cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.15079528.v1
title: Additional file 3 of Circular RNA circIKBKB promotes breast cancer bone metastasis through sustaining NF-κB/bone remodeling factors signaling

description: Additional file 3: Table S3. Pathways of the Cignal Finder 45‐Pathway Arrays.
DOI: 10.6084/m9.figshare.15079687
title: Additional file 2 of Circulating vitamin C concentration and risk of cancers: a Mendelian randomization study

description: Additional file 2: Supplemental Table 2a. Selection of cancer-related genetic variants used for the reverse MR analyses. Supplemental Table 2b. Selected instrumental variables or their proxies for the reverse MR analyses.
DOI: 10.6084/m9.figshare.15079642.v1
title: Additional file 5 of Comparative transcriptome analysis reveals regulatory network and regulators associated with proanthocyanidin accumulation in persimmon

description: Additional file 5.
DOI: 10.6084/m9.figshare.21895725
title: Neoproterozoic subduction-related active rifting in the South China Craton: insights from geochemical and zircon Hf isotopic data

description: Active and passive continental rifts are generally attributed to plume and subduction mechanisms, respectively. However, controversy surrounding the role of the two mechanisms continues, especially for the mid-Neoproterozoic rifts in the South China Craton. Here, we use geochemical and zircon Hf isotope data from the craton’s rift successions to examine the mechanism of rifting. The compiled geochemical data support the existence of subduction-related magmatic belts along the Jiangnan Orogen and western Yangtze margin of the craton during the mid-Neoproterozoic, consistent with a conventional subduction-related passive rift mechanism. But evidence of asthenospheric upwelling and subsequent lithospheric uplift, metamorphism, volcanism and magma-rich rift infill indicate rifting was active. Compiled zircon εHf(t) values and crustal incubation times suggest a ca. 830–780 Ma transition from advancing to retreating subduction that coincides with rifting across the craton. We therefore propose a subduction-related active rifting model in which the onset of transitionalsubduction triggered mantle convection and plume activity that led to the mid-Neoproterozoic initiation of active rifting in the South China Craton. This suggests a mixed mechanism for rifting rather than two distinct end-members.
DOI: 10.6084/m9.figshare.21895725.v1
title: Neoproterozoic subduction-related active rifting in the South China Craton: insights from geochemical and zircon Hf isotopic data

description: Active and passive continental rifts are generally attributed to plume and subduction mechanisms, respectively. However, controversy surrounding the role of the two mechanisms continues, especially for the mid-Neoproterozoic rifts in the South China Craton. Here, we use geochemical and zircon Hf isotope data from the craton’s rift successions to examine the mechanism of rifting. The compiled geochemical data support the existence of subduction-related magmatic belts along the Jiangnan Orogen and western Yangtze margin of the craton during the mid-Neoproterozoic, consistent with a conventional subduction-related passive rift mechanism. But evidence of asthenospheric upwelling and subsequent lithospheric uplift, metamorphism, volcanism and magma-rich rift infill indicate rifting was active. Compiled zircon εHf(t) values and crustal incubation times suggest a ca. 830–780 Ma transition from advancing to retreating subduction that coincides with rifting across the craton. We therefore propose a subduction-related active rifting model in which the onset of transitionalsubduction triggered mantle convection and plume activity that led to the mid-Neoproterozoic initiation of active rifting in the South China Craton. This suggests a mixed mechanism for rifting rather than two distinct end-members.
DOI: 10.5281/zenodo.7701144
title: Pooled CRISPR Screening of High-content Cellular Phenotypes by Ghost Cytometry_01

description: Pooled CRISPR screening of high-content cellular phenotypes by ghost cytometry (NFkB NGS data, conventional flow cytometer data, Amnis data)
DOI: 10.5281/zenodo.7701145
title: Pooled CRISPR Screening of High-content Cellular Phenotypes by Ghost Cytometry_01

description: Pooled CRISPR screening of high-content cellular phenotypes by ghost cytometry (NFkB NGS data, conventional flow cytometer data, Amnis data)
DOI: 10.6084/m9.figshare.15079687.v1
title: Additional file 2 of Circulating vitamin C concentration and risk of cancers: a Mendelian randomization study

