bluuebunny/crossref_metadata_2025 huggingface dataset:
The modulation of disjunctive assertions
Authors: Quelhas Ana Cristina , Johnson-Laird P.N.
Published: February 2016

The theory of mental models postulates that disjunctions of the sort, A or B, where A and B are sensible everyday clauses, have a core meaning that allows an inclusive interpretation, referring to three possibilities: A and not-B, not-A and B, and A and B. The meaning of the clauses and knowledge can modulate this meaning by blocking the construction of at least one model of a possibility—for example, “Rui is playing tennis or he is surfing” blocks the model of Rui doing both activities. This theory is implemented in a computer program. Three experiments investigated the core interpretation and interpretations in which the contents of the clauses should block the model of A and B (as in the preceding example), the model of A and not-B, or the model of not-A and B. In Experiment 1, the participants listed the possibilities for each of the four sorts of disjunction. The results corroborated the predicted modulations. In Experiment 2, these predicted interpretations governed the conclusions that participants accepted from disjunctions and categorical premises. In Experiment 3, the predicted interpretations yielded reliable effects on the conclusions that the participants drew for themselves. We relate these results to theories of reasoning.
OEFinder: a user interface to identify and visualize ordering effects in single-cell RNA-seq data
Authors: Leng Ning , Choi Jeea , Chu Li-Fang , Thomson James A. , Kendziorski Christina , Stewart Ron
Published: February 2016

Summary: A recent article identified an artifact in multiple single-cell RNA-seq (scRNA-seq) datasets generated by the Fluidigm C1 platform. Specifically, Leng et al. showed significantly increased gene expression in cells captured from sites with small or large plate output IDs. We refer to this artifact as an ordering effect (OE). Including OE genes in downstream analyses could lead to biased results. To address this problem, we developed a statistical method and software called OEFinder to identify a sorted list of OE genes. OEFinder is available as an R package along with user-friendly graphical interface implementations which allows users to check for potential artifacts in scRNA-seq data generated by the Fluidigm C1 platform.

Availability and implementation: OEFinder is freely available at https://github.com/lengning/OEFinder

Contact:  rstewart@morgridge.org or lengning1@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
MMseqs software suite for fast and deep clustering and searching of large protein sequence sets
Authors: Hauser Maria , Steinegger Martin , Söding Johannes
Published: February 2016

Motivation: Sequence databases are growing fast, challenging existing analysis pipelines. Reducing the redundancy of sequence databases by similarity clustering improves speed and sensitivity of iterative searches. But existing tools cannot efficiently cluster databases of the size of UniProt to 50% maximum pairwise sequence identity or below. Furthermore, in metagenomics experiments typically large fractions of reads cannot be matched to any known sequence anymore because searching with sensitive but relatively slow tools (e.g. BLAST or HMMER3) through comprehensive databases such as UniProt is becoming too costly.

Results: MMseqs (Many-against-Many sequence searching) is a software suite for fast and deep clustering and searching of large datasets, such as UniProt, or 6-frame translated metagenomics sequencing reads. MMseqs contains three core modules: a fast and sensitive prefiltering module that sums up the scores of similar k-mers between query and target sequences, an SSE2- and multi-core-parallelized local alignment module, and a clustering module.

In our homology detection benchmarks, MMseqs is much more sensitive and 4–30 times faster than UBLAST and RAPsearch, respectively, although it does not reach BLAST sensitivity yet. Using its cascaded clustering workflow, MMseqs can cluster large databases down to ∼30% sequence identity at hundreds of times the speed of BLASTclust and much deeper than CD-HIT and USEARCH. MMseqs can also update a database clustering in linear instead of quadratic time. Its much improved sensitivity-speed trade-off should make MMseqs attractive for a wide range of large-scale sequence analysis tasks.

Availability and implementation: MMseqs is open-source software available under GPL at https://github.com/soedinglab/MMseqs

Contact:  martin.steinegger@mpibpc.mpg.de, soeding@mpibpc.mpg.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
lnCaNet: pan-cancer co-expression network for human lncRNA and cancer genes
Authors: Liu Yining , Zhao Min
Published: February 2016

Summary: Thousands of human long non-coding RNAs (lncRNAs) have been identified in cancers and played important roles in a wide range of tumorigenesis. However, the functions of vast majority of human lncRNAs are still elusive. Emerging studies revealed that the expression level of majority lncRNAs shows discordant expression pattern with their protein-coding gene neighbors in various model organisms. Therefore, it may be useful to infer lncRNAs’ potential biological function in cancer development by more comprehensive functional views of co-expressed cancer genes beyond mere physical proximity of genes. To this aim, we performed thorough searches and analyses of the interactions between lncRNA and non-neighboring cancer genes and provide a comprehensive co-expression data resource, LnCaNet. In current version, LnCaNet contains the pre-computed 8 494 907 significant co-expression pairs of 9641 lncRNAs and 2544 well-classified cancer genes in 2922 matched TCGA samples. In detail, we integrated 10 cancer gene lists from public database and calculate the co-expression with all the lncRNAs in 11 TCGA cancer types separately. Based on the resulted 110 co-expression networks, we identified 17 common regulatory pairs related to extracellular space shared in 11 cancers. We expect LnCaNet will enable researcher to explore lncRNA expression pattern, their affected cancer genes and pathways, biological significance in the context of specific cancer types and other useful annotation related to particular kind of lncRNA-cancer gene interaction.

