bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using hospital network-based surveillance for antimicrobial resistance as a more robust alternative to self-reporting
Authors: Donker Tjibbe , Smieszek Timo , Henderson Katherine L. , Walker Timothy M. , Hope Russell , Johnson Alan P. , Woodford Neil , Crook Derrick W. , Peto Tim E.A. , Walker A. Sarah , Robotham Julie V. 
Published: February 2019

AbstractHospital performance is often measured using self-reported statistics, such as the incidence of hospital-transmitted micro-organisms or those exhibiting antimicrobial resistance (AMR), encouraging hospitals with high levels to improve their performance. However, hospitals that increase screening efforts will appear to have a higher incidence and perform poorly, undermining comparison between hospitals and disincentivising testing, thus hampering infection control. We propose a surveillance system in which hospitals test patients previously discharged from other hospitals and report observed cases. Using NHS Hospital Episode Statistics data, we analysed patient movements across England and assessed the number of hospitals required to participate in such a reporting scheme to deliver robust estimates of incidence. With over 1.2 million admissions to English hospitals previously discharged from other hospitals annually, even when only a fraction of hospitals (41/155) participate (each screening at least 1000 of these admissions), the proposed surveillance system can estimate incidence across all hospitals. By reporting on other hospitals, the reporting of incidence is separated from the task of improving own performance. Therefore the incentives for increasing performance can be aligned to increase (rather than decrease) screening efforts, thus delivering both more comparable figures on the AMR problems across hospitals and improving infection control efforts.
Segment 2 from influenza A(H1N1)pdm09 viruses confers temperature sensitive HA yield on candidate vaccine virus growth in eggs that is complemented by PB2 701D
Authors: Hussain Saira , Turnbull Matthew L. , Pinto Rute M. , McCauley John W. , Engelhardt Othmar G. , Digard Paul 
Published: February 2019

AbstractCandidate vaccine viruses (CVVs) for seasonal influenza A virus are made by reassortment of the antigenic virus with a high-yielding egg-adapted strain, typically A/Puerto Rico/8/34 (PR8). Many 2009 H1N1 pandemic (pdm09) high-growth reassortants (HGRs) selected by this process contain pdm09 segment 2 in addition to the antigenic genes. To investigate this, we made CVV mimics by reverse genetics (RG) that were either 6:2 or 5:3 reassortants between PR8 and two pdm09 strains, A/California/7/2009 (Cal7) and A/England/195/2009, differing in the source of segment 2. The 5:3 viruses replicated better in MDCK-SIAT1 cells than the 6:2 viruses, but the 6:2 CVVs gave higher HA antigen yields from eggs. This unexpected phenomenon reflected temperature sensitivity conferred by pdm09 segment 2, as HA yields from eggs for the 5:3 viruses improved substantially when viruses were grown at 35°C compared with 37.5°C, whereas 6:2 virus yield did not. Authentic 5:3 pdm09 HGRs, X-179A and X-181, were not markedly temperature-sensitive however, despite their PB1 sequences being identical to that of Cal7, suggestive of compensatory mutations elsewhere in the genome. Sequence comparisons of the PR8-derived backbone genes identified single changes in PB2 and NP, 5 in NS1, and 1 in NS2. PB2 N701D but not NP T130A affected the temperature dependency of viral transcription. Furthermore, introducing the PB2 701D change into a 5:3 CVV mimic improved and drastically reduced the temperature sensitivity of HA yield. We conclude that RG PR8 backbones used for vaccine manufacture in eggs should contain PB2 701D to maximise virus yield.
The impact of the “World’s 25 Most Endangered Primates” list on scientific publications and media
Authors: Kerhoas Daphneé , Acerbi Alberto , Webber Amanda D. , McCabe Gráinne , Mittermeier Russell A. , Schwitzer Christoph 
Published: February 2019

