Miracle-dz/UniFAR-FTUs huggingface dataset:
Expression and Function of Four Carbonic Anhydrase Homologs in the Deep-Sea Chemolithoautotroph Thiomicrospira crunogena

ABSTRACT The hydrothermal vent chemolithoautotroph Thiomicrospira crunogena grows rapidly in the presence of low concentrations of dissolved inorganic carbon (DIC) (= CO2 + HCO3− + CO3−2). Its genome encodes α-carbonic anhydrase (α-CA), β-CA, carboxysomal β-like CA (CsoSCA), and a protein distantly related to γ-CA. The purposes of this work were to characterize the gene products, determine whether they were differentially expressed, and identify those that are necessary for DIC uptake and fixation. When expressed in Escherichia coli, CA activity was detectable for α-CA, β-CA, and CsoSCA but not for the γ-CA-like protein. α-CA and CsoSCA but not β-CA were inhibited by sulfonamide inhibitors. CsoSCA was also inhibited by dithiothreitol. When grown under DIC limitation in chemostats, T. crunogena transcribed csoSCA more frequently than when ammonia limited, while genes encoding α-CA and β-CA were not differentially transcribed under these conditions. Cell extracts from T. crunogena grown under both DIC- and ammonia-limited conditions had CA activity that was strongly inhibited by sulfonamides, though extracts from nitrogen-limited cells had some CA activity that was resistant, perhaps due to a higher level of β-CA activity. Based on predictions from the SignalP software program, subcellular location when expressed in E. coli, and carbonic anhydrase assays conducted on intact T. crunogena cells, α-CA is located in the periplasm. However, inhibition of α-CA by acetazolamide had only a minor impact on rates of DIC uptake or fixation. Conversely, inhibition of CsoSCA with ethoxyzolamide inhibited carbon fixation but not DIC uptake, consistent with this enzyme functioning to facilitate DIC interconversion and fixation within carboxysomes.
Liver enzymes, nonalcoholic fatty liver disease, and incident cardiovascular disease: A narrative review and clinical perspective of prospective data

In recent years, a strong link has been established between nonalcoholic fatty liver disease (NAFLD) and the pathogenesis of type 2 diabetes mellitus. The potential role of NAFLD in cardiovascular disease (CVD) has also attracted interest. Published studies have tended to use biochemical and imaging surrogate markers of NAFLD, such as elevated gamma glutamyl transpeptidase (GGT) and alanine aminotransferase (ALT) and fatty liver on ultrasound, when investigating associations with incident CVD events. Positive associations between both baseline GGT and temporal change in GGT, as well as cardiovascular events and cardiovascular mortality independent of alcohol intake, have been reported in several prospective studies. However, adjustment for confounders is often incomplete, and there is scant evidence of improvement in cardiovascular risk prediction beyond established risk scores when incorporating such data. There also appears to be a strong and underrecognized age interaction, with associations between GGT and incident coronary heart disease (CHD) being strong in young individuals but relatively weak in the elderly. By contrast, ALT appears to be only weakly associated with incident CHD and may exhibit a U‐shaped association with total mortality. Finally, although some studies have linked imaging‐defined and biopsy‐confirmed NAFLD with CVD risk, the evidence is inconsistent, with few incident events and/or insufficient potential confounders. Conclusion: A diagnosis of NAFLD is insufficient to consider patients as being at high risk for CVD. The presence of NAFLD should be a clear indication for diabetes screening, but cardiovascular risk screening should be performed with the use of existing risk calculators and should be guided by established cardiovascular risk factors. (HEPATOLOGY 2010;)
p‐Coumaric Acid Activates the GABA‐A Receptor In Vitro and is Orally Anxiolytic In Vivo

