bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enteric disease episodes and the risk of acquiring a future sexually transmitted infection: a prediction model in Montreal residents
Authors: Caron Melissa , Allard Robert , Bédard Lucie , Latreille Jérôme , Buckeridge David L 
Published: March 2016

AbstractObjective. The sexual transmission of enteric diseases poses an important public health challenge. We aimed to build a prediction model capable of identifying individuals with a reported enteric disease who could be at risk of acquiring future sexually transmitted infections (STIs).Materials and Methods. Passive surveillance data on Montreal residents with at least 1 enteric disease report was used to construct the prediction model. Cases were defined as all subjects with at least 1 STI report following their initial enteric disease episode. A final logistic regression prediction model was chosen using forward stepwise selection.Results. The prediction model with the greatest validity included age, sex, residential location, number of STI episodes experienced prior to the first enteric disease episode, type of enteric disease acquired, and an interaction term between age and male sex. This model had an area under the curve of 0.77 and had acceptable calibration.Discussion. A coordinated public health response to the sexual transmission of enteric diseases requires that a distinction be made between cases of enteric diseases transmitted through sexual activity from those transmitted through contaminated food or water. A prediction model can aid public health officials in identifying individuals who may have a higher risk of sexually acquiring a reportable disease. Once identified, these individuals could receive specialized intervention to prevent future infection.Conclusion. The information produced from a prediction model capable of identifying higher risk individuals can be used to guide efforts in investigating and controlling reported cases of enteric diseases and STIs.
The dynamic landscape of fission yeast meiosis alternative-splice isoforms
Authors: Kuang Zheng , Boeke Jef D. , Canzar Stefan 
Published: March 2016

AbstractAlternative splicing increases the diversity of transcriptomes and proteomes in metazoans. The extent to which alternative splicing is active and functional in unicellular organisms is less understood. Here we exploit a single-molecule long-read sequencing technique and develop an open-source software program called SpliceHunter, to characterize the transcriptome in the meiosis of fission yeast. We reveal 17017 alternative splicing events in 19741 novel isoforms at different stages of meiosis, including antisense and read-through transcripts. Intron retention is the major type of alternative splicing, followed by “alternate intron in exon”. 887 novel transcription units are detected; 60 of the predicted proteins show homology in other species and form theoretical stable structures. We compare the dynamics of novel isoforms based on the number of supporting full-length reads with those of annotated isoforms and explore the translational capacity and quality of novel isoforms. The evaluation of these factors indicates that the majority of novel isoforms are unlikely to be both condition-specific and translatable but the possibility of functional novel isoforms is not excluded. Moreover, the co-option of these unusual transcripts into newly born genes seems likely. Together, this study highlights the diversity and dynamics at the isoform level in the sexual development of fission yeast.
Genome-wide measurement of spatial expression in patterning mutants ofDrosophila melanogaster
Authors: Combs Peter A. , Eisen Michael B. 
Published: March 2016

AbstractGenome sequencing has become commonplace, but the understanding of how those genomes ultimately specify cell fate during development is still elusive. Extrapolating insights from deep investigation of a handful of developmentally important Drosophila genes to understanding the regulation of all genes is a major challenge. The developing embryo provides a unique opportunity to study the role of gene expression in pattern specification; the precise and consistent spatial positioning of key transcription factors essentially provides separate transcriptional-readout experiments at a critical point in development.We cryosectioned and sequenced mRNA from single Drosophila melanogaster embryos at the blastoderm stage to screen for spatially-varying regulation of transcription. Expanding on our previous screening of wild type embryos, here we present data from dosage mutants for key maternally provided regulators, including depletion of zelda and hunchback and both over-expression and depletion of bicoid. These data recapitulate all of the expected patterning changes driven by these regulators; for instance, we show spatially-confined up-regulation of expression in the bicoid over-expression condition, and down-regulation of those genes in the bicoid knock-down case, consistent with bicoid’s known function as an anterior-localized activator.Our data highlight the role of combinatorial regulation of patterning gene expression. When comparing changes in multiple conditions, genes responsive to one mutation tend to respond to other mutations in a similar fashion. Furthermore, genes that respond differently to these mutations tend to have more complex patterns of TF binding.
SAMSA: A comprehensive metatranscriptome analysis pipeline
Authors: Westreich Samuel T , Korf Ian , Mills David A. , Lemay Danielle G 
Published: March 2016

