Miracle-dz/UniFAR-FTUs huggingface dataset:
Motor Axon Regeneration and Muscle Reinnervation in Young Adult and Aged Animals

Injuries to peripheral nerves can cause paralysis and sensory disturbances, but such functional impairments are often short lived because of efficient regeneration of damaged axons. The time required for functional recovery, however, increases with advancing age (Verdú et al., 2000; Kawabuchi et al., 2011). Incomplete or delayed recovery after peripheral nerve damage is a major health concern in the aging population because it can severely restrict a person's mobility and independence. A variety of possible causes have been suggested to explain why nervous systems in aged individuals recover more slowly from nerve damage. Potential causes include age-related declines in the regenerative potential of peripheral axons and decreases in the supply or responsivity to trophic and/or tropic factors. However, there have been few direct analyses of age-related axon regeneration. Our aim here was to observe axons directly in young and old mice as they regenerate and ultimately reoccupy denervated neuromuscular synaptic sites to learn what changes in this process are age related. We find that damaged nerves in aged animals clear debris more slowly than nerves in young animals and that the greater number of obstructions regenerating axons encounter in the endoneurial tubes of old animals give rise to slower regeneration. Surprisingly, however, axons from aged animals regenerate quickly when not confronted by debris and reoccupy neuromuscular junction sites efficiently. These results imply that facilitating clearance of axon debris might be a good target for the treatment of nerve injury in the aged.
A non-canonical adenosinergic pathway led by CD38 in human melanoma cells induces suppression of T cell proliferation

Nucleotide-metabolizing ectoenzymes are endowed with an extracellular catalytic domain, which is involved in regulating the extracellular nucleotide/nucleoside balance. The tumor microenvironment contains high levels of adenosine (ADO) generated by this enzymatic network, thus promoting tumor growth by inhibiting anti-tumor immune responses. ADO inhibition in melanoma murine models limits tumor metastases and restores anti-tumor immune responses. This work investigates the expression and function of ectoenzymes in primary human melanoma cell lines. All of latter cells expressed CD38, CD39, CD73, and CD203a/PC-1, and produced ADO from AMP and NAD+. Melanoma cells inhibited T cell proliferation through an ADO-dependent mechanism, since such inhibition was reverted using CD38/CD73 specific inhibitors. Melanoma cells abolished the function of effector memory, central memory and reduced naïve CD4+ T cell proliferation. Accordingly, phosphorylation of S6 ribosomal protein, p38 and Stat1 was lower in activated memory cells than in naïve CD4+ T lymphocytes. Melanoma cells also inhibited proliferation of naïve, memory and -to a lesser extent- of effector CD8+ T cells. These different inhibitory effects correlated with distinct patterns of expression of the ADO receptor A2a and A2b. These results show that primary human melanoma cell lines suppress in vitro T cell proliferation through an adenosinergic pathway in which CD38 and CD73 play a prominent role.
Signal mapping designs for bit-interleaved coded modulation with iterative decoding (BICM-ID)

Bit-interleaved coded modulation with iterative decoding (BICM-ID) is a spectral efficient coded modulation technique to improve the performance of digital communication systems. It has been widely known that for fixed signal constellation, interleaver and error control code, signal mapping plays an important role in determining the error performance of a BICM-ID system. This thesis concentrates on signal mapping designs for BICM-ID systems. To this end, the distance criteria to find the best mapping in terms of the asymptotic performance are first analytically derived for different channel models. Such criteria are then used to find good mappings for various twodimensional 8-ary constellations. The usefulness of the proposed mappings of 8-ary constellations is verified by both the error floor bound and simulation results. Moreover, new mappings are also proposed for BICM-ID systems employing the quadrature phase shift keying (QPSK) constellation. The new mappings are obtained by considering many QPSK symbols over a multiple symbol interval, which essentially creates hypercube constellations. Analytical and simulation results show that the use
Whittaker Functors for Gsp 4 Sergey Lysenko

