bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fitness Landscapes Reveal Simple Strategies for Steering Evolution to Minimize Antibiotic Resistance
Authors: Smith Maria , Cobey Sarah 
Published: December 2016

AbstractThe evolution of antibiotic resistance presents a practical and theoretical challenge: the design of strategies that limit the risk of evolved resistance while effectively treating current patients. Sequentially cycling antibiotics has been proposed as a way to slow the evolution of resistance by reducing the extent of adaptation to a given drug, and clinical trials have demonstrated its effectiveness in some settings. Empirical fitness landscapes in theory allow the sequence of drugs to be refined to maximize tradeoffs between drugs and thereby slow adaptation even further. Using the measured growth rates of 16 genotypes ofEscherichia coliin the presence ofβ-lactam antibiotics, we test an adaptive strategy, based on a Markov chain transition matrix, to select drug sequences that continuously minimize resistance. Cycling is never selected over the long term. Instead, monotherapy with the antibiotic that permits the least growth in its landscape’s absorbing state is rapidly selected from different starting conditions. Analysis of a synthetic fitness landscape shows that cycling drugs that induce sensitivity to one other could, in theory, outperform monotherapy. These results underscore the importance of considering the specific topologies of fitness landscape in determining whether to cycle drugs and suggest a general computational approach to identify high performing, practical strategies to manage resistance.
Cell-to-cell variability in the yeast pheromone response: high throughput screen identifies genes with different effects on transmitted signal and response
Authors: Pesce C. G. , Peria W. , Zdraljevic S. , Rockwell D. , Yu R. C. , Colman-Lerner A. , Brent R. 
Published: December 2016

AbstractPopulations of isogenic cells often respond coherently to signals despite differences in protein abundance and cell state. Our previous work in theSaccharomyces cerevisiaepheromone response system (PRS) uncovered processes that reduced cell-to-cell variation in signal and response. To understand these and other processes that controlled variation, we generated a whole-genome collection of haploid strains with deletions in non-essential genes and used high-throughput flow cytometry to screen more than 1000. We identified 50 “variation genes” required for normal cell-to-cell variability in signal and response. Some genes affected only signal variability, signal strength, or system output, defining these quantities as separable “axes” of system behavior. Two genes affected cytoplasmic microtubule function.
Microbial Genome-Wide Association Studies: Lessons from Human GWAS
Authors: Power Robert A. , Parkhill Julian , de Oliveira Tulio 
Published: December 2016

AbstractThe reduced costs of sequencing have led to the availability of whole genome sequences for a large number of microorganisms, enabling the application of microbial genome wide association studies (GWAS). Given the successes of human GWAS in understanding disease aetiology and identifying potential drug targets, microbial GWAS is likely to further advance our understanding of infectious diseases. By building on the success of GWAS, microbial GWAS have the potential to rapidly provide important insights into pressing global health problems, such as antibiotic resistance and disease transmission. In this review, we outline the methodologies of GWAS, the state of the field of microbial GWAS today, and how lessons from GWAS can direct the future of the field.
Knowledge management and total quality management: a reciprocal relationship
Authors: Honarpour Amir , Jusoh Ahmad , Long Choi Sang 
Published: December 2016

Purpose
This research is an effort to conceptualize the relationship between total quality management (TQM) and knowledge management in a new way. While some researchers considered knowledge management as a facilitator of TQM other scholars concerned TQM as an antecedent for knowledge management. The purpose of this paper is to propose a reciprocal causation between TQM and knowledge management.

Design/methodology/approach
The main focus of literature review is focusing on common practices of TQM and knowledge management. In the next step, joint variance analysis method is used to reanalyze the results of the empirical studies linking TQM to knowledge management. This approach aims to divide the multiple correlation squared and demonstrate what portion is distinctly connected to predictor variables and what portion is on account of common variance among predictors.

Findings
The result indicates that nearly half of all explained variances in empirical studies that considered the relationship between TQM and knowledge management disregarding the criteria are accounted for the joint variance of TQM and knowledge management processes. Therefore a reciprocal causation between TQM and knowledge management can be formulated.

