bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide Marginal Epistatic Association Mapping in Case-Control Studies
Authors: Crawford Lorin , Zhou Xiang 
Published: July 2018

AbstractEpistasis, commonly defined as the interaction between genetic loci, is an important contributor to the genetic architecture underlying many complex traits and common diseases. Most existing epistatic mapping methods in genome-wide association studies explicitly search over all pairwise or higher-order interactions. However, due to the potentially large search space and the resulting multiple testing burden, these conventional approaches often suffer from heavy computational cost and low statistical power. A recently proposed attractive alternative for mapping epistasis focuses instead on detecting marginal epistasis, which is defined as the combined pairwise interaction effects between a given variant and all other variants. By searching for marginal epistatic effects, one can identify genetic variants that are involved in epistasis without the need to identify the exact partners with which the variants interact — thus, potentially alleviating much of the statistical and computational burden associated with conventional epistatic mapping procedures. However, previous marginal epistatic mapping methods are based on quantitative trait models. As we will show here, these lack statistical power in case-control studies. Here, we develop a liability threshold mixed model that extends marginal epistatic mapping to case-control studies. Our method properly accounts for case-control ascertainment and the binary nature of case-control data. We refer to this method as the liability threshold marginal epistasis test (LT-MAPIT). With simulations, we illustrate the benefits of LT-MAPIT in terms of providing effective type I error control, and being more powerful than both existing marginal epistatic mapping methods and conventional explicit search-based approaches in case-control data. We finally apply LT-MAPIT to identify both marginal and pairwise epistasis in seven complex diseases from the Wellcome Trust Case Control Consortium (WTCCC) 1 study.
Tumor extracellular vesicles are required for tumor-associated macrophage programming
Authors: Rabe Daniel C , Rustandy Felicia D , Lee Jiyoung , Rosner Marsha Rich 
Published: July 2018

SummaryTriple-negative breast cancers (TNBC) are highly infiltrated by tumor-associated macrophages (TAMs) that promote tumor growth, survival, metastasis and therapeutic resistance. Although cytokines such as CCL5 have been implicated in TAM recruitment to TNBC tumors, the mechanism by which tumor cells educate TAMs is not understood. Here we show that tumor EVs are both necessary and sufficient for programming TAMs toward a pro-metastatic phenotype. The mechanism involves CCL5 regulation of tumor extracellular vesicles (EVs), which activate TLR2 and TLR3, leading to secretion of a common set of cytokines that further stimulate tumor cell invasion and metastasis as well as alter the tumor microenvironment. Cytokine expression is significantly correlated to CCL5 expression and up-regulated in TNBC patient tumors. These results demonstrate for the first time that tumor EVs are key mediators of TAM education, phenocopy the pro-metastatic and drug resistant state of the tumors to TAMs, and illustrate the potential clinical relevance of these findings to TNBC patients.HighlightsTumor extracellular vesicles (EVs) are required for pro-metastatic programming of tumor-associated macrophages (TAMs)Tumor CCL5 and macrophage TLR signaling mediate tumor EV programming of TAMs in TNBCsTumor EVs mediate drug resistance in TAMs and alter recruitment of regulatory T-cells.Cytokines expressed by EV-educated TAMs are enriched and correlate with CCL5 in human TNBC patients.eTOCChemokines such as CCL5 recruit tumor-associated macrophages (TAMs) that are required for metastasis, but TAM programming is not understood. Rabe et al. show that tumor extracellular vesicles (EVs) are required for programming TAMs via Toll-like Receptors (TLRs) to phenocopy the tumor, rewire the microenvironment, drive metastasis and promote immune cell evasion.
Transient DNA Binding Induces RNA Polymerase II Compartmentalization During Herpesviral Infection Distinct From Phase Separation
Authors: McSwiggen David T , Hansen Anders S , Marie-Nelly Hervé , Teves Sheila , Heckert Alec B , Dugast-Darzacq Claire , Hao Yvonne , Umemoto Kayla K , Tjian Robert , Darzacq Xavier 
Published: July 2018

SummaryDuring lytic infection, Herpes Simplex Virus 1 generates replication compartments (RCs) in host nuclei that efficiently recruit protein factors, including host RNA Polymerase II (Pol II). Pol II and other cellular factors form hubs in uninfected cells that are proposed to phase separate via multivalent protein-protein interactions mediated by their intrinsically disordered regions. Using a battery of live cell microscopic techniques, we show that although RCs superficially exhibit many characteristics of phase separation, the recruitment of Pol II instead derives from nonspecific interactions with the viral DNA. We find that the viral genome remains nucleosome-free, profoundly affecting the way Pol II explores RCs by causing it to repetitively visit nearby binding sites, thereby creating local Pol II accumulations. This mechanism, distinct from phase separation, allows viral DNA to outcompete host DNA for cellular proteins. Our work provides new insights into the strategies used to create local molecular hubs in cells.
Species Designations Belie Phenotypic and Genotypic Heterogeneity in Oral Streptococci
Authors: Velsko Irina M. , Chakraborty Brinta , Nascimento Marcelle M. , Burne Robert A. , Richards Vincent P. 
Published: July 2018

