bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gender impact on transcranial magnetic stimulation-based cortical excitability and cognition relationship in healthy individuals
Authors: Akilan Kosalan , Kumar Sanjeev , Zomorrodi Reza , Blumberger Daniel M. , Daskalakis Zafiris J. , Rajji Tarek K. 
Published: January 2020

Objective
We sought to determine whether cortical excitability, measured via transcranial magnetic stimulation (TMS), is associated with cognition in healthy individuals and whether gender and education have an impact on this relationship.

Methods
Fifty-four healthy individuals (31 males, mean age = 41.94, SD = 21.98; 23 females, mean age 48.57; SD = 22.84) underwent TMS to assess their resting motor threshold (RMT) and the Repeatable Battery for the Assessment of Neuropsychological Status (RBANS) to assess cognition. Multiple regression analyses were conducted to assess the association between RMT, education, gender and cognition.

Results
The multiple regression model revealed a significant association between RBANS Total Index Score and RMT in the female group (B = 0.624, β = 0.602, P = 0.001) and not the male group (B = 0.048, β = 0.034, P = 0.858).

Conclusion
This study demonstrated that lower cortical excitability is associated with better global cognition in healthy female and not male individuals. RMT could be further studied as a tool to better personalize brain stimulation protocols that aim at enhancing cognition.
Twelve Platinum-Standard Reference Genomes Sequences (PSRefSeq) that complete the full range of genetic diversity of Asian rice
Authors: Zhou Yong , Chebotarov Dmytro , Kudrna Dave , Llaca Victor , Lee Seunghee , Rajasekar Shanmugam , Mohammed Nahed , Al-Bader Noor , Sobel-Sorenson Chandler , Parakkal Praveena , Arbelaez Lady Johanna , Franco Natalia , Alexandrov Nickolai , Hamilton N. Ruaraidh Sackville , Leung Hei , Mauleon Ramil , Lorieux Mathias , Zuccolo Andrea , McNally Kenneth , Zhang Jianwei , Wing Rod A. 
Published: January 2020

AbstractAs the human population grows from 7.8 billion to 10 billion over the next 30 years, breeders must do everything possible to create crops that are highly productive and nutritious, while simultaneously having less of an environmental footprint. Rice will play a critical role in meeting this demand and thus, knowledge of the full repertoire of genetic diversity that exists in germplasm banks across the globe is required. To meet this demand, we describe the generation, validation and preliminary analyses of transposable element and long-range structural variation content of 12 near-gap-free reference genome sequences (RefSeqs) from representatives of 12 of 15 subpopulations of cultivated rice. When combined with 4 existing RefSeqs, that represent the 3 remaining rice subpopulations and the largest admixed population, this collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a pan-genome template to map resequencing data to detect virtually all standing natural variation that exists in the pan-cultivated rice genome.
An optimality principle for locomotor central pattern generators
Authors: Ryu Hansol X. , Kuo Arthur D. 
Published: January 2020

AbstractTwo types of neural circuits contribute to legged locomotion:central pattern generators(CPGs) that produce rhythmic motor commands (even in the absence of feedback, termed “fictive locomotion”), andreflex circuitsdriven by sensory feedback. Each circuit alone serves a clear purpose, and the two together are understood to cooperate during normal locomotion. The difficulty is in explaining their relative balance objectively within a control model, as there are infinite combinations that could produce the same nominal motor pattern. Here we propose that optimization in the presence of uncertainty can explain how the circuits should best be combined for locomotion. The key is to re- interpret the CPG in the context of state estimator-based control: an internal model of the limbs that predicts their state, using sensory feedback to optimally balance competing effects of environmental and sensory uncertainties. We demonstrate use of optimally predicted state to drive a simple model of bipedal, dynamic walking, which thus yields minimal energetic cost of transport and best stability. The internal model may be implemented with classic neural half-center circuitry, except with neural parameters determined by optimal estimation principles. Fictive locomotion also emerges, but as a side effect of estimator dynamics rather than an explicit internal rhythm. Uncertainty could be key to shaping CPG behavior and governing optimal use of feedback.New and NoteworthySensory feedback modulates the central pattern generator (CPG) rhythm in locomotion, but there lacks an explanation for how much feedback is appropriate. We propose destabilizing noise as a determinant, where an uncertain environment demands more feedback, but noisy sensors demand less. We reinterpret the CPG as an internal model for predicting body state despite noise. Optimizing its feedback yields robust and economical gait in a walking model, and explains the advantages of feedback-driven CPG control.
Engineering indel and substitution variants of diverse and ancient enzymes using Graphical Representation of Ancestral Sequence Predictions (GRASP)
Authors: Foley Gabriel , Mora Ariane , Ross Connie M. , Bottoms Scott , Sützl Leander , Lamprecht Marnie L. , Zaugg Julian , Essebier Alexandra , Balderson Brad , Newell Rhys , Thomson Raine E. S. , Kobe Bostjan , Barnard Ross T. , Guddat Luke , Schenk Gerhard , Carsten Jörg , Gumulya Yosephine , Rost Burkhard , Haltrich Dietmar , Sieber Volker , Gillam Elizabeth M. J. , Bodén Mikael 
Published: January 2020

