bluuebunny/crossref_metadata_2025 huggingface dataset:
A Simulation Assessment of Model-Assisted Estimation of Steelhead Redd Abundance
Authors: McCormick Joshua L. , Ruzycki James R.
Published: July 2016

Redd abundance for steelhead Oncorhynchus mykiss is frequently estimated using design-based redd surveys. Redd abundance estimates may be biased low because redds may not be distinguishable prior to or in between sampling events (i.e., removal bias). Removal bias is typically mitigated by increasing temporal sampling intensity, thereby potentially reducing the level of spatial replication. In this study a model-assisted estimation technique to correct for removal bias was described and evaluated. Parametric survival time models were fit to redd data to estimate redd longevity and parameterize a simulation to evaluate the model-assisted estimation approach. The simulation showed increasing negative bias in redd counts not adjusted for removal bias as redd longevity decreased and as sampling intervals increased. Average bias among simulated datasets was as high as 43% using raw counts when redd longevity was relatively short at a 25-d sampling interval. Average bias was reduced to as low 1.3% using the model-assisted approach. Relative benefits of the model-assisted approach compared with traditional estimates decreased as redd longevity increased, and the accuracy of model-assisted estimates were sensitive to the function used to estimate redd longevity. The results of this study suggest that commonly used sampling intervals can potentially be increased with no appreciable increase in bias when using model-assisted estimation techniques.

Received October 7, 2015; accepted March 21, 2016 Published online July 20, 2016
Injuries during football tournaments in 45,000 children and adolescents
Authors: Kolstrup Line Agger , Koopmann Kristian Ugelvig , Nygaard Uffe Harboe , Nygaard Rie Harboe , Agger Peter
Published: July 2016

Four percent of the world's population, or 265 million people, play football, and many players are injured every year. The present study investigated more than 1800 injuries in over 45,000 youth players participating in three consecutive international football tournaments in Denmark in 2012–2014. The aim was to investigate the injury types and locations in children and adolescent football players and the differences between genders and age groups (11–15 and 16–19 years of age). An overall injury rate of 15.3 per 1000 player hours was found. The most common injury location was lower extremities (66.7%), and the most common injury type was contusion (24.4%). Girls had a relative risk of injury of 1.5 compared with boys, p < .001, and they had a higher proportion of injuries to knee and lower leg, 23.8%, than boys, 19.0%, p < .01. Boys had a higher proportion of fracture, 6.8%, as opposed to 3.3% among girls, p < .001. In conclusion, we found the youngest girls to have a higher incidence of almost all injury categories than any other group. In general, the incidence of injury decreased with age. The study provides a detailed insight into the injuries that may be expected at a large youth football tournament. These findings are of great value for organizations and healthcare professionals planning similar events and for planning injury prevention strategies, which would be of special interest in the youngest female players in general.
Validation studies of gyrokinetic ITG and TEM turbulence simulations in a JT-60U tokamak using multiple flux matching
Authors: Nakata Motoki , Honda Mitsuru , Yoshida Maiko , Urano Hajime , Nunami Masanori , Maeyama Shinya , Watanabe Tomo-Hiko , Sugama Hideo
Published: July 2016

Quantitative validation studies of flux-tube gyrokinetic Vlasov simulations on ion and electron heat transport are carried out for the JT-60U tokamak experiment. The ion temperature gradient (ITG) and/or trapped electron modes (TEM) driven turbulent transport and zonal flow generations are investigated for an L-mode plasma in the local turbulence limit with a sufficiently small normalized ion thermal gyroradius and weak mean radial electric fields. Nonlinear turbulence simulations by the GKV code successfully reproduce radial profiles of the ion and electron energy fluxes in the core region. The numerical results show that the TEM-driven zonal flow generation in the outer region is more significant than that in the core region with ITG- and ITG–TEM-dominated turbulence, leading to moderate transport shortfall of the ion energy flux. Error levels in the prediction of the ion and electron temperature gradient profiles in the core region are estimated as less than

±

30
%

, based on a multiple flux matching technique, where the simulated ion and electron energy fluxes are simultaneously matched to the experimental values.
Lipschitz slices versus linear slices in Banach spaces
Authors: Guerrero Julio , López-Pérez Ginés , Zoca Abraham
Published: July 2016

The aim of this note is to study the topology generated by Lipschitz slices in the unit sphere of a Banach space. We prove that the above topology agrees with the weak topology in the unit sphere and, as a consequence, we obtain easy Lipschitz characterizations of classical linear topics in Banach spaces as the Daugavet property, Radon-Nikodym property, convex point of continuity property and strong regularity, which shows that the above classical linear properties depend only on the natural uniformity in the Banach space given by the metric and the linear structure.
Variance adaptive shrinkage (vash): flexible empirical Bayes estimation of variances
Authors: Lu Mengyin , Stephens Matthew
Published: July 2016

Motivation: Genomic studies often involve estimation of variances of thousands of genes (or other genomic units) from just a few measurements on each. For example, variance estimation is an important step in gene expression analyses aimed at identifying differentially expressed genes. A common approach to this problem is to use an Empirical Bayes (EB) method that assumes the variances among genes follow an inverse-gamma distribution. This distributional assumption is relatively inflexible; for example, it may not capture ‘outlying’ genes whose variances are considerably bigger than usual. Here we describe a more flexible EB method, capable of capturing a much wider range of distributions. Indeed, the main assumption is that the distribution of the variances is unimodal (or, as an alternative, that the distribution of the precisions is unimodal). We argue that the unimodal assumption provides an attractive compromise between flexibility, computational tractability and statistical efficiency.

