cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12671558
title: Additional file 3 of Integrating RNA-Seq with GWAS reveals novel insights into the molecular mechanism underpinning ketosis in cattle

description: Additional file 3: Table S3. Gene Ontology (GO) enrichment analysis of five gene modules.
DOI: 10.6084/m9.figshare.12671558.v1
title: Additional file 3 of Integrating RNA-Seq with GWAS reveals novel insights into the molecular mechanism underpinning ketosis in cattle

description: Additional file 3: Table S3. Gene Ontology (GO) enrichment analysis of five gene modules.
DOI: 10.6084/m9.figshare.16866145.v2
title: Balancing socioeconomic development with ecological conservation towards rural sustainability: a case study in semiarid rural China

description: Despite the dramatic progress in poverty reduction, China‘s vast rural areas of backwardness, environmental degradation and low labour productivity are a long-standing challenge to achieve common prosperity and sustainable development. Finding a balance between ecological conservation and socioeconomic development is a solution. However, previous studies have largely neglected the concept. Here, we proposed a framework that integrates the ecological environment and socioeconomic wellbeing via farm management and the use of ecosystem services (ES) to assess rural sustainability and explore a suitable balance and pathways from the perspective of the human dimension. Taking Yan’he Township in China’s Loess Plateau as an example, a clustering analysis was performed to group farm households based on their behaviour in cropping, land rental, and off-farm work. A composite index was built to assess rural sustainability at the farm household level, while a structural equation model was performed to estimate the effect of land-use practices on rural sustainability and explore adequate farm management and policy interventions. The results show that households with different farm management and land-use strategies had divergent agricultural performance, use of ES, and environmental and wellbeing outcomes. Increasing legume cropping with conservation approaches (e.g., rotation) and extended irrigation while encouraging migrant work with ensured equal urban-rural social welfare and property rights may contribute to balancing socioeconomic development with ecological conservation. The findings indicate that both interventionist policies and independent market support are vital for individual and community capacity building and public infrastructure development to stimulate agricultural adaptation and rural transformation towards sustainability.
DOI: 10.6084/m9.figshare.7428563
title: Additional file 6: of NmeCas9 is an intrinsically high-fidelity genome-editing platform

description: Table S4. Summary of potential off-target sites detected by SITE-seq analysis. The table includes sites for both NmeCas9 and SpyCas9 for the DTS3, DTS7 and DTS8 sgRNAs, as well as for other sgRNAs used in this study. (XLSX 3308 kb)
DOI: 10.6084/m9.figshare.12671561.v1
title: Additional file 4 of Integrating RNA-Seq with GWAS reveals novel insights into the molecular mechanism underpinning ketosis in cattle

description: Additional file 4: Table S4. Tissue enrichment analysis of all gene modules.
DOI: 10.6084/m9.figshare.22626212
title: Additional file 9 of SRSF1 regulates primordial follicle formation and number determination during meiotic prophase I

description: Additional file 9. Individual data values.
DOI: 10.6084/m9.figshare.12671570
title: Additional file 7 of Integrating RNA-Seq with GWAS reveals novel insights into the molecular mechanism underpinning ketosis in cattle

description: Additional file 7: Table S6. Phenome-wide analysis results for five candidate genes.
DOI: 10.6084/m9.figshare.12671570.v1
title: Additional file 7 of Integrating RNA-Seq with GWAS reveals novel insights into the molecular mechanism underpinning ketosis in cattle

description: Additional file 7: Table S6. Phenome-wide analysis results for five candidate genes.
DOI: 10.6084/m9.figshare.12671552.v1
title: Additional file 1 of Integrating RNA-Seq with GWAS reveals novel insights into the molecular mechanism underpinning ketosis in cattle

description: Additional file 1: Table S1. Summary of RNA-Seq data mapping information.
DOI: 10.6084/m9.figshare.12671555
title: Additional file 2 of Integrating RNA-Seq with GWAS reveals novel insights into the molecular mechanism underpinning ketosis in cattle

description: Additional file 2: Table S2. Summary of seven blood bio-indicators across 24 samples.
DOI: 10.6084/m9.figshare.12671555.v1
title: Additional file 2 of Integrating RNA-Seq with GWAS reveals novel insights into the molecular mechanism underpinning ketosis in cattle

description: Additional file 2: Table S2. Summary of seven blood bio-indicators across 24 samples.
DOI: 10.5281/zenodo.10635338
title: DMLR @ ICLR 2024 Dataset for Arbitrary Threshold-Confidence Decisions Paper

description: Use the most recent up-to-date version in the right-hand sidebar of this page.

