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2,096 results for “Tracts”
Data from: Quantitative proteomics reveals rapid divergence in the postmating response of female reproductive tracts among sibling species
<p><span><span><span><span><span><span><span><span><span><span><span>Fertility depends, in part, on interactions between male and female reproductive proteins inside the female reproductive tract (FRT) that mediate postmating changes in female behavior, morphology, and physiology. Coevolution between interacting proteins within species may drive reproductive incompatibilities between species, yet the mechanisms underlying postmating-prezygotic isolating barriers remain poorly resolved. Here, we used quantitative proteomics in sibling <i>Drosophila</i> species to investigate the molecular composition of the FRT environment and its role in mediating species-specific postmating responses. We found that (1) FRT proteomes in <i>D. simulans</i> and<i> D. mauritiana</i> virgin females express unique combinations of secreted proteins and are enriched for distinct functional categories, (2) mating induces substantial changes to the FRT proteome in <i>D. mauritiana</i> but not in <i>D. simulans</i>, and (3) the <i>D. simulans </i>FRT proteome exhibits limited postmating changes irrespective of whether females mate with conspecific or heterospecific males, suggesting an active female role in mediating reproductive interactions. Comparisons with similar data in the closely related outgroup species <i>D. melanogaster </i>suggest that divergence is concentrated on the <i>D. simulans </i>lineage. Our study suggests that divergence in the FRT extracellular environment and postmating response contribute to previously described patterns of postmating-prezygotic isolation and the maintenance of species boundaries.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria
Objective: Recognizing increasing interest in community disease surveillance globally, the goal of this study was to investigate whether respiratory viruses circulating in the community may be represented through clinical (hospital) surveillance in Nigeria. Results: Children were selected via convenience sampling from communities and a tertiary care center (n = 91) during spring 2017 in Ilorin, Nigeria. Nasal swabs were collected and tested using polymerase chain reaction. The majority (79.1%) of subjects were under 6 years old, of whom 46 were infected (63.9%). A total of 33 of the 91 subjects had one or more respiratory tract virus; there were 10 cases of triple infection and 5 of quadruple. Parainfluenza virus 4, respiratory syncytial virus B and enterovirus were the most common viruses in the clinical sample; present in 93.8% (15/16) of clinical subjects, and 6.7% (5/75) of community subjects (significant difference, p < 0.001). Coronavirus OC43 was the most common virus detected in community members (13.3%, 10/75). A different strain, Coronavirus OC 229 E/NL63 was detected among subjects from the clinic (2/16) and not detected in the community. This pilot study provides evidence that data from the community can potentially represent different information than that sourced clinically, suggesting the need for community surveillance to enhance public health efforts and scientific understanding of respiratory infections.
Dipolar EPR distance distribution libraries from a T4-lysozime and polypyrimidine-tract binding protein 1 (PTBP1) MMM simulations
<p>These datasets are part of the Supplementary Information of<br> <br> Compactness regularization in the analysis of dipolar EPR spectroscopy data<br> Luis Fábregas-Ibáñez, Gunnar Jeschke, Stefan Stoll<br> Journal of Magnetic Resonance, 2022</p> <p>The datasets contain libraries of distributions of distances between nitroxide labels in a T4-Lysozyme protein (2LZM) and the polypyrimidine-tract binding protein 1 (PTBP1) simulated with the MMM software package.</p> <p>The libraries are saved in .mat (MATLAB) format and contain a structure with the distance axis `r0` and distance distributions `P0` and other statistical quantities of the distance distributions.</p>
Realistic 3D avian vocal tract model demonstrates how shape affects sound filtering (Passer domesticus)
