bluuebunny/crossref_metadata_2025_split huggingface dataset:
Learning at variable attentional load requires cooperation between working memory, meta-learning and attention-augmented reinforcement learning
Authors: Womelsdorf Thilo , Watson Marcus R. , Tiesinga Paul 
Published: September 2020

AbstractFlexible learning of changing reward contingencies can be realized with different strategies. A fast learning strategy involves using working memory of recently rewarded objects to guide choices. A slower learning strategy uses prediction errors to gradually update value expectations to improve choices. How the fast and slow strategies work together in scenarios with real-world stimulus complexity is not well known. Here, we disentangle their relative contributions in rhesus monkeys while they learned the relevance of object features at variable attentional load. We found that learning behavior across six subjects is consistently best predicted with a model combining (i) fast working memory (ii) slower reinforcement learning from differently weighted positive and negative prediction errors, as well as (iii) selective suppression of non-chosen feature values and (iv) a meta-learning mechanism adjusting exploration rates based on a memory trace of recent errors. These mechanisms cooperate differently at low and high attentional loads. While working memory was essential for efficient learning at lower attentional loads, enhanced weighting of negative prediction errors and meta-learning were essential for efficient learning at higher attentional loads. Together, these findings pinpoint a canonical set of learning mechanisms and demonstrate how they cooperate when subjects flexibly adjust to environments with variable real-world attentional demands.Significance statementLearning which visual features are relevant for achieving our goals is challenging in real-world scenarios with multiple distracting features and feature dimensions. It is known that in such scenarios learning benefits significantly from attentional prioritization. Here we show that beyond attention, flexible learning uses a working memory system, a separate learning gain for avoiding negative outcomes, and a meta-learning process that adaptively increases exploration rates whenever errors accumulate. These subcomponent processes of cognitive flexibility depend on distinct learning signals that operate at varying timescales, including the most recent reward outcome (for working memory), memories of recent outcomes (for adjusting exploration), and reward prediction errors (for attention augmented reinforcement learning). These results illustrate the specific mechanisms that cooperate during cognitive flexibility.
Genetic improvement of wheat early vigor promote weed-competitiveness under Mediterranean climate
Authors: Aharon Shlomi , Fadida-Myers Aaviya , Nashef Kamal , Ben-David Roi , Lati Ran N. , Peleg Zvi 
Published: September 2020

AbstractChemical weed-control is the most effective practice for wheat, however, rapid evolution of herbicide-resistant weeds threat food-security and calls for integration of non-chemical practices. We hypothesis that integration of GAR dwarfing-genes into elite wheat cultivars can promote early vigor and weed-competitiveness under Mediterranean climate. We develop near-isogenic lines of bread wheat cultivars with GAR dwarfing genes and evaluate them for early vigor and weed-competitiveness under various environmental and management conditions to identify promising NIL for weed-competitiveness and grain yield. While all three NILs, OC1 (Rht8,12), ZC4 (Rht12,13), and BNMF12 (Rht12), responded to gibberellic acid, they exhibited differences in early vigor. Greenhouse and field evaluation highlighted OC1 as a promising line, with significant advantage in early vigor over its parental. To facilitate accurate and continuous early vigor data collection, we applied non-destructive image-based phenotyping approaches which offers non-expensive and end-user friendly solution for selection. NIL OC1 was tested under different weed density level, infestation waves, and temperatures and highlight the complex genotypic × environmental × management interactions. Our findings demonstrate the potential of genetic modification of dwarfing genes as promising approach to improve weed-competitiveness, and serve as basis for future breeding efforts to support sustainable wheat production under semi-arid Mediterranean climate.
Signal separability in integrated neurophotonics
Authors: Yatsenko Dimitri , Moreaux Laurent C. , Choi Jaebin , Tolias Andreas S. , Shepard Kenneth L. , Roukes Michael L. 
Published: September 2020

