bluuebunny/crossref_metadata_2025_split huggingface dataset:
Safety and Efficacy of Antiviral Drugs for the Treatment of Patients with SARS-CoV-2 Infection: A Systematic Review and Meta-analyses
Authors: Torres Zuleika Aponte , Leon Sandra Lopez , Muthuvel Thirumugam , Manivannan Subha , Srivastava Krutika , Pavesi Marco 
Published: September 2020

ABSTRACTObjectiveTo systematically review the safety and efficacy outcomes of using antivirals for the treatment of COVID-19.MethodsFive databases were screened from inception to 27-Aug-2020. The effects of specific drug interventions on safety and efficacy were assessed in COVID-19 patients. Risk Ratios (RRs) with corresponding 95% confidence intervals (CIs) were pooled using random-effects models.ResultsA total of 10 studies were identified which fulfill the inclusion criteria. Patients taking antivirals had 26% less risk of having a severe adverse event (SAE) compared to controls (RR, 0.74, CI:0.62 to 0.89, P=0.002). Clinical improvement at day 14 was observed among the cases treated with antivirals compared to the control group (RR 1.24, CI: 1.00 to 1.53 p=0.05).ConclusionThere is evidence that Remdesivir and LPV/r reduces the hospital length of stay and that patients to which antivirals were administered had less SAE and improvement when compared to patients not prescribed with antivirals. Due to a lack of power and the quality of the studies, it was not possible to determine which antivirals have a greater risk-benefit balance, and therefore the optimal approach to antiviral treatment is still uncertain.
Fish avoid visually noisy environments that reduce their perceptual abilities
Authors: Attwell Joanna R. , Ioannou Christos C. , Reid Chris R. , Herbert-Read James E. 
Published: September 2020

AbstractThe environment contains different forms of ecological noise that can reduce the ability of animals to detect information. Here we ask whether animals can adapt their behaviour to either exploit or avoid areas of their environment with increased dynamic visual noise. By immersing three-spined sticklebacks (Gasterosteus aculeatus) into environments with a simulated form of naturally occurring visual noise – light bands created by the refraction of light from surface waves termed caustic networks – we tested how such visual noise affected the movements, habitat use, and perceptual abilities of these fish. Fish avoided areas of higher visual noise, and achieved this by increasing their activity as a function of the locally perceived noise level, resulting in individuals moving away from noisier areas. By projecting virtual prey into the environment with different levels of visual noise, we found that the fish’s ability to visually detect prey decreased as visual noise increased. We found no evidence that fish increased their exploration (and decreased their refuge use) in environments with increased visual noise, which would have been predicted if they were exploiting increased visual noise to reduce their own likelihood of being detected. Our results indicate that animals can use simple behavioural strategies to mitigate the impacts of dynamic visual noise on their perceptual abilities, thereby improving their likelihood of gathering information in dynamically changing and noisy environments.
Nutrient Export and Periphyton Biomass in a Stream-Lake Basin from the Patagonian Andean Region
Authors: Sosnovsky Alejandro , Lallement Mailén Elizabeth , Rechencq Magalí , Fernández María Valeria , Zattara Eduardo Enrique , Feijoó Claudia Silvina 
Published: September 2020

AbstractWe characterized how land use influenced dissolved nutrients and periphytic algal biomass in an Andean basin from Northwest Patagonia. Nutrient export, especially dissolved inorganic nitrogen increased with human population density. However, no correlation between nutrient concentration and algal biomass was found, which could instead be limited by light availability. Our results suggest that local N-limited ecosystems are liable to eutrophication by increased demographic pressure and that alternative wastewater treatment strategies are necessary for sustainable growth.
Fine–mapping identifiesNAD–ME1as a candidate underlying a major locus controlling temporal variation in primary and specialized metabolism in Arabidopsis
Authors: Francisco Marta , Kliebenstein Daniel J. , Rodríguez Víctor M. , Soengas Pilar , Abilleira Rosaura , Cartea María E. 
Published: September 2020

