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Whole blood RNA-seq demonstrates an increased host immune response in individuals with cystic fibrosis who develop nontuberculous mycobacterial pulmonary disease
<p><strong>Background </strong></p> <p>Individuals with cystic fibrosis have an elevated lifetime risk of colonization, infection, and disease caused by nontuberculous mycobacteria. A prior study involving non-cystic fibrosis individuals reported a gene expression signature associated with susceptibility to nontuberculous mycobacteria pulmonary disease (NTM-PD). In this study, we determined whether people living with cystic fibrosis who progress to NTM-PD have a gene expression pattern similar to the one seen in the non-cystic fibrosis population. <strong> </strong></p> <p><strong>Methods</strong></p> <p>We evaluated whole blood transcriptomics using bulk RNA-seq in a cohort of cystic fibrosis patients with samples collected closest in timing to the first isolation of nontuberculous mycobacteria. The study population included patients who did (n = 12) and did not (n = 30) develop NTM-PD following the first mycobacterial growth. Progression to NTM-PD was defined by a consensus of two expert clinicians based on reviewing clinical, microbiological, and radiological information. Differential gene expression was determined by DESeq2.</p> <p><strong>Results</strong></p> <p>No differences in demographics or composition of white blood cell populations between groups were identified at baseline. Out of 213 genes associated with NTM-PD in the non-CF population, only two were significantly different in our cystic fibrosis NTM-PD cohort. Gene set enrichment analysis of the differential expression results showed that CF individuals who developed NTM-PD had higher expression levels of genes involved in the interferon (α and γ), tumor necrosis factor, and IL6-STAT3-JAK pathways. <strong> </strong></p> <p><strong>Conclusion</strong></p> <p>In contrast to the non-cystic fibrosis population, the gene expression signature of patients with cystic fibrosis who develop NTM-PD is characterized by increased innate immune responses.</p>
African elephants address one another with individually specific name-like calls
<div> <p>Personal names are a universal feature of human language, yet few analogs exist in other species. While dolphins and parrots address conspecifics by imitating the calls of the addressee, human names are not imitations of the sounds typically made by the named individual. Labeling objects or individuals without relying on imitation of the sounds made by that object or individual radically expands the expressive power of language. Thus, if non-imitative name analogs were found in other species, this could have important implications for our understanding of language evolution. Here, we present evidence that wild African elephants address one another with individually specific calls without imitation. We used machine learning to demonstrate that the receiver of a call could be predicted from the call's acoustic structure and found little evidence that calls addressed to a given receiver imitate the receiver's own calls. Moreover, elephants differentially responded to playbacks of calls originally addressed to them relative to calls addressed to a different individual, indicating that they can determine from a call's structure if it was addressed to them. Our findings offer the first evidence for a non-human species individually addressing conspecifics without imitating the receiver.</p> </div>
Individual variation in spawning migration timing in a salmonid fish—exploring roles of environmental and social cues
<p><span>Describing and explaining patterns of individual animal behaviors in situ, and their repeatability over the annual cycle, is an emerging field in ecology owing largely to advances in tagging technology. We describe individual movements of adult Sakhalin taimen, <em>Parahucho</em> <em>perryi</em>, an endangered salmonid fish, in the headwaters of a river in northern Japan during the spring spawning season over two years. Migration timing, separated into stages prior to, during, and following the spawning period, was found to be more consistent and repeatable for females than males. We hypothesized that the observed coordinated movement within seasons, and repeatability in migration timing across seasons, could result from 1) individual-specific responsiveness resulting from endogenous, biological traits that are mediated by environmental factors, or 2) social interactions among comigrating individuals. We found that water temperature and water level experienced by fish near the river mouth approximately a week before arrival at the spawning ground explained variability in run timing between years for females but not males. We found no evidence of conspecific attraction or repulsion resulting from social interactions among the spawners and post-spawners. We conclude that individual-specific responsiveness to environmental cues was the likely mechanism underpinning the observed migration timing and movement patterns.</span></p>
