bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis
Authors: Wen Dingqiao , Yu Yun , Hahn Matthew W. , Nakhleh Luay 
Published: January 2016

AbstractThe role of hybridization and subsequent introgression has been demonstrated in an increasing number of species. Recently, Fontaine et al. (Science, 347, 2015, 1258524) conducted a phylogenomic analysis of six members of the Anopheles gambiae species complex. Their analysis revealed a reticulate evolutionary history and pointed to extensive introgression on all four autosomal arms. The study further highlighted the complex evolutionary signals that the co‐occurrence of incomplete lineage sorting (ILS) and introgression can give rise to in phylogenomic analyses. While tree‐based methodologies were used in the study, phylogenetic networks provide a more natural model to capture reticulate evolutionary histories. In this work, we reanalyse the Anopheles data using a recently devised framework that combines the multispecies coalescent with phylogenetic networks. This framework allows us to capture ILS and introgression simultaneously, and forms the basis for statistical methods for inferring reticulate evolutionary histories. The new analysis reveals a phylogenetic network with multiple hybridization events, some of which differ from those reported in the original study. To elucidate the extent and patterns of introgression across the genome, we devise a new method that quantifies the use of reticulation branches in the phylogenetic network by each genomic region. Applying the method to the mosquito data set reveals the evolutionary history of all the chromosomes. This study highlights the utility of ‘network thinking’ and the new insights it can uncover, in particular in phylogenomic analyses of large data sets with extensive gene tree incongruence.
Development of broad virus resistance in non‐transgenic cucumber using CRISPR/Cas9 technology
Authors: Chandrasekaran Jeyabharathy , Brumin Marina , Wolf Dalia , Leibman Diana , Klap Chen , Pearlsman Mali , Sherman Amir , Arazi Tzahi , Gal‐On Amit 
Published: January 2016

SummaryGenome editing in plants has been boosted tremendously by the development of CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats) technology. This powerful tool allows substantial improvement in plant traits in addition to those provided by classical breeding. Here, we demonstrate the development of virus resistance in cucumber (Cucumis sativus L.) using Cas9/subgenomic RNA (sgRNA) technology to disrupt the function of the recessive eIF4E (eukaryotic translation initiation factor 4E) gene. Cas9/sgRNA constructs were targeted to the N′ and C′ termini of the eIF4E gene. Small deletions and single nucleotide polymorphisms (SNPs) were observed in the eIF4E gene targeted sites of transformed T1 generation cucumber plants, but not in putative off‐target sites. Non‐transgenic heterozygous eif4e mutant plants were selected for the production of non‐transgenic homozygous T3 generation plants. Homozygous T3 progeny following Cas9/sgRNA that had been targeted to both eif4e sites exhibited immunity to Cucumber vein yellowing virus (Ipomovirus) infection and resistance to the potyviruses Zucchini yellow mosaic virus and Papaya ring spot mosaic virus‐W. In contrast, heterozygous mutant and non‐mutant plants were highly susceptible to these viruses. For the first time, virus resistance has been developed in cucumber, non‐transgenically, not visibly affecting plant development and without long‐term backcrossing, via a new technology that can be expected to be applicable to a wide range of crop plants.
Echinocandin resistance and population structure of invasive Candida glabrata isolates from two university hospitals in Germany and Austria
Authors: Klotz Ulrike , Schmidt Dirk , Willinger Birgit , Steinmann Eike , Buer Jan , Rath Peter‐Michael , Steinmann Joerg 
Published: January 2016

