cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.26083456.v1
title: Supplementary Material for: Whole-genome sequencing reveals a novel pathogenic GRIN2B variant in a patient with neurodevelopmental disorder and an inv(6)(p24p11.2)pat

description: Introduction: Neurodevelopmental disorders (NDDs) are diverse and can be explained by either genomic aberrations or single nucleotide variants (SNVs). Most likely due to methodological approaches and/or disadvantages, the concurrence of both genetic events in a single patient has hardly been reported and even more rarely the pathogenic variant has been regarded as the cause of the phenotype when a chromosomal alteration is initially identified. Case Presentation: Here, we describe a NDD patient with a 6p non-pathogenic paracentric inversion paternally transmitted and a de novo pathogenic variant in the GRIN2B gene. Molecular-cytogenetic studies characterized the familial 6p inversion and revealed a paternal 9q inversion not transmitted to the patient. Subsequent whole-genome sequencing (WGS) in the patient-father dyad corroborated the previous findings, discarded inversions-related cryptic genomic rearrangements as causative of the patient’s phenotype, and unveiled a novel heterozygous GRIN2B variant (p.(Ser570Pro)) only in the proband. In addition, Sanger sequencing ruled out such a variant in her mother and thereby confirmed its de novo origin. Due to predicted disturbances in the local secondary structure, this variant may alter the ion channel function of the M1 transmembrane domain. Other pathogenic variants in GRIN2B have been related to the autosomal dominant neurodevelopmental disorder MRD6 (Intellectual developmental disorder, autosomal dominant 6, with or without seizures), which presents with a high variability ranging from mild intellectual disability (ID) without seizures to a more severe encephalopathy. In comparison, our patient's clinical manifestations include, among others, mild ID and brain anomalies previously documented in subjects with MRD6. Conclusion: Occasionally, gross chromosomal abnormalities can be coincidental findings rather than a prime cause of a clinical phenotype (even though they appear to be the causal agent). In brief, this case underscores the importance of comprehensive genomic analysis in unraveling the wide-ranging genetic causes of NDDs and may bring new insights into the MRD6 variability.
DOI: 10.6084/m9.figshare.3558222.v1
title: Supplement 1. R script with annotations for simulation and analysis of simulation output.

description: File List R_script_simulation.r (MD5: 3b20e3f347a136eb3c3470bbb57101b1) Description The supplement is a script (R_script_simulation.r) demonstrating the implementation of our simulations and subsequent analysis of asymmetry. The simulation method we utilized is nonparametric and user-defined. For this reason we have included the script. As described in the methods section of our associated manuscript, the simulation involves imposing species extinctions in our post-mixing communities and using the output as a null model against which we compare our observed results. The script includes annotations describing the function of each section of code.
DOI: 10.6084/m9.figshare.12954488.v1
title: FASTQ: DREAM SMC-RNA Challenge, smc_rna_sim45

description: Simulated FASTQ data from the DREAM SMC-RNA Challenge
DOI: 10.6084/m9.figshare.6820643.v2
title: Dataset 3 from Phylogenetic and functional evidence suggests that deep-ocean ecosystems are highly sensitive to environmental change and direct human disturbance.

description: Functional trait matrix (Matrix of functional traits by peracarid family).
DOI: 10.6084/m9.figshare.21585543.v1
title: Zarr files for PCA

description: Zarr files for constructing PCA
DOI: 10.6084/m9.figshare.5124151.v1
title: Supplementary Material for: CD4+ T Lymphocytes, Especially Th2 Cells, Contribute to the Progress of Renal Fibrosis