The increasing prevalence and social burden of subclinical anxiety in the western world represents a significant psychosocial and financial cost. Consumers are favouring a more natural and nonpharmacological approach for alleviating the effects of everyday stress and anxiety. The gamma‐aminobutyric acid (GABA) receptor is the primary mediator of central inhibitory neurotransmission, and GABA‐receptor agonists are well known to convey anxiolytic effects. Using an in vitro screening approach to identify naturally occurring phytochemical GABA agonists, we discovered the plant secondary metabolite p‐coumaric acid to have significant GABAergic activity, an effect that could be blocked by co‐administration of the specific GABA‐receptor antagonist, picrotoxin. Oral administration of p‐coumaric acid to rodents induced a significant anxiolytic effect in vivo as measured using the elevated plus paradigm, in line with the effects of oral diazepam. Given that p‐coumaric acid is reasonably well absorbed following oral consumption in man and is relatively nontoxic, it may be suitable for the formulation of a safe and effective anxiolytic functional food. Copyright © 2013 John Wiley & Sons, Ltd.
Neural correlates of fair behavior in interpersonal bargaining

Research findings show that proposers make surprisingly fair offers in the ultimatum and dictator games, an observation that contradicts predictions of classical game theory. The present functional magnetic resonance imaging (fMRI) study examines brain activities of proposers that contribute to fair and unfair behaviors. We hypothesized that egoistic and altruistic motives of proposers affect fairness differentially in the two games. fMRI analysis revealed that the 28% of fair offers in the present ultimatum game were related to enhanced activity in prefrontal areas, in particular, in regions involved in reward and theory of mind. This corroborates the idea that egoistic motives are primarily responsible for fair offers in this game, which we denote as strategic fairness. Fair offers in the dictator game, however, were related to increased activity in the dorsal anterior cingulate cortex and the posterior cingulate cortex. This supports the idea that altruistic motives primarily drive fair offers in the dictator game, denoted here as altruistic fairness.
Periodic reversal of direction allows Myxobacteria to swarm

Many bacteria can rapidly traverse surfaces from which they are extracting nutrient for growth. They generate flat, spreading colonies, called swarms because they resemble swarms of insects. We seek to understand how members of any dense swarm spread efficiently while being able to perceive and interfere minimally with the motion of others. To this end, we investigate swarms of the myxobacterium, Myxococcus xanthus. Individual M. xanthus cells are elongated; they always move in the direction of their long axis; and they are in constant motion, repeatedly touching each other. Remarkably, they regularly reverse their gliding directions. We have constructed a detailed cell- and behavior-based computational model of M. xanthus swarming that allows the organization of cells to be computed. By using the model, we are able to show that reversals of gliding direction are essential for swarming and that reversals increase the outflow of cells across the edge of the swarm. Cells at the swarm edge gain maximum exposure to nutrient and oxygen. We also find that the reversal period predicted to maximize the outflow of cells is the same (within the errors of measurement) as the period observed in experiments with normal M. xanthus cells. This coincidence suggests that the circuit regulating reversals evolved to its current sensitivity under selection for growth achieved by swarming. Finally, we observe that, with time, reversals increase the cell alignment, and generate clusters of parallel cells.
Developing measures of food and nutrition security within an Australian context

Abstract Objective To develop a measure of food and nutrition security for use among an Australian population that measures all pillars of food security and to establish its content validity. Design The study consisted of two phases. Phase 1 involved focus groups with experts working in the area of food security. Data were assessed using content analysis and results informed the development of a draft tool. Phase 2 consisted of a series of three online surveys using the Delphi technique. Findings from each survey were used to establish content validity and progressively modify the tool until consensus was reached for all items. Setting Australia. Subjects Phase 1 focus groups involved twenty-five experts working in the field of food security, who were attending the Dietitians Association of Australia National Conference, 2013. Phase 2 included twenty-five experts working in food security, who were recruited via email. Results Findings from Phase 1 supported the need for an Australian-specific tool and highlighted the failure of current tools to measure across all pillars of food security. Participants encouraged the inclusion of items to measure barriers to food acquisition and the previous single item to enable comparisons with previous data. Phase 2 findings informed the selection and modification of items for inclusion in the final tool. Conclusions The results led to the development of a draft tool to measure food and nutrition security, and supported its content validity. Further research is needed to validate the tool among the Australian population and to establish inter- and intra-rater reliability.
Regulation of neuronal survival by DNA methyltransferases

