bluuebunny/crossref_metadata_2025_split huggingface dataset:
Repeat aware evaluation of scaffolding tools
Authors: Mandric Igor , Knyazev Sergey , Zelikovsky Alex 
Published: June 2017

AbstractSummaryGenomic sequences are assembled into a variable, but large number of contigs that should be scaffolded (ordered and oriented) for facilitating comparative or functional analysis. Finding scaffolding is computationally challenging due to misassemblies, inconsistent coverage across the genome, and long repeats. An accurate assessment of scaffolding tools should take into account multiple locations of the same contig on the reference scaffolding rather than matching a repeat to a single best location. This makes mapping of inferred scaffoldings onto the reference a computationally challenging problem. This paper formulates the repeat-aware scaffolding evaluation problem which is to find a mapping of the inferred scaffolding onto the reference maximizing number of correct links and proposes a scalable algorithm capable of handling large whole-genome datasets. Our novel scaffolding validation pipeline has been applied to assess the most of state-of-the-art scaffolding tools on the representative subset of GAGE datasets.AvailabilityThe source code of this evaluation framework is available athttps://github.com/mandricigor/repeat-aware. The documentation is hosted athttps://mandricigor.github.io/repeat-aware.
Parallel Computing to Speed up Whole-Genome Bayesian Regression Analyses Using Orthogonal Data Augmentation
Authors: Hao Cheng , Dorian Garrick , Fernando Rohan 
Published: June 2017

1 AbstractBayesian multiple regression methods are widely used in whole-genome analyses to solve the problem that the numberpof marker covariates is usually larger than the numbernof observations. Inferences from most Bayesian methods are based on Markov chain Monte Carlo methods, where statistics are computed from a Markov chain constructed to have a stationary distribution equal to the posterior distribution of the unknown parameters. In practice, chains of about fifty thousand steps are typically used in whole-genome Bayesian regression analyses, which is computationally intensive. In this paper, we have shown how the sampling of marker effects can be made independent within each step of the chain. This is done by augmenting the marker covariate matrix by addingpnew rows to it such that columns of the augmented marker covariate matrix are orthogonal. The phenotypes corresponding to the augmented rows of marker covariate matrix are considered missing. Ideally, the computations at each step of the MCMC chain, can be speeded up by the numberkof computer processors up to the numberpof markers. Addressing the heavy computational burden associated with Bayesian methods by parallel computing will lead to greater use of these methods.
The Ras-like GTPase Rem2 is a potent endogenous inhibitor of calcium/calmodulin-dependent kinase II activity
Authors: Royer Leandro , Herzog Josiah J. , Kenny Katelyn , Tzvetkova Boriana , Cochrane Jesse C. , Marr Michael T. , Paradis Suzanne 
Published: June 2017

AbstractCaMKII is a well-characterized, abundant protein kinase that regulates a diverse set of functions in a tissue specific manner. For example, in heart muscle, CaMKII regulates Ca2+homeostasis while in neurons CaMKII regulates activity-dependent dendritic remodeling and Long Term Potentiation (LTP), a biological correlate of learning and memory. Previously, we identified the noncanonical GTPase Rem2 as a critical regulator of dendrite branching and synapse formation in the vertebrate nervous system. Here, we report that Rem2 directly interacts with CaMKII and potently inhibits the activity of the intact holoenzyme, a previously undescribed function for the Rem2 protein. To date, only one other endogenous inhibitor of CaMKII has been described: CaMKIIN, which blocks CaMKII activity through binding to the catalytic domain. Our data suggest that Rem2 inhibits CaMKII through a novel mechanism, as inhibition requires the presence of the association domain of CaMKII. Our biochemical finding that Rem2 is a direct, endogenous inhibitor of CaMKII activity, coupled with known functions of Rem2 in neurons, provides a framework which will enable future experiments probing the physiological role of CaMKII inhibition in a cellular context.
Visual experience shapes the neural networks remapping touch into external space
Authors: Crollen Virginie , Lazzouni Latifa , Rezk Mohamed , Bellemare Antoine , Lepore Franco , Collignon Olivier 
Published: June 2017