Availability and implementation: http://lncanet.bioinfo-minzhao.org/

Contact: m.zhao@uq.edu.au

Supplementary information:  Supplementary data are available at Bioinformatics online.
SIRAH tools: mapping, backmapping and visualization of coarse-grained models
Authors: Machado Matías R. , Pantano Sergio
Published: February 2016

Summary: Coarse-grained (CG) models reduce the cost of molecular dynamics simulations keeping the essence of molecular interactions. Still, the diversity of CG representations (sizes, connectivity, naming, etc.) hampers the handling and visualization of such models. SIRAH Tools comprises a set of utilities to convert all-atoms coordinates to arbitrary residue-based CG schemes, write GROMACS’ topological information at any resolution into PSF format and a VMD plugin to visualize, analyze and retrieve pseudo-atomistic information from CG trajectories performed with the SIRAH force field. These tools facilitate the use of intricate CG force fields outside the small developer’s community.

Availability and implementation: Different utilities of SIRAH Tools are written in Perl, Tcl, or R. Documentation and source codes are freely distributed at http://www.sirahff.com.

Contact: mmachado@pasteur.edu.uy or spantano@pasteur.edu.uy
Library of binding protein scaffolds (LibBP): a computational platform for selection of binding protein scaffolds
Authors: Hong Seungpyo , Kim Dongsup
Published: February 2016

Motivation: Developments in biotechnology have enabled the in vitro evolution of binding proteins. The emerging limitations of antibodies in binding protein engineering have led to suggestions for other proteins as alternative binding protein scaffolds. Most of these proteins were selected based on human intuition rather than systematic analysis of the available data. To improve this strategy, we developed a computational framework for finding desirable binding protein scaffolds by utilizing protein structure and sequence information.

Results: For each protein, its structure and the sequences of evolutionarily-related proteins were analyzed, and spatially contiguous regions composed of highly variable residues were identified. A large number of proteins have these regions, but leucine rich repeats (LRRs), histidine kinase domains and immunoglobulin domains are predominant among them. The candidates suggested as new binding protein scaffolds include histidine kinase, LRR, titin and pentapeptide repeat protein.

Availability and implementation: The database and web-service are accessible via http://bcbl.kaist.ac.kr/LibBP.

Contact:  kds@kaist.ac.kr

Supplementary data:  Supplementary data are available at Bioinformatics online.
Alloscore: a method for predicting allosteric ligand–protein interactions
Authors: Li Shuai , Shen Qiancheng , Su Minyi , Liu Xinyi , Lu Shaoyong , Chen Zhongjie , Wang Renxiao , Zhang Jian
Published: February 2016

Summary: Allosteric ligands have increasingly gained attention as potential therapeutic agents due to their higher target selectivity and lower toxicity compared with classic orthosteric ligands. Despite the great interest in the development of allosteric drugs as a new tactic in drug discovery, the understanding of the ligand–protein interactions underlying allosteric binding represents a key challenge. Herein, we introduce Alloscore, a web server that predicts the binding affinities of allosteric ligand–protein interactions. This method exhibits prominent performance in describing allosteric binding and could be useful in allosteric virtual screening and the structural optimization of allosteric agonists/antagonists.

Availability and implementation: The Alloscore server and tutorials are freely available at http://mdl.shsmu.edu.cn/alloscore

Contact:  jian.zhang@sjtu.edu.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
BISQUE: locus- and variant-specific conversion of genomic, transcriptomic and proteomic database identifiers
Authors: Meyer Michael J. , Geske Philip , Yu Haiyuan
Published: February 2016

Summary: Biological sequence databases are integral to efforts to characterize and understand biological molecules and share biological data. However, when analyzing these data, scientists are often left holding disparate biological currency—molecular identifiers from different databases. For downstream applications that require converting the identifiers themselves, there are many resources available, but analyzing associated loci and variants can be cumbersome if data is not given in a form amenable to particular analyses. Here we present BISQUE, a web server and customizable command-line tool for converting molecular identifiers and their contained loci and variants between different database conventions. BISQUE uses a graph traversal algorithm to generalize the conversion process for residues in the human genome, genes, transcripts and proteins, allowing for conversion across classes of molecules and in all directions through an intuitive web interface and a URL-based web service.

Availability and implementation: BISQUE is freely available via the web using any major web browser (http://bisque.yulab.org/). Source code is available in a public GitHub repository (https://github.com/hyulab/BISQUE).

Contact:  haiyuan.yu@cornell.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Predicting physiologically relevant SH3 domain mediated protein–protein interactions in yeast
Authors: Jain Shobhit , Bader Gary D.
Published: February 2016

Motivation: Many intracellular signaling processes are mediated by interactions involving peptide recognition modules such as SH3 domains. These domains bind to small, linear protein sequence motifs which can be identified using high-throughput experimental screens such as phage display. Binding motif patterns can then be used to computationally predict protein interactions mediated by these domains. While many protein–protein interaction prediction methods exist, most do not work with peptide recognition module mediated interactions or do not consider many of the known constraints governing physiologically relevant interactions between two proteins.

