bluuebunny/crossref_metadata_2025_split huggingface dataset:
ChimPipe: Accurate detection of fusion genes and transcription-induced chimeras from RNA-seq data
Authors: Rodríguez-Martín Bernardo , Palumbo Emilio , Marco-Sola Santiago , Griebel Thasso , Ribeca Paolo , Alonso Graciela , Rastrojo Alberto , Aguado Begoña , Guigó Roderic , Djebali Sarah 
Published: August 2016

AbstractBackgroundChimeric transcripts are commonly defined as transcripts linking two or more different genes in the genome, and can be explained by various biological mechanisms such as genomic rearrangement, read-through or trans-splicing, but also by technical or biological artefacts. Several studies have shown their importance in cancer, cell pluripotency and motility. Many programs have recently been developed to identify chimeras from Illumina RNA-seq data (mostly fusion genes in cancer). However outputs of different programs on the same dataset can be widely inconsistent, and tend to include many false positives. Other issues relate to simulated datasets restricted to fusion genes, real datasets with limited numbers of validated cases, result inconsistencies between simulated and real datasets, and gene rather than junction level assessment.ResultsHere we present ChimPipe, a modular and easy-to-use method to reliably identify chimeras from paired-end Illumina RNA-seq data. We have also produced realistic simulated datasets for three different read lengths, and enhanced two gold-standard cancer datasets by associating exact junction points to validated gene fusions. Benchmarking ChimPipe together with four other state-of-the-art tools on this data showed ChimPipe to be the top program at identifying exact junction coordinates for both kinds of datasets, and the one showing the best trade-off between sensitivity and precision. Applied to 106 ENCODE human RNA-seq datasets, ChimPipe identified 137 high confidence chimeras connecting the protein coding sequence of their parent genes. In subsequent experiments, three out of four predicted chimeras, two of which recurrently expressed in a large majority of the samples, could be validated. Cloning and sequencing of the three cases revealed several new chimeric transcript structures, 3 of which with the potential to encode a chimeric protein for which we hypothesized a new role.ConclusionsChimPipe combines spanning and paired end RNA-seq reads to detect any kind of chimeras, including read-throughs, and shows an excellent trade-off between sensitivity and precision. The chimeras found by ChimPipe can be validatedin-vitrowith high accuracy.
Crystal structure of Re-substituted lanthanum tungstate La5.4W1−yReyO12–δ(0 ≤y≤ 0.2) studied by neutron diffraction
Authors: Fantin Andrea , Scherb Tobias , Seeger Janka , Schumacher Gerhard , Gerhards Uta , Ivanova Mariya E. , Meulenberg Wilhelm A. , Dittmeyer Roland , Banhart John 
Published: August 2016

A precise determination of sample composition and water uptake of La6−xWO12−δ(0.4 ≤x≤ 0.8) and Re-substituted La5.4W1−yReyO12−δ(0 ≤y ≤ 0.2) lanthanum tungstate is carried out. Sample compositions and water uptake were determined by electron probe micro-analysis and thermogravimetry, respectively. A single-phase region of Re-substituted lanthanum tungstates is reported. The crystal structure of two selected specimens produced by the citrate-complexation route based on the Pechini method, namely La5.4WO12−δand La5.4W0.8Re0.2O12−δ, was investigated by neutron diffraction in the temperature range 1.5 ≤T≤ 1200 K. The structural model for lanthanum tungstates is validated, according to which the Wyckoff site shared by La and W (Fm{\overline 3}m space group, 24dsite) is split with half-site occupancies (Fm{\overline 3}m space group, 48hsite). Replacement of W by up to 20 mol% Re does not change the lattice structure, and Re atoms substitute for W statistically in both 4aand 48hWyckoff sites of the Fm{\overline 3}m space group, as shown by combining the average neutron scattering length procedure, thermogravimetry and electron probe micro-analysis. Using the Willis and Pryor approach to anisotropic displacement parameters it is shown that the remaining static disorder in the unit cell found in La5.4WO12−δand La5.4W0.8Re0.2O12−δstructures is comparable, when the Fm{\overline 3}m space group with split 48hsite is employed. Through the estimation of the Debye temperature for both compounds, extracted from the analysis of thermal expansion coefficients and from the Willis and Pryor approach, anion anharmonic vibrations like those in yttria-stabilized zirconia are proven to exist in LaWO for the first time.
Internship impact on career consideration among business students
Authors: Rothman Miriam , Sisman Ruth 
Published: August 2016

Purpose
The purpose of this paper is to report on the impact of the internship experience on business students’ career intentions in regard to pursuing a career path in the same job function or industry as their internship.

Design/methodology/approach
After completing and reflecting on an internship, 198 undergraduate students responded to the prompt: “discuss the impact of the internship on your career consideration.” Responses were analyzed using a content analysis methodology in order to determine whether or not interns would pursue the same job functions (e.g. sales) or industry (e.g. non-profit) as their internship in their post-graduation job search.

