bluuebunny/crossref_metadata_2025_split huggingface dataset:
Parallelized Inference for Single Cell Transcriptomic Clustering with Split Merge Sampling on DPMM Model
Authors: Duan Tiehang , Pinto José P. , Xie Xiaohui 
Published: February 2018

Motivation:With the development of droplet based systems, massive single cell transcriptome data has become available, which enables analysis of cellular and molecular processes at single cell resolution and is instrumental to understanding many biological processes. While state-of-the-art clustering methods have been applied to the data, they face challenges in the following aspects: (1) the clustering quality still needs to be improved; (2) most models need prior knowledge on number of clusters, which is not always available; (3) there is a demand for faster computational speed.Results:We propose to tackle these challenges withParallelized Split Merge Sampling onDirichletProcessMixtureModel (the Para-DPMM model). Unlike classic DPMM methods that perform sampling on each single data point, the split merge mechanism samples on the cluster level, which significantly improves convergence and optimality of the result. The model is highly parallelized and can utilize the computing power of high performance computing (HPC) clusters, enabling massive inference on huge datasets. Experiment results show the model achieves about 7% improvement in clustering accuracy for small datasets and more than 20% improvement for large challenging datasets compared with current widely used models. In the mean time, the model’s computing speed is significantly faster.Availability:Source code is publicly available onhttps://github.com/tiehangd/Para_DPMM/tree/master/Para_DPMM_package
GTSF-1 is required for the formation of a functional RNA-dependent RNA Polymerase complex in C. elegans
Authors: Almeida Miguel Vasconcelos , Dietz Sabrina , Redl Stefan , Karaulanov Emil , Hildebrandt Andrea , Renz Christian , Ulrich Helle D. , König Julian , Butter Falk , Ketting René F. 
Published: February 2018

AbstractIn every domain of life, Argonaute proteins and their associated small RNAs regulate gene expression. Despite great conservation of Argonaute proteins throughout evolution, many proteins acting in small RNA pathways are not widely conserved. Gametocyte-specific factor 1 (Gtsf1) proteins, characterized by two tandem CHHC zinc fingers and an unstructured, acidic C-terminal tail, are conserved in animals and act in small RNA pathways. In fly and mouse, they are required for fertility and have been shown to interact with Piwi clade Argonautes. We identified T06A10.3 as the Caenorhabditis elegans Gtsf1 homolog and named it gtsf-1. Given its conserved nature and roles in Piwi-mediated gene silencing, we sought out to characterize GTSF-1 in the context of the small RNA pathways of C. elegans. Like its homologs, GTSF-1 is required for normal fertility. Surprisingly, we report that GTSF-1 is not required for Piwi-mediated gene silencing. Instead, gtsf-1 mutants show strong depletion of a class of endogenous small RNAs, known as 26G-RNAs, and fully phenocopy mutants lacking RRF-3, the RNA-dependent RNA Polymerase that synthesizes 26G-RNAs. We show, both in vivo and in vitro, that GTSF-1 specifically and robustly interacts with RRF-3 via its tandem CHHC zinc fingers. Furthermore, we demonstrate that GTSF-1 is required for the assembly of a larger RRF-3 and DCR-1-containing complex, also known as ERIC, thereby allowing for 26G-RNA generation. We propose that GTSF-1 homologs may similarly act to drive the assembly of larger complexes that subsequently act in small RNA production and/or in imposing small RNA-mediated silencing activities.
A bHLH-PAS protein regulates light-dependent diurnal rhythmic processes in the marine diatomPhaeodactylum tricornutum
Authors: Annunziata Rossella , Ritter Andrés , Fortunato Antonio Emidio , Cheminant-Navarro Soizic , Agier Nicolas , Huysman Marie J. J. , Winge Per , Bones Atle , Bouget François-Yves , Lagomarsino Marco Cosentino , Bouly Jean Pierre , Falciatore Angela 
Published: February 2018

