Miracle-dz/UniFAR-FTUs huggingface dataset:
Fast spectral algorithms of invariants calculation

The recognition of objects independent of their position, size and orientation is an important problem in pattern recognition. In this paper we propose a new fast algorithm of moment invariant computation, which needs almost no multiplications. We use modular arithmetic of the finite Galois field GF(Q) to map the geometrical moments calculation to a fast Fourier-Mellin-Galois transform, which reduces the computational complexity of moments from O(N/sup 4/) to O(N/sup 2/log/sub 2/N). We introduce orthogonal Fourier-Mellin-Galois moments based on a complete set of orthogonal characters of the multiplicative group of the GF(Q). These moments are modular remainders modulo Q of the classical geometrical moments.
Community detection in dynamic networks via adaptive label propagation

An adaptive label propagation algorithm (ALPA) is proposed to detect and monitor communities in dynamic networks. Unlike the traditional methods by re-computing the whole community decomposition after each modification of the network, ALPA takes into account the information of historical communities and updates its solution according to the network modifications via a local label propagation process, which generally affects only a small portion of the network. This makes it respond to network changes at low computational cost. The effectiveness of ALPA has been tested on both synthetic and real-world networks, which shows that it can successfully identify and track dynamic communities. Moreover, ALPA could detect communities with high quality and accuracy compared to other methods. Therefore, being low-complexity and parameter-free, ALPA is a scalable and promising solution for some real-world applications of community detection in dynamic networks.
The Region Adjacent to the C-end of the Inner Gate in Transient Receptor Potential Melastatin 8 (TRPM8) Channels Plays a Central Role in Allosteric Channel Activation*

Background: The gating mechanism of transient receptor potential melastatin 8 (TRPM8) channels remains elusive. Results: Mutations neighboring the C-end region of the TRPM8 channel inner gate modulate allosteric coupling. Conclusion: The region adjacent to the inner gate in TRPM8 channels is pivotal for allosteric channel activation. Significance: These findings increase our understanding of the allosteric mechanism of TRPM8 channel gating. The ability of transient receptor potential (TRP) channels to sense and respond to environmental and endogenous cues is crucial in animal sensory physiology. The molecular mechanism of channel gating is yet elusive. The TRP box, a conserved region in the N-end of the C terminus domain, has been signaled as pivotal for allosteric activation in TRP channels. Here, we have examined the role of the linker region between the TRPM8 inner gate and the TRP box (referred to as the S6-TRP box linker) to identify structural determinants of channel gating. Stepwise substitutions of segments in the S6-TRP box linker of TRPM8 channel with the cognate TRPV1 channel sequences produced functional chimeric channels, and identified Tyr981 as a central molecular determinant of channel function. Additionally, mutations in the 986–990 region had a profound impact on channel gating by voltage and menthol, as evidenced by the modulation of the conductance-to-voltage (G-V) relationships. Simulation of G-V curves using an allosteric model for channel activation revealed that these mutations altered the allosteric constants that couple stimuli sensing to pore opening. A molecular model of TRPM8, based on the recently reported TRPV1 structural model, showed that Tyr981 may lie in a hydrophobic pocket at the end of the S6 transmembrane segment and is involved in inter-subunit interactions with residues from neighbor subunits. The 986–990 region holds intrasubunit interactions between the TRP domain and the S4–S5 linker. These findings substantiate a gating mechanism whereby the TRP domain acts as a coupling domain for efficient channel opening. Furthermore, they imply that protein-protein interactions of the TRP domain may be targets for channel modulation and drug intervention.
The Privacy Badge Revisited-Enhancement of a Privacy-Awareness User Interface for Small Devices

In this paper, we present enhancements of the Privacy Badge, which is a privacy-awareness user interface for small devices with limited capabilities. The Privacy Badge was created to visualize privacy loss in ubiquitous and pervasive computing environments and to enable users to do privacy settings in an easy and understandable way. We introduce the service anticipation as a new feature and present enhancements of existing features. We evaluated the enhanced Privacy Badge with a user evaluation whose results approve the overall system as well as the modifications.
Characterization of Caulobacter crescentus FtsZ Protein Using Dynamic Light Scattering*

