cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24174624.v1
title: The limited effect of deforestation on stabilized subsoil organic carbon in a subtropical catchment

description: Dataset of the study "The limited effect of deforestation on stabilized subsoil organic carbon in a subtropical catchment" <br><br>Predicting the quantity of soil organic carbon (SOC) requires understanding about how different factors control the amount of SOC. Land use has a major influence on the function of the soil as a carbon sink, as shown by substantial organic carbon (OC) losses from the soil upon deforestation. Yet, predicting the degree to which land use change affects the OC content in soils, and the depth down to which this occurs, requires context-specific information related to, for example, climate, geochemistry, and land use history. In this study, 266 samples from forests and agricultural fields were collected from 94 soil profiles down to 300 cm depth in a subtropical region (Arvorhezina, southern Brazil) to study the impact of land use on the amount of stabilized OC along the soil profile. We found that the stabilized OC content was not affected by land use below a depth of 90 cm. Along the soil profile, the amount of stabilized OC was predominantly controlled by land use and depth, in addition to the silt and clay content, and aluminum ion concentrations. Below 100 cm, none of the soil profiles reached a concentration of stabilized OC above 50% of the stabilized OC saturation point (i.e., the maximum OC concentration that can physically be stabilized in these soils). Based on these results, we argue that it is unlikely that deeper soil layers can serve as an OC sink over a time scale relevant to global climate change, due to the limited OC input in these deeper layers. Furthermore, we found that soil weathering degree was not a relevant control on the amount of stabilized OC in our profiles because of the high weathering degree of the studied soils. It is therefore suggested that while the soil weathering degree might be an effective controlling factor of OC stabilization over large spatial scale, it is not an informative measure for this process at regional and local scales (with similar climate, bedrock, and weathering history) in highly weathered soils.
DOI: 10.6084/m9.figshare.9810632.v1
title: networks and gender - Díaz-Faes et al.

description: Data from a questionnaire, administered to biomedical scientists and technicians in Spain, which enquired into multiple aspects of personal research networks
DOI: 10.6084/m9.figshare.20401323.v1
title: Supplementary Material for: How to Improve Training in Descriptive Psychopathology for Psychiatry Residents: A Delphi Study

description: <b><i>Purpose:</i></b> Descriptive psychopathology (DP) is the language of psychiatry and is dedicated to the description of mental symptoms. Despite its core importance, a systematic review identified a series of shortcomings in its training. This Delphi study seeks to provide guidance for better didactic and clinical training in DP. <b><i>Method:</i></b> The authors used the Delphi method in order to gather, pool, and optimize the knowledgeable opinion of a highly qualified panel of international experts on how to improve DP training. A preliminary phase with open-ended questions was the basis to elaborate a Delphi questionnaire consisting of 14 questions on didactic and clinical training, which was then used in two successive Delphi rounds. Twenty-nine international experts in DP participated throughout the study. <b><i>Results:</i></b> A series of hierarchical lists on how to improve DP training were elaborated. Regarding didactic training, the experts valued the contents and educational methods, as well as recommended authors and texts. Regarding clinical training, the experts valued educational methods, desirable characteristics in clinical supervisors, how to improve the supervisors’ expertise, useful aspects and facilitating questions for direct supervision, and the suitability of including other evaluators besides the supervisor. In the final survey, 94% of the experts considered that the Delphi method had been effective to obtain and improve their opinions. <b><i>Conclusions:</i></b> Insufficient direct supervision in live interviews was considered the most important problem. A series of general measures were proposed to improve DP training: (i) adapting DP training throughout residency, with introductory and advanced levels; (ii) making DP training compulsory in psychiatry curricula; (iii) assessing residents’ DP knowledge and clinical use; and (iv) training the trainers/supervisors in both content (DP) and form (how to train/supervise residents). Within didactic training, epistemology of DP and contemporary and classic authors/texts were the highest rated contents, while supervised discussions based on cases, videos, or readings were the highest rated methods. Within clinical training, 8 aspects of DP that could guide the supervisor were highly rated: mental state examination, dialogue, empathy and understanding, attitude/willingness, knowledge-practice bridge, mental symptom formation, implications for decision-making, and the written report of the encounter.
DOI: 10.6084/m9.figshare.28691963.v1
title: Raw Data

