bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of genomic DNA methylation and gene transcription modulation induced byDNMT3Adeficiency in HEK293 cells
Authors: Zhang Mengxiao , Wang Jiaxian , Tian Qiuxiang , Feng Lei , Yang Hui , Zhu Nan , Pan Xingchen , Zhu Jianwei , Chen Peng , Lu Huili 
Published: July 2020

AbstractDNA methylation is an important epigenetic modification associated with transcriptional repression, and plays key roles in normal cell growth as well as oncogenesis. Among the three main DNA methyltransferases (DNMT1, DNMT3A, and DNMT3B), DNMT3A mediatesde novoDNA methylation with partial functional redundancy with DNMT3B. However, the general effects of DNMT3A and its downstream gene regulation profile are yet to be unveiled. In the present study, we used CRISPR/Cas9 technology to successfully create DNMT3A deficient human embryonic kidney cell line HEK293, with frameshift mutations in its catalytic domain. Our results showed that the cell growth slowed down inDNMT3Aknockout cells. UPLC-MS analysis of DNMT3A deficient cells showed that the genome-level DNA methylation was reduced by 21.5% and led to an impairment of cell proliferation as well as a blockage of MAPK and PI3K-Akt pathways. Whole genome RNA-seq revealed thatDNMT3Aknockout up-regulated expression of genes and pathways related to cell metabolism but down-regulated those involved in ribosome function, which explained the inhibition of cell growth and related signal pathways. Further, bisulfite DNA treatment showed thatDNMT3Aablation reduced the methylation level ofDNMT3Bgene as well, indicating the higher DNMT3B activity and thereby explaining those down-regulated profiles of genes.
Individual differences in frontal midline theta activity during visuomotor adaptation are related to execution noise
Authors: Jonker Zeb D. , van der Vliet Rick , Maquelin Guido , van der Cruijsen Joris , Ribbers Gerard M. , Selles Ruud W. , Donchin Opher , Frens Maarten A. 
Published: July 2020

ABSTRACTFrontal midline EEG activity has been found to correlate with error magnitude during motor adaptation. We replicated a previous visuomotor adaptation experiment with very small perturbations, likely to invoke implicit adaptation, in a new group of 60 participants and combined it with EEG recordings. We used this data to explore 1) whether frontal midline activity will be evoked in the absence of awareness of the perturbation; 2) whether frontal midline activity is related to implicit adaptation; 3) whether individual differences in frontal midline activity are related to individual differences in motor learning. The results showed that frontal midline theta activity (FMΘ) is also present during small perturbations, does not drive between-trial error correction, and that the sensitivity of FMΘ to error magnitude was smaller for participants with greater execution noise. This relation between FMΘ-error-sensitivity and execution noise could be fully explained by looking at the relationship between FMΘ and error probability. This implies that frontal midline theta activity represents a surprise-like saliency signal, potentially driving awareness and cognitive control in situations with more salient errors.
FADS2-mediated fatty acid desaturation and cholesterol esterification are signatures of metabolic reprogramming during melanoma progression
Authors: Lee Hyeon Jeong , Chen Zhicong , Collard Marianne , Chen Jiaji G , Wu Muzhou , Alani Rhoda M , Cheng Ji-Xin 
Published: July 2020

AbstractIdentifying metabolic alterations in disease progression has been challenged by difficulties in tracking metabolites at sub-cellular level. Here, by high-resolution stimulated Raman scattering and pump-probe imaging and spectral phasor analysis of melanoma cells grouped by MITF/AXL expression pattern and of human patient tissues paired by primary and metastatic status, we identify a metabolic switch from a pigment-containing phenotype in low-grade melanoma to a lipid-rich phenotype in metastatic melanoma. The lipids found in MITFlow/AXLhighmelanoma cells contain high levels of cholesteryl ester (CE) and unsaturated fatty acid species. Elevated fatty acid uptake activity in MITFlow/AXLhighmelanoma contributes to the lipid-rich phenotype, and inhibiting fatty acid uptake suppresses cell migration. Importantly, monounsaturated sapienate is identified as an essential fatty acid that effectively promotes cancer migration. Blocking either FADS2-mediated lipid desaturation or SOAT-mediated cholesterol esterification effectively suppresses the migration capacity of melanomain vitroandin vivo, indicating the therapeutic potential of targeting these metabolic pathways in metastatic melanoma. Collectively, our results reveal metabolic reprogramming during melanoma progression, and highlight metabolic signatures that could serve as targets for metastatic melanoma treatment and diagnosis.
SUMOylation contributes to proteostasis of the chloroplast protein import receptor TOC159 during early development
Authors: Accossato Sonia , Kessler Felix , Shanmugabalaji Venkatasalam 
Published: July 2020

