cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14337783.v1
title: Additional file 6 of Thousands of previously unknown phages discovered in whole-community human gut metagenomes

description: Additional file 5. Candidate anti-CRISPR (Acr) proteins encoded on each phage genome. Proteins predicted to be an Acr with high confidence (score &gt; 0.9) and meeting all other heuristic criteria are listed along with their inferred host. For the Bifidobacteria phages (see the main text), the nucleotide coordinates of closely related prophages integrated in their host genome are provided in columns 6-8.
DOI: 10.6084/m9.figshare.13653836.v1
title: Pseudmonas cannabina pv. alisalensis TrpA is required for virulence in multiple host plants

description: Tryptophan contribution ti Pcal virulence<br>
DOI: 10.6084/m9.figshare.13653836
title: Pseudmonas cannabina pv. alisalensis TrpA is required for virulence in multiple host plants

description: Tryptophan contribution ti Pcal virulence<br>
DOI: 10.18112/openneuro.ds003397.v1.0.2
title: Monash-vis2PET-MR
DOI: 10.5281/zenodo.4646506
title: Measured SCFAs from feces of infants

description: This dataset is the average concentration of SCFAs in feces of infants. This dataset was used to study the differences of gut microbiome in early childhood with atopic dermatitis. The information of sample ID can be obtained from raw sequence dataset in ERA database and manuscript.
DOI: 10.6084/m9.figshare.14337947.v1
title: Taiwan and Okinawa are genetic diversity museums rather than cradles for Cycas sect. Asiorientales

description: The project includes two files in structure format: 1. 3sp_filtered_SNP.str: the file include ALL SNP after filtering criteria described in manuscript. 2. 3sp_filtered_SNP_neutral.str: the file include NEUTRAL SNP after filtering criteria described in manuscript.
DOI: 10.6084/m9.figshare.14337947
title: Taiwan and Okinawa are genetic diversity museums rather than cradles for Cycas sect. Asiorientales

description: The project includes two files in structure format: 1. 3sp_filtered_SNP.str: the file include ALL SNP after filtering criteria described in manuscript. 2. 3sp_filtered_SNP_neutral.str: the file include NEUTRAL SNP after filtering criteria described in manuscript.
DOI: 10.18112/openneuro.ds003592.v1.0.0
title: Neurocognitive aging data release with behavioral, structural, and multi-echo functional MRI measures
DOI: 10.6084/m9.figshare.14338613
title: Well log

description: A3 well contains DEN, GR, and porosity. ZJ11 and LX1 are training set and test set, respectively.
DOI: 10.6084/m9.figshare.14338613.v1
title: A3 well log

description: A well log contains DEN, GR, and porosity.
DOI: 10.25345/c58r43
title: MassIVE MSV000087125 - GNPS_2 FF TCM Practice practice FF TCM Practice practice FF TCM Practice practice
title: practice practice practice practice practice practice practice practice
DOI: 10.25919/kttc-x397
title: Deep Reef Substrata at Ningaloo Marine Park - Area 5

description: Data from multibeam echosounder surveys taken as part of the Ningaloo Outlook project are classified into various seafloor cover types according to their hardness, rugosity and depth. The classifications are validated with towed video ground truth where it is available. Three AOIs are classified, two that were explicitly part of the Ningaloo Outlook Deep Reefs project and a third transect that was acquired incidentally while RV Investigator was transiting between locations. Due to the nature of the acquired data, two different approaches were taken for the classification, the first approach used multibeam backscatter angular response curves along with rugosity as input to a maximum likelihood classifier. The second approach used flattened multibeam backscatter (i.e. with the angular effects removed), along with rugosity as inputs to a Random Forest Classifier. Estimates of the accuracy of the classifiers are produced, where possible, along with area statistics for the different substratum observed in the classified maps. The maps are GeoTIFFs with text based classification keys. [Note:] Area 5 only
DOI: 10.25919/8m65-7k26
title: Deep Reef Substrata at Ningaloo Marine Park - 120m Transect

