cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9034229.v1
title: Chimpanzee adenoviral vector prime-boost regimen elicits potent immune responses against Ebola virus in mice and rhesus macaques

description: In the last few decades, Ebola virus (EBOV) has emerged periodically and infected people in Africa, resulting in an extremely high mortality rate. With no available prophylaxis or cure so far, a highly effective Ebola vaccine is urgently needed. In this study, we developed a novel chimpanzee adenovirus-based prime-boost vaccine by exploiting two recombinant replication-deficient chimpanzee adenoviral vectors, AdC7 and AdC68, which express glycoproteins (GP) of the EBOV strain identified in the 2014 outbreak. Our results indicated that a single immunization using AdC7 or AdC68 could stimulate potent EBOV-specific antibody responses, whereas the AdC7 prime-AdC68 boost regimen induced much stronger and sustained humoral and cellular immune responses in both mice and rhesus monkeys, compared with AdC7 or AdC68 single vaccination or the AdC68 prime-AdC7 boost regimen. This prime-boost vaccine could also protect mice from the simulated infection with EBOV-like particle (EBOVLP) in biosafety level 2 (BSL-2) laboratories, and antibodies from the prime-boost immunized rhesus macaques could passively provide protection against EBOVLP infection. Altogether, our results show that the AdC7 prime-AdC68 boost vaccine is a promising candidate for further development to combat EBOV infections.
DOI: 10.25549/usctheses-c89-288172
title: The Development of a Second Victim Toolkit for Programs in Nurse Anesthesia.pdf
DOI: 10.6084/m9.figshare.7985894
title: Additional file 2: of Genome-wide association study and candidate gene analysis of alkalinity tolerance in japonica rice germplasm at the seedling stage

description: Table S2. Geographical distribution of 295 japonica rice varieties (XLSX 22 kb)
DOI: 10.6084/m9.figshare.23714269
title: Additional file 5 of Identification of cell subpopulations associated with disease phenotypes from scRNA-seq data using PACSI

description: Additional file 5. Table with differential expression genes in PACSI-identified cells associated with COVID-19 versus all other cells. Table with the Reactome pathways enrichment of upregulated genes in PACSI-identified cells associated with COVID-19. Table with full list of genes in COVID-19 signature. Table with the specificity scores of regulons in PACSI-identified cells associated with COVID-19.
DOI: 10.6084/m9.figshare.23714275.v1
title: Additional file 6 of Identification of cell subpopulations associated with disease phenotypes from scRNA-seq data using PACSI

description: Additional file 6. Table with differential expression genes in PACSI-identified spots associated with poor survival versus all other spots. Table with the Reactome pathways enrichment of upregulated genes in PACSI-identified spots associated with poor survival. Table with full list of the upregulated genes in PACSI-identified spots associated with poor survival versus all other spots.
DOI: 10.6084/m9.figshare.23714263
title: Additional file 3 of Identification of cell subpopulations associated with disease phenotypes from scRNA-seq data using PACSI

description: Additional file 3. Table with differential expression genes in PACSI-identified cells associated with poor survival versus all other cells. Table with the Reactome pathways enrichment of upregulated genes in PACSI-identified cells associated with poor survival. Table with full list of genes in prognostic signature. Table with the specificity scores of regulons in PACSI-identified cells associated with poor survival.
DOI: 10.6084/m9.figshare.9034343
title: Estimating the Number of Clusters Using Cross-Validation

description: Many clustering methods, including <i>k</i>-means, require the user to specify the number of clusters as an input parameter. A variety of methods have been devised to choose the number of clusters automatically, but they often rely on strong modeling assumptions. This article proposes a data-driven approach to estimate the number of clusters based on a novel form of cross-validation. The proposed method differs from ordinary cross-validation, because clustering is fundamentally an unsupervised learning problem. Simulation and real data analysis results show that the proposed method outperforms existing methods, especially in high-dimensional settings with heterogeneous or heavy-tailed noise. In a yeast cell cycle dataset, the proposed method finds a parsimonious clustering with interpretable gene groupings. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.21617273
title: Buried Jurassic rift system in the middle segment of the northern Qaidam Basin: Implications for Mesozoic landforms of the northern Tibetan Plateau

