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TABLE 3 in Horses in the suburbs of a medieval city - a case study from Brno (Czech Republic)
<p>TABLE 3. — Modřice: list of horse burials</p><table><tbody><tr><th><b>Skeleton Number Preservation</b></th><th><b>Pit description Dating Figure</b></th></tr></tbody><tbody><tr><th>M_802</th><td>Postcranial skeleton and seven loose teeth (3 x I1-3, 1 x C, 2 x upper P2,</td><td>Oval.</td><td>15th-16th century.</td><td>12</td></tr><tr><th></th><td>1 x upper P3). Four horse shoes <i>in situ</i>.</td><td></td><td></td><td></td></tr><tr><th>M_803</th><td>Complete skeleton of a newborn foal.</td><td>Oval.</td><td>15th-16th century.</td><td>12</td></tr></tbody></table>
Data from: Association between aspirin dose and subarachnoid hemorrhage from saccular aneurysms: a case-control study
Objective: We aimed to determine the association between ruptured saccular aneurysms and aspirin use/aspirin dose. Methods: 4,701 patients who were diagnosed at the Massachusetts General Hospital and Brigham and Women's Hospital between 1990 and 2016 with 6,411 unruptured and ruptured saccular intracranial aneurysms were evaluated. Univariable and multivariable logistic regression analyses were performed to determine the association between aSAH and aspirin use, including aspirin dose. Inverse probability weighting using propensity scores was used to adjust for potential differences in baseline characteristics between cases and controls. Additional analyses were performed to examine the association of aspirin use and re-rupture prior to treatment. Results: In multivariate analysis with propensity score weighting, aspirin use (OR 0.60, 95% CI 0.45-0.80) was significantly associated with decreased risk of ruptured intracranial aneurysms. There was a significant inverse dose-response relationship between aspirin dose and aneurysmal subarachnoid hemorrhage (OR 0.65, 95% CI 0.53-0.81). In contrast, there was a significant association between aspirin use and increased risk of re-rupture prior to treatment (OR 8.15, 95% CI 2.22-30.0). Conclusions: In this large case-control study, aspirin therapy at diagnosis was associated with a significantly decreased risk of subarachnoid hemorrhage, with an inverse dose-response relationship among aspirin users. However, once rupture has occurred, aspirin is associated with an increased risk of re-rupture prior to treatment.
Data from: A whole-transcriptome approach to evaluating reference genes for quantitative gene expression studies: a case study in Mimulus
While quantitative PCR (qPCR) is widely recognized as being among the most accurate methods for quantifying gene expression, it is highly dependent on the use of reliable, stably expressed reference genes. With the increased availability of high-throughput methods for measuring gene expression, whole-transcriptome approaches may be increasingly utilized for reference gene selection and validation. In this study, RNA-seq was used to identify a set of novel qPCR reference genes and evaluate a panel of traditional "housekeeping" reference genes in two species of the evolutionary model plant genus Mimulus. More broadly, the methods proposed in this study can be used to harness the power of transcriptomes to identify appropriate reference genes for qPCR in any study organism, including emerging and nonmodel systems. We find that RNA-seq accurately estimates gene expression means in comparison to qPCR, and that expression means are robust to moderate environmental and genetic variation. However, measures of expression variability were only in agreement with qPCR for samples obtained from a shared environment. This result, along with transcriptome-wide comparisons, suggests that environmental changes have greater impacts on expression variability than on expression means. We discuss how this issue can be addressed through experimental design, and suggest that the ever-expanding pool of published transcriptomes represents a rich and low-cost resource for developing better reference genes for qPCR.
