Miracle-dz/UniFAR-FTUs huggingface dataset:
Structures and interaction energies of stacked graphene-nucleobase complexes.

The noncovalent interactions of nucleobases and hydrogen-bonded (Watson-Crick) base-pairs on graphene are investigated with the DFT-D method, i.e., all-electron density functional theory (DFT) in generalized gradient approximation (GGA) combined with an empirical correction for dispersion (van der Waals) interactions. Full geometry optimization is performed for complexes with graphene sheet models of increasing size (up to C(150)H(30)). Large Gaussian basis sets of at least polarized triple-zeta quality are employed. The interaction energies are extrapolated to infinite lateral size of the sheets. Comparisons are made with B2PLYP-D and SCS-MP2 single point energies for coronene and C(54)H(18) substrates. The contributions to the binding (Pauli exchange repulsion, electrostatic and induction, dispersion) are analyzed. At a frozen inter-fragment distance, the interaction energy surface of the rigid C(96)H(24) and base monomers is explored in three dimensions (two lateral and one rotational). Methodologically and also regarding the results of an energy decomposition analysis, the complexes behave like other pi-stacked systems examined previously. The sequence obtained for the interaction energy of bases with graphene (G > A > T > C > U) is the same for all methods and supports recent experimental findings. The absolute values are rather large (about -20 to -25 kcal mol(-1)) but in the expected range for pi-systems of that size. The relatively short equilibrium inter-plane distance (about 3 A) is consistent with atomic force microscopy results of monolayer guanine and adenine on graphite. In graphene . Watson-Crick pair complexes, the bases lie differently from their isolated energy minima leading to geometrical anti-cooperativity. Together with an electronic contribution of 2 and 6%, this adds up to total binding anti-cooperativities of 7 and 12% for AT and CG, respectively, on C(96)H(24). Hydrogen bonds themselves are merely affected by binding on graphene.
DIANA-miRPath v3.0: deciphering microRNA function with experimental support

The functional characterization of miRNAs is still an open challenge. Here, we present DIANA-miRPath v3.0 (http://www.microrna.gr/miRPathv3) an online software suite dedicated to the assessment of miRNA regulatory roles and the identification of controlled pathways. The new miRPath web server renders possible the functional annotation of one or more miRNAs using standard (hypergeometric distributions), unbiased empirical distributions and/or meta-analysis statistics. DIANA-miRPath v3.0 database and functionality have been significantly extended to support all analyses for KEGG molecular pathways, as well as multiple slices of Gene Ontology (GO) in seven species (Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Caenorhabditis elegans, Gallus gallus and Danio rerio). Importantly, more than 600 000 experimentally supported miRNA targets from DIANA-TarBase v7.0 have been incorporated into the new schema. Users of DIANA-miRPath v3.0 can harness this wealth of information and substitute or combine the available in silico predicted targets from DIANA-microT-CDS and/or TargetScan v6.2 with high quality experimentally supported interactions. A unique feature of DIANA-miRPath v3.0 is its redesigned Reverse Search module, which enables users to identify and visualize miRNAs significantly controlling selected pathways or belonging to specific GO categories based on in silico or experimental data. DIANA-miRPath v3.0 is freely available to all users without any login requirement.
Finite Control Set Model Predictive Control for Dynamic Reactive Power Compensation With Hybrid Active Power Filters

This paper applies finite control set model predictive control (FCS-MPC) for dynamic reactive power compensation using a hybrid active power filter (HAPF). The FCS-MPC uses a model based on LCL-filter equations to predict the system behavior and optimize the control action. In fact, the application of FCS-MPC in grid-connected converters with LCL-Filter is quite recent. This algorithm is a very promising control technique for power electronics converters and its use for reactive power control of hybrid filter has not been reported in the literature yet. This paper uses the FCS-MPC in a multivariable structure along with an adaptive notch filter to damp resonance. The main purpose is to improve the dynamic response of the HAPF. Simulation as well as practical results prove the feasibility of FCS-MPC application in HAPF reactive power control. The dynamic response of the equipment was significantly improved and represents the main contribution of this paper. As a result, the FCS-MPC allows tracking fluctuations and abrupt changes in load reactive power.
Regulation of T Lymphocyte Metabolism

