Miracle-dz/UniFAR-FTUs huggingface dataset:
Matefin/SUN-1 Phosphorylation Is Part of a Surveillance Mechanism to Coordinate Chromosome Synapsis and Recombination with Meiotic Progression and Chromosome Movement

Faithful chromosome segregation during meiosis I depends on the establishment of a crossover between homologous chromosomes. This requires induction of DNA double-strand breaks (DSBs), alignment of homologs, homolog association by synapsis, and repair of DSBs via homologous recombination. The success of these events requires coordination between chromosomal events and meiotic progression. The conserved SUN/KASH nuclear envelope bridge establishes transient linkages between chromosome ends and cytoskeletal forces during meiosis. In Caenorhabditis elegans, this bridge is essential for bringing homologs together and preventing nonhomologous synapsis. Chromosome movement takes place during synapsis and recombination. Concomitant with the onset of chromosome movement, SUN-1 clusters at chromosome ends associated with the nuclear envelope, and it is phosphorylated in a chk-2- and plk-2-dependent manner. Identification of all SUN-1 phosphomodifications at its nuclear N terminus allowed us to address their role in prophase I. Failures in recombination and synapsis led to persistent phosphorylations, which are required to elicit a delay in progression. Unfinished meiotic tasks elicited sustained recruitment of PLK-2 to chromosome ends in a SUN-1 phosphorylation–dependent manner that is required for continued chromosome movement and characteristic of a zygotene arrest. Furthermore, SUN-1 phosphorylation supported efficient synapsis. We propose that signals emanating from a failure to successfully finish meiotic tasks are integrated at the nuclear periphery to regulate chromosome end–led movement and meiotic progression. The single unsynapsed X chromosome in male meiosis is precluded from inducing a progression delay, and we found it was devoid of a population of phosphorylated SUN-1. This suggests that SUN-1 phosphorylation is critical to delaying meiosis in response to perturbed synapsis. SUN-1 may be an integral part of a checkpoint system to monitor establishment of the obligate crossover, inducible only in leptotene/zygotene. Unrepaired DSBs and unsynapsed chromosomes maintain this checkpoint, but a crossover intermediate is necessary to shut it down.
Lateral inhibition based holistic approach to adaptive image enhancement

We present a physiologically inspired adaptive algorithm for noise removal in an image while preserving significant amount of edge details. The algorithm is motivated by the classical lateral inhibition based receptive field in the visual system as well as the holistic approach of the well known bilateral filter. We propose an adaptive difference of Gaussian (DoG) filter with varying window size depending upon the edge strengths in the image. Our algorithm has advantages over similar other techniques such as simple Gaussian filter, DoG filter, and is comparable to the bilateral filter in terms of edge enhancement. Furthermore, time complexity of our algorithm is much less than the bilateral filter.
The Sun’s Preferred Longitudes and the Coupling of Magnetic Dynamo Modes

Observations show that solar activity is distributed nonaxisymmetrically, concentrating at "preferred longitudes. " This indicates the important role of nonaxisymmetric magnetic fields in the origin of solar activity. We investigate the generation of the nonaxisymmetric fields and their coupling with the axisymmetric solar magnetic field. Our kinematic generation (dynamo) model operating in a sphere includes a model of solar differential rotation, as obtained by inversion of helioseismic data, modeled distributions of the turbulent resistivity, nonaxisymmetric mean helicity, and meridional circulation in the convection zone. We find that (1) the nonaxisymmetric modes are localized near the base of the convection zone, where the formation of active regions starts, and at latitudes around 30°; (2) the coupling of nonaxisymmetric and axisymmetric modes causes the nonaxisymmetric mode to follow the solar cycle; the phase relations between the modes are found; and (3) the rate of rotation of the first nonaxisymmetric mode is close to that determined in interplanetary space.
Improved community network node design using a DLEP based radio-to-router interface

Using a static link state routing metric in wireless mesh and mobile ad hoc networks without major efforts in optimizing the physical link properties has proven to be inefficient. It does not take into account link quality information. While some link metrics try to estimate channel properties based on layer-3 observations, more sophisticated metrics need to access layer-2 information directly. The new 802.11 netlink interface provides a common local interface for Linux based systems and thus the basis for practical usage in community networks. However, a standardized radio-to-router communication protocol to access layer-2 information will allow to go beyond the limitations of having all radio interfaces built directly into the router device. While the PPPoE protocol generally can be applied to this scenario, it has some drawbacks when used in wireless mesh networks. The new DLEP protocol is supported by the IETF MANET group to fill this gap. In this paper we describe the advantages of a flexible node design for community networks based on the DLEP protocol. In addition, we present our implementation of the DLEP protocol and discuss some important deviations from the current draft version of the standard.
Eigenfunctions of the Laplace operator Eigenfunctions of the Laplace operator