description: Data from multibeam echosounder surveys taken as part of the Ningaloo Outlook project are classified into various seafloor cover types according to their hardness, rugosity and depth. The classifications are validated with towed video ground truth where it is available. Three AOIs are classified, two that were explicitly part of the Ningaloo Outlook Deep Reefs project and a third transect that was acquired incidentally while RV Investigator was transiting between locations. Due to the nature of the acquired data, two different approaches were taken for the classification, the first approach used multibeam backscatter angular response curves along with rugosity as input to a maximum likelihood classifier. The second approach used flattened multibeam backscatter (i.e. with the angular effects removed), along with rugosity as inputs to a Random Forest Classifier. Estimates of the accuracy of the classifiers are produced, where possible, along with area statistics for the different substratum observed in the classified maps. The maps are GeoTIFFs with text based classification keys. [Note:] 120m Transect only
DOI: 10.25919/kssa-5b46
title: Deep Reef Substrata at Ningaloo Marine Park - Area 3a

description: Data from multibeam echosounder surveys taken as part of the Ningaloo Outlook project are classified into various seafloor cover types according to their hardness, rugosity and depth. The classifications are validated with towed video ground truth where it is available. Three AOIs are classified, two that were explicitly part of the Ningaloo Outlook Deep Reefs project and a third transect that was acquired incidentally while RV Investigator was transiting between locations. Due to the nature of the acquired data, two different approaches were taken for the classification, the first approach used multibeam backscatter angular response curves along with rugosity as input to a maximum likelihood classifier. The second approach used flattened multibeam backscatter (i.e. with the angular effects removed), along with rugosity as inputs to a Random Forest Classifier. Estimates of the accuracy of the classifiers are produced, where possible, along with area statistics for the different substratum observed in the classified maps. The maps are GeoTIFFs with text based classification keys. [Note:] Area 3a only
DOI: 10.5281/zenodo.4646611
title: Population estimates for the UK 2019 - ONS

description: Population estimates for the UK, England and Wales, Scotland and Northern Ireland: mid-2019, using April 2020 local authority district codes. It contains the following sheets: MYE1 Population estimates: Summary for the UK, mid-2019<br> MYE2 - Persons Population estimates: Persons by single year of age and sex for local authorities in the UK, mid-2019<br> MYE2 - Males Population estimates: Males by single year of age and sex for local authorities in the UK, mid-2019 MYE2 - Females Population estimates: Females by single year of age and sex for local authorities in the UK, mid-2019<br> MYE3 Components of population change for local authorities in the UK, mid-2019<br> MYE4 Population estimates: Summary for the UK, mid-1971 to mid-2019<br> MYE5 Population estimates: Population density for local authorities in the UK, mid-2001 to mid-2019<br> MYE6 Median age of population for local authorities in the UK, mid-2001 to mid-2019<br> Related publications Provides links to further population statistics and related publications <br> <br>
DOI: 10.5281/zenodo.4646610
title: Population estimates for the UK 2019 - ONS

description: Population estimates for the UK, England and Wales, Scotland and Northern Ireland: mid-2019, using April 2020 local authority district codes. It contains the following sheets: MYE1 Population estimates: Summary for the UK, mid-2019<br> MYE2 - Persons Population estimates: Persons by single year of age and sex for local authorities in the UK, mid-2019<br> MYE2 - Males Population estimates: Males by single year of age and sex for local authorities in the UK, mid-2019 MYE2 - Females Population estimates: Females by single year of age and sex for local authorities in the UK, mid-2019<br> MYE3 Components of population change for local authorities in the UK, mid-2019<br> MYE4 Population estimates: Summary for the UK, mid-1971 to mid-2019<br> MYE5 Population estimates: Population density for local authorities in the UK, mid-2001 to mid-2019<br> MYE6 Median age of population for local authorities in the UK, mid-2001 to mid-2019<br> Related publications Provides links to further population statistics and related publications <br> <br>
DOI: 10.6084/m9.figshare.14338721
title: Supplementary Material for: Beta-Trace Protein as a Potential Marker of Acute Kidney Injury: A Pilot Study

