Variableselectioninmultivariatecalibrationbasedonclusteringofvariableconcept

Recentlywehaveproposedanewvariableselectionalgorithm,basedonclusteringofvariableconcept(CLoVA)inclassificationproblem.Withthesameidea,thisnewconcepthasbeenappliedtoaregres-sionproblemandthentheobtainedresultshavebeencomparedwithconventionalvariableselectionstrategiesforPLS.Thebasicideabehindtheclusteringofvariableisthat,theinstrumentchannelsareclusteredintodifferentclustersviaclusteringalgorithms.Then,thespectraldataofeachclusteraresubjectedtoPLSregression.Differentrealdatasets(Cargillcorn,Biscuitdough,ACEQSAR,Soy,andTablet)havebeenusedtoevaluatetheinfluenceoftheclusteringofvariablesonthepredictionper-formancesofPLS.Almostintheallcases,thestatisticalparameterespeciallyinpredictionerrorshowsthesuperiorityofCLoVA-PLSrespecttoothervariableselectionstrategies.Finallythesynergyclusteringofvariable(sCLoVA-PLS),whichisusedthecombinationofcluster,hasbeenproposedasanefficientandmodificationofCLoVAalgorithm.Theobtainedstatisticalparameterindicatesthatvariableclusteringcansplitusefulpartfromredundantones,andthenbasedoninformativecluster;stablemodelcanbereache

Leukemia and small round blue-cell tumor cancer detection using microarray gene expression data set: Combining data dimension reduction and variable selection technique

Using gene expression data in cancer classification plays an important role for solving the fundamental problems relating to cancer diagnosis. Because of high throughput of gene expression data for healthy and patient samples, a variable selection method can be applied to reduce complexity of the model and improve the classification performance. Since variable selection procedures pose a risk of over-fitting, when a large number of variables with respect to sample are used,we have proposed a method for coupling data dimension reduction and variable selection in the present study. This approach uses the concept of variable clustering for the original data set. Significant components of local principal component analysis models have just been retained from all clusters. Then, the variable selection algorithm is performed on these locally derived principal component variables. The proposed algorithm has been evaluated on two gene expression data sets; namely, acute Leukemia and small round blue-cell tumor (SRBCT). Our results confirmed that the classification models achieved on the reduced data were better than those obtained on the entire microarray gene expression profile

Molecular Dynamics and Docking Investigations of Several Zoanthamine- Type Marine Alkaloids as Matrix Metaloproteinase-1 Inhibitors

Zoanthamine-type alkaloids display a wide spectrum of biological effects. This study aimed to examine the inhibitory effects of norzoanthamine and its ten homologues of zoanthamine class on human fibroblast collagenase by modeling a three-dimensional structure of the ligands at collagenase using energy minimization, docking, molecular dynamics simulation and MM-PB/GBSA binding free energy calculations. The results showed that zoanthamide, zooxathellamine and enol-iminium form of norzoanthamine, with lower binding free energies than other compounds, are potent inhibitors of collagenase. However, the enol-iminium form of norzoanthamine showed a more inhibitory activity against collagenase than its keto form. This suggests that it can be used for treatment of many diseases such as osteoporosis, autoimmune diseases, and cancer. Zinc-binding residues such as His 118, His 122 and His 128 for hydrogen bonds and Leu 81, Tyr 110, Val 115, Leu 126, Pro 138, Ser 139 for hydrophobic interactions should be considered for designing an inhibitor for collagenase. Our theoretical results and MM/GBSA binding free energy calculations are consistent with experimental studies. Abbreviation MD: Molecular dynamics; RMSD: Root mean square deviation; MM-PB/GBSA: Molecular mechanics Poisson-Boltzmann/General Born surface area, DFT: density functional theory, B3LYP: Becke, three-parameter, Lee-Yang-Parr, RESP: Restrained electrostatic surfacepotentia

Catalytic Cycle of Multicopper Oxidases Studied by Combined Quantum- and Molecular-Mechanical Free-Energy Perturbation Methods.

