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Sample records for shorter amplicons compared

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

    Science.gov (United States)

    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.

  2. 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.

  3. 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

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

    Science.gov (United States)

    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.

  5. 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

  6. 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...

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

    Science.gov (United States)

    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

  8. 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.)

  9. Optimal Activation of Isopsoralen To Prevent Amplicon Carryover

    OpenAIRE

    Fahle, Gary A.; Gill, Vee J.; Fischer, Steven H.

    1999-01-01

    We compared the efficiencies of activation of the photochemical isopsoralen compound 10 and its resulting amplicon neutralizations under conditions with a UV transilluminator box at room temperature (RT) and a HRI-300 UV photothermal reaction chamber at RT and at 5°C. Our data suggest that use of the HRI-300 reaction chamber at 5°C results in a statistically significantly higher degree of amplicon neutralization.

  10. Removing Noise From Pyrosequenced Amplicons

    Directory of Open Access Journals (Sweden)

    Davenport Russell J

    2011-01-01

    Full Text Available Abstract Background In many environmental genomics applications a homologous region of DNA from a diverse sample is first amplified by PCR and then sequenced. The next generation sequencing technology, 454 pyrosequencing, has allowed much larger read numbers from PCR amplicons than ever before. This has revolutionised the study of microbial diversity as it is now possible to sequence a substantial fraction of the 16S rRNA genes in a community. However, there is a growing realisation that because of the large read numbers and the lack of consensus sequences it is vital to distinguish noise from true sequence diversity in this data. Otherwise this leads to inflated estimates of the number of types or operational taxonomic units (OTUs present. Three sources of error are important: sequencing error, PCR single base substitutions and PCR chimeras. We present AmpliconNoise, a development of the PyroNoise algorithm that is capable of separately removing 454 sequencing errors and PCR single base errors. We also introduce a novel chimera removal program, Perseus, that exploits the sequence abundances associated with pyrosequencing data. We use data sets where samples of known diversity have been amplified and sequenced to quantify the effect of each of the sources of error on OTU inflation and to validate these algorithms. Results AmpliconNoise outperforms alternative algorithms substantially reducing per base error rates for both the GS FLX and latest Titanium protocol. All three sources of error lead to inflation of diversity estimates. In particular, chimera formation has a hitherto unrealised importance which varies according to amplification protocol. We show that AmpliconNoise allows accurate estimates of OTU number. Just as importantly AmpliconNoise generates the right OTUs even at low sequence differences. We demonstrate that Perseus has very high sensitivity, able to find 99% of chimeras, which is critical when these are present at high

  11. 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.

  12. BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS.

    Science.gov (United States)

    Fosso, Bruno; Santamaria, Monica; Marzano, Marinella; Alonso-Alemany, Daniel; Valiente, Gabriel; Donvito, Giacinto; Monaco, Alfonso; Notarangelo, Pasquale; Pesole, Graziano

    2015-07-01

    Substantial advances in microbiology, molecular evolution and biodiversity have been carried out in recent years thanks to Metagenomics, which allows to unveil the composition and functions of mixed microbial communities in any environmental niche. If the investigation is aimed only at the microbiome taxonomic structure, a target-based metagenomic approach, here also referred as Meta-barcoding, is generally applied. This approach commonly involves the selective amplification of a species-specific genetic marker (DNA meta-barcode) in the whole taxonomic range of interest and the exploration of its taxon-related variants through High-Throughput Sequencing (HTS) technologies. The accessibility to proper computational systems for the large-scale bioinformatic analysis of HTS data represents, currently, one of the major challenges in advanced Meta-barcoding projects. BioMaS (Bioinformatic analysis of Metagenomic AmpliconS) is a new bioinformatic pipeline designed to support biomolecular researchers involved in taxonomic studies of environmental microbial communities by a completely automated workflow, comprehensive of all the fundamental steps, from raw sequence data upload and cleaning to final taxonomic identification, that are absolutely required in an appropriately designed Meta-barcoding HTS-based experiment. In its current version, BioMaS allows the analysis of both bacterial and fungal environments starting directly from the raw sequencing data from either Roche 454 or Illumina HTS platforms, following two alternative paths, respectively. BioMaS is implemented into a public web service available at https://recasgateway.ba.infn.it/ and is also available in Galaxy at http://galaxy.cloud.ba.infn.it:8080 (only for Illumina data). BioMaS is a friendly pipeline for Meta-barcoding HTS data analysis specifically designed for users without particular computing skills. A comparative benchmark, carried out by using a simulated dataset suitably designed to broadly represent

  13. Polyadenylated Sequencing Primers Enable Complete Readability of PCR Amplicons Analyzed by Dideoxynucleotide Sequencing

    Directory of Open Access Journals (Sweden)

    Martin Beránek

    2012-01-01

    Full Text Available Dideoxynucleotide DNA sequencing is one of the principal procedures in molecular biology. Loss of an initial part of nucleotides behind the 3' end of the sequencing primer limits the readability of sequenced amplicons. We present a method which extends the readability by using sequencing primers modified by polyadenylated tails attached to their 5' ends. Performing a polymerase chain reaction, we amplified eight amplicons of six human genes (AMELX, APOE, HFE, MBL2, SERPINA1 and TGFB1 ranging from 106 bp to 680 bp. Polyadenylation of the sequencing primers minimized the loss of bases in all amplicons. Complete sequences of shorter products (AMELX 106 bp, SERPINA1 121 bp, HFE 208 bp, APOE 244 bp, MBL2 317 bp were obtained. In addition, in the case of TGFB1 products (366 bp, 432 bp, and 680 bp, respectively, the lengths of sequencing readings were significantly longer if adenylated primers were used. Thus, single strand dideoxynucleotide sequencing with adenylated primers enables complete or near complete readability of short PCR amplicons.

  14. Efficient error correction for next-generation sequencing of viral amplicons.

    Science.gov (United States)

    Skums, Pavel; Dimitrova, Zoya; Campo, David S; Vaughan, Gilberto; Rossi, Livia; Forbi, Joseph C; Yokosawa, Jonny; Zelikovsky, Alex; Khudyakov, Yury

    2012-06-25

    Next-generation sequencing allows the analysis of an unprecedented number of viral sequence variants from infected patients, presenting a novel opportunity for understanding virus evolution, drug resistance and immune escape. However, sequencing in bulk is error prone. Thus, the generated data require error identification and correction. Most error-correction methods to date are not optimized for amplicon analysis and assume that the error rate is randomly distributed. Recent quality assessment of amplicon sequences obtained using 454-sequencing showed that the error rate is strongly linked to the presence and size of homopolymers, position in the sequence and length of the amplicon. All these parameters are strongly sequence specific and should be incorporated into the calibration of error-correction algorithms designed for amplicon sequencing. In this paper, we present two new efficient error correction algorithms optimized for viral amplicons: (i) k-mer-based error correction (KEC) and (ii) empirical frequency threshold (ET). Both were compared to a previously published clustering algorithm (SHORAH), in order to evaluate their relative performance on 24 experimental datasets obtained by 454-sequencing of amplicons with known sequences. All three algorithms show similar accuracy in finding true haplotypes. However, KEC and ET were significantly more efficient than SHORAH in removing false haplotypes and estimating the frequency of true ones. Both algorithms, KEC and ET, are highly suitable for rapid recovery of error-free haplotypes obtained by 454-sequencing of amplicons from heterogeneous viruses.The implementations of the algorithms and data sets used for their testing are available at: http://alan.cs.gsu.edu/NGS/?q=content/pyrosequencing-error-correction-algorithm.

  15. Improved sensitivity of circulating tumor DNA measurement using short PCR amplicons

    DEFF Research Database (Denmark)

    Andersen, Rikke Fredslund; Spindler, Karen-Lise Garm; Brandslund, Ivan

    2015-01-01

    , however, presents a number of challenges that require attention. The amount of DNA is low and highly fragmented and analyses need to be optimized accordingly. KRAS ARMS-qPCR assays with amplicon lengths of 120 and 85 base pairs, respectively, were compared using positive control material (PCR fragments...

  16. 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

  17. A novel ultra high-throughput 16S rRNA gene amplicon sequencing library preparation method for the Illumina HiSeq platform.

    Science.gov (United States)

    de Muinck, Eric J; Trosvik, Pål; Gilfillan, Gregor D; Hov, Johannes R; Sundaram, Arvind Y M

    2017-07-06

    Advances in sequencing technologies and bioinformatics have made the analysis of microbial communities almost routine. Nonetheless, the need remains to improve on the techniques used for gathering such data, including increasing throughput while lowering cost and benchmarking the techniques so that potential sources of bias can be better characterized. We present a triple-index amplicon sequencing strategy to sequence large numbers of samples at significantly lower c ost and in a shorter timeframe compared to existing methods. The design employs a two-stage PCR protocol, incorpo rating three barcodes to each sample, with the possibility to add a fourth-index. It also includes heterogeneity spacers to overcome low complexity issues faced when sequencing amplicons on Illumina platforms. The library preparation method was extensively benchmarked through analysis of a mock community in order to assess biases introduced by sample indexing, number of PCR cycles, and template concentration. We further evaluated the method through re-sequencing of a standardized environmental sample. Finally, we evaluated our protocol on a set of fecal samples from a small cohort of healthy adults, demonstrating good performance in a realistic experimental setting. Between-sample variation was mainly related to batch effects, such as DNA extraction, while sample indexing was also a significant source of bias. PCR cycle number strongly influenced chimera formation and affected relative abundance estimates of species with high GC content. Libraries were sequenced using the Illumina HiSeq and MiSeq platforms to demonstrate that this protocol is highly scalable to sequence thousands of samples at a very low cost. Here, we provide the most comprehensive study of performance and bias inherent to a 16S rRNA gene amplicon sequencing method to date. Triple-indexing greatly reduces the number of long custom DNA oligos required for library preparation, while the inclusion of variable length

  18. Strong selective sweeps associated with ampliconic regions in great ape X chromosomes

    DEFF Research Database (Denmark)

    Nam, Kiwoong; Munch, Kasper; Hobolth, Asger

    2014-01-01

    The unique inheritance pattern of X chromosomes makes them preferential targets of adaptive evolution. We here investigate natural selection on the X chromosome in all species of great apes. We find that diversity is more strongly reduced around genes on the X compared with autosomes...... with ampliconic sequences we propose that intra-genomic conflict between the X and the Y chromosomes is a major driver of X chromosome evolution....

  19. High throughput 16S rRNA gene amplicon sequencing

    DEFF Research Database (Denmark)

    Nierychlo, Marta; Larsen, Poul; Jørgensen, Mads Koustrup

    S rRNA gene amplicon sequencing has been developed over the past few years and is now ready to use for more comprehensive studies related to plant operation and optimization thanks to short analysis time, low cost, high throughput, and high taxonomic resolution. In this study we show how 16S r......RNA gene amplicon sequencing can be used to reveal factors of importance for the operation of full-scale nutrient removal plants related to settling problems and floc properties. Using optimized DNA extraction protocols, indexed primers and our in-house Illumina platform, we prepared multiple samples...... be correlated to the presence of the species that are regarded as “strong” and “weak” floc formers. In conclusion, 16S rRNA gene amplicon sequencing provides a high throughput approach for a rapid and cheap community profiling of activated sludge that in combination with multivariate statistics can be used...

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

    Directory of Open Access Journals (Sweden)

    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.

  1. 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...

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

    Directory of Open Access Journals (Sweden)

    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.

  3. 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

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

    Directory of Open Access Journals (Sweden)

    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.

  5. 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

  6. Analysis and Visualization Tool for Targeted Amplicon Bisulfite Sequencing on Ion Torrent Sequencers.

    Directory of Open Access Journals (Sweden)

    Stephan Pabinger

    Full Text Available Targeted sequencing of PCR amplicons generated from bisulfite deaminated DNA is a flexible, cost-effective way to study methylation of a sample at single CpG resolution and perform subsequent multi-target, multi-sample comparisons. Currently, no platform specific protocol, support, or analysis solution is provided to perform targeted bisulfite sequencing on a Personal Genome Machine (PGM. Here, we present a novel tool, called TABSAT, for analyzing targeted bisulfite sequencing data generated on Ion Torrent sequencers. The workflow starts with raw sequencing data, performs quality assessment, and uses a tailored version of Bismark to map the reads to a reference genome. The pipeline visualizes results as lollipop plots and is able to deduce specific methylation-patterns present in a sample. The obtained profiles are then summarized and compared between samples. In order to assess the performance of the targeted bisulfite sequencing workflow, 48 samples were used to generate 53 different Bisulfite-Sequencing PCR amplicons from each sample, resulting in 2,544 amplicon targets. We obtained a mean coverage of 282X using 1,196,822 aligned reads. Next, we compared the sequencing results of these targets to the methylation level of the corresponding sites on an Illumina 450k methylation chip. The calculated average Pearson correlation coefficient of 0.91 confirms the sequencing results with one of the industry-leading CpG methylation platforms and shows that targeted amplicon bisulfite sequencing provides an accurate and cost-efficient method for DNA methylation studies, e.g., to provide platform-independent confirmation of Illumina Infinium 450k methylation data. TABSAT offers a novel way to analyze data generated by Ion Torrent instruments and can also be used with data from the Illumina MiSeq platform. It can be easily accessed via the Platomics platform, which offers a web-based graphical user interface along with sample and parameter storage

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

    Science.gov (United States)

    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.

  8. 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.

  9. Swarm: robust and fast clustering method for amplicon-based studies

    Science.gov (United States)

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

    2014-01-01

    Popular de novo amplicon clustering methods suffer from two fundamental flaws: arbitrary global clustering thresholds, and input-order dependency induced by centroid selection. Swarm was developed to address these issues by first clustering nearly identical amplicons iteratively using a local threshold, and then by using clusters’ internal structure and amplicon abundances to refine its results. This fast, scalable, and input-order independent approach reduces the influence of clustering parameters and produces robust operational taxonomic units. PMID:25276506

  10. Swarm: robust and fast clustering method for amplicon-based studies

    Directory of Open Access Journals (Sweden)

    Frédéric Mahé

    2014-09-01

    Full Text Available Popular de novo amplicon clustering methods suffer from two fundamental flaws: arbitrary global clustering thresholds, and input-order dependency induced by centroid selection. Swarm was developed to address these issues by first clustering nearly identical amplicons iteratively using a local threshold, and then by using clusters’ internal structure and amplicon abundances to refine its results. This fast, scalable, and input-order independent approach reduces the influence of clustering parameters and produces robust operational taxonomic units.

  11. 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...

  12. Deep amplicon sequencing reveals mixed phytoplasma infection within single grapevine plants

    DEFF Research Database (Denmark)

    Nicolaisen, Mogens; Contaldo, Nicoletta; Makarova, Olga

    2011-01-01

    The diversity of phytoplasmas within single plants has not yet been fully investigated. In this project, deep amplicon sequencing was used to generate 50,926 phytoplasma sequences from 11 phytoplasma-infected grapevine samples from a PCR amplicon in the 5' end of the 16S region. After clustering ...

  13. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  15. 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.

  16. 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.

  17. High-throughput sequencing of 16S rRNA gene amplicons: effects of extraction procedure, primer length and annealing temperature.

    Science.gov (United States)

    Sergeant, Martin J; Constantinidou, Chrystala; Cogan, Tristan; Penn, Charles W; Pallen, Mark J

    2012-01-01

    The analysis of 16S-rDNA sequences to assess the bacterial community composition of a sample is a widely used technique that has increased with the advent of high throughput sequencing. Although considerable effort has been devoted to identifying the most informative region of the 16S gene and the optimal informatics procedures to process the data, little attention has been paid to the PCR step, in particular annealing temperature and primer length. To address this, amplicons derived from 16S-rDNA were generated from chicken caecal content DNA using different annealing temperatures, primers and different DNA extraction procedures. The amplicons were pyrosequenced to determine the optimal protocols for capture of maximum bacterial diversity from a chicken caecal sample. Even at very low annealing temperatures there was little effect on the community structure, although the abundance of some OTUs such as Bifidobacterium increased. Using shorter primers did not reveal any novel OTUs but did change the community profile obtained. Mechanical disruption of the sample by bead beating had a significant effect on the results obtained, as did repeated freezing and thawing. In conclusion, existing primers and standard annealing temperatures captured as much diversity as lower annealing temperatures and shorter primers.

  18. Dynamic Copy Number Evolution of X- and Y-Linked Ampliconic Genes in Human Populations

    DEFF Research Database (Denmark)

    Lucotte, Elise A; Skov, Laurits; Jensen, Jacob Malte

    2018-01-01

    we explore the evolution of human X- and Y-linked ampliconic genes by investigating copy number variation (CNV) and coding variation between populations using the Simons Genome Diversity Project. We develop a method to assess CNVs using the read-depth on modified X and Y chromosome targets containing...... related Y haplogroups, that diversified less than 50,000 years ago. Moreover, X and Y-linked ampliconic genes seem to have a faster amplification dynamic than autosomal multicopy genes. Looking at expression data from another study, we also find that XY-linked ampliconic genes with extensive copy number...

  19. 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

  20. 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.

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  3. JRC GMO-Amplicons: a collection of nucleic acid sequences related to genetically modified organisms.

    Science.gov (United States)

    Petrillo, Mauro; Angers-Loustau, Alexandre; Henriksson, Peter; Bonfini, Laura; Patak, Alex; Kreysa, Joachim

    2015-01-01

    The DNA target sequence is the key element in designing detection methods for genetically modified organisms (GMOs). Unfortunately this information is frequently lacking, especially for unauthorized GMOs. In addition, patent sequences are generally poorly annotated, buried in complex and extensive documentation and hard to link to the corresponding GM event. Here, we present the JRC GMO-Amplicons, a database of amplicons collected by screening public nucleotide sequence databanks by in silico determination of PCR amplification with reference methods for GMO analysis. The European Union Reference Laboratory for Genetically Modified Food and Feed (EU-RL GMFF) provides these methods in the GMOMETHODS database to support enforcement of EU legislation and GM food/feed control. The JRC GMO-Amplicons database is composed of more than 240 000 amplicons, which can be easily accessed and screened through a web interface. To our knowledge, this is the first attempt at pooling and collecting publicly available sequences related to GMOs in food and feed. The JRC GMO-Amplicons supports control laboratories in the design and assessment of GMO methods, providing inter-alia in silico prediction of primers specificity and GM targets coverage. The new tool can assist the laboratories in the analysis of complex issues, such as the detection and identification of unauthorized GMOs. Notably, the JRC GMO-Amplicons database allows the retrieval and characterization of GMO-related sequences included in patents documentation. Finally, it can help annotating poorly described GM sequences and identifying new relevant GMO-related sequences in public databases. The JRC GMO-Amplicons is freely accessible through a web-based portal that is hosted on the EU-RL GMFF website. Database URL: http://gmo-crl.jrc.ec.europa.eu/jrcgmoamplicons/. © The Author(s) 2015. Published by Oxford University Press.

  4. Generic Amplicon Deep Sequencing to Determine Ilarvirus Species Diversity in Australian Prunus.

    Science.gov (United States)

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

    2017-01-01

    The distribution of Ilarvirus species populations amongst 61 Australian Prunus trees was determined by next generation sequencing (NGS) of amplicons generated using a genus-based generic RT-PCR targeting a conserved region of the Ilarvirus RNA2 component that encodes the RNA dependent RNA polymerase (RdRp) gene. Presence of Ilarvirus sequences in each positive sample was further validated by Sanger sequencing of cloned amplicons of regions of each of RNA1, RNA2 and/or RNA3 that were generated by species specific PCRs and by metagenomic NGS. Prunus necrotic ringspot virus (PNRSV) was the most frequently detected Ilarvirus , occurring in 48 of the 61 Ilarvirus -positive trees and Prune dwarf virus (PDV) and Apple mosaic virus (ApMV) were detected in three trees and one tree, respectively. American plum line pattern virus (APLPV) was detected in three trees and represents the first report of APLPV detection in Australia. Two novel and distinct groups of Ilarvirus -like RNA2 amplicon sequences were also identified in several trees by the generic amplicon NGS approach. The high read depth from the amplicon NGS of the generic PCR products allowed the detection of distinct RNA2 RdRp sequence variant populations of PNRSV, PDV, ApMV, APLPV and the two novel Ilarvirus -like sequences. Mixed infections of ilarviruses were also detected in seven Prunus trees. Sanger sequencing of specific RNA1, RNA2, and/or RNA3 genome segments of each virus and total nucleic acid metagenomics NGS confirmed the presence of PNRSV, PDV, ApMV and APLPV detected by RNA2 generic amplicon NGS. However, the two novel groups of Ilarvirus -like RNA2 amplicon sequences detected by the generic amplicon NGS could not be associated to the presence of sequence from RNA1 or RNA3 genome segments or full Ilarvirus genomes, and their origin is unclear. This work highlights the sensitivity of genus-specific amplicon NGS in detection of virus sequences and their distinct populations in multiple samples, and the

  5. Generic Amplicon Deep Sequencing to Determine Ilarvirus Species Diversity in Australian Prunus

    Directory of Open Access Journals (Sweden)

    Wycliff M. Kinoti

    2017-06-01

    Full Text Available The distribution of Ilarvirus species populations amongst 61 Australian Prunus trees was determined by next generation sequencing (NGS of amplicons generated using a genus-based generic RT-PCR targeting a conserved region of the Ilarvirus RNA2 component that encodes the RNA dependent RNA polymerase (RdRp gene. Presence of Ilarvirus sequences in each positive sample was further validated by Sanger sequencing of cloned amplicons of regions of each of RNA1, RNA2 and/or RNA3 that were generated by species specific PCRs and by metagenomic NGS. Prunus necrotic ringspot virus (PNRSV was the most frequently detected Ilarvirus, occurring in 48 of the 61 Ilarvirus-positive trees and Prune dwarf virus (PDV and Apple mosaic virus (ApMV were detected in three trees and one tree, respectively. American plum line pattern virus (APLPV was detected in three trees and represents the first report of APLPV detection in Australia. Two novel and distinct groups of Ilarvirus-like RNA2 amplicon sequences were also identified in several trees by the generic amplicon NGS approach. The high read depth from the amplicon NGS of the generic PCR products allowed the detection of distinct RNA2 RdRp sequence variant populations of PNRSV, PDV, ApMV, APLPV and the two novel Ilarvirus-like sequences. Mixed infections of ilarviruses were also detected in seven Prunus trees. Sanger sequencing of specific RNA1, RNA2, and/or RNA3 genome segments of each virus and total nucleic acid metagenomics NGS confirmed the presence of PNRSV, PDV, ApMV and APLPV detected by RNA2 generic amplicon NGS. However, the two novel groups of Ilarvirus-like RNA2 amplicon sequences detected by the generic amplicon NGS could not be associated to the presence of sequence from RNA1 or RNA3 genome segments or full Ilarvirus genomes, and their origin is unclear. This work highlights the sensitivity of genus-specific amplicon NGS in detection of virus sequences and their distinct populations in multiple samples

  6. 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...

