bluuebunny/crossref_metadata_2025 huggingface dataset:
Improved long read correction for denovoassembly using an FM-index
Authors: Holt James M. , Wang Jeremy R. , Jones Corbin D. , McMillan Leonard
Published: August 2016

1

Long read sequencing is changing the landscape of genomic research, especiallyde novoassembly. Despite the high error rate inherent to long read technologies, increased read lengths dramatically improve the continuity and accuracy of genome assemblies. However, the cost and throughput of these technologies limits their application to complex genomes. One solution is to decrease the cost and time to assemble novel genomes by leveraging “hybrid” assemblies that use long reads for scaffolding and short reads for accuracy. To this end, we describe a novel application of a multi-string Burrows-Wheeler Transform with auxiliary FM-index to correct errors in long read sequences using a set of complementary short reads. We show that our method efficiently produces significantly higher quality corrected sequence than existing hybrid error-correction methods. We demonstrate the effectiveness of our method compared to state-of-the-art hybrid and long-read onlyde novoassembly methods.
A Scalable Data Access Layer to Manage Structured Heterogeneous Biomedical Data
Authors: Delussu Giovanni , Lianas Luca , Frexia Francesca , Zanetti Gianluigi
Published: August 2016

This work presents a scalable data access layer, called PyEHR, intended for building data management systems for secondary use of structured heterogeneous biomedical and clinical data. PyEHR adopts openEHR formalisms to guarantee the decoupling of data descriptions from implementation details and exploits structures indexing to speed up searches. The persistence is guarantee by a driver layer with a common driver interface. Presently, are implemented the interfaces with two NoSQL DBMS: MongoDB and Elasticsearch. The scalability of PyEHR has been evaluated experimentally through two types of tests, namely constant load and constant number of records, with queries of increasing complexity on a two synthetic datasets of ten millions records each, containing very complex openEHR archetype structures, distributed on up to ten working nodes.
NUCLEAR FACTOR Y, subunit C (NF-YC) transcription factors are positive regulators of photomorphogenesis inArabidopsis thaliana
Authors: Myers Zachary A. , Kumimoto Roderick W. , Siriwardana Chamindika L. , Gayler Krystal K. , Risinger Jan R. , Pezzetta Daniela , Holt Ben F.
Published: August 2016

Recent reports suggested that NF-Y transcription factors are positive regulators of skotomorphogenesis inArabidopsis thaliana. ThreeNF-YCgenes (NF-YC3, NF-YC4, andNF-YC9) are known to have overlapping functions in photoperiod dependent flowering and previous studies demonstrated that they interact with basic leucine zipper (bZIP) transcription factors. This included ELONGATED HYPOCOTYL 5 (HY5), which has well-demonstrated roles in photomorphogenesis. Similar tohy5mutants, we report thatnf-yc3 nf-yc4 nf-yc9triple mutants failed to inhibit hypocotyl elongation in all tested light wavelengths. Surprisingly,nf-yc3 nf-yc4 nf-yc9 hy5mutants had synergistic defects in light perception, suggesting that NF-Ys represent a parallel light signaling pathway. As with other photomorphogenic transcription factors,nf-yc3 nf-yc4 nf-yc9triple mutants also partially suppress the short hypocotyl and dwarf rosette phenotypes of CONSTITUTIVE PHOTOMORPHOGENIC 1 (cop1) mutants. Thus, our data strongly suggest that NF-Y transcription factors have important roles as positive regulators of photomorphogenesis, and in conjunction with other recent reports implies that the NF-Y are multifaceted regulators of early seedling development.

Author Summary

Light perception is critically important for the fitness of plants in both natural and agricultural settings. Plants not only use light for photosynthesis, but also as a cue for proper development. As a seedling emerges from soil it must determine the light environment and adopt an appropriate growth habit. When blue and red wavelengths are the dominant sources of light, plants will undergo photomorphogenesis. Photomorphogenesis describes a number of developmental responses initiated by light in a seedling, and includes shortened stems and establishing the ability to photosynthesize. The genes regulating photomorphogenesis have been studied extensively, but a complete picture remains elusive. Here we describe the finding that NUCLEAR FACTOR-Y (NF-Y) genes are positive regulators of photomorphogenesis - i.e., in plants where NF-Y genes are mutated, they display some characteristics of dark grown plants, even though they are in the light. Our data suggests that the roles of NF-Y genes in light perception do not fit in easily with those of other described pathways. Thus, studying these genes promises to help develop a more complete picture of how light drives plant development.
Cancer treatment scheduling and dynamic heterogeneity in social dilemmas of tumour acidity and vasculature
Authors: Kaznatcheev Artem , Velde Robert Vander , Scott Jacob G. , Basanta David
Published: August 2016

Background

Tumours are diverse ecosystems with persistent heterogeneity in various cancer hallmarks like self-sufficiency of growth factor production for angiogenesis and reprogramming of energy-metabolism for aerobic glycolysis. This heterogeneity has consequences for diagnosis, treatment, and disease progression.

