cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14743155.v1
title: Supplementary Material for: Analysis of axial length in young patients with Marfan syndrome and bilateral ectopia lentis by Z-scores

description: Medicine
DOI: 10.5281/zenodo.4905030
title: Catalogue of lensed gravitational wave events

description: Catalogue of 1 million strongly lensed gravitational wave events + example analysis code. Requires roughly ~400 MB of free disk space.
DOI: 10.6084/m9.figshare.14743086
title: Supplementary Material for: Therapeutic Effects of Add-On Tenapanor for Hemodialysis Patients with Refractory Hyperphosphatemia

description: <b><i>Introduction:</i></b> Phosphate binders are used to treat hyperphosphatemia. Some patients have inappropriately controlled serum phosphorus levels, which may occur for many reasons, including a high pill burden and adverse events (AEs). Tenapanor selectively inhibits the passive paracellular transfer of phosphate in the gastrointestinal tract, thereby reducing serum phosphorus levels. This novel mechanism of action may contribute to improved phosphate management. The efficacy and safety of tenapanor have not been evaluated in Japanese patients with high serum phosphorus levels despite treatment with phosphate binders. This study aimed to assess the efficacy and safety of add-on tenapanor therapy for reducing serum phosphorus levels in this population. <b><i>Methods:</i></b> This multicenter, double-blind, randomized, placebo-controlled trial enrolled patients with refractory hyperphosphatemia undergoing hemodialysis. Patients were randomly assigned in a 1:1 ratio to receive tenapanor or placebo as an add-on to their phosphate binder regimen for 6 weeks. Change in serum phosphorus levels at week 6 (day 43) compared with the baseline value (day 1, week 0) (primary endpoint), achievement of target serum phosphorus levels (serum phosphorus level ≤6.0 or ≤5.5 mg/dL), and safety, based on all AEs and drug-related AEs, were among the outcomes evaluated. <b><i>Results:</i></b> In total, 24 patients were randomly assigned to the placebo group and 23 to the tenapanor group. The mean serum phosphorus level decreased from 7.01 mg/dL on day 1 to 6.69 mg/dL on day 43 in the placebo group and from 6.77 mg/dL on day 1 to 4.67 mg/dL on day 43 in the tenapanor group. In the placebo and tenapanor groups (modified intent-to-treat population), the mean (standard deviation) change in the serum phosphorus level at day 43 (last observation carried forward [LOCF]) was 0.08 (1.52) mg/dL and −1.99 (1.24) mg/dL, respectively, with a between-group difference of −2.07 (95% confidence interval: −2.89, −1.26; <i>p</i> &lt; 0.001). The target achievement rate (serum phosphorus level ≤6.0 mg/dL at week 6 [LOCF]) was 37.5 and 87.0% in the placebo and tenapanor groups, respectively. Diarrhea was the most common drug-related AE, and it occurred in 8.3 and 65.2% of patients in the placebo and tenapanor groups, respectively. No specific AEs were observed with add-on tenapanor or with phosphate binders. <b><i>Discussion/Conclusion:</i></b> Therapy with existing phosphate binders and add-on tenapanor resulted in a significant decrease in serum phosphorus level compared with the placebo group in patients with refractory hyperphosphatemia despite treatment with phosphate binders. No new safety signals were raised, and add-on tenapanor was generally well tolerated.
DOI: 10.6084/m9.figshare.14743110
title: Supplementary Material for: Postural Control in Subjects with Incomplete Partition Inner Ear Malformations: A Comparison of Incomplete Partition Types

description: <b><i>Introduction:</i></b> Children with inner ear malformation (IEM) are at risk of vestibular loss as well as hearing loss. Incomplete partition (IP) anomalies constitute about 41% of all IEMs. This study aimed to investigate the postural control in subjects with the same type of IP on both sides and to compare their results with cochlear implant (CI) users without IEM and healthy peers. <b><i>Methods:</i></b> The study group consists of 17 subjects with the same IP types on both sides and using auditory implants on at least one side, with the following 3 groups: 6 IP-I subjects (mean age 12.28 ± 6.25), 6 IP-II subjects (mean age 12.90 ± 3.23), and 5 IP-III subjects (mean age 6.98 ± 3.10). Six unilateral CI users (mean age 11.38 ± 3.57) with normal inner ear structures were included in the CI control group, and 6 healthy peers (10.20 ± 4.79) were included in the healthy control group. The postural control was measured using the Bruininks-Oseretsky Test of Motor Proficiency Second Edition (BOT-2) balance subtest. All devices were turned off during the balance test. <b><i>Results:</i></b> The BOT-2 balance scale scores were observed to be significantly different between the IP-I and healthy control group (medians of balance scores being 3.00 and 16.00, respectively, <i>p</i> &lt; 0.001) and the IP-III and healthy control group (medians of balance scores being 6.60 and 16.00, respectively, <i>p</i> = 0.04). The IP-II group had better balance scores (median = 8.00) than those of the other IP groups, although there were no significant differences between the IP-II and other groups (<i>p</i> &gt; 0.05). <b><i>Conclusion:</i></b> This study demonstrated that subjects with the same IP type on both sides and with early implantation may differ in terms of their postural control abilities depending on their IP type. Subjects with IP should be regularly followed up by the vestibular assessment and supported by their postural control ability by vestibular rehabilitation.
DOI: 10.6084/m9.figshare.14742963
title: Supplementary Material for: Ischemic Preconditioning for Liver Transplantation: A Systematic Review and Meta-Analysis of Randomized Controlled Trials

