Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection and phylogenetic characterization of porcine circovirus 2 from pigs in Mozambique

Porcine circovirus–associated diseases (PCVADs), caused by porcine circovirus 2 (PCV-2), have a significant economic impact on the swine industry worldwide. In Africa, there is little information, to date, regarding the occurrence of PCV-2, and it has not been reported in Mozambique’s swine population. We randomly collected mesenteric lymph nodes (n = 111) from slaughtered pigs from 9 districts in southern Mozambique. PCV-2 DNA was detected in 54% (62 of 111) of the samples and 78% (23 of 31) of the farms. PCV-2 antigen was detected by immunohistochemistry in lymph nodes (6 of 62; 10%) that were positive for PCV-2 by PCR. Histopathologic changes observed in these lymph nodes were lymphoid depletion, multifocal nodal necrosis, and infiltrates of histiocytes and multinucleate giant cells. One positive sample from each district was selected in order to obtain sequences covering the ORF2 region. Five sequences clustered with PCV-2d, of which 3 sequences from Maputo, Namaacha, and Moamba were grouped with PCV-2d-2; 2 sequences from Manhiça and Matola were grouped as PCV-2d-1; and 4 sequences from Boane, Matutuíne, Chibuto, and Xai-Xai were closely related to PCV-2b-1A/B genotypes. Our study indicates that a diversity of PCV-2 viruses is circulating in the Mozambican swine population.
Queer currents, steady rhythms, and drunken da neurons. Focus on "hyperpolarization-activated cation current (Ih) is an ethanol target in midbrain dopamine neurons of mice".

Currents derived from hyperpolarization-activated cation channels ( I h channels) were once referred to as “queer currents ( I q)” because they were unusual in their large amplitudes, their activation by hyperpolarization, and their lack of inactivation during sustained hyperpolarization of the
DINIES: drug–target interaction network inference engine based on supervised analysis

DINIES (drug–target interaction network inference engine based on supervised analysis) is a web server for predicting unknown drug–target interaction networks from various types of biological data (e.g. chemical structures, drug side effects, amino acid sequences and protein domains) in the framework of supervised network inference. The originality of DINIES lies in prediction with state-of-the-art machine learning methods, in the integration of heterogeneous biological data and in compatibility with the KEGG database. The DINIES server accepts any ‘profiles’ or precalculated similarity matrices (or ‘kernels’) of drugs and target proteins in tab-delimited file format. When a training data set is submitted to learn a predictive model, users can select either known interaction information in the KEGG DRUG database or their own interaction data. The user can also select an algorithm for supervised network inference, select various parameters in the method and specify weights for heterogeneous data integration. The server can provide integrative analyses with useful components in KEGG, such as biological pathways, functional hierarchy and human diseases. DINIES (http://www.genome.jp/tools/dinies/) is publicly available as one of the genome analysis tools in GenomeNet.
No Free Lunch Theorem and Bayesian probability theory: two sides of the same coin. Some implications for black-box optimization and metaheuristics

Challenging optimization problems, which elude acceptable solution via conventional calculus methods, arise commonly in different areas of industrial design and practice. Hard optimization problems are those who manifest the following behavior: a) high number of independent input variables; b) very complex or irregular multi-modal fitness; c) computational expensive fitness evaluation. This paper will focus on some theoretical issues that have strong implications for practice. I will stress how an interpretation of the No Free Lunch theorem leads naturally to a general Bayesian optimization framework. The choice of a prior over the space of functions is a critical and inevitable step in every black-box optimization.
Static analysis and compiler design for idempotent processing

Recovery functionality has many applications in computing systems, from speculation recovery in modern microprocessors to fault recovery in high-reliability systems. Modern systems commonly recover using checkpoints. However, checkpoints introduce overheads, add complexity, and often save more state than necessary. This paper develops a novel compiler technique to recover program state without the overheads of explicit checkpoints. The technique breaks programs into idempotent regions---regions that can be freely re-executed---which allows recovery without checkpointed state. Leveraging the property of idempotence, recovery can be obtained by simple re-execution. We develop static analysis techniques to construct these regions and demonstrate low overheads and large region sizes for an LLVM-based implementation. Across a set of diverse benchmark suites, we construct idempotent regions close in size to those that could be obtained with perfect runtime information. Although the resulting code runs more slowly, typical performance overheads are in the range of just 2-12%. The paradigm of executing entire programs as a series of idempotent regions we call idempotent processing, and it has many applications in computer systems. As a concrete example, we demonstrate it applied to the problem of compiler-automated hardware fault recovery. In comparison to two other state-of-the-art techniques, redundant execution and checkpoint-logging, our idempotent processing technique outperforms both by over 15%.
A MHz electronic ballast for automotive-type HID lamps

