bluuebunny/crossref_metadata_2025_split huggingface dataset:
The SEK-1 p38 MAP kinase pathway modulates Gq signaling inC. elegans
Authors: Hoyt Jill M. , Wilson Samuel K. , Kasa Madhuri , Rise Jeremy S. , Topalidou Irini , Ailion Michael 
Published: December 2016

AbstractGq is a heterotrimeric G protein that is widely expressed in neurons and regulates neuronal activity. To identify pathways regulating neuronal Gq signaling we performed a forward genetic screen inCaenorhabditis elegansfor suppressors of activated Gq. One of the suppressors is an allele ofsek-1,which encodes a mitogen-activated protein kinase kinase (MAPKK) in the p38 MAPK pathway. Here we show thatsek-1mutants have a slow locomotion rate and thatsek-1acts in acetylcholine neurons to modulate both locomotion rate and Gq signaling. Furthermore, we find thatsek-1acts in mature neurons to modulate locomotion. Using genetic and behavioral approaches we demonstrate that other components of the p38 MAPK pathway also play a positive role in modulating locomotion and Gq signaling. Finally, we find that mutants in the SEK-1 p38 MAPK pathway partially suppress an activated mutant of the sodium leak channel NCA-1/NALCN, a downstream target of Gq signaling. Our results suggest that the SEK-1 p38 pathway may modulate the output of Gq signaling through NCA-1.
Parkin knockout inhibits neuronal development via regulation of proteasomal degradation of p21
Authors: Park Mi Hee , Lee Hwa Jeong , Lee Hye Lim , Son Dong Ju , Ju Jung Hoon , Hyun Byung Kook , Jung Sung Hee , Song Ju-Kyoung , Lee Dong-Hoon , Hwang Chul-Ju , Han Sang Bae , Kim Sanghyeon , Hong Jin Tae 
Published: December 2016

AbstractPARK2 encodes for the E3 ubiquitin ligase parkin and iimplicates in the development of Parkinson’s disease (PD). Although the neuroprotective role of parkin is well known, the mechanism of parkin’s function in neural stem differentiation is not clear. Co-expressions network analysis showed that SNAP25 and BDNF were positively correlated with parkin, but negatively correlated with p21 in human patient brain. Therefore, we investigated a link between the ubiquitin E3 ligase parkin and proteasomal degradation of p21 for the control of neural stem cell differentiation. We discovered that p21 directly binds with parkin and is ubiquitinated by parkin resulting in the loss of cell differentiation ability. Tranfection of p21 shRNA in PARK2 KO mice significantly rescued the differentiation efficacy as well as SNAP25 and BDNF expression. We also defined the decreased p21 ubiquitination and differentiation ability were reversed after treatment with JNK inhibitor, SP600125 in PARK2 KO mice derived neural stem cells. Thus, the present study indicated that parkin knockout inhibits neural stem cell differentiation by JNK-dependent proteasomal degradation of p21.Summary statementThe present study indicated that parkin knockout inhibits neural stem cell differentiation by JNK-dependent proteasomal degradation of p21.
BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes
Authors: de Santiago Ines , Liu Wei , O’Reilly Martin , Yuan Ke , Chilamakuri Chandra Sekhar Reddy , Ponder Bruce A.J. , Meyer Kerstin B. , Markowetz Florian 
Published: December 2016

AbstractAllele-specific measurements of transcription factor binding from ChIP-seq data are key to dissecting the allelic effects of non-coding variants and their contribution to phenotypic diversity. However, most methods to detect allelic imbalance assume diploid genomes. This assumption severely limits their applicability to cancer samples with frequent DNA copy number changes. Here we present a Bayesian statistical approach called BaalChIP to correct for the effect of background allele frequency on the observed ChIP-seq read counts. BaalChIP allows the joint analysis of multiple ChIP-seq samples across a single variant and outperforms competing approaches in simulations. Using 548 ENCODE ChIP-seq and 6 targeted FAIRE-seq samples we show that BaalChIP effectively corrects allele-specific analysis for copy number variation and increases the power to detect putative cis-acting regulatory variants in cancer genomes.
Stochastic Model for Direction Changes of Swimming Bacteria
Authors: Fier G. , Hansmann D. , Buceta R. C. 
Published: December 2016

