bluuebunny/crossref_metadata_2025 huggingface dataset:
MVSE: an R-package that estimates a climate-driven mosquito-borne viral suitability index
Authors: Obolski Uri , Perez Pablo N , Villabona-Arenas Christian J , Faria Nuno R , Lourenço José
Published: July 2018

Background

Viruses such as dengue, Zika, yellow fever and chikungunya depend on mosquitoes for transmission. Their epidemics typically present periodic patterns, linked to the underlying mosquito population dynamics, which are known to be driven by natural climate fluctuations. Understanding how climate dictates the timing and potential of viral transmission is essential for preparedness of public health systems and design of control strategies.

Results

We developed theMosquito-borneViralSuitabilityEstimator (MVSE) software package for the R programming environment. The package estimates a suitability index based on a climate-driven mathematical expression for the basic reproductive number (R0) of a well established mathematical model for the transmission dynamics of mosquito-borne viruses. By accounting for local humidity and temperature, as well as viral, vector and human priors, suitability can be estimated for specific host and viral species, as well as different regions of the globe.

Conclusions

Here, we describe the background theory and biological interpretation of the new suitability index, as well as the implementation, basic functionality, research and educational potentials of the MVSE R-package. The package is freely available under the GPL 3.0 license.
Clinical data specification and coding for cross-analyses with omics data in autoimmune disease trials
Authors: Roberta Lorenzon , Iannis Drakos , Ribet Claire , Harris Sophie , Maeva Cordoba , Olivia Tran , Eric Dasque , Patrice Cacoub , Agnes Hartemann , Bahram Bodaghi , David Saadoun , Francis Berenbaum , Gilles Grateau , Pierre Ronco , Olivier Benveniste , Kuberaka Mariampillai , Jeremie Sellam , Philippe Seksik , Michelle Rosenzwajg , Adrien Six , Claude Bernard , Caroline Aheng , Eric Vicaut , David Klatzmann , Encarnita Mariotti-Ferrandiz
Published: July 2018

Objectives

Autoimmune and inflammatory diseases (AIDs) form a continuum of autoimmune and inflammatory diseases, yet AIDs’ nosology is based on syndromic classification. The TRANSIMMUNOM trial (NCT02466217) was designed to re-evaluate AIDs nosology through clinic-biological and multi-omics investigations of patients with one of 19 selected AIDs. To allow cross-analyses of clinic-biological data together with omics data, we needed to integrate clinical data in a harmonized database.

Materials and Methods

We assembled a clinical expert consortium (CEC) to select relevant clinic-biological features to be collected for all patients and a cohort management team comprising biologists, clinicians and computer scientists to design an electronic case report form (eCRF). The eCRF design and implementation has been done on OpenClinica, an open-source CFR-part11compliant electronic data capture system.

Results

The CEC selected 865 clinical and biological parameters. The CMT selected coded the items using CDISC standards into 5835 coded values organized in 28 structured eCRFs. Examples of such coding are check boxes for clinical investigation, numerical values with units, disease scores as a result of an automated calculations, and coding of possible treatment formulas, doses and dosage regimens per disease.

Discussion

21 CRFs were designed using OpenClinica v3.14 capturing the 5835 coded values per patients. Technical adjustment have been implemented to allow data entry and extraction of this amount of data, rarely achieved in classical eCRFs designs.

Conclusions

A multidisciplinary endeavour offers complete and harmonized CRFs for AID clinical investigations that are used in TRANSIMMUNOM and will benefit translational research team.
Ade2functions in theDrosophilafat body to promote sleep
Authors: Yurgel Maria E. , Shah Kreesha D. , Brown Elizabeth B. , Bennick Ryan A. , DiAngelo Justin R. , Keene Alex C.
Published: July 2018

Metabolic state is a potent modulator of sleep and circadian behavior and animals acutely modulate their sleep in accordance with internal energy stores and food availability. Across phyla, hormones secreted from adipose tissue act in the brain to control neural physiology and behavior to modulate sleep and metabolic state. Growing evidence suggests the fat body is a critical regulator of complex behaviors, but little is known about the genes that function within the fat body to regulate sleep. To identify molecular factors functioning in the periphery to regulate sleep, we performed an RNAi screen selectively knocking down genes in the fat body. We found that knockdown ofPhosphoribosylformylglycinamidine synthase/Pfas(Ade2), a highly conserved gene involved the biosynthesis of purines, reduces sleep and energy stores. Flies heterozygous for multipleAde2mutations are also short sleepers and this effect is partially rescued by restoringAde2to the fat body. Targeted knockdown ofAde2in the fat body does not alter arousal threshold or the homeostatic response to sleep deprivation, suggesting a specific role in modulating baseline sleep duration. Together, these findings suggestAde2functions within the fat body to promote both sleep and energy storage, providing a functional link between these processes.
Matrilineal Transmission of Familial Excess Longevity (mtFEL): Effects on Cause-specific Mortality in Utah, 1904 - 2002
Authors: O’Brien Elizabeth , Cawthon Richard M. , Smith Ken R. , Kerber Richard A.
Published: July 2018

