bluuebunny/crossref_metadata_2025 huggingface dataset:
Secondary Ossification Center Appearance and Closure in the Pelvis and Proximal Femur
Authors: Parvaresh Kevin C. , Upasani Vidyadhar V. , Bomar James D. , Pennock Andrew T.
Published: July 2016

Introduction:

Variable ossification patterns of the pelvis in skeletally immature patients can make the interpretation of pelvic radiographs challenging. Inconsistencies among prior studies and lack of sex comparisons underscore the need for a more comprehensive characterization of the secondary ossification centers. This study evaluates the chronology and sex differences for appearance and closure of pelvic and proximal femoral secondary ossification centers using computed tomography (CT).

Methods:

Patients who underwent abdominal and pelvic CT scans between January 2009 and December 2014 at 2 tertiary level 1 trauma centers were retrospectively reviewed. Patients between the ages of 2 and 32 years with adequate imaging of the pelvis and proximal femurs were included. Patients with a history of orthopaedic trauma or pathology affecting ossification were excluded. CT scans were assessed for the appearance and closure of the following secondary ossification centers: anterior inferior iliac spine (AIIS), anterior superior iliac spine (ASIS), femoral head (FH), greater trochanter (GT), iliac crest (IC), ischial tuberosity (IT), lesser trochanter (LT), posterior superior iliac spine (PSIS), symphysis pubis (SP), and triradiate cartilage (TRC). Basic descriptive statistics are reported.

Results:

A total of 496 CT scans met inclusion criteria (240 males and 256 females). The order of appearance of the secondary ossification centers was: (male) GT, LT, AIIS, IT, ASIS, PSIS, IC, and SP; (female) GT, LT, IT, AIIS, PSIS, IC, ASIS, and SP. The order of closure was similar: (male) TRC, LT, FH, AIIS, GT, ASIS, PSIS, IT, IC, and SP; (female) LT, TRC, AIIS, FH, GT, ASIS, PSIS, IT, IC, and SP. Female ossification centers appeared ∼1 to 2 years before males in all locations. Female ossification centers closed ∼1 to 2 years before males in all locations except TRC, IC, and SP.

Conclusions:

The appearance and closure of the pelvis and proximal femur secondary ossification centers follow a predictable pattern of development, occurring slightly earlier in females than males. Knowledge of more precise ages of development and sex differences better characterize this complex skeletal development. Future studies may use secondary ossification centers to further evaluate skeletal maturity, assess pediatric pathology, and aid surgical management.

Level of Evidence:

Level III.
Catcher’s Knee: Posterior Femoral Condyle Juvenile Osteochondritis Dissecans in Children and Adolescents
Authors: McElroy Mark J. , Riley Patrick M. , Tepolt Frances A. , Nasreddine Adam Y. , Kocher Mininder S.
Published: July 2016

Background:

Juvenile osteochondritis dissecans is an idiopathic condition involving subchondral bone and articular cartilage in skeletally immature patients in whom the growth plates are open, potentially leading to lesion instability. Because of the differing forces experienced by baseball/softball catchers versus position players, the age at which lesions develop and the characteristics of the lesions themselves may differ between these 2 populations. The purpose of the study was to examine relative age and characteristics of osteochondritis dissecans (OCD) knee lesions in catchers compared with position players.

Methods:

Using a text-based search tool that queries clinic notes and operative reports, computerized medical records from 1990 to 2014 from the Sports Medicine Program of a tertiary care Children’s Hospital were searched to find children and adolescents who had OCD of the knee, played baseball/softball, had a specified field position, and had magnetic resonance imaging of the knee. Ultimately, 98 knees (78 patients) were identified: 33 knees (29 patients) in catchers and 65 knees (49 patients) in noncatchers. Data collected included position played (catcher/noncatcher), demographics (age, unilateral/bilateral, and sex), lesion severity, and sagittal and coronal lesion location.

Results:

When compared with noncatchers, catchers presented at a younger age (P=0.035) but were similar with respect to bilateral involvement (P=0.115), sex (P=0.457), and lesion severity (P=0.484). Lesions in catchers were more posterior on the femoral condyle in the sagittal plane (P=0.004) but similar in location in the coronal plane (P=0.210).

Conclusions:

Catchers developed OCD at a younger age and in a more posterior location on the medial and lateral femoral condyles than noncatchers. These results may represent the effects of repetitive and persistent loading of the knees in the hyperflexed position required of catchers. Increased awareness of this risk may lead to surveillance and prevention programs.