  7. 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.

  8. 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

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

    Science.gov (United States)

    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.

  10. 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

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

    Directory of Open Access Journals (Sweden)

    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.

  12. 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...

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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/

  15. Absolute estimation of initial concentrations of amplicon in a real-time RT-PCR process

    Directory of Open Access Journals (Sweden)

    Kohn Michael

    2007-10-01

    Full Text Available Abstract Background Since real time PCR was first developed, several approaches to estimating the initial quantity of template in an RT-PCR reaction have been tried. While initially only the early thermal cycles corresponding to exponential duplication were used, lately there has been an effort to use all of the cycles in a PCR. The efforts have included both fitting empirical sigmoid curves and more elaborate mechanistic models that explore the chemical reactions taking place during each cycle. The more elaborate mechanistic models require many more parameters than can be fit from a single amplification, while the empirical models provide little insight and are difficult to tailor to specific reactants. Results We directly estimate the initial amount of amplicon using a simplified mechanistic model based on chemical reactions in the annealing step of the PCR. The basic model includes the duplication of DNA with the digestion of Taqman probe and the re-annealing between previously synthesized DNA strands of opposite orientation. By modelling the amount of Taqman probe digested and matching that with the observed fluorescence, the conversion factor between the number of fluorescing dye molecules and observed fluorescent emission can be estimated, along with the absolute initial amount of amplicon and the rate parameter for re-annealing. The model is applied to several PCR reactions with known amounts of amplicon and is shown to work reasonably well. An expanded version of the model allows duplication of amplicon without release of fluorescent dye, by adding 1 more parameter to the model. The additional process is helpful in most cases where the initial primer concentration exceeds the initial probe concentration. Software for applying the algorithm to data may be downloaded at http://www.niehs.nih.gov/research/resources/software/pcranalyzer/ Conclusion We present proof of the principle that a mechanistically based model can be fit to observations

  16. 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...

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

    Directory of Open Access Journals (Sweden)

    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

  18. 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

  19. 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.

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

    Science.gov (United States)

    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

  1. 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.

  2. 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...

  3. 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...

  4. Ultra-high resolution HLA genotyping and allele discovery by highly multiplexed cDNA amplicon pyrosequencing

    Directory of Open Access Journals (Sweden)

    Lank Simon M

    2012-08-01

    Full Text Available Abstract Background High-resolution HLA genotyping is a critical diagnostic and research assay. Current methods rarely achieve unambiguous high-resolution typing without making population-specific frequency inferences due to a lack of locus coverage and difficulty in exon-phase matching. Achieving high-resolution typing is also becoming more challenging with traditional methods as the database of known HLA alleles increases. Results We designed a cDNA amplicon-based pyrosequencing method to capture 94% of the HLA class I open-reading-frame with only two amplicons per sample, and an analogous method for class II HLA genes, with a primary focus on sequencing the DRB loci. We present a novel Galaxy server-based analysis workflow for determining genotype. During assay validation, we performed two GS Junior sequencing runs to determine the accuracy of the HLA class I amplicons and DRB amplicon at different levels of multiplexing. When 116 amplicons were multiplexed, we unambiguously resolved 99%of class I alleles to four- or six-digit resolution, as well as 100% unambiguous DRB calls. The second experiment, with 271 multiplexed amplicons, missed some alleles, but generated high-resolution, concordant typing for 93% of class I alleles, and 96% for DRB1 alleles. In a third, preliminary experiment we attempted to sequence novel amplicons for other class II loci with mixed success. Conclusions The presented assay is higher-throughput and higher-resolution than existing HLA genotyping methods, and suitable for allele discovery or large cohort sampling. The validated class I and DRB primers successfully generated unambiguously high-resolution genotypes, while further work is needed to validate additional class II genotyping amplicons.

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

    Science.gov (United States)

    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.

  6. 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)

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

    Science.gov (United States)

    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

  8. 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.

  9. 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.

  10. 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...

  11. 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...

  12. 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/.

  13. Shorter Decentralized Attribute-Based Encryption via Extended Dual System Groups

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    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.

  16. 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...

  17. 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.

  18. 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.

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

    Science.gov (United States)

    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.

  20. 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.

  1. 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

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

  4. 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...

  5. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  7. 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.

  8. 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...

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    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.

  12. 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.

  13. COMPAR

    International Nuclear Information System (INIS)

    Kuefner, K.

    1976-01-01

    COMPAR works on FORTRAN arrays with four indices: A = A(i,j,k,l) where, for each fixed k 0 ,l 0 , only the 'plane' [A(i,j,k 0 ,l 0 ), i = 1, isub(max), j = 1, jsub(max)] is held in fast memory. Given two arrays A, B of this type COMPAR has the capability to 1) re-norm A and B ind different ways; 2) calculate the deviations epsilon defined as epsilon(i,j,k,l): =[A(i,j,k,l) - B(i,j,k,l)] / GEW(i,j,k,l) where GEW (i,j,k,l) may be chosen in three different ways; 3) calculate mean, standard deviation and maximum in the array epsilon (by several intermediate stages); 4) determine traverses in the array epsilon; 5) plot these traverses by a printer; 6) simplify plots of these traverses by the PLOTEASY-system by creating input data blocks for this system. The main application of COMPAR is given (so far) by the comparison of two- and three-dimensional multigroup neutron flux-fields. (orig.) [de

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

    Science.gov (United States)

    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.

  15. 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.

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

    Science.gov (United States)

    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.

  17. 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.

  18. 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.

  19. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    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.

  3. 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.

  4. 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.

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

    Science.gov (United States)

    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.

  6. 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...

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

    Directory of Open Access Journals (Sweden)

    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.

  8. 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.

  9. Prerequisites for Amplicon Pyrosequencing of Microbial Methanol Utilizers in the Environment

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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

  11. 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:

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

    Directory of Open Access Journals (Sweden)

    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

  13. 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...

  14. 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.

  15. 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)

  16. 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...

  17. 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

  18. 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

  19. 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....

  20. 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....

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  3. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  5. 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.

  6. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  10. 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.

  11. 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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    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.

  13. 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).

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

    Science.gov (United States)

    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.

  15. 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

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

    Directory of Open Access Journals (Sweden)

    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.

  17. 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....

  18. 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...

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  1. 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.

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

    Directory of Open Access Journals (Sweden)

    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

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

    Science.gov (United States)

    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).

  4. 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...

  5. 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.

  6. 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...

  7. 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

  8. 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...

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  11. 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

  12. 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

  13. 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.

  14. 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.

  15. 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

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

    Science.gov (United States)

    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

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

    Directory of Open Access Journals (Sweden)

    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

  18. 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

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    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.

  1. 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.

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

    Science.gov (United States)

    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.

  3. 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.

  4. 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.

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  7. 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.

  8. 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.

  9. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    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.

  12. 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

  13. 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.

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

    Science.gov (United States)

    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.

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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

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

    Science.gov (United States)

    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

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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

  10. Shorter HBIG administration is not associated to HBV recurrence when receiving combined prophylaxis after liver transplantation.

    Science.gov (United States)

    Lens, Sabela; García-Eliz, María; Fernández, Inmaculada; Castells, Lluis; Bonacci, Martin; Mas, Antoni; Crespo, Gonzalo; Buti, María; Prieto, Martín; Forns, Xavier

    2018-04-16

    The combination of hepatitis B immunoglobulin (HBIG) and a nucleos(t)ide analogs (NA) has markedly reduced the rate of hepatitis B (HBV) recurrence after liver transplantation (LT); however, the optimal duration of HBIG has not been clarified. This lack of consensus perpetuates the use of different strategies. The aim of this study was to evaluate the risk factors associated to HBV recurrence after LT in a large cohort of patients under different HBIG regimens. Retrospective multicenter analysis of HBV-related LT recipients receiving combined prophylaxis (HBIG+NA). The strategy of short-term HBIG was compared to life-long administration. HBV recurrence was defined as positive HBsAg after LT. 338 patients were analyzed. After a median follow-up period of 72 months, 37 patients (11%) developed HBV recurrence. Hepatocellular carcinoma (HCC) recurrence and lamivudine resistance after LT were the only factors independently associated to HBV recurrence (HR 5.4[2.3-12] and 9.3[4.2-20], respectively pHBV recurrence was transient (16 patients), persistent (15) or alternant (6). The HBIG regimen did not have an impact on the rate or evolution of HBV recurrence. Overall, patient survival was good and not influenced by HBV recurrence (82% at 5 years). Fulminant liver failure, hepatitis C coinfection or HCC at LT were independent risk factors for lower survival. LT is an effective treatment for HBV-related liver disease. Since the introduction of combined prophylaxis the rate of HBV recurrence is very low. However, life-long HBIG administration does not seem necessary to reduce HBV recurrence. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  11. 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

  12. 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

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

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    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.

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

    Science.gov (United States)

    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.

  15. 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.

  16. 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

  17. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  4. 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.

  5. 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

  6. '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.

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    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

  9. 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

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  12. 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

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    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.

  15. 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...

  16. 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.

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

    Science.gov (United States)

    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).

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  20. 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....

  1. 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

    Directory of Open Access Journals (Sweden)

    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

  2. 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.)

  3. 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.)

  4. 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)

  5. 16S rRNA amplicon sequencing identifies microbiota associated with oral cancer, Human Papilloma Virus infection and surgical treatment

    NARCIS (Netherlands)

    Guerrero-Preston, Rafael; Godoy-Vitorino, Filipa; Jedlicka, Anne; Rodriguez-Hilario, Arnold; Gonzalez, Herminio; Bondy, Jessica; Lawson, Fahcina; Folawiyo, Oluwasina; Michailidi, Christina; Dziedzic, Amanda; Thangavel, Rajagowthamee; Hadar, Tal; Noordhuis, Maartje G.; Westra, William; Koch, Wayne; Sidransky, David

    2016-01-01

    Systemic inflammatory events and localized disease, mediated by the microbiome, may be measured in saliva as head and neck squamous cell carcinoma (HNSCC) diagnostic and prognostic biomonitors. We used a 16S rRNA V3-V5 marker gene approach to compare the saliva microbiome in DNA isolated from

  6. 16S rRNA amplicon sequencing identifies microbiota associated with oral cancer, human papilloma virus infection and surgical treatment.

    Science.gov (United States)

    Guerrero-Preston, Rafael; Godoy-Vitorino, Filipa; Jedlicka, Anne; Rodríguez-Hilario, Arnold; González, Herminio; Bondy, Jessica; Lawson, Fahcina; Folawiyo, Oluwasina; Michailidi, Christina; Dziedzic, Amanda; Thangavel, Rajagowthamee; Hadar, Tal; Noordhuis, Maartje G; Westra, William; Koch, Wayne; Sidransky, David

    2016-08-09

    Systemic inflammatory events and localized disease, mediated by the microbiome, may be measured in saliva as head and neck squamous cell carcinoma (HNSCC) diagnostic and prognostic biomonitors. We used a 16S rRNA V3-V5 marker gene approach to compare the saliva microbiome in DNA isolated from Oropharyngeal (OPSCC), Oral Cavity Squamous Cell Carcinoma (OCSCC) patients and normal epithelium controls, to characterize the HNSCC saliva microbiota and examine their abundance before and after surgical resection.The analyses identified a predominance of Firmicutes, Proteobacteria and Bacteroidetes, with less frequent presence of Actinobacteria and Fusobacteria before surgery. At lower taxonomic levels, the most abundant genera were Streptococcus, Prevotella, Haemophilus, Lactobacillus and Veillonella, with lower numbers of Citrobacter and Neisseraceae genus Kingella. HNSCC patients had a significant loss in richness and diversity of microbiota species (p<0.05) compared to the controls. Overall, the Operational Taxonomic Units network shows that the relative abundance of OTU's within genus Streptococcus, Dialister, and Veillonella can be used to discriminate tumor from control samples (p<0.05). Tumor samples lost Neisseria, Aggregatibacter (Proteobacteria), Haemophillus (Firmicutes) and Leptotrichia (Fusobacteria). Paired taxa within family Enterobacteriaceae, together with genus Oribacterium, distinguish OCSCC samples from OPSCC and normal samples (p<0.05). Similarly, only HPV positive samples have an abundance of genus Gemellaceae and Leuconostoc (p<0.05). Longitudinal analyses of samples taken before and after surgery, revealed a reduction in the alpha diversity measure after surgery, together with an increase of this measure in patients that recurred (p<0.05). These results suggest that microbiota may be used as HNSCC diagnostic and prognostic biomonitors.

  7. 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.

  8. 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

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  11. Looking for Rhizobacterial Ecological Indicators in Agricultural Soils Using 16S rRNA metagenomic Amplicon Data.

    Directory of Open Access Journals (Sweden)

    José R Valverde

    Full Text Available Biological communities present in soil are essential to sustainable and productive agricultural practices; however, an accurate determination of the ecological status of agricultural soils remains to date an elusive task. An ideal indicator should be pervasive, play a relevant role in the ecosystem, show a rapid and proportional answer to external perturbations and be easily and economically measurable. Rhizobacteria play a major role in determining soil properties, becoming an attractive candidate for the detection of ecological indicators. The application of massive sequencing technologies to metagenomic analysis is providing an increasingly more precise view of the structure and composition of soil communities. In this work, we analyse soil rhizobacterial composition under various stress levels to search for potential ecological indicators.Our results suggest that the Shannon index requires observation of a relatively large number of individuals to be representative of the true population diversity, and that the Simpson index may underestimate rare taxa in rhizobacterial environments.Detection of indicator taxa requires comparison of taxonomical classification of sequences. We have compared RDP classifier, RTAX and similarity-based taxonomical classification and selected the latter for taxonomical assignment because it provides larger detail.The study of significant variations in common, clearly identified, taxa, using paired datasets allows minimization of non-treatment effects and avoidance of false positives. We have identified taxa associated to specific perturbations as well as taxa generally affected in treated soils. Changes in these taxa, or combinations of them, may be used as ecological indicators of soil health. The overall number and magnitude of changes detected in taxonomic groups does also increase with stress. These changes constitute an alternative indicator to measuring specific taxa, although their determination requires

  12. 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...

  13. 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

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

    Directory of Open Access Journals (Sweden)

    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.

  15. 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.

  16. 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.

  17. (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 ...

  18. Measuring single constructs by single items: Constructing an even shorter version of the "Short Five" personality inventory.

    Directory of Open Access Journals (Sweden)

    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

  19. 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

  20. Shorter CAG repeat length in the AR gene is associated with poor outcome in head and neck cancer

    DEFF Research Database (Denmark)

    Rosa, Fabíola Encinas; dos Santos, Rodrigo Mattos; Poli-Frederico, Regina Célia

    2007-01-01

    microsatellite instability (MSI) and loss of heterozygosity (LOH) in these tumors. DESIGN: Matched samples of blood and head and neck tumors were evaluated using two methodologies, silver-stained gels to perform the analyses of MSI and LOH, and automated analysis to confirm these results and for genotyping...... of the AR [CAG](n) repeat length. Sixty-nine individuals without cancer were used as a control group for both procedures. The Log-rank test was used to compare overall survival and disease-free survival curves. The Cox proportional hazards regression models were performed to determine the [CAG](n) repeats......: These results suggest that short [CAG](n) repeat length (poor prognosis in a subset of male patients with head and neck cancer and that AR gene microsatellite instability is uncommon in these tumors....

  1. Shorter Duration of Post-Operative Antibiotics for Cecal Ligation and Puncture Does Not Increase Inflammation or Mortality.

    Directory of Open Access Journals (Sweden)

    Kendra N Iskander

    Full Text Available Antimicrobial therapy for sepsis has beneficial effects, but prolonged use fosters emergence of resistant microorganisms, increases cost, and secondary infections. We tested whether 3 days versus 5 days of antibiotics in the murine model of cecal ligation and puncture (CLP negatively influences outcomes. Following CLP mice were randomized to receive the antibiotic imipenem-cilastatin (25mg/kg in dextrose 5% in Lactated Ringer's solution every 12 hours for either three or five days. Serial monitoring over 28 days included body weight, temperature, pulse oximetry, and facial vein sampling for hematological analysis and glucose. A separate group of mice were euthanized on post-CLP day 5 to measure cytokines and peritoneal bacterial counts. The first study examined no antimicrobial therapy and demonstrated that antibiotics significantly improved survival compared to fluids only (p = 0.004. We next tested imipenem-cilastatin therapy for 3 days versus 5 days. Body weight, temperature, glucose, and pulse oximetry measurements remained generally consistent between both groups as did the hematological profile. Pro-inflammatory plasma cytokines were comparable between both groups for IL-6, IL-1β, MIP-2 and anti-inflammatory cytokines IL-10, and TNF SRI. At 5 days post-CLP, i.e. 2 days after the termination of antibiotics in the 3 day group, there were no differences in the number of peritoneal bacteria. Importantly, shortening the course of antibiotics by 40% (from 5 days to 3 days did not decrease survival. Our results indicate that reducing the duration of broad-spectrum antibiotics in murine sepsis did not increase inflammation or mortality.

  2. Shorter maintenance therapy in childhood Acute Lymphoblastic Leukemia. The experience of the prospective, randomized Brazilian GBTLI ALL-93 protocol.

    Directory of Open Access Journals (Sweden)

    Silvia Regina Brandalise

    2016-10-01

    Full Text Available Maintenance therapy is an important phase of the childhood ALL treatment, requiring 2-year long therapy adherence of the patients and families. Weekly methotrexate (MTX with daily 6-mercaptopurine (6MP constitutes the backbone of maintenance therapy. Reduction in the maintenance therapy could overweight problems related with poverty of children with ALL living in Limited-Income countries (LIC. Objective: To compare, prospectively, the EFS rates of children with ALL treated according to two maintenance regimens: 18 vs 24 months duration. Materials and Methods: From October 1993 to September 1999, 867 consecutive untreated ALL patients 10 years and high WBC at diagnosis. Overall death in remission rate was 6.85% (56 patients. Deaths during maintenance were 13 in group 1 and 12 in group 2, all due to infection. Over 15 years of follow-up, two patients both from Group 2 presented a second malignancy (Hodgkin’s disease and thyroid carcinoma after 8.3 and 11 years off therapy, respectively. Conclusion: Six-month reduction of maintenance therapy in ALL children treated according to the GBTLI ALL-93 protocol, provided the same overall outcome as 2-year duration regimen.

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

    Directory of Open Access Journals (Sweden)

    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.

  4. Influence of a Shorter Duration of Post-Operative Antibiotic Prophylaxis on Infectious Complications in Patients Undergoing Elective Liver Resection.

    Science.gov (United States)

    Sakoda, Masahiko; Iino, Satoshi; Mataki, Yuko; Kawasaki, Yota; Kurahara, Hiroshi; Maemura, Kosei; Ueno, Shinichi; Natsugoe, Shoji

    Antibiotic prophylaxis has been recommended to reduce post-operative infectious complications. Discontinuation of post-operative antibiotic administration within 24 hours of operation is currently recommended. Many surgeons, however, conventionally tend to extend the duration of prophylactic antibiotic use. In this study, we performed a retrospective analysis to assess the efficacy of extended post-operative antibiotic use in patients who underwent elective liver resection. A total of 208 consecutive patients who underwent liver resection without biliary reconstruction were investigated. Patients were divided into two groups according to the duration of post-operative antibiotic use: Only once after the operation (the post-operative day [POD] 0 group) and until three days after the operation (the POD 3 group). Post-operative complications in the two groups were analyzed and compared. Incisional surgical site infections (SSIs) were observed in 5% of the POD 0 group and 3% of the POD 3 group (p = 0.517). Organ/space SSIs were observed in 2% of the POD 0 group and 3% of the POD 3 group (p = 0.694). Overall infectious complications including SSIs and remote site infections were observed in 12% of the POD 0 group and 11% of the POD 3 group. Multi-variable analyses revealed that the short-term post-operative antibiotic regimen did not confer additional risk for infectious complications. In elective liver resection, the administration of prophylactic antibiotics on the operative day alone appears to be sufficient, because no additional benefit in the incidence of post-operative infectious complications was conferred on patients given antibiotic agents for three days.

  5. 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.

    Directory of Open Access Journals (Sweden)

    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.

  6. 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

  7. 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.

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    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

  10. 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.

  11. 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.

  12. 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.

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

    Directory of Open Access Journals (Sweden)

    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

  14. Family History of Early Infant Death Correlates with Earlier Age at Diagnosis But Not Shorter Time to Diagnosis for Severe Combined Immunodeficiency

    Directory of Open Access Journals (Sweden)

    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

  15. One Gene and Two Proteins: a Leaderless mRNA Supports the Translation of a Shorter Form of the Shigella VirF Regulator.

    Science.gov (United States)

    Di Martino, Maria Letizia; Romilly, Cédric; Wagner, E Gerhart H; Colonna, Bianca; Prosseda, Gianni

    2016-11-08

    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, VirF 30 (30 kDa), and the shorter VirF 21 (21 kDa), lacking the N-terminal segment. By site-specific mutagenesis and toeprint analysis, we identified the translation start sites of VirF 30 and VirF 21 and showed that the two different forms of VirF arise from differential translation. Interestingly, in vitro and in vivo translation experiments showed that VirF 21 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 VirF 21 The llmRNA is transcribed from a gene-internal promoter, which we identified here. Functional analysis revealed that while VirF 30 is responsible for activation of the virulence system, VirF 21 negatively autoregulates virF expression itself. Since VirF 21 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. Shigella spp. are a major cause of dysentery in humans. In bacteria of this genus, the activation of the invasive program involves a multitude of signals that act on all layers of the gene regulatory hierarchy. By controlling the essential genes for host cell invasion, VirF is the key regulator of the switch from the noninvasive to the invasive phenotype. Here, we show that the Shigella virF gene encodes two proteins of different sizes, VirF 30 and VirF 21 , that are functionally distinct. The major form, VirF 30 , activates the genes

  16. 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.

    Directory of Open Access Journals (Sweden)

    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.

  17. 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.

