cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.25972078
title: Supplementary Material for: Association between serum magnesium levels and risk of acute kidney injury in patients with traumatic brain injury: A retrospective cohort study from the MIMIC-Ⅳ database

description: Introduction: The occurrence of acute kidney injury (AKI) is associated with a higher risk of mortality in patients with traumatic brain injury (TBI). This study aimed to explore the relationship between serum magnesium levels and the risk of AKI in patients with TBI.
Methods: Patients with TBI were identified from the Medical Information Mart Intensive Care Ⅳ (MIMIC-Ⅳ) 2008-2019. The relationship between serum magnesium levels at admission and magnesium coefficient of variation (CV) during hospitalization and the risk of AKI was analyzed using multivariable logistic regression analysis and expressed as odds ratio (OR) and 95% confidence interval (CI). Subgroup analyses were performed according to Glasgow Coma Scale (GCS) score (&lt;14, ≥14), sepsis (no, yes), and estimated glomerular filtration rate (eGFR; &lt;60, ≥60).
Results: Of the 991 patients included, 140 (14.13%) developed AKI during hospitalization. Patients with magnesium levels ≤1.7 mg/dL (tertile 1) (OR=1.68, 95%CI: 1.01-2.81) were associated with a higher risk of AKI compared to those with magnesium levels of 1.7-2.0 mg/dL (tertile 2), but no association was found in those with magnesium levels &gt;2.0 mg/dL (tertile 3) (P=0.479). For magnesium CV, patients with magnesium CV &gt;10% (tertile 3) (OR=2.26, 95%CI: 1.16-4.41) were linked to an increased risk of AKI compared to those with magnesium CV ≤4% (tertile 1), but there may be a slight association between magnesium CV of 4%-10% (tertile 2) and AKI risk (OR=1.86, 95%CI: 0.99-3.48; P=0.053). Subgroup analyses showed that lower magnesium levels (≤1.7 mg/dL) or greater magnesium CV (&gt;10%) were associated with a higher risk of AKI only in patients with a GCS score ≥14, non-sepsis, or eGFR ≥60 mL/min/per1.73m2 (P&lt;0.05).
Conclusion: Lower serum magnesium levels at admission or greater magnesium CV during hospitalization were associated with a higher risk of AKI in patients with TBI.
DOI: 10.6084/m9.figshare.25981951
title: Supplementary Material for: Comorbidity and medication trends in chronic kidney disease and incident atrial fibrillation – A Nationwide Cohort Study

description: Introduction
Chronic kidney disease (CKD) is associated with increased incidence of atrial fibrillation (AF). Also, patients with AF are prone to adverse kidney outcomes. We examined comorbidities and medication use in patients with CKD and incident AF. 
Methods
The Finnish AntiCoagulation in Atrial Fibrillation (FinACAF) is a nationwide retrospective register-linkage study including data from 168 233 patients with incident AF from 2007 to 2018, with laboratory data from 2010 onwards. Estimated glomerular filtration rate (eGFR) was available for 124 936 patients. The cohort was divided into 5 CKD stages with separate groups for dialysis and kidney transplantation.
Results
At AF diagnosis eGFR &lt;60ml/min/1.73m2 was found in 27%, while 318 (0.3%) patients were on dialysis, and 188 (0.2%) had a functioning kidney transplant. Lowering eGFR yielded to more comorbidities and medications. During 2010-2018 in patients with eGFR &lt;60ml/min/1.73m2 prevalence of hypertension, dyslipidaemia and diabetes increased from 82% to 88 %, from 50% to 66% and from 25% to 33%, respectively (&lt;0.001). Throughout the observation period, lipid-lowering medication was underused. 
Conclusions
More than one-fourth of patients with incident AF also had CKD stage 3-5 (eGFR &lt;60ml/min/1.73m2). Both comorbidities and medication use increased with worsening kidney function. Prevalence of major cardiovascular (CV) risk factors increased during 2010-2018, but use of survival affecting medications, such as lipid-lowering medication, was suboptimal at all stages of CKD. More attention should be given to the optimal treatment of risk factors in this high CV risk population.
DOI: 10.6084/m9.figshare.26302075
title: <b>Simultaneous and </b><b><i>in situ</i></b><b> syntheses of an enantiomeric pair of homochiral polymers as their perfect stereocomplex in </b><b>a </b><b>crystal</b>

