Miracle-dz/UniFAR-FTUs huggingface dataset:
Applications of RNA Interference in Mammalian

RNA interference (RNAi) can mediate the long- or short-term si- lencing of gene expression at the DNA, RNA, and/or protein level. Although several triggers of RNAi have been identified, the best characterized of these are small interfering RNAs (siRNAs), which can decrease gene expression through mRNA transcript cleavage, and endogenous microRNAs (miRNAs), which primarily inhibit protein translation. An improved understanding of RNAi has pro- vided new, powerful tools for conducting functional studies in a gene- specific manner. In various applications, RNAi has been used to cre- ate model systems, to identify novel molecular targets, to study gene function in a genome-wide fashion, and to create new avenues for clinical therapeutics. Here, we review many of the ongoing applica- tions of RNAi in mammalian and human systems, and discuss how advances in our knowledge of the RNAi machinery have enhanced the use of these technologies.
PRECISO: A Reverse Engineering Tool to Discover Web Services from Relational Databases

There is a real need for SOA principles, such as those offering software as services, in the software industry. In this effort, databases (one of the most important artifacts in Information Systems) can be also seen as a set of services offering access to the stored information. This paper presents PRECISO, a reverse engineering tool to discover and generate Web Services automatically from relational databases. PRECISO makes it possible to modernize legacy databases by introducing them in an SOA context by means of the generated services. This tool was used in a real-life case study in the context of a software company.
Mapping of environment , Detection and Tracking of Moving Objects using Occupancy Grids

In this paper, we present a real-time algorithm for local simultaneous localization and mapping (SLAM) with detection and tracking of moving objects (DATMO) in dynamic outdoor environments from a moving vehicle equipped with a laser scanner and two radars. To correct vehicle location from odometry we introduce a new fast implementation of incremental scan matching method that can work reliably in dynamic outdoor environments. After a good vehicle location is estimated, the surrounding map is updated incrementally and moving objects are detected without a priori knowledge of the targets. Detected moving objects are finally tracked by a Multiple Hypothesis Tracker (MHT) coupled with an adaptive IMM (Interacting Multiple Models) Filter. The experimental results on datasets collected from different scenarios such as: urban streets, country roads and highways demonstrate the efficiency of the proposed algorithm on a Daimler Mercedes demonstrator in the framework of the European Project PReVENT-ProFusion2.
PTEN enters the nucleus by diffusion

Despite much evidence for phosphatidylinositol phosphate (PIP)‐triggered signaling pathways in the nucleus, there is little understanding of how the levels and activities of these proteins are regulated. As a first step to elucidating this problem, we determined whether phosphatase and tensin homolog deleted on chromosome 10 (PTEN) enters the nucleus by passive diffusion or active transport. We expressed various PTEN fusion proteins in tsBN2, HeLa, LNCaP, and U87MG cells and determined that the largest PTEN fusion proteins showed little or no nuclear localization. Because diffusion through nuclear pores is limited to proteins of 60,000 Da or less, this suggests that nuclear translocation of PTEN occurs via diffusion. We examined PTEN mutants, seeking to identify a nuclear localization signal (NLS) for PTEN. Mutation of K13 and R14 decreased nuclear localization, but these amino acids do not appear to be part of an NLS. We used fluorescence recovery after photobleaching (FRAP) to demonstrate that GFP‐PTEN can passively pass through nuclear pores. Diffusion in the cytoplasm is retarded for the PTEN mutants that show reduced nuclear localization. We conclude that PTEN enters the nucleus by diffusion. In addition, sequestration of PTEN in the cytoplasm likely limits PTEN nuclear translocation. © 2005 Wiley‐Liss, Inc.
Logging in the Age of Web Services

In today's age of Web applications connected via Web services, accountability has become both crucial and harder to achieve. The management of authentication, authorization, and accountability in these applications is therefore a very important and difficult problem to solve. In this article, we describe how audit logging can be built into the Web services infrastructure.
Face recognition using extended local binary patterns and fuzzy information fusion