AbstractAncestral sequence reconstruction is a technique that is gaining widespread use in molecular evolution studies and protein engineering. Accurate reconstruction requires the ability to handle appropriately large numbers of sequences, as well as insertion and deletion (“indel”) events, but available approaches exhibit limitations. To address these limitations, we developed Graphical Representation of Ancestral Sequence Predictions (GRASP), which efficiently implements maximum likelihood methods to enable the inference of ancestors of families with more than 10,000 members. GRASP implements partial order graphs (POGs) to represent and infer insertion and deletion events across ancestors, enabling the identification of building blocks for protein engineering.To validate the capacity to engineer novel proteins from realistic data, we predicted ancestor sequences across three distinct enzyme families: glucose-methanol-choline (GMC) oxidoreductases, cytochromes P450, and dihydroxy/sugar acid dehydratases (DHAD). All tested ancestors demonstrated enzymatic activity. Our study demonstrates the ability of GRASP (1) to support large data sets over 10,000 sequences and (2) to employ insertions and deletions to identify building blocks for engineering biologically active ancestors, by exploring variation over evolutionary time.Author summaryMassive sequencing projects expose the extent of natural, genetic diversity. Here, we describe a method with capacity to perform ancestor sequence reconstruction from data sets in excess of 10,000 sequences, poised to recoverancestraldiversity, including the evolutionary events that determine present-time biological function and structure.We introduce a novel strategy for suggesting “indel variants” that are distinct from, but can be explored alongside, substitution variants for creating ancestral libraries. We demonstrate how indels can be used as building blocks to form “hybrid ancestors”; based on this strategy, we synthesise ancestor variants, with varying enzymatic activities, for wide-ranging applications in the biotechnology sector.
Effect of high-frequency low-intensity pulsed electric field on protecting SH-SY5Y cells against hydrogen peroxide and β-amyloid-induced cell injury via ERK pathway
Authors: Chen Wei-Ting , Lin Guan-Bo , Kuo Yu-Yi , Hsieh Chih-Hsiung , Lu Chueh-Hsuan , Sun Yi-Kun , Chao Chih-Yu 
Published: January 2020

AbstractAs the most common type of neurodegenerative diseases (NDDs), Alzheimer’s disease (AD) is thought to be caused mainly by the excessive aggregation of β-amyloid protein (Aβ). However, a growing number of studies have found that reactive oxygen species (ROS) play a key role in the onset and progression of AD. The present study aimed to probe the neuroprotective effect of high-frequency low-intensity pulsed electric field (H-LIPEF) for SH-SY5Y cells against hydrogen peroxide (H2O2) and Aβ-induced cytotoxicity. By looking in a systematic way into the frequency- and amplitude-dependent neuroprotective effect of pulsed electric field (PEF), the study finds that H-LIPEF at 200 Hz produces the optimal protective effect for SH-SY5Y cells. The underlying mechanisms were confirmed to be due to the activation of extracellular signal-regulated kinase (ERK) pathway and the downstream prosurvival and antioxidant proteins. Because the electric field can be modified to focus on specific area in a non-contact manner, the study suggests that H-LIPEF holds great potential for treating NDDs, whose effect can be further augmented with the administering of drugs or natural compounds at the same time.
Stock mislabelling and its impact on phylogenomic analysis in theDrosophila nasutasubgroup/species complex
Authors: Waddell Peter J. , Wang Jeremy , Jones Corbin D. 
Published: January 2020