The heritable component to a long and healthy life is likely to involve the actions and interactions of both nuclear and mitochondrial genetic variants. Using computerized genealogical records with accompanying cause of death information from the Utah population, we previously reported cause-specific mortality rate distributions associated with the nuclear genetic component of familial exceptional longevity. Here we identify Utah matrilineages (mitochondrial lineages) in which overall survival is better than expected, and compare cause-specific mortality rates in those matrilineages to cause-specific mortality rates in the general population. We also examine the effects on cause-specific mortality of interactions between the nuclear and mitochondrial components of familial excess longevity (nuclear FEL and mtFEL). Among individuals from the bottom quartile of nuclear FEL, those who were also in the top quartile for mtFEL had lower all-cause, heart disease, cancer, stroke, and diabetes mortality rates than those in the bottom quartile of mtFEL. In contrast, among individuals from the top quartile of nuclear FEL, the mortality rates from these diseases were similar for those also in the top quartile of mtFEL vs. those also in the bottom quartile of mtFEL, with the exception of diabetes mortality, which was dramatically suppressed in the high nuclear FEL + high mtFEL group as compared to the high nuclear FEL + low mtFEL group. Moreover, the highest mortality rates from diabetes were found in individuals aged 90 years or older who were members of both the high nuclear FEL and low mtFEL quartiles. These results support the hypothesis that some nuclear genetic variants contributing to long life carry an increased risk of dying from diabetes that is strongly ameliorated by some mitochondrial DNA variants.
Heliaphen, an outdoor high-throughput phenotyping platform designed to integrate genetics and crop modeling
Authors: Gosseau Florie , Blanchet Nicolas , Varès Didier , Burger Philippe , Campergue Didier , Colombety Céline , Gody Louise , Liévin Jean-François , Mangin Brigitte , Tison Gilles , Vincourt Patrick , Casadebaig Pierre , Langlade Nicolas
Published: July 2018

Heliaphen is an outdoor pot platform designed for high-throughput phenotyping. It allows automated management of drought scenarios and plant monitoring during the whole plant cycle. A robot moving between plants growing in 15L pots monitors plant water status and phenotypes plant or leaf morphology, from which we can compute more complex traits such as the response of leaf expansion (LE) or plant transpiration (TR) to water deficit. Here, we illustrate the platform capabilities for sunflower on two practical cases: a genetic and genomics study for the response to drought of yield-related traits and a simulation study, where we use measured parameters as inputs for a crop simulation model. For the genetic study, classical measurements of thousand-kernel weight (TKW) were done on a sunflower bi-parental population under water stress and control conditions managed automatically. The association study using the TKW drought-response highlighted five genetic markers. A complementary transcriptomic experiment identified closeby candidate genes differentially expressed in the parental backgrounds in drought conditions. For the simulation study, we used the SUNFLO crop simulation model to assess the impact of two traits measured on the platform (LE and TR) on crop yield in a large population of environments. We conducted simulations in 42 contrasted locations across Europe and 21 years of climate data. We defined the pattern of abiotic stresses occurring at this continental scale and identified ideotypes (i.e. genotypes with specific traits values) that are more adapted to specific environment types. This study exemplifies how phenotyping platforms can help with the identification of the genetic architecture of complex response traits and the estimation of eco-physiological model parameters in order to define ideotypes adapted to different environmental conditions.
An open-sourcek-mer based machine learning tool for fast and accurate subtyping of HIV-1 genomes
Authors: Solis-Reyes Stephen , Avino Mariano , Poon Art F.Y. , Kari Lila
Published: July 2018

For many disease-causing virus species, global diversity is clustered into a taxonomy of subtypes with clinical significance. In particular, the classification of infections among the subtypes of human immunodeficiency virus type 1 (HIV-1) is a routine component of clinical management, and there are now many classification algorithms available for this purpose. Although several of these algorithms are similar in accuracy and speed, the majority are proprietary and require laboratories to transmit HIV-1 sequence data over the network to remote servers. This potentially exposes sensitive patient data to unauthorized access, and makes it impossible to determine how classifications are made and to maintain the data provenance of clinical bioinformatic workflows. We propose an open-source supervised and alignment-free subtyping method (KAMERIS) that operates onk-mer frequencies in HIV-1 sequences. We performed a detailed study of the accuracy and performance of subtype classification in comparison to four state-of-the-art programs. Based on our testing data set of manually curated real-world HIV-1 sequences (n= 2, 784), Kameris obtained an overall accuracy of 97%, which matches or exceeds all other tested software, with a processing rate of over 1,500 sequences per second. Furthermore, our fully standalone general-purpose software provides key advantages in terms of data security and privacy, transparency and reproducibility. Finally, we show that our method is readily adaptable to subtype classification of other viruses including dengue, influenza A, and hepatitis B and C virus.
The contrasting response to drought and waterlogging is underpinned by divergent DNA methylation programs associated with gene expression in sesame
Authors: Dossa Komivi , Mmadi Marie Ali , Zhou Rong , Zhou Qi , Yang Mei , Cisse Ndiaga , Diouf Diaga , Wang Linhai , Zhang Xiurong
Published: July 2018

