cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8223371
title: Supplementary Material for: Interruption or Discontinuation of Tyrosine Kinase Inhibitor Treatment in Chronic Myeloid Leukaemia: A Retrospective Cohort Study (SPARKLE) in Belgium

description: <b><i>Objectives:</i></b> To assess interruptions/discontinuations of tyrosine kinase inhibitor (TKI) treatment in Belgian patients with chronic myeloid leukaemia (CML). <b><i>Methods:</i></b> This retrospective study included patients with TKI interruptions/discontinuations of ≥4 continuous weeks (no clinical trial context) between May 2013 and May 2016. Data collection took place between October 2016 and February 2017. <b><i>Results:</i></b> All 60 participants (69 interruptions/discontinuations) had chronic-phase CML and 75% had at least a major molecular response (≥MMR) at interruption/discontinuation. Most interruptions/discontinuations occurred while on imatinib (36/69; 49%) and dasatinib (20/69; 29%). Most interruptions/discontinuations occurred due to side effects/intolerance (46/69; 67%); other reasons included a wish to conceive (6/69; 9%) and attempts to achieve treatment-free remission (TFR) (6/69; 9%). Interruptions due to side effects occurred later for imatinib- or dasatinib-treated patients than for those on nilotinib or ponatinib. Treatment was re-initiated in 62% (43/69) of cases. Most interruptions caused by side effects/intolerance were followed by treatment changes. All 4 patients with ≥MR 4.5 at interruption/discontinuation and ≥11-month follow-up who had not restarted treatment maintained the response. <b><i>Conclusion:</i></b> Although TKIs are used for long-term CML treatment, physicians sometimes recommend interruptions/discontinuations. In this study, interruptions/discontinuations were mainly caused by side effects or intolerance, rather than TFR attempts.
DOI: 10.6084/m9.figshare.8223371.v1
title: Supplementary Material for: Interruption or Discontinuation of Tyrosine Kinase Inhibitor Treatment in Chronic Myeloid Leukaemia: A Retrospective Cohort Study (SPARKLE) in Belgium

description: <b><i>Objectives:</i></b> To assess interruptions/discontinuations of tyrosine kinase inhibitor (TKI) treatment in Belgian patients with chronic myeloid leukaemia (CML). <b><i>Methods:</i></b> This retrospective study included patients with TKI interruptions/discontinuations of ≥4 continuous weeks (no clinical trial context) between May 2013 and May 2016. Data collection took place between October 2016 and February 2017. <b><i>Results:</i></b> All 60 participants (69 interruptions/discontinuations) had chronic-phase CML and 75% had at least a major molecular response (≥MMR) at interruption/discontinuation. Most interruptions/discontinuations occurred while on imatinib (36/69; 49%) and dasatinib (20/69; 29%). Most interruptions/discontinuations occurred due to side effects/intolerance (46/69; 67%); other reasons included a wish to conceive (6/69; 9%) and attempts to achieve treatment-free remission (TFR) (6/69; 9%). Interruptions due to side effects occurred later for imatinib- or dasatinib-treated patients than for those on nilotinib or ponatinib. Treatment was re-initiated in 62% (43/69) of cases. Most interruptions caused by side effects/intolerance were followed by treatment changes. All 4 patients with ≥MR 4.5 at interruption/discontinuation and ≥11-month follow-up who had not restarted treatment maintained the response. <b><i>Conclusion:</i></b> Although TKIs are used for long-term CML treatment, physicians sometimes recommend interruptions/discontinuations. In this study, interruptions/discontinuations were mainly caused by side effects or intolerance, rather than TFR attempts.
DOI: 10.6084/m9.figshare.8223329
title: Additional file 2: of Chromatin accessibility plays a key role in selective targeting of Hox proteins

description: Table S6. Hox group peak regions. (XLSX 3054 kb)
DOI: 10.6084/m9.figshare.8223329.v1
title: Additional file 2: of Chromatin accessibility plays a key role in selective targeting of Hox proteins