description: This study designs an "I-shaped" pneumatic flexible tree-climbing robot with adjustable joints and anchors, enabling efficient tree climbing and stable load handling across various tree sizes and conditions.
DOI: 10.6084/m9.figshare.10116041.v1
title: Raw datasets on chronic toxicity tests of nickel by using Daphnia pulex and D. galeata

description: Data for the work titled "Chronic Effects of Nickel on <i>Daphnia pulex</i> and <i>D. galeata</i>". The datasets on chronic toxicity tests of nickel by using <i>D. pulex</i> and <i>D. galeata</i> are in excel files titled "Dpulex_nickel.xlsx" and "Dgaleata_nickel.xlsx", respectively.<br>Produced by Hiroyuki Mano and Naohide Shinohara<br>Research Institute of Science for Safety and Sustainability (RISS)National Institute of Advanced Industrial Science and Technology (AIST)Tsukuba, Japan<br>
DOI: 10.6084/m9.figshare.12901538.v2
title: Orthology species and databases.xlsx

description: List of organisms used in orthology searches and the databases the sequences were obtained from.
DOI: 10.6084/m9.figshare.14442170.v1
title: Korso_CDS_representative.fa.gz

description: Korso representative CDS sequences
DOI: 10.6084/m9.figshare.27043720.v1
title: Supplementary Material for: Is Baricitinib Effective and Safe for Patients with Difficult-to-Treat Rheumatoid Arthritis? Comparative Data with the RA Group of Rheumatoid Arthritis not Difficult to Treat

description: Objective: This study investigates the efficacy and safety of baricitinib, an oral targeted synthetic Disease Modifying Anti-Rheumatic Drugs (DMARD), in patients with difficult-to-treat rheumatoid arthritis (D2T RA) compared to those without, aiming to determine its potential as an alternative treatment for D2T RA. Subject and Methods: A total of 78 patients participated in this retrospective cohort study, with 33 meeting the D2T RA criteria and 45 were in the non-D2T RA group. Various clinical and laboratory parameters, adverse events, and disease activity indices were assessed, alongside drug efficacy and survival rates. Results: Patients with D2T RA exhibited higher seronegativity, prior use of bDMARDs and cDMARDs, and longer disease duration. Both groups experienced reductions in VAS and DAS28 scores, as well as SDAI, CDAI, HAQ, CRP, and ESR levels at baseline and 3, 6, and 12 months post-baricitinib initiation, with sustained efficacy observed over 12 months. The most prevalent adverse event was infection (28.21%). Although initial drug survival rates were similar between groups, the non-D2T RA group demonstrated higher rates at 24 months (46.70% vs. 59.40%). Subgroup analyses showed comparable survival rates between D2T RA and non-D2T RA groups, whether treated with baricitinib alone or in combination with methotrexate or leflunomide. Conclusion: Despite potential treatment resistance, patients meeting the D2T RA criteria shared similar safety and efficacy profiles with those non-D2T RA. Baricitinib emerges as a promising treatment option for D2T RA patients, offering effectiveness and safety comparable to the non-D2T RA group.
DOI: 10.6084/m9.figshare.27684789.v1
title: Supplementary Material for: Worldwide burden of retinoblastoma from 1990-2021

description: Introduction: To report the global, regional, and national burden of retinoblastoma between 1990 and 2021, by age, sex, and sociodemographic index (SDI).
Methods: We leveraged the Global Burden of Disease 2021 Study to elucidate the epidemiological landscape of retinoblastoma, encompassing prevalence, incidence, mortality, and disability-adjusted life years (DALYs) across 204 nations and territories spanning the period from 1990 to 2021. The SDI was employed to evaluate the interplay between socio-economic development and the burden of retinoblastoma.
Results: In 2021, global estimates unveiled 57,333 prevalent cases of retinoblastoma, yielding 6,274 incident cases, 2,762 deaths, and 243,204 DALYs. Globally, the age-standardized prevalence, incidence, mortality, and DALY rates for retinoblastoma in 2021 were 0.86, 0.09, 0.04, and 3.65 per 100,000 population, respectively. Tokelau, Kenya, and Portugal demonstrated the highest age-standardized prevalence and incidence rates of retinoblastoma in 2021. The global prevalence of retinoblastoma peaks among children aged 2 to 4 years and subsequently declines with increasing age. At the regional level, the correlation between SDI and age-standardized prevalence rates for retinoblastoma manifested a V-shaped pattern.
Conclusions: This comprehensive examination of retinoblastoma epidemiological trends underscores the imperative for heightened vigilance and more efficacious therapeutic interventions, especially within resource-limited environments. The findings accentuate the need for targeted strategies to address the disparate burden of retinoblastoma across diverse socioeconomic landscapes.
DOI: 10.6084/m9.figshare.28351808.v2
title: [Dataset] Fire and Herbivory as Architects of Mediterranean Biodiversity. Lestienne et al. submitted

