Full-length high-temperature severe fuel damage test No. 2

International Nuclear Information System (INIS)

Hesson, G.M.; Lombardo, N.J.; Pilger, J.P.; Rausch, W.N.; King, L.L.; Hurley, D.E.; Parchen, L.J.; Panisko, F.E.

1993-09-01

Hazardous conditions associated with performing the Full-Length High- Temperature (FLHT). Severe Fuel Damage Test No. 2 experiment have been analyzed. Major hazards that could cause harm or damage are (1) radioactive fission products, (2) radiation fields, (3) reactivity changes, (4) hydrogen generation, (5) materials at high temperature, (6) steam explosion, and (7) steam pressure pulse. As a result of this analysis, it is concluded that with proper precautions the FLHT- 2 test can be safely conducted

A new strategy for full-length Ebola virus glycoprotein expression in E.coli.

Science.gov (United States)

Zai, Junjie; Yi, Yinhua; Xia, Han; Zhang, Bo; Yuan, Zhiming

2016-12-01

Ebola virus (EBOV) causes severe hemorrhagic fever in humans and non-human primates with high rates of fatality. Glycoprotein (GP) is the only envelope protein of EBOV, which may play a critical role in virus attachment and entry as well as stimulating host protective immune responses. However, the lack of expression of full-length GP in Escherichia coli hinders the further study of its function in viral pathogenesis. In this study, the vp40 gene was fused to the full-length gp gene and cloned into a prokaryotic expression vector. We showed that the VP40-GP and GP-VP40 fusion proteins could be expressed in E.coli at 16 °C. In addition, it was shown that the position of vp40 in the fusion proteins affected the yields of the fusion proteins, with a higher level of production of the fusion protein when vp40 was upstream of gp compared to when it was downstream. The results provide a strategy for the expression of a large quantity of EBOV full-length GP, which is of importance for further analyzing the relationship between the structure and function of GP and developing an antibody for the treatment of EBOV infection.

Full-length cDNA sequences from Rhesus monkey placenta tissue: analysis and utility for comparative mapping

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Lee Sang-Rae

2010-07-01

Full Text Available Abstract Background Rhesus monkeys (Macaca mulatta are widely-used as experimental animals in biomedical research and are closely related to other laboratory macaques, such as cynomolgus monkeys (Macaca fascicularis, and to humans, sharing a last common ancestor from about 25 million years ago. Although rhesus monkeys have been studied extensively under field and laboratory conditions, research has been limited by the lack of genetic resources. The present study generated placenta full-length cDNA libraries, characterized the resulting expressed sequence tags, and described their utility for comparative mapping with human RefSeq mRNA transcripts. Results From rhesus monkey placenta full-length cDNA libraries, 2000 full-length cDNA sequences were determined and 1835 rhesus placenta cDNA sequences longer than 100 bp were collected. These sequences were annotated based on homology to human genes. Homology search against human RefSeq mRNAs revealed that our collection included the sequences of 1462 putative rhesus monkey genes. Moreover, we identified 207 genes containing exon alterations in the coding region and the untranslated region of rhesus monkey transcripts, despite the highly conserved structure of the coding regions. Approximately 10% (187 of all full-length cDNA sequences did not represent any public human RefSeq mRNAs. Intriguingly, two rhesus monkey specific exons derived from the transposable elements of AluYRa2 (SINE family and MER11B (LTR family were also identified. Conclusion The 1835 rhesus monkey placenta full-length cDNA sequences described here could expand genomic resources and information of rhesus monkeys. This increased genomic information will greatly contribute to the development of evolutionary biology and biomedical research.

Full-length high-temperature severe fuel damage test No. 5

International Nuclear Information System (INIS)

Lanning, D.D.; Lombardo, N.J.; Hensley, W.K.; Fitzsimmons, D.E.; Panisko, F.E.; Hartwell, J.K.

1993-09-01

This report describes and presents data from a severe fuel damage test that was conducted in the National Research Universal (NRU) reactor at Chalk River Nuclear Laboratories (CRNL), Ontario, Canada. The test, designated FLHT-5, was the fourth in a series of full-length high-temperature (FLHT) tests on light-water reactor fuel. The tests were designed and performed by staff from the US Department of Energy's Pacific Northwest Laboratory (PNL), operated by Battelle Memorial Institute. The test operation and test results are described in this report. The fuel bundle in the FLHT-5 experiment included 10 unirradiated full-length pressurized-water reactor (PWR) rods, 1 irradiated PWR rod and 1 dummy gamma thermometer. The fuel rods were subjected to a very low coolant flow while operating at low fission power. This caused coolant boilaway, rod dryout and overheating to temperatures above 2600 K, severe fuel rod damage, hydrogen generation, and fission product release. The test assembly and its effluent path were extensively instrumented to record temperatures, pressures, flow rates, hydrogen evolution, and fission product release during the boilaway/heatup transient. Post-test gamma scanning of the upper plenum indicated significant iodine and cesium release and deposition. Both stack gas activity and on-line gamma spectrometer data indicated significant (∼50%) release of noble fission gases. Post-test visual examination of one side of the fuel bundle revealed no massive relocation and flow blockage; however, rundown of molten cladding was evident

Pulp regeneration in a full-length human tooth root using a hierarchical nanofibrous microsphere system.

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Li, Xiangwei; Ma, Chi; Xie, Xiaohua; Sun, Hongchen; Liu, Xiaohua

2016-04-15

While pulp regeneration using tissue engineering strategy has been explored for over a decade, successful regeneration of pulp tissues in a full-length human root with a one-end seal that truly simulates clinical endodontic treatment has not been achieved. To address this challenge, we designed and synthesized a unique hierarchical growth factor-loaded nanofibrous microsphere scaffolding system. In this system, vascular endothelial growth factor (VEGF) binds with heparin and is encapsulated in heparin-conjugated gelatin nanospheres, which are further immobilized in the nanofibers of an injectable poly(l-lactic acid) (PLLA) microsphere. This hierarchical microsphere system not only protects the VEGF from denaturation and degradation, but also provides excellent control of its sustained release. In addition, the nanofibrous PLLA microsphere integrates the extracellular matrix-mimicking architecture with a highly porous injectable form, efficiently accommodating dental pulp stem cells (DPSCs) and supporting their proliferation and pulp tissue formation. Our in vivo study showed the successful regeneration of pulp-like tissues that fulfilled the entire apical and middle thirds and reached the coronal third of the full-length root canal. In addition, a large number of blood vessels were regenerated throughout the canal. For the first time, our work demonstrates the success of pulp tissue regeneration in a full-length root canal, making it a significant step toward regenerative endodontics. The regeneration of pulp tissues in a full-length tooth root canal has been one of the greatest challenges in the field of regenerative endodontics, and one of the biggest barriers for its clinical application. In this study, we developed a unique approach to tackle this challenge, and for the first time, we successfully regenerated living pulp tissues in a full-length root canal, making it a significant step toward regenerative endodontics. This study will make positive scientific

Full-length genomic characterization and molecular evolution of canine parvovirus in China.

Science.gov (United States)

Zhou, Ling; Tang, Qinghai; Shi, Lijun; Kong, Miaomiao; Liang, Lin; Mao, Qianqian; Bu, Bin; Yao, Lunguang; Zhao, Kai; Cui, Shangjin; Leal, Élcio

2016-06-01

Canine parvovirus type 2 (CPV-2) can cause acute haemorrhagic enteritis in dogs and myocarditis in puppies. This disease has become one of the most serious infectious diseases of dogs. During 2014 in China, there were many cases of acute infectious diarrhoea in dogs. Some faecal samples were negative for the CPV-2 antigen based on a colloidal gold test strip but were positive based on PCR, and a viral strain was isolated from one such sample. The cytopathic effect on susceptible cells and the results of the immunoperoxidase monolayer assay, PCR, and sequencing indicated that the pathogen was CPV-2. The strain was named CPV-NY-14, and the full-length genome was sequenced and analysed. A maximum likelihood tree was constructed using the full-length genome and all available CPV-2 genomes. New strains have replaced the original strain in Taiwan and Italy, although the CPV-2a strain is still predominant there. However, CPV-2a still causes many cases of acute infectious diarrhoea in dogs in China.

Scalable production in human cells and biochemical characterization of full-length normal and mutant huntingtin.

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Bin Huang

Full Text Available Huntingtin (Htt is a 350 kD intracellular protein, ubiquitously expressed and mainly localized in the cytoplasm. Huntington's disease (HD is caused by a CAG triplet amplification in exon 1 of the corresponding gene resulting in a polyglutamine (polyQ expansion at the N-terminus of Htt. Production of full-length Htt has been difficult in the past and so far a scalable system or process has not been established for recombinant production of Htt in human cells. The ability to produce Htt in milligram quantities would be a prerequisite for many biochemical and biophysical studies aiming in a better understanding of Htt function under physiological conditions and in case of mutation and disease. For scalable production of full-length normal (17Q and mutant (46Q and 128Q Htt we have established two different systems, the first based on doxycycline-inducible Htt expression in stable cell lines, the second on "gutless" adenovirus mediated gene transfer. Purified material has then been used for biochemical characterization of full-length Htt. Posttranslational modifications (PTMs were determined and several new phosphorylation sites were identified. Nearly all PTMs in full-length Htt localized to areas outside of predicted alpha-solenoid protein regions. In all detected N-terminal peptides methionine as the first amino acid was missing and the second, alanine, was found to be acetylated. Differences in secondary structure between normal and mutant Htt, a helix-rich protein, were not observed in our study. Purified Htt tends to form dimers and higher order oligomers, thus resembling the situation observed with N-terminal fragments, although the mechanism of oligomer formation may be different.

Evaluation of full-length, cleaved and nitrosylated serum surfactant protein D as biomarkers for COPD

DEFF Research Database (Denmark)

Duvoix, Annelyse; Miranda, Elena; Perez, Juan

2011-01-01

. Serum levels of SP-D are raised in individuals with COPD but there is no correlation between the serum level of SP-D and the severity of airflow obstruction. Serum SP-D is present in different forms that may have more utility as a biomarker for COPD. We report here the development of new monoclonal...... antibodies to full length and cleaved SP-D. We have assessed these and existing antibodies in 98 individuals with COPD recruited to the Evaluation of COPD Longitudinally to Identify Predictive Surrogate Endpoints (ECLIPSE) cohort. Our data show that neither monoclonal antibodies to full length nor cleaved SP...

Insertion of Introns: A Strategy to Facilitate Assembly of Infectious Full Length Clones

DEFF Research Database (Denmark)

Johansen, Ida Elisabeth; Lund, Ole Søgaard

2008-01-01

Some DNA fragments are difficult to clone in Escherichia coli by standard methods. It has been speculated that unintended transcription and translation result in expression of proteins that are toxic to the bacteria. This problem is frequently observed during assembly of infectious full-length vi...

Impaired heat shock response in cells expressing full-length polyglutamine-expanded huntingtin.

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Sidhartha M Chafekar

Full Text Available The molecular mechanisms by which polyglutamine (polyQ-expanded huntingtin (Htt causes neurodegeneration in Huntington's disease (HD remain unclear. The malfunction of cellular proteostasis has been suggested as central in HD pathogenesis and also as a target of therapeutic interventions for the treatment of HD. We present results that offer a previously unexplored perspective regarding impaired proteostasis in HD. We find that, under non-stress conditions, the proteostatic capacity of cells expressing full length polyQ-expanded Htt is adequate. Yet, under stress conditions, the presence of polyQ-expanded Htt impairs the heat shock response, a key component of cellular proteostasis. This impaired heat shock response results in a reduced capacity to withstand the damage caused by cellular stress. We demonstrate that in cells expressing polyQ-expanded Htt the levels of heat shock transcription factor 1 (HSF1 are reduced, and, as a consequence, these cells have an impaired a heat shock response. Also, we found reduced HSF1 and HSP70 levels in the striata of HD knock-in mice when compared to wild-type mice. Our results suggests that full length, non-aggregated polyQ-expanded Htt blocks the effective induction of the heat shock response under stress conditions and may thus trigger the accumulation of cellular damage during the course of HD pathogenesis.

Performance of initial full-length RHIC [Relativistic Heavy Ion Collider] dipoles

International Nuclear Information System (INIS)

Dahl, P.; Cottingham, J.; Garber, M.

1987-01-01

The first four full-length (9.7 m) R and D dipoles for the proposed Relativistic Heavy Ion Collider (RHIC) have been successfully tested. The magnets reached a quench plateau of approximately 4.5 T with very reasonable training - a field level comfortably above the design field of 3.45 T required for operation with beams of 100 GeV/amu gold nuclei. Measured field multipoles are considered to be quite acceptable for this series of R and D magnets

XenDB: Full length cDNA prediction and cross species mapping in Xenopus laevis

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Giegerich Robert

2005-09-01

Full Text Available Abstract Background Research using the model system Xenopus laevis has provided critical insights into the mechanisms of early vertebrate development and cell biology. Large scale sequencing efforts have provided an increasingly important resource for researchers. To provide full advantage of the available sequence, we have analyzed 350,468 Xenopus laevis Expressed Sequence Tags (ESTs both to identify full length protein encoding sequences and to develop a unique database system to support comparative approaches between X. laevis and other model systems. Description Using a suffix array based clustering approach, we have identified 25,971 clusters and 40,877 singleton sequences. Generation of a consensus sequence for each cluster resulted in 31,353 tentative contig and 4,801 singleton sequences. Using both BLASTX and FASTY comparison to five model organisms and the NR protein database, more than 15,000 sequences are predicted to encode full length proteins and these have been matched to publicly available IMAGE clones when available. Each sequence has been compared to the KOG database and ~67% of the sequences have been assigned a putative functional category. Based on sequence homology to mouse and human, putative GO annotations have been determined. Conclusion The results of the analysis have been stored in a publicly available database XenDB http://bibiserv.techfak.uni-bielefeld.de/xendb/. A unique capability of the database is the ability to batch upload cross species queries to identify potential Xenopus homologues and their associated full length clones. Examples are provided including mapping of microarray results and application of 'in silico' analysis. The ability to quickly translate the results of various species into 'Xenopus-centric' information should greatly enhance comparative embryological approaches. Supplementary material can be found at http://bibiserv.techfak.uni-bielefeld.de/xendb/.

Full-length Dysferlin Transfer by the Hyperactive Sleeping Beauty Transposase Restores Dysferlin-deficient Muscle

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Helena Escobar

2016-01-01

Full Text Available Dysferlin-deficient muscular dystrophy is a progressive disease characterized by muscle weakness and wasting for which there is no treatment. It is caused by mutations in DYSF, a large, multiexonic gene that forms a coding sequence of 6.2 kb. Sleeping Beauty (SB transposon is a nonviral gene transfer vector, already used in clinical trials. The hyperactive SB system consists of a transposon DNA sequence and a transposase protein, SB100X, that can integrate DNA over 10 kb into the target genome. We constructed an SB transposon-based vector to deliver full-length human DYSF cDNA into dysferlin-deficient H2K A/J myoblasts. We demonstrate proper dysferlin expression as well as highly efficient engraftment (>1,100 donor-derived fibers of the engineered myoblasts in the skeletal muscle of dysferlin- and immunodeficient B6. Cg-Dysfprmd Prkdcscid/J (Scid/BLA/J mice. Nonviral gene delivery of full-length human dysferlin into muscle cells, along with a successful and efficient transplantation into skeletal muscle are important advances towards successful gene therapy of dysferlin-deficient muscular dystrophy.

Species-Specific Expression of Full-Length and Alternatively Spliced Variant Forms of CDK5RAP2.

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John S Y Park

Full Text Available CDK5RAP2 is one of the primary microcephaly genes that are associated with reduced brain size and mental retardation. We have previously shown that human CDK5RAP2 exists as a full-length form (hCDK5RAP2 or an alternatively spliced variant form (hCDK5RAP2-V1 that is lacking exon 32. The equivalent of hCDK5RAP2-V1 has been reported in rat and mouse but the presence of full-length equivalent hCDK5RAP2 in rat and mouse has not been examined. Here, we demonstrate that rat expresses both a full length and an alternatively spliced variant form of CDK5RAP2 that are equivalent to our previously reported hCDK5RAP2 and hCDK5RAP2-V1, repectively. However, mouse expresses only one form of CDK5RAP2 that is equivalent to the human and rat alternatively spliced variant forms. Knowledge of this expression of different forms of CDK5RAP2 in human, rat and mouse is essential in selecting the appropriate model for studies of CDK5RAP2 and primary microcephaly but our findings further indicate the evolutionary divergence of mouse from the human and rat species.

Highly efficient full-length hepatitis C virus genotype 1 (strain TN) infectious culture system

DEFF Research Database (Denmark)

Li, Yi-Ping; Ramirez, Santseharay; Jensen, Sanne B

2012-01-01

Chronic infection with hepatitis C virus (HCV) is an important cause of end stage liver disease worldwide. In the United States, most HCV-related disease is associated with genotype 1 infection, which remains difficult to treat. Drug and vaccine development was hampered by inability to culture...... full-length TN infection dose-dependently. Given the unique importance of genotype 1 for pathogenesis, this infectious 1a culture system represents an important advance in HCV research. The approach used and the mutations identified might permit culture development for other HCV isolates, thus......) culture systems in Huh7.5 cells. Here, we developed a highly efficient genotype 1a (strain TN) full-length culture system. We initially found that the LSG substitutions conferred viability to an intergenotypic recombinant composed of TN 5' untranslated region (5'UTR)-NS5A and JFH1 NS5B-3'UTR; recovered...

Purification and Fibrillation of Full-Length Recombinant PrP.

Science.gov (United States)

Makarava, Natallia; Savtchenko, Regina; Baskakov, Ilia V

2017-01-01

Misfolding and aggregation of prion protein are related to several neurodegenerative diseases in humans such as Creutzfeldt-Jakob disease, fatal familial insomnia, and Gerstmann-Straussler-Scheinker disease. A growing number of applications in the prion field including assays for detection of PrP Sc and methods for production of PrP Sc de novo require recombinant prion protein (PrP) of high purity and quality. Here, we report an experimental procedure for expression and purification of full-length mammalian prion protein. This protocol has been proved to yield PrP of extremely high purity that lacks PrP adducts, oxidative modifications, or truncation, which is typically generated as a result of spontaneous oxidation or degradation. We also describe methods for preparation of amyloid fibrils from recombinant PrP in vitro. Recombinant PrP fibrils can be used as a noninfectious synthetic surrogate of PrP Sc for development of prion diagnostics including generation of PrP Sc -specific antibody.

Full-length mRNA sequencing uncovers a widespread coupling between transcription initiation and mRNA processing.

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Anvar, Seyed Yahya; Allard, Guy; Tseng, Elizabeth; Sheynkman, Gloria M; de Klerk, Eleonora; Vermaat, Martijn; Yin, Raymund H; Johansson, Hans E; Ariyurek, Yavuz; den Dunnen, Johan T; Turner, Stephen W; 't Hoen, Peter A C

2018-03-29

The multifaceted control of gene expression requires tight coordination of regulatory mechanisms at transcriptional and post-transcriptional level. Here, we studied the interdependence of transcription initiation, splicing and polyadenylation events on single mRNA molecules by full-length mRNA sequencing. In MCF-7 breast cancer cells, we find 2700 genes with interdependent alternative transcription initiation, splicing and polyadenylation events, both in proximal and distant parts of mRNA molecules, including examples of coupling between transcription start sites and polyadenylation sites. The analysis of three human primary tissues (brain, heart and liver) reveals similar patterns of interdependency between transcription initiation and mRNA processing events. We predict thousands of novel open reading frames from full-length mRNA sequences and obtained evidence for their translation by shotgun proteomics. The mapping database rescues 358 previously unassigned peptides and improves the assignment of others. By recognizing sample-specific amino-acid changes and novel splicing patterns, full-length mRNA sequencing improves proteogenomics analysis of MCF-7 cells. Our findings demonstrate that our understanding of transcriptome complexity is far from complete and provides a basis to reveal largely unresolved mechanisms that coordinate transcription initiation and mRNA processing.

Non-destructive testing of full-length bonded rock bolts based on HHT signal analysis

Science.gov (United States)

Shi, Z. M.; Liu, L.; Peng, M.; Liu, C. C.; Tao, F. J.; Liu, C. S.

2018-04-01

Full-length bonded rock bolts are commonly used in mining, tunneling and slope engineering because of their simple design and resistance to corrosion. However, the length of a rock bolt and grouting quality do not often meet the required design standards in practice because of the concealment and complexity of bolt construction. Non-destructive testing is preferred when testing a rock bolt's quality because of the convenience, low cost and wide detection range. In this paper, a signal analysis method for the non-destructive sound wave testing of full-length bonded rock bolts is presented, which is based on the Hilbert-Huang transform (HHT). First, we introduce the HHT analysis method to calculate the bolt length and identify defect locations based on sound wave reflection test signals, which includes decomposing the test signal via empirical mode decomposition (EMD), selecting the intrinsic mode functions (IMF) using the Pearson Correlation Index (PCI) and calculating the instantaneous phase and frequency via the Hilbert transform (HT). Second, six model tests are conducted using different grouting defects and bolt protruding lengths to verify the effectiveness of the HHT analysis method. Lastly, the influence of the bolt protruding length on the test signal, identification of multiple reflections from defects, bolt end and protruding end, and mode mixing from EMD are discussed. The HHT analysis method can identify the bolt length and grouting defect locations from signals that contain noise at multiple reflected interfaces. The reflection from the long protruding end creates an irregular test signal with many frequency peaks on the spectrum. The reflections from defects barely change the original signal because they are low energy, which cannot be adequately resolved using existing methods. The HHT analysis method can identify reflections from the long protruding end of the bolt and multiple reflections from grouting defects based on mutations in the instantaneous

Cost-effective sequencing of full-length cDNA clones powered by a de novo-reference hybrid assembly.

Science.gov (United States)

Kuroshu, Reginaldo M; Watanabe, Junichi; Sugano, Sumio; Morishita, Shinichi; Suzuki, Yutaka; Kasahara, Masahiro

2010-05-07

Sequencing full-length cDNA clones is important to determine gene structures including alternative splice forms, and provides valuable resources for experimental analyses to reveal the biological functions of coded proteins. However, previous approaches for sequencing cDNA clones were expensive or time-consuming, and therefore, a fast and efficient sequencing approach was demanded. We developed a program, MuSICA 2, that assembles millions of short (36-nucleotide) reads collected from a single flow cell lane of Illumina Genome Analyzer to shotgun-sequence approximately 800 human full-length cDNA clones. MuSICA 2 performs a hybrid assembly in which an external de novo assembler is run first and the result is then improved by reference alignment of shotgun reads. We compared the MuSICA 2 assembly with 200 pooled full-length cDNA clones finished independently by the conventional primer-walking using Sanger sequencers. The exon-intron structure of the coding sequence was correct for more than 95% of the clones with coding sequence annotation when we excluded cDNA clones insufficiently represented in the shotgun library due to PCR failure (42 out of 200 clones excluded), and the nucleotide-level accuracy of coding sequences of those correct clones was over 99.99%. We also applied MuSICA 2 to full-length cDNA clones from Toxoplasma gondii, to confirm that its ability was competent even for non-human species. The entire sequencing and shotgun assembly takes less than 1 week and the consumables cost only approximately US$3 per clone, demonstrating a significant advantage over previous approaches.

Sequencing, mapping, and analysis of 27,455 maize full-length cDNAs.

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Carol Soderlund

2009-11-01

Full Text Available Full-length cDNA (FLcDNA sequencing establishes the precise primary structure of individual gene transcripts. From two libraries representing 27 B73 tissues and abiotic stress treatments, 27,455 high-quality FLcDNAs were sequenced. The average transcript length was 1.44 kb including 218 bases and 321 bases of 5' and 3' UTR, respectively, with 8.6% of the FLcDNAs encoding predicted proteins of fewer than 100 amino acids. Approximately 94% of the FLcDNAs were stringently mapped to the maize genome. Although nearly two-thirds of this genome is composed of transposable elements (TEs, only 5.6% of the FLcDNAs contained TE sequences in coding or UTR regions. Approximately 7.2% of the FLcDNAs are putative transcription factors, suggesting that rare transcripts are well-enriched in our FLcDNA set. Protein similarity searching identified 1,737 maize transcripts not present in rice, sorghum, Arabidopsis, or poplar annotated genes. A strict FLcDNA assembly generated 24,467 non-redundant sequences, of which 88% have non-maize protein matches. The FLcDNAs were also assembled with 41,759 FLcDNAs in GenBank from other projects, where semi-strict parameters were used to identify 13,368 potentially unique non-redundant sequences from this project. The libraries, ESTs, and FLcDNA sequences produced from this project are publicly available. The annotated EST and FLcDNA assemblies are available through the maize FLcDNA web resource (www.maizecdna.org.

The ability to form full-length intron RNA circles is a general property of nuclear group I introns

DEFF Research Database (Denmark)

Nielsen, Henrik; Fiskaa, Tonje; Birgisdottir, Asa Birna

2003-01-01

at the expense of the host. The circularization pathway has distinct structural requirements that differ from those of splicing and appears to be specifically suppressed in vivo. The ability to form full-length circles is found in all types of nuclear group I introns, including those from the Tetrahymena...... ribosomal DNA. The biological function of the full-length circles is not known, but the fact that the circles contain the entire genetic information of the intron suggests a role in intron mobility....

Novel full-length major histocompatibility complex class I allele discovery and haplotype definition in pig-tailed macaques.

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Semler, Matthew R; Wiseman, Roger W; Karl, Julie A; Graham, Michael E; Gieger, Samantha M; O'Connor, David H

2017-11-13

Pig-tailed macaques (Macaca nemestrina, Mane) are important models for human immunodeficiency virus (HIV) studies. Their infectability with minimally modified HIV makes them a uniquely valuable animal model to mimic human infection with HIV and progression to acquired immunodeficiency syndrome (AIDS). However, variation in the pig-tailed macaque major histocompatibility complex (MHC) and the impact of individual transcripts on the pathogenesis of HIV and other infectious diseases is understudied compared to that of rhesus and cynomolgus macaques. In this study, we used Pacific Biosciences single-molecule real-time circular consensus sequencing to describe full-length MHC class I (MHC-I) transcripts for 194 pig-tailed macaques from three breeding centers. We then used the full-length sequences to infer Mane-A and Mane-B haplotypes containing groups of MHC-I transcripts that co-segregate due to physical linkage. In total, we characterized full-length open reading frames (ORFs) for 313 Mane-A, Mane-B, and Mane-I sequences that defined 86 Mane-A and 106 Mane-B MHC-I haplotypes. Pacific Biosciences technology allows us to resolve these Mane-A and Mane-B haplotypes to the level of synonymous allelic variants. The newly defined haplotypes and transcript sequences containing full-length ORFs provide an important resource for infectious disease researchers as certain MHC haplotypes have been shown to provide exceptional control of simian immunodeficiency virus (SIV) replication and prevention of AIDS-like disease in nonhuman primates. The increased allelic resolution provided by Pacific Biosciences sequencing also benefits transplant research by allowing researchers to more specifically match haplotypes between donors and recipients to the level of nonsynonymous allelic variation, thus reducing the risk of graft-versus-host disease.

High yield purification of full-length functional hERG K+ channels produced in Saccharomyces cerevisiae

DEFF Research Database (Denmark)

Molbaek, Karen; Scharff-Poulsen, Peter; Hélix-Nielsen, Claus

2015-01-01

knowledge this is the first reported high-yield production and purification of full length, tetrameric and functional hERG. This significant breakthrough will be paramount in obtaining hERG crystal structures, and in establishment of new high-throughput hERG drug safety screening assays....

Evidence for a Complex Mosaic Genome Pattern in a Full-length Hepatitis C Virus Sequence

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R.S. Ross

2008-01-01

Full Text Available The genome of the hepatitis C virus (HCV exhibits a high genetic variability. This remarkable heterogeneity is mainly attributed to the gradual accumulation of mutational changes, whereas the contribution of recombination events to the evolution of HCV remains controversial so far. While performing phylogenetic analyses including a large number of sequences deposited in the GenBank, we encountered a full-length HCV sequence (AY651061 that showed evidence for inter-subtype recombination and was, therefore, subjected to a detailed analysis of its molecular structure. The obtained results indicated that AY651061 does not represent a “simple” HCV 1c isolate, but a complex 1a/1c mosaic genome, showing five putative breakpoints in the core to NS3 regions. To our knowledge, this is the first report on a mosaic HCV full- length sequence with multiple breakpoints. The molecular structure of AY651061 is reminiscent of complex homologous recombinant variants occurring among other members of the flaviviridae family, e.g. GB virus C, dengue virus, and Japanese encephalitis virus. Our finding of a mosaic HCV sequence may have important implications for many fields of current HCV research which merit careful consideration.

dsRNA binding characterization of full length recombinant wild type and mutants Zaire ebolavirus VP35.

Science.gov (United States)

Zinzula, Luca; Esposito, Francesca; Pala, Daniela; Tramontano, Enzo

2012-03-01

The Ebola viruses (EBOVs) VP35 protein is a multifunctional major virulence factor involved in EBOVs replication and evasion of the host immune system. EBOV VP35 is an essential component of the viral RNA polymerase, it is a key participant of the nucleocapsid assembly and it inhibits the innate immune response by antagonizing RIG-I like receptors through its dsRNA binding function and, hence, by suppressing the host type I interferon (IFN) production. Insights into the VP35 dsRNA recognition have been recently revealed by structural and functional analysis performed on its C-terminus protein. We report the biochemical characterization of the Zaire ebolavirus (ZEBOV) full-length recombinant VP35 (rVP35)-dsRNA binding function. We established a novel in vitro magnetic dsRNA binding pull down assay, determined the rVP35 optimal dsRNA binding parameters, measured the rVP35 equilibrium dissociation constant for heterologous in vitro transcribed dsRNA of different length and short synthetic dsRNA of 8bp, and validated the assay for compound screening by assessing the inhibitory ability of auryntricarboxylic acid (IC(50) value of 50μg/mL). Furthermore, we compared the dsRNA binding properties of full length wt rVP35 with those of R305A, K309A and R312A rVP35 mutants, which were previously reported to be defective in dsRNA binding-mediated IFN inhibition, showing that the latter have measurably increased K(d) values for dsRNA binding and modified migration patterns in mobility shift assays with respect to wt rVP35. Overall, these results provide the first characterization of the full-length wt and mutants VP35-dsRNA binding functions. Copyright © 2012 Elsevier B.V. All rights reserved.

Quench start localization in full-length SSC R ampersand D dipoles

International Nuclear Information System (INIS)

Devred, A.; Chapman, M.; Cortella, J.; Desportes, A.; Kaugerts, J.; Kirk, T.; Mirk, K.; Schermer, R.; Tompkins, J.C.; Turner, J.; Bleadon, M.; Brown, B.C.; Hanft, R.; Kuchnir, M.; Lamm, M.; Mantsch, P.; Mazur, P.O.; Orris, D.; Peoples, J.; Strait, J.; Tool, G.; Caspi, S.; Gilbert, W.; Meuser, R.; Peters, C.; Rechen, J.; Royet, J.; Scanlan, R.; Taylor, C.; Zbasnik, J.

1989-04-01

Full-length SSC R ampersand D dipole magnets instrumented with four voltage taps on each turn of the inner quarter coils have been tested. These voltage taps enable accurate location of the point at which the quenches start and detailed studies of quench development in the coil. Attention here is focused on localizing the quench source. After recalling the basic mechanism of a quench (why it occurs and how it propagates), the method of quench origin analysis is described: the quench propagation velocity on the turn where the quench occurs is calculated, and the quench location is then verified by reiterating the analysis on the adjacent turns. Last, the velocity value, which appears to be higher than previously measured, is discussed

Characterization of full-length sequenced cDNA inserts (FLIcs from Atlantic salmon (Salmo salar

Directory of Open Access Journals (Sweden)

Lunner Sigbjørn

2009-10-01

Full Text Available Abstract Background Sequencing of the Atlantic salmon genome is now being planned by an international research consortium. Full-length sequenced inserts from cDNAs (FLIcs are an important tool for correct annotation and clustering of the genomic sequence in any species. The large amount of highly similar duplicate sequences caused by the relatively recent genome duplication in the salmonid ancestor represents a particular challenge for the genome project. FLIcs will therefore be an extremely useful resource for the Atlantic salmon sequencing project. In addition to be helpful in order to distinguish between duplicate genome regions and in determining correct gene structures, FLIcs are an important resource for functional genomic studies and for investigation of regulatory elements controlling gene expression. In contrast to the large number of ESTs available, including the ESTs from 23 developmental and tissue specific cDNA libraries contributed by the Salmon Genome Project (SGP, the number of sequences where the full-length of the cDNA insert has been determined has been small. Results High quality full-length insert sequences from 560 pre-smolt white muscle tissue specific cDNAs were generated, accession numbers [GenBank: BT043497 - BT044056]. Five hundred and ten (91% of the transcripts were annotated using Gene Ontology (GO terms and 440 of the FLIcs are likely to contain a complete coding sequence (cCDS. The sequence information was used to identify putative paralogs, characterize salmon Kozak motifs, polyadenylation signal variation and to identify motifs likely to be involved in the regulation of particular genes. Finally, conserved 7-mers in the 3'UTRs were identified, of which some were identical to miRNA target sequences. Conclusion This paper describes the first Atlantic salmon FLIcs from a tissue and developmental stage specific cDNA library. We have demonstrated that many FLIcs contained a complete coding sequence (cCDS. This

The full-length form of the Drosophila amyloid precursor protein is involved in memory formation.

Science.gov (United States)

Bourdet, Isabelle; Preat, Thomas; Goguel, Valérie

2015-01-21

The APP plays a central role in AD, a pathology that first manifests as a memory decline. Understanding the role of APP in normal cognition is fundamental in understanding the progression of AD, and mammalian studies have pointed to a role of secreted APPα in memory. In Drosophila, we recently showed that APPL, the fly APP ortholog, is required for associative memory. In the present study, we aimed to characterize which form of APPL is involved in this process. We show that expression of a secreted-APPL form in the mushroom bodies, the center for olfactory memory, is able to rescue the memory deficit caused by APPL partial loss of function. We next assessed the impact on memory of the Drosophila α-secretase kuzbanian (KUZ), the enzyme initiating the nonamyloidogenic pathway that produces secreted APPLα. Strikingly, KUZ overexpression not only failed to rescue the memory deficit caused by APPL loss of function, it exacerbated this deficit. We further show that in addition to an increase in secreted-APPL forms, KUZ overexpression caused a decrease of membrane-bound full-length species that could explain the memory deficit. Indeed, we observed that transient expression of a constitutive membrane-bound mutant APPL form is sufficient to rescue the memory deficit caused by APPL reduction, revealing for the first time a role of full-length APPL in memory formation. Our data demonstrate that, in addition to secreted APPL, the noncleaved form is involved in memory, raising the possibility that secreted and full-length APPL act together in memory processes. Copyright © 2015 the authors 0270-6474/15/351043-09$15.00/0.

Near Full-Length Identification of a Novel HIV-1 CRF01_AE/B/C Recombinant in Northern Myanmar.

Science.gov (United States)

Zhou, Yan-Heng; Chen, Xin; Liang, Yue-Bo; Pang, Wei; Qin, Wei-Hong; Zhang, Chiyu; Zheng, Yong-Tang

2015-08-01

The Myanmar-China border appears to be the "hot spot" region for the occurrence of HIV-1 recombination. The majority of the previous analyses of HIV-1 recombination were based on partial genomic sequences, which obviously cannot reflect the reality of the genetic diversity of HIV-1 in this area well. Here, we present a near full-length characterization of a novel HIV-1 CRF01_AE/B/C recombinant isolated from a long-distance truck driver in Northern Myanmar. It is the first description of a near full-length genomic sequence in Myanmar since 2003, and might be one of the most complicated HIV-1 chimeras ever detected in Myanmar, containing four CRF01_AE, six B segments, and five C segments separated by 14 breakpoints throughout its genome. The discovery and characterization of this new CRF01_AE/B/C recombinant indicate that intersubtype recombination is ongoing in Myanmar, continuously generating new forms of HIV-1. More work based on near full-length sequence analyses is urgently needed to better understand the genetic diversity of HIV-1 in these regions.

Pharmacological efficacy of anti-IL-1β scFv, Fab and full-length antibodies in treatment of rheumatoid arthritis.

Science.gov (United States)

Qi, Jianying; Ye, Xianlong; Ren, Guiping; Kan, Fangming; Zhang, Yu; Guo, Mo; Zhang, Zhiyi; Li, Deshan

2014-02-01

Rheumatoid arthritis (RA) is a chronic autoimmune inflammatory disease that mainly causes the synovial joint inflammation and cartilage destruction. Interleukin-1β (IL-1β) is an important proinflammatory cytokine involved in the pathogenesis of RA. In this study, we constructed and expressed anti-IL-1β-full-length antibody in CHO-K1-SV, anti-IL-1β-Fab and anti-IL-1β-scFv in Rosetta. We compared the therapeutic efficacy of three anti-IL-1β antibodies for CIA mice. Mice with CIA were subcutaneously injected with humanized anti-IL-1β-scFv, anti-IL-1β-Fab or anti-IL-1β-full-length antibody. The effects of treatment were determined by arthritis severity score, autoreactive humoral, cellular immune responses, histological lesion and cytokines production. Compared with anti-IL-1β-scFv treatments, anti-IL-1β-Fab and anti-IL-1β-full-length antibody therapy resulted in more significant effect in alleviating the severity of arthritis by preventing bone damage and cartilage destruction, reducing humoral and cellular immune responses, and down-regulating the expression of IL-1β, IL-6, IL-2, IFN-γ, TNF-α and MMP-3 in inflammatory tissue. The therapeutic effects of anti-IL-1β-Fab and anti-IL-1β-full-length antibodies on CIA mice had no significant difference. However, production of anti-IL-1β-full-length antibody in eukaryotic system is, in general, time-consuming and more expensive than that of anti-IL-1β-Fab in prokaryotic systems. In conclusion, as a small molecule antibody, anti-IL-1β-Fab is an ideal candidate for RA therapy. Copyright © 2013 Elsevier Ltd. All rights reserved.

Cocrystallization studies of full-length recombinant butyrylcholinesterase (BChE) with cocaine

Energy Technology Data Exchange (ETDEWEB)

Asojo, Oluwatoyin Ajibola; Asojo, Oluyomi Adebola; Ngamelue, Michelle N.; Homma, Kohei; Lockridge, Oksana (Nebraska-Med)

2011-09-16

Human butyrylcholinesterase (BChE; EC 3.1.1.8) is a 340 kDa tetrameric glycoprotein that is present in human serum at about 5 mg l{sup -1} and has well documented therapeutic effects on cocaine toxicity. BChE holds promise as a therapeutic that reduces and finally eliminates the rewarding effects of cocaine, thus weaning an addict from the drug. There have been extensive computational studies of cocaine hydrolysis by BChE. Since there are no reported structures of BChE with cocaine or any of the hydrolysis products, full-length monomeric recombinant wild-type BChE was cocrystallized with cocaine. The refined 3 {angstrom} resolution structure appears to retain the hydrolysis product benzoic acid in sufficient proximity to form a hydrogen bond to the active-site Ser198.

Failure Mode and Effects Analysis (FMEA) of the solid state full length rod control system

International Nuclear Information System (INIS)

Shopsky, W.E.

1977-01-01

The Full Length Rod Control System (FLRCS) controls the power to the rod drive mechanisms for rod movement in response to signals received from the Reactor Control System or from signals generated through Reactor Operator action. Rod movement is used to control reactivity of the reactor during plant operation. The Full Length Rod Control System is designed to perform its reactivity control function in conjunction with the Reactor Control and Protection System, to maintain the reactor core within design safety limits. By the use of a Failure Mode and Effects Analysis, it is shown that the FLRCS will perform its reactivity control functions considering the loss of single active components. That is, sufficient fault limiting control circuits are provided which blocks control rod movement and/or indicates presence of a fault condition at the Control Board. Reactor operator action or automatic reactor trip will thus mitigate the consequences of potential failure of the FLRCS. The analysis also qualitatively demonstrates the reliability of the FLRCS to perform its intended function

A Novel Strategy to Engineer Pre-Vascularized Full-Length Dental Pulp-like Tissue Constructs.

Science.gov (United States)

Athirasala, Avathamsa; Lins, Fernanda; Tahayeri, Anthony; Hinds, Monica; Smith, Anthony J; Sedgley, Christine; Ferracane, Jack; Bertassoni, Luiz E

2017-06-12

The requirement for immediate vascularization of engineered dental pulp poses a major hurdle towards successful implementation of pulp regeneration as an effective therapeutic strategy for root canal therapy, especially in adult teeth. Here, we demonstrate a novel strategy to engineer pre-vascularized, cell-laden hydrogel pulp-like tissue constructs in full-length root canals for dental pulp regeneration. We utilized gelatin methacryloyl (GelMA) hydrogels with tunable physical and mechanical properties to determine the microenvironmental conditions (microstructure, degradation, swelling and elastic modulus) that enhanced viability, spreading and proliferation of encapsulated odontoblast-like cells (OD21), and the formation of endothelial monolayers by endothelial colony forming cells (ECFCs). GelMA hydrogels with higher polymer concentration (15% w/v) and stiffness enhanced OD21 cell viability, spreading and proliferation, as well as endothelial cell spreading and monolayer formation. We then fabricated pre-vascularized, full-length, dental pulp-like tissue constructs by dispensing OD21 cell-laden GelMA hydrogel prepolymer in root canals of extracted teeth and fabricating 500 µm channels throughout the root canals. ECFCs seeded into the microchannels successfully formed monolayers and underwent angiogenic sprouting within 7 days in culture. In summary, the proposed approach is a simple and effective strategy for engineering of pre-vascularized dental pulp constructs offering potentially beneficial translational outcomes.

Purification and characterization of recombinant full-length and protease domain of murine MMP-9 expressed in Drosophila S2 cells

DEFF Research Database (Denmark)

Rasch, Morten G; Lund, Ida K; Illemann, Martin

2010-01-01

MMP-9. Constructs encoding zymogens of full-length murine MMP-9 and a version lacking the O-glycosylated linker region and hemopexin domains were therefore generated and expressed in stably transfected Drosophila S2 insect cells. After 7 days of induction the expression levels of the full......-length and truncated versions were 5 mg/l and 2 mg/l, respectively. The products were >95% pure after gelatin Sepharose chromatography and possessed proteolytic activity when analyzed by gelatin zymography. Using the purified full-length murine MMP-9 we raised polyclonal antibodies by immunizations of rabbits......Matrix metalloproteinase-9 (MMP-9) is a 92-kDa soluble pro-enzyme implicated in pathological events including cancer invasion. It is therefore an attractive target for therapeutic intervention studies in mouse models. Development of inhibitors requires sufficient amounts of correctly folded murine...

Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

Directory of Open Access Journals (Sweden)

Tadashi Imanishi

2004-06-01

Full Text Available The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/. It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs, identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA

Assessment and optimization of theileria parva sporozoite full-length p67 antigen expression in mammalian cells

Science.gov (United States)

Delivery of various forms of recombinant Theileria parva sporozoite antigen (p67) has been shown to elicit antibody responses in cattle capable of providing protection against East Coast fever, the clinical disease caused by T. parva. Previous formulations of full-length and shorter recombinant vers...

A comparative phylogenetic analysis of full-length mariner elements ...

Indian Academy of Sciences (India)

Unknown

recent study showing non-occurance of inter-subfamily excisions because of .... length shown in our figure is greater because of the gaps introduced to maintain an ... to test the feasibility of transforming silkmoths with a foreign gene of ...

Virtually full-length subtype F and F/D recombinant HIV-1 from Africa and South America

NARCIS (Netherlands)

Laukkanen, T.; Carr, J. K.; Janssens, W.; Liitsola, K.; Gotte, D.; McCutchan, F. E.; Op de Coul, E.; Cornelissen, M.; Heyndrickx, L.; van der Groen, G.; Salminen, M. O.

2000-01-01

For reliable classification of HIV-1 strains appropriate reference sequences are needed. The HIV-1 genetic subtype F has a wide geographic spread, causing significant epidemics in South America, Africa, and some regions of Europe. Previously only two full-length sequences of each of the HIV-1

Salmo salar and Esox lucius full-length cDNA sequences reveal changes in evolutionary pressures on a post-tetraploidization genome

Directory of Open Access Journals (Sweden)

Holt Robert A

2010-04-01

Full Text Available Abstract Background Salmonids are one of the most intensely studied fish, in part due to their economic and environmental importance, and in part due to a recent whole genome duplication in the common ancestor of salmonids. This duplication greatly impacts species diversification, functional specialization, and adaptation. Extensive new genomic resources have recently become available for Atlantic salmon (Salmo salar, but documentation of allelic versus duplicate reference genes remains a major uncertainty in the complete characterization of its genome and its evolution. Results From existing expressed sequence tag (EST resources and three new full-length cDNA libraries, 9,057 reference quality full-length gene insert clones were identified for Atlantic salmon. A further 1,365 reference full-length clones were annotated from 29,221 northern pike (Esox lucius ESTs. Pairwise dN/dS comparisons within each of 408 sets of duplicated salmon genes using northern pike as a diploid out-group show asymmetric relaxation of selection on salmon duplicates. Conclusions 9,057 full-length reference genes were characterized in S. salar and can be used to identify alleles and gene family members. Comparisons of duplicated genes show that while purifying selection is the predominant force acting on both duplicates, consistent with retention of functionality in both copies, some relaxation of pressure on gene duplicates can be identified. In addition, there is evidence that evolution has acted asymmetrically on paralogs, allowing one of the pair to diverge at a faster rate.

Characterization of full-length sequenced cDNA inserts (FLIcs) from Atlantic salmon (Salmo salar)

Science.gov (United States)

Andreassen, Rune; Lunner, Sigbjørn; Høyheim, Bjørn

2009-01-01

Background Sequencing of the Atlantic salmon genome is now being planned by an international research consortium. Full-length sequenced inserts from cDNAs (FLIcs) are an important tool for correct annotation and clustering of the genomic sequence in any species. The large amount of highly similar duplicate sequences caused by the relatively recent genome duplication in the salmonid ancestor represents a particular challenge for the genome project. FLIcs will therefore be an extremely useful resource for the Atlantic salmon sequencing project. In addition to be helpful in order to distinguish between duplicate genome regions and in determining correct gene structures, FLIcs are an important resource for functional genomic studies and for investigation of regulatory elements controlling gene expression. In contrast to the large number of ESTs available, including the ESTs from 23 developmental and tissue specific cDNA libraries contributed by the Salmon Genome Project (SGP), the number of sequences where the full-length of the cDNA insert has been determined has been small. Results High quality full-length insert sequences from 560 pre-smolt white muscle tissue specific cDNAs were generated, accession numbers [GenBank: BT043497 - BT044056]. Five hundred and ten (91%) of the transcripts were annotated using Gene Ontology (GO) terms and 440 of the FLIcs are likely to contain a complete coding sequence (cCDS). The sequence information was used to identify putative paralogs, characterize salmon Kozak motifs, polyadenylation signal variation and to identify motifs likely to be involved in the regulation of particular genes. Finally, conserved 7-mers in the 3'UTRs were identified, of which some were identical to miRNA target sequences. Conclusion This paper describes the first Atlantic salmon FLIcs from a tissue and developmental stage specific cDNA library. We have demonstrated that many FLIcs contained a complete coding sequence (cCDS). This suggests that the remaining c

Fiscal 2000 report on result of the full-length cDNA structure analysis; 2000 nendo kanzen cho cDNA kozo kaiseki seika hokokusho

Energy Technology Data Exchange (ETDEWEB)

NONE

2001-03-01

This paper explains the results of research on full-length cDNA structure analysis for the period from April, 2000 to March, 2001. The outline of human genome sequence was published in June, 2000. In Japan, human gene analysis was such that, as the basic technology of the bio industry, a millennium project was decided in the budget of fiscal 2000. The full-length cDNA structure analysis is the core of the project. The libraries of cDNA were prepared using full-length and more than 4-5kbp-long cDNAs by oligo-capping method. It began from determining partial sequence data at end cDNA, and then, with new clones selected therefrom, full-length human cDNA sequence data were determined. The partial sequence data determined by fiscal 2000 were 1,035,000 clones while the full-length sequence data were 12,144 clones. The sequence data obtained were analyzed by homology search and translated into amino acid coding sequences, with predictions conducted on protein functions. A clustering method was examined that selects new clones from partial sequences. Database was constructed on gene expression profiles and disease-related gene sequence data. (NEDO)

Diversity, distribution and dynamics of full-length Copia and Gypsy LTR retroelements in Solanum lycopersicum.

Science.gov (United States)

Paz, Rosalía Cristina; Kozaczek, Melisa Eliana; Rosli, Hernán Guillermo; Andino, Natalia Pilar; Sanchez-Puerta, Maria Virginia

2017-10-01

Transposable elements are the most abundant components of plant genomes and can dramatically induce genetic changes and impact genome evolution. In the recently sequenced genome of tomato (Solanum lycopersicum), the estimated fraction of elements corresponding to retrotransposons is nearly 62%. Given that tomato is one of the most important vegetable crop cultivated and consumed worldwide, understanding retrotransposon dynamics can provide insight into its evolution and domestication processes. In this study, we performed a genome-wide in silico search of full-length LTR retroelements in the tomato nuclear genome and annotated 736 full-length Gypsy and Copia retroelements. The dispersion level across the 12 chromosomes, the diversity and tissue-specific expression of those elements were estimated. Phylogenetic analysis based on the retrotranscriptase region revealed the presence of 12 major lineages of LTR retroelements in the tomato genome. We identified 97 families, of which 77 and 20 belong to the superfamilies Copia and Gypsy, respectively. Each retroelement family was characterized according to their element size, relative frequencies and insertion time. These analyses represent a valuable resource for comparative genomics within the Solanaceae, transposon-tagging and for the design of cultivar-specific molecular markers in tomato.

Full-Length High-Temperature Severe Fuel Damage Test No. 5: Final safety analysis

International Nuclear Information System (INIS)

Lanning, D.D.; Lombardo, N.J.; Panisko, F.E.

1993-09-01

This report presents the final safety analysis for the preparation, conduct, and post-test discharge operation for the Full-Length High Temperature Experiment-5 (FLHT-5) to be conducted in the L-24 position of the National Research Universal (NRU) Reactor at Chalk River Nuclear Laboratories (CRNL), Ontario, Canada. The test is sponsored by an international group organized by the US Nuclear Regulatory Commission. The test is designed and conducted by staff from Pacific Northwest Laboratory with CRNL staff support. The test will study the consequences of loss-of-coolant and the progression of severe fuel damage

Purification and characterization of recombinant full-length and protease domain of murine MMP-9 expressed in Drosophila S2 cells

DEFF Research Database (Denmark)

Rasch, Morten G; Lund, Ida K.; Illemann, Martin

2010-01-01

-length and truncated versions were 5 mg/l and 2 mg/l, respectively. The products were >95% pure after gelatin Sepharose chromatography and possessed proteolytic activity when analyzed by gelatin zymography. Using the purified full-length murine MMP-9 we raised polyclonal antibodies by immunizations of rabbits...

Functional characterization of a full length pregnane X receptor, expression in vivo, and identification of PXR alleles, in Zebrafish (Danio rerio)

Energy Technology Data Exchange (ETDEWEB)

Bainy, Afonso C.D. [Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543 (United States); Departamento de Bioquímica, CCB, Universidade Federal de Santa Catarina, Florianópolis, SC 88040-900 (Brazil); Kubota, Akira; Goldstone, Jared V. [Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543 (United States); Lille-Langøy, Roger [Department of Biology, University of Bergen, N-5020 Bergen (Norway); Karchner, Sibel I. [Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543 (United States); Celander, Malin C. [Department of Biological and Environmental Sciences, University of Gothenburg, SE 405 30 Göteborg (Sweden); Hahn, Mark E. [Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543 (United States); Goksøyr, Anders [Department of Biology, University of Bergen, N-5020 Bergen (Norway); Stegeman, John J., E-mail: jstegeman@whoi.edu [Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543 (United States)

2013-10-15

Highlights: •Full-length pxr has been cloned from zebrafish. •Alleles of pxr were identified in zebrafish. •Full length Pxr was activated less strongly than ligand binding domain in cell-based reporter assays. •High levels of pxr expression were found in eye and brain as well as in liver. •TCPOBOP and PB did not significantly alter expression of pxr in liver. -- Abstract: The pregnane X receptor (PXR) (nuclear receptor NR1I2) is a ligand activated transcription factor, mediating responses to diverse xenobiotic and endogenous chemicals. The properties of PXR in fish are not fully understood. Here we report on cloning and characterization of full-length PXR of zebrafish, Danio rerio, and pxr expression in vivo. Initial efforts gave a cDNA encoding a 430 amino acid protein identified as zebrafish pxr by phylogenetic and synteny analysis. The sequence of the cloned Pxr DNA binding domain (DBD) was highly conserved, with 74% identity to human PXR-DBD, while the ligand-binding domain (LBD) of the cloned sequence was only 44% identical to human PXR-LBD. Sequence variation among clones in the initial effort prompted sequencing of multiple clones from a single fish. There were two prominent variants, one sequence with S183, Y218 and H383 and the other with I183, C218 and N383, which we designate as alleles pxr*1 (nr1i2*1) and pxr*2 (nr1i2*2), respectively. In COS-7 cells co-transfected with a PXR-responsive reporter gene, the full-length Pxr*1 (the more common variant) was activated by known PXR agonists clotrimazole and pregnenolone 16α-carbonitrile but to a lesser extent than the full-length human PXR. Activation of full-length Pxr*1 was only 10% of that with the Pxr*1 LBD. Quantitative real time PCR analysis showed prominent expression of pxr in liver and eye, as well as brain and intestine of adult zebrafish. The pxr was expressed in heart and kidney at levels similar to that in intestine. The expression of pxr in liver was weakly induced by ligands for

Thousands of primer-free, high-quality, full-length SSU rRNA sequences from all domains of life

DEFF Research Database (Denmark)

Karst, Soeren M; Dueholm, Morten S; McIlroy, Simon J

2016-01-01

Ribosomal RNA (rRNA) genes are the consensus marker for determination of microbial diversity on the planet, invaluable in studies of evolution and, for the past decade, high-throughput sequencing of variable regions of ribosomal RNA genes has become the backbone of most microbial ecology studies...... (SSU) rRNA genes and synthetic long read sequencing by molecular tagging, to generate primer-free, full-length SSU rRNA gene sequences from all domains of life, with a median raw error rate of 0.17%. We generated thousands of full-length SSU rRNA sequences from five well-studied ecosystems (soil, human...... gut, fresh water, anaerobic digestion, and activated sludge) and obtained sequences covering all domains of life and the majority of all described phyla. Interestingly, 30% of all bacterial operational taxonomic units were novel, compared to the SILVA database (less than 97% similarity...

Construction of occluded recombinant baculoviruses containing the full-length cry1Ab and cry1Ac genes from Bacillus thuringiensis

Directory of Open Access Journals (Sweden)

B.M. Ribeiro

1998-06-01

Full Text Available The administration of baculoviruses to insects for bioassay purposes is carried out, in most cases, by contamination of food surfaces with a known amount of occlusion bodies (OBs. Since per os infection is the natural route of infection, occluded recombinant viruses containing crystal protein genes (cry1Ab and cry1Ac from Bacillus thuringiensis were constructed for comparison with the baculovirus prototype Autographa californica nucleopolyhedrovirus (AcNPV. The transfer vector pAcUW2B was used for construction of occluded recombinant viruses. The transfer vector containing the crystal protein genes was cotransfected with linearized DNA from a non-occluded recombinant virus. The isolation of recombinant viruses was greatly facilitated by the reduction of background "wild type" virus and the increased proportion of recombinant viruses. Since the recombinant viruses containing full-length and truncated forms of the crystal protein genes did not seem to improve the pathogenicity of the recombinant viruses when compared with the wild type AcNPV, and in order to compare expression levels of the full-length crystal proteins produced by non-occluded and occluded recombinant viruses the full-length cry1Ab and cry1Ac genes were chosen for construction of occluded recombinant viruses. The recombinant viruses containing full-length and truncated forms of the crystal protein genes did not seem to improve its pathogenicity but the size of the larvae infected with the recombinant viruses was significantly smaller than that of larvae infected with the wild type virus.

Genetic characterization of human herpesvirus type 1: Full-length genome sequence of strain obtained from an encephalitis case from India

Directory of Open Access Journals (Sweden)

Vijay P Bondre

2016-01-01

Interpretation & conclusions: Our results showed that the full-length genome sequence generated from an Indian HSV-1 isolate shared close genetic relationship with the American KOS and Chinese CR38 strains which belonged to the Asian genetic lineage. Recombination analysis of Indian isolate demonstrated multiple recombination crossover points throughout the genome. This full-length genome sequence amplified from the Indian isolate would be helpful to study HSV evolution, genetic basis of differential pathogenesis, host-virus interactions and viral factors contributing towards differential clinical outcome in human infections.

Secretory production of tetrameric native full-length streptavidin with thermostability using Streptomyces lividans as a host.

Science.gov (United States)

Noda, Shuhei; Matsumoto, Takuya; Tanaka, Tsutomu; Kondo, Akihiko

2015-01-13

Streptavidin is a tetrameric protein derived from Streptomyces avidinii, and has tight and specific biotin binding affinity. Applications of the streptavidin-biotin system have been widely studied. Streptavidin is generally produced using protein expression in Escherichia coli. In the present study, the secretory production of streptavidin was carried out using Streptomyces lividans as a host. In this study, we used the gene encoding native full-length streptavidin, whereas the core region is generally used for streptavidin production in E. coli. Tetrameric streptavidin composed of native full-length streptavidin monomers was successfully secreted in the culture supernatant of S. lividans transformants, and had specific biotin binding affinity as strong as streptavidin produced by E. coli. The amount of Sav using S. lividans was about 9 times higher than using E. coli. Surprisingly, streptavidin produced by S. lividans exhibited affinity to biotin after boiling, despite the fact that tetrameric streptavidin is known to lose its biotin binding ability after brief boiling. We successfully produced a large amount of tetrameric streptavidin as a secretory-form protein with unique thermotolerance.

PCR-based isolation and identification of full-length low-molecular-weight glutenin subunit genes in bread wheat (Triticum aestivum L.).

Science.gov (United States)

Zhang, Xiaofei; Liu, Dongcheng; Jiang, Wei; Guo, Xiaoli; Yang, Wenlong; Sun, Jiazhu; Ling, Hongqing; Zhang, Aimin

2011-12-01

Low-molecular-weight glutenin subunits (LMW-GSs) are encoded by a multi-gene family and are essential for determining the quality of wheat flour products, such as bread and noodles. However, the exact role or contribution of individual LMW-GS genes to wheat quality remains unclear. This is, at least in part, due to the difficulty in characterizing complete sequences of all LMW-GS gene family members in bread wheat. To identify full-length LMW-GS genes, a polymerase chain reaction (PCR)-based method was established, consisting of newly designed conserved primers and the previously developed LMW-GS gene molecular marker system. Using the PCR-based method, 17 LMW-GS genes were identified and characterized in Xiaoyan 54, of which 12 contained full-length sequences. Sequence alignments showed that 13 LMW-GS genes were identical to those found in Xiaoyan 54 using the genomic DNA library screening, and the other four full-length LMW-GS genes were first isolated from Xiaoyan 54. In Chinese Spring, 16 unique LMW-GS genes were isolated, and 13 of them contained full-length coding sequences. Additionally, 16 and 17 LMW-GS genes in Dongnong 101 and Lvhan 328 (chosen from the micro-core collections of Chinese germplasm), respectively, were also identified. Sequence alignments revealed that at least 15 LMW-GS genes were common in the four wheat varieties, and allelic variants of each gene shared high sequence identities (>95%) but exhibited length polymorphism in repetitive regions. This study provides a PCR-based method for efficiently identifying LMW-GS genes in bread wheat, which will improve the characterization of complex members of the LMW-GS gene family and facilitate the understanding of their contributions to wheat quality.

Hibiscus latent Fort Pierce virus in Brazil and synthesis of its biologically active full-length cDNA clone.

Science.gov (United States)

Gao, Ruimin; Niu, Shengniao; Dai, Weifang; Kitajima, Elliot; Wong, Sek-Man

2016-10-01

A Brazilian isolate of Hibiscus latent Fort Pierce virus (HLFPV-BR) was firstly found in a hibiscus plant in Limeira, SP, Brazil. RACE PCR was carried out to obtain the full-length sequences of HLFPV-BR which is 6453 nucleotides and has more than 99.15 % of complete genomic RNA nucleotide sequence identity with that of HLFPV Japanese isolate. The genomic structure of HLFPV-BR is similar to other tobamoviruses. It includes a 5' untranslated region (UTR), followed by open reading frames encoding for a 128-kDa protein and a 188-kDa readthrough protein, a 38-kDa movement protein, 18-kDa coat protein, and a 3' UTR. Interestingly, the unique feature of poly(A) tract is also found within its 3'-UTR. Furthermore, from the total RNA extracted from the local lesions of HLFPV-BR-infected Chenopodium quinoa leaves, a biologically active, full-length cDNA clone encompassing the genome of HLFPV-BR was amplified and placed adjacent to a T7 RNA polymerase promoter. The capped in vitro transcripts from the cloned cDNA were infectious when mechanically inoculated into C. quinoa and Nicotiana benthamiana plants. This is the first report of the presence of an isolate of HLFPV in Brazil and the successful synthesis of a biologically active HLFPV-BR full-length cDNA clone.

RT-PCR and sequence analysis of the full-length fusion protein of Canine Distemper Virus from domestic dogs.

Science.gov (United States)

Romanutti, Carina; Gallo Calderón, Marina; Keller, Leticia; Mattion, Nora; La Torre, José

2016-02-01

During 2007-2014, 84 out of 236 (35.6%) samples from domestic dogs submitted to our laboratory for diagnostic purposes were positive for Canine Distemper Virus (CDV), as analyzed by RT-PCR amplification of a fragment of the nucleoprotein gene. Fifty-nine of them (70.2%) were from dogs that had been vaccinated against CDV. The full-length gene encoding the Fusion (F) protein of fifteen isolates was sequenced and compared with that of those of other CDVs, including wild-type and vaccine strains. Phylogenetic analysis using the F gene full-length sequences grouped all the Argentinean CDV strains in the SA2 clade. Sequence identity with the Onderstepoort vaccine strain was 89.0-90.6%, and the highest divergence was found in the 135 amino acids corresponding to the F protein signal-peptide, Fsp (64.4-66.7% identity). In contrast, this region was highly conserved among the local strains (94.1-100% identity). One extra putative N-glycosylation site was identified in the F gene of CDV Argentinean strains with respect to the vaccine strain. The present report is the first to analyze full-length F protein sequences of CDV strains circulating in Argentina, and contributes to the knowledge of molecular epidemiology of CDV, which may help in understanding future disease outbreaks. Copyright © 2015 Elsevier B.V. All rights reserved.

Human microcephaly protein RTTN interacts with STIL and is required to build full-length centrioles.

Science.gov (United States)

Chen, Hsin-Yi; Wu, Chien-Ting; Tang, Chieh-Ju C; Lin, Yi-Nan; Wang, Won-Jing; Tang, Tang K

2017-08-15

Mutations in many centriolar protein-encoding genes cause primary microcephaly. Using super-resolution and electron microscopy, we find that the human microcephaly protein, RTTN, is recruited to the proximal end of the procentriole at early S phase, and is located at the inner luminal walls of centrioles. Further studies demonstrate that RTTN directly interacts with STIL and acts downstream of STIL-mediated centriole assembly. CRISPR/Cas9-mediated RTTN gene knockout in p53-deficient cells induce amplification of primitive procentriole bodies that lack the distal-half centriolar proteins, POC5 and POC1B. Additional analyses show that RTTN serves as an upstream effector of CEP295, which mediates the loading of POC1B and POC5 to the distal-half centrioles. Interestingly, the naturally occurring microcephaly-associated mutant, RTTN (A578P), shows a low affinity for STIL binding and blocks centriole assembly. These findings reveal that RTTN contributes to building full-length centrioles and illuminate the molecular mechanism through which the RTTN (A578P) mutation causes primary microcephaly.Mutations in many centriolar protein-encoding genes cause primary microcephaly. Here the authors show that human microcephaly protein RTTN directly interacts with STIL and acts downstream of STIL-mediated centriole assembly, contributing to building full-length centrioles.

Molecular cloning and expression of full-length DNA copies of the genomic RNAs of cowpea mosaic virus

NARCIS (Netherlands)

Vos, P.

1987-01-01

The experiments described in this thesis were designed to unravel various aspects of the mechanism of gene expression of cowpea mosaic virus (CPMV). For this purpose full-length DNA copies of both genomic RNAs of CPMV were constructed. Using powerful invitro

TypeLoader: A fast and efficient automated workflow for the annotation and submission of novel full-length HLA alleles.

Science.gov (United States)

Surendranath, V; Albrecht, V; Hayhurst, J D; Schöne, B; Robinson, J; Marsh, S G E; Schmidt, A H; Lange, V

2017-07-01

Recent years have seen a rapid increase in the discovery of novel allelic variants of the human leukocyte antigen (HLA) genes. Commonly, only the exons encoding the peptide binding domains of novel HLA alleles are submitted. As a result, the IPD-IMGT/HLA Database lacks sequence information outside those regions for the majority of known alleles. This has implications for the application of the new sequencing technologies, which deliver sequence data often covering the complete gene. As these technologies simplify the characterization of the complete gene regions, it is desirable for novel alleles to be submitted as full-length sequences to the database. However, the manual annotation of full-length alleles and the generation of specific formats required by the sequence repositories is prone to error and time consuming. We have developed TypeLoader to address both these facets. With only the full-length sequence as a starting point, Typeloader performs automatic sequence annotation and subsequently handles all steps involved in preparing the specific formats for submission with very little manual intervention. TypeLoader is routinely used at the DKMS Life Science Lab and has aided in the successful submission of more than 900 novel HLA alleles as full-length sequences to the European Nucleotide Archive repository and the IPD-IMGT/HLA Database with a 95% reduction in the time spent on annotation and submission when compared with handling these processes manually. TypeLoader is implemented as a web application and can be easily installed and used on a standalone Linux desktop system or within a Linux client/server architecture. TypeLoader is downloadable from http://www.github.com/DKMS-LSL/typeloader. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Construction of a full-length infectious bacterial artificial chromosome clone of duck enteritis virus vaccine strain

Science.gov (United States)

2013-01-01

Background Duck enteritis virus (DEV) is the causative agent of duck viral enteritis, which causes an acute, contagious and lethal disease of many species of waterfowl within the order Anseriformes. In recent years, two laboratories have reported on the successful construction of DEV infectious clones in viral vectors to express exogenous genes. The clones obtained were either created with deletion of viral genes and based on highly virulent strains or were constructed using a traditional overlapping fosmid DNA system. Here, we report the construction of a full-length infectious clone of DEV vaccine strain that was cloned into a bacterial artificial chromosome (BAC). Methods A mini-F vector as a BAC that allows the maintenance of large circular DNA in E. coli was introduced into the intergenic region between UL15B and UL18 of a DEV vaccine strain by homologous recombination in chicken embryoblasts (CEFs). Then, the full-length DEV clone pDEV-vac was obtained by electroporating circular viral replication intermediates containing the mini-F sequence into E. coli DH10B and identified by enzyme digestion and sequencing. The infectivity of the pDEV-vac was validated by DEV reconstitution from CEFs transfected with pDEV-vac. The reconstructed virus without mini-F vector sequence was also rescued by co-transfecting the Cre recombinase expression plasmid pCAGGS-NLS/Cre and pDEV-vac into CEF cultures. Finally, the in vitro growth properties and immunoprotection capacity in ducks of the reconstructed viruses were also determined and compared with the parental virus. Results The full genome of the DEV vaccine strain was successfully cloned into the BAC, and this BAC clone was infectious. The in vitro growth properties of these reconstructions were very similar to parental DEV, and ducks immunized with these viruses acquired protection against virulent DEV challenge. Conclusions DEV vaccine virus was cloned as an infectious bacterial artificial chromosome maintaining full-length

Generation and Analysis of Full-length cDNA Sequences from Elephant Shark (Callorhinchus milii)

KAUST Repository

Kodzius, Rimantas

2009-03-17

Cartilaginous fishes are the oldest living group of jawed vertebrates and therefore is an important group for understanding the evolution of vertebrate genomes including the human genome. Our laboratory has proposed elephant shark (C. milii) as a model cartilaginous fish genome because of its relatively small genome size (910 Mb). The whole genome of C. milii is being sequenced (first cartilaginous fish genome to be sequenced completely). To characterize the transcriptome of C. milii and to assist in annotating exon-intron boundaries, transcriptional start sites and alternatively spliced transcripts, we are generating full-length cDNA sequences from C. milii.

