bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring the human tear fluid: Discovery of new biomarkers in multiple sclerosis
Authors: Salvisberg Cindy , Tajouri Nadja , Hainard Alexandre , Burkhard Pierre R. , Lalive Patrice H. , Turck Natacha 
Published: February 2014

PurposeMultiple sclerosis is the first cause of progressive neurological disability among young adults living in Western countries. Its diagnosis is mostly based on clinical evaluation, neuroimaging, and in some cases cerebrospinal fluid (CSF) analysis, but no definitive diagnostic test exists. We proposed here that the exploration of tears from multiple sclerosis patients could lead to the discovery of new biomarkers.Experimental designThirty multiple sclerosis patients (20% men) recruited to the Geneva University Hospitals were included in our study (mean age ± SD [years]: 42.4 ± 15.9). Twenty‐five control patients (32% men) were also enrolled (mean age ± SD [years]: 42.7±15.1). Tears, CSF or blood was collected for each patient. Three independent quantitative (tandem mass tag) experiments were carried out between tears from multiple sclerosis and control patients. Protein verification was performed by Western blot on tears and CSF and by ELISA on serum samples.ResultsCombined proteomics analyses provided 185 identified tear proteins. Among the differential proteins, alpha‐1 antichymotrypsin was the only one to be significantly increased in the three experiments with similar ratios (ratios 1.6 to 2.5, p < 0.05). Its tear, CSF and serum elevation were further confirmed by Western blot and ELISA, respectively.Conclusions and clinical relevanceThis study supports the concept that modifications of the tear proteome can reflect biological abnormalities associated with multiple sclerosis and perhaps other inflammatory conditions affecting the CNS. In addition, alpha‐1 antichymotrypsin elevation in tear fluid emerges as a promising biomarker for the diagnosis of multiple sclerosis.
A decade of crystallization drops: Crystallization of the cbb3 cytochrome c oxidase from Pseudomonas stutzeri
Authors: Buschmann Sabine , Richers Sebastian , Ermler Ulrich , Michel Hartmut 
Published: February 2014

AbstractThe cbb3 cytochrome c oxidases are distant members of the superfamily of heme copper oxidases. These terminal oxidases couple O2 reduction with proton transport across the plasma membrane and, as a part of the respiratory chain, contribute to the generation of an electrochemical proton gradient. Compared with other structurally characterized members of the heme copper oxidases, the recently determined cbb3 oxidase structure at 3.2 Å resolution revealed significant differences in the electron supply system, the proton conducting pathways and the coupling of O2 reduction to proton translocation. In this paper, we present a detailed report on the key steps for structure determination. Improvement of the protein quality was achieved by optimization of the number of lipids attached to the protein as well as the separation of two cbb3 oxidase isoenzymes. The exchange of n‐dodecyl‐β‐d‐maltoside for a precisely defined mixture of two α‐maltosides and decanoylsucrose as well as the choice of the crystallization method had a most profound impact on crystal quality. This report highlights problems frequently encountered in membrane protein crystallization and offers meaningful approaches to improve crystal quality.
Regeneration of reptilian scales after wounding: neogenesis, regional difference, and molecular modules
Authors: Wu Ping , Alibardi Lorenzo , Chuong Cheng‐Ming 
Published: February 2014

AbstractLizard skin can produce scales during embryonic development, tail regeneration, and wound healing; however, underlying molecular signaling and extracellular matrix protein expression remains unknown. We mapped cell proliferation, signaling and extracellular matrix proteins in regenerating and developing lizard scales in different body regions with different wound severity. Following lizard tail autotomy (self‐amputation), de novo scales regenerate from regenerating tail blastema. Despite topological differences between embryonic and adult scale formation, asymmetric cell proliferation produces the newly formed outer scale surface. Regionally different responses to wounding were observed; open wounds induced better scale regeneration from tail skin than trunk skin. Molecular studies suggest that neural cell adhesion molecule enriched dermal regions exhibit higher cell proliferation associated with scale growth. β‐catenin may be involved in epidermal scale differentiation. Dynamic tenascin‐C expression suggests its involvement in regeneration. We conclude that different skin regions exhibit different competence for de novo scale formation. While cellular and morphogenetic paths differ during development and regeneration of lizard scale formation, they share general proliferation patterns, epithelial−mesenchymal interactions and similar molecular modules composed of adhesion and extracellular matrix molecules.
Accuracy of radiographs in assessment of displacement in lateral humeral condyle fractures
Authors: Knutsen Ashleen , Avoian Tigran , Borkowski Sean L. , Ebramzadeh Edward , Zionts Lewis E. , Sangiorgio Sophia N. 
Published: February 2014

