cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.4231/d3z02z836
title: Functional enrichment analyses and construction of functional similarity networks with high confidence function prediction by PFP

description: &lt;p&gt;BACKGROUND: A new paradigm of biological investigation takes advantage of technologies that produce large high throughput datasets, including genome sequences, interactions of proteins, and gene expression. The ability of biologists to analyze and interpret such data relies on functional annotation of the included proteins, but even in highly characterized organisms many proteins can lack the functional evidence necessary to infer their biological relevance. RESULTS: Here we have applied high confidence function predictions from our automated prediction system, PFP, to three genome sequences, Escherichia coli, Saccharomyces cerevisiae, and Plasmodium falciparum (malaria). The number of annotated genes is increased by PFP to over 90% for all of the genomes. Using the large coverage of the function annotation, we introduced the functional similarity networks which represent the functional space of the proteomes. Four different functional similarity networks are constructed for each proteome, one each by considering similarity in a single Gene Ontology (GO) category, i.e. Biological Process, Cellular Component, and Molecular Function, and another one by considering overall similarity with the funSim score. The functional similarity networks are shown to have higher modularity than the protein-protein interaction network. Moreover, the funSim score network is distinct from the single GO-score networks by showing a higher clustering degree exponent value and thus has a higher tendency to be hierarchical. In addition, examining function assignments to the protein-protein interaction network and local regions of genomes has identified numerous cases where subnetworks or local regions have functionally coherent proteins. These results will help interpreting interactions of proteins and gene orders in a genome. Several examples of both analyses are highlighted. CONCLUSION: The analyses demonstrate that applying high confidence predictions from PFP can have a significant impact on a researchers&#39; ability to interpret the immense biological data that are being generated today. The newly introduced functional similarity networks of the three organisms show different network properties as compared with the protein-protein interaction networks.&lt;/p&gt;
description: Supplementary Material for the Paper: Functional similarity network with high confidence protein function prediction by PFP. BMC Bioinformatics. 2010 May 19;11:265. doi: 10.1186/1471-2105-11-265.
DOI: 10.4231/d3pk0719w
title: Threading Without Optimizing Weighting Factor for the Scoring Function Proteins

description: &lt;p&gt;Optimizing weighting factors for a linear combination of terms in a scoring function is a crucial step for success in developing a threading algorithm. Usually weighting factors are optimized to yield the highest success rate on a training dataset, and the determined constant values for the weighting factors are used for any target sequence. Here we explore completely different approaches to handle weighting factors for a scoring function of threading. Throughout this study we use a model system of gapless threading using a scoring function with two terms combined by a weighting factor, a main chain angle potential and a residue contact potential. First, we demonstrate that the optimal weighting factor for recognizing the native structure differs from target sequence to target sequence. Then, we present three novel threading methods which circumvent training dataset-based weighting factor optimization. The basic idea of the three methods is to employ different weighting factor values and finally select a template structure for a target sequence by examining characteristics of the distribution of scores computed by using the different weighting factor values. Interestingly, the success rate of our approaches is comparable to the conventional threading method where the weighting factor is optimized based on a training dataset. Moreover, when the size of the training set available for the conventional threading method is small, our approach often performs better. In addition, we predict a target-specific weighting factor optimal for a target sequence by an artificial neural network from features of the target sequence. Finally, we show that our novel methods can be used to assess the confidence of prediction of a conventional threading with an optimized constant weighting factor by considering consensus prediction between them. Implication to the underlined energy landscape of protein folding is discussed.&lt;/p&gt;
description: Supplementary Material for the Paper: Threading Without Optimizing Weighting Factor for the Scoring Function Proteins, in revision (2008). Proteins. 2008 Nov 15;73(3):581-96. doi: 10.1002/prot.22082.
DOI: 10.4231/d3dr2p83h
title: Statistical Potential based Amino Acid Similarity Matrices for Aligning Distantly Related Protein Sequences

