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A vigiPoint characterisation of female versus male reports in VigiBase, the WHO global database of individual case safety reports
<p><strong>General information</strong></p> <p>This data is supplementary material to the paper by Watson <em>et al</em>. on sex differences in global reporting of adverse drug reactions [1]. Readers are referred to this paper for a detailed description of the context in which the data was generated. Anyone intending to use this data for any purpose should read the publicly available information on the VigiBase source data [2, 3]. The conditions specified in the caveat document [3] must be adhered to.</p> <p><b>Source dataset</b></p> <p>The dataset published here is based on analyses performed in VigiBase, the WHO global database of individual case safety reports [4]. All reports entered into VigiBase from its inception in 1967 up to 2 January 2018 with patient sex coded as either female or male have been included, except suspected duplicate reports [5]. In total, the source dataset contained 9,056,566 female and 6,012,804 male reports.</p> <p><strong>Statistical analysis</strong></p> <p>The characteristics of the female reports were compared to those of the male reports using a method called vigiPoint [6]. This is a method for comparing two or more sets of reports (here female and male reports) on a large set of reporting variables, and highlight any feature in which the sets are different in a statistically and clinically relevant manner. For example, patient age group is a reporting variable, and the different age groups 0 - 27 days, 28 days - 23 months et cetera are features within this variable. The statistical analysis is based on shrinkage log odds ratios computed as a comparison between the two sets of reports for each feature, including all reports without missing information for the variable under consideration. The specific output from vigiPoint is defined precisely below. Here, the results for 18 different variables with a total of 44,486 features are presented. 74 of these features were highlighted as so called vigiPoint key features, suggesting a statistically and clinically significant difference between female and male reports in VigiBase.</p> <p><strong>Description of published dataset</strong></p> <p>The dataset is provided in the form of a MS Excel spreadsheet (.xlsx file) with nine columns and 44,486 rows (excluding the header), each corresponding to a specific feature. Below follows a detailed description of the data included in the different columns.</p> <p><em>Variable</em>: This column indicates the reporting variable to which the specific feature belongs. Six of these variables are described in the original publication by Watson <em>et al</em>.: <em>country of origin</em>, <em>geographical region of origin</em>, <em>type of reporter</em>, <em>patient age group</em>, <em>MedDRA SOC</em>, <em>ATC level 2 of reported drugs</em>, <em>seriousness</em>, and <em>fatality </em>[1]. The remaining 12 are described here:</p> <ul> <li> <em>MedDRA HLGT</em> (high-level group term), <em>MedDRA HLT </em>(high-level term) and <em>MedDRA PT</em> (preferred term) are defined analogously to the <em>MedDRA SOC</em> (system organ class) [1], only at lower levels of the <a href="https://www.meddra.org/">MedDRA </a>(Medical Dictionary for Regulatory Activities) hierarchy. Here, MedDRA version 20.1 has been used.</li> <li> <em>ATC level 3 of reported drugs</em> is defined analogously to the variable <em>ATC level 2 of reported drugs </em>[1], only one step further down in the <a href="https://www.whocc.no/atc/structure_and_principles">ATC</a> (Anatomical Therapeutical Classification) hierarchy.</li> <li>The vigiGrade <i>completeness score</i> is a measure of how complete each report is with respect to certain report fields useful for causality assessment [7]. The completeness score has been dichotomised into two features, 'Above or equal to 0.8' and 'Below 0.8'. The maximum possible score for an individual report is 1.0.</li> <li>The <em>date of VigiBase entry </em>is simply the time when a report was entered into VigiBase. This variable is divided into 14 features that are either individual years or ranges of years.</li> <li> The <em>number of reported drugs</em> is the number of unique drugs that are coded on a report as either suspected, interacting, or concomitant. A drug is here defined as an entry at the preferred base (i.e. substance) level of the WHODRUG terminology. The variable is divided into four features: 'One drug', 'Two drugs', '3-5 drugs', and 'More than 5 drugs'.</li> <li> The <em>number of reported MedDRA PTs</em> is the number of unique MedDRA preferred terms that are coded as events on a report. This variable is divided into four features in exactly the same way as the reported drugs.</li> <li> A <i>reported drug</i> is a drug coded on a report as either suspected, interacting, or concomitant. As above, a drug is defined as an entry at the preferred base (i.e. substance) level of the WHODRUG terminology. This variable has almost 23,000 features, one for each drug that occurs in at least one female or one male report.</li> <li> The <em>type of report</em> indicates the type of individual case report. The vast majority belongs to the feature 'Spontaneous', but there are four other possible features for this variable.</li> </ul> <p>The <em>Variable </em>column can be useful for filtering the data, for example if one is interested in one or a few specific variables.</p> <p><i>Feature: </i>This column contains each of the 44,486 included features. The vast majority should be self-explanatory, or else they have been explained above, or in the original paper [1].</p> <p><em>Female reports</em> and <em>Male reports</em>: These columns show the number of female and male reports, respectively, for which the specific feature is present.