cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7863008.v1
title: Supplementary Material for: Bariatric Surgery Is a Safe and Effective Option for Patients with Inflammatory Bowel Diseases: A Case Series and Systematic Review of the Literature

description: <b><i>Background:</i></b><i></i> Questions remain regarding both the safety and efficacy of bariatric surgery in patients with inflammatory bowel diseases (IBD), including the effects of bariatric surgery on the course of disease. We report a case series from a tertiary care IBD referral center and review the existing literature regarding the safety and efficacy of bariatric surgery in IBD patients. <b><i>Objectives:</i></b> Examine the safety and efficacy of bariatric surgery in IBD patients. Explore possible effects of weight loss on postoperative IBD course. <b><i>Method:</i></b> We performed a retrospective review of patients at our center undergoing bariatric surgery with a concurrent IBD diagnosis, collecting baseline characteristics, surgery type, and postoperative course (including IBD outcomes and weight loss). Data from these patients were combined with available data from the existing literature to calculate standardized means with standard error, variance, and confidence intervals (CI). <b><i>Results:</i></b> Data from 13 patients who had undergone bariatric surgery at our facility were combined with data from 8 other studies to create a study population of 101 patients. Of these, 61 had Crohn’s disease, 37 ulcerative colitis, and 3 IBD-unspecified, with a mean preoperative BMI of 44.2 (95% CI 42.9–45.7). Following surgery, a mean excess weight loss of 68.4% was demonstrated (95% CI, 65.7–71.2). Of the 101 patients, 22 experienced early and 20 experienced late postoperative complications. Postoperatively, 10 patients experienced a flare of IBD, 20 remained in remission, and 7 patients were able to discontinue immunosuppressive therapy. <b><i>Conclusions:</i></b> Based on available studies, bariatric surgery appears to be both an effective and safe option for weight loss in patients with IBD.
DOI: 10.6084/m9.figshare.7863065.v1
title: What is important for the sustained implementation of evidence-based brief psychotherapy interventions in psychiatric care? A quantitative evaluation of a real-world programme

description: <b>Purpose:</b> Behavioural activation and motivational interviewing, both evidence-based treatments (EBTs), were implemented in secondary psychiatric care. This longitudinal evaluation of a real-world programme focused on the penetration of EBT adoption and its associations with therapist-related and perceived intervention-related variables. The implementation plan was also compared to sub-processes of Normalization Process Theory. <b>Material and methods:</b> Six participating units employed 72 therapists regularly and they comprise the target group. Due to staff turnover, a total of 84 therapists were trained stepwise. Three survey points (q1, q2, q3) were set for a four-year cycle beginning a year after the initial training and completed 4–5 months after closing patient recruitment. The implementation plan included two workshop days, one for each EBT, and subsequent case consultation groups and other more general strategies. <b>Results:</b> Fifty-seven (68%) of programme-trained therapists responded to one or more of three questionnaires. The self-reported penetration covers about a third of the target group a few months after the completion of the programme. Therapists' favourable perceptions of the EBTs regarding relative advantage, compatibility and complexity were associated with their sustained adoption. Therapists’ background factors (e.g. work experience) and positive adoption intention at q1 did not predict the actual adoption of the EBTs at q3. No specific sustainment strategies were included in the implementation plan. <b>Conclusion:</b> Brief but multi-faceted training with subsequent case consultations promoted the adoption of EBTs in a real-world setting. Adding specific sustainment strategies to the implementation plan is proposed to ensure the long-term survival of the implementation outcomes. <b>Trial registration:</b>ClinicalTrials.gov identifier: NCT02520271.
DOI: 10.6084/m9.figshare.7862936
title: Whole-genome sequences of 9 African samples

description: This is the medatada associated with the European Nucleotide Archive (ENA) entry PRJEB28198.<br>We sequenced 9 blood samples from different African populations on an Illumina HiSeq2000 sequencing platform. <br>An in depth analysis of these and 16 other African sequences is included in "Whole-genome sequence analysis of a Pan African set of samples reveals archaic gene flow from an extinct basal population of modern humans into sub-Saharan populations", to be published in Genome Biology.
DOI: 10.6084/m9.figshare.12881519
title: Drosophila innubila genome

description: The genome is fasta format for Drosophila innubila, as well as the annotation of genes and repeats
DOI: 10.6084/m9.figshare.12881519.v1
title: Drosophila innubila genome