Background: Self-assembly of the tubulin-homologue FtsZ is critical in bacterial cell division. Results: Dynamic light scattering (DLS) measurements provide insight into the kinetics and stable length of Caulobacter crescentus FtsZ in vitro. Conclusion: C. crescentus FtsZ forms short linear polymers in solution with the assembly rate depending on the concentrations of GTP and GDP. Significance: DLS is a valuable technique for studying the polymerization of cytoskeletal proteins. The self-assembly of the tubulin homologue FtsZ at the mid-cell is a critical step in bacterial cell division. We introduce dynamic light scattering (DLS) spectroscopy as a new method to study the polymerization kinetics of FtsZ in solution. Analysis of the DLS data indicates that the FtsZ polymers are remarkably monodisperse in length, independent of the concentrations of GTP, GDP, and FtsZ monomers. Measurements of the diffusion coefficient of the polymers demonstrate that their length is remarkably stable until the free GTP is consumed. We estimated the mean size of the FtsZ polymers within this interval of stable length to be between 9 and 18 monomers. The rates of FtsZ polymerization and depolymerization are likely influenced by the concentration of GDP, as the repeated addition of GTP to FtsZ increased the rate of polymerization and slowed down depolymerization. Increasing the FtsZ concentration did not change the size of FtsZ polymers; however, it increased the rate of the depolymerization reaction by depleting free GTP. Using transmission electron microscopy we observed that FtsZ forms linear polymers in solutions which rapidly convert to large bundles upon contact with surfaces at time scales as short as several seconds. Finally, the best studied small molecule that binds to FtsZ, PC190723, had no stabilizing effect on Caulobacter crescentus FtsZ filaments in vitro, which complements previous studies with Escherichia coli FtsZ and confirms that this class of small molecules binds Gram-negative FtsZ weakly.
Detection in Living Cells of Ca2+-dependent Changes in the Fluorescence Emission of an Indicator Composed of Two Green Fluorescent Protein Variants Linked by a Calmodulin-binding Sequence

We have designed a novel fluorescent indicator composed of two green fluorescent protein variants joined by the calmodulin-binding domain from smooth muscle myosin light chain kinase. When (Ca2+)4-calmodulin is bound to the indicator (K d = 0.4 nm), fluorescence resonance energy transfer between the two fluorophores is attenuated; the ratio of the fluorescence intensity measured at 505 nm to the intensity measured at 440 nm decreases 6-fold. Images of microinjected living cells demonstrate that emission ratios can be used to monitor spatio-temporal changes in the fluorescence of the indicator. Changes in indicator fluorescence in these cells are coupled with no discernible lag (<1 s) to changes in the cytosolic free Ca2+ ion concentration, ranging from below 50 nm to ∼1 μm. This observation suggests that the activity of a calmodulin target with a typical 1 nmaffinity for (Ca2+)4-calmodulin is responsive to changes in the intracellular Ca2+ concentration over the physiological range. It is likely that the indicator we describe can be modified to detect the levels of ligands and proteins in the cell other than calmodulin.
Changes in signal molecules and maturation promoting factor levels associate with spontaneous resumption of meiosis in rat oocytes

The present study was aimed to find out changes in signal molecules and maturation promoting factor (MPF) levels during meiotic cell cycle progression from diplotene and metaphase‐II (M‐II) arrest, a period during which oocyte achieves meiotic competency. Data suggest that high levels of adenosine 3′‐5′‐cyclic monophosphate (cAMP), guanosine 3′‐5′‐cyclic monophosphate (cGMP), and nitric oxide (NO) are associated with diplotene arrest, while reduction in their levels correlates with reduced MPF level and meiotic resumption from diplotene arrest. On the other hand, increased intracellular NO, calcium (Ca2+) as well as hydrogen peroxide (H2O2) levels correlate with decreased cAMP, Thr‐161 phosphorylated cyclin‐dependent kinase‐1 (Cdk1) as well as cyclin B1 levels. The decreased Thr‐161 phosphorylated Cdk1 and cyclin B1 level reduce MPF level leading to exit from M‐II arrest in oocytes cultured in vitro. These data suggest that the decrease of cAMP level and increase of cytosolic free Ca2+ as well as H2O2 levels associate with the reduced MPF level and meiotic resumption from diplotene arrest. On the other hand, increase of NO, cGMP, Ca2+ as well as H2O2 levels are associated with reduced MPF and spontaneous exit from M‐II arrest in rat oocytes cultured in vitro.
A Possible Metric for Semantic Similarity of Object-Oriented Analysis Models and Its Use to Estimate the Predictability of Object-Oriented Analysis Methods

