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1.
Nat Genet ; 53(3): 403-411, 2021 03.
Artigo em Inglês | MEDLINE | ID: mdl-33633365

RESUMO

The advent of single-cell chromatin accessibility profiling has accelerated the ability to map gene regulatory landscapes but has outpaced the development of scalable software to rapidly extract biological meaning from these data. Here we present a software suite for single-cell analysis of regulatory chromatin in R (ArchR; https://www.archrproject.com/ ) that enables fast and comprehensive analysis of single-cell chromatin accessibility data. ArchR provides an intuitive, user-focused interface for complex single-cell analyses, including doublet removal, single-cell clustering and cell type identification, unified peak set generation, cellular trajectory identification, DNA element-to-gene linkage, transcription factor footprinting, mRNA expression level prediction from chromatin accessibility and multi-omic integration with single-cell RNA sequencing (scRNA-seq). Enabling the analysis of over 1.2 million single cells within 8 h on a standard Unix laptop, ArchR is a comprehensive software suite for end-to-end analysis of single-cell chromatin accessibility that will accelerate the understanding of gene regulation at the resolution of individual cells.


Assuntos
Cromatina , Análise de Célula Única/métodos , Software , Animais , Cromatina/genética , Cromatina/metabolismo , Análise por Conglomerados , Regulação da Expressão Gênica , Genoma , Humanos , Camundongos , Análise de Sequência de RNA/métodos , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Interface Usuário-Computador , Navegador
2.
Methods Mol Biol ; 2229: 167-174, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33405221

RESUMO

Restriction digest analysis and Sanger sequencing are among the most commonly used techniques to check the sequence of synthetic DNA constructs. However, both require careful preparation to select restriction enzymes or DNA primers adapted to the expected constructs sequences. In projects involving manufacturing of large batches of synthetic constructs, the task can be tedious and error-prone. This chapter demonstrates the use of two free and open-source web applications providing fast and automated selection of enzymes and sequencing primers for DNA construct verification.


Assuntos
Biologia Computacional/métodos , DNA/genética , Análise de Sequência de DNA/métodos , Desenho Assistido por Computador , Enzimas de Restrição do DNA/metabolismo , Software , Biologia Sintética , Navegador
3.
Methods Mol Biol ; 2226: 259-264, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33326108

RESUMO

Within sarcomas 50 different histological subtypes exist, each with their own molecular and clinical characteristics. The combination of tumor subtype heterogeneity and often a limited number of clinical cases make detailed molecular sarcoma studies challenging, particularly when focusing on individual cohorts. However, the increasing number of publicly available genomics data opens inroads to overcome this obstacle. The international public repositories for high-throughput microarray and next-generation sequence functional genomic data sets submitted by the research community create resources that are freely available for download in a variety of formats. Here, we describe the selected web resources for sarcoma genomics research. These resources support archiving of raw data, processed data, and metadata which are indexed, cross-linked, and searchable.


Assuntos
Bases de Dados Factuais , Bases de Dados Genéticas , Pesquisa , Sarcoma de Ewing , Perfilação da Expressão Gênica/métodos , Genômica/métodos , Humanos , Sarcoma de Ewing/diagnóstico , Sarcoma de Ewing/etiologia , Sarcoma de Ewing/terapia , Software , Transcriptoma , Navegador
4.
Methods Mol Biol ; 2226: 285-302, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33326110

RESUMO

Ewing sarcoma is a highly malignant tumor characterized by a chromosomal translocation that modifies the activity of an ETS family transcription factor. The most prevalent translocation product, EWSR1-FLI1, exploits a permissive and unique chromatin environment of stem cells, and transforms them into an oncogenic state through alterations to gene expression and gene regulatory programs. Though the transformation ability of, and subsequent reliance on EWSR1-FLI1 had been previously described, the advent of genome-wide sequencing technologies allowed for the specific identification of genomic loci and genes targeted by EWSR1-FLI1. Furthermore, the characterization of the chromatin environment in these, and other, cell types could not have been accomplished without the computational and statistical methods that enable large-scale data analysis. Here, we outline in detail the tools and steps needed to analyze genome-wide transcription factor binding and histone modification data (chromatin immunoprecipitation, ChIP-seq), as well as chromatin accessibility data (assay for transposase-accessible chromatin, ATAC-seq) from Ewing sarcoma cells. Our protocol includes a compilation of data quality control metrics, trimming of adapter sequences, reference genome alignment, identification of enriched sites ("peaks") and motifs, as well as annotation and visualization, using real-world data. These steps should provide a platform on which molecular biologists can build their own analytical pipelines to aid in data processing, analysis, and interpretation.


