bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quaternary structure evaluation tool for protein assemblies
Authors: Korkmaz Selcuk , Duarte Jose M. , Prlić Andreas , Goksuluk Dincer , Zararsiz Gokmen , Saracbasi Osman , Burley Stephen K. , Rose Peter W. 
Published: November 2017

AbstractThe Protein Data Bank (PDB) is the single worldwide archive of experimentally-determined three-dimensional (3D) structures of proteins and nucleic acids. As of January 2017, the PDB housed more than 125,000 structures and was growing by more than 11,000 structures annually. Since the 3D structure of a protein is vital to understand the mechanisms of biological processes, diseases, and drug design, correct oligomeric assembly information is of critical importance. For example, it makes a difference if the protein is normally a dimer and not a monomer or a trimer or a tetramer or a hexamer in nature. Unfortunately, the biologically relevant oligomeric form of a 3D structure is not directly obtainable by X-ray crystallography. Instead, this information may be provided by the PDB Depositor as metadata coming from additional experiments, be inferred by sequence-sequence comparisons with similar proteins of known oligomeric state, or predicted using software, such as PISA (Proteins, Interfaces, Structures and Assemblies) or EPPIC (Evolutionary Protein Protein Interface Classifier). Despite significant efforts by professional PDB Biocurators during data deposition, there remain a number of structures in the archive with incorrect quaternary structure descriptions (or annotations). Further investigation is, therefore, needed to evaluate the correctness of quaternary structure annotations. In this study, we aim to identify the most probable oligomeric states for proteins represented in the PDB. Our approach evaluated the performance of four independent prediction methods, including text mining of primary publications, inference from homologous protein structures, and two computational methods (PISA and EPPIC). Aggregating predictions to give consensus results outperformed all four of the independent prediction methods, yielding 86% correct, 9% incorrect, and 5% inconclusive predictions, when tested with a well-curated benchmark dataset. We have developed a freely-available web-based tool to make this approach accessible to researchers and PDB Biocurators (http://quatstruct.rcsb.org).
Cyclic nature of the REM-like state in the cuttlefish Sepia officinalis
Authors: Iglesias T. L. , Boal J. G. , Frank M.G. , Zeil J. , Hanlon R.T. 
Published: November 2017

AbstractSleep is a state of immobility characterized by three key criteria: an increased threshold of arousal, rapid reversal to an alert state, and evidence of homeostatic “rebound sleep” in which there is an increase of time spent in this quiescent state following sleep deprivation. Common European cuttlefish, Sepia officinalis, show states of quiescence during which they meet the last two of these three criteria, yet also show spontaneous bursts of arm and eye movements that accompany rapid changes in chromatophore patterns in the skin. Here we report that this rapid-eye-movement (REM)-like state is cyclic in nature. Iterations of the REM-like state last 2.42 ± 0.22 min (±SE) and alternate with 34.01 ± 1.49 min of the quiescent sleep-like state. These states alternate for durations lasting 176.89 ± 36.71 min. We found clear evidence that this REM-like state (i) occurs in animals younger than previously reported; (ii) follows an ultradian pattern; (iii) includes intermittent dynamic chromatophore patterning, representing fragments of normal patterning seen in the waking state for a wide range of signaling and camouflage; and (iv) shows variability in the intensity of expression of these skin patterns between and within individuals. These data suggest that cephalopods, which are molluscs with an elaborate brain and complex behavior, possess a sleep-like state that resembles behaviorally the vertebrate REM sleep state, although the exact nature and mechanism of this form of sleep may differ from that of vertebrates.
A Phylogenomic Study Quantifies Competing Mechanisms for Pseudogenization in Prokaryotes
Authors: Avni Eliran , Montoya Dennis , Lopez David , Modlin Robert , Pellegrini Matteo , Snir Sagi 
Published: November 2017

AbstractBackgroundPseudogenes are non-functional sequences in the genome with homologous sequences that are functional (i.e. genes). They are abundant in eukaryotes where they have been extensively investigated, while in prokaryotes they are significantly scarcer and less well studied. Here we conduct a comprehensive analysis of the evolution of pseudogenes in prokaryotes. For this analysis we consider a broad range of bacteria, but also focus on the leprosy pathogenMycobacterium leprae, which contains an unusually large number of pseudogenes which comprise approximately 40% of its entire genome.ResultsWe have developed an informatics-based approach to characterize the evolution of pseudogenes. This approach combines tools from phylogenomics, genomics, and transcriptomics. The results we obtain suggest the presence of two mechanisms for pseudogene formation: failed horizontal gene transfer events and disruption of native genes.ConclusionsWe conclude that while in most bacteria the former is most likely responsible for the majority of pseudogenization events, in mycobacteria, and in particular inM. lepraewith its exceptionally high pseudogene numbers, the latter predominates. We believe that our study sheds new light on the evolution of pseudogenes in bacteria, by utilizing new methodologies that are applied to the unusually abundantM. lepraepseudogenes and their orthologs. As such, we anticipate that it will be of broad interest to both evolutionary biologists as well as microbiologists.
Digitalization in retailing: multi-sided platforms as drivers of industry transformation
Authors: Hänninen Mikko , Smedlund Anssi , Mitronen Lasse 
Published: November 2017

