cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20289156
title: Additional file 2 of Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections

description: Additional file 2: Table S2. mNGS detection of respiratory pathogens compared to a reference standard of clinical microbiological testing.
DOI: 10.6084/m9.figshare.20289159.v1
title: Additional file 3 of Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections

description: Additional file 3: Dataset 1. AMR gene database utilized for analyses.
DOI: 10.6084/m9.figshare.20289162.v1
title: Additional file 4 of Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections

description: Additional file 4: Dataset 2. AMR genes and guide RNAs for FLASH targeted mNGS. AMR genes and guide RNAs for FLASH targeted mNGS. A) AMR genes targeted by FLASH. B) AMR alleles and guide RNA targets. Legend: Bla = beta lactam; MLS = macrolide, Tmp/Sul = trimethoprim/sulfamethoxazole.
DOI: 10.6084/m9.figshare.20289168
title: Additional file 6 of Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections

description: Additional file 6: Table S4. AMR genes detected by mNGS.
DOI: 10.6084/m9.figshare.20289174
title: Additional file 8 of Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections

description: Additional file 8: Table S6. Pathogen AMR genes detected by FLASH-mNGS.
DOI: 10.6084/m9.figshare.20289165
title: Additional file 5 of Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections

description: Additional file 5: Table S3. Time to return of clinical antimicrobial susceptibility testing results for culture-confirmed bacterial pathogens.
DOI: 10.6084/m9.figshare.20289168.v1
title: Additional file 6 of Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections

description: Additional file 6: Table S4. AMR genes detected by mNGS.
DOI: 10.6084/m9.figshare.20289171.v1
title: Additional file 7 of Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections

description: Additional file 7: Table S5. Performance of RNA-seq, DNA-seq and combined RNA-seq + DNA-seq for AMR prediction compared to clinical antimicrobial susceptibility testing.
DOI: 10.6084/m9.figshare.20289171
title: Additional file 7 of Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections

description: Additional file 7: Table S5. Performance of RNA-seq, DNA-seq and combined RNA-seq + DNA-seq for AMR prediction compared to clinical antimicrobial susceptibility testing.
DOI: 10.6084/m9.figshare.20289174.v1
title: Additional file 8 of Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections

description: Additional file 8: Table S6. Pathogen AMR genes detected by FLASH-mNGS.
DOI: 10.6084/m9.figshare.20289177
title: Additional file 9 of Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections

description: Additional file 9: Table S7. AMR genes detected by FLASH coupled with Nanopore mNGS.
DOI: 10.6084/m9.figshare.20289177.v1
title: Additional file 9 of Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections

description: Additional file 9: Table S7. AMR genes detected by FLASH coupled with Nanopore mNGS.
DOI: 10.5519/qd.87vm9h1e
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1 records)
DOI: 10.6084/m9.figshare.20289219
title: R values in Search Space.xlsx

description: Reliability Values in Search Space
DOI: 10.6084/m9.figshare.20289198.v1
title: A high-performance cellular automata model for urban expansion simulation based on convolution and GPU

description: GPU_conv_CA
DOI: 10.6084/m9.figshare.20071994
title: Supplementary Material for: A prospective study on defining the indications of prophylactic level IB radiotherapy in nasopharyngeal carcinoma based on a risk score model

description: Objective: To investigate clinical evidence for defining the indications of prophylactic level IB radiotherapy in nasopharyngeal carcinoma (NPC). Methods: We conducted a phase 2 prospective study in 116 newly diagnosed patients with NPC treated by intensity-modulated radiotherapy (IMRT). Whether level IB was irradiated based on the risk score model (RSM). Two groups based on RSM were obtained: low risk and high risk. Omission of level IB irradiation was conducted in low risk group, otherwise level IB was contoured as part of the treatment target. Grade 2 or worse xerostomia at 12 months was assessed by the European Organization for Research and Treatment of Cancer (EORTC) QLQ-H&N35 questionnaire. Results: At a median follow-up of 16months (range, 1-26 months). None patients developed failures at level IB. The 1-year overall survival (OS), locoregional recurrence-free survival (LRRFS) and distant metastasis-free survival (DMFS) rates were 98.3%, 97.2% and 95.8%, respectively. At 12 months xerostomia side-effects were reported 90 of 126 alive patients, grade 2 or worse xerostomia at 12 months was significantly lower in the low risk group than in the high risk group. Conclusion: Omission of level IB irradiation was feasible for patients with low-risk IB lymph nodes metastasis.
DOI: 10.6084/m9.figshare.20289234
title: pb_466_001.reads_of_insert.fastq.gz

