bluuebunny/crossref_metadata_2025 huggingface dataset:
Use of microfasteners to produce damage tolerant composite structures
Authors: Partridge Ivana K. , Hallett Stephen R.
Published: May 2016

The paper concerns the mechanical performance of continuous fibre/thermosetting polymer matrix composites reinforced in the through-thickness direction with fibrous or metallic rods or threads in order to mitigate against low delamination resistance. Specific illustrations of the effects of microfasteners in reducing delamination crack growth are made for Z-pinned and tufted composites. Response to loading in such ‘structured materials’ is subject to multiple parameters defining their in-plane and out-of-plane properties. Single microfastener mechanical tests are well suited to establish the crack bridging laws under a range of loading modes, from simple delamination crack opening to shear, and provide the basis for predicting the corresponding response of microfastener arrays, within a given material environment. The fundamental experiments on microfasteners can be used to derive analytical expressions to describe the crack bridging behaviour in a general sense, to cover all possible loadings. These expressions can be built into cohesive element constitutive laws in a finite-element framework for modelling the effects of microfastener arrays on the out-of-plane mechanical response of reinforced structural elements, including the effects of known manufacturing imperfections. Such predictive behaviour can then be used to assess structural integrity under complex loading, as part of the component design process.

This article is part of the themed issue ‘Multiscale modelling of the structural integrity of composite materials’.
Multiscale characterization and representation of composite materials during processing
Authors: Zobeiry Navid , Forghani Alireza , Li Chao , Gordnian Kamyar , Thorpe Ryan , Vaziri Reza , Fernlund Goran , Poursartip Anoush
Published: May 2016

Given the importance of residual stresses and dimensional changes in composites manufacturing, process simulation has been the focus of many studies in recent years. Consequently, various constitutive models and simulation approaches have been developed and implemented for composites process simulation. In this paper, various constitutive models, ranging from elastic to nonlinear viscoelastic; and simulation approaches ranging from separated flow/solid phases to multiscale integrated phases are presented and their applicability for process simulation is discussed. Attention has been paid to practical aspects of the problem where the complexity of the model coupled with the complexity and size scaling of the structure increases the characterization and simulation costs. Two specific approaches and their application are presented in detail: the pseudo-viscoelastic cure hardening instantaneously linear elastic (CHILE) and linear viscoelastic (VE). It is shown that CHILE can predict the residual stress formation in simple cure cycles such as the one-hold cycle for HEXCEL AS4/8552 where the material does not devitrify during processing. It is also shown that using this simple approach, the cure cycle can be modified to lower the residual stress level and therefore increase the mechanical performance of the composite laminate. For a more complex cure cycle where the material is devitrified during a post-cure, it is shown that a more complex model such as VE is required.

This article is part of the themed issue ‘Multiscale modelling of the structural integrity of composite materials’.
Quantitative cross-linking/mass spectrometry using isotope-labeled cross-linkers and MaxQuant
Authors: Chen Zhuo A. , Fischer Lutz , Cox Jüergen , Rappsilber Juri
Published: May 2016

Abstract

The conceptually simple step from cross-linking/mass spectrometry (CLMS) to quantitative cross-linking/mass spectrometry (QCLMS) is compounded by technical challenges. Currently, quantitative proteomics software is tightly integrated with the protein identification workflow. This prevents automatically quantifying other m/z features in a targeted manner including those associated with cross-linked peptides. Here we present a new release of MaxQuant that permits starting the quantification process from an m/z feature list. Comparing the automated quantification to a carefully manually curated test set of cross-linked peptides obtained by cross-linking C3 and C3b with BS3and isotope-labeled BS3-d4 revealed a number of observations: 1) Fully automated process using MaxQuant can quantify cross-links in our reference dataset with 68% recall rate and 88% accuracy. 2) Hidden quantification errors can be converted into exposed failures by label-swap replica, which makes label-swap replica an essential part of QCLMS. 3) Cross-links that failed during automated quantification can be recovered by semi-automated re-quantification. The integrated workflow of MaxQuant and semi-automated assessment provides the maximum of quantified cross-links. In contrast, work on larger data sets or by less experienced users will benefit from full automation in MaxQuant.

Abbreviations

BS3

Bis[sulfosuccinimidyl] suberate

CLMS

Cross-linking/mass spectrometry

MS1

the initial mass-to-charge-ratio (m/z) spectrum collected for all components in a sample.