Level of Evidence:

Level III—case-control study.
Ex Vivo Assessment of a Parabolic-Tip Inflow Cannula for Pediatric Continuous-Flow VADs
Authors: Griffin Michael T. , Grzywinski Matthew F. , Voorhees Hannah J. , Kameneva Marina V. , Olia Salim E.
Published: July 2016

To address the challenge of unloading the left ventricle during pediatric mechanical circulatory support using next-generation rotary blood pumps, a novel inflow cannula was developed. This unique inflow cannula for pediatric, continuous-flow, left ventricular assist devices (VADs) with a parabolic-shaped inlet entrance was evaluated alongside a bevel-tip and fenestrated-tip cannula via an ex vivo, isolated-heart experimental setup. Performance was characterized using two clinical scenarios of over-pumping and hypovolemia, created by varying pump speed and filling preload pressure, respectively, at ideal and off-axis cannula placement to assess ventricular unloading and positional sensitivity. Quantitative and qualitative assessments were performed on the resultant hemodynamics and intra-ventricular boroscopic images to classify conditions of nonsuction, partial, gradual or severe entrainment, and ventricular collapse. The parabolic-tip cannula was found to be significantly less sensitive to placement position (p < 0.001) than the bevel-tip cannula under all conditions, while not statistically different from the fenestrated cannula. Visual analysis of the parabolic-tip cannula showed complete resistance to entrainment, whereas the fenestrated-tip had partial entrainment in 90% and 87% of the over-pumping and hypovolemic studies, respectively. We conclude that future pediatric VAD designs may benefit from incorporating the parabolic-tip inflow cannula design to maximize unloading of the left ventricle in ideal and nonoptimal conditions.
Mucin gene expression in the intestine of ulcerative colitis patients: a systematic review and meta-analysis
Authors: Niv Yaron
Published: July 2016

The mucus layer of the colon is the main barrier between luminal microbes and the mucosa, and plays a significant role in the body defense mechanisms. Several studies have examined mucin gene (MUC) expression in ulcerative colitis (UC) without conclusive results. The aim of the study was to establish the knowledge of mucin expression in UC as a basis for further investigation. English medical literature searches were performed for mucin expression in the colonic mucosa of UC patients in comparison with controls. Case–control studies were included. A meta-analysis was carried out using ‘Comprehensive meta-analysis’ software. Pooled odds ratios (ORs) and 95% confidence intervals were calculated. Altogether, we found 311 eligible studies. Only 10 case–control studies from five countries fulfilled the inclusion criteria. A moderate heterogeneity was found in the studies included: Q=52.703, d.f. (Q)=15.000, I

2
=71.539%. OR for mucin expression in UC patients versus healthy controls was 1.868 with a 95% confidence interval (CI) 1.263–2.764, P=0.002. Thus, we could find a significant increase of 87% of mucin expression in UC patients. OR for MUC2 was 2.520, 95% CI 1.320–4.809, P<0.001. MUC3 was also increased with OR 2.599, 95% CI 1.389–4.861, P=0.003. Funnel plot did not indicate a significant publication bias. We found a global increase in mucin expression in UC patients, specifically in MUC2 and MUC3. Further studies are needed, especially in patients treated with biologics for mucosal healing, to understand the role of mucin expression in the natural history of UC.
Functional Dyspepsia
Authors: Romano Claudio , Valenti Simona , Cardile Sabrina , Benninga Marc A.
Published: July 2016

As defined by Rome III, there are 4 abdominal pain‐related functional gastrointestinal disorders in children: irritable bowel syndrome, functional dyspepsia (FD), abdominal migraine, and functional abdominal pain. Dyspepsia is a constellation of symptoms referable to the gastroduodenal region of the upper gastrointestinal tract. FD refers to dyspeptic symptoms that cannot currently be explained by an organic cause, and affects 25% to 40% of the adult population over a lifetime. In children, this condition results in increased specialist consultations, with reported prevalence between 3% and 27%. The Rome III criteria for pediatric FD include the presence or persistence of recurrent pain or discomfort centered in the upper abdomen, without evidence of organic disease or change in frequency of stools. Symptoms must be chronic, occurring at least weekly and over a period of at least 6 months. The goal of this article is to provide a narrative review of diagnosis and management of the FD in the pediatric population. A comprehensive search of published literature using the PubMed (http://www.ncbi.nlm.nih.gov/pubmed/) database was carried out to identify all articles published in English from 1998 to November 2015, using 3 key terms; “FD,” “functional gastrointestinal disorders,” and “children.”
Reliability and validity of the function in sitting test in nonambulatory individuals with multiple sclerosis
Authors: Sung JongHun , Ousley Cherita M. , Shen Sa , Isaacs Zadok J.K. , Sosnoff Jacob J. , Rice Laura A.
Published: July 2016

