bluuebunny/crossref_metadata_2025_split huggingface dataset:
The financialization of local governments—the case of financial rationality in the management of Norwegian hydroelectric utilities
Authors: Løding Tomas Hostad 
Published: May 2018

Abstract
Research on the diminishing distance between global financial markets and traditional nonfinancial actors has increased dramatically over the last decade, most commonly captured in the notion of ‘financialization’. This literature has largely been preoccupied with a confluence of structural changes in the state and in the economy that advance the power and scope of financial capital. However, scholars have also provided evidence for cultural change in the framework in which people think about finance and property. Despite the fact that governments have increasingly engaged in heterodox financial market practices, this culturalized analysis has not yet been extended to the public sector. Based on interview data from Norwegian municipal owners of hydroelectric utilities, this article suggests that a rationality attuned to a financialized world economy is disseminating into public sector management. The article concludes by discussing what this means in a sector traditionally governed by a logic rather alien to that of global finance.
Deep Bidirectional Recurrent Neural Networks as End-To-End Models for Smoking Status Extraction from Clinical Notes in Spanish
Authors: Esteban Santiago , Tablado Manuel Rodríguez , Peper Francisco E. , Terrasa Sergio A. , Kopitowski Karin S. 
Published: May 2018

AbstractIntroductionAlthough natural language processing (NLP) tools have been available in English for quite some time, this is not the case for many other languages, particularly for texts from specific contexts such as clinical texts. This poses a challenge for tasks such as classifying text in languages other than English. In the absence of basic NLP tools, the development of statistical models that include manually designed variables that capture the semantic information of the documents is a potential solution. However, this process is expensive and slow. Deep recurrent neural networks (RNNs) have been proposed as “end-to-end” models that learn both variables and parameters jointly, thus avoiding manual feature engineering and saving development time.MethodsWe compared the performance of two strategies for labeling clinical notes of an electronic medical record in Spanish according to the patient’s smoking status (current smoker, current non-smoker, text without information on tobacco): 1. A traditional approach using two classifiers (a multilayer perceptron (MLP) and a support vector machine (SVM)) together with a ‘bag-of-words’ text representation that involves intensive manual development of features and, 2. an ’end-to-end’ model which uses a Short-Long-Term Memory bidirectional deep RNN with GloVe word embeddings. The classifiers were trained in the training set (n = 11775 clinical texts) and were evaluated in the test set (n = 2943) by means of macro-averaged recall, precision and F1 score.ResultsThe RNN scored high values of all three metrics in the test set (sensitivity [95% CI]: 0.965 [0.96, 0.97], PPV: 0.963 [0.96, 0.97], F1 score: 0.964 [0.96, 0.97]). It also showed to be slightly superior to the MLP (difference in recall: 0.009 [95% CI: -0.0007, 0.017], precision: 0.007 [95% CI: -0.0015, 0.019] and F1 score: 0.009 [95% CI: 0.0018, 0.016]); comparing the RNN with the SVM, the latter has a better performance in general (recall difference [95% CI]: -0.007 [-0.016, 0.0018], precision: -0.009 [-0.018, 0.00015] and score F1: -0.008 [-0.014, -0.0017]). In both cases only the confidence interval for the F1 score difference excludes zero. In turn, the RNN consumed 80% less overall development time.ConclusionIn our work, the deep bidirectional RNN as end-to-end model, reached similar levels of performance in the classification of clinical texts in Spanish that models with a great manual engineering of variables, although in less than 20% of the development time. This makes them an important tool to streamline text processing in languages where the development of NLP tools has not progressed as much as in English. Areas such as research or public health management could clearly benefit from ’end-to-end’ models that facilitate the exploitation of already available data sources, such as electronic clinical records.
Plant trichomes and a single geneGLABRA1contribute to insect community composition on field-grownArabidopsis thaliana
Authors: Sato Yasuhiro , Shimizu-Inatsugi Rie , Yamazaki Misako , Shimizu Kentaro K. , Nagano Atsushi J. 
Published: May 2018

