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1.
Int J Audiol ; : 1-9, 2023 Sep 28.
Artigo em Inglês | MEDLINE | ID: mdl-37768039

RESUMO

OBJECTIVE: To examine risky leisure noise exposure from listening to music via headphones and to identify potential determinants with special focus on portable listening devices (PLDs) among adolescents over a period of 7.5-years. DESIGN: Data were collected by questionnaires at four equidistant time points (O1-O4). Music exposure via headphones was calculated based on self-reported volume setting and listening duration. Exceeding 85 dB(A) equivalent for a 40-hour working week was defined as risky noise exposure. Determinants of risky headphone and PLD exposure were investigated using generalised estimating equations and accounting for missing data by multiple imputation. STUDY SAMPLE: Closed cohort of 2148 students attending 9th grade of any secondary school type in Regensburg (Germany), during 2009 to 2011. RESULTS: Risky noise exposure from headphone usage was almost twice as high in wave O1 and O2 (at age 15 or 18) compared with 20-23-year-olds in O3 and O4. Risky exposure to headphones and PLDs were associated with younger age, low and medium education, single-parent household and smoking, whereas good self-rated hearing showed a protective effect. Additionally, not being born in Germany was associated with risky PLD exposure. CONCLUSION: Before harmful behaviours become entrenched, starting preventive efforts at a young age is essential.

2.
Int J Audiol ; : 1-9, 2023 May 11.
Artigo em Inglês | MEDLINE | ID: mdl-37167482

RESUMO

OBJECTIVE: To observe total leisure noise (TLN) exposure and to investigate determinants of risky TLN exposure among adolescents and young adults over a ten-year observation period. DESIGN: OHRKAN is a longitudinal study with five equidistantly distributed questionnaires (waves) over ten years. Risky TLN exposure was defined as exceeding ≥85dB(A) averaged over 40h per week. To identify determinants of risky TLN exposure longitudinally, generalised estimating equations were applied. STUDY SAMPLE: A subgroup (n = 661; mean age 25.6 years in the fifth wave; 58.4% female) of the closed cohort study OHRKAN was analysed. Included participants took part in the fifth wave prior to the study break due to COVID-19. RESULTS: Analysis of participants' data from all five waves showed that risky TLN exposure was highest during the second wave (72.0%), when participants were aged 17-19 years, and thereafter steadily declined. Among young adults, attendance at discotheques and private parties, especially, caused very high exposure. Determinants of risky TLN exposure were wave time point, male gender, a higher level of education, and smoking. CONCLUSIONS: As TLN exposure is highest among older adolescents, prevention programs should target younger teenagers and be tailored to the identified risk groups. The risk from private parties should be addressed.

3.
Int J Audiol ; 61(2): 89-96, 2022 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-33787447

RESUMO

OBJECTIVES: To investigate the association between total leisure noise exposure and intermittent tinnitus among young adults. DESIGN: Data were obtained from the Ohrkan study, an ongoing prospective cohort study conducted in South Germany since 2009. Information about exposure to impulse and leisure noise, tinnitus occurrences, sociodemographic variables, and self-rated hearing ability were analysed at four time points over a period of seven and a half years. STUDY SAMPLE: Participants of the Ohrkan cohort study, who provided data about the occurrence of tinnitus for all surveys (n = 1028). RESULTS: Intermittent tinnitus was reported in the majority of the sample (60%). The risk for intermittent tinnitus increased with higher sound pressure levels from exposure to leisure noise (full model (Odds Ratio, 95%CI): 80-<85dB(A): 1.41 [1.13-1.78], 85-<90dB(A): 1.73 [1.38-2.16], >90dB(A): 2.04 [1.59-2.61]). Visiting nightclubs was a major contributor to this relationship. Of the considered covariables, self-rated hearing as "poor", and growing up in a single-parent household were significantly associated with intermittent tinnitus. CONCLUSION: Intermittent tinnitus is very frequent among young adults and is associated with high levels of leisure noise exposure. To prevent intermittent tinnitus, reduced sound pressure levels and the use of hearing protection are necessary.