ABSTRACTPeriodic light-dark cycles govern the timing of basic biological processes in organisms inhabiting land as well as the sea, where life evolved. Although prominent marine phytoplanktonic organisms such as diatoms show robust diurnal rhythms in growth, cell cycle and gene expression, the molecular foundations controlling these processes are still obscure. By exploring the regulatory landscape of diatom diurnal rhythms, we unveil the function of aPhaeodactylum tricornutumbHLH-PAS protein,PtbHLH1a, in the regulation of light-dependent diurnal rhythms. Peak expression ofPtbHLH1amRNA occurs toward the end of the light period and it adjusts to photoperiod changes. Ectopic over-expression ofPtbHLH1a results in lines showing a phase shift in diurnal cell fluorescence, compared to the wild-type cells, and with altered cell cycle progression and gene expression. Reduced oscillations in gene expression are also observed in overexpression lines compared to wild-type in continuous darkness, showing that the regulation of rhythmicity byPtbHLH1a is not directly dependent on light inputs and cell division.PtbHLH1a homologs are widespread in diatom genomes which may indicate a common function in many species. This study adds new elements to understand diatom biology and ecology and offers new perspectives to elucidate timekeeping mechanisms in marine organisms belonging to a major, but underinvestigated branch of the tree of life.SIGNIFICANCE STATEMENTMost organisms experience diurnal light-dark changes and show rhythms of basic biological processes such that they occur at optimal times of the day. The ocean harbours a huge diversity of organisms showing light-dependent rhythms, but their molecular foundations are still largely unknown. In this study, we discover a novel protein,PtbHLH1a that regulates cell division, gene expression and the diurnal timing of these events in the marine diatomPhaedoactylum tricornutum. The identification ofPtbHLH1a-like genes in many diatom species suggests a conserved function in diurnal rhythm regulation in the most species-rich group of algae in the ocean. This study unveils critical features of diatom biology and advances the field of marine rhythms and their environmental regulation.
The role of AP-1 in self-sufficient proliferation and migration of cancer cells and its potential impact on an autocrine/paracrine loop
Authors: Ibrahim Abd El-Fattah Sherif , Abudu Aierken , Jonhson Eugenia , Aftab Neelum , Fluck Michele 
Published: February 2018

ABSTRACTThe activating protein-1 (AP-1) family members are highly expressed in invasive cancers, but the consequences of this are not completely understood. The aim of this study was to explore the significance of elevated levels of AP-1 family members under conditions that restrict growth. We observed that invasive MDA-MB-231 cells express high levels of Fra-1, c-Jun and, Jun-D during serum starvation and throughout the cell cycle compared to non-tumorigenic and non-invasive cell lines. We then analyzed Fra-1 levels in additional breast and other cancer cell lines. We found a correlation between the high levels of Fra-1 during serum starvation and the ability of the cells to proliferate and migrate under these conditions. Utilizing a dominant negative construct of AP-1, we demonstrated that proliferation and migration of MDA-MB-231 in the absence of serum requires AP-1 activity. Finally, we observed that MDA-MB-231 cells secrete factors(s) that induce Fra-1 expression and migration in non-tumorigenic and non-metastatic cells and that both the expression of and response to these factors require AP-1 activity. These results suggest the presence of an autocrine/paracrine loop that maintains high Fra-1 levels in aggressive cancer cells, enhancing their proliferative and metastatic ability and affecting neighbors to alter the tumor environment.
The exon junction complex regulates the release and phosphorylation of paused RNA polymerase II
Authors: Akhtar Junaid , Kreim Nastasja , Marini Federico , Kumar Mohana Giriram , Brune Daniel , Binder Harald , Roignant Jean-Yves 
Published: February 2018

SUMMARYPromoter proximal pausing of RNA polymerase II (Pol II) is a widespread transcriptional regulatory step across metazoans. Here we find that the nuclear exon junction complex (pre-EJC) plays a critical and conserved role in this process. Depletion of pre-EJC subunits leads to a global decrease in Pol II pausing and to premature entry into elongation. This effect occurs, at least in part, via non-canonical recruitment of pre-EJC components at promoters. Failure to recruit the pre-EJC at promoters results in increased binding of the positive transcription elongation complex (P-TEFb) and in enhanced Pol II release. Notably, restoring pausing is sufficient to rescue exon skipping and the photoreceptor differentiation defect associated with depletion of pre-EJC componentsin vivo. We propose that the pre-EJC serves as an early transcriptional checkpoint to prevent premature entry into elongation, ensuring proper recruitment of RNA processing components that are necessary for exon definition.
Seafood export as a relationship-oriented supply network
Authors: Glavee-Geo Richard , Engelseth Per 
Published: February 2018