 

This dataset contains the data needed to recreate the machine learning evaluations contained in the paper Arbitrary Threshold-Confidence Decisions in Digital Hardware Design via Binary Classification Trees.
DOI: 10.5281/zenodo.10635339
title: DMLR @ ICLR 2024 Dataset for Arbitrary Threshold-Confidence Decisions Paper

description: Use the most recent up-to-date version in the right-hand sidebar of this page.

 

This dataset contains the data needed to recreate the machine learning evaluations contained in the paper Arbitrary Threshold-Confidence Decisions in Digital Hardware Design via Binary Classification Trees.
DOI: 10.6084/m9.figshare.20011750.v1
title: ROLE OF ENTERPRISE ARCHITECTURE IN HEALTHCARE ORGANIZATIONS AND KNOWLEDGE-BASED MEDICAL DIAGNOSIS SYSTEM

description: ABSTRACT Enterprise architecture (EA) is a tool that aligns organization’s business-process with application and information technology (IT) through EAmodels. This EA model allows the organization to cut off unnecessary IT expenses and determines the future and current IT requirements and boosts organizational performance. Enterprise architecture may be employed in every firm where the firm or organization requires configurations between information technology and business functions. This research investigates the role of enterprise architecture in healthcare organizations and suggests the suitable EA framework for knowledge-based medical diagnostic system for EA modeling by comparing the two most widely used EA frameworks. The results of the comparison identified that the proposed EA has a better framework for knowledge-based medical diagnostic system.
DOI: 10.6084/m9.figshare.22626311.v1
title: Additional file 2 of Selenite as a dual apoptotic and ferroptotic agent synergizes with EGFR and KRAS inhibitors with epigenetic interference

description: Additional file 2: Table S1 Antibodies used in this study. Table S2 Primers for RT-qPCR.
DOI: 10.6084/m9.figshare.7428767.v1
title: Additional file 2: of Anticipatory parental effects in a subtropical lizard in response to experimental warming

description: Data used in this study. (XLSX 90 kb)
DOI: 10.6084/m9.figshare.12671522.v1
title: Additional file 1 of LINC00667/miR-449b-5p/YY1 axis promotes cell proliferation and migration in colorectal cancer

description: Additional file 1: Table S1. Ct value for GAPDH and LINC00667.
DOI: 10.6084/m9.figshare.7428848
title: Additional file 4: of STON2 negatively modulates stem-like properties in ovarian cancer cells via DNMT1/MUC1 pathway

description: Table S3. Peptide information from the LC-MS/MS data after analyzing parental cells and spheroids of 3AO cells (FDRâ &lt;â 0.05). Av. Ratio (Lin): the ratio of spheroids to parental cells. (XLS 154 kb)
DOI: 10.6084/m9.figshare.7429154
title: Additional file 8: of Profiling the miRNA-mRNA-lncRNA interaction network in MSC osteoblast differentiation induced by (+)-cholesten-3-one

description: Primer sequences used for qRT-PCR. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.7429169
title: Additional file 1: of Intestinal microbiota mediates Enterotoxigenic Escherichia coli-induced diarrhea in piglets

description: S1. A total of 6 KEGG entries were identified at KEGG level one. S2. A total of 37 KEGG entries were identified at KEGG level two. S3. A total of 236 KEGG Orthology (KO) pathways were identified at KEGG level three. (XLSX 70 kb)
DOI: 10.6084/m9.figshare.7428767
title: Additional file 2: of Anticipatory parental effects in a subtropical lizard in response to experimental warming

description: Data used in this study. (XLSX 90 kb)
DOI: 10.6084/m9.figshare.7428848.v1
title: Additional file 4: of STON2 negatively modulates stem-like properties in ovarian cancer cells via DNMT1/MUC1 pathway

description: Table S3. Peptide information from the LC-MS/MS data after analyzing parental cells and spheroids of 3AO cells (FDRâ &lt;â 0.05). Av. Ratio (Lin): the ratio of spheroids to parental cells. (XLS 154 kb)
DOI: 10.6084/m9.figshare.22626349
title: Additional file 1 of Alternative signal pathways underly fertilization and egg activation in a fish with contrasting modes of spawning