description: &lt;p&gt;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 experimentally solved structures are available as templates for protein structure modeling. Toward this end, recent structure prediction methods employ profile-profile alignments, and various ways of aligning two profiles have been developed. More fundamentally, a better amino acid similarity matrix can improve a profile itself; thereby resulting in more accurate profile-profile alignments. Here we have developed novel amino acid similarity matrices from knowledge-based amino acid contact potentials. Contact potentials are used because the contact propensity to the other amino acids would be one of the most conserved features of each position of a protein structure. The derived amino acid similarity matrices are tested on benchmark alignments at three different levels, namely, the family, the superfamily, and the fold level. Compared to BLOSUM45 and the other existing matrices, the contact potential-based matrices perform comparably in the family level alignments, but clearly outperform in the fold level alignments. The contact potential-based matrices perform even better when suboptimal alignments are considered. Comparing the matrices themselves with each other revealed that the contact potential-based matrices are very different from BLOSUM45 and the other matrices, indicating that they are located in a different basin in the amino acid similarity matrix space.&lt;/p&gt;
description: Supplementary materials for the paper: Statistical Potential based Amino Acid Similarity Matrices for Aligning Distantly Related Protein Sequences. Proteins: Structure, Function and Bioinformatics 64: 587-600. (2006)
DOI: 10.4231/d37659f6q
title: Comparative genomics of small RNAs in bacterial genomes

description: &lt;p&gt;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 that some play important roles in gene regulation. Here we carried out comparative genomics analysis of possible sRNAs that are computationally identified in 30 bacterial genomes from gamma- and alpha-proteobacteria and Deinococcus radiodurans. Identified sRNAs are clustered by a complete-linkage clustering method to see conservation among the organisms. On average, sRNAs are found in approximately 30% of intergenic regions of each genome sequence. Of these, 25.7% are conserved among three or more organisms. Approximately 60% of the conserved sRNAs do not locate in orthologous intergenic regions, implying that sRNAs may be shuffled their positions in genomes. The current study implies that sRNAs may be involved in a more extensive range of functions in bacteria.&lt;/p&gt;
description: Supplemental Material for the paper: Comparative genomics of small RNAs in bacterial genomes. OMICS. 2007 Spring;11(1):58-73.
DOI: 10.4231/d3bz61792
title: Characterization of Local Geometry of Protein Surfaces with the Visibility Criteria

description: &lt;p&gt;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 able to be predicted by conventional sequence-based search. Those uncharacterized protein structures highlight the urgent need of computational methods for annotating proteins from tertiary structures, which include function annotation methods through characterizing protein local surfaces. Toward structure-based protein annotation, we have developed !VisGrid algorithm that uses the visibility criterion to characterize local geometric features of protein surfaces. Unlike existing methods, which only concerns identifying pockets that could be potential ligand-binding sites in proteins, !VisGrid is also aimed to identify large protrusions, hollows, and flat regions, which can characterize geometric features of a protein structure. The visibility used in !VisGrid is defined as the fraction of visible directions from a target position on a protein surface. A pocket or a hollow is recognized as a cluster of positions with a small visibility. A large protrusion in a protein structure is recognized as a pocket in the negative image of the structure. !VisGrid correctly identified 95.0% of ligand-binding sites as one of the three largest pockets in 5616 benchmark proteins. To examine how natural flexibility of proteins affects pocket identification, !VisGrid was tested on distorted structures by molecular dynamics simulation. Sensitivity decreased approximately 20% for structures of a root mean square deviation of 2.0 A to the original crystal structure, but specificity was not much affected. Because of its intuitiveness and simplicity, the visibility criterion will lay the foundation for characterization and function annotation of local shape of proteins.&lt;/p&gt;
description: Supplementary material for the paper: Characterization of Local Geometry of Protein Surfaces with the Visibility Criteria. Proteins. 2008 May 1;71(2):670-83.
DOI: 10.4231/d33f4kn2k
title: Limitations and Potentials of Current Motif Discovery Algorithms

description: &lt;p&gt;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 algorithms, their strengths and weaknesses are not sufficiently understood. Here, we designed a comprehensive set of performance measures and benchmarked five modern sequence-based motif discovery algorithms using large datasets generated from Escherichia coli !RegulonDB. Factors that affect the prediction accuracy, scalability and reliability are characterized. It is revealed that the nucleotide and the binding site level accuracy are very low, while the motif level accuracy is relatively high, which indicates that the algorithms can usually capture at least one correct motif in an input sequence. To exploit diverse predictions from multiple runs of one or more algorithms, a consensus ensemble algorithm has been developed, which achieved 6-45% improvement over the base algorithms by increasing both the sensitivity and specificity. Our study illustrates limitations and potentials of existing sequence-based motif discovery algorithms. Taking advantage of the revealed potentials, several promising directions for further improvements are discussed. Since the sequence-based algorithms are the baseline of most of the modern motif discovery algorithms, this paper suggests substantial improvements would be possible for them.&lt;/p&gt;
description: Supplementary material for the papers: Limitations and Potentials of Current Motif Discovery Algorithms, Nucleic Acids Res. 2005; 33(15): 4899–4913
DOI: 10.4231/d3ww7702p
title: InfoSEAD protocol and sample memo