description: Sequences reads to analyse Tomicus piniperda fungal community
DOI: 10.6084/m9.figshare.20289234.v1
title: pb_466_001.reads_of_insert.fastq.gz

description: Sequences reads to analyse Tomicus piniperda fungal community
DOI: 10.5281/zenodo.6820333
title: PackardChan/ccc2022-heatwave-blocking-CMIP

description: Computer code and data to repeat the results in Chan, Catto and Collins, under minor revision.
DOI: 10.5281/zenodo.6820450
title: Serum osmolality predicts mortality

description: Supplementary Material 1: ICD-9 codes of patients included in this study. Supplementary Material 2: Table S1:Univariate logistics regression analysis of all patients on ICU and in-hospital mortality.Table S2:Univariate Cox regression analysis of all patients on 30-day and 90-day mortality.
DOI: 10.5281/zenodo.6820449
title: Serum osmolality predicts mortality

description: Supplementary Material 1: ICD-9 codes of patients included in this study. Supplementary Material 2: Table S1:Univariate logistics regression analysis of all patients on ICU and in-hospital mortality.Table S2:Univariate Cox regression analysis of all patients on 30-day and 90-day mortality.
DOI: 10.6084/m9.figshare.20289525
title: Data_ASD.csv

description: The dataset for the manuscript – Is Motor Proficiency Overestimated in Performing Complex Movements for Children with and without Autism Spectrum Disorder?
DOI: 10.6084/m9.figshare.20289525.v1
title: Data_ASD.csv

description: The dataset for the manuscript – Is Motor Proficiency Overestimated in Performing Complex Movements for Children with and without Autism Spectrum Disorder?
DOI: 10.6084/m9.figshare.20289198
title: A high-performance cellular automata model for urban expansion simulation based on convolution and GPU

description: GPU_conv_CA
DOI: 10.6084/m9.figshare.20289198.v3
title: A high-performance cellular automata model for urban expansion simulation based on convolution and GPU

description: GPU_conv_CA
DOI: 10.6084/m9.figshare.20289198.v2
title: A high-performance cellular automata model for urban expansion simulation based on convolution and GPU

description: GPU_conv_CA
DOI: 10.34740/kaggle/dsv/2701334
title: Sentiment Analysis
DOI: 10.34808/d2nd-e928
title: Iron deficiency anaemia, unspecified - Female, 34 - Cell image [7120730007984591]

description: This is the histopathological image of HEMATOPOIETIC AND RETICULOENDOTHELIAL SYSTEMS cell sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: VS200 Olympus slide scanner (40x magnification) and saved to DICOM format. The detailed information about the patient, sample, and diagnosis are as follows: Patient:Age: 34Clinical description: Gender: FemaleDiagnosis:Classification: ICD-10_10-20Classification code: Chapter III - Diseases of the blood and blood-forming organs and certain disorders involving the immune mechanismDiagnosis: Iron deficiency anaemia, unspecifiedResult of the histopathological examination: Peripheral blood smear from a patient with iron deficiency anaemia. Significant hypochromia and numerous microcytes are noteworthy. A few elliptocytes, single teardrop-shaped red cells and schistocytes are present. Anisothrombocytosis is also observed. Neutrophils constitute about 50% of WBC. Increased percentage of eosinophils is present (about 10%).Sample:Material: SmearCollecting method: Not availableTopography: HEMATOPOIETIC AND RETICULOENDOTHELIAL SYSTEMSOrgan: HEMATOPOIETIC AND RETICULOENDOTHELIAL SYSTEMSTissue: BloodType of staining: positive/HCStaining: May Grunwald GiemsaAntibody: Not applicableTechnology:Equipment: VS200 OlympusLens: 40xOrganization:Source: Medical University Gdańsk
DOI: 10.34740/kaggle/dsv/3932093
title: MTSOD-dataset
DOI: 10.34808/c15r-k724
title: Iron deficiency anaemia, unspecified - Female, 47 - Cell image [7120730007986771]

