bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel combination of Class-I fumarases and metabolites (α-ketoglutarate and fumarate) signal the DNA damage response inE. coli
Authors: Silas Yardena , Singer Esti , Das Koyeli , Lehming Norbert , Pines Ophry 
Published: August 2020

AbstractClass-II fumarases (Fumarate Hydratase, FH) are dual targeted enzymes, occurring in the mitochondria and cytosol of all eukaryotes. They are essential components in the DNA damage response (DDR) and more specifically, protecting cells from DNA double strand breaks. Similarly, the Gram-positive BacteriumBacillus subtilisClass-II fumarase, in addition to its role in the TCA cycle, also participates in the DDR.Escherichia coli, harbors three fumarase genes; Class-IfumAandfumBand Class-IIfumC. Notably, Class-I fumarases, show no sequence similarity to Class-II fumarases and are of different evolutionary origin. Strikingly, here we show thatE. colifumarase functions are distributed between Class-I fumarases which participate in the DDR, and the Class-II fumarase which participates in respiration. InE. coli, we discover that the signaling molecule, alpha-ketoglutarate (α-KG), has a novel function, complementing DNA damage sensitivity offumnull mutants. Excitingly, we identify theE. coliα-KG dependent DNA repair enzyme AlkB, as the target of this interplay of metabolite signaling. In addition to α-KG, fumarate (fumaric acid) is shown to affect DNA damage repair on two different levels, first by directly inhibiting the DNA damage repair enzyme AlkB demethylase activity, both in vitro and in vivo (countering α-KG). The second is a more global effect on transcription, asfumnull mutants exhibit a decrease in transcription of key DNA damage repair genes. Together these results show evolutionary adaptable metabolic signaling of the DDR, in which fumarases and different metabolites are recruited regardless of the evolutionary enzyme Class preforming the function.Significance StatementClass-II fumarases have been shown to participate in cellular respiration and the DNA damage response. Here we show, for the first time, that in the model prokaryote,Escherichia coli, which harbors both Class-I and Class-II fumarases, it is the Class-I fumarases that participate in DNA damage repair by a mechanism which is different than those described for other fumarases. Strikingly, this mechanism employs a novel signaling molecule, alpha-ketoglutarate (α-KG), and its target is the DNA damage repair enzyme AlkB. In addition, we show that fumarase precursor metabolites, fumarate and succinate, can inhibit the α-KG-dependent DNA damage repair enzyme, AlkB, both in vitro and in vivo. This study provides a new perspective on the function and evolution of metabolic signaling.
Changes in weak pair-wise correlations during running reshapes network state in the main olfactory bulb
Authors: Chockanathan Udaysankar , Crosier Emily J. W. , Waddle Spencer , Lyman Edward , Gerkin Richard C. , Padmanabhan Krishnan 
Published: August 2020

AbstractNeural codes for sensory representations are thought to reside in a broader space defined by the patterns of spontaneous activity that occur when stimuli are not being presented. To understand the structure of this spontaneous activity in the olfactory system, we performed high-density recordings of population activity in the main olfactory bulb of awake mice. We found that spontaneous activity patterns of ensembles of mitral and tufted (M/T) cells in the main olfactory bulb changed dramatically during locomotion, including decreases in pairwise correlations between neurons and increases in the entropy of the population. Maximum entropy models of the ensemble activity revealed that pair-wise interactions were better at predicting patterns of activity when the animal was stationary than while running, suggesting that higher order (3rd, 4th order) interactions between neurons shape activity during locomotion. Taken together, we found that locomotion influenced the structure of spontaneous population activity at the earliest stages of olfactory processing, 1 synapse away from the sensory receptors in the nasal epithelium.New and NoteworthyThe organization and structure of spontaneous population activity in the olfactory system places constraints of how odor information is represented. Using high-density electrophysiological recordings of mitral and tufted cells, we found that running increases the dimensionality of spontaneous activity, implicating higher-order interactions among neurons during locomotion. Behavior thus flexibly alters neuronal activity at the earliest stages of sensory processing.
TREND-DB – A Transcriptome-wide Atlas of the Dynamic Landscape of Alternative Polyadenylation
Authors: Marini Federico , Scherzinger Denise , Danckwardt Sven 
Published: August 2020