Purpose
Digitalization has transformed several industries during the past two decades. In this paper the authors focus on the retail sector, where new business models help retailers and suppliers meet the ever changing and demanding needs of retail shoppers. One example of this business model innovation is multi-sided digital platforms, which have become popular as they connect consumers with suppliers from around the world with a large ecosystem to support the retail platform. The purpose of this paper is to provide an overview of how multi-sided digital platforms are transforming the retail exchange logic and assess the implications and impact of these platform-based businesses on the retail sector, especially for business managers and consumers.

Design/methodology/approach
In this paper, the authors employ literature review, conceptual analysis and qualitative case study methodology. The authors provide an overview of how the platform economy is affecting the retail sector through the illustration of four digital multi-sided platforms: Alibaba Group, Amazon.com, eBay and Rakuten Group, and what differentiates them from incumbent business models in retailing.

Findings
The findings suggest that platforms transform the transaction logic of retailing as they simply intermediate transactions between buyers and suppliers rather than handling the entire supply and logistics chain themselves. The authors highlight the role of consumer understanding and Big Data as one example of how multi-sided digital platforms differentiate from their non-platform competitors.

Practical implications
The paper highlights how incumbent retailers can compete against new forms of business, such as digital platforms, and the authors demonstrate some of the managerial capabilities needed to remain relevant amidst this new digital competition.

Originality/value
Very little empirical studies in marketing and retail literature have focused on multi-sided digital platforms and their business models. The present study fills this gap with an overview of how multi-sided digital platforms transform the retail sector.
An exploration of employer perceptions of graduate student employability
Authors: Chhinzer Nita , Russo Anna Maria 
Published: November 2017

PurposeThe purpose of this paper is to explore employer perceptions of graduate student employability. This study is novel since existing research focused on employability is largely theoretic, remains focused on defining employability of undergraduates and largely fails to determine employer perceptions of factors that increase or decrease employability of graduate students.Design/methodology/approachUsing a two-phased approach, the authors analyzed 122 employer assessments of graduate students at a Canadian university who completed a work-term with the employer in either 2014 or 2015. The authors also collected individual data (e.g. academic achievement, work experience) from student files at the university. Phase 1 involved an exploratory factor analysis to derive factors influencing employer perceptions of employability. Phase 2 expand on factors identified in phase 1 through assessment of 153 written comments using a critical incident technique.FindingsPhase 1 results demonstrate that professional maturity, soft skills + problem solving, continuous learning and academic achievement secure a positive relationship with employer perceptions of graduate employability. Phase 2 results indicate that employers consider generic skills (time management, working in a team, attention to detail), general mental ability, subject-specific knowledge, willingness to work, attitudes and behaviors, and responsiveness to feedback when assessing employability of graduate students.Research limitations/implicationsCollectively, the results of phase 1 and 2 provide a comprehensive awareness of the factors that employers consider when assessing employability of graduate students. Researcher, educational institution, and employer implications are presented.Originality/valueThe authors provide a holistic and empirically grounded understanding of employer perceptions of graduate student employability through reviewing quantitative and qualitative indicators of employability from the employer perspective.
Development of a computer-aided design software for smart garments
Authors: Kim Sungmin 
Published: November 2017

Purpose
The purpose of this paper is to develop a computer-aided design software for smart garments.

Design/methodology/approach
A circuit design software with graphical user interface and an automatic Arduino code generator has been developed.

Findings
Complex circuit design for smart garment can be performed using an intuitive graphical user interface. Sophisticated C codes for activating the smart garment can be generated without in-depth knowledge of C language and electronic devices.

Research limitations/implications
Circuit wiring is performed manually. Further work will be focused on the generation of an algorithm that can find the overlap-free design of complex circuit.

Practical implications
Smart garments with complex functions are expected to be designed more easily without in-depth knowledge of electronic circuits and computer programming.

Social implications
Researchers of smart garment will be able to concentrate on the actual function of smart garments rather than coding the complex C programs.

Originality/value
This is the first computer-aided smart garment design software that can not only design the circuit but also generate the computer codes.
Relationship between resilience and personality traits in paramedics
Authors: Froutan Razieh , Mazlom Reza , Malekzadeh Javad , Mirhaghi Amir 
Published: November 2017

Purpose
Resilience can be of assistance to paramedics in order to maintain their own mental balance in stressful work environments. Since it is not well defined which personality traits are correlated with resilience in these personnel, the purpose of this paper is to explain the relationship between personality traits and levels of resilience.