Upon stimulation, lymphocytes develop from small resting cells into highly proliferative and secretory cells. Although a great deal of study has focused on the genetic program induced by Ag receptor signals, lymphocytes must also regulate their metabolic function to meet the energetic demands of activation. In this review, we discuss the changes in cellular metabolism that accompany lymphocyte activation, with a particular emphasis on glucose metabolism, a major source of both energy and biosynthetic building blocks. We will also cover the signaling pathways that positively and negatively regulate these changes to maintain metabolic homeostasis in cells that are rapidly growing, dividing, and differentiating.
The proportion of unhealthy foodstuffs children are exposed to at the checkout of convenience supermarkets

Abstract Objective To investigate the proportion of foods that are unhealthy to which children are exposed at the checkout of convenience supermarkets. Design We performed a cross-sectional survey of foodstuffs displayed at the checkout. Products displayed at or below children's eye-level were designated as healthy, unhealthy or unclassifiable using the Food Standards Agency's scoring criteria. Setting Thirteen convenience supermarkets from the three leading UK supermarket chains were selected on the basis of proximity to the town hall in Sheffield, England. Subjects Convenience supermarkets were defined as branches of supermarket chains that were identified as being other than superstores on their company's store locator website. Results In almost all of the convenience supermarkets surveyed, the main healthy product on display was sugar-free chewing gum. On average, when chewing gum was not included as a foodstuff, 89% of the products on display at the checkouts of convenience supermarkets were unhealthy using the Food Standards Agency's criteria. One store was a notable outlier, providing only fruit and nuts at its checkout. Conclusions The overwhelming majority of products to which children are exposed at the convenience supermarket checkout are unhealthy. This is despite all the supermarket chains surveyed having signed up to the UK Government's ‘responsibility deal’.
Curing of an R Factor from Escherichia coli by Trimethoprim

R factor 1818, which we have shown previously to be eliminated by thymine starvation, was cured from three strains of Escherichia coli K-12 by overnight exposure to trimethoprim. Elimination was abolished in the presence of added thymine or thymidine, which suggests that curing is the result of the induction of thymineless conditions by trimethoprim. Starvation of the required amino acids proline and histidine had little effect on elimination, whereas methionine deprivation enhanced it. R factor curing was abolished by the presence of chloramphenicol, and it is concluded that protein synthesis is required for elimination to occur. It is suggested that elimination may result from the activity of a nuclease which is synthesized or induced during both direct thymine starvation and by trimethoprim treatment.
Efficient importance sampling for Monte Carlo simulation of multicast networks

We consider the problem of estimating blocking probabilities in a multicast loss system via simulation, applying the static Monte Carlo method with importance sampling. An approach is introduced where the original estimation problem is first decomposed into independent simpler sub-problems, each roughly corresponding to estimating the blocking probability contribution from a single link. Then we apply importance sampling to solve each sub-problem. The importance sampling distribution is the original distribution conditioned on that the state is in the blocking state region of a single link. Samples can be generated from this distribution using the so called inverse convolution method. Finally, a dynamic control algorithm is used for optimally allocating the samples between different sub-problems. The numerical results demonstrate that the variance reduction obtained with the method is remarkable, between 400 and 36000 in the considered examples.
Yield and yield contributing characters of mungbean as influenced by zinc and boron