</p> <p><em>Proportion among female reports</em> and <em>Proportion among male reports</em>: These columns show the proportions within the female and male reports, respectively, for which the specific feature is present. Comparing these crude proportions is the simplest and most intuitive way to contrast the female and male reports, and a useful complement to the specific vigiPoint output.</p> <p><em>Odds ratio</em>: The odds ratio is a basic measure of association between the classification of reports into female and male reports and a given reporting feature, and hence can be used to compare female and male reports with respect to this feature. It is formally defined as <em>a / (bc / d)</em>, where</p> <ul> <li> <em>a</em> is the number of female reports with the feature</li> <li> <em>b</em> is the number of female reports without the feature (excluding reports where the variable is missing)</li> <li> <em>c</em> is the number of male reports with the feature</li> <li> <i>d</i> is the number of male reports without the feature (excluding reports where the variable is missing).</li> </ul> <p>This crude odds ratio can also be computed as <em>(p<sub>female</sub> / (1-p<sub>female</sub>)) / (p<sub>male</sub> / (1-p<sub>male</sub>))</em>, where <em>p<sub>female</sub></em> and <em>p<sub>male</sub></em> are the proportions described earlier. If the odds ratio is above 1, the feature is more common among the female than the male reports; if below 1, the feature is less common among the female than the male reports. Note that the odds ratio can be mathematically undefined, in which case it is missing in the published data.</p> <p><em>vigiPoint score</em>: This score is defined based on an odds ratio with added statistical shrinkage, defined as (<em>a + k) / ((bc / d) + k)</em>, where <em>k</em> is 1% of the total number of female reports, or about 9,000. While the shrinkage adds robustness to the measure of association, it makes interpretation more difficult, which is why the crude proportions and unshrunk odds ratios are also presented. Further, 99% credibility intervals are computed for the shrinkage odds ratios, and these intervals are transformed onto a log<sub>2</sub> scale [6]. The vigiPoint score is then defined as the lower endpoint of the interval, if that endpoint is above 0; as the higher endpoint of the interval, if that endpoint is below 0; and otherwise as 0. The vigiPoint score is useful for sorting the features from strongest positive to strongest negative associations, and/or to filter the features according to some user-defined criteria.</p> <p><em>vigiPoint key feature</em>: Features are classified as vigiPoint key features if their vigiPoint score is either above 0.5 or below -0.5. The specific thereshold of 0.5 is arbitrary, but chosen to identify features where the two sets of reports (here female and male reports) differ in a clinically significant way.</p> <p><strong>References</strong></p> <ol> <li>Watson S, Caster O, Rochon PA, den Ruijter H. Reported adverse drug reactions in women and men: Aggregated evidence from globally collected individual case reports during half a decade. <em>EClinicalMedicine</em> 2019.</li> <li>Uppsala Monitoring Centre. <a href="https://www.who-umc.org/media/164772/guidelineusingvigibaseinstudies.pdf">Guideline for using VigiBase data in studies</a>.</li> <li>Uppsala Monitoring Centre. <a href="https://www.who-umc.org/media/164610/umc_caveat.pdf">Caveat document: Statement of reservations, limitations, and conditions relating to data released from VigiBase, the WHO global database of individual case safety reports (ICSRs)</a>.</li> <li>Lindquist M. VigiBase, the WHO Global ICSR Database System: Basic Facts. <i>The Drug Information Journal</i> 2008; <b>42</b>(5): 409-19.</li> <li>Norén GN, Orre R, Bate A, Edwards IR. Duplicate detection in adverse drug reaction surveillance. <em>Data Mining and Knowledge Discovery</em> 2007; <strong>14</strong>(3): 305-28.</li> <li>Juhlin K, Star K, Norén GN. A method for data-driven exploration to pinpoint key features in medical data and facilitate expert review. <i>Pharmacoepidemiology and Drug Safety</i> 2017; <b>26</b>(10): 1256-65.</li> <li>Bergvall T, Norén GN, Lindquist M. vigiGrade: A tool to identify well-documented individual case reports and highlight systematic data quality issues. <em>Drug Safety </em>2014; <strong>37</strong>(1): 65-77.</li> </ol>
Data from: Individual shifts toward safety explain age-related foraging distribution in a gregarious shorebird
Although age-related spatial segregation is ubiquitous, the underlying mechanisms are poorly understood. Here, we aim to elucidate the processes behind a previously established age-related foraging distribution of red knots (Calidris canutus canutus) in their main wintering area in West Africa (Banc d'Arguin, Mauritania). Based on 10 years of observations of 1232 uniquely color-ringed individuals of 1 to 18+ years old, we examined whether the observed age-related foraging distribution resulted from 1) spatial differences in mortality or 2) age-related shifts in habitat use. Using multistate capture–recapture modeling, we showed that with age foraging red knots moved away from the shoreline, that is, to areas with fewer surprise attacks by raptors. Considering uncertainties in the subjective gradient in predation danger with increasing distance from shore (as assessed from correlations between vigilance and distance from shore in foraging birds), we applied 2 different danger zone boundaries, at 40 m and 500 m from shore. Between years, red knots had a much higher chance to move from the dangerous nearshore area to the "safe" area beyond (71–78% and 26% for 40-m and 500-m danger zone boundary, respectively), than vice versa (4% and 14%). For neither danger zone boundary value did we find differences in annual mortality for individuals using either dangerous or safe zone, so the move away from the shore with age is attributed to individual careers rather than differential mortality. We argue that longitudinal studies like ours will reveal that ontogenetic shifts in habitat use are more common than so far acknowledged.
