bluuebunny/crossref_metadata_2025_split huggingface dataset:
Urea‐temperature phase diagrams capture the thermodynamics of denatured state expansion that accompany protein unfolding
Authors: Tischer Alexander , Auton Matthew 
Published: June 2013

AbstractWe have analyzed the thermodynamic properties of the von Willebrand factor (VWF) A3 domain using urea‐induced unfolding at variable temperature and thermal unfolding at variable urea concentrations to generate a phase diagram that quantitatively describes the equilibrium between native and denatured states. From this analysis, we were able to determine consistent thermodynamic parameters with various spectroscopic and calorimetric methods that define the urea–temperature parameter plane from cold denaturation to heat denaturation. Urea and thermal denaturation are experimentally reversible and independent of the thermal scan rate indicating that all transitions are at equilibrium and the van't Hoff and calorimetric enthalpies obtained from analysis of individual thermal transitions are equivalent demonstrating two‐state character. Global analysis of the urea–temperature phase diagram results in a significantly higher enthalpy of unfolding than obtained from analysis of individual thermal transitions and significant cross correlations describing the urea dependence of
and
that define a complex temperature dependence of the m‐value. Circular dichroism (CD) spectroscopy illustrates a large increase in secondary structure content of the urea‐denatured state as temperature increases and a loss of secondary structure in the thermally denatured state upon addition of urea. These structural changes in the denatured ensemble make up ∼40% of the total ellipticity change indicating a highly compact thermally denatured state. The difference between the thermodynamic parameters obtained from phase diagram analysis and those obtained from analysis of individual thermal transitions illustrates that phase diagrams capture both contributions to unfolding and denatured state expansion and by comparison are able to decipher these contributions.
Sugar nucleotide quantification using multiple reaction monitoring liquid chromatography/tandem mass spectrometry
Authors: Garcia Aldo D. , Chavez Jorge L. , Mechref Yehia 
Published: June 2013

RATIONALEGlycosylation of proteins and lipids is reliant on the availability of monosaccharide‐activated donors known as sugar nucleotides. They are responsible for glycosylation in cells. Reliable quantification of these sugar nucleotides might provide an insight into their biological roles and attributes.METHODSHerein, a method is described for the quantification of sugar nucleotides using ultra high pressure liquid chromatography (UHPLC) tandem mass spectrometry, allowing selective detection of sugar nucleotides in a biological sample. Seven model sugar nucleotide standards commonly associated with lipid and protein glycosylation were separated on a porous graphitic carbon column using an UHPLC system coupled to a triple stage quadrupole mass spectrometer utilizing a multiple reaction monitoring approach.RESULTSSuccessful baseline separation of these metabolites was attained in 6 min using an ammonium formate buffer and acetonitrile, circumventing the use of MS‐unfriendly pairing reagents. The linear dynamic range of this procedure was established over almost three orders of magnitude from 20 pg to 1 ng (40 pg to 2 ng for the isomers UDP‐GlcNAc/GalNAc). The limit of detection ranged from 15 pg to 30 pg while the limit of quantification ranged from 50 pg to 100 pg. Furthermore, viability of this method was tested using three different breast cancer cell lines (MDA‐MB‐231, MDA‐MB‐231‐BR, and MDA‐MB‐361) with the successful identification and quantification of all seven targeted sugar nucleotides.CONCLUSIONSThe described method permitted the quantitative analysis of sugar nucleotides in 10 min, thus allowing the practical use of this approach in high‐throughput settings. The method was also very effective for the quantification of sugar nucleotides derived from three different breast cancer cell lines. The distribution of sugar nucleotides was different among the different cell lines and unique for each cell line. Copyright © 2013 John Wiley & Sons, Ltd.
Local uniformity properties for glauber dynamics on graph colorings
Authors: Hayes Thomas P. 
Published: June 2013

