bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biological Behaviors of Guanidine‐Based Cationic Surfactants
Authors: Song Yongbo , Li Qiuxiao , Li Yunling , Zhi Lifei 
Published: January 2014

AbstractThe biological properties of novel guanidine‐based cationic surfactant including mono‐alkylguanidine (CnG), N,N,N′‐dimethyl alkylguanidine (CnMG), dicephalic guanidine surfactant (CnGQ), heterogemini guanidine surfactant (diCnGQ) were investigated. Antimicrobial activity was determined via the inhibition of cell viability of the prepared compounds, which was measured against three strains of a representative group of microorganisms. The inhibitions of cell viability were basically about 90 % at the concentration of 25 mg L−1 to alkyl guanidium salts (CnG, CnMG), and higher than 95 % at a concentration of 10 mg L−1 to dicephalic guanidine surfactants (CnGQ) and heterogemini guanidine surfactants (diCnGQ). The interactions of bovine serum albumin (BSA) with guanidine surfactants were investigated by fluorescence technology and the effect on BSA conformation follow the order: diC12GQ > C12GQ > C12G > C12MG. At any particular concentration, the biological activity depends on the alkyl chain length to any series of guanidine‐based cationic surfactants.
Matching the Functionality of Single‐Cell Algal Oils with Different Molecular Compositions
Authors: Co Edmund D. , Koutchekinia Mona , Carney John R. , Bond Risha , Rakitsky Walter , Marangoni Alejandro G. 
Published: January 2014

AbstractThe fatty acid composition, triglyceride composition, melting/crystallization profiles, crystallization kinetics, X‐ray diffraction patterns, microstructure and mechanical properties of a pair of algal oils were studied to elucidate structural reasons for the similarity in melting and mechanical properties. Oil A is a predominantly saturated fat, rich in capric, myristic and palmitic acids, composed mostly of trisaturated triglycerides while Oil B contains predominantly palmitic and oleic acids in triglycerides such as POP/OPP and OOP/OPO. The DSC thermogram of Oil A shows similar peak melting temperatures to that of Oil B with Oil B exhibiting a few additional peaks. Both oils exhibit identical SFC‐temperature profiles. Polarized light microscopy revealed a needle‐like morphology for both Oil A and Oil B, with an average length of approximately 3.5–4.0 μm. The similar morphology of the crystals was attributed to a similar polymorphic form (β’) present in both. The fractal dimensions for the distribution of crystalline material within the fat crystal networks of both oils were also similar. The identical melting and mechanical properties of Oil A and Oil B were thus be attributed, respectively, to the presence of different triglycerides (in approximately equal proportions) with similar melting points and the assembly of these triglycerides into crystals of identical shape and size, which are in turn assembled into a network with identical crystal mass distributions. This work suggests that the mechanical and thermal properties of oils with vastly different molecular compositions can be matched by targetting specific TAG combinations which yield similar melting behavior, microstructure and mechanical response.
A TDG/CBP/RARα Ternary Complex Mediates the Retinoic Acid-Dependent Expression of DNA Methylation-Sensitive Genes
Authors: Léger Hélène , Smet-Nocca Caroline , Attmane-Elakeb Amel , Morley-Fletcher Sara , Benecke Arndt G. , Eilebrecht Sebastian 
Published: January 2014

Abstract
The thymine DNA glycosylase (TDG) is a multifunctional enzyme, which is essential for embryonic development. It mediates the base excision repair (BER) of G:T and G:U DNA mismatches arising from the deamination of 5-methyl cytosine (5-MeC) and cytosine, respectively. Recent studies have pointed at a role of TDG during the active demethylation of 5-MeC within CpG islands. TDG interacts with the histone acetylase CREB-binding protein (CBP) to activate CBP-dependent transcription. In addition, TDG also interacts with the retinoic acid receptor α (RARα), resulting in the activation of RARα target genes. Here we provide evidence for the existence of a functional ternary complex containing TDG, CBP and activated RARα. Using global transcriptome profiling, we uncover a coupling of de novo methylation-sensitive and RA-dependent transcription, which coincides with a significant subset of CBP target genes. The introduction of a point mutation in TDG, which neither affects overall protein structure nor BER activity, leads to a significant loss in ternary complex stability, resulting in the deregulation of RA targets involved in cellular networks associated with DNA replication, recombination and repair. We thus demonstrate for the first time a direct coupling of TDG’s epigenomic and transcription regulatory function through ternary complexes with CBP and RARα.
Social Interaction and Atypical Sensory Processing in Children with Autism Spectrum Disorders*
Authors: Matsushima Kanae , Kato Toshihiro 
Published: January 2014

