cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7461749
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.20038713
title: A suppository-base-matrix tablet for time-dependent colon-specific delivery system

description: Our research has focused on the main design features and release performances of time-dependent colon-specific (TDCS) delivery tablets, which relies on the relative constancy that is observed in the small intestinal transit time of dosage forms. But inflammatory bowel disease（IBD）can affect the transit time, and usually results in watery stool. Compared to the TDCS and wax-matrix TDCS tablet, a promising time-dependent colon-specific delivery system was investigated. In our study, a suppository-base-matrix coated tablet was evaluated. Water soluble suppository-base helps the expansion of tablet, facilitates uniform film dissolution and achives high osmotic pressure. Combining the expansion of carboxymethyl starch sodium (CMS-Na) and the moisture absorption of NaCl, the coated TDCS tablet obtained a burst and targeted drug delivery system. A very good correlation between in vitro drug release and in vivo outcome was observed. This TDCS coated tablet provides a promising strategy to control drug release to the desired lower gastrointestinal region.
DOI: 10.6084/m9.figshare.7986182.v1
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.7986200.v1
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.14277695
title: Chemotherapy-Related Anatomical Coronary-Artery Disease in Lung Cancer Patients Evaluated by Coronary-Angiography SYNTAX Score

description: Abstract Background Chemotherapy-related coronary artery disease (CAD) is becoming an emerging issue in clinic. However, the underlying mechanism of chemotherapy-related CAD remains unclear. Objective The study investigated the association between chemotherapy and atherosclerotic anatomical abnormalities of coronary arteries among lung cancer patients. Methods Patients undergoing coronary angiography (CAG) between 2010 and 2017, who previously had lung cancer, were examined. Risk factors associated with CAD and information about lung cancer were evaluated. We assessed coronary-artery abnormalities by SYNTAX score (SXscore) based on CAG. In logistic-regression analysis, we defined high SXscore (SXhigh) grade as positive if ≥22. Data were analyzed through descriptive statistics and regression analysis. Results A total of 94 patients were included in the study. The SXscore was higher in the chemotherapy group than in the non-chemotherapy group (25.25, IQR [4.50–30.00] vs. 16.50, IQR [ 5.00–22.00], p = 0.0195). The SXhigh rate was greater in the chemotherapy group than in the non-chemotherapy group (58.33% vs. 25.86; p = 0.0016). Both univariate (OR:4.013; 95% CI:1.655–9.731) and multivariate (OR:5.868; 95% CI:1.778–19.367) logistic-regression analysis revealed that chemotherapy increased the risk of greater SXhigh rates. Multivariate stepwise logistic-regression analysis showed the risk of more severe anatomical CAD is increased by chemotherapy as a whole by 5.323 times (95% CI: 2.002–14.152), and by platinum-based regimens by 5.850 times (95% CI: 2.027–16.879). Conclusions Chemotherapy is associated with anatomical complexity and severity of CAD, which might partly account for the higher risk of chemotherapy-related CAD among lung cancer patients. (Arq Bras Cardiol. 2020; [online].ahead print, PP.0-0)
DOI: 10.6084/m9.figshare.14277695.v1
title: Chemotherapy-Related Anatomical Coronary-Artery Disease in Lung Cancer Patients Evaluated by Coronary-Angiography SYNTAX Score

description: Abstract Background Chemotherapy-related coronary artery disease (CAD) is becoming an emerging issue in clinic. However, the underlying mechanism of chemotherapy-related CAD remains unclear. Objective The study investigated the association between chemotherapy and atherosclerotic anatomical abnormalities of coronary arteries among lung cancer patients. Methods Patients undergoing coronary angiography (CAG) between 2010 and 2017, who previously had lung cancer, were examined. Risk factors associated with CAD and information about lung cancer were evaluated. We assessed coronary-artery abnormalities by SYNTAX score (SXscore) based on CAG. In logistic-regression analysis, we defined high SXscore (SXhigh) grade as positive if ≥22. Data were analyzed through descriptive statistics and regression analysis. Results A total of 94 patients were included in the study. The SXscore was higher in the chemotherapy group than in the non-chemotherapy group (25.25, IQR [4.50–30.00] vs. 16.50, IQR [ 5.00–22.00], p = 0.0195). The SXhigh rate was greater in the chemotherapy group than in the non-chemotherapy group (58.33% vs. 25.86; p = 0.0016). Both univariate (OR:4.013; 95% CI:1.655–9.731) and multivariate (OR:5.868; 95% CI:1.778–19.367) logistic-regression analysis revealed that chemotherapy increased the risk of greater SXhigh rates. Multivariate stepwise logistic-regression analysis showed the risk of more severe anatomical CAD is increased by chemotherapy as a whole by 5.323 times (95% CI: 2.002–14.152), and by platinum-based regimens by 5.850 times (95% CI: 2.027–16.879). Conclusions Chemotherapy is associated with anatomical complexity and severity of CAD, which might partly account for the higher risk of chemotherapy-related CAD among lung cancer patients. (Arq Bras Cardiol. 2020; [online].ahead print, PP.0-0)
DOI: 10.6084/m9.figshare.7986251
title: MOESM1 of HSP superfamily of genes in the malaria vector Anopheles sinensis: diversity, phylogenetics and association with pyrethroid resistance