description: The genome is fasta format for Drosophila innubila, as well as the annotation of genes and repeats
DOI: 10.6084/m9.figshare.7862909
title: Transects times

description: Times elapsed in the visits to the transects during the 2016 and 2017 campaigns.
DOI: 10.6084/m9.figshare.7862909.v1
title: Transects times

description: Times elapsed in the visits to the transects during the 2016 and 2017 campaigns.
DOI: 10.25345/c5s469
title: MassIVE MSV000086029 - 1_HILIC LC MS_MS of 244 fecal samples of infants_part II
title: Sillner et al. : Longitudinal profiles of dietary and microbial metabolites in formula- and breastfed infants - https://doi.org/10.1101/2020.05.11.086546 HILIC LC-MS/MS for generating non-targeted metabolomics data of 244 fecal samples of infants during first year of life and a follow-up (24 month) Data dependent AutoMSMS of maXis in negative ionisation mode with 35eV collision energy
DOI: 10.6084/m9.figshare.7862699
title: Raw seq data quality control

description: ZIP archive with FastQC-generated quality reports for the short-read libraries used in the assembly and annotation
DOI: 10.6084/m9.figshare.7862699.v1
title: Raw seq data quality control

description: ZIP archive with FastQC-generated quality reports for the short-read libraries used in the assembly and annotation
DOI: 10.6084/m9.figshare.7862693
title: Danionella exome annotation

description: GFF exon annotation file for Danionella
DOI: 10.6084/m9.figshare.7862696
title: Zebrafish exome annotation

description: Ensembl annotation of Zebrafish exome
DOI: 10.6084/m9.figshare.7862687
title: Intron size distribution code.

description: MATLAB code to generate intron size distribution plots.
DOI: 10.6084/m9.figshare.7862690
title: Danionella - Zebrafish orthologs list, removed duplicate Zebrafish hits

description: ortholog protein file with removed duplicate Zebrafish hits.
DOI: 10.6084/m9.figshare.7862696.v1
title: Zebrafish exome annotation

description: Ensembl annotation of Zebrafish exome
DOI: 10.6084/m9.figshare.7862810.v1
title: Improving Spectral Clustering using the Asymptotic Value of the Normalised Cut

description: Spectral clustering is a popular and versatile clustering method based on a relaxation of the normalised graph cut objective. Despite its popularity, selecting the number of clusters and tuning the important scaling parameter remain challenging problems in practical applications of spectral clustering. Popular heuristics have been proposed, but corresponding theoretical results are scarce. In this paper we investigate the asymptotic value of the normalised cut for an increasing sample assumed to arise from an underlying probability distribution. Based on this, we find strong connections between spectral and density clustering. This enables us to provide recommendations for selecting the number of clusters and setting the scaling parameter in a data driven manner. An algorithm inspired by these recommendations is proposed, which we have found to exhibit strong performance in a range of applied domains. An R implementation of the algorithm is available from https://github.com/DavidHofmeyr/spuds.
DOI: 10.6084/m9.figshare.7862684
title: Danionella - Zebrafish orthologs list

description: Tab-separated values file with the CRB-BLAST generated ortholog proteins between zebrafish and DT.
DOI: 10.6084/m9.figshare.7862687.v1
title: Intron size distribution code.

description: MATLAB code to generate intron size distribution plots.
DOI: 10.6084/m9.figshare.7862693.v1
title: Danionella exome annotation

description: GFF exon annotation file for Danionella
DOI: 10.6084/m9.figshare.7862690.v1
title: Danionella - Zebrafish orthologs list, removed duplicate Zebrafish hits

description: ortholog protein file with removed duplicate Zebrafish hits.
DOI: 10.6084/m9.figshare.7862639
title: MAKER-predicted proteins

description: FASTA file with functionally annotated MAKER-derived protein sequences.
DOI: 10.6084/m9.figshare.7862642
title: MAKER-predicted transcripts

description: FASTA file with functionally annotated MAKER-derived transcript sequences.
DOI: 10.6084/m9.figshare.7862684.v1
title: Danionella - Zebrafish orthologs list

description: Tab-separated values file with the CRB-BLAST generated ortholog proteins between zebrafish and DT.
DOI: 10.6084/m9.figshare.7862639.v1
title: MAKER-predicted proteins

