bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diversity of coelomycetous fungi in human infections: a 10-year experience of two European reference centres
Authors: Garcia-Hermoso Dea , Valenzuela-Lopez Nicomedes , Rivero-Menendez Olga , Alastruey-Izquierdo Ana , Guarro Josep , Cano-Lira José F. , Stchigel Alberto M. ,   the French Mycoses Study Group
Published: May 2018

ABSTRACTThe coelomycetous fungi are difficult to properly identify from their phenotypic characterization and their role as etiologic agents of human infections is not clear. We studied the species distribution of these fungi among clinical isolates that had been collected and stored over a ten-year period in two European reference laboratories (France and Spain). We identified phenotypically and molecularly 97 isolates by sequencing the D1-D2 fragment of the 28S nrRNA (LSU) gene. Species of the ordersPleosporalesandGlomerellaleswere present in both collections, andBotryosphaerialesandDiaporthalesonly in the French one. The most prevalent species wereMedicopsis romeroi,Neocucurbitaria keratinophila,Neocucurbitaria unguis-hominisandParaconiothyrium cyclothyrioides, which had been recovered primarily from superficial tissues. TheDidymellaceaewas the most common family represented, with 27 isolates distributed into five genera.
Rapid Pliocene Diversification of Modern Kangaroos
Authors: Couzens Aidan M. C. , Prideaux Gavin J. 
Published: May 2018

Abstract:Differentiating between ancient and rapidly-evolved clades is critical for understanding impacts of environmental change on biodiversity. Australia possesses many aridity-adapted lineages, the origins of which have been linked by molecular evidence to late Miocene drying. Using dental macrowear and molar crown-height measurements spanning the past 25 million years, we show that the most iconic of Australia’s terrestrial mammals, ‘true’ kangaroos and wallabies (Macropodini), diversified in response to Pliocene grassland emergence. In contrast, low-crowned short-faced kangaroos radiated into browsing niches as the late Cenozoic became more arid, contradicting the view that this was a period of global decline among browsers. Our results link warm intervals with bursts of diversification and undermine arguments attributing Pleistocene megafaunal extinction to aridity-forced dietary change.
A segmentation scheme for complex neuronal arbors and application to vibration sensitive neurons in the honeybee brain
Authors: Ikeno Hidetoshi , Kumaraswamy Ajayrama , Kai Kazuki , Wachtler Thomas , Ai Hiroyuki 
Published: May 2018

AbstractThe morphology of a neuron is strongly related to its physiological properties, and thus to information processing functions. Optical microscope images are widely used for extracting the structure of neurons. Although several approaches have been proposed to trace and extract complex neuronal structures from microscopy images, available methods remain prone to errors. In this study, we present a practical scheme for processing confocal microscope images and reconstructing neuronal structures. We evaluated this scheme using image data samples and associated gold standard reconstructions from the BigNeuron Project. In these samples, dendritic arbors belonging to multiple projection branches of the same neuron overlapped in space, making it difficult to automatically and accurately trace their structural connectivity. Our proposed scheme, which combines several software tools for image masking and filtering with an existing tool for dendritic segmentation and tracing, outperformed state-of-the-art automatic methods in reconstructing such neuron structures. For evaluating our scheme, we applied it to a honeybee local interneuron, DL-Int-1, which has complex arbors and is considered to be a critical neuron for encoding the information indicated in the waggle dance of the honeybee.
Targeted induction ofde novoFatty acid synthesis enhances MDV replication in a COX-2/PGE2αdependent mechanism through EP2 and EP4 receptors engagement
Authors: Boodhoo Nitish , Kamble Nitin , Kaufer Benedikt B. , Behboudi Shahriar 
Published: May 2018