<p><span>Despite the complex geometry of songbird's vocal system, it was typically modelled as a tube or with simple mathematical parameters to investigate sound filtering. Here, we developed an adjustable computational acoustic model of a sparrow's upper vocal tract (<em>Passer domesticus</em>), derived from micro-CT scans. We discovered that a 20% tracheal shortening or a 20° beak gape increase caused the vocal tract harmonic resonance to shift towards higher pitch (11.7% or 8.8%, respectively), predominantly in the mid-range frequencies (3-6 kHz). The oropharyngeal-esophageal cavity (OEC), known for its role in sound filtering, was modelled as an adjustable 3D cylinder. For a constant OEC volume, an elongated cylinder induced a higher frequency shift than a wide cylinder (70% versus 37%). We found that the OEC volume adjustments can modify the OEC first harmonic resonance at low frequencies (1.5–3 kHz) and the OEC third harmonic resonance at higher frequencies (6-8 kHz). This work demonstrates the need to consider the realistic geometry of the vocal system to accurately quantify its effect on sound filtering and show that sparrows can tune the entire range of produced sound frequencies to their vocal system resonances, by controlling the vocal tract shape, especially through complex OEC volume adjustments.</span></p>
Antibiotic Prescription in Children with Acute Upper Respiratory Tract Infections-Egypt
<p>This dataset for data collected to study knowledge , attitude and practice of non-specialized physician in Assiut, Egypt as regards antibiotic prescription in cases of children with acute upper respiratory tract infections.<br> Questionnaire of the study has been uploaded with the dataset and for each question the responses were coded in dataset as presented in the questionnaire (i.e No=0, Yes=1).</p>
Lung microbiome in children with hematological malignancies and lower respiratory tract infections
<p><strong>Background</strong>: Respiratory infectious complications remain a major cause of morbidity and mortality in children with hematological malignancies. Knowledge regarding the lung microbiome in the aforementioned children is limited.</p> <p><strong>Methods</strong>: A prospective cohort was conducted, enrolling 16 children with hematological malignancies complicated with moderate to severe lower respiratory tract infections(LRTIs), versus 21 LRTIs children with age, gender, weight, infection severity matched, with no underlying malignancies, to evaluate the lung microbiome from bronchoalveolar lavage fluid samples in different groups.</p> <p><strong>Results</strong>: Lung microbiome from children with hematological malignancies and LRTIs showed obviously decreased α and β diversity, increased microbial function in infectious disease:bacteria/parasite, drug resistance:antimicrobial and human pathogenesis than the control group, and significantly reduced proportion of <em>Firmicutes</em>, <em>Bacteroidota</em>, <em>Actinobacteriota</em> , increased <em>Proteobacteria</em> at the phylum level, distinctly elevated <em>Parabacteroides</em>, <em>Klebsiella</em>, <em>Grimontia</em>, <em>Escherichia_Shigella</em>, <em>unclassified_Enterobacteriaceae</em> at the genus level than the control group. Besides, it was revealed that α diversity (Shannon), β diversity (Bray Curtis dissimilarity), Proteobacteria at the phylum level, and <em>unclassified_Enterobacteriaceae</em> and <em>Escherichia_Shigella</em> at the genus level were significantly negatively associated with hospitalization course, whereas <em>Firmicutes</em> at the phylum level was established positively correlated with hospitalization course.</p> <p><strong>Conclusions</strong>: Children with hematological malignancies and LRTIs showed obviously decreased α and β diversity, significantly increased function in infectious disease pathogenesis, antimicrobial drug resistance, and unfavorable environment tolerance. Besides, α diversity (Shannon), β diversity (Bray Curtis dissimilarity), <em>Proteobacteria</em> may be used as negatively correlated predictors for hospitalization course in these children whereas <em>Firmicutes</em> is a positively correlated predictor. </p>
Etiology of upper respiratory tract infection in outpatients before and during the SARS-CoV-2 pandemic
<p>Illumina MiSeq Viral reads after quality passing and detection in zipped FASTQ format. Files are named by Patient's codes and whether DNA or RNA workflow is used for sample preparation.</p>
Meta-analysis of the human upper respiratory tract microbiome reveals robust taxonomic associations with health and disease.
