cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19130465.v2
title: COins database

description: COins is a database of COI-5P sequences of insects that includes over 532,000 representative sequences of more than 106,000 species specifically formatted for the QIIME2 software platform. It was developed through a combination of automated and manually curated steps, starting from insects COI sequences available in the Barcode of Life Data System selecting sequences that comply to several standards, including a species-level identification. <br> <br> <br> <br> <strong>seq-degapped.qza</strong> --&gt; reference sequences <br> <strong>taxonomy.qza</strong> --&gt; sequences taxonomy <br> <strong>SklearnClassifier_COins_QIIME2_v2022.2.qza</strong> (NEW) --&gt; naïve Bayes taxonomic classifier trained on CO<em>ins</em> (QIIME2 version 2022.2) <br> <strong>Sequences_metadata1.tsv</strong> --&gt; Identification procedure of voucher specimens from which reference sequences were developed. Identification procedure is reported for each sequence included in CO<em>ins</em> (BOLD id reported in <em>BOLDid reference</em> column) and for all identical sequences within haplotypes that were removed at Step 5 of CO<em>ins</em> curation (those for which BOLD id is not available in <em>BOLDid reference </em>column). The haplotype to which each sequence belongs is reported in <em>Haplotype</em> column (haplotypes of each species are labeled with increasing numbers). Identification procedure information derived from sequences associated metadata provided by BOLD system. <br> <strong>Sequences_metadata2.tsv </strong>--&gt; Identical sequences belonging to different species present within CO<em>ins</em>. Each row represents a cluster of identical sequences associated to different species, sequences included in the cluster are labeled with species name and BOLD id. <br>
DOI: 10.6084/m9.figshare.23803929
title: Two-dimensional bilayer ice in coexistence with three-dimensional ice without confinement

description: Temperature-Wettability Phase Diagram of Two-dimensional bilayer ice in coexistence with three-dimensional ice without confinement /Pressure-Wettability Phase Diagram of Two-dimensional bilayer ice in coexistence with three-dimensional ice without confinement
DOI: 10.6084/m9.figshare.25047860.v1
title: Crustal-derived CO<sub>2</sub> production from plutons in carbonate is driven by shallow metamorphic decarbonation not assimilation

description: Data tables S1 through S7 that accompany the following paper submitted to <i>Geochemistry, Geophysics, Geosystems</i> (DOI will be provided once available).Table S1: Bulk-rock major element (wt.%) and trace element (ppm) composition for hand samplesTable S2: <sup>87</sup>Sr/<sup>86</sup>Sr isotope compositions for bulk rock powdersTable S3: Oxygen isotope (d<sup>18</sup>O ‰ VSMOW) compositions for bulk rock powders and clinopyroxeneTable S4: Carbon (d<sup>13</sup>C ‰ VPDB) and isotope (d<sup>18</sup>O ‰ VSMOW) compositions for Quatsino limestoneTable S5: Electron Probe Micro-Analyses Phase CompositionsTable S6: Laser Ablation Inductively Coupled Mass Spectrometry Phase CompositionsTable S7: CO<sub>2</sub> mass and flux calculations<br>
DOI: 10.6084/m9.figshare.25952062
title: Supplementary Material for: Effects and safety of growth hormone treatment in six children with pycnodysostosis

description: Background: Pycnodysostosis is an extremely rare skeletal dysplasia caused by cathepsin K deficiency. It is characterized by extreme short stature with adult height in males typically less than 150 cm and in females less than 130 cm. Our objective was to evaluate the effect and safety of growth hormone (GH) treatment in 6 patients with pycnodysostosis treated according to the Dutch national pycnodysostosis guideline.
Case presentation: 6 subjects (4 boys, 2 girls) with pycnodysostosis, treated with GH 1.4 mg/m2/day (~0.046 mg/kg/day) for ≥1 year. Median (IQR) age at start of GH was 10.4 years (5.7; 12.2) and median height 113.5 cm (93.3; 129.3) (-4.2 SDS (-4.8; -3.6)). All children were prepubertal at start of GH. After 1 year of GH, median height gain was 7.6 cm (6.5; 8.5) (0.3 SDS (-0.3; 0.7)). Three children are still treated with GH and the other three subjects reached adult height (AH): 1 boy reached an AH of 157.0 cm (-3.8 SDS) after 6.3 years of GH, 2 girls reached an AH of 138.5 cm (-5.2 SDS) after 4.8 years of GH and 148.0 cm (-3.6 SDS) after 6.4 years of GH, respectively. This last girl received additional GnRH analogue treatment. In all subjects height SDS remained stable or improved during and after GH treatment. No serious adverse advents were found. Serum IGF-I remained below the +2 SDS.
Conclusion: Our data suggest that GH may prevent the decline in height which can be observed in children with pycnodysostosis. Further research is needed to confirm this. Also, the effect of other growth promoting strategies such as treatment with an additional GnRH analogue warrants further investigation.
DOI: 10.6084/m9.figshare.26047666
title: Supplementary Material for: Impact of Income-to-Poverty Ratio on Long-Term Mortality of Persons with Chronic Liver Disease in the US, 1999-2018

