cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.10326659
title: SNMFSMMA: using symmetric nonnegative matrix factorization and Kronecker regularized least squares to predict potential small molecule-microRNA association

description: Accumulating studies have shown that microRNAs (miRNAs) could be used as targets of small-molecule (SM) drugs to treat diseases. In recent years, researchers have proposed many computational models to reveal miRNA-SM associations due to the huge cost of experimental methods. Considering the shortcomings of the previous models, such as the prediction accuracy of some models is low or some cannot be applied for new SMs (miRNAs), we developed a novel model named Symmetric Nonnegative Matrix Factorization for Small Molecule-MiRNA Association prediction (SNMFSMMA). Different from some models directly applying the integrated similarities, SNMFSMMA first performed matrix decomposition on the integrated similarity matrixes, and calculated the Kronecker product of the new integrated similarity matrixes to obtain the SM-miRNA pair similarity. Further, we applied regularized least square to obtain the mapping function of the SM-miRNA pairs to the associated probabilities by minimizing the objective function. On the basis of Dataset 1 and 2 extracted from SM2miR v1.0 database, we implemented global leave-one-out cross validation (LOOCV), miRNA-fixed local LOOCV, SM-fixed local LOOCV and 5-fold cross-validation to evaluate the prediction performance. Finally, the AUC values obtained by SNMFSMMA in these validation reached 0.9711 (0.8895), 0.9698 (0.8884), 0.8329 (0.7651) and 0.9644 ± 0.0035 (0.8814 ± 0.0033) based on Dataset 1 (Dataset 2), respectively. In the first case study, 5 of the top 10 associations predicted were confirmed. In the second, 7 and 8 of the top 10 predicted miRNAs related with 5-FU and 5-Aza-2ʹ-deoxycytidine were confirmed. These results demonstrated the reliable predictive power of SNMFSMMA.
DOI: 10.6084/m9.figshare.10326659.v1
title: SNMFSMMA: using symmetric nonnegative matrix factorization and Kronecker regularized least squares to predict potential small molecule-microRNA association

description: Accumulating studies have shown that microRNAs (miRNAs) could be used as targets of small-molecule (SM) drugs to treat diseases. In recent years, researchers have proposed many computational models to reveal miRNA-SM associations due to the huge cost of experimental methods. Considering the shortcomings of the previous models, such as the prediction accuracy of some models is low or some cannot be applied for new SMs (miRNAs), we developed a novel model named Symmetric Nonnegative Matrix Factorization for Small Molecule-MiRNA Association prediction (SNMFSMMA). Different from some models directly applying the integrated similarities, SNMFSMMA first performed matrix decomposition on the integrated similarity matrixes, and calculated the Kronecker product of the new integrated similarity matrixes to obtain the SM-miRNA pair similarity. Further, we applied regularized least square to obtain the mapping function of the SM-miRNA pairs to the associated probabilities by minimizing the objective function. On the basis of Dataset 1 and 2 extracted from SM2miR v1.0 database, we implemented global leave-one-out cross validation (LOOCV), miRNA-fixed local LOOCV, SM-fixed local LOOCV and 5-fold cross-validation to evaluate the prediction performance. Finally, the AUC values obtained by SNMFSMMA in these validation reached 0.9711 (0.8895), 0.9698 (0.8884), 0.8329 (0.7651) and 0.9644 ± 0.0035 (0.8814 ± 0.0033) based on Dataset 1 (Dataset 2), respectively. In the first case study, 5 of the top 10 associations predicted were confirmed. In the second, 7 and 8 of the top 10 predicted miRNAs related with 5-FU and 5-Aza-2ʹ-deoxycytidine were confirmed. These results demonstrated the reliable predictive power of SNMFSMMA.
DOI: 10.6084/m9.figshare.7705253
title: First line treatment of adult patients with primary immune thrombocytopenia: a real-world study

