cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.25093394.v1
title: Brasenia schreberi gene annotations

description: Draft genome of Brasenia schreberi, a worldwide distributed and endangered aquatic plant<br>
DOI: 10.6084/m9.figshare.7174931.v1
title: Matlab code from Nonlinear flexure coupling elements for precision control of multibody systems

description: Code for flexure coupling
DOI: 10.6084/m9.figshare.13794008.v1
title: Emiliania huxleyi pan-transcriptome: mRNA, protein, and annotation

description: This project contains the files of the Emiliania huxleyi pan-transcriptome. It was constructed from Illumina reads of the following strains: CCMP2090, CCMP373, CCMP374.<br>Included are the following files:<br>unified_loci_Ehux_v4_May2020.fasta - one representative transcript per locus<br>unified_transcripts_Ehux_v4_May2020.fasta - all transcripts<br>unified_pep_Ehux_v4_Nov2020.fasta - Blast based translation of loci<br>ehux_kegg_reformat_May2020.txt - KEGG pathway annotation<br>blast2go_ehux_annot.ids - GO term annotation (Ontologizer compatible)<br><br>ehux_blast2go_KEGG_merged.xlsx - joint annotation file (KEGG, GO) for loci<br>snps_hard_filtered.recode.vcf - SNPs called and filtered on the representative transcripts, in four strains (CCMP2090, CCMP373, CCMP374, CCMP379)<br>indel_hard_filtered.recode.vcf - Indels called and filtered on the representative transcripts, in four strains (CCMP2090, CCMP373, CCMP374, CCMP379)<br><br><br><br><br>
DOI: 10.6084/m9.figshare.7886549.v1
title: Counttables

description: Counttables for study
DOI: 10.6084/m9.figshare.9786032.v1
title: C. scutulatus-B SVMP exon annotations

description: This tab-delimited text file contains the SVMP gene complex exon coordinates for the C. scutulatus - B contig112058. Pseudo or orphan exons where known are also reported.
DOI: 10.6084/m9.figshare.12750992.v1
title: Covergent_Evolution_Of_Polyploid_Eukaryotes

description: Dataset of the analysis of 10 polyploidy events from across the eukaryotic ToL using the POInT tool. Includes models, trees, orthologous gene inferences, lists of pairs of reciprocal gene losses (RGLs) and synteny blocks.
DOI: 10.6084/m9.figshare.24265024.v1
title: Supplementary Material for: Changes in network size, quality and composition among informal caregivers in different welfare clusters: Longitudinal analyses based on pan-European survey (SHARE)

description: Introduction: This study analyzed the association between transitions into informal caregiving, inside and outside their own household, and changes in network size, quality and composition among older adults (≥50 years) in four different welfare systems in Europe. Methods: Data from wave 4, 6 and 8 of the Survey of Health, Ageing and Retirement in Europe was used and included up to 110,823 participants (aged ≥50 years) from 12 countries. Participants were asked about informal caregiving inside and outside the household and their network size, quality (emotional closeness, contact frequency) and composition (family, friends, men, women). Adjusted Linear and Poisson Fixed Effects regression analyses were conducted. Results: Participants transitioning into any caregiving (inside or outside the household) had a larger network. More women and family members were found among all those transitioning into caregiving, but only outside caregiving was associated with more men and friends in the network. Transitioning into caregiving outside was associated with reduced network closeness and contact. Changes among caregivers outside were similar in all welfare states, but were more pronounced among caregivers inside the household of Eastern Europe. Discussion/Conclusion: Different patterns of changes in network size, quality and composition were found among adults transitioning into caregiving inside, respective, outside the household. All parameters changed among caregivers outside the household. However, the welfare system played a key role for the network changes among inside household caregivers. Thus, the micro as well as the macro context of caregiving is important for the support network of informal caregivers.
DOI: 10.6084/m9.figshare.5890837.v1
title: Supplementary Material for: The Placental Secretome: Identifying Potential Cross-Talk Between Placenta and Islet β-Cells

