bluuebunny/crossref_metadata_2025_split huggingface dataset:
OmicsView: omics data analysis through interactive visual analytics
Authors: Casey Fergal , Negi Soumya , Zhu Jing , Zavodszky Maria , Cheng Derrick , Lin Dongdong , John Sally , Penny Michelle A. , Sexton David , Zhang Baohong 
Published: September 2021

ABSTRACTWith advances in NGS technologies, transcriptional profiling of human tissue across many diseases is becoming more routine, leading to the generation of petabytes of data deposited in public repositories. There is a need for bench scientists with little computational expertise to be able to access and mine this data to understand disease pathology, identify robust biomarkers of disease and the effect of interventions (in vivo or in vitro). To this end we release an open source analytics and visualization platform for expression data called OmicsView, http://omicsview.org.This platform comes preloaded with 1000s of samples across many disease areas and normal tissue, including the GTEx database, all processed with a harmonized pipeline. We demonstrate the power and ease-of-use of the platform by means of a Crohn’s disease data mining exercise where we can quickly uncover disease pathology and identify strong biomarkers of disease and response to treatment.
The rt-TEP tool: real-time visualization of TMS-Evoked Potential to maximize cortical activation and minimize artifacts
Authors: Casarotto S , Fecchio M , Rosanova M , Varone G , D’Ambrosio S , Sarasso S , Pigorini A , Russo S , Comanducci A , Ilmoniemi RJ , Massimini M 
Published: September 2021

ABSTRACTBackgroundThe impact of transcranial magnetic stimulation (TMS) on cortical neurons is currently hard to predict based on a priori biophysical and anatomical knowledge alone. This problem can hamper the reliability and reproducibility of protocols aimed at measuring electroencephalographic (EEG) responses to TMS.New MethodWe introduce and release a novel software tool to facilitate and standardize the acquisition of TMS-evoked potentials (TEPs). The tool, rt-TEP (real-time TEP), interfaces with different EEG amplifiers and offers a series of informative visualization modes to assess in real time the immediate impact of TMS on the underlying neuronal circuits.ResultsWe show that rt-TEP can be used to abolish or minimize magnetic and muscle artifacts contaminating the post-stimulus period thus affording a clear visualization and quantification of the amplitude of the early (<50 ms) EEG response after averaging a limited number of trials. This real-time readout can then be used to adjust TMS parameters (e.g. site, orientation, intensity) and experimental settings (e.g. loudness and/or spectral features of the noise masking) to ultimately maximize direct cortical effects over the undesired sensory effects of the coil’s discharge.Comparison with Existing MethodsThe ensemble of real-time visualization modes of rt-TEP are not implemented in any current commercial software and provide a key readout to titrate TMS parameters beyond the a priori information provided by anatomical models.ConclusionsReal-time optimization of stimulation parameters with rt-TEP can facilitate the acquisition of reliable TEPs with a high signal-to-noise ratio and improve the standardization and reproducibility of data collection across laboratories.Highlightsrt-TEP provides an immediate EEG readout to assess the quality of TEPs in real timert-TEP interfaces with most commercial EEG systemsInformative, real time visualization allows maximising the cortical impact of TMS while minimizing artifactsrt-TEP facilitates the acquisition of reliable TEPs with a high signal-to-noise ratio
Computational capability of ecological dynamics
Authors: Ushio Masayuki , Watanabe Kazufumi , Fukuda Yasuhiro , Tokudome Yuji , Nakajima Kohei 
Published: September 2021

