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View article: OptSurvCutR: Validated Cut-point Selection for Survival Analysis
OptSurvCutR: Validated Cut-point Selection for Survival Analysis Open
The stratification of subjects based on continuous predictors is a common yet challenging task in time-to-event analysis (or survival), particularly when relationships are non-linear and require multiple thresholds. Arbitrary cut-point sel…
View article: Introducing the UK Crop Microbiome Cryobank data resource, AgMicrobiomeBase, with case studies and methods on metabarcoding analyses
Introducing the UK Crop Microbiome Cryobank data resource, AgMicrobiomeBase, with case studies and methods on metabarcoding analyses Open
View article: 157P Nivolumab (NIVO) plus ipilimumab (IPI) vs lenvatinib (LEN) or sorafenib (SOR) as first-line (1L) treatment in Chinese patients with unresectable/advanced hepatocellular carcinoma (HCC): CheckMate 9DW expanded analyses
157P Nivolumab (NIVO) plus ipilimumab (IPI) vs lenvatinib (LEN) or sorafenib (SOR) as first-line (1L) treatment in Chinese patients with unresectable/advanced hepatocellular carcinoma (HCC): CheckMate 9DW expanded analyses Open
View article: Introducing the UK Crop Microbiome Cryobank resource: metabarcoding methods and case studies
Introducing the UK Crop Microbiome Cryobank resource: metabarcoding methods and case studies Open
Background: Here, we describe AgMicrobiomeBase as an output of the UK Crop Microbiome Cryobank (UKCMCB) project, including details of the underlying meta-barcode sequence-based methods and three microbiome analysis case studies. The UKCMCB…
View article: Promoter Methylation Leads to Hepatocyte Nuclear Factor 4A Loss and Pancreatic Cancer Aggressiveness
Promoter Methylation Leads to Hepatocyte Nuclear Factor 4A Loss and Pancreatic Cancer Aggressiveness Open
View article: The UK Crop Microbiome Cryobank: a utility and model for supporting Phytobiomes research
The UK Crop Microbiome Cryobank: a utility and model for supporting Phytobiomes research Open
Plant microbiomes are the microbial communities essential to the functioning of the phytobiome—the system that consist of plants, their environment, and their associated communities of organisms. A healthy, functional phytobiome is critica…
View article: Overview of current detection methods and microRNA potential in <i>Clostridioides difficile</i> infection screening
Overview of current detection methods and microRNA potential in <i>Clostridioides difficile</i> infection screening Open
Clostridioides difficile (formerly called Clostridium difficile, C. difficile) infection (CDI) is listed as an urgent threat on the 2019 antibiotic resistance threats report in the United States by the Centers for Dise…
View article: Supplementary Figure 1 from Identification of microRNA-135b in Stool as a Potential Noninvasive Biomarker for Colorectal Cancer and Adenoma
Supplementary Figure 1 from Identification of microRNA-135b in Stool as a Potential Noninvasive Biomarker for Colorectal Cancer and Adenoma Open
PDF file - 141KB, Flow-chart of exclusion of subjects in the study.
View article: Supplementary Table 2 from Identification of microRNA-135b in Stool as a Potential Noninvasive Biomarker for Colorectal Cancer and Adenoma
Supplementary Table 2 from Identification of microRNA-135b in Stool as a Potential Noninvasive Biomarker for Colorectal Cancer and Adenoma Open
PDF file - 15KB, Characteristics of CRC and advanced adenoma patients in initial microRNA profiling.
View article: Supplementary Table 2 from Identification of microRNA-135b in Stool as a Potential Noninvasive Biomarker for Colorectal Cancer and Adenoma
Supplementary Table 2 from Identification of microRNA-135b in Stool as a Potential Noninvasive Biomarker for Colorectal Cancer and Adenoma Open
PDF file - 15KB, Characteristics of CRC and advanced adenoma patients in initial microRNA profiling.
View article: Supplementary Figure 1 from Identification of microRNA-135b in Stool as a Potential Noninvasive Biomarker for Colorectal Cancer and Adenoma
Supplementary Figure 1 from Identification of microRNA-135b in Stool as a Potential Noninvasive Biomarker for Colorectal Cancer and Adenoma Open
PDF file - 141KB, Flow-chart of exclusion of subjects in the study.
