bluuebunny/crossref_metadata_2025_split huggingface dataset:
Finding functional disease-associated non-coding variation using next-generation sequencing
Authors: Devanna Paolo , Chen Xiaowei Sylvia , Ho Joses , Gajewski Dario , Gialluisi Alessandro , Francks Clyde , Fisher Simon E. , Newbury Dianne , Vernes Sonja C. 
Published: June 2016

ABSTRACTNext generation sequencing has opened the way for the large scale interrogation of cohorts at the whole exome, or whole genome level. Currently, the field largely focuses on potential disease causing variants that fall within coding sequences and that are predicted to cause protein sequence changes, generally discarding non-coding variants. However non-coding DNA makes up~98% of the genome and contains a range of sequences essential for controlling the expression of protein coding genes. Thus, potentially causative non-coding variation is currently being overlooked. To address this, we have designed an approach to assess variation in one class of non-coding regulatory DNA; the 3′UTRome. Variants in the 3'UTR region of genes are of particular interest because 3'UTRs are responsible for modulating protein expression levels via their interactions with microRNAs. Furthermore they are amenable to large scale analysis as 3′UTR-microRNA interactions are based on complementary base pairing and as such can be predictedin silicoat the genome-wide level. We report a strategy for identifying and functionally testing variants in microRNA binding sites within the 3'UTRome and demonstrate the efficacy of this pipeline in a cohort of language impaired children. Using whole exome sequence data from 43 probands, we extracted variants that lay within 3'UTR microRNA binding sites. We identified a common variant (SNP) in a microRNA binding site and found this SNP to be associated with an endophenotype of language impairment (non-word repetition). We showed that this variant disrupted microRNA regulation in cells and was linked to altered gene expression in the brain, suggesting it may represent a risk factor contributing to SLI. This work demonstrates that biologically relevant variants are currently being under-investigated despite the wealth of next-generation sequencing data available and presents a simple strategy for interrogating non-coding regions of the genome. We propose that this strategy should be routinely applied to whole exome and whole genome sequence data in order to broaden our understanding of how non-coding genetic variation underlies complex phenotypes such as neurodevelopmental disorders.
CFEL–ASG Software Suite(CASS): usage for free-electron laser experiments with biological focus
Authors: Foucar Lutz 
Published: June 2016

CASS[Foucaret al.(2012).Comput. Phys. Commun.183, 2207–2213] is a well established software suite for experiments performed at any sort of light source. It is based on a modular design and can easily be adapted for use at free-electron laser (FEL) experiments that have a biological focus. This article will list all the additional functionality and enhancements ofCASSfor use with FEL experiments that have been introduced since the first publication. The article will also highlight some advanced experiments with biological aspects that have been performed.
Islamic bank vs conventional bank: intermediation, fee based service activity and efficiency
Authors: Hardianto Dimas Satria , Wulandari Permata 
Published: June 2016

Purpose
The aim of this research is to compare the differences of intermediation, fee-based service activity and efficiency of conventional banks vs Islamic banks in Indonesia for the 2011-2013 period. Moreover, this study also includes some control variables to find their effect on the dependent variables.

Design/methodology/approach
This research uses two methods, namely, stochastic frontier approach and panel data regression.

Findings
The result indicates that Islamic banks have a higher intermediation ratio, have higher proportion on fee income-to-total operating income and are less efficient. The control variable that has a positively significant effect on intermediation ratio is size; meanwhile, inefficiency and non–loan-earning asset are negatively affecting the intermediation ratio. The control variable that show a positively significant effect on the proportion of fee income-to-total operating income is size; meanwhile, the credit risk variable has no significant effect on the proportion of fee income-to-total operating income. Size and credit risk are the control variables that have a negative relation to efficiency.

Originality/value
This study has significantly contributed to Indonesian Islamic banking based on which the Islamic banking manager should recognize that the intermediation level, fee-based service activity and efficiency are crucially important in establishing competition and maintaining sustainable Islamic banking.
The influence of the UAE context on management practice in UAE business
Authors: de Waal André , Frijns Miriam 
Published: June 2016

Purpose
This paper aims to investigate whether the United Arab Emirates (UAE) business context as described in the literature still matches with the UAE business context in practice. In many managerial publications, and even in quite a few academic ones, warnings are given about the different and difficult business environment which exists in Arab countries. This environment is allegedly characterized by a high religious influence, a definitive centralization of power, a strong family and tribal culture and a strong role of wasta, which makes doing business in the Middle East arduous. However, the context of the UAE is not typical Arab, as it is very much multicultural with many expatriates working in both local and foreign companies.