description: <b><i>Introduction:</i></b> Acute kidney injury (AKI) is a frequent complication among patients in the intensive care unit (ICU). The limitations of serum Cr (sCr) in timely detecting AKI are well known. Beta-trace protein (BTP) is emerging as a novel endogenous glomerular filtration rate marker. The aim of this study was to explore the role of BTP as a marker of AKI. <b><i>Methods:</i></b> Patients admitted to the ICU undergoing surgery were included. BTP, sCr, Cystatin C (CysC), and neutrophil gelatinase-associated lipocalin (NGAL) were measured preoperatively, postoperatively (post-op), and at the first (D1) and second (D2) post-op day. AKI was defined as an increase of sCr to ≥1.5-fold from baseline within 2 days after surgery. <b><i>Results:</i></b> Of the 52 patients studied, 10 patients (19%) developed AKI. Patients with AKI were older (69.6 ± 10.7 vs. 58.1 ± 16.7 years, <i>p</i> = 0.043) and had a longer length of ICU stay (13 [IQR 6–49] vs. 6 [IQR 5–8] days, <i>p</i> = 0.032). Between the 2 groups, the evolution of BTP, sCr, CysC, and NGAL over time differed significantly, with overall higher values in the AKI group. ROC analysis for the detection of AKI within 2 days after surgery showed a great accuracy for BTP. The area under the curve (AUC) for BTP post-op; D1; and D2 was, respectively, 0.869 ± 0.049; 0.938 ± 0.035; and 0.943 ± 0.032. The discriminative power of a BTP measurement on D1 was superior in detecting AKI compared to NGAL (adjusted <i>p</i> value = 0.027). We could not detect a significant difference between the AUCs of other biomarkers (NGAL, sCr, and CysC). <b><i>Conclusion:</i></b> Serum BTP is a promising marker for diagnosing AKI in ICU patients undergoing surgery.
DOI: 10.6084/m9.figshare.14338721.v1
title: Supplementary Material for: Beta-Trace Protein as a Potential Marker of Acute Kidney Injury: A Pilot Study

description: <b><i>Introduction:</i></b> Acute kidney injury (AKI) is a frequent complication among patients in the intensive care unit (ICU). The limitations of serum Cr (sCr) in timely detecting AKI are well known. Beta-trace protein (BTP) is emerging as a novel endogenous glomerular filtration rate marker. The aim of this study was to explore the role of BTP as a marker of AKI. <b><i>Methods:</i></b> Patients admitted to the ICU undergoing surgery were included. BTP, sCr, Cystatin C (CysC), and neutrophil gelatinase-associated lipocalin (NGAL) were measured preoperatively, postoperatively (post-op), and at the first (D1) and second (D2) post-op day. AKI was defined as an increase of sCr to ≥1.5-fold from baseline within 2 days after surgery. <b><i>Results:</i></b> Of the 52 patients studied, 10 patients (19%) developed AKI. Patients with AKI were older (69.6 ± 10.7 vs. 58.1 ± 16.7 years, <i>p</i> = 0.043) and had a longer length of ICU stay (13 [IQR 6–49] vs. 6 [IQR 5–8] days, <i>p</i> = 0.032). Between the 2 groups, the evolution of BTP, sCr, CysC, and NGAL over time differed significantly, with overall higher values in the AKI group. ROC analysis for the detection of AKI within 2 days after surgery showed a great accuracy for BTP. The area under the curve (AUC) for BTP post-op; D1; and D2 was, respectively, 0.869 ± 0.049; 0.938 ± 0.035; and 0.943 ± 0.032. The discriminative power of a BTP measurement on D1 was superior in detecting AKI compared to NGAL (adjusted <i>p</i> value = 0.027). We could not detect a significant difference between the AUCs of other biomarkers (NGAL, sCr, and CysC). <b><i>Conclusion:</i></b> Serum BTP is a promising marker for diagnosing AKI in ICU patients undergoing surgery.
DOI: 10.5281/zenodo.4010525
title: Systems level profiling of chemotherapy-induced stress resolution reveals druggable trade-offs

description: Directory structure: --[ROOT] ----[Kallisto] 50x bootstraped Kallisto-derived estimated counts ----[Library] transcript-to-gene mapping for tximport ----[Metabolomics] normalised metabolyte levels from service provider (Metabolon Inc.) ----[Proteomics] normalised protein levels from service provider (Francis Crick Institute) ----RNAseq.R, produce RNA-seq counts and abundances from Kallisto data ----Metabolomics.R, input + transform + QC metabolomics data ----Proteomics.R, input + QC proteomics da
DOI: 10.5281/zenodo.4010524
title: Systems level profiling of chemotherapy-induced stress resolution reveals druggable trade-offs