Data from: Mental illness, poverty and stigma in India: a case control study
Objective: To assess the effect of experienced stigma on depth of multidimensional poverty of persons with severe mental illness (PSMI) in Delhi, India, controlling for gender, age and caste. Design: Matching case (hospital)–control (population) study. Setting: University Hospital (cases) and National Capital Region (controls), India. Participants: A case–control study was conducted from November 2011 to June 2012. 647 cases diagnosed with schizophrenia or affective disorders were recruited and 647 individuals of same age, sex and location of residence were matched as controls at a ratio of 1:2:1. Individuals who refused consent or provided incomplete interview were excluded. Main outcome measures: Higher risk of poverty due to stigma among PSMI. Results: 38.5% of PSMI compared with 22.2% of controls were found poor on six dimensions or more. The difference in multidimensional poverty index was 69% between groups with employment and income of the main contributors. Multidimensional poverty was strongly associated with stigma (OR 2.60, 95% CI 1.27 to 5.31), scheduled castes/scheduled tribes/other backward castes (2.39, 1.39 to 4.08), mental illness (2.07, 1.25 to 3.41) and female gender (1.87, 1.36 to 2.58). A significant interaction between stigma, mental illness and gender or caste indicates female PSMI or PSMI from 'lower castes' were more likely to be poor due to stigma than male controls (p<0.001) or controls from other castes (p<0.001). Conclusions: Public stigma and multidimensional poverty linked to SMI are pervasive and intertwined. In particular for low caste and women, it is a strong predictor of poverty. Exclusion from employment linked to negative attitudes and lack of income are the highest contributors to multidimensional poverty, increasing the burden for the family. Mental health professionals need to be aware of and address these issues.
Data from: Inferring the origin of populations introduced from a genetically structured native range by approximate Bayesian computation: case study of the invasive ladybird Harmonia axyridis
Correct identification of the source population of an invasive species is a prerequisite for testing hypotheses concerning the factors responsible for biological invasions. The native area of invasive species may be large, poorly known and/or genetically structured. Because the actual source population may not have been sampled, studies based on molecular markers may generate incorrect conclusions about the origin of introduced populations. In this study, we characterized the genetic structure of the invasive ladybird Harmonia axyridis in its native area using various population genetic statistics and methods. We found that H. axyridis native area most likely consisted of two geographically distinct genetic clusters located in eastern and western Asia. We then performed approximate Bayesian computation (ABC) analyses on controlled simulated microsatellite data sets to evaluate: (i) the risk of selecting incorrect introduction scenarios, including admixture between sources, when the populations of the native area are genetically structured and sampling is incomplete, (ii) the ability of ABC analysis to minimize such risks by explicitly including unsampled populations in the scenarios compared. Finally, we performed additional ABC analyses on real microsatellite data sets to retrace the origin of biocontrol and invasive populations of H. axyridis, taking into account the possibility that the structured native area may have been incompletely sampled. We found that the invasive population in eastern North America, which has served as the bridgehead for worldwide invasion by H. axyridis, was probably formed by an admixture between the eastern and western native clusters. This admixture may have facilitated adaptation of the bridgehead population.
Data from: Can perfusion CT unmask postictal stroke mimics? A case-control study of 133 patients
OBJECTIVE: To study the diagnostic value of volume perfusion CT (VPCT) in patients with transient focal neurological deficits following and during epileptic seizures, that mimic symptoms of stroke. METHODS: a retrospective case-control study was performed on 159 patients that presented with a seizure and received an emergency VPCT within the first 3.5 hours of admission, after being misjudged to have an acute stroke. The reference test was a clinical-based, EEG-supported diagnostic algorithm for seizure. RESULTS: We included 133 patients: 94 stroke-mimicking cases with postictal focal neurological deficits ("Todd's phenomenon", n=67) or ongoing seizure on hospital admission ("ictal patients", n=27), and 39 postictal controls without focal neurological deficits. Patients with Todd's phenomenon showed normal (64%), hypo (21%)- and hyperperfusion (14%) on early VPCT. Ictal patients displayed more hyperperfusion compared to postictal patients (p=0.015). Test sensitivity of hyperperfusion for ictal patients is 38% CI [20.7-57.7], specificity 86% CI [77.3-91.7], positive predictive value (ppv) is 42% CI [27.5-58.7], the negative predictive value (npv) 83% CI [78.6-86.9]. A cortical distribution was seen in all hyperperfusion scans, compared to a cortico-subcortical pattern in hypoperfusion (p<0.001). A history of complex focal seizure and age were associated with hyperperfusion (p= 0.046 and 0.038, respectively). CLASSIFICATION OF EVIDENCE: This study provides Class IV evidence that VPCT accurately differentiates ictal stroke mimics from acute ischemic stroke. CONCLUSION: VPCT can differentiate ictal stroke mimics with hyperperfusion from acute ischemic stroke, but not postictal patients who display perfusion patterns overlapping with ischemic stroke.
Figure 1 in The role of artificial ponds in maintaining dragonfly populations in an intensified farmland landscape. A case of study in Zamora, Spain
Figure 1. Location of sampling sites in the study area.