Assuntos
Neoplasias Ósseas/genética , Epigênese Genética , Epigenômica , Regulação Neoplásica da Expressão Gênica , Sarcoma de Ewing/genética , Biomarcadores Tumorais , Sequenciamento de Cromatina por Imunoprecipitação/métodos , Biologia Computacional/métodos , Bases de Dados Genéticas , Epigenômica/métodos , Humanos , Software , Navegador
5.
Methods Mol Biol ; 2226: 303-333, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33326111

RESUMO

Ewing sarcoma (EwS) is a highly aggressive pediatric bone cancer that is defined by a somatic fusion between the EWSR1 gene and an ETS family member, most frequently the FLI1 gene, leading to expression of a chimeric transcription factor EWSR1-FLI1. Otherwise, EwS is one of the most genetically stable cancers. The situation when the major cancer driver is well known looks like a unique opportunity for applying the systems biology approach in order to understand the EwS mechanisms as well as to uncover some general mechanistic principles of carcinogenesis. A number of studies have been performed revealing the direct and indirect effects of EWSR1-FLI1 on multiple aspects of cellular life. Nevertheless, the emerging picture of the oncogene action appears to be highly complex and systemic, with multiple reciprocal influences between the immediate consequences of the driver mutation and intracellular and intercellular molecular mechanisms, including regulation of transcription, epigenome, and tumoral microenvironment. In this chapter, we present an overview of existing molecular profiling resources available for EwS tumors and cell lines and provide an online comprehensive catalogue of publicly available omics and other datasets. We further highlight the systems biology studies of EwS, involving mathematical modeling of networks and integration of molecular data. We conclude that despite the seeming simplicity, a lot has yet to be understood on the systems-wide mechanisms connecting the driver mutation and the major cellular phenotypes of this pediatric cancer. Overall, this chapter can serve as a guide for a systems biology researcher to start working on EwS.


Assuntos
Neoplasias Ósseas/etiologia , Neoplasias Ósseas/metabolismo , Sarcoma de Ewing/etiologia , Sarcoma de Ewing/metabolismo , Biologia de Sistemas , Neoplasias Ósseas/patologia , Bases de Dados Genéticas , Genômica/métodos , Humanos , Metabolômica/métodos , Modelos Teóricos , Proteômica/métodos , Sarcoma de Ewing/patologia , Biologia de Sistemas/métodos , Navegador
6.
Methods Mol Biol ; 2195: 263-275, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-32852769

RESUMO

Germ cell tumors (GCTs) are a rare disease, but they account for 15% of all malignancies diagnosed during adolescence. The biological mechanisms underpinning their development are only starting to be explored. Current GCT treatment may be associated with significant toxicity. Therefore, there is an urgent need to understand the molecular basis of GCT and identify biomarkers to tailor the therapy for individual patients. However, this research is severely hamstrung by the rarity of GCTs in individual hospitals/institutes. A publicly available genomic data commons with GCT datasets compiled from different institutes/studies would be a valuable resource to facilitate such research. In this study, we first reviewed publicly available web portals containing GCT genomics data, focusing on comparing data availability, data access, and analysis tools, and the limitations of using these resources for GCT molecular studies. Next, we specifically designed a GCT data commons with a web portal, GCT Explorer, to assist the research community to store, manage, search, share, and analyze data. The goal of this work is to facilitate GCT molecular basis exploration and translational research.


