Evolutionary Generalized Radial Basis Function neural networks for improving prediction accuracy in gene classification using feature selection

Radial Basis Function Neural Networks (RBFNNs) have been successfully employed in several function approximation and pattern recognition problems. The use of different RBFs in RBFNN has been reported in the literature and here the study centres on the use of the Generalized Radial Basis Function Neural Networks (GRBFNNs). An interesting property of the GRBF is that it can continuously and smoothly reproduce different RBFs by changing a real parameter τ. In addition, the mixed use of different RBF shapes in only one RBFNN is allowed. Generalized Radial Basis Function (GRBF) is based on Generalized Gaussian Distribution (GGD), which adds a shape parameter, τ, to standard Gaussian Distribution. Moreover, this paper describes a hybrid approach, Hybrid Algorithm (HA), which combines evolutionary and gradient-based learning methods to estimate the architecture, weights and node topology of GRBFNN classifiers. The feasibility and benefits of the approach are demonstrated by means of six gene microarray classification problems taken from bioinformatic and biomedical domains. Three filters were applied: Fast Correlation-Based Filter (FCBF), Best Incremental Ranked Subset (BIRS), and Best Agglomerative Ranked Subset (BARS); this was done in order to identify salient expression genes from among the thousands of genes in microarray data that can directly contribute to determining the class membership of each pattern. After different gene subsets were obtained, the proposed methodology was performed using the selected gene subsets as new input variables. The results confirm that the GRBFNN classifier leads to a promising improvement in accuracy.     

Searching in peer-to-peer networks

As peer-to-peer networks are proving capable of handling huge volumes of data, the need for effective search tools is lasting and imperative. During the last years, a number of research studies have been published, which attempt to address the problem of search in large, decentralized networks. In this article, we mainly focus on content and concept-based retrieval. After providing a useful discussion on terminology, we introduce a representative sample of such studies and categorize them according to basic functional and non-functional characteristics. Following our analysis and discussion we conclude that future work should focus on information filtering, re-ranking and merging of results, relevance feedback and content replication as well as on related user-centric aspects of the problem.     

Changes in free amino acids content in albacore (Thunnus alalunga) muscle during thermal processing

Summary The effects of cooking and sterilization at several temperatures on the free amino acids (FAA) content in albacore (Thunnus alalunga) muscle were studied during the processing of canned tuna. FAAs were derivatized witho-phtalaldehyde, separated on a C18 column by HPLC and detected by both fluorescence and ultra-violet detectors. After cooking the loss of FAAs was not significant. However, in the final product sterilized at 115 °C and 110 °C (throughout the whole process) there were significant losses with regard to the start material, but not at 118 °C (all temperatures leading to the same lethal F-value). The influence of the thermal process time at 115 °C was evaluated for 60 and 100 min. Significant losses were found between both canned products (25%) and between the raw fish and the final product (12% and 34%, process time 60 and 100 min, respectively). The determination of the content of FAA present in canned albacore may be a useful indication of the severity of the thermal processing.

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Veränderung im Gehalt an freien Aminosäuren in Thunfischmuskel (Tunnus alalunga) während der Wärmebehandlung

Zusammenfassung Die Wirkung des Kochens und Sterilisierens bei verschiedenen Temperaturen auf den Gehalt an freien Aminosäuren (FAA) im Thunfischmuskel (Thunnus alalunga) wurde während der Herstellung von Thunfischkonserven untersucht. Die freien Aminosäuren wurden mito-Phtalaldehyd derivatisiert, auf einer C-18-Kolonne mit HPLC abgetrennt und durch Fluorescenz und UV-Detektoren nachgewiesen. Nach dem Kochen war der Verlust an FAA nicht signifikant, jedoch in dem bei 110° und 115 °C sterilisierten Endprodukt ergaben sich signifikante Verluste bezogen auf das Ausgangsmaterial, aber nicht auf das bei 118 °C erhitzte; alle Erhitzungstemperaturen führen zu demselben letalen F-Wert. Der Zeiteinfluß der Erhitzung bei 115 °C wurde bei 60 und 100 min bewertet. Signifikante Verluste sind bei beiden Dosenkonserven aufgetreten (25%) und zwischen diesen und dem Rohfisch ( 12% und 34%) bei einer Erhitzungszeit von 60 und 100 min). Die Bestimmung des FAA-Gehalts in Thunfischkonserven kann für den Nachweis der Einwandfreiheit des thermischen Prozesses sehr nützlich sein.