Findings
Across the job functions and industries identified within the internships, 54 and 45 percent of interns confirmed their expectations of career fit, respectively. The implications of confirming and disconfirming these expectations for students are discussed.

Originality/value
Given the value of internships to business students, surprisingly few studies have examined their influence on undergraduates’ career considerations. Students select internships with the intention of learning about job functions or industries for possible career fit, yet the authors know little about whether the experience confirms or disconfirms their expectations. This study seeks to address this gap. The authors suggest that internships, as experiential activities, merit greater attention as they provide students opportunities to learn what they do or do not want to do, where they do or do not want to work and whether their self-concept fits a possible career path – saving themselves and potential employers the cost of job dissatisfaction and turnover.
Teaching self- and social competencies in the retail sector
Authors: Edeling Sabrina , Pilz Matthias 
Published: August 2016

PurposeThe purpose of this paper is to use teaching and learning units specially devised for development of self-competencies and social competencies in the retail sector to explore how learners assess these units in relation to acceptance, quality and self-assessment of improvement in their own performance.Design/methodology/approachThe study focuses on Poland, Italy and Germany, with a total of 1,020 learners undergoing initial vocational training in the retail sector taking part.FindingsThe findings point to high levels of acceptance by participants and to significant appreciation of the quality of the teaching and learning units. Learners also perceived a marked improvement in their performance after completing the units. Differences in outcomes between individual countries can be explained at least in part by the differing training framework in each country.Research limitations/implicationsThe approach did not enable the authors adequately to evaluate the increase in learners’ competencies: participants’ self-assessment is of only limited value for this purpose. Moreover, only three countries were involved in the study. This area in particular will require substantial further research if reliable methods for evaluating competencies are to be developed that improve on the current instruments.Originality/valueThe pedagogical objective of the project was to develop teaching and learning materials that would accelerate the development of self- and social competencies in the retail sector. The aim was that the material should be capable of use right across a range of European countries and be evaluated in a proper way. The findings are based on a very high number of involved students. Also the results are positive and enable teachers in VET-courses to use well tested teaching materials.
Examination of cultural shock, inter-cultural sensitivity and willingness to adapt
Authors: D’Souza Clare , Singaraju Stephen , Halimi Tariq , Sillivan Mort Gillian 
Published: August 2016

PurposeThe purpose of this paper is to identify themes on international experiences that impact culture and how these findings will intervene in understanding cross-cultural training programs. Thereby an attempt is made to: evaluate cross-cultural insensitivity influences on cross-cultural shock and willingness to adapt, identify cultural impressions over a short overseas period, provide some insights on cross-cultural training that will improve training practices for cross-cultural assignments.Design/methodology/approachA diary method was used to analyze the data using NVivo. This research uses diary studies because they have been popular in identifying factors that influence learners to learn, as well as found to be productive to achieve short term experiences. They allow for in-depth analysis, uncovering several findings unlike observation and interviews that cannot reach. In addition, diary text is said to give information on areas of social reality that are not contained in the text. Following this the study used the theme category frequencies to enable us to undertake non-parametric testing of contingency tables.FindingsSeveral descriptors were identified in this study; theχ2-test indicates that there is a difference in cultural shock experiences on negative cultural sensitivity but no difference in positive cultural sensitivity which was found significant at thep=0.05 level. On the other hand there is a significant association between positive cultural sensitivity and willingness to adjust and no significant association between negative cultural sensitivity and willingness to adjust which was found significant at thep=0.05 level.Research limitations/implicationsThis research shows how learning in higher education can take into account the experiences by which learners can use their knowledge and skills for future cross-cultural training in international careers.Practical implicationsThese results can be useful in guiding vocational interests. The results of the research offer descriptors of an exploratory nature which can also be used as a reference analysis for consequent phases in cross-cultural training.Originality/valueResearch provides several descriptors on international culture such as culture shock, positive and negative intercultural sensitivity, and willingness to adapt, some of which were significant. Diary method to analyze data are used which is distinctive and unique to understand behavior.
Trainer attributes as drivers of training effectiveness
Authors: Chukwu Gosim Martin 
Published: August 2016

Purpose
The purpose of this paper is to discover trainer variables that act as driving forces on training effectiveness. This can be a catalyst for improving the quality of training outcomes thereby making training firms more competitive as well as bridge the gap in literature.

Design/methodology/approach
This qualitative research study used the grounded theory methodology. Data analysis was performed using open, axial and selective coding with a discursive set of theoretical propositions emerging. Qualitative data were collected through a focus group, one-on-one interviews and secondary sources. The subjects comprised primarily 26 past participants to the researcher’s firm’s training programs.