AbstractA new modality Photonic probes record fluorescent signals by using arrays of light emitters and detectors embedded in neural tissue. Neither the emitted nor collected light fields are focused. Instead, in proposed configurations, hundreds of emitters will form rapid sequences of structured illumination patterns—providing sufficient spatial and temporal differentiation of neural signals for computational demixing. Here we define criteria for evaluating probe designs for achieving better signal separability. We find that probe geometry has profound, often unintuitive, effects on the separability of neural signals, providing initial design guidelines to achieve separation of individual cells in densely labeled populations.
Defining a Global Map of Functional Group Based 3D Ligand-binding Motifs
Authors: Yang Liu , He Wei , Yun Yuehui , Gao Yongxiang , Zhu Zhongliang , Teng Maikun , Liang Zhi , Niu Liwen 
Published: September 2020

AbstractUncovering conserved 3D protein-ligand binding patterns at the basis of functional groups (FGs) shared by a variety of small molecules can greatly expand our knowledge of protein-ligand interactions. Despite that conserved binding patterns for a few commonly used FGs have been reported in the literature, large-scale identification and evaluation of FG-based 3D binding motifs are still lacking. Here, we developed AFTME, an alignment-free method for automatic mapping of 3D motifs to different FGs of a specific ligand through two-dimensional clustering. Applying our method to 233 nature-existing ligands, we defined 481 FG-binding motifs that are highly conserved across different ligand-binding pockets. Systematic analysis further reveals four main classes of binding motifs corresponding to distinct sets of FGs. Combinations of FG-binding motifs facilitate proteins to bind a wide spectrum of ligands with various binding affinities. Finally, we showed that these general binding patterns are also applicable to target-drug interactions, providing new insights into structure-based drug design.
MicroED structure of the human adenosine receptor determined from a single nanocrystal in LCP
Authors: Martynowycz Michael W. , Shiriaeva Anna , Ge Xuanrui , Hattne Johan , Nannenga Brent L. , Cherezov Vadim , Gonen Tamir 
Published: September 2020

AbstractG Protein-Coupled Receptors (GPCRs), or 7-transmembrane receptors, are a superfamily of membrane proteins that are critically important to physiological processes in the human body. Determining high-resolution structures of GPCRs without signaling partners bound requires crystallization in lipidic cubic phase (LCP). GPCR crystals grown in LCP are often too small for traditional X-ray crystallography. These microcrystals are ideal for investigation by microcrystal electron diffraction (MicroED), but the gel-like nature of LCP makes traditional approaches to MicroED sample preparation insurmountable. Here we show that the structure of a human A2Aadenosine receptor can be determined by MicroED after converting the LCP into the sponge phase followed by cryoFIB milling. We determined the structure of the A2Areceptor to 2.8 Å resolution and resolved an antagonist in its orthosteric ligand-binding site as well as 4 cholesterol molecules bound to the receptor. This study lays the groundwork for future GPCR structural studies using single microcrystals that would otherwise be impossible by other crystallographic methods.One sentence summaryFIB milled LCP-GPCR structure determined by MicroED
Estimating the Impact of Self-Management Education, Influenza Vaccines, Nebulizers, and Spacers on Healthcare Utilization and Expenditures for Medicaid-Enrolled Children with Asthma
Authors: Yildirim Melike , Griffin Paul , Keskinocak Pinar , O’Connor Jean , Swann Julie L 
Published: September 2020