Purpose Determining the magnitude of displacement in pediatric lateral humeral condyle fractures can be difficult. The purpose of this study was to (1) assess the effect of forearm rotation on true fracture displacement using a cadaver model and to (2) determine the accuracy of radiographic measurements of the fracture gap. Methods A non-displaced fracture was created in three human cadaveric arms. The specimens were mounted on a custom apparatus allowing forearm rotation with the humerus fixed. First, the effect of pure rotation on fracture displacement was simulated by rotating the forearm from supination to pronation about the central axis of the forearm, to isolate the effects of muscle pull. Then, the clinical condition of obtaining a lateral oblique radiograph was simulated by rotating the forearm about the medial aspect of the forearm. Fracture displacements were measured using a motion-capture system (true-displacement) and clinical radiographs (apparent-displacement). Results During pure rotation of the forearm, there were no significant differences in fracture displacement between supination and pronation, with changes in displacement of <1.0 mm. During rotation about the medial aspect of the forearm, there was a significant difference in true displacements between supination and pronation at the posterior edge ( p < 0.05). Conclusion Overall, true fracture displacement measurements were larger than apparent radiographic displacement measurements, with differences from 1.6 to 6.0 mm, suggesting that the current clinical methods may not be sensitive enough to detect a displacement of 2.0 mm, especially when positioning the upper extremity for an internal oblique lateral radiograph.
Vacuum ultraviolet photoionization of carbohydrates and nucleotides
Authors: Shin Joong-Won , Bernstein Elliot R. 
Published: February 2014

Carbohydrates (2-deoxyribose, ribose, and xylose) and nucleotides (adenosine-, cytidine-, guanosine-, and uridine-5′-monophosphate) are generated in the gas phase, and ionized with vacuum ultraviolet photons (VUV, 118.2 nm). The observed time of flight mass spectra of the carbohydrate fragmentation are similar to those observed [J.-W. Shin, F. Dong, M. Grisham, J. J. Rocca, and E. R. Bernstein, Chem. Phys. Lett. 506, 161 (2011)] for 46.9 nm photon ionization, but with more intensity in higher mass fragment ions. The tendency of carbohydrate ions to fragment extensively following ionization seemingly suggests that nucleic acids might undergo radiation damage as a result of carbohydrate, rather than nucleobase fragmentation. VUV photoionization of nucleotides (monophosphate-carbohydrate-nucleobase), however, shows that the carbohydrate-nucleobase bond is the primary fragmentation site for these species. Density functional theory (DFT) calculations indicate that the removed carbohydrate electrons by the 118.2 nm photons are associated with endocyclic C–C and C–O ring centered orbitals: loss of electron density in the ring bonds of the nascent ion can thus account for the observed fragmentation patterns following carbohydrate ionization. DFT calculations also indicate that electrons removed from nucleotides under these same conditions are associated with orbitals involved with the nucleobase-saccharide linkage electron density. The calculations give a general mechanism and explanation of the experimental results.
Low-lying excited states and nonradiative processes of 9-methyl-2-aminopurine
Authors: Trachsel Maria A. , Lobsiger Simon , Schär Tobias , Leutwyler Samuel 
Published: February 2014

