Miracle-dz/UniFAR-FTUs huggingface dataset:
KemaDom: a web server for domain prediction using kernel machine with local context

Predicting domains of proteins is an important and challenging problem in computational biology because of its significant role in understanding the complexity of proteomes. Although many template-based prediction servers have been developed, ab initio methods should be designed and further improved to be the complementarity of the template-based methods. In this paper, we present a novel domain prediction system KemaDom by ensembling three kernel machines with the local context information among neighboring amino acids. KemaDom, an alternative ab initio predictor, can achieve high performance in predicting the number of domains in proteins. It is freely accessible at and .
Analysis of de-noising techniques of non-stationary ECG signal based on wavelet and PSO optimized parameters for Savitzky golay filter

The bioelectric signals originate from different organs of human body. Out of these ECG is one of the important bioelectric signals for our concern and for investigation of various heart ailments. ECG demonstrates graphical rendition of activity of the heart and by analyzing the ECG signal several heart diseases can be identified. For analysis of ECG signal, it must be noise free. There are several techniques for filtering out the noise from ECG signal. It is imperative to find out a best possible method for ECG Signal de-noising, which may be investigated by finding and comparing the signal-to-signal-plus-noise ratios (SSNR) and root-mean-square deviations (RMSD). By considering a mother wavelet with different levels and threshold, the values of SSNR and RMSD are calculated and compared to achieve a best possible result. Similarly, by utilizing different frame lengths and polynomial orders, the S-G filter is employed to find SSNR and RMSD. The results of these methods are also compared. Finally, the orders and frame lengths of S-G filters can be obtained by optimizing with the help of particle swarm optimization (PSO) technique.
Security and Privacy : Modest Proposals for Low-Cost RFID Systems #

Low cost Radio Frequency Identification (RFID) systems are increasingly being deployed in industry and commerce. These contactless devices have raised public concern regarding violation of privacy and information security. There is a growing need in the RFID community to discover and develop techniques and methods to overcome several problems posed by the above-mentioned concerns. This paper presents proposals on feasible security mechanisms for low cost RFID systems and analyses them from both security and privacy points of view.
Combined deficiency for MAP kinase-interacting kinase 1 and 2 (Mnk1 and Mnk2) delays tumor development

MAP kinase-interacting kinase 1 and 2 (Mnk1 and Mnk2) are protein-serine/threonine kinases that are activated by ERK or p38 and phosphorylate eIF4E, which is involved in cap-dependent translation initiation. However, Mnk1/2 double knockout (Mnk-DKO) mice show normal cell growth and development despite an absence of eIF4E phosphorylation. Here we show that the tumorigenesis occurring in the Lck-Pten mouse model (referred to here as tPten−/− mice) can be suppressed by the loss of Mnk1/2. Phosphorylation of eIF4E was greatly enhanced in lymphomas of parental tPten−/− mice compared with lymphoid tissues of wild-type mice, but was totally absent in lymphomas of tPten−/−; Mnk-DKO mice. Notably, stable knockdown of Mnk1 in the human glioma cell line U87MG resulted in dramatically decreased tumor formation when these cells were injected into athymic nude mice. Our data demonstrate an oncogenic role for Mnk1/2 in tumor development, and highlight these molecules as potential anticancer drug targets that could be inactivated with minimal side effects.
Complete Chloroplast Genome of Medicinal Plant Lonicera japonica: Genome Rearrangement, Intron Gain and Loss, and Implications for Phylogenetic Studies

