cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23259338.v3
title: Supplementary Material for: Risk Factors for Common Kidney Stones Are Correlated with Kidney Function Independent of Stone Composition

description: Background: Kidney stone type varies with age, sex, season, and medical conditions. Lower estimate glomerular filtration rate (eGFR) leads to changes in urine chemistry, and risk factors for kidney stones are thought to vary by stone type. We explore the association between eGFR, urine risk factors, and common stone compositions. Methods: This was a retrospective cohort study of 811 kidney stone patients seen at Yale Medicine between 1994-2021 with serum chemistries and 24-hour urine chemistries matched within one year of baseline stone analysis. Patients’ eGFR was calculated using the Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) 2021 equation. Demographics and medical history were compared by Chi-squared tests. 24-hour urine chemistries and stone analyses were analyzed by one-way ANOVA. Linear regressions were performed to control for demographics, comorbidities, and stone composition. Results: With lower eGFR, the proportion of calcium stones declined while uric acid stones increased. On univariable analysis, lower eGFR was associated with lower urine pH, calcium, citrate, uric acid, magnesium, phosphorus, and ammonium. On multivariable analysis, controlling for age, sex, ethnicity, BMI, comorbidities, and stone type, these factors remained significant. Stone formers with lower eGFR had elevated supersaturation for uric acid, but reduced supersaturations for calcium-containing stones. Though urine oxalate was significant on univariable analysis, it was not on multivariable analysis. Discussion/Conclusion: Changes in urine parameters are strongly correlated with eGFR regardless of stone type. Renal function may play a key role in modulating kidney stone risk factors. Strategies to mitigate stone risk may need to vary with kidney function, especially when patient urine or stone composition data is unavailable.
DOI: 10.6084/m9.figshare.23259338.v2
title: Supplementary Material for: Risk Factors for Common Kidney Stones Are Correlated with Kidney Function Independent of Stone Composition

description: Background: Kidney stone type varies with age, sex, season, and medical conditions. Lower estimate glomerular filtration rate (eGFR) leads to changes in urine chemistry, and risk factors for kidney stones are thought to vary by stone type. We explore the association between eGFR, urine risk factors, and common stone compositions. Methods: This was a retrospective cohort study of 811 kidney stone patients seen at Yale Medicine between 1994-2021 with serum chemistries and 24-hour urine chemistries matched within one year of baseline stone analysis. Patients’ eGFR was calculated using the Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) 2021 equation. Demographics and medical history were compared by Chi-squared tests. 24-hour urine chemistries and stone analyses were analyzed by one-way ANOVA. Linear regressions were performed to control for demographics, comorbidities, and stone composition. Results: With lower eGFR, the proportion of calcium stones declined while uric acid stones increased. On univariable analysis, lower eGFR was associated with lower urine pH, calcium, citrate, uric acid, magnesium, phosphorus, and ammonium. On multivariable analysis, controlling for age, sex, ethnicity, BMI, comorbidities, and stone type, these factors remained significant. Stone formers with lower eGFR had elevated supersaturation for uric acid, but reduced supersaturations for calcium-containing stones. Though urine oxalate was significant on univariable analysis, it was not on multivariable analysis. Discussion/Conclusion: Changes in urine parameters are strongly correlated with eGFR regardless of stone type. Renal function may play a key role in modulating kidney stone risk factors. Strategies to mitigate stone risk may need to vary with kidney function, especially when patient urine or stone composition data is unavailable.
DOI: 10.6069/q4r7-ec13
title: Assessing the role of trypsin in quantitative plasma- and single-cell
proteomics towards clinical application