Methods

We introduce the double goods game to study the dynamics of these traits using evolutionary game theory. We model glycolytic acid production as a public good for all tumour cells and oxygen from vascularization via VEGF production as a club good benefiting non-glycolytic tumour cells. This results in three viable phenotypic strategies: glycolytic, angiogenic, and aerobic non-angiogenic.

Results

We classify the dynamics into three qualitatively distinct regimes: (1) fully glycolytic, (2) fully angiogenic, or (3) polyclonal in all three cell types. The third regime allows for dynamic heterogeneity even with linear goods, something that was not possible in prior public good models that considered glycolysis or growth-factor production in isolation.

Conclusion

The cyclic dynamics of the polyclonal regime stress the importance of timing for antiglycolysis treatments like lonidamine. The existence of qualitatively different dynamic regimes highlights the order effects of treatments. In particular, we consider the potential of vascular renormalization as a neoadjuvant therapy before follow up with interventions like buffer therapy.
Intrinsic K-Ras dynamics: A novel molecular dynamics data analysis method shows causality between residue pairs
Authors: Vatansever Sezen , Gümüş Zeynep H. , Erman Burak
Published: August 2016

While mutant K-Ras is an important therapeutic target for human cancers, there are still no drugs that directly target it. Recent promising studies emphasize the significance of dynamics data to selectively target its active/inactive states. However, despite tremendous information on K-Ras, the direction of information flow in the allosteric regulation of its dynamics has not yet been elucidated. Here, we present a novel approach that identifies causality in correlated motions of proteins and apply it to K-Ras dynamics. Specifically, we analyze molecular dynamics simulations data and comprehensively investigate nucleotide-dependent intrinsic K-Ras activity. We show that GTP binding leads to characteristic residue correlations with relatively long decay times by stabilizing K-Ras motions. Furthermore, we identify for the first time driver-follower relationships of correlated motions in the regulation of K-Ras activity. Our results can be utilized for directly targeting mutant K-Ras in future studies.
Evolutionary Fates and Dynamic Functionalization of Young Duplicate Genes in Arabidopsis Genomes
Authors: Wang Jun , Tao Feng , Marowsky Nicholas C. , Fan Chuanzhu
Published: August 2016

Gene duplication is a primary means to generate genomic novelties, playing an essential role in speciation and adaptation. Particularly in plants, a high abundance of duplicate genes has been maintained for significantly long periods of evolutionary time. To address the manner in which young duplicate genes were derived primarily from small-scale gene duplication and preserved in plant genomes and to determine the underlying driving mechanisms, we generated transcriptomes to produce the expression profiles of five tissues in Arabidopsis thaliana and the closely related species Arabidopsis lyrata and Capsella rubella. Based on the quantitative analysis metrics, we investigated the evolutionary processes of young duplicate genes in Arabidopsis. We determined that conservation, neofunctionalization, and specialization are three main evolutionary processes for Arabidopsis young duplicate genes. We explicitly demonstrated the dynamic functionalization of duplicate genes along the evolutionary time scale. Upon origination, duplicates tend to maintain their ancestral functions; but as they survive longer, they might be likely to develop distinct and novel functions. The temporal evolutionary processes and functionalization of plant duplicate genes are associated with their ancestral functions, dynamic DNA methylation levels, and histone modification abundances. Furthermore, duplicate genes tend to be initially expressed in pollen and then to gain more interaction partners over time. Altogether, our study provides novel insights into the dynamic retention processes of young duplicate genes in plant genomes.
Surveying innovation in samples of individual end consumers
Authors: de Jong Jeroen P.J.
Published: August 2016

Purpose

– Rather than businesses, individual end consumers may develop innovations for themselves. Innovating consumers generally do not protect their innovations with intellectual property rights and may be generally available – a phenomenon recently coined as “free innovation” (von Hippel, 2016). The purpose of this paper is to take stock of how innovation by individual consumers has been measured, and to propose a survey procedure for future studies of consumer innovation.

Design/methodology/approach

– The author provides a literature review of how innovation by individual end consumers has been measured, and reports on a pilot study conducted in Finland to improve and standardize the measurement of consumer innovation.

Findings

– The survey procedure includes up to six steps which can be tailored to specific research purposes.