Assuntos
Perda Auditiva Provocada por Ruído , Zumbido , Estudos de Coortes , Perda Auditiva Provocada por Ruído/diagnóstico , Perda Auditiva Provocada por Ruído/epidemiologia , Perda Auditiva Provocada por Ruído/etiologia , Humanos , Atividades de Lazer , Estudos Prospectivos , Fatores de Risco , Inquéritos e Questionários , Zumbido/diagnóstico , Zumbido/epidemiologia , Zumbido/etiologia , Adulto Jovem
4.
Nat Methods ; 13(5): 425-30, 2016 05.
Artigo em Inglês | MEDLINE | ID: mdl-27043882

RESUMO

Achieving high accuracy in orthology inference is essential for many comparative, evolutionary and functional genomic analyses, yet the true evolutionary history of genes is generally unknown and orthologs are used for very different applications across phyla, requiring different precision-recall trade-offs. As a result, it is difficult to assess the performance of orthology inference methods. Here, we present a community effort to establish standards and an automated web-based service to facilitate orthology benchmarking. Using this service, we characterize 15 well-established inference methods and resources on a battery of 20 different benchmarks. Standardized benchmarking provides a way for users to identify the most effective methods for the problem at hand, sets a minimum requirement for new tools and resources, and guides the development of more accurate orthology inference methods.


Assuntos
Biologia Computacional/normas , Genômica/normas , Filogenia , Proteômica/normas , Archaea/classificação , Archaea/genética , Bactérias/classificação , Bactérias/genética , Biologia Computacional/métodos , Bases de Dados Genéticas , Eucariotos/classificação , Eucariotos/genética , Ontologia Genética , Genômica/métodos , Modelos Genéticos , Proteômica/métodos , Análise de Sequência de Proteína , Homologia de Sequência , Especificidade da Espécie
5.
Nucleic Acids Res ; 43(W1): W30-8, 2015 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-25943547

RESUMO

The HMMER website, available at http://www.ebi.ac.uk/Tools/hmmer/, provides access to the protein homology search algorithms found in the HMMER software suite. Since the first release of the website in 2011, the search repertoire has been expanded to include the iterative search algorithm, jackhmmer. The continued growth of the target sequence databases means that traditional tabular representations of significant sequence hits can be overwhelming to the user. Consequently, additional ways of presenting homology search results have been developed, allowing them to be summarised according to taxonomic distribution or domain architecture. The taxonomy and domain architecture representations can be used in combination to filter the results according to the needs of a user. Searches can also be restricted prior to submission using a new taxonomic filter, which not only ensures that the results are specific to the requested taxonomic group, but also improves search performance. The repertoire of profile hidden Markov model libraries, which are used for annotation of query sequences with protein families and domains, has been expanded to include the libraries from CATH-Gene3D, PIRSF, Superfamily and TIGRFAMs. Finally, we discuss the relocation of the HMMER webserver to the European Bioinformatics Institute and the potential impact that this will have.


Assuntos
Homologia de Sequência de Aminoácidos , Software , Algoritmos , Bases de Dados de Proteínas , Internet , Cadeias de Markov , Estrutura Terciária de Proteína , Alinhamento de Sequência , Análise de Sequência de Proteína
6.
Nucleic Acids Res ; 42(Database issue): D922-5, 2014 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-24194607

RESUMO

TreeFam (http://www.treefam.org) is a database of phylogenetic trees inferred from animal genomes. For every TreeFam family we provide homology predictions together with the evolutionary history of the genes. Here we describe an update of the TreeFam database. The TreeFam project was resurrected in 2012 and has seen two releases since. The latest release (TreeFam 9) was made available in March 2013. It has orthology predictions and gene trees for 109 species in 15,736 families covering ∼2.2 million sequences. With release 9 we made modifications to our production pipeline and redesigned our website with improved gene tree visualizations and Wikipedia integration. Furthermore, we now provide an HMM-based sequence search that places a user-provided protein sequence into a TreeFam gene tree and provides quick orthology prediction. The tool uses Mafft and RAxML for the fast insertion into a reference alignment and tree, respectively. Besides the aforementioned technical improvements, we present a new approach to visualize gene trees and alternative displays that focuses on showing homology information from a species tree point of view. From release 9 onwards, TreeFam is now hosted at the EBI.