SummaryEchinocandin resistance in Candida glabrata is emerging and is associated with the presence of FKS mutations. In this study, we analysed the antifungal susceptibility, presence of FKS mutations and clonality of C. glabrata blood culture isolates from two hospitals in Germany and Austria. Susceptibility testing of 64 C. glabrata bloodstream isolates from two university hospitals was performed with broth microdilution method according to EUCAST. In addition, all isolates were screened for FKS mutations. Molecular fingerprinting was performed by microsatellite PCR with three separate primer pairs and semiautomated repetitive sequenced‐based PCR (rep‐PCR). One C. glabrata isolate from Germany (1.5%) was echinocandin resistant, with a corresponding mutation in FKS2 gene hot spot 1. The discriminatory power of microsatellite PCR was higher than that of rep‐PCR (Simpson Index of 0.94 vs. 0.88); microsatellite PCR created 31 separate genotypes, whereas rep‐PCR created 17. Predominant genotypes or clusters of isolates from Germany and Austria were present, with no epidemiological evidence of nosocomial transmissions. Although we found a low incidence of echinocandin resistance in C. glabrata in our settings, further surveillance projects in central Europe are warranted for monitoring future epidemiological trends. The genetic population structure of C. glabrata demonstrates overrepresented geographical clusters.
The mysterious case of the public health guideline that is (almost) entirely ignored: call for a research agenda on the causes of the extreme avoidance of physical activity in obesity
Authors: Ekkekakis P. , Vazou S. , Bixby W. R. , Georgiadis E. 
Published: January 2016

SummaryPhysical activity and exercise guidelines for weight management call for at least 60 min of daily activity. However, these documents fail to acknowledge that almost no obese adults meet this target and that non‐adherence and dropout are even higher among obese individuals than the general population. The reasons for this level of activity avoidance among obese individuals remain poorly understood, and there are no evidence‐based methods for addressing the problem. Opinions among exercise scientists are polarized. Some advocate moderate intensity and long duration, whereas others call for high intensity and shorter duration. The latter approach attributes the inactivity and high dropout to limited discretionary time and the slow accrual of visible benefits. However, higher intensity has been associated with non‐adherence and dropout, whereas longer duration has not. A conceptual model is then proposed, according to which obesity interacts with intensity, causing physical activity and exercise to be associated with reduced pleasure among obese individuals. We theorize that, in turn, repeated experiences of reduced pleasure lead to avoidance. On this basis, we call for a research agenda aimed at identifying the causes of activity‐associated and exercise‐associated displeasure in obesity and, by extension, the causes of the extreme physical inactivity among obese individuals.
Anesthetic considerations for patients with Bardet–Biedl syndrome: a case series and review of the literature
Authors: Smith Bradford B. , Barbara David W. , Hyder Joseph A. , Smith Mark M. 
Published: January 2016

SummaryBackgroundBardet–Biedl syndrome (BBS) is a rare genetic condition with manifestations that can impact anesthetic and perioperative care. There is a void of literature describing the perioperative anesthetic management in this complex patient population.ObjectivesThe purpose of this retrospective series was to describe the perioperative care of patients diagnosed with BBS at a large academic tertiary referral center with experience in caring for these patients.MethodsAll patients receiving anesthesia during the time between July 10, 1997 and Jan 1, 2015 were identified. Anesthetic and perioperative records were reviewed in detail for demographic, echocardiographic, preoperative, intraoperative, and postoperative data.ResultsWe identified 12 patients with BBS undergoing 40 anesthetics at our institution. The study identified a high risk for difficult airway with need for advanced airway techniques (67% of patient's ≥18 years of age required either awake fiberoptic or video laryngoscopy techniques), cardiac abnormalities, renal impairment, morbid obesity, and intellectual disability as the main syndrome manifestations of interest to the anesthesiologist. No patient had perioperative complications directly related to BBS; however, each underwent thorough perioperative evaluation with emphasis on the systemic comorbidities associated with the syndrome. This report illustrates that patients with BBS can safely undergo anesthesia, but a detailed and often multidisciplinary preoperative evaluation is prudent.
Cognitive Penetration and the Epistemology of Perception
Authors: Silins Nicholas 
Published: January 2016

AbstractIf our experiences are cognitively penetrable, they can be influenced by our antecedent expectations, beliefs, or other cognitive states. Theorists such as Churchland, Fodor, Macpherson, and Siegel have debated whether and how our cognitive states might influence our perceptual experiences, as well as how any such influences might affect the ability of our experiences to justify our beliefs about the external world. This article surveys views about the nature of cognitive penetration, the epistemological consequences of denying cognitive penetration, and the epistemological consequences of affirming cognitive penetration.
Do restored oyster reefs benefit seagrasses? An experimental study in the Northern Gulf of Mexico
Authors: Sharma Shailesh , Goff Joshua , Moody Ryan M. , Byron Dorothy , Heck Kenneth L. , Powers Sean P. , Ferraro Carl , Cebrian Just 
Published: January 2016

