cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5903479
title: Dataset for: Selective Measurement of 1H-1H Scalar Couplings from Crowded Chemical Shift Regions: Combined Pure Shift and Spin-Echo Modulation approach

description: JHH scalar couplings carry rich structural information and their measurements are fundamental in the 1H NMR based elucidation of small and medium molecules, which, however are hampered in the presence of large J-coupling network. Further, enhanced spectral resolution is often essential for precise determination of a specific set of 1H-1H J-couplings amongst the complex J-multiplets. In the light of the recent advancements in homodecoupling pure shift strategies, here we report absorption mode, band-selective refocused pure shift spin-echo (BSR-PSSE) method, which helps in determining 1H-1H J-couplings from crowded spectral regions. The importance of the present BSR-PSSE experiment is exemplified for two steroid molecules, estradiol and testosterone.
DOI: 10.6084/m9.figshare.5903479.v1
title: Dataset for: Selective Measurement of 1H-1H Scalar Couplings from Crowded Chemical Shift Regions: Combined Pure Shift and Spin-Echo Modulation approach

description: JHH scalar couplings carry rich structural information and their measurements are fundamental in the 1H NMR based elucidation of small and medium molecules, which, however are hampered in the presence of large J-coupling network. Further, enhanced spectral resolution is often essential for precise determination of a specific set of 1H-1H J-couplings amongst the complex J-multiplets. In the light of the recent advancements in homodecoupling pure shift strategies, here we report absorption mode, band-selective refocused pure shift spin-echo (BSR-PSSE) method, which helps in determining 1H-1H J-couplings from crowded spectral regions. The importance of the present BSR-PSSE experiment is exemplified for two steroid molecules, estradiol and testosterone.
DOI: 10.6084/m9.figshare.5903455
title: Dataset for: Olaparib is effective in combination with, and as maintenance therapy after, first-line endocrine therapy in prostate cancer cells.

description: A number of prostate cancer (PCa)-specific genomic aberrations (denominated BRCAness genes) have been discovered implicating sensitivity to PARP inhibition within the concept of synthetic lethality. Recent clinical studies show favorable results for the PARP inhibitor Olaparib used as single agent for treatment of metastatic castration-resistant PCa. Using 2D and 3D cell culture models mimicking the different treatment and progression stages of PCa we evaluated a potential use for Olaparib in combination with first-line endocrine treatments, androgen deprivation and complete androgen blockade and as a maintenance therapy sequenced to endocrine therapy. We demonstrate that the LNCaP cell line possessing multiple aberrations in BRCAness genes is sensitive to Olaparib. Additive effects of Olaparib combined to endocrine treatments in LNCaP are noted. In contrast, we find that the TMPRSS2:ERG-fusion positive cell lines VCaP and DuCaP do not show signs of synthetic lethality, but are sensitive to cytotoxic effects caused by Olaparib. In consequence, additive effects of Olaparib with endocrine therapy were not observable in these cell lines, showing the need for synthetic lethality in combination treatment regimens. Additionally, we show that PCa cells remain sensitive to Olaparib treatment after initial androgen deprivation implicating a possible use of Olaparib as maintenance therapy. In sum, our pre-clinical data recommend Olaparib as a synthetic lethal treatment option in combination or sequenced to first-line endocrine therapy for PCa patients with diagnosed BRCAness.
DOI: 10.6084/m9.figshare.5903455.v1
title: Dataset for: Olaparib is effective in combination with, and as maintenance therapy after, first-line endocrine therapy in prostate cancer cells.