description: Additional file 1: Table S1. Detailed information and intronâ exon organization of An. sinensis HSPs genes.
DOI: 10.6084/m9.figshare.7986251.v1
title: MOESM1 of HSP superfamily of genes in the malaria vector Anopheles sinensis: diversity, phylogenetics and association with pyrethroid resistance

description: Additional file 1: Table S1. Detailed information and intronâ exon organization of An. sinensis HSPs genes.
DOI: 10.6084/m9.figshare.7986296
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.7986359
title: Additional file 1: of A high-performance approach for predicting donor splice sites based on short window size and imbalanced large samples

description: Table S1. The table lists 201 decision rules obtained based on HS3D-train1:135, and lists the number of positive and negative training samples conforming to the decision rules. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.7986359.v1
title: Additional file 1: of A high-performance approach for predicting donor splice sites based on short window size and imbalanced large samples

description: Table S1. The table lists 201 decision rules obtained based on HS3D-train1:135, and lists the number of positive and negative training samples conforming to the decision rules. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.22666426
title: A facile photoinitiated polymerisation route for the preparation of photonic elastomers with chiral nematic order

description: Photonic crystal elastomers that can change colour upon stretching or compression have potential applications in mechanical sensors and optical coatings. However, facile synthetic strategies are required for these materials to be made on a commercially viable scale. To address this issue, we report a photoinitiated polymerisation method to prepare stretchable chiral nematic cellulose nanocrystal (CNC) elastomer composites that exhibit reversible visible colour upon the application of mechanical stress. The initial CNC-elastomer composite is colourless, but when it is stretched (or compressed), the helical pitch of the chiral nematic structure is reduced to lengths corresponding to the wavelengths of the visible region, resulting in colouration. By increasing the percentage elongation of the material (ca. 50–300%), the structural colour can be tuned from red to blue. The colour of the material was characterised by reflectance optical spectroscopy and reflectance circular dichroism to confirm the wavelength and polarisation of the reflected light.
DOI: 10.6084/m9.figshare.22666426.v1
title: A facile photoinitiated polymerisation route for the preparation of photonic elastomers with chiral nematic order

description: Photonic crystal elastomers that can change colour upon stretching or compression have potential applications in mechanical sensors and optical coatings. However, facile synthetic strategies are required for these materials to be made on a commercially viable scale. To address this issue, we report a photoinitiated polymerisation method to prepare stretchable chiral nematic cellulose nanocrystal (CNC) elastomer composites that exhibit reversible visible colour upon the application of mechanical stress. The initial CNC-elastomer composite is colourless, but when it is stretched (or compressed), the helical pitch of the chiral nematic structure is reduced to lengths corresponding to the wavelengths of the visible region, resulting in colouration. By increasing the percentage elongation of the material (ca. 50–300%), the structural colour can be tuned from red to blue. The colour of the material was characterised by reflectance optical spectroscopy and reflectance circular dichroism to confirm the wavelength and polarisation of the reflected light.
DOI: 10.6084/m9.figshare.21617939
title: Eocene mammal tracks from the southeastern Tibetan Plateau

description: Late Eocene artiodactyl and creodont tracks have been reported from the Jianchuan Basin, southeastern Tibetan Plateau, representing the first and the oldest reported mammal tracks in Yunnan Province, China. Sedimentary facies analysis indicates that tracks from the upper Baoxiangsi Formation and the lower Shuanghe Formation occurred in lake shore and flood plain environments, respectively. Based on the morphological analysis, the artiodactyl tracks from the Baoxiangsi Formation are attributed to <i>Anoplotheriipus zeuctus</i>. Combined with fossil records and morphological characteristics, the artiodactyl and creodont tracks were probably produced by entelodonts and mesonychids, respectively. The superimposition of artiodactyl tracks with varying sizes indicates coexistence of juveniles and adults as well as their gregarious behaviour. The co-occurrence of artiodactyl tracks and creodont tracks suggests the predator–prey relationship and ecological chain during the late Eocene. The presence of mammal tracks in the Jianchuan Basin coincides with the climate change from dry to wet in the late Eocene, implying the climatic and ecological effects of the uplift of the Tibetan Plateau.
DOI: 10.6084/m9.figshare.21617939.v1
title: Eocene mammal tracks from the southeastern Tibetan Plateau

