Miracle-dz/UniFAR-FTUs huggingface dataset:
Rad52 SUMOylation affects the efficiency of the DNA repair

Homologous recombination (HR) plays a vital role in DNA metabolic processes including meiosis, DNA repair, DNA replication and rDNA homeostasis. HR defects can lead to pathological outcomes, including genetic diseases and cancer. Recent studies suggest that the post-translational modification by the small ubiquitin-like modifier (SUMO) protein plays an important role in mitotic and meiotic recombination. However, the precise role of SUMOylation during recombination is still unclear. Here, we characterize the effect of SUMOylation on the biochemical properties of the Saccharomyces cerevisiae recombination mediator protein Rad52. Interestingly, Rad52 SUMOylation is enhanced by single-stranded DNA, and we show that SUMOylation of Rad52 also inhibits its DNA binding and annealing activities. The biochemical effects of SUMO modification in vitro are accompanied by a shorter duration of spontaneous Rad52 foci in vivo and a shift in spontaneous mitotic recombination from single-strand annealing to gene conversion events in the SUMO-deficient Rad52 mutants. Taken together, our results highlight the importance of Rad52 SUMOylation as part of a ‘quality control’ mechanism regulating the efficiency of recombination and DNA repair.
A novel method in the induction of reliable experimental acute and chronic ulcerative colitis in mice.

Acute and chronic experimental ulcerative colitis models were produced in mice by providing them with drinking water containing synthetic dextran sulfate sodium. Mice that developed acute colitis showed signs of diarrhea, gross rectal bleeding, and weight loss within 6-10 days after ingesting 3%-10% dextran sulfate sodium. On postmortem examination, multiple erosions and inflammatory changes including crypt abscesses were found on the left side of the large intestine. Mice that developed chronic colitis showed signs of erosions, prominent regenerations of the colonic mucosa including dysplasia, shortening of the large intestine, and frequent formation of lymphoid follicles after 5 administration cycles, where each cycle was composed of 7 days' consumption of drinking water containing 5% dextran sulfate sodium followed by 10 days' consumption of distilled water. The population of intestinal microflora, Bacteroides distasonis and Clostridium spp. , increased significantly in mice with acute and chronic ulcerative colitis. Further, morphological studies suggest that the administered dextran sulfate sodium was partially phagocytized by macrophages in the colonic mucosa.
PERFECTED OPTION MARKETS IN ECONOMIES WITH ADVERSE SELECTION

In economies with adverse selection, Arrow-Debreu contingent commodity contracts must satisfy incentive constraints. Following Prescott and Townsend (in Econometrica, 1984), an Arrow-Debreu economy is considered with a continuum of agents whose feasible sets are artificially restricted by imposing these incentive constraints. Equilibria in such an economy must be incentive-constrained Pareto efficient. It is shown that deterministic equilibria of this kind are achievable through “perfected” option markets with non-linear pricing in a way which makes the incentive constraints self-enforcing. Rothschild, Stiglitz and others have shown, however, that these equilibria must be vulnerable to free entry by profit seeking firms.
Ways of Evaluation of the Annotators in Building the Prague Czech-English Dependency Treebank

In this paper, we present several ways to measure and evaluate the annotation and annotators, proposed and used during the building of the Czech part of the Prague Czech-English Dependency Treebank. At first, the basic principles of the treebank annotation project are introduced (division to three layers: morphological, analytical and tectogrammatical). The main part of the paper describes in detail one of the important phases of the annotation process: three ways of evaluation of the annotators - inter-annotator agreement, error rate and performance. The measuring of the inter-annotator agreement is complicated by the fact that the data contain added and deleted nodes, making the alignment between annotations non-trivial. The error rate is measured by a set of automatic checking procedures that guard the validity of some invariants in the data. The performance of the annotators is measured by a booking web application. All three measures are later compared and related to each other.
Strain partitioning during oblique plate convergence in northern Sumatra: Geodetic and seismologic constraints and numerical modeling

