bluuebunny/crossref_metadata_2025_split huggingface dataset:
Positive Selection and Heat-Response Transcriptomes Reveal Adaptive Features of the Brassicaceae Desert Model, Anastatica hierochuntica
Authors: Eshel Gil , Duppen Nick , Wang Guannan , Oh Dong-Ha , Kazachkova Yana , Herzyk Pawel , Amtmann Anna , Gordon Michal , Chalifa-Caspi Vered , Oscar Michelle Arland , Bar-David Shirli , Marshall-Colon Amy , Dassanayake Maheshi , Barak Simon 
Published: May 2021

SummaryPlant adaptation to a desert environment and its endemic heat stress is poorly understood at the molecular level. The naturally heat-tolerant Brassicaceae species Anastatica hierochuntica is an ideal extremophyte model to identify genetic adaptations that have evolved to allow plants to tolerate heat stress and thrive in deserts.We generated an A. hierochuntica reference transcriptome and pinpointed extremophyte adaptations by comparing Arabidopsis thaliana and A. hierochuntica transcriptome responses to heat and identifying positively selected genes in A. hierochuntica.The two species exhibit similar transcriptome adjustment in response to heat and the A. hierochuntica transcriptome does not exist in a constitutive heat “stress-ready” state. Furthermore, the A. hierochuntica global transcriptome as well as heat-responsive orthologs, display a lower basal and higher heat-induced expression than in A. thaliana. Genes positively selected in multiple extremophytes are associated with stomatal opening, nutrient acquisition, and UV-B induced DNA repair while those unique to A. hierochuntica are consistent with its photoperiod-insensitive, early-flowering phenotype.We suggest that evolution of a flexible transcriptome confers the ability to quickly react to extreme diurnal temperature fluctuations characteristic of a desert environment while positive selection of genes involved in stress tolerance and early flowering could facilitate an opportunistic desert lifestyle.
Hippocampal TRPV1 channels in the modulation of contextual fear conditioning
Authors: Iglesias Lia P. , Fernandes Heliana B. , de Miranda Aline S. , Sorgi Carlos A. , Moreira Fabrício A. 
Published: May 2021

ABSTRACTPsychiatric disorders have been linked to impairments in fear memory circuitry. Thus, pharmacological approaches that impair aversive memories have been investigated as new treatments. The TRPV1 channel modulates biological processes related to memory consolidation and retrieval. However, TRPV1 seems involved in memories generated by high intense conditioning. Anandamide (AEA), the main endocannabinoid, is an agonist of both, TRPV1 channels and CB1 receptors which are colocalized in several brain structures. Remarkably, AEA has twenty-times more affinity for CB1 than for TRPV1, which may be involved in the intensity-dependent recruitment of this channel. In order to evaluate the role of intensity of the conditioning in the recruitment of TRPV1, the animals were submitted to the contextual fear conditioning (CFC) and conditioned with low, moderate or high intensity. Before the retrieval a TRPV1 blocker was administered into the dorsal hippocampus (dHPC). The levels of AEA were quantified by Mass Spectrometry. The RNA levels of Arc, Zif and Trkb, involved in memory and plasticity, were quantified by PCR. Our results showed that TRPV1 blockers impair the retrieval of memory in animals conditioned with moderate and high intensity but not low ones. As revealed by Mass Spectrometry, this different recruitment among intensities seems to be associated with the levels of AEA released. Moreover, the impairment in freezing induced by blocking TRPV1 was prevented by a subeffective dose of the cannabinoid receptor CB1 antagonist which suggest that TRPV1 blockers act increasing AEA availability in the synaptic cleft to act through CB1 receptors. Despite blocking TRPV1 channels impairs freezing in moderate and high intensities, it increases the RNA levels of Arc, Zif and Trkb only in animals conditioned with the moderate intensity. In accordance, the treatment impairs retrieval in both intensities but only in the moderate intensity is able to prevent the reinstatement. Summarizing, our results suggested that intensity of the conditioning modulates AEA levels which in turns determines if TRPV1 will be recruited at the retrieval and which molecular pathways will be engaged due to TRPV1 blocking.
Automated detection of artefacts in neonatal EEG with residual neural networks
Authors: Webb Lachlan , Kauppila Minna , Roberts James A. , Vanhatalo Sampsa , Stevenson Nathan 
Published: May 2021

