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dbMMR-Chinese database: the open-access database for variants in mismatch repair genes in Chinese population
<p>Mutation in mismatch repair genes (MMR) is the genetic predisposition for gastrointestinal cancer represented by the Lynch Syndrome. Identification of the mutation carrier is critical in prevention and treatment of the cancer. Chinese is the largest ethnic population with the largestgastrointestinal cancer cases in the world, but systematic knowledge for the mutation in MMR is lack in Chinese population. Through comprehensive data mining, we collected nearly all MMR data derived from 33,998 Chinese of 23,938 cancer and 10,060 non-cancer cases reported from 1997 to 2019. Upon standardization and re-annotation, the data following international standards, we identified a total of 540 distinct MMR variants including 487 single base change and indel, and 53 large deletion/duplication in four MMR genes of <em>MLH1</em>, <em>MSH2</em>, <em>MSH6</em>and <em>PMS2</em>; 153 of the variants were classified as Pathogenic or Likely Pathogenic. This MMR dataset is the largest collection from a single, non-Caucasian population. We developed an open-access database, dbMMR-Chinese (<a href="https://dbmmr-chinese.fhs.um.edu.mo/">https://dbMMR-chinese.fhs.um.edu.mo</a>), to share with community for MMR mutation-related cancer study and clinical application.</p>
Data_text section 11βHSD2_11β-Hydroxysteroid dehydrogenases control access of 7β,27-dihydroxycholesterol to retinoid-related orphan receptor γ
<p>Data from kinetic characterization (Km and vmaxapp) described in text section 3.2 of 11β-Hydroxysteroid dehydrogenases control access of 7β,27-dihydroxycholesterol to retinoid-related orphan receptor γ</p> <p>Dataset (doi:10.1194/jlr.M092908) contains values from kinetic characterization (Km and vmaxapp) described in text section (kinetic values 11βHSD2.PNG) corresponding to raw data obtained from LC-MS/MS analysis provided as three files in CSV format (31003A-179400_DATE_KB_27Oxysterol_4_7_1-3). All further experiment related information and subsequent data analysis provided as two meta-data-files: (31003A-179400_DATE_KB_27Oxysterol_4_7_M_1-2) as TXT format and PDF format.</p>
Data_supplemental Figure 4_11β-Hydroxysteroid dehydrogenases control access of 7β,27-dihydroxycholesterol to retinoid-related orphan receptor γ
<p>Data of supplemental figure 4 from 11β-Hydroxysteroid dehydrogenases control access of 7β,27-dihydroxycholesterol to retinoid-related orphan receptor γ</p> <p>Dataset (doi:10.1194/jlr.M092908) contains the original figure as PNG-format (10.1194_jlr.M092908_Fig. S4). Corresponding raw data obtained from luminescence analysis provided as six files in CSV format (31003A-179400_DATE_SK_KB_27Oxysterol_18_3-4_1-3). All further experiment related information and subsequent data analysis provided as meta-data-file (31003A-179400_DATE_SK_KB_27Oxysterol_18_3-4_M) as TXT format.</p>
Data_supplemental Figure 2_11β-Hydroxysteroid dehydrogenases control access of 7β,27-dihydroxycholesterol to retinoid-related orphan receptor γ
<p>Data of supplemental figure 2 from 11β-Hydroxysteroid dehydrogenases control access of 7β,27-dihydroxycholesterol to retinoid-related orphan receptor γ</p> <p>Dataset (doi:10.1194/jlr.M092908) contains the original figure as PNG format (10.1194_jlr.M092908_Fig. S2). All further experiment related information and subsequent data analysis provided as two meta-data-files: (31003A-179400_DATE_SK_KB_27Oxysterol_4_5_M_1-2) as TXT format and PDF-Format.</p>
Data_Figure 3 _11β-Hydroxysteroid dehydrogenases control access of 7β,27-dihydroxycholesterol to retinoid-related orphan receptor γ