description: <b><i>Background/Aims:</i></b> Insulin-secreting islet β-cells adapt to the insulin resistance associated with pregnancy by increasing functional β-cell mass, but the placental signals involved in this process are not well defined. In the current study, we analysed expression of G-protein coupled receptor (GPCR) mRNAs in mouse islets and islet GPCR ligand mRNAs in placenta during pregnancy to generate an atlas of potential interactions between the placenta and β-cells to inform future functional studies of islet adaptive responses to pregnancy. <b><i>Methods:</i></b> Quantative RT-PCR arrays were used to measure mRNA expression levels of: (i) 342 GPCRs in islets from non-pregnant mice, and in islets isolated from mice on gestational days 12 and 18; (ii) 126 islet GPCR ligands in mouse placenta at gestational days 12 and 18. <b><i>Results:</i></b> At gestational day 12, a time of rapid expansion of the β-cell mass, 189 islet GPCR mRNAs were quantifiable, while 79 of the 126 known islet GPCR ligand mRNAs were detectable in placental extracts. Approximately half of the quantifiable placental GPCR ligand genes were of unknown function in β-cells. The expression of some islet GPCR and placental ligand mRNAs varied during pregnancy, with altered expression of both GPCR and ligand mRNAs by gestational day 18. <b><i>Conclusion:</i></b> The current study has revealed numerous potential routes for interaction between the placenta and islets, and offers an atlas to inform further functional studies of their roles in adaptive responses to pregnancy, and in the regulation of the β-cell mass.
DOI: 10.6084/m9.figshare.24936399.v1
title: Replies to a questionnaire Nationwide status of progestogen treatment to prevent spontaneous preterm birth: A questionnaire survey for childbirth healthcare facilities in Japan.xlsx

description: <b>Nationwide status of progestogen treatment to prevent spontaneous preterm birth: A questionnaire survey for childbirth healthcare facilities in Japan</b><b>Aim:</b><b> </b>This study aimed to investigate the current status of progestogen treatment for pregnant women at a high risk for preterm birth in childbirth healthcare facilities in Japan.<b>Methods:</b><b> </b>A web-based nationwide questionnaire survey regarding progestogen use for prevention of preterm birth was conducted among childbirth healthcare facilities from 2019 to 2021.<b>Results:</b><b> </b>Valid responses were obtained from 528 facilities (25.2% of those surveyed), including 155 tertiary perinatal facilities (making up 92.3% of all perinatal care facilities). In the survey period, progestogen treatment was implemented in 207 facilities (39.2%) for preterm birth prevention. Regarding types of progestogens, 17α-hydroxyprogesterone caproate was used in 181 facilities (87.4%), with a low dose (125 mg/week) administered in 56.9% of the facilities to comply with the regulations of the national health insurance system, although 250 mg/week is considered the best dose. Vaginal progesterone was used in 32 facilities (15.4%), although the cost of vaginal progesterone was not covered by health insurance. Of the facilities not administering progestogen treatment, approximately 40% expressed that vaginal progesterone would be their first choice for preterm birth prevention in daily practice if it would be covered by health insurance in the future.<b>Conclusions</b>: Due to the current regulations of the Japanese health insurance system, 17α-hydroxyprogesterone caproate, rather than vaginal progesterone, was mainly used for preterm birth prevention. Despite global evidence supporting vaginal progesterone as the approach with the highest efficacy, only a limited number of facilities have utilized it due to the current drug use regulations in Japan.
DOI: 10.6084/m9.figshare.c.3493548_d21.v1
title: Zipped analysis data files of mother cells cultured at 37C

description: A .zip file containing analysis data files (.txt) of mother cells at 37C (after manual correction of erroneous segmentations)
DOI: 10.6084/m9.figshare.12696509.v1
title: Supplementary Material for: Fitness, Strength and Body Composition during Weight Loss in Women with Clinically Severe Obesity: A Randomised Clinical Trial

