bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structure, culture, and predicted function of the gut microbiome of the Mormon cricketAnabrus simplex(Orthoptera: Tettigoniidae)
Authors: Smith Chad C. , Srygley Robert B. , Healy Frank , Swaminath Karthikeyan , Mueller Ulrich G. 
Published: October 2016

SUMMARYThe gut microbiome of insects plays an important role in their ecology and evolution, participating in nutrient acquisition, immunity, and behavior. Microbial community structure within the gut is heavily influenced by differences among gut regions in morphology and physiology, which determine the niches available for microbes to colonize.We present a high-resolution analysis of the structure of the gut microbiome in the Mormon cricketAnabrus simplex,an insect known for its periodic outbreaks in the western United States and nutrition-dependent mating system. The Mormon cricket microbiome was dominated by eleven taxa from the Lactobacillaceae, Enterobacteriaceae, and Streptococcaeae. While most of these were represented in all gut regions, there were marked differences in their relative abundance, with lactic-acid bacteria (Lactobacillaceae) more common in the foregut and midgut and enteric (Enterobacteriaceae) bacteria more common in the hindgut.Differences in community structure were driven by variation in the relative prevalence of three groups: aLactobacillusin the foregut,Pediococcuslactic-acid bacteria in the midgut, andPantoea agglomerans, an enteric bacterium, in the hindgut. These taxa have been shown to have beneficial effects on their hosts in insects and other animals by improving nutrition, increasing resistance to pathogens, and modulating social behavior.Using PICRUSt to predict gene content from our 16S rRNA sequences, we found enzymes that participate in carbohydrate metabolism and pathogen defense in other orthopterans. These were predominately represented in the hindgut and midgut, the most important sites for nutrition and pathogen defense.Phylogenetic analysis of 16S rRNA sequences from cultured isolates indicated low levels of divergence from sequences derived from plants and other insects, suggesting that these bacteria are likely to be exchanged between Mormon crickets and the environment.Our study shows strong spatial variation in microbiome community structure, which influences predicted gene content and thus the potential of the microbiome to influence host function.
Modeling antimicrobial cycling and mixing: Differences arising from an individual-based versus a population-based perspective
Authors: Uecker Hildegard , Bonhoeffer Sebastian 
Published: October 2016

Background:In order to manage bacterial infections in hospitals in the face of antibiotic resistance, the two treatment protocols “mixing” and “cycling” have received considerable attention both from modelers and clinicians. However, the terms are not used in exactly the same way by both groups.Objectives:We aim to investigate a model that comes closer to clinical practice and compare the predictions to the standard model.Methods:We set up two deterministic models, implemented as a set of differential equations, for the spread of bacterial infections in a hospital. Following the traditional approach, the first model takes a population-based perspective. The second model, in contrast, takes the drug use of individual patients into account.Results:The alternative model can indeed lead to different predictions than the standard model. We provide examples for which in the new model, the opposite strategy maximizes the number of uninfected patients or minimizes the rate of spread of double resistance.Conclusions:While the traditional models provide valuable insight, care is needed in the interpretation of results.
A comparative study of metagenomics analysis pipelines at the species level
Authors: Teo Yee Voan , Neretti Nicola 
Published: October 2016

AbstractMany metagenomics classification tools have been developed with the rapid growth of the metagenomics field. However, the classification of closely related species remains a challenge for this field. Here, we compared MetaPhlAn2, kallisto and Kraken for their performances in two metagenomics settings, human metagenomics and environmental metagenomics. Our comparative study showed that kallisto demonstrated higher sensitivity than MetaPhlAn2 and Kraken and better quantification accuracy than Kraken at the species level. We also showed that classification tools that run on full reference genomes misidentified many species that were not truly present. In order to reduce false positives, we introduced marker genes from MetaPhlAn2 into our pipeline, which uses kallisto for the classification step, as an additional filtering step for species detection.
UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing
Authors: Edgar Robert C. 
Published: October 2016