AbstractMany viruses alterde novoFatty Acid (FA) synthesis pathway, which can increase availability of energy for replication and provide specific cellular substrates for particle assembly. Marek’s disease virus (MDV) is a herpesvirus that causes deadly lymphoma and has been linked to alterations of lipid metabolism in MDV-infected chickens. However, the role of lipid metabolism in MDV replication is largely unknown. We demonstrate here that infection of primary chicken embryonic fibroblast with MDV activatesde novolipogenesis, which is required for virus replication. In contrast, activation of Fatty Acid Oxidation (FAO) reduced MDV titer, while inhibition of FAO moderately increased virus replication. Thus optimized virus replication occurs if synthetized fatty acids are not used for generation of energy in the infected cells, and they are likely converted to lipid compounds, which are important for virus replication. We showed that infection with MDV activates COX-2/PGE2αpathway and increases the biosynthesis of PGE2α, a lipid mediator generated from arachidonic acid. Inhibition of COX-2 or PGE2αreceptors, namely EP2 and EP4 receptors, reduced MDV titer, indicating that COX-2/PGE2αpathway are involved in virus replication. Our data show that the FA synthesis pathway inhibitors reduce COX-2 expression level and PGE2αsynthesis in MDV infected cells, arguing that there is a direct link between virus-induced fatty acid synthesis and activation of COX-2/PGE2αpathway. This notion was confirmed by the results showing that PGE2αcan restore MDV replication in the presence of the FA synthesis pathway inhibitors. Taken together, our data demonstrate that MDV uses FA synthesis pathway to enhance PGE2αsynthesis and promote MDV replication through EP2 and EP4 receptors engagement.
Cerox1 and microRNA-488-3p noncoding RNAs jointly regulate mitochondrial complex I catalytic activity
Authors: Sirey Tamara M , Roberts Kenny , Haerty Wilfried , Bedoya-Reina Oscar , Rogatti-Granados Sebastian , Tan Jennifer Y , Li Nick , Heather Lisa C , Cooper Sarah , Marques Ana C , Ponting Chris P 
Published: May 2018

AbstractTo generate energy efficiently, the cell is uniquely challenged to co-ordinate the abundance of electron transport chain protein subunits expressed from both nuclear and mitochondrial genomes. How an effective stoichiometry of this many constituent subunits is co-ordinated post-transcriptionally remains poorly understood. Here we show that Cerox1, an unusually abundant cytoplasmic long noncoding RNA (lncRNA), modulates the levels of mitochondrial complex I subunit transcripts in a manner that requires binding to microRNA-488-3p. Increased abundance of Cerox1 cooperatively elevates complex I subunit protein abundance and enzymatic activity, decreases reactive oxygen species production, and protects against the complex I inhibitor rotenone. Cerox1 function is conserved across placental mammals: human and mouse orthologues effectively modulate complex I enzymatic activity in mouse and human cells, respectively. Cerox1 is the first lncRNA demonstrated, to our knowledge, to regulate mitochondrial oxidative phosphorylation (OXPHOS) and, with miR-488-3p, represent novel targets for the modulation of complex I activity.
PIM-related kinases selectively regulate sensory functions in C. elegans
Authors: Kalichamy Karunambigai S. , Ikkala Kaisa , Pörsti Jonna , Santio Niina M. , Jha Sweta , Holmberg Carina I. , Koskinen Päivi J. 
Published: May 2018

ABSTRACTThe mammalian PIM family of serine/threonine kinases regulate several cellular functions, such as cell survival and motility. Since we have observed PIM expression in the olfactory epithelium and other sensory organs of mice, this has raised the question of whether PIM kinases regulate also sensory cell functions. As our model organism to investigate this question, we used the Caenorhabditis elegans nematodes, which express two PIM-related kinases, PRK-1 and PRK-2. We demonstrated them to be true PIM orthologs with similar substrate specificity as well as sensitivity to PIM-inhibitory compounds. Furthermore, we obtained evidence to indicate that PRKs are selectively involved in regulation of olfactory sensations via AWB or AWCON neurons to volatile attractants or repellants, but do not affect gustatory sensations.
Phenotero: annotate as you write
Authors: Hombach Daniela , Schwarz Jana Marie , Knierim Ellen , Schuelke Markus , Seelow Dominik , Köhler Sebastian 
Published: May 2018