description: Immune thrombocytopenia (ITP) is an autoimmune disease with a mild to severe risk of bleeding complications. First line treatment includes corticosteroids, immunoglobulins, or other. In this large cohort study, first-line strategies for treatment-naive adult primary ITP was studied in a real-world setting. Records from all adult ITP patients who received first-line treatment between January 2010 and December 2017 at Qilu Hospital were reviewed retrospectively (<i>n</i> = 699). During the study period, 271 patients were treated with high-dose dexamethasone (HDD) and 289 patients were treated with conventional prednisone (alone or in combination with other drugs). Initial responses were similar for the two groups (88.56% vs. 86.51%, <i>P</i> = 0.462), but patients in the HDD group responded earlier than the prednisone group (3 days vs. 5 days, <i>P &lt; </i>0.001). The sustained response (SR) at 6 months was lower in the HDD group than in the prednisone group (35.4% vs. 47.1%, <i>P</i> = 0.040). However, the SR at 12 months and at the end of our follow-up were not significantly different between the groups. Overall duration of response (DOR) in the prednisone group was longer than in the HDD group throughout the follow-up period (<i>P = </i>0.007). However, the incidence of SR and overall DOR were not significantly different between the HDD group and the prednisone 3 months group (prednisone terminated within 3 months). The presence of anti-GPIb-IX autoantibodies was a predictive factor for a poor initial response to corticosteroids therapy (<i>P</i> &lt; 0.05). However, neither of the two antiplatelet autoantibodies were correlated with the opportunity to achieve SR and overall DOR in both groups throughout the follow-up period (<i>P</i> &gt; 0.05). Adverse events were more frequent and long-lasting in the prednisone group. Our study showed that HDD provided an effective and more rapid response as initial treatment of ITP, with comparable long-term prognosis and better tolerance when compared with conventional PDN (less than 3 months) in the real-world setting.
DOI: 10.6084/m9.figshare.7705253.v1
title: First line treatment of adult patients with primary immune thrombocytopenia: a real-world study

description: Immune thrombocytopenia (ITP) is an autoimmune disease with a mild to severe risk of bleeding complications. First line treatment includes corticosteroids, immunoglobulins, or other. In this large cohort study, first-line strategies for treatment-naive adult primary ITP was studied in a real-world setting. Records from all adult ITP patients who received first-line treatment between January 2010 and December 2017 at Qilu Hospital were reviewed retrospectively (<i>n</i> = 699). During the study period, 271 patients were treated with high-dose dexamethasone (HDD) and 289 patients were treated with conventional prednisone (alone or in combination with other drugs). Initial responses were similar for the two groups (88.56% vs. 86.51%, <i>P</i> = 0.462), but patients in the HDD group responded earlier than the prednisone group (3 days vs. 5 days, <i>P &lt; </i>0.001). The sustained response (SR) at 6 months was lower in the HDD group than in the prednisone group (35.4% vs. 47.1%, <i>P</i> = 0.040). However, the SR at 12 months and at the end of our follow-up were not significantly different between the groups. Overall duration of response (DOR) in the prednisone group was longer than in the HDD group throughout the follow-up period (<i>P = </i>0.007). However, the incidence of SR and overall DOR were not significantly different between the HDD group and the prednisone 3 months group (prednisone terminated within 3 months). The presence of anti-GPIb-IX autoantibodies was a predictive factor for a poor initial response to corticosteroids therapy (<i>P</i> &lt; 0.05). However, neither of the two antiplatelet autoantibodies were correlated with the opportunity to achieve SR and overall DOR in both groups throughout the follow-up period (<i>P</i> &gt; 0.05). Adverse events were more frequent and long-lasting in the prednisone group. Our study showed that HDD provided an effective and more rapid response as initial treatment of ITP, with comparable long-term prognosis and better tolerance when compared with conventional PDN (less than 3 months) in the real-world setting.
DOI: 10.6084/m9.figshare.7705253.v4
title: First line treatment of adult patients with primary immune thrombocytopenia: a real-world study