AbstractAmplicon sequencing of tags such as 16S and ITS ribosomal RNA is a popular method for investigating microbial populations. In such experiments, sequence errors caused by PCR and sequencing are difficult to distinguish from true biological variation. I describe UNOISE2, an updated version of the UNOISE algorithm for denoising (error-correcting) Illumina amplicon reads and show that it has comparable or better accuracy than DADA2.
Evaluating the accuracy of genomic prediction of growth and wood traits in twoEucalyptusspecies and their F1hybrids
Authors: Tan Biyue , Grattapaglia Dario , Salgado Martins Gustavo , Zamprogno Ferreira Karina , Sundberg Björn , Ingvarsson Pär K. 
Published: October 2016

AbstractBackgroundGenomic prediction is a genomics assisted breeding methodology that can increase genetic gains by accelerating the breeding cycle and potentially improving the accuracy of breeding values. In this study, we used 41,304 informative SNPs genotyped in aEucalyptusbreeding population involving 90E.grandisand 78E.urophyllaparents and their 949 F1hybrids to develop genomic prediction models for eight phenotypic traits - basic density and pulp yield, circumference at breast height and height and tree volume scored at age thee and six years. Based on different genomic prediction methods we assessed the impact of the composition and size of the training/validation sets and the number and genomic location of SNPs on the predictive ability (PA).ResultsHeritabilities estimated using the realized genomic relationship matrix (GRM) were considerably higher than estimates based on the expected pedigree, mainly due to inconsistencies in the expected pedigree that were readily corrected by the GRM. Moreover, GRM more precisely capture Mendelian sampling among related individuals, such that the genetic covariance was based on the actual proportion of the genome shared between individuals. PA improved considerably when increasing the size of the training set and by enhancing relatedness to the validation set. Prediction models trained on pure species parents could not predict well in F1hybrids, indicating that model training has to be carried out in hybrid populations if one is to predict in hybrid selection candidates. The different genomic prediction methods provided similar results for all traits, therefore GBLUP or rrBLUP represents better compromises between computational time and prediction efficiency. Only slight improvement was observed in PA when more than 5,000 SNPs were used for all traits. Using SNPs in intergenic regions provided slightly better PA than using SNPs sampled exclusively in genic regions.ConclusionsEffects of training set size and composition and number of SNPs used are the most important factors for model prediction rather than prediction method and the genomic location of SNPs. Furthermore, training the prediction model on pure parental species provide limited ability to predict traits in interspecific hybrids. Our results provide additional promising perspectives for the implementation of genomic prediction inEucalyptusbreeding programs.
Learning from intelligent conversation
Authors: De Boer Luitzen , Andersen Poul Houman 
Published: October 2016

Purpose
The purpose of the paper is to contribute to further advancing of IMP as a research field by setting up and starting a theoretical conversation between system theory and the IMP.

Design/methodology/approach
The approach is based on a narrative literature study and conceptual research.

Findings
The authors find that system theory and cybernetics can be regarded as important sources of inspiration for early IMP research. The authors identify three specific theoretical “puzzles” in system theory that may serve as useful topics for discussion between system theorists and IMP researchers.

Originality/value
Only a handful of papers have touched upon the relationship between system theory and IMP before. This paper combines a narrative, historical analysis of this relationship with developing specific suggestions for using system theory as a vehicle for further advancement of IMP research.
Interleukin‐1 β‐targeted treatment strategies in inflammatory depression: toward personalized care
Authors: Ellul P. , Boyer L. , Groc L. , Leboyer M. , Fond G. 
Published: October 2016