description: This file contains the complete raw dataset used in the article <i>"Fire and Herbivory as Architects of Mediterranean Biodiversity"</i>, submitted to SCIENCE in February 2025 by Lestienne et al. Access to these data will be under embargo until the study is published.
DOI: 10.6084/m9.figshare.3568425.v1
title: Appendix A. A binomial product model can incorporate spatial aggregation for quadrat sampling.

description: A binomial product model can incorporate spatial aggregation for quadrat sampling.
DOI: 10.6084/m9.figshare.25378897.v1
title: Nomophobia among university students

description: The study examined demographic, psychological, and social factors potentially influencing students' nomophobia. This dataset contains data on the nomophobia status of university students in the Turkish sample. Students' self-reports about their smartphone use before and during Covid-19 are also included in the data set. In addition, responses to the COVID-19 Psychological Distress Scale, Short Form of the UCLA Loneliness Scale, Communication Skills Scale (CSS), Oxford Happiness Scale are also included.
DOI: 10.6084/m9.figshare.20020056.v1
title: Innovation Capability: A Systematic Review of the Literature

description: This work contributes to consolidate academic research on innovation capacity. A systematic methodology was applied to review the literature since 1991. The recovered literature was analyzed and synthesized into a multidimensional framework composed of 7 determinants of innovation capability - transformational leadership; strategic intent to innovate; personnel management innovation; customer and market knowledge; strategic management of technology; organicity of the organizational structure; and project management that results in performance innovation in products and processes. Additionally, an inventory of management practices that characterize and underpin the aforementioned factors was conducted and presented. The framework and the list of management practices can be used as a basis for future empirical research or as a guide for improving firms' innovation capabilities.
DOI: 10.6084/m9.figshare.c.1917842_d8.v1
title: Raw Data.xlsx

description: associated dataset for Data Descriptor: Data Record 2, Raw Data.xlsx
DOI: 10.6084/m9.figshare.28190633.v1
title: Paper-Raw Data.zip

description: Genetic diversity of brucella melitensis in Oman.
DOI: 10.6084/m9.figshare.28722047.v1
title: Analyze Code and U-Net Models For Capturing Subgrid Cold Pool Dynamics with U-Net: Insights fromLarge Eddy Simulation for Storm-Resolving Modeling

description: The ZIP files include the code and the trained U-Net models used to capture subgrid cold pool dynamics. The code for reproducing the figures can be found in draw_function.py, while the code related to deep learning model explainability is provided in explain.py. The trained models are located in the same folder with the prefix following the experimental setup. Those interested in the original CRM output data used to train the U-Net models may contact the authors directly.
DOI: 10.6084/m9.figshare.22787639.v6
title: Supplemental Table S3: The editing steps of diseases and numbers of cows, lactations, and records remaining after each data editing step.

description: Investigating the relationship between fluctuations in daily milk yield as resilience indicators and health traits in Holstein cattle
DOI: 10.6084/m9.figshare.27264324.v1
title: Supplementary Material for: Postnatal outcomes of fetal variants of unknown significance in prenatal CMA: A single-center study

