cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.25323478.v1
title: PRISMA check list

description: This systematic review assesses the effectiveness of treadmill training as an intervention to improve balance and reduce fall risks in the elderly population. Conducted through a comprehensive search across multiple databases from 1980 to 2023, the review synthesized findings from 16 selected studies out of an initial pool of 74. It highlights the multifaceted benefits of treadmill training, such as enhancing balance, mobility, gait, and quality of life, particularly for those with Parkinson's disease, spinal cord injuries, and age-related balance issues. The study underscores treadmill training's potential in geriatric care, noting its adaptability to individual needs and capacities. Despite showing promise, the review calls for further research to optimize training protocols and explore combinations with other interventions for a holistic approach to improving elderly care, indicating a significant step toward promoting healthy aging and reducing fall risks.<br>
DOI: 10.6084/m9.figshare.26420758
title: Supplements to: Learning about AI ethics from cases: A scoping review of AI incident repositories and cases

description: Supplementary materials for the manuscript "Learning about AI ethics from cases: A scoping review of AI incident repositories and cases"Original material in this data repository is licensed as indicated. Third party material included in the ECAT (Sup_05) and data (Sup_04) may be under separate licenses and is not owned by us. We have endeavoured to indicate these licenses where possible, and believe that all material is either under creative commons or equivalent licenses, or where additional material is included it is likely to fall under fair dealing exceptions allowing such excerpting. <br>Supplements comprise:A modified PRISMA flow diagram for the case repository search, and case search within the repositories (Sup_01)A PRISMA checklist for scoping reviews (Sup_02)Data management procedures (Sup_03)The data file of repository descriptions and key case information (Sup_04)The Ethics Case Analysis Tool (ECAT) (Sup_05)<b>Manuscript abstract</b><i>Background</i>: Cases provide a practical resource for learning regarding the uses and challenges of AI applications. Cases give insight into how principles and values are implicated in real contexts, the trade-offs and different perspectives held regarding these contexts, and the – sometimes hidden – relationships between cases, relationships that may support analogical reasoning across contexts.<i>Objective</i>: We aim to (1) provide an approach for structuring ethics cases and (2) investigate how repositories of cases structure those cases and their content.<i>Approach</i>: We motivate a scoping review through a conceptual analysis of ethics case desiderata. The review sought to retrieve repositories, (sometimes known as observatories, catalogues, galleries, or incident databases), and their cases, for analysis of their expression of ethics concepts.<i>Results</i>: We identify n = 14 repositories, extracting the case schema used in each, to identify how this metadata can express ethical concepts. We find that most repositories focus on harm-indicators, with some indicating positive impacts, but with little explicit reference to ethical concepts; a subset (n = 4) includes no structural elements addressing ethical concepts or impacts. We extract a subset of cases from the total cases (n = 2,000) across repositories, identifying and extracting the subset of cases addressing education (n = 100). These are grouped by topic, with a structured content analysis provided of ethical implications from one sub-theme, offering qualitative insights into the ethical coverage.<i>Implications</i>: Our conceptual analysis and empirical review exemplify a model for ethics cases (shorthanded as Ethics-case-CPR), while highlighting gaps both in existing case repositories and specific examples of cases.
DOI: 10.6084/m9.figshare.27073672
title: TFDR corpus: annotated corpus for traditional formula-disease relationships in biomedical articles

description: The Traditional Formula (TF), a combination of herbs prepared in accordance with traditional medicine principles, is increasingly garnering global attention as an alternative to modern medicine. Specifically, there is growing interest in exploring TF's therapeutic effects across various diseases. A significant portion of the state-of-the-art knowledge regarding the relationship between TF and disease is found in scientific publications, where manual knowledge extraction is impractical. Thus, Natural Language Processing (NLP) is being employed to efficiently and accurately search and extract crucial knowledge from unstructured literatures. However, the absence of a high-quality manually annotated corpus focusing on TF-disease relationships hampers the use of NLP in the fields of traditional medicine and modern biomedical science. This article introduces the Traditional Formula-Disease Relationship (TFDR) corpus, a manually annotated corpus designed to facilitate the automatic extraction of TF-disease relationships from biomedical literatures. The TFDR corpus includes information gleaned from 740 PubMed abstracts, encompassing a total of 6,211 TF mentions, 7,166 disease mentions, and 1,109 relationships between them encapsulated within 744 key-sentences.
DOI: 10.6084/m9.figshare.27240009
title: Chromosome-level Genome Assembly of Korean Long-tailed Chicken and Pangenome of 40 Gallus gallus Assemblies