description: Kz_326_poly_bg_subtracted_PXRD and Kz_326_mono_bg_subtracted_PXRD - These data refer to the PXRD image shown as fig. 4d in the main manuscript.kz_326_mono_DSC and kz-326_poly_DSC - These data refer to the DSC image shown as fig. 4c in the main manuscript.kz_mono_326_IR and kz_poly_326_IR_Baselinecrc - These data refer to the IR image shown as fig. 4b in the main manuscript.
DOI: 10.6084/m9.figshare.26493934
title: Supplementary Material for: The Glasgow Prognostic Score as a Predictor of Survival After Chemoradiotherapy for Limited-Disease Small Cell Lung Cancer

description: Introduction: Established biomarkers for predicting chemoradiotherapy efficacy for limited-disease small cell lung cancer (LD-SCLC) are lacking. The inflammation-based Glasgow Prognostic Score (GPS), comprising serum C-reactive protein (CRP) and albumin levels, can predict survival in advanced cancer. This study investigated whether metabolic and inflammatory markers, including the GPS, can predict the efficacy of chemoradiotherapy in patients with LD-SCLC.
Methods: We retrospectively analyzed 124 patients who underwent chemoradiotherapy for LD-SCLC at two institutions between April 2007 and June 2021, and assessed the prognostic significance of various metabolic and inflammatory markers. The GPS was calculated using the CRP and albumin concentrations, and categorized as follows: 0, CRP&lt;1.0 mg/dL and albumin≥3.5 mg/dL; 1, elevated CRP or decreased albumin; and 2, CRP≥1.0 mg/dL and albumin&lt;3.5 mg/dL. Differences in progression-free survival (PFS) and overall survival (OS) were examined using Kaplan–Meier curves and Cox proportional-hazard models.
Results: The overall response rate was 95.1% (95% confidence interval [CI]: 89.6–97.9%). The median PFS and OS from chemoradiotherapy initiation were 12.6 (95% CI: 9.9–15.4) and 29.0 (95% CI: 24.8–45.5) months, respectively. The GPS demonstrated independent predictive ability for the effectiveness of chemoradiotherapy, wherein favorable scores (GPS 0–1) were significantly correlated with superior PFS and OS compared to unfavorable scores (GPS 2: PFS: 14.8 vs. 6.7 months, p=0.0001; OS: 35.4 vs. 11.0 months, p&lt;0.0001).
Conclusion: This preliminary examination revealed that the GPS was significantly associated with PFS and OS in patients undergoing chemoradiotherapy for LD-SCLC, indicating its potential utility in assessing the therapeutic outcomes in LD-SCLC.
DOI: 10.6084/m9.figshare.26494741
title: Supplementary Material for: Linked color imaging with artificial intelligence improves the detection of early gastric cancer

description: Introduction: Esophagogastroduodenoscopy (EGD) is the most important tool to detect gastric cancer (GC). In this study, we developed a computer-aided system (CADe) to detect gastric cancer (GC) with white light imaging (WLI) and linked color imaging (LCI) modes and aimed to compare the performance of CADe with that of endoscopists. Methods: The system was developed based on the deep learning framework from 9021 images in 385 patients between 2017 and 2020. A total of 116 LCI and WLI videos from 110 patients between 2017 and 2023 were used to evaluate per-case sensitivity and per-frame specificity. Results: The per-case sensitivity and per-frame specificity of CADe with a confidence level of 0.5 in detecting GC were 78.6% and 93.4% for WLI and 94.0% and 93.3% for LCI, respectively (P &lt; 0.001). The per-case sensitivities of nonexpert endoscopists for WLI and LCI were 45.8% and 80.4%, whereas those of expert endoscopists were 66.7% and 90.6%, respectively. Regarding detectability between CADe and endoscopists, the per-case sensitivities for WLI and LCI were 78.6% and 94.0% in CADe, respectively, which were significantly higher than those for LCI in experts (90.6%, P = 0.004) and those for WLI and LCI in nonexperts (45.8% and 80.4%, respectively, P &lt; 0.0001); however, no significant difference for WLI was observed between CADe and experts (P = 0.134). Conclusions: Our CADe system showed a significantly better sensitivity in detecting GC when used in LCI compared with WLI mode. Moreover, the sensitivity of CADe using LCI is significantly higher than those of expert endoscopists using LCI.
DOI: 10.6084/m9.figshare.9116732.v1
title: Project SCORE processed with CERES

