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7,378 results for “case”
Opportunities and challenges in achieving co-management in marine protected areas in East Africa: a comparative case study
<p>As marine ecosystems decline globally, scientists recommend increasing the coverage of marine protected areas (MPAs), but many are not effectively managed to deliver benefits. Community integration into MPA decision-making can increase management effectiveness by supporting behaviour change, but this poses implementation challenges. We examine differences in adaptive capacity, community engagement, and perceived MPA benefits using interviews and focal group meetings with two fishing communities from MPAs with different management strategies and geographic settings: a centrally managed MPA in Kenya and a co-managed MPA in Tanzania. We hypothesized that perceptions of MPA benefits and MPA support would be higher among fishers and fish vendors in the more collaboratively designed system in Tanzania, and supported by greater adaptive capacity. Indeed, far fewer Kenyan participants (37%) felt they benefited from the MPA compared to Tanzanian participants (95%). However, agency and trust were largely similar and challenges existed in both systems that reduced collaborative action including low interaction/communication between staff and community, internal leadership challenges, and social conflict. We identified pathways towards improved co-management that transcend systems: institutional prioritization of community integration, investment in community leadership, mapping social networks during MPA establishment, and adequate staffing and operational budgets.</p>
VIBeS Case Studies: Featured Transition Systems and Feature Models
<p>Featured Transition Systems and Feature Models used in the different evaluations presented in: <a href="https://researchportal.unamur.be/en/studentTheses/behavioural-model-based-testing-of-software-product-lines">Behavioural model-based testing of software product lines Devroey, X. (Author). 30 Aug 2017</a></p>
Simulated time series and indicators for the Zambezi River Basin case study
<p>The archive includes:</p> <ul> <li>monthly time series over 2020-2059 time horizon of different physical variables, simulated by the Decision Analytic Framework (DAF) Strategic model of the Zambezi River Basin for the 7 interesting pathways identified in the Negotiation Simulation Lab meeting;</li> <li>a set of evaluation indicators, aggregated at different spatial and temporal scales, for the 7 interesting pathways.</li> </ul> <p>More details on physical variables and indicators included are available in the DAFNE Deliverable D7.3.</p> <p>Files are provided in the <em>csv </em>format, one per each physical variable or indicator: the first 13 rows contain metadata, while data starts at row 14 and use as many columns as the pathways considered. Metadata are the following:</p> <ul> <li><em>name</em>, time series or indicaror label</li> <li><em>author, </em>reference person or team for the specific time series</li> <li><em>created,</em> timestamp of the file creation</li> <li><em>description, </em>description of file content</li> <li><em>unit, </em>unit of measurement</li> <li><em>origin, </em>description of the simulation</li> <li><em>time_sampling,</em> whether the variable is sampled at a given point in time (instantaneous) or represents a time interval (interval)</li> <li><em>frequency, </em>time step of the time series</li> <li><em>scenario, </em>label of scenario</li> <li><em>marker_id, </em>label of the related model component</li> <li><em>id_type, </em>type of time series</li> <li><em>timestart,timeend,P1,P2,P3,P4,P5,P6,P7 : </em>header row of the data, with time information (in the matlab datenum format) at the beginning and pathways on each column</li> </ul>
Data from: The clinical, histological, and genotypic spectrum of SEPN1-related myopathy: a case series
<p><b><span>Objective: </span></b><span>To clarify the prevalence, long-term natural history and severity determinants of SEPN1-related myopathy (SEPN1-RM), we analyzed a large international case series. </span></p> <p><b>Methods: </b>Retrospective clinical, histological and genetic analysis of 132 pediatric and adult patients (2-58 years) followed-up for several decades.