Assuntos
Bases de Dados Genéticas , Família Multigênica , Filogenia , Animais , Genoma , Internet
7.
JACC Adv ; 3(4)2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38770230

RESUMO

BACKGROUND: Understanding the clinical features of myocarditis in various age groups is required to identify age-specific disease patterns. OBJECTIVES: The objective of this study was to examine differences in sex distribution and clinical outcomes in patients with myocarditis of various ages. METHODS: Patients with acute or chronic myocarditis in 3 centers in Berlin, Germany from 2005 to 2021 and in the United States (National Inpatient Sample) from 2010 to 2019 were included. Age groups examined included "prepubescent" (below 11 years for females and below 13 years for males), adolescents (11 [female] or 13 [male] to 18 years), young adults (18-35 years), "middle-aged adults" (35-54 years), and older adults (age >54 years). In patients admitted to the hospital, hospital mortality, length of stay, and medical complication rates were examined. RESULTS: Overall, 6,023 cases in Berlin and 9,079 cases in the U.S. cohort were included. In both cohorts, there were differences in sex distribution among the 5 age categories, and differences in the distribution were most notable in adolescents (69.3% males vs 30.7% females) and in young adults (73.8% males vs 26.3% females). Prepubescent and older adults had the highest rates of in-hospital mortality, hospital length of stay, and medical complications. In the Berlin cohort, prepubescent patients had higher levels of leukocytes (P < 0.001), antistreptolysin antibody (P < 0.001), and NT-proBNP (P < 0.001) when compared to young adults. CONCLUSIONS: In this study, we found that sex differences in myocarditis and clinical features of myocarditis were age-dependent.

8.
Brief Bioinform ; 12(5): 485-8, 2011 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-21666252

RESUMO

There is a great need for standards in the orthology field. Users must contend with different ortholog data representations from each provider, and the providers themselves must independently gather and parse the input sequence data. These burdensome and redundant procedures make data comparison and integration difficult. We have designed two XML-based formats, SeqXML and OrthoXML, to solve these problems. SeqXML is a lightweight format for sequence records-the input for orthology prediction. It stores the same sequence and metadata as typical FASTA format records, but overcomes common problems such as unstructured metadata in the header and erroneous sequence content. XML provides validation to prevent data integrity problems that are frequent in FASTA files. The range of applications for SeqXML is broad and not limited to ortholog prediction. We provide read/write functions for BioJava, BioPerl, and Biopython. OrthoXML was designed to represent ortholog assignments from any source in a consistent and structured way, yet cater to specific needs such as scoring schemes or meta-information. A unified format is particularly valuable for ortholog consumers that want to integrate data from numerous resources, e.g. for gene annotation projects. Reference proteomes for 61 organisms are already available in SeqXML, and 10 orthology databases have signed on to OrthoXML. Adoption by the entire field would substantially facilitate exchange and quality control of sequence and orthology information.


Assuntos
Bases de Dados Factuais , Internet , Proteoma/análise , Software , Anotação de Sequência Molecular , Proteoma/normas , Análise de Sequência
9.
Brief Bioinform ; 12(5): 463-73, 2011 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-21565935

RESUMO

Orthology is one of the most important tools available to modern biology, as it allows making inferences from easily studied model systems to much less tractable systems of interest, such as ourselves. This becomes important not least in the study of genetic diseases. We here review work on the orthology of disease-associated genes and also present an updated version of the InParanoid-based disease orthology database and web site OrthoDisease, with 14-fold increased species coverage since the previous version. Using this resource, we survey the taxonomic distribution of orthologs of human genes involved in different disease categories. The hypothesis that paralogs can mask the effect of deleterious mutations predicts that known heritable disease genes should have fewer close paralogs. We found large-scale support for this hypothesis as significantly fewer duplications were observed for disease genes in the OrthoDisease ortholog groups.


