A neural network-assisted open boundary molecular dynamics simulation method.

A neural network-assisted molecular dynamics method is developed to reduce the computational cost of open boundary simulations. Particle influxes and neural network-derived forces are applied at the boundaries of an open domain consisting of explicitly modeled Lennard-Jones atoms in order to represent the effects of the unmodeled surrounding fluid. Canonical ensemble simulations with periodic boundaries are used to train the neural network and to sample boundary fluxes. The method, as implemented in the LAMMPS, yields temperature, kinetic energy, potential energy, and pressure values within 2.5% of those calculated using periodic molecular dynamics and runs two orders of magnitude faster than a comparable grand canonical molecular dynamics system.

Differential coded aperture single-snapshot spectral imaging.

We propose a novel, to the best of our knowledge, concept of the differential coded aperture snapshot spectral imaging (D-CASSI) technique exploiting the benefits of using a {-1,+1} random mask, which is demonstrated by a broadband single-snapshot hyperspectral camera using compressed sensing. To double the information, we encode the image with two complementary random masks, which proved to be superior to two independent patterns. We utilize dispersed and non-dispersed encoded images captured in parallel on a single detector. We explored several different approaches to processing the measured data, which demonstrates significant improvement in retrieving complex hyperspectral scenes. The experiments were completed by simulations in order to quantify the reconstruction fidelity. The concept of differential CASSI could be easily implemented also by multi-snapshot CASSI without any need for optical system modification.

Enhancement of CASSI by a zero-order image employing a single detector.

Coded aperture snapshot spectral imaging (CASSI) makes it possible to recover 3D hyperspectral data from a single 2D image. However, the reconstruction problem is severely underdetermined, and efforts to improve the compression ratio typically make the imaging system more complex and cause a significant loss of incoming light intensity. In this paper, we propose a novel approach to CASSI that enables capturing both a spectrally sheared and an integrated image of a scene with a single camera. We performed hyperspectral imaging of three different testing scenes in the spectral range of 500-900 nm. We demonstrate the prominent effect of using the nondiffracted image on the reconstruction of data from our camera. The use of the spectrally integrated image improves the reconstruction quality, and we observed an approximately fivefold reduction in reconstruction time.

Superior Role of Waist Circumference to Body-Mass Index in the Prediction of Cardiometabolic Risk in Dyslipidemic Patients.

Coronary risk evaluation by conventional factors (age, gender, smoking, blood pressure and cholesterol) may further be specified by facets of the metabolic syndrome, namely insulin resistance, hypertriglyceridemia and obesity. Although obesity is usually defined as elevated body mass index (BMI), recent data indicate a superior role of waist circumference or hypertri-glyceridemic waist (HTGW) over BMI in the assessment of cardiometabolic risk. In dyslipidemic patients, the specific contributions of risky waist, HTGW or BMI have not been evaluated as yet. 686 dyslipidemic subjects (322 males and 364 females) were enrolled into a cross-sectional study. In each subject basic antropometry (i.e. waist circumference, HTGW, BMI) and laboratory parameters of lipid profile and insulin resistance were determined. Cardiometabolic risk was given by fulfilling the criteria (harmonized definition) of metabolic syndrome. The significance of risky waist, HTGW and BMI were assessed by comparing the respective predictive values for the presence of metabolic syndrome. Dyslipidemic patients with risky waist, HTGW or high BMI have a more atherogenic lipid profile and higher insulin resistance compared to those without risky waist, HTGW or high BMI. Risky waist is stronger predictor of metabolic syndrome (PPV 66 %, NPV 90 %) and thus posesa greater cardiometabolic risk than higher BMI per se does (PPV 42 %, NPV 97 %). The contribution of triglycerides (i.e. HTGW) to these predictive values is marginal (PPV 66 %, NPV 92 %). The present results highlight the superior role of waist circumference as a screening tool over BMI for the evaluation of cardiometabolic risk in dyslipidemic subjects. HTGW brings little additional benefit in risk stratification. Lower BMI proved to be optimal for identifying the subjects with inferior risk.

Antibacterial, mechanical and surface properties of Ag-DLC films prepared by dual PLD for medical applications.

