bluuebunny/crossref_metadata_2025_split huggingface dataset:
Profiling copy number variation and disease associations from 50,726 DiscovEHR Study exomes
Authors: Maxwell Evan K. , Packer Jonathan S. , O’Dushlaine Colm , McCarthy Shane E. , Hare-Harris Abby , Staples Jeffrey , Gonzaga-Jauregui Claudia , Fetterolf Samantha N. , Faucett W. Andrew , Leader Joseph B. , Moreno-De-Luca Andres , Gatta Giusy Della , Scollan Margaret , Persaud Trikaldarshi , Penn John , Hawes Alicia , Bai Xiaodong , Wolf Sarah , Lopez Alexander E. , Ulloa Rick , Sprangel Christopher , Chernomorsky Rostislav , Borecki Ingrid B. , Dewey Frederick E. , Economides Aris N. , Overton John D. , Kirchner H. Lester , Murray Michael F. , Ritchie Marylyn D. , Carey David J. , Ledbetter David H. , Yancopoulos George D. , Shuldiner Alan R. , Baras Aris , Gottesman Omri , Habegger Lukas , Martin Christa Lese , Reid Jeffrey G. 
Published: March 2017

AbstractCopy number variants (CNVs) are a substantial source of genomic variation and contribute to a wide range of human disorders. Gene-disrupting exonic CNVs have important clinical implications as they can underlie variability in disease presentation and susceptibility. The relationship between exonic CNVs and clinical traits has not been broadly explored at the population level, primarily due to technical challenges. We surveyed common and rare CNVs in the exome sequences of 50,726 adult DiscovEHR study participants with linked electronic health records (EHRs). We evaluated the diagnostic yield and clinical expressivity of known pathogenic CNVs, and performed tests of association with EHR-derived serum lipids, thereby evaluating the relationship between CNVs and complex traits and phenotypes in an unbiased, real-world clinical context. We identified CNVs from megabase to exon-level resolution, demonstrating reliable, high-throughput detection of clinically relevant exonic CNVs. In doing so, we created a catalog of high-confidence common and rare CNVs and refined population frequency estimates of known and novel gene-disrupting CNVs. Our survey among an unselected clinical population provides further evidence that neuropathy-associated duplications and deletions in 17p12 have similar population prevalence but are clinically under-diagnosed. Similarly, adults who harbor 22q11.2 deletions frequently had EHR documentation of neurodevelopmental/neuropsychiatric disorders and congenital anomalies, but not a formal genetic diagnosis (i.e., deletion). In an exome-wide association study of lipid levels, we identified a novel five-exon duplication withinLDLRsegregating in a large kindred with features of familial hypercholesterolemia. Exonic CNVs provide new opportunities to understand and diagnose human disease.
Signatures of long-term balancing selection in human genomes
Authors: Bitarello Bárbara Domingues , Filippo Cesare de , Teixeira João Carlos , Schmidt Joshua M. , Kleinert Philip , Meyer Diogo , Andrés Aida M. 
Published: March 2017

AbstractBalancing selection maintains advantageous diversity in populations through various mechanisms. While extensively explored from a theoretical perspective, an empirical understanding of its prevalence and targets lags behind our knowledge of positive selection. Here we describe theNon-Central Deviation(NCD), a simple yet powerful statistic to detect long-term balancing selection (LTBS) that quantifies how close frequencies are to expectations under LTBS, and provides the basis for a neutrality test.NCDcan be applied to a single locus or genomic data, and can be implemented considering only polymorphisms (NCD1) or also considering fixed differences with respect to an outgroup (NCD2) species. Incorporating fixed differences improves power, andNCD2has higher power to detect LTBS in humans under different frequencies of the balanced allele(s) than other available methods. Applied to genome-wide data from African and European human populations, in both cases using chimpanzee as an outgroup,NCD2shows that, albeit not prevalent, LTBS affects a sizable portion of the genome: about 0.6% of analyzed genomic windows and 0.8% of analyzed positions. Significant windows (p< 0.0001) contain 1.6% of SNPs in the genome, which disproportionally fall within exons and change protein sequence, but are not enriched in putatively regulatory sites. These windows overlap about 8% of the protein-coding genes, and these have larger number of transcripts than expected by chance even after controlling for gene length. Our catalog includes known targets of LTBS but a majority of them (90%) are novel. As expected, immune-related genes are among those with the strongest signatures, although most candidates are involved in other biological functions, suggesting that LTBS potentially influences diverse human phenotypes.
Distinguishing among modes of convergent adaptation using population genomic data
Authors: Lee Kristin M. , Coop Graham 
Published: March 2017

