cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/tngrtnvn2p.2
title: Data for: Incidence and Morbidity of Radiation-Induced Hemorrhagic Cystitis in Prostate Cancer

description: We completed an institutional, review board-approved, retrospective chart review of 739 patients who underwent radiation therapy for prostate cancer or bladder cancer from January 1, 2000 to September 20, 2015. Medicare coding for radiation, prostate cancer, and bladder cancer were used to obtain patient records using diagnosis codes 185, 188.0-188.9, V10.51, and V10.46, with procedure codes 92.20 – 92.2. Inpatient and outpatient records from two Detroit Medical Center hospitals (Detroit Receiving and Harper Hutzel Hospital) were reviewed. The primary outcome was the incidence of hemorrhagic cystitis after radiation for prostate cancer. Among patients who developed HC, we analyzed the patient demographics, comorbidities, incidence, radiation modality, morbidity, treatment, and complications
DOI: 10.17632/8js7m95hjx.2
title: Data for: Orientation in Perpetuity: An Online Clinical Decision Support System for Surgical Residents

description: Materials and Methods An internally-developed, web-based CDSS including essential, clinically useful documents was created for use by trainees on a busy pediatric surgery service. A standardized orientation was provided to each resident and fellow upon joining the service, complemented by a summary card to be attached to the trainee’s ID badge. CDSS usage was monitored using web analytics. Trainees who rotated before and after the CDSS launch were surveyed regarding attitudes toward clinical resources and confidence in patient management. Results Documents published to the CDSS included 33 clinical guideline documents and 207 additional educational and support files including reference materials from service orientation were made available to trainees and staff. Goals for resident usage were established by evaluation and adaptation of early traffic patterns. Analysis of web traffic collected over 14 consecutive months revealed utilization above target levels, with 4.0 average weekly page views per trainee (IQR: 1.6-5.6). A total of 60 survey responses were received (54% of trainees invited); majorities of rotating trainees and survey respondents were trainees in general surgery and most were interns. Mean composite scores reflected a trend toward improved satisfaction when seeking CDSM (pre-intervention 3.18 [SD 0.73], post-intervention 3.92 [SD 0.70], range 1-5) which was statistically significant (p=0.005). Mean scores also improved across five out of six components of the composite score (mean improvement 0.75, range: 0.53-0.92), four of which were statistically significant (p=0.001-0.038). A majority (59%) of respondents reported that they used the CDSS frequently. The raw data and analysis products are supplied here.
DOI: 10.17632/2zdpbs6gyh.1
title: Data for: A new numerical approach to the solution of partial differential equations with optimal accuracy on irregular domains and Cartesian meshes. Application to the 3-D wave, heat and Laplace equations with the Dirichlet boundary conditions.

description: Addition to the paper
DOI: 10.17632/c25py4s7dk.1
title: Data for: Insufflation Effects on the Abdominal Wall Dimensions and Incisional/Ventral Hernia Orifice Size

description: List of patient demographics, operation, measurements
DOI: 10.17632/36zgmhhjw2.1
title: Data for: Adequate positioning of the tibial component is key to avoiding bearing impingement in Oxford unicompartmental knee arthroplasty

description: This file include data such as patient age, sex, diagnosis, measurement data (bearing movement, component position, funcitonal outcome etc) for "Adequate positioning of the tibial component is key to avoiding bearing impingement in Oxford unicompartmental knee arthroplasty"
DOI: 10.17632/5rptybw94g.1
title: Data for: Assisted Savings for Retirement: An Experimental Analysis

