bluuebunny/crossref_metadata_2025_split huggingface dataset:
Precisely control mitochondria with light to manipulate cell fate decision
Authors: Ernst Patrick , Xu Ningning , Qu Jing , Chen Herbert , Goldberg Matthew S. , Darley-Usmar Victor , Zhang Jianyi J. , O’Rourke Brian , Liu Xiaoguang , Zhou Lufang 
Published: November 2018

ABSTRACTMitochondrial dysfunction has been implicated in many pathological conditions and diseases. The normal functioning of mitochondria relies on maintaining the inner mitochondrial membrane (IMM) potential (a.k.a.ΔΨm) that is essential for ATP synthesis, Ca2+homeostasis, redox balance and regulation of other key signaling pathways such as mitophagy and apoptosis. However, the detailed mechanisms by which ΔΨmregulates cellular function remain incompletely understood, partially due to difficulty of manipulating ΔΨmwith spatiotemporal resolution, reversibility, or cell type specificity. To address this need, we have developed a next-generation optogenetic-based technique for controllable mitochondrial depolarization with light. We demonstrate successful targeting of the heterologous Channelrhodopsin-2 (ChR2) fusion protein to the IMM and formation of functional cationic channels capable of light-induced selective ΔΨmdepolarization and mitochondrial autophagy. Importantly, we for the first time show that optogenetic-mediated mitochondrial depolarization can be well-controlled to differentially influence the fate of cells expressing mitochondrial ChR2: while sustained moderate light illumination induces substantial apoptotic cell death, transient mild light illumination elicits cytoprotectionviamitochondrial preconditioning. Finally, we show that Parkin overexpression exacerbates, instead of ameliorating, mitochondrial depolarization-mediated cell death in HeLa cells. In summary, we provide evidence that the described mitochondrial-targeted optogenetics may have a broad application for studying the role of mitochondria in regulating cell function and fate decision.
High-throughput interrogation of programmed ribosomal frameshifting in human cells
Authors: Mikl Martin , Pilpel Yitzhak , Segal Eran 
Published: November 2018

SummaryProgrammed ribosomal frameshifting is the controlled slippage of the translating ribosome to an alternative frame. This tightly regulated process is widely employed by human viruses such as HIV and SARS coronavirus and is critical for their life cycle and virulence. It is also utilized from yeast to human to implement a feedback control mechanism to regulate polyamine levels. Here, we developed a high-throughput, fluorescence-based approach to assess the frameshifting potential of a sequence. We designed and tested >12,000 sequences based on 15 viral and human frameshifting events, allowing us to elucidate the rules governing ribosomal frameshifting in a systematic way and to discover novel regulatory inputs based on amino acid properties and tRNA availability. We assessed the natural variation in HIV gag-pol frameshifting rates by testing >500 clinical isolates and identified subtype-specific differences as well as associations between viral load in patients and the optimality of gag-pol frameshifting rates. We further devised computational models that accurately predict frameshifting potential (up to auROC=0.93) and frameshifting rates (up to Pearson r=0.81) of novel variants, including subtle differences between HIV clinical isolates (r=0.60). Taken together, this systematic approach can contribute to the development of antiviral agents acting on programmed ribosomal frameshifting.
Chromatin Compaction by Small RNAs and the Nuclear RNAi Machinery inC. elegans
Authors: Fields Brandon D. , Kennedy Scott 
Published: November 2018

AbstractDNA is organized and compacted into higher-order structures in order to fit within nuclei and to facilitate proper gene regulation. Mechanisms by which higher order chromatin structures are established and maintained are poorly understood. InC. elegans, nuclear-localized small RNAs engage the nuclear RNAi machinery to regulate gene expression and direct the post-translational modification of histone proteins. Here we confirm a recent report suggesting that nuclear small RNAs are required to initiate or maintain chromatin compaction states inC. elegansgerm cells. Additionally, we show that experimentally provided small RNAs are sufficient to direct chromatin compaction and that this compaction requires the small RNA-binding Argonaute NRDE-3, the pre-mRNA associated factor NRDE-2, and the HP1-like protein HPL-2. Our results show that small RNAs, acting via the nuclear RNAi machinery and an HP1-like protein, are capable of driving chromatin compaction inC. elegans.
The structural basis for release factor activation during translation termination revealed by time-resolved cryogenic electron microscopy
Authors: Fu Ziao , Indrisiunaite Gabriele , Kaledhonkar Sandip , Shah Binita , Sun Ming , Chen Bo , Grassucci Robert A. , Ehrenberg Måns , Frank Joachim 
Published: November 2018

