cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12850937.v1
title: Comparison of Intraocular Antibody Measurement, Quantitative Pathogen PCR, and Metagenomic Deep Sequencing of Aqueous Humor in Secondary Glaucoma Associated with Anterior Segment Uveitis

description: To identify viral pathogens in patients with secondary glaucoma associated with anterior segment uveitis and compare metagenomic deep sequencing (MDS) with enzyme-linked immunosorbent assay (ELISA) combined with Witmer-Desmonts coefficient (WDC) evaluation and real-time quantitative polymerase chain reaction (qPCR) on investigating pathogens in aqueous humor. Aqueous humor from 31 patients, including 22 Posner-Schlossman Syndrome and 9 other anterior uveitis, was assessed pathogens by ELISA combined with WDC evaluation, virus deoxyribonucleic acid (DNA) detection by real-time qPCR and MDS. Viral pathogens (HCMV or VZV or RV) were detected in 19 out of 31 eyes (61.3%) by real-time qPCR or WDC evaluation. MDS revealed the presence of HCMV DNA sequences in three PSS patients. Virus is an important pathogen in secondary glaucoma associated with anterior segment uveitis. MDS is a potential etiologic diagnosis tool to seek intraocular viral pathogens for secondary glaucoma associated anterior segment uveitis.
DOI: 10.6084/m9.figshare.7608089
title: Additional file 1: of The landscape of transposable elements and satellite DNAs in the genome of a dioecious plant spinach (Spinacia oleracea L.)

description: Annotation of full-length LTR-REs in spinach genome. (XLS 3011 kb)
DOI: 10.6084/m9.figshare.7608089.v1
title: Additional file 1: of The landscape of transposable elements and satellite DNAs in the genome of a dioecious plant spinach (Spinacia oleracea L.)

description: Annotation of full-length LTR-REs in spinach genome. (XLS 3011 kb)
DOI: 10.6084/m9.figshare.7608110
title: Additional file 3: of The landscape of transposable elements and satellite DNAs in the genome of a dioecious plant spinach (Spinacia oleracea L.)

description: TE concensus sequences generated by RepeatModeler in spinach genome. (FASTA 1073 kb)
DOI: 10.6084/m9.figshare.7608110.v1
title: Additional file 3: of The landscape of transposable elements and satellite DNAs in the genome of a dioecious plant spinach (Spinacia oleracea L.)

description: TE concensus sequences generated by RepeatModeler in spinach genome. (FASTA 1073 kb)
DOI: 10.6084/m9.figshare.7608113
title: Additional file 4: of The landscape of transposable elements and satellite DNAs in the genome of a dioecious plant spinach (Spinacia oleracea L.)

description: TE dataset detected by signature-based methods in spinach genome. (FASTA 122852 kb)
DOI: 10.6084/m9.figshare.7608113.v1
title: Additional file 4: of The landscape of transposable elements and satellite DNAs in the genome of a dioecious plant spinach (Spinacia oleracea L.)

description: TE dataset detected by signature-based methods in spinach genome. (FASTA 122852 kb)
DOI: 10.6084/m9.figshare.12851006
title: Two novel <i>PDE6C</i> gene mutations in Chinese family with achromatopsia

description: <b>Background:</b> Achromatopsia (ACHM) is an inherited retinal disease affecting the cone cell function. To date, six pathogenic genes of ACHM have been identified. However, the diagnostic and therapeutic methods of this disorder remain limited. Herein, to characterize the clinical features and genetic causes of three affected siblings in a Chinese family with ACHM, we used target next-generation sequencing (NGS) and found new pathogenic factors associated with ACHM in this family. <b>Materials and methods:</b> Three patients with ACHM and three healthy family members were included in this study. All participants received comprehensive ophthalmic tests. NGS approach was performed on the patients to determine the causative mutation for this family. The silico analysis was also applied to predict the pathogenesis of identified mutations. <b>Results:</b> Genetic assessments revealed compound heterozygous mutations of the <i>PDE6C</i> gene (c.1413 + 1 G &gt; C, c.305 G &gt; A), carried by all three patients. Both mutations were novel and predicted to be deleterious by six types of online predictive software. The heterozygous <i>PDE6C</i> missense mutation (c.305 G &gt; A) was found from the mother and the heterozygous <i>PDE6C</i> splice site mutation (c.1413 + 1 G &gt; C) was found in the father and all the children. All patients in the family showed typical signs and symptoms of ACHM. <b>Conclusions:</b> We report novel compound heterozygous <i>PDE6C</i> mutations in causing ACHM and further confirm the clinical diagnosis. Our study extends the genotypic spectrums for <i>PDE6C</i>-ACHM and better illustrates its genotype–phenotype correlations, which would help the ACHM patients with better genetic diagnosis, prognosis, and gene treatment.
DOI: 10.6084/m9.figshare.12851006.v1
title: Two novel <i>PDE6C</i> gene mutations in Chinese family with achromatopsia