description: This dataset is the result of 318 cancer cell lines screened with the genome-wide KY1.0/1.1 CRISPR KO library by the Sanger Institute, processed with the Achilles pipeline (except QC). The publication describing the experiment is "Prioritization of cancer therapeutic targets using CRISPR-Cas9 screens," DOI 10.1038/s41586-019-1103-9. <br><br>Readcounts were downloaded from https://score.depmap.sanger.ac.uk/downloads on 8 May 2019. Only cell lines annotated by the authors as passing both QC steps in Supplementary Table 1 were retained. Additionally, only cell lines for which the Broad has copy number data as of 10 May 2019 were retained.<br>For more details on included files, see README
DOI: 10.6084/m9.figshare.9926627
title: OMNI-Net_Dardkiman_Shaked_etal.onnx

description: ONNX file of a deep neural network for 2D phase unwrapping of biological cells in watery medium. Meant for 512x512-pixel images. Distributed for academic non-commercial use only. If you use this network in your manuscript, please cite Dardikman-Yoffe, Shaked, et al. "OMNI-Net: Ready-to-use neural network for unwrapping quantitative phase images of biological cells," Biomedical Optics Express, 2019
DOI: 10.5445/ir/1000136328
title: COM3D: Turbulent Combustion Code User’s Guides

description: COM3D is a three-dimensional code for turbulent reactive flow simulations in complex 3D-geometries. The Favre averaged Navier-Stokes equations are solved together with different models for turbulence and chemical kinetics. COM3D employs different flow solvers. Advanced numerical procedures are provided to facilitate the grid generation for complex 3D computational domains. COM3D was validated on experiments performed on different scales, with and without chemical reaction. Generally good agreement was observed for the important physical quantities. The code was used for combustion analysis of different application problems, ranging from small-scale laboratory tests up to large-scale reactor containment calculations.
DOI: 10.6084/m9.figshare.25975381.v1
title: DendroDataJEcol.xlsx

description: Similar climate-growth relationships but divergent drought resilience strategies in coexisting Mediterranean shrubs
DOI: 10.5066/p91ge4fs
title: Seismic Reflection Profiles Imaging the Seattle Fault Zone Beneath West Seattle, Central Seattle, and Mercer Island, Washington State

description: The U.S. Geological Survey, with funding from the National Earthquakes Hazard Reduction Program, collected ~24 km of north-south trending land-based P-wave seismic reflection profiles gathered across three urban areas in Seattle, Washington: West Seattle, central Seattle, and Mercer Island. The West Seattle profiles were collected with an accelerated weight drop source and 8 Hz vertical component geophone sensors at 5 m spacing along 47th Ave, 44th Ave, 42nd Ave, 39th Ave, and Walnut Ave. The central Seattle profiles were collected with a Minivib I source and 8 Hz vertical component geophone sensors at 5 m spacing along 13th St and Beacon Way. The Mercer Island profiles were collected with a Minivib III source and 8 Hz vertical component geophone sensors at 5 m spacing along 78th Ave SE, 90th Ave SE, 86th Ave SE, and 84th Ave SE. All data are archived in the EarthScope Data Management Center (DMC) in SEGY format. Reports associated with the field records include experiment descriptions and observers logs for each profile. Station location information is in the SEGY file headers. The coordinates are in the UTM Zone 10 N with WGS84 datum. The field records and reports of the West Seattle profiles are available from the DMC, dataset #14-062,  https://ds.iris.edu/mda/14-062/. The central Seattle data are at DMC, dataset #14-038, https://ds.iris.edu/mda/14-038/. The Mercer Island data are at DMC, dataset #15-001, https://ds.iris.edu/mda/15-001/.

Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.
DOI: 10.5281/zenodo.10537319
title: Resting state fMRI and electrophysiology in rats

description: The dataset includes electrophysiology and whole-brain resting-state fMRI simultaneously recorded from adult male Long-Evans rats. Invasive electrophysiology was concurrently recorded from two brain regions: the anterior cingulate cortex (ACC) and the primary motor cortex (M1). This dataset contains 159 resting-state fMRI scans with electrophysiology recorded from both ACC and M1,as well as 13 resting-state fMRI scans with electrophysiology recorded from ACC only.  Each resting-state fMRI scan lasts 20 minutes.
DOI: 10.5281/zenodo.10569208
title: Bioinformatic assignment of PKZILLA ketoreductase (KR) stereochemical outcome based on application of a literature trans-AT KR diagnostic residue heuristic

description: Code, derived files, and results from PKZILLA ketoreductase (KR) stereochemical outcome analysis, based of the heuristic described in Supplementary Figure 4 of (Helfrich et al. 2019).





