bluuebunny/crossref_metadata_2025_split huggingface dataset:
Learning to act by integrating mental simulations and physical experiments
Authors: Dasgupta Ishita , Smith Kevin A. , Schulz Eric , Tenenbaum Joshua B. , Gershman Samuel J. 
Published: May 2018

AbstractPeople can learn about the effects of their actions either by performing physical experiments or by running mental simulations. Physical experiments are reliable but risky; mental simulations are unreliable but safe. We investigate how people negotiate the balance between these strategies. Participants attempted to shoot a ball at a target, and could pay to take practice shots (physical experiments). They could also simply think (run mental simulations), but were incentivized to act quickly by paying for time. We demonstrate that the amount of thinking time and physical experiments is sensitive to trial characteristics in a way that is consistent with a model that integrates information across simulation and experimentation and decides online when to perform each.
Annotation of phenotypes using ontologies: a Gold Standard for the training and evaluation of natural language processing systems
Authors: Dahdul Wasila , Manda Prashanti , Cui Hong , Balhoff James P. , Dececchi T. Alexander , Ibrahim Nizar , Lapp Hilmar , Vision Todd , Mabee Paula M. 
Published: May 2018

AbstractNatural language descriptions of organismal phenotypes - a principal object of study in biology, are abundant in biological literature. Expressing these phenotypes as logical statements using formal ontologies would enable large-scale analysis on phenotypic information from diverse systems. However, considerable human effort is required to make the semantics of phenotype descriptions amenable to machine reasoning by (a) recognizing appropriate on-tological terms for entities in text and (b) stringing these terms into logical statements. Most existing Natural Language Processing tools stop at entity recognition, leaving a need for tools that can assist with both aspects of the task. The recently described Semantic CharaParser aims to meet this need. We describe the first expert-curated Gold Standard corpus for ontology-based annotation of phenotypes from the systematics literature. We use it to evaluate Semantic CharaParser’s annotations and explore differences in performance between humans and machine. We use four annotation accuracy metrics that can account for both semantically identical and similar matches. We found that machine-human consistency was significantly lower than inter-curator (human–human) consistency. Surprisingly, allowing curators access to external information that was not available to Semantic CharaParser did not significantly increase the similarity of their annotations to the Gold Standard nor have a significant effect on inter-curator consistency. We found that the similarity of machine annotations to the Gold Standard increased after new ontology terms relevant to the input text had been added. Evaluation by the original authors of the character descriptions indicated that the Gold Standard annotations came closer to representing their intended meaning than did either the curator or machine annotations. These findings point toward ways to better design of software to augment human curators, and the Gold Standard corpus will allow training and assessment of new tools to improve phenotype annotation accuracy at scale.
Custom hereditary breast cancer gene panel selectively amplifies target genes for reliable variant calling
Authors: Amuzu Setor , Revil Timothée , Foulkes William D. , Ragoussis Jiannis 
Published: May 2018

AbstractBackground: Target enrichment coupled with next generation sequencing provide high-throughput approaches for screening several genes of interest. These approaches facilitate screening a panel of genes for mutations associated with inherited breast cancer for research, diagnostic, and genetic counseling applications.Objective: To evaluate the performance of our custom 13 gene breast cancer panel, based on singleplex PCR, developed by WaferGen BioSystems. The panel was evaluated using patient-derived DNA samples, in terms of target enrichment efficiency, off-target enrichment, uniformity of target capture, effect of GC content of target regions on coverage depth, and concordance with validated variant calls.Results: At least 90% of target sequence for each gene was captured at 30x or greater. We evaluated uniformity of target capture across samples by calculating the percentage of samples with at least 90% of total target captured at 100x or greater and found 92% (33/36 samples) uniformity for our panel. Off-target enrichment ranges between 7.2% and 22.3%. We found perfect concordance between our custom panel and the Qiagen human breast cancer panel for functionally annotated variant calls in high read depth shared target regions. Altogether, there was agreement between the panels for 779 variants at 41 loci. We also confirmed 10 pathogenic mutations, initially discovered by Sanger sequencing, in the appropriate samples following target enrichment using our custom WaferGen panel.Conclusion: Our custom hereditary breast cancer panel is sensitive to the desired target genes and facilitates deep sequencing for reliable variant calling.
Methylation-wide association analysis reveals AIM2, DGUOK, GNAI3, and ST14 genes as potential contributors to the Alzheimer’s disease pathogenesis
Authors: Nazarian Alireza , Yashin Anatoliy I. , Kulminski Alexander M. 
Published: May 2018