description: FASTA file with functionally annotated MAKER-derived protein sequences.
DOI: 10.6084/m9.figshare.7862642.v1
title: MAKER-predicted transcripts

description: FASTA file with functionally annotated MAKER-derived transcript sequences.
DOI: 10.6084/m9.figshare.7862570
title: Pulse Wave Database: version submitted for peer review

description: This provides a link to the version of the Pulse Wave Database which was made available through PhysioNet for the purposes of peer review.
DOI: 10.6084/m9.figshare.7862546
title: Loss of reticulocalbin 2 lowers blood pressure and restrains angiotensin II-induced hypertension in vivo

description: <b>All data associated with the manuscript entitled "</b><b>Loss of reticulocalbin 2 lowers blood pressure and restrains angiotensin II-induced hypertension in vivo" are included in this file. </b>
DOI: 10.17633/rd.brunel.7862522
title: A high-efficiency 2-stroke engine concept: Boosted Uniflow Scavenged Direct Injection Gasoline (BUSDIG) engine with the air hybrid operation

description: The newly generated data used in the following paper is archived here:<br>Wang, X. and Zhao, H., "A high-efficiency 2-stroke engine concept: Boosted Uniflow Scavenged Direct Injection Gasoline (BUSDIG) engine with the air hybrid operation". Engineering. 2019. Accepted.<br>The descriptions for each data are listed in "captions.docx". All the referenced data are achieved in the following links:https://doi.org/10.17633/rd.brunel.5414059.v1https://doi.org/10.17633/rd.brunel.5383951.v1https://doi.org/10.17633/rd.brunel.5371525.v1https://doi.org/10.17633/rd.brunel.5195731.v1https://doi.org/10.17633/rd.brunel.4565158.v1
DOI: 10.6084/m9.figshare.7862546.v1
title: Loss of reticulocalbin 2 lowers blood pressure and restrains angiotensin II-induced hypertension in vivo

description: <b>All data associated with the manuscript entitled "</b><b>Loss of reticulocalbin 2 lowers blood pressure and restrains angiotensin II-induced hypertension in vivo" are included in this file. </b>
DOI: 10.17633/rd.brunel.7862522.v1
title: A high-efficiency 2-stroke engine concept: Boosted Uniflow Scavenged Direct Injection Gasoline (BUSDIG) engine with the air hybrid operation

description: The newly generated data used in the following paper is archived here:<br>Wang, X. and Zhao, H., "A high-efficiency 2-stroke engine concept: Boosted Uniflow Scavenged Direct Injection Gasoline (BUSDIG) engine with the air hybrid operation". Engineering. 2019. Accepted.<br>The descriptions for each data are listed in "captions.docx". All the referenced data are achieved in the following links:https://doi.org/10.17633/rd.brunel.5414059.v1https://doi.org/10.17633/rd.brunel.5383951.v1https://doi.org/10.17633/rd.brunel.5371525.v1https://doi.org/10.17633/rd.brunel.5195731.v1https://doi.org/10.17633/rd.brunel.4565158.v1
DOI: 10.6084/m9.figshare.7862444
title: Springer Nature Librarians 2018 survey

description: Raw data from Springer Nature's 2018 survey of librarians, on their roles, challenges and engagement with faculty. Methodology at https://docs.google.com/document/d/1d1y9Y7mzV7YUGXKFylmfIBfCfrnNwwhDT-QG8RsDzmY/edit?usp=sharing
DOI: 10.6084/m9.figshare.7862216
title: Supplementary Material for: What Do NICU Fellows Identify as Important for Achieving Competency in Neonatal Intubation?