description: Late Eocene artiodactyl and creodont tracks have been reported from the Jianchuan Basin, southeastern Tibetan Plateau, representing the first and the oldest reported mammal tracks in Yunnan Province, China. Sedimentary facies analysis indicates that tracks from the upper Baoxiangsi Formation and the lower Shuanghe Formation occurred in lake shore and flood plain environments, respectively. Based on the morphological analysis, the artiodactyl tracks from the Baoxiangsi Formation are attributed to <i>Anoplotheriipus zeuctus</i>. Combined with fossil records and morphological characteristics, the artiodactyl and creodont tracks were probably produced by entelodonts and mesonychids, respectively. The superimposition of artiodactyl tracks with varying sizes indicates coexistence of juveniles and adults as well as their gregarious behaviour. The co-occurrence of artiodactyl tracks and creodont tracks suggests the predator–prey relationship and ecological chain during the late Eocene. The presence of mammal tracks in the Jianchuan Basin coincides with the climate change from dry to wet in the late Eocene, implying the climatic and ecological effects of the uplift of the Tibetan Plateau.
DOI: 10.6084/m9.figshare.7986494
title: Additional file 1: of DNA methylome profiling of granulosa cells reveals altered methylation in genes regulating vital ovarian functions in polycystic ovary syndrome

description: Hypomethylated CpG sites were representative of 2063 genes. (XLSX 408 kb)
DOI: 10.6084/m9.figshare.7986494.v1
title: Additional file 1: of DNA methylome profiling of granulosa cells reveals altered methylation in genes regulating vital ovarian functions in polycystic ovary syndrome

description: Hypomethylated CpG sites were representative of 2063 genes. (XLSX 408 kb)
DOI: 10.6084/m9.figshare.20038719
title: Reduced bioavailability of cyclosporine A in rats by mung bean seed coat extract

description: Mung bean seed coat (MBSC) is a healthcare product in Asian countries. The aim of this study was to investigate the effect of an MBSC ethanol extract on the bioavailability of cyclosporine A (CsA) in rats. Rats were orally dosed with CsA alone or in combination with MBSC ethanol extracts (500 mg/kg, p.o.). The blood levels of CsA were assayed by liquid chromatography with an electrospray ionization source and tandem mass spectrometry (LC-MS/MS). The everted rat intestinal sac technique was used to determine the influence of MBSC on the absorption of CsA. The results reveal that combined CsA intake with MBSC decreased the Cmax, AUC0-t, t1/2z and MRT0-t values of CsA by 24.96%, 47.28%, 34.73% and 23.58%, respectively (P&lt;0.05), and significantly raised the CL/F by 51.97% (P&lt;0.01). The in vitro results demonstrated that significantly less CsA was absorbed (P&lt;0.05). The overall results indicate that after being concomitantly ingested, MBSC reduced the bioavailability of CsA, at least partially, in the absorption phase.
DOI: 10.6084/m9.figshare.20038731
title: Simultaneous estimation of rosuvastatin and amlodipine in pharmaceutical formulations using stability indicating HPLC method

description: A viable cost-effective and isocratic approach employing C-18 column (250 mm × 4.6 mm, 5 µm) based HPLC has been utilized to separate and estimate the drugs, rosuvastatin, amlodipine and their stress induced degradation products, simultaneously in pharmaceutical formulations. Focused on ICH guideline parameters, the efficient separation of both drugs and their degradation products was achieved by optimizing a 30:70 (v/v) solvent mixture of acetonitrile and 0.1 M ammonium acetate buffer (pH 5) as mobile phase. The flow rate of the mobile phase was 1.5 mL/min and all the detections were carried out at 240 nm using UV detector. The method was linear in the concentration range of 1-200 µg/mL for rosuvastatin with 0.996 coefficient of determination value. For amlodipine, linearity was in the range of 0.5-100 µg/ml with 0.994 coefficient of determination value. Both the drugs along with their degradation products were separated in less than twenty minutes. The results of within-day and between-day precision were varied from 0.72 to 1.81% for rosuvastatin and 0.83 to 1.88% for amlodipine. The results show that this ICH validated method can be employed successfully for the routine as well as stability quantification of both the active ingredients simultaneously in pharmaceutical formulations.
DOI: 10.6084/m9.figshare.19514451
title: Managing retrial queueing systems with boundedly rational customers