Poor seated balance negatively impacts the performance of activities of daily living in nonambulatory individuals with multiple sclerosis (MS) and is frequently a target of rehabilitation interventions. However, there is a lack of clinical measures of seated balance in nonambulatory individuals with MS, thus limiting evaluation of rehabilitation treatments. The aim of this investigation is to determine the reliability and concurrent validity of the Function in Sitting Test (FIST) as a measure of sitting balance in nonambulatory individuals with MS. Twenty nonambulatory individuals with MS [mean age±SD=56.8±10.9 years, women n=15 (75%), mean MS duration±SD=17.8±9.2 years, mean wheelchair usage duration±SD=5.9±4.7 years] underwent a FIST and posturography assessment. The FIST is a 14-item clinical functional assessment of sitting balance validated in adults with acute stroke. The seated posturography assessment involved participants sitting on a force platform without support for 30 s. On the basis of the center of pressure trajectory obtained from the force platform software, two force platform outcomes were quantified: sway area (mm2) of the center of pressure and virtual time to contact to the functional boundary (seconds). Internal consistency reliability was assessed using Cronbach’s coefficient-α. The test–retest reliability was evaluated using the intraclass correlation coefficient (ICC). Concurrent validity of the FIST was assessed by Spearman’s rank correlation analysis. Cronbach’s-α as an index of internal consistency of the FIST was 0.91. The test–retest reliability was found to be excellent (ICC=0.92). The FIST was significantly correlated with virtual time to contact to the functional boundary (ρ=0.487, P=0.02), but not with sway area (ρ=−0.267, P=0.25). The observations provide evidence that the FIST is a reliable and valid tool to assess seated postural control in nonambulatory individuals with MS.
Primary Mediastinal Classical Hodgkin Lymphoma
Authors: Piña-Oviedo Sergio , Moran Cesar A.
Published: July 2016

Primary mediastinal Classical Hodgkin lymphoma (CHL) is rare. Nodular sclerosis CHL (NS-CHL) is the most common subtype involving the anterior mediastinum and/or mediastinal lymph nodes. Primary thymic CHL is exceedingly rare. The disease typically affects young women and is asymptomatic in 30% to 50% of patients. Common symptoms include fatigue, chest pain, dyspnea and cough, but vary depending on the location and size of the tumor. B-symptoms develop in 30% of cases. By imaging, primary mediastinal CHL presents as mediastinal widening/mediastinal mass that does not invade adjacent organs but may compress vital structures as bulky disease. Histopathology is the gold standard for diagnosis. Primary mediastinal NS-CHL consists of nodules of polymorphous inflammatory cells surrounded by broad fibrous bands extending from a thickened lymph node capsule. The cellular nodules contain variable numbers of large Hodgkin/Reed-Sternberg cells, required for diagnosis. Primary thymic CHL may exhibit prominent cystic changes. The histopathologic recognition of NS-CHL can be challenging in cases with prominent fibrosis, scant cellularity, artifactual cell distortion, or an exuberant granulomatous reaction. The differential diagnosis includes primary mediastinal non-HLs, mediastinal germ cell tumors, thymoma, and metastatic carcinoma or melanoma to the mediastinum. Distinction from primary mediastinal non-HLs is crucial for adequate therapeutic decisions. Approximately 95% of patients with primary mediastinal CHL will be alive and free of disease at 10 years after treatment with short courses of combined chemoradiotherapy. In this review, we discuss the history, classification, epidemiology, clinicoradiologic features, histopathology, immunohistochemistry, differential diagnosis, and treatment of primary mediastinal CHL.
Prevalence of the Accessory Cardiac Bronchus on Multidetector Computed Tomography
Authors: Unlu Elif Nisa , Yilmaz Aydin Leyla , Bakirci Sinan , Onbas Omer
Published: July 2016

Purpose:

Accessory cardiac bronchus (ACB) is a very rare congenital anomaly and may cause some clinical complications, such as recurrent episodes of both infection and hemoptysis. The purpose of this study was to assess the multidetector computed tomography (MDCT) characteristics of ACB and to classify this anomaly according to the MDCT aspects.

Materials and Methods:

The routine thoracic CT scans from 5790 patients were evaluated retrospectively. The prevalence, location, length, diameter, division angle, distance from the carina, and the type of ACB were evaluated.

Results:

A total of 12 ACBs were identified, with a prevalence of 0.2%. All ACBs originated from the intermediate bronchus. The median largest diameter of the ACBs was 7.75 mm (range: 5.8 to 10.30 mm), the median length was 12.1 mm (range: 8.6 to 35 mm), the median division angle was 61 degrees (range: 42 to 93 degrees), and the median distance from the carina was 16.95 mm (range: 5.7 to 22.20 mm). Six cases (50%) had a blind extremity (type 1: diverticulum or stump type), 3 cases (25%) had a mutiloculated cystic change at the end (type 2: cystic type), and 3 cases (25%) had a ventilated lobulus demarcated by an anomalous fissure (type 3: ventilated type).

Conclusions:

ACBs can be classified into 3 types according to their MDCT features. Recognition of ACB is important, as it is associated with clinical complications and is also salient in trauma cases.
Levetiracetam and Valproate Retention Rate in Juvenile Myoclonic Epilepsy
Authors: Sala-Padró Jacint , Toledo Manuel , Santamarina Estevo , González-Cuevas Montserrat , Raspall-Chaure Miquel , Sueiras-Gil Maria , Quintana Manolo , Salas-Puig Xavier
Published: July 2016

Background

Valproic acid (VPA) is an effective treatment in juvenile myoclonic epilepsy (JME), but concerns on its use during pregnancy are remarkable. Levetiracetam (LEV) is approved as second-line therapy, and used as monotherapy in clinical practice. Our objective was to analyze the outcome of LEV and VPA in JME.