description: &lt;p&gt;The Information Seeking, Evaluation, Application, and Documentation (InfoSEAD) protocol was developed to assess four areas of student information skills. &#39;&#39;&#39;Seeking:&#39;&#39;&#39; measuring the quantity and variety of information sources used by students &#39;&#39;&#39;Evaluation:&#39;&#39;&#39; identifying the frequency of high-quality information sources used by students &#39;&#39;&#39;Application:&#39;&#39;&#39; how well students use documented information to support an argument &#39;&#39;&#39;Documentation:&#39;&#39;&#39; completeness and accuracy in citation and appropriateness of referencing in the text&lt;/p&gt;
description: Includes a description of the InfoSEAD protocol and an example of how a document can be analyzed using the protocol.
DOI: 10.4231/d3zc7rt9g
title: Measurement of Interfacial Area per Volume for Drainage and Imbibition - S6dc

description: &lt;p&gt;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 two-dimensional pore structures. Within the experimental and analysis error (around 10&ndash;15%), the resulting Pc-Sw-awn surfaces were the same. This suggests that data obtained from either the drainage process or the imbibition process are sufficient to generate the complete functional relationship among Pc-Sw-awn and that the observed hysteresis in Pc-Sw-awn can be modeled by including interfacial area as an additional state variable.&lt;/p&gt;
description: Supplementary materials for the paper: Measurement of interfacial area per volume for drainage and imbibition, Water Resour. Res., 43, W12504, 2007, doi:10.1029/2007WR006021.
DOI: 10.4231/d3pv6b70h
title: Relating Capillary Pressure to Interfacial Areas - S70

description: &lt;p&gt;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 calculated from the observed interfacial curvature of the wetting-nonwetting interface, and these correlated closely to externally measured values of applied pressure. For each applied pressure, the system established mechanical equilibrium characterized by stationary interfaces, uniform curvatures across the model, and random surface normals. To study the relationships among capillary pressure and the interfacial areas, we compare the curvature-based capillary pressure with the differential change in interfacial areas per volume as a function of wetting-phase saturation. The differential pressure contributions calculated from the experimental measurements are found to be nearly independent of the measured capillary pressure. These results suggest that other contributions to the capillary pressure must be significant when imbibition and drainage processes result in saturation gradients.&lt;/p&gt;
description: Supplementary materials for the paper: Relating capillary pressure to interfacial areas, Water Resour. Res., 44, W06408, 2008, doi:10.1029/2007WR006434.
DOI: 10.15468/dl.tgaeen
title: Occurrence Download

description: A dataset containing 60714 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation, Material sample, Material citation, Specimen, Living Specimen, Occurrence evidence)",
 "Continent is Europe",
 "OccurrenceStatus is Present",
 "TaxonKey is Linnaea borealis",
 "Year 2000-2024"
 ]
}

 The dataset includes 60714 records from 163 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059234-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.4231/d3p26q35r
title: Critical Engineering Literacy Test (CELT)

description: 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 version of the CELT. If you wish to use this instrument with your students, please contact a member of the research team to obtain the answers.
description: The CELT download includes the blueprint for writing assessment items, and the content of the assessment itself. This version (4.1) includes 2 parts, one on an engineering topic, and one on a biology topic.
DOI: 10.4231/d3x63b541
title: DAMAGED GIRDER - Supplementary Materials for the Report: Effects of Realistic Heat Straightening Repair on the Properties and Serviceability of Damaged Steel Beam Bridges