AbstractBackground and ObjectiveTo develop a computational algorithm that detects and identifies different artefact types in neonatal electroencephalography (EEG) signals.MethodsAs part of a larger algorithm, we trained a Residual Deep Neural Network on expert human annotations of EEG recordings from 79 term infants recorded in a neonatal intensive care unit (112 h of 18-channel recording). The network was trained using 10 fold cross validation in Matlab. Artefact types included: device interference, EMG, movement, electrode pop, and non-cortical biological rhythms. Performance was assessed by prediction statistics and further validated on a separate independent dataset of 13 term infants (143 h of 3-channel recording). EEG pre-processing steps, and other post-processing steps such as averaging probability over a temporal window, were also included in the algorithm.ResultsThe Residual Deep Neural Network showed high accuracy (95%) when distinguishing periods of clean, artefact-free EEG from any kind of artefact, with a median accuracy for individual patient of 91% (IQR: 81%-96%). The accuracy in identifying the five different types of artefacts ranged from 57%-92%, with electrode pop being the hardest to detect and EMG being the easiest. This reflected the proportion of artefact available in the training dataset. Misclassification as clean was low for each artefact type, ranging from 1%-11%. The detection accuracy was lower on the validation set (87%). We used the algorithm to show that EEG channels located near the vertex were the least susceptible to artefact.ConclusionArtefacts can be accurately and reliably identified in the neonatal EEG using a deep learning algorithm. Artefact detection algorithms can provide continuous bedside quality assessment and support EEG review by clinicians or analysis algorithms.HighlightsWe applied a Residual Deep Neural Network as part of an artefact detection algorithm in neonatal electroencephalograms.The algorithm shows high accuracy in identifying artefactual data in general and for specific artefact types.EEG channels near the top of the head are less prone to artefact.
EVALUATION OF A RAPID ANTIGEN TEST FOR SARS-COV-2 IN SYMPTOMATIC PATIENTS AND THEIR CONTACTS: A MULTICENTER STUDY
Authors: Thirion-Romero Ireri , Guerrero-Zúñiga Selene , Arias-Mendoza Alexandra , Cornejo-TJuárez Dora Patricia , Meza-Meneses Patricia , Torres-Erazo Darwin Stalin , Hernández Thierry , Galindo-Fraga Arturo , Villegas-Mota Isabel , Sepúlveda-Delgado Jesús , Ávila Ríos Santiago , Becerril-Vargas Eduardo , Fernández-Plata Rosario , Midori Pérez-Kawabe TIT , Vázquez Pérez Joel Armando , Kawa Karasik Simón , Terán Gustavo Reyes , Pérez-Padilla José Rogelio ,   Rapid COVID-19 Antigen Test Group
Published: May 2021