description: Additional file 2: Supplemental Table 2a. Selection of cancer-related genetic variants used for the reverse MR analyses. Supplemental Table 2b. Selected instrumental variables or their proxies for the reverse MR analyses.
DOI: 10.5281/zenodo.7703669
title: Pooled CRISPR Screening of High-content Cellular Phenotypes by Ghost Cytometry_02

description: Pooled CRISPR Screening of High-content Cellular Phenotypes by Ghost Cytometry (Macrophage NGS data)
DOI: 10.5281/zenodo.7703670
title: Pooled CRISPR Screening of High-content Cellular Phenotypes by Ghost Cytometry_02

description: Pooled CRISPR Screening of High-content Cellular Phenotypes by Ghost Cytometry (Macrophage NGS data)
DOI: 10.6084/m9.figshare.14555776
title: The RNA structurome in the asexual blood stages of malaria pathogen <i>plasmodium falciparum</i>

description: <i>Plasmodium falciparum</i> is a deadly human pathogen responsible for the devastating disease called malaria. In this study, we measured the differential accumulation of RNA secondary structures in coding and non-coding transcripts from the asexual developmental cycle in <i>P. falciparum</i> in human red blood cells. Our comprehensive analysis that combined high-throughput nuclease mapping of RNA structures by duplex RNA-seq, SHAPE-directed RNA structure validation, immunoaffinity purification and characterization of antisense RNAs collectively measured differentially base-paired RNA regions throughout the parasite’s asexual RBC cycle. Our mapping data not only aligned to a diverse pool of RNAs with known structures but also enabled us to identify new structural RNA regions in the malaria genome. On average, approximately 71% of the genes with secondary structures are found to be protein coding mRNAs. The mapping pattern of these base-paired RNAs corresponded to all regions of mRNAs, including the 5ʹ UTR, CDS and 3ʹ UTR as well as the start and stop codons. Histone family genes which are known to form secondary structures in their mRNAs and transcripts from genes which are important for transcriptional and post-transcriptional control, such as the unique plant-like transcription factor family, <i>ApiAP2</i>, DNA-/RNA-binding protein, <i>Alba3</i> and proteins important for RBC invasion and malaria cytoadherence also showed strong accumulation of duplex RNA reads in various asexual stages in <i>P. falciparum</i>. Intriguingly, our study determined stage-specific, dynamic relationships between mRNA structural contents and translation efficiency in <i>P. falciparum</i> asexual blood stages, suggesting an essential role of RNA structural changes in malaria gene expression programs.
 <b>Abbreviations</b>: CDS: Coding Sequence; DNA: Deoxyribonucleic Acid; dsRNA: double-stranded RNA; IDC: Intra-erythrocytic Developmental Cycle (IDC); m6A: N6-methyladenosine; mRNA: Messenger RNA; ncRNA: Non-coding RNA; RBC: Red Blood cells; RBP: RNA-Binding Protein; REC: Relative Expression Counts; RNA-seq: RNA-sequencing; RNA: Ribonucleic Acid; RNP: Ribonucleoprotein; RPKM: Reads Per Kilobase of transcript Per Million; rRNA: Ribosomal RNA 16. RUFs: RNAs of Unknown Function; SHAPE: Selective 2’-hydroxyl acylation analysed by primer extension; snoRNA: Small Nucleolar RNA; snRNA: Small Nuclear RNA; SRP-RNA: Signal Recognition Particle RNA; ssRNA: (Single-stranded RNA); TE: Translation Efficiency; tRNA: transfer RNA; UTR: Untranslated Region
DOI: 10.6084/m9.figshare.14555776.v1
title: The RNA Structurome in the Asexual Blood Stages of Malaria Pathogen <i>Plasmodium falciparum</i>