Results: We show that this more flexible approach provides competitive performance with existing methods when the variances truly come from an inverse-gamma distribution, and can outperform them when the distribution of the variances is more complex. In analyses of several human gene expression datasets from the Genotype Tissues Expression consortium, we find that our more flexible model often fits the data appreciably better than the single inverse gamma distribution. At the same time we find that in these data this improved model fit leads to only small improvements in variance estimates and detection of differentially expressed genes.

Availability and Implementation: Our methods are implemented in an R package vashr available from http://github.com/mengyin/vashr.

Contact:  mstephens@uchicago.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Sources of Geographic Variation in Health Care: Evidence From Patient
Migration*
Authors: Finkelstein Amy , Gentzkow Matthew , Williams Heidi
Published: July 2016

We study the drivers of geographic variation in U.S. health care utilization, using an empirical strategy that exploits migration of Medicare patients to separate the role of demand and supply factors. Our approach allows us to account for demand differences driven by both observable and unobservable patient characteristics. Within our sample of over-65 Medicare beneficiaries, we find that 40–50% of geographic variation in utilization is attributable to demand-side factors, including health and preferences, with the remainder due to place-specific supply factors.
Effects of Temperature, Humidity, and Wound Age on Valsa mali Infection of Apple Shoot Pruning Wounds
Authors: Chen Chong , Li Bao-Hua , Dong Xiang-Li , Wang Cai-Xia , Lian Sen , Liang Wen-Xing
Published: July 2016

Valsa canker, caused by Valsa mali, is a destructive disease of apple in China. The pathogen infects apple branches, mainly through pruning wounds, and causes branch and tree death. To determine the conditions required for V. mali infection through pruning wounds and growth within the xylem, pruning wounds on 1- to 4-year-old apple branches were inoculated with conidia in vitro under artificially controlled conditions and in vivo in the orchard. The effects of temperature, wetness duration, and wound age on conidial infection through pruning wounds as well as hyphal growth in the xylem were examined. The results showed that, after invading through pruning wounds, V. mali hyphae grew along xylem vessels, tracheids, and rays, expanding longitudinally and laterally. The hyphae could enter adjacent xylem vessels and tracheids through micropores to form a dense hyphal network. Wetness duration did not exhibit an essential effect on conidial infection from pruning wounds. Conidia spread to pruning wounds with rainwater could infect the xylem without any other extra moisture. Temperature for V. mali conidia infection through pruning wounds and hyphal extension in the xylem ranged from 5 to 35°C, with the optimum at 20°C. Pruning wounds made in late March were susceptible to V. mali infection in March, April, and May; the susceptibility was markedly deceased by June, and the pathogen could barely infect through the pruning wounds in November. The infected pruning wounds began to show symptoms from the spring of the following year. More than half of the observed Valsa canker lesions emerged in the spring of the second year, and new canker twigs were also developed from the inoculations in the spring of the third year. March, April, and May are the critical periods for protecting pruning wounds against infection by V. mali in China, and coating pruning wounds with protective film immediately after pruning is an easy and effective measure to protect the pruning wounds.
Validation of Genome-Wide Association Studies as a Tool to Identify Virulence Factors inParastagonospora nodorum
Authors: Gao Yuanyuan , Liu Zhaohui , Faris Justin D. , Richards Jonathan , Brueggeman Robert S. , Li Xuehui , Oliver Richard P. , McDonald Bruce A. , Friesen Timothy L.
Published: July 2016

