bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optogenetically induced low-frequency correlations impair perception
Authors: Nandy Anirvan S. , Nassi Jonathan J. , Reynolds John H. 
Published: January 2018

AbstractDeployment of covert attention to a spatial location can cause large decreases in low-frequency correlated variability among neurons in macaque area V4 whose receptive-fields lie at the attended location. It has been estimated that this reduction accounts for a substantial fraction of the attention-mediated improvement in sensory processing. These estimates depend on assumptions about how population signals are decoded and the conclusion that correlated variability impairs perception, is purely hypothetical. Here we test this proposal directly by optogenetically inducing low-frequency fluctuations, to see if this interferes with performance in an attention-demanding task. We find that low‐ frequency optical stimulation of neurons in V4 elevates correlations among pairs of neurons and impairs the animal’s ability to make fine sensory discriminations. Stimulation at higher frequencies does not impair performance, despite comparable modulation of neuronal responses. These results support the hypothesis that attention-dependent reductions in correlated variability contribute to improved perception of attended stimuli.
Detection of HPV E7 transcription at single-cell resolution in epidermis
Authors: Lukowski SW , Tuong ZK , Noske K , Senabouth A , Nguyen QH , Soyer HP , Frazer IH , Powell JE 
Published: January 2018

SummaryPersistent human papillomavirus (HPV) infection is responsible for at least 5% of human malignancies. Most HPV-associated cancers are initiated by the HPV16 genotype, as confirmed by detection of integrated HPV DNA in cells of oral and anogenital epithelial cancers. However, single-cell RNA-sequencing (scRNA-seq) may enable prediction of HPV involvement in carcinogenesis at other sites. We conducted scRNA-seq on keratinocytes from a mouse transgenic for theE7gene of HPV16, and showed sensitive and specific detection of HPV16-E7mRNA, predominantly in basal keratinocytes. We showed that increasedE7mRNA copy number per cell was associated with increased expression of E7 induced genes. This technique enhances detection of viral transcripts in solid tissue and may clarify possible linkage of HPV infection to development of squamous cell carcinoma.
Charcot-Leyden Crystals activate the NLRP3 inflammasome and cause IL-1β inflammation
Authors: Rodríguez-Alcázar Juan Francisco , Ataide Marco Antonio , Engels Gudrun , Schmitt-Mabmunyo Christine , Garbi Natalio , Kastenmüller Wolfgang , Latz Eicke , Franklin Bernardo S 
Published: January 2018

ABSTRACTCharcot-Leyden crystals (CLCs) are Galectin-10 protein crystals that can form after eosinophils degranule. CLCs can appear and persist in tissues from patients with eosinophilic disorders, such as asthma, allergic reactions, fungal, and helminthic infections. Despite abundant reports of their occurrence in human disease, the inflammatory potential of CLCs has remained unknown. Here we show that CLCs induce IL-1β release upon their uptake by primary human macrophagesin vitro,and that they induce inflammationin vivoin mouse models of acute peritonitis and bronchitis. CLC-induced IL-1β was dependent on NLRP3 and caspase-1, and their instillation in inflammasome reporter mice promoted the assembly of ASC complexes and IL-1β secretion in the lungs. Our findings reveal that CLCs are recognized by the NLRP3 inflammasome, which may sustain inflammation that follows eosinophilic inflammatory processes.
SSPIM: a beam shaping toolbox for structured selective plane illumination microscopy
Authors: Aakhte Mostafa , Akhlaghi Ehsan A. , Müller H.-Arno J. 
Published: January 2018

