Miracle-dz/UniFAR-FTUs huggingface dataset:
Sequential Decisions: A Computational Comparison of Observational and Reinforcement Accounts

Right brain damaged patients show impairments in sequential decision making tasks for which healthy people do not show any difficulty. We hypothesized that this difficulty could be due to the failure of right brain damage patients to develop well-matched models of the world. Our motivation is the idea that to navigate uncertainty, humans use models of the world to direct the decisions they make when interacting with their environment. The better the model is, the better their decisions are. To explore the model building and updating process in humans and the basis for impairment after brain injury, we used a computational model of non-stationary sequence learning. RELPH (Reinforcement and Entropy Learned Pruned Hypothesis space) was able to qualitatively and quantitatively reproduce the results of left and right brain damaged patient groups and healthy controls playing a sequential version of Rock, Paper, Scissors. Our results suggests that, in general, humans employ a sub-optimal reinforcement based learning method rather than an objectively better statistical learning approach, and that differences between right brain damaged and healthy control groups can be explained by different exploration policies, rather than qualitatively different learning mechanisms.
Farnesoid X receptor agonists in biliary tract disease

The farnesoid X receptor (FXR) is a member of ligand-activated nuclear receptor superfamily. FXR is a bile sensor and is part of a complex network of nuclear receptors that includes also the constitutive androstane receptor and the pregnane X receptor. These receptors act coordinately to regulate essential steps of bile acids and xenobiotics uptake, metabolism and excretion in hepatocytes, cholangiocytes and kidney cells. Preclinical models indicate that FXR agonists are effective in reducing liver injury in nonobstructive models of cholestasis. FXR ligands are currently under investigation for treating patients with early stage primary biliary cirrhosis. Although these ligands hold promise, evidence is growing that FXR activation could impair the expression/activity of basolateral transporters such as multidrug resistance protein 4 essential for basolateral secretion of bile constituents in the systemic circulation. Because FXR, pregnane X receptor and constitutive androstane receptor ligands interact with different target genes, it appear that a combination with pregnane X receptor, constitutive androstane receptor ligand/activator or both or ursodeoxycholic acid could prevent possible side-effects of FXR activation in severe cholestasis.
Spectral light absorption by ambient aerosols influenced by biomass burning in the Amazon Basin – I . Comparison and field calibration of absorption measurement techniques

O. Schmid, P. Artaxo, W. P. Arnott, D. Chand, L. V. Gatti, G. P. Frank, A. Hoffer, M. Schnaiter, and M. O. Andreae Max Planck Institute for Chemistry, Department of Biogeochemistry, PO Box 3060, 55020 Mainz, Germany University of São Paulo, Institute of Physics, São Paulo, Brazil Desert Research Institute, Division of Atmospheric Science, Reno, NV, USA Institute of Nuclear Energy Research, Atmospheric Chemistry Laboratory, São Paulo, SP, Brazil Research Center Karlsruhe, Institute of Meteorology and Climate Research, PO Box 3640, 76021 Karlsruhe, Germany
Assessing Agricultural Water Productivity in Desert Farming System of Saudi Arabia

The primary objective of this study was to assess the water productivity (WP) of the annual (wheat, barley, and corn) and biennial (alfalfa and Rhodes grass) crops cultivated under centerpivot irrigation located over desert areas of the Al-Kharj region in Saudi Arabia. The Surface Energy Balance Algorithm for Land (SEBAL) was applied to Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) images to obtain evapotranspiration (ET) for assessing WP and irrigation performance (IP) of crops. Crop productivity (CP) was estimated using Normalized Difference Vegetation Index (NDVI) crop productivity models. The predicted CP (CPP) for corn varied from 12 690 to 14 060 kg/ha and from 6000 to 7370 kg/ha for wheat. The for alfalfa and Rhodes grass was 42 450 and 58 210 (kg/ha/year), respectively. The highest predicted WP was observed in wheat (0.80-2.01 kg/m3) and the lowest was in alfalfa (0.38-0.46 kg/m3). The deviation between SEBAL predicted ET (ETP) and weather station recorded ET (ETW) was 10%. The performance of the prediction models was assessed against the measured data. The overall mean bias/error of the predictions of CP, ET, and WP was 9.4%, , and 9.65%, respectively; the root mean square error (RMSE) was 1996 (kg/ha), 2107 (m3/ha), and 0.09 (kg/m3) for CP, ET, and WP, respectively. When CP was converted into variations between the actual and predicted, the variations were 8% to 12% for wheat, 14% to 20% for corn, 17% to 35% for alfalfa, 3% to 38% for Rhodes grass, and 4% for barley.
Transdiagnostic Clinical Global Impression Scoring for Routine Clinical Settings

