Miracle-dz/UniFAR-FTUs huggingface dataset:
Supporting Online Material Materials and Methods Figs. S1 and S2 Tables S1 and S2 References Temporal Fragmentation of Speciation in Bacteria

Replication of the B. abortus LOV-HK mutant strain was less than the wild-type strain as early as 4 hours after infection. To confirm that this defect in replication was only due to the absence of the BA-LOV-HK gene, the LOV-HK mutant was complemented with a plasmid expressing the wild-type BA-LOV-HK gene. The complemented strain was able to rescue the mutant phenotype (Fig. 4A), confirming that the BA-LOV-HK gene is required for optimal replica-tion of B. abortus in macrophages. Light activation of the LOV-HK requires a reactive cysteine (C69). A C69A mutant in a B. abortus LOV-HK knockout background did not return the replication rate to the wild-type level (Fig. 4A), indicating that formation of the co-valent adduct between FMN and the LOV protein is essential to restore kinase function. Thus, the biological role of the LOV-HK protein is associated with its capacity to sense light and transduce the signal to the output kinase domain. The number of intracellular bacteria increased slightly after 24 hours in culture in the light (Fig. 4B); however, in the dark, roughly an order of magnitude fewer bacteria survived, a survival rate no better than that of the BA-LOV-HK knockout mutant, which suggests clearly that the BA-LOV-HK photoreceptor serves as a virulence factor in Brucella spp. and that light may prepare the bacteria present in the aborted placenta for infection of the next host (28). We have shown that four bacterial LOV-HKs bind a flavin chromophore that, upon illumination , forms the cysteinyl adduct characteristic of LOV domain photochemistry. Unexpectedly , the cysteinyl adduct in Brucella LOV-HK does not break spontaneously in the dark as it does in the other bacterial LOV-HK proteins and the plant phototropin LOV domains (17). Upon illumination in the presence of ATP, the kinases of all four LOV-HKs undergo auto-phosphorylation, likely on a conserved histi-dine, and are activated. The close correlation between cysteinyl-flavin adduct lifetime and kinase activity indicates that the adduct is the signaling state that activates the histidine ki-nase. Furthermore, the BA-LOV-HK appears to function as a photoreceptor that is directly related to Brucella survival and replication within macrophages. Investígación Científica y Tecnológica (ANPCYT-PICT2004-21193). We thank S. Giovannoni and his laboratory and the J. Craig Venter Institute (JCVI) for the E. litoralis HTCC2594 genome sequence, which was determined and deposited in GenBank (CP000157) with support from the Gordon and Betty Moore Foundation. We are indebted to S. Kravitz and …
Monitoring-based validation of functional and performance aspects of a greedy ant colony optimization protocol

Delay Tolerant Networks (DTN) are well adapted for situations where the network nodes suffer from intermittent communications due to the high mobility of the nodes and the constantly changing environment. Several research works tried to address this problem and lately, an ants-based protocol named GrAnt, has been proposed as one of the best solutions. In this paper we firstly assess GrAnt performance in much more challenging conditions than those presented by its authors, and secondly, we present a generic methodology based on MMT, an online security monitoring tool that enables real-time analysis of network traffic, to correlate the performance of a DTN protocol (such as GrAnt) with the information stored in its messages in order to validate the reliability of the protocol.
Effect of the IL-1 Receptor Antagonist Kineret® on Disease Phenotype in mdx Mice

