bluuebunny/crossref_metadata_2025_split huggingface dataset:
PSAT: A web tool to compare genomic neighborhoods of multiple prokaryotic genomes
Authors: Fong Christine , Rohmer Laurence , Radey Matthew , Wasnick Michael , Brittnacher Mitchell J 
Published: March 2008

Abstract

Background
The conservation of gene order among prokaryotic genomes can provide valuable insight into gene function, protein interactions, or events by which genomes have evolved. Although some tools are available for visualizing and comparing the order of genes between genomes of study, few support an efficient and organized analysis between large numbers of genomes. The Prokaryotic Sequence homology Analysis Tool (PSAT) is a web tool for comparing gene neighborhoods among multiple prokaryotic genomes.

Results
PSAT utilizes a database that is preloaded with gene annotation, BLAST hit results, and gene-clustering scores designed to help identify regions of conserved gene order. Researchers use the PSAT web interface to find a gene of interest in a reference genome and efficiently retrieve the sequence homologs found in other bacterial genomes. The tool generates a graphic of the genomic neighborhood surrounding the selected gene and the corresponding regions for its homologs in each comparison genome. Homologs in each region are color coded to assist users with analyzing gene order among various genomes. In contrast to common comparative analysis methods that filter sequence homolog data based on alignment score cutoffs, PSAT leverages gene context information for homologs, including those with weak alignment scores, enabling a more sensitive analysis. Features for constraining or ordering results are designed to help researchers browse results from large numbers of comparison genomes in an organized manner. PSAT has been demonstrated to be useful for helping to identify gene orthologs and potential functional gene clusters, and detecting genome modifications that may result in loss of function.

Conclusion
PSAT allows researchers to investigate the order of genes within local genomic neighborhoods of multiple genomes. A PSAT web server for public use is available for performing analyses on a growing set of reference genomes through any web browser with no client side software setup or installation required. Source code is freely available to researchers interested in setting up a local version of PSAT for analysis of genomes not available through the public server. Access to the public web server and instructions for obtaining source code can be found at http://www.nwrce.org/psat.
LocateP: Genome-scale subcellular-location predictor for bacterial proteins
Authors: Zhou Miaomiao , Boekhorst Jos , Francke Christof , Siezen Roland J 
Published: March 2008

AbstractBackgroundIn the past decades, various protein subcellular-location (SCL) predictors have been developed. Most of these predictors, like TMHMM 2.0, SignalP 3.0, PrediSi and Phobius, aim at the identification of one or a few SCLs, whereas others such as CELLO and Psortb.v.2.0 aim at a broader classification. Although these tools and pipelines can achieve a high precision in the accurate prediction of signal peptides and transmembrane helices, they have a much lower accuracy when other sequence characteristics are concerned. For instance, it proved notoriously difficult to identify the fate of proteins carrying a putative type I signal peptidase (SPIase) cleavage site, as many of those proteins are retained in the cell membrane as N-terminally anchored membrane proteins. Moreover, most of the SCL classifiers are based on the classification of the Swiss-Prot database and consequently inherited the inconsistency of that SCL classification. As accurate and detailed SCL prediction on a genome scale is highly desired by experimental researchers, we decided to construct a new SCL prediction pipeline: LocateP.ResultsLocateP combines many of the existing high-precision SCL identifiers with our own newly developed identifiers for specific SCLs. The LocateP pipeline was designed such that it mimics protein targeting and secretion processes. It distinguishes 7 different SCLs within Gram-positive bacteria: intracellular, multi-transmembrane, N-terminally membrane anchored, C-terminally membrane anchored, lipid-anchored, LPxTG-type cell-wall anchored, and secreted/released proteins. Moreover, it distinguishes pathways for Sec- or Tat-dependent secretion and alternative secretion of bacteriocin-like proteins. The pipeline was tested on data sets extracted from literature, including experimental proteomics studies. The tests showed that LocateP performs as well as, or even slightly better than other SCL predictors for some locations and outperforms current tools especially where the N-terminally anchored and the SPIase-cleaved secreted proteins are concerned. Overall, the accuracy of LocateP was always higher than 90%. LocateP was then used to predict the SCLs of all proteins encoded by completed Gram-positive bacterial genomes. The results are stored in the database LocateP-DBhttp://www.cmbi.ru.nl/locatep-db[1].ConclusionLocateP is by far the most accurate and detailed protein SCL predictor for Gram-positive bacteria currently available.
Snagger: A user-friendly program for incorporating additional information for tagSNP selection
Authors: Edlund Christopher K , Lee Won H , Li Dalin , Van Den Berg David J , Conti David V 
Published: March 2008

