bluuebunny/crossref_metadata_2025_split huggingface dataset:
Measurement of the mapping between intracranial EEG and fMRI recordings in the human brain
Authors: Carmichael DW , Vulliemoz S , Murta T , Chaudhary U. , Perani S , Rodionov R , Rosa MJ , Friston KJ , Lemieux L 
Published: December 2017

AbstractThere are considerable gaps in our understanding of the relationship between human brain activity measured at different temporal and spatial scales by intracranial electroencephalography and fMRI. By comparing individual features and summary descriptions of intracranial EEG activity we determined which best predict fMRI changes in the sensorimotor cortex in two brain states: at rest and during motor performance. We also then examine the specificity of this relationship to spatial colocalisation of the two signals.We acquired electrocorticography and fMRI simultaneously (ECoG-fMRI) in the sensorimotor cortex of 3 patients with epilepsy. During motor activity, high gamma power was the only frequency band where the electrophysiological response was colocalised with fMRI measures across all subjects. The best model of fMRI changes was its principal components, a parsimonious description of the entire ECoG spectrogram. This model performed much better than a model based on the classical frequency bands both during task and rest periods or models derived on a summary of cross spectral changes (e.g. ‘root mean squared EEG frequency’). This suggests that the region specific fMRI signal is reflected in spatially and spectrally distributed EEG activity.
Division of labor during biofilm matrix production
Authors: Dragoš Anna , Kiesewalter Heiko , Martin Marivic , Hsu Chih-Yu , Hartmann Raimo , Wechsler Tobias , Eriksen Carsten , Brix Susanne , Drescher Knut , Stanley-Wall Nicola , Kümmerli Rolf , Kovács Ákos T. 
Published: December 2017

SummaryOrganisms as simple as bacteria can engage in complex collective actions, such as group motility and fruiting body formation. Some of these actions involve a division of labor, where phenotypically specialized clonal subpopulations, or genetically distinct lineages cooperate with each other by performing complementary tasks. Here, we combine experimental and computational approaches to investigate potential benefits arising from division of labor during biofilm matrix production. We show that both phenotypic and genetic strategies for a division of labor can promote collective biofilm formation in the soil bacteriumBacillus subtilis. In this species, biofilm matrix consists of two major components; EPS and TasA. We observed that clonal groups ofB. subtilisphenotypically segregate into three subpopulations composed of matrix non-producers, EPS-producers, and generalists, which produce both EPS and TasA. This incomplete phenotypic specialization was outperformed by a genetic division of labor, where two mutants, engineered as specialists, complemented each other by exchanging EPS and TasA. The relative fitness of the two mutants displayed a negative frequency dependence bothin vitroand on plant roots, with strain frequency reaching a stable equilibrium at 30% TasA-producers, corresponding exactly to the population composition where group productivity is maximized. Using individual-based modelling, we show that asymmetries in strain ratio can arise due to differences in the relative benefits that matrix compounds generate for the collective; and that genetic division of labor can be favored when it breaks metabolic constraints associated with the simultaneous production of two matrix components.Highlights- matrix components EPS and TasA are costly public goods inB. subtilisbiofilms- genetic division of labor using Δepsand ΔtasAfosters maximal biofilm productivity- Δepsand ΔtasAcooperation is evolutionary stable in laboratory and ecological systems- costly metabolic coupling of public goods favors genetic division of labor
Genetic structure and sex-biased gene flow in the history of southern African populations
Authors: Bajić Vladimir , Barbieri Chiara , Hübner Alexander , Güldemann Tom , Naumann Christfried , Gerlach Linda , Berthold Falko , Nakagawa Hirosi , Mpoloka Sununguko W. , Roewer Lutz , Purps Josephine , Stoneking Mark , Pakendorf Brigitte 
Published: December 2017