AbstractWe investigate some local properties which hold with high probability for randomly selected colorings of a fixed graph with no short cycles. In a number of related works, establishing these particular properties has been a crucial step towards proving rapid convergence for the single‐site Glauber dynamics, a Markov chain for sampling colorings uniformly at random. For a large class of graphs, this approach yields the most efficient known algorithms for sampling random colorings. © 2013 Wiley Periodicals, Inc. Random Struct. Alg., 2013
Fibroblasts Cultured on Nanowires Exhibit Low Motility, Impaired Cell Division, and DNA Damage
Authors: Persson Henrik , Købler Carsten , Mølhave Kristian , Samuelson Lars , Tegenfeldt Jonas O. , Oredsson Stina , Prinz Christelle N. 
Published: June 2013

AbstractNanowires are commonly used as tools for interfacing living cells, acting as biomolecule‐delivery vectors or electrodes. It is generally assumed that the small size of the nanowires ensures a minimal cellular perturbation, yet the effects of nanowires on cell migration and proliferation remain largely unknown. Fibroblast behaviour on vertical nanowire arrays is investigated, and it is shown that cell motility and proliferation rate are reduced on nanowires. Fibroblasts cultured on long nanowires exhibit failed cell division, DNA damage, increased ROS content and respiration. Using focused ion beam milling and scanning electron microscopy, highly curved but intact nuclear membranes are observed, showing no direct contact between the nanowires and the DNA. The nanowires possibly induce cellular stress and high respiration rates, which trigger the formation of ROS, which in turn results in DNA damage. These results are important guidelines to the design and interpretation of experiments involving nanowire‐based transfection and electrical characterization of living cells.
Hypericin-photodynamic therapy leads to interleukin-6 secretion by HepG2 cells and their apoptosis via recruitment of BH3 interacting-domain death agonist and caspases
Authors: Barathan M , Mariappan V , Shankar E M , Abdullah B JJ , Goh K L , Vadivelu J 
Published: June 2013

AbstractPhotodynamic therapy (PDT) has emerged as a capable therapeutic modality for the treatment of cancer. PDT is a targeted cancer therapy that reportedly leads to tumor cell apoptosis and/or necrosis by facilitating the secretion of certain pro-inflammatory cytokines and expression of multiple apoptotic mediators in the tumor microenvironment. In addition, PDT also triggers oxidative stress that directs tumor cell killing and activation of inflammatory responses. However, the cellular and molecular mechanisms underlying the role of PDT in facilitating tumor cell apoptosis remain ambiguous. Here, we investigated the ability of PDT in association with hypericin (HY) to induce tumor cell apoptosis by facilitating the induction of reactive oxygen species (ROS) and secretion of Th1/Th2/Th17 cytokines in human hepatocellular liver carcinoma cell line (HepG2) cells. To discover if any apoptotic mediators were implicated in the enhancement of cell death of HY-PDT-treated tumor cells, selected gene profiling in response to HY-PDT treatment was implemented. Experimental results showed that interleukin (IL)-6 was significantly increased in all HY-PDT-treated cells, especially in 1 μg/ml HY-PDT, resulting in cell death. In addition, quantitative real-time PCR analysis revealed that the expression of apoptotic genes, such as BH3-interacting-domain death agonist (BID), cytochrome complex (CYT-C) and caspases (CASP3, 6, 7, 8 and 9) was remarkably higher in HY-PDT-treated HepG2 cells than the untreated HepG2 cells, entailing that tumor destruction of immune-mediated cell death occurs only in PDT-treated tumor cells. Hence, we showed that HY-PDT treatment induces apoptosis in HepG2 cells by facilitating cytotoxic ROS, and potentially recruits IL-6 and apoptosis mediators, providing additional hints for the existence of alternative mechanisms of anti-tumor immunity in hepatocellular carcinoma, which contribute to long-term suppression of tumor growth following PDT.
Nanoscience for the Conservation of Works of Art
Authors:   Royal Society of Chemistry,   Royal Society of Chemistry
Published: June 2013