Silver doped diamond-like carbon layers were deposited by dual pulsed laser deposition using two KrF excimer lasers. The concentration of Ag, determined by XPS and WDS, moved from zero to ~10at%. We found that the sp2/sp3 ratio, film roughness and the number of droplets (SEM and AFM) increased with increasing silver concentration. The sp3 content measurement (XPS) was influenced by ion cluster surface sputtering and varied from 71.0% (undoped DLC) to 36.2% (for 9.3at% Ag). Transmission was measured on the scale from 200nm to 1100nm, and decreased with increasing silver content. An increase of Ag content has an effect on the decrease of the storage modulus (E') and the indentation hardness (HIT). The highest values HIT=51.9GPa and E'=270.6GPa were measured on a sample with 0at% Ag. The lowest values HIT=26.0GPa and E'=180.2GPa were measured on a sample of 9.3at% Ag. Film adhesion was studied using the scratch test and was up to 20.8N for the highest Ag concentration. The contact angle (CA) measurements for water showed that the CA of Ag-DLC films was higher (78°-98°) that of DLC film (77°). The surface free energy of DLC and of Ag-DLC was about 40mJ·m-2. Antibacterial properties were studied using gram positive and gram negative bacteria. The antibacterial effects increased with the Ag concentration and were ~99.9% after 24h for the layers with the highest silver content (9.3at%). Our results demonstrate that the Ag-doped DLC films are potentially useful biomaterials having both good mechanical properties and antimicrobial characteristics. PRIME NOVELTY STATEMENT: Unique manufacturing technique dual pulsed laser deposition was applied on hydrogen-free diamond-like carbon doped by Ag including topological, physical and antibacterial characterization.

Correlation of lipid parameters and markers of insulin resistance: does smoking make a difference?

Insulin resistance associated with dyslipidemia enhances cardiovascular risk. Several atherogenic indexes have been suggested to give more precise information about the risk. The aim of our study was to estimate, which atherogenic index correlates better with parameters of insulin resistance. Furthermore, we compared the parameters of lipid metabolism and insulin resistance between smokers and non-smokers. In our cross-sectional study we enrolled 729 patients with dyslipidemia which were divided into two groups - non-smokers (586) and smokers (143). We measured lipid profile, parameters of insulin resistance (fasting glycemia, insulin, HOMA-IR, C-peptide, proinsulin) and calculated atherogenic indexes - atherogenic index of plasma (log (TAG/HDL-C), AIP), ApoB/ApoA1 index and nonHDL-C. AIP was found out to show stronger correlations with parameters of insulin resistance (p<0.001, correlation coefficients ranging between 0.457 and 0.243) than other indexes (ApoB/ApoA1 or nonHDL cholesterol). AIP correlated with parameters of insulin resistance both in smokers and non-smokers, but after adjustment (for age, body mass index, waist circumference) persisting only in non-smokers. Smokers had a wider waist circumference and a proatherogenic lipid profile. Smoking increases the risk of developing metabolic syndrome. AIP can be used in daily praxis for predicting insulin resistance in patients with dyslipidemia, predominantly in non-smokers.

Evaluation of total adiponectin, adipocyte fatty acid binding protein and fibroblast growth factor 21 levels in individuals with metabolic syndrome.

Although many studies have investigated the relationships of several adipokines to metabolic syndrome (MetS), the interrelationships of adiponectin (ADP), adipocyte fatty acid binding protein (A-FABP) and fibroblast growth factor 21 (FGF 21) have not been described in detail. We examined 209 asymptomatic dyslipidemic patients divided into MetS+ (n=73) and MetS- (n=136) groups. The aim of study was to evaluate the relationships between observed adipokines, to compare the levels of total ADP, A-FABP and FGF 21 in individuals with and without MetS, and to elucidate the relationships of individual adipokines to lipid parameters, markers of insulin resistance and endothelial hemostatic markers in these groups. In MetS+ group, we found the independent positive association ADP with A-FABP (beta=0.4888, p=0.0382), A-FABP with FGF 21 (beta=0.3811, p=0.0002) and von Willebrand factor (beta=0.4502, p=0.0013), and FGF 21 with A-FABP (beta=0.4422, p=0.0002). Our study has confirmed the well-established risk profile of subjects with MetS, although clinically asymptomatic. MetS+ patients had also lower levels of ADP and higher levels of A-FABP and FGF 21. Our study evaluated the interrelationships of ADP, A-FABP and FGF 21 in asymptomatic dyslipidemic subjects with diagnosis of MetS. Especially strong association between A-FABP and FGF 21 needs to be clarified in further studies.

