bluuebunny/crossref_metadata_2025_split huggingface dataset:
Laryngeal tumor volume as a predictor for thyroid cartilage penetration
Authors: Kats Svetlana S. , Muller Susan , Aiken Ashley , Hudgins Patricia A. , Wadsworth J. Trad , Shin Dong M. , Khuri Fadlo , Beitler Jonathan J. 
Published: April 2012

AbstractBackgroundReview of laryngectomy specimens demonstrated that preoperative CT scanning is suboptimal in predicting both thyroid cartilage penetration and extralaryngeal spread. We investigated the association between the CT‐based gross tumor volume (GTV) with pathologic evidence of thyroid cartilage penetration among patients undergoing laryngectomy for squamous cell carcinoma (SCC) of the larynx.MethodsNinety‐four patients were identified who underwent total laryngectomy for SCC of the larynx. GTV, as defined by preoperative diagnostic CT scan, was contoured and analyzed using treatment‐planning software.ResultsAmong the 49 nonirradiated patients, the mean GTVs of patients with (n = 15) and without (n = 34) thyroid cartilage penetration was 60.1 and 28.0 cm3 (p = .004). When the nonirradiated patients were divided into 3 GTV groups (≤25 cm3, 25–50 cm3, >50 cm3), the rates of thyroid cartilage penetration were 23%, 17%, and 78%, respectively (p = .003).ConclusionsLaryngeal tumor volume is associated with pathologic evidence of thyroid cartilage penetration in nonirradiated patients. © 2012 Wiley Periodicals, Inc. Head Neck, 2013
Status dystonicus: Predictors of outcome and progression patterns of underlying disease
Authors: Fasano Alfonso , Ricciardi Lucia , Bentivoglio Anna Rita , Canavese Carlotta , Zorzi Giovanna , Petrovic Igor , Kresojevic Nikola , Kostić Vladimir S. , Svetel Marina , Kovacs Norbert , Balas Istvan , Roubertie Agathe , Mishra Devendra , Mariotti Paolo , Temudo Teresa , Nardocci Nardo 
Published: April 2012

AbstractBackground:Status dystonicus (SD) is a rare, life‐threatening disorder characterized by acute worsening of generalized dystonia.Methods:This study was conducted to characterize the pathogenesis, clinical course, and prognosis of SD. We reviewed the records of six centers and analyzed them together with all the cases previously reported in the literature.Results:Eighty‐nine episodes occurring in 68 patients were studied. The majority of patients were males (64.7%), were <15 years of age (58.8%), and had secondary dystonia as the underlying condition (37.8%). The episodes were mainly characterized by tonic muscle spasms (68.5%), with phasic forms more common in secondary forms and among females. Almost all cases needed a multistaged approach, with surgery being the most successful strategy. Neurological conditions preceding the episode worsened in 16.2% of cases (ending in death in 10.3%).Conclusions:The course and outcome of SD is highly variable; male gender and prevalent tonic phenotype predict a poor outcome © 2012 Movement Disorder Society
Antidot effects on the open‐shell characters and second hyperpolarizabilities of rectangular graphene nanoflakes
Authors: Yoneda Kyohei , Minamide Shu , Yamada Taishi , Ito Soichi , Minami Takuya , Kishi Ryohei , Shigeta Yasuteru , Nakano Masayoshi 
Published: April 2012

AbstractUsing the long‐range corrected spin‐unrestricted density functional theory method, the impact of antidot structure on the open‐shell character and the second hyperpolarizability (γ) of graphene nanoflakes (GNFs) has been investigated for rectangular GNFs with and without antidot structure, referred to as antidot and perfect GNFs, respectively. It is found that the two GNFs exhibit different multiradical characters; the antidot GNF shows intermediate open‐shell character in contrast to the perfect GNF presenting nearly pure tetraradical character. This antidot structure dependence of open‐shell character can be explained in terms of their natural orbital distributions. Such difference in open‐shell characters affects their γ values; the γ of the antidot GNF is about 1.7 times larger than that of the perfect GNF, the feature of which is in agreement with our previous results on the diradical character dependence of γ. © 2012 Wiley Periodicals, Inc.
Hydrogen bonds between pyrazine and RCOOH (R = H, CH3, and C6H5): A theoretical study
Authors: Nascimento Renata X. D. , Belarmino Márcia K. D. L. , Lima Nathália B. D. 
Published: April 2012