The complete chloroplast (cp) genome of Lonicera japonica, a common ornamental and medicinal plant in North America and East Asia, was sequenced and analyzed. The length of the L. japonica cp genome is 155,078 bp, contains a pair of inverted repeat regions (IRa and IRb), of 23,774 bp each, as well as large (LSC, 88,858 bp) and small (SSC, 18,672 bp) single-copy regions. A total of 129 genes were identified in the cp genome, 16 of which were duplicated within the IR regions. Relative to other plant cp genomes, the L. japonica cp genome had a unique rearrangement between trnI-CAU and trnN-GUU. In L. japonica cpDNA, rps19, rpl2, and rpl23 move to the LSC region, from the IR region. The ycf1 pesudogene in the IR region is lost, and only one copy locates in the SSC region. Comparative cp DNA sequence analyses of L. japonica with other cp genomes reveal that the gene order, and the gene and intron contents, are slightly different. The introns in ycf2 and rps18 genes are found for the first time. Four genes (clpP, petB, petD, and rpl16) lost introns. However, its genome structure, GC content, and codon usage were similar to those of typical angiosperm cp genomes. All preferred synonymous codons were found to use codons ending with A/T. The AT-rich sequences were less abundant in the coding regions than in the non-coding ones. A phylogenetic analysis based on 71 protein-coding genes supported the idea that L. japonica is a sister of the Araliaceae species. This study identified unique characteristics of the L. japonica cp genome that contribute to our understanding of the cpDNA evolution. It offers valuable information for the phylogenetic and specific barcoding of this medicinal plant.
ROLE OF microRNAs IN THE REGULATION OF GENE EXPRESSION

First miRNAs were described in a flatworm species C. elegans, which led to an understanding of their important regulatory role in cell differentiation (Lee et al., 1993; Wightmanet al., 1993). Another critical step was the discovery of the second miRNA named let-7, which is a product of expression of a heterochronic switch gene in C. elegans (Reinhart et al., 2000). Loss of let-7 gene activity causes reiteration of larval cell fates during the adult stage, whereas increased let-7 gene dosage causes precocious expression of adult fates during larval stages. Let7 gene encodes a temporally regulated ROLE OF micro-RNAs IN THE REGULATION OF GENE EXPRESSION
Neural-network-based maximum-power-point tracking of coupled-inductor interleaved-boost-converter-supplied PV system using fuzzy controller

The photovoltaic (PV) generator exhibits a nonlinear V-I characteristic and its maximum power (MP) point varies with solar insolation. In this paper, a feedforward MP-point tracking scheme is developed for the coupled-inductor interleaved-boost-converter-fed PV system using a fuzzy controller. The proposed converter has lower switch current stress and improved efficiency over the noncoupled converter system. For a given solar insolation, the tracking algorithm changes the duty ratio of the converter such that the solar cell array voltage equals the voltage corresponding to the MP point. This is done by the feedforward loop, which generates an error signal by comparing the instantaneous array voltage and reference voltage corresponding to the MP point. Depending on the error and change of error signals, the fuzzy controller generates a control signal for the pulsewidth-modulation generator which in turn adjusts the duty ratio of the converter. The reference voltage corresponding to the MP point for the feedforward loop is obtained by an offline trained neural network. Experimental data are used for offline training of the neural network, which employs a backpropagation algorithm. The proposed peak power tracking effectiveness is demonstrated through simulation and experimental results. Tracking performance of the proposed controller is also compared with the conventional proportional-plus-integral-controller-based system. These studies reveal that the fuzzy controller results in better tracking performance.
Back analysis of the multilayer cylindrical HMA samples – height reduction method

ABSTRACT Although the complex modulus is one of the most basic properties used in pavement analysis and design, its accurate measurement for existing pavement layers has always been a challenging task. When samples cut out from the pavement asphalt layers are used for the hot mix asphalt (HMA) complex modulus tests, they are performed separately for each layer. This paper describes an original method for determining the complex moduli of individual asphalt layers. The new idea is tested by applying uniaxial loading–unloading cycle tests to the HMA specimens combined of multiple layers. It was observed that changing the thickness ratios in samples' layers, allows obtaining the sets of load and displacement values (F, u), which effectively enlarge the database needed for the back analysis. For now, the conducted analysis presented in the paper focused on numerical modelling of HMA specimens. The simulated numerical testing conditions were based on viscoelastic parameters of asphalt concrete samples whose values were determined in real laboratory tests. In the case of noisy results of laboratory test simulations with a stochastic Gaussian process, by applying multiple cuts and changing sample's height, the determined values of stiffness moduli of the individual layers do not vary from the reference values by more than 10%.
Development and exploitation of a novel mutant androgen receptor modelling strategy to identify new targets for advanced prostate cancer therapy