DNA methylation is a heritable epigenetic mechanism that participates in gene regulation under abiotic stresses in plants. Sesame (Sesamum indicum L.) is typically considered a drought-tolerant crop but highly susceptible to waterlogging, a property attributed to its presumed origin in Africa or India. Understanding DNA methylation patterns in sesame under drought and waterlogging conditions can provide insights into the regulatory mechanisms underlying its contrasting responses to these principal abiotic stresses. Here, we combined Methylation-Sensitive Amplified Polymorphism and transcriptome analyses to profile cytosine methylation patterns, gene expression alteration, and their interplay in drought-tolerant and waterlogging-tolerant sesame genotypes under control, stress and recovery conditions. Our data showed that drought stress strongly induced de novo methylation (DNM) whereas most of the loci were demethylated (DM) during the recovery phase. In contrast, waterlogging decreased the level of methylation under stress but during the recovery phase, both DM and DNM were concomitantly deployed. In both stresses, the differentially expressed genes (DEGs) were highly correlated with the methylation patterns. We observed that DM was associated with the up-regulation of the DEGs while DNM was correlated with the down-regulation of the DEGs. In addition, we sequenced 44 differentially methylated regions of which 90% overlapped with the promoters and coding sequences of the DEGs. Altogether, we demonstrated that sesame has divergent epigenetic programs that respond to drought and waterlogging stresses. Our results also highlighted the possible interplay among DNA methylation and gene expression, which may modulate the contrasting responses to drought and waterlogging in sesame.
The agony of choice for medical tourists: a patient satisfaction index model
Authors: Rosenbusch Jana , Ismail Ida Rosnita , Ringle Christian Marc
Published: July 2018

Purpose

Grounded on substantial theories and service concept models, this paper aims at proposing a novel patient satisfaction index (PSI) model. This model allows for identifying the key sources of patient satisfaction and for comparing performance results across hospitals competing on the national and international health-care market. The PSI is also an important benchmark instrument for medical tourism.

Design/methodology/approach

The PSI model was initially tested in hospitals in a developed country (the German hospital market). A total of 1,281 complete patient responses were analyzed by means of partial least squares structural equation modeling (PLS-SEM).

Findings

This model’s sources of competitive advantage – doctors’ and nurses’ interaction quality, environmental quality and outcome quality – mostly explain patient satisfaction, which is the key target construct. The results also reveal that the doctors’ and nurses’ interaction quality is the most salient driver of patient satisfaction.

Practical implications

The proposed PSI model can be generally applied to facilitate the comparison of hospitals on a regional, national and even an international level. In addition, the PSI model helps health-care management facilities prioritize their service components’ improvement (e.g. to attract more medical tourists).

Originality/value

Medical tourists are confronted with a variety of health destinations and may find it difficult to choose an appropriate region and health-care provider. This study contributes to medical tourism research by developing a general patient satisfaction index model for medical tourists.
Bridging the gap between supply chain risk management and strategic technology partnering capabilities: insights from social capital theory
Authors: Kilubi Irène , Rogers Helen
Published: July 2018

Purpose

As companies seek to continually innovate to remain globally competitive, they also need to be mindful of the impact of the potential associated supply chain risks. Hence, the purpose of this study is to explore the causal nexus of relationships linking supply chain risk management (SCRM) and strategic technology partnering (STP) capabilities (i.e. organizational capabilities, technological and innovative capabilities, learning and exploitation capabilities, complementary capabilities and network and partnership capabilities) as identified by Kilubi (2016).

Design/methodology/approach

The authors investigate STP capabilities that may positively influence SCRM and in turn foster organizational performance. By using conceptual theory building, the authors create a conceptual framework and use it to guide future investigation through research propositions. Social capital theory serves as the theoretical background.

Findings

Five STP capabilities have been identified as positive mediators for the relationship between SCRM and organizational performance, in particular flexibility and responsiveness.

Originality/value

This paper focuses on bridging the gap and identifying commonalities between two principal research disciplines, STP and SCRM, examining how these can be used to assist in the controlling and management of future risks. This study contributes to the ongoing development of SCRM and STP by integrating insights from social capital theory, supply chain management and strategic management.
Reading on and between the lines: risk identification in collaborative and adversarial buyer–supplier relationships
Authors: Fan Yiyi , Stevenson Mark
Published: July 2018

Purpose

This paper aims to investigate how supply chain risks can be identified in both collaborative and adversarial buyer–supplier relationships (BSRs).

Design/methodology/approach

This research includes a multiple-case study involving ten Chinese manufacturers with two informants per organisation. Data have been interpreted from a multi-level social capital perspective (i.e. from both an individual and organisational level), supplemented by signalling theory.

Findings

Buyers use different risk identification strategies or apply the same strategy in different ways according to the BSR type. The impact of organisational social capital on risk identification is contingent upon the degree to which individual social capital is deployed in a way that benefits an individual’s own agenda versus that of the organisation. Signalling theory generally complements social capital theory and helps further understand how buyers can identify risks, especially in adversarial BSRs, e.g. by using indirect signals from suppliers or other supply chain actors to “read between the lines” and anticipate risks.