QCLMS

Quantitative cross-linking/mass spectrometry
Enhancing synergy of CAR T cell therapy and oncolytic virus therapy for pancreatic cancer
Authors: Walker Rachel , Navas Pedro E. , Friedman Samuel H. , Galliani Simona , Karolak Aleksandra , Macfarlane Fiona , Noble Robert , Poleszczuk Jan , Russell Shonagh , Rejniak Katarzyna A. , Shahmoradi Amir , Ziebell Frederik , Brayer Jason , Abate-Daga Daniel , Enderling Heiko
Published: May 2016

The poor immunogenicity of pancreatic tumors makes them particularly difficult to treat. Standard chemotherapies and single agent immunotherapies have had notoriously little success in this arena. Oncolytic virus therapy has the potential to enhance the penetration of immunotherapeutically-delivered CAR T cells into the tumor and improve treatment outcomes. We evaluate this potential by combining two different mathematical approaches: an ordinary differential equation model to simulate population level tumor response to cytotoxic activity of T cells, coupled with an agent-based model to simulate the enhancement of CAR T cell penetration by oncolytic virus therapy.
Motor control by precisely timed spike patterns
Authors: Srivastava Kyle H. , Holmes Caroline M. , Vellema Michiel , Pack Andrea , Elemans Coen P. H. , Nemenman Ilya , Sober Samuel J.
Published: May 2016

A fundamental problem in neuroscience is to understand how sequences of action potentials (“spikes”) encode information about sensory signals and motor outputs. Although traditional theories of neural coding assume that information is conveyed by the total number of spikes fired (spike rate), recent studies of sensory [1–5] and motor [6] activity have shown that far more information is carried by the millisecond-scale timing patterns of action potentials (spike timing). However, it is unknown whether or how subtle differences in spike timing drive differences in perception or behavior, leaving it unclear whether the information carried by spike timing actually plays a causal role in brain function [1]. Here we demonstrate how a precise spike timing code is read out downstream by the muscles to control behavior. We provide both correlative and causal evidence to show that the nervous system uses millisecond-scale variations in the timing of spikes within multi-spike patterns to regulate a relatively simple behavior – respiration in the Bengalese finch, a songbird. These findings suggest that a fundamental assumption of current theories of motor coding requires revision, and that significant improvements in applications, such as neural prosthetic devices, can be achieved by using precise spike timing information.
Modeling Joint Abundance of Multiple Species Using Dirichlet Process Random Effects
Authors: Johnson Devin S. , Sinclair Elizabeth H.
Published: May 2016

We present a method for modeling multiple species distributions simultaneously using Dirichlet Process random effects to cluster species into guilds. Guilds are ecological groups of species that behave or react similarly to some environmental conditions. By modeling latent guild structure, we capture the cross-correlations in abundance or occurrence of species over surveys. In addition, ecological information about the community structure is obtained as a byproduct of the model. By clustering species into similar functional groups, prediction uncertainty of community structure at additional sites is reduced over treating each species separately. The method is illustrated with a small simulation demonstration, as well as an analysis of a mesopelagic fish survey from the eastern Bering Sea near Alaska. The simulation data analysis shows that guild membership can be extracted as the differences between groups become larger and if guild differences are small the model naturally collapses all the species into a small number of guilds which increases predictive efficiency by reducing the number of parameters to that which is supported by the data.
Creative workplace characteristics and innovative start-up companies
Authors: Lee Young S.
Published: May 2016

Purpose

This study aims to investigate the characteristics of the physical work environment that are known and used in practice to promote creativity for innovative start-up workplaces. The first part of the study identified these characteristics from a content and visual analysis, and examined the current state of implementation of these characteristics in the work environments of innovative start-up companies. The second part of the study examined criticalness and practicality of these characteristics in the workplace with a group of experts in the workplace design, evaluation and management.

Design/methodology/approach

A content and visual analysis for written and visual images was conducted to identify a comprehensive list of characteristics of the physical work environment critical to creativity of the workplace. With the seven characteristics identified, an instrument was developed and interviews were conducted to assess the physical work environments of 22 innovative start-up companies in Michigan. Following up the interviews, an expert group was formed with 26 professionals including architects, interior designers, facility managers and CEOs. A survey was conducted with them to understand the significance and implementation issues among the seven characteristics.

Findings

The most frequently incorporated characteristics in the innovative start-up companies in Michigan were spaces for idea generation, technology interface for collaboration and spaces for a short mental break or social hangout. The three most important physical work environmental characteristics for companies to produce creative, innovative ideas and products/services for growth and market competitiveness were balanced layout, technology interface for collaboration and spaces for idea generation.

Originality/value

The study provides a comprehensive framework to evaluate creative workplace regarding the physical environment. It also offers insights on the work environments of the innovative start-up companies for increased creativity and innovation performance in the workplace.
OLED TV technology forecasting using technology mining and the Fisher-Pry diffusion model
Authors: Cho Yonghee , Daim Tugrul
Published: May 2016

Purpose

Due to rapid technological evolution driven by display manufacturers, the television (TV) market of flat panel displays has been fast growing with the advancement of digital technologies in broadcasting service. Recently, organic light-emitting diode (OLED) successfully penetrated into the large-size TV market, catching up with light-emitting diode (LED)-liquid-crystal display (LCD). This paper aims to investigate the market penetration of OLED technologies by determining their technology adoption rates based on a diffusion model.

Design/methodology/approach

Through the rapid evolution of information and communication technology, as well as a flood of data from diverse sources such as research awards, journals, patents, business press, newspaper and Internet social media, data mining, text mining, tech mining and database tomography have become practical techniques for assisting the forecaster to identify early signs of technological change. The information extracted from a variety of sources can be used in a technology diffusion model, such as Fisher-Pry where emerging technologies supplant older ones. This paper uses a comparison-based prediction method to forecast the adoption and diffusion of next-generation OLED technologies by mining journal and patent databases.