Although there is great interest in the improving the ability to track patients’ change over time in routine clinical care settings, no standardized transdiagnostic measure is currently available for busy clinicians to apply. The Clinical Global Impression (CGI) scales are simple measures widely used as outcomes in psychiatric clinical trials. However, the CGI suffers from poorly defined scoring anchors. Efforts to improve the anchors by enhancing the anchor descriptions have proven useful but are limited by being disease-specific, thereby acting as a barrier to the routine clinical adoption of the CGI. To inform the development of more broadly applicable CGI scoring anchors, we surveyed 24 clinical trial investigators, asking them to rank-order seven elements that inform their CGI-Severity (CGI-S) scoring. Symptom severity emerged as the most important element in determining CGI-S scores; the functional status of the patient emerged as a second element. Less importance was given to self-report symptom scores, staff observations, or side effects. Relative rankings of the elements’ importance did not differ by investigators’ experience nor time usually spent with patients. We integrated these results with published illness-specific CGI anchors to develop the Transdiagnostic CGI (T-CGI), which employs standardized scoring anchors applicable across psychiatric illnesses. Pending validity and reliability evaluations, the T-CGI may prove well-suited for inclusion in routine clinical settings and for incorporation into electronic medical records as a simple and useful measure of treatment efficacy.
Heterogeneity of mprF Sequences in Methicillin-Resistant Staphylococcus aureus Clinical Isolates: Role in Cross-Resistance between Daptomycin and Host Defense Antimicrobial Peptides

ABSTRACT Over the past several years, single-nucleotide polymorphisms (SNPs) within the mprF open reading frame (ORF) have been proposed to be associated with a gain-of-function phenotype in terms of daptomycin (DAP) nonsusceptibility (referred to as daptomycin resistance [DAP-R] herein for ease of presentation) in Staphylococcus aureus. We investigated the frequencies of SNPs within the mprF ORF and the relationships of such SNPs to cross-resistance between DAP and cationic host defense peptides (HDPs). Thirty-five well-characterized, unique DAP-susceptible (DAP-S) and DAP-R methicillin-resistant S. aureus (MRSA) isolates of the clonal complex 5 genotype were used. In addition to mprF SNPs and DAP-HDP cross-resistance, several other key genotypic and phenotypic metrics often associated with DAP-R were delineated, as follows: (i) mprF expression, (ii) membrane phospholipid content, (iii) positive surface charge, (iv) DAP binding, and (v) cell wall thickness profiles. A number of DAP-S strains (MICs of ≤1 μg/ml) exhibited mprF SNPs, occasionally with high-level mprF sequence variation from the genotype reference strain. However, none of these SNPs were localized to well-chronicled mprF hot spot locations associated with DAP-R in S. aureus. In contrast, all 8 DAP-R isolates demonstrated SNPs within such known mprF hot spots. Moreover, only the DAP-R strains showed MprF gain-of-function phenotypes, enhanced mprF expression, higher survival against two prototypical HDPs, and reduced DAP binding. Although a heterogenous array of mprF SNPs were often found in DAP-S strains, only selected hot spot SNPs, combined with concurrent mprF dysregulation, were associated with the DAP-R phenotype.
Innate Lymphoid Cells in HIV/SIV Infections

