Protein multiple sequence alignment by hybrid bio-inspired algorithms

This article presents an immune inspired algorithm to tackle the Multiple Sequence Alignment (MSA) problem. MSA is one of the most important tasks in biological sequence analysis. Although this paper focuses on protein alignments, most of the discussion and methodology may also be applied to DNA alignments. The problem of finding the multiple alignment was investigated in the study by Bonizzoni and Vedova and Wang and Jiang, and proved to be a NP-hard (non-deterministic polynomial-time hard) problem. The presented algorithm, called Immunological Multiple Sequence Alignment Algorithm (IMSA), incorporates two new strategies to create the initial population and specific ad hoc mutation operators. It is based on the ‘weighted sum of pairs’ as objective function, to evaluate a given candidate alignment. IMSA was tested using both classical benchmarks of BAliBASE (versions 1.0, 2.0 and 3.0), and experimental results indicate that it is comparable with state-of-the-art multiple alignment algorithms, in terms of quality of alignments, weighted Sums-of-Pairs (SP) and Column Score (CS) values. The main novelty of IMSA is its ability to generate more than a single suboptimal alignment, for every MSA instance; this behaviour is due to the stochastic nature of the algorithm and of the populations evolved during the convergence process. This feature will help the decision maker to assess and select a biologically relevant multiple sequence alignment. Finally, the designed algorithm can be used as a local search procedure to properly explore promising alignments of the search space

Validity Analysis of Wii Balance Board Versus Baropodometer Platform Using an Open Custom Integrated Application

Abstract Standing balance tests represent the most common way to assess person's functional ability and they were realized by means of specialized and expensive platforms, especially in clinicians' environments. Wii Balance Board (WBB) is video-game based device that measures center of pressure (CoP) oscillations and it showed promising performance compared with 'gold standard' force platforms. In this paper we propose an open integrated custom application to define balance outcomes using WBB. These outcomes were used to execute a validity analysis of WBB performance compared with baropodometer platform (BP). Ten subjects performed two standing balance tests with open and closed eyes respectively on WBB and BP in separate occasion. Validity analysis was carried out using r-Pearson correlation coefficient, ICC analysis, paired-sample t-Test and Bland-Altman plots. Results confirmed that the WBB, although has a fraction of cost of other platforms, represents a tool suitable for some clinician analysi

Monolithic patch antenna for dedicated short-range communications

Dedicated short-range communications (DSRCs) is a novel short- to medium-range wireless protocol designed for automotive use. The DSRC signals are circularly polarised and allocated in the 5.8 GHz band. Described is the development of a monolithic and compact patch antenna with left-hand circular polarisation intended for the on-board unit equipment of a DSRC system. The 40×60×2.455 mm fabricated prototype exhibits a circularly-polarised gain of about 5.52 dBc with a cross-polar discrimination of about 20 dB

Design and efficiency analysis of an LCL Capacitive Power Transfer system with Load-Independent ZPA

This paper proposes a design procedure of an LCL compensation circuit for a capacitive power transfer (CPT) system. The design enables the achievement of load independent zero phase angle (ZPA) operation in order to increase the overall efficiency of the system by using a minimum number of compensation components. The proposed approach is supported and validated by circuital simulations and confirmed by the results of experimental tests carried out on a specifically designed prototype

Self-Equilibrium state of V-Expander Tensegrity Beam

In this paper, we study an innovative class of tensegrity beams, obtained by a suitable assembly of elementary V-Expander tensegrity cells along a longitudinal axis in the three-dimensional space. Tensegrity structures, made by struts in compression and cables in tension, are an innovative structures by itself: they are similar only in appearance to conventional pin-joint structures (trusses), and their mechanics is strongly related to initial feasible self-stress states induced in absence of external loads. In particular, from a kinematical point of view these self-stress states avoid the activation of possible infinitesimal mechanisms. By a numerical study, we analyze the feasible self-stress states for lightweight tensegrity beams made by a suitable assembly of V-Expander elementary cells. Moreover, we analyze the influence on the feasible self-stress states of the addition of struts or cables starting from the simplest V-Expander configuration

Chromosome 18q-Syndrome and 1p terminal duplication in a patient with bilateral vesicoureteral reflux: case report and literature revision