Research limitations/implications

Data collection is focussed on China and is from the buyer side only. Future research could explore other contexts and include the supplier perspective.

Practical implications

The types of relationships that are developed by buyers with their supply chain partners at an organisational and an individual level have implications for risk exposure and how risks can be identified. The multi-level analysis highlights how strategies such as employee rotation and retention can be deployed to support risk identification.

Originality/value

Much of the extant literature on supply chain risk management is focussed on risk mitigation, whereas risk identification is under-represented. A unique case-based insight is provided into risk identification in different types of BSRs by using a multi-level social capital approach complemented by signalling theory.
Key risks in the supply chain of large scale engineering and construction projects
Authors: Rudolf Christian A. , Spinler Stefan
Published: July 2018

Purpose

Large-scale projects are the typical delivery model in the engineering and construction industry, with their very own characteristics. Even though well established, only 1 in 1,000 large-scale projects is successful (Flyvbjerg, 2011). A lack of effective supply chain risk management (SCRM) has repeatedly been identified as one of the main causes. While the SCRM body of knowledge seems increasingly well established, a lack of effective methods meeting the specific requirements of large-scale projects can be observed.

Design/methodology/approach

This paper presents a structured and prioritized view on the supply chain risk portfolio in this sector: first, the authors identified and categorized the key supply chain risks in the recent literature. Next, the authors surveyed large-scale project managers across multiple industries, mainly coming from the domains of supply chain management and project management. Finally, the authors provide a contextualized risk taxonomy for engineering, procurement and construction (EPC) projects.

Findings

The identified risk portfolio deviates from generic projects significantly and shows a very high inherent risk exposure of large-scale projects. In particular, behavioral risks are identified as crucial. Additionally, a bias to considerably underestimate risks at project beginning is found.

Originality/value

The contextualized SCRM taxonomy offers a systematic and structured view on the key supply chain risks in EPC large-scale projects. The identified risks are considerably different in their characteristics compared to generic projects or classical SCRM approaches. The authors thus provide a new perspective on SCRM in this specific setting and complement traditional risk and project risk management techniques.
Structural Breaks and Energy Consumption in the Gulf Cooperation Council Countries: Are Random Shocks Transitory or Permanent?
Authors: Osman Mohamed , Hoque Ariful , Gachino Geoffrey
Published: July 2018

The impact of random shocks on the energy consumption of the Gulf Cooperation Council countries is essentially an empirical question which cannot be determined a priori without properly testing the integration properties of this variable. To this aim, we perform testing the unit root properties of this variable using both traditional unit root tests and the recently developed technique of the Fourier transformation function or simply known as the FADF test developed by Enders and Lee (2012), which not only takes into account for the existence of structural breaks but also that of non‐linearity in the energy consumption series of these countries. The results from the traditional unit root tests fail to reject the null hypothesis of non‐stationarity while that of the Fourier ADF unit root test which is more powerful has strongly rejected the null hypothesis of unit root for all the countries except Bahrain and Qatar. In sum, the results from this test indicate that the energy consumption variables of these countries are characterised by a stationary process and this has important policy implications. This suggests that these random shocks will have only a transitory effect on the energy consumption per capita of these countries.
The Influence of Body Size on the Expression of Sexually Dimorphic Morphological Traits
Authors: Horbaly Haley E. , Kenyhercz Michael W. , Hubbe Mark , Steadman Dawnie W.
Published: July 2018

Skeletal sexual dimorphism manifests as size or shape differences between males and females in a population. Certain dimorphic traits are used in sex estimation methods, and populational variation in the expression of these traits can result in inaccurate sex estimation. However, the underlying causes of variation in trait expression remain unclear. This study explores body size, which also exhibits sexual dimorphism, as a potential factor influencing trait expression. To test this, skeletons of 209 individuals of varying body size were analyzed, and morphological traits were scored according to the Walker (2008), Klales et al. (2012), and Rogers (1999) sex estimation methods. Statistical analyses found significant correlations between body size parameters and expression of traits, with stature explaining more relative variance in trait expression than body mass. However, the relationships are weak and few in number, suggesting that body size has a minimal impact on the expression of these morphological traits.
“Cannot Decide”: The Fine Line Between Appropriate Inconclusive Determinations Versus Unjustifiably Deciding Not To Decide
Authors: Dror Itiel E. , Langenburg Glenn
Published: July 2018

Inconclusive decisions, deciding not to decide, are decisions. We present a cognitive model which takes into account that decisions are an outcome of interactions and intersections between the actual data and human cognition. Using this model it is suggested under which circumstances inconclusive decisions are justified and even warranted (reflecting proper caution and meta‐cognitive abilities in recognizing limited abilities), and, conversely, under what circumstances inconclusive decisions are unjustifiable and should not be permitted. The model further explores the limitations and problems in using categorical decision‐making when the data are actually a continuum. Solutions are suggested within the forensic fingerprinting domain, but they can be applied to other forensic domains, and, with modifications, may also be applied to other expert domains.
Resident and Nonresident Fingernail Isotopes Reveal Diet and Travel Patterns,,
Authors: Mancuso Christy J. , Ehleringer James R.
Published: July 2018

