bluuebunny/crossref_metadata_2025_split huggingface dataset:
Symbiodinium population genetics: testing for species boundaries and analysing samples with mixed genotypes
Authors: Wham Drew C. , LaJeunesse Todd C. 
Published: April 2016

Population genetic markers are increasingly being used to study the diversity, ecology and evolution of Symbiodinium, a group of eukaryotic microbes that are often mutualistic with reef‐building corals. Population genetic markers can resolve individual clones, or strains, from samples of host tissue; however, samples may comprise different species that may confound interpretations of gene flow and genetic structure. Here, we propose a method for resolving species from population genetic data using tests for genetic recombination. Assigning individuals to genetically recombining populations prior to further analyses avoids critical errors in the interpretation of gene flow and dispersal. To demonstrate the effectiveness of the approach, we first apply this method to a simulated data set. We then use the method to resolve two species of host generalist Symbiodinium that commonly co‐occur in reef‐building corals collected from Indo‐West Pacific reefs. We demonstrate that the method is robust even when some hosts contain genotypes from two distinct species. Finally, we examine population genetic data sets from two recently published papers in Molecular Ecology. We show that each strongly supports a two species interpretation, which significantly changes the original conclusions presented in these studies. When combined with available phylogenetic and ecological evidence, the use of population genetic data offers a robust method for unambiguously delimiting morphologically cryptic species.
Labor Market Reforms, Temporary Workers and Wage Inequality
Authors: Kim Hyeon‐Kyeong , Skott Peter 
Published: April 2016

AbstractTemporary workers make up a sizeable part of the labor force in many countries and typically receive wages that are significantly lower than their permanent counterparts. This paper uses an efficiency wage model to explain the wage gap between temporary and permanent workers. High‐performing temporary workers may gain promotion to permanent status, and a high wage to permanent workers therefore serves a dual purpose: it affects the effort of both permanent and temporary workers. Applying the model to the Korean experience, we discuss the effects of the labor market reforms in 1998 on inequality.
A novel flagellar sheath protein, FcpA, determines filament coiling, translational motility and virulence for the Leptospira spirochete
Authors: Wunder Elsio A. , Figueira Cláudio P. , Benaroudj Nadia , Hu Bo , Tong Brian A. , Trajtenberg Felipe , Liu Jun , Reis Mitermayer G. , Charon Nyles W. , Buschiazzo Alejandro , Picardeau Mathieu , Ko Albert I. 
Published: April 2016

SummaryLeptospira are unique among bacteria based on their helical cell morphology with hook‐shaped ends and the presence of periplasmic flagella (PF) with pronounced spontaneous supercoiling. The factors that provoke such supercoiling, as well as the role that PF coiling plays in generating the characteristic hook‐end cell morphology and motility, have not been elucidated. We have now identified an abundant protein from the pathogen L. interrogans, exposed on the PF surface, and named it Flagellar‐coiling protein A (FcpA). The gene encoding FcpA is highly conserved among Leptospira and was not found in other bacteria. fcpA‐ mutants, obtained from clinical isolates or by allelic exchange, had relatively straight, smaller‐diameter PF, and were not able to produce translational motility. These mutants lost their ability to cause disease in the standard hamster model of leptospirosis. Complementation of fcpA restored the wild‐type morphology, motility and virulence phenotypes. In summary, we identified a novel Leptospira 36‐kDa protein, the main component of the spirochete's PF sheath, and a key determinant of the flagella's coiled structure. FcpA is essential for bacterial translational motility and to enable the spirochete to penetrate the host, traverse tissue barriers, disseminate to cause systemic infection and reach target organs.
Cyclic diguanylate regulation of Bacillus cereus group biofilm formation
Authors: Fagerlund Annette , Smith Veronika , Røhr Åsmund K. , Lindbäck Toril , Parmer Marthe P. , Andersson K. Kristoffer , Reubsaet Leon , Økstad Ole Andreas 
Published: April 2016

