cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13889819.v1
title: Incubation onset influences parental investment in eggs and offspring survival in an altricial bird

description: The dataset used in 'Incubation onset influences parental investment in eggs and offspring survival in an altricial bird'.
DOI: 10.5281/zenodo.4708800
title: LOLA11

description: Data belonging to https://lola11.grand-challenge.org/ See license.txt for the data usage rules.
DOI: 10.5281/zenodo.4708799
title: LOLA11

description: Data belonging to https://lola11.grand-challenge.org/ See license.txt for the data usage rules.
DOI: 10.25919/kmr8-d253
title: Parkes observations for project P1038 semester 2021APRS_01

description: PSR~J1759-2402 is one of a small handful of pulsars which are in orbit about high mass stars. Its orbital period is 8.3 years and the orbit is highly eccentric with periastron expected in 2021 March. Although discovered at Parkes, the Lovell telescope has been monitoring the pulsar over many years. However, it’s restricted bandwidth, maintenance schedule and poorer polarization capability make it unsuitable to follow the pulsar as it enters and leaves the eclipse by the companion. In contrast, the UWL on Parkes with its wide- band and excellent polarization characteristics means that we can, and already have determined scattering, polarization, dispersion measure and rotation measure changes as the pulsar enters its companion wind. We request a continuation of our weekly observations of the pulsar to track its progress on the far side of periastron.
DOI: 10.5281/zenodo.4709059
title: Reanalysis of Reynolds 2021 dataset

description: In this repo, we upload the AnnData files necessary for the analysis of Reynolds et al. (2021) dataset. Additionally, we include the Jupyter notebook files used during the analysis, with the cells run to see the results.
DOI: 10.5281/zenodo.4703188
title: The radar-based data and WRF run-files on the convection initiation on Hainan Island in Zhu et al. (2021)

description: <strong>Radar-based data and WRF run-files on the convection initiation on Hainan Island in a manuscript titled "Convection Initiation Associated with Ambient Winds and Local Circulations Over a Tropical Island in South China".</strong> The file <strong>"</strong>Hainan_wrf_files_moist_high_wind.tar.gz" is used to run simulation under high-wind conditions. The file <strong>"</strong>Hainan_wrf_files_moist_low_wind.tar.gz" is used to run simulation under low-wind conditions. The file<strong> "</strong>Radar_based_data_for_Hainan_CI_daily_frequency.tar.gz" is the radar-based data.
DOI: 10.5281/zenodo.4703187
title: The radar-based data and WRF run-files on the convection initiation on Hainan Island in Zhu et al. (2021)

description: <strong>Radar-based data and WRF run-files on the convection initiation on Hainan Island in a manuscript titled "Convection Initiation Associated with Ambient Winds and Local Circulations Over a Tropical Island in South China".</strong> The file <strong>"</strong>Hainan_wrf_files_moist_high_wind.tar.gz" is used to run simulation under high-wind conditions. The file <strong>"</strong>Hainan_wrf_files_moist_low_wind.tar.gz" is used to run simulation under low-wind conditions. The file<strong> "</strong>Radar_based_data_for_Hainan_CI_daily_frequency.tar.gz" is the radar-based data.
DOI: 10.17037/data.00002168
title: Survey data on willingness to participate in COVID-19 vaccine trials among healthcare workers in three Ugandan hospitals

description: Survey data collected as part of a study to investigate willingness to participate in COVID-19 vaccine trials among healthcare workers. Survey was completed by 657 healthcare workers in three hospitals in Uganda. The dataset contains variables on socio-demographic information, willingness to participate in a COVID-19 vaccine trial, motivators and barriers to participation, and the effect of different hypothetical trial characteristics on willingness to participate.
DOI: 10.5281/zenodo.4709121
title: Savanna-forest coexistence across a fire gradient

description: Data accompanying the paper: Bernardino, P. N., Dantas, V. L., Hirota, M., Pausas, J. G. and Oliveira, R. S (2021). Savanna-forest coexistence across a fire gradient. Ecosystems.
DOI: 10.5281/zenodo.3338147
title: Savanna-forest coexistence across a fire gradient