The UV spectrum of the adenine analogue 9-methyl-2-aminopurine (9M-2AP) is investigated with one- and two-color resonant two-photon ionization spectroscopy at 0.3 and 0.05 cm−1 resolution in a supersonic jet. The electronic origin at 32 252 cm−1 exhibits methyl torsional subbands that originate from the $0A_{1}^{{\prime \prime }}$0A1′′ (l = 0) and 1E″ (l = ±1) torsional levels. These and further torsional bands that appear up to $0_0^0+230$000+230 cm−1 allow to fit the threefold (V3) barriers of the torsional potentials as $|V^{\prime \prime }_3|\break = 50$|V3′′|=50 cm−1 in the S0 and $|V^{\prime }_3 |=126$|V3′|=126 cm−1 in the S1 state. Using the B3LYP density functional and correlated approximate second-order coupled cluster CC2 methods, the methyl orientation is calculated to be symmetric relative to the 2AP plane in both states, with barriers of $V^{\prime \prime }_3=20$V3′′=20 cm−1 and $V^{\prime }_3\break =115$V3′=115 cm−1. The $0_0^0$000 rotational band contour is 75% in-plane (a/b) polarized, characteristic for a dominantly long-axis 1ππ* excitation. The residual 25% c-axis polarization may indicate coupling of the 1ππ* to the close-lying 1nπ* state, calculated at 4.00 and 4.01 eV with the CC2 method. However, the CC2 calculated 1nπ oscillator strength is only 6% of that of the 1ππ* transition. The 1ππ* vibronic spectrum is very complex, showing about 40 bands within the lowest 500 cm−1. The methyl torsion and the low-frequency out-of-plane $\nu ^{\prime }_1$ν1′ and $\nu ^{\prime }_2$ν2′ vibrations are strongly coupled in the 1ππ* state. This gives rise to many torsion-vibration combination bands built on out-of-plane fundamentals, which are without precedence in the 1ππ* spectrum of 9H-2-aminopurine [S. Lobsiger, R. K. Sinha, M. Trachsel, and S. Leutwyler, J. Chem. Phys. 134, 114307 (2011)]. From the Lorentzian broadening needed to fit the $0_0^0$000 contour of 9M-2AP, the 1ππ* lifetime is τ ⩾ 120 ps, reflecting a rapid nonradiative transition.
Flows and torques in Brownian ferrofluids subjected to rotating uniform magnetic fields in a cylindrical and annular geometry
Authors: Torres-Diaz I. , Cortes A. , Cedeño-Mattei Y. , Perales-Perez O. , Rinaldi C. 
Published: February 2014

Ferrofluid flow in cylindrical and annular geometries under the influence of a uniform rotating magnetic field was studied experimentally using aqueous ferrofluids consisting of low concentrations (&lt;0.01 v/v) of cobalt ferrite nanoparticles with Brownian relaxation to test the ferrohydrodynamic equations, elucidate the existence of couple stresses, and determine the value of the spin viscosity in these fluids. An ultrasound technique was used to measure bulk velocity profiles in the spin-up (cylindrical) and annular geometries, varying the intensity and frequency of the rotating magnetic field generated by a two pole stator winding. Additionally, torque measurements in the cylindrical geometry were made. Results show rigid-body like velocity profiles in the bulk, and no dependence on the axial direction. Experimental velocity profiles were in quantitative agreement with the predictions of the spin diffusion theory, with a value of the spin viscosity of ∼10−8 kg m/s, two orders of magnitude larger than the value estimated earlier for iron oxide based ferrofluids, and 12 orders of magnitude larger than estimated using dimensional arguments valid in the infinite dilution limit. These results provide further evidence of the existence of couple stresses in ferrofluids and their role in driving the spin-up flow phenomenon.
Population genomics of the honey bee reveals strong signatures of positive selection on worker traits
Authors: Harpur Brock A. , Kent Clement F. , Molodtsova Daria , Lebon Jonathan M. D. , Alqarni Abdulaziz S. , Owayss Ayman A. , Zayed Amro 
Published: February 2014