Duchenne muscular dystrophy (DMD) is an X-linked muscle disease caused by mutations in the dystrophin gene. The pathology of DMD manifests in patients with progressive muscle weakness, loss of ambulation and ultimately death. One of the characteristics of DMD is muscle inflammation, and dystrophin-deficient skeletal muscles produce higher levels of the pro-inflammatory cytokine interleukin 1β (IL-1β) in response to toll like receptor (TLR) stimulation compared to controls; therefore, blocking the IL-1β pathway could improve the disease phenotype in mdx mice, a mouse model of DMD. Kineret® or IL-1Ra is a recombinant IL-1 receptor antagonist approved by the FDA for treating rheumatoid arthritis. To determine the efficacy of IL-1Ra in a DMD model, we administered subcutaneous injections of saline control or IL-1Ra (25 mg/kg/day) to mdx mice daily for 45 days beginning at 5 weeks of age. Functional and histological parameters were measured at the conclusion of the study. IL-1Ra only partially inhibited this signaling pathway in this study; however, there were still interesting observations to be noted. For example, although not significantly changed, splenocytes from the IL-1Ra-treated group secreted less IL-1β after LPS stimulation compared to control mice indicating a blunted response and incomplete inhibition of the pathway (37% decrease). In addition, normalized forelimb grip strength was significantly increased in IL-1Ra-treated mice. There were no changes in EDL muscle-specific force measurements, histological parameters, or motor coordination assessments in the dystrophic mice after IL-1Ra treatment. There was a significant 27% decrease in the movement time and total distance traveled by the IL-1Ra treated mice, correlating with previous studies examining effects of IL-1 on behavior. Our studies indicate partial blocking of IL-1β with IL-1Ra significantly altered only a few behavioral and strength related disease parameters; however, treatment with inhibitors that completely block IL-1β, pathways upstream of IL-1β production or combining various inhibitors may produce more favorable outcomes.
Amino Acid Signaling in Yeast: Post-genome Duplication Divergence of the Stp1 and Stp2 Transcription Factors*

When yeast cells detect external amino acids via their permease-like Ssy1 sensor, the cytosolic precursor forms of Stp1 and Stp2 transcription factors are activated by endoproteolytic removal of their N-terminal domains, a reaction catalyzed by the Ssy5 endoprotease. The processed Stp factors then migrate into the nucleus, where they activate transcription of several amino acid permease genes including AGP1. We report here that the STP1 and STP2 genes most likely derive from the whole genome duplication that occurred in a yeast ancestor. Although Stp1 and Stp2 have been considered redundant, we provide evidence that they functionally diverged during evolution. Stp2 is the only factor processed when amino acids are present at low concentration, and the transcriptional activation of AGP1 promoted by Stp2 is moderate. Furthermore, only Stp2 can sustain Agp1-dependent utilization of amino acids at low concentration. In contrast, Stp1 is only processed when amino acids are present at high concentration, and it promotes higher level transcriptional activation of AGP1. Domain swapping experiments show that the N-terminal domains of Stp1 and Stp2 are responsible for these proteins being cleaved at different amino acid concentrations. Last, induction of the DIP5 permease gene by amino acids depends on Stp2 but not Stp1. We propose that post-whole genome duplication co-conservation of the STP1 and STP2 genes was favored by functional divergence of their products, likely conferring to cells an increased ability to adapt to various amino acid supply conditions.
LTAG Dependency Parsing with Bidirectional Incremental Construction

In this paper, we first introduce a new architecture for parsing, bidirectional incremental parsing. We propose a novel algorithm for incremental construction, which can be applied to many structure learning problems in NLP. We apply this algorithm to LTAG dependency parsing, and achieve significant improvement on accuracy over the previous best result on the same data set.
Flexible ICA approach to the nonlinear blind signal separation in the complex domain

This paper introduces an Independent Component Analysis (ICA) approach to the separation of nonlinear mixtures in the complex domain. Source separation is performed by a complex INFOMAX approach. Nonlinear complex functions involved in the processing are realized by pairs of spline neurons called “splitting functions”, working on the real and the imaginary part of the signal respectively. A simple adaptation algorithm is derived and some experimental results that demonstrate the effectiveness of the proposed method are shown.
Support Vector Gmms for Speaker Verification

This article presents a new approach using the discrimination power of support vectors machines (SVM) in combination with Gaussian mixture models (GMM) for automatic speaker verification (ASV). In this combination SVMs are applied in the GMM model space. Each point of this space represents a GMM speaker model. The kernel which is used for the SVM allows the computation of a similarity between GMM models. It was calculated using the Kullback-Leibler (KL) divergence. The results of this new approach show a clear improvement compared to a simple GMM system on the NIST2005 Speaker Recognition Evaluation primary task
Anopheles gambiae and Anopheles arabiensis population densities and infectivity in Kopere village, Western Kenya.

