Gene Fusions Associated with Recurrent Amplicons Represent a Class of Passenger Aberrations in Breast Cancer

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Shanker Kalyana-Sundaram

2012-08-01

Full Text Available Application of high-throughput transcriptome sequencing has spurred highly sensitive detection and discovery of gene fusions in cancer, but distinguishing potentially oncogenic fusions from random, “passenger” aberrations has proven challenging. Here we examine a distinctive group of gene fusions that involve genes present in the loci of chromosomal amplifications—a class of oncogenic aberrations that are widely prevalent in breast cancers. Integrative analysis of a panel of 14 breast cancer cell lines comparing gene fusions discovered by high-throughput transcriptome sequencing and genome-wide copy number aberrations assessed by array comparative genomic hybridization, led to the identification of 77 gene fusions, of which more than 60% were localized to amplicons including 17q12, 17q23, 20q13, chr8q, and others. Many of these fusions appeared to be recurrent or involved highly expressed oncogenic drivers, frequently fused with multiple different partners, but sometimes displaying loss of functional domains. As illustrative examples of the “amplicon-associated” gene fusions, we examined here a recurrent gene fusion involving the mediator of mammalian target of rapamycin signaling, RPS6KB1 kinase in BT-474, and the therapeutically important receptor tyrosine kinase EGFR in MDA-MB-468 breast cancer cell line. These gene fusions comprise a minor allelic fraction relative to the highly expressed full-length transcripts and encode chimera lacking the kinase domains, which do not impart dependence on the respective cells. Our study suggests that amplicon-associated gene fusions in breast cancer primarily represent a by-product of chromosomal amplifications, which constitutes a subset of passenger aberrations and should be factored accordingly during prioritization of gene fusion candidates.

Function of the EGR-1/TIS8 radiation inducible promoter in a minimal HSV-1 amplicon system

International Nuclear Information System (INIS)

Spear, M.A.; Sakamoto, K.M.; Herrlinger, U.; Pechan, P.; Breakefield, X.O.

1997-01-01

Purpose: To evaluate function of the EGR-1/TIS8 promoter region in minimal HSV-1 amplicon system in order to determine the feasibility of using the system to regulate vector replication with radiation. Materials and Methods: A 600-base pair 5' upstream region of the EGR-1 promoter linked to chloramphenicol acetyltransferase (CAT) was recombined into a minimal HSV-1 amplicon vector system (pONEC). pONEC or a control plasmid was transfected into U87 glioma cells using the Lipofectamine method. Thirty-six hours later one aliquot of cells from each transfection was irradiated to a dose of 20 Gy and another identical aliquot served as a control. CAT activity was assayed 8 hours after irradiation. Results: pONEC transfected cells irradiated with 20 Gy demonstrated 2.0 fold increase in CAT activity compared to non-irradiated cells. Cells transfected with control plasmid showed no change in CAT activity. Unirradiated pONEC cells had CAT activity 1.3 times those transfected with control plasmid. Conclusion: We have previously created HSV-1 gene therapy amplicon vector systems which allow virus-amplicon interdependent replication, with the intent of regulating replication. The above data demonstrates that a minimal amplicon system will allow radiation dependent regulation by the EGR-1 promoter, thus indicating the possibility of using this system to regulate onsite, spatially and temporally regulated vector production. Baseline CAT activity was higher and relative induction lower than other reported expression constructs, which raises concern for the ability of the system to produce a differential in transcription levels sufficient for this purpose. This is possibly the result of residual promoter/enhancer elements remaining in the HSV-1 sequences. We are attempting to create constructs lacking these elements. Addition of secondary promoter sequences may also be of use. We are also currently evaluating the efficacy of the putative IEX-1 radiation inducible promoter region in

Overexpressed Genes/ESTs and Characterization of Distinct Amplicons on 17823 in Breast Cancer Cells

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Ayse E. Erson

2001-01-01

Full Text Available 17823 is a frequent site of gene amplification in breast cancer. Several lines of evidence suggest the presence of multiple amplicons on 17823. To characterize distinct amplicons on 17823 and localize putative oncogenes, we screened genes and expressed sequence tags (ESTs in existing physical and radiation hybrid maps for amplification and overexpression in breast cancer cell lines by semiquantitative duplex PCR, semiquantitative duplex RT-PCR, Southern blot, Northern blot analyses. We identified two distinct amplicons on 17823, one including TBX2 and another proximal region including RPS6KB1 (PS6K and MUL. In addition to these previously reported overexpressed genes, we also identified amplification and overexpression of additional uncharacterized genes and ESTs, some of which suggest potential oncogenic activity. In conclusion, we have further defined two distinct regions of gene amplification and overexpression on 17823 with identification of new potential oncogene candidates. Based on the amplification and overexpression patterns of known and as of yet unrecognized genes on 17823, it is likely that some of these genes mapping to the discrete amplicons function as oncogenes and contribute to tumor progression in breast cancer cells.

Mining environmental high-throughput sequence data sets to identify divergent amplicon clusters for phylogenetic reconstruction and morphotype visualization.

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Gimmler, Anna; Stoeck, Thorsten

2015-08-01

Environmental high-throughput sequencing (envHTS) is a very powerful tool, which in protistan ecology is predominantly used for the exploration of diversity and its geographic and local patterns. We here used a pyrosequenced V4-SSU rDNA data set from a solar saltern pond as test case to exploit such massive protistan amplicon data sets beyond this descriptive purpose. Therefore, we combined a Swarm-based blastn network including 11 579 ciliate V4 amplicons to identify divergent amplicon clusters with targeted polymerase chain reaction (PCR) primer design for full-length small subunit of the ribosomal DNA retrieval and probe design for fluorescence in situ hybridization (FISH). This powerful strategy allows to benefit from envHTS data sets to (i) reveal the phylogenetic position of the taxon behind divergent amplicons; (ii) improve phylogenetic resolution and evolutionary history of specific taxon groups; (iii) solidly assess an amplicons (species') degree of similarity to its closest described relative; (iv) visualize the morphotype behind a divergent amplicons cluster; (v) rapidly FISH screen many environmental samples for geographic/habitat distribution and abundances of the respective organism and (vi) to monitor the success of enrichment strategies in live samples for cultivation and isolation of the respective organisms. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Massively parallel amplicon sequencing reveals isotype-specific variability of antimicrobial peptide transcripts in Mytilus galloprovincialis.

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Umberto Rosani

Full Text Available BACKGROUND: Effective innate responses against potential pathogens are essential in the living world and possibly contributed to the evolutionary success of invertebrates. Taken together, antimicrobial peptide (AMP precursors of defensin, mytilin, myticin and mytimycin can represent about 40% of the hemocyte transcriptome in mussels injected with viral-like and bacterial preparations, and unique profiles of myticin C variants are expressed in single mussels. Based on amplicon pyrosequencing, we have ascertained and compared the natural and Vibrio-induced diversity of AMP transcripts in mussel hemocytes from three European regions. METHODOLOGY/PRINCIPAL FINDINGS: Hemolymph was collected from mussels farmed in the coastal regions of Palavas (France, Vigo (Spain and Venice (Italy. To represent the AMP families known in M. galloprovincialis, nine transcript sequences have been selected, amplified from hemocyte RNA and subjected to pyrosequencing. Hemolymph from farmed (offshore and wild (lagoon Venice mussels, both injected with 10(7 Vibrio cells, were similarly processed. Amplicon pyrosequencing emphasized the AMP transcript diversity, with Single Nucleotide Changes (SNC minimal for mytilin B/C and maximal for arthropod-like defensin and myticin C. Ratio of non-synonymous vs. synonymous changes also greatly differed between AMP isotypes. Overall, each amplicon revealed similar levels of nucleotidic variation across geographical regions, with two main sequence patterns confirmed for mytimycin and no substantial changes after immunostimulation. CONCLUSIONS/SIGNIFICANCE: Barcoding and bidirectional pyrosequencing allowed us to map and compare the transcript diversity of known mussel AMPs. Though most of the genuine cds variation was common to the analyzed samples we could estimate from 9 to 106 peptide variants in hemolymph pools representing 100 mussels, depending on the AMP isoform and sampling site. In this study, no prevailing SNC patterns related

HeurAA: accurate and fast detection of genetic variations with a novel heuristic amplicon aligner program for next generation sequencing.

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Lőrinc S Pongor

Full Text Available Next generation sequencing (NGS of PCR amplicons is a standard approach to detect genetic variations in personalized medicine such as cancer diagnostics. Computer programs used in the NGS community often miss insertions and deletions (indels that constitute a large part of known human mutations. We have developed HeurAA, an open source, heuristic amplicon aligner program. We tested the program on simulated datasets as well as experimental data from multiplex sequencing of 40 amplicons in 12 oncogenes collected on a 454 Genome Sequencer from lung cancer cell lines. We found that HeurAA can accurately detect all indels, and is more than an order of magnitude faster than previous programs. HeurAA can compare reads and reference sequences up to several thousand base pairs in length, and it can evaluate data from complex mixtures containing reads of different gene-segments from different samples. HeurAA is written in C and Perl for Linux operating systems, the code and the documentation are available for research applications at http://sourceforge.net/projects/heuraa/

Ultra-deep pyrosequencing (UDPS data treatment to study amplicon HCV minor variants.

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Josep Gregori

Full Text Available We have investigated the reliability and reproducibility of HCV viral quasispecies quantification by ultra-deep pyrosequencing (UDPS methods. Our study has been divided in two parts. First of all, by UDPS sequencing of clone mixes samples we have established the global noise level of UDPS and fine tuned a data treatment workflow previously optimized for HBV sequence analysis. Secondly, we have studied the reproducibility of the methodology by comparing 5 amplicons from two patient samples on three massive sequencing platforms (FLX+, FLX and Junior after applying the error filters developed from the clonal/control study. After noise filtering the UDPS results, the three replicates showed the same 12 polymorphic sites above 0.7%, with a mean CV of 4.86%. Two polymorphic sites below 0.6% were identified by two replicates and one replicate respectively. A total of 25, 23 and 26 haplotypes were detected by GS-Junior, GS-FLX and GS-FLX+. The observed CVs for the normalized Shannon entropy (Sn, the mutation frequency (Mf, and the nucleotidic diversity (Pi were 1.46%, 3.96% and 3.78%. The mean absolute difference in the two patients (5 amplicons each, in the GS-FLX and GS-FLX+, were 1.46%, 3.96% and 3.78% for Sn, Mf and Pi. No false polymorphic site was observed above 0.5%. Our results indicate that UDPS is an optimal alternative to molecular cloning for quantitative study of HCV viral quasispecies populations, both in complexity and composition. We propose an UDPS data treatment workflow for amplicons from the RNA viral quasispecies which, at a sequencing depth of at least 10,000 reads per strand, enables to obtain sequences and frequencies of consensus haplotypes above 0.5% abundance with no erroneous mutations, with high confidence, resistant mutants as minor variants at the level of 1%, with high confidence that variants are not missed, and highly confident measures of quasispecies complexity.

Use of a novel shorter minimum caliber needle for creating endoscopic tattoos for preoperative localization: a comparative ex vivo study.

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Imai, Kenichiro; Hotta, Kinichi; Ito, Sayo; Yamaguchi, Yuichiro; Kawakami, Takeshi; Wada, Takuya; Igarashi, Kimihiro; Kishida, Yoshihiro; Kinugasa, Yusuke; Kawata, Noboru; Tanaka, Masaki; Kakushima, Naomi; Takizawa, Kohei; Ishiwatari, Hirotoshi; Matsubayashi, Hiroyuki; Ono, Hiroyuki

2017-06-01

In colorectal cancer surgery, inadvertent deep injections during endoscopic tattooing can cause India ink leakage into the peritoneum, leading to complications or to poor visualization of the surgical plane. This ex vivo animal study compared the use of novel shorter, minimum caliber needles versus conventional injection needles for endoscopic tattooing. Four endoscopists used the novel needles and conventional needles to make ten endoscopic tattoos (five tattoos/needle type/endoscopist) in harvested porcine rectum using a saline test-injection method. India ink leakage and the success of the tattoo (i. e. visible, tattoos but for none of the novel needle tattoos ( P  = 0.02). Tattoos created using the novel needles were more successful than those made with the conventional needles: 18/20 (90 %) vs. 11/20 (55 %); P  = 0.01. The use of novel shorter minimum caliber needles may be safe and effective for endoscopic tattooing for preoperative localization prior to colorectal cancer surgery.

Very high resolution single pass HLA genotyping using amplicon sequencing on the 454 next generation DNA sequencers: Comparison with Sanger sequencing.

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Yamamoto, F; Höglund, B; Fernandez-Vina, M; Tyan, D; Rastrou, M; Williams, T; Moonsamy, P; Goodridge, D; Anderson, M; Erlich, H A; Holcomb, C L

2015-12-01

Compared to Sanger sequencing, next-generation sequencing offers advantages for high resolution HLA genotyping including increased throughput, lower cost, and reduced genotype ambiguity. Here we describe an enhancement of the Roche 454 GS GType HLA genotyping assay to provide very high resolution (VHR) typing, by the addition of 8 primer pairs to the original 14, to genotype 11 HLA loci. These additional amplicons help resolve common and well-documented alleles and exclude commonly found null alleles in genotype ambiguity strings. Simplification of workflow to reduce the initial preparation effort using early pooling of amplicons or the Fluidigm Access Array™ is also described. Performance of the VHR assay was evaluated on 28 well characterized cell lines using Conexio Assign MPS software which uses genomic, rather than cDNA, reference sequence. Concordance was 98.4%; 1.6% had no genotype assignment. Of concordant calls, 53% were unambiguous. To further assess the assay, 59 clinical samples were genotyped and results compared to unambiguous allele assignments obtained by prior sequence-based typing supplemented with SSO and/or SSP. Concordance was 98.7% with 58.2% as unambiguous calls; 1.3% could not be assigned. Our results show that the amplicon-based VHR assay is robust and can replace current Sanger methodology. Together with software enhancements, it has the potential to provide even higher resolution HLA typing. Copyright © 2015. Published by Elsevier Inc.

Cytomegalovirus sequence variability, amplicon length, and DNase-sensitive non-encapsidated genomes are obstacles to standardization and commutability of plasma viral load results.

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Naegele, Klaudia; Lautenschlager, Irmeli; Gosert, Rainer; Loginov, Raisa; Bir, Katia; Helanterä, Ilkka; Schaub, Stefan; Khanna, Nina; Hirsch, Hans H

2018-04-22

Cytomegalovirus (CMV) management post-transplantation relies on quantification in blood, but inter-laboratory and inter-assay variability impairs commutability. An international multicenter study demonstrated that variability is mitigated by standardizing plasma volumes, automating DNA extraction and amplification, and calibration to the 1st-CMV-WHO-International-Standard as in the FDA-approved Roche-CAP/CTM-CMV. However, Roche-CAP/CTM-CMV showed under-quantification and false-negative results in a quality assurance program (UK-NEQAS-2014). To evaluate factors contributing to quantification variability of CMV viral load and to develop optimized CMV-UL54-QNAT. The UL54 target of the UK-NEQAS-2014 variant was sequenced and compared to 329 available CMV GenBank sequences. Four Basel-CMV-UL54-QNAT assays of 361 bp, 254 bp, 151 bp, and 95 bp amplicons were developed that only differed in reverse primer positions. The assays were validated using plasmid dilutions, UK-NEQAS-2014 sample, as well as 107 frozen and 69 prospectively collected plasma samples from transplant patients submitted for CMV QNAT, with and without DNase-digestion prior to nucleic acid extraction. Eight of 43 mutations were identified as relevant in the UK-NEQAS-2014 target. All Basel-CMV-UL54 QNATs quantified the UK-NEQAS-2014 but revealed 10-fold increasing CMV loads as amplicon size decreased. The inverse correlation of amplicon size and viral loads was confirmed using 1st-WHO-International-Standard and patient samples. DNase pre-treatment reduced plasma CMV loads by >90% indicating the presence of unprotected CMV genomic DNA. Sequence variability, amplicon length, and non-encapsidated genomes obstruct standardization and commutability of CMV loads needed to develop thresholds for clinical research and management. Besides regular sequence surveys, matrix and extraction standardization, we propose developing reference calibrators using 100 bp amplicons. Copyright © 2018 Elsevier B.V. All

Does universal 16S rRNA gene amplicon sequencing of environmental communities provide an accurate description of nitrifying guilds?

DEFF Research Database (Denmark)

Diwan, Vaibhav; Albrechtsen, Hans-Jørgen; Smets, Barth F.

2018-01-01

amplicon sequencing and from guild targeted approaches. The universal amplicon sequencing provided 1) accurate estimates of nitrifier composition, 2) clustering of the samples based on these compositions consistent with sample origin, 3) estimates of the relative abundance of the guilds correlated...

Analysis of intra-host genetic diversity of Prunus necrotic ringspot virus (PNRSV) using amplicon next generation sequencing.

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Kinoti, Wycliff M; Constable, Fiona E; Nancarrow, Narelle; Plummer, Kim M; Rodoni, Brendan

2017-01-01

PCR amplicon next generation sequencing (NGS) analysis offers a broadly applicable and targeted approach to detect populations of both high- or low-frequency virus variants in one or more plant samples. In this study, amplicon NGS was used to explore the diversity of the tripartite genome virus, Prunus necrotic ringspot virus (PNRSV) from 53 PNRSV-infected trees using amplicons from conserved gene regions of each of PNRSV RNA1, RNA2 and RNA3. Sequencing of the amplicons from 53 PNRSV-infected trees revealed differing levels of polymorphism across the three different components of the PNRSV genome with a total number of 5040, 2083 and 5486 sequence variants observed for RNA1, RNA2 and RNA3 respectively. The RNA2 had the lowest diversity of sequences compared to RNA1 and RNA3, reflecting the lack of flexibility tolerated by the replicase gene that is encoded by this RNA component. Distinct PNRSV phylo-groups, consisting of closely related clusters of sequence variants, were observed in each of PNRSV RNA1, RNA2 and RNA3. Most plant samples had a single phylo-group for each RNA component. Haplotype network analysis showed that smaller clusters of PNRSV sequence variants were genetically connected to the largest sequence variant cluster within a phylo-group of each RNA component. Some plant samples had sequence variants occurring in multiple PNRSV phylo-groups in at least one of each RNA and these phylo-groups formed distinct clades that represent PNRSV genetic strains. Variants within the same phylo-group of each Prunus plant sample had ≥97% similarity and phylo-groups within a Prunus plant sample and between samples had less ≤97% similarity. Based on the analysis of diversity, a definition of a PNRSV genetic strain was proposed. The proposed definition was applied to determine the number of PNRSV genetic strains in each of the plant samples and the complexity in defining genetic strains in multipartite genome viruses was explored.

Analysis of intra-host genetic diversity of Prunus necrotic ringspot virus (PNRSV using amplicon next generation sequencing.

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Wycliff M Kinoti

Full Text Available PCR amplicon next generation sequencing (NGS analysis offers a broadly applicable and targeted approach to detect populations of both high- or low-frequency virus variants in one or more plant samples. In this study, amplicon NGS was used to explore the diversity of the tripartite genome virus, Prunus necrotic ringspot virus (PNRSV from 53 PNRSV-infected trees using amplicons from conserved gene regions of each of PNRSV RNA1, RNA2 and RNA3. Sequencing of the amplicons from 53 PNRSV-infected trees revealed differing levels of polymorphism across the three different components of the PNRSV genome with a total number of 5040, 2083 and 5486 sequence variants observed for RNA1, RNA2 and RNA3 respectively. The RNA2 had the lowest diversity of sequences compared to RNA1 and RNA3, reflecting the lack of flexibility tolerated by the replicase gene that is encoded by this RNA component. Distinct PNRSV phylo-groups, consisting of closely related clusters of sequence variants, were observed in each of PNRSV RNA1, RNA2 and RNA3. Most plant samples had a single phylo-group for each RNA component. Haplotype network analysis showed that smaller clusters of PNRSV sequence variants were genetically connected to the largest sequence variant cluster within a phylo-group of each RNA component. Some plant samples had sequence variants occurring in multiple PNRSV phylo-groups in at least one of each RNA and these phylo-groups formed distinct clades that represent PNRSV genetic strains. Variants within the same phylo-group of each Prunus plant sample had ≥97% similarity and phylo-groups within a Prunus plant sample and between samples had less ≤97% similarity. Based on the analysis of diversity, a definition of a PNRSV genetic strain was proposed. The proposed definition was applied to determine the number of PNRSV genetic strains in each of the plant samples and the complexity in defining genetic strains in multipartite genome viruses was explored.

The bias associated with amplicon sequencing does not affect the quantitative assessment of bacterial community dynamics.

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Federico M Ibarbalz

Full Text Available The performance of two sets of primers targeting variable regions of the 16S rRNA gene V1-V3 and V4 was compared in their ability to describe changes of bacterial diversity and temporal turnover in full-scale activated sludge. Duplicate sets of high-throughput amplicon sequencing data of the two 16S rRNA regions shared a collection of core taxa that were observed across a series of twelve monthly samples, although the relative abundance of each taxon was substantially different between regions. A case in point was the changes in the relative abundance of filamentous bacteria Thiothrix, which caused a large effect on diversity indices, but only in the V1-V3 data set. Yet the relative abundance of Thiothrix in the amplicon sequencing data from both regions correlated with the estimation of its abundance determined using fluorescence in situ hybridization. In nonmetric multidimensional analysis samples were distributed along the first ordination axis according to the sequenced region rather than according to sample identities. The dynamics of microbial communities indicated that V1-V3 and the V4 regions of the 16S rRNA gene yielded comparable patterns of: 1 the changes occurring within the communities along fixed time intervals, 2 the slow turnover of activated sludge communities and 3 the rate of species replacement calculated from the taxa-time relationships. The temperature was the only operational variable that showed significant correlation with the composition of bacterial communities over time for the sets of data obtained with both pairs of primers. In conclusion, we show that despite the bias introduced by amplicon sequencing, the variable regions V1-V3 and V4 can be confidently used for the quantitative assessment of bacterial community dynamics, and provide a proper qualitative account of general taxa in the community, especially when the data are obtained over a convenient time window rather than at a single time point.

Using expected sequence features to improve basecalling accuracy of amplicon pyrosequencing data

DEFF Research Database (Denmark)

Rask, Thomas Salhøj; Petersen, Bent; Chen, Donald S.

2016-01-01

. The new basecalling method described here, named Multipass, implements a probabilistic framework for working with the raw flowgrams obtained by pyrosequencing. For each sequence variant Multipass calculates the likelihood and nucleotide sequence of several most likely sequences given the flowgram data....... This probabilistic approach enables integration of basecalling into a larger model where other parameters can be incorporated, such as the likelihood for observing a full-length open reading frame at the targeted region. We apply the method to 454 amplicon pyrosequencing data obtained from a malaria virulence gene...... family, where Multipass generates 20 % more error-free sequences than current state of the art methods, and provides sequence characteristics that allow generation of a set of high confidence error-free sequences. This novel method can be used to increase accuracy of existing and future amplicon...

Global Perspectives on Activated Sludge Community Composition analyzed using 16S rRNA amplicon sequencing

DEFF Research Database (Denmark)

Nierychlo, Marta; Saunders, Aaron Marc; Albertsen, Mads

communities, and in this study activated sludge sampled from 32 Wastewater Treatment Plants (WWTPs) around the world was described and compared. The top abundant bacteria in the global activated sludge ecosystem were found and the core population shared by multiple samples was investigated. The results......Activated sludge is the most commonly applied bioprocess throughout the world for wastewater treatment. Microorganisms are key to the process, yet our knowledge of their identity and function is still limited. High-througput16S rRNA amplicon sequencing can reliably characterize microbial...

Comparative analyses of amplicon migration behavior in differing denaturing gradient gel electrophoresis (DGGE) systems

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Thornhill, D. J.; Kemp, D. W.; Sampayo, E. M.; Schmidt, G. W.

2010-03-01

Denaturing gradient gel electrophoresis (DGGE) is commonly utilized to identify and quantify microbial diversity, but the conditions required for different electrophoretic systems to yield equivalent results and optimal resolution have not been assessed. Herein, the influence of different DGGE system configuration parameters on microbial diversity estimates was tested using Symbiodinium, a group of marine eukaryotic microbes that are important constituents of coral reef ecosystems. To accomplish this, bacterial clone libraries were constructed and sequenced from cultured isolates of Symbiodinium for the ribosomal DNA internal transcribed spacer 2 (ITS2) region. From these, 15 clones were subjected to PCR with a GC clamped primer set for DGGE analyses. Migration behaviors of the resulting amplicons were analyzed using a range of conditions, including variation in the composition of the denaturing gradient, electrophoresis time, and applied voltage. All tests were conducted in parallel on two commercial DGGE systems, a C.B.S. Scientific DGGE-2001, and the Bio-Rad DCode system. In this context, identical nucleotide fragments exhibited differing migration behaviors depending on the model of apparatus utilized, with fragments denaturing at a lower gradient concentration and applied voltage on the Bio-Rad DCode system than on the C.B.S. Scientific DGGE-2001 system. Although equivalent PCR-DGGE profiles could be achieved with both brands of DGGE system, the composition of the denaturing gradient and application of electrophoresis time × voltage must be appropriately optimized to achieve congruent results across platforms.

Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies

KAUST Repository

Wang, Yong; Qian, Pei-Yuan

2009-01-01

Bacterial 16S ribosomal DNA (rDNA) amplicons have been widely used in the classification of uncultured bacteria inhabiting environmental niches. Primers targeting conservative regions of the rDNAs are used to generate amplicons of variant regions

Herpes simplex virus type 1-derived recombinant and amplicon vectors.

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Fraefel, Cornel; Marconi, Peggy; Epstein, Alberto L

2011-01-01

Herpes simplex virus type 1 (HSV-1) is a human pathogen whose lifestyle is based on a long-term dual interaction with the infected host, being able to establish both lytic and latent infections. The virus genome is a 153 kbp double-stranded DNA molecule encoding more than 80 genes. The interest of HSV-1 as gene transfer vector stems from its ability to infect many different cell types, both quiescent and proliferating cells, the very high packaging capacity of the virus capsid, the outstanding neurotropic adaptations that this virus has evolved, and the fact that it never integrates into the cellular chromosomes, thus avoiding the risk of insertional mutagenesis. Two types of vectors can be derived from HSV-1, recombinant vectors and amplicon vectors, and different methodologies have been developed to prepare large stocks of each type of vector. This chapter summarizes (1) the two approaches most commonly used to prepare recombinant vectors through homologous recombination, either in eukaryotic cells or in bacteria, and (2) the two methodologies currently used to generate helper-free amplicon vectors, either using a bacterial artificial chromosome (BAC)-based approach or a Cre/loxP site-specific recombination strategy.

pyAmpli: an amplicon-based variant filter pipeline for targeted resequencing data.

Science.gov (United States)

Beyens, Matthias; Boeckx, Nele; Van Camp, Guy; Op de Beeck, Ken; Vandeweyer, Geert

2017-12-14

Haloplex targeted resequencing is a popular method to analyze both germline and somatic variants in gene panels. However, involved wet-lab procedures may introduce false positives that need to be considered in subsequent data-analysis. No variant filtering rationale addressing amplicon enrichment related systematic errors, in the form of an all-in-one package, exists to our knowledge. We present pyAmpli, a platform independent parallelized Python package that implements an amplicon-based germline and somatic variant filtering strategy for Haloplex data. pyAmpli can filter variants for systematic errors by user pre-defined criteria. We show that pyAmpli significantly increases specificity, without reducing sensitivity, essential for reporting true positive clinical relevant mutations in gene panel data. pyAmpli is an easy-to-use software tool which increases the true positive variant call rate in targeted resequencing data. It specifically reduces errors related to PCR-based enrichment of targeted regions.

Direct recovery of infectious Pestivirus from a full-length RT-PCR amplicon

DEFF Research Database (Denmark)

Rasmussen, Thomas Bruun; Reimann, Ilona; Hoffmann, Bernd

2008-01-01

This study describes the use of a novel and rapid long reverse transcription (RT)-PCR for the generation of infectious full-length cDNA of pestiviruses. To produce rescued viruses, full-length RT-PCR amplicons of 12.3 kb, including a T7-promotor, were transcribed directly in vitro, and the result......This study describes the use of a novel and rapid long reverse transcription (RT)-PCR for the generation of infectious full-length cDNA of pestiviruses. To produce rescued viruses, full-length RT-PCR amplicons of 12.3 kb, including a T7-promotor, were transcribed directly in vitro......, and the resulting RNA transcripts were electroporated into ovine cells. Infectious virus was obtained after one cell culture passage. The rescued viruses had a phenotype similar to the parental Border Disease virus strain. Therefore, direct generation of infectious pestiviruses from full-length RT-PCR cDNA products...

A priori Considerations When Conducting High-Throughput Amplicon-Based Sequence Analysis

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Aditi Sengupta

2016-03-01

Full Text Available Amplicon-based sequencing strategies that include 16S rRNA and functional genes, alongside “meta-omics” analyses of communities of microorganisms, have allowed researchers to pose questions and find answers to “who” is present in the environment and “what” they are doing. Next-generation sequencing approaches that aid microbial ecology studies of agricultural systems are fast gaining popularity among agronomy, crop, soil, and environmental science researchers. Given the rapid development of these high-throughput sequencing techniques, researchers with no prior experience will desire information about the best practices that can be used before actually starting high-throughput amplicon-based sequence analyses. We have outlined items that need to be carefully considered in experimental design, sampling, basic bioinformatics, sequencing of mock communities and negative controls, acquisition of metadata, and in standardization of reaction conditions as per experimental requirements. Not all considerations mentioned here may pertain to a particular study. The overall goal is to inform researchers about considerations that must be taken into account when conducting high-throughput microbial DNA sequencing and sequences analysis.

Illumina MiSeq 16S amplicon sequence analysis of bovine respiratory disease associated bacteria in lung and mediastinal lymph node tissue.

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Johnston, Dayle; Earley, Bernadette; Cormican, Paul; Murray, Gerard; Kenny, David Anthony; Waters, Sinead Mary; McGee, Mark; Kelly, Alan Kieran; McCabe, Matthew Sean

2017-05-02

Bovine respiratory disease (BRD) is caused by growth of single or multiple species of pathogenic bacteria in lung tissue following stress and/or viral infection. Next generation sequencing of 16S ribosomal RNA gene PCR amplicons (NGS 16S amplicon analysis) is a powerful culture-independent open reference method that has recently been used to increase understanding of BRD-associated bacteria in the upper respiratory tract of BRD cattle. However, it has not yet been used to examine the microbiome of the bovine lower respiratory tract. The objective of this study was to use NGS 16S amplicon analysis to identify bacteria in post-mortem lung and lymph node tissue samples harvested from fatal BRD cases and clinically healthy animals. Cranial lobe and corresponding mediastinal lymph node post-mortem tissue samples were collected from calves diagnosed as BRD cases by veterinary laboratory pathologists and from clinically healthy calves. NGS 16S amplicon libraries, targeting the V3-V4 region of the bacterial 16S rRNA gene were prepared and sequenced on an Illumina MiSeq. Quantitative insights into microbial ecology (QIIME) was used to determine operational taxonomic units (OTUs) which corresponded to the 16S rRNA gene sequences. Leptotrichiaceae, Mycoplasma, Pasteurellaceae, and Fusobacterium were the most abundant OTUs identified in the lungs and lymph nodes of the calves which died from BRD. Leptotrichiaceae, Fusobacterium, Mycoplasma, Trueperella and Bacteroides had greater relative abundances in post-mortem lung samples collected from fatal cases of BRD in dairy calves, compared with clinically healthy calves without lung lesions. Leptotrichiaceae, Mycoplasma and Pasteurellaceae showed higher relative abundances in post-mortem lymph node samples collected from fatal cases of BRD in dairy calves, compared with clinically healthy calves without lung lesions. Two Leptotrichiaceae sequence contigs were subsequently assembled from bacterial DNA-enriched shotgun sequences

FasL and FADD delivery by a glioma-specific and cell cycle-dependent HSV-1 amplicon virus enhanced apoptosis in primary human brain tumors

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Lam Paula Y

2010-10-01

Full Text Available Abstract Background Glioblastoma multiforme is the most malignant cancer of the brain and is notoriously difficult to treat due to the highly proliferative and infiltrative nature of the cells. Herein, we explored the combination treatment of pre-established human glioma xenograft using multiple therapeutic genes whereby the gene expression is regulated by both cell-type and cell cycle-dependent transcriptional regulatory mechanism conferred by recombinant HSV-1 amplicon vectors. Results We demonstrated for the first time that Ki67-positive proliferating primary human glioma cells cultured from biopsy samples were effectively induced into cell death by the dual-specific function of the pG8-FasL amplicon vectors. These vectors were relatively stable and exhibited minimal cytotoxicity in vivo. Intracranial implantation of pre-transduced glioma cells resulted in better survival outcome when compared with viral vectors inoculated one week post-implantation of tumor cells, indicating that therapeutic efficacy is dependent on the viral spread and mode of viral vectors administration. We further showed that pG8-FasL amplicon vectors are functional in the presence of commonly used treatment regimens for human brain cancer. In fact, the combined therapies of pG8-FasL and pG8-FADD in the presence of temozolomide significantly improved the survival of mice bearing intracranial high-grade gliomas. Conclusion Taken together, our results showed that the glioma-specific and cell cycle-dependent HSV-1 amplicon vector is potentially useful as an adjuvant therapy to complement the current gene therapy strategy for gliomas.

SEED 2: a user-friendly platform for amplicon high-throughput sequencing data analyses.

Science.gov (United States)

Vetrovský, Tomáš; Baldrian, Petr; Morais, Daniel; Berger, Bonnie

2018-02-14

Modern molecular methods have increased our ability to describe microbial communities. Along with the advances brought by new sequencing technologies, we now require intensive computational resources to make sense of the large numbers of sequences continuously produced. The software developed by the scientific community to address this demand, although very useful, require experience of the command-line environment, extensive training and have steep learning curves, limiting their use. We created SEED 2, a graphical user interface for handling high-throughput amplicon-sequencing data under Windows operating systems. SEED 2 is the only sequence visualizer that empowers users with tools to handle amplicon-sequencing data of microbial community markers. It is suitable for any marker genes sequences obtained through Illumina, IonTorrent or Sanger sequencing. SEED 2 allows the user to process raw sequencing data, identify specific taxa, produce of OTU-tables, create sequence alignments and construct phylogenetic trees. Standard dual core laptops with 8 GB of RAM can handle ca. 8 million of Illumina PE 300 bp sequences, ca. 4GB of data. SEED 2 was implemented in Object Pascal and uses internal functions and external software for amplicon data processing. SEED 2 is a freeware software, available at http://www.biomed.cas.cz/mbu/lbwrf/seed/ as a self-contained file, including all the dependencies, and does not require installation. Supplementary data contain a comprehensive list of supported functions. daniel.morais@biomed.cas.cz. Supplementary data are available at Bioinformatics online. © The Author(s) 2018. Published by Oxford University Press.

The Napoleon Complex: When Shorter Men Take More.

Science.gov (United States)

Knapen, Jill E P; Blaker, Nancy M; Van Vugt, Mark

2018-05-01

Inspired by an evolutionary psychological perspective on the Napoleon complex, we hypothesized that shorter males are more likely to show indirect aggression in resource competitions with taller males. Three studies provide support for our interpretation of the Napoleon complex. Our pilot study shows that men (but not women) keep more resources for themselves when they feel small. When paired with a taller male opponent (Study 1), shorter men keep more resources to themselves in a game in which they have all the power (dictator game) versus a game in which the opponent also has some power (ultimatum game). Furthermore, shorter men are not more likely to show direct, physical aggression toward a taller opponent (Study 2). As predicted by the Napoleon complex, we conclude that (relatively) shorter men show greater behavioral flexibility in securing resources when presented with cues that they are physically less competitive. Theoretical and practical implications are discussed.

Driving for shorter outages

International Nuclear Information System (INIS)

Tritch, S.

1996-01-01

Nuclear plant outages are necessary to complete activities that cannot be completed during the operating cycle, such as steam generator inspection and testing, refueling, installing modifications, and performing maintenance tests. The time devoted to performing outages is normally the largest contributor to plant unavailability. Similarly, outage costs are a sizable portion of the total plant budget. The scope and quality of work done during outages directly affects operating reliability and the number of unplanned outages. Improved management and planning of outages enhances the margin of safety during the outage and results in increased plant reliability. The detailed planning and in-depth preparation that has become a necessity for driving shorter outage durations has also produced safer outages and improved post-outage reliability. Short outages require both plant and vendor management to focus on all aspects of the outage. Short outage durations, such as 26 days at South Texas or 29 days at North Anna, require power plant inter-department and intra-department teamwork and communication and vendor participation. In this paper shorter and safer outage at the 3-loop plants in the United States are explained. (J.P.N.)

A quantitative and qualitative comparison of illumina MiSeq and 454 amplicon sequencing for genotyping the highly polymorphic major histocompatibility complex (MHC) in a non-model species.

Science.gov (United States)

Razali, Haslina; O'Connor, Emily; Drews, Anna; Burke, Terry; Westerdahl, Helena

2017-07-28

High-throughput sequencing enables high-resolution genotyping of extremely duplicated genes. 454 amplicon sequencing (454) has become the standard technique for genotyping the major histocompatibility complex (MHC) genes in non-model organisms. However, illumina MiSeq amplicon sequencing (MiSeq), which offers a much higher read depth, is now superseding 454. The aim of this study was to quantitatively and qualitatively evaluate the performance of MiSeq in relation to 454 for genotyping MHC class I alleles using a house sparrow (Passer domesticus) dataset with pedigree information. House sparrows provide a good study system for this comparison as their MHC class I genes have been studied previously and, consequently, we had prior expectations concerning the number of alleles per individual. We found that 454 and MiSeq performed equally well in genotyping amplicons with low diversity, i.e. amplicons from individuals that had fewer than 6 alleles. Although there was a higher rate of failure in the 454 dataset in resolving amplicons with higher diversity (6-9 alleles), the same genotypes were identified by both 454 and MiSeq in 98% of cases. We conclude that low diversity amplicons are equally well genotyped using either 454 or MiSeq, but the higher coverage afforded by MiSeq can lead to this approach outperforming 454 in amplicons with higher diversity.

Multiplex PCR, amplicon size and hybridization efficiency on the NanoChip electronic microarray

DEFF Research Database (Denmark)

Børsting, Claus; Sanchez, Juan J; Morling, Niels

2004-01-01

We tested the SNP typing protocol developed for the NanoChip electronic microarray by analyzing the four Y chromosome loci SRY1532, SRY8299, TAT, and 92R7. Amplicons of different lengths containing the same locus were purified and addressed to the NanoChip array and fluorescently labelled reporte...

Shorter height is related to lower cardiovascular disease risk – A narrative review

Directory of Open Access Journals (Sweden)

Thomas T. Samaras

2013-01-01

Full Text Available Numerous Western studies have shown a negative correlation between height and cardiovascular disease. However, these correlations do not prove causation. This review provides a variety of studies showing short people have little to no cardiovascular disease. When shorter people are compared to taller people, a number of biological mechanisms evolve favoring shorter people, including reduced telomere shortening, lower atrial fibrillation, higher heart pumping efficiency, lower DNA damage, lower risk of blood clots, lower left ventricular hypertrophy and superior blood parameters. The causes of increased heart disease among shorter people in the developed world are related to lower income, excessive weight, poor diet, lifestyle factors, catch-up growth, childhood illness and poor environmental conditions. For short people in developed countries, the data indicate that a plant-based diet, leanness and regular exercise can substantially reduce the risk of cardiovascular disease.

Amplicon sequencing for the quantification of spoilage microbiota in complex foods including bacterial spores

NARCIS (Netherlands)

Boer, de P.; Caspers, M.; Sanders, J.W.; Kemperman, R.; Wijman, J.; Lommerse, G.; Roeselers, G.; Montijn, R.; Abee, T.; Kort, R.

2015-01-01

Background
Spoilage of food products is frequently caused by bacterial spores and lactic acid bacteria. Identification of these organisms by classic cultivation methods is limited by their ability to form colonies on nutrient agar plates. In this study, we adapted and optimized 16S rRNA amplicon

Two-stage clustering (TSC: a pipeline for selecting operational taxonomic units for the high-throughput sequencing of PCR amplicons.

Directory of Open Access Journals (Sweden)

Xiao-Tao Jiang

Full Text Available Clustering 16S/18S rRNA amplicon sequences into operational taxonomic units (OTUs is a critical step for the bioinformatic analysis of microbial diversity. Here, we report a pipeline for selecting OTUs with a relatively low computational demand and a high degree of accuracy. This pipeline is referred to as two-stage clustering (TSC because it divides tags into two groups according to their abundance and clusters them sequentially. The more abundant group is clustered using a hierarchical algorithm similar to that in ESPRIT, which has a high degree of accuracy but is computationally costly for large datasets. The rarer group, which includes the majority of tags, is then heuristically clustered to improve efficiency. To further improve the computational efficiency and accuracy, two preclustering steps are implemented. To maintain clustering accuracy, all tags are grouped into an OTU depending on their pairwise Needleman-Wunsch distance. This method not only improved the computational efficiency but also mitigated the spurious OTU estimation from 'noise' sequences. In addition, OTUs clustered using TSC showed comparable or improved performance in beta-diversity comparisons compared to existing OTU selection methods. This study suggests that the distribution of sequencing datasets is a useful property for improving the computational efficiency and increasing the clustering accuracy of the high-throughput sequencing of PCR amplicons. The software and user guide are freely available at http://hwzhoulab.smu.edu.cn/paperdata/.

36 CFR 223.81 - Shorter advertising periods in emergencies.

Science.gov (United States)

2010-07-01

... 36 Parks, Forests, and Public Property 2 2010-07-01 2010-07-01 false Shorter advertising periods... OF AGRICULTURE SALE AND DISPOSAL OF NATIONAL FOREST SYSTEM TIMBER Timber Sale Contracts Advertisement and Bids § 223.81 Shorter advertising periods in emergencies. In emergency situations where prompt...

Evaluation of the reproducibility of amplicon sequencing with Illumina MiSeq platform.

Science.gov (United States)

Wen, Chongqing; Wu, Liyou; Qin, Yujia; Van Nostrand, Joy D; Ning, Daliang; Sun, Bo; Xue, Kai; Liu, Feifei; Deng, Ye; Liang, Yuting; Zhou, Jizhong

2017-01-01

Illumina's MiSeq has become the dominant platform for gene amplicon sequencing in microbial ecology studies; however, various technical concerns, such as reproducibility, still exist. To assess reproducibility, 16S rRNA gene amplicons from 18 soil samples of a reciprocal transplantation experiment were sequenced on an Illumina MiSeq. The V4 region of 16S rRNA gene from each sample was sequenced in triplicate with each replicate having a unique barcode. The average OTU overlap, without considering sequence abundance, at a rarefaction level of 10,323 sequences was 33.4±2.1% and 20.2±1.7% between two and among three technical replicates, respectively. When OTU sequence abundance was considered, the average sequence abundance weighted OTU overlap was 85.6±1.6% and 81.2±2.1% for two and three replicates, respectively. Removing singletons significantly increased the overlap for both (~1-3%, pdeep sequencing increased OTU overlap both when sequence abundance was considered (95%) and when not (44%). However, if singletons were not removed the overlap between two technical replicates (not considering sequence abundance) plateaus at 39% with 30,000 sequences. Diversity measures were not affected by the low overlap as α-diversities were similar among technical replicates while β-diversities (Bray-Curtis) were much smaller among technical replicates than among treatment replicates (e.g., 0.269 vs. 0.374). Higher diversity coverage, but lower OTU overlap, was observed when replicates were sequenced in separate runs. Detrended correspondence analysis indicated that while there was considerable variation among technical replicates, the reproducibility was sufficient for detecting treatment effects for the samples examined. These results suggest that although there is variation among technical replicates, amplicon sequencing on MiSeq is useful for analyzing microbial community structure if used appropriately and with caution. For example, including technical replicates

CLOTU: An online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation

Directory of Open Access Journals (Sweden)

Shalchian-Tabrizi Kamran

2011-05-01

Full Text Available Abstract Background The implementation of high throughput sequencing for exploring biodiversity poses high demands on bioinformatics applications for automated data processing. Here we introduce CLOTU, an online and open access pipeline for processing 454 amplicon reads. CLOTU has been constructed to be highly user-friendly and flexible, since different types of analyses are needed for different datasets. Results In CLOTU, the user can filter out low quality sequences, trim tags, primers, adaptors, perform clustering of sequence reads, and run BLAST against NCBInr or a customized database in a high performance computing environment. The resulting data may be browsed in a user-friendly manner and easily forwarded to downstream analyses. Although CLOTU is specifically designed for analyzing 454 amplicon reads, other types of DNA sequence data can also be processed. A fungal ITS sequence dataset generated by 454 sequencing of environmental samples is used to demonstrate the utility of CLOTU. Conclusions CLOTU is a flexible and easy to use bioinformatics pipeline that includes different options for filtering, trimming, clustering and taxonomic annotation of high throughput sequence reads. Some of these options are not included in comparable pipelines. CLOTU is implemented in a Linux computer cluster and is freely accessible to academic users through the Bioportal web-based bioinformatics service (http://www.bioportal.uio.no.

Implementation of Amplicon Parallel Sequencing Leads to Improvement of Diagnosis and Therapy of Lung Cancer Patients.

Science.gov (United States)

König, Katharina; Peifer, Martin; Fassunke, Jana; Ihle, Michaela A; Künstlinger, Helen; Heydt, Carina; Stamm, Katrin; Ueckeroth, Frank; Vollbrecht, Claudia; Bos, Marc; Gardizi, Masyar; Scheffler, Matthias; Nogova, Lucia; Leenders, Frauke; Albus, Kerstin; Meder, Lydia; Becker, Kerstin; Florin, Alexandra; Rommerscheidt-Fuss, Ursula; Altmüller, Janine; Kloth, Michael; Nürnberg, Peter; Henkel, Thomas; Bikár, Sven-Ernö; Sos, Martin L; Geese, William J; Strauss, Lewis; Ko, Yon-Dschun; Gerigk, Ulrich; Odenthal, Margarete; Zander, Thomas; Wolf, Jürgen; Merkelbach-Bruse, Sabine; Buettner, Reinhard; Heukamp, Lukas C

2015-07-01

The Network Genomic Medicine Lung Cancer was set up to rapidly translate scientific advances into early clinical trials of targeted therapies in lung cancer performing molecular analyses of more than 3500 patients annually. Because sequential analysis of the relevant driver mutations on fixated samples is challenging in terms of workload, tissue availability, and cost, we established multiplex parallel sequencing in routine diagnostics. The aim was to analyze all therapeutically relevant mutations in lung cancer samples in a high-throughput fashion while significantly reducing turnaround time and amount of input DNA compared with conventional dideoxy sequencing of single polymerase chain reaction amplicons. In this study, we demonstrate the feasibility of a 102 amplicon multiplex polymerase chain reaction followed by sequencing on an Illumina sequencer on formalin-fixed paraffin-embedded tissue in routine diagnostics. Analysis of a validation cohort of 180 samples showed this approach to require significantly less input material and to be more reliable, robust, and cost-effective than conventional dideoxy sequencing. Subsequently, 2657 lung cancer patients were analyzed. We observed that comprehensive biomarker testing provided novel information in addition to histological diagnosis and clinical staging. In 2657 consecutively analyzed lung cancer samples, we identified driver mutations at the expected prevalence. Furthermore we found potentially targetable DDR2 mutations at a frequency of 3% in both adenocarcinomas and squamous cell carcinomas. Overall, our data demonstrate the utility of systematic sequencing analysis in a clinical routine setting and highlight the dramatic impact of such an approach on the availability of therapeutic strategies for the targeted treatment of individual cancer patients.

Viability-qPCR for detecting Legionella: Comparison of two assays based on different amplicon lengths.

Science.gov (United States)

Ditommaso, Savina; Giacomuzzi, Monica; Ricciardi, Elisa; Zotti, Carla M

2015-08-01

Two different real-time quantitative PCR (PMA-qPCR) assays were applied for quantification of Legionella spp. by targeting a long amplicon (approx 400 bp) of 16S rRNA gene and a short amplicon (approx. 100 bp) of 5S rRNA gene. Purified DNA extracts from pure cultures of Legionella spp. and from environmental water samples were quantified. Application of the two assays to quantify Legionella in artificially contaminated water achieved that both assays were able to detect Legionella over a linear range of 10 to 10(5) cells ml(-1). A statistical analysis of the standard curves showed that both assays were linear with a good correlation coefficient (R(2) = 0.99) between the Ct and the copy number. Amplification with the reference assay was the most effective for detecting low copy numbers (1 bacterium per PCR mixture). Using selective quantification of viable Legionella by the PMA-qPCR method we obtained a greater inhibition of the amplification of the 400-bp 16S gene fragment (Δlog(10) = 3.74 ± 0.39 log(10) GU ml(-1)). A complete inhibition of the PCR signal was obtained when heat-killed cells in a concentration below 1 × 10(5) cells ml(-1) were pretreated with PMA. Analysing short amplicon sizes led to only 2.08 log reductions in the Legionella dead-cell signal. When we tested environmental water samples, the two qPCR assays were in good agreement according to the kappa index (0.741). Applying qPCR combined with PMA treatment, we also obtained a good agreement (kappa index 0.615). The comparison of quantitative results shows that both assays yielded the same quantification sensitivity (mean log = 4.59 vs mean log = 4.31). Copyright © 2015 Elsevier Ltd. All rights reserved.

Pulmonary Embolism Inpatients Treated With Rivaroxaban Had Shorter Hospital Stays and Lower Costs Compared With Warfarin.

Science.gov (United States)

Margolis, Jay M; Deitelzweig, Steven; Kline, Jeffrey; Tran, Oth; Smith, David M; Crivera, Concetta; Bookhart, Brahim; Schein, Jeff

2016-11-01

Using real-world data, this study compares inpatient length of stay (LOS) and costs for patients with a primary diagnosis of pulmonary embolism (PE) initiating treatment with oral anticoagulation with rivaroxaban versus warfarin. Hospitalizations from MarketScan's Hospital Drug Database were selected from November 1, 2012, through December 31, 2013, for adults with a primary diagnosis of PE initiating treatment with rivaroxaban or warfarin. Warfarin patients were matched 1:1 to rivaroxaban patients using exact and propensity score matching. Hospital LOS, treatment patterns, and hospitalization costs were evaluated. Matched cohorts included 751 rivaroxaban-treated patients and 751 warfarin-treated patients. Adjusted mean LOS was 3.77 days for rivaroxaban patients (95% CI, 3.66-3.87 days) and 5.48 days for warfarin patients (95% CI, 5.33-5.63 days; P < .001). Mean (SD) LOS was shorter for patients taking rivaroxaban whether admission was for provoked PE (rivaroxaban: 5.2 [5.1] days; warfarin: 7.0 [6.5] days; P < .001) or unprovoked PE (rivaroxaban: 3.4 [2.3] days; warfarin: 5.1 [2.7] days; P < .001). Mean (SD) days from first dose to discharge were 2.5 (1.7) (rivaroxaban) and 4.0 (2.9) (warfarin) when initiated with parenteral anticoagulants (P < .001) and 2.7 (1.7) (rivaroxaban) and 4.0 (2.2) (warfarin) without parenteral anticoagulants (P < .001). The rivaroxaban cohort incurred significantly lower unadjusted mean (SD) hospitalization costs (rivaroxaban: $8473 [$9105]; warfarin: $10,291 [$9185]; P < .001), confirmed by covariate adjustment with generalized linear modeling estimating predicted mean hospitalization costs of $8266 for rivaroxaban patients (95% CI, $7851-$8681) and $10,511 for warfarin patients (95% CI, $10,031-$10,992; P < .001). patients with PE treated with rivaroxaban incurred significantly lower hospitalization costs by $2245 per admission compared with patients treated with warfarin, which was attributable to cost offsets from 1.71 fewer days of

Surface density dependence of PCR amplicon hybridization on PNA/DNA probe layers

DEFF Research Database (Denmark)

Yao, Danfeng; Kim, Junyoung; Yu, Fang

2005-01-01

at an intermediate sodium concentration (approximately 100 mM). These effects were mainly ascribed to the electrostatic cross talk among the hybridized DNA molecules and the secondary structure of PCR amplicons. For the negatively charged DNA probes, the hybridization reaction was subjected additionally to the DNA....../DNA electrostatic barrier, particularly in lower ionic strength range (e.g., 10 approximately 150 mM Na(+)). The electrostatic cross talk was shown to be largely reduced if the PNA probe layer was sufficiently diluted by following a strategic templated immobilization method. As a consequence, a pseudo...

Unraveling Core Functional Microbiota in Traditional Solid-State Fermentation by High-Throughput Amplicons and Metatranscriptomics Sequencing

Directory of Open Access Journals (Sweden)

Zhewei Song

2017-07-01

Full Text Available Fermentation microbiota is specific microorganisms that generate different types of metabolites in many productions. In traditional solid-state fermentation, the structural composition and functional capacity of the core microbiota determine the quality and quantity of products. As a typical example of food fermentation, Chinese Maotai-flavor liquor production involves a complex of various microorganisms and a wide variety of metabolites. However, the microbial succession and functional shift of the core microbiota in this traditional food fermentation remain unclear. Here, high-throughput amplicons (16S rRNA gene amplicon sequencing and internal transcribed space amplicon sequencing and metatranscriptomics sequencing technologies were combined to reveal the structure and function of the core microbiota in Chinese soy sauce aroma type liquor production. In addition, ultra-performance liquid chromatography and headspace-solid phase microextraction-gas chromatography-mass spectrometry were employed to provide qualitative and quantitative analysis of the major flavor metabolites. A total of 10 fungal and 11 bacterial genera were identified as the core microbiota. In addition, metatranscriptomic analysis revealed pyruvate metabolism in yeasts (genera Pichia, Schizosaccharomyces, Saccharomyces, and Zygosaccharomyces and lactic acid bacteria (genus Lactobacillus classified into two stages in the production of flavor components. Stage I involved high-level alcohol (ethanol production, with the genus Schizosaccharomyces serving as the core functional microorganism. Stage II involved high-level acid (lactic acid and acetic acid production, with the genus Lactobacillus serving as the core functional microorganism. The functional shift from the genus Schizosaccharomyces to the genus Lactobacillus drives flavor component conversion from alcohol (ethanol to acid (lactic acid and acetic acid in Chinese Maotai-flavor liquor production. Our findings provide

Unraveling Core Functional Microbiota in Traditional Solid-State Fermentation by High-Throughput Amplicons and Metatranscriptomics Sequencing.

Science.gov (United States)

Song, Zhewei; Du, Hai; Zhang, Yan; Xu, Yan

2017-01-01

Fermentation microbiota is specific microorganisms that generate different types of metabolites in many productions. In traditional solid-state fermentation, the structural composition and functional capacity of the core microbiota determine the quality and quantity of products. As a typical example of food fermentation, Chinese Maotai-flavor liquor production involves a complex of various microorganisms and a wide variety of metabolites. However, the microbial succession and functional shift of the core microbiota in this traditional food fermentation remain unclear. Here, high-throughput amplicons (16S rRNA gene amplicon sequencing and internal transcribed space amplicon sequencing) and metatranscriptomics sequencing technologies were combined to reveal the structure and function of the core microbiota in Chinese soy sauce aroma type liquor production. In addition, ultra-performance liquid chromatography and headspace-solid phase microextraction-gas chromatography-mass spectrometry were employed to provide qualitative and quantitative analysis of the major flavor metabolites. A total of 10 fungal and 11 bacterial genera were identified as the core microbiota. In addition, metatranscriptomic analysis revealed pyruvate metabolism in yeasts (genera Pichia, Schizosaccharomyces, Saccharomyces , and Zygosaccharomyces ) and lactic acid bacteria (genus Lactobacillus ) classified into two stages in the production of flavor components. Stage I involved high-level alcohol (ethanol) production, with the genus Schizosaccharomyces serving as the core functional microorganism. Stage II involved high-level acid (lactic acid and acetic acid) production, with the genus Lactobacillus serving as the core functional microorganism. The functional shift from the genus Schizosaccharomyces to the genus Lactobacillus drives flavor component conversion from alcohol (ethanol) to acid (lactic acid and acetic acid) in Chinese Maotai-flavor liquor production. Our findings provide insight into

Shorter Hospital Stays and Lower Costs for Rivaroxaban Compared With Warfarin for Venous Thrombosis Admissions.

Science.gov (United States)

Margolis, Jay M; Deitelzweig, Steven; Kline, Jeffrey; Tran, Oth; Smith, David M; Bookhart, Brahim; Crivera, Concetta; Schein, Jeff

2016-10-06

% confidence interval, $8035-$8739]; warfarin $10 275 [95% confidence interval, $9842-$10 708]). Rivaroxaban was associated with significantly shorter hospital LOS and lower hospitalization costs compared with warfarin. © 2016 The Authors, Janssen Scientific Affairs, LLC, and Truven Health Analytics. Published on behalf of the American Heart Association, Inc., by Wiley Blackwell.

Implications of shorter cells in PEP

International Nuclear Information System (INIS)

Wiedemann, H.

1975-01-01

Further studies on the beam-stay-clear requirements in PEP led to the conclusion that the vertical aperture needed to be enlarged. There are two main reasons for that: Observations at SPEAR indicate that the aperture should be large enough for a fully coupled beam. Full coupling of the horizontal and vertical betatron oscillations occurs not only occasionally when the energy, tune or betatron function at the interaction point is changed but also due to the beam/endash/beam effect of two strong colliding beams. The second reason for an increased aperture requirement is the nonlinear perturbation of the particle trajectories by the sextupoles. This perturbation increases a fully coupled beam by another 50% to 80%. Both effects together with a +-5 mm allowance for closed orbit perturbation result in a vertical beam-stay-clear in the bending magnets of +-4.8 to +-5.6 cm, compared to the present +-2.0 cm. This beam-stay-clear, together with additional space for vacuum chamber, etc., leads to very costly bending magnets. In this note, a shorter cell length is proposed which would reduce considerably the vertical beam-stay-clear requirements in the bending magnets. 7 figs

The risk of shorter fasting time for pediatric deep sedation.

Science.gov (United States)

Clark, Mathew; Birisci, Esma; Anderson, Jordan E; Anliker, Christina M; Bryant, Micheal A; Downs, Craig; Dalabih, Abdallah

2016-01-01

Current guidelines adopted by the American Academy of Pediatrics calls for prolonged fasting times before performing pediatric procedural sedation and analgesia (PSA). PSA is increasingly provided to children outside of the operating theater by sedation trained pediatric providers and does not require airway manipulation. We investigated the safety of a shorter fasting time compared to a longer and guideline compliant fasting time. We tried to identify the association between fasting time and sedation-related complications. This is a prospective observational study that included children 2 months to 18 years of age and had an American Society of Anesthesiologists physical status classification of I or II, who underwent deep sedation for elective procedures, performed by pediatric critical care providers. Procedures included radiologic imaging studies, electroencephalograms, auditory brainstem response, echocardiograms, Botox injections, and other minor surgical procedures. Subjects were divided into two groups depending on the length of their fasting time (4-6 h and >6 h). Complication rates were calculated and compared between the three groups. In the studied group of 2487 subjects, 1007 (40.5%) had fasting time of 4-6 h and the remaining 1480 (59.5%) subjects had fasted for >6 h. There were no statistically significant differences in any of the studied complications between the two groups. This study found no difference in complication rate in regard to the fasting time among our subjects cohort, which included only healthy children receiving elective procedures performed by sedation trained pediatric critical care providers. This suggests that using shorter fasting time may be safe for procedures performed outside of the operating theater that does not involve high-risk patients or airway manipulation.

Prostate-Specific and Tumor-Specific Targeting of an Oncolytic HSV-1 Amplicon/Helper Virus for Prostate Cancer Treatment

Science.gov (United States)

2009-11-01

regulation HSV-1 amplicon and recombinant viruses Molecular cloning Cell culture/gene transfection Xenograft mouse model Histology 20...no herpetic lesions were seen in CMV-ICP4-143T–treated and CMV-ICP4-145T– treated animals, although some gastritis developed 28 days after the viral

A Portable Automatic Endpoint Detection System for Amplicons of Loop Mediated Isothermal Amplification on Microfluidic Compact Disk Platform

Directory of Open Access Journals (Sweden)

Shah Mukim Uddin

2015-03-01

Full Text Available In recent years, many improvements have been made in foodborne pathogen detection methods to reduce the impact of food contamination. Several rapid methods have been developed with biosensor devices to improve the way of performing pathogen detection. This paper presents an automated endpoint detection system for amplicons generated by loop mediated isothermal amplification (LAMP on a microfluidic compact disk platform. The developed detection system utilizes a monochromatic ultraviolet (UV emitter for excitation of fluorescent labeled LAMP amplicons and a color sensor to detect the emitted florescence from target. Then it processes the sensor output and displays the detection results on liquid crystal display (LCD. The sensitivity test has been performed with detection limit up to 2.5 × 10−3 ng/µL with different DNA concentrations of Salmonella bacteria. This system allows a rapid and automatic endpoint detection which could lead to the development of a point-of-care diagnosis device for foodborne pathogens detection in a resource-limited environment.

Imaging Herpes Simplex Virus Type 1 Amplicon Vector–Mediated Gene Expression in Human Glioma Spheroids

OpenAIRE

Christine Kaestle; Alexandra Winkeler; Raphaela Richter; Heinrich Sauer; Jürgen Hescheler; Cornel Fraefel; Maria Wartenberg; Andreas H. Jacobs

2011-01-01

Vectors derived from herpes simplex virus type 1 (HSV-1) have great potential for transducing therapeutic genes into the central nervous system; however, inefficient distribution of vector particles in vivo may limit their therapeutic potential in patients with gliomas. This study was performed to investigate the extent of HSV-1 amplicon vector–mediated gene expression in a three-dimensional glioma model of multicellular spheroids by imaging highly infectious HSV-1 virions expressing green fl...

Analysis of 16S rRNA amplicon sequencing options on the Roche/454 next-generation titanium sequencing platform.

Directory of Open Access Journals (Sweden)

Hideyuki Tamaki

Full Text Available BACKGROUND: 16S rRNA gene pyrosequencing approach has revolutionized studies in microbial ecology. While primer selection and short read length can affect the resulting microbial community profile, little is known about the influence of pyrosequencing methods on the sequencing throughput and the outcome of microbial community analyses. The aim of this study is to compare differences in output, ease, and cost among three different amplicon pyrosequencing methods for the Roche/454 Titanium platform METHODOLOGY/PRINCIPAL FINDINGS: The following three pyrosequencing methods for 16S rRNA genes were selected in this study: Method-1 (standard method is the recommended method for bi-directional sequencing using the LIB-A kit; Method-2 is a new option designed in this study for unidirectional sequencing with the LIB-A kit; and Method-3 uses the LIB-L kit for unidirectional sequencing. In our comparison among these three methods using 10 different environmental samples, Method-2 and Method-3 produced 1.5-1.6 times more useable reads than the standard method (Method-1, after quality-based trimming, and did not compromise the outcome of microbial community analyses. Specifically, Method-3 is the most cost-effective unidirectional amplicon sequencing method as it provided the most reads and required the least effort in consumables management. CONCLUSIONS: Our findings clearly demonstrated that alternative pyrosequencing methods for 16S rRNA genes could drastically affect sequencing output (e.g. number of reads before and after trimming but have little effect on the outcomes of microbial community analysis. This finding is important for both researchers and sequencing facilities utilizing 16S rRNA gene pyrosequencing for microbial ecological studies.

Network analysis of the microorganism in 25 Danish wastewater treatment plants over 7 years using high-throughput amplicon sequencing

DEFF Research Database (Denmark)

Albertsen, Mads; Larsen, Poul; Saunders, Aaron Marc

to link sludge and floc properties to the microbial communities. All data was subjected to extensive network analysis and multivariate statistics through R. The 16S amplicon results confirmed the findings of relatively few core groups of organism shared by all the wastewater treatment plants......Wastewater treatment is the world’s largest biotechnological processes and a perfect model system for microbial ecology as the habitat is well defined and replicated all over the world. Extensive investigations on Danish wastewater treatment plants using fluorescent in situ hybridization have...... a year, totaling over 400 samples. All samples were subjected to 16S rDNA amplicon sequencing using V13 primers on the Illumina MiSeq platform (2x300bp) to a depth of at least 20.000 quality filtered reads per sample. The OTUs were assigned taxonomy based on a manually curated version of the greengenes...

Similar diversity of Alphaproteobacteria and nitrogenase gene amplicons on two related Sphagnum mosses

Directory of Open Access Journals (Sweden)

Anastasia eBragina

2012-01-01

Full Text Available Sphagnum mosses represent a main component in ombrotrophic wetlands. They harbor a specific and diverse microbial community with essential functions for the host. To understand extend and degree of host specificity, Sphagnum fallax and S. angustifolium, two phylogenetically closely related species, which show distinct habitat preference with respect to the nutrient level, were analyzed by a multifaceted approach. Microbial fingerprints obtained by PCR-SSCP (single-strand conformation polymorphism using universal, group-specific and functional primers were highly similar. Similarity was confirmed for colonization patterns obtained by fluorescence in situ hybridization (FISH coupled with confocal laser scanning microscopy (CLSM: Alphaproteobacteria were the main colonizers inside the hyaline cells of Sphagnum leaves. A deeper survey of Alphaproteobacteria by 16S rRNA gene amplicon sequencing reveals a high diversity with Acidocella, Acidisphaera, Rhodopila and Phenylobacterium as major genera for both mosses. Pathogen defense and nitrogen fixation are important functions of Sphagnum-associated bacteria, which are fulfilled by microbial communities of both Sphagna in a similar way. NifH libraries of Sphagnum-associated microbial communities were characterized by high diversity and abundance of Alphaproteobacteria but contained also diverse amplicons of other taxa, e.g. Cyanobacteria, Geobacter and Spirochaeta. Statistically significant differences between the microbial communities of both Sphagnum species could not be discovered in any of the experimental approach. Our results show that the same close relationship, which exists between the physical, morphological and chemical characteristics of Sphagnum mosses and the ecology and function of bog ecosystems, also connects moss plantlets with their associated bacterial communities.

Identification of novel candidate target genes in amplicons of Glioblastoma multiforme tumors detected by expression and CGH microarray profiling

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Hernández-Moneo Jose-Luis

2006-09-01

Full Text Available Abstract Background Conventional cytogenetic and comparative genomic hybridization (CGH studies in brain malignancies have shown that glioblastoma multiforme (GBM is characterized by complex structural and numerical alterations. However, the limited resolution of these techniques has precluded the precise identification of detailed specific gene copy number alterations. Results We performed a genome-wide survey of gene copy number changes in 20 primary GBMs by CGH on cDNA microarrays. A novel amplicon at 4p15, and previously uncharacterized amplicons at 13q32-34 and 1q32 were detected and are analyzed here. These amplicons contained amplified genes not previously reported. Other amplified regions containg well-known oncogenes in GBMs were also detected at 7p12 (EGFR, 7q21 (CDK6, 4q12 (PDGFRA, and 12q13-15 (MDM2 and CDK4. In order to identify the putative target genes of the amplifications, and to determine the changes in gene expression levels associated with copy number change events, we carried out parallel gene expression profiling analyses using the same cDNA microarrays. We detected overexpression of the novel amplified genes SLA/LP and STIM2 (4p15, and TNFSF13B and COL4A2 (13q32-34. Some of the candidate target genes of amplification (EGFR, CDK6, MDM2, CDK4, and TNFSF13B were tested in an independent set of 111 primary GBMs by using FISH and immunohistological assays. The novel candidate 13q-amplification target TNFSF13B was amplified in 8% of the tumors, and showed protein expression in 20% of the GBMs. Conclusion This high-resolution analysis allowed us to propose novel candidate target genes such as STIM2 at 4p15, and TNFSF13B or COL4A2 at 13q32-34 that could potentially contribute to the pathogenesis of these tumors and which would require futher investigations. We showed that overexpression of the amplified genes could be attributable to gene dosage and speculate that deregulation of those genes could be important in the development

Shorter Decentralized Attribute-Based Encryption via Extended Dual System Groups

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Jie Zhang

2017-01-01

Full Text Available Decentralized attribute-based encryption (ABE is a special form of multiauthority ABE systems, in which no central authority and global coordination are required other than creating the common reference parameters. In this paper, we propose a new decentralized ABE in prime-order groups by using extended dual system groups. We formulate some assumptions used to prove the security of our scheme. Our proposed scheme is fully secure under the standard k-Lin assumption in random oracle model and can support any monotone access structures. Compared with existing fully secure decentralized ABE systems, our construction has shorter ciphertexts and secret keys. Moreover, fast decryption is achieved in our system, in which ciphertexts can be decrypted with a constant number of pairings.

Extending 3D near-cloud corrections from shorter to longer wavelengths

International Nuclear Information System (INIS)

Marshak, Alexander; Evans, K. Frank; Várnai, Tamás; Wen, Guoyong

2014-01-01

Satellite observations have shown a positive correlation between cloud amount and aerosol optical thickness (AOT) that can be explained by the humidification of aerosols near clouds, and/or by cloud contamination by sub-pixel size clouds and the cloud adjacency effect. The last effect may substantially increase reflected radiation in cloud-free columns, leading to overestimates in the retrieved AOT. For clear-sky areas near boundary layer clouds the main contribution to the enhancement of clear sky reflectance at shorter wavelengths comes from the radiation scattered into clear areas by clouds and then scattered to the sensor by air molecules. Because of the wavelength dependence of air molecule scattering, this process leads to a larger reflectance increase at shorter wavelengths, and can be corrected using a simple two-layer model [18]. However, correcting only for molecular scattering skews spectral properties of the retrieved AOT. Kassianov and Ovtchinnikov [9] proposed a technique that uses spectral reflectance ratios to retrieve AOT in the vicinity of clouds; they assumed that the cloud adjacency effect influences the spectral ratio between reflectances at two wavelengths less than it influences the reflectances themselves. This paper combines the two approaches: It assumes that the 3D correction for the shortest wavelength is known with some uncertainties, and then it estimates the 3D correction for longer wavelengths using a modified ratio method. The new approach is tested with 3D radiances simulated for 26 cumulus fields from Large-Eddy Simulations, supplemented with 40 aerosol profiles. The results showed that (i) for a variety of cumulus cloud scenes and aerosol profiles over ocean the 3D correction due to cloud adjacency effect can be extended from shorter to longer wavelengths and (ii) the 3D corrections for longer wavelengths are not very sensitive to unbiased random uncertainties in the 3D corrections at shorter wavelengths. - Highlights: �

Biphasic Study to Characterize Agricultural Biogas Plants by High-Throughput 16S rRNA Gene Amplicon Sequencing and Microscopic Analysis.

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Maus, Irena; Kim, Yong Sung; Wibberg, Daniel; Stolze, Yvonne; Off, Sandra; Antonczyk, Sebastian; Pühler, Alfred; Scherer, Paul; Schlüter, Andreas

2017-02-28

Process surveillance within agricultural biogas plants (BGPs) was concurrently studied by high-throughput 16S rRNA gene amplicon sequencing and an optimized quantitative microscopic fingerprinting (QMF) technique. In contrast to 16S rRNA gene amplicons, digitalized microscopy is a rapid and cost-effective method that facilitates enumeration and morphological differentiation of the most significant groups of methanogens regarding their shape and characteristic autofluorescent factor 420. Moreover, the fluorescence signal mirrors cell vitality. In this study, four different BGPs were investigated. The results indicated stable process performance in the mesophilic BGPs and in the thermophilic reactor. Bacterial subcommunity characterization revealed significant differences between the four BGPs. Most remarkably, the genera Defluviitoga and Halocella dominated the thermophilic bacterial subcommunity, whereas members of another taxon, Syntrophaceticus , were found to be abundant in the mesophilic BGP. The domain Archaea was dominated by the genus Methanoculleus in all four BGPs, followed by Methanosaeta in BGP1 and BGP3. In contrast, Methanothermobacter members were highly abundant in the thermophilic BGP4. Furthermore, a high consistency between the sequencing approach and the QMF method was shown, especially for the thermophilic BGP. The differences elucidated that using this biphasic approach for mesophilic BGPs provided novel insights regarding disaggregated single cells of Methanosarcina and Methanosaeta species. Both dominated the archaeal subcommunity and replaced coccoid Methanoculleus members belonging to the same group of Methanomicrobiales that have been frequently observed in similar BGPs. This work demonstrates that combining QMF and 16S rRNA gene amplicon sequencing is a complementary strategy to describe archaeal community structures within biogas processes.

Swarm v2: highly-scalable and high-resolution amplicon clustering.

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Mahé, Frédéric; Rognes, Torbjørn; Quince, Christopher; de Vargas, Colomban; Dunthorn, Micah

2015-01-01

Previously we presented Swarm v1, a novel and open source amplicon clustering program that produced fine-scale molecular operational taxonomic units (OTUs), free of arbitrary global clustering thresholds and input-order dependency. Swarm v1 worked with an initial phase that used iterative single-linkage with a local clustering threshold (d), followed by a phase that used the internal abundance structures of clusters to break chained OTUs. Here we present Swarm v2, which has two important novel features: (1) a new algorithm for d = 1 that allows the computation time of the program to scale linearly with increasing amounts of data; and (2) the new fastidious option that reduces under-grouping by grafting low abundant OTUs (e.g., singletons and doubletons) onto larger ones. Swarm v2 also directly integrates the clustering and breaking phases, dereplicates sequencing reads with d = 0, outputs OTU representatives in fasta format, and plots individual OTUs as two-dimensional networks.

Swarm v2: highly-scalable and high-resolution amplicon clustering

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Frédéric Mahé

2015-12-01

Full Text Available Previously we presented Swarm v1, a novel and open source amplicon clustering program that produced fine-scale molecular operational taxonomic units (OTUs, free of arbitrary global clustering thresholds and input-order dependency. Swarm v1 worked with an initial phase that used iterative single-linkage with a local clustering threshold (d, followed by a phase that used the internal abundance structures of clusters to break chained OTUs. Here we present Swarm v2, which has two important novel features: (1 a new algorithm for d = 1 that allows the computation time of the program to scale linearly with increasing amounts of data; and (2 the new fastidious option that reduces under-grouping by grafting low abundant OTUs (e.g., singletons and doubletons onto larger ones. Swarm v2 also directly integrates the clustering and breaking phases, dereplicates sequencing reads with d = 0, outputs OTU representatives in fasta format, and plots individual OTUs as two-dimensional networks.

Chromosomal Localization of DNA Amplifications in Neuroblastoma Tumors Using cDNA Microarray Comparative Genomic Hybridization

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Ben Beheshti

2003-01-01

Full Text Available Conventional comparative genomic hybridization (CGH profiling of neuroblastomas has identified many genomic aberrations, although the limited resolution has precluded a precise localization of sequences of interest within amplicons. To map high copy number genomic gains in clinically matched stage IV neuroblastomas, CGH analysis using a 19,200-feature cDNA microarray was used. A dedicated (freely available algorithm was developed for rapid in silico determination of chromosomal localizations of microarray cDNA targets, and for generation of an ideogram-type profile of copy number changes. Using these methodologies, novel gene amplifications undetectable by chromosome CGH were identified, and larger MYCN amplicon sizes (in one tumor up to 6 Mb than those previously reported in neuroblastoma were identified. The genes HPCAL1, LPIN1/KIAA0188, NAG, and NSE1/LOC151354 were found to be coamplified with MYCN. To determine whether stage IV primary tumors could be further subclassified based on their genomic copy number profiles, hierarchical clustering was performed. Cluster analysis of microarray CGH data identified three groups: 1 no amplifications evident, 2 a small MYCN amplicon as the only detectable imbalance, and 3 a large MYCN amplicon with additional gene amplifications. Application of CGH to cDNA microarray targets will help to determine both the variation of amplicon size and help better define amplification-dependent and independent pathways of progression in neuroblastoma.

Minimally invasive oesophagectomy more expensive than open despite shorter length of stay.

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Dhamija, Anish; Dhamija, Ankit; Hancock, Jacquelyn; McCloskey, Barbara; Kim, Anthony W; Detterbeck, Frank C; Boffa, Daniel J

2014-05-01

The minimally invasive oesophagectomy (MIO) approach offers a number of advantages over open approaches including reduced discomfort, shorter length of stay and a faster recovery to baseline status. On the other hand, minimally invasive procedures typically are longer and consume greater disposable instrumentation, potentially resulting in a greater overall cost. The objective of this study was to compare costs associated with various oesophagectomy approaches for oesophageal cancer. An institutional Resource Information Management System (RIMS) was queried for cost data relating to hospital expenditures (as opposed to billings or collections). The RIMS was searched for patients undergoing oesophagectomy for oesophageal cancer between 2003 and 2012 via minimally invasive, open transthoracic (OTT) (including Ivor Lewis, modified McKeown or thoracoabdominal) or transhiatal approaches. Patients that were converted from minimally invasive to open, or involved hybrid procedures, were excluded. A total of 160 oesophagectomies were identified, including 61 minimally invasive, 35 open transthoracic and 64 transhiatal. Costs on the day of surgery averaged higher in the MIO group ($12 476 ± 2190) compared with the open groups, OTT ($8202 ± 2512, P < 0.0001) or OTH ($5809 ± 2575, P < 0.0001). The median costs associated with the entire hospitalization also appear to be higher in the MIO group ($25 935) compared with OTT ($24 440) and OTH ($15 248). The average length of stay was lowest in the MIO group (11 ± 9 days) compared with OTT (19 ± 18 days, P = 0.006) and OTH (18 ± 28 days P = 0.07). The operative mortality was similar in the three groups (MIO = 3%, OTT = 9% and OTH = 3%). The operating theatre costs associated with minimally invasive oesophagectomy are significantly higher than OTT or OTH approaches. Unfortunately, a shorter hospital stay after MIO does not consistently offset higher surgical expense, as total hospital costs trend higher in the MIO patients. In

Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform.

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Schirmer, Melanie; Ijaz, Umer Z; D'Amore, Rosalinda; Hall, Neil; Sloan, William T; Quince, Christopher

2015-03-31

With read lengths of currently up to 2 × 300 bp, high throughput and low sequencing costs Illumina's MiSeq is becoming one of the most utilized sequencing platforms worldwide. The platform is manageable and affordable even for smaller labs. This enables quick turnaround on a broad range of applications such as targeted gene sequencing, metagenomics, small genome sequencing and clinical molecular diagnostics. However, Illumina error profiles are still poorly understood and programs are therefore not designed for the idiosyncrasies of Illumina data. A better knowledge of the error patterns is essential for sequence analysis and vital if we are to draw valid conclusions. Studying true genetic variation in a population sample is fundamental for understanding diseases, evolution and origin. We conducted a large study on the error patterns for the MiSeq based on 16S rRNA amplicon sequencing data. We tested state-of-the-art library preparation methods for amplicon sequencing and showed that the library preparation method and the choice of primers are the most significant sources of bias and cause distinct error patterns. Furthermore we tested the efficiency of various error correction strategies and identified quality trimming (Sickle) combined with error correction (BayesHammer) followed by read overlapping (PANDAseq) as the most successful approach, reducing substitution error rates on average by 93%. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Integrated Microfluidic Nucleic Acid Isolation, Isothermal Amplification, and Amplicon Quantification

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Michael G. Mauk

2015-10-01

Full Text Available Microfluidic components and systems for rapid (<60 min, low-cost, convenient, field-deployable sequence-specific nucleic acid-based amplification tests (NAATs are described. A microfluidic point-of-care (POC diagnostics test to quantify HIV viral load from blood samples serves as a representative and instructive example to discuss the technical issues and capabilities of “lab on a chip” NAAT devices. A portable, miniaturized POC NAAT with performance comparable to conventional PCR (polymerase-chain reaction-based tests in clinical laboratories can be realized with a disposable, palm-sized, plastic microfluidic chip in which: (1 nucleic acids (NAs are extracted from relatively large (~mL volume sample lysates using an embedded porous silica glass fiber or cellulose binding phase (“membrane” to capture sample NAs in a flow-through, filtration mode; (2 NAs captured on the membrane are isothermally (~65 °C amplified; (3 amplicon production is monitored by real-time fluorescence detection, such as with a smartphone CCD camera serving as a low-cost detector; and (4 paraffin-encapsulated, lyophilized reagents for temperature-activated release are pre-stored in the chip. Limits of Detection (LOD better than 103 virons/sample can be achieved. A modified chip with conduits hosting a diffusion-mode amplification process provides a simple visual indicator to readily quantify sample NA template. In addition, a companion microfluidic device for extracting plasma from whole blood without a centrifuge, generating cell-free plasma for chip-based molecular diagnostics, is described. Extensions to a myriad of related applications including, for example, food testing, cancer screening, and insect genotyping are briefly surveyed.

Recombinant adeno-associated virus type 2 replication and packaging is entirely supported by a herpes simplex virus type 1 amplicon expressing Rep and Cap.