AbstractIn the course of our 28 de novo genome study of thenasuta-subgroup of theimmigransspecies group, we have come to suspect that several stocks acquired from the major stock centers may have either been mislabeled or mixed up in other ways. This is a short note to indicate which stocks these are, how they were diagnosed, and how an alignment and assembly free (AFAF) phylogenomic analysis sheds further light on what probably occurred.
Single molecule tracking reveals the role of transitory dynamics of nucleoid-associated protein HU in organizing the bacterial chromosome
Authors: Bettridge Kelsey , Verma Subhash , Weng Xiaoli , Adhya Sankar , Xiao Jie 
Published: January 2020

AbstractHU is the most conserved nucleoid-associated protein in eubacteria and has been implicated as a key player in global chromosome organization. The mechanism of HU-mediated nucleoid organization, however, remains poorly understood. Using single molecule tracking coupled with genetic manipulations, we characterized the dynamics of HU in liveEscherichia colicells. We found that native HU dimers bind and unbind chromosomal DNAs weakly and transitorily across the entire nucleoid volume but remain nucleoid-localized, reminiscent of random diffusion in a liquid phase-separated, membrane-less “macro-compartment” distinct from the remaining cytosol. Mutating three key surface lysine residues of HU nearly entirely abolished the weak and transitory interactions of HU with DNA and led to severe cell growth and DNA segregation defects, suggesting the importance of HU’s interactions with chromosomal DNA mediated by the positively charged surface. A conserved proline residue important for recognizing bent and cruciform DNAs such as that in recombination intermediates, similarly abolished HU’s rapid and transitory DNA interaction dynamics but had little impact on its apparent binding stability with nonspecific chromosomal DNAs. Interestingly, the proline residue appeared to be important for HUαβ dimer formation as mutating this residue makes HUαβ behave similarly to HUα2dimers. Finally, we find that while prior evidence has found HU capable of depositing nucleoid-associated noncoding RNAs onto cruciform DNA structures, deletion of these specific naRNAs or inhibition of global transcription had a relatively minor effect on HU dynamics irrespective altered nucleoid compaction. Our results suggest a model of chromosome organization mediated by weak, transient interactions of HU, a substantial deviation from nucleoid-like proteins such as histones. Such collective sum of the numerous weak, transitory binding events of HU with nonspecific chromosome DNAs could generates a “force” to maintain a dynamic, fluid nucleoid with enough flexibility to rapidly facilitate global topological processes such as replication or nucleoid segregation.
What influences treatment response in animal models of non-alcoholic fatty liver disease? A meta-analysis with meta-regression
Authors: Hunter Harriet , de Gracia Hahn Dana , Duret Amedine , Im Yu Ri , Cheah Qinrong , Dong Jiawen , Fairey Madison , Hjalmarsson Clarissa , Li Alice , Lim Hong Kai , McKeown Lorcán , Mitrofan Claudia-Gabriela , Rao Raunak , Utukuri Mrudula , Rowe Ian A. , Mann Jake P. 
Published: January 2020

AbstractThe classical drug development pipeline necessitates studies using animal models of human disease to gauge future efficacy in humans, however, there is a comparatively low conversion rate from success in animals to in humans. Non-alcoholic fatty liver disease (NAFLD) is a complex chronic disease without any licensed therapies and hence a major field of animal research. We performed a meta-analysis of 414 interventional rodent studies (6,575 animals) in NAFLD to assess the mean difference in hepatic triglyceride content. 20 of 21 studied drug classes had similar efficacy with a mean difference of −30% hepatic triglyceride. However, when publication bias was accounted for, this reduced to −16% difference. Study characteristics were only able to account for a minority of variability on meta-regression, and we replicated previous findings of high risk of bias across 82% of cohorts. These findings build on previous work in preclinical neuroscience and help to explain the challenge of reproducibility and translation within the field of metabolism.
RaptRanker:in silicoRNA aptamer selection from HT-SELEX experiment based on local sequence and structure information
Authors: Ishida Ryoga , Adachi Tatsuo , Yokota Aya , Yoshihara Hidehito , Aoki Kazuteru , Nakamura Yoshikazu , Hamada Michiaki 
Published: January 2020