Design/methodology/approach
The theoretical aspects of the UAE business context were derived from a literature study. The aspects of the UAE business context in practice were collected during interviews with 36 Emirati and Western and Eastern expat managers working in the UAE. Subsequently, the theoretical aspects were matched with the practical aspects.

Findings
The matching shows that the typical Arab business setting is still there but that it exists next to the international business setting.

Research limitations/implications
Because of the coexisting cultural business settings, more nuance is needed in describing the typical Arab elements of the UAE business context, to fully understand the way of operating in the UAE.

Originality/value
As during this study a cross section of nationalities working in the UAE, including Emirati, was interviewed, it gives an unique insight into the current state of affairs in the UAE.
The internal challenges facing Islamic finance industry
Authors: Abozaid Abdulazeem 
Published: June 2016

Purpose
The paper aims to highlight the challenges facing Islamic finance industry and outline the prospectus of what constitutes a sound Islamic banking product in terms of both its Shariah control and product development methodology.

Design/methodology/approach
The paper analytically addresses the internal challenges facing Islamic finance industry by highlighting, first, the deficiencies in the existing Shariah supervisory work and, then, the deficiencies in the product development methodology followed in Islamic banks.

Findings
Islamic banking and finance is facing some internal challenges which require immediate action. Although facing the external challenges may be beyond the capacity of the industry players, Islamic banks have no excuse to overlook or turn a blind eye to their internal challenges which can be overcome by enacting Shariah governance for both products and Shariah control and reforming the methodology of product development.

Originality/value
This paper highlights an issue that has not received the needed attention, and it proposes the necessary solutions to the problems it identifies.
Service value optimization of cloud hosted systems using particle swarm technique
Authors: Murad Salah Eddin , Dowaji Salah 
Published: June 2016

Purpose
– Cloud Computing has become a more promising technology with potential opportunities, through reducing the high cost of running the traditional business applications and by leading to new business models. Nonetheless, this technology is fraught with many challenges. From a Software as a Service (SaaS) provider perspective, deployment choices are one of the major perplexing issues in determining the degree to which the application owners’ objectives are met while considering their customers’ targets. The purpose of this paper is to present a new model that allows the service owner to optimize the resources selection based on defined metrics when responding to many customers’ with various priorities.

Design/methodology/approach
– More than 65 academic papers have been collected, a short list of the most related 35 papers have been reviewed, in addition to assessing the functionality of major cloud systems. A potential set of techniques has been investigated to determine the most appropriate ones. Moreover, a new model has been built and a study of different simulation platforms has been conducted.

Findings
– The findings demonstrate that serving many SaaS customer requests, with different agreements and expected outcomes, would have mutual influence that impact the overall provider objectives. Furthermore, this paper investigates how tagging those customers with various priorities, with reflection of their importance to the provider, permits controlling and aligning the selection of computing resources as per the current objectives and defined priorities.

Research limitations/implications
– This study provides researchers with a useful literature, which can assist them in relevant subject. Additionally, it uses a value-based approach and particle swarm technique to model and solve the optimization of the computing resource selection, considering different business objectives for both stakeholders, providers and customers. This study derives priority of a number of factors, by which service providers can make strong and adaptive decisions.

Practical implications
– The paper includes implications on how the SaaS service provider can make decisions to select the needed virtual machines type driven by his own preferences.

Originality/value
– This paper rests on the usage of Particle Swarm Optimization technique to optimize the business value of the service provider, as well as the usage of value-based approach. This will help model that value in order to combine the total profit of the provider and the customer satisfaction, based on the agreed budget and processing time requested by the customer. Another additional approach has been charted by using the customer severity factor that allows the provider to reflect the customer importance while making the placement decision.
The value of strategy and flexibility in new product development
Authors: Fantazy Kamel A. , Salem Mohamed 
Published: June 2016

Purpose
– The purpose of this paper is to examine the relationship between strategy and flexibility in new product development, and the operational and financial performance in the supply chain context. The motives for conducting this research are to introduce the supply chain strategies and new product development flexibility (NPDF) as constructs that could have the potential to contribute to the success of supply chain performance. Based on the relational view of the firm, the authors propose that supply chain strategy is an antecedent of NPDF and can create value for the buying firm in terms of better financial and non-financial performance.