The study of the Laplace operator and its corresponding eigenvalue problem is crucial to understand the foundations of 3D shape analysis. For that reason the most important mathematical properties of the Laplace operator in Euclidean spaces, its eigenvalues and eigenfunctions are summarized and explained in this report. The basic definitions and concepts of infinite dimensional function spaces, that are required are introduced beforehand. In order to motivate the study of the Laplace eigenvalue problem, the connection between the Laplace eigenvalues and the geometry of the domain, to which the operator is applied, is demonstrated by presenting Weyl’s law. Furthermore it is shown how the Fourier transform can be derived from the consequences of the spectral theorem and orthogonal basis functions of the L space. Finally some applications of the Laplace eigenfunctions in 3D shape analysis are demonstrated briefly.
Stochastic optimal control theory

Control theory is a mathematical description of how to act optimally to gain future rewards. In this paper I give an introduction to deterministic and stochastic control theory; partial observability, learning and the combined problem of inference and control. Subsequently, I discuss a class of non-linear stochastic control problems that can be efficiently solved using a path integral. In this control formalism the central concept of cost-to-go becomes a free energy and methods and concepts from probabilistic graphical models and statistical physics can be readily applied. I illustrate the theory with a number of examples. Jointly with Marc Toussaint. TU Berlin
Genetic Structure of Lutzomyia longipalpis Populations in Mato Grosso Do Sul, Brazil, Based on Microsatellite Markers

Background Lutzomyia longipalpis (Diptera: Psychodidae) is the major vector of Leishmania (Leishmania) infantum and thus plays a crucial role in the epidemiology of American visceral leishmaniasis (AVL). This vector is the best studied species of sand fly in the Neotropical region. Many studies claim that this vector is in fact a species complex; however there is still no consensus regarding the number of species that belong into this complex or the geographical distribution of sibling species. The aim of the present study was to analyze the genetic relationships within Lu. longipalpis populations in the state of Mato Grosso do Sul (MS), Brazil. Methodology/Principal Findings We collected 30 Lu. longipalpis (15 females and 15 males) from five localities (Campo Grande, Três Lagoas, Aquidauana, Miranda and Bonito) and 30 Lu. Cruzi from Corumbá, totaling 180 sandflies from MS, and 30 Lu. longipalpis from Estrela de Alagoas, state of Alagoas (AL), Northeast Brazil. We show that eight previously described microsatellite loci were sufficient in distinguishing Lu. longipalpis from Lu. Cruzi, which is a closely related species, and in differentiating between Lu. longipalpis collected in MS versus Estrela de Alagoas. Analyses of the genotypes revealed introgression between sympatric Lu. longipalpis and Lu. Cruzi. Conclusions/Significance Our findings support the hypothesis of cryptic species within the Lu. longipalpis complex. Furthermore, our data revealed introgression between Lu. longipalpis and Lu. cruzi. This phenomenon should be further investigated to determine the level and incidence of hybridization between these two species. We also demonstrated that microsatellite markers are a powerful tool for differentiating sand fly populations and species. The present study has elucidated the population structure of Lu. longipalpis in MS and, by extension, the Neotropical Lu. longipalpis complex itself.
Project Gel a Randomized Rectal Microbicide Safety and Acceptability Study in Young Men and Transgender Women

Objectives The purpose of Project Gel was to determine the safety and acceptability of rectal microbicides in young men who have sex with men (MSM) and transgender women (TGW) at risk of HIV infection. Methods MSM and TGW aged 18–30 years were enrolled at three sites; Pittsburgh, PA; Boston, MA; and San Juan, PR. Stage 1A was a cross-sectional assessment of sexual health and behavior in MSM and TGW. A subset of participants from Stage 1A were then enrolled in Stage 1B, a 12-week evaluation of the safety and acceptability of a placebo rectal gel. This was followed by the final phase of the study (Stage 2) in which a subset of participants from Stage 1B were enrolled into a Phase 1 rectal safety and acceptability evaluation of tenofovir (TFV) 1% gel. Results 248 participants were enrolled into Stage 1A. Participants’ average age was 23.3 years. The most common sexually transmitted infection (STIs) at baseline were Herpes simplex (HSV)-2 (16.1% by serology) and rectal Chlamydia trachomatis (CT) (10.1% by NAAT). 134 participants were enrolled into Stage 1B. During the 12 week period of follow-up 2 HIV, 5 rectal CT, and 5 rectal Neisseria gonorrhea infections were detected. The majority of adverse events (AEs) were infections (N = 56) or gastrointestinal (N = 46) and were mild (69.6%) or moderate (28.0%). Of the participants who completed Stage 1B, 24 were enrolled into Stage 2 and randomized (1:1) to receive TFV or placebo gel. All participants completed Stage 2. The majority of AEs were gastrointestinal (N = 10) and of mild (87.2%) or moderate (10.3%) severity. Conclusions In this study we were able to enroll a sexually active population of young MSM and TGW who were willing to use rectal microbicides. TFV gel was safe and acceptable and should be further developed as an alternative HIV prevention intervention for this population. Trial Registration ClinicalTrials.gov NCT01283360
Structural and Functional Studies of a Phosphatidic Acid-Binding Antifungal Plant Defensin MtDef4: Identification of an RGFRRR Motif Governing Fungal Cell Entry