INTRODUCTION This study was conducted in a sugar belt region of western Kenya interfacing epidemic and endemic malaria transmission. We investigated Anopheles gambiae sensu stricto (ss) and Anopheles arabiensis species compositions and densities, human host choice, and infectivity. METHODOLOGY Mosquitoes were captured using pyrethrum spray catch technique and first identified based on morphology; species were confirmed by PCR. Blood meal preference and sporozoite rates were determined by ELISA. Parity rates and entomological inoculation rates (EIR) were determined. Seasonal densities were compared against environmental temperatures, relative humidity and rainfall. RESULTS In total 2,426 An. gambiae were collected. Out of 1,687 female blood-fed mosquitoes, 272 were randomly selected for entomological tests. An. gambiae ss and An. arabiensis comprised 75% (205/272) and 25% (68/272) of the selection, respectively. An. gambiae ss had higher preference for human blood (97%; n=263/272) compared with An. arabiensis, which mostly fed on bovines (88%; n=239/272). The sporozoite and parity rates were 6% (16/272) and 66% (179/272) for An. gambiae ss and 2% (4/272) and 53% (144/272) for An. arabiensis respectively, while EIR was 0.78 infective bites/person/night. Climate (ANOVA; F=14.2; DF=23) and temperature alone (r=0.626; t=3.75; p=0.001) were significantly correlated with vector densities. CONCLUSION An. gambiae ss are the most efficient malaria vector mosquito species in Kopere village. Because An. gambiae ss largely rests and feeds indoors, use of indoor residual spray and insecticide-treated nets is likely the most suitable approach to malaria vector control in Kopere village and other parts of Kenya where this species is abundant.
A Novel Technique Combining CIP Method With FDTD Method for Implementing Efficient Absorbing Boundary Condition in 3-D High Frequency Electromagnetic Field Analysis

In the high frequency electromagnetic field analysis using the finite-difference time-domain (FDTD), the perfectly matched layer (PML) is often adopted to implement the absorbing boundary condition (ABC). However, it requires much computation time to get enough accuracy of analysis with sufficiently small reflection. In order to overcome such a difficulty, this paper describes a novel technique that combines the constrained interpolation profile (CIP) method with the FDTD method to solve problems faster. As a result of analysis of a typical model of differential transmission line, the computation time could be reduced to 60% compared with the FDTD method with the ordinary PML.
Do developers feel emotions? an exploratory analysis of emotions in software artifacts

Software development is a collaborative activity in which developers interact to create and maintain a complex software system. Human collaboration inevitably evokes emotions like joy or sadness, which can affect the collaboration either positively or negatively, yet not much is known about the individual emotions and their role for software development stakeholders. In this study, we analyze whether development artifacts like issue reports carry any emotional information about software development. This is a first step towards verifying the feasibility of an automatic tool for emotion mining in software development artifacts: if humans cannot determine any emotion from a software artifact, neither can a tool. Analysis of the Apache Software Foundation issue tracking system shows that developers do express emotions (in particular gratitude, joy and sadness). However, the more context is provided about an issue report, the more human raters start to doubt and nuance their interpretation of emotions. More investigation is needed before building a fully automatic emotion mining tool.
Tracking multiple C&C botnets by analyzing DNS traffic

Botnets have been considered as a main source of Internet threats. A common feature of recent botnets is the use of one or more C&C servers with multiple domain names for the purpose of increasing flexibility and survivability. In contrast with single domain botnets, these multi domain botnets are hard to be quarantined because they change domain names regularly for connecting their C&C server(s). In this paper, we introduce a tracking method of botnets by analyzing the relationship of domain names in DNS traffic generated from botnets. By examining the DNS queries from the clients which accessed the known malicious domain names, we can find a set of unknown malicious domain names and their relationship. This method enables to track malicious domain names and clients duplicately infected by multiple bot codes which make botnets revivable against existing quarantine methods. From the experiments with one hour DNS traffic in an ISP network, we find tens of botnets, and each botnet has tens of malicious domains. In addition to botnet domains, we find a set of other domain names used for spamming or advertising servers. The proposed method can be used for quarantining recent botnets and for limiting their survivability by tracking the change of domain names.
Model checking timed automata : techniques and applications