Results: A novel method for predicting physiologically relevant SH3 domain-peptide mediated protein–protein interactions in S. cerevisae using phage display data is presented. Like some previous similar methods, this method uses position weight matrix models of protein linear motif preference for individual SH3 domains to scan the proteome for potential hits and then filters these hits using a range of evidence sources related to sequence-based and cellular constraints on protein interactions. The novelty of this approach is the large number of evidence sources used and the method of combination of sequence based and protein pair based evidence sources. By combining different peptide and protein features using multiple Bayesian models we are able to predict high confidence interactions with an overall accuracy of 0.97.

Availability and implementation: Domain-Motif Mediated Interaction Prediction (DoMo-Pred) command line tool and all relevant datasets are available under GNU LGPL license for download from http://www.baderlab.org/Software/DoMo-Pred. The DoMo-Pred command line tool is implemented using Python 2.7 and C ++.

Contact:  gary.bader@utoronto.ca

Supplementary information:  Supplementary data are available at Bioinformatics online.
Computational approaches to define a human milk metaglycome
Authors: Agravat Sanjay B. , Song Xuezheng , Rojsajjakul Teerapat , Cummings Richard D. , Smith David F.
Published: February 2016

Motivation: The goal of deciphering the human glycome has been hindered by the lack of high-throughput sequencing methods for glycans. Although mass spectrometry (MS) is a key technology in glycan sequencing, MS alone provides limited information about the identification of monosaccharide constituents, their anomericity and their linkages. These features of individual, purified glycans can be partly identified using well-defined glycan-binding proteins, such as lectins and antibodies that recognize specific determinants within glycan structures.

Results: We present a novel computational approach to automate the sequencing of glycans using metadata-assisted glycan sequencing, which combines MS analyses with glycan structural information from glycan microarray technology. Success in this approach was aided by the generation of a ‘virtual glycome’ to represent all potential glycan structures that might exist within a metaglycomes based on a set of biosynthetic assumptions using known structural information. We exploited this approach to deduce the structures of soluble glycans within the human milk glycome by matching predicted structures based on experimental data against the virtual glycome. This represents the first meta-glycome to be defined using this method and we provide a publically available web-based application to aid in sequencing milk glycans.

Availability and implementation:  http://glycomeseq.emory.edu

Contact:  sagravat@bidmc.harvard.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Measuring the spatial correlations of protein binding sites
Authors: Wei Yingying , Wu Hao
Published: February 2016

Motivation: Understanding the interactions of different DNA binding proteins is a crucial first step toward deciphering gene regulatory mechanism. With advances of high-throughput sequencing technology such as ChIP-seq, the genome-wide binding sites of many proteins have been profiled under different biological contexts. It is of great interest to quantify the spatial correlations of the binding sites, such as their overlaps, to provide information for the interactions of proteins. Analyses of the overlapping patterns of binding sites have been widely performed, mostly based on ad hoc methods. Due to the heterogeneity and the tremendous size of the genome, such methods often lead to biased even erroneous results.

Results: In this work, we discover a Simpson’s paradox phenomenon in assessing the genome-wide spatial correlation of protein binding sites. Leveraging information from publicly available data, we propose a testing procedure for evaluating the significance of overlapping from a pair of proteins, which accounts for background artifacts and genome heterogeneity. Real data analyses demonstrate that the proposed method provide more biologically meaningful results.

Availability and implementation: An R package is available at http://www.sta.cuhk.edu.hk/YWei/ChIPCor.html.

Contacts:  ywei@sta.cuhk.edu.hk or hao.wu@emory.edu.

Supplementary information:  Supplementary data are available at Bioinformatics online.
An empirical Bayes change-point model for identifying 3′ and 5′ alternative splicing by next-generation RNA sequencing
Authors: Zhang Jie , Wei Zhi
Published: February 2016

Motivation: Next-generation RNA sequencing (RNA-seq) has been widely used to investigate alternative isoform regulations. Among them, alternative 3′ splice site (SS) and 5′ SS account for more than 30% of all alternative splicing (AS) events in higher eukaryotes. Recent studies have revealed that they play important roles in building complex organisms and have a critical impact on biological functions which could cause disease. Quite a few analytical methods have been developed to facilitate alternative 3′ SS and 5′ SS studies using RNA-seq data. However, these methods have various limitations and their performances may be further improved.

Results: We propose an empirical Bayes change-point model to identify alternative 3′ SS and 5′ SS. Compared with previous methods, our approach has several unique merits. First of all, our model does not rely on annotation information. Instead, it provides for the first time a systematic framework to integrate various information when available, in particular the useful junction read information, in order to obtain better performance. Second, we utilize an empirical Bayes model to efficiently pool information across genes to improve detection efficiency. Third, we provide a flexible testing framework in which the user can choose to address different levels of questions, namely, whether alternative 3′ SS or 5′ SS happens, and/or where it happens. Simulation studies and real data application have demonstrated that our method is powerful and accurate.

Availability and implementation: The software is implemented in Java and can be freely downloaded from http://ebchangepoint.sourceforge.net/.