ABSTRACTBACKGROUNDPoint-of-care rapid tests to identify SARS-CoV-2 can be of great help because, in principle, they allow decisions to be made at the site of care for treatment, or for the separation of cohorts avoiding cross-infection, especially in emergency situations.METHODSA cross sectional study in adults requesting care in Emergency Rooms (ER), or the outpatient clinics of referral hospitals for COVID-19, to define the diagnostic characteristics of a rapid antigen test for SARS-CoV-2 (the Abbott Panbio™) having as a gold standard the RT-PCR for SARS-CoV-2. Health personnel in a routine situation within an active pandemic in several cities of Mexico performed the tests.RESULTSA total of 1,069 participants with a mean age of 47 years (SD 16 years), 47% with a self-reported comorbidity, and an overall prevalence of a positive RT-PCR test of 45%, were recruited from eight hospitals in Mexico. Overall sensitivity of the Panbio test was 54.4% (95%CI 51-57) with a positive likelihood ratio of 35.7, a negative likelihood ratio of 0.46 and a Receiver-Operating Characteristics curve area of 0.77.Positivity for the rapid test depended strongly on an estimate of the viral load (Cycle threshold of RT-PCR, Ct), and the days of symptoms. With a Ct≤25, sensitivity of the rapid test was 0.82 (95%CI, 0.76-0.87). For patients during the first week of symptoms sensitivity was 69.6% (95%CI 66-73). On the other hand, specificity of the rapid test was above 97.8% in all groups.CONCLUSIONSThe Panbio™ rapid antigen test for SARS-CoV-2 has a good specificity, but due to low and heterogeneous sensitivity in real life, a negative test in a person with suggestive symptoms at a time of community transmission of SARS-CoV-2 requires confirmation with RT-PCR, and after the first week of symptoms, sensitivity decreases considerably.
Principles of gene regulation quantitatively connect DNA to RNA and proteins in bacteria
Authors: Balakrishnan Rohan , Mori Matteo , Segota Igor , Zhang Zhongge , Aebersold Ruedi , Ludwig Christina , Hwa Terence 
Published: May 2021

ABSTRACTBacteria allocate their proteome to cellular functions differently in different growth conditions. It is largely unknown how such allocation arises from known mechanisms of gene regulation while constrained by limited translation capacity and fixed protein density. Here, we performed absolute transcriptomic and proteomic analysis forE. coliacross many conditions, obtaining a plethora of results on promoters and mRNAs characteristics that clash with conventional expectations: the majority of mRNAs exhibit similar translational efficiencies, while the promoter strengths are vastly different across genes. These characteristics prescribe two principles of gene regulation guiding bacteria to attain the desired protein allocation under global constraints: Total transcriptional output is tightly coordinated with ribosomal activity, and the concentrations of individual proteins are largely set by transcription. These two principles lead to a quantitative formulation of Central Dogma which unravels the complex relationship between gene regulatory activities and mRNA/protein concentrations across conditions. The knowledge obtained will be invaluable for accurately inferring gene regulatory interactions from ‘omics data, as well as for guiding the design of genetic circuits for synthetic biology applications inE. coliand other organisms.
ZNF146/OZF and ZNF507 target LINE-1 sequences
Authors: Creamer Kevin M. , Larsen Eric C. , Lawrence Jeanne B. 
Published: May 2021

AbstractRepetitive sequences including transposable elements (TEs) and transposon-derived fragments account for nearly half of the human genome. While transposition-competent TEs must be repressed to maintain genomic stability, mutated and fragmented TEs comprising the bulk of repetitive sequences can also contribute to regulation of host gene expression and broader genome organization. Here we analyzed published ChIP-seq data sets to identify proteins broadly enriched on TEs in the human genome. We show two of the proteins identified, C2H2 zinc finger-containing proteins ZNF146 (also known as OZF) and ZNF507, are targeted to distinct sites within LINE-1 ORF2 at thousands of locations in the genome. ZNF146 binding sites are found at old and young LINE-1 elements. In contrast, ZNF507 preferentially binds at young LINE-1 sequences correlated to sequence changes in LINE-1 elements at ZNF507’s binding site. To gain further insight into ZNF146 and ZNF507 function, we disrupt their expression in HEK293 cells using CRISPR/Cas9 and perform RNA sequencing, finding modest gene expression changes in cells where ZNF507 has been disrupted. We further identify a physical interaction between ZNF507 and PRMT5, suggesting ZNF507 may target arginine methylation activity to LINE-1 sequences.
Dynamic trajectories of connectome state transitions are heritable
Authors: Jun Suhnyoung , Alderson Thomas H. , Altmann Andre , Sadaghiani Sepideh 
Published: May 2021