AbstractOyster reefs and seagrass beds are being lost worldwide at alarming rates. These habitats provide many services to humankind and, thus, much effort has been dedicated to their restoration. Here, we examine the efficacy of created oyster reefs at enhancing seagrass beds through the amelioration of hydrographic conditions and water quality. We carried out a field experiment in the Northern Gulf of Mexico where we compared areas shoreward of created reefs with adjacent reef‐free areas over several years using a before‐after control‐impact (BACI) design. The reefs were built with oyster shell, measured 65 m, and were placed at circa 100 m from the shoreline to ensure subtidal conditions and enhance oyster recruitment. The BACI results showed few and disparate effects of the reefs, even when distance from the reef was factored in. However, we found a temporal increase in seagrass cover throughout all the experimental area (i.e. including both reef and control plots) following reef deployment. Interestingly, further analysis with satellite imagery showed the experimental area had higher seagrass cover 5 years after reef deployment than it did before reef deployment, but such increase was not observed for nearby areas. In concert, the results suggest “shadow” effects for the reefs examined, where positive effects on seagrass beds extend beyond the area directly shoreward from the reef. Oyster reef restoration may have positive impacts on shallow seagrass beds in turbid, high‐energy systems; however, more work on the extent and mechanisms for this interaction is needed.
Neutrophil extracellular traps are associated with inflammation in chronic airway disease
Authors: Wright Thomas K. , Gibson Peter G. , Simpson Jodie L. , McDonald Vanessa M. , Wood Lisa G. , Baines Katherine J. 
Published: January 2016

AbstractBackground and objectiveNeutrophil extracellular traps (NETs) are web‐like structures comprising DNA and antimicrobial proteins, expelled from neutrophils during NETosis. Persistence of NETs can be pro‐inflammatory, yet their role in respiratory disease remains unclear. This study aimed to investigate the presence of NETs in sputum from patients with asthma and COPD, and the relationship of NETs with inflammatory phenotype and disease severity.MethodsInduced sputum was collected from healthy controls, asthma and COPD patients. Extracellular DNA (eDNA) was quantified by PicoGreen. LL‐37, α‐defensins1–3, NE, IL‐1β and CXCL8 were quantified by ELISA. PAD4 and NLRP3 gene expression was performed using qPCR. NETs were imaged in sputum smears using immunofluorescence microscopy.ResultsSputum eDNA and NET neutrophil antimicrobial proteins were significantly elevated in asthma and COPD compared with healthy controls. Levels of eDNA and NET components were significantly higher in neutrophilic versus non‐neutrophilic asthma and COPD. NETs were clearly visualized in sputum smears. PAD4 mRNA was upregulated in neutrophilic COPD. The level of eDNA was higher in severe asthma. High eDNA levels were associated with heightened innate immune responses, including elevated CXCL8 and IL‐1β, and NLRP3 gene expression in both COPD and asthma. Antimicrobial proteins and eDNA were positively correlated with airway neutrophils, and negatively correlated with lung function and symptoms.ConclusionNETs are present in the airways of subjects with asthma and COPD. Accumulation of excessive NETs was associated with activation of innate immune responses contributing to disease pathogenesis in chronic airway disease.
Phantoms Never Die: Living with Unreliable Population Data
Authors: Cairns Andrew J. G. , Blake David , Dowd Kevin , Kessler Amy R. 
Published: January 2016