Originality/value
This research is one of the first studies which explores the diverse results of the relationship between TQM and knowledge management from a methodological perspective.
Involvement of high mobility group box‐1 in imiquimod‐induced psoriasis‐like mice model
Authors: Chen Tao , Fu Li‐xin , Guo Zai‐pei , Yin Bin , Cao Na , Qin Sha 
Published: December 2016

AbstractIn the previous work, we have indicated that HMGB1, a pro‐inflammatory cytokine, is closely associated with the pathogenesis of psoriasis. To further clarify the role of HMGB1 in the pathogenesis of psoriasis, we investigated the direct function of HMGB1 application and HMGB1 blockade in imiquimod (IMQ)‐induced psoriatic mouse model in this study. Mice were treated with imiquimod (IMQ) to induce psoriasis‐like inflammation, and consecutively injected with recombinant HMGB1 or phosphate‐buffered saline (PBS) i.d. Abundant cytoplasmic expression of HMGB1 was observed in lesional skin from IMQ‐treated skin. The injection of HMGB1 into the IMQ‐treated skin further aggravated the psoriasis‐like disease, enhanced the infiltration of CD3+ T cells, myeloperoxidase+ neutrophils and CD11c+ dendritic cells, increased the number of γδ T cells, and upregulated the mRNA expression of interleukin (IL)‐6, tumor necrosis factor (TNF)‐α, interferon (IFN)‐γ and IL‐17 compared with the PBS injection. Finally, by using anti‐HMGB1 monoclonal antibody or HMGB1 inhibitor glycyrrhizin, we indicated that HMGB1 blockade reduced the number of γδ T cells, suppressed the mRNA expression of IL‐6, TNF‐α, IFN‐γ and IL‐17, and moderated clinical and histological evolvement in the IMQ‐treated skin. Our data suggest that HMGB1 may act as a pro‐inflammatory cytokine, and contribute to the development of IMQ‐induced psoriasis‐like inflammation. HMGB1 blockade may represent a new direction in the suppression of psoriasis.
Invasive plant removal: assessing community impact and recovery from invasion
Authors: Guido Anaclara , Pillar Valério D. 
Published: December 2016

Summary

Invasive species spread on natural ecosystems is one of the most important causes of biodiversity loss. To disentangle the invasive plant impact on communities it is essential to combine experimental and observation approaches, which enable the correct interpretations of results and lead to the right decisions for management.

We examined the invasion of southern Brazil's grasslands by Eragrostis plana, which is currently the most problematic invasive species in the region. By means of an experiment on invaded communities complemented by observation of non‐invaded communities, we assessed E. plana impact on vegetation, evaluated community response to its removal and discussed the effectiveness of removal methods. Fifty permanent 1 × 1 m plots were located on natural grassland that was partially invaded by E. plana. Removal was done annually from 2012 to 2015 and consisted of five treatments (n = 10): (i) clipping above‐ground biomass on one occasion; (ii) clipping above‐ground biomass periodically; (iii) herbicide and (iv) hand‐pulling, plus (v) control treatment with no‐removal. In addition, 10 plots located in an adjacent non‐invaded area were monitored.

All removal treatments reduced E. plana cover across years, but were not enough to eradicate it. Our results revealed not only differences between invaded and non‐invaded communities, but also an effect of E. plana removal on resident species richness and total cover.

At the local scale, we demonstrated the impact of E. plana invasion on grassland vegetation, suggesting a reduction in resident species richness and total cover. Invasive species removal changed communities differently from invaded ones, but not resembling non‐invaded references, suggesting that community recovery may need more time for reestablishment or that some restoration strategies are required.

Synthesis and applications. This study demonstrated the impact on vegetation of the most important invasive species in southern Brazil's natural grasslands. We highlighted the advantages of combining observations of non‐invaded communities and experimental studies on invaded communities, with and without invasive removal, to help infer causal relationships in ecological invasion research.
Phenotypic plasticity in freshwater picocyanobacteria
Authors: Huber Paula , Diovisalvi Nadia , Ferraro Marcela , Metz Sebastián , Lagomarsino Leonardo , Llames María Eugenia , Royo‐Llonch Marta , Bustingorry José , Escaray Roberto , Acinas Silvia G. , Gasol Josep M. , Unrein Fernando 
Published: December 2016