  18. Diversity of Microbial Communities in Production and Injection Waters of Algerian Oilfields Revealed by 16S rRNA Gene Amplicon 454 Pyrosequencing

    Science.gov (United States)

    Lenchi, Nesrine; İnceoğlu, Özgül; Kebbouche-Gana, Salima; Gana, Mohamed Lamine; Llirós, Marc; Servais, Pierre; García-Armisen, Tamara

    2013-01-01

    The microorganisms inhabiting many petroleum reservoirs are multi-extremophiles capable of surviving in environments with high temperature, pressure and salinity. Their activity influences oil quality and they are an important reservoir of enzymes of industrial interest. To study these microbial assemblages and to assess any modifications that may be caused by industrial practices, the bacterial and archaeal communities in waters from four Algerian oilfields were described and compared. Three different types of samples were analyzed: production waters from flooded wells, production waters from non-flooded wells and injection waters used for flooding (water-bearing formations). Microbial communities of production and injection waters appeared to be significantly different. From a quantitative point of view, injection waters harbored roughly ten times more microbial cells than production waters. Bacteria dominated in injection waters, while Archaea dominated in production waters. Statistical analysis based on the relative abundance and bacterial community composition (BCC) revealed significant differences between production and injection waters at both OTUs0.03 and phylum level. However, no significant difference was found between production waters from flooded and non-flooded wells, suggesting that most of the microorganisms introduced by the injection waters were unable to survive in the production waters. Furthermore, a Venn diagram generated to compare the BCC of production and injection waters of one flooded well revealed only 4% of shared bacterial OTUs. Phylogenetic analysis of bacterial sequences indicated that Alpha-, Beta- and Gammaproteobacteria were the main classes in most of the water samples. Archaeal sequences were only obtained from production wells and each well had a unique archaeal community composition, mainly belonging to Methanobacteria, Methanomicrobia, Thermoprotei and Halobacteria classes. Many of the bacterial genera retrieved had already

  19. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  1. Long span DNA paired-end-tag (DNA-PET sequencing strategy for the interrogation of genomic structural mutations and fusion-point-guided reconstruction of amplicons.

    Directory of Open Access Journals (Sweden)

    Fei Yao

    Full Text Available Structural variations (SVs contribute significantly to the variability of the human genome and extensive genomic rearrangements are a hallmark of cancer. While genomic DNA paired-end-tag (DNA-PET sequencing is an attractive approach to identify genomic SVs, the current application of PET sequencing with short insert size DNA can be insufficient for the comprehensive mapping of SVs in low complexity and repeat-rich genomic regions. We employed a recently developed procedure to generate PET sequencing data using large DNA inserts of 10-20 kb and compared their characteristics with short insert (1 kb libraries for their ability to identify SVs. Our results suggest that although short insert libraries bear an advantage in identifying small deletions, they do not provide significantly better breakpoint resolution. In contrast, large inserts are superior to short inserts in providing higher physical genome coverage for the same sequencing cost and achieve greater sensitivity, in practice, for the identification of several classes of SVs, such as copy number neutral and complex events. Furthermore, our results confirm that large insert libraries allow for the identification of SVs within repetitive sequences, which cannot be spanned by short inserts. This provides a key advantage in studying rearrangements in cancer, and we show how it can be used in a fusion-point-guided-concatenation algorithm to study focally amplified regions in cancer.

  2. Deep nirS amplicon sequencing of San Francisco Bay sediments enables prediction of geography and environmental conditions from denitrifying community composition.

    Science.gov (United States)

    Lee, Jessica A; Francis, Christopher A

    2017-12-01

    Denitrification is a dominant nitrogen loss process in the sediments of San Francisco Bay. In this study, we sought to understand the ecology of denitrifying bacteria by using next-generation sequencing (NGS) to survey the diversity of a denitrification functional gene, nirS (encoding cytchrome-cd 1 nitrite reductase), along the salinity gradient of San Francisco Bay over the course of a year. We compared our dataset to a library of nirS sequences obtained previously from the same samples by standard PCR cloning and Sanger sequencing, and showed that both methods similarly demonstrated geography, salinity and, to a lesser extent, nitrogen, to be strong determinants of community composition. Furthermore, the depth afforded by NGS enabled novel techniques for measuring the association between environment and community composition. We used Random Forests modelling to demonstrate that the site and salinity of a sample could be predicted from its nirS sequences, and to identify indicator taxa associated with those environmental characteristics. This work contributes significantly to our understanding of the distribution and dynamics of denitrifying communities in San Francisco Bay, and provides valuable tools for the further study of this key N-cycling guild in all estuarine systems. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  3. 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/.

  4. Hospital Compare

    Data.gov (United States)

    U.S. Department of Health & Human Services — Hospital Compare has information about the quality of care at over 4,000 Medicare-certified hospitals across the country. You can use Hospital Compare to find...

  5. 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...

  6. An Upgrade on the Rabbit Model of Anthracycline-Induced Cardiomyopathy: Shorter Protocol, Reduced Mortality, and Higher Incidence of Overt Dilated Cardiomyopathy

    Science.gov (United States)

    Talavera, Jesús; Fernández-Del-Palacio, María Josefa; García-Nicolás, Obdulio; Seva, Juan; Brooks, Gavin; Moraleda, Jose M.

    2015-01-01

    Current protocols of anthracycline-induced cardiomyopathy in rabbits present with high premature mortality and nephrotoxicity, thus rendering them unsuitable for studies requiring long-term functional evaluation of myocardial function (e.g., stem cell therapy). We compared two previously described protocols to an in-house developed protocol in three groups: Group DOX2 received doxorubicin 2 mg/kg/week (8 weeks); Group DAU3 received daunorubicin 3 mg/kg/week (10 weeks); and Group DAU4 received daunorubicin 4 mg/kg/week (6 weeks). A cohort of rabbits received saline (control). Results of blood tests, cardiac troponin I, echocardiography, and histopathology were analysed. Whilst DOX2 and DAU3 rabbits showed high premature mortality (50% and 33%, resp.), DAU4 rabbits showed 7.6% premature mortality. None of DOX2 rabbits developed overt dilated cardiomyopathy; 66% of DAU3 rabbits developed overt dilated cardiomyopathy and quickly progressed to severe congestive heart failure. Interestingly, 92% of DAU4 rabbits showed overt dilated cardiomyopathy and 67% developed congestive heart failure exhibiting stable disease. DOX2 and DAU3 rabbits showed alterations of renal function, with DAU3 also exhibiting hepatic function compromise. Thus, a shortened protocol of anthracycline-induced cardiomyopathy as in DAU4 group results in high incidence of overt dilated cardiomyopathy, which insidiously progressed to congestive heart failure, associated to reduced systemic compromise and very low premature mortality. PMID:26788502

  7. Physician Compare

    Data.gov (United States)

    U.S. Department of Health & Human Services — Physician Compare, which meets Affordable Care Act of 2010 requirements, helps you search for and select physicians and other healthcare professionals enrolled in...

  8. The shorter the better? A follow-up analysis of 10-session psychiatric treatment including the motive-oriented therapeutic relationship for borderline personality disorder.

    Science.gov (United States)

    Kramer, Ueli; Stulz, Niklaus; Berthoud, Laurent; Caspar, Franz; Marquet, Pierre; Kolly, Stéphane; De Roten, Yves; Despland, Jean-Nicolas

    2017-05-01

    There is little research on short-term treatments for borderline personality disorder (BPD). While the core changes may occur only in long-term treatments, short-term treatments may enable the study of early generic processes of engagement in therapy and thus inform about effective treatment components. It was shown that a 10-session version of a psychiatric treatment was effective in reducing borderline symptoms at the end of this treatment [Kramer, U., Kolly, S., Berthoud, L., Keller, S., Preisig, M., Caspar, F., … Despland, J.-N. (2014). Effects of motive-oriented therapeutic relationship in a ten-session general psychiatric treatment for borderline personality disorder: A randomized controlled trial. Psychotherapy and Psychosomatics, 83, 176-186.]. Also, it was demonstrated in a randomized design that adding the motive-oriented therapeutic relationship (MOTR), following an individualized case formulation based on Plan Analysis, further increased general outcome after session 10 and had a positive effect on the early changes in self-esteem and alliance. The present study focuses on the follow-up period after this initial treatment, examining treatment density and outcomes after 6 months and service utilization after 12 months. Outcome was measured using the OQ-45. Results on a sub-sample of N = 40 patients with available OQ-45 data at follow-up (n = 21 for MOTR-treatment, n = 19 for comparison treatment) showed maintenance of gains over the follow-up period, which did not differ between both conditions. It appeared for this sample that MOTR treatments, while using the same number of sessions, lasted more weeks (i.e., lower treatment density, defined as the number of sessions per week), when compared to the treatments without MOTR. Density marginally predicted symptom reduction at follow-up. Patients in MOTR treatments had a greater likelihood of entering structured psychotherapy after the initial sessions than patients in the comparison

  9. Comparative Genomics

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 11; Issue 8. Comparative Genomics - A Powerful New Tool in Biology. Anand K Bachhawat. General Article Volume 11 Issue 8 August 2006 pp 22-40. Fulltext. Click here to view fulltext PDF. Permanent link:

  10. Comparative Advantage

    DEFF Research Database (Denmark)

    Zhang, Jie; Jensen, Camilla

    2007-01-01

    that are typically explained from the supply-side variables, the comparative advantage of the exporting countries. A simple model is proposed and tested. The results render strong support for the relevance of supply-side factors such as natural endowments, technology, and infrastructure in explaining international...

  11. Comparative perspectives

    African Journals Online (AJOL)

    IT

    Ideology, policy and implementation: Comparative perspectives from two ... how both political as well as particular language ideologies play a major role in influencing and ..... attitudes as a field of research, many scholars still draw on the concept of .... The data for this study were collected through the use of questionnaires ...

  12. 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.

  13. 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

  14. 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

  15. Video Comparator

    International Nuclear Information System (INIS)

    Rose, R.P.

    1978-01-01

    The Video Comparator is a comparative gage that uses electronic images from two sources, a standard and an unknown. Two matched video cameras are used to obtain the electronic images. The video signals are mixed and displayed on a single video receiver (CRT). The video system is manufactured by ITP of Chatsworth, CA and is a Tele-Microscope II, Model 148. One of the cameras is mounted on a toolmaker's microscope stand and produces a 250X image of a cast. The other camera is mounted on a stand and produces an image of a 250X template. The two video images are mixed in a control box provided by ITP and displayed on a CRT. The template or the cast can be moved to align the desired features. Vertical reference lines are provided on the CRT, and a feature on the cast can be aligned with a line on the CRT screen. The stage containing the casts can be moved using a Boeckleler micrometer equipped with a digital readout, and a second feature aligned with the reference line and the distance moved obtained from the digital display

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. Sequencing and comparing whole mitochondrial genomes ofanimals

    Energy Technology Data Exchange (ETDEWEB)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  2. 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

  3. 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

  4. The power of the kashrut: older but shorter. The impact of religious nutritional and hygienic rules on stature and life expectancy of Jewish conscripts in the early 19th century.

    Science.gov (United States)

    Tassenaar, V; Karel, E H

    2016-06-01

    We test the impact of several demographic, economic and social factors on stature in an early nineteenth century environment. We use a database of conscripts from the period 1818-1860 of a rural province in The Netherlands (Drenthe). This area had a rather high biological standard of living. This database of 413 conscripts contains information about family structure, family rank order, height, tax income, occupation and age of death. Conscripts came from two communities: one from a particular village (Oosterhesselen) and the other was Jewish conscripts that came from the countryside of the province. Our statistical analysis shows a positive significant relationship between family size and height, which confirms the resource dilution theory. Remarkably, the sign of the relation between family size and life expectancy is inverse. Other factors such as the potato crisis and income had the expected effect on conscript heights. The community effect was strong. Jewish conscripts were much shorter than their counterparts. Access to nutrition, the specific food laws and other factors can explain this difference. An increasing sibship size had a negative impact on body height but positive effects on life expectancy when adulthood was reached. Specifically for the Jewish community was the positive effect of the death of the father on conscript height. The mechanisms behind this phenomenon are unclear and open for further research.

  5. 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.

  6. Cats, Cancer and Comparative Oncology

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    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.

  8. 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…

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

    Directory of Open Access Journals (Sweden)

    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.

  10. Illumina amplicon sequencing of 16S rRNA tag reveals bacterial community development in the rhizosphere of apple nurseries at a replant disease site and a new planting site.

    Directory of Open Access Journals (Sweden)

    Jian Sun

    Full Text Available We used a next-generation, Illumina-based sequencing approach to characterize the bacterial community development of apple rhizosphere soil in a replant site (RePlant and a new planting site (NewPlant in Beijing. Dwarfing apple nurseries of 'Fuji'/SH6/Pingyitiancha trees were planted in the spring of 2013. Before planting, soil from the apple rhizosphere of the replant site (ReSoil and from the new planting site (NewSoil was sampled for analysis on the Illumina MiSeq platform. In late September, the rhizosphere soil from both sites was resampled (RePlant and NewPlant. More than 16,000 valid reads were obtained for each replicate, and the community was composed of five dominant groups (Proteobacteria, Acidobacteria, Bacteroidetes, Gemmatimonadetes and Actinobacteria. The bacterial diversity decreased after apple planting. Principal component analyses revealed that the rhizosphere samples were significantly different among treatments. Apple nursery planting showed a large impact on the soil bacterial community, and the community development was significantly different between the replanted and newly planted soils. Verrucomicrobia were less abundant in RePlant soil, while Pseudomonas and Lysobacter were increased in RePlant compared with ReSoil and NewPlant. Both RePlant and ReSoil showed relatively higher invertase and cellulase activities than NewPlant and NewSoil, but only NewPlant soil showed higher urease activity, and this soil also had the higher plant growth. Our experimental results suggest that planting apple nurseries has a significant impact on soil bacterial community development at both replant and new planting sites, and planting on new site resulted in significantly higher soil urease activity and a different bacterial community composition.

  11. AirCompare

    Data.gov (United States)

    U.S. Environmental Protection Agency — AirCompare contains air quality information that allows a user to compare conditions in different localities over time and compare conditions in the same location at...

  12. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    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).

  14. 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).

  15. Comparative Test Case Specification

    DEFF Research Database (Denmark)

    Kalyanova, Olena; Heiselberg, Per

    This document includes the specification on the IEA task of evaluation building energy simulation computer programs for the Double Skin Facades (DSF) constructions. There are two approaches involved into this procedure, one is the comparative approach and another is the empirical one. In the comp....... In the comparative approach the outcomes of different software tools are compared, while in the empirical approach the modelling results are compared with the results of experimental test cases. The comparative test cases include: ventilation, shading and geometry....

  16. 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 ...

  17. Dialysis Facility Compare

    Data.gov (United States)

    U.S. Department of Health & Human Services — Dialysis Facility Compare helps you find detailed information about Medicare-certified dialysis facilities. You can compare the services and the quality of care that...

  18. Approaching comparative company law

    OpenAIRE

    Donald, David C.

    2008-01-01

    This paper identifies some common errors that occur in comparative law, offers some guidelines to help avoid such errors, and provides a framework for entering into studies of the company laws of three major jurisdictions. The first section illustrates why a conscious approach to comparative company law is useful. Part I discusses some of the problems that can arise in comparative law and offers a few points of caution that can be useful for practical, theoretical and legislative comparative ...

  19. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  1. 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.

  2. Comparative Test Case Specification

    DEFF Research Database (Denmark)

    Kalyanova, Olena; Heiselberg, Per

     This document includes a definition of the comparative test cases DSF200_3 and DSF200_4, which previously described in the comparative test case specification for the test cases DSF100_3 and DSF200_3 [Ref.1]....... This document includes a definition of the comparative test cases DSF200_3 and DSF200_4, which previously described in the comparative test case specification for the test cases DSF100_3 and DSF200_3 [Ref.1]....

  3. Text File Comparator

    Science.gov (United States)

    Kotler, R. S.

    1983-01-01

    File Comparator program IFCOMP, is text file comparator for IBM OS/VScompatable systems. IFCOMP accepts as input two text files and produces listing of differences in pseudo-update form. IFCOMP is very useful in monitoring changes made to software at the source code level.

  4. 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 : ...

  5. Women want taller men more than men want shorter women

    NARCIS (Netherlands)

    Stulp, G.; Buunk, A.P.; Pollet, T.V.

    2013-01-01

    Physical characteristics, such as height, play an important role in human mate preferences. Satisfaction with one's own height and one's partner height seem likely to be related to these preferences. Using a student sample (N= 650), we show that women are not only more selective, but also more

  6. Women want taller men more than men want shorter women

    NARCIS (Netherlands)

    Stulp, Gert; Buunk, Abraham P.; Pollet, Thomas V.

    Physical characteristics, such as height, play an important role in human mate preferences. Satisfaction with ones own height and one's partner height seem likely to be related to these preferences. Using a student sample (N = 650), we show that women are not only more selective, but also more

  7. Shorter lines facilitate reading in those who struggle.

    Directory of Open Access Journals (Sweden)

    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.

  8. Introductory Business Textbook Revision Cycles: Are They Getting Shorter?

    Science.gov (United States)

    Zinser, Brian; Brunswick, Gary

    2010-01-01

    The rate of textbook revision cycles is examined in light of the recent trend towards more rapid revisions (and adoptions of textbooks). The authors conduct background research to better understand the context for textbook revision cycles and the environmental forces that have been influencing what appears to be more rapid textbook revisions. A…

  9. A shorter fractionation schedule for postlumpectomy breast cancer patients

    International Nuclear Information System (INIS)

    Shelley, Wendy; Brundage, Michael; Hayter, Charles; Paszat, Lawrence; Zhou, Sam; Mackillop, William

    2000-01-01

    Purpose: The purpose of this retrospective review was to determine the effectiveness of 40 Gy in 16 daily fractions in preventing local recurrence in postlumpectomy invasive breast cancer patients whose margins of resection were clear of tumor by at least 2 mm. Methods: Between September 1989 and December 1993, 294 breasts were treated with this regimen. The entire breast was treated, using a tangential parallel pair, with wedges as necessary, to a dose of 40 Gy in 16 daily fractions. No additional boost was given. The median duration of follow-up of surviving patients is 5.5 years. Recently, the patients' assessment of the cosmetic outcome of their treatment was obtained, using a mailed questionnaire. Results: The 5-year actuarial breast-relapse rate was 3.5%, with an overall 5-year survival and disease-specific survival of 87.8% and 92.1%, respectively. In response to the cosmesis questionnaire, 77% of patients stated they were either extremely or very satisfied with the overall appearance of the breast, 19.5% moderately satisfied, and 3.5% either slightly or not at all satisfied. The corresponding responses for overall level of comfort of the breast were 79%, 16.5%, and 4.5% respectively. Conclusion: This regimen is very effective at preventing recurrent breast cancer in this group of patients, and it provides a high level of patient satisfaction with cosmetic outcome. Its short duration offers the added advantage of a more efficient use of resources and greater patient convenience

  10. Less snow and shorter snow season in the future

    International Nuclear Information System (INIS)

    Vikhamar-Schuler, Dagrun; Beldring, Stein; Foerland, Eirik J.; Roald, Lars A.; Engen-Skaugen, Torill

    2006-01-01

    The article presents some results from the studies of changes in the Norwegian climate made by the project RegClim. Some regional and yearly tendencies are mentioned as well as some macro economical consequences

  11. Shorter duration of breastfeeding at elevated exposures to perfluoroalkyl substances

    DEFF Research Database (Denmark)

    Timmermann, Clara Amalie Gade; Budtz-Jørgensen, Esben; Petersen, Maria Skaalum

    2017-01-01

    . Duration of breastfeeding was assessed by questionnaire and clinical interview. In adjusted linear regression models, a doubling of maternal serum PFASs was associated with a reduction in duration of both total and exclusive breastfeeding, most pronounced for perfluorooctane sulfonic acid (PFOS) where...... a doubling was associated with a reduction in total breastfeeding of 1.4 (95% CI: 0.6; 2.1) months and perfluorooctanoic acid (PFOA) where a doubling was associated with a reduction in exclusive breastfeeding of 0.5 (0.3; 0.7) months. The associations were evident among both primiparous and multiparous women......, and thus cannot be explained by confounding from previous breastfeeding....

  12. Medical necessity for shorter lived radionuclides, specifically pure Iodine-123

    International Nuclear Information System (INIS)

    DeNardo, G.L.; DeNardo, S.J.; Hines, H.H.; Lagunas-Solar, M.C.; Jungerman, J.A.

    1985-01-01

    Iodine-123 has physical and radiochemical characteristics ideal for most tracer procedures performed in patients. Its use is generally preferable to the use of 131 I for diagnosis. The potential for 123 I can be realized only if a radiopharmaceutical of lesser radionuclide contamination is generally and economically available. Iodine-123 produced by direct methods has significant disadvantages relative to quality of procedure and radiation dosimetry. Our experience with 123 I(p,5n) during the past 12 years causes us to vigorously encourage general availability of an 123 I radiopharmaceutical of this quality. Using this product, the authors have prepared radiopharmaceuticals for use in the study of cancer, coagulation, and renal and thyroid diseases

  13. Cannabis use predicts shorter duration of untreated psychosis and ...

    African Journals Online (AJOL)

    Objective: Cannabis use/abuse is a common co-morbid problem in patients experiencing a first episode of psychotic illness (FEP). The relationship between the clinical presentation of FEP and cannabis abuse is complex and warrants further investigation, especially within the South African context. Method: We tested ...

  14. Hospital Compare Data

    Data.gov (United States)

    U.S. Department of Health & Human Services — These are the official datasets used on the Medicare.gov Hospital Compare Website provided by the Centers for Medicare and Medicaid Services. These data allow you to...

  15. Towards Comparative Leadership

    DEFF Research Database (Denmark)

    Jensen, Merete Storgaard

    Globalization is the imitation and adaptation of knowledgesolutions or innovations, as they are diffused from one country to another” (Peter Jarvis 2007) Conducting comparative, educational research of school leadership that effects student achievement in an international perspective is of scient......Globalization is the imitation and adaptation of knowledgesolutions or innovations, as they are diffused from one country to another” (Peter Jarvis 2007) Conducting comparative, educational research of school leadership that effects student achievement in an international perspective...... is of scientific value in qualifying the international and national knowledgebase on effective school leadership. In a methodological perspective comparative analysis in an international setting creates specifically a scientific demand of comparability and a theory based leadership - framework to guide...... the empirical, qualitative research of effective leadership....

  16. Comparing Demonstratives in Kwa

    African Journals Online (AJOL)

    This paper is a comparative study of demonstrative forms in three K wa languages, ... relative distance from the deictic centre, such as English this and that, here and there. ... Mostly, the referents of demonstratives are 'activated' or at least.

  17. Home Health Compare

    Data.gov (United States)

    U.S. Department of Health & Human Services — Home Health Compare has information about the quality of care provided by Medicare-certified home health agencies throughout the nation. Medicare-certified means the...

  18. Nursing Home Compare Data

    Data.gov (United States)

    U.S. Department of Health & Human Services — These are the official datasets used on the Medicare.gov Nursing Home Compare Website provided by the Centers for Medicare and Medicaid Services. These data allow...