Global travel has increased, and having a diagnostic tool to distinguish residents from visitors would be valuable. This study examined stable isotope biomarkers of fingernail tissues of resident (n = 26) and nonresident (n = 22) participants in Salt Lake City (SLC), UT, from 2015 to 2016. The purpose of this research was to determine whether fingernail isotopes could be used for reconstructing geolocation movements and to examine the convergence in nonresident fingernail isotopes to that of the resident signal following their arrival to SLC. Resident isotope values defined a baseline to make comparisons to. Initial nonresident hydrogen and oxygen isotope values were correlated with precipitation isotopes of their prior location. Fingernail isotope turnover rates were rapid and nonresident isotopes were indistinguishable from residents after ~71–90 days. The results of our study highlight the utility of stable isotope measurements of fingernail clippings to examine travel history reconstruction that could aid in identification of human remains.
A Test of Age Estimation Methods on Impacted Third Molars in Males
Authors: Pilloud Marin A. , Heim Kelly
Published: July 2018

This study tests the relationship between third molar impaction and its concomitant effect on age estimation methods. Data were collected on radiographs of males analyzed in the Defense POW/MIA Accounting Agency Laboratory (n = 114). Radiographs of skeletonized individuals were scored for dental development, and age was assigned based on the appropriate ancestry‐based method. Differences between identified age and estimated dental age were assessed to determine whether molar impaction affected root development and age estimations. Results indicate that impacted teeth tend to be underdeveloped and result in age estimates that are too low. While these results are of note to anthropologists and odontologists performing dental age estimates, more work is needed to explore the effect of impaction on development among a more diverse sample.
Comparison of Different Swabs for Sampling Inorganic Gunshot Residue from Gunshot Wounds: Applicability and Reliability for the Determination of Firing Distance
Authors: Merli Daniele , Amadasi Alberto , Mazzarelli Debora , Cappella Annalisa , Castoldi Elisa , Ripa Stefano , Cucca Lucia , Cattaneo Cristina , Profumo Antonella
Published: July 2018

This study concentrates on samples of bare pork skin, with and without bristles, and dried bovine ribs shot with a semi‐automatic pistol to find the best methodology and sampling surface in the search for inorganic gunshot residues (IGSR). Four quadrants of known surface areas were sampled at different distances from the bullet's hole with different swabs: tapes in graphite, Leukosilk® white tape, 3M® transparent tape, and a cotton swab to assess the technique able to collect the highest amounts ofIGSRwith the lowest contribution of the blank. The cotton swab wet in 10%HNO3gave the best results. The highest amounts ofIGSR, measured byICP‐OESandMS, were detected on a surface of 3‐cm radius from the bullet's edge. The amount of metals collected decreased with the firing distance between 20 and 60 cm. The procedure was efficient for sampling different tissues like skin and bones.
Effect of Increased Blood Flow Rate on Hemodialysis Tolerability and Achieved Urea Reduction Ratio
Authors: Ryan Peter , Le Mesurier Lauren , Adams Kelly , Choi Peter , Chacko Bobby
Published: July 2018

Long‐term hemodialysis (HD) imposes a significant burden on the quality of life of end‐stage kidney disease patients. Optimizing dialysis dose is an important consideration in this population; however, evidence exists that suggests that attainment of population dialysis targets is associated with increased intradialytic complications. In this prospective, before‐after study, the blood flow rate (BFR) of 63 maintenance HD patients was increased by 100 mL/min to a maximum BFR of 400 mL/min to determine the impact on patient tolerability and urea reduction ratio (URR) of an increased BFR. Tolerability was assessed by time to recovery (TTR) after dialysis, a validated measure of patient tolerability, and intradialytic complications. Median pre‐increase BFR was 252 mL/min compared to 349 mL/min post‐increase. Mean TTR decreased from 4.67 h to 4.03 h (P = 0.688). No association was observed between percentage change in BFR (R2 = 0.0) or post‐increase BFR (R2 = 0.0) and absolute change in TTR. A significant, positive association was observed between both the absolute and relative changes to BFR and the achieved URR. We found no evidence that increasing BFR by 100 mL/min diminishes patient tolerability.
Viewing obesogenic advertising in children's neighbourhoods using Google Street View
Authors: Egli Victoria , Zinn Caryn , Mackay Lisa , Donnellan Niamh , Villanueva Karen , Mavoa Suzanne , Exeter Daniel J. , Vandevijvere Stefanie , Smith Melody
Published: July 2018