This paper presents a novel and efficient approach for face recognition based on extended local binary patterns (LBP) and fuzzy information fusion. Each facial image in training set is divided into a certain number of sub-regions after a simple image preprocessing, and all training sub-regions from the same position construct a new training subset. The extended LBP method is used to extract local feature of the new training subset independently and then a set of feature histogram vectors can be obtained. For a given unknown facial image, sub-feature histogram vectors of corresponding sub-region are gained after the same preprocessing and partition. The χ2 distances between test sub-regions' histogram and trainings' are obtained to calculate their membership grade. After fuzzy classification of local sub-features, strategy of fuzzy integrate is adopted to fuse each of them. At last the result of classification is determined by the principle of maximum membership. Experimental results on the ORL and FERET databases show competitive performance.
Ultrasonic method of microvibration detection: part II - additional processing method and applications

Introduction: In the last 28 years, the scientific community has been using elastography to evaluate the mechanical properties of biological tissue. The aim of this work was the optimization of the UDmV method, presented in Part I of the series, by means of modifying the technique employed to generate the reference sine and cosine functions, used for phase-quadrature demodulation, and determining how this modification improved the performance of the method. Additionally, the UDmV was employed to characterize the acoustic and mechanical properties of a 7% gelatin phantom. Methods: A focused transducer, F T , with a nominal frequency of 2.25 MHz, was used to induce the shear waves, with frequency of 97.644 Hz. Then, the modified UDmV method was used to extract the phase and quadrature components from ultrasonic RF echo-signals collected from four positions along the propagation path of the shear wave, which allowed the investigation of the medium vibration caused by wave propagation. The phase velocity, s c , and attenuation, as, of the phantom were measured and employed in the calculation of shear modulus, μ, and viscosity, η. Results: The computational simulation demonstrated that the modification in UDmV method resulted in more accurate and precise estimates of the initial phases of the reference sinusoidal functions used for phase-quadrature demodulation. The values for s c and μ of 1.31 ± 0.01 m·s-1 and 1.66 ± 0.01 kPa, respectively, are very close to the values found in the literature (1.32 m·s-1 and 1.61 kPa) for the same material. Conclusion: The UDmV method allowed estimating of the acoustic and viscoelastic parameters of phantom.
Performance Evaluation Metric for Cooperative Sensing in Heterogeneous Radio Environments

Spectrum sensing is a major task for wireless devices in order to improve coexistence among them in heterogeneous radio environments. Wireless communication includes at least two partners: transmitter and receiver. Therefore, cooperation between partners can improve the performance of spectrum sensing by reducing effort, improving sensing result or a combination of both. An optimal cooperative sensing scheme is a first step to achieve complete awareness of the radio environment for wireless devices. To the best of our knowledge, this is the first theoretical work performed in order to understand the problem of developing optimal cooperative sensing schemes for heterogeneous radio environments for multiple users and single channel. We analyze the problem and perform analytical work which results in a cooperative sensing model. The model comprises sensing schedule, data fusion rules, PU's traffic pattern, and detection performance of the sensing device. A new performance evaluation metric is introduced for optimum spectrum sensing in heterogeneous radio environments. An evaluation of available exemplary cooperative sensing schemes shows that none provides optimality in all scenarios.
A Versatile Multilevel Converter Platform for Cancer Treatment Using Irreversible Electroporation

Electroporation is an effective technique based on applying an electric field to cells, commonly used to increase the effectivity of drug and gene delivery. When the applied electric field is strong enough, it can be used for selective cell death with promising results in cancer treatment. This paper proposes the development of a modular multilevel topology in order to provide a high-performance tool for research in electroporation. The proposed converter based on a scalable multicell approach is detailed and analyzed in this paper, and an experimental prototype has been designed and built. The experimental results prove the feasibility of this proposal to enable advanced electroporation techniques.
Temporin-SHf, a New Type of Phe-rich and Hydrophobic Ultrashort Antimicrobial Peptide*