     

Interpretation of long-chain structure from dilute solution properties of ultrahigh molecular weight polymers

Summary Systematic studies on solution properties of ultrahigh molecular weight polymers showed the existence of some special features as compared to usual length polymers. The paper discusses the possible appearance of branched structures in the polymerization process, structures able to influence the mentioned features. From experimental data on poly(methyl methacrylate), poly(butyl methacrylate) and polyacrylonitrile it appears that branching can be excluded, and the very high molecular weight domain considered may be responsible for the modifications observed in the molecular weight dependences on 2>, A₂ or [].     

Electrospun fibers based on porcine plasma: a rheological and morphological study

Iranian Polymer Journal - The present work focuses on the assessment of the ability of porcine plasma protein (PPP) to be electrospun satisfactorily to form fibre mats, and their rheological and...     

Genetic Insight into the Domain Structure and Functions of Dicer-Type Ribonucleases

Ribonuclease Dicer belongs to the family of RNase III endoribonucleases, the enzymes that specifically hydrolyze phosphodiester bonds found in double-stranded regions of RNAs. Dicer enzymes are mostly known for their essential role in the biogenesis of small regulatory RNAs. A typical Dicer-type RNase consists of a helicase domain, a domain of unknown function (DUF283), a PAZ (Piwi-Argonaute-Zwille) domain, two RNase III domains, and a double-stranded RNA binding domain; however, the domain composition of Dicers varies among species. Dicer and its homologues developed only in eukaryotes; nevertheless, the two enzymatic domains of Dicer, helicase and RNase III, display high sequence similarity to their prokaryotic orthologs. Evolutionary studies indicate that a combination of the helicase and RNase III domains in a single protein is a eukaryotic signature and is supposed to be one of the critical events that triggered the consolidation of the eukaryotic RNA interference. In this review, we provide the genetic insight into the domain organization and structure of Dicer proteins found in vertebrate and invertebrate animals, plants and fungi. We also discuss, in the context of the individual domains, domain deletion variants and partner proteins, a variety of Dicers’ functions not only related to small RNA biogenesis pathways.     

Functionalized Reduced Graphene Oxide as a Versatile Tool for Cancer Therapy

Cancer is one of the deadliest diseases in human history with extremely poor prognosis. Although many traditional therapeutic modalities—such as surgery, chemotherapy, and radiation therapy—have proved to be successful in inhibiting the growth of tumor cells, their side effects may vastly limited the actual benefits and patient acceptance. In this context, a nanomedicine approach for cancer therapy using functionalized nanomaterial has been gaining ground recently. Considering the ability to carry various anticancer drugs and to act as a photothermal agent, the use of carbon-based nanomaterials for cancer therapy has advanced rapidly. Within those nanomaterials, reduced graphene oxide (rGO), a graphene family 2D carbon nanomaterial, emerged as a good candidate for cancer photothermal therapy due to its excellent photothermal conversion in the near infrared range, large specific surface area for drug loading, as well as functional groups for functionalization with molecules such as photosensitizers, siRNA, ligands, etc. By unique design, multifunctional nanosystems could be designed based on rGO, which are endowed with promising temperature/pH-dependent drug/gene delivery abilities for multimodal cancer therapy. This could be further augmented by additional advantages offered by functionalized rGO, such as high biocompatibility, targeted delivery, and enhanced photothermal effects. Herewith, we first provide an overview of the most effective reducing agents for rGO synthesis via chemical reduction. This was followed by in-depth review of application of functionalized rGO in different cancer treatment modalities such as chemotherapy, photothermal therapy and/or photodynamic therapy, gene therapy, chemotherapy/phototherapy, and photothermal/immunotherapy.     