AbstractTheoretical calculations using Møller–Plesset perturbation theory (MP2) levels of calculation with a 6‐31++G(d,p) basis set have been performed to determine stable structures and molecular properties for the 1:1 and 1:2 hydrogen complexes involving pyrazine as proton acceptor and RCOOH (R = H, CH3, and C6H5). Six complexes have been characterized as minima as no imaginary frequency was found. As expected, the HO chemical bonds lengths are increased after complexation. For the strongly bound complex, the doubly complexed pyrazine acts as a bridge between the two end molecules while transferring electrons. The vibrational changes that take place in the RCOOH after complexation with pyrazine follow the usual behavior, and the HO stretching frequency is shifted downward whereas its irradiated intensity is much enhanced. As unexpected result, the vibrational modes of the CH stretching of pyrazine has its frequencies shifted to the blue. © 2012 Wiley Periodicals, Inc.
Comparative modeling and QM/MM studies of cysteine protease mutant of Theobroma cacao
Authors: Andrade Deyse Valverde Gomes de , Góes‐Neto Aristóteles , Junior Moacyr Comar , Taranto Alex Gutterres 
Published: April 2012

AbstractThe culture of cacao in Brazil was highly harmed by Moniliophthora perniciosa, the fungus that causes witches' broom disease of cocoa. This disease decreases significantly the cocoa production. An important strategy for control of the witches' broom is the molecular study of the interaction between cacao–M. perniciosa. However, there is little information about of the mechanism of molecular interaction involved in resistance/vulnerability of cacoa tree. To address this problem, the Genome Project showed genes of cysteine protease involved in the mechanism of resistance/vulnerability. Cysteine protease is expressed during the process of the maturation of the seed and it is present in necrofitics period of the disease. Furthermore, proteases have a wide application in feed products, detergents, and pharmaceutical industries. This work constructed the three‐dimensional structure of the cysteine protease of Theobroma cacao by comparative modeling. Thus, the primary sequence of the cysteine protease of T. cacao was submitted to BLASTp obtaining the protein 1PCI with 36% of structural similarity. The model was refined and validated by AMBER 11.0; and evaluated by PROCHECK and ANOLEA software, respectively. This model consists of 171 amino acids, formed by 2693 atoms linked by 2719 chemical bonds. The 3D structure of this enzyme has seven α‐helix, 23 turns, and two β‐sheets. The region of the conserved active site is represented by residues Cys25 and His159. From this model, a mutant model was then generated by replacing His159/Gly. This also was evaluated showing similar characteristics. Studies of the interaction between the mutant structure with the metal ions such as Zn+2, Cu+1, Cu+2, and Cd+2 were performed by Quantum Mechanical/Molecular Mechanical (QM/MM) approach implemented in Gaussian 09W. As a result, the mutant protein is able to complex with all of them, principally with Cd+2 by −3.04 Kcal/mol. This is potentially toxic element present in the environment. Therefore this study suggests that changes in the sequence of the cysteine protease of T. Cacao can lead to development new products of commercial interest. © 2012 Wiley Periodicals, Inc.
Genetic interactions of yeast NEP1 (EMG1), encoding an essential factor in ribosome biogenesis
Authors: Schilling Valeska , Peifer Christian , Buchhaupt Markus , Lamberth Stefanie , Lioutikov Anatoli , Rietschel Benjamin , Kötter Peter , Entian Karl‐Dieter 
Published: April 2012

AbstractNep1 methylates the hypermodified ψ1191 base of 18S rRNA and has an additional essential function during ribosome biogenesis. It is strongly conserved in eukaryotes and a point mutation causes the human Bowen–Conradi syndrome. To identify Δnep1‐specific genetic interactions, viable deletions were screened genome‐wide (SGA). Due to its essential function, we used, for the first time, query strain (Δnep1) with two additive suppressor conditions (mcRPS19B, nop6‐1). Nep1 interacting genes correspond to ribosome biogenesis (RPS18A, RPS18B, RRP8, EFG1, UTP30), to ribosome quality control (UBP3, BRE5, UBP6) and to ribosome functional control (DOM34, no‐go decay). Deletions in ribosome quality and functional control genes were synthetically sick with Δnep1. They cope with malfunctions and the respective deletions strengthen the Δnep1 growth deficiency. Except for Δrps18b, deletions in the identified ribosome biogenesis genes were synthetically lethal with Δnep1. While the synthetic lethalities of Δrrp8 and Δefg1 may result from additive defects, the Δutp30 deletion seems to be in close functional relationship. The Δutp30 deletion itself has no phenotype but it enforced all nep1‐1ts mutant phenotypes. Furthermore, its overexpression partially restored the nep1‐1ts growth deficiency. Our genetic and biochemical data suggest that Utp30 and Nep1 act together during pre‐ribosomal complex formation and, along with Rps18, provide the surface for the Rps19 assembly to the 90S pre‐ribosome. Copyright © 2012 John Wiley & Sons, Ltd.
Single yeast cell vacuolar milieu viscosity assessment by fluorescence polarization microscopy with computer image analysis
Authors: Puchkov Evgeny O. 
Published: April 2012