AbstractControlled vocabularies and ontologies have become a valuable resource for knowledge representation, data integration, and downstream analyses in the biomedical domain. In precision medicine, especially in clinical genetics, the Human Phenotype Ontology (HPO) as well as disease ontologies like the Orphanet Rare Disease Ontology (ORDO) or Medical Subject Headings (MeSH) are often used for deep phenotyping of patients and coding of clinical diagnoses. However, the process of assigning ontology classes (annotating) to patient descriptions is often disconnected from the process of writing patient reports or manuscripts in word processing software such as Microsoft Word or LibreOffice. This additional workload and the requirement to install dedicated software may discourage usage of ontologies for parts of the target audience.To improve this situation, we present Phenotero, a freely available and simple solution to annotate patient phenotypes and diseases at the time of writing clinical reports or manuscripts. We adopt Zotero, a well-established, actively developed citation management software to generate a tool which allows to reference classes from ontologies within clinical reports or manuscripts at the time of writing. We expect this approach to decrease the additional workload to a minimum while ensuring high quality associations with ontology classes. Standardised collection of phenotypic information at the time of describing the patient allows for streamlining of clinic workflow, efficient data entry, and will subsequently promote clinical and molecular diagnosis, remove ambiguousness from manuscripts, and allow sharing of anonymised patient phenotype data with ultimate goal of a better understanding of the disease. Thus, we hope that our integrated approach will further promote the usage of ontologies and controlled vocabularies in the clinical setting and in the biomedical domain.
Neurofibromin is essential to maintain metabolic function and sustain life in the adult mouse
Authors: Turner Ashley N , Johnson Maria S , Brosius Stephanie N , Yoder Brennan S. , Yang Kevin , Yang Qinglin , Moore John F , Yang Qinglin , Moore John F , Sharer J. Daniel , Smith Daniel L , Nagy Tim R , Schoeb Trent R , Korf Bruce R , Kesterson Robert A 
Published: May 2018

AbstractThe consequences of pathogenic variants in the NF1 gene can manifest in numerous tissues as a result of loss of neurofibromin protein function(s). A known function of NF1 is negative regulation of p21ras signaling via a GTPase activating (Ras-GAP) domain. Besides modulation of Ras signaling as a tumor suppressor, other functions of this multi-domain protein are less clear. Biallelic inactivation of NF1 leads to an embryonic lethal phenotype, while neurofibromin is expressed at varying levels in most tissues beyond developmental stages. Taking advantage of the mouse genetics toolkit, we established novel tamoxifen-inducible systemic knockout Nf1 mouse models (C57BL/6) to gain a better understanding of the role of Nf1 in the adult (3-4 months) mouse. Following inactivation of floxed Nf1 alleles, adult CAGGCre-ERTM;Nf14F/4F mice lose function of Nf1 systemically. Both male and female animals do not survive beyond 11 days post-tamoxifen induction and exhibit histological changes in multiple tissues. During this acute crisis, CAGGCre-ERTM;Nf14F/4F mice are not able to maintain body temperature or body mass, and expend all adipose tissue; however, they continue to consume food and absorb calories comparable to littermate-paired controls. Targeted metabolite analyses and indirect calorimetry studies revealed altered fat metabolism, amino acid metabolism and energy expenditure, with animals undergoing metabolic crisis and torpor-like states. Thermoneutral conditions accelerated the acute, lethal phenotype coincident with lower food intake. This study reveals that systemic loss of neurofibromin in the adult mouse induces metabolic dysfunction and lethality, thus highlighting potential functions of this multi-domain protein in addition to tumor suppression.
Neuronal Modulation of Brown Adipose Activity Through Perturbation of White Adipocyte Lipogenesis
Authors: Guilherme Adilson , Pedersen David J , Henriques Felipe , Bedard Alexander H. , Henchey Elizabeth , Kelly Mark , Rahmouni Kamal , Morgan Donald A. , Czech Michael P 
Published: May 2018