Data repository for manuscript "Contacting individual graphene nanoribbons using carbon nanotube electrodes"
<p>This is the raw data for the manuscript "Contacting individual graphene nanoribbons using carbon nanotube electrodes”.</p>
Investigating PhDs' early career occupational outcomes in Italy: individual motivations, role of supervisor and gender differences (Anonymized UniTo dataset)
<p>Anonymized dataset to replicate the UniTo analysis in Carriero <em>et al.</em> (2023).</p> <p><em>If you use the data, please cite</em>:</p> <p>Carriero, R., Coda Zabetta, M., Geuna, A., & Tomatis, F. (2023). Investigating PhDs’ early career occupational outcomes in Italy: Individual motivations, role of supervisor and gender differences. <em>Higher Education</em>. (<a href="https://doi.org/10.1007/s10734-023-01068-y">https://doi.org/10.1007/s10734-023-01068-y</a>)</p>
Data from: Evaluating the importance of individual heterogeneity in reproduction to Weddell seal population dynamics using integral projection models
<ol> <li>Identifying and accounting for unobserved individual heterogeneity in vital rates in demographic models is important for estimating population-level vital rates and identifying diverse life-history strategies, but much less is known about how this individual heterogeneity influences population dynamics.</li> <li>We aimed to understand how the distribution of individual heterogeneity in reproductive and survival rates influenced population dynamics using vital rates from a Weddell seal population by altering the distribution of individual heterogeneity in reproduction, which also altered the distribution of individual survival rates through the incorporation of our estimate of the correlation between the two rates and assessing resulting changes in population growth.</li> <li>We constructed an integral projection model (IPM) structured by age and reproductive state using estimates of vital rates for a long-lived mammal that has recently been shown to exhibit large individual heterogeneity in reproduction. Using output from the IPM, we evaluated how population dynamics changed with different underlying distributions of unobserved individual heterogeneity in reproduction.</li> <li>Results indicate that the changes to the underlying distribution of individual heterogeneity in reproduction cause very small changes in the population growth rate and other population metrics. The largest difference in the estimated population growth rate resulting from changes to the underlying distribution of individual heterogeneity was less than 1%.</li> <li>Our work highlights the differing importance of individual heterogeneity at the population level compared to the individual level. Although individual heterogeneity in reproduction may result in large differences in the lifetime fitness of individuals, changing the proportion of above- or below-average breeders in the population results in much smaller differences in annual population growth rate. For a long-lived mammal with stable and high adult-survival that gives birth to a single offspring, individual heterogeneity in reproduction has a limited effect on population dynamics. We posit that the limited effect of individual heterogeneity on population dynamics may be due to canalization of life-history traits.</li> </ol>
Data files for manuscript "Elucidating the clinical and molecular spectrum of SMARCC2-associated NDD in a cohort of 65 affected individuals"
<p># 2023-06-28<br> # Data files for manuscript "Elucidating the clinical and molecular spectrum of SMARCC2-associated NDD in a cohort of 65 affected individuals"<br> # Summary<br> This ZIP-file contains the supplementary files of our SMARCC2 study "Elucidating the clinical and molecular spectrum of SMARCC2-associated NDD in a cohort of 65 affected individuals". <br> Suppl. File S2 contains comprehensive clinical data<br> Suppl. File S3 contains comprehensive genetic data<br> Suppl. File S4 contains files of the SMARCC2 N-terminal homology model</p> <p># Folder structure<br> ./ (parent directory containing this README file and all subfolders)<br> ./Files/ (contains Excel Suppl. File S2 and Suppl.File S3, and ZIP Suppl.File S4)</p> <p># Files and checksums<br> Algorithm Hash Path<br> --------- ---- ----<br> MD5 003A879AA75CF8B5C4E3E05F76C4EB4C SMARCC2-Supplementary\Files\FileS2_cases_clinical-table.xlsx<br> MD5 73B4F9E83419A8404345101CAA4D2205 SMARCC2-Supplementary\Files\FileS3_variants-and-domains.xlsx<br> MD5 B0A12F36B4801EB6C4D21BA02B4270BB SMARCC2-Supplementary\Files\FileS4_SMARCC2 N-terminal homology model.zip</p>