Findings

In recent years, there has been a drastic reduction of patents related to LCD technologies, which suggests that next-generation OLED technology is penetrating the TV market. A strong industry adoption for OLED has been found. A high level of maturity is expected by 2026.

Research limitations/implications

For OLED technologies that are closely tied to industrial applications such as electronic display devices, it may be better to use more industry-oriented data mining, such as patents, market data, trade shows, number of companies or startups, etc. The Fisher-Pry model does not address the level of sales for each technology. Therefore, the comparison between the Bass model and the Fisher-Pry model would be useful to investigate the market trends of OLED TVs further. Another step for forecasting could include using industry experts and a Delphi model for forecasting (and further validation).

Originality/value

Fisher-Pry growth curves for journal publications and patents follow the expected sequence. Specially, journal publications and patents growth curves are close for OLED technologies, indicating a strong industry adoption.
The hospitality franchise purchase decision making process
Authors: Yeung Ruth M.W. , Brookes Maureen , Altinay Levent
Published: May 2016

Purpose

The purpose of this study is to explore the hospitality franchise purchase decision-making process undertaken by franchisees in Macau as an emerging tourism destination and the role of national culture on purchasing a franchise brand and selecting a potential franchisor.

Design/methodology/approach

Semi-structured in-depth interviews with 18 franchisees in Macau, who purchased international and domestic hospitality franchise brands, were conducted to understand the feelings, attitudes and motivation of franchisees toward purchasing a hospitality franchise.

Findings

The study reveals that national culture can play an important role in franchisees’ decision-making process. Personal networks of friends and family (guanxi) are very influential in introducing and steering aspiring entrepreneurs toward franchising as an option to realize their ambitions, although there may be some limitations to franchisees with this approach. Guanxi was also found to be particularly relevant during negotiations and franchisees’ post-purchase reviews.

Practical implications

International franchisors should understand the importance of guanxi at different stages of the franchisees’ decision-making process. Franchisees should realize how a reliance on guanxi might negatively affect their efforts to undertake sufficient research to thoroughly evaluate the franchisor offer before contract signature.

Originality/value

A comprehensive hospitality franchisee decision-making purchase framework is developed, which includes the cultural context and cultural values. Guanxi, in particular, affects the franchisee decision-making process.
Prospering in the southern Africa’s VUCA world of the nineteenth century
Authors: Mofuoa Khali
Published: May 2016

Purpose

This paper aims to discuss the notion of resilience in the context of the Basotho of Lesotho who managed prospering as a nation in the era of uncertainty during the “VUCA” world of the nineteenth-century southern Africa.

Design/methodology/approach

Using historical data from leadership and organizational behaviour perspectives, the theoretical context of the paper is established to inform discussion on the resilience of the Basotho during the “VUCA” world of the nineteenth-century southern Africa.

Findings

The paper has established that the notion of resilience was synonymous to Basotho’s way of life and livelihood during the “VUCA” world of the nineteenth-century southern Africa. The paper has also established that resilience became the key quality of Basotho as they continued prospering as a nation in the era of uncertainty during the “VUCA” world of the nineteenth-century southern Africa.

Originality/value

From both leadership and organizational behaviour perspectives, the paper uses mainly historical data that are considered to be most relevant, valid and reliable to inform discussions on the notion of resilience as it relates to the Basotho as a nation during the “VUCA” world of the nineteenth-century southern Africa.
Effect of service integration strategy on industrial firm performance
Authors: Kwak Kiho , Kim Wonjoon
Published: May 2016

Purpose

– The purpose of this paper is to examine the relationship between service integration and manufacturing firms’ profitability and to identify profitable services.

Design/methodology/approach

– The study examines the service integration data of 202 firms in the machinery and equipment sector in Korea. Firm profitability comes from secondary data to eliminate common method bias.

Findings

– The relationship between service integration, measured as the service-revenue ratio, and profitability has an inverted U-shape, likely stemming from political costs, a loss of opportunity in manufacturing improvements arising from resource constraints, and an increase in transaction costs. In addition, process operation outsourcing and technical consulting significantly contribute to profitability.

Research limitations/implications

– The authors show that the effect of service integration on profitability diminishes when firms experience both resource constraints and an increase in transaction costs from implementing the strategy. Furthermore, the profitability of services is heterogeneous across different offerings. Further research in other countries and sectors is necessary to refine the relationships suggested herein.

Practical implications

– Managers should strive to minimize the costs and problems stemming from resource constraints and transaction costs. It is also important to utilize external resources to achieve profitability from service integration. Managers also need to realize the different cost-revenue structure of each service.

Originality/value

– The authors find that the relationship between profitability and service integration depends on the degree of resource constraints and transaction costs. The authors also identify which service offerings are highly profitable, which has not been done in previous research.
A double whammy effect of ethnicity and gender on consumer responses to management level service failures
Authors: Wu Laurie , Han Rachel , Mattila Anna S
Published: May 2016

Purpose

– Existing research on demographic stereotypes of employees suggests that ethnicity and gender are important determinants of consumer perceptions and behaviors. Based on the Stereotype Content Model and the Role Congruity Theory, the purpose of this paper is to examine the effect of ethnicity and gender stereotypes on management-level service failures in a US context.