AbstractBackground:Genetic variation in plants alters insect abundance and community structure in the field; however, little is known about the importance of a single gene among diverse plant genotypes. In this context,Arabidopsistrichomes provide an excellent system to discern the roles of natural variation and a key gene,GLABRA1, in shaping insect communities. In this study, we transplanted two independent glabrous mutants (gl1-1andgl1-2) and 17 natural accessions ofArabidopsis thalianato two localities in Switzerland and Japan.Results:Fifteen insect species inhabited plant accessions, with 10–30% broad-sense heritability of community indices being detected, such as species richness and diversity. The total abundance of leaf-chewing herbivores was negatively correlated with trichome density at both the field sites, while glucosinolates had variable effects on leaf chewers between the two sites. Interestingly, there was a parallel tendency for the abundance of leaf chewers to be higher ongl1-1andgl1-2than for their different parental accessions, Ler-1 and Col-0, respectively. Furthermore, the loss of function in theGLABRA1gene significantly decreased the resistance of plants to the two predominant chewers, flea beetles and turnip sawflies.Conclusions:Overall, our results indicate that insect community composition onA. thalianais heritable across two distant field sites, withGLABRA1playing a key role in altering the abundance of leaf-chewing herbivores. Given that such a trichome variation is widely observed in Brassicaceae plants, the present study exemplifies the community-wide impact of a single plant gene on crucifer-feeding insects in the field.
Extracellular HBV RNAs are heterogeneous in length and circulate as virions and capsid-antibody-complexes in chronic hepatitis B patients
Authors: Bai Lu , Zhang Xiaonan , Li Weixia , Wu Min , Liu Jiangxia , Kozlowski Maya , Chen Liang , Zhang Jiming , Huang Yuxian , Yuan Zhenghong 
Published: May 2018

AbstractExtracellular HBV RNA has been detected in both HBV-replicating cell culture media and sera from chronic hepatitis B (CHB) patients, but its exact origin and composition remain controversial. Here, we demonstrated that extracellular HBV RNA species were of heterogeneous lengths, ranging from the length of pregenomic RNA to a few hundred nucleotides. In cell models, these RNAs were predominantly associated with naked capsids although virions also harbored a minority of them. Moreover, HBV RNAs in hepatitis B patients’ blood circulation were localized in unenveloped capsids in the form of capsid-antibody-complexes (CACs) and in virions. Furthermore, we showed that extracellular HBV RNAs could serve as template for viral DNA synthesis. In conclusion, extracellular HBV RNAs mainly consist of pgRNA or the pgRNA species degraded by the RNase H domain of the polymerase in the process of viral DNA synthesis and circulate as CACs and virions. Their presence in the blood circulation of CHB patients may be exploited to develop novel biomarkers for HBV persistence.
Evaluation of two Sigma Transwab® systems for Maintenance of Viability of pathogenic Candida spp. Using the Clinical and Laboratory Standards Institute M40-A2 Standard
Authors: Elcocks E. , Adukwu E.C. 
Published: May 2018

ABSTRACTA key aspect to routine microbiology processes include the retrieval, transport and maintenance of specimens. Swab transport systems (STS) can be utilised for their low cost, ease of use and their ability to recover and maintain specimens over long durations. An increase in healthcare complications due to fungal infections raises the requirement for STS to efficiently recover and preserve pathogens of yeast origin. The Clinical and Laboratory Standards Institute (CLSI) M40-A2 protocol is used to assess the compliance of STS to a quality control standard but at present does not include the recovery of yeast. The aim of this study was to compare the results of two commercial STS and their ability to recover and maintain viability of five clinical and reference strains of Candida spp., including C. auris, when stored at room temperature and 4°C, over 48 h, using the qualitative roll plate method. Findings from this study indicate that the STS used in this study are suitable for the collection and maintenance of the Candida spp. tested, and is very suitable for the recovery of clinical C. auris.
Bifunctional enzyme SpoT is involved in biofilm formation of Helicobacter pylori with multidrug resistance by upregulating efflux pump Hp1174 (gluP)
Authors: Ge Xiaoran , Cai Yuying , Chen Zhenghong , Gao Sizhe , Geng Xiwen , Li Ya , Li Yan , Jia Jihui , Sun Yundong 
Published: May 2018

