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Unsupervised phase mapping of X-ray diffraction data by nonnegative matrix factorization integrated with custom clustering

journals • PubMed • Google Scholar Search for Ichiro Takeuchi in:Nature Research journals • PubMed • Google Scholar Search for Boian S. Alexandrov in:Nature Research journals • PubMed • Google Scholar ... . Competing interests The authors declare no competing interests. Corresponding authors Correspondence to Ichiro Takeuchi or Boian S. Alexandrov. Rights and permissions Open Access This article is

Bayesian-Driven First-Principles Calculations for Accelerating Exploration of Fast Ion Conductors for Rechargeable Battery Application

research by Information Integration (CMI2), Research and Services Division of Materials Data and Integrated System (MaDIS), NIMS, 1-2-1 Sengen, Tsukuba, 305-0047, Ibaraki, JapanRandy Jalem, Ichiro Takeuchi ... AuthorsSearch for Randy Jalem in:Nature Research journals • PubMed • Google Scholar Search for Kenta Kanamori in:Nature Research journals • PubMed • Google Scholar Search for Ichiro Takeuchi in:Nature Research

Identification of CDC42BPG as a novel susceptibility locus for hyperuricemia in a Japanese population

Chronic kidney disease and hyperuricemia are serious global health problems. Recent genome-wide association studies have identified various genetic variants related to these disorders. However, most studies have been conducted in a cross-sectional manner. To identify novel susceptibility loci for chronic kidney disease or hyperuricemia, we performed longitudinal exome-wide...

Comparison of dissimilarity measures for cluster analysis of X-ray diffraction data from combinatorial libraries

Science and Engineering, University of Maryland, College park, MD, 20742, USAA. Gilad Kusne & Ichiro Takeuchi AuthorsSearch for Yuma Iwasaki in:Nature Research journals • PubMed • Google Scholar Search for ... A. Gilad Kusne in:Nature Research journals • PubMed • Google Scholar Search for Ichiro Takeuchi in:Nature Research journals • PubMed • Google Scholar Corresponding author Correspondence to A. Gilad

Description of two species of Caprella (Crustacea: Amphipoda: Caprellidae) from the North Pacific; C. californica Stimpson, 1857 and C. scauroides Mayer, 1903, with a new appraisal of species ranking for C. scauroides

Caprella californica Stimpson, 1857 [sensu lato] is one of the dominant species of Caprella spp. (Crustacea: Amphipoda) along the Pacific coast of Mexico to Canada and Japan to Hong Kong, China, and recently widely reported from the Australian coasts. Detailed morphological comparison of C. californica [sensu lato] collected from California and the Uwa Sea, Japan, revealed...

Label-Free Morphology-Based Prediction of Multiple Differentiation Potentials of Human Mesenchymal Stem Cells for Early Evaluation of Intact Cells

Precise quantification of cellular potential of stem cells, such as human bone marrow–derived mesenchymal stem cells (hBMSCs), is important for achieving stable and effective outcomes in clinical stem cell therapy. Here, we report a method for image-based prediction of the multiple differentiation potentials of hBMSCs. This method has four major advantages: (1) the cells used for...

Multi-parametric solution-path algorithm for instance-weighted support vector machines

An instance-weighted variant of the support vector machine (SVM) has attracted considerable attention recently since they are useful in various machine learning tasks such as non-stationary data analysis, heteroscedastic data modeling, transfer learning, learning to rank, and transduction. An important challenge in these scenarios is to overcome the computational bottleneck...

Discovering combinatorial interactions in survival data

Motivation: Although several methods exist to relate high-dimensional gene expression data to various clinical phenotypes, finding combinations of features in such input remains a challenge, particularly when fitting complex statistical models such as those used for survival studies. Results: Our proposed method builds on existing ‘regularization path-following’ techniques to...