Contact:  zhiwei@njit.edu
Degradation dynamics of microRNAs revealed by a novel pulse-chase approach
Authors: Marzi Matteo J. , Ghini Francesco , Cerruti Benedetta , de Pretis Stefano , Bonetti Paola , Giacomelli Chiara , Gorski Marcin M. , Kress Theresia , Pelizzola Mattia , Muller Heiko , Amati Bruno , Nicassio Francesco
Published: February 2016

The regulation of miRNAs is critical to the definition of cell identity and behavior in normal physiology and disease. To date, the dynamics of miRNA degradation and the mechanisms involved in remain largely obscure, in particular, in higher organisms. Here, we developed a pulse-chase approach based on metabolic RNA labeling to calculate miRNA decay rates at genome-wide scale in mammalian cells. Our analysis revealed heterogeneous miRNA half-lives, with many species behaving as stable molecules (T1/2 > 24 h), while others, including passenger miRNAs and a number (25/129) of guide miRNAs, are quickly turned over (T1/2 = 4–14 h). Decay rates were coupled with other features, including genomic organization, transcription rates, structural heterogeneity (isomiRs), and target abundance, measured through quantitative experimental approaches. This comprehensive analysis highlighted functional mechanisms that mediate miRNA degradation, as well as the importance of decay dynamics in the regulation of the miRNA pool under both steady-state conditions and during cell transitions.
Performance evaluation and optimization of X-ray stress measurement for nickel aluminium bronze based on the Bayesian method
Authors: Zhang Yanhui , Yang Wenyu , Lv Kemao
Published: February 2016

Nickel aluminium bronze is the main material of the controllable pitch propeller in the dynamic positioning system of an ocean-going vessel. When using an X-ray stress measuring instrument to measure the residual stress in this material, measurement failure phenomena often appear since the X-ray diffraction profile of nickel aluminium bronze has a low signal-to-noise ratio. Therefore, the Bragg diffraction angle identified by the traditional method has a large uncertainty, which could cause a large random disturbance of the X-ray stress measurement. Considering the measurement noise and model error, a new approach based on the Bayesian model class framework is proposed to improve the performance of current X-ray stress measurement analysis. For model classes with different peak shape functions, the posterior distributions of the Bragg diffraction angle 2θB are identified first, the posterior probabilities of each model class are computed, a hyper-robust value of 2θB is obtained and finally the residual stress is calculated. Using the confidence intervals of 2θB, the uncertainty of the X-ray stress measuring instrument at each measurement can be determined. Several experiments show that the performance of the proposed method is better than that of the current instrumental method. Of course, the proposed method is also suitable for the residual stress measurement of other new materials and is not limited to nickel aluminium bronze.
Growth of bainitic ferrite and carbon partitioning during the early stages of bainite transformation in a 2 mass% silicon steel studied by in situ neutron diffraction, TEM and APT
Authors: Timokhina I. B. , Liss K. D. , Raabe D. , Rakha K. , Beladi H. , Xiong X. Y. , Hodgson P. D.
Published: February 2016

In situ neutron diffraction, transmission electron microscopy (TEM) and atom probe tomography (APT) have been used to study the early stages of bainite transformation in a 2 mass% Si nano-bainitic steel. It was observed that carbon redistribution between the bainitic ferrite and retained austenite at the early stages of the bainite transformation at low isothermal holding occurred in the following sequence: (i) formation of bainitic ferrite nuclei within carbon-depleted regions immediately after the beginning of isothermal treatment; (ii) carbon partitioning immediately after the formation of bainitic ferrite nuclei but substantial carbon diffusion only after 33 min of bainite isothermal holding; (iii) formation of the carbon-enriched remaining austenite in the vicinity of bainitic laths at the beginning of the transformation; (iv) segregation of carbon to the dislocations near the austenite/ferrite interface; and (v) homogeneous redistribution of carbon within the remaining austenite with the progress of the transformation and with the formation of bainitic ferrite colonies. Bainitic ferrite nucleated at internal defects or bainite/austenite interfaces as well as at the prior austenite grain boundary. Bainitic ferrite has been observed in the form of an individual layer, a colony of layers and a layer with sideplates at the early stages of transformation.
Taking a look at the calibration of a CCD detector with a fiber-optic taper
Authors: Alkire R. W. , Rotella F. J. , Duke N. E. C. , Otwinowski Zbyszek , Borek Dominika
Published: February 2016

At the Structural Biology Center beamline 19BM, located at the Advanced Photon Source, the operational characteristics of the equipment are routinely checked to ensure they are in proper working order. After performing a partial flat-field calibration for the ADSC Quantum 210r CCD detector, it was confirmed that the detector operates within specifications. However, as a secondary check it was decided to scan a single reflection across one-half of a detector module to validate the accuracy of the calibration. The intensities from this single reflection varied by more than 30% from the module center to the corner of the module. Redistribution of light within bent fibers of the fiber-optic taper was identified to be a source of this variation. The degree to which the diffraction intensities are corrected to account for characteristics of the fiber-optic tapers depends primarily upon the experimental strategy of data collection, approximations made by the data processing software during scaling, and crystal symmetry.
The use of noncrystallographic symmetry averaging to solve structures from data affected by perfect hemihedral twinning
Authors: Sabin Charles , Plevka Pavel
Published: February 2016