description: <b>Background:</b> Achromatopsia (ACHM) is an inherited retinal disease affecting the cone cell function. To date, six pathogenic genes of ACHM have been identified. However, the diagnostic and therapeutic methods of this disorder remain limited. Herein, to characterize the clinical features and genetic causes of three affected siblings in a Chinese family with ACHM, we used target next-generation sequencing (NGS) and found new pathogenic factors associated with ACHM in this family. <b>Materials and methods:</b> Three patients with ACHM and three healthy family members were included in this study. All participants received comprehensive ophthalmic tests. NGS approach was performed on the patients to determine the causative mutation for this family. The silico analysis was also applied to predict the pathogenesis of identified mutations. <b>Results:</b> Genetic assessments revealed compound heterozygous mutations of the <i>PDE6C</i> gene (c.1413 + 1 G &gt; C, c.305 G &gt; A), carried by all three patients. Both mutations were novel and predicted to be deleterious by six types of online predictive software. The heterozygous <i>PDE6C</i> missense mutation (c.305 G &gt; A) was found from the mother and the heterozygous <i>PDE6C</i> splice site mutation (c.1413 + 1 G &gt; C) was found in the father and all the children. All patients in the family showed typical signs and symptoms of ACHM. <b>Conclusions:</b> We report novel compound heterozygous <i>PDE6C</i> mutations in causing ACHM and further confirm the clinical diagnosis. Our study extends the genotypic spectrums for <i>PDE6C</i>-ACHM and better illustrates its genotype–phenotype correlations, which would help the ACHM patients with better genetic diagnosis, prognosis, and gene treatment.
DOI: 10.6084/m9.figshare.7608128
title: Additional file 2: of Obesity impacts the regulation of miR-10b and its targets in primary breast tumors

description: Table S1. miRbase miRNAs identified in RNA-seq. The first worksheet lists all miRbase entries identified in 24 samples (normal + tumor) from 12 subjects, with individual values. The second worksheet is an abbreviated list including only the robustly expressed miRNAs (normalized rangeâ &gt;â 10 reads/sample) with group statistics. (XLSX 577 kb)
DOI: 10.6084/m9.figshare.7608128.v1
title: Additional file 2: of Obesity impacts the regulation of miR-10b and its targets in primary breast tumors

description: Table S1. miRbase miRNAs identified in RNA-seq. The first worksheet lists all miRbase entries identified in 24 samples (normal + tumor) from 12 subjects, with individual values. The second worksheet is an abbreviated list including only the robustly expressed miRNAs (normalized rangeâ &gt;â 10 reads/sample) with group statistics. (XLSX 577 kb)
DOI: 10.6084/m9.figshare.8132456
title: Testing and Estimation of Social Network Dependence With Time to Event Data

description: Nowadays, events are spread rapidly along social networks. We are interested in whether people’s responses to an event are affected by their friends’ characteristics. For example, how soon will a person start playing a game given that his/her friends like it? Studying social network dependence is an emerging research area. In this work, we propose a novel latent spatial autocorrelation Cox model to study social network dependence with time-to-event data. The proposed model introduces a latent indicator to characterize whether a person’s survival time might be affected by his or her friends’ features. We first propose a score-type test for detecting the existence of social network dependence. If it exists, we further develop an EM-type algorithm to estimate the model parameters. The performance of the proposed test and estimators are illustrated by simulation studies and an application to a time-to-event dataset about playing a popular mobile game from one of the largest online social network platforms. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement.
DOI: 10.6084/m9.figshare.8132456.v1
title: Testing and Estimation of Social Network Dependence with Time to Event Data