AbstractAlternative polyadenylation (APA) profoundly expands the transcriptome complexity. Perturbations of APA can disrupt biological processes, ultimately resulting in devastating disorders. A major challenge in identifying mechanisms and consequences of APA (and its perturbations) lies in the complexity of RNA 3’end processing, involving poorly conserved RNA motifs and multi-component complexes consisting of far more than 50 proteins. This is further complicated in that RNA 3’end maturation is closely linked to transcription, RNA processing, and even epigenetic (histone/DNA/RNA) modifications. Here we present TREND-DB (http://shiny.imbei.uni-mainz.de:3838/trend-db), a resource cataloging the dynamic landscape of APA after depletion of >170 proteins involved in various facets of transcriptional, co- and posttranscriptional gene regulation, epigenetic modifications, and further processes. TREND-DB visualizes the dynamics of transcriptome 3’end diversification (TREND) in a highly interactive manner; it provides a global APA network map and allows interrogating genes affected by specific APA-regulators, and vice versa. It also permits condition-specific functional enrichment analyses of APA-affected genes, which suggest wide biological and clinical relevance across all RNAi conditions. The implementation of the UCSC Genome Browser provides additional customizable layers of gene regulation accounting for individual transcript isoforms (e.g. epigenetics, miRNA binding sites, RNA-binding proteins). TREND-DB thereby fosters disentangling the role of APA for various biological programs, including potential disease mechanisms, and helps to identify their diagnostic and therapeutic potential.
The sensor hub for detecting the developmental characteristics in reading in children on a white vs. coloured background/coloured overlays
Authors: Jakovljević Tamara , Janković Milica , Savić Andrej , Soldatović Ivan , Todorović Petar , Jakulin Tadeja Jere , Papa Gregor , Ković Vanja 
Published: August 2020

AbstractThe study investigated the influence of white vs 12 background and overlay colours on the reading process in school age children. Previous research reported that colours could affect reading skills as an important factor of the emotional and physiological state of the body and that reading is one of the most important processes in the maturation of children. The aim of the study was to assess developmental differences between second and third grade students of elementary school and to evaluate differences in electroencephalography (EEG), ocular, electrodermal activities (EDA) and heart rate variability (HRV). In the experiment, the responses of 24 children (12 second and 12 third grade students) to different background and overlay colours were summarized using EEG, eye tracking, EDA and HRV signals. Our findings showed a decreasing trend with age regarding EEG power bands (Alpha, Beta, Delta, Theta) and lower scores of reading duration and eye-tracking measures in younger children compared to older children. As shown in the results, HRV parameters showed higher scores in 12 background and overlay colours among second than third grade students which is linearly correlated to the level of stress and readable from EDA measures as well. The existing study showed the calming effect on second graders in turquoise and blue background colours. Considering other colours separately for each parameter, we assumed that there are no systematic differences in Reading duration, EEG power band, Eye-tracking and EDA measures.
18S rDNA Sequence-Structure Phylogeny of the Trypanosomatida (Kinetoplastea, Euglenozoa) with Special Reference onTrypanosoma
Authors: Borges Alyssa R. , Engstler Markus , Wolf Matthias 
Published: August 2020