ABSTRACTWhite adipose tissue (WAT) secretes factors to communicate with other metabolic organs to maintain energy homeostasis. We previously reported that perturbation of adipocyte de novo lipogenesis (DNL) by deletion of fatty acid synthase (FASN) causes expansion of sympathetic neurons within white adipose tissue (WAT) and the appearance of “beige” adipocytes. Here we report evidence that white adipocyte DNL activity is also coupled to neuronal regulation and thermogenesis in brown adipose tissue (BAT). Induced deletion of FASN in all adipocytes in mature mice (iAdFASNKO) enhanced sympathetic innervation and neuronal activity as well as UCP1 expression in both WAT and BAT. In contrast, selective ablation of FASN in brown adipocytes of mice (iUCP1FASNKO) failed to modulate sympathetic innervation and the thermogenic program in BAT. Surprisingly, DNL in brown adipocytes was also dispensable in maintaining euthermia when UCP1FASNKO mice were cold-exposed. These results indicate that DNL in white adipocytes influences long distance signaling to BAT, which can modify BAT sympathetic innervation and expression of genes involved in thermogenesis.
The return of the trophic chain: fundamental vs realized interactions in a simple arthropod food web
Authors: Torres-Campos Inmaculada , Magalhães Sara , Moya-Laraño Jordi , Montserrat Marta 
Published: May 2018

AbstractThe mathematical theory describing small assemblages of interacting species (community modules or motifs) has proved to be essential in understanding the emergent properties of ecological communities. These models use differential equations to study pairwise interactions between species. However, as community modules become more complex, it is not certain that all potential interactions will be effectively realized. Here, we use community modules to experimentally explore whether the number of trophic links among species scales with community complexity (i.e., by adding species known to feed on each other from pair-wise trials). To investigate this question, we used a simple mite community present in avocado orchards (Persea americana), composed of two predators (Euseius stipulatus and Neoseiulus californicus), one herbivore as shared prey (Oligonychus perseae), and pollen of Carpobrotus edulis as an alternative food resource. These configurations enabled the potential for (intraguild) predation and (apparent) competition to be expressed. Using a series of controls, we assessed whether the presence of one species affected the survival of another, or its conversion of food into offspring). We found that increasing the number of potential interactions did not result in more complex realized community modules. Instead, all communities were reduced to one or two linear trophic chains. Our results show that trophic links assumed to occur when species are assembled in pairs do not necessarily occur when other components of the community are present. Consequently, food-web structure may be unrealistic in theoretical community modules that are parameterized based on pair-wise interactions observed when alternative prey is absent. This further suggests the need for empirical research to work in concert with theoretical approaches to develop more realistic and predictive food-web models.
Structural basis for transcript elongation control by NusG/RfaH universal regulators
Authors: Young Kang Jin , Anne Mooney Rachel , Nedialkov Yuri , Saba Jason , Mishanina Tatiana V. , Artsimovitch Irina , Landick Robert , Darst Seth A. 
Published: May 2018

SUMMARYNusG/RfaH/Spt5 transcription elongation factors are the only transcription regulators conserved across all life. In bacteria, NusG regulates RNA polymerase (RNAP) elongation complexes (ECs) across most genes, enhancing elongation by suppressing RNAP backtracking and also coordinating ρ-dependent termination and translation. RfaH is a specialized NusG paralog that engages the EC atopssites and subsequently excludes NusG and suppresses both backtrack and hairpin-stabilized pausing. We used single-particle cryo-EM to determine structures of ECs atopswith NusG or RfaH. Both factors chaperone base pairing of the EC upstream duplex DNA to suppress backtracking. RfaH loads onto the EC by specific recognition of anopshairpin in the single-stranded nontemplate DNA. Binding of both NusG and RfaH is incompatible with the swiveled RNAP conformation necessary for hairpin-stabilized pausing, but only RfaH fully counteracts swiveling to suppress pausing. The universal conservation of NusG/RfaH/Spt5 suggests that the molecular mechanisms uncovered here are widespread.
Market earnings expectation, measurement error in analysts’ consensus forecasts and prediction of stock returns
Authors: Kim Jung Hoon 
Published: May 2018

Purpose
In capital markets research, analysts’ consensus forecasts are widely used as a proxy for unobservable market earnings expectation. However, they measure the market earnings expectation with error that may vary cross-sectionally, as the market does not consistently rely on analysts’ consensus forecasts to form earnings expectation (Walther, 1997). Based on this notion, this paper aims to relate the prediction of future stock returns to the cross-sectional variation of the error in measuring market earnings expectation embedded in analysts’ consensus forecasts.