E. J. N. Helfrich et al., “Automated structure prediction of trans-acyltransferase polyketide synthase products,” Nat Chem Biol, vol. 15, no. 8, Art. no. 8, Aug. 2019, doi: 10.1038/s41589-019-0313-7.
DOI: 10.5281/zenodo.8024696
title: Immobilized fluorescently stained zebrafish through the eXtended Field of view Light Field Microscope 2D-3D dataset

description: <strong>Immobilized fluorescently stained zebrafish through the eXtended Field of view Light Field Microscope 2D-3D dataset</strong> This dataset comprises three immobilized fluorescently stained zebrafish imaged through the eXtended Field of view Light Field Microscope (XLFM, also known as Fourier Light Field Microscope). The images were preprocessed with the SLNet, which extracts the sparse signals from the images (a.k.a. the neural activity). If you intend to use this with Pytorch, you can find a data loader and working source code to load and train networks here. This dataset is part of the publication: Fast light-field 3D microscopy with out-of-distribution detection and adaptation through Conditional Normalizing Flows. The fish present are: 1x NLS GCaMP6s 1x Pan-neuronal nuclear localized GCaMP6s Tg(HuC:H2B:GCaMP6s) 1x Soma localized GCaMP7f Tg(HuC:somaGCaMP7f) The dataset is structured as follows:: XLFM_dataset <em>Dataset/</em> <em>GCaMP6s_NLS_1/</em> <em>SLNet_preprocessed/</em> <em>XLFM_image/</em> <em>XLFM_image_stack.tif</em>: tif stack of 600 preprocessed XLFM images. <em>XLFM_stack/</em> <em>XLFM_stack_nnn.tif</em>: 3D stack corresponding to frame nnn. <em>Neural_activity_coordinates.csv</em>: 3D coordinates of neurons found through the suite2p framework. <em>Raw/</em> <em>XLFM_image/</em> <em>XLFM_image_stack.tif:</em> tif stack of 600 raw XLFM images. (other samples) <em>lenslet_centers_python.txt</em>: 2D coordinates of the lenset in the XLFM images. <em>PSF_241depths_16bit.tif: 3D PSF of the microscope can be used for 3D deconvolution. Spanning 734 × 734 × 550𝜇𝑚3 used to deconvolve this volumes. </em> In this dataset, we provide a subset of the images and volumes. Due to space constraints, we provide the 3D volumes only for: <em>SLNet_preprocessed/XLFM_stack/</em> 10 interleaved frames between frames 0-499 (can be used for training a network). 20 consecutive frames, 500-520 (can be used for testing). <em>raw/</em> No volumes are provided for raw data, but they can be reconstructed through 3D deconvolution. Enjoy, and feel free to contact us for any information request, like the full PSF, 3 more samples or longer image sequences.
description: J. Page Vizcaíno is supported by the Deutsche Forschungsgemeinschaft (LA 3264/2-1). Z. Wang, P. Symvoulidis and E. S. Boyden acknowledge the Alan Foundation, HHMI, Lisa Yang, NIH R01DA029639, NIH 1R01MH123977, NIH R01MH122971, NIH RF1NS113287, NSF 1848029, NIH 1R01DA045549, and John Doerr. P. Favaro acknowledges the interdisciplinary project funding UniBE ID Grant 2018 of the University of Bern.
DOI: 10.6084/m9.figshare.13075097.v1
title: Banni Canid Data

description: Camera trapping data for four canids species (desert fox, Indian fox, domestic dog, and golden jackal) along with habitat covariates measured.<br>
DOI: 10.6084/m9.figshare.26509777
title: Supplementary Material for: Dysregulation of TLR Signaling-Associated Gene Expression in X-linked Agammaglobulinemia: Implications for Correlations Genotype-Phenotype and Disease Expression