Soluble intercellular cell adhesion molecule-1 and vascular cell adhesion molecule-1 in asymptomatic dyslipidemic subjects.

AIM: The plasma levels of soluble intercellular cell adhesion molecule-1 (s-ICAM-1) and soluble vascular cell adhesion molecule-1 (s-VCAM-1) were assessed in clinically asymptomatic subjects to compare them between normolipidemic and various dyslipidemic phenotypes. The associations between soluble cell adhesion molecules (s-CAMs) and risk factors for atherosclerosis, markers of insulin resistance, and the intima-media thickness of the common carotid artery (IMT) were evaluated, too. METHODS: Thwo hundred and thirty-four asymptomatic subjects were divided into four dyslipidemic phenotypes (DLP) according to apolipoprotein B (apoB) and triglycerides (TG): DLP1 (N.=58, apoB<1.2 g/L and TG<1.5 mmol/L), DLP2 (N.=47, apoB<1.2 g/L and TG≥1.5 mmol/L), DLP3 (N.=31, apoB≥1.2 g/L and TG<1.5 mmol/L) and DLP4 (N.=98, apoB≥1.2 g/L and TG≥1.5 mmol/L). DLP1 (normo-apoB /normo-TG) served as a control group. RESULTS: A significant difference in s-ICAM-1 between DLP1 (502.0 [457.1-568.2] ng/mL) and DLP4 (567.9 [502.8-692.1] ng/mL, P<0.001) was found. No significant differences in s-VCAM-1 between DLPs were apparent. S-ICAM-1 was independently predicted by HDL-cholesterol, non-HDL-cholesterol, proinsulin, C-peptide, waist, systolic and diastolic blood pressure. S-VCAM-1 was predicted only by age and systolic blood pressure. Both s-CAMs were detected as independent predictors for IMT, which was significantly increased in DLP 4. CONCLUSION: The elevation of s-ICAM-1 was presented only in patients with simultaneously elevated TG and apoB (DLP4) in comparison with normolipidemic subjects. Patients with DLP 4 had significantly increased IMT, which was independently predicted by levels of s-ICAM-1 and of s-VCAM-1. These findings pointed out DLP4 subjects as individuals with the highest risk for early manifestation of atherosclerosis.

Leptomonas costaricensis sp. n. (Kinetoplastea: Trypanosomatidae), a member of the novel phylogenetic group of insect trypanosomatids closely related to the genus Leishmania.

A flagellate isolated from the intestinal tract of a reduviid bug Ricolla simillima (Heteroptera) in Costa Rica was found to represent a new trypanosomatid species by the phylogenetic analysis of small subunit ribosomal RNA (SSU rRNA), glyceraldehyde phosphate dehydrogenase (GAPDH) and large subunit of RNA polymerase II (RPOIILS) genes. The phylogenetic position of this trypanosomatid, together with its typical promastigote morphology and the host identity, allowed its classification as a species that belongs to the polyphyletic genus Leptomonas. Interestingly, the new species was revealed as a member of the novel phylogenetic clade representing the closest known relative of Leishmania. With the new species used as an outgroup to root the Leishmania RPOIILS phylogenetic tree, the lineage of the Neotropical species L. enriettii was found to branch off early, and was followed by a deep split between the Old World and the remaining New World species. This tree topology supports the hypothesis that the initial transition to dixenous parasitism in this group pre-dated the continental split and that afterwards the Neotropical and the Old World groups evolved largely independently.

In vitro biotransformation of 2,6,9-trisubstituted purine-derived cyclin-dependent kinase inhibitor bohemine by mouse liver microsomes.