The persistence of androgen receptor (AR) signalling in castrate-resistant prostate cancer (CRPC) highlights the unmet clinical need for the development of more effective AR targeting therapies. A key mechanism of therapy-resistance is by selection of AR mutations that convert anti-androgens to agonists enabling the retention of androgenic signalling in CRPC. To improve our understanding of these receptors in advanced disease we developed a physiologically-relevant model to analyse the global functionality of AR mutants in CRPC. Using the bicalutamide-activated ARW741L/C mutation as proof of concept, we demonstrate that this mutant confers an androgenic-like signalling programme and growth promoting phenotype in the presence of bicalutamide. Transcriptomic profiling of ARW741L highlighted key genes markedly up-regulated by the mutant receptor, including TIPARP, RASD1 and SGK1. Importantly, SGK1 expression was found to be highly expressed in the KUCaP xenograft model and a CRPC patient biopsy sample both of which express the bicalutamide-activated receptor mutant. Using an SGK1 inhibitor, ARW741L transcriptional and growth promoting activity was reduced indicating that exploiting functional distinctions between receptor isoforms in our model may provide new and effective therapies for CRPC patients.
Systematic Parameterized Description of Pro-forms in the Prague Dependency Treebank 2 . 0 ∗

A pro-form is a word that is used to replace or substitute other words, phrases, clauses, or sentences etc. Besides pronouns one can also distinguish pro-adjectives, pro-numerals, pro-adverbs, and pro-verbs.1 Pro-forms are related to a wide range of linguistic phenomena, from wordformative principles, through negation and quantification, to anaphoric and deictic functions. As it was recognized a long time ago (among others in Montague grammar), pro-forms are extremely important for studying natural language semantics, even if they constitute only a closed class. Recently, a lot of work has been invested into developing large data resources for exploring natural language semantics, e.g. in the fields of predicate-argument structures or lexical databases. However, the treatment of pro-forms and related phenomena receives only a relatively minor attention in this data-dominated era (perhaps with the only exception of data for anaphora resolution, mostly limited to personal and demonstrative pronouns). Even if tag sets used in various corpora and treebanks clearly indicate some differentiation within the set of pro-forms (e.g.
Variants of BALB/c 3T3 cells lacking complex gangliosides retain a fibronectin matrix and spread normally on fibronectin-coated substrates

Evidence has accumulated that di- and trisialogangliosides are involved in the interaction of cells with fibronectin. We have therefore tested the ability of variants of BALB/c 3T3 deficient in such gangliosides to organize a fibronectin matrix and to spread on fibronectin-coated substrates. Whereas BALB/c 3T3 cells contained gangliosides GM3, GM1, and GD1a, direct chemical analysis showed that five out of six variants isolated contained no detectable GD1a. By the overlaying of thin layer chromatograms of cellular gangliosides with 125I-cholera toxin, these variants were also found to lack ganglioside GM1. In contrast, the sialogalactoprotein profile of these cells, analyzed using an 125I- ricin/SDS polyacrylamide gel overlay technique, was similar to that of the parent cell line. All variants organized an extensive fibronectin matrix comparable to that of BALB/c 3T3, as shown using either immunofluorescence or lactoperoxidase-catalyzed iodination. The variants could also spread on fibronectin-coated substrates and adopt a morphology similar to that of BALB/c 3T3 cells, with little or no difference in the concentration of fibronectin required for 50% cell spreading. Cell spreading of the variants was accompanied by the formation of focal contacts and microfilament bundles, in a manner closely resembling that seen with BALB/c 3T3 cells. Treatment of BALB/c 3T3 cells with neuraminidase, which converts much of the cellular GD1a to GM1, did not affect cell spreading on fibronectin. The results clearly demonstrate that complex gangliosides are not essential for retention of a fibronectin matrix or for spreading on fibronectin- coated substrates.
System dynamics modeling for EFQM excellence model: Case study of a regional electricity company in Iran