Assuntos
Biologia Computacional , Bases de Dados Genéticas , Suscetibilidade a Doenças , Neoplasias Embrionárias de Células Germinativas/etiologia , Biologia Computacional/métodos , Segurança Computacional , Estudos de Associação Genética/métodos , Genoma , Genômica/métodos , Humanos , Neoplasias Embrionárias de Células Germinativas/metabolismo , Neoplasias Embrionárias de Células Germinativas/patologia , Fenótipo , Interface Usuário-Computador , Navegador
7.
Methods Mol Biol ; 2183: 43-62, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-32959240

RESUMO

There is still a lack of vaccines for many bacterial infections for which the best treatment option would be a prophylactic one. On the other hand, effectiveness has been questioned for some existing vaccines, prompting new developments. Therapeutic vaccines are also becoming a treatment option in specific cases where antibiotics tend to fail. In this scenario, refinement and extension of the classical reverse vaccinology approach is allowing scientists to find new and more effective antigens. In this chapter, we describe an in silico methodology that integrates pangenomic, immunoinformatic, structural, and evolutionary approaches for the screening of potential antigens in a given bacterial species. The strategy focuses on targeting relatively conserved epitopes in core proteins to design broadly cross-protective vaccines and avoid allele-specific immunity. The proposed methodological steps and computational tools can be easily implemented in a reverse vaccinology approach not only to identify new leads with strong immune response but also to develop diagnostic assays.


Assuntos
Antígenos de Bactérias/imunologia , Bactérias/imunologia , Proteínas de Bactérias/imunologia , Biologia Computacional , Proteoma , Proteômica , Antígenos de Bactérias/genética , Antígenos de Bactérias/metabolismo , Bactérias/genética , Bactérias/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Vacinas Bacterianas/imunologia , Biologia Computacional/métodos , Bases de Dados Factuais , Genoma Bacteriano , Estudo de Associação Genômica Ampla , Genômica/métodos , Humanos , Anotação de Sequência Molecular , Proteômica/métodos , Vacinologia , Navegador , Fluxo de Trabalho
8.
Viruses ; 12(12)2020 12 10.
Artigo em Inglês | MEDLINE | ID: mdl-33322070

RESUMO

Viruses represent important test cases for data federation due to their genome size and the rapid increase in sequence data in publicly available databases. However, some consequences of previously decentralized (unfederated) data are lack of consensus or comparisons between feature annotations. Unifying or displaying alternative annotations should be a priority both for communities with robust entry representation and for nascent communities with burgeoning data sources. To this end, during this three-day continuation of the Virus Hunting Toolkit codeathon series (VHT-2), a new integrated and federated viral index was elaborated. This Federated Index of Viral Experiments (FIVE) integrates pre-existing and novel functional and taxonomy annotations and virus-host pairings. Variability in the context of viral genomic diversity is often overlooked in virus databases. As a proof-of-concept, FIVE was the first attempt to include viral genome variation for HIV, the most well-studied human pathogen, through viral genome diversity graphs. As per the publication of this manuscript, FIVE is the first implementation of a virus-specific federated index of such scope. FIVE is coded in BigQuery for optimal access of large quantities of data and is publicly accessible. Many projects of database or index federation fail to provide easier alternatives to access or query information. To this end, a Python API query system was developed to enhance the accessibility of FIVE.


Assuntos
Biologia Computacional , Bases de Dados Genéticas , Metagenômica/métodos , Vírus/genética , Biologia Computacional/métodos , Variação Genética , Genoma Viral , Interações Hospedeiro-Patógeno , Humanos , Interface Usuário-Computador , Proteínas Virais/genética , Proteínas Virais/metabolismo , Vírus/metabolismo , Navegador
9.
Blood Adv ; 4(24): 6259-6273, 2020 12 22.
Artigo em Inglês | MEDLINE | ID: mdl-33351119

RESUMO

Thrombosis has emerged as an important complication of coronavirus disease 2019 (COVID-19), particularly among individuals with severe illness. However, the precise incidence of thrombotic events remains uncertain due to differences in study design, patient populations, outcome ascertainment, event definitions, and reporting. In an effort to overcome some of these challenges and promote standardized data collection and reporting in clinical studies, the American Society of Hematology Research Collaborative COVID-19 Non-Malignant Hematology Task Force, in collaboration with the International Society on Thrombosis and Haemostasis COVID-19 Task Force, developed sets of data elements in the following domains: venous thromboembolism, myocardial infarction, stroke/transient ischemic attack, peripheral arterial thrombosis, bleeding, laboratory investigations, and antithrombotic therapy. Data elements in each of these domains were developed with 3 levels of detail to facilitate their incorporation into studies evaluating a range of interventions and outcomes. Previously published data elements were included where possible. The use of standardized variables in a range of clinical studies can enhance the quality of data collection, create efficiency, enhance comparison of results across studies, and facilitate future pooling of data sets.