Originality/value

– The procedure will enable better international/cross-study comparisons and an efficient collection of data.
Modelling student satisfaction and motivation in the integrated educational environment
Authors: Stukalina Yulia
Published: August 2016

Purpose

– The purpose of this paper is to explore some issues related to enhancing the quality of educational services provided by a university in the agenda of integrating quality assurance activities and strategic management procedures.

Design/methodology/approach

– Employing multiple regression analysis the author has examined some factors that are supposed to have an impact on student satisfaction and student motivation in the integrated educational environment.

Findings

– The results of the two-phase empirical research performed in two higher education institutions indicate that student satisfaction and student motivation can be modelled on a number of predictors, which are associated with several indicators related to various aspects of the integrated educational environment.

Research limitations/implications

– The sample in this study included two higher education institutions. Future study with a more diverse student population and the refined scale items is recommended to verify and generalize the findings.

Practical implications

– The research provides useful data for addressing some critical issues in the context of integrating quality assurance activities and strategic management procedures in a university. The results of the empirical study suggest that education managers might carry out regular assessment of their educational environment in the framework of performing strategic analysis, which is aimed at quality enhancement, in order to determine the most significant aspects and associated influences. This would allow them to focus their efforts, time and resources on the issues with the greatest potential for having an impact on the university’s operations, and which may be related to providing qualitative changes in the educational environment in the frame of implementing a number of competitive strategies.

Originality/value

– The relevant literature analysis has allowed the author to explore the research topic from a new (holistic) perspective, and to consider both student satisfaction and student motivation in the integrated educational environment, which was viewed as a complicated multi-level system. In this respect, being related to approaches, ideas and findings in the existing literature, the paper presents an attempt to develop these further in terms of adding value to previous research. The obtained information can be of interest to managers working in the area of higher education.
Exploring academics’ approaches to managing team assessment
Authors: Augar Naomi , Woodley Carolyn J , Whitefield Despina , Winchester Maxwell
Published: August 2016

Purpose

– The purpose of this paper is to develop an understanding of academics’ approaches to managing team assessment at an Australian University with a view to informing policy development and assessment design.

Design/methodology/approach

– The research was conducted using a single exploratory case study approach focussing on the team assessment approach of academics teaching in two colleges at an Australian University. A desktop audit of publicly available assessment policy from 38 Australian universities was conducted alongside a review of relevant college subject guides. The findings of this review framed a subsequent focus group and online survey of academic staff.

Findings

– Results suggest that staff have adopted highly diverse and idiosyncratic approaches to team assessment and have mixed views about varied approaches to managing and assessing teamwork. Findings identify a need for explicit guidance and professional development on designing, managing and grading team assessments. Institutional limits and criteria should be introduced to ensure a whole-of-course approach to developing teamwork skills and ensure students are not burdened with an excessive number of team assessment tasks in a degree.

Research limitations/implications

– The paper reports results from an exploratory case study at a single Australian University. As such, the results are not generalizable.

Practical implications

– The findings could inform guidelines, policies or support resources for designing team assessment tasks.

Originality/value

– The research explores a challenging area for academics: team assessment, which the research indicates is not currently adequately managed through university policy and procedure. The findings highlight options for universities to consider when developing policies and procedures to manage team assessment. The study also provides recommendations for academics to consider when developing and managing team assessment.
School discipline, school uniforms and academic performance
Authors: Baumann Chris , Krskova Hana
Published: August 2016

Purpose

– The purpose of this paper is to examine the role of school discipline in achieving academic performance. The study aims to clarify the role of permissive vis-à-vis authoritative teaching styles with an overarching hypothesis that better discipline leads to better academic performance. The authors also probe whether uniformed students have better discipline.

Design/methodology/approach

– The authors analyse Organisation for Economic Co-operation and Development’s Programme for International Student Assessment data on school discipline dimensions: students listening well, noise levels, teacher waiting time, students working well, class start time. Analysis of variance (ANOVA) with post hoc analysis on five geographic groups established by Baumann and Winzar (2016) was applied to test for geographic differences (Europe, Americas, Far East Asia, Rest of Asia, Anglo-Saxon cluster) in school discipline. ANOVA was further used to test for school discipline and academic performance. Third, t-tests on five discipline dimensions were run to test for differences between students who wear uniforms and those who do not.

Findings

– The results demonstrate differences in school discipline across five geographic clusters, with East Asia leading the way. The authors demonstrate significant differences in discipline for low, medium and high performing students. Peak-performing students have the highest level of discipline. Students wearing a uniform listen better with lower teacher waiting times.