Design/methodology/approach

– Adopting a 2 (ethnicity: Caucasian vs Hispanic) × 2 (gender: male vs female) between-subjects design, two studies were conducted with US consumers to test whether a double whammy effect of ethnicity and gender exists for management-level, but not line-level, service failures.

Findings

– The results of this study suggest that Hispanic female managers suffer from a double whammy effect due to ethnic and gender-based stereotyping in the USA. Furthermore, the findings indicate that the serial mediation via competence perceptions and blame attributions are the underlying psychological mechanism of this effect. As predicted, occupational status functions as a boundary factor to the double whammy effect.

Originality/value

– The findings of this paper contribute to the service management literature by examining the role of demographic characteristics in influencing US consumers’ responses to management-level service failures.
Factors impacting the decision to attend soccer games: an exploratory study
Authors: Karakaya Fahri , Yannopoulos Peter , Kefalaki Margarita
Published: May 2016

Purpose

– As an exploratory study, the purpose of this paper is to examine the underlying motivations for attending soccer games.

Design/methodology/approach

– Attendees at two soccer games in Athens, Greece were surveyed about their frequency of attendance at soccer games and their attitudes toward soccer. In total, 252 people from five randomly selected sections of the stadiums participated in the survey.

Findings

– The results indicate that there are three major motivations – emotional excitement, socialization, and soccer atmospherics – and two identity salience factors – ardent soccer fans and rational soccer fans – for attending soccer games. The most important factor for attendance is being an ardent soccer fan closely followed by the emotional excitement factor. Among the demographic factors considered, only gender significantly affects soccer game attendance.

Originality/value

– In contrast to previous studies that are somewhat descriptive, this research explicitly introduces factors related to social identity theory and attempts to predict soccer game attendance on the basis of a scale of factors that focus on the major motivations for attendance of soccer games, identity salience reasons, and demographic factors. The inclusion of social identity theory as a factor in the attendance of soccer games is a major contribution of this study. Contrary to most of the earlier studies, this study showed that the socialization factor is not related to attendance at soccer games.
Increased blood flow and vasculature in solar lentigo
Authors: Hasegawa Kiyotaka , Fujiwara Rumiko , Sato Kiyoshi , Park Ji‐Youn , Kim Sang Jin , Kim Misun , Kang Hee Young
Published: May 2016

Solar lentigo (SL) is a hallmark of ultraviolet (UV)‐induced photoaged skin and growing evidence implicates blood vessels in UV‐associated pigmentation. In this study, we investigated whether the vasculatures are modified in SL. Twenty‐five women with facial SL were enrolled and colorimetric and blood flow studies were performed. There was a significant increase in erythema which was associated with increased blood flow in the lesional skin compared with perilesional normal skin. Immunohistochemical studies with 24 facial SL biopsies consistently revealed a significant increase in vessel density accompanied by increased levels of vascular endothelial growth factor expression. CD68 immunoreactivity was significantly higher in lesional skin suggesting increased macrophage infiltration in SL. In conclusion, SL is characterized by increased blood flow and vasculature. These findings suggest the possible influence of the characteristics of vasculature on development of SL.
Direct and indirect effects of native range expansion on soil microbial community structure and function
Authors: Collins Courtney G. , Carey Chelsea J. , Aronson Emma L. , Kopp Christopher W. , Diez Jeffrey M.
Published: May 2016

Analogous to the spread of non‐native species, shifts in native species’ ranges resulting from climate and land use change are also creating new combinations of species in many ecosystems. These native range shifts may be facilitated by similar mechanisms that provide advantages for non‐native species and may also have comparable impacts on the ecosystems they invade.

Soil biota, in particular bacteria and fungi, are important regulators of plant community composition and below‐ground ecosystem function. Compared to non‐native plant invasions, there have been relatively few studies examining how soil biota influence – or are influenced by – native species range shifts.

Here, we examined how a native range‐expanding sagebrush species (Artemisia rothrockii) affects below‐ground abiotic conditions and microbial community structure and function using next‐generation sequencing coupled with other biotic and abiotic soil analyses. We utilized a range‐expansion gradient, together with a shrub removal experiment and structural equation models, to determine the direct and indirect drivers of these interconnected processes.

Sagebrush colonization increased bacterial and archaeal richness and diversity and altered community composition across the expansion gradient. Soil organic C and N and soil moisture increased with sagebrush presence; however, results varied across the expansion gradient. We found no relationship between sagebrush and soil pH; however, pH strongly influenced microbial richness and diversity. Microbial (substrate‐induced) respiration was influenced by soil organic N, as well as microbial diversity and functional group relative abundances, highlighting direct and indirect effects of sagebrush on microbial community structure and function. Microbial community composition of soils after 4 years of sagebrush removal was more similar to communities in shrub interspaces than underneath shrubs, suggesting microbial community resilience.