Design/methodology/approach
– The structural equation modeling approach was used to evaluate the proposed model and analyze hypothesized relationships. The analysis, based on data collected from 175 small- and medium-sized (SME) Canadian manufacturing companies.

Findings
– The analysis shows that there are direct positive effects from strategy on NPDF. The findings indicate also a direct positive association between NPDF and performance and showed that the total effect (direct and indirect) positively influenced performance.

Originality/value
– The literature did not reveal any study which attempted to examine strategy, NPDF, and performance in the supply chain context of SMEs. The current study fills this important gap in the literature.
Perception alignment hypothesis: causality of herding?
Authors: Dalko Viktoria 
Published: June 2016

Purpose
The purpose of this paper is to uncover an institutional reason behind herding and the key to successful execution of the accumulation-lift-distribution (ALD) trading strategy.

Design/methodology/approach
The paper proposes the perception alignment hypothesis (PAH), which is based on a large number of empirical episodes. Extensive empirical and theoretical literature of 79 articles is reviewed. These are selected from previously unrelated fields of prosecuted cases in market manipulation, sell-side analysts’ recommendations and internet rumors. These studies are put into a unifying conceptual framework.

Findings
The proposed PAH can explain some herding episodes that were generated for the purpose of executing ALD.

Practical implications
The value of the approach is that while behavioral biases are hard to change, perception alignment can be more responsive to regulation.

Originality/value
This paper is the first to propose the PAH. It provides an explanation for the causality of herding that complements the traditional literature on the psychological weaknesses of investors. This paper opens a debate on whether the stock market is fully competitive because investors have behavioral biases and certain institutions take advantage of those biases.
The effects of monetary policy on the Islamic financial services industry
Authors: Yungucu Burak , Saiti Buerhan 
Published: June 2016

PurposeThe purpose of this paper is to investigate the effects of monetary policy on the Islamic financial service industry by studying the findings of the existed literature.Design/methodology/approachBecause of the unavailability of the empirical models in the existing study, the authors used past studies review and proposed a new theoretical model.FindingsMajority of these studies have documented the negative effects with the exception of a few. The transmission of the monetary policy has been taken place through interest rate risk, asset-liability mismatch, as well as deposit and financing instability. Furthermore, the examined studies have confirmed the viability of the Islamic monetary policy.Originality/valueThe proposed model may offer some insights to policy makers if it is examined empirically.
A qualitative inquiry into the investment decision behaviour of the Malaysian stock market investors
Authors: Jaiyeoba Haruna Babatunde , Haron Razali 
Published: June 2016

Purpose
The main purpose of this study was to examine the investment decision behaviour of retail investors in Malaysia.

Design/methodology/approach
The study adopted semi-structured interviews to solicit an understanding of six retail investors on investment decision behaviour in Malaysia. Content analysis technique was used to analyse the data and verbatim texts were applied in discussing the emergent themes.

Findings
The findings indicate that retail investors in Malaysia are patriotic in nature, and their investment decisions are based on feeling of comfort or convention rather than quantitative analysis. They rely so much on their findings rather than third party’s views for making investment decisions. They were influenced by the psychological biases because they herd on the information. Challenges are solved through experience, and they believe that proper understanding of the financial and economic settings of the country can enhance better investment decision-making.

Research limitations/implications
A more detailed investigation on the investors’ behaviour with more samples may expand our understanding of this issue. Future studies need to examine the investment decision behaviour with more samples.

Practical implications
First, it will prepare hit and run investors to be more ready to remain in the market and improve their skills on how to make sound investment decisions. Second, it helps the investors to know that knowledge of traditional finance theory is not sufficient to excel in stock market, and, hence, they need to know more about behavioural finance. Third, investors are exposed to various reasons as to why investment decisions deviate from expected and different means of solving the challenges faced in making investment decision within the Malaysian context. Fourth, investors are reminded that understanding the financial settings before investing is essential. Finally, policy makers in stock market are able to understand the retail investors’ behaviour.