Understanding the chemistry behind works of art and heritage materials presents an opportunity to apply scientific techniques to their conservation and restoration. Manipulation of materials at the nanoscale affords greater accuracy and minimal disturbance to the original work, while efficiently combating the affects of time and environment.
This book meets the growing demand for an all-encompassing handbook to instruct on the use of today's science on mankind's cultural heritage. The editors have pioneered modern techniques in art conservation over the last four decades, and have brought together expertise from across the globe. Each chapter presents the theoretical background to the topic in question, followed by practical information on its application and relevant case studies.
Introductory chapters present the science behind the physical composition of art materials. Four chapters explore various cleaning techniques now, followed by four chapters describing the application of inorganic nanomaterials. Each chapter is fully referenced to the primary literature and offers suggestions for further reading.
Professional conservators and scientists alike will find this essential reading, as will postgraduate students in the fields of materials and colloid science, art restoration and nanoscience.
Wideband printed slot antenna with polarisation diversity
Authors: Xie J.‐J. , Yin Y.‐Z. , Chen Y. 
Published: June 2013

A single‐layer wideband printed slot antenna with polarisation diversity is presented using a hybrid feeding technique. The antenna consists of an aperture‐coupled feeding element and a coplanar waveguide feeding element. The aperture‐coupled microstrip feed line with a 180° phase difference is used to reduce the cross‐polarisation level and improve the isolation level. A circular patch is connected to the coplanar waveguide feed line for good impedance matching. By introducing a fan‐shaped slot to separate the ground plane of the radiating elements, the measured isolation between the two feeding ports is better than 30 dB in the whole operating band. The measured −10 dB impedance bandwidths are 49% (4.72–7.75 GHz) and 63% (3.96–7.64 GHz) at port 1 and port 2, respectively. Moreover, the proposed antenna has a compact structure and stable gain over the operating band; thus it can be used in the 5.2/5.8 GHz WLAN and 5.5 GHz WiMAX systems.
Fully passivated radial junction nanowire silicon solar cells with submerged nickel‐silicide contact for efficiency enhancement
Authors: Ren R. , Guo Y.X. , Wang J. , Zhu R.H. 
Published: June 2013

Presented is a silicon solar cell model with fully passivated radial junction nanowire surface decoration and submerged nickel‐silicide contact. Numerical simulations using a finite‐difference time‐domain method have been done to investigate the spectral responses of the solar cell model. The experimental results indicate that, with proper nickel‐silicide thickness, the fill factor of the cell can be improved considerably without much degradation on short circuit current density. Under AM 1.5G illumination, the silicon nanowire solar cell device with 50 Å nickel‐silicide contact has short circuit current density of 26.3 mA/cm2, open circuit voltage of 586 mV and fill factor of 70.0%, contributing to power conversion efficiency of 10.8%, which is 19% higher than the control device without the nickel‐silicide contact.
The Impact of a Single Ward for Cohorting Patients with Infection due to Multidrug-Resistant Organisms
Authors: Stumpfs Diego Jung , de Souza Sonia Beatriz Cocaro , Konkewicz Loriane Rita , Lovatto Carem Gorniak , da Silva Cristófer Farias , Macedo Andréia Barcelos Teixeira , dos Santos Rodrigo Pires 
Published: June 2013

Multidrug-resistant organisms (MDROs) are emerging and disseminating around the globe. The guidelines for the management of MDROs support the use of various interventions to reduce the burden of MDROs. We conducted a study to assess the impact of the creation of a unit for cohorting of patients with infection due to MDROs.Hospital de Clínicas de Porto Alegre, a 795-bed university, public hospital, is located in the city of Porto Alegre in southern Brazil. In a quasi-experimental study, we assessed the impact of the creation of an MDRO unit for patient cohorting on the overall hospital incidence of infection due to MDROs.The 34 beds of the unit were located in 16 rooms for adult MDRO-infected patients and 2 additional rooms for respiratory isolation. Patients were transferred to the unit when they were identified as infected or colonized with MDROs. The unit staff was trained for MDRO-infected patient care; unit staff, patients, and families attended weekly meetings for education about MDROs with a multidisciplinary team (doctors, nurses, pharmacists, and social assistants).
ThreaDom: extracting protein domain boundary information from multiple threading alignments
Authors: Xue Zhidong , Xu Dong , Wang Yan , Zhang Yang 
Published: June 2013