AbstractEcological dynamics is driven by an ecological network consisting of complex interactions. Information processing capability of artificial networks has been exploited as a computational resource, yet whether an ecological network possesses a computational capability and how we can exploit it remain unclear. Here, we show that ecological dynamics can be exploited as a computational resource. We call this approach “Ecological Reservoir Computing” (ERC) and developed two types of ERC.In silicoERC reconstructs ecological dynamics from empirical time series and uses simulated system responses as reservoir states, which predicts near future of chaotic dynamics and emulates nonlinear dynamics. The real-time ERC uses population dynamics of a unicellular organism,Tetrahymena thermophila. Medium temperature is an input signal and changes in population abundance are reservoir states. Intriguingly, the real-time ERC has necessary conditions for reservoir computing and is able to make near future predictions of model and empirical time series.
The MultimorbiditY COllaborative Medication Review And DEcision Making (MyComrade) study: A protocol for a cross-border pilot cluster randomised controlled trial
Authors: Hynes Lisa , Murphy Andrew W , Hart Nigel , Kirwan Collette , Mulligan Sarah , Leathem Claire , McQuillan Laura , Maxwell Marina , Carr Emma , Walkin Scott , McCarthy Caroline , Bradley Colin , Byrne Molly , Smith Susan M , Hughes Carmel , Corry Maura , Kearney Patricia M , McCarthy Geraldine , Cupples Margaret , Gillespie Paddy , Newell John , Glynn Liam , Alvarez-Iglesias Alberto , Sinnott Carol 
Published: September 2021

AbstractBackgroundWhile international guidelines recommend medication reviews as part of the management of multimorbidity, evidence on how to implement reviews in practice in primary care is lacking. The MyComrade (MultimorbiditY Collaborative Medication Review And Decision Making) intervention is an evidence-based, theoretically-informed novel intervention which aims to support the conduct of medication reviews for patients with multimorbidity in primary care. Our aim in this pilot study is to evaluate the feasibility of a trial of the intervention with unique modifications accounting for contextual variations in two neighbouring health systems (Republic of Ireland (ROI) and Northern Ireland (NI)).MethodsA pilot cluster randomised controlled trial will be conducted, using a mixed methods process evaluation to investigate the feasibility of a trial of the MyComrade intervention. A total of 16 practices will be recruited (eight in ROI; eight in NI) and four practices in each jurisdiction will be randomly allocated to intervention or control. Twenty people living with multimorbidity and prescribed ≥10 repeat medications will be recruited from each practice prior to practice randomisation. In intervention practices, the MyComrade intervention will be delivered by pairs of GPs in ROI, and a GP and Practice Based Pharmacist (PBP) in NI. The GPs/GP and PBP will schedule time to review medications together using a checklist. Usual care will proceed in practices in the control arm. Data will be collected via electronic health records and postal questionnaires at recruitment, and 4- and 8-months after randomisation. Qualitative interviews to assess the feasibility and acceptability of the intervention, and explore experiences related to multimorbidity management will be conducted with a purposive sample of GPs, PBPs, practice administration staff and patients in intervention and control practices. The feasibility of conducting a health economic evaluation as part of a future definitive trial will be assessed.DiscussionThe findings of this pilot study will assess the feasibility of a trial of the MyComrade intervention in two different health systems. Evaluation of the progression criteria will guide the decision to progress to a definitive trial and inform trial design. The findings will also contribute to the growing evidence-base related to intervention development and feasibility studies.Trial registrationRegistry: ISRCTN,ISRCTN80017020; Date of confirmation 4/11/2019; Retrospectively registered;http://www.isrctn.com/ISRCTN80017020.
Reduction of exposure to simulated respiratory aerosols using ventilation, physical distancing, and universal masking
Authors: Coyle Jayme P. , Derk Raymond C. , Lindsley William G. , Boots Theresa , Blachere Francoise M. , Reynolds Jeffrey S. , McKinney Walter G. , Sinsel Erik W. , Lemons Angela R. , Beezhold Donald H. , Noti John D. 
Published: September 2021