description: Introduction: Chronic liver disease (CLD) is associated with increased morbidity and mortality. Understanding health disparities can inform appropriate interventions. We aimed to study mortality outcomes of those with CLD by income-level (income-to-poverty ratio &lt;5 as lower-income and &gt; 5 as higher-income).
Methods: In this retrospective-cohort study, we analyzed data of adults from the National Health and Nutrition Examination Survey, 1999-2018. CLD included viral hepatitis, nonalcoholic fatty liver disease (NAFLD), and alcohol-associated liver disease (ALD).
Results: We analyzed 59,204 adults: 47,224 without CLD and 11,980 with CLD. The CLD group was older, more likely male, racial/ethnic minority groups or foreign-born, and had lower educational and income levels (P&lt;0.001). Most (80.02%) CLD participants did not have college degrees and had lower-income (79.18%). Among CLD participants, similar differences were observed between lower and higher-income groups. Lower-income participants with CLD had significantly higher 10-year cumulative mortality compared to higher-income CLD participants (15.26% vs 8.00%, P&lt;0.001), with consistent findings in viral hepatitis and NAFLD subgroups (P&lt;0.001) but not ALD (P=0.71). Adjusting for age, sex, race, birthplace, lower-income CLD participants were 2.01 (HR: 2.01; 95% CI: 1.79-2.26) times more likely to die overall and in viral hepatitis (HR: 2.05; 95% CI: 1.31-3.24) and NAFLD subgroups (HR: 2.32; 95% CI: 1.69-3.18) but not ALD (HR: 1.17; 95% CI: 0.55-2.51).
Conclusion: Lower-income, foreign-born, and racial/ethnic minority groups were disproportionately represented among those with CLD, with lower-income and CLD individuals having double the mortality risk compared to their higher-income counterparts. Interventions should be culturally appropriate and address socioeconomic barriers.
DOI: 10.6084/m9.figshare.26062627
title: Supplementary Material for: Reporting practices for animal studies on peritoneal dialysis conducted in 2021-2023 after the introduction of the ARRIVE 2.0 guidelines

description: Introduction. The first version of Animal Research: Reporting of In Vivo Experiments (ARRIVE 1.0) guidelines was introduced to improve reporting of animal research, but did not lead to major improvements in this respect, which applied also to animal studies on peritoneal dialysis (PD). Here, we examined the performance of a revised version of these guidelines (ARRIVE 2.0). 
Methods. 89 relevant articles published in 2018-2020 (ARRIVE 1.0 period) and 97 published in 2021-2023 (ARRIVE 2.0 period) were identified in PubMed® and analyzed for completeness and transparence of reporting. 
Results. In both periods, most studies were carried out in Asia, on rodents, and concerned the peritoneal pathophysiology. During ARRIVE 2.0, more studies were published in higher impact factor journals with the focus on pharmacology and immunology. Compared to ARRIVE 1.0, general aspects of study design and reporting improved during ARRIVE 2.0 period in studies generated in Europe and America, but did not change significantly in Asia. Detailed analysis showed no improvement in completeness of reporting key information included in the ARRIVE 2.0 Essential 10 checklist. Articles from both periods were deficient in sample size calculations, use of blinding, recording adverse events and drop-outs, and specification of appropriate statistical methods. The level of reporting during ARRIVE 2.0 did not correspond to the journal impact factor and the presence of recommendations for the use of ARRIVE 2.0 in their instructions to authors. 
Conclusion. So far, ARRIVE 2.0 has not produced significant improvements in the reporting of animal studies in PD.
DOI: 10.6084/m9.figshare.26075941
title: Supplementary Material for: Side Effects’ Frequency Assessment of low dose oral minoxidil in male androgenetic alopecia patients

