Miracle-dz/UniFAR-FTUs huggingface dataset:
Dimerization of VirD2 Binding Protein Is Essential for Agrobacterium Induced Tumor Formation in Plants

The Type IV Secretion System (T4SS) is the only bacterial secretion system known to translocate both DNA and protein substrates. The VirB/D4 system from Agrobacterium tumefaciens is a typical T4SS. It facilitates the bacteria to translocate the VirD2-T-DNA complex to the host cell cytoplasm. In addition to protein-DNA complexes, the VirB/D4 system is also involved in the translocation of several effector proteins, including VirE2, VirE3 and VirF into the host cell cytoplasm. These effector proteins aid in the proper integration of the translocated DNA into the host genome. The VirD2-binding protein (VBP) is a key cytoplasmic protein that recruits the VirD2–T-DNA complex to the VirD4-coupling protein (VirD4 CP) of the VirB/D4 T4SS apparatus. Here, we report the crystal structure and associated functional studies of the C-terminal domain of VBP. This domain mainly consists of α-helices, and the two monomers of the asymmetric unit form a tight dimer. The structural analysis of this domain confirms the presence of a HEPN (higher eukaryotes and prokaryotes nucleotide-binding) fold. Biophysical studies show that VBP is a dimer in solution and that the HEPN domain is the dimerization domain. Based on structural and mutagenesis analyses, we show that substitution of key residues at the interface disrupts the dimerization of both the HEPN domain and full-length VBP. In addition, pull-down analyses show that only dimeric VBP can interact with VirD2 and VirD4 CP. Finally, we show that only Agrobacterium harboring dimeric full-length VBP can induce tumors in plants. This study sheds light on the structural basis of the substrate recruiting function of VBP in the T4SS pathway of A. tumefaciens and in other pathogenic bacteria employing similar systems.
FTXen: Making hypervisor resilient to hardware faults on relaxed cores

As CMOS technology scales, the Increasingly smaller transistor components are susceptible to a variety of in-field hardware errors. Traditional redundancy techniques to deal with the increasing error rates are expensive and energy inefficient. To address this emerging challenge, many researchers have recently proposed the idea of relaxed hardware design and exposing errors to software. For such relaxed hardware to become a reality, it is crucially important for system software, such as the virtual machine hypervisor, to be resilient to hardware faults. To address the above fundamental software challenge in enabling relaxed hardware design, we are making a major effort in restructuring an important part of system software, namely the virtual machine hypervisor, to be resilient to faulty cores. A fault in a relaxed core can only affect those virtual machines (and applications) running on that core, but the hypervisor and other virtual machines remain intact and continue providing services. We have redesigned every component of Xen, a large, popular virtual machine hypervisor, to achieve such error resiliency. This paper presents our design and implementation of the restructured Xen (we refer to it as FTXen). Our experimental evaluation on real systems shows that FTXen adds minimum application overhead, and scales well to different ratios of reliable and relaxed cores. Our results with random fault injection show that FTXen can successfully survive all injected hardware faults.
(De-)Constructing TLS

TLS is one of the most widely deployed cryptographic protocols on the Internet; it is used to protect the condentiality and integrity of transmitted data in various client-server protocols. Its non-standard use of cryptographic primitives, however, makes it hard to formally assess its security. It is in fact dicult to use traditional (well-understood) security notions for the key-exchange (here: handshake) and the encryption/authentication (here: record layer) parts of the protocol due to the fact that, on the one hand, traditional gamebased notions do not easily support composition, and on the other hand, all TLS versions up to and including 1.2 combine the two phases in a non-standard way. In this paper, we provide a modular security analysis of the handshake in TLS version 1.2 and a slightly sanitized version of the handshake in the current draft of TLS version 1.3, following the constructive cryptography approach of Maurer and Renner (ICS 2011). We provide a deconstruction of the handshake into modular sub-protocols and a security proof for each such sub-protocol. We also show how these results can be combined with analyses of the respective record layer protocols, and the overall result is that in all cases the protocol constructs (unilaterally) secure channels between the two parties from insecure channels and a public-key infrastructure. This approach ensures that (1) each sub-protocol is proven in isolation and independently of the other sub-protocols, (2) the overall security statement proven can easily be used in higher-level protocols, and (3) TLS can be used in any composition with other secure protocols. In more detail, for the key-exchange step of TLS 1.2, we analyze the RSA-based and both Die-Hellman-base d variants (with static and ephemeral server key share) under a non-randomizability assumption for RSA-PKCS and the Gap Die-Hellman assumption, respectively; in all cases we make use of random oracles. For the respective step of TLS 1.3, we prove security under the Decisional Die-Hellman assumption in the standard model. In all statements, we require additional standard computational assumptions on other primitives. In general, since the design of TLS is not modular, the constructive decomposition is less ne-grained than one might wish to have and than it is for a modular design. This paper therefore also suggests new insights into the intrinsic problems incurred by a non-modular protocol design such as that of TLS.
Modeling environmental data by functional principal component logistic regression

