bluuebunny/crossref_metadata_2025 huggingface dataset:
PVAAS: identify variants associated with aberrant splicing from RNA-seq
Authors: Wang Liguo , Nie Jinfu J. , Kocher Jean-Pierre A.
Published: January 2015

Motivation: RNA-seq has been widely used to study the transcriptome. Comparing to microarray, sequencing-based RNA-seq is able to identify splicing variants and single nucleotide variants in one experiment simultaneously. This provides unique opportunity to detect variants that associated with aberrant splicing. Despite the popularity of RNA-seq, no bioinformatics tool has been developed to leverage this advantage to identify variants associated with aberrant splicing.

Results: We have developed PVAAS, a tool to identify single nucleotide variants that associated with aberrant alternative splicing from RNA-seq data. PVAAS works in three steps: (i) identify aberrant splicings; (ii) use user-provided variants or perform variant calling; (iii) assess the significance of association between variants and aberrant splicing events.

Availability and implementation: PVAAS is written in Python and C. Source code and a comprehensive user’s manual are freely available at: http://pvaas.sourceforge.net/.

Contact: wang.liguo@mayo.edu or kocher.jeanpierre@mayo.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
RNA-Rocket: an RNA-Seq analysis resource for infectious disease research
Authors: Warren Andrew S. , Aurrecoechea Cristina , Brunk Brian , Desai Prerak , Emrich Scott , Giraldo-Calderón Gloria I. , Harb Omar , Hix Deborah , Lawson Daniel , Machi Dustin , Mao Chunhong , McClelland Michael , Nordberg Eric , Shukla Maulik , Vosshall Leslie B. , Wattam Alice R. , Will Rebecca , Yoo Hyun Seung , Sobral Bruno
Published: January 2015

Motivation: RNA-Seq is a method for profiling transcription using high-throughput sequencing and is an important component of many research projects that wish to study transcript isoforms, condition specific expression and transcriptional structure. The methods, tools and technologies used to perform RNA-Seq analysis continue to change, creating a bioinformatics challenge for researchers who wish to exploit these data. Resources that bring together genomic data, analysis tools, educational material and computational infrastructure can minimize the overhead required of life science researchers.

Results: RNA-Rocket is a free service that provides access to RNA-Seq and ChIP-Seq analysis tools for studying infectious diseases. The site makes available thousands of pre-indexed genomes, their annotations and the ability to stream results to the bioinformatics resources VectorBase, EuPathDB and PATRIC. The site also provides a combination of experimental data and metadata, examples of pre-computed analysis, step-by-step guides and a user interface designed to enable both novice and experienced users of RNA-Seq data.

Availability and implementation: RNA-Rocket is available at rnaseq.pathogenportal.org. Source code for this project can be found at github.com/cidvbi/PathogenPortal.

Contact:  anwarren@vt.edu

Supplementary information:  Supplementary materials are available at Bioinformatics online.
Inferring single-cell gene expression mechanisms using stochastic simulation
Authors: Daigle Bernie J. , Soltani Mohammad , Petzold Linda R. , Singh Abhyudai
Published: January 2015

Motivation: Stochastic promoter switching between transcriptionally active (ON) and inactive (OFF) states is a major source of noise in gene expression. It is often implicitly assumed that transitions between promoter states are memoryless, i.e. promoters spend an exponentially distributed time interval in each of the two states. However, increasing evidence suggests that promoter ON/OFF times can be non-exponential, hinting at more complex transcriptional regulatory architectures. Given the essential role of gene expression in all cellular functions, efficient computational techniques for characterizing promoter architectures are critically needed.

Results: We have developed a novel model reduction for promoters with arbitrary numbers of ON and OFF states, allowing us to approximate complex promoter switching behavior with Weibull-distributed ON/OFF times. Using this model reduction, we created bursty Monte Carlo expectation-maximization with modified cross-entropy method (‘bursty MCEM2’), an efficient parameter estimation and model selection technique for inferring the number and configuration of promoter states from single-cell gene expression data. Application of bursty MCEM2 to data from the endogenous mouse glutaminase promoter reveals nearly deterministic promoter OFF times, consistent with a multi-step activation mechanism consisting of 10 or more inactive states. Our novel approach to modeling promoter fluctuations together with bursty MCEM2 provides powerful tools for characterizing transcriptional bursting across genes under different environmental conditions.

Availability and implementation: R source code implementing bursty MCEM2 is available upon request.

Contact:  absingh@udel.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Campylobacter iguaniorum sp. nov., isolated from reptiles
Authors: Gilbert Maarten J. , Kik Marja , Miller William G. , Duim Birgitta , Wagenaar Jaap A.
Published: January 2015

During sampling of reptiles for members of the class

Epsilonproteobacteria

, strains representing a member of the genus

Campylobacter

not belonging to any of the established taxa were isolated from lizards and chelonians. Initial amplified fragment length polymorphism, PCR and 16S rRNA sequence analysis showed that these strains were most closely related to

Campylobacter fetus

and

Campylobacter hyointestinalis

. A polyphasic study was undertaken to determine the taxonomic position of five strains. The strains were characterized by 16S rRNA and atpA sequence analysis, matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry and conventional phenotypic testing. Whole-genome sequences were determined for strains 1485ET and 2463D, and the average nucleotide and amino acid identities were determined for these strains. The strains formed a robust phylogenetic clade, divergent from all other species of the genus