AbstractBackgroundAlthough metatranscriptomics—the study of diverse microbial population activity based on RNA-seq data—is rapidly growing in popularity, there are limited options for biologists to analyze this type of data. Current approaches for processing metatranscriptomes rely on restricted databases and a dedicated computing cluster, or metagenome-based approaches that have not been fully evaluated for processing metatranscriptomic datasets. We created a new bioinformatics pipeline, SAMSA, designed specifically for metatranscriptome dataset analysis, which runs either inhouse or in conjunction with Metagenome-RAST (MG-RAST) servers. Designed for use by researchers with relatively little bioinformatics experience, SAMSA offers a breakdown of metatranscriptome activity by organism or transcript function, and is fully open source. We next used this new tool to evaluate best practices for sequencing stool metatranscriptomes.ResultsWorking with the MG-RAST annotation server, we constructed the Simple Annotation of Metatranscriptomes by Sequence Analysis (SAMSA) software package, a complete pipeline for the analysis of gut microbiome data. In creating this package, we determined optimal parameters in data collection and processing. SAMSA can summarize and evaluate raw annotation results, identifying abundant species and significant functional differences between metatranscriptomes.Using pilot data and simulated subsets, we determined experimental requirements for fecal gut metatranscriptomes. Sequences need to be either long reads (longer than 100bp) or paired-end reads that can be joined. Each sample nees 40-50 million raw sequences which can be expected to yield the 5-10 million annotated reads necessary for accurate abundance measures. We also demonstrated that ribosomal RNA depletion does not equally deplete ribosomes from all species within a sample, and remaining rRNA sequences should be discarded. Using publicly available metatranscriptome data in which rRNA was not depleted, we were able to demonstrate that organism activity can be measured using mRNA counts. We were also able to detect significant differences between control and experimental groups in both organism activity and functional activity.ConclusionsBy making this new pipeline publicly available, we have created a powerful new tool for metatranscriptomics research, offering a new method for greater insight into the activity of diverse microbial communities. We further recommend that stool metatranscriptomes be ribodepleted and sequenced in a 100bp paired end format with a minimum of 40 million reads per sample.
The impact of case formulation meetings for teams
Authors: Whitton Clare , Small Michelle , Lyon Hayley , Barker Lyndsie , Akiboh Martina 
Published: March 2016

Purpose– The purpose of this paper is to investigate the impact of psychological case formulation meetings for staff in a secure forensic learning disability and autism service.Design/methodology/approach– In total, 89 of the attendees completed a questionnaire prior to the formulation meeting and then another questionnaire following attendance at a formulation meeting.Findings– The results indicate that staff found these to be a helpful, informative and a positive experience professionally and personally. The results suggest that the formulation meetings developed staffs’ psychological understanding about the patient and their problems, helped to increase their empathy towards the patient, increased consistency in the teams’ views, and that the staff felt listened to.Research limitations/implications– Psychological formulation meetings are established in the current service, and therefore this may be a contributing to factor to the lack of significant change found in some of the items. Therefore, it would be beneficial for future services to complete a service evaluation at a much earlier point of implementation, as this may impact the level of significance.Originality/value– The findings of this service evaluation suggest that formulation is a beneficial and useful tool for teams and would be a helpful tool for psychologists to use in the clinical work with teams.
Effectiveness of individual psychodynamic psychotherapy in disability psychotherapy
Authors: McInnis Erica Elaine 
Published: March 2016

Purpose– The purpose of this paper is to report effectiveness of disability psychotherapy with a male adult with a mild intellectual disability presenting with complex emotional and behavioural problems.Design/methodology/approach– An individual case study was used with repeated analytic, quantitative and qualitative measures. This reported progress from individual weekly disability psychotherapy of psychodynamic orientation within an emotional disability framework.Findings– Disability psychotherapy led to a reduction in emotional and behavioural problems, reduction in emotional disability and facilitated protective psychological growth. In total, 88 sessions resulted in cessation of problem behaviours when other approaches did not. Given this therapy is likely to be reserved for the most complex and severe of cases, this study suggests more sessions of psychotherapy are needed than inferred from previous studies of effectiveness (Beailet al., 2007). This is to promote a sense of self which facilitates psychological well-being.Research limitations/implications– Limitations of a single case study include generalisability, controlling other factors in real life settings and subjectivity from inclusion of analytical measures. Further studies and follow-up would determine longevity of benefits. Nevertheless disability psychotherapy can be effective and should be available in a culturally appropriate service to meet the diverse needs of people with intellectual disabilities.Originality/value– This case study adds to the limited body of evidence on effectiveness of psychotherapy for people with intellectual disabilities. It is novel to report formal outcomes from an emotional disability model (Frankish, 2013a) and the use of analytic and attachment outcome measures.
How to run successful e-internships: a case for organizational learning
Authors: Jeske Debora , Axtell Carolyn M. 
Published: March 2016

Purpose
The purpose of this paper is to outline unique learning experience that virtual/e-internships can offer small and medium-sized enterprises and start-up organizations.