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.11106239
title: Identification of novel CDK2 inhibitors by a multistage virtual screening method based on SVM, pharmacophore and docking model

description: Cyclin-dependent kinase 2 (CDK2) is the family of Ser/Thr protein kinases that has emerged as a highly selective with low toxic cancer therapy target. A multistage virtual screening method combined by SVM, protein-ligand interaction fingerprints (PLIF) pharmacophore and docking was utilised for screening the CDK2 inhibitors. The evaluation of the validation set indicated that this method can be used to screen large chemical databases because it has a high hit-rate and enrichment factor (80.1% and 332.83 respectively). Six compounds were screened out from NCI, Enamine and Pubchem database. After molecular dynamics and binding free energy calculation, two compounds had great potential as novel CDK2 inhibitors and they also showed selective inhibition against CDK2 in the kinase activity assay.
DOI: 10.6084/m9.figshare.11106239.v1
title: Identification of novel CDK2 inhibitors by a multistage virtual screening method based on SVM, pharmacophore and docking model

description: Cyclin-dependent kinase 2 (CDK2) is the family of Ser/Thr protein kinases that has emerged as a highly selective with low toxic cancer therapy target. A multistage virtual screening method combined by SVM, protein-ligand interaction fingerprints (PLIF) pharmacophore and docking was utilised for screening the CDK2 inhibitors. The evaluation of the validation set indicated that this method can be used to screen large chemical databases because it has a high hit-rate and enrichment factor (80.1% and 332.83 respectively). Six compounds were screened out from NCI, Enamine and Pubchem database. After molecular dynamics and binding free energy calculation, two compounds had great potential as novel CDK2 inhibitors and they also showed selective inhibition against CDK2 in the kinase activity assay.
DOI: 10.6084/m9.figshare.12671561
title: Additional file 4 of Integrating RNA-Seq with GWAS reveals novel insights into the molecular mechanism underpinning ketosis in cattle

description: Additional file 4: Table S4. Tissue enrichment analysis of all gene modules.
DOI: 10.6084/m9.figshare.12671564
title: Additional file 5 of Integrating RNA-Seq with GWAS reveals novel insights into the molecular mechanism underpinning ketosis in cattle

description: Additional file 5 Table S5. Connectivity, significance and membership of genes in modules.
DOI: 10.6084/m9.figshare.10057715
title: MOESM1 of Comparative transcriptome and metabolome analyses provide new insights into the molecular mechanisms underlying taproot thickening in Panax notoginseng

description: Additional file 1: Table S1. The pairwise compared DEGs of four developmental stages in P.Â notoginseng taproots.
DOI: 10.25934/00005984
title: Exploring possibilities to improve the risk: benefit balance through analysis of the ocrelizumab phase II extension study 

description: Multiple sclerosis is the major demyelinating disease of the central nervous system. Although considered to be a T cell-mediated autoimmune disease it has been shown that CD20 B cell– depleting antibodies exhibit high efficacy in the control of relapsing MS. We have recently suggested that all current MS drugs act because they target memory B cells, a subset of B cells within the CD20 population. Although the B cell subset depletion potential of ocrelizumab has not been reported, we know that other similar agents deplete memory B cells for months to years.

However, ocrelizumab treatment is given every six months to ensure that all B cells are depleted at a time when there may not be any CD20 positive memory B cells present in the circulation.

Memory B cell depletion can last for years and suggests that treatment effects may therefore last for years also, as found with other multiple sclerosis drugs that similarly deplete memory B cells. Therefore, it may be possible to achieve similar benefit with less frequent drug administration and thus avoiding or reducing potential drug-related side-effects, particularly as it is known that total B cell elimination leaves one susceptible to serious infection.

This study examines the long-term effect, at least 18 months, of a short-term treatment cycle and may provide information on the duration of efficacy and information of the durability of the lymphocyte depletion. Although the study was done many years ago it has not been reported fully, yet based on scientific meetings reports found in the public domain, there may be durability of efficacy offering the possibility of a drug-free pregnancy, and provides insight on how ocrelizumab may be working.