Campylobacter

. In contrast to most currently known members of the genus

Campylobacter

, the strains showed growth at ambient temperatures, which might be an adaptation to their reptilian hosts. The results of this study clearly show that these strains isolated from reptiles represent a novel species within the genus

Campylobacter

, for which the name Campylobacter iguaniorum sp. nov. is proposed. The type strain is 1485ET ( = LMG 28143T = CCUG 66346T).
Should ‘Candidatus Phytoplasma’ be retained within the order Acholeplasmatales?
Authors: Zhao Yan , Davis Robert E. , Wei Wei , Lee Ing-Ming
Published: January 2015

Phytoplasmas are a diverse but phylogenetically coherent group of cell-wall-less bacteria affiliated with the classMollicutes. Due to difficulties in establishing axenic culture, phytoplasmas were assigned to a provisional genus, ‘CandidatusPhytoplasma’, and the genus was embraced within the orderAcholeplasmatales. However, phytoplasmas differ significantly from species of the genusAcholeplasmain their habitat specificities, modes of life, metabolic capabilities, genomic architectures, and phylogenetic positions. This communication describes the unique ecological, nutritional, biochemical, genomic and phylogenetic properties that distinguish phytoplasmas from species of the genusAcholeplasmaand all other taxa in the classMollicutes. Since such distinguishing properties of the phytoplasmas are not referable to the descriptions of the orderAcholeplasmatalesand of all other existing orders, namelyMycoplasmatales,EntomoplasmatalesandAnaeroplasmatales, this communication raises the question of whether ‘CandidatusPhytoplasma’ should be retained in the orderAcholeplasmatalesor whether a novel provisional order and family should be created to accommodate the genus ‘Ca.Phytoplasma’.
Investigating time-of-flight spin-echo modulation for small-angle neutron scattering through experiments and simulation
Authors: Sales Morten , Plomp Jeroen , Habicht Klaus , Strobl Markus
Published: January 2015

A spin-echo-modulated small-angle neutron scattering (SEMSANS) instrument in a time-of-flight (TOF) mode will be able to excel at pulsed neutron sources such as the European Spallation Source (ESS), currently under construction. This work compares experimental data from a TOF SEMSANS setup, where a spatial beam modulation of a white beam is obtained using triangular field coils, with Monte Carlo ray-tracing simulations. The experiments and simulations in accordance demonstrate that a good contrast can be achieved when using a constant field in the triangular coils. In the reported setup only neutrons with certain wavelengths rotate by a Larmor precession angle that spatially modulates their polarization to coincide with the period of a grating installed at the detector position. This is shown by measuring with a broad wavelength range while scanning the echo condition.
Crystallographic analysis of slip transfer mechanisms across the ferrite/cementite interface in carbon steels with fine lamellar structure
Authors: Karkina L. E. , Karkin I. N. , Kabanova I. G. , Kuznetsov A. R.
Published: January 2015

The results of crystallographic analysis of deformation transfer mechanisms across the ferrite/cementite interface in fine lamellar pearlite are presented. The possibility of a strain transfer was evaluated using the LRB criteria that are used for the slip transfer mechanisms across grain boundaries [Lee, Robertson & Birnbaum (1989).Scr. Metall.23, 799–803; (1990).Metall. Trans. A,21, 2437–2447; (1990).Philos. Mag. A,62, 131–153]. Dislocation reactions at the Fe/Fe3C interface were studied, taking into account Bagaryatsky and Isaichev orientation relationships between ferrite and cementite observed for fine lamellar pearlite. Slip planes and Burgers vectors of full and partial dislocations in cementite have been proposed on the basis of the results of atomistic simulations of stacking faults for some planes of cementite. It has been found that strain transfer through the Fe/Fe3C interface is possible only for half of the slip systems 1/2〈111〉{110}Fand for quarter of the slip systems 1/2〈111〉{112}Fof ferrite. Other slip systems do not cross the interface and are involved in the hardening of the ferrite phase of pearlite.
Structural and microstructural interpretations of Zn-doped biocompatible bone-like carbonated hydroxyapatite synthesized by mechanical alloying
Authors: Lala S. , Ghosh M. , Das P. K. , Das D. , Kar T. , Pradhan S. K.
Published: January 2015

Single-phase nanocrystalline biocompatible Zn-dopedA-type carbonated hydroxyapatite (A-cHAp) powder has been synthesizedviamechanical alloying of a stoichiometric mixture of CaCO3, CaHPO4·2H2O and ZnO powders in open air at room temperature by 10 h of milling. TheA-type carbonation in HAp (A-cHAp) is confirmed by Fourier transform IR analysis. The structural and microstructural parameters of the as-milled powders are revealed by Rietveld powder structure refinement analysis and transmission electron microscopy. Zn substitution along with mechanical alloying causes partial amorphization of crystallineA-cHAp, analogous to native bone mineral. Zn2+cations substitute into the ninefold-coordinated Ca2+sites in theA-cHAp unit cell. An assay test using MTT [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide] reveals a high percentage of cell viability and hence confirms the biocompatibility of the sample. The overall results indicate that the processedA-cHAp has a chemical composition very close to that of natural biological apatite.
A new three-dimensional CdIIsupramolecular framework constructed from the 1-[(1H-tetrazol-5-yl)methyl]-1,4-diazoniabicyclo[2.2.2]octane ligand
Authors: Li Qiang , Wang Hui-Ting , Zhou Lin
Published: January 2015

