Total is 1437 Results
Statistical Potential based Amino Acid Similarity Matrices for Aligning Distantly Related Protein Sequences


Daisuke Kihara, H. Huang, Y.H. Tan


Aligning distantly related protein sequences is a long-standing problem in bioinformatics, and a key for successful protein structure prediction. Its importance is increasing recently in the context of structural genomics projects because more and more exp...

Amino Acids/chemistry Biochemistry Bioinformatics Molecular Biosciences Protein Folding

Comparative genomics of small RNAs in bacterial genomes


Daisuke Kihara, Stan Luban


In recent years, various families of small non-coding RNAs (sRNAs) have been discovered by experimental and computational approaches, both in bacterial and eukaryotic genomes. Although most of them await elucidation of their function, it has been reported...

Bacterial Bacterial/Genetics Biochemistry Bioinformatics Deinococcus/Genetics Escherichiacoli/Metabolism Molecular Biosciences Multigene Family RNA

Characterization of Local Geometry of Protein Surfaces with the Visibility Criteria


Bin Li, Daisuke Kihara, Manish Agrawal, Srinivasan Turuvekere


Experimentally determined protein tertiary structures are rapidly accumulating in a database, partly due to the structural genomics projects. Included are proteins of unknown function, whose function has not been investigated by experiments and was not abl...

Argininosuccinate Synthase Binding Sites Biochemistry Bioinformatics Computer Simulation Molecular Biosciences Protein Structure Sensitivity and Specificity Tertiary Tetrahydrofolate Dehydrogenase/chemistry

Limitations and Potentials of Current Motif Discovery Algorithms


Bin Li, Daisuke Kihara, Jianjun Hu


Computational methods for de novo identification of gene regulation elements, such as transcription factor binding sites, have proved to be useful for deciphering genetic regulatory networks. However, despite the availability of a large number of algorithm...

Algorithms Base Sequence Binding Sites Biochemistry Bioinformatics Computational Biology / Methods DNA/Chemistry DNA/methods Escherichia coli/Genetics Factors/Metabolism Markov Chains Markov Chains Regulatory Sequences Molecular Biosciences Regulon Sequence Alignment Sequence Analysis

InfoSEAD protocol and sample memo


Michael Fosmire, Monica E. Cardella, Ruth Wertz, Senay Purzer


The Information Seeking, Evaluation, Application, and Documentation (InfoSEAD) protocol was developed to assess four areas of student information skills. '''Seeking:''' measuring the quantity and variety of information sources used...

Assessment Education Information Literacy Library Science

Measurement of Interfacial Area per Volume for Drainage and Imbibition - S6dc


Daiquan Chen, Jessica Griffin, Laura J. Pyrak-Nolte, Nicholas Giordano


We investigate experimentally the functional relationship between capillary pressure, Pc, wetting phase saturation, Sw, and interfacial area per volume between the wetting and nonwetting phases, awn, for drainage and imbibition processes in micromodels of...

Drainage Physics

Simplicity of K-means versus deepness of Deep Learning. A Case of Unsupervised Feature Learning with Limited Data


Baichuan Zhang, Bartlomiej P. Rajwa, Murat Dundar, Qiang Kou, Yicheng He


We study a biodetection application as a case study to demonstrate that K-means-based unsupervised feature learning can be a simple yet effective alternative to deep learning techniques for small data sets with limited intra- as well as inter-class diversi...

bacterial colonies BARDOT Biomedical Engineering Computer Science deep learning Elastic light scattering Interdisciplinary Research K-Means Clustering Life Sciences Machine Learning representation learning

Relating Capillary Pressure to Interfacial Areas - S70


Daiquan Chen, David Nolte, Laura J. Pyrak-Nolte, Nicholas Giordano


Experiments were performed on transparent two-dimensional microfluidic porous systems to investigate the relationships among capillary pressure and the interfacial areas per volume between two fluid phases and one solid phase. Capillary pressures were calc...

Drainage Physics

Critical Engineering Literacy Test (CELT)


Michael Fosmire, Ruth Wertz, Senay Purzer


The CELT download includes the blueprint for writing assessment items, and the content of the assessment itself. This version (4.1) has 2 parts, one on an engineering topic, and one on a biology topic. The correct responses are not indicated in this versio...

Assessment Education Engineering Education Environmental Engineering

DAMAGED GIRDER - Supplementary Materials for the Report: Effects of Realistic Heat Straightening Repair on the Properties and Serviceability of Damaged Steel Beam Bridges


Amit H. Varma, Young Moo Sohn


Guidelines for conducting heat straightening repair have been developed by FHWA and many DOTS. The guidelines establish limits for: (a) the maximum damage that can be repaired, (b) the maximum restraining force, and %(c%) the maximum heating temperature to...

Civil Engineering Damaged Steel Beam Bridge Heat straightening repair Joint Transportation Research Program JTRP Multiple heat straightening Overheating Overstraining SPR-3105

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