Abstract
Motivation: Protein domains are subunits that can fold and evolve independently. Identification of domain boundary locations is often the first step in protein folding and function annotations. Most of the current methods deduce domain boundaries by sequence-based analysis, which has low accuracy. There is no efficient method for predicting discontinuous domains that consist of segments from separated sequence regions. As template-based methods are most efficient for protein 3D structure modeling, combining multiple threading alignment information should increase the accuracy and reliability of computational domain predictions.
Result: We developed a new protein domain predictor, ThreaDom, which deduces domain boundary locations based on multiple threading alignments. The core of the method development is the derivation of a domain conservation score that combines information from template domain structures and terminal and internal alignment gaps. Tested on 630 non-redundant sequences, without using homologous templates, ThreaDom generates correct single- and multi-domain classifications in 81% of cases, where 78% have the domain linker assigned within ±20 residues. In a second test on 486 proteins with discontinuous domains, ThreaDom achieves an average precision 84% and recall 65% in domain boundary prediction. Finally, ThreaDom was examined on 56 targets from CASP8 and had a domain overlap rate 73, 87 and 85% with the target for Free Modeling, Hard multiple-domain and discontinuous domain proteins, respectively, which are significantly higher than most domain predictors in the CASP8. Similar results were achieved on the targets from the most recently CASP9 and CASP10 experiments.
Availability: http://zhanglab.ccmb.med.umich.edu/ThreaDom/.
Contact: zhng@umich.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Compressive genomics for protein databases
Authors: Daniels Noah M. , Gallant Andrew , Peng Jian , Cowen Lenore J. , Baym Michael , Berger Bonnie 
Published: June 2013

Abstract
Motivation: The exponential growth of protein sequence databases has increasingly made the fundamental question of searching for homologs a computational bottleneck. The amount of unique data, however, is not growing nearly as fast; we can exploit this fact to greatly accelerate homology search. Acceleration of programs in the popular PSI/DELTA-BLAST family of tools will not only speed-up homology search directly but also the huge collection of other current programs that primarily interact with large protein databases via precisely these tools.
Results: We introduce a suite of homology search tools, powered by compressively accelerated protein BLAST (CaBLASTP), which are significantly faster than and comparably accurate with all known state-of-the-art tools, including HHblits, DELTA-BLAST and PSI-BLAST. Further, our tools are implemented in a manner that allows direct substitution into existing analysis pipelines. The key idea is that we introduce a local similarity-based compression scheme that allows us to operate directly on the compressed data. Importantly, CaBLASTP’s runtime scales almost linearly in the amount of unique data, as opposed to current BLASTP variants, which scale linearly in the size of the full protein database being searched. Our compressive algorithms will speed-up many tasks, such as protein structure prediction and orthology mapping, which rely heavily on homology search.
Availability: CaBLASTP is available under the GNU Public License at http://cablastp.csail.mit.edu/
Contact: bab@mit.edu
Stability selection for regression-based models of transcription factor–DNA binding specificity
Authors: Mordelet Fantine , Horton John , Hartemink Alexander J. , Engelhardt Barbara E. , Gordân Raluca 
Published: June 2013

AbstractMotivation: The DNA binding specificity of a transcription factor (TF) is typically represented using a position weight matrix model, which implicitly assumes that individual bases in a TF binding site contribute independently to the binding affinity, an assumption that does not always hold. For this reason, more complex models of binding specificity have been developed. However, these models have their own caveats: they typically have a large number of parameters, which makes them hard to learn and interpret.Results: We propose novel regression-based models of TF–DNA binding specificity, trained using high resolution in vitro data from custom protein-binding microarray (PBM) experiments. Our PBMs are specifically designed to cover a large number of putative DNA binding sites for the TFs of interest (yeast TFs Cbf1 and Tye7, and human TFs c-Myc, Max and Mad2) in their native genomic context. These high-throughput quantitative data are well suited for training complex models that take into account not only independent contributions from individual bases, but also contributions from di- and trinucleotides at various positions within or near the binding sites. To ensure that our models remain interpretable, we use feature selection to identify a small number of sequence features that accurately predict TF–DNA binding specificity. To further illustrate the accuracy of our regression models, we show that even in the case of paralogous TF with highly similar position weight matrices, our new models can distinguish the specificities of individual factors. Thus, our work represents an important step toward better sequence-based models of individual TF–DNA binding specificity.Availability: Our code is available at http://genome.duke.edu/labs/gordan/ISMB2013. The PBM data used in this article are available in the Gene Expression Omnibus under accession number GSE47026.Contact: raluca.gordan@duke.edu
Automated cellular annotation for high-resolution images of adult Caenorhabditis elegans
Authors: Aerni Sarah J. , Liu Xiao , Do Chuong B. , Gross Samuel S. , Nguyen Andy , Guo Stephen D. , Long Fuhui , Peng Hanchuan , Kim Stuart S. , Batzoglou Serafim 
Published: June 2013