AbstractLocalizing touch relies on the activation of skin-based and externally defined spatial frames of references. Psychophysical studies have demonstrated that early visual deprivation prevents the automatic remapping of touch into external space. We used fMRI to characterize how visual experience impacts on the brain circuits dedicated to the spatial processing of touch. Sighted and congenitally blind humans (male and female) performed a tactile temporal order judgment (TOJ) task, either with the hands uncrossed or crossed over the body midline. Behavioral data confirmed that crossing the hands has a detrimental effect on TOJ judgments in sighted but not in blind. Crucially, the crossed hand posture elicited more activity in a fronto-parietal network in the sighted group only. Psychophysiological interaction analysis revealed that the congenitally blind showed enhanced functional connectivity between parietal and frontal regions in the crossed versus uncrossed hand postures. Our results demonstrate that visual experience scaffolds the neural implementation of touch perception.Significance statementAlthough we seamlessly localize tactile events in our daily life, it is not a trivial operation because the hands move constantly within the peripersonal space. To process touch correctly, the brain has therefore to take the current position of the limbs into account and remap them to their location in the external world. In sighted, parietal and premotor areas support this process. However, while visual experience has been suggested to support the implementation of the automatic external remapping of touch, no studies so far have investigated how early visual deprivation alters the brain network supporting touch localization. Examining this question is therefore crucial to conclusively determine the intrinsic role vision plays in scaffolding the neural implementation of touch perception.
Predicting double-strand DNA breaks using epigenome marks or DNA at kilobase resolution
Authors: Mourad Raphaël , Cuvier Olivier 
Published: June 2017

AbstractDouble-strand breaks (DSBs) result from the attack of both DNA strands by multiple sources, including exposure to ionizing radiation or reactive oxygen species. DSBs can cause abnormal chromosomal rearrangements which are linked to cancer development, and hence represent an important issue. Recent techniques allow the genome-wide mapping of DSBs at high resolution, enabling the comprehensive study of DSB origin. However these techniques are costly and challenging. Hence we devised a computational approach to predict DSBs using the epigenomic and chromatin context, for which public data are available from the ENCODE project. We achieved excellent prediction accuracy (AUC= 0.97) at high resolution (< 1 kb), and showed that only chromatin accessibility and H3K4me1 mark were sufficient for highly accurate prediction (AUC= 0.95). We also demonstrated the better sensitivity of DSB predictions compared to BLESS experiments. We identified chromatin accessibility, activity and long-range contacts as best predictors. In addition, our work represents the first step toward unveiling the”cis-DNA repairing” code underlying DSBs, paving the way for future studies ofcis-elements involved in DNA damage and repair.
The effects of mutational processes and selection on driver mutations across cancer types
Authors: Temko Daniel , Tomlinson Ian PM , Severini Simone , Schuster-Böckler Benjamin , Graham Trevor A 
Published: June 2017

ABSTRACTEpidemiological evidence has long associated environmental mutagens with increased cancer risk. However, links between specific mutation-causing processes and the acquisition of individual driver mutations have remained obscure. Here we have used public cancer sequencing data to infer the independent effects of mutation and selection on driver mutation complement. First, we detect associations between a range of mutational processes, including those linked to smoking, ageing, APOBEC and DNA mismatch repair (MMR) and the presence of key driver mutations across cancer types. Second, we quantify differential selection between well-known alternative driver mutations, including differences in selection between distinct mutant residues in the same gene. These results show that while mutational processes play a large role in determining which driver mutations are present in a cancer, the role of selection frequently dominates.
Systematic misperceptions of 3D motion explained by Bayesian inference
Authors: Rokers Bas , Fulvio Jacqueline M. , Pillow Jonathan , Cooper Emily A. 
Published: June 2017

AbstractPeople make surprising but reliable perceptual errors. Here, we provide a unified explanation for errors in the perception of three-dimensional (3D) motion. To do so, we characterized the retinal motion signals produced by objects moving with arbitrary trajectories through arbitrary locations in 3D. Next, we developed a Bayesian model, treating 3D motion perception as optimal inference given sensory noise and the geometry of 3D viewing. The model predicts a wide array of systematic perceptual errors, that depend on stimulus distance, contrast, and eccentricity. We then used a virtual reality (VR) headset as well as a standard 3D display to test these predictions in both traditional psychophysical and more naturalistic settings. We found evidence that people make many of the predicted errors, including a lateral bias in the perception of motion trajectories, a dependency of this bias on stimulus contrast, viewing distance, and eccentricity, and a surprising tendency to misreport approaching motion as receding and vice versa. In sum, we developed a quantitative model that provides a parsimonious account for a range of systematic misperceptions of motion in naturalistic environments.
An intron proximal to a PTC enhances NMD inSaccharomyces cerevisiae
Authors: Wen Jikai , He Muyang , Petric Marija , Marzi Laetitia , Wang Jianming , Piechocki Kim , McLeod Tina , Singh Anand K. , Dwivedi Vibha , Brogna Saverio 
Published: June 2017