AbstractChloroplast biogenesis describes the transition of non-photosynthetic proplastids to photosynthetically active chloroplasts in the cells of germinating seeds. Chloroplast biogenesis requires the import of thousands of nuclear-encoded preproteins and depends on the essential import receptor TOC159, mutation of which results in non-photosynthetic albino plants. We previously showed that ubiquitin-proteasome system (UPS)-dependent regulation of TOC159 levels contributes to the regulation of chloroplast biogenesis during early plant development. Here, we demonstrate that the SUMO (Small Ubiquitin-related Modifier) pathway crosstalks with the ubiquitin-proteasome pathway to affect TOC159 stability during early plant development. We identified a SUMO3-interacting motif (SIM) in the TOC159 GTPase (G-) domain and a SUMO3 covalent SUMOylation site in the membrane (M-) domain. A single K to R substitution (K1370R) in the M-domain disables SUMOylation. Expression of the TOC159K1370R mutant in thetoc159mutant (ppi2) complemented the albino phenotype. Compared to wild type TOC159, TOC159K1370R was destabilized under UPS-inducing stress conditions. However, TOC159K1370R recovered to same protein level as wild type TOC159 in the presence of a proteasome inhibitor. Thus, SUMOylation partially stabilizes TOC159 against UPS-dependent degradation under stress conditions. Our data contribute to the evolving model of tightly controlled proteostasis of the TOC159 import receptor during proplastid to chloroplast transition.
A cost-effective maize ear phenotyping platform enables rapid categorization and quantification of kernels
Authors: Warman Cedar , Sullivan Christopher M. , Preece Justin , Buchanan Michaela E. , Vejlupkova Zuzana , Jaiswal Pankaj , Fowler John E. 
Published: July 2020

AbstractHigh-throughput phenotyping systems are powerful, dramatically changing our ability to document, measure, and detect biological phenomena. Here, we describe a cost-effective combination of a custom-built imaging platform and deep-learning-based computer vision pipeline. A minimal version of the maize ear scanner was built with low-cost and readily available parts. The scanner rotates a maize ear while a cellphone or digital camera captures a video of the surface of the ear. Videos are then digitally flattened into two-dimensional ear projections. Segregating GFP and anthocyanin kernel phenotype are clearly distinguishable in ear projections, and can be manually annotated using image analysis software. Increased throughput was attained by designing and implementing an automated kernel counting system using transfer learning and a deep learning object detection model. The computer vision model was able to rapidly assess over 390,000 kernels, identifying male-specific transmission defects across a wide range of GFP-marked mutant alleles. This includes a previously undescribed defect putatively associated with mutation of Zm00001d002824, a gene predicted to encode a vacuolar processing enzyme (VPE). We show that by using this system, the quantification of transmission data and other ear phenotypes can be accelerated and scaled to generate large datasets for robust analyses.One sentence summaryA maize ear phenotyping system built from commonly available parts creates images of the surface of ears and identifies kernel phenotypes with a deep-learning-based computer vision pipeline.
DBSCAN-SWA: an integrated tool for rapid prophage detection and annotation
Authors: Gan Rui , Zhou Fengxia , Si Yu , Yang Han , Chen Chuangeng , Wu Jiqiu , Zhang Fan , Huang Zhiwei 
Published: July 2020