The compatibility of the current sourcing push pull resonant inverter (CS-PPRI) with the driving requirements of HID lamps designated for automotive headlight applications was investigated theoretically, by simulation and experimentally. The study reveals that a based ballast (CS-PPRI) complies with the automotive requirement of very fast warm up. The experimental ballast was run under zero voltage switching (ZVS) at a nominal switching frequency of 1.29 MHz while the pre-ignition switching frequency was 124 kHz. Warm up time to 80% after cold ignition was about 10 seconds.
Advanced automata-based algorithms for program termination checking

In 2014, Heizmann et al. proposed a novel framework for program termination analysis. The analysis starts with a termination proof of a sample path. The path is generalized to a Büchi automaton (BA) whose language (by construction) represents a set of terminating paths. All these paths can be safely removed from the program. The removal of paths is done using automata difference, implemented via BA complementation and intersection. The analysis constructs in this way a set of BAs that jointly "cover" the behavior of the program, thus proving its termination. An implementation of the approach in Ultimate Automizer won the 1st place in the Termination category of SV-COMP 2017. In this paper, we exploit advanced automata-based algorithms and propose several non-trivial improvements of the framework. To alleviate the complementation computation for BAs---one of the most expensive operations in the framework---, we propose a multi-stage generalization construction. We start with generalizations producing subclasses of BAs (such as deterministic BAs) for which efficient complementation algorithms are known, and proceed to more general classes only if necessary. Particularly, we focus on the quite expressive subclass of semideterministic BAs and provide an improved complementation algorithm for this class. Our experimental evaluation shows that the proposed approach significantly improves the power of termination checking within the Ultimate Automizer framework.
pH-Sensitive Nanoscale Polymers: Highly Efficient Systems for DOX Delivery in Cancer Treatment

Recently, many stimuli-responsive drug delivery systems based on biodegradable and biocompatible polymers have been introduced for controlled release of anticancer drug Doxorubicin. The main role of polymers in these systems is to provide high loading of Doxorubicin and then control the release of the drug in low pH-media. Polymeric micelles and nanoparticles such as magnetic particles, silica and graphene oxide covered with smart polymers include two main categories of Dox-controlled release systems. Herein, we review aforementioned systems which have been used for Doxorubicin release through different response of the system in terms of pH including: swelling or expansion of the polymeric chains, pH-sensitive bond cleavage and loss of electrostatic interactions between the drug and system. The mechanism of drug loading, drug release, advantages and disadvantages of each system are fully discussed.
Inferring Social Disposition by Sound and Surface Appearance in Infancy

ABSTRACT Adults automatically infer a person’s social disposition and future behavior based on the many properties they observe about how they look and sound. The goal of the current study is to explore the developmental origins of this bias. We tested whether 12-month-old infants automatically infer a character’s social disposition (e.g., whether they are likely to “help” or “hinder” another character’s goal) based on the sounds and visual features those characters display. Infants were habituated to 2 characters, 1 that possessed more positive properties (e.g., a soft, fluffy appearance and a happy-sounding laugh) or more negative properties (e.g., a sharp, pointy appearance and a deep, ominous laugh). During test trials, we observed that infants looked longer at events that involved characters engaging in social actions toward another that were inconsistent rather than consistent with the valence of how they looked and sounded during habituation. Two control conditions support the interpretation that infants’ responses were based on an inferred causal relationship between a character’s features and its disposition rather than on some noncausal associations between the positive and negative valences of the characteristics and actions. Together, these studies suggest that infants are biased to connect an agent’s audiovisual features to their social behavior.
Nonlinear Stochastic Biasing from the Formation Epoch Distribution of Dark Halos

We propose a physical model for nonlinear stochastic biasing of one-point statistics resulting from the formation epoch distribution of dark halos. In contrast to previous works based on extensive numerical simulations, our model provides for the first time an analytic expression for the joint probability function. Specifically, we derive the joint probability function of halo and mass density contrasts from the extended Press-Schechter theory. Since this function is derived in the framework of the standard gravitational instability theory assuming the random Gaussianity of the primordial density field alone, we expect that the basic features of the nonlinear and stochastic biasing predicted from our model are fairly generic. As representative examples, we compute the various biasing parameters in cold dark matter models as a function of a redshift and a smoothing length. Our major findings are that (1) the biasing of the variance evolves strongly as redshift, while its scale dependence is generally weak, and a simple linear biasing model provides a reasonable approximation at roughly R ≳ 2(1 + z) h-1 Mpc; and (2) the stochasticity exhibits moderate scale dependence, especially on R ≲ 20 h-1 Mpc, but is almost independent of z. Comparison with the previous numerical simulations shows good agreement with the above behavior, indicating that the nonlinear and stochastic nature of the halo biasing can be essentially understood by taking into account the distribution of the halo mass and the formation epoch.
Grayscale access control: Applying differential privacy to access control for Internet of Thing environment

