bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inferring processes of community assembly from macroscopic patterns: the case for inclusive and mechanistic approaches
Authors: Pontarp Mikael , Brännström Åke , Petchey Owen L 
Published: September 2017

AbstractStatistical techniques exist for inferring community assembly processes from community patterns. Habitat filtering, competition, and biogeographical effects have, for example, been inferred from signals in phenotypic and phylogenetic data. The usefulness of current inference techniques is, however, debated as the causal link between process and pattern is often lacking and processes known to be important are ignored. Here, we revisit current knowledge on community assembly across scales and, in line with several reviews that have outlined the features and challenges associated with current inference techniques, we identify a discrepancy between features of real communities and current inference techniques. We argue, that mechanistic eco-evolutionary models in combination with novel model fitting and model evaluation techniques can provide avenues for more accurate, reliable and inclusive inference. To exemplify, we implement a trait-based and spatially explicit dynamic eco-evolutionary model and discuss steps of model modification, fitting, and evaluation as an iterative approach enabling inference from diverse data sources. This suggested approach can be computationally intensive, and model fitting and parameter estimation can be challenging. We discuss optimization of model implementation, data requirements and availability, and Approximate Bayesian Computation (ABC) as potential solutions to challenges that may arise in our quest for better inference techniques.
Sub-threshold resonance organizes activity and optimizes learning in neural networks
Authors: Roach James P. , Pidde Aleksandra , Katz Eitan , Wu Jiaxing , Ognjanovski Nicolette , Aton Sara J. , Zochowski Michal R. 
Published: September 2017

AbstractNetwork oscillations across and within brain areas are critical for learning and performance in memory tasks. While a large amount of work has focused on the generation of neural oscillations, their effects on neuronal populations’ spiking activity and information encoding is less known. Here, we use computational modeling andin vivorecording to demonstrate that a shift in sub-threshold resonance can interact with oscillating input to ensure that networks of neurons properly encode new information represented in external inputs to the weights of recurrent synaptic connections. Using a neuronal network model, we find that due to an input-current dependent shift in their resonance response, individual neurons in a network will arrange their phases of firing to represent varying strengths of their respective inputs. As networks encode information, neurons fire more synchronously, and this effect limits the extent to which further “learning” (in the form of changes in synaptic strength) can occur. We also demonstrate that sequential patterns of neuronal firing can be accurately stored in the network; these sequences are later reproduced without external input (in the context of sub-threshold oscillations) in both the forward and reverse directions (as has been observed following learningin vivo). To test whether a similar mechanism could actin vivo, we show that periodic stimulation of hippocampal neurons coordinates network activity and functional connectivity in a frequency-dependent manner. We conclude that sub-threshold resonance provides a plausible network-level mechanism to accurately encode and retrieve information without over-strengthening connections between neurons.
Spatially uniform establishment of chromatin accessibility in the earlyDrosophilaembryo
Authors: Haines Jenna E. , Eisen Michael B. 
Published: September 2017

AbstractAs theDrosophilaembryo transitions from the use of maternal RNAs to zygotic transcription, domains of open chromatin, with relatively low nucleosome density and specific histone marks, are established at promoters and enhancers involved in patterned embryonic transcription. However, it remains unclear whether open chromatin is a product of activity - transcription at promoters and patterning transcription factor binding at enhancers - or whether it is established by independent mechanisms. Recent work has implicated the ubiquitously expressed, maternal factor Zelda in this process. To assess the relative contribution of activity in the establishment of chromatin accessibility, we have probed chromatin accessibility across the anterior-posterior axis of earlyDrosophila melanogasterembryos by applying a transposon based assay for chromatin accessibility (ATAC-seq) to anterior and posterior halves of hand-dissected, cellular blastoderm embryos. We find that genome-wide chromatin accessibility is remarkably similar between the two halves. Promoters and enhancers that are active in exclusively one half of the embryo have open chromatin in the other half, demonstrating that chromatin accessibility is not a direct result of activity. However, there is a small skew at enhancers that drive transcription exclusively in either the anterior or posterior half of the embryo, with greater accessibility in the region of activity. Taken together these data support a model in which regions of chromatin accessibility are defined and established by ubiquitous factors, and fine-tuned subsequently by activity.
EAACI Guidelines on allergen immunotherapy: IgE‐mediated food allergy
Authors: Pajno G. B. , Fernandez‐Rivas M. , Arasi S. , Roberts G. , Akdis C. A. , Alvaro‐Lozano M. , Beyer K. , Bindslev‐Jensen C. , Burks W. , Ebisawa M. , Eigenmann P. , Knol E. , Nadeau K. C. , Poulsen L. K. , van Ree R. , Santos A. F. , du Toit G. , Dhami S. , Nurmatov U. , Boloh Y. , Makela M. , O'Mahony L. , Papadopoulos N. , Sackesen C. , Agache I. , Angier E. , Halken S. , Jutel M. , Lau S. , Pfaar O. , Ryan D. , Sturm G. , Varga E.‐M. , van Wijk R. G. , Sheikh A. , Muraro A. ,   EAACI Allergen Immunotherapy Guidelines Group
Published: September 2017