Science.gov (United States)

Conway, J E; Zolotukhin, S; Muzyczka, N; Hayward, G S; Byrne, B J

1997-11-01

Recombinant adeno-associated virus (AAV) type 2 (rAAV) vectors have recently been shown to have great utility as gene transfer agents both in vitro and in vivo. One of the problems associated with the use of rAAV vectors has been the difficulty of large-scale vector production. Low-efficiency plasmid transfection of the rAAV vector and complementing AAV type 2 (AAV-2) functions (rep and cap) followed by superinfection with adenovirus has been the standard approach to rAAV production. The objectives of this study were to demonstrate the ability of a recombinant herpes simplex virus type 1 (HSV-1) amplicon expressing AAV-2 Rep and Cap to support replication and packaging of rAAV vectors. HSV-1 amplicon vectors were constructed which contain the AAV-2 rep and cap genes under control of their native promoters (p5, p19, and p40). An HSV-1 amplicon vector, HSV-RC/KOS or HSV-RC/d27, was generated by supplying helper functions with either wild-type HSV-1 (KOS strain) or the ICP27-deleted mutant of HSV-1, d27-1, respectively. Replication of the amplicon stocks is not inhibited by the presence of AAV-2 Rep proteins, which highlights important differences between HSV-1 and adenovirus replication and the mechanism of providing helper function for productive AAV infection. Coinfection of rAAV and HSV-RC/KOS resulted in the replication and amplification of rAAV genomes. Similarly, rescue and replication of rAAV genomes occurred when rAAV vector plasmids were transfected into cells followed by HSV-RC/KOS infection and when two rAAV proviral cell lines were infected with HSV-RC/KOS or HSV-RC/d27. Production of infectious rAAV by rescue from two rAAV proviral cell lines has also been achieved with HSV-RC/KOS and HSV-RC/d27. The particle titer of rAAV produced with HSV-RC/d27 is equal to that achieved by supplying rep and cap by transfection followed by adenovirus superinfection. Importantly, no detectable wild-type AAV-2 is generated with this approach. These results demonstrate

Improved Efficiency and Reliability of NGS Amplicon Sequencing Data Analysis for Genetic Diagnostic Procedures Using AGSA Software

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Axel Poulet

2016-01-01

Full Text Available Screening for BRCA mutations in women with familial risk of breast or ovarian cancer is an ideal situation for high-throughput sequencing, providing large amounts of low cost data. However, 454, Roche, and Ion Torrent, Thermo Fisher, technologies produce homopolymer-associated indel errors, complicating their use in routine diagnostics. We developed software, named AGSA, which helps to detect false positive mutations in homopolymeric sequences. Seventy-two familial breast cancer cases were analysed in parallel by amplicon 454 pyrosequencing and Sanger dideoxy sequencing for genetic variations of the BRCA genes. All 565 variants detected by dideoxy sequencing were also detected by pyrosequencing. Furthermore, pyrosequencing detected 42 variants that were missed with Sanger technique. Six amplicons contained homopolymer tracts in the coding sequence that were systematically misread by the software supplied by Roche. Read data plotted as histograms by AGSA software aided the analysis considerably and allowed validation of the majority of homopolymers. As an optimisation, additional 250 patients were analysed using microfluidic amplification of regions of interest (Access Array Fluidigm of the BRCA genes, followed by 454 sequencing and AGSA analysis. AGSA complements a complete line of high-throughput diagnostic sequence analysis, reducing time and costs while increasing reliability, notably for homopolymer tracts.

Using surface-enhanced Raman spectroscopy and electrochemically driven melting to discriminate Yersinia pestis from Y. pseudotuberculosis based on single nucleotide polymorphisms within unpurified polymerase chain reaction amplicons.

Science.gov (United States)

Papadopoulou, Evanthia; Goodchild, Sarah A; Cleary, David W; Weller, Simon A; Gale, Nittaya; Stubberfield, Michael R; Brown, Tom; Bartlett, Philip N

2015-02-03

The development of sensors for the detection of pathogen-specific DNA, including relevant species/strain level discrimination, is critical in molecular diagnostics with major impacts in areas such as bioterrorism and food safety. Herein, we use electrochemically driven denaturation assays monitored by surface-enhanced Raman spectroscopy (SERS) to target single nucleotide polymorphisms (SNPs) that distinguish DNA amplicons generated from Yersinia pestis, the causative agent of plague, from the closely related species Y. pseudotuberculosis. Two assays targeting SNPs within the groEL and metH genes of these two species have been successfully designed. Polymerase chain reaction (PCR) was used to produce Texas Red labeled single-stranded DNA (ssDNA) amplicons of 262 and 251 bases for the groEL and metH targets, respectively. These amplicons were used in an unpurified form to hybridize to immobilized probes then subjected to electrochemically driven melting. In all cases electrochemically driven melting was able to discriminate between fully homologous DNA and that containing SNPs. The metH assay was particularly challenging due to the presence of only a single base mismatch in the middle of the 251 base long PCR amplicon. However, manipulation of assay conditions (conducting the electrochemical experiments at 10 °C) resulted in greater discrimination between the complementary and mismatched DNA. Replicate data were collected and analyzed for each duplex on different days, using different batches of PCR product and different sphere segment void (SSV) substrates. Despite the variability introduced by these differences, the assays are shown to be reliable and robust providing a new platform for strain discrimination using unpurified PCR samples.

Photochemical immobilization of anthraquinone conjugated oligonucleotides and PCR amplicons on solid surfaces

DEFF Research Database (Denmark)

Koch, T.; Jacobsen, N.; Fensholdt, J.

2000-01-01

Ligand immobilization on solid surfaces is an essential step in fields such as diagnostics, bio sensor manufacturing, and new material sciences in general. In this paper a photochemical approach based on anthraquinone as the chromophore is presented. Photochemical procedures offer special...... advantages as they are able to generate highly reactive species in an orientation specific manner. As presented here, anthraquinone (AQ) mediated covalent DNA immobilization appears to be superior to currently known procedures. A synthetic procedure providing AQ-phosphoramidites is presented. These reagents...... facilitate AQ conjugation during routine DNA synthesis, thus enabling the AQ-oligonucleotides to be immobilized in a very convenient and efficient manner. AQ-conjugated PCR primers can be used directly in PCR. When the PCR is performed in solution, the amplicons can be immobilized after the PCR. Moreover...

The effect of shorter exposure versus prolonged exposure on treatment outcome in Tourette syndrome and chronic tic disorders - an open trial.

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van de Griendt, Jolande M T M; van Dijk, Maarten K; Verdellen, Cara W J; Verbraak, Marc J P M

2018-01-11

Exposure and response prevention has shown to be an effective strategy and is considered a first-line intervention in the behavioural treatment of tic disorders. Prior research demonstrated significant tic reduction after 12 two hour sessions. In this open trial, the question is addressed whether, relative to these prolonged sessions, exposure sessions of shorter duration yield differential outcome for patients with tic disorders. A total of 29 patients diagnosed with Tourette syndrome (TS) or chronic tic disorder were treated with shorter exposure sessions (1 h), and these data were compared to the data from a study about prolonged exposure (2 h, n = 21). Outcome was measured by the Yale Global Tic Severity Scale (YGTSS). Results suggest that after taking the difference in illness duration between the two groups into account, the effectiveness of shorter exposure sessions is not inferior to that of prolonged exposure. Results suggest that treatment with shorter exposure might be more efficient and more patients can be reached. Future research is needed to gain more insight into the mechanisms underlying the efficacy of behavioural treatments for tics.

The application of amplicon length heterogeneity PCR (LH-PCR) for monitoring the dynamics of soil microbial communities associated with cadaver decomposition.

Science.gov (United States)

Moreno, Lilliana I; Mills, DeEtta; Fetscher, Jill; John-Williams, Krista; Meadows-Jantz, Lee; McCord, Bruce

2011-03-01

The placement of cadavers in shallow, clandestine graves may alter the microbial and geochemical composition of the underlying and adjacent soils. Using amplicon length heterogeneity-PCR (LH-PCR) the microbial community changes in these soils can be assessed. In this investigation, nine different grave sites were examined over a period of 16weeks. The results indicated that measurable changes occurred in the soil bacterial community during the decomposition process. In this study, amplicons corresponding to anaerobic bacteria, not indigenous to the soil, were shown to produce differences between grave sites and control soils. Among the bacteria linked to these amplicons are those that are most often part of the commensal flora of the intestines, mouth and skin. In addition, over the 16week sampling interval, the level of indicator organisms (i.e., nitrogen fixing bacteria) dropped as the body decomposed and after four weeks of environmental exposure they began to increase again; thus differences in the abundance of nitrogen fixing bacteria were also found to contribute to the variation between controls and grave soils. These results were verified using primers that specifically targeted the nifH gene coding for nitrogenase reductase. LH-PCR provides a fast, robust and reproducible method to measure microbial changes in soil and could be used to determine potential cadaveric contact in a given area. The results obtained with this method could ultimately provide leads to investigators in criminal or missing person scenarios and allow for further analysis using human specific DNA assays to establish the identity of the buried body. Copyright © 2010 Elsevier B.V. All rights reserved.

Nitrogenase gene amplicons from global marine surface waters are dominated by genes of non-cyanobacteria

DEFF Research Database (Denmark)

Farnelid, Hanna; Andersson, Anders F.; Bertilsson, Stefan

2011-01-01

analysis of 79,090 nitrogenase (nifH) PCR amplicons encoding 7,468 unique proteins from surface samples (ten DNA samples and two RNA samples) collected at ten marine locations world-wide provides the first in-depth survey of a functional bacterial gene and yield insights into the composition and diversity...... by unicellular cyanobacteria, 42% of the identified non-cyanobacterial nifH clusters from the corresponding DNA samples were also detected in cDNA. The study indicates that non-cyanobacteria account for a substantial part of the nifH gene pool in marine surface waters and that these genes are at least...

High lung cancer surgical procedure volume is associated with shorter length of stay and lower risks of re-admission and death

DEFF Research Database (Denmark)

Møller, Henrik; Riaz, Sharma P; Holmberg, Lars

2016-01-01

It is debated whether treating cancer patients in high-volume surgical centres can lead to improvement in outcomes, such as shorter length of hospital stay, decreased frequency and severity of post-operative complications, decreased re-admission, and decreased mortality. The dataset for this anal......It is debated whether treating cancer patients in high-volume surgical centres can lead to improvement in outcomes, such as shorter length of hospital stay, decreased frequency and severity of post-operative complications, decreased re-admission, and decreased mortality. The dataset...... to their geographical population. Higher volume hospitals had shorter length of stay and the odds of re-admission were 15% lower in the highest hospital volume quintile compared with the lowest quintile. Mortality risks were 1% after 30 d and 3% after 90 d. Patients from hospitals in the highest volume quintile had...

Cowpea mosaic virus RNA-1 acts as an amplicon whose effects can be counteracted by a RNA-2-encoded suppressor of silencing

International Nuclear Information System (INIS)

Liu Li; Grainger, Jef; Canizares, M. Carmen; Angell, Susan M.; Lomonossoff, George P.

2004-01-01

Lines of Nicotiana benthamiana transgenic for full-length copies of both Cowpea mosaic virus (CPMV) genomic RNAs, either singly or together, have been produced. Plants transgenic for both RNAs developed symptoms characteristic of a CPMV infection. When plants transgenic for RNA-1 were agro-inoculated with RNA-2, no infection developed and the plants were also resistant to challenge with CPMV. By contrast, plants transgenic for RNA-2 became infected when agro-inoculated with RNA-1 and were fully susceptible to CPMV infection. The resistance of RNA-1 transgenic plants was shown to be related to the ability of RNA-1 to self-replicate and act as an amplicon. The ability of transgenically expressed RNA-2 to counteract the amplicon effect suggested that it encodes a suppressor of posttranscriptional gene silencing (PTGS). By examining the ability of portions of RNA-2 to reverse PTGS in N. benthamiana, we have identified the small (S) coat protein as the CPMV RNA-2-encoded suppressor of PTGS

Nitrogenase gene amplicons from global marine surface waters are dominated by genes of non-cyanobacteria.

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Hanna Farnelid

Full Text Available Cyanobacteria are thought to be the main N(2-fixing organisms (diazotrophs in marine pelagic waters, but recent molecular analyses indicate that non-cyanobacterial diazotrophs are also present and active. Existing data are, however, restricted geographically and by limited sequencing depths. Our analysis of 79,090 nitrogenase (nifH PCR amplicons encoding 7,468 unique proteins from surface samples (ten DNA samples and two RNA samples collected at ten marine locations world-wide provides the first in-depth survey of a functional bacterial gene and yield insights into the composition and diversity of the nifH gene pool in marine waters. Great divergence in nifH composition was observed between sites. Cyanobacteria-like genes were most frequent among amplicons from the warmest waters, but overall the data set was dominated by nifH sequences most closely related to non-cyanobacteria. Clusters related to Alpha-, Beta-, Gamma-, and Delta-Proteobacteria were most common and showed distinct geographic distributions. Sequences related to anaerobic bacteria (nifH Cluster III were generally rare, but preponderant in cold waters, especially in the Arctic. Although the two transcript samples were dominated by unicellular cyanobacteria, 42% of the identified non-cyanobacterial nifH clusters from the corresponding DNA samples were also detected in cDNA. The study indicates that non-cyanobacteria account for a substantial part of the nifH gene pool in marine surface waters and that these genes are at least occasionally expressed. The contribution of non-cyanobacterial diazotrophs to the global N(2 fixation budget cannot be inferred from sequence data alone, but the prevalence of non-cyanobacterial nifH genes and transcripts suggest that these bacteria are ecologically significant.

Genes encoded within 8q24 on the amplicon of a large extrachromosomal element are selectively repressed during the terminal differentiation of HL-60 cells.

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Hirano, Tetsuo; Ike, Fumio; Murata, Takehide; Obata, Yuichi; Utiyama, Hiroyasu; Yokoyama, Kazunari K

2008-04-02

Human acute myeloblastic leukemia HL-60 cells become resistant to differentiation during long-term cultivation. After 150 passages, double minute chromosomes (dmins) found in early-passaged cells are replaced by large extrachromosomal elements (LEEs). In a DNA library derived from a purified fraction of LEEs, 12.6% (23/183) of clones were assigned to 8q24 and 9.2% (17/183) were assigned to 14q11 in the human genome. Fluorescence in situ hybridization (FISH) revealed a small aberrant chromosome, which had not been found in early-passaged cells, in addition to the purified LEEs. We determined that each LEE consisted of six discontinuous segments in a region that extended for 4.4Mb over the 8q24 locus. Five genes, namely, Myc (a proto-oncogene), NSMCE2 (for a SUMO ligase), CCDC26 (for a retinoic acid-dependent modulator of myeloid differentiation), TRIB1 (for a regulator of MAPK kinase) and LOC389637 (for a protein of unknown function), were encoded by the amplicon. Breaks in the chromosomal DNA within the amplicon were found in the NSMCE2 and CCDC26 genes. The discontinuous structure of the amplicon unit of the LEEs was identical with that of dmins in HL-60 early-passaged cells. The difference between them seemed, predominantly, to be the number (10-15 copies per LEE versus 2 or 3 copies per dmin) of constituent units. Expression of the Myc, NSMCE2, CCDC26 and LOC389637 and TRIB1 genes was constitutive in all lines of HL-60 cells and that of the first four genes was repressed during the terminal differentiation of early-passaged HL-60 cells. We also detected abnormal transcripts of CCDC26. Our results suggest that these genes were selected during the development of amplicons. They might be amplified and, sometimes, truncated to contribute to the maintenance of HL-60 cells in an undifferentiated state.

Wear Fast, Die Young: More Worn Teeth and Shorter Lives in Iberian Compared to Scottish Red Deer.

Science.gov (United States)

Pérez-Barbería, F J; Carranza, J; Sánchez-Prieto, C

2015-01-01

Teeth in Cervidae are permanent structures that are not replaceable or repairable; consequently their rate of wear, due to the grinding effect of food and dental attrition, affects their duration and can determine an animal's lifespan. Tooth wear is also a useful indicator of accumulative life energy investment in intake and mastication and their interactions with diet. Little is known regarding how natural and sexual selection operate on dental structures within a species in contrasting environments and how these relate to life history traits to explain differences in population rates of tooth wear and longevity. We hypothesised that populations under harsh environmental conditions should be selected for more hypsodont teeth while sexual selection may maintain similar sex differences within different populations. We investigated the patterns of tooth wear in males and females of Iberian red deer (Cervus elaphus hispanicus) in Southern Spain and Scottish red deer (C. e. scoticus) across Scotland, that occur in very different environments, using 10343 samples from legal hunting activities. We found higher rates of both incisor and molar wear in the Spanish compared to Scottish populations. However, Scottish red deer had larger incisors at emergence than Iberian red deer, whilst molars emerged at a similar size in both populations and sexes. Iberian and Scottish males had earlier tooth depletion than females, in support of a similar sexual selection process in both populations. However, whilst average lifespan for Iberian males was 4 years shorter than that for Iberian females and Scottish males, Scottish males only showed a reduction of 1 year in average lifespan with respect to Scottish females. More worn molars were associated with larger mandibles in both populations, suggesting that higher intake and/or greater investment in food comminution may have favoured increased body growth, before later loss of tooth efficiency due to severe wear. These results

ATM/RB1 mutations predict shorter overall survival in urothelial cancer.

Science.gov (United States)

Yin, Ming; Grivas, Petros; Emamekhoo, Hamid; Mendiratta, Prateek; Ali, Siraj; Hsu, JoAnn; Vasekar, Monali; Drabick, Joseph J; Pal, Sumanta; Joshi, Monika

2018-03-30

Mutations of DNA repair genes, e.g. ATM/RB1 , are frequently found in urothelial cancer (UC) and have been associated with better response to cisplatin-based chemotherapy. Further external validation of the prognostic value of ATM/RB1 mutations in UC can inform clinical decision making and trial designs. In the discovery dataset, ATM/RB1 mutations were present in 24% of patients and were associated with shorter OS (adjusted HR 2.67, 95% CI, 1.45-4.92, p = 0.002). There was a higher mutation load in patients carrying ATM/RB1 mutations (median mutation load: 6.7 versus 5.5 per Mb, p = 0.072). In the validation dataset, ATM/RB1 mutations were present in 22.2% of patients and were non-significantly associated with shorter OS (adjusted HR 1.87, 95% CI, 0.97-3.59, p = 0.06) and higher mutation load (median mutation load: 8.1 versus 7.2 per Mb, p = 0.126). Exome sequencing data of 130 bladder UC patients from The Cancer Genome Atlas (TCGA) dataset were analyzed as a discovery cohort to determine the prognostic value of ATM/RB1 mutations. Results were validated in an independent cohort of 81 advanced UC patients. Cox proportional hazard regression analysis was performed to calculate the hazard ratio (HR) and 95% confidence interval (CI) to compare overall survival (OS). ATM/RB1 mutations may be a biomarker of poor prognosis in unselected UC patients and may correlate with higher mutational load. Further studies are required to determine factors that can further stratify prognosis and evaluate predictive role of ATM/RB1 mutation status to immunotherapy and platinum-based chemotherapy.

'Mitominis': multiplex PCR analysis of reduced size amplicons for compound sequence analysis of the entire mtDNA control region in highly degraded samples.

Science.gov (United States)

Eichmann, Cordula; Parson, Walther

2008-09-01

The traditional protocol for forensic mitochondrial DNA (mtDNA) analyses involves the amplification and sequencing of the two hypervariable segments HVS-I and HVS-II of the mtDNA control region. The primers usually span fragment sizes of 300-400 bp each region, which may result in weak or failed amplification in highly degraded samples. Here we introduce an improved and more stable approach using shortened amplicons in the fragment range between 144 and 237 bp. Ten such amplicons were required to produce overlapping fragments that cover the entire human mtDNA control region. These were co-amplified in two multiplex polymerase chain reactions and sequenced with the individual amplification primers. The primers were carefully selected to minimize binding on homoplasic and haplogroup-specific sites that would otherwise result in loss of amplification due to mis-priming. The multiplexes have successfully been applied to ancient and forensic samples such as bones and teeth that showed a high degree of degradation.

Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies

DEFF Research Database (Denmark)

Thorsen, Jonathan; Brejnrod, Asker Daniel; Mortensen, Martin Steen

2016-01-01

BACKGROUND: There is an immense scientific interest in the human microbiome and its effects on human physiology, health, and disease. A common approach for examining bacterial communities is high-throughput sequencing of 16S rRNA gene hypervariable regions, aggregating sequence-similar amplicons...

Developing de novo human artificial chromosomes in embryonic stem cells using HSV-1 amplicon technology.

Science.gov (United States)

Moralli, Daniela; Monaco, Zoia L

2015-02-01

De novo artificial chromosomes expressing genes have been generated in human embryonic stem cells (hESc) and are maintained following differentiation into other cell types. Human artificial chromosomes (HAC) are small, functional, extrachromosomal elements, which behave as normal chromosomes in human cells. De novo HAC are generated following delivery of alpha satellite DNA into target cells. HAC are characterized by high levels of mitotic stability and are used as models to study centromere formation and chromosome organisation. They are successful and effective as gene expression vectors since they remain autonomous and can accommodate larger genes and regulatory regions for long-term expression studies in cells unlike other viral gene delivery vectors currently used. Transferring the essential DNA sequences for HAC formation intact across the cell membrane has been challenging for a number of years. A highly efficient delivery system based on HSV-1 amplicons has been used to target DNA directly to the ES cell nucleus and HAC stably generated in human embryonic stem cells (hESc) at high frequency. HAC were detected using an improved protocol for hESc chromosome harvesting, which consistently produced high-quality metaphase spreads that could routinely detect HAC in hESc. In tumour cells, the input DNA often integrated in the host chromosomes, but in the host ES genome, it remained intact. The hESc containing the HAC formed embryoid bodies, generated teratoma in mice, and differentiated into neuronal cells where the HAC were maintained. The HAC structure and chromatin composition was similar to the endogenous hESc chromosomes. This review will discuss the technological advances in HAC vector delivery using HSV-1 amplicons and the improvements in the identification of de novo HAC in hESc.

SHORTER MENSTRUAL CYCLES ASSOCIATED WITH CHLORINATION BY-PRODUCTS IN DRINKING WATER

Science.gov (United States)

Shorter Menstrual Cycles Associated with Chlorination by-Products in Drinking Water. Gayle Windham, Kirsten Waller, Meredith Anderson, Laura Fenster, Pauline Mendola, Shanna Swan. California Department of Health Services.In previous studies of tap water consumption we...

A performance evaluation of Nextera XT and KAPA HyperPlus for rapid Illumina library preparation of long-range mitogenome amplicons.

Science.gov (United States)

Ring, Joseph D; Sturk-Andreaggi, Kimberly; Peck, Michelle A; Marshall, Charla

2017-07-01

Next-generation sequencing (NGS) facilitates the rapid and high-throughput generation of human mitochondrial genome (mitogenome) data to build population and reference databases for forensic comparisons. To this end, long-range amplification provides an effective method of target enrichment that is amenable to library preparation assays employing DNA fragmentation. This study compared the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA) and the KAPA HyperPlus Library Preparation Kit (Kapa Biosystems, Wilmington, MA) for enzymatic fragmentation and indexing of ∼8500bp mitogenome amplicons for Illumina sequencing. The Nextera XT libraries produced low-coverage regions that were consistent across all samples, while the HyperPlus libraries resulted in uniformly high coverage across the mitogenome, even with reduced-volume reaction conditions. The balanced coverage observed from KAPA HyperPlus libraries enables not only low-level variant calling across the mitogenome but also increased sample multiplexing for greater processing efficiency. Copyright © 2017 Elsevier B.V. All rights reserved.

YAOPBM-II: extension to higher degrees and to shorter time series

Energy Technology Data Exchange (ETDEWEB)

Korzennik, S G [Harvard-Smithsonian Center for Astrophysics, Cambridge, MA (United States)], E-mail: skorzennik@cfa.harvard.edu

2008-10-15

In 2005, I presented a new fitting methodology (Yet AnOther Peak Bagging Method -YAOPBM), derived for very-long time series (2088-day-long) and applied it to low degree modes, {iota} {<=} 25. That very-long time series was also sub-divided into shorter segments (728-day-long) that were each fitted over the same range of degrees, to estimate changes with solar activity levels. I present here the extension of this method in several 'directions': a) to substantially higher degrees ({iota} {<=} 125); b) to shorter time series (364- and 182-day-long); and c) to additional 728-day-long segments, covering now some 10 years of observations. I discuss issues with the fitting, namely the leakage matrix, and the f- and p1 mode at very low frequencies, and I present some of the characteristics of the observed temporal changes.

Next-generation sequencing of multiple individuals per barcoded library by deconvolution of sequenced amplicons using endonuclease fragment analysis

DEFF Research Database (Denmark)

Andersen, Jeppe D; Pereira, Vania; Pietroni, Carlotta

2014-01-01

The simultaneous sequencing of samples from multiple individuals increases the efficiency of next-generation sequencing (NGS) while also reducing costs. Here we describe a novel and simple approach for sequencing DNA from multiple individuals per barcode. Our strategy relies on the endonuclease...... digestion of PCR amplicons prior to library preparation, creating a specific fragment pattern for each individual that can be resolved after sequencing. By using both barcodes and restriction fragment patterns, we demonstrate the ability to sequence the human melanocortin 1 receptor (MC1R) genes from 72...... individuals using only 24 barcoded libraries....

Metagenomic Analysis of Slovak Bryndza Cheese Using Next-Generation 16S rDNA Amplicon Sequencing

Directory of Open Access Journals (Sweden)

Planý Matej

2016-06-01

Full Text Available Knowledge about diversity and taxonomic structure of the microbial population present in traditional fermented foods plays a key role in starter culture selection, safety improvement and quality enhancement of the end product. Aim of this study was to investigate microbial consortia composition in Slovak bryndza cheese. For this purpose, we used culture-independent approach based on 16S rDNA amplicon sequencing using next generation sequencing platform. Results obtained by the analysis of three commercial (produced on industrial scale in winter season and one traditional (artisanal, most valued, produced in May Slovak bryndza cheese sample were compared. A diverse prokaryotic microflora composed mostly of the genera Lactococcus, Streptococcus, Lactobacillus, and Enterococcus was identified. Lactococcus lactis subsp. lactis and Lactococcus lactis subsp. cremoris were the dominant taxons in all tested samples. Second most abundant species, detected in all bryndza cheeses, were Lactococcus fujiensis and Lactococcus taiwanensis, independently by two different approaches, using different reference 16S rRNA genes databases (Greengenes and NCBI respectively. They have been detected in bryndza cheese samples in substantial amount for the first time. The narrowest microbial diversity was observed in a sample made with a starter culture from pasteurised milk. Metagenomic analysis by high-throughput sequencing using 16S rRNA genes seems to be a powerful tool for studying the structure of the microbial population in cheeses.

Sequence-specific validation of LAMP amplicons in real-time optomagnetic detection of Dengue serotype 2 synthetic DNA

DEFF Research Database (Denmark)

Minero, Gabriel Khose Antonio; Nogueira, Catarina; Rizzi, Giovanni

2017-01-01

We report on an optomagnetic technique optimised for real-time molecular detection of Dengue fever virus under ideal as well as non-ideal laboratory conditions using two different detection approaches. The first approach is based on the detection of the hydrodynamic volume of streptavidin coated...... magnetic nanoparticles attached to biotinylated LAMP amplicons. We demonstrate detection of sub-femtomolar Dengue DNA target concentrations in the ideal contamination-free lab environment within 20 min. The second detection approach is based on sequence-specific binding of functionalised magnetic...... claim detection of down to 100 fM of Dengue target after 20 min of LAMP with a contamination background....

Hereditary angioedema attacks resolve faster and are shorter after early icatibant treatment.

Directory of Open Access Journals (Sweden)

Marcus Maurer

Full Text Available BACKGROUND: Attacks of hereditary angioedema (HAE are unpredictable and, if affecting the upper airway, can be lethal. Icatibant is used for physician- or patient self-administered symptomatic treatment of HAE attacks in adults. Its mode of action includes disruption of the bradykinin pathway via blockade of the bradykinin B(2 receptor. Early treatment is believed to shorten attack duration and prevent severe outcomes; however, evidence to support these benefits is lacking. OBJECTIVE: To examine the impact of timing of icatibant administration on the duration and resolution of HAE type I and II attacks. METHODS: The Icatibant Outcome Survey is an international, prospective, observational study for patients treated with icatibant. Data on timings and outcomes of icatibant treatment for HAE attacks were collected between July 2009-February 2012. A mixed-model of repeated measures was performed for 426 attacks in 136 HAE type I and II patients. RESULTS: Attack duration was significantly shorter in patients treated <1 hour of attack onset compared with those treated ≥ 1 hour (6.1 hours versus 16.8 hours [p<0.001]. Similar significant effects were observed for <2 hours versus ≥ 2 hours (7.2 hours versus 20.2 hours [p<0.001] and <5 hours versus ≥ 5 hours (8.0 hours versus 23.5 hours [p<0.001]. Treatment within 1 hour of attack onset also significantly reduced time to attack resolution (5.8 hours versus 8.8 hours [p<0.05]. Self-administrators were more likely to treat early and experience shorter attacks than those treated by a healthcare professional. CONCLUSION: Early blockade of the bradykinin B(2 receptor with icatibant, particularly within the first hour of attack onset, significantly reduced attack duration and time to attack resolution.

Identification and Evaluation of Single-Nucleotide Polymorphisms in Allotetraploid Peanut (Arachis hypogaea L.) Based on Amplicon Sequencing Combined with High Resolution Melting (HRM) Analysis.

Science.gov (United States)

Hong, Yanbin; Pandey, Manish K; Liu, Ying; Chen, Xiaoping; Liu, Hong; Varshney, Rajeev K; Liang, Xuanqiang; Huang, Shangzhi

2015-01-01

The cultivated peanut (Arachis hypogaea L.) is an allotetraploid (AABB) species derived from the A-genome (Arachis duranensis) and B-genome (Arachis ipaensis) progenitors. Presence of two versions of a DNA sequence based on the two progenitor genomes poses a serious technical and analytical problem during single nucleotide polymorphism (SNP) marker identification and analysis. In this context, we have analyzed 200 amplicons derived from expressed sequence tags (ESTs) and genome survey sequences (GSS) to identify SNPs in a panel of genotypes consisting of 12 cultivated peanut varieties and two diploid progenitors representing the ancestral genomes. A total of 18 EST-SNPs and 44 genomic-SNPs were identified in 12 peanut varieties by aligning the sequence of A. hypogaea with diploid progenitors. The average frequency of sequence polymorphism was higher for genomic-SNPs than the EST-SNPs with one genomic-SNP every 1011 bp as compared to one EST-SNP every 2557 bp. In order to estimate the potential and further applicability of these identified SNPs, 96 peanut varieties were genotyped using high resolution melting (HRM) method. Polymorphism information content (PIC) values for EST-SNPs ranged between 0.021 and 0.413 with a mean of 0.172 in the set of peanut varieties, while genomic-SNPs ranged between 0.080 and 0.478 with a mean of 0.249. Total 33 SNPs were used for polymorphism detection among the parents and 10 selected lines from mapping population Y13Zh (Zhenzhuhei × Yueyou13). Of the total 33 SNPs, nine SNPs showed polymorphism in the mapping population Y13Zh, and seven SNPs were successfully mapped into five linkage groups. Our results showed that SNPs can be identified in allotetraploid peanut with high accuracy through amplicon sequencing and HRM assay. The identified SNPs were very informative and can be used for different genetic and breeding applications in peanut.

Interstitial lung abnormalities in treatment-naïve advanced non-small-cell lung cancer patients are associated with shorter survival

Energy Technology Data Exchange (ETDEWEB)

Nishino, Mizuki, E-mail: Mizuki_Nishino@DFCI.HARVARD.EDU [Department of Radiology, Brigham and Women' s Hospital, 75 Francis St., Boston, MA 02115 (United States); Department of Imaging, Dana-Farber Cancer Institute, 450 Brookline Ave., Boston, MA 02215 (United States); Cardarella, Stephanie [Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave., Boston, MA 02215, (United States); Dahlberg, Suzanne E. [Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 450 Brookline Ave., Boston, MA 02215 (United States); Araki, Tetsuro [Department of Radiology, Brigham and Women' s Hospital, 75 Francis St., Boston, MA 02115 (United States); Lydon, Christine; Jackman, David M.; Rabin, Michael S. [Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave., Boston, MA 02215, (United States); Hatabu, Hiroto [Department of Radiology, Brigham and Women' s Hospital, 75 Francis St., Boston, MA 02115 (United States); Johnson, Bruce E. [Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave., Boston, MA 02215, (United States)

2015-05-15

Highlights: • Interstitial lung abnormalities were present in 14% of stage IV NSCLC patients. • ILA was more common in older patients with heavier smoking history. • ILA was associated with shorter survival after adjusting for smoking and therapy. • ILA could be an additional independent marker for survival in advanced NSCLC. - Abstract: Objective: Interstitial lung diseases are associated with increased risk of lung cancer. The prevalence of ILA at diagnosis of advanced non-small-cell lung cancer (NSCLC) and its impact on overall survival (OS) remain to be investigated. Materials and method: The study included 120 treatment-naïve stage IV NSCLC patients (53 males, 67 females). ILA was scored on CT prior to any systemic therapy using a 4-point scale [0 = no evidence of ILA, 1 = equivocal for ILA, 2 = suspicious for ILA, 3 = ILA] by a sequential reading method previously reported. ILA scores of 2 or 3 indicated the presence of ILA. Results: ILA was present in 17 patients (14%) with advanced NSCLC prior to any treatment (score3: n = 2, score2: n = 15). These 17 patients were significantly older (median age: 69 vs. 63, p = 0.04) and had a heavier smoking history (median: 40 vs. 15.5 pack-year, p = 0.003) than those with ILA score 0 or 1. Higher ILA scores were associated with shorter OS (p = 0.001). Median OS of the 17 patients with ILA was 7.2 months [95%CI: 2.9–9.4] compared to 14.8 months [95%CI: 11.1–18.4] in patients with ILA score 0 or 1 (p = 0.002). In a multivariate model, the presence of ILA remained significant for increased risk for death (HR = 2.09, p = 0.028) after adjusting for first-line systemic therapy (chemotherapy, p < 0.001; TKI, p < 0.001; each compared to no therapy) and pack years of smoking (p = 0.40). Conclusion: Radiographic ILA was present in 14% of treatment-naïve advanced NSCLC patients. Higher ILA scores were associated with shorter OS, indicating that ILA could be a marker of shorter survival in advanced NSCLC.

Microbial community profiling of fresh basil and pitfalls in taxonomic assignment of enterobacterial pathogenic species based upon 16S rRNA amplicon sequencing.

Science.gov (United States)

Ceuppens, Siele; De Coninck, Dieter; Bottledoorn, Nadine; Van Nieuwerburgh, Filip; Uyttendaele, Mieke

2017-09-18

Application of 16S rRNA (gene) amplicon sequencing on food samples is increasingly applied for assessing microbial diversity but may as unintended advantage also enable simultaneous detection of any human pathogens without a priori definition. In the present study high-throughput next-generation sequencing (NGS) of the V1-V2-V3 regions of the 16S rRNA gene was applied to identify the bacteria present on fresh basil leaves. However, results were strongly impacted by variations in the bioinformatics analysis pipelines (MEGAN, SILVAngs, QIIME and MG-RAST), including the database choice (Greengenes, RDP and M5RNA) and the annotation algorithm (best hit, representative hit and lowest common ancestor). The use of pipelines with default parameters will lead to discrepancies. The estimate of microbial diversity of fresh basil using 16S rRNA (gene) amplicon sequencing is thus indicative but subject to biases. Salmonella enterica was detected at low frequencies, between 0.1% and 0.4% of bacterial sequences, corresponding with 37 to 166 reads. However, this result was dependent upon the pipeline used: Salmonella was detected by MEGAN, SILVAngs and MG-RAST, but not by QIIME. Confirmation of Salmonella sequences by real-time PCR was unsuccessful. It was shown that taxonomic resolution obtained from the short (500bp) sequence reads of the 16S rRNA gene containing the hypervariable regions V1-V3 cannot allow distinction of Salmonella with closely related enterobacterial species. In conclusion 16S amplicon sequencing, getting the status of standard method in microbial ecology studies of foods, needs expertise on both bioinformatics and microbiology for analysis of results. It is a powerful tool to estimate bacterial diversity but amenable to biases. Limitations concerning taxonomic resolution for some bacterial species or its inability to detect sub-dominant (pathogenic) species should be acknowledged in order to avoid overinterpretation of results. Copyright © 2017 Elsevier B

Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies

KAUST Repository

Wang, Yong

2009-10-09

Bacterial 16S ribosomal DNA (rDNA) amplicons have been widely used in the classification of uncultured bacteria inhabiting environmental niches. Primers targeting conservative regions of the rDNAs are used to generate amplicons of variant regions that are informative in taxonomic assignment. One problem is that the percentage coverage and application scope of the primers used in previous studies are largely unknown. In this study, conservative fragments of available rDNA sequences were first mined and then used to search for candidate primers within the fragments by measuring the coverage rate defined as the percentage of bacterial sequences containing the target. Thirty predicted primers with a high coverage rate (>90%) were identified, which were basically located in the same conservative regions as known primers in previous reports, whereas 30% of the known primers were associated with a coverage rate of <90%. The application scope of the primers was also examined by calculating the percentages of failed detections in bacterial phyla. Primers A519-539, E969- 983, E1063-1081, U515 and E517, are highly recommended because of their high coverage in almost all phyla. As expected, the three predominant phyla, Firmicutes, Gemmatimonadetes and Proteobacteria, are best covered by the predicted primers. The primers recommended in this report shall facilitate a comprehensive and reliable survey of bacterial diversity in metagenomic studies. © 2009 Wang, Qian.

Amplicon sequencing of bacterial microbiota in abortion material from cattle.

Science.gov (United States)

Vidal, Sara; Kegler, Kristel; Posthaus, Horst; Perreten, Vincent; Rodriguez-Campos, Sabrina

2017-10-10

Abortions in cattle have a significant economic impact on animal husbandry and require prompt diagnosis for surveillance of epizootic infectious agents. Since most abortions are not epizootic but sporadic with often undetected etiologies, this study examined the bacterial community present in the placenta (PL, n = 32) and fetal abomasal content (AC, n = 49) in 64 cases of bovine abortion by next generation sequencing (NGS) of the 16S rRNA gene. The PL and AC from three fetuses of dams that died from non-infectious reasons were included as controls. All samples were analyzed by bacterial culture, and 17 were examined by histopathology. We observed 922 OTUs overall and 267 taxa at the genus level. No detectable bacterial DNA was present in the control samples. The microbial profiles of the PL and AC differed significantly, both in their composition (PERMANOVA), species richness and Chao-1 (Mann-Whitney test). In both organs, Pseudomonas was the most abundant genus. The combination of NGS and culture identified opportunistic pathogens of interest in placentas with lesions, such as Vibrio metschnikovii, Streptococcus uberis, Lactococcus lactis and Escherichia coli. In placentas with lesions where culturing was unsuccessful, Pseudomonas and unidentified Aeromonadaceae were identified by NGS displaying high number of reads. Three cases with multiple possible etiologies and placentas presenting lesions were detected by NGS. Amplicon sequencing has the potential to uncover unknown etiological agents. These new insights on cattle abortion extend our focus to previously understudied opportunistic abortive bacteria.

Hi-Plex for Simple, Accurate, and Cost-Effective Amplicon-based Targeted DNA Sequencing.

Science.gov (United States)

Pope, Bernard J; Hammet, Fleur; Nguyen-Dumont, Tu; Park, Daniel J

2018-01-01

Hi-Plex is a suite of methods to enable simple, accurate, and cost-effective highly multiplex PCR-based targeted sequencing (Nguyen-Dumont et al., Biotechniques 58:33-36, 2015). At its core is the principle of using gene-specific primers (GSPs) to "seed" (or target) the reaction and universal primers to "drive" the majority of the reaction. In this manner, effects on amplification efficiencies across the target amplicons can, to a large extent, be restricted to early seeding cycles. Product sizes are defined within a relatively narrow range to enable high-specificity size selection, replication uniformity across target sites (including in the context of fragmented input DNA such as that derived from fixed tumor specimens (Nguyen-Dumont et al., Biotechniques 55:69-74, 2013; Nguyen-Dumont et al., Anal Biochem 470:48-51, 2015), and application of high-specificity genetic variant calling algorithms (Pope et al., Source Code Biol Med 9:3, 2014; Park et al., BMC Bioinformatics 17:165, 2016). Hi-Plex offers a streamlined workflow that is suitable for testing large numbers of specimens without the need for automation.

16S rRNA Amplicon Sequencing Demonstrates that Indoor-Reared Bumblebees (Bombus terrestris Harbor a Core Subset of Bacteria Normally Associated with the Wild Host.

Directory of Open Access Journals (Sweden)

Ivan Meeus

Full Text Available A MiSeq multiplexed 16S rRNA amplicon sequencing of the gut microbiota of wild and indoor-reared Bombus terrestris (bumblebees confirmed the presence of a core set of bacteria, which consisted of Neisseriaceae (Snodgrassella, Orbaceae (Gilliamella, Lactobacillaceae (Lactobacillus, and Bifidobacteriaceae (Bifidobacterium. In wild B. terrestris we detected several non-core bacteria having a more variable prevalence. Although Enterobacteriaceae are unreported by non next-generation sequencing studies, it can become a dominant gut resident. Furthermore the presence of some non-core lactobacilli were associated with the relative abundance of bifidobacteria. This association was not observed in indoor-reared bumblebees lacking the non-core bacteria, but having a more standardized microbiota compared to their wild counterparts. The impact of the bottleneck microbiota of indoor-reared bumblebees when they are used in the field for pollination purpose is discussed.

A need for standardization in drinking water analysis – an investigation of DNA extraction procedure, primer choice and detection limit of 16S rRNA amplicon sequencing

DEFF Research Database (Denmark)

Brandt, Jakob; Nielsen, Per Halkjær; Albertsen, Mads

have been made to illuminate the effects specifically related to bacterial communities in drinking water. In this study, we investigated the impact of the DNA extraction and primer choice on the observed community structure, and we also estimated the detection limit of the 16S rRNA amplicon sequencing...

One long chain among shorter chains : the Flory approach revisited

OpenAIRE

Raphaël , E.; Fredrickson , G.; Pincus , P.

1992-01-01

We consider the mean square end-to-end distance of a long chain immersed in a monodisperse, concentrated solution of shorter, chemically identical chains. In contrast with the earlier work of Flory, no simplifying assumption on the wave vector dependence of the effective potential between segments is made. In order to obtain a closed form expression for the dimension of the long chain, we first derive a general expression for the mean square end-to-end distance of a flexible chain with arbitr...

Canary: an atomic pipeline for clinical amplicon assays.

Science.gov (United States)

Doig, Kenneth D; Ellul, Jason; Fellowes, Andrew; Thompson, Ella R; Ryland, Georgina; Blombery, Piers; Papenfuss, Anthony T; Fox, Stephen B

2017-12-15

High throughput sequencing requires bioinformatics pipelines to process large volumes of data into meaningful variants that can be translated into a clinical report. These pipelines often suffer from a number of shortcomings: they lack robustness and have many components written in multiple languages, each with a variety of resource requirements. Pipeline components must be linked together with a workflow system to achieve the processing of FASTQ files through to a VCF file of variants. Crafting these pipelines requires considerable bioinformatics and IT skills beyond the reach of many clinical laboratories. Here we present Canary, a single program that can be run on a laptop, which takes FASTQ files from amplicon assays through to an annotated VCF file ready for clinical analysis. Canary can be installed and run with a single command using Docker containerization or run as a single JAR file on a wide range of platforms. Although it is a single utility, Canary performs all the functions present in more complex and unwieldy pipelines. All variants identified by Canary are 3' shifted and represented in their most parsimonious form to provide a consistent nomenclature, irrespective of sequencing variation. Further, proximate in-phase variants are represented as a single HGVS 'delins' variant. This allows for correct nomenclature and consequences to be ascribed to complex multi-nucleotide polymorphisms (MNPs), which are otherwise difficult to represent and interpret. Variants can also be annotated with hundreds of attributes sourced from MyVariant.info to give up to date details on pathogenicity, population statistics and in-silico predictors. Canary has been used at the Peter MacCallum Cancer Centre in Melbourne for the last 2 years for the processing of clinical sequencing data. By encapsulating clinical features in a single, easily installed executable, Canary makes sequencing more accessible to all pathology laboratories. Canary is available for download as source

Typing of 30 insertion/deletions in Danes using the first commercial indel kit-Mentype(®) DIPplex

DEFF Research Database (Denmark)

Friis, Susanne Lunøe; Børsting, Claus; Rockenbauer, Eszter

2012-01-01

and all amplicon lengths were shorter than 160bp. Full indel profiles were generated from as little as 100pg of DNA. A total of 117 individuals from Danish paternity cases were successfully typed. No deviation from Hardy-Weinberg equilibrium was observed for any of the indels. The combined mean match...

Complete Chloroplast Genome Sequence of Tartary Buckwheat (Fagopyrum tataricum and Comparative Analysis with Common Buckwheat (F. esculentum.

Directory of Open Access Journals (Sweden)

Kwang-Soo Cho

Full Text Available We report the chloroplast (cp genome sequence of tartary buckwheat (Fagopyrum tataricum obtained by next-generation sequencing technology and compared this with the previously reported common buckwheat (F. esculentum ssp. ancestrale cp genome. The cp genome of F. tataricum has a total sequence length of 159,272 bp, which is 327 bp shorter than the common buckwheat cp genome. The cp gene content, order, and orientation are similar to those of common buckwheat, but with some structural variation at tandem and palindromic repeat frequencies and junction areas. A total of seven InDels (around 100 bp were found within the intergenic sequences and the ycf1 gene. Copy number variation of the 21-bp tandem repeat varied in F. tataricum (four repeats and F. esculentum (one repeat, and the InDel of the ycf1 gene was 63 bp long. Nucleotide and amino acid have highly conserved coding sequence with about 98% homology and four genes--rpoC2, ycf3, accD, and clpP--have high synonymous (Ks value. PCR based InDel markers were applied to diverse genetic resources of F. tataricum and F. esculentum, and the amplicon size was identical to that expected in silico. Therefore, these InDel markers are informative biomarkers to practically distinguish raw or processed buckwheat products derived from F. tataricum and F. esculentum.

Lactococcus lactis Diversity in Undefined Mixed Dairy Starter Cultures as Revealed by Comparative Genome Analyses and Targeted Amplicon Sequencing of epsD.

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Frantzen, Cyril A; Kleppen, Hans Petter; Holo, Helge

2018-02-01

Undefined mesophilic mixed (DL) starter cultures are used in the production of continental cheeses and contain unknown strain mixtures of Lactococcus lactis and leuconostocs. The choice of starter culture affects the taste, aroma, and quality of the final product. To gain insight into the diversity of Lactococcus lactis strains in starter cultures, we whole-genome sequenced 95 isolates from three different starter cultures. Pan-genomic analyses, which included 30 publically available complete genomes, grouped the strains into 21 L. lactis subsp . lactis and 28 L. lactis subsp. cremoris lineages. Only one of the 95 isolates grouped with previously sequenced strains, and the three starter cultures showed no overlap in lineage distributions. The culture diversity was assessed by targeted amplicon sequencing using purR , a core gene, and epsD , present in 93 of the 95 starter culture isolates but absent in most of the reference strains. This enabled an unprecedented discrimination of starter culture Lactococcus lactis and revealed substantial differences between the three starter cultures and compositional shifts during the cultivation of cultures in milk. IMPORTANCE In contemporary cheese production, standardized frozen seed stock starter cultures are used to ensure production stability, reproducibility, and quality control of the product. The dairy industry experiences significant disruptions of cheese production due to phage attacks, and one commonly used countermeasure to phage attack is to employ a starter rotation strategy, in which two or more starters with minimal overlap in phage sensitivity are used alternately. A culture-independent analysis of the lactococcal diversity in complex undefined starter cultures revealed large differences between the three starter cultures and temporal shifts in lactococcal composition during the production of bulk starters. A better understanding of the lactococcal diversity in starter cultures will enable the development of

Physical activity during video capsule endoscopy correlates with shorter bowel transit time.

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Stanich, Peter P; Peck, Joshua; Murphy, Christopher; Porter, Kyle M; Meyer, Marty M

2017-09-01

 Video capsule endoscopy (VCE) is limited by reliance on bowel motility for propulsion, and lack of physical activity has been proposed as a cause of incomplete studies. Our aim was to prospectively investigate the association between physical activity and VCE bowel transit.  Ambulatory outpatients receiving VCE were eligible for the study. A pedometer was attached at the time of VCE ingestion and step count was recorded at the end of the procedure. VCE completion was assessed by logistic regression models, which included step count (500 steps as one unit). Total transit time was analyzed by Cox proportional hazards models. The hazard ratios (HR) with 95 % confidence interval (CI) indicated the "hazard" of completion, such that HRs > 1 indicated a reduced transit time.  A total of 100 patients were included. VCE was completed in 93 patients (93 %). The median step count was 2782 steps. Step count was not significantly associated with VCE completion (odds ratio 1.45, 95 %CI 0.84, 2.49). Pedometer step count was significantly associated with shorter total, gastric, and small-bowel transit times (HR 1.09, 95 %CI 1.03, 1.16; HR 1.05, 95 %CI 1.00, 1.11; HR 1.07, 95 %CI 1.01, 1.14, respectively). Higher body mass index (BMI) was significantly associated with VCE completion (HR 1.87, 95 %CI 1.18, 2.97) and shorter bowel transit times (HR 1.05, 95 %CI 1.02, 1.08).  Increased physical activity during outpatient VCE was associated with shorter bowel transit times but not with study completion. In addition, BMI was a previously unreported clinical characteristic associated with VCE completion and should be included as a variable of interest in future studies.

Do shorter wavelengths improve contrast in optical mammography?

International Nuclear Information System (INIS)

Taroni, P; Pifferi, A; Torricelli, A; Spinelli, L; Danesini, G M; Cubeddu, R

2004-01-01

The detection of tumours with time-resolved transmittance imaging relies essentially on blood absorption. Previous theoretical and phantom studies have shown that both contrast and spatial resolution of optical images are affected by the optical properties of the background medium, and high absorption and scattering are generally beneficial. Based on these observations, wavelengths shorter than presently used (680-780 nm) could be profitable for optical mammography. A study was thus performed analysing time-resolved transmittance images at 637, 656, 683 and 785 nm obtained from 26 patients bearing 16 tumours and 15 cysts. The optical contrast proved to increase upon decreasing wavelengths for the detection of cancers in late-gated intensity images, with higher gain in contrast for lesions of smaller size (<1.5 cm diameter). For cysts either a progressive increase or decrease in contrast with wavelength was observed in scattering images

Smoking Topography among Korean Smokers: Intensive Smoking Behavior with Larger Puff Volume and Shorter Interpuff Interval.

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Kim, Sungroul; Yu, Sol

2018-05-18

The difference of smoker's topography has been found to be a function many factors, including sex, personality, nicotine yield, cigarette type (i.e., flavored versus non-flavored) and ethnicity. We evaluated the puffing behaviors of Korean smokers and its association with smoking-related biomarker levels. A sample of 300 participants was randomly recruited from metropolitan areas in South Korea. Topography measures during a 24-hour period were obtained using a CReSS pocket device. Korean male smokers smoked two puffs less per cigarette compared to female smokers (15.0 (13.0⁻19.0) vs. 17.5 (15.0⁻21.0) as the median (Interquartile range)), but had a significantly larger puff volume (62.7 (52.7⁻75.5) mL vs. 53.5 (42.0⁻64.2) mL); p = 0.012). The interpuff interval was similar between men and women (8.9 (6.5⁻11.2) s vs. 8.3 (6.2⁻11.0) s; p = 0.122) but much shorter than other study results. A dose-response association ( p = 0.0011) was observed between daily total puff volumes and urinary cotinine concentrations, after controlling for sex, age, household income level and nicotine addiction level. An understanding of the difference of topography measures, particularly the larger puff volume and shorter interpuff interval of Korean smokers, may help to overcome a potential underestimation of internal doses of hazardous byproducts of smoking.

Systemic lupus erythematosus and vitamin D deficiency are associated with shorter telomere length among African Americans: a case-control study.

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Brett M Hoffecker

Full Text Available Systemic lupus erythematosus (SLE is a chronic systemic autoimmune disease that disproportionately affects African American females. The causes of SLE are unknown but postulated to be a combination of genetic predisposition and environmental triggers. Vitamin D deficiency is one of the possible environmental triggers. In this study we evaluated relationships between vitamin D status, cellular aging (telomere length and anti-telomere antibodies among African American Gullah women with SLE. The study population included African American female SLE patients and unaffected controls from the Sea Island region of South Carolina. Serum 25-hydroxyvitamin D levels were measured using a nonchromatographic radioimmunoassay. Telomere length was measured in genomic DNA of peripheral blood mononuclear cells (PBMCs by monochrome multiplex quantitative PCR. Anti-telomere antibody levels were measured by enzyme-linked immunosorbent assay (ELISA. Patients with SLE had significantly shorter telomeres and higher anti-telomere antibody titers compared to age- and gender-matched unaffected controls. There was a positive correlation between anti-telomere antibody levels and disease activity among patients and a significant correlation of shorter telomeres with lower 25-hydroxyvitamin D levels in both patients and controls. In follow-up examination of a subset of the patients, the patients who remained vitamin D deficient tended to have shorter telomeres than those patients whose 25-hydroxyvitamin D levels were repleted. Increasing 25-hydroxyvitamin D levels in African American patients with SLE may be beneficial in maintaining telomere length and preventing cellular aging. Moreover, anti-telomere antibody levels may be a promising biomarker of SLE status and disease activity.

Differential amplicons (ΔAmp)-a new molecular method to assess RNA integrity.

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Björkman, J; Švec, D; Lott, E; Kubista, M; Sjöback, R

2016-01-01

Integrity of the mRNA in clinical samples has major impact on the quality of measured expression levels. This is independent of the measurement technique being next generation sequencing (NGS), Quantitative real-time PCR (qPCR) or microarray profiling. If mRNA is highly degraded or damaged, measured data will be very unreliable and the whole study is likely a waste of time and money. It is therefore common strategy to test the quality of RNA in samples before conducting large and costly studies. Most methods today to assess the quality of RNA are ignorant to the nature of the RNA and, therefore, reflect the integrity of ribosomal RNA, which is the dominant species, rather than of mRNAs, microRNAs and long non-coding RNAs, which usually are the species of interest. Here, we present a novel molecular approach to assess the quality of the targeted RNA species by measuring the differential amplification (ΔAmp) of an Endogenous RNase Resistant (ERR) marker relative to a reference gene, optionally combined with the measurement of two amplicons of different lengths. The combination reveals any mRNA degradation caused by ribonucleases as well as physical, chemical or UV damage. ΔAmp has superior sensitivity to common microfluidic electrophoretic methods, senses the integrity of the actual targeted RNA species, and allows for a smoother and more cost efficient workflow.

Differential amplicons (ΔAmp—a new molecular method to assess RNA integrity

Directory of Open Access Journals (Sweden)

J. Björkman

2016-01-01

Full Text Available Integrity of the mRNA in clinical samples has major impact on the quality of measured expression levels. This is independent of the measurement technique being next generation sequencing (NGS, Quantitative real-time PCR (qPCR or microarray profiling. If mRNA is highly degraded or damaged, measured data will be very unreliable and the whole study is likely a waste of time and money. It is therefore common strategy to test the quality of RNA in samples before conducting large and costly studies. Most methods today to assess the quality of RNA are ignorant to the nature of the RNA and, therefore, reflect the integrity of ribosomal RNA, which is the dominant species, rather than of mRNAs, microRNAs and long non-coding RNAs, which usually are the species of interest. Here, we present a novel molecular approach to assess the quality of the targeted RNA species by measuring the differential amplification (ΔAmp of an Endogenous RNase Resistant (ERR marker relative to a reference gene, optionally combined with the measurement of two amplicons of different lengths. The combination reveals any mRNA degradation caused by ribonucleases as well as physical, chemical or UV damage. ΔAmp has superior sensitivity to common microfluidic electrophoretic methods, senses the integrity of the actual targeted RNA species, and allows for a smoother and more cost efficient workflow.

The Change of the Family Life Affected by the Shorter Working Time : From the Point of View of the Home Management

OpenAIRE

平田, 道憲

1994-01-01

In Japan, the working time has been decreasing. However, Japanese working people spend more hours per year to work than those in Western countries. The policy of the shorter working time is conducted by the Japanese Government in order that the working people get more free time. This paper examines whether the shorter working time of working members in the family enrich the time use of the other members of the family. Especially, the effect of the shorter working time of husbands to wives...

Representativeness of shorter measurement sessions in long-term indoor air monitoring.

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Maciejewska, M; Szczurek, A

2015-02-01

Indoor air quality (IAQ) considerably influences health, comfort and the overall performance of people who spend most of their lives in confined spaces. For this reason, there is a strong need to develop methods for IAQ assessment. The fundamental issue in the quantitative determination of IAQ is the duration of measurements. Its inadequate choice may result in providing incorrect information and this potentially leads to wrong conclusions. The most complete information may be acquired through long-term monitoring. However it is typically perceived as impractical due to time and cost load. The aim of this study was to determine whether long-term monitoring can be adequately represented by a shorter measurement session. There were considered three measurable quantities: temperature, relative humidity and carbon dioxide concentration. They are commonly recognized as indicatives for IAQ and may be readily monitored. Scaled Kullback-Leibler divergence, also called relative entropy, was applied as a measure of data representativeness. We considered long-term monitoring in a range from 1 to 9 months. Based on our work, the representative data on CO2 concentration may be acquired while performing measurements during 20% of time dedicated to long-term monitoring. In the case of temperature and relative humidity the respective time demand was 50% of long-term monitoring. From our results, in indoor air monitoring strategies, there could be considered shorter measurement sessions, while still collecting data which are representative for long-term monitoring.

Discrimination of Urban Spaces with Different Level of Restorativeness Based on the Original and on a Shorter Version of Hartig et al.’s Perceived Restorativeness Scale

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Fátima Negrín

2017-10-01

Full Text Available Restorativeness is defined as the potential of the environment to re-establish certain cognitive capacities related to human information processing. The most frequently used instrument for evaluating the restorativeness of places is the Perceived Restorativeness Scale, proposed by Hartig et al. (1991. Later on, shorter versions of the Perceived Restorativeness Scale were proposed. The aim of this work is to evaluate the discriminatory capacity of the original and of a shorter Spanish version of the PRS, considering urban settings previously selected for having different level of restorativeness, according to expert’s criteria. The study involved 244 students and used a 3 × 2 mixed experimental design, with two independent variables: Restorativeness of a place (between-subjects, which was manipulated by showing pictures of settings selected with varying levels of restorativeness (high, medium, low, and length of the scale (within-subjects, which was manipulated by asking subjects to fill in both the original and a shorter version of the PRS. The order of presentation of the two scales was counterbalanced. Results show an appropriate reliability for both version of the scale. Items of being-away, fascination, and coherence of the shorter scale correlate more strongly with the corresponding factor of the original scale, compared to the others factors. Both scales produce similar values for the perceived restorativeness of the different places, except for places with low restorativeness.

Long-Term Costs and Health Consequences of Issuing Shorter Duration Prescriptions for Patients with Chronic Health Conditions in the English NHS.

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Martin, Adam; Payne, Rupert; Wilson, Edward Cf

2018-06-01

The National Health Service (NHS) in England spends over £9 billion on prescription medicines dispensed in primary care, of which over two-thirds is accounted for by repeat prescriptions. Recently, GPs in England have been urged to limit the duration of repeat prescriptions, where clinically appropriate, to 28 days to reduce wastage and hence contain costs. However, shorter prescriptions will increase transaction costs and thus may not be cost saving. Furthermore, there is evidence to suggest that shorter prescriptions are associated with lower adherence, which would be expected to lead to lower clinical benefit. The objective of this study is to estimate the cost-effectiveness of 3-month versus 28-day repeat prescriptions from the perspective of the NHS. We adapted three previously developed UK policy-relevant models, incorporating transaction (dispensing fees, prescriber time) and drug wastage costs associated with 3-month and 28-day prescriptions in three case studies: antihypertensive medications for prevention of cardiovascular events; drugs to improve glycaemic control in patients with type 2 diabetes; and treatments for depression. In all cases, 3-month prescriptions were associated with lower costs and higher QALYs than 28-day prescriptions. This is driven by assumptions that higher adherence leads to improved disease control, lower costs and improved QALYs. Longer repeat prescriptions may be cost-effective compared with shorter ones. However, the quality of the evidence base on which this modelling is based is poor. Any policy rollout should be within the context of a trial such as a stepped-wedge cluster design.

"Taller and Shorter": Human 3-D Spatial Memory Distorts Familiar Multilevel Buildings.

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Thomas Brandt

Full Text Available Animal experiments report contradictory findings on the presence of a behavioural and neuronal anisotropy exhibited in vertical and horizontal capabilities of spatial orientation and navigation. We performed a pointing experiment in humans on the imagined 3-D direction of the location of various invisible goals that were distributed horizontally and vertically in a familiar multilevel hospital building. The 21 participants were employees who had worked for years in this building. The hypothesis was that comparison of the experimentally determined directions and the true directions would reveal systematic inaccuracy or dimensional anisotropy of the localizations. The study provides first evidence that the internal representation of a familiar multilevel building was distorted compared to the dimensions of the true building: vertically 215% taller and horizontally 51% shorter. This was not only demonstrated in the mathematical reconstruction of the mental model based on the analysis of the pointing experiments but also by the participants' drawings of the front view and the ground plan of the building. Thus, in the mental model both planes were altered in different directions: compressed for the horizontal floor plane and stretched for the vertical column plane. This could be related to human anisotropic behavioural performance of horizontal and vertical navigation in such buildings.

"Taller and Shorter": Human 3-D Spatial Memory Distorts Familiar Multilevel Buildings.

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Brandt, Thomas; Huber, Markus; Schramm, Hannah; Kugler, Günter; Dieterich, Marianne; Glasauer, Stefan

2015-01-01

Animal experiments report contradictory findings on the presence of a behavioural and neuronal anisotropy exhibited in vertical and horizontal capabilities of spatial orientation and navigation. We performed a pointing experiment in humans on the imagined 3-D direction of the location of various invisible goals that were distributed horizontally and vertically in a familiar multilevel hospital building. The 21 participants were employees who had worked for years in this building. The hypothesis was that comparison of the experimentally determined directions and the true directions would reveal systematic inaccuracy or dimensional anisotropy of the localizations. The study provides first evidence that the internal representation of a familiar multilevel building was distorted compared to the dimensions of the true building: vertically 215% taller and horizontally 51% shorter. This was not only demonstrated in the mathematical reconstruction of the mental model based on the analysis of the pointing experiments but also by the participants' drawings of the front view and the ground plan of the building. Thus, in the mental model both planes were altered in different directions: compressed for the horizontal floor plane and stretched for the vertical column plane. This could be related to human anisotropic behavioural performance of horizontal and vertical navigation in such buildings.

Prerequisites for Amplicon Pyrosequencing of Microbial Methanol Utilizers in the Environment

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Steffen eKolb

2013-09-01

Full Text Available The commercial availability of next generation sequencing (NGS technologies facilitated the assessment of functional groups of microorganisms in the environment with high coverage, resolution, and reproducibility. Soil methylotrophs were among the first microorganisms in the environment that were assessed with molecular tools, and nowadays, as well with NGS technologies. Studies in the past years re-attracted notice to the pivotal role of methylotrophs in global conversions of methanol, which mainly originates from plants, and is involved in oxidative reactions and ozone formation in the atmosphere. Aerobic methanol utilizers belong to Bacteria, yeasts, Ascomycota, and molds. Numerous bacterial methylotrophs are facultatively aerobic, and also contribute to anaerobic methanol oxidation in the environment, whereas strict anaerobic methanol utilizers belong to methanogens and acetogens. The diversity of enzymes catalyzing the initial oxidation of methanol is considerable, and comprises at least five different enzyme types in aerobes, and one in strict anaerobes. Only the gene of the large subunit of PQQ-dependent methanol dehydrogenase (mxaF has been analyzed by environmental pyrosequencing. To enable a comprehensive assessment of methanol utilizers in the environment, new primers targeting genes of the PQQ MDH in Methylibium (mdh2, of the NAD-dependent MDH (mdh, of the methanol oxidoreductase of Actinobacteria (mdo, of the fungal FAD-dependent alcohol oxidase (mod1, mod2, and homologues, and of the gene of the large subunit of the methanol:corrinoid methyltransferases (mtaC in methanogens and acetogens need to be developed. Combined stable isotope probing of nucleic acids or proteins with amplicon-based NGS are straightforward approaches to reveal insights into functions of certain methylotrophic taxa in the global methanol cycle.

The role of romantic attraction and conflict resolution in predicting shorter and longer relationship maintenance among adolescents.

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Appel, Israel; Shulman, Shmuel

2015-04-01

This study examined the role of romantic attraction and conflict resolution patterns in shorter and longer relationship maintenance among adolescent couples. Data were used from 55 couples aged 15-18 years. Partners completed the Romantic Attraction scale and were observed negotiating a disagreement. Three and 6 months later, they were asked to report whether they were still together. Findings indicated that partners' romantic attraction and the tendency to minimize disagreements during interaction predicted shorter relationship maintenance. In contrast, longer relationship maintenance was predicted by partners' capability to resolve conflicts constructively in a positive atmosphere. Findings are embedded and discussed within Fisher's (2004) evolutionary theory of love.

Hypermetabolism in ALS is associated with greater functional decline and shorter survival.

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Steyn, Frederik J; Ioannides, Zara A; van Eijk, Ruben P A; Heggie, Susan; Thorpe, Kathryn A; Ceslis, Amelia; Heshmat, Saman; Henders, Anjali K; Wray, Naomi R; van den Berg, Leonard H; Henderson, Robert D; McCombe, Pamela A; Ngo, Shyuan T

2018-04-29

To determine the prevalence of hypermetabolism, relative to body composition, in amyotrophic lateral sclerosis (ALS) and its relationship with clinical features of disease and survival. Fifty-eight patients with clinically definite or probable ALS as defined by El Escorial criteria, and 58 age and sex-matched control participants underwent assessment of energy expenditure. Our primary outcome was the prevalence of hypermetabolism in cases and controls. Longitudinal changes in clinical parameters between hypermetabolic and normometabolic patients with ALS were determined for up to 12 months following metabolic assessment. Survival was monitored over a 30-month period following metabolic assessment. Hypermetabolism was more prevalent in patients with ALS than controls (41% vs 12%, adjusted OR=5.4; pALS. Mean lower motor neuron score (SD) was greater in hypermetabolic patients when compared with normometabolic patients (4 (0.3) vs 3 (0.7); p=0.04). In the 12 months following metabolic assessment, there was a greater change in Revised ALS Functional Rating Scale score in hypermetabolic patients when compared with normometabolic patients (-0.68 points/month vs -0.39 points/month; p=0.01). Hypermetabolism was inversely associated with survival. Overall, hypermetabolism increased the risk of death during follow-up to 220% (HR 3.2, 95% CI 1.1 to 9.4, p=0.03). Hypermetabolic patients with ALS have a greater level of lower motor neuron involvement, faster rate of functional decline and shorter survival. The metabolic index could be important for informing prognosis in ALS. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

N-Terminal Domains in Two-Domain Proteins Are Biased to Be Shorter and Predicted to Fold Faster Than Their C-Terminal Counterparts

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Etai Jacob

2013-04-01

Full Text Available Computational analysis of proteomes in all kingdoms of life reveals a strong tendency for N-terminal domains in two-domain proteins to have shorter sequences than their neighboring C-terminal domains. Given that folding rates are affected by chain length, we asked whether the tendency for N-terminal domains to be shorter than their neighboring C-terminal domains reflects selection for faster-folding N-terminal domains. Calculations of absolute contact order, another predictor of folding rate, provide additional evidence that N-terminal domains tend to fold faster than their neighboring C-terminal domains. A possible explanation for this bias, which is more pronounced in prokaryotes than in eukaryotes, is that faster folding of N-terminal domains reduces the risk for protein aggregation during folding by preventing formation of nonnative interdomain interactions. This explanation is supported by our finding that two-domain proteins with a shorter N-terminal domain are much more abundant than those with a shorter C-terminal domain.

Real-time PCR Detection of Brucella Abortus: A Comparative Study of SYBR Green I, 5'-exonuclease, and Hybridization Probe Assays

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Newby, Deborah Trishelle; Hadfield, Ted; Roberto, Francisco Figueroa

2003-08-01

Real-time PCR provides a means of detecting and quantifying DNA targets by monitoring PCR product accumulation during cycling as indicated by increased fluorescence. A number of different approaches can be used to generate the fluorescence signal. Three approaches—SYBR Green I (a double-stranded DNA intercalating dye), 5'-exonuclease (enzymatically released fluors), and hybridization probes (fluorescence resonance energy transfer)—were evaluated for use in a real-time PCR assay to detect Brucella abortus. The three assays utilized the same amplification primers to produce an identical amplicon. This amplicon spans a region of the B. abortus genome that includes portions of the alkB gene and the IS711 insertion element. All three assays were of comparable sensitivity, providing a linear assay over 7 orders of magnitude (from 7.5 ng down to 7.5 fg). However, the greatest specificity was achieved with the hybridization probe assay.

Targeted amplicon sequencing (TAS): a scalable next-gen approach to multilocus, multitaxa phylogenetics.

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Bybee, Seth M; Bracken-Grissom, Heather; Haynes, Benjamin D; Hermansen, Russell A; Byers, Robert L; Clement, Mark J; Udall, Joshua A; Wilcox, Edward R; Crandall, Keith A

2011-01-01

Next-gen sequencing technologies have revolutionized data collection in genetic studies and advanced genome biology to novel frontiers. However, to date, next-gen technologies have been used principally for whole genome sequencing and transcriptome sequencing. Yet many questions in population genetics and systematics rely on sequencing specific genes of known function or diversity levels. Here, we describe a targeted amplicon sequencing (TAS) approach capitalizing on next-gen capacity to sequence large numbers of targeted gene regions from a large number of samples. Our TAS approach is easily scalable, simple in execution, neither time-nor labor-intensive, relatively inexpensive, and can be applied to a broad diversity of organisms and/or genes. Our TAS approach includes a bioinformatic application, BarcodeCrucher, to take raw next-gen sequence reads and perform quality control checks and convert the data into FASTA format organized by gene and sample, ready for phylogenetic analyses. We demonstrate our approach by sequencing targeted genes of known phylogenetic utility to estimate a phylogeny for the Pancrustacea. We generated data from 44 taxa using 68 different 10-bp multiplexing identifiers. The overall quality of data produced was robust and was informative for phylogeny estimation. The potential for this method to produce copious amounts of data from a single 454 plate (e.g., 325 taxa for 24 loci) significantly reduces sequencing expenses incurred from traditional Sanger sequencing. We further discuss the advantages and disadvantages of this method, while offering suggestions to enhance the approach.

Spindle assembly checkpoint protein expression correlates with cellular proliferation and shorter time to recurrence in ovarian cancer.

LENUS (Irish Health Repository)

McGrogan, Barbara

2014-07-01

Ovarian carcinoma (OC) is the most lethal of the gynecological malignancies, often presenting at an advanced stage. Treatment is hampered by high levels of drug resistance. The taxanes are microtubule stabilizing agents, used as first-line agents in the treatment of OC that exert their apoptotic effects through the spindle assembly checkpoint. BUB1-related protein kinase (BUBR1) and mitotic arrest deficient 2 (MAD2), essential spindle assembly checkpoint components, play a key role in response to taxanes. BUBR1, MAD2, and Ki-67 were assessed on an OC tissue microarray platform representing 72 OC tumors of varying histologic subtypes. Sixty-one of these patients received paclitaxel and platinum agents combined; 11 received platinum alone. Overall survival was available for all 72 patients, whereas recurrence-free survival (RFS) was available for 66 patients. Increased BUBR1 expression was seen in serous carcinomas, compared with other histologies (P = .03). Increased BUBR1 was significantly associated with tumors of advanced stage (P = .05). Increased MAD2 and BUBR1 expression also correlated with increased cellular proliferation (P < .0002 and P = .02, respectively). Reduced MAD2 nuclear intensity was associated with a shorter RFS (P = .03), in ovarian tumors of differing histologic subtype (n = 66). In this subgroup, for those women who received paclitaxel and platinum agents combined (n = 57), reduced MAD2 intensity also identified women with a shorter RFS (P < .007). For the entire cohort of patients, irrespective of histologic subtype or treatment, MAD2 nuclear intensity retained independent significance in a multivariate model, with tumors showing reduced nuclear MAD2 intensity identifying patients with a poorer RFS (P = .05).

The association between post-traumatic stress disorder and shorter telomere length: A systematic review and meta-analysis.

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Li, Xuemei; Wang, Jiang; Zhou, Jianghua; Huang, Pan; Li, Jiping

2017-08-15

Post-traumatic stress disorder (PTSD) is a common psychiatric disorder, which may accelerate aging. Many study have investigated the association between telomeres length and PTSD, but results from published studies are contradictory. Therefore, Meta-analysis approaches were conducted to give more precise estimate of relationship between telomere length and PTSD. We systematically reviewed the databases of PUBMED, PsycINFO, Medline(Ovid SP) and EMBASE for all articles on the association between telomere length and PTSD. Data were summarized by using random-effects in the meta-analysis. The heterogeneity among studies were examined by using Cochrane's Q statistic and I-squared. Five eligible studies containing 3851 participants were included in our meta-analysis. Shorten telomere length was significantly associated with PTSD with mean difference of -0.19( 95% CI: -0.27, -0.01; P<0.001) with I-square of 96%. The results from subgroup analysis demonstrated that shorter telomere length was significantly associated with PTSD across all gender groups, with mean difference of -0.15( 95% CI: -0.29, -0.01; P=0.04) for female, mean difference of -0.17( 95% CI: -0.19, -0.15; P<0.001) for male. Meanwhile, shorten telomere length was significantly associated with sexual assault(mean difference =-0.15, 95% CI: -0.29, -0.01), childhood trauma (mean difference =-0.08, 95% CI: -0.19, -0.07), but not combat (mean difference =-0.39, 95% CI: -0.83, 0.05). Compared to the individuals without PTSD, individuals with PTSD have shorter telomere length, which has implications for early intervention and timely treatment to prevent future adverse health outcomes. Copyright © 2017. Published by Elsevier B.V.

How do shorter working hours affect employee wellbeing? : Shortening working time in Finland

OpenAIRE

Lahdenperä, Netta

2017-01-01

The way work is done is dramatically changing due to digital breakthroughs. Generation Y is entering the workforce with a changed attitude towards work as organizations are increasing their focus towards employee wellbeing. Organizations who adopt the new model of work and understand the importance of the wellbeing of their staff are leading the transition to a more efficient business, better working life and a healthier planet. The thesis explores the numerous effects of shorter working...

Greater reproductive investment, but shorter lifespan, in agrosystem than in natural-habitat toads

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Francisco Javier Zamora-Camacho

2017-09-01

Full Text Available Global amphibian decline is due to several factors: habitat loss, anthropization, pollution, emerging diseases, and global warming. Amphibians, with complex life cycles, are particularly susceptible to habitat alterations, and their survival may be impaired in anthropized habitats. Increased mortality is a well-known consequence of anthropization. Life-history theory predicts higher reproductive investment when mortality is increased. In this work, we compared age, body size, and different indicators of reproductive investment, as well as prey availability, in natterjack toads (Epidalea calamita from agrosystems and adjacent natural pine groves in Southwestern Spain. Mean age was lower in agrosystems than in pine groves, possibly as a consequence of increased mortality due to agrosystem environmental stressors. Remarkably, agrosystem toads were larger despite being younger, suggesting accelerated growth rate. Although we detected no differences in prey availability between habitats, artificial irrigation could shorten aestivation in agrosystems, thus increasing energy trade. Moreover, agrosystem toads exhibited increased indicators of reproductive investment. In the light of life-history theory, agrosystem toads might compensate for lesser reproductive events—due to shorter lives—with a higher reproductive investment in each attempt. Our results show that agrosystems may alter demography, which may have complex consequences on both individual fitness and population stability.

Applicability of the shorter ‘Bangladesh regimen’ in high multidrug-resistant tuberculosis settings

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Giovanni Sotgiu

2017-03-01

Full Text Available In spite of the recent introduction of two new drugs (delamanid and bedaquiline and a few repurposed compounds to treat multidrug-resistant and extensively drug-resistant tuberculosis (MDR- and XDR-TB, clinicians are facing increasing problems in designing effective regimens in severe cases. Recently a 9 to 12-month regimen (known as the ‘Bangladesh regimen’ proved to be effective in treating MDR-TB cases. It included an initial phase of 4 to 6 months of kanamycin, moxifloxacin, prothionamide, clofazimine, pyrazinamide, high-dose isoniazid, and ethambutol, followed by 5 months of moxifloxacin, clofazimine, pyrazinamide, and ethambutol. However, recent evidence from Europe and Latin America identified prevalences of resistance to the first-line drugs in this regimen (ethambutol and pyrazinamide exceeding 60%, and of prothionamide exceeding 50%. Furthermore, the proportions of resistance to the two most important pillars of the regimen – quinolones and kanamycin – were higher than 40%. Overall, only 14 out of 348 adult patients (4.0% were susceptible to all of the drugs composing the regimen, and were therefore potentially suitable for the ‘shorter regimen’. A shorter, cheaper, and well-tolerated MDR-TB regimen is likely to impact the number of patients treated and improve adherence if prescribed to the right patients through the systematic use of rapid MTBDRsl testing.

Amplicon-based semiconductor sequencing of human exomes: performance evaluation and optimization strategies.

Science.gov (United States)

Damiati, E; Borsani, G; Giacopuzzi, Edoardo

2016-05-01

The Ion Proton platform allows to perform whole exome sequencing (WES) at low cost, providing rapid turnaround time and great flexibility. Products for WES on Ion Proton system include the AmpliSeq Exome kit and the recently introduced HiQ sequencing chemistry. Here, we used gold standard variants from GIAB consortium to assess the performances in variants identification, characterize the erroneous calls and develop a filtering strategy to reduce false positives. The AmpliSeq Exome kit captures a large fraction of bases (>94 %) in human CDS, ClinVar genes and ACMG genes, but with 2,041 (7 %), 449 (13 %) and 11 (19 %) genes not fully represented, respectively. Overall, 515 protein coding genes contain hard-to-sequence regions, including 90 genes from ClinVar. Performance in variants detection was maximum at mean coverage >120×, while at 90× and 70× we measured a loss of variants of 3.2 and 4.5 %, respectively. WES using HiQ chemistry showed ~71/97.5 % sensitivity, ~37/2 % FDR and ~0.66/0.98 F1 score for indels and SNPs, respectively. The proposed low, medium or high-stringency filters reduced the amount of false positives by 10.2, 21.2 and 40.4 % for indels and 21.2, 41.9 and 68.2 % for SNP, respectively. Amplicon-based WES on Ion Proton platform using HiQ chemistry emerged as a competitive approach, with improved accuracy in variants identification. False-positive variants remain an issue for the Ion Torrent technology, but our filtering strategy can be applied to reduce erroneous variants.

Metagenomes provide valuable comparative information on soil microeukaryotes

DEFF Research Database (Denmark)

Jacquiod, Samuel Jehan Auguste; Stenbæk, Jonas; Santos, Susana

2016-01-01

has been identified. Our analyses suggest that publicly available metagenome data can provide valuable information on soil microeukaryotes for comparative purposes when handled appropriately, complementing the current view provided by ribosomal amplicon sequencing methods......., providing microbiologists with substantial amounts of accessible information. We took advantage of public metagenomes in order to investigate microeukaryote communities in a well characterized grassland soil. The data gathered allowed the evaluation of several factors impacting the community structure......, including the DNA extraction method, the database choice and also the annotation procedure. While most studies on soil microeukaryotes are based on sequencing of PCR-amplified taxonomic markers (18S rRNA genes, ITS regions), this work represents, to our knowledge, the first report based solely...

Imaging Herpes Simplex Virus Type 1 Amplicon Vector–Mediated Gene Expression in Human Glioma Spheroids

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Christine Kaestle

2011-05-01

Full Text Available Vectors derived from herpes simplex virus type 1 (HSV-1 have great potential for transducing therapeutic genes into the central nervous system; however, inefficient distribution of vector particles in vivo may limit their therapeutic potential in patients with gliomas. This study was performed to investigate the extent of HSV-1 amplicon vector–mediated gene expression in a three-dimensional glioma model of multicellular spheroids by imaging highly infectious HSV-1 virions expressing green fluorescent protein (HSV-GFP. After infection or microscopy-guided vector injection of glioma spheroids at various spheroid sizes, injection pressures and injection times, the extent of HSV-1 vector–mediated gene expression was investigated via laser scanning microscopy. Infection of spheroids with HSV-GFP demonstrated a maximal depth of vector-mediated GFP expression at 70 to 80 μm. A > 80% transduction efficiency was reached only in small spheroids with a diameter of 90%. The results demonstrated that vector-mediated gene expression in glioma spheroids was strongly dependent on the mode of vector application—injection pressure and injection time being the most important parameters. The assessment of these vector application parameters in tissue models will contribute to the development of safe and efficient gene therapy protocols for clinical application.

Is Alcohol Use Disorder Identification Test (AUDIT or its shorter versions more useful to identify risky drinkers in a Chinese population? A diagnostic study.

Directory of Open Access Journals (Sweden)

Benjamin H K Yip

Full Text Available To examine the diagnostic performance of shorter versions of Alcohol Use Disorder Identification Test (AUDIT, including Alcohol Consumption (AUDIT-C, in identifying risky drinkers in primary care settings using conventional performance measures, supplemented by decision curve analysis and reclassification table.A cross-sectional study of adult males in general outpatient clinics in Hong Kong. The study included only patients who reported at least sometimes drinking alcoholic beverages. Timeline follow back alcohol consumption assessment method was used as the reference standard. A Chinese translated and validated 10-item AUDIT (Ch-AUDIT was used as a screening tool of risky drinking.Of the participants, 21.7% were classified as risky drinkers. AUDIT-C has the best overall performance among the shorter versions of Ch-AUDIT. The AUC of AUDIT-C was comparable to Ch-AUDIT (0.898 vs 0.901, p-value = 0.959. Decision curve analysis revealed that when the threshold probability ranged from 15-30%, the AUDIT-C had a higher net-benefit than all other screens. AUDIT-C improved the reclassification of risky drinking when compared to Ch-AUDIT (net reclassification improvement = 0.167. The optimal cut-off of AUDIT-C was at ≥5.Given the rising levels of alcohol consumption in the Chinese regions, this Chinese translated 3-item instrument provides convenient and time-efficient risky drinking screening and may become an increasingly useful tool.

PipeCraft: Flexible open-source toolkit for bioinformatics analysis of custom high-throughput amplicon sequencing data.

Science.gov (United States)

Anslan, Sten; Bahram, Mohammad; Hiiesalu, Indrek; Tedersoo, Leho

2017-11-01

High-throughput sequencing methods have become a routine analysis tool in environmental sciences as well as in public and private sector. These methods provide vast amount of data, which need to be analysed in several steps. Although the bioinformatics may be applied using several public tools, many analytical pipelines allow too few options for the optimal analysis for more complicated or customized designs. Here, we introduce PipeCraft, a flexible and handy bioinformatics pipeline with a user-friendly graphical interface that links several public tools for analysing amplicon sequencing data. Users are able to customize the pipeline by selecting the most suitable tools and options to process raw sequences from Illumina, Pacific Biosciences, Ion Torrent and Roche 454 sequencing platforms. We described the design and options of PipeCraft and evaluated its performance by analysing the data sets from three different sequencing platforms. We demonstrated that PipeCraft is able to process large data sets within 24 hr. The graphical user interface and the automated links between various bioinformatics tools enable easy customization of the workflow. All analytical steps and options are recorded in log files and are easily traceable. © 2017 John Wiley & Sons Ltd.