AbstractGeographically separated populations can convergently adapt to the same selection pressure. Convergent evolution at the level of a gene may arise via three distinct modes. The selected alleles can (1) have multiple independent mutational origins, (2) be shared due to shared ancestral standing variation, or (3) spread throughout subpopulations via gene flow. We present a model-based, statistical approach that utilizes genomic data to detect cases of convergent adaptation at the genetic level, identify the loci involved and distinguish among these modes. To understand the impact of convergent positive selection on neutral diversity at linked loci, we make use of the fact that hitchhiking can be modeled as an increase in the variance in neutral allele frequencies around a selected site within a population. We build on coalescent theory to show how shared hitchhiking events between subpopulations act to increase covariance in allele frequencies between subpopulations at loci near the selected site, and extend this theory under different models of migration and selection on the same standing variation. We incorporate this hitchhiking effect into a multivariate normal model of allele frequencies that also accounts for population structure. Based on this theory, we present a composite-likelihood-based approach that utilizes genomic data to identify loci involved in convergence, and distinguishes among alternate modes of convergent adaptation. We illustrate our method on genome-wide polymorphism data from two distinct cases of convergent adaptation. First, we investigate the adaptation for copper toxicity tolerance in two populations of the common yellow monkey flower,Mimulus guttatus. We show that selection has occurred on an allele that has been standing in these populations prior to the onset of copper mining in this region. Lastly, we apply our method to data from four populations of the killifish,Fundulus heteroclitus, that show very rapid convergent adaptation for tolerance to industrial pollutants. Here, we identify a single locus at which both independent mutation events and selection on an allele shared via gene flow, either slightly before or during selection, play a role in adaptation across the species’ range.
Adaptive reuse: a review and analysis of its relationship to the 3 Es of sustainability
Authors: Mohamed Rayman , Boyle Robin , Yang Allan Yilun , Tangari Joseph 
Published: March 2017

Purpose
There is a resurgence in the adaptive reuse of buildings. However, there is a lack of literature that pulls all the strands of adaptive reuse together. Furthermore, despite claims that it is motivated by the 3 Es of the sustainability triangle, the authors could find no research that critiques adaptive reuse from this perspective. The purpose of this study is to review the literature to collect pertinent information in a single place and to critically examine whether adaptive reuse incorporates the 3 Es of sustainability.

Design/methodology/approach
The methodological approach of this study is a literature review and a critical analysis of the practice of adaptive review.

Findings
Adaptive reuse is concentrated at the environment and economic development corners of the sustainability triangle. There are positive interactions along this edge. The authors attribute this to the fact that the same actors – the private and public sectors – are located at both corners of the triangle, and they have shared interests. This is different from the wider sustainability literature, where major actors at each corner are different and tensions along each edge are resolved through mediation. In adaptive reuse, there are no actors at the equity corner of the triangle, and there are minimal attempts to address concerns along the equity–environment and equity–economic development edges of the triangle.

Research limitations/implications
This study focuses on the USA.

Practical implications
This study suggests policy interventions that address the equity issue in adaptive reuse.