Originality/value

– Students peak perform when teachers create a disciplined atmosphere where students listen to teachers, where noise levels in the classroom are low and they do not have to wait to start class and teach. Good discipline allows students to work well and this ultimately leads to better academic performance. Uniforms contribute to better discipline in everyday school operations. The findings support that in general, implementing school uniforms at schools might enhance discipline and allow for better learning. The authors recommend keeping uniforms where they are already used and to consider introducing uniforms where they are not yet common.
Beyond the marginalization thesis
Authors: Williams Colin C , Horodnic Ioana Alexandra
Published: August 2016

Purpose

– Grounded in an emergent recognition that those people in formal employment conduct the vast majority of work in the shadow economy, the purpose of this paper is to evaluate for the first time the degree to which shadow work is conducted by those in formal jobs and the characteristics of those in formal employment who participate in the shadow economy.

Design/methodology/approach

– To do this, the authors report a 2007 survey of participation in the shadow economy involving 26,659 face-to-face interviews conducted in 27 European Union (EU) member states.

Findings

– The finding is that in the EU, the formally employed undertake a disproportionate share of work in the shadow economy. Analysing the characteristics of the employed most likely to work in the shadow economy, however, it is those who benefit least from the formal economy, namely, younger unmarried men and on lower incomes living in rural areas, working in the construction sector and in small firms.

Research limitations/implications

– The outcome is a tentative call for recognition that although people in formal employment conduct the vast majority of work in the shadow economy, these are mostly particular vulnerable and weaker groups of the formally employed. Whether similar findings prevail at other spatial scales and in other global regions now needs investigating.

Practical implications

– This survey displays the need for policy not to target the unemployed but particular groups of the formally employed.

Originality/value

– The first extensive evaluation of the extent to which shadow work is conducted by those in formal jobs and the characteristics of those in formal employment who participate in the shadow economy.
Integrated care transitions: emergency to primary health care
Authors: Day Carolina Baltar , Witt Regina Rigatto , Oelke Nelly D
Published: August 2016

Purpose

– The purpose of this paper is to focus on the Integrated Care Transitions Project between the emergency department (ED) of a university hospital and primary health care (PHC) services in a large city in Southern Brazil was the focus of this study. Care transitions occurred through telephone contact for patients discharged from the ED to PHC.

Design/methodology/approach

– This descriptive, exploratory qualitative research collected data via semi-structured interviews (n=14) including interns of health disciplines, advisors for interns, nurses, and physicians from the ED and PHC Family Unit. A thematic analysis of the data were conducted.

Findings

– ED providers felt they gained increased knowledge of the care networks available for patients in the community. Connection between the providers in ED and PHC facilitated confidence in the services provided in the community and increased continuity of care for patients’ needs. The PHC providers recognized integration promoted communication and better care planning for patients discharged from ED. Integrated care made the work in the PHC easier and benefited the users.

Research limitations/implications

– The study evaluated a program available in one hospital. Generalizability may be limited as services in the ED were provided by professional residents and their advisors, not employees of the hospital.

Practical implications

– Shared information by different health services leads to better care for patients and greater job satisfaction for providers.

Originality/value

– Care transitions are not well-managed in health care; there is limited research focusing on care transitions from ED to community. For providers and patients, this program assisted in building capacity and networks for transitions in care.
Ba virtual and inter-organizational evolution: a case study from a EU research project
Authors: Bartolacci Chiara , Cristalli Cristina , Isidori Daniela , Niccolini Federico
Published: August 2016

Purpose

Taking Nonaka’s SECI model as the main reference, this paper aims to offer reflections on the virtual evolution of ba, the places for knowledge creation. Indeed, looking at the current scenario, widening the knowledge spiral to the inter-organizational epistemological level is inevitable. To this aim, information technology tools and virtual communities can establish effective interactions to exchange knowledge, making ba evolve congruently.

Design/methodology/approach

The paper takes the exemplary case of a platform developed during a European research project called “BIVEE: Business Innovation in Virtual Enterprise Environments”. The investigative approach chosen is participatory action research (PAR), with two researchers conducting PAR in real time, and two others involved ex post.

Findings

The paper shows that the virtual evolution of ba can lead the SECI model towards an inter-organizational level. Moreover, through a learning history, it describes how all the phases of the SECI process, even the Socialization one, can take place or be supported in virtual spaces.

Research limitations/implications

Taking into account just one single exemplary case study provides a rich, contextualized understanding of phenomena, while allowing only some theoretical generalizations.