<p>Data of figure 3 from 11β-Hydroxysteroid dehydrogenases control access of 7β,27-dihydroxycholesterol to retinoid-related orphan receptor γ</p> <p>Dataset (doi:10.1194/jlr.M092908) contains the original figure as TIF-format (10.1194_jlr.M092908_Fig. 3). Corresponding raw data obtained from LC-MS/MS analysis provided as three files in CSV format (31003A-179400_DATE_KB_ 27Oxysterol_4_3_1-3). All further experiment related information and subsequent data analysis provided as two meta-data-files (31003A-179400_DATE_KB_27Oxysterol_4_3_M_1-2) as TXT format and PDF format.</p> <p> </p> <p> </p>
Data_supplemental Figure 1_11β-Hydroxysteroid dehydrogenases control access of 7β,27-dihydroxycholesterol to retinoid-related orphan receptor γ
<p>Data of supplemental figure 1 from 11β-Hydroxysteroid dehydrogenases control access of 7β,27-dihydroxycholesterol to retinoid-related orphan receptor γ</p> <p>Dataset (doi:10.1194/jlr.M092908) contains the original figure as TIF-format (10.1194_jlr.M092908_Fig. S1). All further experiment related information and subsequent data analysis provided as two meta-data-files (31003A-179400_DATE_KB_27Oxysterol_4_4_M_1-2) as TXT format and PDF format.</p>
Data_Figure 2_11β-Hydroxysteroid dehydrogenases control access of 7β,27-dihydroxycholesterol to retinoid-related orphan receptor γ
<p>Data of figure 2 from 11β-Hydroxysteroid dehydrogenases control access of 7β,27-dihydroxycholesterol to retinoid-related orphan receptor γ</p> <p>Dataset (doi:10.1194/jlr.M092908) contains the original figure as TIF-format (10.1194_jlr.M092908_Fig. 2). Corresponding raw data obtained from LC-MS/MS analysis provided as three files in CSV format (31003A-179400_ DATE _KB_ 27Oxysterol_4_2_1-3). All further experiment related information and subsequent data analysis provided as two meta-data-files (31003A-179400_ DATE _KB_27Oxysterol_4_2_M_1-2) as TXT format and PDF format.</p>
Data_Figure 4_11β-Hydroxysteroid dehydrogenases control access of 7β,27-dihydroxycholesterol to retinoid-related orphan receptor γ
<p>Data of figure 4 from 11β-Hydroxysteroid dehydrogenases control access of 7β,27-dihydroxycholesterol to retinoid-related orphan receptor γ</p> <p>Dataset (doi:10.1194/jlr.M092908) contains the original figure as TIF-format (10.1194_jlr.M092908_Fig. 4). Corresponding raw data obtained from liquid scintillation analysis provided as nine files in CSV format (31003A-179400_DATE_KB_27Oxysterol_11_1-3_1-3). All further experiment related information and subsequent data analysis provided as three meta-data-files (31003A-179400_DATE_KB_27Oxysterol_11_1-3_M_1) as TXT format.</p>
Data_Figure 7_11β-Hydroxysteroid dehydrogenases control access of 7β,27-dihydroxycholesterol to retinoid-related orphan receptor γ
<p>Data of figure 7 from 11β-Hydroxysteroid dehydrogenases control access of 7β,27-dihydroxycholesterol to retinoid-related orphan receptor γ</p> <p>Dataset (doi:10.1194/jlr.M092908) contains the original figure as TIF-format (10.1194_jlr.M092908_Fig. 7). Corresponding raw data obtained from docking calculation analysis and calculation provided as two files in TXT format (31003A-179400_DATE_KB_27Oxysterol_19_5-6_1). All further experiment related information and subsequent data analysis provided as two meta-data-files (31003A-179400_DATE_KB_27Oxysterol_19_5-6_M) as TXT format.</p>
Data_Figure 9_11β-Hydroxysteroid dehydrogenases control access of 7β,27-dihydroxycholesterol to retinoid-related orphan receptor γ
<p>Data of figure 9 from 11β-Hydroxysteroid dehydrogenases control access of 7β,27-dihydroxycholesterol to retinoid-related orphan receptor γ</p> <p>Dataset (doi:10.1194/jlr.M092908) contains the original figure as TIF-format (10.1194_jlr.M092908_Fig. 9). Graphical abstract.</p>
Participatory Design of Usability Requirements for Access Control in an Evolutionary-Teal Organization Workshop Data Set