description: Introduction
In X-linked agammaglobulinemia (XLA), the diversity of BTK variants complicates the study of genotype-phenotype correlations. Since BTK negatively regulates toll-like receptors (TLRs), we investigated if distinct BTK mutation types selectively modulate TLR pathways, affecting disease expression.
Methods
Using RT-qPCR, we quantified ten TLR signaling-related genes in XLA patients with missense (n=3) and nonsense (n=5) BTK mutations and healthy controls (n=17).
Results 
BTK, IRAK2, PIK3R4, REL, TFRC, and UBE2N were predominantly downregulated, while RIPK2, TLR3, TLR10, and TLR6 showed variable regulation. The missense XLA group exhibited significant downregulation of IRAK2, PIK3R4, REL, and TFRC, and upregulation of TLR3 and/or TLR6.
Conclusion
Hypo-expression of TLR3, TLR6, and TLR10 may increase susceptibility to infections, while hyper-expression might contribute to chronic inflammatory conditions like arthritis or inflammatory bowel disease. Our findings shed light on the important inflammatory component characteristic of some XLA patients, even under optimal therapeutic conditions.
DOI: 10.15468/dl.xxdb7j
title: Occurrence Download

description: A dataset containing 1813 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "TaxonKey is Salvinia ×molesta D.S.Mitch."
 ]
}

 The dataset includes 1813 records from 49 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0049863-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.1594/pangaea.354681
title: Geochemical analysis of surface sediments along the Portuguese Margin

description: Twenty-nine surface samples from the Portuguese shelf, recovered offshore from the mouths of the Ave, Douro, Lis and Mira rivers, were analysed using ICP–OES for selected major and trace elements, after total dissolution. Organic carbon, carbonate content and grain size were also determined. Five evaluation tools have been applied in order to compare the three study areas and to evaluate sediment geochemistry and other sediment compositional variability in the acquired samples: (1) empirical methods based on comparison with standard reference criteria, e.g. the NOAA sediment quality guidelines, (2) normalisation ratios using a grain-size proxy element, (3) “Gradient Method”, plotting contaminant vs. organic matter or Al, (4) definition of a regional geochemical baseline from a compiled database, and (5) enrichment factors.The evaluation of element and component associations indicates differences related both to the onshore drainage areas and to the environmental shelf setting. Despite the considerable variability in total metal contents indicated by our results, the sediment metal composition is largely of natural origin. Metal enrichments observed in the Mira area are associated with the drainage of mineralised areas rich in Cu, Pb, Zn, Fe and Mn. The near absence of human impact on shelf sediments, despite the vicinity to urban areas with high industrialisation levels, such as the Ave-Douro and Lis areas, is attributed to effective trapping in the estuaries and coastal zones, as well dilution with less contaminated sediments shelf sediments and removal with fine fractions due to grain-size sorting. The character of the contaminated sediments transported to these shelf areas is further influenced by grain-size sorting as well as by dilution with less contaminated marine sediments. The results obtained individually by the different methods complement each other and allow more specific interpretations.
description: Supplement to: Mil-Homens, Mário; Stevens, R L; Abrantes, Fatima F; Cato, I (2006): Heavy metal assessment for surface sediments from three areas of the Portuguese continental shelf. Continental Shelf Research, 26(10), 1184-1205
DOI: 10.17609/n8mq0n
title: 2015 Aerial Laser and Photogrammetry Datasets for Dublin, Ireland's City Center
DOI: 10.21227/ps5q-8m55
title: Cophy: Counterfactual Learning of Physical Dynamics

description: Understanding causes and effects in mechanical systems is an essential component of reasoning in the physical world. This work poses a new problem of counterfactual learning of object mechanics from visual input. We develop the COPHY benchmark to assess the capacity of the state-of-the-art models for causal physical reasoning in a synthetic 3D environment and propose a model for learning the physical dynamics in a counterfactual setting. Having observed a mechanical experiment that involves, for example, a falling tower of blocks, a set of bouncing balls or colliding objects, we learn to predict how its outcome is affected by an arbitrary intervention on its initial conditions, such as displacing one of the objects in the scene. The alternative future is predicted given the altered past and a latent representation of the confounders learned by the model in an end-to-end fashion with no supervision. We compare against feedforward video prediction baselines and show how observing alternative experiences allows the network to capture latent physical properties of the environment, which results in significantly more accurate predictions at the level of super human performance.
DOI: 10.34740/kaggle/ds/2160743
title: Non-Native Children Speech Mini Corpus
DOI: 10.48786/edbt.2022.14
title: Gamma Probabilistic Databases: Learning from Exchangeable Query-Answers
DOI: 10.5281/zenodo.12667650
title: Dataset: Use of bioresorbable fibers for short-wave infrared spectroscopy using time-domain diffuse optics