Assuntos
/epidemiologia , Bases de Dados Factuais , Trombose/epidemiologia , Interface Usuário-Computador , Navegador , Anticoagulantes/uso terapêutico , /virologia , Gerenciamento Clínico , Suscetibilidade a Doenças , Humanos , Avaliação de Resultados em Cuidados de Saúde , Vigilância em Saúde Pública , Trombose/diagnóstico , Trombose/etiologia , Trombose/terapia
10.
Nucleic Acids Res ; 48(19): 11030-11039, 2020 11 04.
Artigo em Inglês | MEDLINE | ID: mdl-33045750

RESUMO

Synonymous codon usage significantly impacts translational and transcriptional efficiency, gene expression, the secondary structure of both mRNA and proteins, and has been implicated in various diseases. However, population-specific differences in codon usage biases remain largely unexplored. Here, we present a web server, https://cubap.byu.edu, to facilitate analyses of codon usage biases across populations (CUBAP). Using the 1000 Genomes Project, we calculated and visually depict population-specific differences in codon frequencies, codon aversion, identical codon pairing, co-tRNA codon pairing, ramp sequences, and nucleotide composition in 17,634 genes. We found that codon pairing significantly differs between populations in 35.8% of genes, allowing us to successfully predict the place of origin for African and East Asian individuals with 98.8% and 100% accuracy, respectively. We also used CUBAP to identify a significant bias toward decreased CTG pairing in the immunity related GTPase M (IRGM) gene in East Asian and African populations, which may contribute to the decreased association of rs10065172 with Crohn's disease in those populations. CUBAP facilitates in-depth gene-specific and codon-specific visualization that will aid in analyzing candidate genes identified in genome-wide association studies, identifying functional implications of synonymous variants, predicting population-specific impacts of synonymous variants and categorizing genetic biases unique to certain populations.


Assuntos
Uso do Códon , Bases de Dados Genéticas , Genética Populacional , Estudo de Associação Genômica Ampla , Humanos , Navegador
11.
BMC Bioinformatics ; 21(1): 464, 2020 Oct 19.
Artigo em Inglês | MEDLINE | ID: mdl-33076821

RESUMO

BACKGROUND: Genome browsers are widely used for locating interesting genomic regions, but their interactive use is obviously limited to inspecting short genomic portions. An ideal interaction is to provide patterns of regions on the browser, and then extract other genomic regions over the whole genome where such patterns occur, ranked by similarity. RESULTS: We developed SimSearch, an optimized pattern-search method and an open source plugin for the Integrated Genome Browser (IGB), to find genomic region sets that are similar to a given region pattern. It provides efficient visual genome-wide analytics computation in large datasets; the plugin supports intuitive user interactions for selecting an interesting pattern on IGB tracks and visualizing the computed occurrences of similar patterns along the entire genome. SimSearch also includes functions for the annotation and enrichment of results, and is enhanced with a Quickload repository including numerous epigenomic feature datasets from ENCODE and Roadmap Epigenomics. The paper also includes some use cases to show multiple genome-wide analyses of biological interest, which can be easily performed by taking advantage of the presented approach. CONCLUSIONS: The novel SimSearch method provides innovative support for effective genome-wide pattern search and visualization; its relevance and practical usefulness is demonstrated through a number of significant use cases of biological interest. The SimSearch IGB plugin, documentation, and code are freely available at https://deib-geco.github.io/simsearch-app/ and https://github.com/DEIB-GECO/simsearch-app/ .