description: Table S6. Hox group peak regions. (XLSX 3054 kb)
DOI: 10.6084/m9.figshare.8223224
title: Additional file 6: of Events of alternative splicing in head and neck cancer via RNA sequencing â an update

description: Functional enrichment and hub genes. (XLS 47 kb)
DOI: 10.6084/m9.figshare.8223224.v1
title: Additional file 6: of Events of alternative splicing in head and neck cancer via RNA sequencing â an update

description: Functional enrichment and hub genes. (XLS 47 kb)
DOI: 10.6084/m9.figshare.8223209
title: Additional file 4: of Events of alternative splicing in head and neck cancer via RNA sequencing â an update

description: Table S1. describing the reason for including or excluding each study. (XLS 232 kb)
DOI: 10.6084/m9.figshare.8223203
title: Additional file 1: of Bridging the gap between reference and real transcriptomes

description: Table S1. Overview of major eukaryotic transcriptome databases. Table S2. Large-scale RNA-seq projects (human). Table S3. Sequencing methods providing insight on specific events shown in Fig 2. Table S4. Transcript variations related to cancer and other diseases; and software for retrieving these variations from RNA-seq data. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.8223209.v1
title: Additional file 4: of Events of alternative splicing in head and neck cancer via RNA sequencing â an update

description: Table S1. describing the reason for including or excluding each study. (XLS 232 kb)
DOI: 10.6084/m9.figshare.8223200
title: Additional file 2 of Integrative analysis of DNA methylation suggests down-regulation of oncogenic pathways and reduced somatic mutation rates in survival outliers of glioblastoma

description: : Table S2.Â The list of 161,794 significant sites showing the DNA 145 methylationdifference between LTS and STS. (CSV 8954 kb)
DOI: 10.6084/m9.figshare.8223200.v1
title: Additional file 2 of Integrative analysis of DNA methylation suggests down-regulation of oncogenic pathways and reduced somatic mutation rates in survival outliers of glioblastoma

description: : Table S2.Â The list of 161,794 significant sites showing the DNA 145 methylationdifference between LTS and STS. (CSV 8954 kb)
DOI: 10.6084/m9.figshare.8223203.v1
title: Additional file 1: of Bridging the gap between reference and real transcriptomes

description: Table S1. Overview of major eukaryotic transcriptome databases. Table S2. Large-scale RNA-seq projects (human). Table S3. Sequencing methods providing insight on specific events shown in Fig 2. Table S4. Transcript variations related to cancer and other diseases; and software for retrieving these variations from RNA-seq data. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.8223182
title: MOESM9 of PD-L1 and PD-L2 expression correlated genes in non-small-cell lung cancer

description: Additional file 9: Table S7. Gene lists used for various analyses.
DOI: 10.6084/m9.figshare.8223182.v1
title: MOESM9 of PD-L1 and PD-L2 expression correlated genes in non-small-cell lung cancer

description: Additional file 9: Table S7. Gene lists used for various analyses.
DOI: 10.6084/m9.figshare.8223161
title: MOESM5 of PD-L1 and PD-L2 expression correlated genes in non-small-cell lung cancer

description: Additional file 5: Table S4. Expression correlated genes for IRF1 and IRF9.
DOI: 10.6084/m9.figshare.8223161.v1
title: MOESM5 of PD-L1 and PD-L2 expression correlated genes in non-small-cell lung cancer

description: Additional file 5: Table S4. Expression correlated genes for IRF1 and IRF9.
DOI: 10.6084/m9.figshare.8223134
title: MOESM1 of PD-L1 and PD-L2 expression correlated genes in non-small-cell lung cancer

description: Additional file 1: Table S1. Expression correlated genes for PD-L1, PD-L2, and both.
DOI: 10.6084/m9.figshare.8223134.v1
title: MOESM1 of PD-L1 and PD-L2 expression correlated genes in non-small-cell lung cancer

