Miracle-dz/UniFAR-FTUs huggingface dataset:
RegAnalyst: a web interface for the analysis of regulatory motifs, networks and pathways

RegAnalyst is a user-friendly web interface that integrates MoPP (Motif Prediction Program), MyPatternFinder (pattern detection tool) and MycoRegDB (mycobacterial promoter and regulatory elements database). Since motif discovery is a challenging task, numerous tools have been developed over the past few years. Strikingly, the existing programs were not successful in detecting the known consensus in all mycobacterial (epitomizing degenerate) datasets even in the absence of noise and their performance was further reduced in the presence of noise. Consequently, MoPP, a de novo and greedy (for degeneracy) ‘inexact’ word-based tool that is tailored to enumerate significantly conserved degenerate oligonucleotide motifs was developed. Benchmarking on datasets from MycoRegDB and SCPD (http://rulai.cshl.edu/SCPD/) indicate that MoPP (i) consistently outperforms other motif discovery tools on highly degenerate as well as less degenerate datasets and (ii) successfully detects completely degenerate motifs (with no two instances of a pattern being exactly the same) even in the presence of noise. We have also developed another accessory program, MyPatternFinder, that scans a given sequence or genome to find exact or approximate matches to a query motif of any length identified by MoPP or any other user-defined motif. RegAnalyst will be a valuable tool for in silico analysis of regulatory networks and can be accessed at http://www.nii. ac.in/~deepak/RegAnalyst.
Minimax Analysis for Finite Horizon Inventory Models

We consider stochastic nite-horizon inventory models with discrete distributions that are incompletely speciied by selected moments, percentiles, or a combination of moments and per-centiles. The objective is to determine an inventory policy that minimizes the maximum expected cost over the class of demand distributions satisfying the speciications described above. We show that many inventory models of this form can be solved by a sequence of linear programs.
Clustering of non-polar contacts in proteins

MOTIVATION Hydrophobic or non-polar contacts in proteins are important for protein folding, protein stability and protein-protein interactions. In particular, in the interior of a protein, in the hydrophobic core, a large number of such contacts are found. The residues involved in these contacts often form a tightly packed cluster of atoms. It is useful for the understanding of protein structure to be able to identify and analyse such clusters. RESULTS Tools for hierarchical cluster analysis of non-polar contacts in proteins are described. These tools allow for efficient identification of clusters of non-polar interactions in proteins, both internal clusters and clusters involved in protein-protein contacts. The non-polar contacts are represented by a dendrogram structure, which is a simple approach for flexible identification of clusters by visual inspection. The tools are demonstrated on the structure of crambin, the structure of the complex between human growth hormone and the human growth hormone binding protein, and a pair of lipase/esterase structures. AVAILABILITY On request from the author.
The Effects of Enterprise Resource Planning Systems on Firm's Performance: A Survey of Commercial Banks in Kenya

Enterprise Resource Planning (ERP) systems have transformed the way organizations go about the process of providing Information systems. This research discusses the issues of introducing ERPs into small and medium enterprises with the aim of finding the best ways to manage the change process to get a competitive advantage over its rivals. The study had five objectives of finding out how the financial resource availability, organizational complexities, employees perceptions, regulatory requirements, and having a top management support affects the effective implementation of an ERP system which in turn will affect the firm’s performance. The research adopted a descriptive design employing the use of mainly questionnaires as the primary data collection tool. Data was collected using questionnaires and analyzed by finding out the mean, maximum, minimum, standard deviation and the correlation between the variables in the findings. The presentation of data was done by use of tables while hypothesis test was done by chisquare test of independence. All this was achieved by the use of Statistical Package for Social Science (SPSS V 20). This study found that financial resource availability, organizational complexities, employee’s perceptions, regulatory requirements, and having a top management support all affects the effective implementation of an ERP system which in turn will affect the firm’s performance.
C-Peptide and Vascular Complications in Type 2 Diabetic Subjects