Assuntos
Algoritmos , Epigenômica , Genoma , Reconhecimento Automatizado de Padrão , Navegador , Humanos , Anotação de Sequência Molecular , Ligação Proteica , Sequências Reguladoras de Ácido Nucleico/genética , Fatores de Transcrição/metabolismo
12.
BMC Bioinformatics ; 21(1): 465, 2020 Oct 19.
Artigo em Inglês | MEDLINE | ID: mdl-33076824

RESUMO

BACKGROUND: oposSOM is a comprehensive, machine learning based open-source data analysis software combining functionalities such as diversity analyses, biomarker selection, function mining, and visualization. RESULTS: These functionalities are now available as interactive web-browser application for a broader user audience interested in extracting detailed information from high-throughput omics data sets pre-processed by oposSOM. It enables interactive browsing of single-gene and gene set profiles, of molecular 'portrait landscapes', of associated phenotype diversity, and signalling pathway activation patterns. CONCLUSION: The oposSOM-Browser makes available interactive data browsing for five transcriptome data sets of cancer (melanomas, B-cell lymphomas, gliomas) and of peripheral blood (sepsis and healthy individuals) at www.izbi.uni-leipzig.de/opossom-browser .


Assuntos
Assistência à Saúde , Genômica , Software , Navegador , Humanos , Linfoma de Células B/genética , Aprendizado de Máquina
13.
Nat Commun ; 11(1): 5394, 2020 10 26.
Artigo em Inglês | MEDLINE | ID: mdl-33106483

RESUMO

FRET experiments can provide state-specific structural information of complex dynamic biomolecular assemblies. However, to overcome the sparsity of FRET experiments, they need to be combined with computer simulations. We introduce a program suite with (i) an automated design tool for FRET experiments, which determines how many and which FRET pairs should be used to minimize the uncertainty and maximize the accuracy of an integrative structure, (ii) an efficient approach for FRET-assisted coarse-grained structural modeling, and all-atom molecular dynamics simulations-based refinement, and (iii) a quantitative quality estimate for judging the accuracy of FRET-derived structures as opposed to precision. We benchmark our tools against simulated and experimental data of proteins with multiple conformational states and demonstrate an accuracy of ~3 Å RMSDCα against X-ray structures for sets of 15 to 23 FRET pairs. Free and open-source software for the introduced workflow is available at https://github.com/Fluorescence-Tools . A web server for FRET-assisted structural modeling of proteins is available at http://nmsim.de .


Assuntos
Transferência Ressonante de Energia de Fluorescência/métodos , Proteínas/química , Automação , Simulação por Computador , Transferência Ressonante de Energia de Fluorescência/instrumentação , Modelos Estruturais , Conformação Proteica , Software , Navegador
14.
Am Heart J ; 229: 121-126, 2020 11.
Artigo em Inglês | MEDLINE | ID: mdl-32957030

RESUMO

Myocarditis Disease Unit (MDU) is a functional multidisciplinary network designed to offer multidisciplinary assistance to patients with myocarditis. More than 300 patients coming from the whole Country are currently followed up at a specialized multidisciplinary outpatient clinic. Following the pandemic outbreak of the SARS-CoV-2 infection in Italy, we present how the MDU rapidly evolved to a "tele-MDU", via a dedicated multitasking digital health platform.


Assuntos
Betacoronavirus , Infecções por Coronavirus/epidemiologia , Unidades Hospitalares/organização & administração , Comunicação Interdisciplinar , Miocardite/terapia , Equipe de Assistência ao Paciente/organização & administração , Pneumonia Viral/epidemiologia , Telemedicina/organização & administração , Adulto , Assistência Ambulatorial/organização & administração , Arritmias Cardíacas/terapia , Feminino , Sistemas de Informação Hospitalar , Humanos , Pacientes Internados , Itália/epidemiologia , Masculino , Pessoa de Meia-Idade , Pandemias , Centros de Atenção Terciária/organização & administração , Navegador
15.
PLoS One ; 15(8): e0237324, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32813701