Abstract
Motivation: Advances in high-resolution microscopy have recently made possible the analysis of gene expression at the level of individual cells. The fixed lineage of cells in the adult worm Caenorhabditis elegans makes this organism an ideal model for studying complex biological processes like development and aging. However, annotating individual cells in images of adult C.elegans typically requires expertise and significant manual effort. Automation of this task is therefore critical to enabling high-resolution studies of a large number of genes.
Results: In this article, we describe an automated method for annotating a subset of 154 cells (including various muscle, intestinal and hypodermal cells) in high-resolution images of adult C.elegans. We formulate the task of labeling cells within an image as a combinatorial optimization problem, where the goal is to minimize a scoring function that compares cells in a test input image with cells from a training atlas of manually annotated worms according to various spatial and morphological characteristics. We propose an approach for solving this problem based on reduction to minimum-cost maximum-flow and apply a cross-entropy–based learning algorithm to tune the weights of our scoring function. We achieve 84% median accuracy across a set of 154 cell labels in this highly variable system. These results demonstrate the feasibility of the automatic annotation of microscopy-based images in adult C.elegans.
Contact: saerni@cs.stanford.edu
Information-theoretic evaluation of predicted ontological annotations
Authors: Clark Wyatt T. , Radivojac Predrag 
Published: June 2013

Abstract
Motivation: The development of effective methods for the prediction of ontological annotations is an important goal in computational biology, with protein function prediction and disease gene prioritization gaining wide recognition. Although various algorithms have been proposed for these tasks, evaluating their performance is difficult owing to problems caused both by the structure of biomedical ontologies and biased or incomplete experimental annotations of genes and gene products.
Results: We propose an information-theoretic framework to evaluate the performance of computational protein function prediction. We use a Bayesian network, structured according to the underlying ontology, to model the prior probability of a protein’s function. We then define two concepts, misinformation and remaining uncertainty, that can be seen as information-theoretic analogs of precision and recall. Finally, we propose a single statistic, referred to as semantic distance, that can be used to rank classification models. We evaluate our approach by analyzing the performance of three protein function predictors of Gene Ontology terms and provide evidence that it addresses several weaknesses of currently used metrics. We believe this framework provides useful insights into the performance of protein function prediction tools.
Contact: predrag@indiana.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Inference of historical migration rates via haplotype sharing
Authors: Palamara Pier Francesco , Pe’er Itsik 
Published: June 2013

Abstract
Summary: Pairs of individuals from a study cohort will often share long-range haplotypes identical-by-descent. Such haplotypes are transmitted from common ancestors that lived tens to hundreds of generations in the past, and they can now be efficiently detected in high-resolution genomic datasets, providing a novel source of information in several domains of genetic analysis. Recently, haplotype sharing distributions were studied in the context of demographic inference, and they were used to reconstruct recent demographic events in several populations. We here extend the framework to handle demographic models that contain multiple demes interacting through migration. We extensively test our formulation in several demographic scenarios, compare our approach with methods based on ancestry deconvolution and use this method to analyze Masai samples from the HapMap 3 dataset.
Availability: DoRIS, a Java implementation of the proposed method, and its source code are freely available at http://www.cs.columbia.edu/∼pier/doris.
Contact: itsik@cs.columbia.edu