A new tetrazole–metal supramolecular compound, di-μ-chlorido-bis(trichlorido{1-[(1H-tetrazol-5-yl-κN2)methyl]-1,4-diazoniabicyclo[2.2.2]octane}cadmium(II)), [Cd2(C8H16N6)2Cl8], has been synthesized and structurally characterized by single-crystal X-ray diffraction. In the structure, each CdIIcation is coordinated by five Cl atoms (two bridging and three terminal) and by one N atom from the 1-[(1H-tetrazol-5-yl)methyl]-1,4-diazoniabicyclo[2.2.2]octane ligand, adopting a slightly distorted octahedral coordination geometry. The bridging bicyclo[2.2.2]octane and chloride ligands link the CdIIcations into one-dimensional ribbon-like N—H...Cl hydrogen-bonded chains along thebaxis. An extensive hydrogen-bonding network formed by N—H...Cl and C—H...Cl hydrogen bonds, and interchain π–π stacking interactions between adjacent tetrazole rings, consolidate the crystal packing, linking the poymeric chains into a three-dimensional supramolecular network.
A linear heterometallic bismuth–copper coordination polymer containing two types of organic ligands
Authors: Yue Zi-Long , Feng Yu-Quan , Ng Seik Weng
Published: January 2015

In the linear coordination polymercatena-poly[[[aqua(1,10-phenanthroline-κ2N,N′)copper(II)]-μ-pyridine-2,6-dicarboxylato-κ4O2:O2′,N,O6-[(nitrato-κ2O,O′)bismuth(III)]-μ-pyridine-2,6-dicarboxylato-κ4O2,N,O6:O6′] dihydrate], {[BiIIICuII(C7H3NO4)2(NO3)(C12H8N2)(H2O)]·2H2O}n, the BiIIIcation isO,N,O′-chelated by the two pyridine-2,6-dicarboxylate ligands andO,O′-chelated by the nitrate anion, the nine coordinating atoms conferring a tricapped trigonal prismatic environment on the metal centre. Each pyridine-2,6-dicarboxylate ligand uses one of its carboxylate O atoms to bind to an aqua(1,10-phenanthroline)copper(II) unit, the Cu—O dative bonds giving rise to the formation of a ribbon motif. The CuIIcation exhibits a square-pyramidal geometry. The ribbon motif propagates along the shortest axis of the triclinic unit cell and the solvent water molecules are hydrogen bonded to the same ribbon.
Crystal structure of 3-[2-(4-methylphenyl)ethynyl]-2H-chromen-2-one
Authors: Caracelli Ignez , Maganhi Stella H. , Stefani Hélio A. , Gueogjian Karina , Tiekink Edward R. T.
Published: January 2015

The coumarin ring system in the title asymmetric alkyne, C18H12O2, is approximately planar (r.m.s. deviation of the 11 non-H atoms = 0.048 Å), and is inclined with respect to the methylbenzene ring, forming a dihedral angle of 33.68 (4)°. In the crystal, supramolecular zigzag chains along thec-axis direction are formedviaweak C—H...O hydrogen bonds, and these are connected into double layersviaweak C—H...π interactions; these stack along theaaxis.
Crystal structure of 1-(2-aminophenyl)-3-phenylurea
Authors: Mague Joel T. , Mohamed Shaaban K. , Akkurt Mehmet , Omran Omran A. , Albayati Mustafa R.
Published: January 2015

In the title compound, C13H13N3O, the phenyl ring makes a dihedral angle of 47.0 (1)° with the mean plane of the –NC(=O)N– unit, while the dihedral angle between the latter mean plane and the aminophenyl ring is 84.43 (7)°. In the crystal, molecules are linkedviaN—H...O hydrogen bonds involving the central –NHC(=O)NH– units, forming chains running parallel to thebaxis. These chains associate with one anotherviaN—H...O and N—H...N hydrogen bonds, from the pendant amino groups to the –NHC(=O)NH– units of adjacent molecules, forming columns propagating along [010]. The structure was refined as a two-component twin with a 0.933 (3):0.067 (3) domain ratio.
Crystal structures of two decavanadates(V) with pentaaquamanganese(II) pendant groups: (NMe4)2[V10O28{Mn(H2O)5}2]·5H2O and [NH3C(CH2OH)3]2[V10O28{Mn(H2O)5}2]·2H2O
Authors: Franco Maurício P. , Rüdiger André Luis , Soares Jaísa F. , Nunes Giovana G. , Hughes David L.
Published: January 2015