description: Mass spectrometry-based bottom-up proteomics is rapidly evolving and routinely applied in large biomedical studies. Proteases are a central component of every bottom-up proteomics experiment, digesting proteins into peptides. Trypsin has been the most widely applied protease in proteomics, due to its characteristics. With ever-larger cohort sizes and possible future clinical application of mass spectrometry-based proteomics, the technical impact of trypsin becomes increasingly relevant. To assess possible biases introduced by trypsin digestion, we evaluated the impact of eight commercially available trypsins in a variety of bottom-up proteomics experiments, and across a range of protease concentrations and storage times. To investigate the universal impact of these technical attributes, we included bulk HeLa-cell lysate, human plasma and single HEK293 cells, which were analyzed over a range of Selected Reaction Monitoring (SRM), Data-Independent Acquisition (DIA), and Data-Dependent Acquisition (DDA) instrument methods on three LC-MS instruments. Quantification methods employed encompassed both label-free approaches and absolute quantification utilizing spike-in heavy-labeled recombinant protein fragment standards. Based on this extensive dataset, we report variations between commercial trypsins, their source, as well as their concentration. Furthermore, we provide suggestions on the handling of trypsin in large scale studies.
DOI: 10.5517/ccdc.csd.cc2fdvpd
title: CCDC 2246684: Experimental Crystal Structure Determination

description: Related Article: Ram Prasad Bhatta, Vishal Kachwal, Clàudia Climent, Mayank Joshi, Pere Alemany, A. Roy Choudhury, Inamur Rahaman Laskar|2023|J.Mater.Chem.C|11|11399|doi:10.1039/D3TC01584J
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2fsgl9
title: CCDC 2257841: Experimental Crystal Structure Determination

description: Related Article: Steffen Kühn, Benedikt Köstler, Celine True, Lena Albers, Matthias Wagner, Thomas Müller, Christoph Marschner|2023|Chemical Science|14|8956|doi:10.1039/D3SC03301E
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2fx8d1
title: CCDC 2261493: Experimental Crystal Structure Determination

description: Related Article: Yazhou Li, Yongkun Wang, Feifei Fang, Yu Zhang, Chunpu Li, Tao Yu, Qiangqiang Chen, Jiang Wang, Hong Liu|2023|Org.Lett.|25|6018|doi:10.1021/acs.orglett.3c02166
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.23741352.v1
title: Supplementary Material for: Detection of Hybrid Fusion Transcripts, Aberrant Transcript Expression and Specific Single Nucleotide Variants in Acute Leukemia and Myeloid Disorders with Recurrent Gene Rearrangements.

description: Introduction: A variety of gene rearrangements and molecular alterations are key drivers in the pathobiology of acute leukemia and myeloid disorders; current classification systems increasingly incorporate these findings in diagnostic algorithms. Therefore, clinical laboratories require versatile tools, which can detect an increasing number and variety of molecular and cytogenetic alterations of clinical significance. Methods: We validated an RNA-based NGS assay that enables the detection of: i) numerous hybrid fusion transcripts (including rare/novel gene partners), ii) aberrantly expressed EVI1(MECOM) and IKZF1 (Del Exons 4-7) transcripts, and iii) hotspot variants in KIT, ABL1, NPM1 (relevant in the context of gene rearrangement status). Results: For hybrid fusion transcripts, the assay showed 98-100% concordance for known positive and negative samples, with an analytical sensitivity (ie, limit of detection) of approximately 0.8% cells. Cases with underlying EVI1 (MECOM) translocations demonstrated increased EVI1(MECOM) expression. Aberrant IKZF1 (Del Exons 4-7) transcripts detectable with the assay were also present on orthogonal RT-PCR. Specific hotspot mutations in KIT, ABL1 and NPM1 detected with the assay showed 100% concordance with orthogonal testing. Lastly, several illustrative cases are included to highlight the assay’s clinically relevant contributions to patient work-up. Discussion/Conclusion: Through its ability to simultaneously detect various gene rearrangements, aberrantly expressed transcripts and hotspot mutations, this RNA-based NGS assay is a valuable tool for clinical laboratories to supplement other molecular and cytogenetic methods used in the diagnostic workup, and in clinical research, for patients with acute leukemia and myeloid disorders.
DOI: 10.6084/m9.figshare.24043299
title: Data and analysis codes of "<i>Forestation at the right time with the right species can generate persistent carbon benefits in China</i>"