AbstractHealth-associated oralStreptococcusspecies are promising probiotic candidates to protect against dental caries. Ammonia production through the arginine deiminase system (ADS), which can increase the pH of oral biofilms, and direct antagonism of caries-associated bacterial species are desirable properties for oral probiotic strains. ADS and antagonistic activities can vary dramatically among individuals, but the genetic basis for these differences is unknown. We sequenced whole genomes of a diverse set of clinical oralStreptococcusisolates and examined the genetic basis of variability in ADS and antagonistic activities. A total of 113 isolates were included and represented ten species:S. australis, A12-like,S. cristatus,S. gordonii,S. intermedius,S. mitis,S. oralisincludingS. oralissubsp.dentisani,S. parasanguinis, S. salivarius, andS. sanguinis. Mean ADS activity and antagonism onStreptococcus mutansUA159 were measured for each isolate, and each isolate was whole genome-shotgun sequenced on an Illumina MiSeq. Phylogenies were built of genes known to be involved in ADS activity and antagonism. Several approaches to correlate the pan-genome with phenotypes were performed. Phylogenies of genes previously identified in ADS activity and antagonism grouped isolates by species but not by phenotype. GWAS identified additional genes potentially involved in ADS activity or antagonism across all the isolates we sequenced as well as within several species. Phenotypic heterogeneity in oral streptococci is not necessarily reflected by genotype and is not species-specific. Probiotic strains must be carefully selected based on characterization of each strain, and not based on inclusion within a certain species.ImportanceRepresentative type strains are commonly used to characterize bacterial species, yet species are phenotypically and genotypically heterogeneous. Conclusions about strain physiology and activity based on a single strain therefore may be inappropriate and misleading. When selecting strains for probiotic use, the assumption that all strains within a species share the same desired probiotic characteristics share those characteristics may result in selection of a strain that lacks the desired traits, and therefore makes a minimally effective or ineffective probiotic. Health-associated oral streptococci are promising candidates for anti-caries probiotics, but strains need to be carefully selected based on observed phenotypes. We characterized the genotype and anti-caries phenotypes of strains from ten species of oral Streptococci and demonstrate poor correlation between genotype and phenotype across all species.
A framework for intelligent Twitter data analysis with non-negative matrix factorization
Authors: Casalino Gabriella , Castiello Ciro , Del Buono Nicoletta , Mencar Corrado 
Published: July 2018

Purpose
The purpose of this paper is to propose a framework for intelligent analysis of Twitter data. The purpose of the framework is to allow users to explore a collection of tweets by extracting topics with semantic relevance. In this way, it is possible to detect groups of tweets related to new technologies, events and other topics that are automatically discovered.

Design/methodology/approach
The framework is based on a three-stage process. The first stage is devoted to dataset creation by transforming a collection of tweets in a dataset according to the vector space model. The second stage, which is the core of the framework, is centered on the use of non-negative matrix factorizations (NMF) for extracting human-interpretable topics from tweets that are eventually clustered. The number of topics can be user-defined or can be discovered automatically by applying subtractive clustering as a preliminary step before factorization. Cluster analysis and word-cloud visualization are used in the last stage to enable intelligent data analysis.

Findings
The authors applied the framework to a case study of three collections of Italian tweets both with manual and automatic selection of the number of topics. Given the high sparsity of Twitter data, the authors also investigated the influence of different initializations mechanisms for NMF on the factorization results. Numerical comparisons confirm that NMF could be used for clustering as it is comparable to classical clustering techniques such as spherical k-means. Visual inspection of the word-clouds allowed a qualitative assessment of the results that confirmed the expected outcomes.

Originality/value
The proposed framework enables a collaborative approach between users and computers for an intelligent analysis of Twitter data. Users are faced with interpretable descriptions of tweet clusters, which can be interactively refined with few adjustable parameters. The resulting clusters can be used for intelligent selection of tweets, as well as for further analytics concerning the impact of products, events, etc. in the social network.
Parameters of automated fraud detection techniques during online transactions
Authors: Khattri Vipin , Singh Deepak Kumar 
Published: July 2018

