bluuebunny/crossref_metadata_2025_split huggingface dataset:
Institutionalizing an Evidence-Based Practice in a Selected Government Agency in Nigeria
Authors: Nwaichi E. O. , Chidebe I. , Osuoha J. O. , Chimezie E. , Mbaoji C. , Ifeanyi-Obi C. C. , Ugwoha E.O. , Odogwu B. , Okengwu U. , Olua V. , Oghenekaro L U. , Agbagwa O. E. , Frank-Peterside N. , Ozah M. A. , Raphael C. , Ugiomoh I. , Nwoha P. A. , Akpoji B. A. 
Published: December 2020

AbstractThe need to tackle the discrepancy between research outputs and the execution of the findings into real practice is a crucial factor in establishing evidence-based practice in a selected government agency. There is a need to increase the number of experts in our education sector who can synthesise, translate, and package the evidence for ready use by decision-makers and to foster entrepreneurship in Africa. To achieve this, the activities of a 28-man Evidence Leaders in Africa (ELA) team were recruited to drive the project through capacity building training and workshop sessions. Thereafter, a non-random purposive sampling technique targeted at policy makers at various government and non-governmental organizations was adopted as the study design. In all, purposive administration of 424 copies of questionnaire to individuals in different governmental and non-governmental organizations was done by the recruited personnel. The retrieved data from the questionnaire were analyzed using standard statistical method. Socio-demographic characteristics of respondents reveal 34% representation of (31-40 years) age bracket, with (57%) of them working in the University spanning over 2 to 5years (47%) work experience. Approximately 64% of the respondents are not aware of EIDM while 71% had no understanding of EIDM. As regards knowledge of EIDM, 36% had no knowledge of EIDM, 29% had moderate knowledge, 34% were beginners while approximately 1% had advanced knowledge of EIDM. Also, approximately 99% of the respondents have neither been trained nor involved in training others in EIDM. It was also observed that 8.5% of the respondents were policy-makers in the organization, yet 90.7% of the respondents agree that EIDM is useful in policy-making while 81.3% of the respondents engage their colleagues in EIDM. From this study, it is safe to infer that institutionalizing EIDM in NNMDA has numerous benefits as shown by the findings of this study. This will only be possible when all parties involved in producing and using research evidence are well informed and knowledgeable in EIDM.
Classification of protein binding ligands using structural dispersion of binding site atoms from principal axes
Authors: Premarathna Galkande Iresha , Ellingson Leif 
Published: December 2020

AbstractMany researchers have studied the relationship between the biological functions of proteins and the structures of both their overall backbones of amino acids and their binding sites. A large amount of the work has focused on summarizing structural features of binding sites as scalar quantities, which can result in a great deal of information loss since the structures are three-dimensional. Additionally, a common way of comparing binding sites is via aligning their atoms, which is a computationally intensive procedure that substantially limits the types of analysis and modeling that can be done. In this work, we develop a novel encoding of binding sites as covariance matrices of the distances of atoms to the principal axes of the structures. This representation is invariant to the chosen coordinate system for the atoms in the binding sites, which removes the need to align the sites to a common coordinate system, is computationally efficient, and permits the development of probability models. These can then be used to both better understand groups of binding sites that bind to the same ligand and perform classification for these ligand groups. We demonstrate the effectiveness of our method through classification studies with two benchmark datasets using nearest mean and polytomous logistic regression classifiers.
What we can and what we cannot see with extracellular multielectrodes
Authors: Chintaluri Chaitanya , Bejtka Marta , Średniawa Władysław , Czerwiński Michał , Dzik Jakub M. , Jędrzejewska-Szmek Joanna , Kondrakiewicz Kacper , Kublik Ewa , Wójcik Daniel K. 
Published: December 2020