The objective of the study is to examine whether ocrelizumab has a durability of action longer than 6 months and to obtain data that will help to justify future studies that can may make ocrelizumab even safer.
DOI: 10.5281/zenodo.8407779
title: The files for "RlmI-c-di-GMP" molecular dynamics simulation

description: The crystal structure files (protein RlmI), MD simulation files (input files, parameter files, topology files etc) and structures of c-Di-GMP.
DOI: 10.5281/zenodo.8407778
title: The files for "RlmI-c-di-GMP" molecular dynamics simulation

description: The crystal structure files (protein RlmI), MD simulation files (input files, parameter files, topology files etc) and structures of c-Di-GMP.
DOI: 10.26030/h013-6y72
title: Toward countering muscle and bone loss with spaceflight: GSK3 as a potential target (Tibia, RR9 and HLU, MicroCT and DXA Scanning)

description: We examined the effects of ~30 days of spaceflight on glycogen synthase kinase 3 (GSK3) content and inhibitory serine phosphorylation in murine muscle and bone samples from four separate missions (BION-M1, Rodent Research missions RR1, RR9, and RR18). Spaceflight reduced GSK3b content across all missions, whereas its serine phosphorylation was elevated with RR18 and BION-M1. The reduction in GSK3b was linked to the reduction in type IIA fibers commonly observed with spaceflight as these fibers are particularly enriched with GSK3. We then tested the effects of inhibiting GSK3 before this fiber type shift, and we demonstrate that muscle-specific Gsk3 knockdown increased muscle mass, preserved muscle strength, and promoted the oxidative fiber type with Earth-based hindlimb unloading. In bone, GSK3 activation was enhanced after spaceflight; and strikingly, muscle-specific Gsk3 deletion increased bone mineral density in response to hindlimb unloading. Thus, future studies should test the effects of GSK3 inhibition during spaceflight. This study derives results from the DXA and micro computed tomography assays using tibia tissue from the RR9 mission and hindlimb unloaded/suspended (HLU/HLS) animals. The tibia data in this study are related to other studies using data from the same experiment; OSD-660 (Tibialis Anterior), OSD-661 (Lumbar Spine), OSD-662 (Soleus), OSD-663 (Femur), and OSD-664 (Extensor Digitorum Longus).
DOI: 10.25934/00006041
title: Histologic Predictors of Endoscopic Healing in Crohn's Disease

description: Crohn's disease (CD) is an inflammatory bowel disease that can affect any part of the gastrointestinal tract and is characterized by periods of relapse and remission. Unfortunately, patients with CD often experience disease progression, including fistulas, strictures, and symptoms including worsening abdominal pain and/or diarrhea.(1)

The Crohn’s Disease Activity Index (CDAI) is a widely used tool in clinical trials for CD as primary endpoints, namely clinical remission (CR) and response.(2,3) While the CDAI has demonstrated drug efficacy through these endpoints, histologic endpoints are lacking. Several studies have identified a disconnect between patient reported symptoms and endoscopic evidence of disease, which may be attributed to the presence of comorbid gastrointestinal disorders. 

Treatment goals have evolved to include endoscopic-based endpoints, using tools such as the Crohn’s Disease Endoscopic Index of Severity (CDEIS) and Simple Endoscopic Score for CD (SES-CD).(4,5) However, evidence of histologic inflammation is present in approximately one third of patients achieving endoscopic healing.(6,7) Therefore, the relationship between clinical, histologic and endoscopic measures of CD activity require further investigation. The Global Histology Activity Score (GHAS) is a widely used tool that grades biopsies of the ileum and colonic segments (collected at baseline, week 12 and 54 in EXTEND).(8) Therefore, regional and global GHAS can be separated and compared. 

Recently, the efficacy of ustekinumab on histologic improvement in CD patients have been explored, using data from the phase 3 induction and maintenance UNITI trials (ClinicalTrials.gov NCT01369329, NCT01369342, and NCT01369355) (9). However, to date, no study has investigated the relationship between baseline histologic disease activity and ability to attain endoscopic healing in CD.

The primary objective of this study is to evaluate the association between baseline histologic characteristics and endoscopic measures of disease activity at week 54 using data from the EXTEND trial. The secondary objectives of this study include assessing alternative definitions of mucosal healing (SES-CD of 0 and/or absence of mucosal ulcerations) and endoscopic response (SES-CD reduction at least 50% from baseline) at week 12 and 54. Planned exploratory analyses with immunohistochemistry may be done. Logistic regression will be used and models will be adjusted for confounders, such as disease duration, treatment allocation, concomitant corticosteroid use and concomitant immunomodulator use.
DOI: 10.25934/00006064
title: Comparative Effectiveness of Vedolizumab vs. Infliximab in Ulcerative Colitis

description: Ulcerative colitis (UC) is an inflammatory bowel disease that affects the large intestine and is characterized by diarrhea, rectal bleeding, abdominal pain, urgency, and tenesmus (Tenesmus is the feeling of incomplete evacuation of stool). (1,2) Patients with severe UC and/or corticosteroid-refractory disease are candidates for biologic monoclonal antibody treatments. 