<p>Contains all intermediate data files for the article <strong>Meta-analysis of the human upper respiratory tract microbiome reveals robust taxonomic associations with health and disease, </strong>Quinn-Bohmann et al. 2024. </p> <p>NP and OP refers to nasopharyngeal or oropharyngeal samples, respectively. As some study identifiers are duplicated across these groups, qiime_NP and qiime_OP should be unzipped in distinct directories. The same applies for metadata data files. </p> <p>Analyses of these data can be found at https://github.com/Gibbons-Lab/2023_URTmetaanalysis/tree/main. </p>
Data from: Mating system variation and gene expression in the male reproductive tract of Peromyscus mice
<p>Genes involved in reproduction often evolve rapidly at the sequence level due to postcopulatory sexual selection (PCSS) driven by male-male competition and male-female sexual conflict, but the impact of PCSS on gene expression has been under-explored. Further, though multiple tissues contribute to male reproductive success, most studies have focused on the testes. To explore the influence of mating system variation on reproductive tract gene expression in natural populations, we captured adult males from monogamous <em>Peromyscus californicus</em> and polygynandrous<em> P. boylii</em> and <em>P. maniculatus</em>. We generated RNAseq libraries, quantified gene expression in the testis, seminal vesicle, epididymis, and liver, and identified 3,627 mating system-associated differentially expressed genes (MS-DEGs), where expression shifted in the same direction in <em>P. maniculatus</em> and <em>P. boylii</em> relative to <em>P. californicus</em>. Gene expression variation was most strongly associated with mating behavior in the seminal vesicles, where 89% of differentially expressed genes were MS-DEGs, including key seminal fluid proteins <em>Svs2</em> and <em>Pate4</em>. We also used published rodent genomes to test for positive and relaxed selection on <em>Peromyscus</em>-expressed genes. Though we did not observe more overlap than expected by chance between MS-DEGs and positively selected genes, 203 MS-DEGs showed evidence of positive selection. Fourteen reproductive genes were under tree-wide positive selection but convergent relaxed selection in <em>P. californicus</em> and <em>Microtus ochrogaster</em>, a distantly related monogamous species. Changes in transcript abundance and gene sequence evolution in association with mating behavior suggest that male mice may respond to sexual selection intensity by altering aspects of sperm motility, sperm-egg binding, and copulatory plug formation.</p>
Fig. 2 in Landscape Ecological Analysis Of Taurkalne Forest Tract Fragmentation
Fig. 2. Road network length (km) by category.
Audio from: 'Modeling Voiced Stop Consonants using the 3D Dynamic Digital Waveguide Mesh Vocal Tract Model'
<p>Audio files associated with the paper 'Modeling Voiced Stop Consonants using the 3D Dynamic Digital Waveguide Mesh Vocal Tract Model', presented at the International Congress of Phonetic Sciences 2019, Melbourne, Australia.</p>
MOVIE S1. Normal clearance of murine respiratory tract is mediated by discontinuous Muc5b and Muc5ac mucus clouds
<p>Movie S1. Mucus transport in healthy WT mouse trachea. The mucus on the mounted trachea was submerged in a buffer containing Alcian blue, the tissue tilted, and the mucus movement recorded by video microscopy.</p>
Figure 3 in Occurrence of microplastics in the gastrointestinal tracts of some edible fish species along the Turkish coast
Figure 3. MP particles extracted from edible fish species present in Turkish seas.
Figure 9 in Microplastics in commercial fish digestive tracts from freshwater habitats in Northern Thailand
Figure 9. Microplastic type and shape in the GIT of fish samples confirmed by FTIR.
Figure 5 in Microplastics in commercial fish digestive tracts from freshwater habitats in Northern Thailand
Figure 5. Composition of microplastic found in freshwater fish; a) size b) morphotype c) color.