<p>In order to enable members of a socio-technical evolutionary-teal organization to design the technical component for access control, we conducted a workshop that structures the requirement engineering with members. The workshop aims to illustrate user needs, challenges and potential solutions that can be used to infer usability requirements for the development of a prototype of the user interface for access control in the form of "problem statements" and clustered mind-maps.</p> <p>The workshop is setup as a standalone, five-and-a-half-hour group discussion. It uses the methods of Design Thinking and Participatory Design.<br> The workshop has been recorded in video and this data set contains a textual German transcript and transcripts of the moderation cards that have been created during the workshop for various guiding topics.</p> <p>We hope that the material can be used to (a) comprehend the interpretation used in our qualitative research, (b) to adapt the workshop model by other volunteers of our case study Viva con Agua de St. Pauli e.V. (<a href="https://www.vivaconagua.org/">https://www.vivaconagua.org/</a>), and (c) investigate other interesting research questions.</p> <p>Some material, such as timetables and storyboard, has been omitted in the publication due to privacy restrictions.</p>
FIGURE 8 in Accessing cryptic diversity in Neotropical rattlesnakes (Serpentes: Viperidae: Crotalus) with the description of two new species
FIGURE 8. Crotalus ehecatl in life, (A) ECO-CH-H 3778, holotype from San José Tintonishac, Las Margaritas, Chiapas; (B) adult specimen from Tuxtla Gutiérrez, Chiapas; (C) UTA-R 51456, adult male from Santa Inés, Santa María Chimalapa, Oaxaca; (D) neonate specimen from Santa María Mixtequilla, Oaxaca; (E) neonate specimen from San Pedro Tapanatepec, Oaxaca; (F) adult specimen from San Pedro Totolápam, Oaxaca. Photos by J.A. Hidalgo García (A), E.B. Jiménez Díaz (B), E.N. Smith courtesy of J.A. Campbell (C), I.T. Ahumada Carrillo (D), HERP.MX (E), and F. Martínez Belmar (F).
FIGURE 5 in Accessing cryptic diversity in Neotropical rattlesnakes (Serpentes: Viperidae: Crotalus) with the description of two new species
FIGURE 5. Dorsal and lateral view of the head of the holotype of Crotalus mictlantecuhtli (SDNHM 22416).
FIGURE 3 in Accessing cryptic diversity in Neotropical rattlesnakes (Serpentes: Viperidae: Crotalus) with the description of two new species
FIGURE 3. (A), Results of the principal component analyses between the members of the Crotalus durissus species complex with 95% confidence regions. PC1 and PC2 together explain 33.4% of the total variance. (B), Reanalysis including only members of norhten clade (Crotalus culminatus); (C), members of southern clade (Crotalus durissus) with morphological data available. (D), Bivariate plots with 95% confidence regions for the first two axes derived from scores of discriminant analyses for members of Crotalus durissus species complex.
FIGURE 1 in Accessing cryptic diversity in Neotropical rattlesnakes (Serpentes: Viperidae: Crotalus) with the description of two new species
FIGURE 1. (A) Maximum-likelihood phylogram of the four genes (cyt b, ND4, ND2, c-mos, 2596 bp) analysis (-ln L=- 17,270.83). Tip labels are as follows: 3-letter subspecies code for the Crotalus durissus species complex, following Campbell & Lamar (2004), locality and haplotypes in parentheses, see Appendix 1. Numbers along branches indicate bootstrap support-ML and Bayesian posterior probability. For clarity, support is only shown for important nodes. (B) Maximum-likelihood phylogram of the four genes (cyt b, ND4, ND2, c-mos, 2596 bp) analysis (-ln L=-17,270.83). Tip labels are as follows: 3-letter subspecies code for the Crotalus molossus species complex and outgroups, following Campbell & Lamar (2004) and Anderson & Greenbaum (2012), locality and haplotypes in parentheses, see Appendix 1. Numbers along branches indicate bootstrap support-ML and Bayesian posterior probability. For clarity, support is only shown for important nodes.