Design/methodology/approach
This study uses empirical analyses based on stock returns and annual analysts’ consensus forecasts.

Findings
Based on the analytical work by Abarbanell et al. (1995), this study reports that when the measurement error in annual analysts’ consensus forecasts is the smallest, forward earnings-to-price ratio (constructed with annual analysts’ consensus forecasts) best explains future stock returns, and the forward earnings-to-price ratio-based investment strategy is the most profitable.

Originality/value
Findings of this study are useful to capital markets research that relies on the market earnings expectation and to practitioners seeking more profitable investment strategies.
Determinants of non-performing loans in banking sector in small developing island states
Authors: Kumar Ronald Ravinesh , Stauvermann Peter Josef , Patel Arvind , Prasad Selvin Sanil 
Published: May 2018

PurposeThe banking sector stability depends in large part on the size of non-performing loans (NPLs). Hence, the factors which explain the problem loans are very useful information for banks. Notably, studies in this regard with respect to the small developing countries’ banking sector have received less attention. Therefore, this study aims to examine the determinants of NPLs with a case of Fiji’s banking sector, over the period 2000-2013.Design/methodology/approachThe balanced sample consists of the entire banking sector (five commercial banks and two non-bank financial institutions). First, the authors estimate a base model which comprise bank-specific indicators that are related to bank management and then they extend the estimations to include macroeconomic/structural factors such as economic growth, inflation, changes of the real effective exchange rate, unemployment, remittances, political instability and external events like the global financial crisis. The estimations are done using pooled OLS, the random effects and the fixed effects regression methods.FindingsThe results show that the following indicators have negative association with NPL and are statistically significant with the conventional levels: return on equity, capital adequacy requirement, market share based on assets, unemployment and time. On the other hand, the net interest margin has a positive and statistically significant association with NPL.Research limitations/implicationsSubsequently, the stability of the banking sector in small developing countries such as Fiji is largely dependent on banks’ profitability, solvency, size in terms of market share and the presence of a learning curve and keeping a close tab on the interest rate spread between loans and deposits.Practical implicationsThe paper highlights the specific factors determining NPL in small developing economy of Fiji.Originality/valueThis study is the first to examine specific factors determining NPLs with respect to small developing economies in the Oceania region.
Company reputation and auditor choice: evidence from fortune 1000 companies
Authors: Huang Xuan , Kang Fei 
Published: May 2018

PurposeThe purpose of this paper is to investigate how companies’ reputation affects their selection of auditors.Design/methodology/approachThis paper measures company reputation using the reputation scores from Fortune’s “America’s Most Admired Companies” list. Multivariate analysis is performed to examine the impact of company reputation on public companies’ auditor choice. Robustness checks include conducting Heckman procedures and instrumental-variable two-stage least square regressions to control for self-selection bias and using alternative measures to proxy for company reputation and auditor industry expertise.FindingsThis paper finds that companies with higher reputations are more likely to hire industry-specialist auditors than their counterparts. The results suggest that because of reputation concerns, high-reputation companies have strong incentives to maintain and signal their financial reporting quality, which in turn increase their demand for audit quality.Practical implicationThis paper suggests that company reputation constitutes an important determinant of auditor selection and, therefore, has both policy and practical implications for the demand of audit services. The paper provides policy-makers and practitioners with insights into critical factors influencing companies’ complex decision process of auditor selection.Originality/valueThe findings of this paper on the empirical link between company reputation and auditor choice contribute to the auditing literature by enhancing the understanding of the effects of different company-level characteristics in financial reporting and audit planning process. This paper also adds to the growing literature on the influence of company reputation on corporate behavior by documenting the important role that company reputation plays in the managerial decision-making process.