bluuebunny/crossref_metadata_2025 huggingface dataset:
Dynamic Architecture of DNA Repair Complexes and the Synaptonemal Complex at Sites of Meiotic Recombination
Authors: Woglar Alexander , Villeneuve Anne M.
Published: October 2017

Meiotic double-strand breaks (DSBs) are generated and repaired in a highly regulated manner to ensure formation of crossovers (COs) while also enabling efficient non-CO repair to restore genome integrity. Here we use Structured-Illumination Microscopy to investigate the dynamic architecture of DSB repair complexes at meiotic recombination sites in relationship to the synaptonemal complex (SC). DSBs resected at both ends are rapidly converted into inter-homolog repair intermediates harboring two populations of BLM helicase and RPA, flanking a single population of MutSγ. These intermediates accumulate until late pachytene, when repair proteins disappear from non-CO sites and CO-designated sites become enveloped by SC-central region proteins, acquire a second MutSγpopulation, and lose RPA. These and other data suggest that the SC protects CO intermediates from being dismantled inappropriately and promotes step-wise CO maturation by generating a transient CO-specific repair compartment, thereby enabling differential timing and outcome of repair at CO and non-CO sites
Transcriptome-wide association studies: opportunities and challenges
Authors: Wainberg Michael , Sinnott-Armstrong Nasa , Mancuso Nicholas , Barbeira Alvaro N. , Knowles David A , Golan David , Ermel Raili , Ruusalepp Arno , Quertermous Thomas , Hao Ke , Björkegren Johan LM , Kyung Im Hae , Pasaniuc Bogdan , Rivas Manuel A , Kundaje Anshul
Published: October 2017

Transcriptome-wide association studies (TWAS) integrate GWAS and gene expression datasets to find gene-trait associations. In this Perspective, we explore properties of TWAS as a potential approach to prioritize causal genes, using simulations and case studies of literature-curated candidate causal genes for schizophrenia, LDL cholesterol and Crohn’s disease. We explore risk loci where TWAS accurately prioritizes the likely causal gene, as well as loci where TWAS prioritizes multiple genes, some of which are unlikely to be causal, because they share the same variants as eQTLs. We illustrate that TWAS is especially prone to spurious prioritization when using expression data from tissues or cell types that are less related to the trait, due to substantial variation in both expression levels and eQTL strengths across cell types. Nonetheless, TWAS prioritizes candidate causal genes at GWAS loci more accurately than simple baselines based on proximity to lead GWAS variant and expression in trait-related tissue. We discuss current strategies and future opportunities for improving the performance of TWAS for causal gene prioritization. Our results showcase the strengths and limitations of using expression variation across individuals to determine causal genes at GWAS loci and provide guidelines and best practices when using TWAS to prioritize candidate causal genes.
IMPPAT: A curated database of Indian Medicinal Plants, Phytochemistry And Therapeutics
Authors: Mohanraj Karthikeyan , Karthikeyan Bagavathy Shanmugam , Vivek-Ananth R.P. , Bharath Chand R.P. , Aparna S.R. , Mangalapandi P. , Samal Areejit
Published: October 2017

Phytochemical constituents of medicinal plants encompass a diverse space of chemical scaffolds which can be used for rational design of novel drugs. India is rich with a flora of indigenous medicinal plants that have been used for centuries in traditional Indian medicine to treat human maladies. A comprehensive online database on the phytochemistry of Indian medicinal plants will enable the application of systems biology and cheminformatic approaches towards natural product based drug discovery. In this direction, we here present, IMPPAT, a manually curated database ofIndianMedicinalPlants,Phytochemistry,AndTherapeutics. IMPPAT contains 1742 Indian medicinal plants, 9596 phytochemicals and 1124 therapeutic uses which span across 27074 plant-phytochemical associations and 11514 plant-therapeutic associations. Notably, the curation effort led to a non-redundantin silicochemical library of 9596 phytochemicals with standard chemical identifiers and structure information. Using cheminformatic approaches, we have computed the physicochemical properties and drug-likeliness of the phytochemicals in IMPPAT which led to a filtered subset of 960 potential druggable phytochemicals. Moreover, a comparative analysis against FDA approved drugs suggests that majority of the druggable phytochemicals in IMPPAT are good candidates for novel prospective drugs as they have little or no structural similarity with existing drugs. The IMPPAT database is openly accessible at:https://www.imsc.res.in/~asamal/resources/imppat/home.
Effects of demographic stochasticity and life-history strategies on times and probabilities to fixation: an individual-based model
Authors: Abu Awad Diala , Coron Camille
Published: October 2017