Originality/value
This study examines the experience and prospect to remain as stock market investors, their priorities in selecting the right company for investment purposes, the kind of information seeking from third parties, the challenges faced by them and other important considerations in investment decisions. These have never been examined together in this way in investigation of retail investors’ investment behaviour.
Pathways to de‐extinction: how close can we get to resurrection of an extinct species?
Authors: Shapiro Beth 
Published: June 2016

Summary

De‐extinction, the idea that extinct species might soon be resurrected, receives considerable attention in both popular and scientific literature, in particular with regard to its potential ecological and ethical consequences.

Here, I review the three main pathways that are being considered at present for de‐extinction: back‐breeding, cloning via somatic cell nuclear transfer (SCNT) and genetic engineering. I present the state of the art in each pathway and discuss the limitations of each approach as a mechanism to resurrect extinct species.

Back‐breeding aims to concentrate ancestral traits that persist within a population into a single individual using selective breeding. In back‐breeding, ancestral phenotypes may be resurrected after many generations, but the genes that underlie these phenotypes may differ from those that were present in the extinct species.

Cloning aims to create genetically identical copies of an extinct species from preserved somatic cells. These somatic cells are fused with egg cells from a closely related and living donor species, which causes cellular reprogramming and embryogenesis, a scientific process known as SCNT. The developing embryo is then brought to term within a surrogate host. Because biological remains degrade post‐mortem, cloning of long‐dead organisms is not likely to be feasible.

Genetic engineering aims to edit the genome sequence within cells of living species so that these genome sequences closely resemble that of a closely related extinct species. This approach draws on recent advances in both ancient DNA and genome editing technologies and is a particularly promising approach to de‐extinction. After the genome of a living cell is edited, that living cell can then be used for SCNT.

Because the phenotype of an organism is the consequence of the interaction between its genotype and the environment in which it develops and lives, even species with cloned nuclear genomes will not be exact copies of the extinct species on which they are modelled. We should therefore consider de‐extinction as a means to create ecological proxies for extinct species.

A lay summary is available for this article.
Leafing intensity and the fruit size/number trade‐off in woody angiosperms
Authors: Dombroskie Sarah L. , Tracey Amanda J. , Aarssen Lonnie W. 
Published: June 2016

Summary

A sample of woody angiosperm species was used to test a central prediction of the ‘leafing intensity premium’ hypothesis: higher leafing intensity (number of leaves produced per unit dry mass of shoot vegetative tissue produced in the same growing season) confers a larger bud bank (i.e. number of axillary meristems per unit shoot tissue) that can be deployed for reproduction, and thus confers generally greater fruit numbers, and hence higher potential fecundity allocation (i.e. fecundity per unit size of the supporting shoot tissue that is produced in the same growing season.

Current‐year shoots (i.e. bearing leaves) were collected to record: shoot dry mass, total number of leaves, total number of fruits or fruit clusters (if derived from inflorescences), mean individual leaf dry mass and mean individual fruit dry mass. Sampled individuals (shrubs and trees) were also measured for body size (main stem height and circumference).

Species with larger individual fruit (or fruit cluster) mass have generally larger leaves, but they also have a negative trade‐off relationship with ‘fruiting intensity’ – that is the total number of reproductive meristems producing fruits (or fruit clusters) per unit dry mass of shoot vegetative tissue produced in the same growing season. Variation in fruiting intensity, however, is better predicted by a positive relationship with variation in bud bank size.

Species with smaller leaf size (dry mass) have generally higher leafing intensity; species with higher leafing intensity in turn have generally higher fruiting intensity; and species with higher fruiting intensity in turn have generally higher potential fecundity allocation (based on the typical species maximum number of seeds per fruit, obtained from published floras). Species with smaller body size have generally higher potential fecundity allocation, but body size had no significant relationships with other measured traits when controlling for phylogeny (using phylogenetically independent contrasts).

Synthesis. Our results indicate that bud bank size is an important functional trait for defining adaptive strategy in woody angiosperms. A larger bud bank is generated by higher leafing intensity, which in turn generates higher fruiting intensity, thus generating greater potential fecundity allocation. These traits will be important for maximizing reproductive economy – that is capacity to produce offspring despite growth or body size limitation (e.g. due to crowding/competition, or because of limited time available for growth, flowering, pollination or fruit/seed maturation).