Data from: Bias in phylogenetic measurements of extinction and a case study of end-Permian tetrapods
Extinction risk in the modern world and extinction in the geological past are often linked to aspects of life history or other facets of biology that are phylogenetically conserved within clades. These links can result in phylogenetic clustering of extinction, a measurement comparable across different clades and time periods that can be made in the absence of detailed trait data. This phylogenetic approach is particularly suitable for vertebrate taxa, which often have fragmentary fossil records, but robust, cladistically-inferred trees. Here we use simulations to investigate the adequacy of measures of phylogenetic clustering of extinction when applied to phylogenies of fossil taxa while assuming a Brownian motion model of trait evolution. We characterize expected biases under a variety of evolutionary and analytical scenarios. Recovery of accurate estimates of extinction clustering depends heavily on the sampling rate, and results can be highly variable across topologies. Clustering is often underestimated at low sampling rates, whereas at high sampling rates it is always overestimated. Sampling rate dictates which cladogram timescaling method will produce the most accurate results, as well as how much of a bias ancestor–descendant pairs introduce. We illustrate this approach by applying two phylogenetic metrics of extinction clustering (Fritz and Purvis's D and Moran's I) to three tetrapod clades across an interval including the Permo-Triassic mass extinction event. These groups consistently show phylogenetic clustering of extinction, unrelated to change in other quantitative metrics such as taxonomic diversity or extinction intensity.
FIGURES 9A. Gloeocapsa compacta. Colony collected from a in How diverse are coccoid cyanobacteria? A case study of terrestrial habitats from the Atlantic Rainforest (São Paulo, Brazil)
FIGURES 9A. Gloeocapsa compacta. Colony collected from a tree bark.
Figure 1 from: Samyn Y, Sonet G, d'Acoz C (2021) Exploring the use of micro-computed tomography (micro-CT) in the taxonomy of sea cucumbers: a case-study on the gravel sea cucumber Neopentadactyla mixta (Östergren, 1898) (Echinodermata, Holothuroidea, Phyllophoridae). ZooKeys 1054: 173-184. https://doi.org/10.3897/zookeys.1054.67088
Figure 1 Neopentadactyla mixta (Östergren, 1898) A focus-stacked view of the dorsal-lateral view of dissected specimen B focus-stacked view of the ventral–lateral view of dissected specimen C focus-stacked view of the dorsal–lateral view of a non-dissected specimen D focus-stacked view of the ventral–lateral view of a non-dissected specimen ESEM view of the rosettes from the shaft of a tentacle FSEM view of the 2-pillared tables from the introvert GSEM view of the rods and rosettes from a tentacle tip HSEM view of the 4-pillared tables from the dorsal body wall ISEM view of the 4-pillared tables from the ventral body wall JSEM view of the plates from the dorsal tube feet KSEM view of the plates from the ventral tube feet LSEM view of half of an end-plate from a ventral tube foot. Scale bars: 1 cm (A–D); 50 μm (E–L).
Figure 2 from: Samyn Y, Sonet G, d'Acoz C (2021) Exploring the use of micro-computed tomography (micro-CT) in the taxonomy of sea cucumbers: a case-study on the gravel sea cucumber Neopentadactyla mixta (Östergren, 1898) (Echinodermata, Holothuroidea, Phyllophoridae). ZooKeys 1054: 173-184. https://doi.org/10.3897/zookeys.1054.67088
Figure 2 Neopentadactyla mixta (Östergren, 1898) A micro-CT scan visualizing the position of the calcareous ring B lateral view with micro-CT imaging of the anterior part of the calcareous ring (AR: most anterior radial piece; AIR: most anterior interradial pieces; SAR: subsequent anterior radial pieces; SAIR: subsequent interradial anterior pieces; Mesh: meshwork of radial and interradial median to distal pieces) C oblique view with micro-CT imaging showing a guttered internal side of the calcareous ring D focus-stacked view of the calcareous ring and associated structures (T: tentacles; LM: longitudinal muscle with bifurcation point (BfP); PV: Polian vesicle: SC: stone canal). Scale bars: 1 cm (A–D).
Fig. 5 in Barcoding cryptic bumblebee taxa: B. lucorum, B. crytarum and B. magnus, a case study (Hymenoptera: Apidae: Bombus)
Fig. 5: Comparison of ABI colour traces of fresh (CRY-09) and 100 year old museum DNA (B. magnus turkestanicus), with two miscoding lesions of type T → C, one marked by Y (mixed bases IUPAC code for T/C) in the ABI output file, and one miscoding lesion of type G → A marked by R (mixed bases IUPAC code for G/A) in the ABI output file.