AbstractWhen the mRNA translating ribosome encounters a stop codon in its aminoacyl site (A site), it recruits a class-1 release factor (RF) to induce hydrolysis of the ester bond between peptide chain and peptidyl-site (P-site) tRNA. This process, called termination of translation, is under strong selection pressure for high speed and accuracy. Class-1 RFs (RF1, RF2 in bacteria, eRF1 in eukarya and aRF1 in archaea), have structural motifs that recognize stop codons in the decoding center (DC) and a universal GGQ motif for induction of ester bond hydrolysis in the peptidyl transfer center (PTC) 70 Å away from the DC. The finding that free RF2 is compact with only 20 Å between its codon reading and GGQ motifs came therefore as a surprise1. Cryo-electron microscopy (cryo-EM) then showed that ribosome-bound RF1 and RF2 have extended structures2,3, suggesting that bacterial RFs are compact when entering the ribosome and switch to the extended form in a stop signal-dependent manner3. FRET4, cryo-EM5,6 and X-ray crystallography7, along with a rapid kinetics study suggesting a pre-termination conformational change on the millisecond time-scale of ribosome-bound RF1 and RF28, have lent indirect support to this proposal. However, direct experimental evidence for such a short-lived compact conformation on the native pathway to RF-dependent termination is missing due to its transient nature. Here we use time-resolved cryo-EM9,10,11,12,13 to visualize compact and extended forms of RF1 and RF2 at 3.5 and 4 Å resolution, respectively, in the codon-recognizing complex on the pathway to termination. About 25% of ribosomal complexes have RFs in the compact state at 24 ms reaction time after mixing RF and ribosomes, and within 60 ms virtually all ribosome-bound RFs are transformed to their extended forms.
The landscape of DNA methylation associated with the transcriptomic network in laying hens and broilers generates insight into embryonic muscle development in chicken
Authors: Liu Zihao , Shen Xiaoxu , Han Shunshun , Wang Yan , Zhu Qing , Cui Can , He Haorong , Zhao Jing , Chen Yuqi , Zhang Yao , Ye Lin , Zhang Zhichao , Li Diyan , Zhao Xiaoling , Yin Huadong 
Published: November 2018

AbstractAs DNA methylation is one of the key epigenetic mechanisms involved in embryonic development, elucidating its relationship with non-coding RNA and genes is essential for understanding early development. In this study, we performed single-base-resolution bisulfite sequencing together with RNA-seq to explore the genetic basis of embryonic muscle development in chicken. Comparison of methylome profiles between broilers and laying hens revealed that lower methylation in broilers might contribute to muscle development. Differential methylated region (DMR) analysis between two chicken lines showed that the majority of DMRs were hypo-DMRs for broilers. Differential methylated genes were significantly enriched in muscle development-related terms at E13 and E19. Furthermore, by constructing the network of the lncRNAs, we identified a lncRNA, which we named MYH1-AS, that potentially regulated muscle development. These findings reveal an integrative landscape of late period of embryonic myogenesis in chicken and give rise to a comprehensive understanding of epigenetic and transcriptional regulation, in skeletal muscle development. Our study provides a reliable data resource for further muscle studies.
On a Unifying ‘Reverse’ Regression for Robust Association Studies and Allele Frequency Estimation with Related Individuals
Authors: Zhang Lin , Sun Lei 
Published: November 2018

AbstractFor genetic association studies with related individuals, standard linear mixed-effect model is the most popular approach. The model treats a complex trait (phenotype) as the response variable while a genetic variant (genotype) as a covariate. An alternative approach is to reverse the roles of phenotype and genotype. This class of tests includes quasi-likelihood based score tests. In this work, after reviewing these existing methods, we propose a general, unifying ‘reverse’ regression framework. We then show that the proposed method can also explicitly adjust for potential departure from Hardy–Weinberg equilibrium. Lastly, we demonstrate the additional flexibility of the proposed model on allele frequency estimation, as well as its connection with earlier work of best linear unbiased allele-frequency estimator. We conclude the paper with supporting evidence from simulation and application studies.
Business case for diversification – Adult Basic Education society (ABES), Pakistan
Authors: Dogar Muhammad Nadeem 
Published: November 2018

Supplementary materials
I would recommend the following two readings: Kotter, J. P. 2001. “What leaders really do” Harvard Business Review, vol, December 2001, pp. 85-96 and MIntzberg, H. & Waters, J. A. 1985. “Of strategies, deliberate and emergent” Strategic Management Journal, Vol. 6, pp. 257-272 Teaching Notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes.

