cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.6242512
title: LipidMS v3.0.3: source code and example of lipidomics dataset for human serum

description: Source code and example dataset for LipidMS v3.0.3: a commercially available pooled human serum sample was analyzed in positive and negative detection modes and using MS1, DIA and DDA approaches. The obtained datasets were processed using LipidMS v3.0, MS-DIAL v4.80 or a combination of data pre-processing in XCMS v3.16 and lipid annotation in LipidMS v3.0. This repository contains: - Raw data for positive and negative polarities using MS scan, DIA and DDA acquisition modes. - R scripts for processing with LipidMS v3.0.3 and XCMS v3.16.1 and parameters used for processing with MS-DIAL v4.80. - Source code for LipidMS v3.0.3. - Results obtained for the 3 different softwares employed. - Tutorials for LipidMS R package and online application. - Human pooled serum analysis Raw data for positive and negative polarities using MS scan, DIA and DDA acquisition modes for a human pooled serum sample with or without the addition of 68 lipid standars Results for the data processing and annotation of the lipid standards using LipidMS 3.0, XCMS 3.16 and MS-DIAL 4.80 Results for the manual curation of the total lipid annotations provided by both LipidMS 3.0 and MS-DIAL 4.80
DOI: 10.6084/m9.figshare.19614438.v1
title: Supplementary Material for: Small RNA sequencing reveals exosomal miRNAs as unique feature markers in unprovoked venous thromboembolism

description: Introduction: Venous thromboembolism (VTE) is a common cardiovascular disease. miRNAs play a key role in VTE; however, the role of exosomal miRNAs in VTE remains unknown. Therefore, we aimed to identify key exosomal miRNAs and their potential mechanisms in VTE. Methods: We collected 31 samples from unprovoked VTE patients and 25 samples from healthy individuals. Exosomal miRNA sequencing was performed on 11 unprovoked VTE samples and 9 normal samples, and remaining samples to verify the expression level of candidate 9 miRNAs in VTE and normal samples. The sequencing data were used to analyze exosomal miRNA expression. Meanwhile, GO and KEGG analyses were performed to determine the potential biological functions of differentially expressed miRNA target genes. Results: A total of 32 differentially expressed miRNAs were identified by sequencing. Among the 32 miRNAs, 23 miRNAs were upregulated (72%), and 9 miRNAs were downregulated (28%). In addition, we found that the biological functions and metabolic pathways of the target genes were related to hemostatic factors involved in VTE, indicating the regulation of differentially expressed miRNAs. We identified key miRNAs by constructing a miRNA-mRNA regulatory network and found that the target genes were related to VTE. We finally determined that the abnormal expression of 9 miRNAs is closely related to VTE, and the expression level between VTE and normal was verified through other samples.
DOI: 10.6084/m9.figshare.19614438
title: Supplementary Material for: Small RNA sequencing reveals exosomal miRNAs as unique feature markers in unprovoked venous thromboembolism

description: Introduction: Venous thromboembolism (VTE) is a common cardiovascular disease. miRNAs play a key role in VTE; however, the role of exosomal miRNAs in VTE remains unknown. Therefore, we aimed to identify key exosomal miRNAs and their potential mechanisms in VTE. Methods: We collected 31 samples from unprovoked VTE patients and 25 samples from healthy individuals. Exosomal miRNA sequencing was performed on 11 unprovoked VTE samples and 9 normal samples, and remaining samples to verify the expression level of candidate 9 miRNAs in VTE and normal samples. The sequencing data were used to analyze exosomal miRNA expression. Meanwhile, GO and KEGG analyses were performed to determine the potential biological functions of differentially expressed miRNA target genes. Results: A total of 32 differentially expressed miRNAs were identified by sequencing. Among the 32 miRNAs, 23 miRNAs were upregulated (72%), and 9 miRNAs were downregulated (28%). In addition, we found that the biological functions and metabolic pathways of the target genes were related to hemostatic factors involved in VTE, indicating the regulation of differentially expressed miRNAs. We identified key miRNAs by constructing a miRNA-mRNA regulatory network and found that the target genes were related to VTE. We finally determined that the abnormal expression of 9 miRNAs is closely related to VTE, and the expression level between VTE and normal was verified through other samples.
DOI: 10.34808/dy5k-t831
title: Transitional cell carcinoma, NOS - Male, 72 - Tissue image [6160730013041781]