Objective/Background Many children with autism spectrum disorders (ASDs) have sensory processing disorders (SPDs), which may limit many facets of daily life, including social interaction, an important domain of occupational therapy. Therefore, we examined the relationship between social interaction deficits and SPD in 4—6-year-old children with ASD without intellectual disorders. Methods The Social Responsiveness Scale (SRS) and the Japanese Sensory Inventory-Revised (JSI-R) questionnaires were administered to parents of children with ASD and children in the control group (n = 42 each). Results Response analyses revealed significant intergroup differences in scores for the questionnaires, with more atypical sensory processing patterns and social interaction deficits observed in children with ASD. Significant correlations were observed between the SRS total raw scores and subcategory scores of all sensory modalities of the JSI-R in the entire experimental group. The SPD symptoms were significantly associated with social interaction deficits in children with ASD. Conclusion It is important that occupational therapists consider SPD symptoms in children with ASD to provide early intervention for social interaction deficits.
Emotionale Erschöpfung und Wohlbefinden bei Gesundheitsfachberufen
Authors: Zimmermann Linda , Körner Mirjam 
Published: January 2014

Einleitung
Die gesundheitliche Gefährdung ist für Beschäftigte der Gesundheitsversorgung im Vergleich zu anderen Branchen erhöht. Ziel dieser Befragung ist die Erfassung des Ist-Zustandes emotionaler Erschöpfung und des Wohlbefindens aus Sicht der Gesundheitsfachberufe in 9 Rehabilitationskliniken (N = 306). Ein Viertel der Befragten gibt an, „oft“ bzw. „immer“ emotional erschöpft zu sein. Betriebliche Gesundheitsförderungsmaßnahmen sollten im Gesundheitsversorgungsbereich mehr Beachtung finden.
Changing banking relationships and client‐firm performance: Evidence from Japan for the 1990s
Authors: Tsuruta Daisuke 
Published: January 2014

AbstractThe extant literature generally suggests that the performance of client firms deteriorates if their distressed main bank reduces the supply of credit. However, this insight is only consistent with the notion that main banks have an information advantage over other banks to the extent that a client firm has trouble getting access to credit if the firm changes its main bank. This paper shows that Japanese firms did change their main banking relationship when their main banks become distressed in a period with financial shocks. Surprisingly, these firms did not suffer from loss of access to credit and actually their performance significantly improved after their change of main banks.
REGIONAL VARIATIONS IN INFANT AND CHILD MORTALITY IN NIGERIA: A MULTILEVEL ANALYSIS
Authors: ADEDINI SUNDAY A. , ODIMEGWU CLIFFORD , IMASIKU EUNICE N. S. , ONONOKPONO DOROTHY N. , IBISOMI LATIFAT 
Published: January 2014