RESUMO

Flood inundation maps provide valuable information towards flood risk preparedness, management, communication, response, and mitigation at the time of disaster, and can be developed by harnessing the power of satellite imagery. In the present study, Sentinel-1 Synthetic Aperture RADAR (SAR) data and Otsu method were utilized to map flood inundation areas. Google Earth Engine (GEE) was used for implementing Otsu algorithm and processing Sentinel-1 SAR data. The results were assessed by (i) calculating a confusion matrix; (ii) comparing the submerge water areas of flooded (Aug 2018), non-flooded (Jan 2018) and previous year's flooded season (Aug 2016, Aug 2017), and (iii) analyzing historical rainfall patterns to understand the flood event. The overall accuracy for the Sentinel-1 SAR flood inundation maps of 9th and 21st August 2018 was observed as 94.3% and 94.1% respectively. The submerged area (region under water) classified significant flooding as compared to the non-flooded (January 2018) and previous year's same season (August 2015-2017) classified outputs. Summing up, observations from Sentinel-1 SAR data using Otsu algorithm in GEE can act as a powerful tool for mapping flood inundation areas at the time of disaster, and enhance existing efforts towards saving lives and livelihoods of communities, and safeguarding infrastructure and businesses.


Assuntos
Monitoramento Ambiental/métodos , Inundações/estatística & dados numéricos , Imagens de Satélites , Navegador , Monitoramento Ambiental/estatística & dados numéricos , Índia , Rios
16.
J Med Internet Res ; 22(8): e20673, 2020 08 25.
Artigo em Inglês | MEDLINE | ID: mdl-32748790

RESUMO

BACKGROUND: Although "infodemiological" methods have been used in research on coronavirus disease (COVID-19), an examination of the extent of infodemic moniker (misinformation) use on the internet remains limited. OBJECTIVE: The aim of this paper is to investigate internet search behaviors related to COVID-19 and examine the circulation of infodemic monikers through two platforms-Google and Instagram-during the current global pandemic. METHODS: We have defined infodemic moniker as a term, query, hashtag, or phrase that generates or feeds fake news, misinterpretations, or discriminatory phenomena. Using Google Trends and Instagram hashtags, we explored internet search activities and behaviors related to the COVID-19 pandemic from February 20, 2020, to May 6, 2020. We investigated the names used to identify the virus, health and risk perception, life during the lockdown, and information related to the adoption of COVID-19 infodemic monikers. We computed the average peak volume with a 95% CI for the monikers. RESULTS: The top six COVID-19-related terms searched in Google were "coronavirus," "corona," "COVID," "virus," "corona virus," and "COVID-19." Countries with a higher number of COVID-19 cases had a higher number of COVID-19 queries on Google. The monikers "coronavirus ozone," "coronavirus laboratory," "coronavirus 5G," "coronavirus conspiracy," and "coronavirus bill gates" were widely circulated on the internet. Searches on "tips and cures" for COVID-19 spiked in relation to the US president speculating about a "miracle cure" and suggesting an injection of disinfectant to treat the virus. Around two thirds (n=48,700,000, 66.1%) of Instagram users used the hashtags "COVID-19" and "coronavirus" to disperse virus-related information. CONCLUSIONS: Globally, there is a growing interest in COVID-19, and numerous infodemic monikers continue to circulate on the internet. Based on our findings, we hope to encourage mass media regulators and health organizers to be vigilant and diminish the use and circulation of these infodemic monikers to decrease the spread of misinformation.


Assuntos
Betacoronavirus , Infecções por Coronavirus , Redes Sociais Online , Pandemias , Pneumonia Viral , Ferramenta de Busca , Navegador , Comunicação , Humanos , Internet , Meios de Comunicação de Massa
17.
PLoS One ; 15(7): e0235249, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32649696

RESUMO

Online experiments are growing in popularity. This study aimed to determine the timing accuracy of web technologies and investigate whether they can be used to support high temporal precision psychology experiments. A dynamic sinusoidal grating and flashes were produced by setInterval, CSS3, and requestAnimationFrame (hereafter, rAF) technologies. They were run at normal or real-time priority processing in Chrome, Firefox, Edge, and Internet Explorer on Windows, macOS, and Linux. Timing accuracies were compared with that of Psychtoolbox which was chosen as gold standard. It was found that rAF with real-time priority had the best timing accuracy compared to the other web technologies and had a similar timing accuracy as Psychtoolbox in traditional experiments in most cases. However, rAF exhibited poor timing accuracy on Linux. Therefore, rAF can be used as technical basis for accuracy of millisecond timing sequences in online experiments, thereby benefiting the psychology field.