description: Immune thrombocytopenia (ITP) is an autoimmune disease with a mild to severe risk of bleeding complications. First line treatment includes corticosteroids, immunoglobulins, or other. In this large cohort study, first-line strategies for treatment-naive adult primary ITP was studied in a real-world setting. Records from all adult ITP patients who received first-line treatment between January 2010 and December 2017 at Qilu Hospital were reviewed retrospectively (<i>n</i> = 699). During the study period, 271 patients were treated with high-dose dexamethasone (HDD) and 289 patients were treated with conventional prednisone (alone or in combination with other drugs). Initial responses were similar for the two groups (88.56% vs. 86.51%, <i>P</i> = 0.462), but patients in the HDD group responded earlier than the prednisone group (3 days vs. 5 days, <i>P &lt; </i>0.001). The sustained response (SR) at 6 months was lower in the HDD group than in the prednisone group (35.4% vs. 47.1%, <i>P</i> = 0.040). However, the SR at 12 months and at the end of our follow-up were not significantly different between the groups. Overall duration of response (DOR) in the prednisone group was longer than in the HDD group throughout the follow-up period (<i>P = </i>0.007). However, the incidence of SR and overall DOR were not significantly different between the HDD group and the prednisone 3 months group (prednisone terminated within 3 months). The presence of anti-GPIb-IX autoantibodies was a predictive factor for a poor initial response to corticosteroids therapy (<i>P</i> &lt; 0.05). However, neither of the two antiplatelet autoantibodies were correlated with the opportunity to achieve SR and overall DOR in both groups throughout the follow-up period (<i>P</i> &gt; 0.05). Adverse events were more frequent and long-lasting in the prednisone group. Our study showed that HDD provided an effective and more rapid response as initial treatment of ITP, with comparable long-term prognosis and better tolerance when compared with conventional PDN (less than 3 months) in the real-world setting.
DOI: 10.6084/m9.figshare.15568410.v1
title: Additional file 2 of Easy-Prime: a machine learning–based prime editor design tool

description: Additional file 2: Table S1. Summary of PE2 and PE3 features. Feature rankings for the PE2 and PE3 model were provided.
DOI: 10.6084/m9.figshare.7181120
title: Additional file 2: of CRISPR-mediated deletion of prostate cancer risk-associated CTCF loop anchors identifies repressive chromatin loops

description: Table S1. List of ChIP-seq and RNA-seq datasets. 18Â KB (XLSX 17 kb)
DOI: 10.6084/m9.figshare.7705424
title: MOESM3 of Sequential phototrophicâ mixotrophic cultivation of oleaginous microalga Graesiella sp. WBG-1 in a 1000Â m2 open raceway pond

description: Additional file 3. Changes of residual nitrate and phosphate during the Graesiella cultivation in open raceway pond.
DOI: 10.6084/m9.figshare.7705424.v1
title: MOESM3 of Sequential phototrophicâ mixotrophic cultivation of oleaginous microalga Graesiella sp. WBG-1 in a 1000Â m2 open raceway pond

description: Additional file 3. Changes of residual nitrate and phosphate during the Graesiella cultivation in open raceway pond.
DOI: 10.6084/m9.figshare.15567958
title: Additional file 1 of Experimental colitis promotes sustained, sex-dependent, T-cell-associated neuroinflammation and parkinsonian neuropathology

description: Additional file 1. Characteristics of subjects from whom colon biopsies were collected for evaluation of inflammatory markers.
DOI: 10.6084/m9.figshare.7181138.v1
title: Additional file 4: of CRISPR-mediated deletion of prostate cancer risk-associated CTCF loop anchors identifies repressive chromatin loops

description: Table S3. Annotated SNPs. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.15568410
title: Additional file 2 of Easy-Prime: a machine learning–based prime editor design tool

description: Additional file 2: Table S1. Summary of PE2 and PE3 features. Feature rankings for the PE2 and PE3 model were provided.
DOI: 10.6084/m9.figshare.15568431
title: Additional file 3 of Easy-Prime: a machine learning–based prime editor design tool

description: Additional file 3: Table S2. Paired PE design comparison between Easy-Prime (EP) and PrimeDesign (PD).
DOI: 10.6084/m9.figshare.15568431.v1
title: Additional file 3 of Easy-Prime: a machine learning–based prime editor design tool

description: Additional file 3: Table S2. Paired PE design comparison between Easy-Prime (EP) and PrimeDesign (PD).
DOI: 10.6084/m9.figshare.15567958.v1
title: Additional file 1 of Experimental colitis promotes sustained, sex-dependent, T-cell-associated neuroinflammation and parkinsonian neuropathology

description: Additional file 1. Characteristics of subjects from whom colon biopsies were collected for evaluation of inflammatory markers.
DOI: 10.6084/m9.figshare.21330500
title: Spectral Clustering via Adaptive Layer Aggregation for Multi-Layer Networks