SummaryBiofilm formation can be considered a bacterial virulence mechanism. In a range of Gram‐negatives, increased levels of the second messenger cyclic diguanylate (c‐di‐GMP) promotes biofilm formation and reduces motility. Other bacterial processes known to be regulated by c‐di‐GMP include cell division, differentiation and virulence. Among Gram‐positive bacteria, where the function of c‐di‐GMP signalling is less well characterized, c‐di‐GMP was reported to regulate swarming motility in Bacillus subtilis while having very limited or no effect on biofilm formation. In contrast, we show that in the Bacillus cereus group c‐di‐GMP signalling is linked to biofilm formation, and to several other phenotypes important to the lifestyle of these bacteria. The Bacillus thuringiensis 407 genome encodes eleven predicted proteins containing domains (GGDEF/EAL) related to c‐di‐GMP synthesis or breakdown, ten of which are conserved through the majority of clades of the B. cereus group, including Bacillus anthracis. Several of the genes were shown to affect biofilm formation, motility, enterotoxin synthesis and/or sporulation. Among these, cdgF appeared to encode a master diguanylate cyclase essential for biofilm formation in an oxygenated environment. Only two cdg genes (cdgA, cdgJ) had orthologs in B. subtilis, highlighting differences in c‐di‐GMP signalling between B. subtilis and B. cereus group bacteria.
Immune responses induced by oligogalacturonides are differentially affected by AvrPto and loss of BAK1/BKK1 and PEPR1/PEPR2
Authors: Gravino Matteo , Locci Federica , Tundo Silvio , Cervone Felice , Savatin Daniel Valentin , De Lorenzo Giulia 
Published: April 2016

SummaryPlants possess an innate immune system capable of restricting invasion by most potential pathogens. At the cell surface, the recognition of microbe‐associated molecular patterns (MAMPs) and/or damage‐associated molecular patterns (DAMPs) by pattern recognition receptors (PRRs) represents the first event for the prompt mounting of an effective immune response. Pathogens have evolved effectors that block MAMP‐triggered immunity. The Pseudomonas syringae effector AvrPto abolishes immunity triggered by the peptide MAMPs flg22 and elf18, derived from the bacterial flagellin and elongation factor Tu, respectively, by inhibiting the kinase function of the corresponding receptors FLS2 and EFR, as well as their co‐receptors BAK1 and BKK1. Oligogalacturonides (OGs), a well‐known class of DAMPs, are oligomers of α‐1,4‐linked galacturonosyl residues, released on partial degradation of the plant cell wall homogalacturonan. We show here that AvrPto affects only a subset of the OG‐triggered immune responses and that, among these responses, only a subset is affected by the concomitant loss of BAK1 and BKK1. However, the antagonistic effect on auxin‐related responses is not affected by either AvrPto or the loss of BAK1/BKK1. These observations reveal an unprecedented complexity among the MAMP/DAMP response cascades. We also show that the signalling system mediated by Peps, another class of DAMPs, and their receptors PEPRs, contributes to OG‐activated immunity. We hypothesize that OGs are sensed through multiple and partially redundant perception/transduction complexes, some targeted by AvrPto, but not necessarily comprising BAK1 and BKK1.
Production and turnover of ectomycorrhizal extramatrical mycelial biomass and necromass under elevated CO2 and nitrogen fertilization
Authors: Ekblad Alf , Mikusinska Anna , Ågren Göran I. , Menichetti Lorenzo , Wallander Håkan , Vilgalys Rytas , Bahr Adam , Eriksson Ulrika 
Published: April 2016

Summary

Extramatrical mycelia (EMM) of ectomycorrhizal fungi are important in carbon (C) and nitrogen (N) cycling in forests, but poor knowledge about EMM biomass and necromass turnovers makes the quantification of their role problematic.

We studied the impacts of elevated CO2 and N fertilization on EMM production and turnover in a Pinus taeda forest. EMM C was determined by the analysis of ergosterol (biomass), chitin (total bio‐ and necromass) and total organic C (TOC) of sand‐filled mycelium in‐growth bags. The production and turnover of EMM bio‐ and necromass and total C were estimated by modelling.

N fertilization reduced the standing EMM biomass C to 57% and its production to 51% of the control (from 238 to 122 kg C ha−1 yr−1), whereas elevated CO2 had no detectable effects. Biomass turnover was high (˜13 yr−1) and unchanged by the treatments. Necromass turnover was slow and was reduced from 1.5 yr−1 in the control to 0.65 yr−1 in the N‐fertilized treatment. However, TOC data did not support an N effect on necromass turnover.