Parastagonospora nodorum is a necrotrophic fungal pathogen causing Septoria nodorum blotch on wheat. We have identified nine necrotrophic effector–host dominant sensitivity gene interactions, and we have cloned three of the necrotrophic effector genes, including SnToxA, SnTox1, and SnTox3. Because sexual populations of P. nodorum are difficult to develop under lab conditions, genome-wide association study (GWAS) is the best population genomic approach to identify genomic regions associated with traits using natural populations. In this article, we used a global collection of 191 P. nodorum isolates from which we identified 2,983 single-nucleotide polymorphism (SNP) markers and gene markers for SnToxA and SnTox3 to evaluate the power of GWAS on two popular wheat breeding lines that were sensitive to SnToxA and SnTox3. Strong marker trait associations (MTA) with P. nodorum virulence that mapped to SnTox3 and SnToxA were first identified using the marker set described above. A novel locus in the P. nodorum genome associated with virulence was also identified as a result of this analysis. To evaluate whether a sufficient level of marker saturation was available, we designed a set of primers every 1 kb in the genomic regions containing SnToxA and SnTox3. Polymerase chain reaction amplification was performed across the 191 isolates and the presence/absence polymorphism was scored and used as the genotype. The marker proximity necessary to identify MTA flanking SnToxA and SnTox3 ranged from 4 to 5 and 1 to 7 kb, respectively. Similar analysis was performed on the novel locus. Using a 45% missing data threshold, two more SNP were identified spanning a 4.6-kb genomic region at the novel locus. These results showed that the rate of linkage disequilibrium (LD) decay in P. nodorum and, likely, other fungi is high compared with plants and animals. The fast LD decay in P. nodorum is an advantage only if sufficient marker density is attained. Based on our results with the SnToxA and SnTox3 regions, markers are needed every 9 or 8 kb, respectively, or in every gene, to guarantee that genes associated with a quantitative trait such as virulence are not missed.
Elevated Intraoperative Serum Lactate During Craniotomy Is Associated With New Neurological Deficit and Longer Length of Stay
Authors: Brallier Jess W. , Dalal Pavan J. , McCormick Patrick J. , Lin Hung-Mo , Deiner Stacie G.
Published: July 2016

Background:

Hundreds of thousands of craniotomies are performed annually in the United States. During craniotomy, elevated serum lactate is a concerning and not infrequent occurrence. Elevated intraoperative serum lactate may occur as a result of global hypoperfusion or localized intracerebral ischemia from surgical retraction or inadequate blood supply. The distinction between systemic and hypoperfusion confined to the brain is important because the treatment differs. For example, fluid resuscitation may be indicated in the former but not the latter.

Methods:

To address whether elevated intraoperative serum lactate is associated with hypoperfusion confined to the brain or systemic hypoperfusion, we performed a retrospective cohort study of elective adult (age above 18) craniotomy cases. These included 436 surgeries which were performed at our institution under general anesthesia between May 2011 and August 2013.

Results:

Elevated intraoperative serum lactate in craniotomy patients is associated with new neurological deficits (odds ratio, 2.11) and longer length of stay (20% less likely to be discharged on a given day). Elevated lactate was not associated with systemic complications such as myocardial infarction or mortality.

Conclusions:

Our findings highlight the importance of conducting a definitive prospective study analyzing the clinical impact and mechanism behind hyperlactatemia in the craniotomy population. Knowledge of the serum lactate level may be of value in guiding intraoperative anesthetic and surgical decision-making.
Association Between Perioperative Hyperglycemia and Survival in Patients With Glioblastoma
Authors: Hagan Katherine , Bhavsar Shreyas , Arunkumar Radha , Grasu Roxana , Dang Anh , Carlson Richard , Cowles Charles , Arnold Benjamin , Potylchansky Yuri , Rahlfs Thomas F. , Lipski Ian , Walsh Caroline , Jimenez Federico , Nguyen Anh T. , Feng Lei , Cata Juan P.
Published: July 2016

Background:

Several studies have examined the association between hyperglycemia in the first 10 to 12 weeks following surgery and postoperative survival in glioblastoma multiforme (GBM) patients. We hypothesize that episodes of hyperglycemia before, during and/or following surgery for primary GBM are independent predictors of disease progression and mortality.

Materials and Methods:

A total of 162 adult patients were included in the analysis. All patients received adjuvant temozolamide. The progression free survival (PFS) and overall survival (OS) rates at 1 and 5 years were analyzed using different glycemic cutoff values. Multivariate analyses were conducted to test the association between preoperative, intraoperative and postoperative hyperglycemia with PFS and OS.

Results:

Kaplan-Meier curves revealed a trend toward increased PFS and OS with lower glucose concentrations with the exception of glucose concentrations >180 mg/dL in the intraoperative/postoperative day 0 time period. Univariate analysis of blood glucose levels did not demonstrate a statistically significant effect on PFS in any time period, however hyperglycemia was statistically significant for OS in the preoperative time period. Although, multivariate analysis showed no statistically significant association with hyperglycemia on PFS, a statistically significant decrease in OS was seen for plasma glucose concentrations >112 mg/dL (P=0.01) and >180 mg/dL (P=0.01) in the preoperative period. There was a decreasing effect on OS with blood glucose concentrations greater than the median in multiple time periods (P=0.02).