description: Directory structure: --[ROOT] ----[Kallisto] 50x bootstraped Kallisto-derived estimated counts ----[Library] transcript-to-gene mapping for tximport ----[Metabolomics] normalised metabolyte levels from service provider (Metabolon Inc.) ----[Proteomics] normalised protein levels from service provider (Francis Crick Institute) ----RNAseq.R, produce RNA-seq counts and abundances from Kallisto data ----Metabolomics.R, input + transform + QC metabolomics data ----Proteomics.R, input + QC proteomics da
DOI: 10.6084/m9.figshare.12946919
title: Nonalcoholic fatty liver disease and sarcopenia: pathophysiological connections and therapeutic implications

description: Nonalcoholic fatty liver disease (NAFLD) is currently one of the most common liver diseases worldwide. Recent data suggest that loss of skeletal muscle mass and function (i.e. sarcopenia) is highly prevalent and frequently overlooked in NAFLD patients. Experimental and clinical data suggest that the relationship between NAFLD and sarcopenia is pathophysiologically complex and bi-directional and there is a growing interest in unveiling how sarcopenia could influence NAFLD development and progression. PubMed/MEDLINE was searched for articles related to concomitant occurrence of NAFLD and sarcopenia between January 2013 and April 2020. Areas covered in this review include: (1) updated sarcopenia diagnosis strategy, (2) discussion of current data on pathophysiological connections between NAFLD and sarcopenia, and (3) analysis of current and future therapeutic implications of this knowledge. Clinical studies describe a consistent association between NAFLD and sarcopenia, although a cause–effect relation remains to be determined. Active implementation of current diagnosis algorithms and optimized treatment can prevent sarcopenia related complications in subjects with NAFLD. Pathogenic pathways implicated in this relation are multiple and complex, a better understanding of them can provide novel biomarkers and targeted therapies that will hopefully have an important impact in NAFLD management.
DOI: 10.6084/m9.figshare.12946919.v1
title: Nonalcoholic fatty liver disease and sarcopenia: pathophysiological connections and therapeutic implications

description: Nonalcoholic fatty liver disease (NAFLD) is currently one of the most common liver diseases worldwide. Recent data suggest that loss of skeletal muscle mass and function (i.e. sarcopenia) is highly prevalent and frequently overlooked in NAFLD patients. Experimental and clinical data suggest that the relationship between NAFLD and sarcopenia is pathophysiologically complex and bi-directional and there is a growing interest in unveiling how sarcopenia could influence NAFLD development and progression. PubMed/MEDLINE was searched for articles related to concomitant occurrence of NAFLD and sarcopenia between January 2013 and April 2020. Areas covered in this review include: (1) updated sarcopenia diagnosis strategy, (2) discussion of current data on pathophysiological connections between NAFLD and sarcopenia, and (3) analysis of current and future therapeutic implications of this knowledge. Clinical studies describe a consistent association between NAFLD and sarcopenia, although a cause–effect relation remains to be determined. Active implementation of current diagnosis algorithms and optimized treatment can prevent sarcopenia related complications in subjects with NAFLD. Pathogenic pathways implicated in this relation are multiple and complex, a better understanding of them can provide novel biomarkers and targeted therapies that will hopefully have an important impact in NAFLD management.
DOI: 10.5517/ccdc.csd.cc242f4t
title: CCDC 1968535: Experimental Crystal Structure Determination

description: Related Article: Ni Putu Ariantari, Marian Frank, Ying Gao, Fabian Stuhldreier, Anna-Lene Kiffe-Delf, Rudolf Hartmann, Simon-Patrick Höfert, Christoph Janiak, Sebastian Wesselborg, Werner E.G. Müller, Rainer Kalscheuer, Zhen Liu, Peter Proksch|2021|Tetrahedron|85|132065|doi:10.1016/j.tet.2021.132065
DOI: 10.5517/ccdc.csd.cc242f5v
title: CCDC 1968536: Experimental Crystal Structure Determination

description: Related Article: Ni Putu Ariantari, Marian Frank, Ying Gao, Fabian Stuhldreier, Anna-Lene Kiffe-Delf, Rudolf Hartmann, Simon-Patrick Höfert, Christoph Janiak, Sebastian Wesselborg, Werner E.G. Müller, Rainer Kalscheuer, Zhen Liu, Peter Proksch|2021|Tetrahedron|85|132065|doi:10.1016/j.tet.2021.132065
DOI: 10.5517/ccdc.csd.cc279rt4
title: CCDC 2064966: Experimental Crystal Structure Determination