Hemihedral twinning is a crystal-growth anomaly in which a specimen is composed of two crystal domains that coincide with each other in three dimensions. However, the orientations of the crystal lattices in the two domains differ in a specific way. In diffraction data collected from hemihedrally twinned crystals, each observed intensity contains contributions from both of the domains. With perfect hemihedral twinning, the two domains have the same volumes and the observed intensities do not contain sufficient information to detwin the data. Here, the use of molecular replacement and of noncrystallographic symmetry (NCS) averaging to detwin a 2.1 Å resolution data set forAichi virus 1affected by perfect hemihedral twinning is described. The NCS averaging enabled the correction of errors in the detwinning introduced by the differences between the molecular-replacement model and the crystallized structure. The procedure permitted the structure to be determined from a molecular-replacement model that had 16% sequence identity and a 1.6 Å r.m.s.d. for Cαatoms in comparison to the crystallized structure. The same approach could be used to solve other data sets affected by perfect hemihedral twinning from crystals with NCS.
Structure of a truncated form of leucine zipper II of JIP3 reveals an unexpected antiparallel coiled-coil arrangement
Authors: Llinas Paola , Chenon Mélanie , Nguyen T. Quyen , Moreira Catia , de Régibus Annélie , Coquard Aline , Ramos Maria J. , Guérois Raphaël , Fernandes Pedro A. , Ménétrey Julie
Published: February 2016

JIP3 and JIP4, two highly related scaffolding proteins for MAP kinases, are binding partners for two molecular motors as well as for the small G protein ARF6. The leucine zipper II (LZII) region of JIP3/4 is the binding site for these three partners. Previously, the crystal structure of ARF6 bound to JIP4 revealed LZII in a parallel coiled-coil arrangement. Here, the crystal structure of an N-terminally truncated form of LZII of JIP3 alone shows an unexpected antiparallel arrangement. Using molecular dynamics and modelling, the stability of this antiparallel LZII arrangement, as well as its specificity for ARF6, were investigated. This study highlights that N-terminal truncation of LZII can change its coiled-coil orientation without affecting its overall stability. Further, a conserved buried asparagine residue was pinpointed as a possible structural determinant for this dramatic structural rearrangement. Thus, LZII of JIP3/4 is a versatile structural motif, modifications of which can impact partner recognition and thus biological function.
The application of a resilience assessment approach to promote campus environmental management
Authors: Muller Irene , Tempelhoff Johann
Published: February 2016

Purpose

– This paper aims to outline the benefits of using resilience assessment instead of command and control mechanisms to evaluate sustainable campus environments.

Design/methodology/approach

– An exploratory mixed-method design was followed for the purposes of the project. During the first qualitative phase, a historical timeline of the focal system was created. In the quantitative phase, the resilience assessment guided the investigation. To collect data, the case study research strategy included a heuristic process of collecting and reviewing documents, semi-structured interviews, observations and the systematic implementation of the resilience assessment approach.

Findings

– Based on the resilience assessment approach, it is argued that the environmental status of university campuses can be considered relevant to the local community and immediate environment. Knowledge of the finite resources and their capacity in the context of the social-ecological system may increase the resilience of a campus.

Originality/value

– This research study explores the use of an alternative approach to environmental practices at university campuses. The resilience assessment is usually performed on large ecosystems. By applying this approach to a small ecosystem, the study fills a gap in the applicability of the resilience approach.
Too many compromises: survey research and the spectre of communism
Authors: Schwarzkopf Stefan
Published: February 2016

Purpose

– This paper aims to chart the influence of McCarthyism and of FBI surveillance practices on a number of prominent American social scientists, market researchers, opinion pollsters and survey research practitioners during the post-war years. Hitherto disparate sets of historical evidence on how Red Scare tactics influenced social researchers and marketing scientists are brought together and updated with evidence from original archival research.

Design/methodology/approach

– The paper draws on the existing secondary literature on how social research practitioners and social scientists reacted to the unusually high pressures on academic freedom during the McCarthy era. It supplements this review with evidence obtained from archival research, including declassified FBI files. The focus of this paper is set on prominent individuals, mainly Bernard Berelson, Samuel Stouffer, Hadley Cantril, Robert S. Lynd, Paul F. Lazarsfeld, Herta Herzog, Ernest Dichter, but also the Frankfurt School in exile.

Findings

– Although some of the historiography presents American social scientists and practitioners in the marketing research sector as victims of McCarthyism and FBI surveillance, it can also be shown that virtually all individuals in focus here also developed strategies of accommodation, compromise and even opportunism to benefit from the climate of suspicion brought about by the prevailing anti-Communism.

Social implications

– Anyone interested in questions about the morality of marketing, market research and opinion polling as part of the social sciences practicedin vivowill need to pay attention to the way these social-scientific practices became tarnished by the way prominent researchers accommodated and at times even abetted McCarthyism.