SummaryPicocyanobacteria can occur as single‐cell (Pcy) or as colonies (CPcy). Published evidence suggests that some Pcy strains have the capability to aggregate under certain culture conditions, however this has not been demonstrated to occur in natural environments. We investigated whether the Pcy and CPcy belong to the same species (i.e. phylotype), and the factors that determine their morphological and genetic variability in a hypertrophic shallow lake dominated by picocyanobacteria. Six main different morphologies and >30 phylotypes were observed. All sequences retrieved belonged to the ‘Anathece + Cyanobium’ clade (Synechococcales) that are known to have the capability of aggregation/disaggregation. The temporal variation of picocyanobacteria morphotype composition was weakly correlated with the DGGE temporal pattern, and could be explained by the composition of the zooplankton assemblage. Laboratory experiments confirmed that the small cladoceran Bosmina favoured the dominance of CPcy, i.e. Cyanodictyon doubled the size of the colonies when present, most likely through the aggregation of single‐cell picocyanobacteria into colonies. Flow cytometry cell sorting and 16S rRNA + ITS sequencing of the Pcy and CPcy cytometrically‐defined populations revealed that some phylotypes could be found in both sorted populations, suggesting phenotypic plasticity in which various Synechococcales phylotypes could be found in situ either as single‐cells or as colonies.
Characterization of the first cultured representative of a Bacteroidetes clade specialized on the scavenging of cyanobacteria
Authors: Ben Hania Wajdi , Joseph Manon , Bunk Boyke , Spröer Cathrin , Klenk Hans‐Peter , Fardeau Marie‐Laure , Spring Stefan 
Published: December 2016

SummaryThe anaerobic, mesophilic and moderately halophilic strain L21‐Spi‐D4T was recently isolated from the suboxic zone of a hypersaline cyanobacterial mat using protein‐rich extracts of Arthrospira (formerly Spirulina) platensis as substrate. Phylogenetic analyses based on 16S rRNA genes indicated an affiliation of the novel strain with the Bacteroidetes clade MgMjR‐022, which is widely distributed and abundant in hypersaline microbial mats and heretofore comprised only sequences of uncultured bacteria. Analyses of the complete genome sequence of strain L21‐Spi‐D4T revealed a possible specialization on the degradation of cyanobacterial biomass. Besides genes for enzymes degrading specific cyanobacterial proteins a conspicuous transport complex for the polypeptide cyanophycin could be identified that is homologous to typical polysaccharide utilization loci of Bacteroidetes. A distinct and reproducible co‐occurrence pattern of environmental 16S rRNA gene sequences of the MgMjR‐022 clade and cyanobacteria in the suboxic zone of hypersaline mats points to a specific dependence of members of this clade on decaying cyanobacteria. Based on a comparative analysis of phenotypic, genomic and ecological characteristics we propose to establish the novel taxa Salinivirga cyanobacteriivorans gen. nov., sp. nov., represented by the type strain L21‐Spi‐D4T, and Salinivirgaceae fam. nov., comprising sequences of the MgMjR‐022 clade.
Impact of Christmas on bowel preparation for endoscopic examination of the lower gastrointestinal tract
Authors: Sutton Paul A. , Burley Natalie M.Y. , Glover Jane , Titu Liviu V. 
Published: December 2016

AimThe aim of the present study was to evaluate the impact of Christmas on the efficacy of bowel cleansing performed prior to endoscopic examination of the lower gastrointestinal tract.Patients and methodsA retrospective review of contemporaneous endoscopy reports at a single institution was undertaken. The quality of bowel preparation in patients undergoing lower gastrointestinal endoscopy over a period of 7 days immediately following 25 December in 2013, 2014 and 2015 was compared to the unit average for the corresponding year.ResultsThe proportion of patients with poor bowel preparation was significantly higher in each of the Christmas weeks compared to the unit average for the corresponding year, specifically 36.6 per cent vs 21.1 per cent in 2013 (
P
= 0.032), 22 per cent vs 17.8 per cent in 2014 (
P
= 0.011) and 24.4 per cent vs 17.4 per cent in 2015 (
P
= 0.008). Pooling data over the study period suggested that the incidence of poor preparation between Christmas and New Year was 26.4 per cent vs 18.7 per cent for the remainder of the year (
P
= 0.006).ConclusionChristmas results in a higher proportion of poor bowel preparation. While causality cannot be determined in the present study, we suggest that the residue from Christmas dinner combined with poor compliance with bowel preparation due to satiety from overconsumption are likely to be responsible. Endoscopy units should consider providing additional and specific dietary advice to patients who are undergoing examination during the festive period.
UV reflectance is associated with environmental conditions in Palaearctic Pieris napi (Lepidoptera: Pieridae)
Authors: Stella David , Pecháček Pavel , Meyer‐Rochow Victor Benno , Kleisner Karel 
Published: December 2016