PurposeThis paper aims to provide information of parameters and techniques used in the automated fraud detection system during online transaction. With the increase in the use of online transactions, the concerns regarding data security have also increased. To tackle the frauds, lot of research has been done and plethora of papers are available on the related topics. The purpose of this paper is to provide the clear pathway for researchers to move in the direction of development of automated fraud detection system to prevent the fraud during online transaction.Design/methodology/approachThis literature review analyses and compares the different types of techniques for detecting fraud during online transaction. An in-depth study of the most prominent journals has been done and the core methodology of the papers has been presented. This article also shed some light on different types of parameters used in fraud detection techniques during online transaction.FindingsThere are vast varieties of various fraud detection techniques, and every technique has completed task in its own way. After studying approximately 41 research papers, 14 books and four reports, in total 30 parameters have been identified and a detailed study of the parameters has been presented. The parameters are also listed with their details that how these parameters are used in the security system for detecting online transaction fraud.Research limitations/implicationsThis paper provides empirical insight about the parameters and their prominence in the development of automated fraud detection security system of online transaction. This paper encourages the researchers to development of improved fraud detection system.Practical implicationsThis paper will pave the way for researchers to do a focused research on the fraud detection methodologies. The analysis will help in zeroing down the most prevalent topic of research in this field. The researchers will be able to understand the internal details of parameters and techniques used in the fraud detection systems. This literature also helps the research to think in a variety of ways that how these parameters will be used in the development of fraud detection system.Originality/valueThis paper is one of the most comprehensive reviews in its field. It tries and attempts to fill a void created because of lack of compilation of the laid fraud detection parameters.
The battle against fraud: do reporting mechanisms work?
Authors: Peltier-Rivest Dominic 
Published: July 2018

PurposeThis paper aims to explore how well reporting mechanisms work, investigate current trends and develop a framework for implementing effective mechanisms.Design/methodology/approachThis study is based on primary and secondary data, criminology theory and best corporate strategies.FindingsThis study shows that the median number of annual reports equals 1.2 per cent of the number of employees in an organization and that 40 per cent of these reports have merit (Navex Global, 2014). In addition, 42.2 per cent of all frauds are detected through internal reports, whatever their form. Organizations with formal reporting mechanisms sustain fraud losses that are 40.5 per cent less than other organizations (ACFE, 2014). Moreover, employees are more willing to report theft, human resource and workplace issues than fraud and corruption, while 21 per cent of all whistleblowers have experienced some form of retaliation for reporting wrongdoing (Ethics Resource Center, 2014). Results from primary data show that the option to remain anonymous is offered only by 74 per cent of all reporting mechanisms. This paper argues that effective reporting mechanisms should actively encourage whistleblowing, that all credible allegations should be independently investigated and that whistleblowers should be offered the option to remain anonymous. The oversight and the daily administration of reporting mechanisms should be given to two different parties who are independent from management and who do not participate in incentive compensation plans (Lipman, 2012).Research limitations/implicationsThis paper extends previous research by reporting on current hotline trends and integrating various factors into a framework to implement effective reporting mechanisms.Originality/valueIt is the first paper to investigate the effectiveness of reporting mechanisms and current policy trends.
Understanding fraud in Malaysian SMEs
Authors: N’Guilla Sow Abdoulaye , Basiruddin Rohaida , Abdul Rasid Siti Zaleha , Husin Maizaitulaidawati Md 
Published: July 2018

Purpose
The paper aims to provide an overview of fraud risk among Malaysian small- and medium-sized enterprises (SMEs). In particular, the authors investigate the understanding of SME owners and managers on fraud schemes and the usage of antifraud measures.

Design/methodology/approach
A sample of 126 Malaysian SMEs from different industries participated in this study.

Findings
The results suggest that Malaysian SMEs are exposed to a broad range of fraud schemes, yet few take actions to prevent these frauds.

Practical implications
The findings should be useful to academic researchers, entrepreneurs, regulators and others who are interested in understanding the fraud risk in small businesses.

Originality/value
This study extends and contributes to prior literature by linking the state of fraud and SMEs in developing countries.
Social influences on survival and reproduction: Insights from a long‐term study of wild baboons
Authors: Alberts Susan C. 
Published: July 2018

Abstract

For social species, the environment has two components: physical and social. The social environment modifies the individual's interaction with the physical environment, and the physical environment may in turn impact individuals’ social relationships. This interplay can generate considerable variation among individuals in survival and reproduction. Here, I synthesize more than four decades of research on the baboons of the Amboseli basin in southern Kenya to illustrate how social and physical environments interact to affect reproduction and survival.

For immature baboons, social behaviour can both mitigate and exacerbate the challenge of survival. Only c. 50% of live‐born females and c. 44% of live‐born males reach the median age of first reproduction. Variation in pre‐adult survival, growth and development is associated with multiple aspects of the social environment. For instance, conspecifics provide direct care and are a major source of social knowledge about food and the environment, but conspecifics can also represent a direct threat to survival through infanticide.

In adulthood, both competition (within and between social groups) and cooperative affiliation (i.e. collective action and/or the exchange of social resources such as grooming) are prominent features of baboon social life and have important consequences for reproduction and survival. For instance, adult females with higher social dominance ranks have accelerated reproduction, and adult females that engage in more frequent affiliative social interactions have higher survival throughout adulthood.