Data used in the study "mRNA vaccination boosts spike-specific T cell memory and promotes expansion of CD45RAint TEMRA-like CD8+ T cells in COVID-19 recovered individuals"
<p>Data associated with an original research study examining T cell responses to mRNA vaccination in COVID-19 recovered individuals. 10X Cell Ranger outputs, bulk TCR sequencing data, and T cell functional (ICS) data in this study have been deposited. Authors KMB and HR contributed equally to this effort. Address correspondence to EWN.</p>
Fig. 1 in Infection with Toxoplasma gondii can promote chronic liver diseases in HIV-infected individuals
Fig. 1. Frequency of different liver pathologies in deceased patients from cohorts seropositive and seronegative to Toxoplasma gondii (Nicolle et Manceaux, 1908). * – difference between the indices for the entire cohort of seropositive patients and for the group of deceased patients from this cohort (p <0.05); ^ – difference between the indices for the entire cohort of seronegative patients and for the group of deceased patients from this cohort (p <0.05)
BioRodDis project - Individual information on rodent samples - Jura (France) 2020/2022
<p>This xlxs file contains 190 rodent individuals for which the serological statut for the Puumala (PUUV) orthohantavirus was assessed by immunofluorescence assay (IFA) and enzyme-linked immunosorbent assay (ELISA). </p> <p>The table is organized with the sequencing code in row and the different individual variables in column:</p> <p>Corresponding abbreviations:</p> <p>- CodeID : the unique identifier of each individual</p> <p>- Species: the rodent species</p> <p>- Locality: the sampling locations: La Glacière=”FRFGLA”, Mignovillard=”FRFMIG”</p> <p>- Sex: the sex (F=female; M=male)</p> <p>- Season: the season of sampling</p> <p>- Year: the year of sampling</p> <p>- Period: the season and year of sampling</p> <p>- Weight: the weight (g)</p> <p>- Body_length: the body length (cm)</p> <p>- Tail_length: the tail lenght (cm)</p> <p>- Testes_position: the testes position status (0/1)</p> <p>- Testes_length: the testes lenght (mm)</p> <p>- Seminal_ves_dev: the seminal vesicles development status(0/1)</p> <p>- Vulva: the vulva opening status (0/1)</p> <p>- Lactation: the lactation status (0/1)</p> <p>- Placental_scars: presence of placental scars (0/1)</p> <p>- Uterus_dev: the uterus development status (0/1)</p> <p>- Gestation: the gestation status (0/1)</p> <p>- Sexual_Maturity: the sexual maturity (Mature or immature)</p> <p>- IFA_PUUV: the PUUV serological status by IFA (0= negative; 1= positive)</p> <p>- Serology: the PUUV serological status by ELISA (0= negative; 1= positive)</p>
Sex-specific effects of psychoactive pollution on behavioural individuality and plasticity in fish
<p>The global rise of pharmaceutical contaminants in the aquatic environment poses a serious threat to ecological and evolutionary processes. Studies have traditionally focused on the collateral (average) effects of psychoactive pollutants on ecologically-relevant behaviours of wildlife, often neglecting effects among and within individuals, and whether they differ between males and females. We tested whether psychoactive pollutants have sex-specific effects on behavioural individuality and plasticity in guppies (<em>Poecilia</em> <em>reticulata</em>), a freshwater species that inhabits contaminated waterways in the wild. Fish were exposed to fluoxetine (Prozac) for two years across multiple generations before their activity and stress-related behaviour were repeatedly assayed. Using a Bayesian statistical approach that partitions the effects among and within individuals, we found that males—but not females—in fluoxetine-exposed populations differed less from each other in their behaviour (lower behavioural individuality) than unexposed males. In sharp contrast, effects on behavioural plasticity were observed in females—but not in males—whereby exposure to even low levels of fluoxetine resulted in a substantial decrease (activity) and increase (freezing behaviour) in the behavioural plasticity of females. Our evidence reveals that psychoactive pollution has sex-specific effects on the individual behaviour of fish, suggesting that males and females might not be equally vulnerable to global pollutants.</p>
Figures 1–3 in Individual variation in the advertisement call of Aplastodiscus albosignatus (Anura: Hylidae) is correlated with body size and environmental temperature
Figures 1–3. Location of the study area: (1) map of Brazil highlighting the state of Paraná; (2) map of Paraná indicating the study area; (3) map of Paraná highlighting the physiognomy of the vegetation.