description: This is the histopathological image of OTHER AND UNSPECIFIED MALE GENITAL ORGANS 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: 72Clinical description: Tumor of the urinary bladder.Gender: MaleDiagnosis:Classification: ICD-O_3.2Classification code: TRANSITIONAL CELL PAPILLOMAS AND CARCINOMASDiagnosis: Transitional cell carcinoma, NOSResult of the histopathological examination: Invasive urothelial carcinoma high grade. The cancer is invading the seminal vesicle.Sample:Material: FFPECollecting method: Surgical specimenTopography: MALE GENITAL ORGANSOrgan: OTHER AND UNSPECIFIED MALE GENITAL ORGANSTissue: Seminal vesicleType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: Pannoramic 250 3DHistechLens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.34808/n9sm-c609
title: Transitional cell carcinoma, NOS - Male, 72 - Tissue image [6160730013049481]

description: This is the histopathological image of BLADDER 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: 72Clinical description: Tumor of the urinary bladder.Gender: MaleDiagnosis:Classification: ICD-O_3.2Classification code: TRANSITIONAL CELL PAPILLOMAS AND CARCINOMASDiagnosis: Transitional cell carcinoma, NOSResult of the histopathological examination: Invasive urothelial carcinoma high grade. The cancer is invading fat tissue.Sample:Material: FFPECollecting method: Surgical specimenTopography: URINARY TRACTOrgan: BLADDERTissue: Urinary bladder, NOSType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: Pannoramic 250 3DHistechLens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.34808/9m7k-dy22
title: Transitional cell carcinoma, NOS - Male, 72 - Tissue image [6160730013049271]

description: This is the histopathological image of URETER 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: 72Clinical description: Tumor of the urinary bladder.Gender: MaleDiagnosis:Classification: ICD-O_3.2Classification code: TRANSITIONAL CELL PAPILLOMAS AND CARCINOMASDiagnosis: Transitional cell carcinoma, NOSResult of the histopathological examination: Invasive urothelial carcinoma high grade. The cancer is invading the prostate.Sample:Material: FFPECollecting method: Surgical specimenTopography: URINARY TRACTOrgan: URETERTissue: UreterType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: Pannoramic 250 3DHistechLens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.34808/wncy-sf21
title: LYMPH NODES, Obturator lymph node - Male, 80 - Tissue image [6160730013039831]

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: 80Clinical description: Tumor of the urinary bladder.Gender: MaleDiagnosis:Classification: HealthyClassification code: Diagnosis: Result of the histopathological examination: The lymph nodes are free of metastases.Sample:Material: FFPECollecting method: Surgical specimenTopography: LYMPH NODESOrgan: LYMPH NODESTissue: Obturator lymph nodeType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: Pannoramic 250 3DHistechLens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.34808/zdbd-0t12
title: URETER, Ureter - Male, 72 - Tissue image [6160730013049441]

description: This is the histopathological image of URETER 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: 72Clinical description: Tumor of the urinary bladder.Gender: MaleDiagnosis:Classification: HealthyClassification code: Diagnosis: Result of the histopathological examination: The surgical margin of the left ureter is negative.Sample:Material: FFPECollecting method: Surgical specimenTopography: URINARY TRACTOrgan: URETERTissue: UreterType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: Pannoramic 250 3DHistechLens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.34808/ry0x-8638
title: Transitional cell carcinoma, NOS - Male, 72 - Tissue image [6160730013042831]

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: 72Clinical description: Tumor of the urinary bladder.Gender: MaleDiagnosis:Classification: ICD-O_3.2Classification code: TRANSITIONAL CELL PAPILLOMAS AND CARCINOMASDiagnosis: Transitional cell carcinoma, NOSResult of the histopathological examination: The lymph node with the metastasis of high grade urothelial carcinoma.Sample:Material: FFPECollecting method: Surgical specimenTopography: LYMPH NODESOrgan: LYMPH NODESTissue: Iliac lymph nodeType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: Pannoramic 250 3DHistechLens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.34808/r5j5-aq61
title: Transitional cell carcinoma, NOS - Male, 72 - Tissue image [6160730013044361]