AbstractAssessing the impact of conservation campaigns is of high importance for optimizing the use of limited resources. Lists of threatened species are often used as media outreach tools, but their usefulness is rarely tested. We investigated whether the inclusion of a species in the list “World’s 25 Most Endangered Primates”, published biannually by the International Primatological Society, the International Union for Conservation of Nature’s Species Survival Commission Primate Specialist Group, and Conservation International from 2000, had an effect both on scientific publications and on the general public. We analyzed a database of 40 million articles from major scientific publishers (Elsevier, Springer, Nature, Plos, Pubmed, Biomed Central) finding an increase in the number of papers mentioning a species after its inclusion in the list. We also analyzed media penetration (data from Google News), and online interest (data from Google Blogs, Twitter, and Google Trends), collecting daily data for one month before and one after the official launch of the 2014-2016 list (24th November 2015). The results show a short spike of interest on Google News and Twitter but no long term effect, indicating a limited effect on the general public. Our results are important for the understanding of the impact of current conservation campaigns and to provide strategies for future campaigns.
Differential side-effects ofBacillus thuringiensisbioinsecticide on non-targetDrosophilaflies
Authors: Babin Aurélie , Nawrot-Esposito Marie-Paule , Gallet Armel , Gatti Jean-Luc , Poirié Marylène 
Published: February 2019

AbstractBiopesticides based onBacillus thuringiensis(Bt) spores and toxins are alternate pest management solutions widely used to control insect pests. Their increasing use could lead to accumulation in the environment, hence leading to chronic exposure of non-target organisms. Here, we tested for potential non-intentional side-effects of chronic exposure toBtbiopesticide on larvae of non-targetDrosophilaspecies present inBt-treated areas. Doses up to those recommended for field application (106CFU/g of fly medium) had no effect on the fly development, whereas doses 10 to 100-fold higher (107-108CFU/g) increased developmental time and decreased adult emergence rates in a dose-dependent manner and with varying effect amplitudes for all the species and strains tested. For all them, all larvae died before pupation at the highest dose tested (109CFU/g). Focusing onD. melanogaster, delayed development and reduced emergence resulted from stage-dependent larval mortality, and fitness-related traits of adult flies emerging from survivingBtbiopesticide exposure were moderately increased. The effects ofBtbiopesticide seemed to result from the spores/cleaved toxins synergy, and possibly additives. While recommended doses had no effect on non-targetDrosophilaspecies, misuse or local accumulation ofBtbioinsecticides in the environment could have non-intentional side-effects on fly populations with potential implications for their associated communities.
Descriptive epidemiology of energy expenditure in the UK: Findings from the National Diet and Nutrition Survey 2008 – 2015
Authors: Brage Soren , Lindsay Tim , Venables Michelle , Wijndaele Katrien , Westgate Kate , Collins David , Bluck Les , Wareham Nick , Page Polly 
Published: February 2019

AbstractBackgroundLittle is known about population levels of energy expenditure as national surveillance systems typically employ only crude measures. The National Diet and Nutrition Survey (NDNS) in the UK measures energy expenditure in a 10% subsample by gold-standard doubly-labelled water (DLW).MethodsDLW-subsample participants from the NDNS (383 males, 387 females) aged 4-91yrs were recruited between 2008 and 2015. Height and weight were measured, and bodyfat percentage was estimated by deuterium dilution.ResultsAbsolute Total Energy Expenditure (TEE) increases steadily throughout childhood, ranging from 6.3 and 7.2 MJ/day in 4-7yr-old to 9.9 and 11.8 MJ/day for 14-16yr-old girls and boys, respectively. TEE peaked in 17-27yr-old women (10.9 MJ/day) and 28-43yr-old men (14.4 MJ/day), before decreasing gradually in old age. Physical Acitivty Energy Expenditure (PAEE) declines steadily with age from childhood (87.7 kJ/day/kg in 4-7yr olds) through to old age (38.9 kJ/day/kg in 71-91yr olds). Bodyfat percentage was strongly inversely associated with PAEE throughout life, irrespective of expressing PAEE relative to bodymass or fat-free mass. Compared to females with <30% bodyfat, females >40% recorded 28 kJ/day/kg and 17 kJ/day/kg fat-free mass less PAEE in analyses adjusted for age, geographical region, and time of assessment. Similarly, compared to males with <25% bodyfat, males >35% recorded 26 kJ/day/kg and 10 kJ/day/kg fat-free mass less PAEE.ConclusionsThis first nationally representative study reports levels of human energy expenditure as measured by gold-standard methodology; values may serve as reference for other population studies. Age, sex and body composition are main biological determinants of energy expenditure.Key messagesFirst nationally representative study of human energy expenditure, covering the UK in the period 2008-2015Total Energy Expenditure (MJ/day) increases steadily with age thoughout childhood and adolescence, peaks in the 3rd decade of life in women and 4th decade of life in men, before decreasing gradually in old agePhysical Acitivty Energy Expenditure (kJ/day/kg or kJ/day/kg fat-free mass) declines steadily with age from childhood to old age, more steeply so in malesBodyfat percentage is strongly inversely associated with physical activity energy expenditure
Using extreme gradient boosting (XGBoost) to evaluate the importance of a suite of environmental variables and to predict recruitment of young-of-the-year spotted seatrout in Florida
Authors: Herdter Smith Elizabeth 
Published: February 2019