description: <b><i>Background:</i></b> Renal tubulointerstitial fibrosis is the final common stage of renal failure. CD4+ T lymphocyte recruitment and activation after injury could be the very important early event that mediates the onset of renal fibrogenesis. But the role of CD4+ T lymphocytes in renal fibrosis is controversial and its cellular mechanism needs to be further investigated. <b><i>Methods:</i></b> Biopsy specimens were from patients with minimal-change or IgA nephropathy. Mouse renal fibrosis was induced by unilateral ureteral obstruction (UUO). CD4+ T lymphocytes of wild BALB/c mice were depleted with anti-CD4 antibody. BALB/c Nu/Nu mice were reconstituted with polarized Th1 or Th2 cells by tail vein injection. <b><i>Results:</i></b> Our study demonstrated that massive CD4+ T lymphocytes infiltrated fibrotic kidneys of patients. The depletion of CD4+ T lymphocytes inhibited UUO-induced mouse renal fibrosis. In the process of UUO-induced renal fibrosis, the ratios of Th2/Th1 increased with time. Results have also shown that Th2-reconstituted mice developed renal fibrosis more easily than Th1-reconstituted mice, which manifested by interstitial expansion and collagen deposition, higher expression of α-SMA and vimentin and increased expression of fibronectin, TGF-β and collagen I. We also found that CD4+ T cells from Th1-reconstitued mice tended to secrete IL-4 and IL-13 Th2-like cytokines. <b><i>Conclusion:</i></b> In conclusion, our study demonstrated the importance of CD4+ T lymphocytes in renal fibrosis and gave the first direct evidence that Th2 cells play a pivotal role in UUO-induced renal fibrosis. Inhibition of CD4+ T lymphocyte differentiation to Th2 would be a potential therapeutic intervention to prevent renal fibrosis.
DOI: 10.6084/m9.figshare.14188466.v1
title: SUPPLEMENTARY DATA-AJP-GI

description: Supplementary text
DOI: 10.6084/m9.figshare.12153528.v1
title: Body condition nesting females

description: Study of body condition of nestng females<br>
DOI: 10.5281/zenodo.15315396
title: Unique transcriptional profiles of adult human immature neurons in healthy aging, Alzheimer's disease, and cognitive resilience

description: Following files submitted:1. adult_raw.RDS : Raw seurat object of the processed adult (n=24) snRNA-seq samples.2. adult_filtered.RDS : Filtered (after QC) seurat object of the processed adult (n=24) snRNA-seq samples.3. adultgc_filtered.RDS : Seurat object of adult granule cell subset after additional filtering (See Fig3A). 4. fetal_raw.RDS : Raw seurat object of the processed fetal (n=3) snRNA-seq samples.5. fetal_filtered.RDS : Filtered (after QC) seurat object of the processed fetal (n=3) snRNA-seq samples.6. neurolin.RDS : Seurat object of fetal neurogenic lineage subset (See Fig2D). 7. Functions.R : Helper functions written for running scripts.8. Fig1_script.Rmd : Script to reproduce analysis in Figure 1 and its supplementaries.9. Fig2_script.Rmd : Script to reproduce analysis in Figure 2 and its supplementaries.10. Fig3_script.Rmd : Script to reproduce analysis in Figure 3 and its supplementaries.11. Fig4_script.Rmd : Script to reproduce analysis in Figure 4 and its supplementaries.12. Fig5_script.Rmd : Script to reproduce analysis in Figure 5 and its supplementaries.13. Fig6_script.Rmd : Script to reproduce analysis in Figure 6 and its supplementaries.
DOI: 10.6084/m9.figshare.28705496.v1
title: self-supervised framework.zip

description: Data and code for paper "<i>Self-Supervised Graph Learning for Bicycle OD Flow Semantic Awareness: Harnessing High-Order Relationships via Trajectory Chains and POI Contexts</i>"
DOI: 10.6084/m9.figshare.26972611.v1
title: Chemosynthetic_SppCounts

description: Workbook containing density data by taxon from known-volume community collections from biogenic cold seep habitats including tubeworm bushes and mussel beds. 'Meta' tab shows the depth for each site in the study, while 'Chemos_SppDens' tab contains densities of associated taxa.
DOI: 10.6084/m9.figshare.1136081_d155
title: Ex6R15C2 YFP-1 from Synaptic molecular imaging in spared and deprived columns of mouse barrel cortex with array tomography.

description: This data represents repeated immunohistochemical staining and stripping (elution) cycles of an array tomography tissue ribbon from mouse barrel cortex following chessboard deprivation. Included are images from consecutive 70 nm serial sections aligned to produce a high-resolution volumetric reconstruction of a given antibody stain.
DOI: 10.6084/m9.figshare.23498426.v1
title: <strong>Non-Tuberculous</strong> <strong>Mycobacterium isolations from</strong> <strong>Tuberculosis</strong> <strong>presumptive cases at the</strong> <strong>National Tuberculosis Reference Laboratory Kenya, 2018 </strong>–<strong>2019</strong>