Human papillomavirus detection using the Abbott RealTime high-risk HPV tests compared with conventional nested PCR coupled to high-throughput sequencing of amplification products in cervical smear specimens from a Gabonese female population.

Science.gov (United States)

Moussavou-Boundzanga, Pamela; Koumakpayi, Ismaël Hervé; Labouba, Ingrid; Leroy, Eric M; Belembaogo, Ernest; Berthet, Nicolas

2017-12-21

Cervical cancer is the fourth most common malignancy in women worldwide. However, screening with human papillomavirus (HPV) molecular tests holds promise for reducing cervical cancer incidence and mortality in low- and middle-income countries. The performance of the Abbott RealTime High-Risk HPV test (AbRT) was evaluated in 83 cervical smear specimens and compared with a conventional nested PCR coupled to high-throughput sequencing (HTS) to identify the amplicons. The AbRT assay detected at least one HPV genotype in 44.57% of women regardless of the grade of cervical abnormalities. Except for one case, good concordance was observed for the genotypes detected with the AbRT assay in the high-risk HPV category determined with HTS of the amplicon generated by conventional nested PCR. The AbRT test is an easy and reliable molecular tool and was as sensitive as conventional nested PCR in cervical smear specimens for detection HPVs associated with high-grade lesions. Moreover, sequencing amplicons using an HTS approach effectively identified the genotype of the hrHPV identified with the AbRT test.

Nation-Scale Adoption of Shorter Breast Radiation Therapy Schedules Can Increase Survival in Resource Constrained Economies: Results From a Markov Chain Analysis

Energy Technology Data Exchange (ETDEWEB)

Khan, Atif J., E-mail: atif.j.khan@rutgers.edu [Department of Radiation Oncology, Robert Wood Johnson Medical School/Cancer Institute of New Jersey, New Brunswick, New Jersey (United States); Rafique, Raza [Suleman Dawood School of Business, Lahore University of Management Sciences, Lahore (Pakistan); Zafar, Waleed [Shaukat Khanum Memorial Cancer Hospital and Research Centre, Lahore (Pakistan); Shah, Chirag [Department of Radiation Oncology, Cleveland Clinic, Cleveland, Ohio (United States); Haffty, Bruce G. [Department of Radiation Oncology, Robert Wood Johnson Medical School/Cancer Institute of New Jersey, New Brunswick, New Jersey (United States); Vicini, Frank [Michigan HealthCare Professionals, Farmington Hills, Michigan (United States); Jamshed, Arif [Shaukat Khanum Memorial Cancer Hospital and Research Centre, Lahore (Pakistan); Zhao, Yao [Rutgers University School of Business, Newark, New Jersey (United States)

2017-02-01

Purpose: Hypofractionated whole breast irradiation and accelerated partial breast irradiation (APBI) offer women options for shorter courses of breast radiation therapy. The impact of these shorter schedules on the breast cancer populations of emerging economies with limited radiation therapy resources is unknown. We hypothesized that adoption of these schedules would improve throughput in the system and, by allowing more women access to life-saving treatments, improve patient survival within the system. Methods and Materials: We designed a Markov chain model to simulate the different health states that a postlumpectomy or postmastectomy patient could enter over the course of a 20-year follow-up period. Transition rates between health states were adapted from published data on recurrence rates. We used primary data from a tertiary care hospital in Lahore, Pakistan, to populate the model with proportional use of mastectomy versus breast conservation and to estimate the proportion of patients suitable for APBI. Sensitivity analyses on the use of APBI and relative efficacy of APBI were conducted to study the impact on the population. Results: The shorter schedule resulted in more women alive and more women remaining without evidence of disease (NED) compared with the conventional schedule, with an absolute difference of about 4% and 7% at 15 years, respectively. Among women who had lumpectomies, the chance of remaining alive and with an intact breast was 62% in the hypofractionation model and 54% in the conventional fractionation model. Conclusions: Increasing throughput in the system can result in improved survival, improved chances of remaining without evidence of disease, and improved chances of remaining alive with a breast. These findings are significant and suggest that adoption of hypofractionation in emerging economies is not simply a question of efficiency and cost but one of access to care and patient survivorship.

Nation-Scale Adoption of Shorter Breast Radiation Therapy Schedules Can Increase Survival in Resource Constrained Economies: Results From a Markov Chain Analysis

International Nuclear Information System (INIS)

Khan, Atif J.; Rafique, Raza; Zafar, Waleed; Shah, Chirag; Haffty, Bruce G.; Vicini, Frank; Jamshed, Arif; Zhao, Yao

2017-01-01

Purpose: Hypofractionated whole breast irradiation and accelerated partial breast irradiation (APBI) offer women options for shorter courses of breast radiation therapy. The impact of these shorter schedules on the breast cancer populations of emerging economies with limited radiation therapy resources is unknown. We hypothesized that adoption of these schedules would improve throughput in the system and, by allowing more women access to life-saving treatments, improve patient survival within the system. Methods and Materials: We designed a Markov chain model to simulate the different health states that a postlumpectomy or postmastectomy patient could enter over the course of a 20-year follow-up period. Transition rates between health states were adapted from published data on recurrence rates. We used primary data from a tertiary care hospital in Lahore, Pakistan, to populate the model with proportional use of mastectomy versus breast conservation and to estimate the proportion of patients suitable for APBI. Sensitivity analyses on the use of APBI and relative efficacy of APBI were conducted to study the impact on the population. Results: The shorter schedule resulted in more women alive and more women remaining without evidence of disease (NED) compared with the conventional schedule, with an absolute difference of about 4% and 7% at 15 years, respectively. Among women who had lumpectomies, the chance of remaining alive and with an intact breast was 62% in the hypofractionation model and 54% in the conventional fractionation model. Conclusions: Increasing throughput in the system can result in improved survival, improved chances of remaining without evidence of disease, and improved chances of remaining alive with a breast. These findings are significant and suggest that adoption of hypofractionation in emerging economies is not simply a question of efficiency and cost but one of access to care and patient survivorship.

Shorter duration of non-rapid eye movement sleep slow waves in EphA4 knockout mice.

Science.gov (United States)

Freyburger, Marlène; Poirier, Gaétan; Carrier, Julie; Mongrain, Valérie

2017-10-01

Slow waves occurring during non-rapid eye movement sleep have been associated with neurobehavioural performance and memory. In addition, the duration of previous wakefulness and sleep impacts characteristics of these slow waves. However, molecular mechanisms regulating the dynamics of slow-wave characteristics remain poorly understood. The EphA4 receptor regulates glutamatergic transmission and synaptic plasticity, which have both been linked to sleep slow waves. To investigate if EphA4 regulates slow-wave characteristics during non-rapid eye movement sleep, we compared individual parameters of slow waves between EphA4 knockout mice and wild-type littermates under baseline conditions and after a 6-h sleep deprivation. We observed that, compared with wild-type mice, knockout mice display a shorter duration of positive and negative phases of slow waves under baseline conditions and after sleep deprivation. However, the mutation did not change slow-wave density, amplitude and slope, and did not affect the sleep deprivation-dependent changes in slow-wave characteristics, suggesting that EphA4 is not involved in the response to elevated sleep pressure. Our present findings suggest a role for EphA4 in shaping cortical oscillations during sleep that is independent from sleep need. © 2017 European Sleep Research Society.

The Glycated Albumin (GA) to HbA1c Ratio Reflects Shorter-Term Glycemic Control than GA: Analysis of Patients with Fulminant Type 1 Diabetes.

Science.gov (United States)

Koga, Masafumi; Inada, Shinya; Nakao, Taisei; Kawamori, Ryuzo; Kasayama, Soji

2017-01-01

Glycated albumin (GA) reflects shorter-term glycemic control than HbA1c. We have reported that HbA1c is paradoxically increased in diabetic patients whose glycemic control deteriorated before ameliorating. In this study, we analyzed paradoxical increases of glycemic control indicators after treatment in patients with fulminant type 1 diabetes (FT1D). We also investigated whether the GA/HbA1c ratio may reflect shorter-term glycemic control than GA. Five FT1D patients whose post-treatment HbA1c and GA levels were measured were enrolled. We also used a formula to estimate HbA1c and GA from the fictitious models of changes in plasma glucose in FT1D patients. In this model, the periods during which HbA1c, GA, and the GA/HbA1c ratio were higher than at the first visit were compared. In addition, the half-life for the GA/HbA1c ratio was calculated in accordance with the half-lives for HbA1c and GA (36 and 14 days, respectively). In all FT1D patients, HbA1c levels 2-4 weeks after treatment were increased, with three patients (60%) experiencing an increase of GA levels. In contrast, an increase of the GA/HbA1c ratio was observed in only one patient. In all of the different models of changes in plasma glucose in FT1D patients, the length of time during which the values were higher than at the first visit was in the order of HbA1c > GA > GA/HbA1c ratio. The half-life for the GA/HbA1c ratio was 9 days, shorter than GA. These findings suggest that the GA/HbA1c ratio reflects shorter-term glycemic control than GA. © 2016 Wiley Periodicals, Inc.

Evolution of MHC class I genes in the endangered loggerhead sea turtle (Caretta caretta) revealed by 454 amplicon sequencing.

Science.gov (United States)

Stiebens, Victor A; Merino, Sonia E; Chain, Frédéric J J; Eizaguirre, Christophe

2013-04-30

In evolutionary and conservation biology, parasitism is often highlighted as a major selective pressure. To fight against parasites and pathogens, genetic diversity of the immune genes of the major histocompatibility complex (MHC) are particularly important. However, the extensive degree of polymorphism observed in these genes makes it difficult to conduct thorough population screenings. We utilized a genotyping protocol that uses 454 amplicon sequencing to characterize the MHC class I in the endangered loggerhead sea turtle (Caretta caretta) and to investigate their evolution at multiple relevant levels of organization. MHC class I genes revealed signatures of trans-species polymorphism across several reptile species. In the studied loggerhead turtle individuals, it results in the maintenance of two ancient allelic lineages. We also found that individuals carrying an intermediate number of MHC class I alleles are larger than those with either a low or high number of alleles. Multiple modes of evolution seem to maintain MHC diversity in the loggerhead turtles, with relatively high polymorphism for an endangered species.

Shedding light on the microbial community of the macropod foregut using 454-amplicon pyrosequencing.

Directory of Open Access Journals (Sweden)

Lisa-Maree Gulino

Full Text Available Twenty macropods from five locations in Queensland, Australia, grazing on a variety of native pastures were surveyed and the bacterial community of the foregut was examined using 454-amplicon pyrosequencing. Specifically, the V3/V4 region of 16S rRNA gene was examined. A total of 5040 OTUs were identified in the data set (post filtering. Thirty-two OTUs were identified as 'shared' OTUS (i.e. present in all samples belonging to either Firmicutes or Bacteroidetes (Clostridiales/Bacteroidales. These phyla predominated the general microbial community in all macropods. Genera represented within the shared OTUs included: unclassified Ruminococcaceae, unclassified Lachnospiraceae, unclassified Clostridiales, Peptococcus sp. Coprococcus spp., Streptococcus spp., Blautia sp., Ruminoccocus sp., Eubacterium sp., Dorea sp., Oscillospira sp. and Butyrivibrio sp. The composition of the bacterial community of the foregut samples of each the host species (Macropus rufus, Macropus giganteus and Macropus robustus was significantly different allowing differentiation between the host species based on alpha and beta diversity measures. Specifically, eleven dominant OTUs that separated the three host species were identified and classified as: unclassified Ruminococcaceae, unclassified Bacteroidales, Prevotella spp. and a Syntrophococcus sucromutans. Putative reductive acetogens and fibrolytic bacteria were also identified in samples. Future work will investigate the presence and role of fibrolytics and acetogens in these ecosystems. Ideally, the isolation and characterization of these organisms will be used for enhanced feed efficiency in cattle, methane mitigation and potentially for other industries such as the biofuel industry.

Shedding light on the microbial community of the macropod foregut using 454-amplicon pyrosequencing.

Science.gov (United States)

Gulino, Lisa-Maree; Ouwerkerk, Diane; Kang, Alicia Y H; Maguire, Anita J; Kienzle, Marco; Klieve, Athol V

2013-01-01

Twenty macropods from five locations in Queensland, Australia, grazing on a variety of native pastures were surveyed and the bacterial community of the foregut was examined using 454-amplicon pyrosequencing. Specifically, the V3/V4 region of 16S rRNA gene was examined. A total of 5040 OTUs were identified in the data set (post filtering). Thirty-two OTUs were identified as 'shared' OTUS (i.e. present in all samples) belonging to either Firmicutes or Bacteroidetes (Clostridiales/Bacteroidales). These phyla predominated the general microbial community in all macropods. Genera represented within the shared OTUs included: unclassified Ruminococcaceae, unclassified Lachnospiraceae, unclassified Clostridiales, Peptococcus sp. Coprococcus spp., Streptococcus spp., Blautia sp., Ruminoccocus sp., Eubacterium sp., Dorea sp., Oscillospira sp. and Butyrivibrio sp. The composition of the bacterial community of the foregut samples of each the host species (Macropus rufus, Macropus giganteus and Macropus robustus) was significantly different allowing differentiation between the host species based on alpha and beta diversity measures. Specifically, eleven dominant OTUs that separated the three host species were identified and classified as: unclassified Ruminococcaceae, unclassified Bacteroidales, Prevotella spp. and a Syntrophococcus sucromutans. Putative reductive acetogens and fibrolytic bacteria were also identified in samples. Future work will investigate the presence and role of fibrolytics and acetogens in these ecosystems. Ideally, the isolation and characterization of these organisms will be used for enhanced feed efficiency in cattle, methane mitigation and potentially for other industries such as the biofuel industry.

Effect of Group Exercising and Adjusting the Brace at Shorter Intervals on Cobb Angle and Quality of Life of Patients with Idiopathic Scoliosis

Directory of Open Access Journals (Sweden)

Zahra Hedayati

2016-01-01

Full Text Available Objective: Bracing along with exercising is the most effective protocol in patients with idiopathic scoliosis which have Cobb angles of 25 to 45 degrees. However, since the psychological aspects of scoliosis treatment may affect the quality of life, and the exact time for adjusting the pads of Milwaukee brace is unknown; Therefore the aim of this study was evaluating the effect of exercising in a group, with adjusting the brace in shorter intervals, in compare to routine protocol, in the treatment of idiopathic scoliosis. Matterials & Methods: Thirty-four patients with idiopathic scoliosis which had Cobb angles of 50 to 15 degrees were included in this study and were divided into experimental and control groups. The patients of two groups participated in an eleven-week treatment program, differ between the two groups. Quality of life scores of both groups were evaluated before and after intervention using SRS-22 questionnaire, as well as scoliosis angles before and after the intervention according to the primary and secondary radiographic X-rays. Results: Statistical analysis was performed using Paired T-Test in each group, and Independent T-Test between the two groups before and after treatment. The severity of scoliosis curvature and satisfaction domain of the experimental group was reduced significantly in compared with the control group, after intervention (P=0.04. Moreover in the case of  the quality of life in patients with Cobb angles less than 30 degrees, compared with patients with Cobb angles greater than 31 degrees, in the domains of self-image, satisfaction, and total score, the difference was significant (P<0.05. Conclusion: Adjusting the brace at shorter intervals along with exercising as a group, during the eleven weeks of treatment, has increased satisfaction and reduced the scoliosis Cobb angles of patients.

Investigations of model polymers: Dynamics of melts and statics of a long chain in a dilute melt of shorter chains

International Nuclear Information System (INIS)

Bishop, M.; Ceperley, D.; Frisch, H.L.; Kalos, M.H.

1982-01-01

We report additional results on a simple model of polymers, namely the diffusion in concentrated polymer systems and the static properties of one long chain in a dilute melt of shorter chains. It is found, for the polymer sizes and time scales amenable to our computer calculations, that there is as yet no evidence for a ''reptation'' regime in a melt. There is some indication of reptation in the case of a single chain moving through fixed obstacles. No statistically significant effect of the change, from excluded volume behavior of the long chain to ideal behavior as the shorter chains grow, is observed

Extracellular DNA amplicon sequencing reveals high levels of benthic eukaryotic diversity in the central Red Sea

KAUST Repository

Pearman, John K.

2015-11-01

The present study aims to characterize the benthic eukaryotic biodiversity patterns at a coarse taxonomic level in three areas of the central Red Sea (a lagoon, an offshore area in Thuwal and a shallow coastal area near Jeddah) based on extracellular DNA. High-throughput amplicon sequencing targeting the V9 region of the 18S rRNA gene was undertaken for 32 sediment samples. High levels of alpha-diversity were detected with 16,089 operational taxonomic units (OTUs) being identified. The majority of the OTUs were assigned to Metazoa (29.2%), Alveolata (22.4%) and Stramenopiles (17.8%). Stramenopiles (Diatomea) and Alveolata (Ciliophora) were frequent in a lagoon and in shallower coastal stations, whereas metazoans (Arthropoda: Maxillopoda) were dominant in deeper offshore stations. Only 24.6% of total OTUs were shared among all areas. Beta-diversity was generally lower between the lagoon and Jeddah (nearshore) than between either of those and the offshore area, suggesting a nearshore–offshore biodiversity gradient. The current approach allowed for a broad-range of benthic eukaryotic biodiversity to be analysed with significantly less labour than would be required by other traditional taxonomic approaches. Our findings suggest that next generation sequencing techniques have the potential to provide a fast and standardised screening of benthic biodiversity at large spatial and temporal scales.

Association of mutations in the hemochromatosis gene with shorter life expectancy

DEFF Research Database (Denmark)

Bathum, L; Christiansen, L; Nybo, H

2001-01-01

BACKGROUND: To investigate whether the frequency of carriers of mutations in the HFE gene associated with hereditary hemochromatosis diminishes with age as an indication that HFE mutations are associated with increased mortality. It is of value in the debate concerning screening for hereditary...... hemochromatosis to determine the significance of heterozygosity. METHODS: Genotyping for mutations in exons 2 and 4 of the HFE gene using denaturing gradient gel electrophoresis in 1784 participants aged 45 to 100 years from 4 population-based studies: all 183 centenarians from the Danish Centenarian Study, 601...... in the distribution of mutations in exon 2 in the different age groups. CONCLUSIONS: In a high-carrier frequency population like Denmark, mutations in HFE show an age-related reduction in the frequency of heterozygotes for C282Y, which suggests that carrier status is associated with shorter life expectancy....

Taxonomy of anaerobic digestion microbiome reveals biases associated with the applied high throughput sequencing strategies

DEFF Research Database (Denmark)

Campanaro, Stefano; Treu, Laura; Kougias, Panagiotis

2018-01-01

In the past few years, many studies investigated the anaerobic digestion microbiome by means of 16S rRNA amplicon sequencing. Results obtained from these studies were compared to each other without taking into consideration the followed procedure for amplicons preparation and data analysis...... specifically, the microbial compositions of three laboratory scale biogas reactors were analyzed before and after addition of sodium oleate by sequencing the microbiome with three different approaches: 16S rRNA amplicon sequencing, shotgun DNA and shotgun RNA. This comparative analysis revealed that......, in amplicon sequencing, abundance of some taxa (Euryarchaeota and Spirochaetes) was biased by the inefficiency of universal primers to hybridize all the templates. Reliability of the results obtained was also influenced by the number of hypervariable regions under investigation. Finally, amplicon sequencing...

Is equity confined to the shorter term projects - and if not, what does it need?

International Nuclear Information System (INIS)

Cryan, T.

1996-01-01

There are two types of equity investor generally found in shorter term energy projects: energy project developers or sponsors who view a given project as buying or building a business; and financial investors who have viewed an investment as buying a stream of cash flows. This article examines the objectives and needs of these two investor groups, and discusses the principal issues which govern their respective decision-making process. (author)

Electrochemical genosensing of Salmonella, Listeria and Escherichia coli on silica magnetic particles

Energy Technology Data Exchange (ETDEWEB)

Liébana, Susana; Brandão, Delfina [Grup de Sensors i Biosensors, Departament de Química, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès (Bellaterra) (Spain); Cortés, Pilar; Campoy, Susana [Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès (Bellaterra) (Spain); Alegret, Salvador [Grup de Sensors i Biosensors, Departament de Química, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès (Bellaterra) (Spain); Pividori, María Isabel, E-mail: Isabel.Pividori@uab.cat [Grup de Sensors i Biosensors, Departament de Química, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès (Bellaterra) (Spain)

2016-01-21

A magneto-genosensing approach for the detection of the three most common pathogenic bacteria in food safety, such as Salmonella, Listeria and Escherichia coli is presented. The methodology is based on the detection of the tagged amplified DNA obtained by single-tagging PCR with a set of specific primers for each pathogen, followed by electrochemical magneto-genosensing on silica magnetic particles. A set of primers were selected for the amplification of the invA (278 bp), prfA (217 bp) and eaeA (151 bp) being one of the primers for each set tagged with fluorescein, biotin and digoxigenin coding for Salmonella enterica, Listeria monocytogenes and E. coli, respectively. The single-tagged amplicons were then immobilized on silica MPs based on the nucleic acid-binding properties of silica particles in the presence of the chaotropic agent as guanidinium thiocyanate. The assessment of the silica MPs as a platform for electrochemical magneto-genosensing is described, including the main parameters to selectively attach longer dsDNA fragments instead of shorter ssDNA primers based on their negative charge density of the sugar-phosphate backbone. This approach resulted to be a promising detection tool with sensing features of rapidity and sensitivity very suitable to be implemented on DNA biosensors and microfluidic platforms. - Highlights: • Silica magnetic particles were used for the first time as carrier in electrochemical magneto-genosensing of single-tagged amplicons. • They demonstrated to be a robust platform for the electrochemical detection of PCR products. • Differential adsorption properties for longer dsDNA amplicon incorporating the tagging primers over shorter ssDNA tagged primers were observed due to the negative charge density. • Electrochemical magneto-genosensing of Salmonella enterica, Listeria monocytogenes and Escherichia coli was successfully performed.

Electrochemical genosensing of Salmonella, Listeria and Escherichia coli on silica magnetic particles

International Nuclear Information System (INIS)

Liébana, Susana; Brandão, Delfina; Cortés, Pilar; Campoy, Susana; Alegret, Salvador; Pividori, María Isabel

2016-01-01

A magneto-genosensing approach for the detection of the three most common pathogenic bacteria in food safety, such as Salmonella, Listeria and Escherichia coli is presented. The methodology is based on the detection of the tagged amplified DNA obtained by single-tagging PCR with a set of specific primers for each pathogen, followed by electrochemical magneto-genosensing on silica magnetic particles. A set of primers were selected for the amplification of the invA (278 bp), prfA (217 bp) and eaeA (151 bp) being one of the primers for each set tagged with fluorescein, biotin and digoxigenin coding for Salmonella enterica, Listeria monocytogenes and E. coli, respectively. The single-tagged amplicons were then immobilized on silica MPs based on the nucleic acid-binding properties of silica particles in the presence of the chaotropic agent as guanidinium thiocyanate. The assessment of the silica MPs as a platform for electrochemical magneto-genosensing is described, including the main parameters to selectively attach longer dsDNA fragments instead of shorter ssDNA primers based on their negative charge density of the sugar-phosphate backbone. This approach resulted to be a promising detection tool with sensing features of rapidity and sensitivity very suitable to be implemented on DNA biosensors and microfluidic platforms. - Highlights: • Silica magnetic particles were used for the first time as carrier in electrochemical magneto-genosensing of single-tagged amplicons. • They demonstrated to be a robust platform for the electrochemical detection of PCR products. • Differential adsorption properties for longer dsDNA amplicon incorporating the tagging primers over shorter ssDNA tagged primers were observed due to the negative charge density. • Electrochemical magneto-genosensing of Salmonella enterica, Listeria monocytogenes and Escherichia coli was successfully performed.

Shorter preschool, leukocyte telomere length is associated with obesity at age 9 in Latino children.

Science.gov (United States)

Kjaer, T W; Faurholt-Jepsen, D; Mehta, K M; Christensen, V B; Epel, E; Lin, J; Blackburn, E; Wojcicki, J M

2018-04-01

The aim of this study was to determine the potential role of leukocyte telomere length as a biomarker for development of childhood obesity in a low-income Latino population. A birth cohort of Latino children (N = 201) in San Francisco (recruited May 2006-May 2007) was followed until age 9 and assessed annually for obesity and dietary intake. Leukocyte telomere length was measured at 4 and 5 years (n = 102) and assessed as a predictor for obesity at age 9, adjusting for known risk factors. Furthermore, leukocyte telomere length at age 4 and 5 was evaluated as a possible mediator of the relationship between excessive sugar-sweetened beverage consumption and obesity at age 9. Shorter leukocyte telomere length in preschoolers was associated with obesity at age 9 (adjusted odds ratio 0.35, 95% confidence interval 0.13-0.94) after adjustment for known risk factors. Telomere length mediated 11% of the relationship between excessive sugar-sweetened beverage consumption and obesity. Shorter leukocyte telomere length may be an indicator of future obesity risk in high-risk populations as it is particularly sensitive to damage from oxidative stress exposure, including those from sugar-sweetened beverages. © 2017 World Obesity Federation.

Are Shorter Versions of the Positive and Negative Syndrome Scale (PANSS) Doable? A Critical Review.

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Lindenmayer, Jean-Pierre

2017-12-01

The Positive and Negative Syndrome Scale (PANSS) is a well-established assessment tool for measuring symptom severity in schizophrenia. Researchers and clinicians have been interested in the development of a short version of the PANSS that could reduce the burden of its administration for patients and raters. The author presents a comprehensive overview of existing brief PANSS measures, including their strengths and limitations, and discusses some possible next steps. There are two available scales that offer a reduced number of original PANSS items: PANSS-14 and PANSS-19; and two shorter versions that include six items: Brief PANSS and PANSS-6. The PANSS-6 has been tested quite extensively in established trials and appears to demonstrate high sensitivity to change and an established cut off definition for remission. Prospective testing in new antipsychotic treatment trials is still required for these shorter versions of PANSS. In addition, they need to be supplemented with interview guides, as well as provide conversion formulas to translate total scores from the short PANSS versions to the PANSS-30. Both short versions of the PANSS are essentially designed to evaluate response to antipsychotic treatment. Future PANSS scale development needs to address specific measurement of treatment-responsive positive symptoms by including treatment-sensitive items, as well as illness-phase specific PANSS tools.

Bacterial tag encoded FLX titanium amplicon pyrosequencing (bTEFAP based assessment of prokaryotic diversity in metagenome of Lonar soda lake, India

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Pravin Dudhagara

2015-06-01

Full Text Available Bacterial diversity and archaeal diversity in metagenome of the Lonar soda lake sediment were assessed by bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP. Metagenome comprised 5093 sequences with 2,531,282 bp and 53 ± 2% G + C content. Metagenome sequence data are available at NCBI under the Bioproject database with accession no. PRJNA218849. Metagenome sequence represented the presence of 83.1% bacterial and 10.5% archaeal origin. A total of 14 different bacteria demonstrating 57 species were recorded with dominating species like Coxiella burnetii (17%, Fibrobacter intestinalis (12% and Candidatus Cloacamonas acidaminovorans (11%. Occurrence of two archaeal phyla representing 24 species, among them Methanosaeta harundinacea (35%, Methanoculleus chikugoensis (12% and Methanolinea tarda (11% were dominating species. Significant presence of 11% sequences as an unclassified indicated the possibilities for unknown novel prokaryotes from the metagenome.

Robot-Assisted Hybrid Esophagectomy Is Associated with a Shorter Length of Stay Compared to Conventional Transthoracic Esophagectomy

DEFF Research Database (Denmark)

Rolff, Hans C; Ambrus, Rikard B; Belmouhand, Mohammed

2017-01-01

Aim: To compare the peri- and postoperative data between a hybrid minimally invasive esophagectomy (HMIE) and the conventional Ivor Lewis esophagectomy. Methods: Retrospective comparison of perioperative characteristics, postoperative complications, and survival between HMIE and Ivor Lewis esopha...

De novo origin of VCY2 from autosome to Y-transposed amplicon.

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Peng-Rong Cao

Full Text Available The formation of new genes is a primary driving force of evolution in all organisms. The de novo evolution of new genes from non-protein-coding genomic regions is emerging as an important additional mechanism for novel gene creation. Y chromosomes underlie sex determination in mammals and contain genes that are required for male-specific functions. In this study, a search was undertaken for Y chromosome de novo genes derived from non-protein-coding sequences. The Y chromosome orphan gene variable charge, Y-linked (VCY2, is an autosome-derived gene that has sequence similarity to large autosomal fragments but lacks an autosomal protein-coding homolog. VCY2 locates in the amplicon containing long DNA fragments that were transposed from autosomes to the Y chromosome before the ape-monkey split. We confirmed that VCY2 cannot be encoded by autosomes due to the presence of multiple disablers that disrupt the open reading frame, such as the absence of start or stop codons and the presence of premature stop codons. Similar observations have been made for homologs in the autosomes of the chimpanzee, gorilla, rhesus macaque, baboon and out-group marmoset, which suggests that there was a non-protein-coding ancestral VCY2 that was common to apes and monkeys that predated the transposition event. Furthermore, while protein-coding orthologs are absent, a putative non-protein-coding VCY2 with conserved disablers was identified in the rhesus macaque Y chromosome male-specific region. This finding implies that VCY2 might have not acquired its protein-coding ability before the ape-monkey split. VCY2 encodes a testis-specific expressed protein and is involved in the pathologic process of male infertility, and the acquisition of this gene might improve male fertility. This is the first evidence that de novo genes can be generated from transposed autosomal non-protein-coding segments, and this evidence provides novel insights into the evolutionary history of the Y

Shorter telomeres in peripheral blood mononuclear cells from older persons with sarcopenia: results from an exploratory study

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Emanuele eMarzetti

2014-08-01

Full Text Available Background. Telomere shortening in peripheral blood mononuclear cells (PBMCs has been associated with biological age and several chronic degenerative diseases. However, the relationship between telomere length and sarcopenia, a hallmark of the aging process, is unknown. The aim of the present study was therefore to determine whether PBMC telomeres obtained from sarcopenic older persons were shorter relative to non-sarcopenic peers. We further explored if PBMC telomere length was associated with frailty, a major clinical correlate of sarcopenia.Methods. Analyses were conducted in 142 persons aged >/= 65 years referred to a geriatric outpatient clinic (University Hospital. The presence of sarcopenia was established according to the European Working Group on Sarcopenia in Older People criteria, with bioelectrical impedance analysis used for muscle mass estimation. The frailty status was determined by both the Fried’s criteria (physical frailty, PF and a modified Rockwood’s frailty index (FI. Telomere length was measured in PBMCs by quantitative real-time polymerase chain reaction according to the Telomere/Single copy gene ratio (T/S method.Results. Among 142 outpatients (mean age 75.0 ± 6.5 years, 59.2% women, sarcopenia was diagnosed in 23 individuals (19.3%. The PF phenotype was detected in 74 participants (52.1%. The average FI score was 0.46 ± 0.17. PBMC telomeres were shorter in sarcopenic subjects (T/S = 0.21; 95% CI: 0.18 – 0.24 relative to non-sarcopenic individuals (T/S = 0.26; 95%: CI: 0.24 – 0.28; p = 0.01, independent of age, gender, smoking habit, or comorbidity. No significant associations were determined between telomere length and either PF or FI.Conclusion. PBMC telomere length, expressed as T/S values, is shorter in older outpatients with sarcopenia. The cross-sectional assessment of PBMC telomere length is not sufficient at capturing the complex, multidimensional syndrome of frailty.

Dyslexics' faster decay of implicit memory for sounds and words is manifested in their shorter neural adaptation.

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Jaffe-Dax, Sagi; Frenkel, Or; Ahissar, Merav

2017-01-24

Dyslexia is a prevalent reading disability whose underlying mechanisms are still disputed. We studied the neural mechanisms underlying dyslexia using a simple frequency-discrimination task. Though participants were asked to compare the two tones in each trial, implicit memory of previous trials affected their responses. We hypothesized that implicit memory decays faster among dyslexics. We tested this by increasing the temporal intervals between consecutive trials, and by measuring the behavioral impact and ERP responses from the auditory cortex. Dyslexics showed a faster decay of implicit memory effects on both measures, with similar time constants. Finally, faster decay of implicit memory also characterized the impact of sound regularities in benefitting dyslexics' oral reading rate. Their benefit decreased faster as a function of the time interval from the previous reading of the same non-word. We propose that dyslexics' shorter neural adaptation paradoxically accounts for their longer reading times, since it reduces their temporal window of integration of past stimuli, resulting in noisier and less reliable predictions for both simple and complex stimuli. Less reliable predictions limit their acquisition of reading expertise.

High Numbers of Stromal Cancer-Associated Fibroblasts Are Associated With a Shorter Survival Time in Cats With Oral Squamous Cell Carcinoma.

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Klobukowska, H J; Munday, J S

2016-11-01

Cancer-associated fibroblasts (CAFs) are fibroblastic cells that express α-smooth muscle actin and have been identified in the stroma of numerous epithelial tumors. The presence of CAFs within the tumor stroma has been associated with a poorer prognosis in some human cancers, including oral squamous cell carcinomas (SCCs). Cats frequently develop oral SCCs, and although these are generally highly aggressive neoplasms, there is currently a lack of prognostic markers for these tumors. The authors investigated the prognostic value of the presence of CAFs within the stroma of oral SCC biopsy specimens from 47 cats. In addition, several epidemiologic, clinical, and histologic variables were also assessed for prognostic significance. A CAF-positive stroma was identified in 35 of 47 SCCs (74.5%), and the median survival time (ST) of cats with CAF-positive SCCs (35 days) was significantly shorter than that of cats with CAF-negative SCCs (48.5 days) (P = .031). ST was also associated with the location of the primary tumor (P = .0018): the median ST for oropharyngeal SCCs (179 days) was significantly longer than for maxillary (43.5 days; P = .047), mandibular (42 days; P = .022), and sublingual SCCs (22.5 days; P = .0005). The median ST of sublingual SCCs was also shorter compared with maxillary SCCs (P = .0017). Furthermore, a significant association was identified between site and the presence of stromal CAFs (P = .025). On the basis of this retrospective study, evaluating the tumor stroma for CAFs in feline oral SCC biopsy specimens may be of potential prognostic value. © The Author(s) 2016.

Optimization of a shorter variable-acquisition time for legs to achieve true whole-body PET/CT images.

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Umeda, Takuro; Miwa, Kenta; Murata, Taisuke; Miyaji, Noriaki; Wagatsuma, Kei; Motegi, Kazuki; Terauchi, Takashi; Koizumi, Mitsuru

2017-12-01

The present study aimed to qualitatively and quantitatively evaluate PET images as a function of acquisition time for various leg sizes, and to optimize a shorter variable-acquisition time protocol for legs to achieve better qualitative and quantitative accuracy of true whole-body PET/CT images. The diameters of legs to be modeled as phantoms were defined based on data derived from 53 patients. This study analyzed PET images of a NEMA phantom and three plastic bottle phantoms (diameter, 5.68, 8.54 and 10.7 cm) that simulated the human body and legs, respectively. The phantoms comprised two spheres (diameters, 10 and 17 mm) containing fluorine-18 fluorodeoxyglucose solution with sphere-to-background ratios of 4 at a background radioactivity level of 2.65 kBq/mL. All PET data were reconstructed with acquisition times ranging from 10 to 180, and 1200 s. We visually evaluated image quality and determined the coefficient of variance (CV) of the background, contrast and the quantitative %error of the hot spheres, and then determined two shorter variable-acquisition protocols for legs. Lesion detectability and quantitative accuracy determined based on maximum standardized uptake values (SUV max ) in PET images of a patient using the proposed protocols were also evaluated. A larger phantom and a shorter acquisition time resulted in increased background noise on images and decreased the contrast in hot spheres. A visual score of ≥ 1.5 was obtained when the acquisition time was ≥ 30 s for three leg phantoms, and ≥ 120 s for the NEMA phantom. The quantitative %errors of the 10- and 17-mm spheres in the leg phantoms were ± 15 and ± 10%, respectively, in PET images with a high CV (scan mean SUV max of three lesions using the current fixed-acquisition and two proposed variable-acquisition time protocols in the clinical study were 3.1, 3.1 and 3.2, respectively, which did not significantly differ. Leg acquisition time per bed position of even 30-90�

Shorter Leukocyte Telomere Length in Relation to Presumed Nonalcoholic Fatty Liver Disease in Mexican-American Men in NHANES 1999–2002

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Janet M. Wojcicki

2017-01-01

Full Text Available Leukocyte telomere length is shorter in response to chronic disease processes associated with inflammation such as diabetes mellitus and coronary artery disease. Data from the National Health and Nutrition Examination Survey (NHANES from 1999 to 2002 was used to explore the relationship between leukocyte telomere length and presumed NAFLD, as indicated by elevated serum alanine aminotransferase (ALT levels, obesity, or abdominal obesity. Logistic regression models were used to evaluate the relationship between telomere length and presumed markers of NAFLD adjusting for possible confounders. There was no relationship between elevated ALT levels, abdominal obesity, or obesity and telomere length in adjusted models in NHANES (OR 1.13, 95% CI 0.48–2.65; OR 1.17, 95% CI 0.52–2.62, resp.. Mexican-American men had shorter telomere length in relation to presumed NAFLD (OR 0.07, 95% CI 0.006–0.79 and using different indicators of NAFLD (OR 0.012, 95% CI 0.0006–0.24. Mexican origin with presumed NAFLD had shorter telomere length than men in other population groups. Longitudinal studies are necessary to evaluate the role of telomere length as a potential predictor to assess pathogenesis of NALFD in Mexicans.

Disparate patterns of age-related changes in lipid peroxidation in long-lived naked mole-rats and shorter-lived mice.

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Andziak, Blazej; Buffenstein, Rochelle

2006-12-01

A key tenet of the oxidative stress theory of aging is that levels of accrued oxidative damage increase with age. Differences in damage generation and accumulation therefore may underlie the natural variation in species longevity. We compared age-related profiles of whole-organism lipid peroxidation (urinary isoprostanes) and liver lipid damage (malondialdehyde) in long living naked mole-rats [maximum lifespan (MLS) > 28.3 years] and shorter-living CB6F1 hybrid mice (MLS approximately 3.5 years). In addition, we compared age-associated changes in liver non-heme iron to assess how intracellular conditions, which may modulate oxidative processes, are affected by aging. Surprisingly, even at a young age, concentrations of both markers of lipid peroxidation, as well as of iron, were at least twofold (P naked mole tats than in mice. This refutes the hypothesis that prolonged naked mole-rat longevity is due to superior protection against oxidative stress. The age-related profiles of all three parameters were distinctly species specific. Rates of lipid damage generation in mice were maintained throughout adulthood, while accrued damage in old animals was twice that of young mice. In naked mole-rats, urinary isoprostane excretion declined by half with age (P naked mole-rats is independent of oxidative stress parameters.

Fungi Sailing the Arctic Ocean: Speciose Communities in North Atlantic Driftwood as Revealed by High-Throughput Amplicon Sequencing.

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Rämä, Teppo; Davey, Marie L; Nordén, Jenni; Halvorsen, Rune; Blaalid, Rakel; Mathiassen, Geir H; Alsos, Inger G; Kauserud, Håvard

2016-08-01

High amounts of driftwood sail across the oceans and provide habitat for organisms tolerating the rough and saline environment. Fungi have adapted to the extremely cold and saline conditions which driftwood faces in the high north. For the first time, we applied high-throughput sequencing to fungi residing in driftwood to reveal their taxonomic richness, community composition, and ecology in the North Atlantic. Using pyrosequencing of ITS2 amplicons obtained from 49 marine logs, we found 807 fungal operational taxonomic units (OTUs) based on clustering at 97 % sequence similarity cut-off level. The phylum Ascomycota comprised 74 % of the OTUs and 20 % belonged to Basidiomycota. The richness of basidiomycetes decreased with prolonged submersion in the sea, supporting the general view of ascomycetes being more extremotolerant. However, more than one fourth of the fungal OTUs remained unassigned to any fungal class, emphasising the need for better DNA reference data from the marine habitat. Different fungal communities were detected in coniferous and deciduous logs. Our results highlight that driftwood hosts a considerably higher fungal diversity than currently known. The driftwood fungal community is not a terrestrial relic but a speciose assemblage of fungi adapted to the stressful marine environment and different kinds of wooden substrates found in it.

Induction of a shorter compression phase is correlated with a deeper chest compression during metronome-guided cardiopulmonary resuscitation: a manikin study.

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Chung, Tae Nyoung; Bae, Jinkun; Kim, Eui Chung; Cho, Yun Kyung; You, Je Sung; Choi, Sung Wook; Kim, Ok Jun

2013-07-01

Recent studies have shown that there may be an interaction between duty cycle and other factors related to the quality of chest compression. Duty cycle represents the fraction of compression phase. We aimed to investigate the effect of shorter compression phase on average chest compression depth during metronome-guided cardiopulmonary resuscitation. Senior medical students performed 12 sets of chest compressions following the guiding sounds, with three down-stroke patterns (normal, fast and very fast) and four rates (80, 100, 120 and 140 compressions/min) in random sequence. Repeated-measures analysis of variance was used to compare the average chest compression depth and duty cycle among the trials. The average chest compression depth increased and the duty cycle decreased in a linear fashion as the down-stroke pattern shifted from normal to very fast (pmetronome-guided cardiopulmonary resuscitation.

Cost-effectiveness of longer-term versus shorter-term provision of antibiotics in patients with persistent symptoms attributed to Lyme disease

NARCIS (Netherlands)

Berende, A.; Nieuwenhuis, L.; Hofstede, H.J.M. ter; Vos, F.J.; Vogelaar, M.L.; Tromp, M.A.; Middendorp, H. van; Donders, A.R.T.; Evers, A.W.M.; Kullberg, B.J.; Adang, E.M.M.

2018-01-01

BACKGROUND: The treatment of persistent symptoms attributed to Lyme disease remains controversial. Recently, the PLEASE study did not demonstrate any additional clinical benefit of longer-term versus shorter-term antibiotic treatment. However, the economic impact of the antibiotic strategies has not

Homework schedule: an important factor associated with shorter sleep duration among Chinese school-aged children.

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Li, Shenghui; Yang, Qian; Chen, Zhe; Jin, Xingming; Jiang, Fan; Shen, Xiaoming

2014-09-03

This study was designed to examine the hypothesis that homework schedule has adverse impacts on Chinese children's sleep-wake habits and sleep duration. A random sample of 19,299 children aged 5.08 to 11.99 years old participated in a large, cross-sectional survey. A parent-administered questionnaire was completed to quantify children's homework schedule and sleep behaviors. Generally, it was demonstrated that more homework schedule was significantly associated with later bedtime, later wake time, and shorter sleep duration. Among all sleep variables, bedtime and sleep duration during weekdays appeared to be most affected by homework schedule, especially homework schedule during weekdays.

Competitive amplification of differentially melting amplicons (CADMA improves KRAS hotspot mutation testing in colorectal cancer

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Kristensen Lasse

2012-11-01

Full Text Available Abstract Background Cancer is an extremely heterogeneous group of diseases traditionally categorized according to tissue of origin. However, even among patients with the same cancer subtype the cellular alterations at the molecular level are often very different. Several new therapies targeting specific molecular changes found in individual patients have initiated the era of personalized therapy and significantly improved patient care. In metastatic colorectal cancer (mCRC a selected group of patients with wild-type KRAS respond to antibodies against the epidermal growth factor receptor (EGFR. Testing for KRAS mutations is now required prior to anti-EGFR treatment, however, less sensitive methods based on conventional PCR regularly fail to detect KRAS mutations in clinical samples. Methods We have developed sensitive and specific assays for detection of the seven most common KRAS mutations based on a novel methodology named Competitive Amplification of Differentially Melting Amplicons (CADMA. The clinical applicability of these assays was assessed by analyzing 100 colorectal cancer samples, for which KRAS mutation status has been evaluated by the commercially available TheraScreen® KRAS mutation kit. Results The CADMA assays were sensitive to at least 0.5% mutant alleles in a wild-type background when using 50 nanograms of DNA in the reactions. Consensus between CADMA and the TheraScreen kit was observed in 96% of the colorectal cancer samples. In cases where disagreement was observed the CADMA result could be confirmed by a previously published assay based on TaqMan probes and by fast COLD-PCR followed by Sanger sequencing. Conclusions The high analytical sensitivity and specificity of CADMA may increase diagnostic sensitivity and specificity of KRAS mutation testing in mCRC patients.

The return trip is felt shorter only postdictively: A psychophysiological study of the return trip effect [corrected].

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Ryosuke Ozawa

Full Text Available The return trip often seems shorter than the outward trip even when the distance and actual time are identical. To date, studies on the return trip effect have failed to confirm its existence in a situation that is ecologically valid in terms of environment and duration. In addition, physiological influences as part of fundamental timing mechanisms in daily activities have not been investigated in the time perception literature. The present study compared round-trip and non-round-trip conditions in an ecological situation. Time estimation in real time and postdictive estimation were used to clarify the situations where the return trip effect occurs. Autonomic nervous system activity was evaluated from the electrocardiogram using the Lorenz plot to demonstrate the relationship between time perception and physiological indices. The results suggest that the return trip effect is caused only postdictively. Electrocardiographic analysis revealed that the two experimental conditions induced different responses in the autonomic nervous system, particularly in sympathetic nervous function, and that parasympathetic function correlated with postdictive timing. To account for the main findings, the discrepancy between the two time estimates is discussed in the light of timing strategies, i.e., prospective and retrospective timing, which reflect different emphasis on attention and memory processes. Also each timing method, i.e., the verbal estimation, production or comparative judgment, has different characteristics such as the quantification of duration in time units or knowledge of the target duration, which may be responsible for the discrepancy. The relationship between postdictive time estimation and the parasympathetic nervous system is also discussed.

Comparative Characterization of Multiscale Carbon Fiber Composite with Long and Short MWCNTs at Higher Weight Fractions

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Michael Zimmer

2012-01-01

Full Text Available There are documented advantages to using carbon nanotubes (CNTs in composites for various property enhancements. However, to date, only limited studies have been conducted on using of longer CNTs over 1 mm in length. This study used long multiwalled carbon nanotubes (LMWCNTs and their longer extended networks to test multiple properties in thermal conductivity, electrical conductivity, mechanical strength, and modulus and then compared these properties to those of shorter multi-walled carbon nanotubes (SMWCNTs. For carbon fiber-reinforced composites, the longer graphite paths from LMWCNTs in the matrix were expected to improve all properties. The longer networks were expected to allow for more undisturbed phonon transportation to improve thermal conductivity. This in turn relates to improved electrical conductivity and better mechanical properties. However, results have shown that the LMWCNTs do not improve or decrease thermal conductivity, whereas the shorter MWCNTs provide mixed results. LMWCNTs did show improvements in electrical, mechanical, and physical properties, but compared to shorter MWCNTs, the results in other certain properties varied. This perplexing outcome resides in the functioning of the networks made by both the LMWCNTs and shorter MWCNTs.

At least 10% shorter C–H bonds in cryogenic protein crystal structures than in current AMBER forcefields

Energy Technology Data Exchange (ETDEWEB)

Pang, Yuan-Ping, E-mail: pang@mayo.edu

2015-03-06

High resolution protein crystal structures resolved with X-ray diffraction data at cryogenic temperature are commonly used as experimental data to refine forcefields and evaluate protein folding simulations. However, it has been unclear hitherto whether the C–H bond lengths in cryogenic protein structures are significantly different from those defined in forcefields to affect protein folding simulations. This article reports the finding that the C–H bonds in high resolution cryogenic protein structures are 10–14% shorter than those defined in current AMBER forcefields, according to 3709 C–H bonds in the cryogenic protein structures with resolutions of 0.62–0.79 Å. Also, 20 all-atom, isothermal–isobaric, 0.5-μs molecular dynamics simulations showed that chignolin folded from a fully-extended backbone formation to the native β-hairpin conformation in the simulations using AMBER forcefield FF12SB at 300 K with an aggregated native state population including standard error of 10 ± 4%. However, the aggregated native state population with standard error reduced to 3 ± 2% in the same simulations except that C–H bonds were shortened by 10–14%. Furthermore, the aggregated native state populations with standard errors increased to 35 ± 3% and 26 ± 3% when using FF12MC, which is based on AMBER forcefield FF99, with and without the shortened C–H bonds, respectively. These results show that the 10–14% bond length differences can significantly affect protein folding simulations and suggest that re-parameterization of C–H bonds according to the cryogenic structures could improve the ability of a forcefield to fold proteins in molecular dynamics simulations. - Highlights: • Cryogenic crystal structures are commonly used in computational studies of proteins. • C–H bonds in the cryogenic structures are shorter than those defined in forcefields. • A survey of 3709 C–H bonds shows that the cryogenic bonds are 10–14% shorter. • The

A shorter and more specific oral sensitization-based experimental model of food allergy in mice.

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Bailón, Elvira; Cueto-Sola, Margarita; Utrilla, Pilar; Rodríguez-Ruiz, Judith; Garrido-Mesa, Natividad; Zarzuelo, Antonio; Xaus, Jordi; Gálvez, Julio; Comalada, Mònica

2012-07-31

Cow's milk protein allergy (CMPA) is one of the most prevalent human food-borne allergies, particularly in children. Experimental animal models have become critical tools with which to perform research on new therapeutic approaches and on the molecular mechanisms involved. However, oral food allergen sensitization in mice requires several weeks and is usually associated with unspecific immune responses. To overcome these inconveniences, we have developed a new food allergy model that takes only two weeks while retaining the main characters of allergic response to food antigens. The new model is characterized by oral sensitization of weaned Balb/c mice with 5 doses of purified cow's milk protein (CMP) plus cholera toxin (CT) for only two weeks and posterior challenge with an intraperitoneal administration of the allergen at the end of the sensitization period. In parallel, we studied a conventional protocol that lasts for seven weeks, and also the non-specific effects exerted by CT in both protocols. The shorter protocol achieves a similar clinical score as the original food allergy model without macroscopically affecting gut morphology or physiology. Moreover, the shorter protocol caused an increased IL-4 production and a more selective antigen-specific IgG1 response. Finally, the extended CT administration during the sensitization period of the conventional protocol is responsible for the exacerbated immune response observed in that model. Therefore, the new model presented here allows a reduction not only in experimental time but also in the number of animals required per experiment while maintaining the features of conventional allergy models. We propose that the new protocol reported will contribute to advancing allergy research. Copyright © 2012 Elsevier B.V. All rights reserved.

Reemission spectra and inelastic processes at interaction of attosecond and shorter duration electromagnetic pulses with atoms

International Nuclear Information System (INIS)

Makarov, D.N.; Matveev, V.I.

2017-01-01

Inelastic processes and the reemission of attosecond and shorter electromagnetic pulses by atoms have been considered within the analytical solution of the Schrödinger equation in the sudden perturbation approximation. A method of calculations with the exact inclusion of spatial inhomogeneity of the field of an ultrashort pulse and the momenta of photons in the reemission processes has been developed. The probabilities of inelastic processes and spectra of reemission of ultrashort electromagnetic pulses by one- and many-electron atoms have been calculated. The results have been presented in the form of analytical formulas.

A molecular-beacon-based asymmetric PCR assay for easy visualization of amplicons in the diagnosis of trichomoniasis.

Science.gov (United States)

Sonkar, Subash C; Sachdev, Divya; Mishra, Prashant K; Kumar, Anita; Mittal, Pratima; Saluja, Daman

2016-12-15

The currently available nucleic acid amplification tests (NAATs) for trichomoniasis are accurate, quick and confirmative with superior sensitivity than traditional culture-based microbiology assays. However, these assays are associated with problems of carry over contamination, false positive results, requirement of technical expertise for performance and detection of end product. Hence, a diagnostic assay with easy visualization of the amplified product will be profitable. An in-house, rapid, sensitive, specific molecular-beacon-based PCR assay, using primers against pfoB gene of Trichomonas vaginalis, was developed and evaluated using dry ectocervical swabs (n=392) from symptomatic females with vaginal discharge. Total DNA was isolated and used as template for the PCR assays. The performance and reproducibility of PCR assay was evaluated by composite reference standard (CRS). For easy visualization of the amplified product, molecular-beacon was designed and amplicons were visualized directly using fluorescent handheld dark reader or by Micro-Plate Reader. Molecular-beacons are single-stranded hairpin shaped nucleic acid probes composed of a stem, with fluorophore/quencher pair and a loop region complementary to the desired DNA. The beacon-based PCR assay designed in the present study is highly specific as confirmed by competition experiments and extremely sensitive with detection limit of 20fg of genomic DNA (3-4 pathogens). The minimum infrastructure requirement and ease to perform the assay makes this method highly useful for resource poor countries for better disease management. Copyright © 2016 Elsevier B.V. All rights reserved.

Shorter time since inflammatory bowel disease diagnosis in children is associated with lower mental health in parents.

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Werner, H; Braegger, Cp; Buehr, P; Koller, R; Nydegger, A; Spalinger, J; Heyland, K; Schibli, S; Landolt, Ma

2015-01-01

This study assessed the mental health of parents of children with inflammatory bowel disease (IBD), compared their mental health with age-matched and gender-matched references and examined parental and child predictors for mental health problems. A total of 125 mothers and 106 fathers of 125 children with active and inactive IBD from the Swiss IBD multicentre cohort study were included. Parental mental health was assessed by the Symptom Checklist 27 and child behaviour problems by the Strengths and Difficulties Questionnaire. Child medical data were extracted from hospital records. While the mothers reported lower mental health, the fathers' mental health was similar, or even better, than in age-matched and gender-matched community controls. In both parents, shorter time since the child's diagnosis was associated with poorer mental health. In addition, the presence of their own IBD diagnosis and child behaviour problems predicted maternal mental health problems. Parents of children with IBD may need professional support when their child is diagnosed, to mitigate distress. This, in turn, may help the child to adjust better to IBD. Particular attention should be paid to mothers who have their own IBD diagnosis and whose children display behaviour problems. ©2014 Foundation Acta Paediatrica. Published by John Wiley & Sons Ltd.

Towards shorter wavelength x-ray lasers using a high power, short pulse pump laser

International Nuclear Information System (INIS)

Tighe, W.; Krushelnick, K.; Valeo, E.; Suckewer, S.

1991-05-01

A near-terawatt, KrF* laser system, focussable to power densities >10 18 W/cm 2 has been constructed for use as a pump laser in various schemes aimed at the development of x-ray lasing below 5nm. The laser system along with output characteristics such as the pulse duration, the focal spot size, and the percentage of amplified spontaneous emission (ASE) emitted along with the laser pulse will be presented. Schemes intended to lead to shorter wavelength x-ray emission will be described. The resultant requirements on the pump laser characteristics and the target design will be outlined. Results from recent solid target experiments and two-laser experiments, showing the interaction of a high-power, short pulse laser with a preformed plasma, will be presented. 13 refs., 5 figs

Two populations of double minute chromosomes harbor distinct amplicons, the MYC locus at 8q24.2 and a 0.43-Mb region at 14q24.1, in the SW613-S human carcinoma cell line.

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Guillaud-Bataille, M; Brison, O; Danglot, G; Lavialle, C; Raynal, B; Lazar, V; Dessen, P; Bernheim, A

2009-01-01

High-level amplifications observed in tumor cells are usually indicative of genes involved in oncogenesis. We report here a high resolution characterization of a new amplified region in the SW613-S carcinoma cell line. This cell line contains tumorigenic cells displaying high-level MYC amplification in the form of double minutes (DM(+) cells) and non tumorigenic cells exhibiting low-level MYC amplification in the form of homogeneously staining regions (DM(-) cells). Both cell types were studied at genomic and functional levels. The DM(+) cells display a second amplification, corresponding to the 14q24.1 region, in a distinct population of DMs. The 0.43-Mb amplified and overexpressed region contains the PLEK2, PIGH, ARG2, VTI1B, RDH11, and ZFYVE26 genes. Both amplicons were stably maintained upon in vitro and in vivo propagation. However, the 14q24.1 amplicon was not found in cells with high-level MYC amplification in the form of HSRs, either obtained after spontaneous integration of endogenous DM MYC copies or after transfection of DM(-) cells with a MYC gene expression vector. These HSR-bearing cells are highly tumorigenic. The 14q24.1 amplification may not play a role in malignancy per se but might contribute to maintaining the amplification in the form of DMs. Copyright 2009 S. Karger AG, Basel.

Minimally invasive compared to conventional approach for coronary artery bypass grafting improves outcome

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Jitumoni Baishya

2017-01-01

Full Text Available Introduction: Minimally invasive (MI cardiac surgery is a rapidly gaining popularity, globally as well as in India. We aimed to compare the outcome of MI to the conventional approach for coronary artery bypass graft (CABG surgery. Methods: This prospective, comparative study was conducted at a tertiary care cardiac surgical center. All patients who underwent CABG surgery via MI approach (MI group from July 2015 to December 2015 were enrolled and were compared against same number of EuroSCORE II matched patients undergoing CABG through conventional mid-sternotomy approach (CON group. Demographic, intra- and post-operative variables were collected. Results: In MI group, duration of the surgery was significantly longer (P = 0.029. Intraoperative blood loss lesser (P = 0.002, shorter duration of ventilation (P = 0.002, shorter Intensive Care Unit stay (P = 0.004, shorter hospital stay (P = 0.003, lesser postoperative analgesic requirements (P = 0.027, and lower visual analog scale scores on day of surgery (P = 0.032 and 1 st postoperative day (P = 0.025. No significant difference in postoperative blood loss, blood transfusion, or duration of inotrope requirement observed. There was no conversion to mid-sternotomy in any patients, 8% of patients had desaturation intraoperatively. There was no operative mortality. Conclusion: MI surgery is associated with lesser intraoperative blood loss, better analgesia, and faster recovery.

Comparing robotic, laparoscopic and open cystectomy: a systematic review and meta-analysis

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Thomas Fonseka

2015-03-01

Full Text Available Objective: To conduct a systematic review and meta-analysis comparing outcomes between Open Radical Cystectomy (ORC, Laparoscopic Radical Cystectomy (LRC and Robot-assisted Radical Cystectomy (RARC. RARC is to be compared to LRC and ORC and LRC compared to ORC. Material and methods: A systematic review of the literature was conducted, collating studies comparing RARC, LRC and ORC. Surgical and oncological outcome data were extracted and a meta-analysis was performed. Results: Twenty-four studies were selected with total of 2,104 cases analyzed. RARC had a longer operative time (OPT compared to LRC with no statistical difference between length of stay (LOS and estimated blood loss (EBL. RARC had a significantly shorter LOS, reduced EBL, lower complication rate and longer OPT compared to ORC. There were no significant differences regarding lymph node yield (LNY and positive surgical margins (PSM. LRC had a reduced EBL, shorter LOS and increased OPT compared to ORC. There was no significant difference regarding LNY. Conclusion: RARC is comparable to LRC with better surgical results than ORC. LRC has better surgical outcomes than ORC. With the unique technological features of the robotic surgical system and increasing trend of intra-corporeal reconstruction it is likely that RARC will become the surgical option of choice.

Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene amplicons.

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Lagkouvardos, Ilias; Fischer, Sandra; Kumar, Neeraj; Clavel, Thomas

2017-01-01

The importance of 16S rRNA gene amplicon profiles for understanding the influence of microbes in a variety of environments coupled with the steep reduction in sequencing costs led to a surge of microbial sequencing projects. The expanding crowd of scientists and clinicians wanting to make use of sequencing datasets can choose among a range of multipurpose software platforms, the use of which can be intimidating for non-expert users. Among available pipeline options for high-throughput 16S rRNA gene analysis, the R programming language and software environment for statistical computing stands out for its power and increased flexibility, and the possibility to adhere to most recent best practices and to adjust to individual project needs. Here we present the Rhea pipeline, a set of R scripts that encode a series of well-documented choices for the downstream analysis of Operational Taxonomic Units (OTUs) tables, including normalization steps, alpha - and beta -diversity analysis, taxonomic composition, statistical comparisons, and calculation of correlations. Rhea is primarily a straightforward starting point for beginners, but can also be a framework for advanced users who can modify and expand the tool. As the community standards evolve, Rhea will adapt to always represent the current state-of-the-art in microbial profiles analysis in the clear and comprehensive way allowed by the R language. Rhea scripts and documentation are freely available at https://lagkouvardos.github.io/Rhea.

Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene amplicons

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Ilias Lagkouvardos

2017-01-01

Full Text Available The importance of 16S rRNA gene amplicon profiles for understanding the influence of microbes in a variety of environments coupled with the steep reduction in sequencing costs led to a surge of microbial sequencing projects. The expanding crowd of scientists and clinicians wanting to make use of sequencing datasets can choose among a range of multipurpose software platforms, the use of which can be intimidating for non-expert users. Among available pipeline options for high-throughput 16S rRNA gene analysis, the R programming language and software environment for statistical computing stands out for its power and increased flexibility, and the possibility to adhere to most recent best practices and to adjust to individual project needs. Here we present the Rhea pipeline, a set of R scripts that encode a series of well-documented choices for the downstream analysis of Operational Taxonomic Units (OTUs tables, including normalization steps, alpha- and beta-diversity analysis, taxonomic composition, statistical comparisons, and calculation of correlations. Rhea is primarily a straightforward starting point for beginners, but can also be a framework for advanced users who can modify and expand the tool. As the community standards evolve, Rhea will adapt to always represent the current state-of-the-art in microbial profiles analysis in the clear and comprehensive way allowed by the R language. Rhea scripts and documentation are freely available at https://lagkouvardos.github.io/Rhea.

Marital disruption is associated with shorter salivary telomere length in a probability sample of older adults.

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Whisman, Mark A; Robustelli, Briana L; Sbarra, David A

2016-05-01

Marital disruption (i.e., marital separation, divorce) is associated with a wide range of poor mental and physical health outcomes, including increased risk for all-cause mortality. One biological intermediary that may help explain the association between marital disruption and poor health is accelerated cellular aging. This study examines the association between marital disruption and salivary telomere length in a United States probability sample of adults ≥50 years of age. Participants were 3526 individuals who participated in the 2008 wave of the Health and Retirement Study. Telomere length assays were performed using quantitative real-time polymerase chain reaction (qPCR) on DNA extracted from saliva samples. Health and lifestyle factors, traumatic and stressful life events, and neuroticism were assessed via self-report. Linear regression analyses were conducted to examine the associations between predictor variables and salivary telomere length. Based on their marital status data in the 2006 wave, people who were separated or divorced had shorter salivary telomeres than people who were continuously married or had never been married, and the association between marital disruption and salivary telomere length was not moderated by gender or neuroticism. Furthermore, the association between marital disruption and salivary telomere length remained statistically significant after adjusting for demographic and socioeconomic variables, neuroticism, cigarette use, body mass, traumatic life events, and other stressful life events. Additionally, results revealed that currently married adults with a history of divorce evidenced shorter salivary telomeres than people who were continuously married or never married. Accelerated cellular aging, as indexed by telomere shortening, may be one pathway through which marital disruption is associated with morbidity and mortality. Copyright © 2016 Elsevier Ltd. All rights reserved.

Risky family processes prospectively forecast shorter telomere length mediated through negative emotions.

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Brody, Gene H; Yu, Tianyi; Shalev, Idan

2017-05-01

This study was designed to examine prospective associations of risky family environments with subsequent levels of negative emotions and peripheral blood mononuclear cell telomere length (TL), a marker of cellular aging. A second purpose was to determine whether negative emotions mediate the hypothesized link between risky family processes and diminished telomere length. Participants were 293 adolescents (age 17 years at the first assessment) and their primary caregivers. Caregivers provided data on risky family processes when the youths were age 17 years, youths reported their negative emotions at age 18 years, and youths' TL was assayed from a blood sample at age 22 years. The results revealed that (a) risky family processes forecast heightened negative emotions (β = .316, p emotions forecast shorter TL (β = -.187, p = .012), and (c) negative emotions served as a mediator connecting risky family processes with diminished TL (indirect effect = -0.012, 95% CI [-0.036, -0.002]). These findings are consistent with the hypothesis that risky family processes presage premature cellular aging through effects on negative emotions, with potential implications for lifelong health. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Robotic assisted gastrectomy compared with open resection: a case-matched study.

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Caruso, Riccardo; Vicente, Emilio; Quijano, Yolanda; Ielpo, Benedetto; Duran, Hipolito; Diaz, Eduardo; Fabra, Isabel; Ferri, Valentina

2018-05-04

In recent years, increasingly sophisticated tools have allowed for more complex robotic surgery. Robotic gastrectomy, however, is adopted in only a few selected centers. The goals of this study were to examine the adoption of robotic gastrectomy and to compare outcomes between open and robotic gastric resections. This is a case-matched analysis of patients who underwent robotic and open gastric resection performed at Sanchinarro University Hospital, Madrid from November 2011 to February 2017. Patient data were obtained retrospectively. Clinicopathologic characteristics and perioperative and postoperative outcomes were recorded and analyzed. Two groups of demographically similar patients were analyzed: the robotic group (n = 20) and the open surgery group (n = 19). The patient characteristics of the two groups have been compared. Robotic resection resulted in less blood loss, shorter postoperative hospital stay, and a longer operating time. The two groups had similar complication rates. Pathological data were similar for both procedures. Robotic gastrectomy for locally advanced gastric carcinoma is safe, and long-term outcomes are comparable to those patients who underwent open resection. Robotic gastrectomy resulted in a shorter hospital stay, less blood loss and morbidity comparable with the outcomes of open gastrectomy.

Self-produced Time Intervals Are Perceived as More Variable and/or Shorter Depending on Temporal Context in Subsecond and Suprasecond Ranges

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Keita eMitani

2016-06-01

Full Text Available The processing of time intervals is fundamental for sensorimotor and cognitive functions. Perceptual and motor timing are often performed concurrently (e.g., playing a musical instrument. Although previous studies have shown the influence of body movements on time perception, how we perceive self-produced time intervals has remained unclear. Furthermore, it has been suggested that the timing mechanisms are distinct for the sub- and suprasecond ranges. Here, we compared perceptual performances for self-produced and passively presented time intervals in random contexts (i.e., multiple target intervals presented in a session across the sub- and suprasecond ranges (Experiment 1 and within the sub- (Experiment 2 and suprasecond (Experiment 3 ranges, and in a constant context (i.e., a single target interval presented in a session in the sub- and suprasecond ranges (Experiment 4. We show that self-produced time intervals were perceived as shorter and more variable across the sub- and suprasecond ranges and within the suprasecond range but not within the subsecond range in a random context. In a constant context, the self-produced time intervals were perceived as more variable in the suprasecond range but not in the subsecond range. The impairing effects indicate that motor timing interferes with perceptual timing. The dependence of impairment on temporal contexts suggests multiple timing mechanisms for the subsecond and suprasecond ranges. In addition, violation of the scalar property (i.e., a constant variability to target interval ratio was observed between the sub- and suprasecond ranges. The violation was clearer for motor timing than for perceptual timing. This suggests that the multiple timing mechanisms for the sub- and suprasecond ranges overlap more for perception than for motor. Moreover, the central tendency effect (i.e., where shorter base intervals are overestimated and longer base intervals are underestimated disappeared with subsecond

Polymicrobial nature of chronic diabetic foot ulcer biofilm infections determined using bacterial tag encoded FLX amplicon pyrosequencing (bTEFAP.

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Scot E Dowd

Full Text Available BACKGROUND: Diabetic extremity ulcers are associated with chronic infections. Such ulcer infections are too often followed by amputation because there is little or no understanding of the ecology of such infections or how to control or eliminate this type of chronic infection. A primary impediment to the healing of chronic wounds is biofilm phenotype infections. Diabetic foot ulcers are the most common, disabling, and costly complications of diabetes. Here we seek to derive a better understanding of the polymicrobial nature of chronic diabetic extremity ulcer infections. METHODS AND FINDINGS: Using a new bacterial tag encoded FLX amplicon pyrosequencing (bTEFAP approach we have evaluated the bacterial diversity of 40 chronic diabetic foot ulcers from different patients. The most prevalent bacterial genus associated with diabetic chronic wounds was Corynebacterium spp. Findings also show that obligate anaerobes including Bacteroides, Peptoniphilus, Fingoldia, Anaerococcus, and Peptostreptococcus spp. are ubiquitous in diabetic ulcers, comprising a significant portion of the wound biofilm communities. Other major components of the bacterial communities included commonly cultured genera such as Streptococcus, Serratia, Staphylococcus and Enterococcus spp. CONCLUSIONS: In this article, we highlight the patterns of population diversity observed in the samples and introduce preliminary evidence to support the concept of functional equivalent pathogroups (FEP. Here we introduce FEP as consortia of genotypically distinct bacteria that symbiotically produce a pathogenic community. According to this hypothesis, individual members of these communities when they occur alone may not cause disease but when they coaggregate or consort together into a FEP the synergistic effect provides the functional equivalence of well-known pathogens, such as Staphylococcus aureus, giving the biofilm community the factors necessary to maintain chronic biofilm infections

Urdu translation and validation of shorter version of Positive Affect and Negative Affect Schedule (PANAS) on Pakistani bank employees.

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Akhter, Noreen

2017-10-01

To translate, adapt and validate shorter version of positive affect and negative affect scale on Pakistani corporate employees. This cross-sectional study was conducted in the twin cities of Islamabad and Rawalpindi from October 2014 to December 2015. The study was completed into two independent parts. In part one, the scale was translated by forward translation. Then it was pilot-tested and administered on customer services employees from commercial banks and the telecommunication sector. Data of the pilot study was analysed by using exploratory factor analysis to extract the initial factor of positive affect and negative affect scale. Part two comprised the main study. Commercial bank employees were included in the sample using convenient sampling technique. Data of the main study was analysed using confirmatory factor analysis in order to establish construct validity of positive affect and negative affect scale. There were145 participants in the first part of the study and 495 in the second. Results of confirmatory factor analysis confirmed the two-factor structure of positive affect and negative affect scale suggesting that the scale has two distinct domains, i.e. positive affect and negative affect. The shorter version of positive affect and negative affect scale was found to be a valid and reliable measure.

Characteristics of MHC class I genes in house sparrows Passer domesticus as revealed by long cDNA transcripts and amplicon sequencing.

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Karlsson, Maria; Westerdahl, Helena

2013-08-01

In birds the major histocompatibility complex (MHC) organization differs both among and within orders; chickens Gallus gallus of the order Galliformes have a simple arrangement, while many songbirds of the order Passeriformes have a more complex arrangement with larger numbers of MHC class I and II genes. Chicken MHC genes are found at two independent loci, classical MHC-B and non-classical MHC-Y, whereas non-classical MHC genes are yet to be verified in passerines. Here we characterize MHC class I transcripts (α1 to α3 domain) and perform amplicon sequencing using a next-generation sequencing technique on exon 3 from house sparrow Passer domesticus (a passerine) families. Then we use phylogenetic, selection, and segregation analyses to gain a better understanding of the MHC class I organization. Trees based on the α1 and α2 domain revealed a distinct cluster with short terminal branches for transcripts with a 6-bp deletion. Interestingly, this cluster was not seen in the tree based on the α3 domain. 21 exon 3 sequences were verified in a single individual and the average numbers within an individual were nine and five for sequences with and without a 6-bp deletion, respectively. All individuals had exon 3 sequences with and without a 6-bp deletion. The sequences with a 6-bp deletion have many characteristics in common with non-classical MHC, e.g., highly conserved amino acid positions were substituted compared with the other alleles, low nucleotide diversity and just a single site was subject to positive selection. However, these alleles also have characteristics that suggest they could be classical, e.g., complete linkage and absence of a distinct cluster in a tree based on the α3 domain. Thus, we cannot determine for certain whether or not the alleles with a 6-bp deletion are non-classical based on our present data. Further analyses on segregation patterns of these alleles in combination with dating the 6-bp deletion through MHC characterization across the

42 CFR 137.78 - May a Self-Governance Tribe negotiate a funding agreement for a term longer or shorter than one...

Science.gov (United States)

2010-10-01

... 42 Public Health 1 2010-10-01 2010-10-01 false May a Self-Governance Tribe negotiate a funding agreement for a term longer or shorter than one year? 137.78 Section 137.78 Public Health PUBLIC HEALTH... SERVICES TRIBAL SELF-GOVERNANCE Funding General § 137.78 May a Self-Governance Tribe negotiate a funding...

A comparative study of craniofacial morphology of cleft lip children with or without palate

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Cho, Su Beom; Kim, Young Ju; Koh, Kwang Joon [Dept. of Oral Radiology, College of Dentistry, Chonbuk National University, Chonju (Korea, Republic of)

1995-08-15

The purpose of this study was to determine whether any difference existed in craniofacial morphology between cleft children and normal subjects. Thirty three measurements of the various regions of cranium and face were obtained from lateral cephalometric radiograms in 40 cleft children (27 males, 13 females) and 40 normal subjects (23 males, 17 females) in our dental hospital from Jan. 1988 to Dec. 1995. The measurements were compared with those in control subjects who had no history of craniofacial abnormalities.. The obtained results were as follows; l. In the cranium, the cleft children had significantly shorter posterior cranial base length (S-Ba) and total antero-posterior cranial base length (N-Ba) (P<0.05). 2. In the upper face, the cleft children had significantly shorter upper anterior facial height (N-ANS) and upper posterior facial height (Ptm'-SNL) (P<0.05). 3. In the lower face, the cleft children had significantly shorter antero-posterior mandibular length (Pog-Ar) and antero-posterior mandibular body length (Pog-Go) (P<0.05). 4. In the facial profile, the cleft children had significantly shorter total facial height (N-Me) and posterior facial height (S-Go) (P<0.05).

A comparative study of craniofacial morphology of cleft lip children with or without palate

International Nuclear Information System (INIS)

Cho, Su Beom; Kim, Young Ju; Koh, Kwang Joon

1995-01-01

The purpose of this study was to determine whether any difference existed in craniofacial morphology between cleft children and normal subjects. Thirty three measurements of the various regions of cranium and face were obtained from lateral cephalometric radiograms in 40 cleft children (27 males, 13 females) and 40 normal subjects (23 males, 17 females) in our dental hospital from Jan. 1988 to Dec. 1995. The measurements were compared with those in control subjects who had no history of craniofacial abnormalities.. The obtained results were as follows; l. In the cranium, the cleft children had significantly shorter posterior cranial base length (S-Ba) and total antero-posterior cranial base length (N-Ba) (P<0.05). 2. In the upper face, the cleft children had significantly shorter upper anterior facial height (N-ANS) and upper posterior facial height (Ptm'-SNL) (P<0.05). 3. In the lower face, the cleft children had significantly shorter antero-posterior mandibular length (Pog-Ar) and antero-posterior mandibular body length (Pog-Go) (P<0.05). 4. In the facial profile, the cleft children had significantly shorter total facial height (N-Me) and posterior facial height (S-Go) (P<0.05).

The Effect of Shorter Treatment Regimens for Hepatitis C on Population Health and Under Fixed Budgets.

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Morgan, Jake R; Kim, Arthur Y; Naggie, Susanna; Linas, Benjamin P

2018-01-01

Direct acting antiviral hepatitis C virus (HCV) therapies are highly effective but costly. Wider adoption of an 8-week ledipasvir/sofosbuvir treatment regimen could result in significant savings, but may be less efficacious compared with a 12-week regimen. We evaluated outcomes under a constrained budget and cost-effectiveness of 8 vs 12 weeks of therapy in treatment-naïve, noncirrhotic, genotype 1 HCV-infected black and nonblack individuals and considered scenarios of IL28B and NS5A resistance testing to determine treatment duration in sensitivity analyses. We developed a decision tree to use in conjunction with Monte Carlo simulation to investigate the cost-effectiveness of recommended treatment durations and the population health effect of these strategies given a constrained budget. Outcomes included the total number of individuals treated and attaining sustained virologic response (SVR) given a constrained budget and incremental cost-effectiveness ratios. We found that treating eligible (treatment-naïve, noncirrhotic, HCV-RNA budget among both black and nonblack individuals, and our results suggested that NS5A resistance testing is cost-effective. Eight-week therapy provides good value, and wider adoption of shorter treatment could allow more individuals to attain SVR on the population level given a constrained budget. This analysis provides an evidence base to justify movement of the 8-week regimen to the preferred regimen list for appropriate patients in the HCV treatment guidelines and suggests expanding that recommendation to black patients in settings where cost and relapse trade-offs are considered.

Sequencing and comparing whole mitochondrial genomes ofanimals

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Boore, Jeffrey L.; Macey, J. Robert; Medina, Monica

2005-04-22

Comparing complete animal mitochondrial genome sequences is becoming increasingly common for phylogenetic reconstruction and as a model for genome evolution. Not only are they much more informative than shorter sequences of individual genes for inferring evolutionary relatedness, but these data also provide sets of genome-level characters, such as the relative arrangements of genes, that can be especially powerful. We describe here the protocols commonly used for physically isolating mtDNA, for amplifying these by PCR or RCA, for cloning,sequencing, assembly, validation, and gene annotation, and for comparing both sequences and gene arrangements. On several topics, we offer general observations based on our experiences to date with determining and comparing complete mtDNA sequences.

Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine.

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Marcus J Claesson

Full Text Available BACKGROUND: Variations in the composition of the human intestinal microbiota are linked to diverse health conditions. High-throughput molecular technologies have recently elucidated microbial community structure at much higher resolution than was previously possible. Here we compare two such methods, pyrosequencing and a phylogenetic array, and evaluate classifications based on two variable 16S rRNA gene regions. METHODS AND FINDINGS: Over 1.75 million amplicon sequences were generated from the V4 and V6 regions of 16S rRNA genes in bacterial DNA extracted from four fecal samples of elderly individuals. The phylotype richness, for individual samples, was 1,400-1,800 for V4 reads and 12,500 for V6 reads, and 5,200 unique phylotypes when combining V4 reads from all samples. The RDP-classifier was more efficient for the V4 than for the far less conserved and shorter V6 region, but differences in community structure also affected efficiency. Even when analyzing only 20% of the reads, the majority of the microbial diversity was captured in two samples tested. DNA from the four samples was hybridized against the Human Intestinal Tract (HIT Chip, a phylogenetic microarray for community profiling. Comparison of clustering of genus counts from pyrosequencing and HITChip data revealed highly similar profiles. Furthermore, correlations of sequence abundance and hybridization signal intensities were very high for lower-order ranks, but lower at family-level, which was probably due to ambiguous taxonomic groupings. CONCLUSIONS: The RDP-classifier consistently assigned most V4 sequences from human intestinal samples down to genus-level with good accuracy and speed. This is the deepest sequencing of single gastrointestinal samples reported to date, but microbial richness levels have still not leveled out. A majority of these diversities can also be captured with five times lower sampling-depth. HITChip hybridizations and resulting community profiles correlate

TIA model is attainable in Wistar rats by intraluminal occlusion of the MCA for 10min or shorter.

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Durukan Tolvanen, A; Tatlisumak, E; Pedrono, E; Abo-Ramadan, U; Tatlisumak, T

2017-05-15

Transient ischemic attack (TIA) has received only little attention in the experimental research field. Recently, we introduced a TIA model for mice, and here we set similar principles for simulating this human condition in Wistar rats. In the model: 1) transient nature of the event is ensured, and 2) 24h after the event animals are free from any sensorimotor deficit and from any detectable lesion by magnetic resonance imaging (MRI). Animals experienced varying durations of ischemia (5, 10, 12.5, 15, 25, and 30min, n=6-8pergroup) by intraluminal middle cerebral artery occlusion (MCAO). Ischemia severity and reperfusion rates were controlled by cerebral blood flow measurements. Sensorimotor neurological evaluations and MRI at 24h differentiated between TIA and ischemic stroke. Hematoxylin and eosin staining and apoptotic cell counts revealed pathological correlates of the event. We found that already 12.5min of ischemia was long enough to induce ischemic stroke in Wistar rats. Ten min or shorter durations induced neither gross neurological deficits nor infarcts visible on MRI, but histologically caused selective neuronal necrosis. A separate group of animals with 10min of ischemia followed up to 1week after reperfusion remained free of infarction and any MRI signal change. Thus, 10min or shorter focal cerebral ischemia induced by intraluminal MCAO in Wistar rats provides a clinically relevant TIA the rat. This model is useful for studying molecular correlates of TIA. Copyright © 2017 Elsevier B.V. All rights reserved.

Comparative assessment of genetic diversity in Sesamum indicum L. using RAPD and SSR markers.

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Dar, Aejaz Ahmad; Mudigunda, Sushma; Mittal, Pramod Kumar; Arumugam, Neelakantan

2017-05-01

Sesame (Sesamum indicum L.) is an ancient oilseed crop known for its nutty seeds and high-quality edible oil. It is an unexplored crop with a great economic potential. The present study deals with assessment of genetic diversity in the crop. Twenty two RAPD and 18 SSR primers were used for analysis of the 47 different sesame accessions grown in different agroclimatic zones of India. A total of 256 bands were obtained with RAPD primers, of which 191 were polymorphic. SSR primers gave 64 DNA bands, of which all of were polymorphic. The Jaccard's similarity coefficient of RAPD, SSR, and pooled RAPD and SSR data ranged from 0.510 to 0.885, 0.167 to 0.867, and 0.505 to 0.853, respectively. Maximum polymorphic information content was reported with SSRs (0.194) compared to RAPDs (0.186). Higher marker index was observed with RAPDs (1.426) than with SSRs (0.621). Similarly, maximum resolving power was found with RAPD (4.012) primers than with SSRs (0.884). The RAPD primer RPI-B11 and SSR primer S16 were the most informative in terms of describing genetic variability among the varieties under study. At a molecular level, the seed coat colour was distinguishable by the presence and absence of a group of marker amplicon/s. White and brown seeded varieties clustered close to each other, while black seeded varieties remained distanced from the cluster. In the present study, we found higher variability in Sesamum indicum L. using RAPD and SSR markers and these could assist in DNA finger printing, conservation of germplasm, and crop improvement.