  19. Hospital Compare - Archived Data

    Data.gov (United States)

    U.S. Department of Health & Human Services — Hospital Compare is a consumer-oriented website that provides information on how well hospitals provide recommended care to their patients. This information can help...

  20. Home Health Compare Data

    Data.gov (United States)

    U.S. Department of Health & Human Services — These are the official datasets used on the Medicare.gov Home Health Compare Website provided by the Centers for Medicare and Medicaid Services. These data allow you...

  1. Nursing Home Compare

    Data.gov (United States)

    U.S. Department of Health & Human Services — The data that is used by the Nursing Home Compare tool can be downloaded for public use. This functionality is primarily used by health policy researchers and the...

  2. Comparative Climatic Data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Comparative Climatic Data is a publication containing data tables of meteorological elements; the publication outlines the climatic conditions at major weather...

  3. Dialysis Facility Compare Data

    Data.gov (United States)

    U.S. Department of Health & Human Services — These are the official datasets used on the Medicare.gov Dialysis Facility Compare Website provided by the Centers for Medicare and Medicaid Services. These data...

  4. Comparing Political Communication

    OpenAIRE

    Pfetsch, Barbara; Esser, Frank

    2012-01-01

    This chapter describes the maturation of comparative political communications as a sub-discipline and defines its conceptual core. It then lays out the concept of “political communication system”. At the macro-level, this model captures the patterns of interaction between media and politics as social systems; at the micro-level it captures the interactions between media and political actors as individuals or organizations. Comparative research in this tradition focuses on the structure of pol...

  5. Comparing chess strategies

    OpenAIRE

    Kacz, Kristián

    2010-01-01

    The aim of this work is to provide an overview of approaches in computer chess. It designs and implements a chess engine for multiplayer network chess program ChessNet. Within the engine implements several search algorithms like Negamax, Alpha-beta, Negascout and points to their weaknesses. Adds a possibility to the ChessNet environment to compare chess engines. Compares implemented algorithms in terms of time complexity. Shows several factors wich we have to take into consideration during th...

  6. Competitive versus comparative advantage

    OpenAIRE

    Neary, J. Peter

    2002-01-01

    I explore the interactions between comparative, competitive and absolute advantage in a two-country model of oligopoly in general equilibrium. Comparative advantage always determines the direction of trade, but both competitive and absolute advantage affect resource allocation, trade patterns and trade volumes. Competitive advantage in the sense of more home firms drives foreign firms out of marginal sectors but also makes some marginal home sectors uncompetitive. Absolute advantage in the se...

  7. Comparative approaches to gentrification

    Science.gov (United States)

    Phillips, Martin; Smith, Darren P

    2018-01-01

    The epistemologies and politics of comparative research are prominently debated within urban studies, with ‘comparative urbanism’ emerging as a contemporary lexicon of urban studies. The study of urban gentrification has, after some delay, come to engage with these debates, which can be seen to pose a major challenge to the very concept of gentrification. To date, similar debates or developments have not unfolded within the study of rural gentrification. This article seeks to address some of the challenges posed to gentrification studies through an examination of strategies of comparison and how they might be employed within a comparative study of rural gentrification. Drawing on Tilly (Big structures Large Processes Huge Comparisons. New York: Russell Sage), examples of four ‘strategies of comparison’ are identified within studies of urban and rural gentrification, before the paper explores how ‘geographies of the concept’ and ‘geographies of the phenomenon’ of rural gentrification in the United Kingdom, United States and France may be investigated using Latour’s (Pandora’s Hope. London: Harvard University Press) notion of ‘circulatory sociologies of translation’. The aim of our comparative discussion is to open up dialogues on the challenges of comparative studies that employ conceptions of gentrification and also to promote reflections of the metrocentricity of recent discussions of comparative research. PMID:29657708

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

    Directory of Open Access Journals (Sweden)

    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.

  9. Comparing Political Journalism

    DEFF Research Database (Denmark)

    Comparing Political Journalism is a systematic, in-depth study of the factors that shape and influence political news coverage today. Using techniques drawn from the growing field of comparative political communication, an international group of contributors analyse political news content drawn...... Comparing Political Journalism offers an unparalleled scope in assessing the implications for the ongoing transformation of Western media systems, and addresses core concepts of central importance to students and scholars of political communication world-wide....... from newspapers, television news, and news websites from 16 countries, to assess what kinds of media systems are most conducive to producing quality journalism. Underpinned by key conceptual themes, such as the role that the media are expected to play in democracies and quality of coverage...

  10. A Prospective Study Comparing Ligasure and Open Hemorrhoidectomy

    Directory of Open Access Journals (Sweden)

    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.

  11. Contesting Citizenship: Comparative Analyses

    DEFF Research Database (Denmark)

    Siim, Birte; Squires, Judith

    2007-01-01

    importance of particularized experiences and multiple ineequality agendas). These developments shape the way citizenship is both practiced and analysed. Mapping neat citizenship modles onto distinct nation-states and evaluating these in relation to formal equality is no longer an adequate approach....... Comparative citizenship analyses need to be considered in relation to multipleinequalities and their intersections and to multiple governance and trans-national organisinf. This, in turn, suggests that comparative citizenship analysis needs to consider new spaces in which struggles for equal citizenship occur...

  12. Comparative Nivkh Dictionary

    DEFF Research Database (Denmark)

    Fortescue, Michael David

    This dictionary undertakes to reconstruct the lexis and morphology of the Nivkh proto-language by marshaling and organizing all the data available in published form on the contemporary dialects. It builds upon a considerable body of descriptive and comparative work carried out by scholars who have...... World is a subject of continuing interest to both linguists and anthropologists. The dictionary does not address this question directly. Reconstructing the proto-language is an essential step, however, to any further comparative work – in particular to sorting out the relationship between Nivkh...

  13. Comparing chemical reaction networks

    DEFF Research Database (Denmark)

    Cardelli, Luca; Tribastone, Mirco; Tschaikowski, Max

    2017-01-01

    We study chemical reaction networks (CRNs) as a kernel model of concurrency provided with semantics based on ordinary differential equations. We investigate the problem of comparing two CRNs, i.e., to decide whether the solutions of a source and of a target CRN can be matched for an appropriate...... choice of initial conditions. Using a categorical framework, we extend and unify model-comparison approaches based on dynamical (semantic) and structural (syntactic) properties of CRNs. Then, we provide an algorithm to compare CRNs, running linearly in time with respect to the cardinality of all possible...... comparisons. Finally, using a prototype implementation, CAGE, we apply our results to biological models from the literature....

  14. Comparative Contract Law & Economics

    NARCIS (Netherlands)

    Kovac, M.

    2008-01-01

    This work is a search for deeper understanding of established differences and similarities among compared legal systems. The application of economically inspired optimal model rule as a uniform term of comparison provides additional insights into some of the most often discussed legal issues. The

  15. Comparing East and West

    DEFF Research Database (Denmark)

    Razeto, Anna

    2014-01-01

    This chapter explores the archaeological and literary evidence for marketplaces and urban forms connected to the manufacturing of bricks and metalworking in the capital cities of the contemporary empires of Rome and Han China (ca. 200 BC-200 AD). The comparative analysis of the physical aspects...... was involved in the social and political processes that characterized the production of space in ancient cities....

  16. Ebolavirus comparative genomics

    DEFF Research Database (Denmark)

    Jun, Se-Ran; Leuze, Michael R.; Nookaew, Intawat

    2015-01-01

    The 2014 Ebola outbreak in West Africa is the largest documented for this virus. To examine the dynamics of this genome, we compare more than 100 currently available ebolavirus genomes to each other and to other viral genomes. Based on oligomer frequency analysis, the family Filoviridae forms...

  17. Comparing contracting performance

    DEFF Research Database (Denmark)

    Lindholst, Andrej Christian

    . Hypotheses are suggested for the role of culture, competition, contracts, capabilities and collaboration for contracting performance between and across the countries. Arguments are tested against data from on four comparable national surveys of private delivery of park and road maintenance services in local...

  18. Dermatologia comparativa Comparative Dermatology

    Directory of Open Access Journals (Sweden)

    Hiram Larangeira de Almeida Jr

    2005-06-01

    Full Text Available Demonstra-se o quadro exuberante dos angiofibromas faciais em paciente do sexo masculino, de 32 anos, com esclerose tuberosa, os quais podem ser comparados com amoras.The impressive facial angiofibromas, from a 32 year-old male paciente, with the classical features of tuberous sclerosis, were compared with mulberries.

  19. Comparative cardiac imaging

    International Nuclear Information System (INIS)

    Brundage, B.H.

    1990-01-01

    This book is designed to compare all major cardiac imaging techniques. All major imaging techniques - including conventional angiography, digital angiography, echocardiography and Doppler imaging, conventional radioisotope techniques, computed tomography, and magnetic resonance imaging - are covered in this text as they apply to the major cardiovascular disorders. There is brief coverage of positron emission tomography and an extensive presentation of ultrafast computed tomography

  20. Comparing Harmonic Similarity Measures

    NARCIS (Netherlands)

    de Haas, W.B.; Robine, M.; Hanna, P.; Veltkamp, R.C.; Wiering, F.

    2010-01-01

    We present an overview of the most recent developments in polyphonic music retrieval and an experiment in which we compare two harmonic similarity measures. In contrast to earlier work, in this paper we specifically focus on the symbolic chord description as the primary musical representation and

  1. Comparative Genomics of Eukaryotes.

    NARCIS (Netherlands)

    Noort, V. van

    2007-01-01

    This thesis focuses on developing comparative genomics methods in eukaryotes, with an emphasis on applications for gene function prediction and regulatory element detection. In the past, methods have been developed to predict functional associations between gene pairs in prokaryotes. The challenge

  2. Comparative International Management

    NARCIS (Netherlands)

    Sorge, Arndt; Noorderhaven, Niels; Koen, Carla

    2015-01-01

    The use of comparisons to explain, analyze and understand social and economic phenomena is recognized as a valuable social science tool. This textbook deals with the differences in management and organization between nations and their effects on multinational enterprises. In comparing management

  3. Comparative Political Communication Research

    NARCIS (Netherlands)

    de Vreese, C.H.; Kenski, K.; Jamieson, K.H.

    2017-01-01

    This chapter provides an overview of comparative political communication research (CPCR). CPCR is a growing field since there is wide acknowledgement that many questions are not answered satisfactorily with single case studies. The chapter explains why political communication researchers should care

  4. Comparative and Translatorly

    Directory of Open Access Journals (Sweden)

    Anna Rosen Guercio

    2011-12-01

    Full Text Available World literature’s natural home is comparative literature, a discipline born from and shaped by, as Vilashini Cooppan elegantly puts it, “scholarly engagements with the categories of migration, exile, diaspora, and globalization” (15. However, world literature has frequently been framed as a problem for the discipline, in large part because of its dependence on the ever-vexing and still mistrusted specter of translation. In light of the long-standing anxiety toward both world literature and translation, I propose here that comparatists do ourselves a terrible disservice if we do not urgently take up the questions raised by this disciplinary tension. Translation – in all of its attendant struggles with ethics, aesthetics, appropriation, authority – is not the problem, but, rather, should be understood as a key critical lens for comparative and world literature.In order to establish academia’s frustration with this subject, one need look no further than the “Three Reports to the America Comparative Literature Association on ‘Professional Standards’” (dating from 1965, 1975, and 1993, which return repeatedly to the problem of reading translated literature, circling around it with intense ambivalence. The moral of their story seems to be that translated texts are integral to comparative literature at the same time that they threaten its existence by undermining disciplinary exclusivity in foreign language expertise and by shining a sort of spotlight on all that literature which comparative literature may sometimes “condone” (as one of the reports puts it but to which it does not often actively attend. Even Goethe had Western European languages and literatures firmly in mind when he coined the term, “Weltliteratur.” Translations can’t help but point up the limits of the “four [likely European] languages” proposed as minimal standards for graduate students by the Green and Bernheimer reports, and on the strength of

  5. Comparing apples and pears?

    DEFF Research Database (Denmark)

    Waite, Sue; Bølling, Mads; Bentsen, Peter

    2016-01-01

    Using a conceptual model focused on purposes, aims, content, pedagogy, outcomes, and barriers, we review and interpret literature on two forms of outdoor learning: Forest Schools in England and udeskole in Denmark. We examine pedagogical principles within a comparative analytical framework and co...... to pedagogical principles are necessary to ensure better alignment of purpose and practice to elicit specific outcomes and enable comparison between different types.......Using a conceptual model focused on purposes, aims, content, pedagogy, outcomes, and barriers, we review and interpret literature on two forms of outdoor learning: Forest Schools in England and udeskole in Denmark. We examine pedagogical principles within a comparative analytical framework...... and consider how adopted pedagogies reflect and refract the culture in which they are embedded. Despite different national educational and cultural contexts, English Forest Schools and Danish udeskole share several commonalities within a naturalistic/progressive pedagogical tradition; differences appear...

  6. On comparative inquiry

    DEFF Research Database (Denmark)

    Moutsios, Stavros

    of self‐reflexivity and self-questioning in the Greek polis gave also rise to the genuine interest in the institutions of the cultural ‘other’. Impartiality in the study of the others’ institutions started in Greece and it was closely associated with the signification that physis (nature) should......The paper explores the origins of comparative studies, which as it argues are located in Ancient Greece. Greece is not only the place where the school was born, but it is also there where the interest in and inquiry of the institutions of other societies, including education, emerged. The rise...... to know better their own society through comparison. Cross-cultural examination in this regard informed further the Greeks’ self-reflexivity. By going through a set of historical sources and contemporary literature, the paper will elaborate on the emergence of cross-cultural and comparative inquiry...

  7. Banking: shop and compare.

    Science.gov (United States)

    O'Brien, Jennifer A; DeJarnette, Sherry

    2014-01-01

    There are many reasons to take a critical look at the practice's banking relationship(s)--technology advancements, security measures, improvements in available services, recent banking enhancements designed specifically for medical practices, the impact of the financial crisis on bank ratings and stability, changing practice needs, opportunities for operational automation at the practice--and it is just simply smart to periodically evaluate and compare the features, pricing, and potential savings offered by vendors.

  8. Josephson comparator switching time

    Energy Technology Data Exchange (ETDEWEB)

    Herr, Quentin P; Miller, Donald L; Przybysz, John X [Northrop Grumman, Baltimore, MD (United States)

    2006-05-15

    Comparator performance can be characterized in terms of both sensitivity and decision time. Delta-sigma analogue-to-digital converters are tolerant of sensitivity errors but require short decision time due to feedback. We have analysed the Josephson comparator using the numerical solution of the Fokker-Planck equation, which describes the time evolution of the ensemble probability distribution. At balance, the result is essentially independent of temperature in the range 5-20 K. There is a very small probability, 1 x 10{sup -14}, that the decision time will be longer than seven single-flux-quantum pulse widths, defined as Phi{sub 0}/(I{sub c}R{sub n}). For junctions with a critical current density of 4.5 kA, this decision time is only 20 ps. Decision time error probability decreases rapidly with lengthening time interval, at a rate of two orders of magnitude per pulse width. We conclude that Josephson comparator performance is quite favourable for analogue-to-digital converter applications.

  9. 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.

  10. Comparative risk analysis

    International Nuclear Information System (INIS)

    Niehaus, F.

    1988-01-01

    In this paper, the risks of various energy systems are discussed considering severe accidents analysis, particularly the probabilistic safety analysis, and probabilistic safety criteria, and the applications of these criteria and analysis. The comparative risk analysis has demonstrated that the largest source of risk in every society is from daily small accidents. Nevertheless, we have to be more concerned about severe accidents. The comparative risk analysis of five different energy systems (coal, oil, gas, LWR and STEC (Solar)) for the public has shown that the main sources of risks are coal and oil. The latest comparative risk study of various energy has been conducted in the USA and has revealed that the number of victims from coal is 42 as many than victims from nuclear. A study for severe accidents from hydro-dams in United States has estimated the probability of dam failures at 1 in 10,000 years and the number of victims between 11,000 and 260,000. The average occupational risk from coal is one fatal accident in 1,000 workers/year. The probabilistic safety analysis is a method that can be used to assess nuclear energy risks, and to analyze the severe accidents, and to model all possible accident sequences and consequences. The 'Fault tree' analysis is used to know the probability of failure of the different systems at each point of accident sequences and to calculate the probability of risks. After calculating the probability of failure, the criteria for judging the numerical results have to be developed, that is the quantitative and qualitative goals. To achieve these goals, several systems have been devised by various countries members of AIEA. The probabilistic safety ana-lysis method has been developed by establishing a computer program permit-ting to know different categories of safety related information. 19 tabs. (author)

  11. Comparative pharmacognosy of Pashanbhed

    Directory of Open Access Journals (Sweden)

    Poonam Verma

    2014-01-01

    Full Text Available Background: Pashanbhed is a commercially available diuretic and lithotropic drug, used to treat renal problems. It is a controversial name as it is assigned to various plants such as Bergenia ligulata, Kalanchoe pinnata, Coleus aromaticus and Rotula aquatica. Objective: To perform the comparative preliminary phytochemical screening, diuretic activity, and thin layer chromatography (TLC finger printing profile of three plants (B. ligulata, C. aromaticus, and K. pinnata, most commonly used as Pashanbhed. Materials and Methods: Diuretic potential of methanolic extract (ME of three plants were evaluated at two dose levels (500 and 1,000 mg/kg p.o., using normal Wistar rats (Lipschitz method. Furosemide (20 mg/kg p.o. was used as a standard drug. The effect on urine output and electrolyte changes were measured for 24 h and compared. All MEs were screened preliminarily for their constituents and their TLC finger printing profiles were prepared. One-way analysis of variance (ANOVA followed by Bonferroni′s multiple comparison test. P < 0.05 was considered statistically significant. Results: The MEs of all three plants have shown diuresis in normal rats. However, in intercomparison of the ME C. aromaticus (1,000 mg/kg p.o. produced more significant diuresis (P < 0.05 and electrolyte excretion compared to other test groups, the effect was at par with furosemide. The ME of these plants showed presence of alkaloids, glycosides, steroids, terpenoids, saponins, flavonoids, etc. Conclusion: The ME of C. aromaticus (1,000 mg/kg p.o. has showed highest diuretic action (4.2 among the tested extracts. This suggests the use of C. aromaticus leaves as "Pashanbhed"; the most effective diuretic drug.

  12. Comparative pharmacognosy of Pashanbhed

    Science.gov (United States)

    Verma, Poonam; Gauttam, Vinod; Kalia, Ajudhia N.

    2014-01-01

    Background: Pashanbhed is a commercially available diuretic and lithotropic drug, used to treat renal problems. It is a controversial name as it is assigned to various plants such as Bergenia ligulata, Kalanchoe pinnata, Coleus aromaticus and Rotula aquatica. Objective: To perform the comparative preliminary phytochemical screening, diuretic activity, and thin layer chromatography (TLC) finger printing profile of three plants (B. ligulata, C. aromaticus, and K. pinnata), most commonly used as Pashanbhed. Materials and Methods: Diuretic potential of methanolic extract (ME) of three plants were evaluated at two dose levels (500 and 1,000 mg/kg p.o.), using normal Wistar rats (Lipschitz method). Furosemide (20 mg/kg p.o.) was used as a standard drug. The effect on urine output and electrolyte changes were measured for 24 h and compared. All MEs were screened preliminarily for their constituents and their TLC finger printing profiles were prepared. One-way analysis of variance (ANOVA) followed by Bonferroni's multiple comparison test. P < 0.05 was considered statistically significant. Results: The MEs of all three plants have shown diuresis in normal rats. However, in intercomparison of the ME C. aromaticus (1,000 mg/kg p.o.) produced more significant diuresis (P < 0.05) and electrolyte excretion compared to other test groups, the effect was at par with furosemide. The ME of these plants showed presence of alkaloids, glycosides, steroids, terpenoids, saponins, flavonoids, etc. Conclusion: The ME of C. aromaticus (1,000 mg/kg p.o.) has showed highest diuretic action (4.2) among the tested extracts. This suggests the use of C. aromaticus leaves as “Pashanbhed”; the most effective diuretic drug. PMID:24948861

  13. Comparative Genome Viewer

    International Nuclear Information System (INIS)

    Molineris, I.; Sales, G.

    2009-01-01

    The amount of information about genomes, both in the form of complete sequences and annotations, has been exponentially increasing in the last few years. As a result there is the need for tools providing a graphical representation of such information that should be comprehensive and intuitive. Visual representation is especially important in the comparative genomics field since it should provide a combined view of data belonging to different genomes. We believe that existing tools are limited in this respect as they focus on a single genome at a time (conservation histograms) or compress alignment representation to a single dimension. We have therefore developed a web-based tool called Comparative Genome Viewer (Cgv): it integrates a bidimensional representation of alignments between two regions, both at small and big scales, with the richness of annotations present in other genome browsers. We give access to our system through a web-based interface that provides the user with an interactive representation that can be updated in real time using the mouse to move from region to region and to zoom in on interesting details.

  14. Comparative Studies for What?

    Directory of Open Access Journals (Sweden)

    Pedro Guedes de Carvalho

    2017-12-01

    Full Text Available ISCPES stands for International Society for Comparative Physical Education and Sports and it is going to celebrate its 40th anniversary in 2018. Since the beginning (Israel 1978 the main goals of the Society were established under a worldwide mind set considering five continents and no discrimination of any kind. The founders wanted to compare Physical Education and Sports across the world, searching for the best practices deserving consideration and applied on the purpose of improving citizen quality of life. The mission still stands for “Compare to learn and improve”. As all the organizations lasting for 39 years, ISCPES experienced several vicissitudes, usually correlated with world economic cycles, social and sports changes, which are in ISS journal articles - International Sport Studies. ISS journal is Scopus indexed, aiming to improve its quality (under evaluation to reach more qualified students, experts, professionals and researchers; doing so it will raise its indexation, which we know it is nowadays a more difficult task. First, because there are more journals trying to compete on this academic fierce competitive market; secondly, because the basic requirements are getting more and more hard to gather in the publishing environment around Physical Education and Sports issues. However, we can promise this will be one of our main strategic goals. Another goal I would like to address on this Editorial is the language issue. We have this second strategic goal, which is to reach most of languages spoken in different continents; besides the English language, we will reach Chinese, Spanish and Portuguese speaking countries. For that reason, we already defined that all the abstracts in English will be translated into Chinese, Spanish and Portuguese words so people can find them on any search browser. That will expand the demand for our journal and articles, increasing the number of potential readers. Of course this opportunity, given by

  15. Comparing solar energy alternatives

    Energy Technology Data Exchange (ETDEWEB)

    White, J R

    1984-01-01

    The paper outlines a computational procedure for comparing the merits of alternative processes to convert solar radiation to heat, electrical power, or chemical energy. The procedure uses the ratio of equipment investment to useful work as an index. Comparisons with conversion counterparts based on conventional fuels are also facilitated by examining this index. The procedure is illustrated by comparisons of (1) photovoltaic converters of differing efficiencies; (2) photovoltaic converters with and without focusing concentrators; (3) photovoltaic conversion plus electrolysis vs photocatalysis for the production of hydrogen; (4) photovoltaic conversion plus plasma arcs vs photocatalysis for nitrogen fixation. Estimates for conventionally-fuelled processes are included for comparison. The reasons why solar-based concepts fare poorly in such comparisons are traced to the low energy density of solar radiation and its low stream time factor resulting from the limited number of daylight hours available and clouds obscuring the sun.