AbstractFood allergy can result in considerable morbidity, impairment of quality of life, and healthcare expenditure. There is therefore interest in novel strategies for its treatment, particularly food allergen immunotherapy (FA‐AIT) through the oral (OIT), sublingual (SLIT), or epicutaneous (EPIT) routes. This Guideline, prepared by the European Academy of Allergy and Clinical Immunology (EAACI) Task Force on Allergen Immunotherapy for IgE‐mediated Food Allergy, aims to provide evidence‐based recommendations for active treatment of IgE‐mediated food allergy with FA‐AIT. Immunotherapy relies on the delivery of gradually increasing doses of specific allergen to increase the threshold of reaction while on therapy (also known as desensitization) and ultimately to achieve post‐discontinuation effectiveness (also known as tolerance or sustained unresponsiveness). Oral FA‐AIT has most frequently been assessed: here, the allergen is either immediately swallowed (OIT) or held under the tongue for a period of time (SLIT). Overall, trials have found substantial benefit for patients undergoing either OIT or SLIT with respect to efficacy during treatment, particularly for cow's milk, hen's egg, and peanut allergies. A benefit post‐discontinuation is also suggested, but not confirmed. Adverse events during FA‐AIT have been frequently reported, but few subjects discontinue FA‐AIT as a result of these. Taking into account the current evidence, FA‐AIT should only be performed in research centers or in clinical centers with an extensive experience in FA‐AIT. Patients and their families should be provided with information about the use of FA‐AIT for IgE‐mediated food allergy to allow them to make an informed decision about the therapy.
Families’ perceived benefits of home visits for managing paediatric obesity outweigh the potential costs and barriers
Authors: Gehring Nicole D. , Ball Geoff D. C. , Perez Arnaldo , Holt Nicholas L. , Neuman Daniel , Spence Nicholas , Mercier Laura , Jetha Mary 
Published: September 2017

AbstractAimHome visits have successfully been used to deliver various health services, but what role could they play in paediatric weight management? Low treatment initiation and high attrition prompted our multidisciplinary paediatric weight management clinic to investigate how families perceived the benefits and barriers of home visits.MethodsWe focused on children with obesity aged 2–17 who were enrolled in our tertiary‐level clinic in Alberta, Canada. None had received a home visit. The families were interviewed face‐to‐face from October 2015 to October 2016, and we used a qualitative description methodological framework and manifest content analysis. The parents were the main interviewees.ResultsOf the 56 families, 89% were interested in a home visit, 82% wanted support from a dietician and 54% from an exercise specialist. The perceived benefits of home visits included comprehensive assessment (95%), convenience (86%), tailored care (29%) and family involvement (13%), while the costs and barriers included clinicians’ potential judgmental attitudes (30%), loss of privacy (19%) and distractions (10%). Some thought clinicians would find home visits inconvenient (25%), with bureaucratic challenges (14%) and sustainability issues (5%).ConclusionFamilies felt home visits were a convenient option for managing paediatric obesity and identified important benefits and barriers that could guide such interventions.
Strong antimicrobial activity of xanthohumol and other derivatives from hops (Humulus lupulus L.) on gut anaerobic bacteria
Authors: Cermak Pavel , Olsovska Jana , Mikyska Alexandr , Dusek Martin , Kadleckova Zuzana , Vanicek Jiri , Nyc Otakar , Sigler Karel , Bostikova Vanda , Bostik Pavel 
Published: September 2017