SummaryThere are substantial regional disparities in under-five mortality in Nigeria, and evidence suggests that both individual- and community-level characteristics have an influence on health outcomes. Using 2008 Nigeria Demographic and Health Survey data, this study (1) examines the effects of individual- and community-level characteristics on infant/child mortality in Nigeria and (2) determines the extent to which characteristics at these levels influence regional variations in infant/child mortality in the country. Multilevel Cox proportional hazard analysis was performed on a nationally representative sample of 28,647 children nested within 18,028 mothers of reproductive age, who were also nested within 886 communities. The results indicate that community-level variables (such as region, place of residence, community infrastructure, community hospital delivery and community poverty level) and individual-level factors (including child's sex, birth order, birth interval, maternal education, maternal age and wealth index) are important determinants of infant/child mortality in Nigeria. For instance, the results show a lower risk of death in infancy for children of mothers residing in communities with a high proportion of hospital delivery (HR: 0.70, p<0.05) and for children whose mothers had secondary or higher education (HR: 0.84, p<0.05). Although community factors appear to influence the association between individual-level factors and death during infancy and childhood, the findings consistently indicate that community-level characteristics are more important in explaining regional variations in child mortality, while individual-level factors are more important for regional variations in infant mortality. The results of this study underscore the need to look beyond the influence of individual-level factors in addressing regional variations in infant and child mortality in Nigeria.
Engineered antibody fragments for immuno-PET imaging of endogenous CD8
+
T cells in vivo
Authors: Tavaré Richard , McCracken Melissa N. , Zettlitz Kirstin A. , Knowles Scott M. , Salazar Felix B. , Olafsen Tove , Witte Owen N. , Wu Anna M. 
Published: January 2014

Significance
Anti-CD8 immuno-PET imaging agents provide the potential to monitor the localization, migration, and expansion of CD8-expressing cells noninvasively in vivo. Shown here is the successful generation of functional anti-CD8 imaging agents based on engineered antibodies for use in a variety of preclinical disease and immunotherapeutic models.
Estimation of fluorescence-tagged RNA numbers from spot intensities
Authors: Häkkinen Antti , Kandhavelu Meenakshisundaram , Garasto Stefania , Ribeiro Andre S. 
Published: January 2014

AbstractMotivation: Present research on gene expression using live cell imaging and fluorescent proteins or tagged RNA requires accurate automated methods of quantification of these molecules from the images. Here, we propose a novel automated method for classifying pixel intensities of fluorescent spots to RNA numbers.Results: The method relies on a new model of intensity distributions of tagged RNAs, for which we estimated parameter values in maximum likelihood sense from measurement data, and constructed a maximum a posteriori classifier to estimate RNA numbers in fluorescent RNA spots. We applied the method to estimate the number of tagged RNAs in individual live Escherichia coli cells containing a gene coding for an RNA with MS2-GFP binding sites. We tested the method using two constructs, coding for either 96 or 48 binding sites, and obtained similar distributions of RNA numbers, showing that the method is adaptive. We further show that the results agree with a method that uses time series data and with quantitative polymerase chain reaction measurements. Lastly, using simulated data, we show that the method is accurate in realistic parameter ranges. This method should, in general, be applicable to live single-cell measurements of low-copy number fluorescence-tagged molecules.Availability and implementation: MATLAB extensions written in C for parameter estimation and finding decision boundaries are available under Mozilla public license at http://www.cs.tut.fi/%7ehakkin22/estrna/.Contact: andre.ribeiro@tut.fi
Inference with viral quasispecies diversity indices: clonal and NGS approaches
Authors: Gregori Josep , Salicrú Miquel , Domingo Esteban , Sanchez Alex , Esteban Juan I. , Rodríguez-Frías Francisco , Quer Josep 
Published: January 2014

Abstract
Given the inherent dynamics of a viral quasispecies, we are often interested in the comparison of diversity indices of sequential samples of a patient, or in the comparison of diversity indices of virus in groups of patients in a treated versus control design. It is then important to make sure that the diversity measures from each sample may be compared with no bias and within a consistent statistical framework. In the present report, we review some indices often used as measures for viral quasispecies complexity and provide means for statistical inference, applying procedures taken from the ecology field. In particular, we examine the Shannon entropy and the mutation frequency, and we discuss the appropriateness of different normalization methods of the Shannon entropy found in the literature. By taking amplicons ultra-deep pyrosequencing (UDPS) raw data as a surrogate of a real hepatitis C virus viral population, we study through in-silico sampling the statistical properties of these indices under two methods of viral quasispecies sampling, classical cloning followed by Sanger sequencing (CCSS) and next-generation sequencing (NGS) such as UDPS. We propose solutions specific to each of the two sampling methods—CCSS and NGS—to guarantee statistically conforming conclusions as free of bias as possible.
Contact: josep.gregori@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online
SNPdryad: predicting deleterious non-synonymous human SNPs using only orthologous protein sequences
Authors: Wong Ka-Chun , Zhang Zhaolei 
Published: January 2014