Shorter epilepsy duration is associated with better seizure outcome in temporal lobe epilepsy surgery

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Lucas Crociati Meguins

2015-03-01

Full Text Available Objective To investigate the influence of patient’s age and seizure onset on surgical outcome of temporal lobe epilepsy (TLE. Method A retrospective observational investigation performed from a cohort of patients from 2000 to 2012. Results A total of 229 patients were included. One-hundred and eleven of 179 patients (62% were classified as Engel I in the group with < 50 years old, whereas 33 of 50 (66% in the group with ≥ 50 years old group (p = 0.82. From those Engel I, 88 (61% reported epilepsy duration inferior to 10 years and 56 (39% superior to 10 years (p < 0.01. From the total of patients not seizure free, 36 (42% reported epilepsy duration inferior to 10 years and 49 (58% superior to 10 years (p < 0.01. Conclusion Patients with shorter duration of epilepsy before surgery had better postoperative seizure control than patients with longer duration of seizures.

Amplicon-Based Pyrosequencing Reveals High Diversity of Protistan Parasites in Ships' Ballast Water: Implications for Biogeography and Infectious Diseases.

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Pagenkopp Lohan, K M; Fleischer, R C; Carney, K J; Holzer, K K; Ruiz, G M

2016-04-01

Ships' ballast water (BW) commonly moves macroorganisms and microorganisms across the world's oceans and along coasts; however, the majority of these microbial transfers have gone undetected. We applied high-throughput sequencing methods to identify microbial eukaryotes, specifically emphasizing the protistan parasites, in ships' BW collected from vessels calling to the Chesapeake Bay (Virginia and Maryland, USA) from European and Eastern Canadian ports. We utilized tagged-amplicon 454 pyrosequencing with two general primer sets, amplifying either the V4 or V9 domain of the small subunit (SSU) of the ribosomal RNA (rRNA) gene complex, from total DNA extracted from water samples collected from the ballast tanks of bulk cargo vessels. We detected a diverse group of protistan taxa, with some known to contain important parasites in marine systems, including Apicomplexa (unidentified apicomplexans, unidentified gregarines, Cryptosporidium spp.), Dinophyta (Blastodinium spp., Euduboscquella sp., unidentified syndinids, Karlodinium spp., Syndinium spp.), Perkinsea (Parvilucifera sp.), Opisthokonta (Ichthyosporea sp., Pseudoperkinsidae, unidentified ichthyosporeans), and Stramenopiles (Labyrinthulomycetes). Further characterization of groups with parasitic taxa, consisting of phylogenetic analyses for four taxa (Cryptosporidium spp., Parvilucifera spp., Labyrinthulomycetes, and Ichthyosporea), revealed that sequences were obtained from both known and novel lineages. This study demonstrates that high-throughput sequencing is a viable and sensitive method for detecting parasitic protists when present and transported in the ballast water of ships. These data also underscore the potential importance of human-aided dispersal in the biogeography of these microbes and emerging diseases in the world's oceans.

Shorter Versus Longer Shift Durations to Mitigate Fatigue and Fatigue-Related Risks in Emergency Medical Services Personnel and Related Shift Workers: A Systematic Review

Science.gov (United States)

2018-01-11

Background: This study comprehensively reviewed the literature on the impact of shorter versus longer shifts on critical and important outcomes for Emergency Medical Services (EMS) personnel and related shift worker groups. Methods: Six databases (e....

Prenatal paracetamol exposure is associated with shorter anogenital distance in male infants

Science.gov (United States)

Fisher, B.G.; Thankamony, A.; Hughes, I.A.; Ong, K.K.; Dunger, D.B.; Acerini, C.L.

2016-01-01

STUDY QUESTION What is the relationship between maternal paracetamol intake during the masculinisation programming window (MPW, 8–14 weeks of gestation) and male infant anogenital distance (AGD), a biomarker for androgen action during the MPW? SUMMARY ANSWER Intrauterine paracetamol exposure during 8–14 weeks of gestation is associated with shorter AGD from birth to 24 months of age. WHAT IS ALREADY KNOWN The increasing prevalence of male reproductive disorders may reflect environmental influences on foetal testicular development during the MPW. Animal and human xenograft studies have demonstrated that paracetamol reduces foetal testicular testosterone production, consistent with reported epidemiological associations between prenatal paracetamol exposure and cryptorchidism. STUDY DESIGN, SIZE, DURATION Prospective cohort study (Cambridge Baby Growth Study), with recruitment of pregnant women at ~12 post-menstrual weeks of gestation from a single UK maternity unit between 2001 and 2009, and 24 months of infant follow-up. Of 2229 recruited women, 1640 continued with the infancy study after delivery, of whom 676 delivered male infants and completed a medicine consumption questionnaire. PARTICIPANTS/MATERIALS, SETTING, METHOD Mothers self-reported medicine consumption during pregnancy by a questionnaire administered during the perinatal period. Infant AGD (measured from 2006 onwards), penile length and testicular descent were assessed at 0, 3, 12, 18 and 24 months of age, and age-specific Z scores were calculated. Associations between paracetamol intake during three gestational periods (14 weeks) and these outcomes were tested by linear mixed models. Two hundred and twenty-five (33%) of six hundred and eighty-one male infants were exposed to paracetamol during pregnancy, of whom sixty-eight were reported to be exposed during 8–14 weeks. AGD measurements were available for 434 male infants. MAIN RESULTS AND THE ROLE OF CHANCE Paracetamol exposure during 8–14

Do Dysphagic Patients with an Absent Pharyngeal Swallow Have a Shorter Survival than Dysphagic Patients with Pharyngeal Swallow? Prognostic Importance of a Therapeutic Videoradiographic Swallowing Study (TVSS)

International Nuclear Information System (INIS)

Buelow, M.; Olsson, R.; Ekberg, O.

2005-01-01

Purpose: To study survival in two groups of dysphagic patients - one group unable to elicit the pharyngeal stage of swallow (APS) and another group with pharyngeal swallow (WPS) - and to compare recommendations regarding nutrition and therapeutic strategies based on the therapeutic swallowing study. Material and Methods: In this retrospective study, the records of dysphagic patients who have undergone a therapeutic videoradiographic swallowing study (TVSS) were reviewed. Forty patients without pharyngeal swallow were matched for age and gender with 40 patients with pharyngeal swallow; altogether 80 patients were included in the study. Survival was registered at 3, 12, and 72 months after the TVSS. Results: In this study, the APS group had a significantly shorter survival time compared to the WPS group when followed-up at 12 months. In the APS group, most patients (37.5% (15/40)) died within the 3 months after TVSS. At 72 months, 62.5% (25/40) of the patients in the APS group had died. In the WPS group, 5% (2/40) had died within 3 months and 47.4% (19/40) after 12 months. At 72 months, 52.5% (21/40) of the patients in the WPS group had died. Regarding nutritional and therapeutic recommendations based on TVSS, 34/40 in the APS group were recommended no oral intake. Eighteen naso-gastric tubes were placed directly after TVSS. The therapeutic strategies recommended were head-positioning, thermal tactile stimulation, and tongue exercises (in 8 patients). In the WPS group, all patients were recommended oral intake. Diet modification was recommended in 29 patients. The therapeutic strategies recommended were head-positioning, thermal tactile stimulation, tongue exercises, supraglottic swallow, and effortful swallow (in 24 patients). Conclusion: Patients unable to elicit the pharyngeal stage of swallow had a shorter survival time than patients with pharyngeal swallow, probably due to a more severe underlying disease. Tube feeding was more frequent in the APS group. Fewer

Lab-on-a-chip-based PCR-RFLP assay for the confirmed detection of short-length feline DNA in food.

Science.gov (United States)

Ali, Md Eaqub; Al Amin, Md; Hamid, Sharifah Bee Abd; Hossain, M A Motalib; Mustafa, Shuhaimi

2015-01-01

Wider availability but lack of legal market trades has given feline meat a high potential for use as an adulterant in common meat and meat products. However, mixing of feline meat or its derivatives in food is a sensitive issue, since it is a taboo in most countries and prohibited in certain religions such as Islam and Judaism. Cat meat also has potential for contamination with of severe acute respiratory syndrome, anthrax and hepatitis, and its consumption might lead to an allergic reaction. We developed a very short-amplicon-length (69 bp) PCR assay, authenticated the amplified PCR products by AluI-restriction digestion followed by its separation and detection on a lab-on-a-chip-based automated electrophoretic system, and proved its superiority over the existing long-amplicon-based assays. Although it has been assumed that longer DNA targets are susceptible to breakdown under compromised states, scientific evidence for this hypothesis has been rarely documented. Strong evidence showed that shorter targets are more stable than the longer ones. We confirmed feline-specificity by cross-challenging the primers against 10 different species of terrestrial, aquatic and plant origins in the presence of a 141-bp site of an 18S rRNA gene as a universal eukaryotic control. RFLP analysis separated 43- and 26-bp fragments of AluI-digest in both the gel-image and electropherograms, confirming the original products. The tested detection limit was 0.01% (w/w) feline meat in binary and ternary admixed as well as meatball matrices. Shorter target, better stability and higher sensitivity mean such an assay would be valid for feline identification even in degraded specimens.

Time to Detection with BacT/Alert FA Plus Compared to BacT/Alert FA Blood Culture Media.

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Nutman, A; Fisher Even-Tsur, S; Shapiro, G; Braun, T; Schwartz, D; Carmeli, Y

2016-09-01

Rapid identification of the causative pathogen in patients with bacteremia allows adjustment of antibiotic therapy and improves patient outcomes. We compared in vitro and real-life time to detection (TTD) of two blood culture media, BacT/Alert FA (FA) and BacT/Alert FA Plus (FA Plus), for the nine most common species of bacterial pathogens recovered from blood samples. Experimental data from simulated cultures was compared with microbiology records of TTD for both culture media with growth of the species of interest in clinical blood cultures. In the experimental conditions, median TTD was 3.8 hours (23.9 %) shorter using FA Plus media. The magnitude of reduction differed between species. Similarly, in real life data, FA Plus had shorter TTD than FA media; however, the difference between culture media was smaller, and median TTD was only 1 hour (8.5 %) less. We found shorter TTD with BacT/Alert FA Plus culture media, both experimentally and in real-life conditions and unrelated to antibiotic neutralization, highlighting the importance of appropriate blood culture media selection.

The use of genus-specific amplicon pyrosequencing to assess phytophthora species diversity using eDNA from soil and water in Northern Spain.

Science.gov (United States)

Català, Santiago; Pérez-Sierra, Ana; Abad-Campos, Paloma

2015-01-01

Phytophthora is one of the most important and aggressive plant pathogenic genera in agriculture and forestry. Early detection and identification of its pathways of infection and spread are of high importance to minimize the threat they pose to natural ecosystems. eDNA was extracted from soil and water from forests and plantations in the north of Spain. Phytophthora-specific primers were adapted for use in high-throughput Sequencing (HTS). Primers were tested in a control reaction containing eight Phytophthora species and applied to water and soil eDNA samples from northern Spain. Different score coverage threshold values were tested for optimal Phytophthora species separation in a custom-curated database and in the control reaction. Clustering at 99% was the optimal criteria to separate most of the Phytophthora species. Multiple Molecular Operational Taxonomic Units (MOTUs) corresponding to 36 distinct Phytophthora species were amplified in the environmental samples. Pyrosequencing of amplicons from soil samples revealed low Phytophthora diversity (13 species) in comparison with the 35 species detected in water samples. Thirteen of the MOTUs detected in rivers and streams showed no close match to sequences in international sequence databases, revealing that eDNA pyrosequencing is a useful strategy to assess Phytophthora species diversity in natural ecosystems.

Shorter preschool, leukocyte telomere length is associated with obesity at age 9 in Latino children

DEFF Research Database (Denmark)

Kjaer, Thora Wesenberg; Faurholt-Jepsen, D; Mehta, K M

2018-01-01

The aim of this study was to determine the potential role of leukocyte telomere length as a biomarker for development of childhood obesity in a low-income Latino population. A birth cohort of Latino children (N = 201) in San Francisco (recruited May 2006-May 2007) was followed until age 9...... and assessed annually for obesity and dietary intake. Leukocyte telomere length was measured at 4 and 5 years (n = 102) and assessed as a predictor for obesity at age 9, adjusting for known risk factors. Furthermore, leukocyte telomere length at age 4 and 5 was evaluated as a possible mediator...... of the relationship between excessive sugar-sweetened beverage consumption and obesity at age 9. Shorter leukocyte telomere length in preschoolers was associated with obesity at age 9 (adjusted odds ratio 0.35, 95% confidence interval 0.13-0.94) after adjustment for known risk factors. Telomere length mediated 11...

First-line intra-arterial versus intravenous chemotherapy in unilateral sporadic group D retinoblastoma: evidence of better visual outcomes, ocular survival and shorter time to success with intra-arterial delivery from retrospective review of 20 years of treatment.

Science.gov (United States)

Munier, Francis L; Mosimann, Pascal; Puccinelli, Francesco; Gaillard, Marie-Claire; Stathopoulos, Christina; Houghton, Susan; Bergin, Ciara; Beck-Popovic, Maja

2017-08-01

The introduction of intra-arterial chemotherapy (IAC) as salvage treatment has improved the prognosis for eye conservation in group D retinoblastoma. The aim of this study was to compare the outcomes of consecutive patients with advanced unilateral disease treated with either first-line intravenous chemotherapy (IVC) or first-line IAC. This is a retrospective mono-centric comparative review of consecutive patients. Sporadic unilateral retinoblastoma group D cases treated conservatively at Jules-Gonin Eye Hospital and CHUV between 1997 and 2014. From January 1997 to August 2008, IVC, combined with focal treatments, was the primary treatment approach. From September 2008 to October 2014, IAC replaced IVC as first-line therapy. 48 patients met the inclusion criteria, receiving only either IAC or IVC as primary treatment modality. Outcomes of 23 patients treated by IVC were compared with those of 25 treated by IAC; mean follow-up was 105.3 months (range 29.2-218.6) and 41.7 months (range 19.6-89.5), respectively. Treatment duration was significantly shorter in the IAC group (pchemotherapy treatment. Despite this, the results reported here imply that eyes treated with first-line IAC will have shorter treatment period, better ocular survival and visual acuity than first-line IVC. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

A comparative study of Averrhoabilimbi extraction method

Science.gov (United States)

Zulhaimi, H. I.; Rosli, I. R.; Kasim, K. F.; Akmal, H. Muhammad; Nuradibah, M. A.; Sam, S. T.

2017-09-01

In recent year, bioactive compound in plant has become a limelight in the food and pharmaceutical market, leading to research interest to implement effective technologies for extracting bioactive substance. Therefore, this study is focusing on extraction of Averrhoabilimbi by different extraction technique namely, maceration and ultrasound-assisted extraction. Fewplant partsof Averrhoabilimbiweretaken as extraction samples which are fruits, leaves and twig. Different solvents such as methanol, ethanol and distilled water were utilized in the process. Fruit extractsresult in highest extraction yield compared to other plant parts. Ethanol and distilled water have significant role compared to methanol in all parts and both extraction technique. The result also shows that ultrasound-assisted extraction gave comparable result with maceration. Besides, the shorter period on extraction process gives useful in term of implementation to industries.

Nuclear Species-Diagnostic SNP Markers Mined from 454 Amplicon Sequencing Reveal Admixture Genomic Structure of Modern Citrus Varieties

Science.gov (United States)

Curk, Franck; Ancillo, Gema; Ollitrault, Frédérique; Perrier, Xavier; Jacquemoud-Collet, Jean-Pierre; Garcia-Lor, Andres; Navarro, Luis; Ollitrault, Patrick

2015-01-01

Most cultivated Citrus species originated from interspecific hybridisation between four ancestral taxa (C. reticulata, C. maxima, C. medica, and C. micrantha) with limited further interspecific recombination due to vegetative propagation. This evolution resulted in admixture genomes with frequent interspecific heterozygosity. Moreover, a major part of the phenotypic diversity of edible citrus results from the initial differentiation between these taxa. Deciphering the phylogenomic structure of citrus germplasm is therefore essential for an efficient utilization of citrus biodiversity in breeding schemes. The objective of this work was to develop a set of species-diagnostic single nucleotide polymorphism (SNP) markers for the four Citrus ancestral taxa covering the nine chromosomes, and to use these markers to infer the phylogenomic structure of secondary species and modern cultivars. Species-diagnostic SNPs were mined from 454 amplicon sequencing of 57 gene fragments from 26 genotypes of the four basic taxa. Of the 1,053 SNPs mined from 28,507 kb sequence, 273 were found to be highly diagnostic for a single basic taxon. Species-diagnostic SNP markers (105) were used to analyse the admixture structure of varieties and rootstocks. This revealed C. maxima introgressions in most of the old and in all recent selections of mandarins, and suggested that C. reticulata × C. maxima reticulation and introgression processes were important in edible mandarin domestication. The large range of phylogenomic constitutions between C. reticulata and C. maxima revealed in mandarins, tangelos, tangors, sweet oranges, sour oranges, grapefruits, and orangelos is favourable for genetic association studies based on phylogenomic structures of the germplasm. Inferred admixture structures were in agreement with previous hypotheses regarding the origin of several secondary species and also revealed the probable origin of several acid citrus varieties. The developed species-diagnostic SNP

Heuristics for Comparing the Lengths of Completed E-TSP Tours: Crossings and Areas

Science.gov (United States)

MacGregor, James N.

2017-01-01

The article reports three experiments designed to explore heuristics used in comparing the lengths of completed Euclidean Traveling Salesman Problem (E-TSP) tours. The experiments used paired comparisons in which participants judged which of two completed tours of the same point set was shorter. The first experiment manipulated two factors, the…

Prescreening of microbial populations for the assessment of sequencing potential.

Science.gov (United States)

Hanning, Irene B; Ricke, Steven C

2011-01-01

Next-generation sequencing (NGS) is a powerful tool that can be utilized to profile and compare microbial populations. By amplifying a target gene present in all bacteria and subsequently sequencing amplicons, the bacteria genera present in the populations can be identified and compared. In some scenarios, little to no difference may exist among microbial populations being compared in which case a prescreening method would be practical to determine which microbial populations would be suitable for further analysis by NGS. Denaturing density-gradient electrophoresis (DGGE) is relatively cheaper than NGS and the data comparing microbial populations are ready to be viewed immediately after electrophoresis. DGGE follows essentially the same initial methodology as NGS by targeting and amplifying the 16S rRNA gene. However, as opposed to sequencing amplicons, DGGE amplicons are analyzed by electrophoresis. By prescreening microbial populations with DGGE, more efficient use of NGS methods can be accomplished. In this chapter, we outline the protocol for DGGE targeting the same gene (16S rRNA) that would be targeted for NGS to compare and determine differences in microbial populations from a wide range of ecosystems.

A Kinetic Model Explains Why Shorter and Less Affine Enzyme-recruiting Oligonucleotides Can Be More Potent

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Lykke Pedersen

2014-01-01

Full Text Available Antisense oligonucleotides complementary to RNA targets promise generality and ease of drug design. The first systemically administered antisense drug was recently approved for treatment and others are in clinical development. Chemical modifications that increase the hybridization affinity of oligonucleotides are reasoned to confer higher potency, i.e., modified oligonucleotides can be dosed at lower concentrations to achieve the same effect. Surprisingly, shorter and less affine oligonucleotides sometimes display increased potency. To explain this apparent contradiction, increased uptake or decreased propensity to form structures have been suggested as possible mechanisms. Here, we provide an alternative explanation that invokes only the kinetics behind oligonucleotide-mediated cleavage of RNA targets. A model based on the law of mass action predicts, and experiments support, the existence of an optimal binding affinity. Exaggerated affinity, and not length per se, is detrimental to potency. This finding clarifies how to optimally apply high-affinity modifications in the discovery of potent antisense oligonucleotide drugs.

Effects of shorter versus longer storage time of transfused red blood cells in adult ICU patients

DEFF Research Database (Denmark)

Rygård, Sofie L; Jonsson, Andreas B; Madsen, Martin B

2018-01-01

on the effects of shorter versus longer storage time of transfused RBCs on outcomes in ICU patients. METHODS: We conducted a systematic review with meta-analyses and trial sequential analyses (TSA) of randomised clinical trials including adult ICU patients transfused with fresher versus older or standard issue...... blood. RESULTS: We included seven trials with a total of 18,283 randomised ICU patients; two trials of 7504 patients were judged to have low risk of bias. We observed no effects of fresher versus older blood on death (relative risk 1.04, 95% confidence interval (CI) 0.97-1.11; 7349 patients; TSA......-adjusted CI 0.93-1.15), adverse events (1.26, 0.76-2.09; 7332 patients; TSA-adjusted CI 0.16-9.87) or post-transfusion infections (1.07, 0.96-1.20; 7332 patients; TSA-adjusted CI 0.90-1.27). The results were unchanged by including trials with high risk of bias. TSA confirmed the results and the required...

A Prospective Study Comparing Ligasure and Open Hemorrhoidectomy

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Rahimi M

2011-11-01

Full Text Available Background: Hemorrhoid is among the most common anorectal diseases and patients with high-grade disease conditions need surgical treatment. Many surgical procedures are available to treat the disease. The aim of this study was to compare the operative time and outcomes, (post-operative pain and complications of LigaSure hemorrhoidectomy with those of the open conventional method.Methods : This randomized single-blind clinical trial included 57 patients (28 in LigaSure and 29 in the open group. The primary variable was the operative time for the excision of a single hemorrhoidal packet. The other variables were post-operative pain measured by morphine doses administered to control pain, scores of visual analogue scale (VAS used to measure pain severity, pain during home stay measured by doses of oral ibuprofen and the mean daily VAS scores, early complications including bleeding and urinary retention, longer-term complications and time to return to work.Results : The demographic data were comparatively the same between the two groups. The average time to excise a single packet of hemorrhoid was significantly shorter in the LigaSure group (8.91 min vs. 17.35 min, P<0.001. Post-operative pain measurements (morphine doses and VAS scores were lower in the LigaSure group, but the differences were not statistically significant (P=0.055 and 0.077, respectively. Complications of the two procedures were also comparable. Neither of the groups returned to work in a shorter time.Conclusion: LigaSure hemorrhoidectomy seems to be a safe method and it can reduce the operative time significantly. It may also have a modest effect on post-operative pain.

The usefulness of two-port video-assisted thoracosopic surgery in low-risk patients with secondary spontaneous pneumothorax compared with open thoracotomy

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Kyoung Taek Park

2014-01-01

Conclusion: In selected patients with secondary spontaneous pneumothorax treated with surgical approach, two-port VATS resulted in shorter postoperative drainage period and hospital stay compared with open thoracotomy.

Shorter Fallow Cycles Affect the Availability of Noncrop Plant Resources in a Shifting Cultivation System

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Sarah Paule. Dalle

2006-12-01

Full Text Available Shifting cultivation systems, one of the most widely distributed forms of agriculture in the tropics, provide not only crops of cultural significance, but also medicinal, edible, ritual, fuel, and forage resources, which contribute to the livelihoods, health, and cultural identity of local people. In many regions across the globe, shifting cultivation systems are undergoing important changes, one of the most pervasive being a shortening of the fallow cycle. Although there has been much attention drawn to declines in crop yields in conjunction with reductions in fallow times, little if any research has focused on the dynamics of noncrop plant resources. In this paper, we use a data set of 26 fields of the same age, i.e., ~1.5 yr, but differing in the length and frequency of past fallow cycles, to examine the impact of shorter fallow periods on the availability of noncrop plant resources. The resources examined are collected in shifting cultivation fields by the Yucatec Maya in Quintana Roo, Mexico. These included firewood, which is cut from remnant trees and stumps spared at the time of felling, and 17 forage species that form part of the weed vegetation. Firewood showed an overall decrease in basal area with shorter fallow cycles, which was mostly related to the smaller diameter of the spared stumps and trees in short-fallow milpas. In contrast, forage species showed a mixed response. Species increasing in abundance in short-fallow milpas tended to be short-lived herbs and shrubs often with weedy habits, whereas those declining in abundance were predominantly pioneer trees and animal-dispersed species. Coppicing tree species showed a neutral response to fallow intensity. Within the cultural and ecological context of our study area, we expect that declines in firewood availability will be most significant for livelihoods because of the high reliance on firewood for local fuel needs and the fact that the main alternative source of firewood, forest

Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons

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Christopher Ryan Penton

2016-06-01

Full Text Available We examined the effect of different soil sample sizes obtained from an agricultural field, under a single cropping system uniform in soil properties and aboveground crop responses, on bacterial and fungal community structure and microbial diversity indices. DNA extracted from soil sample sizes of 0.25, 1, 5 and 10 g using MoBIO kits and from 10 and 100 g sizes using a bead-beating method (SARDI were used as templates for high-throughput sequencing of 16S and 28S rRNA gene amplicons for bacteria and fungi, respectively, on the Illumina MiSeq and Roche 454 platforms. Sample size significantly affected overall bacterial and fungal community structure, replicate dispersion and the number of operational taxonomic units (OTUs retrieved. Richness, evenness and diversity were also significantly affected. The largest diversity estimates were always associated with the 10 g MoBIO extractions with a corresponding reduction in replicate dispersion. For the fungal data, smaller MoBIO extractions identified more unclassified Eukaryota incertae sedis and unclassified glomeromycota while the SARDI method retrieved more abundant OTUs containing unclassified Pleosporales and the fungal genera Alternaria and Cercophora. Overall, these findings indicate that a 10 g soil DNA extraction is most suitable for both soil bacterial and fungal communities for retrieving optimal diversity while still capturing rarer taxa in concert with decreasing replicate variation.

Highly parallel and short-acting amplification with locus-specific primers to detect single nucleotide polymorphisms by the DigiTag2 assay.

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Nao Nishida

Full Text Available The DigiTag2 assay enables analysis of a set of 96 SNPs using Kapa 2GFast HotStart DNA polymerase with a new protocol that has a total running time of about 7 hours, which is 6 hours shorter than the previous protocol. Quality parameters (conversion rate, call rate, reproducibility and concordance were at the same levels as when genotype calls were acquired using the previous protocol. Multiplex PCR with 192 pairs of locus-specific primers was available for target preparation in the DigiTag2 assay without the optimization of reaction conditions, and quality parameters had the same levels as those acquired with 96-plex PCR. The locus-specific primers were able to achieve sufficient (concentration of target amplicon ≥5 nM and specific (concentration of unexpected amplicons <2 nM amplification within 2 hours, were also able to achieve detectable amplifications even when working in a 96-plex or 192-plex form. The improved DigiTag2 assay will be an efficient platform for screening an intermediate number of SNPs (tens to hundreds of sites in the replication analysis after genome-wide association study. Moreover, highly parallel and short-acting amplification with locus-specific primers may thus facilitate widespread application to other PCR-based assays.

SHORTER, Aylward. African recruits and missionary conscripts: the White Fathers and the Great War (1914 – 1922. London: Missionaries of Africa History Project, 2007. 270 p. ISBN: 9780955523502

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Jefferson Olivatto da Silva

2011-09-01

Full Text Available Resenha do livroSHORTER, Aylward. African recruits and missionary conscripts: the White Fathers and the Great War (1914 – 1922. London: Missionaries of Africa History Project, 2007. 270 p. ISBN: 9780955523502

Aiming for a shorter rheumatoid arthritis MRI protocol: can contrast-enhanced MRI replace T2 for the detection of bone marrow oedema?

Energy Technology Data Exchange (ETDEWEB)

Stomp, Wouter; Bloem, Johan L.; Reijnierse, Monique [Leiden University Medical Center, Department of Radiology, P.O. Box 9600, Leiden (Netherlands); Krabben, Annemarie; Heijde, Desiree van der; Huizinga, Tom W.J.; Helm-van Mil, Annette H.M. van der [Leiden University Medical Center, Department of Rheumatology, P.O. Box 9600, Leiden (Netherlands)

2014-10-15

To determine whether T1 post-gadolinium chelate images (T1Gd) can replace T2-weighted images (T2) for evaluating bone marrow oedema (BME), thereby allowing a shorter magnetic resonance imaging (MRI) protocol in rheumatoid arthritis (RA). In 179 early arthritis patients and 43 advanced RA patients, wrist and metacarpophalangeal joints were examined on a 1.5-T extremity MRI system with a standard protocol (coronal T1, T2 fat-saturated and coronal and axial T1 fat-saturated after Gd). BME was scored according to OMERACT RAMRIS by two observers with and without T2 images available. Agreement was assessed using intraclass correlation coefficients (ICCs) for semi-quantitative scores and test characteristics with T2 images as reference. Agreement between scores based on T2 and T1Gd images was excellent ICC (0.80-0.99). At bone level, sensitivity and specificity of BME on T1Gd compared to T2 were high for both patient groups and both readers (all ≥80 %). T1Gd and T2 images are equally suitable for evaluating BME. Because contrast is usually administered to assess (teno)synovitis, a short MRI protocol of T1 and T1Gd is sufficient in RA. (orig.)

Aiming for a shorter rheumatoid arthritis MRI protocol: can contrast-enhanced MRI replace T2 for the detection of bone marrow oedema?

International Nuclear Information System (INIS)

Stomp, Wouter; Bloem, Johan L.; Reijnierse, Monique; Krabben, Annemarie; Heijde, Desiree van der; Huizinga, Tom W.J.; Helm-van Mil, Annette H.M. van der

2014-01-01

To determine whether T1 post-gadolinium chelate images (T1Gd) can replace T2-weighted images (T2) for evaluating bone marrow oedema (BME), thereby allowing a shorter magnetic resonance imaging (MRI) protocol in rheumatoid arthritis (RA). In 179 early arthritis patients and 43 advanced RA patients, wrist and metacarpophalangeal joints were examined on a 1.5-T extremity MRI system with a standard protocol (coronal T1, T2 fat-saturated and coronal and axial T1 fat-saturated after Gd). BME was scored according to OMERACT RAMRIS by two observers with and without T2 images available. Agreement was assessed using intraclass correlation coefficients (ICCs) for semi-quantitative scores and test characteristics with T2 images as reference. Agreement between scores based on T2 and T1Gd images was excellent ICC (0.80-0.99). At bone level, sensitivity and specificity of BME on T1Gd compared to T2 were high for both patient groups and both readers (all ≥80 %). T1Gd and T2 images are equally suitable for evaluating BME. Because contrast is usually administered to assess (teno)synovitis, a short MRI protocol of T1 and T1Gd is sufficient in RA. (orig.)

Feasibility of a shorter Goal Attainment Scaling method for a pediatric spasticity clinic - The 3-milestones GAS.

Science.gov (United States)

Krasny-Pacini, A; Pauly, F; Hiebel, J; Godon, S; Isner-Horobeti, M-E; Chevignard, M

2017-07-01

Goal Attainment Scaling (GAS) is a method for writing personalized evaluation scales to quantify progress toward defined goals. It is useful in rehabilitation but is hampered by the experience required to adequately "predict" the possible outcomes relating to a particular goal before treatment and the time needed to describe all 5 levels of the scale. Here we aimed to investigate the feasibility of using GAS in a clinical setting of a pediatric spasticity clinic with a shorter method, the "3-milestones" GAS (goal setting with 3 levels and goal rating with the classical 5 levels). Secondary aims were to (1) analyze the types of goals children's therapists set for botulinum toxin treatment and (2) compare the score distribution (and therefore the ability to predict outcome) by goal type. Therapists were trained in GAS writing and prepared GAS scales in the regional spasticity-management clinic they attended with their patients and families. The study included all GAS scales written during a 2-year period. GAS score distribution across the 5 GAS levels was examined to assess whether the therapist could reliably predict outcome and whether the 3-milestones GAS yielded similar distributions as the original GAS method. In total, 541 GAS scales were written and showed the expected score distribution. Most scales (55%) referred to movement quality goals and fewer (29%) to family goals and activity domains. The 3-milestones GAS method was feasible within the time constraints of the spasticity clinic and could be used by local therapists in cooperation with the hospital team. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Structure of the Bacterial Community in Different Stages of Early Childhood Caries.

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Ximenes, Marcos; Armas, Rafael Dutra de; Triches, Thaisa Cezária; Cardoso, Mariane; Vieira, Ricardo de Souza

2018-01-15

To characterise in vivo the structure of bacterial communities in decayed and sound primary teeth. Samples of biofilms were collected from three groups of patients with complete and exclusively primary dentition (n = 45): G1: sound teeth (n = 15); G2: enamel lesion (n = 15); G3: dentin lesion (n = 15). DNA was extracted (CTAB 2%) from the biofilm, the partial 16S rRNA gene was amplified with Bacteria Universal Primers (BA338fGC - UN518r) and subjected to DGGE (denaturing gradient gel electrophoresis). Multidimensional scaling and ANOSIM (analysis of similarity) were employed to determine the structure of the bacterial communities. The amplicon richness was determined by averaging amplicons, with the differences between treatments determined with ANOVA, while means were compared using Tukey's test (p < 0.05). Compared to sound teeth, a greater variety of bacterial communities was found in decayed teeth. Despite the differences between the bacterial communities of sound teeth and decayed teeth, the Venn diagram showed that the samples had 38 amplicons in common. Greater amplicon richness was observed in samples of decayed teeth (enamel: 20.5 ± 2.7; dentin: 20.1 ± 2.8) compared with the sound samples (12.0 ± 4.3) (p <0.05), indicating enhanced growth for specific groups of bacteria on decayed teeth. Although there is less bacterial diversity on sound than ECC-decayed teeth, the bacterial communities are very similar.

Cancer-Related Constituents of Strawberry Jam as Compared with Fresh Fruit

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Gema Flores

2016-01-01

Full Text Available The health awareness recently shown by consumers has led to a demand for health beneficial products. In particular, researchers are currently focusing their studies on the search for foods for cancer prevention activity. In the present work, we study comparatively the effect of two different processing methods on the contents of phenolic compounds (i.e., ellagic acid, myricetin, quercetin and kaempferol with antioxidant and antitumor properties in strawberry jams. In turn, the results obtained were compared with those of unprocessed fruit. Additionally carcinogenic heat-induced compounds formed by the two jam making methods were evaluated. Decreases of total ellagic acid from 138.4 µg/g to 86.5 µg/g were measured in jam as compared with the intact fruit. Even higher losses of up to 90% of total flavonols were found in strawberry after the jam-making process. A comparison between the two processing methods proved shorter heating periods (around 60 min even at temperatures as high as 100 °C enabled losses of antioxidant phenolics to be minimized. Carcinogenic heat-induced volatile compounds, mainly Maillard reaction products, were formed as a result of thermal treatment during jam processing. However, shorter heating periods also helped reduce the formation of these harmful compounds. These results are deeply discussed. From a practical standpoint, the processing conditions here proposed can be used by industry to obtain strawberry jam with higher content of antioxidant flavonoids and, at the same time, reduced amounts of carcinogenic compounds.

Shorter Ground Contact Time and Better Running Economy: Evidence From Female Kenyan Runners.

Science.gov (United States)

Mooses, Martin; Haile, Diresibachew W; Ojiambo, Robert; Sang, Meshack; Mooses, Kerli; Lane, Amy R; Hackney, Anthony C

2018-06-25

Mooses, M, Haile, DW, Ojiambo, R, Sang, M, Mooses, K, Lane, AR, and Hackney, AC. Shorter ground contact time and better running economy: evidence from female Kenyan runners. J Strength Cond Res XX(X): 000-000, 2018-Previously, it has been concluded that the improvement in running economy (RE) might be considered as a key to the continued improvement in performance when no further increase in V[Combining Dot Above]O2max is observed. To date, RE has been extensively studied among male East African distance runners. By contrast, there is a paucity of data on the RE of female East African runners. A total of 10 female Kenyan runners performed 3 × 1,600-m steady-state run trials on a flat outdoor clay track (400-m lap) at the intensities that corresponded to their everyday training intensities for easy, moderate, and fast running. Running economy together with gait characteristics was determined. Participants showed moderate to very good RE at the first (202 ± 26 ml·kg·km) and second (188 ± 12 ml·kg·km) run trials, respectively. Correlation analysis revealed significant relationship between ground contact time (GCT) and RE at the second run (r = 0.782; p = 0.022), which represented the intensity of anaerobic threshold. This study is the first to report the RE and gait characteristics of East African female athletes measured under everyday training settings. We provided the evidence that GCT is associated with the superior RE of the female Kenyan runners.

RNA-Based Amplicon Sequencing Reveals Microbiota Development during Ripening of Artisanal versus Industrial Lard d'Arnad.

Science.gov (United States)

Ferrocino, Ilario; Bellio, Alberto; Romano, Angelo; Macori, Guerrino; Rantsiou, Kalliopi; Decastelli, Lucia; Cocolin, Luca

2017-08-15

Valle d'Aosta Lard d'Arnad is a protected designation of origin (PDO) product produced from fat of the shoulder and back of heavy pigs. Its manufacturing process can be very diverse, especially regarding the maturation temperature and the NaCl concentration used for the brine; thereby, the main goal of this study was to investigate the impact of those parameters on the microbiota developed during curing and ripening. Three farms producing Lard d'Arnad were selected. Two plants, reflecting the industrial process characterized either by low maturation temperature (plant A [10% NaCl, 2°C]) or by using a low NaCl concentration (plant B [2.5% NaCl, 4°C]), were selected, while the third was characterized by an artisanal process (plant C [30% NaCl, 8°C]). Lard samples were obtained at time 0 and after 7, 15, 30, 60, and 90 days of maturation. From each plant, 3 independent lots were analyzed. The diversity of live microbiota was evaluated by using classical plate counts and amplicon target sequencing of small subunit (SSU) rRNA. The main taxa identified by sequencing were Acinetobacter johnsonii , Psychrobacter , Staphylococcus equorum , Staphylococcus sciuri , Pseudomonas fragi , Brochothrix , Halomonas , and Vibrio , and differences in their relative abundances distinguished samples from the individual plants. The composition of the microbiota was more similar among plants A and B, and it was characterized by the higher presence of taxa recognized as undesired bacteria in food-processing environments. Oligotype analysis of Halomonas and Acinetobacter revealed the presence of several characteristic oligotypes associated with A and B samples. IMPORTANCE Changes in the food production process can drastically affect the microbial community structure, with a possible impact on the final characteristics of the products. The industrial processes of Lard d'Arnad production are characterized by a reduction in the salt concentration in the brines to address a consumer demand

Conditional inactivation of TNFα-converting enzyme in chondrocytes results in an elongated growth plate and shorter long bones.

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Kenta Saito

Full Text Available TNFα-converting enzyme (TACE is a membrane-bound proteolytic enzyme with essential roles in the functional regulation of TNFα and epidermal growth factor receptor (EGFR ligands. Previous studies have demonstrated critical roles for TACE in vivo, including epidermal development, immune response, and pathological neoangiogenesis, among others. However, the potential contribution of TACE to skeletal development is still unclear. In the present study, we generated a Tace mutant mouse in which Tace is conditionally disrupted in chondrocytes under the control of the Col2a1 promoter. These mutant mice were fertile and viable but all exhibited long bones that were approximately 10% shorter compared to those of wild-type animals. Histological analyses revealed that Tace mutant mice exhibited a longer hypertrophic zone in the growth plate, and there were fewer osteoclasts at the chondro-osseous junction in the Tace mutant mice than in their wild-type littermates. Of note, we found an increase in osteoprotegerin transcripts and a reduction in Rankl and Mmp-13 transcripts in the TACE-deficient cartilage, indicating that dysregulation of these genes is causally related to the skeletal defects in the Tace mutant mice. Furthermore, we also found that phosphorylation of EGFR was significantly reduced in the cartilage tissue lacking TACE, and that suppression of EGFR signaling increases osteoprotegerin transcripts and reduces Rankl and Mmp-13 transcripts in primary chondrocytes. In accordance, chondrocyte-specific abrogation of Egfr in vivo resulted in skeletal defects nearly identical to those observed in the Tace mutant mice. Taken together, these data suggest that TACE-EGFR signaling in chondrocytes is involved in the turnover of the growth plate during postnatal development via the transcriptional regulation of osteoprotegerin, Rankl, and Mmp-13.

Comparing the Healthy Nose and Nasopharynx Microbiota Reveals Continuity As Well As Niche-Specificity

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Ilke De Boeck

2017-11-01

Full Text Available To improve our understanding of upper respiratory tract (URT diseases and the underlying microbial pathogenesis, a better characterization of the healthy URT microbiome is crucial. In this first large-scale study, we obtained more insight in the URT microbiome of healthy adults. Hereto, we collected paired nasal and nasopharyngeal swabs from 100 healthy participants in a citizen-science project. High-throughput 16S rRNA gene V4 amplicon sequencing was performed and samples were processed using the Divisive Amplicon Denoising Algorithm 2 (DADA2 algorithm. This allowed us to identify the bacterial richness and diversity of the samples in terms of amplicon sequence variants (ASVs, with special attention to intragenus variation. We found both niches to have a low overall species richness and uneven distribution. Moreover, based on hierarchical clustering, nasopharyngeal samples could be grouped into some bacterial community types at genus level, of which four were supported to some extent by prediction strength evaluation: one intermixed type with a higher bacterial diversity where Staphylococcus, Corynebacterium, and Dolosigranulum appeared main bacterial members in different relative abundances, and three types dominated by either Moraxella, Streptococcus, or Fusobacterium. Some of these bacterial community types such as Streptococcus and Fusobacterium were nasopharynx-specific and never occurred in the nose. No clear association between the nasopharyngeal bacterial profiles at genus level and the variables age, gender, blood type, season of sampling, or common respiratory allergies was found in this study population, except for smoking showing a positive association with Corynebacterium and Staphylococcus. Based on the fine-scale resolution of the ASVs, both known commensal and potential pathogenic bacteria were found within several genera – particularly in Streptococcus and Moraxella – in our healthy study population. Of interest, the

Comparative bacterial community analysis in relatively pristine and anthropogenically influenced mangrove ecosystems on the Red Sea.

Science.gov (United States)

Ullah, Riaz; Yasir, Muhammad; Khan, Imran; Bibi, Fehmida; Sohrab, Sayed Sartaj; Al-Ansari, Ahmed; Al-Abbasi, Fahad; Al-Sofyani, Abdulmohsin A; Daur, Ihsanullah; Lee, Seon-Woo; Azhar, Esam I

2017-08-01

Mangrove habitats are ecologically important ecosystems that are under severe pressure worldwide because of environmental changes and human activities. In this study, 16S rRNA gene amplicon deep-sequencing was used to compare bacterial communities in Red Sea mangrove ecosystems at anthropogenically influenced coastal sites with those at a relatively pristine island site. In total, 32 phyla were identified from the mangrove rhizospheres, with Proteobacteria predominating at each of the studied sites; however, the relative abundance was significantly decreased at the coastal sites (Mastorah, MG-MS; Ar-Rayis, MG-AR) compared with the pristine island site near Dhahban (MG-DBI). The phyla Actinobacteria, Firmicutes, Acidobacteria, Chloroflexi, Spirochetes, and Planctomycetes were present at a relative abundance of >1% at the MG-MS and MG-AR sites, but their concentration was <1% at the MG-DBI site. A total of 1659 operational taxonomic units (OTUs) were identified at the species level, and approximately 945 OTUs were shared across the different sampling sites. Multivariate principal coordinate data analysis separated the MG-DBI site from the MG-AR and MG-MS cluster. Specific bacterial taxa were enriched at each location, and in particular, the genera Pseudoalteromonas and Cobetia were predominantly identified in the MG-DBI site compared with the anthropogenically influenced coastal sites.

In Vitro Comparison of Holmium Lasers: Evidence for Shorter Fragmentation Time and Decreased Retropulsion Using a Modern Variable-pulse Laser.

Science.gov (United States)

Bell, John Roger; Penniston, Kristina L; Nakada, Stephen Y

2017-09-01

To compare the performance of variable- and fixed-pulse lasers on stone phantoms in vitro. Seven-millimeter stone phantoms were made to simulate calcium oxalate monohydrate stones using BegoStone plus. The in vitro setting was created with a clear polyvinyl chloride tube. For each trial, a stone phantom was placed at the open end of the tubing. The Cook Rhapsody H-30 variable-pulse laser was tested on both long- and short-pulse settings and was compared to the Dornier H-20 fixed-pulse laser; 5 trials were conducted for each trial arm. Fragmentation was accomplished with the use of a flexible ureteroscope and a 273-micron holmium laser fiber using settings of 1 J × 12 Hz. The treatment time (in minute) for complete fragmentation was recorded as was the total retropulsion distance (in centimeter) during treatment. Laser fibers were standardized for all repetitions. The treatment time was significantly shorter with the H-30 vs the H-20 laser (14.3 ± 2.5 vs 33.1 ± 8.9 minutes, P = .008). There was no difference between the treatment times using the long vs short pulse widths of the H-30 laser (14.4 ± 3.4 vs 14.3 ± 1.7 minutes, P = .93). Retropulsion differed by laser type and pulse width, H-30 long pulse (15.8 ± 5.7 cm), H-30 short pulse (54.8 ± 7.1 cm), and H-20 (33.2 ± 12.5 cm) (P laser fragmented stone phantoms in half the time of the H-20 laser regardless of the pulse width. Retropulsion effects differed between the lasers, with the H-30 causing the least retropulsion. Longer pulse widths result in less stone retropulsion. Copyright © 2017 Elsevier Inc. All rights reserved.

Comparative study of total shoulder arthroplasty versus total shoulder surface replacement for glenohumeral osteoarthritis with minimum 2-year follow-up

NARCIS (Netherlands)

Kooistra, B.W.; Willems, W.J.H.; Lemmens, E.; Hartel, B.P.; Bekerom, M.P. van den; Deurzen, D.F.P. van

2017-01-01

BACKGROUND: Compared with total shoulder arthroplasty (TSA), total shoulder surface replacement (TSSR) may offer the advantage of preservation of bone stock and shorter surgical time, possibly at the expense of glenoid component positioning and increasing lateral glenohumeral offset. We hypothesized

Comparing the demands of destination entry using Google Glass and the Samsung Galaxy S4 during simulated driving.

Science.gov (United States)

Beckers, Niek; Schreiner, Sam; Bertrand, Pierre; Mehler, Bruce; Reimer, Bryan

2017-01-01

The relative impact of using a Google Glass based voice interface to enter a destination address compared to voice and touch-entry methods using a handheld Samsung Galaxy S4 smartphone was assessed in a driving simulator. Voice entry (Google Glass and Samsung) had lower subjective workload ratings, lower standard deviation of lateral lane position, shorter task durations, faster remote Detection Response Task (DRT) reaction times, lower DRT miss rates, and resulted in less time glancing off-road than the primary visual-manual interaction with the Samsung Touch interface. Comparing voice entry methods, using Google Glass took less time, while glance metrics and reaction time to DRT events responded to were similar. In contrast, DRT miss rate was higher for Google Glass, suggesting that drivers may be under increased distraction levels but for a shorter period of time; whether one or the other equates to an overall safer driving experience is an open question. Copyright © 2016 Elsevier Ltd. All rights reserved.

Diagnostic time in digital pathology: A comparative study on 400 cases

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Aleksandar Vodovnik

2016-01-01

Full Text Available Background: Numerous validation studies in digital pathology confirmed its value as a diagnostic tool. However, a longer time to diagnosis than traditional microscopy has been seen as a significant barrier to the routine use of digital pathology. As a part of our validation study, we compared a digital and microscopic diagnostic time in the routine diagnostic setting. Materials and Methods: One senior staff pathologist reported 400 consecutive cases in histology, nongynecological, and fine needle aspiration cytology (20 sessions, 20 cases/session, over 4 weeks. Complex, difficult, and rare cases were excluded from the study to reduce the bias. A primary diagnosis was digital, followed by traditional microscopy, 6 months later, with only request forms available for both. Microscopic slides were scanned at ×20, digital images accessed through the fully integrated laboratory information management system (LIMS and viewed in the image viewer on double 23” displays. A median broadband speed was 299 Mbps. A diagnostic time was measured from the point slides were made available to the point diagnosis was made or additional investigations were deemed necessary, recorded independently in minutes/session and compared. Results: A digital diagnostic time was 1841 and microscopic 1956 min; digital being shorter than microscopic in 13 sessions. Four sessions with shorter microscopic diagnostic time included more cases requiring extensive use of magnifications over ×20. Diagnostic time was similar in three sessions. Conclusions: A diagnostic time in digital pathology can be shorter than traditional microscopy in the routine diagnostic setting, with adequate and stable network speeds, fully integrated LIMS and double displays as default parameters. This also related to better ergonomics, larger viewing field, and absence of physical slide handling, with effects on both diagnostic and nondiagnostic time. Differences with previous studies included a design

Elevated CD147 expression is associated with shorter overall survival in non-small cell lung cancer.

Science.gov (United States)

Zhang, Xiaojun; Tian, Tian; Zhang, Xiaofeng; Liu, Changting; Fang, Xiangqun

2017-06-06

A number of studies have reported on the prognostic role of CD147 expression in non-small cell lung cancer (NSCLC); however, the results remain controversial. This study aims to investigate the impact of CD147 on the prognosis of NSCLC by means of a meta-analysis. A literature search was performed for relevant studies published before October 29, 2016. The hazard ratios (HRs), odds ratios (ORs), and 95% confidence intervals (CIs) were calculated as effective measures. Sensitivity analysis and publication bias examination were also conducted. Ten eligible studies with a total of 1605 patients were included in this meta-analysis. CD147 overexpression was correlated with poor overall survival (OS) (HR=1.59, 95% CI=1.32-1.91, pCD147 expression was associated with the presence of lymph node metastasis (OR=2.31, 95% CI=1.74-3.07, pCD147 and sex, age, differentiation, or histology was found. No evidence of significant publication bias was identified. This meta-analysis revealed that overexpression of CD147 was associated with shorter OS, the presence of lymph node metastasis and advanced TNM stage in NSCLC. Therefore, CD147 could serve as a potential prognostic marker for NSCLC.

Selective binding of carotenoids with a shorter conjugated chain to the LH2 antenna complex and those with a longer conjugated chain to the reaction center from Rubrivivax gelatinosus.

Science.gov (United States)

Kakitani, Yoshinori; Fujii, Ritsuko; Hayakawa, Yoshihiro; Kurahashi, Masahiro; Koyama, Yasushi; Harada, Jiro; Shimada, Keizo

2007-06-19

Rubrivivax gelatinosus having both the spheroidene and spirilloxanthin biosynthetic pathways produces carotenoids (Cars) with a variety of conjugated chains, which consist of different numbers of conjugated double bonds (n), including the C=C (m) and C=O (o) bonds. When grown under anaerobic conditions, the wild type produces Cars for which n = m = 9-13, whereas under semiaerobic conditions, it additionally produces Cars for which n = m + o = 10 + 1, 13 + 1, and 13 + 2. On the other hand, a mutant, in which the latter pathway is genetically blocked, produces only Cars for which n = 9 and 10 under anaerobic conditions and n = 9, 10, and 10 + 1 under semianaerobic conditions. Those Cars that were extracted from the LH2 complex (LH2) and the reaction center (RC), isolated from the wild-type and the mutant Rvi. gelatinosus, were analyzed by HPLC, and their structures were determined by mass spectrometry and 1H NMR spectroscopy. The selective binding of Cars to those pigment-protein complexes has been characterized as follows. (1) Cars with a shorter conjugated chain are selectively bound to LH2 whereas Cars with a longer conjugated chain to the RC. (2) Shorter chain Cars with a hydroxyl group are bound to LH2 almost exclusively. This rule holds either in the absence or in the presence of the keto group. The natural selection of shorter chain Cars by LH2 and longer chain Cars by the RC is discussed, on the basis of the results now available, in relation to the light-harvesting and photoprotective functions of Cars.

A newly constructed primer pair for the PCR amplification, cloning and sequencing of the flagellin (flaA) gene from isolatesof urease-negative Campylobacter lari.

Science.gov (United States)

Sekizuka, Tsuyoshi; Yokoi, Taeko; Murayama, Ohoshi; Millar, B Cherie; Moore, Johne; Matsuda, Motoo

2005-08-01

A newly constructed primer pair (lari-Af/lari-Ar) designed to generate a product of the flagellin (flaA) gene for urease-negative Campylobacter lari produced a PCR amplicon of about 1700 bp for 16 isolates from 7 seagulls, 5 humans, 3 food animals and one mussel in Japan and Northern Ireland. Nucleotide sequencing and alignments of the flaA amplicons from these isolates demonstrated that the deduced amino acid sequences of the possible open reading frame were 564-572 amino acid residues in length with calculated molecular weights of 58,804 to 59,463. The deduced amino acid sequence similarity analysis strongly suggested that the ORF of the flaA from the 16 isolates showed 70-75% sequence similarities to those of Campylobacter jejuni isolates. The approximate Mr of the flagellin purified from some of the isolates of urease-negative C. lari was estimated to range from 59.6 to 61.8 kDa. Thus, flagellin from the isolates of urease-negative C. lari was shown for the first time to have a molecular size similar to those of C. jejuni and Campylobacter coli isolates, but to be different from the shorter flaA and smaller flagellin of urease-positive thermophilic Campylobacter (UPTC) isolates. Flagellins from C. lari spp., consisting of the two representative taxa of urease-negative C. lari and UPTC, thus show genotypic and phenotypic diversity.

MO-E-BRD-02: Accelerated Partial Breast Irradiation in Brachytherapy: Is Shorter Better?

International Nuclear Information System (INIS)

Todor, D.

2015-01-01

Is Non-invasive Image-Guided Breast Brachytherapy Good? – Jess Hiatt, MS Non-invasive Image-Guided Breast Brachytherapy (NIBB) is an emerging therapy for breast boost treatments as well as Accelerated Partial Breast Irradiation (APBI) using HDR surface breast brachytherapy. NIBB allows for smaller treatment volumes while maintaining optimal target coverage. Considering the real-time image-guidance and immobilization provided by the NIBB modality, minimal margins around the target tissue are necessary. Accelerated Partial Breast Irradiation in brachytherapy: is shorter better? - Dorin Todor, PhD VCU A review of balloon and strut devices will be provided together with the origins of APBI: the interstitial multi-catheter implant. A dosimetric and radiobiological perspective will help point out the evolution in breast brachytherapy, both in terms of devices and the protocols/clinical trials under which these devices are used. Improvements in imaging, delivery modalities and convenience are among the factors driving the ultrashort fractionation schedules but our understanding of both local control and toxicities associated with various treatments is lagging. A comparison between various schedules, from a radiobiological perspective, will be given together with a critical analysis of the issues. to review and understand the evolution and development of APBI using brachytherapy methods to understand the basis and limitations of radio-biological ‘equivalence’ between fractionation schedules to review commonly used and proposed fractionation schedules Intra-operative breast brachytherapy: Is one stop shopping best?- Bruce Libby, PhD. University of Virginia A review of intraoperative breast brachytherapy will be presented, including the Targit-A and other trials that have used electronic brachytherapy. More modern approaches, in which the lumpectomy procedure is integrated into an APBI workflow, will also be discussed. Learning Objectives: To review past and current

MO-E-BRD-02: Accelerated Partial Breast Irradiation in Brachytherapy: Is Shorter Better?

Energy Technology Data Exchange (ETDEWEB)

Todor, D. [Virginia Commonwealth University (United States)

2015-06-15

Is Non-invasive Image-Guided Breast Brachytherapy Good? – Jess Hiatt, MS Non-invasive Image-Guided Breast Brachytherapy (NIBB) is an emerging therapy for breast boost treatments as well as Accelerated Partial Breast Irradiation (APBI) using HDR surface breast brachytherapy. NIBB allows for smaller treatment volumes while maintaining optimal target coverage. Considering the real-time image-guidance and immobilization provided by the NIBB modality, minimal margins around the target tissue are necessary. Accelerated Partial Breast Irradiation in brachytherapy: is shorter better? - Dorin Todor, PhD VCU A review of balloon and strut devices will be provided together with the origins of APBI: the interstitial multi-catheter implant. A dosimetric and radiobiological perspective will help point out the evolution in breast brachytherapy, both in terms of devices and the protocols/clinical trials under which these devices are used. Improvements in imaging, delivery modalities and convenience are among the factors driving the ultrashort fractionation schedules but our understanding of both local control and toxicities associated with various treatments is lagging. A comparison between various schedules, from a radiobiological perspective, will be given together with a critical analysis of the issues. to review and understand the evolution and development of APBI using brachytherapy methods to understand the basis and limitations of radio-biological ‘equivalence’ between fractionation schedules to review commonly used and proposed fractionation schedules Intra-operative breast brachytherapy: Is one stop shopping best?- Bruce Libby, PhD. University of Virginia A review of intraoperative breast brachytherapy will be presented, including the Targit-A and other trials that have used electronic brachytherapy. More modern approaches, in which the lumpectomy procedure is integrated into an APBI workflow, will also be discussed. Learning Objectives: To review past and current

Always look on both sides: phylogenetic information conveyed by simple sequence repeat allele sequences.

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Stéphanie Barthe

Full Text Available Simple sequence repeat (SSR markers are widely used tools for inferences about genetic diversity, phylogeography and spatial genetic structure. Their applications assume that variation among alleles is essentially caused by an expansion or contraction of the number of repeats and that, accessorily, mutations in the target sequences follow the stepwise mutation model (SMM. Generally speaking, PCR amplicon sizes are used as direct indicators of the number of SSR repeats composing an allele with the data analysis either ignoring the extent of allele size differences or assuming that there is a direct correlation between differences in amplicon size and evolutionary distance. However, without precisely knowing the kind and distribution of polymorphism within an allele (SSR and the associated flanking region (FR sequences, it is hard to say what kind of evolutionary message is conveyed by such a synthetic descriptor of polymorphism as DNA amplicon size. In this study, we sequenced several SSR alleles in multiple populations of three divergent tree genera and disentangled the types of polymorphisms contained in each portion of the DNA amplicon containing an SSR. The patterns of diversity provided by amplicon size variation, SSR variation itself, insertions/deletions (indels, and single nucleotide polymorphisms (SNPs observed in the FRs were compared. Amplicon size variation largely reflected SSR repeat number. The amount of variation was as large in FRs as in the SSR itself. The former contributed significantly to the phylogenetic information and sometimes was the main source of differentiation among individuals and populations contained by FR and SSR regions of SSR markers. The presence of mutations occurring at different rates within a marker's sequence offers the opportunity to analyse evolutionary events occurring on various timescales, but at the same time calls for caution in the interpretation of SSR marker data when the distribution of within

Bacterial diversity of the Colombian fermented milk "Suero Costeño" assessed by culturing and high-throughput sequencing and DGGE analysis of 16S rRNA gene amplicons.

Science.gov (United States)

Motato, Karina Edith; Milani, Christian; Ventura, Marco; Valencia, Francia Elena; Ruas-Madiedo, Patricia; Delgado, Susana

2017-12-01

"Suero Costeño" (SC) is a traditional soured cream elaborated from raw milk in the Northern-Caribbean coast of Colombia. The natural microbiota that characterizes this popular Colombian fermented milk is unknown, although several culturing studies have previously been attempted. In this work, the microbiota associated with SC from three manufacturers in two regions, "Planeta Rica" (Córdoba) and "Caucasia" (Antioquia), was analysed by means of culturing methods in combination with high-throughput sequencing and DGGE analysis of 16S rRNA gene amplicons. The bacterial ecosystem of SC samples was revealed to be composed of lactic acid bacteria belonging to the Streptococcaceae and Lactobacillaceae families; the proportions and genera varying among manufacturers and region of elaboration. Members of the Lactobacillus acidophilus group, Lactocococcus lactis, Streptococcus infantarius and Streptococcus salivarius characterized this artisanal product. In comparison with culturing, the use of molecular in deep culture-independent techniques provides a more realistic picture of the overall bacterial communities residing in SC. Besides the descriptive purpose, these approaches will facilitate a rational strategy to follow (culture media and growing conditions) for the isolation of indigenous strains that allow standardization in the manufacture of SC. Copyright © 2017 Elsevier Ltd. All rights reserved.

Gain of chromosome arm 1q in atypical meningioma correlates with shorter progression-free survival.

LENUS (Irish Health Repository)

2012-02-01

Aims: Atypical (WHO grade II) meningiomas have moderately high recurrence rates; even for completely resected tumours, approximately one-third will recur. Post-operative radiotherapy (RT) may aid local control and improve survival, but carries the risk of side effects. More accurate prediction of recurrence risk is therefore needed for patients with atypical meningioma. Previously, we used high-resolution array CGH to identify genetic variations in 47 primary atypical meningiomas and found that approximately 60% of tumors show gain of 1q at 1q25.1 and 1q25.3 to 1q32.1 and that 1q gain appeared to correlate with shorter progression-free survival. This study aimed to validate and extend these findings in an independent sample. Methods: 86 completely resected atypical meningiomas (with 25 recurrences) from two neurosurgical centres in Ireland were identified and clinical follow up was obtained. Utilizing a dual-colour interphase FISH assay, 1q gain was assessed using BAC probes directed against 1q25.1 and 1q32.1. Results: The results confirm the high prevalence of 1q gain at these loci in atypical meningiomas. We further show that gain at 1q32.1 and age each correlate with progression-free survival in patients who have undergone complete surgical resection of atypical meningiomas. Conclusions: These independent findings suggest that assessment of 1q copy number status can add clinically useful information for the management of patients with atypical meningiomas.

Comparative thermometric coagulation studies of plasmas from normal outbred Swiss Webster mice and persons.

Science.gov (United States)

Tsang, V C; Wyatt, C R; Damian, R T

1979-06-01

The functional capabilities of a thermometric clot-timer have been demonstrated in a comparative study of human and mouse plasma coagulation. The influence of some variables on coagulation times of mouse and human plasmas were examined in activated partial thromboplastin time, one-stage prothrombin time, and Russell's viper venom time assays. Mouse plasma coagulation times were generally shorter and more reproducible than those of human plasma. Optimal assay conditions are also described.

New fat suppression RF pulse with shorter duration

International Nuclear Information System (INIS)

Yamaguchi, Kojiro; Ukai, Hiroyuki

2010-01-01

The fat suppression radio frequency pulse currently employed for MRI, which selectively saturates the frequency of the fat, has the narrow-band frequency characteristics. Therefore, the application duration for the pulse employed tends to be prolonged. In the present study, we designed a new fat suppression radiofrequency (RF) pulse using the Laguerre function in order to shorten the duration for fat suppression RF pulse and conducted an evaluation with the clinical equipment. The length of the RF pulse that we created allowed to reduce the duration by 47.3% compared with that employed for the clinical equipment. In addition, in the MR imaging evaluation, the new pulse was confirmed to have the fat suppression effect equivalent to that employed for the clinical equipment. (author)

Comparative Short-Term Clinical Outcomes of Mediastinum Tumor Excision Performed by Conventional VATS and Single-Port VATS: Is It Worthwhile?

Science.gov (United States)

Wu, Ching-Feng; Gonzalez-Rivas, Diego; Wen, Chih-Tsung; Liu, Yun-Hen; Wu, Yi-Cheng; Chao, Yin-Kai; Hsieh, Ming-Ju; Wu, Ching-Yang; Chen, Wei-Hsun

2015-11-01

Single-port video-assisted thoracoscopic surgery (VATS) has been widely applied recently. However, there are still only few reports describing its use in mediastinum tumor resection. We present the technique of single-port video-assisted thoracoscopic mediastinum tumor resection and compare it with conventional VATS with regard to short-term outcome.We retrospectively enrolled 105 patients who received mediastinum surgery in Chang Gung Memorial Hospital. Sixteen patients received sternotomy or thoracotomy, 29 patients received single-port VATS, and 60 patients received conventional VATS (3 ports). The operative time, blood loss, postoperation day 1 pain score, discharge day pain score, and postoperative hospital stay were compared. In order to establish a well balanced cohort study, we also use propensity scores match (1:1) to compare the short-term clinical outcome in 2 groups.No operative deaths occurred in this study. Single-port VATS was associated with shorter operative time, lower postoperation day 1 pain score, and shorter postoperation hospital stay in our cohort study (P = 0.001, short-term outcome not inferior to conventional VATS in our cohort study. The long-term oncology outcome may require time and more enrolled patients to be further evaluated.

Areca nut is associated with younger age of diagnosis, poor chemoradiotherapy response, and shorter overall survival in esophageal squamous cell carcinoma.

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Chang-Han Chen

Full Text Available Areca nut chewing is carcinogenic to humans. However, little is known about the impact of areca nut chewing on esophageal squamous cell carcinoma (ESCC.We retrospectively reviewed 286 ESCC patients who received surgery or preoperative chemoradiotherapy followed by surgery at our institution. Background characteristics including areca nut chewing history were analyzed. The 4-nitroquinoline 1-oxide (4-NQO-induced murine ESCC model was used to test the impact of arecoline, a main constituent of areca nut, on ESCC.Compared to patients without areca nut chewing history, patients with areca nut chewing history had overall a younger age of onset (Mean age: 56.75 versus 52.68 yrs, P<0.001 and significantly worse overall survival than those without areca nut chewing history (P = 0.026. Among patients who received surgery, the overall survival rates were not significantly different between those with or without areca nut chewing history. Among patients who received preoperative chemoradiotherapy followed by surgery, those with areca nut chewing history had a significantly lower pathologic complete response rate (P = 0.002 and lower overall survival rate (P = 0.002 than those without. In the murine ESCC model, the incidence of esophageal invasive squamous cell carcinoma was 40% in mice exposed to concomitant 4-NQO and arecoline treatment for 8 weeks and 6% in mice exposed to 4-NQO only for 8 weeks (P = 0.037.Our results indicate that areca nut chewing history is significantly associated with younger age of onset, poor response to chemoradiotherapy, and shorter overall survival in ESCC patients. Arecoline, a main constituent of areca nut, accelerates esophageal tumorigenesis in the 4-NQO-induced murine ESCC model.

Human capital gains associated with robotic assisted laparoscopic pyeloplasty in children compared to open pyeloplasty.

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Behan, James W; Kim, Steve S; Dorey, Frederick; De Filippo, Roger E; Chang, Andy Y; Hardy, Brian E; Koh, Chester J

2011-10-01

Robotic assisted laparoscopic pyeloplasty is an emerging, minimally invasive alternative to open pyeloplasty in children for ureteropelvic junction obstruction. The procedure is associated with smaller incisions and shorter hospital stays. To our knowledge previous outcome analyses have not included human capital calculations, especially regarding loss of parental workdays. We compared perioperative factors in patients who underwent robotic assisted laparoscopic and open pyeloplasty at a single institution, especially in regard to human capital changes, in an institutional cost analysis. A total of 44 patients 2 years old or older from a single institution underwent robotic assisted (37) or open (7) pyeloplasty from 2008 to 2010. We retrospectively reviewed the charts to collect demographic and perioperative data. The human capital approach was used to calculate parental productivity losses. Patients who underwent robotic assisted laparoscopic pyeloplasty had a significantly shorter average hospital length of stay (1.6 vs 2.8 days, p human capital gains, eg decreased lost parental wages, and lower hospitalization expenses. Future comparative outcome analyses in children should include financial factors such as human capital loss, which can be especially important for families with young children. Copyright © 2011 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

Shorter exposures to harder X-rays trigger early apoptotic events in Xenopus laevis embryos.

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JiaJia Dong

Full Text Available BACKGROUND: A long-standing conventional view of radiation-induced apoptosis is that increased exposure results in augmented apoptosis in a biological system, with a threshold below which radiation doses do not cause any significant increase in cell death. The consequences of this belief impact the extent to which malignant diseases and non-malignant conditions are therapeutically treated and how radiation is used in combination with other therapies. Our research challenges the current dogma of dose-dependent induction of apoptosis and establishes a new parallel paradigm to the photoelectric effect in biological systems. METHODOLOGY/PRINCIPAL FINDINGS: We explored how the energy of individual X-ray photons and exposure time, both factors that determine the total dose, influence the occurrence of cell death in early Xenopus embryo. Three different experimental scenarios were analyzed and morphological and biochemical hallmarks of apoptosis were evaluated. Initially, we examined cell death events in embryos exposed to increasing incident energies when the exposure time was preset. Then, we evaluated the embryo's response when the exposure time was augmented while the energy value remained constant. Lastly, we studied the incidence of apoptosis in embryos exposed to an equal total dose of radiation that resulted from increasing the incoming energy while lowering the exposure time. CONCLUSIONS/SIGNIFICANCE: Overall, our data establish that the energy of the incident photon is a major contributor to the outcome of the biological system. In particular, for embryos exposed under identical conditions and delivered the same absorbed dose of radiation, the response is significantly increased when shorter bursts of more energetic photons are used. These results suggest that biological organisms display properties similar to the photoelectric effect in physical systems and provide new insights into how radiation-mediated apoptosis should be understood and

Mini vs standard percutaneous nephrolithotomy for renal stones: a comparative study.

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ElSheemy, Mohammed S; Elmarakbi, Akram A; Hytham, Mohammed; Ibrahim, Hamdy; Khadgi, Sanjay; Al-Kandari, Ahmed M

2018-03-16

To compare the outcome of mini-percutaneous nephrolithotomy (Mini-PNL) versus standard-PNL for renal stones. Retrospective study was performed between March 2010 and May 2013 for patients treated by Mini-PNL or standard-PNL through 18 and 30 Fr tracts, respectively, using pneumatic lithotripsy. Semirigid ureteroscope (8.5/11.5 Fr) was used for Mini-PNL and 24 Fr nephroscope for standard-PNL. Both groups were compared in stone free rate(SFR), complications and operative time using Student-t, Mann-Whitney, Chi square or Fisher's exact tests as appropriate in addition to logistic regression analysis. P PNL (378) and standard-PNL (151) were nearly comparable in patients and stones criteria including stone burden (3.77 ± 2.21 vs 3.77 ± 2.43 cm 2 ; respectively). There was no significant difference in number of tracts or supracostal puncture. Mini-PNL had longer operative time (68.6 ± 29.09 vs 60.49 ± 11.38 min; p = 0.434), significantly shorter hospital stay (2.43 ± 1.46 vs 4.29 ± 1.28 days) and significantly higher rate of tubeless PNL (75.1 vs 4.6%). Complications were significantly higher in standard-PNL (7.9 vs 20.5%; p PNL (89.9 vs 96%; p = 0.022). This significant difference was found with multiple stones and large stone burden (> 2 cm 2 ), but the SFR was comparable between both groups with single stone or stone burden ≤ 2 cm. Logistic regression analysis confirmed significantly higher complications and SFR with standard-PNL but with significantly shorter operative time. Mini-PNL has significantly lower SFR when compared to standard-PNL (but clinically comparable) with markedly reduced complications and hospital stay. Most of cases can be performed tubeless. The significant difference in SFR was found with multiple stones or large stone burden (> 2 cm 2 ), but not with single stones or stone burden ≤ 2 cm 2 .

Microfluidic PCR Amplification and MiSeq Amplicon Sequencing Techniques for High-Throughput Detection and Genotyping of Human Pathogenic RNA Viruses in Human Feces, Sewage, and Oysters

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Mamoru Oshiki

2018-04-01

Full Text Available Detection and genotyping of pathogenic RNA viruses in human and environmental samples are useful for monitoring the circulation and prevalence of these pathogens, whereas a conventional PCR assay followed by Sanger sequencing is time-consuming and laborious. The present study aimed to develop a high-throughput detection-and-genotyping tool for 11 human RNA viruses [Aichi virus; astrovirus; enterovirus; norovirus genogroup I (GI, GII, and GIV; hepatitis A virus; hepatitis E virus; rotavirus; sapovirus; and human parechovirus] using a microfluidic device and next-generation sequencer. Microfluidic nested PCR was carried out on a 48.48 Access Array chip, and the amplicons were recovered and used for MiSeq sequencing (Illumina, Tokyo, Japan; genotyping was conducted by homology searching and phylogenetic analysis of the obtained sequence reads. The detection limit of the 11 tested viruses ranged from 100 to 103 copies/μL in cDNA sample, corresponding to 101–104 copies/mL-sewage, 105–108 copies/g-human feces, and 102–105 copies/g-digestive tissues of oyster. The developed assay was successfully applied for simultaneous detection and genotyping of RNA viruses to samples of human feces, sewage, and artificially contaminated oysters. Microfluidic nested PCR followed by MiSeq sequencing enables efficient tracking of the fate of multiple RNA viruses in various environments, which is essential for a better understanding of the circulation of human pathogenic RNA viruses in the human population.

The prosurvival activity of ascites against TRAIL is associated with a shorter disease-free interval in patients with ovarian cancer

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Lane Denis

2010-01-01

associated with shorter disease-free interval. Conclusions The prosurvival activity of ascites against TRAIL is associated with shorter disease-free interval, which may be explained, at least in part, by ascites-induced cisplatin/paclitaxel resistance. Our findings suggest that ascites may contain prosurvival factors that protect against TRAIL and chemotherapy and consequently affect disease progression.

Time to pediatric epilepsy surgery is longer and developmental outcomes lower for government compared with private insurance.

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Hauptman, Jason S; Dadour, Andrew; Oh, Taemin; Baca, Christine B; Vickrey, Barbara G; Vassar, Stefanie; Sankar, Raman; Salamon, Noriko; Vinters, Harry V; Mathern, Gary W

2013-07-01

It is unclear if socioeconomic factors like type of insurance influence time to referral and developmental outcomes for pediatric patients undergoing epilepsy surgery. This study determined whether private compared with state government insurance was associated with shorter intervals of seizure onset to surgery and better developmental quotients for pediatric patients undergoing epilepsy surgery. A consecutive cohort (n = 420) of pediatric patients undergoing epilepsy surgery were retrospectively categorized into those with Medicaid (California Children's Services; n = 91) or private (Preferred Provider Organization, Health Maintenance Organization, Indemnity; n = 329) insurance. Intervals from seizure onset to referral and surgery and Vineland developmental assessments were compared by insurance type with the use of log-rank tests. Compared with private insurance, children with Medicaid had longer intervals from seizure onset to referral for evaluation (log-rank test, P = .034), and from seizure onset to surgery (P = .017). In a subset (25%) that had Vineland assessments, children with Medicaid compared with private insurance had lower Vineland scores presurgery (P = .042) and postsurgery (P = .003). Type of insurance was not associated with seizure severity, types of operations, etiology, postsurgical seizure-free outcomes, and complication rate. Compared with Medicaid, children with private insurance had shorter intervals from seizure onset to referral and to epilepsy surgery, and this was associated with lower Vineland scores before surgery. These findings may reflect delayed access for uninsured children who eventually obtained state insurance. Reasons for the delay and whether longer intervals before epilepsy surgery affect long-term cognitive and developmental outcomes warrant further prospective investigations.

A comparative study of working memory: immediate serial spatial recall in baboons (Papio papio) and humans.

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Fagot, Joël; De Lillo, Carlo

2011-12-01

Two experiments assessed if non-human primates can be meaningfully compared to humans in a non-verbal test of serial recall. A procedure was used that was derived from variations of the Corsi test, designed to test the effects of sequence structure and movement path length in humans. Two baboons were tested in Experiment 1. The monkeys showed several attributes of human serial recall. These included an easier recall of sequences with a shorter number of items and of sequences characterized by a shorter path length when the number of items was kept constant. However, the accuracy and speed of processing did not indicate that the monkeys were able to benefit from the spatiotemporal structure of sequences. Humans tested in Experiment 2 showed a quantitatively longer memory span, and, in contrast with monkeys, benefitted from sequence structure. The results are discussed in relation to differences in how human and non-human primates segment complex visual patterns. Copyright © 2011 Elsevier Ltd. All rights reserved.

Cleavage of SNAP25 and its shorter versions by the protease domain of serotype A botulinum neurotoxin.

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Rahman M Mizanur

Full Text Available Various substrates, catalysts, and assay methods are currently used to screen inhibitors for their effect on the proteolytic activity of botulinum neurotoxin. As a result, significant variation exists in the reported results. Recently, we found that one source of variation was the use of various catalysts, and have therefore evaluated its three forms. In this paper, we characterize three substrates under near uniform reaction conditions using the most active catalytic form of the toxin. Bovine serum albumin at varying optimum concentrations stimulated enzymatic activity with all three substrates. Sodium chloride had a stimulating effect on the full length synaptosomal-associated protein of 25 kDa (SNAP25 and its 66-mer substrates but had an inhibitory effect on the 17-mer substrate. We found that under optimum conditions, full length SNAP25 was a better substrate than its shorter 66-mer or 17-mer forms both in terms of kcat, Km, and catalytic efficiency kcat/Km. Assay times greater than 15 min introduced large variations and significantly reduced the catalytic efficiency. In addition to characterizing the three substrates, our results identify potential sources of variations in previous published results, and underscore the importance of using well-defined reaction components and assay conditions.

Assessment of DNA degradation induced by thermal and UV radiation processing: implications for quantification of genetically modified organisms.

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Ballari, Rajashekhar V; Martin, Asha

2013-12-01

DNA quality is an important parameter for the detection and quantification of genetically modified organisms (GMO's) using the polymerase chain reaction (PCR). Food processing leads to degradation of DNA, which may impair GMO detection and quantification. This study evaluated the effect of various processing treatments such as heating, baking, microwaving, autoclaving and ultraviolet (UV) irradiation on the relative transgenic content of MON 810 maize using pRSETMON-02, a dual target plasmid as a model system. Amongst all the processing treatments examined, autoclaving and UV irradiation resulted in the least recovery of the transgenic (CaMV 35S promoter) and taxon-specific (zein) target DNA sequences. Although a profound impact on DNA degradation was seen during the processing, DNA could still be reliably quantified by Real-time PCR. The measured mean DNA copy number ratios of the processed samples were in agreement with the expected values. Our study confirms the premise that the final analytical value assigned to a particular sample is independent of the degree of DNA degradation since the transgenic and the taxon-specific target sequences possessing approximately similar lengths degrade in parallel. The results of our study demonstrate that food processing does not alter the relative quantification of the transgenic content provided the quantitative assays target shorter amplicons and the difference in the amplicon size between the transgenic and taxon-specific genes is minimal. Copyright © 2013 Elsevier Ltd. All rights reserved.

Evaluation on the effects of ageing factor, sampling and preservation methods on Asiatic black bear (Ursus thibetanus noninvasive DNA amplification

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Chih-Chin SHIH

2017-11-01

Full Text Available Noninvasive genetic sampling allows studying wildlife without having to catch, handle or even observe individuals. In this study, factors which may affect the quality of noninvasive samples of Asiatic black bear (Ursus thibetanus in the subtropical areas were identified. We collected hair and faecal samples from captive Asiatic black bears and quantitatively evaluated the effects of hair age (from fresh to 60 days, faeces age (from fresh to 14 days, faeces sampling locations (i.e. sample collected from either the surface, inside or a mixture of both the surface and inside of faeces, and faeces preservation methods (frozen or kept at room temperature in 95% ethanol on amplification success rates of mitochondrial DNA fragments of different sizes (450bp, 900bp, and 1600bp. The results showed that the amplification success rates decreased with sample age and amplicon size in both hair and faecal DNA. In subtropical environment, there was no significant difference between amplification success of DNA extracted from fresh and 7-day-old samples of either the hair or faeces. The amplification success rates were not influenced by sampling location of faeces. For faeces preserved in 95% ethanol, the amplification success appeared unaffected by frozen at -20 °C or kept at room temperature in shorter mtDNA fragments, but was significantly influenced when amplicon size was 1600bp. The results of this study will reinforce the optimization of noninvasive sampling approaches in Asiatic black bear research, especially in the subtropics.

Comparative analysis of conventional and eversion carotid endarterectomy: Prospective randomized study

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Marković Dragan M.

2008-01-01

often needed during the conventional carotid endarterectomy (34.7% compared to eversion endarterectomy (3.9%. χ2-test showed a statistically highly significant difference. CONCLUSION Eversion carotid endarectomy represents a statistically significantly shorter procedure. Distal intimal fixation demanded by this procedure is very rare, clammping of the internal carotid artery is significantly shorter, and it also has a lower rate of the early neurological complications. Based on the results of this study, as well as the opinions of other authors, it can be concluded that the eversion carotid endarterectomy has an advantage over the conventional procedure. We recommend conventional procedure only in cases when retrograde pressure indicates the use of the intraluminal shunting.

Alternative promoter usage generates novel shorter MAPT mRNA transcripts in Alzheimer's disease and progressive supranuclear palsy brains.

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Huin, Vincent; Buée, Luc; Behal, Hélène; Labreuche, Julien; Sablonnière, Bernard; Dhaenens, Claire-Marie

2017-10-03

Alternative promoter usage is an important mechanism for transcriptome diversity and the regulation of gene expression. Indeed, this alternative usage may influence tissue/subcellular specificity, protein translation and function of the proteins. The existence of an alternative promoter for MAPT gene was considered for a long time to explain differential tissue specificity and differential response to transcription and growth factors between mRNA transcripts. The alternative promoter usage could explain partly the different tau proteins expression patterns observed in tauopathies. Here, we report on our discovery of a functional alternative promoter for MAPT, located upstream of the gene's second exon (exon 1). By analyzing genome databases and brain tissue from control individuals and patients with Alzheimer's disease or progressive supranuclear palsy, we identified novel shorter transcripts derived from this alternative promoter. These transcripts are increased in patients' brain tissue as assessed by 5'RACE-PCR and qPCR. We suggest that these new MAPT isoforms can be translated into normal or amino-terminal-truncated tau proteins. We further suggest that activation of MAPT's alternative promoter under pathological conditions leads to the production of truncated proteins, changes in protein localization and function, and thus neurodegeneration.

Comparative efficacy and safety of different circumcisions for patients with redundant prepuce or phimosis: A network meta-analysis.