AbstractEnvironmental factors strongly influence the success of juvenile fish recruitment and productivity, but species-specific environment-recruitment relationships have eluded researchers for decades. Most likely, this is because the environment-recruitment relationship is nonlinear, there are multi-level interactions between factors, and environmental variability may differentially affect recruitment among populations due to spatial heterogeneity. Identifying the most influential environmental variables may result in more accurate predictions of future recruitment and productivity of managed species. Here, gradient tree boosting was implemented using XGBoost to identify the most important predictors of recruitment for six estuary populations of spotted seatrout (Cynoscion nebulosus), an economically valuable marine resource in Florida. XGBoost, a machine learning method for regression and classification, was employed because it inherently models variable interactions and seamlessly deals with multi-collinearity, both of which are common features of ecological datasets. Additionally, XGBoost operates at a speed faster than many other gradient boosting algorithms due to a regularization factor and parallel computing functionality. In this application of XGBoost, the results indicate that the abundance of pre-recruit, juvenile spotted seatrout in spatially distinct estuaries is influenced by nearly the same set of environmental predictors. But perhaps of greater importance is that the results of this study show that this algorithm is highly effective at predicting species abundance and identifying important environmental factors (i.e. predictors of recruitment). It is strongly encouraged that future research explore the applicability of the XGBoost algorithm to other topics in marine and fisheries science and compare its performance to that of other statistical methods.
Single-cell profiling of tumor-reactive CD4+T-cells reveals unexpected transcriptomic diversity
Authors: Magen Assaf , Nie Jia , Ciucci Thomas , Tamoutounour Samira , Zhao Yongmei , Mehta Monika , Tran Bao , McGavern Dorian B. , Hannenhalli Sridhar , Bosselut Rémy 
Published: February 2019

AbstractMost current tumor immunotherapy strategies leverage cytotoxic CD8+T cells. Despite evidence for clinical potential of CD4+tumor-infiltrating lymphocytes (TILs), their functional diversity has limited our ability to harness their activity. To address this issue, we have used single-cell mRNA sequencing to analyze the response of CD4+T cells specific for a defined recombinant tumor antigen, both in the tumor microenvironment and draining lymph nodes (dLN). Designing new computational approaches to characterize subpopulations, we identify TIL transcriptomic patterns strikingly distinct from those elicited by responses to infection, and dominated by diversity among T-bet-expressing T helper type 1 (Th1)-like cells. In contrast, the dLN response includes follicular helper (Tfh)-like cells but lacks Th1 cells. We identify a type I interferon-driven signature in Th1-like TILs, and show that it is found in human liver cancer and melanoma, in which it is negatively associated with response to checkpoint therapy. Our study unveils unsuspected differences between tumor and virus CD4+T cell responses, and provides a proof-of-concept methodology to characterize tumor specific CD4+T cell effector programs. Targeting these programs should help improve immunotherapy strategies.One Sentence SummarySingle-cell RNA sequencing reveals novel and highly diverse transcriptomic patterns characteristic of CD4+T cell responses to tumors.
Attention updates the perceived position of moving objects
Authors: Nakayama Ryohei , Holcombe Alex O. 
Published: February 2019