AbstractIn this work we introduce a stochastic model to describe directional changes in the movement of swimming bacteria. We use the probability density function (PDF) of turn angles, measured on tumblingE. coliwild-type, to build a Langevin equation for the deflection of the bacterial body swimming in isotropic media. We solved analytically this equation by means of the Green function method and show that three parameters are sufficient to describe the movement: a characteristic time, the steady-state solution and a control parameter. We conclude that the tumble motion, which is manifested as abrupt turns, is primarily caused by the rotational boost generated by the flagellar motor and complementarily by the rotational diffusion introduced by noise. We show that, in the tumble motion, the deflection is a non-stationary stochastic processes during times where the tumble occurs. By tuning the control parameter our model is able to explain small turns of the bacteria around their centers of mass along the run. We show that the deflection during the run is an Ornstein-Uhlenbeck process, which for typical run times is stationary. We conclude that, along the run, the rotational boosts do not exist or are neglectable and that only the rotational diffusion remains. Thus we have a single model to explain the turns of the bacterium during the run or tumble movements, through a control parameter that can be tuned through a critical value that can explain the transition between the two turn behaviours. This model is also able to explain very satisfactory all available statistical experimental data, such as PDFs and average values of turning angles and times, of both run and tumble motions.
A bioinformatic panel to interrogate thousands of ExAC variants with minor reference allele that are missed by conventional variant calling
Authors: Koko Mahmoud , Abdallah Mohammed O. E. , Amin Mutaz , Ibrahim Muntaser 
Published: December 2016

AbstractIn variation sites with minor reference alleles, overlooking the detection of homozygous reference genotypes results in inadequate identification of potential disease variants. Current variant calling practices miss these clinically relevant alleles warranting new approaches. More than 26,000 Eome Aggregation Consortium (ExAC) variants have a minor reference allele including 44 variants with known ClinVar disease alleles. We demonstrated how the current variant calling standards miss homozygous reference disease variants in these sites. We developed a bioinformatic panel that can be used to screen these variants using commonly available variant callers. We provide here a simple strategy to screen potential disease-causing variants when present in homozygous reference state.
Does disclosure of food inspections affect business compliance? The case of Berlin, Germany
Authors: Bavorova Miroslava , Fietz Anica Veronika , Hirschauer Norbert 
Published: December 2016

PurposeA whole series of food scandals indicates that misdirected incentives continue to be a source of food risks. Lacking market transparency and the opportunistic use of seemingly profitable opportunities to break the rules cause negative externalities and failure of markets. The purpose of this paper is to investigate the influence of mandatory transparency schemes on food businesses’ behavioural drivers and thus on compliance.Design/methodology/approachThe authors use an adopted analytical framework developed by Hirschaueret al.(2012) as the theoretical background. The authors provide an empirical analysis of the effects of a disclosure system on businesses’ behavioural drivers in three urban parts of the German capital Berlin. The authors conducted a pen-and-paper survey among food businesses to collect data and used a generalized ordered logit regression model to analyse them.FindingsThe results show that the higher the businesses assess the possible negative effects of a negative smiley on sales, the higher the probability of compliance. Considering the immaterial behavioural drivers (protective factors) the authors find the statistical significant influence of a feeling of embarrassment in case of disclosure and the feeling of a fair evaluation on compliance. Thus, the study supports the expectation that disclosure policies affect behavioural drivers and have the potential to steer food businesses’ compliance.Practical implicationsThe study supports the expectation that hygiene controls’ disclosure positively affects food businesses’ compliance. These findings should be taken into consideration in the ongoing discussion about disclosure. Nowadays, there is no mandatory transparency in Germany due to a strong opposition from businesses and their lobbying groups.Originality/valueThe authors conducted a pen-and-paper survey among food businesses in three urban districts of the German capital Berlin, namely, Pankow, Lichtenberg and Marzahn-Hellersdorf in 2014. The food authorities in these districts were the only ones in Germany that had introduced and run a mandatory disclosure system (smiley-system) for food businesses. The results of the inspections were published on the authorities’ homepages in the internet, and were displayed in businesses. Thus the data mirror the unique experiences of the only German food businesses that participated in a mandatory transparency scheme.
Halal integrity in the food supply chain
Authors: Soon Jan Mei , Chandia Mahmood , Regenstein Joe Mac 
Published: December 2016

Purpose
This paper argues that there is an absence of halal integrity within the conventional stages of a food chain. This paper adapts the understanding of the different stages and argues the need to develop a critical consciousness for halal integrity within the food chain to address the needs of the ever-growing Muslim consumers’ market. The purpose of this paper is to propose a definition of halal integrity using farm to fork and global food supply chain models.

Design/methodology/approach
The study includes a review of priori literature and media reports regarding cross-contamination of food products with haram (forbidden) components. This background will be used to conceptualise halal integrity using farm to fork and global supply chain models.