AbstractMotivation: The recent advances in genome sequencing have revealed an abundance of non-synonymous polymorphisms among human individuals; subsequently, it is of immense interest and importance to predict whether such substitutions are functional neutral or have deleterious effects. The accuracy of such prediction algorithms depends on the quality of the multiple-sequence alignment, which is used to infer how an amino acid substitution is tolerated at a given position. Because of the scarcity of orthologous protein sequences in the past, the existing prediction algorithms all include sequences of protein paralogs in the alignment, which can dilute the conservation signal and affect prediction accuracy. However, we believe that, with the sequencing of a large number of mammalian genomes, it is now feasible to include only protein orthologs in the alignment and improve the prediction performance.Results: We have developed a novel prediction algorithm, named SNPdryad, which only includes protein orthologs in building a multiple sequence alignment. Among many other innovations, SNPdryad uses different conservation scoring schemes and uses Random Forest as a classifier. We have tested SNPdryad on several datasets. We found that SNPdryad consistently outperformed other methods in several performance metrics, which is attributed to the exclusion of paralogous sequence. We have run SNPdryad on the complete human proteome, generating prediction scores for all the possible amino acid substitutions.Availability and implementation: The algorithm and the prediction results can be accessed from the Web site: http://snps.ccbr.utoronto.ca:8080/SNPdryad/.Contact: Zhaolei.Zhang@utoronto.caSupplementary information: Supplementary data are available at Bioinformatics online.
PeaKDEck: a kernel density estimator-based peak calling program for DNaseI-seq data
Authors: McCarthy Michael T. , O’Callaghan Christopher A. 
Published: January 2014

Abstract
Summary: Hypersensitivity to DNaseI digestion is a hallmark of open chromatin, and DNaseI-seq allows the genome-wide identification of regions of open chromatin. Interpreting these data is challenging, largely because of inherent variation in signal-to-noise ratio between datasets. We have developed PeaKDEck, a peak calling program that distinguishes signal from noise by randomly sampling read densities and using kernel density estimation to generate a dataset-specific probability distribution of random background signal. PeaKDEck uses this probability distribution to select an appropriate read density threshold for peak calling in each dataset. We benchmark PeaKDEck using published ENCODE DNaseI-seq data and other peak calling programs, and demonstrate superior performance in low signal-to-noise ratio datasets.
Availability and implementation: PeaKDEck is written in standard Perl and runs on any platform with Perl installed. PeaKDEck is also available as a standalone application written in Perl/Tk, which does not require Perl to be installed. Files, including a user guide, can be downloaded at: www.ccmp.ox.ac.uk/peakdeck.
Contact: chris.ocallaghan@ndm.ox.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Impact of deep-sea fishery for Greenland halibut (Reinhardtius hippoglossoides) on non-commercial fish species off West Greenland
Authors: Jørgensen Ole A. , Bastardie François , Eigaard Ole R. 
Published: January 2014

Abstract
Since the late 1980s, a deep-sea fishery for Greenland halibut (Reinhardtius hippoglossoides) has been developing gradually in West Greenland. Deep-sea fish species are generally long-lived and characterized by late age of maturity, low fecundity, and slow growth, features that probably cause low resilience following overexploitation. In order to evaluate whether populations of nine potential bycatch species are negatively affected by the commercial fishery for Greenland halibut, scientific data from bottom-trawl surveys conducted in the same area and period as the commercial fishery were analysed. During the period 1988–2011, population abundance and size composition changed as catch and effort in the Greenland halibut fishery increased. Two species showed a significant decrease in abundance, and four populations showed a significant reduction in mean weight of individuals (p < 0.05). Correlation analyses show that most of the observed trends in abundance are probably not related to increasing fishing effort for Greenland halibut. The analysis did, however, show that most of the observed decreases in mean weight were significantly correlated with fishing effort during the 24-year period.
Black hole spin measurements through the relativistic precession model: XTE J1550-564
Authors: Motta S. E. , Muñoz-Darias T. , Sanna A. , Fender R. , Belloni T. , Stella L. 
Published: January 2014