description: Related Article: Arathy Jose, Raysa Khan Tareque, Martin Mortensen, Remi Legay, Simon J. Coles, Graham J. Tizzard, Barnaby W. Greenland, Trevor G. Smart, Mark C. Bagley, John Spencer|2021|Tetrahedron|85|132020|doi:10.1016/j.tet.2021.132020
DOI: 10.6084/m9.figshare.14338760
title: Kurokawa+2021_Asteroids.zip

description: Observation and modeling data used in the paper: Kurokawa et al. (2021) Distant formation and differentiation of outer main belt asteroids and carbonaceous chondrites' parent bodie.
DOI: 10.6084/m9.figshare.14338766
title: Supplementary Material for: Diagnosis and Management of Severe Asthma in Switzerland: Analysis of Survey Results Conducted with Specialists and General Practitioners

description: <b><i>Background:</i></b> Severe asthma commonly affects 5–10% of the asthmatic population and accounts for approximately 50% of the overall asthma costs. <b><i>Objective:</i></b> This analysis investigated how severe asthma is diagnosed, treated, and managed by specialists and general practitioners (GPs) in Switzerland. <b><i>Methods:</i></b> Two surveys, one each among specialists (<i>N</i> = 44) and GPs (<i>N</i> = 153), were conducted to understand their self-perception on diagnosis, treatment, and management of severe asthma. <b><i>Results:</i></b> Fifty-five percent of the specialists felt very confident and 43% confident in recognizing the symptoms of severe asthma and diagnosing severe asthma. In contrast, 9% of the GPs were very confident and 59% confident in diagnosing severe asthma. More specific diagnostic tests for severe asthma, like total and specific immunoglobulin E levels and measurement of the fraction of exhaled nitric oxide, were run by specialists (χ<sup>2</sup> = 171.4; df = 15, <i>p</i> &lt; 0.001). GPs and specialists were using different measurements to assess severe asthma (χ<sup>2</sup> = 385.2; df = 13, <i>p</i> &lt; 0.001) and their prescribing patterns differed significantly (χ<sup>2</sup> = 189.8; df = 10, <i>p</i> &lt; 0.001). GPs referred patients with severe asthma if the diagnosis was unclear (24%), if treatment failure occurred (26%), and if the patients were at high risk (41%). <b><i>Conclusions:</i></b> Oral corticosteroids (OCSs) are considered as background therapy for severe asthma by GPs and specialists. In order to reduce the OCS burden, there is a need to improve the awareness for other add-on therapies. A joint collaboration between GPs and specialists is the key to leverage therapeutic strategies together.
DOI: 10.6084/m9.figshare.14338766.v1
title: Supplementary Material for: Diagnosis and Management of Severe Asthma in Switzerland: Analysis of Survey Results Conducted with Specialists and General Practitioners

description: <b><i>Background:</i></b> Severe asthma commonly affects 5–10% of the asthmatic population and accounts for approximately 50% of the overall asthma costs. <b><i>Objective:</i></b> This analysis investigated how severe asthma is diagnosed, treated, and managed by specialists and general practitioners (GPs) in Switzerland. <b><i>Methods:</i></b> Two surveys, one each among specialists (<i>N</i> = 44) and GPs (<i>N</i> = 153), were conducted to understand their self-perception on diagnosis, treatment, and management of severe asthma. <b><i>Results:</i></b> Fifty-five percent of the specialists felt very confident and 43% confident in recognizing the symptoms of severe asthma and diagnosing severe asthma. In contrast, 9% of the GPs were very confident and 59% confident in diagnosing severe asthma. More specific diagnostic tests for severe asthma, like total and specific immunoglobulin E levels and measurement of the fraction of exhaled nitric oxide, were run by specialists (χ<sup>2</sup> = 171.4; df = 15, <i>p</i> &lt; 0.001). GPs and specialists were using different measurements to assess severe asthma (χ<sup>2</sup> = 385.2; df = 13, <i>p</i> &lt; 0.001) and their prescribing patterns differed significantly (χ<sup>2</sup> = 189.8; df = 10, <i>p</i> &lt; 0.001). GPs referred patients with severe asthma if the diagnosis was unclear (24%), if treatment failure occurred (26%), and if the patients were at high risk (41%). <b><i>Conclusions:</i></b> Oral corticosteroids (OCSs) are considered as background therapy for severe asthma by GPs and specialists. In order to reduce the OCS burden, there is a need to improve the awareness for other add-on therapies. A joint collaboration between GPs and specialists is the key to leverage therapeutic strategies together.