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203 results for “longitudinal data”
Data from: A longitudinal genetic survey identifies temporal shifts in the population structure of Dutch house sparrows
Dutch house sparrow (Passer domesticus) densities dropped by nearly 50% since the early 1980s, and similar collapses in population sizes have been reported across Europe. Whether, and to what extent, such relatively recent demographic changes are accompanied by concomitant shifts in the genetic population structure of this species needs further investigation. Therefore, we here explore temporal shifts in genetic diversity, genetic structure and effective sizes of seven Dutch house sparrow populations. To allow the most powerful statistical inference, historical populations were resampled at identical locations and each individual bird was genotyped using nine polymorphic microsatellites. Although the demographic history was not reflected by a reduction in genetic diversity, levels of genetic differentiation increased over time, and the original, panmictic population (inferred from the museum samples) diverged into two distinct genetic clusters. Reductions in census size were supported by a substantial reduction in effective population size, although to a smaller extent. As most studies of contemporary house sparrow populations have been unable to identify genetic signatures of recent population declines, results of this study underpin the importance of longitudinal genetic surveys to unravel cryptic genetic patterns.
Data from: An archive of longitudinal recordings of the vocalizations of adult Gombe chimpanzees
Studies of chimpanzee vocal communication provide valuable insights into the evolution of communication in complex societies, and also comparative data for understanding the evolution of human language. One particularly valuable dataset of recordings from free-living chimpanzees was collected by Frans X. Plooij and the late Hetty van de Rijt-Plooij at Gombe National Park, Tanzania (1971–73). These audio specimens, which have not yet been analysed, total over 10 h on 28 tapes, including 7 tapes focusing on adult individuals with a total of 605 recordings. In 2014 the first part of that collection of audio specimens covering the vocalizations of the immature Gombe chimpanzees was made available. The data package described here covers the vocalizations of the adult chimpanzees. We expect these recordings will prove useful for studies on topics including referential signalling and the emergence of dialects. The digitized sound recordings were stored in the Macaulay Library and the Dryad Repository. In addition, the original notes on the contexts of the calls were translated and transcribed from Dutch into English.
Data from: Fungal communities in Scandinavian lakes along a longitudinal gradient
This study investigates the diversity and distribution of fungal communities in 77 oligotrophic lakes in southern Norway and Sweden using 454-sequencing with fungal-specific primers targeting ITS2 region of the rRNA gene. A total of 232 operational taxonomic units (OTUs) belonging to four recognized phyla were detected. A large proportion (70.69%) of the detected OTUs were Dikarya (Ascomycota and Basidiomycota), while Chytridiomycota dominated quantitatively (63.37% reads). The most abundant aquatic fungi were taxonomically assigned to Chytridiomycota, whose members are known to be saprobes on a large variety of substrates and parasites of phytoplankton, zooplankton, fungi and invertebrates, suggesting that resident fungi strictly depend on surfaces and, therefore, are closely associated with other types of aquatic organisms. Our results indicate that surface waters of oligotrophic lakes harbour a diverse pool of fungi, both with tentative terrestrial and true aquatic origin. Longitude and environmental factors were important in structuring the fungal community composition.
Data from: Longitudinal recordings of the vocalizations of immature Gombe chimpanzees for developmental studies
Many researchers are interested in chimpanzee vocal communication, both as an important aspect of chimpanzee social behavior and as a source of insights into the evolution of human language. Nonetheless, very little is known about how chimpanzee vocal communication develops from infancy to adulthood. The largest dataset of audiorecordings from free-living immature chimpanzees was collected by the late Hetty van de Rijt-Plooij and Frans X. Plooij at Gombe National Park, Tanzania (1971–1973). These recordings have not yet been analysed. Therefore, the most extensive effort to study the development of chimpanzee vocalizations remains unfinished. The audiospecimens total over 10 h on 28 tapes, including 20 tapes focusing on 17 specific immature individuals with a total of 1,136 recordings. In order to make this dataset available to more researchers, the analogue sound recordings were digitized and stored in the Macaulay Library and the Dryad Repository. In addition, the original notes on the contexts of the calls were translated and transcribed from Dutch into English.