description: This is the histopathological image of HEMATOPOIETIC AND RETICULOENDOTHELIAL SYSTEMS cell sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: VS200 Olympus slide scanner (40x magnification) and saved to DICOM format. The detailed information about the patient, sample, and diagnosis are as follows: Patient:Age: 47Clinical description: Gender: FemaleDiagnosis:Classification: ICD-10_10-20Classification code: Chapter III - Diseases of the blood and blood-forming organs and certain disorders involving the immune mechanismDiagnosis: Iron deficiency anaemia, unspecifiedResult of the histopathological examination: Peripheral blood smear with presence 75% of neutrophils. Numerous microcytic and hypochromic red blood cells are noteworthy. Single ovalocytes, elliptocytes and echinocytes are also observed.Sample:Material: SmearCollecting method: Not availableTopography: HEMATOPOIETIC AND RETICULOENDOTHELIAL SYSTEMSOrgan: HEMATOPOIETIC AND RETICULOENDOTHELIAL SYSTEMSTissue: BloodType of staining: positive/HCStaining: May Grunwald GiemsaAntibody: Not applicableTechnology:Equipment: VS200 OlympusLens: 40xOrganization:Source: Medical University Gdańsk
DOI: 10.34808/w1fm-tk18
title: Vitamin B12 deficiency anaemia, unspecified - Male, 52 - Cell image [7120730007975601]

description: This is the histopathological image of HEMATOPOIETIC AND RETICULOENDOTHELIAL SYSTEMS cell sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: VS200 Olympus slide scanner (40x magnification) and saved to DICOM format. The detailed information about the patient, sample, and diagnosis are as follows: Patient:Age: 52Clinical description: Gender: MaleDiagnosis:Classification: ICD-10_10-20Classification code: Chapter III - Diseases of the blood and blood-forming organs and certain disorders involving the immune mechanismDiagnosis: Vitamin B12 deficiency anaemia, unspecifiedResult of the histopathological examination: Peripheral blood smear shows predominant population of granulocytes with slight "left shift". Nuclear hypersegmentation is present in most mature granulocytes. Significant anisopoikilocytosis is also observed - numerous ovalocytes and oval macrocytes, a few teardrop-shaped red cells.Sample:Material: SmearCollecting method: Not availableTopography: HEMATOPOIETIC AND RETICULOENDOTHELIAL SYSTEMSOrgan: HEMATOPOIETIC AND RETICULOENDOTHELIAL SYSTEMSTissue: BloodType of staining: positive/HCStaining: May Grunwald GiemsaAntibody: Not applicableTechnology:Equipment: VS200 OlympusLens: 40xOrganization:Source: Medical University Gdańsk
DOI: 10.34808/kmzf-7e31
title: Other autoimmune haemolytic anaemias - Female, 81 - Cell image [7120730007983911]

description: This is the histopathological image of HEMATOPOIETIC AND RETICULOENDOTHELIAL SYSTEMS cell sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: VS200 Olympus slide scanner (40x magnification) and saved to DICOM format. The detailed information about the patient, sample, and diagnosis are as follows: Patient:Age: 81Clinical description: Gender: FemaleDiagnosis:Classification: ICD-10_10-20Classification code: Chapter III - Diseases of the blood and blood-forming organs and certain disorders involving the immune mechanismDiagnosis: Other autoimmune haemolytic anaemiasResult of the histopathological examination: Peripheral blood smear from a patient with AIHA. Presence of red blood cell autoagglutination is noteworthy. Granulocytic lineage cells constitute about 75% of WBC.  Anisocytosis is observed.Sample:Material: SmearCollecting method: Not availableTopography: HEMATOPOIETIC AND RETICULOENDOTHELIAL SYSTEMSOrgan: HEMATOPOIETIC AND RETICULOENDOTHELIAL SYSTEMSTissue: BloodType of staining: positive/HCStaining: May Grunwald GiemsaAntibody: Not applicableTechnology:Equipment: VS200 OlympusLens: 40xOrganization:Source: Medical University Gdańsk
DOI: 10.6084/m9.figshare.20289099
title: Global Production and Trends in Nighttime Oxidants – Increases in China, Decreases Elsewhere

description: Datasets that support the findings of the study "Global Production and Trends in Nighttime Oxidants – Increases in China, Decreases Elsewhere"
DOI: 10.6084/m9.figshare.20289099.v1
title: Global Production and Trends in Nighttime Oxidants – Increases in China, Decreases Elsewhere