description: Introduction: Hair loss is a very common complaint in dermatologists' offices, requiring the use of proven safe and effective therapies to improve the condition without jeopardizing patients’ health and well-being. 
Methods: We selected 100 male patients with androgenetic alopecia beginning treatment with oral minoxidil (dosage: 0,5mg - to 5 mg) to observe incidence and frequency of side effects.
Results: The side-effects/symptoms observed in the assessed patients included body and facial hypertrichosis (most incident – 16 and 11% respectively), lower legs oedema (4%), periorbital oedema (4%), fatigue (1%), tachycardia (1%), and insomnia (3%). Dizziness, hypotension, respiratory changes, and diarrhea were expected although not found in the assessed participants. No life-threatening adverse effects were observed.
Conclusion: the doses administered in current research of oral minoxidil presented good safety profile as hair loss treatment, with the most incident side-effect being related to hypertrichosis. Systemic side-effects were infrequent.
DOI: 10.6084/m9.figshare.26104786
title: Supplementary Material for: Managing children and adolescents with type 1 diabetes and coexisting celiac disease: Real-world data from a global survey

description: Objectives: Celiac disease (CD) is among the diseases most commonly associated with type 1 diabetes (T1D). This study aimed to evaluate the worldwide practices and attitudes of physicians involved in pediatric diabetes care regarding diagnosing and managing CD in children with T1D. 
Methods: The 30-item survey was conducted between July and December 2023 aimed at targeting pediatricians with special interest in T1D and CD. It was shared by the JENIOUS- young investigators group of the International Society of Pediatric and Adolescent Diabetes (ISPAD) and the YES- early career group of the European Society for Pediatric Endocrinology (ESPE).
Results: 180 physicians (67.8% female) from 25 countries responded. Among respondents, 62.2% expected sustaining optimal glycemic control in children with T1D and CD (T1D+CD) to be more difficult than in children with T1D alone. Majority (81.1%) agreed that more specific guidelines are needed. The follow-up routine for patients with T1D+CD differed, and one-quarter of physicians scheduled more frequent follow-up checkups for these patients. Seventy percent agreed multidisciplinary outpatient clinics for their follow-up is needed. In the multivariate ordinal logistic regression model, a statistically significant predictor of a higher degree of practice according to ISPAD 2022 guidelines was a higher level of country income (OR=3.34; p&lt;0.001). 
Conclusions: These results showed variations in physicians' practices regarding managing CD in children with T1D, emphasising the need for more specific guidelines and intensive education of physicians in managing this population, especially in lower-income countries. Our data also suggest the implementation of multidisciplinary outpatient clinics for their follow-up.
DOI: 10.6084/m9.figshare.26159680
title: Supplementary Material for: Lack of nuclear localization of the Creb3l1 transcription factor causes defects in caudal fin bifurcation in zebrafish Danio rerio

description: The formation of normal bone and bone healing require the cAMP-responsive element binding protein 3-like-1 (Creb3l1) transmembrane transcription factor, as deletion of the murine CREB3L1 results in osteopenic animals with limited capacity to repair bone after fracture. Creb3l1 undergoes regulated intra-membrane proteolysis (RIP) to release the N-terminal transcription activating (TA) fragment that enters the nucleus and regulates the expression of target genes. To expand our understanding of Creb3l1 role in skeletal development and skeletal patterning, we aimed to generate animals expressing only the TA fragment of Creb3l1 lacking the transmembrane domain and thereby not regulated through RIP. However, the CRISPR/Cas9-mediated genome editing in zebrafish D. rerio caused a frame-shift mutation that added 56 random amino acids at the C-terminus of the TA fragment (TA+), making it unable to enter the nucleus. Thus, TA+ doesn’t regulate transcription, and the creb3l1TA+/TA+ fish animals are creb3l1 transcriptional nulls. We document that the creb3l1TA+/TA+ fish exhibit defects in the patterning of caudal fin lepidotrichia, with significantly distalized points of proximal bifurcation and decreased secondary bifurcations. Moreover, using the caudal fin amputation model, we show that creb3l1TA+/TA+ fish have decreased capacity for regeneration, and that their regenerates replicate the distalization and bifurcation defects observed in intact fins of creb3l1TA+/TA+ animals. These defects correlate with altered expression of the shha and ptch2 components of the Sonic Hedgehog signaling pathway in creb3l1TA+/TA+ regenerates. Together, our results uncover a previously unknown intersection between Creb3l1 and the Sonic Hedgehog pathway, and document a novel role of Creb3l1 in tissue patterning.
DOI: 10.1285/i24212113v8i2p59
title: The photo diaries method to catch the daily experience of Italian university students during COVID-19 lockdown