Design/methodology/approach
The authors interviewed 18 experts on e-internships (interns and managers of internships) across several countries to learn more about the learning experiences for both organizations and interns. The information from these interviews was also used to formulate a number of recommendations.

Findings
The interviews outlined the various development opportunities that e-internships may produce for interns, managers and staff within these organizations. One important benefit pertains to the skill development of both interns and managers. The interns get unique working experiences that also benefit the organizations in terms of their creativity, input and feedback. In return, managers get a unique learning experience that helps them expand their project management skills, interpersonal skills and mentoring.

Practical implications
The authors outline a number of recommendations that consider skill development, the benefit of diversity in numerous forms as well as mutual benefits for enterprises and start-ups.

Originality/value
The discussion of the various benefits and conditions under which virtual internships will succeed in organizations provides practitioners an insight into the organizational opportunities available to them given the right investment into e-interns and internship schemes.
In touch with the softer side of MBAs
Authors: Beal Brian 
Published: March 2016

Purpose
Considering that Master of Business Administration (MBA) programs have been the focus of many evaluations and much criticism in recent years, the purpose of this paper is to investigate the objective and subjective effects on careers experienced by part-time MBA students and graduates.

Design/methodology/approach
The authors conducted an empirical research, involving more than 700 students and graduates of three part-time MBA programs in Brazil.

Findings
The authors found that students and graduates experience more subjective than objective effects of such programs in their careers, and that the subjective effects are primarily related to self-confidence, employability, expansion of business view and ability to “play the game”.

Originality/value
This study makes three contributions to the knowledge of the effects of MBAs. First, it provides insight into students’ perspectives. Second, it increases the knowledge of the subjective effects of MBAs on the careers of students. And third, it focuses on part-time programs in a developing nation rather than on full-time programs in a developed nation such as the USA, as is often the case.
Cultural values and consumers’ expectations and perceptions of service encounter quality
Authors: Karami Masoud , Maleki Mohamad Mehdi , Dubinsky Alan J. 
Published: March 2016

Purpose
The purpose of the study is to explore the impact of cultural values on perceptions of service encounter quality by examining the potentially mediating role of service encounter expectations.

Design/methodology/approach
A questionnaire was designed to collect data from 30 cosmetic clinic patients in Tehran, Iran. Confirmatory factor analysis was used to test the convergent and discriminant validity of the scales. Moreover, path modeling and bootstrapping were implemented using Smartpls 2.0 (M3) software to analyze the collected data and to assess the research model (Figure 1).

Findings
Cultural values have a significant impact on both expectations and perceptions of service encounter quality. Moreover, findings show that expectations of service encounter quality have an impact on perceptions of service encounter quality. The mediating role of service encounter expectations was confirmed.

Research limitations/implications
There are additional issues that should be addressed about different aspects of service encounters in developing countries. Moreover, subcultures provide attractive context for service quality perception research; subcultures comprise a large consumer market having its own cultural values that future research could examine.

Practical implications
Healthcare service providers should understand the cultural values of patients that may differ by social demographic characteristics. Providing a service that enhances patient cultural values might enhance success in the plastic surgery market, because such surgery may assist one in gaining recognition and improving their relationships with others. Clinic managers should consider Iran as a developing country, with its considerable young population having modern self-oriented demands, should be a desirable market for cosmetics and beauty care products.

Originality/value
Using the concept of Schwartz’s basic human values model to assess consumers’ cultural values and its impact on service encounter quality was the study’s main contribution. Moreover, it is among few studies conducted in the cosmetic surgery industry in a developing country’s context.
Time preference and the process of civilization
Authors: Howden David , Kampe Joakim 
Published: March 2016