PurposeThe purpose of this paper is to examine the role of relationships and networking in the international flow of seafood products through export processes and practices using empirical case examples.Design/methodology/approachThis paper provides an insight into seafood export through ten case studies of seafood exporters from Norway and a freight forwarder working with most of these companies.FindingsThe international seafood business is characterised by coordination, interactions, and exchange such that economic and social interactions among network members transcend national boundaries into international/global markets. The findings reveal how studied seafood exports are in line with the learning-based Uppsala internationalisation model, embedded in international buyer-seller relationship structures and networks, which is also a particularity of this food-producing industry. To secure long-term business in distant markets, small- and medium-sized (SME) seafood exporters have shifted the focus from transactional approaches to relationships and networking as a means of improving export performance. This paper suggests how logistics and marketing have become closely and strategically interconnected, and so marketing strategies depend on logistics strategies and the two cannot be separated in a typical global seafood supply network.Practical implicationsPurposeful collaborative interaction between exporter and importer helps in risk mitigation. Increased interactions in distant markets by SMEs can also be achieved using social media networking.Originality/valueThis paper offers an insight into the global seafood supply network using empirical case examples from Norway, an important seafood producing country.
Supply chain agility: a mediator for absorptive capacity
Authors: Martinez-Sanchez Angel , Lahoz-Leo Fernando 
Published: February 2018

PurposeThe purpose of this paper is to analyse the mediating effect of supply chain agility (SCA) in the relationship between absorptive capacity (AC) and firm performance.Design/methodology/approachThe authors use data from 231 Spanish firms and test the hypothesis by structural equation modelling.FindingsSCA mediates the relationship between AC and firm performance.Research limitations/implicationsThe cross-sectional survey and the use of managerial perceptions may need to use longitudinal and real measures in future studies to validate causal relationships.Practical implicationsSCA may contribute to explain why AC improves firm performance. Firms with more agile supply chains may benefit more from their efforts in AC to improve firm performance.Originality/valueA conceptual framework has been developed to explain the relationships of the main constructs of the study (AC and SCA) with firm performance and whether SCA mediates the relationship between AC and firm performance.
Use of Big Four auditors and fund raising: evidence from developing and emerging markets
Authors: Beisland Leif Atle , Mersland Roy , Strøm Øystein 
Published: February 2018

PurposeThis study is motivated by recent research suggesting that the funding benefits of using Big Four auditors may not be as uniform as were previously assumed. The purpose of this paper is to analyze the relationship between use of Big Four auditors and access to debt capital by applying data from microfinance institutions (MFIs) in emerging countries, a population typically not investigated in accounting research.Design/methodology/approachThe authors apply a unique hand-collected data set from 60 emerging markets and empirically investigate whether access to various debt categories is related to the use of Big Four auditors.FindingsThe authors find that access to international commercial debt, international subsidized debt and government agency debt is positively related to the use of a Big Four auditor. For local commercial debt, the authors find no association between auditor type and access to debt capital. The association between auditor choice and access to debt capital is stronger for nonprofit than for-profit MFIs.Originality/valueThis is the first audit quality study to include a broad sample of emerging countries, which in itself is an important contribution. As far as general audit quality research is concerned, the authors take the literature one step further by showing that the benefits of using a Big Four auditor may be dependent on the specific source of debt financing a firm or organization seeks to use. Moreover, the authors demonstrate that the for-profit vs nonprofit dimension influences the relationship between auditor choice and access to capital.
Continuous glucose monitoring: a systematic review of sensor systems and prospects
Authors: Ray Partha Pratim 
Published: February 2018