AbstractSummaryAs an intracellular form of a bacteriophage in the bacterial host genome, a prophage is usually integrated into bacterial DNA with high specificity and contributes to horizontal gene transfer (HGT). Phage therapy has been widely applied, for example, using phages to kill bacteria to treat pathogenic and resistant bacterial infections. Therefore, it is necessary to develop effective tools for the fast and accurate identification of prophages. Here, we introduce DBSCAN-SWA, a command line software tool developed to predict prophage regions of bacterial genomes. DBSCAN-SWA runs faster than any previous tool. Importantly, it has great detection power based on analysis using 184 manually curated prophages, with a recall of 85% compared with Phage_Finder (63%), VirSorter (74%) and PHASTER (82%) for raw DNA sequences. DBSCAN-SWA also provides user-friendly visualizations including a circular prophage viewer and interactive DataTables.Availability and implementationDBSCAN-SWA is implemented in Python3 and is freely available under an open source GPLv2 license fromhttps://github.com/HIT-ImmunologyLab/DBSCAN-SWA/.
Tafenoquine inhibits replication of SARS-Cov-2 at pharmacologically relevant concentrations in vitro
Authors: Dow Geoffrey S. , Luttick Angela , Fenner Jen , Wesche David , Yeo Karen Rowland , Rayner Craig 
Published: July 2020

ABSTRACTTafenoquine [TQ] exhibited EC50/90s of ~ 2.6/5.1 μM against SARS-CoV-2 in VERO E6 cells and was 4-fold more potent than hydroxychloroquine [HCQ]. Time-of-addition experiments were consistent with a different mechanism for TQ v HCQ. Physiologically based pharmacokinetic (PBPK) modeling suggested that lung unbound concentrations of TQ in COVID-19 patients may exceed the EC90 for at least 8 weeks after administration. The therapeutic potential for TQ in management of COVID-19 should be further evaluated.
Apoptosis-induced FGF signalling promotes non-cell autonomous resistance to cell death
Authors: Bock Florian J. , Cloix Catherine , Zerbst Desiree , Tait Stephen W.G. 
Published: July 2020

AbstractDamaged or superfluous cells are often eliminated by apoptosis. Although a cell-autonomous process, apoptotic cells communicate with their environment in different ways. However, the extent to which apoptotic cells alerting their neighbours to potential danger is unclear. Addressing this question, here we describe a mechanism whereby dying cells can promote survival of neighbouring cells. We find that during apoptosis, cells release the growth factor FGF2, leading to MEK/ERK-dependent transcriptional upregulation of pro-survival BCL-2 proteins in a non-cell autonomous manner. This transient upregulation of prosurvival BCL-2 proteins in turn can protect neighbouring cells from apoptosis. Accordingly, we find in certain cancer types a correlation between FGF-signalling, BCL-2 expression and worse prognosis. Importantly, either co-treatment with FGF-receptor inhibitors or removal of apoptotic stress restores apoptotic sensitivity. These data reveal a pathway by which dying cells can increase resistance to cell death in surrounding cells. Beyond mediating cytotoxic drug resistance, this process may serve additional roles, for instance limiting tissue damage in response to stress.
Tobacco harm reduction in the 21st century
Authors: O'Leary Renée , Polosa Riccardo 
Published: July 2020

Purpose
This paper aims to overview the need for tobacco harm reduction, the consumer products that facilitate tobacco harm reduction and the barriers to its implementation. The worldwide endemic of tobacco smoking results in the death of over seven million smokers a year. Cigarette quit rates are very low, from 3%–12%, and relapse rates are high, from 75%–80% in the first six months and 30%–40% even after one year of abstinence. In addition, some smokers do not desire to quit. Cigarette substitution in tobacco harm reduction is one strategy that may reduce the burden of morbidity and mortality.

Design/methodology/approach
This review examines the displacement of smoking through substitution of non-combustible low-risk products such as snus, heated tobacco products and e-cigarettes.