ABSTRACTIntroduction:Alzheimer’s disease (AD) is a progressive complex neurodegenerative disorder with devastating impact on cognitive abilities. It is among the top 10 leading causes of death in the United States with no curative medications. Exploring genetic and non-genetic contributors to AD development is, therefore, of great importance.Methods:We investigated the AD-associated epigenetic changes by combing results from publicly available genome-wide association analyses and a large-scale methylation quantitative trait loci study.Results:Probes mapped to 133 genes were associated with AD with < 2.50E-06. Of these, four genes (i.e., GNAI3, AIM2, DGUOK and ST14) provided stronger evidence of possible role in AD pathogenesis as they were also significantly associated with AD in previous expression quantitative trait loci analyses and/or mouse model studies.Discussion:Although the identified associations do not prove any definitive causal relationships with AD, they provide a list of prioritized genes for follow-up functional studies.
Glucocorticoid-mediated Aβ and SCG10 upregulation evoke microtubule dysfunction and memory deficits
Authors: Choi Gee Euhn , Oh Ji Young , Lee Hyun Jik , Chae Chang Woo , Kim Jun Sung , Jung Young Hyun , Han Ho Jae 
Published: May 2018

AbstractWe investigated glucocorticoid, a major risk factor of Alzheimer’s disease, promoted microtubule instability that culminates in memory deficits. Mice group exposed to corticosteroid had reduced trafficking of AMPAR1/2 and mitochondria into the synapse due to microtubule destabilization, which finally impaired cognitive function. Furthermore, cortisol reduced microtubule stability through the mitochondria glucocorticoid receptor (GR)-dependent pathway in SH-SY5Y cells. Cortisol translocated the Hsp70-bound GR into mitochondria before stimulating ER-mitochondria interaction via increasing GR-Bcl-2 complex. Subsequently, Aβ was produced since γ-secretase activity was upregulated by increased ER-mitochondria connectivity. Mitochondrial Ca2+ influx was also elevated due to ER-mitochondria bridging, resulting in activation of mTOR pathway. Subsequent autophagy inhibition failed to remove Aβ and led to its accumulation. Moreover, selective autophagy through ubiquitination of SCG10 was suppressed. We eventually showed that both elevated Aβ and SCG10 levels drive cells to fail trafficking AMPAR1/2 and mitochondria into the cell terminus. In conclusion, glucocorticoid regulates ER-mitochondria coupling, which evokes Aβ generation and SCG10 upregulation. Subsequent microtubule destabilization leads to memory impairment through failure of AMPAR1/2 or mitochondria transport into cell periphery.
Learning the sequence of influenza A genome assembly during viral replication using point process models and fluorescence in situ hybridization
Authors: Majarian Timothy D. , Murphy Robert F. , Lakdawala Seema S. 
Published: May 2018