Excellence models, such as European Foundation for Quality Management (EFQM) provide a framework for the self-assessment. The EFQM model consists of two main domains: Enablers and Results. Feedback from the results makes the organization to correct the system. Hence, a dynamic model could be appropriate in analyzing the interrelated behavior of the two main domains as well as those within the criteria and sub-criteria. In this paper, a dynamic model is presented in which the EFQM model items are linked through the causal relationships. The case study described in this article is concerned about Yazd regional electricity company in Iran. The advantage is that by changing one parameter in the model, one can find how it could affect other parts of the model including the key results. By this analysis, it could be expected that the efficiency of EFQM model would be improved.
Hospital Culture of Transitions in Care: Survey Development

Understanding hospital culture is important to effectively manage patient flow. The purpose of this study was to develop a survey instrument that can assess a hospital's culture related to in-hospital transitions in care. Key transition themes were identified using a multidisciplinary team of experts from 3 health care systems. Candidate items were rigorously evaluated using a modified Delphi technique. Findings indicate 8 themes associated with hospital culture-mediating transitions. Forty-four items reflect the themes.
Resource-Based Theory and Market-Driven Management

Market-Driven Management poses the question of the relationship between markets and competitive advantage. Market-driven firms reveal a superior ability to understand, attract and maintain, a supply of products/services that offer more value for the customer than competitors. The Resource-Based Theory originates from Penrose’s idea (1959) of the firm as a coordinated ‘bundle’ of resources that the business has at its disposal or has access to (inside out), which are valuable, rare and inimitable. In global markets, MDM strives towards continuous innovation processes that can enable the company to escape the potential pressure of the competition, by identifying new customer needs to satisfy (outside in). The market-driven company is not only oriented to the market, but also tends to orient the market.
Directional Adaptive Multilevel Median Filter for Salt–and-Pepper Noise Reduction

This paper presents a novel two-stage adaptive noise reduction scheme for images corrupted by salt and pepper noise. The first stage identifies the impulse noise in the image by classifying the pixels into two classesthe ‘noise-free pixels’ and the ‘noise corrupted pixels’, based on the intensity values of the pixels. The second stage aims to reduce the impulse noise from the image by processing the ‘noise corrupted pixels’ while the ‘noise-free pixels’ are kept intact. This stage consists of two steps. In the first step, the denoised value of each ‘noise corrupted pixel’ is calculated using adaptive multilevel median filter. The second step enhances the image quality by applying directional filtering to the denoised image of the first step. Extensive computer simulations indicate that this technique provides significant improvement over many other existing techniques in terms of PSNR.
Kernel-based multifactor analysis for image synthesis and recognition

In many vision problems, the appearances of the observed images, e.g. the human facial images, are often influenced by multiple underlying factors. In this paper, a kernel-based factorization framework is proposed to analyze a multifactor dataset. Specifically, we perform N-mode singular value decomposition (N-mode SVD) in a higher dimensional feature space instead of the input space by using kernel approaches. Given an input sample, its specific underlying factors which may be all absent in the training set can be extracted and translated from one sample to another by using kernel-based 'translation'. Therefore our framework is suitable for tasks of new image synthesis and underlying factor recognition. We demonstrate the capabilities of our framework on ensembles of facial images subjected to different person identities, viewpoints and illuminations with high-quality synthetic faces and high face recognition accuracy.
Impact characteristics of simulated hailstones during ingestion by turbofan aero-engines