description: This is the histopathological image of BLADDER 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: 72Clinical description: Tumor of the urinary bladder.Gender: MaleDiagnosis:Classification: ICD-O_3.2Classification code: TRANSITIONAL CELL PAPILLOMAS AND CARCINOMASDiagnosis: Transitional cell carcinoma, NOSResult of the histopathological examination: Invasive urothelial carcinoma high grade. The cancer is invading fat tissue.Sample:Material: FFPECollecting method: Surgical specimenTopography: URINARY TRACTOrgan: BLADDERTissue: Urinary bladder, NOSType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: Pannoramic 250 3DHistechLens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.34808/wqcg-vx79
title: Transitional cell carcinoma, NOS - Male, 72 - Tissue image [61607300130401]

description: This is the histopathological image of BLADDER 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: 72Clinical description: Tumor of the urinary bladder.Gender: MaleDiagnosis:Classification: ICD-O_3.2Classification code: TRANSITIONAL CELL PAPILLOMAS AND CARCINOMASDiagnosis: Transitional cell carcinoma, NOSResult of the histopathological examination: Invasive urothelial carcinoma high grade. The cancer is invading fat tissue and the ureter.Sample:Material: FFPECollecting method: Surgical specimenTopography: URINARY TRACTOrgan: BLADDERTissue: Urinary bladder, NOSType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: Pannoramic 250 3DHistechLens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.34808/bn83-rd08
title: BLADDER, Bladder, NOS - Male, 80 - Tissue image [6160730013036651]

description: This is the histopathological image of BLADDER 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: 80Clinical description: Tumor of the urinary bladder.Gender: MaleDiagnosis:Classification: HealthyClassification code: Diagnosis: Result of the histopathological examination: The radial surgical margin of the fat tissue is negative.Sample:Material: FFPECollecting method: Surgical specimenTopography: URINARY TRACTOrgan: BLADDERTissue: Bladder, NOSType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: Pannoramic 250 3DHistechLens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.34808/edcf-bs42
title: Transitional cell carcinoma, NOS - Male, 72 - Tissue image [6160730013049691]

description: This is the histopathological image of BLADDER 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: 72Clinical description: Tumor of the urinary bladder.Gender: MaleDiagnosis:Classification: ICD-O_3.2Classification code: TRANSITIONAL CELL PAPILLOMAS AND CARCINOMASDiagnosis: Transitional cell carcinoma, NOSResult of the histopathological examination: Invasive urothelial carcinoma high grade. The cancer is invading fat tissue and the ureter.Sample:Material: FFPECollecting method: Surgical specimenTopography: URINARY TRACTOrgan: BLADDERTissue: Urinary bladder, NOSType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: Pannoramic 250 3DHistechLens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.34808/3ecv-6c85
title: Transitional cell carcinoma, NOS - Male, 72 - Tissue image [6160730013044701]

description: This is the histopathological image of BLADDER 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: 72Clinical description: Tumor of the urinary bladder.Gender: MaleDiagnosis:Classification: ICD-O_3.2Classification code: TRANSITIONAL CELL PAPILLOMAS AND CARCINOMASDiagnosis: Transitional cell carcinoma, NOSResult of the histopathological examination: Invasive urothelial carcinoma high grade. The cancer is invading fat tissue and the ureter.Sample:Material: FFPECollecting method: Surgical specimenTopography: URINARY TRACTOrgan: BLADDERTissue: Urinary bladder, NOSType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: Pannoramic 250 3DHistechLens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.34808/q3ts-jp10
title: Pemphigoid - Female, 66 - Tissue image [6160730013046591]

description: This is the histopathological image of SKIN 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: 66Clinical description: Suspicious of pemphigus vulgaris, dermatitis herpetiformis.Gender: FemaleDiagnosis:Classification: ICD-10_10-20Classification code: Chapter XII - Diseases of the skin and subcutaneous tissueDiagnosis: PemphigoidResult of the histopathological examination: In the examined skin sections  shows a subepidermal blister beneath of which there are fibrin masses and mixed inflammatory infiltrate with a predominance of eosinophils .
The morphology is suggestive of bullous pemphigoid.Sample:Material: FFPECollecting method: Surgical biopsyTopography: SKINOrgan: SKINTissue: Skin of umbilicusType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: Pannoramic 250 3DHistechLens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.34808/vajq-w264
title: Transitional cell carcinoma, NOS - Male, 80 - Tissue image [6160730013032911]