description: Additional file 1: Table S1. Expression correlated genes for PD-L1, PD-L2, and both.
DOI: 10.6084/m9.figshare.8223104
title: Additional file 3: of Concurrent measurement of microbiome and allergens in the air of bedrooms of allergy disease patients in the Chicago area

description: Table S2. Differentially Abundance OTUs between households with and without dogs. (CSV 56 kb)
DOI: 10.6084/m9.figshare.8223104.v1
title: Additional file 3: of Concurrent measurement of microbiome and allergens in the air of bedrooms of allergy disease patients in the Chicago area

description: Table S2. Differentially Abundance OTUs between households with and without dogs. (CSV 56 kb)
DOI: 10.6084/m9.figshare.8223089
title: Additional file 1: of Concurrent measurement of microbiome and allergens in the air of bedrooms of allergy disease patients in the Chicago area

description: Table S1. Community diversity based on selected abiotic variables. (CSV 343 b)
DOI: 10.6084/m9.figshare.8223089.v1
title: Additional file 1: of Concurrent measurement of microbiome and allergens in the air of bedrooms of allergy disease patients in the Chicago area

description: Table S1. Community diversity based on selected abiotic variables. (CSV 343 b)
DOI: 10.6084/m9.figshare.8222930
title: Feedback for patients reporting adverse drug reactions; satisfaction and expectations

description: <b><i>Objective:</i></b> Due to the rising number of patient reports in pharmacovigilance, the manner in which feedback is provided to patients is an element to be considered. The objective is to explore the satisfaction of patients towards personalized and general feedback in response to their reported adverse drug reactions (ADRs). <b><i>Methods:</i></b> Patients who reported an ADR to the Dutch Pharmacovigilance Centre for the first time in the period between October 2012 and April 2013 were included. Reporters received personalized feedback or a general acknowledgement letter. Satisfaction towards the received feedback, expressed on a 5-point Likert scale (1 very good to 5 very poor), was studied using a web-based questionnaire. Data were analyzed using Pearson Chi-square test and linear regression analysis. Statistical significance was based on p &lt; 0.05. <b><i>Results:</i></b> A total of 471 patient-reporters were contacted with a total response of 52.5%. Respondents of both groups were satisfied with the received feedback, average score 2 (good). Respondents of the personalized feedback-group were however more satisfied score 2.0 versus 2.5 (p &lt; 0.001) and considered the feedback more clear and useful compared with respondents of the acknowledgement letter-group, respectively score 1.6 versus 1.7 (p = 0.01) and score 2.1 versus 2.5 (p &lt; 0.001). <b><i>Conclusion:</i></b> Patients reporting ADRs are satisfied with feedback received from the pharmacovigilance centre, whether this is a personalized feedback or a general acknowledgment letter. They find it clear, useful and it meets their expectation. Although differences were found between the two types of feedback, these differences did not indicate dissatisfaction towards the received feedback.
DOI: 10.6084/m9.figshare.8222930.v1
title: Feedback for patients reporting adverse drug reactions; satisfaction and expectations