Two heterometallic decavanadate(V) compounds, bis(tetramethylammonium) decaaquadi-μ4-oxido-tetra-μ3-oxido-hexadeca-μ2-oxido-hexaoxidodimanganese(II)decavanadate(V) pentahydrate, (Me4N)2[V10O28{Mn(H2O)5}2]·5H2O,A, and bis{[tris(hydroxymethyl)methyl]ammonium} decaaquadi-μ4-oxido-tetra-μ3-oxido-hexadeca-μ2-oxido-hexaoxidodimanganese(II)decavanadate(V) dihydrate, [NH3C(CH2OH)3]2[V10O28{Mn(H2O)5}2]·2H2O,B, have been synthesized under mild reaction conditions in an aqueous medium. Both polyanions present two [Mn(OH2)5]2+complex units bound to the decavanadate cluster through oxide bridges. InA, the decavanadate unit has 2/msymmetry, whereas inBit has twofold symmetry. Apart from this, the main differences betweenAandBrest on the organic cations, tetramethylammonium and [tris(hydroxymethyl)methyl]ammonium, respectively, and on the number and arrangement of the water molecules of crystallization. In both compounds, the H atoms from the coordinating water molecules participate in extensive three-dimensional hydrogen-bonding networks, which link the cluster units both directly and through solvent molecules and, inB, through the `tris' cation hydroxyl groups. The cation inBalso participates in N—H...O hydrogen bonds. A number of C—H...O interactions are also observed in both structures.
Crystal structure of 7,7-dimethyl-6-methylidenetricyclo[6.2.1.01,5]undecane-2-carboxylic acid
Authors: Beghidja Noureddine , Benayache Samir , Benayache Fadila , Knight David W. , Kariuki Benson M.
Published: January 2015

In the title compound, C15H22O2, both five-membered rings display an envelope conformation whereas the six-membered ring displays a chair conformation. In the crystal, pairs of O—H...O hydrogen bonds between carboxylic groups link molecules, related by a twofold rotation axis, into supramolecular dimers.
Crystal structure of cholest-5-en-3β-yl 3-(2,4-dimethoxy-3-methylphenyl)prop-2-enoate
Authors: Bugenhagen Bernhard , Munk Ariane , Vill Volkmar , Al Jasem Yosef , Thiemann Thies
Published: January 2015

In the title compound, C39H58O4, the steroid ringsAandCadopt a chair conformation, while ringBadopts a half-chair conformation, and ringDhas an envelope conformation, with the methyl-substituted C atom as the flap. In the crystal, molecules pack within layers parallel to (100), with their long axis parallel to the [101] direction. Adjacent layers are linkedviaC—H...O hydrogen bonds and C—H...π interactions, forming a three-dimensional framework.
Crystal structure of isobutyl 4-(2-chlorophenyl)-5-cyano-6-{(E)-[(dimethylamino)methylidene]amino}-2-methyl-4H-pyran-3-carboxylate
Authors: Mohandas T. , Kumar C. Udhaya , Devi S. Aruna , Prakasam B. Arul , Sakthivel P. , Vidhyasagar T.
Published: January 2015

In the title compound, C21H24ClN3O3, the dihedral angle between the pyran ring (r.m.s. deviation = 0.037 Å) and the chlorobenzene ring is 88.56 (14)°. In the crystal, the molecules are linked by C—H...O interactions, generatingC(7) (001) chains.
Achieving employee commitment for continuous improvement initiatives
Authors: Lam Marco , O'Donnell Mark , Robertson Dan
Published: January 2015

Purpose

– Although prior research has found that employee participation is key to successfully implementing quality management initiatives (Baird et al., 2011; de Menezes, 2012; Lagrosen and Lagrosen, 2005), little research in operations management exists that investigates which management actions and behaviors lead to employee commitment to such initiatives. The purpose of this paper is to address this gap in the operations management literature by investigating which influence tactics are the most effective in soliciting employee commitment to continuous improvement tasks. The paper also examines how influence tactics affect the supervisor-subordinate relationship and the manager’s effectiveness in implementing continuous improvement initiatives.

Design/methodology/approach

– A survey instrument was used to measure supervisor-subordinate relationship quality, usage of influence behaviors and participants’ task commitment to continuous improvement initiatives.

Findings

– The results indicate that five of the 11 influence tactics identified in the prior literature, i.e., collaboration, consultation, ingratiation, inspirational appeals, and rational persuasion, are significant and strong predictors of employee commitment to continuous improvement initiatives. Further, analyses show that these influence tactics are significant drivers of the quality of the supervisor-subordinate relationship, which was found to partially mediate the relationship between influence tactics and the supervisor’s effectiveness in implementing continuous improvement projects.

Research limitations/implications

– Since the extant CI and Total Quality Management literature has looked at the plant or program level rather than the worker-level as in the research, the findings offer one explanation as to why earlier studies investigating the relationship between quality management programs and increased organizational performance reported mixed results.

Practical implications

– Increasing managers’ awareness and usage of influence tactics may increase the success rate of continuous improvement projects as well the quality of the relationship with the manager’s subordinates.

Originality/value

– While the extant literature has argued that management support and employee commitment are key components of a continuous improvement project implementation, little has been written about the specific management actions and behaviors that lead to success.
Music, musicians and information seeking behaviour
Authors: Kostagiolas Petros A. , Lavranos Charilaos , Korfiatis Nikolaos , Papadatos Joseph , Papavlasopoulos Sozon
Published: January 2015

Purpose

– The purpose of this paper is to examine information seeking behaviour targeted to music information seeking by amateur musicians, accompanied with empirical evidence from a survey on a community concert band. While several studies in the literature have examined information seeking in the context of hedonic motives (e.g. entertainment oriented), music information can also be used for utilitarian purposes by providing amateur musicians the necessary tools to improve their skill and become better in their practice.

Design/methodology/approach

– A review of the literature on music information seeking and an empirical study on members of an amateur concert band are presented. The theoretical construct of the survey is informed by Wilsons’ macro model of information seeking behaviour. This is employed in order to understand information motives and needs, as well as obstacles in information seeking of musicians.

Findings

– Musicians seek information not only for entertainment but for educational purposes as well as for the acquisition of certain music works. The use of the internet for information seeking as well as the gradual adoption of online social networks has provided access to new musical resources within the digital music networks.

