Miracle-dz/UniFAR-FTUs huggingface dataset:
Candidate gene molecular markers as tools for analyzing genetic susceptibility to morbillivirus infection in stranded Cetaceans

Morbilliviruses, such as Cetacean morbillivirus (CeMV) or Phocine distemper virus (PDV), represent a growing threat for marine mammals on both hemispheres. Because free‐ranging animal populations strongly rely on natural resistance mechanisms, innate immunity‐related genes and virus cell entry receptor genes may represent key factors involved in susceptibility to CeMV in Cetaceans. Using the next generation sequencing technology, we have sequenced 11 candidate genes in two model species, Stenella coeruleoalba and Phocoena phocoena. Suitable single nucleotide polymorphism markers of potential functional importance, located in genes coding for basigin (BSG, CD147), the signaling lymphocyte activating molecule (SLAMF1), the poliovirus‐related receptor‐4 (NECTIN4, PVRL4), toll‐like receptors 3, 7, 8 (TLR3, TLR7, TLR8), natural resistance‐associated macrophage protein (SLC11A1) and natural cytotoxicity triggering receptor 1 (NCR1), were identified in each model species, along with MHC‐DQB haplotypes unique for each species. This set of molecular markers represents a potentially useful tool for studying host genetic variation and susceptibility to morbillivirus infection in Cetaceans as well as for studying functionally important genetic diversity of selected Cetacean populations.
Distributed denial of service detection using TCP/IP header and traffic measurement analysis

Recently, the detection of distributed denial of service (DDoS) and the discovery of DDoS attacking signature used the mean of traffic measurement analysis at protocol level. This technique is not suited to find the signatures of DDoS attack, which is formless. Also, DDoS is in general the combination of different forms of denial of service (DoS). As a result, it is difficult to find the exact signature of attack. Moreover, it is very difficult to distinguish the difference between an unusual high traffic which is caused by the attack, and the flash crowds which normally occur when a huge number of users use the target machine at the same time. In fact, this difference should only be observed from analyzing the data in the packet header. In this paper, we propose to discover the DDoS attacking signature by analyzing the TCP/IP packet header against the well defined rules and conditions, and distinguish the difference between normal and abnormal traffic. We here observe three groups or delegates of DDoS attacking, i.e., ICMP flood, UDP flood and TCP SYN flood, and present convincing preliminary experiments.
Assessment Center Practices in Indonesia: An Exploratory Study

Although assessment centers (AC) continue to spread to Asian countries, no published study exists that evaluates AC practices in an Asian country, and none within the largest populous country within the region of Indonesia. Therefore, we conducted an exploratory survey of Indonesian organizations to examine how ACs are designed, executed, implemented, and evaluated in the target country. In this article, we show first how political, economic, and cultural circumstances have an impact on the use of AC programs in Indonesia. Second, we report a broad spectrum of AC features within Indonesian organizations. Third, we compare selected results of our study with prior findings in other countries and regions to identify advantages and disadvantages in current Indonesian AC practices. Finally, implications for both future AC research and practice in both this region, and more widely, are discussed.
Compartment modeling of dynamic brain PET--the impact of scatter corrections on parameter errors.