description: <b><i>Introduction:</i></b> To determine whether combined exercise training with an energy-restricted diet leads to improved physical fitness and body composition when compared to energy restriction alone in free-living premenopausal women with clinically severe obesity. <b><i>Methods:</i></b> Sixty premenopausal women (BMI of 40.4 ± 6.7) were randomised to energy restriction only (ER) or to exercise plus energy restriction (EXER) for 12 months. Body composition and fitness were measured at baseline, 3, 6 and 12 months. <b><i>Results:</i></b> VO<sub>2 peak</sub> improved more for EXER compared to ER at 3 (mean difference ± SEM 2.5 ± 0.9 mL ∙ kg<sup>–1</sup> ∙ min<sup>–1</sup>, <i>p</i> = 0.006) and 6 (3.1 ± 1.2 mL ∙ kg<sup>–1</sup> ∙ min<sup>–1</sup>, <i>p</i> = 0.007) but not 12 months (2.3 ± 1.6 mL ∙ kg<sup>–1</sup> ∙ min<sup>–1</sup>, <i>p</i> = 0.15). Muscle strength improved more for EXER compared to ER at all time points. No differences between groups for lean mass were observed at 12 months. <b><i>Conclusion:</i></b> Combining exercise training with an energy-restricted diet did not lead to greater aerobic power, total body mass, fat mass or limit lean body mass loss at 12 months when compared to energy restriction alone for premenopausal women with clinically severe obesity in free-living situations. Future research should aim to determine an effective lifestyle approach which can be applied in the community setting for this high-risk group.
DOI: 10.6084/m9.figshare.13689652.v1
title: Supplementary Material for: Renal Sympathetic Denervation Attenuates Congestive Heart Failure in Angiotensin II-Dependent Hypertension: Studies with Ren-2 Transgenic Hypertensive Rats with Aortocaval Fistula

description: <b><i>Objective:</i></b> We examined if renal denervation (RDN) attenuates the progression of aortocaval fistula (ACF)-induced heart failure or improves renal hemodynamics in Ren-2 transgenic rats (TGR), a model of angiotensin II (ANG II)-dependent hypertension. <b><i>Methods:</i></b> Bilateral RDN was performed 1 week after creation of ACF. The animals studied were ACF TGR and sham-operated controls, and both groups were subjected to RDN or sham denervation. In separate groups, renal artery blood flow (RBF) responses were determined to intrarenal ANG II (2 and 8 ng), norepinephrine (NE) (20 and 40 ng) and acetylcholine (Ach) (10 and 40 ng) 3 weeks after ACF creation. <b><i>Results:</i></b> In nondenervated ACF TGR, the final survival rate was 10 versus 50% in RDN rats. RBF was significantly lower in ACF TGR than in sham-operated TGR (6.2 ± 0.3 vs. 9.7 ± 0.5 mL min<sup>−1</sup> g<sup>−1</sup>, <i>p</i> &lt; 0.05), the levels unaffected by RDN. Both doses of ANG II decreased RBF more in ACF TGR than in sham-operated TGR (−19 ± 3 vs. −9 ± 2% and −47 ± 3 vs. −22 ± 2%, <i>p</i> &lt; 0.05 in both cases). RDN did not alter RBF responses to the lower dose, but increased it to the higher dose of ANG II in sham-operated as well as in ACF TGR. NE comparably decreased RBF in ACF TGR and sham-operated TGR, and RDN increased RBF responsiveness. Intrarenal Ach increased RBF significantly more in ACF TGR than in sham-operated TGR (29 ± 3 vs. 17 ± 3%, <i>p</i> &lt; 0.05), the changes unaffected by RDN. ACF creation induced marked bilateral cardiac hypertrophy and lung congestion, both attenuated by RDN. In sham-operated but not in ACF TGR, RDN significantly decreased mean arterial pressure. <b><i>Conclusion:</i></b> The results show that RDN significantly improved survival rate in ACF TGR; however, this beneficial effect was not associated with improvement of reduced RBF or with attenuation of exaggerated renal vascular responsiveness to ANG II.
DOI: 10.6084/m9.figshare.7388777.v1
title: Père David deer gut microbiome

description: <b>Père David deer gut microbiome changes across captive and translocated populations: implications for conservation</b>
DOI: 10.6084/m9.figshare.22056647.v1
title: Introduced and invasive alien species of Antarctica and the Southern Ocean Islands

description: This dataset provides current and comprehensive information available on the identity, localities, establishment, eradication status, dates of introduction, habitat, and evidence of impact of known introduced and invasive alien species for the terrestrial and freshwater Antarctic and Southern Ocean region. It includes 3066 records for 1204 taxa and 36 localities. This dataset is intended to be an updateable, versioned repository for information on the occurrence and status of alien species in the broader Antarctic region. <br> The data fields were populated from a systematic search of the scientific and grey literature between March 2021 and January 2023, including peer-reviewed publications, existing species checklists, and government reports and other documents containing species lists, such as management plans. Information sources are included in four fields in the main dataset: occurrenceReference, eradicationReference, firstRecordReference, and invasiveReference. The values in these reference fields correspond to a full list of resources used to compile the dataset, provided in the “AntarcticAliens_references.csv” file (total 384 sources). <br> A full description of the dataset, data collection and validation methods, and usage notes are provided in the manuscript.
DOI: 10.6084/m9.figshare.7889996.v1
title: gVCF_HG02973