Abstract

Background
There has been considerable effort focused on developing efficient programs for tagging single-nucleotide polymorphisms (SNPs). Many of these programs do not account for potential reduced genomic coverage resulting from genotyping failures nor do they preferentially select SNPs based on functionality, which may be more likely to be biologically important.

Results
We have developed a user-friendly and efficient software program, Snagger, as an extension to the existing open-source software, Haploview, which uses pairwise r
2 linkage disequilibrium between single nucleotide polymorphisms (SNPs) to select tagSNPs. Snagger distinguishes itself from existing SNP selection algorithms, including Tagger, by providing user options that allow for: (1) prioritization of tagSNPs based on certain characteristics, including platform-specific design scores, functionality (i.e., coding status), and chromosomal position, (2) efficient selection of SNPs across multiple populations, (3) selection of tagSNPs outside defined genomic regions to improve coverage and genotyping success, and (4) picking of surrogate tagSNPs that serve as backups for tagSNPs whose failure would result in a significant loss of data. Using HapMap genotype data from ten ENCODE regions and design scores for the Illumina platform, we show similar coverage and design score distribution and fewer total tagSNPs selected by Snagger compared to the web server Tagger.

Conclusion
Snagger improves upon current available tagSNP software packages by providing a means for researchers to select tagSNPs that reliably capture genetic variation across multiple populations while accounting for significant genotyping failure risk and prioritizing on SNP-specific characteristics.
Both selective and neutral processes drive GC content evolution in the human genome
Authors: Pozzoli Uberto , Menozzi Giorgia , Fumagalli Matteo , Cereda Matteo , Comi Giacomo P , Cagliani Rachele , Bresolin Nereo , Sironi Manuela 
Published: March 2008

Abstract

Background
Mammalian genomes consist of regions differing in GC content, referred to as isochores or GC-content domains. The scientific debate is still open as to whether such compositional heterogeneity is a selected or neutral trait.

Results
Here we analyze SNP allele frequencies, retrotransposon insertion polymorphisms (RIPs), as well as fixed substitutions accumulated in the human lineage since its divergence from chimpanzee to indicate that biased gene conversion (BGC) has been playing a role in within-genome GC content variation. Yet, a distinct contribution to GC content evolution is accounted for by a selective process. Accordingly, we searched for independent evidences that GC content distribution does not conform to neutral expectations. Indeed, after correcting for possible biases, we show that intron GC content and size display isochore-specific correlations.

Conclusion
We consider that the more parsimonious explanation for our results is that GC content is subjected to the action of both weak selection and BGC in the human genome with features such as nucleosome positioning or chromatin conformation possibly representing the final target of selective processes. This view might reconcile previous contrasting findings and add some theoretical background to recent evidences suggesting that GC content domains display different behaviors with respect to highly regulated biological processes such as developmentally-stage related gene expression and programmed replication timing during neural stem cell differentiation.
Influence of leukotriene gene polymorphisms on chronic rhinosinusitis
Authors: Al-Shemari Hasan , Bossé Yohan , Hudson Thomas J , Cabaluna Myrna , Duval Melanie , Lemire Mathieu , Vallee-Smedja Sophie , Frenkiel Saul , Desrosiers Martin 
Published: March 2008

Abstract

Background
Chronic rhinosinusitis (CRS) is increasingly viewed as an inflammatory condition of the sinonasal mucosa interacting with bacteria and/or fungi. However, factors conferring susceptibility to disease remain unknown. Advances in genomics offer powerful tools to explore this disorder. The goal of this study was to evaluate the effect of single nucleotide polymorphisms (SNP) on CRS in a panel of genes related to cysteinyl leukotriene metabolism.