Materials and Methods

We analyzed patients with JME attending our epilepsy unit between 2010 and 2014, including all patients treated with LEV and/or VPA at some point of the disease course. The primary end point was drug retention rate in monotherapy after the final analysis.

Results

We identified 58 patients (62% women). All had myoclonic seizures, 86% had generalized tonic-clonic seizures (GTCS) before the diagnosis, and 9% also had absences. All had generalized spike and wave on the interictal electroencephalogram, and 86% of them also had generalized polyspike and wave discharges. In total, LEV monotherapy was maintained in 15 (65%) of 23 patients, and VPA was maintained in 37 (74%) of 50 patients (P = 0.062). In women younger than 35 years, LEV had a similar retention rate with VPA (P = 0.939). More VPA patients achieved seizure freedom during follow-up (P < 0.01), whereas LEV patients showed a trend toward higher myoclonic freedom (0.085).

Conclusions

Levetiracetam showed lower retention rate than VPA, primarily due to poorer seizure control during long-term follow-up. More LEV patients achieved myoclonic seizure freedom than VPA patients. In women younger than 35 years, LEV and VPA had comparable retention rate; therefore, LEV could be a good option for women with JME with prominent myoclonic seizures.
A physical model for low-frequency electromagnetic induction in the near field based on direct interaction between transmitter and receiver electrons
Authors: Smith Ray T. , Jjunju Fred P. M. , Young Iain S. , Taylor Stephen , Maher Simon
Published: July 2016

A physical model of electromagnetic induction is developed which relates directly the forces between electrons in the transmitter and receiver windings of concentric coaxial finite coils in the near-field region. By applying the principle of superposition, the contributions from accelerating electrons in successive current loops are summed, allowing the peak-induced voltage in the receiver to be accurately predicted. Results show good agreement between theory and experiment for various receivers of different radii up to five times that of the transmitter. The limitations of the linear theory of electromagnetic induction are discussed in terms of the non-uniform current distribution caused by the skin effect. In particular, the explanation in terms of electromagnetic energy and Poynting’s theorem is contrasted with a more direct explanation based on variable filament induction across the conductor cross section. As the direct physical model developed herein deals only with forces between discrete current elements, it can be readily adapted to suit different coil geometries and is widely applicable in various fields of research such as near-field communications, antenna design, wireless power transfer, sensor applications and beyond.
Origami mechanical metamaterials based on the Miura-derivative fold patterns
Authors: Zhou Xiang , Zang Shixi , You Zhong
Published: July 2016

This paper presents two new types of origami-inspired mechanical metamaterials based on the Miura-derivative fold patterns that consist of non-identical parallelogram facets. The analytical models to predict dimension changes and deformation kinematics of the proposed metamaterials are developed. Furthermore, by modelling the creases as revolute hinges with certain rotational spring constants, we derived analytical models for stretching and bulk moduli. The analytical models are validated through finite-element simulation results. Numerical examples reveal that the proposed metamaterials possess some intriguing properties, including negative Poisson’s ratios and bulk modulus. The work presented in this paper can provide a highly flexible framework for the design of versatile tunable mechanical metamaterials.
Weather explains high annual variation in butterfly dispersal
Authors: Kuussaari Mikko , Rytteri Susu , Heikkinen Risto K. , Heliölä Janne , von Bagh Peter
Published: July 2016

Weather conditions fundamentally affect the activity of short-lived insects. Annual variation in weather is therefore likely to be an important determinant of their between-year variation in dispersal, but conclusive empirical studies are lacking. We studied whether the annual variation of dispersal can be explained by the flight season's weather conditions in a Clouded Apollo (Parnassius mnemosyne) metapopulation. This metapopulation was monitored using the mark–release–recapture method for 12 years. Dispersal was quantified for each monitoring year using three complementary measures: emigration rate (fraction of individuals moving between habitat patches), average residence time in the natal patch, and average distance moved. There was much variation both in dispersal and average weather conditions among the years. Weather variables significantly affected the three measures of dispersal and together with adjusting variables explained 79–91% of the variation observed in dispersal. Different weather variables became selected in the models explaining variation in three dispersal measures apparently because of the notable intercorrelations. In general, dispersal rate increased with increasing temperature, solar radiation, proportion of especially warm days, and butterfly density, and decreased with increasing cloudiness, rainfall, and wind speed. These results help to understand and model annually varying dispersal dynamics of species affected by global warming.
Genetics of complex traits: prediction of phenotype, identification of causal polymorphisms and genetic architecture
Authors: Goddard M. E. , Kemper K. E. , MacLeod I. M. , Chamberlain A. J. , Hayes B. J.
Published: July 2016