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Huang, Chuiguo; Song, Pan; Xu, Changbao; Wang, Ruofan; Wei, Lei; Zhao, Xinghua

2017-07-01

Phimosis and redundant prepuce are defined as the inability of the foreskin to be retracted behind the glans penis in uncircumcised males. To synthesize the evidence and provide the hierarchies of different circumcisions for phimosis and redundant prepuce, we performed an overall network meta-analysis (NMA) based on their comparative efficacy and safety. Electronic databases including PubMed, Embase, Wan Fang, VIP, CNKI and CBM database were researched from randomized controlled trials (RCTs) for redundant prepuce or phimosis. We conducted the direct and indirect comparisons by aggregate data drug information system (ADDIS) software. Moreover, consistency models were applied to assess the differences among the male circumcision practices, and the ranks based on probabilities of intervention for the different endpoints were performed. Node-splitting analysis was used to test inconsistency. Eighteen RCTs were included with 6179 participants. Compared with the conventional circumcision(CC), two new styles of circumcisions, the disposable circumcision suture device(DCSD) and Shang Ring circumcision(SRC), provided significantly shorter operation time[DCSD: standardized mean difference (SMD) = -20.60, 95% credible interval(CI) (-23.38, -17.82); SRC: SMD = -19.16, 95%CI (-21.86, -16.52)], shorter wound healing time [DCSD:SMD = -4.19, 95%CI (-8.24,-0.04); SRC: SMD = 4.55, 95%CI (1.62, 7.57); ] and better postoperative penile appearance [DCSD: odds ratios odds ratios (OR) = 11.42, 95%CI (3.60, 37.68); SRC: OR = 3.85,95%CI (1.29, 12.79)]. Additionally, DCSD showed a lower adverse events rate than other two treatments. However, no significant difference was shown in all surgeries for 24 h postoperative pain score. Node-splitting analysis showed that no significant inconsistency was existed (P > 0.05). Based on the results of NMA, DCSD may be a most effective and safest choice for phimosis and redundant prepuce. DCSD has the advantages of a shorter operation

Laparoscopic versus open radical cystectomy in bladder cancer: a systematic review and meta-analysis of comparative studies.

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Kun Tang

Full Text Available BACKGROUND AND OBJECTIVE: More recently laparoscopic radical cystectomy (LRC has increasingly been an attractive alternative to open radical cystectomy (ORC and many centers have reported their early experiences in the treatment of bladder cancer. Evaluate the safety and efficacy of LRC compared with ORC in the treatment of bladder cancer. METHODS: A systematic search of Medline, Scopus, and the Cochrane Library was performed up to Mar 1, 2013. Outcomes of interest assessing the two techniques included demographic and clinical baseline characteristics, perioperative, pathologic and oncological variables, and post-op neobladder function and complications. RESULTS: Sixteen eligible trials evaluating LRC vs ORC were identified including seven prospective and nine retrospective studies. Although LRC was associated with longer operative time (p<0.001, patients might benefit from significantly fewer overall complications (p<0.001, less blood loss (p<0.001, shorter length of hospital stay (p<0.001, less need of blood transfusion (p<0.001, less narcotic analgesic requirement (p<0.001, shorter time to ambulation (p = 0.03, shorter time to regular diet (p<0.001, fewer positive surgical margins (p = 0.006, fewer positive lymph node (p = 0.05, lower distant metastasis rate (p = 0.05 and fewer death (p = 0.004. There was no significant difference in other demographic parameters except for a lower ASA score (p = 0.01 in LRC while post-op neobladder function were similar between the two groups. CONCLUSIONS: Our data suggest that LRC appears to be a safe, feasible and minimally invasive alternative to ORC with reliable perioperative safety, pathologic & oncologic efficacy, comparable post-op neobladder function and fewer complications. Because of the inherent limitations of the included studies, further large sample prospective, multi-centric, long-term follow-up studies and randomized control trials should be undertaken to confirm our

Access to Electric Light Is Associated with Shorter Sleep Duration in a Traditionally Hunter-Gatherer Community.

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de la Iglesia, Horacio O; Fernández-Duque, Eduardo; Golombek, Diego A; Lanza, Norberto; Duffy, Jeanne F; Czeisler, Charles A; Valeggia, Claudia R

2015-08-01

Access to electric light might have shifted the ancestral timing and duration of human sleep. To test this hypothesis, we studied two communities of the historically hunter-gatherer indigenous Toba/Qom in the Argentinean Chaco. These communities share the same ethnic and sociocultural background, but one has free access to electricity while the other relies exclusively on natural light. We fitted participants in each community with wrist activity data loggers to assess their sleep-wake cycles during one week in the summer and one week in the winter. During the summer, participants with access to electricity had a tendency to a shorter daily sleep bout (43 ± 21 min) than those living under natural light conditions. This difference was due to a later daily bedtime and sleep onset in the community with electricity, but a similar sleep offset and rise time in both communities. In the winter, participants without access to electricity slept longer (56 ± 17 min) than those with access to electricity, and this was also related to earlier bedtimes and sleep onsets than participants in the community with electricity. In both communities, daily sleep duration was longer during the winter than during the summer. Our field study supports the notion that access to inexpensive sources of artificial light and the ability to create artificially lit environments must have been key factors in reducing sleep in industrialized human societies. © 2015 The Author(s).

Are Shorter Article Titles More Attractive for Citations? Cross-sectional Study of 22 Scientific Journals

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Habibzadeh, Farrokh; Yadollahie, Mahboobeh

2010-01-01

Aim To investigate the correlation between the length of the title of a scientific article and the number of citations it receives, in view of the common editorial call for shorter titles. Methods Title and the number of citations to all articles published in 2005 in 22 arbitrarily chosen English-language journals (n = 9031) were retrieved from citation database Scopus. The 2008 journal impact factors of these 22 journals were also retrieved from Thomson Reuters’ Journal Citation Report (JCR). Assuming the article title length as the independent variable, and the number of citations to the article as the dependent variable, a linear regression model was applied. Results The slope of the regression line for some journals (n = 6, when titles were measured in characters but 7 when titles were measured in words) was negative – none was significantly different from 0. The overall slope for all journals was 0.140 (when titles were measured in characters) and 0.778 (when titles were measured in words), significantly different from 0 (P articles with longer titles received more citations – Spearman ρ = 0.266 – when titles were measured in characters, and ρ = 0.244 when titles were measured in words (P 10 and for 2 out of 14 journals with impact factor <10 (P < 0.001, Fisher exact test). Conclusion Longer titles seem to be associated with higher citation rates. This association is more pronounced for journals with high impact factors. Editors who insist on brief and concise titles should perhaps update the guidelines for authors of their journals and have more flexibility regarding the length of the title. PMID:20401960

Clinical benefit of ertapenem compared to flomoxef for the treatment of cefotaxime-resistant Enterobacteriaceae bacteremia.

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Lee, Chen-Hsiang; Chen, I-Ling; Li, Chia-Chin; Chien, Chun-Chih

2018-01-01

Cefotaxime-resistant Enterobacteriaceae (CE) infections are intractable, with limited treatment options. Though carbapenems are frequently prescribed for CE infections, the emergence of carbapenem-resistant Enterobacteriaceae is of huge concern. Flomoxef is effective against CE in vitro, and some clinical data on its demonstrated effectiveness against CE bloodstream infections (BSIs) exists. We conducted a retrospective study on adults with BSI caused by flomoxef-susceptible CE to investigate the efficacy of flomoxef compared with that of ertapenem. The outcome was evaluated with propensity score-based matching and logistic regression analysis. Demographic and clinical characteristics of patients treated with flomoxef (n = 58) or ertapenem (n = 188) were compared. In the multivariate analysis, severe sepsis (adjusted odds ratio [AOR] = 3.84; 95% confidence interval [CI], 1.16-12.78; p = 0.03), high BSI mortality score (AOR = 5.59; 95% CI, 2.37-13.21; p flomoxef-treated patients were matched to 116 ertapenem-treated patients. There were no intergroup differences in BSI severity, comorbidity, or BSI sources. The 28-day mortality rates (20.7% vs 13.8%, p = 0.28) did not differ significantly. However, hospitalization length was shorter in the ertapenem group (10.2 ± 8.5 vs. 14.6 ± 9.4 days, p < 0.01). Although similar outcomes were observed between the groups, ertapenem therapy was associated with a shorter hospitalization time in adults after CE BSI.

A thaumatin-like genomic sequence identification in Vitis vinifera l., stormy wines and musts based on direct pcr

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Jana Žiarovská

2018-03-01

Full Text Available Normal 0 21 false false false MicrosoftInternetExplorer4 Direct polymerase chain reaction method was use to amplify a thaumatin-like sequence of Vitis vinifera L. in grapes as well as in stormy wines and musts. Thaumatin-like proteins (TLPs of Vitis vinifera possess beside its function in abiotic and biotic stress response another one - they are able to cause protein haze in wine unless removed prior to bottling. Direct PCR is an approach where omission of DNA extraction is typical prior the amplification of the target site of plant genome. Crude extract or small pieces of plant tissues are used in the analysis directly without steps of extraction and purification of gDNA. The biological material that was used in analysis was collected during August - October 2017 in local stores and winery Sabo and comprises from cultivars Iršai, Muškát, Savignon Blanc, Svätovavrinecké, Dornfelder and Pálava. Direct PCR was performed by a cutted piece of grape tissue and a dilution buffer was use in 1:2 for stormy wine or must, respectively. Direct amplification of thaumatin-like protein sequence of Vitis vinifera was performed along with the control reactions with the primers for conserved region of plant chloroplast. Possitive amplification of thaumatin-like allergen sequence resulted in 570 bp amplicon. The most abundant amplicons were amplified in stormy wines, followed by musts and the amplicons from grapes were weaker when comparing them to others. The amplicon specificity checking of obtained PCR product of thaumatin-like allergen was performed by restriction cleavage by Psi I and resulted in restriction amplicons of the 80 bp, 81 bp, 94 bp and 315 bp in length. Confirmation of the amplicon specificity by restriction cleavage support the potential of direct PCR to become a reproducible method that will be fully applicable in routine analysis of not only plant genomes in the future, but it was demonstrated, that it works in liquids, too.  

Ultralow lattice thermal conductivity in monolayer C3N as compared to graphene

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Sarath Kumar, S. R.

2017-09-21

Using density functional theory and the Boltzmann transport equation for phonons, we demonstrate that the thermal conductivity is massively reduced in monolayer CN as compared to isostructural graphene. We show that larger phase space for three-phonon scattering processes is available in monolayer CN, which results in much shorter phonon life-times. Although both materials are characterized by sp hybridisation, anharmonicity effects are found to be enhanced for the C-N and C-C bonds in monolayer CN, reflected by a Grüneisen parameter of -8.5 as compared to -2.2 in graphene. The combination of these properties with the fact that monolayer CN is organic, non-toxic, and built of earth abundant elements gives rise to great potential in thermoelectric applications.

Progesterone-releasing devices for cattle estrus induction and synchronization: Device optimization to anticipate shorter treatment durations and new device developments.

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de Graaff, W; Grimard, B

2018-05-01

Synchronization programs using progesterone-releasing intravaginal devices that allow for fixed time artificial insemination are still finding increasing application in bovine reproduction. This practice is useful for rationalizing livestock management because an increased number of cows can be inseminated in one session without the need for estrus detection. Although much of the innovation related to the design and development of intravaginal devices for use in cattle took place in the previous century, progress in understanding the physiology of the bovine estrous cycle resulted in shorter treatment durations, a trend which is still continuing. In this competitive market, with little functional differentiation between the existing devices, the shorter treatment duration prompted for optimization of the progesterone content in the device, as the cost of the drug significantly contributes to the price per unit. For CIDR ® a reduction of the progesterone content of about 30 per cent was realized. Price reduction remained an important target for further device development. Next to reduction of progesterone content, cheaper and easier to process materials like polyethylene vinyl acetate (EVA) copolymers have been explored to replace the commonly used silicone elastomers. The reengineering effort of CIDR ® demonstrated that knowledge of release kinetics and insight into gradual depletion patterns in the device is critical for optimization of drug content without compromising performance (blood levels). More recent publications related to the use of alternative polymers like EVA and polyisoprene (IP) indicated encouraging results regarding further reduction of progesterone content. The use of EVA seems most promising, because it is in principle a low-cost polymer available in many grades and this thermoplastic polymer can be processed easily by means of commonly used techniques like injection molding and extrusion. The use of thermoplastic polymers, however, requires

[Meta-analysis of randomized controlled trials comparing procedure for prolapse and hemorrhoids with Milligan-Morgan hemorrhoidectomy in the treatment of prolapsed hemorrhoids].

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He, Ping; Chen, Hongliang

2015-12-01

To compare the safety and efficacy of procedure for prolapse and hemorrhoids (PPH) with Milligan-Morgan hemorrhoidectomy (MMH) in the treatment of prolapsed hemorrhoids. All the randomized controlled trials (RCT) comparing PPH with MMH in the treatment of prolapsed hemorrhoids published between January 1998 and January 2015 were retrieved from PubMed, Embase, Cochrane Library, CBM, CNKI, Wangfang, VIP databases. Hand search was applied in Chinese Journal of Gastrointestinal Surgery, Chinese Journal of Coloproctology and Journal of Colorectal and Anal Surgery from the library of Chengdu University of Traditional Chinese Medicine. Associated reference documents in enrolled trials were reviewed. The methodological quality of enrolled trials was evaluated according to the Cochrane handbook for systematic reviews of interventions. Meta-analysis was performed using RevMan 5.3 software. Sixteen RCTs recruiting 1411 patients were identified. Among them, 702 patients underwent PPH, and other 709 patients MMH. Meta-analysis showed that as compared to MMH, PPH had shorter operating time(WMD=-12.34, 95% CI:-17.87 to -6.80, P=0.000], shorter hospital stay (WMD=-1.48, 95% CI: -1.81 to -1.14, P=0.000) and shorter time to recover normal activity (WMD=-14.11, 95% CI: -24.51 to -3.70, P=0.008). Patients in PPH group experienced less pain at postoperative 24 h, postoperative 1 week and the first postoperative bowel movement (all P0.05). Satisfaction degree of patients in PPH group was better than that in MMH group (OR=2.36, 95% CI:1.36 to 4.07, P=0.002). Procedure for prolapse and hemorrhoids offers some short-term benefits over Milligan-Morgan hemorrhoidectomy, but is associated with a higher rate of recurrent disease.

Phylogenetic Analysis of a Novel Molecular Isolate of Spotted Fever Group Rickettsiae from Northern Peru

National Research Council Canada - National Science Library

Jiang, Ju; Blair, Patrick J; Felices, Vidal; Moron, Cecilia; Cespedes, Manuel; Anaya, Elizabeth; Schoeler, George B; Sumner, John W; Olson, James G; Richards, Allen L

2005-01-01

... (SFG) rickettsia. Following nested polymerase chain reaction (PCR) amplification of the 17-kDa gene, gltA, ompB, ompA, and sca4, amplicons were purified, sequenced, and compared to those downloaded from GenBank...

Influence of heavy metals on rhizosphere microbial communities of Siam weed (Chromolaena odorata (L. using a 16S rRNA gene amplicon sequencing approach

Directory of Open Access Journals (Sweden)

Thanyaporn Ruangdech

2017-06-01

Full Text Available A 16S rRNA amplicon sequencing approach was used to assess the impacts of cadmium (Cd and zinc (Zn contamination on populations of rhizobacteria on Siam weed (Chromolaena odorata (L.. Bacterial communities were characterized using the Illumina MiSeq platform and the V6 hypervariable region of the 16S rRNA gene. Among the 54,026 unique operational taxonomic units (OTUs identified, 99.7% were classified as bacteria and the rest were classified as archaea. Several dominant bacterial phyla were observed in all samples—Proteobacteria, Actinobacteria, Acidobacteria, Firmicutes and Bacteroidetes. These five phyla accounted for 89.2% of all OTUs identified among all sites, and only two OTUs could not be classified to a phylum. Comparison among samples containing low and high levels of Cd contamination using nonparametric Shannon and Shannon diversity indices showed that soils with low levels of diversity had a higher level of Cd (p < 0.05. These results indicated that levels of Cd may significantly alter bacterial species selection. The Cd- and Zn-resistant bacteria from each sample were subjected to heavy-metal minimum inhibitory concentration (MIC analyses. The MIC values obtained from 1152 isolates were used to individually analyze the pattern of gene function using the BioNumerics software. The results of this analysis showed that 26.7% of the bacteria were resistant to Cd concentrations up to 320 mg/L and only 2.3% of bacteria were resistant to Zn at concentrations up to 3200 mg/L. The MIC analyses indicated that the number of resistant bacteria decreased with increasing metal concentrations and those bacteria resistant to Cd and Zn may contain more than one group of metal-resistance genes.

Less is more: latent learning is maximized by shorter training sessions in auditory perceptual learning.

Science.gov (United States)

Molloy, Katharine; Moore, David R; Sohoglu, Ediz; Amitay, Sygal

2012-01-01

The time course and outcome of perceptual learning can be affected by the length and distribution of practice, but the training regimen parameters that govern these effects have received little systematic study in the auditory domain. We asked whether there was a minimum requirement on the number of trials within a training session for learning to occur, whether there was a maximum limit beyond which additional trials became ineffective, and whether multiple training sessions provided benefit over a single session. We investigated the efficacy of different regimens that varied in the distribution of practice across training sessions and in the overall amount of practice received on a frequency discrimination task. While learning was relatively robust to variations in regimen, the group with the shortest training sessions (∼8 min) had significantly faster learning in early stages of training than groups with longer sessions. In later stages, the group with the longest training sessions (>1 hr) showed slower learning than the other groups, suggesting overtraining. Between-session improvements were inversely correlated with performance; they were largest at the start of training and reduced as training progressed. In a second experiment we found no additional longer-term improvement in performance, retention, or transfer of learning for a group that trained over 4 sessions (∼4 hr in total) relative to a group that trained for a single session (∼1 hr). However, the mechanisms of learning differed; the single-session group continued to improve in the days following cessation of training, whereas the multi-session group showed no further improvement once training had ceased. Shorter training sessions were advantageous because they allowed for more latent, between-session and post-training learning to emerge. These findings suggest that efficient regimens should use short training sessions, and optimized spacing between sessions.

Comparative Studies on the Stenogamous and Eurygamous Behavior of Eight Anopheles Species of the Hyrcanus Group (Diptera: Culicidae in Thailand

Directory of Open Access Journals (Sweden)

Adulsak Wijit

2016-03-01

Full Text Available Establishment of laboratory colony is essential for mosquito-borne-disease research. Mating behavior of stenogamous Anopheles peditaeniatus and seven eurygamous species (Anopheles argyropus, Anopheles crawfordi, Anopheles nigerrimus, Anopheles nitidus, Anopheles paraliae (=An. lesteri, Anopheles pursati and Anopheles sinensis, were investigated and compared in this study. The self-mating success of adult mosquitoes in different size cages at two density resting surface (DRS values, 3.6 and 7.2, was statistically significant between stenogamous and eurygamous species. The results obtained from comparative measurements of specific characters in adult females (maxillary palpomere and antennal sensilla characters and males (wing and genitalia indicate those characters might influence the mating success of An. peditaeniatus in a small cage. The gonostylus of An. peditaeniatus was shorter than the eurygamous species. Additionally, the lower frequency of clasper movement and shorter mating time could be important mechanisms that control the stenogamous behavior of An. peditaeniatus. Interestingly, for the first time, a cluster of large sensilla coeloconica was recorded on the antenna of An. argyropus and An. peditaeniatus females. There was no statistically significant difference in the mean number per female of those large antennal sensilla coeloconica among six of the eurygamous species.

A comparative study of cancer patients with short and long sick-leave after primary treatment.

Science.gov (United States)

Gudbergsson, Saevar Berg; Torp, Steffen; Fløtten, Tone; Fosså, Sophie D; Nielsen, Roy; Dahl, Alv A

2011-04-01

Sick-leave after primary cancer treatment has hardly been studied. This study compares Norwegian cancer patients (CPs) with shorter (≤8 months) and longer (≥9 months) sick-leave after primary cancer treatment. Our aim was to characterize factors associated with these two types of sick-leave in order to identify possible factors for interventions by which long-term sick-leaves may be avoided. A mailed questionnaire was completed by a sample of Norwegian CPs 15 to 39 months after primary treatment of the ten most common invasive types of cancer. The groups with shorter (n=359) and longer (n=481) sick-leaves (SSL vs LSL) were compared with each other by self-reported information as to socio-demographic and cancer-related variables, health, quality of life, work ability, work situation and supportive interventions. The LSL consisted of 78% females, and 76% of them had breast or gynaecological cancer. A higher proportion of patients with low level of education, economical problems, treated with chemotherapy, hormones and multimodal treatment belonged to LSL compared to SSL. Significantly more LSL had recurrences of cancer, co-morbidity, regular use of medication, and poorer self-rated health, quality of life and work ability. Compared to SSL, more LSL reported needs for and offers of supportive care such as physiotherapy, physical activities and psychosocial support. A multivariate regression analysis showed that reduced work ability, changes in employment due to cancer, lack of support from supervisors at work, and having had combined treatment were significantly associated with being LSL. Longer sick-leave after primary cancer treatment is associated with combined cancer treatment, lack of support from supervisors and reduced overall work ability. Interventions and counselling related to the work place and reduced work ability could be of value for prevention of long-term sick-leaves.

The Anthropometric Characteristics of Futsal Players Compared with Professional Soccer Players

Directory of Open Access Journals (Sweden)

Burdukiewicz Anna

2014-08-01

Full Text Available Purpose. The aim of the study was to compare the morphological characteristics of experienced futsal players with professional soccer players. Methods. The research sample included 22 university futsal players and 22 professional soccer players. Parameters including body height and mass, skinfold thicknesses of the trunk and extremities, lower limb length, trunk width, humerus and femur bone breadths, and the circumferences of the chest, hips, thighs, and calves were used to calculate various somatic indices. Somatotyping was performed using the Heath–carter method. Differences in the characteristics between the futsal and soccer players were analyzed using Student’s t test. Intragroup analysis was also performed on futsal players depending on player position and compared with the arithmetic means and standard deviations of all variables of the entire sample. Results. compared with their soccer-playing peers, the futsal players were shorter, weighed less, had shorter lower limbs, narrower hips, and smaller hip circumference and bone breadth values. In contrast, higher levels of body fat and endomorphy were noted in this group. The proportion of mesomorphs and ectomorphs were similar in both groups. Futsal goalkeepers were differentiated by greater subcutaneous adiposity and body mass. Defenders had the slimmest body shape, with relatively narrower shoulders and hips, smaller bone breadths, and lower levels of adiposity. The body build of wingers was slightly larger. Pivoters were characterized by greater body height and larger values for the characteristics measuring the lateral trunk dimensions. Conclusions. The observed morphological differences between futsal and soccer players were mainly in body height and height-associated characteristics. This indicates that no specialized approach in futsal recruitment is currently used. This points to the need to develop a specialized approach in the player recruitment stage, as the tactical and

Utility of a rapid immunochromatographic strip test in detecting canine parvovirus infection compared with polymerase chain reaction

Directory of Open Access Journals (Sweden)

Sundaran S. Tinky

2015-04-01

Full Text Available Aim: The present study was undertaken to detect the presence of canine parvovirus (CPV in fecal samples of diarrheic dogs by conventional polymerase chain reaction (PCR and immunochromatographic (IC strip test and to compare the diagnostic potential of these tests. Materials and Methods: A total of 50 fecal samples collected from diarrheic dogs suspected for CPV infection were subjected to PCR using CPV-555 primer amplifying the gene coding for the VP1 protein. These samples were also tested by IC strip test using a commercial rapid Ag test kit. The results were statistically analyzed using McNemar test. Results: A total of 22 samples (44% were detected as positive by PCR, which yielded a specific amplicon of 583 bp. In IC strip test, 18 (36% samples were found to be positive. The sensitivity of the test as compared to PCR was found to be 72.22% and specificity was 92.86%. Positive predictive value and negative predictive value of IC strip test was found to be 88.89% and 81.25%, respectively. Statistical analysis of the results of PCR and IC assay using McNemar test revealed no significant difference (p>0.05. Conclusion: The IC strip test could be employed as a rapid field level diagnostic tool for the diagnosis of canine parvoviral diarrhea.

Pseudogene of dihydrolipoyl succinyltransferase (E2k) found by PCR amplification and direct sequencing of rodent-human cell hybrid DNAs

Energy Technology Data Exchange (ETDEWEB)

Cai, X.; Ali, G.; Blass, J.P. [Cornell Univ. Medical College, White Plains, NY (United States); Szabo, P. [Cornell Univ. Medical College, New York, NY (United States); Tanzi, R.E. [Massachusetts General Hospital, Boston, MA (United States)

1994-07-01

Previous studies have indicated that the cDNA for the E2k component of the human {alpha}-ketoglutarate dehydrogenase complex (KGDHC) hybridized not only to a major locus on chromosome 14q24.3 in a region associated with familial Alzheimer`s disease and with Joseph-Machado disease, but also to another locus on chromosome 1p31. The authors now report that PCR of genomic DNA and direct sequencing indicated that the chromosome 1 locus is an intronless pseudogene. PCR of genomic DNA amplified E2k fragments from mouse-human cell hybrids containing human chromosome 1 DNA but not from hybrids containing human chromosome 14 DNA. The resulting amplicons were of comparable sizes to those when the cDNA was used to template. The direct sequencing of these amplicons confirmed the lack of introns and indicated a frame shift, which led to the presence of four termination codons early in the coding region. PCR followed by direct sequencing of the amplicons appears to be a convenient method for identifying intronless pseudogenes.

Denoising PCR-amplified metagenome data

Directory of Open Access Journals (Sweden)

Rosen Michael J

2012-10-01

Full Text Available Abstract Background PCR amplification and high-throughput sequencing theoretically enable the characterization of the finest-scale diversity in natural microbial and viral populations, but each of these methods introduces random errors that are difficult to distinguish from genuine biological diversity. Several approaches have been proposed to denoise these data but lack either speed or accuracy. Results We introduce a new denoising algorithm that we call DADA (Divisive Amplicon Denoising Algorithm. Without training data, DADA infers both the sample genotypes and error parameters that produced a metagenome data set. We demonstrate performance on control data sequenced on Roche’s 454 platform, and compare the results to the most accurate denoising software currently available, AmpliconNoise. Conclusions DADA is more accurate and over an order of magnitude faster than AmpliconNoise. It eliminates the need for training data to establish error parameters, fully utilizes sequence-abundance information, and enables inclusion of context-dependent PCR error rates. It should be readily extensible to other sequencing platforms such as Illumina.

Laparoscopic versus open splenectomy for portal hypertension: a systematic review of comparative studies.

Science.gov (United States)

Cai, Yunqiang; Liu, Zhihong; Liu, Xubao

2014-08-01

Laparoscopic splenectomy has become the gold-standard procedure for normal to moderately enlarged spleens. However, the safety of laparoscopic splenectomy for patients with portal hypertension remains controversial. We carried out this systematic review to identify the feasibility and safety of laparoscopic splenectomy in treating portal hypertension. A systematic search for comparative studies that compared laparoscopic splenectomy with open splenectomy for portal hypertension was carried out. Studies were independently reviewed for quality, inclusion and exclusion criteria, demographic characteristics, and perioperative outcomes. Although laparoscopic splenectomy is associated with longer operating time, it offers advantages over the open procedure in terms of less blood loss, lower operative complications, earlier resumption of oral intake, and shorter posthospital stay. Therefore, laparoscopic splenectomy is a safe and feasible intervention for portal hypertension. © The Author(s) 2014.

Comparative costs of coal and nuclear-generated electricity in the united states

International Nuclear Information System (INIS)

Brandfon, W.W.

1987-01-01

This paper compares the future first-year operating costs and lifetime levelized costs of producing baseload coal- and nuclear-generated electricity under schedules shorter than those recently experienced at U.S. plants. Nuclear appears to have a clear economic advantage. Coal is favorable only when it is assumed that the units will operate at very low capacity factors and/or when the capital cost differential between nuclear and coal is increased far above the recent historical level. Nuclear is therefore a cost-competitive electric energy option for utilities and should be considered as an alternative to coal when large baseload capacity is required. (author)

Prognostic relevance of gemistocytic grade II astrocytoma: gemistocytic component and MR imaging features compared to non-gemistocytic grade II astrocytoma

Energy Technology Data Exchange (ETDEWEB)

Heo, Young Jin [Inje University, Busan Paik Hospital, Department of Radiology, Busan (Korea, Republic of); Park, Ji Eun; Kim, Ho Sung; Lee, Ji Ye; Jung, Seung Chai; Choi, Choong Gon; Kim, Sang Joon [University of Ulsan College of Medicine, Asan Medical Center, Department of Radiology and Research Institute of Radiology, Seoul (Korea, Republic of); Nam, Soo Jeong [University of Ulsan College of Medicine, Asan Medical Center, Department of Pathology, Seoul (Korea, Republic of)

2017-07-15

To determine if gemistocytic grade II astrocytoma (GemA) and its MR imaging characteristics are associated with a shorter time-to-progression (TTP) compared with non-gemistocytic grade II astrocytoma (non-GemA). We enrolled 78 patients who were followed up more than 5 years (29 pathologically proven GemA and 49 non-GemA) during a 10-year period. Contrast-enhanced T1-weighted, diffusion-weighted imaging (DWI), dynamic susceptibility contrast (DSC), and MR spectroscopy (MRS) and clinical data were retrospectively reviewed. Clinical and MR imaging features were analyzed as possible prognostic factors of high-grade transformation, and multivariate analysis of TTP was performed using Cox proportional modeling. GemA showed more frequent high-grade features than non-GemA, including diffusion restriction (P <.001), increased choline/creatine (P =.02), and increased choline/NAA ratio (P =.015). Patients with GemA had a significantly shorter median TTP (53.1 vs 68 months; P <.001). A gemistocytic histopathology (hazard ratio = 3.42; P =.015) and low ADC (hazard ratio = 3.61; P =.001) were independently associated with a shorter TTP. GemA can present with MR imaging findings mimicking high-grade glioma at initial diagnosis and transforms to high-grade disease earlier than non-GemA. Low ADC on DWI might be useful in stratifying the risk of progression in patients with grade II astrocytoma. (orig.)

A comparative study of craniofacial morphology of parents with and without cleft lip and/or palate children

International Nuclear Information System (INIS)

Lim, Sug Young; Koh, Kwang Joon

1993-01-01

The purpose of this study was to determine whether any difference existed in craniofacial morphology between parents of children with cleft lip and/or palate and parents of children without cleft lip and/or palate. Thirty three measurements of the various regions of cranium and face were obtained from lateral cephalometric radiograms in parents of 28 children with cleft lip and palate, 18 children with cleft lip, and 22 children with cleft palate. There were 28 couples and 40 single parents in this sample. There were 92 individuals including 41 males and 51 females. The measurements were compared with those in control subjects, including 40 adult males and 40 adult females, who had no history of craniofacial abnormalities. The total sample was compared for the sex independently. The obtained results were as follows. 1. In the cranium, both parents of cleft children had significantly shorter posterior cranial base length (S-Ba). 2. In the upper face, a significantly shorter anteroposterior length of maxilla (A'-Ptm'), particularly in the anterior region (A'-K'), anterior facial depth (A-SBaL), posterior facial height (Ptm'-SNL) and relation of subnasale to the cranial base (BaN S n) were noted in fathers of cleft children. But, all measurements were not found to be significantly different between experimental group and control group in all mothers. 3. In the lower face, both parents of cleft children showed a significantly greater Y axis angle (NSGn) and ramal plane angle (SNL-RP) in faters of cleft children. Thus both parents showed a posteriorly rotation of mandible. The thickness of the lower lip (B-B ) was significantly thicker in fathers of cleft children. 4. In the facial profile, a significantly shorter posterior facial height (S-Go) and greater angle of soft tissue facial convexity (BaN P og ) were noted in the fathers of cleft children. But, all measurements were not found to be significantly different between experimental group and control group in all

A comparative study of craniofacial morphology of parents with and without cleft lip and/or palate children

Energy Technology Data Exchange (ETDEWEB)

Lim, Sug Young; Koh, Kwang Joon [Dept. of Oral and Maxillofacial Radiology, College of Dentistry, Chonbuk National University, Chonju (Korea, Republic of)

1993-02-15

The purpose of this study was to determine whether any difference existed in craniofacial morphology between parents of children with cleft lip and/or palate and parents of children without cleft lip and/or palate. Thirty three measurements of the various regions of cranium and face were obtained from lateral cephalometric radiograms in parents of 28 children with cleft lip and palate, 18 children with cleft lip, and 22 children with cleft palate. There were 28 couples and 40 single parents in this sample. There were 92 individuals including 41 males and 51 females. The measurements were compared with those in control subjects, including 40 adult males and 40 adult females, who had no history of craniofacial abnormalities. The total sample was compared for the sex independently. The obtained results were as follows. 1. In the cranium, both parents of cleft children had significantly shorter posterior cranial base length (S-Ba). 2. In the upper face, a significantly shorter anteroposterior length of maxilla (A'-Ptm'), particularly in the anterior region (A'-K'), anterior facial depth (A-SBaL), posterior facial height (Ptm'-SNL) and relation of subnasale to the cranial base (BaN{sup S}n) were noted in fathers of cleft children. But, all measurements were not found to be significantly different between experimental group and control group in all mothers. 3. In the lower face, both parents of cleft children showed a significantly greater Y axis angle (NSGn) and ramal plane angle (SNL-RP) in faters of cleft children. Thus both parents showed a posteriorly rotation of mandible. The thickness of the lower lip (B-B) was significantly thicker in fathers of cleft children. 4. In the facial profile, a significantly shorter posterior facial height (S-Go) and greater angle of soft tissue facial convexity (BaN'Pog') were noted in the fathers of cleft children. But, all measurements were not found to be significantly different between

(SELAX strain) B2 amplicon

African Journals Online (AJOL)

USER

2010-07-12

Jul 12, 2010 ... enzyme was inactivated by heating at 75°C for 10 min after the addition of 2 µl of ... material of the vector DNA and the partial genomic digests were packaged in ... tubes. The tubes were incubated for 15 min at 37°C. Molten LB ... Plaque transfer was carried out for 2 min with ink markings made on the agar ...

Unlabeled probes for the detection and typing of herpes simplex virus.

Science.gov (United States)

Dames, Shale; Pattison, David C; Bromley, L Kathryn; Wittwer, Carl T; Voelkerding, Karl V

2007-10-01

Unlabeled probe detection with a double-stranded DNA (dsDNA) binding dye is one method to detect and confirm target amplification after PCR. Unlabeled probes and amplicon melting have been used to detect small deletions and single-nucleotide polymorphisms in assays where template is in abundance. Unlabeled probes have not been applied to low-level target detection, however. Herpes simplex virus (HSV) was chosen as a model to compare the unlabeled probe method to an in-house reference assay using dual-labeled, minor groove binding probes. A saturating dsDNA dye (LCGreen Plus) was used for real-time PCR. HSV-1, HSV-2, and an internal control were differentiated by PCR amplicon and unlabeled probe melting analysis after PCR. The unlabeled probe technique displayed 98% concordance with the reference assay for the detection of HSV from a variety of archived clinical samples (n = 182). HSV typing using unlabeled probes was 99% concordant (n = 104) to sequenced clinical samples and allowed for the detection of sequence polymorphisms in the amplicon and under the probe. Unlabeled probes and amplicon melting can be used to detect and genotype as few as 10 copies of target per reaction, restricted only by stochastic limitations. The use of unlabeled probes provides an attractive alternative to conventional fluorescence-labeled, probe-based assays for genotyping and detection of HSV and might be useful for other low-copy targets where typing is informative.

Déjà-vu all over again: using simulation to evaluate the impact of shorter shelf life for red blood cells at Héma-Québec.

Science.gov (United States)

Blake, John T; Hardy, Matthew; Delage, Gilles; Myhal, Geneviève

2013-07-01

Since the 1970s red blood cells (RBCs) have had a rated shelf life of 42 days. Recently, studies have suggested poorer patient outcomes when older blood is transfused. However, shortening the shelf life of RBCs may increase costs and lead to greater instances of outdates and shortages. A simulation method to evaluate the impact of a shorter shelf life for RBCs on a regional blood network was developed. A network model of the production and distribution system in the province of Quebec was built and validated. The model suggests that a shelf life of 21 or 28 days will have modest impact on outdate and shortage rates. A shelf life of 14 days will create significant challenges for both blood suppliers and hospitals and will result in systemwide outdate rates of 6.64% and shortage rates of 2.75%. The impact of a shorter shelf life for RBCs will disproportionately affect smaller and midsize hospitals. A shelf life of 28 or 21 days is feasible without excessive increases to systemwide outdate, shortage, or emergency ordering rates. Large hospitals will see minimal impact; smaller hospitals will see larger increases and may be unable to find inventory policies that maintain both low outdate and shortage rates. Reducing the shelf life to 14 days, or lower, results in significant challenges for suppliers and hospitals of all sizes. All hospitals will see an impact on outdate and shortage rates; overall systemwide outdate rates (6% or more) will reach levels that would currently be considered unacceptably high. © 2012 American Association of Blood Banks.

Intracellular diversity of the V4 and V9 regions of the 18S rRNA in marine protists (radiolarians) assessed by high-throughput sequencing.

Science.gov (United States)

Decelle, Johan; Romac, Sarah; Sasaki, Eriko; Not, Fabrice; Mahé, Frédéric

2014-01-01

Metabarcoding is a powerful tool for exploring microbial diversity in the environment, but its accurate interpretation is impeded by diverse technical (e.g. PCR and sequencing errors) and biological biases (e.g. intra-individual polymorphism) that remain poorly understood. To help interpret environmental metabarcoding datasets, we investigated the intracellular diversity of the V4 and V9 regions of the 18S rRNA gene from Acantharia and Nassellaria (radiolarians) using 454 pyrosequencing. Individual cells of radiolarians were isolated, and PCRs were performed with generalist primers to amplify the V4 and V9 regions. Different denoising procedures were employed to filter the pyrosequenced raw amplicons (Acacia, AmpliconNoise, Linkage method). For each of the six isolated cells, an average of 541 V4 and 562 V9 amplicons assigned to radiolarians were obtained, from which one numerically dominant sequence and several minor variants were found. At the 97% identity, a diversity metrics commonly used in environmental surveys, up to 5 distinct OTUs were detected in a single cell. However, most amplicons grouped within a single OTU whereas other OTUs contained very few amplicons. Different analytical methods provided evidence that most minor variants forming different OTUs correspond to PCR and sequencing artifacts. Duplicate PCR and sequencing from the same DNA extract of a single cell had only 9 to 16% of unique amplicons in common, and alignment visualization of V4 and V9 amplicons showed that most minor variants contained substitutions in highly-conserved regions. We conclude that intracellular variability of the 18S rRNA in radiolarians is very limited despite its multi-copy nature and the existence of multiple nuclei in these protists. Our study recommends some technical guidelines to conservatively discard artificial amplicons from metabarcoding datasets, and thus properly assess the diversity and richness of protists in the environment.

Comparing local TV news with national TV news in cancer coverage: an exploratory content analysis.

Science.gov (United States)

Lee, Chul-Joo; Long, Marilee; Slater, Michael D; Song, Wen

2014-12-01

The authors compared local TV news with national TV news in terms of cancer coverage using a nationally representative sample of local nightly TV and national network TV (i.e., ABC, CBS, NBC, and CNN) cancer news stories that aired during 2002 and 2003. Compared with national TV news, local TV cancer stories were (a) much shorter in length, (b) less likely to report on cancer prevention (i.e., preventive behaviors and screening tests), and (c) less likely to reference national organizations (i.e., National Cancer Institute, American Cancer Society, National Institutes of Health, Centers for Disease Control and Prevention, Food and Drug Administration) that have made clear recommendations about ways to prevent cancer. The implications of these findings for health communication research and cancer education were discussed.

Region of interest methylation analysis: a comparison of MSP with MS-HRM and direct BSP.

Science.gov (United States)

Akika, Reem; Awada, Zainab; Mogharbil, Nahed; Zgheib, Nathalie K

2017-07-01

The aim of this study was to compare and contrast three DNA methylation methods of a specific region of interest (ROI): methylation-specific PCR (MSP), methylation-sensitive high resolution melting (MS-HRM) and direct bisulfite sequencing (BSP). The methylation of a CpG area in the promoter region of Estrogen receptor alpha (ESR1) was evaluated by these three methods with samples and standards of different methylation percentages. MSP data were neither reproducible nor sensitive, and the assay was not specific due to non-specific binding of primers. MS-HRM was highly reproducible and a step forward into categorizing the methylation status of the samples as percent ranges. Direct BSP was the most informative method regarding methylation percentage of each CpG site. Though not perfect, it was reproducible and sensitive. We recommend the use of either method depending on the research question and target amplicon, and provided that the designed primers and expected amplicons are within recommendations. If the research question targets a limited number of CpG sites and simple yes/no results are enough, MSP may be attempted. For short amplicons that are crowded with CpG sites and of single melting domain, MS-HRM may be the method of choice though it only indicates the overall methylation percentage of the entire amplicon. Although the assay is highly reproducible, being semi-quantitative makes it of lesser interest to study ROI methylation of samples with little methylation differences. Direct BSP is a step forward as it gives information about the methylation percentage at each CpG site.

3D Vision Provides Shorter Operative Time and More Accurate Intraoperative Surgical Performance in Laparoscopic Hiatal Hernia Repair Compared With 2D Vision.

Science.gov (United States)

Leon, Piera; Rivellini, Roberta; Giudici, Fabiola; Sciuto, Antonio; Pirozzi, Felice; Corcione, Francesco

2017-04-01

The aim of this study is to evaluate if 3-dimensional high-definition (3D) vision in laparoscopy can prompt advantages over conventional 2D high-definition vision in hiatal hernia (HH) repair. Between September 2012 and September 2015, we randomized 36 patients affected by symptomatic HH to undergo surgery; 17 patients underwent 2D laparoscopic HH repair, whereas 19 patients underwent the same operation in 3D vision. No conversion to open surgery occurred. Overall operative time was significantly reduced in the 3D laparoscopic group compared with the 2D one (69.9 vs 90.1 minutes, P = .006). Operative time to perform laparoscopic crura closure did not differ significantly between the 2 groups. We observed a tendency to a faster crura closure in the 3D group in the subgroup of patients with mesh positioning (7.5 vs 8.9 minutes, P = .09). Nissen fundoplication was faster in the 3D group without mesh positioning ( P = .07). 3D vision in laparoscopic HH repair helps surgeon's visualization and seems to lead to operative time reduction. Advantages can result from the enhanced spatial perception of narrow spaces. Less operative time and more accurate surgery translate to benefit for patients and cost savings, compensating the high costs of the 3D technology. However, more data from larger series are needed to firmly assess the advantages of 3D over 2D vision in laparoscopic HH repair.

Comparative photoluminescence study of close-packed and colloidal InP/ZnS quantum dots

Science.gov (United States)

Thuy, Ung Thi Dieu; Thuy, Pham Thi; Liem, Nguyen Quang; Li, Liang; Reiss, Peter

2010-02-01

This letter reports on the comparative photoluminescence study of InP/ZnS quantum dots in the close-packed solid state and in colloidal solution. The steady-state photoluminescence spectrum of the close-packed InP/ZnS quantum dots peaks at a longer wavelength than that of the colloidal ones. Time-resolved photoluminescence shows that the close-packed quantum dots possess a shorter luminescence decay time and strongly increased spectral shift with the time delayed from the excitation moment in comparison with the colloidal ones. The observed behavior is discussed on the basis of energy transfer enabled by the short interparticle distance between the close-packed quantum dots.

Comparing the Effectiveness of a Clinical Registry and a Clinical Data Warehouse for Supporting Clinical Trial Recruitment: A Case Study

Science.gov (United States)

Weng, Chunhua; Bigger, J Thomas; Busacca, Linda; Wilcox, Adam; Getaneh, Asqual

2010-01-01

This paper reports a case study comparing the relative efficiency of using a Diabetes Registry or a Clinical Data Warehouse to recruit participants for a diabetes clinical trial, TECOS. The Clinical Data Warehouse generated higher positive predictive accuracy (31% vs. 6.6%) and higher participant recruitment than the Registry (30 vs. 14 participants) in a shorter time period (59 vs. 74 working days). We identify important factors that increase clinical trial recruitment efficiency and lower cost. PMID:21347102

Subgingival microbiome in smokers and non-smokers in periodontitis: an exploratory study using traditional targeted techniques and a next-generation sequencing

NARCIS (Netherlands)

Bizzarro, S.; Loos, B.G.; Laine, M.L.; Crielaard, W.; Zaura, E.

2013-01-01

Aim To compare the results of two targeted techniques to an open-ended technique in periodontitis patients, differentiated on the basis of smoking habit. Materials & Methods Thirty periodontitis patients (15 smokers and 15 non-smokers) provided subgingival plaque samples for 16S rRNA gene amplicon

Urban blackbirds have shorter telomeres

NARCIS (Netherlands)

Ibanez-Alamo, Juan Diego; Pineda-Pampliega, Javier; Thomson, Robert L.; Aguirre, Jose I.; Diez-Fernandez, Alazne; Faivre, Bruno; Figuerola, Jordi; Verhulst, Simon

Urbanization, one of the most extreme human-induced environmental changes, represents a major challenge for many organisms. Anthropogenic habitats can have opposing effects on different fitness components, for example, by decreasing starvation risk but also health status. Assessment of the net

Shorter Perceived Outpatient MRI Wait Times Associated With Higher Patient Satisfaction.

Science.gov (United States)

Holbrook, Anna; Glenn, Harold; Mahmood, Rabia; Cai, Qingpo; Kang, Jian; Duszak, Richard

2016-05-01

The aim of this study was to assess differences in perceived versus actual wait times among patients undergoing outpatient MRI examinations and to correlate those times with patient satisfaction. Over 15 weeks, 190 patients presenting for outpatient MR in a radiology department in which "patient experience" is one of the stated strategic priorities were asked to (1) estimate their wait times for various stages in the imaging process and (2) state their satisfaction with their imaging experience. Perceived times were compared with actual electronic time stamps. Perceived and actual times were compared and correlated with standardized satisfaction scores using Kendall τ correlation. The mean actual wait time between patient arrival and examination start was 53.4 ± 33.8 min, whereas patients perceived a mean wait time of 27.8 ± 23.1 min, a statistically significant underestimation of 25.6 min (P perceived wait times at all points during patient encounters were correlated with higher satisfaction scores (P perceived and actual wait times were both correlated with higher satisfaction scores. As satisfaction surveys play a larger role in an environment of metric transparency and value-based payments, better understanding of such factors will be increasingly important. Copyright © 2016 American College of Radiology. Published by Elsevier Inc. All rights reserved.

Shorter Exciton Lifetimes via an External Heavy-Atom Effect: Alleviating the Effects of Bimolecular Processes in Organic Light-Emitting Diodes.

Science.gov (United States)

Einzinger, Markus; Zhu, Tianyu; de Silva, Piotr; Belger, Christian; Swager, Timothy M; Van Voorhis, Troy; Baldo, Marc A

2017-10-01

Multiexcited-state phenomena are believed to be the root cause of two exigent challenges in organic light-emitting diodes; namely, efficiency roll-off and degradation. The development of novel strategies to reduce exciton densities under heavy load is therefore highly desirable. Here, it is shown that triplet exciton lifetimes of thermally activated delayed-fluorescence-emitter molecules can be manipulated in the solid state by exploiting intermolecular interactions. The external heavy-atom effect of brominated host molecules leads to increased spin-orbit coupling, which in turn enhances intersystem crossing rates in the guest molecule. Wave function overlap between the host and the guest is confirmed by combined molecular dynamics and density functional theory calculations. Shorter triplet exciton lifetimes are observed, while high photoluminescence quantum yields and essentially unaltered emission spectra are maintained. A change in the intersystem crossing rate ratio due to increased dielectric constants leads to almost 50% lower triplet exciton densities in the emissive layer in the steady state and results in an improved onset of the photoluminescence quantum yield roll-off at high excitation densities. Efficient organic light-emitting diodes with better roll-off behavior based on these novel hosts are fabricated, demonstrating the suitability of this concept for real-world applications. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Lumbar facet anatomy changes in spondylolysis: a comparative skeletal study

Science.gov (United States)

Dar, Gali; Peleg, Smadar; Steinberg, Nili; Alperovitch-Najenson, Dvora; Salame, Khalil; Hershkovitz, Israel

2007-01-01

Opinions differ as to the exact mechanism responsible for spondylolysis (SP) and whether individuals with specific morphological characteristics of the lumbar vertebral neural arch are predisposed to SP. The aim of our study was to reveal the association between SP and the architecture of lumbar articular facets and the inter-facet region. Methods: Using a Microscribe three-dimensional apparatus (Immersion Co., San Jose, CA, USA), length, width and depth of all articular facets and all inter-facet distances in the lumbar spine (L1–L5) were measured. From the Hamann-Todd Human Osteological Collection (Cleveland Museum of Natural History, OH, USA) 120 normal male skeletons with lumbar spines in the control group and 115 with bilateral SP at L5 were selected. Analysis of variance was employed to examine the differences between spondylolytic and normal spines. Results: Three profound differences between SP and the norm appeared: (1) in individuals with SP, the size and shape of L4’s neural arch had significantly greater inter-facet widths, significantly shorter inter-facet heights and significantly shorter and narrower articular facets; (2) only in the L4 vertebra in individuals with SP was the inferior inter-facet width greater in size than the superior inter-facet width of the vertebra below (L5) (38.7 mm versus 40 mm); (3) in all lumbar vertebrae, the right inferior articular facets in individuals with SP were flatter compared to the control group. Conclusions: Individuals with L4 “SP” characteristics are at a greater risk of developing fatigue fractures in the form of spondylolysis at L5. PMID:17440753

A randomised trial comparing laparoscopy with laparotomy in the ...

African Journals Online (AJOL)

time to normal activity, total hospital costs,[8] shorter hospital stay and quicker recovery in ... with laparoscopy in the surgical management of women with REP in any setting. ..... Regression analysis accounting for the learning curve shows that.

Clinical application of RT-nested PCR integrated with RFLP in Hantavirus detection and genotyping: a prospective study in Shandong Province, PR China.

Science.gov (United States)

Liu, Yun-Xi; Zhao, Zhong-Tang; Cao, Wu-Chun; Xu, Xiao-Qun; Suo, Ji-Jiang; Xing, Yu-Bin; Jia, Ning; Du, Ming-Mei; Liu, Bo-Wei; Yao, Yuan

2013-01-01

The aim of the present study was to evaluate the clinical usefulness of applying RT-nested PCR along with RFLP as a method for diagnosis and genotypic differentiation of Hantavirus in the acute-stage sera of HFRS patients as compared to the ELISA technique. A prospective study of patients with suspected HFRS patients was carried out. Sera were collected for serological evaluation by ELISA and RT-nested PCR testing. Primers were selected from the published sequence of the S segment of HTNV strain 76-118 and SEOV strain SR-11, which made it possible to obtain an amplicon of 403 bp by RT-nested PCR. The genotypic differentiations of the RT-nested PCR amplicons were carried out by RFLP. Sequence analyses of the amplicons were used to confirm the accuracy of the results obtained by RFLP. Of the 48 acute-stage sera from suspected HFRS patients, 35 were ELISA-positive while 41 were positive by RT-nested PCR. With Hind III and Hinf I, RFLP profiles of the RT-nested PCR amplicons of the 41 positive sera exhibited two patterns. 33 had RFLP profiles similar to the reference strain R22, and thus belonged to the SEOV type. The other 8 samples which were collected during October-December had RFLP profiles similar to the reference strain 76-118, and thus belonged to the HTNV type. Sequence phylogenetic analysis of RT-nested PCR amplicons revealed sdp1, sdp2 YXL-2008, and sdp3 as close relatives of HTNV strain 76-118, while sdp22 and sdp37 as close relatives of SEOV strain Z37 and strain R22 located in two separate clusters in the phylogenetic tree. These results were identical to those acquired by RFLP. RT-nested PCR integrated with RFLP was a rapid, simple, accurate method for detecting and differentiating the genotypes of Hantavirus in the acute-stage sera of suspected HFRS patients. In Shandong province, the main genotypes of Hantavirus belonged to the SEOV types, while the HTNV types were observed during the autumn-winter season.

Cats, Cancer and Comparative Oncology

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Claire M. Cannon

2015-06-01

Full Text Available Naturally occurring tumors in dogs are well-established models for several human cancers. Domestic cats share many of the benefits of dogs as a model (spontaneous cancers developing in an immunocompetent animal sharing the same environment as humans, shorter lifespan allowing more rapid trial completion and data collection, lack of standard of care for many cancers allowing evaluation of therapies in treatment-naïve populations, but have not been utilized to the same degree in the One Medicine approach to cancer. There are both challenges and opportunities in feline compared to canine models. This review will discuss three specific tumor types where cats may offer insights into human cancers. Feline oral squamous cell carcinoma is common, shares both clinical and molecular features with human head and neck cancer and is an attractive model for evaluating new therapies. Feline mammary tumors are usually malignant and aggressive, with the ‘triple-negative’ phenotype being more common than in humans, offering an enriched population in which to examine potential targets and treatments. Finally, although there is not an exact corollary in humans, feline injection site sarcoma may be a model for inflammation-driven tumorigenesis, offering opportunities for studying variations in individual susceptibility as well as preventative and therapeutic strategies.

Ease of intubation: A randomized, double-blind study to compare two doses of rocuronium bromide for endotracheal intubation.

Science.gov (United States)

Shukla, Aparna; Misra, Shilpi

2016-01-01

Clinical need for a nondepolarizing agent with a rapid onset time and a brief duration of action has led to the development of rocuronium bromide. The aim of this study was to evaluate optimal dose of rocuronium bromide for intubation and to compare the onset time, duration of action, intubating conditions, and hemodynamic effects of two doses of rocuronium bromide. A prospective, randomized, double-blind study. All the patients were divided in a randomized, double-blind fashion into two groups of twenty patients each. Group I patients received rocuronium bromide 0.6 mg/kg intravenously and intubated at 60 s, Group II patients received rocuronium bromide 0.9 mg/kg and intubated at 60 s. The neuromuscular block was assessed using single twitch stimulation of 0.1 Hz at adductor pollicis muscle of hand at every 10 s. The results were compiled and analyzed statistically using Chi-square test for qualitative data and Student's t -test for quantitative data. Time of onset was significantly shorter ( P Rocuronium bromide 0.9 mg/kg is a safer alternative to rocuronium bromide 0.6 mg/kg for endotracheal intubation with shorter time of onset and better intubating conditions.

Evaluation of Coflex interspinous stabilization following decompression compared with decompression and posterior lumbar interbody fusion for the treatment of lumbar degenerative disease: A minimum 5-year follow-up study.

Science.gov (United States)

Yuan, Wei; Su, Qing-Jun; Liu, Tie; Yang, Jin-Cai; Kang, Nan; Guan, Li; Hai, Yong

2017-01-01

Few studies have compared the clinical and radiological outcomes between Coflex interspinous stabilization and posterior lumbar interbody fusion (PLIF) for degenerative lumbar disease. We compared the at least 5-year clinical and radiological outcomes of Coflex stabilization and PLIF for lumbar degenerative disease. Eighty-seven consecutive patients with lumbar degenerative disease were retrospectively reviewed. Forty-two patients underwent decompression and Coflex interspinous stabilization (Coflex group), 45 patients underwent decompression and PLIF (PLIF group). Clinical and radiological outcomes were evaluated. Coflex subjects experienced less blood loss, shorter hospital stays and shorter operative time than PLIF (all pdisease was higher in the PLIF group, but this did not achieve statistical significance (11.1% vs. 4.8%, p=0.277). Both groups provided sustainable improved clinical outcomes for lumbar degenerative disease through at least 5-year follow-up. The Coflex group had significantly better early efficacy than the PLIF group. Coflex interspinous implantation after decompression is safe and effective for lumbar degenerative disease. Copyright © 2016 Elsevier Ltd. All rights reserved.

The Optimal Approach for Laparoscopic Adrenalectomy through Mono Port regarding Left or Right Sides: A Comparative Study

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Wooseok Byon

2014-01-01

Full Text Available Introduction. Several studies have shown the feasibility and safety of both transperitoneal and posterior retroperitoneal approaches for single incision laparoscopic adrenalectomy, but none have compared the outcomes according to the left- or right-sided location of the adrenal glands. Materials and Methods. From 2009 to 2013, 89 patients who received LAMP (laparoscopic adrenalectomy through mono port were analyzed. The surgical outcomes attained using the transperitoneal approach (TPA and posterior retroperitoneal approach (PRA were analyzed and compared. Results and Discussion. On the right side, no significant differences were found between the LAMP-TPA and LAMP-PRA groups in terms of patient characteristics and clinicopathological data. However, outcomes differed in which LAMP-PRA group had a statistically significant shorter mean operative time (84.13 ± 41.47 min versus 116.84 ± 33.17 min; P=0.038, time of first oral intake (1.00 ± 0.00 days versus 1.21 ± 0.42 days; P=0.042, and length of hospitalization (2.17 ± 0.389 days versus 3.68 ± 1.38 days; P≤0.001, whereas in left-sided adrenalectomies LAMP-TPA had a statistically significant shorter mean operative time (83.85 ± 27.72 min versus 110.95 ± 29.31 min; P=0.002. Conclusions. We report that LAMP-PRA is more appropriate for right-sided laparoscopic adrenalectomies due to anatomical characteristics and better surgical outcomes. For left-sided laparoscopic adrenalectomies, however, we propose LAMP-TPA as a more suitable method.

A comparison of 454 sequencing and clonal sequencing for the characterization of hepatitis C virus NS3 variants

NARCIS (Netherlands)

Ho, Cynthia K. Y.; Welkers, Matthijs R. A.; Thomas, Xiomara V.; Sullivan, James C.; Kieffer, Tara L.; Reesink, Henk W.; Rebers, Sjoerd P. H.; de Jong, Menno D.; Schinkel, Janke; Molenkamp, Richard

2015-01-01

We compared 454 amplicon sequencing with clonal sequencing for the characterization of intra-host hepatitis C virus (HCV) NS3 variants. Clonal and 454 sequences were obtained from 12 patients enrolled in a clinical phase I study for telaprevir, an NS3-4a protease inhibitor. Thirty-nine datasets were

COMPARATIVE STUDY OF HEALTH STATUS BETWEEN COUNTRIES ALONG THE NEW SILK ROAD

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Ju’e Yan

2016-04-01

Full Text Available Using World Statistics Data from the year 2012, health status differences between countries along the “New Silk Road” were compared and analyzed. Life expectancy at birth, life expectancy at age 60, healthy life expectancy, neonatal mortality rate, infant mortality rate, under-five mortality rate, maternal mortality ratio, as well as certain disease incidence rates were used. The study indicated that the 12 countries along the New Silk Road had longer life expectancy at birth. Females had longer life expectancy at birth than males, but life expectancy at age 60 was shorter than the global average, and healthy life expectancy at birth was also shorter. Maternal health status was generally good in each country. China, Russia, and 4 other countries had better children’s health status than India, Tajikistan, Pakistan, and Afghanistan. Non-communicable diseases caused higher mortality than communicable diseases and accidental injuries. However, the age standardized mortality rates of communicable diseases in India, Tajikistan, Pakistan, and Afghanistan were still relatively high. Communicable diseases were also the leading cause of reduction in life expectancy. Tuberculosis had a more significant impact on health status. In conclusion, health status varies among the New Silk Road countries. Countries including China and Iran have relatively better health status, and non communicable diseases were the predominant risk factor impacting health. However, in countries such as India and Afghanistan, mortality caused by communicable diseases is still prominent. Under the current trend of globalization, New Silk Road countries are supposed to collaborate to expand their healthcare systems, and improve the health conditions for their people.

Comparison of different real-time PCR chemistries and their suitability for detection and quantification of genetically modified organisms

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Žel Jana

2008-03-01

Full Text Available Abstract Background The real-time polymerase chain reaction is currently the method of choice for quantifying nucleic acids in different DNA based quantification applications. It is widely used also for detecting and quantifying genetically modified components in food and feed, predominantly employing TaqMan® and SYBR® Green real-time PCR chemistries. In our study four alternative chemistries: Lux™, Plexor™, Cycling Probe Technology and LNA® were extensively evaluated and compared using TaqMan® chemistry as a reference system. Results Amplicons were designed on the maize invertase gene and the 5'-junction of inserted transgene and plant genomic DNA in MON 810 event. Real-time assays were subsequently compared for their efficiency in PCR amplification, limits of detection and quantification, repeatability and accuracy to test the performance of the assays. Additionally, the specificity of established assays was checked on various transgenic and non-transgenic plant species. The overall applicability of the designed assays was evaluated, adding practicability and costs issues to the performance characteristics. Conclusion Although none of the chemistries significantly outperformed the others, there are certain characteristics that suggest that LNA® technology is an alternative to TaqMan® when designing assays for quantitative analysis. Because LNA® probes are much shorter they might be especially appropriate when high specificity is required and where the design of a common TaqMan® probe is difficult or even impossible due to sequence characteristics. Plexor™ on the other hand might be a method of choice for qualitative analysis when sensitivity, low cost and simplicity of use prevail.

Comparative bio-ecological studies among two species of Urentius lace bugs (Hemiptera: Tingidae in Sudan

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Abdalla Abdelrahim Satti

2012-06-01

Full Text Available Among the prevalent lace bugs in Sudan, Urentius hystricellus and Urentius euonymus are important pests of eggplant and pigeon pea, respectively. They attack alternative hosts, but some plants were reported as common hosts for both species. In fact, the identity of these pests and their actual host plants seems to be confusing. Therefore, the main objectives of this work were to; differentiate between such pest species based on certain morpho-biological investigations, verify their hosts’ ranges and study their intra-host distributions and seasonal trends through field surveys and experiments. The results showed clear morphological and biological differences among the two lace bug species. The durations of pre-imaginal stages of U. hystricellus were shorter than those of U. euonymus, while each pest took shorter durations in autumn as compared with winter season. Each pest has its own host range, and no shared hosts were detected, as believed. Hence, the mistaken hosts were corrected and new hosts were added. Such new records included Solanum incanum for U. hystricellus, and two hosts (Chrozophora plicata and Rhynchosia memnonia for U. euonymus. Counts of insects on either leaf sides have revealed variable distributions in different hosts. The seasonal trends of the two pests showed peak populations during autumn and summer seasons. In conclusion, the study made clear distinctions between U. hystricellus and U. euonymus, and gave supportive findings for ecological management.

Ship Lock Control System Optimization using GA, PSO and ABC: A Comparative Review

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Željko Kanović

2014-02-01

Full Text Available This paper presents the comparison of some well-known global optimization techniques in optimization of an expert system controlling a ship locking process. The purpose of the comparison is to find the best algorithm for optimization of membership function parameters of fuzzy expert system for the ship lock control. Optimization was conducted in order to achieve better results in local distribution of ship arrivals, i.e. shorter waiting times for ships and less empty lockages. Particle swarm optimization, artificial bee colony optimization and genetic algorithm were compared. The results shown in this paper confirmed that all these procedures show similar results and provide overall improvement of ship lock operation performance, which speaks in favour of their application in similar transportation problem optimization.

Illumina MiSeq Phylogenetic Amplicon Sequencing Shows a Large Reduction of an Uncharacterised Succinivibrionaceae and an Increase of the Methanobrevibacter gottschalkii Clade in Feed Restricted Cattle.

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Matthew Sean McCabe

Full Text Available Periodic feed restriction is used in cattle production to reduce feed costs. When normal feed levels are resumed, cattle catch up to a normal weight by an acceleration of normal growth rate, known as compensatory growth, which is not yet fully understood. Illumina Miseq Phylogenetic marker amplicon sequencing of DNA extracted from rumen contents of 55 bulls showed that restriction of feed (70% concentrate, 30% grass silage for 125 days, to levels that caused a 60% reduction of growth rate, resulted in a large increase of relative abundance of Methanobrevibacter gottschalkii clade (designated as OTU-M7, and a large reduction of an uncharacterised Succinivibrionaceae species (designated as OTU-S3004. There was a strong negative Spearman correlation (ρ = -0.72, P = <1x10(-20 between relative abundances of OTU-3004 and OTU-M7 in the liquid rumen fraction. There was also a significant increase in acetate:propionate ratio (A:P in feed restricted animals that showed a negative Spearman correlation (ρ = -0.69, P = <1x10(-20 with the relative abundance of OTU-S3004 in the rumen liquid fraction but not the solid fraction, and a strong positive Spearman correlation with OTU-M7 in the rumen liquid (ρ = 0.74, P = <1x10(-20 and solid (ρ = 0.69, P = <1x10(-20 fractions. Reduced A:P ratios in the rumen are associated with increased feed efficiency and reduced production of methane which has a global warming potential (GWP 100 years of 28. Succinivibrionaceae growth in the rumen was previously suggested to reduce methane emissions as some members of this family utilise hydrogen, which is also utilised by methanogens for methanogenesis, to generate succinate which is converted to propionate. Relative abundance of OTU-S3004 showed a positive Spearman correlation with propionate (ρ = 0.41, P = <0.01 but not acetate in the liquid rumen fraction.

Impact of Dose Reductions, Delays Between Chemotherapy Cycles, and/or Shorter Courses of Adjuvant Chemotherapy in Stage II and III Colorectal Cancer Patients: a Single-Center Retrospective Study.

Science.gov (United States)

Sgouros, Joseph; Aravantinos, Gerasimos; Kouvatseas, George; Rapti, Anna; Stamoulis, George; Bisvikis, Anastasios; Res, Helen; Samantas, Epameinondas

2015-12-01

Most stage II or III colorectal cancer patients are receiving nowadays a 4 to 6-month course of adjuvant chemotherapy. However, delays between cycles, reductions in the doses of chemotherapy drugs, or even permanent omissions of chemotherapy cycles might take place due to side effects or patient's preference. We examined the impact of these treatment modifications on recurrence-free survival (RFS) and overall survival (OS). We retrospectively collected data from colorectal cancer patients who had received adjuvant chemotherapy in our Department. Patients were categorized in five groups based on whether they had or not delays between chemotherapy cycles, dose reductions, and permanent omissions of chemotherapy cycles. Three-year RFS and OS of the five different groups were compared using the log-rank test and the Sidak approach. Five hundred and eight patients received treatment. Twenty seven percent of the patients had the full course of chemotherapy; the others had delays, dose reductions, or early termination of the treatment. No statistically significant differences were observed in 3-year RFS and OS between the five groups. A trend for worse RFS was noticed with early termination of treatment. A similar trend was also noticed for OS but only for stage II patients. In colorectal cancer patients, receiving adjuvant chemotherapy, delays between chemotherapy cycles, dose reductions of chemotherapy drugs, or even early termination of the treatment course do not seem to have a negative impact in 3-year RFS and OS; however, due to the trend of worse RFS in patients receiving shorter courses of chemotherapy, further studies are needed.

Comparative Study between Standard and Totally Tubeless Percutaneous Nephrolithotomy.

Science.gov (United States)

Yun, Sung Il; Lee, Yoon Hyung; Kim, Jae Soo; Cho, Sung Ryong; Kim, Bum Soo; Kwon, Joon Beom

2012-11-01

Several recent studies have reported the benefits of tubeless percutaneous nephrolithotomy (PNL). Postoperatively, tubeless PNL patients have an indwelling ureteral stent placed, which is often associated with stent-related morbidity. We have performed totally tubeless (tubeless and stentless) PNL in which no nephrostomy tube or ureteral stent is placed postoperatively. We evaluated the safety, effectiveness, and feasibility of totally tubeless PNL. From March 2008 to February 2012, 57 selected patients underwent standard or totally tubeless PNL. Neither a nephrostomy tube nor a ureteral stent was placed in the totally tubeless PNL group. We compared patient and stone characteristics, operation time, length of hospitalization, analgesia requirements, stone-free rate, blood loss, change in creatinine, and perioperative complications between the standard and totally tubeless PNL groups. There were no significant differences in preoperative patient characteristics, postoperative complications, or the stone-free rate between the two groups, but the totally tubeless PNL group showed a shorter hospitalization and a lesser analgesic requirement compared with the standard PNL group. Blood loss and change in creatinine were not significantly different between the two groups. Totally tubeless PNL appears to be a safe and effective alternative for the management of renal stone patients and is associated with a decrease in length of hospital stay.

Evolution of the DAZ gene and the AZFc region on primate Y chromosomes

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Yu Jane-Fang

2008-03-01

Full Text Available Abstract Background The Azoospermia Factor c (AZFc region of the human Y chromosome is a unique product of segmental duplication. It consists almost entirely of very long amplicons, represented by different colors, and is frequently deleted in subfertile men. Most of the AZFc amplicons have high sequence similarity with autosomal segments, indicating recent duplication and transposition to the Y chromosome. The Deleted in Azoospermia (DAZ gene within the red-amplicon arose from an ancestral autosomal DAZ-like (DAZL gene. It varies significantly between different men regarding to its copy number and the numbers of RNA recognition motif and DAZ repeat it encodes. We used Southern analyses to study the evolution of DAZ and AZFc amplicons on the Y chromosomes of primates. Results The Old World monkey rhesus macaque has only one DAZ gene. In contrast, the great apes have multiple copies of DAZ, ranging from 2 copies in bonobos and gorillas to at least 6 copies in orangutans, and these DAZ genes have polymorphic structures similar to those of their human counterparts. Sequences homologous to the various AZFc amplicons are present on the Y chromosomes of some but not all primates, indicating that they arrived on the Y chromosome at different times during primate evolution. Conclusion The duplication and transposition of AZFc amplicons to the human Y chromosome occurred in three waves, i.e., after the branching of the New World monkey, the gorilla, and the chimpanzee/bonobo lineages, respectively. The red-amplicon, one of the first to arrive on the Y chromosome, amplified by inverted duplication followed by direct duplication after the separation of the Old World monkey and the great ape lineages. Subsequent duplication/deletion in the various lineages gave rise to a spectrum of DAZ gene structure and copy number found in today's great apes.

Psoralen-mediated virus photoinactivation in platelet concentrates: enhanced specificity of virus kill in the absence of shorter UVA wavelengths

International Nuclear Information System (INIS)

Margolis-Nunno, Henrietta; Robinson, Richard; Horowitz, Bernard; Ben-Hur, Ehud; Geacintov, N.E.

1995-01-01

Treatments with psoralens and long-wavelength ultraviolet radiation (UVA, 320-400 nm; PUVA) have shown efficacy for virus sterilization of platelet concentrates (PC). We have employed the psoralen derivative 4'-aminomethyl-4,5',8-trimethylpsoralen (AMT), and have found that platelet integrity is best preserved when rutin, a flavonoid that quenches multiple reactive oxygen species, is present during AMT/UVA treatment of PC. In this report, we examine the effects of different UVA spectra under our standard PC treatment conditions (i.e. 50 μg/mL AMT, 0.35 mM rutin and 38 J/cm 2 UVA). Added vesicular stomatitis virus (VSV; ≥ 5.5 log 10 ) was completely inactivated with the simultaneous maintenance of the platelet aggregation response (> 90% of control) when a UVA light source with transmission mainly between 360 and 370 nm (narrow UVA1) was used. In contrast, with a broad-band UVA (320-400 nm; broad UVA) light source, the aggregation response was greatly compromised (< 50% of control) with only a minor increase in the rate of VSV kill. With this lamp, platelet function could be improved to about 75% of the control by adding a long-pass filter, which reduced the transmission of shorter (≤ 345 nm) UVA wavelengths (340-400 nm; UVA1). At equivalent levels of virus kill, aggregation function was always best preserved when narrow UVA1 was used for PUVA treatment. Even in the absence of AMT, and with or without rutin present, narrow UVA1 irradiation was better tolerated by platelets than was broad UVA. (author)

CHAPTER 1

African Journals Online (AJOL)

Dr Olaleye

The amplicons were sequenced and subjected to basic local alignment search tool ... Out of the 12 amplicons in agarose gel, there were 6 sharp and 6 faint bands .... A: Consensus sequence with (-) and (*) signs representing gaps and points ...

Midterm Clinical and First Reproductive Results of a Randomized Controlled Trial Comparing Uterine Fibroid Embolization and Myomectomy

International Nuclear Information System (INIS)

Mara, Michal; Maskova, Jana; Fucikova, Zuzana; Kuzel, David; Belsan, Tomas; Sosna, Ondrej

2008-01-01

The purpose of this study was to compare the midterm results of a radiological and surgical approach to uterine fibroids. One hundred twenty-one women with reproductive plans who presented with an intramural fibroid(s) larger than 4 cm were randomly selected for either uterine artery embolization (UAE) or myomectomy. We compared the efficacy and safety of the two procedures and their impact on patient fertility. Fifty-eight embolizations and 63 myomectomies (42 laparoscopic, 21 open) were performed. One hundred eighteen patients have finished at least a 12-month follow-up; the mean follow-up in the entire study population was 24.9 months. Embolized patients underwent a significantly shorter procedure and required a shorter hospital stay and recovery period. They also presented with a lower CRP concentration on the second day after the procedure (p < 0.0001 for all parameters). There were no significant differences between the two groups in the rate of technical success, symptomatic effectiveness, postprocedural follicle stimulating hormone levels, number of reinterventions for fibroid recurrence or regrowth, or complication rates. Forty women after myomectomy and 26 after UAE have tried to conceive, and of these we registered 50 gestations in 45 women. There were more pregnancies (33) and labors (19) and fewer abortions (6) after surgery than after embolization (17 pregnancies, 5 labors, 9 abortions) (p < 0.05). Obstetrical and perinatal results were similar in both groups, possibly due to the low number of labors after UAE to date. We conclude that UAE is less invasive and as symptomatically effective and safe as myomectomy, but myomectomy appears to have superior reproductive outcomes in the first 2 years after treatment

Operative treatment of acute acromioclavicular dislocations Rockwood III and V-Comparative study between K-wires combined with FiberTape(®) vs. TightRope System(®).

Science.gov (United States)

Vrgoč, G; Japjec, M; Jurina, P; Gulan, G; Janković, S; Šebečić, B; Starešinić, M

2015-11-01

Acromioclavicular (AC) joint dislocations usually occur in a young active population as a result of a fall on the shoulder. Rockwood divided these dislocations into six types. Optimal treatment is still a matter of discussion. Many operative techniques have been developed, but the main choice is between open and minimally-invasive arthroscopic procedures. The aim of this study was to compare two different surgical methods on two groups of patients to find out which method is superior in terms of benefit to the patient. The methods were evaluated through objective and subjective scores, with a focus on complications and material costs. A retrospective two-centre study was conducted in patients with acute AC joint dislocation Rockwood types III and V. The two methods conducted were an open procedure using K-wires combined with FiberTape(®) (Arthrex, Naples, USA) (Group 1) and an arthroscopic procedure using the TightRope System(®) (Arthrex, Naples, USA) (Group 2). Groups underwent procedures during a two-year period. Diagnosis was based on the clinical and radiographic examination of both AC joints. Surgical treatment and rehabilitation were performed. Sixteen patients were included in this study: Group 1 comprised 10 patients, all male, average age 41.6 years (range 17-64 years), Rockwood type III (eight patients) and Rockwood type V (two patients); Group 2 had six patients, one female and five male, average age 37.8 years (range 18-58 years), Rockwood type III (two patients) and Rockwood type V (four patients). Time from injury to surgery was shorter and patients needed less time to return to daily activities in Group 1. Duration of the surgical procedure was shorter in Group 2 compared with Group 1. Complications of each method were noted. According to the measured scores and operative outcome between dislocation Rockwood type III and V, no significant difference was found. Implant material used in Group 2 was 4.7 times more expensive than that used in Group 1

25G compared with 20G vitrectomy under Resight non-contact wide-angle lenses for Terson syndrome.

Science.gov (United States)

Mao, Xinbang; You, Zhipeng

2017-08-01

The aim of the present study was to compare the effectiveness of 25G vitrectomy to standard 20G vitrectomy for treatment of Terson syndrome under Resight non-contact wide-angle lenses. This was a case-control study of 20 patients with Terson syndrome (study group) that underwent 25G vitrectomy under Resight non-contact wide-angle lenses, with those of 20 matched patients that underwent 20G vitrectomy (control group). Medical records were reviewed from between July 2011 and October 2013. Data included results of the Early Treatment Diabetic Retinopathy Study examination, ophthalmology B-scan ultrasonography and fundus photography. The mean age, follow-up time, the preoperative visual acuity of LogMAR and the preoperative intraocular pressure (IOP) were all comparable in the two groups (all P>0.05). There were statistically significant differences in postoperative visual acuity of LogMAR compared with preoperative visual acuity (Pcontact wide-angle lenses can achieve a significantly shorter operative time and lower post-operative IOP compared with 20G Vitrectomy.

Comparing Part-time Employment in Germany, Sweden, Ireland and the Netherland

DEFF Research Database (Denmark)

Bekker, Sonja; Hipp, Lena; Leschke, Janine

2017-01-01

In the current discussions on combining work and family, the idea of shorter working hours is becoming ever more popular. However, much of the research on part-time employment has looked at women and mothers in particular. Much less is known about part-time work among men or fathers. Therefore......, this paper aims to establish the differences and similarities between men and women and particularly between mothers and fathers in their choices to work parttime, taking into account different household contexts and welfare state institutions. By analysing part-time work in Germany, Sweden, Ireland...... and the Netherlands in 2014 using individual level data from the European Labour Force Survey, we show that for men a lower earning capacity compared to their partner or family responsibilities do not seem to lead to higher part-time shares. This is the opposite of what we find for women. According to our analysis...

Bilateral Breast Reduction Without Opioid Analgesics: A Comparative Study.

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Parsa, Fereydoun Don; Cheng, Justin; Stephan, Brad; Castel, Nikki; Kim, Leslie; Murariu, Daniel; Parsa, Alan A

2017-09-01

Breast reduction has traditionally been performed under general anesthesia with adjunct opioid use. However, opioids are associated with a wide variety of adverse effects, including nausea, vomiting, constipation, postoperative sedation, dizziness, and addiction. This study compares bilateral breast reduction using a multimodal opioid-free pain management regimen vs traditional general anesthesia with adjunct opioids. A total of 83 female patients were enrolled in this study. Group 1 includes a retrospective series of 39 patients that underwent breast reduction via general anesthesia with adjunct opioid use. This series was compared to 2 prospective groups of patients who did not receive opioids either preoperatively or intraoperatively. In group 2, twenty-six patients underwent surgery under intravenous sedation and local anesthesia. In group 3, eighteen patients underwent surgery with general anesthesia. All patients in groups 2 and 3 received preoperative gabapentin and celecoxib along with infiltration of local anesthetics during the operation and prior to discharge to the Post-Anesthesia Care Unit (PACU). Primary outcome measures included the duration of surgery, time from end of operation to discharge home, postoperative opioid and antiemetic use, and unplanned postoperative hospitalizations. When compared to group 1, groups 2 and 3 experienced a shorter time from end of operation to discharge home (P opioid use (P opioid-free bilateral breast reduction either under local or general anesthesia as an outpatient. This method resulted in significantly less morbidity, use of opioids postoperatively, as well as unplanned hospital admissions compared to "traditional" breast reduction under general anesthesia with the use of opioids. 3. © 2017 The American Society for Aesthetic Plastic Surgery, Inc. Reprints and permission: journals.permissions@oup.com

A comparative study of contractility of the heart ventricle in some ectothermic vertebrates

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Sergey Kharin

2009-07-01

Full Text Available The purpose of this study was to analyze contractility of the heart ventricle in selected reptilian and amphibian species having the same ventricular excitation pattern. Systolic time intervals and indices of contractility of the heart ventricle were measured in anaesthetized frogs, snakes, and tortoises by use of polycardiography. The electromechanical delay was significantly shorter in tortoises compared with the other two species. The isovolumetric contraction time in frogs was approximately twofold longer than in reptiles. The pre-ejection period was the longest in frogs and the shortest in tortoises, whereas snakes were intermediate. The ejection time was slightly longer in tortoises compared with the other two species. The greatest isovolumetric contraction index and the smallest myocardial tension index corresponded to the frog and tortoise heart ventricle, respectively. The intrasystolic index in tortoises was significantly greater than in frogs, whereas quite similar to that in snakes. The frog ventricle had lower contractility compared with the reptilian one. Although ventricular contractility tended to be lower in snakes compared with tortoises, this difference was not statistically significant. Possible causes for these differences are discussed. We suppose a large variety in ventricular contractility among amphibian and reptilian species having the same ventricular activation pattern. This variety may be conditioned by heart anatomy, intracardiac shunting, lifestyles, and habitats. It can only be hypothesized that on the average, ventricular contractility is higher in reptiles compared with amphibians and in chelonians compared with snakes.

DNA Extraction and Primer Selection

DEFF Research Database (Denmark)

Karst, Søren Michael; Nielsen, Per Halkjær; Albertsen, Mads

Talk regarding pitfalls in DNA extraction and 16S amplicon primer choice when performing community analysis of complex microbial communities. The talk was a part of Workshop 2 "Principles, Potential, and Limitations of Novel Molecular Methods in Water Engineering; from Amplicon Sequencing to -omics...

Premature infants display increased noxious-evoked neuronal activity in the brain compared to healthy age-matched term-born infants.

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Slater, Rebeccah; Fabrizi, Lorenzo; Worley, Alan; Meek, Judith; Boyd, Stewart; Fitzgerald, Maria

2010-08-15

This study demonstrates that infants who are born prematurely and who have experienced at least 40days of intensive or special care have increased brain neuronal responses to noxious stimuli compared to healthy newborns at the same postmenstrual age. We have measured evoked potentials generated by noxious clinically-essential heel lances in infants born at term (8 infants; born 37-40weeks) and in infants born prematurely (7 infants; born 24-32weeks) who had reached the same postmenstrual age (mean age at time of heel lance 39.2+/-1.2weeks). These noxious-evoked potentials are clearly distinguishable from shorter latency potentials evoked by non-noxious tactile sensory stimulation. While the shorter latency touch potentials are not dependent on the age of the infant at birth, the noxious-evoked potentials are significantly larger in prematurely-born infants. This enhancement is not associated with specific brain lesions but reflects a functional change in pain processing in the brain that is likely to underlie previously reported changes in pain sensitivity in older ex-preterm children. Our ability to quantify and measure experience-dependent changes in infant cortical pain processing will allow us to develop a more rational approach to pain management in neonatal intensive care. Copyright (c) 2010 Elsevier Inc. All rights reserved.

Rapid discrimination of Isaria javanica and Isaria poprawskii from Isaria spp. using high resolution DNA melting assays

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The current study evaluates the potential of using high resolution DNA melting assays to discriminate species in the genus, Isaria. The study utilizes a previously identified 103 base pair PCR amplicon, which was reported to be selective for Isaria fumosorosea. Our study finds the amplicon selective...

Direct amplification, sequencing and profiling of Chlamydia trachomatis strains in single and mixed infection clinical samples.