Data from: Gray matter volume modifications in migraine: a cross-sectional and longitudinal study
Objective. To explore cross-sectional and longitudinal gray matter (GM) volume changes in migraine patients and their association with patients' clinical characteristics and disease activity. Methods. Brain T2-weighted and 3D T1-weighted scans were acquired from 73 episodic migraineurs and 46 age- and sex-matched non-migraine controls at baseline. Twenty-four migraineurs and 25 controls agreed to be re-examined after a mean follow-up of 4 years. Using a general linear model and SPM12, a whole-brain analysis was performed to assess GM volume modifications. Results. At baseline, compared to controls, migraine patients showed lower cerebellar GM volume and higher volume of regions of the fronto-temporal lobes. At follow-up, migraineurs were significantly older than controls. Over the follow-up, migraineurs developed an increased volume of fronto-temporo-parietal regions, which was more prominent in patients with a higher baseline disease activity: long disease duration and high attack frequency. Migraineurs also developed decreased GM volume of visual areas, which was related to higher pain severity. Patients with an increased attack frequency at follow-up experienced both increased and decreased volume of nociceptive regions. In migraineurs, reduced GM volume of extrastriate visual areas during the follow-up was significantly correlated to baseline disease activity: shorter disease duration and lower attack frequency. Conclusion. In this cohort, the migraine brain changes dynamically over time and different pathophysiological mechanisms can occur in response to patients' disease severity. The interaction between predisposing brain traits and experience-dependent responses might vary across different nociceptive and visual areas, thus leading to distinct patterns of longitudinal GM volume changes.
Data from: Longitudinal study of performance on the Ruff Figural Fluency Test in persons aged 35 years or older
The Ruff Figural Fluency Test (RFFT) is a cognitive test to measure executive function. Longitudinal studies have shown that repeated testing improves performance on the RFFT. Such a practice effect may hinder the interpretation of test results in a clinical setting. Therefore, we investigated the longitudinal performance on the RFFT in persons aged 35–82 years. Performance on the RFFT was measured three times over an average follow-up period of six years in 2,515 participants of the Prevention of REnal and Vascular ENd-stage Disease (PREVEND) study in Groningen, the Netherlands: 53% men; mean age (SD), 53 (10) years. The effect of consecutive measurements on performance on the RFFT was investigated with linear multilevel regression models that also included age, gender, educational level and the interaction term consecutive measurement number x age as independent variables. It was found that the mean (SD) number of unique designs on the RFFT increased from 73 (26) at the first measurement to 79 (27) at the second measurement and to 83 (26) at the third measurement (p<0.001). However, the increase per consecutive measurement number was negatively associated with age and decreased with 0.23 per one-year increment of age (p<0.001). The increase per consecutive measurement number was not dependent on educational level. Similar results were found for the median (IQR) number of perseverative errors which showed a small but statistically significant increase with repeating testing: 7 (3–13) at the first measurement, 7 (4–14) at the second measurement and 8 (4–15) at the third measurement (ptrend = 0.002). In conclusion, the performance on the RFFT improved by repeating the test over an average follow-up period of three to six years. This practice effect was the largest in young adults and not dependent on educational level.
Data from: Complex longitudinal diversification across South China and Vietnam in Stejneger's pit viper, Viridovipera stejnegeri (Schmidt, 1925) (Reptilia: Serpentes: Viperidae)
Viridovipera stejnegeri is one of the most common pit vipers in Asia, with a wide distribution in southern China and Vietnam. We investigated historical demography and explored how the environment and climatic factors have shaped genetic diversity and the evolutionary history of this venomous snake. A total of 171 samples from 47 localities were sequenced and analysed for two mitochondrial gene fragments and three nuclear genes. Gene trees reveal the existence of two well-supported clades (Southwest China and Southeast China) with seven distinct and strongly supported, geographically structured subclades within V. stejnegeri. Estimation of divergence time and ancestral area suggests that V. stejnegeri originated at ~6.0 Ma in the late Miocene on the Yunnan–Guizhou Plateau. The estimated date of origin and divergence of the island populations of Taiwan and Hainan closely matches the geological origin of the both islands. The mtDNA gene tree reveals the presence of west–east diversification in V. stejnegeri populations. Complex orogenesis and heterogeneous habitats, as well as climate-mediated habitat differentiation including glacial cycles, all have influenced population structure and the distribution of this taxon. The validity of V. stejnegeri chenbihuii is questionable, and this subspecies most probably represents an invalid taxon.