PURPOSE The aim of this study was to investigate the effect of scatter and its correction on kinetic parameters in dynamic brain positron emission tomography (PET) tumor imaging. The 2-tissue compartment model was used, and two different reconstruction methods and two scatter correction (SC) schemes were investigated. METHODS The gate Monte Carlo (MC) software was used to perform 2 × 15 full PET scan simulations of a voxelized head phantom with inserted tumor regions. The two sets of kinetic parameters of all tissues were chosen to represent the 2-tissue compartment model for the tracer 3'-deoxy-3'-((18)F)fluorothymidine (FLT), and were denoted FLT1 and FLT2. PET data were reconstructed with both 3D filtered back-projection with reprojection (3DRP) and 3D ordered-subset expectation maximization (OSEM). Images including true coincidences with attenuation correction (AC) and true+scattered coincidences with AC and with and without one of two applied SC schemes were reconstructed. Kinetic parameters were estimated by weighted nonlinear least squares fitting of image derived time-activity curves. Calculated parameters were compared to the true input to the MC simulations. RESULTS The relative parameter biases for scatter-eliminated data were 15%, 16%, 4%, 30%, 9%, and 7% (FLT1) and 13%, 6%, 1%, 46%, 12%, and 8% (FLT2) for K1, k2, k3, k4, Va, and Ki, respectively. As expected, SC was essential for most parameters since omitting it increased biases by 10 percentage points on average. SC was not found necessary for the estimation of Ki and k3, however. There was no significant difference in parameter biases between the two investigated SC schemes or from parameter biases from scatter-eliminated PET data. Furthermore, neither 3DRP nor OSEM yielded the smallest parameter biases consistently although there was a slight favor for 3DRP which produced less biased k3 and Ki estimates while OSEM resulted in a less biased Va. The uncertainty in OSEM parameters was about 26% (FLT1) and 12% (FLT2) larger than for 3DRP although identical postfilters were applied. CONCLUSIONS SC was important for good parameter estimations. Both investigated SC schemes performed equally well on average and properly corrected for the scattered radiation, without introducing further bias. Furthermore, 3DRP was slightly favorable over OSEM in terms of kinetic parameter biases and SDs.
Simulating supply chain activities in multi-agent based supply chain management system with plasma simulator

To implement the multifarious real-time business scenario in the supply chain management system is very complex task. The supply chain management system contains multiple interdependent entities along with goals of maximized organizational goals and the maximized customer satisfaction. The multi-agent system approach offers the guarantee to assist the design and development of complex supply chain management system. In this paper, we introduce the simulation middleware PlaSMA which extends the JADE agent framework with a simulation control that validate the proper functioning of the intelligent agents in the MAS based SCM system. We illustrate the benefits of the PlaSMA simulation for SCM design and discuss further gains to be expected from the performance view point of MAS based SCM system.
ppk23-Dependent Chemosensory Functions Contribute to Courtship Behavior in Drosophila melanogaster

Insects utilize diverse families of ion channels to respond to environmental cues and control mating, feeding, and the response to threats. Although degenerin/epithelial sodium channels (DEG/ENaC) represent one of the largest families of ion channels in Drosophila melanogaster, the physiological functions of these proteins are still poorly understood. We found that the DEG/ENaC channel ppk23 is expressed in a subpopulation of sexually dimorphic gustatory-like chemosensory bristles that are distinct from those expressing feeding-related gustatory receptors. Disrupting ppk23 or inhibiting activity of ppk23-expressing neurons did not alter gustatory responses. Instead, blocking ppk23-positive neurons or mutating the ppk23 gene delayed the initiation and reduced the intensity of male courtship. Furthermore, mutations in ppk23 altered the behavioral response of males to the female-specific aphrodisiac pheromone 7(Z), 11(Z)-Heptacosadiene. Together, these data indicate that ppk23 and the cells expressing it play an important role in the peripheral sensory system that determines sexual behavior in Drosophila.
Columbia-UCF TRECVID2010 Multimedia Event Detection: Combining Multiple Modalities, Contextual Concepts, and Temporal Matching

Summary TRECVID Multimedia Event Detection offers an interesting but very challenging task in detecting high- level complex events (Figure 1) in user-generated videos. In this paper, we will present an overview and comparative analysis of our results, which achieved top performance among all 45 submissions in TRECVID 2010. Our aim is to answer the following questions. What kind of feature is more effective for multimedia event detection? Are features from different feature modalities (e.g., audio and visual) complementary for event detection? Can we benefit from generic concept detection of background scenes, human actions, and audio concepts? Are sequence matching and event-specific object detectors critical? Our findings indicate that spatial-temporal feature is very effective for event detection, and it's also very complementary to other features such as static SIFT and audio features. As a result, our baseline run combining these three features already achieves very impressive results, with a mean minimal normalized cost (MNC) of 0.586. Incorporating the generic concept detectors using a graph diffusion algorithm provides marginal gains (mean MNC 0.579). Sequence matching with Earth Mover's Distance (EMD) further improves the results (mean MNC 0.565). The event-specific detector ("batter"), however, didn't prove useful from our current re-ranking tests. We conclude that it is important to combine strong complementary features from multiple modalities for multimedia event detection, and cross-frame matching is helpful in coping with temporal order variation. Leveraging contextual concept detectors and foreground activities remains a very attractive direction requiring further research.
Fibropapilloma of the Glans Penis in a Horse