SignificanceMost hypotheses explaining the evolution of sociality in insects assume that positive selection drives the evolution of worker traits. Yet we know little about the extent of natural selection acting on social insects. We produced a map of positive selection for the honey bee through analysis of 40 individual genomes. We found strong evidence of positive selection acting on genes and regulatory sequences, and we discovered that mutations in worker-biased proteins tend to have greater fitness effects than mutations in queen-biased proteins. We also found many instances of positive selection acting on genes that influence worker traits, suggesting that worker phenotypes represent a major vector for adaptation in social insects.
Two Patterns of Cannabis Use among Adolescents: Results of a 10-Year Prospective Study Using a Growth Mixture Model
Authors: Grevenstein Dennis , Kröninger-Jungaberle Henrik 
Published: February 2014

Background The present study aimed to distinguish cannabis consumption patterns among adolescents and to relate these to life satisfaction, academic achievement, and the use of other psychoactive substances. Methods This study used a prospective design. Cannabis use was measured 14 times over the course of 10 years. Participants were 318 adolescents aged 14 to 15 at the beginning of the study. Results Growth mixture modeling identified 2 latent classes. Class 1 was defined by phases of high-frequency cannabis use, and Class 2 was defined by low-frequency use or nonuse. Class 1 reported decreased satisfaction with life and one's own academic and professional achievement at the age of 24 as well as higher use of tobacco and illicit substances. Conclusions High-frequency use of cannabis predicts a decreased satisfaction with life and one's own academic and professional achievement as well as an increased use of other substances.
Differences in Alcohol Brand Consumption between Underage Youth and Adults—United States, 2012
Authors: Siegel Michael , Chen Kelsey , DeJong William , Naimi Timothy S. , Ostroff Joshua , Ross Craig S. , Jernigan David H. 
Published: February 2014

Background The alcohol brand preferences of US underage drinkers have recently been identified, but it is not known whether youth are simply mimicking adult brand choices or whether other factors are impacting their preferences. This study is the first to compare the alcohol brand preferences of underage drinkers and adults. Methods The authors conducted a cross-sectional assessment of youth and adult alcohol brand preferences. A 2012 Internet-based survey of a nationally representative sample of 1032 underage drinkers, ages 13–20, was used to determine the prevalence of past-30-day consumption for each of 898 alcohol brands, and each brand's youth market share, based on the total number of standard drinks consumed. Data on the brand-specific prevalence of past-30-day or past-7-day consumption among older youth (ages 18–20), adults (ages 21+), and young adults (ages 21–34) was obtained from Gfk MRI's Survey of the Adult Consumer for the years 2010–2012. Overall market shares for each brand, also measured by the total number of standard drinks consumed, were estimated from national data compiled by Impact Databank for the year 2010. Results Although most alcohol brands popular among underage drinkers were also popular among adult drinkers, there were several brands that appeared to be disproportionately consumed by youth. Conclusions This article provides preliminary evidence that youth do not merely mimic the alcohol brand choices of adults. Further research using data derived from fully comparable data sources is necessary to confirm this finding.
Comparing DNA integration site clusters with scan statistics
Authors: Berry Charles C. , Ocwieja Karen E. , Malani Nirav , Bushman Frederic D. 
Published: February 2014

Abstract
Motivation: Gene therapy with retroviral vectors can induce adverse effects when those vectors integrate in sensitive genomic regions. Retroviral vectors are preferred that target sensitive regions less frequently, motivating the search for localized clusters of integration sites and comparison of the clusters formed by integration of different vectors. Scan statistics allow the discovery of spatial differences in clustering and calculation of false discovery rates providing statistical methods for comparing retroviral vectors.
Results: A scan statistic for comparing two vectors using multiple window widths is proposed with software to detect clustering differentials and compute false discovery rates. Application to several sets of experimentally determined HIV integration sites demonstrates the software. Simulated datasets of various sizes and signal strengths are used to determine the power to discover clusters and evaluate a convenient lower bound. This provides a toolkit for planning evaluations of new gene therapy vectors.
Availability and implementation: The geneRxCluster R package containing a simple tutorial and usage hints is available from http://www.bioconductor.org.
Contact: ccberry@ucsd.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
StochHMM: a flexible hidden Markov model tool and C++ library
Authors: Lott Paul C. , Korf Ian 
Published: February 2014