AbstractNonsense mediated mRNA decay (NMD) is regarded as the function of a specialized cytoplasmic translation-coupled mRNA decay pathway in eukaryotes, however, whether a premature translation termination codon (PTC) will lead to NMD often depends on splicing a downstream intron in the nucleus. Deposition of the exon junction complex (EJC) on mRNA is understood to mediate such splicing-dependent NMD in mammalian cells. The budding yeast,Saccharomyces cerevisiae, which has introns in only 5% of its genes, characteristically at the start of the coding region, and lacks proteins essential for EJC assembly, is not expected to undergo splicing-dependent NMD. However, we found that the presence of an intron near a PTC can also enhance NMD in this organism, regardless of whether it is downstream or upstream. These data provide evidence for a hitherto unsuspected EJC-independent mechanism linking translation and pre-mRNA inS. cerevisiae.
Amplifying the practicality of contemporary building information modelling (BIM) implementations for New Zealand green building certification (Green Star)
Authors: GhaffarianHoseini Ali , Tien Doan Dat , Naismith Nicola , Tookey John , GhaffarianHoseini Amirhosein 
Published: June 2017

PurposeGreen Star is becoming a broadly accepted mark of design quality and environmental sustainability. Compared to other green tools, Green Star is considered as one of main streams green assessment tools, which cover almost sustainable criteria. Simultaneously, building information modelling (BIM) has also been introduced into the industry. BIM is expected to aid designers to shift the construction industry towards more environmentally and economically sustainable construction practice. Whilst the aspirations of Green Star rating and BIM implementation are broadly aligned, in the context of New Zealand this has led to some disconnects in design strategy and process. The purpose of this paper is to improve the practicality of BIM implementations for delivering Green Star certification in New Zealand.Design/methodology/approachThe extensive literature review is conducted through a series of incremental steps. A conceptual framework focussing on the relationship between benefits and challenges of BIM and Green Star is then developed.FindingsBIM supports practitioners to achieve the majority of Green Star criteria (75 per cent). Energy efficiency criterion is the key factor affecting the assessment process of Green Star and National Australian Built Environment Rating System in New Zealand. Research questions about lessening the challenges which can be encountered during the BIM and Green Star implementation are developed.Research limitations/implicationsThis paper is limited to a conceptual research. Further empirical research should be conducted to validate and modify the conceptual framework and the propositions presented in this paper to provide an initial insight into BIM and Green Star connectivity within the context of New Zealand.Originality/valueThis paper provided a clear picture for investors, developers, practitioners about benefits and challenges of BIM and Green Star implementation. The outcomes are anticipated to deliver visions for shifting the country further towards development of sustainable future cities.
Improving the performance profile of energy conservation measures at the Penn State University Park Campus
Authors: Kazemi Rad Melissa , Riley David , Asadi Somayeh , Delgoshaei Parhum 
Published: June 2017

Purpose
The purpose of this paper is to examine significant steps taken by the Pennsylvania State University (Penn State) to account for both energy cost savings and greenhouse gas (GHG) emissions reduction goals through strategic investments in energy conservation measures (ECMs) in campus buildings. Through an analysis of multiple years of investment in facility upgrades across the university, the impacts of ECMs of various types are characterized by building type. The standards and criteria for ECMs investments are also evaluated with the goal to develop a predictive tool to support decision making pertaining to an annual investment in a portfolio of ECMs that will maintain a trajectory to achieve both financial return on investment as well as GHG reduction goals.

Design/methodology/approach
This study is comprised of three main parts: analyzing the energy costs saving and GHG emissions reduction contribution of various building types in which ECMs were conducted, analyzing costs saving and GHG emissions reduction contribution of each ECM while considering the average annual investments made in them and estimating the impact of upgrading Penn State’s steam plants from firing a mixture of coal and natural gas to natural gas only on the GHG emissions.

Findings
These analyses help identify which types of buildings and ECMs would have larger savings and emissions reduction contributions. A calculator is also created to enable forecasting of costs saving and GHG emissions reduction of investment distribution strategy among ECMs. This study demonstrates that the calculator based on data from previous years will benefit decision makers in more wisely configuring the investment portfolio.

Originality/value
This paper fulfills an identical need to couple energy efficiency strategies coupled with the environmental impacts associated with different fossil fuel energy sources.
Military lives: coaching transitions
Authors: Beech Nick , Gold Jeff , Beech Susan 
Published: June 2017

PurposeThe purpose of this paper is to first consider how veterans use talk to shape interpretations of personal and social identify. Second, this paper seeks to gain an understanding of how veterans see themselves in a civilian world, their ability to re-conceptualise and realign their perspective on life to support their transition in to a civilian world.

Design/methodology/approachUnderpinned by Ricoeur’s theory of narrative identity, the work provides a qualitative analysis data from coaching interviews with five veterans.

FindingsThe findings revealed the on-going legacy of military life and how its distinctiveness and belief centred on kinship shapes personal identity and the way they see their civilian world. The work sheds light on to the benefits of this Ricoeur’s self-reflexive approach and how it can be used to provide a deeper insight in to the nature of personal transitions and how narrative can be used to expose complexities of the narratives of personal history and meaning as the narrator becomes both the seeker and what is sought.