Whole-genome sequencing reveals contribution of rare and common variation to structural kidney and urinary tract malformations
<p>Supplementary tables detailing analysis of whole-genome sequencing data from 992 patients with congenital anomalies of the kidneys and urinary tract (CAKUT). </p>
Pathogen non-planktonic phases within the urinary tract impact early infection and resistance evolution - Data
<p>This upload contains data that is necessary to re-create the figures for the manuscript "<strong>Infection dynamics in the urinary tract - The importance of non-planktonic phases during early infection and resistance evolution</strong>" by Raatz et al. published in The ISME Journal (<a href="https://doi.org/10.1093/ismejo/wrae191">https://doi.org/10.1093/ismejo/wrae191</a>).</p> <p>This manuscript is available as a bioRxiv preprint at https://www.biorxiv.org/content/10.1101/2023.10.23.563535.</p> <p>The related upload with DOI 10.5281/zenodo.10025282 contains the scripts to compute this data set, as well as the scripts for plotting.</p> <p> </p>
Dataset - Dynamic persistence of intracellular bacterial communities of uropathogenic Escherichia coli in a human bladder-chip model of urinary tract infections
<p>Dataset for manuscript posted at biorxiv: https://doi.org/10.1101/2021.01.03.42483 and in revision for eLife. Data corresponding to each main figure and its associated figure supplements are in seperate .zip folders.</p>
SARS-CoV-2 viral loads across the upper and lower respiratory tract, sex, disease severity and age groups for adult and pediatric COVID-19
<p>This dataset shows SARS-CoV-2 respiratory viral loads (viral RNA concentration in the respiratory tract) in the upper and lower respiratory tract for age, sex and COVID-19 severity groups. The data were obtained from a systematic review. The model outputs show the Weibull distributions, case percentiles, and sensitivity & specificity when using SARS-CoV-2 viral load (URT or LRT) as a prognostic indicator. See our paper for more information.</p>
Philosophy [IO Bijapur 181A] Glosses and tracts
<ul> <li><strong>Philosophy.</strong></li> <li><strong>This manuscript is now IO Bijapur 181A </strong><strong>in the India Office collections.</strong></li> <li><strong>[metadata:</strong><a href="https://de.wikipedia.org/wiki/Otto_Loth"> <strong>Otto Loth, </strong></a><strong><em><a href="http://doi.org/10.5281/zenodo.3923636">A Catalogue of the Arabic Manuscripts in the Library of the India Office</a></em>, (volume 1), no. 525 here with further notations and hyperlinks]</strong>. <p> </p> <p>525.</p> <p>B 181A. Size 7<sup>1/4</sup> in. by 5<sup>1/2</sup> in.; foll. 173. Seventeen lines in a page.</p> <p>Glosses on the preceding Commentary of <em>Ḳuṭb al-dîn</em>, by SAIYID SHARÎF JURJÂNÎ (d. A.H. 816). See Ḥ. Kh. v. 595, and Casiri, i. 188, no. DCXXXVIII [= <a href="http://worldcat.org/identities/lccn-no2005040879/">Miguel Casiri</a>, <a href="https://archive.org/details/bibliothecaarabi01esco/page/n3/mode/2up"><em>Bibliotheca Arabico-Hispana Escurialensis</em></a> (2 vols, Madrid, 1760–1770)]; cf. Cat. Lugd. iii. 373. These Glosses extend in this, as well as all the following copies, and also in the MS. of Casiri, only over the first part of the Logic, on the apprehensions, التصوّرات.</p> <p>The work begins:</p> <p>قال فريد عصره ووحيد زمانه<sup>1</sup><sup> </sup>الحمدلله فيّاض ذوارف العوارف الفياض الوهاب.</p> <p>The single glosses are not introduced by قوله , as usual , but the text to which they refer is marked with red lines.</p> <p>Neatly written, by Taḳî al-dîn الحصنى , who died A.H. 881 , according to a note on the title-page, which was written by the subsequent owner of this copy.</p> <p>Marginal notes.</p> <p>The last two foll. are filled with various notes and tracts, viz.---</p> <p><em>a</em>. An arithmetical rule, which begins:</p> <p> بسط التركات التي فيها الكسر</p> <p><em>b</em>. A short tract by JURJÂNÎ on the definition of غاية , فائدة, and other words. It is inscribed:</p> <p>الفوائد الشريفة للحضرة الشريفية قدّس سرّه</p> <p><em>c</em>. (fol.173) A list of the ‘’seventy and odd’’ articles of the Creed, beginning :</p> <p>ذكر الشعب البضع و السبعين الايمان</p> <p>It is followed by</p> <p>صلوة الاستخارة</p> <p><em>d</em>. Another tract on the Creed. At the end the signature of ‘Alî b. Maḥmûd Gîlânî.</p> <p>Bîj. Libr., A. H. 1025. Seal of Ibrâhîm Nauras (‘Âdil Shâh II.).</p> <p>On the title-page is an ornament in colours, which contains the title of the book, and a note, according to which it was presented by Mîr Zâhid, A.H. 994.</p> <p> </p> <p><sup>1</sup> This commencement slightly varies from the following copies and Casiri, l.c.</p> <p> </p> <p> </p> <p> </p> <p> </p> </li> </ul> <p> </p>
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.