Model checking is a technique to automatically analyse systems that have been modeled in a formal language. The timed automaton framework is such a formal language. It is suitable to model many realistic problems in which time plays a central role. Examples are distributed algorithms, protocols, embedded software and scheduling problems. The main problem with model checking is the exponential growth of the state space as models become larger (also known as the 'state space explosion' problem). This thesis consists of six research papers. Three of these contribute theory to alleviate the state space explosion problem. The other three demonstrate the practical use of model checking technology by applying it to realistic case studies.
Clustering via Random Walk Hitting Time on Directed Graphs

In this paper, we present a general data clustering algorithm which is based on the asymmetric pairwise measure of Markov random walk hitting time on directed graphs. Unlike traditional graph based clustering methods, we do not explicitly calculate the pairwise similarities between points. Instead, we form a transition matrix of Markov random walk on a directed graph directly from the data. Our algorithm constructs the probabilistic relations of dependence between local sample pairs by studying the local distributions of the data. Such dependence relations are asymmetric, which is a more general measure of pairwise relations than the similarity measures in traditional undirected graph based methods in that it considers both the local density and geometry of the data. The probabilistic relations of the data naturally result in a transition matrix of Markov random walk. Based on the random walk viewpoint, we compute the expected hitting time for all sample pairs, which explores the global information of the structure of the underlying directed graph. An asymmetric measure based clustering algorithm, called K-destinations, is proposed for partitioning the nodes of the directed graph into disjoint sets. By utilizing the local distribution information of the data and the global structure information of the directed graph, our method is able to conquer some limitations of traditional pairwise similarity based methods. Experimental results are provided to validate the effectiveness of the proposed approach.
Gene Conversion and Evolution of Gene Families: An Overview

The importance of gene conversion for the evolution of gene families is reviewed. Four problems concerning gene conversion, i.e., concerted evolution, generation of useful variation, deleterious effects, and relation to neofunctionalization, are discussed by surveying reported examples of evolving gene families. Emphasis is given toward understanding interactive effects of gene conversion and natural selection.
Gi‐mediated activation of the Ras/MAP kinase pathway involves a 100 kDa tyrosine‐phosphorylated Grb2 SH3 binding protein, but not Src nor Shc

Mitogenic G protein‐coupled receptors, such as those for lysophosphatidic acid (LPA) and thrombin, activate the Ras/MAP kinase pathway via pertussis toxin (PTX)‐sensitive Gi, tyrosine kinase activity and recruitment of Grb2, which targets guanine nucleotide exchange activity to Ras. Little is known about the tyrosine phosphorylations involved, although Src activation and Shc phosphorylation are thought to be critical. We find that agonist‐induced Src activation in Rat‐1 cells is not mediated by Gi and shows no correlation with Ras/MAP kinase activation. Furthermore, LPA‐induced tyrosine phosphorylation of Shc is PTX‐insensitive and Ca2+‐dependent in COS cells, but undetectable in Rat‐1 cells. Expression of dominant‐negative Src or Shc does not affect MAP kinase activation by LPA. Thus, Gi‐mediated Ras/MAP kinase activation in fibroblasts and COS cells involves neither Src nor Shc. Instead, we detect a 100 kDa tyrosine‐phosphorylated protein (p100) that binds to the C‐terminal SH3 domain of Grb2 in a strictly Gi‐ and agonist‐dependent manner. Tyrosine kinase inhibitors and wortmannin, a phosphatidylinositol (PI) 3‐kinase inhibitor, prevent p100–Grb2 complex formation and MAP kinase activation by LPA. Our results suggest that the p100–Grb2 complex, together with an upstream non‐Src tyrosine kinase and PI 3‐kinase, couples Gi to Ras/MAP kinase activation, while Src and Shc act in a different pathway.
The European Software Piracy: An Empirical Application ⁄