C-peptide is a small peptide comprised of 31 amino acids, with a short half-life of approximately 30 minutes. It was first identified by Steiner et al. [1] as a by-product of proinsulin and its main role is in assisting in the arrangement of the correct structure of insulin. Proinsulin consists of an A chain, connecting peptide (C-peptide), and B chain. C-peptide has a central glycine-rich region that allows the correct positioning of the A and B chains for insulin to achieve its tertiary structure [1]. It is secreted into the bloodstream in equimolar amounts together with insulin in response to glucose stimulation. C-peptide has been long considered an inactive peptide; however, over the last two decades, numerous studies have revealed that C-peptide displays a physiological role in different cell types [2,3]. The C-terminal pentapeptide of C-peptide obtains the full activity of intact C-peptide in stimulating Na+/K+-ATPase [4]. The amino acid sequence of C-peptide can vary by species, although it has several conserved sequences, such as its N-terminal acidic region, glycine-rich central segment, and C-terminal pentapeptide [5]. Moreover, evidence indicates that C-peptide is not merely an inactive by-product of insulin biosynthesis but also a hormonally-active peptide itself [3,4].
On Restricted Leibniz Algebras

In this article we prove that in prime characteristic there is a functor − p− Leib from the category of diassociative algebras to the category of restricted Leibniz algebras, generalizing the functor from associative algebras to restricted Lie algebras. Moreover, we define the notion of restricted universal enveloping diassociative algebra Ud p (𝔤) of a restricted Leibniz algebra 𝔤 and we show that Ud p is left adjoint to the functor − p− Leib . We also construct the restricted enveloping algebra, which classifies the restricted Leibniz modules. In the last section we put a restricted pre-Lie structure on the tensor product of a Leibniz algebra by a Zinbiel algebra.
Journal of Geophysical Research: Solid Earth Seismic interferometry and stationary phase at caustics

Waves that propagate between two receivers can be extracted by cross correlating noise recorded at these receivers if the noise is generated by sources on a closed surface surrounding the receivers. This concept is called seismic interferometry. Of all these noise sources, those for whom the travel time diﬀerence for propagation to the two receivers is in the stationary phase zone, give the dominant contribution. In this paper we analyze the stationary phase properties when one receiver is at a caustic for waves leaving the other receiver. A simple model for a waveguide and a general treatment of caustics show that, at a caustic, the curvature of the travel time diﬀerence at the stationary phase zone vanishes. As a result the stationary phase region is considerably wider at a caustic than at other points, and it is more likely that noise sources are present in the stationary phase region. This explains why it is easier to extract waves from seismic interferometry when the receivers are at caustics such as antipodal receivers on the Earth.
Experimental testbed for seawater channel characterization

Shallow seawaters are problematic for acoustic and optical communications. Sensor networks based on electromagnetic (EM) communications are evaluated in this environment. In order to characterize the underwater channel, several measurement systems have been designed, built and tested in the sea obtaining very reliable results. Experiments carried out with dipoles and loop antennas showed serious disagreement with the state of the art, especially when dipole antennas are used. Dipoles performance was poor while magnetic loops showed much lower attenuation. A measurement system is described in detail and real attenuation of the underwater channel is obtained for several distances and antennas. Finally, measured and simulated results are compared and reveal good agreement.
Employee Reactions to Electronic Control Systems

This field study considered proposed relationships between perceived procedural fairness and employee reactions to a relatively novel organizational phenomenon, electronic control systems (ECSs). In a sample (N= 151) of employees, perceptions of ECSs' procedural fairness explained variance in ECSs' satisfaction beyond that accounted for in previous studies. In turn, ECSs' satisfaction was associated with job satisfaction. Results generally show that procedural fairness, which has a history of strong relationships with important organization outcomes, enhances existing models of employee reactions to ECSs.
Inclination-dependent Luminosity Function of Spiral Galaxies in the Sloan Digital Sky Survey: Implications for Dust Extinction