  16. Comparing solar energy alternatives

    Energy Technology Data Exchange (ETDEWEB)

    White, J R

    1984-01-01

    This paper outlines a computational procedure for comparing the merits of alternative processes to convert solar radiation to heat, electrical power, or chemical energy. The procedure uses the ratio of equipment investment to useful work as an index. Comparisons with conversion counterparts based on conventional fuels are also facilitated by examining this index. The procedure is illustrated by comparisons of (1) photovoltaic converters of differing efficiencies; (2) photovoltaic converters with and without focusing concentrators; (3) photovoltaic conversion plus electrolysis vs photocatalysis for the production of hydrogen; (4) photovoltaic conversion plus plasma arcs vs photocatalysis for nitrogen fixation. Estimates for conventionally-fuelled processes are included for comparison. The reasons why solar-based concepts fare poorly in such comparisons are traced to the low energy density of solar radiation and its low stream time factor resulting from the limited number of daylight hours available and clouds obscuring the sun. 11 references.

  17. Comparing new anticoagulants.

    Science.gov (United States)

    Wooten, James M

    2012-12-01

    For years, the pharmaceutical industry has been trying to find a safe and effective drug to replace warfarin. Although warfarin is an effective anticoagulant, its pharmacology, adverse effects, and risk profiles dictate that patients taking this medication must be monitored judiciously. The US Food and Drug Administration has approved two drugs for commercial use, dabigatran and rivaroxaban, that will compete directly with warfarin for use in specific indications. Because of direct marketing to patients, physicians are being asked to comment on these new medications. This brief review illustrates the data available for the two new drugs when compared to warfarin for the specified indications. For some patients, these drugs may be highly beneficial and offer an excellent alternative to warfarin. For others, warfarin may still be the preferred drug.

  18. Comparative RNA genomics

    DEFF Research Database (Denmark)

    Backofen, Rolf; Gorodkin, Jan; Hofacker, Ivo L.

    2018-01-01

    Over the last two decades it has become clear that RNA is much more than just a boring intermediate in protein expression. Ancient RNAs still appear in the core information metabolism and comprise a surprisingly large component in bacterial gene regulation. A common theme with these types of mostly...... small RNAs is their reliance of conserved secondary structures. Large scale sequencing projects, on the other hand, have profoundly changed our understanding of eukaryotic genomes. Pervasively transcribed, they give rise to a plethora of large and evolutionarily extremely flexible noncoding RNAs...... that exert a vastly diverse array of molecule functions. In this chapter we provide a—necessarily incomplete—overview of the current state of comparative analysis of noncoding RNAs, emphasizing computational approaches as a means to gain a global picture of the modern RNA world....

  19. Manipulator comparative testing program

    International Nuclear Information System (INIS)

    Draper, J.V.; Handel, S.J.; Sundstrom, E.; Herndon, J.N.; Fujita, Y.; Maeda, M.

    1986-01-01

    The Manipulator Comparative Testing Program examined differences among manipulator systems from the United States and Japan. The manipulator systems included the Meidensha BILARM 83A, the Model M-2 of Central Research Laboratories Division of Sargent Industries (CRL), and the GCA Corporation PaR Systems Model 6000. The site of testing was the Remote Operations Maintenance Demonstration (ROMD) facility, operated by the Fuel Recycle Division in the Consolidated Fuel Reprocessing Program at the Oak Ridge National Laboratory (ORNL). In all stages of testing, operators using the CRL Model M-2 manipulator had consistently lower times to completion and error rates than they did using other machines. Performance was second best with the Meidensha BILARM 83A in master-slave mode. Performance with the BILARM in switchbox mode and the PaR 6000 manipulator was approximately equivalent in terms of criteria recorded in testing. These data show no impact of force reflection on task performance

  20. Comparative Failure in Science

    Directory of Open Access Journals (Sweden)

    Barney Glaser, PhD, Hon Phd

    2017-06-01

    Full Text Available A perennial problem for some scientists is their feeling of comparative failure as scientists. This problem becomes clearer if we consider two major sources of this feeling that are inherent in the vary nature of scientific work. (i In science, strong emphasis is placed on the achievement of recognition; (ii the typical basic scientist works in a community filled with “great men” who have made important and decisive discoveries in their respective fields; they are the acknowledge guiding lights. These esteemed scientists, who have attained honors beyond the reach of most of their colleagues, tend to become models for those who have been trained by them or who have worked under them. As Eiduson has put it in her recent psychological study of basic research scientists “Scientists: are idols-oriented.”

  1. Comparative Failure in Science

    Directory of Open Access Journals (Sweden)

    Barney G. Glaser, Ph.D., Hon. Ph.D

    2008-03-01

    Full Text Available A perennial problem for some scientists is their feeling of comparative failure as scientists. This problem becomes clearer if we consider two major sources of this feeling that are inherent in the vary nature of scientific work. (i In science, strong emphasis is placed on the achievement of recognition; (ii the typical basic scientist works in a community filled with “great men” who have made important and decisive discoveries in their respective fields; they are the acknowledge guiding lights. These esteemed scientists, who have attained honors beyond the reach of most of their colleagues, tend to become models for those who have been trained by them or who have worked under them. As Eiduson has put it in her recent psychological study of basic research scientists “Scientists: are idols-oriented.”

  2. Comparability of prostate trials

    DEFF Research Database (Denmark)

    Suciu, S; Sylvester, R; Iversen, P

    1993-01-01

    The present overview of advanced prostate cancer required the identification of randomized clinical trials studying the question of maximal androgen blockade versus the classic castration therapy. The heterogeneity of the trials concerned the type of castration (surgical or chemical) and the type...... of antiandrogen (flutamide, Anandron, or cyproterone acetate) added to castration. This paper reviews the different types of heterogeneity that might exist among trials that are involved in the overview: study design, randomization procedure, treatment evaluation, statistical evaluation, and data maturity....... In order to overcome these various types of heterogeneity and to compare like with like, the treatment comparison should be stratified a posteriori by question (i.e., type of castration or type of anti-androgen studied) and by study. In this way, one may draw valid conclusions. Of course, those trials...

  3. 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

  4. Operations dashboard: comparative study

    Science.gov (United States)

    Ramly, Noor Nashriq; Ismail, Ahmad Zuhairi; Aziz, Mohd Haris; Ahmad, Nurul Haszeli

    2011-10-01

    In this present days and age, there are increasing needs for companies to monitor application and infrastructure health. Apart from having proactive measures to secure their application and infrastructure, many see monitoring dashboards as crucial investment in disaster preparedness. As companies struggle to find the best solution to cater for their needs and interest for monitoring their application and infrastructure's health, this paper summarizes the studies made on several known off-the-shelf operations dashboard and in-house developed dashboard. A few criteria of good dashboard are collected from previous studies carried out by several researchers and rank them according to importance and business needs. The finalized criteria that will be discussed in later sections are data visualization, performance indicator, dashboard personalization, audit capability and alert/ notification. Comparative studies between several popular dashboards were then carried out to determine whether they met these criteria that we derived from the first exercise. The findings hopefully can be used to educate and provide an overview of selecting the best IT application and infrastructure operations dashboard that suit business needs, thus become the main contribution of this paper.

  5. Comparative genomic hybridization.

    Science.gov (United States)

    Pinkel, Daniel; Albertson, Donna G

    2005-01-01

    Altering DNA copy number is one of the many ways that gene expression and function may be modified. Some variations are found among normal individuals ( 14, 35, 103 ), others occur in the course of normal processes in some species ( 33 ), and still others participate in causing various disease states. For example, many defects in human development are due to gains and losses of chromosomes and chromosomal segments that occur prior to or shortly after fertilization, whereas DNA dosage alterations that occur in somatic cells are frequent contributors to cancer. Detecting these aberrations, and interpreting them within the context of broader knowledge, facilitates identification of critical genes and pathways involved in biological processes and diseases, and provides clinically relevant information. Over the past several years array comparative genomic hybridization (array CGH) has demonstrated its value for analyzing DNA copy number variations. In this review we discuss the state of the art of array CGH and its applications in medical genetics and cancer, emphasizing general concepts rather than specific results.

  6. Comparative Supreme Justice

    Directory of Open Access Journals (Sweden)

    Ditlev Tamm

    2011-12-01

    Full Text Available This article deals with the great variety of Supreme Courts in the world today and presents some selected courts. Supreme Courts are found in most countries both as only apex courts or in a courts’ system where also supreme administrative courts or constitutional courts are found. The starting point is the variation of supreme justice in the Nordic countries where one apex court is the system of Denmark and Norway whereas administrative courts are found in Sweden and Finland. Constitutional courts stem from the European tradition and are most abundant in Europe and in countries with a civil law system but especially in Africa they are also found in common law countries. Mexico is mentioned as a specific example of a Supreme Court that has taken upon itself to be a main player in the endeavour to communicate the law to a general audience. The article is a presentation with samples of what is going to be a project on comparative supreme justice in which the position of supreme courts in the various states, the recruitment scheme and competence of the courts and other such factors will be analyzed on a global basis.

  7. Comparative waste forms study

    International Nuclear Information System (INIS)

    Wald, J.W.; Lokken, R.O.; Shade, J.W.; Rusin, J.M.

    1980-12-01

    A number of alternative process and waste form options exist for the immobilization of nuclear wastes. Although data exists on the characterization of these alternative waste forms, a straightforward comparison of product properties is difficult, due to the lack of standardized testing procedures. The characterization study described in this report involved the application of the same volatility, mechanical strength and leach tests to ten alternative waste forms, to assess product durability. Bulk property, phase analysis and microstructural examination of the simulated products, whose waste loading varied from 5% to 100% was also conducted. The specific waste forms investigated were as follows: Cold Pressed and Sintered PW-9 Calcine; Hot Pressed PW-9 Calcine; Hot Isostatic Pressed PW-9 Calcine; Cold Pressed and Sintered SPC-5B Supercalcine; Hot Isostatic pressed SPC-5B Supercalcine; Sintered PW-9 and 50% Glass Frit; Glass 76-68; Celsian Glass Ceramic; Type II Portland Cement and 10% PW-9 Calcine; and Type II Portland Cement and 10% SPC-5B Supercalcine. Bulk property data were used to calculate and compare the relative quantities of waste form volume produced at a spent fuel processing rate of 5 metric ton uranium/day. This quantity ranged from 3173 L/day (5280 Kg/day) for 10% SPC-5B supercalcine in cement to 83 L/day (294 Kg/day) for 100% calcine. Mechanical strength, volatility, and leach resistance tests provide data related to waste form durability. Glass, glass-ceramic and supercalcine ranked high in waste form durability where as the 100% PW-9 calcine ranked low. All other materials ranked between these two groupings

  8. Ebolavirus comparative genomics

    Science.gov (United States)

    Jun, Se-Ran; Leuze, Michael R.; Nookaew, Intawat; Uberbacher, Edward C.; Land, Miriam; Zhang, Qian; Wanchai, Visanu; Chai, Juanjuan; Nielsen, Morten; Trolle, Thomas; Lund, Ole; Buzard, Gregory S.; Pedersen, Thomas D.; Wassenaar, Trudy M.; Ussery, David W.

    2015-01-01

    The 2014 Ebola outbreak in West Africa is the largest documented for this virus. To examine the dynamics of this genome, we compare more than 100 currently available ebolavirus genomes to each other and to other viral genomes. Based on oligomer frequency analysis, the family Filoviridae forms a distinct group from all other sequenced viral genomes. All filovirus genomes sequenced to date encode proteins with similar functions and gene order, although there is considerable divergence in sequences between the three genera Ebolavirus, Cuevavirus and Marburgvirus within the family Filoviridae. Whereas all ebolavirus genomes are quite similar (multiple sequences of the same strain are often identical), variation is most common in the intergenic regions and within specific areas of the genes encoding the glycoprotein (GP), nucleoprotein (NP) and polymerase (L). We predict regions that could contain epitope-binding sites, which might be good vaccine targets. This information, combined with glycosylation sites and experimentally determined epitopes, can identify the most promising regions for the development of therapeutic strategies. This manuscript has been authored by UT-Battelle, LLC under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan (http://energy.gov/downloads/doe-public-access-plan). PMID:26175035

  9. Comparative Healthcare: Diabetes Mellitus.

    Directory of Open Access Journals (Sweden)

    Dr Mohammed Ali

    2009-05-01

    Full Text Available In the third in this series of ‘comparative healthcare’ medical practitioners explore the approach to diabetes inBangaldesh and Australia respectively. The social and medical consequences of this chronic conditionare highlighted through the approach to patients at various stages of the disease from two nationalperspectives. An astonishing 7% of the 153 million people are reported to have diabetes in Bangladesh. Manyremain undiagnosed. Delays in diagnosis or management of diabetes have life limiting consequences for thosewho can ill afford private health care in the poorer nation. Screening and early intervention appear to bedenied to many in the developing country. The context is very different with Australians very fortunate to havea coordinated primary health care sector. The outlook for Bangladeshis with uncontrolled diabetes or withtreatable sequela would be unacceptable in Australia. At every stage in the disease trajectory the doctorsemphasise the importance of life style modification, a particular challenge in affluent Australia with its growingincidence of life style related pre morbid conditions in an increasingly sedentary population. A corner stone ofthe support of people with diabetes is the role of nurses and allied health professionals. With a fundedcommitment to multidisciplinary care in the community people with diabetes in Australia have access tosupport closer to home whereas those in Bangladesh remain heavily dependent on specialist, hospital basedservices. One can only speculate how Bangladesh will cope as its population ages and there are an everincreasing proportion of people who require urgent and expensive medical interventions. At the very leastthere is a strong case for greater investment in primary care especially to limit the economic consequences ofdiabetes and other chronic conditions. Finally as in other articles in this series we would like to emphasise that,the views expressed are those of the authors and do

  10. 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

  11. Non-comparative and comparative advertising in oligopolistic markets

    OpenAIRE

    Alipranti, Maria; Mitrokostas, Evangelos; Petrakis, Emmanuel

    2016-01-01

    We study firms' advertising strategies in an oligopolistic market in which both non-comparative and comparative advertising are present. We show that in equilibrium firms mix over the two types of advertising, with the intensity of comparative advertising exceeding that of non-comparative advertising; moreover, that the intensity of comparative increases relatively to non-comparative advertising as market competition intensifies. Interestingly, the use of comparative advertising may lead to h...

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

    Science.gov (United States)

    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.

  13. Comparative Magma Oceanography

    Science.gov (United States)

    Jones, J. H.

    1999-01-01

    The question of whether the Earth ever passed through a magma ocean stage is of considerable interest. Geochemical evidence strongly suggests that the Moon had a magma ocean and the evidence is mounting that the same was true for Mars. Analyses of martian (SNC) meteorites have yielded insights into the differentiation history of Mars, and consequently, it is interesting to compare that planet to the Earth. Three primary features of Mars contrast strongly to those of the Earth: (i) the extremely ancient ages of the martian core, mantle, and crust (about 4.55 b.y.); (ii) the highly depleted nature of the martian mantle; and (iii) the extreme ranges of Nd isotopic compositions that arise within the crust and depleted mantle. The easiest way to explain the ages and diverse isotopic compositions of martian basalts is to postulate that Mars had an early magma ocean. Cumulates of this magma ocean were later remelted to form the SNC meteorite suite and some of these melts assimilated crustal materials enriched in incompatible elements. The REE pattern of the crust assimilated by these SNC magmas was LREE enriched. If this pattern is typical of the crust as a whole, the martian crust is probably similar in composition to melts generated by small degrees of partial melting (about 5%) of a primitive source. Higher degrees of partial melting would cause the crustal LREE pattern to be essentially flat. In the context of a magma ocean model, where large degrees of partial melting presumably prevailed, the crust would have to be dominated by late-stage, LREE-enriched residual liquids. Regardless of the exact physical setting, Nd and W isotopic evidence indicates that martian geochemical reservoirs must have formed early and that they have not been efficiently remixed since. The important point is that in both the Moon and Mars we see evidence of a magma ocean phase and that we recognize it as such. Several lines of theoretical inference point to an early Earth that was also hot

  14. 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)

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

    Science.gov (United States)

    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.

  16. Comparative law as method and the method of comparative law

    NARCIS (Netherlands)

    Hage, J.C.; Adams, M.; Heirbaut, D.

    2014-01-01

    This article addresses both the justificatory role of comparative law within legal research (comparative law as method) and the method of comparative law itself. In this connection two questions will be answered: 1. Is comparative law a method, or a set of methods, for legal research? 2. Does

  17. Pre-hospital electrocardiogram triage with tele-cardiology support is associated with shorter time-to-balloon and higher rates of timely reperfusion even in rural areas: data from the Bari- Barletta/Andria/Trani public emergency medical service 118 registry on primary angioplasty in ST-elevation myocardial infarction.

    Science.gov (United States)

    Brunetti, Natale Daniele; Di Pietro, Gaetano; Aquilino, Ambrogio; Bruno, Angela I; Dellegrottaglie, Giulia; Di Giuseppe, Giuseppe; Lopriore, Claudio; De Gennaro, Luisa; Lanzone, Saverio; Caldarola, Pasquale; Antonelli, Gianfranco; Di Biase, Matteo

    2014-09-01

    We report the preliminary data from a regional registry on ST-elevation myocardial infarction (STEMI) patients treated with primary angioplasty in Apulia, Italy; the region is covered by a single public health-care service, a single public emergency medical service (EMS), and a single tele-medicine service provider. Two hundred and ninety-seven consecutive patients with STEMI transferred by regional free public EMS 1-1-8 for primary-PCI were enrolled in the study; 123 underwent pre-hospital electrocardiograms (ECGs) triage by tele-cardiology support and directly referred for primary-PCI, those remaining were just transferred by 1-1-8 ambulances for primary percutaneous coronary intervention (PCI) (diagnosis not based on tele-medicine ECG; already hospitalised patients, emergency-room without tele-medicine support). Time from first ECG diagnostic for STEMI to balloon was recorded; a time-to-balloon primary-PCI). Pre-hospital triage with tele-cardiology ECG in an EMS registry from an area with more than one and a half million inhabitants was associated with shorter time-to-balloon and higher rates of timely treated patients, even in 'rural' areas. © The European Society of Cardiology 2014.

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

    Directory of Open Access Journals (Sweden)

    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.

  19. 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.

  20. Next generation sequencing and comparative analyses of Xenopus mitogenomes

    Directory of Open Access Journals (Sweden)

    Lloyd Rhiannon E

    2012-09-01

    Full Text Available Abstract Background Mitochondrial genomes comprise a small but critical component of the total DNA in eukaryotic organisms. They encode several key proteins for the cell’s major energy producing apparatus, the mitochondrial respiratory chain. Additonally, their nucleotide and amino acid sequences are of great utility as markers for systematics, molecular ecology and forensics. Their characterization through nucleotide sequencing is a fundamental starting point in mitogenomics. Methods to amplify complete mitochondrial genomes rapidly and efficiently from microgram quantities of tissue of single individuals are, however, not always available. Here we validate two approaches, which combine long-PCR with Roche 454 pyrosequencing technology, to obtain two complete mitochondrial genomes from individual amphibian species. Results We obtained two new xenopus frogs (Xenopus borealis and X. victorianus complete mitochondrial genome sequences by means of long-PCR followed by 454 of individual genomes (approach 1 or of multiple pooled genomes (approach 2, the mean depth of coverage per nucleotide was 9823 and 186, respectively. We also characterised and compared the new mitogenomes against their sister taxa; X. laevis and Silurana tropicalis, two of the most intensely studied amphibians. Our results demonstrate how our approaches can be used to obtain complete amphibian mitogenomes with depths of coverage that far surpass traditional primer-walking strategies, at either the same cost or less. Our results also demonstrate: that the size, gene content and order are the same among xenopus mitogenomes and that S. tropicalis form a separate clade to the other xenopus, among which X. laevis and X. victorianus were most closely related. Nucleotide and amino acid diversity was found to vary across the xenopus mitogenomes, with the greatest diversity observed in the Complex 1 gene nad4l and the least diversity observed in Complex 4 genes (cox1-3. All protein

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  3. Bilateral Breast Reduction Without Opioid Analgesics: A Comparative Study.

    Science.gov (United States)

    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

  4. 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.

  5. The C-terminal domain of Nrf1 negatively regulates the full-length CNC-bZIP factor and its shorter isoform LCR-F1/Nrf1β; both are also inhibited by the small dominant-negative Nrf1γ/δ isoforms that down-regulate ARE-battery gene expression.

    Science.gov (United States)

    Zhang, Yiguo; Qiu, Lu; Li, Shaojun; Xiang, Yuancai; Chen, Jiayu; Ren, Yonggang

    2014-01-01

    The C-terminal domain (CTD, aa 686-741) of nuclear factor-erythroid 2 p45-related factor 1 (Nrf1) shares 53% amino acid sequence identity with the equivalent Neh3 domain of Nrf2, a homologous transcription factor. The Neh3 positively regulates Nrf2, but whether the Neh3-like (Neh3L) CTD of Nrf1 has a similar role in regulating Nrf1-target gene expression is unknown. Herein, we report that CTD negatively regulates the full-length Nrf1 (i.e. 120-kDa glycoprotein and 95-kDa deglycoprotein) and its shorter isoform LCR-F1/Nrf1β (55-kDa). Attachment of its CTD-adjoining 112-aa to the C-terminus of Nrf2 yields the chimaeric Nrf2-C112Nrf1 factor with a markedly decreased activity. Live-cell imaging of GFP-CTD reveals that the extra-nuclear portion of the fusion protein is allowed to associate with the endoplasmic reticulum (ER) membrane through the amphipathic Neh3L region of Nrf1 and its basic c-tail. Thus removal of either the entire CTD or the essential Neh3L portion within CTD from Nrf1, LCR-F1/Nrf1β and Nrf2-C112Nrf1, results in an increase in their transcriptional ability to regulate antioxidant response element (ARE)-driven reporter genes. Further examinations unravel that two smaller isoforms, 36-kDa Nrf1γ and 25-kDa Nrf1δ, act as dominant-negative inhibitors to compete against Nrf1, LCR-F1/Nrf1β and Nrf2. Relative to Nrf1, LCR-F1/Nrf1β is a weak activator, that is positively regulated by its Asn/Ser/Thr-rich (NST) domain and acidic domain 2 (AD2). Like AD1 of Nrf1, both AD2 and NST domain of LCR-F1/Nrf1β fused within two different chimaeric contexts to yield Gal4D:Nrf1β607 and Nrf1β:C270Nrf2, positively regulate their transactivation activity of cognate Gal4- and Nrf2-target reporter genes. More importantly, differential expression of endogenous ARE-battery genes is attributable to up-regulation by Nrf1 and LCR-F1/Nrf1β and down-regulation by Nrf1γ and Nrf1δ.