Assuntos
Doença/genética , Predisposição Genética para Doença , Animais , Bases de Dados Genéticas , Doença/classificação , Modelos Animais de Doenças , Genoma , Humanos , Filogenia , Software , Especificidade da Espécie
10.
Mol Phylogenet Evol ; 67(1): 223-33, 2013 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-23353073

RESUMO

Molecular phylogenetic analyses have produced a plethora of controversial hypotheses regarding the patterns of diversification of non-bilaterian animals. To unravel the causes for the patterns of extreme inconsistencies at the base of the metazoan tree of life, we constructed a novel supermatrix containing 122 genes, enriched with non-bilaterian taxa. Comparative analyses of this supermatrix and its two non-overlapping multi-gene partitions (including ribosomal and non-ribosomal genes) revealed conflicting phylogenetic signals. We show that the levels of saturation and long branch attraction artifacts in the two partitions correlate with gene sampling. The ribosomal gene partition exhibits significantly lower saturation levels than the non-ribosomal one. Additional systematic errors derive from significant variations in amino acid substitution patterns among the metazoan lineages that violate the stationarity assumption of evolutionary models frequently used to reconstruct phylogenies. By modifying gene sampling and the taxonomic composition of the outgroup, we were able to construct three different yet well-supported phylogenies. These results show that the accuracy of phylogenetic inference may be substantially improved by selecting genes that evolve slowly across the Metazoa and applying more realistic substitution models. Additional sequence-independent genomic markers are also necessary to assess the validity of the phylogenetic hypotheses.


Assuntos
Ctenóforos/classificação , Filogenia , Placozoa/classificação , Poríferos/classificação , Ribossomos/genética , Animais , Teorema de Bayes , Ctenóforos/genética , Genômica , Funções Verossimilhança , Modelos Genéticos , Placozoa/genética , Poríferos/genética
11.
Nucleic Acids Res ; 39(Web Server issue): W518-23, 2011 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-21622656

RESUMO

Analyzing the functional potential of newly sequenced genomes and metagenomes has become a common task in biomedical and biological research. With the advent of high-throughput sequencing technologies comparative metagenomics opens the way to elucidate the genetically determined similarities and differences of complex microbial communities. We developed the web server 'CoMet' (http://comet.gobics.de), which provides an easy-to-use comparative metagenomics platform that is well-suitable for the analysis of large collections of metagenomic short read data. CoMet combines the ORF finding and subsequent assignment of protein sequences to Pfam domain families with a comparative statistical analysis. Besides comprehensive tabular data files, the CoMet server also provides visually interpretable output in terms of hierarchical clustering and multi-dimensional scaling plots and thus allows a quick overview of a given set of metagenomic samples.


Assuntos
Metagenômica/métodos , Software , Análise por Conglomerados , Interpretação Estatística de Dados , Internet , Metagenoma , Estrutura Terciária de Proteína , Análise de Sequência de DNA , Análise de Sequência de Proteína
12.
Stud Health Technol Inform ; 294: 575-576, 2022 May 25.
Artigo em Inglês | MEDLINE | ID: mdl-35612151

RESUMO

Standardized fall risk scores have not proven to reliably predict falls in clinical settings. Machine Learning offers the potential to increase the accuracy of such predictions, possibly vastly improving care for patients at high fall risks. We developed a boosting algorithm to predict both recurrent falls and the severity of fall injuries. The model was trained on a dataset including extensive information on fall events of patients who had been admitted to Charité - Universitätsmedizin Berlin between August 2016 and July 2020. The data were recorded according to the German expert standard for fall documentation. Predictive power scores were calculated to define optimal feature sets. With an accuracy of 74% for recurrent falls and 86% for injury severity, boosting demonstrated the best overall predictive performance of all models assessed. Given that our data contain initially rated risk scores, our results demonstrate that well trained ML algorithms possibly provide tools to substantially reduce fall risks in clinical care settings.


Assuntos
Acidentes por Quedas/estatística & dados numéricos , Algoritmos , Aprendizado de Máquina , Acidentes por Quedas/prevenção & controle , Alemanha/epidemiologia , Hospitalização , Humanos , Recidiva , Estudos Retrospectivos , Fatores de Risco
13.
Bioinformatics ; 26(7): 960-1, 2010 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-20172941

RESUMO

SUMMARY: Assessment of phylogenetic diversity is a key element to the analysis of microbial communities. Tools are needed to handle next-generation sequencing data and to cope with the computational complexity of large-scale studies. Here, we present Treephyler, a tool for fast taxonomic profiling of metagenomes. Treephyler was evaluated on real metagenome to assess its performance in comparison to previous approaches for taxonomic profiling. Results indicate that Treephyler is in terms of speed and accuracy prepared for next-generation sequencing techniques and large-scale analysis. AVAILABILITY: Treephyler is implemented in Perl; it is portable to all platforms and applicable to both nucleotide and protein input data. Treephyler is freely available for download at http://www.gobics.de/fabian/treephyler.php.