An estimated EMM production ranging from 2.5 to 6% of net primary production stresses the importance of its inclusion in C models. A slow EMM necromass turnover indicates an importance in building up forest humus.
Signals of speciation: volatile organic compounds resolve closely related sagebrush taxa, suggesting their importance in evolution
Authors: Jaeger Deidre M. , Runyon Justin B. , Richardson Bryce A. 
Published: April 2016

Summary

Volatile organic compounds (VOCs) play important roles in the environmental adaptation and fitness of plants. Comparison of the qualitative and quantitative differences in VOCs among closely related taxa and assessing the effects of environment on their emissions are important steps to deducing VOC function and evolutionary importance.

Headspace VOCs from five taxa of sagebrush (Artemisia, subgenus Tridentatae) growing in two common gardens were collected and analyzed using GC‐MS.

Of the 74 total VOCs emitted, only 15 were needed to segregate sagebrush taxa using Random Forest analysis with a low error of 4%. All but one of these 15 VOCs showed qualitative differences among taxa. Ordination of results showed strong clustering that reflects taxonomic classification. Random Forest identified five VOCs that classify based on environment (2% error), which do not overlap with the 15 VOCs that segregated taxa.

We show that VOCs can discriminate closely related species and subspecies of Artemisia, which are difficult to define using molecular markers or morphology. Thus, it appears that changes in VOCs either lead the way or follow closely behind speciation in this group. Future research should explore the functions of VOCs, which could provide further insights into the evolution of sagebrushes.
Helper and cytotoxic T‐cell subsets (Th1, Th2, Tc1, and Tc2) in benign and malignant salivary gland tumors
Authors: Haghshenas MR , Khademi B , Ashraf MJ , Ghaderi A , Erfani N 
Published: April 2016

ObjectiveThe objective of this study was to explore the prevalence of T helper type 1 (Th1; CD4+IFN‐γ +) and Th2 (CD4+IL‐4+) cells, as well as cytotoxic T cell type 1 (Tc1; CD8+IFN‐γ+) and Tc2 cells (CD8+IL‐4+) in peripheral blood of the patients with salivary gland tumors (SGTs).Subjects and Methods: Thirty new patients with SGTs and 15 healthy controls were recruited. After intracellular cytokine staining, data acquisition and analysis were performed by flow cytometry.ResultsThe mean percentages of Th1 and Tc1 cells, as well as the ratios of Th1/Th2 and Tc1/Tc2, were observed to be significantly lower in patients with malignant SGTs in comparison with controls. Furthermore, the geometric mean fluorescent intensity (geometric MFI, representing the cytokine expression intensity) for IL‐4 production by Th2 and Tc2 lymphocytes was significantly higher in patients with malignant tumors than controls. Positive correlations were observed between the mean percentage of Tc2 cells with Th2 cells, and with the tumor size in patients with benign and malignant tumors, respectively.ConclusionThe findings suggest that the imbalance of Th1/Th2 and Tc1/Tc2 ratios, as well as the increase in the expression of IL‐4 by Th2 and Tc2 lymphocytes, may contribute to the pathogenesis of SGTs, especially in malignant cases.
The art of attrition: development of robust oat microsatellites
Authors: Dumlupinar Ziya , Brown Ryan , Campbell Robert , Jellen Eric N. , Anderson Joe , Bonman J. Michael , Carson Martin , Chao Shiaoman , Obert Don , Jackson Eric 
Published: April 2016

AbstractMicrosatellite or simple sequence repeat (SSR) markers are important tools for genetic analyses, especially those targeting diversity. The primary objective of this study was to develop robust oat‐based microsatellite markers from newly enriched genomic libraries to expand on a relatively small existing oat SSR toolbox. Microsatellite motifs characterized by (CA/GT), (AAT/TTA), (ATG/TAC) and (CATC/GTAG) repeats were targeted for enrichment. Preliminary screening showed that 90% of clones from the (CA/GT) and 79% of the clones from the (ATG/TAC) libraries contained repeats, while < 11% of the clones from (AAT/TTA) and (CATC/GTAG) libraries contained repeats. Subsequent sequencing of 1536 clones from the (CA/GT) and (ATG/TAC) libraries resulted in 539 and 578 SSRs for which primers were designed, respectively. A total of 246 SSRs were polymorphic across 11 oat lines. One hundred and twenty‐five of the markers produced highly reproducible assays that interrogated 369 alleles at 193 loci. Of these, 79 robust assays interrogated 146 codominant alleles. These markers will be useful for a wide range of genetic analyses in oat including assessment of diversity and marker‐assisted breeding.
Rare presentation of small bowel intussusception in childhood
Authors: Chan Chung‐Yan Grace , Tsang Pui‐Ki Jane , Chu Ping‐Yung , Wong Yiu‐chung 
Published: April 2016