AbstractWithin influenza virus infected cells, viral genomic RNA are selectively packed into progeny virions, which predominantly contain a single copy of 8 viral RNA segments. Intersegmental RNA-RNA interactions are thought to mediate selective packaging of each viral ribonucleoprotein complex (vRNP). Clear evidence of a specific interaction network culminating in the full genomic set has yet to be identified. Using multi-color fluorescence in situ hybridization to visualize four vRNP segments within a single cell, we developed image-based models of vRNP-vRNP spatial dependence. These models were used to construct likely sequences of vRNP associations resulting in the full genomic set. Our results support the notion that selective packaging occurs during cytoplasmic transport and identifies the formation of multiple distinct vRNP sub-complexes that likely form as intermediate steps toward full genomic inclusion into a progeny virion. The methods employed demonstrate a statistically driven, model based approach applicable to other interaction and assembly problems.Author SummaryInfluenza virus consists of eight viral ribonucleoproteins (vRNPs) that are assembled by infected cells to produce new virions. The process by which all eight vRNPs are assembled is not yet understood. We therefore used images from a previous study in which up to four vRNPs had been visualized in the same cell to construct spatial point process models that measure how well the subcellular distribution of one vRNP can be predicted from one or more other vRNPs. We used the likelihood of these models as an estimate of the extent of association between vRNPs and thereby constructed likely sequences of vRNP assembly that would produce full virions. Our work identifies the formation of multiple distinct vRNP sub-complexes that likely form as intermediate steps toward production of a virion. The results may be of use in designing strategies to interfere with virus assembly. We also anticipate that the approach may be useful for studying other assembly processes, especially for complexes with modest affinities and more components than can be visualized simultaneously.
Flow-wise or path-wise: diffusion in a fragmented dendritic network and implications for eels
Authors: Domange J. , Lambert P. , Beaulaton L. , Drouineau H. 
Published: May 2018

AbstractThe European eel (Anguilla anguilla) is a catadromous species that reproduces at sea and inhabits continental waters during its growth phase. River fragmentation due to obstacles is considered one cause of the decline of this species. However, the colonization process of river catchments by eels is still poorly understood. In this article, we compare two scenarios for the diffusion of eels within river catchments: a path-wise scenario, in which movements are totally random, and a flow-wise scenario, in which movements are partially oriented. Based on these two scenarios, we attempted to predict the distribution of eels within dendritic river catchments, explicitly accounting for the presence of obstacles to movement. The model was fitted to a long-time series of electro-fishing data. The results suggest that the path-wise scenario is more predominant than the flow-wise scenario. Moreover, results show that the distribution of eels in river catchment depends on (i) the types of movements carried out by eels, (ii) the configuration of river networks and (iii) the positions of obstacles within catchments.
Effect of fosfomycin,Cynara scolymusextract, deoxynivalenol and their combinations on intestinal health of weaned piglets
Authors: Martínez Guadalupe , Diéguez Susana N. , Fernández Paggi María B. , Riccio María B. , Pérez Gaudio Denisa S. , Decundo Julieta M. , Romanelli Agustina , Amanto Fabián A. , Tapia María O. , Soraci Alejandro L. 
Published: May 2018

AbstractIntestinal health of weaning piglets was studied after oral treatments with fosfomycin (FOS),Cynara scolymusextract (CSE), deoxynivalenol (DON) and their combinations. Piglets were divided in groups and received different treatments during 15 days, namely DON (1mg/kg of feed), FOS administered into the drinking water (30 mg/kg b.w.), CSE (300 g/ton of feed) and all possible combinations including a control group that received clean balanced diet. At day 15, three piglets from each group were euthanized and gastrointestinal tract samples were immediately taken to evaluate pH, bacteriology (enterobacteria and lactic acid bacteria), volatile fatty acids concentration (VFAs), disaccharidases activity (lactase, sucrase and maltase), histology (intestinal absorptive area [IAA] and goblet cells count) and adherence of bacteria to intestinal mucus. Animals receiving FOS and CSE treatments exhibited evident beneficial intestinal effects compared to animals receiving diets free from these compounds. This was revealed by a lower enterobacteria population together with a lower E/L, an enhanced production of butyric acid, an increased enzymatic activity (particularly maltase), and a greater IAA and goblet cells count along with an increase in pathogenic bacteria adherence to intestinal mucus. Interactions between both treatments resulted in similar beneficial effects as their individual administration. On the contrary, DON produced detrimental effects on intestinal health as a decrease was observed on volatile fatty acids production, enzymatic activity and goblet cells count in animals receiving diets containing sub- toxic concentrations of this mycotoxin. The knowledge of the intestinal effects of these compounds contributes to understand the physiological and pathological gut changes and their potential productive consequences.
Group reporting as a tool to enhance the quality of courses
Authors: Crisanto Mari Anjeli Lubrica 
Published: May 2018