Previous works has suggested that the harmonic mean population size can summarize the consequences of demographic fluctuations on the genetic frequencies of populations. We test this hypothesis by studying a model in which the demography and genetic composition of the population are both determined by the behavior of the individuals within the population. We propose an effective population size that allows us to compare our model with the classical Wright-Fisher diffusion both for neutral alleles and those under selection. We find that using our approximation for the effective population size, the Wright-Fisher diffusion provides good results for the times to absorption and probabilities of fixation of a given neutral allele and in cases where selection is not too strong. However, the times and laws to fixation are not always well predicted due to large fluctuations in population size caused by small growth rates or strong competition between individuals, that cannot be captured by the constant population size approximation. The discrepancy between our model and the Wright-Fisher diffusion is accentuated in the presence of demo-genetic feed-back. Our results imply that the Wright-Fisher diffusion is not appropriate when studying probabilities and times to fixation in long-lived species with low reproductive rates.
Estradiol and luteinizing hormone reverse memory loss in phencyclidine model of schizophrenia: Evidence for hippocampal GABA action
Authors: Riordan Alexander J. , Schaler Ari W. , Fried Jackson B. , Paine Tracie A. , Thornton Janice E.
Published: October 2017

The cognitive symptoms of schizophrenia are poorly understood and difficult to treat. Estrogens may mitigate these symptoms via unknown mechanisms. To examine these mechanisms, we tested whether increasing estradiol (E) or decreasing luteinizing hormone (LH) could rescue declarative memory in a phencyclidine (PCP) model of schizophrenia. We then assessed whether changes in cortical or hippocampal GABA may underlie these effects. Female rats were ovariectomized and injected subchronically with PCP. To modulate E and LH, animals received hormone capsules or Antide injections. Short-term episodic memory was assessed using the novel object recognition task. Brain expression of GAD67 was analyzed via western blot, and parvalbumin-containing cells were counted using immunohistochemistry. Some rats received hippocampal infusions of a GABAA agonist, GABAA antagonist, or GAD inhibitor before behavioral testing. We found that PCP reduced hippocampal GAD67 and abolished object recognition. Antide restored hippocampal GAD67 and rescued recognition memory in PCP-treated animals. Estradiol reversed PCP’s amnesic effect but failed to restore hippocampal GAD67. PCP did not cause significant differences in number of parvalbumin-expressing cells or cortical expression of GAD67. Hippocampal infusions of a GABAA agonist restored memory in PCP-treated rats. Blocking hippocampal GAD or GABAA receptors in ovx animals reproduced memory loss similar to PCP and inhibited estradiol’s memory rescue in PCP-treated animals. In summary, decreasing LH or increasing E can reverse memory loss in a PCP model of schizophrenia. Alterations in hippocampal GABA may contribute to both PCP’s effects on declarative memory and the hormones’ ability to reverse them.
An unusual nucleosomal sequence pattern is enriched in mammalian genes
Authors: Wright Gregory M. , Cui Feng
Published: October 2017

Nucleosomal DNA sequences generally follow a well-known pattern with ∼10-bp periodic WW (where W is A or T) dinucleotides that oscillate in phase with each other and out of phase with SS (where S is G or C) dinucleotides. However, nucleosomes having a DNA sequence pattern inverse to the conventional one have not been systematically analyzed in eukaryotes. Here, we show that anti-WW/SS nucleosomes are widespread and exhibit a species- and context-specific distribution in the genomes. The enrichment of anti-WW/SS nucleosomes in mammalian genomes is positively correlated with RNA Pol II transcriptional levels, but negatively correlated with the presence of the periodic WW or SS sequence patterns. In addition, chromatin remodeling complexes have an impact on the abundance of anti-WW/SS nucleosomes. The data reveal distinct roles ofcis- andtrans-acting factors in the rotational positioning of nucleosomes between non-mammals and mammals. Implications of the anti-WW/SS sequence pattern for RNA Pol II transcription are discussed.
So you think you can PLS-DA?
Authors: Ruiz-Perez Daniel , Guan Haibin , Madhivanan Purnima , Mathee Kalai , Narasimhan Giri
Published: October 2017

Background

Partial Least-Squares Discriminant Analysis (PLS-DA) is a popular machine learning tool that is gaining increasing attention as a useful feature selector and classifier. In an effort to understand its strengths and weaknesses, we performed a series of experiments with synthetic data and compared its performance to its close relative from which it was initially invented, namely Principal Component Analysis (PCA).

Results

We demonstrate that even though PCA ignores the information regarding the class labels of the samples, this unsupervised tool can be remarkably effective as a feature selector. In some cases, it outperforms PLS-DA, which is made aware of the class labels in its input. Our experiments range from looking at the signal-to-noise ratio in the feature selection task, to considering many practical distributions and models encountered when analyzing bioinformatics and clinical data. Other methods were also evaluated. Finally, we analyzed an interesting data set from 396 vaginal microbiome samples where the ground truth for the feature selection was available. All the 3D figures shown in this paper as well as the supplementary ones can be viewed interactively at http://biorg.cs.fiu.edu/plsda

Conclusions

Our results highlighted the strengths and weaknesses of PLS-DA in comparison with PCA for different underlying data models.
APOLIPOPROTEIN-E (APOE) ε4 AND COGNITIVE DECLINE OVER THE ADULT LIFE COURSE
Authors: Rawle Mark James , Davis Daniel , Bendayan Rebecca , Wong Andrew , Kuh Diana , Richards Marcus
Published: October 2017