Complex or quantitative traits are important in medicine, agriculture and evolution, yet, until recently, few of the polymorphisms that cause variation in these traits were known. Genome-wide association studies (GWAS), based on the ability to assay thousands of single nucleotide polymorphisms (SNPs), have revolutionized our understanding of the genetics of complex traits. We advocate the analysis of GWAS data by a statistical method that fits all SNP effects simultaneously, assuming that these effects are drawn from a prior distribution. We illustrate how this method can be used to predict future phenotypes, to map and identify the causal mutations, and to study the genetic architecture of complex traits. The genetic architecture of complex traits is even more complex than previously thought: in almost every trait studied there are thousands of polymorphisms that explain genetic variation. Methods of predicting future phenotypes, collectively known as genomic selection or genomic prediction, have been widely adopted in livestock and crop breeding, leading to increased rates of genetic improvement.
Blood thicker than water: kinship, disease prevalence and group size drive divergent patterns of infection risk in a social mammal
Authors: Benton Clare H. , Delahay Richard J. , Robertson Andrew , McDonald Robbie A. , Wilson Alastair J. , Burke Terry A. , Hodgson Dave
Published: July 2016

The importance of social- and kin-structuring of populations for the transmission of wildlife disease is widely assumed but poorly described. Social structure can help dilute risks of transmission for group members, and is relatively easy to measure, but kin-association represents a further level of population sub-structure that is harder to measure, particularly when association behaviours happen underground. Here, using epidemiological and molecular genetic data from a wild, high-density population of the European badger (Meles meles), we quantify the risks of infection withMycobacterium bovis(the causative agent of tuberculosis) in cubs. The risk declines with increasing size of its social group, but this net dilution effect conceals divergent patterns of infection risk. Cubs only enjoy reduced risk when social groups have a higher proportion of test-negative individuals. Cubs suffer higher infection risk in social groups containing resident infectious adults, and these risks are exaggerated when cubs and infectious adults are closely related. We further identify key differences in infection risk associated with resident infectious males and females. We link our results to parent–offspring interactions and other kin-biased association, but also consider the possibility that susceptibility to infection is heritable. These patterns of infection risk help to explain the observation of a herd immunity effect in badgers following low-intensity vaccination campaigns. They also reveal kinship and kin-association to be important, and often hidden, drivers of disease transmission in social mammals.
A neo-W chromosome in a tropical butterfly links colour pattern, male-killing, and speciation
Authors: Smith David A. S. , Gordon Ian J. , Traut Walther , Herren Jeremy , Collins Steve , Martins Dino J. , Saitoti Kennedy , Ireri Piera , ffrench-Constant Richard
Published: July 2016

Sexually antagonistic selection can drive both the evolution of sex chromosomes and speciation itself. The tropical butterfly the African Queen,Danaus chrysippus, shows two such sexually antagonistic phenotypes, the first being sex-linked colour pattern, the second, susceptibility to a male-killing, maternally inherited mollicute,Spiroplasma ixodeti, which causes approximately 100% mortality in male eggs and first instar larvae. Importantly, this mortality is not affected by the infection status of the male parent and the horizontal transmission ofSpiroplasmais unknown. In East Africa, male-killing of the Queen is prevalent in a narrow hybrid zone centred on Nairobi. This hybrid zone separates otherwise allopatric subspecies with different colour patterns. Here we show that a neo-W chromosome, a fusion between the W (female) chromosome and an autosome that controls both colour pattern and male-killing, links the two phenotypes thereby driving speciation across the hybrid zone. Studies of the population genetics of the neo-W around Nairobi show that the interaction between colour pattern and male-killer susceptibility restricts gene flow between two subspecies ofD. chrysippus. Our results demonstrate how a complex interplay between sex, colour pattern, male-killing, and a neo-W chromosome, has set up a genetic ‘sink' that keeps the two subspecies apart. The association between the neo-W and male-killing thus provides a ‘smoking gun' for an ongoing speciation process.
Relaxed selection during a recent human expansion
Authors: Peischl S. , Dupanloup I. , Foucal A. , Jomphe M. , Bruat V. , Grenier J.-C. , Gouy A. , Gbeha E. , Bosshard L. , Hip-Ki E. , Agbessi M. , Hodgkinson A. , Vézina H. , Awadalla P. , Excoffier L.
Published: July 2016

Humans have colonized the planet through a series of range expansions, which deeply impacted genetic diversity in newly settled areas and potentially increased the frequency of deleterious mutations on expanding wave fronts. To test this prediction, we studied the genomic diversity of French Canadians who colonized Quebec in the 17thcentury. We used historical information and records from ∼4000 ascending genealogies to select individuals whose ancestors lived mostly on the colonizing wave front and individuals whose ancestors remained in the core of the settlement. Comparison of exomic diversity reveals that i) both new and low frequency variants are significantly more deleterious in front than in core individuals, ii) equally deleterious mutations are at higher frequencies in front individuals, and iii) front individuals are two times more likely to be homozygous for rare very deleterious mutations present in Europeans. These differences have emerged in the past 6-9 generations and cannot be explained by differential inbreeding, but are consistent with relaxed selection on the wave front. Modeling the evolution of rare variants allowed us to estimate their associated selection coefficients as well as front and core effective sizes. Even though range expansions had a limited impact on the overall fitness of French Canadians, they could explain the higher prevalence of recessive genetic diseases in recently settled regions. Since we show that modern human populations are experiencing differential strength of purifying selection, similar processes might have happened throughout human history, contributing to a higher mutation load in populations that have undergone spatial expansions.
KAT: A K-mer Analysis Toolkit to quality control NGS datasets and genome assemblies
Authors: Mapleson Daniel , Garcia Accinelli Gonzalo , Kettleborough George , Wright Jonathan , Clavijo Bernardo J.
Published: July 2016

Motivation

De novoassembly of whole genome shotgun (WGS) next-generation sequencing (NGS) data beneﬁts from high-quality input with high coverage. However, in practice, determining the quality and quantity of useful reads quickly and in a reference-free manner is not trivial. Gaining a better understanding of the WGS data, and how that data is utilised by assemblers, provides useful insights that can inform the assembly process and result in better assemblies.