SummaryThe analysis of national mortality trends is critically dependent on the quality of the population, exposures and deaths data that underpin death rates. We develop a framework that allows us to assess data reliability and to identify anomalies, illustrated, by way of example, using England and Wales population data. First, we propose a set of graphical diagnostics that help to pinpoint anomalies. Second, we develop a simple Bayesian model that allows us to quantify objectively the size of any anomalies. Two-dimensional graphical diagnostics and modelling techniques are shown to improve significantly our ability to identify and quantify anomalies. An important conclusion is that significant anomalies in population data can often be linked to uneven patterns of births of people in cohorts born in the distant past. In the case of England and Wales, errors of more than 9% in the estimated size of some birth cohorts can be attributed to an uneven pattern of births. We propose methods that can use births data to improve estimates of the underlying population exposures. Finally, we consider the effect of anomalies on mortality forecasts and annuity values, and we find significant effects for some cohorts. Our methodology has general applicability to other sources of population data, such as the Human Mortality Database.
Effects of Ageing on the Immune System: Infants to Elderly
Authors: Valiathan R. , Ashman M. , Asthana D. 
Published: January 2016

AbstractPhysiological ageing is accompanied by decline in immune system function and immune alteration during ageing increases susceptibility to infections. We retrospectively analysed the data for complete blood count (CBC) and lympho‐cyte subsets from infant to elderly age groups to determine changes during ageing. Data from dual‐platform flow cytometry and CBC were analysed to determine the percentage (%) and absolute cell counts (Abs) of peripheral blood lymphocyte subsets (CD3, CD4, CD8, CD19 and CD56+16+ cells) in infants (1 month to 1 year), children (1 year to 6 years), adolescents (12 years to 18 years), adults (21 years to 50) and elderly (70 years to 92 years). Differences in plasma cytokine levels in adults and elderly were also analysed using Randox system. Comparisons among age groups from infants through adults revealed progressive declines in the percentage of total lymphocytes and absolute numbers of T and B cells. The NK cells declined from infancy to adulthood but increased in elderly participants. The percentages of T cells increased with age from infant to adulthood and then declined. Pro‐inflammatory cytokines, TNF‐α and IL‐6, were higher in elderly people compared to adults. The elderly group had significantly higher levels of monocyte chemoattractant protein‐1 (MCP‐1) and lower levels of epidermal growth factor (EGF) compared to adults. Our findings confirm and extend earlier reports on age‐related changes in lymphocyte subpopulations and data generated from this study is useful for clinicians and researchers, patient management in various age groups for the interpretation of disease‐related changes, as well as therapy‐dependent alterations.
Follicular fluorescence quantity to characterize acne severity: a validation study
Authors: Richter C. , Trojahn C. , Dobos G. , Blume‐Peytavi U. , Kottner J. 
Published: January 2016

BackgroundPorphyrins are native fluorophores in the follicle openings, visible under ultraviolet‐A light. Acne severity might be associated with increased Propionibacterium acnes colonization and porphyrin production. Aim of this study was to investigate whether the parameter fluorescence quantity can be used to measure acne severity.MethodsA validation study was conducted in 24 patients with acne using split‐face design. Acne severity was measured using Investigator Static Global Assessment scores and lesion counts. Reliability, construct validity and sensitivity to change in fluorescence quantity were investigated.ResultsMean baseline Investigator Static Global Assessment score was 2.7 (SD 0.1). Mean baseline fluorescence quantities were 24.8 (SD 4.0) on the cheek and 20.3 (SD 4.6) on the chin. On day 25, values ranged from 6.0 (SD 6.0) to 18.1 (SD 18.4) on the cheek and from 2.6 (SD 4.4) to 14.7 (SD 16.2) on the chin. The intraclass correlation coefficients of fluorescence quantity ranged from 0.513 to 0.987. Effect sizes for fluorescence measurements were highest on the chin and cheek ranging from 0.24 to 0.77 and 0.32 to 0.75, respectively.ConclusionFluorescence quantity indicates acne severity, especially on the inner cheek and chin areas. Fluorescence quantity is reliable but is not as sensitive as manual lesion counting.
Informal Governance Arrangements in the Southern Randstad: Understanding the Dynamics in a Polycentric Region
Authors: Spaans Marjolein , Zonneveld Wil 
Published: January 2016