We tested the association between APOE-ε4 and processing speed and memory between ages 43 and 69 in a population-based birth cohort. Analyses of processing speed (using a timed letter search task) and episodic memory (a 15-item word learning test) were conducted at ages 43, 53, 60-64 and 69 years using linear and multivariable regression, adjusting for gender and childhood cognition. Linear mixed models, with random intercepts and slopes, were conducted to test the association between APOE and the rate of decline in these cognitive scores from age 43 to 69. Model fit was assessed with the Bayesian Information Criterion. A cross-sectional association between APOE-ε4 and memory scores was detected at age 69 for both heterozygotes and homozygotes (β=−0.68 & β=−1.38 respectively, p=.03) with stronger associations in homozygotes; no associations were observed before this age. Homozygous carriers of APOE-ε4 had a faster rate of decline in memory between ages 43 and 69, when compared to noncarriers, after adjusting for gender and childhood cognition (β=−0.05, p=.04). There were no cross-sectional or longitudinal associations between APOE-ε4 and processing speed. We conclude that APOE-ε4 is associated with a subtly faster rate of memory decline from midlife to early old age; this may be due to effects of APOE-ε4 becoming manifest around the latter stage of life. Continuing follow-up will determine what proportion of this increase will become clinically significant.
Impact of non-LTR retrotransposons in the differentiation and evolution of Anatomically Modern Humans
Authors: Guichard Etienne , Peona Valentina , Malagoli-Tagliazucchi Guidantonio , Abitante Lucia , Jagoda Evelyn , Musella Margherita , Ricci Marco , Rubio-Roldán Alejandro , Sarno Stefania , Luiselli Donata , Pettener Davide , Taccioli Cristian , Pagani Luca , Garcia-Perez Jose Luis , Boattini Alessio
Published: October 2017

Transposable Elements are biologically important components of eukaryote genomes. In particular, non-LTR retrotransposons (N-LTRrs) extensively shaped the human genome throughout evolution. In this study, we compared retrotransposon insertions differentially present in the genomes of Anatomically Modern Humans, Neanderthals, Denisovans and Chimpanzees, in order to assess the possible impact of retrotransposition in the differentiation of the human lineage. Briefly, we first identified species-specific N-LTRrs and established their distribution in present day human populations. These analyses shortlisted a group of N-LTRr insertions that were found exclusively in Anatomically Modern Humans. Notably, these insertions targeted genes more frequently than randomly expected and are associated with an increase in the number of transcriptional/splicing variants of those genes they inserted in. The analysis of the functionality of genes targeted by human-specific N-LTRr insertions seems to reflect phenotypic changes that occurred during human evolution. Furthermore, the expression of genes containing the most recent N-LTRr insertions is enriched in the brain, especially in undifferentiated neurons, and these genes associate in networks related to neuron maturation and migration. Additionally, we also identified candidate N-LTRr insertions that have likely produced new functional variants exclusive to modern humans, which show traces of positive selection and are now fixed in all present-day human populations. In sum, our results strongly suggest that N-LTRr impacted our differentiation as a species and have been a constant source of genomic variability all throughout the evolution of the human lineage.
DDK has a primary role in processing stalled replication forks to initiate downstream checkpoint signaling
Authors: Sasi Nanda Kumar , Coquel Flavie , Lin Yea-Lih , MacKeigan Jeffrey P , Pasero Philippe , Weinreich Michael
Published: October 2017

CDC7-DBF4 kinase (DDK) is required to initiate DNA replication in eukaryotes by activating the replicative MCM helicase. DDK has also been reported to have diverse and sometimes conflicting roles in the replication checkpoint response in various organisms but the underlying mechanisms are far from settled. Here we show that human DDK promotes limited resection of newly synthesized DNA at stalled replication forks or sites of DNA damage to initiate replication checkpoint signaling. DDK is also required for efficient fork restart and G2/M cell cycle arrest. DDK exhibits genetic interactions with the ssDNA exonuclease EXO1, and we show that EXO1 is also required for nascent strand degradation following exposure to HU, raising the possibility that DDK regulates EXO1 directly. Thus, DDK has a primary and previously undescribed role in the replication checkpoint to promote ssDNA accumulation at stalled forks, which is required to initiate a robust checkpoint response and cell cycle arrest to maintain genome integrity.
Role of the pre-initiation complex in Mediator recruitment and dynamics
Authors: Knoll Elisabeth R. , Zhu Z. Iris , Landsman David , Morse Randall H.
Published: October 2017