description: The Jurassic is one of the most important periods generating hydrocarbon source rocks and coals in Northwest China, and the Qaidam Basin is an important petroliferous and coal-forming basin. However, a series of explorations in the Qaidam Basin targeting Jurassic source rocks have failed over the past several years. These failures were mainly caused by missing the targeted Jurassic strata, suggesting that the current understanding of the Jurassic distribution in the Qaidam Basin is still limited. Therefore, this study conducts detailed analyses of the drilling wells and seismic data in the middle segment of the northern Qaidam Basin. The seismic profiles and borehole data indicate a rifting tectonic setting with discontinuous deposition and rapid facies transition during the Jurassic. A well-preserved buried rift valley proved in the Hongnan region reveals that the Jurassic deposits are mainly restricted in the narrow rift system. Therefore, further exploration targeting the Jurassic source rocks should focus on delineating the distribution of the Jurassic rift system in the Qaidam Basin, combined with the recovery of the complex Cenozoic tectonic overprinting.
DOI: 10.6084/m9.figshare.23714263.v1
title: Additional file 3 of Identification of cell subpopulations associated with disease phenotypes from scRNA-seq data using PACSI

description: Additional file 3. Table with differential expression genes in PACSI-identified cells associated with poor survival versus all other cells. Table with the Reactome pathways enrichment of upregulated genes in PACSI-identified cells associated with poor survival. Table with full list of genes in prognostic signature. Table with the specificity scores of regulons in PACSI-identified cells associated with poor survival.
DOI: 10.6084/m9.figshare.7986002.v1
title: Additional file 3: of Proliferation of hydrocarbon-degrading microbes at the bottom of the Mariana Trench

description: Accession numbers of protein sequences used as query sequence against the metagenomic datasets in this study (XLSX 12 kb)
DOI: 10.6084/m9.figshare.9034343.v1
title: Estimating the number of clusters using cross-validation

description: Many clustering methods, including <i>k</i>-means, require the user to specify the number of clusters as an input parameter. A variety of methods have been devised to choose the number of clusters automatically, but they often rely on strong modeling assumptions. This paper proposes a data-driven approach to estimate the number of clusters based on a novel form of cross-validation. The proposed method differs from ordinary cross-validation, because clustering is fundamentally an unsupervised learning problem. Simulation and real data analysis results show that the proposed method outperforms existing methods, especially in high-dimensional settings with heterogeneous or heavy-tailed noise. In a yeast cell cycle dataset, the proposed method finds a parsimonious clustering with interpretable gene groupings.
DOI: 10.6084/m9.figshare.7985918
title: Additional file 5: of Genome-wide association study and candidate gene analysis of alkalinity tolerance in japonica rice germplasm at the seedling stage

description: Table S3. Summary of functional annotation of the genes in the candidate region on chromosome 3 (XLSX 12 kb)
DOI: 10.6084/m9.figshare.7985924
title: Additional file 6: of Genome-wide association study and candidate gene analysis of alkalinity tolerance in japonica rice germplasm at the seedling stage

description: Table S4. GO enrichment analysis of the genes in candidate region. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.7986500
title: Additional file 2: of DNA methylome profiling of granulosa cells reveals altered methylation in genes regulating vital ovarian functions in polycystic ovary syndrome

description: Hypermethylated sites were linked to a total of 1777 genes (XLSX 354 kb)
DOI: 10.6084/m9.figshare.14277345
title: Electrocardiographic effect of artemisinin-piperaquine, dihydroartemisinin-piperaquine, and artemether-lumefantrine treatment in falciparum malaria patients

description: Abstract INTRODUCTION: Artemisinin-based combination therapy (ACT), such as artemisinin-piperaquine (AP), dihydroartemisinin-piperaquine (DP), and artemether-lumefantrine (AL), is the first-line treatment for malaria in many malaria-endemic areas. However, we lack a detailed evaluation of the cardiotoxicity of these ACTs. This study aimed to analyze the electrocardiographic effects of these three ACTs in malaria patients. METHODS: We analyzed the clinical data of 89 hospitalized patients with falciparum malaria who had received oral doses of three different ACTs. According to the ACTs administered, these patients were divided into three treatment groups: 27 treated with AP (Artequick), 31 with DP (Artekin), and 31 with AL (Coartem). Electrocardiograms and other indicators were recorded before and after the treatment. The QT interval was calculated using Fridericia’s formula (QTcF) and Bazett’s formula (QTcB). RESULTS: Both QTcF and QTcB interval prolongation occurred in all three groups. The incidence of such prolongation between the three groups was not significantly different. The incidence of both moderate and severe prolongation was not significantly different between the three groups. The ΔQTcF and ΔQTcB of the three groups were not significantly different. The intra-group comparison showed significant prolongation of QTcF after AL treatment. CONCLUSIONS: Clinically recommended doses of DP, AL, and AP may cause QT prolongation in some malaria patients but do not cause torsades de pointes ventricular tachycardia or other arrhythmias.
DOI: 10.6084/m9.figshare.14278002
title: Prognostic Value of Lung Ultrasound for Clinical Outcomes in Heart Failure Patients: A Systematic Review and Meta-Analysis