description: <br> Mycobacterial pathogens are among the top causes of diseases in humans. In Kenya, incidences of Non-Tuberculous Mycobacteria (NTM) species have steadily been on the increase. Most NTMs are resistant to first line treatment of tuberculosis and have a challenge in timely and accurate diagnosis. Misdiagnosis has led to prescribing anti-tuberculosis regimens to patients suffering from NTM. We aimed to determine the most prevalent Non-Tuberculous <em>Mycobacterium</em> in Kenya. <br>
DOI: 10.6084/m9.figshare.28544036.v1
title: KleinmanFoster_2025_eLife

description: Data set for Kleinman and Foster, 2025, "Spatial localization of hippocampal replay requires dopamine signaling"
DOI: 10.15468/dl.uqagpj
title: Occurrence Download

description: A dataset containing 3194 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Observation, Human Observation, Machine Observation, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Watsonalla cultraria (Fabricius, 1775)"
 ]
}

 The dataset includes 3194 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009552-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.21081031.v1
title: Supplementary Material for: Does Sickle Cell Disease Protect against HIV Infection: A Systematic Review

description: Objective: The aim of this systematic review was to investigate if SCD protects against HIV infection by determining the association between SCD and the incidence and virulence of HIV infection. Methods: This is a systematic review that used MEDLINE, PubMed, CINAHL, and Academic Search Complete as data sources. Articles describing the relationship of SCD with HIV infection were included in this review. Hence, the effect measures were converted to correlation coefficients and synthesized accordingly to examine the putative protective role of SCD over HIV infection. Independent full-text screening and data extraction were conducted on all eligible studies. The risk of bias was assessed using the mixed methods appraisal tool. We employed a random-effects model of meta-analysis to estimate the pooled prevalence. We computed Cochrane's Q statistics, I2, and prediction interval to quantify effect size heterogeneity. Results: SCD reduces the risk of HIV infection by 75% (OR = 0.25; r = -0.36, p &lt; 0.001; I2 = 71.65). There was no publication bias (Egger’s t-value = 0.411; p = 0.721) (Figure 2). Similarly, risk of HIV virulence was reduced by 77% (OR = 0.23; r= -0.38; p &lt; 0.001; I2 = 63.07).The mechanisms implicated in the protective influence of SCD include autosplenectomy, reduced CCR5 expression, and increased expression of heme and iron-regulated genes. Conclusions: Sickle cell disease appears protective of HIV infection and slows HIV progression. PROSPERO registration Number: CRD42022304490
DOI: 10.6084/m9.figshare.19719421.v1
title: MIMA study - Palbociclib

description: spatially registered images of multiplex IHC staining of MMTV-PyMT mammary carcinoma tissue three days after local Palbociclib drug delivery. Drug release is from the bottom to the top.
DOI: 10.6084/m9.figshare.25470154.v1
title: Supplementary Material for: The impact of statin treatment duration on the risk of new-onset diabetes mellitus and recurrent vascular events in ischemic stroke patients: a linked data analysis

description: Introduction: Although statin therapy reduces cardiovascular events, statin use is associated with the risk of new-onset diabetes mellitus (NODM). Using a linked dataset, we evaluated the effect of statin treatment on vascular outcomes and NODM development in patients with ischemic stroke. 
Methods: From the dataset, we identified 20,250 patients with acute ischemic stroke who had neither a prior history of DM nor a previous history of statin use before the index stroke. Patients were divided into statin users and non-users. The outcomes were NODM and vascular outcomes, including recurrent ischemic stroke and acute myocardial infarction (AMI). 
Results: Of the 20,250 patients, 13,706 (67.7%) received statin treatment after the index stroke. For the risk of NODM, a time-response relationship was observed between the use of statins and NODM; a longer post-stroke follow-up duration substantially increased the risk of NODM. Among those with ischemic stroke exceeding 3 years, statin users had an approximately 1.7-fold greater risk of NODM than statin non-users. Statin therapy significantly reduced the risk of recurrent ischemic stroke by 54% (HR 0.46, 95% CI, 0.43–0.50, P &lt; 0.001) across all stroke subtypes. 
Conclusion: Statin therapy following ischemic stroke increased the occurrence of NODM in patients over a period of 3 years. Despite the increased risk of NODM, statin therapy shows a beneficial effect in reducing major cardiovascular events such as recurrent ischemic stroke and AMI in patients with ischemic stroke.
DOI: 10.6084/m9.figshare.26879650.v1
title: Supplementary Material for: Outcomes of Patients with Critical Limb Ischemia and Chronic Kidney Disease: A National Perspective