Originality/value

This paper contextualizes the SECI model within a Web platform for open innovation, to investigate whether the knowledge creation process can take place entirely within a virtual environment linking subjects from different organizations. In so doing, it applies the SECI model to the phases of the innovation process, called waves.
Innovation in service ecosystems
Authors: Aal Kotaiba , Di Pietro Laura , Edvardsson Bo , Renzi Maria Francesca , Guglielmetti Mugion Roberta
Published: August 2016

Purpose

– The purpose of this paper is to extend the understanding of innovation in service ecosystems by focussing on the role of values resonance in relation to the integration of brands, service systems and experience rooms.

Design/methodology/approach

– An empirical, explorative case study of an innovative service system is carried out using a narrative approach and presented in the form of a saga.

Findings

– Insights gleaned from the empirical study are used for conceptual developments. Analysis of the empirical case study is presented as four lessons linked to values, brands, service systems and experience rooms.

Originality/value

– The paper extends a conceptual framework of innovative resource integration in service ecosystems. The paper also contributes four propositions to inform theory: values resonance is a basis for service innovation, the innovative integration of brands based on values resonance can foster innovation, the integration of resources across service system boundaries grounded in values resonance can enable innovation and the integration of experience rooms into a coherent servicescape based on values resonance can support novel forms of resource integration and value co-creation efforts in service ecosystems.
Perceived prevalence and personal impact of negative online reviews
Authors: Bradley Graham L. , Sparks Beverley A. , Weber Karin
Published: August 2016

Purpose

– Technological advancement and growth in social media have meant that customers are increasingly using the internet to write a review or express opinions about products and services. Many of these online reviews are critical of service organizations and workers. The purpose of this paper is to document the experiences that service industry personnel have of negatively valenced, customer-authored, online reviews, the personal impact of these reviews, and the manner in which participants respond emotionally and behaviorally to these reviews.

Design/methodology/approach

– This research drew on the stress, coping, and service literature, with particular emphasis on stress appraisal theory. The study involved the completion of an anonymous online questionnaire by 421 restaurant owners, managers, and employees.

Findings

– Many respondents reported feelings of anger and use of maladaptive coping strategies in response to negative online reviews (NORs). Smaller numbers reported feelings of embarrassment and guilt, and thoughts of leaving the industry. Factors pertaining to respondents’ online review exposure, emotional responses, and coping strategies predicted the effects of negative reviews on thoughts of exiting current employment.

Research limitations/implications

– The findings have implications for protecting worker well-being and job tenure in an industry deeply affected by electronic word-of-mouth. Replication is recommended using a longitudinal design and more objective data obtained from validated instruments and independent sources.

Originality/value

– This survey provides the first known evidence of the personal impact of NORs on business owners, managers, and employees.
Explaining social exchanges in information-based online communities (IBOCs)
Authors: Benoit (née Moeller) Sabine , Bilstein Nicola , Hogreve Jens , Sichtmann Christina
Published: August 2016

Purpose

– The purpose of this paper is to scrutinize platforms for members to exchange information by information-based online communities (IBOCs, like LinkedIn or Facebook). Because member participation is vital for IBOCs, this research aims to identify and validate factors that drive member participation.

Design/methodology/approach

– With reference to social exchange theory the authors developed a model of antecedents of participation in IBOCs that was tested with survey data using PLS. Because some of the results contradicted the theory, the authors examined those results in a mainly qualitative study with online community providers. These experts offered explanations that inform the discussion and managerial implications.

Findings

– Role clarity, provider’s responsiveness, and enjoyment all influence member participation. Contrary to theory, the cooperation of other members affects member participation negatively while a member’s ability shows no effect.

Practical implications

– This research has several implications for IBOC providers. Because ability does not affect participation directly, providers do not need to worry about lacking ability and can effectively target all potential members. The importance of provider responsiveness signals that IBOC providers should proactively monitor members’ compliance with social norms to lower the social risk for members. The impact of community-specific knowledge and enjoyment on participation puts emphasis on careful community design and the thoughtful implementation of new features that might enhance enjoyment, but reduce role clarity.

Originality/value

– Whereas most of the participation literature focusses on a dyadic relationship, the research investigates the triadic relationship in which the provider is only an enabler of exchange. Furthermore, the authors bring together two streams of the literature: the participation literature, which tends to focus on offline participation; and the online community literature, which has not yet investigated participation. This is also the first paper to investigate nonlinear effects on participation.
Engineering social media driven intelligent systems through crowdsourcing
Authors: Sykora Martin
Published: August 2016

Purpose

The purpose of this paper is to explore implicit crowdsourcing, leveraging social media in real-time scenarios for intelligent systems.

Design/methodology/approach

A case study using an illustrative example system, which systematically used a custom social media platform for automated financial news analysis and summarisation was developed, evaluated and discussed. Literature review related to crowdsourcing and collective intelligence in intelligent systems was also conducted to provide context and to further explore the case study.