description: Data accompanying the paper: Bernardino, P. N., Dantas, V. L., Hirota, M., Pausas, J. G. and Oliveira, R. S (2021). Savanna-forest coexistence across a fire gradient. Ecosystems.
DOI: 10.6084/m9.figshare.13636577
title: Supporting data for "Genomic contextualisation of ancient DNA molecular data from an Argentinian fifth pandemic Vibrio cholerae infection"

description: Specific lineages of serogroup O1 <i>Vibrio cholerae </i>are notorious for causing cholera pandemics, of which there have been seven since the 1800s. Much is known about the sixth pandemic (1899-1923) and the ongoing seventh pandemic (1961-present), but we know very little about the bacteriology of pandemics 1 to 5. Moreover, although we are learning about the contribution of non-O1 non-pandemic <i>V. cholerae</i> to cholera dynamics during the current pandemic, we know almost nothing about their role in the past. A recent ancient DNA study has presented what may be the first molecular evidence of a <i>V. cholerae </i>infection from the fifth cholera pandemic period (1886-1887 AD) in Argentina. Here, we place the molecular evidence from that study into the genomic context of non-pandemic <i>V. cholerae</i> from Latin America and elsewhere, and show that a gene fragment amplified from ancient DNA is most similar to that of <i>V. cholerae</i> from the Americas, and from Argentina. Our results corroborate and reinforce the findings of the original study, and collectively suggest that even in the 1880s, non-pandemic <i>V. cholerae</i> local to the Americas may have caused sporadic infections in Argentina, just as we know to have happened during the seventh pandemic in Latin America.
DOI: 10.6084/m9.figshare.13636577.v1
title: Supporting data for "Genomic contextualisation of ancient DNA molecular data from an Argentinian fifth pandemic Vibrio cholerae infection"

description: Specific lineages of serogroup O1 <i>Vibrio cholerae </i>are notorious for causing cholera pandemics, of which there have been seven since the 1800s. Much is known about the sixth pandemic (1899-1923) and the ongoing seventh pandemic (1961-present), but we know very little about the bacteriology of pandemics 1 to 5. Moreover, although we are learning about the contribution of non-O1 non-pandemic <i>V. cholerae</i> to cholera dynamics during the current pandemic, we know almost nothing about their role in the past. A recent ancient DNA study has presented what may be the first molecular evidence of a <i>V. cholerae </i>infection from the fifth cholera pandemic period (1886-1887 AD) in Argentina. Here, we place the molecular evidence from that study into the genomic context of non-pandemic <i>V. cholerae</i> from Latin America and elsewhere, and show that a gene fragment amplified from ancient DNA is most similar to that of <i>V. cholerae</i> from the Americas, and from Argentina. Our results corroborate and reinforce the findings of the original study, and collectively suggest that even in the 1880s, non-pandemic <i>V. cholerae</i> local to the Americas may have caused sporadic infections in Argentina, just as we know to have happened during the seventh pandemic in Latin America.
DOI: 10.6084/m9.figshare.12478700
title: Datasets and supplemental information for: Modified Band Alignment Method to Obtain Hybrid Functional Accuracy from Standard DFT: Application to Defects in Highly Mismatched III-V:Bi Alloys.

description: Datasets and supplemental information for paper: <br>Modified Band Alignment Method to Obtain Hybrid Functional Accuracy from Standard DFT: Application to Defects in Highly Mismatched III-V:Bi Alloys.<br><br>by Maciej P. Polak, Robert Kudrawiec, Ryan Jacobs, Izabela Szlufarska, and Dane Morgan<br>Published in:<br><br>
DOI: 10.6084/m9.figshare.12478700.v2
title: Datasets and supplemental information for: Modified Band Alignment Method to Obtain Hybrid Functional Accuracy from Standard DFT: Application to Defects in Highly Mismatched III-V:Bi Alloys.

