cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10574839
title: Specialized public database of barrier situations for people with sensory disabilities in public transport

description: The database offers a set of specific situations related to the use of urban public transport that represent a barrier for people with visual or hearing impairment. The database is based on the user experience of people with sensory disabilities in Brno. Although, it contains references to the realities of the Transport Company of the City of Brno, it describes situations that go beyond these locally specific realities and offers inspiration for developing more accessible urban public transport across the Czech Republic. It contains 178 unique barrier situations that were identified through in-depth interviews and focus groups with 30 visually and 20 hearing impaired users of the Brno City Transport Company's services conducted during 2023. The database mainly captures the variability of barrier situations, but does not address the frequency of their occurrence. Thus, situations that may occur very rarely or very often are juxtaposed.
DOI: 10.5281/zenodo.10590759
title: Specialized public database of barrier situations for people with sensory disabilities in public transport

description: The database offers a set of specific situations related to the use of urban public transport that represent a barrier for people with visual or hearing impairment. The database is based on the user experience of people with sensory disabilities in Brno. Although, it contains references to the realities of the Transport Company of the City of Brno, it describes situations that go beyond these locally specific realities and offers inspiration for developing more accessible urban public transport across the Czech Republic. It contains 178 unique barrier situations that were identified through in-depth interviews and focus groups with 30 visually and 20 hearing impaired users of the Brno City Transport Company's services conducted during 2023. The database mainly captures the variability of barrier situations, but does not address the frequency of their occurrence. Thus, situations that may occur very rarely or very often are juxtaposed.
DOI: 10.5281/zenodo.10574838
title: Specialized public database of barrier situations for people with sensory disabilities in public transport

description: The database offers a set of specific situations related to the use of urban public transport that represent a barrier for people with visual or hearing impairment. The database is based on the user experience of people with sensory disabilities in Brno. Although, it contains references to the realities of the Transport Company of the City of Brno, it describes situations that go beyond these locally specific realities and offers inspiration for developing more accessible urban public transport across the Czech Republic. It contains 178 unique barrier situations that were identified through in-depth interviews and focus groups with 30 visually and 20 hearing impaired users of the Brno City Transport Company's services conducted during 2023. The database mainly captures the variability of barrier situations, but does not address the frequency of their occurrence. Thus, situations that may occur very rarely or very often are juxtaposed.
DOI: 10.5281/zenodo.10615464
title: Group A streptococcus, Escherichia coli, Streptococcus pneumoniae and Haemophilus influenzae genome vs Human genome @ 6p21.3 Blastn - Hedgehogs or Bystanders?

description: The genome of Group A streptococcus, Escherichia coli, Streptococcus pneumoniae, and Haemophilus influenzae were analyzed with human genome hg38 at locus 6p21.3 using blastn. Megablast, somewhat similar sequences, dissimilar blast and short blast were the methods used. Blastn showed some overlaps of the respective genome with the human genome. The results are shown in the accompanying dataset. Amongst the four organisms, streptococcus pneumoniae genome had the maximal overlaps with human genome at 6p21.3. The locus 6p21.3 of the human genome is known for major histocompatibility antigen expression (MHC-1) and human leukocyte antigen (HLA) molecules, which are associated with many autoimmune disorders. Some of the common disorders associated with this locus include type 1 diabetes, celiac disease, myasthenia gravis, autoimmune pernicious anemia, vitiligo, etc. These common commensal cum pathogenic microorganisms can influence the expression of the MHC-1 complex, and thereby may change the phenotypic or clinical expression of diseases. These concepts have the potential for further research and analysis in the future.
DOI: 10.5281/zenodo.10615463
title: Group A streptococcus, Escherichia coli, Streptococcus pneumoniae and Haemophilus influenzae genome vs Human genome @ 6p21.3 Blastn - Hedgehogs or Bystanders?

description: The genome of Group A streptococcus, Escherichia coli, Streptococcus pneumoniae, and Haemophilus influenzae were analyzed with human genome hg38 at locus 6p21.3 using blastn. Megablast, somewhat similar sequences, dissimilar blast and short blast were the methods used. Blastn showed some overlaps of the respective genome with the human genome. The results are shown in the accompanying dataset. Amongst the four organisms, streptococcus pneumoniae genome had the maximal overlaps with human genome at 6p21.3. The locus 6p21.3 of the human genome is known for major histocompatibility antigen expression (MHC-1) and human leukocyte antigen (HLA) molecules, which are associated with many autoimmune disorders. Some of the common disorders associated with this locus include type 1 diabetes, celiac disease, myasthenia gravis, autoimmune pernicious anemia, vitiligo, etc. These common commensal cum pathogenic microorganisms can influence the expression of the MHC-1 complex, and thereby may change the phenotypic or clinical expression of diseases. These concepts have the potential for further research and analysis in the future.
DOI: 10.6084/m9.figshare.7865828
title: Investigation on Ruthenium(II) Bipyridine/AgIII Complexes Chemiluminescence System and Its Application for Sensitive Norfloxacin and Ofloxacin Detection