description: The aim of this research was to explore Italian students' lockdown experience during the COVID-19 pandemic to understand their emotions and the coping strategies they played out during their daily lives at home through photo diaries. The research was carried out in six Italian universities involving 109 participants. The task required each student to take one photo per day for one week in T1 and one in T2, representing their mood during their daily life at home and to give it a title and a brief description. Overall, 1,526 photographs with texts were collected. The main subjects of the photographs were objects, the most frequent coping strategy was self-distraction, and most participants expressed emotions of joy and anticipation but also sadness and fear. Then, the associations between the characteristics of their photos and the emotions and coping strategies from their diary entries were analyzed. For example, emotional support and joy were positively associated with family, pets, and food, while fear and sadness were represented with objects. Implications of the results are discussed, including considerations about using photo diaries during collective disasters.
DOI: 10.13020/52cc-k949
title: Effects of Landscape Position on Perennial Biomass and Food Crop Performance in Buffer Areas

description: Due to the environmental consequences of annual-dominated cropping systems, there is an increasing need to identify agronomic strategies which incorporate perennial crops. One strategy for increasing perennial cover is through the targeted use of annually-harvested perennial food and bioproducts crops in buffer strips, which has the potential to create new revenue streams for farmers and substantially mitigate agricultural nutrient pollution from conventional cropping systems. As buffers are typically installed on marginal land, it is critical to understand how landscape position influences the success of perennial crops. The objectives in this study were to determine the relatively early influence of landscape position on the productivity of a variety of perennial crops and their subsequent soil nutrients and soil water storing capabilities. In this experiment, nine perennial (alfalfa, alsike clover, indiangrass, switchgrass, big bluestem, prairie cordgrass, intermediate wheatgrass, high diversity polyculture, low diversity polyculture) and two annual (corn, soybean) crops were planted across two landscape positions (hillslope and deposition). Plant biomass, plant tissue nitrogen, soil moisture, and soil NO3-N and NH4-N were measured and compared at two different locations in Minnesota. Overall, the polyculture mixes, and to some extent intermediate wheatgrass, performed the best with respect to biomass production while also providing ecosystem services across most soil by landscape position combinations tested in this study. However, there were some important findings specific to each soil and landscape position combination, mainly oriented towards biomass production. We also observed temporal patterns in soil moisture and depth-related patterns in soil N reductions. This study presents an opportunity to optimize the use of perennial crops on marginal agricultural lands for improved environmental and economic benefit.
description: Files contain all data collected over a 2-year period at two locations in Minnesota.
DOI: 10.15129/9ab14b0e-19ac-4279-938f-27f643078cec
title: REFIT: Electrical Load Measurements (Cleaned)

description: The REFIT Electrical Load Measurements dataset includes cleaned electrical consumption data in Watts for 20 households at aggregate and appliance level, timestamped and sampled at 8 second intervals. This dataset is intended to be used for research into energy conservation and advanced energy services, ranging from non-intrusive appliance load monitoring, demand response measures, tailored energy and retrofit advice, appliance usage analysis, consumption and time-use statistics and smart home/building automation. When using this dataset please cite the following paper in Scientific Data, http://dx.doi.org/10.1038/sdata.2016.122 This version of the dataset has been cleaned in the following ways: - Timestamp duplicates have been merged. - IAM (Individual Appliance Monitor) readings set to 0 Watts if above 4000 Watts (above the rated limit of the sensor). - Each IAM has been processed to ensure that it only shows readings for one appliance, where possible. - The ReadMe file has been updated with information about monitored appliance changes. - NaN values have been forward filled (&lt; 2 minute gaps) or zeroed (&gt; 2 minute gaps). This work has been carried out as part of the REFIT project (`Personalised Retrofit Decision Support Tools for UK Homes using Smart Home Technology', Grant Reference EP/K002368/1/1). REFIT is a consortium of three universities - Loughborough, Strathclyde and East Anglia - and ten industry stakeholders funded by the Engineering and Physical Sciences Research Council (EPSRC) under the Transforming Energy Demand in Buildings through Digital Innovation (BuildTEDDI) funding programme. A raw data version of this dataset (deposited 23/09/2015) is also available from the Data Sets link below.
DOI: 10.15468/dl.2znkdu
title: Occurrence Download