description: GFA file of 40- chicken pangenome. 40 chickens are consisted of bGalGal1.mat.broiler.GRCg7b, bGalGal1.pat.whiteleghornlayer.GRCg7w_WZ, bGalGal5.pri, bGalGal4.pri, Ggswu, P17_new_chr_level_genome, F025_new_chr_level_genome, W17_new_chr_level_genome, H3_ncbi, CVASU_Gallus_Gallus_GG1F, KLC, CVASU_Gallus_Gallus_GG1M, CAU_Silkie_1.0, Ogye1.0, ASM2537063v1, ASM2465302v1, ASM2465299v1, ASM2465304v1, GRCg6a, ASM2465303v1, ASM2465298v1, bGalGal5.alt, bGalGal4.alt, ASM2468635v1, ASM2468646v1, ASM2468628v1, ASM2467976v1, ASM2467932v1, ASM2467990v1, ASM2468700v1, ASM2467941v1, ASM2468629v1, ASM2468631v1, ASM2467935v1, ASM2467939v1, ASM2467937v1, ASM2468627v1, ASM3450986v1, ASM3450984v1, ASM3450988v1 breeds. The assemblies used to make this graph is all available on NCBI
DOI: 10.6084/m9.figshare.28162235
title: Supplementary Material for: Patient Preferences for HR+/HER2‒ Early Breast Cancer Adjuvant Treatment: A Multicountry Discrete Choice Experiment

description: Introduction: More adjuvant treatment options are becoming available for hormone receptor–positive/human epidermal growth factor receptor 2–negative (HR+/HER2–) early breast cancer (EBC) based on results of clinical trials. This study quantified the importance of different attributes of EBC adjuvant therapies to patients and the benefit-risk tradeoffs patients were willing to make.
Methods: Women with HR+/HER2– EBC completed an online discrete choice experiment (DCE) survey; the design was informed by clinical data, qualitative interviews (n=40), and pre-testing interviews (n=40). Participants (pts) made 10 choices between pairs of hypothetical treatments described by varying levels of 6 attributes. DCE data were analyzed using a correlated mixed logit model. Relative attribute importance scores captured the impact of each attribute across clinically relevant ranges. Benefit-risk tradeoffs were captured as the minimum improvements in 5-y invasive disease–free survival (iDFS) that pts would require to tolerate increases in therapy-associated adverse event (AE) risks.
Results: A total of 866 patients from the US, France, Spain, Canada, the UK, Germany, South Korea, and Australia completed the DCE (mean age: 57.7 y; 76% postmenopausal; 29% stage I disease, 55% stage II, 16% stage III). Improved 5-y iDFS (75.4-82.7% range; associated with combination regimens [CRs] vs endocrine therapy [ET] alone) contributed the most to treatment preferences (clinically relevant relative attribute importance: 38.4%), followed by reduced risks of venous thromboembolic events (VTEs) (20.4%), neutropenia (20.3%), and diarrhea (15.0%). Treatment type + duration (3.7%) and fatigue (2.3%) were less important. Pts required the largest improvement in 5-y iDFS (3.9%) to tolerate increased risks of VTE (0.7% to 2.5%) or neutropenia (5.6% to 46%); willingness to accept tradeoffs depended on the AE. Preference heterogeneity was observed across subgroups, but 5-y iDFS improvement was consistently the most impactful on treatment choice in all subgroups.
Conclusion: A multicountry sample of patients most valued adjuvant therapies with higher 5-y iDFS and may therefore prefer CRs over ET alone. The value of CRs depends on their specific safety profiles, and shared decision-making should consider this to select treatment options that align with individual preferences.
DOI: 10.6084/m9.figshare.28163324
title: Supplementary Material for: In vivo Predictors of Focal Type In-stent Restenosis: A Clinical, Angiographical and Optical Coherence Tomography Study