Over the past several years, new populations of innate lymphocytes have been described in mice and primates that are critical for mucosal homeostasis, microbial regulation, and immune defense. Generally conserved from mice to humans, innate lymphoid cells (ILC) have been divided primarily into three subpopulations based on phenotypic and functional repertoires: ILC1 bear similarities to natural killer cells; ILC2 have overlapping functions with TH2 cells; and ILC3 that share many functions with TH17/TH22 cells. ILC are specifically enriched at mucosal surfaces and are possibly one of the earliest responders during viral infections besides being involved in the homeostasis of gut-associated lymphoid tissue and maintenance of gut epithelial barrier integrity. Burgeoning evidence also suggests that there is an early and sustained abrogation of ILC function and numbers during HIV and pathogenic SIV infections, most notably ILC3 in the gastrointestinal tract, which leads to disruption of the mucosal barrier and dysregulation of the local immune system. A better understanding of the direct or indirect mechanisms of loss and dysfunction will be critical to immunotherapeutics aimed at restoring these cells. Herein, we review the current literature on ILC with a particular emphasis on ILC3 and their role(s) in mucosal immunology and the significance of disrupting the ILC niche during HIV and SIV infections.
Comparative analysis of non-autonomous effects of tasiRNAs and miRNAs in Arabidopsis thaliana

In plants, small interfering RNAs (siRNAs) can trigger a silencing signal that may spread within a tissue to adjacent cells or even systemically to other organs. Movement of the signal is initially limited to a few cells, but in some cases the signal can be amplified and travel over larger distances. How far silencing initiated by other classes of plant small RNAs (sRNAs) than siRNAs can extend has been less clear. Using a system based on the silencing of the CH42 gene, we have tracked the mobility of silencing signals initiated in phloem companion cells by artificial microRNAs (miRNA) and trans-acting siRNA (tasiRNA) that have the same primary sequence. In this system, both the ta-siRNA and the miRNA act at a distance. Non-autonomous effects of the miRNA can be triggered by several different miRNA precursors deployed as backbones. While the tasiRNA also acts non-autonomously, it has a much greater range than the miRNA or hairpin-derived siRNAs directed against CH42, indicating that biogenesis can determine the non-autonomous effects of sRNAs. In agreement with this hypothesis, the silencing signals initiated by different sRNAs differ in their genetic requirements.
Neuroanatomic Connectivity of the Human Ascending Arousal System Critical to Consciousness and Its Disorders

Abstract The ascending reticular activating system (ARAS) mediates arousal, an essential component of human consciousness. Lesions of the ARAS cause coma, the most severe disorder of consciousness. Because of current methodological limitations, including of postmortem tissue analysis, the neuroanatomic connectivity of the human ARAS is poorly understood. We applied the advanced imaging technique of high angular resolution diffusion imaging (HARDI) to elucidate the structural connectivity of the ARAS in 3 adult human brains, 2 of which were imaged postmortem. High angular resolution diffusion imaging tractography identified the ARAS connectivity previously described in animals and also revealed novel human pathways connecting the brainstem to the thalamus, the hypothalamus, and the basal forebrain. Each pathway contained different distributions of fiber tracts from known neurotransmitter-specific ARAS nuclei in the brainstem. The histologically guided tractography findings reported here provide initial evidence for human-specific pathways of the ARAS. The unique composition of neurotransmitter-specific fiber tracts within each ARAS pathway suggests structural specializations that subserve the different functional characteristics of human arousal. This ARAS connectivity analysis provides proof of principle that HARDI tractography may affect the study of human consciousness and its disorders, including in neuropathologic studies of patients dying in coma and the persistent vegetative state.
NLTE abundances of Mn in a sample of metal-poor stars ⋆

Aims. Following our solar work, we perform NLTE calculations of the Mn abundance for fourteen stars with [Fe/H] from 0 to -2.5, mainly to show how NLTE affects Mn abundances in cool stars of different metallicities. Methods. The spectrum synthesis and Mn abundances are based on statistical equilibrium calculations using various estimates fo r the influence of hydrogen collisions. Results. The NLTE abundances of Mn in all studied stars are systematically higher than the LTE abundances. At low metallicities, the NLTE abundance corrections may run up to 0.5 - 0.7 dex. Instead of a strong depletion of Mn relative to Fe in metal-poor stars as found by the other authors, we only find slightly subsolar values of [Mn /Fe] throughout the range of metallicities analyzed here. Conclusions. The [Mn/Fe] trend in metal-poor stars is inconsistent with the predi ctions of galactic chemical evolution models, where Mn is less produced than Fe.
Differential Actions of PAR2 and PAR1 in Stimulating Human Endothelial Cell Exocytosis and Permeability: The Role of Rho-GTPases