Data from: Incidence of influenza A(H3N2) virus infections in Hong Kong in a longitudinal sero-epidemiological study, 2009-2015
Background: Many serologic studies were done during and after the 2009 influenza pandemic, to estimate the cumulative incidence of influenza A(H1N1)pdm09 virus infections, but there are few comparative estimates of the incidence of influenza A(H3N2) virus infections during epidemics. Methods: We conducted a longitudinal serologic study in Hong Kong. We collected sera annually and tested samples from 2009-13 by HAI against the A/Perth/16/2009(H3N2) virus, and samples from 2013-15 against the A/Victoria/361/2011(H3N2) virus using the hemagglutination inhibition (HAI) assay. We estimated the cumulative incidence of infections based on 4-fold or greater rises in HAI titers in consecutive sera. Results: There were four major H3N2 epidemics: (1) Aug-Oct 2010; (2) Mar-Jun 2012; (3) Jul-Oct 2013; and (4) Jun-Jul 2014. Between 514 516 and 614 619 relevant pairs of sera were available for each epidemic. We estimated that 98%, 2019%, 57% and 7% of the population were infected in each epidemic, respectively, with higher incidence in children in epidemics 1 and 4. Conclusions: We estimatedfound that around 5% to 20% of the Hong Kong population were infectedre-infections in each of the four H3N2 epidemics that occurred from 2010 through 2014 were rare. The largest H3N2 epidemic occurred with the lowest level of pre-epidemic immunity.
Data from: Within guild co-infections influence parasite community membership: a longitudinal study in African Buffalo
1. Experimental studies in laboratory settings have demonstrated a critical role of parasite interactions in shaping parasite communities. The sum of these interactions can produce diverse effects on individual hosts as well as influence disease emergence and persistence at the population level. 2. A predictive framework for the effects of parasite interactions in the wild remains elusive, largely because of limited longitudinal or experimental data on parasite communities of free-ranging hosts. 3. This four year study followed a community of haemoparasites in free-ranging African buffalo (Syncerus caffer). We detected infection by 11 haemoparasite species using PCR-based diagnostic techniques, and analyzed drivers of infection patterns using generalized linear mixed models to understand the role of host characteristics and season on infection likelihood. We tested for (1) effects of co-infection by other haemoparasites (within guild) and (2) effects of parasites infecting different tissue types (across guild). 4. We found that within guild co-infections were the strongest predictors of haemoparasite infections in the buffalo; but that seasonal and host characteristics also had important effects. In contrast, the evidence for across-guild effects of parasites utilizing different tissue on haemoparasite infection was weak. 5. These results provide a nuanced view of the role of co-infections in determining haemoparasite infection patterns in free living mammalian hosts. Our findings suggest a role for interactions among parasites infecting a single tissue type in determining infection patterns.