Findings

It was shown how, and that useful intelligent systems can be constructed from appropriately engineered custom social media platforms which are integrated with intelligent automated processes. A recent inter-rater agreement measure for evaluating quality of implicit crowd contributions was also explored and found to be of value.

Practical implications

This paper argues that when social media platforms are closely integrated with other automated processes into a single system, this may provide a highly worthwhile online and real-time approach to intelligent systems through implicit crowdsourcing. Key practical issues, such as achieving high-quality crowd contributions, challenges of efficient workflows and real-time crowd integration into intelligent systems, were discussed. Important ethical and related considerations were also covered.

Originality/value

A contribution to existing theory was made by proposing how social media Web platforms may benefit crowdsourcing. As opposed to traditional crowdsourcing platforms, the presented approach and example system has a set of social elements that encourages implicit crowdsourcing. Instances of crowdsourcing with existing social media, such as Twitter, often also called crowd piggybacking, have been used in the past; however, using an entirely custom-built social media system for implicit crowdsourcing is relatively novel and has several advantages. Some of the discussion in context of intelligent systems construction are novel and contribute to the existing body of literature in this field.
Remarkable lives: Jen Waring in conversation with Jerome Carson
Authors: Waring Jen , Carson Jerome
Published: August 2016

Purpose

– The purpose of this paper is to provide a profile of Jen Waring.

Design/methodology/approach

– Jen provides a short biographical description of her life. She is then interviewed by Jerome.

Findings

– Jen talks about her long battle with mental health problems and what has sustained her over this time. She talks about the crucial importance of support from both loved ones and professionals, as well as medication.

Research limitations/implications

– Single case studies are of course just one person’s story. Given Jen is an academic biologist, she not only has a unique way of looking at mental illness, she can see the potential of developing approaches in the biological understanding for people experiencing mental distress.

Practical implications

– Jen’s account shows the need for long-term support for more severe mental health problems. There are no quick fixes! It also highlights the need for interventions at biological, psychological and social levels.

Social implications

– People need “somewhere to live, someone to love and something meaningful to do” (Rachel Perkins). Many sufferers do not have all three. Services may only be able to provide two of these.

Originality/value

– Accounts of mental illness recovery by academics can often provide the authors with amazing insights into the world of the mentally distressed. They can also serve as an inspiration to the many students who experience mental distress.
Understanding library users’ preferences and expectations of online help
Authors: Zhang Tao , Stonebraker Ilana , Promann Marlen
Published: August 2016

Purpose

Online help and tutorials are an important part of library services, yet they are often studied in specific contexts and disciplines like subject-specific research guides. The objective of this study was to examine users’ common preferences and expectations of library help channels in general and online help in particular.

Design/methodology/approach

The authors conducted a qualitative survey with 45 library users. The survey asked users how they seek library help, their preferences and expectations of online help, content format and general help channels and later, a content analysis of survey responses was performed.

Findings

Results showed that survey participants have different prioritizations of library help channels. Half of the respondents preferred conceptual help that emphasizes concepts and underlying principles, while the other half preferred procedural (step-by-step) help or mixed. The survey also indicated reliance by participants on expert help, even when online help was available.

Originality/value

Based on the results, the authors identified users’ behavioral preferences, attitudes and expectations toward library help channels and online help content. They also discussed the unique challenge of creating online help for libraries, as users have a dynamic range of help-seeking preferences and mixed expectations of help content depending on the context.
OPRM1 genotype interacts with serotonin system dysfunction to predict alcohol‐heightened aggression in primates
Authors: Driscoll Carlos A , Lindell Stephen G. , Schwandt Melanie L , Suomi Stephen J , Higley J Dee , Heilig Markus , Barr Christina S
Published: August 2016

Although the notion that alcohol promotes violence is widespread, not all individuals are aggressive while intoxicated. Genetic variation could be a contributing factor to individual differences in alcohol‐heightened aggression. The present study examines the effects of OPRM1C77G genotype on responses to threat in rhesus macaques under normal conditions and following alcohol administration. Prior studies have shown that a low CSF level of 5‐HIAA is a trait marker for individuals prone to escalated aggression. We wanted to examine whether the predictive value for this marker on aggression was moderated by OPRM1 genotype. Animals were administered alcohol (BAC 100–200 mg%), were provoked by a human intruder, and aggressive responses were recorded. Factor analysis was performed to generate aggressive response factors, which were then used as dependent variables for ANOVA, with OPRM1 genotype and CSF 5‐HIAA as independent variables. Factor analysis generated three factors (‘Threatening’, ‘Distance Decreasing’ and ‘High Intensity’). We found that High Intensity aggression was increased among carriers of the OPRM1 G allele, especially among individuals with low CSF levels of 5‐HIAA. Aggression in the non‐intoxicated state was predicted by 5‐HIAA, but not by genotype. This study demonstrates that OPRM1 genotype predicts alcohol‐heightened aggression in rhesus macaques with low CSF levels of 5‐HIAA. Because OPRM1 variation predicts similar effects on alcohol response and behavior in humans and macaques, this study could suggest a role for OPRM1 genotype in alcohol‐heightened aggression in humans. If so, it may be that compounds that block this receptor could reduce alcohol‐associated violence in selected patient populations.
Intravenous self‐administration of alcohol in rats—problems with translation to humans
Authors: Lê Anh D. , Kalant Harold
Published: August 2016