Results

We present the K-mer Analysis Toolkit (KAT): a multi-purpose software toolkit for reference-free quality control (QC) of WGS reads andde novogenome assemblies, primarily via their k-mer frequencies and GC composition. KAT enables users to assess levels of errors, bias and contamination at various stages of the assembly process. In this paper we highlight KAT’s ability to provide valuable insights into assembly composition and quality of genome assemblies through pairwise comparison of k-mers present in both input reads and the assemblies.

Availability

KAT is available under the GPLv3 license at:https://github.com/TGAC/KAT.

Contact

bernardo.clavijo@earlham.ac.uk

Supplementary Information

Supplementary Information (SI) is available at Bioinformatics online. In addition, the software documentation is available online at:http://kat.readthedocs.io/en/latest/.
An aging-independent replicative lifespan in a symmetrically dividing eukaryote
Authors: Spivey Eric C. , Jones Stephen K. , Rybarski James R. , Saifuddin Fatema A. , Finkelstein Ilya J.
Published: July 2016

The replicative lifespan (RLS) of a cell—defined as the number of generations a cell divides before death—has informed our understanding of the molecular mechanisms of cellular aging. Nearly all RLS studies have been performed on budding yeast and little is known about the mechanisms of aging and longevity in symmetrically dividing eukaryotic cells. Here, we describe a multiplexed fission yeast (Schizosaccharomyces pombe) lifespan micro-dissector (FYLM); a microfluidic platform for performing automated micro-dissection and high-content single-cell analysis in well-defined culture conditions. Using the FYLM, we directly observe continuous and robust replication of hundreds of individual fission yeast cells for over seventy-five cell divisions. Surprisingly, cells die without any classic hallmarks of cellular aging such as changes in cell morphology, increased doubling time, or reduced sibling health. Genetic perturbations and longevity-enhancing drugs can further extend the replicative lifespan (RLS) via an aging-independent mechanism. We conclude that despite occasional sudden death of individual cells, fission yeast does not age. These results highlight that cellular aging and replicative lifespan can be uncoupled in a eukaryotic cell.
In silico phylogenomics using complete genomes: a case study on the evolution of hominoids
Authors: Costa Igor Rodrigues , Prosdocimi Francisco , Jennings W. Bryan
Published: July 2016

The increasing availability of complete genome data is facilitating the acquisition of phylogenomic data sets, but the process of obtaining orthologous sequences from other genomes and assembling multiple sequence alignments remains piecemeal and arduous. We designed software that performs these tasks and outputs anonymous loci (AL) or anchored enrichment/ultraconserved element loci (AE/UCE) data sets in ready-to-analyze formats. We demonstrate our program by applying it to the hominoids. Starting with human, chimpanzee, gorilla, and orangutan genomes, our software generated an exhaustive data set of 292 ALs (∼1 kb each) in ∼3 h. Not only did analyses of our AL data set validate the program by yielding a portrait of hominoid evolution in agreement with previous studies, but the accuracy and precision of our estimated ancestral effective population sizes and speciation times represent improvements. We also used our program with a published set of 512 vertebrate-wide AE “probe” sequences to generate data sets consisting of 171 and 242 independent loci (∼1 kb each) in 11 and 13 min, respectively. The former data set consisted of flanking sequences 500 bp from adjacent AEs, while the latter contained sequences bordering AEs. Although our AE data sets produced the expected hominoid species tree, coalescent-based estimates of ancestral population sizes and speciation times based on these data were considerably lower than estimates from our AL data set and previous studies. Accordingly, we suggest that loci subjected to direct or indirect selection may not be appropriate for coalescent-based methods. Complete in silico approaches, combined with the burgeoning genome databases, will accelerate the pace of phylogenomics.
Stability of TaC precipitates in a Co–Re-based alloy being developed for ultra-high-temperature applications
Authors: Gilles Ralph , Mukherji Debashis , Karge Lukas , Strunz Pavel , Beran Premysl , Barbier Bruno , Kriele Armin , Hofmann Michael , Eckerlebe Helmut , Rösler Joachim
Published: July 2016