AbstractThe information used by conscious perception may be somewhat different from that which drives certain actions. In support of this notion, recent studies reported that although internal grating motion can accumulate over seconds into a large illusory position shift, this position shift is not reflected in saccade targeting (action). Another possibility however is that rather than saccades and other actions having privileged access to the correct position, the attention shift thought to precede saccades resets the accumulated position shift to zero. Here we found that the accumulation of illusory position shift can be reset by transients near the moving object and also by the observer pressing a button at the time the object is perceived to reach a particular position. This creates a striking impression of the object jumping back to near its actual position. These results suggest that both stimulus-driven attention and attention associated with control of action may update the perceived position of moving objects and mediate the previously reported dissociation between conscious perception and saccades.
RapidAIM: A culture- and metaproteomics-based Rapid Assay of Individual Microbiome responses to drugs
Authors: Li Leyuan , Ning Zhibin , Zhang Xu , Mayne Janice , Cheng Kai , Stintzi Alain , Figeys Daniel 
Published: February 2019

AbstractThe gut microbiome has been associated with a growing list of diseases. Drugs and other compounds can affect the microbiome, but our understanding of drug-induced changes in individual microbiomes is limited due to a lack of rapid and effective high-throughput assay methods. We developed an approach named Rapid Assay of Individual Microbiome (RapidAIM) to screen xenobiotics against individual microbiomes. RapidAIM was evaluated by testing 43 compounds against five individual microbiomes using a metaproteomic approach. We show that our workflow enables quantitative profiling of the microbiome. The tested compounds significantly affected overall microbiome abundance, microbiome composition and functional pathways at multiple taxonomic levels. The microbiome responses to berberine, metformin, diclofenac, fructooligosaccharide and most antibiotics were consistent among most individuals. Interestingly, most of our tested NSAIDs, statins, and histamine-2 blockers induced strong and individually distinct responses. Our workflow offers an effective solution to systematically study the effects of many different compounds on individual microbiomes.
Optimal biochemical information processing at criticality
Authors: Stanoev Angel , Nandan Akhilesh P. , Koseska Aneta 
Published: February 2019

AbstractHow cells utilize surface receptors for chemoreception is a recurrent question spanning between physics and biology over the past few decades. However, the dynamical mechanism for processing time-varying signals is still unclear. Using dynamical systems formalism to describe criticality in non-equilibrium systems, we propose generic principle for temporal information processing through phase-space trajectories using dynamic transient memory. In contrast to short-term memory, dynamic memory generated via ghost attractor enables signal integration depending on stimulus history, and thus balance between stability and plasticity in receptor responses. We propose that self-organization at criticality can arise through fluctuation-sensing mechanism, illustrated for the experimentally established epidermal growth factor sensing system. This framework applies irrespective of the intrinsic node dynamics or network size, as we show using also a basic neuronal model. Processing of non-stationary signals, a feature previously attributed only to neuronal networks, thus uniquely emerges for biochemical networks organized at criticality.
hicap:in silicoserotyping of theHaemophilus influenzaecapsule locus
Authors: Watts Stephen C. , Holt Kathryn E. 
Published: February 2019