In recent years, many studies have dealt with predicting a response variable based on the information provided by a functional variable. When the response variable is binary, different problems arise, such as multicollinearity and high dimensionality, which prejudice the estimation of the model and the interpretation of its parameters. In this article we address these problems by using functional logistic regression and principal component analysis. In order to obtain a unique solution for the maximum likelihood estimation of the parameter function, quasi‐natural cubic spline interpolation of sample paths on their discrete time observations is proposed. We also introduce a new interpretation of the relationship between the response variable and the functional predictor where the change in the odds of success is evaluated from the estimated parameter function. An analysis of climatological data is finally presented to illustrate the practical performance of the proposed methodologies. Copyright © 2004 John Wiley & Sons, Ltd.
Multi-camera calibration using multi-view constraints

A new calibration algorithm for multi-camera systems using a small 3D reference rig is proposed. Extrinsic and intrinsic parameters of the cameras are recovered only by capturing the reference rig placed at different locations. Thus the proposed method yields a simple calibration means for multi-camera systems while not using large reference rig, which should occupy the image capture volume as full as possible for accuracy. The algorithm is based on factorization of projection matrices into the camera and rig pose parameters. The obtained parameters are further refined by a non-linear optimization process. The results of the experiments with real images are presented to demonstrate the feasibility of the proposed method.
Estomatitis subprótesis y efectividad del OLEOZON® en su tratamiento

espanolIntroduccion: La Estomatitis subprotesis es una patologia inflamatoria que afecta a la mucosa oral localizada en intimo contacto con la protesis dental. Existe un alto porcentaje de pacientes aquejados de estomatitis subprotesis, lo que constituye un serio problema de salud. Su etiologia esta determinada por diversos factores lo que hace su estudio muy complejo. El aceite ozonizado (Oleozon) dado a sus propiedades es una nueva opcion terapeutica para los pacientes portadores de esta entidad. Objetivo: Demostrar la efectividad del aceite ozonizado en la estomatitis subprotesis. Metodos: Se realizo un estudio experimental secuencial controlado con grupos paralelos de Junio de 2017 a Mayo de 2018 a los que se administro Oleozon y nistatina en crema. Resultados: Ambos tratamientos son efectivos en el tratamiento de la estomatitis subprotesis grados I y II, aunque con el Oleozon se logra la curacion en menor tiempo. EnglishIntroduction: The Stomatitis Subprosthesis is an inflammatory pathology that affects the localized oral mucosa in intimate contact with the dental prosthesis. There is a high percentage of patients suffering from subprosthesis stomatitis, which constitutes a serious health problem. Its etiology is determined by several factors which makes its study very complex. The ozonized oil (Oleozon) given to its properties is a new therapeutic option for the patients carriers of this entity. Objetive: To demonstrate the effectiveness of ozonized oil in the stomatitis subprosthesis. Methods: A controlled sequential experimental study was carried out with parallel groups from June 2017 to May 2018, to which Oleozon and nystatin cream were administered. Results: Both treatments are effective in the treatment of grade I and II subprosthesis stomatitis, although with Oleozon healing is achieved in less time.
Markerless identification and tracking for scalable image database

In this paper we present a novel approach for object identification and tracking in large image datasets. Objects of interest are represented by feature points and descriptors extracted and compared to a set of reference data. An optimized matching paradigm is designed to deal with scalable image databases while keeping a good recognition rate in real-life environment conditions. Experiments are conducted to evaluate the effectiveness of the method and the obtained results demonstrate a true interest of the proposed approach.
CC1, a Novel Crenarchaeal DNA Binding Protein

ABSTRACT The genomes of the related crenarchaea Pyrobaculum aerophilum and Thermoproteus tenax lack any obvious gene encoding a single-stranded DNA binding protein (SSB). SSBs are essential for DNA replication, recombination, and repair and are found in all other genomes across the three domains of life. These two archaeal genomes also have only one identifiable gene encoding a chromatin protein (the Alba protein), while most other archaea have at least two different abundant chromatin proteins. We performed a biochemical screen for novel nucleic acid binding proteins present in cell extracts of T. tenax. An assay for proteins capable of binding to a single-stranded DNA oligonucleotide resulted in identification of three proteins. The first protein, Alba, has been shown previously to bind single-stranded DNA as well as duplex DNA. The two other proteins, which we designated CC1 (for crenarchaeal chromatin protein 1), are very closely related to one another, and homologs are restricted to the P. aerophilum and Aeropyrum pernix genomes. CC1 is a 6-kDa, monomeric, basic protein that is expressed at a high level in T. tenax. This protein binds single- and double-stranded DNAs with similar affinities. These properties are consistent with a role for CC1 as a crenarchaeal chromatin protein.
Temporally structured replay of neural activity in a model of entorhinal cortex, hippocampus and postsubiculum