Morphology-Based Prediction of Osteogenic Differentiation Potential of Human Mesenchymal Stem Cells

Human bone marrow mesenchymal stem cells (hBMSCs) are widely used cell source for clinical bone regeneration. Achieving the greatest therapeutic effect is dependent on the osteogenic differentiation potential of the stem cells to be implanted. However, there are still no practical methods to characterize such potential non-invasively or previously. Monitoring cellular morphology...

Expression of proteins associated with adipocyte lipolysis was significantly changed in the adipose tissues of the obese spontaneously hypertensive/NDmcr-cp rat

Background The etiology of the metabolic syndrome is complex, and is determined by the interplay of both genetic and environmental factors. The present study was designed to identify genes and proteins in the adipose tissues with altered expression in the spontaneously hypertensive/NIH –corpulent rat, SHR/NDmcr-cp (CP) and to find possible molecular targets associated with the...

Genomic Profiling of Oral Squamous Cell Carcinoma by Array-Based Comparative Genomic Hybridization

We designed a study to investigate genetic relationships between primary tumors of oral squamous cell carcinoma (OSCC) and their lymph node metastases, and to identify genomic copy number aberrations (CNAs) related to lymph node metastasis. For this purpose, we collected a total of 42 tumor samples from 25 patients and analyzed their genomic profiles by array-based comparative...

Baseline cardiac magnetic resonance imaging versus baseline endomyocardial biopsy for the prediction of left ventricular reverse remodeling and prognosis in response to therapy in patients with idiopathic dilated cardiomyopathy

Endomyocardial biopsy (EMB) and late gadolinium enhancement cardiovascular magnetic resonance (LGE-CMR) imaging performed at baseline are both used to evaluate the extent of myocardial fibrosis. However, no study has directly compared the effectiveness of these diagnostic tools in the prediction of left ventricular reverse remodeling (LVRR) and prognosis in response to therapy in...

Altered gene and protein expression in liver of the obese spontaneously hypertensive/NDmcr-cp rat

Background It is difficult to study the mechanisms of the metabolic syndrome in humans due to the heterogeneous genetic background and lifestyle. The present study investigated changes in the gene and protein profiles in an animal model of the metabolic syndrome to identify the molecular targets associated with the pathogenesis and progression of obesity related to the metabolic...

Epigenetic subclassification of meningiomas based on genome-wide DNA methylation analyses

Meningiomas are among the most common intracranial tumors and are mostly curable by surgical resection. However, some populations of meningiomas with benign histological profiles show malignant behavior. The reasons for this inconsistency are yet to be ascertained, and novel diagnostic criteria other than the histological one are urgently needed. The aim of the present study is...

Downregulation of SAV1 plays a role in pathogenesis of high-grade clear cell renal cell carcinoma

Background Clinical outcome of patients with high-grade ccRCC (clear cell renal cell carcinoma) remains still poor despite recent advances in treatment strategies. Molecular mechanism of pathogenesis in developing high-grade ccRCC must be clarified. In the present study, we found that SAV1 was significantly downregulated with copy number loss in high-grade ccRCCs. Therefore, we...

Integrated analysis of genetic and epigenetic alterations reveals CpG island methylator phenotype associated with distinct clinical characters of lung adenocarcinoma

DNA methylation affects the aggressiveness of human malignancies. Cancers with CpG island methylator phenotype (CIMP), a distinct group with extensive DNA methylation, show characteristic features in several types of tumors. In this study, we initially defined the existence of CIMP in 41 lung adenocarcinomas (AdCas) through genome-wide DNA methylation microarray analysis. DNA...

Genomic Profiling of Submucosal-Invasive Gastric Cancer by Array-Based Comparative Genomic Hybridization

Genomic copy number aberrations (CNAs) in gastric cancer have already been extensively characterized by array comparative genomic hybridization (array CGH) analysis. However, involvement of genomic CNAs in the process of submucosal invasion and lymph node metastasis in early gastric cancer is still poorly understood. In this study, to address this issue, we collected a total of...