ABSTRACTThe drug resistance of Helicobacter pylori (H. pylori) is gradually becoming a serious problem. Biofilm formation is an important factor that leads to multidrug resistance in bacteria. The ability of H. pylori to form biofilms on the gastric mucosa has been known. However, there are few studies on the regulation mechanisms of H. pylori biofilm formation and multidrug resistance. Guanosine 3’-diphosphate 5’-triphosphate and guanosine 3’,5’-bispyrophosphate [(p)ppGpp] are global regulatory factors and are synthesized in H. pylori by the bifunctional enzyme SpoT. It has been reported that (p)ppGpp is involved in the biofilm formation and multidrug resistance of various bacteria. In this study, we found that SpoT also plays an important role in H. pylori biofilm formation and multidrug resistance. Therefore, it is necessary to carry out some further studies regarding its regulatory mechanism. Considering that efflux pumps are of great importance in the biofilm formation and multidrug resistance of bacteria, we tried to find if efflux pumps controlled by SpoT participate in these activities. Then, we found that Hp1174 (glucose/galactose transporter, gluP), an efflux pump of the MFS family, is highly expressed in biofilm-forming and multi-drug resistance (MDR) H. pylori and is upregulated by SpoT. Through further research, we determined that gluP involved in H. pylori biofilm formation and multidrug resistance. Furthermore, the average expression level of gluP in clinical MDR strains was considerably higher than that in clinical drug-sensitive strains. Taken together, our results revealed a novel molecular mechanism of H. pylori tolerance to multidrug.
Self-regulation of the Dopaminergic Reward Circuit in Cocaine Users with Mental Imagery and Neurofeedback
Authors: Kirschner Matthias , Sladky Ronald , Haugg Amelie , Stäempfli Philipp , Jehli Elisabeth , Hodel Martina , Engeli Etna , Höesli Sarah , Baumgartner Markus R. , Sulzer James , Huys Quentin J.M. , Seifritz Erich , Quednow Boris B. , Scharnowski Frank , Herdener Marcus 
Published: May 2018

AbstractBackground: Enhanced drug-related reward sensitivity accompanied by impaired sensitivity to non-drug related rewards in the mesolimbic dopamine system are thought to underlie the broad motivational deficits and dysfunctional decision-making frequently observed in cocaine use disorder (CUD). Effective approaches to modify this imbalance and reinstate non-drug reward responsiveness are urgently needed. Here we examine whether cocaine users (CU) can use mental imagery of non-drug rewards to self-regulate the ventral tegmental area and substantia nigra (VTA/SN). We expected that compulsive and obsessive thoughts about cocaine consumption would hamper the ability to self-regulate the VTA/SN. Finally, we tested if self-regulation of the VTA/SN can be improved with real-time fMRI (rtfMRI) neurofeedback (NFB).Methods: Twenty-two CU and 28 healthy controls (HC) were asked to voluntarily up-regulate VTA/SN activity with rewarding non-drug imagery alone, or combined with rtfMRI NFB of VTA/SN activity. Obsessive-compulsive drug use was measured with the Obsessive Compulsive Cocaine Use Scale (OCCUS).Results: CU were able to induce activity in the dopaminergic midbrain and other reward regions with reward imagery. The ability to self-regulate the VTA/SN was reduced in those with more severe obsessive-compulsive drug use. NFB enhanced the effect of non-drug imagery.Conclusion: CU can voluntary activate their reward system through non-drug related imagery and improve this ability with rtfMRI NFB. Combining reward imagery and rtFMRI NFB has great potential for modifying the maladapted reward sensitivity and reinstating non-drug reward responsiveness. This motivates further work to examine the therapeutic potential of cognitive neurostimulation in CUD.
Environmental drivers of ranavirus in free-living amphibians in constructed ponds
Authors: Youker-Smith T.E. , Boersch-Supan P.H. , Whipps C.M. , Ryan S.J. 
Published: May 2018