The spiking activity of hippocampal neurons during rapid eye movement (REM) sleep exhibits temporally structured replay of spiking occurring during previously experienced trajectories. Here, temporally structured replay of place cell activity during REM sleep is modeled in a large‐scale network simulation of grid cells, place cells and head direction cells. During simulated waking behavior, the movement of the simulated rat drives activity of a population of head direction cells that updates the activity of a population of entorhinal grid cells. The population of grid cells drives the activity of place cells coding individual locations. Associations between location and movement direction are encoded by modification of excitatory synaptic connections from place cells to speed modulated head direction cells. During simulated REM sleep, the population of place cells coding an experienced location activates the head direction cells coding the associated movement direction. Spiking of head direction cells then causes frequency shifts within the population of entorhinal grid cells to update a phase representation of location. Spiking grid cells then activate new place cells that drive new head direction activity. In contrast to models that perform temporally compressed sequence retrieval similar to sharp wave activity, this model can simulate data on temporally structured replay of hippocampal place cell activity during REM sleep at time scales similar to those observed during waking. These mechanisms could be important for episodic memory of trajectories.
Indexing Strings and Rulesets An Exploration Leading to an Enumeration

An enumeration of strings is developed, in which all strings of finite length of symbols from any alphabet appear, with no upper bounds for string length or alphabet size. A bijective indexing function and its inverse are found for the string enumeration, allowing iteration through the set of all strings, as well as identification of arbitrary strings by the associated index. The method is then extended to sequences of strings and to sequential substitution system (SSS) rulesets, providing a welldefined, relatively dense enumeration of all possible valid SSS rulesets for strings of arbitrary length and any number of symbols used in rulesets of any length, although in this case the indexing function is not one-to-one.
Development of an embedded system for real time Heart Rate Variability analysis

Electrocardiogram (ECG) is the most preferably used noninvasive test for diagnosis of cardiac rhythm. Irregular rhythm of heart beats is measured in terms of Heart Rate Variability (HRV). Analysis of HRV plays an important role in automated diagnosis of cardiac status. This paper deals with development of an embedded system suitable for real time HRV analysis. A low cost embedded system for monitoring an ECG has been developed using operational amplifiers and a Microchip's microcontroller. Digitized ECG has been transmitted serially to computer for real time analysis of HRV. Nonlinear energy associated with QRS complex is highest amongst the ECG beat. This feature has been utilized for QRS detection. Rest all the statistical markers for HRV are then computed with reference to the detected QRS. HRV analysis of 10 real subjects has been carried out using the embedded system. Results show that the proposed low cost embedded system is suitable for real time HRV analysis.
Point-to Analysis for Object-Oriented Language

Pointer analysis is the problem of statically determining the runtime targets of pointer variables in a program. This information has a wide variety of client applications in optimizing compilers and software engineering tools. This paper focuses on precise pointsto analysis for Object Oriented Languages (OOL) such as Java, C#, Scala, etc based on Andersen's points-to analysis for C language, which validates the performance of the analysis on a large set of Java programs. Implementation of this analysis is done by using a subset-based approach which is done by using Binary Decision Diagrams (BDDs). This paper first introduces BDDs and operations on BDDs using some simple points-to examples. Then, a complete subsetbased points-to algorithm is presented, expressed completely using BDDs and BDD operations.
Mindfulness Trait Predicts Neurophysiological Reactivity Associated with Negativity Bias: An ERP Study

This study explored the relationship of mindfulness trait with the early and late stages of affective processing, by examining the two corresponding ERP components, P2 and LPP, collected from twenty-two male Chinese participants with a wide range of meditation experiences. Multiple regression analyses was performed on the mindfulness scores, as measured by CAMS-R, with the subjective affective ratings and ERP data collected during an emotion processing task. The results showed that increased mindfulness scores predicted increased valence ratings of negative stimuli (less negative), as well as increased P2 amplitudes at the frontocentral location for positive compared to negative stimuli. Based on these findings, a plausible mechanism of mindfulness in reducing negativity bias was discussed. Moreover, our results replicated previous findings on the age-related increase of P2 amplitudes at the frontal sites for positive compared to neutral stimuli. Since the locations at which P2 amplitudes were found as associated with age and mindfulness differed, as did the emotional contents of the stimuli being compared, indicating that the effect of age did not confound our findings on mindfulness and the two factors might operate on early affective processing from distinct sources and mechanisms.
Estimation and Prediction Metrics for Adaptive Maintenance Effort of Object-Oriented Systems