Abstract
We present a systematic analysis of the complete set of observations of the black hole (BH) binary XTE J1550-564 obtained by the Rossi X-ray Timing Explorer. We study the fast time variability properties of the source and determine the spin of the BH through the relativistic precession model. Similarly to what is observed in the BH binary GRO J1655-40, the frequencies of the QPOs and broad-band noise components match the general relativistic frequencies of particle motion close to the compact object predicted by the relativistic precession model. The combination of two simultaneously observed quasi-periodic oscillation (QPO) frequencies together with the dynamical BH mass from optical/infrared observations yields a spin equal to a = 0.34 ± 0.01, consistent with previous determinations from X-ray spectroscopy. Based on the derived BH parameters, the low-frequency QPO emission radii vary from ∼30 gravitational radii (Rg) to the innermost stable orbit for this spin (∼5 Rg), where they sharply disappear as observed for the case of GRO J1655-40.
Grain Number,Plant Height,and Heading Date7Is a Central Regulator of Growth, Development, and Stress Response
Authors: Weng Xiaoyu , Wang Lei , Wang Jia , Hu Yong , Du Hao , Xu Caiguo , Xing Yongzhong , Li Xianghua , Xiao Jinghua , Zhang Qifa 
Published: January 2014

AbstractGrain number, plant height, and heading date7 (Ghd7) has been regarded as an important regulator of heading date and yield potential in rice (Oryza sativa). In this study, we investigated functions of Ghd7 in rice growth, development, and environmental response. As a long-day dependent negative regulator of heading date, the degree of phenotypic effect of Ghd7 on heading date and yield traits is quantitatively related to the transcript level and is also influenced by both environmental conditions and genetic backgrounds. Ghd7 regulates yield traits through modulating panicle branching independent of heading date. Ghd7 also regulates plasticity of tiller branching by mediating the PHYTOCHROME B-TEOSINTE BRANCHED1 pathway. Drought, abscisic acid, jasmonic acid, and high-temperature stress strongly repressed Ghd7 expression, whereas low temperature enhanced Ghd7 expression. Overexpression of Ghd7 increased drought sensitivity, whereas knock-down of Ghd7 enhanced drought tolerance. Gene chip analysis of expression profiles revealed that Ghd7 was involved in the regulation of multiple processes, including flowering time, hormone metabolism, and biotic and abiotic stresses. This study suggests that Ghd7 functions to integrate the dynamic environmental inputs with phase transition, architecture regulation, and stress response to maximize the reproductive success of the rice plant.
Financial constraints for investment in Brazil
Authors: Lima Crisóstomo Vicente , Javier López Iturriaga Félix , Vallelado González Eleuterio 
Published: January 2014

Purpose– The purpose of this paper is to verify the existence of financial constraints for investment in Brazil, an emerging market with growing international visibility.Design/methodology/approach– Using panel data methodology and generalized method of moments (GMM), the paper estimates dynamic investment models based on the Euler equation and Tobin'sqfor a panel data set of 199 Brazilian non-financial firms for the time period 1995-2006.Findings– Results show that Brazilian firms face financial constraints since their investments depend on internally generated funds. Results are robust to different investment models based on the Euler equation, also controlling for growth opportunities. Significant investment-cash flow sensitivity has been found for the whole sample of firms. Subsamples of firms considered as under financial constraints, according to dividend payout and equity issuance policies, have higher investment-cash flow sensitivity. Investment-cash flow sensitivity of financially constrained firms in Brazil is higher than that in the UK and in Romania, a transition economy.Originality/value– The results extend empirical evidence of financial constraints in Brazil. The paper contributes to the literature by assessing the firms’ financial constraint status on an annual basis, and by using panel data methodology and GMM to estimate dynamic models of investment that take into account the proposals of the hierarchy of finance theory. In addition, the paper controls for growth opportunities. Capital market imperfections affect firm investment in Brazil and such effects are even stronger for financially constrained firms.