Practical implicationsThe work reinforces the value of Ricoeur’s self-reflexive approach identifying narrative mediating between two “poles” of identity and the act of mimesis; prefiguration, configuration and refiguration as veterans project stories of their world and their place within it.

Originality/valueThe paper provides new insights in to the importance of narrative identify broadening its potential application with engagement across diverse communities, thereby providing depth and rigour of its conceptual understanding of personal identify. The work further provides insights in to the challenges facing veterans to integrate within a civilian society.
Patients’ expectations and solutions for improving primary diabetes care
Authors: Vachon Brigitte , Huynh Ai-Thuy , Breton Mylaine , Quesnel Louise , Camirand Michel , Leblanc Jeannette , Tardif Sylvie 
Published: June 2017

Purpose
The purpose of this paper is to document health care needs expressed by people living with diabetes, describe the solutions they envisaged for improving the quality of primary care (PC) services and empower them to make better use of PC services.

Design/methodology/approach
A participatory research approach was used. Six workshops were organised to provide diabetes patients with knowledge on available services and to engage them in sharing their experience. Group discussions were recorded. Data were analysed using the thematic analysis method.

Findings
In total, 79 persons living with diabetes for a mean of 13 years participated. Needs expressed were grouped under seven themes: assurance of satisfactory follow-up by a family physician, continuous access to services adapted to evolving needs, motivation to adopt and maintain healthy behaviours, maintenance of knowledge about diabetes, psychological support, financial constraints, and collaboration with secondary-level services. Patients proposed solutions for improving services that were grouped under five themes: facilitating access to services, disseminating information about available services, centralising diabetes information on the internet, offering personalised services and improving interprofessional collaboration.

Practical implications
Needs expressed by diabetic patients concern different aspects of care such as accessibility, organisation, coordination, and better dissemination and visibility of services. The solutions proposed by patients focussed on better access to information and interprofessional services.

Originality/value
The workshop format used in this study offers an original and interesting approach and tool for actively engaging patients in quality improvement of services.
Sustaining Thai SMEs through perceived benefits and happiness
Authors: Winit Warat , Kantabutra Sooksan 
Published: June 2017

Purpose
This paper aims to examine the relationship between stakeholders’ perceived benefits and happiness of small and medium-sized enterprises (SMEs) that follow Thai’s corporate sustainability practices, called sufficiency economy, and their impact on stakeholder–company relationship quality and firm performance outcomes.

Design/methodology/approach
Derived from the literature, a structural model, expressing the relationship between stakeholders’ perceived benefits and happiness of SMEs and their impact on stakeholder–company relationship quality and firm performance outcomes, was developed. A questionnaire survey was conducted with 636 stakeholders from sufficiency economy SMEs in Thailand. Structural equation modeling was used to test the model.

Findings
Results indicate that utilitarian benefits, and hedonic and eudaimonic happiness impact enhanced stakeholder–company relationship quality with the firm to varying degrees. Different levels of relationship quality also impact perceived corporate reputation and perceived brand equity differently.

Originality/value
This study is among the first that identifies the positive impact of happiness on corporate sustainability performance.
The governance role of institutional investors in information disclosure
Authors: Lin Yuchen , Song Yangbo , Tan Jinsong 
Published: June 2017

Purpose
As an important participant in capital market, institutional investors play a principal role in improving corporate governance. Most existing studies have focused on institutional ownership and its economic consequences. Nevertheless, they have not provided sufficient insight on the governance behavior of institutional investors as well as the underlying incentive mechanism. This paper aims to analyze the governance role of institutional investors in information disclosure and provide related evidence.

Design/methodology/approach
The authors propose a novel theory to analyze the institutional investors’ behavior of active governance and shows that such behavior significantly improves the quality of corporate information disclosure. The authors then conduct an empirical test by using the hand-collected data of institutional investors’ corporate visits during 2009-2014 in ChiNext.

Findings
This paper finds that the firms visited by institutional investors are more likely to have a greater tendency of disclosing more information than the firms that have never been visited. In particular, a higher frequency of visits or a larger number of participating institutional investors leads to a higher degree of disclosure. Consistent with the notion that on-site visits endow institutional investors with more frequent and active interaction with the firms, the authors find that the results are stronger for firms which are visited on-site, when compared with other information acquisition activities such as online meetings, conference calls and investor meetings. In addition, the effect of a site visit is greater when the site visit is conducted by securities companies or funds rather than insurance companies or QFIIs. Finally, the test of the direction of causality suggests that visits conducted by institutional investors leads to more information disclosure, rather than the reverse. Collectively, these results show that institutional investors’ participation enhances corporate information disclosure.

Originality/value
This paper explores the internal mechanism that institutional investors affect corporate governance by improving information disclosure through their corporate visits. This is the first study to investigate the influence of institutional investors’ corporate visits and their economic consequences.