As the essential role of data analysis in obtaining valuable information increases, the importance of acquiring useful data has also increased, especially within an Internet of Things (IoT) era. In this context, proper access control technique is required, because excessive data collection and analysis can lead to security breaches. However, existing access permission/denial binary access control techniques are not only unable to guarantee security, they can also significantly reduce information availability. In this paper, we propose a grayscale access control scheme that aims to minimize the trade-off between information usability and security by applying the differential privacy. We also propose a noise parameter determination algorithm that uses a Stackelberg game to determine the appropriate amount of noise insertion in differential privacy. We demonstrate that the proposed technique can determine the appropriate noise parameter values and achieve fine-grained access control through experiments.
Fast trajectory planning of reactive operation considering manipulability for a humanoid

For humanoid robots, there exist a class of challenging tasks, e.g. playing table tennis, which are non-repeatedly, triggered randomly by sensor events, and compelling the robots to produce reactive operations in very short time. Additionally, some key poses of the robot are partially constrained to accomplish the operations, and are usually adjusted during the operation execution. In this paper, efforts are made to generate trajectory for these operations. Firstly, an extended manipulability index is proposed to optimize the key poses so that the humanoid robot has the manipulability considering joint limits at the key poses, which makes it convenient to adjust the trajectory. Secondly, a fast approach to generating the whole trajectory consisting of all the key poses and the strategies to realize the trajectory adjustment when specifications change are proposed. Finally, the ZMP (Zero Moment Point) displacement excited by the reactive operations is also given to decide whether the generated trajectory is feasible. The effectiveness of the method is demonstrated through simulations.
Mapping Cognitive Rehabilitation in Diffuse Axonal Injury (DAI): A Case Study

There has been no report on detailed temporal mapping of traumatic brain injury (TBI), especially diffuse axonal injury (DAI), rehabilitation process. A case study is presented here on four-year tracking of a 24-year old male adolescent with severe DAI. The study aimed to develop a theoretical visual model of TBI (DAI) cognitive rehabilitation, and to validate this model by mapping out the sequence of significant behaviour events. The ensuing spiral cone model concurs with two well-known TBI rehabilitation sequels. The sequence of cognitive rehabilitation should aid in planning interventions in other similar or comparable TBI (DAI) patients.
A neural basis for the spatial suppression of visual motion perception

In theory, sensory perception should be more accurate when more neurons contribute to the representation of a stimulus. However, psychophysical experiments that use larger stimuli to activate larger pools of neurons sometimes report impoverished perceptual performance. To determine the neural mechanisms underlying these paradoxical findings, we trained monkeys to discriminate the direction of motion of visual stimuli that varied in size across trials, while simultaneously recording from populations of motion-sensitive neurons in cortical area MT. We used the resulting data to constrain a computational model that explained the behavioral data as an interaction of three main mechanisms: noise correlations, which prevented stimulus information from growing with stimulus size; neural surround suppression, which decreased sensitivity for large stimuli; and a read-out strategy that emphasized neurons with receptive fields near the stimulus center. These results suggest that paradoxical percepts reflect tradeoffs between sensitivity and noise in neuronal populations.
THE PATTERNS OF THE ARTERIAL PRESSURE PULSE

During the past ten years there have accumulated in this laboratory a large number of records of the arterial pressure pulses taken with the Hypodermic Manometer (4). These are faithful records of the changes in the pressure of the blood in various arteries of man and of other animals. The form of the pressure pulse curve is quite variable. Some of the types are drawn roughly to scale in the figures presented herewitOh, but, there are many intergrading examples which can not be shown for lack of space. It is the purpose of this paper t,o describe the manner in which these typical patterns tlake form and to present a simple hypothesis that will account physically for t,he variations seen in the pressure pulses in different arteries and under differ-ent? conditions. The simplest pulse form is that seen in very small animals such as the mouse, canary, frog or turtle (1). During early systole the ejection from the heart is rapid, blood is coming into the arterial tree faster than it is leaving through the arterioles and the pressure in the arteries rises abruptly. Later the rate of ejection falls, the arterial pressure rise continues but becomes less abrupt. Toward the end of systole there is a balance between the rate of ejection and the rate of arteriolar drainage. The curve is then horizontal. An actual decline in the curve is sometlimes seen during late systole, when ejection falls to a rate that is less than arteriolar drainage. During diastole the curve is a perfectly smooth fall of pressure with time. falls faster at first when the pressure is high. It Blood drains out of the arterioles more rapidly and each unit of blood leaving the arterioles makes a greater pressure diff'erence when the pressure is high than when the pressure is low. This smooth pressure curve is the simple consequence of filling and emptying of the aiterial compression chamber. However it is seen only in small animals. The t,inv arteries of these creatures respond so quickly that tlhey follow faithfully t,he pressure changes which are produced by the heart. In ordinary laboratory animals such as the dog and in man the form of the pressure pulse is much more complex. Superimposed upon the first described filling and emptying curve are waves of arterial origin. This is because the mass of the arberial blood column is so large and the …
Exploring Multiple Evidences to Infer Users Location in Twitter