  6. Right $P$-comparable semigroups

    OpenAIRE

    Halimi, Nazer. H.

    2009-01-01

    In this paper we introduce the notion of right waist and right comparizer ideals for semigroups. In particular, we study the ideal theory of semigroups containing right waists and right comparizer ideals. We also study those properties of right cones that can be carried over to right $P$-comparable semigroups. We give sufficient and necessary conditions on the set of nilpotent elements of a semigroup to be an ideal. We provide several equivalent characterizations for a right ideal being a rig...

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

    Directory of Open Access Journals (Sweden)

    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.

  8. 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

  9. Comparative Education Histories: A Postscript

    Science.gov (United States)

    Manzon, Maria

    2018-01-01

    Comparative education is two centuries old. Many mainstream historical narratives claim that the field began with the iconic opus of Marc-Antoine Jullien de Paris (1817). This article offers to re-theorise the histories of comparative education. It suggests casting a far-sighted and panoramic look at the field's origins. An underlying assumption…

  10. Comparable Worth Theory and Policy.

    Science.gov (United States)

    Wittig, Michele Andrisin; Lowe, Rosemary Hays

    1989-01-01

    Provides different perspectives on comparable worth issues. Covers the following topics: (1) competing explanations for the wage gap; (2) indirect approaches to wage equity; (3) the need for a direct approach to wage equity; (4) job evaluation; (5) application of comparable worth principles to compensation systems; and (6) strategies for adopting…

  11. 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.

  12. 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.

  13. Ultralow lattice thermal conductivity in monolayer C3N as compared to graphene

    KAUST Repository

    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.

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  16. 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.

  17. Comparing word and face recognition

    DEFF Research Database (Denmark)

    Robotham, Ro Julia; Starrfelt, Randi

    2017-01-01

    included, as a control, which makes designing experiments all the more challenging. Three main strategies have been used to overcome this problem, each of which has limitations: 1) Compare performances on typical tests of the three stimulus types (e.g., a Face Memory Test, an Object recognition test...... this framework to classify tests and experiments aiming to compare processing across these categories, it becomes apparent that core differences in characteristics (visual and semantic) between the stimuli make the problem of designing comparable tests an insoluble conundrum. By analyzing the experimental...

  18. Comparing neutrino and antineutrino scattering

    International Nuclear Information System (INIS)

    Barish, B.C.

    1977-01-01

    The charged current interaction is considered. The present situation with respect to the indications of new physics at high energies, especially in the context of what can be learned by comparing neutrino with antineutrino production is reviewed

  19. Ethnography and comparative housing research

    NARCIS (Netherlands)

    Ronald, R.

    2011-01-01

    Housing systems across advanced societies are typically compared in terms of quantitative measures of aggregate variables, with little regard for local complexity, diversity and cultural contingency. This paper seeks, through the exploration of ethnographic techniques, to reflect on both the

  20. Physician Compare National Downloadable File

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Physician Compare National Downloadable File is organized at the individual eligible professional level; each line is unique at the professional/enrollment...

  1. CompareTests-R package

    Science.gov (United States)

    CompareTests is an R package to estimate agreement and diagnostic accuracy statistics for two diagnostic tests when one is conducted on only a subsample of specimens. A standard test is observed on all specimens.

  2. Comparing long term energy scenarios

    International Nuclear Information System (INIS)

    Cumo, M.; Simbolotti, G.

    2001-01-01

    Major projection studies by international organizations and senior analysts have been compared with reference to individual key parameters (population, energy demand/supply, resources, technology, emissions and global warming) to understand trends and implications of the different scenarios. Then, looking at the long term (i.e., 2050 and beyond), parameters and trends have been compared together to understand and quantify whether and when possible crisis or market turbulence might occur due to shortage of resources or environmental problems [it

  3. Comparative Methodology and Postmodern Relativism

    Science.gov (United States)

    Young, Robert

    1997-09-01

    The author addresses the problems of conducting comparative studies in education if one adopts a viewpoint of postmodern relativism. While acknowledging the value of postmodernist thought in opening up a new understanding of the educational process, he finds that postmodernism raises difficulties when one attempts to deal with the differences and interactions between cultures. He rejects the extremes of both relativism and universalism and argues that comparative studies should be based on a balance between the two.

  4. Corporate Finance and Comparative Advantage

    OpenAIRE

    Peter Egger; Christian Keuschnigg

    2009-01-01

    Since innovative firms are often financially constrained, access to external funds is important for the expansion of innovative industries. This paper reports four important results. First, comparative advantage is shaped by factor endowments as well as fundamental determinants of corporate finance. In particular, a larger equity ratio of firms and tough governance standards relax finance constraints and create a comparative advantage in innovative industries. Second, factor price equalizatio...

  5. 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.

  6. Comparing Microbiome Sampling Methods in a Wild Mammal: Fecal and Intestinal Samples Record Different Signals of Host Ecology, Evolution

    Directory of Open Access Journals (Sweden)

    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.

  7. 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.

  8. 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

  9. Cloud computing for comparative genomics

    Directory of Open Access Journals (Sweden)

    Pivovarov Rimma

    2010-05-01

    Full Text Available Abstract Background Large comparative genomics studies and tools are becoming increasingly more compute-expensive as the number of available genome sequences continues to rise. The capacity and cost of local computing infrastructures are likely to become prohibitive with the increase, especially as the breadth of questions continues to rise. Alternative computing architectures, in particular cloud computing environments, may help alleviate this increasing pressure and enable fast, large-scale, and cost-effective comparative genomics strategies going forward. To test this, we redesigned a typical comparative genomics algorithm, the reciprocal smallest distance algorithm (RSD, to run within Amazon's Elastic Computing Cloud (EC2. We then employed the RSD-cloud for ortholog calculations across a wide selection of fully sequenced genomes. Results We ran more than 300,000 RSD-cloud processes within the EC2. These jobs were farmed simultaneously to 100 high capacity compute nodes using the Amazon Web Service Elastic Map Reduce and included a wide mix of large and small genomes. The total computation time took just under 70 hours and cost a total of $6,302 USD. Conclusions The effort to transform existing comparative genomics algorithms from local compute infrastructures is not trivial. However, the speed and flexibility of cloud computing environments provides a substantial boost with manageable cost. The procedure designed to transform the RSD algorithm into a cloud-ready application is readily adaptable to similar comparative genomics problems.

  10. Cloud computing for comparative genomics.

    Science.gov (United States)

    Wall, Dennis P; Kudtarkar, Parul; Fusaro, Vincent A; Pivovarov, Rimma; Patil, Prasad; Tonellato, Peter J

    2010-05-18

    Large comparative genomics studies and tools are becoming increasingly more compute-expensive as the number of available genome sequences continues to rise. The capacity and cost of local computing infrastructures are likely to become prohibitive with the increase, especially as the breadth of questions continues to rise. Alternative computing architectures, in particular cloud computing environments, may help alleviate this increasing pressure and enable fast, large-scale, and cost-effective comparative genomics strategies going forward. To test this, we redesigned a typical comparative genomics algorithm, the reciprocal smallest distance algorithm (RSD), to run within Amazon's Elastic Computing Cloud (EC2). We then employed the RSD-cloud for ortholog calculations across a wide selection of fully sequenced genomes. We ran more than 300,000 RSD-cloud processes within the EC2. These jobs were farmed simultaneously to 100 high capacity compute nodes using the Amazon Web Service Elastic Map Reduce and included a wide mix of large and small genomes. The total computation time took just under 70 hours and cost a total of $6,302 USD. The effort to transform existing comparative genomics algorithms from local compute infrastructures is not trivial. However, the speed and flexibility of cloud computing environments provides a substantial boost with manageable cost. The procedure designed to transform the RSD algorithm into a cloud-ready application is readily adaptable to similar comparative genomics problems.

  11. Sociological analysis and comparative education

    Science.gov (United States)

    Woock, Roger R.

    1981-12-01

    It is argued that comparative education is essentially a derivative field of study, in that it borrows theories and methods from academic disciplines. After a brief humanistic phase, in which history and philosophy were central for comparative education, sociology became an important source. In the mid-50's and 60's, sociology in the United States was characterised by Structural Functionalism as a theory, and Social Survey as a dominant methodology. Both were incorporated into the development of comparative education. Increasingly in the 70's, and certainly today, the new developments in sociology are characterised by an attack on Positivism, which is seen as the philosophical position underlying both functionalism and survey methods. New or re-discovered theories with their attendant methodologies included Marxism, Phenomenological Sociology, Critical Theory, and Historical Social Science. The current relationship between comparative education and social science is one of uncertainty, but since social science is seen to be returning to its European roots, the hope is held out for the development of an integrated social theory and method which will provide a much stronger basis for developments in comparative education.

  12. 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

  13. Nuclear power ecology: comparative analysis

    International Nuclear Information System (INIS)

    Trofimenko, A.P.; Lips'ka, A.Yi.; Pisanko, Zh.Yi.

    2005-01-01

    Ecological effects of different energy sources are compared. Main actions for further nuclear power development - safety increase and waste management, are noted. Reasons of restrained public position to nuclear power and role of social and political factors in it are analyzed. An attempt is undertaken to separate real difficulties of nuclear power from imaginary ones that appear in some mass media. International actions of environment protection are noted. Risk factors at different energy source using are compared. The results of analysis indicate that ecological influence and risk for nuclear power are of minimum

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

    Directory of Open Access Journals (Sweden)

    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

  15. Comparative analyses reveal discrepancies among results of commonly used methods for Anopheles gambiaemolecular form identification

    Directory of Open Access Journals (Sweden)

    Pinto João

    2011-08-01

    Full Text Available Abstract Background Anopheles gambiae M and S molecular forms, the major malaria vectors in the Afro-tropical region, are ongoing a process of ecological diversification and adaptive lineage splitting, which is affecting malaria transmission and vector control strategies in West Africa. These two incipient species are defined on the basis of single nucleotide differences in the IGS and ITS regions of multicopy rDNA located on the X-chromosome. A number of PCR and PCR-RFLP approaches based on form-specific SNPs in the IGS region are used for M and S identification. Moreover, a PCR-method to detect the M-specific insertion of a short interspersed transposable element (SINE200 has recently been introduced as an alternative identification approach. However, a large-scale comparative analysis of four widely used PCR or PCR-RFLP genotyping methods for M and S identification was never carried out to evaluate whether they could be used interchangeably, as commonly assumed. Results The genotyping of more than 400 A. gambiae specimens from nine African countries, and the sequencing of the IGS-amplicon of 115 of them, highlighted discrepancies among results obtained by the different approaches due to different kinds of biases, which may result in an overestimation of MS putative hybrids, as follows: i incorrect match of M and S specific primers used in the allele specific-PCR approach; ii presence of polymorphisms in the recognition sequence of restriction enzymes used in the PCR-RFLP approaches; iii incomplete cleavage during the restriction reactions; iv presence of different copy numbers of M and S-specific IGS-arrays in single individuals in areas of secondary contact between the two forms. Conclusions The results reveal that the PCR and PCR-RFLP approaches most commonly utilized to identify A. gambiae M and S forms are not fully interchangeable as usually assumed, and highlight limits of the actual definition of the two molecular forms, which might

  16. BOOK REVIEW: The Current Comparator

    Science.gov (United States)

    Petersons, Oskars

    1989-01-01

    This 120-page book is a concise, yet comprehensive, clearly-written and well-illustrated monograph that covers the subject matter from basic principles through design, construction and calibration details to the principal applications. The book will be useful, as a primer, to the uninitiated and, as a reference book to the practitioner involved with transformer-type ratio devices. The length of the book and the style of presentation will not overburden any informed reader. The described techniques and the cited references are primarily from the work at the National Research Council, Canada (NRC). Any omissions, however, are not serious with respect to coverage of the subject matter, since most of the development work has been done at NRC. The role of transformers and transformer-like devices for establishing accurate voltage and current ratios has been recognized for over half a century. Transformer techniques were much explored and developed in the fifties and sixties for accuracy levels suitable for standards laboratories. Three-winding voltage transformers were developed for scaling of impedances in connection with the calculable Thompson Lampard capacitor; three-winding current transformers or current comparators were initially explored for the calibration of current transformers and later for specialized impedance measurements. Extensive development of the current comparator and its applications has been and is still being conducted at the NRC by a team that was started and, until his retirement, led by N L Kusters. The team is now led by W J M Moore. He and P N Miljanic, the authors of this book, have had the principal roles in the development of the current comparator. It is fortunate for the field of metrology that considerabe resources and a talented group of researchers were available to do this development along with mechanisms that were available to transfer this technology to a private sector instrument manufacturer and, thus, disseminate it world wide

  17. Comparative study Beamnrc VS Pinnacle

    International Nuclear Information System (INIS)

    Moreno Reyes, J. C.; Macias Jaen, J.; Jimenez Ortega, E.

    2013-01-01

    Has been developed in JAVA a software application called JJGAMMA, capable of manipulating the environment BEAMNRC and Pinnacle output formats 3 , comfortable, fast and accurately. As particular application you can use to compare dose distributions (plans for treatments, checking fields for modeling and clinical accelerators Commissioner) using, as objective criteria, function or Gamma index. (Author)

  18. Analysing and Comparing Encodability Criteria

    Directory of Open Access Journals (Sweden)

    Kirstin Peters

    2015-08-01

    Full Text Available Encodings or the proof of their absence are the main way to compare process calculi. To analyse the quality of encodings and to rule out trivial or meaningless encodings, they are augmented with quality criteria. There exists a bunch of different criteria and different variants of criteria in order to reason in different settings. This leads to incomparable results. Moreover it is not always clear whether the criteria used to obtain a result in a particular setting do indeed fit to this setting. We show how to formally reason about and compare encodability criteria by mapping them on requirements on a relation between source and target terms that is induced by the encoding function. In particular we analyse the common criteria full abstraction, operational correspondence, divergence reflection, success sensitiveness, and respect of barbs; e.g. we analyse the exact nature of the simulation relation (coupled simulation versus bisimulation that is induced by different variants of operational correspondence. This way we reduce the problem of analysing or comparing encodability criteria to the better understood problem of comparing relations on processes.

  19. The Economics of Comparable Worth.

    Science.gov (United States)

    Killingsworth, Mark R.

    This document concludes that the basic difficulty with comparable worth is that it is an ill-conceived solution to a serious problem and that alternative policies, such as equal employment opportunity legislation or application of antitrust laws, provide means of addressing employment discrimination that are both more effective and less likely to…

  20. Countries compared on public performance

    NARCIS (Netherlands)

    Jedid-Jah Jonker

    2012-01-01

    How well is the public sector performing? Are citizens being well served? This report compares the performance of nine public services in 28 developed countries over the period 1995-2009. Four sectors - education, health care, social safety and housing - are studied in some detail, while the

  1. Job Satisfaction in Fisheries Compared

    Science.gov (United States)

    Pollnac, Richard; Bavinck, Maarten; Monnereau, Iris

    2012-01-01

    This article draws comparative lessons from seven job satisfaction studies on marine capture fishing that were recently carried out in nine countries and three geographical regions--Asia, Africa, and the Caribbean. The seven studies made use of an identical job satisfaction assessment tool and present information on a selection of metiers mainly…

  2. Paracetamol suppositories: a comparative study.

    Science.gov (United States)

    Cullen, S; Kenny, D; Ward, O C; Sabra, K

    1989-01-01

    Paracetamol suppositories in two different bases were given to children who had fever after operations. Plasma concentrations and the effect on temperature were compared. There was a significant correlation between peak plasma concentrations and maximum drop in temperature. A lipophilic base produced better results than a hydrophilic base. PMID:2817936

  3. Paracetamol suppositories: a comparative study.

    OpenAIRE

    Cullen, S; Kenny, D; Ward, O C; Sabra, K

    1989-01-01

    Paracetamol suppositories in two different bases were given to children who had fever after operations. Plasma concentrations and the effect on temperature were compared. There was a significant correlation between peak plasma concentrations and maximum drop in temperature. A lipophilic base produced better results than a hydrophilic base.

  4. Teaching Strategy: Comparing Rights Documents.

    Science.gov (United States)

    Shiman, David A.

    1998-01-01

    Engages students in comparing the rights proclaimed in the Universal Declaration of Human Rights (UDHR) with those present in the United States Bill of Rights and other constitutional amendments. Challenges the students to explore reasons for the presence or absence of certain rights and to reflect on the role of the government. (CMK)

  5. Comparative dermatology: acquired digital fibrokeratoma

    OpenAIRE

    Cunha Filho, Roberto Rheingantz da

    2008-01-01

    Demonstra-se quadro característico de fibroqueratoma digital adquirido em trabalhadora rural de 42 anos de idade, que se compara a corno de rinoceronte.It is presented a case of a 42 year-old white female farmer with the classical feature of acquired digital fibrokeratoma, which is compared to rhinoceros horn.

  6. Comparing Candidate Hospital Report Cards

    Energy Technology Data Exchange (ETDEWEB)

    Burr, T.L.; Rivenburgh, R.D.; Scovel, J.C.; White, J.M.

    1997-12-31

    We present graphical and analytical methods that focus on multivariate outlier detection applied to the hospital report cards data. No two methods agree which hospitals are unusually good or bad, so we also present ways to compare the agreement between two methods. We identify factors that have a significant impact on the scoring.

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

    Directory of Open Access Journals (Sweden)

    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.

  8. COGNATE: comparative gene annotation characterizer.

    Science.gov (United States)

    Wilbrandt, Jeanne; Misof, Bernhard; Niehuis, Oliver

    2017-07-17

    The comparison of gene and genome structures across species has the potential to reveal major trends of genome evolution. However, such a comparative approach is currently hampered by a lack of standardization (e.g., Elliott TA, Gregory TR, Philos Trans Royal Soc B: Biol Sci 370:20140331, 2015). For example, testing the hypothesis that the total amount of coding sequences is a reliable measure of potential proteome diversity (Wang M, Kurland CG, Caetano-Anollés G, PNAS 108:11954, 2011) requires the application of standardized definitions of coding sequence and genes to create both comparable and comprehensive data sets and corresponding summary statistics. However, such standard definitions either do not exist or are not consistently applied. These circumstances call for a standard at the descriptive level using a minimum of parameters as well as an undeviating use of standardized terms, and for software that infers the required data under these strict definitions. The acquisition of a comprehensive, descriptive, and standardized set of parameters and summary statistics for genome publications and further analyses can thus greatly benefit from the availability of an easy to use standard tool. We developed a new open-source command-line tool, COGNATE (Comparative Gene Annotation Characterizer), which uses a given genome assembly and its annotation of protein-coding genes for a detailed description of the respective gene and genome structure parameters. Additionally, we revised the standard definitions of gene and genome structures and provide the definitions used by COGNATE as a working draft suggestion for further reference. Complete parameter lists and summary statistics are inferred using this set of definitions to allow down-stream analyses and to provide an overview of the genome and gene repertoire characteristics. COGNATE is written in Perl and freely available at the ZFMK homepage ( https://www.zfmk.de/en/COGNATE ) and on github ( https

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

    Directory of Open Access Journals (Sweden)

    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

  10. Episodic Memory: A Comparative Approach

    Science.gov (United States)

    Martin-Ordas, Gema; Call, Josep

    2013-01-01

    Historically, episodic memory has been described as autonoetic, personally relevant, complex, context-rich, and allowing mental time travel. In contrast, semantic memory, which is theorized to be free of context and personal relevance, is noetic and consists of general knowledge of facts about the world. The field of comparative psychology has adopted this distinction in order to study episodic memory in non-human animals. Our aim in this article is not only to reflect on the concept of episodic memory and the experimental approaches used in comparative psychology to study this phenomenon, but also to provide a critical analysis of these paradigms. We conclude the article by providing new avenues for future research. PMID:23781179

  11. Comparative Genomics in Homo sapiens.

    Science.gov (United States)

    Oti, Martin; Sammeth, Michael

    2018-01-01

    Genomes can be compared at different levels of divergence, either between species or within species. Within species genomes can be compared between different subpopulations, such as human subpopulations from different continents. Investigating the genomic differences between different human subpopulations is important when studying complex diseases that are affected by many genetic variants, as the variants involved can differ between populations. The 1000 Genomes Project collected genome-scale variation data for 2504 human individuals from 26 different populations, enabling a systematic comparison of variation between human subpopulations. In this chapter, we present step-by-step a basic protocol for the identification of population-specific variants employing the 1000 Genomes data. These variants are subsequently further investigated for those that affect the proteome or RNA splice sites, to investigate potentially biologically relevant differences between the populations.

  12. Enhancer Identification through Comparative Genomics

    Energy Technology Data Exchange (ETDEWEB)

    Visel, Axel; Bristow, James; Pennacchio, Len A.

    2006-10-01

    With the availability of genomic sequence from numerousvertebrates, a paradigm shift has occurred in the identification ofdistant-acting gene regulatory elements. In contrast to traditionalgene-centric studies in which investigators randomly scanned genomicfragments that flank genes of interest in functional assays, the modernapproach begins electronically with publicly available comparativesequence datasets that provide investigators with prioritized lists ofputative functional sequences based on their evolutionary conservation.However, although a large number of tools and resources are nowavailable, application of comparative genomic approaches remains far fromtrivial. In particular, it requires users to dynamically consider thespecies and methods for comparison depending on the specific biologicalquestion under investigation. While there is currently no single generalrule to this end, it is clear that when applied appropriately,comparative genomic approaches exponentially increase our power ingenerating biological hypotheses for subsequent experimentaltesting.

  13. Introduction to SamplerCompare

    Directory of Open Access Journals (Sweden)

    Madeleine B. Thompson

    2011-08-01

    Full Text Available SamplerCompare is an R package for comparing the performance of Markov chain Monte Carlo (MCMC samplers. It samples from a collection of distributions with a collection of MCMC methods over a range of tuning parameters. Then, using log density evaluations per uncorrelated observation as a figure of merit, it generates a grid of plots showing the results of the simulation. It comes with a collection of predefined distributions and samplers and provides R and C interfaces for defining additional ones. It also provides the means to import simulation data generated by external systems. This document provides background on the package and demonstrates the basics of running simulations, visualizing results, and defining distributions and samplers in R.