description: The reaction mechanism of AgIII complex ([Ag(HIO6)2]5–) with ruthenium(II) bipyridine (Ru(bpy)32+) in acid medium was investigated. A novel flow injection chemiluminescence (CL) analysis method was developed for the detection of norfloxacin (NFLX) and ofloxacin (OFLX) in commercial drug, milk and human urine samples based on AgIII-ruthenium(II) bipyridine in acidic solution. Under optimal conditions, CL intensities were proportional to drug concentrations in the range of 1.6 × 10-9 to 8 × 10-6 g mL-1 for NFLX and 1.0 × 10-9 to 4 × 10-6 g mL-1 for OFLX. The detection limit was 1.0 × 10-9 g mL-1 for NFLX and 0.8 × 10-9 g mL-1 for OFLX. On the basis of the CL, UV and fluorescence spectra, possible reaction mechanisms were proposed.
DOI: 10.6084/m9.figshare.7865828.v1
title: Investigation on Ruthenium(II) Bipyridine/AgIII Complexes Chemiluminescence System and Its Application for Sensitive Norfloxacin and Ofloxacin Detection

description: The reaction mechanism of AgIII complex ([Ag(HIO6)2]5–) with ruthenium(II) bipyridine (Ru(bpy)32+) in acid medium was investigated. A novel flow injection chemiluminescence (CL) analysis method was developed for the detection of norfloxacin (NFLX) and ofloxacin (OFLX) in commercial drug, milk and human urine samples based on AgIII-ruthenium(II) bipyridine in acidic solution. Under optimal conditions, CL intensities were proportional to drug concentrations in the range of 1.6 × 10-9 to 8 × 10-6 g mL-1 for NFLX and 1.0 × 10-9 to 4 × 10-6 g mL-1 for OFLX. The detection limit was 1.0 × 10-9 g mL-1 for NFLX and 0.8 × 10-9 g mL-1 for OFLX. On the basis of the CL, UV and fluorescence spectra, possible reaction mechanisms were proposed.
DOI: 10.6084/m9.figshare.6817256
title: Additional file 2: of Recurrent tumor-specific regulation of alternative polyadenylation of cancer-related genes

description: Supplementary tables. It includes all supplementary tables. Table S1.List of 114 cancer-related genes. Table S2. Summary of the 33 cancer types. Table S3. Summary of the reported 33 genes involved in 77 events of tumor-specific cleavage patterns. Table S4. Details of all CSs involved in the reported 77 APA events. Table S5. Mapping relations between diseases in TCGA and those in COSMIC (Supplementary Methods). (XLSX 235 kb)
DOI: 10.6084/m9.figshare.6817256.v1
title: Additional file 2: of Recurrent tumor-specific regulation of alternative polyadenylation of cancer-related genes

description: Supplementary tables. It includes all supplementary tables. Table S1.List of 114 cancer-related genes. Table S2. Summary of the 33 cancer types. Table S3. Summary of the reported 33 genes involved in 77 events of tumor-specific cleavage patterns. Table S4. Details of all CSs involved in the reported 77 APA events. Table S5. Mapping relations between diseases in TCGA and those in COSMIC (Supplementary Methods). (XLSX 235 kb)
DOI: 10.6084/m9.figshare.17827307
title: RNA sequencing of age-related fertility decrease

description: High-throughput transcriptome sequencing was
used to identify differentially
expressed genes in the ovarian granulosa cells of older women with infertility.
DOI: 10.6084/m9.figshare.13632941
title: Additional file 1 of Comparing tuberculosis gene signatures in malnourished individuals using the TBSignatureProfiler

description: Additional file 1. Supplementary signature list and references. This file contains the TBSignatureProfiler software doucmentation, list of signatures  and references for all the signatures in the TBSignatureProfiler.
DOI: 10.6084/m9.figshare.13632941.v1
title: Additional file 1 of Comparing tuberculosis gene signatures in malnourished individuals using the TBSignatureProfiler