Findings
Different interpretations of halal – what is permitted and what is prohibited – exist for the different schools of Islamic legal thought and within the customs of different countries. In order to ensure that food production is embracive of the religious needs of the global Muslim customer market, this paper utilises the farm to fork and global supply chain models to foster a critical awareness of halal needs. Halal integrity should be clearly presenting the details of the halal status of the product and assuring that the requirements for halal as stated are met. Halal integrity not only deals with permitted and prohibited foods, but that the halal status of the food products (i.e. from raw materials until it reaches the consumers) should not be breached (i.e. no cross-contamination with haram products/methods and no ill intents). A formal definition of halal integrity has been proposed.

Research limitations/implications
The SWOT analyses serve as a guideline as the analysis done may be outdated as the environments are constantly changing.

Originality/value
This research although academic is meant to have a real value in improving the integrity of the halal food supply chain, providing value to the food industry, to countries that are concerned about this supply chain and to Muslim consumers. Halal integrity is crucial to the success of the emerging halal market.
Fraud and counterfeit wines in France: an overview and perspectives
Authors: Lecat Benoit , Brouard Joelle , Chapuis Claude 
Published: December 2016

Purpose
The purpose of this paper is to analyze the specificities of wine forgery today and to show the perspectives offered to the different stakeholders in the wine industry.

Design/methodology/approach
Owing to the technical aspects of this paper, a literature review based on academic papers (history) and articles coming from the professional press, internet websites and public organizations was made.

Findings
It was found that frauds have always existed. Forgers are constantly in search of new ways of counterfeiting wines. Producers have had to adapt to the various forms of counterfeiting, mainly by resorting to modern technology. As the traceability of great wines is becoming crucial, a new type of relationships between producers anxious to offer genuine estate wines and consumers anxious to drink the bottles they ordered has developed. This new constraint became a marketing opportunity for producers.

Research limitations/implications
It was difficult to obtain official data (interviews or surveys) because of the sensitiveness of the topic.

Practical implications
This paper, which offers an inventory of the methods used by forgers to deceive customers, makes both producers and consumers aware of the extent of the problem. The counterfeiting phenomenon is dangerous for producers’ image and the technological changes are a tool allowing producers to protect their wine and reinforce their relationships with consumers.

Originality/value
This paper gives an overview of forgers’ ploys in France. It opens a discussion about perspectives for the different stakeholders while most of the research tends to focus on technical solutions and the analysis of specific affairs which received media coverage.
Strategic assets in technology-based incubators in Brazil
Authors: Fernandes Carolina Cristina , Oliveira Jr Moacir de Miranda , Sbragia Roberto , Borini Felipe Mendes 
Published: December 2016

PurposeThe purpose of this paper is to analyze the relationship between strategic assets and the launch of new products in technology-based incubators (TBIs) in Brazil.Design/methodology/approachThe authors applied two surveys, one for the universe of TBIs’ managers in the state of Sao Paulo, Brazil, and the other to the incubated firms’ managers/owners. Two statistical techniques were used: correlation analysis and multiple linear regression.FindingsThe main finding of this paper is that TBIs’ strategies focusing on the supply of knowledge assets and the creation of relationship assets are more effective than strategies focused only on the supply of physical infrastructure for firms located in incubators.Research limitations/implicationsBecause the sample of 100 respondents of incubated companies was the result of a non-probabilistic convenience sampling, the outcomes also cannot be generalized.Practical implicationsFor managers of TBIs, there is a challenge to focus on the supply of intangible and high value added assets for incubated firms. For managers/owners of incubated firms, the authors provide an orientation to what they should seek or demand when deciding where to place their business in a TBI. For the government, the results of this research may help to formulate public policies to support and incentivize TBIs. For investors, the results can help to define where to seek the most innovative projects.Social implicationsInnovation and entrepreneurship are understood as sources of wealth creation and social development.Originality/valueThe authors propose in this paper that there is a theoretical gap between traditional theories of innovation and entrepreneurship and the strategic behavior and performance of business incubators and their interconnected stakeholders. Here the authors seek to bridge this gap.
Accelerating chemical start-ups in ecosystems: the need for biotopes
Authors: van Gils Maarten J.G.M. , Rutjes Floris P.J.T. 
Published: December 2016

