cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12844389.v2
title: Improving Dose-Finding for New Agents as Monotherapy and Add-On Therapy

description: With the recent advancement in immuno-oncology, next-stage early oncology development is focusing on identifying the best combinations of established immunotherapies with new agents to either overcome drug resistance or achieve synergic effects. Although the combination is the focus, safety profile of the new agent alone must be explored. Therefore, many trials have both monotherapy and add-on combination therapy arms. Finding the maximum tolerable dose (MTD) for the new agent in both arms is critical. Traditional oncology dose-finding methods and MTD estimation algorithm do not handle the correlation and interplay between the two arms and the selected MTDs may contradict with each other. To overcome these issues, we applied a two-dimensional pool-adjacent-violators algorithm to MTD estimation and modified the standard Bayesian optimal interval design (BOIN) to allow for information flow between arms during dose-finding. We also showed that a naïve adaptation of standard BOIN that is much simpler to implement demonstrated empirically similar performance. These new approaches were assessed with simulations and demonstrated improvement for trials with both monotherapy and add-on combination therapy arms. Albeit proposed in the context with immunotherapy as the backbone drug, our approaches can be applied to any new agent in combination with a fixed dose of another drug. Supplementary materials for this article are available online.
DOI: 10.5281/zenodo.10663333
title: Descriptive statistics supplement: Influence of shoulder morphology and rotator cuff tear type on load-induced glenohumeral biomechanics – a Sawbone simulator study

description: The dataset "descriptive_statistics.xlsx" contains the desctiptive statistics for our planned publication with the title: Influence of shoulder morphology and rotator cuff tear type on load-induced glenohumeral biomechanics – a Sawbone simulator study
DOI: 10.6084/m9.figshare.19135913
title: Additional file 3 of Dual CRISPR interference and activation for targeted reactivation of X-linked endogenous FOXP3 in human breast cancer cells

description: Additional file 3: Table S1. Gene copy number, mutation and expression of the FOXP3 gene in human breast cancer cell lines
DOI: 10.6084/m9.figshare.19135913.v1
title: Additional file 3 of Dual CRISPR interference and activation for targeted reactivation of X-linked endogenous FOXP3 in human breast cancer cells

description: Additional file 3: Table S1. Gene copy number, mutation and expression of the FOXP3 gene in human breast cancer cell lines
DOI: 10.6084/m9.figshare.19135919
title: Additional file 4 of Dual CRISPR interference and activation for targeted reactivation of X-linked endogenous FOXP3 in human breast cancer cells

description: Additional file 4: Table S2. CRISPR/dCas9-KRAB-, VPR-, XIST-sgRNA, and FOXP3-sgRNA stably expressed cell models
DOI: 10.6084/m9.figshare.19135919.v1
title: Additional file 4 of Dual CRISPR interference and activation for targeted reactivation of X-linked endogenous FOXP3 in human breast cancer cells

description: Additional file 4: Table S2. CRISPR/dCas9-KRAB-, VPR-, XIST-sgRNA, and FOXP3-sgRNA stably expressed cell models
DOI: 10.6084/m9.figshare.19135925
title: Additional file 5 of Dual CRISPR interference and activation for targeted reactivation of X-linked endogenous FOXP3 in human breast cancer cells

description: Additional file 5: Table S3a. The potential off-targets of FOXP3 accessed using the Cas-OFFinder off-target searching tool. b. The potential off-targets of XIST accessed using the Cas-OFFinder off-target searching tool. c. The potential mismatch ≤4 off-target regions accessed using the Cas-OFFinder off-target searching tool. d. The potential mismatch ≤4 off-target regions accessed using the Cas-OFFinder off-target searching tool.
DOI: 10.6084/m9.figshare.19135925.v1
title: Additional file 5 of Dual CRISPR interference and activation for targeted reactivation of X-linked endogenous FOXP3 in human breast cancer cells

description: Additional file 5: Table S3a. The potential off-targets of FOXP3 accessed using the Cas-OFFinder off-target searching tool. b. The potential off-targets of XIST accessed using the Cas-OFFinder off-target searching tool. c. The potential mismatch ≤4 off-target regions accessed using the Cas-OFFinder off-target searching tool. d. The potential mismatch ≤4 off-target regions accessed using the Cas-OFFinder off-target searching tool.
DOI: 10.6084/m9.figshare.19135928
title: Additional file 6 of Dual CRISPR interference and activation for targeted reactivation of X-linked endogenous FOXP3 in human breast cancer cells