AbstractAn important aim of the development of selective plane illumination microscopy (SPIM) is to present a completely open and flexible microscope set-up for nonspecialist users. Here, we report Structured SPIM (SSPIM), which provides an open-source, user-friendly and compact toolbox for beam shaping that can generate digital patterns for a wide range of illumination beams. SSPIM represents a toolbox to produce static, spherical Gaussian, Bessel and Airy beams by simple control of a Spatial Light Modulator (SLM). In addition, it is able to produce patterns for incoherent and coherent (lattice beam) array beam formation and tiling for all types of beams supported. We demonstrate the workflow and experimental and simulation results using the SSPIM toolbox. In final, the capability of the SSPIM is investigated with 3D imaging of Drosophila embryo using three different illumination beams such as scanned/dithered Gaussian, Bessel and Lattice beam which engineered with SSPIM. SSPIM toolbox is easy to use and applicable for a wide range of applications to generate and optimize the desired beam pattern and thus can help developing adaptation of the Open SPIM system towards a wider range of biological samples.
Structure-guided design of a cell penetrating peptide preventing cAMP modulation of HCN channels
Authors: Saponaro Andrea , Cantini Francesca , Porro Alessandro , Bucchi Annalisa , Di Francesco Dario , Maione Vincenzo , Donadoni Chiara , Introini Bianca , Mesirca Pietro , Mangoni Matteo E. , Thiel Gerhard , Banci Lucia , Santoro Bina , Moroni Anna 
Published: January 2018

AbstractThe auxiliary subunit TRIP8b prevents cAMP activation of HCN channels by antagonizing its binding to their cyclic-nucleotide binding domain (CNBD). By determining an NMR-derived structure of the complex formed by the HCN2 channel CNBD and a minimal TRIP8b fragment, TRIPnano, we show here a bipartite interaction between the peptide and CNBD which prevents cAMP binding in two ways: through direct competition for binding at the distal C-helix of the CNBD; and through an allosteric reduction in cAMP affinity induced by TRIP8b binding to the CNBD N-bundle loop. TRIPnano abolishes cAMP binding in all three isoforms, HCN1, HCN2 and HCN4 and can be used to prevent cAMP stimulation in native f-channels. Application of TRIP8bnano, or its delivery via a cell-penetrating sequence, in sinoatrial node myocytes, selectively inhibits beta-adrenergic stimulation of the native If current and mimics the physiological concentrations of acetylcholine leading to a 30% reduction in the spontaneus rate of action potential firing.
Beyond synthetic lethality: charting the landscape of clinically relevant genetic interactions in cancer
Authors: Magen Assaf , Das Avinash , Lee Joo Sang , Sharmin Mahfuza , Lugo Alexander , Gutkind J. Silvio , Schäffer Alejandro A. , Ruppin Eytan , Hannenhalli Sridhar 
Published: January 2018

AbstractThe phenotypic effect of perturbing a gene’s activity depends on the activity level of other genes, reflecting the notion that phenotypes are emergent properties of a network of functionally interacting genes. In the context of cancer, contemporary investigations have primarily focused on just one type of functional genetic interaction (GI) – synthetic lethality (SL). However, there may be additional types of GIs whose systematic identification would enrich the molecular and functional characterization of cancer. Here, we describe a novel data-driven approach called EnGIne, that applied to TCGA data identifies 71,946 GIs spanning 12 distinct types, only a small minority of which are SLs. The detected GIs explain cancer driver genes’ tissue-specificity and differences in patients’ response to drugs, and stratify breast cancer tumors into refined subtypes. These results expand the scope of cancer GIs and lay a conceptual and computational basis for future studies of additional types of GIs and their translational applications. The GI network is accessible online via a web portal [https://amagen.shinyapps.io/cancerapp/].
Comparing complex variants in family trios
Authors: Toptaş Berke Ç. , Rakocevic Goran , Kómár Péter , Kural Deniz 
Published: January 2018