Using a sample of 61,506 spiral galaxies selected from the SDSS DR2, we examine the luminosity function (LF) of spiral galaxies with different inclination angles. We find that the characteristic luminosity of the LF, L*, decreases with increasing inclination, while the faint-end slope, α, depends only weakly on it. The inclination dependence of the LF is consistent with that expected from a simple model in which the optical depth is proportional to the cosine of the inclination angle, and we use a likelihood method to recover both the coefficient in front of the cosine, γ, and the LF for galaxies viewed face-on. The value of γ is quite independent of galaxy luminosity in a given band, and the values of γ obtained in this way for the five SDSS bands give an extinction curve that is a power law of wavelength (τ ∝ λ-n), with a power index of n = 0.96 ± 0.04. Using the dust extinction for galaxies obtained by Kauffmann and coworkers, we derive an "extinction-corrected" luminosity function for spiral galaxies. Dust extinction makes M* dimmer by ~0.5 mag in the z band and by ~1.2 mag in the u band. Since our analysis is based on a sample in which selection effects are well under control, the dimming of edge-on galaxies relative to face-on galaxies is best explained by assuming that galaxy disks are optically thick in dust absorption.
Information Flow Control for Intrusion Detection Derived from MAC Policy

Most of today's MAC implementations can be turned into permissive mode, where no enforcement is performed but alerts are raised instead. This behavior is very close to an anomaly IDS except that the system is configured through a MAC policy. MAC implementations such as SELinux and AppArmor come with a default policy including real life and practical rules ready to be used as is or as a basis for a custom policy. In this paper, we first propose an extension of an IDS based on information flow control. We address issues concerning programs execution and improve its expressiveness in terms of security policy. This extended model can be configured to reach a wide variety of different security goals. Particularly, it allows for information flow checking based on users and/or programs dependent policy rules. Furthermore, suspicious modification of binary programs can be detected to avoid malware execution. We also propose an algorithm for deriving an AppArmor MAC policy into an information flow policy, and thus get the advantage of having a ready to use policy offering good security. We finally show a practical example of deriving such a policy in order to configure our IDS.
Magnetic field amplification by SN-driven interstellar turbulence

Supernovae are known to be the dominant energy source for driving turbulence in the interstellar medium. Yet, their effect on magnetic field amplification in spiral galaxies is still poorly understood. Analytical models based on the uncorrelated-ensemble approach predicted that any created field will be expelled from the disk before a significant amplification can occur. By means of direct simulations of supernova-driven turbulence, we demonstrate that this is not the case. Accounting for vertical stratification and galactic differential rotation, we find an exponential amplification of the mean field on timescales of 100 Myr. We highlight the importance of rotation in the generation of helicity by showing that a similar mechanism based on Cartesian shear does not lead to a sustained amplification of the mean magnetic field.
THE EFFECT OF BALANCE TRAINING ON POSTURE SWAY IN MULTIPLE SCLEROSIS PATIENTS

Purpose: The multiple sclerosis disease is one of the most common progressive neurological diseases in young adults. According to this matter, that risk possibility is two or three times more than healthy people. The purpose of current study is to survey the effect of balance training on posture sway in multiple sclerosis patients Study method: The current study is semi-experimental. In this regard, 20 patients with multiple sclerosis from MS Society of Iran with age range of (41/8512/59) and scale score of disability progression (0-5) were participated in this study during 10 weeks (three times a week and Each session 1.5 hour). The posture sway in subjects were measured before and after practicing with static stabilometer machine, and also the paired sample t test with (P≤0.05) for results comparison was used. Results: The results of research showed that the effect of balance training on general fluctuations decrement (P= 0.000), anterior - posterior (P=0.02) and sway speed range (P=0.01) was meaningful but the exercises effect on medio-lateral sway (P=0.07) was meaningful. Conclusion: The achieved results from the study showed that the selected balance training was effective on general posture sway especially anterior–posterior. Article visualizations:
A General Framework for Content-enhanced Network Representation Learning