Because issues of cost and bioavailability have hampered the development of gene-encoded antimicrobial peptides to combat infectious diseases, short linear peptides with high microbial cell selectivity have been recently considered as antibiotic substitutes. A new type of short antimicrobial peptide, designated temporin-SHf, was isolated and cloned from the skin of the frog Pelophylax saharica. Temporin-SHf has a highly hydrophobic sequence (FFFLSRIFa) and possesses the highest percentage of Phe residues of any known peptide or protein. Moreover, it is the smallest natural linear antimicrobial peptide found to date, with only eight residues. Despite its small size and hydrophobicity, temporin-SHf has broad-spectrum microbicidal activity against Gram-positive and Gram-negative bacteria and yeasts, with no hemolytic activity. CD and NMR spectroscopy combined with restrained molecular dynamics calculations showed that the peptide adopts a well defined non-amphipathic α-helical structure from residue 3 to 8, when bound to zwitterionic dodecyl phosphocholine or anionic SDS micelles. Relaxation enhancement caused by paramagnetic probes showed that the peptide adopts nearly parallel orientations to the micelle surface and that the helical structure is stabilized by a compact hydrophobic core on one face that penetrates into the micelle interior. Differential scanning calorimetry on multilamellar vesicles combined with membrane permeabilization assays on bacterial cells indicated that temporin-SHf disrupts the acyl chain packing of anionic lipid bilayers, thereby triggering local cracks and microbial membrane disintegration through a detergent-like effect probably via the carpet mechanism. The short length, compositional simplicity, and broad-spectrum activity of temporin-SHf make it an attractive candidate to develop new antibiotic agents.
Fourier Transform Infrared (FTIR) Spectroscopy of Biological Tissues

Abstract This article reviews some of the recent advances on FTIR spectroscopy in areas related to natural tissues and cell biology. It is the second review publication resulting from a detailed study on the applications of spectroscopic methods in biological studies and summarizes some of the most widely used peak frequencies and their assignments. The aim of these studies is to prepare a database of molecular fingerprints, which will help researchers in defining the chemical structure of the biological tissues introducing most of the important peaks present in the natural tissues. In spite of applying different methods, there seems to be a considerable similarity in defining the peaks of identical areas of the FTIR spectra. As a result, it is believed that preparing a unique collection of the frequencies encountered in FTIR spectroscopic studies can lead to significant improvements both in the quantity and quality of research and their outcomes. This article is the first review of its kind that provides a precise database on the most important FTIR characteristic peak frequencies for researchers aiming to analyze natural tissues by FTIR spectroscopy and will be of considerable assistance to those who are focusing on the analysis of cancerous tissues by FTIR spectroscopy.
Genetic Correlations of Brain Lesion Distribution in Multiple Sclerosis: An Exploratory Study

BACKGROUND AND PURPOSE: In MS, the total brain lesion volume and spatial distribution of lesions across the brain vary widely among individual patients. We hypothesized that spatial distribution may be partially driven by genetic predisposition, and we aimed to explore relations among candidate genes and the spatial distribution of white matter brain lesions in MS. MATERIAL AND METHODS: Genotypes of 69 SNPs in 208 patients with MS were related to the spatial distribution of T2 brain lesions. Lesions were manually outlined on MR images, and binary lesion masks were produced and registered to a common space. With Randomise software, the lesion masks were related to genotype by using a voxelwise nonparametric GLM approach, followed by clusterwise analysis. We used a DNA chip with SNPs selected from the literature on MS susceptibility, severity, and phenotypes. RESULTS: For 11 of these SNPs, 1 of the genotypes expressed significant clusters of increased or decreased lesion probability in varying, predominantly periventricular, brain regions. When we statistically controlled the voxelwise analyses for effects of total brain lesion volume, only 1 SNP remained significant: rs2227139, located within the MHC class II region. This SNP retained its periventricular cluster of significantly increased lesion probability for the heterozygote genotype. CONCLUSIONS: Heterozygosity of rs2227139 (MHC class II region) is associated with increased right frontal periventricular lesion probability (P < .01). Ten other SNPs showed associations between genotype and spatial lesion distribution that are partly explained by total lesion volume.
Hidden conic representation of indefinite linear quadratic control