description: <i>Plasmodium falciparum</i> is a deadly human pathogen responsible for the devastating disease called malaria. In this study, we measured the differential accumulation of RNA secondary structures in coding and noncoding transcripts from the asexual developmental cycle in <i>P. falciparum</i> in human red blood cells. Our comprehensive analysis that combined high-throughput nuclease mapping of RNA structures by duplex RNA-seq, SHAPE-directed RNA structure validation, immunoaffinity purification and characterization of antisense RNAs collectively measured differentially base-paired RNA regions throughout the parasite’s asexual RBC cycle. Our mapping data not only aligned to a diverse pool of RNAs with known structures but also enabled us to identify new structural RNA regions in the malaria genome. On average, approximately 71% of the genes with secondary structures are found to be protein coding mRNAs. The mapping pattern of these base-paired RNAs corresponded to all regions of mRNAs, including the 5ʹ UTR, CDS and 3ʹ UTR as well as the start and stop codons. Histone family genes which are known to form secondary structures in their mRNAs and transcripts from genes which are important for transcriptional and post-transcriptional control, such as the unique plant-like transcription factor family, <i>ApiAP2</i>, DNA/RNA binding protein, <i>Alba3</i> and proteins important for RBC invasion and malaria cytoadherence also showed strong accumulation of duplex RNA reads in various asexual stages in <i>P. falciparum</i>. Intriguingly, our study determined stage-specific, dynamic relationships between mRNA structural contents and translation efficiency in <i>P. falciparum</i> asexual blood stages, suggesting an essential role of RNA structural changes in malaria gene expression programs.
DOI: 10.6084/m9.figshare.25272538.v1
title: Supplementary Material for: Understanding Social, Cultural, and Religious Factors Influencing Medical Decision-Making on BRCA1/2 Genetic Testing in the Orthodox Jewish Community

description: Introduction. Although the prevalence of a pathogenic variant in the BRCA1 and BRCA2 genes is about 1:400 (0.25%) in the general population, the prevalence is as high as 1:40 (2.5%) among the Ashkenazi Jewish population. Despite cost-effective preventive measures for mutation carriers, Orthodox Jews constitute a cultural and religious group that requires different approaches to BRCA1 and BRCA2 genetic testing relative to other groups. This study analyzed a dialogue of key stakeholders and community members to explore factors that influence decision-making about BRCA1 and BRCA2 genetic testing in the New York Orthodox Jewish community. 
Methods. Qualitative research methods, based on Grounded Theory and Narrative Research, were utilized to analyze the narrative data collected from 49 key stakeholders and community members. A content analysis was conducted to identify themes; inter-rater reliability was 71%.
Results. Facilitators of genetic testing were a desire for preventive interventions and education, while barriers to genetic testing included negative emotions, feared impact on family/romantic relationships, cost, and stigma. Views differed on the role of religious leaders and healthcare professionals in medical decision-making. Education, health, and community were discussed as influential factors, and concerns were expressed about disclosure, implementation, and information needs. 
Conclusion. This study elicited the opinions of Orthodox Jewish women (decision-makers) and key stakeholders (influencers) who play critical roles in the medical decision-making process. The findings have broad implications for engaging community stakeholders within faith-based or culturally distinct groups to ensure better utilization of healthcare services for cancer screening and prevention designed to improve population health.
DOI: 10.6084/m9.figshare.25272538
title: Supplementary Material for: Understanding Social, Cultural, and Religious Factors Influencing Medical Decision-Making on BRCA1/2 Genetic Testing in the Orthodox Jewish Community

description: Introduction. Although the prevalence of a pathogenic variant in the BRCA1 and BRCA2 genes is about 1:400 (0.25%) in the general population, the prevalence is as high as 1:40 (2.5%) among the Ashkenazi Jewish population. Despite cost-effective preventive measures for mutation carriers, Orthodox Jews constitute a cultural and religious group that requires different approaches to BRCA1 and BRCA2 genetic testing relative to other groups. This study analyzed a dialogue of key stakeholders and community members to explore factors that influence decision-making about BRCA1 and BRCA2 genetic testing in the New York Orthodox Jewish community. 
Methods. Qualitative research methods, based on Grounded Theory and Narrative Research, were utilized to analyze the narrative data collected from 49 key stakeholders and community members. A content analysis was conducted to identify themes; inter-rater reliability was 71%.
Results. Facilitators of genetic testing were a desire for preventive interventions and education, while barriers to genetic testing included negative emotions, feared impact on family/romantic relationships, cost, and stigma. Views differed on the role of religious leaders and healthcare professionals in medical decision-making. Education, health, and community were discussed as influential factors, and concerns were expressed about disclosure, implementation, and information needs. 
Conclusion. This study elicited the opinions of Orthodox Jewish women (decision-makers) and key stakeholders (influencers) who play critical roles in the medical decision-making process. The findings have broad implications for engaging community stakeholders within faith-based or culturally distinct groups to ensure better utilization of healthcare services for cancer screening and prevention designed to improve population health.
DOI: 10.5281/zenodo.7709845
title: Pooled CRISPR Screening of High-content Cellular Phenotypes by Ghost Cytometry_03