This paper provides empirical evidence on the link between piracy and software protection, taking piracy determinants in cross‐country regressions as basic reference. For that purpose, we use a panel data set for 24 countries over three years, 1994, 1997 and 2000, relating piracy rates to an index of software protection, per capita income and a set of country fixed effects. Results display that software piracy is sensitive to income and software protection changes.
Is the Thatcher Illusion Modulated by Face Familiarity? Evidence from an Eye Tracking Study

Thompson (1980) first detected and described the Thatcher Illusion, where participants instantly perceive an upright face with inverted eyes and mouth as grotesque, but fail to do so when the same face is inverted. One prominent but controversial explanation is that the processing of configural information is disrupted in inverted faces. Studies investigating the Thatcher Illusion either used famous faces or non-famous faces. Highly familiar faces were often thought to be processed in a pronounced configural mode, so they seem ideal candidates to be tested in one Thatcher study against unfamiliar faces–but this has never been addressed so far. In our study, participants evaluated 16 famous and 16 non-famous faces for their grotesqueness. We tested whether familiarity (famous/non-famous faces) modulates reaction times, correctness of grotesqueness assessments (accuracy), and eye movement patterns for the factors orientation (upright/inverted) and Thatcherisation (Thatcherised/non-Thatcherised). On a behavioural level, familiarity effects were only observable via face inversion (higher accuracy and sensitivity for famous compared to non-famous faces) but not via Thatcherisation. Regarding eye movements, however, Thatcherisation influenced the scanning of famous and non-famous faces, for instance, in scanning the mouth region of the presented faces (higher number, duration and dwell time of fixations for famous compared to non-famous faces if Thatcherised). Altogether, famous faces seem to be processed in a more elaborate, more expertise-based way than non-famous faces, whereas non-famous, inverted faces seem to cause difficulties in accurate and sensitive processing. Results are further discussed in the face of existing studies of familiar vs. unfamiliar face processing.
Bridging the gap between visual exploration and agent-based pedestrian simulation in a virtual environment

We present a system to evaluate and improve visual guidance systems and signage for pedestrians inside large buildings. Given a 3D model of an actual building we perform agent-based simulations mimicking the decision making process and navigation patterns of pedestrians trying to find their way to predefined locations. Our main contribution is to enable agents to base their decisions on realistic threedimensional visibility and occlusion cues computed from the actual building geometry with added semantic annotations (e.g. meaning of signs, or purpose of inventory), as well as an interactive visualization of simulated movement trajectories and accompanying visibility data tied to the underlying 3D model. This enables users of the system to quickly pinpoint and solve problems within the simulation by watching, exploring and understanding emergent behavior inside the building. This insight gained from introspection can in turn inform planning and thus improve the effectiveness of guidance systems.
Concordance Between Hybrid Capture 2 Results Performed on Cervical Samples Obtained Before and Immediately After Visual Inspection with Acetic Acid Test

Background: VIA is a simple, inexpensive test widely advocated for resource-limited settings. Major limitation of VIA is its low specificity. HPV DNA testing can be used to triage VIA-positive women if the facilities are available. The major concern for such strategy would be whether sample collection after acetic acid wash will alter HPV test characteristics. This study aimed to evaluate whether samples for HPV testing by Hybrid Capture 2 (HC2) technology can be collected immediately after VIA without altering test performance. Methods: Total 204 VIA-positive women were recruited. Cervical samples were collected for HC2 test before and after VIA at the same sitting by the same provider. The paired samples were analyzed at the same laboratory by the same technician in the same batch of testing. Agreement in HC2 results between pre-VIA and post-VIA samples was estimated using kappa statistics. All women had colposcopy and biopsies were obtained if colposcopy was suspicious of neoplasia. Sensitivity and specificity of HC2 test in detecting CIN2+ lesions were calculated using negative colposcopy or biopsy as the gold standard and were compared between the pre and post VIA samples. Results: Almost perfect agreement in HC2 results (kappa=0.85) and RLU/Cut off ratios (correlation coefficient=0.92) was observed between samples collected before and after VIA. The sensitivity and specificity to detect CIN2+ lesions remained unaltered even when cervical samples were collected after VIA. This confirmed that acetic acid wash did not alter HC2 performance. Conclusions: Collection of samples for HC2 test is feasible immediately after VIA.