Alcohol is consumed orally by humans, and oral self‐administration has been successfully modeled in laboratory animals. Over the last several years, attempts have been made to develop a procedure for the reliable intravenous (IV) self‐administration of alcohol in rodents. IV self‐administration would provide a better tool for investigating neurobiological mechanisms of alcohol reinforcement and dependence because confounding factors associated with oral self‐administration, such as variations in orosensory sensitivity to alcohol and/or its absorption, are avoided. A review of the literature shows that rats, mice and non‐human primates can initiate and maintain IV self‐administration of alcohol. However, there are 50‐ to 100‐fold interspecies differences in the reported alcohol infusion doses required. Most surprising is that the infusion dose (1–2 mg/kg) that reliably maintains IV alcohol self‐administration in rats results in total alcohol intakes of only 20–25 mg/kg/hour, which are unlikely to have significant pharmacological effects. The evidence to support IV self‐administration of such low doses of alcohol in rats as well as the potential biological mechanisms underlying such self‐administration are discussed. The minute amounts of alcohol shown to reliably maintain IV self‐administration behavior in rats challenge the relationship between their blood alcohol levels and the rewarding and reinforcing effects of alcohol.
Variation in plant functional traits across and within four species of Western Australian Banksia (Proteaceae) along a natural climate gradient
Authors: Cochrane Anne , Hoyle Gemma L. , Yates Colin J. , Neeman Teresa , Nicotra Adrienne B.
Published: August 2016

Plant traits are fundamental components of the ecological strategies of plants, relating to how plants acquire and use resources. Their study provides insight into the dynamics of species geographical ranges in changing environments. Here, we assessed the variation in trait values at contrasting points along an environmental gradient to provide insight into the flexibility of species response to environmental heterogeneity. Firstly, we identified how commonly measured functional traits of four congeneric species (Banksia baxteri, B. coccinea, B. media and B. quercifolia) varied along a longitudinal gradient in the South Western Australian Floristic Region. This regional gradient provides significant variation in moisture, temperature and soil nutrients: soil nitrogen content decreases with declining rainfall and increasing temperature. We hypothesized that (i) the regional pattern in trait–environment associations across the species would match those observed on a global scale and (ii) that the direction and slopes of the within‐species relationships would be similar to those across species for each of the measured traits. Along the regional gradient we observed strong shifts in trait values, and cross‐species relationships followed the expected trend: specific leaf area was significantly lower, and leaf Narea and seed dry mass significantly higher, at the drier end of the rainfall gradient. However, traits within species were generally not well correlated with habitat factors: we found weak patterns among populations, either due to the small ecological gradient or perhaps because fine‐scale structuring among populations (at a micro‐evolutionary scale) was low due to high gene flow within species. Understanding how species traits shift as a result of climatic influences, both at the regional (across species) and local (within species) scale, provides insight into plant adaptation to the environment. Such studies have important applications for conservation biology and population management in the face of global change.
Serum cell death biomarker mirrors liver cancer regression after transarterial chemoembolisation
Authors: Bock B. , Hasdemir D. , Wandrer F. , Rodt T. , Manns M. P. , Schulze‐Osthoff K. , Bantel H.
Published: August 2016

Background

Hepatocellular carcinoma (HCC) represents an increasing health problem with limited therapeutic options. In patients with intermediate disease stage, transarterial chemoembolisation (TACE) is widely applied. Treatment response is routinely assessed by imaging techniques according to the international response evaluation criteria in solid tumours (RECIST), which consider tumour regression or additionally tumour necrosis (modified RECIST). Evaluation of treatment response, however, by these methods is time‐ and cost‐intensive and usually performed at earliest several months following TACE.

Aim

To investigate the suitability of novel non‐invasive cell death biomarkers for an earlier prediction of TACE response.