AbstractExtracellular recording is an accessible technique used in animals and humans to study the brain physiology and pathology. As the number of recording channels and their density grows it is natural to ask how much improvement the additional channels bring in and how we can optimally use the new capabilities for monitoring the brain. Here we show that for any given distribution of electrodes we can establish exactly what information about current sources in the brain can be recovered and what information is strictly unobservable.We demonstrate this in the general setting of previously proposed kernel Current Source Density method and illustrate it with simplified examples as well as using evoked potentials from the barrel cortex obtained with a Neuropixels probe and with compatible model data.Author SummaryEvery set of measurements is a window into reality rendering its incomplete or distorted picture. It is often difficult to relate the obtained representation of the world to underlying ground truth. Here we show, for brain electrophysiology, for arbitrary experimental setup (distribution of electrodes), and arbitrary analytical setup (function space of current source densities), that one can identify distributions of current sources which can be recovered precisely, and those which are invisible in the system. This shows what is and what is not observable in the studied system for a given setup, allows to improve the analysis results by modifying analytical setup, and facilitates interpretation of the measured sets of LFP, ECoG and EEG recordings.
CLEC-2 promotes inflammatory peritoneal macrophage emigration to draining lymph nodes during endotoxemia
Authors: Bourne Joshua H. , Beristain-Covarrubias Nonantzin , Zuidscheroude Malou , Campos Joana , Di Ying , Garlick Evelyn , Colicchia Martina , Terry Lauren V. , Thomas Steven G. , Brill Alexander , Bayry Jagadeesh , Watson Steve P. , Rayes Julie 
Published: December 2020

AbstractMacrophage recruitment during sterile inflammation and infection is essential to clear pathogens, apoptotic cells and debris. However, persistent macrophage accumulation leads to chronic inflammation. Platelets are emerging as key modulators of the inflammatory response. Here, we identify that platelet C-type-lectin-like receptor-2 (CLEC-2) is a crucial immunomodulatory receptor through the interaction with podoplanin, upregulated on inflammatory macrophages.Mechanistically, platelet CLEC-2 upregulates the expression of podoplanin and its co-ligands CD44 and ERM proteins, leading to actin rearrangement and promotion of cell migration; this is mimicked by recombinant CLEC-2-Fc (rCLEC-2-Fc). Treatment of LPS-challenged mice with rCLEC-2-Fc induces a rapid emigration of peritoneal macrophages to mesenteric lymph nodes, through a gradient generated by the podoplanin ligand, CCL21, to prime T cells. We propose that crosslinking podoplanin using rCLEC-2-Fc is a novel, cell-specific strategy to accelerate macrophage removal from the site of inflammation, and hence promote the resolution of the inflammatory response.Visual AbstractSummaryPersistent macrophage accumulation in inflamed tissue leads to chronic inflammation and organ damage. Bourne et al. identify recombinant CLEC-2-Fc crosslinking podoplanin on inflammatory macrophages, as a cell-specific strategy to accelerate their emigration to draining lymph nodes, and reduce local inflammation.
To See, Not to See, or to See Poorly: Perceptual Quality and Guess Rate as a Function of Electroencephalography (EEG) Brain Activity in an Orientation Perception Task
Authors: Sheldon Sarah S. , Mathewson Kyle E. 
Published: December 2020

AbstractDetection of visual stimuli fluctuates over time, and these fluctuations have been shown to correlate with time-domain evoked activity and frequency-domain periodic activity. However, it is unclear if these fluctuations are related to a change in guess rate, perceptual quality, or both. Here we determined whether the quality of perception randomly varies across trials or is fixed so that the variability is the same. Then we estimated how perceptual quality and guess rate on an orientation perception task relates to EEG activity. Response errors were fitted to variable precision models and the standard mixture model to determine whether perceptual quality is from a varying or fixed distribution. Overall, the best fit was the standard mixture model that assumes response variability can be defined by a fixed distribution.The power and phase of 2-7 Hz post-target activities were found to vary along with task performance in that more accurate trials had greater power, and the preferred phase differed significantly between accurate and guess trials. Guess rate and σ were significantly lower on trials with high 2-3 Hz power than low and the difference started around 250 ms post-target.These effects coincide with changes in the P3 ERP: there was a more positive deflection in the accurate trials vs guesses. These results suggest that the spread of errors (perceptual quality) can be characterized by a fixed range of values. Where the errors fall within that range is modulated by the post-target power in the lower frequency bands and their analogous ERPs.
Age-related reductions in the number of serial sarcomeres contribute to shorter fascicle lengths but not elevated passive tension
Authors: Power Geoffrey A. , Crooks Sean , Fletcher Jared R. , Macintosh Brian R. , Herzog Walter 
Published: December 2020