The limited regenerative capacity of neuronal cells requires tight orchestration of cell death and survival regulation in the context of longevity, age-associated diseases as well as during the development of the nervous system. Subordinate to genetic networks epigenetic mechanisms like DNA methylation and histone modifications are involved in the regulation of neuronal development, function and aging. DNA methylation by DNA methyltransferases (DNMTs), mostly correlated with gene silencing, is a dynamic and reversible process. In addition to their canonical actions performing cytosine methylation, DNMTs influence gene expression by interactions with histone modifying enzymes or complexes increasing the complexity of epigenetic transcriptional networks. DNMTs are expressed in neuronal progenitors, post-mitotic as well as adult neurons. In this review, we discuss the role and mode of actions of DNMTs including downstream networks in the regulation of neuronal survival in the developing and aging nervous system and its relevance for associated disorders.
Economic Correlates of Suicide Rates in OECD Countries

This paper investigates how economic conditions are associated with age-sex group specific suicide rates in a panel of 28 OECD countries over the period 1980-2002. We consider the trend and cyclical components of income, unemployment, income inequality, inflation, as well as various socio-demographic control variables. Results depend on whether stationarity properties are adequately accommodated or not. Estimating models in first differences we find that the cyclical component of income is negatively associated with suicide rates of men, while suicide rates of women are primarily affected by unemployment. Moreover, our estimations show that the effects of the cyclical component of income and unemployment are most pronounced in OECD countries with low public social security spending.
An Empirical Comparative Study on Two Large-Scale Hierarchical Text Classification Approaches

Patent classification is a large scale hierarchical text classification (LSHTC) task. Though comprehensive comparisons, either learning algorithms or feature selection strategies, have been fully made in the text categorization field, few work was done for a LSHTC task due to high computational cost and complicated structural label characteristics. For the first time, this paper compares two popular learning frameworks, namely, hierarchical support vector machine (SVM) and k-nearest neighbor (k-NN) that are applied to a LSHTC task. Our experimental results show that the latter outperforms the former for the LSHTC task, which is quite different from the existing results for normal text categorization tasks. In addition, this paper compares different similarity measures and ranking strategies in k-NN framework for LSHTC task. From our empirical study, conclusions can be drawn that k-NN is more appropriate for the LSHTC task than hierarchical SVM. BM25 outperforms other similarity measures and ListWeak gains a better performance than other ranking strategies. Our empirical results also indicate that using all the labels of the retrieved neighbors can remarkably improve classification performance over only using the first label of the retrieved neighbors.
Exploring the DNA-binding specificities of zinc fingers with DNA microarrays

A key step in the regulation of networks that control gene expression is the sequence-specific binding of transcription factors to their DNA recognition sites. A more complete understanding of these DNA–protein interactions will permit a more comprehensive and quantitative mapping of the regulatory pathways within cells, as well as a deeper understanding of the potential functions of individual genes regulated by newly identified DNA-binding sites. Here we describe a DNA microarray-based method to characterize sequence-specific DNA recognition by zinc-finger proteins. A phage display library, prepared by randomizing critical amino acid residues in the second of three fingers of the mouse Zif268 domain, provided a rich source of zinc-finger proteins with variant DNA-binding specificities. Microarrays containing all possible 3-bp binding sites for the variable zinc fingers permitted the quantitation of the binding site preferences of the entire library, pools of zinc fingers corresponding to different rounds of selection from this library, as well as individual Zif268 variants that were isolated from the library by using specific DNA sequences. The results demonstrate the feasibility of using DNA microarrays for genome-wide identification of putative transcription factor-binding sites.
Three new ascomycetes from freshwater in China