Transformation of Cowpea Vigna unguiculata with a Full-Length DNA Copy of Cowpea Mosaic Virus M-RNA

NARCIS (Netherlands)

Hille, Jacques; Goldbach, Rob

1987-01-01

A full-length DNA copy of the M-RNA of cowpea mosaic virus (CPMV), supplied with either the 35S promoter from cauliflower mosaic virus (CaMV) or the nopaline synthase promoter from Agrobacterium tumefaciens, was introduced into the T-DNA region of a Ti-plasmid-derived gene vector and transferred to

An analysis of expressed sequence tags of developing castor endosperm using a full-length cDNA library

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Wallis James G

2007-07-01

Full Text Available Abstract Background Castor seeds are a major source for ricinoleate, an important industrial raw material. Genomics studies of castor plant will provide critical information for understanding seed metabolism, for effectively engineering ricinoleate production in transgenic oilseeds, or for genetically improving castor plants by eliminating toxic and allergic proteins in seeds. Results Full-length cDNAs are useful resources in annotating genes and in providing functional analysis of genes and their products. We constructed a full-length cDNA library from developing castor endosperm, and obtained 4,720 ESTs from 5'-ends of the cDNA clones representing 1,908 unique sequences. The most abundant transcripts are genes encoding storage proteins, ricin, agglutinin and oleosins. Several other sequences are also very numerous, including two acidic triacylglycerol lipases, and the oleate hydroxylase (FAH12 gene that is responsible for ricinoleate biosynthesis. The role(s of the lipases in developing castor seeds are not clear, and co-expressing of a lipase and the FAH12 did not result in significant changes in hydroxy fatty acid accumulation in transgenic Arabidopsis seeds. Only one oleate desaturase (FAD2 gene was identified in our cDNA sequences. Sequence and functional analyses of the castor FAD2 were carried out since it had not been characterized previously. Overexpression of castor FAD2 in a FAH12-expressing Arabidopsis line resulted in decreased accumulation of hydroxy fatty acids in transgenic seeds. Conclusion Our results suggest that transcriptional regulation of FAD2 and FAH12 genes maybe one of the mechanisms that contribute to a high level of ricinoleate accumulation in castor endosperm. The full-length cDNA library will be used to search for additional genes that affect ricinoleate accumulation in seed oils. Our EST sequences will also be useful to annotate the castor genome, which whole sequence is being generated by shotgun sequencing at

Global identification of the full-length transcripts and alternative splicing related to phenolic acid biosynthetic genes in Salvia miltiorrhiza

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Zhichao eXu

2016-02-01

Full Text Available Salvianolic acids are among the main bioactive components in Salvia miltiorrhiza, and their biosynthesis has attracted widespread interest. However, previous studies on the biosynthesis of phenolic acids using next-generation sequencing platforms are limited with regard to the assembly of full-length transcripts. Based on hybrid-seq (next-generation and single molecular real-time sequencing of the S. miltiorrhiza root transcriptome, we experimentally identified 15 full-length transcripts and 4 alternative splicing events of enzyme-coding genes involved in the biosynthesis of rosmarinic acid. Moreover, we herein demonstrate that lithospermic acid B accumulates in the phloem and xylem of roots, in agreement with the expression patterns of the identified key genes related to rosmarinic acid biosynthesis. According to co-expression patterns, we predicted that 6 candidate cytochrome P450s and 5 candidate laccases participate in the salvianolic acid pathway. Our results provide a valuable resource for further investigation into the synthetic biology of phenolic acids in S. miltiorrhiza.

The effect of two different renal denervation strategies on blood pressure in resistant hypertension: Comparison of full-length versus proximal renal artery ablation.

Science.gov (United States)

Chen, Weijie; Ling, Zhiyu; Du, Huaan; Song, Wenxin; Xu, Yanping; Liu, Zengzhang; Su, Li; Xiao, Peilin; Yuan, Yuelong; Lu, Jiayi; Zhang, Jianhong; Li, Zhifeng; Shao, Jiang; Zhong, Bin; Zhou, Bei; Woo, Kamsang; Yin, Yuehui

2016-11-01

Renal denervation (RDN) is used to manage blood pressure (BP) in patients with resistant hypertension (rHT), but effectiveness is still a concern, and key arterial portion for successful RDN is not clear. The aim of this study was to investigate the efficacy and safety of proximal versus full-length renal artery ablation in patients with resistant hypertension (rHT). Forty-seven patients with rHT were randomly assigned to receive full-length ablation (n = 23) or proximal ablation (n = 24) of the renal arteries. All lesions were treated with radiofrequency energy via a saline-irrigated catheter. Office BP was measured during 12 months of follow-up and ambulatory BP at baseline and 6 months (n = 15 in each group). Compared with full-length ablation, proximal ablation reduced the number of ablation points in both the right (6.1 ± 0.7 vs. 3.3 ± 0.6, P renal arteries (6.2 ± 0.7 vs. 3.3 ± 0.8, P  0.5). Similar office BPs was reduced by -39.4 ± 11.5/-20.9 ± 7.1 mm Hg at 6 months and -38.2 ± 10.3/-21.5 ± 5.8 mm Hg at 12 months in the full-length group (P efficacy and safety profile compared with full-length RDN, and propose the proximal artery as the key portion for RDN. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Genetic deletion of muscle RANK or selective inhibition of RANKL is not as effective as full-length OPG-fc in mitigating muscular dystrophy.

Science.gov (United States)

Dufresne, Sébastien S; Boulanger-Piette, Antoine; Bossé, Sabrina; Argaw, Anteneh; Hamoudi, Dounia; Marcadet, Laetitia; Gamu, Daniel; Fajardo, Val A; Yagita, Hideo; Penninger, Josef M; Russell Tupling, A; Frenette, Jérôme

2018-04-24

Although there is a strong association between osteoporosis and skeletal muscle atrophy/dysfunction, the functional relevance of a particular biological pathway that regulates synchronously bone and skeletal muscle physiopathology is still elusive. Receptor-activator of nuclear factor κB (RANK), its ligand RANKL and the soluble decoy receptor osteoprotegerin (OPG) are the key regulators of osteoclast differentiation and bone remodelling. We thus hypothesized that RANK/RANKL/OPG, which is a key pathway for bone regulation, is involved in Duchenne muscular dystrophy (DMD) physiopathology. Our results show that muscle-specific RANK deletion (mdx-RANK mko ) in dystrophin deficient mdx mice improves significantly specific force [54% gain in force] of EDL muscles with no protective effect against eccentric contraction-induced muscle dysfunction. In contrast, full-length OPG-Fc injections restore the force of dystrophic EDL muscles [162% gain in force], protect against eccentric contraction-induced muscle dysfunction ex vivo and significantly improve functional performance on downhill treadmill and post-exercise physical activity. Since OPG serves a soluble receptor for RANKL and as a decoy receptor for TRAIL, mdx mice were injected with anti-RANKL and anti-TRAIL antibodies to decipher the dual function of OPG. Injections of anti-RANKL and/or anti-TRAIL increase significantly the force of dystrophic EDL muscle [45% and 17% gains in force, respectively]. In agreement, truncated OPG-Fc that contains only RANKL domains produces similar gains, in terms of force production, than anti-RANKL treatments. To corroborate that full-length OPG-Fc also acts independently of RANK/RANKL pathway, dystrophin/RANK double-deficient mice were treated with full-length OPG-Fc for 10 days. Dystrophic EDL muscles exhibited a significant gain in force relative to untreated dystrophin/RANK double-deficient mice, indicating that the effect of full-length OPG-Fc is in part independent of the RANKL

Human uroporphyrinogen III synthase: Molecular cloning, nucleotide sequence, and expression of a full-length cDNA

International Nuclear Information System (INIS)

Tsai, Shihfeng; Bishop, D.F.; Desnick, R.J.

1988-01-01

Uroporphyrinogen III synthase, the fourth enzyme in the heme biosynthetic pathway, is responsible for conversion of the linear tetrapyrrole, hydroxymethylbilane, to the cyclic tetrapyrrole, uroporphyrinogen III. The deficient activity of URO-synthase is the enzymatic defect in the autosomal recessive disorder congenital erythropoietic porphyria. To facilitate the isolation of a full-length cDNA for human URO-synthase, the human erythrocyte enzyme was purified to homogeneity and 81 nonoverlapping amino acids were determined by microsequencing the N terminus and four tryptic peptides. Two synthetic oligonucleotide mixtures were used to screen 1.2 x 10 6 recombinants from a human adult liver cDNA library. Eight clones were positive with both oligonucleotide mixtures. Of these, dideoxy sequencing of the 1.3 kilobase insert from clone pUROS-2 revealed 5' and 3' untranslated sequences of 196 and 284 base pairs, respectively, and an open reading frame of 798 base pairs encoding a protein of 265 amino acids with a predicted molecular mass of 28,607 Da. The isolation and expression of this full-length cDNA for human URO-synthase should facilitate studies of the structure, organization, and chromosomal localization of this heme biosynthetic gene as well as the characterization of the molecular lesions causing congenital erythropoietic porphyria

Full splitting of the first zero-field steps in the I-V curve of Josephson junctions of intermediate length

International Nuclear Information System (INIS)

Hansen, J.B.; Divin, Y.Y.; Mygind, J.

1986-01-01

We report on the observation of full splitting of the first zero-field steps in the I-V curves of Josephson transmission lines of intermediate length Lroughly-equal(3--5)lambda/sub J/, where lambda/sub J/ is the Josephson penetration length. We study in detail how this splitting of the step into two branches depends on the temperature of the junction and on a weak applied magnetic field. We relate the splitting to excitations in the junctions whose behavior is described by the perturbed Sine-Gordon equation

Potency of full-length MGF to induce maximal activation of the IGF-I R Is similar to recombinant human IGF-I at high equimolar concentrations

NARCIS (Netherlands)

J.A.M.J.L. Janssen (Joseph); L.J. Hofland (Leo); C.J. Strasburger; E.S.R.D. Van Dungen (Elisabeth S.R. Den); M. Thevis (Mario)

2016-01-01

textabstractAims To compare full-length mechano growth factor (full-length MGF) with human recombinant insulin-like growth factor-I (IGF-I) and human recombinant insulin (HI) in their ability to activate the human IGF-I receptor (IGF-IR), the human insulin receptor (IR-A) and the human insulin

Copper Coordination in the Full-Length, Recombinant Prion Protein†

Science.gov (United States)

Burns, Colin S.; Aronoff-Spencer, Eliah; Legname, Giuseppe; Prusiner, Stanley B.; Antholine, William E.; Gerfen, Gary J.; Peisach, Jack; Millhauser, Glenn L.

2010-01-01

The prion protein (PrP) binds divalent copper at physiologically relevant conditions and is believed to participate in copper regulation or act as a copper-dependent enzyme. Ongoing studies aim at determining the molecular features of the copper binding sites. The emerging consensus is that most copper binds in the octarepeat domain, which is composed of four or more copies of the fundamental sequence PHGGGWGQ. Previous work from our laboratory using PrP-derived peptides, in conjunction with EPR and X-ray crystallography, demonstrated that the HGGGW segment constitutes the fundamental binding unit in the octarepeat domain [Burns et al. (2002) Biochemistry 41, 3991–4001; Aronoff-Spencer et al. (2000) Biochemistry 39, 13760–13771]. Copper coordination arises from the His imidazole and sequential deprotonated glycine amides. In this present work, recombinant, full-length Syrian hamster PrP is investigated using EPR methodologies. Four copper ions are taken up in the octarepeat domain, which supports previous findings. However, quantification studies reveal a fifth binding site in the flexible region between the octarepeats and the PrP globular C-terminal domain. A series of PrP peptide constructs show that this site involves His96 in the PrP(92–96) segment GGGTH. Further examination by X-band EPR, S-band EPR, and electron spin–echo envelope spectroscopy, demonstrates coordination by the His96 imidazole and the glycine preceding the threonine. The copper affinity for this type of binding site is highly pH dependent, and EPR studies here show that recombinant PrP loses its affinity for copper below pH 6.0. These studies seem to provide a complete profile of the copper binding sites in PrP and support the hypothesis that PrP function is related to its ability to bind copper in a pH-dependent fashion. PMID:12779334

Beam test of a full-length prototype of the BESIII drift chamber with the readout electronics

International Nuclear Information System (INIS)

Qin, Z.H.; Chen, Y.B.; Sheng, H.Y.; Wu, L.H.; Liu, J.B.; Zhuang, B.A.; Jiang, X.S.; Zhao, Y.B.; Zhu, K.J.; Yan, Z.K.; Chen, C.; Xu, M.H.; Wang, L.; Ma, X.Y.; Tang, X.; Liu, R.G.; Jin, Y.; Zhu, Q.M.; Zhang, G.F.; Wu, Z.; Li, R.Y.; Zhao, P.P.; Dai, H.L.; Li, X.P.; Li, J.

2007-01-01

A full-length prototype of the BESIII drift chamber together with its readout electronics was built and a beam test was performed. Two different methods, namely 'single-threshold method' and 'double-threshold method' for timing measurement, were studied. Test results show that the BESIII drift chamber and its readout electronics can reach their design specifications. The 'double-threshold method' results in a better timing accuracy and noise suppression capabilities as compared with the 'single-threshold method'

Assessment of adaptive evolution between wheat and rice as deduced from full-length common wheat cDNA sequence data and expression patterns

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Hayashizaki Yoshihide

2009-06-01

Full Text Available Abstract Background Wheat is an allopolyploid plant that harbors a huge, complex genome. Therefore, accumulation of expressed sequence tags (ESTs for wheat is becoming particularly important for functional genomics and molecular breeding. We prepared a comprehensive collection of ESTs from the various tissues that develop during the wheat life cycle and from tissues subjected to stress. We also examined their expression profiles in silico. As full-length cDNAs are indispensable to certify the collected ESTs and annotate the genes in the wheat genome, we performed a systematic survey and sequencing of the full-length cDNA clones. This sequence information is a valuable genetic resource for functional genomics and will enable carrying out comparative genomics in cereals. Results As part of the functional genomics and development of genomic wheat resources, we have generated a collection of full-length cDNAs from common wheat. By grouping the ESTs of recombinant clones randomly selected from the full-length cDNA library, we were able to sequence 6,162 independent clones with high accuracy. About 10% of the clones were wheat-unique genes, without any counterparts within the DNA database. Wheat clones that showed high homology to those of rice were selected in order to investigate their expression patterns in various tissues throughout the wheat life cycle and in response to abiotic-stress treatments. To assess the variability of genes that have evolved differently in wheat and rice, we calculated the substitution rate (Ka/Ks of the counterparts in wheat and rice. Genes that were preferentially expressed in certain tissues or treatments had higher Ka/Ks values than those in other tissues and treatments, which suggests that the genes with the higher variability expressed in these tissues is under adaptive selection. Conclusion We have generated a high-quality full-length cDNA resource for common wheat, which is essential for continuation of the

Studies of nontarget-mediated distribution of human full-length IgG1 antibody and its FAb fragment in cardiovascular and metabolic-related tissues.

Science.gov (United States)

Davidsson, Pia; Söderling, Ann-Sofi; Svensson, Lena; Ahnmark, Andrea; Flodin, Christine; Wanag, Ewa; Screpanti-Sundqvist, Valentina; Gennemark, Peter

2015-05-01

Tissue distribution and pharmacokinetics (PK) of full-length nontargeted antibody and its antigen-binding fragment (FAb) were evaluated for a range of tissues primarily of interest for cardiovascular and metabolic diseases. Mice were intravenously injected with a dose of 10 mg/kg of either human IgG1or its FAb fragment; perfused tissues were collected at a range of time points over 3 weeks for the human IgG1 antibody and 1 week for the human FAb antibody. Tissues were homogenized and antibody concentrations were measured by specific immunoassays on the Gyros system. Exposure in terms of maximum concentration (Cmax ) and area under the curve was assessed for all nine tissues. Tissue exposure of full-length antibody relative to plasma exposure was found to be between 1% and 10%, except for brain (0.2%). Relative concentrations of FAb antibody were the same, except for kidney tissue, where the antibody concentration was found to be ten times higher than in plasma. However, the absolute tissue uptake of full-length IgG was significantly higher than the absolute tissue uptake of the FAb antibody. This study provides a reference PK state for full-length whole and FAb antibodies in tissues related to cardiovascular and metabolic diseases that do not include antigen or antibody binding. © 2015 Wiley Periodicals, Inc. and the American Pharmacists Association.

Conformational change in full-length mouse prion: A site-directed spin-labeling study

International Nuclear Information System (INIS)

Inanami, Osamu; Hashida, Shukichi; Iizuka, Daisuke; Horiuchi, Motohiro; Hiraoka, Wakako; Shimoyama, Yuhei; Nakamura, Hideo; Inagaki, Fuyuhiko; Kuwabara, Mikinori

2005-01-01

The structure of the mouse prion (moPrP) was studied using site-directed spin-labeling electron spin resonance (SDSL-ESR). Since a previous NMR study by Hornemanna et al., [Hornemanna, Korthb, Oeschb, Rieka, Widera, Wuethricha, Glockshubera, Recombinant full-length murine prion protein, mPrP (23-231): purification and spectroscopic characterization, FEBS Lett. 413 (1997) 277-281] has indicated that N96, D143, and T189 in moPrP are localized in a Cu 2+ binding region, Helix1 and Helix2, respectively, three recombinant moPrP mutations (N96C, D143C, and T189C) were expressed in an Escherichia coli system, and then refolded by dialysis under low pH and purified by reverse-phase HPLC. By using the preparation, we succeeded in preserving a target cystein residue without alteration of the α-helix structure of moPrP and were able to apply SDSL-ESR with a methane thiosulfonate spin label to the full-length prion protein. The rotational correlation times (τ) of 1.1, 3.3, and 4.8 ns were evaluated from the X-band ESR spectra at pH 7.4 and 20 deg C for N96R1, D143R1, and T189R1, respectively. τ reflects the fact that the Cu 2+ binding region is more flexible than Helix1 or Helix2. ESR spectra recorded at various temperatures revealed two phases together with a transition point at around 20 deg C in D143R1 and T189R1, but not in N96R1. With the variation of pH from 4.0 to 7.8, ESR spectra of T189R1 at 20 deg C showed a gradual increase of τ from 2.9 to 4.8 ns. On the other hand, the pH-dependent conformational changes in N96R1 and D143R1 were negligible. These results indicated that T189 located in Helix2 possessed a structure sensitive to physiological pH changes; simultaneously, N96 in the Cu 2+ binding region and D143 in Helix1 were conserved

Caspase 3 inactivates biologically active full length interleukin-33 as a classical cytokine but does not prohibit nuclear translocation

International Nuclear Information System (INIS)

Ali, Shafaqat; Nguyen, Dang Quan; Falk, Werner; Martin, Michael Uwe

2010-01-01

IL-33 is a member of the IL-1 family of cytokines with dual function which either activates cells via the IL-33 receptor in a paracrine fashion or translocates to the nucleus to regulate gene transcription in an intracrine manner. We show that full length murine IL-33 is active as a cytokine and that it is not processed by caspase 1 to mature IL-33 but instead cleaved by caspase 3 at aa175 to yield two products which are both unable to bind to the IL-33 receptor. Full length IL-33 and its N-terminal caspase 3 breakdown product, however, translocate to the nucleus. Finally, bioactive IL-33 is not released by cells constitutively or after activation. This suggests that IL-33 is not a classical cytokine but exerts its function in the nucleus of intact cells and only activates others cells via its receptor as an alarm mediator after destruction of the producing cell.

Construction and characterization of a full-length cDNA library for the wheat stripe rust pathogen (Puccinia striiformis f. sp. tritici

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Chen Xianming

2007-06-01

Full Text Available Abstract Background Puccinia striiformis is a plant pathogenic fungus causing stripe rust, one of the most important diseases on cereal crops and grasses worldwide. However, little is know about its genome and genes involved in the biology and pathogenicity of the pathogen. We initiated the functional genomic research of the fungus by constructing a full-length cDNA and determined functions of the first group of genes by sequence comparison of cDNA clones to genes reported in other fungi. Results A full-length cDNA library, consisting of 42,240 clones with an average cDNA insert of 1.9 kb, was constructed using urediniospores of race PST-78 of P. striiformis f. sp. tritici. From 196 sequenced cDNA clones, we determined functions of 73 clones (37.2%. In addition, 36 clones (18.4% had significant homology to hypothetical proteins, 37 clones (18.9% had some homology to genes in other fungi, and the remaining 50 clones (25.5% did not produce any hits. From the 73 clones with functions, we identified 51 different genes encoding protein products that are involved in amino acid metabolism, cell defense, cell cycle, cell signaling, cell structure and growth, energy cycle, lipid and nucleotide metabolism, protein modification, ribosomal protein complex, sugar metabolism, transcription factor, transport metabolism, and virulence/infection. Conclusion The full-length cDNA library is useful in identifying functional genes of P. striiformis.

Full-Length Fibronectin Drives Fibroblast Accumulation at the Surface of Collagen Microtissues during Cell-Induced Tissue Morphogenesis.

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Jasper Foolen

Full Text Available Generating and maintaining gradients of cell density and extracellular matrix (ECM components is a prerequisite for the development of functionality of healthy tissue. Therefore, gaining insights into the drivers of spatial organization of cells and the role of ECM during tissue morphogenesis is vital. In a 3D model system of tissue morphogenesis, a fibronectin-FRET sensor recently revealed the existence of two separate fibronectin populations with different conformations in microtissues, i.e. 'compact and adsorbed to collagen' versus 'extended and fibrillar' fibronectin that does not colocalize with the collagen scaffold. Here we asked how the presence of fibronectin might drive this cell-induced tissue morphogenesis, more specifically the formation of gradients in cell density and ECM composition. Microtissues were engineered in a high-throughput model system containing rectangular microarrays of 12 posts, which constrained fibroblast-populated collagen gels, remodeled by the contractile cells into trampoline-shaped microtissues. Fibronectin's contribution during the tissue maturation process was assessed using fibronectin-knockout mouse embryonic fibroblasts (Fn-/- MEFs and floxed equivalents (Fnf/f MEFs, in fibronectin-depleted growth medium with and without exogenously added plasma fibronectin (full-length, or various fragments. In the absence of full-length fibronectin, Fn-/- MEFs remained homogenously distributed throughout the cell-contracted collagen gels. In contrast, in the presence of full-length fibronectin, both cell types produced shell-like tissues with a predominantly cell-free compacted collagen core and a peripheral surface layer rich in cells. Single cell assays then revealed that Fn-/- MEFs applied lower total strain energy on nanopillar arrays coated with either fibronectin or vitronectin when compared to Fnf/f MEFs, but that the presence of exogenously added plasma fibronectin rescued their contractility. While collagen

First full length sequences of the S gene of European isolates reveal further diversity among turkey coronaviruses.

OpenAIRE

2011-01-01

Abstract An increasing incidence of enteric disorders clinically evocative of the poult enteritis complex has been observed in turkeys in France since 2003. Using a newly designed real-time RT-PCR assay specific for the nucleocapsid (N) gene of infectious bronchitis virus (IBV) and turkey coronaviruses (TCoV), coronaviruses were identified in 37 % of the intestinal samples collected from diseased turkey flocks. The full length Spike (S) gene of these viruses was amplified, cloned a...

Sequencing and analysis of full-length cDNAs, 5'-ESTs and 3'-ESTs from a cartilaginous fish, the elephant shark (Callorhinchus milii).

KAUST Repository

Brenner, Sydney

2012-10-08

Cartilaginous fishes are the most ancient group of living jawed vertebrates (gnathostomes) and are, therefore, an important reference group for understanding the evolution of vertebrates. The elephant shark (Callorhinchus milii), a holocephalan cartilaginous fish, has been identified as a model cartilaginous fish genome because of its compact genome (∼910 Mb) and a genome project has been initiated to obtain its whole genome sequence. In this study, we have generated and sequenced full-length enriched cDNA libraries of the elephant shark using the \\'oligo-capping\\' method and Sanger sequencing. A total of 6,778 full-length protein-coding cDNA and 10,701 full-length noncoding cDNA were sequenced from six tissues (gills, intestine, kidney, liver, spleen, and testis) of the elephant shark. Analysis of their polyadenylation signals showed that polyadenylation usage in elephant shark is similar to that in mammals. Furthermore, both coding and noncoding transcripts of the elephant shark use the same proportion of canonical polyadenylation sites. Besides BLASTX searches, protein-coding transcripts were annotated by Gene Ontology, InterPro domain, and KEGG pathway analyses. By comparing elephant shark genes to bony vertebrate genes, we identified several ancient genes present in elephant shark but differentially lost in tetrapods or teleosts. Only ∼6% of elephant shark noncoding cDNA showed similarity to known noncoding RNAs (ncRNAs). The rest are either highly divergent ncRNAs or novel ncRNAs. In addition to full-length transcripts, 30,375 5\\'-ESTs and 41,317 3\\'-ESTs were sequenced and annotated. The clones and transcripts generated in this study are valuable resources for annotating transcription start sites, exon-intron boundaries, and UTRs of genes in the elephant shark genome, and for the functional characterization of protein sequences. These resources will also be useful for annotating genes in other cartilaginous fishes whose genomes have been targeted for

Sequencing and analysis of full-length cDNAs, 5'-ESTs and 3'-ESTs from a cartilaginous fish, the elephant shark (Callorhinchus milii).

KAUST Repository

Brenner, Sydney; Kodzius, Rimantas; Tan, Yue Ying; Tay, Alice; Tay, Boon-Hui; Venkatesh, Byrappa

2012-01-01

Cartilaginous fishes are the most ancient group of living jawed vertebrates (gnathostomes) and are, therefore, an important reference group for understanding the evolution of vertebrates. The elephant shark (Callorhinchus milii), a holocephalan cartilaginous fish, has been identified as a model cartilaginous fish genome because of its compact genome (∼910 Mb) and a genome project has been initiated to obtain its whole genome sequence. In this study, we have generated and sequenced full-length enriched cDNA libraries of the elephant shark using the 'oligo-capping' method and Sanger sequencing. A total of 6,778 full-length protein-coding cDNA and 10,701 full-length noncoding cDNA were sequenced from six tissues (gills, intestine, kidney, liver, spleen, and testis) of the elephant shark. Analysis of their polyadenylation signals showed that polyadenylation usage in elephant shark is similar to that in mammals. Furthermore, both coding and noncoding transcripts of the elephant shark use the same proportion of canonical polyadenylation sites. Besides BLASTX searches, protein-coding transcripts were annotated by Gene Ontology, InterPro domain, and KEGG pathway analyses. By comparing elephant shark genes to bony vertebrate genes, we identified several ancient genes present in elephant shark but differentially lost in tetrapods or teleosts. Only ∼6% of elephant shark noncoding cDNA showed similarity to known noncoding RNAs (ncRNAs). The rest are either highly divergent ncRNAs or novel ncRNAs. In addition to full-length transcripts, 30,375 5'-ESTs and 41,317 3'-ESTs were sequenced and annotated. The clones and transcripts generated in this study are valuable resources for annotating transcription start sites, exon-intron boundaries, and UTRs of genes in the elephant shark genome, and for the functional characterization of protein sequences. These resources will also be useful for annotating genes in other cartilaginous fishes whose genomes have been targeted for whole

Full length articles published in BJOMS during 2010-11--an analysis by sub-specialty and study type.

Science.gov (United States)

Arakeri, Gururaj; Colbert, Serryth; Rosenbaum, Gavin; Brennan, Peter A

2012-12-01

Full length articles such as prospective and retrospective studies, case series, laboratory-based research and reviews form the majority of papers published in the British Journal of Oral and Maxillofacial Surgery (BJOMS). We were interested to evaluate the breakdown of these types of articles both by sub-specialty and the type of study as well as the proportion that are written by UK colleagues compared to overseas authors over a 2 year period (2010-11). A total of 191 full length articles across all sub-specialties of our discipline were published, with 107 papers (56%) coming from UK authors. There were proportionately more oncology papers arising from the UK than overseas (60 and 30% of total respectively) while the opposite was found for cleft/deformity studies (10% and 22%). There was only one laboratory-based study published from the UK compared with 27 papers from overseas. The number of quality papers being submitted to the Journal continues to increase, and the type of article being published between UK and overseas probably reflects different practices and case-loads amongst colleagues. The relatively few UK laboratory based studies published in BJOMS compared to overseas authors are most likely due to authors seeking the most prestigious journals possible for their work. Copyright © 2012 The British Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.

Particle infectivity of HIV-1 full-length genome infectious molecular clones in a subtype C heterosexual transmission pair following high fidelity amplification and unbiased cloning

Energy Technology Data Exchange (ETDEWEB)

Deymier, Martin J., E-mail: mdeymie@emory.edu [Emory Vaccine Center, Yerkes National Primate Research Center, 954 Gatewood Road NE, Atlanta, GA 30329 (United States); Claiborne, Daniel T., E-mail: dclaibo@emory.edu [Emory Vaccine Center, Yerkes National Primate Research Center, 954 Gatewood Road NE, Atlanta, GA 30329 (United States); Ende, Zachary, E-mail: zende@emory.edu [Emory Vaccine Center, Yerkes National Primate Research Center, 954 Gatewood Road NE, Atlanta, GA 30329 (United States); Ratner, Hannah K., E-mail: hannah.ratner@emory.edu [Emory Vaccine Center, Yerkes National Primate Research Center, 954 Gatewood Road NE, Atlanta, GA 30329 (United States); Kilembe, William, E-mail: wkilembe@rzhrg-mail.org [Zambia-Emory HIV Research Project (ZEHRP), B22/737 Mwembelelo, Emmasdale Post Net 412, P/BagE891, Lusaka (Zambia); Allen, Susan, E-mail: sallen5@emory.edu [Zambia-Emory HIV Research Project (ZEHRP), B22/737 Mwembelelo, Emmasdale Post Net 412, P/BagE891, Lusaka (Zambia); Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA (United States); Hunter, Eric, E-mail: eric.hunter2@emory.edu [Emory Vaccine Center, Yerkes National Primate Research Center, 954 Gatewood Road NE, Atlanta, GA 30329 (United States); Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA (United States)

2014-11-15

The high genetic diversity of HIV-1 impedes high throughput, large-scale sequencing and full-length genome cloning by common restriction enzyme based methods. Applying novel methods that employ a high-fidelity polymerase for amplification and an unbiased fusion-based cloning strategy, we have generated several HIV-1 full-length genome infectious molecular clones from an epidemiologically linked transmission pair. These clones represent the transmitted/founder virus and phylogenetically diverse non-transmitted variants from the chronically infected individual's diverse quasispecies near the time of transmission. We demonstrate that, using this approach, PCR-induced mutations in full-length clones derived from their cognate single genome amplicons are rare. Furthermore, all eight non-transmitted genomes tested produced functional virus with a range of infectivities, belying the previous assumption that a majority of circulating viruses in chronic HIV-1 infection are defective. Thus, these methods provide important tools to update protocols in molecular biology that can be universally applied to the study of human viral pathogens. - Highlights: • Our novel methodology demonstrates accurate amplification and cloning of full-length HIV-1 genomes. • A majority of plasma derived HIV variants from a chronically infected individual are infectious. • The transmitted/founder was more infectious than the majority of the variants from the chronically infected donor.

Particle infectivity of HIV-1 full-length genome infectious molecular clones in a subtype C heterosexual transmission pair following high fidelity amplification and unbiased cloning

International Nuclear Information System (INIS)

Deymier, Martin J.; Claiborne, Daniel T.; Ende, Zachary; Ratner, Hannah K.; Kilembe, William; Allen, Susan; Hunter, Eric

2014-01-01

The high genetic diversity of HIV-1 impedes high throughput, large-scale sequencing and full-length genome cloning by common restriction enzyme based methods. Applying novel methods that employ a high-fidelity polymerase for amplification and an unbiased fusion-based cloning strategy, we have generated several HIV-1 full-length genome infectious molecular clones from an epidemiologically linked transmission pair. These clones represent the transmitted/founder virus and phylogenetically diverse non-transmitted variants from the chronically infected individual's diverse quasispecies near the time of transmission. We demonstrate that, using this approach, PCR-induced mutations in full-length clones derived from their cognate single genome amplicons are rare. Furthermore, all eight non-transmitted genomes tested produced functional virus with a range of infectivities, belying the previous assumption that a majority of circulating viruses in chronic HIV-1 infection are defective. Thus, these methods provide important tools to update protocols in molecular biology that can be universally applied to the study of human viral pathogens. - Highlights: • Our novel methodology demonstrates accurate amplification and cloning of full-length HIV-1 genomes. • A majority of plasma derived HIV variants from a chronically infected individual are infectious. • The transmitted/founder was more infectious than the majority of the variants from the chronically infected donor

Inconsistencies of genome annotations in apicomplexan parasites revealed by 5'-end-one-pass and full-length sequences of oligo-capped cDNAs

Directory of Open Access Journals (Sweden)

Sugano Sumio

2009-07-01

Full Text Available Abstract Background Apicomplexan parasites are causative agents of various diseases including malaria and have been targets of extensive genomic sequencing. We generated 5'-EST collections for six apicomplexa parasites using our full-length oligo-capping cDNA library method. To improve upon the current genome annotations, as well as to validate the importance for physical cDNA clone resources, we generated a large-scale collection of full-length cDNAs for several apicomplexa parasites. Results In this study, we used a total of 61,056 5'-end-single-pass cDNA sequences from Plasmodium falciparum, P. vivax, P. yoelii, P. berghei, Cryptosporidium parvum, and Toxoplasma gondii. We compared these partially sequenced cDNA sequences with the currently annotated gene models and observed significant inconsistencies between the two datasets. In particular, we found that on average 14% of the exons in the current gene models were not supported by any cDNA evidence, and that 16% of the current gene models may contain at least one mis-annotation and should be re-evaluated. We also identified a large number of transcripts that had been previously unidentified. For 732 cDNAs in T. gondii, the entire sequences were determined in order to evaluate the annotated gene models at the complete full-length transcript level. We found that 41% of the T. gondii gene models contained at least one inconsistency. We also identified and confirmed by RT-PCR 140 previously unidentified transcripts found in the intergenic regions of the current gene annotations. We show that the majority of these discrepancies are due to questionable predictions of one or two extra exons in the upstream or downstream regions of the genes. Conclusion Our data indicates that the current gene models are likely to still be incomplete and have much room for improvement. Our unique full-length cDNA information is especially useful for further refinement of the annotations for the genomes of

Patient-Specific Instruments Based on Knee Joint Computed Tomography and Full-Length Lower Extremity Radiography in Total Knee Replacement

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Hua Tian

2018-01-01

Conclusions: The use of PSIs based on knee joint CT and standing full-length lower extremity radiography in TKR resulted in acceptable alignment compared with the use of conventional instruments, although the marginal advantage was not statistically different. Surgical time and clinical results were also similar between the two groups. However, the PSI group had less postoperative drainage.

An RNA-Seq strategy to detect the complete coding and non-coding transcriptome including full-length imprinted macro ncRNAs.

Directory of Open Access Journals (Sweden)

Ru Huang

Full Text Available Imprinted macro non-protein-coding (nc RNAs are cis-repressor transcripts that silence multiple genes in at least three imprinted gene clusters in the mouse genome. Similar macro or long ncRNAs are abundant in the mammalian genome. Here we present the full coding and non-coding transcriptome of two mouse tissues: differentiated ES cells and fetal head using an optimized RNA-Seq strategy. The data produced is highly reproducible in different sequencing locations and is able to detect the full length of imprinted macro ncRNAs such as Airn and Kcnq1ot1, whose length ranges between 80-118 kb. Transcripts show a more uniform read coverage when RNA is fragmented with RNA hydrolysis compared with cDNA fragmentation by shearing. Irrespective of the fragmentation method, all coding and non-coding transcripts longer than 8 kb show a gradual loss of sequencing tags towards the 3' end. Comparisons to published RNA-Seq datasets show that the strategy presented here is more efficient in detecting known functional imprinted macro ncRNAs and also indicate that standardization of RNA preparation protocols would increase the comparability of the transcriptome between different RNA-Seq datasets.

An integrated PCR colony hybridization approach to screen cDNA libraries for full-length coding sequences.

Science.gov (United States)

Pollier, Jacob; González-Guzmán, Miguel; Ardiles-Diaz, Wilson; Geelen, Danny; Goossens, Alain

2011-01-01

cDNA-Amplified Fragment Length Polymorphism (cDNA-AFLP) is a commonly used technique for genome-wide expression analysis that does not require prior sequence knowledge. Typically, quantitative expression data and sequence information are obtained for a large number of differentially expressed gene tags. However, most of the gene tags do not correspond to full-length (FL) coding sequences, which is a prerequisite for subsequent functional analysis. A medium-throughput screening strategy, based on integration of polymerase chain reaction (PCR) and colony hybridization, was developed that allows in parallel screening of a cDNA library for FL clones corresponding to incomplete cDNAs. The method was applied to screen for the FL open reading frames of a selection of 163 cDNA-AFLP tags from three different medicinal plants, leading to the identification of 109 (67%) FL clones. Furthermore, the protocol allows for the use of multiple probes in a single hybridization event, thus significantly increasing the throughput when screening for rare transcripts. The presented strategy offers an efficient method for the conversion of incomplete expressed sequence tags (ESTs), such as cDNA-AFLP tags, to FL-coding sequences.

Pre-Steady-State Kinetic Analysis of Truncated and Full-Length Saccharomyces cerevisiae DNA Polymerase Eta

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Jessica A. Brown

2010-01-01

Full Text Available Understanding polymerase fidelity is an important objective towards ascertaining the overall stability of an organism's genome. Saccharomyces cerevisiae DNA polymerase η (yPolη, a Y-family DNA polymerase, is known to efficiently bypass DNA lesions (e.g., pyrimidine dimers in vivo. Using pre-steady-state kinetic methods, we examined both full-length and a truncated version of yPolη which contains only the polymerase domain. In the absence of yPolη's C-terminal residues 514–632, the DNA binding affinity was weakened by 2-fold and the base substitution fidelity dropped by 3-fold. Thus, the C-terminus of yPolη may interact with DNA and slightly alter the conformation of the polymerase domain during catalysis. In general, yPolη discriminated between a correct and incorrect nucleotide more during the incorporation step (50-fold on average than the ground-state binding step (18-fold on average. Blunt-end additions of dATP or pyrene nucleotide 5′-triphosphate revealed the importance of base stacking during the binding of incorrect incoming nucleotides.

A new set of ESTs and cDNA clones from full-length and normalized libraries for gene discovery and functional characterization in citrus

Directory of Open Access Journals (Sweden)

Alamar Santiago

2009-09-01

Full Text Available Abstract Background Interpretation of ever-increasing raw sequence information generated by modern genome sequencing technologies faces multiple challenges, such as gene function analysis and genome annotation. Indeed, nearly 40% of genes in plants encode proteins of unknown function. Functional characterization of these genes is one of the main challenges in modern biology. In this regard, the availability of full-length cDNA clones may fill in the gap created between sequence information and biological knowledge. Full-length cDNA clones facilitate functional analysis of the corresponding genes enabling manipulation of their expression in heterologous systems and the generation of a variety of tagged versions of the native protein. In addition, the development of full-length cDNA sequences has the power to improve the quality of genome annotation. Results We developed an integrated method to generate a new normalized EST collection enriched in full-length and rare transcripts of different citrus species from multiple tissues and developmental stages. We constructed a total of 15 cDNA libraries, from which we isolated 10,898 high-quality ESTs representing 6142 different genes. Percentages of redundancy and proportion of full-length clones range from 8 to 33, and 67 to 85, respectively, indicating good efficiency of the approach employed. The new EST collection adds 2113 new citrus ESTs, representing 1831 unigenes, to the collection of citrus genes available in the public databases. To facilitate functional analysis, cDNAs were introduced in a Gateway-based cloning vector for high-throughput functional analysis of genes in planta. Herein, we describe the technical methods used in the library construction, sequence analysis of clones and the overexpression of CitrSEP, a citrus homolog to the Arabidopsis SEP3 gene, in Arabidopsis as an example of a practical application of the engineered Gateway vector for functional analysis. Conclusion The new

Characterization of near full-length genomes of HIV type 1 strains in Denmark: Basis for a universal therapeutic vaccine

DEFF Research Database (Denmark)

Andresen, Betina S.; Vinner, Lasse; Tang, Sheila Tuyet

2007-01-01

We report here the near full-length sequence characterization of 17 Danish clinical HIV-1 strains isolated from HLA-A02 patients not in need of ART, with relatively low viral loads and normal CD4 cell counts. Sequencing was performed directly on DNA extracted from short-term cocultures of PBMCs...... of a universal immunotherapeutic vaccine construct based on these epitopes....

Binding site analysis of full-length α1a adrenergic receptor using homology modeling and molecular docking

International Nuclear Information System (INIS)

Pedretti, Alessandro; Elena Silva, Maria; Villa, Luigi; Vistoli, Giulio

2004-01-01

The recent availability of crystal structure of bovine rhodopsin offers new opportunities in order to approach the construction of G protein coupled receptors. This study focuses the attention on the modeling of full-length α 1a adrenergic receptor (α 1a -AR) due to its biological role and significant implications in pharmacological treatment of benign prostate hyperplasia. This work could be considered made up by two main steps: (a) the construction of full structure of α 1a -AR, through homology modeling methods; (b) the automated docking of an endogenous agonist, norepinephrine, and of an antagonist, WB-4101, using BioDock program. The obtained results highlight the key residues involved in binding sites of both agonists and antagonists, confirming the mutagenesis data and giving new suggestions for the rational design of selective ligands

Rational Design of High-Number dsDNA Fragments Based on Thermodynamics for the Construction of Full-Length Genes in a Single Reaction.

Directory of Open Access Journals (Sweden)

Bhagyashree S Birla

Full Text Available Gene synthesis is frequently used in modern molecular biology research either to create novel genes or to obtain natural genes when the synthesis approach is more flexible and reliable than cloning. DNA chemical synthesis has limits on both its length and yield, thus full-length genes have to be hierarchically constructed from synthesized DNA fragments. Gibson Assembly and its derivatives are the simplest methods to assemble multiple double-stranded DNA fragments. Currently, up to 12 dsDNA fragments can be assembled at once with Gibson Assembly according to its vendor. In practice, the number of dsDNA fragments that can be assembled in a single reaction are much lower. We have developed a rational design method for gene construction that allows high-number dsDNA fragments to be assembled into full-length genes in a single reaction. Using this new design method and a modified version of the Gibson Assembly protocol, we have assembled 3 different genes from up to 45 dsDNA fragments at once. Our design method uses the thermodynamic analysis software Picky that identifies all unique junctions in a gene where consecutive DNA fragments are specifically made to connect to each other. Our novel method is generally applicable to most gene sequences, and can improve both the efficiency and cost of gene assembly.

VP1u phospholipase activity is critical for infectivity of full-length parvovirus B19 genomic clones

OpenAIRE

Filippone, Claudia; Zhi, Ning; Wong, Susan; Lu, Jun; Kajigaya, Sachiko; Gallinella, Giorgio; Kakkola, Laura; Söderlund-Venermo, Maria; Young, Neal S.; Brown, Kevin E.

2008-01-01

Three full-length genomic clones (pB19-M20, pB19-FL and pB19-HG1) of parvovirus B19 were produced in different laboratories. pB19-M20 was shown to produce infectious virus. To determine the differences in infectivity, all three plasmids were tested by transfection and infection assays. All three clones were similar in viral DNA replication, RNA transcription, and viral capsid protein production. However, only pB19-M20 and pB19-HG1 produced infectious virus. Comparison of viral sequences showe...

Differing Efficacies of Lead Group A Streptococcal Vaccine Candidates and Full-Length M Protein in Cutaneous and Invasive Disease Models

Directory of Open Access Journals (Sweden)

Tania Rivera-Hernandez

2016-06-01

Full Text Available Group A Streptococcus (GAS is an important human pathogen responsible for both superficial infections and invasive diseases. Autoimmune sequelae may occur upon repeated infection. For this reason, development of a vaccine against GAS represents a major challenge, since certain GAS components may trigger autoimmunity. We formulated three combination vaccines containing the following: (i streptolysin O (SLO, interleukin 8 (IL-8 protease (Streptococcus pyogenes cell envelope proteinase [SpyCEP], group A streptococcal C5a peptidase (SCPA, arginine deiminase (ADI, and trigger factor (TF; (ii the conserved M-protein-derived J8 peptide conjugated to ADI; and (iii group A carbohydrate lacking the N-acetylglucosamine side chain conjugated to ADI. We compared these combination vaccines to a “gold standard” for immunogenicity, full-length M1 protein. Vaccines were adjuvanted with alum, and mice were immunized on days 0, 21, and 28. On day 42, mice were challenged via cutaneous or subcutaneous routes. High-titer antigen-specific antibody responses with bactericidal activity were detected in mouse serum samples for all vaccine candidates. In comparison with sham-immunized mice, all vaccines afforded protection against cutaneous challenge. However, only full-length M1 protein provided protection in the subcutaneous invasive disease model.

A new set of ESTs and cDNA clones from full-length and normalized libraries for gene discovery and functional characterization in citrus

Science.gov (United States)

Marques, M Carmen; Alonso-Cantabrana, Hugo; Forment, Javier; Arribas, Raquel; Alamar, Santiago; Conejero, Vicente; Perez-Amador, Miguel A

2009-01-01

Background Interpretation of ever-increasing raw sequence information generated by modern genome sequencing technologies faces multiple challenges, such as gene function analysis and genome annotation. Indeed, nearly 40% of genes in plants encode proteins of unknown function. Functional characterization of these genes is one of the main challenges in modern biology. In this regard, the availability of full-length cDNA clones may fill in the gap created between sequence information and biological knowledge. Full-length cDNA clones facilitate functional analysis of the corresponding genes enabling manipulation of their expression in heterologous systems and the generation of a variety of tagged versions of the native protein. In addition, the development of full-length cDNA sequences has the power to improve the quality of genome annotation. Results We developed an integrated method to generate a new normalized EST collection enriched in full-length and rare transcripts of different citrus species from multiple tissues and developmental stages. We constructed a total of 15 cDNA libraries, from which we isolated 10,898 high-quality ESTs representing 6142 different genes. Percentages of redundancy and proportion of full-length clones range from 8 to 33, and 67 to 85, respectively, indicating good efficiency of the approach employed. The new EST collection adds 2113 new citrus ESTs, representing 1831 unigenes, to the collection of citrus genes available in the public databases. To facilitate functional analysis, cDNAs were introduced in a Gateway-based cloning vector for high-throughput functional analysis of genes in planta. Herein, we describe the technical methods used in the library construction, sequence analysis of clones and the overexpression of CitrSEP, a citrus homolog to the Arabidopsis SEP3 gene, in Arabidopsis as an example of a practical application of the engineered Gateway vector for functional analysis. Conclusion The new EST collection denotes an

EXPRESSION AND CHARACTERIZATION OF FULL-LENGTH HUMAN HEME OXYGENASE-1: PRESENCE OF INTACT MEMBRANE-BINDING REGION LEADS TO INCREASED BINDING AFFINITY FOR NADPH-CYTOCHROME P450 REDUCTASE

Science.gov (United States)

Huber, Warren J.; Backes, Wayne L.

2009-01-01

Heme oxygenase (HO) is the chief regulatory enzyme in the oxidative degradation of heme to biliverdin. In the process of heme degradation, this NADPH and cytochrome P450 reductase (CPR)-dependent oxidation of heme also releases free iron and carbon monoxide. Much of the recent research involving heme oxygenase is done using a 30-kDa soluble form of the enzyme, which lacks the membrane binding region (C-terminal 23 amino acids). The goal of this study was to express and purify a full-length human HO-1 (hHO-1) protein; however, due to the lability of the full-length form, a rapid purification procedure was required. This was accomplished by use of a GST-tagged hHO-1 construct. Although the procedure permitted the generation of a full-length HO-1, this form was contaminated with a 30-kDa degradation product that could not be eliminated. Therefore, we attempted to remove a putative secondary thrombin cleavage site by a conservative mutation of amino acid 254, which replaces lysine with arginine. This mutation allowed the expression and purification of a full length hHO-1 protein. Unlike wild-type HO-1, the K254R mutant could be purified to a single 32-kDa protein capable of degrading heme at the same rate as the wild-type enzyme. The K254R full-length form had a specific activity of ~200–225 nmol bilirubin hr−1nmol−1 HO-1 as compared to ~140–150 nmol bilirubin hr−1nmol−1 for the WT form, which contains the 30-kDa contaminant. This is a 2–3-fold increase from the previously reported soluble 30-kDa HO-1, suggesting that the C-terminal 23 amino acids are essential for maximal catalytic activity. Because the membrane spanning domain is present, the full-length hHO-1 has the potential to incorporate into phospholipid membranes, which can be reconstituted at known concentrations, in combination with other ER-resident enzymes. PMID:17915953

Construction of a normalized full-length cDNA library of cephalopod Amphioctopus fangsiao and development of microsatellite markers

Science.gov (United States)

Feng, Yanwei; Liu, Wenfen; Xu, Xin; Yang, Jianmin; Wang, Weijun; Wei, Xiumei; Liu, Xiangquan; Sun, Guohua

2017-10-01

Amphioctopus fangsiao is one of the most economically important species and has been considered to be a candidate for aquaculture. In order to facilitate its fine-scale genetic analyses, we constructed a normalized full-length library successfully and developed a set of microsatellite markers in this study. The normalized full-length library had a storage capacity of 6.9×105 independent clones. The recombination efficiency was 95% and the average size of inserted fragments was longer than 1000 bp. A total of 3440 high quality ESTs were obtained, which were assembled into 1803 unigenes. Of these unigenes, 450 (25%) were assigned into 33 Gene Ontology terms, 576 (31.9%) into 153 Kyoto Encyclopedia of Genes and Genomes pathways, and 275 (15.3%) into 22 Clusters of Orthologous Groups. Seventy-six polymorphic microsatellite markers were identified. The number of alleles per locus ranged from 4 to 17, and the observed and expected heterozygosities varied between 0.167 and 0.967 and between 0.326 and 0.944, respectively. Twelve loci were significantly deviated from Hardy-Weinberg equilibrium after Bonferroni correction and no linkage disequilibrium was found between different loci. This study provided not only a useful resource for the isolation of the functional genes, but also a set of informative microsatellites for the assessment of population structure and conservation genetics of A. fangsiao.

A Novel mouse model of enhanced proteostasis: Full-length human heat shock factor 1 transgenic mice

International Nuclear Information System (INIS)

Pierce, Anson; Wei, Rochelle; Halade, Dipti; Yoo, Si-Eun; Ran, Qitao; Richardson, Arlan

2010-01-01

Research highlights: → Development of mouse overexpressing native human HSF1 in all tissues including CNS. → HSF1 overexpression enhances heat shock response at whole-animal and cellular level. → HSF1 overexpression protects from polyglutamine toxicity and favors aggresomes. → HSF1 overexpression enhances proteostasis at the whole-animal and cellular level. -- Abstract: The heat shock response (HSR) is controlled by the master transcriptional regulator heat shock factor 1 (HSF1). HSF1 maintains proteostasis and resistance to stress through production of heat shock proteins (HSPs). No transgenic model exists that overexpresses HSF1 in tissues of the central nervous system (CNS). We generated a transgenic mouse overexpressing full-length non-mutant HSF1 and observed a 2-4-fold increase in HSF1 mRNA and protein expression in all tissues studied of HSF1 transgenic (HSF1 +/0 ) mice compared to wild type (WT) littermates, including several regions of the CNS. Basal expression of HSP70 and 90 showed only mild tissue-specific changes; however, in response to forced exercise, the skeletal muscle HSR was more elevated in HSF1 +/0 mice compared to WT littermates and in fibroblasts following heat shock, as indicated by levels of inducible HSP70 mRNA and protein. HSF1 +/0 cells elicited a significantly more robust HSR in response to expression of the 82 repeat polyglutamine-YFP fusion construct (Q82YFP) and maintained proteasome-dependent processing of Q82YFP compared to WT fibroblasts. Overexpression of HSF1 was associated with fewer, but larger Q82YFP aggregates resembling aggresomes in HSF1 +/0 cells, and increased viability. Therefore, our data demonstrate that tissues and cells from mice overexpressing full-length non-mutant HSF1 exhibit enhanced proteostasis.

Computational Insight Into the Structural Organization of Full-Length Toll-Like Receptor 4 Dimer in a Model Phospholipid Bilayer

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Mahesh Chandra Patra

2018-03-01

Full Text Available Toll-like receptors (TLRs are a unique category of pattern recognition receptors that recognize distinct pathogenic components, often utilizing the same set of downstream adaptors. Specific molecular features of extracellular, transmembrane (TM, and cytoplasmic domains of TLRs are crucial for coordinating the complex, innate immune signaling pathway. Here, we constructed a full-length structural model of TLR4—a widely studied member of the interleukin-1 receptor/TLR superfamily—using homology modeling, protein–protein docking, and molecular dynamics simulations to understand the differential domain organization of TLR4 in a membrane-aqueous environment. Results showed that each functional domain of the membrane-bound TLR4 displayed several structural transitions that are biophysically essential for plasma membrane integration. Specifically, the extracellular and cytoplasmic domains were partially immersed in the upper and lower leaflets of the membrane bilayer. Meanwhile, TM domains tilted considerably to overcome the hydrophobic mismatch with the bilayer core. Our analysis indicates an alternate dimerization or a potential oligomerization interface of TLR4-TM. Moreover, the helical properties of an isolated TM dimer partly agree with that of the full-length receptor. Furthermore, membrane-absorbed or solvent-exposed surfaces of the toll/interleukin-1 receptor domain are consistent with previous X-ray crystallography and biochemical studies. Collectively, we provided a complete structural model of membrane-bound TLR4 that strengthens our current understanding of the complex mechanism of receptor activation and adaptor recruitment in the innate immune signaling pathway.

High avidity antibodies to full-length VAR2CSA correlate with absence of placental malaria

DEFF Research Database (Denmark)

Tutterrow, Yeung Lo; Salanti, Ali; Avril, Marion

2012-01-01

VAR2CSA mediates sequestration of Plasmodium falciparum-infected erythrocytes in the placenta, increasing the risk of poor pregnancy outcomes. Naturally acquired antibodies (Ab) to placental parasites at delivery have been associated with improved pregnancy outcomes, but Ab levels and how early...... in pregnancy Ab must be present in order to eliminate placental parasites before delivery remains unknown. Antibodies to individual Duffy-binding like domains of VAR2CSA have been studied, but the domains lack many of the conformational epitopes present in full-length VAR2CSA (FV2). Thus, the purpose...... of this study was to describe the acquisition of Ab to FV2 in women residing in high and low transmission areas and determine how Ab levels during pregnancy correlate with clearance of placental parasites. Plasma samples collected monthly throughout pregnancy from pregnant women living in high and low...

Retrieval of a million high-quality, full-length microbial 16S and 18S rRNA gene sequences without primer bias

DEFF Research Database (Denmark)

Karst, Søren Michael; Dueholm, Morten Simonsen; McIlroy, Simon Jon

2018-01-01

Small subunit ribosomal RNA (SSU rRNA) genes, 16S in bacteria and 18S in eukaryotes, have been the standard phylogenetic markers used to characterize microbial diversity and evolution for decades. However, the reference databases of full-length SSU rRNA gene sequences are skewed to well-studied e...

Molecular comparisons of full length metapneumovirus (MPV genomes, including newly determined French AMPV-C and -D isolates, further supports possible subclassification within the MPV Genus.

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Paul A Brown

Full Text Available Four avian metapneumovirus (AMPV subgroups (A-D have been reported previously based on genetic and antigenic differences. However, until now full length sequences of the only known isolates of European subgroup C and subgroup D viruses (duck and turkey origin, respectively have been unavailable. These full length sequences were determined and compared with other full length AMPV and human metapneumoviruses (HMPV sequences reported previously, using phylogenetics, comparisons of nucleic and amino acid sequences and study of codon usage bias. Results confirmed that subgroup C viruses were more closely related to HMPV than they were to the other AMPV subgroups in the study. This was consistent with previous findings using partial genome sequences. Closer relationships between AMPV-A, B and D were also evident throughout the majority of results. Three metapneumovirus "clusters" HMPV, AMPV-C and AMPV-A, B and D were further supported by codon bias and phylogenetics. The data presented here together with those of previous studies describing antigenic relationships also between AMPV-A, B and D and between AMPV-C and HMPV may call for a subclassification of metapneumoviruses similar to that used for avian paramyxoviruses, grouping AMPV-A, B and D as type I metapneumoviruses and AMPV-C and HMPV as type II.

Use of Dried Blood Spots to Elucidate Full-Length Transmitted/Founder HIV-1 Genomes

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Jesus F. Salazar-Gonzalez

2016-07-01

Full Text Available Background: Identification of HIV-1 genomes responsible for establishing clinical infection in newly infected individuals is fundamental to prevention and pathogenesis research. Processing, storage, and transportation of the clinical samples required to perform these virologic assays in resource-limited settings requires challenging venipuncture and cold chain logistics. Here, we validate the use of dried-blood spots (DBS as a simple and convenient alternative to collecting and storing frozen plasma. Methods: We performed parallel nucleic acid extraction, single genome amplification (SGA, next generation sequencing (NGS, and phylogenetic analyses on plasma and DBS. Results: We demonstrated the capacity to extract viral RNA from DBS and perform SGA to infer the complete nucleotide sequence of the transmitted/founder (TF HIV-1 envelope gene and full-length genome in two acutely infected individuals. Using both SGA and NGS methodologies, we showed that sequences generated from DBS and plasma display comparable phylogenetic patterns in both acute and chronic infection. SGA was successful on samples with a range of plasma viremia, including samples as low as 1,700 copies/ml and an estimated ~50 viral copies per blood spot. Further, we demonstrated reproducible efficiency in gp160 env sequencing in DBS stored at ambient temperature for up to three weeks or at -20ºC for up to five months. Conclusions: These findings support the use of DBS as a practical and cost-effective alternative to frozen plasma for clinical trials and translational research conducted in resource-limited settings.

Single-molecule study of full-length NaChBac by planar lipid bilayer recording.

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Andrew Jo

Full Text Available Planar lipid bilayer device, alternatively known as BLM, is a powerful tool to study functional properties of conducting membrane proteins such as ion channels and porins. In this work, we used BLM to study the prokaryotic voltage-gated sodium channel (Nav NaChBac in a well-defined membrane environment. Navs are an essential component for the generation and propagation of electric signals in excitable cells. The successes in the biochemical, biophysical and crystallographic studies on prokaryotic Navs in recent years has greatly promoted the understanding of the molecular mechanism that underlies these proteins and their eukaryotic counterparts. In this work, we investigated the single-molecule conductance and ionic selectivity behavior of NaChBac. Purified NaChBac protein was first reconstituted into lipid vesicles, which is subsequently incorporated into planar lipid bilayer by fusion. At single-molecule level, we were able to observe three distinct long-lived conductance sub-states of NaChBac. Change in the membrane potential switches on the channel mainly by increasing its opening probability. In addition, we found that individual NaChBac has similar permeability for Na+, K+, and Ca2+. The single-molecule behavior of the full-length protein is essentially highly stochastic. Our results show that planar lipid bilayer device can be used to study purified ion channels at single-molecule level in an artificial environment, and such studies can reveal new protein properties that are otherwise not observable in in vivo ensemble studies.

Calculation of evolutionary correlation between individual genes and full-length genome: a method useful for choosing phylogenetic markers for molecular epidemiology.

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Shuai Wang

Full Text Available Individual genes or regions are still commonly used to estimate the phylogenetic relationships among viral isolates. The genomic regions that can faithfully provide assessments consistent with those predicted with full-length genome sequences would be preferable to serve as good candidates of the phylogenetic markers for molecular epidemiological studies of many viruses. Here we employed a statistical method to evaluate the evolutionary relationships between individual viral genes and full-length genomes without tree construction as a way to determine which gene can match the genome well in phylogenetic analyses. This method was performed by calculation of linear correlations between the genetic distance matrices of aligned individual gene sequences and aligned genome sequences. We applied this method to the phylogenetic analyses of porcine circovirus 2 (PCV2, measles virus (MV, hepatitis E virus (HEV and Japanese encephalitis virus (JEV. Phylogenetic trees were constructed for comparisons and the possible factors affecting the method accuracy were also discussed in the calculations. The results revealed that this method could produce results consistent with those of previous studies about the proper consensus sequences that could be successfully used as phylogenetic markers. And our results also suggested that these evolutionary correlations could provide useful information for identifying genes that could be used effectively to infer the genetic relationships.

Rational Design of High-Number dsDNA Fragments Based on Thermodynamics for the Construction of Full-Length Genes in a Single Reaction.

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Birla, Bhagyashree S; Chou, Hui-Hsien

2015-01-01

Gene synthesis is frequently used in modern molecular biology research either to create novel genes or to obtain natural genes when the synthesis approach is more flexible and reliable than cloning. DNA chemical synthesis has limits on both its length and yield, thus full-length genes have to be hierarchically constructed from synthesized DNA fragments. Gibson Assembly and its derivatives are the simplest methods to assemble multiple double-stranded DNA fragments. Currently, up to 12 dsDNA fragments can be assembled at once with Gibson Assembly according to its vendor. In practice, the number of dsDNA fragments that can be assembled in a single reaction are much lower. We have developed a rational design method for gene construction that allows high-number dsDNA fragments to be assembled into full-length genes in a single reaction. Using this new design method and a modified version of the Gibson Assembly protocol, we have assembled 3 different genes from up to 45 dsDNA fragments at once. Our design method uses the thermodynamic analysis software Picky that identifies all unique junctions in a gene where consecutive DNA fragments are specifically made to connect to each other. Our novel method is generally applicable to most gene sequences, and can improve both the efficiency and cost of gene assembly.

The length-weight and length-length relationships of bluefish, Pomatomus saltatrix (Linnaeus, 1766 from Samsun, middle Black Sea region

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Melek Özpiçak

2017-10-01

Full Text Available In this study, length-weight relationship (LWR and length-length relationship (LLR of bluefish, Pomatomus saltatrix were determined. A total of 125 specimens were sampled from Samsun, the middle Black Sea in 2014 fishing season. Bluefish specimens were monthly collected from commercial fishing boats from October to December 2014. All captured individuals (N=125 were measured to the nearest 0.1 cm for total, fork and standard lengths. The weight of each fish (W was recorded to the nearest 0.01 g. According to results of analyses, there were no statistically significant differences between sexes in term of length and weight (P˃0.05. The minimum and maximum total, fork and standard lengths of bluefish ranged between 13.5-23.6 cm, 12.50-21.80 cm and 10.60-20.10 cm, respectively. The equation of length-weight relationship were calculated as W=0.008TL3.12 (r2>0.962. Positive allometric growth was observed for bluefish (b>3. Length-length relationship was also highly significant (P<0.001 with coefficient of determination (r2 ranging from 0.916 to 0.988.

Expression and characterization of full-length human heme oxygenase-1: the presence of intact membrane-binding region leads to increased binding affinity for NADPH cytochrome P450 reductase.

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Huber, Warren J; Backes, Wayne L

2007-10-30

Heme oxygenase-1 (HO-1) is the chief regulatory enzyme in the oxidative degradation of heme to biliverdin. In the process of heme degradation, HO-1 receives the electrons necessary for catalysis from the flavoprotein NADPH cytochrome P450 reductase (CPR), releasing free iron and carbon monoxide. Much of the recent research involving heme oxygenase has been done using a 30 kDa soluble form of the enzyme, which lacks the membrane binding region (C-terminal 23 amino acids). The goal of this study was to express and purify a full-length human HO-1 (hHO-1) protein; however, due to the lability of the full-length form, a rapid purification procedure was required. This was accomplished by use of a glutathione-s-transferase (GST)-tagged hHO-1 construct. Although the procedure permitted the generation of a full-length HO-1, this form was contaminated with a 30 kDa degradation product that could not be eliminated. Therefore, attempts were made to remove a putative secondary thrombin cleavage site by a conservative mutation of amino acid 254, which replaces arginine with lysine. This mutation allowed the expression and purification of a full-length hHO-1 protein. Unlike wild type (WT) HO-1, the R254K mutant could be purified to a single 32 kDa protein capable of degrading heme at the same rate as the WT enzyme. The R254K full-length form had a specific activity of approximately 200-225 nmol of bilirubin h-1 nmol-1 HO-1 as compared to approximately 140-150 nmol of bilirubin h-1 nmol-1 for the WT form, which contains the 30 kDa contaminant. This is a 2-3-fold increase from the previously reported soluble 30 kDa HO-1, suggesting that the C-terminal 23 amino acids are essential for maximal catalytic activity. Because the membrane-spanning domain is present, the full-length hHO-1 has the potential to incorporate into phospholipid membranes, which can be reconstituted at known concentrations, in combination with other endoplasmic reticulum resident enzymes.

Significance of urinary full-length megalin in patients with IgA nephropathy.

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Takuto Seki

Full Text Available BACKGROUND AND OBJECTIVES: Megalin is highly expressed at the apical membranes of proximal tubular epithelial cells. A urinary full-length megalin (C-megalin assay is linked to the severity of diabetic nephropathy in type 2 diabetes. This study examined the relationship between levels of urinary C-megalin and histological findings in adult patients with IgA nephropathy (IgAN. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS: Urine samples voided in the morning on the day of renal biopsy were obtained from 73 patients with IgAN (29 men and 44 women; mean age, 33 years and 5 patients with membranous nephropathy (MN. Renal pathologic variables were analyzed using the Oxford classification of IgAN, the Shigematsu classification and the Clinical Guidelines of IgAN in Japan. The levels of urinary C-megalin were measured by sandwich ELISA. RESULTS: Histological analysis based on the Oxford classification revealed that the levels of urinary C-megalin were correlated with mesangial hypercellularity in IgAN patients (OR = 1.76, 95% CI: 1.04-3.27, P<0.05. There was a significant correlation between the levels of urinary C-megalin and the severity of chronic extracapillary abnormalities according to the Shigematsu classification in IgAN patients (β = 0.33, P = 0.008. The levels of urinary C-megalin were significantly higher in all risk levels of IgAN patients requiring dialysis using the Clinical Guidelines of IgAN in Japan than in the control group. The levels of urinary C-megalin were significantly higher in the high risk and very high risk grades than in the low risk grade (P<0.05. The levels of urinary C-megalin were significantly higher in MN patients compared to the control group. CONCLUSIONS: The levels of urinary C-megalin are associated with histological abnormalities in adult IgAN patients. There is a possibility that urinary C-megalin is an independent predictor of disease progression of IgAN. In addition, our results suggest that

Cloning and sequencing of full-length cDNAs of RNA1 and RNA2 of a Tomato black ring virus isolate from Poland.