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Sandeep J Joseph

Full Text Available Sequencing bacterial genomes from DNA isolated directly from clinical samples offers the promise of rapid and precise acquisition of informative genetic information. In the case of Chlamydia trachomatis, direct sequencing is particularly desirable because it obviates the requirement for culture in mammalian cells, saving time, cost and the possibility of missing low abundance strains. In this proof of concept study, we developed methodology that would allow genome-scale direct sequencing, using a multiplexed microdroplet PCR enrichment technology to amplify a 100 kb region of the C. trachomatis genome with 500 1.1-1.3 kb overlapping amplicons (5-fold amplicon redundancy. We integrated comparative genomic data into a pipeline to preferentially select conserved sites for amplicon design. The 100 kb target region could be amplified from clinical samples, including remnants from diagnostics tests, originating from the cervix, urethra and urine, For rapid analysis of these data, we developed a framework for whole-genome based genotyping called binstrain. We used binstrain to estimate the proportion of SNPs originating from 14 C. trachomatis reference serotype genomes in each sample. Direct DNA sequencing methods such as the one described here may have an important role in understanding the biology of C. trachomatis mixed infections and the natural genetic variation of the species within clinically relevant ecological niches.

Nitrogen Cycle Evaluation (NiCE) Chip for the Simultaneous Analysis of Multiple N-Cycle Associated Genes.

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Oshiki, Mamoru; Segawa, Takahiro; Ishii, Satoshi

2018-02-02

Various microorganisms play key roles in the Nitrogen (N) cycle. Quantitative PCR (qPCR) and PCR-amplicon sequencing of the N cycle functional genes allow us to analyze the abundance and diversity of microbes responsible in the N transforming reactions in various environmental samples. However, analysis of multiple target genes can be cumbersome and expensive. PCR-independent analysis, such as metagenomics and metatranscriptomics, is useful but expensive especially when we analyze multiple samples and try to detect N cycle functional genes present at relatively low abundance. Here, we present the application of microfluidic qPCR chip technology to simultaneously quantify and prepare amplicon sequence libraries for multiple N cycle functional genes as well as taxon-specific 16S rRNA gene markers for many samples. This approach, named as N cycle evaluation (NiCE) chip, was evaluated by using DNA from pure and artificially mixed bacterial cultures and by comparing the results with those obtained by conventional qPCR and amplicon sequencing methods. Quantitative results obtained by the NiCE chip were comparable to those obtained by conventional qPCR. In addition, the NiCE chip was successfully applied to examine abundance and diversity of N cycle functional genes in wastewater samples. Although non-specific amplification was detected on the NiCE chip, this could be overcome by optimizing the primer sequences in the future. As the NiCE chip can provide high-throughput format to quantify and prepare sequence libraries for multiple N cycle functional genes, this tool should advance our ability to explore N cycling in various samples. Importance. We report a novel approach, namely Nitrogen Cycle Evaluation (NiCE) chip by using microfluidic qPCR chip technology. By sequencing the amplicons recovered from the NiCE chip, we can assess diversities of the N cycle functional genes. The NiCE chip technology is applicable to analyze the temporal dynamics of the N cycle gene

ATLAS: Adjuvant Tamoxifen Longer Against Shorter

Science.gov (United States)

1998-09-01

largely tunaffected by other these 30 000 women during about 10 years of follow-up patient characteristics or treatments. were 21% (SD 3), 29% (SD 2...for both types of mosted to stop part of the eduon y epatient . most of them did stop, part of the reduction in the The right side of figure 4...patient characteristics (e.g. high/ low-risk, ER+/ER-, pre/post-menopausal) recorded at entry. Other trials of tamoxifen duration The Atlas collaboration

Movement and touch make plants shorter

NARCIS (Netherlands)

Heuvelink, E.; Kierkels, T.

2017-01-01

Plants in the greenhouse are increasingly on the move. More attention is being paid to air circulation and mobile cultivation is on the rise. Research shows that movement and touch (also as plants rub against each other) slow down growth. That can be frustrating but you can also use it to your

Sterol 27-Hydroxylase Polymorphism Significantly Associates With Shorter Telomere, Higher Cardiovascular and Type-2 Diabetes Risk in Obese Subjects

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Sofia Pavanello

2018-06-01

Full Text Available Background/objectivesThe pathologic relationship linking obesity and lipid dismetabolism with earlier onset of aging-related disorders, including cardiovascular disease (CVD and type-2 diabetes (T2D, is not fully elucidate. Chronic inflammatory state, in obese individuals, may accelerate cellular aging. However, leukocyte telomere length (LTL, the cellular biological aging indicator, is elusively linked with obesity. Recent studies indicate that sterol 27-hydroxylase (CYP27A1 is an emerging antiatherogenic enzyme, that, by converting extrahepatic cholesterol to 27-hydroxycholesterol, facilitates cholesterol removal via high-density lipoprotein-cholesterol (HDL-C. We tested the hypothesis that obese subjects who carry at least three copies of CYP27A1 low-hydroxylation (LH activity genome-wide-validated alleles (rs4674345A, rs1554622A, and rs4674338G present premature aging, as reflected in shorter LTL and higher levels of CVD/T2D risk factors, including reduced HDL-C.Subjects/methodsObese subjects from SPHERE project {n = 1,457; overweight [body mass index (BMI 25–30 kg/m2] 65.8% and severe-obese (BMI > 30 kg/m2 34.2%} were characterized for the presence from 0 to 6 LH-CYP27A1 allele copy number. Univariate and multivariable sex–age–smoking-adjusted linear-regression models were performed to compare CVD/T2D risk factors and biological aging (LTL in relation to the combined BMI-LH groups: overweight-LH: 0–2, overweight-LH: 3–6, severe-obese-LH: 0–2, and severe-obese-LH: 3–6.ResultsHigher LTL attrition was found in severe-obese than overweight individuals (p < 0.001. Multivariable model reveals that among severe-obese patients those with LH: 3–6 present higher LTL attrition than LH: 0–2 (p < 0.05. Univariate and multivariable models remarkably show that insulin resistance is higher both in overweight-LH: 3–6 vs overweight-LH: 0–2 (p < 0.001 and in severe-obese-LH: 3–6 vs severe-obese-LH: 0–2 (p�

A comparative analysis of conventional and SurePath liquid-based cervicovaginal cytology: A study of 140 cases

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Jyotsna Sharma

2016-01-01

Full Text Available Background: The role of Papanicolaou (Pap test in cervical cancer screening need not be overemphasized. While most Western countries have adopted the liquid-based cytology (LBC, which is considered superior, many developing countries are still using the conventional Pap smear (CPS technique. Objective: To compare the staining and cytomorphological features on conventional versus liquid-based cervicovaginal smears. Materials and Methods: One hundred and forty cervicovaginal smears prepared by the standard conventional and LBC techniques were interpreted as per the Bethesda system of reporting cervicovaginal smears. Twelve parameters were studied, compared, and statistically analyzed. A P value <0.05 was considered to be statistically significant. Results: 129/140 (92% of CPSs and 130/140 (93% LBC smears were satisfactory. LBC had a significantly shorter screening time (2.0 ± 0.08 vs 4.0 ± 0.65 and better representative material than that of CPS (50% vs 42%. Neutrophils were significantly more in CPS than LBC (96% vs 92% with a P value <0.05 while hemorrhagic background and red blood cells (RBCs were more prominent in CPS. LBC showed significant artifactual changes in squamous epithelial cells. Epithelial abnormalities ranging from atypical squamous cells of undetermined significance (ASCUS to high grade squamous intraepithelial lesion (HSIL were seen in 3% (4 and 2% (2 of CPSs and LBCs, respectively. Organisms were better picked up in CPS (99% in CPS vs 73% LBC with a value of P = 0.0001. Conclusion: Although a shorter screening time and cleaner background are the major advantages of LBC, CPS is not inferior to LBC. Considering the high cost, rather than the advantages associated with LBC, we feel that CPS is a better option for developing countries.

Prospective clinical study comparing intraligamentary anesthesia and inferior alveolar nerve block for extraction of posterior mandibular teeth.

Science.gov (United States)

Kämmerer, P W; Adubae, A; Buttchereit, I; Thiem, D G E; Daubländer, M; Frerich, B

2018-04-01

The aim of the study was to compare the efficacy of intraligamentary anesthesia (ILA) with conventional inferior alveolar nerve block (IANB) for extraction of mandibular posterior teeth. In a prospective clinical trial, a total of 301 mandibular posterior teeth were extracted in 266 patients. Randomization was conducted into those who received ILA (patients n = 98; teeth n = 105) and those who received IANB (patient n = 140; teeth n = 140). Twenty-eight patients were subjected to bilateral mandibular dental extractions and received both ILA und IANB (teeth n = 56 (ILA n = 28; IANB n = 28)). The primary objective was to evaluate the differences in pain during injection, in pain during tooth extraction (numeric rating scale (NRS)), and in anesthetic quality (complete/sufficient vs. insufficient/no effect). Differences in latency time, amount of anesthetic solution, need for second injection, and duration of local numbness as well as in the incidence of dry socket were assessed. ILA had significant lower pain of injection (p < 0.001), shorter latency time (p < 0.001), and shorter duration of local numbness (p < 0.001) and required lesser amount of local anesthetic solution (p < 0.001) together with a similar anesthetic quality (p = 0.082) compared to IANB. Concerning pain during extraction (p = 0.211), frequency of second injection (p = 0.197), and incidence of dry socket (p = 0.178), no significant differences were detected. ILA fulfills the requirements of a minimal invasive and patient-friendly local anesthetic technique. In accordance, it represents a safe and reliable alternative to IANB for extraction of mandibular posterior teeth. ILA can be recommended for routine dental extractions.

Integrity of nuclear genomic deoxyribonucleic acid in cooked meat: Implications for food traceability.

Science.gov (United States)

Aslan, O; Hamill, R M; Sweeney, T; Reardon, W; Mullen, A M

2009-01-01

It is essential to isolate high-quality DNA from muscle tissue for PCR-based applications in traceability of animal origin. We wished to examine the impact of cooking meat to a range of core temperatures on the quality and quantity of subsequently isolated genomic (specifically, nuclear) DNA. Triplicate steak samples were cooked in a water bath (100 degrees C) until their final internal temperature was 75, 80, 85, 90, 95, or 100 degrees C, and DNA was extracted. Deoxyribonucleic acid quantity was significantly reduced in cooked meat samples compared with raw (6.5 vs. 56.6 ng/microL; P 800 bp) were observed only when using DNA from raw meat and steak cooked to lower core temperatures. Small amplicons (food authentication, it is less abundant, and results suggest that analyses should be designed to use small amplicon sizes for meat cooked to high core temperatures.

Testing genotyping strategies for ultra-deep sequencing of a co-amplifying gene family: MHC class I in a passerine bird.

Science.gov (United States)

Biedrzycka, Aleksandra; Sebastian, Alvaro; Migalska, Magdalena; Westerdahl, Helena; Radwan, Jacek

2017-07-01

Characterization of highly duplicated genes, such as genes of the major histocompatibility complex (MHC), where multiple loci often co-amplify, has until recently been hindered by insufficient read depths per amplicon. Here, we used ultra-deep Illumina sequencing to resolve genotypes at exon 3 of MHC class I genes in the sedge warbler (Acrocephalus schoenobaenus). We sequenced 24 individuals in two replicates and used this data, as well as a simulated data set, to test the effect of amplicon coverage (range: 500-20 000 reads per amplicon) on the repeatability of genotyping using four different genotyping approaches. A third replicate employed unique barcoding to assess the extent of tag jumping, that is swapping of individual tag identifiers, which may confound genotyping. The reliability of MHC genotyping increased with coverage and approached or exceeded 90% within-method repeatability of allele calling at coverages of >5000 reads per amplicon. We found generally high agreement between genotyping methods, especially at high coverages. High reliability of the tested genotyping approaches was further supported by our analysis of the simulated data set, although the genotyping approach relying primarily on replication of variants in independent amplicons proved sensitive to repeatable errors. According to the most repeatable genotyping method, the number of co-amplifying variants per individual ranged from 19 to 42. Tag jumping was detectable, but at such low frequencies that it did not affect the reliability of genotyping. We thus demonstrate that gene families with many co-amplifying genes can be reliably genotyped using HTS, provided that there is sufficient per amplicon coverage. © 2016 John Wiley & Sons Ltd.

A Comparative Study of Applying Active-Set and Interior Point Methods in MPC for Controlling Nonlinear pH Process

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Syam Syafiie

2014-06-01

Full Text Available A comparative study of Model Predictive Control (MPC using active-set method and interior point methods is proposed as a control technique for highly non-linear pH process. The process is a strong acid-strong base system. A strong acid of hydrochloric acid (HCl and a strong base of sodium hydroxide (NaOH with the presence of buffer solution sodium bicarbonate (NaHCO3 are used in a neutralization process flowing into reactor. The non-linear pH neutralization model governed in this process is presented by multi-linear models. Performance of both controllers is studied by evaluating its ability of set-point tracking and disturbance-rejection. Besides, the optimization time is compared between these two methods; both MPC shows the similar performance with no overshoot, offset, and oscillation. However, the conventional active-set method gives a shorter control action time for small scale optimization problem compared to MPC using IPM method for pH control.

Bupivacaine compared with etidocaine for vaginal delivery.

Science.gov (United States)

Moore, D C; Bridenbaugh, P O; Bridenbaugh, L D; Thompson, G E; Balfour, R I; Lysons, D F

1975-01-01

A comparison of 0.5 percent etidocaine with 0.25 and 0.5 percent bupivacaine, using continuous (intermittent) caudal block in 60 vaginal deliveries, showed the latter two solutions to be the agents of choice. All solutions contained a final concentration of 1:2000,000 epihephrine. In 40 parturients given either 0.25 or 0.5 percent bupivacaine, all had pain relief after the initial dose, while 5 of 20 given etidocaine required a refill dose within 30 to 50 minutes for complete pain relief. The duration of action of the initial dose with both concentrations of bupivacaine was longer than that of etidocaine. The degree of motor blockade with 0.5 percent etidocaine was greater than with 0.5 percent bupivacaine, and with 0.5 percent concentrations of either etidocaine or bupivacaine was greater than with 0.25 percent bupivacaine. The duration of motor blockade of 0.5 percent etidocaine and bupivacaine was comparable. The duration of motor blockade of the 0.25 percent concentration of bupivacaine was shorter than with the 0.5 percent concentration of both etidocaine and bupivacaine; and with both bupivacaine concentrations the duration of sensory anesthesia in the extremities was longer than motor blockade; with etidocaine, the opposite occurred.

Comparative Analysis between Conventional PI and Fuzzy LogicPI Controllers for Indoor Benzene Concentrations

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Nun Pitalúa-Díaz

2015-05-01

Full Text Available Exposure to hazardous concentrations of volatile organic compounds indoors in small workshops could affect the health of workers, resulting in respirative diseases, severe intoxication or even cancer. Controlling the concentration of volatile organic compounds is required to prevent harmful conditions for workers in indoor environments. In this document, PI and fuzzy PI controllers were used to reduce hazardous indoor air benzene concentrations in small workplaces. The workshop is represented by means of a well-mixed room model. From the knowledge obtained from the model, PI and fuzzy PI controllers were designed and their performances were compared. Both controllers were able to maintain the benzene concentration within secure levels for the workers. The fuzzy PI controller performed more efficiently than the PI controller. Both approaches could be expanded to control multiple extractor fans in order to reduce the air pollution in a shorter time. The results from the comparative analysis showed that implementing a fuzzy logic PI controller is promising for assuring indoor air quality in this kind of hazardous work environment.

Comparative study of oncologic outcomes for laparoscopic vs. open surgery in transverse colon cancer.

Science.gov (United States)

Kim, Woo Ram; Baek, Se Jin; Kim, Chang Woo; Jang, Hyun A; Cho, Min Soo; Bae, Sung Uk; Hur, Hyuk; Min, Byung Soh; Baik, Seung Hyuk; Lee, Kang Young; Kim, Nam Kyu; Sohn, Seung Kuk

2014-01-01

Laparoscopic resection for transverse colon cancer is a technically challenging procedure that has been excluded from various large randomized controlled trials of which the long-term outcomes still need to be verified. The purpose of this study was to evaluate long-term oncologic outcomes for transverse colon cancer patients undergoing laparoscopic colectomy (LAC) or open colectomy (OC). This retrospective review included patients with transverse colon cancer who received a colectomy between January 2006 and December 2010. Short-term and five-year oncologic outcomes were compared between these groups. A total of 131 patients were analyzed in the final study (LAC, 84 patients; OC, 47 patients). There were no significant differences in age, gender, body mass index, tumor location, operative procedure, or blood loss between groups, but the mean operative time in LAC was significantly longer (LAC, 246.8 minutes vs. OC, 213.8 minutes; P = 0.03). Hospital stay was much shorter for LAC than OC (9.1 days vs. 14.5 days, P transverse colon cancer is feasible and safe with comparable short- and long-term outcomes.

Comparative study of intrathecal hyperbaric versus isobaric ropivacaine: A randomized control trial

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Rajni Gupta

2013-01-01

Full Text Available Background: Hyperbaric ropivacaine produce more reliable sensory and motor block, with faster onset, better quality of muscles relaxation than isobaric ropivacaine. So, this study was designed to compare the efficacy of hyperbaric ropivacaine with isobaric ropivacaine in patients undergoing lower abdominal surgery. Methods: A randomized controlled double blind study in two groups of patients. group A (n=35 received 3 ml of isobaric ropivacaine 6 mg/ml (18 mg. Group B (n=35 received 3 ml of hyperbaric ropivacaine 6 mg/ml (18 mg. The onset and duration of sensory block at dermatome level T10, maximum upper and lower spread of sensory block, intensity, and duration of motor block were recorded. Statistical Analysis: Block characteristics were compared using the two-tailed Mann - Whitney U-test. The proportion of side effects was compared using the Chi-square test. Results: The median time of onset of sensory block at the T10 dermatome was 4.4±1.3 min in group B and 6.0±1.03 min in group A. The median time to maximum block height was 16.7±3.7 min in group A and 12.03±1.96 min in group B. The median duration of complete motor recovery (B0 was significantly shorter in the heavy ropivacaine group (166.5±11.7 min compared with the isobaric ropivacaine group (192.9±9.6 min. Conclusions: Intrathecal hyperbaric ropivacaine provides more rapid, adequate, and good quality of sensory and motor block with rapid post-operative recovery as compare to isobaric ropivacaine.

The location of the mandibular canal in prognathic patients compared to subjects with normal occlusion

Energy Technology Data Exchange (ETDEWEB)

Jung, Yun Hoa; Nah, Kyung Soo; Cho, Bong Hae [Pusan National Univ. College of Dentistry, Pusan (Korea, Republic of)

2007-12-15

The purpose of this study was to compare the location of the mandibular canal in Class {iota}{iota}{iota} patients and 26 normal patients were observed. Four measurements were taken on cross sectional tomography between the first and second molars: the distance from the mandibular canal to the inner surface of both the buccal and lingual cortices, the distance from the mandibular canal to the inferior border of the mandible, and the buccolingual width of the mandible. The buccolingual location of the canals was classified as lingual, central, of buccal. Each measurement was analyzed with an independent test to compare Class {iota}{iota}{iota} malocclusion to normal occlusion. Compared to the control group, the prognathic group had a shorter distance from the canal to the inner surface of the lingual cortex and to the base of the mandible. A higher percentage of the canals were located lingually in the prognathic group. This study showed that the mandibular canal was located more lingually and interiorly in prognathic patients than in patients with normal occlusion. These results could help surgeons to reduce injuries to the inferior alveolar nerve.

Comparing ImmunoCard with two EIA assays for Clostridium difficile toxins.

Science.gov (United States)

Chan, Edward L; Seales, Diane; Drum, Hong

2009-01-01

To compare three Clostridium difficile EIA kits for the detection of C. difficile toxins from clinical specimens. A total of 287 fresh and stored stool specimens were tested using all three assays. Stools with discrepant results were sent to a reference laboratory for tissue cytotoxin assay. Trinity Medical Center, a community hospital with network hospitals. Patients with diarrhea submitted stools for detection of C. difficile toxins. Of the 287 stool specimens, 116 were positive and 171 negative for C. difficile toxins. The sensitivity, specificity, and positive and negative predictive values of Meridian EIA assay were 99.1, 97.7, 96.6, and 99.4%; ImmunoCard were 100, 98.2, 97.5, and 100%; BioStar OIA assay were 94, 98.8, 98.2, and 96% respectively. ImmunoCardprovides the best sensitivity (100%) for C. difficile toxins A and B detection. The BioStar OIA rapid test missed seven positive stool specimens possibly due to failure to detect toxin B. ImmunoCard has slightly higher predictive values, shorter turnaround time and greater convenience compared to the Meridian EIA Assay. ImmunoCard may be cost effective not only in smaller laboratories, but also in high volume laboratories, when used on a STAT basis or single request.

Comparative Analysis between Simultaneous Resection and Staged Resection for Synchronous Colorectal Liver Metastases - A Single Center Experience on 300 Consecutive Patients.

Science.gov (United States)

Alexandrescu, Sorin; Diaconescu, Andrei; Ionel, Zenaida; Zlate, Cristian; Grigorie, Răzvan; Hrehoreţ, Doina; Braşoveanu, Vladislav; Dima, Simona; Botea, Florin; Ionescu, Mihnea; Tomescu, Dana; Droc, Gabriela; Fota, Ruxandra; Croitoru, Adina; Gramaticu, Iulia; Buica, Florina; Iacob, Razvan; Gheorghe, Cristian; Herlea, Vlad; Grasu, Mugur; Dumitru, Radu; Boroş, Mirela; Popescu, Irinel

2017-01-01

Introduction: In synchronous colorectal liver metastases (SCLMs), simultaneous resection (SR) of the primary tumor and liver metastases has not gained wide acceptance. Most authors prefer staged resections (SgR), especially in patients presenting rectal cancer or requiring major hepatectomy. Methods: Morbidity, mortality, survival rates and length of hospital stay were compared between the two groups of patients (SR vs. SgR). A subgroup analysis was performed for patients with similar characteristics (e.g. rectal tumor, major hepatectomy, bilobar metastases, metastatic lymph nodes, preoperative chemotherapy). Results: Between 1995 and 2016, SR was performed in 234 patients, while 66 patients underwent SgR. Comparative morbidity (41% vs. 31.8%, respectively, p = 0.1997), mortality (3.8% vs. 3%, respectively, p = 1) and overall survival rates (85.8%, 51.3% and 30% vs. 87%, 49.6% and 22.5%, at 1-, 3- and 5-years, respectively, p = 0.386) were similar between the SR and SgR group. Mean hospital stay was significantly shorter in patients undergoing SR than SgR (15.11 ‚+- 8.60 vs. 19.42 ‚+- 7.36 days, respectively, p 0.0001). The characteristics of SR and SgR groups were similar, except the following parameters: rectal tumor (34.1% vs. 19.7%, respectively, p = 0.0245), metastatic lymph nodes (68.1% vs. 86.3%, respectively, p = 0.0383), bilobar liver metastases (22.6% vs. 37.8%, respectively, p = 0.0169), major hepatectomies (13.2% vs. 30.3%, respectively, p= 0.0025) and neo-adjuvant chemotherapy (13.2% vs. 77.2%, respectively, p 0.0001). A comparative analysis of morbidity, mortality and survival rates between SR and SgR was performed for subgroups of patients presenting these parameters. In each of these subgroups, SR was associated with similar morbidity, mortality and survival rates compared with SgR (p value 0.05). In patients with SCLMs, SR provides similar short-term and long-term outcomes as SgR, with a shorter hospital stay. Therefore, in most patients with

Comparative metagenomic analysis of soil microbial communities across three hexachlorocyclohexane contamination levels.

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Naseer Sangwan

Full Text Available This paper presents the characterization of the microbial community responsible for the in-situ bioremediation of hexachlorocyclohexane (HCH. Microbial community structure and function was analyzed using 16S rRNA amplicon and shotgun metagenomic sequencing methods for three sets of soil samples. The three samples were collected from a HCH-dumpsite (450 mg HCH/g soil and comprised of a HCH/soil ratio of 0.45, 0.0007, and 0.00003, respectively. Certain bacterial; (Chromohalobacter, Marinimicrobium, Idiomarina, Salinosphaera, Halomonas, Sphingopyxis, Novosphingobium, Sphingomonas and Pseudomonas, archaeal; (Halobacterium, Haloarcula and Halorhabdus and fungal (Fusarium genera were found to be more abundant in the soil sample from the HCH-dumpsite. Consistent with the phylogenetic shift, the dumpsite also exhibited a relatively higher abundance of genes coding for chemotaxis/motility, chloroaromatic and HCH degradation (lin genes. Reassembly of a draft pangenome of Chromohalobacter salaxigenes sp. (∼8X coverage and 3 plasmids (pISP3, pISP4 and pLB1; 13X coverage containing lin genes/clusters also provides an evidence for the horizontal transfer of HCH catabolism genes.

Typing of 49 autosomal SNPs by single base extension and capillary electrophoresis for forensic genetic testing

DEFF Research Database (Denmark)

Børsting, Claus; Tomas Mas, Carmen; Morling, Niels

2012-01-01

of the amplicons range from 65 to 115 bp. The high sensitivity and the short amplicon sizes make the assay very suitable for typing of degraded DNA samples, and the low mutation rate of SNPs makes the assay very useful for relationship testing. Combined, these advantages make the assay well suited for disaster...

Comparison of the biometric values obtained by two different A-mode ultrasound devices (Eye Cubed vs. PalmScan): a transversal, descriptive, and comparative study.

Science.gov (United States)

Velez-Montoya, Raul; Shusterman, Eugene Mark; López-Miranda, Miriam Jessica; Mayorquin-Ruiz, Mariana; Salcedo-Villanueva, Guillermo; Quiroz-Mercado, Hugo; Morales-Cantón, Virgilio

2010-03-24

To assess the reliability of the measurements obtained with the PalmScan, when compared with another standardized A-mode ultrasound device, and assess the consistency and correlation between the two methods. Transversal, descriptive, and comparative study. We recorded the axial length (AL), anterior chamber depth (ACD) and lens thickness (LT) obtained with two A-mode ultrasounds (PalmScan A2000 and Eye Cubed) using an immersion technique. We compared the measurements with a two-sample t-test. Agreement between the two devices was assessed with Bland-Altman plots and 95% limits of agreement. 70 eyes of 70 patients were enrolled in this study. The measurements with the Eye Cubed of AL and ACD were shorter than the measurements taken by the PalmScan. The differences were not statistically significant regarding AL (p < 0.4) but significant regarding ACD (p < 0.001). The highest agreement between the two devices was obtained during LT measurement. The PalmScan measurements were shorter, but not statistically significantly (p < 0.2). The values of AL and LT, obtained with both devices are not identical, but within the limits of agreement. The agreement is not affected by the magnitude of the ocular dimensions (but only between range of 20 mm to 27 mm of AL and 3.5 mm to 5.7 mm of LT). A correction of about 0.5 D could be considered if an intraocular lens is being calculated. However due to the large variability of the results, the authors recommend discretion in using this conversion factor, and to adjust the power of the intraocular lenses based upon the personal experience of the surgeon.

Community Structure Comparisons of Hydrothermal Vent Microbial Mats Along the Mariana Arc and Back-arc

Science.gov (United States)

Hager, K. W.; Fullerton, H.; Moyer, C. L.

2015-12-01

Hydrothermal vents along the Mariana Arc and back-arc represent a hotspot of microbial diversity that has not yet been fully recognized. The Mariana Arc and back-arc contain hydrothermal vents with varied vent effluent chemistry and temperature, which translates to diverse community composition. We have focused on iron-rich sites where the dominant primary producers are iron oxidizing bacteria. Because microbes from these environments have proven elusive in culturing efforts, we performed culture independent analysis among different microbial communities found at these hydrothermal vents. Terminal-restriction fragment length polymorphism (T-RFLP) and Illumina sequencing of small subunit ribosomal gene amplicons were used to characterize community members and identify samples for shotgun metagenomics. Used in combination, these methods will better elucidate the composition and characteristics of the bacterial communities at these hydrothermal vent systems. The overarching goal of this study is to evaluate and compare taxonomic and metabolic diversity among different communities of microbial mats. We compared communities collected on a fine scale to analyze the bacterial community based on gross mat morphology, geography, and nearby vent effluent chemistry. Taxa richness and evenness are compared with rarefaction curves to visualize diversity. As well as providing a survey of diversity this study also presents a juxtaposition of three methods in which ribosomal small subunit diversity is compared with T-RFLP, next generation amplicon sequencing, and metagenomic shotgun sequencing.

Shorter or longer text in Ezekiel 6: The role of genre

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Godwin Mushayabasa

2014-08-01

Full Text Available The text of Ezekiel continues to present some challenges to students studying it. This is in view of what one school of thought identify in the Ezekiel text as extensive redactions and revisions, whilst another school of thought is hesitant to subject the Masoretic Text (MT to such critical analysis. Amidst these differing viewpoints, I have discussed by means of literary analysis, the possibility that chapter 6 of Ezekiel may have been intended as a prophetic poetic message, or was later edited to conform to the genre of prophetic poetry. This is in the light of the so-called repetitions or ‘additions’ reflected in the MT if compared against the LXX, as well as the general problems associated with the Hebrew text of Ezekiel. The findings indicate that the text of Ezekiel 6 probably already had a complete theological corpus when it left the hand of the prophet Ezekiel or those who penned his words down. However, scribes saw it necessary to restructure, organise and colour the prophetic oracle in a literary form and structure they thought was necessary. This finding could be vital for solving literary and text critical problems in Ezekiel.

Laparoscopic colectomy for transverse colon cancer: comparative analysis of short- and long-term outcomes.

Science.gov (United States)

Sheng, Weizheng; Zhang, Bo; Chen, Weifeng; Gu, Dayong; Gao, Weidong

2015-01-01

This study evaluated the short- and long-term outcomes of laparoscopic colectomy compared with open colectomy for patients with transverse colon cancer by matched-pair analysis. This study enrolled 59 patients who underwent laparoscopic colectomy and compared them with 59 matched patients who underwent open colectomy for transverse colon cancer. The following parameters were matched: clinical stage and type of resection. Both short- and long-term outcomes of laparoscopic colectomy were compared with those of open colectomy. No difference was observed between the two groups in terms of age, gender, ASA score, comorbidity, clinical stage and operative procedures. Regarding short-term outcomes, blood loss, time to first flatus, time to liquid diet and postoperative stay were significantly shorter in the laparoscopy group than in the open group, while operation time was significantly longer in the laparoscopy group than in the open group. Postoperative complication was similar between the two groups. With respect to long-term outcomes, the two groups did not differ significantly in terms of 5-year overall and disease-free survival. In summary, laparoscopic colectomy is a safe and feasible option for selected patients with transverse colon cancer. The short- and long-term outcomes of laparoscopic colectomy are considered to be acceptable.

Partial and Full PCR-Based Reverse Genetics Strategy for Influenza Viruses

Science.gov (United States)

Chen, Hongjun; Ye, Jianqiang; Xu, Kemin; Angel, Matthew; Shao, Hongxia; Ferrero, Andrea; Sutton, Troy; Perez, Daniel R.

2012-01-01

Since 1999, plasmid-based reverse genetics (RG) systems have revolutionized the way influenza viruses are studied. However, it is not unusual to encounter cloning difficulties for one or more influenza genes while attempting to recover virus de novo. To overcome some of these shortcomings we sought to develop partial or full plasmid-free RG systems. The influenza gene of choice is assembled into a RG competent unit by virtue of overlapping PCR reactions containing a cDNA copy of the viral gene segment under the control of RNA polymerase I promoter (pol1) and termination (t1) signals – herein referred to as Flu PCR amplicons. Transfection of tissue culture cells with either HA or NA Flu PCR amplicons and 7 plasmids encoding the remaining influenza RG units, resulted in efficient virus rescue. Likewise, transfections including both HA and NA Flu PCR amplicons and 6 RG plasmids also resulted in efficient virus rescue. In addition, influenza viruses were recovered from a full set of Flu PCR amplicons without the use of plasmids. PMID:23029501

Development of a multiplex qPCR in real time for quantification and differential diagnosis of Salmonella Gallinarum and Salmonella Pullorum.

Science.gov (United States)

Rubio, Marcela da Silva; Penha Filho, Rafael Antonio Casarin; Almeida, Adriana Maria de; Berchieri, Angelo

2017-12-01

Currently there are 2659 Salmonella serovars. The host-specific biovars Salmonella Pullorum and Salmonella Gallinarum cause systemic infections in food-producing and wild birds. Fast diagnosis is crucial to control the dissemination in avian environments. The present work describes the development of a multiplex qPCR in real time using a low-cost DNA dye (SYBr Green) to identify and quantify these biovars. Primers were chosen based on genomic regions of difference (RoD) and optimized to control dimers. Primers pSGP detect both host-specific biovars but not other serovars and pSG and pSP differentiate biovars. Three amplicons showed different melting temperatures (Tm), allowing differentiation. The pSGP amplicon (97 bp) showed Tm of 78°C for both biovars. The pSG amplicon (273 bp) showed a Tm of 86.2°C for S. Gallinarum and pSP amplicon (260 bp) dissociated at 84.8°C for S. Pullorum identification. The multiplex qPCR in real time showed high sensitivity and was capable of quantifying 10 8 -10 1 CFU of these biovars.

A randomized study comparing skin closure in cesarean sections: staples vs subcuticular sutures.

Science.gov (United States)

Rousseau, Julie-Anne; Girard, Karine; Turcot-Lemay, Lucile; Thomas, Nancy

2009-03-01

We sought to compare postoperative pain according to the skin closure method (subcuticular sutures vs staples) after an elective term cesarean section. A randomized controlled trial of 101 women was performed. Women were randomly assigned to subcuticular sutures or staples. Operative technique and postoperative analgesia were standardized. Stratification was used for primary vs repeat cesareans. Analog pain and satisfaction scales ranging from 0-10 were completed at postoperative days 1 and 3, and at 6 weeks postoperatively. A digital photograph of the incision was taken at 6 weeks postoperatively and evaluated by 3 independent blinded observers. Pain at 6 weeks postoperatively was significantly less in the staple group (0.17 vs 0.51; P = .04). Operative time was shorter in that group (24.6 vs 32.9 minutes; P women's satisfaction. Staples are the method of choice for skin closure for elective term cesareans in our population.

DNA barcode for genetic traceability of Nile Perch and Nile Tilapia

International Nuclear Information System (INIS)

Avossa, Valeria

2017-01-01

For this study, mitochondrial DNA was extracted from 55 fish samples (26 Nile Perch Samples and 29 Nile Tilapia Samples collected from 3 different Ugandan regions of Lake Victoria. In order to optimize the PCR method, we also extracted DNA from two other different fish samples: one from Italy and one from a Viennese market. The COI gene was amplified using universal primers (COI2, COI3, cocktails of 8 and 4 primers respectively). After the amplification step, the amplicons were analysed using gel electrophoresis , in order to establish that the set primers worked well in the samples. The positive results of an agarose gel electrophoresis analysis with the PCR amplicons (amplicons length ~700pb) are shown.

Shorter dialysis session length was not associated with lower mental health and physical functioning in elderly hemodialysis patients: Results from the Japan Dialysis Outcome and Practice Patterns Study (J-DOPPS.

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Masashi Kitagawa

Full Text Available Health-related quality of life (HRQOL is often prioritized over long-term survival in elderly patients. Although a longer dialysis session length (DSL has been shown to reduce mortality, its effects on improving the HRQOL are unknown.Using data from the Japan Dialysis Outcomes and Practice Patterns Study (J-DOPPS, patients aged ≥ 65 years on maintenance hemodialysis were enrolled. DSL was categorized as short (240 minutes. The primary outcomes were changes in mental health (ΔMH and physical functioning (ΔPF scores assessed using the Japanese version of SF-12, in one year. The differences in the ΔMH and ΔPF among the three groups were assessed via regression (beta coefficients derived using a linear regression model.Of 1,187 patients at baseline, 319 (26.9% had a short length, 686 (57.8% a medium length, and 182 (15.3% a long length. We assessed the ΔMH data from 793 patients and the ΔPF data from 738. No significant differences in the ΔMH were noted for the short or long groups compared with the medium group (score difference: 0.26, 95% confidence interval [CI]: -4.17 to 4.69 for short; score difference: -1.15, 95% CI: -6.17 to 3.86 for long. Similarly, no significant differences were noted for these groups versus the medium group in ΔPF either (score difference: -1.43, 95% CI: -6.73 to 3.87 for short; score difference: -1.71, 95% CI: -7.63 to 4.22 for long.A shorter DSL might have no adverse effects on MH or PF for elderly patients.

Aberrations of ERBB2 and TOP2A Genes in Breast Cancer

DEFF Research Database (Denmark)

Nielsen, Kirsten Vang; Müller, Sven; Møller, Susanne

2009-01-01

genes and the other by having amplification of ERBB2 and deletion of TOP2A. The characteristics are compared to findings on paired ERBB2 and TOP2A data from 649 patients with invasive breast cancer from a previously published biomarker study. The physical localization of FISH signals in metaphase...... spreads from cell lines showed that simultaneous amplification is not a simple co-amplification of a whole amplicon containing both genes. Most gene signals are translocated to abnormal marker chromosomes. ERBB2 genes but not TOP2A genes are present in tandem amplicons, leading to a higher ERBB2 ratio....... This observation was confirmed by patient FISH data: among 276 (43% of all patients) abnormal tumors, 67% had different ERBB2 and TOP2A status. ERBB2 amplification with normal TOP2A status was found in 36% of the abnormal tumors (15% of all patients). Simultaneous amplification of both genes was found in 28...

Evaluation of three methods of DNA extraction from paraffin-embedded material for the amplification of genomic DNA by means of the PCR technique

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MESQUITA Ricardo Alves

2001-01-01

Full Text Available There are several protocols reported in the literature for the extraction of genomic DNA from formalin-fixed paraffin-embedded samples. Genomic DNA is utilized in molecular analyses, including PCR. This study compares three different methods for the extraction of genomic DNA from formalin-fixed paraffin-embedded (inflammatory fibrous hyperplasia and non-formalin-fixed (normal oral mucosa samples: phenol with enzymatic digestion, and silica with and without enzymatic digestion. The amplification of DNA by means of the PCR technique was carried out with primers for the exon 7 of human keratin type 14. Amplicons were analyzed by means of electrophoresis in an 8% polyacrylamide gel with 5% glycerol, followed by silver-staining visualization. The phenol/enzymatic digestion and the silica/enzymatic digestion methods provided amplicons from both tissue samples. The method described is a potential aid in the establishment of the histopathologic diagnosis and in retrospective studies with archival paraffin-embedded samples.

A comparative planning study of step-and-shoot IMRT versus helical tomotherapy for whole-pelvis irradiation in cervical cancer

International Nuclear Information System (INIS)

Chitapanarux, Imjai; Tharavichitkul, Ekkasit; Nobnop, Wannapa; Wanwilairat, Somsak; Vongtama, Roy; Traisathit, Patrinee

2015-01-01

The aim of this study was to compare the dosimetric parameters of whole-pelvis radiotherapy (WPRT) for cervical cancer between step-and-shoot IMRT (SaS-IMRT) and Helical Tomotherapy TM (HT). Retrospective analysis was performed on 20 cervical cancer patients who received WPRT in our center between January 2011 and January 2014. SaS-IMRT and HT treatment plans were generated for each patient. The dosimetric values for target coverage and organ-at-risk (OAR) sparing were compared according to the criteria of the International Commission on Radiation Units and Measurements 83 (ICRU 83) guidelines. Differences in beam-on time (BOT) were also compared. All the PTV dosimetric parameters (D5%, D50% and D95%) for the HT plan were (statistically significantly) of better quality than those for the SaS-IMRT plan (P-value < 0.001 in all respects). HT was also significantly more accurate than SaS-IMRT with respect to the D98% and Dmean of the CTV (P-values of 0.008 and <0.001, respectively). The median Conformity Index (CI) did not differ between the two plans (P-value = 0.057). However, the Uniformity Index for HT was significantly better than that for SaS-IMRT (P-value < 0.001). The median of D50% for the bladder, rectum and small bowel were significantly lower in HT planning than SaS-IMRT (P-value < 0.001). For D2%, we found that HT provided better sparing to the rectum and bladder (P-value < 0.001). However, the median of D2% for the small bowel was comparable for both plans. The median of Dmax of the head of the left femur was significantly lower in the HT plan, but this did not apply for the head of the right femur. BOT for HT was significantly shorter than for SaS-IMRT (P-value < 0.001). HT provided highly accurate plans, with more homogeneous PTV coverage and superior sparing of OARs than SaS-IMRT. In addition, HT enabled a shorter delivery time than SaS-IMRT. (author)

Shorter or longer text in Ezekiel 6: The role of genre

Directory of Open Access Journals (Sweden)

Godwin Mushayabasa

2014-08-01

Full Text Available The text of Ezekiel continues to present some challenges to students studying it. This is in view of what one school of thought identify in the Ezekiel text as extensive redactions and revisions, whilst another school of thought is hesitant to subject the Masoretic Text (MT to such critical analysis. Amidst these differing viewpoints, I have discussed by means of literary analysis, the possibility that chapter 6 of Ezekiel may have been intended as a prophetic poetic message, or was later edited to conform to the genre of prophetic poetry. This is in the light of the so-called repetitions or ‘additions’ reflected in the MT if compared against the LXX, as well as the general problems associated with the Hebrew text of Ezekiel. The findings indicate that the text of Ezekiel 6 probably already had a complete theological corpus when it left the hand of the prophet Ezekiel or those who penned his words down. However, scribes saw it necessary to restructure, organise and colour the prophetic oracle in a literary form and structure they thought was necessary. This finding could be vital for solving literary and text critical problems in Ezekiel.

Photodynamic Therapy Plus Chemotherapy Compared with Photodynamic Therapy Alone in Hilar Nonresectable Cholangiocarcinoma.

Science.gov (United States)

Wentrup, Robert; Winkelmann, Nicola; Mitroshkin, Andrey; Prager, Matthias; Voderholzer, Winfried; Schachschal, Guido; Jürgensen, Christian; Büning, Carsten

2016-05-23

Standard treatments are not available for hilar nonresectable cholangiocarcinoma (NCC). It is unknown whether combination therapy of photodynamic therapy (PDT) plus systemic chemotherapy is superior to PDT alone. We retrospectively reviewed 68 patients with hilar NCC treated with either PDT plus chemotherapy (PTD-C) or PDT monotherapy (PDT-M). The primary endpoint was the mean overall survival rate. Secondary endpoints included the 1-year survival rate, risk of cholangitic complications, and outcomes, which were evaluated according to the chemotherapy protocol. More than 90% of the study population had advanced hilar NCC Bismuth type III or IV. In the PDT-M group (n=35), the mean survival time was 374 days compared with 520 days in the PDT-C group (n=33, p=0.021). The 1-year survival rate was significantly higher in the PDT-C group compared with the PDT-M group (88% vs 58%, p=0.001) with a significant reduction of mortality (hazard ratio, 0.20; 95% confidence interval, 0.07 to 0.58; p=0.003). Gemcitabine monotherapy resulted in a shorter survival time compared with the gemcitabine combination therapy (mean, 395 days vs 566 days; p=0.09). Cholangitic complications were observed at a similar frequency in the PDT-C and PDT-M groups. Combining repeated PDT with a gemcitabine-based combination therapy might offer a significant survival benefit in patients with hilar NCC.

Rapid sequence induction and intubation with rocuronium-sugammadex compared with succinylcholine

DEFF Research Database (Denmark)

Sørensen, M K; Bretlau, C; Gätke, M R

2012-01-01

An unanticipated difficult airway may arise during rapid sequence induction and intubation (RSII). The aim of the trial was to assess how rapidly spontaneous ventilation could be re-established after RSII. We hypothesized that the time period from tracheal intubation to spontaneous ventilation wo...... would be shorter with rocuronium-sugammadex than with succinylcholine....

A prospective randomized study comparing percutaneous nephrolithotomy under combined spinal-epidural anesthesia with percutaneous nephrolithotomy under general anesthesia.

Science.gov (United States)

Singh, Vishwajeet; Sinha, Rahul Janak; Sankhwar, S N; Malik, Anita

2011-01-01

A prospective randomized study was executed to compare the surgical parameters and stone clearance in patients who underwent percutaneous nephrolithotomy (PNL) under combined spinal-epidural anesthesia (CSEA) versus those who underwent PNL under general anesthesia (GA). Between January 2008 to December 2009, 64 patients with renal calculi were randomized into 2 groups and evaluated for the purpose of this study. Group 1 consisted of patients who underwent PNL under CSEA and Group 2 consisted of patients who underwent PNL under GA. The operative time, stone clearance rate, visual pain analog score, mean analgesic dose and mean hospital stay were compared amongst other parameters. The difference between visual pain analog score after the operation and the dose of analgesic requirement was significant on statistical analysis between both groups. PNL under CSEA is as effective and safe as PNL under GA. Patients who undergo PNL under CESA require lesser analgesic dose and have a shorter hospital stay. Copyright © 2011 S. Karger AG, Basel.

Comparative sacral morphology and the reconstructed tail lengths of five extinct primates: Proconsul heseloni, Epipliopithecus vindobonensis, Archaeolemur edwardsi, Megaladapis grandidieri, and Palaeopropithecus kelyus.

Science.gov (United States)

Russo, Gabrielle A

2016-01-01

This study evaluated the relationship between the morphology of the sacrum-the sole bony link between the tail or coccyx and the rest of the body-and tail length (including presence/absence) and function using a comparative sample of extant mammals spanning six orders (Primates, Carnivora, Rodentia, Diprotodontia, Pilosa, Scandentia; N = 472). Phylogenetically-informed regression methods were used to assess how tail length varied with respect to 11 external and internal (i.e., trabecular) bony sacral variables with known or suspected biomechanical significance across all mammals, only primates, and only non-primates. Sacral variables were also evaluated for primates assigned to tail categories ('tailless,' 'nonprehensile short-tailed,' 'nonprehensile long-tailed,' and 'prehensile-tailed'). Compared to primates with reduced tail lengths, primates with longer tails generally exhibited sacra having larger caudal neural openings than cranial neural openings, and last sacral vertebrae with more mediolaterally-expanded caudal articular surfaces than cranial articular surfaces, more laterally-expanded transverse processes, more dorsally-projecting spinous processes, and larger caudal articular surface areas. Observations were corroborated by the comparative sample, which showed that shorter-tailed (e.g., Lynx rufus [bobcat]) and longer-tailed (e.g., Acinonyx jubatus [cheetah]) non-primate mammals morphologically converge with shorter-tailed (e.g., Macaca nemestrina) and longer-tailed (e.g., Macaca fascicularis) primates, respectively. 'Prehensile-tailed' primates exhibited last sacral vertebrae with more laterally-expanded transverse processes and greater caudal articular surface areas than 'nonprehensile long-tailed' primates. Internal sacral variables performed poorly compared to external sacral variables in analyses of extant primates, and were thus deemed less useful for making inferences concerning tail length and function in extinct primates. The tails lengths of

Anterior Versus Posterolateral Approach for Total Laparoscopic Splenectomy: A Comparative Study

Science.gov (United States)

Ji, Bai; Wang, Yingchao; Zhang, Ping; Wang, Guangyi; Liu, Yahui

2013-01-01

Objective: Although the anterior approach is normally used for elective laparoscopic splenectomy (LS), the posterolateral approach may be superior. We have retrospectively compared the effectiveness and safety of these approaches in patients with non-severe splenomegaly scheduled for elective total LS. Methods: Patients with surgical spleen disorders scheduled for elective LS between March 2005 and June 2011 underwent laparoscopic splenic mobilization via the posterolateral or anterior approach. Main outcome measures included operation time, intraoperative blood loss, frequency of postoperative pancreatic leakage, and length of hospital stay. Results: During the study period, 203 patients underwent LS, 58 (28.6%) via the posterolateral and 145 (71.4%) via the anterior approach. Three patients (1.5%) required conversion to laparotomy due to extensive perisplenic adhesions. The posterolateral approach was associated with significantly shorter operation time (65.0 ± 12.3 min vs. 95.0 ± 21.3 min, P 0.05) Conclusions: The posterolateral approach is more effective and safer than the anterior approach in patients without severe splenomegaly (< 30 cm). PMID:23372427

A novel photoinduced electron transfer (PET) primer technique for rapid real-time PCR detection of Cryptosporidium spp

Energy Technology Data Exchange (ETDEWEB)

Jothikumar, N., E-mail: jin2@cdc.gov; Hill, Vincent R.

2013-06-28

Highlights: •Uses a single-labeled fluorescent primer for real-time PCR. •The detection sensitivity of PET PCR was comparable to TaqMan PCR. •Melt curve analysis can be performed to confirm target amplicon production. •Conventional PCR primers can be converted to PET PCR primers. -- Abstract: We report the development of a fluorescently labeled oligonucleotide primer that can be used to monitor real-time PCR. The primer has two parts, the 3′-end of the primer is complimentary to the target and a universal 17-mer stem loop at the 5′-end forms a hairpin structure. A fluorescent dye is attached to 5′-end of either the forward or reverse primer. The presence of guanosine residues at the first and second position of the 3′ dangling end effectively quenches the fluorescence due to the photo electron transfer (PET) mechanism. During the synthesis of nucleic acid, the hairpin structure is linearized and the fluorescence of the incorporated primer increases several-fold due to release of the fluorescently labeled tail and the absence of guanosine quenching. As amplicons are synthesized during nucleic acid amplification, the fluorescence increase in the reaction mixture can be measured with commercially available real-time PCR instruments. In addition, a melting procedure can be performed to denature the double-stranded amplicons, thereby generating fluorescence peaks that can differentiate primer dimers and other non-specific amplicons if formed during the reaction. We demonstrated the application of PET-PCR for the rapid detection and quantification of Cryptosporidium parvum DNA. Comparison with a previously published TaqMan® assay demonstrated that the two real-time PCR assays exhibited similar sensitivity for a dynamic range of detection of 6000–0.6 oocysts per reaction. PET PCR primers are simple to design and less-expensive than dual-labeled probe PCR methods, and should be of interest for use by laboratories operating in resource

A novel photoinduced electron transfer (PET) primer technique for rapid real-time PCR detection of Cryptosporidium spp

International Nuclear Information System (INIS)

Jothikumar, N.; Hill, Vincent R.

2013-01-01

Highlights: •Uses a single-labeled fluorescent primer for real-time PCR. •The detection sensitivity of PET PCR was comparable to TaqMan PCR. •Melt curve analysis can be performed to confirm target amplicon production. •Conventional PCR primers can be converted to PET PCR primers. -- Abstract: We report the development of a fluorescently labeled oligonucleotide primer that can be used to monitor real-time PCR. The primer has two parts, the 3′-end of the primer is complimentary to the target and a universal 17-mer stem loop at the 5′-end forms a hairpin structure. A fluorescent dye is attached to 5′-end of either the forward or reverse primer. The presence of guanosine residues at the first and second position of the 3′ dangling end effectively quenches the fluorescence due to the photo electron transfer (PET) mechanism. During the synthesis of nucleic acid, the hairpin structure is linearized and the fluorescence of the incorporated primer increases several-fold due to release of the fluorescently labeled tail and the absence of guanosine quenching. As amplicons are synthesized during nucleic acid amplification, the fluorescence increase in the reaction mixture can be measured with commercially available real-time PCR instruments. In addition, a melting procedure can be performed to denature the double-stranded amplicons, thereby generating fluorescence peaks that can differentiate primer dimers and other non-specific amplicons if formed during the reaction. We demonstrated the application of PET-PCR for the rapid detection and quantification of Cryptosporidium parvum DNA. Comparison with a previously published TaqMan® assay demonstrated that the two real-time PCR assays exhibited similar sensitivity for a dynamic range of detection of 6000–0.6 oocysts per reaction. PET PCR primers are simple to design and less-expensive than dual-labeled probe PCR methods, and should be of interest for use by laboratories operating in resource

The Effects of Biocompatible Compared with Standard Peritoneal Dialysis Solutions on Peritonitis Microbiology, Treatment, and Outcomes: the balANZ Trial

Science.gov (United States)

Johnson, David W.; Brown, Fiona G.; Clarke, Margaret; Boudville, Neil; Elias, Tony J.; Foo, Marjorie W.Y.; Jones, Bernard; Kulkarni, Hemant; Langham, Robyn; Ranganathan, Dwarakanathan; Schollum, John; Suranyi, Michael G.; Tan, Seng H.; Voss, David

2012-01-01

♦ Background: A multicenter, multi-country randomized controlled trial (the balANZ study) recently reported that peritonitis rates significantly improved with the use of neutral-pH peritoneal dialysis (PD) solutions low in glucose degradation products (“biocompatible”) compared with standard solutions. The present paper reports a secondary outcome analysis of the balANZ trial with respect to peritonitis microbiology, treatment, and outcomes. ♦ Methods: Adult incident PD patients with residual renal function were randomized to receive either biocompatible or conventional (control) PD solutions for 2 years. ♦ Results: The safety population analysis for peritonitis included 91 patients in each group. The unadjusted geometric mean peritonitis rates in those groups were 0.30 [95% confidence interval (CI): 0.22 to 0.41] episodes per patient-year for the biocompatible group and 0.49 (95% CI: 0.39 to 0.62) episodes per patient-year for the control group [incidence rate ratio (IRR): 0.61; 95% CI: 0.41 to 0.90; p = 0.01]. When specific causative organisms were examined, the rates of culture-negative, gram-positive, gram-negative, and polymicrobial peritonitis episodes were not significantly different between the biocompatible and control groups, although the biocompatible group did experience a significantly lower rate of non-pseudomonal gram-negative peritonitis (IRR: 0.41; 95% CI: 0.18 to 0.92; p = 0.03). Initial empiric antibiotic regimens were comparable between the groups. Biocompatible fluid use did not significantly reduce the risk of peritonitis-associated hospitalization (adjusted odds ratio: 0.80; 95% CI: 0.48 to 1.34), but did result in a shorter median duration of peritonitis-associated hospitalization (6 days vs 11 days, p = 0.05). Peritonitis severity was more likely to be rated as mild in the biocompatible group (37% vs 10%, p = 0.001). Overall peritonitis-associated technique failures and peritonitis-related deaths were comparable in the two groups

{sup 177}Lu- labeled MOv18 as compared to {sup 131}I- or {sup 90}Y-labeled MOv18 has the better therapeutic effect in eradication of alpha folate receptor-expressing tumor xenografts

Energy Technology Data Exchange (ETDEWEB)

Zacchetti, Alberto [Unit of Molecular Therapies, Department of Experimental Oncology and Laboratories, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan 20133 (Italy); Coliva, Angela [Department of Imaging and Nuclear Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan 20133 (Italy); Luison, Elena [Unit of Molecular Therapies, Department of Experimental Oncology and Laboratories, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan 20133 (Italy); Seregni, Ettore; Bombardieri, Emilio [Department of Imaging and Nuclear Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan 20133 (Italy); Giussani, Augusto [Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg (Germany); Figini, Mariangela [Unit of Molecular Therapies, Department of Experimental Oncology and Laboratories, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan 20133 (Italy); Canevari, Silvana [Unit of Molecular Therapies, Department of Experimental Oncology and Laboratories, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan 20133 (Italy)], E-mail: silvana.canevari@istitutotumori.mi.it

2009-10-15

Introduction: The mouse monoclonal antibody MOv18, directed against the {alpha}-isoform of folate receptor (FR), was investigated to identify the optimal radioconjugate for radioimmunotherapy of minimal residual disease in ovarian cancer. Methods: Pharmacokinetics, biodistribution, long-term therapeutic efficacy and toxicity of MOv18, labeled with the beta-emitters {sup 131}I, {sup 90}Y and {sup 177}Lu, were compared in a xenografted mouse model, composed by two cell lines, A431FR and A431MK, differing only for FR expression. Results: A shorter blood clearance and a higher tumor uptake were observed for {sup 90}Y- and {sup 177}Lu- compared to {sup 131}I-MOv18, and a shorter blood pharmacokinetics was recorded in A431FR-bearing animals. At equitoxic maximum tolerable doses, the general irradiation by {sup 131}I- and {sup 90}Y-MOv18 gives rise to strong targeted effects on A431FR and nontargeted effects on A431MK tumors, while {sup 177}Lu-MOv18 was able to eradicate small size tumor masses expressing the antigen of interest exerting only mild non-targeted effects. Conclusion: {sup 177}Lu-MOv18 at the maximal tolerated dose is the immunoradioconjugate with the best therapeutic window in experimental conditions of small tumor volume.

Comparative study of diode-pumping self-injection and injection-locking Tm:YAG lasers

International Nuclear Information System (INIS)

Wu, C T; Chen, F; Ju, Y L; Wang, Y Z

2013-01-01

A comparative study of the laser characteristics of self-injection and injection-locking Tm:YAG lasers is given in this paper. At a pump energy of 145 mJ and Q-switched repetition rate of 100 Hz, an output energy of 2.39 mJ was obtained for an injection-locking Tm:YAG laser, with a pulse width of 403.2 ns and a pulse building-up time of 2.12 μs. Under the same conditions, the output energy, pulse width and pulse build-up time for a self-injection Tm:YAG laser were 2.21 mJ, 407.0 ns and 3.95 μs, respectively. The threshold of the Q-switched injection-locking Tm:YAG laser was much lower than that of the self-injection laser, and the pulse width was narrower and the pulse build-up time shorter. Additionally, the output spectrum was much purer for the injection-locking laser. (paper)

Heat transfer system safety: Comparing the effectiveness of batch venting and a light-ends removal kit (LERK

Directory of Open Access Journals (Sweden)

Christopher Ian Wright

2014-11-01

Full Text Available Heat transfer fluids (HTF should be analysed at least once per year to determine the extent of thermal degradation. Under normal operating conditions, mineral-based HTFs will thermally degrade and the bonds between hydrocarbons break to form shorter-chain hydrocarbons known as “light-ends”. These light-ends accumulate in a HTF system and present a future potential fire risk. Light-ends can be removed from a HTF system via a batch vent or installation of a temporary or permanently installed light-ends removal kit (LERK. Data was collected prior to and following batch venting or installation of a LERK. The main study parameter was closed flash temperature as open flash temperature and fire point did not change considerably. Analysis showed that both methods increased closed flash temperature in excess of 130 °C three months after the intervention, so both methods were deemed effective. Data showed that the percentage change achieved with the LERK, compared to batch venting, was 2-fold higher at three months and 10-fold higher at 6 months. The duration of effect was longer with the LERK with closed flash temperature being stable and consistently above 130 °C for 50 months after being permanently installed. This case highlights the effectiveness of a permanently fitted LERK which is effective for the longer-term control of closed flash temperature. However, mobile LERKs could be an option for manufacturers looking to manage closed flash temperature on a shorter-term basis or as an alternative to batch venting.

Comparing fixation used for calcaneal displacement osteotomies: a look at removal rates and cost.

Science.gov (United States)

Lucas, Douglas E; Simpson, G Alex; Philbin, Terrence M

2015-02-01

The calcaneal displacement osteotomy is a procedure frequently used by foot and ankle surgeons for hindfoot angular deformity. Traditional techniques use compression screw fixation that can result in prominent hardware. While the results of the procedure are generally good, a common concern is the development of plantar heel pain related to prominent hardware. The primary purpose of this study is to retrospectively compare clinical outcomes of 2 fixation methods for the osteotomy. Secondarily a cost analysis will compare implant costs to hardware removal costs. Records were reviewed for patients who had undergone a calcaneal displacement osteotomy fixated with either lag screw or a locked lateral compression plate (LLCP). Neuropathy, previous ipsilateral calcaneus surgery, heel pad trauma, or incomplete radiographic follow-up were exclusionary. Thirty-two patients (19.4%) required hardware removal from the screw fixation group compared to 1 (1.6%) of the LLCP group, which is significant (P cost was remarkably different with screw fixation costing on average $247.12, compared to the LLCP costing $1175.59. Although the LLCP cost was significantly higher, cost savings were identified when the cost of removal and removal rates were included. This study demonstrates that this device provides adequate stabilization for healing in equivalent time to screw fixation. The LLCP required decreased rates of hardware removal with fewer postoperative visits over a shorter period of time. Significant savings were demonstrated in the LLCP group despite the higher implant cost. Therapeutic, Level III, Retrospective Comparative Study. © 2014 The Author(s).

Systematic review of robotic surgery in gynecology: robotic techniques compared with laparoscopy and laparotomy.

Science.gov (United States)

Gala, Rajiv B; Margulies, Rebecca; Steinberg, Adam; Murphy, Miles; Lukban, James; Jeppson, Peter; Aschkenazi, Sarit; Olivera, Cedric; South, Mary; Lowenstein, Lior; Schaffer, Joseph; Balk, Ethan M; Sung, Vivian

2014-01-01

The Society of Gynecologic Surgeons Systematic Review Group performed a systematic review of both randomized and observational studies to compare robotic vs nonrobotic surgical approaches (laparoscopic, abdominal, and vaginal) for treatment of both benign and malignant gynecologic indications to compare surgical and patient-centered outcomes, costs, and adverse events associated with the various surgical approaches. MEDLINE and the Cochrane Central Register of Controlled Trials were searched from inception to May 15, 2012, for English-language studies with terms related to robotic surgery and gynecology. Studies of any design that included at least 30 women who had undergone robotic-assisted laparoscopic gynecologic surgery were included for review. The literature yielded 1213 citations, of which 97 full-text articles were reviewed. Forty-four studies (30 comparative and 14 noncomparative) met eligibility criteria. Study data were extracted into structured electronic forms and reconciled by a second, independent reviewer. Our analysis revealed that, compared with open surgery, robotic surgery consistently confers shorter hospital stay. The proficiency plateau seems to be lower for robotic surgery than for conventional laparoscopy. Of the various gynecologic applications, there seems to be evidence that renders robotic techniques advantageous over traditional open surgery for management of endometrial cancer. However, insofar as superiority, conflicting data are obtained when comparing robotics vs laparoscopic techniques. Therefore, the specific method of minimally invasive surgery, whether conventional laparoscopy or robotic surgery, should be tailored to patient selection, surgeon ability, and equipment availability. Copyright © 2014 AAGL. Published by Elsevier Inc. All rights reserved.

ESPRIT-Forest: Parallel clustering of massive amplicon sequence data in subquadratic time.

Science.gov (United States)

Cai, Yunpeng; Zheng, Wei; Yao, Jin; Yang, Yujie; Mai, Volker; Mao, Qi; Sun, Yijun

2017-04-01

The rapid development of sequencing technology has led to an explosive accumulation of genomic sequence data. Clustering is often the first step to perform in sequence analysis, and hierarchical clustering is one of the most commonly used approaches for this purpose. However, it is currently computationally expensive to perform hierarchical clustering of extremely large sequence datasets due to its quadratic time and space complexities. In this paper we developed a new algorithm called ESPRIT-Forest for parallel hierarchical clustering of sequences. The algorithm achieves subquadratic time and space complexity and maintains a high clustering accuracy comparable to the standard method. The basic idea is to organize sequences into a pseudo-metric based partitioning tree for sub-linear time searching of nearest neighbors, and then use a new multiple-pair merging criterion to construct clusters in parallel using multiple threads. The new algorithm was tested on the human microbiome project (HMP) dataset, currently one of the largest published microbial 16S rRNA sequence dataset. Our experiment demonstrated that with the power of parallel computing it is now compu- tationally feasible to perform hierarchical clustering analysis of tens of millions of sequences. The software is available at http://www.acsu.buffalo.edu/∼yijunsun/lab/ESPRIT-Forest.html.

One Gene and Two Proteins: a Leaderless mRNA Supports the Translation of a Shorter Form of the Shigella VirF Regulator

Directory of Open Access Journals (Sweden)

Maria Letizia Di Martino

2016-11-01

Full Text Available VirF, an AraC-like activator, is required to trigger a regulatory cascade that initiates the invasive program of Shigella spp., the etiological agents of bacillary dysentery in humans. VirF expression is activated upon entry into the host and depends on many environmental signals. Here, we show that the virF mRNA is translated into two proteins, the major form, VirF30 (30 kDa, and the shorter VirF21 (21 kDa, lacking the N-terminal segment. By site-specific mutagenesis and toeprint analysis, we identified the translation start sites of VirF30 and VirF21 and showed that the two different forms of VirF arise from differential translation. Interestingly, in vitro and in vivo translation experiments showed that VirF21 is also translated from a leaderless mRNA (llmRNA whose 5′ end is at position +309/+310, only 1 or 2 nucleotides upstream of the ATG84 start codon of VirF21. The llmRNA is transcribed from a gene-internal promoter, which we identified here. Functional analysis revealed that while VirF30 is responsible for activation of the virulence system, VirF21 negatively autoregulates virF expression itself. Since VirF21 modulates the intracellular VirF levels, this suggests that transcription of the llmRNA might occur when the onset of the virulence program is not required. We speculate that environmental cues, like stress conditions, may promote changes in virF mRNA transcription and preferential translation of llmRNA.

A first study comparing preservation of a ready-to-eat soup under pressure (hyperbaric storage) at 25°C and 30°C with refrigeration.

Science.gov (United States)

Moreira, Sílvia A; Fernandes, Pedro A R; Duarte, Ricardo; Santos, Diana I; Fidalgo, Liliana G; Santos, Mauro D; Queirós, Rui P; Delgadillo, Ivonne; Saraiva, Jorge A

2015-11-01

Hyperbaric storage (HS), storage under pressure at 25°C and 30°C, of a ready-to-eat (RTE) soup was studied and compared with refrigeration. Soup was stored at different time (4 and 8 h), temperature (4°C, 25°C, and 30°C), and pressure (0.1, 100, and 150 MPa) conditions, to compare microbial loads and physicochemical parameters. HS resulted in similar (microbial growth inhibition) to better (microbial inactivation) results compared to refrigeration, leading to equal and lower microbial loads, respectively, at the end of storage. Lower/higher pressure (100 vs. 150 MPa) and shorter/longer storage times (4 vs. 8 h) resulted in more pronounced microbial growth inhibition/microbial inactivation. Aerobic mesophiles showed less susceptibility to HS, compared to Enterobacteriaceae and yeast and molds. HS maintained generally the physicochemical parameters at values similar to refrigeration. Thus, HS with no need for temperature control throughout storage and so basically energetically costless, is a potential alternative to refrigeration.

Detection of hepatitis A virus by the nucleic acid sequence-based amplification technique and comparison with reverse transcription-PCR.

Science.gov (United States)

Jean, J; Blais, B; Darveau, A; Fliss, I

2001-12-01

A nucleic acid sequence-based amplification (NASBA) technique for the detection of hepatitis A virus (HAV) in foods was developed and compared to the traditional reverse transcription (RT)-PCR technique. Oligonucleotide primers targeting the VP1 and VP2 genes encoding the major HAV capsid proteins were used for the amplification of viral RNA in an isothermal process resulting in the accumulation of RNA amplicons. Amplicons were detected by hybridization with a digoxigenin-labeled oligonucleotide probe in a dot blot assay format. Using the NASBA, as little as 0.4 ng of target RNA/ml was detected per comparison to 4 ng/ml for RT-PCR. When crude HAV viral lysate was used, a detection limit of 2 PFU (4 x 10(2) PFU/ml) was obtained with NASBA, compared to 50 PFU (1 x 10(4) PFU/ml) obtained with RT-PCR. No interference was encountered in the amplification of HAV RNA in the presence of excess nontarget RNA or DNA. The NASBA system successfully detected HAV recovered from experimentally inoculated samples of waste water, lettuce, and blueberries. Compared to RT-PCR and other amplification techniques, the NASBA system offers several advantages in terms of sensitivity, rapidity, and simplicity. This technique should be readily adaptable for detection of other RNA viruses in both foods and clinical samples.

Next-Generation Mitogenomics: A Comparison of Approaches Applied to Caecilian Amphibian Phylogeny

OpenAIRE

Maddock, Simon T.; Briscoe, Andrew G.; Wilkinson, Mark; Waeschenbach, Andrea; San Mauro, Diego; Day, Julia J.; Littlewood, D. Tim J.; Foster, Peter G.; Nussbaum, Ronald A.; Gower, David J.

2016-01-01

Mitochondrial genome (mitogenome) sequences are being generated with increasing speed due to the advances of next-generation sequencing (NGS) technology and associated analytical tools. However, detailed comparisons to explore the utility of alternative NGS approaches applied to the same taxa have not been undertaken. We compared a ‘traditional’ Sanger sequencing method with two NGS approaches (shotgun sequencing and non-indexed, multiplex amplicon sequencing) on four different sequencing pla...

Mid-term follow-up outcomes of 2-staged hybrid coronary revascularization compared with off-pump coronary artery bypass for patients with multivessel coronary artery disease.

Science.gov (United States)

Wu, Song; Ling, Yunpeng; Fu, Yuanhao; Zhang, Lufeng; Yang, Hang; Guo, Lijun; Gao, Wei; Wan, Feng

2017-06-01

Two-staged hybrid coronary revascularization (HCR) is a novel procedure in selected patients with multivessel coronary artery disease. However, few studies are available on the mid-term or long-term outcomes of this 2-staged procedure as compared to off-pump coronary artery bypass (OPCAB). To compare in-hospital and mid-term follow-up outcomes of 2-staged HCR with OPCAB in patients with multivessel coronary artery disease. The present retrospective study analyzed the data from 73 patients who underwent the 2-staged HCR (HCR group) during 2012-2014 at the heart center. Three hundred and eighty-three patients who underwent conventional OPCAB by the same surgeon were selected for the comparative analysis performed on in-hospital and mid-term follow-up outcomes between the two groups. No significant difference was observed in the preoperative outcome between the two groups. The HCR group had a shorter operation duration (152.9 ±43.8 vs. 262.6 ±51.8 min, p < 0.05), less bleeding (558.6 ±441.3 vs. 1035.5 ±613.3 ml, p < 0.05), shorter mechanical ventilation (9.4 ±7.4 vs. 19.0 ±18.3 h, p < 0.05), and less blood transfusion (12 (16.4%) vs. 200 (52.2%), p < 0.05). The mean follow-up duration was 25.0 ±9.6 months in the HCR group and 22.8 ±10.6 months in the OPCAB group. The incidence of major adverse cardiac or cerebrovascular events (MACCE) was similar in both groups (4 (5.5%) vs. 10 (2.8%), p = 0.408). The estimated 3-year survival was similar in both groups (log-rank χ 2 = 1.041, p = 0.308). The 2-staged HCR is a safe and effective surgical procedure and may offer similar mid-term follow-up outcomes to OPCAB.

Assessing the Accuracy of Quantitative Molecular Microbial Profiling

Directory of Open Access Journals (Sweden)

Denise M. O'Sullivan

2014-11-01

Full Text Available The application of high-throughput sequencing in profiling microbial communities is providing an unprecedented ability to investigate microbiomes. Such studies typically apply one of two methods: amplicon sequencing using PCR to target a conserved orthologous sequence (typically the 16S ribosomal RNA gene or whole (metagenome sequencing (WGS. Both methods have been used to catalog the microbial taxa present in a sample and quantify their respective abundances. However, a comparison of the inherent precision or bias of the different sequencing approaches has not been performed. We previously developed a metagenomic control material (MCM to investigate error when performing different sequencing strategies. Amplicon sequencing using four different primer strategies and two 16S rRNA regions was examined (Roche 454 Junior and compared to WGS (Illumina HiSeq. All sequencing methods generally performed comparably and in good agreement with organism specific digital PCR (dPCR; WGS notably demonstrated very high precision. Where discrepancies between relative abundances occurred they tended to differ by less than twofold. Our findings suggest that when alternative sequencing approaches are used for microbial molecular profiling they can perform with good reproducibility, but care should be taken when comparing small differences between distinct methods. This work provides a foundation for future work comparing relative differences between samples and the impact of extraction methods. We also highlight the value of control materials when conducting microbial profiling studies to benchmark methods and set appropriate thresholds.

A new restriction endonuclease-based method for highly-specific detection of DNA targets from methicillin-resistant Staphylococcus aureus.

Directory of Open Access Journals (Sweden)

Maria W Smith

Full Text Available PCR multiplexing has proven to be challenging, and thus has provided limited means for pathogen genotyping. We developed a new approach for analysis of PCR amplicons based on restriction endonuclease digestion. The first stage of the restriction enzyme assay is hybridization of a target DNA to immobilized complementary oligonucleotide probes that carry a molecular marker, horseradish peroxidase (HRP. At the second stage, a target-specific restriction enzyme is added, cleaving the target-probe duplex at the corresponding restriction site and releasing the HRP marker into solution, where it is quantified colorimetrically. The assay was tested for detection of the methicillin-resistant Staphylococcus aureus (MRSA pathogen, using the mecA gene as a target. Calibration curves indicated that the limit of detection for both target oligonucleotide and PCR amplicon was approximately 1 nM. Sequences of target oligonucleotides were altered to demonstrate that (i any mutation of the restriction site reduced the signal to zero; (ii double and triple point mutations of sequences flanking the restriction site reduced restriction to 50-80% of the positive control; and (iii a minimum of a 16-bp target-probe dsDNA hybrid was required for significant cleavage. Further experiments showed that the assay could detect the mecA amplicon from an unpurified PCR mixture with detection limits similar to those with standard fluorescence-based qPCR. Furthermore, addition of a large excess of heterologous genomic DNA did not affect amplicon detection. Specificity of the assay is very high because it involves two biorecognition steps. The proposed assay is low-cost and can be completed in less than 1 hour. Thus, we have demonstrated an efficient new approach for pathogen detection and amplicon genotyping in conjunction with various end-point and qPCR applications. The restriction enzyme assay may also be used for parallel analysis of multiple different amplicons from the same

Clinical benefit of ertapenem compared to flomoxef for the treatment of cefotaxime-resistant Enterobacteriaceae bacteremia

Directory of Open Access Journals (Sweden)

Lee C

2018-02-01

Full Text Available Chen-Hsiang Lee,1,2 I-Ling Chen,3 Chia-Chin Li,4 Chun-Chih Chien4 1Department of Internal Medicine, Division of Infectious Diseases, Kaohsiung Chang Gung Memorial, Hospital, 2Chang Gung University, College of Medicine, 3Department of Pharmacy, 4Department of Laboratory Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan Objectives: Cefotaxime-resistant Enterobacteriaceae (CE infections are intractable, with limited treatment options. Though carbapenems are frequently prescribed for CE infections, the emergence of carbapenem-resistant Enterobacteriaceae is of huge concern. Flomoxef is effective against CE in vitro, and some clinical data on its demonstrated effectiveness against CE bloodstream infections (BSIs exists.Patients and methods: We conducted a retrospective study on adults with BSI caused by flomoxef-susceptible CE to investigate the efficacy of flomoxef compared with that of ertapenem. The outcome was evaluated with propensity score-based matching and logistic regression analysis.Results: Demographic and clinical characteristics of patients treated with flomoxef (n = 58 or ertapenem (n = 188 were compared. In the multivariate analysis, severe sepsis (adjusted odds ratio [AOR] = 3.84; 95% confidence interval [CI], 1.16–12.78; p = 0.03, high BSI mortality score (AOR = 5.59; 95% CI, 2.37–13.21; p < 0.01, ultimately or rapidly fatal comorbidity (AOR = 10.60; 95% CI, 3.43–32.75; p < 0.01, and pneumonia (AOR = 10.11; 95% CI, 3.43–29.81; p < 0.01 were independently associated with 28-day mortality. Using propensity scores, 58 flomoxef-treated patients were matched to 116 ertapenem-treated patients. There were no intergroup differences in BSI severity, comorbidity, or BSI sources. The 28-day mortality rates (20.7% vs 13.8%, p = 0.28 did not differ significantly. However, hospitalization length was shorter in the ertapenem group (10.2 ± 8.5 vs. 14.6 ± 9.4 days, p < 0.01.Conclusion: Although similar outcomes were

Effect of inner membrane tearing in the treatment of adult chronic subdural hematoma: a comparative study.

Science.gov (United States)

Kayaci, Selim; Kanat, Ayhan; Koksal, Vaner; Ozdemir, Bulent

2014-01-01

The postoperative results of chronic subdural hematoma (CSDH) procedures using catheterization and tearing of inner membrane (CTIM) technique have not previously been discussed in the literature. This article compares the effects of CTIM technique on brain re-expansion and re-accumulation with cases operated on with a burr-hole craniotomy and outer membrane incision (BCOMI) technique. The study involved operations on 144 patients (Group 1) using the CTIM technique and 108 patients (Group 2) using the BCOMI technique. In the operations using the CTIM technique in Group 1, the mean effusion measured in the subdural space (SDS) was 10.0 ± 0.2 mm, and for Group 2, 14.3 ± 0.6 mm in the postoperative period on the first and third days and this difference was found to be significant (p subdural effusion and pneumocephalus, and shorter hospital stays.

Comparative measurements of independent yields of 239Pu fission fragments induced by thermal and resonance neutrons

International Nuclear Information System (INIS)

Gundorin, N.A.; Kopach, Y.N.; Telezhnikov, S.A.

1994-01-01

The independent yields of 239 Pu fission fragments by means of gamma-spectroscopy method were measured for light and heavy groups on the IBR-30 reactor in Dubna. Comparative analysis of experimental data for fission induced by thermal and resonance neutrons was performed. The possibilities to increase the measurement's precision consist of the employment of a HPGe detector with high efficiency and its open-quotes activeclose quotes shielding in the gamma spectrometer, as well as a high speed electronics system. In this way the number of identified fragments will be increased and independent yields will be measured to a precision of 1-3%. Measurements at the source with shorter neutron pulse duration to increase neutron energy resolution will be possible after the reconstruction of a modern neutron source in Dubna in accordance with the IREN project

A Benchmark Study on Error Assessment and Quality Control of CCS Reads Derived from the PacBio RS.

Science.gov (United States)

Jiao, Xiaoli; Zheng, Xin; Ma, Liang; Kutty, Geetha; Gogineni, Emile; Sun, Qiang; Sherman, Brad T; Hu, Xiaojun; Jones, Kristine; Raley, Castle; Tran, Bao; Munroe, David J; Stephens, Robert; Liang, Dun; Imamichi, Tomozumi; Kovacs, Joseph A; Lempicki, Richard A; Huang, Da Wei

2013-07-31

PacBio RS, a newly emerging third-generation DNA sequencing platform, is based on a real-time, single-molecule, nano-nitch sequencing technology that can generate very long reads (up to 20-kb) in contrast to the shorter reads produced by the first and second generation sequencing technologies. As a new platform, it is important to assess the sequencing error rate, as well as the quality control (QC) parameters associated with the PacBio sequence data. In this study, a mixture of 10 prior known, closely related DNA amplicons were sequenced using the PacBio RS sequencing platform. After aligning Circular Consensus Sequence (CCS) reads derived from the above sequencing experiment to the known reference sequences, we found that the median error rate was 2.5% without read QC, and improved to 1.3% with an SVM based multi-parameter QC method. In addition, a De Novo assembly was used as a downstream application to evaluate the effects of different QC approaches. This benchmark study indicates that even though CCS reads are post error-corrected it is still necessary to perform appropriate QC on CCS reads in order to produce successful downstream bioinformatics analytical results.

High-definition resolution three-dimensional imaging systems in laparoscopic radical prostatectomy: randomized comparative study with high-definition resolution two-dimensional systems.

Science.gov (United States)

Kinoshita, Hidefumi; Nakagawa, Ken; Usui, Yukio; Iwamura, Masatsugu; Ito, Akihiro; Miyajima, Akira; Hoshi, Akio; Arai, Yoichi; Baba, Shiro; Matsuda, Tadashi

2015-08-01

Three-dimensional (3D) imaging systems have been introduced worldwide for surgical instrumentation. A difficulty of laparoscopic surgery involves converting two-dimensional (2D) images into 3D images and depth perception rearrangement. 3D imaging may remove the need for depth perception rearrangement and therefore have clinical benefits. We conducted a multicenter, open-label, randomized trial to compare the surgical outcome of 3D-high-definition (HD) resolution and 2D-HD imaging in laparoscopic radical prostatectomy (LRP), in order to determine whether an LRP under HD resolution 3D imaging is superior to that under HD resolution 2D imaging in perioperative outcome, feasibility, and fatigue. One-hundred twenty-two patients were randomly assigned to a 2D or 3D group. The primary outcome was time to perform vesicourethral anastomosis (VUA), which is technically demanding and may include a number of technical difficulties considered in laparoscopic surgeries. VUA time was not significantly shorter in the 3D group (26.7 min, mean) compared with the 2D group (30.1 min, mean) (p = 0.11, Student's t test). However, experienced surgeons and 3D-HD imaging were independent predictors for shorter VUA times (p = 0.000, p = 0.014, multivariate logistic regression analysis). Total pneumoperitoneum time was not different. No conversion case from 3D to 2D or LRP to open RP was observed. Fatigue was evaluated by a simulation sickness questionnaire and critical flicker frequency. Results were not different between the two groups. Subjective feasibility and satisfaction scores were significantly higher in the 3D group. Using a 3D imaging system in LRP may have only limited advantages in decreasing operation times over 2D imaging systems. However, the 3D system increased surgical feasibility and decreased surgeons' effort levels without inducing significant fatigue.

Comparative analysis of arthroscopic debridement in osseous versus soft tissue anterior ankle impingement.

Science.gov (United States)

Devgan, Ashish; Rohilla, Rajesh; Tanwar, Milind; Jain, Aditya; Siwach, Karan; Devgan, Radika

2016-01-01

Arthroscopic debridement has been a gold standard procedure for anterior ankle impingement, both in cases of osseous and soft tissue impingement. There is sparse literature on comparative outcome with respect to functional results between the two types of impingement post-arthroscopic debridement. Our study included 14 patients diagnosed as cases of anterior ankle impingement on the basis of clinical and radiological examination. They were segregated into two groups (on the basis of cause of impingement (osseous versus soft tissue)). Both groups were treated by arthroscopic debridement. Primary outcome was patient satisfaction, which was assessed by Likert scale and clinical outcomes were measured using AOFAS ankle-hind foot scale, VAS score, range of motion and time to return to pre-injury activity level in both groups. Mean follow-up was of 15 months where eleven patients reported an excellent recovery, two patients had good recovery while one patient reported poor outcome. Mean AOFAS ankle hind foot scale improved from 50.5 preoperatively to 85.71 postoperatively (statistically significant; p value - 0.0001). Mean Likert scale value post-operative was 4.21. VAS score showed significant improvement in patients of both the groups. Range of motion was slightly better in soft tissue impingement type with a relatively shorter time to return to sports or preinjury activity level as compared to osseous impingement group. The patients in both the groups had comparable outcomes with no statistically significant difference with regard to patient satisfaction and clinical outcome.