</p> <p><b><span>Results: </span></b><span>The clinical phenotype was marked by severe axial muscle weakness, spinal rigidity and scoliosis (86.1%, from 8.9±4 years), with relatively-preserved limb strength and previously-unreported ophthalmoparesia in severe cases. All patients developed respiratory failure (from 10.1±6 years), 81.7% requiring ventilation while ambulant. Histopathologically, 79 muscle biopsies showed large variability, partly determined by site of biopsy and age. Multi-minicores were the most common lesion (59.5%), often associated with mild dystrophic features and occasionally with eosinophilic inclusions. Identification of 65 SEPN1 mutations, including 32 novel ones and the first pathogenic CNV, unveiled exon 1 as the main mutational hotspot and revealed the first genotype-phenotype correlations, bi-allelic null mutations being significantly associated with disease severity (<i>p</i>=0.017). SEPN1-RM was more severe and progressive than previously thought, leading to loss of ambulation in 10% cases, systematic functional decline from the end of the third decade and reduced lifespan even in mild cases. The main prognosis determinants were scoliosis/respiratory management, <i>SEPN1</i> mutations and body mass abnormalities, which correlated with disease severity. Finally, we propose a set of severity criteria, provide quantitative data for outcome identification and establish a need for age stratification.</span></p> <p><b><span>Conclusion</span></b><span>: Our results inform clinical practice, improving diagnosis and management, and represent a major breakthrough for clinical trial readiness in this not-so-rare disease.</span></p>
Simulated time series and indicators for the Omo-Turkana Basin case study
<p>The archive includes:</p> <ul> <li>daily time series over 2021-2099 time horizon of different physical variables, simulated by the Water Energy Food Integrated Model on the Omo Turkana River Basin for the 6 interesting pathways identified in the Negotiation Simulation Lab meeting;</li> <li>a set of evaluation indicators, aggregated at different spatial and temporal scales, for the 6 interesting pathways.</li> </ul> <p>More details on physical variables and indicators included are available in the DAFNE Deliverable D7.3.</p> <p>Files are provided in the <em>csv </em>format, one per each physical variable or indicator: the first 13 rows contain metadata, while data starts at row 14 and use as many columns as the pathways considered. Metadata are the following:</p> <ul> <li><em>name</em>, time series or indicaror label</li> <li><em>author, </em>reference person or team for the specific time series</li> <li><em>created,</em> timestamp of the file creation</li> <li><em>description, </em>description of file content</li> <li><em>unit, </em>unit of measurement</li> <li><em>origin, </em>description of the simulation</li> <li><em>time_sampling,</em> whether the variable is sampled at a given point in time (instantaneous) or represents a time interval (interval)</li> <li><em>frequency, </em>time step of the time series</li> <li><em>scenario, </em>label of scenario</li> <li><em>marker_id, </em>label of the related model component</li> <li><em>id_type, </em>type of time series</li> <li><em>timestart,timeend,P1,P2,P3,P4,P5,P6 : </em>header row of the data, with time information (in the matlab datenum format) at the beginning and pathways on each column</li> </ul>
Genome-wide association results from: Transcriptomic stratification of late-onset Alzheimer's cases reveals novel genetic modifiers of disease pathology
<p>Late-Onset Alzheimer's disease (LOAD) is a common, complex genetic disorder well-known for its heterogeneous pathology. The genetic heterogeneity underlying common, complex diseases poses a major challenge for targeted therapies and the identification of novel disease-associated variants. Case-control approaches are often limited to examining a specific outcome in a group of heterogenous patients with different clinical characteristics. Here, we developed a novel approach to define relevant transcriptomic endophenotypes and stratify decedents based on molecular profiles in three independent human LOAD cohorts. By integrating post-mortem brain gene co-expression data from 2114 human samples with LOAD, we developed a novel quantitative, composite phenotype that can better account for the heterogeneity in genetic architecture underlying the disease. We used iterative weighted gene co-expression network analysis (WGCNA) to reduce data dimensionality and to isolate gene sets that are highly co-expressed within disease subtypes and represent specific molecular pathways. We then performed single variant association testing using whole genome-sequencing data for the novel composite phenotype in order to identify genetic loci that contribute to disease heterogeneity. Distinct LOAD subtypes were identified for all three study cohorts (two in ROSMAP, three in Mayo Clinic, and two in Mount Sinai Brain Bank). Single variant association analysis identified a genome-wide significant variant in <i>TMEM106B</i> (p-value < 5´10<sup>-8</sup>, rs1990620<sup><span><span>G</span></span></sup>) in the ROSMAP cohort that confers protection from the inflammatory LOAD subtype. Taken together,<b> </b>our novel approach can be used to stratify LOAD into distinct molecular subtypes based on affected disease pathways.</p>
