cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14798097.v1
title: Supplementary Material for: Association of Vitamin D Receptor Gene Polymorphisms with Serum Vitamin D Levels in a Greek Rural Population (Velestino Study)

description: <b><i>Background/Aim:</i></b> An alarming increase in vitamin D deficiency even in sunny regions highlights the need for a better understanding of the genetic background of the vitamin D endocrine system and the molecular mechanisms of gene polymorphisms of the vitamin D receptor (VDR). In this study, the serum levels of 25(OH)D<sub>3</sub> were correlated with common VDR polymorphisms (<i>ApaI, BsmI, FokI</i>, and <i>TaqI</i>) in 98 subjects of a Greek homogeneous rural population. <b><i>Methods:</i></b> 25(OH)D<sub>3</sub> concentration was measured by ultra-HPLC, and the VDR gene polymorphisms were identified by quantitative real-time PCR followed by amplicon high-resolution melting analysis. <b><i>Results:</i></b> Subjects carrying either the B <i>BsmI</i> (OR: 0.52, 95% CI: 0.27–0.99) or t <i>TaqI</i> (OR: 2.06, 95%: 1.06–3.99) allele presented twice the risk for developing vitamin D deficiency compared to the reference allele. Moreover, subjects carrying 1, 2, or all 3 of these genotypes (BB/Bb, Tt/tt, and FF) demonstrated 2-fold (OR: 2.04, 95% CI: 0.42–9.92), 3.6-fold (OR: 3.62, 95% CI: 1.07–12.2), and 7-fold (OR: 6.92, 95% CI: 1.68–28.5) increased risk for low 25(OH)D<sub>3</sub> levels, respectively. <b><i>Conclusions:</i></b> Our findings reveal a cumulative effect of specific VDR gene polymorphisms that may regulate vitamin D concentrations explaining, in part, the paradox of vitamin D deficiency in sunny regions, with important implications for precision medicine.
DOI: 10.6084/m9.figshare.24233629.v14
title: <b>Unlocking Optimal ORM Designs: Accelerated Tradeoff </b><b>Analysis with Transformers</b>

description: Optimizing object-relational database mapping (ORM) design is essential for software system performance. However, current ORM design tools widely used in practice offer limited support for evaluating performance implications. State-of-the-art relying on systematic tradeoff analysis provides greater assistance but becomes impractical for large-scale, real-world systems. In this paper, we introduce an innovative solution grounded in machine learning to efficiently and scalably identify optimal ORM database tradeoffs.Our approach involves training a transformer model using a dataset of formally analyzed object-relational database designs to identify Pareto-optimal design tradeoffs, significantly reducing the number of design candidates. The extensive experiments across various software database systems demonstrate the high effectiveness of the approach in identifying optimal design alternatives overlooked by leading ORM tools. Additionally, our results show a remarkable 98.21 % improvement in analysis efficiency compared to the current state-of-the-art, reducing tradeoff analysis time from over 15 days to around 18 minutes on average.<br><br>
DOI: 10.6084/m9.figshare.24515095.v4
title: <b>Data</b>_<b><i>Boundary-Layer Meteorology</i></b> (Guo et al., 2024)

description: Please read "Readme_FYI.txt" prior to your use of our data, as are published in support of Figures 4, 5b,d, 9, 11 & 12 of the following peer-reviewed article.Material <sup><strong>1</strong></sup> links to: Eddy scale-wise topology underlying turbulence anisotropy illuminates the dissimilar transport of momentum, heat, and moisture in a stably stratified katabatic flow<br>
DOI: 10.6084/m9.figshare.28007000.v2
title: Supplementary Dataset Files

description: Refer to the Methods & Results section of the thesis
DOI: 10.6084/m9.figshare.28553744.v1
title: <i>Porphyromonas gingivalis</i> suppresses interferon signaling

description: Interferon signaling is a critical defense mechanism in host cells against intracellular pathogens. In macrophages, interferon-gamma stimulates the expression of numerous genes to enhance bactericidal activity. However, how <i>Porphyromonas gingivalis</i>, a key periodontal pathogen, evades this immune response remains unclear. This study investigated the molecular mechanisms by which <i>P. gingivalis</i> suppresses interferon signaling in macrophages, focusing on STAT1, a vital interferon transcription factor. RNA-seq and RT-qPCR analyses revealed that <i>P. gingivalis</i> infection suppressed nearly half of the interferon-gamma-induced genes, including STAT1.
DOI: 10.6084/m9.figshare.14191244.v1
title: Supplementary Material for: A New Concept for Central Wedge Resection in Labiaplasty