description: One of the fundamental problems in network analysis is detecting community structure in multi-layer networks, of which each layer represents one type of edge information among the nodes. We propose integrative spectral clustering approaches based on effective convex layer aggregations. Our aggregation methods are strongly motivated by a delicate asymptotic analysis of the spectral embedding of weighted adjacency matrices and the downstream <i>k</i>-means clustering, in a challenging regime where community detection consistency is impossible. In fact, the methods are shown to estimate the optimal convex aggregation, which minimizes the misclustering error under some specialized multi-layer network models. Our analysis further suggests that clustering using Gaussian mixture models is generally superior to the commonly used <i>k</i>-means in spectral clustering. Extensive numerical studies demonstrate that our adaptive aggregation techniques, together with Gaussian mixture model clustering, make the new spectral clustering remarkably competitive compared to several popularly used methods. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.21330500.v1
title: Spectral clustering via adaptive layer aggregation for multi-layer networks*

description: One of the fundamental problems in network analysis is detecting community structure in multi-layer networks, of which each layer represents one type of edge information among the nodes. We propose integrative spectral clustering approaches based on effective convex layer aggregations. Our aggregation methods are strongly motivated by a delicate asymptotic analysis of the spectral embedding of weighted adjacency matrices and the downstream <i>k</i>-means clustering, in a challenging regime where community detection consistency is impossible. In fact, the methods are shown to estimate the optimal convex aggregation, which minimizes the mis-clustering error under some specialized multi-layer network models. Our analysis further suggests that clustering using Gaussian mixture models is generally superior to the commonly used <i>k</i>-means in spectral clustering. Extensive numerical studies demonstrate that our adaptive aggregation techniques, together with Gaussian mixture model clustering, make the new spectral clustering remarkably competitive compared to several popularly used methods.
DOI: 10.6084/m9.figshare.7705586
title: Additional file 2: of Prevalence of human papillomavirus infection of 65,613 women in East China

description: Table S2. The all multiple HPV infection mode in participants. (XLSX 29â kb)
DOI: 10.12751/g-node.if5rg3
title: Dataset - Effects of chronic ingestion of soy peptide supplementation on juvenile social isolation

description: This dataset is supplementing a research paper. We provide all numeric data and 16S rRNA sequencing data (fastq files) generated and analyzed during the study.
description: IsSupplementTo: Tamura et al., Chronic ingestion of soy peptide supplementation reduces aggressive behavior and abnormal fear memory caused by juvenile social isolation that is not published yet. Scientific Reports, submitted.
DOI: 10.6084/m9.figshare.25249777.v1
title: Supplementary Material for: Opinions over targets for blood pressure control after mechanical thrombectomy in patients with acute ischemic stroke: baseline survey for the ENCHANTED2/MT trial in China

description: Background: Although guidelines recommend a target blood pressure 185-180/105-110 mmHg after mechanical thrombectomy for acute ischemic stroke (AIS), there is limited randomized evidence to support this level. We surveyed candidate institutions about the approach to blood pressure management in this patient group in preparation for inviting them to participate in the Enhanced Blood Pressure Control after Endovascular Thrombectomy for the Acute Ischemic Stroke Trial (ENCHANTED2/MT). 
Methods: Physicians from a professional network of institutions that met mechanical thrombectomy qualification requirements were invited to participate in an online questionnaire covering basic clinical information as well as questions on blood pressure management. 
Results: We invited 88 sites to participate with 44 (50%) ultimately joining the trial, and a total of 88 physicians finished the survey. The median number of annual mechanical thrombectomy cases performed per site was 89 [IQR 65-150]. Only 38 (43%) institutions strictly adhere to guidelines when managing the blood pressure of mechanical thrombectomy patients. The most popular blood pressure target for reperfusion patients was 140-160 mmHg (n=47, 53%), and &lt;120 mmHg (n=28, 32%). Fewer hospital stroke beds (40 [21–57] vs. 60 [39–110], p = 0.01) and lower proportion of elevated blood pressure after mechanical thrombectomy (25% [10%–50%] vs. 50% [20%–70%], p = 0.02) were related to a more aggressive blood pressure target (&lt;120 mmHg). Urapidil (n=82, 93%) and calcium channel blockers (CCBs) (n = 87, 99%), were the most widely used antihypertensive drugs, respectively.
Conclusions: According to the survey, unstandardized blood pressure management protocols are performed in mechanical thrombectomy patients at institutions across China, which is different from prior survey from another country. More high-quality studies are needed to guide clinical practice.
DOI: 10.6084/m9.figshare.16617440.v1
title: Is a Classification Procedure Good Enough?-A Goodness-of-Fit Assessment Tool for Classification Learning