Data from: Inferring longitudinal hierarchies: framework and methods for studying the dynamics of dominance
1. Social inequality is a consistent feature of animal societies, often manifesting as dominance hierarchies, in which each individual is characterized by a dominance rank denoting its place in the network of competitive relationships among group‐members. Most studies treat dominance hierarchies as static entities despite their true longitudinal, and sometimes highly dynamic, nature. 2. To guide study of the dynamics of dominance, we propose the concept of a longitudinal hierarchy: the characterization of a single, latent hierarchy and it's dynamics over time. Longitudinal hierarchies describe the hierarchy position (r) and dynamics (∆) associated with each individual as a property of its interaction data, the periods into which these data are divided based on a period delineation rule (p), and the method chosen to infer the hierarchy. Hierarchy dynamics result from both active (∆a) and passive (∆p) processes. Methods that infer longitudinal hierarchies should optimize accuracy of rank dynamics as well as of the rank orders themselves, but no studies have yet evaluated the accuracy with which different methods infer hierarchy dynamics. 3. We modify three popular ranking approaches to make them better suited for inferring longitudinal hierarchies. Our three 'informed' methods assign ranks that are informed by data from the prior period rather than calculating ranks de novo in each observation period, and use prior knowledge of dominance correlates to inform placement of new individuals in the hierarchy. These methods are provided in an R package. 4. Using both a simulated dataset and a long‐term empirical dataset from a species with two distinct sex‐based dominance structures, we compare the performance of these methods and their unmodified counterparts. We show that choice of method has dramatic impacts on inference of hierarchy dynamics via differences in estimates of ∆a. Methods that calculate ranks de novo in each period overestimate hierarchy dynamics, but incorporation of prior information leads to more accurately inferred ∆a. Of the modified methods, Informed MatReorder infers the most conservative estimates of hierarchy dynamics and Informed Elo infers the most dynamic hierarchies. 5. This work provides crucially needed conceptual framing and methodological validation for studying social dominance and its dynamics.
Data set from longitudinal survey: ySKILLS' first wave
<p>This document provides the data set and information concerning the first wave of data collection of ySKILLS longitudinal survey items conducted within Task 4.2. in six countries: Estonia, Finland, Germany, Italy, Poland, and Portugal. The aim of Task 4.2. was to develop a robust longitudinal survey to measure both short and medium-term impact of information and communication technologies (ICT) on youth. The data is collected in three waves. The survey focuses on four dimensions of well-being (cognitive, physical, psychological, and social) and several areas related to ICT use. Specifically, the questionnaire is divided into sections. For a detailed overview of each section, see the data dictionary. </p> <p>Upon first request, users will be granted access to the dataset. As the project is still in progress, and the data collection of the follow-up waves is still ongoing the dataset is not yet open access. Once all survey waves are completed, the dataset is merged and cleaned, and the report on the three waves is published, the data of all waves will be open access. </p>
Data for the paper "Longitudinal Filtering, Sponge Layers, and Equatorial Jet Formation in a General Circulation Model of Gaseous Exoplanets"
<p>GCM data for the paper "Longitudinal Filtering, Sponge Layers, and Equatorial Jet Formation in a General Circulation Model of Gaseous Exoplanets" published in Monthly Notices of the Royal Astronomical Society. Data are in the pp format used by the Met Office Unified Model GCM and can be loaded using the Iris python package.<br><br>The individual files correspond to simulations done in the following parts of the paper<br><br>eta75_study.tgz - Simulations from Section 3.1.1 investigating changing the value of t_K with eta_s=0.75<br>Keff_flat.tgz - The simulation with a flattened Keff, as outlined in Section 3.1.2<br>eta9_study.tgz - Simulations from Section 3.2 investigating increasing eta_s to 0.9<br>resolution_study.tgz - The simulations from the resolution study found in Appendix B.</p>
Metadata from database covering longitudinal data from patients with subarachnoid hemorrhage
<p>Data from patient history, lab values (low-resolution data) and from multiple biosensors (high-resolution data) were prospectively collected from patients with aneurysmal subarachnoid hemorrhage (aSAH) who were admitted to the neurosurgical intensive care unit at the University Hospital of Zurich since October 2016. The cohort covers data from about 300 patients. The data collection was carried out via a CNS data collector (Moberg ICU Solutions, Ambler, PA) and the processing and storage of the high-resolution data was realized on the dedicated information technology infrastructure "ICU Cockpit" [doi.org/10.1093/jamia/ocac064].</p> <p><span>With the present project, highly sensitive patient data in need of protection is collected. Data cannot be made publicly available. However, for specific research questions, data may be made available upon request with the appropriate ethics committee approval and after completion of a DTA.</span></p>