An 18-year-old Arabian stallion was presented for recent onset of stranguria. Physical examination of the distal portion of the glans penis revealed multiple, smooth, glistening, grayish-pink, variably sized, exophytic, nodular masses circumferentially surrounding the external urethral orifice. Partial penile amputation was performed, and the entire specimen was submitted for histological evaluation. Microscopically, the masses consisted of abundant amounts of loosely arranged fibrovascular stroma with low numbers of spindloid to stellate fibrocytes. The overlying epithelium was mildly to moderately hyperplastic with short anastomosing rete ridges (pseudoepitheliomatous hyperplasia). The lesion was diagnosed as fibropapilloma because of features similar to bovine penile fibropapilloma including anatomical location, gross appearance, and histological characteristics. A sarcoid was considered but negated as the lesion lacked the classical streaming and interlacing spindle cell population, “picket-fence” appearance at the epithelial interface, and long, thin, dissecting rete ridges typical of most equine sarcoids. Polymerase chain reaction for the Bovine papillomavirus-1 and Bovine papillomavirus-2 E5 gene and for Equine herpesvirus 1, 3, and 4 was negative on formalin-fixed tissue specimens.
Compute-and-Forward Network Coding Design over Multi-Source Multi-Relay Channels

Network coding is a new and promising paradigm for modern communication networks by allowing intermediate nodes to mix messages received from multiple sources. Compute-and-forward strategy is one category of network coding in which a relay will decode and forward a linear combination of source messages according to the observed channel coefficients, based on the algebraic structure of lattice codes. The destination will recover all transmitted messages if enough linear equations are received. In this work, we design in a system level, the compute-and-forward network coding coefficients by Fincke-Pohst based candidate set searching algorithm and network coding system matrix constructing algorithm, such that by those proposed algorithms, the transmission rate of the multi-source multi-relay system is maximized. Numerical results demonstrate the effectiveness of our proposed algorithms.
Self-sustained Ionization and Vanishing Dead Zones in Protoplanetary Disks

We analyze the ionization state of the magnetohydrodynamically turbulent protoplanetary disks and propose a new mechanism of sustaining ionization. First, we show that in the quasi-steady state of turbulence driven by magnetorotational instability in a typical protoplanetary disk with dust grains, the amount of energy dissipation should be sufficient for providing the ionization energy that is required for activating magnetorotational instability. Second, we show that in the disk with dust grains the energetic electrons that compose electric currents in weakly ionized gas can provide collisional ionization, depending on the actual saturation state of magnetorotational turbulence. On the other hand, we show that in the protoplanetary disks with the reduced effect of dust grains, the turbulent motion can homogenize the ionization degree, which can activate magnetorotational instability even in the absence of other ionization processes. The results in this Letter indicate that most of the regions in protoplanetary disks remain magnetically active, and we thus require a change in the theoretical modeling of planet formation.
Counting independent sets up to the tree threshold