This paper investigates the problem of network embedding, which aims at learning low-dimensional vector representation of nodes in networks. Most existing network embedding methods rely solely on the network structure, i.e., the linkage relationships between nodes, but ignore the rich content information associated with it, which is common in real world networks and beneficial to describing the characteristics of a node. In this paper, we propose content-enhanced network embedding (CENE), which is capable of jointly leveraging the network structure and the content information. Our approach integrates text modeling and structure modeling in a general framework by treating the content information as a special kind of node. Experiments on several real world net- works with application to node classification show that our models outperform all existing network embedding methods, demonstrating the merits of content information and joint learning.
Interaction of dietary protein, cholesterol and age on lipid metabolism of the rat

1. Male rats at 1 (young) and 9 months (adult) of age were fed on purified diets, supplemented with or without cholesterol, containing 200 g protein/kg (casein (CAS), whey protein (WHY) or soya-bean protein (SOY)) for 4 weeks. 2. SOY exerted a hypocholesterolaemic effect in young rats regardless of dietary cholesterol, whereas in adult rats it was observed only when a cholesterol-enriched diet was given. WHY was also hypocholesterolaemic in rats of both ages given cholesterol. SOY tended to reduce the liver cholesterol both in young and adult rats. 3. The liver hydroxymethylglutaryl-CoA reductase (NADPH) (EC 1.1.1.34) activity tended to be lower in the vegetable-protein groups than in the animal-protein groups in young rats, but the age-related reduction was observed only in the latter groups. 4. There was no significant age-related difference in the activity of liver cholesterol 7α-monooxygenase (EC 1.14.13.17) in response to diets. However, when cholesterol was given, activity tended to decrease with age. Rats given SOY excreted more faecal steroids than those given casein, particularly adult rats. 5. The fatty acid profile of phosphatidylcholine and the Δ6-desaturase activity of liver microsomes indicated the reduced desaturation of linoleate in the SOY and WHY groups compared with the CAS groups. 6. The results thus showed a complex interaction of protein type, cholesterol and age on cholesterol homeostasis.
A Basis Size Dependence Study of Carbon-13 Nuclear Magnetic Resonance Spectroscopic Shielding in Alanyl and Valyl Fragments: Toward Protein Shielding Hypersurfaces

We have investigated the effects of basis set quality on the accuracy and speed of ab initio calculations of Cat CB chemical shifts (or shieldings) of alanine and valine residues in proteins. Five basis set combinations were studied: a uniform 3-21G and a 4-31G/3-21G “locally dense” basis, both producing 88 contracted functions; a 6-31 lG+(2d)/3-21G and a 6-311G+(2d)/6-31G basis, each giving a total of 108 contracted functions; and a uniform STO-3G basis, giving 48 contracted functions. We find that results obtained by using small Gaussian basis sets correlate well with calculations performed using very large (6-31 lG++(2d,2~)/6-31G) basis sets, with only changes in slope and offset being required in order to bring results into excellent agreement, while the time necessary for the calculations is significantly reduced. This marked decrease in computational time using small, locally dense basis sets has permitted the first calculation of a three-dimensional chemical shielding hypersurface for valine. Chemical shifts predicted by using the @,v,xl shielding hypersurface are in good accord with chemical shift values detennined experimentally. These results open up new opportunities for the relatively rapid evaluation of amino acid shielding hypersurfaces for future use in protein structure prediction and refinement.
A nested sequence of projectors and corresponding braid matrices R̂(θ). 1. Odd dimensions