AbstractThe subject of our investigation was the visual features of wing color with special focus on the UV reflectance in the green‐veined white butterfly (Pieris napi). Previous studies had concluded that UV reflectance on dorsal wing surfaces is found only in the female P. napi. Based on UV sensitive photography, we analyzed a correlation between 12 geographic and environmental factors and UV reflectance patterns on 3 patches on the forewings of 407 P. napi specimens from the Palaearctic region. Results had shown that females significantly differ from males: they exhibit a 25% higher UV reflectance. To investigate whether and how UV reflectance levels on the forewings and hindwings of both sexes are influenced by the environment, we performed a principal component analysis (PCA) with several environmental variables. For several variables (in particular, latitude and longitude, mean annual temperature and precipitation, and temperature annual range and altitude), the generalized linear model (GLM) model revealed a significant correlation in both sexes. This suggests a link between UV reflectance levels and the environment and distribution of P. napi. We found that stronger UV reflectance is associated with generally more hostile environments and concluded that large‐scale environmental factors influence the UV reflectance on the forewings of both male and female green‐veined white butterflies.
HLA‐DRB1shared epitope alleles in patients with rheumatoid arthritis: relation to autoantibodies and disease severity in a south Indian population
Authors: Konda Mohan Vasanth , Ganesan Nalini , Gopalakrishnan Rajasekhar , Venkatesan Vettriselvi 
Published: December 2016

AbstractAimTo investigate the presence of the ‘shared epitope’ (SE) in theHLA‐DRB1alleles in patients withRAand to ascertain the frequency of theHLA‐DRB1alleles with autoantibodies (anti‐cyclic citrullinated peptide [anti‐CCP] rheumatoid factor [RF]) and disease severity.MethodsA total of 200RApatients and 200 apparently healthy subjects participated in the study.HLA‐DRB1were genotyped using polymerase chain reaction with sequence‐specific primer (PCR‐SSP). Anti‐CCPandRFin serum were determined byin vitroquantitative enzyme‐linked immunosorbent assay (ELISA) method. Erythrocyte sedimentation rate (ESR) was measured by Westergren method. Disease activity was assessed by using the disease activity score‐28 (DAS‐28). Chi‐square test and Student'st‐test were used in the statistical analysis.ResultsA significant increase in the frequency ofHLA‐DRB1*01, *04, *10 and *14 were identified inRApatients and showed a strong association with the disease susceptibility. While the frequencies ofHLA‐DRB1*03, *07, *11 and *13 were significantly lower inRApatients than in controls. The otherHLA‐DRB1alleles *08, *09, *12, *15 and *16 showed no significant difference. The frequency of anti‐CCPandRFantibodies did not showed significant difference inSE‐positive patients compared withSE‐negative patients.DAS‐28 values ofRApatients showed no significant difference betweenSE‐positive andSE‐negative groups.ConclusionOur results indicate thatHLA‐DRB1*01, *04, *10 and *14 alleles are related withRA, whileHLA‐DRB1*03, *07, *11 and *13 protect againstRAin our population. On the other hand, we failed to provide evidence for the association of the autoantibodies andDAS‐28 withSE‐positiveRApatients.
Smokers and ex‐smokers have shared differences in the neural substrates for potential monetary gains and losses
Authors: Nestor Liam J. , McCabe Ella , Jones Jennifer , Clancy Luke , Garavan Hugh 
Published: December 2016