description: Introduction：Few studies have evaluated different patterns of in-stent restenosis by optical coherence tomography (OCT). This study aims to identify in vivo predictors for focal restenosis in patients with in-stent restenosis (ISR).
Methods: The study recruited patients with ISR who underwent OCT examination in the Cardiology Department of the Affiliated Hospital of Zunyi Medical University from October 2018 to December 2022. Based on the angiographic classification of ISR lesions, the patients were divided into two groups: the focal group (n=58) and the non-focal group (n=158).
Results： The white blood cell count was higher in the non-focal group than those in focal type (7.8±3.0 vs. 6.6±2.1, P = 0.007). The prevalence of lipid rich plaque was higher in patients with focal ISR (65.5% vs. 42.4%, P = 0.003). The occurrence of red thrombus (27.8% vs. 12.1%, P = 0.016) and white thrombus (41.1% vs. 24.1%, P = 0.021) was higher in the non-focal group. Multivariate analysis showed that low density lipoprotein cholesterol C (odds ratio [OR]:3.341, 95% confidence interval [CI]: 1.714-9.784, P = 0.046) was independently associated with focal restenosis. While white blood cell count (OR: 0.814, 95% CI: 0.657-0.913, P = 0.047) and stent malapposition (OR: 0.228, 95% CI: 0.057-0.896, P = 0.037) were independently associated with non-focal restenosis.
Conclusion：There were significant differences in clinical baselines and OCT identified morphological characteristics in patients between focal and non-focal group. Low density lipoprotein cholesterol C was independent associated with focal restenosis. White blood cell count and stent malapposition were correlated with non-focal restenosis.
DOI: 10.6084/m9.figshare.7938170
title: Platinum and palladium tetranuclear acetates: DFT optimized geometries

description: Supporting information for upcoming article.<br><br>The geometries were optimized with the hybrid PBE0 functional and various basis sets using GAMESS-US program. The basis sets were obtained from the EMSL Basis Set Library (https://bse.pnl.gov/bse/portal).<br>Figure1b shows simplified view of the crystal solvate 5 Pt<sub>4</sub>(OOCMe)<sub>8</sub>×13 C<sub>6</sub>H<sub>6</sub>.
DOI: 10.17026/dans-2cj-nvwu
title: Nederlandse gedragscode wetenschappelijke integriteit
title: Netherlands Code of Conduct for Research Integrity

description: Voor het goed functioneren van wetenschap is wetenschappelijke integriteit van essentieel belang. Dit geldt voor alle disciplines. Wetenschappelijk onderzoek ontleent zijn status immers aan het feit dat het gaat om een normatief gereguleerd proces, waarbij die normativiteit deels methodologisch en deels ethisch van aard is en gearticuleerd kan worden in een aantal leidende principes: eerlijkheid, zorgvuldigheid, transparantie, onafhankelijkheid, verantwoordelijkheid. 

Het is van groot belang dat de principes van goede en integere wetenschapsbeoefening en de daaruit voortvloeiende normen voor goede onderzoekspraktijken helder geformuleerd zijn en breed onderwezen, gekend en toegepast worden. Deze gedragscode is daarop gericht en vervult een drieledige rol:

(i) Aan onderzoekers, onderzoekers in opleiding en studenten biedt hij een educatief en normatief kader (hoofdstukken 2 en 3) dat zij geacht worden te internaliseren en leidend te laten zijn bij hun onderzoeksactiviteiten. 
(ii) Aan instellingsbesturen en commissies voor wetenschappelijke integriteit levert de code een toetsingskader bij de beoordeling van vermeende schendingen van de wetenschappelijke integriteit (hoofdstukken 3 en 5). 
(iii) Voor de instellingen formuleert deze code bovendien een aantal zorgplichten (hoofdstuk 4).
DOI: 10.17632/pvgrvxh243.1
title: T-Bolt preload and load

description: Bolt stress is very sensitive to load eccentricity. Three uniaxial strain gauges were placed in the "Y" direction on the external surface of the reduced section of the bolt. The strain gauges were placed 120° apart. If there is no eccentricity, all three strains are to be equals.

The application of preload on the bolt was performed by tightening the hexagonal nut with the torque tool. The specification of the average torque in the hexagonal nut was 888.7 Nm. Subsequently, the static test corresponding to the application of the test loads was carried out, which generates an extreme bending moment of 3.1 MNm on the blade root and a load FA on each of the 56 bolted joints.