IntroductionWe quantify the effect of a set of interventions including asthma self-management education, influenza vaccination, spacers, and nebulizers on healthcare utilization and expenditures for Medicaid-enrolled children with asthma in New York and Michigan.MethodsWe obtained patients’ data from Medicaid Analytic eXtract files and evaluated patients with persistent asthma in 2010 and 2011. We used difference-in-difference regression to quantify the effect of the intervention on the probability of asthma-related healthcare utilization, asthma medication, and utilization costs. We estimated the average change in outcome measures from pre-intervention/intervention (2010) to post-intervention (2011) periods for the intervention group by comparing this with the average change in the control group over the same time horizon.ResultsAll of the interventions reduced both utilization and asthma medication costs. Asthma self-management education, nebulizer, and spacer interventions reduced the probability of emergency department (20.8-1.5 %, 95%CI 19.7-21.9% vs. 0.5-2.5% respectively) and inpatient (3.5-0.8%, 95%CI 2.1-4.9% vs. 0.4-1.2%, respectively) utilizations. Influenza vaccine decreased the probability of primary care physician (6-3.5%, 95%CI 4.4-7.6% vs. 1.5-5.5%, respectively) visit. The reductions varied by state and intervention.ConclusionsPromoting asthma self-management education, influenza vaccinations, nebulizers, and spacers can decrease the frequency of healthcare utilization and asthma-related expenditures while improving medication adherence.
No evidence ofToxoplasma gondiiinfection in urban and rural squirrels
Authors: Kinnunen Riikka P , Schmidt Chloé , Hernández-Ortiz Adrián , Garroway Colin J 
Published: September 2020

AbstractWildlife in cities can act as reservoirs for parasites that can infect domestic pets and have implications for human health. For example, the Coccidian parasiteToxoplasma gondiican infect all mammalian species, with felids acting as the only definitive hosts. Rodents, such as squirrels, could play an important role in urban infection dynamics ofT. gondii, as squirrels occur at higher densities in cities than in natural environments and regularly share their territories with cats. In urban and suburban areas squirrels can encounter infectious oocysts shed in cat feces in contaminated soil or in the food they eat. They are also preyed upon by cats making them a potentially important species for completing theT. gondiilife cycle in cities. We hypothesized that due to increased exposure to cats, urban squirrels would be more susceptible toT. gondiiinfection relative to squirrels in more natural areas. We investigated this using molecular and serological methods on samples collected from American red squirrels (Tamiasciurus hudsonicus), eastern grey squirrels (Sciurus carolinensis), northern flying squirrels (Glaucomys sabrinus), and least chipmunks (Tamias minimus) in and around the city of Winnipeg, Manitoba, Canada. We tested a total of 230 tissue samples from 46 squirrels forT. gondiiDNA using quantitative PCR and supplemented these data with analyses of 13 serum samples from grey squirrels (Sciurus carolinensis) testing forT. gondiiantibodies by indirect ELISA. We found no evidence ofT. gondiiinfection in any squirrel. This suggests that squirrels may not be important intermediate hosts ofT. gondiiin cities and do not need to be considered as sources of infection to cats.
Striatal seeding of protofibrillar alpha-synuclein causes cortical hyperreactivity in behaving mice
Authors: Blumenstock Sonja , Sun Fanfan , Marinković Petar , Sgobio Carmelo , Liebscher Sabine , Herms Jochen 
Published: September 2020

SummaryAlpha-synucleinopathies are characterized by self-aggregation of the protein alpha-synuclein (a-syn), causing alterations on the molecular and cellular level. To unravel the impact of transneuronal spreading and templated misfolding of a-syn on the microcircuitry of remotely connected brain areas, we investigated cortical neuron function in awake mice 9 months after a single intrastriatal injection of a-syn preformed fibrils (PFFs), usingin vivotwo-photon calcium imaging. We found altered function of layer 2/3 cortical neurons in somatosensory cortex (S1) of PFF-inoculated mice, as witnessed by an enhanced response to whisking and increased synchrony, accompanied by a decrease in baseline Ca2+levels. Stereological analyses revealed a reduction in GAD67-positive inhibitory cells in S1 in PFF-injected brains. These findings point to a disturbed excitation/inhibition balance as an important pathomechanism in alpha-synucleinopathies and demonstrate a clear association between the spread of toxic proteins and the initiation of altered neuronal function in remotely connected areas.
Shifts in the thermal niche of fruit trees under climate change: the case of peach cultivation in France
Authors: Vanalli C. , Casagrandi R. , Gatto M. , Bevacqua D. 
Published: September 2020