description: Introduction:Chromosome microarray analysis(CMA) can identify clinically significant microdeletions and microduplications, providing valuable insights into the genetic basis of various disorders. Our study was to evaluate clinical management and prognosis of fetuses with prenatal variants of unknown significance (VOUS) and determine diagnostic approaches for subsequent pregnancies.
Methods: This study included 2,953 fetuses undergoing chromosome microarray analysis (CMA) at the Prenatal Diagnostic Center of Changzhou Maternal and Child Health Care Hospital from January 2018 to December 2022, identifying 162 cases with VOUS. Parent-of-origin testing determined the origin of copy number variations (CNVs). Prenatal genetic counseling was provided, and outcomes were followed for 3-36 months post-birth.
Results: All 162 VOUS cases received prenatal genetic counseling. Among these, 123 continued the pregnancy; 22 chose termination, and 17 were lost to follow-up. Of the continuations, 116 delivered at term, and 7 preterm. Post-birth follow-up showed 5/123 live-born fetuses developed relevant clinical phenotypes. Parent-of-origin testing in 21 cases identified 18 hereditary and 3 de novo variants. Additionally, five subsequent pregnancies were monitored, with two undergoing amniocentesis and three receiving low-risk non-invasive prenatal testing (NIPT), all with positive outcomes.
Conclusion: VOUS, occurring in approximately 5% of cases, require comprehensive prenatal genetic counseling and show generally favorable outcomes. Despite low association with adverse clinical phenotypes, the importance of postnatal follow-up and regular report updates is emphasized to detect potential clinical associations early.
DOI: 10.6084/m9.figshare.27933987.v1
title: ChatGPT Data JP.pdf

description: Input and output data from long-term learning in mathematical statistics using ChatGPT
DOI: 10.6084/m9.figshare.8287082.v1
title: Additional file 14: of A systematic analysis of genomics-based modeling approaches for prediction of drug response to cytotoxic chemotherapies

description: Spearman Correlations for NLSVR CTR1 models from 10 to 1000 genes presented in figure for section E and Fig.Â 6. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.22698655.v3
title: PMTransformer pre-trained model

description: Pretrained Machine learning models for MOFTransformer and PMTransformer.
DOI: 10.6084/m9.figshare.26978050.v1
title: GVHD RAG Data with Production

description: A classic retrieval augmented generation (RAG) Q&A bot that answers questions about the GVHD medical condition.
DOI: 10.6084/m9.figshare.11671617.v1
title: Orthosilicic acid Inhibits RANKL-Induced Osteoclastogenesis and Reverses Ovariectomy-Induced Bone Loss in Vivo

description: Silicon is essential for bone formation. Numerous experiments in vitro and in vivo have shown that an appropriate increase intake of silicon can facilitate the synthesis of collagen and its stabilization, and promote the differentiation and mineralization of osteoblasts. However, its effect on osteoclast-associated osteoporosis and the underlying mechanisms remain unclear. In this study, we examined whether orthosilicic acid restrain the differentiation of osteoclast through the receptor activator of nuclear factor κB ligand (RANKL)/ receptor activator of nuclear factor κB (RANK)/ osteoprotegerin(OPG) signaling pathway by investigating its effect in vitro and in vivo. By using an in vitro bone marrow macrophage (BMM)-derived osteoclast culture system, we found that orthosilicic acid inhibited osteoclast differentiation and RANKL-induced osteoclast marker gene and protein expression including c-Fos, nuclear factor of activated T cells cl (NFATcl), tumor necrosis factor receptor-associated factor 6(TRAF6), nuclear factor kappa B P50(NF- κB P50), NF- κB P52, RANK, Integrin β3, cathepsin K(CTSK). And we treated ovariectomized (OVX) mice with orthosilicic acid and revealed a protective effect of orthosilicic acid on osteoporosis in vivo. In conclusion, our finding demonstrated that orthosilicic acid suppresses RANKL-induced osteoclastogenesis and has potential value as a therapeutic agent for OVX-induced bone loss.
DOI: 10.6084/m9.figshare.27931818.v1
title: DIPPY Supplemental table

description: Please see https://www.biorxiv.org/content/10.1101/2024.04.15.589492v1.abstract
DOI: 10.6084/m9.figshare.7679885.v1
title: Supplementary Material for: Unmet Medical Needs in Ulcerative Colitis: An Expert Group Consensus