description: This collection contains the datasets used in our study ‘<b>Forestation at the right time with the right species can generate persistent carbon benefits in China</b>’.<i><b>Part A: Data</b></i>Most of the data presented here are after pre-processing, such as transforming the projection, extracting variables, clipping to the study region (70<sup>o</sup>E-140<sup>o</sup>E,15<sup>o</sup>N-55<sup>o</sup>N), and resampling to 1-km.The original source of these data sets (usually global, at different resolutions) is given in 'data_original.txt' as well as in the 'Data availability' of the main text.1. MaxEnt_average_results.rar: contains all the model results of the MaxEnt model in ’.tif’ (average of the 10-folds results)2. potential_china_forest_1km.zip: contains the potential forest distributions for China at 1-km resolution from multiple source (Random Forest, WRI and ORCHIDEE). Note: the forest distribution is in the form of logical variables in the .mat file, where a value of 1 or true means that the grid point is potentially forestable, and a value of 0 or false means this grid is not suitable for forest.3. existing_china_forest_1km.zip: contains the existing forest distributions for China at 1-km resolution from multiple source (FI2013-2017, Hansen, MODIS, ESA-CCI, CNLUCC, GLC-FCS30 and GlobeLand30). Note: the existing forest distribution is in the form of logical variables in the .mat file, where a value of 1 or true means there is forest distribution, and a value of 0 or false means there is currently no forest distribution.4. masks_area_china_1km.zip: area mask and the shp files of the national and provincial boundaries of China.5. ori_carbon_all_grid_1km.mat: Living biomass carbon densities in 2010 for China at 1-km (unit: Mg C ha-1). Both aboveground and belowground biomass carbon are included. The original biomass map is from Spawn et al. 2020.6. Forest_inventory_data_5th_9th.xlsx: 1) The forest area reported in 5th to 9th national forest inventory 2) The forest area of different age classes derived form the 9th national forest inventory.7. Forest_age_CN2019.tif: the forest stand age map for China updated to 2019.8. data_original.txt: the original source of these data sets<b>Part B: MATLAB Code</b>This file (Matlab_code.rar) contains the code, functions and parameters for our analysis of the data, mainly MATLAB files (.m or mat)<b>Part C: Demo/Example data and code</b>This file (Demo.7z) contains the demo of our code running, which includes the demo code along with code comments, input data for the demo, and the expected output results.<b>Part D: Docs</b>Reference and guidelines (Docs.rar).If you have any questions or suggestions, please contact xuhaotony@pku.edu.cn
DOI: 10.6084/m9.figshare.24043299.v2
title: Data and analysis codes of "<i>Forestation at the right time with the right species can generate persistent carbon benefits in China</i>"

description: This collection contains the datasets used in our study ‘<b>Forestation at the right time with the right species can generate persistent carbon benefits in China</b>’.<i><b>Part A: Data</b></i>Most of the data presented here are after pre-processing, such as transforming the projection, extracting variables, clipping to the study region (70<sup>o</sup>E-140<sup>o</sup>E,15<sup>o</sup>N-55<sup>o</sup>N), and resampling to 1-km.The original source of these data sets (usually global, at different resolutions) is given in 'data_original.txt' as well as in the 'Data availability' of the main text.1. MaxEnt_average_results.rar: contains all the model results of the MaxEnt model in ’.tif’ (average of the 10-folds results)2. potential_china_forest_1km.zip: contains the potential forest distributions for China at 1-km resolution from multiple source (Random Forest, WRI and ORCHIDEE). Note: the forest distribution is in the form of logical variables in the .mat file, where a value of 1 or true means that the grid point is potentially forestable, and a value of 0 or false means this grid is not suitable for forest.3. existing_china_forest_1km.zip: contains the existing forest distributions for China at 1-km resolution from multiple source (FI2013-2017, Hansen, MODIS, ESA-CCI, CNLUCC, GLC-FCS30 and GlobeLand30). Note: the existing forest distribution is in the form of logical variables in the .mat file, where a value of 1 or true means there is forest distribution, and a value of 0 or false means there is currently no forest distribution.4. masks_area_china_1km.zip: area mask and the shp files of the national and provincial boundaries of China.5. ori_carbon_all_grid_1km.mat: Living biomass carbon densities in 2010 for China at 1-km (unit: Mg C ha-1). Both aboveground and belowground biomass carbon are included. The original biomass map is from Spawn et al. 2020.6. Forest_inventory_data_5th_9th.xlsx: 1) The forest area reported in 5th to 9th national forest inventory 2) The forest area of different age classes derived form the 9th national forest inventory.7. Forest_age_CN2019.tif: the forest stand age map for China updated to 2019.8. data_original.txt: the original source of these data sets<b>Part B: MATLAB Code</b>This file (Matlab_code.rar) contains the code, functions and parameters for our analysis of the data, mainly MATLAB files (.m or mat)<b>Part C: Demo/Example data and code</b>This file (Demo.7z) contains the demo of our code running, which includes the demo code along with code comments, input data for the demo, and the expected output results.<b>Part D: Docs</b>Reference and guidelines (Docs.rar).If you have any questions or suggestions, please contact xuhaotony@pku.edu.cn
DOI: 10.6084/m9.figshare.24050034
title: tests.zip