Learning outcomes
This case study aims to provide following four learning outcomes: enhanced understanding of organizational leadership style/approach in terms of rigidness or flexibility to bring modifications in organizational vision to tap current opportunities, enhanced understanding of the use of emotions and rationality in organizational decision-making to strike a balance between organizational needs and community needs in the context of organizational priority framework, enhanced understanding of issue of integration to meet community needs smartly particularly in social development organizations and enhanced understanding of leadership strategies for successful business diversification.

Case overview/synopsis
This case study highlights and discusses three issues: first, it explores issues related to change in organizational vision and aims keeping in mind the needs of community rather than sticking to organizational needs (flexibility versus rigidity). Second, it explores the role of emotions and rationality in organizational decision-making by its leadership. Third, it discusses the role of leadership in successfully transforming one-dimensional organization into multidimensional organization by adding new avenues for future growth by mobilizing existing organizational strengths and competencies. Finally, this case discusses theories of leadership and change management in the context of social development organizations to align their activities with community’s emerging needs.

Complexity academic level
Master Level - Master of Business Administration and Master of Management. This case provides sufficient material to be discussed at master level courses such as change leadership and change management in social development organizations.

Supplementary materials
Teaching Notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes.

Subject code
Management science
What’s in a name? Family violence involving older adults
Authors: Benbow Susan M. , Bhattacharyya Sharmi , Kingston Paul 
Published: November 2018

Purpose
The purpose of this paper is to review the terminology used to describe family violence involving older adults in order to stimulate a discussion that may assist in the use of a more appropriate and clearer terminology.

Design/methodology/approach
Different definitions of terms used to describe violence are considered and the contexts in which they are used. Two cases are described to illustrate the use of overlapping terms, the assumptions that lie behind them and the different actions that they lead to.

Findings
The authors argue that legal, relational, health (physical and mental) and social perspectives are all useful and integration contributes to a fuller understanding of violence.

Originality/value
The importance of terminology used to describe family violence involving older adults has been neglected in the past, yet it influences understanding about violent incidents and shapes responses to them.
Sukukrisks – a structured review of theoretical research
Authors: Hasan Rashedul , Ahmad Abu Umar Faruq , Parveen Tamiza 
Published: November 2018

PurposeThe key purpose of this study is to make awareness for faithful Muslims who are interested to invest in Islamic capital markets so as to enable them making right decision while considering investment inSukukover conventional interest-bearing bonds.Design/methodology/approachThis study reviews past literature to analyse contemporarySukukrisks and discusses several mechanisms to mitigate those risks.FindingsThe study shows thatSukukcan be good alternatives to conventional bonds.Sukukstructures need to be further developed to fulfil theSharīʿahcompliance requirements.Research limitations/implicationsThis study is exploratory in nature, and as such, it seeks to identify the risks related toSukukissuance. Given this limitation, it did not provide empirical evidences relating to any specific category ofSukukrisks.Practical implicationsAn in-depth knowledge ofSukukrisks would help both academicians and investors understand the potential problems related toSukukstructures and take precautions in the early stage to prevent causes of being defaulted or bankrupt.Originality/valueThe risks related toSukukhave been explored in all potential roots. This study has offered some significant techniques to prevent the relevant risks for investors’ benefits. Information being provided throughout this study is expected to serve potential investors inSukukas a guide to make right decisions and enable them to minimise the risk to secure healthy returns on their investments.
Accountability in Islamic financial institution
Authors: Aribi Zakaria Ali , Arun Thankom , Gao Simon 
Published: November 2018

PurposeThe purpose of this paper is to explore whether any discrepancy exists between the disclosed in SSB reports of Islamic banks and the disclosure index which was based on stakeholders’ expectation.Design/methodology/approachThis study uses contents analysis as the research method to explore Shariâ’ah audit reporting practices of Islamic Banks.FindingsThe study finds that the level of disclosures overall by IFIs in the sample is rather low compared to the stakeholder expectations.Practical implicationsThis paper has important implication for policy makers as it contribute to the debate on that uniform disclosure standards across the globe need to be implemented to ensure a uniform level of disclosure by Islamic banks.Originality/valueThis study is amongst the few studies that examine and explore the nature and extent ofShari’ahSupervisory Board in Islamic banks.
The influence of culture on service quality leading to customer satisfaction and moderation role of type of bank
Authors: Endara Yousef Mohamed , Ali Asbi B. , Yajid Mohd Shukri Ab 
Published: November 2018