description: <b><i>Objective:</i></b> The aim of the study was to develop a new concept for central wedge resection to improve surgical results. Currently, the most common postoperative complications of the regular central wedge (RV) resection technique are wound dehiscence and scar contracture. <b><i>Methods:</i></b> A case-control study was applied to randomly divide 119 patients with labia minora hypertrophy deformities into 2 groups: new central wedge (NV) (<i>n</i> = 57) and RV (<i>n</i> = 62). All patients underwent the corresponding corrective surgery to repair the deformity. During the NV procedure, we changed the direction of the scalpel to form 2 inclined sections and sutured these sections together to achieve nonparallel closure lines. The patients in the 2 groups were followed up at 1 and 6 months postoperatively. We described the details of this method and evaluated the treatment outcomes of the 2 groups. <b><i>Results:</i></b> Patient age, labia minora width, and procedure time were not significantly different between the 2 groups (<i>p</i> &gt; 0.05). However, the visual analog scale (VAS) scores in the 2 groups were significantly different (<i>p</i> &lt; 0.05). Two patients in the NV group were somewhat dissatisfied because of lymphoedema and asymmetry; 6 patients in the RV group expressed dissatisfaction with scarring, healing complications, and asymmetry. A minor corrective operation was performed for asymmetry, and the dehiscence healed spontaneously. The patient with edema is still being followed up. <b><i>Conclusion:</i></b> The surgical method we introduced was indicated to be a simple and effective procedure that avoided wound dehiscence and scar contracture, which are common with the regular approach.
DOI: 10.6084/m9.figshare.28308620.v1
title: Source data for the Figures in Kono et al. (2025)

description: Kono et al. (2025), Gravitational stability of iron-rich peridotite melt at Mars's core-mantle boundary, Communications Earth & Environment.
DOI: 10.6084/m9.figshare.7676903.v1
title: Biomonitoring of Toxic Elements in Plants Collected Near Leather Tanning Industry

description: The present work aimed the study of atmospheric deposition of toxic elements near to a tannery industry by collecting black material deposited on leaf surfaces of cinnamon trees (Cinnamomum zeylanicum). Elements such as As, Ba, Cr, Cu, Fe, Ni, Pb, Sb, V, and Zn were analyzed by inductively coupled plasma mass spectrometry (ICP-MS). For comparison purpose, black particles deposited on the leaf surface of lemon trees (Citrus lemon) collected away from the tannery industry were also analyzed. Results showed that the amount of toxic elements found in the black particles collected near tannery area was significantly higher than the amount of those measured in the comparison site. Enrichment factors (EF) of As and Cr were markedly impacted by anthropogenic emissions, whereas the other elements were moderately/slightly enriched. Cluster analysis (CA) identified the leather industry as the anthropogenic source, while As possibly comes from the wide use of pesticides and herbicides in agricultural practices. The results indicated that emissions from the leather industry and agricultural activities are the main source of pollution in this area.
DOI: 10.6084/m9.figshare.1582639.v1
title: Raw data for Kuntz and Eisen, 2015 ‘Oxygen changes drive non-uniform scaling in Drosophila melanogaster embryogenesis’

description: Time-lapse imaging of developing Drosophila melanogaster embryos. Please see README.txt for a summary and specific details of the files contained in the compressed folder.
DOI: 10.6084/m9.figshare.23275817.v1
title: The transcriptome of human PBMCs incubated with or without Indoxyl sulfate-(Trans.fpkm) The pharmacokinetics of tacrolimus in PBMCs and whole blood of the two rat models of CKD-(MS data)