description: Bohr, Holt, and Schubert: “Assisted Savings for Retirement: An Experimental Analysis” The 12 sessions for the main experiment are listed as AS_1, AS_2,…,AS_6 for the assisted savings treatment and PS_1, PS_2,…,PS_6 for the private savings treatment. These labels appear in the “label” column on the left of the file. Even though the “AS” and “PS” indicate the treatment, there is a separate column for the treatment as well. The “Vecon Lab Session Name” column refers to the name used for each session in the VeconLab database, which is for recordkeeping purposes only and can be ignored. The subjects in each session have ID labels 1.. 9, as shown in the “id” column, and the data for each session are sorted by round in the “round” column. The “market price” column shows the call market-clearing price that is the same for each person in a given round. As noted in the paper, if there were no trades and a bid-ask spread was defined, the price was determined to be the midpoint of that spread. In each round, each trader can make a bid characterized by a limit price and number of units, which are shown in the “bid price” and “bid quantity” columns. Similarly, offers to sell are shown in the “offer price” and “offer quantity” columns. The “fundamental value” column shows 28 in all periods for this flat value design. There are also columns for “quantity bought” “quantity sold” and “final share holdings” that list numbers of shares in these categories. The “cash” column shows the subject’s final cash position at the end of the round, after interest and dividends are paid and balances are adjusted for share purchases, share sales, and consumption expenditures. “Change in lab cash” refers to how much more cash holdings a subject has compared to the prior period. The “dividend” shows which dividend was realized in that round, the “interest received” column lists interest income for that person in that round. The individual’s consumption expenditure in a round is listed in the “consumption” column. “Consumption earnings” refers to the earnings amount resulting from converting lab dollars into take home pay (US dollars). Those period-by-period earnings in US dollars are accumulated in the “cumulative earnings column.” The cumulative earnings for the final period 18 include final share redemptions and all consumed lab cash as described in the paper.
DOI: 10.17632/8wts94bpg9.1
title: Data for: Assisted Savings for Retirement: An Experimental Analysis

description: Read Me File European Economic Review Guide to Data Appendix Bohr, Holt, and Schubert: “Assisted Savings for Retirement: An Experimental Analysis” The 12 sessions for the main experiment are listed as AS_1, AS_2,…,AS_6 for the assisted savings treatment and PS_1, PS_2,…,PS_6 for the private savings treatment. These labels appear in the “label” column on the left of the file. Even though the “AS” and “PS” indicate the treatment, there is a separate column for the treatment as well. The “Vecon Lab Session Name” column refers to the name used for each session in the VeconLab database, which is for recordkeeping purposes only and can be ignored. The subjects in each session have ID labels 1.. 9, as shown in the “id” column, and the data for each session are sorted by round in the “round” column. The “market price” column shows the call market-clearing price that is the same for each person in a given round. As noted in the paper, if there were no trades and a bid-ask spread was defined, the price was determined to be the midpoint of that spread. In each round, each trader can make a bid characterized by a limit price and number of units, which are shown in the “bid price” and “bid quantity” columns. Similarly, offers to sell are shown in the “offer price” and “offer quantity” columns. The “fundamental value” column shows 28 in all periods for this flat value design. There are also columns for “quantity bought” “quantity sold” and “final share holdings” that list numbers of shares in these categories. The “cash” column shows the subject’s final cash position at the end of the round, after interest and dividends are paid and balances are adjusted for share purchases, share sales, and consumption expenditures. “Change in lab cash” refers to how much more cash holdings a subject has compared to the prior period. The “dividend” shows which dividend was realized in that round, the “interest received” column lists interest income for that person in that round. The individual’s consumption expenditure in a round is listed in the “consumption” column. “Consumption earnings” refers to the earnings amount resulting from converting lab dollars into take home pay (US dollars). Those period-by-period earnings in US dollars are accumulated in the “cumulative earnings column.” The cumulative earnings for the final period 18 include final share redemptions and all consumed lab cash as described in the paper.
DOI: 10.6084/m9.figshare.14417612
title: Silurian (Aeronian) rhynchonelliform brachiopods of Shabdjereh, south-west Central Iran and their significance for early spiriferide evolution

description: The Silurian (Aeronian) post-extinction recovery brachiopod fauna of Iran and Afghanistan is characterized by a proliferation of the <i>Stegocornu</i> Brachiopod Association, which includes prominent endemic rhynchonellide and spiriferide components. A local variety of that association, recently recovered from the Shabdjereh Formation of Kerman Province, East-Central Iran, contains eight brachiopod species, including the rhynchonellide <i>Kermanirhyncha granulata</i> gen. et sp. nov., and the spiriferides <i>Levanispirifer alatus</i> gen. et sp. nov. and <i>Mictospirifer obtusus</i> sp. nov. A new phylogenetic analysis of the earliest Late Ordovician to Aeronian spiriferides, within the general context of the Ordovician radiation of rhynchonelliform brachiopods with calcified brachial supports, reveals the following two major centres of biodiversification and dispersal: (1) the Laurentian palaeocontinent, which is the likely place of origin and initial diversification of the atrypide suborders Lissatrypidina and Anazygidina; and (2) the assemblage of Kazakh island arcs and microplates (known also as Kazakh Archipelago), which was the centre of origin and initial dispersal of the atrypid suborder Atrypidina and the order Spiriferida. South China represents a major refuge, where spiriferides survived the terminal Ordovician extinction and from where they dispersed towards adjacent parts of Gondwana including the Iranian terranes. The latter areas were an important secondary centre of spiriferide biodiversification during the Aeronian Age. http://zoobank.org/urn:lsid:zoobank.org.pub:B8726A08-7D90-4AAF-8ECF-B81E78119712
DOI: 10.6084/m9.figshare.14452987
title: New data on early Oligocene dormice (Rodentia, Gliridae) from southern Europe: phylogeny and diversification of the family