Recent in-flight instances of aircraft engine power loss involving hail ingestion have forced the manufacturers to demonstrate successful engine operation whilst ingesting hail. The main objective of this research project has been to obtain an understanding of the basic characteristics of hailstone impacts. A hail gun was designed to fire simulated hailstones at speeds up to 175 m/s. Three measurement techniques were used to determine the impact characteristics of the hailstones, i.e: patternator, high speed cine-photography, and still photography with short duration flashes. Using these techniques, the basic impact characteristics in terms of post-impact particle size, velocity and mass distribution were obtained for a variety of target configurations. The influence of seemingly important parameters on the impact characteristics were investigated, including approach angle and velocity, target curvature, and target rotation. Studies were further made into multiple impacts, and the effect of target curvature and rotation on the impact characteristics. Based on the experimental results, a set of empirical rules and a mathematical model describing hailstone break-up were defined.
Time vs. space in fault-tolerant distributed systems

Algorithms for solving agreement problems can be classified in two categories: (1) those relying on failure detectors (FDs), which we call FD-based, and (2) those that rely on a group membership service (GMS), which we call GMS-based. This paper discusses the advantages and limitations of these two approaches and proposes an extension to the GMS approach that combines the advantages of both approaches, without their drawbacks. This extension leads us to distinguish between time-triggered suspicions of processes and space-triggered exclusions.
Laser-assisted nanoceramics reinforced polymer scaffolds for tissue engineering: additional heating and stem cells behavior

The conditions of selective laser melting (SLM) of tissue engineering scaffolds affect cell response and must be engineered to support cell adhesion, proliferation, and differentiation. In the present study, the influence of additional heating during SLM process on stem cell viability near biopolymer matrix reinforced by nanoceramics additives was carried out. We used the biocompatible and bioresorbable polymers (polyetheretherketone /PEEK/ and polycaprolactone /PCL/) as a matrix and nano-oxide ceramics - TiO2, Al2O3, ZrO2, FexOy and/or hydroxyapatite as a basis of the additives. The rate of pure PEEK and PCL bio-resorption and in mixtures with nano oxides on the matrix was studied by the method of mass loss on bacteria of hydroxylase and enzyme complex. The stem cellular morphology, proliferative MMSC activity, and adhesion of the 2D and 3D nanocomposite matrices were the subjects of comparison. Medical potential of the SLS/M-fabricated nano-oxide ceramics after additional heating as the basis for tissue engineering scaffolds and cell targeting systems were discussed.
Solving Geometry Friends using Monte-Carlo Tree Search with directed graph representation

Geometry Friends is a platform game with two different objects (rectangle and circle). Players can control the geometries to collect all the diamonds in the level. It requires both of efficient path planning and careful objects control with physics law. It has been revealed that it is not easy to achieve human-level performance for the game. In our early work, we show that simple A* search can be used for the problem. Although it's useful, it sometimes falls into local optimum. In this work, we propose to use Monte-Carlo Tree Search (MCTS) to generate plans for the game object. Because the game levels are not suitable for the MCTS, we propose to represent them into a directed graph with special properties. Experimental results demonstrate the potential of the MCTS approach for the Geometry Friends game.
Induction of Inducible Nitric Oxide (NO) Synthase mRNA and NO Production in Macrophages Infected with Influenza A/PR/8 Virus and Stimulated with Its Ether‐Split Product

We investigated the inductive activity of infective influenza A/PR/8/34 (PR8) virus and its ether‐split product (ESP) on the expression of inducible nitric oxide (NO) synthase (iNOS) and NO production in RAW264.7 (RAW) cells, a murine macrophage (MΦ) cell line, and thioglycolate‐elicited peritoneal MΦ (TPM). In both cells, PR8 virus infection induced iNOS mRNA between 4 hr and 24 hr, attaining a peak value at 12 hr. In correlation with induction of iNOS mRNA, NO amounts increased significantly from 12 to 24 hr. Moreover, this study demonstrated that ESP with the same hemagglutination titer as PR8 virus could induce iNOS mRNA and NO production, although the inductive activity of ESP was weaker than that of PR8 virus. Considering the dual role (beneficial and detrimental roles) of NO on certain inflammatory disorders and virus infections, the inductive activity of influenza virus on the iNOS‐mediated NO production independent of its infectivity might contribute to a modification of influenza virus infection.