FIGURE 5 in Problems with the taxonomy of Phytoptus tetratrichus Nalepa 1890 (Acari: Eriophyoidea) inhabiting Tilia spp.: Analysis based on morphological variation among individuals
FIGURE 5. Leaf damage caused by Phytoptus tetratrichus on Tilia americana.
Parameters of RSF law and AE activity for the individual sliding-rate steps
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MtDNA genomes from Ranis individuals aligned with previously published ancient & modern humans
<p>The Middle to Upper Palaeolithic transition in Europe is associated with the regional disappearance of Neanderthals and the spread of Homo sapiens. Archaeological evidence indicates the presence of technocomplexes at the interface of this transition, complicating our understanding of the period and the association of those with specific hominin groups. One such technocomplex where the maker is unknown is the Lincombian-Ranisian-Jerzmanowician (LRJ), which covers an area in northwestern and central Europe from the UK to Poland. This paper presents the morphological and proteomic species identification, mitochondrial DNA analysis, and direct radiocarbon dating of human remains directly associated to an LRJ assemblage at the cave site of Ilsenhöhle in Ranis (Germany). </p>
Dataset on the validation of individuals' intention to engagement in philanthropic activities measure
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Individual .ttl files for plate VGF139 samples
Individual .ttl files for plate VGF139 samples processed using the ENPKG framework
Unveiling Heterogeneity in Individual Thresholds: Validation Using Urinary Prostaglandin D2 Metabolite in Food Allergy Reactions
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NCT05930912 Individual Participant Data
<p>The data is composed of MRI & MRA results of the participant, data monitoring, and hematology result.</p>
Quantifying the contribution of individual inputs used in Zero Budget Natural Farming
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Individual tree biomass by components for small black spruce trees growing on the wetlands of the Boreal and Taiga Plains of Canada
<p>New tree mensuration data and biomass component data from destructive sampling of 679 trees, were collected at 58 black spruce boreal wetland sites within the Boreal Plains and Taiga Plains of Canada. These data have been used to:</p> <p> Develop individual small black spruce trees allometric models. These models will focus on relationships between basal and breast height diameter, years-to-breast height, and height as function of basal diameter or breast height diameter, taper equation, and individual tree volume compilation.<br> Develop individual small black spruce trees biomass models. These equations will focus on estimating biomass of single trees based on diameters (basal and breast height diameter) and/or height). </p> <p> </p>
De lo individual a lo social: compartir conocimiento en organizaciones de investigación
<p>Ponencia - IV Congreso Latinoamericano de Marketing Social</p>
Data analysis file for the manuscript "Assessing the speed of individual bacteria dispersing on mycelial networks"
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LENGTH DIFFERENCES OF INDIVIDUAL YARN AND SINGLE YARN ELONGATION DEFORMATIONS IN COOKED YARN COMPOSITION.