The Mediator complex functions in eukaryotic transcription by stimulating the cooperative assembly of a pre-initiation complex (PIC) and recruitment of RNA Polymerase II (Pol II) for gene activation. The core Mediator complex is organized into head, middle, and tail modules, and in budding yeast (Saccharomyces cerevisiae), Mediator recruitment has generally been ascribed to sequence-specific activators engaging the tail module triad of Med2-Med3-Med15 at upstream activating sequences (UASs). We show that med2Δ med3Δ med15Δ yeast are viable and that Mediator lacking Med2-Med3-Med15 is associated with active promoters genome-wide. To test whether Mediator might alternatively be recruited via interactions with the PIC, we examined Mediator association genome-wide after depleting PIC components. We found that depletion of Taf1, Rpb3, and TBP profoundly affected Mediator association at active gene promoters, with TBP being critical for transit of Mediator from UAS to promoter, while Pol II and Taf1 stabilize Mediator association at proximal promoters.
Systematic Dissection of Sequence Elements Controlling σ70 Promoters Using a Genomically-Encoded Multiplexed Reporter Assay inE. coli
Authors: Urtecho Guillaume , Tripp Arielle D. , Insigne Kimberly D. , Kim Hwangbeom , Kosuri Sriram
Published: October 2017

Promoters are the key drivers of gene expression and are largely responsible for the regulation of cellular responses to time and environment. InE. coli,decades of studies have revealed most, if not all, of the sequence elements necessary to encode promoter function. Despite our knowledge of these motifs, it is still not possible to predict the strength and regulation of a promoter from primary sequence alone. Here we develop a novel multiplexed assay to study promoter function inE. coliby building a site-specific genomic recombination-mediated cassette exchange (RMCE) system that allows for the facile construction and testing of large libraries of genetic designs integrated into precise genomic locations. We build and test a library of 10,898 σ70 promoter variants consisting of all combinations of a set of eight ‐35 elements, eight ‐10 elements, three UP elements, eight spacers, and eight backgrounds. We find that the ‐35 and ‐10 sequence elements can explain approximately 74% of the variance in promoter strength within our dataset using a simple log-linear statistical model. Simple neural network models explain greater than 95% of the variance in our dataset by capturing nonlinear interactions with the spacer, background, and UP elements.
Majority of choice-related variability in perceptual decisions is present in early sensory cortex
Authors: Morais Michael J. , Michelson Charles D. , Chen Yuzhi , Pillow Jonathan W. , Seidemann Eyal
Published: October 2017

While performing challenging perceptual tasks such as detecting a barely visible target, our perceptual reports vary across presentations of identical stimuli. This perceptual variability is presumably caused by neural variability in our brains. How much of the neural variability that correlates with the perceptual variability is present in the primary visual cortex (V1), the first cortical processing stage of visual information? To address this question, we recorded neural population responses from V1 using voltage-sensitive dye imaging while monkeys performed a challenging reaction-time visual detection task. We found that V1 population responses in the period leading to the decision correspond more closely to the monkey’s report than to the visual stimulus. These results, together with a simple computational model that allows one to quantify the captured choice-related variability, suggest that most of this variability is present in V1 as additive noise, and that areas downstream to V1 contain relatively little independent choice-related variability.
Reliability and correlation of fMRI, ECoG and EEG during natural stimulus processing
Authors: Haufe Stefan , DeGuzman Paul , Henin Simon , Arcaro Michael , Honey Christopher J. , Hasson Uri , Parra Lucas C.
Published: October 2017

Human brain mapping relies heavily on fMRI, ECoG and EEG, which capture different physiological signals. Relationships between these signals have been established in the context of specific tasks or during resting state, often using spatially confined concurrent recordings in animals. But it is not certain whether these correlations generalize to other contexts relevant for human cognitive neuroscience. Here, we address the case of complex naturalistic stimuli and ask two basic questions. First, how reliable are the responses evoked by a naturalistic audio-visual stimulus in each of these imaging methods, and second, how similar are stimulus-related responses across methods? To this end, we investigated a wide range of brain regions and frequency bands. We presented the same movie clip twice to three different cohorts of subjects (NEEG = 45, NfMRI = 11, NECoG = 5) and assessed stimulus-driven correlations across viewings and between imaging methods, thereby ruling out task-irrelevant confounds. All three imaging methods had similar repeat-reliability across viewings when fMRI and EEG data were averaged across subjects, highlighting the potential to achieve large signal-to-noise ratio by leveraging large sample sizes. The fMRI signal correlated positively with high-frequency ECoG power across multiple task-related cortical structures but positively with low-frequency EEG and ECoG power. In contrast to previous studies, these correlations were as strong for low-frequency as for high frequency ECoG. We also observed links between fMRI and infra-slow EEG voltage fluctuations. These results extend previous findings to the case of natural stimulus processing.
Identity exploration during the transition to motherhood: facilitating factors and outcomes
Authors: Gross Spector Michal , Cinamon Rachel Gali
Published: October 2017

Purpose

The purpose of this paper is to expand our understanding about the way women shape their career decisions during their transition to motherhood, through the exploration process, its facilitating factors and outcomes.

Design/methodology/approach

A longitudinal, quantitative method was used to investigate the vocational and maternal exploration processes. Workplace, spousal and family support served as facilitating factors, and vocational decisions and well-being as outcomes. Participants were 326 Israeli women during their transition to motherhood.

Findings

SEM analysis revealed a good model fit to the data. Workplace support had a positive effect on maternal exploration. Increased maternal exploration was positively associated with keeping working patterns before motherhood, and negatively associated with well-being.