Many software systems built in recent years have been developed using object-oriented technology and, in some cases, they already need adaptive maintenance in order to satisfy market and customer needs. In most cases, the estimation and prediction of maintenance effort is performed with difficulty due to the lack of metrics and suitable models. In this paper, a model and metrics for estimation/prediction of adaptive maintenance effort are presented and compared with some other solutions taken from the literature. The model proposed can be used as a general approach for adopting well-known metrics (typically used for the estimation of development effort) for the estimation/prediction of adaptive maintenance effort. The model and metrics proposed have been validated against real data by using multilinear regression analysis. The validation has shown that several well-known metrics can be profitably employed for the estimation/prediction of maintenance effort.
Discrete-time control framework for robots over unreliable packet-switching communication network

This paper presents a control framework for networked robotic systems with the consideration of discrete nature of communication network and controller. In order to enhance regulation performance, a local controller is developed to transform the dynamics of robotic systems so that the output signal includes both position and velocity information. For the input/output signals of the robot, a discretization block is exploited to convert continuous-time signals to discrete-time signals, and vice versa. The issue of communication delay is coped with by utilizing wave-variable transformation, while the adverse effects of packet losses are ameliorated by a novel packet modulation. Based on the proposed control framework, the passivity of the interconnected control system and steadystate position regulation are studied. The performance of the proposed networked control system is evaluated by numerical simulations.
A STRUCTURED ANALYSIS ON MORPHEME SEGMENTATION FOR AGGLUTINATIVE LANGUAGES

The learning of morphology through unsupervised methods helps to identify automatically affixes, morphological segmentation of words with engendered paradigms which can list all affixes that are combined with a list of stems. The role of unsupervised morpheme segmentation is to segment the words into stem and affix. This paper illustrates the importance of unsupervised morphological segmentation for the problem of morpheme boundary detection for resource poor languages which are highly inflectional and agglutinative in morphology. It specially focuses on few approaches which are based on their performance with highly agglutinative language.
Enhancing The Performance of Nonuniformly Deployed Sensor Network by Locating Bottleneck Areas for Partial Redeployment

The distribution of the sensor locations may be nonuniform under some terrain imposed physical constraints or different sensing quality requirements in different parts of a wireless sensor network. Given such a nonuniformly deployed sensor network, some bottleneck areas will form soon after the network becomes operational. Those areas will severely decrease the lifetime of the network. We propose an algorithm to locate those areas prior to operation. The algorithm progressively tries to form compact clusters whose borders do not intersect. We show, using different scenarios, that by means of small redeployments over the areas that separate these clusters, we increase the lifetime considerably.
THE PARENTAL PREDICTORS OF CHILD S ATTACHMENT SECURITY AND THE MODERATION ROLE OF CHILD S DISABILITY: REFRAMING PARENTING PROGRAMS FOR FAMILIES WITH CHILDREN AFFECTED BY NEUROLOGICAL ILLNESS

Introduction Disability appears to challenge parents, undermining sensitivity, and increasing the chances that children with neurological conditions will be insecurely attached. Aim The study aims at exploring the role of parental perceptions in predicting child‟s attachment security, and whether their effects persist and control the presence of the child‟s disability, specifically if there isa neurological illness. Further, the potential moderation role of the child‟s disability in the relationship between parental perceptions and child‟s attachment security is also tested.
SHriMP views: an interactive environment for information visualization and navigation

The SHriMP (Simple Hierarchical Multi-Perspective) visualization technique was designed to enhance how people browse and explore complex information spaces. SHriMP uses a nested graph view to present information that is hierarchically structured. It introduces the concept of nested interchangeable views to allow a user to explore multiple perspectives of information at different levels of abstraction. SHriMP combines a hypertext following metaphor with animated panning and zooming motions over the nested graph to provide continuous orientation and contextual cues for the user. In this demo, we show how these ideas are proving useful in the areas of software visualization, knowledge management and flow diagram visualization.
Secure Encrypted Image Search in Mobile Cloud Computing

Mobile could computing is an area of cloud computing which considers resource constrained devices. Therefore there naturally appears a new design goal which is efficiency of mobile client applications. In this paper we consider encrypted image search schemes. In particular, we design a scheme for which distances between encrypted images are close to distances between images in plaintexts, which allows for more efficient search mechanisms. At the same time, this scheme can ensure privacy of image content. Previous solutions achieve this goal by exploiting homomorphic encryption schemes, which are far to inefficient and hard to realize on the resource constrained mobile devices. In this paper, we introduce a novel encryption search scheme for CBIR (Content-Based Image Retrieval) by using comparable encryption. Our scheme greatly reduces the amount of computation on the client side, and improves the distance consistency and precision of fuzzy search, compared to previous solutions.