AbstractAptamers are short single-stranded RNA/DNA molecules that bind to specific target molecules. Aptamers with high binding-affinity and target specificity are identified using anin vitroprocedure called high throughput systematic evolution of ligands by exponential enrichment (HT-SELEX). However, the development of aptamer affinity reagents takes a considerable amount of time and is costly because HT-SELEX produces a large dataset of candidate sequences, some of which have insufficient binding-affinity. Here, we present RNA aptamer Ranker (RaptRanker), a novel insilicomethod for identifying high binding-affinity aptamers from HT-SELEX data by scoring and ranking. RaptRanker analyzes HT-SELEX data by evaluating the nucleotide sequence and secondary structure simultaneously, and by ranking according to scores reflecting local structure and sequence frequencies. To evaluate the performance of RaptRanker, we performed two new HT-SELEX experiments, and evaluated binding affinities of a part of sequences that include aptamers with low binding-affinity. In both datasets, the performance of RaptRanker was superior to Frequency, Enrichment and MPBind. We also confirmed that the consideration of secondary structures is effective in HT-SELEX data analysis, and that RaptRanker successfully predicted the essential subsequence motifs in each identified sequence.
Movement-assisted localization from acoustic telemetry data
Authors: Hostetter Nathan J. , Royle J. Andrew 
Published: January 2020

AbstractBackgroundAcoustic telemetry technologies are being rapidly deployed to study a variety of aquatic taxa including fishes, reptiles, and marine mammals. Large cooperative telemetry networks produce vast quantities of data useful in the study of movement, resource selection and species distribution. Efficient use of acoustic telemetry data requires estimation of acoustic source locations from detections at sensors (i.e. localization). Multiple processes provide information for localization estimation including detection/non-detection data at sensors, information on signal rate, and an underlying movement model describing how individuals move and utilize space. Frequently, however, localization methods only integrate a subset of these processes and do not utilize the full spatial encounter history information available from sensor arrays.MethodsIn this paper we draw analogies between the challenges of acoustic telemetry localization and newly developed methods of spatial capture-recapture (SCR). We develop a framework for localization that integrates explicit sub-models for movement, signal (or cue) rate, and detection probability, based on acoustic telemetry spatial encounter history data. This method, which we call movement-assisted localization, makes efficient use of the full encounter history data available from acoustic sensor arrays, provides localizations with fewer than three detections, and even allows for predictions to be made of the position of an individual when it wasnotdetected at all. We demonstrate these concepts by developing generalizable Bayesian formulations of the SCR movement-assisted localization model to address study-specific challenges common in acoustic telemetry studies.ResultsSimulation studies show that movement-assisted localization models improve point-wise RMSE of localization estimates by > 50% and greatly increased the precision of estimated trajectories compared to localization using only the detection history of a given signal. Additionally, integrating a signal rate sub-model reduced biases in the estimation of movement, signal rate, and detection parameters observed in independent localization models.ConclusionsMovement-assisted localization provides a flexible framework to maximize the use of acoustic telemetry data. Conceptualizing localization within an SCR framework allows extensions to a variety of data collection protocols, improves the efficiency of studies interested in movement, resource selection, and space-use, and provides a unifying framework for modeling acoustic data.
A Splice Site-Sensing Conformational Switch in U2AF2 is Modulated by U2AF1 and its Recurrent Myelodysplasia-Associated Mutation
Authors: Warnasooriya Chandani , Glasser Eliezra , Feeney Callen F. , Laird Kholiswa M. , Jenkins Jermaine L. , Ermolenko Dmitri N. , Kielkopf Clara L. 
Published: January 2020