Methods

We analysed activation of pro‐apoptotic caspases and the proteolytic cleavage of the caspase substrate CK‐18 in liver tissues and sera from HCC patients by immunohistochemistry, a luminometric substrate assay and ELISA.

Results

Both caspase activity and caspase‐cleaved CK‐18 fragments were elevated in HCC patients compared to healthy controls. CK‐18 serum levels significantly increased during the first 3 days and peaked at day two following TACE. Interestingly, we found significant differences in CK‐18 levels between patients with and without tumour regression. Detection of CK‐18 fragments revealed a promising performance for the early prediction of TACE response with an area under the curve value of 0.76.

Conclusions

Caspase‐cleaved CK‐18 levels mirror liver cancer regression and allow an earlier prediction of TACE response. The concordance with mRECIST suggests that the detection of CK‐18 levels immediately after TACE might be used as a short‐term decision guide to continue or change HCC therapy.
Sexual objectification in women's daily lives: A smartphone ecological momentary assessment study
Authors: Holland Elise , Koval Peter , Stratemeyer Michelle , Thomson Fiona , Haslam Nick
Published: August 2016

Sexual objectification, particularly of young women, is highly prevalent in modern industrialized societies. Although there is plenty of experimental and cross‐sectional research on objectification, prospective studies investigating the prevalence and psychological impact of objectifying events in daily life are scarce. We used ecological momentary assessment to track the occurrence of objectifying events over 1 week in the daily lives of young women (N = 81). Participants reported being targeted by a sexually objectifying event – most often the objectifying gaze – approximately once every 2 days and reported witnessing sexual objectification of others approximately 1.35 times per day. Further, multilevel linear regression analyses showed that being targeted by sexual objectification was associated with a substantial increase in state self‐objectification. Overall, individual differences had little impact in moderating these effects.
Synsedimentary broken‐foreland tectonics during the Paleogene in the Andes of NW Argentine: new evidence from regional to centimetre‐scale deformation features
Authors: Montero‐López Carolina , del Papa Cecilia , Hongn Fernando , Strecker Manfred R. , Aramayo Alejandro
Published: August 2016

Unravelling the spatiotemporal evolution of the Cenozoic Andean (Altiplano‐Puna) plateau has been one of the most intriguing problems of South American geology. Despite a number of investigations, the early deformation and uplift history of this area remained largely enigmatic. This paper analyses the Paleogene tectono‐sedimentary history of the Casa Grande Basin, in the present‐day transition zone between the northern sector of the Puna Plateau and the northern part of the Argentine Eastern Cordillera. Our detailed mapping of synsedimentary structures records the onset of regional contractional deformation during the middle Eocene, revealing reactivation of Cretaceous extensional structures and the development of doubly vergent thrusts. This is in agreement with records from other southern parts of the Puna Plateau and the Eastern Cordillera. These observations indicate the existence of an Eocene broken foreland setting within the region, characterized by low‐lying compressional basins and ranges with spatially disparate sectors of deformation, which was subsequently subjected to regional uplift resulting in the attainment of present‐day elevations during the Neogene.
A hierarchical model of whole assemblage island biogeography
Authors: Lasky Jesse R. , Keitt Timothy H. , Weeks Brian C. , Economo Evan P.
Published: August 2016

Island systems have long played a central role in the development of ecology and evolutionary biology. However, while many empirical studies suggest species differ in vital biogeographic rates, such as dispersal abilities, quantitative methods have had difficulty incorporating such differences into analyses of whole‐assemblages. In particular, differences in dispersal abilities among species can cause variation in the spatial clustering and localization of species distributions. Here, we develop a single, hierarchical Bayes, assemblage‐wide model of 252 bird species distributions on the islands of northern Melanesia and use it to investigate a) whether dispersal limitation structures bird assemblages across the archipelago, b) whether species differ in dispersal ability, and c) test the hypothesis that wing aspect ratio, a trait linked to flight efficiency, predicts differences inferred by the model. Consistent with island biogeographic theory, we found that individual species were more likely to occur on islands with greater area, and on islands near to other islands where the species also occurred. However, species showed wide variation in the importance and spatial scale of these clustering effects. The importance of clustering in distributions was greater for species with low wing aspect ratios, and the spatial scale of clustering was also smaller for low aspect ratio species. These findings suggest that the spatial configuration of islands interacts with species dispersal ability to affect contemporary distributions, and that these species differences are detectable in occurrence patterns. More generally, our study demonstrates a quantitative, hierarchical approach that can be used to model the influence of dispersal heterogeneity in diverse assemblages and test hypotheses for how traits drive dispersal differences, providing a framework for deconstructing ecological assemblages and their drivers.