Background: Vesico-ureteral reflux (VUR) is a dynamic event in which a retrograde flow of urine is present into the upper tracts. VUR may occur isolated or in association with other congenital abnormalities or as part of syndromic entities. We present a patient with a bilateral primary VUR, syndromic disease caused by a large deletion of 18q (18q21.3-qter) and terminal duplication of 1p (1p36.32-p36.33). Case report: The patient was 8 years old female with a disease including moderate growth retardation, psychomotor retardation, facial dysmorphism, single umbilical artery, umbilical hernia, urachal remnant, bilateral congenital clubfeet and renal-urinary disease. Chromosomal analysis and Array-CGH revealed two heterozygous chromosomal rearrangements: 1p terminal duplication and de novo 18q terminal deletion. She referred to our clinic to evaluation of bilateral hydronephrosis and right renal cortex thinning. Voiding cystourethrography demonstrated bilateral grade IV VUR and dimercaptosuccinic acid renal scintigraphy confirmed right renal cortex thinning and showed a cortical uptake of 75% of the left kidney and 25% of the right kidney. The patient underwent ureterovesical reimplantation after failure of 3 endoscopic submeatal Deflux injections with VUR resolution. Conclusions: This is the first report involving a patient with 18q-syndrome and contemporary presence of 1p chromosomal terminal duplication. The coexistence of two chromosomal rearrangements complicates the clinical picture and creates a chimeric disorder (marked by characteristics of both chromosomal anomalies). Kidney problems, primarily VUR is reported in 15% of patients affected by 18-q syndrome and no cases is reported in the literature regarding a correlation between VUR and 1p36 chromosomal duplication

Acute Glomerulonephritis in a Child with Chlamydia pneumoniae Infection: A Case Report.

Background. Infectious diseases seem to be an important and independent risk factor for renal failure, but the underlying mechanism of renal involvement during some kinds of infectious diseases is still unclear, even if the literature data report immunomediated and/or autoimmune mechanisms to explain the pathogenic relationship between the two diseases. In paediatric patients, Chlamydia pneumoniae is a rare cause of renal complications and it may manifest in several ways, mainly involving the respiratory system, even if also renal and glomerulalr complications, have been described. Case Diagnosis/Treatment. Herein we report a case of a 3-year-old child who developed an acute glomerulonephritis that was chronologically, clinically, and biologically related to a previous Chlamydia pneumoniae infection. On our knowledge, in the literature it is the youngest patient with renal involvement during course of Chlamydia pneumoniae infection ever reported. Conclusions. The present case supports the hypothesis of a rather close causal relationship between this infective agent and renal and glomerular symptoms occurred in this child, during an acute episode of respiratory disease

Discovering anomalies in big data: a review focused on the application of metaheuristics and machine learning techniques

With the increase in available data from computer systems and their security threats, interest in anomaly detection has increased as well in recent years. The need to diagnose faults and cyberattacks has also focused scientific research on the automated classification of outliers in big data, as manual labeling is difficult in practice due to their huge volumes. The results obtained from data analysis can be used to generate alarms that anticipate anomalies and thus prevent system failures and attacks. Therefore, anomaly detection has the purpose of reducing maintenance costs as well as making decisions based on reports. During the last decade, the approaches proposed in the literature to classify unknown anomalies in log analysis, process analysis, and time series have been mainly based on machine learning and deep learning techniques. In this study, we provide an overview of current state-of-the-art methodologies, highlighting their advantages and disadvantages and the new challenges. In particular, we will see that there is no absolute best method, i.e., for any given dataset a different method may achieve the best result. Finally, we describe how the use of metaheuristics within machine learning algorithms makes it possible to have more robust and efficient tools

Molecular Mechanisms Mediating Antiangiogenic Action of the Urokinase Receptor-Derived Peptide UPARANT in Human Retinal Endothelial Cells

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Learning Robust Dynamic Networks in Prokaryotes by Gene Expression Networks Iterative Explorer (GENIE)

Genetic and genomic approaches have been used successfully to assign genes to distinct regulatory networks, but the uncertainty concerning the connec tions between genes, the ambiguity inherent to the biological processes, and the impossibility of experimentally determining the underlying biological properties only allow a rough prediction of the dynamics of genes. Here we describe the GE NIE methodology that formulates alternative models of genetic regulatory networks based on the available literature and transcription factor binding site evidence. It also provides a framework for the analysis of these models optimized by genetic algorithms, inferring their optimal parameters, simulating their behavior, evaluat ing them by integrating robustness, realness and flexibility criteria, and contrasting the predictions to experimentally results obtained by Gene Fluorescence Protein analysis. The application of this method to the regulatory network of the bacterium Salmonella enterica uncovered new mechanisms that enable the inter-connection of the PhoP/PhoQ and the PmrA/PmrB two component systems. The predictions were experimentally verified to establish that both transcriptional and post-transcriptional mechanisms are employed to connect these two systems.Ministerio de Ciencia y Tecnología BIO2004-0270-