A basis of N2 projectors, each an N2×N2 matrix with constant elements, is implemented to construct a class of braid matrices R(θ), θ being the spectral parameter. Only odd values of N are considered here. Our ansatz for the projectors Pα appearing in the spectral decomposition of R(θ) leads to exponentials exp(mαθ) as the coefficient of Pα. The sums and differences of such exponentials on the diagonal and the antidiagonal, respectively, provide the (2N2−1) nonzero elements of R(θ). One element at the center is normalized to unity. A class of supplementary constraints imposed by the braid equation leaves 12(N+3)(N−1) free parameters mα. The diagonalizer of R(θ) is presented for all N. Transfer matrices t(θ) and L(θ) operators corresponding to our R(θ) are studied. Our diagonalizer signals specific combinations of the components of the operators that lead to a quadratic algebra of N2 constant N×N matrices. The θ dependence factors out for such combinations. R(θ) is developed in a power series in θ. Th.
Convective core mixing: A metallicity dependence?

The main purpose of this paper is to investigate the possible existence of a metallicity dependence of the overshooting from main sequence star turbulent cores. We focus on objects with masses in the range ~$ 2.5~{M}_{\odot}$–~$25~{M}_{\odot}$. Evolutionary time scale ratios are compared with star number ratios on the main sequence. Star populations are synthesized using grids of evolutionary tracks computed with various overshooting amounts. Observational material is provided by the large and homogeneous photometric database of the OGLE 2 project for the Magellanic clouds. Attention is paid to the study of uncertainties: distance modulus, intergalactic and interstellar reddening, IMF slope and average binarity rate. Rotation and the chemical composition gradient are also considered. The result for the overshooting distance is $l_{\mathrm{over}}^{\mathrm{\tiny SMC}}= 0.40^{+0.12}_{-0.06}~\mathrm{H}_{\mathrm{p}}$ ($Z_{0}=0.004$) and $l_{\mathrm{over}}^{\mathrm{\tiny LMC}}= 0.10^{+0.17}_{-0.10}~\mathrm{H}_{\mathrm{p}}$ ($Z_{0}=0.008$) suggesting a possible dependence of the extent of the mixed central regions with metallicity within the considered mass range. Unfortunately it is not yet possible to fully disentangle the effects of mass and chemical composition.
On effective actions for the bosonic tachyon

We extend the analysis of [24] to the bosonic case and find the one-derivative effective action valid in the vicinity of rolling tachyons with an energy not larger than that of the original D-brane. For on-shell tachyons rolling down the well-behaved side of the potential in this theory, the energy is conserved and the pressure eventually decreases exponentially. For tachyons rolling down the ``wrong'' side, the pressure instead blows up in a finite time.
Context-sensitive program analysis as database queries

Program analysis has been increasingly used in software engineering tasks such as auditing programs for security vulnerabilities and finding errors in general. Such tools often require analyses much more sophisticated than those traditionally used in compiler optimizations. In particular, context-sensitive pointer alias information is a prerequisite for any sound and precise analysis that reasons about uses of heap objects in a program. Context-sensitive analysis is challenging because there are over 1014 contexts in a typical large program, even after recursive cycles are collapsed. Moreover, pointers cannot be resolved in general without analyzing the entire program. This paper presents a new framework, based on the concept of deductive databases, for context-sensitive program analysis. In this framework, all program information is stored as relations; data access and analyses are written as Datalog queries. To handle the large number of contexts in a program, the database represents relations with binary decision diagrams (BDDs). The system we have developed, called bddbddb, automatically translates database queries into highly optimized BDD programs. Our preliminary experiences suggest that a large class of analyses involving heap objects can be described succinctly in Datalog and implemented efficiently with BDDs. To make developing application-specific analyses easy for programmers, we have also created a language called PQL that makes a subset of Datalog queries more intuitive to define. We have used the language to find many security holes in Web applications.
Investigation on multiuser diversity in spectrum sharing based cognitive radio networks

A new form of multiuser diversity, named multiuser interference diversity, is investigated for opportunistic communications in cognitive radio (CR) networks by exploiting the mutual interference between the CR and the existing primary radio (PR) links. The multiuser diversity gain and ergodic throughput are analyzed for different types of CR networks and compared against those in the conventional networks without the PR link.