Purpose
Group reporting, a form of cooperative learning, is a learning tool often employed in residential teaching to facilitate quality learning. Like other cooperative learning methods, it enhances learning in classrooms by allowing students work on activities in small groups to receive rewards based on their group’s performance. However, though group reporting is often done in face-to-face settings, few up-to-date literature has shown its application in online learning. Moreover, the question as to whether online cooperative learning through group reports yields positive or negative response from students has to be studied further. The paper aims to discuss these issues.

Design/methodology/approach
This study focuses on the students’ response to the group reporting activity carried throughout one semester. A course offered by the University of the Philippines Open University on database management systems made use of group reporting to add to the students’ learning experience. Group meetings along with regular online lectures were carried out during the first half of the semester. The output group reports were then presented during the second half and served as the main resource for those weeks’ study modules. An online survey with Likert scales drawing out the student reactions on the learning activity impact was administered to volunteer respondents at the end of classes.

Findings
In total, 71.9 percent of 32 respondents observed changes in their behavior after using peer and cooperative learning technologies. The respondents also indicated that they enjoyed the group reporting activity (14 agreeing strongly, 14 agreeing moderately). They also indicated that they were motivated to learn the course through the group reports (8 agreeing strongly, 14 agreeing moderately). However, when asked if they preferred to have all the modules in group report format 9 agreed moderately, 8 disagreed moderately, 7 disagreed strongly, 4 agreed strongly, and 4 neither agreed nor disagreed. Still, overall, online cooperative learning facilitated quality learning based on this study’s results.

Originality/value
This study contributes to the body of knowledge by showing how group reporting can be applied online and how students have responded to it. The study also provides recommendations on how to conduct online cooperative learning in order to enhance the quality of courses, with implications for further research to look into variations with respect to the technology used for reporting and its suitability to a given course.
The “comply or explain” principle in the Republic of Slovenia
Authors: Djokic Danila , Duh Mojca 
Published: May 2018

Purpose
This paper aims to provide an overview of the quality of corporate governance (CG) disclosures in the framework of CGS and the “comply or explain” code principle in Slovenia. It aims to observe the differences among companies of the prime, standard and entry markets in terms of the differences in governance standards and regulatory frameworks.

Design/methodology/approach
This paper analyzes the historical development, legal approach and methods used in the regulation of the “comply or explain” principle in Slovenia. In the 2014 SEECGAN research – Slovenia, we measured the quality of CG by applying the newly created SEECGAN index methodology covering seven segments of CG and assessing 98 attributes. This paper upgrades the results of this research with additional case study research.

Findings
The analysis from 2011 to 2014 on the “comply or explain” principle showed a gradual improvement of transparency in Slovenian public companies. The 2014 SEECGAN research – Slovenia revealed that the number of specific and high-quality explanations of deviations has increased. The study in this paper showed that the governance practice in some cases is still not in line with code recommendations and does not disclose the deviations from the code.

Originality/value
Disclosures of the Slovenian public companies are presented for the period 2004-2018. This paper points out the improvements to be realized to change unsatisfactory practices. The measurement of the quality of CG by the 2014 SEECGAN research – Slovenia introduced a methodology, which could be recognized and improved by the EU and/or its member states.
Smart HR 4.0 – how industry 4.0 is disrupting HR
Authors: Sivathanu Brijesh , Pillai Rajasshrie 
Published: May 2018

Purpose
This paper aims to highlight the importance of Smart Human Resources 4.0 (Smart HR 4.0) and its role as a catalyst in the disruption process in the human resource domain. This paper illustrates the advantages of Smart HR 4.0 in the HR domain by using the example of Credit Suisse, which has extensively used people analytics to reduce employee attrition.