AbstractBackgroundParasites of the order Trypanosomatida are known due to their medical relevance. Trypanosomes cause African sleeping sickness and Chagas disease in South America, andLeishmaniaRoss, 1903 species mutilate and kill hundreds of thousands of people each year. However, human pathogens are very few when compared to the great diversity of trypanosomatids. Despite the progresses made in the past decades on understanding the evolution of this group of organisms, there are still many open questions which require robust phylogenetic markers to increase the resolution of trees.MethodsUsing two known 18S rDNA template structures (fromTrypanosoma cruziChagas, 1909 andTrypanosoma bruceiPlimmer& Bradford, 1899), individual 18S rDNA secondary structures were predicted by homology modeling. Sequences and their secondary structures, automatically encoded by a 12-letter alphabet (each nucleotide with its three structural states, paired left, paired right, unpaired), were simultaneously aligned. Sequence-structure trees were generated by neighbor joining and/or maximum likelihood.ResultsWith a few exceptions, all nodes within a sequence-structure maximum likelihood tree of 43 representative 18S rDNA sequence-structure pairs are robustly supported (bootstrap support >75). Even a quick and easy sequence-structure neighbor-joining analysis yields accurate results and enables reconstruction and discussion of the big picture for all 240 18S rDNA sequence-structure pairs of trypanosomatids that are currently available.ConclusionsWe reconstructed the phylogeny of a comprehensive sampling of trypanosomes evaluated in the context of trypanosomatid diversity, demonstrating that the simultaneous use of 18S rDNA sequence and secondary structure data can reconstruct robust phylogenetic trees.
Transient Room Lighting for Ambient Light Multiphoton Microscopy
Authors: Velten A. , Uselmann A.J. , Prajapati S. , Bredfeldt J.S. , Mackie T.R. , Eliceiri K.W. 
Published: August 2020

AbstractLaser scanning microscopy techniques such as confocal and multiphoton fluorescence microscopy have been widely adopted by the biological research community due to their ability to monitor intact specimens at high spatial and temporal resolution. However, they have been limited for many biomedical, clinical and industrial applications by their fundamental need to operate in near absolute darkness. We present a lighting system that allows the use of light-sensitive imaging techniques in a fully-lit room by interleaving capture and illumination at a high frequency and exploiting the light averaging properties of the human eye. We use this system with a multiphoton fluorescence microscope to illustrate that this method is capable of image capture in a well-lit room on par with capture in absolute darkness. This comparison is quantified through noise analysis of the images. This system has been implemented for laser scanning microscopy but has potential for widefield fluorescence imaging suitable for open-field surgery.
Pathogenetic Perspective of Missense Mutations of ORF3a Protein of SARS-CoV2
Authors: Hassan Sk. Sarif , Attrish Diksha , Ghosh Shinjini , Choudhury Pabitra Pal , Roy Bidyut 
Published: August 2020

AbstractOne of the most important proteins for COVID-19 pathogenesis in SARS-CoV2 is the ORF3a protein which is the largest accessory protein among others accessory proteins coded by coronavirus genome. The major roles of the protein include virulence, infectivity, ion channel activity, morphogenesis and virus release. The coronavirus, SARS-CoV2 is continuously evolving naturally and thereby the encoded proteins are also mutating rapidly. Therefore, critical study of mutations in ORF3a is certainty important from the pathogenetic perspective. Here, a sum of 175 various non-synonymous mutations in the ORF3a protein of SARS-CoV2 are identified and their corresponding effects in structural stability and functions of the protein ORF3a are studied. Broadly three different classes of mutations, such as neutral, disease and mixed (neutral and disease) type mutations were observed. Consecutive mutations in some ORF3a proteins are established based on timeline of detection of mutations. Considering the amino acid compositions over the ORF3a primary protein sequences, twenty clusters are detected based on K-means clustering method. Our findings on 175 novel mutations of ORF3a proteins will extend our knowledge of ORF3a, a vital accessory protein in SARS-CoV2, which would assist to enlighten on the pathogenicity of this life-threatening COVID-19.
Paradoxical relationships between active transport and global protein distributions in neurons
Authors: Bellotti A. , Murphy J. , Lin L. , Petralia R. , Wang Y-X , Hoffman D. , O’Leary T. 
Published: August 2020