description: Rodents of the extant family Gliridae, commonly called dormice, are common in European faunas since the early Eocene. Here we study for the first time specimens from St-Martin-de-Castillon C (France, early Oligocene) previously reported as <i>Gliravus</i> aff. <i>majori</i> and <i>Pseudodryomys</i> aff. <i>fugax</i>. We now refer them to <i>Butseloglis tenuis</i> and <i>Microdyromys misonnei</i>. Besides the French material, new specimens from Montalbán 1D (Spain, early Oligocene) are studied. They include: <i>Butseloglis montisalbani</i> and <i>M. misonnei</i> already known in the locality, but also <i>Oligodyromys libanicus</i> and <i>Glirudinus</i> aff<i>. glirulus</i> reported here for the first time. Previous phylogenies of the family only focused on extant taxa. Here we propose the first phylogenetic analysis of Gliridae including both extant and fossil taxa. The relationships between the taxa show several paraphylies at the generic level and suggest that the classification of the family needs a revision. Two main clades are revealed in our analysis, including most extant taxa, both of them being closely related to the Oligocene genus <i>Microdyromys</i>. By comparing the phylogeny to the evolution of species-richness through time, we show that glirids underwent three major diversification phases. The first diversification event involves several clades of late Eocene and early Oligocene glirids. The second diversification event involves the two main clades still represented today. They both started diversifying in the late Oligocene and led the species richness of the family to reach a peak at the end of the early Miocene. Finally, the third diversification starts in the middle Pliocene and involves mostly extant genera. These diversification phases might have been triggered by successive glaciation events that occurred in the Oligocene, Miocene and Pliocene. A potential evolutionary advantage of this family successfully facing cold climatic events could be the ability to hibernate, acquired as early as the early Oligocene.
DOI: 10.6084/m9.figshare.14452987.v1
title: New data on early Oligocene dormice (Rodentia, Gliridae) from southern Europe: phylogeny and diversification of the family

description: Rodents of the extant family Gliridae, commonly called dormice, are common in European faunas since the early Eocene. Here we study for the first time specimens from St-Martin-de-Castillon C (France, early Oligocene) previously reported as <i>Gliravus</i> aff. <i>majori</i> and <i>Pseudodryomys</i> aff. <i>fugax</i>. We now refer them to <i>Butseloglis tenuis</i> and <i>Microdyromys misonnei</i>. Besides the French material, new specimens from Montalbán 1D (Spain, early Oligocene) are studied. They include: <i>Butseloglis montisalbani</i> and <i>M. misonnei</i> already known in the locality, but also <i>Oligodyromys libanicus</i> and <i>Glirudinus</i> aff<i>. glirulus</i> reported here for the first time. Previous phylogenies of the family only focused on extant taxa. Here we propose the first phylogenetic analysis of Gliridae including both extant and fossil taxa. The relationships between the taxa show several paraphylies at the generic level and suggest that the classification of the family needs a revision. Two main clades are revealed in our analysis, including most extant taxa, both of them being closely related to the Oligocene genus <i>Microdyromys</i>. By comparing the phylogeny to the evolution of species-richness through time, we show that glirids underwent three major diversification phases. The first diversification event involves several clades of late Eocene and early Oligocene glirids. The second diversification event involves the two main clades still represented today. They both started diversifying in the late Oligocene and led the species richness of the family to reach a peak at the end of the early Miocene. Finally, the third diversification starts in the middle Pliocene and involves mostly extant genera. These diversification phases might have been triggered by successive glaciation events that occurred in the Oligocene, Miocene and Pliocene. A potential evolutionary advantage of this family successfully facing cold climatic events could be the ability to hibernate, acquired as early as the early Oligocene.
DOI: 10.6084/m9.figshare.14417612.v1
title: Silurian (Aeronian) rhynchonelliform brachiopods of Shabdjereh, south-west Central Iran and their significance for early spiriferide evolution