Originality/value

– A person-centred approach for information seeking behaviour is studied and adapted for musicians. The survey provides new information behaviour results for designers of music information spaces which in turn are creating a new model of the relationship between music and society.
Image descriptions and their relational expressions: a review of the literature and the issues
Authors: Benson Allen C
Published: January 2015

Purpose

– The purpose of this paper is to survey the treatment of relationships, relationship expressions and the ways in which they manifest themselves in image descriptions.

Design/methodology/approach

– The term “relationship” is construed in the broadest possible way to include spatial relationships (“to the right of”), temporal (“in 1936,” “at noon”), meronymic (“part of”), and attributive (“has color,” “has dimension”). The intentions of these vaguely delimited categories with image information, image creation, and description in libraries and archives is complex and in need of explanation.

Findings

– The review brings into question many generally held beliefs about the relationship problem such as the belief that the semantics of relationships are somehow embedded in the relationship term itself and that image search and retrieval solutions can be found through refinement of word-matching systems.

Originality/value

– This review has no hope of systematically examining all evidence in all disciplines pertaining to this topic. It instead focusses on a general description of a theoretical treatment in Library and Information Science.
Domain knowledge and data quality perceptions in genome curation work
Authors: Huang Hong
Published: January 2015

Purpose

– The purpose of this paper is to understand genomics scientists’ perceptions in data quality assurances based on their domain knowledge.

Design/methodology/approach

– The study used a survey method to collect responses from 149 genomics scientists grouped by domain knowledge. They ranked the top-five quality criteria based on hypothetical curation scenarios. The results were compared using χ2 test.

Findings

– Scientists with domain knowledge of biology, bioinformatics, and computational science did not reach a consensus in ranking data quality criteria. Findings showed that biologists cared more about curated data that can be concise and traceable. They were also concerned about skills dealing with information overloading. Computational scientists on the other hand value making curation understandable. They paid more attention to the specific skills for data wrangling.

Originality/value

– This study takes a new approach in comparing the data quality perceptions for scientists across different domains of knowledge. Few studies have been able to synthesize models to interpret data quality perception across domains. The findings may help develop data quality assurance policies, training seminars, and maximize the efficiency of genome data management.
The interplay of affective and cognitive factors in information seeking and use
Authors: Savolainen Reijo
Published: January 2015

Purpose

– The purpose of this paper is to elaborate the conceptual picture of the relationships between the affective and cognitive factors in information seeking and use.

Design/methodology/approach

– Conceptual analysis focusing on the ways in which the affective and cognitive factors and their interplay are approached in the Information Search Process model developed by Carol Kuhlthau, and the Social-Biological Information Technology model elaborated by Diane Nahl.

Findings

– Kuhlthau’s model approaches the cognitive factors (thoughts) and affective factors (feelings) and affective-cognitive factors (mood) as integral constituents of the six-stage information search process. Thoughts determine the valence of feelings (positive or negative), while mood opens or closes the range of possibilities in a search. Nahl’s taxonomic model defines the affective and cognitive factors as components of a biologically determined process serving the ends of adaptation to information ecology. The interplay of the above factors is conceptualized by focusing on their mutual roles in the cognitive and affective appraisal of information.

Research limitations/implications

– The findings are based on the comparison of two models only.

Originality/value

– So far, information scientists have largely ignored the study of the interplay between affective and cognitive factors in information seeking and use. The findings indicate that the examination of these factors together rather than separately holds a good potential to elaborate the holistic picture of information seeking and use.
Variants in SELL,MRPS36P2,TP63,DDB2,CACNA1H,ADAM19,GNAI1,CDH13 and GABRG2 interact to confer risk of acne in Chinese population
Authors: Wang HongYan , Guo MeiHua , Shen SongKe , He Li , Zhang XueJun , Zuo XianBo , Yang Sen
Published: January 2015

Acne vulgaris is a common skin disease characterized by chronic inflammation of the pilosebaceous unit resulting from androgen‐induced increased sebum production, altered keratinization, inflammation and bacterial colonization of hair follicles by propionibacterium acnes. Our previous genome‐wide association study on acne has identified two new susceptibility loci. To search for potential gene–gene interactions and investigate the best‐fit association models for the single nucleotide polymorphisms (SNP) from these interacting genes, we implemented logistic regression analysis in the combined sample of 2916 cases with severe acne and 4716 controls. The most significant association evidence was observed under an additive model for rs6896064 and under a dominant model the rest of these SNP. Significant interactions between these SNP were observed in this study: the SELL × MRPS36P2 (Padjusted = 4.15 × 10−10), TP63 × DDB2 (Padjusted = 7.62 × 10−08), DDB2 × CACNA1H (Padjusted = 1.89 × 10−07), ADAM19 × GNAI1 × CDH13 (Padjusted = 1.22 × 10−04) and ADAM19 × GABRG2 × GNAI2 × CDH13 (Pad justed = 6.33 × 10−05). These results may contribute to our understanding of acne genetic etiology and account for the additional risk of certain patients.
Gravimetric survey terrain correction using linear analytical approximation
Authors: Bychkov S.G. , Dolgal A.S. , Kostitsyn V.I. , Simanov A.A.
Published: January 2015

