Clustering with neural networks

Partitioning a set ofN patterns in ad-dimensional metric space intoK clusters — in a way that those in a given cluster are more similar to each other than the rest — is a problem of interest in many fields, such as, image analysis, taxonomy, astrophysics, etc. As there are approximatelyK ^N/K! possible ways of partitioning the patterns amongK clusters, finding the best solution is beyond exhaustive search whenN is large. We show that this problem, in spite of its exponential complexity, can be formulated as an optimization problem for which very good, but not necessarily optimal, solutions can be found by using a Hopfield model of neural networks. To obtain a very good solution, the network must start from many randomly selected initial states. The network is simulated on the MPP, a 128 × 128 SIMD array machine, where we use the massive parallelism not only in solving the differential equations that govern the evolution of the network, but also in starting the network from many initial states at once thus obtaining many solutions in one run. We achieve speedups of two to three orders of magnitude over serial implementations and the promise through Analog VLSI implementations of further speedups of three to six orders of magnitude.Supported by a National Research Council-NASA Research Associatship     

Soluble Sema4D cleaved from osteoclast precursors by TACE suppresses osteoblastogenesis

Bone remodelling is mediated by orchestrated communication between osteoclasts and osteoblasts which, in part, is regulated by coupling and anti-coupling factors. Amongst formally known anti-coupling factors, Semaphorin 4D (Sema4D), produced by osteoclasts, plays a key role in downmodulating osteoblastogenesis. Sema4D is produced in both membrane-bound and soluble forms; however, the mechanism responsible for producing sSema4D from osteoclasts is unknown. Sema4D, TACE and MT1-MMP are all expressed on the surface of RANKL-primed osteoclast precursors. However, only Sema4D and TACE were colocalized, not Sema4D and MT1-MMP. When TACE and MT1-MMP were either chemically inhibited or suppressed by siRNA, TACE was found to be more engaged in shedding Sema4D. Anti-TACE-mAb inhibited sSema4D release from osteoclast precursors by ~90%. Supernatant collected from osteoclast precursors (OC-sup) suppressed osteoblastogenesis from MC3T3-E1 cells, as measured by alkaline phosphatase activity, but OC-sup harvested from the osteoclast precursors treated with anti-TACE-mAb restored osteoblastogenesis activity in a manner that compensates for diminished sSema4D. Finally, systemic administration of anti-TACE-mAb downregulated the generation of sSema4D in the mouse model of critical-sized bone defect, whereas local injection of recombinant sSema4D to anti-TACE-mAb-treated defect upregulated local osteoblastogenesis. Therefore, a novel pathway is proposed whereby TACE-mediated shedding of Sema4D expressed on the osteoclast precursors generates functionally active sSema4D to suppress osteoblastogenesis.     

Genome-wide comparative analysis of Mg transporter gene family between Triticum turgidum and Camelina sativa

Magnesium (Mg) as a bimetal plays critical roles in biochemical processes, membrane stability, and enzyme activity. Mg transporters (MGTs) are involving in maintaining Mg homeostasis in cells. Although the MGT family members have been identified in different plant species, there is no comprehensive analysis of the other plants' MGT genes. In the current study, 62 and 41 non-redundant putative MGT proteins were recognized into the genome of Camelina sativa, and Triticum turgidum and they were compared based on physicochemical properties, protein structure, expression, and interaction. All identified MGTs were classified into three subgroups, NIPA, CorA, and MRS2/MGT, based on conserved-motifs distribution. The results showed that the secondary structure pattern in NIPA and MRS2 subfamily members in both studied plant species were highly similar. Furthermore, MGTs encompass the conserved structures and the critical sites mainly in the metal ion and Mg²⁺ binding centers as well as the catalytic sites were observed. The highest numbers of protein channels were predicted in CorA proteins in both C. sativa and T. turgidum with 24 and 17 channel numbers, respectively. The Ser, Pro, Gly, Lys, Tyr, and Arg amino acids were predicted as the binding residues in MGTs channel regions. The expression pattern of identified genes demonstrated that MGT genes have diverse tissue-specific expression and stress response expression patterns. Besides, 147 co-expressed genes with MGTs were clustered into the eight co-expression nodes involved in N-glycan biosynthesis, protein processing in the endoplasmic reticulum, carbon metabolism, biosynthesis of amino acids, and endocytosis. In the present study, all interpretations are based on in silico predictions, which can be used in further studies related to functional genomics of MGT genes.