Global Positioning System (GPS) measurements along the subduction zone of northern Sumatra (2°S to 3°N) reveal that the strain associated with the oblique convergence of the Australian plate with Eurasia is almost fully partitioned between trench-normal contraction within the forearc and trench-parallel shear strain within a few tens of kilometers of the Sumatran fault Kinematic analyses of interplate earthquake slip vectors provide slip rates on the Sumatran fault within a few millimeters per year of GPS and geologic rates, giving us more confidence in the use of slip vectors for inferring slip partitioning elsewhere. The inferred slip rate on the Sumatran fault is ∼1/3 less than the full margin parallel component of plate motion. An across-forearc rotation in the slip vectors suggests that the missing arc-parallel shear occurs seaward of the geodetic network, between the forearc islands and the trench. Simple finite element models are used to explore the conditions under which the change in the principal strain rate directions between the forearc and the arc region can occur. Modeling suggests that neither a preexisting strike-slip fault nor a zone of thermally induced lithospheric weakness in the overriding plate is needed for strain partitioning to occur. In general, forearc slivers form over the region of interplate coupling and are driven along strike by the basal shear. A volcanic arc can help the partitioning process by localizing the margin-parallel shear strain in the upper plate if its crust and mantle are weaker than its surroundings. Interplate slip vectors and geodetic results from Sumatra together suggest that the highest coupling on the plate boundary occurs beneath and seaward of the forearc islands, consistent with inferences about the rupture zones of great nineteenth century earthquakes there. The Sumatra example suggests that geodetic measurements of interseismic, margin-parallel shear strain at oblique convergent margins can be used to map the landward extent of the relatively high basal stress beneath the overriding plate if one can correct for strain localization caused by weak upper plate strike-slip faults.
Please Scroll down for Article International Journal of Human-computer Interaction Qn-aces: Integrating Queueing Network and Act-r, Caps, Epic, and Soar Architectures for Multitask Cognitive Modeling Qn-aces: Integrating Queueing Network and Act-r, Caps, Epic, and Soar Architectures for Multitask Co

This article may be used for research, teaching and private study purposes. Any substantial or systematic reproduction, redistribution , reselling , loan or sub-licensing, systematic supply or distribution in any form to anyone is expressly forbidden. The publisher does not give any warranty express or implied or make any representation that the contents will be complete or accurate or up to date. The accuracy of any instructions, formulae and drug doses should be independently verified with primary sources. The publisher shall not be liable for any loss, actions, claims, proceedings, demand or costs or damages whatsoever or howsoever caused arising directly or indirectly in connection with or arising out of the use of this material. Comprehensive and computational models of human performance have both scientific and practical importance to human–machine system design and human-centered computing. This article describes QN-ACES, a cognitive architecture that aims to integrate two complementary classes of cognitive architectures: Queueing network (QN) mathematical architecture and ACT–R, CAPS, EPIC, and Soar (ACES) symbolic architectures. QN-ACES represents the fourth major step along the QN architecture development for theoretical and methodological unification in cognitive and human–computer interaction modeling. The first three steps—QN architecture for response time, QN-RMD (Reflected Multidimensional Diffusions) for response time, response accuracy, and mental architecture, and QN-MHP (Model Human Processor) for mathematical analysis and real time simulation of procedural tasks— are summarized first, followed by a discussion of the rationale, importance and specific research issues of QN-ACES.
Agent-based models of financial markets