Ideally, the results of a mature engineering process are predictable, i.e., independent applications of the process produce results that are the same within certain controlled limits. We suggest estimating the predictability of domain models produced using an object-oriented analysis method by comparing how semantically similar and complete are the domain models produced by independent analysts applying the method to the same problem. We introduce a possible measure of semantic similarity and evaluate it by using it to compare the predictability of two object-oriented analysis methods applied to 65 independently specified domain models of a large Voice-over-IP system and its supporting information management system.
The Open Framework for Developing Knowledge Base And Question Answering System

Developing a question answering (QA) system is a task of implementing and integrating modules of different technologies and evaluating an integrated whole system, which inevitably goes with a collaboration among experts of different domains. For supporting a easy collaboration, this demonstration presents the open framework that aims to support developing a QA system in collaborative and intuitive ways. The demonstration also shows the QA system developed by our novel framework.
Unified form for multi-scale top-hat transform based algorithms

Multi-scale operation has been one efficient way to improve the performance of top-hat transform. The key of multi-scale top-hat transform is appropriately organizing and using multi-scale top-hat transform to extract the multi-scale image features. If a unified form of multi-scale top-hat transform can be proposed, the application of multi-scale top-hat transform could be focused on the decision of some functions of the unified form. This would simplify the algorithm design. In this paper, a unified form of multi-scale top-hat transform based algorithms is given. To prove the unified form, some applications of multi-scale tophat transform based algorithms are integrated into the unified form by specifying the key functions of the unified form. These examples not only prove the unified form, but also provide the way of how to determine the key functions of the unified form for different applications.
OCR for Script Identification of Hindi (Devnagari) Numerals using Feature Sub Selection by Means of End-Point with Neuro-Memetic Model

Recognition of Indian languages scripts is challenging problems. In Optical Character Recognition [OCR], a character or symbol to be recognized can be machine printed or handwritten characters/numerals. There are several approaches that deal with problem of recognition of numerals/character depending on the type of feature extracted and different way of extracting them. This paper proposes a recognition scheme for handwritten Hindi (devnagiri) numerals; most admired one in Indian subcontinent. Our work focused on a technique in feature extraction i.e. global based approach using end-points information, which is extracted from images of isolated numerals. These feature vectors are fed to neuromemetic model [18] that has been trained to recognize a Hindi numeral. The archetype of system has been tested on varieties of image of numerals. In proposed scheme data sets are fed to neuromemetic algorithm, which identifies the rule with highest fitness value of nearly 100 % & template associates with this rule is nothing but identified numerals. Experimentation result shows that recognition rate is 92-97 % compared to other models. Keywords—OCR, Global Feature, End-Points, Neuro-Memetic model.
Jordan-Wigner Fermionization and the Theory of Low-Dimensional Quantum Spin Models.: Dynamic Properties

