PARAMETRIC STUDY OF REAXFF SIMULATION PARAMETERS FOR MOLECULAR DYNAMICS MODELING OF REACTIVE CARBON GASES

Abstract The development of innovative carbon-based materials can be greatly facilitated by molecular modeling techniques. Although the Reax Force Field (ReaxFF) can be used to simulate the chemical behavior of carbon-based systems, the simulation settings required for accurate predictions have not been fully explored. Using the ReaxFF, molecular dynamics (MD) simulations are used to simulate the chemical behavior of pure carbon and hydrocarbon reactive gases that are involved in the formation of carbon structures such as graphite, buckyballs, amorphous carbon, and carbon nanotubes. It is determined that the maximum simulation time step that can be used in MD simulations with the ReaxFF is dependent on the simulated temperature and selected parameter set, as are the predicted reaction rates. It is also determined that different carbon-based reactive gases react at different rates, and that the predicted equilibrium structures are generally the same for the different ReaxFF parameter sets, except in the case of the predicted formation of large graphitic structures with the Chenoweth parameter set under specific conditions.

Autoinducer-2 plays a crucial role in gut colonization and probiotic functionality of Bifidobacterium breve UCC2003

In the present study we show that luxS of Bifidobacterium breve UCC2003 is involved in the production of the interspecies signaling molecule autoinducer-2 (AI-2), and that this gene is essential for gastrointestinal colonization of a murine host, while it is also involved in providing protection against Salmonella infection in Caenorhabditis elegans. We demonstrate that a B. breve luxS-insertion mutant is significantly more susceptible to iron chelators than the WT strain and that this sensitivity can be partially reverted in the presence of the AI-2 precursor DPD. Furthermore, we show that several genes of an iron starvation-induced gene cluster, which are downregulated in the luxS-insertion mutant and which encodes a presumed iron-uptake system, are transcriptionally upregulated under in vivo conditions. Mutation of two genes of this cluster in B. breve UCC2003 renders the derived mutant strains sensitive to iron chelators while deficient in their ability to confer gut pathogen protection to Salmonella-infected nematodes. Since a functional luxS gene is present in all tested members of the genus Bifidobacterium, we conclude that bifidobacteria operate a LuxS-mediated system for gut colonization and pathogen protection that is correlated with iron acquisition.

A comparative study of the structural, mechanical and tribological characteristics of TiSiC-Cr coatings prepared in CH4 and C2H2 reactive atmosphere by cathodic vacuum arc

TiSiC-Cr coatings, with Cr and Si as additional elements, were deposited on Si, C 45 and 316 L steel substrates via cathodic arc evaporation. Two series of coatings with thicknesses in the range of 3.6–3.9 μm were produced, using either CH4 or C2H2 as carbon containing gas. For each series, different coatings were prepared by varying the carbon rich gas flow rate between 90 and 130 sccm, while maintaining constant cathode currents (110 and 100 A at TiSi and Cr cathodes, respectively), substrate bias (–200 V) and substrate temperature (∼320 °C). The coatings were analyzed for their mechanical characteristics (hardness, adhesion) and tribological performance (friction, wear), along with their elemental and phase composition, chemical bonds, crystalline structure and cross-sectional morphology. The coatings were found to be formed with nano-scale composite structures consisting of carbide crystallites (grain size of 3.1–8.2 nm) and amorphous hydrogenated carbon. The experimental results showed significant differences between the two coating series, where the films formed from C2H2 exhibited markedly superior characteristics in terms of microstructure, morphology, hardness, friction behaviour and wear resistance. For the coatings prepared using CH4, the measured values of crystallite size, hardness, friction coefficient and wear rate were in the ranges of 7.2–8.2 nm, 26–30 GPa, 0.3–0.4 and 2.1–4.8 × 10−6 mm3 N−1 m−1, respectively, while for the coatings grown in C2H2, the values of these characteristics were found to be in the ranges of 3.1–3.7 nm, 41–45 GPa, 0.1–0.2 and 1.4–3.0 × 10−6 mm3 N−1 m−1, respectively. Among the investigated coatings, the one produced using C2H2 at the highest flow rate (130 sccm) exhibited the highest hardness (45.1 GPa), the lowest friction coefficient (0.10) and the best wear resistance (wear rate of 1.4 × 10−6 mm3 N−1 m−1).