Conclusions:

Preoperative hyperglycemia is associated with poor OS after GBM surgery.
Unlocking the Doors to Patient Satisfaction in Pediatric Orthopaedics
Authors: Peng Frederick B. , Burrows James F. , Shirley Eric D. , Rosen Paul
Published: July 2016

Background:

Despite efforts to enhance the patient experience, many health care providers continue to struggle to improve patient satisfaction as the identification of tangible quality improvement areas remains difficult. This dilemma is particularly relevant in pediatric settings, where patient satisfaction measures have not been as thoroughly studied in subspecialties such as orthopaedics. We investigate this issue to identify the major drivers of patient satisfaction in pediatric orthopaedics, which has significant financial and professional implications for both hospital administrators and health care providers. Although recent patient experience studies emphasize on improving access to care and nurturing hospitality by facilities upgrades or staff development, we hypothesized that the patient-physician relationship remains the most important factor in patients’ assessment of their experiences.

Methods:

Patient satisfaction surveys were collected from outpatient visits to pediatric orthopaedic practices at 5 locations in 3 states. Data were aggregated as monthly percentages of responses on a 5-point Likert scale. Month over month Pearson product-moment correlation coefficients were generated between top responses for “Likelihood of Your Recommending Our Practice to Others” (LTR) and other variables.

Results:

In total, 6195 families completed satisfaction surveys. The variables most predictive of likelihood to recommend the practice were “Staff Worked Together” (r=0.82), “Friendliness/Courtesy of Care Provider” (r=0.80), “Cheerfulness of Practice” (r=0.80), “Likelihood of Recommending Care Provider” (r=0.80), and “Care Provider’s Information about Medications” (r=0.78).

Conclusions:

Measurements of the patient-physician relationship, along with overall cheerfulness and staff collaboration, have the strongest relationships to LTR. These results suggest that patient satisfaction is influenced by more than just the patient-physician relationship, and may have significance in aiding pediatric orthopaedic clinics in their quality assurance/quality improvement plans of enhancing the patient experience.

Level of Evidence:

Level III—prognostic.
Pulmonary Hypertension in the Era of Mechanical Circulatory Support
Authors: Krishnamurthy Yamini , Cooper Lauren B. , Parikh Kishan S. , Felker G. Michael , Milano Carmelo A. , Rogers Joseph G. , Hernandez Adrian F. , Patel Chetan B.
Published: July 2016

Left heart disease (LHD) represents the most common cause of pulmonary hypertension (PH), and is associated with worse prognosis compared with LHD without PH. In addition, PH due to LHD may prevent patients from receiving heart transplantation, because of risk of perioperative right ventricular failure. Current literature lacks comprehensive descriptions and management strategies of PH due to LHD. In this review, we summarize the literature that is available to highlight the definition, pathogenesis, and prognosis of PH due to LHD. Furthermore, we discuss the use of mechanical circulatory support (MCS) in this population. Finally, we provide recommendations regarding the management and reassessment of PH due to LHD in the specific context of MCS.
Risk Categorization Predicts Disability in Pain‐associated Functional Gastrointestinal Disorders After 6 Months
Authors: Cunningham Natoshia R. , Jagpal Anjana , Peugh James , Farrell Michael K. , Cohen Mitchell B. , Mezoff Adam G. , Lynch‐Jordan Anne , Kashikar‐Zuck Susmita
Published: July 2016

Introduction:

For a large portion of youth, pain‐associated functional gastrointestinal disorders (FGIDs) are associated with significant impairment over time. Clinically feasible methods to categorize youth with FGIDs at greatest risk for persistent pain‐related impairment have not yet been identified.

Methods:

Measures of functional disability, pain intensity, and anxiety were collected on 99 patients with FGIDs (ages 8–18) during a visit to a pediatric gastroenterology office to assess for the presence of risk. Follow‐up data were obtained on a subset of this sample (n = 64) after 6 months, either in person or via mail. The present study examined whether a greater number of risk factors at baseline predicted greater pain‐related disability at follow‐up.

Results:

Patients were divided into 4 groups based on number of risk factors present at the initial assessment: 0 (18.2%), 1 (24.2%), 2 (26.3%), and 3 (31.3%). The presence of 2 or 3 risk factors significantly predicted greater disability at follow‐up compared to those with 0 risk factors (R2 = 0.311) and those with just 1 risk factor (Cohen's d values of –1.07 and –1.44, respectively).

Discussion:

A simple approach to risk categorization can identify youth with FGIDs who are most likely to report increased levels of pain‐related impairment over time. These findings have important clinical implications that support the utility of a brief screening process during medical care to inform referral for targeted treatment approaches to FGIDs.
The cohort effect in childhood disease dynamics
Authors: He Daihai , Earn David J. D.
Published: July 2016