Findings
Toxicological testing, population studies, clinical trials and randomized controlled trials demonstrate the potential reductions in exposures for smokers. Many barriers impede the implementation of product substitution in tobacco harm reduction. These products have been subjected to regulatory bans and heavy taxation and are rejected by smokers and society based on misperceptions about nicotine, sensational media headlines and unsubstantiated fears of youth addiction. These barriers will need to be addressed if tobacco harm reduction is to make the maximum impact on the tobacco endemic.

Originality/value
This review provides the rationale for tobacco harm reduction, evaluates the current products available and identifies the barriers to implementation.
What makes employees participate in volunteering programs? The role of organizational support
Authors: Sekar Srinivasan , Dyaram Lata 
Published: July 2020

Purpose
The purpose of this paper is to identify some of the critical organizational support factors and efforts that facilitate better employee participation in corporate volunteering (CV) programs. There is a growing interest to understand the role of organization in enhancing better employee participation in volunteering programs.

Design/methodology/approach
The authors conducted an empirical investigation with (n = 461) employee volunteers, who participated in company sponsored volunteering programs. The authors tested the hypothesized relationship using structural equation modelling (SEM).

Findings
The SEM results indicate that cultural fit, organizational CV communication and implementation of CV programmes facilitate better employee participation.

Research limitations/implications
This study provides insights for organizations in terms of increased internal communication and alignment of organizational values with CV programmes to attract better employee participation in volunteering programmes.

Originality/value
This study contributes to the literature on the phenomenon of employee volunteering by examining various organizational efforts that facilitate better employee participation in volunteering programmes.
Supplier selection using hybrid multicriteria decision-making methods
Authors: Tusnial Anirudh , Sharma Satyendra Kumar , Dhingra Parth , Routroy Srikanta 
Published: July 2020

PurposeThe paper develops a decision-making model for supplier selection combining quality function deployment (QFD), analytic hierarchy process (AHP) and technique for order preference by similarity to ideal solution (TOPSIS). The efficacy of the model was demonstrated by applying it for supplier selection of lithium ion batteries.Design/methodology/approachThe proposed methodology involved identifying customer requirements for lithium ion batteries and translating them to requisite technical characteristics using QFD. Further, separate sourcing, safety and sustainability-related supplier parameters were proposed taking into account the manufacturer's point of view. The relative weight of each parameter was then calculated using AHP, and finally, TOPSIS was used to select the best supplier.FindingsThe proposed methodology was applied to six suppliers of lithium ion batteries, and the obtained results were used to select the most and least preferred suppliers.Practical implicationsThe obtained results cannot be generalized and are valid to the case environment. However, the proposed approach can be used for any environment related to supplier selection after capturing the corresponding parameters. The proposed approach does not restrict the number of parameters to be considered.Originality/valueMany researches related to supplier evaluation are reported in literature, but few studies are available related to supplier performance evaluation for lithium ion batteries using QFD, AHP and TOPSIS. The study will provide a guideline for comparing and selecting supplier on the basis of performance in general and its application to lithium ion batteries in specific.
Numerical study of heat transfer in 90° bend tube by AI2O3 nano fluids using fluid injection
Authors: Mahdizadeh Hadi , Adam Nor Mariah 
Published: July 2020

Purpose
This paper aims to investigate increasing heat transfer in bend tube 90° by fluid injection using nano fluid flow that was performed by expending varying Reynolds number. This paper studies the increased heat transfer in the bent tube that used some parameters to examine the effects of volume fraction, nanoparticle diameter, fluid injection, Reynolds number on heat transfer and flow in a bend pipe.

Design/methodology/approach
Designing curved tubes increases the thermal conductivity amount between fluid and wall. It is used the finite volume method and simple algorithms to solve the conservation equations of mass, momentum and energy. The results showed that the nanoparticles used in bent tube transfusion increase the heat transfer performance by increasing the volume fraction; it has a direct impact on enhancing the heat transfer coefficient.

Findings
Heat transfer coefficient enhanced 1.5% when volume fraction increased from 2 % to 6%, the. It is due to the impact of nanoparticles on the thermal conductivity of the fluid. The fluid is injected into the boundary layer flow due to jamming that enhances heat transfer. Curved lines used create a centrifugal force due to the bending and lack of development that increase the heat transfer.