AbstractSmall bowel intussusception complicated simultaneously by volvulus in an older child is rare but clinically significant, necessitating urgent operative management. We report a local case of jejuno‐jejunal intussusception complicated by volvulus and bowel infarction in a 9‐year‐old Chinese girl, with diagnosis made on preoperative computed tomography and confirmed at laparotomy. An intestinal polyp as the lead point for intussusception was identified operatively.
Blue rubber bleb nevus syndrome with knee joint disorder
Authors: Doi Takehiko , Masumoto Natsuko , Sonoda Motoshi , Nakayama Hideki , Mizuno Yuji 
Published: April 2016

AbstractBlue rubber bleb nevus syndrome (BRBNS) involves cutaneous vascular malformation characterized by multiple venous malformations. This commonly affects the skin and gastrointestinal tract. BRBNS is associated with anemia and occasionally involves orthopedic manifestations. A 6‐year‐old boy was referred to hospital for evaluation of anemia. He presented with a rubber‐like soft‐tissue mass in the left knee and the right side of the neck, recurrent pain, and fixed flexion contracture of the knee. Blood examination indicated consumption coagulopathy and anemia caused by not only iron‐deficiency anemia but also microangiopathy. Endoscopy of the gastrointestinal tract indicated multiple bluish‐black sessile venous malformations. Ultrasonography and magnetic resonance imaging of the knee showed intra‐articular and intramuscular involvement. Based on these findings, BRBNS with knee joint disorder was diagnosed. With regard to vascular malformations, like other diseases such as inflammatory arthropathy, ultrasonography of the joint may become a new diagnostic approach for evaluating orthopedic manifestations.
Differences in constitutive and inducible defences in pine species determining susceptibility to pinewood nematode
Authors: Pimentel C. S. , Gonçalves E. V. , Firmino P. N. , Calvão T. , Fonseca L. , Abrantes I. , Correia O. , Máguas C. 
Published: April 2016

The pinewood nematode, Bursaphelenchus xylophilus, originating from North America (NA), is a major invasive pine pest in Eurasia. It was first detected in Portugal in 1999 associated with maritime pine, Pinus pinaster, and has been differently affecting the main local pine species, P. pinaster and P. pinea. Field studies and direct inoculation experiments in Pinus spp. seedlings, under controlled conditions, were performed to assess whether the differences in constitutive and inducible defences are determining the different susceptibility of pine host species to B. xylophilus. Host co‐evolution with the pathogen was also assessed, including the NA P. radiata, widely used in forestry in the northeast of the Iberian peninsula. Pine mortality in the field was positively related with the abundance of B. xylophilus, and concentration of phenolics and condensed tannins in pines. In the greenhouse assay, seedling tissues were analysed for constitutive investment in defences, as well as the potential inducibility of those defences as driven by B. xylophilus inoculation. Slower growing P. pinea presented higher levels of constitutive defences than faster growing P. pinaster, with only P. pinaster being affected by B. xylophilus. Furthermore, co‐evolution with the pathogen is important, with the fast‐growing NA P. radiata presenting an inducible and effective response to B. xylophilus. Results point to the importance of integrating data on pine life history traits, including growth rate, and production of constitutive and inducible defences, into predictive models for this invasive forest pest.
What's wrong with the back of the envelope? A call for simple (and timely) benefit–cost analysis
Authors: Carrigan Christopher , Shapiro Stuart 
Published: April 2016

AbstractObservers across the ideological spectrum have criticized benefit–cost analysis for as long as it has been part of the rulemaking process. Still, proponents and detractors agree that analysis has morphed into a mechanism often used by agencies to justify regulatory decisions already made. We argue that a simpler analysis of more alternatives conducted earlier in the regulatory process can resuscitate it as a tool to inform policy. Recognizing that requiring a procedure does not ensure that regulators will follow it, we offer possible remedies, including strengthening or relaxing subsequent review of proposed rules, which raise the cost of circumventing the reform or lower the cost of following it.
Probabilistic Multi-Resolution Scanning for Two-Sample Differences
Authors: Soriano Jacopo , Ma Li 
Published: April 2016