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Jończyk, M; Le Gall, O; Pałucha, A; Borodynko, N; Pospieszny, H

2004-04-01

Full-length cDNA clones corresponding to the RNA1 and RNA2 of the Polish isolate MJ of Tomato black ring virus (TBRV, genus Nepovirus) were obtained using a direct recombination strategy in yeast, and their complete nucleotide sequences were established. RNA1 is 7358 nucleotides and RNA2 is 4633 nucleotides in length, excluding the poly(A) tails. Both RNAs contain a single open reading frame encoding polyproteins of 254 kDa and 149 kDa for RNA1 and RNA2 respectively. Putative cleavage sites were identified, and the relationships between TBRV and related nepoviruses were studied by sequence comparison.

Effect of Full-Length Carbon Fiber Insoles on Lower Limb Kinetics in Patients With Midfoot Osteoarthritis: A Pilot Study.

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Yi, Taeim; Kim, Jung Hyun; Oh-Park, Mooyeon; Hwang, Ji Hye

2018-03-01

We investigated the effects of full-length carbon fiber (FCF) insoles on gait, muscle activity, kinetics, and pain in patients with midfoot osteoarthritis (OA). We enrolled 13 patients with unilateral midfoot OA (mild: Visual Analog Scale [VAS] range, 1-3; moderate, VAS range, 4-7) and healthy controls. All participants were asked to walk under two conditions: with and without FCF insole. The outcome measures were ground reaction force, quantitative gait parameters, electromyography activities and pain severity (VAS). In the patients with moderate midfoot OA, significantly longer gait cycle and higher muscle activity of lower limb during loading-response phase were observed while walking without FCF insoles. In the mild midfoot OA group, there was no significant difference in VAS score (without, 2.0 ± 1.0 vs. with, 2.0 ± 0.5) with FCF insole use. However, significantly reduced VAS score (without, 5.5 ± 1.4 vs. with, 2.0 ± 0.5) and muscle activity of the tibialis anterior and increased muscle activity of gastrocnemius were observed in the moderate midfoot OA group by using an FCF insole (P < 0.05). Full-length carbon fiber insoles can improve pain in individuals with moderate midfoot OA, which might be associated with changes in the kinetics and muscle activities of the lower limb. Taken together, the results of the present study suggest that FCF insoles may be used as a helpful option for midfoot OA.

A full-length Plasmodium falciparum recombinant circumsporozoite protein expressed by Pseudomonas fluorescens platform as a malaria vaccine candidate.

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Amy R Noe

Full Text Available The circumsporozoite protein (CSP of Plasmodium falciparum is a major surface protein, which forms a dense coat on the sporozoite's surface. Preclinical research on CSP and clinical evaluation of a CSP fragment-based RTS, S/AS01 vaccine have demonstrated a modest degree of protection against P. falciparum, mediated in part by humoral immunity and in part by cell-mediated immunity. Given the partial protective efficacy of the RTS, S/AS01 vaccine in a recent Phase 3 trial, further improvement of CSP-based vaccines is crucial. In this report, we describe the preclinical development of a full-length, recombinant CSP (rCSP-based vaccine candidate against P. falciparum malaria suitable for current Good Manufacturing Practice (cGMP production. Utilizing a novel high-throughput Pseudomonas fluorescens expression platform, we demonstrated greater efficacy of full-length rCSP as compared to N-terminally truncated versions, rapidly down-selected a promising lead vaccine candidate, and developed a high-yield purification process to express immunologically active, intact antigen for clinical trial material production. The rCSP, when formulated with various adjuvants, induced antigen-specific antibody responses as measured by enzyme-linked immunosorbent assay (ELISA and immunofluorescence assay (IFA, as well as CD4+ T-cell responses as determined by ELISpot. The adjuvanted rCSP vaccine conferred protection in mice when challenged with transgenic P. berghei sporozoites containing the P. falciparum repeat region of CSP. Furthermore, heterologous prime/boost regimens with adjuvanted rCSP and an adenovirus type 35-vectored CSP (Ad35CS showed modest improvements in eliciting CSP-specific T-cell responses and anti-malarial protection, depending on the order of vaccine delivery. Collectively, these data support the importance of further clinical development of adjuvanted rCSP, either as a stand-alone product or as one of the components in a heterologous prime

Construction of a Full-Length Enriched cDNA Library and Preliminary Analysis of Expressed Sequence Tags from Bengal Tiger Panthera tigris tigris

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Changqing Liu

2013-05-01

Full Text Available In this study, a full-length enriched cDNA library was successfully constructed from Bengal tiger, Panthera tigris tigris, the most well-known wild Animal. Total RNA was extracted from cultured Bengal tiger fibroblasts in vitro. The titers of primary and amplified libraries were 1.28 × 106 pfu/mL and 1.56 × 109 pfu/mL respectively. The percentage of recombinants from unamplified library was 90.2% and average length of exogenous inserts was 0.98 kb. A total of 212 individual ESTs with sizes ranging from 356 to 1108 bps were then analyzed. The BLASTX score revealed that 48.1% of the sequences were classified as a strong match, 45.3% as nominal and 6.6% as a weak match. Among the ESTs with known putative function, 26.4% ESTs were found to be related to all kinds of metabolisms, 19.3% ESTs to information storage and processing, 11.3% ESTs to posttranslational modification, protein turnover, chaperones, 11.3% ESTs to transport, 9.9% ESTs to signal transducer/cell communication, 9.0% ESTs to structure protein, 3.8% ESTs to cell cycle, and only 6.6% ESTs classified as novel genes. By EST sequencing, a full-length gene coding ferritin was identified and characterized. The recombinant plasmid pET32a-TAT-Ferritin was constructed, coded for the TAT-Ferritin fusion protein with two 6× His-tags in N and C-terminal. After BCA assay, the concentration of soluble Trx-TAT-Ferritin recombinant protein was 2.32 ± 0.12 mg/mL. These results demonstrated that the reliability and representativeness of the cDNA library attained to the requirements of a standard cDNA library. This library provided a useful platform for the functional genome and transcriptome research of Bengal tigers.

The Effect of Casting Ring Liner Length and Prewetting on the Marginal Adaptation and Dimensional Accuracy of Full Crown Castings.

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Haralur, Satheesh B; Hamdi, Osama A; Al-Shahrani, Abdulaziz A; Alhasaniah, Sultan

2017-01-01

To evaluate the effect of varying cellulose casting ring liner length and its prewetting on the marginal adaptation and dimensional accuracy of full veneer metal castings. The master die was milled in stainless steel to fabricate the wax pattern. Sixty wax patterns were fabricated with a uniform thickness of 1.5 mm at an occlusal surface and 1 mm axial surface, cervical width at 13.5 mm, and 10 mm cuspal height. The samples were divided into six groups ( n = 10). Groups I and II samples had the full-length cellulose prewet and dry ring liner, respectively. The groups III and IV had 2 mm short prewet and dry cellulose ring liner, respectively, whereas groups V and VI were invested in 6 mm short ring liner. The wax patterns were immediately invested in phosphate bonded investment, and casting procedure was completed with nickel-chrome alloy. The castings were cleaned and mean score of measurements at four reference points for marginal adaption, casting height, and cervical width was calculated. The marginal adaption was calculated with Imaje J software, whereas the casting height and cervical width was determined using a digital scale. The data was subjected to one-way analysis of varaince and Tukey post hoc statistical analysis with Statistical Package for the Social Sciences version 20 software. The group II had the best marginal adaption with a gap of 63.786 μm followed by group I (65.185 μm), group IV (87.740 μm), and group III (101.455 μm). A large marginal gap was observed in group V at 188.871 μm. Cuspal height was more accurate with group V (10.428 mm), group VI (10.421 mm), and group II (10.488 mm). The cervical width was approximately similar in group I, group III, and group V. Statistically significant difference was observed in Tukey post hoc analysis between group V and group VI with all the other groups with regards to marginal adaptation. The dry cellulose ring liners provided better marginal adaptation in comparison to prewet cellulose ring

Tula hantavirus isolate with the full-length ORF for nonstructural protein NSs survives for more consequent passages in interferon-competent cells than the isolate having truncated NSs ORF.

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Jääskeläinen, Kirsi M; Plyusnina, Angelina; Lundkvist, Ake; Vaheri, Antti; Plyusnin, Alexander

2008-01-11

The competitiveness of two Tula hantavirus (TULV) isolates, TULV/Lodz and TULV/Moravia, was evaluated in interferon (IFN) -competent and IFN-deficient cells. The two isolates differ in the length of the open reading frame (ORF) encoding the nonstructural protein NSs, which has previously been shown to inhibit IFN response in infected cells. In IFN-deficient Vero E6 cells both TULV isolates survived equally well. In contrast, in IFN-competent MRC5 cells TULV/Lodz isolate, that possesses the NSs ORF for the full-length protein of 90 aa, survived for more consequent passages than TULV/Moravia isolate, which contains the ORF for truncated NSs protein (66-67 aa). Our data show that expression of a full-length NSs protein is beneficial for the virus survival and competitiveness in IFN-competent cells and not essential in IFN-deficient cells. These results suggest that the N-terminal aa residues are important for the full activity of the NSs protein.

Full-Length Characterization of Hepatitis C Virus Subtype 3a Reveals Novel Hypervariable Regions under Positive Selection during Acute Infection▿

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Humphreys, Isla; Fleming, Vicki; Fabris, Paolo; Parker, Joe; Schulenberg, Bodo; Brown, Anthony; Demetriou, Charis; Gaudieri, Silvana; Pfafferott, Katja; Lucas, Michaela; Collier, Jane; Huang, Kuan-Hsiang Gary; Pybus, Oliver G.; Klenerman, Paul; Barnes, Eleanor

2009-01-01

Hepatitis C virus subtype 3a is a highly prevalent and globally distributed strain that is often associated with infection via injection drug use. This subtype exhibits particular phenotypic characteristics. In spite of this, detailed genetic analysis of this subtype has rarely been performed. We performed full-length viral sequence analysis in 18 patients with chronic HCV subtype 3a infection and assessed genomic viral variability in comparison to other HCV subtypes. Two novel regions of int...

Construction and evaluation of normalized cDNA libraries enriched with full-length sequences for rapid discovery of new genes from Sisal (Agave sisalana Perr.) different developmental stages.

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Zhou, Wen-Zhao; Zhang, Yan-Mei; Lu, Jun-Ying; Li, Jun-Feng

2012-10-12

To provide a resource of sisal-specific expressed sequence data and facilitate this powerful approach in new gene research, the preparation of normalized cDNA libraries enriched with full-length sequences is necessary. Four libraries were produced with RNA pooled from Agave sisalana multiple tissues to increase efficiency of normalization and maximize the number of independent genes by SMART™ method and the duplex-specific nuclease (DSN). This procedure kept the proportion of full-length cDNAs in the subtracted/normalized libraries and dramatically enhanced the discovery of new genes. Sequencing of 3875 cDNA clones of libraries revealed 3320 unigenes with an average insert length about 1.2 kb, indicating that the non-redundancy of libraries was about 85.7%. These unigene functions were predicted by comparing their sequences to functional domain databases and extensively annotated with Gene Ontology (GO) terms. Comparative analysis of sisal unigenes and other plant genomes revealed that four putative MADS-box genes and knotted-like homeobox (knox) gene were obtained from a total of 1162 full-length transcripts. Furthermore, real-time PCR showed that the characteristics of their transcripts mainly depended on the tight expression regulation of a number of genes during the leaf and flower development. Analysis of individual library sequence data indicated that the pooled-tissue approach was highly effective in discovering new genes and preparing libraries for efficient deep sequencing.

The full-length E1-circumflexE4 protein of human papillomavirus type 18 modulates differentiation-dependent viral DNA amplification and late gene expression

International Nuclear Information System (INIS)

Wilson, Regina; Ryan, Gordon B.; Knight, Gillian L.; Laimins, Laimonis A.; Roberts, Sally

2007-01-01

Activation of the productive phase of the human papillomavirus (HPV) life cycle in differentiated keratinocytes is coincident with high-level expression of E1-circumflexE4 protein. To determine the role of E1-circumflexE4 in the HPV replication cycle, we constructed HPV18 mutant genomes in which expression of the full-length E1-circumflexE4 protein was abrogated. Undifferentiated keratinocytes containing mutant genomes showed enhanced proliferation when compared to cells containing wildtype genomes, but there were no differences in maintenance of viral episomes. Following differentiation, cells with mutant genomes exhibited reduced levels of viral DNA amplification and late gene expression, compared to wildtype genome-containing cells. This indicates that HPV18 E1-circumflexE4 plays an important role in regulating HPV late functions, and it may also function in the early phase of the replication cycle. Our finding that full-length HPV18 E1-circumflexE4 protein plays a significant role in promoting viral genome amplification concurs with a similar report with HPV31, but is in contrast to an HPV11 study where viral DNA amplification was not dependent on full-length E1-circumflexE4 expression, and to HPV16 where only C-terminal truncations in E1-circumflexE4 abrogated vegetative genome replication. This suggests that type-specific differences exist between various E1-circumflexE4 proteins

Production of a full-length infectious GFP-tagged cDNA clone of Beet mild yellowing virus for the study of plant-polerovirus interactions.

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Stevens, Mark; Viganó, Felicita

2007-04-01

The full-length cDNA of Beet mild yellowing virus (Broom's Barn isolate) was sequenced and cloned into the vector pLitmus 29 (pBMYV-BBfl). The sequence of BMYV-BBfl (5721 bases) shared 96% and 98% nucleotide identity with the other complete sequences of BMYV (BMYV-2ITB, France and BMYV-IPP, Germany respectively). Full-length capped RNA transcripts of pBMYV-BBfl were synthesised and found to be biologically active in Arabidopsis thaliana protoplasts following electroporation or PEG inoculation when the protoplasts were subsequently analysed using serological and molecular methods. The BMYV sequence was modified by inserting DNA that encoded the jellyfish green fluorescent protein (GFP) into the P5 gene close to its 3' end. A. thaliana protoplasts electroporated with these RNA transcripts were biologically active and up to 2% of transfected protoplasts showed GFP-specific fluorescence. The exploitation of these cDNA clones for the study of the biology of beet poleroviruses is discussed.

Assessing the genetic diversity of Cu resistance in mine tailings through high-throughput recovery of full-length copA genes

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Li, Xiaofang; Zhu, Yong-Guan; Shaban, Babak; Bruxner, Timothy J. C.; Bond, Philip L.; Huang, Longbin

2015-01-01

Characterizing the genetic diversity of microbial copper (Cu) resistance at the community level remains challenging, mainly due to the polymorphism of the core functional gene copA. In this study, a local BLASTN method using a copA database built in this study was developed to recover full-length putative copA sequences from an assembled tailings metagenome; these sequences were then screened for potentially functioning CopA using conserved metal-binding motifs, inferred by evolutionary trace analysis of CopA sequences from known Cu resistant microorganisms. In total, 99 putative copA sequences were recovered from the tailings metagenome, out of which 70 were found with high potential to be functioning in Cu resistance. Phylogenetic analysis of selected copA sequences detected in the tailings metagenome showed that topology of the copA phylogeny is largely congruent with that of the 16S-based phylogeny of the tailings microbial community obtained in our previous study, indicating that the development of copA diversity in the tailings might be mainly through vertical descent with few lateral gene transfer events. The method established here can be used to explore copA (and potentially other metal resistance genes) diversity in any metagenome and has the potential to exhaust the full-length gene sequences for downstream analyses. PMID:26286020

Pre-Steady-State Kinetic Analysis of Truncated and Full-Length Saccharomyces cerevisiae DNA Polymerase Eta

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Brown, Jessica A.; Zhang, Likui; Sherrer, Shanen M.; Taylor, John-Stephen; Burgers, Peter M. J.; Suo, Zucai

2010-01-01

Understanding polymerase fidelity is an important objective towards ascertaining the overall stability of an organism's genome. Saccharomyces cerevisiae DNA polymerase η (yPolη), a Y-family DNA polymerase, is known to efficiently bypass DNA lesions (e.g., pyrimidine dimers) in vivo. Using pre-steady-state kinetic methods, we examined both full-length and a truncated version of yPolη which contains only the polymerase domain. In the absence of yPolη's C-terminal residues 514–632, the DNA binding affinity was weakened by 2-fold and the base substitution fidelity dropped by 3-fold. Thus, the C-terminus of yPolη may interact with DNA and slightly alter the conformation of the polymerase domain during catalysis. In general, yPolη discriminated between a correct and incorrect nucleotide more during the incorporation step (50-fold on average) than the ground-state binding step (18-fold on average). Blunt-end additions of dATP or pyrene nucleotide 5′-triphosphate revealed the importance of base stacking during the binding of incorrect incoming nucleotides. PMID:20798853

Construction of phosphorylation interaction networks by text mining of full-length articles using the eFIP system.

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Tudor, Catalina O; Ross, Karen E; Li, Gang; Vijay-Shanker, K; Wu, Cathy H; Arighi, Cecilia N

2015-01-01

Protein phosphorylation is a reversible post-translational modification where a protein kinase adds a phosphate group to a protein, potentially regulating its function, localization and/or activity. Phosphorylation can affect protein-protein interactions (PPIs), abolishing interaction with previous binding partners or enabling new interactions. Extracting phosphorylation information coupled with PPI information from the scientific literature will facilitate the creation of phosphorylation interaction networks of kinases, substrates and interacting partners, toward knowledge discovery of functional outcomes of protein phosphorylation. Increasingly, PPI databases are interested in capturing the phosphorylation state of interacting partners. We have previously developed the eFIP (Extracting Functional Impact of Phosphorylation) text mining system, which identifies phosphorylated proteins and phosphorylation-dependent PPIs. In this work, we present several enhancements for the eFIP system: (i) text mining for full-length articles from the PubMed Central open-access collection; (ii) the integration of the RLIMS-P 2.0 system for the extraction of phosphorylation events with kinase, substrate and site information; (iii) the extension of the PPI module with new trigger words/phrases describing interactions and (iv) the addition of the iSimp tool for sentence simplification to aid in the matching of syntactic patterns. We enhance the website functionality to: (i) support searches based on protein roles (kinases, substrates, interacting partners) or using keywords; (ii) link protein entities to their corresponding UniProt identifiers if mapped and (iii) support visual exploration of phosphorylation interaction networks using Cytoscape. The evaluation of eFIP on full-length articles achieved 92.4% precision, 76.5% recall and 83.7% F-measure on 100 article sections. To demonstrate eFIP for knowledge extraction and discovery, we constructed phosphorylation-dependent interaction

Molecular Comparisons of Full Length Metapneumovirus (MPV) Genomes, Including Newly Determined French AMPV-C and –D Isolates, Further Supports Possible Subclassification within the MPV Genus

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Brown, Paul A.; Lemaitre, Evelyne; Briand, François-Xavier; Courtillon, Céline; Guionie, Olivier; Allée, Chantal; Toquin, Didier; Bayon-Auboyer, Marie-Hélène; Jestin, Véronique; Eterradossi, Nicolas

2014-01-01

Four avian metapneumovirus (AMPV) subgroups (A–D) have been reported previously based on genetic and antigenic differences. However, until now full length sequences of the only known isolates of European subgroup C and subgroup D viruses (duck and turkey origin, respectively) have been unavailable. These full length sequences were determined and compared with other full length AMPV and human metapneumoviruses (HMPV) sequences reported previously, using phylogenetics, comparisons of nucleic and amino acid sequences and study of codon usage bias. Results confirmed that subgroup C viruses were more closely related to HMPV than they were to the other AMPV subgroups in the study. This was consistent with previous findings using partial genome sequences. Closer relationships between AMPV-A, B and D were also evident throughout the majority of results. Three metapneumovirus “clusters” HMPV, AMPV-C and AMPV-A, B and D were further supported by codon bias and phylogenetics. The data presented here together with those of previous studies describing antigenic relationships also between AMPV-A, B and D and between AMPV-C and HMPV may call for a subclassification of metapneumoviruses similar to that used for avian paramyxoviruses, grouping AMPV-A, B and D as type I metapneumoviruses and AMPV-C and HMPV as type II. PMID:25036224

Drug resistance is conferred on the model yeast Saccharomyces cerevisiae by expression of full-length melanoma-associated human ATP-binding cassette transporter ABCB5.

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Keniya, Mikhail V; Holmes, Ann R; Niimi, Masakazu; Lamping, Erwin; Gillet, Jean-Pierre; Gottesman, Michael M; Cannon, Richard D

2014-10-06

ABCB5, an ATP-binding cassette (ABC) transporter, is highly expressed in melanoma cells, and may contribute to the extreme resistance of melanomas to chemotherapy by efflux of anti-cancer drugs. Our goal was to determine whether we could functionally express human ABCB5 in the model yeast Saccharomyces cerevisiae, in order to demonstrate an efflux function for ABCB5 in the absence of background pump activity from other human transporters. Heterologous expression would also facilitate drug discovery for this important target. DNAs encoding ABCB5 sequences were cloned into the chromosomal PDR5 locus of a S. cerevisiae strain in which seven endogenous ABC transporters have been deleted. Protein expression in the yeast cells was monitored by immunodetection using both a specific anti-ABCB5 antibody and a cross-reactive anti-ABCB1 antibody. ABCB5 function in recombinant yeast cells was measured by determining whether the cells possessed increased resistance to known pump substrates, compared to the host yeast strain, in assays of yeast growth. Three ABCB5 constructs were made in yeast. One was derived from the ABCB5-β mRNA, which is highly expressed in human tissues but is a truncation of a canonical full-size ABC transporter. Two constructs contained full-length ABCB5 sequences: either a native sequence from cDNA or a synthetic sequence codon-harmonized for S. cerevisiae. Expression of all three constructs in yeast was confirmed by immunodetection. Expression of the codon-harmonized full-length ABCB5 DNA conferred increased resistance, relative to the host yeast strain, to the putative substrates rhodamine 123, daunorubicin, tetramethylrhodamine, FK506, or clorgyline. We conclude that full-length ABCB5 can be functionally expressed in S. cerevisiae and confers drug resistance.

Full-length genome sequences of five hepatitis C virus isolates representing subtypes 3g, 3h, 3i and 3k, and a unique genotype 3 variant.

Science.gov (United States)

Lu, Ling; Li, Chunhua; Yuan, Jie; Lu, Teng; Okamoto, Hiroaki; Murphy, Donald G

2013-03-01

We characterized the full-length genomes of five distinct hepatitis C virus (HCV)-3 isolates. These represent the first complete genomes for subtypes 3g and 3h, the second such genomes for 3k and 3i, and of one novel variant presently not assigned to a subtype. Each genome was determined from 18-25 overlapping fragments. They had lengths of 9579-9660 nt and each contained a single ORF encoding 3020-3025 aa. They were isolated from five patients residing in Canada; four were of Asian origin and one was of Somali origin. Phylogenetic analysis using 64 partial NS5B sequences differentiated 10 assigned subtypes, 3a-3i and 3k, and two additional lineages within genotype 3. From the data of this study, HCV-3 full-length sequences are now available for six of the assigned subtypes and one unassigned. Our findings should add insights to HCV evolutionary studies and clinical applications.

Correlated evolution of sternal keel length and ilium length in birds

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Tao Zhao

2017-07-01

Full Text Available The interplay between the pectoral module (the pectoral girdle and limbs and the pelvic module (the pelvic girdle and limbs plays a key role in shaping avian evolution, but prior empirical studies on trait covariation between the two modules are limited. Here we empirically test whether (size-corrected sternal keel length and ilium length are correlated during avian evolution using phylogenetic comparative methods. Our analyses on extant birds and Mesozoic birds both recover a significantly positive correlation. The results provide new evidence regarding the integration between the pelvic and pectoral modules. The correlated evolution of sternal keel length and ilium length may serve as a mechanism to cope with the effect on performance caused by a tradeoff in muscle mass between the pectoral and pelvic modules, via changing moment arms of muscles that function in flight and in terrestrial locomotion.

Full-length model of the human galectin-4 and insights into dynamics of inter-domain communication

Science.gov (United States)

Rustiguel, Joane K.; Soares, Ricardo O. S.; Meisburger, Steve P.; Davis, Katherine M.; Malzbender, Kristina L.; Ando, Nozomi; Dias-Baruffi, Marcelo; Nonato, Maria Cristina

2016-09-01

Galectins are proteins involved in diverse cellular contexts due to their capacity to decipher and respond to the information encoded by β-galactoside sugars. In particular, human galectin-4, normally expressed in the healthy gastrointestinal tract, displays differential expression in cancerous tissues and is considered a potential drug target for liver and lung cancer. Galectin-4 is a tandem-repeat galectin characterized by two carbohydrate recognition domains connected by a linker-peptide. Despite their relevance to cell function and pathogenesis, structural characterization of full-length tandem-repeat galectins has remained elusive. Here, we investigate galectin-4 using X-ray crystallography, small- and wide-angle X-ray scattering, molecular modelling, molecular dynamics simulations, and differential scanning fluorimetry assays and describe for the first time a structural model for human galectin-4. Our results provide insight into the structural role of the linker-peptide and shed light on the dynamic characteristics of the mechanism of carbohydrate recognition among tandem-repeat galectins.

First full-length genome sequence of the polerovirus luffa aphid-borne yellows virus (LABYV) reveals the presence of at least two consensus sequences in an isolate from Thailand.

Science.gov (United States)

Knierim, Dennis; Maiss, Edgar; Kenyon, Lawrence; Winter, Stephan; Menzel, Wulf

2015-10-01

Luffa aphid-borne yellows virus (LABYV) was proposed as the name for a previously undescribed polerovirus based on partial genome sequences obtained from samples of cucurbit plants collected in Thailand between 2008 and 2013. In this study, we determined the first full-length genome sequence of LABYV. Based on phylogenetic analysis and genome properties, it is clear that this virus represents a distinct species in the genus Polerovirus. Analysis of sequences from sample TH24, which was collected in 2010 from a luffa plant in Thailand, reveals the presence of two different full-length genome consensus sequences.

Gene discovery from Jatropha curcas by sequencing of ESTs from normalized and full-length enriched cDNA library from developing seeds

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Sugantham Priyanka Annabel

2010-10-01

Full Text Available Abstract Background Jatropha curcas L. is promoted as an important non-edible biodiesel crop worldwide. Jatropha oil, which is a triacylglycerol, can be directly blended with petro-diesel or transesterified with methanol and used as biodiesel. Genetic improvement in jatropha is needed to increase the seed yield, oil content, drought and pest resistance, and to modify oil composition so that it becomes a technically and economically preferred source for biodiesel production. However, genetic improvement efforts in jatropha could not take advantage of genetic engineering methods due to lack of cloned genes from this species. To overcome this hurdle, the current gene discovery project was initiated with an objective of isolating as many functional genes as possible from J. curcas by large scale sequencing of expressed sequence tags (ESTs. Results A normalized and full-length enriched cDNA library was constructed from developing seeds of J. curcas. The cDNA library contained about 1 × 106 clones and average insert size of the clones was 2.1 kb. Totally 12,084 ESTs were sequenced to average high quality read length of 576 bp. Contig analysis revealed 2258 contigs and 4751 singletons. Contig size ranged from 2-23 and there were 7333 ESTs in the contigs. This resulted in 7009 unigenes which were annotated by BLASTX. It showed 3982 unigenes with significant similarity to known genes and 2836 unigenes with significant similarity to genes of unknown, hypothetical and putative proteins. The remaining 191 unigenes which did not show similarity with any genes in the public database may encode for unique genes. Functional classification revealed unigenes related to broad range of cellular, molecular and biological functions. Among the 7009 unigenes, 6233 unigenes were identified to be potential full-length genes. Conclusions The high quality normalized cDNA library was constructed from developing seeds of J. curcas for the first time and 7009 unigenes coding

Crystal Structure of the Full-Length Feline Immunodeficiency Virus Capsid Protein Shows an N-Terminal β-Hairpin in the Absence of N-Terminal Proline

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Christelle Folio

2017-11-01

Full Text Available Feline immunodeficiency virus (FIV is a member of the Retroviridae family. It is the causative agent of an acquired immunodeficiency syndrome (AIDS in cats and wild felines. Its capsid protein (CA drives the assembly of the viral particle, which is a critical step in the viral replication cycle. Here, the first atomic structure of full-length FIV CA to 1.67 Å resolution is determined. The crystallized protein exhibits an original tetrameric assembly, composed of dimers which are stabilized by an intermolecular disulfide bridge induced by the crystallogenesis conditions. The FIV CA displays a standard α-helical CA topology with two domains, separated by a linker shorter than other retroviral CAs. The β-hairpin motif at its amino terminal end, which interacts with nucleotides in HIV-1, is unusually long in FIV CA. Interestingly, this functional β-motif is formed in this construct in the absence of the conserved N-terminal proline. The FIV CA exhibits a cis Arg–Pro bond in the CypA-binding loop, which is absent in known structures of lentiviral CAs. This structure represents the first tri-dimensional structure of a functional, full-length FIV CA.

Efficient generation of recombinant RNA viruses using targeted recombination-mediated mutagenesis of bacterial artificial chromosomes containing full-length cDNA

DEFF Research Database (Denmark)

Rasmussen, Thomas Bruun; Risager, Peter Christian; Fahnøe, Ulrik

2013-01-01

Background Infectious cDNA clones are a prerequisite for directed genetic manipulation of RNA viruses. Here, a strategy to facilitate manipulation and rescue of classical swine fever viruses (CSFVs) from full-length cDNAs present within bacterial artificial chromosomes (BACs) is described....... This strategy allows manipulation of viral cDNA by targeted recombination-mediated mutagenesis within bacteria. Results A new CSFV-BAC (pBeloR26) derived from the Riems vaccine strain has been constructed and subsequently modified in the E2 coding sequence, using the targeted recombination strategy to enable...

Production of full length and splicing form of chymosin using pETexpression system in E-coli and investigation its enzyme activity and preplasmic secretion

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M. Ahmadi Zeydabadi

2008-05-01

Full Text Available Introduction: Chymosin (Rennin EC 3.4.23.4 is an aspartyl proteinas (the major proteolyticenzyme in the fourth stomach of the unweaned calf that is formed by proteolytic activation fromzymogene prochymosin. The aim of his study was to produce the full length and splicing form ofchymosin using pETexpression system in E-coli and to assay the activity of expressed enzyme andpreplasmic secretion.Materials and Methods: The sense primer F-prochy(+ (5´-ggggccatgGCTGAGATCACCAGGAincluding NCOI restriction site. The anti sense R-prochy(- (5´-gggcggccgcGATGGCTTTGGCCAGC -3´ hybridizing to the C-terminal end of calf preprocymosincDNA and contains an additional NotI restriction site at its 5´-end . The cells were disrupted bysonication and proteins were purified by using Ni-NTA beads from Qiagen under native conditional.The preprochymosin and AS6 preprochymosin were activated at pH 4.7. The enzyme solutions werediluted 20-fold with 50 mM phosphate buffer .Results: Sequencing data analysis showed that the exon six has been spliced out and, therefore thegene product is 114 bp shorter in length, both chymosin forms were expressed together in E.coli.Under the same expression conditions, at least AS6 preprochymosin was produced 7-fold highexpression in comparison to a full-length recombinant chymosin. Following acid activation andneutralization, the purified fractions were tested in a qualitative milk clotting assay. The clottingactivity of preprochymosin and exon6-less preprochymosin were comparable.Conclusion: High expression of this alternatively expressed transcript in bacteria, and properfolding of the AS6 chymosin protein molecule in the absence of exon six are the two most importantaspects distinguished in this research.

Stable preparations of tyrosine hydroxylase provide the solution structure of the full-length enzyme

Science.gov (United States)

Bezem, Maria T.; Baumann, Anne; Skjærven, Lars; Meyer, Romain; Kursula, Petri; Martinez, Aurora; Flydal, Marte I.

2016-01-01

Tyrosine hydroxylase (TH) catalyzes the rate-limiting step in the biosynthesis of catecholamine neurotransmitters. TH is a highly complex enzyme at mechanistic, structural, and regulatory levels, and the preparation of kinetically and conformationally stable enzyme for structural characterization has been challenging. Here, we report on improved protocols for purification of recombinant human TH isoform 1 (TH1), which provide large amounts of pure, stable, active TH1 with an intact N-terminus. TH1 purified through fusion with a His-tagged maltose-binding protein on amylose resin was representative of the iron-bound functional enzyme, showing high activity and stabilization by the natural feedback inhibitor dopamine. TH1 purified through fusion with a His-tagged ZZ domain on TALON is remarkably stable, as it was partially inhibited by resin-derived cobalt. This more stable enzyme preparation provided high-quality small-angle X-ray scattering (SAXS) data and reliable structural models of full-length tetrameric TH1. The SAXS-derived model reveals an elongated conformation (Dmax = 20 nm) for TH1, different arrangement of the catalytic domains compared with the crystal structure of truncated forms, and an N-terminal region with an unstructured tail that hosts the phosphorylation sites and a separated Ala-rich helical motif that may have a role in regulation of TH by interacting with binding partners. PMID:27462005

Preparation of a differentially expressed, full-length cDNA expression library by RecA-mediated triple-strand formation with subtractively enriched cDNA fragments

NARCIS (Netherlands)

Hakvoort, T. B.; Spijkers, J. A.; Vermeulen, J. L.; Lamers, W. H.

1996-01-01

We have developed a fast and general method to obtain an enriched, full-length cDNA expression library with subtractively enriched cDNA fragments. The procedure relies on RecA-mediated triple-helix formation of single-stranded cDNA fragments with a double-stranded cDNA plasmid library. The complexes

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Dr Ahmed

other areas of business administration. ... mathematics, real estate, insurance, actuarial science and business administration (McCutcheon & Scott, 1989). Most textbooks written in these ..... Mathematics of Finance; Heinemann; Oxford. Murray ...

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ABSTRACT. This paper considered contamination of aquifer resulting from petroleum spillage, which is a common phenomenal in the. Niger Delta area of Nigeria. We used the model given by. Bestman (1987) and assumed that some endogenous variables are built into the system. To achieve a level of desirable state, we ...

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Mbah & Amao (SWJ):11-14. Natural Foods and Feeding Habits Of The African Honey bee ... Keywords: natural food, nectar, pollen, african honeybee, Apis mellifera adansonii ..... Crailsheim, K. (1990). The Protein balance of the honeybee.

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... Solarin (SWJ):1-6. On Existence Of Control For A Class Of Uncertain Dynamical Systems ... .m We apply the Conjugate Gradient Method. (C.G.M) in ...... Numerical Technique .... Some of its Applications; Journal of Mathematical Analysis and.

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providing energy storage and metabolic fuel, acting as functional and structural ... zoonotic and non-zoonotic diseases are been imported and exported in and out ..... rabbits infected with T. brucie and Gow et al., (2007) in which dog naturally ...

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In recent years, a new technique was introduced that combines both hydrolysis and ... Cassava Starch Preparation: The cassava starch used for this investigation was prepared ... One normal HCl and one normal NaOH were used to adjust the ...

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Administrator

chemical oxidation and reduction, electro-chemical treatment and ion-pair extraction were extensively used ... The present study is an effort to develop a fungal-based treatment system for the cleaning of dye industrial ..... Biochemical and Biophysical Research Communications 178:1056-. 1063. Raju, N. S., Venkataramana ...

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SPECKLED PIGEON (Columba guinea HARTLAUB AND. FINSCH ... area of the Nigerian northern guinea savanna (Fry, 1965). The habit of the .... defined by Margolis et al., (1982). Chi-square ..... Southern Africa, Academic Press, London.. 4 ...

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Marcos

2012-08-21

Aug 21, 2012 ... Cut flowers have a very limited life after they have been cut off from the mother plant, as survival on their own reserves is ... One of the techniques used for the removal ... and vegetables (Pellegrini and Belle, 2008). There are ...

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inorganic, synthetic organic polymer and naturally occurring coagulants .... Flash fast mixing was done for 2 mins at a speed of 100rpm, followed by slow mixing for ..... Moringa leaves from germplasm to plant, to food, to health. Symposium on ...

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The isotope techniques used in hydrology may be classified into three groups: environmental ..... In that case a solution may be found in measurements of 14C content of groundwaters. ... Applied Isotope Hydrogeology. Elsevier, New. York.

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some rural communities of Zaria, Nigeria for microbial index of water quality in relation to ... These factors, together with the inadequate waste treatment facilities and ..... The Need for an Integrated Approach to Water Supply and. Sanitation in ...

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Marcos

2012-08-21

Aug 21, 2012 ... 1Universidade Estadual Paulista, Faculdade de Ciências Agronômicas, CEP: 18601-060, Botucatu, SP, Brasil. 2Universidade Federal de Alagoas, Centro de Ciências Agrárias-CECA, Maceio, AL, Brasil. 3Universidade Federal Rural do Semi-Árido, Departamento de Ciências Vegetais, Mossoró, RN, Brasil ...

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markovian process could be reduced to a markovian chain with the homogenous .... x and y respectively. n= the value of the strategy i.e. number of dummies/virtual ..... Groove, CA. Feinberg, E. A. & Shwartz, A. (2002), Handbook of Markov.

Molecular Cloning and Characterization of Full-Length cDNA of Calmodulin Gene from Pacific Oyster Crassostrea gigas

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Xing-Xia Li

2016-01-01

Full Text Available The shell of the pearl oyster (Pinctada fucata mainly comprises aragonite whereas that of the Pacific oyster (Crassostrea gigas is mainly calcite, thereby suggesting the different mechanisms of shell formation between above two mollusks. Calmodulin (CaM is an important gene for regulating the uptake, transport, and secretion of calcium during the process of shell formation in pearl oyster. It is interesting to characterize the CaM in oysters, which could facilitate the understanding of the different shell formation mechanisms among mollusks. We cloned the full-length cDNA of Pacific oyster CaM (cgCaM and found that the cgCaM ORF encoded a peptide of 113 amino acids containing three EF-hand calcium-binding domains, its expression level was highest in the mantle, hinting that the cgCaM gene is probably involved in shell formation of Pacific oyster, and the common ancestor of Gastropoda and Bivalvia may possess at least three CaM genes. We also found that the numbers of some EF hand family members in highly calcified species were higher than those in lowly calcified species and the numbers of these motifs in oyster genome were the highest among the mollusk species with whole genome sequence, further hinting the correlation between CaM and biomineralization.

Characterization of a Full-Length Endogenous Beta-Retrovirus, EqERV-Beta1, in the Genome of the Horse (Equus caballus

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Antoinette C. van der Kuyl

2011-06-01

Full Text Available Information on endogenous retroviruses fixed in the horse (Equus caballus genome is scarce. The recent availability of a draft sequence of the horse genome enables the detection of such integrated viruses by similarity search. Using translated nucleotide fragments from gamma-, beta-, and delta-retroviral genera for initial searches, a full-length beta-retrovirus genome was retrieved from a horse chromosome 5 contig. The provirus, tentatively named EqERV-beta1 (for the first equine endogenous beta-retrovirus, was 10434 nucleotide (nt in length with the usual retroviral genome structure of 5’LTR-gag-pro-pol-env-3’LTR. The LTRs were 1361 nt long, and differed approximately 1% from each other, suggestive of a relatively recent integration. Coding sequences for gag, pro and pol were present in three different reading-frames, as common for beta-retroviruses, and the reading frames were completely open, except that the env gene was interrupted by a single stopcodon. No reading frame was apparent downstream of the env gene, suggesting that EqERV-beta1 does not encode a superantigen like mouse mammary tumor virus (MMTV. A second proviral genome of EqERV-beta1, with no stopcodon in env, is additionally integrated on chromosome 5 downstream of the first virus. Single EqERV-beta1 LTRs were abundantly present on all chromosomes except chromosome 24. Phylogenetically, EqERV-beta1 most closely resembles an unclassified retroviral sequence from cattle (Bos taurus, and the murine beta-retrovirus MMTV.

Study of canine parvovirus evolution: comparative analysis of full-length VP2 gene sequences from Argentina and international field strains.

Science.gov (United States)

Gallo Calderón, Marina; Wilda, Maximiliano; Boado, Lorena; Keller, Leticia; Malirat, Viviana; Iglesias, Marcela; Mattion, Nora; La Torre, Jose

2012-02-01

The continuous emergence of new strains of canine parvovirus (CPV), poorly protected by current vaccination, is a concern among breeders, veterinarians, and dog owners around the world. Therefore, the understanding of the genetic variation in emerging CPV strains is crucial for the design of disease control strategies, including vaccines. In this paper, we obtained the sequences of the full-length gene encoding for the main capsid protein (VP2) of 11 canine parvovirus type 2 (CPV-2) Argentine representative field strains, selected from a total of 75 positive samples studied in our laboratory in the last 9 years. A comparative sequence analysis was performed on 9 CPV-2c, one CPV-2a, and one CPV-2b Argentine strains with respect to international strains reported in the GenBank database. In agreement with previous reports, a high degree of identity was found among CPV-2c Argentine strains (99.6-100% and 99.7-100% at nucleotide and amino acid levels, respectively). However, the appearance of a new substitution in the 440 position (T440A) in four CPV-2c Argentine strains obtained after the year 2009 gives support to the variability observed for this position located within the VP2, three-fold spike. This is the first report on the genetic characterization of the full-length VP2 gene of emerging CPV strains in South America and shows that all the Argentine CPV-2c isolates cluster together with European and North American CPV-2c strains.

Development of three full-length infectious cDNA clones of distinct brassica yellows virus genotypes for agrobacterium-mediated inoculation.

Science.gov (United States)

Zhang, Xiao-Yan; Dong, Shu-Wei; Xiang, Hai-Ying; Chen, Xiang-Ru; Li, Da-Wei; Yu, Jia-Lin; Han, Cheng-Gui

2015-02-02

Brassica yellows virus is a newly identified species in the genus of Polerovirus within the family Luteoviridae. Brassica yellows virus (BrYV) is prevalently distributed throughout Mainland China and South Korea, is an important virus infecting cruciferous crops. Based on six BrYV genomic sequences of isolates from oilseed rape, rutabaga, radish, and cabbage, three genotypes, BrYV-A, BrYV-B, and BrYV-C, exist, which mainly differ in the 5' terminal half of the genome. BrYV is an aphid-transmitted and phloem-limited virus. The use of infectious cDNA clones is an alternative means of infecting plants that allows reverse genetic studies to be performed. In this study, full-length cDNA clones of BrYV-A, recombinant BrYV5B3A, and BrYV-C were constructed under control of the cauliflower mosaic virus 35S promoter. An agrobacterium-mediated inoculation system of Nicotiana benthamiana was developed using these cDNA clones. Three days after infiltration with full-length BrYV cDNA clones, necrotic symptoms were observed in the inoculated leaves of N. benthamiana; however, no obvious symptoms appeared in the upper leaves. Reverse transcription-PCR (RT-PCR) and western blot detection of samples from the upper leaves showed that the maximum infection efficiency of BrYVs could reach 100%. The infectivity of the BrYV-A, BrYV-5B3A, and BrYV-C cDNA clones was further confirmed by northern hybridization. The system developed here will be useful for further studies of BrYV, such as host range, pathogenicity, viral gene functions, and plant-virus-vector interactions, and especially for discerning the differences among the three genotypes. Copyright © 2014 Elsevier B.V. All rights reserved.

Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum cultivar Micro-Tom, a reference system for the Solanaceae genomics

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Kikuchi Mari

2010-03-01

Full Text Available Abstract Background The Solanaceae family includes several economically important vegetable crops. The tomato (Solanum lycopersicum is regarded as a model plant of the Solanaceae family. Recently, a number of tomato resources have been developed in parallel with the ongoing tomato genome sequencing project. In particular, a miniature cultivar, Micro-Tom, is regarded as a model system in tomato genomics, and a number of genomics resources in the Micro-Tom-background, such as ESTs and mutagenized lines, have been established by an international alliance. Results To accelerate the progress in tomato genomics, we developed a collection of fully-sequenced 13,227 Micro-Tom full-length cDNAs. By checking redundant sequences, coding sequences, and chimeric sequences, a set of 11,502 non-redundant full-length cDNAs (nrFLcDNAs was generated. Analysis of untranslated regions demonstrated that tomato has longer 5'- and 3'-untranslated regions than most other plants but rice. Classification of functions of proteins predicted from the coding sequences demonstrated that nrFLcDNAs covered a broad range of functions. A comparison of nrFLcDNAs with genes of sixteen plants facilitated the identification of tomato genes that are not found in other plants, most of which did not have known protein domains. Mapping of the nrFLcDNAs onto currently available tomato genome sequences facilitated prediction of exon-intron structure. Introns of tomato genes were longer than those of Arabidopsis and rice. According to a comparison of exon sequences between the nrFLcDNAs and the tomato genome sequences, the frequency of nucleotide mismatch in exons between Micro-Tom and the genome-sequencing cultivar (Heinz 1706 was estimated to be 0.061%. Conclusion The collection of Micro-Tom nrFLcDNAs generated in this study will serve as a valuable genomic tool for plant biologists to bridge the gap between basic and applied studies. The nrFLcDNA sequences will help annotation of the

Construction of a Full-Length Enriched cDNA Library and Preliminary Analysis of Expressed Sequence Tags from Bengal Tiger Panthera tigris tigris

Science.gov (United States)

Liu, Changqing; Liu, Dan; Guo, Yu; Lu, Taofeng; Li, Xiangchen; Zhang, Minghai; Ma, Jianzhang; Ma, Yuehui; Guan, Weijun

2013-01-01

In this study, a full-length enriched cDNA library was successfully constructed from Bengal tiger, Panthera tigris tigris, the most well-known wild Animal. Total RNA was extracted from cultured Bengal tiger fibroblasts in vitro. The titers of primary and amplified libraries were 1.28 × 106 pfu/mL and 1.56 × 109 pfu/mL respectively. The percentage of recombinants from unamplified library was 90.2% and average length of exogenous inserts was 0.98 kb. A total of 212 individual ESTs with sizes ranging from 356 to 1108 bps were then analyzed. The BLASTX score revealed that 48.1% of the sequences were classified as a strong match, 45.3% as nominal and 6.6% as a weak match. Among the ESTs with known putative function, 26.4% ESTs were found to be related to all kinds of metabolisms, 19.3% ESTs to information storage and processing, 11.3% ESTs to posttranslational modification, protein turnover, chaperones, 11.3% ESTs to transport, 9.9% ESTs to signal transducer/cell communication, 9.0% ESTs to structure protein, 3.8% ESTs to cell cycle, and only 6.6% ESTs classified as novel genes. By EST sequencing, a full-length gene coding ferritin was identified and characterized. The recombinant plasmid pET32a-TAT-Ferritin was constructed, coded for the TAT-Ferritin fusion protein with two 6× His-tags in N and C-terminal. After BCA assay, the concentration of soluble Trx-TAT-Ferritin recombinant protein was 2.32 ± 0.12 mg/mL. These results demonstrated that the reliability and representativeness of the cDNA library attained to the requirements of a standard cDNA library. This library provided a useful platform for the functional genome and transcriptome research of Bengal tigers. PMID:23708105

The Dalles Dam, Columbia River: Spillway Improvement CFD Study

Energy Technology Data Exchange (ETDEWEB)

Cook, Chris B.; Richmond, Marshall C.; Serkowski, John A.

2006-06-01

was then applied to address specific SIS design questions. Specifically, the CFD models were used to evaluate flow deflectors, baffle block removal and the effects of spillwalls. The CFD models were also used to evaluate downstream differences at other locations, such as at the Highway 197 bridge piers and Oregon shore islands, due to alterations in spill pattern. CFD model results were analyzed to quantitatively compare impacts of the spillwall that has subsequently been constructed between bays 6 and 7. CFD model results provided detailed information about how the spillwall would impact downstream flow patterns that complemented results from the 1:80 scale physical model. The CFD model was also used to examine relative differences between the juvenile spill pattern used in previous years and the anticipated spill pattern that will be applied once the wall is complete. In addition, the CFD model examined velocity magnitudes over the downstream basalt shelf to investigate potential for erosion under high flow conditions (e.g., 21 kcfs/bay for bays 1 through 6) with the spillwall in place. Several appendices follow the results and discussion sections of this report. These appendices document the large number of CFD simulations that have been performed by PNNL; both spillway improvement study (SIS) related and those performed for related biological tests.

Generation of Length Distribution, Length Diagram, Fibrogram, and Statistical Characteristics by Weight of Cotton Blends

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B. Azzouz

2007-01-01

Full Text Available The textile fibre mixture as a multicomponent blend of variable fibres imposes regarding the proper method to predict the characteristics of the final blend. The length diagram and the fibrogram of cotton are generated. Then the length distribution, the length diagram, and the fibrogram of a blend of different categories of cotton are determined. The length distributions by weight of five different categories of cotton (Egyptian, USA (Pima, Brazilian, USA (Upland, and Uzbekistani are measured by AFIS. From these distributions, the length distribution, the length diagram, and the fibrogram by weight of four binary blends are expressed. The length parameters of these cotton blends are calculated and their variations are plotted against the mass fraction x of one component in the blend .These calculated parameters are compared to those of real blends. Finally, the selection of the optimal blends using the linear programming method, based on the hypothesis that the cotton blend parameters vary linearly in function of the components rations, is proved insufficient.

Construction of a full-length prototype of the BESIII drift chamber and on-detector test for the BESIII drift chamber electronics

International Nuclear Information System (INIS)

Qin Zhonghua; Wu Linghui; Liu Jianbei; Chinese Academy of Sciences, Beijing; Yan Zhikang; Hunan Univ., Changsha; Chen Yuanbo; Chen Chang; Xu Meihang; Wang Lan; Ma Xiaoyan; Jin Yan; Liu Rongguang; Tang Xiao; Zhang Guifang; Zhu Qiming; Sheng Huayi; Zhu Kejun

2007-01-01

A full-length prototype of the BESIII drift chamber was built. The experience gained on gas sealing, high voltage supply and front-end electronics installation should be greatly beneficial to the successful construction of the BESIII drift chamber. An on-detector test of the BESIII drift chamber electronics was carried out with the constructed prototype chamber. The noise performance, drift time and charge measurements, and electronics gains were examined specifically. The final test results indicate that the electronics have a good performance and can satisfy their design requirements. (authors)

The small FOXP1 isoform predominantly expressed in activated B cell-like diffuse large B-cell lymphoma and full-length FOXP1 exert similar oncogenic and transcriptional activity in human B cells.

Science.gov (United States)

van Keimpema, Martine; Grüneberg, Leonie J; Schilder-Tol, Esther J M; Oud, Monique E C M; Beuling, Esther A; Hensbergen, Paul J; de Jong, Johann; Pals, Steven T; Spaargaren, Marcel

2017-03-01

The forkhead transcription factor FOXP1 is generally regarded as an oncogene in activated B cell-like diffuse large B-cell lymphoma. Previous studies have suggested that a small isoform of FOXP1 rather than full-length FOXP1, may possess this oncogenic activity. Corroborating those studies, we herein show that activated B cell-like diffuse large B-cell lymphoma cell lines and primary activated B cell-like diffuse large B-cell lymphoma cells predominantly express a small FOXP1 isoform, and that the 5'-end of the Foxp1 gene is a common insertion site in murine lymphomas in leukemia virus- and transposon-mediated insertional mutagenesis screens. By combined mass spectrometry, (quantative) reverse transcription polymerase chain reaction/sequencing, and small interfering ribonucleic acid-mediated gene silencing, we determined that the small FOXP1 isoform predominantly expressed in activated B cell-like diffuse large B-cell lymphoma lacks the N-terminal 100 amino acids of full-length FOXP1. Aberrant overexpression of this FOXP1 isoform (ΔN100) in primary human B cells revealed its oncogenic capacity; it repressed apoptosis and plasma cell differentiation. However, no difference in potency was found between this small FOXP1 isoform and full-length FOXP1. Furthermore, overexpression of full-length FOXP1 or this small FOXP1 isoform in primary B cells and diffuse large B-cell lymphoma cell lines resulted in similar gene regulation. Taken together, our data indicate that this small FOXP1 isoform and full-length FOXP1 have comparable oncogenic and transcriptional activity in human B cells, suggesting that aberrant expression or overexpression of FOXP1, irrespective of the specific isoform, contributes to lymphomagenesis. These novel insights further enhance the value of FOXP1 for the diagnostics, prognostics, and treatment of diffuse large B-cell lymphoma patients. Copyright© Ferrata Storti Foundation.

Full-length genome sequences of porcine epidemic diarrhoea virus strain CV777; Use of NGS to analyse genomic and sub-genomic RNAs

DEFF Research Database (Denmark)

Rasmussen, Thomas Bruun; Boniotti, Maria Beatrice; Papetti, Alice

2018-01-01

Porcine epidemic diarrhoea virus, strain CV777, was initially characterized in 1978 as the causative agent of a disease first identified in the UK in 1971. This coronavirus has been widely distributed among laboratories and has been passaged both within pigs and in cell culture. To determine...... the variability between different stocks of the PEDV strain CV777, sequencing of the full-length genome (ca. 28kb) has been performed in 6 different laboratories, using different protocols. Not surprisingly, each of the different full genome sequences were distinct from each other and from the reference sequence...... the analysis of sub-genomic mRNAs from infected cells. It is clearly important to know the features of the specific sample of CV777 being used for experimental studies....

Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomics.

Science.gov (United States)

Aoki, Koh; Yano, Kentaro; Suzuki, Ayako; Kawamura, Shingo; Sakurai, Nozomu; Suda, Kunihiro; Kurabayashi, Atsushi; Suzuki, Tatsuya; Tsugane, Taneaki; Watanabe, Manabu; Ooga, Kazuhide; Torii, Maiko; Narita, Takanori; Shin-I, Tadasu; Kohara, Yuji; Yamamoto, Naoki; Takahashi, Hideki; Watanabe, Yuichiro; Egusa, Mayumi; Kodama, Motoichiro; Ichinose, Yuki; Kikuchi, Mari; Fukushima, Sumire; Okabe, Akiko; Arie, Tsutomu; Sato, Yuko; Yazawa, Katsumi; Satoh, Shinobu; Omura, Toshikazu; Ezura, Hiroshi; Shibata, Daisuke

2010-03-30

The Solanaceae family includes several economically important vegetable crops. The tomato (Solanum lycopersicum) is regarded as a model plant of the Solanaceae family. Recently, a number of tomato resources have been developed in parallel with the ongoing tomato genome sequencing project. In particular, a miniature cultivar, Micro-Tom, is regarded as a model system in tomato genomics, and a number of genomics resources in the Micro-Tom-background, such as ESTs and mutagenized lines, have been established by an international alliance. To accelerate the progress in tomato genomics, we developed a collection of fully-sequenced 13,227 Micro-Tom full-length cDNAs. By checking redundant sequences, coding sequences, and chimeric sequences, a set of 11,502 non-redundant full-length cDNAs (nrFLcDNAs) was generated. Analysis of untranslated regions demonstrated that tomato has longer 5'- and 3'-untranslated regions than most other plants but rice. Classification of functions of proteins predicted from the coding sequences demonstrated that nrFLcDNAs covered a broad range of functions. A comparison of nrFLcDNAs with genes of sixteen plants facilitated the identification of tomato genes that are not found in other plants, most of which did not have known protein domains. Mapping of the nrFLcDNAs onto currently available tomato genome sequences facilitated prediction of exon-intron structure. Introns of tomato genes were longer than those of Arabidopsis and rice. According to a comparison of exon sequences between the nrFLcDNAs and the tomato genome sequences, the frequency of nucleotide mismatch in exons between Micro-Tom and the genome-sequencing cultivar (Heinz 1706) was estimated to be 0.061%. The collection of Micro-Tom nrFLcDNAs generated in this study will serve as a valuable genomic tool for plant biologists to bridge the gap between basic and applied studies. The nrFLcDNA sequences will help annotation of the tomato whole-genome sequence and aid in tomato functional

Dither Cavity Length Controller with Iodine Locking

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Lawson Marty

2016-01-01

Full Text Available A cavity length controller for a seeded Q-switched frequency doubled Nd:YAG laser is constructed. The cavity length controller uses a piezo-mirror dither voltage to find the optimum length for the seeded cavity. The piezo-mirror dither also dithers the optical frequency of the output pulse. [1]. This dither in optical frequency is then used to lock to an Iodine absorption line.

High avidity antibodies to full-length VAR2CSA correlate with absence of placental malaria.

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Yeung Lo Tutterrow

Full Text Available VAR2CSA mediates sequestration of Plasmodium falciparum-infected erythrocytes in the placenta, increasing the risk of poor pregnancy outcomes. Naturally acquired antibodies (Ab to placental parasites at delivery have been associated with improved pregnancy outcomes, but Ab levels and how early in pregnancy Ab must be present in order to eliminate placental parasites before delivery remains unknown. Antibodies to individual Duffy-binding like domains of VAR2CSA have been studied, but the domains lack many of the conformational epitopes present in full-length VAR2CSA (FV2. Thus, the purpose of this study was to describe the acquisition of Ab to FV2 in women residing in high and low transmission areas and determine how Ab levels during pregnancy correlate with clearance of placental parasites. Plasma samples collected monthly throughout pregnancy from pregnant women living in high and low transmission areas in Cameroon were evaluated for Ab to FV2 and the proportion of high avidity Ab (i.e., Ab that remain bound in the presence of 3M NH(4SCN was assessed. Ab levels and proportion of high avidity Ab were compared between women with placental malaria (PM(+ and those without (PM(- at delivery. Results showed that PM(- women had significantly higher Ab levels (p = 0.0047 and proportion of high avidity Ab (p = 0.0009 than PM(+ women throughout pregnancy. Specifically, women with moderate to high Ab levels (>5,000 MFI and those with ≥ 35% high avidity Ab at 5-6 months were found to have 2.3 (95% CI, 1.0-4.9 and 7.6-fold (p = 0.0013, 95% CI: 1.2-50.0 reduced risk of placental malaria, respectively. These data show that high levels of Ab to FV2, particularly those with high avidity for FV2, produced by mid-pregnancy are important in clearing parasites from the placenta. Both high Ab levels and proportion of high avidity Ab to FV2 may serve as correlates of protection for assessing immunity against placental malaria.

Full-length VP2 gene analysis of canine parvovirus reveals emergence of newer variants in India.

Science.gov (United States)

Nookala, Mangadevi; Mukhopadhyay, Hirak Kumar; Sivaprakasam, Amsaveni; Balasubramanian, Brindhalakshmi; Antony, Prabhakar Xavier; Thanislass, Jacob; Srinivas, Mouttou Vivek; Pillai, Raghavan Madhusoodanan

2016-12-01

The canine parvovirus (CPV) infection is a highly contagious and serious enteric disease of dogs with high fatality rate. The present study was taken up to characterize the full-length viral polypeptide 2 (VP2) gene of CPV of Indian origin along with the commercially available vaccines. The faecal samples from parvovirus suspected dogs were collected from various states of India for screening by PCR assay and 66.29% of samples were found positive. Six CPV-2a, three CPV-2b, and one CPV-2c types were identified by sequence analysis. Several unique and existing mutations have been noticed in CPV types analyzed indicating emergence of newer variants of CPV in India. The phylogenetic analysis revealed that all the field CPV types were grouped in different subclades within two main clades, but away from the commercial vaccine strains. CPV-2b and CPV-2c types with unique mutations were found to be establishing in India apart from the prevailing CPV-2a type. Mutations and the positive selection of the mutants were found to be the major mechanism of emergence and evolution of parvovirus. Therefore, the incorporation of local strain in the vaccine formulation may be considered for effective control of CPV infections in India.

Structure and function of the first full-length murein peptide ligase (Mpl cell wall recycling protein.

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Debanu Das

2011-03-01

Full Text Available Bacterial cell walls contain peptidoglycan, an essential polymer made by enzymes in the Mur pathway. These proteins are specific to bacteria, which make them targets for drug discovery. MurC, MurD, MurE and MurF catalyze the synthesis of the peptidoglycan precursor UDP-N-acetylmuramoyl-L-alanyl-γ-D-glutamyl-meso-diaminopimelyl-D-alanyl-D-alanine by the sequential addition of amino acids onto UDP-N-acetylmuramic acid (UDP-MurNAc. MurC-F enzymes have been extensively studied by biochemistry and X-ray crystallography. In gram-negative bacteria, ∼30-60% of the bacterial cell wall is recycled during each generation. Part of this recycling process involves the murein peptide ligase (Mpl, which attaches the breakdown product, the tripeptide L-alanyl-γ-D-glutamyl-meso-diaminopimelate, to UDP-MurNAc. We present the crystal structure at 1.65 Å resolution of a full-length Mpl from the permafrost bacterium Psychrobacter arcticus 273-4 (PaMpl. Although the Mpl structure has similarities to Mur enzymes, it has unique sequence and structure features that are likely related to its role in cell wall recycling, a function that differentiates it from the MurC-F enzymes. We have analyzed the sequence-structure relationships that are unique to Mpl proteins and compared them to MurC-F ligases. We have also characterized the biochemical properties of this enzyme (optimal temperature, pH and magnesium binding profiles and kinetic parameters. Although the structure does not contain any bound substrates, we have identified ∼30 residues that are likely to be important for recognition of the tripeptide and UDP-MurNAc substrates, as well as features that are unique to Psychrobacter Mpl proteins. These results provide the basis for future mutational studies for more extensive function characterization of the Mpl sequence-structure relationships.

Revised genomic consensus for the hypermethylated CpG island region of the human L1 transposon and integration sites of full length L1 elements from recombinant clones made using methylation-tolerant host strains

DEFF Research Database (Denmark)

Crowther, P J; Doherty, J P; Linsenmeyer, M E

1991-01-01

preferentially from L1 members which have accumulated mutations that have removed sites of methylation. We present a revised consensus from the 5' presumptive control region of these elements. This revised consensus contains a consensus RNA polymerase III promoter which would permit the synthesis of transcripts......Efficient recovery of clones from the 5' end of the human L1 dispersed repetitive elements necessitates the use of deletion mcr- host strains since this region contains a CpG island which is hypermethylated in vivo. Clones recovered with conventional mcr+ hosts seem to have been derived...... from the 5' end of full length L1 elements. Such potential transcripts are likely to exhibit a high degree of secondary structure. In addition, we have determined the flanking sequences for 6 full length L1 elements. The majority of full length L1 clones show no convincing evidence for target site...

Diagnostic value of newborn foot length to predict gestational age

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Mutia Farah Fawziah

2017-08-01

Full Text Available Background  Identification of gestational age, especially within 48 hours of birth, is crucial for newborns, as the earlier preterm status is detected, the earlier the child can receive optimal management. Newborn foot length is an anthropometric measurement which is easy to perform, inexpensive, and potentially efficient for predicting gestational age. Objective  To analyze the diagnostic value of newborn foot length in predicting gestational age. Methods  This diagnostic study was performed between October 2016 and February 2017 in the High Care Unit of Neonates at Dr. Moewardi General Hospital, Surakarta. A total of 152 newborns were consecutively selected and underwent right foot length measurements before 96 hours of age. The correlation between newborn foot length to classify as full term and gestational age was analyzed with Spearman’s correlation test because of non-normal data distribution. The cut-off point of newborn foot length was calculated by receiver operating characteristic (ROC curve and diagnostic values of newborn foot length were analyzed by 2 x 2 table with SPSS 21.0 software. Results There were no significant differences between male and female newborns in terms of gestational age, birth weight, choronological age, and newborn foot length (P>0.05. Newborn foot length and gestational age had a significant correlation (r=0.53; P=0.000. The optimal cut-off newborn foot length to predict full term status was 7.1 cm. Newborn foot length below 7.1 cm had sensitivity 75%, specificity 98%, positive predictive value 94.3%, negative predictive value 90.6%, positive likelihood ratio 40.5, negative likelihood ratio 0.25, and post-test probability 94.29%, to predict preterm status in newborns. Conclusion  Newborn foot length can be used to predict gestational age, especially for the purpose of differentiating between preterm and full term newborns.

Cutting Whole Length or Partial Length of Internal Anal Sphincter in Managementof Fissure in Ano

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Furat Shani Aoda

2017-12-01

Full Text Available A chronic anal fissure is a common painful perianal condition.The main operative procedure to treat this painful condition is a lateral internal sphincteretomy (LIS.The aim of study is to compare the outcome and complications of closed LIS up to the dentate line (whole length of internal sphincter or up to the fissure apex (partial length of internal sphincter in the treatment of anal fissure.It is a prospective comparativestudy including 100 patients with chronic fissure in ano. All patients assigned to undergo closed LIS. Those patients were randomly divided into two groups: 50 patients underwent LIS to the level of dentate line (whole length and other 50 patients underwent LIS to the level of fissure apex (partial length. Patients were followed up weekly in the 1st month, twice monthly in the second month then monthly   for next 2 months and finally after 1 year. There was satisfactory relief of pain in all patients in both groups & complete healing of the fissure occurred. Regarding post operative incontinence no major degree of incontinence occur in both group but minor degree of incontinence persists In 7 patients after whole length LIS after one year. In conclusion, both whole length & partial length LIS associated with improvement of pain, good chance of healing but whole length LIS associated with more chance of long term  flatus incontinence. Hence,we recommend partial length LIS as treatment forchronic anal fissure.

FULL LENGTH RESEARCH ARTICLE Yoriyo et al.(2008) SWJ:35 ...

African Journals Online (AJOL)

Dr. Ahmed

poultry industry to its full capacity. These factors include poor management systems and diseases. Poultry diseases are the major cause of financial loss in poultry production (Oluyemi & Rober, 1979). Intestinal parasitism is a common problem in poultry especially those reared under extensive systems. Ajayi & Ajayi (1983) ...

Identification of the full-length β-actin sequence and expression profiles in the tree shrew (Tupaia belangeri).

Science.gov (United States)

Zheng, Yu; Yun, Chenxia; Wang, Qihui; Smith, Wanli W; Leng, Jing

2015-02-01

The tree shrew (Tupaia belangeri) diverges from the primate order (Primates) and is classified as a separate taxonomic group of mammals - Scandentia. It has been suggested that the tree shrew can be used as an animal model for studying human diseases; however, the genomic sequence of the tree shrew is largely unidentified. In the present study, we reported the full-length cDNA sequence of the housekeeping gene, β-actin, in the tree shrew. The amino acid sequence of β-actin in the tree shrew was compared to that of humans and other species; a simple phylogenetic relationship was discovered. Quantitative polymerase chain reaction (qPCR) and western blot analysis further demonstrated that the expression profiles of β-actin, as a general conservative housekeeping gene, in the tree shrew were similar to those in humans, although the expression levels varied among different types of tissue in the tree shrew. Our data provide evidence that the tree shrew has a close phylogenetic association with humans. These findings further enhance the potential that the tree shrew, as a species, may be used as an animal model for studying human disorders.

Impedance of finite length resistive cylinder

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S. Krinsky

2004-11-01

Full Text Available We determine the impedance of a cylindrical metal tube (resistor of radius a, length g, and conductivity σ attached at each end to perfect conductors of semi-infinite length. Our main interest is in the asymptotic behavior of the impedance at high frequency (k≫1/a. In the equilibrium regime, ka^{2}≪g, the impedance per unit length is accurately described by the well-known result for an infinite length tube with conductivity σ. In the transient regime, ka^{2}≫g, where the contribution of transition radiation arising from the discontinuity in conductivity is important, we derive an analytic expression for the impedance and compute the short-range wakefield. The analytic results are shown to agree with numerical evaluation of the impedance.

Isolation of full-length putative rat lysophospholipase cDNA using improved methods for mRNA isolation and cDNA cloning

International Nuclear Information System (INIS)

Han, J.H.; Stratowa, C.; Rutter, W.J.

1987-01-01

The authors have cloned a full-length putative rat pancreatic lysophospholipase cDNA by an improved mRNA isolation method and cDNA cloning strategy using [ 32 P]-labelled nucleotides. These new methods allow the construction of a cDNA library from the adult rat pancreas in which the majority of recombinant clones contained complete sequences for the corresponding mRNAs. A previously recognized but unidentified long and relatively rare cDNA clone containing the entire sequence from the cap site at the 5' end to the poly(A) tail at the 3' end of the mRNA was isolated by single-step screening of the library. The size, amino acid composition, and the activity of the protein expressed in heterologous cells strongly suggest this mRNA codes for lysophospholipase

Signal sequence and keyword trap in silico for selection of full-length human cDNAs encoding secretion or membrane proteins from oligo-capped cDNA libraries.