MtDef4 is a 47-amino acid cysteine-rich evolutionary conserved defensin from a model legume Medicago truncatula. It is an apoplast-localized plant defense protein that inhibits the growth of the ascomycetous fungal pathogen Fusarium graminearum in vitro at micromolar concentrations. Little is known about the mechanisms by which MtDef4 mediates its antifungal activity. In this study, we show that MtDef4 rapidly permeabilizes fungal plasma membrane and is internalized by the fungal cells where it accumulates in the cytoplasm. Furthermore, analysis of the structure of MtDef4 reveals the presence of a positively charged γ-core motif composed of β2 and β3 strands connected by a positively charged RGFRRR loop. Replacement of the RGFRRR sequence with AAAARR or RGFRAA abolishes the ability of MtDef4 to enter fungal cells, suggesting that the RGFRRR loop is a translocation signal required for the internalization of the protein. MtDef4 binds to phosphatidic acid (PA), a precursor for the biosynthesis of membrane phospholipids and a signaling lipid known to recruit cytosolic proteins to membranes. Amino acid substitutions in the RGFRRR sequence which abolish the ability of MtDef4 to enter fungal cells also impair its ability to bind PA. These findings suggest that MtDef4 is a novel antifungal plant defensin capable of entering into fungal cells and affecting intracellular targets and that these processes are mediated by the highly conserved cationic RGFRRR loop via its interaction with PA.
Energy Efficient Multipath Routing Protocol for Wireless Mobile Ad Hoc Networks May

energy. Due to limited battery power nodes die out early and affect the network lifetime. So, energy efficiency is one of the main problems in a mobile ad hoc network, especially designing a routing protocol. In this paper, we propose an efficient routing algorithm and we call it EEM-AOMDV. The proposed algorithm aims to increase the network lifetime and minimize the energy consumption during the source to destination route establishment. The algorithm which we propose considers two energy metrics in route selection and integrates these metrics into AOMDV. This system is implemented by using NS-2.34. Simulation results show that the proposed routing protocol can extend the lifetime of the network and can achieve higher performance when compared to conventional ad hoc on-demand multipath distance vector (AOMDV) routing protocol.
The Honeynet Project : Trapping the Hackers What specific threats do computer networks face from hackers ? Who ’ s perpetrating these threats and how ?

15 O ne of the greatest challenges we face in the security community involves informa-tion—specifically, intelligence that identifies our enemies, how they operate, and why. Traditionally, we have understood cyberthreats solely based on the exploits used because after an incident occurs, the only data we have is what's left on the compromised system. Unfortunately, this information is extremely limited and tells us little about the overall threat. How can we defend against and defeat an enemy, for example , when we don't know who that enemy is? The Honeynet Project provides a new method for answering this question by luring hackers to a system and then analyzing their activities from the start. This approach effectively complements other well-known intrusion detection and prevention technologies. Moreover, it improves on the more conventional approaches that the security community has studied and implemented during the past 35 years. The organizations most interested in this technology are research oriented, such as universities, government, and military. This article describes how the Honeynet Project works, provides some examples of the kind of information that honeynets and honeypots collect, and details a future plan for distributed honeynet deployment. The Honeynet Project (www.honeynet.org) is a security research organization dedicated to learning the black-hat community's tools, tactics, and motives and then sharing any lessons learned. The organization comprises international security professionals who volunteer their time and resources to deploy networks (or honeynets) that are designed to be attacked. The team then analyzes the information collected from these attacks. The Honeynet Project began in 1999 as an informal mailing list of a small group of individuals, but the group soon realized that no single person had all the experience necessary to analyze the information collected from attacks. The mailing list grew as the need for expertise in areas such as exploit analysis, worms, Linux, Windows, and networking increased. Over time, this group evolved, officially calling itself the Honeynet Project in June 2000. Over the next two years, the group formalized. It limited its membership to 30 members, incorporated as a nonprofit organization, and founded a board of directors, States. The alliance dramatically increased the Honeynet Project's ability to gather data and gave it a global perspective on the threats the Internet faces.
WEIGHTED VOTING OF MULTIPLE ALN CLASSIFIERS FOR OCR