Harrap's shorter dictionary English-French, French-English

CERN Document Server

2004-01-01

Maîtrisez parfaitement l'Anglais et l'Américain modernes. Les évolutions les plus récentes du vocabulaire. 350 000 mots et expressions 600 000 traductions. Nouveau : des centaines de mots nouveaux issus des grands thèmes de l'actualité (altermondialisme, bioterrorisme, coparentalité, bibande...). Une couverture complète du vocabulaire technique et idiomatique des deux langues. Un traitement détaillé des variantes régionales (irlandaises, australiennes, québécoises, belges, etc.). Les sigles, abréviations et noms propres. De nombreuses aides à la traduction : nouveau, 400 entrées longues introduites par des menus pour accéder sans ambiguïté à la bonne traduction ; nouveau, des notes culturelles pour comprendre mots et expressions liés à la civilisation anglo-saxonne ; des centaines de notes d'usage pour éviter les pièges de la traduction : faux amis, mots difficiles à traduire... Des milliers d'exemples pour illustrer les différents sens des mots. L'indication des niveaux de langue : ...

Hypofractionated Breast Radiation: Shorter Scheme, Lower Toxicity.

Science.gov (United States)

Linares, Isabel; Tovar, María Isabel; Zurita, Mercedes; Guerrero, Rosario; Expósito, Manuela; Del Moral, Rosario

2016-08-01

We analyzed the toxicity and cosmetic outcomes for patients who had undergone 3-dimensional conformal radiotherapy with a hypofractionated schedule and identified the risk factors associated with such a schedule. A total of 143 patients were treated for breast cancer (stage 0-III) with a hypofractionated radiation schedule after breast-conserving surgery from 2006 to 2011. Most patients received 42.4 Gy in 16 daily fractions, 2.65 Gy per fraction to the whole breast plus an additional simultaneous integrated or sequential boost to the tumor bed. The median follow-up period was 36 months. Mild acute skin toxicity was observed in 62%; 7% of the patients developed moderate skin toxicity, but no grade 4 toxicity was observed. The prevalence of fibrosis within the boost area was 5%, but no grade ≥ 2 was observed. The prevalence of fibrosis of any grade was greater in the nonboost (23%) than in the boost area. Of all the patients, 91% had good or excellent cosmetic outcomes. From the multivariate analysis, the incidence of epithelitis correlated with the patient's treated volume (P = .044). The incidence of acute toxicity correlated with the boost type to the tumor bed and the total treatment dose (P = .012 and P = .002, respectively). Also, a poor to fair cosmetic outcome was significantly associated statistically with the surgery type (P = .05), boost type (P = .004), and total dose (P = .001). Delivering whole-breast irradiation with a hypofractionated schedule of 42.4 Gy plus a simultaneous integrated boost to the tumor bed appears to be a safe and effective technique, with good cosmetic results and lower toxicity. Copyright © 2015 Elsevier Inc. All rights reserved.

Comparative data from young men and women on masseter muscle fibres, function and facial morphology

DEFF Research Database (Denmark)

Tuxen, A.; Bakke, M.; Pinholt, E. M.

1999-01-01

The primary aim was to relate information about masseter muscle fibres and function to aspects of facial morphology in a group of healthy young men. The secondary aim was to investigate possible sex differences using data previously obtained from a comparable group of age-matched, healthy women......, and the tissue examined for myosin ATPase activity. Further, the cross-sectional areas of the different fibre types were measured. In spite of using age-matched healthy men and women with a full complement of teeth, statistically significant sex differences were found among measures related to muscle function...... and some measures of facial morphology. Thus data from men and women should not be pooled uncritically. The greater bite force in men than women corresponded with the greater diameter and cross-sectional area of type II fibres. Further, the males had more anteriorly inclined mandibles and shorter anterior...

Outcome of Peroral Endoscopic Myotomy (POEM) for Treating Achalasia Compared With Laparoscopic Heller Myotomy (LHM).

Science.gov (United States)

Peng, Lijun; Tian, Shuni; Du, Chao; Yuan, Ziying; Guo, Mingxiao; Lu, Lin

2017-02-01

Peroral endoscopic myotomy (POEM) is an emerging endoscopic treatment for achalasia and the long-term efficacy of POEM remains to be evaluated. This study compared the outcomes of POEM with that of the standard laparoscopic Heller myotomy (LHM) for achalasia. Achalasia patients treated by POEM or LHM were retrospectively analyzed, with a minimum postoperative follow-up of 3 years. Perioperative outcomes and long-term outcomes including treatment success (Eckardt score ≤3), occurrence of gastroesophageal reflux disease (GERD) (GerdQ score ≥9) and quality of life (36-item short form) were compared. Thirteen patients who underwent POEM were compared with 18 patients who received LHM. These patients were similar in age, sex, symptoms duration, Eckardt score, and previous therapy (all P>0.05). Mean myotomy lengths were similar (P=0.73). Operation time was shorter in the POEM group (P=0.001). One patient (7.7%) developed pneumothorax after POEM and 1 patient (5.6%) experienced postoperative infection after LHM (P=1.00). Treatment success was achieved in 83.3% (9/12) of POEM patients and 80.0% (12/15) of LHM patients (P=1.00). Both POEM and LHM significantly reduced Eckardt score (both P=0.00). GERD rate was similar (8.3% vs. 6.7%, P=1.00). There was no difference in all aspects of quality of life between the 2 groups. Long-term outcomes indicate that POEM is an effective treatment that is comparable with LHM. More data of randomized trials comparing POEM with LHM will enrich the existing evidence.

Software-assisted quantitative analysis of small bowel motility compared to manual measurements

International Nuclear Information System (INIS)

Bickelhaupt, S.; Froehlich, J.M.; Cattin, R.; Raible, S.; Bouquet, H.; Bill, U.; Patak, M.A.

2014-01-01

Aim: To validate a newly developed software prototype that automatically analyses small bowel motility by comparing it directly with manual measurement. Material and methods: Forty-five patients with clinical indication for small bowel magnetic resonance imaging (MRI) were retrospectively included in this institutional review board-approved study. MRI was performed using a 1.5 T system following a standard MR-enterography protocol. Small bowel motility parameters (contractions-per-minute, luminal diameter, amplitude) were measured three times each in identical segments using the manual and the semiautomatic software-assisted method. The methods were compared for agreement, repeatability, and time needed for each measurement. All parameters were compared between the methods. Results: A total of 91 small-bowel segments were analysed. No significant intra-individual difference (p > 0.05) was found for peristaltic frequencies between the methods (mean: 4.14/min manual; 4.22/min software-assisted). Amplitudes (5.14 mm; 5.57 mm) and mean lumen diameters (17.39 mm; 14.68) differed due to systematic differences in the definition of the bowel wall. Mean duration of single measurement was significantly (p < 0.01) shorter with the software (6.25 min; 1.30 min). The scattering of repeated measurements was significantly (p < 0.05) lower using the software. Conclusion: The software-assisted method accomplished highly reliable, fast and accurate measurement of small bowel motility. Measurement precision and duration differed significantly between the two methods in favour of the software-assisted technique

Production, fertility, survival, and body measurements of Montbéliarde-sired crossbreds compared with pure Holsteins during their first 5 lactations.

Science.gov (United States)

Hazel, A R; Heins, B J; Seykora, A J; Hansen, L B

2014-01-01

Two-breed crossbreds of Montbéliarde and Holstein (MO × HO) as well as 3-breed crossbreds of Montbéliarde and Jersey/Holstein (MO × JH) were compared with pure Holstein (HO) cows for production, somatic cell score (SCS), fertility, survival to subsequent calving, mortality, and body measurements during their first 5 lactations. Cows calved for the first time between 2005 and 2010 and were housed in either a confinement herd or a herd that had access to pasture for 165d of the year in the north central region of the United States. Body, hoof, and udder measurements of cows were also objectively measured. The MO × HO crossbred cows were not different from pure HO cows for fat-plus-protein production during any lactation. However, the MO × JH crossbred cows had 5% lower fat-plus-protein production compared with pure HO cows in the confinement herd. On the other hand, the MO × JH crossbred cows were not different for fat-plus-protein production in the third to fifth lactation compared with pure HO cows in the seasonal pasture herd. Across the 2 herds, the MO × HO and MO × JH crossbred cows had 21% higher first-service conception rate, 41 fewer days open, and 12% higher pregnancy rate compared with the pure HO cows. Furthermore, the MO × HO (5%) and MO × JH (12%) crossbred cows had lower mortality rates than the pure HO cows (18%). Because of superior fertility and lower mortality rates, the MO × HO and MO × JH crossbred cows, combined, had greater survival to second (+13%), third (+24%), fourth (+25%), and fifth (+17%) lactation compared with pure HO cows. For body measurements, MO × HO were similar to pure HO cows for hip height and heart girth, but MO × HO cows had more body condition and greater body weight (+39kg) across the first 5 lactations. The MO × JH cows had more body condition but 5cm shorter hip height and 28kg less body weight than pure HO cows across the first 5 lactations. Foot angle was steeper and hoof length was shorter for MO × HO

Comparative effectiveness of open versus minimally invasive sacroiliac joint fusion.

Science.gov (United States)

Ledonio, Charles Gt; Polly, David W; Swiontkowski, Marc F; Cummings, John T

2014-01-01

The mainstay of sacroiliac joint disruption/degenerative sacroiliitis therapy has been nonoperative management. This nonoperative management often includes a regimen of physical therapy, chiropractic treatment, therapeutic injections, and possibly radiofrequency ablation at the discretion of the treating physician. When these clinical treatments fail, sacroiliac joint fusion has been recommended as the standard treatment. Open and minimally invasive (MIS) surgical techniques are typical procedures. This study aims to compare the perioperative measures and Oswestry Disability Index (ODI) outcomes associated with each of these techniques. A comparative retrospective chart review of patients with sacroiliac joint fusion and a minimum of 1 year of follow-up was performed. Perioperative measures and ODI scores were compared using the Fisher's exact test and two nonparametric tests, ie, the Mann-Whitney U test and the Wilcoxon signed-rank test. The results are presented as percent or median with range, as appropriate. Forty-nine patients from two institutions underwent sacroiliac joint fusion between 2006 and 2012. Ten patients were excluded because of incomplete data, leaving 39 evaluable patients, of whom 22 underwent open and 17 underwent MIS sacroiliac joint fusion. The MIS group was significantly older (median age 66 [39-82] years) than the open group (median age 51 [34-74] years). Surgical time and hospital stay were significantly shorter in the MIS group than in the open group. Preoperative ODI was significantly greater in the open group (median 64 [44-78]) than in the MIS group (median 53 [14-84]). Postoperative improvement in ODI was statistically significant within and between groups, with MIS resulting in greater improvement. The open and MIS sacroiliac joint fusion techniques resulted in statistically and clinically significant improvement for patients with degenerative sacroiliitis refractory to nonoperative management. However, the number of patients

Highly efficient pulsed power supply system with a two-stage LC generator and a step-up transformer for fast capillary discharge soft x-ray laser at shorter wavelength

International Nuclear Information System (INIS)

Sakai, Yusuke; Takahashi, Shnsuke; Komatsu, Takanori; Song, Inho; Watanabe, Masato; Hotta, Eiki

2010-01-01

Highly efficient and compact pulsed power supply system for a capillary discharge soft x-ray laser (SXRL) has been developed. The system consists of a 2.2 μF two-stage LC inversion generator, a 2:54 step-up transformer, a 3 nF water capacitor, and a discharge section with a few tens of centimeter length capillary. Adoption of the pulsed transformer in combination with the LC inversion generator enables us to use only one gap switch in the circuit for charging the water capacitor up to about 0.5 MV. Furthermore, step-up ratio of a water capacitor voltage to a LC inversion generator initial charging voltage is about 40 with energy transfer efficiency of about 50%. It also leads to good reproducibility of a capillary discharge which is necessary for lasing a SXRL stably. For the study of the possibility of lasing a SXRL at shorter wavelength in a small laboratory scale, high-density and high-temperature plasma column suitable for the laser can be generated relatively easily with this system.

Live Zika virus chimeric vaccine candidate based on a yellow fever 17-D attenuated backbone

OpenAIRE

Nougairede, Antoine; Klitting, Raphaelle; Aubry, Fabien; Gilles, Magali; Touret, Franck; De Lamballerie, Xavier

2018-01-01

Zika virus (ZIKV) recently dispersed throughout the tropics and sub-tropics causing epidemics associated with congenital disease and neurological complications. There is currently no commercial vaccine for ZIKV. Here we describe the initial development of a chimeric virus containing the prM/E proteins of a ZIKV epidemic strain incorporated into a yellow fever 17-D attenuated backbone. Using the versatile and rapid ISA (Infectious Subgenomic Amplicons) reverse genetics method, we compared diff...

Volumetric Modulated Arc Therapy for Spine Radiosurgery: Superior Treatment Planning and Delivery Compared to Static Beam Intensity Modulated Radiotherapy.

Science.gov (United States)

Zach, Leor; Tsvang, Lev; Alezra, Dror; Ben Ayun, Maoz; Harel, Ran

2016-01-01

Spine stereotactic radiosurgery (SRS) delivers an accurate and efficient high radiation dose to vertebral metastases in 1-5 fractions. We aimed to compare volumetric modulated arc therapy (VMAT) to static beam intensity modulated radiotherapy (IMRT) for spine SRS. Ten spine lesions of previously treated SRS patients were planned retrospectively using both IMRT and VMAT with a prescribed dose of 16 Gy to 100% of the planning target volume (PTV). The plans were compared for conformity, homogeneity, treatment delivery time, and safety (spinal cord dose). All evaluated parameters favored the VMAT plan over the IMRT plans. D min in the IMRT was significantly lower than in the VMAT plan (7.65 Gy/10.88 Gy, p DSC) was found to be significantly better for the VMAT plans compared to the IMRT plans (0.77/0.58, resp., p  value < 0.01), and an almost 50% reduction in the net treatment time was calculated for the VMAT compared to the IMRT plans (6.73 min/12.96 min, p < 0.001). In our report, VMAT provides better conformity, homogeneity, and safety profile. The shorter treatment time is a major advantage and not only provides convenience to the painful patient but also contributes to the precision of this high dose radiation therapy.

EUS-directed Transgastric ERCP (EDGE) Versus Laparoscopy-assisted ERCP (LA-ERCP) for Roux-en-Y Gastric Bypass (RYGB) Anatomy: A Multicenter Early Comparative Experience of Clinical Outcomes.

Science.gov (United States)

Kedia, Prashant; Tarnasky, Paul R; Nieto, Jose; Steele, Stephen L; Siddiqui, Ali; Xu, Ming-Ming; Tyberg, Amy; Gaidhane, Monica; Kahaleh, Michel

2018-04-17

The standard of care for managing pancreaticobiliary disease in altered Roux-en-Y gastric bypass patients is laparoscopy-assisted endoscopic retrograde cholangiopancreatography (LA-ERCP), but is limited by cost and adverse events. Recently a minimally invasive, completely endoscopic approach using endoscopic ultrasound (EUS) directed transgastric ERCP (EDGE) has been described. We aim to compare EDGE to LA-ERCP in this study. Patients from May 2005 to June 2017 with Roux-en-Y gastric bypass anatomy having undergone LA-ERCP or EDGE at 4 tertiary centers were captured in a registry. Patient demographics, procedural details, and clinical outcomes were measured for each group. Seventy-two patients (n=29 EDGE, n=43 LA-ERCP) were included in this study. There was no significant difference in the technical success of EDGE gastrogastric fistula (96.5%) versus LA-gastrostomy creation (100%). The success rate of achieving therapeutic ERCP (EDGE 96.5% vs. LA-ERCP 97.7%) and number of ERCP (EDGE 1.2 vs. LA-ERCP 1.02) needed to achieve clinical resolution was similar between both groups. Adverse event rate for EDGE, 24% (7/29) and LA-ERCP, 19% (8/43) was similar. The total procedure time (73 vs. 184 min) and length of hospital stay (0.8 vs. 2.65 d) was significantly shorter for EDGE compared to LA-ERCP. The overall weight change after EDGE was -6.6 lbs at an average 28-week follow-up. This study suggests that the EDGE procedure has similar technical success and adverse events compared with LA-ERCP with the benefit of significantly shorter procedure times and hospital stay. EDGE may offer a minimally invasive, effective option, with less resource utilization, and without significant weight gain.

Voluntary resistance running induces increased hippocampal neurogenesis in rats comparable to load-free running.

Science.gov (United States)

Lee, Min Chul; Inoue, Koshiro; Okamoto, Masahiro; Liu, Yu Fan; Matsui, Takashi; Yook, Jang Soo; Soya, Hideaki

2013-03-14

Recently, we reported that voluntary resistance wheel running with a resistance of 30% of body weight (RWR), which produces shorter distances but higher work levels, enhances spatial memory associated with hippocampal brain-derived neurotrophic factor (BDNF) signaling compared to wheel running without a load (WR) [17]. We thus hypothesized that RWR promotes adult hippocampal neurogenesis (AHN) as a neuronal substrate underlying this memory improvement. Here we used 10-week-old male Wistar rats divided randomly into sedentary (Sed), WR, and RWR groups. All rats were injected intraperitoneally with the thymidine analogue 5-Bromo-2'-deoxuridine (BrdU) for 3 consecutive days before wheel running. We found that even when the average running distance decreased by about half, the average work levels significantly increased in the RWR group, which caused muscular adaptation (oxidative capacity) for fast-twitch plantaris muscle without causing any negative stress effects. Additionally, immunohistochemistry revealed that the total BrdU-positive cells and newborn mature cells (BrdU/NeuN double-positive) in the dentate gyrus increased in both the WR and RWR groups. These results provide new evidence that RWR has beneficial effects on AHN comparable to WR, even with short running distances. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Facial Expression Enhances Emotion Perception Compared to Vocal Prosody: Behavioral and fMRI Studies.

Science.gov (United States)

Zhang, Heming; Chen, Xuhai; Chen, Shengdong; Li, Yansong; Chen, Changming; Long, Quanshan; Yuan, Jiajin

2018-05-09

Facial and vocal expressions are essential modalities mediating the perception of emotion and social communication. Nonetheless, currently little is known about how emotion perception and its neural substrates differ across facial expression and vocal prosody. To clarify this issue, functional MRI scans were acquired in Study 1, in which participants were asked to discriminate the valence of emotional expression (angry, happy or neutral) from facial, vocal, or bimodal stimuli. In Study 2, we used an affective priming task (unimodal materials as primers and bimodal materials as target) and participants were asked to rate the intensity, valence, and arousal of the targets. Study 1 showed higher accuracy and shorter response latencies in the facial than in the vocal modality for a happy expression. Whole-brain analysis showed enhanced activation during facial compared to vocal emotions in the inferior temporal-occipital regions. Region of interest analysis showed a higher percentage signal change for facial than for vocal anger in the superior temporal sulcus. Study 2 showed that facial relative to vocal priming of anger had a greater influence on perceived emotion for bimodal targets, irrespective of the target valence. These findings suggest that facial expression is associated with enhanced emotion perception compared to equivalent vocal prosodies.

A Comparative Study between Universal Eclectic Septoplasty Technique and Cottle

Science.gov (United States)

Amaral Neto, Odim Ferreira do; Mizoguchi, Flavio Massao; Freitas, Renato da Silva; Maniglia, João Jairney; Maniglia, Fábio Fabrício; Maniglia, Ricardo Fabrício

2017-01-01

Introduction  Since the last century surgical correction of nasal septum deviation has been improved. The Universal Eclectic Technique was recently reported and there are still few studies dedicated to address this surgical approach. Objective  The objective of this study is to compare the results of septal deviation correction achieved using the Universal Eclectic Technique (UET) with those obtained through Cottle's Technique. Methods  This is a prospective study with two consecutive case series totaling 90 patients (40 women and 50 men), aged between 18 and 55 years. We divided patients into two groups according to the surgical approach. Fifty-three patients underwent septoplasty through Universal Eclectic Technique (UET) and thirty-seven patients were submitted to classical Cottle's septoplasty technique. All patients have answered the Nasal Obstruction Symptom Evaluation Scale (NOSE) questionnaire to assess pre and postoperative nasal obstruction. Results  Statistical analysis showed a significantly shorter operating time for the UET group. Nasal edema assessment performed seven days after the surgery showed a prevalence of mild edema in UET group and moderate edema in Cottle's technique group. In regard to complication rates, UET presented a single case of septal hematoma while in Cottle's technique group we observed: 02 cases of severe edemas, 01 case of incapacitating headache, and 01 complaint of nasal pain. Conclusion  The Universal Eclectic Technique (UET) has proven to be a safe and effective surgical technique with faster symptomatic improvement, low complication rates, and reduced surgical time when compared with classical Cottle's technique. PMID:28680499

Seed quality and water use characteristics of maize landraces compared with selected commercial hybrids

Directory of Open Access Journals (Sweden)

Farai Mazvimbakupa

2015-03-01

Full Text Available Understanding seed quality and water use characteristics of maize (Zea mays L. landraces will improve food security among subsistence farmers who still cultivate them. The objective of this study was to evaluate seed quality and water use characteristics of two maize landraces (GQ1 and GQ2 compared with two commercial hybrids (SC701 and PAN53. Seed quality was determined by the standard germination, electrical conductivity, and tetrazolium tests. A controlled environment study was conducted in which the landraces were compared with hybrids across three water treatments (30% ETc; 50% ETc, and 80% ETc. Although landrace GQ2 performed at par with the hybrids, overall, seed quality tests showed that hybrids had superior seed quality than landraces. This was also confirmed by highly significant emergence results (P < 0.001 from pot trials where SC701 and PAN53 had higher emergence (100% and 94.44%, respectively compared with GQ2 (86.11% and GQ1 (61.11%. Subjecting landraces and hybrids to water stress (50% and 30% ETc resulted in shorter plants with fewer leaves and earlier tasselling compared with non-stressed plants (80% ETc. Plant height for the 30% ETc water treatment was 156.1 cm compared with 175.8 cm for the 80% ETc water treatment, while plants under the 30% ETc water treatment tasseled at 105.4 d compared with 129.5 d for the 80% ETc water treatment. The GQ2 landrace continued to perform similar to, and often better, than the hybrid varieties, especially under stress conditions. Yield was poor under controlled conditions. Performance of the GQ2 landrace for both seed quality tests and under controlled conditions shows that landraces remain an important germplasm resource.

Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification.

Science.gov (United States)

Ziesemer, Kirsten A; Mann, Allison E; Sankaranarayanan, Krithivasan; Schroeder, Hannes; Ozga, Andrew T; Brandt, Bernd W; Zaura, Egija; Waters-Rist, Andrea; Hoogland, Menno; Salazar-García, Domingo C; Aldenderfer, Mark; Speller, Camilla; Hendy, Jessica; Weston, Darlene A; MacDonald, Sandy J; Thomas, Gavin H; Collins, Matthew J; Lewis, Cecil M; Hofman, Corinne; Warinner, Christina

2015-11-13

To date, characterization of ancient oral (dental calculus) and gut (coprolite) microbiota has been primarily accomplished through a metataxonomic approach involving targeted amplification of one or more variable regions in the 16S rRNA gene. Specifically, the V3 region (E. coli 341-534) of this gene has been suggested as an excellent candidate for ancient DNA amplification and microbial community reconstruction. However, in practice this metataxonomic approach often produces highly skewed taxonomic frequency data. In this study, we use non-targeted (shotgun metagenomics) sequencing methods to better understand skewed microbial profiles observed in four ancient dental calculus specimens previously analyzed by amplicon sequencing. Through comparisons of microbial taxonomic counts from paired amplicon (V3 U341F/534R) and shotgun sequencing datasets, we demonstrate that extensive length polymorphisms in the V3 region are a consistent and major cause of differential amplification leading to taxonomic bias in ancient microbiome reconstructions based on amplicon sequencing. We conclude that systematic amplification bias confounds attempts to accurately reconstruct microbiome taxonomic profiles from 16S rRNA V3 amplicon data generated using universal primers. Because in silico analysis indicates that alternative 16S rRNA hypervariable regions will present similar challenges, we advocate for the use of a shotgun metagenomics approach in ancient microbiome reconstructions.

Evaluating Clonal Expansion of HIV-Infected Cells: Optimization of PCR Strategies to Predict Clonality

Science.gov (United States)

Laskey, Sarah B.; Pohlmeyer, Christopher W.; Bruner, Katherine M.; Siliciano, Robert F.

2016-01-01

In HIV-infected individuals receiving suppressive antiretroviral therapy, the virus persists indefinitely in a reservoir of latently infected cells. The proliferation of these cells may contribute to the stability of the reservoir and thus to the lifelong persistence of HIV-1 in infected individuals. Because the HIV-1 replication process is highly error-prone, the detection of identical viral genomes in distinct host cells provides evidence for the clonal expansion of infected cells. We evaluated alignments of unique, near-full-length HIV-1 sequences to determine the relationship between clonality in a short region and clonality in the full genome. Although it is common to amplify and sequence short, subgenomic regions of the viral genome for phylogenetic analysis, we show that sequence identity of these amplicons does not guarantee clonality across the full viral genome. We show that although longer amplicons capture more diversity, no subgenomic region can recapitulate the diversity of full viral genomes. Consequently, some identical subgenomic amplicons should be expected even from the analysis of completely unique viral genomes, and the presence of identical amplicons alone is not proof of clonally expanded HIV-1. We present a method for evaluating evidence of clonal expansion in the context of these findings. PMID:27494508

Evaluating Clonal Expansion of HIV-Infected Cells: Optimization of PCR Strategies to Predict Clonality.

Directory of Open Access Journals (Sweden)

Sarah B Laskey

2016-08-01

Full Text Available In HIV-infected individuals receiving suppressive antiretroviral therapy, the virus persists indefinitely in a reservoir of latently infected cells. The proliferation of these cells may contribute to the stability of the reservoir and thus to the lifelong persistence of HIV-1 in infected individuals. Because the HIV-1 replication process is highly error-prone, the detection of identical viral genomes in distinct host cells provides evidence for the clonal expansion of infected cells. We evaluated alignments of unique, near-full-length HIV-1 sequences to determine the relationship between clonality in a short region and clonality in the full genome. Although it is common to amplify and sequence short, subgenomic regions of the viral genome for phylogenetic analysis, we show that sequence identity of these amplicons does not guarantee clonality across the full viral genome. We show that although longer amplicons capture more diversity, no subgenomic region can recapitulate the diversity of full viral genomes. Consequently, some identical subgenomic amplicons should be expected even from the analysis of completely unique viral genomes, and the presence of identical amplicons alone is not proof of clonally expanded HIV-1. We present a method for evaluating evidence of clonal expansion in the context of these findings.

Survey for collagenase gene prtC in Porphyromonas gingivalis and Porphyromonas endodontalis isolated from endodontic infections.

Science.gov (United States)

Odell, L J; Baumgartner, J C; Xia, T; David, L L

1999-08-01

Collagenase is a potential virulence factor shown to be expressed by Porphyromonas gingivalis associated with periodontal disease. The purpose of this study was to use the polymerase chain reaction (PCR) to detect the presence of the collagenase gene (prtC) in 21 strains of Porphyromonas species isolated from endodontic infections. Type strains for P. gingivalis (ATCC 33277), P. endodontalis (ATCC 35406), Prevotella intermedia (ATCC 25611), and Prevotella nigrescens (ATCC 33563) were used as controls. When PCR primers specific for the 16S ribosomal RNA gene of P. gingivalis or P. endodontalis were used, 16 of the strains were identified as P. gingivalis, and five strains were identified as P. endodontalis. The presence of the prtC gene for collagenase was detected using PCR. Amplicons were analyzed by agarose gel electrophoresis, with an 815 bp amplicon representing the presence of the collagenase gene. Type strain ATCC 33277 and all 16 clinical isolates of P. gingivalis produced the collagenase gene amplicon. Neither type strain ATCC 35406 nor the five strains from clinical isolates of P. endodontalis produced the collagenase gene amplicon. These results indicate that P. gingivalis from endodontic infections possesses the prtC gene. P. endodontalis does not seem to exhibit prtC. The virulence of P. gingivalis may be related to its production of collagenase.

High-resolution melt-curve analysis of random-amplified-polymorphic-DNA markers, for the characterisation of pathogenic Leptospira

DEFF Research Database (Denmark)

Tulsiani, Suhella; Craig, S B; Graham, G C

2010-01-01

A new test for pathogenic Leptospira isolates, based on RAPD-PCR and high-resolution melt (HRM) analysis (which measures the melting temperature of amplicons in real time, using a fluorescent DNA-binding dye), has recently been developed. A characteristic profile of the amplicons can be used...... typed against 13 previously published RAPD primers, using a real-time cycler (the Corbett Life Science RotorGene 6000) and the optimised reagents from a commercial kit (Quantace SensiMix). RAPD-HRM at specific temperatures generated defining amplicon melt profiles for each of the tested serovars....... These profiles were evaluated as difference-curve graphs generated using the RotorGene software package, with a cut-off of at least 8 'U' (plus or minus). The results demonstrated that RAPD-HRM can be used to measure serovar diversity and establish identity, with a high degree of stability. The characterisation...

Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage

Czech Academy of Sciences Publication Activity Database

Amps, K.; Andrews, P.W.; Anyfantis, G.; Armstrong, L.; Avery, S.; Baharvand, H.; Baker, J.; Baker, D.; Munoz, M. N.; Beil, S.; Benvenisty, N.; Ben-Yosef, D.; Biancotti, J. C.; Bosman, A.; Brena, R. M.; Brison, D.; Caisander, G.; Camarasa, M. V.; Chen, J. M.; Chiao, E.; Choi, Y. M.; Choo, E.; Collins, D.; Colman, A.; Crook, J. M.; Daley, G. Q.; Dalton, A.; De Sousa, P. A.; Denning, C.; Downie, J.; Dvořák, P.; Hampl, Aleš

2011-01-01

Roč. 29, č. 12 (2011), s. 1132-1144 ISSN 1087-0156 Institutional research plan: CEZ:AV0Z50390703 Keywords : comparative genomic hybridization * copy number variation * human es cells Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 23.268, year: 2011

OFFGEL electrophoresis and tandem mass spectrometry approach compared with DNA-based PCR method for authentication of meat species from raw and cooked ground meat mixtures containing cattle meat, water buffalo meat and sheep meat.

Science.gov (United States)

Naveena, Basappa M; Jagadeesh, Deepak S; Jagadeesh Babu, A; Madhava Rao, T; Kamuni, Veeranna; Vaithiyanathan, S; Kulkarni, Vinayak V; Rapole, Srikanth

2017-10-15

The present study compared the accuracy of an OFFGEL electrophoresis and tandem mass spectrometry-based proteomic approach with a DNA-based method for meat species identification from raw and cooked ground meat mixes containing cattle, water buffalo and sheep meat. The proteomic approach involved the separation of myofibrillar proteins using OFFGEL electrophoresis, SDS-PAGE and protein identification by MALDI-TOF MS. Species-specific peptides derived from myosin light chain-1 and 2 were identified for authenticating buffalo meat spiked at a minimum 0.5% level in sheep meat with high confidence. Relative quantification of buffalo meat mixed with sheep meat was done by quantitative label-free mass spectrometry using UPLC-QTOF and PLGS search engine to substantiate the confidence level of the data. In the DNA-based method, PCR amplification of mitochondrial D loop gene using species specific primers found 226bp and 126bp product amplicons for buffalo and cattle meat, respectively. The method was efficient in detecting a minimum of 0.5% and 1.0% when buffalo meat was spiked with cattle meat in raw and cooked meat mixes. Copyright © 2017 Elsevier Ltd. All rights reserved.

Vibrio plantisponsor sp. nov., a diazotrophic bacterium isolated from a mangrove associated wild rice (Porteresia coarctata Tateoka)

Digital Repository Service at National Institute of Oceanography (India)

Rameshkumar, N.; Gomez-Gil, B.; Sproer, C.; Lang, E.; Kumar, N.D.; Krishnamurthi, S.; Nair, S.; Roque, A.

nifH amplicon was purified using Eppendorf Perfectprep Gel Cleanup Kit (according to the manufacturer’s instructions). The purified nifH amplicon was used directly for DNA sequencing with the dideoxy chain termination method with the Big...Dye terminator kit (Applied Biosystems) using the above mentioned nifH primers, and the reaction products were analysed by capillary electrophoresis on an ABI 310 Genetic Analyzer (Applied Biosystems). For phylogenetic analysis, partial nifH nucleotide...

Comparative health technology assessment of robotic-assisted, direct manual laparoscopic and open surgery: a prospective study.

Science.gov (United States)

Turchetti, Giuseppe; Pierotti, Francesca; Palla, Ilaria; Manetti, Stefania; Freschi, Cinzia; Ferrari, Vincenzo; Cuschieri, Alfred

2017-02-01

Despite many publications reporting on the increased hospital cost of robotic-assisted surgery (RAS) compared to direct manual laparoscopic surgery (DMLS) and open surgery (OS), the reported health economic studies lack details on clinical outcome, precluding valid health technology assessment (HTA). The present prospective study reports total cost analysis on 699 patients undergoing general surgical, gynecological and thoracic operations between 2011 and 2014 in the Italian Public Health Service, during which period eight major teaching hospitals treated the patients. The study compared total healthcare costs of RAS, DMLS and OS based on prospectively collected data on patient outcome in addition to healthcare costs incurred by the three approaches. The cost of RAS operations was significantly higher than that of OS and DMLS for both gynecological and thoracic operations (p DMLS. Total costs of general surgery RAS were significantly higher than those of OS (p DMLS general surgery. Indirect costs were significantly lower in RAS compared to both DMLS general surgery and OS gynecological surgery due to the shorter length of hospital stay of RAS approach (p < 0.001). Additionally, in all specialties compared to OS, patients treated by RAS experienced a quicker recovery and significantly less pain during the hospitalization and after discharge. The present HTA while confirming higher total healthcare costs for RAS operations identified significant clinical benefits which may justify the increased expenditure incurred by this approach.

The POINT-AGAPE Survey: Comparing Automated Searches of Microlensing Events toward M31

CERN Document Server

Tsapras, Y; Weston, M J; Kerins, E; Baillon, P; Gould, A; Paulin-Henriksson, S

2010-01-01

Searching for microlensing in M31 using automated superpixel surveys raises a number of difficulties which are not present in more conventional techniques. Here we focus on the problem that the list of microlensing candidates is sensitive to the selection criteria or "cuts" imposed and some subjectivity is involved in this. Weakening the cuts will generate a longer list of microlensing candidates but with a greater fraction of spurious ones; strengthening the cuts will produce a shorter list but may exclude some genuine events. We illustrate this by comparing three analyses of the same data-set obtained from a 3-year observing run on the INT in La Palma. The results of two of these analyses have been already reported: Belokurov et al. (2005) obtained between 3 and 22 candidates, depending on the strength of their cuts, while Calchi Novati et al. (2005) obtained 6 candidates. The third analysis is presented here for the first time and reports 10 microlensing candidates, 7 of which are new. Only two of the cand...

Systematic review and meta-analysis of published, randomized, controlled trials comparing suture anastomosis to stapled anastomosis for ileostomy closure.

Science.gov (United States)

Sajid, M S; Craciunas, L; Baig, M K; Sains, P

2013-12-01

The objective of this article is to systematically analyze the randomized, controlled trials comparing the effectiveness of suture anastomosis (SUA) versus stapled anastomosis (STA) in patients undergoing ileostomy closure. Randomized, controlled trials comparing the effectiveness of SUA versus STA in patients undergoing ileostomy closure were analyzed using RevMan(®), and combined outcomes were expressed as odds risk ratio (OR) and standardized mean difference (SMD). Four randomized, controlled trials that recruited 645 patients were retrieved from electronic databases. There were 327 patients in the STA group and 318 patients in the SUA group. There was significant heterogeneity among included trials. Operative time (SMD -1.02; 95 % CI -1.89, -0.15; z = 2.29; p infection, reoperation and readmission were similar following STA and SUA in patients undergoing ileostomy closure. Length of hospital stay was also similar between STA and SUA groups. In ileostomy closure, STA was associated with shorter operative time and lower risk of postoperative small bowel obstruction. However, STA and SUA were similar in terms of anastomotic leak, surgical site infection, readmission, reoperations and length of hospital stay.

Comparison of 454 Ultra-Deep Sequencing and Allele-Specific Real-Time PCR with Regard to the Detection of Emerging Drug-Resistant Minor HIV-1 Variants after Antiretroviral Prophylaxis for Vertical Transmission.

Directory of Open Access Journals (Sweden)

Andrea Hauser

Full Text Available Pregnant HIV-infected women were screened for the development of HIV-1 drug resistance after implementation of a triple-antiretroviral transmission prophylaxis as recommended by the WHO in 2006. The study offered the opportunity to compare amplicon-based 454 ultra-deep sequencing (UDS and allele-specific real-time PCR (ASPCR for the detection of drug-resistant minor variants in the HIV-1 reverse transcriptase (RT.Plasma samples from 34 Tanzanian women were previously analysed by ASPCR for key resistance mutations in the viral RT selected by AZT, 3TC, and NVP (K70R, K103N, Y181C, M184V, T215Y/F. In this study, the RT region of the same samples was investigated by amplicon-based UDS for resistance mutations using the 454 GS FLX System.Drug-resistant HIV-variants were identified in 69% (20/29 of women by UDS and in 45% (13/29 by ASPCR. The absolute number of resistance mutations identified by UDS was twice that identified by ASPCR (45 vs 24. By UDS 14 of 24 ASPCR-detected resistance mutations were identified at the same position. The overall concordance between UDS and ASPCR was 61.0% (25/41. The proportions of variants quantified by UDS were approximately 2-3 times lower than by ASPCR. Amplicon generation from samples with viral loads below 20,000 copies/ml failed more frequently by UDS compared to ASPCR (limit of detection = 650 copies/ml, resulting in missing or insufficient sequence coverage.Both methods can provide useful information about drug-resistant minor HIV-1 variants. ASPCR has a higher sensitivity than UDS, but is restricted to single resistance mutations. In contrast, UDS is limited by its requirement for high viral loads to achieve sufficient sequence coverage, but the sequence information reveals the complete resistance patterns within the genomic region analysed. Improvements to the UDS limit of detection are in progress, and UDS could then facilitate monitoring of drug-resistant minor variants in the HIV-1 quasispecies.

Amplicon restriction patterns associated with nitrogenase activity of ...

Indian Academy of Sciences (India)

2013-10-01

Oct 1, 2013 ... Nitrogen-fixing actinomycete micro-symbiont Frankia nodulates roots of ... the tree is useful in stabilizing nitrogen-depleted soils. Two species of genus .... labelled plastic bags, brought to the laboratory and stored at. −80°C for ...

Meckel's cave access: anatomic study comparing the endoscopic transantral and endonasal approaches.

Science.gov (United States)

Van Rompaey, Jason; Suruliraj, Anand; Carrau, Ricardo; Panizza, Benedict; Solares, C Arturo

2014-04-01

Recent advances in endonasal endoscopy have facilitated the surgical access to the lateral skull base including areas such as Meckel's cave. This approach has been well documented, however, few studies have outlined transantral specific access to Meckel's. A transantral approach provides a direct pathway to this region obviating the need for extensive endonasal and transsphenoidal resection. Our aim in this study is to compare the anatomical perspectives obtained in endonasal and transantral approaches. We prepared 14 cadaveric specimens with intravascular injections of colored latex. Eight cadavers underwent endoscopic endonasal transpterygoid approaches to Meckel's cave. Six additional specimens underwent an endoscopic transantral approach to the same region. Photographic evidence was obtained for review. 30 CT scans were analyzed to measure comparative distances to Meckel's cave for both approaches. The endoscopic approaches provided a direct access to the anterior and inferior portions of Meckel's cave. However, the transantral approach required shorter instrumentation, and did not require clearing of the endonasal corridor. This approach gave an anterior view of Meckel's cave making posterior dissection more difficult. A transantral approach to Meckel's cave provides access similar to the endonasal approach with minimal invasiveness. Some of the morbidity associated with extensive endonasal resection could possibly be avoided. Better understanding of the complex skull base anatomy, from different perspectives, helps to improve current endoscopic skull base surgery and to develop new alternatives, consequently, leading to improvements in safety and efficacy.

Comparative study on aerosol removal by natural processes in containment in severe accident for AP1000 reactor

International Nuclear Information System (INIS)

Sun, Xiaohui; Cao, Xinrong; Shi, Xingwei; Yan, Jin

2017-01-01

Highlights: • Characteristics of aerosol distribution in containment are obtained. • Aerosol removal by natural processes is comparative studied by two methods. • Traditional rapid assessment method is conservative and can be applied in AP1000 reactor. - Abstract: Focusing on aerosol removal by naturally occurring processes in containment in severe accident for AP1000, integral severe accident code MELCOR and rapid assessment method mentioned in NUREG/CR-6189 are utilized to study aerosol removal by natural processes, respectively. Three typical severe accidents, induced by large break loss of coolant accident (LBLOCA), small break loss of coolant accident (SBLOCA) and steam generator tube rupture (SGTR), respectively, are selected for the study. The results obtained by two methods were further compared in the following several aspects: efficiency of aerosol removal by natural processes, peak time of aerosol suspended in containment atmosphere, peak amount of aerosol suspended in containment atmosphere, time when aerosol removal efficiency by natural processes is up to 99.9%. It was further concluded that results obtained by rapid assessment with shorter calculation process are more conservative. The analysis results provide reference to assessment method selection of severe accident source term for AP1000 nuclear emergency.

EFFECTIVENESS OF AGILE COMPARED TO WATERFALL IMPLEMENTATION METHODS IN IT PROJECTS: ANALYSIS BASED ON BUSINESS INTELLIGENCE PROJECTS

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Kisielnicki Jerzy

2017-10-01

Full Text Available The global Business Intelligence (BI market grew by 7.3% in 2016 according to the Gartner report (2017. Today, organizations require better use of data and analytics to support their business decisions. Internet power and business trend changes have provided a broad term for data analytics - Big Data. To be able to handle it and leverage a value of having access to Big Data, organizations have no other choice than to get proper systems implemented and working. However, traditional methods are not efficient for changing business needs. Long time between project start and go-live causes a gap between initial solution blueprint and actual user requirements at the end of the project. This article presents the latest market trends in BI systems implementation by comparing agile with traditional methods. It presents a case study provided in a large telecommunications company (350 BI users and the results of a pilot research provided in the three large companies: media, digital, and insurance. Both studies prove that agile methods might be more effective in BI projects from an end-user perspective and give first results and added value in a much shorter time compared to a traditional approach.

Two new mini-slings compared with transobturator tension-free vaginal tape for treatment of stress urinary incontinence: A 1-year follow-up randomized controlled trial.

Science.gov (United States)

Gaber, Mohamed E; Borg, Tamer; Samour, Hazem; Nawara, Mai; Reda, Ahmed

2016-12-01

The aim of this study was to compare the outcome of two single-incision mini-slings (the Contasure-Needleless [C-NDL] and the endopelvic free anchorage) with the standard midurethral transobturator tension-free vaginal tape (TVT-O) procedure. A double blind randomized controlled study was conducted at Ain Shams University Maternity Hospital from August 2014 until July 2015. A total of 209 patients were randomized into three groups. The first group underwent the TVT-O procedure, the second group underwent the endopelvic free anchorage procedure and the third group underwent the C-NDL procedure. Patients were followed up for 12 months in terms of subjective cure, objective cure, and complications rate. After 12 months of follow-up, there were no differences among the three groups in terms of objective cure rate, subjective cure rate, patient satisfaction, or incidence of complications (de novo urge, hemorrhage, infection, and mesh erosion). The C-NDL was associated with a shorter operative time (P < 0.001) and less blood loss (P = 0.021) than the standard TVT-O. The new single-incision mini-slings showed similar efficacy and patient acceptance to that of the standard TVT-O for up to 12 months postoperatively with no difference in the complications rate. The C-NDL is associated with shorter operative time and less blood loss. © 2016 Japan Society of Obstetrics and Gynecology.

Percutaneous closure of patent ductus arteriosus in small infants with significant lung disease may offer faster recovery of respiratory function when compared to surgical ligation.

Science.gov (United States)

Abu Hazeem, Anas A; Gillespie, Matthew J; Thun, Haley; Munson, David; Schwartz, Matthew C; Dori, Yoav; Rome, Jonathan J; Glatz, Andrew C

2013-10-01

To describe our experience with percutaneous closure of patent ductus arteriosus (PDA) in small infants and compare outcomes to matched surgical patients. Ligation via thoracotomy has been used to close PDAs in small infants, but has been associated with respiratory and hemodynamic compromise. We hypothesized that percutaneous closure would offer faster recovery of respiratory function. Patients closure between January 2000 and April 2012 were reviewed and matched to contemporary surgical patients on gestational age (GA), birth weight (BW), procedure weight (WT), and ventilation mode. Patients returned to baseline respiratory status when the product of mean airway pressure and FiO2 returned to pre-procedural levels. Eight matched pairs were included. Median BW, GA, and WT were 1.43 kg (0.52-2.97), 29.8 weeks (24-39), and 2.8 kg (2.2-3.9) for catheter patients and 1.55 kg (0.48-3.04), 29 weeks (23-37), and 2.75 kg (2.3-4.2) for surgical patients. Complete PDA closure occurred in all. The median time to return to baseline respiratory status was significantly shorter in the percutaneous group (17 hr (range 0-113) vs. 53 hr (range 13-219), P closure of PDA in small infants on respiratory support is equivalent in safety and efficacy and may offer shorter recovery time than surgical ligation. Copyright © 2013 Wiley Periodicals, Inc.

Incubation period and immune function: A comparative field study among coexisting birds

Science.gov (United States)

Palacios, M.G.; Martin, T.E.

2006-01-01

Developmental periods are integral components of life history strategies that can have important fitness consequences and vary enormously among organisms. However, the selection pressures and mechanisms causing variation in length of developmental periods are poorly understood. Particularly puzzling are prolonged developmental periods, because their selective advantage is unclear. Here we tested the hypotheses that immune function is stronger in species that are attacked at a higher rate by parasites and that prolonged embryonic development allows the development of this stronger immune system. Through a comparative field study among 12 coexisting passerine bird species, we show that species with higher blood parasite prevalence mounted stronger cellular immune responses than species with lower prevalence. These results provide support for the hypothesis that species facing greater selection pressure from parasites invest more in immune function. However, species with longer incubation periods mounted weaker cellular immune responses than species with shorter periods. Therefore, cellular immune responses do not support the hypothesis that longer development time enhances immunocompentence. Future studies should assess other components of the immune system and test alternative causes of variation in incubation periods among bird species. ?? Springer-Verlag 2005.

Accelerated Comparative Fatigue Strength Testing of Belt Adhesive Joints

Science.gov (United States)

Bajda, Miroslaw; Blazej, Ryszard; Jurdziak, Leszek

2017-12-01

Belt joints are the weakest link in the serial structure that creates an endless loop of spliced belt segments. This affects not only the lower strength of adhesive joints of textile belts in comparison to vulcanized splices, but also the replacement of traditional glues to more ecological but with other strength parameters. This is reflected in the lowered durability of adhesive joints, which in underground coal mines is nearly twice shorter than the operating time of belts. Vulcanized splices require high precision in performance, they need long time to achieve cross-linking of the friction mixture and, above all, they require specialized equipment (vulcanization press) which is not readily available and often takes much time to be delivered down, which means reduced mining output or even downtime. All this reduces the reliability and durability of adhesive joints. In addition, due to the consolidation on the Polish coal market, mines are joined into large economic units serviced by a smaller number of processing plants. The consequence is to extend the transport routes downstream and increase reliability requirements. The greater number of conveyors in the chain reduces reliability of supply and increases production losses. With high fixed costs of underground mines, the reduction in mining output is reflected in the increase in unit costs, and this at low coal prices on the market can mean substantial losses for mines. The paper describes the comparative study of fatigue strength of shortened samples of adhesive joints conducted to compare many different variants of joints (various adhesives and materials). Shortened samples were exposed to accelerated fatigue in the usually long-lasting dynamic studies, allowing more variants to be tested at the same time. High correlation between the results obtained for shortened (100 mm) and traditional full-length (3×250 mm) samples renders accelerated tests possible.

Measurement of gastric emptying time: a comparative study between nonisotopic aspiration method and new radioisotopic technique

International Nuclear Information System (INIS)

Chaudhuri, T.K.; Greenwald, A.J.; Heading, R.C.; Chaudhuri, T.K.

1975-01-01

A comparative study between modified conventional saline load test and the more recently introduced radioisotopic method was run in 8 normal volunteers. Each subject underwent at least three studies by each of the two methods: (1) aspiration method Goldstein and Boyle incorporating our modification, and (2) an isotopic method employing a gamma camera with a computer. A liquid metal of isotonic saline was used with or without /sup 99m/Tc-DTPA. The results indicated that the gastric emptying T 1 / 2 (8.8 +- 3.5 min) obtained by saline load test was shorter than that obtained by isotopic method (12 +- 3 min). This discrepancy was most likely due to inherent error (incomplete aspiration of the gastric fluid) in the former method giving rise to a false faster emptying time. Moreover, the variations in T 1 / 2 value in the same individual was much more in the aspiration method than it was in the isotopic method

A morphogenetic survey on ciliate plankton from a mountain lake pinpoints the necessity of lineage-specific barcode markers in microbial ecology.

Science.gov (United States)

Stoeck, Thorsten; Breiner, Hans-Werner; Filker, Sabine; Ostermaier, Veronika; Kammerlander, Barbara; Sonntag, Bettina

2014-02-01

Analyses of high-throughput environmental sequencing data have become the 'gold-standard' to address fundamental questions of microbial diversity, ecology and biogeography. Findings that emerged from sequencing are, e.g. the discovery of the extensive 'rare microbial biosphere' and its potential function as a seed-bank. Even though applied since several years, results from high-throughput environmental sequencing have hardly been validated. We assessed how well pyrosequenced amplicons [the hypervariable eukaryotic V4 region of the small subunit ribosomal RNA (SSU rRNA) gene] reflected morphotype ciliate plankton. Moreover, we assessed if amplicon sequencing had the potential to detect the annual ciliate plankton stock. In both cases, we identified significant quantitative and qualitative differences. Our study makes evident that taxon abundance distributions inferred from amplicon data are highly biased and do not mirror actual morphotype abundances at all. Potential reasons included cell losses after fixation, cryptic morphotypes, resting stages, insufficient sequence data availability of morphologically described species and the unsatisfying resolution of the V4 SSU rRNA fragment for accurate taxonomic assignments. The latter two underline the necessity of barcoding initiatives for eukaryotic microbes to better and fully exploit environmental amplicon data sets, which then will also allow studying the potential of seed-bank taxa as a buffer for environmental changes. © 2013 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Volumetric Modulated Arc Therapy for Spine Radiosurgery: Superior Treatment Planning and Delivery Compared to Static Beam Intensity Modulated Radiotherapy

Directory of Open Access Journals (Sweden)

Leor Zach

2016-01-01

Full Text Available Purpose. Spine stereotactic radiosurgery (SRS delivers an accurate and efficient high radiation dose to vertebral metastases in 1–5 fractions. We aimed to compare volumetric modulated arc therapy (VMAT to static beam intensity modulated radiotherapy (IMRT for spine SRS. Methods and Materials. Ten spine lesions of previously treated SRS patients were planned retrospectively using both IMRT and VMAT with a prescribed dose of 16 Gy to 100% of the planning target volume (PTV. The plans were compared for conformity, homogeneity, treatment delivery time, and safety (spinal cord dose. Results. All evaluated parameters favored the VMAT plan over the IMRT plans. Dmin in the IMRT was significantly lower than in the VMAT plan (7.65 Gy/10.88 Gy, p<0.001, the Dice Similarity Coefficient (DSC was found to be significantly better for the VMAT plans compared to the IMRT plans (0.77/0.58, resp., p  value<0.01, and an almost 50% reduction in the net treatment time was calculated for the VMAT compared to the IMRT plans (6.73 min/12.96 min, p<0.001. Conclusions. In our report, VMAT provides better conformity, homogeneity, and safety profile. The shorter treatment time is a major advantage and not only provides convenience to the painful patient but also contributes to the precision of this high dose radiation therapy.

Patients with Duchenne muscular dystrophy are significantly shorter than those with Becker muscular dystrophy, with the higher incidence of short stature in Dp71 mutated subgroup.

Science.gov (United States)

Matsumoto, Masaaki; Awano, Hiroyuki; Lee, Tomoko; Takeshima, Yasuhiro; Matsuo, Masafumi; Iijima, Kazumoto

2017-11-01

Duchenne and Becker muscular dystrophy (DMD/BMD) are caused by mutations in the dystrophin gene and are characterized by severe and mild progressive muscle wasting, respectively. Short stature has been reported as a feature of DMD in the Western hemisphere, but not yet confirmed in Orientals. Height of young BMD has not been fully characterized. Here, height of ambulant and steroid naive Japanese 179 DMD and 42 BMD patients between 4 and 10 years of age was retrospectively examined using height standard deviation score (SDS). The mean height SDS of DMD was -1.08 SD that was significantly smaller than normal (p < 0.001), indicating short stature of Japanese DMD. Furthermore, the mean height SDS of BMD was -0.27 SD, suggesting shorter stature than normal. Remarkably, the mean height SDS of DMD was significantly smaller than that of BMD (p < 0.0001). In DMD higher incidence of short stature (height SDS < -2.5 SD) was observed in Dp71 subgroup having mutations in dystrophin exons 63-79 than others having mutations in exons 1-62 (27.8% vs. 7.5%, p = 0.017). These suggested that height is influenced by dystrophin in not only DMD but also BMD and that dystrophin Dp71 has a role in height regulation. Copyright © 2017 Elsevier B.V. All rights reserved.

Centrosome clustering and cyclin D1 gene amplification in double minutes are common events in chromosomal unstable bladder tumors

International Nuclear Information System (INIS)

Rey, Javier del; Prat, Esther; Ponsa, Immaculada; Lloreta, Josep; Gelabert, Antoni; Algaba, Ferran; Camps, Jordi; Miró, Rosa

2010-01-01

Aneuploidy, centrosome abnormalities and gene amplification are hallmarks of chromosome instability (CIN) in cancer. Yet there are no studies of the in vivo behavior of these phenomena within the same bladder tumor. Twenty-one paraffin-embedded bladder tumors were analyzed by conventional comparative genome hybridization and fluorescence in situ hybridization (FISH) with a cyclin D1 gene (CCND1)/centromere 11 dual-color probe. Immunofluorescent staining of α, β and γ tubulin was also performed. Based on the CIN index, defined as the percentage of cells not displaying the modal number for chromosome 11, tumors were classified as CIN-negative and CIN-positive. Fourteen out of 21 tumors were considered CIN-positive. All T1G3 tumors were included in the CIN-positive group whereas the majority of Ta samples were classified as CIN-negative tumors. Centrosome clustering was observed in six out of 12 CIN-positive tumors analyzed. CCND1 amplification in homogeneously staining regions was present in six out of 14 CIN-positive tumors; three of them also showed amplification of this gene in double minutes. Complex in vivo behavior of CCND1 amplicon in bladder tumor cells has been demonstrated by accurate FISH analysis on paraffin-embedded tumors. Positive correlation between high heterogeneity, centrosome abnormalities and CCND1 amplification was found in T1G3 bladder carcinomas. This is the first study to provide insights into the coexistence of CCND1 amplification in homogeneously staining regions and double minutes in primary bladder tumors. It is noteworthy that those patients whose tumors showed double minutes had a significantly shorter overall survival rate (p < 0.001)

Comparative assessment of alignment efficiency and space closure of active and passive self-ligating vs conventional appliances in adolescents: a single-center randomized controlled trial.

Science.gov (United States)

Songra, Goldie; Clover, Matthew; Atack, Nikki E; Ewings, Paul; Sherriff, Martyn; Sandy, Jonathan R; Ireland, Anthony J

2014-05-01

The aim of this study was to compare the time to initial alignment and extraction space closure using conventional brackets and active and passive self-ligating brackets. One hundred adolescent patients 11 to 18 years of age undergoing maxillary and mandibular fixed appliance therapy after the extraction of 4 premolars were randomized with stratification of 2 age ranges (11-14 and 15-18 years) and 3 maxillomandibular plane angles (high, medium, and low) with an allocation ratio of 1:2:2. Restrictions were applied using a block size of 10. Allocation was to 1 of 3 treatment groups: conventional brackets, active self-ligating, or passive self-ligating brackets. All subjects were treated with the same archwire sequence and space-closing mechanics in a district general hospital setting. The trial was a 3-arm parallel design. Labial-segment alignment and space closure were measured on study models taken every 12 weeks throughout treatment. All measurements were made by 1 operator who was blinded to bracket type. The patients and other operators were not blinded to bracket type during treatment. Ninety-eight patients were followed to completion of treatment (conventional, n = 20; active self-ligating brackets, n = 37; passive self-ligating brackets, n = 41). The data were analyzed using linear mixed models and demonstrated a significant effect of bracket type on the time to initial alignment (P = 0.001), which was shorter with the conventional brackets than either of the self-ligating brackets. Sidak's adjustment showed no significant difference in effect size (the difference in average response in millimeters) between the active and passive self-ligating brackets (the results are presented as effect size, 95% confidence intervals, probabilities, and intraclass correlation coefficients) (-0.42 [-1.32, 0.48], 0.600, 0.15), but the conventional bracket was significantly different from both of these (-1.98 [-3.19, -0.76], 0.001, 0.15; and -1.56 [-2.79, -0.32], 0.001, 0

Efficiency of levobupivacaine and bupivacaine for supraclavicular block: a randomized double-blind comparative study

Directory of Open Access Journals (Sweden)

Cenk Ilham

2014-06-01

Full Text Available Background and objectives: Success rate of catheter applications is low in supraclavicular block. Thus, bupivacaine and levobupivacaine become important with their long effect time in single injection practices. In this study, we aimed to compare the effectiveness, side effects and complications of bupivacaine and levobupivacaine in supraclavicular block. Methods: Sixty patients aged between 20 and 65, with body weight between 50 and 100 kg, in the ASA I-II-III group who were scheduled for hand, forearm and arm surgery using supraclavicular block were randomized into two groups of 30. The patients received 30 ml 0.5% bupivacaine (Group B or 30 ml 0.5% levobupivacaine (Group L. Motor and sensory blocks were evaluated. Motor and sensory block onset times, total block durations, postoperative pain, amount of postoperative analgesic used and patient satisfaction were recorded. Results: Demographic data, distribution of surgical area and hemodynamic data were similar between the two groups. Surgery, motor and sensory block durations of Group B and L patients did not vary statistically significantly. However, motor and sensory block onset times in Group B were significantly shorter than Group L (p 0.05. Conclusion: 30 ml 0.5% bupivacaine and levobupivacaine provide similar block characteristics for supraclavicular block. Bupivacaine leads to faster motor and sensory block onset compared to levobupivacaine however similar duration of postoperative analgesia.

Complete Genomes of Classical Swine Fever Virus Cloned into Bacterial Artificial Chromosomes

DEFF Research Database (Denmark)

Rasmussen, Thomas Bruun; Reimann, I.; Uttenthal, Åse

Complete genome amplification of viral RNA provides a new tool for the generation of modified pestiviruses. We have used our full-genome amplification strategy for generation of amplicons representing complete genomes of classical swine fever virus. The amplicons were cloned directly into a stabl...... single-copy bacterial artificial chromosome (BAC) generating full-length pestivirus DNAs from which infectious RNA transcripts could be also derived. Our strategy allows construction of stable infectious BAC DNAs from a single full-length PCR product....

Comparing Outcomes and Cost of 3 Surgical Treatments for Sagittal Synostosis: A Retrospective Study Including Procedure-Related Cost Analysis.

Science.gov (United States)

Garber, Sarah T; Karsy, Michael; Kestle, John R W; Siddiqi, Faizi; Spanos, Stephen P; Riva-Cambrin, Jay

2017-10-01

Neurosurgical techniques for repair of sagittal synostosis include total cranial vault (TCV) reconstruction, open sagittal strip (OSS) craniectomy, and endoscopic strip (ES) craniectomy. To evaluate outcomes and cost associated with these 3 techniques. Via retrospective chart review with waiver of informed consent, the last consecutive 100 patients with sagittal synostosis who underwent each of the 3 surgical correction techniques before June 30, 2013, were identified. Clinical, operative, and process of care variables and their associated specific charges were analyzed along with overall charge. The study included 300 total patients. ES patients had fewer transfusion requirements (13% vs 83%, P cost savings compared with the TCV reconstruction. The charges were similar to those incurred with OSS craniectomy, but patients had a shorter length of stay and fewer revisions. Copyright © 2017 by the Congress of Neurological Surgeons

Effectiveness of sublingual nitroglycerin before puncture compared with conventional intra-arterial nitroglycerin in transradial procedures: a randomized trial

Energy Technology Data Exchange (ETDEWEB)

Turan, Burak, E-mail: drburakturan@gmail.com; Daşlı, Tolga; Erkol, Ayhan; Erden, İsmail

2015-10-15

Aim: Sublingual (SL) nitroglycerin administered before radial artery puncture can improve cannulation success and decrease the incidence of radial artery spasm (RAS) compared with intra-arterial (IA) nitroglycerin in transradial procedures. Methods: Patients undergoing diagnostic transradial angiography were randomized to IA (200 mcg) or SL (400 mcg) nitroglycerin. Primary endpoints were puncture time and puncture attempts. Secondary endpoint was the incidence of RAS. Results: Total of 101 participants (mean age 60 ± 11 years, 53% male) were randomized (51 in IA and 50 in SL groups). Puncture time (50 [36–75] vs 50 [35–90] sec), puncture attempts (1.18 ± 0.48 vs 1.20 ± 0.49), multiple punctures (13.7 vs 16.0%) and RAS (19.6 vs 24.0%) were not statistically different between IA vs SL groups respectively. A composite endpoint of all adverse events related to transradial angiography (multiple punctures, RAS, access site crossover, hypotension/bradycardia associated with nitroglycerin and radial artery occlusion) was very similar in IA vs SL groups (39 vs 40%, respectively). However puncture time was significantly longer with SL nitroglycerin in patients < 1.65 m height (47 [36–66] vs 63 [41–110] sec, p = 0.042). Multiple punctures seemed higher with SL nitroglycerin in patients with diabetes (0 vs 30%, p = 0.028) or in patients < 1.65 m height (7.4 vs 25%, p = 0.085). Likewise, RAS with SL nitroglycerin seemed more frequent in smokers compared to IA nitroglycerin (0 vs 27%, p = 0.089). Conclusions: SL nitroglycerin was not different from IA nitroglycerin in terms of efficiency and safety in overall study population. However it may be inferior to IA nitroglycerin in certain subgroups (shorter individuals, diabetics and smokers). - Highlights: • Improvement in radial artery puncture time and success with subcutaneous nitrate was reported. • Giving nitrate sublingually may have vasodilation along entire length of radial artery and may prevent RAS

Inferior Pedicle Reduction Mammoplasty with or without Tourniquet: A Comparative Study.

Science.gov (United States)

Demir, Canser Yilmaz; Sultanoglu, Yılmaz; Kocak, Omer Faruk; Ersoz, Muhammet Eren

2017-10-01

To compare the perioperative findings of inferior pedicle reduction mammoplasty (IPRM) performed with or without a tourniquet. This study was carried out in the plastic and reconstructive surgery department at a tertiary care center on a total of 42 consecutive women scheduled for IPRM. Patients in Group I (n = 21) underwent surgery using a tourniquet, whereas patients in Group II (n = 21) were operated on without a tourniquet. Levels of hemoglobin (Hb), hematocrit (Hct), Hct/Hb ratio, and platelet counts were noted preoperatively and on postoperative 24th and 48th h. Numbers of surgical pads and gauze sponges completely used and dripping with blood were recorded. Duration of operation, the amount of breast tissue excised on both sides, and fluid collected in hemovac drains on 48th h after operation were documented. In Group I, the operative time was significantly shorter (p usage is practical and safe, and it may also improve the cost-effectiveness of the procedure. This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .

Shorter sleep duration is associated with social impairment and comorbidities in ASD.

Science.gov (United States)

Veatch, Olivia J; Sutcliffe, James S; Warren, Zachary E; Keenan, Brendan T; Potter, Melissa H; Malow, Beth A

2017-07-01

Sleep disturbance, particularly insomnia, is common in children with autism spectrum disorders (ASD). Furthermore, disturbed sleep affects core symptoms and other related comorbidities. Understanding the causes and consequences of sleep disturbances in children with ASD is an important step toward mitigating these symptoms. To better understand the connection between sleep duration and ASD severity, we analyzed ASD-related symptoms using the Autism Diagnostic Interview-Revised (ADI-R), Autism Diagnostic Observation Schedule (ADOS), IQ scores, and parent reports of the average amount of time slept per night that were available in the medical histories of 2,714 children with ASD in the Simons Simplex Collection (SSC). The mean (SD) sleep duration was 555 minutes. Sleep duration and severity of core ASD symptoms were negatively correlated, and sleep duration and IQ scores were positively correlated. Regression results indicated that more severe social impairment, primarily a failure to develop peer relationships, is the core symptom most strongly associated with short sleep duration. Furthermore, increased severity for numerous maladaptive behaviors assessed on the Child Behavior Checklist, as well as reports of attention deficit disorder, depressive disorder, and obsessive compulsive disorder were associated with short sleep duration. Severity scores for social/communication impairment and restricted and repetitive behaviors (RRB) were increased, and IQ scores were decreased, for children reported to sleep ≤420 minutes per night (lower 5th percentile) compared to children sleeping ≥660 minutes (upper 95th percentile). Our results indicate that reduced amounts of sleep are related to more severe symptoms in children with ASD. Autism Res 2017. © 2017 International Society for Autism Research, Wiley Periodicals, Inc. Autism Res 2017, 10: 1221-1238. © 2017 International Society for Autism Research, Wiley Periodicals, Inc. © 2017 International Society for Autism

Primary infectious spondylodiscitis in 51 patients over 75 years old: A comparative study.

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Dubost, Jean-Jacques; Lopez, Julien; Pereira, Bruno; Castagne, Benjamin; Tournadre, Anne; Soubrier, Martin; Couderc, Marion

2018-05-23

The incidence of infectious spondylodiscitis has been shown to rise with age; however, they had not been extensively investigated in the very elderly. This retrospective, monocentric study included patients hospitalized in our department of rheumatology for primary infectious spondylodiscitis between 2000 and 2015, and compared over 75-year-olds with younger patients. Of the 152 patients, 51 (33.6%) were≥75 years old, 59 were 61-74, and 42 were≤60. Patients≥75 years old were more often institutionalized (7.8 vs. 0; P=.02), were less often subject to infection risk factors (27.5 vs. 54.5%; P=.02), but did not differ from the others as regards the frequency of diabetes and cancer. Time to diagnosis was shorter for the under 60-year-olds (23 vs. 30 vs. 30 day for each age group, respectively; P<.05). There were no differences among the age groups in terms of spondylodiscitis localization, frequency of neurological symptoms and fever, frequency or intensity of inflammatory syndrome, imaging use, frequency of microorganism identification, blood culture positivity, or use and efficacy of disco-vertebral biopsy. Microorganism distribution was comparable among the groups, except for Gram-negative bacilli, with Escherichia coli more common in over 75-year-olds (7/8 vs. 4/14; P=.02). Duration of antibiotherapy and hospitalization was comparable across the age groups. Five patients died, all over 75 years old (5/51 vs. 0/101; P=.001). Age is a risk factor for primary spondylodiscitis, associated with significant mortality in over 75-year-olds (10%). For these elderly patients, spondylodiscitis does not bear any other distinguishing features. Copyright © 2017 Elsevier España, S.L.U. All rights reserved.

Comparing Microbiome Sampling Methods in a Wild Mammal: Fecal and Intestinal Samples Record Different Signals of Host Ecology, Evolution.

Science.gov (United States)

Ingala, Melissa R; Simmons, Nancy B; Wultsch, Claudia; Krampis, Konstantinos; Speer, Kelly A; Perkins, Susan L

2018-01-01

The gut microbiome is a community of host-associated symbiotic microbes that fulfills multiple key roles in host metabolism, immune function, and tissue development. Given the ability of the microbiome to impact host fitness, there is increasing interest in studying the microbiome of wild animals to better understand these communities in the context of host ecology and evolution. Human microbiome research protocols are well established, but wildlife microbiome research is still a developing field. Currently, there is no standardized set of best practices guiding the collection of microbiome samples from wildlife. Gut microflora are typically sampled either by fecal collection, rectal swabbing, or by destructively sampling the intestinal contents of the host animal. Studies rarely include more than one sampling technique and no comparison of these methods currently exists for a wild mammal. Although some studies have hypothesized that the fecal microbiome is a nested subset of the intestinal microbiome, this hypothesis has not been formally tested. To address these issues, we examined guano (feces) and distal intestinal mucosa from 19 species of free-ranging bats from Lamanai, Belize, using 16S rRNA amplicon sequencing to compare microbial communities across sample types. We found that the diversity and composition of intestine and guano samples differed substantially. In addition, we conclude that signatures of host evolution are retained by studying gut microbiomes based on mucosal tissue samples, but not fecal samples. Conversely, fecal samples retained more signal of host diet than intestinal samples. These results suggest that fecal and intestinal sampling methods are not interchangeable, and that these two microbiotas record different information about the host from which they are isolated.

Comparing Microbiome Sampling Methods in a Wild Mammal: Fecal and Intestinal Samples Record Different Signals of Host Ecology, Evolution

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Melissa R. Ingala

2018-05-01

Full Text Available The gut microbiome is a community of host-associated symbiotic microbes that fulfills multiple key roles in host metabolism, immune function, and tissue development. Given the ability of the microbiome to impact host fitness, there is increasing interest in studying the microbiome of wild animals to better understand these communities in the context of host ecology and evolution. Human microbiome research protocols are well established, but wildlife microbiome research is still a developing field. Currently, there is no standardized set of best practices guiding the collection of microbiome samples from wildlife. Gut microflora are typically sampled either by fecal collection, rectal swabbing, or by destructively sampling the intestinal contents of the host animal. Studies rarely include more than one sampling technique and no comparison of these methods currently exists for a wild mammal. Although some studies have hypothesized that the fecal microbiome is a nested subset of the intestinal microbiome, this hypothesis has not been formally tested. To address these issues, we examined guano (feces and distal intestinal mucosa from 19 species of free-ranging bats from Lamanai, Belize, using 16S rRNA amplicon sequencing to compare microbial communities across sample types. We found that the diversity and composition of intestine and guano samples differed substantially. In addition, we conclude that signatures of host evolution are retained by studying gut microbiomes based on mucosal tissue samples, but not fecal samples. Conversely, fecal samples retained more signal of host diet than intestinal samples. These results suggest that fecal and intestinal sampling methods are not interchangeable, and that these two microbiotas record different information about the host from which they are isolated.

Patients with gout have short telomeres compared with healthy participants: association of telomere length with flare frequency and cardiovascular disease in gout.

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Vazirpanah, N; Kienhorst, L B E; Van Lochem, E; Wichers, C; Rossato, M; Shiels, P G; Dalbeth, N; Stamp, L K; Merriman, T R; Janssen, M; Radstake, T R D J; Broen, J Ca

2017-07-01

Chronic inflammation associates with increased senescence, which is a strong predictor for cardiovascular disease. We hypothesised that inflammation accelerates senescence and thereby enhances the risk of cardiovascular disease in gout. We assessed replicative senescence by quantifying telomere length (TL) in a discovery cohort of 145 Dutch patients with gout and 273 healthy individuals and validated our results in 474 patients with gout and 293 healthy participants from New Zealand. Subsequently, we investigated the effect of cardiovascular disease on TL of all participants. Also, we measured TL of CD4 + and CD8 + T lymphocytes, B lymphocytes, monocytes, natural killer cells and plasmacytoid dendritic cells. Additionally, we assessed the potential temporal difference in TL and telomerase activity. TL in PBMCs of healthy donors decreased over time, reflecting normal ageing. Patients with gout demonstrated shorter telomeres (p=0.001, R 2 =0.01873). In fact, the extent of telomere erosion in patients with gout was higher at any age compared with healthy counterparts at any age (pgout with cardiovascular disease had the shortest telomeres and TL was an independent risk factor for cardiovascular disease in patients with gout (p=0.001). TL was inversely associated with the number of gouty flares (p=0.005). Patients with gout have shorter telomeres than healthy participants, reflecting increased cellular senescence. Telomere shortening was associated with the number of flares and with cardiovascular disease in people with gout. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

A set of 14 DIP-SNP markers to detect unbalanced DNA mixtures.

Science.gov (United States)

Liu, Zhizhen; Liu, Jinding; Wang, Jiaqi; Chen, Deqing; Liu, Zidong; Shi, Jie; Li, Zeqin; Li, Wenyan; Zhang, Gengqian; Du, Bing

2018-03-04

Unbalanced DNA mixture is still a difficult problem for forensic practice. DIP-STRs are useful markers for detection of minor DNA but they are not widespread in the human genome and having long amplicons. In this study, we proposed a novel type of genetic marker, termed DIP-SNP. DIP-SNP refers to the combination of INDEL and SNP in less than 300bp length of human genome. The multiplex PCR and SNaPshot assay were established for 14 DIP-SNP markers in a Chinese Han population from Shanxi, China. This novel compound marker allows detection of the minor DNA contributor with sensitivity from 1:50 to 1:1000 in a DNA mixture of any gender with 1 ng-10 ng DNA template. Most of the DIP-SNP markers had a relatively high probability of informative alleles with an average I value of 0.33. In all, we proposed DIP-SNP as a novel kind of genetic marker for detection of minor contributor from unbalanced DNA mixture and established the detection method by associating the multiplex PCR and SNaPshot assay. DIP-SNP polymorphisms are promising markers for forensic or clinical mixture examination because they are shorter, widespread and higher sensitive. Copyright © 2018 Elsevier Inc. All rights reserved.

Sensor Systems with Magnetic and Optomagnetic Readout of Rolling Circle Amplification Products

DEFF Research Database (Denmark)

Hansen, Mikkel Fougt; Donolato, Marco; Fock, Jeppe

2016-01-01

We are developing robust biosensors for homogeneous detection of rolling cirle amplification (RCA) products with magnetic and/or optomagnetic readouts based on surface-functionalized magnetic nanoparticles. Binding of RCA amplicons to nanoparticles modifies their ability to rotate in response...... to an applied oscillating magnetic field. As a result, magnetic or optical measurements of these changes in the rotational response of nanoparticles vs. frequency of the magnetic field can be used to quantitate the number of amplicons, and, hence, the concentration of target nucleic acid analytes. After...

Postoperative Analgesia in Children- Comparative Study between Caudal Bupivacaine and Bupivacaine plus Tramadol

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Meena Doda

2009-01-01

Full Text Available Thirty children, ASAI-II, aged between 2yrs-5yrs, undergoing sub umbilical operation (inguinal and penile surgery were selected for this double blind study. They were randomly divided in two groups, group Aand group B. Group A(n15 received 0.25%bupivacaine 0.5ml.kg -1 and Group B (n=15 received 0.25% bupivaeaine 0.5ml.kg -1 and tramadol 2mg.kg -1 as single shot caudal block. Postoperative pain was assessed by a modified TPPPS (Toddler-Preschool Postoperative Pain Scale and analgesic given only when the score was more than 3. In the first 24 hrs it was observed that the mean duration of time interval between the caudal block and first dose of analgesic was significantly long(9. lhrs in Group B as compared to Group A (6.3hrs which was much shorter(p< 0.01.There was no significant haemodynamie changes, motor weakness or respiratory depression in both groups. This study con-cluded that addition of tramadol 2mg.kg -1 to caudal 0.25% bupivacaine 0.5ml.kg -1 significantly prolong the duration of postoperative analgesia in children withoutprodueing much adverse effects.

Microbial diversity and evidence of novel homoacetogens in the gut of both geriatric and adult giant pandas (Ailuropoda melanoleuca.

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Hein Min Tun

Full Text Available Recent studies have described the bacterial community residing in the guts of giant pandas, together with the presence of lignocellulolytic enzymes. However, a more comprehensive understanding of the intestinal microbial composition and its functional capacity in giant pandas remains a major goal. Here, we conducted a comparison of bacterial, fungal and homoacetogenic microbial communities from fecal samples taken from two geriatric and two adult captive giant pandas. 16S rDNA amplicon pyrosequencing revealed that Firmicutes and Proteobacteria are the most abundant microbiota in both geriatric and adult giant pandas. However, members of phylum Actinobacteria found in adult giant pandas were absent in their geriatric counterparts. Similarly, ITS1 amplicon pyrosequencing identified developmental changes in the most abundant fungal classes from Sordariomycetes in adult pandas to Saccharomycetes in geriatric pandas. Geriatric pandas exhibited significantly higher abundance of a potential probiotic fungus (Candida tropicalis as compared to adult pandas, indicating their importance in the normal digestive physiology of aged pandas. Our study also reported the presence of a lignocellulolytic white-rot fungus, Perenniporia medulla-panis, and the evidence of novel homoacetogens residing in the guts of giant pandas.

Impact of management protocols of intrauterine fetal death on perceived stress: A comparative study

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Mita Mandal

2017-01-01

Full Text Available Background: Pregnancy loss is a distressing problem and retention of dead fetus in utero has its own ill effects on physical, psychological, and social aspects, and hence, it is better to recommend medical induction, provided this can be safely undertaken. Aims: The aim of this study is to compare the efficacy, tolerability, induction-delivery interval, and perceived stress scores between induction methods in late intrauterine fetal death (IUFD with misoprostol alone and mifepristone with misoprostol combination in a rural population of Eastern India. Materials and Methods: This pilot study was conducted on 125 patients after taking institutional ethical clearance and informed consent of the patients in a time span of 1 year. Group 2 patients received 200 mg of mifepristone per orally and observed for 48 h, followed by 50 μg misoprostol administered in the posterior vaginal fornix, and repeated 6th hourly up to a maximum of four doses. Group 1 received 50 μg misoprostol per vaginally 6 hourly for four doses. Induction-delivery interval was calculated. Perceived stress level was calculated on admission and before discharge. Results: Significantly lower induction-delivery interval was observed in Group 2 as compared to Group 1 with P < 0.001. There was no significant difference of Cohen's perceived stress scores on admission, but the difference was significantly lower in Group 2 on discharge with the value of P = 0.03. Group 1 had significantly lower hospital stay in days as compared to Group 2 of patients with P < 0.001. Conclusions: Patients with IUFD administered misoprostol per vaginally only may require shorter hospital stay as compared to patients administered with oral mifepristone followed by misoprostol vaginally but the delivery induction time increases significantly and may increase perceived stress levels which may have short- and long-term negative psychological impact.

Shorter lines facilitate reading in those who struggle.

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Matthew H Schneps

Full Text Available People with dyslexia, who ordinarily struggle to read, sometimes remark that reading is easier when e-readers are used. Here, we used eye tracking to observe high school students with dyslexia as they read using these devices. Among the factors investigated, we found that reading using a small device resulted in substantial benefits, improving reading speeds by 27%, reducing the number of fixations by 11%, and importantly, reducing the number of regressive saccades by more than a factor of 2, with no cost to comprehension. Given that an expected trade-off between horizontal and vertical regression was not observed when line lengths were altered, we speculate that these effects occur because sluggish attention spreads perception to the left as the gaze shifts during reading. Short lines eliminate crowded text to the left, reducing regression. The effects of attention modulation by the hand, and of increased letter spacing to reduce crowding, were also found to modulate the oculomotor dynamics in reading, but whether these factors resulted in benefits or costs depended on characteristics, such as visual attention span, that varied within our sample.

How empathic are vegan medical professionals compared to others? Leads from a paper-pencil-survey.

Science.gov (United States)

Kessler, Christian S; Michalsen, Andreas; Holler, Sophie; Murthy, Vijayendra S; Cramer, Holger

2018-05-01

The aim of this survey was to examine differences in personality profiles among 198 vegan (n = 64; 32.3%), vegetarian (n = 78; 39.4%) and omnivore (n = 55; 27.8%) medical professionals. Outcomes were motives for the nutritional approaches, WHO QoL-BREF, Big Five SOEP Inventory, Portraits Value Questionnaire, and Empathizing Scale. Regarding motives for particular diets, omnivores rated influence of guardians (p vegans and vegetarians. Vegans and vegetarians consumed less coffee (p = 0.007) and alcohol compared to omnivores (p = 0.017). The duration of adhering to a specific diet was significantly shorter in vegans. Data suggest that vegan medical professionals do not differ from vegetarians or omnivores regarding empathy, values or personality traits. Differences to a related internet sample were observed for a number of outcomes. Given the small sample size and potential selection bias through the specific subpopulation attending a plant-based nutrition conference, further studies are warranted to confirm these results. Particularly, potential reciprocities between empathy and individual nutritional choices deserve further attention.