description: Additional file 1. Supplementary signature list and references. This file contains the TBSignatureProfiler software doucmentation, list of signatures  and references for all the signatures in the TBSignatureProfiler.
DOI: 10.6084/m9.figshare.13632953
title: Additional file 4 of Comparing tuberculosis gene signatures in malnourished individuals using the TBSignatureProfiler

description: Additional file 4. Percentage of overlapping genes between the multigene TB signatures. The values are calculated as the percentage of the genes from the signature that are present in the column signature, e.g. row 45, column 3 designates that 93.8% (15/16) of the Zak_RISK_16 genes are in the Berry_393 list, whereas row 3 column 45 shows that only 5.2% of the Berry_393 are in the smaller Zak_RISK_16 list. The large number of yellow cells indicates that there is not a lot of overlap between existing signatures.
DOI: 10.6084/m9.figshare.13632953.v1
title: Additional file 4 of Comparing tuberculosis gene signatures in malnourished individuals using the TBSignatureProfiler

description: Additional file 4. Percentage of overlapping genes between the multigene TB signatures. The values are calculated as the percentage of the genes from the signature that are present in the column signature, e.g. row 45, column 3 designates that 93.8% (15/16) of the Zak_RISK_16 genes are in the Berry_393 list, whereas row 3 column 45 shows that only 5.2% of the Berry_393 are in the smaller Zak_RISK_16 list. The large number of yellow cells indicates that there is not a lot of overlap between existing signatures.
DOI: 10.6084/m9.figshare.9963023
title: Cholesterol depletion sensitizes gallbladder cancer to cisplatin by impairing DNA damage response

description: Gallbladder cancer (GBC) is the common malignancy of the bile tract system with extremely poor clinical outcomes, owing to its metastatic property and intrinsic resistance to the first-line drugs. Although it is well-established that cholesterol abnormity contributes to gallstone formation, a leading risk factor for GBC, the link of cholesterol homeostasis with GBC has not been investigated. The present study systematically examined the genes implicated in cholesterol homeostasis, and revealed altered gene expressions of <i>de novo</i> cholesterol biosynthesis and sterol sulfonation (SULT2B1), reduced bile acid synthesis (CYP7B1 and CYP39A1) and impaired sterol efflux (ABCA1, ABCG5, LCAT, and CETP) in GBC tissues. Suppression of cholesterol biosynthesis by lovastatin inhibited GBC cell proliferation possibly through attenuating the DNA repair process. Further investigation revealed lovastatin sensitized GBC cells to cisplatin-induced apoptosis and suppressed the activation of CHK1, CHK2, and H2AX during DNA damage response. By using chemically distinct statins, HMGCR depletion or supplementing mevalonate, the product of HMGCR, we showed the inhibitory effects on DNA repair process of lovastatin were due to the blockage of the mevalonate pathway. Subcutaneous xenograft mice model suggested lovastatin promoted the therapeutic efficacy of cisplatin, and significantly prolonged the survival times of tumor-bearing mice. Moreover, HMGCR ablation repressed tumor growth <i>in vivo</i>, which can be rescued partially by restored expression of HMGCR, suggesting the on-target effects of lovastatin. Therefore, our study provides the clinical relevance of cholesterol homeostasis with GBC progression, and highlights a novel intervention of combined use of lovastatin and cisplatin for GBC.
DOI: 10.6084/m9.figshare.13633019
title: Additional file 2 of Systemic inflammation and chronic kidney disease in a patient due to the RNASEH2B defect

description: Additional file 2.
DOI: 10.6084/m9.figshare.13633019.v1
title: Additional file 2 of Systemic inflammation and chronic kidney disease in a patient due to the RNASEH2B defect

description: Additional file 2.
DOI: 10.6084/m9.figshare.9963023.v1
title: Cholesterol depletion sensitizes gallbladder cancer to cisplatin by impairing DNA damage response