AbstractWe investigated age-related changes to fascicle length (FL), sarcomere length (SL), and serial sarcomere number (SSN), and how this affects passive force. Following mechanical testing to determine passive force, the medial gastrocnemius muscle of young (n=9) and old (n=8) Fisher 344BN hybrid rats was chemically fixed at the optimal muscle length for force production; individual fascicles were dissected for length measurement, and laser diffraction was used to assess SL. Old rats had ∼14% shorter FLthan young, which was driven by a ∼10% reduction in SSN, with no difference in SL (∼4%). Passive force was greater in the old compared to young rats at long muscle lengths. Shorter FLand reduced SSN in the old rats could not entirely explain increased passive forces for absolute length changes, owing to a slight reduction in SL in old, resulting in similar SL at long muscle lengths.Summary StatementThis study sought to explain the increased passive tension observed for muscles of older individuals owing to age-related changes to muscle architecture.
The ENIGMA Toolbox: Cross-disorder integration and multiscale neural contextualization of multisite neuroimaging datasets
Authors: Larivière Sara , Paquola Casey , Park Bo-yong , Royer Jessica , Wang Yezhou , Benkarim Oualid , Vos de Wael Reinder , Valk Sofie L. , Thomopoulos Sophia I. , Kirschner Matthias ,   ENIGMA Consortium, Lewis Lindsay B. , Evans Alan C. , Sisodiya Sanjay M. , McDonald Carrie R. , Thompson Paul M. , Bernhardt Boris C. 
Published: December 2020

Among ‘big data’ initiatives, the ENIGMA (Enhancing NeuroImaging Genetics through Meta-Analysis) Consortium—a worldwide alliance of over 2,000 scientists diversified into over 50 Working Groups—has yielded some of the largest studies of the healthy and diseased brain. Integration of multisite datasets to assess transdiagnostic similarities and differences and to contextualize findings with respect to neural organization, however, have been limited. Here, we introduce the ENIGMA Toolbox, a Python/Matlab ecosystem for (i) accessing 100+ ENIGMA datasets, facilitating cross-disorder analysis, (ii) visualizing data on brain surfaces, and (iii) contextualizing findings at the microscale (postmortem cytoarchitecture and gene expression) and macroscale (structural and functional connectomes). Our Toolbox equips scientists with tutorials to explore molecular, histological, and network correlates of noninvasive neuroimaging markers of brain disorders. Moreover, our Toolbox bridges the gap between standardized data processing protocols and analytic workflows and facilitates cross-consortia initiatives. The Toolbox is documented and openly available at http://enigma-toolbox.readthedocs.io.Abstract Figure
Effect of Lauric Acid on the Stability of Aβ42-Oligomers
Authors: Khatua Prabir , Jana Asis , Hansmann Ulrich H. E. 
Published: December 2020

AbstractWhile Alzheimer’s disease is correlated with the presence of Aβfibrils in patient brains, the more likely agents are their precursors, soluble oligomers that may form pores or otherwise distort cell membranes. Using all-atom molecular dynamics simulation we study how presence of fatty acids such as lauric acid changes the stability of pore-forming oligomers built from three-stranded Aβ42chains. Such a change would alter the distribution of amyloids in the fatty-acid rich brain environment, and therefore could explain the lower polymorphism observed in Aβ-fibrils derived from brains of patients with Alzheimer’s disease. We find that lauric acid stabilizes both ring-like and barrel-shaped models, with the effect being stronger for barrel-like models than for ring-like oligomers.
Dispersal rate and riverine network connectivity shape the genetic diversity of freshwater amphipod metapopulations
Authors: Alther Roman , Fronhofer Emanuel A. , Altermatt Florian 
Published: December 2020