A field experiment was carried out during February to April 2014 at the Crop Museum plot, Department of Agronomy, Hajee Mohammad Danesh Science and Technology University (HSTU), Dinajpur to investigate the effect of zinc and boron on growth and yield characteristics of mungbeen (BARI mung-5). In this study mungbean plant was affected by three zinc levels (0, 1.5 and 3.0 kgha -1 ) and three boron levels (0, 1.0 and 2.0 kgha -1 ). It was conducted by RCBD with three replications. The yield and yield contributing characteristics of mungbean plant was significantly affected by the different levels of zinc and boron. The maximum plant height, number of branches plant -1 , number of pod plant -1 , pod length, number of grains pod -1 , 100-grains weight, grain yield, stover yield, biological yield and harvest index were recorded from in the treatment combination of Zn 1 B 1 (1.5 kg Zn ha -1 and 1.0 kg B ha -1 ) among all the treatments. From the yield and yield traits, it is clear that 1.5 kg Zn ha -1 + 1.0 kg B ha -1 of was congenial for the cultivation of mungbean.
Altered Precipitation Impacts on Above- and Below-Ground Grassland Invertebrates: Summer Drought Leads to Outbreaks in Spring

Climate change is predicted to result in altered precipitation patterns, which may reshape many grassland ecosystems. Rainfall is expected to change in a number of different ways, ranging from periods of prolonged drought to extreme precipitation events, yet there are few community wide studies to accurately simulate future changes. We aimed to test how above- and below-ground grassland invertebrate populations were affected by contrasting future rainfall scenarios. We subjected a grassland community to potential future rainfall scenarios including ambient, increased amount (+50% of ambient), reduced amount (–50% of ambient), reduced frequency (no water for 21 days, followed by the total ambient rainfall applied in a single application) and summer drought (no rainfall for 13 weeks during the growing season). During Austral spring (September 2015), we sampled aboveground invertebrates, belowground macro invertebrates and nematodes. Aboveground communities showed a significant response to altered rainfall regime with the greatest effects observed in summer drought plots. This was mostly due to a large increase in sucking herbivores (658% higher than ambient plots). Plots experiencing summer droughts also had higher populations of parasitoids, chewing herbivores and detritivores. These plots had 92% more plant biomass suggesting that primary productivity increased rapidly following the end of the summer drought 5 months earlier. We interpret these results as supporting the plant vigor hypothesis (i.e., that rapid plant growth is beneficial to aboveground invertebrates). While belowground invertebrates were less responsive to altered precipitation, we observed a number of correlations between the abundances of above- and below-ground invertebrate groups under ambient rainfall that dissipated under altered rainfall regimes. Mechanisms underpinning these associations, and reasons for them to become decoupled under altered precipitation regimes (we term this ‘climatic decoupling’), remain speculative, but they provide the basis for formulating hypotheses and future work. In conclusion, we predict that shifts in rainfall patterns, especially summer drought, will likely have large, but probably short-term, impacts on grassland invertebrate communities. In particular, sucking herbivores show sensitivity to precipitation changes, which have the potential to cascade through the food chain and affect higher trophic levels.
How absent negativity relates to affect and motivation: an integrative relief model

The present paper concerns the motivational underpinnings and behavioral correlates of the prevention or stopping of negative stimulation – a situation referred to as relief. Relief is of great theoretical and applied interest. Theoretically, it is tied to theories linking affect, emotion, and motivational systems. Importantly, these theories make different predictions regarding the association between relief and motivational systems. Moreover, relief is a prototypical antecedent of counterfactual emotions, which involve specific cognitive processes compared to factual or mere anticipatory emotions. Practically, relief may be an important motivator of addictive and phobic behaviors, self destructive behaviors, and social influence. In the present paper, we will first provide a review of conflicting conceptualizations of relief. We will then present an integrative relief model (IRMO) that aims at resolving existing theoretical conflicts. We then review evidence relevant to distinctive predictions regarding the moderating role of various procedural features of relief situations. We conclude that our integrated model results in a better understanding of existing evidence on the affective and motivational underpinnings of relief, but that further evidence is needed to come to a more comprehensive evaluation of the viability of IRMO.
Unconventional Myosin Myo1c Promotes Membrane Fusion in a Regulated Exocytic Pathway