The ash dieback invasion of Europe was founded by two genetically divergent individuals (https://doi.org/10.1038/s41559-018-0548-9)
<p>Hymenoscyphus fraxineus, genome, annotation and genetic diversity data used in analysis of the ash dieback invasion of Europe (McMullan et al., 2018; see README.txt)</p> <p>McMullan M, Rafiqi M, Kaithakottil G, Clavijo BJ, Bilham L, Orton E, et al. The ash dieback invasion of Europe was founded by two genetically divergent individuals. Nat Ecol Evol. 2018; Available from: https://doi.org/10.1038/s41559-018-0548-9</p>
FOR-instance: a UAV laser scanning benchmark dataset for semantic and instance segmentation of individual trees
<p>The challenge of accurately segmenting individual trees from laser scanning data hinders the assessment of crucial tree parameters necessary for effective forest management, impacting many downstream applications. While dense laser scanning offers detailed 3D representations, automating the segmentation of trees and their structures from point clouds remains difficult. The lack of suitable benchmark datasets and reliance on small datasets have limited method development. The emergence of deep learning models exacerbates the need for standardized benchmarks. Addressing these gaps, the FOR-instance data represent a novel benchmarking dataset to enhance forest measurement using dense airborne laser scanning data, aiding researchers in advancing segmentation methods for forested 3D scenes.</p> <p>In this repository, users will find forest laser scanning point clouds from unamnned aerial vehicle (using Riegl sensors) that are manually segmented according to the individual trees (1130 trees) and semantic classes. The point clouds are subdivided into five data collections representing different forests in Norway, the Czech Republic, Austria, New Zealand, and Australia. </p> <p>These data are meant to be used either for developement of new methods (using the dev data) or for testing of exisitng methods (test data). The data splits are provided in the data_split_metadata.csv file.</p> <p>A full description of the FOR-instance data can be found at <a href="http://arxiv.org/abs/2309.01279">http://arxiv.org/abs/2309.01279</a> </p>
Atlantic cod individual spatial behaviour and stable isotope associations in a no-take marine reserve
<ol> <li>Foraging is a behavioural process and, therefore, individual behaviour and diet are theorized to covary. However, few comparisons of individual behaviour type and diet exist in the wild.</li> <li>We tested whether behaviour type and diet covary in a protected population of Atlantic cod, <em>Gadus</em> <em>morhua</em>. </li> <li>Working in a no-take marine reserve, we could collect data on natural behavioural variation and diet choice with minimal anthropogenic disturbance. We inferred behaviour using acoustic telemetry and diet from stable isotope compositions (expressed as δ<sup>13</sup>C and δ<sup>15</sup>N values). We further investigated whether behaviour and diet could have survival costs.</li> <li>We found cod with shorter diel vertical migration distances fed at higher trophic levels. Cod δ<sup>13</sup>C and δ<sup>15</sup>N values scaled positively with body size. Neither behaviour nor diet predicted survival, indicating phenotypic diversity is maintained without survival costs for cod in a protected ecosystem.</li> <li>The links between diet and diel vertical migration highlight that future work is needed to understand whether the shifts in this behaviour during environmental change (e.g. fishing or climate), could lead to trophic cascades. </li> </ol>
Terrestrial laser scanning data of urban trees in Milton Keynes, UK: individual trees and Treegraph model outputs
