Scaling success: Linking public breeding with private enterprise

<p>The known Downstream Promoter Element and Initiator site motifs are shown in boldface.</p

PeakRegressor Identifies Composite Sequence Motifs Responsible for STAT1 Binding Sites and Their Potential rSNPs

How to identify true transcription factor binding sites on the basis of sequence motif information (e.g., motif pattern, location, combination, etc.) is an important question in bioinformatics. We present “PeakRegressor,” a system that identifies binding motifs by combining DNA-sequence data and ChIP-Seq data. PeakRegressor uses L1-norm log linear regression in order to predict peak values from binding motif candidates. Our approach successfully predicts the peak values of STAT1 and RNA Polymerase II with correlation coefficients as high as 0.65 and 0.66, respectively. Using PeakRegressor, we could identify composite motifs for STAT1, as well as potential regulatory SNPs (rSNPs) involved in the regulation of transcription levels of neighboring genes. In addition, we show that among five regression methods, L1-norm log linear regression achieves the best performance with respect to binding motif identification, biological interpretability and computational efficiency

ゲノム、メタゲノムに潜む潜在的機能ポテンシャルの評価

この要旨は日本ゲノム微生物学会の年会で2012年3月12日に発表したものである（口頭発表O-37, ポスター発表2P-59

Walsh spectral analysis of multiple dyadic stationary processes and its applications

In this paper, we investigate some properties of multiple dyadic stationary processes from the viewpoint of their Walsh spectral analysis. It is shown that under certain conditions a dyadic autoregressive and moving average process of finite order is expressed as a dyadic autoregressive process of finite order and also as a dyadic moving average process of finite order. We can see that the principal component process of such a dyadic stationary process has a simple finite structure in the sense that a dyadic filter which generates the principal component process has only one-side finite lags.Walsh spectral analysis dyadic stationary process finite parametric spectral model principal component analysis canonical correlation analysis

Experimental investigation on steel-concrete composite beams with expansion joints in concrete slab

Funding Information: The loading tests were performed at Nippon Steel Echo-Tech Corporation in Chiba, Japan. The assistance of the laboratory staff and the financial support are gratefully acknowledged. The author(s) disclosed receipt of the following financial support for the research, authorship, and/or publication of this article: This work was supported by the Kajima Foundation (Japan). Funding Information: The loading tests were performed at Nippon Steel Echo-Tech Corporation in Chiba, Japan. The assistance of the laboratory staff and the financial support are gratefully acknowledged. Publisher Copyright: © The Author(s) 2022.This study examines experimentally the mechanical performance of composite steel and concrete beams with expansion joints in the concrete slab. Four composite beams with expansion joints in the concrete slab were tested, and various aspects of such beams including the effects of expansion joint locations ((Formula presented.), (Formula presented.), and (Formula presented.), where (Formula presented.)), expansion joint sizes (through and half-through of the concrete depth), and loading conditions (positive bending moment and negative bending) etc., were investigated. Load versus vertical deflection responses at key sections, and the strain development and distribution on the steel beam were measured. To explore the behavior of shear connectors on or near the expansion joint sections, the normal strain on shear connectors was measured. The bending strain and axial strain of shear connectors on joint sections were also discussed in detail. The theoretical methods for predicting the rigidities and ultimate load-carrying capacities of the composite beams were examined, and it was found that the current AASHTO-LRFD criterion without considering expansion joints in a concrete slab can still provide conservative estimations of ultimate loads of such beams under a negative moment. For composite beams under a positive bending moment, however, they are not applicable, due to the different failure modes. The test results from this research provide new information for improving the design, construction, management, maintenance, and structural health assessment of such beams that can be used in bridges and buildings, etc.Peer reviewe

CellMontage: similar expression profile search server

Summary: The establishment and rapid expansion of microarray databases has created a need for new search tools. Here we present CellMontage, the first server for expression profile similarity search over a large database—69 000 microarray experiments derived from NCBI’s GEO site. CellMontage provides a novel, content-based search engine for accessing gene expression data. Microarray experiments with similar overall expression to a user-provided expression profile (e.g. microarray experiment) are computed and displayed—usually within 20 s. The core search engine software is downloadable from the site