This review deals with several microscopic (‘agent-based’) models of financial markets which have been studied by economists and physicists over the last decade: Kim–Markowitz, Levy–Levy–Solomon, Cont–Bouchaud, Solomon–Weisbuch, Lux–Marchesi, Donangelo–Sneppen and Solomon–Levy–Huang. After an overview of simulation approaches in financial economics, we first give a summary of the Donangelo–Sneppen model of monetary exchange and compare it with related models in economics literature. Our selective review then outlines the main ingredients of some influential early models of multi-agent dynamics in financial markets (Kim–Markowitz, Levy–Levy–Solomon). As will be seen, these contributions draw their inspiration from the complex appearance of investors' interactions in real-life markets. Their main aim is to reproduce (and, thereby, provide possible explanations) for the spectacular bubbles and crashes seen in certain historical episodes, but they lack (like almost all the work before 1998 or so) a perspective in terms of the universal statistical features of financial time series. In fact, awareness of a set of such regularities (power-law tails of the distribution of returns, temporal scaling of volatility) only gradually appeared over the nineties. With the more precise description of the formerly relatively vague characteristics (e.g. moving from the notion of fat tails to the more concrete one of a power law with index around three), it became clear that financial market dynamics give rise to some kind of universal scaling law. Showing similarities with scaling laws for other systems with many interacting sub-units, an exploration of financial markets as multi-agent systems appeared to be a natural consequence. This topic has been pursued by quite a number of contributions appearing in both the physics and economics literature since the late nineties. From the wealth of different flavours of multi-agent models that have appeared up to now, we discuss the Cont–Bouchaud, Solomon–Levy–Huang and Lux–Marchesi models. Open research questions are discussed in our concluding section.
HWPDE: Novel Approach for Data Extraction from Structured Web Pages

Diving into the World Wide Web for the purpose of fetching precious stones (relevant information) is a tedious task under the limitations of current diving equipments (Current Browsers). While a lot of work is being carried out to improve the quality of diving equipments, a related area of research is to devise a novel approach for mining. This paper describes a novel approach to extract the web data from the hidden websites so that it can be used as a free service to a user for a better and improved experience of searching relevant data. Through the proposed method, relevant data (Information) contained in the web pages of hidden websites is extracted by the crawler and stored in the local database so as to build a large repository of structured and indexed and ultimately relevant data. Such kind of extracted data has a potential to optimally satisfy the relevant Information starving end user.
A Multi-Agent strategy for automatic 3 D object recognition based on the fusion of Lidar range and intensity data

Three dimensional object recognition and extraction from Lidar and other airborne or space borne data have been an area of major interest in photogrammetry for quite a long time. Therefore, many researchers have been trying to study and develop automatic or semi-automatic approaches for object extraction based on sensory data in urban areas. Lidar data have proved to be a promising data source for various mapping and 3D modeling of objects. But, according to the complicated relationships between objects in urban areas, especially buildings and trees, the performance of obtained results from ordinary object recognition algorithms based on Lidar data, is still dependent on several assumptions and simplifications. In this paper a multi-agent strategy has been proposed for automatic building and tree recognition based on the fusion of textural and spatial information extracted from Lidar range and intensity data. In this multi-agent methodology, two different groups of object recognition agents are defined for building and tree recognition in parallel and the algorithm has two different operational levels based on the types of contextual information. According to the difficulties in the field of building and tree detection based on the textural descriptors or spatial context, using the communicational behaviors and other capabilities of the multi-agent systems can be so useful in the field of 3D object recognition in dense urban areas. The evaluation of obtained results of the proposed methodology confirms the high capabilities of Lidar data and this multi-agent algorithm to decrease the conflicts in the field of building and tree recognition in parallel.
Synthesis and Evaluation of Non-peptidic Cysteine Protease Inhibitors of P. falciparum Derived from Etacrynic Acid

A series of etacrynic acid derivatives was synthesized and screened for their in vitro activity against Plasmodium falciparum, as well as their activity against recombinantly expressed falcipain-2 and -3. The two most active compounds of the series displayed IC50 values of 9.0 and 18.8 μM against Plasmodia.
A realistic model of emergent phonology