Science.gov (United States)

Otsuki, Tetsuji; Ota, Toshio; Nishikawa, Tetsuo; Hayashi, Koji; Suzuki, Yutaka; Yamamoto, Jun-ichi; Wakamatsu, Ai; Kimura, Kouichi; Sakamoto, Katsuhiko; Hatano, Naoto; Kawai, Yuri; Ishii, Shizuko; Saito, Kaoru; Kojima, Shin-ichi; Sugiyama, Tomoyasu; Ono, Tetsuyoshi; Okano, Kazunori; Yoshikawa, Yoko; Aotsuka, Satoshi; Sasaki, Naokazu; Hattori, Atsushi; Okumura, Koji; Nagai, Keiichi; Sugano, Sumio; Isogai, Takao

2005-01-01

We have developed an in silico method of selection of human full-length cDNAs encoding secretion or membrane proteins from oligo-capped cDNA libraries. Fullness rates were increased to about 80% by combination of the oligo-capping method and ATGpr, software for prediction of translation start point and the coding potential. Then, using 5'-end single-pass sequences, cDNAs having the signal sequence were selected by PSORT ('signal sequence trap'). We also applied 'secretion or membrane protein-related keyword trap' based on the result of BLAST search against the SWISS-PROT database for the cDNAs which could not be selected by PSORT. Using the above procedures, 789 cDNAs were primarily selected and subjected to full-length sequencing, and 334 of these cDNAs were finally selected as novel. Most of the cDNAs (295 cDNAs: 88.3%) were predicted to encode secretion or membrane proteins. In particular, 165(80.5%) of the 205 cDNAs selected by PSORT were predicted to have signal sequences, while 70 (54.2%) of the 129 cDNAs selected by 'keyword trap' preserved the secretion or membrane protein-related keywords. Many important cDNAs were obtained, including transporters, receptors, and ligands, involved in significant cellular functions. Thus, an efficient method of selecting secretion or membrane protein-encoding cDNAs was developed by combining the above four procedures.

The comparison between the length of vertical dimension of occlusion and the length of thumb on undergraduate Mongoloid students

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Goh Li Teng

2011-03-01

Full Text Available The Thumb Rule of Leonardo da Vinci states that many proportions of the face show relationship with the length of thumb which is measured from the proximal tip of the proximal phalanx to the distal tip of the distal phalanx. Previous studies have shown that the length of the vertical dimension of occlusion (VDO is similar to the length of thumb of the Caucasoid race. The purpose of this study is to determine whether the length of VDO have correlations with the length of thumb among those of the Mongoloid race. This study took a survey method with the analytical cross-sectional approach. A total of 80 students of Faculty of Dentistry who have fulfilled all population criteria were randomly chosen to measure the length of VDO and the length of the thumb. Results analyzed with Student's t-test statistic revealed that there was a significant difference between males and females in the length of VDO and the length of the thumb, however, there was no significant difference between the length of VDO and the length of the thumb. There were very strong correlations (P<0.05 between the length of VDO and the length of the thumb. As a conclusion, the length of thumb can be suggested as an objective method to determine the length of VDO in this population.

Employment of Near Full-Length Ribosome Gene TA-Cloning and Primer-Blast to Detect Multiple Species in a Natural Complex Microbial Community Using Species-Specific Primers Designed with Their Genome Sequences.

Science.gov (United States)

Zhang, Huimin; He, Hongkui; Yu, Xiujuan; Xu, Zhaohui; Zhang, Zhizhou

2016-11-01

It remains an unsolved problem to quantify a natural microbial community by rapidly and conveniently measuring multiple species with functional significance. Most widely used high throughput next-generation sequencing methods can only generate information mainly for genus-level taxonomic identification and quantification, and detection of multiple species in a complex microbial community is still heavily dependent on approaches based on near full-length ribosome RNA gene or genome sequence information. In this study, we used near full-length rRNA gene library sequencing plus Primer-Blast to design species-specific primers based on whole microbial genome sequences. The primers were intended to be specific at the species level within relevant microbial communities, i.e., a defined genomics background. The primers were tested with samples collected from the Daqu (also called fermentation starters) and pit mud of a traditional Chinese liquor production plant. Sixteen pairs of primers were found to be suitable for identification of individual species. Among them, seven pairs were chosen to measure the abundance of microbial species through quantitative PCR. The combination of near full-length ribosome RNA gene library sequencing and Primer-Blast may represent a broadly useful protocol to quantify multiple species in complex microbial population samples with species-specific primers.

Full-Length Sequence of Mouse Acupuncture-Induced 1-L (Aig1l Gene Including Its Transcriptional Start Site

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Mika Ohta

2011-01-01

Full Text Available We have been investigating the molecular efficacy of electroacupuncture (EA, which is one type of acupuncture therapy. In our previous molecular biological study of acupuncture, we found an EA-induced gene, named acupuncture-induced 1-L (Aig1l, in mouse skeletal muscle. The aims of this study consisted of identification of the full-length cDNA sequence of Aig1l including the transcriptional start site, determination of the tissue distribution of Aig1l and analysis of the effect of EA on Aig1l gene expression. We determined the complete cDNA sequence including the transcriptional start site via cDNA cloning with the cap site hunting method. We then analyzed the tissue distribution of Aig1l by means of northern blot analysis and real-time quantitative polymerase chain reaction. We used the semiquantitative reverse transcriptase-polymerase chain reaction to examine the effect of EA on Aig1l gene expression. Our results showed that the complete cDNA sequence of Aig1l was 6073 bp long, and the putative protein consisted of 962 amino acids. All seven tissues that we analyzed expressed the Aig1l gene. In skeletal muscle, EA induced expression of the Aig1l gene, with high expression observed after 3 hours of EA. Our findings thus suggest that the Aig1l gene may play a key role in the molecular mechanisms of EA efficacy.

The length of the male urethra

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Tobias. S. Kohler

2008-08-01

Full Text Available PURPOSE: Catheter-based medical devices are an important component of the urologic armamentarium. To our knowledge, there is no population-based data regarding normal male urethral length. We evaluated the length of the urethra in men with normal genitourinary anatomy undergoing either Foley catheter removal or standard cystoscopy. MATERIALS AND METHODS: Male urethral length was obtained in 109 men. After study permission was obtained, the subject's penis was placed on a gentle stretch and the catheter was marked at the tip of the penis. The catheter was then removed and the distance from the mark to the beginning of the re-inflated balloon was measured. Alternatively, urethral length was measured at the time of cystoscopy, on removal of the cystoscope. Data on age, weight, and height was obtained in patients when possible. RESULTS: The mean urethral length was 22.3 cm with a standard deviation of 2.4 cm. Urethral length varied between 15 cm and 29 cm. No statistically significant correlation was found between urethral length and height, weight, body mass index (BMI, or age. CONCLUSIONS: Literature documenting the length of the normal male adult urethra is scarce. Our data adds to basic anatomic information of the male urethra and may be used to optimize genitourinary device design.

FULL LENGTH RESEARCH ARTICLE Gnut

African Journals Online (AJOL)

Dr Ahmed

. Peanuts, Groundnuts microflora and pathogenesis of peanut pod. Root Phytopathology, 55(4):359-367. Halima, A. S. 2000. Isolation and preliminary Identification of fungi in stored groundnut. HND project. Department of Science Laboratory.

Economic issues of broiler production length

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Szőllősi László

2014-01-01

Full Text Available The length of broiler production cycle is also an important factor when profitability is measured. This paper is to determine the effects of different market ages and down-time period, overall broiler production cycle length on performance and economic parameters based on Hungarian production and financial circumstances. A deterministic model was constructed to manage the function-like correlations of age-related daily weight gain, daily feed intake and daily mortality data. The results show that broiler production cycle length has a significant effect on production and economic performance. Cycle length is determined by the length of down-time and grow-out periods. If down-time period is reduced by one day, an average net income of EUR 0.55 per m2 is realizable. However, the production period is not directly proportional either with emerging costs or obtainable revenues. Profit maximization is attainable if the production period is 41-42 days.

Relativistic length agony continued

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Redžić D.V.

2014-01-01

Full Text Available We made an attempt to remedy recent confusing treatments of some basic relativistic concepts and results. Following the argument presented in an earlier paper (Redžić 2008b, we discussed the misconceptions that are recurrent points in the literature devoted to teaching relativity such as: there is no change in the object in Special Relativity, illusory character of relativistic length contraction, stresses and strains induced by Lorentz contraction, and related issues. We gave several examples of the traps of everyday language that lurk in Special Relativity. To remove a possible conceptual and terminological muddle, we made a distinction between the relativistic length reduction and relativistic FitzGerald-Lorentz contraction, corresponding to a passive and an active aspect of length contraction, respectively; we pointed out that both aspects have fundamental dynamical contents. As an illustration of our considerations, we discussed briefly the Dewan-Beran-Bell spaceship paradox and the ‘pole in a barn’ paradox. [Projekat Ministarstva nauke Republike Srbije, br. 171028

Molecular Cloning and Characterization of Full-Length cDNA of Calmodulin Gene from Pacific Oyster Crassostrea gigas.

Science.gov (United States)

Li, Xing-Xia; Yu, Wen-Chao; Cai, Zhong-Qiang; He, Cheng; Wei, Na; Wang, Xiao-Tong; Yue, Xi-Qing

2016-01-01

The shell of the pearl oyster ( Pinctada fucata ) mainly comprises aragonite whereas that of the Pacific oyster ( Crassostrea gigas ) is mainly calcite, thereby suggesting the different mechanisms of shell formation between above two mollusks. Calmodulin (CaM) is an important gene for regulating the uptake, transport, and secretion of calcium during the process of shell formation in pearl oyster. It is interesting to characterize the CaM in oysters, which could facilitate the understanding of the different shell formation mechanisms among mollusks. We cloned the full-length cDNA of Pacific oyster CaM (cgCaM) and found that the cgCaM ORF encoded a peptide of 113 amino acids containing three EF-hand calcium-binding domains, its expression level was highest in the mantle, hinting that the cgCaM gene is probably involved in shell formation of Pacific oyster, and the common ancestor of Gastropoda and Bivalvia may possess at least three CaM genes. We also found that the numbers of some EF hand family members in highly calcified species were higher than those in lowly calcified species and the numbers of these motifs in oyster genome were the highest among the mollusk species with whole genome sequence, further hinting the correlation between CaM and biomineralization.

VP1u phospholipase activity is critical for infectivity of full-length parvovirus B19 genomic clones.

Science.gov (United States)

Filippone, Claudia; Zhi, Ning; Wong, Susan; Lu, Jun; Kajigaya, Sachiko; Gallinella, Giorgio; Kakkola, Laura; Söderlund-Venermo, Maria; Young, Neal S; Brown, Kevin E

2008-05-10

Three full-length genomic clones (pB19-M20, pB19-FL and pB19-HG1) of parvovirus B19 were produced in different laboratories. pB19-M20 was shown to produce infectious virus. To determine the differences in infectivity, all three plasmids were tested by transfection and infection assays. All three clones were similar in viral DNA replication, RNA transcription, and viral capsid protein production. However, only pB19-M20 and pB19-HG1 produced infectious virus. Comparison of viral sequences showed no significant differences in ITR or NS regions. In the capsid region, there was a nucleotide sequence difference conferring an amino acid substitution (E176K) in the phospholipase A2-like motif of the VP1-unique (VP1u) region. The recombinant VP1u with the E176K mutation had no catalytic activity as compared with the wild-type. When this mutation was introduced into pB19-M20, infectivity was significantly attenuated, confirming the critical role of this motif. Investigation of the original serum from which pB19-FL was cloned confirmed that the phospholipase mutation was present in the native B19 virus.

VP1u phospholipase activity is critical for infectivity of full-length parvovirus B19 genomic clones✰

Science.gov (United States)

Filippone, Claudia; Zhi, Ning; Wong, Susan; Lu, Jun; Kajigaya, Sachiko; Gallinella, Giorgio; Kakkola, Laura; Venermo, Maria S Söderlund; Young, Neal S.; Brown, Kevin E.

2008-01-01

Three full-length genomic clones (pB19-M20, pB19-FL and pB19-HG1) of parvovirus B19 were produced in different laboratories. pB19-M20 was shown to produce infectious virus. To determine the differences in infectivity, all three plasmids were tested by transfection and infection assays. All three clones were similar in viral DNA replication, RNA transcription, and viral capsid protein production. However, only pB19-M20 and pB19-HG1 produced infectious virus. Comparison of viral sequences showed no significant differences in ITR or NS regions. In the capsid region, there was a nucleotide sequence difference conferring an amino acid substitution (E176K) in the phospholipase A2-like motif of the VP1-unique (VP1u) region. The recombinant VP1u with the E176K mutation had no catalytic activity as compared with the wild-type. When this mutation was introduced into pB19-M20, infectivity was significantly attenuated, confirming the critical role of this motif. Investigation of the original serum from which pB19-FL was cloned confirmed that the phospholipase mutation was present in the native B19 virus. PMID:18252260

Fundamental length and relativistic length

International Nuclear Information System (INIS)

Strel'tsov, V.N.

1988-01-01

It si noted that the introduction of fundamental length contradicts the conventional representations concerning the contraction of the longitudinal size of fast-moving objects. The use of the concept of relativistic length and the following ''elongation formula'' permits one to solve this problem

Effect of heated length on the Critical Heat Flux of subcooled flow boiling. 2. Effective heated length under axially nonuniform heating condition

International Nuclear Information System (INIS)

Kinoshita, Hidetaka; Yoshida, Takuya; Nariai, Hideki; Inasaka, Fujio

1998-01-01

Effect of heated length on the Critical Heat Flux (CHF) of subcooled flow boiling with water was experimentally investigated by using direct current heated tube made of stainless steel a part of whose wall thickness was axially cut for realizing nonuniform heat flux condition. The higher enhancement of the CHF was derived for shorter tube length. The effective heated length was determined for the tube under axially nonuniform heat flux condition. When the lower heat flux part below the Net Vapor Generation (NVG) heat flux exists at the middle of tube length, then the effective heated length becomes the tube length downstream the lower heat flux parts. However, when the lower heat flux part is above the NVG, then the effective heated length is full tube length. (author)

Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray.

Directory of Open Access Journals (Sweden)

Kouji Satoh

Full Text Available Rice (Oryza sativa L. is a model organism for the functional genomics of monocotyledonous plants since the genome size is considerably smaller than those of other monocotyledonous plants. Although highly accurate genome sequences of indica and japonica rice are available, additional resources such as full-length complementary DNA (FL-cDNA sequences are also indispensable for comprehensive analyses of gene structure and function. We cross-referenced 28.5K individual loci in the rice genome defined by mapping of 578K FL-cDNA clones with the 56K loci predicted in the TIGR genome assembly. Based on the annotation status and the presence of corresponding cDNA clones, genes were classified into 23K annotated expressed (AE genes, 33K annotated non-expressed (ANE genes, and 5.5K non-annotated expressed (NAE genes. We developed a 60mer oligo-array for analysis of gene expression from each locus. Analysis of gene structures and expression levels revealed that the general features of gene structure and expression of NAE and ANE genes were considerably different from those of AE genes. The results also suggested that the cloning efficiency of rice FL-cDNA is associated with the transcription activity of the corresponding genetic locus, although other factors may also have an effect. Comparison of the coverage of FL-cDNA among gene families suggested that FL-cDNA from genes encoding rice- or eukaryote-specific domains, and those involved in regulatory functions were difficult to produce in bacterial cells. Collectively, these results indicate that rice genes can be divided into distinct groups based on transcription activity and gene structure, and that the coverage bias of FL-cDNA clones exists due to the incompatibility of certain eukaryotic genes in bacteria.

Effects of Conjugate Gradient Methods and Step-Length Formulas on the Multiscale Full Waveform Inversion in Time Domain: Numerical Experiments

Science.gov (United States)

Liu, Youshan; Teng, Jiwen; Xu, Tao; Badal, José; Liu, Qinya; Zhou, Bing

2017-05-01

We carry out full waveform inversion (FWI) in time domain based on an alternative frequency-band selection strategy that allows us to implement the method with success. This strategy aims at decomposing the seismic data within partially overlapped frequency intervals by carrying out a concatenated treatment of the wavelet to largely avoid redundant frequency information to adapt to wavelength or wavenumber coverage. A pertinent numerical test proves the effectiveness of this strategy. Based on this strategy, we comparatively analyze the effects of update parameters for the nonlinear conjugate gradient (CG) method and step-length formulas on the multiscale FWI through several numerical tests. The investigations of up to eight versions of the nonlinear CG method with and without Gaussian white noise make clear that the HS (Hestenes and Stiefel in J Res Natl Bur Stand Sect 5:409-436, 1952), CD (Fletcher in Practical methods of optimization vol. 1: unconstrained optimization, Wiley, New York, 1987), and PRP (Polak and Ribière in Revue Francaise Informat Recherche Opertionelle, 3e Année 16:35-43, 1969; Polyak in USSR Comput Math Math Phys 9:94-112, 1969) versions are more efficient among the eight versions, while the DY (Dai and Yuan in SIAM J Optim 10:177-182, 1999) version always yields inaccurate result, because it overestimates the deeper parts of the model. The application of FWI algorithms using distinct step-length formulas, such as the direct method ( Direct), the parabolic search method ( Search), and the two-point quadratic interpolation method ( Interp), proves that the Interp is more efficient for noise-free data, while the Direct is more efficient for Gaussian white noise data. In contrast, the Search is less efficient because of its slow convergence. In general, the three step-length formulas are robust or partly insensitive to Gaussian white noise and the complexity of the model. When the initial velocity model deviates far from the real model or the

A novel copper(II) coordination at His186 in full-length murine prion protein

Energy Technology Data Exchange (ETDEWEB)

Watanabe, Yasuko [Laboratory of Radiation Biology, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo 060-0818 (Japan); Hiraoka, Wakako [Laboratory of Biophysics, School of Science and Technology, Meiji University, Kawasaki 214-8571 (Japan); Igarashi, Manabu; Ito, Kimihito [Department of Global Epidemiology, Hokkaido University Research Center for Zoonosis Control, Sapporo 001-0020 (Japan); Shimoyama, Yuhei [Soft-Matter Physics Laboratory, Graduate School of Emergent Science, Muroran Institute of Technology, Muroran 050-8585 (Japan); Horiuchi, Motohiro [Laboratory of Prion Diseases, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo 060-0818 (Japan); Yamamori, Tohru; Yasui, Hironobu; Kuwabara, Mikinori [Laboratory of Radiation Biology, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo 060-0818 (Japan); Inagaki, Fuyuhiko [Laboratory of Structural Biology, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812 (Japan); Inanami, Osamu, E-mail: inanami@vetmed.hokudai.ac.jp [Laboratory of Radiation Biology, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo 060-0818 (Japan)

2010-04-09

To explore Cu(II) ion coordination by His{sup 186} in the C-terminal domain of full-length prion protein (moPrP), we utilized the magnetic dipolar interaction between a paramagnetic metal, Cu(II) ion, and a spin probe introduced in the neighborhood of the postulated binding site by the spin labeling technique (SDSL technique). Six moPrP mutants, moPrP(D143C), moPrP(Y148C), moPrP(E151C), moPrP(Y156C), moPrP(T189C), and moPrP(Y156C,H186A), were reacted with a methane thiosulfonate spin probe and a nitroxide residue (R1) was created in the binding site of each one. Line broadening of the ESR spectra was induced in the presence of Cu(II) ions in moPrP(Y148R1), moPrP(Y151R1), moPrP(Y156R1), and moPrP(T189R1) but not moPrP(D143R1). This line broadening indicated the presence of electron-electron dipolar interaction between Cu(II) and the nitroxide spin probe, suggesting that each interspin distance was within 20 A. The interspin distance ranges between Cu(II) and the spin probes of moPrP(Y148R1), moPrP(Y151R1), moPrP(Y156R1), and moPrP(T189R1) were estimated to be 12.1 A, 18.1 A, 10.7 A, and 8.4 A, respectively. In moPrP(Y156R1,H186A), line broadening between Cu(II) and the spin probe was not observed. These results suggest that a novel Cu(II) binding site is involved in His186 in the Helix2 region of the C-terminal domain of moPrP{sup C}.

A novel copper(II) coordination at His186 in full-length murine prion protein

International Nuclear Information System (INIS)

Watanabe, Yasuko; Hiraoka, Wakako; Igarashi, Manabu; Ito, Kimihito; Shimoyama, Yuhei; Horiuchi, Motohiro; Yamamori, Tohru; Yasui, Hironobu; Kuwabara, Mikinori; Inagaki, Fuyuhiko; Inanami, Osamu

2010-01-01

To explore Cu(II) ion coordination by His 186 in the C-terminal domain of full-length prion protein (moPrP), we utilized the magnetic dipolar interaction between a paramagnetic metal, Cu(II) ion, and a spin probe introduced in the neighborhood of the postulated binding site by the spin labeling technique (SDSL technique). Six moPrP mutants, moPrP(D143C), moPrP(Y148C), moPrP(E151C), moPrP(Y156C), moPrP(T189C), and moPrP(Y156C,H186A), were reacted with a methane thiosulfonate spin probe and a nitroxide residue (R1) was created in the binding site of each one. Line broadening of the ESR spectra was induced in the presence of Cu(II) ions in moPrP(Y148R1), moPrP(Y151R1), moPrP(Y156R1), and moPrP(T189R1) but not moPrP(D143R1). This line broadening indicated the presence of electron-electron dipolar interaction between Cu(II) and the nitroxide spin probe, suggesting that each interspin distance was within 20 A. The interspin distance ranges between Cu(II) and the spin probes of moPrP(Y148R1), moPrP(Y151R1), moPrP(Y156R1), and moPrP(T189R1) were estimated to be 12.1 A, 18.1 A, 10.7 A, and 8.4 A, respectively. In moPrP(Y156R1,H186A), line broadening between Cu(II) and the spin probe was not observed. These results suggest that a novel Cu(II) binding site is involved in His186 in the Helix2 region of the C-terminal domain of moPrP C .

Blind sequence-length estimation of low-SNR cyclostationary sequences

CSIR Research Space (South Africa)

Vlok, JD

2014-06-01

Full Text Available Several existing direct-sequence spread spectrum (DSSS) detection and estimation algorithms assume prior knowledge of the symbol period or sequence length, although very few sequence-length estimation techniques are available in the literature...

Stochastic Simulation of a Full-Chain Reptation Model with Constraint Release, Chain-Length Fluctuations and Chain Stretching

DEFF Research Database (Denmark)

Neergaard, Jesper; Schieber, Jay D.

1999-01-01

A self-consistent reptation model that includes chain stretching, chain-length fluctuations, segment connectivity and constraint release is used to predict transient and steady flows. Quantitative comparisons are made with entangledsolution data. The model is able to capture quantitatively all...

WebPrInSeS: automated full-length clone sequence identification and verification using high-throughput sequencing data.

Science.gov (United States)

Massouras, Andreas; Decouttere, Frederik; Hens, Korneel; Deplancke, Bart

2010-07-01

High-throughput sequencing (HTS) is revolutionizing our ability to obtain cheap, fast and reliable sequence information. Many experimental approaches are expected to benefit from the incorporation of such sequencing features in their pipeline. Consequently, software tools that facilitate such an incorporation should be of great interest. In this context, we developed WebPrInSeS, a web server tool allowing automated full-length clone sequence identification and verification using HTS data. WebPrInSeS encompasses two separate software applications. The first is WebPrInSeS-C which performs automated sequence verification of user-defined open-reading frame (ORF) clone libraries. The second is WebPrInSeS-E, which identifies positive hits in cDNA or ORF-based library screening experiments such as yeast one- or two-hybrid assays. Both tools perform de novo assembly using HTS data from any of the three major sequencing platforms. Thus, WebPrInSeS provides a highly integrated, cost-effective and efficient way to sequence-verify or identify clones of interest. WebPrInSeS is available at http://webprinses.epfl.ch/ and is open to all users.

Generation and analysis of large-scale expressed sequence tags (ESTs from a full-length enriched cDNA library of porcine backfat tissue

Directory of Open Access Journals (Sweden)

Lee Hae-Young

2006-02-01

Full Text Available Abstract Background Genome research in farm animals will expand our basic knowledge of the genetic control of complex traits, and the results will be applied in the livestock industry to improve meat quality and productivity, as well as to reduce the incidence of disease. A combination of quantitative trait locus mapping and microarray analysis is a useful approach to reduce the overall effort needed to identify genes associated with quantitative traits of interest. Results We constructed a full-length enriched cDNA library from porcine backfat tissue. The estimated average size of the cDNA inserts was 1.7 kb, and the cDNA fullness ratio was 70%. In total, we deposited 16,110 high-quality sequences in the dbEST division of GenBank (accession numbers: DT319652-DT335761. For all the expressed sequence tags (ESTs, approximately 10.9 Mb of porcine sequence were generated with an average length of 674 bp per EST (range: 200–952 bp. Clustering and assembly of these ESTs resulted in a total of 5,008 unique sequences with 1,776 contigs (35.46% and 3,232 singleton (65.54% ESTs. From a total of 5,008 unique sequences, 3,154 (62.98% were similar to other sequences, and 1,854 (37.02% were identified as having no hit or low identity (Sus scrofa. Gene ontology (GO annotation of unique sequences showed that approximately 31.7, 32.3, and 30.8% were assigned molecular function, biological process, and cellular component GO terms, respectively. A total of 1,854 putative novel transcripts resulted after comparison and filtering with the TIGR SsGI; these included a large percentage of singletons (80.64% and a small proportion of contigs (13.36%. Conclusion The sequence data generated in this study will provide valuable information for studying expression profiles using EST-based microarrays and assist in the condensation of current pig TCs into clusters representing longer stretches of cDNA sequences. The isolation of genes expressed in backfat tissue is the

Functional PAK-2 knockout and replacement with a caspase cleavage-deficient mutant in mice reveals differential requirements of full-length PAK-2 and caspase-activated PAK-2p34.

Science.gov (United States)

Marlin, Jerry W; Chang, Yu-Wen E; Ober, Margaret; Handy, Amy; Xu, Wenhao; Jakobi, Rolf

2011-06-01

p21-Activated protein kinase 2 (PAK-2) has both anti- and pro-apoptotic functions depending on its mechanism of activation. Activation of full-length PAK-2 by the monomeric GTPases Cdc42 or Rac stimulates cell survival, whereas caspase activation of PAK-2 to the PAK-2p34 fragment is involved in the apoptotic response. In this study we use functional knockout of PAK-2 and gene replacement with the caspase cleavage-deficient PAK-2D212N mutant to differentiate the biological functions of full-length PAK-2 and caspase-activated PAK-2p34. Knockout of PAK-2 results in embryonic lethality at early stages before organ development, whereas replacement with the caspase cleavage-deficient PAK-2D212N results in viable and healthy mice, indicating that early embryonic lethality is caused by deficiency of full-length PAK-2 rather than lack of caspase activation to the PAK-2p34 fragment. However, deficiency of caspase activation of PAK-2 decreased spontaneous cell death of primary mouse embryonic fibroblasts and increased cell growth at high cell density. In contrast, stress-induced cell death by treatment with the anti-cancer drug cisplatin was not reduced by deficiency of caspase activation of PAK-2, but switched from an apoptotic to a nonapoptotic, caspase-independent mechanism. Homozygous PAK-2D212N primary mouse embryonic fibroblasts that lack the ability to generate the proapoptotic PAK-2p34 show less activation of the effector caspase 3, 6, and 7, indicating that caspase activation of PAK-2 amplifies the apoptotic response through a positive feedback loop resulting in more activation of effector caspases.

Zero-point length from string fluctuations

International Nuclear Information System (INIS)

Fontanini, Michele; Spallucci, Euro; Padmanabhan, T.

2006-01-01

One of the leading candidates for quantum gravity, viz. string theory, has the following features incorporated in it. (i) The full spacetime is higher-dimensional, with (possibly) compact extra-dimensions; (ii) there is a natural minimal length below which the concept of continuum spacetime needs to be modified by some deeper concept. On the other hand, the existence of a minimal length (zero-point length) in four-dimensional spacetime, with obvious implications as UV regulator, has been often conjectured as a natural aftermath of any correct quantum theory of gravity. We show that one can incorporate the apparently unrelated pieces of information-zero-point length, extra-dimensions, string T-duality-in a consistent framework. This is done in terms of a modified Kaluza-Klein theory that interpolates between (high-energy) string theory and (low-energy) quantum field theory. In this model, the zero-point length in four dimensions is a 'virtual memory' of the length scale of compact extra-dimensions. Such a scale turns out to be determined by T-duality inherited from the underlying fundamental string theory. From a low energy perspective short distance infinities are cutoff by a minimal length which is proportional to the square root of the string slope, i.e., α ' . Thus, we bridge the gap between the string theory domain and the low energy arena of point-particle quantum field theory

Full length SSC R and D dipole magnet test results

International Nuclear Information System (INIS)

Strait, J.; Bleadon, M.; Brown, B.C.

1989-03-01

Four full scale SSC development dipole magnets have been tested for mechanical and quench behavior. Two are of a design similar to previous magnets but contain a number of improvements, including more uniform coil size, higher pre-stress and a redesigned inner-outer coil splice. One exceeds the SSC operating current on the second quench but the other appears to be limited by damaged superconductor to a lower current. The other two magnets are of alternate designs. One trains erratically and fails to reach a plateau and the other reaches plateau after four quenches. 12 refs., 4 figs

Lyso-myristoyl phosphatidylcholine micelles sustain the activity of Dengue non-structural (NS) protein 3 protease domain fused with the full-length NS2B.

Science.gov (United States)

Huang, Qiwei; Li, Qingxin; Joy, Joma; Chen, Angela Shuyi; Ruiz-Carrillo, David; Hill, Jeffrey; Lescar, Julien; Kang, Congbao

2013-12-01

Dengue virus (DENV), a member of the flavivirus genus, affects 50-100 million people in tropical and sub-tropical regions. The DENV protease domain is located at the N-terminus of the NS3 protease and requires for its enzymatic activity a hydrophilic segment of the NS2B that acts as a cofactor. The protease is an important antiviral drug target because it plays a crucial role in virus replication by cleaving the genome-coded polypeptide into mature functional proteins. Currently, there are no drugs to inhibit DENV protease activity. Most structural and functional studies have been conducted using protein constructs containing the NS3 protease domain connected to a soluble segment of the NS2B membrane protein via a nine-residue linker. For in vitro structural and functional studies, it would be useful to produce a natural form of the DENV protease containing the NS3 protease domain and the full-length NS2B protein. Herein, we describe the expression and purification of a natural form of DENV protease (NS2BFL-NS3pro) containing the full-length NS2B protein and the protease domain of NS3 (NS3pro). The protease was expressed and purified in detergent micelles necessary for its folding. Our results show that this purified protein was active in detergent micelles such as lyso-myristoyl phosphatidylcholine (LMPC). These findings should facilitate further structural and functional studies of the protease and will facilitate drug discovery targeting DENV. Copyright © 2013 Elsevier Inc. All rights reserved.

Analysis of ureteral length in adult cadavers

Directory of Open Access Journals (Sweden)

Hugo F. F. Novaes

2013-04-01

Full Text Available Introduction In some occasions, correlations between human structures can help planning surgical intra-abdominal interventions. The previous determination of ureteral length helps pre-operatory planning of surgeries, reduces costs of auxiliary exams, the correct choice of double-J catheter with low morbidity and fewer symptoms, and an adequate adhesion to treatment. Objective To evaluate ureteral length in adult cadavers and to analyze its correlation with anthropometric measures. Materials and Methods: From April 2009 to January 2012 we determined ureteral length of adult cadavers submitted to necropsy and obtained the following measures: height, distance from shoulder to wrist, elbow-wrist, xiphoid appendix-umbilicus, umbilicus-pubis, xiphoid appendix-pubis and between iliac spines. We analyzed the correlations between ureteral length and those anthropometric measures. Results We dissected 115 ureters from 115 adult corpses from April 2009 to January 2012. Median ureteral length didn't vary between sexes or according to height. It was observed no correlation among ureteral length and all considered anthropometric measures in all analyzed subgroups and in general population. There were no significant differences between right and left ureteral measures. Conclusions There is no difference of ureteral length in relation to height or gender (male or female. There is no significant correlation among ureteral length and the considered anthropometric measures.

Divergence of host range and biological properties between natural isolate and full-length infectious cDNA clone of the Beet mild yellowing virus 2ITB.

Science.gov (United States)

Klein, Elodie; Brault, Véronique; Klein, Delphine; Weyens, Guy; Lefèbvre, Marc; Ziegler-Graff, Véronique; Gilmer, David

2014-01-01

Plant infection by poleroviruses is restricted to phloem tissues, preventing any classical leaf rub inoculation with viral RNA or virions. Efficient virus inoculation to plants is achieved by viruliferous aphids that acquire the virus by feeding on infected plants. The use of promoter-driven infectious cDNA is an alternative means to infect plants and allows reverse genetic studies to be performed. Using Beet mild yellowing virus isolate 2ITB (BMYV-2ITB), we produced a full-length infectious cDNA clone of the virus (named BMYV-EK) placed under the control of the T7 RNA polymerase and the Cauliflower mosaic virus 35S promoters. Infectivity of the engineered BMYV-EK virus was assayed in different plant species and compared with that of the original virus. We showed that in vitro- or in planta-derived transcripts were infectious in protoplasts and in whole plants. Importantly, the natural aphid vector Myzus persicae efficiently transmitted the viral progeny produced in infected plants. By comparing agroinoculation and aphid infection in a host range assay, we showed that the engineered BMYV-EK virus displayed a similar host range to BMYV-2ITB, except for Nicotiana benthamiana, which proved to be resistant to systemic infection with BMYV-EK. Finally, both the BMYV-EK P0 and the full-length clone were able to strongly interfere with post-transcriptional gene silencing. © 2013 BSPP AND JOHN WILEY & SONS LTD.

Extreme telomere length dimorphism in the Tasmanian devil and related marsupials suggests parental control of telomere length.

Directory of Open Access Journals (Sweden)

Hannah S Bender

Full Text Available Telomeres, specialised structures that protect chromosome ends, play a critical role in preserving chromosome integrity. Telomere dynamics in the Tasmanian devil (Sarcophilus harrisii are of particular interest in light of the emergence of devil facial tumour disease (DFTD, a transmissible malignancy that causes rapid mortality and threatens the species with extinction. We used fluorescent in situ hybridisation to investigate telomere length in DFTD cells, in healthy Tasmanian devils and in four closely related marsupial species. Here we report that animals in the Order Dasyuromorphia have chromosomes characterised by striking telomere length dimorphism between homologues. Findings in sex chromosomes suggest that telomere length dimorphism may be regulated by events in the parental germlines. Long telomeres on the Y chromosome imply that telomere lengthening occurs during spermatogenesis, whereas telomere diminution occurs during oogenesis. Although found in several somatic cell tissue types, telomere length dimorphism was not found in DFTD cancer cells, which are characterised by uniformly short telomeres. This is, to our knowledge, the first report of naturally occurring telomere length dimorphism in any species and suggests a novel strategy of telomere length control. Comparative studies in five distantly related marsupials and a monotreme indicate that telomere dimorphism evolved at least 50 million years ago.

Pseudo-polyprotein translated from the full-length ORF1 of capillovirus is important for pathogenicity, but a truncated ORF1 protein without variable and CP regions is sufficient for replication.

Science.gov (United States)

Hirata, Hisae; Yamaji, Yasuyuki; Komatsu, Ken; Kagiwada, Satoshi; Oshima, Kenro; Okano, Yukari; Takahashi, Shuichiro; Ugaki, Masashi; Namba, Shigetou

2010-09-01

The first open-reading frame (ORF) of the genus Capillovirus encodes an apparently chimeric polyprotein containing conserved regions for replicase (Rep) and coat protein (CP), while other viruses in the family Flexiviridae have separate ORFs encoding these proteins. To investigate the role of the full-length ORF1 polyprotein of capillovirus, we generated truncation mutants of ORF1 of apple stem grooving virus by inserting a termination codon into the variable region located between the putative Rep- and CP-coding regions. These mutants were capable of systemic infection, although their pathogenicity was attenuated. In vitro translation of ORF1 produced both the full-length polyprotein and the smaller Rep protein. The results of in vivo reporter assays suggested that the mechanism of this early termination is a ribosomal -1 frame-shift occurring downstream from the conserved Rep domains. The mechanism of capillovirus gene expression and the very close evolutionary relationship between the genera Capillovirus and Trichovirus are discussed. Copyright (c) 2010. Published by Elsevier B.V.

The MX/G/1 queue with queue length dependent service times

Directory of Open Access Journals (Sweden)

Bong Dae Choi

2001-01-01

Full Text Available We deal with the MX/G/1 queue where service times depend on the queue length at the service initiation. By using Markov renewal theory, we derive the queue length distribution at departure epochs. We also obtain the transient queue length distribution at time t and its limiting distribution and the virtual waiting time distribution. The numerical results for transient mean queue length and queue length distributions are given.

Full-length characterization of A1/D intersubtype recombinant genomes from a therapy-induced HIV type 1 controller during acute infection and his noncontrolling partner

DEFF Research Database (Denmark)

Fomsgaard, A.; Vinner, L.; Therrien, D.

2008-01-01

To increase the understanding of mechanisms of HIV control we have genetically and immunologically characterized a full-length HIV-1 isolated from an acute infection in a rare case of undetectable viremia. The subject, a 43-year-old Danish white male (DK1), was diagnosed with acute HIV-1 infection...... and phylogenic trees were constructed and diversity and evolutionary distances were calculated. Intracellular IFN-gamma in CD8(+)CD3(+) T-lymphocyte reactions was investigated by intracellular flow cytometry (IC-FACS). Virus isolates from both patients were A1D intersubtype recombinants showing 98% sequence...

Association of murine lupus and thymic full-length endogenous retroviral expression maps to a bone marrow stem cell

International Nuclear Information System (INIS)

Krieg, A.M.; Gourley, M.F.; Steinberg, A.D.

1991-01-01

Recent studies of thymic gene expression in murine lupus have demonstrated 8.4-kb (full-length size) modified polytropic (Mpmv) endogenous retroviral RNA. In contrast, normal control mouse strains do not produce detectable amounts of such RNA in their thymuses. Prior studies have attributed a defect in experimental tolerance in murine lupus to a bone marrow stem cell rather than to the thymic epithelium; in contrast, infectious retroviral expression has been associated with the thymic epithelium, rather than with the bone marrow stem cell. The present study was designed to determine whether the abnormal Mpmv expression associated with murine lupus mapped to thymic epithelium or to a marrow precursor. Lethally irradiated control and lupus-prone mice were reconstituted with T cell depleted bone marrow; one month later their thymuses were studied for endogenous retroviral RNA and protein expression. Recipients of bone marrow from nonautoimmune donors expressed neither 8.4-kb Mpmv RNA nor surface MCF gp70 in their thymuses. In contrast, recipients of bone marrow from autoimmune NZB or BXSB donors expressed thymic 8.4-kb Mpmv RNA and mink cell focus-forming gp70. These studies demonstrate that lupus-associated 8.4-kb Mpmv endogenous retroviral expression is determined by bone marrow stem cells

Comparison of Newly Assembled Full Length HIV-1 Integrase With Prototype Foamy Virus Integrase: Structure-Function Prospective.

Science.gov (United States)

Dayer, Mohammad Reza

2016-05-01

Drug design against human immunodeficiency virus type 1 (HIV-1) integrase through its mechanistic study is of great interest in the area in biological research. The main obstacle in this area is the absence of the full-length crystal structure for HIV-1 integrase to be used as a model. A complete structure, similar to HIV-1 of a prototype foamy virus integrase in complex with DNA, including all conservative residues, is available and has been extensively used in recent investigations. The aim of this study was to determine whether the above model is precisely representative of HIV-1 integrase. This would critically determine the success of any designed drug using the model in deactivation of integrase and AIDS treatment. Primarily, a new structure for HIV-1 was constructed, using a crystal structure of prototype foamy virus as the starting structure. The constructed structure of HIV-1 integrase was simultaneously simulated with a prototype foamy virus integrase on a separate occasion. Our results indicate that the HIV-1 system behaves differently from the prototype foamy virus in terms of folding, hydration, hydrophobicity of binding site and stability. Based on our findings, we can conclude that HIV-1 integrase is vastly different from the prototype foamy virus integrase and does not resemble it, and the modeling output of the prototype foamy virus simulations could not be simply generalized to HIV-1 integrase. Therefore, our HIV-1 model seems to be more representative and more useful for future research.

The relationship of protein conservation and sequence length

Directory of Open Access Journals (Sweden)

Panchenko Anna R

2002-11-01

Full Text Available Abstract Background In general, the length of a protein sequence is determined by its function and the wide variance in the lengths of an organism's proteins reflects the diversity of specific functional roles for these proteins. However, additional evolutionary forces that affect the length of a protein may be revealed by studying the length distributions of proteins evolving under weaker functional constraints. Results We performed sequence comparisons to distinguish highly conserved and poorly conserved proteins from the bacterium Escherichia coli, the archaeon Archaeoglobus fulgidus, and the eukaryotes Saccharomyces cerevisiae, Drosophila melanogaster, and Homo sapiens. For all organisms studied, the conserved and nonconserved proteins have strikingly different length distributions. The conserved proteins are, on average, longer than the poorly conserved ones, and the length distributions for the poorly conserved proteins have a relatively narrow peak, in contrast to the conserved proteins whose lengths spread over a wider range of values. For the two prokaryotes studied, the poorly conserved proteins approximate the minimal length distribution expected for a diverse range of structural folds. Conclusions There is a relationship between protein conservation and sequence length. For all the organisms studied, there seems to be a significant evolutionary trend favoring shorter proteins in the absence of other, more specific functional constraints.

Quench propagation study for the BNL-built, full-length, 50mm aperture SSC model dipoles

International Nuclear Information System (INIS)

Muratore, J.; Anerella, M.; Cottingham, G.

1993-01-01

As part of the program to build and test SSC 50mm aperture prototype dipole magnets, a series of seven full-length dipoles were built and tested at BNL. Important part of the testing program was the study of quench propagation velocity and hot spot temperature over a range of experimental conditions in order to characterize the safety of the conductor during quenches experienced under different circumstances. Such studies are important tools in design, implementation, and verification of quench protection strategies in superconducting accelerator magnets. This investigation was facilitated by artificially inducing quenches under controlled experimental conditions with spot heaters placed at carefully chosen locations on the magnet coils. Such studies were done as part of the 15m-long magnet test program and were performed on five of the magnets in the series. All were equipped with spot heaters on an inner coil, and two of these also had spot heaters on an outer coil. Therefore, in addition to the studies in the inner coils, it was also possible to study quench propagation in the outer coils, where slower quench velocities and higher conductor temperatures are expected, in comparison to that in the inner coils. In spontaneous quenches, where there may be no voltage taps, it is not possible to measure the conductor hot spot temperature. It is straightforward to measure the number of MIITs generated, since only the magnet current and voltage need be measured. The concept of MIITs then becomes a valuable diagnostic tool which can characterize the temperature behavior of a conductor during quench and can be used to determine limits for safe operation of the coil. With spot heaters placed at known locations and closely bracketed by voltage taps, hot spot temperature can be measured. Research such as is described in this paper is therefore important in order to determine the validity of the MIITs approach and to establish a correlation between temperature and MIITs

The Length-Weight, Length-Length Relationship and Condition Factor of Angora Loach, Oxynoemacheilus angorae (Steindachner, 1897 Inhabiting Kılıçözü Stream in Kızılırmak River Basin (Central Anatolia-Turkey

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Okan Yazıcıoğlu

2016-12-01

Full Text Available In this study, length-weight relationship (LWR, length- length relationship (LLR and condition factor (K of Angora loach, Oxynoemacheilus angorae were determined. A total of 103 specimens were sampled from Kılıçözü Stream in 2014. The length and weight of specimens were ranged 3.5-9.8 cm and 0.38-6.58 g, respectively. Length-weight relationships for female, male and all samples were found as W= 0.01056.TL2.896 (r²= 0.923, W= 0.00963.TL2.940 (r²= 0.978 and W= 0.00987.TL2.929 (r²= 0.963, respectively. LWRs indicated an isometric growth in female, male and all samples. The values of Fulton’s condition factor (K ranged from 0.699 to 1.246 for females and from 0.654 to 1.072 for males. All length-length relationships were statistically significant.

Structure and function of the first full-length murein peptide ligase (Mpl) cell wall recycling protein.

Science.gov (United States)

Das, Debanu; Hervé, Mireille; Feuerhelm, Julie; Farr, Carol L; Chiu, Hsiu-Ju; Elsliger, Marc-André; Knuth, Mark W; Klock, Heath E; Miller, Mitchell D; Godzik, Adam; Lesley, Scott A; Deacon, Ashley M; Mengin-Lecreulx, Dominique; Wilson, Ian A

2011-03-18

Bacterial cell walls contain peptidoglycan, an essential polymer made by enzymes in the Mur pathway. These proteins are specific to bacteria, which make them targets for drug discovery. MurC, MurD, MurE and MurF catalyze the synthesis of the peptidoglycan precursor UDP-N-acetylmuramoyl-L-alanyl-γ-D-glutamyl-meso-diaminopimelyl-D-alanyl-D-alanine by the sequential addition of amino acids onto UDP-N-acetylmuramic acid (UDP-MurNAc). MurC-F enzymes have been extensively studied by biochemistry and X-ray crystallography. In gram-negative bacteria, ∼30-60% of the bacterial cell wall is recycled during each generation. Part of this recycling process involves the murein peptide ligase (Mpl), which attaches the breakdown product, the tripeptide L-alanyl-γ-D-glutamyl-meso-diaminopimelate, to UDP-MurNAc. We present the crystal structure at 1.65 Å resolution of a full-length Mpl from the permafrost bacterium Psychrobacter arcticus 273-4 (PaMpl). Although the Mpl structure has similarities to Mur enzymes, it has unique sequence and structure features that are likely related to its role in cell wall recycling, a function that differentiates it from the MurC-F enzymes. We have analyzed the sequence-structure relationships that are unique to Mpl proteins and compared them to MurC-F ligases. We have also characterized the biochemical properties of this enzyme (optimal temperature, pH and magnesium binding profiles and kinetic parameters). Although the structure does not contain any bound substrates, we have identified ∼30 residues that are likely to be important for recognition of the tripeptide and UDP-MurNAc substrates, as well as features that are unique to Psychrobacter Mpl proteins. These results provide the basis for future mutational studies for more extensive function characterization of the Mpl sequence-structure relationships.

Transgenic Parasites Stably Expressing Full-Length Plasmodium falciparum Circumsporozoite Protein as a Model for Vaccine Down-Selection in Mice Using Sterile Protection as an Endpoint

Science.gov (United States)

Porter, Michael D.; Nicki, Jennifer; Pool, Christopher D.; DeBot, Margot; Illam, Ratish M.; Brando, Clara; Bozick, Brooke; De La Vega, Patricia; Angra, Divya; Spaccapelo, Roberta; Crisanti, Andrea; Murphy, Jittawadee R.; Bennett, Jason W.; Schwenk, Robert J.; Ockenhouse, Christian F.

2013-01-01

Circumsporozoite protein (CSP) of Plasmodium falciparum is a protective human malaria vaccine candidate. There is an urgent need for models that can rapidly down-select novel CSP-based vaccine candidates. In the present study, the mouse-mosquito transmission cycle of a transgenic Plasmodium berghei malaria parasite stably expressing a functional full-length P. falciparum CSP was optimized to consistently produce infective sporozoites for protection studies. A minimal sporozoite challenge dose was established, and protection was defined as the absence of blood-stage parasites 14 days after intravenous challenge. The specificity of protection was confirmed by vaccinating mice with multiple CSP constructs of differing lengths and compositions. Constructs that induced high NANP repeat-specific antibody titers in enzyme-linked immunosorbent assays were protective, and the degree of protection was dependent on the antigen dose. There was a positive correlation between antibody avidity and protection. The antibodies in the protected mice recognized the native CSP on the parasites and showed sporozoite invasion inhibitory activity. Passive transfer of anti-CSP antibodies into naive mice also induced protection. Thus, we have demonstrated the utility of a mouse efficacy model to down-select human CSP-based vaccine formulations. PMID:23536694

Potts ferromagnet correlation length in hypercubic lattices: Renormalization - group approach

International Nuclear Information System (INIS)

Curado, E.M.F.; Hauser, P.R.

1984-01-01

Through a real space renormalization group approach, the q-state Potts ferromagnet correlation length on hierarchical lattices is calculated. These hierarchical lattices are build in order to simulate hypercubic lattices. The high-and-low temperature correlation length asymptotic behaviours tend (in the Ising case) to the Bravais lattice correlation length ones when the size of the hierarchical lattice cells tends to infinity. It is conjectured that the asymptotic behaviours several values of q and d (dimensionality) so obtained are correct. Numerical results are obtained for the full temperature range of the correlation length. (Author) [pt

Telomere Length – a New Biomarker in Medicine

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Agnieszka Kozłowska

2015-12-01

Full Text Available A number of xenobiotics in the environment and workplace influences on our health and life. Biomarkers are tools for measuring such exposures and their effects in the organism. Nowadays, telomere length, epigenetic changes, mutations and changes in gene expression pattern have become new molecular biomarkers. Telomeres play the role of molecular clock, which influences on expectancy of cell life and thus aging, the formation of damages, development diseases and carcinogenesis. The telomere length depends on mechanisms of replication and the activity of telomerase. Telomere length is currently used as a biomarker of susceptibility and/or exposure. This paper describes the role of telomere length as a biomarker of aging cells, oxidative stress, a marker of many diseases including cancer, and as a marker of environmental and occupational exposure.

The X-ray Crystal Structure of Full-Length Human Plasminogen

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Ruby H.P. Law

2012-03-01

Full Text Available Plasminogen is the proenzyme precursor of the primary fibrinolytic protease plasmin. Circulating plasminogen, which comprises a Pan-apple (PAp domain, five kringle domains (KR1-5, and a serine protease (SP domain, adopts a closed, activation-resistant conformation. The kringle domains mediate interactions with fibrin clots and cell-surface receptors. These interactions trigger plasminogen to adopt an open form that can be cleaved and converted to plasmin by tissue-type and urokinase-type plasminogen activators. Here, the structure of closed plasminogen reveals that the PAp and SP domains, together with chloride ions, maintain the closed conformation through interactions with the kringle array. Differences in glycosylation alter the position of KR3, although in all structures the loop cleaved by plasminogen activators is inaccessible. The ligand-binding site of KR1 is exposed and likely governs proenzyme recruitment to targets. Furthermore, analysis of our structure suggests that KR5 peeling away from the PAp domain may initiate plasminogen conformational change.

Full scale demonstration of air-purifying pavement

NARCIS (Netherlands)

Ballari, M.; Brouwers, H.J.H.

2013-01-01

Experiments concerning a full-scale demonstration of air purifying pavement in Hengelo, The Netherlands, are reported. The full width of the street was provided with concrete pavement containing TiO2 over a length of 150 m ("DeNOx street"). Another part of the street, about 100 m, was paved with

Full Length R esearch A rticle

African Journals Online (AJOL)

Germ tube tests were performed for identification of the isolates. Susceptibility ... agents for the treatment of genitourinary tract infections caused by Candida species. Keywords: ..... contraceptives, drug abuse or even due to sexual promiscuity.

Blue light-excited LOV1 and LOV2 domains cooperatively regulate the kinase activity of full-length phototropin2 from Arabidopsis.

Science.gov (United States)

Oide, Mao; Okajima, Koji; Nakagami, Hirofumi; Kato, Takayuki; Sekiguchi, Yuki; Oroguchi, Tomotaka; Hikima, Takaaki; Yamamoto, Masaki; Nakasako, Masayoshi

2018-01-19

Phototropin2 (phot2) is a blue-light (BL) receptor that regulates BL-dependent activities for efficient photosynthesis in plants. phot2 comprises two BL-receiving light-oxygen-voltage-sensing domains (LOV1 and LOV2) and a kinase domain. BL-excited LOV2 is thought to be primarily responsible for the BL-dependent activation of the kinase. However, the molecular mechanisms by which small BL-induced conformational changes in the LOV2 domain are transmitted to the kinase remain unclear. Here, we used full-length wild-type and mutant phot2 proteins from Arabidopsis to study their molecular properties in the dark and under BL irradiation. Phosphorylation assays and absorption measurements indicated that the LOV1 domain assists the thermal relaxation of BL-excited LOV2 and vice versa. Using small-angle X-ray scattering and electron microscopy, we observed that phot2 forms a dimer and has a rod shape with a maximum length of 188 Å and a radius of gyration of 44 Å. Under BL, phot2 displayed large conformational changes that bent the rod shape. By superimposing the crystal structures of the LOV1 dimer, LOV2, and a homology model of the kinase to the observed changes, we inferred that the BL-dependent change consisted of positional shifts of both LOV2 and the kinase relative to LOV1. Furthermore, phot2 mutants lacking the photocycle in LOV1 or LOV2 still exhibited conformational changes under BL, suggesting that LOV1 and LOV2 cooperatively contribute to the conformational changes that activate the kinase. These results suggest that BL-activated LOV1 contributes to the kinase activity of phot2. We discuss the possible intramolecular interactions and signaling mechanisms in phot2. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

Tube Length and Water Flow

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Ben Ruktantichoke

2011-06-01

Full Text Available In this study water flowed through a straight horizontal plastic tube placed at the bottom of a large tank of water. The effect of changing the length of tubing on the velocity of flow was investigated. It was found that the Hagen-Poiseuille Equation is valid when the effect of water entering the tube is accounted for.

ASC-J9 Suppresses Castration-Resistant Prostate Cancer Growth through Degradation of Full-length and Splice Variant Androgen Receptors

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Shinichi Yamashita

2012-01-01

Full Text Available Early studies suggested androgen receptor (AR splice variants might contribute to the progression of prostate cancer (PCa into castration resistance. However, the therapeutic strategy to target these AR splice variants still remains unresolved. Through tissue survey of tumors from the same patients before and after castration resistance, we found that the expression of AR3, a major AR splice variant that lacks the AR ligand-binding domain, was substantially increased after castration resistance development. The currently used antiandrogen, Casodex, showed little growth suppression in CWR22Rv1 cells. Importantly, we found that AR degradation enhancer ASC-J9 could degrade both full-length (fAR and AR3 in CWR22Rv1 cells as well as in C4-2 and C81 cells with addition of AR3. The consequences of such degradation of both fAR and AR3 might then result in the inhibition of AR transcriptional activity and cell growth in vitro. More importantly, suppression of AR3 specifically by short-hairpin AR3 or degradation of AR3 by ASC-J9 resulted in suppression of AR transcriptional activity and cell growth in CWR22Rv1-fARKD (fAR knockdown cells in which DHT failed to induce, suggesting the importance of targeting AR3. Finally, we demonstrated the in vivo therapeutic effects of ASC-J9 by showing the inhibition of PCa growth using the xenografted model of CWR22Rv1 cells orthotopically implanted into castrated nude mice with undetectable serum testosterone. These results suggested that targeting both fAR- and AR3-mediated PCa growth by ASC-J9 may represent the novel therapeutic approach to suppress castration-resistant PCa. Successful clinical trials targeting both fAR and AR3 may help us to battle castration-resistant PCa in the future.

Length of a Hanging Cable

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Eric Costello

2011-01-01

Full Text Available The shape of a cable hanging under its own weight and uniform horizontal tension between two power poles is a catenary. The catenary is a curve which has an equation defined by a hyperbolic cosine function and a scaling factor. The scaling factor for power cables hanging under their own weight is equal to the horizontal tension on the cable divided by the weight of the cable. Both of these values are unknown for this problem. Newton's method was used to approximate the scaling factor and the arc length function to determine the length of the cable. A script was written using the Python programming language in order to quickly perform several iterations of Newton's method to get a good approximation for the scaling factor.

Progress in Long Scale Length Laser-Plasma Interactions

International Nuclear Information System (INIS)

Glenzer, S H; Arnold, P; Bardsley, G; Berger, R L; Bonanno, G; Borger, T; Bower, D E; Bowers, M; Bryant, R; Buckman, S.; Burkhart, S C; Campbell, K; Chrisp, M P; Cohen, B I; Constantin, G; Cooper, F; Cox, J; Dewald, E; Divol, L; Dixit, S; Duncan, J; Eder, D; Edwards, J; Erbert, G; Felker, B; Fornes, J; Frieders, G; Froula, D H; Gardner, S D; Gates, C; Gonzalez, M; Grace, S; Gregori, G; Greenwood, A; Griffith, R; Hall, T; Hammel, B A; Haynam, C; Heestand, G; Henesian, M; Hermes, G; Hinkel, D; Holder, J; Holdner, F; Holtmeier, G; Hsing, W; Huber, S; James, T; Johnson, S; Jones, O S; Kalantar, D; Kamperschroer, J H; Kauffman, R; Kelleher, T; Knight, J; Kirkwood, R K; Kruer, W L; Labiak, W; Landen, O L; Langdon, A B; Langer, S; Latray, D; Lee, A; Lee, F D; Lund, D; MacGowan, B; Marshall, S; McBride, J; McCarville, T; McGrew, L; Mackinnon, A J; Mahavandi, S; Manes, K; Marshall, C; Mertens, E; Meezan, N; Miller, G; Montelongo, S; Moody, J D; Moses, E; Munro, D; Murray, J; Neumann, J; Newton, M; Ng, E; Niemann, C; Nikitin, A; Opsahl, P; Padilla, E; Parham, T; Parrish, G; Petty, C; Polk, M; Powell, C; Reinbachs, I; Rekow, V; Rinnert, R; Riordan, B; Rhodes, M.

2003-01-01

The first experiments on the National Ignition Facility (NIF) have employed the first four beams to measure propagation and laser backscattering losses in large ignition-size plasmas. Gas-filled targets between 2 mm and 7 mm length have been heated from one side by overlapping the focal spots of the four beams from one quad operated at 351 nm (3ω) with a total intensity of 2 x 10 15 W cm -2 . The targets were filled with 1 atm of CO 2 producing of up to 7 mm long homogeneously heated plasmas with densities of n e = 6 x 10 20 cm -3 and temperatures of T e = 2 keV. The high energy in a NIF quad of beams of 16kJ, illuminating the target from one direction, creates unique conditions for the study of laser plasma interactions at scale lengths not previously accessible. The propagation through the large-scale plasma was measured with a gated x-ray imager that was filtered for 3.5 keV x rays. These data indicate that the beams interact with the full length of this ignition-scale plasma during the last ∼1 ns of the experiment. During that time, the full aperture measurements of the stimulated Brillouin scattering and stimulated Raman scattering show scattering into the four focusing lenses of 6% for the smallest length (∼2 mm). increasing to 12% for ∼7 mm. These results demonstrate the NIF experimental capabilities and further provide a benchmark for three-dimensional modeling of the laser-plasma interactions at ignition-size scale lengths

CEPF Western Ghats Special Series: Length-weight and length-length relationship of three species of snakehead fish, Channa diplogramma, C. marulius and C. striata from the riverine reaches of Lake Vembanad, Kerala, India.

Directory of Open Access Journals (Sweden)

A. Ali

2013-09-01

Full Text Available The length-weight relationship (LWR and length-length relationships (LLR of three snakehead fishes, Channa diplogramma, C. marulius and C. striata, exploited by small-scale fishers in the riverine reaches of Lake Vembanad, Kerala were studied using the allometric growth equation Y = aXb. Our analysis shows that the LWR of C. diplogramma and C. marulius is nonisometric with exponents much smaller than the cubic value (b = 3, while that of C. striata is isometric. Channa marulius showed a definite change in LWR with size, with smaller fish growing with positive allometric exponents (b greater than 3 and larger individuals having negative allometric relationship (b less than 3, indicating a possible age-related change in growth pattern. In the case of LLR, all three snakehead species showed non-isometric growth patterns. The caudal fin did not grow substantially with increasing fish length.

discouraged by queue length

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P. R. Parthasarathy

2001-01-01

Full Text Available The transient solution is obtained analytically using continued fractions for a state-dependent birth-death queue in which potential customers are discouraged by the queue length. This queueing system is then compared with the well-known infinite server queueing system which has the same steady state solution as the model under consideration, whereas their transient solutions are different. A natural measure of speed of convergence of the mean number in the system to its stationarity is also computed.

The full-length microRNA cluster in the intron of large latency transcript is associated with the virulence of pseudorabies virus.

Science.gov (United States)

Wang, Xin; Zhang, Mei-Mei; Yan, Kai; Tang, Qi; Wu, Yi-Quan; He, Wen-Bo; Chen, Huan-Chun; Liu, Zheng-Fei

2018-07-01

Pseudorabies virus (PRV), the etiological pathogen of Aujeszky's disease, belongs to the Alphaherpesvirus subfamily. Large latency transcript (LLT), the most abundant PRV transcript, harbors a ~ 4.6 kb microRNA (miRNA) cluster-encoding intron. To investigate the function of the LLT miRNA cluster during the life cycle of PRV, we generated a miRNA cluster mutation virus (PRV-∆miR cluster) and revertant virus. Analysis of the growth kinetics of PRV-ΔmiR cluster-infected cells revealed significantly smaller plaques and lower titers than the wild-type and revertant viruses. The mutation virus exhibited increased IE180 and decreased EP0 expression. The clinical symptoms observed in mice infected with PRV-ΔmiR cluster revealed that the miRNA cluster is involved in the pathogenesis of PRV. Physical parameters, virus shedding assays, and the SN 50 titers revealed that the miRNA cluster enhances PRV virulence in pigs. Collectively, our findings suggest that the full-length miRNA cluster is involved in PRV replication and virulence. Copyright © 2018 Elsevier Inc. All rights reserved.

A New Concept of Full Employment

NARCIS (Netherlands)

Delsen, L.W.M.

1997-01-01

The target of full employment depends upon the goals regarding labour force participation rates, the length of the work week and frictional unemployment. Although nearly all social groups agree that stronger economic growth would contribute most to solving the unemployment problem, the prospects for

Minimal Length Scale Scenarios for Quantum Gravity

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Sabine Hossenfelder

2013-01-01

Full Text Available We review the question of whether the fundamental laws of nature limit our ability to probe arbitrarily short distances. First, we examine what insights can be gained from thought experiments for probes of shortest distances, and summarize what can be learned from different approaches to a theory of quantum gravity. Then we discuss some models that have been developed to implement a minimal length scale in quantum mechanics and quantum field theory. These models have entered the literature as the generalized uncertainty principle or the modified dispersion relation, and have allowed the study of the effects of a minimal length scale in quantum mechanics, quantum electrodynamics, thermodynamics, black-hole physics and cosmology. Finally, we touch upon the question of ways to circumvent the manifestation of a minimal length scale in short-distance physics.

The Length of Maternity Leave and Family Health

OpenAIRE

Beuchert, Louise Voldby; Humlum, Maria Knoth; Vejlin, Rune Majlund

2014-01-01

We study the relationship between the length of maternity leave and the physical and psychological health of the family. Using a reform of the parental leave scheme in Denmark that increased the number of weeks of leave with full benefit compensation,we estimate the effect of the length of maternity leave on a range of health indicators including the number of hospital admissions for both mother and child and the probability of the mother receiving antidepressants. The reform led to an increa...

Amplification and pyrosequencing of near-full-length hepatitis C virus for typing and monitoring antiviral resistant strains.

Science.gov (United States)

Trémeaux, P; Caporossi, A; Ramière, C; Santoni, E; Tarbouriech, N; Thélu, M-A; Fusillier, K; Geneletti, L; François, O; Leroy, V; Burmeister, W P; André, P; Morand, P; Larrat, S

2016-05-01

Directly acting antiviral drugs have contributed considerable progress to hepatitis C virus (HCV) treatment, but they show variable activity depending on virus genotypes and subtypes. Therefore, accurate genotyping including recombinant form detection is still of major importance, as is the detection of resistance-associated mutations in case of therapeutic failure. To meet these goals, an approach to amplify the HCV near-complete genome with a single long-range PCR and sequence it with Roche GS Junior was developed. After optimization, the overall amplification success rate was 73% for usual genotypes (i.e. HCV 1a, 1b, 3a and 4a, 16/22) and 45% for recombinant forms RF_2k/1b (5/11). After pyrosequencing and subsequent de novo assembly, a near-full-length genomic consensus sequence was obtained for 19 of 21 samples. The genotype and subtype were confirmed by phylogenetic analysis for every sample, including the suspected recombinant forms. Resistance-associated mutations were detected in seven of 13 samples at baseline, in the NS3 (n = 3) or NS5A (n = 4) region. Of these samples, the treatment of one patient included daclatasvir, and that patient experienced a relapse. Virus sequences from pre- and posttreatment samples of four patients who experienced relapse after sofosbuvir-based therapy were compared: the selected variants seem too far from the NS5B catalytic site to be held responsible. Although tested on a limited set of samples and with technical improvements still necessary, this assay has proven to be successful for both genotyping and resistance-associated variant detection on several HCV types. Copyright © 2016 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Use of Full-Length Recombinant Calflagin and Its C Fragment for Improvement of Diagnosis of Trypanosoma cruzi Infection†

Science.gov (United States)

Marcipar, Iván S.; Roodveldt, Cintia; Corradi, Gerardo; Cabeza, María L.; Brito, Maria Edileuza F.; Winter, Lucile M. Floeter; Marcipar, Alberto J.; Silber, Ariel M.

2005-01-01

Serological diagnosis of Trypanosoma cruzi infection is hampered by issues related to test specificity due to the cross-reactivity of most antigens with proteins of related parasites such as Leishmania spp. The recombinant calflagins are considered relevant antigens for the diagnosis of infection by Trypanosoma cruzi. In the present work, we describe two genes coding for putative calflagins in Leishmania major with the N-terminal moieties presenting high similarity with T. cruzi genes. This fact raised questions about their role in some cross-recognition of this antigen by sera from Leishmania spp.-infected individuals. The complete T. cruzi calflagin and two fragments of the protein, consisting of 146 amino acids of the N-terminal and 65 amino acids of the C-terminal regions, were expressed and evaluated against a panel of sera, which included well-characterized samples from T. cruzi, and Leishmania-infected patients. We were able to show that sera from Leishmania (Viannia) braziliensis-infected individuals recognized the recombinant full-length calflagin. Both the N-terminal and the complete protein presented the same high sensitivity (98.5% of sera from T. cruzi-infected patients was detected) but different specificities (94% and 98%, respectively, when evaluated against sera from people not infected by T. cruzi, including 15 sera from people infected with L. braziliensis). The C-terminal fragment presented low sensitivity (70%) but 100% specificity. We propose the use of these antigens in two sequential assays to optimize the serological diagnosis of T. cruzi infection in humans in geographic areas where Leishmania spp. infection is coendemic. PMID:16272476

A simple strategy for the purification of native recombinant full-length human RPL10 protein from inclusion bodies.

Science.gov (United States)

Pereira, Larissa M; Silva, Luana R; Alves, Joseane F; Marin, Nélida; Silva, Flavio Sousa; Morganti, Ligia; Silva, Ismael D C G; Affonso, Regina

2014-09-01

The L10 ribosomal protein (RPL10) plays a role in the binding of the 60 S and 40 S ribosomal subunits and in mRNA translation. The evidence indicates that RPL10 also has multiple extra-ribosomal functions, including tumor suppression. Recently, the presence of RPL10 in prostate and ovarian cancers was evaluated, and it was demonstrated to be associated with autistic disorders and premature ovarian failure. In the present work, we successfully cloned and expressed full-length human RPL10 (hRPL10) protein and isolated inclusion bodies containing this protein that had formed under mild growth conditions. The culture produced 376mg of hRPL10 protein per liter of induced bacterial culture, of which 102.4mg was present in the soluble fraction, and 25.6mg was recovered at approximately 94% purity. These results were obtained using a two-step process of non-denaturing protein extraction from pelleted inclusion bodies. We studied the characteristics of this protein using circular dichroism spectroscopy and by monitoring the changes induced by the presence or absence of zinc ions using fluorescence spectrometry. The results demonstrated that the protein obtained using these non-conventional methods retained its secondary and tertiary structure. The conformational changes induced by the incorporation of zinc suggested that this protein could interact with Jun or the SH3 domain of c-yes. The results suggested that the strategy used to obtain hRPL10 is simple and could be applied to obtaining other proteins that are susceptible to degradation. Copyright © 2014 Elsevier Inc. All rights reserved.