ABSTRACT Glucose homeostasis is controlled in part by regulation of glucose uptake into muscle and adipose tissue. Intracellular membrane vesicles containing the GLUT4 glucose transporter move towards the cell cortex in response to insulin and then fuse with the plasma membrane. Here we show that the fusion step is retarded by the inhibition of phosphatidylinositol (PI) 3-kinase. Treatment of insulin-stimulated 3T3-L1 adipocytes with the PI 3-kinase inhibitor LY294002 causes the accumulation of GLUT4-containing vesicles just beneath the cell surface. This accumulation of GLUT4-containing vesicles near the plasma membrane prior to fusion requires an intact cytoskeletal network and the unconventional myosin motor Myo1c. Remarkably, enhanced Myo1c expression under these conditions causes extensive membrane ruffling and overrides the block in membrane fusion caused by LY294002, restoring the display of GLUT4 on the cell exterior. Ultrafast microscopic analysis revealed that insulin treatment leads to the mobilization of GLUT4-containing vesicles to these regions of Myo1c-induced membrane ruffles. Thus, localized membrane remodeling driven by the Myo1c motor appears to facilitate the fusion of exocytic GLUT4-containing vesicles with the adipocyte plasma membrane.
A comprehensive view of polyamine and histamine metabolism to the light of new technologies

Polyamines and histamine are biogenic amines with multiple biological roles. In spite of the evidence for the involvement of both polyamines and histamine metabolism impairment in several highly prevalent pathological conditions multiple questions concerning the molecular processes behind these effects remain to be elucidated. More comprehensive and systemic studies intergrating molecular biology, biophysical and bioinformatics tools could contribute to accelerate the advances in this research area. This review is designed to underscore the main questions to be answered in polyamine and histamine research and how these new systemic approaches could help to find these answers.
Infrared Properties of Star-forming Dwarf Galaxies. II. Blue Compact Dwarf Galaxies in the Virgo Cluster

A sample of 16 blue compact dwarf galaxies (BCDs) in the Virgo Cluster has been imaged in the near-infrared (NIR) in J and Ks on the 2.1 m telescope at the Observatorio Astronómico Nacional in the Sierra San Pedro Mártir in Mexico. Isophotes as faint as μJ = 24 mag arcsec-2 and μ = 23 mag arcsec-2 have been reached in most of the targets. Surface brightness profiles can be fitted across the whole range of radii by the sum of two components: a hyperbolic secant (sech) function, which is known to fit the light profiles of dwarf irregular galaxies (dIs), and a Gaussian component, which quantifies the starburst near the center. Isophotal and total fitted NIR magnitudes have been calculated, along with semimajor axes at μJ = 23 mag arcsec-2 and μ = 22 mag arcsec-2. The diffuse underlying component and the young starburst have been quantified using the profile fitting. Most color profiles show a constant color, between J - Ks = 0.7 and 0.9 mag. The diffuse component represents the overwhelming majority of the NIR light for most BCDs, with the starburst enhancing the flux by less than about 0.3 mag. Linear correlations were found between the sech scale length and the sech magnitude and between the sech semimajor axis and the sech magnitude. Overall, galaxies with more luminous diffuse components are larger and brighter in the center. The central burst correlates with the diffuse component, with brighter BCDs having stronger starbursts, suggesting that more massive objects are forming stars more efficiently. BCDs lie on the "fundamental plane" defined by dIs in Paper I, following the same relation between sech absolute magnitude, sech central surface brightness, and the hydrogen line width W20, although the scatter is larger than for the dIs. On the other hand, correlations between the sech absolute magnitude and the sech central surface brightness in Ks for BCDs and dIs are equally good, indicating that BCD line widths may be enhanced by turbulence or winds.
Iterated Limiting Recursion and the Program Minimization Problem