  14. BANK RATING. A COMPARATIVE ANALYSIS

    Directory of Open Access Journals (Sweden)

    Batrancea Ioan

    2015-07-01

    Full Text Available Banks in Romania offers its customers a wide range of products but which involves both risk taking. Therefore researchers seek to build rating models to help managers of banks to risk of non-recovery of loans and interest. In the following we highlight rating Raiffeisen Bank, BCR-ERSTE Bank and Transilvania Bank, based on the models CAAMPL and Stickney making a comparative analysis of the two rating models.

  15. Detecting selection needs comparative data

    DEFF Research Database (Denmark)

    Nielsen, Rasmus; Hubisz, Melissa J.

    2005-01-01

    Positive selection at the molecular level is usually indicated by an increase in the ratio of non-synonymous to synonymous substitutions (dN/dS) in comparative data. However, Plotkin et al. 1 describe a new method for detecting positive selection based on a single nucleotide sequence. We show here...... that this method is particularly sensitive to assumptions regarding the underlying mutational processes and does not provide a reliable way to identify positive selection....

  16. School bullying - A comparative approach -

    OpenAIRE

    Kosevaliska, Olga; Buzarovska - Lazetik, Gordana; Nanev, Lazar

    2014-01-01

    The modest purpose of this paper is to elaborate the phenomenon of school bullying and to try to give an answer to questions that remain open over time because of the seriousness of this issue. A child is being bullied when he or she is exposed repeatedly over time to aggressive behavior that intentionally inflicts injury or discomfort through physical contact, verbal attacks, fighting or psychological manipulation. Besides finding the proper definition of bullying, we’ll give a comparative a...

  17. Comparative optimism about healthy eating.

    Science.gov (United States)

    Sproesser, Gudrun; Klusmann, Verena; Schupp, Harald T; Renner, Britta

    2015-07-01

    The present study investigated people's perception of their own as compared to their peers' healthy eating and related these perceptions to actual healthy eating, BMI, and subsequent healthy eating behavior. Data were collected within the framework of the longitudinal cohort study Konstanz Life Study (T1: N = 770; T2: N = 510). Our results demonstrated an optimistic bias on the group level. Specifically, people rated their own eating behavior as healthier on average than that of their average peers. This comparative optimism occurred even when actual healthy eating was unfavorable and BMI was high. However, it increased with actual healthy eating behavior. Importantly, optimistic perceptions were positively related to the intention to eat healthily and healthy eating six months later. Hence, the results suggest that an optimistic comparative view of one's own healthy eating is grounded in reality and boosts rather than deters subsequent health behavior. This implies that there might not be a need to reduce optimistic perceptions of healthy eating behavior. Copyright © 2015 Elsevier Ltd. All rights reserved.

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. 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

  3. 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...

  4. 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...

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

    Directory of Open Access Journals (Sweden)

    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.

  6. EARLY ENTERAL FEEDING AND DELAYED ENTERAL FEEDING- A COMPARATIVE STUDY

    Directory of Open Access Journals (Sweden)

    Alli Muthiah

    2017-03-01

    Full Text Available BACKGROUND Nutrients form the fuel for the body, which comes in the form of carbohydrates, proteins and lipids. The body is intended to burn fuels in order to perform work. Starvation with malnutrition affects the postoperative patients and patients with acute pancreatitis. There is an increased risk of nosocomial infections and a delay in the wound healing may be noted. They are more prone for respiratory tract infections. Enteral Nutrition (EN delivers nutrition to the body through gastrointestinal tract. This also includes the oral feeding. This study will review the administration, rationale and assess the pros and cons associated with the early initiation of enteral feeding. The aim of this study is to evaluate if early commencement of enteral nutrition compared to traditional management (delayed enteral feeding is associated with fewer complications and improved outcome-  In patients undergoing elective/emergency gastrointestinal surgery.  In patients with acute pancreatitis. It is also used to determine whether a period of starvation (nil by mouth after gastrointestinal surgery or in the early days of acute pancreatitis is beneficial in terms of specific outcomes. MATERIALS AND METHODS A prospective cohort interventional study was conducted using 100 patients from July 2012 to November 2012. Patients satisfying the inclusion and exclusion criteria were included in the study. Patients admitted in my unit for GIT surgeries or acute pancreatitis constituted the test group, while patients admitted in other units for similar disease processes constituted the control group. RESULTS Our study concluded that early enteral feeding resulted in reduced incidence of surgical site infections. When the decreased length of stay, shorter convalescent period and the lesser post-interventional fatigue were taken into account, early enteral feeding has a definite cost benefit.CONCLUSION Early enteral feeding was beneficial associated with fewer

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

    Science.gov (United States)

    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

  8. 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.)

  9. 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.

  10. 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.

  11. Phytozome Comparative Plant Genomics Portal

    Energy Technology Data Exchange (ETDEWEB)

    Goodstein, David; Batra, Sajeev; Carlson, Joseph; Hayes, Richard; Phillips, Jeremy; Shu, Shengqiang; Schmutz, Jeremy; Rokhsar, Daniel

    2014-09-09

    The Dept. of Energy Joint Genome Institute is a genomics user facility supporting DOE mission science in the areas of Bioenergy, Carbon Cycling, and Biogeochemistry. The Plant Program at the JGI applies genomic, analytical, computational and informatics platforms and methods to: 1. Understand and accelerate the improvement (domestication) of bioenergy crops 2. Characterize and moderate plant response to climate change 3. Use comparative genomics to identify constrained elements and infer gene function 4. Build high quality genomic resource platforms of JGI Plant Flagship genomes for functional and experimental work 5. Expand functional genomic resources for Plant Flagship genomes

  12. Building and using comparable corpora

    CERN Document Server

    Sharoff, Serge; Zweigenbaum, Pierre; Fung, Pascale

    2013-01-01

    The 1990s saw a paradigm change in the use of corpus-driven methods in NLP. In the field of multilingual NLP (such as machine translation and terminology mining) this implied the use of parallel corpora. However, parallel resources are relatively scarce: many more texts are produced daily by native speakers of any given language than translated. This situation resulted in a natural drive towards the use of comparable corpora, i.e. non-parallel texts in the same domain or genre. Nevertheless, this research direction has not produced a single authoritative source suitable for researchers and stu

  13. Body mass in comparative primatology.

    Science.gov (United States)

    Smith, R J; Jungers, W L

    1997-06-01

    Data are presented on adult body mass for 230 of 249 primate species, based on a review of the literature and previously unpublished data. The issues involved in collecting data on adult body mass are discussed, including the definition of adults, the effects of habitat and pregnancy, the strategy for pooling data on single species from multiple studies, and use of an appropriate number of significant figures. An analysis of variability in body mass indicates that the coefficient of variation for body mass increases with increasing species mean mass. Evaluation of several previous body mass reviews reveals a number of shortcomings with data that have been used often in comparative studies.

  14. Comparing India and the West

    Directory of Open Access Journals (Sweden)

    S.N. Balagangadhara

    2008-10-01

    Full Text Available During the last two decades, I have been pursuing an unorthodox way of studying cultural differences, focusing mainly on the Indian and the western cultures. Because I believe that one can answer questions about the circumscription of the words ‘Indian’ and ‘western’ cultures satisfactorily (Balangangadhara, 1994, I will assume their intelligibility in what follows. In this paper, I want to raise a rather intriguing problem about comparing these two cultures. I shall do that without looking at other approaches to the issue and in the form of an argument. In order to come to the point quickly, let me make use of Said’s 'Orientalism.'

  15. 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).

  16. 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.

  17. Forest ownership in comparative law

    Directory of Open Access Journals (Sweden)

    Üstüner Birben

    2015-07-01

    Full Text Available Efficient and sustainable use of forest resources depend on various factors. However, one of the most emphasized and discussed topics among these factors is forest ownership. Comparative law is an important way of analyzing and understanding legal systems of different countries, and identifying different aspects of the current legal systems. This study tries to analyze forest ownership with regard to comparative law. France for the Continental-European legal system, Great Britain for the Anglo-Saxon legal system, and Russia Federation for the Socialist legal system are taken respectively as a base. Thus, how right to ownership is evaluated in different legal systems and what are the main features of that are indicated. As a result, private forest ownership is common in the Continental-European legal system and Anglo-Saxon legal system while state ownership is common in the Socialist legal system. Prevalence of private forest ownership in the Continental-European and the Anglo-Saxon legal systems is also closely related to the previous use rights transferred into right to ownership. In addition, it is concluded regarding the historical process that many changes occurred on forest ownership types without considering differences in legal systems.

  18. Comparing Civilian Support for Terrorism

    Directory of Open Access Journals (Sweden)

    Srobana Bhattacharya

    2017-06-01

    Full Text Available Terrorism is an extreme form of political violence, that is inherently abhorrent in nature. Yet, it continues to attain enough support to continue and survive. The recent proliferation of Islamic State and its ever increasing domestic and international civilian support base urges immediate attention to this question. While most research holds that provision of public goods by terrorist groups is the primary cause for high levels of civilian support, I argue that, terrorist groups are more interested in resource extraction rather than resource provision. Additionally, these studies pay scant attention to existing resource structure, especially territorial and political control to explain terrorist-civilian interaction. This paper emphasizes the bi-directional nature of this interaction – a. perception of civilians by the terrorist group and b. terrorist group’s perception of the civilians. To analyze levels of civilian support for terrorism, I compare fifteen terrorist groups using qualitative comparative analysis and show how territory, political competition, ethnicity, target selection and organizational structure combine to explain conditions that lead terrorist groups to include or exclude civilian population for support. Based on the variance in support networks of terrorist groups, counter-terrorism policies should also differ. High civilian support indicates the need to use non-military methods to decrease the appeal of terrorist groups. However, terrorist groups with more diffused and multiple support structures need more collaborative and coercive measures to intercept all the possible links to the main group.

  19. 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

  20. Comparative toxicity of sodium carbonate peroxyhydrate to freshwater organisms.

    Science.gov (United States)

    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

  1. Comparative transcriptomics in the Triticeae

    Directory of Open Access Journals (Sweden)

    Waugh Robbie

    2009-06-01

    Full Text Available Abstract Background Barley and particularly wheat are two grass species of immense agricultural importance. In spite of polyploidization events within the latter, studies have shown that genotypically and phenotypically these species are very closely related and, indeed, fertile hybrids can be created by interbreeding. The advent of two genome-scale Affymetrix GeneChips now allows studies of the comparison of their transcriptomes. Results We have used the Wheat GeneChip to create a "gene expression atlas" for the wheat transcriptome (cv. Chinese Spring. For this, we chose mRNA from a range of tissues and developmental stages closely mirroring a comparable study carried out for barley (cv. Morex using the Barley1 GeneChip. This, together with large-scale clustering of the probesets from the two GeneChips into "homologous groups", has allowed us to perform a genomic-scale comparative study of expression patterns in these two species. We explore the influence of the polyploidy of wheat on the results obtained with the Wheat GeneChip and quantify the correlation between conservation in gene sequence and gene expression in wheat and barley. In addition, we show how the conservation of expression patterns can be used to elucidate, probeset by probeset, the reliability of the Wheat GeneChip. Conclusion While there are many differences in expression on the level of individual genes and tissues, we demonstrate that the wheat and barley transcriptomes appear highly correlated. This finding is significant not only because given small evolutionary distance between the two species it is widely expected, but also because it demonstrates that it is possible to use the two GeneChips for comparative studies. This is the case even though their probeset composition reflects rather different design principles as well as, of course, the present incomplete knowledge of the gene content of the two species. We also show that, in general, the Wheat GeneChip is not able

  2. Ensembl 2002: accommodating comparative genomics.

    Science.gov (United States)

    Clamp, M; Andrews, D; Barker, D; Bevan, P; Cameron, G; Chen, Y; Clark, L; Cox, T; Cuff, J; Curwen, V; Down, T; Durbin, R; Eyras, E; Gilbert, J; Hammond, M; Hubbard, T; Kasprzyk, A; Keefe, D; Lehvaslaiho, H; Iyer, V; Melsopp, C; Mongin, E; Pettett, R; Potter, S; Rust, A; Schmidt, E; Searle, S; Slater, G; Smith, J; Spooner, W; Stabenau, A; Stalker, J; Stupka, E; Ureta-Vidal, A; Vastrik, I; Birney, E

    2003-01-01

    The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of human, mouse and other genome sequences, available as either an interactive web site or as flat files. Ensembl also integrates manually annotated gene structures from external sources where available. As well as being one of the leading sources of genome annotation, Ensembl is an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements. These range from sequence analysis to data storage and visualisation and installations exist around the world in both companies and at academic sites. With both human and mouse genome sequences available and more vertebrate sequences to follow, many of the recent developments in Ensembl have focusing on developing automatic comparative genome analysis and visualisation.

  3. Challenges in Comparative Oral Epic

    Directory of Open Access Journals (Sweden)

    John Miles Foley

    2012-10-01

    Full Text Available Originally written in 2001 and subsequently published in China, this collaborative essay explores five questions central to comparative oral epic with regard to Mongolian, South Slavic, ancient Greek, and Old English traditions: “What is a poem in oral epic tradition?” “What is a typical scene or theme in oral epic tradition?” “What is a poetic line in oral epic tradition?” “What is a formula in an oral epic tradition?” “What is the register in oral epic poetry?” Now available for the first time in English, this essay reflects a foundational stage of what has become a productive and long-term collaboration between the Center for Studies in Oral Tradition and the Institute of Ethnic Literature of the Chinese Academy of Social Sciences.

  4. Lupus nephritis management guidelines compared.

    Science.gov (United States)

    Wilhelmus, Suzanne; Bajema, Ingeborg M; Bertsias, George K; Boumpas, Dimitrios T; Gordon, Caroline; Lightstone, Liz; Tesar, Vladimir; Jayne, David R

    2016-06-01

    In the past years, many (randomized) trials have been performed comparing the treatment strategies for lupus nephritis. In 2012, these data were incorporated in six different guidelines for treating lupus nephritis. These guidelines are European, American and internationally based, with one separate guideline for children. They offer information on different aspects of the management of lupus nephritis including induction and maintenance treatment of the different histological classes, adjunctive treatment, monitoring of the patient, definitions of response and relapse, indications for (repeat) renal biopsy, and additional challenges such as the presence of vascular complications, the pregnant SLE patient, treatment in children and adolescents and considerations about end-stage renal disease and transplantation. In this review, we summarize the guidelines, determine the common ground between them, highlight the differences and discuss recent literature. © The Author 2015. Published by Oxford University Press on behalf of ERA-EDTA. All rights reserved.

  5. Comparing Methods for Cardiac Output

    DEFF Research Database (Denmark)

    Graeser, Karin; Zemtsovski, Mikhail; Kofoed, Klaus F

    2018-01-01

    of the left ventricular outflow tract. METHODS: The primary aim was a systematic comparison of CO with Doppler-derived 3D TEE and CO by thermodilution in a broad population of patients undergoing cardiac surgery. A subanalysis was performed comparing cross-sectional area by TEE with cardiac computed...... tomography (CT) angiography. Sixty-two patients, scheduled for elective heart surgery, were included; 1 was subsequently excluded for logistic reasons. Inclusion criteria were coronary artery bypass surgery (N = 42) and aortic valve replacement (N = 19). Exclusion criteria were chronic atrial fibrillation......, left ventricular ejection fraction below 0.40 and intracardiac shunts. Nineteen randomly selected patients had a cardiac CT the day before surgery. All images were stored for blinded post hoc analyses, and Bland-Altman plots were used to assess agreement between measurement methods, defined as the bias...

  6. Becoming fit for transnational comparability

    DEFF Research Database (Denmark)

    Krejsler, John Benedicto; Ulf, Olsson; Kenneth, Petersson

    2018-01-01

    . Consequently, Danish teacher education discourse has emerged from a distinctly national vocational seminary tradition, into a modernized university college discourse that increasingly fits the transnational templates of comparability, albeit at a slower pace than her Swedish neighbor. It is often difficult...... of modern nations, if they are to succeed in “an increasingly competitive global race among knowledge economies.” In the case of the Bologna Process, the transformative effects are often rather direct. More often, however, effects touch upon national educational agendas in indirect ways, in terms......This chapter traces how national teacher education policy discourse in Denmark and Sweden is being transformed by opaque, albeit often inclusive, processes in transnational policy forums, such as the Bologna Process, OECD, and EU. This is facilitated by “soft law” surrounding the imagined needs...

  7. Military Retention. A Comparative Outlook

    Directory of Open Access Journals (Sweden)

    Vasile Sminchise

    2016-06-01

    Full Text Available One of the main goals for human resources management structures and for armed forces leaders is to maintain all necessary personnel, both qualitatively and quantitatively for operational needs or for full required capabilities. The retention of military personnel is essential to keep morale and unit readiness and to reduce the costs for recruiting, training, replacement of manpower. Retention rates depend not only on money or other social measures. The goal for retention is to keep in use the most valuable resource that belongs to an organization: the human beings and their knowledge. The aim pf this paper is to provide a comparative analysis of retention measures in various countries based on Research and Technology Organisation report released in 2007 and, thus, provide more examples of retention measures as far as the Romanian military system is concerned.

  8. [Comparative studies of face recognition].

    Science.gov (United States)

    Kawai, Nobuyuki

    2012-07-01

    Every human being is proficient in face recognition. However, the reason for and the manner in which humans have attained such an ability remain unknown. These questions can be best answered-through comparative studies of face recognition in non-human animals. Studies in both primates and non-primates show that not only primates, but also non-primates possess the ability to extract information from their conspecifics and from human experimenters. Neural specialization for face recognition is shared with mammals in distant taxa, suggesting that face recognition evolved earlier than the emergence of mammals. A recent study indicated that a social insect, the golden paper wasp, can distinguish their conspecific faces, whereas a closely related species, which has a less complex social lifestyle with just one queen ruling a nest of underlings, did not show strong face recognition for their conspecifics. Social complexity and the need to differentiate between one another likely led humans to evolve their face recognition abilities.

  9. COMPARATIVE HABITABILITY OF TRANSITING EXOPLANETS

    Energy Technology Data Exchange (ETDEWEB)

    Barnes, Rory; Meadows, Victoria S.; Evans, Nicole, E-mail: rory@astro.washington.edu [Astronomy Department, University of Washington, Box 951580, Seattle, WA 98195 (United States)

    2015-12-01

    Exoplanet habitability is traditionally assessed by comparing a planet’s semimajor axis to the location of its host star’s “habitable zone,” the shell around a star for which Earth-like planets can possess liquid surface water. The Kepler space telescope has discovered numerous planet candidates near the habitable zone, and many more are expected from missions such as K2, TESS, and PLATO. These candidates often require significant follow-up observations for validation, so prioritizing planets for habitability from transit data has become an important aspect of the search for life in the universe. We propose a method to compare transiting planets for their potential to support life based on transit data, stellar properties and previously reported limits on planetary emitted flux. For a planet in radiative equilibrium, the emitted flux increases with eccentricity, but decreases with albedo. As these parameters are often unconstrained, there is an “eccentricity-albedo degeneracy” for the habitability of transiting exoplanets. Our method mitigates this degeneracy, includes a penalty for large-radius planets, uses terrestrial mass–radius relationships, and, when available, constraints on eccentricity to compute a number we call the “habitability index for transiting exoplanets” that represents the relative probability that an exoplanet could support liquid surface water. We calculate it for Kepler objects of interest and find that planets that receive between 60% and 90% of the Earth’s incident radiation, assuming circular orbits, are most likely to be habitable. Finally, we make predictions for the upcoming TESS and James Webb Space Telescope missions.

  10. COMPARATIVE HABITABILITY OF TRANSITING EXOPLANETS

    International Nuclear Information System (INIS)

    Barnes, Rory; Meadows, Victoria S.; Evans, Nicole

    2015-01-01

    Exoplanet habitability is traditionally assessed by comparing a planet’s semimajor axis to the location of its host star’s “habitable zone,” the shell around a star for which Earth-like planets can possess liquid surface water. The Kepler space telescope has discovered numerous planet candidates near the habitable zone, and many more are expected from missions such as K2, TESS, and PLATO. These candidates often require significant follow-up observations for validation, so prioritizing planets for habitability from transit data has become an important aspect of the search for life in the universe. We propose a method to compare transiting planets for their potential to support life based on transit data, stellar properties and previously reported limits on planetary emitted flux. For a planet in radiative equilibrium, the emitted flux increases with eccentricity, but decreases with albedo. As these parameters are often unconstrained, there is an “eccentricity-albedo degeneracy” for the habitability of transiting exoplanets. Our method mitigates this degeneracy, includes a penalty for large-radius planets, uses terrestrial mass–radius relationships, and, when available, constraints on eccentricity to compute a number we call the “habitability index for transiting exoplanets” that represents the relative probability that an exoplanet could support liquid surface water. We calculate it for Kepler objects of interest and find that planets that receive between 60% and 90% of the Earth’s incident radiation, assuming circular orbits, are most likely to be habitable. Finally, we make predictions for the upcoming TESS and James Webb Space Telescope missions

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

    Science.gov (United States)

    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 .

  12. Expanding Comparative Literature into Comparative Sciences Clusters with Neutrosophy and Quad-stage Method

    Directory of Open Access Journals (Sweden)

    Fu Yuhua

    2016-08-01

    Full Text Available By using Neutrosophy and Quad-stage Method, the expansions of comparative literature include: comparative social sciences clusters, comparative natural sciences clusters, comparative interdisciplinary sciences clusters, and so on. Among them, comparative social sciences clusters include: comparative literature, comparative history, comparative philosophy, and so on; comparative natural sciences clusters include: comparative mathematics, comparative physics, comparative chemistry, comparative medicine, comparative biology, and so on.

  13. Comparative cytotoxicity of periodontal bacteria

    International Nuclear Information System (INIS)

    Stevens, R.H.; Hammond, B.F.