ABSTRACTAn essential heterodimer of the U2AF1 and U2AF2 pre-mRNA splicing factors nucleates spliceosome assembly at polypyrimidine (Py) signals preceding the major class of 3ʹ splice sites. Among myelodysplastic syndromes (MDS), U2AF1 frequently acquires an S34F-encoding mutation. The influence of the U2AF1 subunit and its S34F mutation on the U2AF2 conformations remains unknown. Here, we employ single molecule Förster resonance energy transfer (FRET) to determine the influence of wild-type or S34F-substituted U2AF1 on the conformational dynamics of U2AF2 and its splice site RNA complexes. In the absence of RNA, the U2AF1 subunit stabilizes a high FRET value, which by structure-guided mutagenesis corresponds to a closed conformation of the tandem U2AF2 RNA recognition motifs (RRMs). When the U2AF heterodimer is bound to a strong, uridine-rich splice site, U2AF2 switches to a lower FRET value characteristic of an open, side-by-side arrangement of the RRMs. Remarkably, the U2AF heterodimer binds weak, uridine-poor Py tracts as a mixture of closed and open U2AF2 conformations, which are modulated by the S34F mutation. Shifts between open and closed U2AF2 may underlie U2AF1-dependent splicing of degenerate Py tracts and contribute to a subset of S34F-dysregulated splicing events in MDS patients.
Auxin-dependent alleviation of oxidative stress and growth promotion ofScenedesmus obliquusC1S byAzospirillum brasilense
Authors: Pagnussat L.A. , Maroniche G. , Curatti L. , Creus C. 
Published: January 2020

AbstractThere is currently an increasing interest in the use of microalgae for wastewater treatment and the use of its biomass as a feedstock for biofuels. Both of these applications are often performed more efficiently by microalgal-bacteria consortia. However, the mechanisms that account for the stability and robustness of this kind of interactions are poorly understood. In this study, we confirmed the growth promotion activity of the plant growth-promoting bacteriumAzospirillum brasilenseSp245 on the microalgaeScenedesmus obliquusC1S. We show that this activity is critically dependent on bacterial indole-3 acetic acid (IAA) production, which results in a decrease in algal reactive oxygen species (ROS) levels, higher cell densities and ameliorates algal cells bleaching after nitrogen deprivation. We also show a close inter-species interaction between both partners and an active expression of the bacterialipdCgene involved in production of IAA when co-cultivated.This study extends the current knowledge of the mechanisms underlying bacteria-microalgae consortia to improve their technological applications and to better understand ecological relationships in the environment.
Deep evolutionary analysis reveals the design principles of fold A glycosyltransferases
Authors: Taujale Rahil , Venkat Aarya , Huang Liang-Chin , Yeung Wayland , Rasheed Khaled , Edison Arthur S. , Moremen Kelley W. , Kannan Natarajan 
Published: January 2020

AbstractGlycosyltransferases (GTs) are prevalent across the tree of life and regulate nearly all aspects of cellular functions by catalyzing synthesis of glycosidic linkages between diverse donor and acceptor substrates. Despite the availability of GT sequences from diverse organisms, the evolutionary basis for their complex and diverse modes of catalytic and regulatory functions remain enigmatic. Here, based on deep mining of over half a million GT-A fold sequences from diverse organisms, we define a minimal core component shared among functionally diverse enzymes. We find that variations in the common core and the emergence of hypervariable loops extending from the core contributed to the evolution of catalytic and functional diversity. We provide a phylogenetic framework relating diverse GT-A fold families for the first time and show that inverting and retaining mechanisms emerged multiple times independently during the course of evolution. We identify conserved modes of donor and acceptor recognition in evolutionarily divergent families and pinpoint the sequence and structural features for functional specialization. Using the evolutionary information encoded in primary sequences, we trained a machine learning classifier to predict donor specificity with nearly 88% accuracy and deployed it for the annotation of understudied GTs in five model organisms. Our studies provide an evolutionary framework for investigating the complex relationships connecting GT-A fold sequence, structure, function and regulation.
Synergic coordination of stem cells is required to induce a regenerative response in anthozoan cnidarians
Authors: Amiel Aldine R. , Foucher Kevin , Ferreira Solène , Röttinger Eric 
Published: January 2020

AbstractLittle is known about the origin of the inductive signal that translates the amputation stress into a cooperative cellular response. By studying the process underlying the reformation of lost body parts in the anthozoan cnidarianNematostella vectensis, we identified a regeneration-inducing structure that, via a tissue crosstalk, is responsible for the initiation of the repair program. We further revealed for the first time in anthozoan cnidarians, that fast and slow-cycling/quiescent stem cells respond to the amputation stress and actively participate in the reformation of lost body parts. Importantly, a synergic interaction of both stem cell populations is required to complete the regeneration process. Our findings suggest that the emergence/loss of structure complexity/compartmentalization influences the proprieties of tissue plasticity, changes the competence of a tissue to reprogram and, in the context of regeneration, the capacity of the tissue to emit or respond to a regeneration-inducing signal.