Various methods for computing the terrain correction in a high‐precision gravity survey are currently available. The present paper suggests a new method that uses linear analytical terrain approximations. In this method, digital terrain models for the near‐station topographic masses are obtained by vectorizing scan images of large‐scaled topographic maps, and the terrain correction computation is carried out using a Fourier series approximation of discrete height values. Distant topography data are represented with the help of digital GTOPO30 and Shuttle Radar Topography Mission cartographic information. We formulate linear analytical approximations of terrain corrections for the whole region using harmonic functions as the basis of our computational algorithm. Stochastic modelling allows effective assessment of the accuracy of terrain correction computation. The Perm Krai case study has shown that our method makes full use of all the terrain data available from topographic maps and digital terrain models and delivers a digital terrain correction computed to a priori precision. Our computer methodology can be successfully applied for the terrain correction computation in different survey areas.
Flowering phenology and mating success of the heterodichogamous tree Machilus thunbergii Sieb. et Zucc (Lauraceae)
Authors: Watanabe Shuntaro , Noma Naohiko , Nishida Takayoshi
Published: January 2015

Heterodichogamy is defined as the presence of two flower morphs that exhibit male and female functions at different times among individuals within a population, and is regarded as an adaptation to promote outbreeding through enhanced intermorph pollination. In highly fragmented populations in which the morph frequency is biased, heterodichogamy may hamper population growth by reducing seed sets of the more numerous morph, and enhancing seed sets of the less numerous morph. In such situations, we hypothesize that individual plants experience greater seed sets if the opposite sexual morphs are nearby, and that individuals of a less numerous sexual morph have greater seed sets. After confirming heterodichogamy by observing flowering behavior and phenology, we tested these two hypotheses in a highly fragmented population of Machilus thunbergii, a putative heterodichogamous evergreen laurel tree. Our observations confirmed that M. thunbergii is heterodichogamous, consisting of two types of protogynous and bisexual flowers: a morning female (MF)–afternoon male morph and a morning male (MM)–afternoon female morph at the individual level. Sexual expression of the two morphs was highly synchronized and reciprocal. Investigation of seed‐set rates revealed greater rates of both morphs if the opposite morph was nearby. The less numerous sexual morph (MF) showed a greater seed‐set rate than the more numerous sexual morph (MM).
Modernising Adult Protection in an Age of Choice
Authors: Chesterman John
Published: January 2015

This article examines the effect that two important legal and social policy developments are having on adult protection laws and practices in Australia. The first concerns the increasing reach of human rights norms, which encourage minimal reliance to be placed on substitute decision‐making arrangements, such as adult guardianship, in favour of providing greater support for people to make and implement their own decisions. The second concerns the consumer choice focus of current aged care and disability reforms in Australia. While both these developments will lead to improvements in the lives of many people, they also present regulatory challenges when it comes to protecting the well‐being of at‐risk adults, especially adults with significant cognitive impairments or with significant mental ill health. The article draws on work undertaken as part of a Churchill Fellowship and contains reform suggestions that seek to improve our protection of at‐risk adults in an era increasingly characterised by freedom of choice.
Individual and Institutional Accountability: The Case of Research Assessment
Authors: Lewis Jenny M
Published: January 2015

Performance measurement is a particular type of accountability, which might be imposed by governments but is institutionally implemented and individually experienced. Over the last three decades, the emphasis on measuring the performance of publicly funded services has risen, along with concerns about the need to demonstrate a wise use of public funds. This paper examines the dynamic interaction of the institutional and individual levels of accountability, by focusing on research assessment systems. A study of three universities in different nations reveals that the perceived impacts of these systems relate to specific institutional contexts, but that individuals’ views from within the same context also vary considerably. Professionals understand and interact with accountability systems in a manner that reflects their own values, and this ensures that they will interpret and react to them in different ways. This makes designing accountability systems without negative affects on individuals a difficult task.
Accountability and the Enforcement of Ethical Values in Finance: Insights from Islamic Finance
Authors: Lai Jikon
Published: January 2015

Vivid debates on the ethical foundations of contemporary financial practices followed the global financial crisis of 2007–8, with many questioning whether narrow self‐interest and profit maximisation should serve as primary drivers of behaviour in finance. This coincides with a resurgent research interest in finance ethics that has investigated whether ethical standards can or should be applied to financial practices and identified types of ethical principles that can or should be adopted. This paper contributes to this literature by investigating how ethical standards could be enforced in the financial sector by focussing on the example of Islamic finance in Malaysia. To facilitate the analysis, the paper adopts a broad understanding of the principal‐agent relationship and uses the lens of accountability as a conceptual bridge between ethical standards and their enforcement. The paper concludes by drawing out broad implications of this analysis for ‘conventional finance’.
Singing on the wings! Male wing fanning performances affect female willingness to copulate in the aphid parasitoid Lysiphlebus testaceipes (Hymenoptera: Braconidae: Aphidiinae)
Authors: Benelli Giovanni , Kavallieratos Nickolas G. , Donati Elisa , Giunti Giulia , Stefanini Cesare , Canale Angelo
Published: January 2015