description: Introduction: Studies exploring the relationship between peripheral arterial disease (PAD), critical limb ischemia (CLI), and chronic kidney disease (CKD) and its effect on in-hospital outcomes are limited. We aimed to analyze the outcomes of patients with CKD and PAD who are admitted for CLI.
Methods: We utilized the National Inpatient Sample (NIS) to capture hospitalizations for CLI from 2012-2020 and then identified cases with concomitant CKD. The primary outcome was mortality, and secondary outcomes were cerebrovascular accident, major bleeding, vasopressor requirement, percutaneous coronary intervention, cardiac arrest, acute respiratory failure, transfusion, length of stay (LOS), and total hospital charges. Multivariable logistic regression was performed to adjust for covariates.
Results: A total of 441,245 patients with CLI were identified, of which 122,370 (27.7%) reported concomitant CKD. Patients with CKD had a higher in-patient mortality (OR 1.68, CI, 1.17-1.68, p &lt; 0.001), vascular complications (OR 1.31, 95% CI, 1.17-1.48, p&lt;0.001), acute kidney injury requiring hemodialysis (OR 3.17, 95% CI, 2.64-3.80, p&lt; 0.001) and major bleeding (OR 1.12, 95% CI 1.05-1.19, p&lt;0.001). Patients with CKD underwent minimally-invasive endovascular therapy (31.08% vs 36.73%, p&lt;0.0001) and invasive procedures (14.73% vs 23.55%, p&lt;0.0001) less often. PAD-CLI with CKD was associated with major (20.54% vs. 16.17%, OR 1.04; p&lt;0.0001) and minor (26.87% vs. 19.53%, OR 1.2, p&lt;0.0001) amputations more often. 
Conclusion: Patients admitted for PAD-CLI with concomitant CKD have significantly higher in-hospital mortality as compared to patients without CKD. Moreover, patients with CKD and PAD-CLI are less likely to receive revascularization and more likely to undergo amputation.
DOI: 10.6084/m9.figshare.28660310.v1
title: Supplementary Material for: Decreased Lactococcus lactis and propionic acid in feces of patients with Moyamoya disease: Possible implications of immune dysregulation

description: Introduction: Moyamoya disease (MMD) is a cerebrovascular disease characterized by progressive steno-occlusive lesions in the terminal portion of the internal carotid artery. Despite its unknown etiology, immune dysregulation is regarded as a critical trigger for delineating the pathophysiology of MMD. The gut microbiota produces short-chain fatty (SCFA) and organic acids, influencing immune regulation and vascular remodeling. We aimed to characterize the gut microbiota in patients with MMD.
Methods: Sixteen patients with MMD and sixteen healthy controls were included in this study. We performed 16S rRNA sequencing of fecal samples and analyzed microbiome diversity and composition, and quantified SCFA and organic acid levels using liquid chromatography.
Results: There were no significant differences in α- and b-diversities among feces from the MMD patients and controls. However, 16S rRNA sequencing identified defective Lactococcus lactis (0 ± 0 in the MMD patients vs. 0.026 ± 0.084 in healthy controls, p = 0.0181) and abundant Gordinobacter pamelaeae (0.030±0.039 in the patients vs. 0.001±0.005 in healthy controls, p = 0.003) are strongly linked to MMD. Propionic acid levels were significantly lower in feces of the MMD patients compared to healthy controls (0.83 ± 0.34 mg/g in the MMD patients vs. 1.20 ± 0.55 mg/g in healthy controls, p = 0.028). 
Conclusion: Decreased Lactococcus lactis can result in reduced lactic acid and propionic acid levels in the feces of the patients. This imbalance in the gut microbiome and SCFA/organic acid levels could contribute to immune dysregulation underlying the vascular remodeling seen in MMD.
DOI: 10.6084/m9.figshare.c.3606911_d3.v1
title: Additional file 3: Table S3. of Elucidating the molecular physiology of lantibiotic NAI-107 production in Microbispora ATCC-PTA-5024

description: Description, functional classification, abundance profile and mass spectrometry identification parameters of differentially represented Microbispora ATCC-PTA-5024 proteins identified from membrane proteome analysis at A substages. (XLSX 37 kb)
DOI: 10.6084/m9.figshare.21485682.v1
title: GDP2020.rar

description: China's GDP in 2020
DOI: 10.6084/m9.figshare.26831803.v1
title: heritageMeta.csv