Originality/value

– Against the view of social scientists as harassed academic minority, evidence is presented in this paper which shows American social scientists who researched market-related phenomena, like media, voters choices and consumer behaviour, in a different light. Most importantly, this paper for the first time presents archival evidence on the scale of Paul F. Lazarsfeld’s surveillance by the FBI.
Marketing and the Cold War: an overview
Authors: Tadajewski Mark , Stole Inger L.
Published: February 2016

Purpose

– This paper aims to examine the contents of the special issue, situating the material in appropriate historical context.

Design/methodology/approach

– The account is based on a close reading of each manuscript. Links to the wider academic literature are created, and a narrative thread is provided to introduce readers to the imbrication of marketing with the Cold War geopolitical climate.

Originality/value

– The debates surrounding the Cold War, marketing theory and marketing practice have been reviewed.
Association of anti‐RNA polymerase III antibody and silicone breast implants in patients with systemic sclerosis
Authors: Saigusa Ryosuke , Asano Yoshihide , Nakamura Kouki , Yamashita Takashi , Ichimura Yohei , Takahashi Takehiro , Toyama Tetsuo , Taniguchi Takashi , Yoshizaki Ayumi , Miyazaki Miki , Tamaki Zenshiro , Sato Shinichi
Published: February 2016

Systemic sclerosis (SSc) is believed to be caused by a complex interplay between genetic factors and environmental influences. Although silicone has been considered to be a candidate of environmental agents, clinical data presented so far fail to show a significant association between silicone breast implant (SBI) and the development of SSc. Because we recently experienced two consecutive SSc patients with anti‐RNA polymerase III (RNAP III) antibody who underwent SBI, we here investigated the association of SBI history with the development of SSc positive for anti‐RNAP III antibody. Among 262 Japanese SSc patients, of note, the frequency of SBI history was significantly higher in the anti‐RNAP III antibody group (16.0% [4/25]) than in the anti‐topoisomerase I antibody group (0% [0/87], P < 0.005) and in the anticentromere antibody group (1.2% [2/150], P < 0.005). These results suggest that SBI could influence the development of SSc in a certain subset of patients with anti‐RNAP III antibody.
Suppression of Mcl‐1 induces apoptosis in mouse peritoneal macrophages infected with Mycobacterium tuberculosis
Authors: Wang Fei‐yu , Wang Xin‐min , Wang Chan , Wang Xiao‐fang , Zhang Yu‐qing , Wu Jiang‐dong , Wu Fang , Zhang Wan‐jiang , Zhang Le
Published: February 2016

The effect of myeloid cell leukemia‐1 (Mcl‐1) inhibition on apoptosis of peritoneal macrophages in mice infected with Mycobacterium tuberculosis was investigated and the primary signaling pathway associated with the transcriptional regulation of Mcl‐1 was identified. Real‐time PCR and western blotting indicated that Mcl‐1 transcript and protein expression are upregulated during infection with virulent M. tuberculosis H37Rv and Xinjiang strains but not with attenuated M. tuberculosis strain H37Ra or Bacillus Calmette–Guérin. Mcl‐1 transcript and protein expression were downregulated by specific inhibitors of the Janus kinase/signal transducer and activator of transcription (JAK/STAT), mitogen‐activated protein kinase (MAPK) and phosphoinositol 3‐kinase (PI3K) pathways (AG490, PD98059 and LY294002, respectively). The strongest inhibitor of Mcl‐1 expression was PD98059, the MAPK inhibitor. Flow cytometry demonstrated that the rate of apoptosis in peritoneal macrophages is significantly higher in mice infected with M. tuberculosis and the rate of apoptosis is correlated with the virulence of the strain of M. tuberculosis. Apoptosis was found to be upregulated by AG490, PD98059 and LY294002, whereas inhibition of the MAPK pathway sensitized the infected macrophages to apoptosis. Taken together, these results suggest that specific downregulation of Mcl‐1 significantly increases apoptosis of peritoneal macrophages and that the MAPK signaling pathway is the primary mediator of Mcl‐1 expression.
Self‐weighing and simple dietary advice for overweight and obese pregnant women to reduce obstetric complications without impact on quality of life: a randomised controlled trial
Authors: McCarthy EA , Walker SP , Ugoni A , Lappas M , Leong O , Shub A
Published: February 2016

Objective

To determine the effect of serial weighing and dietary advice compared with standard antenatal care on obstetric outcomes.

Design

Randomised controlled clinical trial.

Setting

Australian tertiary obstetric hospital.

Population

Three hundred and eighty‐two overweight or obese non‐diabetic pregnant women at less than 20 weeks gestation with a singleton pregnancy.

Methods

Women were randomised to targeted, serial self‐weighing and simple dietary advice, (intervention), or standard antenatal care (control).

Main outcomes measures

The primary outcome was a reduction in a composite of obstetric complications: gestational hypertension, pre‐eclampsia, diabetes, assisted or caesarean birth, shoulder dystocia, severe perineal trauma, postpartum haemorrhage and maternal high dependency care. Secondary outcomes were gestational weight gain at 36 weeks' gestation, quality of life (QOL) and maternal serum levels of 28‐week leptin, adiponectin and C‐reactive protein (CRP).