description: Abstract Background There is conflicting information about whether lung ultrasound assessed by B-lines has prognostic value in patients with heart failure (HF). Objectives To evaluate the prognostic value of lung ultrasound assessed by B-lines in HF patients. Methods Four databases (PubMed, EMBASE, Cochrane Library, and Scopus) were systematically searched to identify relevant articles. We pooled the hazard ratio (HR) and 95% confidence interval (CI) from eligible studies and carried out heterogeneity, quality assessment, and publication bias analyses. Data were pooled using a fixed-effects or random-effect model. A p value &lt; 0.05 was considered to indicate statistical significance. Results Nine studies involving 1,212 participants were included in the systematic review. B-lines &gt; 15 and &gt; 30 at discharge were significantly associated with increased risk of combined outcomes of all-cause mortality or HF hospitalization (HR, 3.37, 95% CI, 1.52-7.47; p = 0.003; HR, 4.01, 95% CI, 2.29-7.01; p &lt; 0.001, respectively). A B-line &gt; 30 cutoff at discharge was significantly associated with increased risk of HF hospitalization (HR, 9.01, 95% CI, 2.80-28.93; p &lt; 0.001). Moreover, a B-line &gt; 3 cutoff significantly increased the risk for combined outcomes of all-cause mortality or HF hospitalization in HF outpatients (HR, 3.21, 95% CI, 2.09-4.93; I2 = 10%; p &lt; 0.00001). Conclusion B-lines could predict all-cause mortality and HF hospitalizations in patients with HF. Further large randomized controlled trials are needed to explore whether dealing with B-lines would improve the prognosis in clinical settings.
DOI: 10.6084/m9.figshare.7985933.v1
title: Additional file 7: of Genome-wide association study and candidate gene analysis of alkalinity tolerance in japonica rice germplasm at the seedling stage

description: Table S5. RNA-seq dates of the genes in candidate region. (XLSX 12 kb)
DOI: 10.25549/usctheses-c89-289252
title: etd-VillegasCh-8315a
DOI: 10.6084/m9.figshare.7985906
title: MOESM1 of PITX2 enhances progression of lung adenocarcinoma by transcriptionally regulating WNT3A and activating Wnt/Î˛-catenin signaling pathway

description: Additional file 1: Table S1. 317 genes used for pathway analysis.
DOI: 10.6084/m9.figshare.7986596
title: MOESM3 of Trends in insecticide resistance in Culex pipiens pallens over 20Â years in Shandong, China

description: Additional file 3: Table S3. Multiple comparisons by Dunnettâ s T3 test.
DOI: 10.6084/m9.figshare.14277251.v1
title: Imputation method to reduce undetected severe acute respiratory infection cases during the coronavirus disease outbreak in Brazil

description: Abstract INTRODUCTION: The coronavirus disease (COVD-19) outbreak has overburdened the surveillance of severe acute respiratory infections (SARIs), including the laboratory network. This study was aimed at correcting the absence of laboratory results of reported SARI deaths. METHODS: The imputation method was applied for SARI deaths without laboratory information using clinico-epidemiological characteristics. RESULTS: Of 84,449 SARI deaths, 51% were confirmed with COVID-19 while 3% with other viral respiratory diseases. After the imputation method, 95% of deaths were reclassified as COVID-19 while 5% as other viral respiratory diseases. CONCLUSIONS: The imputation method was a useful and robust solution (sensitivity and positive predictive value of 98%) for missing values through clinical & epidemiological characteristics.
DOI: 10.6084/m9.figshare.14277261
title: Clinical characteristics and therapeutic procedure for a critical case of novel coronavirus pneumonia treated with glucocorticoids and non-invasive ventilator treatment