description: The Silurian (Aeronian) post-extinction recovery brachiopod fauna of Iran and Afghanistan is characterized by a proliferation of the <i>Stegocornu</i> Brachiopod Association, which includes prominent endemic rhynchonellide and spiriferide components. A local variety of that association, recently recovered from the Shabdjereh Formation of Kerman Province, East-Central Iran, contains eight brachiopod species, including the rhynchonellide <i>Kermanirhyncha granulata</i> gen. et sp. nov., and the spiriferides <i>Levanispirifer alatus</i> gen. et sp. nov. and <i>Mictospirifer obtusus</i> sp. nov. A new phylogenetic analysis of the earliest Late Ordovician to Aeronian spiriferides, within the general context of the Ordovician radiation of rhynchonelliform brachiopods with calcified brachial supports, reveals the following two major centres of biodiversification and dispersal: (1) the Laurentian palaeocontinent, which is the likely place of origin and initial diversification of the atrypide suborders Lissatrypidina and Anazygidina; and (2) the assemblage of Kazakh island arcs and microplates (known also as Kazakh Archipelago), which was the centre of origin and initial dispersal of the atrypid suborder Atrypidina and the order Spiriferida. South China represents a major refuge, where spiriferides survived the terminal Ordovician extinction and from where they dispersed towards adjacent parts of Gondwana including the Iranian terranes. The latter areas were an important secondary centre of spiriferide biodiversification during the Aeronian Age. http://zoobank.org/urn:lsid:zoobank.org.pub:B8726A08-7D90-4AAF-8ECF-B81E78119712
DOI: 10.5281/zenodo.4721951
title: Risultati della valutazione del corso "Praticare l'Open Science nelle Scienze della Terra e dell'ambiente"

description: Risultati della valutazione del corso "Praticare l'Open Science nelle Scienze della Terra e dell'ambiente"
DOI: 10.5281/zenodo.4721950
title: Risultati della valutazione del corso "Praticare l'Open Science nelle Scienze della Terra e dell'ambiente"

description: Risultati della valutazione del corso "Praticare l'Open Science nelle Scienze della Terra e dell'ambiente"
DOI: 10.17632/gt6692jm6w.2
title: Data for: Elemental proxies for paleosalinity analysis of ancient shales and mudrocks

description: modern and ancient data for paleosalinity research
DOI: 10.17632/7dcd797nmp.3
title: Data for: Indoleamine 2,3-dioxygenase-1 (IDO-1) expression in Adrenocortical Carcinoma

description: Data for IDO-1 and PDL-2 expression in adrenocortical carcinoma
DOI: 10.17632/878bddysry.2
title: Data for: Protective efficacy of peptides from Plasmodium vivax circumsporozoite protein

description: Vivax malaria is a major cause of morbidity and mortality worldwide, with several million clinical cases per year and 2.5 billion at risk of infection. A vaccine is urgently needed but the most advanced malaria vaccine, VMP001, confers only very low levels of protection against vivax malaria challenge in humans. VMP001 is based on the circumsporozoite protein (CSP) of Plasmodium vivax. Here a virus-like particle, Qβ, is used as a platform to generate very high levels of antibody against peptides from PvCSP in mice, in order to answer questions important to further development of P. vivax CSP (PvCSP) vaccines. Minimal peptides from the VK210 and VK247 allelic variants of PvCSP are found to be highly protective as Qβ-peptide vaccines, using transgenic P. berghei parasites expressing the homologous PvCSP allelic variant. A target of neutralising antibodies within the nonamer unit repeat of VK210, AGDR, is found, as a Qβ-peptide vaccine, to provide partial protection against malaria challenge, and enhances protective efficacy when combined with full-length PvCSP vaccination. A truncated form of PvCSP, missing the N-terminal domain, is found to confer much higher levels of protective efficacy than full-length PvCSP. Peptides derived from highly conserved areas of PvCSP, RI and RII, are found not to confer protective efficacy as Qβ-peptide vaccines.
DOI: 10.5281/zenodo.4721974
title: CoVaxxy Tweet IDs data set