Three new freshwater ascomycetes, Diaporthe aquatica sp. nov. (Diaporthaceae), Ophioceras aquaticus sp. nov. (Magnaporthaceae) and Togninia aquatica sp. nov. (Togniniaceae), are described and illustrated based on morphological and molecular data (ITS, 18S, 28S rDNA sequences). Diaporthe aquatica is characterized by globose to subglobose, black ascomata with long necks, broadly cylindrical to obclavate asci, and small, ellipsoidal to fusiform, one-septate, hyaline ascospores; it is unusual among Diaporthe species in the fact that it lacks a stroma and has freshwater habitat. Ophioceras aquaticus is characterized by globose ascomata with a long beak, cylindrical, eight-spored asci with J- subapical rings and 3–5-septate filiform ascospores with slightly acute ends. Togninia aquatica is characterized by globose ascomata with long necks, clavate and truncate asci clustered on distinct ascogenous hyphae, and small, reniform, hyaline ascospores. Differences among the new taxa and similar species are discussed.
Pathogenesis of non-alcoholic fatty liver disease

Non-alcoholic fatty liver disease (NAFLD) represents a spectrum of disease ranging from hepatocellular steatosis through steatohepatitis to fibrosis and irreversible cirrhosis. The prevalence of NAFLD has risen rapidly in parallel with the dramatic rise in obesity and diabetes,1,2 and is rapidly becoming the most common cause of liver disease in Western countries.3 Indeed, NAFLD is now recognized to be the aetiology in many cases previously labelled as cryptogenic cirrhosis.4 In Western populations, estimates of NAFLD prevalence vary between 20 and 30%,5,6 rising up to 90% in morbidly obese individuals.7 The more severe, and clinically significant form of NAFLD, non-alcoholic steatohepatitis (NASH) is less common, affecting an estimated 2–3% of the general population,8 and up to 37% of the morbidly obese.7 Of particular concern, and with significant implications for future disease burden, is the increasing prevalence of NAFLD in children and young adults. Studies have reported a 3% prevalence of NAFLD in the general paediatric population, rising to 53% in obese children.9,10 NAFLD has a strong association with type 2 diabetes, with steatosis present in 70% of type 2 diabetics screened with ultrasound,11 and thus it is now recognized to represent the hepatic manifestation of the metabolic syndrome. NAFLD occurs in all ethnic groups although it appears to have a lower prevalence in African-Americans compared with Hispanic and European Americans. This difference remains even after controlling for obesity and insulin resistance (IR)5,12 and may be related to ethnic differences in lipid homeostasis.5 There are no laboratory, imaging or histological findings which can accurately distinguish between NAFLD and alcohol-induced steatosis or steatohepatitis, and the diagnosis can therefore only be made in the absence of a history of significant alcohol intake. Other specific causes … Address correspondence to J. K. Dowman, Centre for Liver Research, Institute of Biomedical Research, University of Birmingham, Wolfson Drive, B15 2TT, Birmingham, UK. email: j.k. dowman{at}bham.ac. uk
In situ estimates of submesoscale horizontal eddy diffusivity across an ocean front

In the last decade, the rapid advancements in computational power have favored the development of high-resolution numerical models capable of directly resolving small-scale structures such as fronts and filaments. Such models have greatly improved our understanding of submesoscale dynamics. At the same time, the small dimensions and short duration of these structures still pose major challenges for small-scale dedicated field experiments. For this reason, submesoscale studies from in situ observations are still relatively scarce and quantitative estimates of key physical parameters for high-resolution numerical models, such as horizontal eddy diffusivity, are still lacking. This study presents a novel approach for computing in situ horizontal eddy diffusivity associated with frontal structures by combining cross-front widths derived from surface thermosalinograph sections with stirring rates estimated from Lagrangian drifter trajectories. The method is applied to the measurements collected across a frontal structure observed in the western part of the Gulf of Lion during the Latex10 campaign (LAgrangian Transport EXperiment, 1-24 September 2010). A total of 76 estimates of eddy diffusivity were obtained for strain rates of 0.70 and 1.21 day −1 and front widths (horizontal scales) ranging between 1 and 4 km. The estimates are log-normally distributed, with 70% of the values ranging between 0.4 and 5 m 2 s −1 . Further analysis based on high-resolution simulations and remote sensed observations, as well as dedicated field experiments will help to assess the robustness of some of the assumptions at the base of the proposed approach, and to extend the results to different ocean regions.
Three-Dimensional Finite Element Analysis of the Effect of 1-Piece Superstructure on Mandibular Flexure