Processed SpectrumDocuments from AllPositive (case study for MS2Query)
<p>Processed SpectrumDocuments of the "AllPositive" dataset created from GNPS positive ionmode mass spectra. They are used in a case study for MS2Query: https://github.com/iomega/ms2query.</p> <p>Reading this pickle file in python will give a tuple of two lists of spec2vec.SpectrumDocument. The first list contains 2,000 spectra and the second list contains 93,320 spectra that are used as query and library spectra in the case study.</p>
Implementation of ATP and Microbial Indicator Testing for Hygiene Monitoring in a Tofu Production Facility Improves Product Quality and Hygienic Conditions of Food Contact Surfaces: A Case Study
<p>This is the code and associated data that was used to generate conclusions for the following manuscript published in Applied and Environmental Microbiology:</p> <p>DOI: 10.1128/AEM.02278-20</p> <p>Implementation of ATP and Microbial Indicator Testing for Hygiene Monitoring in a Tofu Production Facility Improves Product Quality and Hygienic Conditions of Food Contact Surfaces: A Case Study</p> <p>Authors: Jonathan H. Sogin(a), Gabriela Lopez Velasco(b), Burcu Yordem(b), Cari K. Lingle(b), John M. David(b), Mario Cobo(a), Randy W. Worobo(a)</p> <p>(a)Department of Food Science, Cornell University, Ithaca, NY, USA</p> <p>(b)3M Company, St. Paul, MN, USA</p> <p>Address correspondence to Jonathan H. Sogin, jhs397@cornell.edu</p>
The Marginal Latin (LaM) readings of 2 Samuel - all the cases collected
<p>Collected textual cases for my SBL 2020 paper "The Marginal Latin (LaM) readings of 2 Samuel".</p>
A rare entity - percutaneous lead extraction in a very late onset pacemaker endocarditis - case report and review of literature
<p><strong>Video 1.</strong> Transthoracic two-dimensional echocardiography apical 4-chamber view: large hypoechogenic hyper-pedunculated mobile mass at the level of tricuspid valve; <strong>Video 2.</strong> Transesophageal two-dimensional echocardiography: low echogenicity pedunculated mass attached to the pacemaker lead, with multiple sites of binding, with no supplementary involvement of the tricuspid valve and myxomatous appearance of the posterior leaflet with hypermobility and rupture of chordae; <strong>Video 3. </strong>Fluoroscopy during the lead extraction procedure, after freeing the lead from adhesions: traction of the lead from the right ventricular apex, through the tricuspid valve, right atrium, superior vena cava and left subclavian vein, to complete lead removal; <strong>Video 4.</strong> Postprocedural transesophageal two-dimensional echocardiography: posterior leaflet chordae rupture, no residual vegetation, no pericardial effusion; <strong>Video 5.</strong> Transthoracic two-dimensional echocardiography parasternal short axis, no additional cardiac masses, posterior leaflet chordae rupture of the tricuspid valve; <strong>Video 6.</strong> Transthoracic two-dimensional echocardiography parasternal short axis, color Doppler: mild tricuspid regurgitation, with two small thin jets.</p>
Deadly dormmate: a case study on Bungarus candidus living among a student dormitory with implications for human safety
<p>Movement and observation data gained through radio-telemetry of a single Malayan krait (<em>Bungarus candidus</em>) among a suburban landscape (a university dormitory complex) in NE Thailand. Included: movement spatial data .csv file and photographic evidence of foraging observations, a predation events, and conflicts with humans, camera trap footage, and snakebite incident data .csv file.</p> <p> </p> <p>B.candidus_observation_data.csv file column headings:</p> <p>folderID: The Zenodo folder ID containing the photographic evidence of events.</p> <p>obvdate: Date of observation (mm/dd/yyyy)</p> <p>obvtime: Time of observation (24hr)</p> <p>easting_utm: UTM easting (UTM Zone 48N; Datum WGS84)</p> <p>northing_utm: UTM northing (UTM Zone 48N; Datum WGS84)</p> <p>gps_accuracy: Accuracy of GPS location (m)</p> <p>notes: Comments and details on events/observations</p> <p> </p> <p>BUCA28_movement_data.csv file column headings:</p> <p>Datetime: Date and time when the snake was located (mm/dd/yyyy hh:mm)</p> <p>Easting: UTM easting (UTM Zone 48N; Datum WGS84)</p> <p>Northing: UTM northing (UTM Zone 48N; Datum WGS84)</p> <p>Behavior: Either the animal’s behavior observed during the location check (sheltering, foraging, or feeding) or type of other significant locations (capture or release sites)</p> <p>Habitat_Type: Land-use type where the snake was located</p> <p> </p> <p>Snakebite_incident_data_SUT_Dormitories.csv file column headings:</p> <p>Date: Date the snakebite occurred was located (mm/dd/yyyy)</p> <p>Time: Time (ICT) the snakebite occurred (hh:mm)</p> <p>Location: Brief location description where the incident occurred at Suranaree University of Technology</p> <p>Mesohabitat Description: Brief description of the scene where the bite occurred</p> <p> Snake species confirmed?: if responsible species known (Yes) or unknown (No)</p> <p>Snake Species: Identified responsible snake species (if known)</p> <p>If not confirmed, suspected species responsible: Species most likely to be responsible based on known snake species at SUT, the time the bite occurred, and bite symptoms.