Consider the problem of approximately counting weighted independent sets of a graph G with activity λ, i.e., where the weight of an independent set I is λ<sup>|I|</sup>. We present a novel analysis yielding a deterministic approximation scheme which runs in polynomial time for <i>any</i> graph of maximum degree Δ and λ< λ<sub>c</sub>=(Δ-1)<sup>Δ-1</sup>/(Δ-2)<sup>Δ</sup>. This improves on the previously known general bound of λ ≤ (2 ‾ Δ-2). The new regime includes the interesting case of λ=1 (uniform weights) and Δ ≤ 5. The previous bound required Δ ≤ 4 for uniform approximate counting and there is evidence that for Δ ≥ 6 the problem is hard. Note that λ<sub>c</sub> is the critical activity for uniqueness of the <i>Gibbs</i> measure on the regular tree of degree Δ, i.e., for λ ≤ λ<sub>c</sub> the probability that the root is in the independent set is asymptotically independent of the configuration on the leaves far below. Indeed, our analysis is focused on establishing decay of correlations with distance in the above weighted distribution. We show that on any graph of maximum degree Δ correlations decay with distance at least as fast as they do on the regular tree of the same degree. This resolves an open conjecture in statistical physics. Our comparison of a general graph with the tree uses an algorithmic argument yielding the approximation scheme mentioned above. Also, by existing arguments, establishing decay of correlations for all graphs and λ<λ<sub>c</sub> gives that the <i>Glauber</i> dynamics is rapidly mixing in this regime. However, the implication from decay of correlations to rapid mixing of the dynamics is only known to hold for graphs of subexponential growth, and hence, our result regarding the Glauber dynamics is limited to this class of graphs.
Structural basis for the prion-like MAVS filaments in antiviral innate immunity

Mitochondrial antiviral signaling (MAVS) protein is required for innate immune responses against RNA viruses. In virus-infected cells MAVS forms prion-like aggregates to activate antiviral signaling cascades, but the underlying structural mechanism is unknown. Here we report cryo-electron microscopic structures of the helical filaments formed by both the N-terminal caspase activation and recruitment domain (CARD) of MAVS and a truncated MAVS lacking part of the proline-rich region and the C-terminal transmembrane domain. Both structures are left-handed three-stranded helical filaments, revealing specific interfaces between individual CARD subunits that are dictated by electrostatic interactions between neighboring strands and hydrophobic interactions within each strand. Point mutations at multiple locations of these two interfaces impaired filament formation and antiviral signaling. Super-resolution imaging of virus-infected cells revealed rod-shaped MAVS clusters on mitochondria. These results elucidate the structural mechanism of MAVS polymerization, and explain how an α-helical domain uses distinct chemical interactions to form self-perpetuating filaments. DOI: http://dx.doi. org/10.7554/eLife.01489. 001
Accurate Timing Analysis using SAT and Pattern-Dependent Delay Models

Accurate delay modeling beyond static models is critical to garnering better correlation with post-silicon analysis. Furthermore, post-silicon timing validation requires a pattern-dependent timing model to generate patterns. To address these issues, a timing analysis tool was proposed that integrates a data-dependent delay model into its analysis. The approach solves for the delay by using the concept of circuit unrolling and formulation of timing questions as decision problems for input into a SAT solver. The effectiveness and validity of the proposed methodology is illustrated through experiments on benchmark circuits
LDL receptor-related protein-1 is a sialic-acid-independent receptor for myelin-associated glycoprotein that functions in neurite outgrowth inhibition by MAG and CNS myelin

Summary In the injured adult mammalian central nervous system (CNS), products are generated that inhibit neuronal sprouting and regeneration. In recent years, most attention has focused on the myelin-associated inhibitory proteins (MAIs) Nogo-A, OMgp, and myelin-associated glycoprotein (MAG). Binding of MAIs to neuronal cell-surface receptors leads to activation of RhoA, growth cone collapse, and neurite outgrowth inhibition. In the present study, we identify low-density lipoprotein (LDL) receptor-related protein-1 (LRP1) as a high-affinity, endocytic receptor for MAG. In contrast with previously identified MAG receptors, binding of MAG to LRP1 occurs independently of terminal sialic acids. In primary neurons, functional inactivation of LRP1 with receptor-associated protein, depletion by RNA interference (RNAi) knock-down, or LRP1 gene deletion is sufficient to significantly reverse MAG and myelin-mediated inhibition of neurite outgrowth. Similar results are observed when LRP1 is antagonized in PC12 and N2a cells. By contrast, inhibiting LRP1 does not attenuate inhibition of neurite outgrowth caused by chondroitin sulfate proteoglycans. Mechanistic studies in N2a cells showed that LRP1 and p75NTR associate in a MAG-dependent manner and that MAG-mediated activation of RhoA may involve both LRP1 and p75NTR. LRP1 derivatives that include the complement-like repeat clusters CII and CIV bind MAG and other MAIs. When CII and CIV were expressed as Fc-fusion proteins, these proteins, purified full-length LRP1 and shed LRP1 all attenuated the inhibition of neurite outgrowth caused by MAG and CNS myelin in primary neurons. Collectively, our studies identify LRP1 as a novel MAG receptor that functions in neurite outgrowth inhibition.
Genome Partitioning of Genetic Variation for Milk Production and Composition Traits in Holstein Cattle