The advertising of unhealthy food and beverages forms an important component of obesogenic environments. Such marketing to children is a key health determinant because of its impact on dietary preference and food purchasing behaviour. The location of outdoor advertising is important in exploring obesogenic environments and children's neighbourhoods. The aim of this study is to explore issues involved in the use of Google Street View to examine outdoor food and beverage advertising. The implications for using Google Street View in the context of neighbourhood built environment research and grass‐roots advocacy are discussed. The study was conducted within walkable distances from 19 primary and intermediate schools in Auckland, New Zealand, where “walkable” was defined as limited by 800 m road network boundaries, which are equivalent to school buffer boundaries. Google Street View allows for centrality of data collection, coding, and storage. However, challenges exist with the method because 727 (29.4%) of a total of 2,474 outdoor advertisements that were identified were not able to be categorised because images were unclear, not in English, blocked, or at angles where detail cannot be deciphered. Specific to outdoor advertising for food and beverages, the results presented here show that children are exposed to a significantly greater number of unhealthy advertising than other advertising, P=0.001, eta‐squared statistic (0.45) indicates a large effect size. Overall, the results show promise for the use of Google Street View in the study of obesogenic environments.
A novel, easy method for estimating pheromone trap attraction range: application to the pine sawyer beetle Monochamus galloprovincialis
Authors: Jactel Herve , Bonifacio Luis , van Halder Inge , Vétillard Fabrice , Robinet Christelle , David Guillaume
Published: July 2018

Pheromone traps are widely used for monitoring or managing insect pest populations. However, it is important to know their range of attraction to optimize the setting of pheromone trap networks.

We propose an easy method based on the use of pairs of adjacent traps located at decreasing distance from each other. The range of attraction is deduced from the observation of reduced trap capture when the attraction range of two adjacent traps starts overlapping. The relationship between the relative trap capture and the distance between paired traps is fitted with a logistic curve.

To empirically test these predictions, we conducted trapping experiments with the beetle Monochamus galloprovincialis, the insect vector of the pine wood nematode. Fifteen pairs of traps separated by 25 to 300 m, in France, and 18 pairs of traps distant from 25 to 400 m, in Portugal, were installed in maritime pine plantation landscapes.

In both countries, the relative percentage of capture per trap per week was best fitted by a logistic model with two parameters. The estimated attraction ranges were 92 m (confidence interval = 62–211 m) in France and 123 m (confidence interval = 64–491 m) in Portugal.

The interference between paired traps thus provides a simple and robust method for estimating the attraction range of pheromone traps.
Accuracy of genotype imputation in Labrador Retrievers
Authors: Friedrich J. , Antolín R. , Edwards S. M. , Sánchez‐Molano E. , Haskell M. J. , Hickey J. M. , Wiener P.
Published: July 2018

The dog is a valuable model species for the genetic analysis of complex traits, and the use of genotype imputation in dogs will be an important tool for future studies. It is of particular interest to analyse the effect of factors like single nucleotide polymorphism (SNP) density of genotyping arrays and relatedness between dogs on imputation accuracy due to the acknowledged genetic and pedigree structure of dog breeds. In this study, we simulated different genotyping strategies based on data from 1179 Labrador Retriever dogs. The study involved 5826 SNPs on chromosome 1 representing the high density (HighD) array; the low‐density (LowD) array was simulated by masking different proportions of SNPs on the HighD array. The correlations between true and imputed genotypes for a realistic masking level of 87.5% ranged from 0.92 to 0.97, depending on the scenario used. A correlation of 0.92 was found for a likely scenario (10% of dogs genotyped using HighD, 87.5% of HighD SNPs masked in the LowD array), which indicates that genotype imputation in Labrador Retrievers can be a valuable tool to reduce experimental costs while increasing sample size. Furthermore, we show that genotype imputation can be performed successfully even without pedigree information and with low relatedness between dogs in the reference and validation sets. Based on these results, the impact of genotype imputation was evaluated in a genome‐wide association analysis and genomic prediction in Labrador Retrievers.
Management of primary spontaneous pneumothorax: a review
Authors: Wong Amy , Galiabovitch Elena , Bhagwat Krishna
Published: July 2018

Primary spontaneous pneumothorax is a common problem faced by doctors in medical practice. It is a significant global health problem affecting adolescent and young adults. This article will review the etiopathology, diagnosis and current management guidelines. It aims to improve clinical practice and compliance to the complexities of procedures involved in management.
Potential involvement of ubiquitin‐proteasome system dysfunction associated with oxidative stress in the pathogenesis of sickle cell disease
Authors: Warang Prashant , Homma Takujiro , Pandya Riddhi , Sawant Anuja , Shinde Nikhil , Pandey Debjeet , Fujii Junichi , Madkaikar Manisha , Mukherjee Malay B.
Published: July 2018

The ubiquitin‐proteasome system (UPS) is an important intracellular proteolytic pathway responsible for the degradation of proteins and oxidative damage; hence it plays a central role in maintaining homeostasis of red blood cells (RBCs). The present study investigated the levels of polyubiquitination, the function of proteasomes and effect of hydroxycarbamide (HC) therapy in RBCs from sickle cell disease (SCD) patients. Polyubiquitinated proteins were found to be elevated in untreated SCD (UT‐SCD) patients compared to those in HC‐treated SCD patients (HC‐SCD) and controls. Activities of β1 and β2 subunits were a little higher in UT‐SCD patients, and much higher proteolytic activities were observed in all three subunits (β1, β2 and β5) of RBCs in HC‐SCD patients compared to those of UT‐SCD patients and controls, although the protein levels of these subunits remained approximately the same. It is notable that, despite HC therapy, some patients showed persistent complications and accumulation of polyubiquitinated proteins. The enhanced proteasomal activity among HC‐treated patients might remove the polyubiquitinated protein and could be one of the important mechanisms of therapeutic action. These findings could be useful to understand the pathophysiology of SCD and its clinical heterogeneity and identify a suitable therapeutic target for the better management of these patients.
Advances in understanding the pathogenesis of acquired aplastic anaemia
Authors: Luzzatto Lucio , Risitano Antonio M.
Published: July 2018