description: Additional file 6: Table S4. CRISPR/dCas9 DNA constructs for targeted repression of XIST and activation of FOXP3
DOI: 10.6084/m9.figshare.19135928.v1
title: Additional file 6 of Dual CRISPR interference and activation for targeted reactivation of X-linked endogenous FOXP3 in human breast cancer cells

description: Additional file 6: Table S4. CRISPR/dCas9 DNA constructs for targeted repression of XIST and activation of FOXP3
DOI: 10.6084/m9.figshare.19135931
title: Additional file 7 of Dual CRISPR interference and activation for targeted reactivation of X-linked endogenous FOXP3 in human breast cancer cells

description: Additional file 7: Table S5. The sequences of PCR primers and CRISPR sgRNAs used in this study
DOI: 10.6084/m9.figshare.19135931.v1
title: Additional file 7 of Dual CRISPR interference and activation for targeted reactivation of X-linked endogenous FOXP3 in human breast cancer cells

description: Additional file 7: Table S5. The sequences of PCR primers and CRISPR sgRNAs used in this study
DOI: 10.6084/m9.figshare.19135934
title: Additional file 8 of Dual CRISPR interference and activation for targeted reactivation of X-linked endogenous FOXP3 in human breast cancer cells

description: Additional file 8: Table S6. Specific primary antibodies used in this study
DOI: 10.6084/m9.figshare.19135934.v1
title: Additional file 8 of Dual CRISPR interference and activation for targeted reactivation of X-linked endogenous FOXP3 in human breast cancer cells

description: Additional file 8: Table S6. Specific primary antibodies used in this study
DOI: 10.6084/m9.figshare.12844517
title: An Efficient Algorithm for Minimizing Multi Non-Smooth Component Functions

description: Many problems in statistics and machine learning can be formulated as an optimization problem of a finite sum of nonsmooth convex functions. We propose an algorithm to minimize this type of objective functions based on the idea of alternating linearization. Our algorithm retains the simplicity of contemporary methods without any restrictive assumptions on the smoothness of the loss function. We apply our proposed method to solve two challenging problems: overlapping group lasso and convex regression with sharp partitions. Numerical experiments show that our method is superior to the state-of-the-art algorithms, many of which are based on the accelerated proximal gradient method. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.12844517.v1
title: An efficient algorithm for minimizing multi non-smooth component functions

description: Many problems in statistics and machine learning can be formulated as an optimization problem of a finite sum of non-smooth convex functions. We propose an algorithm to minimize this type of objective functions based on the idea of alternating linearization. Our algorithm retains the simplicity of contemporary methods without any restrictive assumptions on the smoothness of the loss function. We apply our proposed method to solve two challenging problems: overlapping group Lasso and convex regression with sharp partitions (CRISP). Numerical experiments show that our method is superior to the state-of-the-art algorithms, many of which are based on the accelerated proximal gradient method.
DOI: 10.6084/m9.figshare.12844517.v2
title: An Efficient Algorithm for Minimizing Multi Non-Smooth Component Functions

description: Many problems in statistics and machine learning can be formulated as an optimization problem of a finite sum of nonsmooth convex functions. We propose an algorithm to minimize this type of objective functions based on the idea of alternating linearization. Our algorithm retains the simplicity of contemporary methods without any restrictive assumptions on the smoothness of the loss function. We apply our proposed method to solve two challenging problems: overlapping group lasso and convex regression with sharp partitions. Numerical experiments show that our method is superior to the state-of-the-art algorithms, many of which are based on the accelerated proximal gradient method. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.12844526
title: Sparse Single Index Models for Multivariate Responses

description: Joint models are popular for analyzing data with multivariate responses. We propose a sparse multivariate single index model, where responses and predictors are linked by unspecified smooth functions and multiple matrix level penalties are employed to select predictors and induce low-rank structures across responses. An alternating direction method of multipliers based algorithm is proposed for model estimation. We demonstrate the effectiveness of proposed model in simulation studies and an application to a genetic association study. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.12844526.v2
title: Sparse Single Index Models for Multivariate Responses