</p> <p>Bite Location: Where on the body the victim was bitten</p> <p>Envenomation Symptoms: Brief description of bite symptoms (note: none were severe/dangerous cases)</p> <p>Fang Puncture Marks?: Brief description of whether fang puncture marks were visible, and if so, how many punctures</p> <p>Notes and Photos: Brief further notes on how the bite occurred, and in the case of the bite by C. maculiceps, the corresponding Zenodo folder ID containing the photographic evidence (of the snake and dormitory bite location [during daylight]).</p> <p> </p> <p> </p>
FIG.1 in Socio-economic changes and their implication in the consumption and trade of meat during the La Tène period in Northern France: the cases of the Villeneuve-Saint-Germain and Condé-sur-Suippe (Aisne) oppida
FIG.1. — Distribution of some late Iron Age sites in the study region.
FIG. 4 in Socio-economic changes and their implication in the consumption and trade of meat during the La Tène period in Northern France: the cases of the Villeneuve-Saint-Germain and Condé-sur-Suippe (Aisne) oppida
FIG. 4. — Plan of the living zone on the site of Villeneuve-Saint-Germain. Scale bar: 5 m.
Distant Gatherings: A Text-Case for Digital Manuscript Collaborations
<p>The restrictions imposed by COVID19 have challenged all who work in academia, and particularly those who work with material sources like medieval manuscripts, to reconsider normal practices of research exchange and how they might transfer to the online environment. Rather than slavishly replicating previous in-person formats which are invariably less effective when staged virtually, we have the chance instead to think creatively about how to capitalize on the digital medium, to investigate why people already willingly dedicate so much of their time to computer-based forms of communication. By identifying and co-opting what makes some kinds of virtual exchange successful, we can inspire new forms of academic exchange that re-invent rather than mimic older forms of teaching, research, and learning.</p> <p> </p>
Contrasting association of Leptin receptor polymorphisms and haplotypes with polycystic ovary syndrome in Bahraini and Tunisian women: a case–control study
<p><span><b>Background</b>. This study examined the contribution of ethnicity to the association of leptin receptor gene (<i>LEPR)</i> genetic variants with polycystic ovary syndrome (PCOS) in Tunisian and Bahraini Arabic-speaking women.<b> </b></span></p> <p><span><b>Methods. </b>Subjects consisted of 320 women with PCOS, and 446 eumenorrhic women from Tunisia, and 242 women with PCOS and 238 controls from Bahrain. Genotyping of (exonic) rs1137100 and rs1137101 and (intronic) rs2025804 <i>LEPR</i> variants was done by allelic exclusion.<b> </b></span></p> <p><span><b>Results. </b>The minor allele frequencies of rs1137100 and rs1137101 were significantly different between PCOS cases and control women from Bahrain but not Tunisia, and <i>LEPR</i> rs1137101 was associated with increased PCOS susceptibility only in Bahraini subjects. Furthermore, rs1137100 was associated with decreased PCOS risk among Bahrainis under codominant and recessive models; rs1137100 was negatively associated with PCOS in Tunisians after controlling for testosterone. In addition, rs2025804 was associated with increased PCOS risk among Tunisian but not Bahraini women, after adjusting for key covariates. Negative correlation was seen between rs1137101 and triglycerides in Tunisians, while HOMA-IR and insulin correlated with rs2025804 and rs1137101 among Bahraini subjects, and rs1137101 correlated with estradiol and prolactin. Taking TAG haplotype as common, positive association of TAA and negative association of TGG haplotype with PCOS was seen among Bahraini women; no three-locus PCOS-associated haplotypes were found in Tunisians.<b> </b></span></p> <p><span><b>Conclusions. </b>T<span>his study is the first to demonstrate the contribution of ethnicity to the association of <i>LEPR</i> gene variants with PCOS</span>, thereby highlighting the significance of controlling for ethnicity in gene association investigations.</span></p>
Identifying diagnostic genetic markers for a cryptic invasive agricultural pest: a test case using the apple maggot fly, Rhagoletis pomonella (Diptera: Tephritidae)