Lysiphlebus testaceipes (Hymenoptera: Braconidae: Aphidiinae) is a generalist endoparasitoid attacking more than 100 aphid species. In L. testaceipes, wing fanning is a main male courtship display evoked by a female‐borne sex pheromone. However, no information is available on the characteristics and behavioral role of male fanning during courtship in this parasitoid. Here, the courtship behavior of a wild strain of L. testaceipes was quantified and the male wing fanning performances were analyzed through high‐speed video recordings and examined in relation to mating success. Courtship sequence of wild L. testaceipes did not substantially differ from that previously reported for other populations mass reared on aphids. We observed that the male courtship duration did not affect mating success. However, video analysis revealed that the males producing high‐frequency fanning signals achieved higher mating success over those that display low‐frequency fanning. Wing fanning before successful and unsuccessful courtship differed in amplitude of wing movements and alignment toward the mate, highlighting that frontal courtship positively influence the female mating decisions. This study increases knowledge on sexual behavior in a key parasitoid of aphids, highlighting the importance of wing fanning among the range of sensory modalities used in the sexual communication of L. testaceipes. From a practical point of view, this information is useful in L. testaceipes‐based biocontrol strategies, since it can help to establish parameters for quality checking of mass‐reared wasps over time.
Contribution of Chlorophyll to Photooxidation of Soybean Oil at Specific Visible Wavelengths of Light
Authors: Bianchi Laurie M. , Duncan Susan E. , Webster Janet B. , Neilson Andrew P. , O'Keefe Sean F.
Published: January 2015

Photosensitizers in foods and beverages are important considerations when selecting packaging materials. Chlorophyll is found at low concentrations in many food products. The objective of this study was to determine the photosensitizing effect of chlorophyll on soybean oil (SO) using broad‐spectrum light and 3 visible wavelength regions of light. SO with added chlorophyll (0, 1, or 2 μg chlorophyll added/mL SO) was exposed to 5 light conditions, using a photochemical reactor (10 °C; 4 h). Light treatments included broad‐spectrum (BS; no filter; 157.6 ± 4.7 mW intensity), 430 nm (10 nm; 1.8 ± 0.7 mW), and 660 nm (10 nm; 0.332 ± 0.05 mW) wavelengths compared to a no‐light control. Chlorophyll a (but not b) absorbs light in the selected visible wavelength regions. Chlorophyll degradation was evaluated. Oxidative changes in SO were assessed by peroxide value (PV) and thiobarbituric acid‐reactive substances (TBARS) assay, which measures malondialdehyde (MDA). Chlorophyll was completely degraded at BS and 430 nm conditions and degraded to 36% of original concentration at 660 nm wavelength. PV and MDA concentration significantly increased with chlorophyll addition (1 μg/mL) at BS and 430 nm wavelengths compared to no‐light control. Lower light intensity at 660 nm initiated oxidation reactions as measured by PV, but not significantly. There were differences in PV (BS, 430 nm) and TBARS (BS) between the no‐light and light‐exposed SO without chlorophyll added. There was very little effect at 450 nm. This study suggests that broad‐spectrum light and at least light wavelengths at or near 430 nm and 660 nm excite chlorophyll, resulting in initiation of oxidation reactions. Packaging material selection for foods and beverages should consider blocking excitation wavelengths of photosensitizing molecules, including chlorophyll, to protect product quality.
Discrimination between Bacillus and Alicyclobacillus Isolates in Apple Juice by Fourier Transform Infrared Spectroscopy and Multivariate Analysis
Authors: Al‐Holy Murad A. , Lin Mengshi , Alhaj Omar A. , Abu‐Goush Mahmoud H.
Published: January 2015

Alicyclobacillus is a causative agent of spoilage in pasteurized and heat‐treated apple juice products. Differentiating between this genus and the closely related Bacillus is crucially important. In this study, Fourier transform infrared spectroscopy (FT‐IR) was used to identify and discriminate between 4 Alicyclobacillus strains and 4 Bacillus isolates inoculated individually into apple juice. Loading plots over the range of 1350 and 1700 cm−1 reflected the most distinctive biochemical features of Bacillus and Alicyclobacillus. Multivariate statistical methods (for example, principal component analysis and soft independent modeling of class analogy) were used to analyze the spectral data. Distinctive separation of spectral samples was observed. This study demonstrates that FT‐IR spectroscopy in combination with multivariate analysis could serve as a rapid and effective tool for fruit juice industry to differentiate between Bacillus and Alicyclobacillus and to distinguish between species belonging to these 2 genera.
Progression after spontaneous regression in lung large cell neuroendocrine carcinoma: Report of a curative resection
Authors: Tomizawa Kenji , Suda Kenichi , Takemoto Toshiki , Iwasaki Takuya , Sakaguchi Masahiro , Kuwano Hiroyuki , Mitsudomi Tetsuya
Published: January 2015

We present the first reported case of lung large cell neuroendocrine carcinoma (LCNEC) with spontaneous regression followed by progression. An 85‐year‐old woman presented with a 2.8‐cm nodule in the right upper lung lobe on chest computed tomography. After four months, the tumor decreased to 1.8 cm and remained unchanged in size for the next three months, but it grew to 8.6 cm and invaded the mediastinal fat tissue after approximately one year. Ultrasound echo‐guided percutaneous biopsy revealed the tumor to be LCNEC. The patient underwent a right upper lobectomy with lymph node dissection. She had a good postoperative course with no complications. Physicians and surgeons should be aware that radiographic regression of a pulmonary nodule does not necessarily exclude the possibility of lung cancer.
A cixiid survey for natural potential vectors of ‘Candidatus Phytoplasma phoenicium’ in Lebanon and preliminary transmission trials
Authors: Tedeschi R. , Picciau L. , Quaglino F. , Abou‐Jawdah Y. , Molino Lova M. , Jawhari M. , Casati P. , Cominetti A. , Choueiri E. , Abdul‐Nour H. , Bianco P.A. , Alma A.
Published: January 2015