Assuntos
Genômica/métodos , Metagenoma , Filogenia , Software , Bases de Dados Factuais
14.
Bioinformatics ; 26(11): 1409-15, 2010 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-20400454

RESUMO

MOTIVATION: Existing coalescent models and phylogenetic tools based on them are not designed for studying the genealogy of sequences like those of HIV, since in HIV recombinants with multiple cross-over points between the parental strains frequently arise. Hence, ambiguous cases in the classification of HIV sequences into subtypes and circulating recombinant forms (CRFs) have been treated with ad hoc methods in lack of tools based on a comprehensive coalescent model accounting for complex recombination patterns. RESULTS: We developed the program ARGUS that scores classifications of sequences into subtypes and recombinant forms. It reconstructs ancestral recombination graphs (ARGs) that reflect the genealogy of the input sequences given a classification hypothesis. An ARG with maximal probability is approximated using a Markov chain Monte Carlo approach. ARGUS was able to distinguish the correct classification with a low error rate from plausible alternative classifications in simulation studies with realistic parameters. We applied our algorithm to decide between two recently debated alternatives in the classification of CRF02 of HIV-1 and find that CRF02 is indeed a recombinant of Subtypes A and G. AVAILABILITY: ARGUS is implemented in C++ and the source code is available at http://gobics.de/software.


Assuntos
Algoritmos , HIV/classificação , HIV/genética , HIV-1/classificação , Cadeias de Markov , Filogenia , Análise de Sequência de DNA
15.
Nucleic Acids Res ; 37(Web Server issue): W185-8, 2009 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-19491309

RESUMO

In the absence of whole genome sequences for many organisms, the use of expressed sequence tags (EST) offers an affordable approach for researchers conducting phylogenetic analyses to gain insight about the evolutionary history of organisms. Reliable alignments for phylogenomic analyses are based on orthologous gene sequences from different taxa. So far, researchers have not sufficiently tackled the problem of the completely automated construction of such datasets. Existing software tools are either semi-automated, covering only part of the necessary data processing, or implemented as a pipeline, requiring the installation and configuration of a cascade of external tools, which may be time-consuming and hard to manage. To simplify data set construction for phylogenomic studies, we set up a web server that uses our recently developed OrthoSelect approach. To the best of our knowledge, our web server is the first web-based EST analysis pipeline that allows the detection of orthologous gene sequences in EST libraries and outputs orthologous gene alignments. Additionally, OrthoSelect provides the user with an extensive results section that lists and visualizes all important results, such as annotations, data matrices for each gene/taxon and orthologous gene alignments. The web server is available at http://orthoselect.gobics.de.


Assuntos
Etiquetas de Sequências Expressas/química , Filogenia , Alinhamento de Sequência , Software , Genes , Genômica , Internet , Interface Usuário-Computador
16.
Int J Hyg Environ Health ; 233: 113688, 2021 04.
Artigo em Inglês | MEDLINE | ID: mdl-33530011