AbstractThe brain’s functional connectome is dynamic, constantly reconfiguring in an individual-specific manner. However, which characteristics of such reconfigurations are subject to genetic effects, and to what extent, is largely unknown. Here, we identified heritable dynamic features, quantified their heritability, and determined their association with cognitive phenotypes. In resting-state fMRI, we obtained multivariate features, each describing a temporal or spatial characteristic of connectome dynamics jointly over a set of connectome states. We found strong evidence for heritability of temporal features, particularly fractional occupancy (FO) and transition probability (TP), describing the trajectory of state transitions. Genetic effects explained a substantial proportion of phenotypic variance of these features (h2=.39, 95% CI= [.24,.54] for FO; h2=.43, 95% CI=[.29,.57] for TP). Moreover, these temporal phenotypes were associated with cognitive performance. Contrarily, we found no robust evidence for heritability of spatial features of the dynamic states (i.e., states’ Modularity and connectivity pattern). Genetic effects may therefore primarily contribute to how the connectome transitions across states, rather than the precise spatial instantiation of the states in individuals. In sum, genetic effects impact the duration spent in each connectivity configuration and the frequency of shifting between configurations, and such temporal features may act as endophenotypes for cognitive abilities.
Quantifying brain state transition cost via Schrödinger bridge
Authors: Kawakita Genji , Kamiya Shunsuke , Sasai Shuntaro , Kitazono Jun , Oizumi Masafumi 
Published: May 2021

AbstractQuantifying brain state transition cost is a fundamental problem in systems neuroscience. Previous studies utilized network control theory to measure the cost by considering a neural system as a deterministic dynamical system. However, this approach does not capture the stochasticity of neural systems, which is important for accurately quantifying brain state transition cost. Here, we propose a novel framework based on optimal control in stochastic systems. In our framework, we quantify the transition cost as the Kullback-Leibler divergence from an uncontrolled transition path to the optimally controlled path, which is known as Schrödinger bridge. To test its utility, we applied this framework to functional magnetic resonance imaging data from the Human Connectome Project and computed the brain state transition cost in cognitive tasks. We demonstrate correspondence between brain state transition cost and the difficulty of tasks. The results suggest that our framework provides a general theoretical tool for investigating cognitive functions from the viewpoint of transition cost.Author SummaryIn our daily lives, we perform numerous tasks with different kinds and levels of cognitive demand. To successfully perform these tasks, the brain needs to modulate its spontaneous activity to reach an appropriate state for each task. Previous studies utilized optimal control in deterministic systems to measure cost for brain state transition. However, there has not been a unified framework for quantifying brain state transition cost that takes account of stochasticity of neural activities. Here, we propose a novel framework for measuring brain state transition cost, utilizing the idea of optimal control in stochastic systems. We assessed the utility of our framework for quantifying the cost of transitioning between various cognitive tasks. Our framework can be applied to very diverse settings due to its generality.
Kinetic Monitoring Of Neuronal Stress Response To Proteostasis Dysfunction
Authors: Santiago-Lopez Angel J. , Berglund Ken , Gross Robert E. , Gutekunst Claire-Anne N. 
Published: May 2021

ABSTRACTProteostasis dysfunction and activation of the unfolded protein response (UPR) are characteristic of all major neurodegenerative diseases. Nevertheless, although the UPR and proteostasis dysfunction has been studied in great detail in model organisms like yeast and mammalian cell lines, it has not yet been examined in neurons. In this study, we applied a viral vector-mediated expression of a reporter protein based on a UPR transcription factor, ATF4, and time-lapse fluorescent microscopy to elucidate how mouse primary neurons respond to pharmacological and genetic perturbations to neuronal proteostasis. In in vitro models of endoplasmic reticulum (ER) stress and proteasome inhibition, we used the ATF4 reporter to reveal the time course of the neuronal stress response relative to neurite degeneration and asynchronous cell death. We showed how potential neurodegenerative disease co-factors, ER stress and mutant α-synuclein overexpression, impacted neuronal stress response and overall cellular health. This work therefore introduces a viral vector-based reporter that yields a quantifiable readout suitable for non-cell destructive kinetic monitoring of proteostasis dysfunction in neurons by harnessing ATF4 signaling as part of the UPR activation.
The influence of second language learning motivation on students' understandability of textbooks
Authors: Zhang Yuqian , De Zoysa Anura , Jagoda Kalinga 
Published: May 2021