View article: Supplementary Table 4 from Identification of microRNA-135b in Stool as a Potential Noninvasive Biomarker for Colorectal Cancer and Adenoma
Supplementary Table 4 from Identification of microRNA-135b in Stool as a Potential Noninvasive Biomarker for Colorectal Cancer and Adenoma Open
PDF file - 16KB, Sensitivity and specificity of miRNA markers.
View article: Supplementary Table 3 from Identification of microRNA-135b in Stool as a Potential Noninvasive Biomarker for Colorectal Cancer and Adenoma
Supplementary Table 3 from Identification of microRNA-135b in Stool as a Potential Noninvasive Biomarker for Colorectal Cancer and Adenoma Open
XLSX file - 585KB, miRNA microarray data from 5 pairs of CRCs and 2 pairs of adenomas.
View article: Supplementary Table 1 from Identification of microRNA-135b in Stool as a Potential Noninvasive Biomarker for Colorectal Cancer and Adenoma
Supplementary Table 1 from Identification of microRNA-135b in Stool as a Potential Noninvasive Biomarker for Colorectal Cancer and Adenoma Open
XLSX file - 33KB, The characteristics of CRC and advancent adenoma patients in tissue miRNA assay.
View article: Supplementary Table 1 from Identification of microRNA-135b in Stool as a Potential Noninvasive Biomarker for Colorectal Cancer and Adenoma
Supplementary Table 1 from Identification of microRNA-135b in Stool as a Potential Noninvasive Biomarker for Colorectal Cancer and Adenoma Open
XLSX file - 33KB, The characteristics of CRC and advancent adenoma patients in tissue miRNA assay.
View article: Supplementary Table 4 from Identification of microRNA-135b in Stool as a Potential Noninvasive Biomarker for Colorectal Cancer and Adenoma
Supplementary Table 4 from Identification of microRNA-135b in Stool as a Potential Noninvasive Biomarker for Colorectal Cancer and Adenoma Open
PDF file - 16KB, Sensitivity and specificity of miRNA markers.
View article: Data from Identification of microRNA-135b in Stool as a Potential Noninvasive Biomarker for Colorectal Cancer and Adenoma
Data from Identification of microRNA-135b in Stool as a Potential Noninvasive Biomarker for Colorectal Cancer and Adenoma Open
Purpose: Detecting microRNA (miRNA) in stool is a novel approach for colorectal cancer (CRC) screening. This study aimed to identify stool-based miRNA as noninvasive biomarkers for detection of CRC and adenoma.Experimental Design…
View article: Data from Identification of microRNA-135b in Stool as a Potential Noninvasive Biomarker for Colorectal Cancer and Adenoma
Data from Identification of microRNA-135b in Stool as a Potential Noninvasive Biomarker for Colorectal Cancer and Adenoma Open
Purpose: Detecting microRNA (miRNA) in stool is a novel approach for colorectal cancer (CRC) screening. This study aimed to identify stool-based miRNA as noninvasive biomarkers for detection of CRC and adenoma.Experimental Design…
View article: Supplementary Table 3 from Identification of microRNA-135b in Stool as a Potential Noninvasive Biomarker for Colorectal Cancer and Adenoma
Supplementary Table 3 from Identification of microRNA-135b in Stool as a Potential Noninvasive Biomarker for Colorectal Cancer and Adenoma Open
XLSX file - 585KB, miRNA microarray data from 5 pairs of CRCs and 2 pairs of adenomas.