Design/methodology/approach
This cross-sectional study was conducted on paramedics in Eastern Iran through field research. The study participants were selected by convenience sampling method. The data collection instruments included NEO-Five Factor Inventory-Short Form and Connor-Davidson Resilience Scale. The data obtained were also analyzed using descriptive and inferential statistics (correlation and regression analysis) through the SPSS 16.0 software.

Findings
A total of 252 paramedics with a mean age of 28.9±5.1 years participated in this study. The personality traits of neuroticism (r=−0.24), openness to experience (r=−0.22), and agreeableness (r=−0.18) were significantly correlated with resilience. In contrast, extraversion (r=0.26) and conscientiousness (r=0.32) were in a significant relationship with resilience. In this respect, the given personality traits could account for 31.5 percent of changes in resilience.

Research limitations/implications
It was concluded that the paramedics with lower scores of neuroticism had higher levels of resilience and they could similarly show better compliance with their work conditions in stressful situations and consequently maintain their mental health.

Practical implications
It is recommended to conduct psychological examinations of personality traits in recruitment and selection stages of medical emergency personnel and to implement psychological interventions for those medical emergency staff with the personality trait of neuroticism.

Social implications
Resilient paramedics may also perceive less stress and it may be negatively associated with burnout.

Originality/value
The study examined the relationship between personality traits and resiliency in order to clarifying recruitment criteria in emergency medical services.
Mood, religious experience and the Ramadan effect
Authors: Wasiuzzaman Shaista , Al-Musehel Noura Abdullah 
Published: November 2017

Purpose
The purpose of this paper is to focus on the influence of mood/emotions and religious experience on Islamic stock markets during the Ramadan month.

Design/methodology/approach
This study uses stock returns data of two countries – Saudi Arabia and Iran – from January 2008 to September 2014 and the ARMA-GARCH models to study impact of the Ramadan month on the return and volatility of the stock market in these two countries.

Findings
The results of this study show some differences in the impact of the Ramadan month on the return and volatility of the stock market in these two countries. While the Ramadan month has a significant positive influence on the mean returns and the volatility of the Saudi market, its influence on the Iranian market is found to be insignificant. Further analysis on the last ten days of the Ramadan month provides a similar result for the Saudi market. However, for the Iranian market, volatility is significantly negatively affected during these last ten days.

Originality/value
Most prior studies have found significant changes in returns during the Ramadan month but a deeper understanding of this stock market anomaly is needed. The results point toward the influence of mood/emotions and religious experience in explaining the existence of the Ramadan anomaly.
The determinants of corporate profitability: an investigation of Indian manufacturing firms
Authors: Nanda Swagatika , Panda Ajaya Kumar 
Published: November 2017

PurposeThe purpose of this paper is to examine the firm-specific and macroeconomic determinants of profitability of Indian manufacturing firms. It assesses the main determinants of firm’s profitability in the pre-crisis and post-crisis period from 2000 to 2015.Design/methodology/approachThis methodology splits the factors that influence firm profitability in two groups: firm-specific (internal) factors and macroeconomic indicators. It further aims to look at the consistency of the factors in the pre-crisis and post-crisis period. The return on assets and the net profit margin are considered as proxy for corporate profits. The panel generalized least square and panel vector auto-regression model have been employed, and it is observed that the exchange rate seems to have played a major role in the crisis period by explaining the earning quotient for Indian firms.FindingsThis paper concludes that the firm-specific variables and exchange rate channels are quite relevant in explaining the profitability of Indian manufacturing firms. It accepts the hypotheses that size and liquidity enhances whereas leverage discourages the profitability. Few exceptions have been observed during the crisis period. The study also concludes that in the short run, the changes in exchange rate are not increasing profitability, but in the long run, it increases profitability as the volatility of nominal exchange rate is positively impacting profitability. Moreover, the study finds that the nominal exchange rate index is more informative and explains that profitability is better than real exchange rate index in the case of Indian manufacturing firms over the study period.Research limitations/implicationsThe managers and the policy makers should give utmost importance to the firm-specific determinants, especially after the crisis period, and consider the appropriate exchange rate to evaluate firm performance for making any change in the policy to make any business profitable.Originality/valueThis study has been conducted over a longer time by using advanced panel data analysis techniques on the recent data. The study period properly captures the crisis time and the research includes different selection of profitability that highlights corporate earnings pattern. Moreover, validation of the exchange rate sensitivity of profitability over nominal and real exchange rate increases the robustness of the study. Moreover, on Indian manufacturing firms, the study is very significant and unique.
Network position of independent director in cross-border mergers and acquisitions
Authors: Guo Chenxi , Lv Ping 
Published: November 2017