ABSTRACTTo limit community spread of SARS-CoV-2, CDC recommends universal masking indoors, maintaining 1.8 m of physical distancing, adequate ventilation, and avoiding crowded indoor spaces. Several studies have examined the independent influence of each control strategy in mitigating transmission in isolation, yet controls are often implemented concomitantly within an indoor environment. To address the influence of physical distancing, universal masking, and ventilation on very fine respiratory droplets and aerosol particle exposure, a simulator that coughed and exhaled aerosols (the source) and a second breathing simulator (the recipient) were placed in an exposure chamber. When controlling for the other two mitigation strategies, universal masking with 3-ply cotton masks reduced exposure to 0.3–3 µm coughed and exhaled aerosol particles by > 77% compared to unmasked tests, whereas physical distancing (0.9 or 1.8 m) significantly changed exposure to cough but not exhaled aerosols. The effectiveness of ventilation depended upon the respiratory activity, i.e., coughing or breathing, as well as the duration of exposure time. Our results demonstrate that a combination of administrative and engineering controls can reduce personal inhalation exposure to potentially infectious very fine respiratory droplets and aerosol particles within an indoor environment.PRACTICAL IMPLICATIONSUniversal masking provided the most effective strategy in reducing inhalational exposure to simulated aerosols.Physical distancing provided limited reductions in exposure to small aerosol particles.Ventilation promotes air mixing in addition to aerosol removal, thus altering the exposure profile to individuals.A combination of mitigation strategies can effectively reduce exposure to potentially infectious aerosols.
Influence of Rule and Reward-based Strategies on Inferences of Serial Order by Monkeys
Authors: Ferhat Allain-Thibeault , Jensen Greg , Terrace Herbert S. , Ferrera Vincent P. 
Published: September 2021

ABSTRACTKnowledge of transitive relationships between items can contribute to learning the order of a set of stimuli from pairwise comparisons. However, cognitive mechanisms of transitive inferences based on rank order remain unclear, as are contributions of reward magnitude and rule-based inference. To explore these issues, we created a conflict between rule- and reward-based learning during a serial ordering task. Rhesus macaques learned two lists, each containing five stimuli, that were trained exclusively with adjacent pairs. Selection of the higher-ranked item resulted in rewards. “Small reward” lists yielded 2 drops of fluid reward, while “large reward” lists yielded 5 drops. Following training of adjacent pairs, monkeys were tested on novels pairs. One item was selected from each list, such that a ranking rule could conflict with preferences for large rewards. Differences in associated reward magnitude had a strong influence on accuracy, but we also observed a symbolic distance effect. That provided evidence of a rule-based influence on decisions. Reaction time comparisons suggested a conflict between rule and reward-based processes. We conclude that performance reflects the contributions of two strategies, and that a model-based strategy is employed in the face of a strong countervailing reward incentive.
Water stress-associated isolation barriers between two sympatric oak species
Authors: Le Provost Grégoire , Brachi Benjamin , Lesur Isabelle , Lalanne Céline , Labadie Karine , Aury Jean-Marc , Da Silva Corinne , Postolache Dragos , Leroy Thibault , Plomion Christophe 
Published: September 2021

AbstractDrought and waterlogging impede tree growth and may even lead to tree death. With climate change, these environmental factors are a growing source of concern, particularly for temperate forests. Oaks, an emblematic group of tree species, have evolved a range of adaptations to cope with these constraints. The two most widely distributed European species — pedunculate oak (PO) and sessile oaks (SO) — have overlapping ranges, but are highly constrained locally by soil water content variation. These differences in local ecological requirements provide a powerful biological model for studying the role of ecological barriers in speciation. We used an experimental set-up mimicking the ecological preferences of these species, in which seedlings were subjected to waterlogging and drought. We studied gene expression in roots by RNA-seq and identified genes differentially expressed between treatments with different outcomes depending on species. These “species x environment”-responsive genes revealed adaptive molecular strategies involving adventitious and lateral root formation, aerenchyma formation in PO, and osmoregulation and ABA regulation in SO. With this experimental design, we also identified genes with expression profiles presenting a “species” effect regardless of imposed constraints with important roles in intrinsic reproductive barriers. Finally, we compared our findings with those for a genome scan of species divergence and found that the candidate genes were enriched in highly differentiated SNPs. This suggests that many of the genes involved in the contrasting transcriptomic responses are subject to natural selection and that gene regulation helps to maintain these two different oak species in sympatry.
Task-Level Value Affects Trial-Level Reward Processing
Authors: Hassall Cameron D. , Hunt Laurence T. , Holroyd Clay B. 
Published: September 2021