AbstractAmphibian ranaviruses occur globally, but we are only beginning to understand mechanisms for emergence. Ranaviruses are aquatic pathogens which can cause > 90% mortality in larvae of many aquatic-breeding amphibians, making them important focal host taxa. Host susceptibilities and virulence of ranaviruses have been studied extensively in controlled laboratory settings, but research is needed to identify drivers of infection in natural environments. Constructed ponds, essential components of wetland restoration, have been associated with higher ranavirus prevalence than natural ponds, posing a conundrum for conservation efforts, and emphasizing the need to understand potential drivers. In this study, we analyzed four years of Frog virus 3 prevalence and associated environmental parameters in populations of wood frogs (Lithobates sylvaticus) and green frogs (Lithobates clamitans) in a constructed pond system. High prevalence was best predicted by low temperature, high host density, low zooplankton concentrations, and Gosner stages approaching metamorphosis. This study identified important variables to measure in assessments of ranaviral infection risk in newly constructed ponds, including effects of zooplankton, which have not been previously quantified in natural settings. Examining factors mediating diseases in natural environments, particularly in managed conservation settings, is important to both validate laboratory findings in situ, and to inform future conservation planning, particularly in the context of adaptive management.
Translational control through differential ribosome pausing during amino acid limitation in mammalian cells
Authors: Darnell Alicia M. , Subramaniam Arvind R. , O’Shea Erin K. 
Published: May 2018

SummaryLimitation for amino acids is thought to regulate translation in mammalian cells primarily by signaling through the kinases mTORC1 and GCN2. We find that limitation for the amino acid arginine causes a selective loss of tRNA charging, which regulates translation through ribosome pausing at two of six arginine codons. Surprisingly, limitation for leucine, an essential and abundant amino acid in protein, results in little or no ribosome pausing. Chemical and genetic perturbation of mTORC1 and GCN2 signaling revealed that their robust response to leucine limitation prevents ribosome pausing, while an insufficient response to arginine limitation led to loss of arginine tRNA charging and ribosome pausing. Codon-specific ribosome pausing decreased protein production and triggered premature ribosome termination without significantly reducing mRNA levels. Together, our results suggest that amino acids which are not optimally sensed by the mTORC1 and GCN2 pathways still regulate translation through an evolutionarily conserved mechanism based on codon-specific ribosome pausing.
Topological Skeletonization and Tree-Summarization of Neurons Using Discrete Morse Theory
Authors: Wang Suyi , Li Xu , Mitra Partha , Wang Yusu 
Published: May 2018

AbstractNeuroscientific data analysis has classically involved methods for statistical signal and image processing, drawing on linear algebra and stochastic process theory. However, digitized neuroanatomical data sets containing labelled neurons, either individually or in groups labelled by tracer injections, do not fully fit into this classical framework. The tree-like shapes of neurons cannot mathematically be adequately described as points in a vector space (eg, the subtraction of two neuronal shapes is not a meaningful operation). There is therefore a need for new approaches. Methods from computational topology and geometry are naturally suited to the analysis of neuronal shapes. Here we introduce methods from Discrete Morse Theory to extract tree-skeletons of individual neurons from volumetric brain image data, or to summarize collections of neurons labelled by localized anterograde tracer injections. Since individual neurons are topologically trees, it is sensible to summarize the collection of neurons labelled by a localized anterograde tracer injection using a consensus tree-shape. This consensus tree provides a richer information summary than the regional or voxel-based “connectivity matrix” approach that has previously been used in the literature.The algorithmic procedure includes an initial pre-processing step to extract a density field from the raw volumetric image data, followed by initial skeleton extraction from the density field using a discrete version of a 1-(un)stable manifold of the density field. Heuristically, if the density field is regarded as a mountainous landscape, then the 1-(un)stable manifold follows the “mountain ridges” connecting the maxima of the density field. We then simplify this skeletongraph into a tree using a shortest-path approach and methods derived from persistent homology. The advantage of this approach is that it uses global information about the density field and is therefore robust to local fluctuations and non-uniformly distributed input signals. To be able to handle large data sets, we use a divide-and-conquer approach. The resulting software DiMorSC is available on Github[40]. To the best of our knowledge this is currently the only publicly available code for the extraction of the 1-unstable manifold from an arbitrary simplicial complex using the Discrete Morse approach.
Characteristics of the mitochondrial and cellular uptake of MPP+, as probed by the fluorescent mimic, 4′I-MPP+
Authors: Mapa Mapa S.T. , Le Viet Q. , Wimalasena Kandatege 
Published: May 2018