description: This is the histopathological image of OTHER AND UNSPECIFIED MALE GENITAL ORGANS 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: 80Clinical description: Tumor of the urinary bladder.Gender: MaleDiagnosis:Classification: ICD-O_3.2Classification code: TRANSITIONAL CELL PAPILLOMAS AND CARCINOMASDiagnosis: Transitional cell carcinoma, NOSResult of the histopathological examination: The perivesical fat tissu with the infiltration of urothelial high grade carcinoma. The seminal vesicle is of normal histological structure.Sample:Material: FFPECollecting method: Surgical specimenTopography: MALE GENITAL ORGANSOrgan: OTHER AND UNSPECIFIED MALE GENITAL ORGANSTissue: Seminal vesicleType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: Pannoramic 250 3DHistechLens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.34808/8sr9-4023
title: Transitional carcinoma - Male, 80 - Tissue image [616073001303771]

description: This is the histopathological image of BLADDER 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: 80Clinical description: Tumor of the urinary bladder.Gender: MaleDiagnosis:Classification: ICD-O_3.2Classification code: TRANSITIONAL CELL PAPILLOMAS AND CARCINOMASDiagnosis: Transitional carcinomaResult of the histopathological examination: High grade urothelial carcinoma with squamous metaplasia. The tumor invades the musclar wall of the bladder.Sample:Material: FFPECollecting method: Surgical specimenTopography: URINARY TRACTOrgan: BLADDERTissue: Urinary bladder, NOSType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: Pannoramic 250 3DHistechLens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.34808/ejfy-xe63
title: Transitional cell carcinoma, NOS - Male, 72 - Tissue image [6160730013041611]

description: This is the histopathological image of PROSTATE GLAND 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: 72Clinical description: Tumor of the urinary bladder.Gender: MaleDiagnosis:Classification: ICD-O_3.2Classification code: TRANSITIONAL CELL PAPILLOMAS AND CARCINOMASDiagnosis: Transitional cell carcinoma, NOSResult of the histopathological examination: Invasive urothelial carcinoma high grade. The cancer is invading the prostate.Sample:Material: FFPECollecting method: Surgical specimenTopography: MALE GENITAL ORGANSOrgan: PROSTATE GLANDTissue: Prostate glandType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: Pannoramic 250 3DHistechLens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.34808/ja84-jy29
title: BLADDER, Bladder, NOS - Male, 80 - Tissue image [6160730013034961]

description: This is the histopathological image of BLADDER 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: 80Clinical description: Tumor of the urinary bladder.Gender: MaleDiagnosis:Classification: HealthyClassification code: Diagnosis: Result of the histopathological examination: The radial surgical margin of the fat tissue is negative.Sample:Material: FFPECollecting method: Surgical specimenTopography: URINARY TRACTOrgan: BLADDERTissue: Bladder, NOSType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: Pannoramic 250 3DHistechLens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.34808/rt1m-nv20
title: Transitional cell carcinoma, NOS - Male, 72 - Tissue image [616073001304841]

description: This is the histopathological image of BLADDER 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: 72Clinical description: Tumor of the urinary bladder.Gender: MaleDiagnosis:Classification: ICD-O_3.2Classification code: TRANSITIONAL CELL PAPILLOMAS AND CARCINOMASDiagnosis: Transitional cell carcinoma, NOSResult of the histopathological examination: Invasive urothelial carcinoma high grade. The cancer is invading fat tissue and the ureter.Sample:Material: FFPECollecting method: Surgical specimenTopography: URINARY TRACTOrgan: BLADDERTissue: Urinary bladder, NOSType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: Pannoramic 250 3DHistechLens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.34808/xac5-gb10
title: Transitional cell carcinoma, NOS - Male, 72 - Tissue image [6160730013045341]

description: This is the histopathological image of BLADDER 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: 72Clinical description: Tumor of the urinary bladder.Gender: MaleDiagnosis:Classification: ICD-O_3.2Classification code: TRANSITIONAL CELL PAPILLOMAS AND CARCINOMASDiagnosis: Transitional cell carcinoma, NOSResult of the histopathological examination: Invasive urothelial carcinoma high grade. The cancer is invading fat tissue and the ureter.Sample:Material: FFPECollecting method: Surgical specimenTopography: URINARY TRACTOrgan: BLADDERTissue: Urinary bladder, NOSType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: Pannoramic 250 3DHistechLens: 20xOrganization:Source: Medical University Gdańsk