bluuebunny/crossref_metadata_2025_split huggingface dataset:
GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, miRNA, and mRNA data in GDC
Authors: Li Ruidong , Qu Han , Wang Shibo , Wei Julong , Zhang Le , Ma Renyuan , Lu Jianming , Zhu Jianguo , Zhong Wei-De , Jia Zhenyu 
Published: December 2017

AbstractThe large-scale multidimensional omics data in the Genomic Data Commons (GDC) provides opportunities to investigate the crosstalk among different RNA species and their regulatory mechanisms in cancers. Easy-to-use bioinformatics pipelines are needed to facilitate such studies. We have developed a user-friendly R/Bioconductor package, named GDCRNATools, to facilitate downloading, organizing, and analyzing RNA data in GDC with an emphasis on deciphering the lncRNA-mRNA related competing endogenous RNAs (ceRNAs) regulatory network in cancers. Many widely used bioinformatics tools and databases are utilized in our package. Users can easily pack preferred downstream analysis pipelines or integrate their own pipelines into the workflow. Interactive shiny web apps built in GDCRNATools greatly improve visualization of results from the analysis.AvailabilityGDCRNATools is an R/Bioconductor package that is freely available at https://github.com/Jialab-UCR/GDCRNATools
Physical mechanisms of ultrasonic neurostimulation of the retina
Authors: Menz Mike D. , Ye Patrick , Firouzi Kamyar , Pauly Kim Butts , Khuri-Yakub Butrus T. , Baccus Stephen A. 
Published: December 2017

AbstractFocused ultrasound has been shown to be effective at stimulating neurons in vivo, ex vivo and in vitro preparations. Ultrasonic neuromodulation is the only non-invasive method of stimulation that could reach deep in the brain with high spatial-temporal resolution, and thus has potential for use in clinical applications and basic studies of the nervous system. Understanding the physical mechanism by which energy in a high acoustic frequency wave is delivered to stimulate neurons will be important to optimize this technology. Two primary candidates for a physical mechanism are radiation force, the delivery of momentum by the acoustic wave, and cavitation, oscillating gas bubbles. We imaged the isolated salamander retina during ultrasonic stimuli that drive ganglion cell activity and observed micron scale displacements consistent with radiation force. We recorded ganglion cell spiking activity with a planar multielectrode array and changed the acoustic carrier frequency across a broad range (0.5 - 43 MHz), finding that increased stimulation occurs at higher acoustic frequencies, a result that is consistent with radiation force but not cavitation. A quantitative radiation force model can explain retinal responses, and could potentially explain previous in vivo results in the mouse, suggesting a new hypothesis to be tested in vivo. Finally, we found that neural activity was strongly modulated by the distance between the transducer and the electrode array showing the influence of standing waves on the response. We conclude that radiation force is the physical mechanism underlying ultrasonic neurostimulation in the ex vivo retina, and that the control of standing waves is a new potential method to modulate these effects.
Microhabitats shape diversity-productivity relationships in freshwater bacterial communities
Authors: Schmidt Marian L. , Biddanda Bopaiah A. , Weinke Anthony D. , Chiang Edna , Januska Fallon , Props Ruben , Denef Vincent J. 
Published: December 2017

AbstractEukaryotic communities commonly display a positive relationship between biodiversity and ecosystem function (BEF) but the results have been mixed when assessed in bacterial communities. Habitat heterogeneity, a factor in eukaryotic BEFs, may explain these variable observations but it has not been thoroughly evaluated in bacterial communities. Here, we examined the impact of habitat on the relationship between diversity assessed based on richness, evenness, or phylogenetic diversity, and heterotrophic productivity. We sampled co-occurring free-living (more homogenous) and particle-associated (more heterogeneous) bacterial habitats in a freshwater, estuarine lake. Diversity measures, and not environmental variables, were the best predictors of particle-associated heterotrophic production. There was a strong, positive, linear relationship between particle-associated bacterial richness and heterotrophic productivity that strengthened with evenness. There were no observable BEF trends in free-living bacterial communities. Across both habitats, communities with more phylogenetically related taxa had higher per-capita heterotrophic production than communities of phylogenetically distantly related taxa. Our findings show that heterotrophic bacterial productivity is positively correlated with evenness and richness, negatively with phylogenetic diversity, and that BEF relationships are contingent on microhabitats. Our work adds to the understanding of the highly distinct contributions to community diversity and ecosystem functioning contributed by bacteria in free-living and particle-associated aquatic habitats.
Remembrance of Inferences Past
Authors: Dasgupta Ishita , Schulz Eric , Goodman Noah D. , Gershman Samuel J. 
Published: December 2017