Findings
Seven major trainer attributes – facilitator disposition, real life examples, group work, interaction, participant involvement, stories/illustrations and demonstrations – were recognized by trainees whose post-training appraisals confirm that the training was effective. These trainer attributes combine with environmental factors to trigger trainee characteristics leading to behavior change and performance improvement.

Research limitations/implications
The paper makes a significant contribution to training evaluation literature. Researchers can take up any of the discovered attributes to further refine training evaluation theories or models.

Practical implications
New knowledge can be utilized to improve quality training presentations to improve learning outcomes. Organizational performance improvement, which is the desired return on investment of training, can better be achieved.

Originality/value
The paper goes beyond conceptual models to empirical discovery.
Effect of the fabric color on the visual perception of pilling
Authors: Barakzehi Marjan , Asadi Fatemeh , Ghareh Aghaji Ali Akbar 
Published: August 2016

Purpose
Pilling is a fabric surface fault comprising of small, fuzzy balls on the surface of a fabric that leads to poor handle and quality. The purpose of this paper is to investigate the effect of the fabric color in terms of depth and hue on the visual perception of pilling on the fabric surface.

Design/methodology/approach
Acrylic fabrics were prepared at various color depths and hues and then were applied with relatively equal amount of pilling on the surface of samples. The amount of perceived pilling was evaluated by human observers by employing paired comparison method and the results were analyzed using statistical methods.

Findings
According to the results, color depth and the visual perception of pilling in achromatic sample were nearly independent. Color hue can be considered as an important factor in the visual perception of pilling so when the color contrast between the pill and background decreases, the visual perception of pilling decreases as well. Hence, the achromatic sample have the most amount of pilling perception whereas green and blue samples show less pilling, in visual sensation.

Originality/value
There is a strong demand for acrylic fabrics in apparel industry but they have high tendency for pilling formation. To overcome this problem, experts have suggested some methods to prevent or reduce pilling. If it is proved that color influences on pilling perception, an useful instruction will be available for acrylic fabric manufacturers in order to satisfy their customer with good quality of products. In this work, the authors tried to find such relationships between the color and the pilling perception for human observers.
Modeling employee-based brand equity (EBBE) and perceived environmental uncertainty (PEU) on a firm’s performance
Authors: Poulis Athanasios , Wisker Zazli 
Published: August 2016

PurposeThis paper aims to examine the impact of employee-based brand equity (EBBE) and perceived environmental uncertainty (PEU) on firm performance.Design/methodology/approachData were collected through an e-mail survey from fast-moving consumer goods (FMCG) firms in the UK and UAE. Sample sectors included cosmetics and toiletries, household care products, packaged food, soft drinks and tobacco firms. Quantitative data were analyzed using structural equation modeling.FindingsThe results suggest strong support for the hypothesized relationships, thereby providing strong validation for the proposed model. One interesting finding was that the PEU affected employee brand equity significantly stronger in the UK than in the UAE. This phenomenon is explained in the discussion section.Research limitations/implicationsAlthough several studies have indicated several other elements for EBBE, such as brand commitment and brand citizen behavior, the authors borrowed Kinget al.’s (2012) EBBE concept and limited their variables on EBBE for brand endorsement, brand allegiance and brand consistent behavior.Practical implicationsKnowledge is expanded through an empirical study validating the proposed model, which provides meaningful insights for developing training tools for internal brand management. Firms have to increase the brand manager’s commitment to increase the employee brand equity, which in turn increases the firm’s performance.Originality/valueThis paper makes three imperative contributions to the branding literature: expanding the existing brand equity literature to incorporate employee brand equity; being the first known empirically tested PEU on employee brand equity; and empirically testing employee brand equity, which has been ignored in branding literature on firm performance.
Validating a scale to measure consumer’s luxury brand aspiration
Authors: S. Sreejesh , Sarkar Abhigyan , Roy Subhadip 
Published: August 2016

Purpose
The purpose of this study was to conceptualize consumer’s luxury brand aspiration and develop a psychometrically reliable scale to measure the construct. This study aims to extend the existing research in luxury branding domain through validating a scale to measure consumer’s luxury brand aspiration.

Design/methodology/approach
Initially, the dimensions of consumer’s luxury brand aspiration were identified through prior literature review and qualitative investigations. This was followed by a series of scale development studies suggested by Churchill (1979).

Findings
The results supported that the second-order measure of consumer’s luxury brand aspiration consist of four related first-order dimensions, namely, identity signaling, social recognition, self-esteem and achievement signaling. Luxury brand aspiration was found to have direct positive influences on brand commitment and brand attachment. Brand commitment and attachment in turn significantly influence intention to pay price premium.

Originality/value
Value of this research article lies in validating a scale to measure individual’s luxury brand aspiration for the first time in branding literature.
The impact of employee work perceptions on purchase intentions from a company store
Authors: Bodkin Charles D. , Peters Cara , Thomas Jane 
Published: August 2016

Purpose
Company stores market to their internal employees via the distribution of branded promotional products. The purpose of this study is to investigate factors that may influence when an employee is more likely to purchase from a company store.