Research limitations/implications

The sample of the current study was limited to highly educated Israeli working women.

Practical implications

The results of the current study can serve career counselors policymakers and organizations in their efforts to encourage first-time mothers to retain their paid work patterns by supporting maternal exploration through creating family-friendly policies.

Originality/value

The current findings have demonstrated that social support factors contribute to the enhancement of the exploration process also in later developmental stages. Furthermore, these findings showed differential effects of managerial support on maternal exploration and vocational exploration.
Innovations in human resource practices: measurement development and validation
Authors: Agarwal Sonal , Chawla Ginni , Singh Rupali
Published: October 2017

Purpose

The purpose of this study is to develop innovations in human resource (InHR) framework in the context of Indian banking industry and further develop a scale for its measurement.

Design/methodology/approach

A non-response bias test is conducted on a sample of 300 employees, and the assumptions of constant variance, outliers and normality are tested. Further, the InHR scale is validated through exploratory factor analysis (EFA) and confirmatory factor analysis (CFA) tests.

Findings

EFA confirms the existence of five empirically distinct constructs at banking industry in India, and CFA affirms the dependability of the arrived constructs. It is concluded that the InHR framework constructs possess high reliability and validity.

Research limitations/implications

The authors duly recognize the limitations of survey-based research, the exploratory research design and the use of single method.

Practical implications

The proposed InHR scale and its constructs are an important input to guide managers and human resources (HR) policymakers to devise strategies for the Indian banking industry. Banks can also benchmark existing HR policies by applying the proposed InHR framework constructs.

Social implications

The InHR constructs provide academicians and practitioners with a better approach of understanding the InHR practices.

Originality/value

Despite the significance of Indian banking industry for the socio-economic capital, academic research focusing on this industry’s innovative practices has been limited. This study reveals originality and value by proposing an InHR framework in the context of Indian banking industry which integrates all the major innovative practices. Further a scale has been developed for its measurement.
Antecedents of e-business adoption intention: an empirical study
Authors: Sarmah Bijoylaxmi , Sharma Shreekant , Gupta Shivam
Published: October 2017

Purpose

Recent advances in information and communication technologies has driven emergence and expansion of the internet with decreased computing and communication costs and paved the way for exploring, creating and delivering value to the stakeholders through e-business adoption by the hotel service providers. Keeping this context in mind, this study aims to develop a conceptual model to investigate the antecedent factors of e-business adoption intention among the owners/managers of Indian micro, small and medium hotel enterprises and empirically validates it.

Design/methodology/approach

Data were gathered from micro, small and medium hotel owners/managers with the help online survey method that resulted into 116 usable questionnaires. Structural equation modeling technique was applied to examine the appropriateness of the hypotheses.

Findings

Findings reveal that attitude toward e-business, subjective norm and perceived behavioral control positively influences e-business adoption intention among the owners/managers of micro, small and medium hotel enterprises in India.

Research limitations/implications

The context of this study is micro, small and medium hotel enterprises in India only and thereby limits the generalizability of results to other industry and country context.

Practical implications

This study offers theoretical and managerial implications to be applied by academicians and micro, small and medium enterprise owners/managers for e-business adoption in Indian hotel industry.

Originality value

This study can be considered as an extension of the study of Crespo and del Bosque (2008) in which they applied the theory of planned behavior to understand the psychological factors that determine e-business adoption among the managers and, thereby, contribute the existing literature, as empirical studies on e-business adoption intention by micro, small and medium hotel enterprises are scantly available.
Relationship between foreign agent operations and performance in SME exporters
Authors: Ahn Se-Hwa
Published: October 2017

Purpose

The purpose of this paper is to examine the effects of small and medium-sized enterprises’ (SMEs) foreign agent operations on their international performance. This study thus investigates a mechanism in which market information obtained through agents is interpreted, transformed and applied for decision making and presents outcomes. In particular, the study focuses on the mediating role of adaptive capability on the relationship between market information management and export performance.

Design/methodology/approach

Drawing upon the theories of knowledge-based view and contingency paradigm, a research model is developed for linking the key constructs of foreign agent operations, information management, adaptive capability and performance. Structural equation modeling is applied for testing the model using data collected from a sample of 152 Korean SME exporters.

Findings

The results indicate that a firm’s operation quality of foreign agents strongly affects the quality of market information management which consequently impacts export performance. In the relationship between market information management and export performance, in particular, adaptive capability is found to play a mediating role. This implies that export performance is, for the most part, achieved by the mediation of adaptive capability, although market information leads directly to export performance to some degree. The results also confirm the existence of reciprocal causation between a firm’s export performance and foreign agent operations. The finding suggests that the outcome of SME export performance continues to provide feedback to its operations of foreign agents and consistently influence each other.