FIG. 2 in First Systematic Study using the Variability of the Residual Colour Patterns: The Case of the Paleogene Seraphsidae (Mollusca, Gastropoda, Stromboidea)
FIG. 2. — Variability of the extant species Terebellum terebellum (Linnaeus, 1758) in dorsal view and normal light: A-D, T. terebellum form punctulorum (RÖding, 1798); E, T. terebellum form delicatum Kuroda & Kawamoto, 1961, MNHN IM, Segond Channel, Santo, Vanuatu; F-J, T. terebellum form nebulosum (RÖding, 1798); A, MNHN IM, Grand Récif Sud, New Caledonia; B, MNHN IM, Grand Récif Sud, New Caledonia; C, MNHN IM, Secteur de Balabio, New Caledonia; D, MNHN IM, Grand Récif Sud, New Caledonia; F, MNHN IM, Plateau des Chesterfield; G, MNHN IM, Plateau des Chesterfield); H, MNHN IM, Aésé Island, Santo, Vanuatu; I, MNHN IM, Baie des Citrons, Nouméa, New Caledonia; J, MNHN IM, Quatre Bancs de l'Ouest, lagoon of Nouméa, New Caledonia; K, T. terebellum, MNHN IM, Plateau des Chesterfield. Scale bars: 10 mm. Photographs by C. Lemzaouda (MNHN).
Figure 1 in Congruence and conflict: case studies of morphotaxonomy versus rDNA gene tree phylogeny among articulate brachiopods (Brachiopoda: Rhynchonelliformea), with description of a new genus
Figure 1. Locality map.
Figure 4 in Amblypygi parthenogenesis, embryonic and post-embryonic development: a case study with the Amazonian species Charinus guto Giupponi and Miranda, 2016 (Amblypygi: Charinidae)
Figure 4. Number of individuals of Charinus guto Giupponi and Miranda, 2016 with egg sac per month.
Digital representation of measurement uncertainty: a case study linking an RMO key comparison with a CIPM Key Comparison
<pre>This dataset is associated with a publication of the same name (currently submitted to the MDPI journal Metrology). It contains digital records (JSON files) of participant results as well as DoE results obtained from data processing. Python modules to display the contents of these files are provided as are modules for the comparison analyses. The GUM Tree Calculator (GTC) Python software package is required (version~1.3.6, or above: https://github.com/MSLNZ/GTC).</pre>
Drought stress and plant cultivar type affect demographic responses of herbivorous insects: a case study with the rose-grain aphid, Metopolophium dirhodum, (Hemiptera: Aphididae)
<p>Raw data files of "the effect of water stress on demographic features of aphid <em>Metopolophium dirhodum on two cultivars"</em></p>
Case study 13: Why is lentil (Lens culinaris) cultivation a success story in south-west Germany? Case study 14: Why is soybean (Glycine max) cultivation a success story in south-west Germany?
<p>Case Study 13<br> Though lentils (Lens culinaris) are a traditional crop in many temperate European countries, the crop disappeared from European cropping systems in the mid-20th century. Lentils are still an important food in traditional and modern cuisine, and they currently gain importance based on the demand for vegetarian and vegan food. The revival of lentil growing and lentil consumption in parts of Germany for the last 10 years is an unprecedented story of success. We want to use this experience to push the re-introduction and expansion of lentil in modern farming all over Europe, particularly in those countries from where the crop has disappeared in the last decades. We seek to multiply the lentil acreage, to increase and stabilize yields, and to network European lentil growers. Due to agronomic reasons, growers cannot easily extent their lentil acreage, although there are many obvious benefits for the stability of agro-ecosystems such as the mixed cropping of lentils, diversification of crop rotations and N-fixation. If we want to keep lentil growing running and expanding, we have to understand these settings if growing should be promoted. On-farm research and data compilation from existing field trials will help to develop new and ecological sound techniques for lentil growing in modern farming systems. In a broad on-farm survey data will be collected for the first time to describe the impact of lentil growing on the agro-ecosystem and to determine and describe factors for successful lentil growing. This will improve the cropping system and the willingness of farmers to adopt lentil growing and thus increase the lentil acreage. Main challenges of lentil growing will be identifie in order to ease the adoption of lentil growing. The results will be a basis for decision-makers in European policy and society to develop tools for improving and maintaining ecological value of farmland, and for generally maintaining and improving agriculture in Europe, particularly in economically in underdeveloped regions. Lentil is exceptional in comparison to other pulses concerning their use: they are exclusively used for human consumption, their amount of anti-nutritive compounds is lowest among all pulses grown in Europe, grains can be consumed without complex processing, and consumers will directly benefit from the results of the project. Particularly the increasing trend of vegetarian or vegan diet can be satisfied easily and best with lentils. The overall outcome of the study would be(i)identification of agronomic key factors for successful lentil growing; (ii)stabilising and improving lentil growing based on(iii)to export the idea of lentil growing and improved cropping systems to other regions and countries in Europe based on (i)and(ii).