description: A dataset containing 264 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Squilla chydaea Manning, 1962"
 ]
}

 The dataset includes 264 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006297-240425142415019/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3n89yp
title: Occurrence Download

description: A dataset containing 188 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lysiosquilla scabricauda (Lamarck, 1818)"
 ]
}

 The dataset includes 188 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010676-230918134249559/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bzerym
title: Occurrence Download

description: A dataset containing 3386 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Squilla empusa Say, 1818"
 ]
}

 The dataset includes 3386 records from 56 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010485-230918134249559/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.1594/pangaea.777976
title: Names of oceans and seas as digitized table

description: The dataset contains the names of all oceans and seas in the "Limits of Oceans and Seas" (IHO, 1953). An automatic algorithm gives an area centroid for each polygon (ocean or sea). The dataset consists of four columns. The first column contains the name of the ocean or sea, column 2 and 3 contain the position of each polygon point (latitude, longitude). Column 4 contains an area index. With this index a link to the polygons is possible.
DOI: 10.17882/100104
title: Lagrangian drifters in the Southwestern Atlantic Ocean

description: "55 drifters were deployed along two zonal transects centered at 47 and 47.25ºS on September 8, 2021(Fig. 1). Spacing between the initial deployment positions of the drifters varied between 14 km and 18 km in the continental shelf providing the position every 30 minutes and between 3 km and 6 km over the continental slope with temporal resolution of 10 minutes. The shortest distances between deployment positions correspond to drifters deployed close to the 200 m isobath. The drifters have a 6 m long, 1 m diameter holey sock drogue centered at 15 m depth to track currents at that depth. Each file contains a drifter trajectory in the NetCDF format with the ID number, longitude, latitude and time.
The dataset includes raw positions; For details about the data processing, e.g. the methodology applied to detect the drogue loss, see https://doi.org/10.1016/j.dsr.2024.104319 and https://doi.org/10.1029/2023JC020446
DOI: 10.25625/aqy3si
title: Overhauser enhanced liquid state nuclear magnetic resonance spectroscopy in one and two dimensions

description: Here deposits data for the publication entitled "Overhauser enhanced liquid state nuclear magnetic resonance spectroscopy in one and two dimensions" accepted in Nature Communications. Please see readme.rtf for contents.
DOI: 10.26302/sshade/experiment_op_20181105_002
title: Ni K edge XAS transmission of Ni metallic foil reference at ambient conditions
DOI: 10.5281/zenodo.10086216
title: Accompanying data for "The Response of Tropical Rainfall to Idealized Small-Scale Thermal and Mechanical Forcing", by Martin Velez-Pardo and Timothy W. Cronin

description: Data accompanying the manuscript "The Response of Tropical Rainfall to Idealized Small-Scale Thermal and Mechanical Forcing", by Martin Velez-Pardo and Timothy W. Cronin.
DOI: 10.5281/zenodo.10126627
title: Slow slip as an indicator of fault stress criticality

description: This dataset contains simulated data used in Lambert (submitted): Slow slip as an indicator of fault stress criticality.
DOI: 10.5281/zenodo.10578630
title: IBDmix calls of introgressed Neanderthal sequences in individuals from the 1000 Genomics Project populations

description: This submission provides DNA sequence regions predicted to be introgressed from Neanderthals in individuals from the 1000 Genomes Project. The calls were generated using a new IBDmix (https://github.com/PrincetonUniversity/IBDmix) analysis framework that uses genetic distance as opposed to physical distance in measuring segment size. Calls are provided using Altai, Vindija, and Chagyrskaya as the Neanderthal archaic reference genome.