Under the application of the preload F at 54.9%, it was observed that eccentricity, did not present significant variations when going from the preloading stage to the extreme load stage. This fact led to a second experiment with the application of the preload at 100.8 % with F =217,432 N. For this 100.8% preload condition, the eccentricity increased to 1.367 mm. It was also observed that during tightening there was a crossing of the strain signal 1 and 2; that is, the torque wrench tilted the bolt, and the eccentricity went from e=0.86 mm to e=1.367 mm.  The load eccentricity can be used to stress and fatigue calculation.
DOI: 10.17882/99432
title: Global conversion of the M2-tide (modes 1-10) and the role of supercritical slopes

description: This data set represents an extension of earlier computations of the internal M2-tide generation  (for mode 1, Pollmann and Nycander, 2023; data set: 10.17882/92304) for the modes 2-10. The methodology is based on linear theory and is explained in Pollmann et al., 2019.  In addition, we address the role of slope criticality in the open-ocean and identify which conversion rate estimates fall into (i) the linear regime, where linear theory is valid; (ii) the weakly nonlinear regime, where linear theory might underestimate, but does not strongly overestimate the nonlinear conversion; (iii) the strongly nonlinear regime, where linear theory might substantially overestimate the nonlinear conversion. Details on the procedure can be found in the associated manuscript (Geoffroy, Pollmann and Nycander, currently under revision for J. Phys. Oceanogr.). Please cite this as well as the papers mentioned above when using this data set.
This data set includes the global conversion rate estimates of modes 1-10 below 400m, 700m, and 1000 m depth. We include the uncorrected estimates as well as those in the linear regime (i) and in the regime combining linear and weakly nonlinear conditions (i+ii). The associated masks, also differentiating between ridges and canyons, are also included. Note that there is no weakly nonlinear regime (ii) for canyons and that there is no strongly nonlinear regime (iii) for ridges for the first mode. Conversion rate estimates from topography patches with canyons deeper than the patch mean depth are also masked. For reasons of completeness, we add the mode-1 estimates and the mask for land and continental slopes of Pollmann & Nycander, 2023 (data set: 10.17882/92304).
DOI: 10.18739/a2jh3d23r
title: Surface Mass Balance and Snow Depth on Sea Ice Working Group (SUMup) snow density subdataset, Greenland and Antartica, 1950-2018
DOI: 10.3886/e201821v4
title: ECIN Replication Package for "How policing incentives affect crime, measurement, and justice"

description: In this paper we develop a model where the police choose between investigating and patrolling, while civilians choose between producing and stealing. We derive a truth table for the equilibrium numbers of criminals and producers, punished or not, that can holistically evaluate the effects of police performance incentives. To test the model, we conduct an experiment that varies how severely an officer is reprimanded for false punishments. We find that stronger reprimands do not change crime, increase civilian incomes, and decrease false positives. We also find that the clearance rate, a measure of performance used widely in econometric studies, suggests police performance is better when it is unambiguously worse.
DOI: 10.3886/e209325v2
title: ECIN Replication Package for "Trade and Ethnolinguistic Differences: A Replication and Extension"

description: This repository contains the data and code used in the paper "Trade and Ethnolinguistic Differences: A Replication and Extension", published in Economic Inquiry
DOI: 10.5063/f1765csf
title: Avian species list and eBird checklists for 10 long-term ecological research study sites in Central California Drylands

description: Citizen science data, such as eBird, is broadly accessible and has been underutilized in the study of fine-scale avian populations and distributions. eBird data offers opportunities for examining avian diversity and abundance across ecological gradients. Using these data, we compiled the abundance and diversity of bird communities throughout Central California drylands at 10 established long-term research sites.years2018-2021sites 10 unique instancesSpecies list and checklist from these primary data.Zoë Hillier-Weltman, CJ Lortie, Mario Zuliani, & Bridget Stutchbury. (2023). eBird Observations in Central California. Knowledge Network for Biocomplexity. doi:10.5063/F1DJ5D3W.
DOI: 10.5063/f1bc3x0n
title: Geolocations of all Ephedra californica shrubs at key ecological areas within the San Joaquin Desert.

description: The geolocation of all Ephedra californica shrubs withing key ecological areas within the San Joaquin Desert. All shrubs have been geolocated via the Google earth satellite.
DOI: 10.5063/f1dj5d3w
title: eBird Observations in Central California

description: eBird data for 10 sites located across the Central California desert, from 2018-2021. eBird Basic Dataset. Version: EBD_relOct-2022. Cornell Lab of Ornithology, Ithaca, New York. Oct 2022.
DOI: 10.5063/f1n29vd5
title: Diversity and distribution of terrestrial arthropods on BLM lands across the San Joaquin Valley, California

description: Arthropods were collected at nine sites within the San Joaquin Valley using pitfall and malaise traps, and by sweeping open area vegetation and shrub canopies.
DOI: 10.5063/f1w957mg
title: A set of Keyhole Markup Language polygons to describe site-level ecoregional differences in the plants and animals of Central California Deserts.