Social networks are valuable sources of information to monitor real-time events, such as earthquakes and epidemics. For this type of surveillance, users location is an essential piece of information, but a substantial number of users choose not to disclose their geographical information. However, characteristics of the users’ behavior, such as the friends they associate with and the types of messages published may hint on their spatial location. In this paper, we present a method to infer the spatial location of Twitter users. Unlike the approaches proposed so far, we incorporate two sources of information to learn geographical position: the text posted by users and their friendship network. We propose a probabilistic approach that jointly models the geographical labels and Twitter texts of users organized in the form of a graph representing the friendship network. We use the Markov random ﬁeld probability model to represent the network and learning is carried out through a Markov chain Monte Carlo simulation technique to approximate the posterior probability distribution of the missing geographical labels. We show the accuracy of the model in a large dataset of Twitter users, where the ground truth is the location given by the GPS position. The method is evaluated and compared to two baseline algorithms that employ either of these two types of information. The results obtained are signiﬁcantly better than those of the baseline methods.
Gene Related to Anergy in Lymphocytes (GRAIL) Expression in CD4+ T Cells Impairs Actin Cytoskeletal Organization during T Cell/Antigen-presenting Cell Interactions*

GRAIL (gene related to anergy in lymphocytes), is an E3 ubiquitin ligase with increased expression in anergic CD4+ T cells. The expression of GRAIL has been shown to be both necessary and sufficient for the induction of T cell (T) anergy. To date, several subsets of anergic T cells have demonstrated altered interactions with antigen-presenting cells (APC) and perturbed TCR-mediated signaling. The role of GRAIL in mediating these aspects of T cell anergy remains unclear. We used flow cytometry and confocal microscopy to examine T/APC interactions in GRAIL-expressing T cells. Increased GRAIL expression resulted in reduced T/APC conjugation efficiency as assessed by flow cytometry. Examination of single T/APC conjugates by confocal microscopy revealed altered polarization of polymerized actin and LFA-1 to the T/APC interface. When GRAIL expression was knocked down, actin polarization to the T/APC interface was restored, demonstrating that GRAIL is necessary for alteration of actin cytoskeletal rearrangement under anergizing conditions. Interestingly, proximal TCR signaling including calcium flux and phosphorylation of Vav were not disrupted by expression of GRAIL in CD4+ T cells. In contrast, interrogation of distal signaling events demonstrated significantly decreased JNK phosphorylation in GRAIL-expressing T cells. In sum, GRAIL expression in CD4+ T cells mediates alterations in the actin cytoskeleton during T/APC interactions. Moreover, in this model, our data dissociates proximal T cell signaling events from functional unresponsiveness. These data demonstrate a novel role for GRAIL in modulating T/APC interactions and provide further insight into the cell biology of anergic T cells.
Rock›Scissors›Paper Game on Complex Networks

In ecological and social systems, dieren t species often compete with each other so that their relative strength is characterized by a cyclic dominance relation. Because of the absence of an absolute winner, cyclically dominating population dynamics often show neutrally stable or unstable oscillations, which may in practical mar stable coexistence of various species. We show that networks with heterogeneous degree distributions facilitate stable coexistence in the rockscissors-paper game, which is a standard model of cyclic competition.
A REVIEW OF TRAIT-MEDIATED INDIRECT INTERACTIONS IN ECOLOGICAL COMMUNITIES

In this paper we review the empirical studies documenting trait-mediated indirect interactions (TMIIs) in food webs. Basic models and empirical approaches that form the foundation of our conceptualization of species interactions generally assume that interactions are an intrinsic property of the two interacting species and therefore are governed by their respective densities. However, if a species reacts to the presence of a second species by altering its phenotype, then the trait changes in the reacting species can alter the per capita effect of the reacting species on other species and, consequently, population density or fitness of the other species. Such trait-mediated indirect interactions can reinforce or oppose density-mediated effects and have been largely overlooked by community ecologists. We first briefly develop the case for the broad mechanistic basis for TMIIs and then review the direct evidence for TMIIs in various permutations of simple three- to four-species food webs. We find strong evid.