description: Human PBMCs were isolated from a healthy male Chinese volunteer, then resuspended in RPMI containing 10% FBS under standard cell culture conditions (humidified atmosphere, 5% CO2, and 37 ℃). Indoxyl sulfate (Sigma) was dissolved in RPMI containing 10% FBS and diluted to 0.2 mM in the range of recipients with CKD. Transcriptome analysis of PBMCs was then performed. Tac blood concentration measurement was performed using an HPLC-MS/MS system comprising an Agilent-1260 system and an API4000 triple quadrupole mass spectrometer (Applied Biosystems, Singapore) in positive mode. The analyte was separated on an ACE C18 column (20×2.1 mm, 2 μm) with an XDB pre-column. The mobile phase consisted of Phase A (water containing 10 mM Ammonium acetate with 0.1% Formic acid) and Phase B (Acetonitrile containing 0.1% Formic acid) at 20% (0-0.01 minutes), 40% (0.3 minutes), 60% (0.8 minutes), 80% (1.2 minutes), 95% (1.5 minutes), 98% (1.8 minutes), 95% (4.5 minutes), 60% (4.6 minutes), 40% (4.8 minutes), 20% (5-6 minutes). Multiple reaction monitoring modes had the m/z transitions of 821.8/768.6 (TAC); 931.8/864.7 (sirolimus [IS]). The linear range for the calibration curve in WB was 0.5-150 ng∙mL-1, and the lower limit of quantitation was 0.5 ng∙mL-1 PBMCs TAC concentration measurement was performed using a UPLC-MS/MS system comprising an LC30-AD (Shimadzu, Kyoto, Japan) system and an API5500 triple quadrupole mass spectrometer (Applied Biosystems, Singapore) in positive mode. The analyte was separated on a Waters C18 column (50×2.1 mm, 1.7 μm). The mobile phase consisted of Phase A (water containing 2 mM Ammonium format with 0.1% Formic acid) and Phase B (methanol) at 25% (0-0.5 minutes), 40% (1 minute), 60% (1.2 minutes), 80% (1.5 minutes), 95% (2 minutes), 95% (4.5 minutes), 60% (4.6 minutes), 40% (4.8 minutes), 25% (5-6 minutes). Multiple reaction monitoring modes had the m/z transitions of 821.8/768.6 (TAC); 931.8/864.7 (sirolimus [IS]). The method was validated according to Clinical Laboratory Standard Institute (CLSI) guidelines and showed high sensitivity and specificity over a range of 0.005-2.5 ng∙10-6 PBMCs in PBMC.
DOI: 10.6084/m9.figshare.11416899.v1
title: Supplementary Material for: Linking Colony Size with Foraging Behavior and Brain Investment in Odorous Ants (Formicidae: Dolichoderinae)

description: Superorganisms represent a unique level of biological organization in which the phenotype of the reproductive unit, the colony, results from traits expressed at the level of individual workers. Because body size scaling has important consequences for cell diversity and system complexity in solitary organisms, colony size is a trait of particular interest in superorganism evolution. In some instances, division of labor and worker polymorphism scale with colony size, but in general little is known about how colony size drives differences in individual-level behavior or neural traits. Ants represent the greatest diversity of superorganisms and provide a manner of natural experiment to test trends in trait evolution across multiple instances of colony size expansion. In this study, we control for environmental differences and worker size polymorphism to test if colony size correlates with measures of foraging behavior and brain size in dolichoderine ants. We present data from 3 species ranked by colony size. Our results suggest colony size correlates with measures of exploratory behavior and brain investment, with small-colony ants showing higher exploratory drive and faster exploration rate than the larger colony species, and greater relative investment in the primary olfactory brain region, the antennal lobe, than the larger colony species.
DOI: 10.6084/m9.figshare.21517662.v1
title: Supplementary Material for: Development and validation of a cardiovascular disease risk prediction model for patients with non-dialysis-dependent chronic kidney diseases based on the nomogram

description: Introduction Most CKD patients experience cardiovascular issues before commencing renal replacement therapy. An accuracy prediction model is helpful for physicians to assess cardiovascular prognoses in each individual, and to provide insights on how to outline individualized lines of therapy. Method This study enrolled 1138 participants with non-dialysis-dependent chronic kidney disease (NDD-CKD). Following a proportion of 7:3, patients were randomly assigned to training and validation cohorts. The relevant predictors of cardiovascular events were screened using the least absolute shrinkage and selection operator (Lasso) regression. The area under the receiver operating characteristic curve (AUC) and the calibration curve with 1000 bootstraps resamples were used to assess the nomogram's performance. Tests on the discrimination of the prediction model used Kaplan-Meier (KM) curve. Results After screening all the predictors by lasso regression, the five remaining ones (albumin, estimated glomerular filtration rate, etiology of CKD, cardiovascular disease history, and age) were used to construct the prediction model. The AUC of 1-year, 2-year, and 3-year was 0.81 (95% CI = 0.75–0.87), 0.80 (95% CI = 0.75–0.86), and 0.80 (95% CI = 0.73–0.86), respectively. The calibration curve and the KM curve showed good prediction features, and the external validation also had a good prediction performance (AUC of 1-, 2-, and 3-years were 0.77, 0.84, and 0.82, respectively). Conclusion We successfully developed a novel nomogram that has decent prediction performance and can be used for assessing the probability of cardiovascular events in patients with NDD-CKD, displaying valuable potential for clinical application.
DOI: 10.6084/m9.figshare.28801208.v1
title: Perceiving Multidimensional Disaster Damages from Street-View Images Using Visual-Language Models