The traditional linear quadratic control can be solved elegantly via the classical algebraic Riccati equation. Unfortunately, this Riccati approach is rather limitation to handle the indefinite linear quadratic control, since the inverse(generalized inverse) of indefinite matrix is hard to express. The semidefinite programming(or linear matrix inequality) based approach could tackle indefinite linear quadratic control in a few cases, however, the complexity of solving the semidefinite programming is impractical for real-time control, especial in large scale problem. In this paper, we discuss two classes of indefinite linear quadratic control, the corresponding conic quadratic formulations are derived. An attractive feature of the proposed formulations is the numerical tractability, especially when compared to approaches based on semidefinite programming.
Performance analysis of an MPEG-II audio/video player

An MPEG audio/video player in software is implemented on a commercial operating system and is detailed evaluated. The primary purpose of this work is to explore new system technologies in quality-of-service (QoS) support for advanced multimedia applications. Here, we address the performance analysis of this software-MPEC-II player and report the experiences in performance tuning and QoS enhancements via empirical experiments.
Impact of buffer composition on the dynamic on-state resistance of high-voltage AlGaN/GaN HFETs

Switching experiments with normally-off GaN-HFETs using a carbon-doped GaN buffer or an AlGaN buffer showed very different magnitudes of increased dynamic on-state resistance. The dynamic on-state resistance is analyzed for variations in buffer composition and set into relation to the buffer voltage-blocking strength. Also, the impact of p-GaN gate normally-off and Schottky-gate normally-on device technologies on the dispersion is studied. It is concluded that a buffer with less trap sites and lower breakdown strength is more favorable for high-voltage switching than a buffer with incorporated acceptors to increase the buffer breakdown strength.
Secure data transmission in wireless sensor networks

Today a growing number of applications, in particular in the area of cyber-physical systems (CPS), depend on data collected by wireless sensor networks. The individual nodes of these networks have severe resource limitations, concerning storage, processing, and transmission capabilities, but also concerning energy available for communication functions. Supporting the required protocol functionality in combination with the goal of energy-saving operation typically results in the development of proprietary, highly specialized communication protocols for wireless sensor networks. However, with Internet technology as the dominating communication paradigm for a wide range of application areas, it became an attractive goal to be able to use Internet protocols within wireless sensor networks. An important functionality within wireless sensor networks is data gathering and aggregation. An Internet protocol standardized within IETF that supports this functionality is the ‘IP Flow Information Export’ (IPFIX) protocol. In this thesis, concepts for adapting the IPFIX protocol to the needs of wireless sensor networks have been investigated, resulting in the development of the protocol TinyIPFIX, which is an adaptation of the ‘IP Flow Information Export’ (IPFIX) protocol. The new protocol has been assessed in a representative use case involving a building application. TinyIPFIX has been extended by compression capabilities and by aggregation functionality. Furthermore, extensions to support secure data transmission have been developed, using the protocol ‘Datagram Transport Layer Security’ (DTLS). This solution ensures that data collected by sensor nodes is transmitted via secure channels to a global data sink, and that authorised access is ensured from a data sink to a wireless sensor network. For validation, a system has been realized that allows configuration of the networks components dynamically, and that supports visualization of the current network status and the collected data in real time.
Typing of clinical herpes simplex virus isolates with mouse monoclonal antibodies to herpes simplex virus types 1 and 2: comparison with type-specific rabbit antisera and restriction endonuclease analysis of viral DNA