description: <b><i>Background:</i></b> Tracheal intubation (TI) is one of the most important interventions for the stabilization of critically ill neonates. Competency in airway management is essential for neonatal fellows. No studies have assessed which educational models, techniques, or instructions are perceived by neonatal fellows as the most beneficial for achieving competency in TI. <b><i>Objectives:</i></b> This study identifies which factors are considered most helpful in achieving intubation competency. <b><i>Method:</i></b> This was a mixed-method study. Semi-structured phone interviews addressed training experience for neonatal intubation. Through qualitative analysis, common themes were identified. RedCap electronic surveys and procedure logs were used to assess procedural experience. <b><i>Results:</i></b> Forty-two fellows from 5 programs completed phone interviews. Fellows recalled 6–10 intubation attempts before fellowship. Independent statements related to achieving intubation competency were analyzed and coded into 5 main themes (Procedure, Practice, Perceptual Environment, Personnel, and Preparation). A large proportion of the statements focused on the use of video laryngoscopy. <b><i>Conclusions:</i></b> The themes identified by neonatal-perinatal medicine (NPM) fellows as being the most beneficial in achieving proficiency in neonatal TI are categorized as “The 5 Ps.” Careful review of these themes may be utilized to develop validated curriculums that enhance the teaching of TI and optimize the achievement of TI competency among NPM fellows.
DOI: 10.6084/m9.figshare.7862192
title: Data tables for Inia araguaiaensis acoustic signals

description: Data tables for Inia araguaiaensis acoustic signals, including the results of the ARTwarp analysis, and the table used to built the rarefaction curve and Whittaker diagram.
DOI: 10.6084/m9.figshare.7862192.v1
title: Data tables for Inia araguaiaensis acoustic signals

description: Data tables for Inia araguaiaensis acoustic signals, including the results of the ARTwarp analysis, and the table used to built the rarefaction curve and Whittaker diagram.
DOI: 10.6084/m9.figshare.12881525
title: DiNV genome

description: The genome and annotation of Drosophila innubila nudivirus in fata format
DOI: 10.6084/m9.figshare.7862153
title: Partial Mechanical Restraint video files of juvenile Japanese quail (first half)

description: Partial Mechanical Restraint was performed on juvenile Japanese quail (40 days of age). Test consisted in restricting the movement of the animal between two walls of a melamine box of 20 x 10 cm (height per width, respectively) with the characteristic that the front wall was made of glass, and the back wall was adjustable to induce immobility in such a way that the animal cannot open the wings, but can move the head and legs. The experimenters retreated out of the birds' sight, and the test was during 5 minutes recorded with a video camera place in front of the box. All the birds were tested in 31 batches of 4 animals each, where the birds had no visual or physical contact between each other. File name includes the ID number of the four birds tested.
DOI: 10.6084/m9.figshare.7862126
title: Supplementary Data from Increased frequency of travel in the presence of cross-immunity may act to decrease the chance of a global pandemic

description: The high frequency of modern travel has led to concerns about a devastating pandemic since a lethal pathogen strain could spread worldwide quickly. Many historical pandemics have arisen following pathogen evolution to a more virulent form. However, some pathogen strains invoke immune responses that provide partial cross-immunity against infection with related strains. Here, we consider a mathematical model of successive outbreaks of two strains—a low virulence (LV) strain outbreak followed by a high virulence (HV) strain outbreak. Under these circumstances, we investigate the impacts of varying travel rates and cross-immunity on the probability that a major epidemic of the HV strain occurs, and the size of that outbreak. Frequent travel between subpopulations can lead to widespread immunity to the HV strain, driven by exposure to the LV strain. As a result, major epidemics of the HV strain are less likely, and can potentially be smaller, with more connected subpopulations. Cross-immunity may be a factor contributing to the absence of a global pandemic as severe as the 1918 influenza pandemic in the century since.This article is part of the theme issue ‘Detection, forecasting and control of infectious disease epidemics: modelling outbreaks in humans, animals and plants Part 1’.
DOI: 10.6084/m9.figshare.7862117
title: Observational and weather data from Predicting plant disease epidemics from functionally represented weather series

description: A RData file with the data for fitting all models in Predicting plant disease epidemics from functionally-represented weather series
DOI: 10.6084/m9.figshare.7862120
title: README for supplementary material to Predicting plant disease epidemics from functionally-represented weather series from Predicting plant disease epidemics from functionally represented weather series

description: Descriptions of each of the supplementary files
DOI: 10.6084/m9.figshare.7862126.v1
title: Supplementary Data from Increased frequency of travel in the presence of cross-immunity may act to decrease the chance of a global pandemic