SummaryPlant metabolism is modulated by a complex interplay between internal signals and external cues. A major goal of all quantitative metabolomic studies is to clone the underlying genes to understand the mechanistic basis of this variation. Using fine-scale genetic mapping, in this work we report the identification and initial characterization ofNAD-DEPENDENT MALIC ENZYME 1(NAD-ME1) as the candidate gene underlying the pleiotropic network Met.II.15 QTL controlling variation in plant metabolism and circadian clock outputs in the Bay × Sha Arabidopsis population. Transcript abundance and promoter analysis inNAD-ME1Bay-0andNAD-ME1Shaalleles confirmed allele-specific expression that appears to be due a polymorphism disrupting a putative circadian cis-element binding site. Analysis of T-DNA insertion lines and heterogeneous inbred families (HIFs) showed that transcript variation of theNAD-ME1gene led to temporal shifts of tricarboxylic acid cycle (TCA) intermediates, glucosinolate (GSL) accumulation and altered regulation of several GSL biosynthesis pathway genes. Untargeted metabolomics analyses reveal complex regulatory networks ofNAD-ME1dependent upon the day-time. The mutant lead to shifts in plant primary metabolites, cell-wall components, isoprenoids, fatty acids and plant immunity phytochemicals, among others. Our findings suggest thatNAD-ME1may act as a key component to coordinate plant primary and secondary metabolism in a time-dependent manner.
The power to detect cultural transmission in the Nuclear Twin Family design with and without polygenic risk scores and in the Transmitted-Non-transmitted (alleles) design
Authors: Bruins S. , Dolan C. V. , Boomsma D. I. 
Published: September 2020

AbstractThe aim of our study is to compare the power of two different approaches to detect passive genotype-environment covariance originating from simultaneous cultural and genetic transmission. In the traditional Nuclear Twin Family Design cultural transmission is estimated on the basis of the phenotypic covariance matrices of the mono- and dizygotic twins and their parents, where phenotyping is required in all family members. A more recent method is the Transmitted-Nontransmitted allele design, which exploits measured genetic variants in parents and offspring to test for effects of nontransmitted alleles from parents. This design requires genome-wide data and a powerful GWA (genome-wide association) study for the phenotype in addition to phenotyping in offspring. We compared the power of both designs. Using exact data simulation, we demonstrate that compared to the Transmitted-Nontransmitted design, the Nuclear Twin Family Design is relatively well-powered to detect cultural transmission and genotype-environment covariance. The power of the Transmitted-Nontransmitted design depends on the predictive power of polygenic risk scores. Adding polygenic risk scores of realistic effect size to the Nuclear Twin Family Design did not result in an appreciable increase the power to detect cultural transmission.
Information-based signal selection improves decoding of attention spotlight from multi-units & local field potentials and enhances correlation with behavior
Authors: De Sousa Ferreira C. , Gaillard C. , Di Bello F. , Ben Hadj Hassen S. , Ben Hamed S. 
Published: September 2020

AbstractThe ability to access brain information in real-time is crucial both for a better understanding of cognitive functions and for the development of therapeutic applications based on brain-machine interfaces. Great success has been achieved in the field of neural motor prosthesis. Progress is still needed in the real-time decoding of higher-order cognitive processes such as covert attention. Recently, we showed that we can track the location of the attentional spotlight using classification methods applied to prefrontal multi-unit activity (MUA) in the non-human primate (Astrand et al., 2016). Importantly, we demonstrated that the decoded (x,y) attentional spotlight parametrically correlates with the behavior of the monkeys thus validating our decoding of attention. We also demonstrate that this spotlight is extremely dynamic (Gaillard et al., 2020). Here, in order to get closer to non-invasive decoding applications, we extend our previous work to local field potential signals (LFP). Specifically, we achieve, for the first time, high decoding accuracy of the (x,y) location of the attentional spotlight from prefrontal LFP signals, to a degree comparable to that achieved from MUA signals, and we show that this LFP content is predictive of behavior. This LFP attention-related information is maximal in the gamma band. In addition, we introduce a novel two-step decoding procedure based on the labelling of maximally attention-informative trials during the decoding procedure. This procedure strongly improves the correlation between our real-time MUA and LFP based decoding and behavioral performance, thus further refining the functional relevance of this real-time decoding of the (x,y) locus of attention. This improvement is more marked for LFP signals than for MUA signals, suggesting that LFP signals may contain other sources of task-related variability than spatial attention information. Overall, this study demonstrates that the attentional spotlight can be accessed from LFP frequency content, in real-time, and can be used to drive high-information content cognitive brain machine interfaces for the development of new therapeutic strategies.HighlightsWe use machine learning to decode attention spotlight from prefrontal MUA & LFP.We achieve high decoding accuracy of (x,y) spatial attention spotlight.(x,y) attention spotlight position accuracy is maximal from LFP gamma frequency range.MUA and LFP decoded attention position predicts behavioral performances.Selecting high information signals improves decoding and behavioral correlates.
Parallel evolution of direct development in frogs – Skin and thyroid gland development in African Squeaker Frogs (Anura: Arthroleptidae:Arthroleptis)
Authors: Naumann Benjamin , Schweiger Susan , Hammel Jörg U. , Müller Hendrik 
Published: September 2020