description: Data compiling the speakers' linguistic profile
DOI: 10.6084/m9.figshare.12480479.v1
title: Supplementary Material for: Major Predictive Factors for Progression of Early to Late Age-Related Macular Degeneration

description: <b><i>Introduction:</i></b> We present a prediction model for progression from early/intermediate to advanced age-related macular degeneration (AMD) within 5.9 years. <b><i>Objectives:</i></b> To evaluate the combined role of genetic, nongenetic, and phenotypic risk factors for conversion from early to late AMD over ≥5 years. <b><i>Methods:</i></b> Baseline phenotypic characteristics were evaluated based on color fundus photography, spectral-domain optical coherence tomography, and infrared images. Genotyping for 36 single-nucleotide polymorphisms as well as systemic lipid and complement measurements were performed. Multivariable backward logistic regression resulted in a final prediction model. <b><i>Results and Conclusions:</i></b> During a mean of 5.9 years of follow-up, 22.4% (<i>n</i> = 52) of the patients (<i>n</i> = 232) showed progression to late AMD. The multivariable prediction model included age, <i>CFH</i> variant rs1061170, pigment abnormalities, drusenoid pigment epithelial detachment (DPED), and hyperreflective foci (HRF). The model showed an area under the curve of 0.969 (95% confidence interval 0.948–0.990) and adequate calibration (Hosmer-Lemeshow test, <i>p</i> = 0.797). In addition to advanced age and carrying a <i>CFH</i> variant, pigment abnormalities, DPED, and HRF are relevant imaging biomarkers for conversion to late AMD. In clinical routine, an intensified monitoring of patients with a high-risk phenotypic profile may be suitable for the early detection of conversion to late AMD.
DOI: 10.6084/m9.figshare.22548538.v1
title: Attitude towards Technical and Vocational Education and Training (TVET): Examining the Effect of Behavioral Insights Approach - Underlying data for phase 1

description: Underlying data for phase 1 (survey)
DOI: 10.6084/m9.figshare.27430458.v1
title: Supplementary Material for: Developing a core outcome set for Netherton syndrome: An international multi-stakeholder e-Delphi consensus study

description: Introduction: Netherton syndrome (NS; OMIM#256500) is a rare and severe disorder of epidermal maturation and keratinization caused by pathogenic variants in the serine protease inhibitor Kazal type 5 (SPINK5), leading to severe skin barrier impairment. Although effective treatment is crucial for NS patients, there is a lack of knowledge on what the best treatment options are for these patients. Large heterogeneity in reported outcomes and measurement instruments hinders accurate comparison of treatment results across studies and the development of a treatment guideline. Therefore, we aimed to develop a core outcome set (COS) for NS that can be used in clinical care and research.

Methods: This study was performed in accordance with the recommendations of the Core Outcome Measures in Effectiveness Trials (COMET) initiative. After identification of outcomes through a literature search and classification based on the International Classification of Functioning and taxonomies published by the COMET initiative, discussion groups were organized at the 2nd International Netherton Congress 2022 to finalize the provisional outcome list. Through a 2-round e-Delphi, 41 stakeholders (patients and family members, professionals, and representatives of industry) from 14 countries rated the importance of the outcomes using a 9-point Likert scale. An online consensus meeting attended by 14 stakeholders finalized the COS.

Results: The core outcome set for NS comprised 21 outcomes in 10 domains. These included four ‘skin’ outcomes, two ‘sensation’ outcomes, two ‘side-effects of treatment’ outcomes, one ‘vitality’ outcome, one ‘emotional functioning’ outcome, two ‘physical development’ outcomes, two ‘nutrition’ outcomes, two ‘infections’ outcomes, two ‘allergies’ outcomes, and three ‘assessment results’ outcomes.

Conclusion: In this study, consensus was reached on 21 outcomes to be included in the COS for NS. The selection of outcomes in the COS underlines that NS not only affects the skin, but is a disease requiring a broad multidisciplinary approach in clinical care and research. International implementation of this COS will lead to more uniform reporting, thereby enabling comparison of study results, which may facilitate future treatment guideline development. The next step is to further conceptually define the outcomes and reach consensus on how the measure these.
DOI: 10.6084/m9.figshare.25951720.v1
title: Lattice optimization, electron-phonon properties, and EPC results of few-hydrogen metal-bonded perovskites

description: Full DFT calculations of few-hydrogen metal-bonded perovskites by using QE, including lattice optimization, electron-phonon properties, and EPC results