ObjectivesIt is unknown whether a cytokine signature may help the identification of subgroup of patient who would respond to personalized treatment. As interleukin‐1 beta (Il‐1β) seems to play a major role in mood disorder, a systematic review and meta‐analysis of its potential role in major depressive disorder (MDD) was carried out.MethodsA systematic search was performed to identify appropriate MDD vs. control studies pertaining to Il‐1β. Methodological quality and possible moderators were also assessed.ResultsA total of 1922 studies were identified, and 53 articles were selected. Results showed an association between increased blood IL‐1β and MDD in high‐quality studies only. No association with age was found. No IL‐1β gene‐related polymorphisms has been associated with MDD. No effect of antidepressant on IL‐1β level has been found, although the antidepressants investigated were various. Qualitative analyses indicate that MDD coupled to a history of childhood trauma may be a subgroup for IL‐1β ‐targeted therapies. No difference in studies utilizing a stimulation method has been identified to date.ConclusionsThe present work has confirmed IL‐1β as a biological marker of interest for innovative MDD treatments. However, further studies are needed to clarify the patients with MDD who may benefit from these therapies.
Incidence, characteristics and course of narrow phenotype paediatric bipolar I disorder in the British Isles
Authors: Sharma A. , Neely J. , Camilleri N. , James A. , Grunze H. , Le Couteur A. 
Published: October 2016

ObjectiveTo estimate the surveillance incidence of first‐time diagnosis of narrow phenotype bipolar I disorder (NPBDI) in young people under 16 years by consultants in child and adolescent psychiatry (CCAP) in the British Isles and describe symptoms, comorbidity, associated factors, management strategies and clinical outcomes at 1‐year follow‐up.MethodActive prospective surveillance epidemiology was utilised to ask 730 CCAP to report cases of NPBDI using the child and adolescent psychiatry surveillance system.ResultsOf the 151 cases of NPBDI reported, 33 (age range 10–15.11 years) met the DSM‐IV analytical case definition with 60% having had previously undiagnosed mood episodes. The minimum 12‐month incidence of NPBDI in the British Isles was 0.59/100 000 (95% CI 0.41–0.84). Irritability was reported in 72% cases and comorbid conditions in 51.5% cases with 48.5% cases requiring admission to hospital. Relapses occurred in 56.67% cases during the 1‐year follow‐up.ConclusionsThese rates suggest that the first‐time diagnosis of NPBDI in young people <16 years of age by CCAP in the British Isles is infrequent; however, the rates of relapse and admission to hospital warrant close monitoring.
Hidden diversity: parasites of stream arthropods
Authors: Grabner Daniel S. 
Published: October 2016

Summary

Parasite communities of aquatic macroinvertebrates have so far rarely been studied, even if these host organisms are of high relevance for the ecology of freshwater systems and their parasites likely affect the host populations and communities. Therefore, this study addresses this ‘hidden diversity’ in aquatic arthropods of a stream ecosystem in North Rhine‐Westphalia, Germany.

Samples of benthic organisms were taken, and the most abundant host species of major invertebrate groups (amphipods and larvae of chironomids, beetles, caddisflies, mayflies, stoneflies) were tested by PCR for different parasite taxa [microsporidians, acanthocephalans (only amphipods), trematodes, nematodes]. Furthermore, the possible link between prevalence and host feeding type was investigated for each parasite group using a newly developed ‘feeding type score’.

In total, 10 species of aquatic insect larvae and two amphipods of the genus Gammarus spp. were tested and 16 different isolates of microsporidians, three acanthocephalan species, six species of trematodes and one nematode were found. Microsporidians were present in all host species with prevalences ranging from 20 to 100%. Only one presumably specific host–microsporidian association was found for the mayfly Ephemera danica and three isolates were detected exclusively in amphipods. Three acanthocephalan species were detected in the amphipods with prevalences of up to 5.3%. All tested host species were infected with trematodes (prevalences 25–100%), except the caddisfly Sericostoma sp. Nematodes were detected in five host species with prevalences ranging from 14 to 80%. For several positive samples, no sequencing result could be obtained, especially for trematodes and nematodes, therefore, the actual parasite diversity might be even higher.

Active filter feeding showed the highest feeding type prevalence score for microsporidia and nematodes, and passive filter feeders for trematodes, but these results have to be interpreted cautiously as only one active and one passive filter feeder species each were present in the sample.