AbstractDespite disagreement about how anterior cingulate cortex (ACC) supports decision making, a recent hypothesis suggests that activity in this region is best understood in the context of a task or series of tasks. One important task-level variable is average reward because it is both a known driver of effortful behaviour and an important determiner of the tasks in which we choose to engage. Here we asked how average task value affects reward-related ACC activity. To answer this question, we measured a reward-related signal said to be generated in ACC called the reward positivity (RewP) while participants gambled in three tasks of differing average value. The RewP was reduced in the high-value task, an effect that was not explainable by either reward magnitude or outcome expectancy. This result suggests that ACC does not evaluate outcomes and cues in isolation, but in the context of the value of the current task.
Named Entity Recognition and Linking: a Portuguese and Spanish Oncological Parallel Corpus
Authors: Andrade Vitor D.T , Ruas Pedro , Couto Francisco M. 
Published: September 2021

AbstractBiomedical literature is the main mean of communication for researchers to share their findings. Since biomedical literature is composed of a large collection of text expressed in natural language, the usage of text mining tools to extract information from those texts automatically is of utmost importance. The problem is that the majority of the state-of-the-art tools were not developed to deal with other languages besides English, which in biomedical literature is even more critical since a significant part of health-related texts is written in the author’s native language. To address this issue, this work presents a deep learning NERL (Named Entity Recognition and Linking) system and a parallel corpus for the Spanish and Portuguese languages focused on the oncological domain. Both the system and the corpus are available at https://github.com/lasigeBioTM/ICERL_system-ICR_Corpus.
Molecular plasticity to soil water deficit differs between sessile oak (Quercus Petraea (Matt.) Liebl.) high- and low-water use efficiency genotypes
Authors: Provost Gregoire Le , Gerardin Theo , Plomion Christophe , Brendel Oliver 
Published: September 2021

AbstractBackgroundWater use efficiency (WUE) is an important adaptive trait for soil water deficit. The molecular and physiological bases of WUE regulation in crops have been studied in detail in the context of plant breeding. Knowledge for most forest tree species lags behind, despite the need to identify populations or genotypes able to cope with the longer, more intense drought periods likely to result from climate warming.ResultsWe aimed to bridge this gap in knowledge for sessile oak (Quercus Petraeae Matt. L.), one of the most ecologically and economically important tree species in Europe, using a factorial design including two genotypes (low and high WUE) and two watering regimes (control and drought). By monitoring the ecophysiological response, we were able to identify groups of genotypes with high and low WUE. We then performed RNA-seq to quantify gene expression for the most extreme genotypes exposed to two watering regimes. By analyzing the interaction term, we were able to capture the molecular strategy of each group of plants for coping with drought. Regardless of water availability, the high WUE genotypes overexpressed genes associated with drought responses, and the control of stomatal density and distribution, and displayed a downregulation of genes associated with early stomatal closure and high transpiration rate. High-WUE genotypes, thus, coped with drought by fine-tuning the expression of genes with known functions in the regulation of stomatal size, density, movement or aperture and transpiration rate.ConclusionFine physiological screening of sessile oaks with contrasting WUE, and their molecular characterization i) highlighted subtle differences in transcription between low and high WUE genotypes, identifying key molecular players in the genetic control of this trait, and ii) revealed the genes underlying the molecular strategy that had evolved in each group to cope with water deficit, providing new insight into the value of WUE for adaptation to drought.
A distinctive ligand recognition mechanism by the human vasoactive intestinal polypeptide receptor 2
Authors: Xu Yingna , Feng Wenbo , Zhou Qingtong , Liang Anyi , Li Jie , Dai Antao , Zhao Fenghui , Zhao Lihua , Xia Tian , Jiang Yi , Xu H. Eric , Yang Dehua , Wang Ming-Wei 
Published: September 2021