description: <b><i>Objective:</i></b> Due to the rising number of patient reports in pharmacovigilance, the manner in which feedback is provided to patients is an element to be considered. The objective is to explore the satisfaction of patients towards personalized and general feedback in response to their reported adverse drug reactions (ADRs). <b><i>Methods:</i></b> Patients who reported an ADR to the Dutch Pharmacovigilance Centre for the first time in the period between October 2012 and April 2013 were included. Reporters received personalized feedback or a general acknowledgement letter. Satisfaction towards the received feedback, expressed on a 5-point Likert scale (1 very good to 5 very poor), was studied using a web-based questionnaire. Data were analyzed using Pearson Chi-square test and linear regression analysis. Statistical significance was based on p &lt; 0.05. <b><i>Results:</i></b> A total of 471 patient-reporters were contacted with a total response of 52.5%. Respondents of both groups were satisfied with the received feedback, average score 2 (good). Respondents of the personalized feedback-group were however more satisfied score 2.0 versus 2.5 (p &lt; 0.001) and considered the feedback more clear and useful compared with respondents of the acknowledgement letter-group, respectively score 1.6 versus 1.7 (p = 0.01) and score 2.1 versus 2.5 (p &lt; 0.001). <b><i>Conclusion:</i></b> Patients reporting ADRs are satisfied with feedback received from the pharmacovigilance centre, whether this is a personalized feedback or a general acknowledgment letter. They find it clear, useful and it meets their expectation. Although differences were found between the two types of feedback, these differences did not indicate dissatisfaction towards the received feedback.
DOI: 10.6084/m9.figshare.8222852
title: Additional file 2: of Temporal proteome dynamics of Clostridium cellulovorans cultured with major plant cell wall polysaccharides

description: Coefficients of correlation between different biological replicates. Coefficients of correlation were calculated between different biological replicates. As an example, GluTP1_N1 indicates protein samples prepared at time point 1 and biological replicate 1 (XLSX 12 kb)
DOI: 10.6084/m9.figshare.8222855
title: Additional file 3: of Temporal proteome dynamics of Clostridium cellulovorans cultured with major plant cell wall polysaccharides

description: Detailed description of KEGG orthology analysis. We conducted KEGG orthology analysis to categorize the functional classes of each protein cluster with cellular proteins, and detailed information is shown. We highlighted the category of the functional class of each protein cluster described in the main manuscript. KEGG orthology term is shown in KEGG. At the # of identified proteins, the number of proteins categorized at the KEGG orthology term is described. At the percentage of total, we show the proportion of proteins belonging to each KEGG orthology term (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8222852.v1
title: Additional file 2: of Temporal proteome dynamics of Clostridium cellulovorans cultured with major plant cell wall polysaccharides

description: Coefficients of correlation between different biological replicates. Coefficients of correlation were calculated between different biological replicates. As an example, GluTP1_N1 indicates protein samples prepared at time point 1 and biological replicate 1 (XLSX 12 kb)
DOI: 10.6084/m9.figshare.8222855.v1
title: Additional file 3: of Temporal proteome dynamics of Clostridium cellulovorans cultured with major plant cell wall polysaccharides

description: Detailed description of KEGG orthology analysis. We conducted KEGG orthology analysis to categorize the functional classes of each protein cluster with cellular proteins, and detailed information is shown. We highlighted the category of the functional class of each protein cluster described in the main manuscript. KEGG orthology term is shown in KEGG. At the # of identified proteins, the number of proteins categorized at the KEGG orthology term is described. At the percentage of total, we show the proportion of proteins belonging to each KEGG orthology term (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8222843
title: Additional file 1: of Temporal proteome dynamics of Clostridium cellulovorans cultured with major plant cell wall polysaccharides

description: List of identified proteins under each condition. All proteins identified in our proteome analysis under each condition are shown. We show quantitative values and assigned k-means cluster, as represented in Fig. 4. CAZy family is obtained from CAZY Database ( www.cazy.org ). As an example, TP1_N1 indicates the sample obtained with time point 1 and biological replicates 1 (XLSX 1267 kb)
DOI: 10.6084/m9.figshare.8222843.v1
title: Additional file 1: of Temporal proteome dynamics of Clostridium cellulovorans cultured with major plant cell wall polysaccharides

description: List of identified proteins under each condition. All proteins identified in our proteome analysis under each condition are shown. We show quantitative values and assigned k-means cluster, as represented in Fig. 4. CAZy family is obtained from CAZY Database ( www.cazy.org ). As an example, TP1_N1 indicates the sample obtained with time point 1 and biological replicates 1 (XLSX 1267 kb)
DOI: 10.6084/m9.figshare.8222816
title: Additional file 9 of LtrDetector: A tool-suite for detecting long terminal repeat retrotransposons de-novo