AbstractCases of parallel evolution offer the possibility to identify adaptive traits and to uncover developmental constraints on the evolutionary trajectories of these traits. The independent evolution of direct development, from the ancestral biphasic life history in frogs is such a case of parallel evolution. In frogs, aquatic larvae (tadpoles) differ profoundly from their adult forms and exhibit a stunning diversity regarding their habitats, morphology and feeding behaviors. The transition from the tadpole to the adult is a climactic, thyroid hormone (TH)-dependent process of profound and fast morphological rearrangement called metamorphosis. One of the organ systems that experiences the most comprehensive metamorphic rearrangements is the skin. Direct-developing frogs lack a free-swimming tadpole and hatch from terrestrial eggs as fully formed froglets. In the few species examined, development is characterized by the condensed and transient formation of some tadpole-specific features and the early formation of adult-specific features during a “cryptic” metamorphosis. In this study we show that skin in direct-developing African squeaker frogs (Arthroleptis) is also repatterned from a tadpole-like to an adult-like histology during a cryptic metamorphosis. This repatterning correlates with an increase of thyroid gland activity. A comparison with data from the Puerto Rican coqui (Eleutherodactylus coqui) reveals that direct development might have evolved in parallel in these frogs by a comparable heterochronic shift of thyroid gland activity. This suggests that the development of many adult-features is still constrained by the ancestral dependency on thyroid hormone signaling.
Model-informed COVID-19 vaccine prioritization strategies by age and serostatus
Authors: Bubar Kate M. , Kissler Stephen M. , Lipsitch Marc , Cobey Sarah , Grad Yonatan H. , Larremore Daniel B. 
Published: September 2020

AbstractWhen a vaccine for COVID-19 becomes available, limited initial supply will raise the question of how to prioritize the available doses and thus underscores the need for transparent, evidence-based strategies that relate knowledge of, and uncertainty in, disease transmission, risk, vaccine efficacy, and existing population immunity. Here, we employ a model-informed approach to vaccine prioritization that evaluates the impact of prioritization strategies on cumulative incidence and mortality and accounts for population factors such as age, contact structure, and seroprevalence, and vaccine factors including imperfect and age-varying efficacy. This framework can be used to evaluate and compare existing strategies, and it can also be used to derive an optimal prioritization strategy to minimize mortality or incidence. We find that a transmission-blocking vaccine should be prioritized to adults ages 20-49y to minimize cumulative incidence and to adults over 60y to minimize mortality. Direct vaccination of adults over 60y minimizes mortality for vaccines that do not block transmission. We also estimate the potential benefit of using individual-level serological tests to redirect doses to only seronegative individuals, improving the marginal impact of each dose. We argue that this serology-informed vaccination approach may improve the efficiency of vaccination efforts while partially addressing existing inequities in COVID-19 burden and impact.
Transcranial direct current stimulation over the left inferior frontal gyrus improves sentence comprehension
Authors: Peristeri Eleni , Wang Zeyi , Herrmann Olivia , Caffo Brian , Frangakis Constantine , Tsapkini Kyrana 
Published: September 2020