The structure of school terms is well known to influence seasonality of transmission rates of childhood infectious diseases in industrialized countries. A less well-studied aspect of school calendars that influences disease dynamics is that all children enter school on the same day each year. Rather than a continuous inflow, there is a sudden increase in the number of susceptible individuals in schools at the start of the school year. Based on the standard susceptible–exposed–infectious–recovered (SEIR) model, we show that school cohort entry alone is sufficient to generate a biennial epidemic pattern, similar to many observed time series of measles incidence. In addition, cohort entry causes an annual decline in the effective transmission that is evident in observed time series, but not in models without the cohort effect. Including both cohort entry and school terms yields a model fit that is significantly closer to observed measles data than is obtained with either cohort entry or school terms alone (and just as good as that obtained with Schenzle's realistic age-structured model). Nevertheless, we find that the bifurcation structure of the periodically forced SEIR model is nearly identical, regardless of whether forcing arises from cohort entry, school terms and any combination of the two. Thus, while detailed time-series fits are substantially improved by including both cohort entry and school terms, the overall qualitative dynamic structure of the SEIR model appears to be insensitive to the origin of periodic forcing.
State-space reduction and equivalence class sampling for a molecular self-assembly model
Authors: Packwood Daniel M. , Han Patrick , Hitosugi Taro
Published: July 2016

Direct simulation of a model with a large state space will generate enormous volumes of data, much of which is not relevant to the questions under study. In this paper, we consider a molecular self-assembly model as a typical example of a large state-space model, and present a method for selectively retrieving ‘target information’ from this model. This method partitions the state space into equivalence classes, as identified by an appropriate equivalence relation. The set of equivalence classes
H
, which serves as a reduced state space, contains none of the superfluous information of the original model. After construction and characterization of a Markov chain with state space
H
, the target information is efficiently retrieved via Markov chain Monte Carlo sampling. This approach represents a new breed of simulation techniques which are highly optimized for studying molecular self-assembly and, moreover, serves as a valuable guideline for analysis of other large state-space models.
Alcohol discrimination and preferences in two species of nectar-feeding primate
Authors: Gochman Samuel R. , Brown Michael B. , Dominy Nathaniel J.
Published: July 2016

Recent reports suggest that dietary ethanol, or alcohol, is a supplemental source of calories for some primates. For example, slow lorises (
Nycticebus coucang
) consume fermented nectars with a mean alcohol concentration of 0.6% (range: 0.0–3.8%). A similar behaviour is hypothesized for aye-ayes (
Daubentonia madagascariensis
) based on a single point mutation (A294V) in the gene that encodes alcohol dehydrogenase class IV (ADH4), the first enzyme to catabolize alcohol during digestion. The mutation increases catalytic efficiency 40-fold and may confer a selective advantage to aye-ayes that consume the nectar of
Ravenala madagascariensis
. It is uncertain, however, whether alcohol exists in this nectar or whether alcohol is preferred or merely tolerated by nectarivorous primates. Here, we report the results of a multiple-choice food preference experiment with two aye-ayes and a slow loris. We conducted observer-blind trials with randomized, serial dilutions of ethanol (0–5%) in a standard array of nectar-simulating sucrose solutions. We found that both species can discriminate varying concentrations of alcohol; and further, that both species prefer the highest available concentrations. These results bolster the hypothesized adaptive function of the A294V mutation in ADH4, and a connection with fermented foods, both in aye-ayes and the last common ancestor of African apes and humans.
Force per cross-sectional area from molecules to muscles: a general property of biological motors
Authors: Rospars Jean-Pierre , Meyer-Vernet Nicole
Published: July 2016

We propose to formally extend the notion of specific tension, i.e. force per cross-sectional area—classically used for muscles, to quantify forces in molecular motors exerting various biological functions. In doing so, we review and compare the maximum tensions exerted by about 265 biological motors operated by about 150 species of different taxonomic groups. The motors considered range from single molecules and motile appendages of microorganisms to whole muscles of large animals. We show that specific tensions exerted by molecular and non-molecular motors follow similar statistical distributions, with in particular, similar medians and (logarithmic) means. Over the 1019mass (M) range of the cell or body from which the motors are extracted, their specific tensions vary asMαwithαnot significantly different from zero. The typical specific tension found in most motors is about 200 kPa, which generalizes to individual molecular motors and microorganisms a classical property of macroscopic muscles. We propose a basic order-of-magnitude interpretation of this result.
A clonally reproducing generalist aphid pest colonises diverse host plants by rapid transcriptional plasticity of duplicated gene clusters
Authors: Mathers Thomas C. , Chen Yazhou , Kaithakottil Gemy , Legeai Fabrice , Mugford Sam T. , Baa-Puyoulet Patrice , Bretaudeau Anthony , Clavijo Bernardo , Colella Stefano , Collin Olivier , Dalmay Tamas , Derrien Thomas , Feng Honglin , Gabaldón Toni , Jordan Anna , Julca Irene , Kettles Graeme J. , Kowitwanich Krissana , Lavenier Dominique , Lenzi Paolo , Lopez-Gomollon Sara , Loska Damian , Mapleson Daniel , Mauster Florian , Moxon Simon , Price Daniel R. G. , Sugio Akiko , van Munster Manuella , Uzest Marilyne , Waite Darren , Jander Georg , Tagu Denis , Wilson Alex C. C. , van Oosterhout Cock , Swarbreck David , Hogenhout Saskia A.
Published: July 2016

Background

The prevailing paradigm of host-parasite evolution is that arms races lead to increasing specialisation via genetic adaptation. Insect herbivores are no exception, and the majority have evolved to colonise a small number of closely related host species. Remarkably, the green peach aphid,Myzus persicae, colonises plant species across 40 families and singleM. persicaeclonal lineages can colonise distantly related plants. This remarkable ability makesM. persicaea highly destructive pest of many important crop species.