In this report, ongoing research into the explanation of universal characteristics of human sound systems is presented. The characteristics are explained through a theory which is called emergent phonology. This theory is based on the ideas of Luc Steels (Steels 1995, 1996, 1997) that language is an emergent adaptive system in a population of language users in which coherence is maintained through self-organisation. Complexity is an emergent property of the interactions (called language games) between the agents. Two simulations are presented. The first is of vowel systems. This simulation has been completed and the system, as well as its results, in which universal characteristics of vowel systems do emerge, are presented. The second simulation is designed for more complex utterances that consist of multiple syllables with consonants. This is ongoing research. The technical details of the production and perception systems are provided in some detail. The first results of the combination of the production and perception parts are presented.
Flow cytometric immunofluorescence assay for detection of antibodies to human immunodeficiency virus type 1 using insoluble precursor forms of recombinant polyproteins as carriers and antigens

A new serological assay, the recombinant flow cytometric immunofluorescence assay (r-FIFA), was developed for the early detection of human immunodeficiency virus type 1 (HIV-1) antibodies by using recombinant insoluble forms of HIV-1 Gag-p45, Gag-gp41 chimeric protein, gp160, Po197 polyprotein as antigens and autologous carriers through flow cytometry. These recombinant proteins were expressed in insect cells by a baculovirus expression system. Eight anti-HIV-1 seroconversion panels, a low-titer anti-HIV-1 panel from Boston Biomedica Inc. (BBI), and three HIV-1 seroconversion specimens from the Provincial Health Laboratory of Ontario, Toronto, Ontario, Canada (PHL), were tested and analyzed by r-FIFA. In sensitivity comparisons between r-FIFA and tests licensed by the U.S. Food and Drug Administration, which were used to test all of the HIV-1 panels from BBI, detection of HIV-1 antibody by r-FIFA was on average greater than 20 days earlier than that by enzyme immunoassay. The sensitivity of r-FIFA has permitted the detection of HIV-1-specific immunoglobulin G (IgG), IgM, and IgA antibodies during seroconversion. A kinetic analysis of HIV-1 antibody production of r-FIFA has shown that either IgG or IgM, or both, can be detected, depending on the phase and type of the immune response in the HIV-1-infected individual. Both primary and secondary immune responses were observed during this period. The r-FIFA results suggest that implementation of r-FIFA may significantly reduce the "window" period from the time of infection to the time of seroconversion, with earlier detection of antibodies after initial infection. This would also make it possible for us to understand the immune response and the precise mechanisms of immunopathogenesis in the early period of HIV-1 infection.
The Characterization of the Olf-1/EBF-Like HLH Transcription Factor Family: Implications in Olfactory Gene Regulation and Neuronal Development

The Olf-1/EBF helix-loop-helix (HLH) transcription factor has been implicated in olfactory gene regulation and in B-cell development. Using homology screening methods, we identified two additional Olf-1/EBF-like cDNAs from a mouse embryonic cDNA library. The Olf-1/EBF-like (O/E) proteins O/E-1, O/E-2, and O/E-3 define a family of transcription factors that share structural similarities and biochemical activities. Although these O/E genes are expressed within olfactory epithelium in an identical pattern, they exhibit different patterns of expression in the developing nervous system. Although O/E-1 mRNA is present in several tissues in addition to olfactory neurons and developing B-cells, O/E-2 and O/E-3 are expressed at high levels only in olfactory tissue. In O/E-1 knock-out animals, the presence of two additional O/E family members in olfactory neurons may provide redundancy and allow normal olfactory neurodevelopment. Further, the identification of the O/E family of HLH transcription factors and their embryonic expression patterns suggest that the O/E proteins may have a more general function in neuronal development.
Numerical experiments with a salt dome

A salt dome is a familiar example of a three‐dimensional (3-D) geologic structure. Surprisingly, most of the literature devoted to the investigation of salt domes deals only with cross‐sectional views of the domes. This is particularly true for seismic work. A notable exception is the work of French (1974) which discusses inaccuracies in focusing introduced by performing two‐dimensional (2-D) migration of data obtained over a 3-D model structure.
Registration of blurred images for image mosaic