AbstractBayesian models of cognition assume that people compute probability distributions over hypotheses. However, the required computations are frequently intractable or prohibitively expensive. Since people often encounter many closely related distributions, selective reuse of computations (amortized inference) is a computationally efficient use of the brain’s limited resources. We present three experiments that provide evidence for amortization in human probabilistic reasoning. When sequentially answering two related queries about natural scenes, participants’ responses to the second query systematically depend on the structure of the first query. This influence is sensitive to the content of the queries, only appearing when the queries are related. Using a cognitive load manipulation, we find evidence that people amortize summary statistics of previous inferences, rather than storing the entire distribution. These findings support the view that the brain trades off accuracy and computational cost, to make efficient use of its limited cognitive resources to approximate probabilistic inference.
Value Encoding in the Globus Pallidus: fMRI reveals an interaction effect between reward and dopamine drive
Authors: Fiore Vincenzo G. , Nolte Tobias , Rigoli Francesco , Smittenaar Peter , Gu Xiaosi , Dolan Raymond J. 
Published: December 2017

AbstractThe external part of the globus pallidus (GPe) is a core nucleus of the basal ganglia (BG) whose activity is disrupted under conditions of low dopamine release, as in Parkinson’s disease. Current models assume decreased dopamine release in the dorsal striatum results in deactivation of dorsal GPe, which in turn affects motor expression via a regulatory effect on other nuclei of the BG. However, recent studies in healthy and pathological animal models have reported neural dynamics that do not match with this view of the GPe as a relay in the BG circuit. Thus, the computational role of the GPe in the BG is still to be determined. We previously proposed a neural model that revisits the functions of the nuclei of the BG, and this model predicts that GPe encodes values which are amplified under a condition of low striatal dopaminergic drive. To test this prediction, we used an fMRI paradigm involving a within-subject placebo-controlled design, using the dopamine antagonist risperidone, wherein healthy volunteers performed a motor selection and maintenance task under low and high reward conditions. ROI-based fMRI analysis revealed an interaction between reward and dopamine drive manipulations, with increased BOLD activity in GPe in a high compared to low reward condition, and under risperidone compared to placebo. These results confirm the core prediction of our computational model, and provide a new perspective on neural dynamics in the BG and their effects on motor selection and motor disorders.
Transplacental protection against asthma by maternal treatment with a bacterial-derived immunomodulatory agent
Authors: Mincham Kyle T. , Scott Naomi M. , Lauzon-Joset Jean-Francois , Leffler Jonatan , Larcombe Alexander N. , Stumbles Philip A. , Robertson Sarah A. , Pasquali Christian , Holt Patrick G. , Strickland Deborah H. 
Published: December 2017

ABSTRACTStudies in European and US farming populations have documented major reductions in asthma prevalence in offspring of mothers exposed to microbial breakdown products present in farm dusts and unprocessed foods. This was associated with enhancement of innate immune competence in the offspring. We sought to (i) identify a safe therapeutic that would reproduce these immunomodulatory effects in a murine model, (ii) elucidate underlying mechanism(s)-of-action, and (iii) develop a scientific rationale for progressing this approach to human trials. We demonstrate in mice that maternal treatment during pregnancy with the microbial-derived immunomodulator OM85, which has been used clinically in adults and children in Europe for >30 years for bolstering resistance to infection-associated airways inflammation, markedly reduces the susceptibility of the offspring of treated mothers to development of experimental atopic asthma. We identify bone marrow precursors of the dendritic cell populations responsible for airway mucosal immune surveillance as the primary targets for the asthma-protective effects of maternal OM85 treatment in the offspring.
Prometheus: omics portals for interkingdom comparative genomic analyses
Authors: Ko Gunhwan , Jang Insu , Koo Namjin , Park Seong-Jin , Oh Sangho , Kim Min-Seo , Choi Jin-Hyuk , Kim Hyeongmin , Sim Young Mi , Byeon Iksu , Kim Pan-Gyu , Kim Kye Young , Han Gukhee , Yoon Jong-Cheol , Hong Yunji , Mun Kyung-Lok , Lee Banghyuk , Ko Deayeon , Song Wangho , Kim Yong-Min 
Published: December 2017

AbstractFunctional analyses of genes are crucial for unveiling biological responses, for genetic engineering, and for developing new medicines. However, functional analyses have largely been restricted to model organisms, representing a major hurdle for functional studies and industrial applications. To resolve this, comparative genome analyses can be used to provide clues to gene functions as well as their evolutionary history. To this end, we present Prometheus (http://prometheus.kobic.re.kr),web-based omics portal that contains more than 17,215 sequences from prokaryotic and eukaryotic genomes. This portal supports interkingdom comparative analyses via a domain architecture-based gene identification system, Gene Search, and users can easily and rapidly identify single or entire gene sets in specific pathways. Bioinformatics tools for further analyses are provided in Prometheus or through BioExpress, a cloud-based bioinformatics analysis platform. Prometheus suggests a new paradigm for comparative analyses with large amounts of genomic information.
Does index futures trading cause market fluctuations?
Authors: Dong Shanshan , Feng Yun 
Published: December 2017