Results

To investigate the exceptional phenotypic plasticity ofM. persicae, we sequenced theM. persicaegenome and assessed how one clonal lineage responds to host plant species of different families. We show that genetically identical individuals are able to colonise distantly related host species through the differential regulation of genes belonging to aphid-expanded gene families. Multigene clusters collectively up-regulate in single aphids within two days upon host switch. Furthermore, we demonstrate the functional significance of this rapid transcriptional change using RNA interference (RNAi)-mediated knock-down of genes belonging to the cathepsin B gene family. Knock-down of cathepsin B genes reduced aphid fitness, but only on the host that induced up-regulation of these genes.

Conclusions

Previous research has focused on the role of genetic adaptation of parasites to their hosts. Here we show that the generalist aphid pestM. persicaeis able to colonise diverse host plant species in the absence of genetic specialisation. This is achieved through rapid transcriptional plasticity of genes that have duplicated during aphid evolution.
Postmortem genetic screening for the identification, verification, and reporting of genetic variants contributing to the sudden death of the young
Authors: Methner D. Nicole R. , Scherer Steven E. , Welch Katherine , Walkiewicz Magdalena , Eng Christine M. , Belmont John W. , Powell Mark C. , Korchina Viktoriya , Doddapaneni Harsha Vardhan , Muzny Donna M. , Gibbs Richard A. , Wolf Dwayne A. , Sanchez Luis A. , Kahn Roger
Published: July 2016

Each year in the United States, thousands of cases of sudden and unexpected deaths of infants, children, and young adults are assigned an undetermined cause of death after postmortem investigation and autopsy. Heritable genetic variants have been suggested as the cause of up to a third of sudden death (SD) cases. Elucidation of the genetic variants involved in SD cases is important to not only help establish cause and manner of death of these individuals, but to also aid in determining whether familial genetic testing should be considered. Previously, these types of postmortem screenings have not been a feasible option for most county medical examiners’ and coroners’ offices. We sequenced full exons of 64 genes associated with SD in the largest known cohort (351) of infant and young SD decedents using massively parallel sequencing at <$600 per sample. Genetic variants were assessed through literature review and clinical evaluation by a multidisciplinary consortium of experts. Thirteen individuals (3.7%), eight infants (2.8% of those <1 yr of age) and five children/young adults (7.0% of those >1 yr of age), were found to have a reportable genetic variant contributing to SD. These percentages represent an estimate lower than those previously reported. Overall yields and results likely vary between studies due to differences in evaluation techniques and reporting. Additionally, we recommend ongoing assessment of data, including nonreported novel variants, as technology and literature continually advance. This study demonstrates a strategy to implement molecular autopsies in medicolegal investigations of young SD decedents.
SMARCA4 regulates gene expression and higher-order chromatin structure in proliferating mammary epithelial cells
Authors: Barutcu A. Rasim , Lajoie Bryan R. , Fritz Andrew J. , McCord Rachel P. , Nickerson Jeffrey A. , van Wijnen Andre J. , Lian Jane B. , Stein Janet L. , Dekker Job , Stein Gary S. , Imbalzano Anthony N.
Published: July 2016

The packaging of DNA into chromatin plays an important role in transcriptional regulation and nuclear processes. Brahma-related gene-1 SMARCA4 (also known as BRG1), the essential ATPase subunit of the mammalian SWI/SNF chromatin remodeling complex, uses the energy from ATP hydrolysis to disrupt nucleosomes at target regions. Although the transcriptional role of SMARCA4 at gene promoters is well-studied, less is known about its role in higher-order genome organization.SMARCA4knockdown in human mammary epithelial MCF-10A cells resulted in 176 up-regulated genes, including many related to lipid and calcium metabolism, and 1292 down-regulated genes, some of which encode extracellular matrix (ECM) components that can exert mechanical forces and affect nuclear structure. ChIP-seq analysis of SMARCA4 localization and SMARCA4-bound super-enhancers demonstrated extensive binding at intergenic regions. Furthermore, Hi-C analysis showed extensive SMARCA4-mediated alterations in higher-order genome organization at multiple resolutions. First,SMARCA4knockdown resulted in clustering of intra-and inter-subtelomeric regions, demonstrating a novel role for SMARCA4 in telomere organization. SMARCA4 binding was enriched at topologically associating domain (TAD) boundaries, andSMARCA4knockdown resulted in weakening of TAD boundary strength. Taken together, these findings provide a dynamic view of SMARCA4-dependent changes in higher-order chromatin organization and gene expression, identifying SMARCA4 as a novel component of chromatin organization.
Crystal structure of modulated martensite and crystallographic correlations between martensite variants of Ni50Mn38Sn12alloy
Authors: Lin Chunqing , Yan Haile , Zhang Yudong , Esling Claude , Zhao Xiang , Zuo Liang
Published: July 2016