AbstractThis study was undertaken to evaluate the apparent viscosity within the vacuoles of single Saccharomyces cerevisiae cells by steady‐state fluorescence anisotropy measurements of quinacrine, using wide‐field fluorescence polarization microscopy combined with computer image analysis. Quinacrine was shown to be rather specifically accumulated within the vacuoles of the cells. This accumulation was effectively reversed by ATP depletion of the cells, with no detectable binding of the dye within the vacuoles. Quinacrine fluorescence anisotropy in the sucrose solutions of various viscosities obeyed the Perrin equation. The fluorescence anisotropy of quinacrine was measured in the vacuoles of 39 cells. From cell to cell, this parameter changed in the range 0.032–0.086. Using the Perrin plot as a calibration curve, apparent viscosity values of the vacuolar milieu were calculated for each cell. The population of the cells studied was heterogeneous with regard to vacuolar viscosity, which was in the range 3.5 ± 0.4–14.06 ± 0.64 cP. There was a characteristic distribution of the frequencies of cells with apparent viscosities within certain limits, and cells with viscosity values in the range 5–6 cP were the most frequent. No relationship was found between the sizes of the vacuoles and their apparent viscosities. Copyright © 2012 John Wiley & Sons, Ltd.
Gesundheit und integrierte Stadtentwicklung
Authors: Böhme Christa 
Published: April 2012

Einleitung
Die Gesundheit des Menschen wird von verschiedenen Faktoren determiniert. Neben Alter, Geschlecht und genetischen Dispositionen, Lebensstil und Verhaltensweisen sowie sozialen Netzwerken sind dies vor allem die Lebensbedingungen und -verhältnisse der Menschen. Aufgabe der Stadtentwicklung ist es, diese Lebensverhältnisse vor Ort in den Kommunen zu gestalten. Entscheidungen zur Stadtentwicklung haben daher seit jeher die Gesundheit der Menschen in den Städten beeinflusst.
Bayesian integration of networks without gold standards
Authors: Weile Jochen , James Katherine , Hallinan Jennifer , Cockell Simon J. , Lord Phillip , Wipat Anil , Wilkinson Darren J. 
Published: April 2012

Abstract
Motivation: Biological experiments give insight into networks of processes inside a cell, but are subject to error and uncertainty. However, due to the overlap between the large number of experiments reported in public databases it is possible to assess the chances of individual observations being correct. In order to do so, existing methods rely on high-quality ‘gold standard’ reference networks, but such reference networks are not always available.
Results: We present a novel algorithm for computing the probability of network interactions that operates without gold standard reference data. We show that our algorithm outperforms existing gold standard-based methods. Finally, we apply the new algorithm to a large collection of genetic interaction and protein–protein interaction experiments.
Availability: The integrated dataset and a reference implementation of the algorithm as a plug-in for the Ondex data integration framework are available for download at http://bio-nexus.ncl.ac.uk/projects/nogold/
Contact: darren.wilkinson@ncl.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Matrix eQTL: ultra fast eQTL analysis via large matrix operations
Authors: Shabalin Andrey A. 
Published: April 2012

