cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7986269
title: MOESM3 of HSP superfamily of genes in the malaria vector Anopheles sinensis: diversity, phylogenetics and association with pyrethroid resistance

description: Additional file 3: Fig. S2. Phylogenetic relationships of HSP genes from four insect species. The phylogenetic tree was constructed using the maximum-likelihood method based on predicted amino acid sequences. Analysis was performed with the program package MEGA5.0. The number at the branch point of the node represents the bootstrap values calculated from 1000 replications, and the gaps were deleted with pairwise deletion method. As, An. sinensis; Ag, An. gambiae; Cq, Cx. quinquefasciatus and Ae, Ae. aegypti. (A) HSP90 family; (B) HSP70 family; (C) Chaperonins family; (D) HSP40 family; (E) sHSP family.
DOI: 10.6084/m9.figshare.14277251
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.7986281.v1
title: Additional file 4: of Comparative genomic analysis of Bacillus paralicheniformis MDJK30 with its closely related species reveals an evolutionary relationship between B. paralicheniformis and B. licheniformis

description: Table S2. Genetic characteristics of strains in the current research. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.7986296.v1
title: Additional file 6: of Comparative genomic analysis of Bacillus paralicheniformis MDJK30 with its closely related species reveals an evolutionary relationship between B. paralicheniformis and B. licheniformis

description: Table S4. Table S4. Average Nucleotide Identity (ANI) (%) based on whole-genome alignments. ANI values of lineage L are in blue and lineage P are in purple. (XLSX 62 kb).
DOI: 10.6084/m9.figshare.21617311.v1
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: 10.5281/zenodo.7756569
title: A Pan-European, Quantile Machine learning (QML) based, Total, Fine-Mode and Coarse-Mode Aerosol Optical Depth dataset (QML AOD))

description: The V 1.1.0 product is an improved Aerosol Optical Depth (AOD) product based on Gap-filled MAIAC AOD, which provide first full-coverage, high-resolution monitoring of fine-mode and coarse-mode aerosols in Europe from 2003-20. This dataset has successfully rectified the previously identified issue of weak associations between satellite AOD and PM2.5 in Europe, which was primarily attributable to current limitations of AOD data. Our innovative approach has yielded stronger correlations with PM10, PM2.5, and PMcoarse than previous AOD product, laying a critical groundwork for improving PM10, PM2.5, and PMcoarse predictions in further epidemiological studies or environmental monitoring.

We have uploaded three QML AOD datasets in Geotiff format, covering the region from -27° to 72° latitude and from -25° to 45° longitude. These datasets will be useful for researchers and policymakers to better understand the impacts of aerosols on the environment and human health.

 Note: v1.0.0 product do not include MAIAC AOD in their models.

Please read more details in our paper 

Estimation of pan-European, daily total, fine-mode and coarse-mode Aerosol Optical Depth at 0.1° resolution to facilitate air quality assessments

https://doi.org/10.1016/j.scitotenv.2024.170593
DOI: 10.5281/zenodo.8315721
title: A Pan-European, Quantile Machine learning (QML) based, Total, Fine-Mode and Coarse-Mode Aerosol Optical Depth dataset (QML AOD))

description: The V 1.1.0 product is an improved Aerosol Optical Depth (AOD) product based on Gap-filled MAIAC AOD, which provide first full-coverage, high-resolution monitoring of fine-mode and coarse-mode aerosols in Europe from 2003-20. This dataset has successfully rectified the previously identified issue of weak associations between satellite AOD and PM2.5 in Europe, which was primarily attributable to current limitations of AOD data. Our innovative approach has yielded stronger correlations with PM10, PM2.5, and PMcoarse than previous AOD product, laying a critical groundwork for improving PM10, PM2.5, and PMcoarse predictions in further epidemiological studies or environmental monitoring.