The magnitude of the snow-sourced reactive nitrogen flux to the boundary layer in the Uintah Basin, Utah, USA

Reactive nitrogen (Nr=NO, NO2, HONO) and volatile organic carbon emissions from oil and gas extraction activities play a major role in wintertime ground-level ozone exceedance events of up to 140 ppb in the Uintah Basin in eastern Utah. Such events occur only when the ground is snow covered, due to the impacts of snow on the stability and depth of the boundary layer and ultraviolet actinic flux at the surface. Recycling of reactive nitrogen from the photolysis of snow nitrate has been observed in polar and mid-latitude snow, but snow-sourced reactive nitrogen fluxes in mid-latitude regions have not yet been quantified in the field. Here we present vertical profiles of snow nitrate concentration and nitrogen isotopes (δ15N) collected during the Uintah Basin Winter Ozone Study 2014 (UBWOS 2014), along with observations of insoluble light-absorbing impurities, radiation equivalent mean ice grain radii, and snow density that determine snow optical properties. We use the snow optical properties and nitrate concentrations to calculate ultraviolet actinic flux in snow and the production of Nr from the photolysis of snow nitrate. The observed δ15N(NO3-) is used to constrain modeled fractional loss of snow nitrate in a snow chemistry column model, and thus the source of Nr to the overlying boundary layer. Snow-surface δ15N(NO3-) measurements range from -5‰ to 10‰ and suggest that the local nitrate burden in the Uintah Basin is dominated by primary emissions from anthropogenic sources, except during fresh snowfall events, where remote NOx sources from beyond the basin are dominant. Modeled daily-averaged snow-sourced Nr fluxes range from 5.6-71x107 molec cm-2 s-1 over the course of the field campaign, with a maximum noon-time value of 3.1x109 molec cm-2 s-1. The top-down emission estimate of primary, anthropogenic NOx in the Uintah and Duchesne counties is at least 300 times higher than the estimated snow NOx emissions presented in this study. Our results suggest that snow-sourced reactive nitrogen fluxes are minor contributors to the Nr boundary layer budget in the highly-polluted Uintah Basin boundary layer during winter 2014.

Alpha oscillations index the functionality and the plastic changes of the visual system

Alpha oscillations are linked to visual awareness and to the periodical sampling of visual information, suggesting that alpha rhythm reflect an index of the functionality of the posterior cortices, and hence of the visual system. Therefore, the present work described a series of studies investigating alpha oscillations as a biomarker of the functionality and the plastic modifications of the visual system in response to lesions to the visual cortices or to external stimulations. The studies presented in chapter 5 and 6 showed that posterior lesions alter alpha oscillations in hemianopic patients, with reduced alpha reactivity at the eyes opening and decreased alpha functional connectivity, especially in right-lesioned hemianopics, with concurrent dysfunctions in the theta range, suggesting a specialization of the right hemisphere in orchestrating alpha oscillations and coordinating complex interplays among different brain rhythms. The study presented in chapter 7 investigated a mechanism of rhythmical attentional sampling of visual information in healthy participants, showing that perceptual performance is influenced by a rhythmical mechanism of attentional allocation, occurring at lower-alpha frequencies (i.e., 7 Hz), when a single spatial location is monitored, and at lower frequencies (i.e., 5 Hz), when attention is allocated to two spatial locations. Moreover, the right hemisphere seemed to have a dominance in this rhythmical attentional sampling, distributing attentional resources to the entire visual field. Finally, the study presented in chapter 8 showed that prolonged visual entrainment induce long-term modulations of resting-state alpha activity in healthy participants, suggesting that persistent modifications in the functionality of the visual system are possible. Altogheter, these findings show that functional processes and plastic changes of the visual system are reflected in alpha oscillatory patterns. Therefore, investigating and promoting alpha oscillations may contribute to the development of rehabilitative protocols to ameliorate the functionality of the visual system, in brain lesioned patients.

Role of organic acids and phytonutrients as natural alternatives to antibiotics in supporting intestinal functionality

The gastrointestinal tract (GIT) represents the major portion of the body that interfaces with the external environment, with the double function of food processing and line of defense of the body. Numerous components support and regulate the barrier function of the GIT, such as tight junctions (TJs), cytokines, commensal and pathogenic microorganisms, and other systems of the organism, as the endocannabinoid system (ECS). The ECS can control several gastrointestinal functions, as well as the regulation of intestinal inflammation. Failure of the intestinal barrier function triggers an increase of the concentration of pro-inflammatory cytokines and leads to a reduction in intestinal functionality. This thesis aimed to explore the potential of natural compounds as a new alternative approach to antibiotics not only as antimicrobial, but also supporting intestinal maturation and integrity, and as immune-boosting agents. Different experiments were performed to evaluate the potential of nature-identical compounds (NICs), organic acids (OAs), and essential oils (EOs) to support and fight various stressful stimuli. In vitro, a well characterized blend of NICs and OAs were able to improve TJs and transepithelial electrical resistance (TEER) in an intestinal cell line, exerting an anti-inflammatory potential. EOs enhanced TEER and TJs mRNA levels, with a reduction of paracellular permeability, showing antioxidant and antimicrobial properties. In vivo, thymol modulates the gene expression of ECS and gut chemosensing in the GIT of piglets, where the precise localization of the cannabinoid receptors was immunohistochemically confirmed, suggesting an anti-inflammatory potential. In conclusion, natural alternative molecules represent an effective alternative to support or replace the classical pharmacological prophylaxis. These alternative molecules act not only as antimicrobial agents, but also exerted a crucial role in supporting the intestinal barrier function, preventing oxidative stress, and reducing inflammation. Moreover, thymol seems able to modulate the ECS, representing a novel frontier to support animal health and productivity.

Lung Age Is Related To Carotid Structural Alterations In Hypertensive Subjects.