AbstractBackgroundThe left inferior frontal gyrus (IFG) has been shown to be involved in sentence comprehension in many studies through its involvement in both semantic and syntactic computations. However, causal evidence for its involvement in sentence comprehension is scarce. We used transcranial direct current stimulation (tDCS) to test the causal involvement of the left IFG in sentence comprehension in a group of individuals with primary progressive aphasia (PPA). These individuals participated in a tDCS study targeting lexical retrieval only, not sentence comprehension, therefore in the present study we report on far-transfer effects of tDCS in sentence comprehension.ObjectiveWe sought to determine whether tDCS over the left inferior frontal gyrus (IFG) coupled with lexical retrieval treatment may improve sentence comprehension in PPA.MethodWithin a sham-controlled, double-blind design, we tested whether 15 daily sessions of anodal tDCS over the left IFG may improve sentence comprehension in 27 people with PPA, and whether the tDCS effects were sustained up to two months post-treatment.ResultsWe found that immediately post-treatment, and up to 2-months post-treatment, there was significantly larger improvement of sentence comprehension in the tDCS condition compared to sham. There were, however, differential effects of tDCS in each PPA variant and sentence-type. Importantly, participants with the epicenter of atrophy over the stimulated area (non-fluent PPA) benefited most from tDCS.ConclusionTDCS over the left IFG induces far-transfer effects and may improve sentence comprehension in PPA. We provide causal evidence that left IFG is a critical area for sentence comprehension.
Periodic variations in the Covid-19 infection and fatality rates
Authors: Peirani S. , Icard Ph. , de Freitas Pacheco J.A. 
Published: September 2020

AbstractPower spectra of infection and mortality rate curves for nineteen countries of different continents were computed. Nine of them show the presence of oscillations with a period of about seven says either in the infection or in the mortality data sets. The computed power spectra for seven countries do no indicate any significant signal of periodicity while the three remaining countries indicate periodic oscillations only in the infection or only in the mortality curve. Data indicate that minima occur generally on weekends. The seven-day periodicity present in infection data of nine countries is robust and seems to be the consequence of different factors as, for instance, higher testing frequency during weekdays or/and an enhanced contamination during social activities during weekends. For the moment, there is no convincing explanation for the seven-day oscillations observed in the mortality curves of some countries.
Examining the relationship between adolescent health behaviors, brain health, and academic achievement using fNIRS
Authors: Papasideris Mia , Safati Adrian , Ayaz Hasan , Morita Plinio , Hall Peter 
Published: September 2020

AbstractBackgroundSeveral adolescent health behaviors have been hypothesized to improve academic performance via their beneficial impact on cognitive control and functional aspects of the prefrontal cortex (PFC). Specifically, exercise, restorative sleep, and proper diet are thought to improve PFC function, while substance abuse is thought to reduce it. Few studies have examined the relationships among all of these in the same sample, while quantifying downstream impacts on academic performance.ObjectiveThe primary objective of this study is to examine the association between lifestyle behaviors and academic performance in a sample of adolescents, and to examine the extent to which activity within the PFC and behavioural indices of inhibition may mediate this relationship.MethodsSixty-seven adolescents underwent two study sessions five days apart. Sleep and physical activity were measured using wrist-mounted accelerometry; eating habits, substance use and academic achievement were measured by self-report. Prefrontal function was quantified by performance on the Multi-Source Interference Task (MSIT), and task-related brain activity via functional near-infrared spectroscopy (fNIRS).ResultsHigher levels of accelerometer-assessed physical activity predicted higher MSIT accuracy scores (ϐ= .321,ρ= 0.019) as well as greater task-related increases in activation within the right dlPFC (ϐ=.008,SE= .004,ρ=.0322). Frequency of fast-food consumption and substance use were both negatively associated with MSIT accuracy scores (ϐ= −.307,ρ= .023) and Math grades (β= −3.702,SE= 1.563,ρ= .022) respectively. However, these effects were not mediated by indicators of PFC function.ConclusionPhysical activity and eating behaviors predicted better interference task performance in adolescents, with the former mediated by greater task-related increases in right dlPFC activation. Substance use predicted worse Math grades, however, no other reliable effects of health behaviors on academic outcomes were evident.
Label-free imaging and classification of liveP. falciparum
Authors: Lebel Paul M. , Dial Rebekah L. , Vemuri Venkata N. P. , Garcia Valentina , DeRisi Joseph , Gómez-Sjöberg Rafael 
Published: September 2020