description: Post-disaster street-view imagery has increasingly become a critical resource for ground-level damage assessment and disaster perception classification tasks, significantly contributing to disaster reporting. However, existing approaches face notable limitations, such as the requirement for extensive manual annotations and limited interpretability inherent in pretrained image classification models. Recently, Large Language Models (LLMs) have attracted considerable interest due to their robust natural disaster-related domain knowledge, powerful text generation abilities, and advanced capabilities in visual comprehension. This study explores and expands the potential of LLMs for perceiving multi-dimensional disaster impacts through street-view imagery. Specifically, we collected 2,556 street-view images taken post-hurricane from regions in Florida. For experimental purposes, these images were annotated directly by GPT-4 mini (via prompt engineering) to quantify disaster impacts, alongside parallel annotations by human experts.
DOI: 10.6084/m9.figshare.11948691.v1
title: Supplementary Material for: Clinical Utility and Global Applicability of Prolonged Grief Disorder in the ICD-11 from the Perspective of Chinese and German-Speaking Health Care Professionals

description: <b><i>Background:</i></b> Prolonged grief disorder (PGD) is included in the ICD-11 (11th edition of the International Classification of Diseases). The new PGD criteria reflect the requirements and recommendations of the World Health Organization for improved clinical utility and international applicability. Even though the ICD classification system is globally used, no research has investigated how healthcare professionals (HP) in non-Western countries may adopt this change for their own practice. <b><i>Objective:</i></b> The present study explored the extent to which the new PGD criteria were accepted and perceived to meet the standards for clinical utility and international applicability among Chinese and German-speaking HP. <b><i>Methods:</i></b> Individual semistructured interviews were conducted in person, by phone, or online (e.g., via Skype), with 24 Chinese (<i>n</i> = 10) and German-speaking (<i>n</i> = 14) HP working with bereaved populations in China and Switzerland, and analyzed using a qualitative framework analysis. Questions included “what items are currently missing from the PGD criteria?”. <b><i>Results:</i></b> Across all HP, the majority supported the inclusion of PGD and were generally aligned with the current criteria. HP found that the criteria distinguished between normal and abnormal grief and considered the criteria easy to use if their modifications were considered. Merits included, among others, improved clinical decision making, research promotion, and social acknowledgment. Main concerns included misdiagnosis, pathologization, and a lack of specificity of criteria. The importance of international applicability was emphasized across Chinese and German-speaking HP. Different grief-specific symptoms were identified by German-speaking and Chinese HP. <b><i>Conclusions:</i></b> These findings provide evidence for the clinical utility and international applicability of ICD-11 PGD criteria among German-speaking and Chinese HP, as well as cultural similarities and differences in the barriers to implementation of these criteria.
DOI: 10.6084/m9.figshare.19687213.v1
title: Additional file 2 of The impact of a digital joint school educational programme on post-operative outcomes following lower limb arthroplasty: a retrospective comparative cohort study

description: Additional file 2.
DOI: 10.6084/m9.figshare.27101089.v1
title: Raw data of "prey bioluminescence-mediated visual luring in a sit and wait predator"

description: File spectrum.csvThe spectrum of luminescence signals produced by male (<code>Source == Male firefly</code>) and female (<code>Source == Female</code>) <i>Diaphanes lampyroides</i> and that of the LED device (<code>Source == LED</code>) used in the field experiments. Spectrum of wavelength lower than 450 nm are trimmed.File LED-experiment.csvThe numbers of firefly/non-firefly attraction and interception events between control and LED treatments. The web area, date, and video duration of each observed web are also recorded.
DOI: 10.6084/m9.figshare.28093631.v1
title: Supplementary Material for: BEYOND THE LIMIT: SALVAGING THE POSTERIOR CIRCULATION TERRITORY VIA LATE ENDOVASCULAR THROMBECTOMY