The objective of this study was to estimate the contribution of each autosome to genetic variation of milk yield, fat, and protein percentage and somatic cell score in Holstein cattle. Data on 2294 Holstein bulls genotyped for 39,557 autosomal markers were used. Three approaches were applied to estimate the proportion of genetic variance attributed to each chromosome. In two of them, marker-derived kinship coefficients were computed, using either marker genotypes observed on the whole genome or on subsets relative to each chromosome. Variance components were then estimated using residual maximum likelihood in method 1 or a regression-based approach in method 2. In method 3, genetic variances associated to each marker were estimated in a linear multiple regression approach, and then were summed up chromosome-wise. Generally, all chromosomes contributed to genetic variation. For most of the chromosomes, the amount of variance attributed to a chromosome was found to be proportional to its physical length. Nevertheless, for traits influenced by genes with very large effects a larger proportion of the genetic variance is expected to be associated with the chromosomes where these genes are. This is illustrated with the DGAT1 gene on BTA14 which is known to have a large effect on fat percentage in milk. The proportion of genetic variance for fat percentage associated with chromosome 14 was two to sevenfold (depending on the method) larger than would be predicted from chromosome size alone. Based on method 3 an approach is suggested to estimate the effective number of genes underlying the inheritance of the studied traits, yielding numbers between N ≈ 400 (for fat percentage) to N ≈ 900 (for milk yield). It is argued that these numbers are conservative lower bound estimates, but are in line with recent findings suggesting a highly polygenic background of production traits in dairy cattle.
Inverse optimal control for a hybrid dynamical system with impacts

In this paper, we develop an approach to inverse optimal control for a class of hybrid dynamical system with impacts. As it is usually posed, the problem of inverse optimal control is to find a cost function that is consistent with an observed sequence of decisions, under the assumption that these decisions are optimal. We assume instead that observed decisions are only approximately optimal and find a cost function that minimizes the extent to which these decisions violate first-order necessary conditions for optimality. For the hybrid dynamical system that we consider with a cost function that is a linear combination of known basis functions, this minimization is a convex program. In fact, it reduces to a simple least-squares computation that - unlike most other forms of inverse optimal control - can be solved very efficiently. We apply our approach to a dynamic bipedal climbing robot in simulation, showing that we can recover cost functions from observed trajectories that are consistent with two different modes of locomotion.
Functional Domain Mapping and Selective Trans-dominant Effects Exhibited by Cx26 Disease-causing Mutations*

Mutations in Cx26 are a major cause of autosomal dominant and recessive forms of sensorineural deafness. Some mutations in Cx26 are associated not only with deafness but also with skin disease. We examined the subcellular localization and function of two green fluorescent protein (GFP)-tagged Cx26 point mutants that exhibit both phenotypes, G59A-GFP and D66H-GFP. D66H-GFP was retained within the brefeldin A-insensitive trans-Golgi network, whereas a population of G59A-GFP was transported to the cell surface. Neither G59A nor D66H formed gap junctions that were permeable to small fluorescent dyes, suggesting they are loss-of-function mutations. When co-expressed with wild-type Cx26, both G59A and D66H exerted dominant-negative effects on Cx26 function. G59A also exerted a trans-dominant negative effect on co-expressed wild type Cx32 and Cx43, whereas D66H exerted a trans-dominant negative effect on Cx43 but not Cx32. We propose that the severity of the skin disease is dependent on the specific nature of the Cx26 mutation and the trans-dominant selectivity of the Cx26 mutants on co-expressed connexins. Additional systematic mutations at residue D66, in which the overall charge of this motif was altered, suggested that the first extracellular loop is critical for Cx26 transport to the cell surface as well as function of the resulting gap junction channels.