The Jordan-Wigner transformation is known as a powerful tool in condensed matter theory, especially in the theory of low-dimensional quantum spin systems. The aim of this chapter is to review the application of the Jordan-Wigner fermionization technique for calculating dynamic quantities of low-dimensional quantum spin models. After a brief introduction of the Jordan-Wigner transformation for one-dimensional spin one-half systems and some of its extensions for higher dimensions and higher spin values we focus on the dynamic properties of several low-dimensional quantum spin models. We start from the famous s=1/2 XX chain. As a first step we recall well-known results for dynamics of the z-spin-component fluctuation operator and then turn to the dynamics of the dimer and trimer fluctuation operators. The dynamics of the trimer fluctuations involves both the two-fermion (one particle and one hole) and the four-fermion (two particles and two holes) excitations. We discuss some properties of the two-fermion and four-fermion excitation continua. The four-fermion dynamic quantities are of intermediate complexity between simple two-fermion (like the zz dynamic structure factor) and enormously complex multi-fermion (like the xx or xy dynamic structure factors) dynamic quantities. Further we discuss the effects of dimerization, anisotropy of XY interaction, and additional Dzyaloshinskii-Moriya interaction on various dynamic quantities. Finally we consider the dynamic transverse spin structure factor $S_{zz}({\bf{k}},\omega)$ for the s=1/2 XX model on a spatially anisotropic square lattice which allows one to trace a one-to-two-dimensional crossover in dynamic quantities.
EQUILIBRIUM FLUCTUATIONS FOR ∇ϕ INTERFACE MODEL

unchen We study the large scale space–time fluctuations ofan interface which is modeled by a massless scalar field with reversible Langevin dynamics. For a strictly convex interaction potential we prove that on a large space–time scale these fluctuations are governed by an infinite-dimensional Ornstein–Uhlenbeck process. Its effective diffusion type covariance matrix is characterized through a variational formula. 1. Introduction. It is a common phenomenon that at low temperature two pure thermodynamic phases spatially coexist and are separated by an interface, which is very sharp with a width of a few atomic distances. In thermal equilibrium such an interface is planar and local deformations will relax back diffusively in order to minimize surface tension. To build a statistical mechanics model for the interface, one assumes that transverse deviations from the perfectly flat interface are given through a scalar field ϕ, that is, ϕ� � 2 → � with ϕ ≡ 0 corresponding to the flat interface. To have a mathematically well-defined model we discretize � 2 . We also generalize to arbitrary dimension. Then ϕ� � d → � with ϕ x is the height ofthe interf ace at site x ∈ � d . Neighboring heights are connected through an elastic potential V. While we need more stringent assumptions later on, at this point V should be bounded from below and increase sufficiently rapidly for large arguments. To each configuration ϕ we associate the (elastic) energy H� ϕ �= 1 � � x−y�= 1
Automatic Path and Trajectory Planning for Robotic Spray Painting

In this paper, a new automated optimum path and trajectory generation system for robotic painting process is presented. Usually, a direct self-learning manual method is usually adopted, i.e. the operator drives the robot manually through a complete spraying cycle. Recently, in order to-avoid this time-consuming procedure, CAD-based or "acquire-comparerecognize" methods have been developed. Here, a general technique that avoids the need for manual programming or CAD drawings and allows to obtain an optimal path and trajectory by using the graph theory and operative research methods is developed. After an image acquisition phase, a partitioner splits the object into a set of primitives, then the proposed algorithm is run on the graph in order to generate the optimal path; then, a optimum trajectory planning phase is performed. Kinematic and dynamic simulators of the CMA Robotics robots have been developed and validated in order to allow a correct planning and evaluation of the results. The new path planning algorithm has been implemented in Matlab and Visual-Studio.NET environments. Practical applications are presented.
Pharmacophore Fingerprint-Based Approach to Binding Site Subpocket Similarity and Its Application to Bioisostere Replacement

Bioisosteres have been defined as structurally different molecules or substructures that can form comparable intermolecular interactions, and therefore, fragments that bind to similar protein structures exhibit a degree of bioisosterism. We present KRIPO (Key Representation of Interaction in POckets): a new method for quantifying the similarities of binding site subpockets based on pharmacophore fingerprints. The binding site fingerprints have been optimized to improve their performance for both intra- and interprotein family comparisons. A range of attributes of the fingerprints was considered in the optimization, including the placement of pharmacophore features, whether or not the fingerprints are fuzzified, and the resolution and complexity of the pharmacophore fingerprints (2-, 3-, and 4-point fingerprints). Fuzzy 3-point pharmacophore fingerprints were found to represent the optimal balance between computational resource requirements and the identification of potential replacements. The complete PDB was converted into a database comprising almost 300,000 optimized fingerprints of local binding sites together with their associated ligand fragments. The value of the approach is demonstrated by application to two crystal structures from the Protein Data Bank: (1) a MAP kinase P38 structure in complex with a pyridinylimidazole inhibitor (1A9U) and (2) a complex of thrombin with melagatran (1K22). Potentially valuable bioisosteric replacements for all subpockets of the two studied protein are identified.
Surprise-Based Intrinsic Motivation for Deep Reinforcement Learning