description: Gallbladder cancer (GBC) is the common malignancy of the bile tract system with extremely poor clinical outcomes, owing to its metastatic property and intrinsic resistance to the first-line drugs. Although it is well-established that cholesterol abnormity contributes to gallstone formation, a leading risk factor for GBC, the link of cholesterol homeostasis with GBC has not been investigated. The present study systematically examined the genes implicated in cholesterol homeostasis, and revealed altered gene expressions of <i>de novo</i> cholesterol biosynthesis and sterol sulfonation (SULT2B1), reduced bile acid synthesis (CYP7B1 and CYP39A1) and impaired sterol efflux (ABCA1, ABCG5, LCAT, and CETP) in GBC tissues. Suppression of cholesterol biosynthesis by lovastatin inhibited GBC cell proliferation possibly through attenuating the DNA repair process. Further investigation revealed lovastatin sensitized GBC cells to cisplatin-induced apoptosis and suppressed the activation of CHK1, CHK2, and H2AX during DNA damage response. By using chemically distinct statins, HMGCR depletion or supplementing mevalonate, the product of HMGCR, we showed the inhibitory effects on DNA repair process of lovastatin were due to the blockage of the mevalonate pathway. Subcutaneous xenograft mice model suggested lovastatin promoted the therapeutic efficacy of cisplatin, and significantly prolonged the survival times of tumor-bearing mice. Moreover, HMGCR ablation repressed tumor growth <i>in vivo</i>, which can be rescued partially by restored expression of HMGCR, suggesting the on-target effects of lovastatin. Therefore, our study provides the clinical relevance of cholesterol homeostasis with GBC progression, and highlights a novel intervention of combined use of lovastatin and cisplatin for GBC.
DOI: 10.6084/m9.figshare.9963023.v3
title: Cholesterol depletion sensitizes gallbladder cancer to cisplatin by impairing DNA damage response

description: Gallbladder cancer (GBC) is the common malignancy of the bile tract system with extremely poor clinical outcomes, owing to its metastatic property and intrinsic resistance to the first-line drugs. Although it is well-established that cholesterol abnormity contributes to gallstone formation, a leading risk factor for GBC, the link of cholesterol homeostasis with GBC has not been investigated. The present study systematically examined the genes implicated in cholesterol homeostasis, and revealed altered gene expressions of <i>de novo</i> cholesterol biosynthesis and sterol sulfonation (SULT2B1), reduced bile acid synthesis (CYP7B1 and CYP39A1) and impaired sterol efflux (ABCA1, ABCG5, LCAT, and CETP) in GBC tissues. Suppression of cholesterol biosynthesis by lovastatin inhibited GBC cell proliferation possibly through attenuating the DNA repair process. Further investigation revealed lovastatin sensitized GBC cells to cisplatin-induced apoptosis and suppressed the activation of CHK1, CHK2, and H2AX during DNA damage response. By using chemically distinct statins, HMGCR depletion or supplementing mevalonate, the product of HMGCR, we showed the inhibitory effects on DNA repair process of lovastatin were due to the blockage of the mevalonate pathway. Subcutaneous xenograft mice model suggested lovastatin promoted the therapeutic efficacy of cisplatin, and significantly prolonged the survival times of tumor-bearing mice. Moreover, HMGCR ablation repressed tumor growth <i>in vivo</i>, which can be rescued partially by restored expression of HMGCR, suggesting the on-target effects of lovastatin. Therefore, our study provides the clinical relevance of cholesterol homeostasis with GBC progression, and highlights a novel intervention of combined use of lovastatin and cisplatin for GBC.
DOI: 10.6084/m9.figshare.9963023.v2
title: Cholesterol depletion sensitizes gallbladder cancer to cisplatin by impairing DNA damage response

description: Gallbladder cancer (GBC) is the common malignancy of the bile tract system with extremely poor clinical outcomes, owing to its metastatic property and intrinsic resistance to the first-line drugs. Although it is well-established that cholesterol abnormity contributes to gallstone formation, a leading risk factor for GBC, the link of cholesterol homeostasis with GBC has not been investigated. The present study systematically examined the genes implicated in cholesterol homeostasis, and revealed altered gene expressions of <i>de novo</i> cholesterol biosynthesis and sterol sulfonation (SULT2B1), reduced bile acid synthesis (CYP7B1 and CYP39A1) and impaired sterol efflux (ABCA1, ABCG5, LCAT, and CETP) in GBC tissues. Suppression of cholesterol biosynthesis by lovastatin inhibited GBC cell proliferation possibly through attenuating the DNA repair process. Further investigation revealed lovastatin sensitized GBC cells to cisplatin-induced apoptosis and suppressed the activation of CHK1, CHK2, and H2AX during DNA damage response. By using chemically distinct statins, HMGCR depletion or supplementing mevalonate, the product of HMGCR, we showed the inhibitory effects on DNA repair process of lovastatin were due to the blockage of the mevalonate pathway. Subcutaneous xenograft mice model suggested lovastatin promoted the therapeutic efficacy of cisplatin, and significantly prolonged the survival times of tumor-bearing mice. Moreover, HMGCR ablation repressed tumor growth <i>in vivo</i>, which can be rescued partially by restored expression of HMGCR, suggesting the on-target effects of lovastatin. Therefore, our study provides the clinical relevance of cholesterol homeostasis with GBC progression, and highlights a novel intervention of combined use of lovastatin and cisplatin for GBC.
DOI: 10.6084/m9.figshare.6817316
title: Additional file 5: of Recurrent tumor-specific regulation of alternative polyadenylation of cancer-related genes