Short fetal leukocyte telomere length and preterm prelabor rupture of the membranes.

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Ramkumar Menon

Full Text Available BACKGROUND: Rupture of the fetal membranes is a common harbinger of imminent labor and delivery. Telomere shortening is a surrogate for oxidative stress (OS and senescence. Fetal leukocyte and placental membrane DNA telomere lengths were evaluated to determine their association with preterm prelabor rupture of the membranes (pPROM or spontaneous preterm births with intact membranes (PTB, compared to term birth. METHODS: Telomere lengths were quantified in cord blood leukocytes (n = 133 from three major groups: 1 pPROM (n = 28, 2 PTB (n = 69 and 3 uncomplicated full term births (controls, n = 35, using real-time quantitative PCR. Placental membrane specimens (n = 18 were used to correlate fetal leukocyte and placental telomere lengths. Telomere length differences among the groups were analyzed by ANOVA. Pearson correlation coefficients determined relationships between leukocyte and placental membrane telomere lengths. RESULTS: In pregnancies with intact membranes, fetal leukocyte telomere length was inversely proportional to gestational age. The mean telomere length decreased as gestation progressed, with the shortest at term. pPROM had telomere lengths (9962 ± 3124 bp that were significantly shorter than gestational age-matched PTB (11546 ± 4348 bp, p = 0.04, but comparable to term births (9011 ± 2497 bp, p = 0.31. Secondary analyses revealed no effects of race (African American vs. Caucasian or intraamniotic infection on telomere length. A strong Pearson's correlation was noted between fetal leukocyte and placental membrane telomere lengths (ρ = 0.77; p<0.01. CONCLUSIONS: Fetal leukocyte telomere length is reduced in pPROM compared to PTB but is similar to term births. pPROM represents a placental membrane disease likely mediated by OS-induced senescence.

Minimal Length Effects on Tunnelling from Spherically Symmetric Black Holes

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Benrong Mu

2015-01-01

Full Text Available We investigate effects of the minimal length on quantum tunnelling from spherically symmetric black holes using the Hamilton-Jacobi method incorporating the minimal length. We first derive the deformed Hamilton-Jacobi equations for scalars and fermions, both of which have the same expressions. The minimal length correction to the Hawking temperature is found to depend on the black hole’s mass and the mass and angular momentum of emitted particles. Finally, we calculate a Schwarzschild black hole's luminosity and find the black hole evaporates to zero mass in infinite time.

Utility of telomere length measurements for age determination of humpback whales

Directory of Open Access Journals (Sweden)

Morten Tange Olsen

2014-12-01

Full Text Available This study examines the applicability of telomere length measurements by quantitative PCR as a tool for minimally invasive age determination of free-ranging cetaceans. We analysed telomere length in skin samples from 28 North Atlantic humpback whales (Megaptera novaeangliae, ranging from 0 to 26 years of age. The results suggested a significant correlation between telomere length and age in humpback whales. However, telomere length was highly variable among individuals of similar age, suggesting that telomere length measured by quantitative PCR is an imprecise determinant of age in humpback whales. The observed variation in individual telomere length was found to be a function of both experimental and biological variability, with the latter perhaps reflecting patterns of inheritance, resource allocation trade-offs, and stochasticity of the marine environment.

Short Rayleigh length free electron lasers

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W. B. Colson

2006-03-01

Full Text Available Conventional free electron laser (FEL oscillators minimize the optical mode volume around the electron beam in the undulator by making the resonator Rayleigh length about one third to one half of the undulator length. This maximizes gain and beam-mode coupling. In compact configurations of high-power infrared FELs or moderate power UV FELs, the resulting optical intensity can damage the resonator mirrors. To increase the spot size and thereby reduce the optical intensity at the mirrors below the damage threshold, a shorter Rayleigh length can be used, but the FEL interaction is significantly altered. We model this interaction using a coordinate system that expands with the rapidly diffracting optical mode from the ends of the undulator to the mirrors. Simulations show that the interaction of the strongly focused optical mode with a narrow electron beam inside the undulator distorts the optical wave front so it is no longer in the fundamental Gaussian mode. The simulations are used to study how mode distortion affects the single-pass gain in weak fields, and the steady-state extraction in strong fields.

RiceFOX: a database of Arabidopsis mutant lines overexpressing rice full-length cDNA that contains a wide range of trait information to facilitate analysis of gene function.

Science.gov (United States)

Sakurai, Tetsuya; Kondou, Youichi; Akiyama, Kenji; Kurotani, Atsushi; Higuchi, Mieko; Ichikawa, Takanari; Kuroda, Hirofumi; Kusano, Miyako; Mori, Masaki; Saitou, Tsutomu; Sakakibara, Hitoshi; Sugano, Shoji; Suzuki, Makoto; Takahashi, Hideki; Takahashi, Shinya; Takatsuji, Hiroshi; Yokotani, Naoki; Yoshizumi, Takeshi; Saito, Kazuki; Shinozaki, Kazuo; Oda, Kenji; Hirochika, Hirohiko; Matsui, Minami

2011-02-01

Identification of gene function is important not only for basic research but also for applied science, especially with regard to improvements in crop production. For rapid and efficient elucidation of useful traits, we developed a system named FOX hunting (Full-length cDNA Over-eXpressor gene hunting) using full-length cDNAs (fl-cDNAs). A heterologous expression approach provides a solution for the high-throughput characterization of gene functions in agricultural plant species. Since fl-cDNAs contain all the information of functional mRNAs and proteins, we introduced rice fl-cDNAs into Arabidopsis plants for systematic gain-of-function mutation. We generated >30,000 independent Arabidopsis transgenic lines expressing rice fl-cDNAs (rice FOX Arabidopsis mutant lines). These rice FOX Arabidopsis lines were screened systematically for various criteria such as morphology, photosynthesis, UV resistance, element composition, plant hormone profile, metabolite profile/fingerprinting, bacterial resistance, and heat and salt tolerance. The information obtained from these screenings was compiled into a database named 'RiceFOX'. This database contains around 18,000 records of rice FOX Arabidopsis lines and allows users to search against all the observed results, ranging from morphological to invisible traits. The number of searchable items is approximately 100; moreover, the rice FOX Arabidopsis lines can be searched by rice and Arabidopsis gene/protein identifiers, sequence similarity to the introduced rice fl-cDNA and traits. The RiceFOX database is available at http://ricefox.psc.riken.jp/.

Intersubunit distances in full-length, dimeric, bacterial phytochrome Agp1, as measured by pulsed electron-electron double resonance (PELDOR) between different spin label positions, remain unchanged upon photoconversion.

Science.gov (United States)

Kacprzak, Sylwia; Njimona, Ibrahim; Renz, Anja; Feng, Juan; Reijerse, Edward; Lubitz, Wolfgang; Krauss, Norbert; Scheerer, Patrick; Nagano, Soshichiro; Lamparter, Tilman; Weber, Stefan

2017-05-05

Bacterial phytochromes are dimeric light-regulated histidine kinases that convert red light into signaling events. Light absorption by the N-terminal photosensory core module (PCM) causes the proteins to switch between two spectrally distinct forms, Pr and Pfr, thus resulting in a conformational change that modulates the C-terminal histidine kinase region. To provide further insights into structural details of photoactivation, we investigated the full-length Agp1 bacteriophytochrome from the soil bacterium Agrobacterium fabrum using a combined spectroscopic and modeling approach. We generated seven mutants suitable for spin labeling to enable application of pulsed EPR techniques. The distances between attached spin labels were measured using pulsed electron-electron double resonance spectroscopy to probe the arrangement of the subunits within the dimer. We found very good agreement of experimental and calculated distances for the histidine-kinase region when both subunits are in a parallel orientation. However, experimental distance distributions surprisingly showed only limited agreement with either parallel- or antiparallel-arranged dimer structures when spin labels were placed into the PCM region. This observation indicates that the arrangements of the PCM subunits in the full-length protein dimer in solution differ significantly from that in the PCM crystals. The pulsed electron-electron double resonance data presented here revealed either no or only minor changes of distance distributions upon Pr-to-Pfr photoconversion. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Minimal Length, Measurability and Gravity

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Alexander Shalyt-Margolin

2016-03-01

Full Text Available The present work is a continuation of the previous papers written by the author on the subject. In terms of the measurability (or measurable quantities notion introduced in a minimal length theory, first the consideration is given to a quantum theory in the momentum representation. The same terms are used to consider the Markov gravity model that here illustrates the general approach to studies of gravity in terms of measurable quantities.

Production of enzymatically active recombinant full-length barley high pI alpha-glucosidase of glycoside family 31 by high cell-density fermentation of Pichia pastoris and affinity purification

DEFF Research Database (Denmark)

Næsted, Henrik; Kramhøft, Birte; Lok, F.

2006-01-01

Recombinant barley high pI alpha-glucosidase was produced by high cell-density fermentation of Pichia pastoris expressing the cloned full-length gene. The gene was amplified from a genomic clone and exons (coding regions) were assembled by overlap PCR. The resulting cDNA was expressed under contr...... nM x s(-1), and 85 s(-1) using maltose as substrate. This work presents the first production of fully active recombinant alpha-glucosidase of glycoside hydrolase family 31 from higher plants. (c) 2005 Elsevier Inc. All rights reserved....

Maximum length scale in density based topology optimization

DEFF Research Database (Denmark)

Lazarov, Boyan Stefanov; Wang, Fengwen

2017-01-01

The focus of this work is on two new techniques for imposing maximum length scale in topology optimization. Restrictions on the maximum length scale provide designers with full control over the optimized structure and open possibilities to tailor the optimized design for broader range...... of manufacturing processes by fulfilling the associated technological constraints. One of the proposed methods is based on combination of several filters and builds on top of the classical density filtering which can be viewed as a low pass filter applied to the design parametrization. The main idea...

Normal standards for kidney length as measured with US in premature infants

International Nuclear Information System (INIS)

Schlesinger, A.E.; Hedlund, G.L.; Pierson, W.P.; Null, D.M.

1986-01-01

In order to develop normal standards for kidney length in premature infants, the authors measured kidney length by US imaging in 39 (to date) premature infants less than 72 hours old and without known renal disease. Kidney length was compared with four different parameters of body size, including gestational age, birth weight, birth length, and body surface area. Similar standards have been generated previously for normal renal length as measured by US imaging in full-term infants and older children. These standards have proven utility in cases of congenital and acquired disorders that abnormally increase or decrease renal size. Scatter plots of kidney length versus body weight and kidney length versus body surface area conformed well to a logarithmic distribution, with a high correlation coefficient and close-fitting 95% confidence limits (SEE = 2.05)

The length-weight and length-length relationships of bluefish, Pomatomus saltatrix (Linnaeus, 1766) from Samsun, middle Black Sea region

OpenAIRE

Özpiçak, Melek; Saygın, Semra; Polat, Nazmi

2017-01-01

In this study, length-weight relationship (LWR) and length-length relationship (LLR) of bluefish,Pomatomus saltatrix were determined. A total of 125 specimens were sampled from Samsun, themiddle Black Sea in 2014 fishing season. Bluefish specimens were monthly collected fromcommercial fishing boats from October to December 2014. All captured individuals (N=125) weremeasured to the nearest 0.1 cm for total, fork and standard lengths. The weight of each fish (W)was recorded to the nearest 0.01 ...

Generation and analysis of a large-scale expressed sequence Tag database from a full-length enriched cDNA library of developing leaves of Gossypium hirsutum L.

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Min Lin

Full Text Available BACKGROUND: Cotton (Gossypium hirsutum L. is one of the world's most economically-important crops. However, its entire genome has not been sequenced, and limited resources are available in GenBank for understanding the molecular mechanisms underlying leaf development and senescence. METHODOLOGY/PRINCIPAL FINDINGS: In this study, 9,874 high-quality ESTs were generated from a normalized, full-length cDNA library derived from pooled RNA isolated from throughout leaf development during the plant blooming stage. After clustering and assembly of these ESTs, 5,191 unique sequences, representative 1,652 contigs and 3,539 singletons, were obtained. The average unique sequence length was 682 bp. Annotation of these unique sequences revealed that 84.4% showed significant homology to sequences in the NCBI non-redundant protein database, and 57.3% had significant hits to known proteins in the Swiss-Prot database. Comparative analysis indicated that our library added 2,400 ESTs and 991 unique sequences to those known for cotton. The unigenes were functionally characterized by gene ontology annotation. We identified 1,339 and 200 unigenes as potential leaf senescence-related genes and transcription factors, respectively. Moreover, nine genes related to leaf senescence and eleven MYB transcription factors were randomly selected for quantitative real-time PCR (qRT-PCR, which revealed that these genes were regulated differentially during senescence. The qRT-PCR for three GhYLSs revealed that these genes express express preferentially in senescent leaves. CONCLUSIONS/SIGNIFICANCE: These EST resources will provide valuable sequence information for gene expression profiling analyses and functional genomics studies to elucidate their roles, as well as for studying the mechanisms of leaf development and senescence in cotton and discovering candidate genes related to important agronomic traits of cotton. These data will also facilitate future whole-genome sequence

A novel method for length of chirped fiber Bragg grating sensor

Science.gov (United States)

Li, Zhenwei; Wei, Peng; Liu, Taolin

2018-03-01

Length of chirped fiber Bragg grating sensor is very important for detonation velocity. Different from other ways, we proposed a novel method based on the optical frequency domain reflection theory to measure the length of chirped fiber grating sensor in non-contact condition. This method adopts a tunable laser source to provide wavelength scanning laser, which covers the Full Width at Half Maximum of spectrum of the chirped fiber Bragg grating sensor. A Michelson interferometer is used to produce optical interference signal. Finally, the grating's length is attainable by distance domain signal. In theory, length resolution of chirped fiber Bragg grating sensor could be 0.02 mm. We perform a series of length measurement experiments for chirped fiber grating sensor, including comparison experiments with hot-tip method. And the experiment results show that the novel method could accurately measure the length of chirped fiber Bragg grating sensors, and the length differences between the optical frequency domain reflection method and the hot-tip probe method are very small.

Cross-dimensional mapping of number, length and brightness by preschool children.

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Maria Dolores de Hevia

Full Text Available Human adults in diverse cultures, children, infants, and non-human primates relate number to space, but it is not clear whether this ability reflects a specific and privileged number-space mapping. To investigate this possibility, we tested preschool children in matching tasks where the dimensions of number and length were mapped both to one another and to a third dimension, brightness. Children detected variation on all three dimensions, and they reliably performed mappings between number and length, and partially between brightness and length, but not between number and brightness. Moreover, children showed reliably better mapping of number onto the dimension of length than onto the dimension of brightness. These findings suggest that number establishes a privileged mapping with the dimension of length, and that other dimensions, including brightness, can be mapped onto length, although less efficiently. Children's adeptness at number-length mappings suggests that these two dimensions are intuitively related by the end of the preschool years.

Telomere length analysis.

Science.gov (United States)

Canela, Andrés; Klatt, Peter; Blasco, María A

2007-01-01

Most somatic cells of long-lived species undergo telomere shortening throughout life. Critically short telomeres trigger loss of cell viability in tissues, which has been related to alteration of tissue function and loss of regenerative capabilities in aging and aging-related diseases. Hence, telomere length is an important biomarker for aging and can be used in the prognosis of aging diseases. These facts highlight the importance of developing methods for telomere length determination that can be employed to evaluate telomere length during the human aging process. Telomere length quantification methods have improved greatly in accuracy and sensitivity since the development of the conventional telomeric Southern blot. Here, we describe the different methodologies recently developed for telomere length quantification, as well as their potential applications for human aging studies.

BACHD rats expressing full-length mutant huntingtin exhibit differences in social behavior compared to wild-type littermates.

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Giuseppe Manfré

Full Text Available Huntington disease (HD is a devastating inherited neurodegenerative disorder characterized by progressive motor, cognitive, and psychiatric symptoms without any cure to slow down or stop the progress of the disease. The BACHD rat model for HD carrying the human full-length mutant huntingtin protein (mHTT with 97 polyQ repeats has been recently established as a promising model which reproduces several HD-like features. While motor and cognitive functions have been characterized in BACHD rats, little is known about their social phenotype.This study focuses especially on social behavior since evidence for social disturbances exists in human patients. Our objective was to compare social behavior in BACHD and wild-type (WT rats at different ages, using two different measures of sociability.Animals were tested longitudinally at the age of 2, 4 and 8 months in the social interaction test to examine different parameters of sociability. A separate cohort of 7 month old rats was tested in the three chamber social test to measure both sociability and social novelty. Gene expression analyses in 8 months old animals were performed by real time qRT-PCR to evaluate a potential involvement of D1 and D2 dopaminergic receptors and the contribution of Brain-derived neurotrophic factor (BDNF to the observed behavioral alterations.In the social interaction test, BACHD rats showed age-dependent changes in behaviour when they were-re introduced to their cagemate after a 24 hours-period of individual housing. The time spent on nape attacks increased with aging. Furthermore, a significant higher level of pinning at 2 months of age was shown in the BACHD rats compared to wild-types, followed by a reduction at 4 and 8 months. On the other hand, BACHD rats exhibited a decreased active social behaviour compared to wild-types, reflected by genotype-effects on approaching, following and social nose contact. In the three chamber social test, BACHD rats seemed to show a mild

Length of urethra in the Indian adult male population

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Venkatesh Krishnamoorthy

2012-01-01

Full Text Available Objective: The urethral length has not been measured in the Indian population. Even the international literature in this arena is very sparse. This paper is an attempt to develop a simple anatomical database for urethral length. Materials and Methods: Between January 2010 and April 2011, the urethral lengths of 422 adult male patients who required catheterization as part of regular treatment at our hospital, were recorded after obtaining consent from the patients and from the scientific and ethics review boards of the institution. Patients with history of prostatic or urethral abnormalities were excluded. The balloon of a sterile Foley′s catheter was inflated using 10 cc of saline. The length from the junction of the balloon to the ′Y′ junction of the Foley was measured. The catheter was then passed into the bladder and re-inflated to same volume. The penis was gently straightened and the length of the catheter outside the penis was measured till the premarked point at the ′Y′ junction. Subtracting this from the original length gave the length of the urethra. Results: The mean length of the urethra was 17.55 + 1.42 cm with a range between 14 and 22.5 cm. Conclusions: Literature in which the length of the normal adult male urethra is recorded for a significant sample size is very scarce. Our data adds to basic anatomic information of the male urethra specific to the Indian population. Statistical Methods: Descriptive statistical analysis was performed. The non-linear regression analysis was employed to find the normative values of urethral length according to age class.

Frequency Characteristics of Double-Walled Carbon Nanotube Resonator with Different Length

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Jun-Ha LEE

2016-05-01

Full Text Available In this paper, we have conducted classical molecular dynamics simulations for DWCNTs of various wall lengths to investigate their use as ultrahigh frequency nano-mechanical resonators. We sought to determine the variations in the frequency of these resonators according to changes in the DWCNT wall lengths. For a double-walled carbon nanotube resonator with a shorter inner nanotube, the shorter inner nanotube can be considered to be a flexible core, and thus, the length influences the fundamental frequency. In this paper, we analyze the variation in frequency of ultra-high frequency nano-mechnical resonators constructed from DWCNTs with different wall lengths.DOI: http://dx.doi.org/10.5755/j01.ms.22.2.12951

Relationships of body lengths with mouth opening and prey length of nemipterid fishes (Regan, 1913 in the Gulf of Thailand

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Mithun Paul

2017-12-01

Full Text Available This study aims to investigate the relationship among total length (TL of fish with mouth opening namely horizontal opening (MH, vertical opening (VH, mouth area (MA and fork length (FL of seven sympatric nemipterid fish species and to know the relationship between total length and consumed prey length of five sympatric species sampled from the Gulf of Thailand in 2015. A total 883 fish were investigated collected from both cruise surveys and fishing port survey. TL was linearly and log-linearly related with both MV and MH for three and four species, respectively. MA’s were always the log linear relation of TL and shapes were nearly oval for all species. FL in all TL-FL relationships were proportional to the TL’s in all species (r2 = 0.94, P  .5 and in invertebrate prey items for N. tambuloides (P > .5. So, this study clearly confirms that nemipterid fishes of different sizes feed on all different specific prey items according to its own body size and feed according to size class for prey items available nearby.

Construction of cold mass assembly for full-length dipoles for the SSC [Superconducting Super Collider] accelerator

International Nuclear Information System (INIS)

Dahl, P.; Cottingham, J.; Garber, M.

1986-10-01

Four of the initial six 17m long demonstration dipole magnets for the proposed Superconducting Super Collider have been constructed, and the first one is now being tested. This paper describes the magnet design and construction of the cold mass assembly. The magnets are cold iron (and cold bore) 1-in-1 dipoles, wound with partially keystoned current density-graded high homogeneity NbTi cable in a two-layer cos θ coil of 40 mm inner diameter. The magnetic length is 16.6 m. The coil is prestressed by 15 mm wide stainless steel collars, and mounted in a circular, split iron yoke of 267 mm outer diameter, supported by a cylindrical yoke (and helium) containment vessel of stainless steel. The magnet bore tube assembly incorporates superconducting sextupole trim coils produced by an industrial, automatic process akin to printed circuit fabrication

Length-weight and length-length relationships of common carp (Cyprinus carpio L.) in the middle and southern Iraq provinces

Science.gov (United States)

Al-jebory, Taymaa A.; Das, Simon K.; Usup, Gires; Bakar, Y.; Al-saadi, Ali H.

2018-04-01

In this study, length-weight and length-length relationships of common carp (Cyprinus carpio L.) in the middle and southern Iraq provinces were determined. Fish specimens were procured from seven provinces from July to December, 2015. A negative and positive allometric growth pattern was obtained, where the total length (TL) ranged from 25.60 cm to 33.53 cm, and body weight (BW) ranged from 700 g to 1423 g. Meanwhile, the lowest of 1.03 and highest of 3.54 in "b" value was recorded in group F and group C, respectively. Therefore, Fulton condition factor (K) range from 2.57 to 4.94. While, relative condition factor (Kn) was in the ranged of 0.95 to 1.01. A linear relationship between total length (TL) and standard length (SL) among the provinces for fish groups was obtained. The variances in "b" value ranged from 0.10 to 0.93 with correlation coefficient (r2) of 0.02 to 0.97. This research could be used as a guide to study the ecology and biology of common Carp (Cyprinus carpio L.) in the middle and southern Iraq provinces.

Modelling length of hospital stay in motor victims

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Mercedes Ayuso-Gutiérrez

2015-03-01

Full Text Available Objective. To analyze which socio-demographic and other factors related to motor injuries affect the length of hospital recovery stay. Materials and methods. In the study a sample of 17 932 motor accidents was used. All the crashes occurred in Spain between 2000 and 2007. Different regression models were fitted to data to identify and measure the impact of a set of explanatory regressors. Results. Time of hospital stay for men is on average 41% larger than for women. When the victim has a fracture as a consequence of the accident, the mean time of hospital stay is multiplied by five. Injuries located in lower extremities, the head and abdomen are associated with greater hospitalization lengths. Conclusions. Gender, age and type of victim, as well as the location and nature of injuries, are found to be factors that have significant impact on the expected length of hospital stay.

Evaluation of Efficient Line Lengths for Better Readability

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Zahid Hussain

2012-01-01

Full Text Available In this paper the major findings of a formal experiment about onscreen text line lengths are presented. The experiment examined the effects of four different line lengths on the reading speed and the reading efficiency. Efficiency is defined as a combination of reading speed and accuracy. Sixteen people between the age of 24 and 36 participated at the experiment. The subjects had to read four different texts with an average line length around 2000 characters. The texts contained substitution words, which had to be detected by the subjects to measure reading accuracy. Besides objective measures like reading speed and accuracy, the subjects were asked to subjectively vote on their reading experience. The results from our objective measures show strong similarities to those of the work done previously by different researchers. The absolute reading speed grows when the line length grows from CPL (Characters Per Line 30-120. The measured reading efficiency, however, doesn\\\\\\'t grow steadily, although a growing trend can be seen. This is due to the fact, that the test persons found in average more substitution words from the 60 CPL text than they did from the 30 and 90 CPL texts. The reading speed seems to increase while the line length increases but the overall comprehension seems to peak at medium line lengths. As in the previous studies, our test persons also prefer the medium (60 and 90 CPL line lengths, although they perform better when reading longer lines. In the overall subjective opinion 13 out of 16 test persons selected the 60 or 90 CPL line length as their favorite. The literature doesn\\\\\\'t truly provide a scientific explanation for the difference between the objective performance and the subjective preference. A natural hypothesis would be that the line length that is the fastest to read would also feel most comfortable to the readers but in the light of this and the earlier research it seems like this is not the case.

Musculoskeletal pain and posture decrease step length in young adults

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Maria Regina Rachmawati

2009-08-01

Full Text Available Pain of the musculoskeletal system, especially low back pain, is one of the most frequent problems with a high risk of disability. The aim of this research study was to determine the existence of an association between low back pain on one hand, posture and step length on the other. This cross-sectional study was conducted on 77 healthy young adult subjects. Step length was measured with the Biodex Gait Trainer 2 (230 VAC. The study results indicate that 62.3% of the young adult subjects had suffered from low back pain. There was no significant association between gender and pain. In male subjects no significant association was found between pain on one hand and mean difference in step length and posture on the other. However, in female subjects with abnormal posture, there was a highly significant difference in left step length between subjects with back pain and those without (p=0.007. The results of a multiple regression analysis indicate that posture has the greatest influence on left step length (B=4.135; 95% Confidence Interval 0.292-7.977. It is recommended that in the examination of low back pain an assessment be made of posture, step length and difference in step lengths.

Musculoskeletal pain and posture decrease step length in young adults

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Maria Regina Rachmawati

2016-02-01

Full Text Available Pain of the musculoskeletal system, especially low back pain, is one of the most frequent problems with a high risk of disability. The aim of this research study was to determine the existence of an association between low back pain on one hand,  posture and step length on the other. This cross-sectional study was conducted on 77 healthy young adult subjects. Step length was measured with the Biodex Gait Trainer 2 (230 VAC. The study results indicate that 62.3% of the young adult subjects had suffered from low back pain. There was no significant association between gender and pain. In male subjects no significant association was found between pain on one hand and mean difference in step length and posture on the other. However, in female subjects with abnormal posture, there was a highly significant difference in left step length between subjects with back pain and those without (p=0.007.  The results of a multiple regression analysis indicate that posture has the greatest influence on left step length (B=4.135; 95% Confidence Interval 0.292-7.977. It is recommended that in the examination of low back pain an assessment be made of posture, step length and difference in step lengths.

Relation of Stump Length with Various Gait Parameters in Trans-tibial Amputee

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Koyel Majumdar

2008-07-01

Full Text Available The purpose of this paper is evaluating the impact of stump length of unilateral below knee amputees (BKA on different gait parameters. Nine unilateral BKA were chosen and divided into three groups comprising patients with short, medium, and long stump length. Each of them underwent gait analysis test by Computer Dynography (CDG system to measure the gait parameters. It was found that the ground reaction force is higher in the patients with medium stump length whereas the velocity, step length both for the prosthetic and sound limb and cadence were high in longer stump length. Statistical analysis shows a significant difference (p<0.05 between the gait parameters of BKA with medium and longer stump length. The patients with longer stump length were more efficient than medium and short stump patients as they consumed comparatively lesser energy while walking with self-selected velocity and conventional (Solid ankle cushioned heel SACH foot.

Anatomic and functional leg-length inequality: A review and recommendation for clinical decision-making. Part I, anatomic leg-length inequality: prevalence, magnitude, effects and clinical significance

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Knutson Gary A

2005-07-01

Full Text Available Abstract Background Leg-length inequality is most often divided into two groups: anatomic and functional. Part I of this review analyses data collected on anatomic leg-length inequality relative to prevalence, magnitude, effects and clinical significance. Part II examines the functional "short leg" including anatomic-functional relationships, and provides an outline for clinical decision-making. Methods Online database – Medline, CINAHL and MANTIS – and library searches for the time frame of 1970–2005 were done using the term "leg-length inequality". Results and Discussion Using data on leg-length inequality obtained by accurate and reliable x-ray methods, the prevalence of anatomic inequality was found to be 90%, the mean magnitude of anatomic inequality was 5.2 mm (SD 4.1. The evidence suggests that, for most people, anatomic leg-length inequality does not appear to be clinically significant until the magnitude reaches ~ 20 mm (~3/4". Conclusion Anatomic leg-length inequality is near universal, but the average magnitude is small and not likely to be clinically significant.

RESEARCH ARTICLE Full length sequencing and novel ...

Indian Academy of Sciences (India)

Navya

2016-12-16

Dec 16, 2016 ... TOLONE, ANNA MARIA SUTERA, MARIA TERESA SARDINA, BALDASSARE ... finding of novel SNPs that might be important in future studies and laid the .... power, precision and quality to assess the relationship between ...

FULL LENGTH RESEARCH ARTICLE Adamu & Babatunde (2008 ...

African Journals Online (AJOL)

Dr. Ahmed

standards which now appear in BS 1006 (standard method 1978). These properties are fundamental in the ... to increase its affinity for disperse colours and make it possible to dye the fibre easily. Determination of dye ... Colour fastness to washing test results are shown in Table 4. The procedure was also repeated for dye ...

FULL LENGTH RESEARCH ARTICLE Onuh & Ohazurike (2008 ...

African Journals Online (AJOL)

Dr. Ahmed

flasks containing 50 ml of Reese and Levinson's solution, consisting of Sodium Polypectate (NaPP) as carbon source, and incubated for 7 days at 38oC. ... containing 50ml of Reese and Levinson's medium with Carboxylmethyl. Cellulose (CMC) as the .... from the brown rot fungus Postia placenta. Applied Microbiology and.

The Length of the Day: A Cosmological Perspective

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Arbab A. I.

2009-01-01

Full Text Available We have found an empirical law for the variation of the length of the Earth’s day with geologic time employing Wells’s data. We attribute the lengthening of the Earth’s day to the present cosmic expansion of the Universe. The prediction of law has been found to be in agreement with the astronomical and geological data. The day increases at a present rate of 0.002 sec / century. The length of the day is found to be 6 hours when the Earth formed. We have also found a new limit for the value of the Hubble constant and the age of the Universe.

Telomere Length Reprogramming in Embryos and Stem Cells

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Keri Kalmbach

2014-01-01

Full Text Available Telomeres protect and cap linear chromosome ends, yet these genomic buffers erode over an organism’s lifespan. Short telomeres have been associated with many age-related conditions in humans, and genetic mutations resulting in short telomeres in humans manifest as syndromes of precocious aging. In women, telomere length limits a fertilized egg’s capacity to develop into a healthy embryo. Thus, telomere length must be reset with each subsequent generation. Although telomerase is purportedly responsible for restoring telomere DNA, recent studies have elucidated the role of alternative telomeres lengthening mechanisms in the reprogramming of early embryos and stem cells, which we review here.

Does Reproductive Investment Decrease Telomere Length in Menidia menidia?

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Jin Gao

Full Text Available Given finite resources, intense investment in one life history trait is expected to reduce investment in others. Although telomere length appears to be strongly tied to age in many taxa, telomere maintenance requires energy. We therefore hypothesize that telomere maintenance may trade off against other life history characters. We used natural variation in laboratory populations of Atlantic silversides (Menidia menidia to study the relationship between growth, fecundity, life expectancy, and relative telomere length. In keeping with several other studies on fishes, we found no clear dependence of telomere length on age. However, we did find that more fecund fish tended to have both reduced life expectancy and shorter telomeres. This result is consistent with the hypothesis that there is a trade-off between telomere maintenance and reproductive output.

Crystal structure of full-length Zika virus NS5 protein reveals a conformation similar to Japanese encephalitis virus NS5

Energy Technology Data Exchange (ETDEWEB)

Upadhyay, Anup K.; Cyr, Matthew; Longenecker, Kenton; Tripathi, Rakesh; Sun, Chaohong; Kempf, Dale J. (AbbVie)

2017-02-21

The rapid spread of the recentZika virus(ZIKV) epidemic across various countries in the American continent poses a major health hazard for the unborn fetuses of pregnant women. To date, there is no effective medical intervention. The nonstructural protein 5 ofZika virus(ZIKV-NS5) is critical for ZIKV replication through the 5'-RNA capping and RNA polymerase activities present in its N-terminal methyltransferase (MTase) and C-terminal RNA-dependent RNA polymerase (RdRp) domains, respectively. The crystal structure of the full-length ZIKV-NS5 protein has been determined at 3.05 Å resolution from a crystal belonging to space groupP2₁2₁2 and containing two protein molecules in the asymmetric unit. The structure is similar to that reported for the NS5 protein fromJapanese encephalitis virusand suggests opportunities for structure-based drug design targeting either its MTase or RdRp domain.

The queue-length in GI/G/s queues

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Le Gall Pierre

2000-01-01

Full Text Available The distribution of the queue-length in the stationary symmetrical GI/G/s queue is given with an application to the M/G/s queue, particularly in the case of the combination of several packet traffics, with various constant service times, to dimension the buffer capacity.

Telomere Length and Mortality

DEFF Research Database (Denmark)

Kimura, Masayuki; Hjelmborg, Jacob V B; Gardner, Jeffrey P

2008-01-01

Leukocyte telomere length, representing the mean length of all telomeres in leukocytes, is ostensibly a bioindicator of human aging. The authors hypothesized that shorter telomeres might forecast imminent mortality in elderly people better than leukocyte telomere length. They performed mortality...

Importance of Viral Sequence Length and Number of Variable and Informative Sites in Analysis of HIV Clustering.

Science.gov (United States)

Novitsky, Vlad; Moyo, Sikhulile; Lei, Quanhong; DeGruttola, Victor; Essex, M

2015-05-01

To improve the methodology of HIV cluster analysis, we addressed how analysis of HIV clustering is associated with parameters that can affect the outcome of viral clustering. The extent of HIV clustering and tree certainty was compared between 401 HIV-1C near full-length genome sequences and subgenomic regions retrieved from the LANL HIV Database. Sliding window analysis was based on 99 windows of 1,000 bp and 45 windows of 2,000 bp. Potential associations between the extent of HIV clustering and sequence length and the number of variable and informative sites were evaluated. The near full-length genome HIV sequences showed the highest extent of HIV clustering and the highest tree certainty. At the bootstrap threshold of 0.80 in maximum likelihood (ML) analysis, 58.9% of near full-length HIV-1C sequences but only 15.5% of partial pol sequences (ViroSeq) were found in clusters. Among HIV-1 structural genes, pol showed the highest extent of clustering (38.9% at a bootstrap threshold of 0.80), although it was significantly lower than in the near full-length genome sequences. The extent of HIV clustering was significantly higher for sliding windows of 2,000 bp than 1,000 bp. We found a strong association between the sequence length and proportion of HIV sequences in clusters, and a moderate association between the number of variable and informative sites and the proportion of HIV sequences in clusters. In HIV cluster analysis, the extent of detectable HIV clustering is directly associated with the length of viral sequences used, as well as the number of variable and informative sites. Near full-length genome sequences could provide the most informative HIV cluster analysis. Selected subgenomic regions with a high extent of HIV clustering and high tree certainty could also be considered as a second choice.

Inertial Effects on Finite Length Pipe Seismic Response

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Virginia Corrado

2012-01-01

Full Text Available A seismic analysis for soil-pipe interaction which accounts for length and constraining conditions at the ends of a continuous pipe is developed. The Winkler model is used to schematize the soil-structure interaction. The approach is focused on axial strains, since bending strains in a buried pipe due to the wave propagation are typically a second-order effect. Unlike many works, the inertial terms are considered in solving equations. Accurate numerical simulations are carried out to show the influence of pipe length and constraint conditions on the pipe seismic strain. The obtained results are compared with results inferred from other models present in the literature. For free-end pipelines, inertial effects have significant influence only for short length. On the contrary, their influence is always important for pinned pipes. Numerical simulations show that a simple rigid model can be used for free-end pipes, whereas pinned pipes need more accurate models.

Focal Length Affects Depicted Shape and Perception of Facial Images.

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Vít Třebický

Full Text Available Static photographs are currently the most often employed stimuli in research on social perception. The method of photograph acquisition might affect the depicted subject's facial appearance and thus also the impression of such stimuli. An important factor influencing the resulting photograph is focal length, as different focal lengths produce various levels of image distortion. Here we tested whether different focal lengths (50, 85, 105 mm affect depicted shape and perception of female and male faces. We collected three portrait photographs of 45 (22 females, 23 males participants under standardized conditions and camera setting varying only in the focal length. Subsequently, the three photographs from each individual were shown on screen in a randomized order using a 3-alternative forced-choice paradigm. The images were judged for attractiveness, dominance, and femininity/masculinity by 369 raters (193 females, 176 males. Facial width-to-height ratio (fWHR was measured from each photograph and overall facial shape was analysed employing geometric morphometric methods (GMM. Our results showed that photographs taken with 50 mm focal length were rated as significantly less feminine/masculine, attractive, and dominant compared to the images taken with longer focal lengths. Further, shorter focal lengths produced faces with smaller fWHR. Subsequent GMM revealed focal length significantly affected overall facial shape of the photographed subjects. Thus methodology of photograph acquisition, focal length in this case, can significantly affect results of studies using photographic stimuli perhaps due to different levels of perspective distortion that influence shapes and proportions of morphological traits.

Application of Displacement Height and Surface Roughness Length to Determination Boundary Layer Development Length over Stepped Spillway

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Xiangju Cheng

2014-12-01

Full Text Available One of the most uncertain parameters in stepped spillway design is the length (from the crest of boundary layer development. The normal velocity profiles responding to the steps as bed roughness are investigated in the developing non-aerated flow region. A detailed analysis of the logarithmic vertical velocity profiles on stepped spillways is conducted through experimental data to verify the computational code and numerical experiments to expand the data available. To determine development length, the hydraulic roughness and displacement thickness, along with the shear velocity, are needed. This includes determining displacement height d and surface roughness length z0 and the relationship of d and z0 to the step geometry. The results show that the hydraulic roughness height ks is the primary factor on which d and z0 depend. In different step height, step width, discharge and intake Froude number, the relations d/ks = 0.22–0.27, z0/ks = 0.06–0.1 and d/z0 = 2.2–4 result in a good estimate. Using the computational code and numerical experiments, air inception will occur over stepped spillway flow as long as the Bauer-defined boundary layer thickness is between 0.72 and 0.79.

Sonographic Measurement of Fetal Ear Length in Turkish Women with a Normal Pregnancy

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Mucize Eriç Özdemir

2014-12-01

Full Text Available Background: Abnormal fetal ear length is a feature of chromosomal disorders. Fetal ear length measurement is a simple measurement that can be obtained during ultrasonographic examinations. Aims: To develop a nomogram for fetal ear length measurements in our population and investigate the correlation between fetal ear length, gestational age, and other standard fetal biometric measurements. Study Design: Cohort study. Methods: Ear lengths of the fetuses were measured in normal singleton pregnancies. The relationship between gestational age and fetal ear length in millimetres was analysed by simple linear regression. In addition, the correlation of fetal ear length measurements with biparietal diameter, head circumference, abdominal circumference, and femur length were evaluated.Ear length measurements were obtained from fetuses in 389 normal singleton pregnancies ranging between 16 and 28 weeks of gestation. Results: A nomogram was developed by linear regression analysis of the parameters ear length and gestational age. Fetal ear length (mm = y = (1.348 X gestational age-12.265, where gestational ages is in weeks. A high correlation was found between fetal ear length and gestational age, and a significant correlation was also found between fetal ear length and the biparietal diameter (r=0.962; p<0.001. Similar correlations were found between fetal ear length and head circumference, and fetal ear length and femur length. Conclusion: The results of this study provide a nomogram for fetal ear length. The study also demonstrates the relationship between ear length and other biometric measurements.

Static correlation lengths in QCD at high temperatures and finite densities

CERN Document Server

Hart, A; Philipsen, O

2000-01-01

We use a perturbatively derived effective field theory and three-dimensional lattice simulations to determine the longest static correlation lengths in the deconfined QCD plasma phase at high temperatures (T\\gsim 2 Tc) and finite densities (\\mu\\lsim 4 T). For vanishing chemical potential, we refine a previous determination of the Debye screening length, and determine the dependence of different correlation lengths on the number of massless flavours as well as on the number of colours. For non-vanishing but small chemical potential, the existence of Debye screening allows us to carry out simulations corresponding to the full QCD with two (or three) massless dynamical flavours, in spite of a complex action. We investigate how the correlation lengths in the different quantum number channels change as the chemical potential is switched on.

Dividing the Force Concept Inventory into two equivalent half-length tests

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Jing Han

2015-05-01

Full Text Available The Force Concept Inventory (FCI is a 30-question multiple-choice assessment that has been a building block for much of the physics education research done today. In practice, there are often concerns regarding the length of the test and possible test-retest effects. Since many studies in the literature use the mean score of the FCI as the primary variable, it would be useful then to have different shorter tests that can produce FCI-equivalent scores while providing the benefits of being quicker to administer and overcoming the test-retest effects. In this study, we divide the 1995 version of the FCI into two half-length tests; each contains a different subset of the original FCI questions. The two new tests are shorter, still cover the same set of concepts, and produce mean scores equivalent to those of the FCI. Using a large quantitative data set collected at a large midwestern university, we statistically compare the assessment features of the two half-length tests and the full-length FCI. The results show that the mean error of equivalent scores between any two of the three tests is within 3%. Scores from all tests are well correlated. Based on the analysis, it appears that the two half-length tests can be a viable option for score based assessment that need to administer tests quickly or need to measure short-term gains where using identical pre- and post-test questions is a concern.

Probiotics supplementation and length of hospital stay in neonates with gastrointestinal surgery

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Veronica Mugarab-Samedi

Full Text Available Any manipulation on open bowel causes interventional impact on gut microbiome, and surgical stress triggers bacterial translocation; thus, it will be fundamental to determine gut microbiome after surgery. Monitoring dynamic changes in microbiome of post-surgical infants who received probiotics and placebo could provide with important information about gut colonization and potential bacterial overgrowth.The purpose of this study is to assess the effect of probiotics supplementation on length of hospital stay, duration of parenteral nutrition, and feed tolerance in neonates after gastrointestinal surgery. Keywords: Neonates, Surgery, Probiotics, Microbiome, Length of hospital stay, Full enteral feeds

Foot length measurements of newborns of high and low risk pregnancies

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Ana Karina Marques Salge

Full Text Available Abstract OBJECTIVE Comparing foot length measurements of newborns in high and low risk pregnancies at a public hospital in Goiânia, GO, Brazil. METHOD A cross-sectional study carried out between April, 2013 and May, 2015, with a sample consisting of 180 newborns; 106 infants of women from high-risk pregnancies and 74 of women from low-risk pregnancies. Data were descriptively analyzed. Foot length measurement was performed using a stiff transparent plastic ruler, graduated in millimeters. The length of both feet was measured from the tip of the hallux (big toe to the end of the heel. RESULTS A statistically significant relationship was found between the foot length and newborn’s weight, between the cephalic and thoracic perimeters in the high-risk group and between the cephalic perimeter in the control group. CONCLUSION There is a need for creating cut-off points to identify newborns with intrauterine growth disorders using foot length.

Why the Length of a Quantum String Cannot Be Lorentz Contracted

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Antonio Aurilia

2013-01-01

Full Text Available We propose a quantum gravity-extended form of the classical length contraction law obtained in special relativity. More specifically, the framework of our discussion is the UV self-complete theory of quantum gravity. We show how our results are consistent with (i the generalized form of the uncertainty principle (GUP, (ii the so-called hoop-conjecture, and (iii the intriguing notion of “classicalization” of trans-Planckian physics. We argue that there is a physical limit to the Lorentz contraction rule in the form of some minimal universal length determined by quantum gravity, say the Planck Length, or any of its current embodiments such as the string length, or the TeV quantum gravity length scale. In the latter case, we determine the critical boost that separates the ordinary “particle phase,” characterized by the Compton wavelength, from the “black hole phase,” characterized by the effective Schwarzschild radius of the colliding system.

Determination of Onramp Weaving Length for Resolving Merging Dilemma

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Chiu Liu

2012-03-01

Full Text Available It is physically known that onramp merging may turn out to be difficult if the onramp (weaving/merging length is too short because a driver under certain driving circumstances may find that either merging ahead or merging behind a neighboring vehicle on the adjacent highway lane cannot be completed. Various existing guidelines or design manuals provide no clear physical understanding and explanations to the design onramp weaving length but often based on evolved empirical experiences. By integrating human factors, vehicle dynamic characteristics, roadway surface condition, and the onramp weaving design into a single unified analytic framework, the onramp length required for a driver to merge into the highway traffic successfully is determined exactly with formulas and physical solutions to avoid the merging dilemma and enhance driving safety at highway interchanges. The design onramp weaving length is examined and evaluated with various foreseeable merging scenarios and physical examples. This analytic framework sheds light on the understanding of the onramp weaving the first time strictly on a physical human-vehicle-roadway interaction setting. Practitioners can easily apply these user friendly formulae and equations derived from the unified framework to calculate the onramp weaving length to resolve the merging dilemma and enhance driving safety for any highway interchanges.

Full Len gth Res earc h Arti cle Full Length Research Article

African Journals Online (AJOL)

functioning of adults as well as children, often with significant ... learning disability particularly in children (Albert,. 1999 ... Signs and Symptoms of this infection include, mild to ..... Isolation and Antimicrobial ... Bayesian Statistics for Social.

Does length or neighborhood size cause the word length effect?

Science.gov (United States)

Jalbert, Annie; Neath, Ian; Surprenant, Aimée M

2011-10-01

Jalbert, Neath, Bireta, and Surprenant (2011) suggested that past demonstrations of the word length effect, the finding that words with fewer syllables are recalled better than words with more syllables, included a confound: The short words had more orthographic neighbors than the long words. The experiments reported here test two predictions that would follow if neighborhood size is a more important factor than word length. In Experiment 1, we found that concurrent articulation removed the effect of neighborhood size, just as it removes the effect of word length. Experiment 2 demonstrated that this pattern is also found with nonwords. For Experiment 3, we factorially manipulated length and neighborhood size, and found only effects of the latter. These results are problematic for any theory of memory that includes decay offset by rehearsal, but they are consistent with accounts that include a redintegrative stage that is susceptible to disruption by noise. The results also confirm the importance of lexical and linguistic factors on memory tasks thought to tap short-term memory.

Fundamental length

International Nuclear Information System (INIS)

Pradhan, T.

1975-01-01

The concept of fundamental length was first put forward by Heisenberg from purely dimensional reasons. From a study of the observed masses of the elementary particles known at that time, it is sumrised that this length should be of the order of magnitude 1 approximately 10 -13 cm. It was Heisenberg's belief that introduction of such a fundamental length would eliminate the divergence difficulties from relativistic quantum field theory by cutting off the high energy regions of the 'proper fields'. Since the divergence difficulties arise primarily due to infinite number of degrees of freedom, one simple remedy would be the introduction of a principle that limits these degrees of freedom by removing the effectiveness of the waves with a frequency exceeding a certain limit without destroying the relativistic invariance of the theory. The principle can be stated as follows: It is in principle impossible to invent an experiment of any kind that will permit a distintion between the positions of two particles at rest, the distance between which is below a certain limit. A more elegant way of introducing fundamental length into quantum theory is through commutation relations between two position operators. In quantum field theory such as quantum electrodynamics, it can be introduced through the commutation relation between two interpolating photon fields (vector potentials). (K.B.)

A cryogenic test stand for full length SSC magnets with superfluid capability

International Nuclear Information System (INIS)

Peterson, T.J.; Mazur, P.O.

1989-02-01

The Fermilab Magnet Test Facility performs testing of the full scale SSC magnets on test stands capable of simulating the cryogenic environment of the SSC main ring. One of these test stands, Stand 5, also has the ability to operate the magnet under test at temperatures from 1.8K to 4.5K with either supercritical helium or subcooled liquid, providing at least 25 Watts of refrigeration. At least 50 g/s flow is available from 2.3K to 4.5K, whereas superfluid operation occurs with zero flow. Cooldown time from 4.5K to 1.8K is 1.5 hours. A maximum current capability of 10,000 amps is provided, as is instrumentation to monitor and control the cryogenic conditions. This paper describes the cryogenic design of this test stand. 8 refs., 6 figs

Diffusion length in nanoporous TiO2 films under above-band-gap illumination

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J. D. Park

2014-06-01

Full Text Available We determined the carrier diffusion lengths in TiO2 nanoporous layers of dye-sensitized solar cells by using scanning photocurrent microscopy using an ultraviolet laser. Here, we excited the carrier directly in the nanoporous layers where the diffusion lengths were found to 140 μm as compared to that of visible illumination measured at 90 μm. The diffusion length decreased with increasing laser modulation frequency, in which we determined the electron lifetimes and the diffusion coefficients for both visible and UV illuminations. The diffusion lengths have been studied in terms of the sintering temperatures for both cells with and without binding molecules. We found a strong correlation between the diffusion length and the overall light-to-current conversion efficiency, proving that improving the diffusion length and hence the interparticle connections, is key to improving cell efficiency.

Characterization of a new full length TMPRSS3 isoform and identification of mutant alleles responsible for nonsyndromic recessive deafness in Newfoundland and Pakistan

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Shotland Lawrence I

2004-09-01

Full Text Available Abstract Background Mutant alleles of TMPRSS3 are associated with nonsyndromic recessive deafness (DFNB8/B10. TMPRSS3 encodes a predicted secreted serine protease, although the deduced amino acid sequence has no signal peptide. In this study, we searched for mutant alleles of TMPRSS3 in families from Pakistan and Newfoundland with recessive deafness co-segregating with DFNB8/B10 linked haplotypes and also more thoroughly characterized the genomic structure of TMPRSS3. Methods We enrolled families segregating recessive hearing loss from Pakistan and Newfoundland. Microsatellite markers flanking the TMPRSS3 locus were used for linkage analysis. DNA samples from participating individuals were sequenced for TMPRSS3. The structure of TMPRSS3 was characterized bioinformatically and experimentally by sequencing novel cDNA clones of TMPRSS3. Results We identified mutations in TMPRSS3 in four Pakistani families with recessive, nonsyndromic congenital deafness. We also identified two recessive mutations, one of which is novel, of TMPRSS3 segregating in a six-generation extended family from Newfoundland. The spectrum of TMPRSS3 mutations is reviewed in the context of a genotype-phenotype correlation. Our study also revealed a longer isoform of TMPRSS3 with a hitherto unidentified exon encoding a signal peptide, which is expressed in several tissues. Conclusion Mutations of TMPRSS3 contribute to hearing loss in many communities worldwide and account for 1.8% (8 of 449 of Pakistani families segregating congenital deafness as an autosomal recessive trait. The newly identified TMPRSS3 isoform e will be helpful in the functional characterization of the full length protein.

Dorsal Phalloplasty to Preserve Penis Length after Penile Prosthesis Implantation

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Osama Shaeer

2017-03-01

Full Text Available Objectives: Following penile prosthesis implantation (PPI, patients may complain of a decrease in visible penis length. A dorsal phalloplasty defines the penopubic junction by tacking pubic skin to the pubis, revealing the base of the penis. This study aimed to evaluate the efficacy of a dorsal phalloplasty in increasing the visible penis length following PPI. Methods: An inflatable penile prosthesis was implanted in 13 patients with severe erectile dysfunction (ED at the Kamal Shaeer Hospital, Cairo, Egypt, from January 2013 to May 2014. During the surgery, nonabsorbable tacking sutures were used to pin the pubic skin to the pubis through the same penoscrotal incision. Intraoperative penis length was measured before and after the dorsal phalloplasty. Overall patient satisfaction was measured on a 5-point rating scale and patients were requested to subjectively compare their postoperative penis length with memories of their penis length before the onset of ED. Results: Intraoperatively, the dorsal phalloplasty increased the visible length of the erect penis by an average of 25.6%. The average length before and after tacking was 10.2 ± 2.9 cm and 13.7 ± 2.8 cm, respectively (P <0.002. Postoperatively, seven patients (53.8% reported a longer penis, five patients (38.5% reported no change in length and one patient (7.7% reported a slightly shorter penis. The mean overall patient satisfaction score was 4.9 ± 0.3. None of the patients developed postoperative complications. Conclusion: A dorsal phalloplasty during PPI is an effective method of increasing visible penis length, therefore minimising the impression of a shorter penis after implantation.

Improvement of genome assembly completeness and identification of novel full-length protein-coding genes by RNA-seq in the giant panda genome.

Science.gov (United States)

Chen, Meili; Hu, Yibo; Liu, Jingxing; Wu, Qi; Zhang, Chenglin; Yu, Jun; Xiao, Jingfa; Wei, Fuwen; Wu, Jiayan

2015-12-11

High-quality and complete gene models are the basis of whole genome analyses. The giant panda (Ailuropoda melanoleuca) genome was the first genome sequenced on the basis of solely short reads, but the genome annotation had lacked the support of transcriptomic evidence. In this study, we applied RNA-seq to globally improve the genome assembly completeness and to detect novel expressed transcripts in 12 tissues from giant pandas, by using a transcriptome reconstruction strategy that combined reference-based and de novo methods. Several aspects of genome assembly completeness in the transcribed regions were effectively improved by the de novo assembled transcripts, including genome scaffolding, the detection of small-size assembly errors, the extension of scaffold/contig boundaries, and gap closure. Through expression and homology validation, we detected three groups of novel full-length protein-coding genes. A total of 12.62% of the novel protein-coding genes were validated by proteomic data. GO annotation analysis showed that some of the novel protein-coding genes were involved in pigmentation, anatomical structure formation and reproduction, which might be related to the development and evolution of the black-white pelage, pseudo-thumb and delayed embryonic implantation of giant pandas. The updated genome annotation will help further giant panda studies from both structural and functional perspectives.

Experimental validation of 3D reconstructed pin-power distributions in full-scale BWR fuel assemblies with partial length rods

Energy Technology Data Exchange (ETDEWEB)

Giust, F. D. [Axpo Kernenergie, Parkstrasse 23, CH-5401 Baden (Switzerland); Swiss Federal Inst. of Technology EPFL, CH-1015 Lausanne (Switzerland); Grimm, P. [Paul Scherrer Inst., CH-5232 Villigen (Switzerland); Chawla, R. [Paul Scherrer Inst., CH-5232 Villigen (Switzerland); Swiss Federal Inst. of Technology (EPFL), CH-1015 Lausanne (Switzerland)

2012-07-01

Total fission rate measurements have been performed on full-size BWR fuel assemblies of type SVEA-96 Optima2 in the framework of Phase III of the LWR-PROTEUS experimental program at the Paul Scherrer Inst.. This paper presents comparisons of calculated, nodal reconstructed, pin-wise total-fission rate distributions with experimental results. Radial comparisons have been performed for the three sections of the assembly (96, 92 and 84 fuel pins), while three-dimensional effects have been investigated at pellet-level for the two transition regions, i.e. the tips of the short (1/3) and long (2/3) partial length rods. The test zone has been modeled using two different code systems: HELIOS/PRESTO-2 and CASMO-5/SIMULATE-5. The first is presently used for core monitoring and design at the Leibstadt Nuclear Power Plant (KKL). The second represents the most recent generation of the widely applied CASMO/SIMULATE system. For representing the PROTEUS test-zone boundaries, Partial Current Ratios (PCRs) - derived from a 3D MCNPX model of the entire reactor - have been applied to the PRESTO-2 and SIMULATE-5 models in the form of 2- and 5-group diagonal albedo matrices, respectively. The MCNPX results have also served as a reference, high-order transport solution in the calculation/experiment comparisons. It is shown that the performance of the nodal methodologies in predicting the global distribution of the total-fission rate is very satisfactory. Considering the various radial comparisons, the standard deviations of the calculated/experimental (C/E) distributions do not exceed 1.9% for any of the three methodologies - PRESTO-2, SIMULATE-5 and MCNPX. For the three-dimensional comparisons at pellet-level, the corresponding standard deviations are 2.7%, 2.0% and 2.1%, respectively. (authors)

Heritable circadian period length in a wild bird population

NARCIS (Netherlands)

Helm, B.; Visser, M.E.

2010-01-01

Timing is essential, but circadian clocks, which play a crucial role in timekeeping, are almost unaddressed in evolutionary ecology. A key property of circadian clocks is their free-running period length (τ), i.e. the time taken for a full cycle under constant conditions. Under laboratory

Direct Numerical Simulations of a Full Stationary Wind-Turbine Blade

Science.gov (United States)

Qamar, Adnan; Zhang, Wei; Gao, Wei; Samtaney, Ravi

2014-11-01

Direct numerical simulation of flow past a full stationary wind-turbine blade is carried out at Reynolds number, Re = 10,000 placed at 0 and 5 (degree) angle of attack. The study is targeted to create a DNS database for verification of solvers and turbulent models that are utilized in wind-turbine modeling applications. The full blade comprises of a circular cylinder base that is attached to a spanwise varying airfoil cross-section profile (without twist). An overlapping composite grid technique is utilized to perform these DNS computations, which permits block structure in the mapped computational space. Different flow shedding regimes are observed along the blade length. Von-Karman shedding is observed in the cylinder shaft region of the turbine blade. Along the airfoil cross-section of the blade, near body shear layer breakdown is observed. A long tip vortex originates from the blade tip region, which exits the computational plane without being perturbed. Laminar to turbulent flow transition is observed along the blade length. The turbulent fluctuations amplitude decreases along the blade length and the flow remains laminar regime in the vicinity of the blade tip. The Strouhal number is found to decrease monotonously along the blade length. Average lift and drag coefficients are also reported for the cases investigated. Supported by funding under a KAUST OCRF-CRG grant.

Electron bunch length measurement with a wakefield radiation decelerator

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Weiwei Li

2014-03-01

Full Text Available In this paper, we propose a novel method to measure the electron bunch length with a dielectric wakefield radiation (DWR decelerator which is composed of two dielectric-lined waveguides (DLWs and an electron spectrometer. When an electron beam passes through a DLW, the DWR is excited which leads to an energy loss of the electron beam. The energy loss is found to be largely dependent on the electron bunch length and can be easily measured by an electron spectrometer which is essential for a normal accelerator facility. Our study shows that this method has a high resolution and a great simplicity.

The determinants of IPO firm prospectus length in Africa

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Bruce Hearn

2013-04-01

Full Text Available This paper studies the differential impact on IPO firm listing prospectus length from increasing proportions of foreign directors from civil as opposed to common law societies and social elites. Using a unique hand-collected and comprehensive sample of 165 IPO firms from across 18 African countries the evidence suggests that increasing proportions of directors from civil code law countries is associated with shorter prospectuses while the opposite is true for their common law counterparts. Furthermore increasing proportions of directors drawn from elevated social positions in indigenous society is related to increasing prospectus length in North Africa while being insignificant in SSA.

Generation of recombinant pestiviruses using a full genome amplification strategy

DEFF Research Database (Denmark)

Rasmussen, Thomas Bruun; Reimann, Ilona; Uttenthal, Åse

Aim Complete genome amplification of viral RNA provides a new tool for generation of modified pestiviruses. We have recently reported a full genome amplification strategy for direct recovery of infectious pestivirus (Rasmussen et al., 2008). This comprised rescue of BDV strain “Gifhorn” from a full......-length RT-PCR amplicon demonstrating that long RT-PCR can be used for direct generation of an infectious pestivirus. The strategy is not limited to amplification of BDV “Gifhorn”, but can be further utilized for amplification of a diverse selection of pestivirus strains and for the generation of modified...... was reverse transcribed to cDNA at 50C for 90 minutes using SuperScript III reverse transcriptase (Invitrogen). Full-length PCR amplification was performed using primers specific for the extreme 5’- and 3’-ends of the viral genomes. A T7 promoter was incorporated in the 5’-primers for direct in vitro...

Association of Telomere Length with Breast Cancer Prognostic Factors.

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Kaoutar Ennour-Idrissi

Full Text Available Telomere length, a marker of cell aging, seems to be affected by the same factors thought to be associated with breast cancer prognosis.To examine associations of peripheral blood cell-measured telomere length with traditional and potential prognostic factors in breast cancer patients.We conducted a cross-sectional analysis of data collected before surgery from 162 breast cancer patients recruited consecutively between 01/2011 and 05/2012, at a breast cancer reference center. Data on the main lifestyle factors (smoking, alcohol consumption, physical activity were collected using standardized questionnaires. Anthropometric factors were measured. Tumor biological characteristics were extracted from pathology reports. Telomere length was measured using a highly reproducible quantitative PCR method in peripheral white blood cells. Spearman partial rank-order correlations and multivariate general linear models were used to evaluate relationships between telomere length and prognostic factors.Telomere length was positively associated with total physical activity (rs = 0.17, P = 0.033; Ptrend = 0.069, occupational physical activity (rs = 0.15, P = 0.054; Ptrend = 0.054 and transportation-related physical activity (rs = 0.19, P = 0.019; P = 0.005. Among post-menopausal women, telomere length remained positively associated with total physical activity (rs = 0.27, P = 0.016; Ptrend = 0.054 and occupational physical activity (rs = 0.26, P = 0.021; Ptrend = 0.056 and was only associated with transportation-related physical activity among pre-menopausal women (rs = 0.27, P = 0.015; P = 0.004. No association was observed between telomere length and recreational or household activities, other lifestyle factors or traditional prognostic factors.Telomeres are longer in more active breast cancer patients. Since white blood cells are involved in anticancer immune responses, these findings suggest that even regular low-intensity physical activity, such as that

Porosity effects in flame length of the porous burners

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Fatemeh Bahadori

2014-10-01

Full Text Available Furnaces are the devices for providing heat to the industrial systems like boilers, gas turbines and etc. The main challenge of furnaces is emission of huge air pollutants. However, porous burners produce less contaminant compared to others. The quality of the combustion process in the porous burners depends on the length of flame in the porous medium. In this paper, the computational fluid dynamic (CFD is used to investigate the porosity effects on the flame length of the combustion process in porous burner. The simulation results demonstrate that increasing the porosity increases the flame length and the combustion zone extends forward. So, combustion quality increases and production of carbon monoxide decrease. It is possible to conclude that temperature distribution in low porosity burner is lower and more uniform than high porosity one. Therefore, by increasing the porosity of the burner, the production of nitrogen oxides increases. So, using an intermediate porosity in the burner appears to be reasonable.

Measurement of Telomere Length in Colorectal Cancers for Improved Molecular Diagnosis

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Eric Le Balc’h

2017-08-01

Full Text Available All tumors have in common to reactivate a telomere maintenance mechanism to allow for unlimited proliferation. On the other hand, genetic instability found in some tumors can result from the loss of telomeres. Here, we measured telomere length in colorectal cancers (CRCs using TRF (Telomere Restriction Fragment analysis. Telomeric DNA content was also quantified as the ratio of total telomeric (TTAGGG sequences over that of the invariable Alu sequences. In most of the 125 CRCs analyzed, there was a significant diminution in telomere length compared with that in control healthy tissue. Only 34 tumors exhibited no telomere erosion and, in some cases, a slight telomere lengthening. Telomere length did not correlate with age, gender, tumor stage, tumor localization or stage of tumor differentiation. In addition, while telomere length did not correlate with the presence of a mutation in BRAF (V-raf murine sarcoma viral oncogene homolog B, PIK3CA (phosphatidylinositol 3-kinase catalytic subunit, or MSI status, it was significantly associated with the occurrence of a mutation in KRAS. Interestingly, we found that the shorter the telomeres in healthy tissue of a patient, the larger an increase in telomere length in the tumor. Our study points to the existence of two types of CRCs based on telomere length and reveals that telomere length in healthy tissue might influence telomere maintenance mechanisms in the tumor.

Effect of the electrostatic surface potential on the oligomerization of full-length human recombinant prion protein at single-molecule level

Energy Technology Data Exchange (ETDEWEB)

Wang, Bin; Xu, Bingqian, E-mail: bxu@engr.uga.edu [Single Molecule Study Laboratory, College of Engineering and Nanoscale Science, and Engineering Center, University of Georgia, Athens, Georgia 30605 (United States); Lou, Zhichao [Single Molecule Study Laboratory, College of Engineering and Nanoscale Science, and Engineering Center, University of Georgia, Athens, Georgia 30605 (United States); College of Materials Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing 210016 (China); Zhang, Haiqian [College of Materials Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing 210016 (China)

2016-03-21

The electrostatic surface potential (ESP) of prion oligomers has critical influences on the aggregating processes of the prion molecules. The atomic force microscopy (AFM) and structural simulation were combined to investigate the molecular basis of the full-length human recombinant prion oligomerization on mica surfaces. The high resolution non-intrusive AFM images showed that the prion oligomers formed different patterns on mica surfaces at different buffer pH values. The basic binding units for the large oligomers were determined to be prion momoners (Ms), dimers (Ds), and trimers (Ts). The forming of the D and T units happened through the binding of hydrophobic β-sheets of the M units. In contrast, the α-helices of these M, D, and T units were the binding areas for the formation of large oligomers. At pH 4.5, the binding units M, D, and T showed clear polarized ESP distributions on the surface domains, while at pH 7.0, they showed more evenly distributed ESPs. Based on the conformations of oligomers observed from AFM images, the D and T units were more abundantly on mica surface at pH 4.5 because the ESP re-distribution of M units helped to stabilize these larger oligomers. The amino acid side chains involved in the binding interfaces were stabilized by hydrogen bonds and electrostatic interactions. The detailed analysis of the charged side chains at pH 4.5 indicated that the polarized ESPs induced the aggregations among M, D, and T to form larger oligomers. Therefore, the hydrogen bonds and electrostatic interactions worked together to form the stabilized prion oligomers.

Effect of the electrostatic surface potential on the oligomerization of full-length human recombinant prion protein at single-molecule level

International Nuclear Information System (INIS)

Wang, Bin; Xu, Bingqian; Lou, Zhichao; Zhang, Haiqian

2016-01-01

The electrostatic surface potential (ESP) of prion oligomers has critical influences on the aggregating processes of the prion molecules. The atomic force microscopy (AFM) and structural simulation were combined to investigate the molecular basis of the full-length human recombinant prion oligomerization on mica surfaces. The high resolution non-intrusive AFM images showed that the prion oligomers formed different patterns on mica surfaces at different buffer pH values. The basic binding units for the large oligomers were determined to be prion momoners (Ms), dimers (Ds), and trimers (Ts). The forming of the D and T units happened through the binding of hydrophobic β-sheets of the M units. In contrast, the α-helices of these M, D, and T units were the binding areas for the formation of large oligomers. At pH 4.5, the binding units M, D, and T showed clear polarized ESP distributions on the surface domains, while at pH 7.0, they showed more evenly distributed ESPs. Based on the conformations of oligomers observed from AFM images, the D and T units were more abundantly on mica surface at pH 4.5 because the ESP re-distribution of M units helped to stabilize these larger oligomers. The amino acid side chains involved in the binding interfaces were stabilized by hydrogen bonds and electrostatic interactions. The detailed analysis of the charged side chains at pH 4.5 indicated that the polarized ESPs induced the aggregations among M, D, and T to form larger oligomers. Therefore, the hydrogen bonds and electrostatic interactions worked together to form the stabilized prion oligomers.