Methods
Severe cases of CRS and postal code match controls were recruited prospectively. A total of 206 cases and 200 controls were available for the present study. Using a candidate gene approach, five genes related to cysteinyl leukotriene metabolism were assessed. For each gene, we selected the maximally informative set of common SNPs (tagSNPs) using the European-derived (CEU) HapMap dataset. These SNPs are in arachidonate 5-lipoxygenase (ALOX5), arachidonate 5-lipoxygenase-activating protein (ALOX5AP), leukotriene C4 synthase (LTC4S), cysteinyl leukotriene receptor 1 (CYSLTR1) and cysteinyl leukotriene receptor 2 (CYSLTR2) genes.

Results
A total of 59 SNPs were genotyped to capture the common genetic variations within these genes. Three SNPs located within the ALOX5, CYSLTR1 and ALOX5AP genes reached the nominal p-value threshold (p < 0.05) for association with CRS. However, none of these SNPs resist multiple testing adjustment.

Conclusion
While these initial results do not support that polymorphsims in genes assessed involved in the leukotriene pathways are contributing to the pathogenesis of CRS, this initial study was not powered to detect polymorphisms with relative risk of 2.0 or less, where we could expect many gene effects for complex diseases to occur. Thus, despite this lack of significant association noted in this study, we believe that validation with external populations and the use of better-powered studies in the future may allow more conclusive findings.
Surveillance study of vector species on board passenger ships, Risk factors related to infestations
Authors: Mouchtouri Varvara A , Anagnostopoulou Rimma , Samanidou-Voyadjoglou Anna , Theodoridou Kalliopi , Hatzoglou Chrissi , Kremastinou Jenny , Hadjichristodoulou Christos 
Published: March 2008

Abstract

Background
Passenger ships provide conditions suitable for the survival and growth of pest populations. Arthropods and rodents can gain access directly from the ships' open spaces, can be carried in shiploads, or can be found on humans or animals as ectoparasites. Vectors on board ships may contaminate stored foods, transmit illness on board, or, introduce diseases in new areas. Pest species, ship areas facilitating infestations, and different risk factors related to infestations were identified in 21 ferries.

Methods
486 traps for insects and rodents were placed in 21 ferries. Archives of Public Health Authorities were reviewed to identify complaints regarding the presence of pest species on board ferries from 1994 to 2004. A detail questionnaire was used to collect data on ship characteristics and pest control practices.

Results
Eighteen ferries were infested with flies (85.7%), 11 with cockroaches (52.3%), three with bedbugs, and one with fleas. Other species had been found on board were ants, spiders, butterflies, beetles, and a lizard. A total of 431 Blattella germanica species were captured in 28 (9.96%) traps, and 84.2% of them were nymphs. One ship was highly infested. Cockroach infestation was negatively associated with ferries in which Hazard Analysis Critical Control Point system was applied to ensure food safety on board (Relative Risk, RR = 0.23, p = 0.03), and positively associated with ferries in which cockroaches were observed by crew (RR = 4.09, p = 0.007), no cockroach monitoring log was kept (RR = 5.00, p = 0.02), and pesticide sprays for domestic use were applied by crew (RR = 4.00, p = 0.05). Cockroach infested ships had higher age (p = 0.03). Neither rats nor mice were found on any ship, but three ferries had been infested with a rodent in the past.