description: Datasets that support the findings of the study "Global Production and Trends in Nighttime Oxidants – Increases in China, Decreases Elsewhere"
DOI: 10.26066/rds.1973179
title: Debris cover glacier melt in the Karakoram during 2021

description: The assessment of meltwater sourcing from the clean and debris-covered glaciers is scarce in High Mountain Asia (HMA). The melting rate varies with the debris cover thickness and glacier orientation. The present study quantifies glacier melting rate attributed to varying thickness of debris cover in the Karakoram. We observed the melting rates by installing ablation stakes on Hinarchi and Sachen glaciers over debris-free and debris-covered ice during a field expedition. The stakes were installed on clean ice and glacier surface with debris cover thickness ranges between 0.5 and 2 cm at selected experimental sites between 2700 and 3100 m a.s.l. during July 2021.
DOI: 10.6084/m9.figshare.18497600.v2
title: FROM-GLC Plus

description: Building on the earlier Global Land Cover Mapping (Finer Resolution Observation and Monitoring - Global Land Cover, FROM-GLC), we developed the improved Global Land Cover Change Monitoring Platform (FROM-GLC Plus) using methods such as multi-season sample space-time migration, multi-source data time series reconstruction, and machine learning. The FROM-GLC Plus system provides a capacity for producing global land cover change data set from the 1980s with flexibility in spatio–temporal details. The preliminary results of multi-resolution land cover maps in Chicago, U. S. is given here.<br>Values in the files: 10-cropland20-forest30-grassland40-shrubland50-wetland60-water70-tundra80-impervious90-bare land100-ice/snow120-clouds
DOI: 10.5283/epub.41303
title: Data archive of "How sequential changes in reward expectation modulate cognitive control: Pupillometry as a tool to monitor dynamic changes in reward expectation", International Journal of Psychophysiology

description: Data archive with pupillometry and behavioral raw data from two experiments
description: Pupillometry and behavioral raw data files from two experiments with description / Pupillometrie- und Verhaltensrohdaten zweier Experimente mit Beschreibung
DOI: 10.11588/data/eixopn
title: Key Signature Genes of Early Terminal Granulocytic Differentiation Distinguish Sepsis from SIRS on ICU Admission

description: Background: Infection can induce granulopoiesis. This process potentially gives rise to blood gene classifiers of sepsis in systemic inflammatory response syndrome (SIRS) patients. The aim of this study was to identify sepsis signature genes in blood granulocytes from patients with sepsis and SIRS on intensive care unit (ICU) admission. Methods: CD15+ cells encompassing all stage of terminal granulocytic differentiation were analyzed. CD15 transcriptomes from patients with sepsis and SIRS on ICU admission and presurgical controls (discovery cohort) were subjected to differential gene expression and pathway enrichment analyses. Differential expression was validated by bead array in independent sepsis and SIRS patients (validation cohort). We referred to the GeneCards database for subcellular gene associations and Grassi et al. (Cell Rep 2018; 24: 2784-2794) for granule signature genes. Blood counts of granulocyte precursors were determined by flow cytometry in a validation cohort subset. Results: Despite similar transcriptional CD15 responses in sepsis and SIRS, enrichment of pathways known to decline at the metamyelocyte stage (mitochondrial, lysosome, cell cycle, proteasome) was associated with sepsis but not SIRS. Twelve of 30 validated genes, from 100 selected for changes in response to sepsis rather than SIRS, were endo-lysosomal. Revisiting the discovery transcriptomes revealed elevated expression of promyelocyte-restricted azurophilic granule genes in sepsis and myelocyte-restricted specific granule genes in sepsis followed by SIRS. Blood counts of promyelocytes and myelocytes were higher in sepsis than SIRS. Conclusions: Sepsis-induced granulopoiesis and signature genes of early terminal granulocytic differentiation provide a rationale for classifiers of sepsis in patients with SIRS on ICU admission. Yet, distinction of this process from non-infectious tissue injury-induced granulopoiesis remains to be investigated.
DOI: 10.34740/kaggle/dsv/3932323
title: Russian Invasion of Ukraine
DOI: 10.5281/zenodo.6820581
title: Assessment of the FAIR-ness of the VAMDC infrastructure following RDA guidelines.