AbstractDespite an increased understanding of nicotine addiction, there is a scarcity of research comparing the neural correlates of non‐drug reward between smokers and ex‐smokers. Long‐term changes in reward‐related brain functioning for non‐drug incentives may elucidate patterns of functioning that potentially contribute to ongoing smoking behaviour in current smokers. Similarly, examining the effects of previous chronic nicotine exposure during a period of extended abstinence may reveal whether there are neural correlates responsible for non‐drug reward processing that are different from current smokers. The current study, therefore, sets out to examine the neural correlates of reward and loss anticipation, and their respective outcomes, in smokers, ex‐smokers and matched controls using a monetary incentive delay task during functional magnetic resonance imaging. Here, we report that in the absence of any significant behavioural group differences, both smokers and ex‐smokers showed a significantly greater activation change in the lateral orbitofrontal/anterior insular cortex compared with smokers when anticipating both potential monetary gains and losses. We further report that ex‐smokers showed a significantly greater activation change in the ventral putamen compared with both controls and smokers and in the caudate compared with controls during the anticipation of potential monetary losses only. The results suggest that smoking may sensitize striato‐orbitofrontal circuitry subserving motivational processes for loss avoidance and reward gain in nicotine addiction.
Statin potency and the risk of hospitalization for community‐acquired pneumonia
Authors: Shin Ju‐Young , Eberg Maria , Ernst Pierre , Filion Kristian B. 
Published: December 2016

AimPrevious studies suggest that statins may have beneficial respiratory effects. However, it is unclear if these purported benefits vary with statin potency. Our objective was to determine if higher potency statins, compared with lower potency statins, were associated with a reduced risk of hospitalization for community‐acquired pneumonia (HCAP).MethodsWe conducted a nested case–control analysis of a retrospective, population‐based cohort of new users of statins using data extracted from the UK's Clinical Practice Research Datalink and Hospital Episode Statistics. For each HCAP case, we used risk set sampling to randomly select up to 10 controls, matched on sex, age, cohort entry date and follow‐up duration. We used conditional logistic regression with high‐dimensional propensity scores to estimate hazard ratios (HRs) and 95% confidence intervals (CIs) for HCAP with current use of higher potency statin vs. lower potency statins.ResultsA total of 217 721 patients entered the cohort on a lower potency statin and 130 707 entered on a higher potency statin; these patients resulted in 2251 cases of HCAP during 561 886 person‐years of observation (rate: 4.0 HCAP per 1000 persons per year, 95% CI: 3.8–4.2). The analysis included 22 178 matched controls. Compared with lower potency statins, higher potency statins were associated with an increased rate of HCAP (HR: 1.14, 95% CI: 1.03–1.27). Higher potency statins were also associated with an increased rate of fatal HCAP (HR: 1.29, 95% CI: 1.04–1.59).ConclusionsHigher potency statins were not associated with a decreased risk of HCAP compared with lower potency statins.
The Bothnian Sea ice stream: early Holocene retreat dynamics of the south‐central Fennoscandian Ice Sheet
Authors: Greenwood Sarah L. , Clason Caroline C. , Nyberg Johan , Jakobsson Martin , Holmlund Per 
Published: December 2016

The Gulf of Bothnia hosted a variety of palaeo‐glaciodynamic environments throughout the growth and decay of the last Fennoscandian Ice Sheet, from the main ice‐sheet divide to a major corridor of marine‐ and lacustrine‐based deglaciation. Ice streaming through the Bothnian and Baltic basins has been widely assumed, and the damming and drainage of the huge proglacial Baltic Ice Lake has been implicated in major regional and hemispheric climate changes. However, the dynamics of palaeo‐ice flow and retreat in this large marine sector have until now been inferred only indirectly, from terrestrial, peripheral evidence. Recent acquisition of high‐resolution multibeam bathymetry opens these basins up, for the first time, to direct investigation of their glacial footprint and palaeo‐ice sheet behaviour. Here we report on a rich glacial landform record: in particular, a palaeo‐ice stream pathway, abundant traces of high subglacial meltwater volumes, and widespread basal crevasse squeeze ridges. The Bothnian Sea ice stream is a narrow flow corridor that was directed southward through the basin to a terminal zone in the south‐central Bothnian Sea. It was activated after initial margin retreat across the Åland sill and into the Bothnian basin, and the exclusive association of the ice‐stream pathway with crevasse squeeze ridges leads us to interpret a short‐lived stream event, under high extension, followed by rapid crevasse‐triggered break‐up. We link this event with a c. 150‐year ice‐rafted debris signal in peripheral varved records, at c. 10.67 cal. ka BP. Furthermore, the extensive glacifluvial system throughout the Bothnian Sea calls for considerable input of surface meltwater. We interpret strongly atmospherically driven retreat of this marine‐based ice‐sheet sector.