View article: The first discovery of Tc1 transposons in yeast
The first discovery of Tc1 transposons in yeast Open
Background Identification of transposons without close homologs is still a difficult task. IS630/Tc1/mariner transposons, classified into a superfamily, are probably the most widespread DNA transposons in nature. Tc1/mariner transposons ha…
View article: Immune dysfunction signatures predict outcomes and define checkpoint blockade–unresponsive microenvironments in acute myeloid leukemia
Immune dysfunction signatures predict outcomes and define checkpoint blockade–unresponsive microenvironments in acute myeloid leukemia Open
BackgroundImmune exhaustion and senescence are dominant dysfunctional states of effector T cells and major hurdles for the success of cancer immunotherapy. In the current study, we characterized how acute myeloid leukemia (AML) promotes th…
View article: The first nonclassical Tc1 transposon discovered in yeast
The first nonclassical Tc1 transposon discovered in yeast Open
Background Identification of transposons or retrotransposons is still a difficult task and can not be accomplished without specialist knowledge. Tc1/mariner is a superfamily of DNA transposons that have been discovered in animals, plants, …
View article: Full-Length Genome of an Ogataea polymorpha Strain CBS4732 ura3Δ Reveals Large Duplicated Segments in Subtelomeric Regions
Full-Length Genome of an Ogataea polymorpha Strain CBS4732 ura3Δ Reveals Large Duplicated Segments in Subtelomeric Regions Open
Background Currently, methylotrophic yeasts (e.g., Pichia pastoris , Ogataea polymorpha , and Candida boindii ) are subjects of intense genomics studies in basic research and industrial applications. In the genus Ogataea , most research is…
View article: Signatures of immune senescence predict outcomes and define checkpoint blockade-unresponsive microenvironments in acute myeloid leukemia
Signatures of immune senescence predict outcomes and define checkpoint blockade-unresponsive microenvironments in acute myeloid leukemia Open
Summary The function of senescent-like T cells, transcriptomic features of immune effector senescence (IES) and their influence on therapeutic response were investigated in independent AML clinical cohorts comprising 1,864 patients treated…
View article: Hyperactive neutrophil chemotaxis contributes to anti‐tumor necrosis factor‐α treatment resistance in inflammatory bowel disease
Hyperactive neutrophil chemotaxis contributes to anti‐tumor necrosis factor‐α treatment resistance in inflammatory bowel disease Open
Background and Aim Anti‐tumor necrosis factor‐α (anti‐TNF‐α) agents have been used for inflammatory bowel disease; however, it has up to 30% nonresponse rate. Identifying molecular pathways and finding reliable diagnostic biomarkers for pa…
View article: A Multi-Factorial Observational Study on Sequential Fecal Microbiota Transplant in Patients with Medically Refractory Clostridioides difficile Infection
A Multi-Factorial Observational Study on Sequential Fecal Microbiota Transplant in Patients with Medically Refractory Clostridioides difficile Infection Open
Fecal microbiota transplantation (FMT) is highly effective in recurrent Clostridioides difficile infection (CDI); increasing evidence supports FMT in severe or fulminant Clostridioides difficile infection (SFCDI). However, the multifactori…
View article: Hyperactive chemotaxis contributes to anti-TNFα treatment resistance in inflammatory bowel disease
Hyperactive chemotaxis contributes to anti-TNFα treatment resistance in inflammatory bowel disease Open
Background & Aims Anti-tumour necrosis factor-alpha (anti-TNFα) agents have been used for inflammatory bowel disease (IBD), however, it has up to 30% non-response rate. Identifying molecular pathways and finding reliable diagnostic biomark…
View article: Multiomics Profiling Reveals Signatures of Dysmetabolism in Urban Populations in Central India
Multiomics Profiling Reveals Signatures of Dysmetabolism in Urban Populations in Central India Open
Background: Non-communicable diseases (NCDs) have become a major cause of morbidity and mortality in India. Perturbation of host–microbiome interactions may be a key mechanism by which lifestyle-related risk factors such as tobacco use, al…
View article: Precise annotation of <i>Drosophila</i> mitochondrial genomes leads to insights into AT-rich regions
Precise annotation of <i>Drosophila</i> mitochondrial genomes leads to insights into AT-rich regions Open
In the present study, we performed precise annotation of Drosophila melanogaster , D. simulans , D. grimshawi , Bactrocera oleae mitochondrial (mt) genomes by pan RNA-seq analysis. Our new annotations corrected or modified some of the prev…
View article: Full-length Genome of the Ogataea polymorpha strain HU-11 reveals large duplicated segments in subtelomeric regions
Full-length Genome of the Ogataea polymorpha strain HU-11 reveals large duplicated segments in subtelomeric regions Open
Background: Currently, methylotrophic yeasts (e.g., Pichia pastoris, Hansenula polymorpha, and Candida boindii) are subjects of intense genomics studies in basic research and industrial applications. In the genus Ogataea, most research is …