description: &lt;p&gt;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 prevent the side effects of heat straightening repair process. However the heat straightening guidelines are violated in the field due to time and economic issues. These violations include, but are not limited to: (a) under heating below 1200&deg;F, (b) over heating above 1200&deg;F, %(c%) over straining above restraining force limit (0.5 M,,p,,) and (d) multiple heat straightening of the same beam more than two times. Currently, there is a lack of knowledge of the effects of these imperfections in the heat straightening repair process on the condition and serviceability of the damaged-repaired beams. This knowledge is needed to develop more realistic guidelines for evaluating and replacing bridge members subjected to damage followed by imperfect heat straightening repair. The overall goal of this research is to develop recommendations and guidelines for evaluating steel beam bridges in Indiana subjected to damage followed by heat straightening repair with imperfections (overstraining, overheating, or multiple heat straightening).&lt;/p&gt;
description: Supplementary Materials for the Report: Effects of Realistic Heat Straightening Repair on the Properties and Serviceability of Damaged Steel Bridges
DOI: 10.4231/d3ns0kx8z
title: FORCE SYSTEM 1 - Supplementary Materials for the Report: Effects of Realistic Heat Straightening Repair on the Properties and Serviceability of Damaged Steel Beam Bridges

description: &lt;p&gt;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 prevent the side effects of heat straightening repair process. However the heat straightening guidelines are violated in the field due to time and economic issues. These violations include, but are not limited to: (a) under heating below 1200&deg;F, (b) over heating above 1200&deg;F, %(c%) over straining above restraining force limit (0.5 M,,p,,) and (d) multiple heat straightening of the same beam more than two times. Currently, there is a lack of knowledge of the effects of these imperfections in the heat straightening repair process on the condition and serviceability of the damaged-repaired beams. This knowledge is needed to develop more realistic guidelines for evaluating and replacing bridge members subjected to damage followed by imperfect heat straightening repair. The overall goal of this research is to develop recommendations and guidelines for evaluating steel beam bridges in Indiana subjected to damage followed by heat straightening repair with imperfections (overstraining, overheating, or multiple heat straightening).&lt;/p&gt;
description: Supplementary Materials for the Report: Effects of Realistic Heat Straightening Repair on the Properties and Serviceability of Damaged Steel Bridges
DOI: 10.4231/d3j09w45g
title: FORCE SYSTEM 2 - Supplementary Materials for the Report: Effects of Realistic Heat Straightening Repair on the Properties and Serviceability of Damaged Steel Beam Bridges

description: &lt;p&gt;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 prevent the side effects of heat straightening repair process. However the heat straightening guidelines are violated in the field due to time and economic issues. These violations include, but are not limited to: (a) under heating below 1200&deg;F, (b) over heating above 1200&deg;F, %(c%) over straining above restraining force limit (0.5 M,,p,,) and (d) multiple heat straightening of the same beam more than two times. Currently, there is a lack of knowledge of the effects of these imperfections in the heat straightening repair process on the condition and serviceability of the damaged-repaired beams. This knowledge is needed to develop more realistic guidelines for evaluating and replacing bridge members subjected to damage followed by imperfect heat straightening repair. The overall goal of this research is to develop recommendations and guidelines for evaluating steel beam bridges in Indiana subjected to damage followed by heat straightening repair with imperfections (overstraining, overheating, or multiple heat straightening).&lt;/p&gt;
description: Supplementary Materials for the Report: Effects of Realistic Heat Straightening Repair on the Properties and Serviceability of Damaged Steel Bridges
DOI: 10.4231/d3sf2mc0w
title: ADJUSTING FORCE - Supplementary Materials for the Report: Effects of Realistic Heat Straightening Repair on the Properties and Serviceability of Damaged Steel Beam Bridges

description: &lt;p&gt;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 prevent the side effects of heat straightening repair process. However the heat straightening guidelines are violated in the field due to time and economic issues. These violations include, but are not limited to: (a) under heating below 1200&deg;F, (b) over heating above 1200&deg;F, %(c%) over straining above restraining force limit (0.5 Mp) and (d) multiple heat straightening of the same beam more than two times. Currently, there is a lack of knowledge of the effects of these imperfections in the heat straightening repair process on the condition and serviceability of the damaged-repaired beams. This knowledge is needed to develop more realistic guidelines for evaluating and replacing bridge members subjected to damage followed by imperfect heat straightening repair. The overall goal of this research is to develop recommendations and guidelines for evaluating steel beam bridges in Indiana subjected to damage followed by heat straightening repair with imperfections (overstraining, overheating, or multiple heat straightening).&lt;/p&gt;
description: Supplementary Materials for the Report: Effects of Realistic Heat Straightening Repair on the Properties and Serviceability of Damaged Steel Bridges