Synthesis. Our results suggest that native range expansions can have important impacts on soil biological communities, soil chemistry and hydrology which can further impact below‐ground ecosystem processes such as nutrient cycling and litter decomposition. The combination of high‐throughput sequencing and structural equation modelling used here offers an exciting yet underutilized approach to understanding how both native and non‐native species’ range expansions may affect the structure and function of soil ecosystems.
Alterations and correlations of the gut microbiome, metabolism and immunity in patients with primary biliary cirrhosis
Authors: Lv Long‐Xian , Fang Dai‐Qiong , Shi Ding , Chen De‐Ying , Yan Ren , Zhu Yi‐Xin , Chen Yan‐Fei , Shao Li , Guo Fei‐Fei , Wu Wen‐Rui , Li Ang , Shi Hai‐Yan , Jiang Xia‐Wei , Jiang Hui‐Yong , Xiao Yong‐Hong , Zheng Shu‐Sen , Li Lan‐Juan
Published: May 2016

We selected 42 early‐stage primary biliary cirrhosis (PBC) patients and 30 healthy controls (HC). Metagenomic sequencing of the 16S rRNA gene was used to characterize the fecal microbiome. UPLC‐MS/MS assaying of small molecules was used to characterize the metabolomes of the serum, urine and feces. Liquid chip assaying of serum cytokines was used to characterize the immune profiles. The gut of PBC patients were depleted of some potentially beneficial bacteria, such as Acidobacteria, Lachnobacterium sp., Bacteroides eggerthii and Ruminococcus bromii, but were enriched in some bacterial taxa containing opportunistic pathogens, such as γ‐Proteobacteria, Enterobacteriaceae, Neisseriaceae, Spirochaetaceae, Veillonella, Streptococcus, Klebsiella, Actinobacillus pleuropneumoniae, Anaeroglobus geminatus, Enterobacter asburiae, Haemophilus parainfluenzae, Megasphaera micronuciformis and Paraprevotella clara. Several altered gut bacterial taxa exhibited potential interactions with PBC through their associations with altered metabolism, immunity and liver function indicators, such as those of Klebsiella with IL‐2A and Neisseriaceae with urinary indoleacrylate. Many gut bacteria, such as some members of Bacteroides, were altered in their associations with the immunity and metabolism of PBC patients, although their relative abundances were unchanged. Consequently, the gut microbiome is altered and may be critical for the onset or development of PBC by interacting with metabolism and immunity.
Shelf‐Life Extension of Chill‐Stored Beef Longissimus Steaks Packaged under Modified Atmospheres with 50% O2 and 40% CO2
Authors: Yang Xiaoyin , Niu Lebao , Zhu Lixian , Liang Rongrong , Zhang Yimin , Luo Xin
Published: May 2016

This study was conducted to compare the shelf‐life of beef steaks stored in different packaging conditions: overwrapped (OW) packaging and 2 modified atmosphere packaging systems (MAP): 80% O2 MAP (80% O2/20% CO2) and 50% O2 MAP (50% O2/40% CO2/10% N2). Steaks were stored at 2 °C for 20 d. Headspace gas composition, microbial counts, color stability, pH, purge loss, and lipid oxidation were monitored. Among the packaging types, 50% O2 MAP was superior to OW packaging and 80% O2 MAP in delaying bacterial growth and extending shelf‐life to 20 d. 50% O2 MAP also gave steaks an acceptable color during storage. No significant differences were observed in color stability of steaks packaged in both 50% O2 MAP and 80% O2 MAP. This study reveals 50% O2 MAP is a realistic alternative to preserve beef steaks efficiently.
Analysis of Duplicated Multiple‐Samples Rank Data Using the Mack–Skillings Test
Authors: Carabante Kennet Mariano , Alonso‐Marenco Jose Ramon , Chokumnoyporn Napapan , Sriwattana Sujinda , Prinyawiwatkul Witoon
Published: May 2016

Appropriate analysis for duplicated multiple‐samples rank data is needed. This study compared analysis of duplicated rank preference data using the Friedman versus Mack–Skillings tests. Panelists (n = 125) ranked twice 2 orange juice sets: different‐samples set (100%, 70%, vs. 40% juice) and similar‐samples set (100%, 95%, vs. 90%). These 2 sample sets were designed to get contrasting differences in preference. For each sample set, rank sum data were obtained from (1) averaged rank data of each panelist from the 2 replications (n = 125), (2) rank data of all panelists from each of the 2 separate replications (n = 125 each), (3) jointed rank data of all panelists from the 2 replications (n = 125), and (4) rank data of all panelists pooled from the 2 replications (n = 250); rank data (1), (2), and (4) were separately analyzed by the Friedman test, although those from (3) by the Mack–Skillings test. The effect of sample sizes (n = 10 to 125) was evaluated. For the similar‐samples set, higher variations in rank data from the 2 replications were observed; therefore, results of the main effects were more inconsistent among methods and sample sizes. Regardless of analysis methods, the larger the sample size, the higher the χ2 value, the lower the P‐value (testing H0: all samples are not different). Analyzing rank data (2) separately by replication yielded inconsistent conclusions across sample sizes, hence this method is not recommended. The Mack–Skillings test was more sensitive than the Friedman test. Furthermore, it takes into account within‐panelist variations and is more appropriate for analyzing duplicated rank data.
CoMuS: simulating coalescent histories and polymorphic data from multiple species
Authors: Papadantonakis S. , Poirazi P. , Pavlidis P.
Published: May 2016