description: Datasets and supplemental information for paper: <br>Modified Band Alignment Method to Obtain Hybrid Functional Accuracy from Standard DFT: Application to Defects in Highly Mismatched III-V:Bi Alloys.<br><br>by Maciej P. Polak, Robert Kudrawiec, Ryan Jacobs, Izabela Szlufarska, and Dane Morgan<br>Published in:<br><br>
DOI: 10.6084/m9.figshare.14464767
title: Supplementary Material for: Shifts in the Skin Microbiota after UVB Treatment in Adult Atopic Dermatitis

description: <b><i>Background:</i></b> The pathophysiology in atopic dermatitis (AD) is not fully understood, but immune dysfunction, skin barrier defects, and alterations of the skin microbiota are thought to play important roles. AD skin is frequently colonized with <i>Staphylococcus aureus</i> (<i>S. aureus</i>) and microbial diversity on lesional skin (LS) is reduced compared to on healthy skin. Treatment with narrow-band ultraviolet B (nb-UVB) leads to clinical improvement of the eczema and reduced abundance of <i>S. aureus</i>. However, in-depth knowledge of the temporal dynamics of the skin microbiota in AD in response to nb-UVB treatment is lacking and could provide important clues to decipher whether the microbial changes are primary drivers of the disease, or secondary to the inflammatory process. <b><i>Objectives:</i></b> To map the temporal shifts in the microbiota of the skin, nose, and throat in adult AD patients after nb-UVB treatment. <b><i>Methods:</i></b> Skin swabs were taken from lesional AD skin (<i>n</i> = 16) before and after 3 treatments of nb-UVB, and after 6–8 weeks of full-body treatment. We also obtained samples from non-lesional skin (NLS) and from the nose and throat. All samples were characterized by 16S rRNA gene sequencing. <b><i>Results:</i></b> We observed shifts towards higher diversity in the microbiota of lesional AD skin after 6–8 weeks of treatment, while the microbiota of NLS and of the nose/throat remained unchanged. After only 3 treatments with nb-UVB, there were no significant changes in the microbiota. <b><i>Conclusion:</i></b> Nb-UVB induces changes in the skin microbiota towards higher diversity, but the microbiota of the nose and throat are not altered.
DOI: 10.6084/m9.figshare.14464839
title: Information on surveyed populations and stomach contents from two mainland Speleomantes: data from summer 2020

description: 565 salamanders stomach contents of two European cave salamanders (Hydromantes strinatii and H. ambrosii), subdivided in 313 individuals with empty stomach, 37 with non-recognizable contents, and 215 individuals with full stomach, including information on 978 recognized prey items.
DOI: 10.6084/m9.figshare.14464818
title: Supplementary Material for: Kisspeptin Levels in Girls with Precocious Puberty: A Systematic Review and Meta-Analysis

description: <b><i>Background/Aims:</i></b> Kisspeptin (KP) is a key player in the regulation of the release of gonadotropin-releasing hormone (GnRH), which increases the secretion of gonadotropin during puberty to establish reproductive function and regulate the hypothalamic-pituitary-gonadal axis. Premature activation of GnRH secretion leads to idiopathic/central gonadotropin-dependent precocious puberty (CPP). We aimed to compare the blood KP concentrations in girls with CPP and healthy controls. <b><i>Methods:</i></b> A systematic review and meta-analysis was performed. We searched MEDLINE, EMBASE, The Cochrane Library, and SciELO. Random-effects model and standardized mean difference (SMD) were used. Heterogeneity was assessed through <i>I</i><sup>2</sup>. Meta-regression considered patient age, KP fraction, and analytical method for KP measurement. <b><i>Results:</i></b> The 11 studies included comprised 316 CPP patients and 251 controls. Higher KP levels in the CPP group were found (SMD 1.53; CI 95% = 0.56–2.51). Subgroup analysis revealed association with patient age (<i>p</i> = 0.048), indicating a positive correlation between elevation in KP concentration and age in CPP group. A group of patients with precocious thelarche (PT) from 5 of the included studies comprising 121 patients showed higher levels of KP (1.10; −0.25–2.45: CI 95%) and high heterogeneity (<i>I</i><sup>2</sup> = 91%). The CPP/PT ratio for KP level indicates KP 36% higher on CPP than PT patients. <b><i>Conclusions:</i></b> A consistent difference in KP levels between girls with CPP and controls was identified. While there are important limitations in KP assays which argue against its use as a diagnostic tool, the KP levels in CPP versus control and PT children are consistent with the predicted mechanisms and pathophysiology of CPP.
DOI: 10.5519/qd.kcbxdwq4
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (435 records)
DOI: 10.25919/rc75-6n22
title: Parkes observations for project P885 semester 2021APRS_01