Anaerobic bacteria, such as Bacteroides fragilis or Clostridium perfringens, are part of indigenous human flora. However, Clostridium difficile represents also an important causative agent of nosocomial infectious antibiotic‐associated diarrhoea. Treatment of C. difficile infection is problematic, making it imperative to search for new compounds with antimicrobial properties. Hops (Humulus lupulus L.) contain substances with antibacterial properties. We tested antimicrobial activity of purified hop constituents humulone, lupulone and xanthohumol against anaerobic bacteria. The antimicrobial activity was established against B. fragilis, C. perfringens and C. difficile strains according to standard testing protocols (CLSI, EUCAST), and the minimum inhibitory concentrations (MICs) and minimum bactericidal concentrations (MBC) were calculated. All C. difficile strains were toxigenic and clinically relevant, as they were isolated from patients with diarrhoea. Strongest antimicrobial effects were observed with xanthohumol showing MIC and MBC values of 15–107 μg/mL, which are close to those of conventional antibiotics in the strains of bacteria with increased resistance. Slightly higher MIC and MBC values were obtained with lupulone followed by higher values of humulone. Our study, thus, shows a potential of purified hop compounds, especially xanthohumol, as alternatives for treatment of infections caused by select anaerobic bacteria, namely nosocomial diarrhoea caused by resistant strains.
Frame Rate vs Resolution: A Subjective Evaluation of Spatiotemporal Perceived Quality Under Varying Computational Budgets
Authors: Debattista K. , Bugeja K. , Spina S. , Bashford‐Rogers T. , Hulusic V. 
Published: September 2017

AbstractMaximizing performance for rendered content requires making compromises on quality parameters depending on the computational resources available . Yet, it is currently unclear which parameters best maximize perceived quality. This work investigates perceived quality across computational budgets for the primary spatiotemporal parameters of resolution and frame rate. Three experiments are conducted. Experiment 1 (n = 26) shows that participants prefer fixed frame rates of 60 frames per second (fps) at lower resolutions over 30 fps at higher resolutions. Experiment 2 (n = 24) explores the relationship further with more budgets and quality settings and again finds 60 fps is generally preferred even when more resources are available. Experiment 3 (n = 25) permits the use of adaptive frame rates, and analyses the resource allocation across seven budgets. Results show that while participants allocate more resources to frame rate at lower budgets the situation reverses once higher budgets are available and a frame rate of around 40 fps is achieved. In the overall, the results demonstrate a complex relationship between frame rate and resolution's effects on perceived quality. This relationship can be harnessed, via the results and models presented, to obtain more cost‐effective virtual experiences.
Increased adult neurogenesis associated with reactive astrocytosis occurs prior to neuron loss in a mouse model of neurodegenerative disease
Authors: Liu Ting‐Ting , Ye Xiao‐Lian , Zhang Jin‐Ping , Yu Ting‐Ting , Cheng Shan‐Shan , Zou Xiao‐Chuan , Xu Yun , Chen Gui‐Quan , Yin Zhen‐Yu 
Published: September 2017