We have uploaded three QML AOD datasets in Geotiff format, covering the region from -27° to 72° latitude and from -25° to 45° longitude. These datasets will be useful for researchers and policymakers to better understand the impacts of aerosols on the environment and human health.

 Note: v1.0.0 product do not include MAIAC AOD in their models.

Please read more details in our paper 

Estimation of pan-European, daily total, fine-mode and coarse-mode Aerosol Optical Depth at 0.1° resolution to facilitate air quality assessments

https://doi.org/10.1016/j.scitotenv.2024.170593
DOI: 10.6084/m9.figshare.7461734.v2
title: D-CCA: A Decomposition-Based Canonical Correlation Analysis for High-Dimensional Datasets

description: A typical approach to the joint analysis of two high-dimensional datasets is to decompose each data matrix into three parts: a low-rank common matrix that captures the shared information across datasets, a low-rank distinctive matrix that characterizes the individual information within a single dataset, and an additive noise matrix. Existing decomposition methods often focus on the orthogonality between the common and distinctive matrices, but inadequately consider the more necessary orthogonal relationship between the two distinctive matrices. The latter guarantees that no more shared information is extractable from the distinctive matrices. We propose decomposition-based canonical correlation analysis (D-CCA), a novel decomposition method that defines the common and distinctive matrices from the ℓ2 space of random variables rather than the conventionally used Euclidean space, with a careful construction of the orthogonal relationship between distinctive matrices. D-CCA represents a natural generalization of the traditional canonical correlation analysis. The proposed estimators of common and distinctive matrices are shown to be consistent and have reasonably better performance than some state-of-the-art methods in both simulated data and the real data analysis of breast cancer data obtained from The Cancer Genome Atlas. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.7986182
title: Additional file 2: of Whole genome sequencing reveals complexity in both HPV sequences present and HPV integrations in HPV-positive oropharyngeal squamous cell carcinomas

description: Table S1. The summary of the whole genome sequencing data in each tumor sample. The table included the total raw reads, the clean reads, the average number of SNPs and indels in each tumor sample. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.7985915.v1
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.7986224.v1
title: Additional file 1: of Systematic identification and validation of the reference genes from 60 RNA-Seq libraries in the scallop Mizuhopecten yessoensis

description: Table S1. Detailed information on the RNA-Seq datasets (XLSM 9 kb)
DOI: 10.6084/m9.figshare.14278002.v1
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.7985921.v1
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.7986233
title: Additional file 2: of Systematic identification and validation of the reference genes from 60 RNA-Seq libraries in the scallop Mizuhopecten yessoensis

description: Table S2. Detailed information on the expression variability and annotation of the candidate reference genes in early development, adult tissues and gonadal development of the Yesso scallop (XLSM 330 kb)
DOI: 10.6084/m9.figshare.7985924.v1
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.7986305
title: Additional file 7: of Comparative genomic analysis of Bacillus paralicheniformis MDJK30 with its closely related species reveals an evolutionary relationship between B. paralicheniformis and B. licheniformis

description: Table S5. List of 1718 single-copy core genes shared by 14 lineage P strains. (XLSX 97 kb).
DOI: 10.6084/m9.figshare.14277808.v1
title: Atorvastatin Reduces Accumulation of Vascular Smooth Muscle Cells to Inhibit Intimal Hyperplasia via p38 MAPK Pathway Inhibition in a Rat Model of Vein Graft