Originality/value
This is the first study to provide a succinct review of contemporary adaptive reuse and that places the practice within the framework of the 3 Es of sustainability.
Digital making with “At-Risk” youth
Authors: Hughes Janette Michelle 
Published: March 2017

PurposeThe purpose of this paper is to explore how a small group of adolescents in an alternative care and treatment program develop digital literacy skills over time while immersed in a rich media setting. It also explores how the students use new media tools and affordances to “perform” their identities and to present themselves within their classroom community.Design/methodology/approachThis ethnographic case study research involved seven students from a Canadian alternative school that provides educational programming for students from government approved care, treatment, custody and correctional facilities. Through an integrated arts-based curriculum, with a thematic focus on community and identity, the students used a variety to digital tools and media to create an “All About Me” book.FindingsThe students used inquiry-based learning and multiple modes of expression, facilitated by the multimodal, multimedia nature of digital media, including both screen-based and tangibles as essential components of knowing and communicating. The maker pedagogies employed in this intervention facilitated self-directed learning, as well as the development of perseverance and self-confidence.Originality/valueIn many work environments individuals are required to have knowledge of emerging technologies, and to employ this expertise in their work. Teaching students how to navigate their way through unfamiliar technology, to reflect on the process, and to communicate effectively, are important in both academics and future work environments. The authors continue to work with this group of students in the STEAM-3D Maker Lab and emphasize learning through discovery, design and the development of important skills such as perseverance, troubleshooting, resilience and collaboration.
A comparison of MOOC development and delivery approaches
Authors: Smith Neil , Caldwell Helen , Richards Mike , Bandara Arosha 
Published: March 2017

Purpose
The purpose of this paper is to present a comparison of two ways of developing and delivering massive open online courses (MOOCs). One was developed by The Open University in collaboration with FutureLearn; the other was developed independently by a small team at the Northampton University.

Design/methodology/approach
The different approaches had very different profiles of pedagogic flexibility, cost, development processes, institutional support and participant numbers.

Findings
MOOCs on existing large platforms can reach thousands of people, but constrain pedagogical choice. Self-made MOOCs have smaller audiences but can target them more effectively.

Originality/value
This comparison shows that, several years after MOOCs became prominent, there are many viable approaches for MOOCs.
Corporate attributes affecting sustainability reporting: an Indian perspective
Authors: Bhatia Aparna , Tuli Siya 
Published: March 2017

Purpose
This paper aims to examine the relationship between sustainability reporting by companies and selected corporate specific attributes. It also highlights that the scope of sustainability reporting differs from company to company and industry to industry.

Design/methodology/approach
Methodology is based on content analysis of 158 Indian companies selected from BSE 200. It uses multiple regression analysis to identify significant corporate attributes.

Findings
The analysis in this study reveals that companies with large size, older age, having multinational operations and belonging to Software, IT and ITES and Oil and Gas industry have significant sustainability disclosure. However, company’s profits, leverage, growth and advertising intensity are negatively related with the extent of sustainability disclosure. Other variables are found to be insignificant.

Research limitations/implications
As content analysis technique has been used for gathering sustainability information, subjective judgment involved in identifying and classifying the nature of reported sustainability information cannot be ruled out.

Practical/implications
This study adds to the growing literature on international sustainability disclosure practices and their determinants. Hence, it has its implications for a number of interested groups as investors, accounting bodies, regulatory authorities, companies, government, stock exchanges, general public, academicians and researchers.

Originality/value
As an emerging trend, there are few empirical studies exploring the determinants of sustainability reporting. To the best of the authors’ knowledge, this paper covers the impact of large number of corporate attributes in wholesome.
Customer responses towards disabled frontline employees
Authors: Rosenbaum Mark Scott , Baniya Rojan , Seger-Guttmann Tali 
Published: March 2017

Purpose
The purpose of this paper is to investigate the impact of disabled service providers on customers’ evaluations of service quality and behavioural intentions.

Design/methodology/approach
The authors conducted a qualitative analysis of online reviews from samples collected in a “dining-in-the-dark” restaurant, which employs blind waiters, and from a restaurant that employs deaf servers. The authors also put forth three quantitative analyses that use survey methodology.