Summary
We propose a multi-resolution scanning approach to identifying two-sample differences. Windows of multiple scales are constructed through nested dyadic partitioning on the sample space and a hypothesis regarding the two-sample difference is defined on each window. Instead of testing the hypotheses on different windows independently, we adopt a joint graphical model, namely a Markov tree, on the null or alternative states of these hypotheses to incorporate spatial correlation across windows. The induced dependence allows borrowing strength across nearby and nested windows, which we show is critical for detecting high resolution local differences. We evaluate the performance of the method through simulation and show that it substantially outperforms other state of the art two-sample tests when the two-sample difference is local, involving only a small subset of the data. We then apply it to a flow cytometry data set from immunology, in which it successfully identifies highly local differences. In addition, we show how to control properly for multiple testing in a decision theoretic approach as well as how to summarize and report the inferred two-sample difference. We also construct hierarchical extensions of the framework to incorporate adaptivity into the construction of the scanning windows to improve inference further.
Oral habits, dental trauma, and occlusal characteristics among 4‐ to 12‐year‐old institutionalized orphan children in Riyadh, Saudi Arabia
Authors: AlSadhan Salwa A. , Al‐Jobair Asma M. 
Published: April 2016

ABSTRACTThe aim of this study was to assess the oral habit practices, dental trauma, and occlusal characteristics of 4‐ to 12‐year‐old orphans living in governmental orphanages in Riyadh. This cross‐sectional study was conducted in three government orphanages and three ordinary schools. All 90 orphans, residing in the orphanage, were included. Ninety schoolchildren were selected to serve as the controls. Demographic data, oral habit history, and dental trauma history were obtained through a questionnaire. All children were examined to confirm the presence of signs of oral habits, dental trauma, and associated occlusal characteristics. Pearson chi‐square was used for statistical analysis. Orphans were found to have more digit sucking and oral self‐mutilation habits; however, the control children were found to have more nail biting habit. Nearly 21% of the orphans had dental trauma compared to 10% of the control group. About 70% of the dental trauma affected permanent teeth among orphans, whereas, 85% affected primary teeth in the control children. Dental trauma increased as the orphans got older; however, it decreased significantly as the control children got older. Orphans were found to have more cross‐bite, increased over‐jet, and open‐bite. Digit sucking habit was positively associated with class II molar relation, presence of posterior cross‐bite, and open‐bite. Orphans had increased prevalence of digit sucking habit, self‐mutilation, dental trauma, and malocclusion.
Exploring the relationships between maternal and child metacognitions and child anxiety
Authors: Esbjørn Barbara Hoff , Normann Nicoline , Lønfeldt Nicole Nadine , Tolstrup Marie , Reinholdt‐Dunne Marie Louise 
Published: April 2016

Research has shown that anxiety may be transmitted through verbal information pathways, for example, when parents share their anxious cognitions with their child. Less is known about the influence of parental metacognitions, that is, beliefs regarding thoughts, on child anxiety. We explored the relations between metacognitions in mothers and their children and anxiety in the children. Our study included 111 non‐clinical children aged 8 to 12 years and their mothers. Children rated their metacognitions, worry and anxiety, and mothers rated their metacognitions. Results indicated agreement between maternal and child metacognitions. Maternal metacognitions were positively associated with children's anxiety symptoms and worry, and this relation was mediated by the children's metacognitions. Our results warrant further examination of the role of parental metacognitions in child anxiety.
Deciphering Deservedness: Canadian Employment Insurance Reforms in Historical Perspective
Authors: Grundy John , Laliberte Rudman Debbie 
Published: April 2016

AbstractIn 2012, the Government of Canada introduced reforms to Employment Insurance (EI), Canada's primary income security programme for the unemployed. The changes entailed new requirements for particular types of claimants to apply for and accept jobs of increasingly less pay, and codified the efforts claimants must demonstrate in job searches to maintain benefits. These measures leave many claimants little choice but to accept precarious employment as a means of financial survival. The central claim of the article is that recent EI reforms are not adequately understood as an instance of neo‐liberal activation. Instead, they must be situated in a long history of attempts to categorize the unemployed as deserving or undeserving of income security on the basis of their work history and perceptions of their willingness to work. Through a survey of different periods of unemployment policy in Canada, we demonstrate continuity in authorities' efforts to differentiate the unemployed into categories of worthy and unworthy. Within this history, however, the 2012 reforms are unprecedented in the extent to which they reorient the EI programme to service low wage labour markets. By way of conclusion, we suggest that the current EI programme exacerbates insecurities for the growing segment of workers in precarious employment.