description: We propose to continue observing the magnetars 1E 1547.0-5408 and PSR J1622-4950 weekly, to track their rotation, flux density, and polarisation. The revolutionary UWL capabilities promise new opportunities to disentangle still mysterious radio emission mechanisms in magnetars. This promise is supported by the recent follow up of XTE J1810-197, again a radio magnetar after 10 years dormant, and of the hot-off-the-press magnetar Swift J1818.0-1607, for which our exciting recent results with UWL motivate an increased monitoring cadence to once weekly.
DOI: 10.6084/m9.figshare.14464743
title: Kass-et-al-2021-MEE-ENMeval_v2-Appendix3

description: In the paper, we describe a literature review we conducted of articles citing ENMeval to understand how the package has been used and inform recommendations for the use of version 2.0. We had searched Web of Science (accessed June 2019) for articles that cited the original publication from October 2015 to May 2019. The search returned 214 studies, and of these we reviewed a total of 182 ( some were omitted due to access constraints).<br><br>This comma-separated values (.csv) file contains the date of publication, citation, and DOI for all publications we reviewed in the paper.<br>
DOI: 10.6084/m9.figshare.14464965
title: Supplementary Material for: Outcomes of Interleukin-2 Receptor Antagonist Induction Therapy in Standard-Risk Renal Transplant Recipients Maintained on Tacrolimus: A Systematic Review and Meta-Analysis

description: <b><i>Introduction:</i></b> The additive benefit of interleukin-2 receptor antagonist (IL2-RA) induction in standard-risk kidney transplant recipients, while maintained on tacrolimus-based immunosuppressive therapy, is uncertain. <b><i>Methods:</i></b> We divided the studies included in this meta-analysis into 2 groups: group A (included studies that used same dose of tacrolimus in both arms of each study) and group B (included studies that compared patients who received induction therapy and low-dose tacrolimus vs. those who received no-induction therapy and high dose of tacrolimus). <b><i>Results:</i></b> In group A, 11 studies were included (<i>n</i> = 2,886). IL2-RA induction therapy was not associated with significant differences in comparison to no-induction therapy in terms of acute rejection rates at 6 months post-transplant (risk ratio = 1.12 and 95% confidence interval [CI] range: 0.94–1.35) or graft survival at 1 year post-transplant (risk ratio = 0.78 and 95% CI range: 0.45–1.36). In group B, 2 studies were included (<i>n</i> = 669). There was no difference between both arms in terms of acute rejection rates (risk ratio = 0.62, with 95% CI range: 0.33–1.14) or graft survival (risk ratio = 1 and 95% CI range: 0.57–1.74). <b><i>Conclusion:</i></b> IL2-RA induction therapy does not improve outcomes in patients maintained on tacrolimus-based immunotherapy in standard-risk population.
DOI: 10.6084/m9.figshare.12174102.v1
title: OTU by sample matrices

description: Operational taxonomic unit (OTU) by sample matrices from the publication: Miller et al. 2021 "Land-use intensity affects the potential for apparent competition within and between habitats" in The Journal of Animal Ecology DOI:TBCOTUs comprise arthropod taxa (predominantly herbivorous hosts and parasitoids) and samples are individual herbivores. <br>For further information see publicationData under a CC BY-NC-SA (Attribution-NonCommercial-ShareAlike) licence.
DOI: 10.6084/m9.figshare.12174102
title: OTU by sample matrices

description: Operational taxonomic unit (OTU) by sample matrices from the publication: Miller et al. 2021 "Land-use intensity affects the potential for apparent competition within and between habitats" in The Journal of Animal Ecology DOI:TBCOTUs comprise arthropod taxa (predominantly herbivorous hosts and parasitoids) and samples are individual herbivores. <br>For further information see publicationData under a CC BY-NC-SA (Attribution-NonCommercial-ShareAlike) licence.
DOI: 10.6084/m9.figshare.14034971
title: Adjuvant therapy following neoadjuvant chemotherapy and surgery for oesophageal adenocarcinoma in patients with clear resection margins