Findings
Based on word clouds generated by online data, the findings show that customers treat the hiring of disabled service providers as the most prominent clue in their perceptions of organizational service quality. The quantitative results further illustrate that customers who hold more favourable attitudes towards disabled employees are more likely than other customers to spread positive word-of-mouth (WOM). Another analysis reveals that attitudes towards disabled employees are a separate construct from human compassion.

Research limitations/implications
Customers’ attitudes towards disabled frontline service employees represent a service quality driver. The authors offer researchers an exploratory scale on consumer attitudes towards the hiring of disabled employees to further refine and develop for future validation.

Practical implications
Retail organizations may be able to obtain a competitive advantage by employing frontline disabled people through customer WOM communications. These communications are linked to positive organizational outcomes.

Originality/value
Retail and service researchers know considerably little about customers’ perceptions of interacting with disabled employees. This paper represents original research that encourages retail and service organization to employ disabled frontline employees.
Implementing workplace health promotion – role of middle managers
Authors: Justesen Just Bendix , Eskerod Pernille , Christensen Jeanette Reffstrup , Sjøgaard Gisela 
Published: March 2017

Purpose
The purpose of this paper is to address a missing link between top management and employees when it comes to understanding how to successfully implement and embed workplace health promotion (WHP) as a strategy within organizations: the role of the middle managers.

Design/methodology/approach
A conceptual framework based on review of theory is applied within an empirical multi-case study that is part of a health intervention research project on increased physical activity among office workers. The study involves six Danish organizations.

Findings
Middle managers play a key role in successful implementation of WHP, but feel uncertain about their role, especially when it comes to engaging with their employees. Uncertainty about their role appears to make middle managers reluctant to take action on WHP and leave further action to top management instead.

Research limitations/implications
Limitations included the middle managers’ low attendance at the half-day seminar on strategic health (50 percent attendance), the fact that they were all office workers and they were all from Denmark.

Practical implications
Middle managers ask for more knowledge and skills if they are to work with WHP in daily business.

Social implications
Implementing and embedding WHP as a health strategy raises ethical issues of interfering with employees’ health, is seen as the employee’s personal responsibility.

Originality/value
This study adds to knowledge of the difficulties of implementing and embedding WHP activities in the workplace and suggests an explicit and detailed research design.
Wear behaviour of copper/carbon nanotubes
Authors: Shaari Nor Shamimi , Md Said Jamaliah , Jumahat Aidah , Ismail Muhammad Hussain 
Published: March 2017

Purpose
The purpose of this paper is to study the wear behaviour of copper matrix composites reinforced with carbon nanotubes (CNTs) prepared by powder metallurgy route.

Design/methodology/approach
The CNTs were treated by sulphuric acid and nitric acid to deagglomerate the CNTs prior mixing with copper powder. The composites comprised 0 to 4 Vol.% pristine CNTs (PCNTs) and also after acid-treated CNTs (ACNTs). The optimum value (pure Cu, 3 Vol.% PCNTs, 3 Vol.% ACNTs) evaluated by micro-hardness test was selected for wear test analysis.

Findings
The results showed that the enhancement of hardness, weight loss, coefficient of friction, wear depth and surface roughness (Ra) was due to the effect of homogenous distribution of ACNTs in Cu matrix and significant bonding compared to pure Cu and Cu-reinforced PCNTs. The scanning electron microscopy micrograph of worn surfaces and wear depth of the specimens also showed that the addition of ACNTs in Cu resulted in better wear performances.

Originality/value
CNTs were treated prior processing to improve hardness and wear properties of Cu/CNTs composites.
Fabrication of dimple structured surface of A390 Al-Si alloy using turning process
Authors: Mohd Dali Mohd Nor Azam , Ghani Jaharah A. , Che Haron Che Hassan , Hassan Sharudin 
Published: March 2017

Purpose
The purpose of this paper is to produce dimple structure on a cylindrical surface for Aluminium-Silicon (Al-Si) alloy piston (A390) using turning process. The process selection is based on factors such as the capability of machining process, low cost process, minimum set up time and green working environment.