    1988-01-01

    The direct cytotoxicity of sonic extracts (SE) from nine periodontal bacteria for human gingival fibroblasts (HGF) was compared. Equivalent dosages (in terms of protein concentration) of SE were used to challenge HGF cultures. The cytotoxic potential of each SE was assessed by its ability to (1) inhibit HGF proliferation, as measured by direct cell counts; (2) inhibit 3H-thymidine incorporation in HGF cultures; or (3) cause morphological alterations of the cells in challenged cultures. The highest concentration (500 micrograms SE protein/ml) of any of the SEs used to challenge the cells was found to be markedly inhibitory to the HGFs by all three of the criteria of cytotoxicity. At the lowest dosage tested (50 micrograms SE protein/ml); only SE from Actinobacillus actinomycetemcomitans, Bacteroides gingivalis, and Fusobacterium nucleatum caused a significant effect (greater than 90% inhibition or overt morphological abnormalities) in the HGFs as determined by any of the criteria employed. SE from Capnocytophaga sputigena, Eikenella corrodens, or Wolinella recta also inhibited cell proliferation and thymidine incorporation at this dosage; however, the degree of inhibition (5-50%) was consistently, clearly less than that of the first group of three organisms named above. The SE of the three other organisms tested (Actinomyces odontolyticus, Bacteroides intermedius, and Streptococcus sanguis) had little or no effect (0-10% inhibition) at this concentration. The data suggest that the outcome of the interaction between bacterial components and normal resident cells of the periodontium is, at least in part, a function of the bacterial species

  14. Sex work: a comparative study.

    Science.gov (United States)

    McCarthy, Bill; Benoit, Cecilia; Jansson, Mikael

    2014-10-01

    Explanations of adult involvement in sex work typically adopt one of two approaches. One perspective highlights a variety of negative experiences in childhood and adolescence, including physical and sexual abuse, family instability, poverty, associations with "pimps" and other exploiters, homelessness, and drug use. An alternative account recognizes that some of these factors may be involved, but underscores the contribution of more immediate circumstances, such as current economic needs, human capital, and employment opportunities. Prior research offers a limited assessment of these contrasting claims: most studies have focused exclusively on people working in the sex industry and they have not assessed the independent effects of life course variables central to these two perspectives. We add to this literature with an analysis that drew on insights from life course and life-span development theories and considered the contributions of factors from childhood, adolescence, and adulthood. Our comparative approach examined predictors of employment in sex work relative to two other low-income service or care work occupations: food and beverage serving and barbering and hairstyling. Using data from a study of almost 600 workers from two cities, one in Canada and the other in the United States, we found that both immediate circumstances and negative experiences from early life are related to current sex work involvement: childhood poverty, abuse, and family instability were independently associated with adult sex work, as were limited education and employment experience, adult drug use, and marital status.

  15. Sonourethrography compared to retrograde urethrography

    International Nuclear Information System (INIS)

    Kim, Jong Chul; Chang, Nam Sik; Park, Cheong Hee; Rhee, Byung Chul; Kong, Jae Chul; Park, Jong Yoon

    1989-01-01

    A total of 15 patients with suspected urethral stricture or fistula underwent conventional retrograde urethrography and following sonourethrography with saline infusion or voiding against Eschmann penile clamp, in Gyeongsang and Chungnam National University Hospital from July, 1989 to June, 1989. The sonographic findings were as diagnostic as the roentgen findings in 12 patients. When the length of the strictures assessed by each imaging modality was compared to measurement at open urothroplasty of 2 patients, sonourethrography was consistently more accurate. Urethroscopy was done in all cases. Sonourethrography using distension technique of the urethra enabled classification of the degree of spongiofibrosis, thus provided the guidance of direct vision internal urethrotomy in 9 patients. In 2 patients, the sonourethrogram identified periurethral tumor and urethral polyp which were not definitely analysed on the retrograde urethrogram. In the patient of posttraumatic postoperative urethrorectal fistula, residual fistuous tract was seen on both examinations. In 1 patient of stricture with severe periurethral scar, urethral stricture recurred after graft. No patient reported significant discomfort during the sonourethrogram. The sonourethrogram provided valuable, dynamic. 3 dimensional information about the luminal and extraluminal anatomy and pathology of the anterior urethra. The new method of sonourethrogram allows for the appropriate decision to be made easier for optimal treatment of urethal stricture, etc, and can be used as a follow up study

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

    Science.gov (United States)

    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.

  17. Comparative pathogenomics of Clostridium tetani.

    Directory of Open Access Journals (Sweden)

    Jonathan E Cohen

    Full Text Available Clostridium tetani and Clostridium botulinum produce two of the most potent neurotoxins known, tetanus neurotoxin and botulinum neurotoxin, respectively. Extensive biochemical and genetic investigation has been devoted to identifying and characterizing various C. botulinum strains. Less effort has been focused on studying C. tetani likely because recently sequenced strains of C. tetani show much less genetic diversity than C. botulinum strains and because widespread vaccination efforts have reduced the public health threat from tetanus. Our aim was to acquire genomic data on the U.S. vaccine strain of C. tetani to better understand its genetic relationship to previously published genomic data from European vaccine strains. We performed high throughput genomic sequence analysis on two wild-type and two vaccine C. tetani strains. Comparative genomic analysis was performed using these and previously published genomic data for seven other C. tetani strains. Our analysis focused on single nucleotide polymorphisms (SNP and four distinct constituents of the mobile genome (mobilome: a hypervariable flagellar glycosylation island region, five conserved bacteriophage insertion regions, variations in three CRISPR (clustered regularly interspaced short palindromic repeats-Cas (CRISPR-associated systems, and a single plasmid. Intact type IA and IB CRISPR/Cas systems were within 10 of 11 strains. A type IIIA CRISPR/Cas system was present in two strains. Phage infection histories derived from CRISPR-Cas sequences indicate C. tetani encounters phages common among commensal gut bacteria and soil-borne organisms consistent with C. tetani distribution in nature. All vaccine strains form a clade distinct from currently sequenced wild type strains when considering variations in these mobile elements. SNP, flagellar glycosylation island, prophage content and CRISPR/Cas phylogenic histories provide tentative evidence suggesting vaccine and wild type strains share a

  18. Comparing records with related chronologies

    Science.gov (United States)

    Bronk Ramsey, Christopher; Albert, Paul; Kearney, Rebecca; Staff, Richard A.

    2016-04-01

    In order to integrate ice, terrestrial and marine records, it is necessary to deal with records on different timescales. These timescales can be grouped into those that use a common fundamental chronometer (such as Uranium-Thorium dating or Radiocarbon) and can also be related to one another where we have chronological tie points such as tephra horizons. More generally we can, through a number of different methodologies, derive relationships between different timescales. A good example of this is the use of cosmogenic isotope production, specifically 10Be and 14C to relate the calibrated radiocarbon timescale to that of the Greenland ice cores. The relationships between different timescales can be mathematically expressed in terms of time-transfer functions. This formalism allows any related record to be considered against any linked timescale with an appropriate associated uncertainty. The prototype INTIMATE chronological database allows records to be viewed and compared in this way and this is now being further developed, both to include a wider range of records and also to provide better connectivity to other databases and chronological tools. These developments will also include new ways to use tephra tie-points to constrain the relationship between timescales directly, without needing to remodel each associated timescale. The database as it stands allows data for particular timeframes to be recalled and plotted against any timescale, or exported in spreadsheet format. New functionality will be added to allow users to work with their own data in a private space and then to publish it when it has been through the peer-review publication process. In order to make the data easier to use for other further analysis and plotting, and with data from other sources, the database will also act as a server to deliver data in a JSON format. The aim of this work is to make the comparison of integrated data much easier for researchers and to ensure that good practice in

  19. Comparative Climatology of Terrestrial Planets

    Science.gov (United States)

    Mackwell, Stephen J.; Simon-Miller, Amy A.; Harder, Jerald W.; Bullock, Mark A.

    to a future volume. Our authors have taken on the task to look at climate on the terrestrial planets in the broadest sense possible — by comparing the atmospheric processes at work on the four terrestrial bodies, Earth, Venus, Mars, and Titan (Titan is included because it hosts many of the common processes), and on terrestrial planets around other stars. These processes include the interactions of shortwave and thermal radiation with the atmosphere, condensation and vaporization of volatiles, atmospheric dynamics, chemistry and aerosol formation, and the role of the surface and interior in the long-term evolution of climate. Chapters herein compare the scientific questions, analysis methods, numerical models, and spacecraft remote sensing experiments of Earth and the other terrestrial planets, emphasizing the underlying commonality of physical processes. We look to the future by identifying objectives for ongoing research and new missions. Through these pages we challenge practicing planetary scientists, and most importantly new students of any age, to find pathways and synergies for advancing the field. In Part I, Foundations, we introduce the fundamental physics of climate on terrestrial planets. Starting with the best studied planet by far, Earth, the first chapters discuss what is known and what is not known about the atmospheres and climates of the terrestrial planets of the solar system and beyond. In Part II, Greenhouse Effect and Atmospheric Dynamics, we focus on the processes that govern atmospheric motion and the role that general circulation models play in our current understanding. In Part III, Clouds and Hazes, we provide an in-depth look at the many effects of clouds and aerosols on planetary climate. Although this is a vigorous area of research in the Earth sciences, and very strongly influences climate modeling, the important role that aerosols and clouds play in the climate of all planets is not yet well constrained. This section is intended to

  20. Comparative pathogenomics of Clostridium tetani.

    Science.gov (United States)

    Cohen, Jonathan E; Wang, Rong; Shen, Rong-Fong; Wu, Wells W; Keller, James E

    2017-01-01

    Clostridium tetani and Clostridium botulinum produce two of the most potent neurotoxins known, tetanus neurotoxin and botulinum neurotoxin, respectively. Extensive biochemical and genetic investigation has been devoted to identifying and characterizing various C. botulinum strains. Less effort has been focused on studying C. tetani likely because recently sequenced strains of C. tetani show much less genetic diversity than C. botulinum strains and because widespread vaccination efforts have reduced the public health threat from tetanus. Our aim was to acquire genomic data on the U.S. vaccine strain of C. tetani to better understand its genetic relationship to previously published genomic data from European vaccine strains. We performed high throughput genomic sequence analysis on two wild-type and two vaccine C. tetani strains. Comparative genomic analysis was performed using these and previously published genomic data for seven other C. tetani strains. Our analysis focused on single nucleotide polymorphisms (SNP) and four distinct constituents of the mobile genome (mobilome): a hypervariable flagellar glycosylation island region, five conserved bacteriophage insertion regions, variations in three CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) systems, and a single plasmid. Intact type IA and IB CRISPR/Cas systems were within 10 of 11 strains. A type IIIA CRISPR/Cas system was present in two strains. Phage infection histories derived from CRISPR-Cas sequences indicate C. tetani encounters phages common among commensal gut bacteria and soil-borne organisms consistent with C. tetani distribution in nature. All vaccine strains form a clade distinct from currently sequenced wild type strains when considering variations in these mobile elements. SNP, flagellar glycosylation island, prophage content and CRISPR/Cas phylogenic histories provide tentative evidence suggesting vaccine and wild type strains share a common ancestor.

  1. Comparative Genomics of Carp Herpesviruses

    Science.gov (United States)

    Kurobe, Tomofumi; Gatherer, Derek; Cunningham, Charles; Korf, Ian; Fukuda, Hideo; Hedrick, Ronald P.; Waltzek, Thomas B.

    2013-01-01

    Three alloherpesviruses are known to cause disease in cyprinid fish: cyprinid herpesviruses 1 and 3 (CyHV1 and CyHV3) in common carp and koi and cyprinid herpesvirus 2 (CyHV2) in goldfish. We have determined the genome sequences of CyHV1 and CyHV2 and compared them with the published CyHV3 sequence. The CyHV1 and CyHV2 genomes are 291,144 and 290,304 bp, respectively, in size, and thus the CyHV3 genome, at 295,146 bp, remains the largest recorded among the herpesviruses. Each of the three genomes consists of a unique region flanked at each terminus by a sizeable direct repeat. The CyHV1, CyHV2, and CyHV3 genomes are predicted to contain 137, 150, and 155 unique, functional protein-coding genes, respectively, of which six, four, and eight, respectively, are duplicated in the terminal repeat. The three viruses share 120 orthologous genes in a largely colinear arrangement, of which up to 55 are also conserved in the other member of the genus Cyprinivirus, anguillid herpesvirus 1. Twelve genes are conserved convincingly in all sequenced alloherpesviruses, and two others are conserved marginally. The reference CyHV3 strain has been reported to contain five fragmented genes that are presumably nonfunctional. The CyHV2 strain has two fragmented genes, and the CyHV1 strain has none. CyHV1, CyHV2, and CyHV3 have five, six, and five families of paralogous genes, respectively. One family unique to CyHV1 is related to cellular JUNB, which encodes a transcription factor involved in oncogenesis. To our knowledge, this is the first time that JUNB-related sequences have been reported in a herpesvirus. PMID:23269803

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

    Directory of Open Access Journals (Sweden)

    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.

  3. Comparing recent uranium supply scenarios

    International Nuclear Information System (INIS)

    Arnold, N.; Gufler, K.

    2014-01-01

    For more than one decade – even after the Fukushima accidents - an increase in global nuclear energy generation capacity is widely expected. At the same time a variety of uranium supply scenarios were published by industry, academics or international organizations, drawing different pictures of future uranium supply. They were created with the background of a uranium market facing several challenges. First an excursion in the uranium market price, in 2007, then reduced nuclear growth expectations after 2011, at least in non-Asian countries, also implying considerable changes to the supply side. For this publication a meta-study was carried out identifying, evaluating and comparing different recent scenarios on the availability of uranium. While there are some differences in the frame conditions (e.g. the expected uranium demand, the time fame, the considered mining projects,..), there are also notable similarities in these scenarios. This concerns long lead times for mine openings as well as the dependence on large mining projects (e.g. Olympic Dam, Cigar Lake). Generally, a decline in production in about 10 years is assumed, and thus the necessity of the timely development of mining projects is pointed out. In addition the omission of uranium from Russian nuclear weapons and the chances of keeping the changes in secondary supplies in balance with primary production have been widely discussed. Here, the production growth in Kazakhstan but also the role of the current market situation are central aspects. As another aspect the possible contribution from unconventional resources is of interest, particularly against the background of rising production costs for conventional resources. Finally, it shall be reflected how well older scenarios were able to map the reality and which trends could or could not be anticipated. It is relevant to identify which aspects in the development of mining capacities are essential for security of supply, and can therefore be regarded

  4. 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.

  5. 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.

  6. 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.

  7. Genome wide characterization of simple sequence repeats in watermelon genome and their application in comparative mapping and genetic diversity analysis.

    Science.gov (United States)

    Zhu, Huayu; Song, Pengyao; Koo, Dal-Hoe; Guo, Luqin; Li, Yanman; Sun, Shouru; Weng, Yiqun; Yang, Luming

    2016-08-05

    Microsatellite markers are one of the most informative and versatile DNA-based markers used in plant genetic research, but their development has traditionally been difficult and costly. The whole genome sequencing with next-generation sequencing (NGS) technologies provides large amounts of sequence data to develop numerous microsatellite markers at whole genome scale. SSR markers have great advantage in cross-species comparisons and allow investigation of karyotype and genome evolution through highly efficient computation approaches such as in silico PCR. Here we described genome wide development and characterization of SSR markers in the watermelon (Citrullus lanatus) genome, which were then use in comparative analysis with two other important crop species in the Cucurbitaceae family: cucumber (Cucumis sativus L.) and melon (Cucumis melo L.). We further applied these markers in evaluating the genetic diversity and population structure in watermelon germplasm collections. A total of 39,523 microsatellite loci were identified from the watermelon draft genome with an overall density of 111 SSRs/Mbp, and 32,869 SSR primers were designed with suitable flanking sequences. The dinucleotide SSRs were the most common type representing 34.09 % of the total SSR loci and the AT-rich motifs were the most abundant in all nucleotide repeat types. In silico PCR analysis identified 832 and 925 SSR markers with each having a single amplicon in the cucumber and melon draft genome, respectively. Comparative analysis with these cross-species SSR markers revealed complicated mosaic patterns of syntenic blocks among the genomes of three species. In addition, genetic diversity analysis of 134 watermelon accessions with 32 highly informative SSR loci placed these lines into two groups with all accessions of C.lanatus var. citorides and three accessions of C. colocynthis clustered in one group and all accessions of C. lanatus var. lanatus and the remaining accessions of C. colocynthis

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

    Science.gov (United States)

    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.

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

    Czech Academy of Sciences Publication Activity Database

    Bjorkman, J.; Švec, David; Kubista, Mikael; Sjöback, R.

    2016-01-01

    Roč. 6, Jan 2016 (2016), s. 4-12 ISSN 2214-7535 R&D Projects: GA ČR GA13-02154S; GA MŠk(CZ) ED1.1.00/02.0109 Institutional support: RVO:86652036 Keywords : RNA integrity * RNA quality * Endogenous RNase resistant marker Subject RIV: EB - Genetics ; Molecular Biology

  10. Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing

    Directory of Open Access Journals (Sweden)

    Luisa W. Hugerth

    2017-09-01

    Full Text Available Microbial ecology as a scientific field is fundamentally driven by technological advance. The past decade's revolution in DNA sequencing cost and throughput has made it possible for most research groups to map microbial community composition in environments of interest. However, the computational and statistical methodology required to analyse this kind of data is often not part of the biologist training. In this review, we give a historical perspective on the use of sequencing data in microbial ecology and restate the current need for this method; but also highlight the major caveats with standard practices for handling these data, from sample collection and library preparation to statistical analysis. Further, we outline the main new analytical tools that have been developed in the past few years to bypass these caveats, as well as highlight the major requirements of common statistical practices and the extent to which they are applicable to microbial data. Besides delving into the meaning of select alpha- and beta-diversity measures, we give special consideration to techniques for finding the main drivers of community dissimilarity and for interaction network construction. While every project design has specific needs, this review should serve as a starting point for considering what options are available.

  11. screening of new isolates of bt and cloning of their dna amplicons

    African Journals Online (AJOL)

    NEMAPPA

    2012-09-18

    Sep 18, 2012 ... Nine new indigenous isolates of Bacillus thuringiensis (Bt) were characterized for their colony type, ... Bt. New gene sequences encoding more active toxins could be ..... Toxicity of a Bacillus thuringiensis israelensis-like strain.

  12. Functional Analysis of Frequent Lung Cancer Amplicons Under Current Genome Annotation

    Science.gov (United States)

    2015-12-01

    Zhang, Z., Wang, T., Winter, D., Keefe , D., Birney, E., Iyer, V. R., Lieb, J. D., Crawford, G. E., Li, G., Sandhu, K. S., Zheng, M., Wang, P., Luo, O...Herrero, J., Johnson, N., Keefe , D., Lukk, M., Luscombe, N. M., Sobral, D., Vaquerizas, J. M., Wilder, S. P., Batzoglou, S., Sidow, A., Hussami, N

  13. Fifteen novel FBN1 mutations causing Marfan syndrome detected by heteroduplex analysis of genomic amplicons

    Energy Technology Data Exchange (ETDEWEB)

    Nijbroek, G.; Sood, S.; McIntosh, I. [John Hopkins Univ. School of Medicine, Baltimore, MD (United States)] [and others

    1995-07-01

    Mutations in the gene encoding fibrillin-1 (FBN1), a component of the extracellular microfibril, cause the Marfan syndrome (MFS). This statement is supported by the observations that the classic Marfan phenotype cosegregates with intragenic and/or flanking marker alleles in all families tested and that a significant number of FBN1 mutations have been identified in affected individuals. We have now devised a method to screen the entire coding sequence and flanking splice junctions of FBN1. On completion for a panel of nine probands with classic MFS, six new mutations were identified that accounted for disease in seven (78%) of nine patients. Nine additional new mutations have been characterized in the early stages of a larger screening project. These 15 mutations were equally distributed throughout the gene and, with one exception, were specific to single families. One-third of mutations created premature termination codons, and 6 of 15 substituted residues with putative significance for calcium finding to epidermal growth factor (EGF)-like domains. Mutations causing severe and rapidly progressive disease that presents in the neonatal period can occur in a larger region of the gene than previously demonstrated, and the nature of the mutation is as important a determinant as its location, in predisposing to this phenotype. 56 refs., 5 figs., 3 tabs.

  14. Genome editing using FACS enrichment of nuclease-expressing cells and indel detection by amplicon analysis

    DEFF Research Database (Denmark)

    Lonowski, Lindsey A; Narimatsu, Yoshiki; Riaz, Anjum

    2017-01-01

    , FACS enrichment of cells expressing nucleases linked to fluorescent proteins can be used to maximize knockout or knock-in editing efficiencies or to balance editing efficiency and toxic/off-target effects. The two methods can be combined to form a pipeline for cell-line editing that facilitates...

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

    KAUST Repository

    Pearman, John K.; Irigoien, Xabier; Carvalho, Susana

    2015-01-01

    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

  16. Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates

    DEFF Research Database (Denmark)

    Froslev, Tobias Guldberg; Kjoller, Rasmus; Bruun, Hans Henrik

    2017-01-01

    by high-throughput sequencing of amplified marker genes. LULU identifies errors by combining sequence similarity and co-occurrence patterns. To validate the LULU method, we use a unique data set of high quality survey data of vascular plants paired with plant ITS2 metabarcoding data of DNA extracted from...

  17. Laboratory Tests of Multiplex Detection of PCR Amplicons Using the Luminex 100 Flow Analyzer

    Energy Technology Data Exchange (ETDEWEB)

    Venkateswaran, K.S.; Nasarabadi, S.; Langlois, R.G.

    2000-05-05

    Lawrence Livermore National Laboratory (LLNL) demonstrated the power of flow cytometry in detecting the biological agents simulants at JFT III. LLNL pioneered in the development of advanced nucleic acid analyzer (ANM) for portable real time identification. Recent advances in flow cytometry provide a means for multiplexed nucleic acid detection and immunoassay of pathogenic microorganisms. We are presently developing multiplexed immunoassays for the simultaneous detection of different simulants. Our goal is to build an integrated instrument for both nucleic acid analysis and immuno detection. In this study we evaluated the Luminex LX 100 for concurrent identification of more than one PCR amplified product. ANAA has real-time Taqman fluorescent detection capability for rapid identification of field samples. However, its multiplexing ability is limited by the combination of available fluorescent labels. Hence integration of ANAA with flow cytometry can give the rapidity of ANAA amplification and the multiplex capability of flow cytometry. Multiplexed flow cytometric analysis is made possible using a set of fluorescent latex microsphere that are individually identified by their red and infrared fluorescence. A green fluorochrome is used as the assay signal. Methods were developed for the identification of specific nucleic acid sequences from Bacillus globigii (Bg), Bacillus thuringensis (Bt) and Erwinia herbicola (Eh). Detection sensitivity using different reporter fluorochromes was tested with the LX 100, and also different assay formats were evaluated for their suitability for rapid testing. A blind laboratory trial was carried out December 22-27, 1999 to evaluate bead assays for multiplex identification of Bg and Bt PCR products. This report summarizes the assay development, fluorochrome comparisons, and the results of the blind trial conducted at LLNL for the laboratory evaluation of the LX 100 flow analyzer.

  18. 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.

  19. 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.

  20. 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.