PurposeThe purpose of this paper is to clarify the relationship between start-ups and an innovation ecosystem. Start-ups need resources available in the ecosystem to grow, but experience organizational capacity limitations during their open innovation practices. This study frames the “open innovation” interface and discloses ways to accelerate the process of connecting start-ups’ demands to ecosystem’s supplies.Design/methodology/approachA case study was used to describe the development of a conceptual ecosystem model to frame the “open innovation” interface and its subsequent implementation at nine start-up hotspots in the Dutch chemical industry. To develop the ecosystem model, the system of innovation concept was enriched with the perspective of a chemical start-up to pinpoint critical resources for growth.FindingsIt is suggested that the most relevant “open innovation” interface for start-ups looking to grow is an innovation biotope: a well-defined, business-oriented cross-section of an ecosystem. All stakeholders in a biotope are carefully selected based on the entrepreneurial issue at stake: they can only enter the secured marketplace if they are able to provide dedicated solutions to start-ups. The biotope enables “open innovation in a closed system” which results in acceleration of the innovation process.Originality/valueThis is the first study to report on the definition and implementation of an innovation biotope as the “open innovation” interface between an ecosystem and start-ups. In addition, it provides a powerful tool, the ecosystem canvas, that can help both regional and national innovation systems to visualize their ecosystem and identify blind spots.
Open innovation for start-ups
Authors: Michelino Francesca , Cammarano Antonello , Lamberti Emilia , Caputo Mauro 
Published: December 2016

PurposeThe purpose of this paper is to provide a methodological framework for evaluating the impact of open innovation (OI) adoption on start-up ventures at the knowledge domain level, taking into account the technological specialization and the quality of innovation output.Design/methodology/approachThe framework employs patent data for investigating joint development activities between start-ups and partners, thus defining an openness degree of R&D. The partner typology and the levels of specialization on the knowledge fields affected by each invention are investigated. The methodology is tested on a sample of bio-pharmaceutical start-ups.FindingsOn average, the openness level in the start-up phase is higher than the consolidation one. Furthermore, the higher the level of openness during the start-up phase, the higher the propensity to collaborate with scientific organizations. And yet, the occurrence of R&D collaborations is positively correlated to the level of specialization on the knowledge fields involved in joint development activities.Practical implicationsOI strategies are valuable for start-ups, particularly in the bio-pharmaceutical industry, since their adoption improves the quality of innovation output. This is particularly true when R&D collaborations are established with scientific entities.Originality/valueThis work investigates the impact of OI adoption on start-up ventures at the knowledge domain level, by employing objective and standardized data. Hence, the methodology can be considered as a first step in developing a useful tool for managers, researchers and business analysts.
Trust in open innovation – the case of a med-tech start-up
Authors: Hasche Nina , Linton Gabriel , Öberg Christina 
Published: December 2016

PurposeThe literature has shown great interest in open innovation (OI), and also discussed its degree of openness based on, for example, the number of parties involved. Less is known, however, about what makes OI processes work. The purpose of this paper is to describe and discuss the importance of trust in OI, and the paper specifically focusses on a start-up company’s OI processes with collaboration parties. The paper points out how a lack of trust antecedents may disable such OI processes.Design/methodology/approachThe empirical part of the paper consists of a case study on a medicine technology start-up. Interviews and analyses of secondary sources made up the main data capturing methods. Each collaboration between the start-up and another party is analysed through three trust antecedents: contractual, competence based, and goodwill.FindingsThe paper shows how either party may have chosen to discontinue the collaboration, based on the lack of competence or goodwill antecedents to trust. Specifically, the case indicates how the start-up discontinues the collaboration based on a perceived lack of goodwill, while the collaboration party bases its decision on competence deficits by the start-up.Originality/valueThe paper contributes to previous research through describing OI related to start-ups, and introducing trust antecedents as prerequisites for OI. To the literature on trust, trust mutuality makes a research contribution.
Startups and open innovation: a review of the literature
Authors: Spender John-Christopher , Corvello Vincenzo , Grimaldi Michele , Rippa Pierluigi 
Published: December 2016

Purpose
Startup companies represent a powerful engine of open innovation (OI) processes. The purpose of this paper is to represent a first step in building a map of the state-of-the-art knowledge of the “startups in an OI context” phenomenon. Through the selection and analysis of relevant literature, this study aims at deepening our understanding of the theme and at providing directions for future research.

Design/methodology/approach
By using an explicit method for the review (Pittaway et al., 2004) the authors selected a set of papers, which cover the knowledge domain object of this study. In total, 41 articles about “startups and OI” have been selected and the full papers have been analysed.

Findings
The analysed literature has been synthesized in seven sub-topics, which have been evaluated as the most relevant in explaining the phenomenon of startups in relation to OI. Implications for research, for managers and for policy makers conclude the paper.

Practical implications
The review produced valuable knowledge for both managers and policy decision-makers. The paper allows a better understanding of the role of startups in OI processes. This improved understanding can help managers of large firms as well as policy makers involved in OI in making their decisions. Besides, implications of OI strategies for startup managers have been singled-out.

Originality/value
Startup companies are intrinsically open organizations, necessarily engaged in innovation processes. Research at the intersection between the themes of OI and startups is gaining momentum. This review of the literature represents the first attempt to organize the scientific knowledge related to the intersection between the startups and OI phenomena systematically.