Co–Re alloys are being developed for ultra-high-temperature applications to supplement Ni-based superalloys in future gas turbines. The main goal of the alloy development is to increase the maximum service temperature of the alloy beyond 1473 K,i.e.at least 100 K more than the present single-crystal Ni-based superalloy turbine blades. Co–Re alloys are strengthened by carbide phases, particularly the monocarbide of Ta. The binary TaC phase is stable at very high temperatures, much greater than the melting temperature of superalloys and Co–Re alloys. However, its stability within the Co–Re–Cr system has never been studied systematically. In this study an alloy with the composition Co–17Re–23Cr–1.2Ta–2.6C was investigated using complementary methods of small-angle neutron scattering (SANS), scanning electron microscopy, X-ray diffraction and neutron diffraction. Samples heat treated externally and samples heatedin situduring diffraction experiments exhibited stable TaC precipitates at temperatures up to 1573 K. The size and volume fraction of fine TaC precipitates (up to 100 nm) were characterized at high temperatures within situSANS measurements. Moreover, SANS was used to monitor precipitate formation during cooling from high temperatures. When the alloy is heated the matrix undergoes an allotropic phase transformation from the ∊ phase (hexagonal close-packed) to the γ phase (face-centred cubic), and the influence on the strengthening TaC precipitates was also studied within situSANS. The results show that the TaC phase is stable and at these high temperatures the precipitates coarsen but still remain. This makes the TaC precipitates attractive and the Co–Re alloys a promising candidate for high-temperature application.
Discursive constructions of women managers in German mass media in the gender quota debate 2011-2013
Authors: Lang Rainhart , Rybnikova Irma
Published: July 2016

Purpose

This study aims to explore the main discursive images of women managers as reproduced by selected German newspapers at the time of the political debate surrounding gender quota on management boards between 2011 and 2013.

Design/methodology/approach

Drawing on critical discourse analysis according to Wodak (2001), an empirical analysis of media articles on women managers in two German newspapers, Welt and Bild, has been conducted.

Findings

The results of the study show that despite the diversity of images fabricated by the media in reference to women managers, the debate surrounding the issue of establishing a gender quota in management boards is dominated by dualistic categories and reductionist identity ascriptions, like women managers as being “over-feminine” or “over-masculine”, “exclusive” or “outsiders”.

Research limitations/implications

As the empirical focus of the study lays on two right-wing newspapers in Germany, the results do not allow for generalizations regarding the German media landscape.

Social implications

Public dispute surrounding gender quota in German companies tends to reproduce stereotypical discursive figures regarding women managers instead of challenging them. A fundamental change in the media reports on women managers is needed.

Originality/value

The research contributes to the analysis of media representations of women managers, by providing context-sensitive results from the current political debate in Germany. The findings reveal the stability of discursive structures over time, particularly gendered bias in the case of media representations of women managers, notwithstanding political aspirations to change established practices.
Bodies, sexualities and women leaders in popular culture: from spectacle to metapicture
Authors: Bell Emma , Sinclair Amanda
Published: July 2016

Purpose

This paper focuses on visual representation of women leaders and how women leaders’ bodies and sexualities are rendered visible in particular ways.

Design/methodology/approach

The arguments are based on a reading of the Danish television drama series, Borgen. The authors interpret the meaning of this text and consider what audiences might gain from watching it.

Findings

The analysis of Borgen highlights the role of popular culture in resisting patriarchal values and enabling women to reclaim leadership.

Originality/value

The metaphor of the spectacle enables explanation of the representation of women leaders in popular culture as passive, fetishised objects of the masculine gaze. These pervasive representational practices place considerable pressure on women leaders to manage their bodies and sexualities in particular ways. However, popular culture also provides alternative representations of women leaders as embodied and agentic. The notion of the metapicture offers a means of destabilising confining notions of female leadership within popular culture and opening up alternatives.
Toward a research roadmap for construction mediation
Authors: Ilter Deniz , Irlayici Cakmak Pinar , Arici Ustuner Yaprak , Tas Elcin
Published: July 2016

Purpose

This paper aims to outline the state-of-the-art and research contributions in the construction mediation domain to determine whether existing research is compatible with a future scenario envisioning a wider adoption and more systemised use of mediation in the construction industry and to develop a research agenda based on key challenges facing mediation.

Design/methodology/approach

A systematic procedure based on keywords was adopted for the selection of relevant research contributions in the area, and a meta-classification framework has been designed based on independent classifications of the content, method and authorship to analyse the publications.

Findings

Research contributions in the past decade mostly focused on perceptions of professionals on mediation and the dynamics of the mediation process and mediator tactics. Based on the challenges identified, proposed research agenda includes court-connected mediation, mediation in public projects, project mediation, documentation of case studies of mediation applications and use of IT in mediation.

Research limitations/implications

The publications investigated in this study are limited to scholarly articles published in the mainstream construction management journals and can be expanded to books or articles published in law journals if required.

Originality/value

Existing literature includes important contributions regarding many aspects of construction mediation, however, a holistic agenda is lacking to overcome the key challenges to the widespread use of mediation in the construction sector. The research directions presented in this paper is expected to contribute to the proliferation of the neglected areas and constitute the basis for the development of a research roadmap in the construction mediation domain.
Construction mediation in Scotland
Authors: Trushell Ian , Clark Bryan , Agapiou Andrew
Published: July 2016

Purpose

This paper aims to address the knowledge gap, by exploring the attitudes and experiences of mediators relative to the process, based on research with practitioners in Scotland. Recent research on construction mediation in Scotland has focused exclusively on construction lawyers’ and contractors’ interaction with the process, without reference to the views of mediators themselves.