The simultaneous analysis of intra‐ and interspecies variation is challenging mainly because our knowledge about patterns of polymorphisms where both intra‐ and interspecies samples coexist is limited. In this study, we present CoMuS (Coalescent of Multiple Species), a multispecies coalescent software that can simulate intra‐ and interspecies polymorphisms. CoMuS supports a variety of speciation models and demographic scenarios related to the history of each species. In CoMuS, speciation can be accompanied by either instant or gradual isolation between sister species. Sampling may also occur in the past, and thus, we can study simultaneously extinct and extant species. Our software supports both the infinite‐ and the finite‐site model, with substitution rate heterogeneity among sites and a user‐defined proportion of invariable sites. We demonstrate the usage of CoMuS in various applications: species delimitation, software testing, model selection and parameter inference involving present‐day and ancestral samples, comparison between gradual and instantaneous isolation models, estimation of speciation time between human and chimpanzee using both intra‐ and interspecies variation. We expect that CoMuS will be particularly useful for studies where species have been separated recently from their common ancestor and phenomena such as incomplete lineage sorting or introgression still occur.
Oral administration of recombinant Mycobacterium smegmatis expressing a tripeptide construct derived from endogenous and microbial antigens prevents atherosclerosis in ApoE−/− mice
Authors: Deshpande Vrushali , Krishnan Rameshkumar , Philip Sheena , Faludi Ildiko , Ponnusamy Thiruvelselvan , Thota Lakshmi Narasimha Rao , Endresz Valeria , Lu Xinjie , Kakkar Vijay V. , Mundkur Lakshmi A.
Published: May 2016

Introduction

Immunotherapy by inducing oral tolerance to atherogenic self‐antigens is gaining importance as an alternative treatment modality for atherosclerosis. The use of live bacterial vectors to express the recombinant antigen in vivo will obviate the need for large‐scale purification of recombinant protein and may also augment the efficacy of oral tolerance induction.

Aim

The objective of the study was to explore the use of recombinant Mycobacterium smegmatis as a live vector for oral delivery of antigens to induce immune tolerance.

Method and Results

We developed a M. smegmatis vector to secrete a recombinant tripeptide construct (AHC; peptides from Apolipoprotein B, Heat‐shock protein 60 and Chlamydia pneumoniae outer membrane protein) expressed in a dendroaspin protein scaffold in pJH154 background. Immune response and oral tolerance to the cloned peptides were studied in C57/BL6 mice. The efficacy of this live vaccine to control atherosclerosis was studied in ApoE−/− knockout mice in C57/BL6 background. Oral administration of M. smegmatis secreting the cloned AHC antigen was found to induce tolerance to cloned protein and reduce the development of atherosclerosis by 24.0% compared to control. Protection against atherosclerosis was associated with increase in expression of regulatory T cell‐associated markers including CTLA4 (1.8‐fold), Foxp3 (2.6‐fold), TGF‐β (2.8‐fold), IL10 (2.9‐fold), and reduction in lipids, macrophage infiltration, and expression of inflammatory mediators in aorta.

Conclusions

Our results suggest that M. smegmatis can be developed as an oral carrier of recombinant proteins to treat inflammatory autoimmune diseases.
Proton pump inhibitors use and change in bone mineral density
Authors: Arj Abbas , Razavi Zade Mohsen , Yavari Maryam , Akbari Hossein , Zamani Batol , Asemi Zatollah
Published: May 2016

Objective

Limited data are available reporting the effect of proton pump inhibitor (PPI) use on changes in bone mineral density (BMD). The aim of this study was to investigate the relationship between PPI use and BMD.

Methods

The current cross‐sectional study included 80 patients (31 male and 49 female) aged 20–45 years old without history of hip fracture with a follow‐up of at least 2 years. The study was carried out in 40 daily PPI users and 40 PPI non‐users. Femur and posterior‐anterior spine BMD were quantified by dual‐energy X‐ray absorptiometry in all participants. The relationship between use of PPI and BMD was tested by multivariate linear regression analysis adjusted for age, sex, BMI and serum vitamin D levels.

Results

Our study demonstrated that mean femoral T‐scores were significant between PPI and non‐user groups (−0.44 ± 1.11 vs. +0.19 ± 0.95, P = 0.007). In addition, the frequency of femoral osteoporosis and osteopenia in the exposed group was significantly more in the control group (P = 0.04). Mean femoral Z‐scores, lumbar spine T‐score and lumbar spine Z‐score were not statistically different between PPI and non‐user groups. The linear regression analysis revealed that there was no association between PPI and non‐users, and lumbar spine T‐score.