1.1 One of the important technical tools in D. Gaitsgory’s proof of the Vanishing Conjecture appearing in the geometric Langlands correspondence ([3]) is the theory of Whittaker functors for GLn. In this paper we define analogous functors for GSp4 and study their properties. Let us first review the situation at the level of automorphic forms on G = Sp4. Let X be a smooth projective absolutely irreducible curve over Fq, F = Fq(X) and A be the adeles ring of F . Let B be a Borel subgroup of G and U ⊂ B its unipotent radical. For a character ψ : U(F )\U(A)→ C∗ one has a global Whittaker module over G(A) WMψ = {f : U(F )\G(A) → C | f(ug) = ψ(u)f(g) for u ∈ U(A), f is smooth} Let Acusp(G(F )\G(A)) be the space of cusp forms on G(F )\G(A). The usual Whittaker operator Wψ : Acusp(G(F )\G(A)) →WMψ is given by
The Limits of De Novo DNA Motif Discovery

A major challenge in molecular biology is reverse-engineering the cis-regulatory logic that plays a major role in the control of gene expression. This program includes searching through DNA sequences to identify “motifs” that serve as the binding sites for transcription factors or, more generally, are predictive of gene expression across cellular conditions. Several approaches have been proposed for de novo motif discovery–searching sequences without prior knowledge of binding sites or nucleotide patterns. However, unbiased validation is not straightforward. We consider two approaches to unbiased validation of discovered motifs: testing the statistical significance of a motif using a DNA “background” sequence model to represent the null hypothesis and measuring performance in predicting membership in gene clusters. We demonstrate that the background models typically used are “too null,” resulting in overly optimistic assessments of significance, and argue that performance in predicting TF binding or expression patterns from DNA motifs should be assessed by held-out data, as in predictive learning. Applying this criterion to common motif discovery methods resulted in universally poor performance, although there is a marked improvement when motifs are statistically significant against real background sequences. Moreover, on synthetic data where “ground truth” is known, discriminative performance of all algorithms is far below the theoretical upper bound, with pronounced “over-fitting” in training. A key conclusion from this work is that the failure of de novo discovery approaches to accurately identify motifs is basically due to statistical intractability resulting from the fixed size of co-regulated gene clusters, and thus such failures do not necessarily provide evidence that unfound motifs are not active biologically. Consequently, the use of prior knowledge to enhance motif discovery is not just advantageous but necessary. An implementation of the LR and ALR algorithms is available at http://code.google. com/p/likelihood-ratio-motifs/.
Vitamins, stress and growth: the availability of antioxidants in early life influences the expression of cryptic genetic variation

Environmental inputs during early development can shape the expression of phenotypes, which has long‐lasting consequences in physiology and life history of an organism. Here, we study whether experimentally manipulated availability of dietary antioxidants, vitamins C and E, influences the expression of genetic variance for antioxidant defence, endocrine signal and body mass in yellow‐legged gull chicks using quantitative genetic models based on full siblings. Our experimental study in a natural population reveals that the expression of genetic variance in total antioxidant capacity in plasma increased in chicks supplemented with vitamins C and E despite the negligible effects on the average phenotype. This suggests that individuals differ in their ability to capture and transport dietary antioxidants or to respond to these extra resources, and importantly, this ability has a genetic basis. Corticosterone level in plasma and body mass were negatively correlated at the phenotypic level. Significant genetic variance of corticosterone level appeared only in control chicks nonsupplemented with vitamins, suggesting that the genetic variation of endocrine system, which transmits environmental cues to adaptively control chick development, appeared in stressful conditions (i.e. poor antioxidant availability). Therefore, environmental inputs may shape evolutionary trajectories of antioxidant capacity and endocrine system by affecting the expression of cryptic genetic variation.
Activation of the Mitogen-activated Protein Kinase, Slt2p, at Bud Tips Blocks a Late Stage of Endoplasmic Reticulum Inheritance in Saccharomyces cerevisiae

We explore the role of components that act both upstream and downstream of Slt2p in the Ptc1p-dependent regulation of ER inheritance and mitochondrial inheritance. Our findings are that Ptc1p is needed to inactivate the pool of Slt2p associated with the bud tip to promote the cortical distribution of the ER in daughter cells.
Should I stay or should I go? Conceptual underpinnings of goal-directed actions