ABSTRACTObjectivesWe investigated the genetic history of southern African populations with a special focus on their paternal history. We reexamined previous claims that the Y-chromosome haplogroup E1b1b was brought to southern Africa by pastoralists from eastern Africa, and investigated patterns of sex-biased gene flow in southern Africa.Material and MethodsWe analyzed previously published complete mtDNA genome sequences and ~900 kb of NRY sequences from 23 populations from Namibia, Botswana and Zambia, as well as haplogroup frequencies from a large sample of southern African populations and 23 newly genotyped Y-linked STR loci for samples assigned to haplogroup E1b1b.ResultsOur results support an eastern African origin for Y-chromosome haplogroup E1b1b; however, its current distribution in southern Africa is not strongly associated with pastoralism, suggesting a more complex origin for pastoralism in this region. We confirm that the Bantu expansion had a notable genetic impact in southern Africa, and that in this region it was probably a rapid, male-dominated expansion. Furthermore, we find a significant increase in the intensity of sex-biased gene flow from north to south, which may reflect changes in the social dynamics between Khoisan and Bantu groups over time.ConclusionsOur study shows that the population history of southern Africa has been very complex, with different immigrating groups mixing to different degrees with the autochthonous populations. The Bantu expansion led to heavily sex-biased admixture as a result of interactions between Khoisan females and Bantu males, with a geographic gradient which may reflect changes in the social dynamics between Khoisan and Bantu groups over time.
Characterizing co-expression networks underpinning maize stalk rot virulence inFusarium verticillioidesthrough computational subnetwork module analyses
Authors: Kim Man S. , Zhang Huan , Yan Huijuan , Yoon Byung-Jun , Shim Won Bo 
Published: December 2017

AbstractFusarium verticillioidesis recognized as an important stalk rot pathogen of maize worldwide, but our knowledge of genetic mechanisms underpinning this pathosystem is limited. Previously, we identified a striatin-like protein Fsr1 that plays an important role in stalk rot. To further characterize transcriptome networks downstream of Fsr1, we performed next-generation sequencing (NGS) to investigate relative read abundance and also to infer co-expression networks utilizing the preprocessed expression data through partial correlation. We used a probabilistic pathway activity inference strategy to identify functional subnetwork modules likely involved in virulence. Each subnetwork modules consisted of multiple correlated genes with coordinated expression patterns, but the collective activation levels were significantly different inF. verticillioideswild type versus the mutant. We also identified putative hub genes from predicted subnetworks for functional validation and network robustness studies through mutagenesis, virulence and qPCR studies. Our results suggest that these genes are important virulence genes that regulate the expression of closely correlated genes, demonstrating that these are important hubs of their respective subnetworks. Lastly, we used keyF. verticillioidesvirulence genes to computationally predict a subnetwork of maize genes that potentially respond to fungal genes by applying cointegration-correlation-expression strategy.
A Molecular Odorant Transduction Model and the Complexity of Combinatorial Encoding in the Drosophila Antenna
Authors: Lazar Aurel A. , Yeh Chung-Heng 
Published: December 2017