description: Abstract Background: The rate of saphenous vein graft failure one year after coronary artery bypass grafting ranges from 10% to 25%. The aim of this study was to explore whether atorvastatin can reduce accumulation of vascular smooth muscle cells to inhibit intimal hyperplasia via p38 MAPK pathway inhibition. Methods: Forty-five Sprague-Dawley rats were randomized to three groups. Thirty rats received a vein graft operation, and they were randomized to be treated with vehicle or atorvastatin; fifteen rats received a sham operation. We detected intimal hyperplasia by hematoxylin-eosin staining and related protein expression by immunohistochemical and Western blot analysis. Comparisons were analyzed by single-factor analysis of variance and Fisher's least significant difference test, with p &lt; 0.05 considered significant. Results: The intima analyzed by hematoxylin-eosin staining was dramatically thicker in the control group than in the atorvastatin group and sham group (p &lt; 0.01). The outcomes of immunohistochemical staining of α-SMA demonstrated that the percentage of α-SMA-positive cells in the control group was higher than in the atorvastatin group (p &lt; 0.01). We also evaluated α-SMA, PCNA, p38 MAPK, and phosphorylation of p38 MAPK after statin treatment by Western blot analysis, and the results indicated that atorvastatin did not lead to p38 MAPK reduction (p &lt; 0.05); it did, however, result in inhibition of p38 MAPK phosphorylation (p &lt; 0.01), and it significantly reduced α-SMA and PCNA levels, in comparison with the control group (p &lt; 0.01). Conclusion: We have demonstrated that atorvastatin can inhibit accumulation of vascular smooth muscle cells by inhibiting the p38 MAPK pathway, and it is capable of inhibiting intimal hyperplasia in a rat vein graft model.
DOI: 10.6084/m9.figshare.7985933
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: 10.6084/m9.figshare.14277808
title: Atorvastatin Reduces Accumulation of Vascular Smooth Muscle Cells to Inhibit Intimal Hyperplasia via p38 MAPK Pathway Inhibition in a Rat Model of Vein Graft

description: Abstract Background: The rate of saphenous vein graft failure one year after coronary artery bypass grafting ranges from 10% to 25%. The aim of this study was to explore whether atorvastatin can reduce accumulation of vascular smooth muscle cells to inhibit intimal hyperplasia via p38 MAPK pathway inhibition. Methods: Forty-five Sprague-Dawley rats were randomized to three groups. Thirty rats received a vein graft operation, and they were randomized to be treated with vehicle or atorvastatin; fifteen rats received a sham operation. We detected intimal hyperplasia by hematoxylin-eosin staining and related protein expression by immunohistochemical and Western blot analysis. Comparisons were analyzed by single-factor analysis of variance and Fisher's least significant difference test, with p &lt; 0.05 considered significant. Results: The intima analyzed by hematoxylin-eosin staining was dramatically thicker in the control group than in the atorvastatin group and sham group (p &lt; 0.01). The outcomes of immunohistochemical staining of α-SMA demonstrated that the percentage of α-SMA-positive cells in the control group was higher than in the atorvastatin group (p &lt; 0.01). We also evaluated α-SMA, PCNA, p38 MAPK, and phosphorylation of p38 MAPK after statin treatment by Western blot analysis, and the results indicated that atorvastatin did not lead to p38 MAPK reduction (p &lt; 0.05); it did, however, result in inhibition of p38 MAPK phosphorylation (p &lt; 0.01), and it significantly reduced α-SMA and PCNA levels, in comparison with the control group (p &lt; 0.01). Conclusion: We have demonstrated that atorvastatin can inhibit accumulation of vascular smooth muscle cells by inhibiting the p38 MAPK pathway, and it is capable of inhibiting intimal hyperplasia in a rat vein graft model.
DOI: 10.6084/m9.figshare.7986587
title: MOESM1 of Trends in insecticide resistance in Culex pipiens pallens over 20Â years in Shandong, China

description: Additional file 1: Table S1. Mosquito sampling sites and times.
DOI: 10.6084/m9.figshare.7986587.v1
title: MOESM1 of Trends in insecticide resistance in Culex pipiens pallens over 20Â years in Shandong, China

description: Additional file 1: Table S1. Mosquito sampling sites and times.
DOI: 10.6084/m9.figshare.21087273
title: Additional file 5 of Overexpression of cotton GhNAC072 gene enhances drought and salt stress tolerance in transgenic Arabidopsis