description: LTR retrotransposons found by LtrDetector in Zea mays. This compressed file (.tar.gz) includes the LTR retrotransposons found by LtrDetector in BED format. (TAR.GZ 4278 kb)
DOI: 10.6084/m9.figshare.8222810
title: Additional file 8 of LtrDetector: A tool-suite for detecting long terminal repeat retrotransposons de-novo

description: LTR retrotransposons found by LtrDetector in Sorghum bicolor. This compressed file (.tar.gz) includes the LTR retrotransposons found by LtrDetector in BED format. (TAR.GZ 891 kb)
DOI: 10.6084/m9.figshare.8222816.v1
title: Additional file 9 of LtrDetector: A tool-suite for detecting long terminal repeat retrotransposons de-novo

description: LTR retrotransposons found by LtrDetector in Zea mays. This compressed file (.tar.gz) includes the LTR retrotransposons found by LtrDetector in BED format. (TAR.GZ 4278 kb)
DOI: 10.6084/m9.figshare.8222804
title: Additional file 7 of LtrDetector: A tool-suite for detecting long terminal repeat retrotransposons de-novo

description: LTR retrotransposons found by LtrDetector in Oryza sativa Japonica. This compressed file (.tar.gz) includes the LTR retrotransposons found by LtrDetector in BED format. (TAR.GZ 268 kb)
DOI: 10.6084/m9.figshare.8222810.v1
title: Additional file 8 of LtrDetector: A tool-suite for detecting long terminal repeat retrotransposons de-novo

description: LTR retrotransposons found by LtrDetector in Sorghum bicolor. This compressed file (.tar.gz) includes the LTR retrotransposons found by LtrDetector in BED format. (TAR.GZ 891 kb)
DOI: 10.6084/m9.figshare.8222798
title: Additional file 5 of LtrDetector: A tool-suite for detecting long terminal repeat retrotransposons de-novo

description: LTR retrotransposons found by LtrDetector in Glycine max. This compressed file (.tar.gz) includes the LTR retrotransposons found by LtrDetector in BED format. (TAR.GZ 929 kb)
DOI: 10.6084/m9.figshare.8222801
title: Additional file 6 of LtrDetector: A tool-suite for detecting long terminal repeat retrotransposons de-novo

description: LTR retrotransposons found by LtrDetector in Hordeum vulgare. This compressed file (.tar.gz) includes the LTR retrotransposons found by LtrDetector in BED format. (TAR.GZ 7488 kb)
DOI: 10.6084/m9.figshare.8222804.v1
title: Additional file 7 of LtrDetector: A tool-suite for detecting long terminal repeat retrotransposons de-novo

description: LTR retrotransposons found by LtrDetector in Oryza sativa Japonica. This compressed file (.tar.gz) includes the LTR retrotransposons found by LtrDetector in BED format. (TAR.GZ 268 kb)
DOI: 10.6084/m9.figshare.8222795
title: Additional file 6: of Breast cancer PAM50 signature: correlation and concordance between RNA-Seq and digital multiplexed gene expression technologies in a triple negative breast cancer series

description: Code. Normalization and PAM50 scripts for both platforms. Scripts used to perform the PAM50 assay in RNA-Seq and NanoString nCounter® platforms, along with additional technique-specific and transcript ID files. (ZIP 91 kb)
DOI: 10.6084/m9.figshare.8222792
title: Additional file 4 of LtrDetector: A tool-suite for detecting long terminal repeat retrotransposons de-novo

description: Long Terminal Repeat (LTR) retrotransposons found by LtrDetector in Arabidopsis thaliana. This compressed file (.tar.gz) includes the LTR retrotransposons found by LtrDetector in BED format. (TAR.GZ 62 kb)
DOI: 10.6084/m9.figshare.8222798.v1
title: Additional file 5 of LtrDetector: A tool-suite for detecting long terminal repeat retrotransposons de-novo