SummaryAimsThis study was to investigate whether cell proliferation and adult neurogenesis are affected at early neurodegenerative stage when neuron loss has not begun to display.Methods and ResultsForebrain‐specific nicastrin (NCT) conditional knockout (cKO) mice were generated by crossing NCTf/f with CaMKIIα‐Cre Tg mice. BrdU was used as a lineage tracer to label proliferating neural progenitor cells (NPCs). Immunohistochemistry (IHC) on BrdU indicated that the total number of BrdU positive (+) cells was increased in NCT cKO mice. IHC on doublecortin (DCX) showed that the total number of DCX+ cells was also increased in NCT cKO mice. NCT cKO mice displayed significant astrogliosis as well. However, NCT cKO mice at 3 months did not show significant neuronal death or synaptic loss.ConclusionsNCT‐dependent γ‐secretase activity plays an important role in cell proliferation and immature neuron generation. Enhanced neurogenesis and astrogliosis may be early cellular events prior to the occurrence of neuronal death in neurodegenerative disease.
Schisandrin B down‐regulated lncRNA BCYRN1 expression of airway smooth muscle cells by improving miR‐150 expression to inhibit the proliferation and migration of ASMC in asthmatic rats
Authors: Zhang Xiao‐yu , Tang Xue‐yi , Ma Li‐jun , Guo Ya‐li , Li Xiao‐su , Zhao Li‐min , Tian Cui‐jie , Cheng Dong‐Jun , Chen Zhuo‐chang , Zhang Luo‐xian 
Published: September 2017

AbstractObjectiveThe mechanism of Schisandrin B on the proliferation and migration of airway smooth muscle cells (ASMCs) in asthmatic rats was explored.MethodsSD rats were divided into three groups: control (group 1), model (group 2) and model + Schisandrin B (group 3). miR‐150 and lncRNA BCYRN1 levels were measured by qRT‐PCR. The combination of BCYRN1 and miR‐150 was detected by RNA pull down. ASMCs’ viability/proliferation/migration were examined by WST‐1 assay and 24‐well Transwell system.ResultsSchisandrin B up‐regulated miR‐150 expression and down‐regulated BCYRN1 expression in sensitized rats. Schisandrin B reversed the expression of miR‐150 and BCYRN1 in MV‐treated ASMCs. In addition, Schisandrin B inhibited the viability, proliferation and migration of MV‐induced ASMCs. We also found miR‐150 inhibited BCYRN1 expression which was proved by experiments using ASMCs transfected with miR‐150 inhibitor.ConclusionSchisandrin B increased miR‐150 expression and decreased BCYRN1, and BCYRN1 expression was inhibited by miR‐150, which indicated that Schisandrin B could regulate BCYRN1 through miR‐150.
Expression of connexin 43 in the human hair follicle: emphasis on the connexin 43 protein levels in the bulge and through the keratinization process
Authors: Flores Angel Fernandez , Varela‐Vazquez Adrian , Mayan Maria D. , Fonseca Eduardo 
Published: September 2017

BackgroundGap junctions form communication compartments between cells. These channels assemble from connexin subunits.ObjectiveTo investigate the immunoexpression of connexin 43 (Cx43) in adult human hair follicles.MethodsCases were retrospectively obtained from our archives.ResultsWe identified immunoexpression of Cx43 in the matrix, the papilla, the outer root sheath, the bulge, the medulla, the cortex, the shaft and the secretory part of the sebaceous gland. There was very low expression (VLE) of Cx43 in the perifollicular sheath, the mantle and the arrector pili muscle. The internal root sheath showed high‐density expression in the bulb. Such expression abruptly decreased at different points in each of its layers at the point of keratinization. The isthmus showed Cx43‐positive staining in the middle layers and all along, whereas there was VLE in the two outermost layers. The infundibulum showed expression all along the middle layers, whereas it showed VLE in the 2 outermost layers and in the 2 or 3 innermost layers.ConclusionsThe bulge contains Cx43. Our results suggest that keratinization in the hair follicle is closely related to the decrease in Cx43 expression.
Phenotypic plasticity in the morphology of small benthic Icelandic Arctic charr (Salvelinus alpinus)
Authors: Kristjánsson Bjarni K. , Leblanc Camille A.‐L. , Skúlason Skúli , Snorrason Sigurður S. , Noakes David L.G. 
Published: September 2017