Results

There was no difference in the rate of the primary composite outcome of obstetric complications: 124/184 (67% control), 124/187 (66% intervention) [relative risk 0.98 (95% confidence interval (CI) 0.85–1.14)]. There was no difference in mean gestational weight gain [−0.9 kg (95% CI −2.0, 0.25)], QOL or leptin, adiponectin or CRP levels between intervention and control groups.

Conclusions

This low‐cost, pragmatic intervention failed to prevent obstetric complications or modify maternal biochemistry or gestational weight gain in overweight or obese pregnant women. Participation in the study did not impair participants' QOL.

Tweetable abstract

Serial self‐weighing and dietary advice failed to reduce obstetric complications in overweight pregnant women.
INSTITUTIONAL INEFFECTIVENESS, ILLEGITIMACY, AND PUBLIC SUPPORT FOR VIGILANTISM IN LATIN AMERICA
Authors: NIVETTE AMY E.
Published: February 2016

Why do individuals or groups support vigilantism as a means of conflict resolution? Most researchers tend to agree that support for and participation in vigilantism occurs in “stateless locations,” that is, when formal justice institutions are weak or absent. Despite this general consensus, quantitative evidence of this relationship is limited to a handful of country‐specific studies that used only subjective survey‐based measures of institutional weakness. This study seeks to extend research on vigilantism by assessing the relationship between subjective and objective conditions of formal justice institutions and public support for vigilantism across 323 provinces in 18 Latin American countries by using the 2012 AmericasBarometer Survey. Specifically, this study uses multilevel logistic regression techniques to examine the variability of public support for lethal vigilantism within and across Latin American countries. When controlling for a wide range of potential confounds, the results show that the most robust predictors of support for violent vigilantism are subjective indicators of institutional illegitimacy, personal victimization, and punitive attitudes. Evidence also exists that objective insecurity, as measured by province‐level homicide rates, fosters public support for violent vigilantism in certain situations.
Characterization of Antibodies for Grain‐Specific Gluten Detection
Authors: Sharma Girdhari M. , Rallabhandi Prasad , Williams Kristina M. , Pahlavan Autusa
Published: February 2016

Gluten ingestion causes immunoglobulin E (IgE)‐mediated allergy or celiac disease in sensitive individuals, and a strict gluten‐free diet greatly limits food choices. Immunoassays such as enzyme‐linked immunosorbent assay (ELISA) are used to quantify gluten to ensure labeling compliance of gluten‐free foods. Anti‐gluten antibodies may not exhibit equal affinity to gluten from wheat, rye, and barley. Moreover, because wheat gluten is commonly used as a calibrator in ELISA, accurate gluten quantitation from rye and barley contaminated foods may be compromised. Immunoassays utilizing grain‐specific antibodies and calibrators may help improve gluten quantitation. In this study, polyclonal antibodies raised against gluten‐containing grain‐specific peptides were characterized for their immunoreactivity to gluten from different grain sources. Strong immunoreactivity to multiple gluten polypeptides from wheat, rye, and barley was observed in the range 34 to 43 kDa with anti‐gliadin, 11 to 15 and 72 to 95 kDa with anti‐secalin, and 30 to 43 kDa with anti‐hordein peptide antibodies, respectively. Minimal or no cross‐reactivity with gluten from other grains was observed among these antibodies. The anti‐consensus peptide antibody raised against a repetitive amino acid sequence of proline and glutamine exhibited immunoreactivity to gluten from wheat, rye, barley, and oat. The antibodies exhibited similar immunoreactivity with most of the corresponding grain cultivars by ELISA. The high specificity and minimal cross‐reactivity of grain‐specific antibodies suggest their potential use in immunoassays for accurate gluten quantitation.
The righteous and the rightful: The technomoral politics of NGOs, social movements, and the state in India
Authors: BORNSTEIN ERICA , SHARMA ARADHANA
Published: February 2016

Civil society groups today are honored and relied on by governments, as well as tightly regulated and scrutinized for challenging state policies and agencies. In contemporary India, political dynamics of collaboration and confrontation between state and nonstate actors increasingly unfold in legal‐social fields, taking “technomoral” forms. Mixing technocratic languages of law and policy with moral pronouncements, these actors assert themselves as virtuous agents, marking their political legitimacy as keepers of the public interest. Using ethnographic research with Indian NGOs, social movements, and a political party, we show that as civil society groups interact with state bodies, they redefine institutional boundaries and claim moral authority over public stewardship. Technomoral strategies are neither depoliticized nor antipolitical, but constitute a righteous and rightful form of politics. [NGOs, state, India, morality, activist politics, neoliberalism, law]
Rituals of care for the elderly in northern Thailand: Merit, morality, and the everyday of long‐term care
Authors: AULINO FELICITY
Published: February 2016

Caregivers’ quotidian actions challenge prevailing views of care that rely on the emotional or attentive orientation of the caregiver. The routinized care tasks provided by two middle‐aged women for their bedridden mother in northern Thailand reveal the realities of long‐term caregiving. For these sisters, care transforms “merit” and “karma” without reliance on internal conviction. This context in turn reflects how people enact values and maintain social worlds through habituated physical practices of providing for others. Ordinary care in practice—termed “rituals of care”—dislodges fixation on particular personal sentiments and affirms the study of care as a powerful tool for assessing enduring modes of moral experience as well as subtle forms of social change. [care,ritual,phenomenology,Buddhism,Thailand,embodiment,morality]
Molecular characterization of clear cell renal cell carcinoma identifies CSNK2A1, SPP1 and DEFB1 as promising novel prognostic markers
Authors: Rabjerg Maj , Bjerregaard Henriette , Halekoh Ulrich , Jensen Boye L. , Walter Steen , Marcussen Niels
Published: February 2016