description: The high frequency of modern travel has led to concerns about a devastating pandemic since a lethal pathogen strain could spread worldwide quickly. Many historical pandemics have arisen following pathogen evolution to a more virulent form. However, some pathogen strains invoke immune responses that provide partial cross-immunity against infection with related strains. Here, we consider a mathematical model of successive outbreaks of two strains—a low virulence (LV) strain outbreak followed by a high virulence (HV) strain outbreak. Under these circumstances, we investigate the impacts of varying travel rates and cross-immunity on the probability that a major epidemic of the HV strain occurs, and the size of that outbreak. Frequent travel between subpopulations can lead to widespread immunity to the HV strain, driven by exposure to the LV strain. As a result, major epidemics of the HV strain are less likely, and can potentially be smaller, with more connected subpopulations. Cross-immunity may be a factor contributing to the absence of a global pandemic as severe as the 1918 influenza pandemic in the century since.This article is part of the theme issue ‘Detection, forecasting and control of infectious disease epidemics: modelling outbreaks in humans, animals and plants Part 1’.
DOI: 10.6084/m9.figshare.7862114
title: Modelling background and fitted model statistics from Predicting plant disease epidemics from functionally represented weather series

description: A html file produced from running the Markdown script for Predicting plant disease epidemics from functionally-represented weather series
DOI: 10.6084/m9.figshare.7862120.v1
title: README for supplementary material to Predicting plant disease epidemics from functionally-represented weather series from Predicting plant disease epidemics from functionally represented weather series

description: Descriptions of each of the supplementary files
DOI: 10.6084/m9.figshare.7862111
title: Code for model fitting from Predicting plant disease epidemics from functionally represented weather series

description: R Markdown script for reproducing all analyses in Predicting plant disease epidemics from functionally-represented weather series
DOI: 10.6084/m9.figshare.7862111.v1
title: Code for model fitting from Predicting plant disease epidemics from functionally represented weather series

description: R Markdown script for reproducing all analyses in Predicting plant disease epidemics from functionally-represented weather series
DOI: 10.6084/m9.figshare.7862114.v1
title: Modelling background and fitted model statistics from Predicting plant disease epidemics from functionally represented weather series

description: A html file produced from running the Markdown script for Predicting plant disease epidemics from functionally-represented weather series
DOI: 10.6084/m9.figshare.7862087
title: Data Collected from Incorporating intraspecific variation into dental microwear texture analysis

description: This spreadsheet contains all data collected, summary statistics and results of Liner Mixed-Effect modelling.
DOI: 10.6084/m9.figshare.7862081
title: Scripts used in modelling DMTA data from Incorporating intraspecific variation into dental microwear texture analysis

description: R scripts used in this manuscript. Specifically the sections on subsampling and Linear Mixed-Effect Modelling
DOI: 10.6084/m9.figshare.7862087.v1
title: Data Collected from Incorporating intraspecific variation into dental microwear texture analysis

description: This spreadsheet contains all data collected, summary statistics and results of Liner Mixed-Effect modelling.
DOI: 10.6084/m9.figshare.7862072
title: <i>Tupelocetus palmeri</i>, a new species of protocetid whale (Mammalia, Cetacea) from the middle Eocene of South Carolina

description: We describe <i>Tupelocetus palmeri</i>, a new genus and species of archaeocete whale, based on a single specimen from the Cross Member of the middle Eocene Tupelo Bay Formation (Bartonian). The holotype consists of a partial cranium with complete petrosals, posterior processes of tympanics, the posterior ends of the nasals, a part of the right orbit, and what are interpreted as the right and left P2s. The incomplete skull was collected from the Martin Marietta Cross Quarry (Berkeley County, South Carolina), which has also furnished the holotype of <i>Carolinacetus gingerichi</i>. The new species differs from all other protocetids in having a deep cavity on the occiput, as well as having the following combination of features: large nasal processes of frontals, single-cusped P2, and premaxilla terminates at level of P2 or P3. A phylogenetic analysis places <i>T. palmeri</i> in a large polytomy along the cetacean stem, more closely related to crown Cetacea than <i>Maiacetus</i>, <i>Artiocetus</i>, and <i>Rodhocetus</i>, but more basal than <i>Georgiacetus</i>, <i>Babiacetus</i>, and <i>Eocetus</i>. Another member of this polytomy is <i>Natchitochia jonesi</i>, and although specimens of <i>Natchitochia</i> and <i>T. palmeri</i> do not share any elements, what is preserved suggests that they are similar in size and among the largest of all protocetids. Although we are unable to differentiate these two species, we outline future data that could resolve this question.