The early life environment also has important consequences for adult reproduction and survival, as in a number of other bird and mammal species. In seasonal breeders, early life effects often apply to entire cohorts; in contrast, in nonseasonal and highly social species such as baboons, early life effects are more individual‐specific, stemming from considerable variation not only in the early physical environment (even if they are born in the same year) but also in the particulars of their social environment.
Variation in reproductive modes and population genetic structures of a monocarpic perennial herb, Cardiocrinum cordatum, in relation to habitat fragmentation
Authors: Narumi Tadashi , Ohara Masashi 
Published: July 2018

AbstractReproductive systems are recognized as having a profound influence on the extent and structure of genetic variation in plant populations. To investigate the spatiotemporal variation in the reproductive modes (sexual and vegetative reproduction) and population genetic structures of a monocarpic perennial herb, Cardiocrinum cordatum (liliaceae), we selected a variety of habitats (e.g. large forested area including primeval forest, small fragmented secondary forest, and so on) around Sapporo City, Japan. We conducted breeding experiments, monitored the fate and growth of marked individuals for 3 years, and also analyzed the spatiotemporal genetic variation of flowering plants within the populations using allozyme variation. Plants emasculated prior to anthesis produced mature fruits in all populations examined. However, seed production was significantly lower in the small fragmented populations, possibly because of the low availability of pollinators and subsequent pollen limitation. In these fragmented populations, the mature flowering plants tended to be more dependent on vegetative reproduction for their recruitment, because they can only produce flowers once in their lifetime. Genetic diversity using samples from mature flowering plants in each population was lower in the small fragmented populations than in the large populations. In addition, although genotypic compositions in the fragmented populations were more or less similar during the 3 years of the study, the dominant genotypes changed temporally and spatially every year in the large populations. The present study demonstrated that the reproductive features of C. cordatum can be altered in various environmental conditions, such as habitat fragmentation, and these changes considerably affected the population genetic structures and vice versa.
Ten‐year trends in the price differential between healthier and less healthy foods in New Zealand
Authors: Mackay Sally , Vandevijvere Stefanie , Lee Arier 
Published: July 2018

AimTo measure the relative change in price of healthier and less healthy foods over 10 years in New Zealand.MethodsFoods in the New Zealand food price index were classified as healthy and less healthy (WHO Europe Nutrient Profile Model) and by degree of processing (according to the NOVA classification). The change in price from February 2007 to January 2017 was analysed using a mixed model for repeated measures with healthiness (or level of processing), season and time added as covariates.ResultsEighty‐eight (of 155) relevant items had sufficient information on weight and healthiness. The trend of increasing food prices over time was similar for healthier and less healthy foods and between the three categories of processing. There was a statistically significant interaction (P = 0.014) between seasons and healthiness of foods, and seasons and degrees of processing (P < 0.001). The price of healthy foods and minimally processed foods fluctuated more by season compared to less healthy foods and processed foods.ConclusionsFood prices increased over time with no significant difference in the rate of change for healthier and less healthy foods, and between foods of different degrees of processing. This method can be used to routinely monitor relative changes in food prices according to healthiness.
Seasonal changes in fish catch and environmental variables in a large Tropical Lake, Volta, Ghana
Authors: Mensah Emmanuel T‐D. , Dankwa Hederick R. , Lauridsen Torben L. , Asmah Ruby , Campion Benjamin B. , Edziyie Regina 
Published: July 2018

AbstractFish species assemblage and selected environmental variables were monitored in Lake Volta from September 2014 to August 2016 to determine seasonal variability in species composition, catch and environmental variables that determine the structure of the fish community. A total of 1,557 individual fish belonging to 41 species, 25 genera and 13 families were recorded. The important fish species with respect to frequency of occurrence, abundance and weight, respectively, were as follows: Chrysichthys (100%; 43.03%; 17.93%), tilapias (100%; 28.97%; 17.86%), Alestes (100%; 14.13%; 32.10%) and Bagrus (91.67%; 5.65%; 12.80%) in that order. The composition of fish species and their temporal variation in experimental catches were similar to that of commercial catches. There were no significant differences (p > 0.05) in species abundance, weight and diversity indices between the dry and wet seasons. The modal class of length frequency distribution of the dominant species in the catch, Chrysichthys, reduced from 125 mm in 2006 to 95 mm in the current study indicating overfishing. Environmental variables considered showed little variation and within optimal ranges for fish survival and did not differ significantly between seasons. Canonical Correspondence Analysis showed that environmental variables explained 43.30% of the variation in species abundance with Lake water level, nitrite‐nitrogen and total dissolved solids being the main environmental factors influencing the structure of the fish community.