description: <b><i>Background:</i></b> In recent decades, liver transplantation (LTx) has increased the survival and quality of life of patients with end-stage organ failure. Unfortunately, LTx is limited due to the shortage of donors. A lot of effort is put into finding new ways to reduce ischemia-reperfusion injury (IRI) in liver grafts to increase the number of suitable organs procured from expanded-criteria donors (ECD). The aim of this study was to systematically review the literature reporting LTx outcomes when using ischemic preconditioning (IPC) or remote ischemic preconditioning (RIPC) to reduce IRI in liver grafts. <b><i>Methods:</i></b> A literature search was performed in the MEDLINE, Web of Science, and EMBASE databases. The following combination was used: “Liver” OR “Liver Transplantation” AND “Ischemic preconditioning” OR “occlusion” OR “clamping” OR “Pringle.” The following outcome data were retrieved: the rates of graft primary nonfunction (PNF), retransplantation, graft loss, and mortality; stay in hospital and the intensive care unit; and postoperative serum liver damage parameters. <b><i>Results:</i></b> The initial search retrieved 4,522 potentially relevant studies. After evaluating 17 full-text articles, a total of 9 randomized controlled trials (RCTs) were included (7 IPC and 2 RIPC studies) in the qualitative synthesis; the meta-analysis was only performed on the data from the IPC studies. RIPC studies had considerable methodological differences. The meta-analysis revealed the beneficial effect of IPC when comparing postoperative aspartate aminotransferase (AST) corresponding to a statistically lower mortality rate in the IPC group (odds ratio [OR] 0.51; 95% confidence interval [CI] 0.27–0.98; <i>p</i> = 0.04). <b><i>Conclusion:</i></b> IPC lowers postoperative AST levels and reduces the mortality rate; however, data on the benefits of RIPC are lacking.
DOI: 10.6084/m9.figshare.14740959.v1
title: FORGOTTEN LINEAGES AND RECURRENT HYBRIDIZATIONS WITHIN THE KELP GENUS ALARIA (PHAEOPHYCEAE) REVEALED BY WHOLE GENOME SEQUENCING

description: Provided in this project are vcf files and occurrence data related to phylogenomic analysis of the kelp <i>Alaria</i>. All detailed methods, including filtering parameters, can be found in the article sharing this project title (article currently in review).<br>Alaria_occurence_data_2iv20.csv: occurrence data used for Fig. 1 map, sourced from records from Luning 1990 (Biogeography of Seaweeds), Barcode of Life Data Systems, and Macroalgal Portal.<br><br>Alaria_phylogenomics_SNP_final.fasta: Final SNP dataset in fasta format used for phylogenetic analysis of Alaria, mapping reads to reference nuclear scaffolds (KU-791D_nuclear_scaffolds_fasta).<br><br>Alaria_phylogenomics_SNP_final.vcf.gz: Final SNP dataset in vcf format used for phylogenetic analysis of Alaria, mapping reads to reference nuclear scaffolds (KU-791D_nuclear_scaffolds_fasta).<br><br>Alaria_phylogenomics_SNP_final_LD.fasta: Final SNP dataset in fasta format used for phylogenetic analysis of Alaria, with additional filter for linkage disequilibrium, mapping reads to reference nuclear scaffolds (KU-791D_nuclear_scaffolds_fasta).<br><br>Alaria_phylogenomics_SNP_final_LD.vcf.gz: Final SNP dataset in vcf format used for phylogenetic analysis of Alaria, with additional filter for linkage disequilibrium, mapping reads to reference nuclear scaffolds (KU-791D_nuclear_scaffolds_fasta).<br><br>Alaria_phylogenomics_SNP_raw.vcf.gz: Raw vcf file after compiling bam files and calling SNPs, after read mapping of Alaria samples to KU-791D_nuclear_scaffolds.fasta. This file has no SNP filters applied to it.<br><br>Alaria_Undaria_final_raw.vcf.gz: Raw vcf file after compiling bam files and calling SNPs, after read mapping of Alaria samples to Undaria pinnatifida genome (Shan et al. 2020). This file has no SNP filters applied to it.<br><br>Alaria_Undaria_SNP_final.fasta: Final SNP dataset in fasta format used for phylogenetic analysis of Alaria, including Undaria pinnatifida to act as an outgroup taxon, mapping reads to Undaria pinnatifida genome (Shan et al. 2020).<br><br>Alaria_Undaria_SNP_final.vcf.gz: Final SNP dataset in vcf format used for phylogenetic analysis of Alaria, including Undaria pinnatifida to act as an outgroup taxon, mapping reads to Undaria pinnatifida genome (Shan et al. 2020).<br><br>KU-791D_nuclear_scaffolds.fasta: reference nuclear scaffolds for Alaria esculenta used for mapping reads from various species of Alaria.<br>
DOI: 10.6084/m9.figshare.14740959
title: FORGOTTEN LINEAGES AND RECURRENT HYBRIDIZATIONS WITHIN THE KELP GENUS ALARIA (PHAEOPHYCEAE) REVEALED BY WHOLE GENOME SEQUENCING