Almond witches'‐broom (AlmWB) disease, associated with ‘Candidatus Phytoplasma phoenicium’, is an emerging threat with real risk of introduction in Euro‐Mediterranean Countries. Its rapid spread over large geographical areas suggests the presence of efficient insect vector(s). In the present work, a survey on cixiids was carried out in Lebanon in the years 2010–2013 in AlmWB‐infested almond and nectarine orchards. Insects were collected by means of different methods, identified with a stereo microscope, and analysed for phytoplasma identification through 16S rDNA PCR‐based amplification and nucleotide sequence analyses. Preliminary transmission trials were performed with the most abundant species. A list of the cixiid genera and species present in the studied area is given as well as some information about their biology. ‘Ca. Phytoplasma phoenicium’ strains were detected in the genera Cixius, Tachycixius, Eumecurus and Hyalesthes. Preliminary trials revealed that Tachycixius specimens were able to transmit the detected strains to healthy peach potted seedlings. Further studies are required to better clarify the taxonomic status and the bio‐ethology of collected planthoppers and deeply study their role as phytoplasma vectors.
Distinct intrinsic network connectivity patterns of post‐traumatic stress disorder symptom clusters
Authors: Tursich M. , Ros T. , Frewen P. A. , Kluetsch R. C. , Calhoun V. D. , Lanius R. A.
Published: January 2015

Objective

Post‐traumatic stress disorder (PTSD) is considered a multidimensional disorder, with distinct symptom clusters including re‐experiencing, avoidance/numbing, hyperarousal, and most recently depersonalization/derealization. However, the extent of differing intrinsic network connectivity underlying these symptoms has not been fully investigated. We therefore investigated the degree of association between resting connectivity of the salience (SN), default mode (DMN), and central executive (CEN) networks and PTSD symptom severity.

Method

Using resting‐state functional MRI data from PTSD participants (n = 21), we conducted multivariate analyses to test whether connectivity of extracted independent components varied as a function of re‐experiencing, avoidance/numbing, hyperarousal, and depersonalization/derealization.

Results

Hyperarousal symptoms were associated with reduced connectivity of posterior insula/superior temporal gyrus within SN [peak Montréal Neurological Institute (MNI): −44, −8, 0, t = −4.2512, k = 40]. Depersonalization/derealization severity was associated with decreased connectivity of perigenual anterior cingulate/ventromedial prefrontal cortex within ventral anterior DMN (peak MNI: 8, 40, −4; t = −3.8501; k = 15) and altered synchrony between two DMN components and between DMN and CEN.

Conclusion

Our results are consistent with prior research showing intrinsic network disruptions in PTSD and imply heterogeneous connectivity patterns underlying PTSD symptom dimensions. These findings suggest possible biomarkers for PTSD and its dissociative subtype.
Immunohistochemical Characterization of Sympathetic Chain Ganglia (SChG) Neurons Supplying the Porcine mammary Gland
Authors: Franke‐Radowiecka A. , Wąsowicz K. , Klimczuk M. , Podlasz P. , Zalecki M. , Sienkiewicz W.
Published: January 2015

The aim of this study was to investigate the chemical coding of mammary gland‐projecting SChG neurons using double‐labelling immunohistochemistry. Earlier observation showed that after injection of the retrograde tracer fast blue (FB) into the second, right thoracic mamma, FB+ mammary gland‐projecting neurons were found in Th1‐3, Th9‐14 and L1‐4 right SChG. The greatest number of FB+ nerve cell bodies was observed in Th10 (approx. 843) and Th11 (approx. 567). Neurons projecting to the last right abdominal mamma were found in L1‐4 SChG. The greatest number of FB+ neurons was observed in L2 (approx. 1200). Immunohistochemistry revealed that the vast majority of FB+ mammary‐projecting neurons contained immunoreactivities to TH (96.97%) and/or DßH (95.92%). Many TH/DßH‐positive neurons stained for SOM (41.5%) or NPY (33.2%), and less numerous nerve cells expressed VIP (16.9%). This observation strongly corresponds to the results of previous studies concerning the immunohistochemical characterization of nerve fibres supplying the porcine mammary gland.
Correlation between corneal and ambient temperature with particular focus on polar conditions
Authors: Slettedal Jon Klokk , Ringvold Amund
Published: January 2015

Purpose

To examine the relationship between human corneal and environmental temperature.

Methods

An infrared camera was used to measure the corneal surface temperature in a group of healthy volunteers as well as in an experimental setting with donor corneas and an artificial anterior chamber, employing circulating saline at +37°C. Liquid nitrogen was used to obtain a very low temperature in the experimental setting. High ambient temperature measurements were performed in a sauna.

Results

In healthy volunteers, the cornea required at least 20–30 min to adapt to change in ambient temperature. The relationship between corneal and external temperature was relatively linear. At the two extremes, +83°C and −40°C, the corneal temperature was +42°C and +25.1°C, respectively. In the experimental setting, corneal temperature was +24.3°C at air temperature −40°C.

Conclusion

A rather stable aqueous humour temperature of +37°C and high thermal conductivity of the corneal tissue prevent corneal frostbite even at extremely low ambient temperatures.