Purpose
Continuous glucose monitoring (CGM) is a notable invention introduced in the biomedical industry. It provides valuable information about intermittent capillary blood glucose that is normally unattainable by regular clinical blood sample tests. CGM includes several progressive facilities such as instantaneous and real-time display of blood glucose level, “24/7” coverage, continuous motion of alerts for actual or impending hypo- and hyperglycemia and the ability to characterize glycemic variability. CGM allows users and physicians to visualize and diagnose more accurate and precise rate of change of glucose by capacitating small, comfortable, user-friendly sensor devices. Sometimes, this vital information is shared to the personal message box over Internet. In short, CGM is capable to inform, educate, motivate and alert (IEMA) people with diabetes. Despite the huge expectation with CGM, the available solutions have not attracted much attention among people. The huge potential of CGM in future diabetic study relies on the successful implication of the CGM. This paper aims at disseminating of state-of-the-art knowledge about existing work around the CGM.

Design/methodology/approach
This paper presents a comprehensive systematic review on the recent developments in CGM development techniques that have been reported in credible sources, namely PubMed, IEEE Xplore, Science Direct, Springer Link, Scopus and Google Scholar. Detailed analysis and systematic comparison are provided to highlight the achievement and future direction of CGM deployment.

Findings
Several key challenges are also portrayed for suitable opportunistic orientation. CGM solutions from four leading manufacturers such as Tandem, Dexcom, Abbott and Medtronic are compared based on the following factors including accuracy (% MARD); sensor lifetime, calibration requirement, smart device, compatibility and remote monitoring. Qualitative and quantitative analyses are performed.

Originality/value
This work can be a valuable source of reference and guidance for future research in this field.
Explaining determinants of Agri-tourism income: evidence from Italy
Authors: Giaccio Vincenzo , Giannelli Agostino , Mastronardi Luigi 
Published: February 2018

PurposeThe purpose of this paper is to analyze the income sources of Italian farm tourism businesses, considering some economic, social and environmental variables that represent internal business factors and highlighting their contribution to the development of this income.Design/methodology/approachThe empirical analysis is based on the Italian section of the Farm Accountancy Data Network (FADN) that includes 365 Italian farm tourism businesses. FADN is an instrument to assess the income of European agricultural holdings and the impacts of the Common Agricultural Policy. The analysis has been carried out through a Multivariate Regression Model.FindingsThe results of this paper have showed that some economic variables (food service, direct selling and public subsidies) determine an increase in farm income, whereas an increased number of family employees may have a negative impact on this income.Research limitations/implicationsExternal factors, such as proximity to urban or cultural centres, may impact on agri-tourism income, but these are not considered in the statistical analyses. Another limit of this paper is the exclusion of tourists’ motivational variables and others mostly referring to the market (pricing policies, promotional strategies, etc.). Furthermore, this paper focuses on a specific country and this could reduce the generalization of its results.Practical implicationsThanks to the selected regression drivers, farmers who offer tourism services could recognize a priori their entrepreneurial opportunities and understand the variables on which to focus to increase their income, which could be in turn strengthened by policies seeking to develop the endogenous potential.Social implicationsAgri-tourism can fulfill various functions in the regional economy, with positive implications for the quality of life of rural societies.Originality/valueOn the European level, there is currently a lack of research studying the variables affecting agri-tourism revenue and entrepreneurial choice that mostly define profitability. This may be the first time that FADN data set has been utilized for researching farm tourism businesses in Europe.
In vivo optical coherence tomography imaging in a case of mucous membrane pemphigoid and a negative Nikolsky's sign
Authors: Capocasale Giorgia , Panzarella Vera , Rodolico Vito , Di Fede Olga , Campisi Giuseppina 
Published: February 2018