AbstractManual microscopic inspection of fixed and stained blood smears has remained the gold standard forPlasmodiumparasitemia analysis for over a century. Unfortunately, smear preparation consumes time and reagents, while manual microscopy is skill-dependent and labor-intensive. Here, we demonstrate that label-free microscopy combined with deep learning enables both life stage classification and accurate parasitemia quantification. Using a custom-built microscope, we find that deep-ultraviolet light enhances image contrast and resolution, achieving four-category classification ofPlasmodium falciparumblood stages at an overall accuracy greater than 99%. To increase accessibility, we extended our method to a commercial brightfield microscope using near-ultraviolet and visible light. Both systems were tested extrinsically by parasitemia titration, revealing superior performance over manually-scored Giemsa-stained smears, and a limit of detection below 0.1%. Our results suggest that label-free microscopy combined with deep learning could eliminate the need for conventional blood smear analysis.
KuLGaP: A Selective Measure for Assessing Therapy Response in Patient-Derived Xenografts
Authors: Ortmann Janosch , Rampášek Ladislav , Tai Elijah , Mer Arvind Singh , Shi Ruoshi , Stewart Erin L , Mascaux Celine , Fares Aline , Pham Nhu-An , Beri Gangesh , Eeles Christopher , Tkachuk Denis , Ho Chantal , Sakashita Shingo , Weiss Jessica , Jiang Xiaoqian , Liu Geoffrey , Cescon David W. , O’Brien Catherine , Guo Sheng , Tsao Ming-Sound , Haibe-Kains Benjamin , Goldenberg Anna 
Published: September 2020

AbstractQuantifying response to drug treatment in mouse models of human cancer is important for treatment development and assignment, and yet remains a challenging task. A preferred measure to quantify this response should take into account as much of the experimental data as possible, i.e. both tumor size over time and the variation among replicates. We propose a theoretically grounded measure, KuLGaP, to compute the difference between the treatment and control arms. KuLGaP is more selective than currently existing measures, reduces the risk of false positive calls and improves translation of the lab results to clinical practice.
Genotypic differences in wheat yield determinants within a NAM population based on elite parents
Authors: Basavaraddi Priyanka A. , Savin Roxana , Sukumaran Sivakumar , Reynolds Matthew P. , Griffiths Simon , Slafer Gustavo A. 
Published: September 2020

AbstractFuture grain yield (GY) improvements require the identification of beneficial traits within the context of high yield potential and not just based on the pleiotropic effect of traits such as crop height and heading date. We evaluated 1937 lines from Nested Association Mapping (NAM) population derived from 13 bi-parental varietal crosses under field conditions. We selected 493 lines with similar time to anthesis to that of the two checks used in the study (across and within each family) which reduced the range of plant height in the selected lines. Yield components were measured in these 493 lines from which 231 lines were selected by excluding lines with lowest number of grains so excluded low yielding lines. Later the subset of 231 lines were evaluated in two field experiments (2016-17, CS1 and 2017-18, CS2). Numerical and physiological components of grain yield were measured. The two-step selection maximised GY within an acceptable range of variation for height and anthesis. GY in 231 lines showed very high G×E interaction. Taking both seasons together, we selected lines from upper and lower quartile GY groups to identify stable beneficial trait combinations for improved GY. Differences in GY were explained by grain number driven by increased spike dry weight at anthesis (SDWa) and fruiting efficiency (FE). Increased GY was accompanied by sink limitation. The data points towards increases in grain number as the route towards future GY increases in wheat breeding.