AbstractIntraspecific phenotypic diversity is the raw material for evolution, so understanding its origin and maintenance is critically important for conservation of biodiversity. Intraspecific diversity in a trait or a suite of traits can result from genetic diversity and/or phenotypic plasticity. The two are, however, not independent as plasticity has been shown to evolve. In this study, we evaluated the importance of phenotypic plasticity in generating morphological diversity in populations of small benthic Arctic charr in Iceland, using a rearing experiment with contrasting modes of feeding. We also examined the association between phenotypic plasticity in offspring groups generated by the contrasting feeding modes and important ecological variables characterising the natural habitats of the respective populations. Although the level of plasticity could not be related to any of the ecological measurements, clear differences in morphological reaction norms among populations suggest that plasticity is an important aspect of morphological diversity of the charr. It is not clear whether that plasticity is adaptive, but it is notable that reaction norms in all populations have similar reaction to the treatments.
Effects of rituximab and dexamethasone on regulatory and proinflammatory B‐cell subsets in patients with primary immune thrombocytopenia
Authors: Gudbrandsdottir Sif , Brimnes Marie , Køllgaard Tania , Hasselbalch Hans C , Nielsen Claus H 
Published: September 2017

AbstractObjectiveTo investigate the cytokine production and surface marker composition of B cells in adult patients with newly diagnosed primary immune thrombocytopenia (ITP) before and 12 months after treatment with rituximab + dexamethasone (RTX+DXM) or dexamethasone (DXM).MethodsPeripheral blood mononuclear cells were isolated from nine patients treated with RTX+DXM, seven patients treated with DXM, and seven healthy donors. Expression of the cell‐surface markers CD5, CD27, CD25, and CD19, and intracellular content of IL‐6 and IL‐10 were measured by flow cytometry.ResultsPBMCs from ITP patients at baseline contained a lower proportion of IL‐10+ B cells (P < .01) and IL‐6+ B cells (P < .01) than healthy controls. All patients responded to therapy and levels were normalized at 12 months. The proportion of CD5+ B cells increased (P < .01) and CD27+ memory B cells decreased (P < .05) 12 months after treatment with RTX+DXM compared to baseline, with an inverse correlation between platelet numbers and the proportion of CD27+ B cells (R = −0.71; P < .05).ConclusionBoth treatment regimens normalized the frequencies of cytokine‐producing B cells. The additional increase in CD5+ B cells after RTX+DXM is compatible with induction of Bregs.
Using spatiotemporal source separation to identify prominent features in multichannel data without sinusoidal filters
Authors: Cohen Michael X 
Published: September 2017

AbstractThe number of simultaneously recorded electrodes in neuroscience is steadily increasing, providing new opportunities for understanding brain function, but also new challenges for appropriately dealing with the increase in dimensionality. Multivariate source separation analysis methods have been particularly effective at improving signal‐to‐noise ratio while reducing the dimensionality of the data and are widely used for cleaning, classifying and source‐localizing multichannel neural time series data. Most source separation methods produce a spatial component (that is, a weighted combination of channels to produce one time series); here, this is extended to apply source separation to a time series, with the idea of obtaining a weighted combination of successive time points, such that the weights are optimized to satisfy some criteria. This is achieved via a two‐stage source separation procedure, in which an optimal spatial filter is first constructed and then its optimal temporal basis function is computed. This second stage is achieved with a time‐delay‐embedding matrix, in which additional rows of a matrix are created from time‐delayed versions of existing rows. The optimal spatial and temporal weights can be obtained by solving a generalized eigendecomposition of covariance matrices. The method is demonstrated in simulated data and in an empirical electroencephalogram study on theta‐band activity during response conflict. Spatiotemporal source separation has several advantages, including defining empirical filters without the need to apply sinusoidal narrowband filters.
Who Are Heritage Writers? Language Experiences and Writing Proficiency
Authors: Gatti Alberta , O'Neill Teresa 
Published: September 2017

AbstractThis article explores the relationship between the writing proficiency of heritage speakers of Mandarin Chinese, Korean, and Spanish and their context of acquisition, educational experiences, and language practices. Biographical data and proficiency ratings obtained with the ACTFL Writing Proficiency Test were collected for 187 adult heritage speakers. These data are analyzed in order to shed light on connections between the writing proficiency of heritage speakers of these three languages and their language experiences, which have implications for placement and pedagogy in the postsecondary setting. The results of the analysis are then deployed in a series of recommendations to support the development of writing proficiency in the classroom. The authors advocate a proficiency‐oriented approach to the teaching of heritage language that leverages the learners’ linguistic resources.