Originality/value
This study has investigated the effect of injection of water into a 90° bend before and after the bend. Specific objectives are to analyze effect of injection on heat transfer of bend tube and pressure drop, evaluate best performance of mixing injection and bend in different positions and analyze effect of nano fluid volume fraction on injection.
Do they really want to leave? A (re)-evaluation of expatriates' and spouses' premature return intention
Authors: Goede Julia 
Published: July 2020

PurposeThe purpose of this study is to (re-)evaluate the explanatory power of the stressor–stress–strain model and its' current operationalization by examining the influence of general and interaction adjustment and the mediating effect of general satisfaction on expatriates' and spouses' intention to prematurely return from an assignment or overseas location. Though expatriates' premature return intention has been well examined in prior literature, this is the first study to focus on spouses' premature return intention from the expatriate's assignment.Design/methodology/approachTo evaluate the hypotheses, a sample of 104 expatriates and a sample of 64 spouses were collected and analysed utilizing structural equation modeling.FindingsThe results show that adjustment, as the opposite of distress, is not a direct negative driver of expatriates' nor spouses' premature return intention. Instead, the findings underscore the relevance of the general satisfaction with the international assignment (IA) as a mediator for both expatriates and spouses, which emphasizes the importance of attitudinal factors in the model. Overall, the results indicate that adjustment, in particular interaction adjustment, might not be a timely measure of distress anymore.Practical implicationsIn order to reduce expatriates' and spouses' premature return intention multinational corporations should aim at maximizing satisfaction levels during the IA. To achieve this, both should be included in the selection process prior to the IA to tailor support mechanisms to satisfy their expectations.Originality/valueThis study is the first to investigate the premature return intention from the expatriates' and spouses' perspectives, while (re-)evaluating the explanatory power of the stressor–stress–strain model at present.
Screening of Murabaha business process through Quran and hadith: a text mining analysis
Authors: Tlemsani Issam , Marir Farhi , Majdalawieh Munir 
Published: July 2020

Purpose
This paper revolves around the usage of data analytics in the Qur’an and Hadith through a new text mining technique to answer the main research question of whether the activities and the data flows of the Murabaha financing contract is compatible with Sharia law. The purpose of this paper is to provide a thorough and comprehensive database that will be used to examine existing practices in Islamic banks’ and improve compliancy with Islamic financial law (Sharia).

Design/methodology/approach
To design a Sharia-compliant Murabaha business process originated on text mining, the authors start by identifying the factors deemed necessary in their text mining techniques of both texts; using a four-step strategy to analyze those text mining analytics; then, they list the three basic approaches in text mining used for new knowledge discovery in databases: the co-occurrence approach based on the recursive co-occurrence algorithm; the machine learning or statistical-based; and the knowledge-based. They identify any variation and association between the Murabaha business processes produced using text mining against the one developed through data collection.

Findings
The main finding attained in this paper is to confirm the compatibility of all activities and the data flows in the Murabaha financing contract produced using data analytics of the Quran and Hadith texts against the Murabaha business process that was developed based on data collection. Another key finding is revealing some shortcomings regarding Islamic banks business process compliance with Sharia law.

Practical implications
Given Murabaha as the most popular mode of Islamic financing with more than 75% in total transactions, this research has managed to touch-base on an area that is interesting to the vast majority of those dealing with Islamic finance instruments. By reaching findings that could improve the existing Islamic Murabaha business process and concluding on Sharia compliance of the existing Murabaha business process, this research is quite relevant and could be used in practice as well as in influencing public policy. In fact, Islamic Sharia law experts, Islamic finance professionals and Islamic banks may find the results of this study very useful in improving at least one aspect of the Islamic finance transactions.

Originality/value
By using a novel, fresh text mining methods built on recursive occurrence of synonym words from the Qur’an and Hadith to enrich Islamic finance, this research study can claim to have been the first of its kind in using machine learning to mine the Quran, Hadith and in extracting valuable knowledge to support and consolidate the Islamic financial business processes and make them more compliant with the i.