ABSTRACTNeural function depends on continual synthesis and targeted trafficking of intracellular components, including ion channel proteins. The detailed biophysics active ion channel transport are increasingly well understood, along with the steady-state distribution of functional channels in the membrane. However we lack a quantitative understanding of how transport mechanisms give rise to stable expression patterns, and how live measurements of active transport relate to static estimates of channel density in neurites. We experimentally measured neuronal transport and expression densities of Kv4.2, a voltage-gated transient potassium channel. Kv4.2 is known to have a highly specific dendritic expression and little or no reported functional expression in axons. Surprisingly, in over 500 hours of quantitative live imaging, we found substantially higher microtubule-based transport of Kv4.2 subunits in axons compared to dendrites. We show that this paradoxical result is expected using a mass action trafficking model of intracellular transport that we calibrate to experimental measurements. Furthermore, we find qualitative differences in axonal and dendritic active transport that are captured in a stochastic model of puncta transport. This reveals that active transport is tuned to efficiently move cargo through axons while promoting mixing in dendrites. Finally, our data reveals trends in transport parameters that can explain the functional density profile of Kv4.2. Puncta velocity bias is directed distally and the magnitude of this bias increases with distance from the soma. These trends are consistent with an analytical solution of a linear transport PDE, corroborating previously unexplained distributions of Kv4.2 subunit localization and A-type current density. Together, our results provide new quantitative data on ion channel trafficking and reveal counterintuitive but mathematically consistent relationships between the distribution of cargo that is in transit and its functional expression.SIGNIFICANCEThis study of ion channel transport reveals a seemingly counterintuitive result: the majority of subunit transport occurs in axons for a cargo whose static distribution is concentrated in dendrites. This disparity is reconciled by a simple mathematical model of transport, which reveals that the local density of actively transported intracellular cargo can show an inverse relationship with its static expression density. Mass action models also reconcile the previously unexplained, highly asymmetric, increasing distribution of Kv4.2 with its measured trafficking density that resembles diffusion with minimal drift. The generality of our analysis prompts caution in how static snapshots of intracellular cargo distributions should be interpreted for any type of intracellular cargo.
The mediating role of boreout in the effects of mobbing on service innovation performance
Authors: Özsungur Fahri 
Published: August 2020

Purpose
The purpose of this paper is to examine the association between mobbing and service innovation performance. In this context, the mediating role of boreout, a new concept in the literature, was examined.

Design/methodology/approach
This study was conducted with 240 participants recruited in manufacturing companies affiliated with Adana Chamber of Industry in the province of Adana Turkey in November 2019. The research was analyzed by the structural equation modeling method with the social exchange theory basis.

Findings
Findings revealed that boreout and mobbing were negatively associated with service innovation performance. Mobbing was positively associated with boreout and job boredom. According to the finding of this study, boreout partially mediated the effect of the mobbing on service innovation performance.

Originality/value
This study reveals the association among mobbing, boreout and service innovation performances of employees of companies operating in manufacturing sector. The findings of this study provide important practical knowledge to businesses and academics regarding the field of management, entrepreneurship and innovation.
Doubly stratified non-Newtonian nanofluid flow featuring nonlinear convection
Authors: Shahzadi Iqra , Kausar Nabeela 
Published: August 2020

Purpose
The formulation of nonlinear convective non-Newtonian material is reported in this communication. Aspects of thermal radiation and heat source are taken into account for heat transport analysis. The novel stratifications (thermal and solutal) and convective conditions are considered simultaneously. The boundary-layer concept is implemented to simplify the complex mathematical expressions.

Design/methodology/approach
The well-known optimal homotopy scheme develops the computations. Optimal values regarding nonzero auxiliary variables are calculated and examined.

Findings
Nonlinear convective flow; Thixotropic non-Newtonian material; Thermal radiation; Heat source; Stratifications and convective conditions; Buongiorno model.