description: In recent years, many non-traditional classification methods, such as Random Forest, Boosting, and neural network, have been widely used in applications. Their performance is typically measured in terms of classification accuracy. While the classification error rate and the like are important, they do not address a fundamental question: Is the classification method underfitted? To our best knowledge, there is no existing method that can assess the goodness-of-fit of a general classification procedure. Indeed, the lack of a parametric assumption makes it challenging to construct proper tests. To overcome this difficulty, we propose a methodology called BAGofT that splits the data into a training set and a validation set. First, the classification procedure to assess is applied to the training set, which is also used to adaptively find a data grouping that reveals the most severe regions of underfitting. Then, based on this grouping, we calculate a test statistic by comparing the estimated success probabilities and the actual observed responses from the validation set. The data splitting guarantees that the size of the test is controlled under the null hypothesis, and the power of the test goes to one as the sample size increases under the alternative hypothesis. For testing parametric classification models, the BAGofT has a broader scope than the existing methods since it is not restricted to specific parametric models (e.g., logistic regression). Extensive simulation studies show the utility of the BAGofT when assessing general classification procedures and its strengths over some existing methods when testing parametric classification models.
DOI: 10.6084/m9.figshare.7180541.v1
title: Kinetic study of the thermal inactivation of <i>Lactobacillus plantarum</i> during bread baking

description: Live probiotics can be supplemented to bread as functional ingredients. The viability of probiotics in bread needs to be sufficient to exert a beneficial effect on human health. To maximize the viability, a kinetic study on the inactivation of probiotics during baking was carried out. The thermal inactivation of <i>Lactobacillus plantarum</i> P8 during bread baking was evaluated with rate-dependent kinetic models. The influences of temperature, moisture content, drying rate, and temperature variation rate on the inactivation kinetics were studied explicitly. A kinetic model kd=ko1+adTdtexp⁡bX−EdRT, which included temperature (<i>T</i>), moisture content (<i>X</i>), and temperature variation rate (<i>dT/dt</i>) as variables, was found to best describe the concave and sigmoidal survival curves of probiotics in bread crust and in crumb during baking, respectively. The drying rate (<i>dX/dt</i>) was of little influence on the kinetics. The application of the proposed model is limited to baking processes, but could be used to maximize the survival of probiotics in bread products.
DOI: 10.6084/m9.figshare.12947695
title: Additional file 3 of Accurate prediction of DNA N4-methylcytosine sites via boost-learning various types of sequence features

description: Additional file 3 Case study results. In Additional File 3, the 4mC-contained DNA sequence and the prediction results of four predictors are reported.
DOI: 10.6084/m9.figshare.7180541
title: Kinetic study of the thermal inactivation of <i>Lactobacillus plantarum</i> during bread baking

description: Live probiotics can be supplemented to bread as functional ingredients. The viability of probiotics in bread needs to be sufficient to exert a beneficial effect on human health. To maximize the viability, a kinetic study on the inactivation of probiotics during baking was carried out. The thermal inactivation of <i>Lactobacillus plantarum</i> P8 during bread baking was evaluated with rate-dependent kinetic models. The influences of temperature, moisture content, drying rate, and temperature variation rate on the inactivation kinetics were studied explicitly. A kinetic model kd=ko1+adTdtexp⁡bX−EdRT, which included temperature (<i>T</i>), moisture content (<i>X</i>), and temperature variation rate (<i>dT/dt</i>) as variables, was found to best describe the concave and sigmoidal survival curves of probiotics in bread crust and in crumb during baking, respectively. The drying rate (<i>dX/dt</i>) was of little influence on the kinetics. The application of the proposed model is limited to baking processes, but could be used to maximize the survival of probiotics in bread products.
DOI: 10.6084/m9.figshare.12947902.v1
title: Additional file 9 of Identification of novel molecular markers of mastitis caused by Staphylococcus aureus using gene expression profiling in two consecutive generations of Chinese Holstein dairy cattle

description: Additional file 9: Table S5. Differentially expressed genes detected in S vs. H
DOI: 10.6084/m9.figshare.12948008.v1
title: Additional file 1 of Circular HER2 RNA positive triple negative breast cancer is sensitive to Pertuzumab

description: Additional file 1: Table S1. All plasmids information.
DOI: 10.6084/m9.figshare.9277760.v1
title: Additional file 3: of Genome-wide identification, expression analysis and functional study of the GRAS gene family in Tartary buckwheat (Fagopyrum tataricum)

description: Table S1. List of the 47 FtGRAS genes identified in this study. (XLS 153 kb)