A comprehensive study on the crystal structure, the microstructure and the crystallographic features of the martensite in an Ni50Mn38Sn12alloy has been conducted in the present work. The results show that the martensite possesses a 4O modulated structure. The martensite is organized into broad plates in the original austenite grain. The plates contain irregularly shaped colonies with two characteristic microstructural patterns: a classical lamellar pattern and a herringbone pattern. Crystallographic analyses by scanning electron microscopy/electron backscatter diffraction demonstrate that in each colony there are four orientation variants (A, B, C and D) and they form three types of twins (type I, type II and compound twin). The interfaces between corresponding variants are coincident with their twinning planeK1. The interface planes of the compound twin pairs A&D and B&C can have one or two different orientations, which leads to the two microstructural patterns. The corresponding variants in neighboring colonies within one broad plate (intra-plate colonies) possess close orientations, but the type I and the type II twin relationships are interchanged. The variants in neighboring colonies situated in adjacent plates (inter-plate colonies) are type I or type II twin related but with some angular deviations. The plate interface is defined by the {221} plane of the variant pair with largest thickness. The results of the present work provide comprehensive microstructural and crystallographic information on modulated martensite in NiMnSn alloys that is useful for the understanding of their specific functionalities and helpful for further investigation on property optimization of these materials.
She’s homely, beautiful and then, hardworking!
Authors: Tijani-Adenle Ganiyat
Published: July 2016

Purpose

There are assumptions in gender-related media research that increased female status would be accompanied by more and better representation of women. There are also expectations that an increase in the number of women working in the news media will increase the positive representation of women. The aim of this paper is to critique the representation of women leaders and managers in the Nigerian press to assess the extent to which these factors have influenced the representation of women in the West African country.

Design/methodology/approach

Using two methods, qualitative content analysis and interview, this chapter critiques the representation of women leaders and managers in Nigerian Guardian Life and Vanguard Allure (over a period of six months – the last half of 2014) to determine the way women in leadership and management are constructed by checking for frames on stereotypes, gender roles and trivialisation themes. The editors of the two publications are then interviewed to consider the philosophies behind the coverage patterns and assess their knowledge and awareness of the implications of the coverage patterns on the status of women in the sub-Saharan African country.

Findings

It was discovered that the Nigerian press are focusing on re-enforcing traditional gender roles and norms rather than challenging them, and women in leadership and management in the country do not apply sufficient agency in challenging the status quo.

Research limitations/implications

Even though information derived from this study cannot be said to represent the realities in all of Africa, it surely provides a good context within which issues about media representation of women in leadership and management in Africa can be better understood to assess how the cultures on the continent’s various countries affect the realities of the lives of women.

Originality/value

The bulk of feminist research is situated in the North. Not much feminist research is being done in the South, and there appears to be an inadequate engagement with the available few in the literature. This chapter bridges the gap by presenting much needed information about gender, media and organisation in Nigeria; a highly populous multi-ethnic and multi-cultural sub-Saharan African country. Even though information derived from this study cannot be said to represent the realities in all of Africa, it will surely provide a good context within which issues about media, gender and organisation in Africa can be better appreciated.
An investigation into the different styles of the lawyer and construction specialist when mediating construction disputes
Authors: Wall Ray , Ankrah Nii , Charlson Jennifer
Published: July 2016

Purpose

The purpose of this paper is to assess the views and experiences of mediators from different professional backgrounds practising in the construction industry. Previous research shows that the legal profession dominates construction mediation in both England and Wales.

Design/methodology/approach

The phenomenological approach was used to capture the lived experiences of the interviewees and gain insight into their views and practices. The data collection was by semi-structured interviews. The data was then analysed using software to establish themes.

Findings

The major difference in mediator practice discovered between the two groups is the use of the evaluative style by lawyer and facilitative style by non-lawyer mediators. Non-lawyer mediators strongly reported their criticisms of the evaluative style in mediation suggesting that it undermines the parties’ ability to self-determine their own dispute and reduces the level of satisfaction experienced by the parties in the process of mediation. Lawyer mediators supported the use of the evaluative style as an acceptable compromise on the parties’ self-determination and feelings of satisfaction in pursuit of achieving the goal of a settlement in mediation, which was significantly better than the escalation of stress and costs to the parties in the event that the dispute escalates to litigation. In addition, mandatory mediation, the role of advisors/advocates, governance and the future of mediation were explored.