Effect of the electrostatic surface potential on the oligomerization of full-length human recombinant prion protein at single-molecule level

Science.gov (United States)

Wang, Bin; Lou, Zhichao; Zhang, Haiqian; Xu, Bingqian

2016-03-01

The electrostatic surface potential (ESP) of prion oligomers has critical influences on the aggregating processes of the prion molecules. The atomic force microscopy (AFM) and structural simulation were combined to investigate the molecular basis of the full-length human recombinant prion oligomerization on mica surfaces. The high resolution non-intrusive AFM images showed that the prion oligomers formed different patterns on mica surfaces at different buffer pH values. The basic binding units for the large oligomers were determined to be prion momoners (Ms), dimers (Ds), and trimers (Ts). The forming of the D and T units happened through the binding of hydrophobic β-sheets of the M units. In contrast, the α-helices of these M, D, and T units were the binding areas for the formation of large oligomers. At pH 4.5, the binding units M, D, and T showed clear polarized ESP distributions on the surface domains, while at pH 7.0, they showed more evenly distributed ESPs. Based on the conformations of oligomers observed from AFM images, the D and T units were more abundantly on mica surface at pH 4.5 because the ESP re-distribution of M units helped to stabilize these larger oligomers. The amino acid side chains involved in the binding interfaces were stabilized by hydrogen bonds and electrostatic interactions. The detailed analysis of the charged side chains at pH 4.5 indicated that the polarized ESPs induced the aggregations among M, D, and T to form larger oligomers. Therefore, the hydrogen bonds and electrostatic interactions worked together to form the stabilized prion oligomers.

Word length, set size, and lexical factors: Re-examining what causes the word length effect.

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Guitard, Dominic; Gabel, Andrew J; Saint-Aubin, Jean; Surprenant, Aimée M; Neath, Ian

2018-04-19

The word length effect, better recall of lists of short (fewer syllables) than long (more syllables) words has been termed a benchmark effect of working memory. Despite this, experiments on the word length effect can yield quite different results depending on set size and stimulus properties. Seven experiments are reported that address these 2 issues. Experiment 1 replicated the finding of a preserved word length effect under concurrent articulation for large stimulus sets, which contrasts with the abolition of the word length effect by concurrent articulation for small stimulus sets. Experiment 2, however, demonstrated that when the short and long words are equated on more dimensions, concurrent articulation abolishes the word length effect for large stimulus sets. Experiment 3 shows a standard word length effect when output time is equated, but Experiments 4-6 show no word length effect when short and long words are equated on increasingly more dimensions that previous demonstrations have overlooked. Finally, Experiment 7 compared recall of a small and large neighborhood words that were equated on all the dimensions used in Experiment 6 (except for those directly related to neighborhood size) and a neighborhood size effect was still observed. We conclude that lexical factors, rather than word length per se, are better predictors of when the word length effect will occur. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

THE NETWORK OF CITY PUBLIC TRANSPORT AS THE BASE FOR TRIP LENGTH DISTRIBUTION DETERMINING

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P. Horbachov

2015-07-01

Full Text Available The up-to-date methods of modelling the demand for public transport services require an objective estimation and improvement. Such an improvement can be achieved by taking into account the trip length distribution during trip matrix calculation that requires determining the reasons of regularities occurance in city population trip lengths.

Lengths of Orthologous Prokaryotic Proteins Are Affected by Evolutionary Factors

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Tatiana Tatarinova

2015-01-01

Full Text Available Proteins of the same functional family (for example, kinases may have significantly different lengths. It is an open question whether such variation in length is random or it appears as a response to some unknown evolutionary driving factors. The main purpose of this paper is to demonstrate existence of factors affecting prokaryotic gene lengths. We believe that the ranking of genomes according to lengths of their genes, followed by the calculation of coefficients of association between genome rank and genome property, is a reasonable approach in revealing such evolutionary driving factors. As we demonstrated earlier, our chosen approach, Bubble-sort, combines stability, accuracy, and computational efficiency as compared to other ranking methods. Application of Bubble Sort to the set of 1390 prokaryotic genomes confirmed that genes of Archaeal species are generally shorter than Bacterial ones. We observed that gene lengths are affected by various factors: within each domain, different phyla have preferences for short or long genes; thermophiles tend to have shorter genes than the soil-dwellers; halophiles tend to have longer genes. We also found that species with overrepresentation of cytosines and guanines in the third position of the codon (GC3 content tend to have longer genes than species with low GC3 content.

Oblique-Length Contraction Factor in the Special Theory of Relativity

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Smarandache F.

2013-01-01

Full Text Available In this paper one generalizes the Lorentz Contraction Factor for the case when the lengths are moving at an oblique angle with respect to the motion direction. One shows that the angles of the moving relativistic objects are distorted.

Llama immunization with full-length VAR2CSA generates cross-reactive and inhibitory single-domain antibodies against the DBL1X domain.

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Nunes-Silva, Sofia; Gangnard, Stéphane; Vidal, Marta; Vuchelen, Anneleen; Dechavanne, Sebastien; Chan, Sherwin; Pardon, Els; Steyaert, Jan; Ramboarina, Stephanie; Chêne, Arnaud; Gamain, Benoît

2014-12-09

VAR2CSA stands today as the leading vaccine candidate aiming to protect future pregnant women living in malaria endemic areas against the severe clinical outcomes of pregnancy associated malaria (PAM). The rational design of an efficient VAR2CSA-based vaccine relies on a profound understanding of the molecular interactions associated with P. falciparum infected erythrocyte sequestration in the placenta. Following immunization of a llama with the full-length VAR2CSA recombinant protein, we have expressed and characterized a panel of 19 nanobodies able to recognize the recombinant VAR2CSA as well as the surface of erythrocytes infected with parasites originating from different parts of the world. Domain mapping revealed that a large majority of nanobodies targeted DBL1X whereas a few of them were directed towards DBL4ε, DBL5ε and DBL6ε. One nanobody targeting the DBL1X was able to recognize the native VAR2CSA protein of the three parasite lines tested. Furthermore, four nanobodies targeting DBL1X reproducibly inhibited CSA adhesion of erythrocytes infected with the homologous NF54-CSA parasite strain, providing evidences that DBL1X domain is part or close to the CSA binding site. These nanobodies could serve as useful tools to identify conserved epitopes shared between different variants and to characterize the interactions between VAR2CSA and CSA.

Gap length distributions by PEPR

International Nuclear Information System (INIS)

Warszawer, T.N.

1980-01-01

Conditions guaranteeing exponential gap length distributions are formulated and discussed. Exponential gap length distributions of bubble chamber tracks first obtained on a CRT device are presented. Distributions of resulting average gap lengths and their velocity dependence are discussed. (orig.)

Targeting the Full Length of the Motor End Plate Regions in the Mouse Forelimb Increases the Uptake of Fluoro-Gold into Corresponding Spinal Cord Motor Neurons

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Andrew Paul Tosolini

2013-05-01

Full Text Available Lower motor neuron dysfunction is one of the most debilitating motor conditions. In this regard, transgenic mouse models of various lower motor neuron dysfunctions provide insight into the mechanisms underlying these pathologies and can also aid the development of new therapies. Viral-mediated gene therapy can take advantage of the muscle-motor neuron topographical relationship to shuttle therapeutic genes into specific populations of motor neurons in these mouse models. In this context, motor end plates (MEPs are highly specialised regions on the skeletal musculature that offer direct access to the pre-synaptic nerve terminals, henceforth to the spinal cord motor neurons. The aim of this study was two-folded. First it was to characterise the exact position of the MEP regions for several muscles of the mouse forelimb using acetylcholinesterase histochemistry. This MEP-muscle map was then used to guide a series of intramuscular injections of Fluoro-Gold (FG in order to characterise the distribution of the innervating motor neurons. This analysis revealed that the MEPs are typically organised in an orthogonal fashion across the muscle fibres and extending throughout the full width of each muscle. Furthermore, targeting the full length of the MEP regions gave rise to a seemingly greater number of labelled motor neurons that are organised into columns spanning through more spinal cord segments than previously reported. The present analysis suggests that targeting the full width of the muscles’ MEP regions with FG increases the somatic availability of the tracer. This process ensures a greater uptake of the tracer by the pre-synaptic nerve terminals, hence maximising the labelling in spinal cord motor neurons. This investigation should have positive implications for future studies involving the somatic delivery of therapeutic genes into motor neurons for the treatment of various motor dysfunctions.

Identification of a truncated nucleoprotein in avian metapneumovirus-infected cells encoded by a second AUG, in-frame to the full-length gene

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Alvarez Rene

2005-04-01

Full Text Available Abstract Background Avian metapneumoviruses (aMPV cause an upper respiratory disease with low mortality, but high morbidity primarily in commercial turkeys. There are three types of aMPV (A, B, C of which the C type is found only in the United States. Viruses related to aMPV include human, bovine, ovine, and caprine respiratory syncytial viruses and pneumonia virus of mice, as well as the recently identified human metapneumovirus (hMPV. The aMPV and hMPV have become the type viruses of a new genus within the Metapneumovirus. The aMPV nucleoprotein (N amino acid sequences of serotypes A, B, and C were aligned for comparative analysis. Based on predicted antigenicity of consensus protein sequences, five aMPV-specific N peptides were synthesized for development of peptide-antigens and antisera. Results The presence of two aMPV nucleoprotein (N gene encoded polypeptides was detected in aMPV/C/US/Co and aMPV/A/UK/3b infected Vero cells. Nucleoprotein 1 (N1 encoded from the first open reading frame (ORF was predicted to be 394 amino acids in length for aMPV/C/US/Co and 391 amino acids in length for aMPV/A/UK/3b with approximate molecular weights of 43.3 kilodaltons and 42.7 kilodaltons, respectively. Nucleoprotein 2 (N2 was hypothesized to be encoded by a second downstream ORF in-frame with ORF1 and encoded a protein predicted to contain 328 amino acids for aMPV/C/US/Co or 259 amino acids for aMPV/A/UK/3b with approximate molecular weights of 36 kilodaltons and 28.3 kilodaltons, respectively. Peptide antibodies to the N-terminal and C-terminal portions of the aMPV N protein confirmed presence of these products in both aMPV/C/US/Co- and aMPV/A/UK/3b-infected Vero cells. N1 and N2 for aMPV/C/US/Co ORFs were molecularly cloned and expressed in Vero cells utilizing eukaryotic expression vectors to confirm identity of the aMPV encoded proteins. Conclusion This is the first reported identification of potential, accessory in-frame N2 ORF gene products among

Ultrashort electron bunch length measurement with diffraction radiation deflector

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Dao Xiang

2007-01-01

Full Text Available In this paper, we propose a novel method to measure electron bunch length with a diffraction radiation (DR deflector which is composed of a DR radiator and three beam position monitors (BPMs. When an electron beam passes through a metallic aperture which is tilted by 45 degrees with respect to its trajectory, backward DR that propagates perpendicular to the beam’s trajectory is generated which adds a transverse deflection to the beam as a result of momentum conservation. The deflection is found to be largely dependent on the bunch length and could be easily observed with a downstream BPM. Detailed investigations show that this method has wide applicability, high temporal resolution, and great simplicity.

Lengths and Positions of the Vermiform Appendix among Sudanese Cadavers

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Ehab I. El-Amin

2015-08-01

Full Text Available Background/objective: The anatomy of vermiform appendix displays great variations in length and position between different populations. The reports relating these variations to a specific etiological factor are few. This study aims to describe the positions and lengths of vermiform appendix among Sudanese cadavers. Methods: This descriptive study was carried out in Omdurman Teaching Hospital Morgue and Omdurman Islamic University-Sudan. Sixty Sudanese cadavers (30 male and 30 female, were dissected in the period from June 2013 to June 2014. The positions and the lengths of vermiform appendix were measured in millimeters. The data was analyzed by SPSS version 20. Results: The cadavers’ age ranged between 20 to 80 years according to their medico-legal reports. Retrocaecal position was mainly observed in 60%, pelvic in 35%, post-ileal in 3.3%, and pre-ileal in 1.7%. The lengths of the appendix was found < 69 mm in 23.3%, 70-110 mm in 60%, and > 110 mm in 16.7%, also the study showed insignificant difference between the lengths and ages (p < 0.08, and between males and females (p = 0.23. Age was the influencing factor for the positions of vermiform appendixes (p = 0.04. Conclusion: The study showed that the commonest lengths of the appendix were 70-110 mm while the common position was retrocaecal regardless to age or gender. This data should be considered in surgical removal of the inflamed appendix.

In vivo myograph measurement of muscle contraction at optimal length

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Ahmed Aminul

2007-01-01

Full Text Available Abstract Background Current devices for measuring muscle contraction in vivo have limited accuracy in establishing and re-establishing the optimum muscle length. They are variable in the reproducibility to determine the muscle contraction at this length, and often do not maintain precise conditions during the examination. Consequently, for clinical testing only semi-quantitative methods have been used. Methods We present a newly developed myograph, an accurate measuring device for muscle contraction, consisting of three elements. Firstly, an element for adjusting the axle of the device and the physiological axis of muscle contraction; secondly, an element to accurately position and reposition the extremity of the muscle; and thirdly, an element for the progressive pre-stretching and isometric locking of the target muscle. Thus it is possible to examine individual in vivo muscles in every pre-stretched, specified position, to maintain constant muscle-length conditions, and to accurately re-establish the conditions of the measurement process at later sessions. Results In a sequence of experiments the force of contraction of the muscle at differing stretching lengths were recorded and the forces determined. The optimum muscle length for maximal force of contraction was established. In a following sequence of experiments with smaller graduations around this optimal stretching length an increasingly accurate optimum muscle length for maximal force of contraction was determined. This optimum length was also accurately re-established at later sessions. Conclusion We have introduced a new technical solution for valid, reproducible in vivo force measurements on every possible point of the stretching curve. Thus it should be possible to study the muscle contraction in vivo to the same level of accuracy as is achieved in tests with in vitro organ preparations.

Telomere length and depression

DEFF Research Database (Denmark)

Wium-Andersen, Marie Kim; Ørsted, David Dynnes; Rode, Line

2017-01-01

BACKGROUND: Depression has been cross-sectionally associated with short telomeres as a measure of biological age. However, the direction and nature of the association is currently unclear. AIMS: We examined whether short telomere length is associated with depression cross-sectionally as well...... as prospectively and genetically. METHOD: Telomere length and three polymorphisms, TERT, TERC and OBFC1, were measured in 67 306 individuals aged 20-100 years from the Danish general population and associated with register-based attendance at hospital for depression and purchase of antidepressant medication....... RESULTS: Attendance at hospital for depression was associated with short telomere length cross-sectionally, but not prospectively. Further, purchase of antidepressant medication was not associated with short telomere length cross-sectionally or prospectively. Mean follow-up was 7.6 years (range 0...

The Allometry of Bee Proboscis Length and Its Uses in Ecology.

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Daniel P Cariveau

Full Text Available Allometric relationships among morphological traits underlie important patterns in ecology. These relationships are often phylogenetically shared; thus quantifying allometric relationships may allow for estimating difficult-to-measure traits across species. One such trait, proboscis length in bees, is assumed to be important in structuring bee communities and plant-pollinator networks. However, it is difficult to measure and thus rarely included in ecological analyses. We measured intertegular distance (as a measure of body size and proboscis length (glossa and prementum, both individually and combined of 786 individual bees of 100 species across 5 of the 7 extant bee families (Hymenoptera: Apoidea: Anthophila. Using linear models and model selection, we determined which parameters provided the best estimate of proboscis length. We then used coefficients to estimate the relationship between intertegular distance and proboscis length, while also considering family. Using allometric equations with an estimation for a scaling coefficient between intertegular distance and proboscis length and coefficients for each family, we explain 91% of the variance in species-level means for bee proboscis length among bee species. However, within species, individual-level intertegular distance was a poor predictor of individual proboscis length. To make our findings easy to use, we created an R package that allows estimation of proboscis length for individual bee species by inputting only family and intertegular distance. The R package also calculates foraging distance and body mass based on previously published equations. Thus by considering both taxonomy and intertegular distance we enable accurate estimation of an ecologically and evolutionarily important trait.

Molecular cloning and characterization of the full-length cDNA encoding the tree shrew (tupaia belangeri) CD28

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Huang, Xiaoyan; Yan, Yan; Wang, Sha; Wang, Qinying; Shi, Jian; Shao, Zhanshe; Dai, Jiejie

2017-11-01

CD28 is one of the most important co-stimulatory molecules expressed by naive and primed T cells. The tree shrews (Tupaia belangeri), as an ideal animal model for analyzing mechanism of human diseases receiving extensive attentions, demands essential research tools, in particular in the study of cellular markers and monoclonal antibodies for immunological studies. However, little is known about tree shrew CD28 (tsCD28) until now. In this study, a 663 bp of the full-length CD28 cDNA, encoding a polypeptide of 220 amino acids was cloned from tree shrew spleen lymphocytes. The nucleotide sequence of the tsCD28 showed 85%, 76%, and 75% similarities with human, rat, and mouse, respectively, which showed the affinity relationship between tree shrew and human is much closer than between human and rodents. The open reading frame (ORF) sequence of tsCD28 gene was predicted to be in correspondence with the signal sequence, immunoglobulin variable-like (IgV) domain, transmembrane domain and cytoplasmic tail, respectively.We also analyzed its molecular characteristics with other mammals by using biology software such as Clustal W 2.0 and so forth. Our results showed that tsCD28 contained many features conserved in CD28 genes from other mammals, including conserved signal peptide and glycosylation sites, and several residues responsible for binding to the CD28R, and the tsCD28 amino acid sequence were found a close genetic relationship with human and monkey. The crystal structure and surface charge revealed most regions of tree shrew CD28 molecule surface charges are similar as human. However, compared with human CD28 (hCD28) regions, in some areas, the surface positive charge of tsCD28 was less than hCD28, which may affect antibody binding. The present study is the first report of cloning and characterization of CD28 in tree shrew. This study provides a theoretical basis for the further study the structure and function of tree shrew CD28 and utilize tree shrew as an effective

A STUDY OF CORRELATION OF FOOT LENGTH AND GESTATIONAL MATURITY IN NEONATES

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M. Bhuvaneswari

2018-03-01

Full Text Available BACKGROUND Gestational age estimation at birth can be done by clinical estimation through careful history of LMP, ultrasonic estimation of gestational age, date of first recorded foetal activity “quickening” first felt at approximately 16-18 weeks, Date of first recorded foetal heart sounds. MATERIALS AND METHODS A study sample of 800 live newborns were selected by simple random sampling technique born at GVR hospital and Government General Hospital, Kurnool from April 2015 to May 2016. Data was collected using standard proforma meeting the objectives of the study. a Gestational age assessment was done using modified Bellard’s score and b Foot length was measured using sliding calipers which is having an accuracy of a millimeter. Following instruments are used: 1 Sliding calipers for measuring foot length, 2 Flexible, non-stretchable measuring tape for head circumference, 3 Infantometer for measuring crown heel length, 4 Electronic weighing scale for measuring weight. RESULTS The foot length of preterm neonates ranged from 4.5-7.8 cm with the mean foot length of 6.1571 cm and 6.6964 cm for preterm SGA and AGA, respectively. The foot length of term neonates ranged from 5.4-8.7 cm with a mean foot length of 7.0471 cm, 7.5703 cm, 8.0391 cm for term SGA, AGA, LGA respectively. The foot length for post term neonates ranged from 6.7-8.8 cm, with a mean foot length of 7.5688 cm, 8.0170 cm and 8.2667 cm for post term SGA, AGA and LGA, respectively. This shows that foot length increases as the gestational age increases. CONCLUSION Foot length can be correlated significantly with the gestational age, birth weight, head circumference and crown heel length.

Numerical analysis of finite Debye-length effects in induced-charge electro-osmosis.

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Gregersen, Misha Marie; Andersen, Mathias Baekbo; Soni, Gaurav; Meinhart, Carl; Bruus, Henrik

2009-06-01

For a microchamber filled with a binary electrolyte and containing a flat unbiased center electrode at one wall, we employ three numerical models to study the strength of the resulting induced-charge electro-osmotic (ICEO) flow rolls: (i) a full nonlinear continuum model resolving the double layer, (ii) a linear slip-velocity model not resolving the double layer and without tangential charge transport inside this layer, and (iii) a nonlinear slip-velocity model extending the linear model by including the tangential charge transport inside the double layer. We show that, compared to the full model, the slip-velocity models significantly overestimate the ICEO flow. This provides a partial explanation of the quantitative discrepancy between observed and calculated ICEO velocities reported in the literature. The discrepancy increases significantly for increasing Debye length relative to the electrode size, i.e., for nanofluidic systems. However, even for electrode dimensions in the micrometer range, the discrepancies in velocity due to the finite Debye length can be more than 10% for an electrode of zero height and more than 100% for electrode heights comparable to the Debye length.

Telomere Length and the Cancer-Atherosclerosis Trade-Off.

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Rivka C Stone

2016-07-01

Full Text Available Modern humans, the longest-living terrestrial mammals, display short telomeres and repressed telomerase activity in somatic tissues compared with most short-living small mammals. The dual trait of short telomeres and repressed telomerase might render humans relatively resistant to cancer compared with short-living small mammals. However, the trade-off for cancer resistance is ostensibly increased age-related degenerative diseases, principally in the form of atherosclerosis. In this communication, we discuss (a the genetics of human telomere length, a highly heritable complex trait that is influenced by genetic ancestry, sex, and paternal age at conception, (b how cancer might have played a role in the evolution of telomere biology across mammals, (c evidence that in modern humans telomere length is a determinant (rather than only a biomarker of cancer and atherosclerosis, and (d the potential influence of relatively recent evolutionary forces in fashioning the variation in telomere length across and within populations, and their likely lasting impact on major diseases in humans. Finally, we propose venues for future research on human telomere genetics in the context of its potential role in shaping the modern human lifespan.

Construction and characterisation of a full-length infectious molecular clone from a fast replicating, X4-tropic HIV-1 CRF02.AG primary isolate

International Nuclear Information System (INIS)

Tebit, Denis M.; Zekeng, Leopold; Kaptue, Lazare; Kraeusslich, Hans-Georg; Herchenroeder, Ottmar

2003-01-01

Based on our previous analysis of HIV-1 isolates from Cameroon, we constructed a full-length infectious molecular clone from a primary isolate belonging to the CRF02.AG group of recombinant viruses which dominate the HIV-epidemic in West and Central Africa. The virus derived by transfection of the proviral clone pBD6-15 replicated with similar efficiency compared to its parental isolate and used CXCR4 as coreceptor as well. Furthermore, HIV-1 BD6-15 exhibited similar replication properties and virus yield as the reference B-type HIV-1 strain NL4-3. Sequence analysis revealed open reading frames for all structural and accessory genes apart from vpr. Phylogenetic and bootscanning analyses confirmed that BD6-15 clusters with CRF02.AG recombinant strains from West and Central Africa with similar cross-over points as described for the CRF02.AG prototype strain lbNG. Thus, pBD6-15 represents the first non-subtype B infectious molecular clone of a fast replicating, high producer, X4-tropic primary HIV-1 isolate, which had only been briefly passaged in primary cells

Full-length cellular β-secretase has a trimeric subunit stoichiometry, and its sulfur-rich transmembrane interaction site modulates cytosolic copper compartmentalization.

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Liebsch, Filip; Aurousseau, Mark R P; Bethge, Tobias; McGuire, Hugo; Scolari, Silvia; Herrmann, Andreas; Blunck, Rikard; Bowie, Derek; Multhaup, Gerd

2017-08-11

The β-secretase (BACE1) initiates processing of the amyloid precursor protein (APP) into Aβ peptides, which have been implicated as central players in the pathology of Alzheimer disease. BACE1 has been described as a copper-binding protein and its oligomeric state as being monomeric, dimeric, and/or multimeric, but the native cellular stoichiometry has remained elusive. Here, by using single-molecule fluorescence and in vitro cross-linking experiments with photo-activatable unnatural amino acids, we show that full-length BACE1, independently of its subcellular localization, exists as trimers in human cells. We found that trimerization requires the BACE1 transmembrane sequences (TMSs) and cytoplasmic domains, with residues Ala 463 and Cys 466 buried within the trimer interface of the sulfur-rich core of the TMSs. Our 3D model predicts that the sulfur-rich core of the trimeric BACE1 TMS is accessible to metal ions, but copper ions did not trigger trimerization. The results of functional assays of endogenous BACE1 suggest that it has a role in intracellular copper compartmentalization by transferring cytosolic copper to intracellular compartments, while leaving the overall cellular copper concentration unaltered. Adding to existing physiological models, our results provide novel insight into the atypical interactions between copper and BACE1 and into its non-enzymatic activities. In conclusion, therapeutic Alzheimer disease prevention strategies aimed at decreasing BACE1 protein levels should be regarded with caution, because adverse effects in copper homeostasis may occur. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Biomass estimates of freshwater zooplankton from length-carbon regression equations

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Patrizia COMOLI

2000-02-01

Full Text Available We present length/carbon regression equations of zooplankton species collected from Lake Maggiore (N. Italy during 1992. The results are discussed in terms of the environmental factors, e.g. food availability, predation, controlling biomass production of particle- feeders and predators in the pelagic system of lakes. The marked seasonality in the length-standardized carbon content of Daphnia, and its time-specific trend suggest that from spring onward food availability for Daphnia population may be regarded as a simple decay function. Seasonality does not affect the carbon content/unit length of the two predator Cladocera Leptodora kindtii and Bythotrephes longimanus. Predation is probably the most important regulating factor for the seasonal dynamics of their carbon biomass. The existence of a constant factor to convert the diameter of Conochilus colonies into carbon seems reasonable for an organism whose population comes on quickly and just as quickly disappears.

Full-Length Venom Protein cDNA Sequences from Venom-Derived mRNA: Exploring Compositional Variation and Adaptive Multigene Evolution.

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Modahl, Cassandra M; Mackessy, Stephen P

2016-06-01

Envenomation of humans by snakes is a complex and continuously evolving medical emergency, and treatment is made that much more difficult by the diverse biochemical composition of many venoms. Venomous snakes and their venoms also provide models for the study of molecular evolutionary processes leading to adaptation and genotype-phenotype relationships. To compare venom complexity and protein sequences, venom gland transcriptomes are assembled, which usually requires the sacrifice of snakes for tissue. However, toxin transcripts are also present in venoms, offering the possibility of obtaining cDNA sequences directly from venom. This study provides evidence that unknown full-length venom protein transcripts can be obtained from the venoms of multiple species from all major venomous snake families. These unknown venom protein cDNAs are obtained by the use of primers designed from conserved signal peptide sequences within each venom protein superfamily. This technique was used to assemble a partial venom gland transcriptome for the Middle American Rattlesnake (Crotalus simus tzabcan) by amplifying sequences for phospholipases A2, serine proteases, C-lectins, and metalloproteinases from within venom. Phospholipase A2 sequences were also recovered from the venoms of several rattlesnakes and an elapid snake (Pseudechis porphyriacus), and three-finger toxin sequences were recovered from multiple rear-fanged snake species, demonstrating that the three major clades of advanced snakes (Elapidae, Viperidae, Colubridae) have stable mRNA present in their venoms. These cDNA sequences from venom were then used to explore potential activities derived from protein sequence similarities and evolutionary histories within these large multigene superfamilies. Venom-derived sequences can also be used to aid in characterizing venoms that lack proteomic profiles and identify sequence characteristics indicating specific envenomation profiles. This approach, requiring only venom, provides

Full-length soluble CD147 promotes MMP-2 expression and is a potential serological marker in detection of hepatocellular carcinoma.

Science.gov (United States)

Wu, Jiao; Hao, Zhi-Wei; Zhao, You-Xu; Yang, Xiang-Min; Tang, Hao; Zhang, Xin; Song, Fei; Sun, Xiu-Xuan; Wang, Bin; Nan, Gang; Chen, Zhi-Nan; Bian, Huijie

2014-07-04

As a surface glycoprotein, CD147 is capable of stimulating the production of matrix metalloproteinases (MMPs) from neighboring fibroblasts. The aim of the present study is to explore the role of soluble CD147 on MMPs secretion from hepatocellular carcinoma (HCC) cells, and to investigate the diagnostic value of serum soluble CD147 in the HCC detection. We identified the form of soluble CD147 in cell culture supernate of HCC cells and serum of patients with HCC, and explored the role of soluble CD147 on MMPs secretion. Serum CD147 levels were detected by the enzyme-linked immunosorbent assay, and the value of soluble CD147 as a marker in HCC detection was analyzed. Full length soluble CD147 was presented in the culture medium of HCC cells and serum of patients with HCC. The extracellular domain of soluble CD147 promoted the expression of CD147 and MMP-2 from HCC cells. Knockdown of CD147 markedly diminished the up-regulation of CD147 and MMP-2 which induced by soluble CD147. Soluble CD147 activated ERK, FAK, and PI3K/Akt pathways, leading to the up-regulation of MMP-2. The level of soluble CD147 in serum of patients with HCC was significantly elevated compared with healthy individuals (P CD147 levels were found to be associated with HCC tumor size (P = 0.007) and Child-Pugh grade (P = 0.007). Moreover, soluble CD147 showed a better performance in distinguishing HCC compared with alpha-fetoprotein. The extracellular domain of soluble CD147 enhances the secretion of MMP-2 from HCC cells, requiring the cooperation of membrane CD147 and activation of ERK, FAK, and PI3K/Akt signaling. The measurement of soluble CD147 may offer a useful approach in diagnosis of HCC.

Characterization of partial and near full-length genomes of HIV-1 strains sampled from recently infected individuals in São Paulo, Brazil.

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Sabri Saeed Sanabani

Full Text Available BACKGROUND: Genetic variability is a major feature of human immunodeficiency virus type 1 (HIV-1 and is considered the key factor frustrating efforts to halt the HIV epidemic. A proper understanding of HIV-1 genomic diversity is a fundamental prerequisite for proper epidemiology, genetic diagnosis, and successful drugs and vaccines design. Here, we report on the partial and near full-length genomic (NFLG variability of HIV-1 isolates from a well-characterized cohort of recently infected patients in São Paul, Brazil. METHODOLOGY: HIV-1 proviral DNA was extracted from the peripheral blood mononuclear cells of 113 participants. The NFLG and partial fragments were determined by overlapping nested PCR and direct sequencing. The data were phylogenetically analyzed. RESULTS: Of the 113 samples (90.3% male; median age 31 years; 79.6% homosexual men studied, 77 (68.1% NFLGs and 32 (29.3% partial fragments were successfully subtyped. Of the successfully subtyped sequences, 88 (80.7% were subtype B sequences, 12 (11% BF1 recombinants, 3 (2.8% subtype C sequences, 2 (1.8% BC recombinants and subclade F1 each, 1 (0.9% CRF02 AG, and 1 (0.9% CRF31 BC. Primary drug resistance mutations were observed in 14/101 (13.9% of samples, with 5.9% being resistant to protease inhibitors and nucleoside reverse transcriptase inhibitors (NRTI and 4.9% resistant to non-NRTIs. Predictions of viral tropism were determined for 86 individuals. X4 or X4 dual or mixed-tropic viruses (X4/DM were seen in 26 (30.2% of subjects. The proportion of X4 viruses in homosexuals was detected in 19/69 (27.5%. CONCLUSIONS: Our results confirm the existence of various HIV-1 subtypes circulating in São Paulo, and indicate that subtype B account for the majority of infections. Antiretroviral (ARV drug resistance is relatively common among recently infected patients. The proportion of X4 viruses in homosexuals was significantly higher than the proportion seen in other study populations.

BACHD rats expressing full-length mutant huntingtin exhibit differences in social behavior compared to wild-type littermates.

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Manfré, Giuseppe; Novati, Arianna; Faccini, Ilaria; Rossetti, Andrea C; Bosch, Kari; Molteni, Raffaella; Riva, Marco A; Van der Harst, Johanneke E; Nguyen, Huu Phuc; Homberg, Judith R

2018-01-01

Huntington disease (HD) is a devastating inherited neurodegenerative disorder characterized by progressive motor, cognitive, and psychiatric symptoms without any cure to slow down or stop the progress of the disease. The BACHD rat model for HD carrying the human full-length mutant huntingtin protein (mHTT) with 97 polyQ repeats has been recently established as a promising model which reproduces several HD-like features. While motor and cognitive functions have been characterized in BACHD rats, little is known about their social phenotype. This study focuses especially on social behavior since evidence for social disturbances exists in human patients. Our objective was to compare social behavior in BACHD and wild-type (WT) rats at different ages, using two different measures of sociability. Animals were tested longitudinally at the age of 2, 4 and 8 months in the social interaction test to examine different parameters of sociability. A separate cohort of 7 month old rats was tested in the three chamber social test to measure both sociability and social novelty. Gene expression analyses in 8 months old animals were performed by real time qRT-PCR to evaluate a potential involvement of D1 and D2 dopaminergic receptors and the contribution of Brain-derived neurotrophic factor (BDNF) to the observed behavioral alterations. In the social interaction test, BACHD rats showed age-dependent changes in behaviour when they were-re introduced to their cagemate after a 24 hours-period of individual housing. The time spent on nape attacks increased with aging. Furthermore, a significant higher level of pinning at 2 months of age was shown in the BACHD rats compared to wild-types, followed by a reduction at 4 and 8 months. On the other hand, BACHD rats exhibited a decreased active social behaviour compared to wild-types, reflected by genotype-effects on approaching, following and social nose contact. In the three chamber social test, BACHD rats seemed to show a mild deficit in

BACHD rats expressing full-length mutant huntingtin exhibit differences in social behavior compared to wild-type littermates

Science.gov (United States)

Manfré, Giuseppe; Novati, Arianna; Faccini, Ilaria; Rossetti, Andrea C.; Bosch, Kari; Molteni, Raffaella; Riva, Marco A.; Van der Harst, Johanneke E.; Homberg, Judith R.

2018-01-01

Background Huntington disease (HD) is a devastating inherited neurodegenerative disorder characterized by progressive motor, cognitive, and psychiatric symptoms without any cure to slow down or stop the progress of the disease. The BACHD rat model for HD carrying the human full-length mutant huntingtin protein (mHTT) with 97 polyQ repeats has been recently established as a promising model which reproduces several HD-like features. While motor and cognitive functions have been characterized in BACHD rats, little is known about their social phenotype. Objective This study focuses especially on social behavior since evidence for social disturbances exists in human patients. Our objective was to compare social behavior in BACHD and wild-type (WT) rats at different ages, using two different measures of sociability. Methods Animals were tested longitudinally at the age of 2, 4 and 8 months in the social interaction test to examine different parameters of sociability. A separate cohort of 7 month old rats was tested in the three chamber social test to measure both sociability and social novelty. Gene expression analyses in 8 months old animals were performed by real time qRT-PCR to evaluate a potential involvement of D1 and D2 dopaminergic receptors and the contribution of Brain-derived neurotrophic factor (BDNF) to the observed behavioral alterations. Results In the social interaction test, BACHD rats showed age-dependent changes in behaviour when they were-re introduced to their cagemate after a 24 hours-period of individual housing. The time spent on nape attacks increased with aging. Furthermore, a significant higher level of pinning at 2 months of age was shown in the BACHD rats compared to wild-types, followed by a reduction at 4 and 8 months. On the other hand, BACHD rats exhibited a decreased active social behaviour compared to wild-types, reflected by genotype-effects on approaching, following and social nose contact. In the three chamber social test, BACHD rats

FULL LENGTH RESEARCH ARTICLE Dr Bayo type set

African Journals Online (AJOL)

Dr Ahmed

WORLD JOURNAL VOL 2(NO2) 2007 www.sciecnceworldjournal.com ... 1Department of Pure and Applied Mathematics. Ladoke Akintola ... This paper presents the simplified version of the Freeman-Tukey test statistic for testing hypothesis ...

FULL LENGTH RESEARCH ARTICLE Agashe & Bodhe(2008) SWJ ...

African Journals Online (AJOL)

Dr. Ahmed

Mobile networks allow users to access services while on the move .... chosen from a random Gaussian distribution with mean equal to zero ... da and. )( db when mobile is at a distance d from A is. ),0(. )6....(. )......... () log(. )( )5.( .... This denial of.

Full Length Research Paper LTR-retrotransposons-based molecular ...

African Journals Online (AJOL)

LTR-retrotransposons possess unique properties that make them appropriate for investigating relationships between closely related species and populations. The aim of the current study was to employ Ty1-copia group retrotransposons as molecular markers in cultivated Egyptian cottons, G. barbadense L. Restriction site ...

Full Length Research Paper Plant regeneration of Michelia ...

African Journals Online (AJOL)

Michelia champaca L. is a woody ornamental tree species which has high commercial value to be used as a basic material for perfume, cosmetic, and medicine. The development of an efficient plant regeneration system for M. champaca is essential for the production of Champaca planting material and precondition for ...

Molecular cloning of full-length coding sequences and ...

African Journals Online (AJOL)

DR TONUKARI NYEROVWO

structure and function of collagen, the distribution patterns of these two characteristic residues in α chains of ... the extracellular matrix. Besides ... number in collagen family and the major matrix protein in ..... Dashes represent missing residues.

The impact of precise robotic lesion length measurement on stent length selection: ramifications for stent savings.

Science.gov (United States)

Campbell, Paul T; Kruse, Kevin R; Kroll, Christopher R; Patterson, Janet Y; Esposito, Michele J

2015-09-01

Coronary stent deployment outcomes can be negatively impacted by inaccurate lesion measurement and inappropriate stent length selection (SLS). We compared visual estimate of these parameters to those provided by the CorPath 200® Robotic PCI System. Sixty consecutive patients who underwent coronary stent placement utilizing the CorPath System were evaluated. The treating physician assessed orthogonal images and provided visual estimates of lesion length and SLS. The robotic system was then used for the same measures. SLS was considered to be accurate when visual estimate and robotic measures were in agreement. Visual estimate SLSs were considered to be "short" or "long" if they were below or above the robotic-selected stents, respectively. Only 35% (21/60) of visually estimated lesions resulted in accurate SLS, whereas 33% (20/60) and 32% (19/60) of the visually estimated SLSs were long and short, respectively. In 5 cases (8.3%), 1 less stent was placed based on the robotic lesion measurement being shorter than the visual estimate. Visual estimate assessment of lesion length and SLS is highly variable with 65% of the cases being inaccurately measured when compared to objective measures obtained from the robotic system. The 32% of the cases where lesions were visually estimated to be short represents cases that often require the use of extra stents after the full lesion is not covered by 1 stent [longitudinal geographic miss (LGM)]. Further, these data showed that the use of the robotic system prevented the use of extra stents in 8.3% of the cases. Measurement of lesions with robotic PCI may reduce measurement errors, need for extra stents, and LGM. Copyright © 2015 Elsevier Inc. All rights reserved.

Full-length cloning and phylogenetic analyses of translationally controlled tumour protein and ferritin genes from the Indian white prawn, Fenneropenaeus indicus (H. Milne Edwards)

Digital Repository Service at National Institute of Oceanography (India)

Nayak, S.; Ramaiah, N.; Meena, R.M.; Sreepada, R.A.

-length sequences of these immune-relevant genes, this study highlighted their conserved natures, which perhaps make them important defence-related proteins in the innate immune system of F. indicus....

Peyronie's Reconstruction for Maximum Length and Girth Gain: Geometrical Principles

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Paulo H. Egydio

2008-01-01

Full Text Available Peyronie's disease has been associated with penile shortening and some degree of erectile dysfunction. Surgical reconstruction should be based on giving a functional penis, that is, rectifying the penis with rigidity enough to make the sexual intercourse. The procedure should be discussed preoperatively in terms of length and girth reconstruction in order to improve patient satisfaction. The tunical reconstruction for maximum penile length and girth restoration should be based on the maximum length of the dissected neurovascular bundle possible and the application of geometrical principles to define the precise site and size of tunical incision and grafting procedure. As penile rectification and rigidity are required to achieve complete functional restoration of the penis and 20 to 54% of patients experience associated erectile dysfunction, penile straightening alone may not be enough to provide complete functional restoration. Therefore, phosphodiesterase inhibitors, self-injection, or penile prosthesis may need to be added in some cases.

Kidney Length in Normal Korean Children

International Nuclear Information System (INIS)

Kim, In One; Cheon, Jung Eun; Lee, Young Seok; Lee, Sun Wha; Kim, Ok Hwa; Kim, Ji Hye; Kim, Hong Dae; Sim, Jung Suk

2010-01-01

Renal length offers important information to detect or follow-up various renal diseases. The purpose of this study was to determine the kidney length of normal Korean children in relation to age, height, weight, body surface area (BSA), and body mass index (BMI). Children between 1 month and 15 years of age without urological abnormality were recruited. Children below 3rd percentile and over 97th percentile for height or weight were excluded. Both renal lengths were measured in the prone position three times and then averaged by experienced radiologists. The mean length and standard deviation for each age group was obtained, and regression equation was calculated between renal length and age, weight, height, BSA, and BMI, respectively. Renal length was measured in 550 children. Renal length grows rapidly until 24 month, while the growth rate is reduced thereafter. The regression equation for age is: renal length (mm) = 45.953 + 1.064 x age (month, ≤ 24 months) (R2 = 0.720) or 62.173 + 0.203 x age (months, > 24 months) (R2 = 0.711). The regression equation for height is: renal length (mm) = 24.494 + 0.457 x height (cm) (R2 = 0.894). The regression equation for weight is: renal length (mm) = 38.342 + 2.117 x weight (kg, ≤18 kg) (R2 = 0.852) or 64.498 + 0.646 x weight (kg, > 18 kg) (R2 = 0.651). The regression equation for BSA is: renal length (mm) = 31.622 + 61.363 x BSA (m2, ≤ 0.7) (R2 = 0.857) or 52.717 + 29.959 x BSA (m2, > 0.7) (R2 = 0.715). The regression equation for BMI is: renal length (mm) = 44.474 + 1.163 x BMI (R2 = 0.079). This study provides data on the normal renal length and its association with age, weight, height, BSA and BMI. The results of this study will guide the detection and follow-up of renal diseases in Korean children

Isolation and characterization of full-length cDNA clones coding for cholinesterase from fetal human tissues

International Nuclear Information System (INIS)

Prody, C.A.; Zevin-Sonkin, D.; Gnatt, A.; Goldberg, O.; Soreq, H.

1987-01-01

To study the primary structure and regulation of human cholinesterases, oligodeoxynucleotide probes were prepared according to a consensus peptide sequence present in the active site of both human serum pseudocholinesterase and Torpedo electric organ true acetylcholinesterase. Using these probes, the authors isolated several cDNA clones from λgt10 libraries of fetal brain and liver origins. These include 2.4-kilobase cDNA clones that code for a polypeptide containing a putative signal peptide and the N-terminal, active site, and C-terminal peptides of human BtChoEase, suggesting that they code either for BtChoEase itself or for a very similar but distinct fetal form of cholinesterase. In RNA blots of poly(A) + RNA from the cholinesterase-producing fetal brain and liver, these cDNAs hybridized with a single 2.5-kilobase band. Blot hybridization to human genomic DNA revealed that these fetal BtChoEase cDNA clones hybridize with DNA fragments of the total length of 17.5 kilobases, and signal intensities indicated that these sequences are not present in many copies. Both the cDNA-encoded protein and its nucleotide sequence display striking homology to parallel sequences published for Torpedo AcChoEase. These finding demonstrate extensive homologies between the fetal BtChoEase encoded by these clones and other cholinesterases of various forms and species

Leukocyte Telomere Length and Cognitive Function in Older Adults

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Emily Frith

2018-04-01

Full Text Available We evaluated the specific association between leukocyte telomere length and cognitive function among a national sample of the broader U.S. older adult population. Data from the 1999-2002 National Health and Nutrition Examination Survey (NHANES were used to identify 1,722 adults, between 60-85 years, with complete data on selected study variables. DNA was extracted from whole blood via the LTL assay, which is administered using quantitative polymerase chain reaction to measure telomere length relative to standard reference DNA (T/S ratio. Average telomere length was recorded, with two to three assays performed to control for individual variability. The DSST (Digit Symbol Substitution Test was used to assess participant executive cognitive functioning tasks of pairing and free recall. Individuals were excluded if they had been diagnosed with coronary artery disease, congestive heart failure, heart attack or stroke at the baseline assessment. Leukocyte telomere length was associated with higher cognitive performance, independent of gender, race-ethnicity, physical activity status, body mass index and other covariates. In this sample, there was a strong association between LTL and cognition; for every 1 T/S ratio increase in LTL, there was a corresponding 9.9 unit increase in the DSST (β = 9.9; 95% CI: 5.6-14.2; P [JCBPR 2018; 7(1.000: 14-18

Full-length U-xPu-10Zr (x = 0, 8, 19 wt.%) fast reactor fuel test in FFTF

Energy Technology Data Exchange (ETDEWEB)

Porter, D.L., E-mail: Douglas.Porter@inl.gov [Idaho National Laboratory, P.O. Box 1625, Idaho Falls, ID 83415-6188 (United States); Tsai Hanchung [Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439-4803 (United States)

2012-08-15

The Integral Fast Reactor-1 (IFR-1) experiment performed in the Fast Flux Test Facility (FFTF) was the only U-Pu-10Zr (Pu-0, 8 and 19 wt.%) metallic fast reactor test with commercial-length (91.4-cm active fuel-column length) conducted to date. With few remaining test reactors, there is little opportunity for performing another test with a long active fuel column. The assembly was irradiated to the goal burnup of 10 at.%. The beginning-of-life (BOL) peak cladding temperature of the hottest pin was 608 Degree-Sign C, cooling to 522 Degree-Sign C at end-of-life (EOL). Selected fuel pins were examined non-destructively using neutron radiography, precision axial gamma scanning, and both laser and spiral contact cladding profilometry. Destructive exams included plenum gas pressure, volume, and gas composition determinations on a number of pins followed by optical metallography, electron probe microanalysis (EPMA), and alpha and beta-gamma autoradiography on a single U-19Pu-10Zr pin. The post-irradiation examinations (PIEs) showed very few differences compared to the short-pin (34.3-cm fuel column) testing performed on fuels of similar composition in Experimental Breeder Reactor-II (EBR-II). The fuel column grew axially slightly less than observed in the short pins, but with the same pattern of decreasing growth with increasing Pu content. There was a difference in the fuel-cladding chemical interaction (FCCI) in that the maximum cladding penetration by interdiffusion with fuel/fission products did not occur at the top of the fuel column where the cladding temperature is highest, as observed in EBR-II tests. Instead, the more exaggerated fission-rate profile of the FFTF pins resulted in a peak FCCI at {approx}0.7 X/L axial location along the fuel column. This resulted from a higher production of rare-earth fission products at this location and a higher {Delta}T between fuel center and cladding than at core center, together providing more rare earths at the cladding and

CORRELATION BETWEEN PENIS LENGTH AND ANTHOPOMETRY OF 5 YEAR OLD CHILDREN

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Doddy Kurnia Indrawan

2013-03-01

Full Text Available Short penis still a problem for parents. Penis lenght is associated with  weight and considered abnormal in obese children. The purpose of this study was to find out the correlation between penis length and the anthropometry children aged 5 years. A cross sectional study was conducted, at the Division of Endocrinology, Department of Child Health, Medical Faculty of Udayana University, Sanglah Hospital Denpasar, during October 2010, at TK Sayang Ibu Sanglah Hospital. The calculation of the sample with a correlation coefficient of weight and  height obtained  9 people, taking in consecutive sampling and analyzed  with Pearson’s correlation. The mean body weight was 23.6 (SD 7.70 kg;  mean child height was 108.4 (SD 5.3 cm, and 47.1% were obese. The mean length of the penis was 4.7(SD1.30 cm. The correlation between weight and penis lenght was strong negative (r = -0.876; P = 0.000 and between penis length and height was r = -0.597; P = 0,011.There was a strong negative correlation between body weight and penis length and also negative correlation between penis length and height in kindergarten children. (MEDICINA 2012;43:19-22.

Three-Dimensional Dirac Oscillator with Minimal Length: Novel Phenomena for Quantized Energy

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Malika Betrouche

2013-01-01

Full Text Available We study quantum features of the Dirac oscillator under the condition that the position and the momentum operators obey generalized commutationrelations that lead to the appearance of minimal length with the order of the Planck length, ∆xmin=ℏ3β+β′, where β and β′ are two positive small parameters. Wave functions of the system and the corresponding energy spectrum are derived rigorously. The presence of the minimal length accompanies a quadratic dependence of the energy spectrum on quantum number n, implying the property of hard confinement of the system. It is shown that the infinite degeneracy of energy levels appearing in the usual Dirac oscillator is vanished by the presence of the minimal length so long as β≠0. Not only in the nonrelativistic limit but also in the limit of the standard case (β=β′=0, our results reduce to well known usual ones.

Amplification of Frequency-Modulated Similariton Pulses in Length-Inhomogeneous Active Fibers

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I. O. Zolotovskii

2012-01-01

Full Text Available The possibility of an effective gain of the self-similar frequency-modulated (FM wave packets is studied in the length-inhomogeneous active fibers. The dynamics of parabolic pulses with the constant chirp has been considered. The optimal profile for the change of the group-velocity dispersion corresponding to the optimal similariton pulse amplification has been obtained. It is shown that the use of FM pulses in the active (gain and length-inhomogeneous optical fibers with the normal group-velocity dispersion can provide subpicosecond optical pulse amplification up to the energies higher than 1 nJ.

Flame Length

Data.gov (United States)

Earth Data Analysis Center, University of New Mexico — Flame length was modeled using FlamMap, an interagency fire behavior mapping and analysis program that computes potential fire behavior characteristics. The tool...

Safety of PEGylated recombinant human full-length coagulation factor VIII (BAX 855) in the overall context of PEG and PEG conjugates.

Science.gov (United States)

Stidl, R; Fuchs, S; Bossard, M; Siekmann, J; Turecek, P L; Putz, M

2016-01-01

BAX 855 is a PEGylated human full-length recombinant factor VIII (rFVIII) based on licensed rFVIII (ADVATE). The applied PEGylation technology has been optimized to retain functionality of the FVIII molecule, improve its pharmacokinetic properties and allow less frequent injections while maintaining efficacy. The aim of this study was to confirm that the excellent safety profile of ADVATE remains unchanged after PEGylation. Non-clinical safety studies with BAX 855 and its respective unbound polyethylene glycol (PEG) were conducted in several species. The distribution of a single dose of radiolabelled BAX 855 was further investigated in rats. Publically available safety data on PEG alone and PEGylated biomolecules were summarized and reviewed for specific safety findings attributable to PEG or PEGylated biopharmaceuticals. Safety pharmacology studies in rabbits and macaques and repeated dose toxicity studies in rats and macaques identified no safety issues. Results of a distribution study in rats administered radiolabelled BAX 855 showed that radioactivity was completely excreted; urine was the major elimination route. A 28-day study in rats dosed with the unbound PEG constituent (PEG2ru20KCOOH) of BAX 855 showed no adverse or non-adverse effects. Safety data for PEG and PEG-protein conjugates indicate no safety concerns associated with PEG at clinically relevant dose levels. Although vacuolation of certain cell types has been reported in mammals, no such vacuolation was observed with BAX 855 or with the unbound PEG constituent. Non-clinical safety evaluation of PEG and BAX 855 identified no safety signals; the compound is now in clinical development for the treatment of patients with haemophilia A. © 2015 Baxalta Innovations GmbH. Haemophilia Published by John Wiley & Sons Ltd.

Exact run length distribution of the double sampling x-bar chart with estimated process parameters

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Teoh, W. L.

2016-05-01

Full Text Available Since the run length distribution is generally highly skewed, a significant concern about focusing too much on the average run length (ARL criterion is that we may miss some crucial information about a control chart’s performance. Thus it is important to investigate the entire run length distribution of a control chart for an in-depth understanding before implementing the chart in process monitoring. In this paper, the percentiles of the run length distribution for the double sampling (DS X chart with estimated process parameters are computed. Knowledge of the percentiles of the run length distribution provides a more comprehensive understanding of the expected behaviour of the run length. This additional information includes the early false alarm, the skewness of the run length distribution, and the median run length (MRL. A comparison of the run length distribution between the optimal ARL-based and MRL-based DS X chart with estimated process parameters is presented in this paper. Examples of applications are given to aid practitioners to select the best design scheme of the DS X chart with estimated process parameters, based on their specific purpose.

Inhibitor discovery of full-length New Delhi metallo-β-lactamase-1 (NDM-1.

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Bingzheng Shen

Full Text Available New Delhi metallo-β-lactmase-1 (NDM-1 has recently attracted extensive attention for its biological activities to catalyze the hydrolysis of almost all of β-lactam antibiotics. To study the catalytic property of NDM-1, the steady-kinetic parameters of NDM-1 toward several kinds of β-lactam antibiotics have been detected. It could effectively hydrolyze most β-lactams (k cat/K m ratios between 0.03 to 1.28 µmol⁻¹.s⁻¹, except aztreonam. We also found that thiophene-carboxylic acid derivatives could inhibit NDM-1 and have shown synergistic antibacterial activity in combination with meropenem. Flexible docking and quantum mechanics (QM study revealed electrostatic interactions between the sulfur atom of thiophene-carboxylic acid derivatives and the zinc ion of NDM-1, along with hydrogen bond between inhibitor and His189 of NDM-1. The interaction models proposed here can be used in rational design of NDM-1 inhibitors.

Off-axis full-field swept-source optical coherence tomography using holographic refocusing

Science.gov (United States)

Hillmann, Dierck; Franke, Gesa; Hinkel, Laura; Bonin, Tim; Koch, Peter; Hüttmann, Gereon

2013-03-01

We demonstrate a full-field swept-source OCT using an off-axis geometry of the reference illumination. By using holographic refocusing techniques, a uniform lateral resolution is achieved over the measurement depth of approximately 80 Rayleigh lengths. Compared to a standard on-axis setup, artifacts and autocorrelation signals are suppressed and the measurement depth is doubled by resolving the complex conjugate ambiguity. Holographic refocusing was done efficiently by Fourier-domain resampling as demonstrated before in inverse scattering and holoscopy. It allowed to reconstruct a complete volume with about 10μm resolution over the complete measurement depth of more than 10mm. Off-axis full-field swept-source OCT enables high measurement depths, spanning many Rayleigh lengths with reduced artifacts.

Intraflagellar transport particle size scales inversely with flagellar length: revisiting the balance-point length control model.

Science.gov (United States)

Engel, Benjamin D; Ludington, William B; Marshall, Wallace F

2009-10-05

The assembly and maintenance of eukaryotic flagella are regulated by intraflagellar transport (IFT), the bidirectional traffic of IFT particles (recently renamed IFT trains) within the flagellum. We previously proposed the balance-point length control model, which predicted that the frequency of train transport should decrease as a function of flagellar length, thus modulating the length-dependent flagellar assembly rate. However, this model was challenged by the differential interference contrast microscopy observation that IFT frequency is length independent. Using total internal reflection fluorescence microscopy to quantify protein traffic during the regeneration of Chlamydomonas reinhardtii flagella, we determined that anterograde IFT trains in short flagella are composed of more kinesin-associated protein and IFT27 proteins than trains in long flagella. This length-dependent remodeling of train size is consistent with the kinetics of flagellar regeneration and supports a revised balance-point model of flagellar length control in which the size of anterograde IFT trains tunes the rate of flagellar assembly.

Controlling the optical path length in turbid media using differential path-length spectroscopy: fiber diameter dependence

NARCIS (Netherlands)

Kaspers, O. P.; Sterenborg, H. J. C. M.; Amelink, A.

2008-01-01

We have characterized the path length for the differential path-length spectroscopy (DPS) fiber optic geometry for a wide range of optical properties and for fiber diameters ranging from 200 mu m to 1000 mu m. Phantom measurements show that the path length is nearly constant for scattering

DFAs and PFAs with long shortest synchronizing word length

NARCIS (Netherlands)

De Bondt, M.; Don, H.; Zantema, H.; Charlier, E.; Leroy, J.; Rigo, M.

2017-01-01

It was conjectured by Černý in 1964, that a synchronizing DFA on n states always has a synchronizing word of length at most (n-1)2 and he gave a sequence of DFAs for which this bound is reached. Until now a full analysis of all DFAs reaching this bound was only given for n ≤ 4 and with bounds on the

Short Rayleigh Length Free Electron Lasers

CERN Document Server

Crooker, P P; Armstead, R L; Blau, J

2004-01-01

Conventional free electron laser (FEL) oscillators minimize the optical mode volume around the electron beam in the undulator by making the resonator Rayleigh length about one third of the undulator length. This maximizes gain and beam-mode coupling. In compact configurations of high-power infrared FELs or moderate power UV FELs, the resulting optical intensity can damage the resonator mirrors. To increase the spot size and thereby reduce the optical intensity at the mirrors below the damage threshold, a shorter Rayleigh length can be used, but the FEL interaction is significantly altered. A new FEL interaction is described and analyzed with a Rayleigh length that is only one tenth the undulator length, or less. The effect of mirror vibration and positioning are more critical in the short Rayleigh length design, but we find that they are still within normal design tolerances.

Changes in root lengths of maxillary incisors during orthodontic retention period

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Ravanmehr H

2006-01-01

Full Text Available Background and Aim: External apical root resorption is a common iatrogenic consequence of orthodontic treatment. Much controversy exists in the literature about changes in root lengths at post treatment periods. Although many practitioners believe that resorption becomes stable after active treatment, quantitative data are scarce. The purpose of this study was to determine quantitative changes in root lengths of maxillary incisors during fixed orthodontic post treatment period, and to assess if it is influenced by gender and factors related to active treatment. Materials and Methods: This was a case cross over study, performed on 80 patients (52 females and 28 males aged between 13 and 22 years. At debonding stage and beginning of retention phase of fixed orthodontic treatment, Hawley type retainer was fabricated for maxillary arch. Periapical radiographs of maxillary incisors using standard parallel technique were obtained immediately after debonding, and 3 and 7 months later. Crown and root lengths of maxillary incisors were measured using computer program. Changes in root lengths were calculated considering correction factors. Also associations between some factors and the change in root lengths during post treatment periods were assessed. These included gender, type of treatment plan (non extraction/extraction, technique (standard edgewise/straight-wire edgewise and duration of active treatment (less than 2 years/2 years and more. T-test and 4-way ANOVA were used for statistical analysis with P0.05 as the limit of significance. Results: No significant relation was found between apical root resorption of maxillary central incisors and time elapsed after treatment. Significant relation was observed between apical root resorption of maxillary lateral incisors and the length of post treatment period. No significant relation was found between root length changes of maxillary incisors during post treatment period and gender, type of treatment

Amplitude-independent flaw length determination using differential eddy current

Science.gov (United States)

Shell, E.

2013-01-01

Military engine component manufacturers typically specify the eddy current (EC) inspection requirements as a crack length or depth with the assumption that the cracks in both the test specimens and inspected component are of a similar fixed aspect ratio. However, differential EC response amplitude is dependent on the area of the crack face, not the length or depth. Additionally, due to complex stresses, in-service cracks do not always grow in the assumed manner. It would be advantageous to use more of the information contained in the EC data to better determine the full profile of cracks independent of the fixed aspect ratio amplitude response curve. A specimen with narrow width notches is used to mimic cracks of varying aspect ratios in a controllable manner. The specimen notches have aspect ratios that vary from 1:1 to 10:1. Analysis routines have been developed using the shape of the EC response signals that can determine the length of a surface flaw of common orientations without use of the amplitude of the signal or any supporting traditional probability of detection basis. Combined with the relationship between signal amplitude and area, the depth of the flaw can also be calculated.

Does length of common limb influence remission of diabetes? Short-term results

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Ramraj V Nagendra Gupta

2016-01-01

Full Text Available Background: Despite strict patient selection criteria, diabetes remission is not seen in all patients after gastric bypass. Can length of the common limb influence diabetes remission? Aim: To find if any correlation exists between the length of the common limb and remission of diabetes. Study Design: Prospective study. Materials and Methods: Twenty-five consecutive patients with Type II diabetes mellitus and a fasting C-peptide >1 ng/ml who underwent laparoscopic Roux-en-y gastric bypass were included. All patients had standard limb lengths and length of the common limb was measured in all patients. Patients were followed up and glycated haemoglobin (HbA1c was repeated at 6 months postoperatively. Pre- and postoperative HbA1c were then correlated with the lengths of common limb to look for any relation. Statistical Analysis: Descriptive and inferential statistical analysis, analysis of variance (ANOVA. Results: Of the 25 patients, 15 were females and 10 were males. The mean age was 44.16 years and the mean body mass index (BMI was 43.96 kg/m 2 . Preoperative HbA1c varied from 5.8 to 12.3%. Length of the common limb varied from 210 to 790 cm (mean 470.4 cm. HbA1c at 6 months ranged from 4.8 to 7.7% (mean 5.81%. On comparison of preoperative and 6 months postoperative HbA1c and correlating with the length of common limb, we found that patients with a common limb of length 600 cm length (P = 0.004. Conclusion: A shorter common limb does appear to have better chances of resolution of Type II diabetes mellitus in our study, thus paving the way for further studies.

Length dependent properties of SNS microbridges

International Nuclear Information System (INIS)

Sauvageau, J.E.; Jain, R.K.; Li, K.; Lukens, J.E.; Ono, R.H.

1985-01-01

Using an in-situ, self-aligned deposition scheme, arrays of variable length SNS junctions in the range of 0.05 μm to 1 μm have been fabricated. Arrays of SNS microbridges of lead-copper and niobium-copper fabricated using this technique have been used to study the length dependence, at constant temperature, of the critical current I and bridge resistance R /SUB d/ . For bridges with lengths pounds greater than the normal metal coherence length xi /SUB n/ (T), the dependence of I /SUB c/ on L is consistent with an exponential dependence on the reduced length l=L/xi /SUB n/ (T). For shorter bridges, deviations from this behavior is seen. It was also found that the bridge resistance R /SUB d/ does not vary linearly with the geometric bridge length but appears to approach a finite value as L→O

Razão peso/comprimento: um bom indicador do estado nutricional em recém-nascidos a termo? Weight/length ratio: is it a good index to assess the nutritional status of full-term newborns?

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Taciana D. de A. Braga

2002-01-01

Full Text Available Objetivo: uma avaliação acurada do estado nutricional da criança ao nascer tem importância na identificação precoce de eventos mórbidos relacionados com a aceleração ou desaceleração do crescimento intra-útero. Os índices antropométricos resultantes das razões entre o peso e o comprimento e aqueles que resultam da razão entre o perímetro braquial e o perímetro cefálico podem ser uma alternativa, dentro da antropometria, para esse fim. O objetivo principal deste estudo foi verificar o grau de correlação entre a prega cutânea triciptal e os índices antropométricos - índice ponderal de Rohrer, índice de massa corpórea, razão peso/comprimento, razão perímetro braquial/perímetro cefálico - utilizados como critério de avaliação do estado nutricional de recém-nascidos. Métodos: realizou-se um estudo de corte transversal em 390 recém-nascidos a termo na maternidade do Centro de Atenção à Saúde da Mulher do Instituto Materno-Infantil de Pernambuco, no período de maio a julho de 1999. Os recém-nascidos foram avaliados quanto ao peso, comprimento, perímetros cefálico e braquial e prega cutânea triciptal. Resultados: os resultados mostraram que os índices antropométricos apresentaram correlação significante com a prega cutânea triciptal, tendo sido a razão simples entre o peso e o comprimento aquele que se correlacionou mais fortemente (r = 0,63; p Objective: An accurate assessment of the nutritional status of an infant at birth is very important, since it provides information on early identification of pathological events related to intrauterine growth acceleration or retardation. Anthropometric ratios such as weight/length and mid-arm circumference/head circumference may be used as alternative tools for this purpose. The main objective of this study was to verify the correlation between triceps skinfold thickness with Rohrer Index, Body Mass Index, weight/length ratio, and mid-arm circumference

Bioinorganic Chemistry of Parkinson's Disease: Affinity and Structural Features of Cu(I) Binding to the Full-Length β-Synuclein Protein.

Science.gov (United States)

Miotto, Marco C; Pavese, Mayra D; Quintanar, Liliana; Zweckstetter, Markus; Griesinger, Christian; Fernández, Claudio O

2017-09-05

Alterations in the levels of copper in brain tissue and formation of α-synuclein (αS)-copper complexes might play a key role in the amyloid aggregation of αS and the onset of Parkinson's disease (PD). Recently, we demonstrated that formation of the high-affinity Cu(I) complex with the N-terminally acetylated form of the protein αS substantially increases and stabilizes local conformations with α-helical secondary structure and restricted motility. In this work, we performed a detailed NMR-based structural characterization of the Cu(I) complexes with the full-length acetylated form of its homologue β-synuclein (βS), which is colocalized with αS in vivo and can bind copper ions. Our results show that, similarly to αS, the N-terminal region of βS constitutes the preferential binding interface for Cu(I) ions, encompassing two independent and noninteractive Cu(I) binding sites. According to these results, βS binds the metal ion with higher affinity than αS, in a coordination environment that involves the participation of Met-1, Met-5, and Met-10 residues (site 1). Compared to αS, the shift of His from position 50 to 65 in the N-terminal region of βS does not change the Cu(I) affinity features at that site (site 2). Interestingly, the formation of the high-affinity βS-Cu(I) complex at site 1 in the N-terminus promotes a short α-helix conformation that is restricted to the 1-5 segment of the AcβS sequence, which differs with the substantial increase in α-helix conformations seen for N-terminally acetylated αS upon Cu(I) complexation. Our NMR data demonstrate conclusively that the differences observed in the conformational transitions triggered by Cu(I) binding to AcαS and AcβS find a correlation at the level of their backbone dynamic properties; added to the potential biological implications of these findings, this fact opens new avenues of investigations into the bioinorganic chemistry of PD.

The crystal structure of full-length Sizzled from Xenopus laevis yields insights into Wnt-antagonistic function of secreted Frizzled-related proteins.

Science.gov (United States)

Bu, Qixin; Li, Zhiqiang; Zhang, Junying; Xu, Fei; Liu, Jianmei; Liu, Heli

2017-09-29

The Wnt-signaling pathway is crucial to cell proliferation, differentiation, and migration. The secreted Frizzled-related proteins (sFRPs) represent the largest family of secreted Wnt inhibitors. However, their function in antagonizing Wnt signaling has remained somewhat controversial. Here, we report the crystal structure of Sizzled from Xenopus laevis , the first full-length structure of an sFRP. Tethered by an inter-domain disulfide bond and a linker, the N-terminal cysteine-rich domain (CRD) and the C-terminal netrin-like domain (NTR) of Sizzled are arranged in a tandem fashion, with the NTR domain occluding the groove of CRD for Wnt accessibility. A Dual-Luciferase assay demonstrated that removing the NTR domain and replacing the CRD groove residues His-116 and His-118 with aromatic residues may significantly enhance antagonistic function of Sizzled in inhibiting Wnt3A signaling. Sizzled is a monomer in solution, and Sizzled CRD exhibited different packing in the crystal, suggesting that sFRPs do not have a conserved CRD dimerization mode. Distinct from the canonical NTR domain, the Sizzled NTR adopts a novel α/β folding with two perpendicular helices facing the central mixed β-sheet. The subgroup of human sFRP1/2/5 and Sizzled should have a similar NTR domain that features a highly positively charged region, opposite the NTR-CRD interface, suggesting that the NTR domain in human sFRPs, at least sFRP1/2/5, is unlikely to bind to Wnt but is likely involved in biphasic Wnt signaling modulation. In summary, the Sizzled structure provides the first insights into how the CRD and the NTR domains relate to each other for modulating Wnt-antagonistic function of sFRPs. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Telomere length modulation in human astroglial brain tumors.