description: Introduction: Posterior circulation infarctions, particularly basilar artery occlusions, contribute significantly to morbidity and mortality in ischemic stroke. However, literature supporting mechanical thrombectomy in the posterior circulation, especially beyond the 24-hour window, is limited. 
Case Presentation: We present the case of a 64-year-old male diagnosed with basilar artery occlusion who underwent a successful mechanical thrombectomy 11 days after symptom onset. Despite complications such as hemorrhagic transformation and herniation, the patient was stabilized and showed functional improvement 3 months post-stroke, 
Conclusion: This case suggests that delayed thrombectomy may provide benefits for selected patients, even beyond the recommended 24-hour window. Further research is essential to refine treatment strategies and potentially extend the intervention window for posterior circulation strokes.
DOI: 10.6084/m9.figshare.28450565.v1
title: Leader Visibility DataLV= Leader VisibilityIB = Innovative Work BehaviorHD = Hierarchical DistanceITQ = Intent to QuitRWYS = Leader Member Exchange

description: This study explores the impact of leader visibility (LV), hierarchical distance (HD), and leader-member exchange (LMX) on employees' innovative work behavior (IWB) and their intent to quit. Despite leadership’s importance, LV and HD have received limited attention. The research also develops a standardized LV questionnaire to address this gap. A survey of 458 employees from innovative U.S. companies was conducted, with data analyzed using correlation and regression methods. Findings show that LV and LMX boost IWB and reduce quitting intentions, while HD has the opposite effect. The new 6-item LV questionnaire meets reliability and validity standards.
DOI: 10.6084/m9.figshare.14823009.v1
title: Supplementary Material for: Human herpesvirus 6 infection and risk of Chronic fatigue syndrome: a systematic review and meta-analysis

description: Medicine
DOI: 10.6084/m9.figshare.27895734.v1
title: Data --- Hot Ion Total Azimuthal Drift, Coupled Ei On

description: This is the set of simulation data including the plasma total azimuthal drift, for the idealized 9-hour solar wind simulation. The effect of inductive electric field is considered.
DOI: 10.6084/m9.figshare.7083389.v2
title: PopPUNK Listeria monocytogenes dataset

description: This is an example set of 128 Listeria monocytogenes genomes, reported in https://doi.org/10.1016/j.cmi.2016.12.008.<br>They are used to demonstrate the function of the software PopPUNK https://poppunk.readthedocs.io/
DOI: 10.6084/m9.figshare.28163363.v1
title: Supplementary Material for: A case of myeloproliferative neoplasm with eosinophilia associated with PCM1-JAK2 rearrangement

description: Introduction: The PCM1-JAK2 rearrangement is generated through the t(8; 9)(p22; p24) translocation event. The myeloid/lymphoid neoplasms with eosinophilia (MLN-eo) with PCM1-JAK2 rearrangement is the common types of MLN-eo with tyrosine kinase fusion genes (MLN-Eo-tk). MLN-Eo with PCM1-JAK2 rearrangement is a rare disease with a poor prognosis and no unified treatment guidelines. The response of disease to ruxolitinib may be transient and it may only serve as a temporary treatment prior to transplantation. Case Presentation: We report one patient diagnosed with MLN-Eo with PCM1-JAK2 rearrangement who exhibited resistance to ruxolitinib, subsequently received pegylated interferon (Peg-IFN) and lenalidomide. The Peg-IFN was discontinued due to adverse effects, the patient has been receiving lenalidomide monotherapy for a duration exceeding two years, achieving complete hematologic remission and molecular response, significant amelioration of symptoms, as well as regression of hepatosplenomegaly. Conclusion: A case of MLN-Eo with PCM1-JAK2 rearrangement underwent continuous oral lenalidomide monotherapy for over two years. The patient achieved complete hematologic remission and molecular response during the long-term follow-up; however, a complete molecular remission was not attained. The underlying mechanism of lenalidomide in these diseases necessitates further comprehensive investigation through fundamental research and clinical trials.