AbstractThe Dutch Randstad is known for its polycentric configuration resulting in regional daily urban systems and planning realities that do not match formal government tiers. Over the years many informal governance structures have been proposed to address this issue. Often the rationale behind such informal arrangements is ‘to get things done’, to overcome the rigidity and inflexibility of formal administrative structures. As many other polycentric urban regions face similar issues, this analysis may help government tiers in the development of a response to the mismatch between urban structure and the architecture of formal government. The southern Randstad is one of the regions which has faced different informal governance arrangements at different scales. We discuss their emergence, aim and the participants involved as well as the reasons for the fact that different arrangements co‐exist for approximately the same area to understand the dynamics in polycentric regions as the southern Randstad.
The Scale of VGI in Map Production: A Perspective on European National Mapping Agencies
Authors: Olteanu‐Raimond Ana‐Maria , Hart Glen , Foody Giles M. , Touya Guillaume , Kellenberger Tobias , Demetriou Demetris 
Published: January 2016

AbstractThe perspective of European National Mapping Agencies (NMA) on the role of citizen sensing in map production was explored. The NMAs varied greatly in their engagement with the community generating volunteered geographic information (VGI) and in their future plans. From an assessment of NMA standard practices, it was evident that much VGI was acquired with a positional accuracy that, while less than that typically acquired by NMAs, actually exceeded the requirements of the nominal data capture scale used by most NMAs. Opportunities for VGI use in map revision and updating were evident, especially for agencies that use a continuous rather than cyclical updating policy. Some NMAs had also developed systems to engage with citizen sensors and examples are discussed. Only rarely was VGI used to collect data on features beyond the standard set used by the NMAs. The potential role of citizen sensing and so its current scale of use by NMAs is limited by a series of concerns, notably relating to issues of data quality, the nature and motivation of the contributors, legal issues, the sustainability of data source, and employment fears of NMA staff. Possible priorities for future research and development are identified to help ensure that the potential of VGI in mapping is realized.
Whooping cough in a renal transplant recipient
Authors: Garbiras M. , Shabaka A. , Calvo N. , Martin L. , Moreno M.A. , Lopez de la Manzanara V. , Sanchez‐Fructuoso A.I. 
Published: January 2016

AbstractWhooping cough is a respiratory infection with a severity that varies with age, immune status, and probably with other factors such as the degree of exposure and the virulence of the organism. The most frequent microorganism responsible for whooping cough is Bordetella pertussis. We present the case of a 62‐year‐old renal transplant recipient presenting with typical and severe manifestations of whooping cough caused by B. pertussis.
Preference Erosion – The Case of Everything But Arms and Sugar
Authors: Kopp Thomas , Prehn Sören , Brümmer Bernhard 
Published: January 2016

AbstractWhile the European Union's Everything But Arms (EBA) agreement has granted unlimited preferential access to the European market for the least developed countries (LDCs) since 2001, the sugar sector has been exempted for the first years. Only from 2009 on, the LDCs were entitled to export an unlimited amount of sugar to the EU, receiving the intervention price. The expected increase in sugar imports led the EU to substantially reduce the intervention price, besides other measures. This caused a disadvantage for countries which had been granted preferential access to the European market already: the African, Caribbean, and Pacific (ACP) countries. Our paper quantifies this erosion of preferences, employing a gravity framework. In terms of methodology we are addressing two fundamental problems well known in the gravity literature. The occurrence of excess zeros in the dependent variable of such disaggregated data is tackled with the employment of the scale‐independent negative binomial quasi generalised pseudo maximum likelihood estimator. The problem of identification is addressed by modelling the policy change with the continuous preference margin instead of using dummy variables. We find that preference erosion did occur. The ACP countries were indeed negatively affected by the consequences following the introduction of the EBA.
PKM2 released by neutrophils at wound site facilitates early wound healing by promoting angiogenesis
Authors: Zhang Yinwei , Li Liangwei , Liu Yuan , Liu Zhi‐Ren 
Published: January 2016

AbstractNeutrophils infiltration/activation following wound induction marks the early inflammatory response in wound repair. However, the role of the infiltrated/activated neutrophils in tissue regeneration/proliferation during wound repair is not well understood. Here, we report that infiltrated/activated neutrophils at wound site release pyruvate kinase M2 (PKM2) by its secretive mechanisms during early stages of wound repair. The released extracellular PKM2 facilitates early wound healing by promoting angiogenesis at wound site. Our studies reveal a new and important molecular linker between the early inflammatory response and proliferation phase in tissue repair process.