Originality/value

This study makes an important contribution to the body of export literature by identifying the mediating effects of adaptive capability on the relationship between market information management and export performance. In addition, the results create a recursive model for SME export performance by verifying the reciprocal relationship between export performance and operating with agents. This study thus helps extend understanding of international operations through foreign agents in the SME context.
Faculty research productivity under alternative appointment types: tenure vs non-tenure track
Authors: Allen Marcus T. , Sweeney Carol A.
Published: October 2017

Purpose

The increasing use of non-tenure employment contracting as a cost savings and/or management flexibility increasing mechanism in colleges and universities raises concerns about the impact of this strategy on other aspects of the higher education system. The purpose of this paper is to document reduced research productivity at a university that uses rolling contracts in comparison to research productivity at another university in the same state university system in the USA that uses tenure track contracting.

Design/methodology/approach

Negative binomial regression analysis allows investigation of the primary variable of interest (appointment type) while controlling for other factors that may also affect research productivity.

Findings

The findings suggest that non-tenure track employment contracting may have other long-term implications for institutions of higher education that warrant consideration.

Originality/value

No prior study has investigated the topic of comparative research productivity in business schools using this methodology or data source.
Molecular typing and occurrence of beta‐lactam resistance genes of Shigella sonnei strains isolated from 1983 to 2014 in the São Paulo state of Brazil
Authors: Seribelli Amanda Ap. , Frazão Miliane R. , Medeiros Marta I. Cazentini , Stehling Eliana G. , Falcão Juliana P.
Published: October 2017

Shigella sonnei, which has generally been associated with dysentery in developed countries, has recently been emerging in developing countries. Specifically, in Brazil few published studies have that molecularly characterized this species. The aims of this study were to analyze the efficacy of typing using multiple‐locus variable‐number tandem‐repeat analysis (MLVA), study the phylogeny by multi‐locus sequence typing (MLST) and assess the presence of some beta‐lactam resistance genes in S. sonnei strains isolated from human diarrhoeic faeces in the São Paulo State in Brazil between 1983 and 2014. Seventy‐two such S. sonnei strains were typed by MLVA and grouped into two clusters. The discrimination index of MLVA was found to be 0.996. Twenty strains were typed by MLST as ST152. In addition, the blaTEM gene was detected in eight (72.7%) of the 11 S. sonnei strains that had previously been shown to be resistant to β‐lactams. However, blaCTX‐M‐1group, blaCTX‐M‐9group and blaSHV genes were not found. MLVA results suggested the existence of two prevalent subtypes in the S. sonnei strains studied, confirming previous results. Moreover, MLVA efficiently discriminated monomorphic S. sonnei species. Because the S. sonnei strains studied belonged to clonal complex 152 and all isolates were typed as ST152, MLST is not a suitable method for studying the population structure of S. sonnei. Although, the rates of β‐lactam resistance were not high in the present study, the frequency of blaTEM may represent a risk for patients receiving antimicrobial treatment. Taken together, the results provide better molecular characterization of this globally clinically important pathogen.
‘Ruins of Modernity’: The Critical Implications of Unfinished Public Works in Italy
Authors: Arboleda Pablo
Published: October 2017

Since the 1950s, the construction of public works has been a significant element of Italy's focus on modernization. Numerous instances of malpractice have resulted in frequent failures of this form of development, with the result that many projects have remained unfinished for decades. In 2007, a group of artists called Alterazioni Video declared these ‘ruins of modernity’ to be a romanticized architectural style; in doing so, their aim is to imbue the sites with new value and dignity. This article uses the artists’ argument as a point of departure to theorize about unfinished public works within the framework of interdisciplinary literatures on modern ruins. In addition, since modern ruins by definition hold a critical meaning––which the artists deliberately excluded from their narrative––the article takes into account the obscure political and economic circumstances causing this phenomenon. After remarking upon specificities and similarities to unfinished neoliberal topographies generated by the 2008 financial crisis, it is concluded that unfinished public works in Italy represent an interesting case serving to enrich debates on incompletion.
Does Enrollment in High‐Deductible Health Plans Encourage Price Shopping?
Authors: Zhang Xinke , Haviland Amelia , Mehrotra Ateev , Huckfeldt Peter , Wagner Zachary , Sood Neeraj
Published: October 2017

Objective

To investigate whether enrollment in high‐deductible health plans (HDHPs) led enrollees to choose lower‐priced providers for office visits and laboratory tests.

Study Setting

Claims data from more than 40 large employers.

Study Design

We compared the change in price for office visits and laboratory tests for enrollees who switched to HDHPs versus enrollees who remained in traditional plans. We estimated separate models for enrollees who changed providers versus those who remained with the same provider to disentangle the effects of HDHPs on provider choice and negotiated prices.

Data Collection

Claims data from 2004 to 2010 on 1.8 million enrollees.

Principal Findings

After enrollment in HDHPs, 28 percent of enrollees changed physicians for office visits (compared to 19 percent in the Traditional Plan group, p < .01); however, this did not result in a statistically significant reduction in price for office visits. About 25 percent of enrollees changed providers for laboratory tests (compared to 23 percent in the Traditional Plan group, p < .01), resulting in savings of about $2.09 or a 12.8 percent reduction in price per laboratory test. We found that HDHPs had lower negotiated prices for office visits but not for laboratory tests.