Purpose:Mandibular flexure may affect the stress distribution in the implant-supported fixed partial dentures, yet the phenomenon has received little attention in finite element analysis studies. The purpose of this study was to evaluate the restraining effects imposed by 1-piece cross-arch superstructure on mandibular flexure and implant stresses. Material:Mandibular deformation and stress distribution in an implant-supported prosthesis (5 implants and 1-piece superstructure with 16.5 mm bilateral distal cantilevers) were analyzed by a 3-dimensional finite element model of a human edentulous mandible. To determine the effect of 1-piece cross-arch superstructure on mandibular flexure restriction, incisal clenching was simulated. During incisal clenching, maximum contraction of dental arch occurs. For this purpose, 9 pairs of mas ticatory muscles were simulated by multiple force vectors over areas of attachment. Results:A significant amount of stress (26.2 MPa) at the cortical bone surrounding the neck of the implant located at the symphysis assumed as a consequence of mandibular flexure. At the same area, maximum strain value of 1680 microstrain was detected. Moreover, maximum deformation of 0.35 mm was observed at the mandibular angle. Conclusions:One-piece implant-supported superstructure restricted mandibular deformation to almost half of the amount observed in unrestricted mandibular models of previous studies. This phenomenon must be considered in finite element analysis studies.
Imprint of DES superstructures on the cosmic microwave background

Small temperature anisotropies in the cosmic microwave background (CMB) can be sourced by density perturbations via the late-time integrated Sachs-Wolfe (ISW) effect. Large voids and superclusters are excellent environments to make a localized measurement of this tiny imprint. In some cases excess signals have been reported. We probed these claims with an independent data set, using the first year data of the Dark Energy Survey (DES) in a different footprint, and using a different superstructure finding strategy. We identified 52 large voids and 102 superclusters at redshifts 0.2 < z < 0.65. We used the Jubilee simulation to a priori evaluate the optimal ISW measurement configuration for our compensated top-hat filtering technique, and then performed a stacking measurement of the CMB temperature field based on the DES data. For optimal configurations, we detected a cumulative cold imprint of voids with DeltaTf ≈ -5.0 ± 3.7 muK and a hot imprint of superclusters DeltaTf ≈ 5.1 ± 3.2 muK; this is ˜1.2sigma higher than the expected |DeltaTf| ≈ 0.6 muK imprint of such superstructures in Lambda cold dark matter (LambdaCDM). If we instead use an a posteriori selected filter size (R/Rv = 0.6), we can find a temperature decrement as large as DeltaTf ≈ -9.8 ± 4.7 muK for voids, which is ˜2sigma above LambdaCDM expectations and is comparable to previous measurements made using Sloan Digital Sky Survey superstructure data.
On The Renewal Input Batch-arrival Queue Under Single And Multiple Working Vacation Policy With Application To EPON

Abstract This paper analyzes renewal input batch arrival queues with multiple and single working vacation policy. We obtain the steady state system-length distributions at pre-arrival and arbitrary epochs. The Laplace-Stieltjes transforms (LST) of the sojourn time distribution for the first customer and an arbitrary customer in an accepted batch have been derived. Also the probability density function of sojourn time distribution for the first customer in an accepted batch has been obtained. The proposed analysis is based on the roots of the characteristics equations formed using the probability generating functions (p.g.f.) of embedded pre-arrival epoch probabilities. Several performance measures such as the mean system-length and mean sojourn times of first and an arbitrary customer in an accepted batch are presented. The suggested queues have potential application in ethernet passive optical network (EPON).