AbstractMotivation: Expression quantitative trait loci (eQTL) analysis links variations in gene expression levels to genotypes. For modern datasets, eQTL analysis is a computationally intensive task as it involves testing for association of billions of transcript-SNP (single-nucleotide polymorphism) pair. The heavy computational burden makes eQTL analysis less popular and sometimes forces analysts to restrict their attention to just a small subset of transcript-SNP pairs. As more transcripts and SNPs get interrogated over a growing number of samples, the demand for faster tools for eQTL analysis grows stronger.Results: We have developed a new software for computationally efficient eQTL analysis called Matrix eQTL. In tests on large datasets, it was 2–3 orders of magnitude faster than existing popular tools for QTL/eQTL analysis, while finding the same eQTLs. The fast performance is achieved by special preprocessing and expressing the most computationally intensive part of the algorithm in terms of large matrix operations. Matrix eQTL supports additive linear and ANOVA models with covariates, including models with correlated and heteroskedastic errors. The issue of multiple testing is addressed by calculating false discovery rate; this can be done separately for cis- and trans-eQTLs.Availability: Matlab and R implementations are available for free at http://www.bios.unc.edu/research/genomic_software/Matrix_eQTLContact: shabalin@email.unc.edu
Rigorous assessment of gene set enrichment tests
Authors: Naeem Haroon , Zimmer Ralf , Tavakkolkhah Pegah , Küffner Robert 
Published: April 2012

Abstract
Motivation: Several statistical tests are available to detect the enrichment of differential expression in gene sets. Such tests were originally proposed for analyzing gene sets associated with biological processes. The objective evaluation of tests on real measurements has not been possible as it is difficult to decide a priori, which processes will be affected in given experiments.
Results: We present a first large study to rigorously assess and compare the performance of gene set enrichment tests on real expression measurements. Gene sets are defined based on the targets of given regulators such as transcription factors (TFs) and microRNAs (miRNAs). In contrast to processes, TFs and miRNAs are amenable to direct perturbations, e.g. regulator over-expression or deletion. We assess the ability of 14 different statistical tests to predict the perturbations from expression measurements in Escherichia coli, Saccharomyces cerevisiae and human. We also analyze how performance depends on the quality and comprehensiveness of the regulator targets via a permutation approach. We find that ANOVA and Wilcoxons test consistently perform better than for instance Kolmogorov–Smirnov and hypergeometric tests. For scenarios where the optimal test is not known, we suggest to combine all evaluated tests into an unweighted consensus, which also performs well in our assessment. Our results provide a guide for the selection of existing tests as well as a basis for the development and assessment of novel tests.
Contact: robert.kueffner@bio.ifi.lmu.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Eoulsan: a cloud computing-based framework facilitating high throughput sequencing analyses
Authors: Jourdren Laurent , Bernard Maria , Dillies Marie-Agnès , Le Crom Stéphane 
Published: April 2012

Abstract
Summary: We developed a modular and scalable framework called Eoulsan, based on the Hadoop implementation of the MapReduce algorithm dedicated to high-throughput sequencing data analysis. Eoulsan allows users to easily set up a cloud computing cluster and automate the analysis of several samples at once using various software solutions available. Our tests with Amazon Web Services demonstrated that the computation cost is linear with the number of instances booked as is the running time with the increasing amounts of data.
Availability and implementation: Eoulsan is implemented in Java, supported on Linux systems and distributed under the LGPL License at: http://transcriptome.ens.fr/eoulsan/
Contact: eoulsan@biologie.ens.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
PaGeFinder: quantitative identification of spatiotemporal pattern genes
Authors: Pan Jian-Bo , Hu Shi-Chang , Wang Hao , Zou Quan , Ji Zhi-Liang 
Published: April 2012

Abstract
Summary: Pattern Gene Finder (PaGeFinder) is a web-based server for on-line detection of gene expression patterns from serial transcriptomic data generated by high-throughput technologies like microarray or next-generation sequencing. Three particular parameters, the specificity measure, the dispersion measure and the contribution measure, were introduced and implemented in PaGeFinder to help quantitative and interactive identification of pattern genes like housekeeping genes, specific (selective) genes and repressed genes. Besides the on-line computation service, the PaGeFinder also provides downloadable Java programs for local detection of gene expression patterns.
Availability: http://bioinf.xmu.edu.cn:8080/PaGeFinder/index.jsp
Contact: appo@xmu.edu.cn; zouquan@xmu.edu.cn
Differential variability improves the identification of cancer risk markers in DNA methylation studies profiling precursor cancer lesions
Authors: Teschendorff Andrew E. , Widschwendter Martin 
Published: April 2012