AbstractIn the past two decades, a substantial amount of work characterized the odorant receptors, neuroanatomy and odorant response properties of the early olfactory system of Drosophila melanogaster. Yet many odorant receptors remain only partially characterized and, the odorant transduction process and the axon hillock spiking mechanism of the olfactory sensory neurons (OSNs) have yet to be fully determined.Identity and concentration, two key aspects of olfactory coding, originate in the odorant transduction process. Detailed molecular models of the odorant transduction process are, however, scarce for fruit flies. To address these challenges we advance a comprehensive model of fruit fly OSNs as a cascade consisting of an odorant transduction process (OTP) and a biophysical spike generator (BSG). We model identity and concentration in OTP using an odorant-receptor binding rate tensor, modulated by the odorant concentration profile, and an odorant-receptor dissociation rate tensor, and quantitatively describe the ligand binding/dissociation process. We model the BSG as a Connor-Stevens point neuron.The resulting combinatorial encoding model of the Drosophila antenna provides a theoretical foundation for understanding the neural code of both odorant identity and odorant concentration and advances the state-of-the-art in a number of ways. First, it quantifies on the molecular level the combinatorial complexity of the transformation taking place in the antennae. The concentration-dependent combinatorial code determines the complexity of the input space driving olfactory processing in the downstream neuropils, such as odorant recognition and olfactory associative learning. Second, the model is biologically validated using multiple electrophysiology recordings. Third, the model demonstrates that the currently available data for odorant-receptor responses only enable the estimation of the affinity of the odorant-receptor pairs. The odorant-dissociation rate is only available for a few odorant-receptor pairs. Finally, our model calls for new experiments for massively identifying the odorant-receptor dissociation rates of relevance to flies.
Functional triplet motifs underlie accurate predictions of single-trial responses in populations of tuned and untuned V1 neurons
Authors: Dechery Joseph B , MacLean Jason N 
Published: December 2017

AbstractVisual stimuli are encoded in the activity patterns of neocortical neuronal populations. Trial-averaged neuronal activity is selectively modulated by particular visual stimulus parameters, such as the direction of a moving bar of light, resulting in well-defined tuning properties. However, a large number of neurons in visual cortex remain unmodulated by any given stimulus parameter, and the role of this untuned population is not well understood. Here, we use two-photon calcium imaging to record, in an unbiased manner, from large populations of layer 2/3 excitatory neurons in mouse primary visual cortex to describe co-varying activity on single trials in populations consisting of tuned and untuned neurons. Specifically, we summarize pairwise covariability with an asymmetric partial correlation coefficient, allowing us to analyze the population correlation structure with graph theory. Using the graph neighbors of a neuron, we find that the local population, including tuned and untuned neurons, are able to predict individual neuron activity on a single trial basis and recapitulate average tuning properties of tuned neurons. We also find that a specific functional triplet motif in the graph results in the best predictions, suggesting a signature of informative correlations in these populations. Variance explained in total population activity scales with the number of neurons imaged, suggesting larger sample sizes are required to fully capture local network interactions. In summary, we show that unbiased sampling of the local population can explain single trial response variability as well as trial-averaged tuning properties in V1, and the ability to predict responses is tied to the occurrence of a functional triplet motif.Author summaryV1 populations have historically been characterized by single cell response properties and pairwise co-variability. Many cells, however, do not show obvious dependencies to a given stimulus or behavioral task, and have consequently gone unanalyzed. We densely record from V1 populations to measure how trial-to-trial response variability relates to these previously understudied neurons. We find that individual neurons, regardless of response properties, are inextricably dependent on the population in which they are embedded. By studying patterns of correlations between groups of neurons, we identify a specific triplet motif that predicts this dependence on local population activity. Only by studying large populations simultaneously were we able to find an emergent property of this information. These results imply that understanding how the visual system operates with substantial trial-to-trial variability will necessitate a network perspective that accounts for both visual stimuli and activity in the local population.
Evaluating two-stage holistic production systems using novel CSDEA approach
Authors: Zhai Dujun , Jin Minyue , Shang Jennifer , Ji Chenfeng 
Published: December 2017

Purpose
The purpose of this paper is to apply data envelopment analysis (DEA) techniques to the collective decision-making environment to appraise two-stage production process under different decision preferences.

Design/methodology/approach
The authors propose a novel multi-criteria group decision-making approach that uses consensus-strategic data envelopment analysis (CSDEA) to appraise two-stage production process under two different decision strategies, which are efficiency- and fairness-based group decision preferences.

Findings
The authors find that the proposed CSDEA model evaluates the performance of the decision-making units (DMUs) not by diminishing other competitors but rather based on group interests of the entire decision set.