AbstractClimate influences plant phenological traits, thus playing a key role in defining the geographical range of crops. Foreseeing the impact of climate change on fruit trees is essential to inform policy decisions to guide the adaptation to new climatic conditions. To this end, we propose and use a phenological process-based model to assess the impacts of climate change upon the phenology, the suitability and the distribution of economically important cultivars of peach (Prunus persica), across the entire continental France. The model combines temperature dependent sub-models of dormancy, blooming, fruit survival and ripening, using chilling units, forcing units, frost occurrence and growing degree days, respectively. We find that climate change will have divergent impacts upon peach production. On the one hand, blooming will occur earlier, warmer temperatures will decrease spring frost occurrence and fruit ripening will be easily achieved before the start of fall. On the other hand, milder winters will impede the plant buds from breaking endodormancy, with consequent abnormal patterns of fruit development or even blooming failure. This latter impact will dramatically shift the geographic range of sites where peach production will be profitable. This shift will mainly be from the south of France (Languedoc-Roussillon, Rhône-Alpes and Provence-Alpes-Côte d’Azur), to northwestern areas where the winter chilling requirement will still be fulfilled. Our study provides novel insights for understanding and forecasting climate change impacts on peach phenology and it is the first framework that maps the ecological thermal niche of peach at national level.
A Multistaged Hyperparallel Optimization of the Fuzzy-Logic Mechanistic Model of Molecular Regulation
Authors: Aiyetan Paul 
Published: September 2020

AbstractMotivationAlthough it circumvents hyperparameter estimation of ordinary differential equation (ODE) based models and the complexities of many other models, the computational time complexity of a fuzzy logic regulatory model inference problem, particularly at higher order of interactions, quickly approaches those of computationally intractable problems. This undermines the benefits inherent in the simplicity and strength of the fuzzy logic-based molecular regulatory inference approach.ResultsFor a sample inference problem – molecular regulation of vorinostat resistance in the HCT116 colon cancer cell lines, our modeled, designed and implemented “multistaged-hyperparallel” optimization approach significantly shortened the time to model inference from about 485.6 hours (20.2 days) to approximately 9.6 hours (0.4 days), compared to an optimized version of a previous implementation.AvailabilityThe multistaged-hyperparallel method is implemented as a plugin in the JFuzzyMachine tool, freely available at the GitHub repository locationshttps://github.com/paiyetan/jfuzzymachineandhttps://github.com/paiyetan/jfuzzymachine/releases/tag/v1.7.21. Source codes and binaries are freely available at the specified URLs.Contactpaiyetan@gmu.edu
Genomic sequencing confirms absence of introgression despite past hybridisation between a common and a critically endangered bird and its common congener
Authors: Forsdick Natalie J. , Martini Denise , Brown Liz , Cross Hugh B. , Maloney Richard F. , Steeves Tammy E. , Knapp Michael 
Published: September 2020

AbstractGenetic swamping resulting from interspecific hybridisation can increase extinction risk for threatened species. The development of high-throughput and reduced-representation genomic sequencing and analyses to generate large numbers of high resolution genomic markers has the potential to reveal introgression previously undetected using small numbers of genetic markers. However, few studies to date have implemented genomic tools to assess the extent of interspecific hybridisation in threatened species. Here we investigate the utility of genome-wide single nucleotide polymorphisms (SNPs) to detect introgression resulting from past interspecific hybridisation in one of the world’s rarest birds. Anthropogenic impacts have resulted in hybridisation and subsequent backcrossing of the critically endangered Aotearoa New Zealand endemic kakī (black stilts;Himantopus novaezelandiae) with the non-threatened self-introduced congeneric poaka (Aotearoa New Zealand population of pied stilts,Himantopus himantopus leucocephalus), yet genetic analyses with a limited set of microsatellite markers revealed no evidence of introgression of poaka genetic material in kakī, excluding one individual. We use genomic data for ∼63% of the wild adult kakī population to reassess the extent of introgression resulting from hybridisation between kakī and poaka. Consistent with previous genetic analyses, we detected no introgression from poaka into kakī. These collective results indicate that, for kakī, existing microsatellite markers provide a robust, cost-effective approach to detect cryptic hybrids. Further, for well-differentiated species, the use of genomic markers may not be required to detect admixed individuals.
Impact of COVID-19 on Hospital Admission of Acute Stroke patients in Bangladesh
Authors: Hasan A T M Hasibul , Das Subir Chandra , Islam Muhammad Sougatul , Mansur Mohaimen , Shawon Md Shajedur Rahman , Hassan Rashedul , Hoque Chowdhury Mohammad Shah Jahirul , Mondal Md Badrul Alam , Mohammad Quazi Deen 
Published: September 2020