Vedolizumab and infliximab are two biologic therapies that have demonstrated efficacy in achieving and maintaining remission through several pivotal placebo-controlled trials, including ACT 1 (NCT00036439), ACT 2 (NCT00096655), and GEMINI 1 (NCT00783718). (3,4)  Recently, the VARSITY trial used an active-comparator approach to demonstrate the superiority of vedolizumab to adalimumab among patients with moderate to severe UC.(5) However, network meta-analyses have suggested superiority of infliximab over adalimumab as a first-line biologic treatment in UC patients.(6)  There are no head-to-head trials comparing vedolizumab and infliximab.

Given the routine use of vedolizumab and infliximab as a treatment for UC, head-to-head comparisons are needed to better understand the positioning of vedolizumab as a treatment for biologic-naïve UC patients. 

The Mayo Score is a tool that is used to determine UC disease activity and is comprised of four patient-reported and endoscopic parameters: stool frequency, rectal bleeding, endoscopic findings, and physician’s global assessment. Each parameter is scored from 0 to 3, with higher scores indicating greater disease severity. The total Mayo Score ranges from 0 to 12, while the partial Mayo Score excludes the endoscopic subscore and thus ranges from 0 to 9. (6) While Mayo Scores have been widely used in clinical trials for UC as primary endpoints, mucosal healing (determined by endoscopy) remains an important target of treatment as well.

The primary objective of this study is to compare the efficacy of vedolizumab and infliximab to achieve post-induction (week 6) clinical remission and one year mucosal healing as determined by the Mayo Score. The secondary objectives of this study include clinical remission at one year, mucosal healing at post-induction (week 6). Additionally, clinical response, reduction in markers of disease activity (e.g. fecal calprotectin, C-reactive protein), and reduction in histologic measures of disease activity at post-induction (week 6) and one year will be analyzed.

Data from GEMINI 1 and VARSITY, which is being requested from Vivli, will be pooled to obtain a cohort of biologic-naïve UC patients treated with vedolizumab. Biologic-naïve patients treated with infliximab in ACT 1 and ACT 2 which is being requested from the Yale University Open Data Access (YODA) Project, will be pooled to comprise the infliximab cohort.
DOI: 10.25934/00006489
title: Tapering strategies of biological and targeted synthetic disease-modifying antirheumatic drugs for patients with inflammatory arthri-tis: a systematic review of randomised controlled trials 


description: Traditionally, standard dosage of biological and targeted synthetic disease-modifying antirheumatic drugs (bDMARDs and tsDMARDs, respectively) are continued lifelong in patients with inflammatory arthritis (i.e. rheumatoid arthritis [RA], psoriatic arthritis [PsA] and axial spondyloarthritis [axSpA]). However, recent studies indicate that a significant proportion of patients in sustained remission or low disease activity (LDA) can taper their bDMARD and maintain disease activity.  This systematic review will evaluate the risk of flare i.e. worsening in arthritis activity after the dosage of biological drugs have been reduced or even discontinued in patients with inflammatory arthriris (e.g. rheumatoid arthritis, psoriatic arthritis and axial spondyloarthritis) in sustained remission or low disease activity. The review will only include randomised controlled trials as these trials have the highest level of evidence.
DOI: 10.5281/zenodo.8408024
title: Codebook - Knowledge-Action Platforms (Data & Policy article) Bream McIntosh et al.,

description: Codebook used for Round 2 coding against key criteria of a 'Platform' definition that responds to matrix coding of Sustainability Knowledge Action Platforms. To accompany the article in Data & Policy 'The role of sustainability knowledge-action platforms in advancing multi-stakeholder engagement on sustainability'.
DOI: 10.5281/zenodo.8408023
title: Codebook - Knowledge-Action Platforms (Data & Policy article) Bream McIntosh et al.,

description: Codebook used for Round 2 coding against key criteria of a 'Platform' definition that responds to matrix coding of Sustainability Knowledge Action Platforms. To accompany the article in Data & Policy 'The role of sustainability knowledge-action platforms in advancing multi-stakeholder engagement on sustainability'.