AbstractSummary: Hidden Markov models (HMMs) are probabilistic models that are well-suited to solve many different classification problems in computation biology. StochHMM provides a command-line program and C++ library that can implement a traditional HMM from a simple text file. StochHMM provides researchers the flexibility to create higher-order emissions, integrate additional data sources and/or user-defined functions into multiple points within the HMM framework. Additional features include user-defined alphabets, ability to handle ambiguous characters in an emission-dependent manner, user-defined weighting of state paths and ability to tie transition probabilities to sequence.Availability and implementation: StochHMM is implemented in C++ and is available under the MIT License. Software, source code, documentation and examples can be found at http://github.com/KorfLab/StochHMM.Contact: ifkorf@ucdavis.edu
Integrative gene set analysis of multi-platform data with sample heterogeneity
Authors: Hu Jun , Tzeng Jung-Ying 
Published: February 2014

AbstractMotivation: Gene set analysis is a popular method for large-scale genomic studies. Because genes that have common biological features are analyzed jointly, gene set analysis often achieves better power and generates more biologically informative results. With the advancement of technologies, genomic studies with multi-platform data have become increasingly common. Several strategies have been proposed that integrate genomic data from multiple platforms to perform gene set analysis. To evaluate the performances of existing integrative gene set methods under various scenarios, we conduct a comparative simulation analysis based on The Cancer Genome Atlas breast cancer dataset.Results: We find that existing methods for gene set analysis are less effective when sample heterogeneity exists. To address this issue, we develop three methods for multi-platform genomic data with heterogeneity: two non-parametric methods, multi-platform Mann–Whitney statistics and multi-platform outlier robust T-statistics, and a parametric method, multi-platform likelihood ratio statistics. Using simulations, we show that the proposed multi-platform Mann–Whitney statistics method has higher power for heterogeneous samples and comparable performance for homogeneous samples when compared with the existing methods. Our real data applications to two datasets of The Cancer Genome Atlas also suggest that the proposed methods are able to identify novel pathways that are missed by other strategies.Availability and implementation: http://www4.stat.ncsu.edu/∼jytzeng/Software/Multiplatform_gene_set_analysis/Contact: john.hu@omicsoft.com, jhu7@ncsu.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Event trigger identification for biomedical events extraction using domain knowledge
Authors: Zhou Deyu , Zhong Dayou , He Yulan 
Published: February 2014

Abstract
Motivation: In molecular biology, molecular events describe observable alterations of biomolecules, such as binding of proteins or RNA production. These events might be responsible for drug reactions or development of certain diseases. As such, biomedical event extraction, the process of automatically detecting description of molecular interactions in research articles, attracted substantial research interest recently. Event trigger identification, detecting the words describing the event types, is a crucial and prerequisite step in the pipeline process of biomedical event extraction. Taking the event types as classes, event trigger identification can be viewed as a classification task. For each word in a sentence, a trained classifier predicts whether the word corresponds to an event type and which event type based on the context features. Therefore, a well-designed feature set with a good level of discrimination and generalization is crucial for the performance of event trigger identification.
Results: In this article, we propose a novel framework for event trigger identification. In particular, we learn biomedical domain knowledge from a large text corpus built from Medline and embed it into word features using neural language modeling. The embedded features are then combined with the syntactic and semantic context features using the multiple kernel learning method. The combined feature set is used for training the event trigger classifier. Experimental results on the golden standard corpus show that &gt;2.5% improvement on F-score is achieved by the proposed framework when compared with the state-of-the-art approach, demonstrating the effectiveness of the proposed framework.
Availability and implementation: The source code for the proposed framework is freely available and can be downloaded at http://cse.seu.edu.cn/people/zhoudeyu/ETI_Sourcecode.zip.
Contact: d.zhou@seu.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.