Originality/value
The authors extend Li’s two-stage model to cases that consider both intermediate inputs and outputs. The authors address the issue of incorporating collective managerial strategy into multi-criteria group decision-making and propose a novel CSDEA model that considers not only the individual-level performance of a DMU but also the group-level or collective decision strategies.
‘Deal’ or ‘No Deal’? Impacts of Alternative Post‐Brexit Trade Agreements on UK Agriculture
Authors: Feng Siyi , Patton Myles , Binfield Julian , Davis John 
Published: December 2017

SummaryBrexit will have important implications for UK agricultural commodity markets due to potentially significant changes to trade flows. We quantify the sectoral impacts on UK agriculture of three illustrative scenarios, which capture a broad range of potential trade arrangements: Bespoke Free Trade Deal, WTO Default and Unilateral Trade Liberalisation. It is estimated that the projected market impacts are relatively small if the UK negotiates a Bespoke Free Trade Agreement with the EU. The projected impacts are much greater under the two other scenarios, which capture potential trade arrangements if ‘no deal’ is reached. The high tariffs imposed under the WTO default scenario lead to significant adjustments in trade between the UK and EU‐27, with the impact on the domestic UK market depending on whether the UK is a net importer or a net exporter of the relevant commodity. All sectors experience price and production declines under the trade liberalisation scenario in which the UK unilaterally sets tariffs on imports from both the EU‐27 and the rest of the world to zero; the impacts are particularly severe in the beef and sheep sectors where international competition is very strong.
Polyethylene glycol‐based bowel preparation before colonoscopy for selected inpatients: A pilot study
Authors: Pontone Stefano , Palma Rossella , Panetta Cristina , Eberspacher Chiara , Angelini Rita , Pironi Daniele , Filippini Angelo , Pontone Paolo 
Published: December 2017

OBJECTIVETo evaluate the impact of a new same‐day, low‐dose 1‐L polyethylene glycol‐based (1‐L PEG) bowel preparation on the diagnostic rating of selected hospitalized patients and its tolerability, with risk factors for inadequate bowel preparation.METHODSA single‐center prospective pilot study was conducted with hospitalized patients scheduled for colonoscopy, presenting risk factors for poor bowel preparation, such as bleeding or subocclusive symptoms. The included patients were randomly divided in two groups, which received either a same‐day 1‐L PEG (group A) or a split‐dose 4‐L PEG (group B), and performed a colonoscopy within 4 h of the last dose.RESULTSIn all, 44 inpatients [27 males; mean age 63.5 years (range 20–94 years)] were enrolled. Optimal bowel cleansing was reached in 64% and 55% (P = 0.64) of patients in groups A and B, respectively. The adenoma detection rate was 14% (group A) and 18% (group B) (P = 0.34). A valid diagnosis was reached in 38 (86%) of 44 patients (21 in group A and 17 in group B) after a mean hospitalization of 3 days for group A and 6 days for group B (P = 0.04).CONCLUSIONSOur data support the conclusion that the schedule protocol proposed in this study enables a clear diagnosis in most of the inpatients at high risk of poor bowel preparation and no statistical differences were found between the two groups in terms of successful bowel cleansing achieved. Therefore, the same‐day, low‐dose 1‐L PEG bowel preparation could be introduced for selected inpatients.
Overserving and Allowed Entry of Obviously Alcohol‐Intoxicated Spectators at Sporting Events
Authors: Elgán Tobias H. , Durbeej Natalie , Holder Harold D. , Gripenberg Johanna 
Published: December 2017