Conclusion

Overall, the results of this study showed that PPI use in subjects without risk factors of osteoporosis determined by the femoral T‐score compared with the control group was associated with increased risk of developing osteoporosis and osteopenia in the femur bones.
Association between depression and anemia in otherwise healthy adults
Authors: Vulser H. , Wiernik E. , Hoertel N. , Thomas F. , Pannier B. , Czernichow S. , Hanon O. , Simon T. , Simon J‐M , Danchin N. , Limosin F. , Lemogne C.
Published: May 2016

Objective

It remains debated whether anemia is associated with depression, independently of physical health factors. We report a large‐scale cross‐sectional study examining this association in adults free of chronic disease and medication from the general population.

Method

Hemoglobin levels were measured among 44 173 healthy participants [63% men; mean [standard deviation] age = 38.4 (11.1) years] from the ‘Investigations Préventives et Cliniques’ (IPC) cohort study. Depression was measured with the Questionnaire of Depression 2nd version, Abridged. Logistic regression analyses were performed to examine the association between anemia and depression, while adjusting for a wide range of sociodemographic characteristics and health‐related factors (i.e., sex, age, living status, education level, occupational status, alcohol intake, smoking status, physical activity, and body mass index).

Results

Depressed participants were significantly more likely to have anemia compared to non‐depressed participants, even after adjustment for sociodemographic and health‐related variables [odds ratio = 1.36; 95% confidence interval = (1.18; 1.57)]. Anemia prevalence increased with depression severity, suggesting a dose–response relationship (P for trend <0.001).

Conclusion

In healthy adults from the general population, we found a significant and robust association between depression and anemia. Further studies are needed to assess the longitudinal relationship between both conditions and determine the mechanisms underlying this association.
Prevalence of obesity in paediatric psoriasis and its impact on disease severity and progression
Authors: Ergun Tulin , Seckin Gencosmanoglu Dilek , Karakoc‐Aydiner Elif , Salman Andac , Tekin Burak , Bulbul‐Baskan Emel , Alpsoy Erkan , Cakıroglu Aylin , Onsun Nahide
Published: May 2016

Background/Objectives

The current literature suggests there is a possible connection between paediatric psoriasis and obesity. However, there is a paucity of research on the influence of increased adiposity on the severity of paediatric psoriasis and disease progression. We aimed to compare the prevalence of being overweight or obese in paediatric psoriasis patients and controls and assess the potential impact of being overweight/obese on disease severity and progression of disease.

Methods

This multicentre prospective case‐control study included 289 psoriasis patients (aged < 18 years) treated and followed up by one of the four university hospitals in Turkey. The control group consisted of 151 consecutive age‐matched and sex‐matched children who lacked a personal or family history of psoriasis. The participants' characteristics, psoriasis‐related parametres (e.g., initial subtype, psoriasis area and severity index, presence of psoriatic arthritis) and body mass index were determined.

Results

The difference between the prevalence of being overweight/obese among psoriatics (28%) and the control group (19%) was significant (P = 0.024). Being overweight/obese had no significant impact on disease severity and unresponsiveness to topical treatment. Within a median follow‐up time of 12 months, 23% of our patients with localised disease at disease onset progressed to generalised disease. The impact of being overweight/obese on disease progression was found to be non‐significant; however, disease duration was found to have a significant impact on disease progression (P = 0.026).

Conclusions

Although it is not associated with disease severity and course, increased bodyweight may be a health problem for psoriatic children.
Formal training in general movement assessment is required to effectively evaluate infants with perinatal asphyxia in outpatient settings
Authors: Brown Annemette K. , Greisen Gorm , Haugsted Ulla , Jonsbo Finn
Published: May 2016

Aim

General movement assessment (GMA) can help to identify children with a high risk of developing neurological dysfunction, such as cerebral palsy, and certified training is provided in this specialism. The aim of this study was to investigate the feasibility and reliability of using video recordings to assess GMA, in a busy Danish outpatient clinic.

Methods

The study comprised 30‐term infants born with perinatal asphyxia, who were video recorded at three months. They were assessed by two certified GMA observers and re‐assessed two weeks later. Interobserver and intra‐observer agreements were analysed using proportional agreement, and nominal kappa statistics were used to calculate 95% confidence intervals (95% CI).

Results

We found substantial and almost perfect interobserver and intra‐observer reliability. Intra‐observer agreement was 0.85 (95% CI: 0.65–1.00; p < 0.0001) and 0.85 (95% CI: 0.62–1.00; p < 0.0001), and interobserver agreement was 0.71 (95% CI: 0.45–0.96; p < 0.0001) at time point one and 0.85 (95% CI: 0.63–1.00; p < 0.0001) two weeks later. All video recordings were completed within our multidisciplinary outpatient clinic without delay.