The impressive number of 26 parasite species (12 microsporidians and 10 helminths) were detected in 12 host species, mostly with surprisingly high prevalences. These results illustrate the ‘hidden diversity’ in aquatic ecosystems and highlight the importance of parasites for aquatic ecological research and the need for studies on the effects of mixed parasite infections on the host populations and communities.
Practice into Pedagogy into Practice: Collaborative Postcards from Hong Kong
Authors: Archer Carol 
Published: October 2016

AbstractA collaborative postcard project completed by 22 students as part of a drawing course conducted at a university in Hong Kong is introduced. The project entailed inviting students into an art practice in which the author was herself engaged as a practitioner as well as a researcher. After introducing the educational context in which the project took place, the author provides an account – informed by ‘participant‐observer’ feedback from students – of how the project unfolded and was experienced. In the second section of the article the creative and pedagogic efficacy of the project is considered with reference to the experience‐centred and dialogic principles expressed in the educational philosophies of John Dewey, Simone Weil, Hannah Arendt and Paulo Freire. The third section draws on insights from scholars working in a range of disciplines – cultural history, anthropology, sociology and psychology – to argue that a particular set of organisational and collaborative dynamics catalysed students’ levels of engagement, creativity and motivation. The article argues that the collaborative postcard project is an example of an experience‐centred and practice‐based pedagogy that is founded on dialogue, mutual generosity and experimental play, and engenders in students the ‘quality of mental process’ that is, for John Dewey, ‘the measure of educative growth’.
Drawing Pedagogies in Higher Education: the Learning Impact of a Collaborative Cross‐disciplinary Drawing Course
Authors: Lyon Philippa , Letschka Patrick , Ainsworth Tom , Haq Inam 
Published: October 2016

AbstractDrawing is taught in higher education across art and design but also, increasingly, in medical education, with a variety of aims and approaches. It is argued that there is a need, in both these disciplinary domains, to make more explicit the underpinning pedagogical approach to drawing and the impact that different approaches have on learning. The research described in this article focuses on an optional drawing course for undergraduate craft students and medical students. The course is run by the College of Arts and Humanities at a UK university and has a thematic focus on the human body. This qualitative case study sets out, in the context of selected theory about the teaching and learning of drawing, to explore what the learning impact of a particular collaborative model of teaching drawing was on a cross‐disciplinary student group. Findings included, with reference to Riley's framework of drawing pedagogies, that a range of philosophical and pedagogical ideas about drawing were blended from the teaching perspective in a way that enabled students from distinct disciplinary backgrounds to engage and learn. A shift was observed in students’ perceptions of drawing, with both sets of students questioning previously held assumptions about the use and value of drawing within their learning. Life drawing and anatomy laboratory drawing, in particular, provoked deep and challenging reflections about different cultural conceptions of the human body and the practice of collaborative drawing, with dialogic reflection, enabling insights to be developed into different disciplinary epistemologies.
HIV‐1 promonocytic and lymphoid cell lines: an in vitro model of in vivo mitochondrial and apoptotic lesion
Authors: Morén Constanza , González‐Casacuberta Ingrid , Álvarez‐Fernández Carmen , Bañó Maria , Catalán‐Garcia Marc , Guitart‐Mampel Mariona , Juárez‐Flores Diana Luz , Tobías Ester , Milisenda José , Cardellach Francesc , Gatell Josep Maria , Sánchez‐Palomino Sonsoles , Garrabou Glòria 
Published: October 2016