PurposeThe purpose of this paper is to consider the impact of network position of independent directors on the decision-making process of cross-border mergers and acquisitions (CBMAs).Design/methodology/approachWith 912 CBMAs constructed by 431 Chinese-listed corporations from 2006 to 2015, the authors provide graph-theoretical methods to quantify directors’ networks and build logistics models of CBMA success and generalized linear model for transaction value.FindingsThe authors find that independent directors in central positions of board networks of CBMA significantly strengthen the possibility of success of CBMA and react more positively to large CBMA. The results reveal that state-owned enterprises reduce the importance of independent directors in central positions in assisting successful CBMA, but strengthen the importance in promoting large CBMA. Specifically, majority shareholders counteract the importance of independent directors in central positions in assisting successful CBMA, but improve the importance in promoting large CBMA.Originality/valueThe findings suggest that independent directors in central positions, which are embedded in sets of board relationships and interactions, lead to efficient external corporate governance as a mechanism to facilitate a Chinese-listed firm’s CBMA decision making.
Bank regulatory capital and liquidity creation: evidence from BRICS countries
Authors: Umar Muhammad , Sun Gang , Shahzad Khurram , Rao Zia-ur-Rehman 
Published: November 2017

Purpose
The purpose of this paper is to explore the relationship between bank regulatory capital and liquidity creation in banks of BIRCS countries.

Design/methodology/approach
Data from all publicly listed banks of BRICS nations for the period 2003-2014 have been collected and analyzed. Two-stage least-squares regression has been used to control endogeneity. The econometric model includes different control variables that have been selected based on the extant literature.

Findings
Increase in bank capital negatively affects bank liquidity creation which implies that “financial fragility-crowding out” hypothesis holds for banks of BRICS countries.

Originality/value
This study provides the evidence of the inverse relationship between bank regulatory capital and liquidity creation from emerging economies. The findings show that there is a trade-off between curtailing bank risk taking and liquidity creation. Therefore, the regulators must formulate policies to strike a balance between the two.
Exchange rate pass-through to consumer prices in Ghana: is there asymmetry?
Authors: Amoah Lordina , Aziakpono Meshach Jesse 
Published: November 2017

Purpose
The purpose of this paper is to reexamine the speed and magnitude of exchange rate pass-through (ERPT) to consumer prices in Ghana.

Design/methodology/approach
The Johansen Maximum Likelihood approach is employed in the estimation of different models of symmetric and asymmetric ERPT. Specifically asymmetric ERPT models with respect to the direction and size of exchange rate changes are estimated.

Findings
Results reveal that even though a depreciation in the nominal effective exchange rate will lead to an increase of consumer prices in the long-run, it is not statistically significant. Evidence also suggests a significant asymmetry with respect to direction and size of exchange rate changes. This indicates that the right ERPT model is an asymmetric model. Specifically ERPT is found to be incomplete but relatively higher in periods of depreciation than in periods of appreciation; that is 53 percent against 3 percent. ERPT is also higher during episodes of large changes (about 51 percent).

Research limitations/implications
It would have been interesting to analyze the impact on consumer prices through changes in import prices. That approach was not adopted due to lack of consistent data on import prices in Ghana.

Practical implications
It is imperative that the monetary authorities critically monitor exchange rate movements in order to be able to take swift policy action so as to counteract any inflationary pressures from the external sector. In particular, much attention should be paid to events and arrangements that could result in large depreciation of the exchange rate.

Originality/value
While previous studies have assumed a symmetric ERPT model for Ghana, this paper is unique in that it investigates the most appropriate model for examining ERPT in Ghana whether symmetric or an asymmetric.
Dividend policy and stock price volatility of industrial products firms in Malaysia
Authors: Zainudin Rozaimah , Mahdzan Nurul Shahnaz , Yet Chee Hong 
Published: November 2017

PurposeThe purpose of this paper is to analyse the relationship between stock price volatility (SPV) and dividend policy of industrial products firms listed on Bursa Malaysia.Design/methodology/approachThe sample comprises 166 industrial products public-listed firms covering a time span from year 2003 to 2012. Using Baskin’s framework, firm’s SPV is related to dividend payout, controlling for earnings volatility, firm size, leverage and growth of assets. Further, the impact of the global financial crisis on the relationship between SPV and the tested variables is examined.FindingsEarning volatility significantly explains SPV of industrial product firms during the crisis period, while dividend payout ratio (PR) predominantly influences volatility during pre- and post-crisis sub-periods. The empirical results indicate that dividend policy is a strong predictor of SPV of industrial products firms in Malaysia, particularly during the post-crisis period.Originality/valueThe paper explores the firm’s SPV and dividend policy for a new set of data focussing on industrial products firms listed on the Malaysian Stock Exchange.