List of tissue specimens of Hipposideros spp. used for cytochrome b sequencing and phylogenetic inference, with geographical data. Voucher refers to the location and/or accession number of the voucher, and tissue collection refers to the collection where the tissue is kept, and accession or collector numbers. Acronyms are as follows: Estación Biológica de DoZana, Sevilla, Spain (EBD), South Australia Museum, Adelaide, Australia (SAM), Senckenberg Museum, Frankfurt am Main, Germany (SMF), Instituto de Ecología, Xalapa, México (IEX), Louisiana State University, Baton Rouge, Louisiana, USA (LSU), Charles M. Francis, Canadian Wildlife Service, Ottawa, Ontario, Canada (CMF), Lao Department of Forestry, Vientiane, Lao PDR, no catalogued (LAO). Next column indicates GenBank accession numbers. More information about the specimens is available in the GenBank records in A new species of bat of the Hipposideros bicolor group (Chiroptera: Hipposideridae) from Central Laos, with evidence of convergent evolution with Sundaic taxa
List of tissue specimens of Hipposideros spp. used for cytochrome b sequencing and phylogenetic inference, with geographical data. Voucher refers to the location and/or accession number of the voucher, and tissue collection refers to the collection where the tissue is kept, and accession or collector numbers. Acronyms are as follows: Estación Biológica de DoZana, Sevilla, Spain (EBD), South Australia Museum, Adelaide, Australia (SAM), Senckenberg Museum, Frankfurt am Main, Germany (SMF), Instituto de Ecología, Xalapa, México (IEX), Louisiana State University, Baton Rouge, Louisiana, USA (LSU), Charles M. Francis, Canadian Wildlife Service, Ottawa, Ontario, Canada (CMF), Lao Department of Forestry, Vientiane, Lao PDR, no catalogued (LAO). Next column indicates GenBank accession numbers. More information about the specimens is available in the GenBank records
Data from: Headache study: The management of chronic headache with referral from primary care to direct access to Magnetic Resonance Imaging (MRI) compared to Neurology services: an observational prospective study in London
<p><b>Objectives</b>. To evaluate the cost, accessibility and patient satisfaction implications of two clinical pathways used in the management of chronic headache.</p> <p><b>Intervention</b>. Management of chronic headache following referral from Primary Care that differed in the first appointment, either a Neurology appointment or an MRI brain scan.</p> <p><b>Design and setting</b>. A pragmatic, non-randomised, prospective, single-center study at a Central Hospital in London.</p> <p><b>Participants. </b>Adult patients with chronic headache referred from Primary to Secondary Care.</p> <p><b>Primary and secondary outcome measures.</b> Participants' use of health care services and costs were estimated using primary and secondary care databases and questionnaires quarterly up to 12 months post-recruitment. Cost analyses were compared using generalised linear models (GLM). Secondary outcomes assessed: access to care, patient satisfaction, headache burden and self-perceived quality of life using headache-specific (MIDAS, HIT-6) and a generic questionnaire (EQ-5D-5L).</p> <p><b>Results. </b>Mean (SD) cost up to 6 months post-recruitment per participant was £578 (£420) for the Neurology group (n=128) and £245 (£172) for the MRI group (n=95), leading to an estimated mean cost difference of £333 (95% CI £253 to £413, p<0.001). The mean cost difference at 12 months increased to £518 (95% CI £401 to £637, p<0.001). When adjusted for baseline and follow-up imbalances between groups, this remained statistically significant. The utilisation of brain MRI improved access to care compared to the Neurology group (p<0.001). Participants in the Neurology group reported higher levels of satisfaction associated with the pathway and led to greater change in care management.</p> <p><b>Conclusion. </b>Direct referral to brain MRI from Primary Care led to cost-savings and quicker access to care but lower satisfaction levels when compared with referral to Neurology services. Further research into the use of brain MRI for a subset of patient population more likely to be reassured by a negative brain scan should be considered.</p>