AbstractThe discovery that 1-methyl-4-phenylpyridinium (MPP+) selectively destroys dopaminergic neurons and causes Parkinson’s disease (PD) symptoms in mammals has strengthened the environmental hypothesis of PD. The current model for the dopaminergic toxicity of MPP+is centered on the uptake into dopaminergic neurons, accumulation into the mitochondria, inhibition of the complex-I leading to ATP depletion, increased reactive oxygen species (ROS) production, and apoptotic cell death. However, some aspects of this mechanism and the details of the cellular and mitochondrial accumulation of MPP+are still poorly understood. The aim of this study was to characterize a structural and functional MPP+mimic which is suitable to study the cellular distribution and mitochondrial uptake of MPP+in live cells and use it to identify the molecular details of these processes to advance the understanding of the mechanism of the selective dopaminergic toxicity of MPP+. Here we report the characterization of the fluorescent MPP+derivative, 1-methyl-4-(4’-iodophenyl)pyridinium (4’I-MPP+), as a suitable candidate for this purpose. Using this novel probe, we show that cytosolic/mitochondrial Ca2+play a critical role through sodium-calcium exchanger (NCX) in the mitochondrial and cellular accumulation of MPP+suggesting for the first time that MPP+and related mitochondrial toxins may also exert their toxic effects through the perturbation of Ca2+homeostasis in dopaminergic cells. We also found that the specific mitochondrial NCX (mNCX) inhibitors protect dopaminergic cells from the MPP+and 4’I-MPP+toxicity, most likely through the inhibition of the mitochondrial uptake, which could potentially be exploited for the development of pharmacological agents to protect the central nervous system (CNS) dopaminergic neurons from PD-causing environmental toxins.
Hierarchical organization of developing HSPC in the human embryonic liver
Authors: Zhang Y. , Clay D. , Mitjavila-Garcia M.T. , Alama A. , Mennesson B. , Berseneff H. , Louache F. , Bennaceur-Griscelli A. , Oberlin E. 
Published: May 2018

ABSTRACTDespite advances to engineer transplantable hematopoietic stem and progenitor cells (HSPCs) for research and therapy, an in depth characterization of the developing human hematopoietic system is still lacking. The human embryonic liver is at the crossroad of several hematopoietic sites and harbours a complex hematopoietic hierarchy including the first, actively dividing, HSPCs that will further seed the definitive hematopoietic organs. However few is known about the hierarchical phenotypic and functional hematopoietic organization operating at these stages of development.Here, by using a combination of four endothelial and hematopoietic surface markers i.e. the endothelial-specific marker VE-cadherin, the pan-leukocyte antigen CD45, the hemato-endothelial marker CD34 and the Angiotensin-Converting Enzyme (ACE, CD143), encompassing all early human HSPCs, we identified a hematopoietic hierarchy and, among it, a population co-expressing the four markers that uniquely harbored a proliferation and differentiation potential bothex vivoandin vivo. Moreover, we traced back this population to the yolk sac and AGM sites of hematopoietic emergence. Taken together, our data will help to identify human HSPC self-renewal and amplification mechanisms for future cell therapies.SUMMARY STATEMENTWe uncover the phenotypic and functional hematopoietic hierarchy operating in the early human embryo. It will bring insights into the mechanisms driving hematopoietic stem cell self-renewal for future cell therapies.