All actions, even the simplest like moving an arm to grasp a pen, are associated with energy costs. Thus all mobile organisms possess the ability to evaluate resources and select those behaviors that are most likely to lead to the greatest accrual of valuable items (reward) in the near or, especially in the case of humans, distant future. The evaluation process is performed at all possible stages of the series of decisions that lead to the building of a goal-directed action or to its suppression. This is because all animals have a limited amount of energy and resources; to survive and be able to reproduce they have to minimize the costs and maximize the outcomes of their actions. These computations are at the root of behavioral flexibility. Two executive functions play a major role in generating flexible behaviors: (i) the ability to predict future outcomes of goal-directed actions; and (ii) the ability to cancel them when they are unlikely to accomplish valuable results. These two processes operate continuously during the entire course of a movement: during its genesis, its planning and even its execution, so that the motor output can be modulated or suppressed at any time before its execution. In this review, functional interactions of the extended neural network subserving generation and inhibition of goal-directed movements will be outlined, leading to the intriguing hypothesis that the performance of actions and their suppression are not specified by independent sets of brain regions. Rather, it will be proposed that acting and stopping are functions emerging from specific interactions between largely overlapping brain regions, whose activity is intimately linked (directly or indirectly) to the evaluations of pros and cons of an action. Such mechanism would allow the brain to perform as a highly efficient and flexible system, as different functions could be computed exploiting the same components operating in different configurations.
Likelihood Inference for a Nonstationary Fractional Autoregressive Model

This paper discusses model based inference in an autoregressive model for fractional processes based on the Gaussian likelihood. The model allows for the process to be fractional of order d or d b; where db > 1=2 are parameters to be estimated. We model the data X1;:::;XT given the initial values X 0 n; n = 0;1;:::, under the assumption that the errors are i.i. d. Gaussian. We consider the like- lihood and its derivatives as stochastic processes in the parameters, and prove that they converge in distribution when the errors are i.i. d. with suitable moment conditions and the initial values are bounded. We use this to prove existence and consistency of the local likelihood estimator, and to …nd the asymptotic distrib- ution of the estimators and the likelihood ratio test of the associated fractional unit root hypothesis, which contains the fractional Brownian motion of type II.
Changes in soil carbon, nitrogen, and phosphorus due to land-use changes in Brazil

Abstract. In this paper, soil carbon, nitrogen and phosphorus concentrations and stocks were investigated in agricultural and natural areas in 17 plot-level paired sites and in a regional survey encompassing more than 100 pasture soils In the paired sites, elemental soil concentrations and stocks were determined in native vegetation (forests and savannas), pastures and crop–livestock systems (CPSs). Nutrient stocks were calculated for the soil depth intervals 0–10, 0–30, and 0–60 cm for the paired sites and 0–10, and 0–30 cm for the pasture regional survey by sum stocks obtained in each sampling intervals (0–5, 5–10, 10–20, 20–30, 30–40, 40–60 cm). Overall, there were significant differences in soil element concentrations and ratios between different land uses, especially in the surface soil layers. Carbon and nitrogen contents were lower, while phosphorus contents were higher in the pasture and CPS soils than in native vegetation soils. Additionally, soil stoichiometry has changed with changes in land use. The soil C : N ratio was lower in the native vegetation than in the pasture and CPS soils, and the carbon and nitrogen to available phosphorus ratio (PME) decreased from the native vegetation to the pasture to the CPS soils. In the plot-level paired sites, the soil nitrogen stocks were lower in all depth intervals in pasture and in the CPS soils when compared with the native vegetation soils. On the other hand, the soil phosphorus stocks were higher in all depth intervals in agricultural soils when compared with the native vegetation soils. For the regional pasture survey, soil nitrogen and phosphorus stocks were lower in all soil intervals in pasture soils than in native vegetation soils. The nitrogen loss with cultivation observed here is in line with other studies and it seems to be a combination of decreasing organic matter inputs, in cases where crops replaced native forests, with an increase in soil organic matter decomposition that leads to a decrease in the long run. The main cause of the increase in soil phosphorus stocks in the CPS and pastures of the plot-level paired site seems to be linked to phosphorus fertilization by mineral and organics fertilizers. The findings of this paper illustrate that land-use changes that are currently common in Brazil alter soil concentrations, stocks and elemental ratios of carbon, nitrogen and phosphorus. These changes could have an impact on the subsequent vegetation, decreasing soil carbon and increasing nitrogen limitation but alleviating soil phosphorus deficiency.
Keratocyte Density: Comparison of Two Confocal Microscopes