description: Provided in this project are vcf files and occurrence data related to phylogenomic analysis of the kelp <i>Alaria</i>. All detailed methods, including filtering parameters, can be found in the article sharing this project title (article currently in review).<br>Alaria_occurence_data_2iv20.csv: occurrence data used for Fig. 1 map, sourced from records from Luning 1990 (Biogeography of Seaweeds), Barcode of Life Data Systems, and Macroalgal Portal.<br><br>Alaria_phylogenomics_SNP_final.fasta: Final SNP dataset in fasta format used for phylogenetic analysis of Alaria, mapping reads to reference nuclear scaffolds (KU-791D_nuclear_scaffolds_fasta).<br><br>Alaria_phylogenomics_SNP_final.vcf.gz: Final SNP dataset in vcf format used for phylogenetic analysis of Alaria, mapping reads to reference nuclear scaffolds (KU-791D_nuclear_scaffolds_fasta).<br><br>Alaria_phylogenomics_SNP_final_LD.fasta: Final SNP dataset in fasta format used for phylogenetic analysis of Alaria, with additional filter for linkage disequilibrium, mapping reads to reference nuclear scaffolds (KU-791D_nuclear_scaffolds_fasta).<br><br>Alaria_phylogenomics_SNP_final_LD.vcf.gz: Final SNP dataset in vcf format used for phylogenetic analysis of Alaria, with additional filter for linkage disequilibrium, mapping reads to reference nuclear scaffolds (KU-791D_nuclear_scaffolds_fasta).<br><br>Alaria_phylogenomics_SNP_raw.vcf.gz: Raw vcf file after compiling bam files and calling SNPs, after read mapping of Alaria samples to KU-791D_nuclear_scaffolds.fasta. This file has no SNP filters applied to it.<br><br>Alaria_Undaria_final_raw.vcf.gz: Raw vcf file after compiling bam files and calling SNPs, after read mapping of Alaria samples to Undaria pinnatifida genome (Shan et al. 2020). This file has no SNP filters applied to it.<br><br>Alaria_Undaria_SNP_final.fasta: Final SNP dataset in fasta format used for phylogenetic analysis of Alaria, including Undaria pinnatifida to act as an outgroup taxon, mapping reads to Undaria pinnatifida genome (Shan et al. 2020).<br><br>Alaria_Undaria_SNP_final.vcf.gz: Final SNP dataset in vcf format used for phylogenetic analysis of Alaria, including Undaria pinnatifida to act as an outgroup taxon, mapping reads to Undaria pinnatifida genome (Shan et al. 2020).<br><br>KU-791D_nuclear_scaffolds.fasta: reference nuclear scaffolds for Alaria esculenta used for mapping reads from various species of Alaria.<br>
DOI: 10.5281/zenodo.4905684
title: A computationally designed chimeric antigen receptor provides a small-molecule safety switch for T-cell therapy