<p><strong>TLS_point_clouds:</strong></p> <p>- Data collection: Terrestrial laser scanning data acquired in leaf-off condition in April 2021.</p> <p>- Scanning instrument: We used a RIEGL VZ-400 with a wavelength of 1550 nm, 0.35 mrad beam divergence and 0.04˚ angular resolution.</p> <p>- Locations: The data were collected from three urban sites in Milton Keynes, UK: Avebury Blvd (Ave), Dansteed Way (Dan), and Overgate (Ove).</p> <p>- File information: Each file is an individual tree point cloud in Polygon File Format (.ply), which can be viewed in software such as CloudCompare.</p> <p> </p> <p><strong>Treegraph_outputs:</strong></p> <p>- Description: Model outputs from <em>Treegraph</em> for individual trees.</p> <p>- File naming convention: [TreeID]-[downsample_voxel_length]-[tip_diameter_if_known].*</p> <ul> <li>*.centres.ply: Skeleton nodes of individual trees.</li> <li>*.mesh.ply: Cylinder model of individual trees.</li> <li>*.json: Geometrical and topological attributes at varying scales, from internode and branch to the whole tree.</li> <li>*.txt: Summary of input parameters, logs of intermediate steps, and a statistical overview of whole-tree structural attributes.</li> </ul>
Linking the metabolic rate of individuals to species ecology and life history in key Arctic copepods
<p>This folder contains data and code for the manuscript "Linking the metabolic rate of individuals to species ecology <br> and life history in key Arctic copepods"</p> <p>The first script to run is the "rolling regression and adding covariates to MR data.R", this will read in all the<br> files with oxygen measurements, dry weight, and species and life stage information. The code will fit and predict <br> estimates for each individual, calculate O2 from calibration data, subtract background respiration, run the rolling regression,<br> and add the covariates DW, species and life stage to the metabolic rate data, and write the resulting data fame to a .txt file.</p> <p>The second script "lme4 Analysis and figures 5 6 7.R" will read in the data from the first script. <br> Here the AMR RMR and aerobic scope is estimated by Density Estimation via Model-Based Clustering. <br> The resulting data is fitted with a mixed model 'lmer'. <br> The remaining part of the script make the predictions that are presented in the text of the manuscript<br> and that are shown in figure 5, 6, and 7.</p> <p>Further information is annotated in the scripts</p>
"I'm something of an untrained, unofficial cultural anthropologist myself. Ihave a business interviewing people to capture their personal histories. I'm always interested how people fit into their world and how they affect their world. I'm a graphic designer who works in the same building as the printing presses that I recorded. Iwalk past the presses every day on my way to talk to the folks in the prepress department. I'm on friendly but not drinking terms with the pressmen. I'm a friend with the prepress manager. Three Heidelberg presses are installed side by side in an open warehouse-like room. The presses are about twenty feet long and about five feet high. With their series of four humps or mounds where each printing cylinder is located, the presses remind one of giant, gray, mechanical caterpillars. Each press has a cyan cylinder, a magenta cylinder, a yellow cylinder and a black cylinder – so the humps are brightly colored. The presses are well lit by banks of fluorescent lights hanging from the ceiling over each press. When you walk into the press room you hear the sound of rock music blaring from a boom box radio mixed with the general din of the presses. It is only when you walk up to a press like Idid for the recordings that you really start to hear the individual strains of clicking, clacking and mechanical, syncopated chattering. When I made my recordings I was intrigued by the subtle variations in the sounds produced by these machines that aren't apparent when you first walk through the door. The pressmen were kind enough to allow me to walk right up to the presses and poke my microphone quite close to the rotating press cylinders. Iuse a Danish Pro Audio microphone about the size of a pencil eraser. An extremely sensitive mic with the capacity for capturing loud sounds such as the presses up close. Rotating the mic to one side or the other focused on the unique sounds coming from one cylinder or the other." [Kevin/KMerrell]18 in Collecting Sounds. Online Sharing of Field Recordings as Cultural Practice