description: Bounded rationality includes potential cognitive deficits that limit human rational behaviour. In this paper, we allow for estimation errors of their utility and consider bounded rationality in queueing models with retrials. Upon arrival, customers decide whether to join the system based on their perceived utility, and their choice behaviour is characterised by a logit choice model. For a revenue-seeking server and a social planner, we investigate corresponding optimal pricing strategies. We find that the revenue-optimal price is no longer socially efficient in general but depends on the retrial rate. There exists a threshold such that the socially optimal price is greater than the revenue-optimal one when the retrial rate is below this threshold; otherwise, the revenue-optimal price is greater. A larger bounded rationality widens the gap between social welfare under the revenue- and socially optimal prices. Furthermore, the server’s revenue may increase or first decrease and then increase with respect to customers’ rationality levels, and the server may find it beneficial to reveal waiting time information when customers’ rationality is high. Finally, failing to account for customers’ bounded rationality can lead a significant revenue loss for the server and the proportion of such a revenue loss is close to 1 as customers become fully boundedly rational.
DOI: 10.6084/m9.figshare.22655441.v1
title: Additional file 15 of Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data

description: Additional file 15: Table S20. GO enrichment for co-eGenes associated with the same eQTL, variation of Supplementary Table 14 with a stricter background
DOI: 10.6084/m9.figshare.24763752
title: City Labour Attraction Statistics

description: Flow intention reflected by job search and job postings.
DOI: 10.6084/m9.figshare.21618087
title: Genome assembly and annotation

description: genome assembly and annotation
DOI: 10.6084/m9.figshare.24763902
title: HGNNPIP: A Hybrid Graph Neural Network framework for Protein-protein Interaction Prediction

description: A deep understanding of Protein-protein interactions (PPIs) can provide comprehensive insights into many biological functions, thereby facilitating drug target identification and novel therapeutic design. Recent developments in artificial intelligence (AI)-driven computational methods have enabled the discovery of previously uncharacterized PPIs from large-scale interactome datasets. Almost all existing machine learning methods rely on Subcellular Localization (SL) to construct balanced datasets based on positive interactions to achieve predictions. Despite high fitting accuracy, the generalization ability of these models is questionable. To solve this problem, we analyzed existing methods and found that the high false positives in these methods are due to the bias in data distribution caused by SL. Therefore, we proposed a new strategy for negative instance sampling in PPI prediction and developed a Hybrid Graph Neural Network framework for Protein-protein Interaction Prediction (HGNNPIP). The experimental results showed that HGNNPIP works well on six benchmark datasets. Comparison analysis demonstrated that our model outperformed the other four existing methods. We also used HGNNPIP to explore the molecular contacts involved in the rice-pathogen interaction system. In vivo experiments confirmed multiple regulations related to disease resistance in rice. In summary, this study provides new insights into establishing a computational framework for PPI prediction with high reliability.
DOI: 10.6084/m9.figshare.14266765
title: Additional file 3 of Revealing taxon-specific heavy metal-resistance mechanisms in denitrifying phosphorus removal sludge using genome-centric metaproteomics

description: Additional file 2: Supplementary dataset. The quality metrics, taxonomy, and abundance of MAGs.
DOI: 10.6084/m9.figshare.16899998
title: Generalized Factor Model for Ultra-High Dimensional Correlated Variables with Mixed Types

description: As high-dimensional data measured with mixed-type variables gradually become prevalent, it is particularly appealing to represent those mixed-type high-dimensional data using a much smaller set of so-called factors. Due to the limitation of the existing methods for factor analysis that deal with only continuous variables, in this article, we develop a generalized factor model, a corresponding algorithm and theory for ultra-high dimensional mixed types of variables where both the sample size <i>n</i> and variable dimension <i>p</i> could diverge to infinity. Specifically, to solve the computational problem arising from the non-linearity and mixed types, we develop a two-step algorithm so that each update can be carried out in parallel across variables and samples by using an existing package. Theoretically, we establish the rate of convergence for the estimators of factors and loadings in the presence of nonlinear structure accompanied with mixed-type variables when both <i>n</i> and <i>p</i> diverge to infinity. Moreover, since the correct specification of the number of factors is crucial to both the theoretical and the empirical validity of factor models, we also develop a criterion based on a penalized loss to consistently estimate the number of factors under the framework of a generalized factor model. To demonstrate the advantages of the proposed method over the existing ones, we conducted extensive simulation studies and also applied it to the analysis of the NFBC1966 dataset and a cardiac arrhythmia dataset, resulting in more predictive and interpretable estimators for loadings and factors than the existing factor model.