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Domenico La Torre

Full Text Available BACKGROUND: Telomeres alteration during carcinogenesis and tumor progression has been described in several cancer types. Telomeres length is stabilized by telomerase (h-TERT and controlled by several proteins that protect telomere integrity, such as the Telomere Repeat-binding Factor (TRF 1 and 2 and the tankyrase-poli-ADP-ribose polymerase (TANKs-PARP complex. OBJECTIVE: To investigate telomere dysfunction in astroglial brain tumors we analyzed telomeres length, telomerase activity and the expression of a panel of genes controlling the length and structure of telomeres in tissue samples obtained in vivo from astroglial brain tumors with different grade of malignancy. MATERIALS AND METHODS: Eight Low Grade Astrocytomas (LGA, 11 Anaplastic Astrocytomas (AA and 11 Glioblastoma Multiforme (GBM samples were analyzed. Three samples of normal brain tissue (NBT were used as controls. Telomeres length was assessed through Southern Blotting. Telomerase activity was evaluated by a telomere repeat amplification protocol (TRAP assay. The expression levels of TRF1, TRF2, h-TERT and TANKs-PARP complex were determined through Immunoblotting and RT-PCR. RESULTS: LGA were featured by an up-regulation of TRF1 and 2 and by shorter telomeres. Conversely, AA and GBM were featured by a down-regulation of TRF1 and 2 and an up-regulation of both telomerase and TANKs-PARP complex. CONCLUSIONS: In human astroglial brain tumours, up-regulation of TRF1 and TRF2 occurs in the early stages of carcinogenesis determining telomeres shortening and genomic instability. In a later stage, up-regulation of PARP-TANKs and telomerase activation may occur together with an ADP-ribosylation of TRF1, causing a reduced ability to bind telomeric DNA, telomeres elongation and tumor malignant progression.

Effective Debye length in closed nanoscopic systems: a competition between two length scales.

Science.gov (United States)

Tessier, Frédéric; Slater, Gary W

2006-02-01

The Poisson-Boltzmann equation (PBE) is widely employed in fields where the thermal motion of free ions is relevant, in particular in situations involving electrolytes in the vicinity of charged surfaces. The applications of this non-linear differential equation usually concern open systems (in osmotic equilibrium with an electrolyte reservoir, a semi-grand canonical ensemble), while solutions for closed systems (where the number of ions is fixed, a canonical ensemble) are either not appropriately distinguished from the former or are dismissed as a numerical calculation exercise. We consider herein the PBE for a confined, symmetric, univalent electrolyte and quantify how, in addition to the Debye length, its solution also depends on a second length scale, which embodies the contribution of ions by the surface (which may be significant in high surface-to-volume ratio micro- or nanofluidic capillaries). We thus establish that there are four distinct regimes for such systems, corresponding to the limits of the two parameters. We also show how the PBE in this case can be formulated in a familiar way by simply replacing the traditional Debye length by an effective Debye length, the value of which is obtained numerically from conservation conditions. But we also show that a simple expression for the value of the effective Debye length, obtained within a crude approximation, remains accurate even as the system size is reduced to nanoscopic dimensions, and well beyond the validity range typically associated with the solution of the PBE.

Sighting optics including an optical element having a first focal length and a second focal length

Science.gov (United States)

Crandall, David Lynn [Idaho Falls, ID

2011-08-01

One embodiment of sighting optics according to the teachings provided herein may include a front sight and a rear sight positioned in spaced-apart relation. The rear sight includes an optical element having a first focal length and a second focal length. The first focal length is selected so that it is about equal to a distance separating the optical element and the front sight and the second focal length is selected so that it is about equal to a target distance. The optical element thus brings into simultaneous focus, for a user, images of the front sight and the target.

Healthy lifestyle and leukocyte telomere length in U.S. women.

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Qi Sun

Full Text Available Whether a healthy lifestyle may be associated with longer telomere length is largely unknown.To examine healthy lifestyle practices, which are primary prevention measures against major age-related chronic diseases, in relation to leukocyte telomere length.Cross-sectional analysis in the Nurses' Health Study (NHS.The population consisted of 5,862 women who participated in multiple prospective case-control studies within the NHS cohort. Z scores of leukocyte telomere length were derived within each case-control study. Based on prior work, we defined low-risk or healthy categories for five major modifiable factors assessed in 1988 or 1990: non-current smoking, maintaining a healthy body weight (body mass index in 18.5-24.9 kg/m(2, engaging in regular moderate or vigorous physical activities (≥150 minutes/week, drinking alcohol in moderation (1 drink/week to <2 drinks/day, and eating a healthy diet (Alternate Healthy Eating Index score in top 50%. We calculated difference (% of the z scores contrasting low-risk groups with reference groups to evaluate the association of interest.Although none of the individual low-risk factors was significantly associated with larger leukocyte telomere length z scores, we observed a significant, positive relationship between the number of low-risk factors and the z scores. In comparison with women who had zero low-risk factors (1.9% of the total population and were, therefore, considered the least healthy group, the leukocyte telomere length z scores were 16.4%, 22.1%, 28.7%, 22.6%, and 31.2% (P for trend = 0.015 higher for women who had 1 to 5 low-risk factors, respectively.Adherence to a healthy lifestyle, defined by major modifiable risk factors, was associated with longer telomere length in leukocytes.

Bruch´s membrane thickness in relationship to axial length.

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Hai Xia Bai

Full Text Available To assess a potential role of Bruch´s membrane (BM in the biomechanics of the eye, we measured its thickness and the density of retinal pigment epithelium (RPE cells in various ocular regions in eyes of varying axial length.Human globes, enucleated because of an ocular tumor or end-stage glaucoma were prepared for histological examination. Using light microscopy, the histological slides were histomorphometrically examined applying a digitized image analysis system.The study included 104 eyes with a mean axial length of 27.9±3.2 mm (range:22.6mm-36.5mm. In eyes without congenital glaucoma, BM was significantly thickest (P<0.001 at the ora serrata, followed by the posterior pole, the midpoint between equator and posterior pole (MBEPP, and finally the equator. BM thickness was not significantly correlated with axial length (ora serrata: P = 0.93; equator:P = 0.31; MBEPP:P = 0.15; posterior pole:P = 0.35. RPE cell density in the pre-equatorial region (P = 0.02; regression coefficient r = -0.24 and in the retro-equatorial region (P = 0.03; r = -0.22 decreased with longer axial length, while RPE cell density at the ora serrata (P = 0.35, the MBEPP (P = 0.06; r = -0.19 and the posterior pole (P = 0.38 was not significantly correlated with axial length. Highly myopic eyes with congenital glaucoma showed a tendency towards lower BM thickness and lower RPE cell density at all locations.BM thickness, in contrast to scleral and choroidal thickness, was independent of axial length in eyes without congenital glaucoma. In association with an axial elongation associated decrease in the RPE cell density in the midperiphery, the findings support the notion of a biomechanical role BM may play in the process of emmetropization/myopization.

length-weight relationhip of freshwater wild fish species

African Journals Online (AJOL)

Dr Naeem

2012-06-21

Jun 21, 2012 ... Length-weight (LWR) and length-length relationships (LLR) were determined for a freshwater catfish ... Key words: Mystus bleekeri, length-weight relationship, length-length relationship, predictive equations. INTRODUCTION. Mystus bleekeri (freshwater catfish Day, 1877), locally ..... fish farmers, Aquacult.

The Effect of Length in Employment Sites’ Web Form Design on User Preferences

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Yu-Ching Wang

2014-06-01

Full Text Available Web form has become a critical component for many Web applications and services. Previous research has investigated into the general design of web form layout without examining the impact of variations in format, length and structure on user experience. This study explores users’ preference and performance over Web forms of different lengths deployed on an employment site. Three types of design of Web forms were developed as the experiment instruments for 48 participants to test and evaluate. Results show that participants’ preferences and satisfaction varied by the length of Web forms. Participants’ preferences were also affected by their previous Internet experiences with job websites. In the end, recommendations for design principles for Web forms used for job sites were presented. [Article content in Chinese

Impact of Lesion Length on Functional Significance in Intermediate Coronary Lesions

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Morteza Safi

2017-07-01

Full Text Available Introduction: The present study aimed at assessing the role of lesion length in predicting Fractional Flow Reserve (FFR value for physiological evaluation of intermediate coronary lesions.Methods: In the current study, 68 patients with 83 coronary lesions were enrolled. All of the patients in this study underwent routine coronary angiography, according to appropriate indications. To evaluate physiologically significant intermediate coronary stenosis (defined between 40% and 70% on visual estimation, the Fractional Flow Reserve (FFR study was performed and the Quantitative Coronary Angiography (QCA data were also assessed for measurement of lesion length. The correlation between QCA data and FFR values was also examined.Results: Eighty-three lesions were evaluated from 68 patients. Stenosis was considered physiologically significant when FFR was lower than 0.75. The FFR was significant in twelve lesions (14.5%. There was a negative correlation between FFR value and lesion length (r = -0.294 and P = 0.013. Moreover, lesion length in physiologically significant FFR group (21.07  ± 6.9 was greater than that of the non-significant FFR group (15.23 ± 6.5 (P value < 0.05. Furthermore, the correlation between QCA data and FFR values was also investigated, yet, there was only a positive correlation between FFR and Minimum Luminal Diameter (MLD values (r = 0.248 and P value = 0.04. The Receiver Operating Characteristic (ROC curve analysis for predicting the significant FFR value demonstrated that a lesion length greater than 17.5 mm was the best cut-off point for prediction of the significant FFR value with acceptable sensitivity and specificity of 83.3% and 68.8%, respectively.Conclusions: There is a negative correlation between lesion length and FFR value in intermediate coronary lesions. In addition, a lesion length greater than 17.5 mm is the best cut- off point for prediction of significant FFR values.

Correcting length-frequency distributions for imperfect detection

Science.gov (United States)

Breton, André R.; Hawkins, John A.; Winkelman, Dana L.

2013-01-01

Sampling gear selects for specific sizes of fish, which may bias length-frequency distributions that are commonly used to assess population size structure, recruitment patterns, growth, and survival. To properly correct for sampling biases caused by gear and other sources, length-frequency distributions need to be corrected for imperfect detection. We describe a method for adjusting length-frequency distributions when capture and recapture probabilities are a function of fish length, temporal variation, and capture history. The method is applied to a study involving the removal of Smallmouth Bass Micropterus dolomieu by boat electrofishing from a 38.6-km reach on the Yampa River, Colorado. Smallmouth Bass longer than 100 mm were marked and released alive from 2005 to 2010 on one or more electrofishing passes and removed on all other passes from the population. Using the Huggins mark–recapture model, we detected a significant effect of fish total length, previous capture history (behavior), year, pass, year×behavior, and year×pass on capture and recapture probabilities. We demonstrate how to partition the Huggins estimate of abundance into length frequencies to correct for these effects. Uncorrected length frequencies of fish removed from Little Yampa Canyon were negatively biased in every year by as much as 88% relative to mark–recapture estimates for the smallest length-class in our analysis (100–110 mm). Bias declined but remained high even for adult length-classes (≥200 mm). The pattern of bias across length-classes was variable across years. The percentage of unadjusted counts that were below the lower 95% confidence interval from our adjusted length-frequency estimates were 95, 89, 84, 78, 81, and 92% from 2005 to 2010, respectively. Length-frequency distributions are widely used in fisheries science and management. Our simple method for correcting length-frequency estimates for imperfect detection could be widely applied when mark–recapture data

Effect of Nanopore Length on the Translocation Process of a Biopolymer: Numerical Study

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Yong Kweon Suh

2013-09-01

Full Text Available In this study, we simulate the electrophoretic motion of a bio-polymer through a synthetic nanopore in the presence of an external bias voltage by considering the hydrodynamic interactions between the polymer and the fluid explicitly. The motion of the polymer is simulated by 3D Langevin dynamics technique by modeling the polymer as a worm-like-chain, while the hydrodynamic interactions are incorporated by the lattice Boltzmann equation. We report the simulation results for three different lengths of the nanopore. The translocation time increases with the pore length even though the electrophoretic force on the polymer is the same irrespective of the pore length. This is attributed to the fact that the translocation velocity of each bead inside the nanopore decreases with the pore length due to the increased fluid resistance force caused by the increase in the straightened portion of the polymer. We confirmed this using a theoretical formula.

The length-weight relationships of three sharks and five batoids in the Lebanese marine waters, eastern Mediterranean

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Myriam Lteif

2016-12-01

Full Text Available Length-weight relationships were estimated for 8 elasmobranchs (3 sharks and 5 batoids in the Lebanese marine waters, eastern Mediterranean. The values of parameter b ranged between 1.752 ± 0.4508 and 3.337 ± 0.2321. Sex influenced the length-weight relationships for the shark Centrophorus uyato (Rafinesque 1801 and the batoid Torpedo marmorata (Risso 1810. These relationships should be used only with the observed length ranges.

MOMENTS OF THE LENGTH OF LINE SEGMENTS IN HOMOGENEOUS PLANAR STIT TESSELLATIONS

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Christoph Thäle

2011-05-01

Full Text Available Homogeneous planar tessellations stable under iteration (STIT tessellations are considered. Using recent results about the joint distribution of direction and length of the typical I-, K- and J-segment we prove closed formulas for the first, second and higher moments of the length of these segments given their direction. This especially leads to themean values and variances of these quantities andmean value relations as well as general moment relationships. Moreover, the relation between these mean values and certain conditional mean values (and also higher moments is discussed. The results are also illustrated for several examples.

Components of genetic variability of ear length of silage maize

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Sečanski Mile

2006-01-01

Full Text Available The objective of this study was to evaluate following parameters of the ear length of silage maize: variability of inbred lines and their diallel hybrids, superior-parent heterosis and genetic components of variability and habitability on the basis of a diallel set. The analysis of genetic variance shows that the additive component (D was lower than the dominant (H1 and H2 genetic variances, while the frequency of dominant genes (u for this trait was greater than the frequency of recessive genes (v Furthermore, this is also confirmed by the dominant to recessive genes ratio in parental inbreeds for the ear length (Kd/Kr> 1, which is greater than unity during both investigation years. The calculated value of the average degree of dominance √H1/D is greater than unity, pointing out to superdominance in inheritance of this trait in both years of investigation, which is also confirmed by the results of Vr/Wr regression analysis of inheritance of the ear length. As a presence of the non-allelic interaction was established it is necessary to study effects of epitasis as it can have a greater significance in certain hybrids. A greater value of dominant than additive variance resulted in high broad-sense habitability for ear length in both investigation years.

Disentangling the effects of alternation rate and maximum run length on judgments of randomness

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Sabine G. Scholl

2011-08-01

Full Text Available Binary sequences are characterized by various features. Two of these characteristics---alternation rate and run length---have repeatedly been shown to influence judgments of randomness. The two characteristics, however, have usually been investigated separately, without controlling for the other feature. Because the two features are correlated but not identical, it seems critical to analyze their unique impact, as well as their interaction, so as to understand more clearly what influences judgments of randomness. To this end, two experiments on the perception of binary sequences orthogonally manipulated alternation rate and maximum run length (i.e., length of the longest run within the sequence. Results show that alternation rate consistently exerts a unique effect on judgments of randomness, but that the effect of alternation rate is contingent on the length of the longest run within the sequence. The effect of maximum run length was found to be small and less consistent. Together, these findings extend prior randomness research by integrating literature from the realms of perception, categorization, and prediction, as well as by showing the unique and joint effects of alternation rate and maximum run length on judgments of randomness.

Experimental investigation of span length for flexural test of fiber reinforced polymer composite laminates

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Akhil Mehndiratta

2018-01-01

Full Text Available Testing and evaluation of mechanical properties for FRP (Fiber Reinforced Polymer composite parts play a significant role to qualify it for the end use. Among the mechanical properties, the flexural strength is significant and vital as it may vary with specimen depth, temperature and the test span length. The flexural strength varies for different materials with varying the test span length hence the current work aims to find an optimum span length to test flexural strength for the specimens made of Glass (7781, EC9756 and Carbon (HTA7, G801 prepreg materials. Experiments are conducted as per the ASTM Standard D 790 for flexural test by varying the span lengths to understand the behavior of the flexural strength and flexural modulus. The experimental data were compared with those obtained from the finite element program software Altair Hyper works 14.0. The results indicate that flexural modulus increases with the span length to a point and then it decreases. Thereby, an optimum span length can be obtained for testing flexural strength, which will be useful to the designers and the composite manufacturers to accomplish better standard testing procedures.

Automatic Determination of Fiber-Length Distribution in Composite Material Using 3D CT Data

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Günther Greiner

2010-01-01

Full Text Available Determining fiber length distribution in fiber reinforced polymer components is a crucial step in quality assurance, since fiber length has a strong influence on overall strength, stiffness, and stability of the material. The approximate fiber length distribution is usually determined early in the development process, as conventional methods require a destruction of the sample component. In this paper, a novel, automatic, and nondestructive approach for the determination of fiber length distribution in fiber reinforced polymers is presented. For this purpose, high-resolution computed tomography is used as imaging method together with subsequent image analysis for evaluation. The image analysis consists of an iterative process where single fibers are detected automatically in each iteration step after having applied image enhancement algorithms. Subsequently, a model-based approach is used together with a priori information in order to guide a fiber tracing and segmentation process. Thereby, the length of the segmented fibers can be calculated and a length distribution can be deduced. The performance and the robustness of the segmentation method is demonstrated by applying it to artificially generated test data and selected real components.

Increased mRNA expression of a laminin-binding protein in human colon carcinoma: Complete sequence of a full-length cDNA encoding the protein

International Nuclear Information System (INIS)

Yow, Hsiukang; Wong, Jau Min; Chen, Hai Shiene; Lee, C.; Steele, G.D. Jr.; Chen, Lanbo

1988-01-01

Reliable markers to distinguish human colon carcinoma from normal colonic epithelium are needed particularly for poorly differentiated tumors where no useful marker is currently available. To search for markers the authors constructed cDNA libraries from human colon carcinoma cell lines and screened for clones that hybridize to a greater degree with mRNAs of colon carcinomas than with their normal counterparts. Here they report one such cDNA clone that hybridizes with a 1.2-kilobase (kb) mRNA, the level of which is ∼9-fold greater in colon carcinoma than in adjacent normal colonic epithelium. Blot hybridization of total RNA from a variety of human colon carcinoma cell lines shows that the level of this 1.2-kb mRNA in poorly differentiated colon carcinomas is as high as or higher than that in well-differentiated carcinomas. Molecular cloning and complete sequencing of cDNA corresponding to the full-length open reading frame of this 1.2-kb mRNA unexpectedly show it to contain all the partial cDNA sequence encoding 135 amino acid residues previously reported for a human laminin receptor. The deduced amino acid sequence suggests that this putative laminin-binding protein from human colon carcinomas consists of 295 amino acid residues with interesting features. There is an unusual C-terminal 70-amino acid segment, which is trypsin-resistant and highly negatively charged

Fragment Length of Circulating Tumor DNA.

Science.gov (United States)

Underhill, Hunter R; Kitzman, Jacob O; Hellwig, Sabine; Welker, Noah C; Daza, Riza; Baker, Daniel N; Gligorich, Keith M; Rostomily, Robert C; Bronner, Mary P; Shendure, Jay

2016-07-01

Malignant tumors shed DNA into the circulation. The transient half-life of circulating tumor DNA (ctDNA) may afford the opportunity to diagnose, monitor recurrence, and evaluate response to therapy solely through a non-invasive blood draw. However, detecting ctDNA against the normally occurring background of cell-free DNA derived from healthy cells has proven challenging, particularly in non-metastatic solid tumors. In this study, distinct differences in fragment length size between ctDNAs and normal cell-free DNA are defined. Human ctDNA in rat plasma derived from human glioblastoma multiforme stem-like cells in the rat brain and human hepatocellular carcinoma in the rat flank were found to have a shorter principal fragment length than the background rat cell-free DNA (134-144 bp vs. 167 bp, respectively). Subsequently, a similar shift in the fragment length of ctDNA in humans with melanoma and lung cancer was identified compared to healthy controls. Comparison of fragment lengths from cell-free DNA between a melanoma patient and healthy controls found that the BRAF V600E mutant allele occurred more commonly at a shorter fragment length than the fragment length of the wild-type allele (132-145 bp vs. 165 bp, respectively). Moreover, size-selecting for shorter cell-free DNA fragment lengths substantially increased the EGFR T790M mutant allele frequency in human lung cancer. These findings provide compelling evidence that experimental or bioinformatic isolation of a specific subset of fragment lengths from cell-free DNA may improve detection of ctDNA.

Characterization of the cloned full-length and a truncated human target of rapamycin: Activity, specificity, and enzyme inhibition as studied by a high capacity assay

International Nuclear Information System (INIS)

Toral-Barza, Lourdes; Zhang Weiguo; Lamison, Craig; LaRocque, James; Gibbons, James; Yu, Ker

2005-01-01

The mammalian target of rapamycin (mTOR/TOR) is implicated in cancer and other human disorders and thus an important target for therapeutic intervention. To study human TOR in vitro, we have produced in large scale both the full-length TOR (289 kDa) and a truncated TOR (132 kDa) from HEK293 cells. Both enzymes demonstrated a robust and specific catalytic activity towards the physiological substrate proteins, p70 S6 ribosomal protein kinase 1 (p70S6K1) and eIF4E binding protein 1 (4EBP1), as measured by phosphor-specific antibodies in Western blotting. We developed a high capacity dissociation-enhanced lanthanide fluorescence immunoassay (DELFIA) for analysis of kinetic parameters. The Michaelis constant (K m ) values of TOR for ATP and the His6-S6K substrate were shown to be 50 and 0.8 μM, respectively. Dose-response and inhibition mechanisms of several known inhibitors, the rapamycin-FKBP12 complex, wortmannin and LY294002, were also studied in DELFIA. Our data indicate that TOR exhibits kinetic features of those shared by traditional serine/threonine kinases and demonstrate the feasibility for TOR enzyme screen in searching for new inhibitors

Does self-regulation of advertisement length improve consumer welfare?

OpenAIRE

Matsubae, Taisuke; Matsushima, Noriaki

2012-01-01

In Japan, TV platforms regulate themselves as to the length of the advertisements they air. Using modified Hotelling models, we investigate whether such self-regulation improves consumer and social welfare or not. When all consumers choose a single TV program (the utility functions of consumers satisfy the standard 'full-coverage' condition), self-regulation always reduces consumer welfare. It improves social welfare only if the advertisement revenue of each platform is not small and the cost...

Austenite Grain Size Estimtion from Chord Lengths of Logarithmic-Normal Distribution

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Adrian H.

2017-12-01

Full Text Available Linear section of grains in polyhedral material microstructure is a system of chords. The mean length of chords is the linear grain size of the microstructure. For the prior austenite grains of low alloy structural steels, the chord length is a random variable of gamma- or logarithmic-normal distribution. The statistical grain size estimation belongs to the quantitative metallographic problems. The so-called point estimation is a well known procedure. The interval estimation (grain size confidence interval for the gamma distribution was given elsewhere, but for the logarithmic-normal distribution is the subject of the present contribution. The statistical analysis is analogous to the one for the gamma distribution.

Neighborhood Disadvantage and Telomere Length: Results from the Fragile Families Study

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Douglas S. Massey

2018-04-01

Full Text Available Telomeres are repetitive nucleotide sequences located at the ends of chromosomes that protect genetic material. We use data from the Fragile Families and Child Wellbeing Study to analyze the relationship between exposure to spatially concentrated disadvantage and telomere length for white and black mothers. We find that neighborhood disadvantage is associated with shorter telomere length for mothers of both races. This finding highlights a potential mechanism through which the unique spatially concentrated disadvantage faced by African Americans contributes to racial health disparities. We conclude that equalizing the health and socioeconomic status of black and white Americans will be very difficult without reducing levels of residential segregation in the United States.

Water Erosion in Different Slope Lengths on Bare Soil

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Bárbara Bagio

Full Text Available ABSTRACT Water erosion degrades the soil and contaminates the environment, and one influential factor on erosion is slope length. The aim of this study was to quantify losses of soil (SL and water (WL in a Humic Cambisol in a field experiment under natural rainfall conditions from July 4, 2014 to June 18, 2015 in individual events of 41 erosive rains in the Southern Plateau of Santa Catarina and to estimate soil losses through the USLE and RUSLE models. The treatments consisted of slope lengths of 11, 22, 33, and 44 m, with an average degree of slope of 8 %, on bare and uncropped soil that had been cultivated with corn prior to the study. At the end of the corn cycle, the stalk residue was removed from the surface, leaving the roots of the crop in the soil. Soil loss by water erosion is related linearly and positively to the increase in slope length in the span between 11 and 44 m. Soil losses were related to water losses and the Erosivity Index (EI30, while water losses were related to rain depth. Soil losses estimated by the USLE and RUSLE model showed lower values than the values observed experimentally in the field, especially the values estimated by the USLE. The values of factor L calculated for slope length of 11, 22, 33, and 44 m for the two versions (USLE and RUSLE of the soil loss prediction model showed satisfactory results in relation to the values of soil losses observed.

Monte Carlo simulation of VHTR particle fuel with chord length sampling

International Nuclear Information System (INIS)

Ji, W.; Martin, W. R.

2007-01-01

The Very High Temperature Gas-Cooled Reactor (VHTR) poses a problem for neutronic analysis due to the double heterogeneity posed by the particle fuel and either the fuel compacts in the case of the prismatic block reactor or the fuel pebbles in the case of the pebble bed reactor. Direct Monte Carlo simulation has been used in recent years to analyze these VHTR configurations but is computationally challenged when space dependent phenomena are considered such as depletion or temperature feedback. As an alternative approach, we have considered chord length sampling to reduce the computational burden of the Monte Carlo simulation. We have improved on an existing method called 'limited chord length sampling' and have used it to analyze stochastic media representative of either pebble bed or prismatic VHTR fuel geometries. Based on the assumption that the PDF had an exponential form, a theoretical chord length distribution is derived and shown to be an excellent model for a wide range of packing fractions. This chord length PDF was then used to analyze a stochastic medium that was constructed using the RSA (Random Sequential Addition) algorithm and the results were compared to a benchmark Monte Carlo simulation of the actual stochastic geometry. The results are promising and suggest that the theoretical chord length PDF can be used instead of a full Monte Carlo random walk simulation in the stochastic medium, saving orders of magnitude in computational time (and memory demand) to perform the simulation. (authors)

Aberrant leukocyte telomere length in Birdshot Uveitis.

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Nadia Vazirpanah

Full Text Available Birdshot Uveitis (BU is an archetypical chronic inflammatory eye disease, with poor visual prognosis, that provides an excellent model for studying chronic inflammation. BU typically affects patients in the fifth decade of life. This suggests that it may represent an age-related chronic inflammatory disease, which has been linked to increased erosion of telomere length of leukocytes.To study this in detail, we exploited a sensitive standardized quantitative real-time polymerase chain reaction to determine the peripheral blood leukocyte telomere length (LTL in 91 genotyped Dutch BU patients and 150 unaffected Dutch controls.Although LTL erosion rates were very similar between BU patients and healthy controls, we observed that BU patients displayed longer LTL, with a median of log (LTL = 4.87 (= 74131 base pair compared to 4.31 (= 20417 base pair in unaffected controls (P<0.0001. The cause underpinning the difference in LTL could not be explained by clinical parameters, immune cell-subtype distribution, nor genetic predisposition based upon the computed weighted genetic risk score of genotyped validated variants in TERC, TERT, NAF1, OBFC1 and RTEL1.These findings suggest that BU is accompanied by significantly longer LTL.

Thermal significance of fission-track length distributions

International Nuclear Information System (INIS)

Crowley, K.D.

1985-01-01

The semi-analytical solution of an equation describing the production and shortening of fission tracks in apatite suggests that certain thermal histories have unique length-distribution 'signatures'. Isothermal-heating histories should be characterized by flattened, length-shortened distributions; step-heating histories should be characterized by bimodal track length distributions; and linear-cooling histories should be characterized by negatively skewed, length-shortened distributions. The model formulated here to investigate track length distributions can be used to constrain the thermal histories of natural samples for which unbiased track length data are available - provided that the geologic history of the system of interest can be used to partially constrain one of the unknowns in the model equations, time or temperature. (author)

Construction and characterization of a full-length infectious cDNA clone of foot-and-mouth disease virus strain O/JPN/2010 isolated in Japan in 2010.

Science.gov (United States)

Nishi, Tatsuya; Onozato, Hiroyuki; Ohashi, Seiichi; Fukai, Katsuhiko; Yamada, Manabu; Morioka, Kazuki; Kanno, Toru

2016-06-01

A full-length infectious cDNA clone of the genome of a foot-and-mouth disease virus isolated from the 2010 epidemic in Japan was constructed and designated pSVL-f02. Transfection of Cos-7 or IBRS-2 cells with this clone allowed the recovery of infectious virus. The recovered virus had the same in vitro characterization as the parental virus with regard to antigenicity in neutralization and indirect immunofluorescence tests, plaque size and one-step growth. Pigs were experimentally infected with the parental virus or the recombinant virus recovered from pSVL-f02 transfected cells. There were no significant differences in clinical signs or antibody responses between the two groups, and virus isolation and viral RNA detection from clinical samples were similar. Virus recovered from transfected cells therefore retained the in vitro characteristics and the in vivo pathogenicity of their parental strain. This cDNA clone should be a valuable tool to analyze determinants of pathogenicity and mechanisms of virus replication, and to develop genetically engineered vaccines against foot-and-mouth disease virus. Copyright © 2016 Elsevier Ltd. All rights reserved.

Axial length elongation in adults with long-standing unilateral traumatic cataract

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Jonel Steffen

2016-09-01

Full Text Available Background: Unilateral eye elongation with resultant axial myopia has been reported to occur secondary to visual deprivation from birth or early childhood. Acquired axial length elongation secondary to visual deprivation in adults has rarely been reported. Aim: To report acquired axial myopia in adults with visual deprivation due to long-standing unilateral traumatic cataract. Methods: Eleven consecutive adult patients who presented for cataract surgery with unilateral, long-standing, mature, traumatic cataracts and an interocular axial length difference of more than 1 mm were studied. Patients with a post-operative best corrected visual acuity (BCVA of < 6/12 were excluded to rule out possible pre-existing anisometropic amblyopia. Results: Of the 11 patients with significant interocular axial length difference, 5 patients were excluded on the basis of possible pre-existing amblyopia. The remaining 6 patients had final BCVA of 6/12 or better. The median length of the cataractous eyes was 2.83 mm longer than the fellow eyes (range 1.12 mm – 3.52 mm. The intraocular lens power required for emmetropia was 6.8 dioptres (range 3.5 dioptres – 11.5 dioptres less in the cataractous eyes. A refractive outcome within 1 dioptre of the target refraction was achieved in all patients. The median delay between ocular trauma and cataract surgery was 20 years (range 8–24 years. Conclusion: Significant unilateral axial length elongation may occur in adults with longstanding traumatic cataracts and visual deprivation. A potential correlation may exist between delay to surgery and degree of axial length difference. This rare phenomenon must be considered when determining intraocular lens power to avoid post-operative refractive surprises.

Urban Aerodynamic Roughness Length Mapping Using Multitemporal SAR Data

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Fengli Zhang

2017-01-01

Full Text Available Aerodynamic roughness is very important to urban meteorological and climate studies. Radar remote sensing is considered to be an effective means for aerodynamic roughness retrieval because radar backscattering is sensitive to the surface roughness and geometric structure of a given target. In this paper, a methodology for aerodynamic roughness length estimation using SAR data in urban areas is introduced. The scale and orientation characteristics of backscattering of various targets in urban areas were firstly extracted and analyzed, which showed great potential of SAR data for urban roughness elements characterization. Then the ground truth aerodynamic roughness was calculated from wind gradient data acquired by the meteorological tower using fitting and iterative method. And then the optimal dimension of the upwind sector for the aerodynamic roughness calculation was determined through a correlation analysis between backscattering extracted from SAR data at various upwind sector areas and the aerodynamic roughness calculated from the meteorological tower data. Finally a quantitative relationship was set up to retrieve the aerodynamic roughness length from SAR data. Experiments based on ALOS PALSAR and COSMO-SkyMed data from 2006 to 2011 prove that the proposed methodology can provide accurate roughness length estimations for the spatial and temporal analysis of urban surface.

Comparison of reconfigurable structures for flexible word-length multiplication

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O. A. Pfänder

2008-05-01

Full Text Available Binary multiplication continues to be one of the essential arithmetic operations in digital circuits. Even though field-programmable gate arrays (FPGAs are becoming more and more powerful these days, the vendors cannot avoid implementing multiplications with high word-lengths using embedded blocks instead of configurable logic. But on the other hand, the circuit's efficiency decreases if the provided word-length of the hard-wired multipliers exceeds the precision requirements of the algorithm mapped into the FPGA. Thus it is beneficial to use multiplier blocks with configurable word-length, optimized for area, speed and power dissipation, e.g. regarding digital signal processing (DSP applications.

In this contribution, we present different approaches and structures for the realization of a multiplication with variable precision and perform an objective comparison. This includes one approach based on a modified Baugh and Wooley algorithm and three structures using Booth's arithmetic operand recoding with different array structures. All modules have the option to compute signed two's complement fix-point numbers either as an individual computing unit or interconnected to a superior array. Therefore, a high throughput at low precision through parallelism, or a high precision through concatenation can be achieved.

Screening length in dusty plasma crystals

International Nuclear Information System (INIS)

Nikolaev, V S; Timofeev, A V

2016-01-01

Particles interaction and value of the screening length in dusty plasma systems are of great interest in dusty plasma area. Three inter-particle potentials (Debye potential, Gurevich potential and interaction potential in the weakly collisional regime) are used to solve equilibrium equations for two dusty particles suspended in a parabolic trap. The inter-particle distance dependence on screening length, trap parameter and particle charge is obtained. The functional form of inter-particle distance dependence on ion temperature is investigated and compared with experimental data at 200-300 K in order to test used potentials applicability to dusty plasma systems at room temperatures. The preference is given to the Yukawa-type potential including effective values of particle charge and screening length. The estimated effective value of the screening length is 5-15 times larger than the Debye length. (paper)

Dynamic Allan Variance Analysis Method with Time-Variant Window Length Based on Fuzzy Control

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Shanshan Gu

2015-01-01

Full Text Available To solve the problem that dynamic Allan variance (DAVAR with fixed length of window cannot meet the identification accuracy requirement of fiber optic gyro (FOG signal over all time domains, a dynamic Allan variance analysis method with time-variant window length based on fuzzy control is proposed. According to the characteristic of FOG signal, a fuzzy controller with the inputs of the first and second derivatives of FOG signal is designed to estimate the window length of the DAVAR. Then the Allan variances of the signals during the time-variant window are simulated to obtain the DAVAR of the FOG signal to describe the dynamic characteristic of the time-varying FOG signal. Additionally, a performance evaluation index of the algorithm based on radar chart is proposed. Experiment results show that, compared with different fixed window lengths DAVAR methods, the change of FOG signal with time can be identified effectively and the evaluation index of performance can be enhanced by 30% at least by the DAVAR method with time-variant window length based on fuzzy control.

Relationships between total length and otolith size of bluefish Pomatomus saltatrix (Linnaeus, 1766 in the Marmara Sea of Turkey

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Habib Bal

2018-01-01

Full Text Available In the present study, bluefish, Pomatomus saltatrix, was monthly collected from commercial fishing boats operating in the Marmara Sea between January and December 2014. The relationship between total length and otolith size of 346 bluefish samples were examined. Total lengths of females, males and unidentified samples were ranged from between 13.2-37.0, 12.3-34.8 and 13.0-31.6 cm, respectively. Otolith lengths were between 3.82-12.60 mm and otolith width were between 1.59-4.34 mm for all samples. It was found that there is a strong correlations between otolith length-total length (r2 =0.88 and otolith width-total length (r2 0.81.

Investigation of entrance length in circular and noncircular conduits by computational fluid dynamics simulation

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Pimpun Tongpun

2014-08-01

Full Text Available This study estimated entrance length of circular and noncircular conduits, including circle, triangle, square and hexagon cross-sectional conduit, by using computational fluid dynamics (CFD. For simulation condition, the length of noncircular conduit was 10 m and the hydraulic diameter was 0.2 m. The laminar flow with Reynolds number of 500 and turbulent flow with Reynolds number of 50,000 were applied to investigate water flow in conduits. The governing equations were solved iteratively by using ANSYS FLUENT 14.0. For turbulent flow simulation, standard k-epsilon and RNG k-epsilon model were employed to simulate turbulence. The preliminary results were validated by comparison with theoretical data. At first, grid independency was evaluated to optimize the model. Norm* was employed to investigate the entrance length, which is related to velocity. The simulated results revealed that the entrance length for laminar flow was longer than turbulent flow.

Sex identification and reconstruction of length of humerus from its fragments: An Egyptian study

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Dalia Mohamed Ali

2016-06-01

Full Text Available The aim of this study was to calculate the total length of the humerus and identify the sex from its fragments in Egyptians. One hundred and fifty dry adult right humeri (75 male and 75 female were studied. The humeri were divided into seven fragments according to specific anatomical landmarks. Data obtained was subjected to descriptive statistical analysis. The longest fragmentary portion revealed a good result with closest proximity to the total length of humerus. All fragments showed significant sexual differences (P < 0.001 between males and females except H2. Total length of humerus revealed the highest percentage of accuracy (93.3% followed by H4 (86.7% and H7 (83.3% for sex identification. Finally, from measurements of different humeral fragments in Egyptian population; the length of the humerus can be estimated and the sex can be identified.

Effect of marital distance on birth weight and length of offspring

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Kozieł Sławomir

2017-09-01

Full Text Available Marital distance (MD, the geographical distance between birthplaces of spouses, is considered an agent favouring occurrence of heterosis and can be used as a measure of its level. Heterosis itself is a phenomenon of hybrid vigour and seems to be an important factor regulating human growth and development. The main aim of the study is to examine potential effects of MD on birth weight and length of offspring, controlling for socioeconomic status (SES, mother’s age and birth order. Birth weight (2562 boys and 2572 girls and length (2526 boys, 2542 girls of children born in Ostrowiec Swietokrzyski (Poland in 1980, 1983, 1985 and 1988 were recorded during cross-sectional surveys carried out between 1994-1999. Data regarding the socio-demographic variables of families were provided by the parents. Analysis of covariance showed that MD significantly affected both birth weight and length, allowing for sex, birth order, mother’s age and SES of family. For both sexes, a greater marital distance was associated with a higher birth weight and a longer birth length. Our results support the hypothesis that a greater geographical distance between the birth places of parents may contribute to the heterosis effects in offspring. Better birth outcomes may be one of the manifestations of these effects.

Structure-guided investigation of lipopolysaccharide O-antigen chain length regulators reveals regions critical for modal length control.

Science.gov (United States)

Kalynych, Sergei; Ruan, Xiang; Valvano, Miguel A; Cygler, Miroslaw

2011-08-01

The O-antigen component of the lipopolysaccharide (LPS) represents a population of polysaccharide molecules with nonrandom (modal) chain length distribution. The number of the repeat O units in each individual O-antigen polymer depends on the Wzz chain length regulator, an inner membrane protein belonging to the polysaccharide copolymerase (PCP) family. Different Wzz proteins confer vastly different ranges of modal lengths (4 to >100 repeat units), despite having remarkably conserved structural folds. The molecular mechanism responsible for the selective preference for a certain number of O units is unknown. Guided by the three-dimensional structures of PCPs, we constructed a panel of chimeric molecules containing parts of two closely related Wzz proteins from Salmonella enterica and Shigella flexneri which confer different O-antigen chain length distributions. Analysis of the O-antigen length distribution imparted by each chimera revealed the region spanning amino acids 67 to 95 (region 67 to 95), region 200 to 255, and region 269 to 274 as primarily affecting the length distribution. We also showed that there is no synergy between these regions. In particular, region 269 to 274 also influenced chain length distribution mediated by two distantly related PCPs, WzzB and FepE. Furthermore, from the 3 regions uncovered in this study, region 269 to 274 appeared to be critical for the stability of the oligomeric form of Wzz, as determined by cross-linking experiments. Together, our data suggest that chain length determination depends on regions that likely contribute to stabilize a supramolecular complex.

Slow oscillation amplitudes and up-state lengths relate to memory improvement.

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Dominik P J Heib

Full Text Available There is growing evidence of the active involvement of sleep in memory consolidation. Besides hippocampal sharp wave-ripple complexes and sleep spindles, slow oscillations appear to play a key role in the process of sleep-associated memory consolidation. Furthermore, slow oscillation amplitude and spectral power increase during the night after learning declarative and procedural memory tasks. However, it is unresolved whether learning-induced changes specifically alter characteristics of individual slow oscillations, such as the slow oscillation up-state length and amplitude, which are believed to be important for neuronal replay. 24 subjects (12 men aged between 20 and 30 years participated in a randomized, within-subject, multicenter study. Subjects slept on three occasions for a whole night in the sleep laboratory with full polysomnography. Whereas the first night only served for adaptation purposes, the two remaining nights were preceded by a declarative word-pair task or by a non-learning control task. Slow oscillations were detected in non-rapid eye movement sleep over electrode Fz. Results indicate positive correlations between the length of the up-state as well as the amplitude of both slow oscillation phases and changes in memory performance from pre to post sleep. We speculate that the prolonged slow oscillation up-state length might extend the timeframe for the transfer of initial hippocampal to long-term cortical memory representations, whereas the increase in slow oscillation amplitudes possibly reflects changes in the net synaptic strength of cortical networks.

Diet, nutrition and telomere length.

Science.gov (United States)

Paul, Ligi

2011-10-01

The ends of human chromosomes are protected by DNA-protein complexes termed telomeres, which prevent the chromosomes from fusing with each other and from being recognized as a double-strand break by DNA repair proteins. Due to the incomplete replication of linear chromosomes by DNA polymerase, telomeric DNA shortens with repeated cell divisions until the telomeres reach a critical length, at which point the cells enter senescence. Telomere length is an indicator of biological aging, and dysfunction of telomeres is linked to age-related pathologies like cardiovascular disease, Parkinson disease, Alzheimer disease and cancer. Telomere length has been shown to be positively associated with nutritional status in human and animal studies. Various nutrients influence telomere length potentially through mechanisms that reflect their role in cellular functions including inflammation, oxidative stress, DNA integrity, DNA methylation and activity of telomerase, the enzyme that adds the telomeric repeats to the ends of the newly synthesized DNA. Copyright © 2011 Elsevier Inc. All rights reserved.

Extended fuel cycle length

International Nuclear Information System (INIS)

Bruyere, M.; Vallee, A.; Collette, C.

1986-09-01

Extended fuel cycle length and burnup are currently offered by Framatome and Fragema in order to satisfy the needs of the utilities in terms of fuel cycle cost and of overall systems cost optimization. We intend to point out the consequences of an increased fuel cycle length and burnup on reactor safety, in order to determine whether the bounding safety analyses presented in the Safety Analysis Report are applicable and to evaluate the effect on plant licensing. This paper presents the results of this examination. The first part indicates the consequences of increased fuel cycle length and burnup on the nuclear data used in the bounding accident analyses. In the second part of this paper, the required safety reanalyses are presented and the impact on the safety margins of different fuel management strategies is examined. In addition, systems modifications which can be required are indicated

Q-FISH measurement of hepatocyte telomere lengths in donor liver and graft after pediatric living-donor liver transplantation: donor age affects telomere length sustainability.

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Youichi Kawano

Full Text Available Along with the increasing need for living-donor liver transplantation (LDLT, the issue of organ shortage has become a serious problem. Therefore, the use of organs from elderly donors has been increasing. While the short-term results of LDLT have greatly improved, problems affecting the long-term outcome of transplant patients remain unsolved. Furthermore, since contradictory data have been reported with regard to the relationship between donor age and LT/LDLT outcome, the question of whether the use of elderly donors influences the long-term outcome of a graft after LT/LDLT remains unsettled. To address whether hepatocyte telomere length reflects the outcome of LDLT, we analyzed the telomere lengths of hepatocytes in informative biopsy samples from 12 paired donors and recipients (grafts of pediatric LDLT more than 5 years after adult-to-child LDLT because of primary biliary atresia, using quantitative fluorescence in situ hybridization (Q-FISH. The telomere lengths in the paired samples showed a robust relationship between the donor and grafted hepatocytes (r = 0.765, p = 0.0038, demonstrating the feasibility of our Q-FISH method for cell-specific evaluation. While 8 pairs showed no significant difference between the telomere lengths for the donor and the recipient, the other 4 pairs showed significantly shorter telomeres in the recipient than in the donor. Multiple regression analysis revealed that the donors in the latter group were older than those in the former (p = 0.001. Despite the small number of subjects, this pilot study indicates that donor age is a crucial factor affecting telomere length sustainability in hepatocytes after pediatric LDLT, and that the telomeres in grafted livers may be elongated somewhat longer when the grafts are immunologically well controlled.

In Vitro Comparative Study of the Working Length Determination with Radiovisiography and Conventional Radiography in Dilacerated Canals

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Ali Bagherpour

2015-06-01

Full Text Available Introduction: The aim of this study was to compare digital and conventional radiography in determining the working length of dilacerated canals.Methods: Thirty nine human extracted single-rooted teeth with root curvature more than 35 degrees were included in this study. After access preparation, a file was inserted into the canal and advanced until the file tip was visualized at the foramen. With measurement of the file length using a millimeter ruler, true canal length was determined for each canal. Then, teeth were mounted in acrylic blocks and canal length was estimated by using on-screen digital radiography with both 3- and 6-clicks measurement and from conventional radiography by conforming a preserved file on the image of the root canal.Results: There were no significant differences in measurement accuracy between the true canal length and conventional radiographic length, but there were significant difference between both digital radiographic techniques with true canal length. There was no significant correlation between root curvature and canal length estimation error of studied methods.Conclusion: In dilacerated canals, the accuracy of determination of working length by using conventional radiography is higher than digital radiography

Generation of recombinant pestiviruses using a full-genome amplification strategy

DEFF Research Database (Denmark)

Rasmussen, Thomas Bruun; Reimann, I.; Uttenthal, Åse

2010-01-01

-Gifhorn genome was generated by long RTPCR and then RNA transcripts derived from this amplicon were used to rescue infectious virus. Here, we have now used this full-genome amplification strategy for efficient and robust amplification of three additional pestivirus strains: the vaccine strain C and the virulent...... Paderborn strain of Classical swine fever virus plus the CP7 strain of Bovine viral diarrhoea virus. The amplicons were cloned directly into a stable single-copy bacterial artificial chromosome generating full-length pestivirus DNAs from which infectious RNA transcripts could be also derived....

Isthmus Dependent Atrial Flutter Cycle Length Correlates with Right Atrial Cross-Sectional Area

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Kousik Krishnan

2009-05-01

Full Text Available Background: Right atrial flutter cycle length can prolong in the presence of antiarrhythmic drug therapy. We hypothesized that the cycle length of right atrial isthmus dependent flutter would correlate with right atrial cross-sectional area measurements. Methods: 60 patients who underwent ablation for electrophysiologically proven isthmus dependent right atrial flutter, who were not on Class I or Class III antiarrhythmic drugs and had recent 2-dimensional echocardiographic data comprised the study group. Right atrial length and width were measured in the apical four chamber view. Cross-sectional area was estimated by multiplying the length and width. 35 patients had an atrial flutter rate ≥250 bpm (Normal Flutter Group and 25 patients had an atrial flutter rate < 250 bpm (Slow Flutter Group. Results: Mean atrial flutter rate was 283 bpm in the normal flutter group and 227 bpm in the slow flutter group. Mean atrial flutter cycle length was 213 ms in the Normal Flutter Group and 265 ms in the Slow Flutter Group (p<0.0001. Mean right atrial cross sectional area was 1845 mm2 in the Normal Flutter group and 2378 mm2 in the Slow Flutter Group, (p< 0.0001. Using linear regression, CSA was a significant predictor of cycle length (β =0.014 p = 0.0045. For every 1 mm2 increase in cross-sectional area, cycle length is 0.014 ms longer.Conclusion: In the absence of antiarrhythmic medications, right atrial cross sectional area enlargement correlates with atrial flutter cycle length. These findings provide further evidence that historical rate-related definitions of typical isthmus dependent right atrial are not mechanistically valid.

Multiple Word-Length High-Level Synthesis

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Coussy Philippe

2008-01-01

Full Text Available Abstract Digital signal processing (DSP applications are nowadays widely used and their complexity is ever growing. The design of dedicated hardware accelerators is thus still needed in system-on-chip and embedded systems. Realistic hardware implementation requires first to convert the floating-point data of the initial specification into arbitrary length data (finite-precision while keeping an acceptable computation accuracy. Next, an optimized hardware architecture has to be designed. Considering uniform bit-width specification allows to use traditional automated design flow. However, it leads to oversized design. On the other hand, considering non uniform bit-width specification allows to get a smaller circuit but requires complex design tasks. In this paper, we propose an approach that inputs a C/C++ specification. The design flow, based on high-level synthesis (HLS techniques, automatically generates a potentially pipeline RTL architecture described in VHDL. Both bitaccurate integer and fixed-point data types can be used in the input specification. The generated architecture uses components (operator, register, etc. that have different widths. The design constraints are the clock period and the throughput of the application. The proposed approach considers data word-length information in all the synthesis steps by using dedicated algorithms. We show in this paper the effectiveness of the proposed approach through several design experiments in the DSP domain.

Multiple Word-Length High-Level Synthesis

Directory of Open Access Journals (Sweden)

Dominique Heller

2008-09-01

Full Text Available Digital signal processing (DSP applications are nowadays widely used and their complexity is ever growing. The design of dedicated hardware accelerators is thus still needed in system-on-chip and embedded systems. Realistic hardware implementation requires first to convert the floating-point data of the initial specification into arbitrary length data (finite-precision while keeping an acceptable computation accuracy. Next, an optimized hardware architecture has to be designed. Considering uniform bit-width specification allows to use traditional automated design flow. However, it leads to oversized design. On the other hand, considering non uniform bit-width specification allows to get a smaller circuit but requires complex design tasks. In this paper, we propose an approach that inputs a C/C++ specification. The design flow, based on high-level synthesis (HLS techniques, automatically generates a potentially pipeline RTL architecture described in VHDL. Both bitaccurate integer and fixed-point data types can be used in the input specification. The generated architecture uses components (operator, register, etc. that have different widths. The design constraints are the clock period and the throughput of the application. The proposed approach considers data word-length information in all the synthesis steps by using dedicated algorithms. We show in this paper the effectiveness of the proposed approach through several design experiments in the DSP domain.

Length and time scales of atmospheric moisture recycling

Directory of Open Access Journals (Sweden)

R. J. van der Ent

2011-03-01

Full Text Available It is difficult to quantify the degree to which terrestrial evaporation supports the occurrence of precipitation within a certain study region (i.e. regional moisture recycling due to the scale- and shape-dependence of regional moisture recycling ratios. In this paper we present a novel approach to quantify the spatial and temporal scale of moisture recycling, independent of the size and shape of the region under study. In contrast to previous studies, which essentially used curve fitting, the scaling laws presented by us follow directly from the process equation. thus allowing a fair comparison between regions and seasons. The calculation is based on ERA-Interim reanalysis data for the period 1999 to 2008. It is shown that in the tropics or in mountainous terrain the length scale of recycling can be as low as 500 to 2000 km. In temperate climates the length scale is typically between 3000 to 5000 km whereas it amounts to more than 7000 km in desert areas. The time scale of recycling ranges from 3 to 20 days, with the exception of deserts, where it is much longer. The most distinct seasonal differences can be observed over the Northern Hemisphere: in winter, moisture recycling is insignificant, whereas in summer it plays a major role in the climate. The length and time scales of atmospheric moisture recycling can be useful metrics to quantify local climatic effects of land use change.

Influence of carbon nanotube length on toxicity to zebrafish embryos

Directory of Open Access Journals (Sweden)

Cheng J

2012-07-01

Full Text Available Jinping Cheng,1,2 Shuk Han Cheng11Department of Biology and Chemistry, City University of Hong Kong, Hong Kong; 2State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, ChinaAbstract: There is currently a large difference of opinion in nanotoxicology studies of nanomaterials. There is concern about why some studies have indicated that there is strong toxicity, while others have not. In this study, the length of carbon nanotubes greatly affected their toxicity in zebrafish embryos. Multiwalled carbon nanotubes (MWCNTs were sonicated in a nitric acid solution for 24 hours and 48 hours. The modified MWCNTs were tested in early developing zebrafish embryo. MWCNTs prepared with the longer sonication time resulted in severe developmental toxicity; however, the shorter sonication time did not induce any obvious toxicity in the tested developing zebrafish embryos. The cellular and molecular changes of the affected zebrafish embryos were studied and the observed phenotypes scored. This study suggests that length plays an important role in the in vivo toxicity of functionalized CNTs. This study will help in furthering the understanding on current differences in toxicity studies of nanomaterials.Keywords: length, carbon nanotubes, sonication, developmental toxicity, zebrafish

Pulse length of ultracold electron bunches extracted from a laser cooled gas

Directory of Open Access Journals (Sweden)

J. G. H. Franssen

2017-07-01

Full Text Available We present measurements of the pulse length of ultracold electron bunches generated by near-threshold two-photon photoionization of a laser-cooled gas. The pulse length has been measured using a resonant 3 GHz deflecting cavity in TM110 mode. We have measured the pulse length in three ionization regimes. The first is direct two-photon photoionization using only a 480 nm femtosecond laser pulse, which results in short (∼15 ps but hot (∼104 K electron bunches. The second regime is just-above-threshold femtosecond photoionization employing the combination of a continuous-wave 780 nm excitation laser and a tunable 480 nm femtosecond ionization laser which results in both ultracold (∼10 K and ultrafast (∼25 ps electron bunches. These pulses typically contain ∼103 electrons and have a root-mean-square normalized transverse beam emittance of 1.5 ± 0.1 nm rad. The measured pulse lengths are limited by the energy spread associated with the longitudinal size of the ionization volume, as expected. The third regime is just-below-threshold ionization which produces Rydberg states which slowly ionize on microsecond time scales.

Word-Length Correlations and Memory in Large Texts: A Visibility Network Analysis

Directory of Open Access Journals (Sweden)

Lev Guzmán-Vargas

2015-11-01

Full Text Available We study the correlation properties of word lengths in large texts from 30 ebooks in the English language from the Gutenberg Project (www.gutenberg.org using the natural visibility graph method (NVG. NVG converts a time series into a graph and then analyzes its graph properties. First, the original sequence of words is transformed into a sequence of values containing the length of each word, and then, it is integrated. Next, we apply the NVG to the integrated word-length series and construct the network. We show that the degree distribution of that network follows a power law, P ( k ∼ k - γ , with two regimes, which are characterized by the exponents γ s ≈ 1 . 7 (at short degree scales and γ l ≈ 1 . 3 (at large degree scales. This suggests that word lengths are much more strongly correlated at large distances between words than at short distances between words. That finding is also supported by the detrended fluctuation analysis (DFA and recurrence time distribution. These results provide new information about the universal characteristics of the structure of written texts beyond that given by word frequencies.

The association between intelligence and telomere length: a longitudinal population based study.

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Eva M Kingma

Full Text Available Low intelligence has been associated with poor health and mortality, but underlying mechanisms remain obscure. We hypothesized that low intelligence is associated with accelerated biological ageing as reflected by telomere length; we suggested potential mediation of this association by unhealthy behaviors and low socioeconomic position. The study was performed in a longitudinal population-based cohort study of 895 participants (46.8% males. Intelligence was measured with the Generalized Aptitude-Test Battery at mean age 52.8 years (33-79 years, SD=11.3. Leukocyte telomere length was measured by PCR. Lifestyle and socioeconomic factors were assessed using written self-report measures. Linear regression analyses, adjusted for age, sex, and telomere length measured at the first assessment wave (T1, showed that low intelligence was associated with shorter leukocyte telomere length at approximately 2 years follow-up (beta= .081, t=2.160, p= .031. Nearly 40% of this association was explained by an unhealthy lifestyle, while low socioeconomic position did not add any significant mediation. Low intelligence may be a risk factor for accelerated biological ageing, thereby providing an explanation for its association with poor health and mortality.

Bond-Length Distortions in Strained Semiconductor Alloys

International Nuclear Information System (INIS)

Woicik, J.C.; Pellegrino, J.G.; Steiner, B.; Miyano, K.E.; Bompadre, S.G.; Sorensen, L.B.; Lee, T.; Khalid, S.

1997-01-01

Extended x-ray absorption fine structure measurements performed at In-K edge have resolved the outstanding issue of bond-length strain in semiconductor-alloy heterostructures. We determine the In-As bond length to be 2.581±0.004 Angstrom in a buried, 213 Angstrom thick Ga 0.78 In 0.22 As layer grown coherently on GaAs(001). This bond length corresponds to a strain-induced contraction of 0.015±0.004 Angstrom relative to the In-As bond length in bulk Ga 1-x In x As of the same composition; it is consistent with a simple model which assumes a uniform bond-length distortion in the epilayer despite the inequivalent In-As and Ga-As bond lengths. copyright 1997 The American Physical Society

Topological analysis of polymeric melts: chain-length effects and fast-converging estimators for entanglement length.

Science.gov (United States)

Hoy, Robert S; Foteinopoulou, Katerina; Kröger, Martin

2009-09-01

Primitive path analyses of entanglements are performed over a wide range of chain lengths for both bead spring and atomistic polyethylene polymer melts. Estimators for the entanglement length N_{e} which operate on results for a single chain length N are shown to produce systematic O(1/N) errors. The mathematical roots of these errors are identified as (a) treating chain ends as entanglements and (b) neglecting non-Gaussian corrections to chain and primitive path dimensions. The prefactors for the O(1/N) errors may be large; in general their magnitude depends both on the polymer model and the method used to obtain primitive paths. We propose, derive, and test new estimators which eliminate these systematic errors using information obtainable from the variation in entanglement characteristics with chain length. The new estimators produce accurate results for N_{e} from marginally entangled systems. Formulas based on direct enumeration of entanglements appear to converge faster and are simpler to apply.

Spatial linear flows of finite length with nonuniform intensity distribution

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Mikhaylov Ivan Evgrafovich

2014-02-01

Full Text Available Irrotational flows produced by spatial linear flows of finite length with different uneven lows of discharge over the flow length are represented in cylindrical coordinate system. Flows with the length 2a are placed in infinite space filled with ideal (inviscid fluid. In “А” variant discharge is fading linearly downward along the length of the flow. In “B” variant in upper half of the flow (length a discharge is fading linearly downward, in lower half of the flow discharge is fading linearly from the middle point to lower end. In “C” variant discharge of the flow is growing linearly from upper and lower ends to middle point.Equations for discharge distribution along the length of the flow are provided for each variant. Equations consist of two terms and include two dimensional parameters and current coordinate that allows integrating on flow length. Analytical expressions are derived for speed potential functions and flow speed components for flow speeds produced by analyzed flows. These analytical expressions consist of dimensional parameters of discharge distribution patterns along the length of the flow. Flow lines equation (meridional sections of flow surfaces for variants “A”, “B”, “C” is unsolvable in quadratures. Flow lines plotting is proposed to be made by finite difference method. Equations for flow line plotting are provided for each variant. Calculations of these equations show that the analyzed flows have the following flow lines: “A” has confocal hyperbolical curves, “B” and “C” have confocal hyperboles. Flow surfaces are confocal hyperboloids produced by rotation of these hyperboles about the axis passing through the flows. In “A” variant the space filled with fluid is separated by vividly horizontal flow surface in two parts. In upper part that includes the smaller part of the flow length flow lines are oriented downward, in lower part – upward. The equation defining coordinate of

Mechanical properties of rubberwood oriented strand lumber (OSL: The effect of strand length

Directory of Open Access Journals (Sweden)

Buhnnum Kyokong

2005-09-01

Full Text Available Effect of strand length on mechanical properties (tension, compression and bending of oriented strand lumber (OSL made of rubberwood (Hevea brasiliensis Muell. Arg. was reported. Three strand lengths of 50 mm, 100 mm, and 150 mm with 1 mm thickness and 15 mm width were used. The strands were mixed with 5% pMDI glue (weight basis in a tumble mixer. The OSL specimens were formed by hot pressing process of unidirectionally aligned strands. Average specific gravity and moisture content were 0.76 and 8.34%, respectively. Tension and compression tests were carried out for directions both parallel and perpendicular to grain while bending test was performed only in parallel direction. Ultimate stresses and moduli of elasticity were examined from the stress-strain curves. It was found that for the parallel-to-grain direction, the longer strand OSL gave higher strength. The role of the strand length did not appear for the direction normal to the grain. The relationship between the mechanical properties of OSL and strand length was well described by the modified Hankinson formula.

Blood and dried blood spot telomere length measurement by qPCR: assay considerations.

Directory of Open Access Journals (Sweden)

DeAnna L Zanet

Full Text Available Measurement of telomere length is crucial for the study of telomere maintenance and its role in molecular pathophysiology of diseases and in aging. Several methods are used to measure telomere length, the choice of which usually depends on the type and size of sample to be assayed, as well as cost and throughput considerations. The goal of this study was to investigate the factors that may influence the reliability of qPCR-based relative telomere length measurements in whole blood. Day to day intra-individual variability, types of blood anticoagulant, sample storage conditions, processing and site of blood draw were investigated. Two qPCR-based methods to measure telomere length (monoplex vs. multiplex were also investigated and showed a strong correlation between them. Freezing and thawing of the blood and storage of the blood at 4°C for up to 4 days did not affect telomere length values. Telomere lengths in dried blood spots were significantly higher than both whole blood and peripheral mononuclear blood cells, and were highly correlated with both. We found that telomere length measurements were significantly higher in dried blood spots collected directly from fingertip prick compared to dried blood spots prepared with anticoagulated whole blood collected from the finger, and non-blotted whole blood taken from both finger and arm venipuncture. This suggests that DNA from cells blotted on paper is not equivalent to that collected from venipuncture whole blood, and caution should be taken when comparing between blood sample types.

The Effect of CFRP Length on the Failure Mode of Strengthened Concrete Beams

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Jun Ding

2014-06-01

Full Text Available This paper reports the effects of carbon fiber-reinforced polymer (CFRP length on the failure process, pattern and crack propagation for a strengthened concrete beam with an initial notch. The experiments measuring load-bearing capacity for concrete beams with various CFRP lengths have been performed, wherein the crack opening displacements (COD at the initial notch are also measured. The application of CFRP can significantly improve the load-bearing capacity, and the failure modes seem different with various CFRP lengths. The stress profiles in the concrete material around the crack tip, at the end of CFRP and at the interface between the concrete and CFRP are then calculated using the finite element method. The experiment measurements are validated by theoretical derivation and also support the finite element analysis. The results show that CFRP can significantly increase the ultimate load of the beam, while such an increase stops as the length reaches 0.15 m. It is also concluded that the CFRP length can influence the stress distribution at three critical stress regions for strengthened concrete beams. However, the optimum CFRP lengths vary with different critical stress regions. For the region around the crack tip, it is 0.15 m; for the region at the interface it is 0.25 m, and for the region at the end of CFRP, it is 0.30 m. In conclusion, the optimum CFRP length in this work is 0.30 m, at which CFRP strengthening is fully functioning, which thus provides a good reference for the retrofitting of buildings.

Length Scales in Bayesian Automatic Adaptive Quadrature

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Adam Gh.

2016-01-01

Full Text Available Two conceptual developments in the Bayesian automatic adaptive quadrature approach to the numerical solution of one-dimensional Riemann integrals [Gh. Adam, S. Adam, Springer LNCS 7125, 1–16 (2012] are reported. First, it is shown that the numerical quadrature which avoids the overcomputing and minimizes the hidden floating point loss of precision asks for the consideration of three classes of integration domain lengths endowed with specific quadrature sums: microscopic (trapezoidal rule, mesoscopic (Simpson rule, and macroscopic (quadrature sums of high algebraic degrees of precision. Second, sensitive diagnostic tools for the Bayesian inference on macroscopic ranges, coming from the use of Clenshaw-Curtis quadrature, are derived.

OC30 - Fracture reduction with nitrous oxide at the children's emergency department shortens the length of stay and reduces the use of full anaesthesia in the operating department.

Science.gov (United States)

Lang, Sigrid; Wentzel, Anna-Pia; Ekstrom, Malin

2016-05-09

Theme: Accreditation and quality improvement. Dislocated fractures are common in the children's emergency department (ER). All forms of fracture reduction are very painful requiring nitrous oxide. The purpose is to shorten the length of stay in the hospital as well as sustain a high quality of care. All nurses received theoretical and practical training in the use of nitrous oxide. Evaluations with the families were made by telephone. A total of 40 enclosed fracture reductions were made at the ER, leading to a reduction of 33 patients in the operating department and the length of stay was shortened - this compared to the same time in 2014. No adverse event was reported and no patient felt any increase in pain during the treatment. All patients would repeat the procedure if necessary. The treatment has reduced the length of stay in the hospital without affecting the other patients in the ER or the quality of care.

Subtype-independent near full-length HIV-1 genome sequencing and assembly to be used in large molecular epidemiological studies and clinical management.

Science.gov (United States)

Grossmann, Sebastian; Nowak, Piotr; Neogi, Ujjwal

2015-01-01

HIV-1 near full-length genome (HIV-NFLG) sequencing from plasma is an attractive multidimensional tool to apply in large-scale population-based molecular epidemiological studies. It also enables genotypic resistance testing (GRT) for all drug target sites allowing effective intervention strategies for control and prevention in high-risk population groups. Thus, the main objective of this study was to develop a simplified subtype-independent, cost- and labour-efficient HIV-NFLG protocol that can be used in clinical management as well as in molecular epidemiological studies. Plasma samples (n=30) were obtained from HIV-1B (n=10), HIV-1C (n=10), CRF01_AE (n=5) and CRF01_AG (n=5) infected individuals with minimum viral load >1120 copies/ml. The amplification was performed with two large amplicons of 5.5 kb and 3.7 kb, sequenced with 17 primers to obtain HIV-NFLG. GRT was validated against ViroSeq™ HIV-1 Genotyping System. After excluding four plasma samples with low-quality RNA, a total of 26 samples were attempted. Among them, NFLG was obtained from 24 (92%) samples with the lowest viral load being 3000 copies/ml. High (>99%) concordance was observed between HIV-NFLG and ViroSeq™ when determining the drug resistance mutations (DRMs). The N384I connection mutation was additionally detected by NFLG in two samples. Our high efficiency subtype-independent HIV-NFLG is a simple and promising approach to be used in large-scale molecular epidemiological studies. It will facilitate the understanding of the HIV-1 pandemic population dynamics and outline effective intervention strategies. Furthermore, it can potentially be applicable in clinical management of drug resistance by evaluating DRMs against all available antiretrovirals in a single assay.

Relativistic distances, sizes, lengths

International Nuclear Information System (INIS)

Strel'tsov, V.N.

1992-01-01

Such notion as light or retarded distance, field size, formation way, visible size of a body, relativistic or radar length and wave length of light from a moving atom are considered. The relation between these notions is cleared up, their classification is given. It is stressed that the formation way is defined by the field size of a moving particle. In the case of the electromagnetic field, longitudinal sizes increase proportionally γ 2 with growing charge velocity (γ is the Lorentz-factor). 18 refs

Wind direction variations in the natural wind – A new length scale

DEFF Research Database (Denmark)

Johansson, Jens; Christensen, Silas Sverre

2018-01-01

During an observation period of e.g. 10min, the wind direction will differ from its mean direction for short periods of time, and a body of air will pass by from that direction before the direction changes once again. The present paper introduces a new length scale which we have labeled the angular...... length scale. This length scale expresses the average size of the body of air passing by from any deviation of wind direction away from the mean direction. Using metrological observations from two different sites under varying conditions we have shown that the size of the body of air relative to the mean...... size decreases linearly with the deviation from the mean wind direction when the deviation is normalized with the standard deviation of the wind direction. It is shown that this linear variation is independent of the standard deviation of the wind direction, and that the two full-scale data sets follow...

Investigation into the effects of steel wire rope specimen length on breaking force

CSIR Research Space (South Africa)

O'Brien, TM

2004-03-01

Full Text Available (2000). The methodology employed was to test different length of triangular strand and non-spin rope to destruction, and to evaluate these results against SABS 0293:1996. For each rope construction, specimens were prepared both with and without cut wires...