description: A number of prostate cancer (PCa)-specific genomic aberrations (denominated BRCAness genes) have been discovered implicating sensitivity to PARP inhibition within the concept of synthetic lethality. Recent clinical studies show favorable results for the PARP inhibitor Olaparib used as single agent for treatment of metastatic castration-resistant PCa. Using 2D and 3D cell culture models mimicking the different treatment and progression stages of PCa we evaluated a potential use for Olaparib in combination with first-line endocrine treatments, androgen deprivation and complete androgen blockade and as a maintenance therapy sequenced to endocrine therapy. We demonstrate that the LNCaP cell line possessing multiple aberrations in BRCAness genes is sensitive to Olaparib. Additive effects of Olaparib combined to endocrine treatments in LNCaP are noted. In contrast, we find that the TMPRSS2:ERG-fusion positive cell lines VCaP and DuCaP do not show signs of synthetic lethality, but are sensitive to cytotoxic effects caused by Olaparib. In consequence, additive effects of Olaparib with endocrine therapy were not observable in these cell lines, showing the need for synthetic lethality in combination treatment regimens. Additionally, we show that PCa cells remain sensitive to Olaparib treatment after initial androgen deprivation implicating a possible use of Olaparib as maintenance therapy. In sum, our pre-clinical data recommend Olaparib as a synthetic lethal treatment option in combination or sequenced to first-line endocrine therapy for PCa patients with diagnosed BRCAness.
DOI: 10.6084/m9.figshare.5903425
title: MOESM5 of Human regulatory proteins associate with non-coding RNAs from the EBV IR1 region

description: Additional file 5. STRING analyses of predicted RBPs. Results from STRING enrichment analyses of 81 RBPmap-identified proteins. Information includes annotations and enrichment data on biological processes, KEGG pathways, molecular functions, cellular components, InterPro, and Pfam.
DOI: 10.6084/m9.figshare.5903425.v1
title: MOESM5 of Human regulatory proteins associate with non-coding RNAs from the EBV IR1 region

description: Additional file 5. STRING analyses of predicted RBPs. Results from STRING enrichment analyses of 81 RBPmap-identified proteins. Information includes annotations and enrichment data on biological processes, KEGG pathways, molecular functions, cellular components, InterPro, and Pfam.
DOI: 10.6084/m9.figshare.5903422
title: MOESM4 of Human regulatory proteins associate with non-coding RNAs from the EBV IR1 region

description: Additional file 4. RBPmap of EBV W1s1W2s2. Human or mouse proteins predicted (RBPmap) to bind W1s1W2s2 RNA (see Fig.Â 2A) from the IR1 region of EBV. Results from both EBV type 1 and type 2 sequences are included as well as a comparison.
DOI: 10.6084/m9.figshare.5903422.v1
title: MOESM4 of Human regulatory proteins associate with non-coding RNAs from the EBV IR1 region

description: Additional file 4. RBPmap of EBV W1s1W2s2. Human or mouse proteins predicted (RBPmap) to bind W1s1W2s2 RNA (see Fig.Â 2A) from the IR1 region of EBV. Results from both EBV type 1 and type 2 sequences are included as well as a comparison.
DOI: 10.6084/m9.figshare.5903419
title: MOESM3 of Human regulatory proteins associate with non-coding RNAs from the EBV IR1 region

description: Additional file 3. Fold enrichment individual experimental results from all RIPs.
DOI: 10.6084/m9.figshare.5903419.v1
title: MOESM3 of Human regulatory proteins associate with non-coding RNAs from the EBV IR1 region

description: Additional file 3. Fold enrichment individual experimental results from all RIPs.
DOI: 10.6084/m9.figshare.5903416
title: MOESM2 of Human regulatory proteins associate with non-coding RNAs from the EBV IR1 region

description: Additional file 2. Mass spectrometry results. List of proteins that bound biotinylated forms of ebv-sisRNA-1 after mass spectrometry from gel slices indicated in Fig.Â 1B. Hits resulting from either the top (60-65 kDa) or bottom (35-40 kDa) are indicated.
DOI: 10.6084/m9.figshare.5903416.v1
title: MOESM2 of Human regulatory proteins associate with non-coding RNAs from the EBV IR1 region

description: Additional file 2. Mass spectrometry results. List of proteins that bound biotinylated forms of ebv-sisRNA-1 after mass spectrometry from gel slices indicated in Fig.Â 1B. Hits resulting from either the top (60-65 kDa) or bottom (35-40 kDa) are indicated.
DOI: 10.6084/m9.figshare.5903410
title: Additional file 9: of Epidemiology of canine gastrointestinal helminths in sub-Saharan Africa

description: Prevalence data sets. (XLSX 32Â kb)
DOI: 10.6084/m9.figshare.5903410.v1
title: Additional file 9: of Epidemiology of canine gastrointestinal helminths in sub-Saharan Africa

description: Prevalence data sets. (XLSX 32Â kb)
DOI: 10.6084/m9.figshare.5903383.v2
title: Additional file 9: of Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes

description: Table S4. List of genes with subtype specific active transcription states. (XLS 44Â kb)
DOI: 10.6084/m9.figshare.5903383.v1
title: Additional file 9: of Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes

description: Table S4. List of genes with subtype specific active transcription states. (XLS 44Â kb)
DOI: 10.6084/m9.figshare.5903374.v2
title: Additional file 7: of Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes

description: Table S5. List of genes with subtype specific active enhancer states. (XLS 212Â kb)
DOI: 10.6084/m9.figshare.5903374.v1
title: Additional file 7: of Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes

description: Table S5. List of genes with subtype specific active enhancer states. (XLS 212Â kb)
DOI: 10.6084/m9.figshare.5903350.v1
title: Additional file 3: of Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes

description: Table S2. ChIP-seq sample replicates correlation. (XLSX 61Â kb)
DOI: 10.6084/m9.figshare.5903350.v2
title: Additional file 3: of Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes

description: Table S2. ChIP-seq sample replicates correlation. (XLSX 61Â kb)
DOI: 10.6084/m9.figshare.5903344.v2
title: Additional file 2: of Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes

description: Table S1. ChIP-seq sample alignment summary. (XLSX 66Â kb)
DOI: 10.6084/m9.figshare.5903344.v1
title: Additional file 2: of Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes

description: Table S1. ChIP-seq sample alignment summary. (XLSX 66Â kb)
DOI: 10.6084/m9.figshare.5903329.v2
title: Additional file 18: of Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes

description: Table S3. Emission probability and transition probability of Chromatin States defined by ChromHMM. (XLSX 46Â kb)
DOI: 10.6084/m9.figshare.5903329.v1
title: Additional file 18: of Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes

description: Table S3. Emission probability and transition probability of Chromatin States defined by ChromHMM. (XLSX 46Â kb)
DOI: 10.6084/m9.figshare.5903320.v2
title: Additional file 17: of Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes

description: Table S10. RNA-seq gene expression read count. (XLSX 8751Â kb)
DOI: 10.6084/m9.figshare.5903320.v1
title: Additional file 17: of Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes

description: Table S10. RNA-seq gene expression read count. (XLSX 8751Â kb)
DOI: 10.6084/m9.figshare.5903290.v2
title: Additional file 14: of Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes

description: Table S6. List of genes with subtype specific repressive polycomb domain states. (XLS 10Â kb)
DOI: 10.6084/m9.figshare.5903290.v1
title: Additional file 14: of Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes

description: Table S6. List of genes with subtype specific repressive polycomb domain states. (XLS 10Â kb)
DOI: 10.6084/m9.figshare.5903257
title: MOESM1 of Mitochondrial dysfunction and autism: comprehensive genetic analyses of children with autism and mtDNA deletion

description: Additional file 1: Table S1. Investigated genes responsible for mtDNA maintenance (intergenomic NGS panel).
DOI: 10.6084/m9.figshare.5903257.v1
title: MOESM1 of Mitochondrial dysfunction and autism: comprehensive genetic analyses of children with autism and mtDNA deletion

description: Additional file 1: Table S1. Investigated genes responsible for mtDNA maintenance (intergenomic NGS panel).
DOI: 10.6084/m9.figshare.5903254.v2
title: Additional file 12: of Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes

description: Table S9 Significant upstream regulators of subtype gene signatures of active transcription states and active transcription flanking states. (XLSX 16Â kb)
DOI: 10.6084/m9.figshare.5903254.v1
title: Additional file 12: of Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes

description: Table S9 Significant upstream regulators of subtype gene signatures of active transcription states and active transcription flanking states. (XLSX 16Â kb)
DOI: 10.6084/m9.figshare.5903236.v2
title: Additional file 11: of Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes

description: Table S8. Significant pathways of subtype gene signatures of active transcription states and active transcription flanking states. (XLSX 18Â kb)
DOI: 10.6084/m9.figshare.5903236.v1
title: Additional file 11: of Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes

description: Table S8. Significant pathways of subtype gene signatures of active transcription states and active transcription flanking states. (XLSX 18Â kb)
DOI: 10.6084/m9.figshare.5903227.v2
title: Additional file 10: of Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes

description: Table S7. Subtype gene signatures of active transcription states and active transcription flanking states. (XLSX 23Â kb)
DOI: 10.6084/m9.figshare.5903227.v1
title: Additional file 10: of Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes

description: Table S7. Subtype gene signatures of active transcription states and active transcription flanking states. (XLSX 23Â kb)
DOI: 10.6084/m9.figshare.5903212
title: Additional file 1: of Development of Two-Dimensional Classroom Discourse Analysis Tool (CDAT): scientific reasoning and dialog patterns in the secondary science classes

description: Quantitative data of the classroom dialogues analyzed in the study. (XLSX 279 kb)
DOI: 10.6084/m9.figshare.5903212.v1
title: Additional file 1: of Development of Two-Dimensional Classroom Discourse Analysis Tool (CDAT): scientific reasoning and dialog patterns in the secondary science classes

description: Quantitative data of the classroom dialogues analyzed in the study. (XLSX 279 kb)
DOI: 10.6084/m9.figshare.5903164
title: Additional file 2: of Gut microbiota trajectory in early life may predict development of celiac disease

description: Table S2. Ecological descriptors and immune parameters. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.5903164.v1
title: Additional file 2: of Gut microbiota trajectory in early life may predict development of celiac disease

description: Table S2. Ecological descriptors and immune parameters. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.5903146
title: Additional file 1: of Gut microbiota trajectory in early life may predict development of celiac disease

description: Table S1. Full list of OTUs and taxonomic classifications. (XLSX 87 kb)
DOI: 10.6084/m9.figshare.5903146.v1
title: Additional file 1: of Gut microbiota trajectory in early life may predict development of celiac disease

description: Table S1. Full list of OTUs and taxonomic classifications. (XLSX 87 kb)
DOI: 10.6084/m9.figshare.5903110
title: Additional file 3: of TERIUS: accurate prediction of lncRNA via high-throughput sequencing data representing RNA-binding protein association

description: TERIUS source code. (GZ 19356 kb)
DOI: 10.6084/m9.figshare.5903110.v1
title: Additional file 3: of TERIUS: accurate prediction of lncRNA via high-throughput sequencing data representing RNA-binding protein association

description: TERIUS source code. (GZ 19356 kb)
DOI: 10.5519/qd.weebl2w2
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1 records)
DOI: 10.6084/m9.figshare.5903086
title: Additional file 2 of Introducing difference recurrence relations for faster semi-global alignment of long sequences

description: This archive file contains input nucleotide sequences used in the benchmark and raw outputs of the benchmarking programs. (ZIP 26,419 kb)
DOI: 10.6084/m9.figshare.5903086.v1
title: Additional file 2 of Introducing difference recurrence relations for faster semi-global alignment of long sequences

description: This archive file contains input nucleotide sequences used in the benchmark and raw outputs of the benchmarking programs. (ZIP 26,419 kb)
DOI: 10.6084/m9.figshare.5903083
title: Additional file 1: Figure S1. of Evaluation of heat-treating heartworm-positive canine serum samples during treatment with Advantage Multi® for Dogs and doxycycline

description: DiroCHEK Heartworm Antigen test results for dogs 43491, 43493, 43494 and 43495 with adult heartworm recoveries of 10, 10, 0 and 2 adults, respectively. The top two wells contain the positive and negative controls. There are two wells per dog with the first well containing the pre-heat-treatment serum sample and the second well containing the post-heat-treatment serum sample for each dog. Figure S2. DiroCHEK Heartworm Antigen test results for dogs 43481, 43482, 43485 and 43486 with adult heartworm recoveries of 11, 0, 1 and 11 adults, respectively. The top two wells contain the positive and negative controls. There are two wells per dog with the first well containing the pre-heat-treatment serum sample and the second well containing the post-heat-treatment serum sample for each dog. Figure S3. DiroCHEK Heartworm Antigen test results for dogs 43480, 43483, 43490 and 43492 with adult heartworm recoveries of 12, 2, 0 and 10 adults, respectively. The top two wells contain the positive and negative controls. There are two wells per dog with the first well containing the pre-heat-treatment serum sample and the second well containing the post-heat-treatment serum sample for each dog. Figure S4. DiroCHEK Heartworm Antigen test results for dogs 43484, 43487, 43488 and 43489 with adult heartworm recoveries of 11, 0, 0 and 10 adults, respectively. The top two wells contain the positive and negative controls. There are two wells per dog with the first well containing the pre-heat-treatment serum sample and the second well containing the post-heat-treatment serum sample for each dog. (ZIP 39142 kb)
DOI: 10.6084/m9.figshare.5903083.v1
title: Additional file 1: Figure S1. of Evaluation of heat-treating heartworm-positive canine serum samples during treatment with Advantage Multi® for Dogs and doxycycline