AbstractTheory predicts that the distribution of genetic diversity in a landscape is strongly dependent on the connectivity of the metapopulation and the dispersal of individuals between patches. However, the influence of explicit spatial configurations such as dendritic landscapes on the genetic diversity and structure of metapopulations is still understudied, and theoretical corroborations of empirical patterns are largely lacking. Here, we used real-world microsatellite data and stochastic simulations of two metapopulations of freshwater amphipods in a 28,000 km2riverine network to study the influence of spatial connectivity and dispersal strategies on their spatial genetic diversity and structure. We found a significant imprint of the riverine network connectivity on the genetic diversity of both amphipod species. Data from 95 sites showed that allelic richness and observed heterozygosity significantly increased towards more central nodes of the network. In simulation models, dispersal rate was suggested to be the key factor explaining the empirically observed distribution of genetic diversity. Contrary to often-claimed expectations, however, the relevance of directionality of dispersal was only minor. Surprisingly, also the consideration of site-specific carrying capacities, for example by assuming a direct dependency of population size with local river size, substantially decreased the model fit to empirical data. This highlights that directional dispersal and the spatial arrangement of population sizes may have a smaller relevance in shaping population genetic diversity of riverine organisms than previously thought, and that dispersal along the river network is the single-most important determinant of population genetic diversity.
Biologically-relevant transfer learning improves transcription factor binding prediction
Authors: Novakovsky Gherman , Saraswat Manu , Fornes Oriol , Mostafavi Sara , Wasserman Wyeth W. 
Published: December 2020

AbstractBackgroundDeep learning has proven to be a powerful technique for transcription factor (TF) binding prediction, but requires large training datasets. Transfer learning can reduce the amount of data required for deep learning, while improving overall model performance, compared to training a separate model for each new task.ResultsWe assess a transfer learning strategy for TF binding prediction consisting of a pre-training step, wherein we train a multi-task model with multiple TFs, and a fine-tuning step, wherein we initialize single-task models for individual TFs with the weights learned by the multi-task model, after which the single-task models are trained at a lower learning rate. We corroborate that transfer learning improves model performance, especially if in the pre-training step the multi-task model is trained with biologically-relevant TFs. We show the effectiveness of transfer learning for TFs with ∼500 ChIP-seq peak regions. Using model interpretation techniques, we demonstrate that the features learned in the pre-training step are refined in the fine-tuning step to resemble the binding motif of the target TF (i.e. the recipient of transfer learning in the fine-tuning step). Moreover, pre-training with biologically-relevant TFs allows single-task models in the fine-tuning step to learn features other than the motif of the target TF.ConclusionsOur results confirm that transfer learning is a powerful technique for TF binding prediction.
Identification and classification of innexin gene transcripts in the central nervous system of the terrestrial slugLimax valentianus
Authors: Sadamoto Hisayo , Takahashi Hironobu , Kobayashi Suguru , Kondoh Hirooki , Tokumaru Hiroshi 
Published: December 2020

AbstractIn invertebrates, innexin is involved in the formation of single-cell membrane channels and intercellular gap junction channels. Generally, there are multiple isoforms of innexin family proteins in various animal species, which enable the precise regulation of channel function. In molluscan species, the sequence information of innexins is still limited and the sequences have not been classified.This study examined the innexin transcripts expressed in the central nervous system of the terrestrial slugLimax valentianusand identified 16 transcripts of 12 innexin isoforms, including the splicing variants. To examine the function of molluscan innexin isoforms, phylogenetic analysis was performed using the innexin sequences of molluscan species. Next, the phosphorylation, N-glycosylation, and S-nitrosylation sites in the isoforms were predicted to characterize the innexin isoforms. Further, 16 circular RNA sequences of nine innexin isoforms were identified in the central nervous system ofLimax. The identification and classification of the gene transcripts of molluscan innexins provided novel insights for understanding the regulatory mechanism of innexins in the central nervous system.
Drinking habits and executive functioning: a propensity score-weighted analysis of 78,832 adults
Authors: Schweren Lizanne JS , Haavik Jan , Li Lin , Solberg Berit Skretting , Larsson Henrik , Hartman Catharina A 
Published: December 2020