AbstractTo characterize mitochondrial/apoptotic parameters in chronically human immunodeficiency virus (HIV‐1)‐infected promonocytic and lymphoid cells which could be further used as therapeutic targets to test pro‐mitochondrial or anti‐apoptotic strategies as in vitro cell platforms to deal with HIV‐infection. Mitochondrial/apoptotic parameters of U1 promonocytic and ACH2 lymphoid cell lines were compared to those of their uninfected U937 and CEM counterparts. Mitochondrial DNA (mtDNA) was quantified by rt‐PCR while mitochondrial complex IV (CIV) function was measured by spectrophotometry. Mitochondrial‐nuclear encoded subunits II–IV of cytochrome‐c‐oxidase (COXII‐COXIV), respectively, as well as mitochondrial apoptotic events [voltage‐dependent‐anion‐channel‐1(VDAC‐1)‐content and caspase‐9 levels] were quantified by western blot, with mitochondrial mass being assessed by spectrophotometry (citrate synthase) and flow cytometry (mitotracker green assay). Mitochondrial membrane potential (JC1‐assay) and advanced apoptotic/necrotic events (AnexinV/propidium iodide) were measured by flow cytometry. Significant mtDNA depletion spanning 57.67% (P < 0.01) was found in the U1 promonocytic cells further reflected by a significant 77.43% decrease of mitochondrial CIV activity (P < 0.01). These changes were not significant for the ACH2 lymphoid cell line. COXII and COXIV subunits as well as VDAC‐1 and caspase‐9 content were sharply decreased in both chronic HIV‐1‐infected promonocytic and lymphoid cell lines (<0.005 in most cases). In addition, U1 and ACH2 cells showed a trend (moderate in case of ACH2), albeit not significant, to lower levels of depolarized mitochondrial membranes. The present in vitro lymphoid and especially promonocytic HIV model show marked mitochondrial lesion but apoptotic resistance phenotype that has been only partially demonstrated in patients. This model may provide a platform for the characterization of HIV‐chronicity, to test novel therapeutic options or to study HIV reservoirs.
Arrival by ambulance explains variation in mortality by time of admission: retrospective study of admissions to hospital following emergency department attendance in England
Authors: Anselmi Laura , Meacock Rachel , Kristensen Søren Rud , Doran Tim , Sutton Matt 
Published: October 2016

BackgroundStudies finding higher mortality rates for patients admitted to hospital at weekends rely on routine administrative data to adjust for risk of death, but these data may not adequately capture severity of illness. We examined how rates of patient arrival at accident and emergency (A&E) departments by ambulance—a marker of illness severity—were associated with in-hospital mortality by day and time of attendance.MethodsRetrospective observational study of 3 027 946 admissions to 140 non-specialist hospital trusts in England between April 2013 and February 2014. Patient admissions were linked with A&E records containing mode of arrival and date and time of attendance. We classified arrival times by day of the week and daytime (07:00 to 18:59) versus night (19:00 to 06:59 the following day). We examined the association with in-hospital mortality within 30 days using multivariate logistic regression.ResultsOver the week, 20.9% of daytime arrivals were in the highest risk quintile compared with 18.5% for night arrivals. Daytime arrivals on Sundays contained the highest proportion of patients in the highest risk quintile at 21.6%. Proportions of admitted patients brought in by ambulance were substantially higher at night and higher on Saturday (61.1%) and Sunday (60.1%) daytimes compared with other daytimes in the week (57.0%). Without adjusting for arrival by ambulance, risk-adjusted mortality for patients arriving at night was higher than for daytime attendances on Wednesday (0.16 percentage points). Compared with Wednesday daytime, risk-adjusted mortality was also higher on Thursday night (0.15 percentage points) and increased throughout the weekend from Saturday daytime (0.16 percentage points) to Sunday night (0.26 percentage points). After adjusting for arrival by ambulance, the raised mortality only reached statistical significance for patients arriving at A&E on Sunday daytime (0.17 percentage points).ConclusionUsing conventional risk-adjustment methods, there appears to be a higher risk of mortality following emergency admission to hospital at nights and at weekends. After accounting for mode of arrival at hospital, this pattern changes substantially, with no increased risk of mortality following admission at night or for any period of the weekend apart from Sunday daytime. This suggests that risk-adjustment based on inpatient administrative data does not adequately account for illness severity and that elevated mortality at weekends and at night reflects a higher proportion of more severely ill patients arriving by ambulance at these times.