Design/methodology/approach
Three main machining parameters that greatly influenced the dimple structure fabrication were identified from previous researches (cutting parameters, vibration and cutting tool geometry). To facilitate dimple structure fabrication using turning process, a dynamic assisted tooling (DATT) was developed. Experiments were conducted on Al-Si A390 material for future application of automotive piston. A three-dimensional surface profiler (Alicona) was used for geometry measurement and analysis of dimple structure. The Taguchi method, with an L8 orthogonal array, was used to accommodate seven parameters used in the fabrication of dimpled structures using turning process. Signal-to-noise (S/N) ratio and observation on the shape of dimple structure array were used to determine the optimum machining condition.

Findings
Optimum parameters obtained using S/N ratio analysis were cutting speed of 9 m/min, depth of cut of 0.01 mm, amplitude displacement of 1 mm, nose radius of 0.4 mm and frequency of (25 Hertz). Whereas feed rate, rake and relief angles were not significant to the size, shape and dimple array; therefore, their selected values depend on requirement of the application. Based on the S/N ratio and uniformity of the array of dimple structure as the main reference, the sixth and eighth experiment conditions almost achieved the optimum condition which are able to produce the width of dimple structure of 396.82 and 560.43 μm, respectively, dimple length of 3,261.6 and 2,422.7 μm, respectively, dimple depth of 63.43 and 65.97 μm, respectively, area ratio of 10 and 10.39 per cent, respectively, and surface roughness of 3.0023 and 3.0054 μm, respectively. These results are within the range of dimple structure obtained by the previous researchers for sliding mechanical components application.

Originality/value
The optimum condition of machining parameters in producing uniform dimple structure led to the compilation of data base in dimple structure research via turning process. Dimple structure produced is similarly obtained with other processes like laser, burnishing, photochemical, etc. DATT developed has the ability to produce repeatable vibration frequency, stable and consistent amplitude displacement using a simple crank concept and structure that can be mounted on all types of lathe machine either conventional or computer numerical control.
Optimized characterization of response surface methodology on lubricant with titanium oxide nanoparticles
Authors: Mohamad Nor Syahirah , Kasolang Salmiah 
Published: March 2017

Purpose
An optimized model is often deployed to reduce trial and error in experimental approach and obtain the multi-variant correlation. In this study, response surface methodology (RSM), namely, Box–Behnken design (BBD) approach, has been used to optimize the characterization of lubricant with additives. BBD is based on multivariate analysis whereby the effects of different parameters are considered simultaneously. It is a non-linear system which is more representative of the actual phenomenon. This study aims to investigate the effect of three independent variables, namely, speed, load and concentration of TiO2, on the coefficient of friction (CoF).

Design/methodology/approach
RSM was applied to get the multiplicity of the self-determining input variables and construct mathematical models. Mathematical models were established to predict the CoF and to conduct a statistical analysis of the independent variables’ interactions on response surface using Minitab 16.0 statistical software. Three parameters were regulated: speed (X1), load (X2) and concentration of TiO2 (X3). The output measured was the CoF.

Findings
The result obtained from BBD has shown that the most influential parameter was speed, followed by concentration of TiO2 nanoparticles and then normal load. Analysis of variance indicated that the proposed experiment from the quadratic model has successfully interpreted the experimental data with a coefficient of determination R2 = 0.9931. From the contour plot of BBD, the optimization zone for interacting variables has been obtained. The zone indicates two regions of lower friction values (<0.04): concentration between 0.5 to 1.0 Wt.% for a speed range of 1,000 to 2,000 rpm, and load between 17 to 20 kg for a speed in the range of 1,200 to 1,900 rpm. The optimized condition shows that the minimum value of CoF (0.0191) is at speed of 1,782 rpm, load of 20 kg and TiO2 concentration of 1.0 Wt.%.

Originality/value
In general, it has been shown that RSM is an effective and powerful tool in experimental optimization of multi-variants.