AbstractMotivation: Several tools exist to count Mendelian violations in family trios by comparing variants at the same genomic positions. This naive variant comparison however, fails to assess regions where multiple variants need to be examined together, resulting in reduced accuracy of existing Mendelian violation checking tools.Results: We introduce VBT, a trio concordance analysis tool, that identifies Mendelian violations by approximately solving the 3-way variant matching problem to resolve variant representation differences in family trios. We show that VBT outperforms previous trio comparison methods by accuracy.Availability: VBT is implemented in C++ and source code is available under GNU GPLv3 license at the following URL: https://github.com/sbg/VBT-TrioAnalysis.gitContact:cagkantoptas@hotmail.comSupplementary information: Supplementary materials are available at Biorxiv.
The Immune Deficiency Pathway Regulates Metabolic Homeostasis inDrosophila
Authors: Davoodi Saeideh , Galenza Anthony , Panteluk Andrew , Deshpande Rujuta , Ferguson Meghan , Grewal Savraj , Foley Edan 
Published: January 2018

ABSTRACTImmune and metabolic pathways collectively influence host responses to microbial invaders, and mutations in one pathway frequently disrupt activity in the other. We used theDrosophilamodel to characterize metabolic homeostasis in flies with modified Immune Deficiency (IMD) pathway activity. The IMD pathway is very similar to the mammalian Tumor Necrosis Factor-alpha pathway, a key regulator of vertebrate immunity and metabolism. We found that persistent activation of IMD resulted in hyperglycemia, depleted fat reserves, and developmental delays, implicating IMD in metabolic regulation. Consistent with this hypothesis, we found thatimdmutants weigh more, are hyperlipidemic, and have impaired glucose tolerance. To test the importance of metabolic regulation for host responses to bacterial infection, we challenged insulin pathway mutants with lethal doses of severalDrosophilapathogens. We found that loss-of-function mutations in the insulin pathway impacted host responses to infection in a manner that depends on the route of infection, and the identity of the infectious microbe. Combined, our results support a role for coordinated regulation of immune and metabolic pathways in host containment of microbial invaders.
Knowledge artifacts: the implications of incommensurable dimensions for their design
Authors: Simone Carla 
Published: January 2018

Purpose
The purpose of this paper is to overcome the confusion generated by a loose definition of the term knowledge artifact (KA) and its impacts on the design of technologies supporting their use.

Design/methodology/approach
The paper looks at the conceptual foundations underpinning the concept of KA that are related to the way in which knowledge is conceived, and revisits the outcomes of empirical investigations to shed light on different aspects of the use of KA in various settings.

Findings
The paper identifies a class of KAs and its role in relation to other classes of KAs, as it emerges from the empirical investigations.

Research limitations/implications
The focus is on documental artifacts that are, however, widely used in different domains and organizations. New empirical work is needed to consider other kinds of artifacts and their role in knowledge-intense activities.

Practical implications
The paper aims to drive the attention of the designer on phenomena that hinder the acceptance, appropriation and effectiveness of the technologies they design to support a crucial aspect of collaboration.

Originality/value
The paper is original in the following ways: first, documenting the interplay between a kind of KA that is poorly considered in the literature with other classes of KAs; second, highlighting a set of principles that should guide the construction of computational KAs of a different nature.
Rigor, relevance, and the knowledge “market”
Authors: Hamet Joanne , Michel Sylvie 
Published: January 2018

PurposeThe “relevance literature” often moans that the publications of top-ranked academic journals are hardly relevant to managers, while actionable research struggles to get published. The purpose of this paper is to propose a theoretical explanation of this phenomenon.Design/methodology/approachThis paper addresses the relevance debate in management science through the theoretical frame of the theories of the firm.FindingsThis paper proposes that business organizations should tend to internalize specific applied research. Applied to management research, this could explain why the “market” for academic publications might be more relevant for generalizable and conceptual research than for applied, contextualized research.Research limitations/implicationsThe paper is conceptual. However, it provides a new prospect to the rigor-relevance debate and to the ranking of researchers and business schools.Practical implicationsBusiness organizations should tend to internalize specific, applied research. Consequently, academic publications should concentrate on generalizable, “Mode 1” research.Social implicationsThe conclusions could justify the evolution of the rating of universities and researchers towards a multi-dimensional rating, including measures of the socio-economic impact of the research, instead on focusing on academic publications only.Originality/valueThis paper offers a new point of view on the rigor-relevance debate. It supports the idea that applied and conceptual research are different forms of knowledge and should be “traded”, produced and rewarded differently.
To what is the review process relevant?
Authors: Babin Barry J. , Moulard Julie Guidry 
Published: January 2018

Purpose
The purpose of this paper is to consider various strengths and weaknesses of the academic review process with an emphasis on the effect the process has on the relevance of business journals, particularly in the marketing literature.