Originality/value

The research is anticipated to be of particular benefit to parties considering referring a construction dispute to mediation.
An outsider’s inside view of ethnic entrepreneurship
Authors: McPherson Mark
Published: July 2016

Purpose

This paper aims to critically reflect upon the qualitative research strategy adopted by an outsider investigating business practices between first and second-generation South Asian entrepreneurs. The paper presents, explains and justifies the methodological design and outsider strategy used to help overcome a number of operational research issues. In addition, for those considering the use of qualitative methodology for similar research, practical advice is offered to researchers whom do not share the same ethnicity as the informants under investigation.

Design/methodology/approach

To implement an outsider strategy, the methodological design draws its theoretical underpinning via a phenomenological paradigm. Issues appertaining to sample design, negotiating access, adopted research instruments are examined, and their uses to overcome potential operational issues justified.

Findings

The complexities, difficulties and successes of an outsider looking in are highlighted. Evident is the impact of personal and structural power relations between researcher and interviewee, as well as potential research problems as a result thereof. The paper stresses the need to ensure the preservation of researcher integrity, credibility and confidentiality, as he/she will encounter situations wherein he/she will be tested to the fullest.

Research limitations/implications

The research environment within the Greater London area where the respondents are located may not be as generalisable when compared with other parts of the UK and ethnic entrepreneurs therein.

Originality/value

The paper presents an evaluation of a qualitative research strategy used by an outsider to gain an inside view of ethnic entrepreneurship.
The impact of market orientation and learning orientation on organisational performance
Authors: Beneke Justin , Blampied Simon , Dewar Nadine , Soriano Linda
Published: July 2016

Purpose

This study aims to consider the impact of market orientation and learning orientation on organisational performance in the context of small- and medium-sized enterprises (SMEs) in Cape Town, South Africa. SMEs play a vital role in developing countries’ economies given their large contribution towards employment and the economic output (gross domestic product). However, many SMEs struggle to implement practices that are used to successful ends by their corporate counterparts. In view of this, this study sought to probe this issue within an emerging market context.

Design/methodology/approach

A survey of 162 enterprises, using partial least squares -structural equation modelling path modelling, was used to link the constructs of market orientation, learning orientation and organisational performance.

Findings

The results revealed a significant relationship between market orientation and organisational performance. However, in contrast to other studies in the developed world, this study found that learning orientation has neither a significant effect on organisational performance nor a moderating effect on the relationship between market orientation and organisational performance of SMEs.

Practical implications

The implications of these findings suggests that, inter alia, the organisation’s implicit marketing plans should be made explicit and shared with employees throughout the enterprise. Moreover, owners and senior managers should embrace a positive marketing philosophy and optimal organisational structure, as well as be willing to assume risks to achieve organisational objectives. However, further research is advocated to understand the nuances distinguishing developing and developed countries.

Originality/value

This is one of the first studies to consider the interrelationships between market orientation, learning orientation and organisational performance in the context of SMEs within an emerging market setting. To the best of the authors’ knowledge, this is pioneering research in the South African domain.
Understanding the midstream environment within a social change systems continuum
Authors: May Cybele , Previte Josephine
Published: July 2016

Purpose

This paper aims to provide guidance on how midstream social marketing can be used to understand and address wicked problems through adopting a collaborative systems integration approach conceptualised from a macromarketing perspective.

Design/methodology/approach

Rothschild’s motivation, opportunity and ability (MOA) framework is applied in this study to understand veterinarians as midstream microactors in the macrosystem of wicked animal welfare issues. Focus group and individual interview data from veterinarians were analysed through the lens of the MOA framework to understand veterinarians’ as midstream microactors within a systems continuum.

Findings

The MOA of veterinarians to engage downstream targets – cat owners – in behaviour change are identified. Fresh insights reveal the challenges and barriers to simply focusing on veterinarians as the key microactor required to address the wicked problem of cat overpopulation. Challenges identified include the cost of sterilisation to both owners and veterinary practices, alongside vying beliefs about the capacity of individual veterinarians to persuade owners about the benefits of sterilisation to improve animal welfare. Additionally, insight into veterinarians’ perceptions of upstream strategies to address the problem – in terms of marketing, education and law – expose further complications on where regulation and law enforcement can be integrated in future social marketing strategies to address the cat overpopulation problem.

Practical implications

The application of the MOA framework improves understanding of the concept and practice of midstream social marketing. It provides a practical and strategic tool that social marketers can apply when approaching behaviour change that leverages midstream actors as part of the social change solution.

Originality/value

Research and theorisation in this paper demonstrates an alternative pathway to address wicked problems via a collaborative systems integration approach conceptualised from a macromarketing perspective. Effective long-term change relies on understanding and coordinating a broad macrosystem of interconnected actors along a downstream, midstream and upstream continuum. This starts by understanding the microactions of individual actors within the macrosystem.