This review examines the evidence that bone marrow failure (BMF) in aplastic anaemia (AA) is due to loss of haematopoietic stem cells (HSCs), which, in turn, is caused by deranged immunity and inflammation. We also consider how the course of the disease and the response to immuno‐suppressive therapy are influenced by the nature and specificity of the pathogenic process. A somatic mutation of thePIGAgene underlies the clonal disease paroxysmal nocturnal haemoglobinuria (PNH): there is direct evidence that the expansion of thePIGAmutant clone results from Darwinian selection exerted by a glycosyl‐phosphatidyl‐inositol ‐specific auto‐immune attack. Thus,PNHpatients are a unique subset of patients withAA, in whom haematopoiesis recovers through this escape mechanism. A similar process, although less effective, may operate when the auto‐immune attack is against a human leucocyte antigen (HLA) molecule and anHLAmutation has produced a clone missing that molecule. We then discuss the significance of other mutant clones that are frequently found inAA, presumably due to a combination of genetic drift and selection. These clones are not causative ofAA, but they emerge inAAand they may be pre‐leukaemic: unlike aPIGAmutant clone, in general they are unable to effectively reconstitute haematopoiesis.
My Village Is Dying? Integrating Methods from the Inside Out
Authors: Peters Paul , Carson Dean , Porter Robert , Vuin Ana , Carson Doris , Ensign Prescott
Published: July 2018

The purpose of this paper is to confront the notion of “decline” at the village level by illustrating a more immersive approach to sociological and demographic research within rural and remote communities. The research uses case studies of three villages in Australia, Canada, and Sweden, all of which have been labeled as “declining villages,” typified by population loss, an aging population, high rates of youth outmigration, and loss of businesses and services. This paper argues that focusing solely on quantitative indicators of demographic change provides a narrow view of rural village trajectories and ignores subtle processes of local adaptation that are hidden from quantitative data sets. Our research integrates quantitative data from the “outside” with qualitative data from the “inside,” including visual ethnography, to develop a more balanced perspective on how villages have been changing and what change could mean locally. These objectives are accomplished by revisiting aDirt Researchmethodology applicable to a broad range of research into rural and remote villages.
Identification of peptides with tolerogenic potential in a hydrolysed whey‐based infant formula
Authors: Gouw Joost W. , Jo Juandy , Meulenbroek Laura A. P. M. , Heijjer T. Sam , Kremer Erica , Sandalova Elena , Knulst André C. , Jeurink Prescilla V. , Garssen Johan , Rijnierse Anneke , Knippels Léon M. J.
Published: July 2018

Background

Failure to induce oral tolerance may result in food allergy. Hydrolysed cow's milk‐based infant formulas are recommended in subjects with a high risk of developing allergic disease. Presentation of T cell epitopes is a prerequisite to generate regulatory T cells that could contribute to oral tolerance.

Objective

To investigate whether a specific hydrolysed whey‐based infant formula contains peptides that function as T cell epitopes to support the development of oral tolerance to whey.

Methods

First, a novel liquid chromatography‐mass spectrometry (LC‐MS) method was developed to characterize β‐lactoglobulin‐derived peptides present in a specific infant formula with a focus on region AA#13‐48 of β‐lactoglobulin, which has previously been described to contain T cell epitopes with tolerogenic potential. Second, the formula was subjected to the ProImmune ProPresent® antigen presentation assay and MHC class II binding algorithm to identify relevant HLA‐DRB1‐restricted peptides. Third, identified peptides were tested on human cow's milk protein‐specific T cell lines to determine T cell recognition.

Results

Thirteen peptides of minimal 9AAs long that overlap with AA#13‐48 of β‐lactoglobulin were identified. Six of them were found across all batches analysed. It was further confirmed that these peptides were processed and presented by human dendritic cells. The identified HLA‐DRB1‐restricted peptides were correlated to AA#11‐30 and AA#23‐39 of β‐lactoglobulin. Importantly, the proliferation assay showed that the synthetic peptides were recognized by cow's milk protein‐specific T cell lines and induced T cell proliferation.