Design/methodology/approach
The authors not only highlight some of the literature addressing the review process but also present insight and opinion largely based on decades of experience editing, reviewing, writing and publishing.

Findings
Reviewers can help develop research papers, but reviewers remain gatekeepers who, theoretically, protect journals from publishing research that would diminish the truthful body of knowledge within a field. However, many inefficiencies, some of which involve volition, allow one to question whether the review process as we know it best accomplishes that purpose.

Practical implications
Recognizing that reviewers affect journal prestige, the paper concludes with a number of ideas for improving the gate-keeping and developmental functions for academic articles.

Social implications
Society should extract value from what appears in publicly circulated, academic, refereed journals. However, to the extent that the publication process interferes with objective dissemination of knowledge, that value is diminished and perhaps even absent.

Originality/value
The paper intends to stimulate frank conversation about the Academy’s refereed publication process and factors that tend to interfere with its function.
Rigorous and Relevant – introducing a critical discourse analysis to the relevance debate
Authors: Bäckström Izabelle , Ahlgren Kajsa 
Published: January 2018

Purpose
The purpose of this paper is to explore how the notion of “relevance” is produced, distributed and consumed in the field of management research by applying a critical discourse analysis (CDA) as a theoretical lens. A CDA perspective offers a way to scrutinize the power relations that emerge with journal rankings and how these influence how the relevance discourse develops.

Design/methodology/approach
This paper illustrates how a CDA perspective can be fruitfully applied to the relevance literature, exemplifying such an application with two illustrative texts. The texts represent two distinct cases; one is a fictive story informally distributed among scholars, and the other is an extract of a published review on the relevance debate.

Findings
A CDA lens sheds light on how academic power relations are maintained in the production, distribution and consumption of the “relevance” notion. It shows the importance of individual awareness among management researchers of how the discourse is shaped.

Research limitations/implications
To increase the generalizability of the study, a CDA lens could be applied to a larger amount of texts in the relevance literature. The findings imply that the relevance literature would benefit from contributions bridging the gap between rigor and relevance, and questioning how power relations are maintained.

Originality/value
CDA adds a new perspective to the relevance debate, revealing how academic power relations are maintained with management scholars’ adherence to journal norms and the implications of this act.
The feasibility of online dispute resolution in the Islamic banking industry in Malaysia
Authors: Oseni Umar A. , Adewale Abideen Adeyemi , Omoola Sodiq O. 
Published: January 2018

PurposeThe paper aims to examine the perceptions of three major stakeholders – bankers, lawyers and customers – in the Islamic banking industry in Malaysia to assess their behavioural intention to use the proposed online dispute resolution (ODR) mechanism.Design/methodology/approachThe study modifies the unified theory of acceptance and use of technology (UTAUT) within the context of ODR and its feasibility in the Malaysian Islamic banking industry. The model was extended to include trust in technology and trust in bank, which might have significant influences on the intentions of major stakeholders to use ODR for banking-related disputes. Actual use of the ODR was not included in the model as specified in the original UTAUT. Based on an internet survey, responses were obtained from about 109 respondents. The data obtained were subjected to multivariate statistical analyses.FindingsResults obtained indicate that trust in technology and effort expectancy are the most influencing determinants of the behavioural intention to use ODR among stakeholders in the Islamic banking industry in Malaysia. However, performance expectancy and social influence did not produce significant effects on behavioural intention.Research limitations/implicationsApplying ODR in the banking industry in Malaysia will contribute to sustainable banking businesses in major Islamic finance jurisdictions. Being the most advanced region in global Islamic banking business, Asia sets the pace through theoretical and empirical studies in exploring innovative ideals such as ODR to promote sustainable business that not only ensures proper customer relationship management but also promotes consume protection.Practical implicationsResults obtained suggest that the increasing use of internet banking will make ODR the preferable mechanism for dispute resolution in small-scale disputes in retail banking. This will also require some form of predictability, enforceability andShari‘ahcompliance in the process of dispute resolution for the major stakeholders to have full confidence in the ODR mechanism. The recently introduced Financial Ombudsman Scheme in the Islamic Financial Services Act 2013 of Malaysia is expected to serve as a good legal basis for the ODR mechanism.Originality/valueThis appears to be one of the earliest attempts to examine the application of ODR in resolving Islamic banking disputes with a detailed analysis on its legal basis and implication.
The role of international investment agreements in attracting FDI to developing countries
Authors: Beebeejaun Ambareen 
Published: January 2018