Originality/value
To the best of authors’ knowledge, no such analysis has yet been reported.
Village savings and loans association participation and impact on off-farm income among rural women
Authors: Bannor Richard Kwasi , Oppong-Kyeremeh Helena , Derkyi Mercy , Adombila Albert Yingura , Amrago Ernest Christlieb 
Published: August 2020

PurposeThis paper aims to examine the factors that influence rural women’s participation in Village Savings and Loans Association (VSLA) and the savings contribution in the Kassena-Nankana West District of Ghana. The study also analysed the impact of VSLA participation on off-farm income and on poverty.Design/methodology/approachIn total, 120 rural women were selected for this study. The probit and heteroskedasticity linear regression models were used to examine the factors that influence VSLA participation and the savings made by members, respectively. The propensity score matching technique, coupled with Rosenbaum Sensitivity analysis, were used to analyse the impact of VSLA on off-farm income and poverty.FindingsDemographic and livelihood factors such as human, natural, financial, physical and social capitals have different influences on the participation and the savings contribution in the VSLA. Moreover, VSLA has a significant impact on off-farm income; however, it did not affect poverty.Originality/valueDespite the numerous studies on VSLA, there is little evidence of literature of its impact on off-farm income of rural women in West Africa, specifically, Ghana. Thus, this paper expands the frontiers of the existing literature on VSLA impact assessment and the factors that influence the savings made by women in the association.
The Big-4’s influence on rules-based accounting standards
Authors: Lysak Amy K. 
Published: August 2020

Purpose
This study aims to evaluate whether the Big-4’s commenting efforts influence the characteristics of Financial Accounting Standards Board’s (FASB’s) Final_Standards using the content of their comment letters. Whether auditors lobby standard-setters to help their clients or to help themselves and whether they are successful are questions highly relevant to issues of auditor independence and audit effectiveness.

Design/methodology/approach
Based on components of Mergenthaler (2009), this study develops a rules-based continuum change score to measure how much more (less) rules-based a Final_Standard is compared to its exposure draft to evaluate the influence of the Big-4 on the FASB’s standard-setting for 63 accounting standards.

Findings
The findings show that extensive comment letters and increased uncertainty language are associated with increases in the rules-based attributes included in Final_Standards. These results suggest the Big-4 prioritize a reduction in their own litigation risk over the possible preferences of their clients for less rigid standards. Moreover, the results are consistent with their comment letters influencing the FASB’s decision to include more rules-based attributes in Final_Standards.

Originality/value
This study develops a potential proxy for audit risk by assessing the changes in the rules-based characteristics of proposed accounting standards and using the content of the comment letters to evaluate whether the Big-4 accounting firms may influence the FASB’s Final_Standards. Overall, this study provides a unique perspective on the influence of constituents on the FASB’s standard-setting.
Exploring the U.S. Coast Guard's stance agility on Twitter during Hurricane Harvey
Authors: Boman Courtney D. , Valiavska Anna , Bramlett Josh C. , Cameron Glen T. 
Published: August 2020

AbstractDrawing on the contingency theory of strategic conflict management, this study examines how the U.S. Coast Guard (USCG) used Twitter to communicate during Hurricane Harvey. A content analysis was conducted on tweets (N = 273) by using stances along the contingency's continuum, finding that the USCG frequently adopted stances on both sides of the continuum's spectrum throughout the disaster event. The analysis of USCG tweets provides a real‐world case study of how Twitter is used by organizations to strategically communicate with the public during a disaster event. Like many disaster aid organizations, the USCG must balance competing goals of assisting the impacted population, while continuing to secure funding from the U.S. government. The current study contributes to contingency theory of strategic conflict management literature by applying the theory to a disaster, providing tangible evidence that disaster communication research should consider incorporating different stances across the continuum, sometimes simultaneously, that could help guide strategies, ultimately helping the organization and public being affected during a disaster.