Design/methodology/approach
The paper discusses the role of Smart HR 4.0 as a disruptor in the human resource domain. With the help of the Smart HR 4.0 conceptual framework, this paper illustrates how Smart HR 4.0 disrupts the talent on-boarding, talent development, and talent off-boarding process.

Findings
An organization would require a successful Smart HR 4.0 strategy to cope up with the challenges of Industry 4.0 transformation. Emerging technologies such as Internet-of-Things, Big Data, and artificial intelligence will automate most of the HR processes, resulting in efficient and leaner HR teams. Both organization structure and leadership style changes would be required for efficient Smart HR 4.0 implementation that would allow HR departments to play a more strategic role in the overall organization growth.

Originality/value
This paper contributes to the existing literature and body of knowledge in the HR domain by developing a Smart HR 4.0 conceptual framework. This paper discusses how Smart HR 4.0 acts as a catalyst in the disruption of talent ion-boarding, talent development, and talent off-boarding process with the help of emerging technologies and change in the employee generation.
Lean leadership in major projects: from “predict and provide” to “predict and prevent”
Authors: Holweg Matthias , Maylor Harvey 
Published: May 2018

Purpose
The purpose of this paper is to understand the context of major projects and their management from an OM perspective; the authors provide a foundation for exploring how the body of work on lean production (the “old” theory) can contribute to the development of major projects (the “new” context). In doing so, it extends the prevailing economic approach to major projects (best described as “predict and provide”) and posits the development of an alternative approach based on extending the lean production logic to this new context (referred to as “predict and prevent”).

Design/methodology/approach
The paper investigates the scope for adopting lean practices in context of major project. To this effect the authors review the current state of both lean thinking and major project management, and use “Universal Credit” as an exploratory case study to illustrate and verify the arguments in practice.

Findings
Two main findings are proposed: first, the authors demonstrate the inherent performance challenge of major projects in OM terms, which the authors argue presents significant scope for the application of OM concepts to improve major project performance. Second, using lean thinking as framing, the authors identify three distinct process levels and common wastes in major projects, and identify five principles how lean could improve the delivery of major projects.

Research limitations/implications
Major projects present an untapped area for OM research; based on the exploratory case the authors propose ways how OM concepts can be applied to this new context. Further research will be needed to validate and generalise.

Practical implications
Major projects, including organisational transformations, IT-enabled change, major events and large infrastructure projects, constitute a large proportion of economic activity. Despite their prominence, however, they are also commonly associated with low success rates. This paper provides one route for exploring how a successful set of principles could be applied to improving their performance.

Originality/value
This work translates a popular set of ideas from OM to strengthening a relatively neglected context within OM. An agenda for further research is suggested to support the development of this application.
Strategic alliances in technology industries: a different rationale
Authors: Li Lee , Qian Gongming 
Published: May 2018

PurposeThe purpose of this paper is to investigate the strategic intentions of strategic alliances in technology industries.Design/methodology/approachThis paper mainly uses case studies as its methodology.FindingsThis paper depicts how the possibilities of firms sharing resources, costs and risks decrease when industry changes grow frequently and unpredictably. More importantly, this study suggests that in technology industries, firms use strategic alliances to keep their existing marketing strategies intact.Research limitations/implicationsFor future studies, the authors will develop and test hypotheses based on the arguments of this paper.Practical implicationsFindings of this paper contradict business executives’ common sense but have important implications for them to manage their strategic alliances.Originality/valueFindings of this paper contradict the traditional belief of strategic alliances and thus advance the knowledge on strategic alliances.