Insect pests destroy ~15% of all USA crops, resulting in losses of $15 billion annually. Thus, developing cheap, quick and reliable methods for detecting harmful species is critical to curtail insect damage and lessen economic impact. The apple maggot fly, Rhagoletis pomonella (Diptera: Tephritidae), is a major invasive pest threatening the multibillion-dollar apple industry in the Pacific Northwest USA. The fly is also sympatric with a benign but morphologically similar and genetically closely related species, R. zephyria, which attacks non-commercial snowberry. Unambiguous species identification is essential due to a zero-infestation policy of apple maggot for fruit export. Mistaking R. zephyria for R. pomonella triggers unnecessary and costly quarantines, diverting valuable control resources. Here we develop and apply a relatively simple and cost-effective diagnostic approach using Illumina sequencing of double digest restriction-site associated DNA markers. We identified five informative single nucleotide polymorphisms (SNPs) and designed a diagnostic test based on agarose gel electrophoresis of restriction enzyme digested polymerase chain reaction amplification products (RFLPs) to distinguish fly species. We demonstrated the utility of this approach for immediate, one day species identification by scoring apple- and snowberry-infesting flies of known host plant identity, reared directly from 11 sites throughout Washington. However, if immediate diagnosis is not required, or hundreds to thousands of specimens must be assessed, then a direct Illumina-based sequencing strategy, similar to that used here for diagnostic SNP identification can be powerful and cost-effective. The genomic strategy we present is effective for R. pomonella and also transferable to many cryptic pests.
Prospects for the natural distribution of crop wild-relatives with limited adaptability: The case of the wild pea Pisum fulvum
<p>Plant breeders and conservationists depend on knowledge about the genetic variation of their species of interest. <em>Pisum</em> <em>fulvum</em>, a wild relative of domesticated pea, has attracted attention as a genetic resource for crop improvement, yet little information about its diversity in the wild has been published hitherto. We sampled 15 populations of <em>P. fulvum </em>from Israeli natural habitats and conducted genotyping by sequencing to analyse their genetic diversity and adaptive state. We also attempted to evaluate the species past demography and the prospects of its future reaction to environmental changes. The results suggest that genetic diversity of <em>P. fulvum</em> is low to medium and is distributed between well diverged populations. Surprisingly, with 56 % in the total population, the selfing rate was found to be significantly lower than expected from a species that is commonly assumed to be a predominant selfer. We found a strong genetic bottleneck during the last glacial period and only limited patterns of isolation by distance and environment, which explained 13 % - 18 % of the genetic variation. Despite the weak signatures of genome-wide IBE, 1354 markers were significantly correlated with environmental factors, 1233 of which were located within known genes with a nonsynonymous to synonymous ratio of 0.382. Species distribution modelling depicted an ongoing fragmentation and decreased habitable area over the next 80 years under two different socio-economic pathways. Our results suggest that complex interactions of substantial drift and selection shaped the genome of <em>P. fulvum</em>. Climate change is likely to cause further erosion of genetic diversity in <em>P. fulvum</em>. Systematic ex-situ conservation may be advisable to safeguard genetic variability for future utilization of this species.</p>
Enhancement of cloud-to-ground lightning activity caused by the urban effect: a case study in the Beijing metropolitan area
<p>The dataset here includes land-surface temperature, wind field, precipitation, UV aerosol index, and lightning information analyzed in the paper "<strong>Enhancement of cloud-to-ground lightning activity </strong><strong>caused by the urban effect: a case study in</strong> <strong>the Beijing metropolitan area</strong>".</p>
Covid19 case data December 2020 - The Netherlands
<p>This data is the daily case data on covid-19 cases in the Netherlands, published by the RIVM (national public health agency). The data covers all case data of December 2020.</p>
Covid19 case data September 2020 - The Netherlands
<p>This data is the daily case data on covid-19 cases in the Netherlands, published by the RIVM (national public health agency). The data covers all case data of September 2020.</p>
ScienceDex guides
Understand access before you commit
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.