description: Joint models are popular for analyzing data with multivariate responses. We propose a sparse multivariate single index model, where responses and predictors are linked by unspecified smooth functions and multiple matrix level penalties are employed to select predictors and induce low-rank structures across responses. An alternating direction method of multipliers based algorithm is proposed for model estimation. We demonstrate the effectiveness of proposed model in simulation studies and an application to a genetic association study. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.12844526.v1
title: Sparse Single Index Models for Multivariate Responses

description: Joint models are popular for analyzing data with multivariate responses. We propose a sparse multivariate single index model, where responses and predictors are linked by unspecified smooth functions and multiple matrix level penalties are employed to select predictors and induce low-rank structures across responses. An alternating direction method of multipliers based algorithm is proposed for model estimation. We demonstrate the effectiveness of proposed model in simulation studies and an application to a genetic association study. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.12844529
title: MCVIS: A New Framework for Collinearity Discovery, Diagnostic, and Visualization

description: Collinearity discovery through diagnostic tools is an important analysis step when performing linear regression. Despite their wide-spread use, collinearity indices such as the variance inflation factor and the condition number have limitations and may not be effective in some applications. In this article, we will contribute to the study of conventional collinearity indices through theoretical and empirical work. We will present mcvis, a new framework that uses resampling techniques to repeatedly learn from these conventional collinearity indices to better understand the causes of collinearity. Our framework is made available in R through the mcvis package which includes new collinearity measures and visualizations, in particular a bipartite plot that informs on the degree and structure of collinearity. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.12844529.v1
title: MCVIS: A New Framework for Collinearity Discovery, Diagnostic, and Visualization

description: Collinearity discovery through diagnostic tools is an important analysis step when performing linear regression. Despite their wide-spread use, collinearity indices such as the variance inflation factor and the condition number have limitations and may not be effective in some applications. In this article, we will contribute to the study of conventional collinearity indices through theoretical and empirical work. We will present mcvis, a new framework that uses resampling techniques to repeatedly learn from these conventional collinearity indices to better understand the causes of collinearity. Our framework is made available in R through the mcvis package which includes new collinearity measures and visualizations, in particular a bipartite plot that informs on the degree and structure of collinearity. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.7867478
title: Additional file 4: of Identifying and exploiting gene-pathway interactions from RNA-seq data for binary phenotype

description: The enriched KEGG pathways from three algorithms. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.7867478.v1
title: Additional file 4: of Identifying and exploiting gene-pathway interactions from RNA-seq data for binary phenotype

description: The enriched KEGG pathways from three algorithms. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.19135955
title: Additional file 1 of Effects of in ovo delivered xylo- and mannan- oligosaccharides on growth performance, intestinal immunity, cecal short-chain fatty acids, and cecal microbiota of broilers

description: Additional file 1 Table S1 Spearman’s correlation between growth performance parameters and major short-chain fatty acids in each treatment in broilers at d 28 post-hatch. Fig. S1 Biplot (individual samples scatter removed) from principal component (PC) analysis of growth performance parameters and the major cecal short-chain fatty acids showing correlations among these variables in different treatment groups in two PC (PC 1 and PC 2). The PC percentage on the x and y-axis indicates the proportions of the variability of the data explained by those components. The angle between the loading arrows and their directions indicates negative, positive, or no association, while the length indicates the value of correlation (e.g., α = 0° and r = 1; α = 90° and r = 0; and α = 180° and r = − 1). See Table S1 for the significant spearman’s correlation coefficient. ADFI: average daily feed intake, ADG: average daily gain, FCR: feed conversion ratio, FBW: final body weight. NSC: normal saline, XOS3: xylotriose, XOS4: xylotetraose, MOS3: mannotriose, MOS4: mannotetraose, NIC: no injection control.
DOI: 10.6084/m9.figshare.19135955.v1
title: Additional file 1 of Effects of in ovo delivered xylo- and mannan- oligosaccharides on growth performance, intestinal immunity, cecal short-chain fatty acids, and cecal microbiota of broilers