description: Abstract The novel coronavirus pneumonia (NCP) outbreak occurred in Wuhan, China at the end of 2019. Here, we report the clinical characteristics and therapeutic procedure for a case of severe NCP. The patient was started on glucocorticoids and non-invasive ventilator treatment. After treatment, the patient’s symptoms improved, and the status was confirmed as NCP negative. Our results may provide clues for the treatment of NCP.
DOI: 10.6084/m9.figshare.14277261.v1
title: Clinical characteristics and therapeutic procedure for a critical case of novel coronavirus pneumonia treated with glucocorticoids and non-invasive ventilator treatment

description: Abstract The novel coronavirus pneumonia (NCP) outbreak occurred in Wuhan, China at the end of 2019. Here, we report the clinical characteristics and therapeutic procedure for a case of severe NCP. The patient was started on glucocorticoids and non-invasive ventilator treatment. After treatment, the patient’s symptoms improved, and the status was confirmed as NCP negative. Our results may provide clues for the treatment of NCP.
DOI: 10.6084/m9.figshare.7985921
title: MOESM3 of PITX2 enhances progression of lung adenocarcinoma by transcriptionally regulating WNT3A and activating Wnt/Î˛-catenin signaling pathway

description: Additional file 3: Table S3. Sequences of shRNAs and miRNA mimics.
DOI: 10.6084/m9.figshare.7986200
title: Additional file 4: of Whole genome sequencing reveals complexity in both HPV sequences present and HPV integrations in HPV-positive oropharyngeal squamous cell carcinomas

description: Table S2. The split reads containing HPV and human sequence junctions. The table listed all the split reads which contains HPV and human sequence junctions. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.14277345.v1
title: Electrocardiographic effect of artemisinin-piperaquine, dihydroartemisinin-piperaquine, and artemether-lumefantrine treatment in falciparum malaria patients

description: Abstract INTRODUCTION: Artemisinin-based combination therapy (ACT), such as artemisinin-piperaquine (AP), dihydroartemisinin-piperaquine (DP), and artemether-lumefantrine (AL), is the first-line treatment for malaria in many malaria-endemic areas. However, we lack a detailed evaluation of the cardiotoxicity of these ACTs. This study aimed to analyze the electrocardiographic effects of these three ACTs in malaria patients. METHODS: We analyzed the clinical data of 89 hospitalized patients with falciparum malaria who had received oral doses of three different ACTs. According to the ACTs administered, these patients were divided into three treatment groups: 27 treated with AP (Artequick), 31 with DP (Artekin), and 31 with AL (Coartem). Electrocardiograms and other indicators were recorded before and after the treatment. The QT interval was calculated using Fridericia’s formula (QTcF) and Bazett’s formula (QTcB). RESULTS: Both QTcF and QTcB interval prolongation occurred in all three groups. The incidence of such prolongation between the three groups was not significantly different. The incidence of both moderate and severe prolongation was not significantly different between the three groups. The ΔQTcF and ΔQTcB of the three groups were not significantly different. The intra-group comparison showed significant prolongation of QTcF after AL treatment. CONCLUSIONS: Clinically recommended doses of DP, AL, and AP may cause QT prolongation in some malaria patients but do not cause torsades de pointes ventricular tachycardia or other arrhythmias.
DOI: 10.6084/m9.figshare.21617311
title: Multiple Palaeozoic–Mesozoic orogenic events in the SE Yangtze Block, China: evidence from the petrogenesis and deformation of gneissic granites from the Nanwenhe metamorphic dome and regional correlation analysis