AbstractHaemophilus influenzaeexclusively colonises the human nasopharynx and can cause a variety of respiratory infections as well as invasive diseases including meningitis and sepsis. A key virulence determinant ofH. influenzaeis the polysaccharide capsule of which six serotypes are known, each encoded by a distinct variation of the capsule biosynthesis locus (cap-a tocap-f).H. influenzaetype b (Hib) was historically responsible for the majority of invasiveH. influenzaedisease and prevalence has been markedly reduced in countries that have implemented vaccination programs targeting this serotype. In the postvaccine era, non-typeableH. influenzaeemerged as the most dominant group causing disease but in recent years a resurgence of encapsulatedH. influenzaestrains has also been observed, most notably serotype a. Given the increasing incidence of encapsulated strains and the high frequency of Hib in countries without vaccination programs, there is growing interest in genomic epidemiology ofH. influenzae. Here we present hicap, a software tool for rapid in silico serotype prediction fromH. influenzaegenome sequences. hicap is written using Python3 and is freely available at github.com/scwatts/hicap under a GPLv3 license. To demonstrate the utility of hicap, we used it to investigate the cap locus diversity and distribution in 691 high-qualityH. influenzaegenomes from GenBank. These analyses identifiedcaploci in 95 genomes and confirmed the general association of each serotype with a unique clonal lineage and also identified occasional recombination between lineages giving rise to hybridcaploci (2% of encapsulated strains).
Long-term vegetation change in species-rich Nardus grasslands of central Germany caused by eutrophication, recovery from acidification and management change
Authors: Peppler-Lisbach Cord , Stanik Nils , Könitz Natali , Rosenthal Gert 
Published: February 2019

AbstractQuestionsThe impact of environmental changes on species-rich Nardus grasslands has been documented from the Atlantic biogeographic region but not from Central Europe. Which patterns and trends of community change in species-rich Nardus grassland of the Continental biogeographic region occurred in past decades? Are patterns and trends similar across areas within the Continental biographic region of Germany? Do they correspond to identified changes in the Atlantic biogeographic region of Europe?LocationEast Hesse Highlands, GermanyMethodsIn 2012/15, we re-surveyed vegetation relevés on quasi-permanent plots originally surveyed between 1971 and 1986/87 and re-measured soil parameters. We tested for differences in species frequency and abundance, mean Ellenberg indicator values, diversity measures and soil variables. Nitrogen and sulphur deposition data were analysed to evaluate effects of atmospheric pollutants. We used regression analyses to identify the contribution of environmental drivers to changes in species composition.ResultsWe found significant increases in soil pH, Ellenberg R and N values, species of agricultural grasslands and grassland fallows. C:N ratio, Nardus grassland specialists and low-nutrient indicators declined, while changes in species composition relate to changes in pH and management. There was a strong decrease in sulphur and a moderate increase in nitrogen deposition. Local patterns in atmospheric depositions did not correlate with local changes in species composition and soil parameters.ConclusionThe findings indicate significant overall eutrophication, a trend towards less acidic conditions, and insufficient management and abandonment. This is widely consistent across study areas and correspond to recent reports on vegetation changes and recovery from acidification in the Atlantic biogeographic region. We strongly assume reduction in sulphur deposition during recent decades to be a major driver of these changes combined with increased nitrogen deposition and reduced management intensity. This suggests a large-scale validity of processes triggering changes in Nardus grasslands across Western and Central Europe.NomenclatureThe nomenclature follows the German taxonomic reference list (GermanSL version 1.3) of Jansen & Dengler (2008).
Temporal switching of species roles in a plant–pollinator network
Authors: Miele Vincent , Ramos-Jiliberto Rodrigo , Vázquez Diego P. 
Published: February 2019

AbstractMutualistic networks are highly dynamic, characterized by high temporal turnover of species and interactions. Yet, we have a limited understanding of how the internal structure of these networks and the roles species play in them vary through time. We used six years of observation data and a novel statistical method (dynamic stochastic block models) to assess how network structure and species roles change across time in a quantitative plant–pollinator network from a dryland ecosystem in Argentina. Our analyses revealed a core–periphery structure persistent through seasons and years. Yet, species roles as core or peripheral were highly dynamic: virtually all species that played a core role in some seasons were also peripheral in other seasons, while many other species remained always peripheral. Our results illuminate our understanding of the dynamics of ecological networks and have important implications for ecosystem management and conservation.