AbstractBackgroundWith the proposed pathophysiologic mechanism of neurologic injury by SARS COV-2 the frequency of stroke and henceforth the related hospital admissions were expected to rise. In this paper we investigate this presumption by comparing the frequency of admissions of stroke cases in Bangladesh before and during the pandemic.MethodsWe conducted a retrospective analysis of stroke admissions in a 100-bed stroke unit at the National Institute of Neurosciences and Hospital (NINS&H) which is considerably a large stroke unit. We considered all the admitted cases from the 1stJanuary to the 30thJune, 2020. We used Poisson regressions to determine whether statistically significant changes in admission counts can be found before and after 25 March since when there is a surge in COVID-19 infections.ResultsA total of 1394 stroke patients got admitted during the study period. Half of the patients were older than 60 years, whereas only 2.6% were 30 years old or younger with a male-female ratio of 1.06:1. From January to March, 2020 the mean rate of admission was 302.3 cases per month which dropped to 162.3 cases per month from April to June with an overall reduction of 46.3% in acute stroke admission per month. In those two periods, reductions in average admission per month for ischemic stroke (IST), intracerebral hemorrhage (ICH), subarachnoid hemorrhage (SAH) and venous stroke (VS) were 45.5%, 37.2%, 71.4% and 39.0%, respectively. Based on weekly data, results of Poisson regressions confirm that the average number of admissions per week dropped significantly during the last three months of the sample period. Further, in the first three months, a total of 22 cases of hyperacute stroke management were done whereas in the last three months there was an 86.4% reduction in the number of hyperacute stroke patients getting reperfusion treatment. Only 38 patients (2.7%) were later found to be RT- PCR for SARS Cov-2 positive based on nasal swab testing.ConclusionOur study revealed more than fifty percent reduction in acute stroke admission during the COVID-19 pandemic. It is still elusive whether the reduction is related to the fear of getting infected by COVID-19 from hospitalization or the overall restriction on public movement and stay-home measures.
Trends in plant ecology research in Ethiopia (1969-2019): Systematic analysis
Authors: Gebrehiwot Kflay , Demissew Sebsebe 
Published: September 2020

AbstractThe objective of this paper was to systematically analyze the trend of plant ecological research in Ethiopia. The inclusion and exclusion of the articles for analysis were performed using Reporting Standards for Systematic Evidence Syntheses (ROSES) flow diagram developed for systematic review/meta-analysis. The number of articles published, authors, and collaboration has increased dramatically since the 1960s. Most of the research largely focused on the Dry evergreen Afromontane Forest and grassland complex (DAF) and Moist evergreen Afromontane Forest (MAF) vegetation types, comprising of about 52.6%. Of the remaining vegetation types, the woodlands (14.3%) i.e.Acacia-Commiphorawoodland and bushland proper (ACW), andCombretum-Terminaliawoodland and wooded grassland (CTW), desert and semi-desert scrubland (DSS) (2.3%), and the Afroalpine (AA) and Ericaceous Belt (EB) (1.5%) received little attention. A descriptive study on plant community ecology revolving on floristic composition and community structure is the dominant research theme, which revealed a narrow theme in contrast to the global trend. Other plant ecological studies such as reproductive and dispersal ecology of invasive plant species, and pollination ecology seems largely a neglected topic by the academia. Furthermore, the recommendations forwarded are not result-based. As a future direction, the Ethiopian government should develop a project database both for completed and ongoing projects.