description: Nowadays, events are spread rapidly along social network. We are interested in whether people’s responses to an event are affected by their friends’ characteristics. For example, how soon will a person starts playing a game given that his/her friends like it? Studying social network dependence is an emerging research area. In this work, we propose a novel latent spatial autocorrelation Cox model to study social network dependence with time-to-event data. The proposed model introduces a latent indicator to characterize whether a person’s survival time might be affected by his or her friends’ features. We first propose a score-type test for detecting the existence of social network dependence. If it exists, we further develop an EM-type algorithm to estimate the model parameters. The performance of the proposed test and estimators are illustrated by simulation studies and an application to a time-to-event data set about playing a popular mobile game from one of the largest online social network platforms.
DOI: 10.6084/m9.figshare.8132456.v2
title: Testing and Estimation of Social Network Dependence With Time to Event Data

description: Nowadays, events are spread rapidly along social networks. We are interested in whether people’s responses to an event are affected by their friends’ characteristics. For example, how soon will a person start playing a game given that his/her friends like it? Studying social network dependence is an emerging research area. In this work, we propose a novel latent spatial autocorrelation Cox model to study social network dependence with time-to-event data. The proposed model introduces a latent indicator to characterize whether a person’s survival time might be affected by his or her friends’ features. We first propose a score-type test for detecting the existence of social network dependence. If it exists, we further develop an EM-type algorithm to estimate the model parameters. The performance of the proposed test and estimators are illustrated by simulation studies and an application to a time-to-event dataset about playing a popular mobile game from one of the largest online social network platforms. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement.
DOI: 10.6084/m9.figshare.8132456.v4
title: Testing and Estimation of Social Network Dependence With Time to Event Data

description: Nowadays, events are spread rapidly along social networks. We are interested in whether people’s responses to an event are affected by their friends’ characteristics. For example, how soon will a person start playing a game given that his/her friends like it? Studying social network dependence is an emerging research area. In this work, we propose a novel latent spatial autocorrelation Cox model to study social network dependence with time-to-event data. The proposed model introduces a latent indicator to characterize whether a person’s survival time might be affected by his or her friends’ features. We first propose a score-type test for detecting the existence of social network dependence. If it exists, we further develop an EM-type algorithm to estimate the model parameters. The performance of the proposed test and estimators are illustrated by simulation studies and an application to a time-to-event dataset about playing a popular mobile game from one of the largest online social network platforms. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement.
DOI: 10.6084/m9.figshare.8132456.v3
title: Testing and Estimation of Social Network Dependence With Time to Event Data

description: Nowadays, events are spread rapidly along social networks. We are interested in whether people’s responses to an event are affected by their friends’ characteristics. For example, how soon will a person start playing a game given that his/her friends like it? Studying social network dependence is an emerging research area. In this work, we propose a novel latent spatial autocorrelation Cox model to study social network dependence with time-to-event data. The proposed model introduces a latent indicator to characterize whether a person’s survival time might be affected by his or her friends’ features. We first propose a score-type test for detecting the existence of social network dependence. If it exists, we further develop an EM-type algorithm to estimate the model parameters. The performance of the proposed test and estimators are illustrated by simulation studies and an application to a time-to-event dataset about playing a popular mobile game from one of the largest online social network platforms. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement.
DOI: 10.6084/m9.figshare.12851051
title: COVID-19 and comorbidities: a systematic review and meta-analysis