Impact of national drug pricing policy 2018 on access to medicines in Lahore Division, Pakistan: A pre-post survey study using WHO/HAI methodology
<p><span><b>Objective: </b>To evaluate the impact of new national drug pricing policy (NDPP) 2018 on the access to medicines in terms of prices, availability, and affordability.<b> </b></span></p> <p><span><b>Design: </b>Two cross-sectional surveys were undertaken before and after the launch of NDPP 2018, using a modified WHO/HAI methodology.</span></p> <p><span><b>Setting: </b>Four districts of Lahore division, Pakistan. </span></p> <p><span><b>Participants: </b>16 public sector hospitals and 16 private sector retail pharmacies. </span></p> <p><span><b>Measures: </b>The pre- and post-survey data on prices and availability of Lowest Price Generics (LPGs) and Originator Brands (OBs) of 50 medicines were obtained by visiting the same public and private sector health facilities (n=32). Out of 50, 46 surveyed medicines were from National Essential Medicines List (NEML). Inflation-adjusted median unit prices (MUPs) and median price ratios (MPRs) from 2019 were used for price comparison. Affordability was calculated in terms of number of days' wages required to get a standard treatment by the lowest paid unskilled government worker.</span></p> <p><span><b>Results:</b> The overall mean percent availabilities remained poor in both years i.e. far less than 80%. In public sector, the mean percent availability of OBs improved from 6.8% to 33.1% whereas, in case of LPGs it was reduced from 35.1% to 9%. In private sector, the mean percent availability of both OBs and LPGs demonstrated slight improvements in 2019 i.e. 55.0% to 58.3% and 20.3% to 32.3%. The adjusted MUPs and MPRs of OBs significantly increased by a median of 4.29% (Wilcoxon test p=0.001, p=0.0001). Whereas, the adjusted MUPs and MPRs of LPGs were increased by a median of 15.7% (p=0.002, p=0.0002). Overall the affordability of many medicines for common ailments reduced significantly in 2019.</span></p> <p><span><b>Conclusion</b><b>s</b><b>: </b>The availability of medicines slightly improved, except in the case of LPGs which was reduced at public sector. The implementation of NDPP 2018 led to increase in drug prices, making the standard treatment for some of the most prevalent ailments unaffordable. So verily, the drug pricing policy must be reviewed to ensure access to essential medicines.</span></p>
Exploring the reach of open access content to non-academic audiences
<p>Raw data from survey run on nature.com, springerlink and biomedcentral.com in association with VSNU. Relates to publication "Exploring the reach of open access content to non-academic audiences"</p> <p><a href="https://www.doi.org/10.5281/zenodo.4143313">https://www.doi.org/10.5281/zenodo.4143313</a></p> <p> </p>
Relations between access to sport and green spaces and Body Mass Index in the canton of Geneva
<p>README.txt</p> <p>-------------------------------------------------<br> Science et Ingénierie de l'Environnement (SIE)<br> Bâtiment GR<br> EPFL ENAC SSIE-GE<br> CH-1015 Lausanne<br> *<br> *<br> ------------------------------------------------.<br> *<br> *<br> "Envdata.csv" contains the data used in the study entitled:<br> "Relations between access to sport and green spaces and Body Mass Index in the canton of Geneva", <br> (C. El Khoury,Y. Frischholz, B. Heutte, V. Remy, M. Schornoz, 2020)<br> *<br> *<br> -------------------------------------------------<br> *<br> *<br> Variables : Description [unit]<br> *<br> ID : Bus Santé participant's ID [-]<br> x_lv03, y_lv03 : Coordinates of participants residence (LV03) [m]<br> year_survey : Bus Santé participation year [-]<br> #SPORT10min : Density of sport infrastructures within a buffer of 10 minutes walk around residences [-]<br> dist_1SPORT : Direct distance to first sport infrastructure from residences [m]<br> meanNDVI10min : Mean NDVI within a buffer of 10 minutes walk (to remove biases due to large water bodies, the lake area was removed from the 10 minutes buffer) [m]<br> BMI_randorder : Values of BMI used in a randomized order for confidentiality reasons [kg/m2]<br> *<br> *<br> -------------------------------------------------</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.