Total versus subtotal Laparoscopic Hysterectomy: A comparative study in Arash Hospital

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Samiei H

2009-09-01

Full Text Available "n Normal 0 false false false EN-US X-NONE AR-SA MicrosoftInternetExplorer4 st1":*{behavior:url(#ieooui } /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin:0in; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:Arial; mso-bidi-theme-font:minor-bidi;} Background: Over the past 50 years, subtotal or supracervical hysterectomy has come to be viewed as a suboptimal procedure reserved for those rare instances in which when concern over blood loss or anatomic distortion dictates limiting the extent of dissection, the aim of this study was to compare total and subtotal laparoscopic hysterectomy. "n"nMethods: The patients who were candidates for hysterectomy with benign disease, with no contraindication for laparoscopic surgery entered the study in Arash Hospital, from March 2007 to April 2009. By simple randomization 45 patients (25 for TLH and 20 for SLH were selected. Demographic Details and intra and post operative complications, were recorded by the staff and were compared between two groups."n"nResults: The average time for TLH operations look significantly longer than SLH operation (148.6±29.7 minutes; 128.5±25.64 minutes, p=0.03. Although, the hemoglobin (gr/dl drop in TLH was significantly higher than SLH (1.54 Versus 0.9, p<0.05 Blood transfusion were common in SLH (1 case Versus 3 Cases. The total length of hospital stay, was significantly shorter after SLH than TLH (3.6±1.47 day and 2.85±0.59, p=0.04. The drug requirements to

A comparative study on optical and magnetic resonance properties of near-surface NV centers in nano and bulk diamond

International Nuclear Information System (INIS)

Frederico Brandao

2014-01-01

Using shallow nitrogen-vacancy (NV) centers in diamond for applications in magnetometry requires the generation of stable defects in the NV charge state in sufficiently high density and high quality spin properties. Recent studies reported about NV defects close to the surface created by ion implantation or during chemical vapor deposition growth technique and in nanodiamonds point to a scenario where defects are stabilized in the neutral charge state and that the minority of negatively charged state defects have poor spin properties, i.e.g shorter coherence times compared to NV defects deeply localized in bulk diamond. This undesirable behavior appears to result from the interaction with rapidly fluctuating electric fields created by moving charges at the surface and with interface effects associated with the termination of the diamond surface. Here we report studies of photoluminescence and magnetic resonance properties of shallow NV ensembles created by low energy nitrogen ion implantation in electronic grade diamond substrate and nanodiamonds with low nitrogen concentration. We verified the shallow NV center spin properties through pulsed optically detected magnetic resonance (ODMR) protocols and found longitudinal time constant (T1) of a few milliseconds and transversal relaxation time constant (T2) of a few microseconds for shallow defects implanted in bulk diamond. For nanodiamonds, the T2 coherence time is similar to the case in bulk sample but on the other hand the T1 coherence time is ten times shorter than in bulk. Additionally was found the T2* is around one microsecond for shallow NV defects in bulk samples meanwhile in nanodiamonds it is around twenty nanoseconds. It worth to mention that all the measurements were performed in NV ensembles which show just two ODMR resonance lines with applied magnetic field as if they were magnetically equivalent. In that sense we are trying to apply chirped pulses and Ramsey pulse sequence to check this assumption

Comparative in vitro toxicity assessment of perfluorinated carboxylic acids.

Science.gov (United States)

Mahapatra, Cecon T; Damayanti, Nur P; Guffey, Samuel C; Serafin, Jennifer S; Irudayaraj, Joseph; Sepúlveda, Maria S

2017-06-01

Perfluoroalkyl and polyfluoroalkyl substances (PFASs) are synthetic fluorinated compounds that are highly bioaccumulative and persistent organic pollutants. Perfluorooctanoic acid (PFOA), an eight-carbon chain perfluorinated carboxylic acid, was used heavily for the production of fluoropolymers, but concerns have led to its replacement by shorter carbon chain homologues such as perfluorohexanoic acid (PFHxA) and perfluorobutanoic acid (PFBA). However, limited toxicity data exist for these substitutes. We evaluated the toxicity of PFOA, PFHxA and PFBA on a zebrafish liver cell line and investigated the effects of exposure on cell metabolism. Gross toxicity after 96 h of exposure was highest for PFOA and PFO - , while PFHxA and PFBA exhibited lower toxicity. Although the structural similarity of these compounds to fatty acids suggests the possibility of interference with the transport and metabolism of lipids, we could not detect any differential expression of peroxisome proliferator-activated receptor (ppar-α, -β and -γ), fabp3 and crot genes after 96 h exposure to up to 10 ppm of the test compounds. However, we observed localized lipid droplet accumulation only in PFBA-exposed cells. To study the effects of these compounds on cell metabolism, we conducted fluorescence lifetime imaging microscopy using naturally fluorescent biomarkers, NADH and FAD. The fluorescence lifetimes of NADH and FAD and the bound/free ratio of each of these coenzymes decreased in a dose- and carbon length-dependent manner, suggesting disruption of cell metabolism. In sum, our study revealed that PFASs with shorter carbon chains are less toxic than PFOA, and that exposure to sublethal dosage of PFOA, PFHxA or PFBA affects cell metabolism. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Measuring single constructs by single items: Constructing an even shorter version of the "Short Five" personality inventory.

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Kenn Konstabel

Full Text Available The aim of this study was to construct a short, 30-item personality questionnaire that would be, in terms of content and meaning of the scores, as comparable as possible with longer, well-established inventories such as NEO PI-R and its clones. To do this, we shortened the formerly constructed 60-item "Short Five" (S5 by half so that each subscale would be represented by a single item. We compared all possibilities of selecting 30 items (preserving balanced keying within each domain of the five-factor model in terms of correlations with well-established scales, self-peer correlations, and clarity of meaning, and selected an optimal combination for each domain. The resulting shortened questionnaire, XS5, was compared to the original S5 using data from student samples in 6 different countries (Estonia, Finland, UK, Germany, Spain, and China, and a representative Finnish sample. The correlations between XS5 domain scales and their longer counterparts from well-established scales ranged from 0.74 to 0.84; the difference from the equivalent correlations for full version of S5 or from meta-analytic short-term dependability coefficients of NEO PI-R was not large. In terms of prediction of external criteria (emotional experience and self-reported behaviours, there were no important differences between XS5, S5, and the longer well-established scales. Controlling for acquiescence did not improve the prediction of criteria, self-peer correlations, or correlations with longer scales, but it did improve internal reliability and, in some analyses, comparability of the principal component structure. XS5 can be recommended as an economic measure of the five-factor model of personality at the level of domain scales; it has reasonable psychometric properties, fair correlations with longer well-established scales, and it can predict emotional experience and self-reported behaviours no worse than S5. When subscales are essential, we would still recommend using the

Comparing the reported burn conditions for different severity burns in porcine models: a systematic review.

Science.gov (United States)

Andrews, Christine J; Cuttle, Leila

2017-12-01

There are many porcine burn models that create burns using different materials (e.g. metal, water) and different burn conditions (e.g. temperature and duration of exposure). This review aims to determine whether a pooled analysis of these studies can provide insight into the burn materials and conditions required to create burns of a specific severity. A systematic review of 42 porcine burn studies describing the depth of burn injury with histological evaluation is presented. Inclusion criteria included thermal burns, burns created with a novel method or material, histological evaluation within 7 days post-burn and method for depth of injury assessment specified. Conditions causing deep dermal scald burns compared to contact burns of equivalent severity were disparate, with lower temperatures and shorter durations reported for scald burns (83°C for 14 seconds) compared to contact burns (111°C for 23 seconds). A valuable archive of the different mechanisms and materials used for porcine burn models is presented to aid design and optimisation of future models. Significantly, this review demonstrates the effect of the mechanism of injury on burn severity and that caution is recommended when burn conditions established by porcine contact burn models are used by regulators to guide scald burn prevention strategies. © 2017 Medicalhelplines.com Inc and John Wiley & Sons Ltd.

Comprehensive evaluation and optimization of amplicon library preparation methods for high-throughput antibody sequencing.

Science.gov (United States)

Menzel, Ulrike; Greiff, Victor; Khan, Tarik A; Haessler, Ulrike; Hellmann, Ina; Friedensohn, Simon; Cook, Skylar C; Pogson, Mark; Reddy, Sai T

2014-01-01

High-throughput sequencing (HTS) of antibody repertoire libraries has become a powerful tool in the field of systems immunology. However, numerous sources of bias in HTS workflows may affect the obtained antibody repertoire data. A crucial step in antibody library preparation is the addition of short platform-specific nucleotide adapter sequences. As of yet, the impact of the method of adapter addition on experimental library preparation and the resulting antibody repertoire HTS datasets has not been thoroughly investigated. Therefore, we compared three standard library preparation methods by performing Illumina HTS on antibody variable heavy genes from murine antibody-secreting cells. Clonal overlap and rank statistics demonstrated that the investigated methods produced equivalent HTS datasets. PCR-based methods were experimentally superior to ligation with respect to speed, efficiency, and practicality. Finally, using a two-step PCR based method we established a protocol for antibody repertoire library generation, beginning from inputs as low as 1 ng of total RNA. In summary, this study represents a major advance towards a standardized experimental framework for antibody HTS, thus opening up the potential for systems-based, cross-experiment meta-analyses of antibody repertoires.

Forensic validation of the PowerPlex® ESI 16 STR Multiplex and comparison of performance with AmpFlSTR® SGM Plus®.

Science.gov (United States)

Tucker, Valerie C; Kirkham, Amanda J; Hopwood, Andrew J

2012-05-01

We describe the forensic validation of Promega's PowerPlex® European Standard Investigator 16 (ESI 16) multiplex kit and compare results generated with the AmpFlSTR® SGM Plus® (SGM+) multiplex. ESI 16 combines the loci contained within the SGM+ multiplex with five additional loci: D2S441, D10S1248, D22S1045, D1S1656, and D12S391. A relative reduction in amplicon size of the SGM+ loci facilitates an increased robustness and amplification success of these amplicons with degraded DNA samples. Tests performed herein supplement ESI 16 data published previously with sensitivity, profile quality, mock casework, inhibitor and mixture study data collected in our laboratories in alignment with our internal technical and quality guidelines and those issued by the Scientific Working Group on DNA Analysis Methods (SWGDAM), the DNA Advisory Board (DAB) and the DNA working group (DNAWG) of the European Network of Forensic Science Institutes (ENFSI). Full profiles were routinely generated from a fully heterozygous single source DNA template using 62.5 pg for ESI 16 and 500 pg for SGM+. This increase in sensitivity has a consequent effect on mixture analyses and the detection of minor mixture components. The improved PCR chemistry confers enhanced tolerance to high levels of laboratory prepared inhibitors compared with SGM+ results. In summary, our results demonstrate that the ESI 16 multiplex kit is more robust and sensitive compared with SGM+ and will be a suitable replacement system for the analysis of forensic DNA samples providing compliance with the European standard set of STR loci.

Anaesthetic induction and recovery characteristics of a diazepam-ketamine combination compared with propofol in dogs

Directory of Open Access Journals (Sweden)

Jacques P. Ferreira

2015-06-01

Full Text Available Induction of anaesthesia occasionally has been associated with undesirable behaviour in dogs. High quality of induction of anaesthesia with propofol has been well described while in contrast variable induction and recovery quality has been associated with diazepam-ketamine. In this study, anaesthetic induction and recovery characteristics of diazepam-ketamine combination with propofol alone were compared in dogs undergoing elective orchidectomy. Thirty-six healthy adult male dogs were used. After habitus scoring (simple descriptive scale [SDS], the dogs were sedated with morphine and acepromazine. Forty minutes later a premedication score (SDS was allocated and general anaesthesia was induced using a combination of diazepam-ketamine (Group D/K or propofol (Group P and maintained with isoflurane. Scores for the quality of induction, intubation and degree of myoclonus were allocated (SDS. Orchidectomy was performed after which recovery from anaesthesia was scored (SDS and times to extubation and standing were recorded. Data were analysed using descriptive statistics and Kappa Reliability and Kendall Tau B tests. Both groups were associated with acceptable quality of induction and recovery from anaesthesia. Group P, however, was associated with a poorer quality of induction (p = 0.014, prolonged induction period (p = 0.0018 and more pronounced myoclonus (p = 0.003, but had better quality of recovery (p = 0.000002 and shorter recovery times (p = 0.035 compared with Group D/K. Diazepam-ketamine and propofol are associated with acceptable induction and recovery from anaesthesia. Propofol had inferior anaesthetic induction characteristics, but superior and quicker recovery from anaesthesia compared with diazepam-ketamine.

The development and validation of a shorter version of the Canadian Health Care Evaluation Project Questionnaire (CANHELP Lite): a novel tool to measure patient and family satisfaction with end-of-life care.

Science.gov (United States)

Heyland, Daren K; Jiang, Xuran; Day, Andrew G; Cohen, S Robin

2013-08-01

The recently developed Canadian Health Care Evaluation Project (CANHELP) questionnaire, which can be used to assess both patient and family satisfaction with end-of-life care, takes 40-60 minutes to complete. The length of the interview may limit its uptake and clinical utility; a shorter version would make its use more feasible. The purpose of this study was to develop and validate a shorter version of the CANHELP questionnaire. Data were collected using a cross-sectional survey of patients with advanced medical diseases and their family members. Participants completed the long version of CANHELP, a global rating of satisfaction with care (GRS), the FAMCARE scale (family members only), and a quality-of-life (QOL) questionnaire. We reduced the items on the long version based on their relationship to the GRS, the frequency of missing data, the distribution of responses, the redundancy of the items, and focus groups with frontline users. With the remaining items, we assessed internal consistency using Cronbach's alpha, and evaluated construct validity by describing the correlation of the new CANHELP Lite with the full version of CANHELP, GRS, FAMCARE, and the QOL questionnaire scores. A total of 363 patients and 193 family members participated in this study. The patient version was reduced from 37 items to 20 items and the caregiver version was reduced from 38 items to 21 items. Cronbach's alphas ranged from 0.68 to 0.93 for all domains of both the patient and caregiver questionnaires. We observed a high degree of correlation between CANHELP Lite domains and overall scores and the same domains and overall scores for the full version of CANHELP. In addition, we observed moderate to strong correlation between the CANHELP Lite overall satisfaction scores and the GRS questions. There was moderate correlation between the overall family member CANHELP Lite score and overall FAMCARE score (r = 0.45) and this was similar to the correlation between the full version of

The Intestinal Eukaryotic and Bacterial Biome of Spotted Hyenas: The Impact of Social Status and Age on Diversity and Composition.

Science.gov (United States)

Heitlinger, Emanuel; Ferreira, Susana C M; Thierer, Dagmar; Hofer, Heribert; East, Marion L

2017-01-01

In mammals, two factors likely to affect the diversity and composition of intestinal bacteria (bacterial microbiome) and eukaryotes (eukaryome) are social status and age. In species in which social status determines access to resources, socially dominant animals maintain better immune processes and health status than subordinates. As high species diversity is an index of ecosystem health, the intestinal biome of healthier, socially dominant animals should be more diverse than those of subordinates. Gradual colonization of the juvenile intestine after birth predicts lower intestinal biome diversity in juveniles than adults. We tested these predictions on the effect of: (1) age (juvenile/adult) and (2) social status (low/high) on bacterial microbiome and eukaryome diversity and composition in the spotted hyena ( Crocuta crocuta ), a highly social, female-dominated carnivore in which social status determines access to resources. We comprehensively screened feces from 35 individually known adult females and 7 juveniles in the Serengeti ecosystem for bacteria and eukaryotes, using a set of 48 different amplicons (4 for bacterial 16S, 44 for eukaryote 18S) in a multi-amplicon sequencing approach. We compared sequence abundances to classical coprological egg or oocyst counts. For all parasite taxa detected in more than six samples, the number of sequence reads significantly predicted the number of eggs or oocysts counted, underscoring the value of an amplicon sequencing approach for quantitative measurements of parasite load. In line with our predictions, our results revealed a significantly less diverse microbiome in juveniles than adults and a significantly higher diversity of eukaryotes in high-ranking than low-ranking animals. We propose that free-ranging wildlife can provide an intriguing model system to assess the adaptive value of intestinal biome diversity for both bacteria and eukaryotes.

Comparative analysis of bacterial community-metagenomics in coastal Gulf of Mexico sediment microcosms following exposure to Macondo oil (MC252)

KAUST Repository

Koo, Hyunmin

2014-09-10

The indigenous bacterial communities in sediment microcosms from Dauphin Island (DI), Petit Bois Island (PB) and Perdido Pass (PP) of the coastal Gulf of Mexico were compared following treatment with Macondo oil (MC252) using pyrosequencing and culture-based approaches. After quality-based trimming, 28,991 partial 16S rRNA sequence reads were analyzed by rarefaction, confirming that analyses of bacterial communities were saturated with respect to species diversity. Changes in the relative abundances of Proteobacteria, Bacteroidetes and Firmicutes played an important role in structuring bacterial communities in oil-treated sediments. Proteobacteria were dominant in oil-treated samples, whereas Firmicutes and Bacteroidetes were either the second or the third most abundant taxa. Tenericutes, members of which are known for oil biodegradation, were detected shortly after treatment, and continued to increase in DI and PP sediments. Multivariate statistical analyses (ADONIS) revealed significant dissimilarity of bacterial communities between oil-treated and untreated samples and among locations. In addition, a similarity percentage analysis showed the contribution of each species to the contrast between untreated and oil-treated samples. PCR amplification using DNA from pure cultures of Exiguobacterium,  Pseudoalteromonas,  Halomonas and Dyadobacter, isolated from oil-treated microcosm sediments, produced amplicons similar to polycyclic aromatic hydrocarbon-degrading genes. In the context of the 2010 Macondo blowout, the results from our study demonstrated that the indigenous bacterial communities in coastal Gulf of Mexico sediment microcosms responded to the MC252 oil with altered community structure and species composition. The rapid proliferation of hydrocarbonoclastic bacteria suggests their involvement in the degradation of the spilt oil in the Gulf of Mexico ecosystem.

Comparative toxicity of sodium carbonate peroxyhydrate to freshwater organisms.

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Geer, Tyler D; Kinley, Ciera M; Iwinski, Kyla J; Calomeni, Alyssa J; Rodgers, John H

2016-10-01

Sodium carbonate peroxyhydrate (SCP) is a granular algaecide containing H2O2 as an active ingredient to control growth of noxious algae. Measurements of sensitivities of target and non-target species to hydrogen peroxide are necessary for water resource managers to make informed decisions and minimize risks for non-target species when treating noxious algae. The objective of this study was to measure and compare responses among a target noxious alga (cyanobacterium Microcystis aeruginosa) and non-target organisms including a eukaryotic alga (chlorophyte Pseudokirchneriella subcapitata), microcrustacean (Ceriodaphnia dubia), benthic amphipod (Hyalella azteca), and fathead minnow (Pimephales promelas) to exposures of hydrogen peroxide as SCP. Hydrogen peroxide exposures were confirmed using the I3(-) method. SCP margins of safety for these organisms were compared with published toxicity data to provide context for other commonly used algaecides and herbicides (e.g. copper formulations, endothall, and diquat dibromide). Algal responses (cell density and chlorophyll a concentrations) and animal mortality were measured after 96h aqueous exposures to SCP in laboratory-formulated water to estimate EC50 and LC50 values, as well as potency slopes. Despite a shorter test duration, M. aeruginosa was more sensitive to hydrogen peroxide as SCP (96h EC50:0.9-1.0mgL(-)(1) H2O2) than the eukaryotic alga P. subcapitata (7-d EC50:5.2-9.2mgL(-1) H2O2), indicating potential for selective control of prokaryotic algae. For the three non-target animals evaluated, measured 96-h LC50 values ranged from 1.0 to 19.7mgL(-1) H2O2. C. dubia was the most sensitive species, and the least sensitive species was P. promelas, which is not likely to be affected by concentrations of hydrogen peroxide as SCP that would be used to control noxious algae (e.g. M. aeruginosa). Based on information from peer-reviewed literature, other algaecides could be similarly selective for cyanobacteria. Of the

Generation of recombinant pestiviruses using a full-genome amplification strategy

DEFF Research Database (Denmark)

Rasmussen, Thomas Bruun; Reimann, I.; Uttenthal, Åse

2010-01-01

-Gifhorn genome was generated by long RTPCR and then RNA transcripts derived from this amplicon were used to rescue infectious virus. Here, we have now used this full-genome amplification strategy for efficient and robust amplification of three additional pestivirus strains: the vaccine strain C and the virulent...... Paderborn strain of Classical swine fever virus plus the CP7 strain of Bovine viral diarrhoea virus. The amplicons were cloned directly into a stable single-copy bacterial artificial chromosome generating full-length pestivirus DNAs from which infectious RNA transcripts could be also derived....

Multiplexed homogeneous proximity ligation assays for high throughput protein biomarker research in serological material

DEFF Research Database (Denmark)

Lundberg, Martin; Thorsen, Stine Buch; Assarsson, Erika

2011-01-01

A high throughput protein biomarker discovery tool has been developed based on multiplexed proximity ligation assays (PLA) in a homogeneous format in the sense of no washing steps. The platform consists of four 24-plex panels profiling 74 putative biomarkers with sub pM sensitivity each consuming...... sequences are united by DNA ligation upon simultaneous target binding forming a PCR amplicon. Multiplex PLA thereby converts multiple target analytes into real-time PCR amplicons that are individually quantificatied using microfluidic high capacity qPCR in nano liter volumes. The assay shows excellent...

Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone

OpenAIRE

Ganesh, Sangita; Parris, Darren J; DeLong, Edward F; Stewart, Frank J

2013-01-01

Marine oxygen minimum zones (OMZs) support diverse microbial communities with roles in major elemental cycles. It is unclear how the taxonomic composition and metabolism of OMZ microorganisms vary between particle-associated and free-living size fractions. We used amplicon (16S rRNA gene) and shotgun metagenome sequencing to compare microbial communities from large (>1.6 μm) and small (0.2–1.6 μm) filter size fractions along a depth gradient in the OMZ off Chile. Despite steep vertical redox ...

Comparing the two Greek archipelagos plant species diversity and endemism patterns highlight the importance of isolation and precipitation as biodiversity drivers.

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Iliadou, Eleni; Kallimanis, Athanasios S; Dimopoulos, Panayotis; Panitsa, Maria

2014-12-01

Greece has two island archipelagos, the Aegean and the Ionian, which host a rich array of plants and wildlife, particularly endemic and threatened plant species. Despite the long history of island biogeographic studies in the Aegean, similar studies in the Ionian remain limited, with the two island archipelagos rarely being compared. The Aegean and Ionian archipelagos share many features, especially regarding total plant diversity, but exhibit different patterns of endemism. For instance, when considering similarly sized islands, those in the Ionian host as many as, if not more, species compared to the Aegean. In contrast, the Ionian Islands are poor in endemics (particularly narrow range endemics, such as single island or regional endemics) and threatened taxa, compared to the Aegean Islands. In the Ionian, endemics only persist on the largest islands, and form a very small proportion of the species pool, compared to the Aegean archipelago. The lack of endemism might be attributed to the more recent separation of the Ionian Islands from the mainland and the shorter distance separating them from the mainland. In addition, the Ionian Islands receive higher levels of precipitation and are typically covered by denser and higher vegetation than the Aegean Islands. These conditions favour greater total species richness, but tend to lead to higher numbers of common species compared to threatened and endemic taxa. This study demonstrates that both isolation and precipitation serve as biodiversity drivers, influencing plant species diversity and endemism patterns, of the two Greek archipelagos.

Effectiveness of ready-to-use therapeutic food compared to a corn/soy-blend-based pre-mix for the treatment of childhood moderate acute malnutrition in Niger.

Science.gov (United States)

Nackers, Fabienne; Broillet, France; Oumarou, Diakité; Djibo, Ali; Gaboulaud, Valérie; Guerin, Philippe J; Rusch, Barbara; Grais, Rebecca F; Captier, Valérie

2010-12-01

Standard nutritional treatment of moderate acute malnutrition (MAM) relies on fortified blended flours though their importance to treat this condition is a matter of discussion. With the newly introduced World Health Organization growth standards, more children at an early stage of malnutrition will be treated following the dietary protocols as for severe acute malnutrition, including ready-to-use therapeutic food (RUTF). We compared the effectiveness of RUTF and a corn/soy-blend (CSB)-based pre-mix for the treatment of MAM in the supplementary feeding programmes (SFPs) supported by Médecins Sans Frontières, located in the Zinder region (south of Niger). Children measuring 65 to childhood MAM in Niger, RUTF resulted in a higher weight gain, a higher recovery rate, a shorter length of stay and a lower transfer rate to the I-TFC compared to a CSB pre-mix. This might have important implications on the efficacy and the quality of SFPs.

Self-expandable metal stents for malignant esophageal obstruction: a comparative study between extrinsic and intrinsic compression.

Science.gov (United States)

Rhee, K; Kim, J-H; Jung, D H; Han, J W; Lee, Y C; Lee, S K; Shin, S K; Park, J C; Chung, H S; Park, J J; Youn, Y H; Park, H

2016-04-01

Self-expandable metal stents (SEMSs) are effective for malignant esophageal obstruction, but usefulness of SEMSs in extrinsic lesions is yet to be elucidated. This study is aimed at evaluating the clinical usefulness of SEMSs in the extrinsic compression compared with intrinsic. A retrospective review was conducted for 105 patients (intrinsic, 85; extrinsic, 20) with malignant esophageal obstruction who underwent endoscopic SEMSs placement. Technical and clinical success rates were evaluated and clinical outcomes were compared between extrinsic and intrinsic group. Extrinsic group was mostly pulmonary origin. Overall technical and clinical success rate was 100% and 91%, respectively, without immediate complications. Extrinsic and intrinsic group did not differ significantly in clinical success rate. The median stent patency time was 131.3 ± 85.8 days in intrinsic group while that of extrinsic was 54.6 ± 45.1 due to shorter survival after stent insertion. The 4-, 8-, and 12-week patency rates were 90.5%, 78.8%, and 64.9% respectively in intrinsic group, while stents of extrinsic group remained patent until death. Uncovered, fully covered, and double-layered stent were used evenly and the types did not influence patency in both groups. In conclusion, esophageal SEMSs can safely and effectively be used for malignant extrinsic compression as well as intrinsic. © 2015 International Society for Diseases of the Esophagus.

Comparative analysis of serial and parallel laser patterning of Ag nanowire thin films

Energy Technology Data Exchange (ETDEWEB)

Oh, Harim; Lee, Myeongkyu, E-mail: myeong@yonsei.ac.kr

2017-03-31

Highlights: • Serial and parallel laser patterning of Ag nanowire thin films is comparatively analyzed. • AgNW film can be directly patterned by a spatially-modulated pulsed Nd:YAG laser beam. • An area of 2.24 cm{sup 2} can be simultaneously patterned by a single pulse with energy of 350 mJ. - Abstract: Ag nanowire (AgNW) films solution-coated on a glass substrate were laser-patterned in two different ways. For the conventional serial process, a pulsed ultraviolet laser of 30 kHz repetition rate and ∼20 ns pulse width was employed as the laser source. For parallel patterning, the film was directly irradiated by a spatially-modulated Nd:YAG laser beam that has a low repetition rate of 10 kHz and a shorter pulse width of 5 ns. While multiple pulses with energy density ranging from 3 to 9 J/cm{sup 2} were required to pattern the film in the serial process, a single pulse with energy density of 0.16 J/cm{sup 2} completely removed AgNWs in the parallel patterning. This may be explained by the difference in patterning mechanism. In the parallel process using short pulses of 5 ns width, AgNWs can be removed in their solid state by the laser-induced thermo-elastic force, while they should be evaporated in the serial process utilizing a high-repetition rate laser. Important process parameters such as threshold energy density, speed, and available feature sizes are comparatively discussed for the two patterning.

Capillary electrophoresis with electrochemiluminescent detection for highly sensitive assay of genetically modified organisms.

Science.gov (United States)

Guo, Longhua; Yang, Huanghao; Qiu, Bin; Xiao, Xueyang; Xue, Linlin; Kim, Donghwan; Chen, Guonan

2009-12-01

A capillary electrophoresis coupled with electrochemiluminescent detection system (CE-ECL) was developed for the detection of polymerase chain reaction (PCR) amplicons. The ECL luminophore, tris(1,10-phenanthroline) ruthenium(II) (Ru(phen)(3)(2+)), was labeled to the PCR primers before amplification. Ru(phen)(3)(2+) was then introduced to PCR amplicons by PCR amplification. Eventually, the PCR amplicons were separated and detected by the homemade CE-ECL system. The detection of a typical genetically modified organism (GMO), Roundup Ready Soy (RRS), was shown as an example to demonstrate the reliability of the proposed approach. Four pairs of primers were amplified by multiple PCR (MPCR) simultaneously, three of which were targeted on the specific sequence of exogenous genes of RRS, and another was targeted on the endogenous reference gene of soybean. Both the conditions for PCR amplification and CE-ECL separation and detection were investigated in detail. Results showed that, under the optimal conditions, the proposed method can accurately identifying RRS. The corresponding limit of detection (LOD) was below 0.01% with 35 PCR cycles.

Rapid Detection of the Chlamydiaceae and Other Families in the Order Chlamydiales: Three PCR Tests

Science.gov (United States)

Everett, Karin D. E.; Hornung, Linda J.; Andersen, Arthur A.

1999-01-01

Few identification methods will rapidly or specifically detect all bacteria in the order Chlamydiales, family Chlamydiaceae. In this study, three PCR tests based on sequence data from over 48 chlamydial strains were developed for identification of these bacteria. Two tests exclusively recognized the Chlamydiaceae: a multiplex test targeting the ompA gene and the rRNA intergenic spacer and a TaqMan test targeting the 23S ribosomal DNA. The multiplex test was able to detect as few as 200 inclusion-forming units (IFU), while the TaqMan test could detect 2 IFU. The amplicons produced in these tests ranged from 132 to 320 bp in length. The third test, targeting the 23S rRNA gene, produced a 600-bp amplicon from strains belonging to several families in the order Chlamydiales. Direct sequence analysis of this amplicon has facilitated the identification of new chlamydial strains. These three tests permit ready identification of chlamydiae for diagnostic and epidemiologic study. The specificity of these tests indicates that they might also be used to identify chlamydiae without culture or isolation. PMID:9986815

Genetic variability and discrimination of low doses of Toxocara spp. from public areas soil inferred by loop-mediated isothermal amplification assay as a field-friendly molecular tool

Directory of Open Access Journals (Sweden)

Maryam Ozlati

2016-12-01

Full Text Available Aim: One of the main diagnostic problems of conventional polymerase chain reaction (PCR is indiscrimination of low parasitic loads in soil samples. The aim of this study is to determine the genetic diversity and identification of Toxocara spp. from public areas soil inferred by loop-mediated isothermal amplification (LAMP assay. Materials and Methods: A total of 180 soil samples were collected from various streets and public parks of northwest Iran. The DNA of recovered Toxocara eggs were extracted and amplified by PCR and LAMP following ZnSO4 flotation technique. The amplicons of internal transcribed spacer-2 gene were sequenced to reveal the heterogeneity traits of Toxocara spp. In addition, Toxocara canis sequences of southwest Iran were directly retrieved to compare gene flow between two distinct populations. Results: Toxocara spp. eggs were found in 57, 14 and 77 of soil samples using the microscopy, PCR and LAMP (detection limit 1-3 eggs/200 g soil, respectively. 7.7% of isolates were identified as T. canis by PCR method, while LAMP was able to detect 27.2%, 15.5% and 12.2% as Toxocara cati, T. canis and mixed infections, respectively. The kappa coefficient between LAMP and microscopy indicated a strong agreement (0.765 but indicated a faint agreement among LAMP-PCR (0.203 and PCR-microscopy (0.308 methods. A pairwise fixation index (Fst as a degree of gene flow was generally low (0.02156 among Toxocara populations of northwest and southwest Iran. Conclusions: The statistically significant Fst value indicates that the T. canis populations are not genetically well differentiated between northwest and southwest Iran. This shows that here is possibly an epidemiological drift due to the transfer of alleles. The LAMP assay because of its shorter reaction time, more sensitivity, and simultaneous detection of environmental contamination to be appears as valuable field diagnosis compared to PCR. Therefore, the detection of low Toxocara spp. loads

Genetic variability and discrimination of low doses of Toxocara spp. from public areas soil inferred by loop-mediated isothermal amplification assay as a field-friendly molecular tool.

Science.gov (United States)

Ozlati, Maryam; Spotin, Adel; Shahbazi, Abbas; Mahami-Oskouei, Mahmoud; Hazratian, Teimour; Adibpor, Mohammad; Ahmadpour, Ehsan; Dolatkhah, Afsaneh; Khoshakhlagh, Paria

2016-12-01

Aim: One of the main diagnostic problems of conventional polymerase chain reaction (PCR) is indiscrimination of low parasitic loads in soil samples. The aim of this study is to determine the genetic diversity and identification of Toxocara spp. from public areas soil inferred by loop-mediated isothermal amplification (LAMP) assay. A total of 180 soil samples were collected from various streets and public parks of northwest Iran. The DNA of recovered Toxocara eggs were extracted and amplified by PCR and LAMP following ZnSO 4 flotation technique. The amplicons of internal transcribed spacer-2 gene were sequenced to reveal the heterogeneity traits of Toxocara spp. In addition, Toxocara canis sequences of southwest Iran were directly retrieved to compare gene flow between two distinct populations. Toxocara spp. eggs were found in 57, 14 and 77 of soil samples using the microscopy, PCR and LAMP (detection limit 1-3 eggs/200 g soil), respectively. 7.7% of isolates were identified as T. canis by PCR method, while LAMP was able to detect 27.2%, 15.5% and 12.2% as Toxocara cati , T. canis and mixed infections, respectively. The kappa coefficient between LAMP and microscopy indicated a strong agreement (0.765) but indicated a faint agreement among LAMP-PCR (0.203) and PCR-microscopy (0.308) methods. A pairwise fixation index ( F st) as a degree of gene flow was generally low (0.02156) among Toxocara populations of northwest and southwest Iran. The statistically significant F st value indicates that the T. canis populations are not genetically well differentiated between northwest and southwest Iran. This shows that here is possibly an epidemiological drift due to the transfer of alleles. The LAMP assay because of its shorter reaction time, more sensitivity, and simultaneous detection of environmental contamination to be appears as valuable field diagnosis compared to PCR. Therefore, the detection of low Toxocara spp. loads from public area soils will help to expand

Efficient generation of mutations mediated by CRISPR/Cas9 in the hairy root transformation system of Brassica carinata.

Science.gov (United States)

Kirchner, Thomas W; Niehaus, Markus; Debener, Thomas; Schenk, Manfred K; Herde, Marco

2017-01-01

A protocol for the induction of site-directed deletions and insertions in the genome of Brassica carinata with CRISPR is described. The construct containing the Cas9 nuclease and the guide RNA (gRNA) was delivered by the hairy root transformation technique, and a successful transformation was monitored by GFP fluorescence. PAGE analysis of an amplified region, presumably containing the deletions and insertions, demonstrated up to seven different indels in one transgenic root and in all analyzed roots a wildtype allele of the modified gene was not detectable. Interestingly, many of these mutations consisted of relatively large indels with up to 112 bp. The exact size of the deletions was determined to allow an estimation whether the targeted gene was not functional due to a considerable deletion or a frame shift within the open reading frame. This allowed a direct phenotypic assessment of the previously characterized roots and, in fact, deletions in FASCICLIN-LIKE ARABINOGALACTAN PROTEIN 1 (BcFLA1)-a gene with an expression pattern consistent with a role in root hair architecture-resulted in shorter root hairs compared to control roots ectopically expressing an allele of the gene that cannot be targeted by the gRNA in parallel to the CRISPR construct. As an additional line of evidence, we monitored BcFLA1 expression with qPCR and detected a significant reduction of the transcript in roots with an active CRISPR construct compared to the control, although residual amounts of the transcript were detected, possibly due to inefficient nonsense-mediated mRNA decay. Additionally, the presence of deletions and insertions were verified by Sanger sequencing of the respective amplicons. In summary we demonstrate the successful application of CRISPR/Cas9 in hairy roots of B. carinata, the proof of its effectiveness and its effect on the root hair phenotype. This study paves the way for experimental strategies involving the phenotypic assessment of gene lesions by CRISPR which

Efficient generation of mutations mediated by CRISPR/Cas9 in the hairy root transformation system of Brassica carinata.

Directory of Open Access Journals (Sweden)

Thomas W Kirchner

Full Text Available A protocol for the induction of site-directed deletions and insertions in the genome of Brassica carinata with CRISPR is described. The construct containing the Cas9 nuclease and the guide RNA (gRNA was delivered by the hairy root transformation technique, and a successful transformation was monitored by GFP fluorescence. PAGE analysis of an amplified region, presumably containing the deletions and insertions, demonstrated up to seven different indels in one transgenic root and in all analyzed roots a wildtype allele of the modified gene was not detectable. Interestingly, many of these mutations consisted of relatively large indels with up to 112 bp. The exact size of the deletions was determined to allow an estimation whether the targeted gene was not functional due to a considerable deletion or a frame shift within the open reading frame. This allowed a direct phenotypic assessment of the previously characterized roots and, in fact, deletions in FASCICLIN-LIKE ARABINOGALACTAN PROTEIN 1 (BcFLA1-a gene with an expression pattern consistent with a role in root hair architecture-resulted in shorter root hairs compared to control roots ectopically expressing an allele of the gene that cannot be targeted by the gRNA in parallel to the CRISPR construct. As an additional line of evidence, we monitored BcFLA1 expression with qPCR and detected a significant reduction of the transcript in roots with an active CRISPR construct compared to the control, although residual amounts of the transcript were detected, possibly due to inefficient nonsense-mediated mRNA decay. Additionally, the presence of deletions and insertions were verified by Sanger sequencing of the respective amplicons. In summary we demonstrate the successful application of CRISPR/Cas9 in hairy roots of B. carinata, the proof of its effectiveness and its effect on the root hair phenotype. This study paves the way for experimental strategies involving the phenotypic assessment of gene lesions

Comparative study between sugammadex and neostigmine in neurosurgical anesthesia in pediatric patients

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Ayman A Ghoneim

2015-01-01

Full Text Available Background: Postoperative recurarization remains a risk following the use of the conventional neuromuscular blocking agents. In addition, none of the commonly used reversal agents, such as neostigmine or edrophonium are capable of reliably reversing profound blockade. The present comparative and randomized study investigated the use of sugammadex for reversing profound neuromuscular blockade (NMB in pediatric neurosurgical patients undergone posterior fossa tumor excision. Patients and Methods: Forty pediatric patients undergoing elective craniotomy for posterior fossa tumor excision were randomly divided into either of neostigmine or sugammadex group in which muscle relaxant was reversed at the end of anesthesia either with neostigmine 0.04 mg/kg added to atropine 0.02 mg/kg or sugammadex 4 mg/kg alone, respectively. The primary endpoint was the time from the administration of sugammadex or neostigmine to recovery of the train of four (TOF ratio to 90% after rocuronium-induced neuromuscular block. Unpaired t-test was used to compare continuous variables between groups. Meanwhile, repeated ANOVA was used to detect intragroup differences. Results: Patients in sugammadex group attained a TOF ratio 90% in statistically shorter time (1.4 ± 1.2 min than those in neostigmine group (25.16 ± 6.49 min for reversal of the rocuronium. Mean arterial pressure and heart rate were significantly higher in neostigmine group at 2, 5 and 10 min after administration of the reversal agents and returned nonsignificantly different after that. With no recurarization in any patient throughout the study period. Conclusion: Sugammadex rapidly and effectively reverses rocuronium-induced NMB in pediatric patients undergoing neurosurgery when administered at reappearance of T2 of TOF at dose 4 mg/kg.

Comparative Reproduction Aspects of the Deep-water Shrimps Aristaeomorpha foliacea and Aristeus antennatus (Decapoda, Aristeidae in the Greek Ionian Sea (Eastern Mediterranean

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K. Kapiris

2009-01-01

Full Text Available In the eastern Ionian Sea, the deep-water shrimps Aristaeomorpha foliacea and Aristeus antennatus constitute a virgin fishing resource, since their maximum abundance depth exceeds commercial exploitation depths. The two sympatric species share a number of common reproductive features, such as summer reproduction. A slight temporal shift in mating activity, ovarian maturation, and spawning period was observed between species. The most notable difference was the more pronounced seasonality in reproductive activity of Aristeus antennatus compared to that of A. foliacea as evidenced by the frequency of inseminated females and functionally mature males, as well as by the shorter ovarian maturation period. Nevertheless, regarding the whole life span, both sexes of Aristeus antennatus exhibit a more extended reproductive activity in comparison to A. foliacea. No notable differentiation of both species existed in comparison to other Mediterranean regions.

Prospective study comparing laparoscopic and open adenomectomy: Surgical and functional results.

Science.gov (United States)

Garcia-Segui, A; Angulo, J C

Open adenomectomy (OA) is the surgery of choice for large volume benign prostatic hyperplasia, and laparoscopic adenomectomy (LA) represents a minimally invasive alternative. We present a long-term, prospective study comparing both techniques. The study consecutively included 199 patients with benign prostatic hyperplasia and prostate volumes>80g who were followed for more than 12 months. The patients underwent OA (n=97) or LA (n=102). We recorded and compared demographic and perioperative data, functional results and complications using a descriptive statistical analysis. The mean age was 69.2±7.7 years (range 42-87), and the mean prostate volume (measured by TRUS) was 112.1±32.7mL (range 78-260). There were no baseline differences among the groups in terms of age, ASA scale, prostate volume, PSA levels, Qmax, IPSS, QoL or treatments prior to the surgery. The surgical time (P<.0001) and catheter time (P<.0002) were longer in the LA group. Operative bleeding (P<.0001), transfusion rate (P=.0015) and mean stay (P<.0001) were significantly lower in the LA group. The LA group had a lower rate of complications (P=.04), but there were no significant differences between the groups in terms of major complications (Clavien score≥3) (P=.13) or in the rate of late complications (at one year) (P=.66). There were also no differences between the groups in the functional postoperative results: IPSS (P=.17), QoL (P=.3) and Qmax (P=.17). LA is a reasonable, safe and effective alternative that results in less bleeding, fewer transfusions, shorter hospital stays and lower morbidity than OA. LA has similar functional results to OA, at the expense of longer surgical times and longer catheter times. Copyright © 2016 AEU. Publicado por Elsevier España, S.L.U. All rights reserved.

Finding the founder of Stockholm - A kinship study based on Y-chromosomal, autosomal and mitochondrial DNA

DEFF Research Database (Denmark)

Malmström, Helena; Vretemark, Maria; Tillmar, Andreas

2012-01-01

-chromosomal and autosomal SNPs and compared the results with haplogroup frequencies of modern Swedes to investigate paternal relations. Possible maternal kinship was investigated by deep FLX-sequencing of overlapping mtDNA amplicons. The authenticity of the sequences was examined using data from independent extractions......, massive clonal data, the c-statistics, and real-time quantitative data. We show that the males carry the same Y-chromosomal haplogroup and thus we cannot reject a father-son type of relation. Further, as shown by the mtDNA analyses, none of the individuals are maternally related. We conclude...

Emergency Physicians Are Able to Detect Right Ventricular Dilation With Good Agreement Compared to Cardiology.

Science.gov (United States)

Rutz, Matt A; Clary, Julie M; Kline, Jeffrey A; Russell, Frances M

2017-07-01

Focused cardiac ultrasound (FOCUS) is a useful tool in evaluating patients presenting to the emergency department (ED) with acute dyspnea. Prior work has shown that right ventricular (RV) dilation is associated with repeat hospitalizations and shorter life expectancy. Traditionally, RV assessment has been evaluated by cardiologist-interpreted comprehensive echocardiography. The primary goal of this study was to determine the inter-rater reliability between emergency physicians (EPs) and a cardiologist for determining RV dilation on FOCUS performed on ED patients with acute dyspnea. This was a prospective, observational study at two urban academic EDs; patients were enrolled if they had acute dyspnea and a computed tomographic pulmonary angiogram without acute disease. All patients had an EP-performed FOCUS to assess for RV dilation. RV dilation was defined as an RV to left ventricular ratio greater than 1. FOCUS interpretations were compared to a blinded cardiologist FOCUS interpretation using agreement and kappa statistics. Of 84 FOCUS examinations performed on 83 patients, 17% had RV dilation. Agreement and kappa, for EP-performed FOCUS for RV dilation were 89% (95% confidence interval [CI] 80-95%) and 0.68 (95% CI 0.48-0.88), respectively. Emergency physician sonographers are able to detect RV dilation with good agreement when compared to cardiology. These results support the wider use of EP-performed FOCUS to evaluate for RV dilation in ED patients with dyspnea. © 2017 by the Society for Academic Emergency Medicine.

Comparative effectiveness of open versus minimally invasive sacroiliac joint fusion

Directory of Open Access Journals (Sweden)

Ledonio CGT

2014-06-01

Full Text Available Charles GT Ledonio,1 David W Polly Jr,1 Marc F Swiontkowski,1 John T Cummings Jr2 1Department of Orthopaedic Surgery, University of Minnesota, Twin Cities, MN, 2Community Neurosurgical Care, Indianapolis, IN, USA Background: The mainstay of sacroiliac joint disruption/degenerative sacroiliitis therapy has been nonoperative management. This nonoperative management often includes a regimen of physical therapy, chiropractic treatment, therapeutic injections, and possibly radiofrequency ablation at the discretion of the treating physician. When these clinical treatments fail, sacroiliac joint fusion has been recommended as the standard treatment. Open and minimally invasive (MIS surgical techniques are typical procedures. This study aims to compare the perioperative measures and Oswestry Disability Index (ODI outcomes associated with each of these techniques. Methods: A comparative retrospective chart review of patients with sacroiliac joint fusion and a minimum of 1 year of follow-up was performed. Perioperative measures and ODI scores were compared using the Fisher's exact test and two nonparametric tests, ie, the Mann–Whitney U test and the Wilcoxon signed-rank test. The results are presented as percent or median with range, as appropriate. Results: Forty-nine patients from two institutions underwent sacroiliac joint fusion between 2006 and 2012. Ten patients were excluded because of incomplete data, leaving 39 evaluable patients, of whom 22 underwent open and 17 underwent MIS sacroiliac joint fusion. The MIS group was significantly older (median age 66 [39–82] years than the open group (median age 51 [34–74] years. Surgical time and hospital stay were significantly shorter in the MIS group than in the open group. Preoperative ODI was significantly greater in the open group (median 64 [44–78] than in the MIS group (median 53 [14–84]. Postoperative improvement in ODI was statistically significant within and between groups, with MIS

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Lifescience Database Archive (English)

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Measuring single constructs by single items: Constructing an even shorter version of the “Short Five” personality inventory

Science.gov (United States)

Konstabel, Kenn; Lönnqvist, Jan-Erik; Leikas, Sointu; García Velázquez, Regina; Qin, Hiaying; Verkasalo, Markku; Walkowitz, Gari

2017-01-01

The aim of this study was to construct a short, 30-item personality questionnaire that would be, in terms of content and meaning of the scores, as comparable as possible with longer, well-established inventories such as NEO PI-R and its clones. To do this, we shortened the formerly constructed 60-item “Short Five” (S5) by half so that each subscale would be represented by a single item. We compared all possibilities of selecting 30 items (preserving balanced keying within each domain of the five-factor model) in terms of correlations with well-established scales, self-peer correlations, and clarity of meaning, and selected an optimal combination for each domain. The resulting shortened questionnaire, XS5, was compared to the original S5 using data from student samples in 6 different countries (Estonia, Finland, UK, Germany, Spain, and China), and a representative Finnish sample. The correlations between XS5 domain scales and their longer counterparts from well-established scales ranged from 0.74 to 0.84; the difference from the equivalent correlations for full version of S5 or from meta-analytic short-term dependability coefficients of NEO PI-R was not large. In terms of prediction of external criteria (emotional experience and self-reported behaviours), there were no important differences between XS5, S5, and the longer well-established scales. Controlling for acquiescence did not improve the prediction of criteria, self-peer correlations, or correlations with longer scales, but it did improve internal reliability and, in some analyses, comparability of the principal component structure. XS5 can be recommended as an economic measure of the five-factor model of personality at the level of domain scales; it has reasonable psychometric properties, fair correlations with longer well-established scales, and it can predict emotional experience and self-reported behaviours no worse than S5. When subscales are essential, we would still recommend using the full version

Interatrial septum pacing decreases atrial dyssynchrony on strain rate imaging compared with right atrial appendage pacing.

Science.gov (United States)

Yasuoka, Yoshinori; Abe, Haruhiko; Umekawa, Seiko; Katsuki, Keiko; Tanaka, Norio; Araki, Ryo; Imanaka, Takahiro; Matsutera, Ryo; Morisawa, Daisuke; Kitada, Hirokazu; Hattori, Susumu; Noda, Yoshiki; Adachi, Hidenori; Sasaki, Tatsuya; Miyatake, Kunio

2011-03-01

Interatrial septum pacing (IAS-P) decreases atrial conduction delay compared with right atrial appendage pacing (RAA-P). We evaluate the atrial contraction with strain rate of tissue Doppler imaging (TDI) during sinus activation or with IAS-P or RAA-P. Fifty-two patients with permanent pacemaker for sinus node disease were enrolled in the study. Twenty-three subjects were with IAS-P and 29 with RAA-P. The time from end-diastole to peak end-diastolic strain rate was measured and corrected with RR interval on electrocardiogram. It was defined as the time from end-diastole to peak end-diastolic strain rate (TSRc), and the balance between maximum and minimum TSRc at three sites (ΔTSRc) was compared during sinus activation and with pacing rhythm in each group. There were no significant differences observed in general characteristics and standard echocardiographic parameters except the duration of pacing P wave between the two groups. The duration was significantly shorter in the IAS-P group compared with the RAA-P group (95 ± 34 vs 138 ± 41; P = 0.001). TSRc was significantly different between sinus activation and pacing rhythm (36.3 ± 35.7 vs 61.6 ± 36.3; P = 0.003) in the RAA-P group, whereas no significant differences were observed in the IAS-P group (25.4 ± 12.1 vs 27.7 ± 14.7; NS). During the follow-up (mean 2.4 ± 0.7 years), the incidence of paroxysmal atrial fibrillation (AF) conversion to permanent AF was not significantly different between the two groups. IAS-P decreased the contraction delay on atrial TDI compared to RAA-P; however, it did not contribute to the reduction of AF incidence in the present study. ©2010, The Authors. Journal compilation ©2010 Wiley Periodicals, Inc.

Computer-designed surgical guide template compared with free-hand operation for mesiodens extraction in premaxilla using “trapdoor” method

Science.gov (United States)

Hu, Ying Kai; Xie, Qian Yang; Yang, Chi; Xu, Guang Zhou

2017-01-01

Abstract The aim of this study was to introduce a novel method of mesiodens extraction using a vascularized pedicled bone flap by piezosurgery and to compare the differences between a computer-aided design surgical guide template and free-hand operation. A total of 8 patients with mesiodens, 4 with a surgical guide (group I), and 4 without it (group II) were included in the study. The surgical design was to construct a trapdoor pedicle on the superior mucoperiosteal attachment with application of piezosurgery. The bone lid was repositioned after mesiodens extraction. Group I patients underwent surgeries based on the preoperative planning with surgical guide templates, while group II patients underwent free-hand operation. The outcome variables were success rate, intraoperative time, anterior nasal spine (ANS) position, changes of nasolabial angle (NLA), and major complications. Data from the 2 groups were compared by SPSS 17.0, using Wilcoxon test. The operative time was significantly shorter in group I patients. All the mesiodentes were extracted successfully and no obvious differences of preoperative and postoperative ANS position and NLA value were found in both groups. The patients were all recovered uneventfully. Surgical guide templates can enhance clinical accuracy and reduce operative time by facilitating accurate osteotomies. PMID:28658139

Comparative Study for Efficacy and Safety of Adenoidectomy according to the Surgical Method: A Prospective Multicenter Study.

Directory of Open Access Journals (Sweden)

Jeong-Whun Kim

Full Text Available There have been several operative techniques for adenoidectomy and their efficacy and morbidity are different according to the technique. This prospective multicenter study was aimed to compare the efficacy and morbidity of coblation adenoidectomy (CA with those of power-assisted adenoidectomy.Prospective multi-institutional study.Children who underwent CA, power-assisted adenoidectomy with cauterization (PAA+C or without cauterization (PAA-C due to adenoid hypertrophy were enrolled from 13 hospitals between July 2013 and June 2014. Mean operation time, degree of intraoperative bleeding and postoperative bleeding rate were evaluated.A total of 388 children (mean age ± standard deviation = 6.6 ± 2.5 years; 245 males and 143 females were included. According to the adenoidectomy technique, the children were classified into 3 groups: (1 CA (n = 116; (2 PAA+C (n = 153; and (3 PAA-C (n = 119. Significant differences were not found in age and sex among three groups. In the CA group, mean operation time was significantly shorter (P < 0.001 and degree of intraoperative bleeding was significantly less (P < 0.001 compared to PAA+C or PAA-C group. Delayed postoperative bleeding rate of PAA-C group was significantly higher than that of CA or PAA+C group (P = 0.016.This prospective multicenter study showed that CA was superior to PAA in terms of mean operation time and degree of intraoperative bleeding.

Vinorelbine-Cyclophosphamide compared to cyclophosphamide in peripheral blood stem cell mobilization for multiple myeloma.

Science.gov (United States)

de Mel, Sanjay; Chen, Yunxin; Lin, Adeline; Soh, Teck Guan; Ooi, Melissa; Yap, Eng Soo; Donato, Lara Kristina Sioco; Halim, Nurul Aidah Abdul; Mah, Joanna; Lim, Karen; Poon, Li Mei; Tan, Belinda; Yelly; Lim, Hui Li; Koh, Liang Piu; Tai, Bee Choo; Chen, Zhaojin; Chng, Wee Joo; Gopalakrishnan, Satish Kumar; Tan, Lip Kun

2018-04-23

High dose Cyclophosphamide (Cy) and Vinorelbine Cyclophosphamide (Vino-Cy) are stem cell (SC) mobilisation options for patients with multiple myeloma (MM). We present a comparison of mobilisation outcomes using these regimens. Vino-Cy patients received Vinorelbine 25 mg/m 2 on day 1, cyclophosphamide 1500 mg/m 2 on day 2, and pegylated GCSF on day 4 or GCSF 10 mcg/kg/day from day 4 onwards. Cy patients were given cyclophosphamide 4000 mg/m 2 on day 1 and GCSF10 mcg/kg/day from day 5 onwards. The target CD34 + SC collection was 5 × 10 6  per kg/BW. 149 patients were included. SC collection was lower in the Vino-Cy group (8.20 × 10 6 /Kg BW) compared to the Cy group (11.43 × 10 6 /Kg BW), with adjusted geometric mean ratio of 0.59 (95% CI 0.41 to 0.86, p = 0.006). Time taken to achieve an adequate PB SC count was shorter for Vino-Cy (9 ± 1 day compared to 12 ± 2 days for Cy, adjusted absolute mean difference -3.95, 95% CI -4.85 to -3.06, P < .001). Mobilisation related toxicities (in particular, neutropaenic fever) were greater for Cy. Vino-Cy is a potential alternative to Cy given the need for effective mobilisation protocols with acceptable toxicity. Copyright © 2018 King Faisal Specialist Hospital & Research Centre. Published by Elsevier Ltd. All rights reserved.

Sources of PCR-induced distortions in high-throughput sequencing data sets

Science.gov (United States)

Kebschull, Justus M.; Zador, Anthony M.

2015-01-01

PCR permits the exponential and sequence-specific amplification of DNA, even from minute starting quantities. PCR is a fundamental step in preparing DNA samples for high-throughput sequencing. However, there are errors associated with PCR-mediated amplification. Here we examine the effects of four important sources of error—bias, stochasticity, template switches and polymerase errors—on sequence representation in low-input next-generation sequencing libraries. We designed a pool of diverse PCR amplicons with a defined structure, and then used Illumina sequencing to search for signatures of each process. We further developed quantitative models for each process, and compared predictions of these models to our experimental data. We find that PCR stochasticity is the major force skewing sequence representation after amplification of a pool of unique DNA amplicons. Polymerase errors become very common in later cycles of PCR but have little impact on the overall sequence distribution as they are confined to small copy numbers. PCR template switches are rare and confined to low copy numbers. Our results provide a theoretical basis for removing distortions from high-throughput sequencing data. In addition, our findings on PCR stochasticity will have particular relevance to quantification of results from single cell sequencing, in which sequences are represented by only one or a few molecules. PMID:26187991

Detection and analysis of hemolysin genes in Aeromonas hydrophila isolated from Gouramy (Osphronemus gouramy) by polymerase chain reaction (PCR)

Science.gov (United States)

Rozi; Rahayu, K.; Daruti, D. N.

2018-04-01

The goal of this study was to detect of Aeromonas hydrophila carrying the hlyA gene in guramy by PCR assay. A total of 5 A. hydrophila strains were isolated from gouramy with different location and furthermore genotypic of all A. hydrophila strains havedetected by PCR assay for 16S rRNA gene. The primers used in the PCR targeted a 592-bp fragment of the hlyA gene coding for the hemolysin gene. Particularly hlyA genes are responsible for haemolysin toxins production in this genus. After gel electrophoresis, the amplicons from representative strains of the A. hydrophila were purified using extraction kit and were subjected to the DNA sequencing analysis. The results showed that: (i) the 592bp amplicon of the hlyA gene was detected in 5/6 of the A. hydrophila; (ii) the nucleotide blast results of hemolysin gene sequences of the strains of A. hydrophila revealed a high homology of 90-97 % with published sequences, and;(iii) the protein blast showed 95-98 % homology when compared to the published sequences. The PCR clearly identified the haemolysin-producing strains of A. hydrophila by detection in hlyA genes and may have application as a rapid species-specific virulence test.

Characterization of a human cell line stably over-expressing the candidate oncogene, dual specificity phosphatase 12.

Directory of Open Access Journals (Sweden)

Erica L Cain

2011-04-01

Full Text Available Analysis of chromosomal rearrangements within primary tumors has been influential in the identification of novel oncogenes. Identification of the "driver" gene(s within cancer-derived amplicons is, however, hampered by the fact that most amplicons contain many gene products. Amplification of 1q21-1q23 is strongly associated with liposarcomas and microarray-based comparative genomic hybridization narrowed down the likely candidate oncogenes to two: the activating transcription factor 6 (atf6 and the dual specificity phosphatase 12 (dusp12. While atf6 is an established transcriptional regulator of the unfolded protein response, the potential role of dusp12 in cancer remains uncharacterized.To evaluate the oncogenic potential of dusp12, we established stable cell lines that ectopically over-express dusp12 in isolation and determined whether this cell line acquired properties frequently associated with transformed cells. Here, we demonstrate that cells over-expressing dusp12 display increased cell motility and resistance to apoptosis. Additionally, over-expression of dusp12 promoted increased expression of the c-met proto-oncogene and the collagen and laminin receptor intergrin alpha 1 (itga1 which is implicated in metastasis.Collectively, these results suggest that dusp12 is oncologically relevant and exposes a potential association between dusp12 and established oncogenes that could be therapeutically targeted.

A massive parallel sequencing workflow for diagnostic genetic testing of mismatch repair genes

Science.gov (United States)

Hansen, Maren F; Neckmann, Ulrike; Lavik, Liss A S; Vold, Trine; Gilde, Bodil; Toft, Ragnhild K; Sjursen, Wenche

2014-01-01

The purpose of this study was to develop a massive parallel sequencing (MPS) workflow for diagnostic analysis of mismatch repair (MMR) genes using the GS Junior system (Roche). A pathogenic variant in one of four MMR genes, (MLH1, PMS2, MSH6, and MSH2), is the cause of Lynch Syndrome (LS), which mainly predispose to colorectal cancer. We used an amplicon-based sequencing method allowing specific and preferential amplification of the MMR genes including PMS2, of which several pseudogenes exist. The amplicons were pooled at different ratios to obtain coverage uniformity and maximize the throughput of a single-GS Junior run. In total, 60 previously identified and distinct variants (substitutions and indels), were sequenced by MPS and successfully detected. The heterozygote detection range was from 19% to 63% and dependent on sequence context and coverage. We were able to distinguish between false-positive and true-positive calls in homopolymeric regions by cross-sample comparison and evaluation of flow signal distributions. In addition, we filtered variants according to a predefined status, which facilitated variant annotation. Our study shows that implementation of MPS in routine diagnostics of LS can accelerate sample throughput and reduce costs without compromising sensitivity, compared to Sanger sequencing. PMID:24689082

Improved assay to detect Plasmodium falciparum using an uninterrupted, semi-nested PCR and quantitative lateral flow analysis

Science.gov (United States)

2013-01-01

Background A rapid, non-invasive, and inexpensive point-of-care (POC) diagnostic for malaria followed by therapeutic intervention would improve the ability to control infection in endemic areas. Methods A semi-nested PCR amplification protocol is described for quantitative detection of Plasmodium falciparum and is compared to a traditional nested PCR. The approach uses primers that target the P. falciparum dihydrofolate reductase gene. Results This study demonstrates that it is possible to perform an uninterrupted, asymmetric, semi-nested PCR assay with reduced assay time to detect P. falciparum without compromising the sensitivity and specificity of the assay using saliva as a testing matrix. Conclusions The development of this PCR allows nucleic acid amplification without the need to transfer amplicon from the first PCR step to a second reaction tube with nested primers, thus reducing both the chance of contamination and the time for analysis to PCR amplicon yield was adapted to lateral flow detection using the quantitative up-converting phosphor (UCP) reporter technology. This approach provides a basis for migration of the assay to a POC microfluidic format. In addition the assay was successfully evaluated with oral samples. Oral fluid collection provides a simple non-invasive method to collect clinical samples. PMID:23433252

Two Different Percutaneous Bone-Anchored Hearing Aid Abutment Systems: Comparative Clinical Study.

Science.gov (United States)

Polat, Beldan; İşeri, Mete; Orhan, Kadir Serkan; Yılmazer, Ayça Başkadem; Enver, Necati; Ceylan, Didem; Kara, Ahmet; Güldiken, Yahya; Çomoğlu, Şenol

2016-04-01

To compare two different percutaneous bone-anchored hearing aid (BAHA) abutment systems regarding operation time, scar healing, quality of life, implant stability, audiologic results, and complications. The study involves a prospective multi-center clinical evaluation. Thirty-two consecutive patients who had undergone BAHA surgery from January 2011 to January 2013 in two tertiary centers were included in the study. The Glasgow Inventory Benefit Score was used to assess the patients at least 6 months after surgery. The operation time and complications were recorded. Implant stability quotient (ISQ) values were recorded using resonance frequency analysis. Holger's classification was used to evaluate skin reactions. The mean length of the operation was 39.2±4 min for standard abutment and 18.3±5.7 min for hydroxyapatite-coated abutment. ISQ scores were significantly better for standard abutment in all tests. The mean total Glasgow Inventory Benefit Score was 39.3±19 for the standard abutment and 46.3±24.5 for the hydroxyapatite-coated abutment groups, but there was no statistical significance between the two groups. There was no difference in audiological improvement between the two groups after surgery. Hydroxyapatite-coated abutment provided a shorter operation time that was significantly different from standard abutment. There were no significant differences between standard abutment and hydroxyapatite-coated abutment regarding audiologic improvement, quality of life, loading time, and complications.

Why shorter half-times of repair lead to greater damage in pulsed brachytherapy

International Nuclear Information System (INIS)

Fowler, J.F.

1993-01-01

Pulsed brachytherapy consists of replacing continuous irradiation at low dose-rate with a series of medium dose-rate fractions in the same overall time and to the same total dose. For example, pulses of 1 Gy given every 2 hr or 2 Gy given every 4 hr would deliver the same 70 Gy in 140 hr as continuous irradiation at 0.5 Gy/hr. If higher dose-rates are used, even with gaps between the pulses, the biological effects are always greater. Provided that dose rates in the pulse do not exceed 3 Gy/hr, and provided that pulses are given as often as every 2 hr, the inevitable increases of biological effect are no larger than a few percent (of biologically effective dose or extrapolated response dose). However, these increases are more likely to exceed 10% (and thus become clinically significant) if the half-time of repair of sublethal damage is short (less than 1 hr) rather than long. This somewhat unexpected finding is explained in detail here. The rise and fall of Biologically Effective Dose (and hence of Relative Effectiveness, for a constant dose in each pulse) is calculated during and after single pulses, assuming a range of values of T 1/2 , the half-time of sublethal damage repair. The area under each curve is proportional to Biologically Effective Dose and therefore to log cell kill. Pulses at 3 Gy/hr do yield greater biological effect (dose x integrated Relative Effectiveness) than lower dose-rate pulses or continuous irradiation at 0.5 Gy/hr. The contrast is greater for the short T 1/2 of 0.5 hr than for the longer T 1/2 of 1.5 hr. More biological damage will be done (compared with traditional low dose rate brachytherapy) in tissues with short T 1/2 (0.1-1 hr) than in tissues with longer T 1/2 values. 8 refs., 3 figs

Systematic review and meta-analysis of published trials comparing the effectiveness of transanal endoscopic microsurgery and radical resection in the management of early rectal cancer.

Science.gov (United States)

Sajid, M S; Farag, S; Leung, P; Sains, P; Miles, W F A; Baig, M K

2014-01-01

A systematic analysis was conducted of trials comparing the effectiveness of transanal endoscopic microsurgery (TEMS) with radical resection (RR) for T1 and T2 rectal cancer. An electronic search was carried out of trials reporting the effectiveness of TEMS and RR in the treatment of T1 and T2 rectal cancers. Ten trials including 942 patients were retrieved. There was a trend toward a higher risk of local recurrence (odds ratio 2.78; 95% confidence interval 1.42, 5.44; z = 2.97; P TEMS compared with RR. The risk of distant recurrence, overall survival (odds ratio 0.90; 95% confidence interval 0.49, 1.66; z = 0.33; P = 0.74) and mortality was similar. TEMS was associated with a shorter operation time and hospital stay and a reduced risk of postoperative complications (P TEMS is superior to RR in the management of early rectal cancer. Larger, better designed and executed prospective studies are needed to answer this question. Colorectal Disease © 2013 The Association of Coloproctology of Great Britain and Ireland.

Comparative performance of double-digest RAD sequencing across divergent arachnid lineages.

Science.gov (United States)

Burns, Mercedes; Starrett, James; Derkarabetian, Shahan; Richart, Casey H; Cabrero, Allan; Hedin, Marshal

2017-05-01

Next-generation sequencing technologies now allow researchers of non-model systems to perform genome-based studies without the requirement of a (often unavailable) closely related genomic reference. We evaluated the role of restriction endonuclease (RE) selection in double-digest restriction-site-associated DNA sequencing (ddRADseq) by generating reduced representation genome-wide data using four different RE combinations. Our expectation was that RE selections targeting longer, more complex restriction sites would recover fewer loci than RE with shorter, less complex sites. We sequenced a diverse sample of non-model arachnids, including five congeneric pairs of harvestmen (Opiliones) and four pairs of spiders (Araneae). Sample pairs consisted of either conspecifics or closely related congeneric taxa, and in total 26 sample pair analyses were tested. Sequence demultiplexing, read clustering and variant calling were performed in the pyRAD program. The 6-base pair cutter EcoRI combined with methylated site-specific 4-base pair cutter MspI produced, on average, the greatest numbers of intra-individual loci and shared loci per sample pair. As expected, the number of shared loci recovered for a sample pair covaried with the degree of genetic divergence, estimated with cytochrome oxidase I sequences, although this relationship was non-linear. Our comparative results will prove useful in guiding protocol selection for ddRADseq experiments on many arachnid taxa where reference genomes, even from closely related species, are unavailable. © 2016 John Wiley & Sons Ltd.

Arthroscopic undersurface rotator cuff repair versus conventional arthroscopic double-row rotator cuff repair - Comparable results at 2-year follow-up.

Science.gov (United States)

Ang, Benjamin Fu Hong; Chen, Jerry Yongqiang; Yeo, William; Lie, Denny Tijauw Tjoen; Chang, Paul Chee Cheng

2018-01-01

The aim of our study is to compare the improvement in clinical outcomes after conventional arthroscopic double-row rotator cuff repair and arthroscopic undersurface rotator cuff repair. A consecutive series of 120 patients who underwent arthroscopic rotator cuff repair was analysed. Sixty-one patients underwent conventional double-row rotator cuff repair and 59 patients underwent undersurface rotator cuff repair. Several clinical outcomes, including numerical pain rating scale (NPRS), constant shoulder score (CSS), Oxford shoulder score (OSS) and University of California Los Angeles shoulder score (UCLASS), were prospectively recorded by a trained healthcare professional preoperatively and at 3, 6, 12 and 24 months after surgery. Comparing both groups, there were no differences in age, gender and preoperative NPRS, CSS, OSS and UCLASS. However, the tear size was 0.7 ± 0.2 (95% confidence interval (CI) 0.3-1.1) cm larger in the conventional group ( p = 0.002). There was no difference in the improvement of NPRS, CSS, OSS and UCLASS at all time points of follow-up, that is, at 3, 6, 12 and 24 months after surgery. The duration of operation was shorter by 35 ± 3 (95% CI 28-42) min in the undersurface group ( p rotator cuff repair and conventional arthroscopic double-row rotator cuff repair showed marked improvements in clinical scores when compared preoperatively, and there was no difference in improvements between both groups. Arthroscopic undersurface rotator cuff repair is a faster technique compared to the conventional arthroscopic double-row rotator cuff repair.

Quality of harvested autologous platelets compared with stored donor platelets for use after cardiopulmonary bypass procedures.

Science.gov (United States)

Crowther, M; Ford, I; Jeffrey, R R; Urbaniak, S J; Greaves, M

2000-10-01

Platelet dysfunction has a major contribution in bleeding after cardiopulmonary bypass (CPB) and transfusion of platelets is frequently used to secure haemostasis. Allogeneic platelets prepared for transfusion are functionally impaired. Autologous platelets harvested preoperatively require a shorter storage time before transfusion and their use also avoids the risks associated with transfusion of allogeneic blood products. For the first time, we have compared the functional quality of autologous platelets with allogeneic platelets prepared by two methods, immediately before infusion. Platelet activation was assessed by P-selectin expression and fibrinogen binding using flow cytometry. We also monitored the effects of CPB surgery and re-infusion of autologous platelets on platelet function. Autologous platelet-rich plasma (PRP) contained a significantly lower (P platelets compared with allogeneic platelet preparations, and also contained a significantly higher (P platelets. Allogeneic platelets prepared by donor apheresis were more activated and less responsive than those produced by centrifugation of whole blood. In patients' blood, the percentage of platelets expressing P-selectin or binding fibrinogen increased significantly after CPB (P platelets responsive to in vitro agonists was decreased (P platelet activation during the procedure. The percentage of activated platelets decreased (statistically not significant) after re-infusion of autologous PRP. P-selectin expression had returned to pre-CPB levels 24 h post-operatively. Autologous platelet preparations display minimal activation, but remain responsive. Conservation of platelet function may contribute to the potential clinical benefits of autologous transfusion in cardiopulmonary bypass.

Modification of Propellant Binder Network for Improvement of Mechanical Properties

Science.gov (United States)

1984-12-01

skeletal atoms) is more beneficial than 22 mole % of the shorter PEG 3350 (230 skeletal atoms) or 25 mole % of shorter PCP 0260 (180 skeletal atoms). One...of the reasons may be that a higher degree of strain-induced crystalliza- tion of PEG 8000 occurs compared with PEG 3350 or PCP 0260. 4.8 Effect of...prepolymer rubbers. Also, the stress capability of the cured rubbers is improved compared to the long chain prepolymer rubbers. Polyethylene glycol 8000 ( PEG

A novel synthetic quantification standard including virus and internal report targets: application for the detection and quantification of emerging begomoviruses on tomato.

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Péréfarres, Frédéric; Hoareau, Murielle; Chiroleu, Frédéric; Reynaud, Bernard; Dintinger, Jacques; Lett, Jean-Michel

2011-08-05

Begomovirus is a genus of phytopathogenic single-stranded DNA viruses, transmitted by the whitefly Bemisia tabaci. This genus includes emerging and economically significant viruses such as those associated with Tomato Yellow Leaf Curl Disease, for which diagnostic tools are needed to prevent dispersion and new introductions. Five real-time PCRs with an internal tomato reporter gene were developed for accurate detection and quantification of monopartite begomoviruses, including two strains of the Tomato yellow leaf curl virus (TYLCV; Mld and IL strains), the Tomato leaf curl Comoros virus-like viruses (ToLCKMV-like viruses) and the two molecules of the bipartite Potato yellow mosaic virus. These diagnostic tools have a unique standard quantification, comprising the targeted viral and internal report amplicons. These duplex real-time PCRs were applied to artificially inoculated plants to monitor and compare their viral development. Real-time PCRs were optimized for accurate detection and quantification over a range of 2 × 10(9) to 2 × 10(3) copies of genomic viral DNA/μL for TYLCV-Mld, TYLCV-IL and PYMV-B and 2 × 10(8) to 2 × 10(3) copies of genomic viral DNA/μL for PYMV-A and ToLCKMV-like viruses. These real-time PCRs were applied to artificially inoculated plants and viral loads were compared at 10, 20 and 30 days post-inoculation. Different patterns of viral accumulation were observed between the bipartite and the monopartite begomoviruses. Interestingly, PYMV accumulated more viral DNA at each date for both genomic components compared to all the monopartite viruses. Also, PYMV reached its highest viral load at 10 dpi contrary to the other viruses (20 dpi). The accumulation kinetics of the two strains of emergent TYLCV differed from the ToLCKMV-like viruses in the higher quantities of viral DNA produced in the early phase of the infection and in the shorter time to reach this peak viral load. To detect and quantify a wide range of begomoviruses, five duplex

A novel synthetic quantification standard including virus and internal report targets: application for the detection and quantification of emerging begomoviruses on tomato

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Lett Jean-Michel

2011-08-01

Full Text Available Abstract Background Begomovirus is a genus of phytopathogenic single-stranded DNA viruses, transmitted by the whitefly Bemisia tabaci. This genus includes emerging and economically significant viruses such as those associated with Tomato Yellow Leaf Curl Disease, for which diagnostic tools are needed to prevent dispersion and new introductions. Five real-time PCRs with an internal tomato reporter gene were developed for accurate detection and quantification of monopartite begomoviruses, including two strains of the Tomato yellow leaf curl virus (TYLCV; Mld and IL strains, the Tomato leaf curl Comoros virus-like viruses (ToLCKMV-like viruses and the two molecules of the bipartite Potato yellow mosaic virus. These diagnostic tools have a unique standard quantification, comprising the targeted viral and internal report amplicons. These duplex real-time PCRs were applied to artificially inoculated plants to monitor and compare their viral development. Results Real-time PCRs were optimized for accurate detection and quantification over a range of 2 × 109 to 2 × 103 copies of genomic viral DNA/μL for TYLCV-Mld, TYLCV-IL and PYMV-B and 2 × 108 to 2 × 103 copies of genomic viral DNA/μL for PYMV-A and ToLCKMV-like viruses. These real-time PCRs were applied to artificially inoculated plants and viral loads were compared at 10, 20 and 30 days post-inoculation. Different patterns of viral accumulation were observed between the bipartite and the monopartite begomoviruses. Interestingly, PYMV accumulated more viral DNA at each date for both genomic components compared to all the monopartite viruses. Also, PYMV reached its highest viral load at 10 dpi contrary to the other viruses (20 dpi. The accumulation kinetics of the two strains of emergent TYLCV differed from the ToLCKMV-like viruses in the higher quantities of viral DNA produced in the early phase of the infection and in the shorter time to reach this peak viral load. Conclusions To detect and

Comparative antinociceptive and sedative effects of epidural romifidine and detomidine in buffalo (Bubalus bubalis).

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Marzok, M A; El-Khodery, S A

2017-07-01

In this study, comparative antinociceptive and sedative effects of epidural administration of romifidine and detomidine in buffalo were evaluated. Eighteen healthy adult buffalo, allocated randomly in three groups (two experimental and one control; n=6) received either 50 μg/kg of romifidine or detomidine diluted in sterile saline (0.9 per cent) to a final volume of 20 ml, or an equivalent volume of sterile saline epidurally. Antinociception, sedation and ataxia parameters were recorded immediately after drug administration. Epidural romifidine and detomidine produced mild to deep sedation and complete antinociception of the perineum, inguinal area and flank, and extended distally to the coronary band of the hindlimbs and cranially to the chest area. Times to onset of antinociception and sedation were significantly shorter with romifidine than with detomidine. The antinociceptive and sedative effects were significantly longer with romifidine than with detomidine. Romifidine or detomidine could be used to provide a reliable, long-lasting and cost-effective method for achieving epidural anaesthesia for standing surgical procedures in buffalo. Romifidine induces a longer antinociceptive effect and a more rapid onset than detomidine. Consequently, epidural romifidine may offer better therapeutic benefits in the management of acute postoperative pain. British Veterinary Association.

Next-Generation DNA Sequencing of VH/VL Repertoires: A Primer and Guide to Applications in Single-Domain Antibody Discovery.

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Henry, Kevin A

2018-01-01

Immunogenetic analyses of expressed antibody repertoires are becoming increasingly common experimental investigations and are critical to furthering our understanding of autoimmunity, infectious disease, and cancer. Next-generation DNA sequencing (NGS) technologies have now made it possible to interrogate antibody repertoires to unprecedented depths, typically by sequencing of cDNAs encoding immunoglobulin variable domains. In this chapter, we describe simple, fast, and reliable methods for producing and sequencing multiplex PCR amplicons derived from the variable regions (V H , V H H or V L ) of rearranged immunoglobulin heavy and light chain genes using the Illumina MiSeq platform. We include complete protocols and primer sets for amplicon sequencing of V H /V H H/V L repertoires directly from human, mouse, and llama lymphocytes as well as from phage-displayed V H /V H H/V L libraries; these can be easily be adapted to other types of amplicons with little modification. The resulting amplicons are diverse and representative, even using as few as 10 3 input B cells, and their generation is relatively inexpensive, requiring no special equipment and only a limited set of primers. In the absence of heavy-light chain pairing, single-domain antibodies are uniquely amenable to NGS analyses. We present a number of applications of NGS technology useful in discovery of single-domain antibodies from phage display libraries, including: (i) assessment of library functionality; (ii) confirmation of desired library randomization; (iii) estimation of library diversity; and (iv) monitoring the progress of panning experiments. While the case studies presented here are of phage-displayed single-domain antibody libraries, the principles extend to other types of in vitro display libraries.

Family History of Early Infant Death Correlates with Earlier Age at Diagnosis But Not Shorter Time to Diagnosis for Severe Combined Immunodeficiency

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Anderson Dik Wai Luk

2017-07-01

Full Text Available BackgroundSevere combined immunodeficiency (SCID is fatal unless treated with hematopoietic stem cell transplant. Delay in diagnosis is common without newborn screening. Family history of infant death due to infection or known SCID (FH has been associated with earlier diagnosis.ObjectiveThe aim of this study was to identify the clinical features that affect age at diagnosis (AD and time to the diagnosis of SCID.MethodsFrom 2005 to 2016, 147 SCID patients were referred to the Asian Primary Immunodeficiency Network. Patients with genetic diagnosis, age at presentation (AP, and AD were selected for study.ResultsA total of 88 different SCID gene mutations were identified in 94 patients, including 49 IL2RG mutations, 12 RAG1 mutations, 8 RAG2 mutations, 7 JAK3 mutations, 4 DCLRE1C mutations, 4 IL7R mutations, 2 RFXANK mutations, and 2 ADA mutations. A total of 29 mutations were previously unreported. Eighty-three of the 94 patients fulfilled the selection criteria. Their median AD was 4 months, and the time to diagnosis was 2 months. The commonest SCID was X-linked (n = 57. A total of 29 patients had a positive FH. Candidiasis (n = 27 and bacillus Calmette–Guérin (BCG vaccine infection (n = 19 were the commonest infections. The median age for candidiasis and BCG infection documented were 3 months and 4 months, respectively. The median absolute lymphocyte count (ALC was 1.05 × 109/L with over 88% patients below 3 × 109/L. Positive FH was associated with earlier AP by 1 month (p = 0.002 and diagnosis by 2 months (p = 0.008, but not shorter time to diagnosis (p = 0.494. Candidiasis was associated with later AD by 2 months (p = 0.008 and longer time to diagnosis by 0.55 months (p = 0.003. BCG infections were not associated with age or time to diagnosis.ConclusionFH was useful to aid earlier diagnosis but was overlooked by clinicians and not by parents. Similarly, typical clinical features of

A single nucleotide mutation in Nppc is associated with a long bone abnormality in lbab mice.

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Jiao, Yan; Yan, Jian; Jiao, Feng; Yang, Hongbin; Donahue, Leah Rae; Li, Xinmin; Roe, Bruce A; Stuart, John; Gu, Weikuan

2007-04-17

The long bone abnormality (lbab) mouse is a new autosomal recessive mutant characterized by overall smaller body size with proportionate dwarfing of all organs and shorter long bones. Previous linkage analysis has located the lbab mutation on chromosome 1 between the markers D1Mit9 and D1Mit488. A genome-based positional approach was used to identify a mutation associated with lbab disease. A total of 122 genes and expressed sequence tags at the lbab region were screened for possible mutation by using genomic DNA from lbabl/lbab, lbab/+, and +/+ B6 mice and high throughput temperature gradient capillary electrophoresis. A sequence difference was identified in one of the amplicons of gene Nppc between lbab/lbab and +/+ mice. One-step reverse transcriptase polymerase chain reaction was performed to validate the difference of Nppc in different types of mice at the mRNA level. The mutation of Nppc was unique in lbab/lbab mice among multiple mouse inbred strains. The mutation of Nppc is co-segregated with lbab disease in 200 progenies produced from heterozygous lbab/+ parents. A single nucleotide mutation of Nppc is associated with dwarfism in lbab/lbab mice. Current genome information and technology allow us to efficiently identify single nucleotide mutations from roughly mapped disease loci. The lbab mouse is a useful model for hereditary human achondroplasia.

A single nucleotide mutation in Nppc is associated with a long bone abnormality in lbab mice

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Roe Bruce A

2007-04-01

Full Text Available Abstract Background The long bone abnormality (lbab mouse is a new autosomal recessive mutant characterized by overall smaller body size with proportionate dwarfing of all organs and shorter long bones. Previous linkage analysis has located the lbab mutation on chromosome 1 between the markers D1Mit9 and D1Mit488. Results A genome-based positional approach was used to identify a mutation associated with lbab disease. A total of 122 genes and expressed sequence tags at the lbab region were screened for possible mutation by using genomic DNA from lbabl/lbab, lbab/+, and +/+ B6 mice and high throughput temperature gradient capillary electrophoresis. A sequence difference was identified in one of the amplicons of gene Nppc between lbab/lbab and +/+ mice. One-step reverse transcriptase polymerase chain reaction was performed to validate the difference of Nppc in different types of mice at the mRNA level. The mutation of Nppc was unique in lbab/lbab mice among multiple mouse inbred strains. The mutation of Nppc is co-segregated with lbab disease in 200 progenies produced from heterozygous lbab/+ parents. Conclusion A single nucleotide mutation of Nppc is associated with dwarfism in lbab/lbab mice. Current genome information and technology allow us to efficiently identify single nucleotide mutations from roughly mapped disease loci. The lbab mouse is a useful model for hereditary human achondroplasia.