description: A collection of Tweet IDs related to Covid-19 Vaccines, gathered from Twitter since Jan 4, 2021. Please see https://arxiv.org/abs/2101.07694 for more information.
DOI: 10.6084/m9.figshare.14489523
title: Gene database of Drosophila melanogaster

description: <i>Drosophila melanogaster</i> is an important fruit fly-based model organism for genetics. This work sought to provide fundamental information about the genetic repertoire of this model organism by parsing its annotated genome sequence downloaded from GenBank. Comprising gene name, gene function, and gene sequence, the database should find use in a variety of workflows seeking to correlate genetic endowment with phenotypic display under varied nutritional and environmental conditions.
DOI: 10.15784/601440
title: NBP1402 JPC43 Diatom Data

description: This dataset includes diatom data, both absolute abundance and relative contribution, for NBP1402 JPC43.
DOI: 10.6084/m9.figshare.14463744
title: gene.fa

description: Caenorhabditis elegans gene
DOI: 10.6084/m9.figshare.14463744.v1
title: gene.fa

description: Caenorhabditis elegans gene
DOI: 10.5281/zenodo.4719173
title: Depth profiles of porosity estimated from electrical resistivity logs at the Nankai Trough

description: This dataset includes depth profiles of porosity estimated from electrical resistivity logs for six sites (sites C0001, C0002, C0004, C0006, C0012, and C0024) at the Nankai Trough. Depth profiles are estimated by Yabe et al. (2020, Earth Planets and Space, doi: 10.1186/s40623-020-01303-1) with the method presented in Yabe et al. (2019, Earth Planets and Space, doi: 10.1186/s40623-019-1097-4). The first column is depth in meters below sea floor (mbsf). The second column is the estimated porosity.
DOI: 10.5281/zenodo.4719172
title: Depth profiles of porosity estimated from electrical resistivity logs at the Nankai Trough

description: This dataset includes depth profiles of porosity estimated from electrical resistivity logs for six sites (sites C0001, C0002, C0004, C0006, C0012, and C0024) at the Nankai Trough. Depth profiles are estimated by Yabe et al. (2020, Earth Planets and Space, doi: 10.1186/s40623-020-01303-1) with the method presented in Yabe et al. (2019, Earth Planets and Space, doi: 10.1186/s40623-019-1097-4). The first column is depth in meters below sea floor (mbsf). The second column is the estimated porosity.
DOI: 10.17608/k6.auckland.13031681
title: Metagenomic data (Gut Bugs Trial)

description: The gut microbiome is a contributing factor in the development of metabolic disorders. The Gut Bugs Trial was conducted to assess the efficacy of using lean multi-donor fecal microbiota transplantation (FMT) to treat adolescents with obesity. <br>The Gut Bugs Trial recruited 87 adolescents with obesity and randomised them 1:1 to receive a single dose of either FMT or placebo capsules. FMT capsules contained concentrated fecal material derived from 4 sex-matched lean donors. Placebo capsules contained saline. Recipients were clinically assessed at baseline, and at 6-, 12-, and 26-weeks post-treatment. The primary objective was a change in BMI SDS at week 6. Secondary objectives included a variety of metabolic health parameters, body composition, and gut microbiome alterations. <br>Microbial DNA was extracted from stool samples collected from donors and recipients throughout the study. Shotgun metagenomic sequencing was performed on 381 samples using an Illumina platform (150bp paired end reads). Raw sequencing files were processed with bioBakery workflows using docker images available at http://huttenhower.sph.harvard.edu/biobakery_workflows. Quality control and pre-processing steps involved removal of adaptor sequences using Trim Galore! followed by removal of low-quality reads and human sequences with KneadData. Taxonomic profiling was performed using MetaPhlAn2; Strain profiling was performed using StrainPhlAn; and functional profiling was performed using HUMAnN2.<br>This dataset contains:(i) Sample metadata(ii) KneadData read count table(iii) MetaPhlAn2 relative abundance table(iv) MetaCyc pathways abundance table (HUMAnN2)(v) SNP haplotype FASTA files (StrainPhlAn)