Conclusions

High‐deductible health plan enrollment may shift enrollees to lower cost providers, resulting in modest savings.
An Integrated Approach to Mandarin Processing: Food Safety and Nutritional Quality, Consumer Preference, and Nutrient Bioaccessibility
Authors: Putnik Predrag , Barba Francisco J. , Lorenzo Jose Manuel , Gabrić Domagoj , Shpigelman Avi , Cravotto Giancarlo , Bursać Kovačević Danijela
Published: October 2017

Mandarins are a member of the Citrus genus and are the focus of growing commercial interest, with satsuma mandarins (Citrus unshiu) and the common mandarin (Citrus reticulata Blanco) being the most important mandarin varieties. The possible health benefits and functional properties of those fruits are often associated with the antioxidative function of vitamin C, carotenoids, and phenolic compounds. While most mandarins are consumed fresh, many are processed into juices (mostly cloudy), usually via thermal processing which can lead to the creation of off‐flavors and may diminish nutritional quality. The aim of this review is to summarize the most significant and recent information on the safety, sensorial properties, and nutritional benefits of mandarins and their processing into juice. The article also discusses recent information regarding the bioaccessibility of valuable, mandarin specific, compounds.
Weapon Use in Korean Homicide: Differences Between Homicides Involving Sharp and Blunt Instruments
Authors: Park Jisun , Son Hyeonseo
Published: October 2017

On the basis of information regarding 276 homicides committed in South Korea between 1987 and 2008, we compared offenders’ and victims’ characteristics, injury locations, weapon‐related behavior, and offending behavior between homicides involving sharp and blunt instruments. The victims of sharp‐force homicide were much younger relative to those of blunt‐force homicide. In addition, homicides involving blunt instruments were more likely to be committed by offenders who lived with the victims. Most sharp‐force homicides involved injuries to the torso, while blunt‐force homicides involved mainly head injuries. Furthermore, perpetrators of sharp‐force homicides tended to preselect their weapons, while those of blunt‐force homicides were likely to use weapons of opportunity. Logistic regression analysis identified a number of factors, including injury location and body transportation, which significantly predicted weapon type. As this was the first South Korean study to compare sharp‐ and blunt‐force homicides, the results have practical implications for homicide investigations.
Lone Actor Terrorist Attack Planning and Preparation: A Data‐Driven Analysis,
Authors: Schuurman Bart , Bakker Edwin , Gill Paul , Bouhana Noémie
Published: October 2017

This article provides an in‐depth assessment of lone actor terrorists’ attack planning and preparation. A codebook of 198 variables related to different aspects of pre‐attack behavior is applied to a sample of 55 lone actor terrorists. Data were drawn from open‐source materials and complemented where possible with primary sources. Most lone actors are not highly lethal or surreptitious attackers. They are generally poor at maintaining operational security, leak their motivations and capabilities in numerous ways, and generally do so months and even years before an attack. Moreover, the “loneness” thought to define this type of terrorism is generally absent; most lone actors uphold social ties that are crucial to their adoption and maintenance of the motivation and capability to commit terrorist violence. The results offer concrete input for those working to detect and prevent this form of terrorism and argue for a re‐evaluation of the “lone actor” concept.
Modeling Changes to Streamflow, Sediment, and Nutrient Loading from Land Use Changes Due to Potential Natural Gas Development
Authors: Hanson Lars , Habicht Steven , Daggupati Prasad , Srinivasan Raghavan , Faeth Paul
Published: October 2017

Natural gas development using hydraulic fracturing has many potential environmental impacts, but among the most certain is the land disturbance required to build the well pads and other infrastructure required to drill and extract the gas. We used the Soil and Water Assessment Tool (SWAT) model to investigate how natural gas development could impact streamflow and sediment, total nitrogen (TN), and total phosphorous (TP) loadings in the upper Delaware River Basin (DRB), a relatively undeveloped watershed of 7,950 km2 that lies above the Marcellus Shale formation. If gas development was permitted, our projections show the DRB could experience development of over 600 well pads to extract natural gas at build out, which, with supporting infrastructure (roads, gathering pipelines), could convert over 5,000 ha from existing land uses in the study area. In subbasins with development activity we found sediment, TN, and TP yields could increase by an average of 15, 0.08, and 0.03 kg/ha/yr, respectively (an increase of 2, 3, and 15%, respectively) for each one percent of subbasin land area converted into natural gas infrastructure. At the study area outlet on the Delaware River at Port Jervis, New York, we found increases in the annual average streamflow and sediment, nitrogen, and phosphorus loads of up to 0.01, 0.2, 0.2, and 1%, respectively, for a rapid development year, and 0.08, 1.3, 2.0, and 11%, respectively, for the full development scenario. Editor's note: This paper is part of the featured series on SWAT Applications for Emerging Hydrologic and Water Quality Challenges. See the February 2017 issue for the introduction and background to the series.
Effects of 12 weeks of treatment with intravenously administered bococizumab, a humanized monoclonal antibody blocking proprotein convertase subtilisin/kexin type 9, in hypercholesterolemic subjects on high‐dose statin
Authors: Fazio Sergio , Robertson David G. , Joh Tenshang , Wan Hong , Riel Tom , Forgues Philippe , Baum Charles M. , Garzone Pamela D. , Gumbiner Barry
Published: October 2017

Aims

Two multiple‐dose phase II studies were conducted in subjects with primary hypercholesterolemia to evaluate the LDL‐C lowering efficacy, safety, and tolerability of bococizumab, a proprotein convertase subtilisin/kexin type 9 (PCSK9) inhibitor.