Purpose. The ConfoScan 3 clinical confocal microscope provides sharper images of cells in the stroma than the Tandem Scanning confocal microscope does. In this study, we compared volumetric densities of stromal cells determined from images recorded by these two instruments. Methods. Fifty corneas of 25 normal subjects were examined by confocal microscopy, first by using a Tandem Scanning confocal microscope and then by using a ConfoScan 3 confocal microscope. Bright objects, assumed to represent keratocytes, were counted in a known area of two frames selected from the mid-stroma. The effective depth of the sample volume represented by each frame was estimated from the number of consecutive frames and the corresponding distance that selected cells were visible and countable during a scan. Density was the number of visible cells in the sample area divided by the effective sample volume. Results. The effective focal depth of the Tandem Scanning microscope was 11.9 ± 2.6 μm (mean ± SD), and was 25.9 ± 7.1 μm for the ConfoScan 3. Mean cell density at mid stroma was 23,013 ± 4,420 cells/mm3 with the Tandem Scanning microscope and 23,996 ± 2,898 cells/mm3 with the ConfoScan 3. This difference was not significant (P = 0.15). Conclusions. In normal corneas, the ConfoScan 3 and the Tandem Scanning confocal microscopes indicate stromal cell densities that are not significantly different from each other. Estimates of cell density from both instruments require an accurate estimate of the effective depth of the sample volume; this depth is approximately 2.2 times greater with the ConfoScan 3. This difference must be considered when comparing results from studies that use one instrument with results from studies that use the other.
Two Antiphase Oscillations Occur in Each Suprachiasmatic Nucleus of Behaviorally Split Hamsters

The suprachiasmatic nuclei (SCNs) control circadian rhythms of numerous behavioral and physiological responses. In hamsters, constant light causes “splitting” of circadian rhythms, such that a single daily bout of activity separates into two components, 12 h apart, with antiphase circadian oscillations in the left and right SCN. Given the phenotypic and functional heterogeneity of the SCN, in which ventrolateral but not dorsomedial neurons are retinorecipient, we asked how these two compartments respond to the constant lighting conditions that produce splitting, using three different phase markers of neuronal activity: PER1 (Period 1), c-FOS, and pERK (phosphorylated extracellular signal-regulated kinase). We report the emergence of a coherent novel network in which each side of the SCN exhibits two antiphase oscillating subregions, here termed “core-like” and “shell-like,” in addition to the known antiphase oscillation between the right and left SCN. The novel SCN response entails a coherent rhythm in a core-like region of the SCN, which otherwise is not cycling. A mathematical model is presented, and this model interprets the observed changes in the proportion of in-phase and antiphase populations of SCN oscillators and suggests novel testable hypotheses. Finally, the functional significance of this network was explored by investigating the adjacent hypothalamus. Activation of the paraventricular nucleus is in-phase with the ipsilateral core-like SCN, whereas activation of the lateral subparaventricular zone is in-phase with the ipsilateral shell-like SCN, pointing to a multiplicity of SCN output signals. These results suggest a neural basis for internal coincidence of SCN oscillators, and a novel mechanism of plasticity in SCN neural networks and outputs.
Sentinel Surveillance of Influenza-Like Illness in Two Hospitals in Maracay, Venezuela: 2006–2010