     

Development of Novel Prime-Boost Strategies Based on a Tri-Gene Fusion Recombinant L. tarentolae Vaccine against Experimental Murine Visceral Leishmaniasis

Visceral leishmaniasis (VL) is a vector-borne disease affecting humans and domestic animals that constitutes a serious public health problem in many countries. Although many antigens have been examined so far as protein- or DNA-based vaccines, none of them conferred complete long-term protection. The use of the lizard non-pathogenic to humans Leishmania (L.) tarentolae species as a live vaccine vector to deliver specific Leishmania antigens is a recent approach that needs to be explored further. In this study, we evaluated the effectiveness of live vaccination in protecting BALB/c mice against L. infantum infection using prime-boost regimens, namely Live/Live and DNA/Live. As a live vaccine, we used recombinant L. tarentolae expressing the L. donovani A2 antigen along with cysteine proteinases (CPA and CPB without its unusual C-terminal extension (CPB^-CTE)) as a tri-fusion gene. For DNA priming, the tri-fusion gene was encoded in pcDNA formulated with cationic solid lipid nanoparticles (cSLN) acting as an adjuvant. At different time points post-challenge, parasite burden and histopathological changes as well as humoral and cellular immune responses were assessed. Our results showed that immunization with both prime-boost A2-CPA-CPB^-CTE-recombinant L. tarentolae protects BALB/c mice against L. infantum challenge. This protective immunity is associated with a Th1-type immune response due to high levels of IFN-γ production prior and after challenge and with lower levels of IL-10 production after challenge, leading to a significantly higher IFN-γ/IL-10 ratio compared to the control groups. Moreover, this immunization elicited high IgG1 and IgG2a humoral immune responses. Protection in mice was also correlated with a high nitric oxide production and low parasite burden. Altogether, these results indicate the promise of the A2-CPA-CPB^-CTE-recombinant L. tarentolae as a safe live vaccine candidate against VL.     

Cell line selection through gamma irradiation combined with multi-walled carbon nanotubes elicitation enhanced phenolic compounds accumulation in Salvia nemorosa cell culture

The current study focused on improving the production of phenolic acids in the Woodland Sage cell suspension culture (CSC) through attaining high-yielding cell lines and carboxyl functionalized multi-walled carbon nanotubes (MWCNT-COOH) elicitation. The leaf-derived callus was irradiated at different doses of gamma irradiation 10 to 100 Gy. The maximum content of rosmarinic acid (RA), salvianolic acid B (SAB), ferulic acid (FA), and cinnamic acid (CA) was recorded in callus cultures irradiated with 70 Gy, which was 18.53, 5.21, 1.9, and 7.59 mg/g DW, respectively. The CSC that established from 70 Gy γ-irradiated calli accumulated 1.7-fold RA more higher irradiated callus culture. The CSC elicited with various concentrations of MWCNT-COOH in range 25 to 100 mg/l significantly increased fresh weight (FW), dry weight (DW), and phenolic acid contents of cells. The highest FW with 268.47 g/l and DW with 22.17 g/l was obtained in 100 mg/l MWCNT-COOH treatment. The RA, SAB, CA and FA content of CSC treated with 100 mg/l MWCNT-COOH were 13-fold, 14.2-fold, 20-fold, and 3- fold higher than wild S. nemorosa plant at flowering stage, respectively. The antioxidant activity of cultures significantly enhanced with both gamma and MWCNT-COOH based on DPPH and FRAP assay. Our results showed that the combination of cell line selection and MWCNT-COOH elicitation significantly improved the production of secondary metabolites in Woodland Sage, which is useful for large-scale production of phenolic compounds.