description: Pooled CRISPR Screening of High-content Cellular Phenotypes by Ghost Cytometry (Ghost Cytometer data)
DOI: 10.5281/zenodo.7709846
title: Pooled CRISPR Screening of High-content Cellular Phenotypes by Ghost Cytometry_03

description: Pooled CRISPR Screening of High-content Cellular Phenotypes by Ghost Cytometry (Ghost Cytometer data)
DOI: 10.5281/zenodo.10472988
title: Pooled CRISPR Screening of High-content Cellular Phenotypes by Ghost Cytometry_04

description: Pooled CRISPR Screening of High-content Cellular Phenotypes by Ghost Cytometry (Python files)
DOI: 10.5281/zenodo.10472989
title: Pooled CRISPR Screening of High-content Cellular Phenotypes by Ghost Cytometry_04

description: Pooled CRISPR Screening of High-content Cellular Phenotypes by Ghost Cytometry (Python files)
DOI: 10.6084/m9.figshare.21897163
title: Differential Proteins Expression Distinguished Between Patients With Infectious and Noninfectious Uveitis

description: We investigated the aqueous humor proteome and associated plasma proteome in patients with infectious or noninfectious uveitis. AH and plasma were obtained from 28 patients with infectious uveitis (IU), 29 patients with noninfectious uveitis (NIU) and 35 healthy controls undergoing cataract surgery. The proteins profile was analyzed by SomaScan technology. We found 1844 and 2484 proteins up-regulated and 124 and 161 proteins down-regulated in the AH from IU and NIU groups, respectively. In the plasma, three proteins were up-regulated in NIU patients, and one and five proteins were down-regulated in the IU and NIU patients, respectively. The results of pathway enrichment analysis for both IU and NIU groups were related mostly to inflammatory and regulatory processes. SomaScan was able to detect novel AH and plasma protein biomarkers in IU and NIU patients. Also, the unique proteins found in both AH and plasma suggest a protein signature that could distinguish between infectious and noninfectious uveitis.
DOI: 10.6084/m9.figshare.21897163.v1
title: Differential Proteins Expression Distinguished Between Patients With Infectious and Noninfectious Uveitis

description: We investigated the aqueous humor proteome and associated plasma proteome in patients with infectious or noninfectious uveitis. AH and plasma were obtained from 28 patients with infectious uveitis (IU), 29 patients with noninfectious uveitis (NIU) and 35 healthy controls undergoing cataract surgery. The proteins profile was analyzed by SomaScan technology. We found 1844 and 2484 proteins up-regulated and 124 and 161 proteins down-regulated in the AH from IU and NIU groups, respectively. In the plasma, three proteins were up-regulated in NIU patients, and one and five proteins were down-regulated in the IU and NIU patients, respectively. The results of pathway enrichment analysis for both IU and NIU groups were related mostly to inflammatory and regulatory processes. SomaScan was able to detect novel AH and plasma protein biomarkers in IU and NIU patients. Also, the unique proteins found in both AH and plasma suggest a protein signature that could distinguish between infectious and noninfectious uveitis.
DOI: 10.6084/m9.figshare.12984286
title: Balancing Unobserved Covariates With Covariate-Adaptive Randomized Experiments