Abstract— Endothelial cell proteinase activated receptors (PARs) belong to a family of heterotrimeric G protein-coupled receptors that are implicated in leukocyte accumulation and potentiation of reperfusion injury. We characterized the effect and the signal transduction pathways recruited after stimulation of endothelial PAR2. We used von Willebrand Factor (vWF) release and monolayer permeability to peroxidase to report Weibel-Palade body (WPB) exocytosis and pore formation, respectively. Human umbilical vein endothelial cells (HUVECs) were stimulated with the selective PAR2 agonist peptide SLIGRL-NH2 or PAR1 agonist peptide TFLLR-NH2. PAR2 stimulation resulted in WPB exocytosis like PAR1 stimulation but, unlike PAR1, failed to increase monolayer permeability. BAPTA-AM inhibited PAR2-induced exocytosis, indicating a PAR2 calcium-dependent signal in ECs. Moreover, PAR2-like PAR1-stimulated exocytosis requires actin cytoskeleton remodeling, because vWF release is inhibited if the cells were pretreated with Jasplakinolide. Rho-GTPase activity is required for PAR-stimulated exocytosis, because inactivation of this family of actin-regulatory proteins with Clostridium difficile toxin B blocked exocytosis. Expression of dominant-negative mutant Cdc4217N inhibited exocytosis whereas neither dominant-negative Rac17N expression nor C3 exotoxin treatment affected vWF release. PAR2 stimulated RhoA-GTP weakly compared with the PAR1 agonist. We conclude that both PAR2 and PAR1 elicit WP body exocytosis in a calcium and Cdc42 GTPase-dependent manner. In contrast, the differential effect of PAR1 versus PAR2 activation to increase monolayer permeability correlates with weak RhoA activation by the PAR2 agonist.
COLLISIONAL STRIPPING AND DISRUPTION OF SUPER-EARTHS

The final stage of planet formation is dominated by collisions between planetary embryos. The dynamics of this stage determine the orbital configuration and the mass and composition of planets in the system. In the solar system, late giant impacts have been proposed for Mercury, Earth, Mars, and Pluto. In the case of Mercury, this giant impact may have significantly altered the bulk composition of the planet. Here we present the results of smoothed particle hydrodynamics simulations of high-velocity (up to ∼5vesc) collisions between 1 and 10 M⊕ planets of initially terrestrial composition to investigate the end stages of formation of extrasolar super-Earths. As found in previous simulations of collisions between smaller bodies, when collision energies exceed simple merging, giant impacts are divided into two regimes: (1) disruption and (2) hit-and-run (a grazing inelastic collision and projectile escape). Disruption occurs when the impact parameter is near zero, when the projectile mass is small compared to the target, or at extremely high velocities. In the disruption regime, we derive the criteria for catastrophic disruption (when half the total colliding mass is lost), the transition energy between accretion and erosion, and a scaling law for the change in bulk composition (iron-to-silicate ratio) resulting from collisional stripping of a mantle.
Comparative Analysis of Conventional, Real and Complex Wavelet Transforms for Face Recognition

recognition has been studied for many years in the context of biometrics and is one of the most successful applications of image analysis and understanding. Various methods, approaches and algorithms for recognition of human faces were proposed. In this paper, independent, comparative study of conventional discrete wavelet transform (DWT), real dual-tree discrete wavelet transform (R-DT-DWT), and complex dual-tree discrete wavelet transform (C-DT-DWT) based features for face recognition is carried out. In 2005, Delac et al. (26) presented an independent comparative study of PCA, ICA, and LDA on the FERET data set where it was concluded that no particular distance-metric combination is the best. In this paper we intend to bring further conclusions. Unlike the contribution by Delac et al., our conclusions are in context of DWT, R-DT-DWT, and C-DT-DWT. Moreover, these approaches are tested on nine different databases at different levels and under three different distance metrics, which allowed us to compare their performance independently. Our simulation results show that no particular distance-metric combination is the best across all standard benchmark face databases. However, the overall performance for city block distance measure was found to be better as compared to the Euclidean and cosine distance. Also, the performance for R-DT-DWT and C-DT-DWT based features were found equivalently efficient in many cases. So taking redundancy into consideration, it may be suggested to opt for R-DT-DWT for face efficient recognition.
Lyapunov-based approach for finite time stability and stabilization