description: Additional file 1 Table S1 Spearman’s correlation between growth performance parameters and major short-chain fatty acids in each treatment in broilers at d 28 post-hatch. Fig. S1 Biplot (individual samples scatter removed) from principal component (PC) analysis of growth performance parameters and the major cecal short-chain fatty acids showing correlations among these variables in different treatment groups in two PC (PC 1 and PC 2). The PC percentage on the x and y-axis indicates the proportions of the variability of the data explained by those components. The angle between the loading arrows and their directions indicates negative, positive, or no association, while the length indicates the value of correlation (e.g., α = 0° and r = 1; α = 90° and r = 0; and α = 180° and r = − 1). See Table S1 for the significant spearman’s correlation coefficient. ADFI: average daily feed intake, ADG: average daily gain, FCR: feed conversion ratio, FBW: final body weight. NSC: normal saline, XOS3: xylotriose, XOS4: xylotetraose, MOS3: mannotriose, MOS4: mannotetraose, NIC: no injection control.
DOI: 10.6084/m9.figshare.24903348
title: CXADR promote epithelial–mesenchymal transition in endometriosis by modulating AKT/GSK-3β signaling

description: Endometriosis is a benign high prevalent disease exhibiting malignant features. However, the underlying pathogenesis and key molecules of endometriosis remain unclear. By integrating and analysis of existing expression profile datasets, we identified coxsackie and adenovirus receptor (CXADR), as a novel key gene in endometriosis. Based on the results of immunohistochemistry (IHC), we confirmed significant down-regulation of CXADR in ectopic endometrial tissues obtained from women with endometriosis compared with healthy controls. Further <i>in vitro</i> investigation indicated that CXADR regulated the stability and function of the phosphatases and AKT inhibitors PHLPP2 (pleckstrin homology domain and leucine-rich repeat protein phosphatase 2) and PTEN (phosphatase and tensin homolog). Loss of CXADR led to phosphorylation of AKT and glycogen synthase kinase-3β (GSK-3β), which resulted in stabilization of an epithelial–mesenchymal transition (EMT) factor, SNAIL1 (snail family transcriptional repressor 1). Therefore, EMT processs was induced, and the proliferation, migration and invasion of Ishikawa cells were enhanced. Over-expression of CXADR showed opposite effects. These findings suggest a previously undefined role of AKT/GSK-3β signaling axis in regulating EMT and reveal the involvement of a CXADR-induced EMT, in pathogenic progression of endometriosis.
DOI: 10.6084/m9.figshare.24903348.v1
title: CXADR promote epithelial–mesenchymal transition in endometriosis by modulating AKT/GSK-3β signaling

description: Endometriosis is a benign high prevalent disease exhibiting malignant features. However, the underlying pathogenesis and key molecules of endometriosis remain unclear. By integrating and analysis of existing expression profile datasets, we identified coxsackie and adenovirus receptor (CXADR), as a novel key gene in endometriosis. Based on the results of immunohistochemistry (IHC), we confirmed significant down-regulation of CXADR in ectopic endometrial tissues obtained from women with endometriosis compared with healthy controls. Further <i>in vitro</i> investigation indicated that CXADR regulated the stability and function of the phosphatases and AKT inhibitors PHLPP2 (pleckstrin homology domain and leucine-rich repeat protein phosphatase 2) and PTEN (phosphatase and tensin homolog). Loss of CXADR led to phosphorylation of AKT and glycogen synthase kinase-3β (GSK-3β), which resulted in stabilization of an epithelial–mesenchymal transition (EMT) factor, SNAIL1 (snail family transcriptional repressor 1). Therefore, EMT processs was induced, and the proliferation, migration and invasion of Ishikawa cells were enhanced. Over-expression of CXADR showed opposite effects. These findings suggest a previously undefined role of AKT/GSK-3β signaling axis in regulating EMT and reveal the involvement of a CXADR-induced EMT, in pathogenic progression of endometriosis.
DOI: 10.6084/m9.figshare.24903351
title: <i>SMAD7</i> gene polymorphisms and their influence on patients with colorectal cancer