description: A set of Keyhole Markup Language (KML) polygons were generated to describe site-level ecological differences in plant and animal communities within California Deserts. All polygons were acquired and generated with Google Earth satellite.
DOI: 10.5063/f1zw1jdg
title: A list of ecological study sites within Central California Drylands

description: Plant-animal ecological interaction research within The Central California Drylands spatial summary list. Data provided describe primary site identifiers with geospatial data for joins to detailed site-level ecological research.
DOI: 10.5066/p91ryez4
title: Quaternary faults offshore of California

description: A comprehensive map of Quaternary faults has been generated for offshore of California. The Quaternary fault map includes mapped geometries and attribute information for offshore fault systems located in California State and Federal waters. The polyline shapefile and matching KML file have been compiled from previously published mapping where relatively dense, high-resolution marine geophysical data exist. The data are accompanied by a PDF containing citations for the compiled source data. Most of the marine geophysical data used for mapping have been processed, merged, and released by the USGS in maps, data releases, and journal publications in support of the California Seafloor Mapping Program and the U.S. West Coast and Alaska Marine Geohazards Project.
DOI: 10.5281/zenodo.11154974
title: Data supporting publication "Metagenomic Immunoglobulin Sequencing (MIG-Seq) Exposes Patterns of IgA Antibody Binding in the Healthy Human Gut Microbiome"

description: Data supporting publication "Metagenomic Immunoglobulin Sequencing (MIG-Seq) Exposes Patterns of IgA Antibody Binding in the Healthy Human Gut Microbiome"
DOI: 10.5281/zenodo.13357634
title: Code and accompanied data for figures in the GET paper
DOI: 10.5281/zenodo.13932035
title: Expert Features
DOI: 10.5281/zenodo.14101797
title: Dataset supporting the tool 'delfies: a Python package for the detection of DNA breakpoints with neo-telomere addition'

description: Purpose

These data can be used to test my tool delfies on real data, to get a concrete sense of its inputs/outputs and test that it is properly installed.

Description

Genome

I downloaded the genome of Oscheius onirici, accession: GCA_932521025.

I subsampled the genome to the last 2kbp of chromosome I, which contains an elimination breakpoint, using `seqkit` v2.8.2, giving the FASTA file in this release.

Sequencing data

I then downloaded the following sequencing data for *O. onirici*, from the European Nucleotide Archive:



ERR5967937: Illumina NovaSeq 6000 paired end short reads. Reads are 2x150bp with average per-base quality of Q27.

ERR10796202: Oxford Nanopore PromethION long reads. Reads have average length 11.9kbp and average per-base quality Q11.4.

ERR7979900: Pacific Biosciences (PacBio) Sequel II long reads. Reads have average length 11.1kbp and average per-base quality Q28.


And aligned them to the above genome with `minimap2` version 2.26-r1175, using the following presets: "map-ont" for the Nanopore data, "map-hifi" for the PacBio data, "sr" for the Illumina data.

After sorting with `samtools`, this gives the BAM files in this release.

Running delfies

I then ran `delfies` version 0.6.0 on each BAM and genome, as:

```shdelfies --threads 16 \    --telo_forward_seq TTAGGC \    --breakpoint_type all \    --min_mapq 20 \    --min_supporting_reads 6 \    \${genome} \${bam} \${odirname}```

The three resulting output directories are in this release, prefixed with `delfies_`.

A single, identical breakpoint is found using all three BAMs (see files '*breakpoint_locations.bed').

Data source

The above raw data were produced and released by the Wellcome Sanger Institute as part of projects PRJEB51305 and PRJEB59023.
DOI: 10.5281/zenodo.14197671
title: Data - Quantifying dynamic linkages between precipitation, groundwater recharge, and streamflow using ensemble rainfall‐runoff analysis

description: The data support the analysis conducted in "Quantifying Dynamic Linkages Between Precipitation, Groundwater Recharge, and Streamflow Using Ensemble Rainfall‐Runoff Analysis", accepted for publication in Water Resources Research (https://doi.org/10.1029/2024WR037821) by Huibin Gao, Qin Ju, Dawei Zhang, Zhenlong Wang, Zhenchun Hao, and James Kirchner.
DOI: 10.5281/zenodo.14202839
title: Global patterns and drivers of coupling between anammox and denitrification processes across inland aquatic ecosystems

description: Here, we reported a dataset regarding global anammox and denitrification rates from inland aquatic ecosystems.