description: The role of adjuvant therapy in patients with oesophagogastric adenocarcinoma treated by neoadjuvant chemotherapy (NAC) and surgery is contentious. In UK practice, surgical resection margin status is often used to classify patients into receiving adjuvant treatment. This study aimed to assess any survival benefit of adjuvant therapy in patients with clear resection margins. This was a retrospective collaborative cohort study combining two prospectively collected UK institutional databases of patients with oesophageal adenocarcinoma. Multivariable Cox regression and propensity matched analyses were used to compare overall and recurrence-free survival according to the adjuvant treatment. Of 374 patients with clear resection margins, 221 patients (59%) had no adjuvant treatment, 137 patients (37%) had adjuvant chemotherapy and 16 patients (4%) had adjuvant chemoradiotherapy. For patients who had received NAC (290, 76%), when adjuvant chemotherapy was compared to no adjuvant treatment, hazard ratios (HRs) favoured adjuvant chemotherapy but did not reach independent significance (overall survival [OS] HR 0.65 95% confidence interval [CI] 0.40–1.06; <i>p</i> .0.087). Responders to NAC (Mandard 1–3) were seemingly more likely to demonstrate a survival benefit from adjuvant chemotherapy (HR 0.42 95% CI 0.15–1.11; <i>p</i> .1.081). Although no independent survival benefit was observed, the point estimates favoured adjuvant treatment, predominantly in patients with chemo-responsive tumours.
DOI: 10.6084/m9.figshare.14034971.v1
title: Adjuvant therapy following neoadjuvant chemotherapy and surgery for oesophageal adenocarcinoma in patients with clear resection margins

description: The role of adjuvant therapy in patients with oesophagogastric adenocarcinoma treated by neoadjuvant chemotherapy (NAC) and surgery is contentious. In UK practice, surgical resection margin status is often used to classify patients into receiving adjuvant treatment. This study aimed to assess any survival benefit of adjuvant therapy in patients with clear resection margins. This was a retrospective collaborative cohort study combining two prospectively collected UK institutional databases of patients with oesophageal adenocarcinoma. Multivariable Cox regression and propensity matched analyses were used to compare overall and recurrence-free survival according to the adjuvant treatment. Of 374 patients with clear resection margins, 221 patients (59%) had no adjuvant treatment, 137 patients (37%) had adjuvant chemotherapy and 16 patients (4%) had adjuvant chemoradiotherapy. For patients who had received NAC (290, 76%), when adjuvant chemotherapy was compared to no adjuvant treatment, hazard ratios (HRs) favoured adjuvant chemotherapy but did not reach independent significance (overall survival [OS] HR 0.65 95% confidence interval [CI] 0.40–1.06; <i>p</i> .0.087). Responders to NAC (Mandard 1–3) were seemingly more likely to demonstrate a survival benefit from adjuvant chemotherapy (HR 0.42 95% CI 0.15–1.11; <i>p</i> .1.081). Although no independent survival benefit was observed, the point estimates favoured adjuvant treatment, predominantly in patients with chemo-responsive tumours.
DOI: 10.6084/m9.figshare.14210564.v1
title: Relapse localization in Danish pediatric patients with Hodgkin lymphoma

description: Pediatric Hodgkin lymphoma (pHL) is highly curable. However, a minority experience relapse and are subjected to toxic salvage regimens. Investigating the patterns of relapse could help to select the patients and/or the involved sites that would benefit from consolidating radiotherapy. The Danish Childhood Cancer Registry was used to identify children &lt;18 years with relapsed pHL from 1990–2018. The lymphoma volumes involved at diagnosis and at relapse were contoured on the patients’ original scans. Rigid image co-registration was used to merge the scans enabling a visual assessment of the anatomical relapse localization relative to the initially involved lymph nodes, and if irradiated, to the radiotherapy field. From 185 patients with pHL, 24 patients with relapse were available for analysis. All patients received combination chemotherapy and seven had consolidating radiotherapy. Relapses exclusively in initially involved sites occurred in 14 patients. Relapses exclusively in new sites were rare and only observed in three irradiated patients. Seven patients relapsed in both initially involved and new sites. The median time to relapse was 6 months (range 2–59 months), however, in-field relapses in irradiated patients occurred later (54 months, range 10–59 months). Neither risk group, initial bulky disease, early response, or metabolic activity seemed to be associated with the site of a later relapse. The number of relapses were small, and conclusions regarding the selection of patients for radiotherapy could not be drawn. Relapse exclusively in initially involved sites were the most common, most often in the exact same initially involved lymph nodes. Hence, modern involved site radiotherapy, focusing on the initially involved lymphoma volume and minimizing the radiation doses to normal tissues, should be applied when consolidating radiotherapy is used in patients with pHL.