description: The test data serves as an example to explain how to use VariaMotif.
DOI: 10.6084/m9.figshare.24050034.v1
title: tests.zip

description: The test data serves as an example to explain how to use VariaMotif.
DOI: 10.5281/zenodo.8289301
title: 25-years dataset of Ageostrophic, Ekman and Stokes surface currents in the Mediterranean Sea (AGESC-Med)

description: One meter integrated depth surface velocity fields for the Mediterranean Sea calculated following the methodology in Morales-Marquez et al.(2020) DOI:10.1029/2022JC019135 and used in Morales-Marquez et al. (2023) DOI: 10.1029/2020JC017104. This dataset provides the total velocity field, the ageostrophic, Ekman and Stokes components.
DOI: 10.5281/zenodo.8289300
title: 25-years dataset of Ageostrophic, Ekman and Stokes surface currents in the Mediterranean Sea (AGESC-Med)

description: One meter integrated depth surface velocity fields for the Mediterranean Sea calculated following the methodology in Morales-Marquez et al.(2020) DOI:10.1029/2022JC019135 and used in Morales-Marquez et al. (2023) DOI: 10.1029/2020JC017104. This dataset provides the total velocity field, the ageostrophic, Ekman and Stokes components.
DOI: 10.6084/m9.figshare.23760057.v1
title: Supplementary Material for: The Role of Biologic Mesh and Fundoplication in the Surgical Management of Hiatal Hernias: A Multicenter Evaluation

description: Introduction- Hiatal hernia repair is associated with substantial recurrence of both hiatal hernia and symptoms of gastroesophageal reflux (GER). While small randomized controlled trials demonstrate limited differences in outcomes with use of mesh or fundoplication type, uncertainty remains. Methods- A multicenter, retrospective review of patients undergoing surgical treatment of hiatal hernias between 2015-2020 was performed. Patients with mesh and with suture only repair were compared, and partial versus complete fundoplication was compared. Primary outcomes were hernia recurrence and occurrence of post-operative GER symptoms and dysphagia. Multivariable regression was performed to assess the effect of each intervention on clinical outcomes. Results- A total of 453 patients from four sites were followed for a median (IQR) of 17 (13) months. On multivariate analysis, mesh had no impact on hernia recurrence (odds ratio 0.993, 95% CI 0.53-1.87, p=0.982), and fundoplication type did not impact recurrence of post-operative GER symptoms (complete: odds ratio 0.607, 95% CI 0.33-1.12, p=0.112) or dysphagia (complete: odds ratio 1.17, 95% CI 0.56-2.43, p=0.677). Conclusion- During hiatal hernia repair, mesh and fundoplication type do not appear to have substantial impact on GER symptoms, dysphagia, or hernia recurrence. This multicenter study provides real-world evidence to support the findings of small RCTs.
DOI: 10.5281/zenodo.8192577
title: The effect of shear strain and shear localization on fault healing

description: This is the ReadMe file corresponding to the study entitled:<br> "The effect of shear strain and shear localization on fault healing"<br> By Noël C., Giorgetti C., Collettini C. and Marone C. This study has been submited to EPSL This Read-Me file has been last edited in July 2023 This readme file describes the data repository and supplementary files accompanying the above publication. <br> For any further queries please contact corentin.noel@geoazur.unice.fr
DOI: 10.5281/zenodo.8192576
title: The effect of shear strain and shear localization on fault healing