1. Biotransformation pathways of the cyclin-dependent kinase inhibitor 6-benzylamino-2-(3-hydroxypropylamino)-9-isopropylpurine (bohemine) by mouse liver microsomes in vitro were investigated. 2. Metabolite profiles of [8-(3)H]-labelled bohemine were established by TLC/(3)H-autoradiography and enzymatic and MS analyses were used to elucidate the chemical structures of the metabolites. The structures of the main primary metabolites were confirmed by synthesis of authentic compounds. 3. A schema of the primary NADPH-dependent pathways has been proposed involving N(2)- and N9-dealkylation, N(6)-debenzylation, aromatic hydroxylation, and C2 side chain oxidation of bohemine. Three of the primary metabolites detected, 6-(benzylamino)-2-(3-hydroxypropylamino)purine (M4), 6-amino-2-(3-hydroxypropylamino)-9-isopropylpurine (M5) and 6-(4-hydroxybenzylamino)-2-(3-hydroxypropylamino)-9-isopropylpurine (M6), all retaining their parent primary hydroxyl group, were subsequently shown to be converted, by a liver cytosolic NAD(+)-dependent system, into their corresponding carboxylic acids. M6 was subject to microsomal glycosidations requiring UDP-sugar donors. NADPH-dependent conversion of M6 into M5 by microsomes was also demonstrated. 4. Cytochrome P450 (CYP) enzymes-selective inhibitors were used to identify CYPs involved in bohemine biotransformation. The findings suggested that CYP2a and CYP3a substantially contributed to the NADPH-dependent bohemine transformation in vitro. 5. The findings will facilitate experiments designed to dissect enzymatic systems catalysing clearance of C2,C6,N9-trisubstituted purine compounds from mammalian tissues.

Trypanosoma avium of raptors (Falconiformes): phylogeny and identification of vectors.

Avian trypanosomes are widespread parasites of birds, the transmission of which remains mostly unclear, with various blood-sucking insects mentioned as possible vectors. A search for vectors of trypanosomes of sparrowhawk (Accipiter nisus), buzzard (Buteo buteo), lesser-spotted eagle (Aquila pomarina) and kestrel (Falco tinnunculus) was performed in Czech and Slovak Republics. Black flies (Eusimulium spp.), hippoboscid flies (Ornithomyia avicularia), mosquitoes (Culex pipiens pipiens) and biting midges (Culicoides spp.), trapped while attempting to feed on raptor nestlings, were found to contain trypanosomatids in their intestine. Trypanosomes from the raptors and blood-sucking insects were isolated, and their 18S rRNA sequences were used for species identification and for the inference of intra- and interspecific relationships. Together with the trypanosome isolated from a black fly, the bird trypanosomes formed a well-supported Trypanosoma avium clade. The isolates derived from hippoboscid flies and mosquitoes are most likely also avian trypanosomes infecting birds other than the studied raptors. Analysis of the kinetoplast, that has features characteristic for the avian trypanosomes (minicircle size; dimensions of the kinetoplast disc), provided further evidence for the identification of vectors. It is suggested that all trypanosomes isolated from raptors included in this study belong to the T. avium complex and are transmitted by the ornithophilic simuliids such as Eusimulium securiforme.

Coprodiagnosis of Hammondia heydorni in dogs by PCR based amplification of ITS 1 rRNA: differentiation from morphologically indistinguishable oocysts of Neospora caninum.

Hammondia heydorni is thought to be a non-pathogenic coccidian parasite of dogs that is closely related to Neospora caninum, an important parasite of cattle and dogs. Oocysts of these two species are morphologically indistinguishable from each other. A population of 2240 dogs in the Czech Republic was screened for the presence of H. heydorni/N. caninum oocysts and five (0.22%), represented by five of 3135 faecal samples (0.16%), were positive. The internal transcribed spacer 1 region of the rRNA gene (ITS1) from two isolates were cloned and the DNA sequences were identical with those of the ITS1 of H. heydorni. Based on the rRNA sequences available for H. heydorni and related coccidia, the primer pair JS4-JS5 was designed to amplify the 3' end of the small subunit (SSU) rRNA gene and ITS1 of H. heydorni. When tested on DNA extracted from a variety of parasites, the primers amplified a specific 267 bp fragment in our isolates only. The presence of DNA equivalent to 10 oocysts was sufficient for the amplification of the ITS1. We present a PCR-based diagnostic method as the only fast and reliable method for the diagnosis of H. heydorni in dogs.