description: Figures available for download. (PDF 86 kb)
DOI: 10.6084/m9.figshare.6817316.v1
title: Additional file 5: of Recurrent tumor-specific regulation of alternative polyadenylation of cancer-related genes

description: Figures available for download. (PDF 86 kb)
DOI: 10.6084/m9.figshare.13633026
title: Additional file 2 of Comparative study of Danshen and Siwu decoction based on the molecular structures of the components and predicted targets

description: Additional file 2: The molecular structure of 129 compounds of Danshen components used in this study.
DOI: 10.6084/m9.figshare.13633026.v1
title: Additional file 2 of Comparative study of Danshen and Siwu decoction based on the molecular structures of the components and predicted targets

description: Additional file 2: The molecular structure of 129 compounds of Danshen components used in this study.
DOI: 10.6084/m9.figshare.13633029
title: Additional file 3 of Comparative study of Danshen and Siwu decoction based on the molecular structures of the components and predicted targets

description: Additional file 3: The molecular structure of 81 compounds of Siwu decoction components.
DOI: 10.6084/m9.figshare.13633029.v1
title: Additional file 3 of Comparative study of Danshen and Siwu decoction based on the molecular structures of the components and predicted targets

description: Additional file 3: The molecular structure of 81 compounds of Siwu decoction components.
DOI: 10.6084/m9.figshare.6817361
title: Additional file 1: of Tau GSTs involved in regulation of leaf abscission by comparison the gene profiling of MeGSTs in various abscission-promoting treatments in cassava abscission zones

description: Data 1. Primers used in qRT-PCR analysis. (XLS 39 kb)
DOI: 10.6084/m9.figshare.7865951
title: A Novel Colorimetric Immunoassay of Ultrasensitive Alpha-Fetoprotein Sensing in Magnetic Bead-Based Mimic Enzyme-Chromogenic Substrate System

description: This work described a simple and feasible colorimetric immunoassay. Using hemin (a horseradish peroxidase (HRP) mimic enzyme) and the mimic enzyme-chromogenic substrate system, it can qualitatively and quantitatively detect a-fetoprotein (AFP) at an ultralow concentration. The glucose oxidase (GOx) catalyzed oxidation of glucose leads to the formation of gluconic acid and hydrogen peroxide (H2O2). The latter can oxidize 4-aminoatipyrine (4-AAP) to chromogenic products, and the reaction was catalyzed by hemin. With the increase of H2O2, the absorbance increased, and the color of the solution changed from colorless to pink. On the basis of the system, monitored by recording the color or absorbance (λ = 505 nm), a new immunoassay protocol with GOx-labeled anti-AFP detection antibody was designed. A wide linear dependence was obtained in the range from 0.075 to 280 ng mL-1 with a low detection limit (LOD) of 0.0247 ng mL-1 (S/N = 3).
DOI: 10.6084/m9.figshare.7865951.v1
title: A Novel Colorimetric Immunoassay of Ultrasensitive Alpha-Fetoprotein Sensing in Magnetic Bead-Based Mimic Enzyme-Chromogenic Substrate System

description: This work described a simple and feasible colorimetric immunoassay. Using hemin (a horseradish peroxidase (HRP) mimic enzyme) and the mimic enzyme-chromogenic substrate system, it can qualitatively and quantitatively detect a-fetoprotein (AFP) at an ultralow concentration. The glucose oxidase (GOx) catalyzed oxidation of glucose leads to the formation of gluconic acid and hydrogen peroxide (H2O2). The latter can oxidize 4-aminoatipyrine (4-AAP) to chromogenic products, and the reaction was catalyzed by hemin. With the increase of H2O2, the absorbance increased, and the color of the solution changed from colorless to pink. On the basis of the system, monitored by recording the color or absorbance (λ = 505 nm), a new immunoassay protocol with GOx-labeled anti-AFP detection antibody was designed. A wide linear dependence was obtained in the range from 0.075 to 280 ng mL-1 with a low detection limit (LOD) of 0.0247 ng mL-1 (S/N = 3).
DOI: 10.6084/m9.figshare.6817376
title: Additional file 2: of Tau GSTs involved in regulation of leaf abscission by comparison the gene profiling of MeGSTs in various abscission-promoting treatments in cassava abscission zones

description: Data 2. The accession numbers of GSTs in cassava. (XLSX 20 kb)