AbstractActivated by physiologically important peptide hormones, class B1 G protein-coupled receptors (GPCRs) modulate key physiological functions and serve as valuable drug targets for many diseases. Among them, vasoactive intestinal polypeptide receptor 2 (VIP2R) is the last member whose full-length 3-dimensional structure has yet to be determined. VIP2R, expressed in the central and peripheral nervous systems and involved in a number of pathophysiological conditions, is implicated in pulmonary arterial hypertension, autoimmune and psychiatric disorders. Here, we report the cryo-electron microscopy structure of the human VIP2R bound to its endogenous ligand PACAP27 and the stimulatory G protein. Different from all reported peptide-bound class B1 GPCR structures, the N-terminal α-helix of VIP2R adopts a unique conformation that deeply inserts into a cleft between PACAP27 and the extracellular loop 1, thereby stabilizing the peptide-receptor interface. Its truncation or extension significantly decreased VIP2R-mediated cAMP accumulation. Our results provide additional information on peptide recognition and receptor activation among class B1 GPCRs and may facilitate the design of better therapeutics.
Enterococcus faecalis persists and replicates within epithelial cells in vitro and in vivo during wound infection
Authors: Tay Wei Hong , da Silva Ronni A.G. , Ho Foo Kiong , Chong Kelvin K.L. , Ludwig Alexander , Kline Kimberly A. 
Published: September 2021

AbstractEnterococcus faecalis is a frequent opportunistic pathogen of wounds, whose infections are associated with biofilm formation, persistence, and recalcitrance toward treatment. We have previously shown that E. faecalis wound infection persists for at least 7 days. Here we report that viable E. faecalis are present within both immune and non-immune cells at the wound site up to 5 days after infection, raising the prospect that intracellular persistence contributes to chronic E. faecalis infection. Using an in vitro keratinocyte infection model, we show that a subpopulation of E. faecalis becomes internalized via macropinocytosis into single membrane-bound compartments, where they can survive and replicate. These intracellular E. faecalis can persist in late endosomes up to 72 hours after infection in the absence of colocalization with the lysosomal protease cathepsin D or apparent fusion with the lysosome, suggesting that E. faecalis blocks endosomal maturation. Indeed, intracellular E. faecalis infection results in a marked reduction in Rab7 expression, a small GTPase required for endosome-lysosome fusion. Finally, we demonstrate that intracellular E. faecalis derived from infected keratinocytes are significantly more efficient in reinfecting new keratinocytes. Together, these data suggest that intracellular proliferation of E. faecalis may contribute to its persistence in the face of a robust immune response, providing a primed reservoir of bacteria for subsequent reinfection.Author SummaryEnterococcus faecalis is often isolated from chronic wounds. Prior to this study, E. faecalis has been observed within different cell types, suggesting that it can successfully colonize intracellular spaces. However, to date, little is known about the mechanisms E. faecalis use to survive intracellularly. Here, we describe key features of the intracellular lifestyle of E. faecalis. We show that E. faecalis exists in an intracellular state within immune cells and non-immune cells during mammalian wound infection. We show that E. faecalis can survive and replicate inside keratinocytes, and intracellularly replicating E. faecalis are primed to more efficiently cause reinfection, potentially contributing to chronic or persistent infections. In order to establish this intracellular lifestyle, E. faecalis is taken up by keratinocytes via macropinocytosis, whereupon it manipulates the endosomal pathway and expression of trafficking molecules required for endo-lysosomal fusion, enabling E. faecalis to avoid lysosomal degradation and consequent death. These results advance our understanding of E. faecalis pathogenesis, demonstrating mechanistically how this classic extracellular pathogen can co-opt host cells for intracellular persistence, and highlight the heterogeneity of mechanisms bacteria can use to avoid host-mediated killing in order to cause disease.