Existing methods for the registration of blurred images are efficient for the artificially blurred images or a planar registration. They are not suitable for image mosaic of the source images from a real camera with an almost fixed optical center. We propose a registration method so that a distortion-free registration on naturally captured images can be obtained. It adopts a multi-resolution and robust feature based inter-layer mosaic together. In each layer, Harris corner detector is chosen to effectively detect features and RANSAC is used to find reliable matches for further calibration as well as an initial homography as the initial motion of next layer. Simplex and subspace trust region methods are used consequently to estimate the stable focal length and rotation matrix through the transformation property of feature matches. Experimental results demonstrate the performance of our proposed method.
Sickle-Cell Anemia Hemoglobin: The Molecular Biology of the First “Molecular Disease”—The Crucial Importance of Serendipity

IN the spring of 1952 I sent 32 letters to England, trying to find a job in academic research. I was finishing my second postdoctoral year in the United States, working in Joseph Fruton's Biochemistry Department at Yale University. My topic was peptide chemistry, in particular the development of a
Jointly learning trajectory generation and hitting point prediction in robot table tennis

This paper proposes a combined learning framework for a table tennis robot. In a typical robot table tennis setup, a single striking point is predicted for the robot on the basis of the ball's initial state. Subsequently, the desired Cartesian racket state and the desired joint states at the striking time are determined. Finally, robot joint trajectories are generated. Instead of predicting a single striking point, we propose to construct a ball trajectory prediction map, which predicts the ball's entire rebound trajectory using the ball's initial state. We construct as well a robot trajectory generation map, which predicts the robot joint movement pattern and the movement duration using the Cartesian racket trajectories without the need of inverse kinematics, where a correlation function is used to adapt these joint movement parameters according to the ball flight trajectory. With joint movement parameters, we can directly generate joint trajectories. Additionally, we introduce a reinforcement learning approach to modify robot joint trajectories such that the robot can return balls well. We validate this new framework in both the simulated and the real robotic systems and illustrate that a seven degree-of-freedom Barrett WAM robot performs well.
Québec, Quebec 1 Faculté Des Sciences De L'administration Université Laval 2 Decision Support Technologies Section Defence R&d Canada -valcartier Effort Allocation Algorithms for Search and Rescue Operations

We present search effort allocation algorithms developed to assist Canadian search mission coordinators in the optimal planning of search and rescue missions. These algorithms are based on search theory, on numerical optimization techniques and on constraint satisfaction programming. We assume that the effort is continuous, that the search object is stationary and that the search is conducted in discrete space. We also propose an algorithm for the definition and assignment of multiple search rectangles to multiple search aircraft.
Encapsulating Multiple Communication-Cost Metrics in Partitioning Sparse Rectangular Matrices for Parallel Matrix-Vector Multiplies

This paper addresses the problem of one-dimensional partitioning of structurally unsymmetric square and rectangular sparse matrices for parallel matrix-vector and matrix-transpose-vector multiplies. The objective is to minimize the communication cost while maintaining the balance on computational loads of processors. Most of the existing partitioning models consider only the total message volume hoping that minimizing this communication-cost metric is likely to reduce other metrics. However, the total message latency (start-up time) may be more important than the total message volume. Furthermore, the maximum message volume and latency handled by a single processor are also important metrics. We propose a two-phase approach that encapsulates all these four communication-cost metrics. The objective in the first phase is to minimize the total message volume while maintaining the computational-load balance. The objective in the second phase is to encapsulate the remaining three communication-cost metrics. We propose communication-hypergraph and partitioning models for the second phase. We then present several methods for partitioning communication hypergraphs. Experiments on a wide range of test matrices show that the proposed approach yields very effective partitioning results. A parallel implementation on a PC cluster verifies that the theoretical improvements shown by partitioning results hold in practice.