Conclusion and Clinical Relevance

This study demonstrates that the tested hydrolysed infant formula contains functional HLA‐DRB1‐restricted T cell epitopes, which can potentially support the development of oral tolerance to whey.
Democratizing Innovation in Organizations: Teaching Design Thinking to Non‐Designers
Authors: Liedtka Jeanne , Salzman Randy , Azer Daisy
Published: July 2018

Designers are comfortable with ambiguity and open‐ended questions. Not so much with industry leaders and managers who decide to take a course in design thinking. Many are risk‐averse individuals fearful of failure to begin with. They need a more structured methodology if they are to feel comfortable with designerly thinking and decision‐making.
Coronary risk assessment using traditional risk factors with CT coronary artery calcium scoring in clinical practice
Authors: Kerut Edmund Kenneth , Hall Michael E. , Turner Michael C. , McMullan Michael R.
Published: July 2018

As coronary artery calcium (CAC) is atherosclerosis and not just a marker of cardiovascular (CV) disease, measurement of a patient's coronary artery calcium score (CACS) is a strong predictor of risk. Clinically performed in asymptomatic patients, the CACS, along with several CV risk factors, namely age, sex, ethnicity, diabetes, tobacco use, family history, cholesterol level, blood pressure, and use of cholesterol or hypertensive medications, provide a predictive model of 10 year risk for CV events. A smartphone “App” makes this quick to obtain and use. This helps the clinician in making recommendations for both lifestyle changes and statin therapy. Those patients in which the most benefit occur from measurement of a CACS are those at an intermediate CV risk. Measurement of the CACS has become an integral part of the clinician's assessment of a patient's CV risk and for guiding preventative therapies.
Shrub shading moderates the effects of weather on arthropod activity in arctic tundra
Authors: Asmus Ashley L. , Chmura Helen E. , Høye Toke T. , Krause Jesse S. , Sweet Shannan K. , Perez Jonathan H. , Boelman Natalie T. , Wingfield John C. , Gough Laura
Published: July 2018

1. Rapid warming has facilitated an increase in deciduous shrub cover in arctic tundra. Because shrubs create a cooler microclimate during the growing season, shrub cover could modulate the effects of global warming on the phenology and activity of ectotherms, including arthropods. This possibility was explored here using two dominant arthropod groups (flies and wolf spiders) in Alaskan tundra.

2. We monitored arthropods with pitfall traps over five summers at four sites that differed in shrub abundance, and used generalised additive mixed models (GAMMs) to separate the two underlying components of pitfall trap catch: the seasonal trend in arthropod density and the effects of short‐term weather variation (air temperature, wind speed, rainfall, solar radiation) on arthropod activity.

3. We found that shrub cover significantly altered the seasonal trend in the abundance of flies by reducing early‐season pitfall catch, in line with observed later snowmelt in shrub‐dominated plots at these sites.

4. Additionally, shrub cover modulated the effects of many weather variables on arthropod activity: shrub cover shifted wolf spiders' temperature–activity relationship, dampened the positive effect of solar radiation on the activity of arthropods in total, and ameliorated the negative effect of wind on the activity of flies.

5. Thus, these results indicate that shrub encroachment will probably be accompanied by altered arthropod responses to warming and other key weather variables. Because the rate of key ecological processes – herbivory, decomposition, predation – are controlled by activity at the organismal level, these effects on arthropods will have long‐term ecosystem‐level consequences.
Increased risk of hospital admission for ICD‐9‐CM psychotic episodes following admission for epilepsy
Authors: Rossi Kyle C. , Kim Anna M. , Jetté Nathalie , Yoo Ji Yeoun , Hung Kenneth , Dhamoon Mandip S.
Published: July 2018

Objective

To determine whether epilepsy admissions are associated with a higher readmission risk for psychotic episodes compared to admissions for other medical causes.

Methods

The Nationwide Readmissions Database is a nationally representative dataset from 2013. We used International Classification of Diseases, Ninth Revision, Clinical Modification (ICD‐9‐CM) codes to identify medical conditions. There were 58 278 index admissions for epilepsy, and this group was compared against admissions for stroke (n = 215 821) and common medical causes (pneumonia, urinary tract infection [UTI], congestive heart failure [CHF], and chronic obstructive pulmonary disease [COPD], n = 973 078). Readmission rates for psychotic episodes within 90 days from discharge for index hospitalizations were calculated. Cox regression was used to test for associations between admission type and readmission for psychotic episodes up to 1 year after index admission, in univariate models and adjusted for multiple medical, social, and psychiatric variables.

Results

Up to 90 days from index admission, there were 683/100 000 readmissions for psychotic episodes in the epilepsy group, 92/100 000 in the stroke group, and 58‐206/100 000 in the medical group. The relative rate of readmission in the epilepsy group was highest in the first 30 days following index admission (311/100 000). Unadjusted hazard ratio (HR) for readmission for psychotic episodes within 1 year in the epilepsy group compared to the stroke group was 6.58 (95% confidence interval [CI] 5.69‐7.61, P < 2 × 10−16), and 4.41 compared to the medical group (95% CI 4.00‐4.85, P < 2 × 10−16). The fully adjusted HR for readmission in the epilepsy group remained elevated at 3.63 compared to the stroke group (95% CI 3.08‐4.28, P < 2 × 10−16), and 1.95 compared to the medical group (95% CI 1.76‐2.15, P < 2 × 10−16). Confounding factors most strongly associated with psychosis readmission were documented psychosis history at the time of index admission, younger age, and lower income quartile.

Significance

An epilepsy admission was independently associated with subsequent hospital readmission for psychotic episodes, even after adjustment for confounding variables.