PurposeConsidering the importance of current Libyan business environment, this paper aims to understand the influence of culture on perceived service quality that leads to customer satisfaction in the Libyan banking industry. In addition, it would be interesting to explore which type of banks, e.g. public or private banks, moderate the relationship between perceived service quality and customer satisfaction.Design/methodology/approachThe data were collected from the customers who are receiving services from the top three private and top three public banks in the cities of Tripoli and Misurata, Libya. About 329 samples were obtained and Smart PLS was used for the statistical analysis.FindingsThe results show that perceived service quality is strongly predicted by collectivism, masculinity and uncertainty avoidance. Perceived service quality also leads to customer satisfaction among the Libyan banking customers. Further, public bank is more concerned on customer satisfaction compared to private banks.Practical implicationThe research has greater implication for the Middle-Eastern bank managers who are pursuing possibilities of newer business strategies.OriginalityThe study provides an interesting viewpoint of the banking service in Libya, especially in the economic uncertainty post-war and political instability. Its focus on culture as a strong influence to the delivery of service quality in such context is admirable especially in relation with the embedded Islamic culture.
Does salience matter in investment decision?
Authors: Chaudary Samra 
Published: November 2018

PurposeThe paper takes a behavioral approach by making use of the prospect theory to unveil the impact of salience on short-term and long-term investment decisions. This paper aims to investigate the group differences for two types of investors’ groups, i.e. individual investors and professional investors.Design/methodology/approachThe study uses partial least square-based structural equation modeling technique, measurement invariance test and multigroup analysis test on a unique data set of 277 active equity traders which included professional money managers and individual investors.FindingsResults showed that salience has a significant positive impact on both short-term and long-term investment decisions. The impact was almost 1.5 times higher for long-term investment decision as compared to short-term decision. Furthermore, multigroup analysis revealed that the two groups (individual investors and professional investors) were statistically significantly different from each other.Research limitations/implicationsThe study has implications for financial regulators, money managers and individual investors as it was found that individual investors suffer more with salience heuristic and may end up with sub-optimal portfolios due to inefficient diversification. Thus, investors should be cautious in fully relying on salience and avoid such bias to improve investment returns.Practical implicationsThe study concludes with a discussion of policy and regulatory implications on how to minimize salience bias to achieve optimum and diversified portfolios.Originality/valueThe study has significantly contributed to the growing body of applied behavioral research in the discipline of finance.
Rare and phylogenetically distinct plant species exhibit less diverse root‐associated pathogen communities
Authors: Chen Yongjian , Jia Pu , Cadotte Marc William , Wang Pandeng , Liu Xiang , Qi Yanling , Jiang Xiaomin , Wang Zihui , Shu Wensheng 
Published: November 2018

Abstract

One of the central questions in ecology is why some species are abundant while others are rare. In plant communities, some studies show that rare plant species are rare because they suffer stronger negative density‐dependent effects from pathogens compared to abundant plant species. Moreover, such pathogen effects are also suggested to be related to phylogenetic distance among plant species. However, the importance of pathogens has been commonly inferred by treating the entire pathogen community as a “black box” without explicitly characterizing pathogen richness and community composition.

Here, we test two predictions. First, if rare plant species are more susceptible to pathogens, we predict that rare plant species are associated with a higher richness of specialists (i.e., pathogens that attack only a single plant species) and/or the total pathogen community. If phylogenetically distinct plant species are less susceptible to pathogens, we predict that plant species with higher phylogenetic distinctiveness (i.e., a measure of how phylogenetically distant a species is from other co‐occurring species) are associated with a lower richness of phylogenetic specialists (i.e., pathogens that attack closely related plant species) and/or the total pathogen community.

We conducted a survey of the root‐associated pathogen communities from 45 plant species in a subtropical forest. We showed that approximately 40% and 25% of the pathogens were specialists and phylogenetic specialists respectively. In contrast to our first prediction, the richness of the total pathogen community but not the richness of the specialists was found to be positively related to plant species abundance, indicating that rare plant species suffer less from pathogens. Consistent with our second prediction, both the richness of the phylogenetic specialists and the total pathogen community were found to be negatively related to plant species phylogenetic distinctiveness. Furthermore, these correlations were stronger at the earlier plant life stages examined.

Synthesis. We found that the root‐associated pathogen communities were less diverse in rare plant species and plant species with few close relatives. These associations varied across multiple plant life stages, suggesting that the strength of the above‐ground–below‐ground interactions change dynamically across plant life span.