description: Balancing important covariates is often critical in clinical trials and causal inference. Stratified permuted block (STR-PB) and covariate-adaptive randomization (CAR) procedures are widely used to balance observed covariates in practice. The balance properties of these procedures with respect to the observed covariates have been well studied. However, it has been questioned whether these methods will also yield a good balance for the unobserved covariates. In this article, we develop a general framework for the analysis of the unobserved covariates imbalance. These results are applicable to develop and compare the balance properties of complete randomization (CR), STR-PB, and CAR procedures with respect to the unobserved covariates. To quantify the improvement obtained by using STR-PB and CAR procedures rather than CR, we introduce the percentage reduction in variance of the unobserved covariates imbalance and compare these quantities. Our results demonstrate the benefits of using CAR or STR-PB (when the number of strata is small relative to the sample size) in terms of balancing unobserved covariates. These results also pave the way for future research into the effect of unobserved covariates in covariate-adaptive randomized experiments in clinical trials, as well as many other applications. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.12984286.v2
title: Balancing Unobserved Covariates With Covariate-Adaptive Randomized Experiments

description: Balancing important covariates is often critical in clinical trials and causal inference. Stratified permuted block (STR-PB) and covariate-adaptive randomization (CAR) procedures are widely used to balance observed covariates in practice. The balance properties of these procedures with respect to the observed covariates have been well studied. However, it has been questioned whether these methods will also yield a good balance for the unobserved covariates. In this article, we develop a general framework for the analysis of the unobserved covariates imbalance. These results are applicable to develop and compare the balance properties of complete randomization (CR), STR-PB, and CAR procedures with respect to the unobserved covariates. To quantify the improvement obtained by using STR-PB and CAR procedures rather than CR, we introduce the percentage reduction in variance of the unobserved covariates imbalance and compare these quantities. Our results demonstrate the benefits of using CAR or STR-PB (when the number of strata is small relative to the sample size) in terms of balancing unobserved covariates. These results also pave the way for future research into the effect of unobserved covariates in covariate-adaptive randomized experiments in clinical trials, as well as many other applications. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.12984286.v1
title: Balancing Unobserved Covariates with Covariate-Adaptive Randomized Experiments

description: Balancing important covariates is often critical in clinical trials and causal inference. Stratified permuted block (STR-PB) and covariate-adaptive randomization (CAR) procedures are widely used to balance observed covariates in practice. The balance properties of these procedures with respect to the observed covariates have been well studied. However, it has been questioned whether these methods will also yield a good balance for the unobserved covariates. In this article, we develop a general framework for the analysis of the unobserved covariates imbalance. These results are applicable to develop and compare the balance properties of complete randomization (CR), STR-PB, and CAR procedures with respect to the unobserved covariates. To quantify the improvement obtained by using STR-PB and CAR procedures rather than CR, we introduce the percentage reduction in variance of the unobserved covariates imbalance and compare these quantities. Our results demonstrate the benefits of using CAR or STR-PB (when the number of strata is small relative to the sample size) in terms of balancing unobserved covariates. These results also pave the way for future research into the effect of unobserved covariates in covariate-adaptive randomized experiments in clinical trials, as well as many other applications.
DOI: 10.6084/m9.figshare.17702978
title: New advances in quantitative proteomics research and current applications in asthma

description: Asthma is the most common chronic respiratory disease and has been declared a global public health problem by the World Health Organization. Due to the high heterogeneity and complexity, asthma can be classified into different ‘phenotypes’ and it is still difficult to assess the phenotypes and stages of asthma by traditional methods. In recent years, mass spectrometry-based proteomics studies have made significant progress in sensitivity and accuracy of protein identification and quantitation, and are able to obtain differences in protein expression across samples, which provides new insights into the mechanisms and classification of asthma. In this article, we summarize research strategies in quantitative proteomics, including labeled, label-free and targeted quantification, and highlight the advantages and disadvantages of each. In addition, new applications of quantitative proteomics and the current status of research in asthma have also been discussed. In this study, online resources such as PubMed and Google Scholar were used for literature retrieval. The application of quantitative proteomics in asthma has an important role in identifying asthma subphenotypes, revealing potential pathogenesis and therapeutic targets. But the proteomic studies on asthma are not sufficient, as most of them are in the phase of biomarker discovery.