description: The Nanwenhe metamorphic dome contains a rare Silurian granitic pluton that developed in the SE Yangtze Block during early Palaeozoic orogenesis, and this pluton comprises the Nanwenhe gneissic granites. The petrogenetic and structural deformation histories of the gneissic granites recorded the multi-stage interaction of the SE Yangtze Block with other blocks during the Palaeozoic and Mesozoic, including the Cathaysia, Indochina, and Paleo-Pacific blocks. Zircon U–Pb and Hf isotopes and geochemical data indicate that the Early Palaeozoic granites (433–420 Ma) are S-type granitic rocks, and they were derived from the partial melting of ancient continental crust with no contribution from mantle material. And the large variations and positive values of ε<sub>Hf</sub>(t) (−12.25 to +10.69) of the gneissic granites are ascribed to a heterogeneous source and disequilibrium melting. Here we compare early Palaeozoic granitoids in the SE Yangtze Block (foreland belt) with those in the orogenic core, and suggest that the SE Yangtze Block underwent limited syn-collisional crustal thickening and metamorphism, and following which post-collisional granitoids were formed through partial melting of continental crust. Structural analysis of the Nanwenhe gneissic granites allows two stages of deformation to be identified: northward detachment (D<sub>1</sub>) and northwestward thrusting (D<sub>2</sub>). <sup>40</sup>Ar–<sup>39</sup>Ar isotope dating of muscovites from the gneissic granites yields a well-defined plateau age of 229.61 Ma, which is interpreted as the timing of Late Triassic structural overprinting associated with the formation of the Nanwenhe metamorphic dome. Integration of our new results with previous research findings from the dome and South China allows us to conclude that the detachment deformation (D<sub>1</sub>) represents Late Triassic post-collisional extension, and D<sub>2</sub> represented Jurassic intracontinental orogeny associated with subduction of the Paleo-Pacific Block.
DOI: 10.6084/m9.figshare.7985894.v1
title: Additional file 2: of Genome-wide association study and candidate gene analysis of alkalinity tolerance in japonica rice germplasm at the seedling stage

description: Table S2. Geographical distribution of 295 japonica rice varieties (XLSX 22 kb)
DOI: 10.6084/m9.figshare.7985906.v1
title: MOESM1 of PITX2 enhances progression of lung adenocarcinoma by transcriptionally regulating WNT3A and activating Wnt/Î˛-catenin signaling pathway

description: Additional file 1: Table S1. 317 genes used for pathway analysis.
DOI: 10.6084/m9.figshare.7985915
title: MOESM2 of PITX2 enhances progression of lung adenocarcinoma by transcriptionally regulating WNT3A and activating Wnt/Î˛-catenin signaling pathway

description: Additional file 2: Table S2. Sequences of qRT-PCR primers.
DOI: 10.6084/m9.figshare.7985918.v1
title: Additional file 5: of Genome-wide association study and candidate gene analysis of alkalinity tolerance in japonica rice germplasm at the seedling stage

description: Table S3. Summary of functional annotation of the genes in the candidate region on chromosome 3 (XLSX 12 kb)
DOI: 10.6084/m9.figshare.7985927
title: MOESM4 of PITX2 enhances progression of lung adenocarcinoma by transcriptionally regulating WNT3A and activating Wnt/Î˛-catenin signaling pathway

description: Additional file 4: Table S4. Clinical data of 60 LUAD patients.
DOI: 10.6084/m9.figshare.7986002
title: Additional file 3: of Proliferation of hydrocarbon-degrading microbes at the bottom of the Mariana Trench

description: Accession numbers of protein sequences used as query sequence against the metagenomic datasets in this study (XLSX 12 kb)
DOI: 10.6084/m9.figshare.7461749.v1
title: Matched Learning for Optimizing Individualized Treatment Strategies Using Electronic Health Records

description: Current guidelines for treatment decision making largely rely on data from randomized controlled trials (RCTs) studying average treatment effects. They may be inadequate to make individualized treatment decisions in real-world settings. Large-scale electronic health records (EHR) provide opportunities to fulfill the goals of personalized medicine and learn individualized treatment rules (ITRs) depending on patient-specific characteristics from real-world patient data. In this work, we tackle challenges with EHRs and propose a machine learning approach based on matching (M-learning) to estimate optimal ITRs from EHRs. This new learning method performs matching instead of inverse probability weighting as commonly used in many existing methods for estimating ITRs to more accurately assess individuals’ treatment responses to alternative treatments and alleviate confounding. Matching-based value functions are proposed to compare matched pairs under a unified framework, where various types of outcomes for measuring treatment response (including continuous, ordinal, and discrete outcomes) can easily be accommodated. We establish the Fisher consistency and convergence rate of M-learning. Through extensive simulation studies, we show that M-learning outperforms existing methods when propensity scores are misspecified or when unmeasured confounders are present in certain scenarios. Lastly, we apply M-learning to estimate optimal personalized second-line treatments for type 2 diabetes patients to achieve better glycemic control or reduce major complications using EHRs from New York Presbyterian Hospital. Supplementary materials for this article are available online.