We have used combined quantum mechanical and molecular mechanical free-energy perturbation methods in combination with explicit solvent simulations to study the reaction mechanism of the multicopper oxidases, in particular, the regeneration of the reduced state from the native intermediate. For 52 putative states of the trinuclear copper cluster, differing in the oxidation states of the copper ions and the protonation states of water- and O2-derived ligands, we have studied redox potentials, acidity constants, isomerization reactions, as well as water- and O2 binding reactions. Thereby, we can propose a full reaction mechanism of the multicopper oxidases with atomic detail. We also show that the two copper sites in the protein communicate so that redox potentials and acidity constants of one site are affected by up to 0.2 V or 3 pKa units by a change in the oxidation state of the other site

SUPPLEMENTARY MATERIAL Marine Natural Products as Acetylcholinesterase Inhibitor: Comparative Quantum Mechanics and Molecular Docking Study

The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr 75147-63448, Ira

Development of a new colorimetric assay for detection of bisphenol-A in aqueous media using green synthesized silver chloride nanoparticles: experimental and theoretical study

In the present study, a cost-effective, green and simple synthesis method was applied for preparation of stable silver chloride nanoparticles (AgCl-NPs). The method was done by forming AgCl-NPs from Ag+ ions using aqueous extract of brown algae (Sargassum boveanum) obtained from the Persian Gulf Sea. This extract served as capping agent during the formation of AgCl-NPs. Creation of AgCl-NPs was confirmed by UV–visible spectroscopy, powder X-ray diffraction, energy-dispersive X-ray spectroscopy, and highresolution transmission electron microscopy, while the morphology and size analyses were characterized using highresolution transmission electron microscopy and dynamic light scattering. After optimization of some experimental conditions, particularly pH, a simple and facile system was developed for the naked-eye detection of bisphenol-A. Moreover, a theoretical study of AgCl interaction with bisphenol-A was performed at the density functional level of theory in both gas and solvent phases. Theoretical results showed that electrostatic and van der Waal interactions play important roles in complexation of bisphenol-Awith AgCl-NPs, which can lead to aggregation of the as-prepared AgCl-NPs and results in color change from specific yellow to dark purple, where a new aggregation band induced at 542 nm appears. The absorbance at 542 nm was found to be linearly dependent on the bisphenol-A concentration in the range of 1 × 10−6–1 × 10−4 M, with limit of detection of 45 nM. In conclusion, obtained results from the present study can open up an innovative application of the green synthesis of AgCl-NPs using brown algae extract as colorimetric sensor

Development of a new colorimetric assay for detection of bisphenol-A in aqueous media using green synthesized silver chloride nanoparticles: experimental and theoretical study.

Abstract In the present study, a cost-effective, green and simple synthesis method was applied for preparation of stable silver chloride nanoparticles (AgCl-NPs). The method was done by forming AgCl-NPs from Ag+ ions using aqueous extract of brown algae (Sargassum boveanum) obtained from the Persian Gulf Sea. This extract served as capping agent during the formation of AgCl-NPs. Creation of AgCl-NPs was confirmed by UV-visible spectroscopy, powder X-ray diffraction, energy-dispersive X-ray spectroscopy, and high-resolution transmission electron microscopy, while the morphology and size analyses were characterized using high-resolution transmission electron microscopy and dynamic light scattering. After optimization of some experimental conditions, particularly pH, a simple and facile system was developed for the naked-eye detection of bisphenol-A. Moreover, a theoretical study of AgCl interaction with bisphenol-A was performed at the density functional level of theory in both gas and solvent phases. Theoretical results showed that electrostatic and van der Waal interactions play important roles in complexation of bisphenol-A with AgCl-NPs, which can lead to aggregation of the as-prepared AgCl-NPs and results in color change from specific yellow to dark purple, where a new aggregation band induced at 542 nm appears. The absorbance at 542 nm was found to be linearly dependent on the bisphenol-A concentration in the range of 1 × 10-6-1 × 10-4 M, with limit of detection of 45 nM. In conclusion, obtained results from the present study can open up an innovative application of the green synthesis of AgCl-NPs using brown algae extract as colorimetric sensors