     

Effects of Pro-Tex® on the expression of Hsp70 gene and immune response parameters in the Persian sturgeon fingerlings,Acipenser persicus,infected with Aeromonas hydrophila

The induction of Hsps (heat shock protein) recognized as a promising approach to limiting disease and improving health in aquaculture. This investigation aimed to study the impacts of Pro-Tex®, an extract from the prickly pear cactus (Opuntia ficus indica), on the expression of Hsp70 gene and induction of immune response parameters in Acipenser persicus infected with Aeromonas hydrophila ATCC^®7966^TM. Fish were pretreated with 25, 50 and 100 mg/L of Pro-Tex and then injected in the intra-peritoneal cavity with A. hydrophila. The expression level of Hsp70 gene, lysozyme activity (LYZ) and complement C3 (C3), and immunoglobulin M (IgM) levels were assessed in liver, gill, and intestine on the days 3 and 7 post-infection. Tex-OE® increased expression of Hsp70 in a dose-dependent way in A. persicus, but this expression significantly reduced on the 7-days post-injection. The Hsp70 expression pattern was variable in each tissue, also, LYZ activity, C3, and IgM increased, depending on the concentration, and showed a decreasing trend in a time-dependent way. In conclusion, our data indicated that Pro-Tex as an Hsp70 inducer increases the resistance of sturgeon fry against fish pathogens by induction of different immunity factors.     

Robust algorithm for brain magnetic resonance image (MRI) classification based on GARCH variances series

In this paper, a robust algorithm for disease type determination in brain magnetic resonance image (MRI) is presented. The proposed method classifies MRI into normal or one of the seven different diseases. At first two-level two-dimensional discrete wavelet transform (2D DWT) of input image is calculated. Our analysis show that the wavelet coefficients of detail sub-bands can be modeled by generalized autoregressive conditional heteroscedasticity (GARCH) statistical model. The parameters of GARCH model are considered as the primary feature vector. After feature vector normalization, principal component analysis (PCA) and linear discriminant analysis (LDA) are used to extract the proper features and remove the redundancy from the primary feature vector. Finally, the extracted features are applied to the K-nearest neighbor (KNN) and support vector machine (SVM) classifiers separately to determine the normal image or disease type. Experimental results indicate that the proposed algorithm achieves high classification rate and outperforms recently introduced methods while it needs less number of features for classification.     

Nanoformulation of curcumin protects HUVEC endothelial cells against ionizing radiation and suppresses their adhesion to monocytes: potential in prevention of radiation-induced atherosclerosis

Objectives

To investigated the potential of a novel dendrosomal nanoformulation of curcumin (DNC) in blocking radiation-induced changes in irradiated human umbilical vein endothelial cells (HUVECs), and their adhesion to human THP-1 monocytoid cells.

Results

Co⁶⁰ gamma rays reduced viability, raised the expression of adhesion molecules, ICAM-1, VCAM-1 and E-selectin (mRNA and protein), augmented the adhesion of THP-1 cells to HUVECs, activated NF-κB binding, increased the release of pro-inflammatory cytokines (IL-6, IL-8 and MCP-1) and induced oxidative damage (reduced glutathione declined, while 8-OHdG and TBARS increased). 5 µM DNC significantly inhibited these radiation-induced changes, activated the Nrf-2 pathway, and effectively suppressed THP-1 adhesion to HUVECs, implicating p38 MAPK signaling.

Conclusion

DNC treatment is a potential preventive method against inflammation and vascular damage from ionizing radiation.

     

Length‐weight and length‐length relationships of the genus Alosa (Clupeoidei: Clupeiformes: Clupeidae) along the southern Caspian Sea coast

Length–weight (LWR) and length–length (LLR) relationships were estimated for four shad species of the genus Alosa, reported from along the southern Caspian Sea coast, north of Iran in a study from March 2014. Two of these species are endemic to the Caspian Sea. The length–weight parameter b for these species ranged from 2.99 to 3.24, with regression coefficients (r²) ranging from 0.91 to 0.99. All LLRs were highly significant (r² > 0.96).