Exploration in complex domains is a key challenge in reinforcement learning, especially for tasks with very sparse rewards. Recent successes in deep reinforcement learning have been achieved mostly using simple heuristic exploration strategies such as $\epsilon$-greedy action selection or Gaussian control noise, but there are many tasks where these methods are insufficient to make any learning progress. Here, we consider more complex heuristics: efficient and scalable exploration strategies that maximize a notion of an agent's surprise about its experiences via intrinsic motivation. We propose to learn a model of the MDP transition probabilities concurrently with the policy, and to form intrinsic rewards that approximate the KL-divergence of the true transition probabilities from the learned model. One of our approximations results in using surprisal as intrinsic motivation, while the other gives the $k$-step learning progress. We show that our incentives enable agents to succeed in a wide range of environments with high-dimensional state spaces and very sparse rewards, including continuous control tasks and games in the Atari RAM domain, outperforming several other heuristic exploration techniques.
Lignocellulose degradation by Phanerochaete chrysosporium: purification and characterization of the main alpha-galactosidase.

The main alpha-galactosidase was purified to homogeneity, in 30% yield, from a solid culture of Phanerochaete chrysosporium on 1 part wheat bran/2 parts thermomechanical softwood pulp. It is a glycosylated tetramer of 50 kDa peptide chains, which gives the N-terminal sequence ADNGLAITPQMG(? W)NT(? W)NHFG(? W)DIS(? W)DTI. It is remarkably stable, with crude extracts losing no activity over 3 h at 80 degrees C, and the purified enzyme retaining its activity over several months at 4 degrees C. The kinetics of hydrolysis at 25 degrees C of various substrates by this retaining enzyme were measured, absolute parameters being obtained by active-site titration with 2',4',6'-trinitrophenyl 2-deoxy-2, 2-difluoro-alpha-D-galactopyranoside. The variation of kcat/Km for 1-naphthyl-alpha-D-galactopyranoside with pH is bell-shaped, with pK1=1.91 and pK2=5.54. The alphaD(V/K) value for p-nitrophenyl-alpha-D-glucopyranoside is 1.031+/-0.007 at the optimal pH of 3.75 and 1.114+/-0.006 at pH7.00, indicating masking of the intrinsic effect at optimal pH. There is no alpha-2H effect on binding galactose [alphaD(Ki)=0.994+/-0.013]. The enzyme hydrolyses p-nitrophenyl beta-L-arabinopyranoside approximately 510 times slower than the galactoside, but has no detectable activity on the alpha-D-glucopyranoside or alpha-D-mannopyranoside. Hydrolysis of alpha-galactosides with poor leaving groups is Michaelian, but that of substrates with good leaving groups exhibits pronounced apparent substrate inhibition, with Kis values similar to Km values. We attribute this to the binding of the second substrate molecule to a beta-galactopyranosyl-enzyme intermediate, forming an E.betaGal. alphaGalX complex which turns over slowly, if at all. 1-Fluoro-alpha-D-galactopyranosyl fluoride, unlike alpha-D-galactopyranosyl fluoride, is a Michaelian substrate, indicating that the effect of 1-fluorine substitution is greater on the first than on the second step of the enzyme reaction.
A Column Generation Approach for the Graph Matching Problem

Graph matching plays a central role in different problems for structural pattern recognition. Examples of applications include matching 3D CAD models, shape matching and medical imaging, to name but a few. In this paper, we present a new integer linear formulation for the problem and employ a combinatorial optimization technique, called “column generation”, in order to solve instances of the problem. We also present computational experiments with generated instances.