Finite time stability is investigated for continuous system ẋ = f(x) which satisfies uniqueness of solutions in forward time. A necessary and sufficient condition is given for this class of systems using Lyapunov functions. Then, a necessary and sufficient condition is developed for finite time stabilization of class CLk-affine systems involving a class CL0−settling time for the closed-loop system. Finally an explicit feedback control is given using a control Lyapunov function verifying a certain inequality.
Increasing Competition and the Winner's Curse: Evidence from Procurement

We empirically measure the effects increasing competition on equilibrium bidding in procurement auctions. In common value auctions, the winner's curse counsels more conservative bidding as the number of competitors increases. First, we estimate the structural parameters of an equilibrium bidding model and test for the importance of common value components in bidders' preferences. Second, we use these estimates to measure the effects on increasing competition on both individual bids as well as winning bids (ie. procurement costs). Methodologically, we have estimated a model which allows bidders' latent valuations for a contract to have both common and private value components. We analyze bid data from construction procurement auctions run by the New Jersey department of transportation in the years 1989-1997. Our results show that different types of contracts differ significantly in the degree that private and/or common value components are important, and these have contrasting implications on the effects of increasing competition on equilibrium bids and expected government procurement outlays. Auctions for highway work contracts are very close to a pure common value auction, while both common value and private value are important in auctions of bridge repair contracts. Furthermore, our results indicate that the winner's curse is particularly strong in these highway contract auctions. Simulated bid functions show that for the median bidder, the percentage markup increases from 50% with 2 bidders to above 70% with 10 bidders. Furthermore, winning bid simulations indicate that the average procurement cost is strictly increasing in the number of bidders as competition intensifies: for example, the median costs rise about 30%, as the number of bidders is increases from 3 to 6. These results emphasize how asymmetric information can overturn the common economic wisdom that more competition is always desirable, and have potentially important policy implications.
Contrast Media with and without Calcium for Cardioangiography in Children

The possible beneficial effects of added calcium ions to contrast media to diminish myocardial toxicity was evaluated in 93 cardiac catheterizations with cardioangiography, performed in 50 children and adolescents. Two contrast media with equal iodine content (370 mg/ml) and similar physical properties were used: Isopawue-370, containing 0.34 mg calcium/ml, and Renografin-76, not containing calcium. It is concluded that addition of calcium to contrast media for cardioangiography in children and adolescents does not alter their myocardial, fluid or electrolyte effects when injected selectively into the cardiac chambers or great vessels.
INFLUENCE OF PRIMARY SOMATOSENSORY CORTEX ON HAND MOTOR CIRCUITRY AND THE ROLE OF STIMULATION PARAMETERS

The primary somatosensory cortex (SI) is important for hand function and influences motor circuitry in the primary motor cortex (M1). Areas 3a, 1 and 2 of SI have direct connectivity with M1. Much of our present knowledge of this connectivity and its relevance to hand function is based on animal research. However, less is known about the neural mechanisms that underpin hand function in humans. The present study investigated the influence of SI on corticospinal excitability as well as inhibitory and excitatory neural circuitry within M1 before and after continuous theta-burst stimulation (cTBS). Additionally, stimulation parameters influence the direction and magnitude of cTBS after-effects. Thus, current direction and frequency of cTBS were manipulated. Two experiments were performed. In Experiment 1, motor-evoked potentials (MEPs) were recorded from the first-dorsal interosseous (FDI) muscle bilaterally before and after 50 Hz cTBS over left SI. In a second condition, the orientation of cTBS was reversed. Experiment 2 measured MEPs, short-latency intracortical inhibition (SICI) and intracortical facilitation (ICF) from the right FDI following a modified 30 Hz cTBS over left SI or M1. The results of Experiment 1 and 2 demonstrate that SI influences M1 circuitry such that MEPs are facilitated following cTBS over SI. However, MEPs are suppressed when the current direction is reversed. CTBS at 30 Hz delivered over M1 suppressed excitatory circuitry that generates MEPs and ICF. The findings from the thesis suggest that SI influences hand motor circuitry and is likely a mechanism by which somatosensory information modulates hand motor function.