Design/methodology/approach

The entire research design of this research was constrained by the small population of practising Scottish construction mediators (thought to be circa. 20 in 2013). The design encompassed a literature search, participant interviews, questionnaire survey and qualitative and quantitative data. The research questionnaire was designed to capture data related to the biography, training and experience of those interviewed before their opinion on the benefits of, and problems with, mediation were sought.

Findings

The results indicate that mediations failed because of ignorance, intransigence and over-confidence of the parties. Barriers to greater use of mediation in construction disputes were identified as the lack of skilled, experienced mediators, the continued popularity of adjudication and both lawyer and party resistance. Notwithstanding the English experience, Scottish mediators gave little support for mandating disputants to mediate before proceeding with court action. A surprising number were willing to give an evaluation of the dispute rather than merely facilitating a settlement.

Originality/value

There are few experienced construction mediators in Scotland, and the continued popularity of statutory adjudication is a significant barrier. Mediators believe that clients’ negative perceptions of mediation are a bigger barrier than lawyers’ perceptions. The mediators wanted judicial encouragement for mediation backed by some legislative support, mediation clauses incorporated into construction contracts and government adoption of mediation as the default process in its own contracts.
Multilevel marketing and entrepreneurship in Thailand
Authors: Hatchaleelaha Somchai , Wongsurawat Winai
Published: July 2016

Purpose

The purpose of this research is to trace the development of a major player in the health/wellness direct sales industry in Thailand and draw lessons about growth strategies and approaches in dealing with common entrepreneurial challenges.

Design/methodology/approach

In preparing the case study narrative, primary data from the direct experience of the company founder were combined with secondary sources of information on the landscape of direct sales industry in Thailand. Key lessons were developed from discussion and reflection on experiences of people involved in the development of the company.

Findings

A multi-billion baht, direct sales business with over 100,000 members was built from the ground up in a span of one decade. Recruiting and retaining members with the right level of entrepreneurial drive is a constant challenge for the growing venture. Incorporating new technology to help manage information about members, customers and stock will play a central role in creating future growth opportunities.

Research limitations/implications

The research represents a single case study so generalization is naturally limited.

Originality/value

Direct sales entails a considerable amount of stigma, resulting in a limited number of frank and detailed analysis of such businesses and their founding entrepreneurs. This study represents an attempt to fill this gap and will hopefully stimulate more investigation into a business model that appears to be thriving in many emerging economies in Southeast Asia.
Emerging market global business model innovation
Authors: Oyedele Adesegun
Published: July 2016

Purpose

Developing a global business model requires a clear understanding of the market conditions in the global marketplace. The aim of this study was to evaluate the effect of emerging market conditions on the key building blocks of Osterwalder’s business model canvas.

Design/methodology/approach

The paper explains the basic framework of Osterwalder’s business model and evaluation of relevant dimensions of emerging market characteristics and the effect of these dimensions on creating global business models in emerging markets.

Findings

Global business models in emerging market must evaluate and account for important market conditions, such as the power of non-governmental institutions, the effect of clientelism and prevalence of informal institutional flux.

Practical implications

When developing a global business model, researchers and managers should understand market conditions will not only shape the cost structure and revenue stream but also make a company to change its value proposition entirely.

Originality/value

The main value of this paper is recognizing and assessing the effects of emerging market conditions on Osterwalder’s business model framework.
Prospects of microbial cell factories developed through systems metabolic engineering
Authors: Gustavsson Martin , Lee Sang Yup
Published: July 2016

While academic‐level studies on metabolic engineering of microorganisms for production of chemicals and fuels are ever growing, a significantly lower number of such production processes have reached commercial‐scale. In this work, we review the challenges associated with moving from laboratory‐scale demonstration of microbial chemical or fuel production to actual commercialization, focusing on key requirements on the production organism that need to be considered during the metabolic engineering process. Metabolic engineering strategies should take into account techno‐economic factors such as the choice of feedstock, the product yield, productivity and titre, and the cost effectiveness of midstream and downstream processes. Also, it is important to develop an industrial strain through metabolic engineering for pathway construction and flux optimization together with increasing tolerance to products and inhibitors present in the feedstock, and ensuring genetic stability and strain robustness under actual fermentation conditions.
ICT Activity, Innovation and Productivity: An Analysis of Data From Australian Businesses
Authors: Reeson Andrew , Rudd Lachlan
Published: July 2016

Longitudinal firm level data are used to examine the short‐term impact of information and communications technology (ICT) investment and innovation on Australian businesses. ICT activity is found to be correlated with increased rates of innovation across all aspects of business. Firms which increase their ICT investment are also more likely to subsequently report increased productivity, though this effect does not appear to be causal. IT investment was most clearly associated with increased productivity and profitability in the manufacturing, construction and transport industry sector. The results suggest that the impact of ICT investment within a firm is mediated by broader innovations in business practice.