PurposeThe study aims to focus on the effectiveness of international investment agreements (IIAs) in helping or facilitating the influx of foreign direct investment (FDI) to host developing countries.Design/methodology/approachTo critically examine the topic, the black letter approach and the socio-legal analysis are adopted. The study has analysed how Mauritius, being a developing country, is responding to FDI needs from various bilateral and multilateral investment treaties concluded, and the research includes the analysis of official data publicly made available by the World Trade Organization, Organisation for Economic Co-operation and Development, International Monetary Fund and Mauritius governmental agencies’ reports.FindingsFrom the methodologies used, it was found that other than IIAs, there are various key determinants which foreign investors consider prior to injecting their capital in developing countries in terms of environmental, social and cultural factors. Also, there are some inherent loopholes mostly in terms of monitoring, in the way IIAs are concluded and are applied in practice by and amongst signatory states.Originality/valueThis research is amongst the first studies to conclude the link between IIAs and FDI flows in developing countries with a particular focus on Mauritius. Additionally, an overwhelming number of studies have emphasised on the efforts to boost FDI, which are inspired mostly by action plans of developed nations, but this research will analyse the policy options adopted by China, being itself a developing country, and the extent to which such recommendations are applicable in the context of Mauritius will also be considered.
Impact of value-adding services on quality, loyalty and brand equity in the brewing industry
Authors: Juga Jari , Juntunen Jouni , Paananen Mikko 
Published: January 2018

Purpose
The purpose of this paper is to investigate the impact of logistics value-adding services and perceived service quality on brand equity among B2B customers of a brewery company.

Design/methodology/approach
A theoretical model is developed and tested using survey data from 173 hotel, restaurant and catering (HoReCa) industry customers of a brewery company in Finland.

Findings
Value-adding services play an important role in building the brewery company’s brand equity through perceived service quality. Besides a direct impact on overall service quality, an indirect impact is detected through the operational dimension of service quality in logistics.

Research limitations/implications
A broader data set would be needed to generalize the findings also beyond the brewery business and the HoReCa industry customers in Finland.

Practical implications
To increase brand equity, value-adding services like logistics can play an important role for B2B customers. This study is important for practitioners and academics, as there has been little quantitative research available regarding value-adding services in the context of service quality and brand equity research.

Originality/value
This paper combines logistics as value-adding service to customers’ willingness to pay extra profits to cooperate with service producer.
Classification model and e-loyalty implications for online services
Authors: Salegna Gary 
Published: January 2018

PurposeThe majority of past classification models for services have failed to account for the different nature of online services, and therefore, they are not helpful in classifying online services. This paper aims to present a new model for classifying online services, and managerial implications for creating customer loyalty to online service organizations are discussed.Design/methodology/approachThis paper presents an overview of the research in service classifications and a classification model for online services based on a review of the services literature.FindingsThe model for online services presented in this paper classifies online services into four categories: online mass services, online mass e-tailing services, online professional and personal services and online service shops.Originality/valueThe classification of online services has received very limited research attention; yet, online services represent a rapidly growing area. The model presented in this paper provides a foundation for the further study and research of online services.