Effectiveness of Group-Delivered Cognitive Therapy and Treatment Length in Women Veterans with PTSD

Directory of Open Access Journals (Sweden)

Diane T. Castillo

2014-01-01

Full Text Available The effectiveness and length of group-delivered cognitive treatment for Posttraumatic Stress Disorder (PTSD was examined in a sample of women veterans. The sample included 271 primarily non-Hispanic white (61% and Hispanic (25% women veterans treated in 8-, 10-, or 12-group length sessions with manualized cognitive therapy for PTSD. Outcome was measured with the PTSD Symptom Checklist (PCL in an intention-to-treat analysis (N = 271, in completer subjects (n = 172, and with group as the unit of analysis (n = 47 groups. Significant decreases in PTSD were found in the full sample (effect size [ES] range = 0.27 to 0.38, completers (ES range = 0.37 to 0.54, and group as the unit of analysis (ES range = 0.71 to 0.92, suggesting effectiveness of cognitive group treatment for PTSD. PCL scores significantly improved in the 8, 10, and 12 group lengths, with no differences between each. Clinical improvement showed a third decreasing 10 or more PCL points and 22% no longer meeting PTSD diagnostic criteria, with the best results in the 10-session group. The results suggest group-delivered cognitive therapy is an effective, efficient, time-limited treatment for PTSD.

Microcomputer system for controlling fuel rod length

International Nuclear Information System (INIS)

Meyer, E.R.; Bouldin, D.W.; Bolfing, B.J.

1979-01-01

A system is being developed at the Oak Ridge National Laboratory (ORNL) to automatically measure and control the length of fuel rods for use in a high temperature gas-cooled reactor (HTGR). The system utilizes an LSI-11 microcomputer for monitoring fuel rod length and for adjusting the primary factor affecting length. Preliminary results indicate that the automated system can maintain fuel rod length within the specified limits of 1.940 +- 0.040 in. This system provides quality control documentation and eliminates the dependence of the current fuel rod molding process on manual length control. In addition, the microcomputer system is compatible with planned efforts to extend control to fuel rod fissile and fertile material contents

Correlation length estimation in a polycrystalline material model

International Nuclear Information System (INIS)

Simonovski, I.; Cizelj, L.

2005-01-01

This paper deals with the correlation length estimated from a mesoscopic model of a polycrystalline material. The correlation length can be used in some macroscopic material models as a material parameter that describes the internal length. It can be estimated directly from the strain and stress fields calculated from a finite-element model, which explicitly accounts for the selected mesoscopic features such as the random orientation, shape and size of the grains. A crystal plasticity material model was applied in the finite-element analysis. Different correlation lengths were obtained depending on the used set of crystallographic orientations. We determined that the different sets of crystallographic orientations affect the general level of the correlation length, however, as the external load is increased the behaviour of correlation length is similar in all the analyzed cases. The correlation lengths also changed with the macroscopic load. If the load is below the yield strength the correlation lengths are constant, and are slightly higher than the average grain size. The correlation length can therefore be considered as an indicator of first plastic deformations in the material. Increasing the load above the yield strength creates shear bands that temporarily increase the values of the correlation lengths calculated from the strain fields. With a further load increase the correlation lengths decrease slightly but stay above the average grain size. (author)

Full-length single-cell RNA-seq applied to a viral human cancer: applications to HPV expression and splicing analysis in HeLa S3 cells.

Science.gov (United States)

Wu, Liang; Zhang, Xiaolong; Zhao, Zhikun; Wang, Ling; Li, Bo; Li, Guibo; Dean, Michael; Yu, Qichao; Wang, Yanhui; Lin, Xinxin; Rao, Weijian; Mei, Zhanlong; Li, Yang; Jiang, Runze; Yang, Huan; Li, Fuqiang; Xie, Guoyun; Xu, Liqin; Wu, Kui; Zhang, Jie; Chen, Jianghao; Wang, Ting; Kristiansen, Karsten; Zhang, Xiuqing; Li, Yingrui; Yang, Huanming; Wang, Jian; Hou, Yong; Xu, Xun

2015-01-01

Viral infection causes multiple forms of human cancer, and HPV infection is the primary factor in cervical carcinomas. Recent single-cell RNA-seq studies highlight the tumor heterogeneity present in most cancers, but virally induced tumors have not been studied. HeLa is a well characterized HPV+ cervical cancer cell line. We developed a new high throughput platform to prepare single-cell RNA on a nanoliter scale based on a customized microwell chip. Using this method, we successfully amplified full-length transcripts of 669 single HeLa S3 cells and 40 of them were randomly selected to perform single-cell RNA sequencing. Based on these data, we obtained a comprehensive understanding of the heterogeneity of HeLa S3 cells in gene expression, alternative splicing and fusions. Furthermore, we identified a high diversity of HPV-18 expression and splicing at the single-cell level. By co-expression analysis we identified 283 E6, E7 co-regulated genes, including CDC25, PCNA, PLK4, BUB1B and IRF1 known to interact with HPV viral proteins. Our results reveal the heterogeneity of a virus-infected cell line. It not only provides a transcriptome characterization of HeLa S3 cells at the single cell level, but is a demonstration of the power of single cell RNA-seq analysis of virally infected cells and cancers.

The relationship between telomere length and mortality in chronic obstructive pulmonary disease (COPD.

Directory of Open Access Journals (Sweden)

Jee Lee

Full Text Available Some have suggested that chronic obstructive pulmonary disease (COPD is a disease of accelerated aging. Aging is characterized by shortening of telomeres. The relationship of telomere length to important clinical outcomes such as mortality, disease progression and cancer in COPD is unknown. Using quantitative polymerase chain reaction (qPCR, we measured telomere length of peripheral leukocytes in 4,271 subjects with mild to moderate COPD who participated in the Lung Health Study (LHS. The subjects were followed for approximately 7.5 years during which time their vital status, FEV(1 and smoking status were ascertained. Using multiple regression methods, we determined the relationship of telomere length to cancer and total mortality in these subjects. We also measured telomere length in healthy "mid-life" volunteers and patients with more severe COPD. The LHS subjects had significantly shorter telomeres than those of healthy "mid-life" volunteers (p<.001. Compared to individuals in the 4(th quartile of relative telomere length (i.e. longest telomere group, the remaining participants had significantly higher risk of cancer mortality (Hazard ratio, HR, 1.48; p = 0.0324 and total mortality (HR, 1.29; p = 0.0425. Smoking status did not make a significant difference in peripheral blood cells telomere length. In conclusion, COPD patients have short leukocyte telomeres, which are in turn associated increased risk of total and cancer mortality. Accelerated aging is of particular relevance to cancer mortality in COPD.

Performance of RC columns with partial length corrosion

International Nuclear Information System (INIS)

Wang Xiaohui; Liang Fayun

2008-01-01

Experimental and analytical studies on the load capacity of reinforced concrete (RC) columns with partial length corrosion are presented, where only a fraction of the column length was corroded. Twelve simply supported columns were eccentrically loaded. The primary variables were partial length corrosion in tensile or compressive zone and the corrosion level within this length. The failure of the corroded column occurs in the partial length, mainly developed from or located nearby or merged with the longitudinal corrosion cracks. For RC column with large eccentricity, load capacity of the column is mainly influenced by the partial length corrosion in tensile zone; while for RC column with small eccentricity, load capacity of the column greatly decreases due to the partial length corrosion in compressive zone. The destruction of the longitudinally mechanical integrality of the column in the partial length leads to this great reduction of the load capacity of the RC column

Full-length sequencing and identification of novel polymorphisms in ...

Indian Academy of Sciences (India)

Rosalia Di Gerlando

2017-08-16

Aug 16, 2017 ... ANNA MARIA SUTERA, MARIA TERESA SARDINA. ∗ ... SNPs that might be important in future studies and laid the basis for further association analyses needed to ..... Haplotype-based analysis can provide higher power,.

Full-length sequencing and identification of novel polymorphisms in ...

Indian Academy of Sciences (India)

The aim of this work was to sequence the entirecoding region of ACACA gene in Valle del Belice sheep breed to identify polymorphic sites. A total of 51 coding exons of ACACA gene were sequenced in 32 individuals of Valle del Belice sheep breed. Sequencing analysis and alignment of obtained sequences showed the ...

Full Length Research Paper Curcumin induces cleavage of -catenin ...

African Journals Online (AJOL)

β-Catenin/Tcf-4 signaling pathway plays important roles in colorectal tumorigenesis. RT-PCR, western blotting and immunoprecipitation were used to study the effects of curcumin on β-catenin/Tcf-4 signaling pathway in HT-29 cells. Treatment of curcumin could induce cleavage of β-catenin and the cleavage could be ...

Cinemeducation: teaching family assessment skills using full-length movies.

Science.gov (United States)

Wilson, Astrid H; Blake, Barbara J; Taylor, Gloria A; Hannings, Glenda

2013-05-01

A thorough family assessment provides a foundation for the nursing process when working with families. Therefore, nurses, along with other health care providers must develop expertise in conducting family assessments to provide the best possible care within the community. This article describes an innovative educational strategy using movies to teach family assessment skills and puts forth recommendations for future research to provide evidence to support this teaching modality. © 2013 Wiley Periodicals, Inc.

Full Length Research Paper Biochemical and textural properties of ...

African Journals Online (AJOL)

Skinned, vacuum packed post-rigor gilthead seabream (Sparus aurata) fillets were stored frozen at -22°C for up to 340 days. Sampling was carried out on fresh fillets at days 34, 91, 183, 266 and 340 of frozen storage. Tests related to muscle integrity (activity of -glucosidase and the protein content of centrifugal tissue fluids), ...

Full-length genomic analysis of korean porcine sapelovirus strains

DEFF Research Database (Denmark)

Son, Kyu-Yeol; Kim, Deok-Song; Kwon, Joseph

2014-01-01

the typical picornavirus genome organization; 5'untranslated region (UTR)-L-VP4-VP2-VP3-VP1-2A-2B-2C-3A-3B-3C-3D-3'UTR. Three distinct cis-active RNA elements, the internal ribosome entry site (IRES) in the 5'UTR, a cis-replication element (CRE) in the 2C coding region and 3'UTR were identified...... and their structures were predicted. Interestingly, the structural features of the CRE and 3'UTR were different between PSV strains. The availability of these first complete genome sequences for PSV strains will facilitate future investigations of the molecular pathogenesis and evolutionary characteristics of PSV....

FULL LENGTH RESEARCH ARTICLE Hassan et al. (2008) SWJ ...

African Journals Online (AJOL)

Dr. Ahmed

1Department of Biological Sciences. Kaduna State University ... From hydrological statistics, the volume of water world-wide amounts to some 1.4 x 109 km3. ... most striking features of the past water assessment procedures has been reliance ...

Full Length Research Paper Production of emodin from Aspergillus ...

African Journals Online (AJOL)

In order to study the chemical constituents in the pigmented culture produced from Aspergillus ochraceus, solid phase extraction method was employed to isolate the pigment molecules from the primary culture, followed by fractionation on preparative liquid chromatography. Structural characterization confirmed that one of ...

Penile length and circumference: an Indian study.

Science.gov (United States)

Promodu, K; Shanmughadas, K V; Bhat, S; Nair, K R

2007-01-01

Apprehension about the normal size of penis is a major concern for men. Aim of the present investigation is to estimate the penile length and circumference of Indian males and to compare the results with the data from other countries. Results will help in counseling the patients worried about the penile size and seeking penis enlargement surgery. Penile length in flaccid and stretched conditions and circumference were measured in a group of 301 physically normal men. Erected length and circumference were measured for 93 subjects. Mean flaccid length was found to be 8.21 cm, mean stretched length 10.88 cm and circumference 9.14 cm. Mean erected length was found to be 13.01 cm and erected circumference was 11.46 cm. Penile dimensions are found to be correlated with anthropometric parameters. Insight into the normative data of penile size of Indian males obtained. There are significant differences in the mean penile length and circumference of Indian sample compared to the data reported from other countries. Study need to be continued with a large sample to establish a normative data applicable to the general population.

ESTIMATION OF STATURE BASED ON FOOT LENGTH

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Vidyullatha Shetty

2015-01-01

Full Text Available BACKGROUND : Stature is the height of the person in the upright posture. It is an important measure of physical identity. Estimation of body height from its segments or dismember parts has important considerations for identifications of living or dead human body or remains recovered from disasters or other similar conditions. OBJECTIVE : Stature is an important indicator for identification. There are numerous means to establish stature and their significance lies in the simplicity of measurement, applicability and accuracy in prediction. Our aim of the study was to review the relationship between foot length and body height. METHODS : The present study reviews various prospective studies which were done to estimate the stature. All the measurements were taken by using standard measuring devices and standard anthropometric techniques. RESULTS : This review shows there is a correlation between stature and foot dimensions it is found to be positive and statistically highly significant. Prediction of stature was found to be most accurate by multiple regression analysis. CONCLUSIONS : Stature and gender estimation can be done by using foot measurements and stud y will help in medico - legal cases in establishing identity of an individual and this would be useful for Anatomists and Anthropologists to calculate stature based on foot length

Isospin breaking in the pion-nucleon coupling constant and the nucleon-nucleon scattering length

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V. A. Babenko

2016-08-01

Full Text Available Charge independence breaking (CIB in the pion-nucleon coupling constant and the nucleon-nucleon scattering length is considered on the basis of the Yukawa meson theory. CIB effect in these quantities is almost entirely explained by the mass difference between the charged and the neutral pions. Therewith charge splitting of the pion-nucleon coupling constant is almost the same as charge splitting of the pion mass. Calculated difference between the proton-proton and the neutron-proton scattering length in this case comprises ∼90% of the experimental value.

Bunch Length Measurements in SPEAR3

Energy Technology Data Exchange (ETDEWEB)

Corbett, W.J.; Fisher, A.; Huang, X.; Safranek, J.; Sebek, J.; /SLAC; Lumpkin, A.; /Argonne; Sannibale, F.; /LBL, Berkeley; Mok, W.; /Unlisted

2007-11-28

A series of bunch length measurements were made in SPEAR3 for two different machine optics. In the achromatic optics the bunch length increases from the low-current value of 16.6ps rms to about 30ps at 25ma/bunch yielding an inductive impedance of -0.17{Omega}. Reducing the momentum compaction factor by a factor of {approx}60 [1] yields a low-current bunch length of {approx}4ps rms. In this paper we review the experimental setup and results.

Walking on inclines: how do desert ants monitor slope and step length

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Seidl Tobias

2008-06-01

Full Text Available Abstract Background During long-distance foraging in almost featureless habitats desert ants of the genus Cataglyphis employ path-integrating mechanisms (vector navigation. This navigational strategy requires an egocentric monitoring of the foraging path by incrementally integrating direction, distance, and inclination of the path. Monitoring the latter two parameters involves idiothetic cues and hence is tightly coupled to the ant's locomotor behavior. Results In a kinematic study of desert ant locomotion performed on differently inclined surfaces we aimed at pinpointing the relevant mechanisms of estimating step length and inclination. In a behavioral experiment with ants foraging on slippery surfaces we broke the otherwise tightly coupled relationship between stepping frequency and step length and examined the animals' ability to monitor distances covered even under those adverse conditions. We show that the ants' locomotor system is not influenced by inclined paths. After removing the effect of speed, slope had only marginal influence on kinematic parameters. Conclusion From the obtained data we infer that the previously proposed monitoring of angles of the thorax-coxa joint is not involved in inclinometry. Due to the tiny variations in cycle period, we also argue that an efference copy of the central pattern generator coding the step length in its output frequency will most likely not suffice for estimating step length and complementing the pedometer. Finally we propose that sensing forces acting on the ant's legs could provide the desired neuronal correlate employed in monitoring inclination and step length.

LENGTH-WEIGHT RELATIONSHIP AND CONDITION FACTOR OF ...

African Journals Online (AJOL)

Data Collection and Analysis. The measurements of length (cm), weight (g) and the condition factor of individual fish sampled were recorded. The relationship between length and weight of the fish was examined by simple linear regression using WINKS software. The variations in the length-weight represented by 'b' were.

πK-scattering lengths

International Nuclear Information System (INIS)

Volkov, M.K.; Osipov, A.A.

1983-01-01

The msub(π)asub(0)sup(1/2)=0.1, msub(π)asub(0)sup(3/2)=-0.1, msub(π)asub(0)sup((-))=0.07, msub(π)sup(3)asub(1)sup(1/2)=0.018, msub(π)sup(3)asub(1)aup(3/2)=0.002, msub(π)sup(3)asub(1)sup((-))=0.0044, msub(π)sup(5)asub(2)sup(1/2)=2.4x10sup(-4) and msub(π)sup(5)asub(2)sup(3/2)=-1.2x10sup(-4) scattering lengths are calculated in the framework of the composite meson model which is based on four-quark interaction. The decay form factors of (rho, epsilon, S*) → 2π, (K tilde, K*) → Kπ are used. The q 2 -terms of the quark box diagrams are taken into account. It is shown that the q 2 -terms of the box diagrams give the main contribution to the s-wave scattering lengths. The diagrams with the intermediate vector mesons begin to play the essential role at calculation of the p- and d-wave scattering lengths

Upscaling of polymer solar cell fabrication using full roll-to-roll processing

DEFF Research Database (Denmark)

Krebs, Frederik C; Tromholt, Thomas; Jørgensen, Mikkel

2010-01-01

factors (excluding bus bars) of 50, 67 and 75% respectively. In addition modules with lengths of 6, 10, 20, 22.5 and 25 cm were explored. The devices were prepared by full roll-to-roll solution processing in a web width of 305 mm and roll lengths of up to 200 m. The devices were encapsulated...... with a barrier material in a full roll-to-roll process using standard adhesives giving the devices excellent stability during storage and operation. The total area of processed polymer solar cell was around 60 m2 per run. The solar cells were characterised using a roll-to-roll system comprising a solar simulator...... to the cost for electricity using existing technologies the levelized cost of electricity (LCOE) is expected to be significantly higher than the existing technologies due to the inferior operational lifetime. The presented devices are thus competitive for consumer electronics but ill-suited for on...

Romantic Relationship Length and its Perceived Quality: Mediating Role of Facebook-Related Conflict

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H. M. Saidur Rahaman

2015-08-01

Full Text Available The purpose of this study was to investigate how Facebook use is leading to negative relationship outcomes such as cheating and breakup by assessing users’ perceived relationship qualities. It was hypothesized that Facebook-related conflict will be negatively related with users’ relationship length and will also be negatively related with their perceived relationship satisfaction, commitment, and love. Facebook-related conflict further mediates the relationship between relationship length and perceived relationship satisfaction, commitment, and love. Self-report data were gathered from participants (N = 101 in an online survey by employing standard questionnaires. A set of regression and mediation analyses confirmed all the hypotheses of the study. That is, Facebook-related conflict mediates the relationship between relationship length and perceived relationship satisfaction, commitment, and love. Moreover, the magnitude of mediation was highest for relationship satisfaction. Implications for future research and contributions are discussed.

Systematic and Cell Type-Specific Telomere Length Changes in Subsets of Lymphocytes

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Jue Lin

2016-01-01

Full Text Available Telomeres, the protective DNA-protein complexes at the ends of linear chromosomes, are important for genome stability. Leukocyte or peripheral blood mononuclear cell (PBMC telomere length is a potential biomarker for human aging that integrates genetic, environmental, and lifestyle factors and is associated with mortality and risks for major diseases. However, only a limited number of studies have examined longitudinal changes of telomere length and few have reported data on sorted circulating immune cells. We examined the average telomere length (TL in CD4+, CD8+CD28+, and CD8+CD28− T cells, B cells, and PBMCs, cross-sectionally and longitudinally, in a cohort of premenopausal women. We report that TL changes over 18 months were correlated among these three T cell types within the same participant. Additionally, PBMC TL change was also correlated with those of all three T cell types, and B cells. The rate of shortening for B cells was significantly greater than for the three T cell types. CD8+CD28− cells, despite having the shortest TL, showed significantly more rapid attrition when compared to CD8+CD28+ T cells. These results suggest systematically coordinated, yet cell type-specific responses to factors and pathways contribute to telomere length regulation.

Fatigue Crack Length Sizing Using a Novel Flexible Eddy Current Sensor Array

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Ruifang Xie

2015-12-01

Full Text Available The eddy current probe, which is flexible, array typed, highly sensitive and capable of quantitative inspection is one practical requirement in nondestructive testing and also a research hotspot. A novel flexible planar eddy current sensor array for the inspection of microcrack presentation in critical parts of airplanes is developed in this paper. Both exciting and sensing coils are etched on polyimide films using a flexible printed circuit board technique, thus conforming the sensor to complex geometric structures. In order to serve the needs of condition-based maintenance (CBM, the proposed sensor array is comprised of 64 elements. Its spatial resolution is only 0.8 mm, and it is not only sensitive to shallow microcracks, but also capable of sizing the length of fatigue cracks. The details and advantages of our sensor design are introduced. The working principal and the crack responses are analyzed by finite element simulation, with which a crack length sizing algorithm is proposed. Experiments based on standard specimens are implemented to verify the validity of our simulation and the efficiency of the crack length sizing algorithm. Experimental results show that the sensor array is sensitive to microcracks, and is capable of crack length sizing with an accuracy within ±0.2 mm.

Cellular Mechanisms of Ciliary Length Control

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Jacob Keeling

2016-01-01

Full Text Available Cilia and flagella are evolutionarily conserved, membrane-bound, microtubule-based organelles on the surface of most eukaryotic cells. They play important roles in coordinating a variety of signaling pathways during growth, development, cell mobility, and tissue homeostasis. Defects in ciliary structure or function are associated with multiple human disorders called ciliopathies. These diseases affect diverse tissues, including, but not limited to the eyes, kidneys, brain, and lungs. Many processes must be coordinated simultaneously in order to initiate ciliogenesis. These include cell cycle, vesicular trafficking, and axonemal extension. Centrioles play a central role in both cell cycle progression and ciliogenesis, making the transition between basal bodies and mitotic spindle organizers integral to both processes. The maturation of centrioles involves a functional shift from cell division toward cilium nucleation which takes place concurrently with its migration and fusion to the plasma membrane. Several proteinaceous structures of the distal appendages in mother centrioles are required for this docking process. Ciliary assembly and maintenance requires a precise balance between two indispensable processes; so called assembly and disassembly. The interplay between them determines the length of the resulting cilia. These processes require a highly conserved transport system to provide the necessary substances at the tips of the cilia and to recycle ciliary turnover products to the base using a based microtubule intraflagellar transport (IFT system. In this review; we discuss the stages of ciliogenesis as well as mechanisms controlling the lengths of assembled cilia.

Study on the Workspace of a 6-DOF Parallel Topology Robot Related to Binary Link Lengths

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Calin-Octavian Miclosina

2016-12-01

Full Text Available The paper presents a study on the workspace of a parallel topology robot with the structure FP3+6•SPS+MP3. The variable parameters are the binary link lengths, from both upper and lower levels, and the driving kinematical joint strokes. The workspace boundary is determined by SolidWorks software simulations. For different binary link lengths, workspace volume is determined and sections through the workspace are presented.

Study Regarding the Correlation between Body Mass and Spur Length in Hunting Pheasant (Males, in October

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Eugenie Grigoroiu

2011-10-01

Full Text Available This work presents a study on the correlation between body mass and spur length in October 2009.October is the month when the pheasant hunting begins. The structure per ages of pheasant cocks is not well known, but we may consider that over 80% are pheasants eclosed during the current year, from the first, second or the third mating, so that the body mass and spur length were different according to age.

Lifetime and Path Length of the Virtual Particle

International Nuclear Information System (INIS)

Lyuboshitz, V.L.; Lyuboshitz, V.V.

2005-01-01

The concepts of the lifetime and path length of a virtual particle are introduced. It is shown that, near the mass surface of the real particle, these quantities constitute a 4-vector. At very high energies, the virtual particle can propagate over considerable (even macroscopic) distances. The formulas for the lifetime and path length of an ultrarelativistic virtual electron in the process of bremsstrahlung in the Coulomb field of a nucleus are obtained. The lifetime and path length of the virtual photon at its conversion into an electron-positron pair are discussed. The connection between the path length of the virtual particle and the coherence length (formation length) is analyzed

Information, polarization and term length in democracy

DEFF Research Database (Denmark)

Schultz, Christian

2008-01-01

This paper considers term lengths in a representative democracy where the political issue divides the population on the left-right scale. Parties are ideologically different and better informed about the consequences of policies than voters are. A short term length makes the government more...... accountable, but the re-election incentive leads to policy-distortion as the government seeks to manipulate swing voters' beliefs to make its ideology more popular. This creates a trade-off: A short term length improves accountability but gives distortions. A short term length is best for swing voters when...

Identification, Characterization and Full-Length Sequence Analysis of a Novel Polerovirus Associated with Wheat Leaf Yellowing Disease

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Peipei Zhang

2017-09-01

Full Text Available To identify the pathogens responsible for leaf yellowing symptoms on wheat samples collected from Jinan, China, we tested for the presence of three known barley/wheat yellow dwarf viruses (BYDV-GAV, -PAV, WYDV-GPV (most likely pathogens using RT-PCR. A sample that tested negative for the three viruses was selected for small RNA sequencing. Twenty-five million sequences were generated, among which 5% were of viral origin. A novel polerovirus was discovered and temporarily named wheat leaf yellowing-associated virus (WLYaV. The full genome of WLYaV corresponds to 5,772 nucleotides (nt, with six AUG-initiated open reading frames, one non-AUG-initiated open reading frame, and three untranslated regions, showing typical features of the family Luteoviridae. Sequence comparison and phylogenetic analyses suggested that WLYaV had the closest relationship with sugarcane yellow leaf virus (ScYLV, but the identities of full genomic nucleotides and deduced amino acid sequence of coat protein (CP were 64.9 and 86.2%, respectively, below the species demarcation thresholds (90% in the family Luteoviridae. Furthermore, agroinoculation of Nicotiana benthamiana leaves with a cDNA clone of WLYaV caused yellowing symptoms on the plant. Our study adds a new polerovirus that is associated with wheat leaf yellowing disease, which would help to identify and control pathogens of wheat.

Decomposing the queue length distribution of processor-sharing models into queue lengths of permanent customer queues

NARCIS (Netherlands)

Cheung, S.K.; van den Berg, Hans Leo; Boucherie, Richardus J.

2005-01-01

We obtain a decomposition result for the steady state queue length distribution in egalitarian processor-sharing (PS) models. In particular, for an egalitarian PS queue with $K$ customer classes, we show that the marginal queue length distribution for class $k$ factorizes over the number of other

Permutations avoiding an increasing number of length-increasing forbidden subsequences

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Elena Barcucci

2000-12-01

Full Text Available A permutation π is said to be τ-avoiding if it does not contain any subsequence having all the same pairwise comparisons as τ. This paper concerns the characterization and enumeration of permutations which avoid a set F j of subsequences increasing both in number and in length at the same time. Let F j be the set of subsequences of the form σ(j+1(j+2, σ being any permutation on {1,...,j}. For j=1 the only subsequence in F 1 is 123 and the 123-avoiding permutations are enumerated by the Catalan numbers; for j=2 the subsequences in F 2 are 1234 2134 and the (1234,2134 avoiding permutations are enumerated by the Schröder numbers; for each other value of j greater than 2 the subsequences in F j are j! and their length is (j+2 the permutations avoiding these j! subsequences are enumerated by a number sequence {a n } such that C n ≤ a n ≤ n!, C n being the n th Catalan number. For each j we determine the generating function of permutations avoiding the subsequences in F j according to the length, to the number of left minima and of non-inversions.

Sonourethrography of anterior urethral strictures: assessment of length and degree

International Nuclear Information System (INIS)

Kim, Jong Chul; Jeong, Youn Sin

1994-01-01

We reviewed out experience of sonourethrography(SUG) in male anterior urethral strictures to correlate the stricture length and degree seen on SUG with those on urethroscopy, surgery or biopsy. During the recent 6 years,both the retrograde urethrography (RUG) and SUG were preformed in 50 occasions for 47 patients with anteriorurethral stricture, that were subsequently evaluated urethroscopically or at surgery. As a whole, the length of the stricture seen on SUG did not correlate very well with that seen on RGU (r2=0.71, p<0.005). Considering the data from the operation as the gold standard, SUG was more accurate than RUG in depicting the exact stricturelength (r2=0.97 and 0.75 respectively,p<0.005). The shorter the lesion, the more accurate the data obtained.Although SUG certainly identified periurethral tissue, it was not adequate in predicting the depth of spongiofibrosis compared with full-depth biopsies in 20 patients. In conclusion, SUG, a dynamic study, accurately defined the stricture site, number and calibre. When compared with RUG, SUG was more accurate in the measurement of stricture length and in the demonstration of periurethral tissue, making it a valuable method in the evaluation of patients with suspected anterior urethral strictures

Walkway Length Determination for Steady State Walking in Young and Older Adults

Science.gov (United States)

Macfarlane, Pamela A.; Looney, Marilyn A.

2008-01-01

The primary purpose of this study was to determine acceleration (AC) and deceleration (DC) distances that would accommodate young and older adults walking at their preferred and fast speeds. A secondary purpose was to determine the minimal walkway length needed to record six steady state (SS) steps (three full gait cycles) for younger and older…

Performance of the S - [chi][squared] Statistic for Full-Information Bifactor Models

Science.gov (United States)

Li, Ying; Rupp, Andre A.

2011-01-01

This study investigated the Type I error rate and power of the multivariate extension of the S - [chi][squared] statistic using unidimensional and multidimensional item response theory (UIRT and MIRT, respectively) models as well as full-information bifactor (FI-bifactor) models through simulation. Manipulated factors included test length, sample…

CEBAF Upgrade Bunch Length Measurements

Energy Technology Data Exchange (ETDEWEB)

Ahmad, Mahmoud [Old Dominion Univ., Norfolk, VA (United States)

2016-05-01

Many accelerators use short electron bunches and measuring the bunch length is important for efficient operations. CEBAF needs a suitable bunch length because bunches that are too long will result in beam interruption to the halls due to excessive energy spread and beam loss. In this work, bunch length is measured by invasive and non-invasive techniques at different beam energies. Two new measurement techniques have been commissioned; a harmonic cavity showed good results compared to expectations from simulation, and a real time interferometer is commissioned and first checkouts were performed. Three other techniques were used for measurements and comparison purposes without modifying the old procedures. Two of them can be used when the beam is not compressed longitudinally while the other one, the synchrotron light monitor, can be used with compressed or uncompressed beam.

Keeping disease at arm's length

DEFF Research Database (Denmark)

Lassen, Aske Juul

2015-01-01

active ageing change everyday life with chronic disease, and how do older people combine an active life with a range of chronic diseases? The participants in the study use activities to keep their diseases at arm’s length, and this distancing of disease at the same time enables them to engage in social...... and physical activities at the activity centre. In this way, keeping disease at arm’s length is analysed as an ambiguous health strategy. The article shows the importance of looking into how active ageing is practised, as active ageing seems to work well in the everyday life of the older people by not giving...... emphasis to disease. The article is based on ethnographic fieldwork and uses vignettes of four participants to show how they each keep diseases at arm’s length....

Waterborne polyurethane single-ion electrolyte from aliphatic diisocyanate and various molecular length of polyethylene glycol

Directory of Open Access Journals (Sweden)

2007-03-01

Full Text Available The waterborne polyurethane (WPU dispersions from the reaction of cycloaliphatic diisocyanates [4,4’-methylenebis(cyclohexyl isocyanate (H12MDI and isophorone diisocyanate (IPDI] and polyethylene glycol (PEG with various molecular lengths were synthesized using our modified acetone process. Differetial scanning calorimeter (DSC and Fourier transform infrared spectroscopy (FTIR were utilized to characterize WPU films for the behavior of their crystallinity and H-bonding of WPU films. The Tg value of WPU increases with increasing the molecular length of PEG, whereas the Tm of WPU decreases with increasing PEG length. Alternating current (AC impedance experiments were performed to determine the ionic conductivities of WPU films. The WPU gel electrolytes exhibits an ionic conductivity as high as ~ 10-5 S/cm at room temperature.

The Effect of Gestational Age on Axial Length of the Eyes of Premature Infants

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Mehmet Ali Sekeroglu

2016-01-01

Full Text Available Aim: The aim of the present study is to evaluate the axial length of the eyes of premature infants without retinopathy of prematurity and to document the relationship with gestational age and changes as infants grew-up. Material and Method: The axial length of the eyes were measured by using a mobile A-scan ultrasonographic biometry device just before the first retinopathy of prematurity screening examination and 4-weeks thereafter. Results: One-hundred and thirty-six infants with a mean gestational age of 31,7±2,7 weeks and a birth-weight of 1561.0±379.3 g were included in the study. Axial length measurements were done at a mean postconceptional age of 35.8 ±2.6 (31-40 and 39.8±2.7 (35-44 weeks, consecutively. The mean axial length at first and second visits were 16.43±0.42 mm (15.28-17.13 and 16.69±0.41 mm (15.60-17.70, consecutively (p

Effect of canal length and curvature on working length alteration with WaveOne reciprocating files.

Science.gov (United States)

Berutti, Elio; Chiandussi, Giorgio; Paolino, Davide Salvatore; Scotti, Nicola; Cantatore, Giuseppe; Castellucci, Arnaldo; Pasqualini, Damiano

2011-12-01

This study evaluated the working length (WL) modification after instrumentation with WaveOne Primary (Dentsply Maillefer, Ballaigues, Switzerland) reciprocating files and the incidence of overinstrumentation in relation to the initial WL. Thirty-two root canals of permanent teeth were used. The angles of curvature of the canals were calculated on digital radiographs. The initial WL with K-files was transferred to the matched WaveOne Primary reciprocating files. After glide paths were established with PathFile (Dentsply Maillefer, Ballaigues, Switzerland), canals were shaped with WaveOne Primary referring to the initial WL. The difference between the postinstrumentation canal length and the initial canal length was analyzed by using a fiberoptic inspection microscope. Data were analyzed with a balanced 2-way factorial analysis of variance (P < .05). Referring to the initial WL, 24 of 32 WaveOne Primary files projected beyond the experimental apical foramen (minimum-maximum, 0.14-0.76 mm). A significant decrease in the canal length after instrumentation (95% confidence interval ranging from -0.34 mm to -0.26 mm) was detected. The canal curvature significantly influenced the WL variation (F(1) = 30.65, P < .001). The interaction between the initial canal length and the canal curvature was statistically significant (F(2) = 4.38, P = .014). Checking the WL before preparation of the apical third of the root canal is recommended when using the new WaveOne NiTi single-file system. Copyright © 2011 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

Maternal telomere length inheritance in the king penguin.

Science.gov (United States)

Reichert, S; Rojas, E R; Zahn, S; Robin, J-P; Criscuolo, F; Massemin, S

2015-01-01

Telomeres are emerging as a biomarker for ageing and survival, and are likely important in shaping life-history trade-offs. In particular, telomere length with which one starts in life has been linked to lifelong survival, suggesting that early telomere dynamics are somehow related to life-history trajectories. This result highlights the importance of determining the extent to which telomere length is inherited, as a crucial factor determining early life telomere length. Given the scarcity of species for which telomere length inheritance has been studied, it is pressing to assess the generality of telomere length inheritance patterns. Further, information on how this pattern changes over the course of growth in individuals living under natural conditions should provide some insight on the extent to which environmental constraints also shape telomere dynamics. To fill this gap partly, we followed telomere inheritance in a population of king penguins (Aptenodytes patagonicus). We tested for paternal and maternal influence on chick initial telomere length (10 days old after hatching), and how these relationships changed with chick age (at 70, 200 and 300 days old). Based on a correlative approach, offspring telomere length was positively associated with maternal telomere length early in life (at 10 days old). However, this relationship was not significant at older ages. These data suggest that telomere length in birds is maternally inherited. Nonetheless, the influence of environmental conditions during growth remained an important factor shaping telomere length, as the maternal link disappeared with chicks' age.

Allometric relationships among body mass, MUZZLE-tail length, and tibia length during the growth of Wistar rats.

Science.gov (United States)

Santiago, Hildemberg Agostinho Rocha de; De Pierro, Lucas Rodolfo; Reis, Rafael Menezes; Caluz, Antônio Gabriel Ricardo Engracia; Ribeiro, Victor Barbosa; Volpon, José Batista

2015-11-01

To investigate allometric relationships among body mass (BM), muzzle-tail length (MTL), and tibia length (TL) in Wistar rats and establish their growth rate change parameters. Eighteen male and 18 female Wistar rats were studied from the 3rd to the 21st week of age. BM, MTL, and TL were measured daily, and relative growth was compared using allometry. A positive correlation between BM and MTL (p<0.05) and BM and TL (p<0.05) was observed. Males and females showed comparable curves; however, females had turning points at a younger age. The allometric relationship between BM and MTL presented a regular increase until reaching a mass of 351 g (males) and 405 g (females). BM and TL showed an initial increase until 185 g (males) and 182 g (females), and then reached a plateau that finished at 412 g (males) and 334 g (females), to display another increase. The allometric relationship of body mass with animal length and tibia length was comparable for male and female rats, with female rats maturing earlier. Animal longitudinal growth occurred in a single stage. In contrast, tibia length depicted two stages of accelerated growth with an intermediate period of deceleration.

Effects of brood size manipulation and common origin on phenotype and telomere length in nestling collared flycatchers

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Voillemot Marie

2012-08-01

Full Text Available Abstract Background Evidence is accumulating that telomere length is a good predictor of life expectancy, especially early in life, thus calling for determining the factors that affect telomere length at this stage. Here, we investigated the relative influence of early growth conditions and origin (genetics and early maternal effects on telomere length of collared flycatchers (Ficedula albicollis at fledging. We experimentally transferred hatchlings among brood triplets to create reduced, control (i.e. unchanged final nestling number and enlarged broods. Results Although our treatment significantly affected body mass at fledging, we found no evidence that increased sibling competition affected nestling tarsus length and telomere length. However, mixed models showed that brood triplets explained a significant part of the variance in body mass (18% and telomere length (19%, but not tarsus length (13%, emphasizing that unmanipulated early environmental factors influenced telomere length. These models also revealed low, but significant, heritability of telomere length (h2 = 0.09. For comparison, the heritability of nestling body mass and tarsus length was 0.36 and 0.39, respectively, which was in the range of previously published estimates for those two traits in this species. Conclusion Those findings in a wild bird population demonstrate that telomere length at the end of the growth period is weakly, but significantly, determined by genetic and/or maternal factors taking place before hatching. However, we found no evidence that the brood size manipulation experiment, and by extension the early growth conditions, influenced nestling telomere length. The weak heritability of telomere length suggests a close association with fitness in natural populations.

Morphometric Characteristics and Length-Weight Relationship of Russian Sturgeon Juveniles Fed with Different Ratio

Directory of Open Access Journals (Sweden)

Raluca Cristina ANDREI(GURIENCU

2017-11-01

Full Text Available The aim of this paper was to analyze some morphometric characteristics and the correlation between them for Russian sturgeon juveniles (Acipenser gueldenstaedtii reared in a recirculating aquaculture system fed at different fed with different ratio: 1% body weight (BW, 1.5% BW, 2% BW and ad libitum feeding (which was around 2.8% BW.Fish, with an average body mass around 248.194 ± 1.59 g. Following biometric measurements were made for each fish, including weight (W, total length (TL, standard length (SL, fork length (FL, maximum body depth (last depth of caudal peduncle, H; preanal distance (AD, predorsal distance (PD, length of head (C, preorbital distance (PO, length of pectoral fin (LPF, interorbital distance (ID, maximum width of head (MH, width of mouth (WM, width of the head at the level of the mouth (WHM. The obtained results showed significant differences between all morphometric measurements (p<0.05 for all the experimental variants, emphasizing that in the ad libitum feeding all morphometric measurements were significantly higher than in the other experimental variants. In order to highlight more eloquent these differences, were developed some linear regressions between the morphometric measurements and significant positive correlation (p<0.05 between dependent and independent variables were found.

Threshold Research on Highway Length under Typical Landscape Patterns Based on Drivers’ Physiological Performance

Directory of Open Access Journals (Sweden)

Xia Zhao

2015-01-01

Full Text Available The appropriately landscaped highway scenes may not only help improve road safety and comfort but also help protect ecological environment. Yet there is very little research data on highway length threshold with consideration of distinctive landscape patterns. Against this backdrop, the paper aims to quantitatively analyze highway landscape’s effect on driving behavior based on drivers’ physiological performance and quantify highway length thresholds under three typical landscape patterns, namely, “open,” “semiopen,” and “vertical” ones. The statistical analysis was based on data collected in a driving simulator and electrocardiograph. Specifically, vehicle-related data, ECG data, and supplemental subjective stress perception were collected. The study extracted two characteristic indices, lane deviation and LF/HF, and extrapolated the drivers’ U-shaped physiological response to landscape patterns. Models on highway length were built based on LF/HF’s variation trend with highway length. The results revealed that the theoretical highway length threshold tended to increase when the landscape pattern was switched to open, semiopen, and vertical ones. And the reliability and accuracy of the results were validated by questionnaires and field operational tests. Findings from this research will assist practitioners in taking active environmental countermeasures pertaining to different roadside landscape patterns.

Leukocyte telomere length and hippocampus volume: a meta-analysis [version 1; referees: 2 approved

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Gustav Nilsonne

2015-10-01

Full Text Available Leukocyte telomere length has been shown to correlate to hippocampus volume, but effect estimates differ in magnitude and are not uniformly positive. This study aimed primarily to investigate the relationship between leukocyte telomere length and hippocampus gray matter volume by meta-analysis and secondarily to investigate possible effect moderators. Five studies were included with a total of 2107 participants, of which 1960 were contributed by one single influential study. A random-effects meta-analysis estimated the effect to r = 0.12 [95% CI -0.13, 0.37] in the presence of heterogeneity and a subjectively estimated moderate to high risk of bias. There was no evidence that apolipoprotein E (APOE genotype was an effect moderator, nor that the ratio of leukocyte telomerase activity to telomere length was a better predictor than leukocyte telomere length for hippocampus volume. This meta-analysis, while not proving a positive relationship, also is not able to disprove the earlier finding of a positive correlation in the one large study included in analyses. We propose that a relationship between leukocyte telomere length and hippocamus volume may be mediated by transmigrating monocytes which differentiate into microglia in the brain parenchyma.

Assessment of a robust model protocol with accelerated throughput for a human recombinant full length estrogen receptor-alpha binding assay: protocol optimization and intralaboratory assay performance as initial steps towards validation.

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Freyberger, Alexius; Wilson, Vickie; Weimer, Marc; Tan, Shirlee; Tran, Hoai-Son; Ahr, Hans-Jürgen

2010-08-01

Despite about two decades of research in the field of endocrine active compounds, still no validated human recombinant (hr) estrogen receptor-alpha (ERalpha) binding assay is available, although hr-ERalpha is available from several sources. In a joint effort, US EPA and Bayer Schering Pharma with funding from the EU-sponsored 6th framework project, ReProTect, developed a model protocol for such a binding assay. Important features of this assay are the use of a full length hr-ERalpha and performance in a 96-well plate format. A full length hr-ERalpha was chosen, as it was considered to provide the most accurate and human-relevant results, whereas truncated receptors could perform differently. Besides three reference compounds [17beta-estradiol, norethynodrel, dibutylphthalate] nine test compounds with different affinities for the ERalpha [diethylstilbestrol (DES), ethynylestradiol, meso-hexestrol, equol, genistein, o,p'-DDT, nonylphenol, n-butylparaben, and corticosterone] were used to explore the performance of the assay. Three independent experiments per compound were performed on different days, and dilutions of test compounds from deep-frozen stocks, solutions of radiolabeled ligand and receptor preparation were freshly prepared for each experiment. The ERalpha binding properties of reference and test compounds were well detected. As expected dibutylphthalate and corticosterone were non-binders in this assay. In terms of the relative ranking of binding affinities, there was good agreement with published data obtained from experiments using a human recombinant ERalpha ligand binding domain. Irrespective of the chemical nature of the compound, individual IC(50)-values for a given compound varied by not more than a factor of 2.5. Our data demonstrate that the assay was robust and reliably ranked compounds with strong, weak, and no affinity for the ERalpha with high accuracy. It avoids the manipulation and use of animals, i.e., the preparation of uterine cytosol as

Homogeneous Field and WKB Approximation in Deformed Quantum Mechanics with Minimal Length

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Jun Tao

2015-01-01

Full Text Available In the framework of the deformed quantum mechanics with a minimal length, we consider the motion of a nonrelativistic particle in a homogeneous external field. We find the integral representation for the physically acceptable wave function in the position representation. Using the method of steepest descent, we obtain the asymptotic expansions of the wave function at large positive and negative arguments. We then employ the leading asymptotic expressions to derive the WKB connection formula, which proceeds from classically forbidden region to classically allowed one through a turning point. By the WKB connection formula, we prove the Bohr-Sommerfeld quantization rule up to Oβ2. We also show that if the slope of the potential at a turning point is too steep, the WKB connection formula is no longer valid around the turning point. The effects of the minimal length on the classical motions are investigated using the Hamilton-Jacobi method. We also use the Bohr-Sommerfeld quantization to study statistical physics in deformed spaces with the minimal length.

Integration of length and curvature in haptic perception.

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Panday, Virjanand; Tiest, Wouter M Bergmann; Kappers, Astrid M L

2014-01-24

We investigated if and how length and curvature information are integrated when an object is explored in one hand. Subjects were asked to explore four types of objects between thumb and index finger. Objects differed in either length, curvature, both length and curvature correlated as in a circle, or anti-correlated. We found that when both length and curvature are present, performance is significantly better than when only one of the two cues is available. Therefore, we conclude that there is integration of length and curvature. Moreover, if the two cues are correlated in a circular cross-section instead of in an anti-correlated way, performance is better than predicted by a combination of two independent cues. We conclude that integration of curvature and length is highly efficient when the cues in the object are combined as in a circle, which is the most common combination of curvature and length in daily life.

Performance Evaluation Of Furrow Lengths And Field Application Techniques

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Issaka

2015-08-01

Full Text Available Abstract The study evaluated performance of furrow lengths and field application techniques. The experiment was conducted on 2000 m2 field at Bontanga irrigation scheme. Randomized Complete Block Design RCBD was used with three replicates. The replicates include Blocks A B and C of furrow lengths 100 m 75 m and 50 m respectively. Each replicate had surge cut-off cut-back and bunds treatments. Water was introduced into the furrows and the advance distances and time were measured. Results of the study showed that at Block A surge technique recorded the highest advance rate of 1.26 minm and opportunity time of 11 min whilst bunds recorded the lowest advance rate of 0.92 minm. Significant difference 3.32 pamp88050.05 occurred between treatment means of field application techniques at Block A 100 m. Significant difference 2.71 pamp88050.05 was also recorded between treatment means. At Block B 75 m there was significant difference 2.71 pamp88050.05 between treatment means. No significant difference 0.14 pamp88040.05 was observed among surge cut-back and bunds techniques. There was significant difference 2.60 pamp88050.05 between treatment means but no significant difference between cut-back and bunds techniques in Block C 50 m. Their performance was ranked in the order Surge Cut-back Cut-off Bunds for furrow lengths 100 m 75 m and 50 m respectively.

Bedside prediction of right subclavian venous catheter insertion length

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Yoon Ji Choi

2014-12-01

Full Text Available Background and objective: The present study aimed to evaluate whether right subclavian vein (SCV catheter insertion depth can be predicted reliably by the distances from the SCV insertion site to the ipsilateral clavicular notch directly (denoted as I-IC, via the top of the SCV arch, or via the clavicle (denoted as I-T-IC and I-C-IC, respectively. Method: In total, 70 SCV catheterizations were studied. The I-IC, I-T-IC, and I-C-IC distances in each case were measured after ultrasound-guided SCV catheter insertion. The actual length of the catheter between the insertion site and the ipsilateral clavicular notch, denoted as L, was calculated by using chest X-ray. Results: L differed from the I-T-IC, I-C-IC, and I-IC distances by 0.14±0.53, 2.19±1.17, and -0.45 ±0.68 cm, respectively. The mean I-T-IC distance was the most similar to the mean L (intraclass correlation coefficient = 0.89. The mean I-IC was significantly shorter than L, while the mean I-C-IC was significantly longer. Linear regression analysis provided the following formula: Predicted SCV catheter insertion length (cm = -0.037 + 0.036 × Height (cm + 0.903 × I-T-IC (cm (adjusted r2 =0.64. Conclusion: The I-T-IC distance may be a reliable bedside predictor of the optimal insertion length for a right SCV cannulation.

The Effect of Height, Wing Length, and Wing Symmetry on Tabebuia rosea Seed Dispersal

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Yasmeen Moussa

2014-12-01

Full Text Available The relationship between the vertical drop height and the horizontal distance traveled (dispersal ratio was investigated for a sample of fifty Tabebuia rosea seeds by dropping the seeds from five heights ranging from 1.00 to 2.00 meters. The dispersal ratio was found to be a constant 0.16 m/m for these heights. The effects of total seed length and asymmetry of seed wings on dispersal ratio were also measured using separate samples of fifty Tabebuia rosea seeds. It was found that neither seed length nor asymmetry had a significant effect on the dispersal ratio.

RUNX2 tandem repeats and the evolution of facial length in placental mammals

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Pointer Marie A

2012-06-01

Full Text Available Abstract Background When simple sequence repeats are integrated into functional genes, they can potentially act as evolutionary ‘tuning knobs’, supplying abundant genetic variation with minimal risk of pleiotropic deleterious effects. The genetic basis of variation in facial shape and length represents a possible example of this phenomenon. Runt-related transcription factor 2 (RUNX2, which is involved in osteoblast differentiation, contains a functionally-important tandem repeat of glutamine and alanine amino acids. The ratio of glutamines to alanines (the QA ratio in this protein seemingly influences the regulation of bone development. Notably, in domestic breeds of dog, and in carnivorans in general, the ratio of glutamines to alanines is strongly correlated with facial length. Results In this study we examine whether this correlation holds true across placental mammals, particularly those mammals for which facial length is highly variable and related to adaptive behavior and lifestyle (e.g., primates, afrotherians, xenarthrans. We obtained relative facial length measurements and RUNX2 sequences for 41 mammalian species representing 12 orders. Using both a phylogenetic generalized least squares model and a recently-developed Bayesian comparative method, we tested for a correlation between genetic and morphometric data while controlling for phylogeny, evolutionary rates, and divergence times. Non-carnivoran taxa generally had substantially lower glutamine-alanine ratios than carnivorans (primates and xenarthrans with means of 1.34 and 1.25, respectively, compared to a mean of 3.1 for carnivorans, and we found no correlation between RUNX2 sequence and face length across placental mammals. Conclusions Results of our diverse comparative phylogenetic analyses indicate that QA ratio does not consistently correlate with face length across the 41 mammalian taxa considered. Thus, although RUNX2 might function as a ‘tuning knob’ modifying face

Factors related to axial length elongation and myopia progression in orthokeratology practice.

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Bingjie Wang

Full Text Available To investigate which baseline factors are predictive for axial length growth over an average period of 2.5 years in a group of children wearing orthokeratology (OK contact lenses.In this retrospective study, the clinical records of 249 new OK wearers between January 2012 and December 2013 from the contact lens clinic at the Eye and ENT Hospital of Fudan University were reviewed. The primary outcome measure was axial length change from baseline to the time of review (July-August 2015. Independent variables included baseline measures of age at initiation of OK wear, gender, refractive error (spherical equivalent, astigmatism, average keratometry, corneal toricity, central corneal thickness, white-to-white corneal diameter, pupil size, corneal topography eccentricity value (e-value, intraocular pressure (IOP and total time in follow-up (months total. The contributions of all independent variables on axial length change at the time of review were assessed using univariate and multivariable regression analyses.Univariate analyses of the right eyes of 249 OK patients showed that smaller increases in axial length were associated with older age at the onset of OK lens wear, greater baseline spherical equivalent myopic refractive error, less time in follow-up and a smaller e-value. Multivariable analyses of the significant right eye variables showed that the factors associated with smaller axial length growth were older age at the onset of OK lens wear (p<0.0001, greater baseline spherical equivalent myopic refractive error (p = 0.0046 and less time in follow-up (p<0.0001.The baseline factors demonstrating the greatest correlation with reduced axial length elongation during OK lens wear in myopic children included greater baseline spherical equivalent myopic refractive error and older age at the onset of OK lens wear.

Microstructure, length, and connection of limbic tracts in normal human brain development

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Qiaowen eYu

2014-08-01

Full Text Available The cingulum and fornix play an important role in memory, attention, spatial orientation and feeling functions. Both microstructure and length of these limbic tracts can be affected by mental disorders such as Alzheimer’s disease, depression, autism, anxiety, and schizophrenia. To date, there has been little systematic characterization of their microstructure, length and functional connectivity in normally developing brains. In this study, diffusion tensor imaging (DTI and resting state functional MRI (rs-fMRI data from 65 normally developing right-handed subjects from birth to young adulthood was acquired. After cingulate gyrus part of the cingulum (cgc, hippocampal part of the cingulum (cgh and fornix (fx were traced with DTI tractography, absolute and normalized tract lengths and DTI-derived metrics including fractional anisotropy, mean, axial and radial diffusivity were measured for traced limbic tracts. Free water elimination (FWE algorithm was adopted to improve accuracy of the measurements of DTI-derived metrics. The role of these limbic tracts in the functional network at birth and adulthood was explored. We found a logarithmic age-dependent trajectory for FWE-corrected DTI metric changes with fast increase of microstructural integrity from birth to 2-year-old followed by a slow increase to 25-year-old. Normalized tract length of cgc increases with age, while no significant relationship with age was found for normalized tract lengths of cgh and fx. Stronger microstructural integrity on the left side compared to that of right side was found. With integrated DTI and rs-fMRI, the key connectional role of cgc and cgh in the default mode network (DMN was confirmed as early as birth. Systematic characterization of length and DTI metrics after FWE correction of limbic tracts offers insight into their morphological and microstructural developmental trajectories. These trajectories may serve as a normal reference for pediatric patients with

Evaluation of the Normal Fetal Kidney Length and Its Correlation with Gestational Age

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Farrokh Seilanian Toosi

2013-05-01

Full Text Available A true estimation of gestational age (GA plays an important role in quality maternity care and scheduling the labor date. This study aimed to evaluate the normal fetal kidney length (KL and its correlation with GA. A cross-sectional study on 92 pregnant women between 8th and 10th week of gestation with normal singleton pregnancy underwent standard ultrasound fetal biometry and kidney length measurement. univariate and multivariate linear regression analysis was used to create a predictive equation to estimate GA on the KL and fetobiometry parameters. A significant correlation was found between GA and KL (r=0.83, P<0.002. The best GA predictor was obtained by combining head circumference, fetal biparietal diameter, femur length and KL with a standard error (SE about 14.2 days. Our findings showed that KL measurements combination with other fetal biometric parameters could predict age of pregnancy with a better precision.

The impact of sound technology on the distribution of shot lengths in Hollywood cinema, 1920 to 1933

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Nick Redfern

2012-11-01

Full Text Available The impact of sound technology on Hollywood is analysed through looking at the median shot lengths of silent films from the 1920s (n = 54 and early sound films (n = 106. The results show a large increase in the median shot lengths with the introduction of sound (Mann Whitney U = 554.0, Z = -8.33, p = <0.01, PS = 0.0968, estimated to be 2.0s (95% CI: 1.6, 2.4. The dispersion of shot lengths measured using the robust estimator Qn shows a similarly large increase in the dispersion of shot lengths with the transition to sound (Mann Whitney U = 319.0, Z = -9.18, p = <0.01, PS = 0.0557, estimated to be 2.0s (95% CI: 1.7, 2.4.

Photoluminescence Enhancement of Poly(3-methylthiophene Nanowires upon Length Variable DNA Hybridization

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Jingyuan Huang

2018-01-01

Full Text Available The use of low-dimensional inorganic or organic nanomaterials has advantages for DNA and protein recognition due to their sensitivity, accuracy, and physical size matching. In this research, poly(3-methylthiophene (P3MT nanowires (NWs are electrochemically prepared with dopant followed by functionalization with probe DNA (pDNA sequence through electrostatic interaction. Various lengths of pDNA sequences (10-, 20- and 30-mer are conjugated to the P3MT NWs respectively followed with hybridization with their complementary target DNA (tDNA sequences. The nanoscale photoluminescence (PL properties of the P3MT NWs are studied throughout the whole process at solid state. In addition, the correlation between the PL enhancement and the double helix DNA with various lengths is demonstrated.

Sarcomere length-dependence of activity-dependent twitch potentiation in mouse skeletal muscle

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MacIntosh Brian R

2002-12-01

Full Text Available Abstract Background It has been reported that potentiation of a skeletal muscle twitch response is proportional to muscle length with a negative slope during staircase, and a positive slope during posttetanic potentiation. This study was done to directly compare staircase and posttetanic responses with measurement of sarcomere length to compare their length-dependence. Methods Mouse extensor digitorum longus (EDL muscles were dissected to small bundles of fibers, which permit measurement of sarcomere length (SL, by laser diffraction. In vitro fixed-end contractions of EDL fiber bundles were elicited at 22°C and 35°C at sarcomere lengths ranging from 2.35 μm to 3.85 μm. Twitch contractions were assessed before and after 1.5 s of 75 Hz stimulation at 22°C or during 10 s of 10 Hz stimulation at 22°C or 35°C. Results Staircase potentiation was greater at 35°C than 22°C, and the relative magnitude of the twitch contraction (Pt*/Pt was proportional to sarcomere length with a negative slope, over the range 2.3 μm – 3.7 μm. Linear regression yielded the following: Pt*/Pt = -0.59·SL+3.27 (r2 = 0.74; Pt*/Pt = -0.39·SL+2.34 (r2 = 0.48; and Pt*/Pt = -0.50·SL+2.45 (r2 = 0.80 for staircase at 35°C, and 22°C and posttetanic response respectively. Posttetanic depression rather than potentiation was present at long SL. This indicates that there may be two processes operating in these muscles to modulate the force: one that enhances and a second that depresses the force. Either or both of these processes may have a length-dependence of its mechanism. Conclusion There is no evidence that posttetanic potentiation is fundamentally different from staircase in these muscles.

Universal and idiosyncratic characteristic lengths in bacterial genomes

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Junier, Ivan; Frémont, Paul; Rivoire, Olivier

2018-05-01

In condensed matter physics, simplified descriptions are obtained by coarse-graining the features of a system at a certain characteristic length, defined as the typical length beyond which some properties are no longer correlated. From a physics standpoint, in vitro DNA has thus a characteristic length of 300 base pairs (bp), the Kuhn length of the molecule beyond which correlations in its orientations are typically lost. From a biology standpoint, in vivo DNA has a characteristic length of 1000 bp, the typical length of genes. Since bacteria live in very different physico-chemical conditions and since their genomes lack translational invariance, whether larger, universal characteristic lengths exist is a non-trivial question. Here, we examine this problem by leveraging the large number of fully sequenced genomes available in public databases. By analyzing GC content correlations and the evolutionary conservation of gene contexts (synteny) in hundreds of bacterial chromosomes, we conclude that a fundamental characteristic length around 10–20 kb can be defined. This characteristic length reflects elementary structures involved in the coordination of gene expression, which are present all along the genome of nearly all bacteria. Technically, reaching this conclusion required us to implement methods that are insensitive to the presence of large idiosyncratic genomic features, which may co-exist along these fundamental universal structures.

Electron Effective-Attenuation-Length Database

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SRD 82 NIST Electron Effective-Attenuation-Length Database (PC database, no charge)   This database provides values of electron effective attenuation lengths (EALs) in solid elements and compounds at selected electron energies between 50 eV and 2,000 eV. The database was designed mainly to provide EALs (to account for effects of elastic-eletron scattering) for applications in surface analysis by Auger-electron spectroscopy (AES) and X-ray photoelectron spectroscopy (XPS).

Roentgenologic investigations for the anterior tooth length

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Cho, Won Pyo; Ahn, Hyung Kyu [College of Dentistry, Seoul National University , Seoul (Korea, Republic of)

1972-11-15

The author measured the length of crown, root and tooth on the films which was taken by intraoral bisecting technic with mesh plate on the films. The films were taken from the dry skulls, dentiform, same patients who had to be removed their upper incisors, and the other patients who admitted for dental care. From this serial experiment the results were made as follows: 1. By using the film and mesh plate in the oral cavity, the real tooth length can be measured easily on the film surfaces. 2. The film distortion in the oral cavity can be avoided when taking the film using the mesh plate and film together. 3. When measuring the film, length of crown was elongated and length of root was shortened. 4. When using the well-trained bisecting technic, the real tooth length can be measured directly on the intraoral film.

Dysregulation of gene expression in the striatum of BACHD rats expressing full-length mutant huntingtin and associated abnormalities on molecular and protein levels.

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Yu-Taeger, Libo; Bonin, Michael; Stricker-Shaver, Janice; Riess, Olaf; Nguyen, Hoa Huu Phuc

2017-05-01

Huntington disease (HD) is an autosomal dominantly inherited neurodegenerative disorder caused by a CAG repeat expansion in the gene coding for the huntingtin protein (HTT). Mutant HTT (mHTT) has been proposed to cause neuronal dysfunction and neuronal loss through multiple mechanisms. Transcriptional changes may be a core pathogenic feature of HD. Utilizing the Affymetrix platform we performed a genome-wide RNA expression analysis in two BACHD transgenic rat lines (TG5 and TG9) at 12 months of age, both of which carry full-length human mHTT but with different expression levels. By defining the threshold of significance at p < 0.01, we found 1608 genes and 871 genes differentially expressed in both TG5 and TG9 rats when compared to the wild type littermates, respectively. We only chose the highly up-/down-regulated genes for further analysis by setting an additional threshold of 1.5 fold change. Comparing gene expression profiles of human HD brains and BACHD rats revealed a high concordance in both functional and IPA (Ingenuity Pathway Analysis) canonical pathways relevant to HD. In addition, we investigated the causes leading to gene expression changes at molecular and protein levels in BACHD rats including the involvement of polyQ-containing transcription factors TATA box-binding protein (TBP), Sp1 and CBP as well as the chromatin structure. We demonstrate that the BACHD rat model recapitulates the gene expression changes of the human disease supporting its role as a preclinical research animal model. We also show for the first time that TFIID complex formation is reduced, while soluble TBP is increased in an HD model. This finding suggests that mHTT is a competitor instead of a recruiter of polyQ-containing transcription factors in the transcription process in HD. Copyright © 2017 Elsevier Ltd. All rights reserved.

Upper bound for the length of commutative algebras

International Nuclear Information System (INIS)

Markova, Ol'ga V

2009-01-01

By the length of a finite system of generators for a finite-dimensional associative algebra over an arbitrary field one means the least positive integer k such that the words of length not exceeding k span this algebra (as a vector space). The maximum length for the systems of generators of an algebra is referred to as the length of the algebra. In the present paper, an upper bound for the length of a commutative algebra in terms of a function of two invariants of the algebra, the dimension and the maximal degree of the minimal polynomial for the elements of the algebra, is obtained. As a corollary, a formula for the length of the algebra of diagonal matrices over an arbitrary field is obtained. Bibliography: 8 titles.

Measuring Crack Length in Coarse Grain Ceramics

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Salem, Jonathan A.; Ghosn, Louis J.

2010-01-01

Due to a coarse grain structure, crack lengths in precracked spinel specimens could not be measured optically, so the crack lengths and fracture toughness were estimated by strain gage measurements. An expression was developed via finite element analysis to correlate the measured strain with crack length in four-point flexure. The fracture toughness estimated by the strain gaged samples and another standardized method were in agreement.

Digital Radiography for Determination of Primary Tooth Length: In Vivo and Ex Vivo Studies

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Maria D. Basso

2015-01-01

Full Text Available Background. Methods for determining the root canal length of the primary tooth should yield accurate and reproducible results. In vitro studies show some limitations, which do not allow their findings to be directly transferred to a clinical situation. Aim. To compare the accuracy of radiographic tooth length obtained from in vivo digital radiograph with that obtained from ex vivo digital radiograph. Method. Direct digital radiographs of 20 upper primary incisors were performed in teeth (2/3 radicular resorption that were radiographed by an intraoral sensor, according to the long-cone technique. Teeth were extracted, measured, and mounted in a resin block, and then radiographic template was used to standardise the sensor-target distance (30 cm. The apparent tooth length (APTL was obtained from the computer screen by means of an electronic ruler accompanying the digital radiography software (CDR 2.0, whereas the actual tooth length (ACTL was obtained by means of a digital calliper following extraction. Data were compared to the ACTL by variance analysis and Pearson’s correlation test. Results. The values for APTL obtained from in vivo radiography were slightly underestimated, whereas those values obtained from ex vivo were slightly overestimated. No significance was observed (P≤0.48 between APTL and ACTL. Conclusion. The length of primary teeth estimated by in vivo and ex vivo comparisons using digital radiography was found to be similar to the actual tooth length.

Upper Bound for Queue length in Regulated Burst Service Scheduling

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Mahmood Daneshvar Farzanegan

2016-01-01

Full Text Available Quality of Service (QoS provisioning is very important in next computer/communication networks because of increasing multimedia services. Hence, very investigations are performed in this area. Scheduling algorithms effect QoS provisioning. Lately, a scheduling algorithm called Regulated Burst Service Scheduling (RBSS suggested by author in [1] to provide a better service to bursty and delay sensitive services such as video. One of the most significant feature in RBSS is considering burstiness of arrival traffic in scheduling algorithm. In this paper, an upper bound of queue length or buffer size and service curve are calculated by Network Calculus analysis for RBSS. Because in RBSS queue length is a parameter that is considered in scheduling arbitrator, analysis results a differential inequality to obtain service curve. To simplify, arrival traffic is assumed to be linear that is defined in the paper clearly. This paper help to analysis delay in RBSS for different traffic with different specifications. Therefore, QoS provisioning will be evaluated.

Investigating the effects of exam length on performance and cognitive fatigue.

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Jamie L Jensen

Full Text Available This study examined the effects of exam length on student performance and cognitive fatigue in an undergraduate biology classroom. Exams tested higher order thinking skills. To test our hypothesis, we administered standard- and extended-length high-level exams to two populations of non-majors biology students. We gathered exam performance data between conditions as well as performance on the first and second half of exams within conditions. We showed that lengthier exams led to better performance on assessment items shared between conditions, possibly lending support to the spreading activation theory. It also led to greater performance on the final exam, lending support to the testing effect in creative problem solving. Lengthier exams did not result in lower performance due to fatiguing conditions, although students perceived subjective fatigue. Implications of these findings are discussed with respect to assessment practices.

Information-theoretic lengths of Jacobi polynomials

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Guerrero, A; Dehesa, J S [Departamento de Fisica Atomica, Molecular y Nuclear, Universidad de Granada, Granada (Spain); Sanchez-Moreno, P, E-mail: agmartinez@ugr.e, E-mail: pablos@ugr.e, E-mail: dehesa@ugr.e [Instituto ' Carlos I' de Fisica Teorica y Computacional, Universidad de Granada, Granada (Spain)

2010-07-30

The information-theoretic lengths of the Jacobi polynomials P{sup ({alpha}, {beta})}{sub n}(x), which are information-theoretic measures (Renyi, Shannon and Fisher) of their associated Rakhmanov probability density, are investigated. They quantify the spreading of the polynomials along the orthogonality interval [- 1, 1] in a complementary but different way as the root-mean-square or standard deviation because, contrary to this measure, they do not refer to any specific point of the interval. The explicit expressions of the Fisher length are given. The Renyi lengths are found by the use of the combinatorial multivariable Bell polynomials in terms of the polynomial degree n and the parameters ({alpha}, {beta}). The Shannon length, which cannot be exactly calculated because of its logarithmic functional form, is bounded from below by using sharp upper bounds to general densities on [- 1, +1] given in terms of various expectation values; moreover, its asymptotics is also pointed out. Finally, several computational issues relative to these three quantities are carefully analyzed.