Early Lipid Raft-Related Changes: Interplay between Unilateral Denervation and Hindlimb Suspension

Muscle disuse and denervation leads to muscle atrophy, but underlying mechanisms can be different. Previously, we have found ceramide (Cer) accumulation and lipid raft disruption after acute hindlimb suspension (HS), a model of muscle disuse. Herein, using biochemical and fluorescent approaches the influence of unilateral denervation itself and in combination with short-term HS on membrane-related parameters of rat soleus muscle was studied. Denervation increased immunoexpression of sphingomyelinase and Cer in plasmalemmal regions, but decreased Cer content in the raft fraction and enhanced lipid raft integrity. Preliminary denervation suppressed (1) HS-induced Cer accumulation in plasmalemmal regions, shown for both nonraft and raft-fractions; (2) HS-mediated decrease in lipid raft integrity. Similar to denervation, inhibition of the sciatic nerve afferents with capsaicin itself increased Cer plasmalemmal immunoexpression, but attenuated the membrane-related effects of HS. Finally, both denervation and capsaicin treatment increased immunoexpression of proapoptotic protein Bax and inhibited HS-driven increase in antiapoptotic protein Bcl-2. Thus, denervation can increase lipid raft formation and attenuate HS-induced alterations probably due to decrease of Cer levels in the raft fraction. The effects of denervation could be at least partially caused by the loss of afferentation. The study points to the importance of motor and afferent inputs in control of Cer distribution and thereby stability of lipid rafts in the junctional and extrajunctional membranes of the muscle.     

Diabetes during Pregnancy: A Maternal Disease Complicating the Course of Pregnancy with Long-Term Deleterious Effects on the Offspring. A Clinical Review

In spite of the huge progress in the treatment of diabetes mellitus, we are still in the situation that both pregestational (PGDM) and gestational diabetes (GDM) impose an additional risk to the embryo, fetus, and course of pregnancy. PGDM may increase the rate of congenital malformations, especially cardiac, nervous system, musculoskeletal system, and limbs. PGDM may interfere with fetal growth, often causing macrosomia, but in the presence of severe maternal complications, especially nephropathy, it may inhibit fetal growth. PGDM may also induce a variety of perinatal complications such as stillbirth and perinatal death, cardiomyopathy, respiratory morbidity, and perinatal asphyxia. GDM that generally develops in the second half of pregnancy induces similar but generally less severe complications. Their severity is higher with earlier onset of GDM and inversely correlated with the degree of glycemic control. Early initiation of GDM might even cause some increase in the rate of congenital malformations. Both PGDM and GDM may cause various motor and behavioral neurodevelopmental problems, including an increased incidence of attention deficit hyperactivity disorder (ADHD) and autism spectrum disorder (ASD). Most complications are reduced in incidence and severity with the improvement in diabetic control. Mechanisms of diabetic-induced damage in pregnancy are related to maternal and fetal hyperglycemia, enhanced oxidative stress, epigenetic changes, and other, less defined, pathogenic mechanisms.     

Ivabradine Induces Cardiac Protection against Myocardial Infarction by Preventing Cyclophilin-A Secretion in Pigs under Coronary Ischemia/Reperfusion

In response to cardiac ischemia/reperfusion, proteolysis mediated by extracellular matrix metalloproteinase inducer (EMMPRIN) and its secreted ligand cyclophilin-A (CyPA) significantly contributes to cardiac injury and necrosis. Here, we aimed to investigate if, in addition to the effect on the funny current (I(f)), Ivabradine may also play a role against cardiac necrosis by reducing EMMPRIN/CyPA-mediated cardiac inflammation. In a porcine model of cardiac ischemia/reperfusion (IR), we found that administration of 0.3 mg/kg Ivabradine significantly improved cardiac function and reduced cardiac necrosis by day 7 after IR, detecting a significant increase in cardiac CyPA in the necrotic compared to the risk areas, which was inversely correlated with the levels of circulating CyPA detected in plasma samples from the same subjects. In testing whether Ivabradine may regulate the levels of CyPA, no changes in tissue CyPA were found in healthy pigs treated with 0.3 mg/kg Ivabradine, but interestingly, when analyzing the complex EMMPRIN/CyPA, rather high glycosylated EMMPRIN, which is required for EMMPRIN-mediated matrix metalloproteinase (MMP) activation and increased CyPA bonding to low-glycosylated forms of EMMPRIN were detected by day 7 after IR in pigs treated with Ivabradine. To study the mechanism by which Ivabradine may prevent secretion of CyPA, we first found that Ivabradine was time-dependent in inhibiting co-localization of CyPA with the granule exocytosis marker vesicle-associated membrane protein 1 (VAMP1). However, Ivabradine had no effect on mRNA expression nor in the proteasome and lysosome degradation of CyPA. In conclusion, our results point toward CyPA, its ligand EMMPRIN, and the complex CyPA/EMMPRIN as important targets of Ivabradine in cardiac protection against IR.