AbstractExcessive alcohol intake compromises cognitive functioning. At the same time, moderate alcohol consumption is reported to protect against Alzheimer’s disease among elderly. Little is known about dose-dependent effects of alcohol consumption on higher-order cognitive functioning among generally healthy adults. Here, we applied propensity weighted analyses to investigate associations between habitual drinking patterns and executive functioning in the general population.A community sample of N=78,832 Dutch adults (age 18-65, 40.9% male) completed the Ruff Figural Fluency Task of executive functioning (range 1-165), and self-reported their past month consumption of alcoholic beverages on a food frequency questionnaire. Participants were stratified according to drinking level (abstinent [22.0%], occasional [<2.5 g/day, 21.4%], light [2.5–14.9 g/day, 42.9%], moderate [15–29.9 g/day, 11.4%], or heavy [>30 g/day, 2.3%]) and binge-drinking (yes [10.6%] vs. no [89.4%]). Groups were equivalised using multinomial propensity score weighing based on demographic, socioeconomic, health-related and psychosocial factors influencing drinking behaviour.Compared to abstinent participants, task performance was better among light drinkers (β[95% CI]=0.056[0.033-0.078] or +1.3 points, p<0.0001) and moderate drinkers (β[95% CI]=0.111[0.079-0.143] or +2.5 points, p<0.0001), but not among occasional drinkers (β[95% CI]=0.018[-0.006-0.043], p=0.1432) or heavy drinkers (β[95% CI]=0.075[-0.009-0.158], p=0.0791). No difference was found between binge-drinkers and non-binge-drinkers (β[95% CI]=0.032[-0.002-0.066], p=0.0654).In conclusion, we observed better executive functioning in light-moderate drinkers compared to abstainers, but not in occasional drinkers, heavy drinkers or binge-drinkers. This non-linear association is reminiscent of the dose-dependent effect of alcohol consumption on cardiovascular risk. Further studies may determine whether cardiovascular, inflammatory and/or other somatic factors mediate the association between moderate drinking and higher-order cognitive functions. Although analyses were adjusted for observed factors that influence drinking behaviours, we cannot exclude a contribution from unobserved residual confounding.
Nudge strategies for behavior-based prevention and control of neglected tropical diseases: a scoping review and ethical assessment
Authors: Velde Fiona Vande , Overgaard Hans J. , Bastien Sheri 
Published: December 2020

AbstractBackgroundNudging, a strategy that uses subtle stimuli to direct people’s behavior, has recently been included as effective and low-cost behavior change strategy in low- and middle- income countries (LMIC), targeting behavior-based prevention and control of neglected tropical diseases (NTDs). Therefore, the present scoping review aims to provide a timely overview of how nudge interventions have been applied within health promotion research, with a specific focus on the prevention and control of NTDs. In addition, the review proposes a framework for the ethical reflection of nudges for behavior-based prevention and control of NTDs, or more broadly global health promotion.MethodsA comprehensive search was performed in the following databases: MEDLINE, PsycINFO, and Embase (Ovid), Web of Science Core Collection, CINAHL, ERIC and Econ.Lit (EBSCO), as well as registered trials and reviews in CENTRAL and PROSPERO to identify ongoing or unpublished studies. Additionally, studies were included through a handpicked search on websites of governmental nudge units and global health or development organizations. A PRISMA flow diagram was used to elaborate on the number of articles retrieved, retained, excluded and reasons for every action.ResultsThis scoping review of studies implementing nudge strategies for behavior-based prevention and control of NTDs identified 33 studies and a total of 67 nudge-type interventions. Most nudges targeted handwashing behavior and were focused on general health practices rather than targeting a disease in specific. The most common nudge techniques were those targeting decision assistance, such as facilitating commitment and reminder actions. The ethical assessment presented favorable results, certainly regarding the health benefits of the included nudges and the trust relationship for the implementers.ConclusionTwo key recommendations that should inform future research when implementing nudge strategies in global health promotion in general. Firstly, aim for the application of robust study designs including rigorous process and impact evaluation which allow for a better understanding of ‘what works’ and ‘how it works’. Secondly, consider the ethical implications of implementing nudge strategies, specifically in LMIC.