PurposeThe purpose of this study is to examine the relationship between the understandability of an accounting textbooks written in English and the language learning motivation of international students. Previous research assumed that native speakers of a language and second-language speakers would understand a given accounting text similarly and little attempt has been made to ascertain any individual differences in users’ capacity to read and understand a foreign language.Design/methodology/approachThe 107 participants in this study comprised of full-time English as a Second Language postgraduate commerce students studying at a major Australian university. The authors used two-part questionnaire to examine the motivation of participants and the understandability of an accounting textbook using the Cloze test.FindingsThe results suggest that most international students have difficulty in understanding the textbook narratives used in this study. Furthermore, the results show that students’ motivation to learn a foreign language impacts on the understandability of an accounting textbook.Practical implicationsThis study will help the educators, textbook publishers and students to understand the needs of ESL students. It is expected to provide guidance for authors and instructors to enhance the effectiveness of the accounting courses.Originality/valueThe accounting literature shows that there have been efforts by accounting researchers to measure the understandability of accounting texts or narratives. This research provided valuable insights of the learning challenges of international students and valuable recommendations to educators and publishers to enhance the delivery.
Solution of the 3D Helmholtz equation using barycentric Lagrange interpolation collocation method
Authors: Yang Miaomiao , Du Xinkun , Ge Yongbin 
Published: May 2021

PurposeThis meshless collocation method is applicable not only to the Helmholtz equation with Dirichlet boundary condition but also mixed boundary conditions. It can calculate not only the high wavenumber problems, but also the variable wave number problems.Design/methodology/approachIn this paper, the authors developed a meshless collocation method by using barycentric Lagrange interpolation basis function based on the Chebyshev nodes to deduce the scheme for solving the three-dimensional Helmholtz equation. First, the spatial variables and their partial derivatives are treated by interpolation basis functions, and the collocation method is established for solving second order differential equations. Then the differential matrix is employed to simplify the differential equations which is on a given test node. Finally, numerical experiments show the accuracy and effectiveness of the proposed method.FindingsThe numerical experiments show the advantages of the present method, such as less number of collocation nodes needed, shorter calculation time, higher precision, smaller error and higher efficiency. What is more, the numerical solutions agree well with the exact solutions.Research limitations/implicationsCompared with finite element method, finite difference method and other traditional numerical methods based on grid solution, meshless method can reduce or eliminate the dependence on grid and make the numerical implementation more flexible.Practical implicationsThe Helmholtz equation has a wide application background in many fields, such as physics, mechanics, engineering and so on.Originality/valueThis meshless method is first time applied for solving the 3D Helmholtz equation. What is more the present work not only gives the relationship of interpolation nodes but also the test nodes.
The mutual impact of university president’s leadership and organizational justice on knowledge sharing: the mediating effect of communication
Authors: Kim Soo Jung , Jang Youjin , Yoo Myunghyun , Song Ji Hoon 
Published: May 2021

Purpose
The purpose of this study is to empirically examine the mediating effect of organizational communication in the relationships among transformational leadership, organizational justice and knowledge sharing within the higher education setting in South Korea.

Design/methodology/approach
A sample of 321 university employees, including 151 faculty members and 170 administrative staff members, from a representative private university, participated in the survey as part of a consulting project for university innovation. Structural equation modeling (SEM) was mainly used for data analysis to identify the structural relationship among the research variables.

Findings
The results of this study confirmed that transformational leadership positively influences organizational justice and knowledge sharing. However, the influence of organizational justice on knowledge sharing was not statistically significant. The mediating effect of organizational communication among those relationships to increase the members’ knowledge sharing behavior was statistically significant.

Originality/value
In this study, holistic aspects of the organization, including leadership, organizational culture and organizational strategy, were examined for encouraging employees’ knowledge sharing behavior while an organization undergoes innovational changes. More practically, this study suggested that organizational communication could be used as one of the critical strategies in the process of university innovation.