A total of 122 clinical isolates of herpes simplex virus (HSV) from 107 patients were typed by using an indirect immunoperoxidase technique with commercially available type-specific rabbit antisera, recently developed mouse monoclonal antibodies to HSV types 1 and 2, and restriction endonuclease analysis of viral DNA. With the commercially available type-specific rabbit antisera, 34% of clinical HSV isolates were of indeterminate type; 63% of them were typed as HSV type 1 and 37% as HSV type 2 by using monoclonal antibody and restriction enzyme typing systems. Typing by immunofluorescence assay with the monoclonal antibodies gave identical results to those obtained by restriction enzyme analysis. Simultaneous infection with both HSV types was demonstrated by monoclonal antibody typing in five isolates from three patients. These findings were subsequently confirmed by plaque purification and restriction endonuclease analysis of viral DNA. Monoclonal antibodies were as sensitive as restriction enzyme analysis for the typing of clinical HSV isolates. Because of their simplicity, they are more amenable to use in clinical laboratories than is restriction endonuclease analysis.
K-nearest neighbor classifier for signature verification system

The paper presents an off-line signature verification system using k-nearest neighbor classifier. Global features from the signatures are extracted using radon transform. For each registered user in the system database a number of reference signatures are enrolled and aligned for statistics information extraction about his signature. Extreme points warping algorithm is used to align two signatures. During the k-nearest neighbor classifier training, a number of genuine and forged signatures are chosen. A test signature's verification is established by first aligning it with each reference signature for the claimed user. The signature is then classified as genuine or forgery, according to the alignment scores which are normalized by reference statistics, using standard pattern classification techniques. Using a database of 2250 signatures (genuine signatures and skilled forgeries) from 75 writers in the proposed signature verification system a performance of approximately 80% is achieved.
Ramp rate control and voltage regulation for grid directly connected wind turbines

This paper introduces a methodology to enhance the quality of the voltage and power produced from fixed-speed direct-connected wind turbines. The method uses an electrolyzer/fuel cell combination to be connected to the point of common coupling via limited rating converters. The control scheme is designed to keep the power ramp rate and voltage fluctuation within their limits and to minimize the rating of the converters used to interface the electrolyzer and the fuel cell. Intensive simulation results are carried out to demonstrate and validate the proposed technique.
Symmetrical criterion of random distribution discrimination

The paper deals with the problem of discrimination of stochastic distributions. In contrast to Kullback's measure, an easily calculated symmetrical metrized criterion is proposed. Its numerical value lies in interval [0,1] irrespective of the type of compared distributions. Examples of calculation of the criterion for typical distributions are given.
A Middle Timnian Nomadic Encampment on the Faynan-Beersheba Road: Excavations and Survey at Nahal Tsafit (Late 5th/Early 4th Millennia B.C.E.)

Excavations at Nahal Tsafit, on the Rotem Plain in the northeastern Negev, have uncovered a Middle Timnian encampment dated to the late 5th/early 4th millennia B.C.E. A large tumulus field, comprising 115 large cairns and three open-air shrines characteristic of the early phases of Timnian culture, was surveyed on the ridge above the site. Although contemporary with the Ghassulian-Beersheba Chalcolithic culture of the settled zone, the architecture revealed and material culture recovered from excavation of the encampment place it clearly in Middle Timnian culture, the desert complement to the Ghassulian. The location of the site on the road between Beersheba and Faynan, and the presence of potsherds originating in Faynan, suggest Timnian involvement in the early copper trade.
Raptor codes on symmetric channels

This paper extends the construction and analysis of Raptor codes originally designed in A. Shokrollahi (2004) for the erasure channel to general symmetric channels. We explicitly calculate the asymptotic fraction of output nodes of degree one and two for capacity-achieving Raptor codes, and discuss techniques to optimize the output degree distribution.