description: SARS-CoV-2 has caused a worldwide pandemic that began with an outbreak of pneumonia cases in the Hubei province of China. Knowledge of those most at risk is integral for treatment, guideline implementation, and resource allocation. We conducted a systematic review and meta-analysis to evaluate comorbidities associated with severe and fatal cases of COVID-19. A search was conducted on PubMed and EmBase on 20 April 2020. Pooled estimates were collected using a random-effects model. Thirty-three studies were included in the systematic review and twenty-two in the meta-analysis. Of the total cases 40.80% (95%CI: 35.49%, 46.11%) had comorbidities, while fatal cases had 74.37% (95%CI: 55.78%, 86.97%). Hypertension was more prevalent in severe [47.65% (95%CI: 35.04%, 60.26%)] and fatal [47.90% (95%CI: 40.33%, 55.48%)] cases compared to total cases [14.34% (95%CI: 6.60%, 28.42%)]. Diabetes was more prevalent among fatal cases [24.89% (95%CI: 18.80%, 32.16%)] compared to total cases [9.65% (95%CI: 6.83%, 13.48%)]. Respiratory diseases had a higher prevalence in fatal cases [10.89% (95%CI: 7.57%, 15.43%)] in comparison to total cases [3.65% (95%CI: 2.16%, 6.1%)]. Studies assessing the mechanisms accounting for the associations between severe cases and hypertension, diabetes, and respiratory diseases are crucial in understanding this new disease, managing patients at risk, and developing policies and guidelines that will reduce future risk of severe COVID-19 disease.
DOI: 10.6084/m9.figshare.12851051.v1
title: COVID-19 and comorbidities: a systematic review and meta-analysis

description: SARS-CoV-2 has caused a worldwide pandemic that began with an outbreak of pneumonia cases in the Hubei province of China. Knowledge of those most at risk is integral for treatment, guideline implementation, and resource allocation. We conducted a systematic review and meta-analysis to evaluate comorbidities associated with severe and fatal cases of COVID-19. A search was conducted on PubMed and EmBase on 20 April 2020. Pooled estimates were collected using a random-effects model. Thirty-three studies were included in the systematic review and twenty-two in the meta-analysis. Of the total cases 40.80% (95%CI: 35.49%, 46.11%) had comorbidities, while fatal cases had 74.37% (95%CI: 55.78%, 86.97%). Hypertension was more prevalent in severe [47.65% (95%CI: 35.04%, 60.26%)] and fatal [47.90% (95%CI: 40.33%, 55.48%)] cases compared to total cases [14.34% (95%CI: 6.60%, 28.42%)]. Diabetes was more prevalent among fatal cases [24.89% (95%CI: 18.80%, 32.16%)] compared to total cases [9.65% (95%CI: 6.83%, 13.48%)]. Respiratory diseases had a higher prevalence in fatal cases [10.89% (95%CI: 7.57%, 15.43%)] in comparison to total cases [3.65% (95%CI: 2.16%, 6.1%)]. Studies assessing the mechanisms accounting for the associations between severe cases and hypertension, diabetes, and respiratory diseases are crucial in understanding this new disease, managing patients at risk, and developing policies and guidelines that will reduce future risk of severe COVID-19 disease.
DOI: 10.6084/m9.figshare.12851060
title: Comparative proteomics analysis indicates that palmatine contributes to transepithelial migration by regulating cellular adhesion

description: Palmatine, a biologically active isoquinoline alkaloid, possesses multiple pharmaceutical activities against mucosal infection and inflammation. There are no reports about the influence of palmatine on uterine mucosal epithelial cells. We used proteomics to analyse differentially expressed proteins (DEPs) in goat endometrial epithelial cells (EECs) stimulated by lipopolysaccharide (LPS, 5 μg/mL, the dosage can induce inflammatory response, according to our previous study) for 12 h and then treated with palmatine (80 μg/mL) for 8 h; the dosage was selected based on MTT assay. The EECs without any treatment were used as controls. Every group was treated in triplicate. A total of 428 DEPs in LPS-stimulated group and 486 DEPs in the palmatine-treated group were identified. Functional annotation analysis showed that palmatine mainly regulated the protein expression of structural molecules involved in the response to stimuli. Pathway analysis showed that cell adhesion molecule (CaM) pathways were most significant enriched due to palmatine treatment. Junction adhesion molecule 1 (JAM1), nectin 1 (NECT1) and cadherin 5 (CDH5), which play important roles in the transepithelial migration (TEpM) of leukocytes, were significantly downregulated by palmatine. Meanwhile, other proteins essential to the maintenance of cell adhesion and those that facilitate leukocyte migration were upregulated after palmatine treatment. <b>Discussion and conclusions:</b> The results suggested that palmatine regulates the expression of CaMs to affect TEpM during uterine mucosal inflammation and provides novel insight to understanding and developing palmatine pharmacology. Palmatine is a promising drug for treatment of mucosal inflammation.
DOI: 10.6084/m9.figshare.12851060.v2
title: Comparative proteomics analysis indicates that palmatine contributes to transepithelial migration by regulating cellular adhesion