PurposeThe purpose of this paper is to study the effect of different parts (predictable and impact) of different types of speculative behavior (intraday speculation, medium-term speculation and long-term speculation) on future fluctuations in the underlying index.Design/methodology/approachThe authors input information about heterogeneous speculative behavior into the HAR-RV model to study the effect of different parts (predictable and impact) of different types of speculative behavior (intraday speculation, medium-term speculation and long-term speculation) on the future fluctuation of the underlying index.FindingsThe authors find that the increase in intraday speculation will exacerbate spot market volatility; and the expected increase of long-term value speculation can reduce market volatility, but the shock of speculation will exacerbate market volatility.Practical implicationsThe authors suggest that regulators should strictly limit speculative intraday trading, and also focus on the long-term value speculation that decreases market volatility, in order to guide the benign development of the markets that stabilize abnormal market fluctuations.Originality/valueFirst, in view of the correlation between the futures and spot markets, the authors put forward a new proxy for the speculation degree. Second, the authors input heterogeneous speculative behavior into the HAR-RV model to study the effects of different parts (predictable and impact) on different types of speculative behavior (intraday speculation, medium-term speculation and long-term speculation) on the future fluctuation of the underlying index.
Relationships between philosophical values and conflict management styles
Authors: Parmer Lucinda 
Published: December 2017

PurposeTo examine the relationships between Boyatzis et al.’s (2000) philosophical value orientations and Rahim’s (1983 & 1995) conflict management styles through an exploratory research study. The philosophical value orientations are identified as pragmatic, intellectual and human. The conflict management styles are represented as integrating, obliging, dominating, avoiding and compromising.Design/methodology/approachThe author collected a sample of 161 participants gathered from Amazon’s mechanical turk digital labor pool. Participants completed a survey measuring their philosophical value orientations, conflict management styles and provided information on demographic characteristics. Statistical analysis was used to explore the relationship between philosophical value orientations, conflict management style scores and demographic characteristics.FindingsThe study demonstrated there were significant associations between the philosophical value orientations and the conflict management styles. Significant associations regarding the philosophical value orientations and conflict management styles were also found across the demographic groups.Research limitations/implicationsThree philosophical value orientations were examined in this study to include pragmatic, intellectual and human; however, there are a multitude of personal and workplace values that could be further studied.Practical implicationsThe practical implications of this study show that employees do bring into the company or organization a set of beliefs and value structures that can influence how they respond and relate to their immediate supervisor in challenging or conflicting situations.Social implicationsThe social implications of this study indicate employees’ behavior and reactions to their immediate supervisor are directly manipulated by the value-based system they have developed prior to joining the organization.Originality/valueNo prior research has examined the relationship between Boyatzis et al.’s (2000) philosophical value orientations of pragmatic, intellectual and human and Rahim’s (1983 & 1995) conflict management styles of integrating, obliging, dominating, avoiding and compromising. This study explores how philosophical value orientations are related to the five conflict management styles manifested within the organizational leader-follower dyadic relationship.
Sustainability reporting experience by universities: a causal configuration approach
Authors: Zorio-Grima Ana , Sierra-García Laura , Garcia-Benau Maria A. 
Published: December 2017

Purpose
The purpose of this research is to identify the combinations of factors leading to experience in sustainability reporting by Spanish public universities.

Design/methodology/approach
Using a sample of 49 public universities in Spain, this paper identifies the combinations of factors on innovation profile, political and internal factors that explain the different degree of corporate social reporting experience with fuzzy-set qualitative comparative analysis.

Findings
The study’s findings are a contribution to existing literature as the results obtained point out three different configurations leading to this expertise, with a combination of different conditions based on innovation profile, political and internal factors. Also, the results reveal new characteristics of sustainable development strategies by universities, such as devoting a specific sustainability reporting section in the university website, creating a sustainability body in the university structure or submitting the sustainability report to external assurance.

Research limitations/implications
This study refers only to Spanish public universities. In the future, new studies can enlarge the sample and analyse country effects and impact of public versus private status of universities on sustainability reporting strategies.

Practical implications
The study’s findings are important for university community, regulators and other stakeholders to start considering the need to somehow promote further sustainability reporting and assurance practices by universities, especially in a context of budget restrictions.

Originality/value
This paper opens up a new line of research on sustainability experience using an innovative methodology (fuzzy-set qualitative comparative analysis) useful with small sample sizes, and provides a complete picture of sustainability reporting by Spanish public universities.
Construction and validation of the customer social participation in brand communities scale
Authors: Kamboj Shampy , Sarmah Bijoylaxmi 
Published: December 2017

Purpose
The purpose of this paper is to construct and validate customer social participation (CSP) scale in the context of brand communities on social media.