description: LTR retrotransposons found by LtrDetector in Glycine max. This compressed file (.tar.gz) includes the LTR retrotransposons found by LtrDetector in BED format. (TAR.GZ 929 kb)
DOI: 10.6084/m9.figshare.8222789
title: Additional file 3 of LtrDetector: A tool-suite for detecting long terminal repeat retrotransposons de-novo

description: The synthetic sequences. This compressed file (.tar.gz) includes the synthetic sequences with different mutation rates. (TAR.GZ 1872 kb)
DOI: 10.6084/m9.figshare.8222795.v1
title: Additional file 6: of Breast cancer PAM50 signature: correlation and concordance between RNA-Seq and digital multiplexed gene expression technologies in a triple negative breast cancer series

description: Code. Normalization and PAM50 scripts for both platforms. Scripts used to perform the PAM50 assay in RNA-Seq and NanoString nCounter® platforms, along with additional technique-specific and transcript ID files. (ZIP 91 kb)
DOI: 10.6084/m9.figshare.8222801.v1
title: Additional file 6 of LtrDetector: A tool-suite for detecting long terminal repeat retrotransposons de-novo

description: LTR retrotransposons found by LtrDetector in Hordeum vulgare. This compressed file (.tar.gz) includes the LTR retrotransposons found by LtrDetector in BED format. (TAR.GZ 7488 kb)
DOI: 10.6084/m9.figshare.8222789.v1
title: Additional file 3 of LtrDetector: A tool-suite for detecting long terminal repeat retrotransposons de-novo

description: The synthetic sequences. This compressed file (.tar.gz) includes the synthetic sequences with different mutation rates. (TAR.GZ 1872 kb)
DOI: 10.6084/m9.figshare.8222783
title: Additional file 5: of Breast cancer PAM50 signature: correlation and concordance between RNA-Seq and digital multiplexed gene expression technologies in a triple negative breast cancer series

description: QC – NanoString. NanoString nCounter data Quality Control. NanoStringQCPro reports in .html files. Technical, control and count-based metrics are reported. Additionally, a table is provided to associate the sample IDs mentioned in the manuscript with the IDs generated during the NanoString nCounter® quantification process. (ZIP 15743 kb)
DOI: 10.6084/m9.figshare.8222783.v1
title: Additional file 5: of Breast cancer PAM50 signature: correlation and concordance between RNA-Seq and digital multiplexed gene expression technologies in a triple negative breast cancer series

description: QC – NanoString. NanoString nCounter data Quality Control. NanoStringQCPro reports in .html files. Technical, control and count-based metrics are reported. Additionally, a table is provided to associate the sample IDs mentioned in the manuscript with the IDs generated during the NanoString nCounter® quantification process. (ZIP 15743 kb)
DOI: 10.6084/m9.figshare.8222792.v1
title: Additional file 4 of LtrDetector: A tool-suite for detecting long terminal repeat retrotransposons de-novo

description: Long Terminal Repeat (LTR) retrotransposons found by LtrDetector in Arabidopsis thaliana. This compressed file (.tar.gz) includes the LTR retrotransposons found by LtrDetector in BED format. (TAR.GZ 62 kb)
DOI: 10.6084/m9.figshare.8222780
title: Additional file 2 of LtrDetector: A tool-suite for detecting long terminal repeat retrotransposons de-novo

description: Script for ground truth generation pipeline. This compressed file (.tar.gz) includes the Python code for the evaluation pipeline. (TAR.GZ 5 kb)
DOI: 10.6084/m9.figshare.8222777
title: Additional file 1 of LtrDetector: A tool-suite for detecting long terminal repeat retrotransposons de-novo

description: The LtrDetector software and the visualization script. This compressed file (.tar.gz) includes the C++ source code of LtrDetector and the Python script for visualizing putative elements as well as instructions on how to compile and run the programs. (TAR.GZ 145 kb)