The general problem of finding minimal programs realizing given “program descriptions” is considered, where program descriptions may be of finite or infinite length and may specify arbitrary program properties. The problem of finding minimal programs consistent with finite or infinite input-output lists is a special case (for infinite input-output lists, this is a variant of E. M. Gold's function identification problem). Although most program minimization problems are not recursively solvable, they are found to be no more difficult than the problem of deciding whether any given program realizes any given description, or the problem of enumerating programs in order of nondecreasing length (whichever is harder). This result is formulated in terms of k-limiting recursive predicates and functionals, defined by repeated application of Gold's limit operator. A simple consequence is that the program minimization problem is limiting recursively solvable for finite input-output lists and 2-limiting recursively solvable for infinite input-output lists, with weak assumptions about the measure of program size. Gold regarded limiting function identification (more generally, “black box” identification) as a model of inductive thought. Intuitively, iterated limiting identification might be regarded as higher-order inductive inference performed collectively by an ever-growing community of lower order inductive inference machines.
Explaining Dioscorides' “Double Difference”: Why Are Some Mushrooms Poisonous, and Do They Signal Their Unprofitability?

The adaptive significance of toxins in mushrooms has received very little consideration, although it is clear that poisons have appeared (and/or disappeared) many times in mushrooms' evolutionary history. One possibility is that poisons have evolved in some mushroom species to deter their consumption by would‐be fungivores before spore dispersal. If this is so, then one might expect poisonous mushrooms to signal their unprofitability in some way. In this study, we have conducted the first formal analysis of the ecological and morphological traits associated with edible and poisonous mushrooms in North America and Europe. Poisonous mushrooms do not tend to be more colorful or aggregated than edible mushrooms, but they are more likely to exhibit distinctive odors even when phylogenetic relationships are accounted for. This raises the intriguing possibility that some poisonous species of mushrooms have evolved warning odors (and perhaps tastes) to enhance avoidance learning by fungivores.
"Strategic" Behavior in a Strategy-proof Environment

A mechanism is said to be strategy-proof if no agent has an incentive to misrepresent her true preferences. This property is considered highly desirable for mechanisms that are used in real-life markets. And indeed, many of the great success stories of market design employ strategy-proof mechanisms, such as the second-price sealed-bid auction (Vickrey 1961), or Deferred Acceptance (DA, Gale and Shapley 1962; Dubins and Freedman 1981; Roth 1982). Specifically, in school-choice settings, the appeal of strategy-proof mechanisms is one of the main reasons many school districts choose the applicant-proposing version of DA over pre-existing mechanisms. At the core of the attractiveness of these mechanisms is the assumption that agents report their preferences truthfully in strategy-proof environments. We present direct field evidence of preference misrepresentation by applicant's under the applicant-proposing DA. Our study is based on the recently redesigned admission process in Israel for graduate studies in psychology (MA or direct PhD track), where several participating institutions offer positions in the same study track, but under different terms. In particular, in some cases only some of the positions are funded.
T Cell-Derived IL-10 Determines Leishmaniasis Disease Outcome and Is Suppressed by a Dendritic Cell Based Vaccine

In the murine model of Leishmania major infection, resistance or susceptibility to the parasite has been associated with the development of a Th1 or Th2 type of immune response. Recently, however, the immunosuppressive effects of IL-10 have been ascribed a crucial role in the development of the different clinical correlates of Leishmania infection in humans. Since T cells and professional APC are important cellular sources of IL-10, we compared leishmaniasis disease progression in T cell-specific, macrophage/neutrophil-specific and complete IL-10-deficient C57BL/6 as well as T cell-specific and complete IL-10-deficient BALB/c mice. As early as two weeks after infection of these mice with L. major, T cell-specific and complete IL-10-deficient animals showed significantly increased lesion development accompanied by a markedly elevated secretion of IFN-γ or IFN-γ and IL-4 in the lymph nodes draining the lesions of the C57BL/6 or BALB/c mutants, respectively. In contrast, macrophage/neutrophil-specific IL-10-deficient C57BL/6 mice did not show any altered phenotype. During the further course of disease, the T cell-specific as well as the complete IL-10-deficient BALB/c mice were able to control the infection. Furthermore, a dendritic cell-based vaccination against leishmaniasis efficiently suppresses the early secretion of IL-10, thus contributing to the control of parasite spread. Taken together, IL-10 secretion by T cells has an influence on immune activation early after infection and is sufficient to render BALB/c mice susceptible to an uncontrolled Leishmania major infection.