Design/methodology/approach
In this study, various tests for reliability and validity have been performed to confirm scale structure. Data were collected using survey method from the student and non-student sample.

Findings
The results confirm a multi-dimensional scale with nine items for measuring customer participation in social media brand communities.

Research limitations/implications
The results of this study present several implications for online brand communities managers and are likely to support future research in the context of social media brand communities.

Originality/value
This paper is the first to develop a multi-dimensional scale of customer participation in social media brand communities. This is a new addition to existing literature, as the majority of empirical studies in this field are from participation other than CSP, and contexts different from social media brand communities.
Tweeting #Leaders
Authors: Huang Lei Vincent , Yeo Tien Ee Dominic 
Published: December 2017

Purpose
To better understand executive communication on social media, the purpose of this paper is to examine the pattern of messages posted by chief executive officers (CEOs) on Twitter and their retweetability (rate of reposting by other users).

Design/methodology/approach
The study data comprises 1,068 original tweets randomly selected from all Fortune 1000 CEOs’ tweets in 2014. The impact of the contextual factors (industry background, activeness, and Twitter age) and content factors (content types, supplementary information, and linguistic features) on retweetability was examined through regression analyses.

Findings
CEOs tweet to share information and insights, to promote their companies or products, to update work or life status, and to interact with the public. Original insights, promotional messages, and seasonal greetings were most likely to be retweeted. CEOs’ backgrounds, usage of hashtags, and certainty of language were also positively associated with retweetability.

Practical implications
CEOs may enhance their online social influence through demonstrating leadership by sharing insights about their organization or industry and posting topical messages (e.g. season’s greetings). Furthermore, CEOs could use hashtags strategically to initiate or participate in discussions and promote their personal visibility.

Originality/value
This study is one of the first to evaluate how leaders of the largest companies in the USA communicate on Twitter. It contributes to a theoretical understanding of the factors underlying online influence – the influence of the status of the online communicator vs the message content on information forwarding.
What drives users’ intentions to purchase a GPS Navigation app
Authors: Wang Yu-Yin , Lin Hsin-Hui , Wang Yi-Shun , Shih Ying-Wei , Wang Ssu-Ting 
Published: December 2017

Purpose
Grounded on the value-based adoption model and innovation diffusion theory, this study examined consumer purchase decisions of mobile Global Positioning System (GPS) navigation apps. In addition, this study also investigated the moderating role that perceived availability of free substitutes (PAFS) plays in the relationship between perceived value and purchase intention. The paper aims to discuss these issues.

Design/methodology/approach
Data collected from 219 mobile users were analyzed against the research model using the partial least squares approach.

Findings
The results showed that compatibility, relative advantage, perceived enjoyment, perceived cost (positively), and complexity (negatively) influenced these users’ value perceptions and purchase decisions. Furthermore, PAFS significantly weakened the positive relationship between perceived value and purchase intentions.

Practical implications
Based on these findings, the authors provide practical suggestions for mobile app developers to increase mobile app sales. This study also helps advance knowledge of mobile internet marketing.

Originality/value
This study is a pioneering effort in explaining consumer purchase intentions in the context of mobile GPS navigation app.
Excellence criteria of services supply chain in management consulting institutes of Iran
Authors: Balouei Jamkhaneh Hadi , Safaei Ghadikolaei Abdol Hamid , Madhoushi Mehrdad , Yahyazadehfar Mahmood 
Published: December 2017

PurposeThe purpose of this study was to identify the excellence criteria of services supply chain (SSC) in Iran and the relationship between them and the importance of each criterion.Design/methodology/approachIn this paper, after reviewing the principles and evaluating models of SSCs, using the fuzzy Delphi method, the criteria for excellence in the supply chain processes were identified. Then, the relationships between these criteria and their significance were evaluated using decision-making trial and evaluation laboratory (DEMATEL) and DEMATEL-based analytic network process methods.FindingsThe results show that 19 evaluation criteria have been identified in Iran in accordance with the SSC process. These criteria were classified according to their nature and based on the Deming Excellence Model and ISO 9004 standards in four areas: Plan, Do, Check and Act. In addition, the Act dimension with the weight of 0.275 has the highest importance and the Plan dimension with the weight of 0.219 has the lowest importance.Practical implicationsThis study attempted to identify appropriate criteria for SSC processes in management consulting firms by examining supply chain assessment models to provide the managers with the right understanding of this industry for performance assessment so that they have a better knowledge of supply chain processes.Originality/valueThe results will be useful for managers to understand the SSC and the ways of SSC excellence in a service organization. This research is a first step for evaluating SSC performance of management consultancy institutes. In fact, after the identification of SSC processes and evaluation criteria, designing a mechanism for the evaluation of the performance of SSCs can be a subject for future research.