description: Additional file 5: Supplementary Table S1. Number of NAC genes and their assembly in G. hirsutum, G. arboreum, and G. raimondii.
DOI: 10.6084/m9.figshare.21087282
title: Additional file 8 of Overexpression of cotton GhNAC072 gene enhances drought and salt stress tolerance in transgenic Arabidopsis

description: Additional file 8: Supplementary Table S4. Physiological traits (ELWL, RLWC, CMS and Chlorophyll content) of transgenic and wildtype during drought and salt stress treatment.
DOI: 10.6084/m9.figshare.7986257
title: Additional file 1: of Comparative genomic analysis of Bacillus paralicheniformis MDJK30 with its closely related species reveals an evolutionary relationship between B. paralicheniformis and B. licheniformis

description: Table S1. The features of prophage, genomic islands, secondary metabolite clusters and CRISPR in MDJK30 genome. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.7986287
title: Additional file 5: of Comparative genomic analysis of Bacillus paralicheniformis MDJK30 with its closely related species reveals an evolutionary relationship between B. paralicheniformis and B. licheniformis

description: Table S3. List of 528 single-copy core genes shared by 56 Bacillus strains. (XLSX 37 kb)
DOI: 10.6084/m9.figshare.7986233.v1
title: Additional file 2: of Systematic identification and validation of the reference genes from 60 RNA-Seq libraries in the scallop Mizuhopecten yessoensis

description: Table S2. Detailed information on the expression variability and annotation of the candidate reference genes in early development, adult tissues and gonadal development of the Yesso scallop (XLSM 330 kb)
DOI: 10.6084/m9.figshare.7986269.v1
title: MOESM3 of HSP superfamily of genes in the malaria vector Anopheles sinensis: diversity, phylogenetics and association with pyrethroid resistance

description: Additional file 3: Fig. S2. Phylogenetic relationships of HSP genes from four insect species. The phylogenetic tree was constructed using the maximum-likelihood method based on predicted amino acid sequences. Analysis was performed with the program package MEGA5.0. The number at the branch point of the node represents the bootstrap values calculated from 1000 replications, and the gaps were deleted with pairwise deletion method. As, An. sinensis; Ag, An. gambiae; Cq, Cx. quinquefasciatus and Ae, Ae. aegypti. (A) HSP90 family; (B) HSP70 family; (C) Chaperonins family; (D) HSP40 family; (E) sHSP family.
DOI: 10.6084/m9.figshare.7461749.v2
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.
DOI: 10.6084/m9.figshare.7986305.v1
title: Additional file 7: of Comparative genomic analysis of Bacillus paralicheniformis MDJK30 with its closely related species reveals an evolutionary relationship between B. paralicheniformis and B. licheniformis

description: Table S5. List of 1718 single-copy core genes shared by 14 lineage P strains. (XLSX 97 kb).
DOI: 10.6084/m9.figshare.7986596.v1
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: 10.5281/zenodo.10639127
title: Model Output for simulations of future Winter Warming events  in the Abisko area.

description: Model Output for simulatuons of future Winter Warming Events in Pascual et al. (2024) Accounting for winter warming events in the ecosystem model LPJ-GUESS: evaluation and outlook. 

The dataset includes monthly output for snow depth, ground temperature, ecosystem fluxes and ground water content in four different ecosystems in the Abisko area: wet fen, peat plateau, birch forest, and tundra.
DOI: 10.5281/zenodo.10639128
title: Model Output for simulations of future Winter Warming events  in the Abisko area.

description: Model Output for simulatuons of future Winter Warming Events in Pascual et al. (2024) Accounting for winter warming events in the ecosystem model LPJ-GUESS: evaluation and outlook. 

The dataset includes monthly output for snow depth, ground temperature, ecosystem fluxes and ground water content in four different ecosystems in the Abisko area: wet fen, peat plateau, birch forest, and tundra.