Assuntos
Coleta de Dados/instrumentação , Intervenção Baseada em Internet , Psicologia Experimental/instrumentação , Tempo de Reação/fisiologia , Navegador , Coleta de Dados/métodos , Estudos de Viabilidade , Humanos , Psicologia Experimental/métodos , Fatores de Tempo
18.
Nat Commun ; 11(1): 3557, 2020 07 16.
Artigo em Inglês | MEDLINE | ID: mdl-32678091

RESUMO

Bacteria of the genus Bacteroides are common members of the human intestinal microbiota and important degraders of polysaccharides in the gut. Among them, the species Bacteroides thetaiotaomicron has emerged as the model organism for functional microbiota research. Here, we use differential RNA sequencing (dRNA-seq) to generate a single-nucleotide resolution transcriptome map of B. thetaiotaomicron grown under defined laboratory conditions. An online browser, called 'Theta-Base' ( www.helmholtz-hiri.de/en/datasets/bacteroides ), is launched to interrogate the obtained gene expression data and annotations of ~4500 transcription start sites, untranslated regions, operon structures, and 269 noncoding RNA elements. Among the latter is GibS, a conserved, 145 nt-long small RNA that is highly expressed in the presence of N-acetyl-D-glucosamine as sole carbon source. We use computational predictions and experimental data to determine the secondary structure of GibS and identify its target genes. Our results indicate that sensing of N-acetyl-D-glucosamine induces GibS expression, which in turn modifies the transcript levels of metabolic enzymes.


Assuntos
Bacteroides thetaiotaomicron/genética , Microbioma Gastrointestinal , Pequeno RNA não Traduzido/genética , Transcriptoma , Acetilglucosamina/metabolismo , Proteínas de Bactérias/genética , Bacteroides thetaiotaomicron/crescimento & desenvolvimento , Bacteroides thetaiotaomicron/metabolismo , Meios de Cultura/metabolismo , Regulação Bacteriana da Expressão Gênica , Humanos , Conformação de Ácido Nucleico , Regiões Promotoras Genéticas , RNA Bacteriano/genética , Pequeno RNA não Traduzido/química , RNA não Traduzido/genética , Reprodutibilidade dos Testes , Navegador
19.
Sci Rep ; 10(1): 8693, 2020 05 26.
Artigo em Inglês | MEDLINE | ID: mdl-32457382

RESUMO

The contrast between consonance and dissonance is vital in making music emotionally meaningful. Consonance typically denotes perceived agreeableness and stability, while dissonance disagreeableness and a need of resolution. This study addresses the perception of consonance/dissonance in single intervals and chords with two empirical experiments conducted online. Experiment 1 explored the perception of a representative sample of intervals and chords to investigate the overlap between the seven most used concepts (Consonance, Smoothness, Purity, Harmoniousness, Tension, Pleasantness, Preference) denoting consonance/dissonance in all the available (60) empirical studies published since 1883. The results show that the concepts exhibit high correlations, albeit these are somewhat lower for non-musicians compared to musicians. In Experiment 2 the stimuli's cultural familiarity was divided into three levels, and the correlations between the key concepts of Consonance, Tension, Harmoniousness, Pleasantness, and Preference were further examined. Cultural familiarity affected the correlations drastically across both musicians and non-musicians, but in different ways. Tension maintained relatively high correlations with Consonance across musical expertise and cultural familiarity levels, making it a useful concept for studies addressing both musicians and non-musicians. On the basis of the results a control for cultural familiarity and musical expertise is recommended for all studies investigating consonance/dissonance perception.


Assuntos
Música , Reconhecimento Psicológico , Adulto , Feminino , Humanos , Masculino , Inquéritos e Questionários , Navegador
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