description: Colorectal cancer (CRC) is a prevalent malignant tumor, and its pathogenesis is still not fully understood. Studies have shown that <i>SMAD7</i> gene polymorphisms can affect CRC susceptibility, but the results have been inconsistent and require additional confirmation. Our study aimed to evaluate the effect of <i>SMAD7</i> variants on the risk of CRC in the Chinese Han population. A total of five single nucleotide polymorphisms (SNPs) in <i>SMAD7</i> were genotyped among 696 CRC patients and 696 healthy participants using the MassARRAY iPLEX platform. SNPs were evaluated for their associations with CRC using logistic regression analysis under multiple genetic models. The false-positive report probability (FPRP) analysis was used to validate the positive findings. Our study indicated that rs11874392 showed an increased association with CRC risk (odds ratio, 1.31; 95% confidence interval, 1.04–1.67; <i>p</i> = 0.024). Stratified analysis showed that rs11874392 might increase the risk of CRC in females (OR = 1.70, <i>p</i> = 0.028), individuals with smoking (OR = 1.87, <i>p</i> = 0.026), and drinking (OR = 1.38, <i>p</i> = 0.027). The rs11874392 was found to be related to an elevated risk of rectal cancer (OR = 1.73, <i>p</i> = 0.003), but not with colon cancer. FPRP analysis demonstrated that all of these associations were statistically significant (FPRP &lt;0.2). Additionally, rs11874392 was the strongest predictive model for CRC. This study provides evidence that the <i>SMAD7</i> rs11874392 is related to an increased susceptibility to CRC.
DOI: 10.6084/m9.figshare.24903351.v1
title: <i>SMAD7</i> gene polymorphisms and their influence on patients with colorectal cancer

description: Colorectal cancer (CRC) is a prevalent malignant tumor, and its pathogenesis is still not fully understood. Studies have shown that <i>SMAD7</i> gene polymorphisms can affect CRC susceptibility, but the results have been inconsistent and require additional confirmation. Our study aimed to evaluate the effect of <i>SMAD7</i> variants on the risk of CRC in the Chinese Han population. A total of five single nucleotide polymorphisms (SNPs) in <i>SMAD7</i> were genotyped among 696 CRC patients and 696 healthy participants using the MassARRAY iPLEX platform. SNPs were evaluated for their associations with CRC using logistic regression analysis under multiple genetic models. The false-positive report probability (FPRP) analysis was used to validate the positive findings. Our study indicated that rs11874392 showed an increased association with CRC risk (odds ratio, 1.31; 95% confidence interval, 1.04–1.67; <i>p</i> = 0.024). Stratified analysis showed that rs11874392 might increase the risk of CRC in females (OR = 1.70, <i>p</i> = 0.028), individuals with smoking (OR = 1.87, <i>p</i> = 0.026), and drinking (OR = 1.38, <i>p</i> = 0.027). The rs11874392 was found to be related to an elevated risk of rectal cancer (OR = 1.73, <i>p</i> = 0.003), but not with colon cancer. FPRP analysis demonstrated that all of these associations were statistically significant (FPRP &lt;0.2). Additionally, rs11874392 was the strongest predictive model for CRC. This study provides evidence that the <i>SMAD7</i> rs11874392 is related to an increased susceptibility to CRC.
DOI: 10.6084/m9.figshare.12844864
title: Synthesis, crystal structure, Hirshfeld surface analysis, DNA binding, DNA cleavage activity and molecular docking of a new Schiff base nickel(II) complex

description: A mononuclear nickel(II) complex, [Ni(<i>o</i>-van-tris)<sub>2</sub>]·2H<sub>2</sub>O (<i>o</i>-van-tris = Schiff base derived from <i>o</i>-vanillin and tris(hydroxymethyl)aminomethane), has been synthesized and structurally characterized. The single crystal structure shows a distorted octahedron geometry coordinated with Ni(II) atom, and 2 D plane structure has formed by O–H···O hydrogen bond interactions. An analysis to ascertain intermolecular interactions of the complex was performed based on the Hirshfeld surfaces and their associated two-dimensional fingerprint plots. The binding properties of the nickel(II) complex with CT-DNA have been investigated by spectroscopic methods and molecular docking. Absorption and fluorescence spectral studies reveal that the complex interacts with DNA through hydrogen bond and hydrophobic interactions with the DNA base pairs. Molecular docking studies show that the complex effectively docks in the major groove of DNA. The DNA cleavage experiment was performed by gel electrophoretic assay, indicating that DNA cleavage activity of the complex is concentration dependent and much sensitive to ionic strength. The efficient cleavage mediated via hydrolytically cleaving pathway. Communicated by Ramaswamy H. Sarma