BackgroundAlcohol intoxication among spectators at sporting events and related problems, such as violence, are of great concern in many countries around the world. However, knowledge is scarce about whether or not alcohol is served to obviously intoxicated spectators at licensed premises inside and outside the sporting arenas, and if obviously intoxicated spectators are allowed entrance to these events. The objective of this study was therefore to examine the occurrences of overserving at licensed premises inside and outside arenas, and of allowed entry of obviously intoxicated spectators into arenas.MethodsAn observational study assessing the rate of denied alcohol service and denied entry to arenas of trained professional actors portraying a standardized scene of obvious alcohol intoxication (i.e., pseudo‐patrons) was conducted. The scene was developed by an expert panel, and each attempt was monitored by an observer. The settings were 2 arenas hosting matches in the Swedish Premier Football League in the largest city in Sweden and 1 arena in the second largest city, including entrances and licensed premises inside and outside the arenas.ResultsThe rates of denied alcohol service were 66.9% at licensed premises outside the arenas (n = 151) and 24.9% at premises inside the arenas (n = 237). The rate of denied entry to the arenas (n = 102) was 10.8%.ConclusionsOverserving and allowed entry of obviously alcohol‐intoxicated spectators are problematic at sporting events in Sweden and may contribute to high overall intoxication levels among spectators. The differences in server intervention rates indicate that serving staff at licensed premises inside the arenas and entrance staff are not likely to have been trained in responsible beverage service. This result underscores the need for server training among staff at the arenas.
Repairability of skeletal alterations induced by sodium valproate in rats
Authors: Kirihata Yuka , Ban Yoshiki , Nakamori Chiaki , Takagi Hironori , Hashimoto Tomonori , Tsutsumi Shunsuke 
Published: December 2017

ABSTRACTThe present study aimed at examining postnatal repairability of sodium valproate‐induced skeletal alterations in rats. Sodium valproate (400 mg/kg) or the vehicle (distilled water) was orally administrated to pregnant Sprague‐Dawley rats from gestation days 9 to 11. Fetuses and pups were obtained on gestation day 21 and postnatal day 11, respectively, and their skeletons were stained with Alizarin red S and Alcian blue and examined. Sodium valproate‐induced costal and vertebral alterations in the fetuses included discontinued rib cartilage, fused rib, full or short supernumerary rib, bipart ossification of thoracic centrum, supernumerary lumbar vertebrae, and lumbarization. In pups, however, discontinued rib cartilage was not observed, and the incidence of a short supernumerary rib was significantly lower than that in the fetuses, suggesting that these alterations are postnatally repairable.
Barriers to care for chronic hepatitis C in the direct-acting antiviral era: a single-centre experience
Authors: Nguyen Peter , Vutien Philip , Hoang Joseph , Trinh Sam , Le An , Yasukawa Lee Ann , Weber Susan , Henry Linda , Nguyen Mindie H 
Published: December 2017

BackgroundCure rates for chronic hepatitis C have improved dramatically with direct-acting antivirals (DAAs), but treatment barriers remain. We aimed to compare treatment initiation rates and barriers across both interferon-based and DAA-based eras.MethodsWe conducted a retrospective cohort study of all patients with chronic hepatitis C seen at an academic hepatology clinic from 1999 to 2016. Patients were identified to have chronic hepatitis C by the International Classification of Diseases, Ninth Revision codes, and the diagnosis was validated by chart review. Patients were excluded if they did not have at least one visit in hepatology clinic, were under 18 years old or had prior treatment with DAA therapy. Patients were placed in the DAA group if they were seen after 1 January 2014 and had not yet achieved virological cure with prior treatment. All others were considered in the interferon group.Results3202 patients were included (interferon era: n=2688; DAA era: n=514). Despite higher rates of decompensated cirrhosis and medical comorbidities in the DAA era, treatment and sustained virological response rates increased significantly when compared with the interferon era (76.7% vs 22.3%, P<0.001; 88.8% vs 55%, P<0.001, respectively). Lack of follow-up remained a significant reason for non-treatment in both groups (DAA era=24% and interferon era=45%). An additional 8% of patients in the DAA era were not treated due to insurance or issues with cost. In the DAA era, African-Americans, compared with Caucasians, had significantly lower odds of being treated (OR=0.37, P=0.02).ConclusionsDespite higher rates of medical comorbidities in the DAA era, considerable treatment challenges remain including cost, loss to follow-up and ethnic disparities.