Methods

The results from the two phase II, double‐blinded, randomized, placebo‐controlled, multicenter studies conducted in the USA and Canada were combined. In Study 1, 90 subjects with LDL‐C ≥100 mg/dL received intravenous (IV) placebo or bococizumab 0.25, 1, 3, or 6 mg/kg. In Study 2, 45 subjects with LDL‐C ≥80 mg/dL received IV placebo or bococizumab 1 or 3 mg/kg. Subjects were treated every 4 weeks for 12 weeks. Dosing was interrupted if LDL‐C dipped to ≤25 mg/dL and resumed if LDL‐C returned to ≥40 mg/dL. The primary endpoint was percent LDL‐C reduction from baseline at Week 12.

Results

At Week 12, the reductions from baseline in LDL‐C vs placebo in the bococizumab 0.25, 1, 3, and 6 mg/kg groups were 9.3%, 10.2%, 41.6%, and 52.0%, respectively (P < .001 vs placebo for all). LDL‐C reductions were greater (69.9%) in subjects who received all three doses of bococizumab 6 mg/kg (P < .001 vs placebo). Pharmacogenomic analysis revealed that 15% of hyperlipidemic subjects carried polymorphisms associated with familial hypercholesterolemia, with maximal LDL‐C reductions being similar between carriers and noncarriers. Adverse events were mild, unrelated to bococizumab, and resolved by Week 12.

Conclusions

These studies demonstrated that bococizumab safely and effectively lowered LDL‐C in hypercholesterolemic subjects on high doses of statin.
Modified method for distinguishing the intersegmental border for lung segmentectomy
Authors: Wang Jun , Xu XinFeng , Wen Wei , Wu WeiBing , Zhu Quan , Chen Liang
Published: October 2017

This paper analyzed the results of a modified and simpler technique for distinguishing the intersegmental border during lung segmentectomy surgery. From January 2013 to December 2015, 539 patients with screening‐detected lung nodules <2 cm in maximum diameter underwent anatomic segmentectomy. With the guidance of preoperative three‐dimensional computed tomography bronchography and angiography, the bronchus, artery, and intrasegmental vein of the targeted segment could be precisely dissected under unilateral differential ventilation, and then intersegmental demarcation was confirmed by the modified inflation‐deflation method. The demarcation presented by this method was highly coincident with the real intersegmental border. Dissection along the border between the collapsed and inflated segments using either electrocautery or staples was safe, with almost no air leak or bleeding. This technique is a simple and effective alternative to previously described intersegmental border marking methods.
Comparative safety of systemic and low‐bioavailability steroids in inflammatory bowel disease: Systematic review and network meta‐analysis
Authors: Bonovas Stefanos , Nikolopoulos Georgios K. , Lytras Theodore , Fiorino Gionata , Peyrin‐Biroulet Laurent , Danese Silvio
Published: October 2017

Aims

Oral systemic corticosteroids have been used to induce remission in patients with active inflammatory bowel disease (IBD) for over 50 years; however, the wide array of adverse events (AEs) associated with these drugs prompted the development of steroid compounds with targeted delivery and low systemic bioavailability. This study assessed corticosteroids' comparative harm using network meta‐analysis.

Methods

We searched PubMed, Scopus, Embase, the Cochrane Library, clinical trial registries, regulatory authorities' websites and major conference proceedings, through March 2017. Randomized controlled trials that recruited adult IBD patients and compared oral systemic corticosteroids (prednisone/prednisolone) or compounds/formulations with low systemic bioavailability (budesonide, budesonide MMX, and beclomethasone dipropionate) with placebo, or against each other, were considered eligible for inclusion. Two reviewers independently extracted study data and outcomes, and rated each trial's risk‐of‐bias.

Results

We identified and synthesized evidence from 31 trials including 5689 IBD patients. Budesonide MMX was associated with significantly fewer corticosteroid‐related AEs than oral systemic corticosteroids [odds ratio (OR): 0.25, 95% confidence interval (CI): 0.13–0.49] and beclomethasone (OR: 0.35, 95% CI: 0.13–1.00), but not significantly fewer AEs than budesonide (OR: 0.64, 95% CI: 0.37–1.11); it performed equally good with placebo. By contrast, the occurrence of serious AEs, and treatment discontinuations due to AEs, did not differ between the comparator treatments.

Conclusions

Budesonide MMX is associated with fewer corticosteroid‐related AEs than its comparator steroid treatments for adult IBD patients. Further high‐quality research is warranted to illuminate the steroid drugs' comparative safety profiles.