RESUMO

BACKGROUND: Due to climate change, the frequency, intensity and severity of extreme weather events, such as heat waves, cold waves, storms, heavy precipitation causing wildfires, floods, and droughts are increasing, which could adversely affect human health. The purpose of this systematic review is therefore to assess the current literature about the association between these extreme weather events and their impact on the health of the European population. METHODS: Observational studies published from January 1, 2007 to May 17, 2020 on health effects of extreme weather events in Europe were searched systematically in Medline, Embase and Cochrane Central Register of Controlled Trials. The exposures of interest included extreme temperature, heat waves, cold waves, droughts, floods, storms and wildfires. The health impacts included total mortality, cardiovascular mortality and morbidity, respiratory mortality and morbidity, and mental health. We conducted the systematic review following PRISMA (Preferred Reporting Items for Systematic Review and Meta-analysis). The quality of the included studies was assessed using the NICE quality appraisal checklist (National Institute for Health and Care Excellence). RESULTS: The search yielded 1472 articles, of which 35 met the inclusion criteria and were included in our review. Studies regarding five extreme weather events (extreme heat events, extreme cold events, wildfires, floods, droughts) were found. A positive association between extreme heat/cold events and overall, cardiovascular and respiratory mortality was reported from most studies. Wildfires are likely to increase the overall and cardiovascular mortality. Floods might be associated with the deterioration of mental health instead of mortality. Depending on their length, droughts could have an influence on both respiratory and cardiovascular mortality. Contradictory evidence was found in heat-associated morbidity and wildfire-associated respiratory mortality. The associations are inconclusive due to the heterogeneous study designs, study quality, exposure and outcome assessment. CONCLUSIONS: Evidence from most of the included studies showed that extreme heat and cold events, droughts, wildfires and floods in Europe have negative impacts on human health including mental health, although some of the associations are not conclusive. Additional high-quality studies are needed to confirm our results and further studies regarding the effects of other extreme weather events in Europe are to be expected.


Assuntos
Clima Extremo , Mudança Climática , Inundações , Temperatura Alta , Humanos , Saúde Mental , Estudos Observacionais como Assunto , Tempo (Meteorologia)
17.
Artif Organs ; 34(11): 904-10, 2010 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-21092033

RESUMO

Extracorporeal membrane oxygenation (ECMO) is a well-established therapy for several lung and heart diseases in the field of neonatal and pediatric medicine (e.g., acute respiratory distress syndrome, congenital heart failure, cardiomyopathy). Current ECMO systems are typically composed of an oxygenator and a separate nonpulsatile blood pump. An oxygenator with an integrated pulsatile blood pump for small infant ECMO was developed, and this novel concept was tested regarding functionality and gas exchange rate. Pulsating silicone tubes (STs) were driven by air pressure and placed inside the cylindrical fiber bundle of an oxygenator to be used as a pump module. The findings of this study confirm that pumping blood with STs is a viable option for the future. The maximum gas exchange rate for oxygen is 48mL/min/L(blood) at a medium blood flow rate of about 300mL/min. Future design steps were identified to optimize the flow field through the fiber bundle to achieve a higher gas exchange rate. First, the packing density of the hollow-fiber bundle was lower than commercial oxygenators due to the manual manufacturing. By increasing this packing density, the gas exchange rate would increase accordingly. Second, distribution plates for a more uniform blood flow can be placed at the inlet and outlet of the oxygenator. Third, the hollow-fiber membranes can be individually placed to ensure equal distances between the surrounding hollow fibers.


Assuntos
Oxigenação por Membrana Extracorpórea/instrumentação , Coração Auxiliar , Oxigenadores de Membrana , Fluxo Pulsátil , Pressão do Ar , Velocidade do Fluxo Sanguíneo , Dióxido de Carbono/sangue , Elasticidade , Desenho de Equipamento , Humanos , Recém-Nascido , Teste de Materiais , Miniaturização , Oxigênio/sangue , Desenho de Prótese , Silicones , Fatores de Tempo
18.
BMC Bioinformatics ; 10: 219, 2009 Jul 16.
Artigo em Inglês | MEDLINE | ID: mdl-19607672