description: 1000 Genomes gVCF mapped to hs37d5 for HG02973. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.16810327.v1
title: S20

description: Data of Subject_20
DOI: 10.6084/m9.figshare.19242810.v1
title: Genetic risk score for plasma uric acid levels is associated with early rapid kidney function decline in type 2 diabetes

description: <b>Abstract</b><b>Context: </b>Observational studies have shown that elevated uric acid (UA) is associated with chronic kidney disease (CKD). However, whether the relationship is causal remains unclear.<b></b><b> </b><b>Objectives </b>: To determine the association of plasma UA and incident CKD and the causal relationship between plasma UA and rapid decline in kidney function (RDKF) in patients with type 2 diabetes (T2D). <b>Design and participants: : </b>Multivariable cox regression was conducted to evaluate the hazard ratio (HR) between plasma UA and incident CKD among 1,300 normoalbuminuric patients in two T2D cohorts (DN=402, SMART2D=898). A weighted genetic risk score (wGRS) was calculated based on ten single nucleotide polymorphism (SNPs) identified in genome-wide association studies of UA in East Asians. Mendelian randomisation (MR) analysis was performed among 1,146 Chinese T2D patients without CKD(estimated glomerular filtration rate (eGFR) &gt;60ml/min/1.73m<sup>2</sup>) at baseline (DN=478, SMART2D=668). The wGRS and individual SNPs were used as genetic instruments and RDKF was defined as eGFR decline of 5ml/min/1.73m<sup>2</sup>/yr or greater. <b>Results : </b>During the mean follow-up of 5.2 and 5.4 years, 81 (9%) and 46 (11%) participants in the SMART2D and DN cohorts developed CKD, respectively. 1-SD increment in plasma UA conferred higher risk of incident CKD (DN, adjusted-HR=1.40, 95%CI 1.02-1.91, P=0.036; SMART2D, adjusted-HR=1.31, 95%CI 1.04-1.64, P=0.018). Higher wGRS was associated with increased odds for RDKF (meta-adjusted odds ratio=1.12, 95%CI 1.01-1.24,P=0.030, P<sub>het</sub>= 0.606).<b> </b><b>Conclusions : </b>Elevated plasma UA is an independent risk factor of incident CKD. Furthermore, plasma UA potentially has a causal role in early eGFR loss in T2D patients.
DOI: 10.6084/m9.figshare.26716459.v1
title: Additional file 1 of Validation of an elicited Imitation test as a measure of Korean language proficiency

description: Additional file 1: Appendix 1
DOI: 10.6084/m9.figshare.21201676.v3
title: Molecular survey of certain protozoan agents that cause diarrhea in children in Sudan

description: data availability
DOI: 10.6084/m9.figshare.25968190.v2
title: codes and data for "Network-informed analysis of a multivariate trait-space reveals optimal trait selection"

description: Trait-based analyses have shown great potential to advance our understanding of terrestrial ecosystem processes and functions. However, challenges remain in adequately synthesising a multidimensional and covarying trait space. Here, we develop a trait reduction procedure based on network analysis of a global trait dataset that covers 27 traits across 262 ecoregions. By applying constraints on previous optimal reduced network in which traits were incrementally added or removed, we established consistent network series. Then, the most cost-efficient trait sets are allowing to identify to represent full trait space when an acquisition cost can be attributed to each trait.<b> </b>We found that that the reduced trait sets properly represented the three main dimensions of full trait space in hydrological safety, leaf economic strategy, and plant reproduction and competition. Then a parsimonious trade-off can also be achieved by selecting a 16-trait network which costs only 42.1% of the full suite of the 27 traits. Our approach can help in revealing important trade-offs and in selecting key traits, thus will potentially enhancing our understanding on the main trade-off dimensions of the multivariate trait space and facilitating trait-based research practically.
DOI: 10.6084/m9.figshare.17701106.v1
title: EEG Dataset for RSVP and P300 Speller Brain-Computer Interfaces

description: EEG dataset for subject 16
DOI: 10.6084/m9.figshare.28027706.v1
title: Credible sets file