Conclusion
Integrated pest control programs should include continuing monitoring for a variety of pest species in different ship locations; pest control measures should be more persistent in older ships. HACCP system aids in the prevention of cockroach infestations on board.
Improved production of human type II procollagen in the yeast Pichia pastoris in shake flasks by a wireless-controlled fed-batch system
Authors: Ruottinen Maria , Bollok Monika , Kögler Martin , Neubauer Antje , Krause Mirja , Hämäläinen Eija-Riitta , Myllyharju Johanna , Vasala Antti , Neubauer Peter 
Published: March 2008

Abstract

Background
Here we describe a new technical solution for optimization of Pichia pastoris shake flask cultures with the example of production of stable human type II collagen. Production of recombinant proteins in P. pastoris is usually performed by controlling gene expression with the strong AOX1 promoter, which is induced by addition of methanol. Optimization of processes using the AOX1 promoter in P. pastoris is generally done in bioreactors by fed-batch fermentation with a controlled continuous addition of methanol for avoiding methanol toxification and carbon/energy starvation. The development of feeding protocols and the study of AOX1-controlled recombinant protein production have been largely made in shake flasks, although shake flasks have very limited possibilities for measurement and control.

Results
By applying on-line pO2 monitoring we demonstrate that the widely used pulse feeding of methanol results in long phases of methanol exhaustion and consequently low expression of AOX1 controlled genes. Furthermore, we provide a solution to apply the fed-batch strategy in shake flasks. The presented solution applies a wireless feeding unit which can be flexibly positioned and allows the use of computer-controlled feeding profiles.
By using the human collagen II as an example we show that a quasi-continuous feeding profile, being the simplest way of a fed-batch fermentation, results in a higher production level of human collagen II. Moreover, the product has a higher proteolytic stability compared to control cultures due to the increased expression of human collagen prolyl 4-hydroxylase as monitored by mRNA and protein levels.

Conclusion
The recommended standard protocol for methanol addition in shake flasks using pulse feeding is non-optimal and leads to repeated long phases of methanol starvation. The problem can be solved by applying the fed-batch technology. The presented wireless feeding unit, together with an on-line monitoring system offers a flexible, simple, and low-cost solution for initial optimization of the production in shake flasks which can be performed in parallel. By this way the fed-batch strategy can be applied from the early screening steps also in laboratories which do not have access to high-cost and complicated bioreactor systems.
Evaluation of the current knowledge limitations in breast cancer research: a gap analysis
Authors: Thompson Alastair , Brennan Keith , Cox Angela , Gee Julia , Harcourt Diana , Harris Adrian , Harvie Michelle , Holen Ingunn , Howell Anthony , Nicholson Robert , Steel Michael , Streuli Charles ,   Breast Cancer Campaign Gap Analysis Meeting (2 November 2006, London, UK)
Published: March 2008

Abstract
Background
A gap analysis was conducted to determine which areas of breast cancer research, if targeted by researchers and funding bodies, could produce the greatest impact on patients.

Methods
Fifty-six Breast Cancer Campaign grant holders and prominent UK breast cancer researchers participated in a gap analysis of current breast cancer research. Before, during and following the meeting, groups in seven key research areas participated in cycles of presentation, literature review and discussion. Summary papers were prepared by each group and collated into this position paper highlighting the research gaps, with recommendations for action.

Results
Gaps were identified in all seven themes. General barriers to progress were lack of financial and practical resources, and poor collaboration between disciplines. Critical gaps in each theme included: (1) genetics (knowledge of genetic changes, their effects and interactions); (2) initiation of breast cancer (how developmental signalling pathways cause ductal elongation and branching at the cellular level and influence stem cell dynamics, and how their disruption initiates tumour formation); (3) progression of breast cancer (deciphering the intracellular and extracellular regulators of early progression, tumour growth, angiogenesis and metastasis); (4) therapies and targets (understanding who develops advanced disease); (5) disease markers (incorporating intelligent trial design into all studies to ensure new treatments are tested in patient groups stratified using biomarkers); (6) prevention (strategies to prevent oestrogen-receptor negative tumours and the long-term effects of chemoprevention for oestrogen-receptor positive tumours); (7) psychosocial aspects of cancer (the use of appropriate psychosocial interventions, and the personal impact of all stages of the disease among patients from a range of ethnic and demographic backgrounds).