description: <b><i>Background:</i></b> The authors aimed to conduct an extensive literature review and consensus meeting to identify unmet needs in ulcerative colitis (UC) and ways to overcome them. UC is a relapsing and remitting inflammatory bowel disease with varied, and changing, incidence rates worldwide. UC has an unpredictable disease course and is associated with a high health economic burden. During 2016 and 2017, a panel of experts was convened to identify, discuss and address areas of unmet need in UC. <b><i>Methods:</i></b> PubMed and Cochrane Library databases were searched for relevant articles describing studies performed in patients with UC. These findings were used to generate a set of statements relating to unmet needs in UC. Consensus on these statements was then sought from a panel of 9 expert gastroenterologists using a modified Delphi review process that consisted of anonymous surveys followed by live meetings. <b><i>Results:</i></b> In 2 literature reviews, over 5,000 unique records were identified and a total of 138 articles were fully reviewed. These were used to consider 26 areas of unmet need, which were explored in 2 face-to-face meetings, in which the statements were debated and amended, resulting in consensus on 30 final statements. The unmet needs identified were categorised into 7 areas: impact of UC on patients’ daily life; importance of early diagnosis and treatment; drawbacks of existing treatments; urgent need for new treatments; and disease-, practice- or patient-focused unmet needs. <b><i>Conclusions:</i></b> These expert group meetings found a number of areas of unmet needs in UC, which is an important first step in tackling them in the future. Future research and development should be focused in these areas for the management of patients with UC.
DOI: 10.6084/m9.figshare.15141021.v1
title: Dataset for handling missing values in well-log curves with a gated graph neural network

description: This is the dataset used in the article titled "Handling missing values in well-log curves with a gated graph neural network".
DOI: 10.6084/m9.figshare.22673581.v1
title: Supplementary Material for: Rate of overlap between ICD-11 Gaming Disorder and DSM-5 Internet Gaming Disorder along with Turkish reliability of the Gaming Disorder Scale for Adolescents (GADIS-A)

description: Introduction: The main aims of the current study were i) to explore the overlap between internet gaming disorder (IGD) and Gaming Disorder (GD) diagnoses, ii) to identify clinical characteristics in clinical settings, and iii) to measure psychometric properties of the Gaming Disorder Scale for Adolescents (GADIS-A). Methods: 222 adolescents who were followed up within a tertiary-care mental health hospital, were included (IGD/GD group [n=111], Clinical Comparison Group [n=90], Healthy Controls [n=21]). The tools used were the Gaming Disorder Scale for Adolescents (GADIS-A), Internet Gaming Disorder Scale – Short-Form, The Difficulties in Emotion Regulation Scale (DERS-36), Children's Global Assessment Scale, and a semi-structured interview for DSM-5 diagnoses. Results: The overlap rate of IGD and GD is 73%. Comorbid ADHD diagnoses were more commonly found in the IGD group compared to the clinical comparison group. Patients who met GD and IGD diagnoses revealed higher scores in DERS-36. Turkish GADIS-A Item-total score correlation coefficients were between 0.627-0.860. In the sample, there was a high level of correlation between between the number of DSM-5 and ICD-11 diagnostic criteria met and GADIS-A scale scores. The Cronbach’s alphas if item deleted ranged between 0.942-0.954. In addition, treatment refusal was more frequent in the IGD group than in the clinical comparison group. Conclusion: The GADIS-A had good to excellent psychometric properties in Turkish adolescents. Despite having a stricter diagnostic criterion, GD overlapped with IGD in a clinical population.
DOI: 10.6084/m9.figshare.28462934.v1
title: Discovering ley activation hotspots in the M2 muscarinic recpetor, ligand binding-induced FTIR difference spectra

description: The M<sub>2</sub> muscarinic receptor (M<sub>2</sub>R) is a prototypical G protein-coupled receptor (GPCR) that serves as a model system for understanding ligand recognition and GPCR activation. Here, using vibrational spectroscopy, we identify the mechanisms governing M<sub>2</sub>R activation by its native agonist, acetylcholine. Combined with mutagenesis, computational chemistry, and organic synthetic chemistry, our analyses found that the precise distance between acetylcholine and Asn404, one of the amino acids constituting the ligand-binding site, is important for M<sub>2</sub>R activation and that the N404Q mutant undergoes partial active state-like conformational changes. We discovered that a water molecule bridging acetylcholine and Asn404 forms a precise and flexible hydrogen bond network, triggering the outward movement of transmembrane helix 6 in M<sub>2</sub>R. Consistent with this observation, disruptions in this hydrogen bond network via chemical modification at the α- or β-position of acetylcholine failed to activate M<sub>2</sub>R. Collectively, our findings pinpoint Asn404 as a critical residue that both senses acetylcholine binding and induces M<sub>2</sub>R activation.
DOI: 10.6084/m9.figshare.9784967.v1
title: Subject 5

description: Data from Subject 5