"I'm something of an untrained, unofficial cultural anthropologist myself. Ihave a business interviewing people to capture their personal histories. I'm always interested how people fit into their world and how they affect their world. I'm a graphic designer who works in the same building as the printing presses that I recorded. Iwalk past the presses every day on my way to talk to the folks in the prepress department. I'm on friendly but not drinking terms with the pressmen. I'm a friend with the prepress manager. Three Heidelberg presses are installed side by side in an open warehouse-like room. The presses are about twenty feet long and about five feet high. With their series of four humps or mounds where each printing cylinder is located, the presses remind one of giant, gray, mechanical caterpillars. Each press has a cyan cylinder, a magenta cylinder, a yellow cylinder and a black cylinder – so the humps are brightly colored. The presses are well lit by banks of fluorescent lights hanging from the ceiling over each press. When you walk into the press room you hear the sound of rock music blaring from a boom box radio mixed with the general din of the presses. It is only when you walk up to a press like Idid for the recordings that you really start to hear the individual strains of clicking, clacking and mechanical, syncopated chattering. When I made my recordings I was intrigued by the subtle variations in the sounds produced by these machines that aren't apparent when you first walk through the door. The pressmen were kind enough to allow me to walk right up to the presses and poke my microphone quite close to the rotating press cylinders. Iuse a Danish Pro Audio microphone about the size of a pencil eraser. An extremely sensitive mic with the capacity for capturing loud sounds such as the presses up close. Rotating the mic to one side or the other focused on the unique sounds coming from one cylinder or the other." [Kevin/KMerrell]18
Targeted social immunity is associated with a pathogen-specific erosion of individual immune function in ants - dataset
<p>Complete dataset of quantitative data and R scripts used to generate the figures and statistics of the publication, sorted by figure panel number. Information about data structure are including in the scripts. </p>
Consensual videos of potentially re-identifiable individuals recorded at the Autonomous Driving Test Area Baden-Württemberg (raw images recorded daytime).
<p>For the purpose of research on data intermediaries and data anonymisation, it is necessary to test these processes with realistic video data containing personal data. For this purpose, the <a href="http://treumoda.de/">TreuMoDa</a> project, funded by the German Federal Ministry of Education and Research (BMBF), has created a dataset of different traffic scenes containing identifiable persons.</p><p>This video data was collected at the <a href="https://taf-bw.de/">Autonomous Driving Test Area Baden-Württemberg</a>. On the one hand, it should be possible to recognise people in traffic, including their line of sight. On the other hand, it should be usable for the demonstration and evaluation of anonymisation techniques.</p><p><strong>The legal basis for the publication of this data set the consent given by the participants as documented in the file Consent.pdf (all purposes) in accordance with Art. 6 1 (a) and Art. 9 2 (a) GDPR. Any further processing is subject to the GDPR.</strong></p><p>We make this dataset available for non-commercial purposes such as teaching, research and scientific communication. Please note that this licence is limited by the provisions of the GDPR. Anyone downloading this data will become an independent controller of the data. This data has been collected with the consent of the identifiable individuals depicted.</p><p>Any consensual use must take into account the purposes mentioned in the uploaded consent forms and in the privacy terms and conditions provided to the participants (see Consent.pdf). All participants consented to all three purposes, and no consent was withdrawn at the time of publication. KIT is unable to provide you with contact details for any of the participants, as we have removed all links to personal data other than that contained in the published images.</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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.