Abstract
Motivation: The standard paradigm in omic disciplines has been to identify biologically relevant biomarkers using statistics that reflect differences in mean levels of a molecular quantity such as mRNA expression or DNA methylation. Recently, however, it has been proposed that differential epigenetic variability may mark genes that contribute to the risk of complex genetic diseases like cancer and that identification of risk and early detection markers may therefore benefit from statistics based on differential variability.
Results: Using four genome-wide DNA methylation datasets totalling 311 epithelial samples and encompassing all stages of cervical carcinogenesis, we here formally demonstrate that differential variability, as a criterion for selecting DNA methylation features, can identify cancer risk markers more reliably than statistics based on differences in mean methylation. We show that differential variability selects features with heterogeneous outlier methylation profiles and that these play a key role in the early stages of carcinogenesis. Moreover, differentially variable features identified in precursor non-invasive lesions exhibit significantly increased enrichment for developmental genes compared with differentially methylated sites. Conversely, differential variability does not add predictive value in cancer studies profiling invasive tumours or whole-blood tissue. Finally, we incorporate the differential variability feature selection step into a novel adaptive index prediction algorithm called EVORA (epigenetic variable outliers for risk prediction analysis), and demonstrate that EVORA compares favourably to powerful prediction algorithms based on differential methylation statistics.
Conclusions: Statistics based on differential variability improve the detection of cancer risk markers in the context of DNA methylation studies profiling epithelial preinvasive neoplasias. We present a novel algorithm (EVORA) which could be used for prediction and diagnosis of precursor epithelial cancer lesions.
Availability: R-scripts implementing EVORA are available from CRAN (www.r-project.org).
Contact: a.teschendorff@ucl.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies
Authors: Gritsenko Alexey A. , Nijkamp Jurgen F. , Reinders Marcel J.T. , Ridder Dick de 
Published: April 2012

Abstract
Motivation: The increasing availability of second-generation high-throughput sequencing (HTS) technologies has sparked a growing interest in de novo genome sequencing. This in turn has fueled the need for reliable means of obtaining high-quality draft genomes from short-read sequencing data. The millions of reads usually involved in HTS experiments are first assembled into longer fragments called contigs, which are then scaffolded, i.e. ordered and oriented using additional information, to produce even longer sequences called scaffolds. Most existing scaffolders of HTS genome assemblies are not suited for using information other than paired reads to perform scaffolding. They use this limited information to construct scaffolds, often preferring scaffold length over accuracy, when faced with the tradeoff.
Results: We present GRASS (GeneRic ASsembly Scaffolder)—a novel algorithm for scaffolding second-generation sequencing assemblies capable of using diverse information sources. GRASS offers a mixed-integer programming formulation of the contig scaffolding problem, which combines contig order, distance and orientation in a single optimization objective. The resulting optimization problem is solved using an expectation–maximization procedure and an unconstrained binary quadratic programming approximation of the original problem. We compared GRASS with existing HTS scaffolders using Illumina paired reads of three bacterial genomes. Our algorithm constructs a comparable number of scaffolds, but makes fewer errors. This result is further improved when additional data, in the form of related genome sequences, are used.
Availability: GRASS source code is freely available from http://code.google.com/p/tud-scaffolding/.
Contact: a.gritsenko@tudelft.nl
Supplementary information: Supplementary data are available at Bioinformatics online.
NASPGHAN Practice Guidelines
Authors: Mack Cara L. , Gonzalez‐Peralta Regino P. , Gupta Nitika , Leung Daniel , Narkewicz Michael R. , Roberts Eve A. , Rosenthal Philip , Schwarz Kathleen B. 
Published: April 2012

ABSTRACTHepatitis C virus (HCV) is an RNA virus that affects >180 million individuals worldwide with a high propensity for chronic infection. Children with HCV infection differ from adults in several ways including some modes of transmission, rates of clearance, progression of fibrosis, and the duration of potential chronic infection when acquired at birth. Since the discovery of HCV in 1989, there have been significant advances in the understanding of the virology and natural history of chronic HCV infection in children. In addition, there are now several treatment options for children with chronic hepatitis C infection and many new therapies on the horizon. As a consequence, the North American Society for Pediatric Gastroenterology, Hepatology, and Nutrition brought together experts in pediatric hepatology to review the available data in children and provide clinicians with approaches to the diagnosis, management, and prevention of HCV infection in children and adolescents. The guideline details the epidemiology and natural history of HCV infection in children, the diagnostic workup, monitoring and treatment of disease, and provides an update on future treatment options and areas of research.