Conclusion

This study demonstrated the reliability of the GMA method in a busy multidisciplinary Danish paediatric outpatient setting, when assessors had been formally trained in the method and used it regularly.
Investigating a Longitudinal Trajectory of Child Obesity and Its Association with Child Maltreatment in South Korea
Authors: Park Aely , Kim Youngmi
Published: May 2016

This study investigated the association between child maltreatment and body mass index (BMI) using data from four waves (wave 2 in 2011 through 5 in 2014) of the Korean Children & Youth Panel Survey collected by the South Korean National Youth Policy Institute. We employed a latent growth curve modeling approach to estimate an unobserved latent trajectory and to test the longitudinal effects of child abuse and neglect on BMI. Our results indicate that child abuse is significantly associated with BMI and children who report higher levels of abuse tend to have higher rates of increase in their BMI. This study addresses a gap in the literature by demonstrating that a parent's maltreatment of their child has a long‐term effect on the rate of change in their BMI over time.
Evaluation of the factors contributing to long‐term survival in canine tonsillar squamous cell carcinoma
Authors: Grant J , North S
Published: May 2016

Objectives

To identify any prognostic factors that may be associated with the long‐term survival of dogs diagnosed with tonsillar squamous cell carcinoma (TSCC).

Methods

The medical records of 15 dogs treated for TSCC were reviewed retrospectively. The signalment, presenting signs, clinical stage, treatments and outcome were documented.

Results

The overall median survival time (MST) of the dogs in the study was 243 days. There was a 1‐and 2‐year survival of 40% and 20%, respectively. The results of initial staging had a significant effect on survival, as dogs with only one tonsil affected and no evidence of metastatic disease had a longer MST (637.5 days) than the dogs with local (MST: 134 days) or distant (MST: 75 days) metastatic disease or bilateral tonsillar involvement at the time of initial presentation. Prolonged survival times were reported for dogs undergoing surgery and adjunctive chemotherapy (MST: 464.5 days) for treatment of their TSCC.

Clinical significance

This is the first veterinary study demonstrating an association between prognosis of patients with TSCC and stage at the time of presentation, with long survival times demonstrated for dogs with early‐stage disease following an initial treatment protocol that included surgery and chemotherapy. There was no clear association between long survival and additional surgeries for progressive disease; however; further investigation is warranted.
High‐quality care improves outcome in recumbent dairy cattle
Authors: Poulton PJ , Vizard AL , Anderson GA , Pyman MF
Published: May 2016

Objective

To investigate the influence of the quality of care on outcome and occurrence of secondary damage in recumbent dairy cows.

Methods

Recumbent dairy cows were monitored during their recumbency under field conditions in South Gippsland, Victoria, Australia. The cause of the original recumbency of 218 downer cows was determined and any secondary damage, day 7 status, final outcome and the nursing conditions of the cows were recorded. A four‐tiered grading system describing nursing quality was developed to allow analysis of its influence on outcome and on the occurrence of secondary damage.

Results

Day 7 outcome, final outcome and occurrence of important secondary damage were very strongly associated with the level of overall care provided to the recumbent cows. There was a decrease in the percentage of cows recovering by day 7 from 33% to 0%, a decrease from 45% to 0% of cows eventually recovering and an increase from 68% to 100% of cows with clinically important secondary damage as overall care decreased.

Conclusion

Management of recumbent cattle is potentially a significant animal welfare issue for the dairy industry and their care is a very important but often under‐appreciated aspect of their management. Recovery is positively influenced by high‐quality care by improving the chances of recovery from the initial cause of recumbency and by reducing the occurrence of secondary damage. Recumbent cows must either be nursed at a high level of care or euthanased promptly.
Severe hyponatraemia in foals: clinical findings, primary diagnosis and outcome
Authors: Collins NM , Axon JE , Carrick JB , Russell CM , Palmer JE
Published: May 2016

Objective

To evaluate severe hyponatraemia in foals presenting as medical emergencies to an intensive care unit (ICU) in order to determine the prevalence, clinical findings, primary diagnosis and outcome.

Design

Retrospective case study of records from Thoroughbred foals aged less than 3 months presenting to anICUas medical emergencies in 2002–12; foals with severe hyponatraemia (serum sodium<122 mmol/L) on admission laboratory data were identified. Data retrieved included signalment, clinical findings, laboratory results, primary diagnosis, treatment and outcome.

Results

Severe hyponatraemia was identified in 69/1718 Thoroughbred foals (4%) presenting to theICUduring the study period. Of the 69 foals, 11 (15.9%) presented with neurological signs attributable to hyponatraemic encephalopathy and 7 of these foals had seizures; other neurological signs included obtundation, ataxia and apparent blindness. The three most common primary diagnoses of the 69 foals with severe hyponatraemia were renal disease (18/69, 26.1%), enterocolitis (16/69, 23.2%) and uroperitoneum (15/69, 21.7%). Treatment was directed at the primary disease and correction of the hyponatraemia. A total of 50 of the 69 foals (72.5%) with severe hyponatraemia survived to hospital discharge and 38 of them (76%) survived at least 12 months following discharge.

Conclusion

The prevalence of severe hyponatraemia in this study population was 4%. The majority of foals with severe hyponatraemia did not demonstrate direct clinical manifestations as a result of the low serum sodium concentration. The outcome of foals with severe hyponatraemia was mostly favourable.