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data (Cognition and vascular endothelial function in hypertensive individuals with and without a history of Covid-19: A Cross-Sectional Study)
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Efficient quantum gates for individual nuclear spin qubits by indirect control
<p>Hybrid quantum registers, such as electron-nuclear spin systems, have emerged as promising hard-<br> ware for implementing quantum information and computing protocols in scalable systems. Neverthe-<br> less, the coherent control of such systems still faces challenges. Particularly, the lower gyromagnetic<br> ratios of the nuclear spins cause them to respond slowly to control fields, resulting in gate times<br> that are generally longer than the coherence time of the electron. Here, we demonstrate a scheme<br> for circumventing this problem by indirect control: We apply a small number of short pulses only<br> to the electron and let the full system undergo free evolution under the hyperfine coupling between<br> the pulses. Using this scheme, we realize robust quantum gates in an electron-nuclear spin system,<br> including a Hadamard gate on the nuclear spin and a controlled-NOT gate with the nuclear spin<br> as the target qubit. The durations of these gates are shorter than the electron coherence time, and<br> thus additional operations to extend the system coherence time are not needed. Our demonstration<br> serves as a proof of concept for achieving efficient coherent control of electron-nuclear spin systems,<br> such as NV centers in diamond. Our scheme is still applicable when the nuclear spins are only<br> weakly coupled to the electron.</p>
Difference in rupture risk between familial and sporadic intracranial aneurysms: an individual patient data meta-analysis
<p><b>Objective:</b> We combined <span>individual patient data (IPD) from prospective cohorts of patients with </span>unruptured intracranial aneurysms (UIA) to assess to what extent patients with familial UIA have a higher rupture risk than those with sporadic UIA.<b> </b></p> <p><b>Methods:</b> For this IPD meta-analysis we performed an Embase and Pubmed search for studies published up to December 1, 2020. We included studies that 1) had a prospective study design; 2) included 50 or more patients with UIA; 3) studied the natural course of UIA and risk factors for aneurysm rupture including family history for aneurysmal subarachnoid haemorrhage and UIA; and 4) had aneurysm rupture as an outcome. Cohorts with available IPD were included. All studies included patients with newly diagnosed UIA visiting one of the study centers. The primary outcome was aneurysmal rupture. Patients with polycystic kidney disease and moyamoya disease were excluded. We compared rupture rates of familial versus sporadic UIA using a Cox proportional hazard regression model adjusted for the PHASES score and smoking. We performed two analyses: 1. only studies defining first-degree relatives as parents, children, and siblings and 2. all studies, thus both including and excluding siblings as first-degree relatives.</p> <p><b>Results:</b> We pooled IPD from eight cohorts with a low and moderate risk of bias. First-degree relatives were defined as parents, siblings and children in six cohorts (29% Dutch, 55% Finnish, 15% Japanese), totalling 2,297 patients (17% familial, 399 patients) with 3,089 UIA and 7,301 person-years follow-up. Rupture occurred in 10 familial patients (rupture rate: 0·89%/person-year; 95% CI:0·45-1·59) and 41 sporadic patients (0·66%/person-year; 95% CI:0·48-0·89); adjusted HR for familial patients 2·56 (95% CI: 1·18–5·56). After adding also the two cohorts excluding siblings as first-degree relatives resulting in 9,511 patients the adjusted HR was 1·44 (95% CI: 0·86–2·40).</p> <p><b>Conclusion:</b> The risk of rupture of UIA is two and a half times higher, with a range from a 1.2 to 5 times higher risk, in familial than in sporadic UIA. When assessing the risk of rupture in UIA, family history should be taken into account.</p>
DRIP: Segmenting Individual Requirements from the Paragraphs in Software Requirement Documents
<p>Software Requirement Document datasets in past 5 years of RE, ICSE, REFSQ, REJ</p>
Oxygen sensing with individual ZnO:Sb Micro-wires: Effects of temperature and light exposure on the sensitivity and stability
<p>Nanostructured ZnO has been widely investigated as a gas sensing material. Antimony is an important dopant for ZnO that catalyzes its surface reactivity and thus strengthens its gas sensing capability. However, there are little to no studies on the gas sensing of antimony-doped ZnO single wires. We fabricated and characterized ZnO/ZnO:Sb core/shell micro-wires and demonstrated that individual wires are sensitive to oxygen gas flow. Temperature and light illumination strongly affect the oxygen gas sensitivity and stability of these individual wires. It was found that these micro- and nano-wire oxygen sensors at 200˚C give the highest response to oxygen, yet a vanishingly small effect of light and temperature variations. The underlying physics and the interplay between these effects are discussed in terms of surface-adsorbed oxygen, oxygen vacancies and hydrogen doping.</p>
Doryteuthis pealeii embyronic transcriptome individual stages 16-27 pooled and annotation
<p>Photoreception is a ubiquitous sensory ability found across the Metazoa, and photoreceptive organs are intricate and diverse in their structure. Although the morphology of the compound eye in Drosophila and the single-chambered eye in vertebrates have elaborated independently, the amount of conservation within the 'eye' gene regulatory network remains controversial, with few taxa studied. To better understand the evolution of photoreceptive organs, we established the cephalopod Doryteuthis pealeii as a lophotrochozoan model for eye development. Utilizing histological, transcriptomic and molecular assays, we characterize eye formation in Doryteuthis pealeii Through lineage tracing and gene expression analyses, we demonstrate that cells expressing Pax and Six genes incorporate into the lens, cornea and iris, and the eye placode is the sole source of retinal tissue. Functional assays demonstrate that Notch signaling is required for photoreceptor cell differentiation and retinal organization. This comparative approach places the canon of eye research in traditional models into perspective, highlighting complexity as a result of both conserved and convergent mechanisms.</p>
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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.