</p> <p>Case Study 14<br> Several attempts have been made in the past to introduce soybean in temperate regions of Europe, which, however, did not lead to a long-lasting establishment of soybean cropping systems in agricultural practice. Now it seems there is a break-through in some regions of Germany, Eastern France, Austria and Switzerland, maybe due to climate change, the breeding and availability of adapted varieties (0,00,000-varieties), the demand for GMO free food and feed, and the demand for vegetarian/vegan food. The aim of the case study is to permanently integrate soybean in farming systems in temperate climates, to increase the stability and sustainability of soybean cropping systems, and thus to increase the soybean acreage in temperate climates in Europe. Currently, we assume that particularly organic farmers benefit from local soybean growing because of pest and disease risks field beans (Vicia faba) and peas (Pisum sativum) on the one hand, and the requirement of legumes for N-fixation in organic rotations on the other hand. In addition, local soy bean growing solves many problems related to the nutrition of monogastric animals in organic farming systems. For further expansion of soybean cropping in (temperate) Europe countries, the driving factors for soybean growing on practical farms (organic and conventional) have to be revealed in more detail. This approach should include experience from, and use contacts to, other European countries such as Austria.<br> As rotational diseases and pests limit the percentage of soybean on farmland, new methods have to be developed to improve and stabilize the agro-ecosystems while growing soybean. On-farm surveys will reveal the status quo of agro-ecological impacts and agronomic success of soybean growing, with focus on major selected factors to improve the agro-ecological value and to increase yields and yield stability. Soybean could be well introduced in regions where maize-monocropping is dominant, such as the southern Rhine valley in Germany, and thus to increase crop diversity in compliance with the overall aims of European policy and public. The outcome of the soybean case study can finally be well combined with the lentil case study from the same<br> stories of success but probably due to different reasons. Other crops which may be introduced in future into European agriculture will benefit from this knowledge and can be introduced more easily. The overall outcome of the study would be(i)identification of agronomic key factors for successful soybean growing in a temperate climate;(ii)stabilisation and improvement of soybean growing basing on (iii)to export the idea of soybean growing and improved cropping systems to other regions.</p>
Engaging Health Sciences Librarians on Data Ethics: Case Study on a Pilot Curriculum (Dataset)
<p>This repository contains de-identified evaluation data collected as part of the Ethical Considerations of Data: A Curriculum for Health Sciences Librarians pilot as well as the data collection instrument used.</p> <p>These files are related to a forthcoming JMLA Case Study titled Engaging Health Sciences Librarians on Data Ethics: Case Study on a Pilot Curriculum. </p> <p><strong>Paper Abstract</strong>: <br> Three medical librarians developed a pilot curriculum designed to address perceived gaps in librarian training in regards to data ethics. One of the team members had additional academic training in ethics and bioethics, which helped to provide an intellectual foundation for this project. Our three-module class aimed to provide students with an overview of major ethical frameworks, skills to apply those frameworks to data issues, and an exploration of ethical considerations and challenges faced in libraries. Participants from library schools and professional library organizations were invited to apply. Twenty-four LIS professionals and students attended the Zoom-based class and shared their thoughts and attitudes by means of a survey after each session and in a focus group after the conclusion of the class.</p>
Figure 3 from: Nader M, El Indary S, Abi Salloum B, Abou Dagher M (2011) Combining non-invasive methods for the rapid assessment of mammalian richness in a transectquadrat survey scheme – Case Study of the Horsh Ehden Nature Reserve, North Lebanon. ZooKeys 119: 63-71. https://doi.org/10.3897/zookeys.119.1040
Figure 3 - Mammalian distribution map showing the location of mammalian activity and the location of the Motion Sensor Cameras.
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.