Conclusion
Through recommendations to address these gaps with future research, the long-term benefits to patients will include: better estimation of risk in families with breast cancer and strategies to reduce risk; better prediction of drug response and patient prognosis; improved tailoring of treatments to patient subgroups and development of new therapeutic approaches; earlier initiation of treatment; more effective use of resources for screening populations; and an enhanced experience for people with or at risk of breast cancer and their families. The challenge to funding bodies and researchers in all disciplines is to focus on these gaps and to drive advances in knowledge into improvements in patient care.
Analysis of repetitive DNA distribution patterns in the Tribolium castaneum genome
Authors: Wang Suzhi , Lorenzen Marcé D , Beeman Richard W , Brown Susan J 
Published: March 2008

Abstract
Background
Insect genomes vary widely in size, a large fraction of which is often devoted to repetitive DNA. Re-association kinetics indicate that up to 42% of the genome of the red flour beetle, Tribolium castaneum, is repetitive. Analysis of the abundance and distribution of repetitive DNA in the recently sequenced genome of T. castaneum is important for understanding the structure and function of its genome.

Results
Using TRF, TEpipe and RepeatScout we found that approximately 30% of the T. castaneum assembled genome is composed of repetitive DNA. Of this, 17% is found in tandem arrays and the remaining 83% is dispersed, including transposable elements, which in themselves constitute 5-6% of the genome. RepeatScout identified 31 highly repetitive DNA elements with repeat units longer than 100 bp, which constitute 7% of the genome; 65% of these highly repetitive elements and 74% of transposable elements accumulate in regions representing 40% of the assembled genome that is anchored to chromosomes. These regions tend to occur near one end of each chromosome, similar to previously described blocks of pericentric heterochromatin. They contain fewer genes with longer introns, and often correspond with regions of low recombination in the genetic map.

Conclusion
Our study found that transposable elements and other repetitive DNA accumulate in certain regions in the assembled T. castaneum genome. Several lines of evidence suggest these regions are derived from the large blocks of pericentric heterochromatin in T. castaneum chromosomes.
Experimental and Modeling Approach of Irradiation Defects Recovery in Zirconium Alloys: Impact of an Applied Stress
Authors: Ribis Joël , Onimus Fabien , Béchade Jean-Luc , Doriot Sylvie , Cappelaere Chantal , Lemaignan Clément , Barbu Alain , Rabouille Olivier 
Published: March 2008

Abstract
During neutron irradiation, both interstitial and vacancy loops are formed in high concentration in zirconium alloys. Due to this high density of loops, the material is considerably hardened, but the recovery of the radiation damage during a heat treatment leads to a progressive softening of the irradiated material. The recovery of the radiation induced hardening has been investigated using microhardness tests. Transmission electron microscopy (TEM) observations performed on irradiated foils have also shown that the loop density falls while the loop size increases during the thermal annealing. Furthermore, the TEM analysis has revealed that only vacancy loops are present in the material after long term annealing, the interstitial loops having entirely disappeared. A numerical cluster dynamic modeling has also been used in order to reproduce the material recovery for various annealing conditions. The microstructural evolution during mechanical testing with various loading conditions has also been studied. It has been shown that during a creep test with low applied stress (130 MPa) and high temperature (450°C), the microstructure evolution can essentially be explained by the thermal recovery of the loops leading to glide of dislocations as found for an non-irradiated material. At intermediate temperature (400°C), it is shown that for low stress level (130 MPa) the microstructure evolution can also be explained by the thermal recovery of loops, whereas for higher stress (250 MPa), sweeping of loops by gliding dislocations can also occur. In addition, for an applied stress of 130 MPa and a temperature of 400°C, dislocation density is higher in the irradiated material than in the non-irradiated material deformed in the same conditions. It is also shown that secondary slip systems are more activated in the irradiated material than in the non-irradiated material. From this detailed analysis, the mechanical behavior during creep is interpreted in terms of microscopic deformation mechanisms.