AbstractThere is currently a growing interest in new diagnostic tools of the oral cavity and mucosa which are non‐invasive, repeatable and reliable. A diagnosis of a suspected, autoimmune pathology was made regarding a 57‐year‐old patient with desquamative gingivitis. However, a negative Nikolsky's sign did not seem to indicate a diagnosis of mucous membrane pemphigoid neither was there any indication as to the optimum location for an incisional biopsy. As an imaging method, the use of optical coherence tomography (OCT) has enabled the obtaining of tomographic (cross‐sectional) scans of tissue. Such images are acquired prior to and after verifying Nikolsky's sign, thereby enabling the clinician to identify the presence (or not) of subepithelial bullae. Thereafter, an assessment of changes in the subepithelium (the split) can be performed, even in the absence of a suitable clinical picture, such as, for example, a negative Nikolsky's sign. Histological analysis and the use of indirect immunofluorescence have facilitated a diagnosis of mucous membrane pemphigoid, an autoimmune pathology, which can be confirmed with the appearance of subepithelial bullae. OCT was found to be a valid, non‐invasive, auxiliary diagnostic device, capable of revealing in vivo and real‐time bullae, which were hitherto clinically undetectable.
Critically ill neonates displayed stable vital parameters and reduced metabolic acidosis during neonatal emergency airborne transport in Sweden
Authors: Frid Ingrid , Ågren Johan , Kjellberg Mattias , Normann Erik , Sindelar Richard 
Published: February 2018

AbstractAimThis study evaluated the medical quality of acute airborne transports carried out by a neonatal emergency transport service in a Swedish healthcare region from 2012 to 2015.MethodsThe transport charts and patient records of all infants transported to the regional centre were reviewed for transport indications and vital parameters and outcomes.ResultsWe identified 187 acute airborne transports and the main indications for referral were therapeutic hypothermia after perinatal asphyxia, extremely preterm birth and respiratory failure. There were 37 deaths, but none of these occurred during transport and none of the deaths that occurred within 24 hours after transport were found to be related to the transport per se. No differences were found in vital parameters or ventilator settings before and after transport, except for an improvement in blood pH (7.22 ± 0.13 versus 7.27 ± 0.13, mean ± SD, p < 0.01), due to a decrease in base deficit (−8.0 ± 6.8 versus −5.4 ± 6.3 mmol, p < 0.001), while the partial pressure of carbon dioxide remained unchanged.ConclusionDuring air transport, critically ill neonates displayed stable vital parameters and reduced metabolic acidosis. No transport‐related mortality was found, but the high number of extremely preterm infants transported indicates the potential for improving in‐utero transport.
Deletion of Uncoupling Protein‐2 reduces renal mitochondrial leak respiration, intrarenal hypoxia and proteinuria in a mouse model of type 1 diabetes
Authors: Friederich‐Persson M. , Persson P. , Hansell P. , Palm F. 
Published: February 2018

AbstractAimUncoupling protein‐2 (UCP‐2) can induce mitochondrial uncoupling in the diabetic kidney. Although mitochondrial uncoupling reduces oxidative stress originating from the mitochondria and can be regarded as a protective mechanism, the increased oxygen consumption occurring secondarily to increased mitochondria uncoupling, that is leak respiration, may contribute to kidney tissue hypoxia. Using UCP‐2−/− mice, we tested the hypothesis that UCP‐2‐mediated leak respiration is important for the development of diabetes‐induced intrarenal hypoxia and proteinuria.MethodsKidney function, in vivo oxygen metabolism, urinary protein leakage and mitochondrial function were determined in wild‐type and UCP‐2−/− mice during normoglycaemia and 2 weeks after diabetes induction.ResultsDiabetic wild‐type mice displayed mitochondrial leak respiration, pronounced intrarenal hypoxia, proteinuria and increased urinary KIM‐1 excretion. However, diabetic UCP‐2−/− mice did not develop increased mitochondrial leak respiration and presented with normal intrarenal oxygen levels, urinary protein and KIM‐1 excretion.ConclusionAlthough functioning as an antioxidant system, mitochondria uncoupling is always in co‐occurrence with increased oxygen consumption, that is leak respiration; a potentially detrimental side effect as it can result in kidney tissue hypoxia; an acknowledged unifying pathway to nephropathy. Indeed, this study demonstrates a novel mechanism in which UCP‐2‐mediated mitochondrial leak respiration is necessary for the development of diabetes‐induced intrarenal tissue hypoxia and proteinuria.