description: Credible sets file across all fine-mapped loci (for different LD panels and fine-mapping methods)
DOI: 10.6084/m9.figshare.23641164.v2
title: National forest carbon harvesting and allocation dataset for the period 2003 to 2018

description: Combining the tree cover loss dataset, the interannual variation of the satellite-based vegetation index, and the provincial statistical harvested wood provided by the China Forestry and Grassland Statistical Yearbook, we produced a Long-term HarvEst and Allocation of Forest Biomass (LEAF) dataset for China, which provides spatial information on forest harvesting at a resolution of 30 m.  Averaged from 2003 to 2018, forest harvesting took away 68.34 Mt C yr<sup>-1</sup>. The validation results demonstrated the accuracy and reliability of the dataset in capturing the spatial variation of harvested carbon. The file format of the product is GeoTIFF with the spatial reference of WGS84 (EPSG:4326).  Each GeoTIFF file represents annual harvested forest carbon (unit: g C m<sup>−2</sup>yr<sup>-1</sup>), the absolute harvested carbon per pixel is obtained by multiplying by the corresponding pixel area. The dataset generated by this study is an important data source for estimating the carbon budget of forest ecosystems in China, which also can provide essential insights for sustainable forest management and climate change mitigation efforts.
DOI: 10.6084/m9.figshare.12291245.v6
title: R code for Leaf senescence exhibits stronger climatic responses during warm than during cold autumns

description: A warmer world could extend growing seasons for plants. Changes in spring phenology have been studied, yet autumn phenology remains poorly understood. Using &gt;500,000 phenological records of four temperate tree species between 1951 and 2013 in Europe, we show that leaf senescence in warm autumns exhibits significantly stronger climate responses, with a higher phenological plasticity, than in cold autumns, indicating a nonlinear response to climate. The onset of leaf senescence in warm autumns was delayed due to the stronger climate response, primarily caused by nighttime warming. However, daytime warming, especially during warm autumns, imposes a drought stress which advances leaf senescence. This may counteract the extension of growing season under global warming. These findings provide guidance for more reliable predictions of plant phenology and biosphere-atmosphere feedbacks in the context of global warming.
DOI: 10.6084/m9.figshare.27308562.v1
title: 原始数据.xlsx

description: <b>Improved detection limit in rapid detection of Porcine Circovirus type 3 by one-pot NGO-RPA-Cas12a assay</b>
DOI: 10.26180/26199917.v1
title: Polymer glass configurations deformed using athermal quasi-static simple shear

description: The zipped folder contains the following files:"information_data.pdf" that details the simulation parameters used to create and deform the polymer glass models“pos.dump” – Contains the configurations for γ = 0 to γ = 0.25 with δγ = 10−3, totaling 251 configurations. These configurations are at T = 0 and represent AQS shear data.• “in.KGmodel” – Parameters for our model used in LAMMPS simulations.• “stress.XZ.dat” – Contains stress versus strain information in shaer plane of the system.“info slice.txt” – Contains information on the number of particles in the xz (shear) slices from y = −9 to y = 9, totaling 73 slices for each γ. Each slice has a width of ∆y = 2, and the central location of the slab y is incremented by 0.25. First 200 configurations are analysed and presented in the article. There are a total of (200 × 73) = 14600 lines.“xz plane/dis2d 98” – Non-affine displacement field of 2D slices at γ = 0.098 in the xz (shear) plane with a width of ∆y = 2 are provided.“xz plane/xx 98” – Interpolated data for each slice from y = −9 to y = 9, totaling 73 slices (y incremented by 0.25) for γ = 0.098. This interpolation is performed using the Python library “grid data” with method=“linear” on a square grid of 80×80 in the range [−10,10] for both x and z.“angle dissection/direction uniform N26.txt” – Contains the unit directions (uniformly distributed on a unit sphere) used to dissect our system.“angle dissection/gamma 98/angle2d j” (j = 1, . . . , 26) – The non-affine displacement field after dissecting alongthe direction corresponding to the j-th line of the data file “direction uniform N26.txt”.“angle dissection/gamma 98/info slice.txt”–The information of the number of particles within the slices.“angle dissection/gamma 98/xx j” (j = 1, . . . , 26) – The grid data of the non-affine displacement field data “angle2d j” after interpolation. For this case we use the 128 × 128 grid in the range [−16, 16] for both the directions in the plane.