description: Data underlying the figures in the publication “A computationally designed chimeric antigen receptor provides a small-molecule safety switch for T-cell therapy”, published in <em>Nat Biotechnol,</em> <strong>2020</strong>, 38, 426–432: https://doi.org/10.1038/s41587-019-0403-9 Table of contents: 1. Table 1; Excel file with the data of the figures in the main text and in the supporting information. 2. STOP-CAR-master; .zip folder with the code used to perform the design simulation. It can also be found at https://github.com/LPDI-EPFL/STOP-CAR.
DOI: 10.6084/m9.figshare.14742948
title: Supplementary Material for: Oncosuppressor-Mutated Cell-Based Diagnostic Platform for Liquid Biopsy Diagnoses Benign Head and Neck Masses and Predicts Malignancy in Thyroid Nodules: Results from a Consecutive Cohort of Patients

description: <b><i>Background:</i></b> We reported that a novel oncosuppressor-mutated cell (OMC)-based platform has the potential for early cancer detection in healthy individuals and for identification of cancer patients at risk of developing metachronous metastases. <b><i>Objective:</i></b> Herein, we sought to determine the diagnostic accuracy of this novel OMC-based platform in a consecutive cohort of patients operated for suspicious head and neck masses. <b><i>Methods:</i></b> OMCs (<i>BRCA1</i>-deficient fibroblasts) were exposed to blood serum from patients with head and neck nodules before surgical removal. These cells were analyzed for their proliferation and survival. Treated OMCs were inoculated subcutaneously in NOD/SCID mice, and tumor growth was monitored over time. <b><i>Results:</i></b> OMCs exposed to serum from patients with malignant lesions displayed increased proliferation compared to those exposed to serum from patients with benign lesions. Only OMCs exposed to serum from patients diagnosed with malignant thyroid neoplasia generated a cancerous mass. The sensitivity of the test was 92%, with only 1 false negative out of 34 patients. Immunohistochemical staining showed that the cancerous masses were poorly differentiated adenocarcinomas with high proliferative index. <b><i>Conclusions:</i></b> These data show that liquid biopsy combined with an OMC-based in vivo platform has the potential to diagnose benign head and neck masses and predict whether a thyroid nodule is malignant. These results strengthen the concept that OMCs can be used to detect circulating malignant factors in cancer patients.
DOI: 10.5281/zenodo.4905683
title: A computationally designed chimeric antigen receptor provides a small-molecule safety switch for T-cell therapy

description: Data underlying the figures in the publication “A computationally designed chimeric antigen receptor provides a small-molecule safety switch for T-cell therapy”, published in <em>Nat Biotechnol,</em> <strong>2020</strong>, 38, 426–432: https://doi.org/10.1038/s41587-019-0403-9 Table of contents: 1. Table 1; Excel file with the data of the figures in the main text and in the supporting information. 2. STOP-CAR-master; .zip folder with the code used to perform the design simulation. It can also be found at https://github.com/LPDI-EPFL/STOP-CAR.
DOI: 10.6084/m9.figshare.14742948.v1
title: Supplementary Material for: Oncosuppressor-Mutated Cell-Based Diagnostic Platform for Liquid Biopsy Diagnoses Benign Head and Neck Masses and Predicts Malignancy in Thyroid Nodules: Results from a Consecutive Cohort of Patients

description: <b><i>Background:</i></b> We reported that a novel oncosuppressor-mutated cell (OMC)-based platform has the potential for early cancer detection in healthy individuals and for identification of cancer patients at risk of developing metachronous metastases. <b><i>Objective:</i></b> Herein, we sought to determine the diagnostic accuracy of this novel OMC-based platform in a consecutive cohort of patients operated for suspicious head and neck masses. <b><i>Methods:</i></b> OMCs (<i>BRCA1</i>-deficient fibroblasts) were exposed to blood serum from patients with head and neck nodules before surgical removal. These cells were analyzed for their proliferation and survival. Treated OMCs were inoculated subcutaneously in NOD/SCID mice, and tumor growth was monitored over time. <b><i>Results:</i></b> OMCs exposed to serum from patients with malignant lesions displayed increased proliferation compared to those exposed to serum from patients with benign lesions. Only OMCs exposed to serum from patients diagnosed with malignant thyroid neoplasia generated a cancerous mass. The sensitivity of the test was 92%, with only 1 false negative out of 34 patients. Immunohistochemical staining showed that the cancerous masses were poorly differentiated adenocarcinomas with high proliferative index. <b><i>Conclusions:</i></b> These data show that liquid biopsy combined with an OMC-based in vivo platform has the potential to diagnose benign head and neck masses and predict whether a thyroid nodule is malignant. These results strengthen the concept that OMCs can be used to detect circulating malignant factors in cancer patients.
DOI: 10.6084/m9.figshare.14743108.v1
title: Table S1 List of amniote species with molecular or molecular cytogenetic evidence for homology of sex chromosomes. from Sex chromosome evolution among amniotes: is the origin of sex chromosomes non-random?