description: This is the ReadMe file corresponding to the study entitled:<br> "The effect of shear strain and shear localization on fault healing"<br> By Noël C., Giorgetti C., Collettini C. and Marone C. This Read-Me file has been last edited in August 2023 This readme file describes the data repository and supplementary files accompanying the above publication. <br> For any further queries please contact corentin.noel@geoazur.unice.fr
DOI: 10.5281/zenodo.8227602
title: The effect of shear strain and shear localization on fault healing

description: This is the ReadMe file corresponding to the study entitled:<br> "The effect of shear strain and shear localization on fault healing"<br> By Noël C., Giorgetti C., Collettini C. and Marone C. This study has been submited to JRG: Solid Earth This Read-Me file has been last edited in July 2023 This readme file describes the data repository and supplementary files accompanying the above publication. <br> For any further queries please contact corentin.noel@geoazur.unice.fr
DOI: 10.5281/zenodo.8297726
title: The effect of shear strain and shear localization on fault healing

description: This is the ReadMe file corresponding to the study entitled:<br> "The effect of shear strain and shear localization on fault healing"<br> By Noël C., Giorgetti C., Collettini C. and Marone C. This Read-Me file has been last edited in August 2023 This readme file describes the data repository and supplementary files accompanying the above publication. <br> For any further queries please contact corentin.noel@geoazur.unice.fr
DOI: 10.6084/m9.figshare.23759928.v1
title: Supplementary Material for: High systemic immune-inflammation index, predicting early allograft dysfunction, indicates high 90-day-mortality for acute-on-chronic liver failure after liver transplantation

description: Introduction: To investigate the relationship between systemic immune-inflammation index (SII) and early allograft dysfunction (EAD) and 90-day-mortality after liver transplantation (LT) in acute-on-chronic liver failure (ACLF). Methods: Retrospective records analysis was done on 114 patients who had LT for ACLF. To identify the ideal SII, the receiver operating characteristic (ROC) curve was used. The incidence of EAD and 90-day-mortality following LT were calculated. The prognostic value of SII was assessed using the Kaplan-Meier technique and the Cox proportional hazards model. Results: The cut-off of SII was 201.5 (AUC=0.728, P&lt;0.001). EAD occurred in 40 (35.1%) patients of the high SII group and 5 (4.4%) patients of the normal SII group, P &lt;0.001. 18(15.8%) deaths occurred in the high SII group and 2(1.8%) deaths occurred in the normal SII group, P =0.008. The multivariate analysis demonstrated that SII ≥201.5, MELD≥27 were independent prognostic factors for 90-day-mortality after LT. Conclusion: SII predicts the occurrence of EAD and is an independent risk factor for 90-day- mortality after LT.
DOI: 10.6084/m9.figshare.23766087.v1
title: Supplementary Material for: Feasibility of using the Global TALES protocol to elicit personal narratives in 10 year-old children in Ireland

description: Introduction. This small-scale study explored the feasibility of the Global TALES protocol in eliciting personal narratives in typically developing monolingual Irish children, using the online Zoom platform. We investigated children’s performance on measures of productivity (total number of utterances; total number of words) and syntactic complexity (MLU in words). We also documented the topics children talked about in response to the six emotion-based prompts contained in the Global TALES protocol. Methods: Nineteen typically developing children (6 male, 13 female), aged between 10,0 and 10,11years produced personal narratives in response to the Global TALES protocol. Given COVID-19 pandemic-related public health restrictions, the language samples were elicited using Zoom. All stories were transcribed and analysed using Systematic Analysis of Language Transcripts software. Qualitative content analysis was used to code the topics of the children’s stories. Results: Sixteen participants responded to all prompts. One participant only responded to three of the six prompts. The prompt that was least successful in eliciting response was the ‘problem’ prompt; 15.7% (n=3) of the children did not provide a response to this prompt. On average, children produced 40 utterances, although individual variability was high. On average, MLU was 8.7, ranging from 6 to 11. Children’s topics closely resembled those reported in the Global TALES feasibility study, despite the fact the current study took place during the COVID-19 pandemic. The most frequent topics were related to family (events, illnesses, relationships, siblings) and finding or fixing something. Conclusion: The Global TALES protocol was successful in eliciting personal narratives from 10 year-old Irish English-speaking children. Future larger scale studies are now needed to investigate if the results generalise to the wider Irish population with the view of creating local benchmarks of personal narrative performance.