description: Palmatine, a biologically active isoquinoline alkaloid, possesses multiple pharmaceutical activities against mucosal infection and inflammation. There are no reports about the influence of palmatine on uterine mucosal epithelial cells. We used proteomics to analyse differentially expressed proteins (DEPs) in goat endometrial epithelial cells (EECs) stimulated by lipopolysaccharide (LPS, 5 μg/mL, the dosage can induce inflammatory response, according to our previous study) for 12 h and then treated with palmatine (80 μg/mL) for 8 h; the dosage was selected based on MTT assay. The EECs without any treatment were used as controls. Every group was treated in triplicate. A total of 428 DEPs in LPS-stimulated group and 486 DEPs in the palmatine-treated group were identified. Functional annotation analysis showed that palmatine mainly regulated the protein expression of structural molecules involved in the response to stimuli. Pathway analysis showed that cell adhesion molecule (CaM) pathways were most significant enriched due to palmatine treatment. Junction adhesion molecule 1 (JAM1), nectin 1 (NECT1) and cadherin 5 (CDH5), which play important roles in the transepithelial migration (TEpM) of leukocytes, were significantly downregulated by palmatine. Meanwhile, other proteins essential to the maintenance of cell adhesion and those that facilitate leukocyte migration were upregulated after palmatine treatment. <b>Discussion and conclusions:</b> The results suggested that palmatine regulates the expression of CaMs to affect TEpM during uterine mucosal inflammation and provides novel insight to understanding and developing palmatine pharmacology. Palmatine is a promising drug for treatment of mucosal inflammation.
DOI: 10.6084/m9.figshare.12851060.v1
title: Comparative proteomics analysis indicates that palmatine contributes to transepithelial migration by regulating cellular adhesion

description: Palmatine, a biologically active isoquinoline alkaloid, possesses multiple pharmaceutical activities against mucosal infection and inflammation. There are no reports about the influence of palmatine on uterine mucosal epithelial cells. We used proteomics to analyse differentially expressed proteins (DEPs) in goat endometrial epithelial cells (EECs) stimulated by lipopolysaccharide (LPS, 5 μg/mL, the dosage can induce inflammatory response, according to our previous study) for 12 h and then treated with palmatine (80 μg/mL) for 8 h; the dosage was selected based on MTT assay. The EECs without any treatment were used as controls. Every group was treated in triplicate. A total of 428 DEPs in LPS-stimulated group and 486 DEPs in the palmatine-treated group were identified. Functional annotation analysis showed that palmatine mainly regulated the protein expression of structural molecules involved in the response to stimuli. Pathway analysis showed that cell adhesion molecule (CaM) pathways were most significant enriched due to palmatine treatment. Junction adhesion molecule 1 (JAM1), nectin 1 (NECT1) and cadherin 5 (CDH5), which play important roles in the transepithelial migration (TEpM) of leukocytes, were significantly downregulated by palmatine. Meanwhile, other proteins essential to the maintenance of cell adhesion and those that facilitate leukocyte migration were upregulated after palmatine treatment. <b>Discussion and conclusions:</b> The results suggested that palmatine regulates the expression of CaMs to affect TEpM during uterine mucosal inflammation and provides novel insight to understanding and developing palmatine pharmacology. Palmatine is a promising drug for treatment of mucosal inflammation.
DOI: 10.6084/m9.figshare.7608194
title: Additional file 1: of Development of a cardiac-centered frailty ontology

description: Frailty ontology concept list. (XLSX 37 kb)
DOI: 10.6084/m9.figshare.7608194.v1
title: Additional file 1: of Development of a cardiac-centered frailty ontology

description: Frailty ontology concept list. (XLSX 37 kb)