description: Sex chromosomes are a great example of a convergent evolution at the genomic level, having evolved dozens of times just within amniotes. An intriguing question is whether this repeated evolution was random, or whether some ancestral syntenic blocks have significantly higher chance to be co-opted for the role of sex chromosomes due to their gene content related to gonad development. Here, we summarize current knowledge on the evolutionary history of sex determination and sex chromosomes in amniotes and evaluate the hypothesis of non-random emergence of sex chromosomes. The current data on the origin of sex chromosomes in amniotes suggest that their evolution is indeed non-random. However, this non-random pattern is not very strong, and many syntenic blocks representing putatively independently evolved sex chromosomes are unique. Still, repeatedly co-opted chromosomes are an excellent model system, as independent co-option of the same genomic region for the role of sex chromosome offers a great opportunity for testing evolutionary scenarios on the sex chromosome evolution under the explicit control for the genomic background and gene identity. Future studies should use these systems more to explore the convergent/divergent evolution of sex chromosomes.This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)’.
DOI: 10.6084/m9.figshare.14743108
title: Table S1 List of amniote species with molecular or molecular cytogenetic evidence for homology of sex chromosomes. from Sex chromosome evolution among amniotes: is the origin of sex chromosomes non-random?

description: Sex chromosomes are a great example of a convergent evolution at the genomic level, having evolved dozens of times just within amniotes. An intriguing question is whether this repeated evolution was random, or whether some ancestral syntenic blocks have significantly higher chance to be co-opted for the role of sex chromosomes due to their gene content related to gonad development. Here, we summarize current knowledge on the evolutionary history of sex determination and sex chromosomes in amniotes and evaluate the hypothesis of non-random emergence of sex chromosomes. The current data on the origin of sex chromosomes in amniotes suggest that their evolution is indeed non-random. However, this non-random pattern is not very strong, and many syntenic blocks representing putatively independently evolved sex chromosomes are unique. Still, repeatedly co-opted chromosomes are an excellent model system, as independent co-option of the same genomic region for the role of sex chromosome offers a great opportunity for testing evolutionary scenarios on the sex chromosome evolution under the explicit control for the genomic background and gene identity. Future studies should use these systems more to explore the convergent/divergent evolution of sex chromosomes.This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)’.
DOI: 10.5517/ccdc.csd.cc11th0c
title: CCDC 977802: Experimental Crystal Structure Determination

description: Related Article: Ying Shi, Ting Wang, Jinping Li, Shuang Wang|2016|Huaxue Tongbao|79|152|
DOI: 10.5517/ccdc.csd.cc12qnct
title: CCDC 1004876: Experimental Crystal Structure Determination

description: Related Article: Manas Layeka, Mahendra Ghosha, Rajat Sahab, Debasis Bandyopadhyay|2016|J.Chem.Pharm.Res.|8|618|
DOI: 10.5517/ccdc.csd.cc141dyj
title: CCDC 1044047: Experimental Crystal Structure Determination

description: Related Article: Fei Ye, Na Li, Li-Xia Zhoa, Shuang Gao, Ying Fu|2016|Ind.J.Heterocycl.Chem.|26|127|
DOI: 10.5281/zenodo.4899253
title: Compilation of Data used in the manuscript "REY Patterns And Their Natural Anomalies In Waters And Brines: The Correlation Of Gd- And Y- Anomalies"

description: Compilation of rare earth element analyses used in the manuscript:<strong> </strong><strong>REY patterns and their natural anomalies in waters and brines: The correlation of Gd- and Y-anomalies </strong>by Peter Möller, Peter Dulski and Marco De Lucia. Primary literature sources are reported in the second tab of the spreadsheet, named "References". The spreadsheets are uploaded in 2 different formats, xlsx and ods.
DOI: 10.5281/zenodo.4899252
title: Compilation of Data used in the manuscript "REY Patterns And Their Natural Anomalies In Waters And Brines: The Correlation Of Gd- And Y- Anomalies"

description: Compilation of rare earth element analyses used in the manuscript:<strong> </strong><strong>REY patterns and their natural anomalies in waters and brines: The correlation of Gd- and Y-anomalies </strong>by Peter Möller, Peter Dulski and Marco De Lucia. Primary literature sources are reported in the second tab of the spreadsheet, named "References". The spreadsheets are uploaded in 2 different formats, xlsx and ods.