Association of Pathogen Burden and Hypertension: The Persian Gulf Healthy Heart Study

background Chronic infection with cytomegalovirus (CMV), Chlamydia pneumoniae, herpes simplex virus 1 (HSV-1), and Helicobacter pylori may contribute to essential hypertension. However, the evidence now available does not clarify whether the aggregate number of pathogens (pathogen burden) may be associated with hypertension. methods Sera from 1,754 men and women aged ≥25  years were analyzed for immunoglobulin G antibodies to C.  pneumoniae, HSV-1, H.  pylori, and CMV using enzyme-linked immunosorbent assay. The aggregate number of seropositives to the studied viral and bacterial agents was defined as pathogen burden. Hypertension was defined according to World Health Organization criteria. results A total of 459 (26.3%) of the subjects had hypertension. In the hypertensive group, 4.2% had 0 or 1 pathogens present, 20.6% had 2, 43.2% had 3, and 32.1% had 4; in the normotensive group, 7.9% had 0 or 1, 28.4% had 2, 42.7% had 3, and 21.0% had 4. Of the 4 studied pathogens, H.  pylori seropositivity showed a significant independent association with hypertension (odds ratio (OR) =1.37; 95% confidence interval (CI) =1.05–1.79; P = 0.02). In multiple logistic regression analyses, the pathogen burden did not show a significant independent association with hypertension. Coinfection with H.  pylori and C.  pneumoniae was significantly associated with hypertension compared with double seronegativity after adjustment for age, sex, chronic low-grade inflammation, and cardiovascular risk factors (OR = 1.68; 95% CI = 1.14–2.47; P = 0.008]. conclusions The pathogen burden was not associated with hypertension. However, coinfection with C. pneumoniae and H. pylori showed a significant association with essential hypertension, independent of cardiovascular risk factors and chronic low-grade inflammation. Keywords: blood pressure; Chlamydia pneumoniae; cytomegalovirus; Helicobacter pylori; herpes simplex virus; hypertension; pathogen

Phospholipase A2 activity of the Persian Gulf upside-down jellyfish venom (Cassiopea andromeda)

Background: The venomous jellyfish Cassiopea andromeda can produce envenomation and different toxicological and biological effects by their nematocysts. The phospholipase A2 enzymes (PLA2) are toxic and induce various pharmacological effects including neurotoxicity, myotoxicity, and anticoagulant activities. The main aim of the current project was to screen the in vitro PLA2 activity of the C. andromeda crude venom. To better understand the experimental result; a molecular docking study was also performed. Materials and methods: The live specimens were collected from Nayband lagoon, by a trawl net, and separation of their tentacles was done according to Bloom 's et al., method. The PLA2 activity of crude venom was performed according to the acidimetric method of Tan and Tan. The lyophilized venom was subjected to Gas Chromatography/ Mass Spectroscopy, and the obtained structures were used for docking study against PLA2. The indoxam was considered as standard control. Results: The PLA2 activity of the jellyfish crude venom was 413 ±0.08 µmol/min/mg. Analysis of the crude venom detected seven compounds (i-vii) using GC-MS. Docking data was also confirmed the experimental results. According to the docking results, the highest affinity [-6.7 (kcal/mol)] was observed in the compound “Pregn-5-ene-3,11-dione, 17,20:20,21 bis [methylenebis(oxy)]-, cyclic 3-(1,2-ethane diyl acetal”. Conclusions: A high PLA2 level was found in the venom of C. andromeda. There was a good correlation between in vitro and in silico studies

Omentin-1, visfatin and adiponectin levels in relation to bone mineral density in Iranian postmenopausal women

The potential link between infection with Chlamydia pneumoniae or Helicobacter pylori and osteoporosis has not been investigated in population-based longitudinal studies. A total of 250 healthy postmenopausal women who participated in a prospective cohort study were evaluated for IgG antibodies directed against C. pneumoniae and H. pylori, osteoprotegerin (OPG), the receptor activator of nuclear factor kappa B ligand (RANKL), CrossLaps, and osteocalcin. Bone mineral density (BMD) was measured at the femoral neck and lumbar spine at baseline and at follow- up 5.8 years later. There were no significant differences in age-adjusted bone turnover markers, OPG, RANKL, the RANKL/OPG ratio, and BMD between the C. pneumoniae and H. pylori IgG seropositive and seronegative subjects (P > 0.05). Neither C. pneumoniae nor H. pylori IgG seropositivity was associated with age-and body massindex-adjusted BMD at the femoral neck and lumbar spine or bone loss at the 5.8-year follow-up. In logistic regression analysis, neither C. pneumoniae nor H. pylori IgG seropositivities predicted incident lumbar or spine osteoporosis 5.8 years later. In conclusion, neither C. pneumoniae nor H. pylori IgG seropositivity was associated with bone turnover markers, the RANKL/OPG ratio, BMD, or bone loss in postmenopausal women. In addition, chronic infection with C. pneumoniae or H. pylori did not predict incident osteoporosis among this group of women