description: This document presents the results of the evaluation of the VAMDC infrastructure, following the FAIR assessment method produced by the Research Data Alliance FAIR Data Maturity Model Working Group (https://doi.org/10.15497/RDA00050).
description: {"references": ["FAIR Data Maturity Model Working Group. (2020). FAIR Data Maturity Model. Specification and Guidelines (1.0). https://doi.org/10.15497/rda00050", "A Decade with VAMDC: Results and Ambitions, Atoms, vol. 8, no. 4, p. 76, 2020. doi:10.3390/atoms8040076."]}
DOI: 10.5281/zenodo.6820580
title: Assessment of the FAIR-ness of the VAMDC infrastructure following RDA guidelines.

description: This document presents the results of the evaluation of the VAMDC infrastructure, following the FAIR assessment method produced by the Research Data Alliance FAIR Data Maturity Model Working Group (https://doi.org/10.15497/RDA00050).
description: {"references": ["FAIR Data Maturity Model Working Group. (2020). FAIR Data Maturity Model. Specification and Guidelines (1.0). https://doi.org/10.15497/rda00050", "A Decade with VAMDC: Results and Ambitions, Atoms, vol. 8, no. 4, p. 76, 2020. doi:10.3390/atoms8040076."]}
DOI: 10.34808/0411-4504
title: Mantle cell lymphoma - Male, 70 - Tissue image [7120837250927171]

description: This is the histopathological image of LYMPH NODES tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format. The detailed information about the patient, sample, and diagnosis are as follows: Patient:Age: 70Clinical description: Generalized lymphadenopathy.Gender: MaleDiagnosis:Classification: ICD-O_3.2Classification code: MATURE B-CELL LYMPHOMASDiagnosis: Mantle cell lymphomaResult of the histopathological examination: WHO: mantle cell lymphoma (MCL).

IHC: CD 20 (+), PAX5 (+), cyclin D1 (+), CD 5(+), bcl 2 (+), CD 23 (-), CD 43 (-/+), CD 3(-), bcl 6 (+/-), MUM 1 (+), Ki 67 20-25%kkSample:Material: FFPECollecting method: Surgical specimenTopography: LYMPH NODESOrgan: LYMPH NODESTissue: Subclavicular lymph nodeType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: Pannoramic 250 3DHistechLens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.34808/kt38-k084
title: Mantle cell lymphoma - Female, 65 - Tissue image [7120837250926661]

description: This is the histopathological image of LYMPH NODES tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: VS200 Olympus slide scanner (20x magnification) and saved to DICOM format. The detailed information about the patient, sample, and diagnosis are as follows: Patient:Age: 65Clinical description: Generalized lymphadenopathy.Gender: FemaleDiagnosis:Classification: ICD-O_3.2Classification code: MATURE B-CELL LYMPHOMASDiagnosis: Mantle cell lymphomaResult of the histopathological examination: Mantle cell lymphoma, blastoid variant.
IHC: CD20+, CD3 (-), bcl2 +, bcl6 (-), CD5 +, CD10 (-), cyclin D1 +, CD23+, cMyc (-), Ki67 70%.Sample:Material: FFPECollecting method: Surgical specimenTopography: LYMPH NODESOrgan: LYMPH NODESTissue: Lymph node axilla, armType of staining: positive/IHCStaining: Not applicableAntibody: c-MycTechnology:Equipment: VS200 OlympusLens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.5281/zenodo.6778139
title: MD simulation trajectory of SDG/POPE bilayer and related files

description: Raw simulation trajectory data of pre-equiblirated SDG/POPE bilayer and related files from all-atom molecular dynamics simulations. Simulations have been performed with GROMACS-2018.6 with Lipid17 forcefield and TIP3P water model. The trajectory is 0-2100 ns, and we have disregarded the first 100 ns in our analysis. The system in the trajectory consists of 12 SDG, 116 POPE and 6400 water molecules. Temperature 310 K, pressure 1 bar.
DOI: 10.5281/zenodo.6778138
title: MD simulation trajectory of SDG/POPE bilayer and related files

description: Raw simulation trajectory data of pre-equiblirated SDG/POPE bilayer and related files from all-atom molecular dynamics simulations. Simulations have been performed with GROMACS-2018.6 with Lipid17 forcefield and TIP3P water model. The trajectory is 0-2100 ns, and we have disregarded the first 100 ns in our analysis. The system in the trajectory consists of 12 SDG, 116 POPE and 6400 water molecules. Temperature 310 K, pressure 1 bar.