Purpose– The authors begin with an admittedly simplistic statement: “civilization” is best represented by the increased availability of utility providing goods and services. In other words, civilization is synonymous with economic development. The purpose of this paper is to concern three questions. First, how does civilization develop? Second, what is time preference and how does it affect the development of civilization, or what the authors call the “process of civilization.” Third, what factors affect time preference, and how do changes in time preference affect this civilizing process? Through these three questions, the authors provide the theoretical answer to why civilization developed, instead of the more common historical how civilization actually developed.Design/methodology/approach– The authors survey a variety of theories of civilization, and then develop an alternative that answers the question of “how civilization develops” rather than the more common “how did civilization develop.”Findings– Endogenous reductions in time preference are determined to be the best explanation of the spark that instigates the process of civilization. It also allows for other approaches to fall under its umbrella, thus providing one general theory in place of the current-specific theories.Originality/value– The value lies in the creation of a general theory of civilization, against which other theories looking at specific factors can be gauged.
Dynamic modeling and sensitivity analysis of dual-robot pneumatic riveting system for fuselage panel assembly
Authors: Huan Honglun , Cheng Liang , Ke Yinglin 
Published: March 2016

Purpose
– The purpose of this paper is to present a dual-robot pneumatic riveting system for fuselage panel assembly, including the system design, dynamic analysis and sensitivity analysis. The dual-robot pneumatic riveting system is designed to improve riveting efficiency and quality, thus finally replace the traditional two-man riveting mode where possible.

Design/methodology/approach
– The dual-robot pneumatic riveting system has been designed by considering vibration reduction for the tools and isolation for robots. Nonlinear multi-body dynamic model including clearance and collision is established for investigating the dynamic performance and analyzing the systemic sensitivities with respect to the key variations. Semi-implicit Runge–Kuta algorithm is used for solving the dynamic equations and shop experiments are implemented to verify the effectiveness of the numerical simulations.

Findings
– The simulation results show the tools can be held stably enough for riveting operation and the system sensitivity with respect to robot gesture can achieve the expected level. The experiment validates the proposed system with a good performance, and the riveting quality could adequately meet the requirements. The system is capable of installing an aluminum alloy countersunk 5 mm diameter rivet in 5 s.

Practical implications
– The dual robot pneumatic riveting system is successfully developed and test. It has been applied in a project of fuselage panel assembly in the aircraft manufacturing industry in China.

Originality/value
– To replace the traditional manual rivet installation, this paper presents a dual robot pneumatic riveting system and includes both the system design and dynamic analysis.
Intelligent method for tuning H2 PID controller of water hydraulic manipulator of CFETR blanket maintenances
Authors: Han Manfen , Wu Huapeng , Song Yuntao , Cheng Yong , Handroos Heikki 
Published: March 2016

Purpose
– The purpose of this paper is to investigate an intelligent control for water hydraulic position servo system which is intent to be used in remote control robot for fusion reactor. The dynamic model of water hydraulic servo control system is built and proportional–integral–derivative (PID) controller is used.

Design/methodology/approach
– PID control is the most common control algorithm used in industry and has been a conventional tool used to operate closed-loop control system; however, it is very difficult to achieve high accuracy and fast response by using the traditional way to tune its perimeters. To improve the control performance, optimization algorithm can be applied to search the best parameters of PID. This paper presents a search algorithm using particle swarm with H2 control standards objective function to optimize PID parameters.

Findings
– By comparing simulation and mock-up experiments’ results from different control methods, the particle swarm optimization algorithm presents better performance and is more effective for tuning PID parameters.

Originality/value
– This paper presents an effective way to ensure safety and efficiency for remote handling maintenances of China Fusion Engineering Test Reactor.
Design of cooling system for inspection manipulator and analysis based on experiment
Authors: Chen Tan , Zhang Wei-jun , Yuan Jian-jun , Du Liang , Zhou Ze-yu 
Published: March 2016

Purpose
– This paper aims to present a different cooling method (water cooling) to protect all the mechanical/electrical components for Tokamak in-vessel inspection manipulator. The method is demonstrated effective through high temperature experiment, which provides an economical and robust approach for manipulators to work normally under high temperature.

Design/methodology/approach
– The design of cooling system uses spiral copper tube structure, which is versatile for all types of key components of manipulator, including motors, encoders, drives and vision systems. Besides, temperature sensors are set at different positions of the manipulator to display temperature data to construct a close-loop feedback control system with cooling components.

Findings
– The cooling system for the whole inspection manipulator working under high temperature is effective. Using insulation material such as rubber foam as component coating can significantly reduce the environmental heat transferred to cooling system.

Originality/value
– Compared with nitrogen gas cooling applied in robotic protection design, although it is of less interest in prior research, water cooling method proves to be effective and economical through our high temperature experiment. This paper also presents an energetic analysis method to probe into the global process of water cooling and to evaluate the cooling system.