Data for: Diagnostic potential of blood plasma longitudinal viscosity measured using Brillouin light scattering
<p>Data for "Diagnostic potential of blood plasma longitudinal viscosity measured using Brillouin light scattering"</p>
Empirical Data from a Longitudinal Software Maintenance Experiment
<p>This dataset contains IDE interaction traces (logs) and screen videos obtained from a comprehensive study conducted to understand in detail how software professionals plan and execute maintenance activities on real-life software.</p>
Data for Fig 1C of PLOS Biology The Cybathlon BCI race: Successful longitudinal mutual learning with two tetraplegic users
<p>The mat file consists of the race completion time data of pilots P1 and P2 and the session date these races took place on.</p>
Data for S5 Fig of PLOS Biology The Cybathlon BCI race: Successful longitudinal mutual learning with two tetraplegic users
<p>The mat file consists of BCI discriminancy data after artifact removal for pilot P2 for three typical sessions of this user</p>
Data from: Identifying patterns of non-communicable diseases in developed eastern coastal China: a longitudinal study of electronic health records from 12 public hospitals
Objective: Few studies have examined the spectrum and trends of non-communicable diseases (NCDs) in inpatients in eastern coastal China, which is transforming from an industrial economy to a service-oriented economy and is the most economically developed region in the country. This study aimed to dynamically elucidate the spectrum and characteristics of severe NCDs in eastern coastal China by analysing patients' longitudinal electronic health records (EHRs). Setting: To monitor the spectrum of NCDs dynamically, we extracted the EHR data from 12 general tertiary hospitals in eastern coastal China from 2003 to 2014. The rankings of and trends in the proportions of different NCDs presented by inpatients in different gender and age groups were calculated and analysed. Participants: We obtained a total sample of 1,907,484 inpatients with NCDs from 2003 to 2014, 50.05% of whom were male and 81.53% were aged 50 years or older. Results: There was an increase in the number of total NCD inpatients in eastern coastal China from 2003 to 2014. However, the proportion of chronic respiratory diseases and cancer inpatients decreased over the 12-year period. Compared with men, women displayed a significant increase in the proportion of mental and behavioural disorders (P<0.001) over time. Additionally, digestive diseases and sensory organ diseases significantly decreased among men, but not women. The older group accounted for a larger and growing proportion of the NCD inpatients, and the most common conditions in this group were cerebral infarctions, coronary heart disease and hypertension. In addition, the proportion of 21- to 50-year-old inpatients with diabetes, blood diseases or endocrine diseases skyrocketed from 2003 to 2014 (P<0.001). Conclusions: The burden of inpatients' NCDs increased rapidly, particularly among women and younger people. The NCD spectrum observed in eastern coastal China is a good source of evidence for developing prevention guides for regions experiencing transition.
Data from: A framework for the identification of long-term social avoidance in longitudinal datasets
Animal sociality is of significant interest to evolutionary and behavioural ecologists, with efforts focused on the patterns, causes and fitness outcomes of social preference. However, individual social patterns are the consequence of both attraction to (preference for) and avoidance of conspecifics. Despite this, social avoidance has received far less attention than social preference. Here, we detail the necessary steps to generate a spatially explicit, iterative null model which can be used to identify non-random social avoidance in longitudinal studies of social animals. We specifically identify and detail parameters which will influence the validity of the model. To test the usability of this model, we applied it to two longitudinal studies of social animals (Eastern water dragons (Intellegama leseurii) and bottlenose dolphins (Tursiops aduncus) to identify the presence of social avoidances. Using this model allowed us to identify the presence of social avoidances in both species. We hope that the framework presented here inspires interest in addressing this critical gap in our understanding of animal sociality, in turn allowing for a more holistic understanding of social interactions, relationships and structure.
Predicting MRI Abnormalities With Longitudinal Data of the Whitehall II Substudy
ClinicalTrials.gov study NCT03335696. IPD Sharing: YES. Countries: 1. Publications: 14.
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.