RESUMO

BACKGROUND: Phylogenetic studies using expressed sequence tags (EST) are becoming a standard approach to answer evolutionary questions. Such studies are usually based on large sets of newly generated, unannotated, and error-prone EST sequences from different species. A first crucial step in EST-based phylogeny reconstruction is to identify groups of orthologous sequences. From these data sets, appropriate target genes are selected, and redundant sequences are eliminated to obtain suitable sequence sets as input data for tree-reconstruction software. Generating such data sets manually can be very time consuming. Thus, software tools are needed that carry out these steps automatically. RESULTS: We developed a flexible and user-friendly software pipeline, running on desktop machines or computer clusters, that constructs data sets for phylogenomic analyses. It automatically searches assembled EST sequences against databases of orthologous groups (OG), assigns ESTs to these predefined OGs, translates the sequences into proteins, eliminates redundant sequences assigned to the same OG, creates multiple sequence alignments of identified orthologous sequences and offers the possibility to further process this alignment in a last step by excluding potentially homoplastic sites and selecting sufficiently conserved parts. Our software pipeline can be used as it is, but it can also be adapted by integrating additional external programs. This makes the pipeline useful for non-bioinformaticians as well as to bioinformatic experts. The software pipeline is especially designed for ESTs, but it can also handle protein sequences. CONCLUSION: OrthoSelect is a tool that produces orthologous gene alignments from assembled ESTs. Our tests show that OrthoSelect detects orthologs in EST libraries with high accuracy. In the absence of a gold standard for orthology prediction, we compared predictions by OrthoSelect to a manually created and published phylogenomic data set. Our tool was not only able to rebuild the data set with a specificity of 98%, but it detected four percent more orthologous sequences. Furthermore, the results OrthoSelect produces are in absolut agreement with the results of other programs, but our tool offers a significant speedup and additional functionality, e.g. handling of ESTs, computing sequence alignments, and refining them. To our knowledge, there is currently no fully automated and freely available tool for this purpose. Thus, OrthoSelect is a valuable tool for researchers in the field of phylogenomics who deal with large quantities of EST sequences. OrthoSelect is written in Perl and runs on Linux/Mac OS X. The tool can be downloaded at (http://gobics.de/fabian/orthoselect.php).


Assuntos
Biologia Computacional/métodos , Genômica , Filogenia , Software , Etiquetas de Sequências Expressas , Genoma , Linguagens de Programação
19.
PLoS One ; 11(5): e0155829, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27192172

RESUMO

Atherosclerotic lesions that critically narrow the artery can necessitate an angioplasty and stent implantation. Long-term therapeutic effects, however, are limited by excessive arterial remodeling. We here employed a miniaturized nitinol-stent coated with star-shaped polyethylenglycole (star-PEG), and evaluated its bio-functionalization with RGD and CXCL1 for improving in-stent stenosis after implantation into carotid arteries of mice. Nitinol foils or stents (bare metal) were coated with star-PEG, and bio-functionalized with RGD, or RGD/CXCL1. Cell adhesion to star-PEG-coated nitinol foils was unaltered or reduced, whereas bio-functionalization with RGD but foremost RGD/CXCL1 increased adhesion of early angiogenic outgrowth cells (EOCs) and endothelial cells but not smooth muscle cells when compared with bare metal foils. Stimulation of cells with RGD/CXCL1 furthermore increased the proliferation of EOCs. In vivo, bio-functionalization with RGD/CXCL1 significantly reduced neointima formation and thrombus formation, and increased re-endothelialization in apoE-/- carotid arteries compared with bare-metal nitinol stents, star-PEG-coated stents, and stents bio-functionalized with RGD only. Bio-functionalization of star-PEG-coated nitinol-stents with RGD/CXCL1 reduced in-stent neointima formation. By supporting the adhesion and proliferation of endothelial progenitor cells, RGD/CXCL1 coating of stents may help to accelerate endothelial repair after stent implantation, and thus may harbor the potential to limit the complication of in-stent restenosis in clinical approaches.


Assuntos
Estenose das Carótidas/prevenção & controle , Quimiocina CXCL1/farmacologia , Endotélio Vascular/efeitos dos fármacos , Oligopeptídeos/farmacologia , Stents/efeitos adversos , Ligas/química , Animais , Estenose das Carótidas/etiologia , Adesão Celular/efeitos dos fármacos , Proliferação de Células/efeitos dos fármacos , Células Cultivadas , Quimiocina CXCL1/química , Endotélio Vascular/fisiologia , Camundongos , Oligopeptídeos/química
20.
F1000Res ; 3: 55, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-25075290

RESUMO

BioJS is a community-based standard and repository of functional components to represent biological information on the web. The development of BioJS has been prompted by the growing need for bioinformatics visualisation tools to be easily shared, reused and discovered. Its modular architecture makes it easy for users to find a specific functionality without needing to know how it has been built, while components can be extended or created for implementing new functionality. The BioJS community of developers currently provides a range of functionality that is open access and freely available. A registry has been set up that categorises and provides installation instructions and testing facilities at http://www.ebi.ac.uk/tools/biojs/. The source code for all components is available for ready use at https://github.com/biojs/biojs.

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