description: DiroCHEK Heartworm Antigen test results for dogs 43491, 43493, 43494 and 43495 with adult heartworm recoveries of 10, 10, 0 and 2 adults, respectively. The top two wells contain the positive and negative controls. There are two wells per dog with the first well containing the pre-heat-treatment serum sample and the second well containing the post-heat-treatment serum sample for each dog. Figure S2. DiroCHEK Heartworm Antigen test results for dogs 43481, 43482, 43485 and 43486 with adult heartworm recoveries of 11, 0, 1 and 11 adults, respectively. The top two wells contain the positive and negative controls. There are two wells per dog with the first well containing the pre-heat-treatment serum sample and the second well containing the post-heat-treatment serum sample for each dog. Figure S3. DiroCHEK Heartworm Antigen test results for dogs 43480, 43483, 43490 and 43492 with adult heartworm recoveries of 12, 2, 0 and 10 adults, respectively. The top two wells contain the positive and negative controls. There are two wells per dog with the first well containing the pre-heat-treatment serum sample and the second well containing the post-heat-treatment serum sample for each dog. Figure S4. DiroCHEK Heartworm Antigen test results for dogs 43484, 43487, 43488 and 43489 with adult heartworm recoveries of 11, 0, 0 and 10 adults, respectively. The top two wells contain the positive and negative controls. There are two wells per dog with the first well containing the pre-heat-treatment serum sample and the second well containing the post-heat-treatment serum sample for each dog. (ZIP 39142 kb)
DOI: 10.5281/zenodo.4008452
title: Genes RNA expression counts for FAIR_Bioinfo courses

description: Counts table of gene expression (assembly GCF_000214015.3) from Bioproject PRJNA304086, runs SRR3099585-87 & SRR3105697-99.
DOI: 10.5281/zenodo.3997136
title: Genes RNA expression counts for FAIR_Bioinfo courses

description: Counts table of gene expression (assembly GCF_000214015.3) from Bioproject PRJNA304086, runs SRR3099585-87 & SRR3105697-99.
DOI: 10.6084/m9.figshare.5903002
title: Additional file 1: of Cholera diagnosis in human stool and detection in water: protocol for a systematic review of available technologies

description: Template for data extraction. (XLSX 22KB)
DOI: 10.6084/m9.figshare.5903002.v1
title: Additional file 1: of Cholera diagnosis in human stool and detection in water: protocol for a systematic review of available technologies

description: Template for data extraction. (XLSX 22KB)
DOI: 10.6084/m9.figshare.5902981
title: Additional file 8: of Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

description: The HMM for the CID domain. (HMM 18 kb)
DOI: 10.6084/m9.figshare.5902981.v1
title: Additional file 8: of Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

description: The HMM for the CID domain. (HMM 18 kb)
DOI: 10.6084/m9.figshare.5902978
title: Additional file 9: of The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification

description: Figures S1–S6. Heat maps of CGJ distances of classified viruses in Baltimore groups I–V and VI/VII. Versions of the summary heat maps shown in Fig. 1 with annotations for families and orders. (ZIP 2051 kb)
DOI: 10.6084/m9.figshare.5902978.v1
title: Additional file 9: of The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification

description: Figures S1–S6. Heat maps of CGJ distances of classified viruses in Baltimore groups I–V and VI/VII. Versions of the summary heat maps shown in Fig. 1 with annotations for families and orders. (ZIP 2051 kb)
DOI: 10.6084/m9.figshare.5902969
title: Additional file 7: of Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

description: Alignment file used to generate HMM for the CID domain. (FA 4 kb)
DOI: 10.6084/m9.figshare.5902969.v1
title: Additional file 7: of Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

description: Alignment file used to generate HMM for the CID domain. (FA 4 kb)