Background Limited information exists on the epidemiology of acute febrile respiratory illnesses in tropical South American countries such as Venezuela. The objective of the present study was to examine the epidemiology of influenza-like illness (ILI) in two hospitals in Maracay, Venezuela. Methodology/Principal Findings We performed a prospective surveillance study of persons with ILI who presented for care at two hospitals in Maracay, Venezuela, from October 2006 to December 2010. A respiratory specimen and clinical information were obtained from each participant. Viral isolation and identification with immunofluorescent antibodies and molecular methods were employed to detect respiratory viruses such as adenovirus, influenza A and B, parainfluenza, and respiratory sincytial virus, among others. There were 916 participants in the study (median age: 17 years; range: 1 month – 86 years). Viruses were identified in 143 (15.6%) subjects, and one participant was found to have a co-infection with more than one virus. Influenza viruses, including pandemic H1N1 2009, were the most frequently detected pathogens, accounting for 67.4% (97/144) of the viruses detected. Adenovirus (15/144), parainfluenza virus (13/144), and respiratory syncytial virus (11/144) were also important causes of ILI in this study. Pandemic H1N1 2009 virus became the most commonly isolated influenza virus during its initial appearance in 2009. Two waves of the pandemic were observed: the first which peaked in August 2009 and the second - higher than the preceding - that peaked in October 2009. In 2010, influenza A/H3N2 re-emerged as the most predominant respiratory virus detected. Conclusions/Significance Influenza viruses were the most commonly detected viral organisms among patients with acute febrile respiratory illnesses presenting at two hospitals in Maracay, Venezuela. Pandemic H1N1 2009 influenza virus did not completely replace other circulating influenza viruses during its initial appearance in 2009. Seasonal influenza A/H3N2 was the most common influenza virus in the post-pandemic phase.
Discrete Fixed Point Analysis and Its Applications 1

We have carried out a thorough study on the existence of discrete fixed points and applications. As a result, we establish several general existence theorems of fixed and zero points on a broad class of subsets of the integer lattice Z and also on arbitrary discrete sets. Most results have their well-known continuous counterparts. One of the major conditions is that of locally gross direction preservation imposed on the mappings under consideration. Furthermore, we establish several theorems for the existence of a unique discrete zero point. In addition, three applications are discussed. We first study a pure exchange competitive economy with indivisibilities and show the existence of a discrete Walrasian equilibrium. Second, we show the existence of a pure strategy Nash equilibrium in games where the set of each player’s strategies is a discrete set and the mixed strategies are not played. Third, we discuss a general Samuelson’s spatial price equilibrium model in a discrete setting.
A Bayesian Approximation Method for Online Ranking

This paper describes a Bayesian approximation method to obtain online ranking algorithms for games with multiple teams and multiple players. Recently for Internet games large online ranking systems are much needed. We consider game models in which a k-team game is treated as several two-team games. By approximating the expectation of teams' (or players') performances, we derive simple analytic update rules. These update rules, without numerical integrations, are very easy to interpret and implement. Experiments on game data show that the accuracy of our approach is competitive with state of the art systems such as TrueSkill, but the running time as well as the code is much shorter.
Effect of Moisture Content and Feed Rate on Size Reduction of Pearl Millet

Pearl millet at various moisture content (6.2, 9.4 and 12.3%, d.b.) and feed rates (3, 6 and 9 kg/h) was ground using hammer mill and its physical properties viz. arithmetic mean diameter, geometric mean diameter, thousand grain weight, aspect ratio, specific surface area, surface area and bulk density were studied. Sieve analysis results showed that the increase in moisture content produced more medium sized particles with decreased percent weight retained in pan. Bond's work index, Kick's constant and average particle size were increased with the decrease in total surface area at higher moisture levels. The highest energy (2.34 KWh/kg) was consumed for 12.3% moisture content. Various grinding characteristics were significantly affected by moisture content and feed rate either individually or in combination and correlated in terms of Bond's work index, Kick's constant, total surface area, average particle size, effectiveness of milling and bulk density. Milling loss was found to be higher at lower moisture level and decreased with the increase of moisture content as well as feed rate. The loose and compact bulk density was ranged between 46.8-199.5 kg m -3 and 53.5-254.1 kg m -3 , respectively among the entire sieve fractions. Water absorption capacity increased with the decrease in particle size.