Design/methodology/approach
A survey was administered to the members of a chamber of commerce located in the southeastern USA. Data were analyzed using regression, and post hoc analyses were conducted using an analysis of covariance.

Findings
Organizational identification and job satisfaction significantly impacted employees’ intentions to purchase from a company store. Gender, education, marital status and years of work experience were personal factors that moderated that relationship. Firm size and employee rank were company factors that moderated the relationship between employee work perceptions and employee purchase intentions at a company store.

Originality/value
No research to date exists on company stores. This study is unique in that it proposes internal branding as a theoretical foundation for understanding company stores and examines factors that impact employees’ intentions to purchase from a company store.
Differential aphid toxicity to ladybeetles is not a function of host plant or facultative bacterial symbionts
Authors: White Jennifer A. , McCord Joshua S. , Jackson Kelly A. , Dehnel Allison C. , Lenhart Paul A. 
Published: August 2016

Summary

Herbivores often defend themselves from predation by transmitting toxic plant‐produced chemicals to their enemies. Polyphagous herbivores sometimes exhibit differential toxicity when found on various host plant species, which is generally assumed to reflect variation in plant chemistry.

Here, however, we provide evidence that host‐associated herbivore lineages can intrinsically differ in their toxic properties. Lineages of Aphis craccivora originating from black locust (Robinia pseudoacacia) are unsuitable food for the ladybeetle Harmonia axyridis, resulting in death of both larvae and adults, whereas aphid lineages originating from alfalfa (Medicago sativa) support larval development and adult reproduction. We show that locust‐origin aphids remain toxic and alfalfa‐origin aphids remain non‐toxic when reared on any of three legume plants (fava, alfalfa or locust).

Furthermore, toxicity is not a function of the facultative bacterial symbiont Arsenophonus, which is naturally present in locust‐origin aphid lineages and facilitates aphid use of locust. Experimentally cured locust‐origin lineages remain toxic, and an experimentally transinfected alfalfa‐origin lineage remains non‐toxic to H. axyridis.

Instead, Arsenophonus plays an indirect role in the distribution of toxic aphid lineages by facilitating aphid use of locust. It is the parthenogenetic coinheritance of Arsenophonus and the toxic trait that observationally correlates locust‐feeding with toxicity in A. craccivora, rather than host plant chemistry per se.

Our results clearly demonstrate that aphid lineages intrinsically vary in their toxic properties in a way that neither plant chemistry nor bacterial symbionts can explain. A more inclusive paradigm is needed for understanding variation in herbivore defence against predators.
Relationship between cladoceran (Crustacea) functional diversity and lake trophic gradients
Authors: Nevalainen Liisa , Luoto Tomi P. 
Published: August 2016

Summary

Functional diversity (FD) as a biodiversity measure has an explicit role in ecosystem functioning because the effects of environmental changes in ecosystems are determined by biological functions, such as feeding type and trophic position, of particular species.

We evaluated the usability of functional characterization and FD of an aquatic keystone group (Crustacea: Cladocera) for enhancing the understanding of long‐term lake functional responses to environmental changes. The aims were to separate ecologically significant functional groups, investigate succession of such functional groups during nutrient enrichment process and determine the relationship between FD and lake productivity using a palaeolimnological approach.

We selected two eutrophicated study lakes from southern Finland for down‐core investigations, one with a centennial (past c. 350 years) and the other with a decadal (past c. 70 years) nutrient enrichment record. Cladoceran microfossils in the sediment cores were used to determine the taxonomic structure of the past communities. Ecologically relevant functional characteristics were determined to separate functional groups by utilizing a functional dendrogram and a weighted community‐based FD index together with a set of multidimensional FD indices. The indices were applied to the down‐core assemblages.

The functional dendrogram separated cladocerans into functional groups where habitat type principally separated open‐water filterers and predators from epibenthic scrapers and detritivores. Further separation in the pelagic branch was based on body size and feeding and among the benthic branch body shape.

Functional assemblages changed markedly during the nutrient enrichment process. In the early stage of eutrophication, the largest functional changes were caused by small planktonic filterers and predators. Small filterers and epibenthos responded strongest during the eutrophic–hypereutrophic succession. FD had a positive long‐term relationship with lake trophic status until eutrophic conditions that was likely caused by diversifying resources and versatile food webs. Under hypereutrophic conditions, and especially at a decadal temporal resolution, alternating predation regimes caused variance to FD.

In the current records, cladoceran FD was positively related to lake productivity and bottom‐up controls during the early stages of eutrophication in the long‐term record but top‐down controls apparently were more important at a decadal scale and under hypereutrophic conditions.