This paper addresses the problem of combining the results of multiple adaptive logic networks that were used as classifiers in OCR system for Macedonian Cyrilli c. Combining is performed by weighted voting of some or all the classifiers. The weights associated to every trained classifier are evaluated on a test sample. As a result of the weighted voting process, a li st of character candidates along with their confidence levels is produced for every pattern. The confidence levels of the character candidates are used in the contextual postprocessing phase for word candidates generation and lexicon lookup.
Social Entropy: a New Metric for Learning Multi-Robot Teams

As robotics research expands into multiagent tasks and learning, investigators need new tools for evaluating the artiicial robot societies they study. Is it enough, for example, just to say a team is \hetero-geneous? " Perhaps heterogeneity is more properly viewed on a sliding scale. To address these issues this paper presents new metrics for learning robot teams. The metrics evaluate diversity in societies of mechanically similar but behaviorally heterogeneous agents. Behavior is an especially important dimension of diversity in learning teams since, as they learn, agents choose between hetero-or homogeneity based solely on their behavior. This paper introduces metrics of behavioral diierence and behavioral diversity. Behav-ioral diierence refers to disparity between two spe-ciic agents, while diversity is a measure of an entire society. Social Entropy, inspired by Shannon's Information Entropy 5], is proposed as a metric of be-havioral diversity. It captures important components of diversity including the number and size of castes in a society. The new metrics are illustrated in the evaluation of an example learning robot soccer team.
The Effect of Coaches’ Controlling Style on the Competitive Anxiety of Young Athletes

Framed on a Self-Determination Theory perspective, the purpose of this study was to explore the predictive capacity of coaches’ interpersonal controlling style on the competitive anxiety of young athletes, considering the mediating effect of the athletes’ controlled motivation on this relationship. The sample consisted of 1166 athletes, aged between 9 and 18, who ranked their perceptions of coaches’ controlling style, as well as the reasons for participating in sport and their competitive anxiety before or during competition. The structural models assessing both the direct effect of the controlling style on the anxiety and the complete mediated effect of the controlled motivation on this relationship revealed good fit indices. However, a significant difference of the chi-square was obtained when comparing these models to the partial mediation model, providing evidence of this last model to be more adequate to describe the relationship between coaches’ controlling style and athletes’ competitive anxiety. Positive significant effects of coach controlling style on the three forms of competitive anxiety were found (βCS-SA = 0.21, p < 0.001; βCS-W= 0.14, p < 0.001; βCS-CD= 0.30, p < 0.001) indicating that coach controlling style could be an antecedent for athletes’ anxiety in a direct way. Although this style also predicts athletes’ motivation to participate, this indirect path seems to predict competitive anxiety in a less clear way. We discuss our results facing them up to Vallerand’s hierarchical model postulates, focusing on the relevant influence of coaches on the young athletes’ experience in the sport context.
Securing Java with Local Policies

We propose an extension to the security model of Java. It allows for specifying, analysing and enforcing history-based policies. Policies are defined by finite state automata recognizing the permitted execution histories. Programmers can sandbox an untrusted piece of code with a policy, which is enforced at run-time through its local scope. A static analysis allows for optimizing the execution monitor, that will only check the program points where some security violation may actually occur.
HeLI, a Word-Based Backoff Method for Language Identification

In this paper we describe the Helsinki language identification method, HeLI, and the resources we created for and used in the 3rd edition of the Discriminating between Similar Languages (DSL) shared task, which was organized as part of the VarDial 2016 workshop. The shared task comprised of a total of 8 tracks, of which we participated in 7. The shared task had a record number of participants, with 17 teams providing results for the closed track of the test set A. Our system reached the 2nd position in 4 tracks (A closed and open, B1 open and B2 open) and in this paper we are focusing on the methods and data used for those tracks. We describe our word-based backoff method in mathematical notation. We also describe how we selected the corpus we used in the open tracks.
Cooperative Strategy for Optimal Management of Smart Grids by Wavelet RNNs and Cloud Computing

Advanced smart grids have several power sources that contribute with their own irregular dynamic to the power production, while load nodes have another dynamic. Several factors have to be considered when using the owned power sources for satisfying the demand, i.e., production rate, battery charge and status, variable cost of externally bought energy, and so on. The objective of this paper is to develop appropriate neural network architectures that automatically and continuously govern power production and dispatch, in order to maximize the overall benefit over a long time. Such a control will improve the fundamental work of a smart grid. For this, status data of several components have to be gathered, and then an estimate of future power production and demand is needed. Hence, the neural network-driven forecasts are apt in this paper for renewable nonprogrammable energy sources. Then, the produced energy as well as the stored one can be supplied to consumers inside a smart grid, by means of digital technology. Among the sought benefits, reduced costs and increasing reliability and transparency are paramount.