The prognosis associated with clear cell renal carcinoma (ccRCC) can vary widely and novel molecular prognostic markers are needed to assess prognosis at an earlier stage. Several gene products have been investigated for this purpose, but none of them have been implemented in clinical practice. Here we hypothesized that we, using TaqMan® Array, could identify superior prognostic messenger RNA (mRNA)s in long‐term follow‐up. Messenger RNA level of 19 candidate genes was investigated in 97 patients with ccRCC. Three genes impacted significantly on prognosis in both univariate and multivariate analysis. In univariate analysis, CSNK2A1 was a strong indicator of a poor overall survival (OS) (HR = 5.01, p < 0.001), disease specific survival (DSS) (HR = 6.21, p = 0.007) and progression free survival (PFS) (HR = 5.93, p = 0.005). High expression of SPP1 was associated to poor PFS (HR = 4.41, p = 0.04). DEFB1 was associated with a better PFS (HR = 0.24, p = 0.006). In multivariate analysis, CSNK2A1 was associated to a worse OS (HR = 3.56, p = 0.008) and PFS (HR = 3.84, p = 0.005), whereas SPP1 was an independent predictor of a worse PFS (HR = 3.46, p = 0.007) and DEFB1 of a better PFS (HR = 0.37, p = 0.027). These results show that with TaqMan® Array we could identify three superior gene products related to prognosis. Further studies are needed to elucidate the pathways and roles of these genes in renal cancer development.
Strategies for Using Plagiarism Software in the Screening of Incoming Journal Manuscripts: Recommendations Based on a Recent Literature Survey
Authors: Lykkesfeldt Jens
Published: February 2016

In recent years, several online tools have appeared capable of identifying potential plagiarism in science. While such tools may help to maintain or even increase the originality and ethical quality of the scientific literature, no apparent consensus exists among editors on the degree of plagiarism or self‐plagiarism necessary to reject or retract manuscripts. In this study, two entire volumes of published original papers and reviews from Basic & Clinical Pharmacology & Toxicology were retrospectively scanned for similarity in anonymized form using iThenticate software to explore measures to predictively identify true plagiarism and self‐plagiarism and to potentially provide guidelines for future screening of incoming manuscripts. Several filters were applied, all of which appeared to lower the noise from irrelevant hits. The main conclusions were that plagiarism software offers a unique opportunity to screen for plagiarism easily but also that it has to be employed with caution as automated or uncritical use is far too unreliable to allow a fair basis for judging the degree of plagiarism in a manuscript. This remains the job of senior editors. Whereas a few cases of self‐plagiarism that would not likely have been accepted with today's guidelines were indeed identified, no cases of fraud or serious plagiarism were found. Potential guidelines are discussed.
Apolipoprotein E genotype is not associated with cognitive impairment in older adults with bipolar disorder
Authors: Kerr Daniel Shikanai , Stella Florindo , Radanovic Márcia , Aprahamian Ivan , Bertollucci Paulo Henrique Ferreira , Forlenza Orestes Vicente
Published: February 2016

Objectives

Cognitive decline is part of the long‐term outcome for many individuals with bipolar disorder (BD). The ε4 allele (APOE*4) of apolipoprotein E (APOE) is a well‐established risk factor for dementia in Alzheimer's disease (AD). However, its contribution to the risk of cognitive deterioration in BD has not yet been determined. Our aim was to analyze the APOE genotype association with cognitive status in a sample of older adults with BD and compare this to the association in individuals with AD, individuals with mild cognitive impairment (MCI), and healthy controls.

Methods

Participants (n = 475) were allocated to four groups: individuals with BD (n = 77), those with AD (n = 211), those with MCI (n = 43), and healthy controls (n = 144) according to clinical and neuropsychological assessment. APOE was genotyped by real‐time polymerase chain reaction. Tukey's honest significant difference test and Pearson's chi‐squared test were used to compare diagnostic groups.

Results

Subjects with BD were similar to controls with respect to the distribution of the APOE genotype (p = 0.636) and allele frequencies (p = 0.481). Significant differences were found when comparing the AD group to the BD group or to controls (APOE genotype: p < 0.0002; allele frequencies: p < 0.001). APOE*4 was significantly increased in the AD group when compared to the BD group (p = 0.031) and controls (p < 0.0001). The cognitively impaired BD subgroup (Mini‐Mental State Examination below the cutoff score and/or neuropsychological assessment compatible with MCI) had a statistically significant higher frequency of APOE*2 compared to the AD group (p = 0.003).

Conclusions

APOE*4 is not associated with the diagnosis of BD and does not impact the occurrence of dementia in BD. Given the distinct clinical and biological features of cognitive impairment in BD, we hypothesized that dementia in BD is unrelated to AD pathological mechanisms.