Hypertensive patients exhibit higher cardiovascular risk and reduced lung function compared with the general population. Whether this association stems from the coexistence of two highly prevalent diseases or from direct or indirect links of pathophysiological mechanisms is presently unclear. This study investigated the association between lung function and carotid features in non-smoking hypertensive subjects with supposed normal lung function. Hypertensive patients (n = 67) were cross-sectionally evaluated by clinical, hemodynamic, laboratory, and carotid ultrasound analysis. Forced vital capacity, forced expired volume in 1 second and in 6 seconds, and lung age were estimated by spirometry. Subjects with ventilatory abnormalities according to current guidelines were excluded. Regression analysis adjusted for age and prior smoking history showed that lung age and the percentage of predicted spirometric parameters associated with common carotid intima-media thickness, diameter, and stiffness. Further analyses, adjusted for additional potential confounders, revealed that lung age was the spirometric parameter exhibiting the most significant regression coefficients with carotid features. Conversely, plasma C-reactive protein and matrix-metalloproteinases-2/9 levels did not influence this relationship. The present findings point toward lung age as a potential marker of vascular remodeling and indicate that lung and vascular remodeling might share common pathophysiological mechanisms in hypertensive subjects.

An Efficient Protocol For The Generation Of Monocyte Derived Dendritic Cells Using Serum-free Media For Clinical Applications In Post Remission Aml Patients.

Protocols for the generation of dendritic cells (DCs) using serum as a supplementation of culture media leads to reactions due to animal proteins and disease transmissions. Several types of serum-free media (SFM), based on good manufacture practices (GMP), have recently been used and seem to be a viable option. The aim of this study was to evaluate the results of the differentiation, maturation, and function of DCs from Acute Myeloid Leukemia patients (AML), generated in SFM and medium supplemented with autologous serum (AS). DCs were analyzed by phenotype characteristics, viability, and functionality. The results showed the possibility of generating viable DCs in all the conditions tested. In patients, the X-VIVO 15 medium was more efficient than the other media tested in the generation of DCs producing IL-12p70 (p=0.05). Moreover, the presence of AS led to a significant increase of IL-10 by DCs as compared with CellGro (p=0.05) and X-Vivo15 (p=0.05) media, both in patients and donors. We concluded that SFM was efficient in the production of DCs for immunotherapy in AML patients. However, the use of AS appears to interfere with the functional capacity of the generated DCs.

Diet Carotenoid Lutein Modulates The Expression Of Genes Related To Oxygen Transporters And Decreases Dna Damage And Oxidative Stress In Mice.

Lutein (LT) is a carotenoid obtained by diet and despite its antioxidant activity had been biochemically reported, few studies are available concerning its influence on the expression of antioxidant genes. The expression of 84 genes implicated in antioxidant defense was quantified using quantitative reverse transcription polymerase chain reaction array. DNA damage was measured by comet assay and glutathione (GSH) and thiobarbituric acid reactive substances (TBARS) were quantified as biochemical parameters of oxidative stress in mouse kidney and liver. cDDP treatment reduced concentration of GSH and increased TBARS, parameters that were ameliorated in treatment associated with LT. cDDP altered the expression of 32 genes, increasing the expression of GPx2, APC, Nqo1 and CCs. LT changed the expression of 37 genes with an induction of 13 mainly oxygen transporters. In treatments associating cDDP and LT, 30 genes had their expression changed with a increase of the same genes of the cDDP treatment alone. These results suggest that LT might act scavenging reactive species and also inducing the expression of genes related to a better antioxidant response, highlighting the improvement of oxygen transport. This improved redox state of the cell through LT treatment could be related to the antigenotoxic and antioxidant effects observed.

Overexpression Of Ucp1 In Tobacco Induces Mitochondrial Biogenesis And Amplifies A Broad Stress Response.

Uncoupling protein one (UCP1) is a mitochondrial inner membrane protein capable of uncoupling the electrochemical gradient from adenosine-5'-triphosphate (ATP) synthesis, dissipating energy as heat. UCP1 plays a central role in nonshivering thermogenesis in the brown adipose tissue (BAT) of hibernating animals and small rodents. A UCP1 ortholog also occurs in plants, and aside from its role in uncoupling respiration from ATP synthesis, thereby wasting energy, it plays a beneficial role in the plant response to several abiotic stresses, possibly by decreasing the production of reactive oxygen species (ROS) and regulating cellular redox homeostasis. However, the molecular mechanisms by which UCP1 is associated with stress tolerance remain unknown. Here, we report that the overexpression of UCP1 increases mitochondrial biogenesis, increases the uncoupled respiration of isolated mitochondria, and decreases cellular ATP concentration. We observed that the overexpression of UCP1 alters mitochondrial bioenergetics and modulates mitochondrial-nuclear communication, inducing the upregulation of hundreds of nuclear- and mitochondrial-encoded mitochondrial proteins. Electron microscopy analysis showed that these metabolic changes were associated with alterations in mitochondrial number, area and morphology. Surprisingly, UCP1 overexpression also induces the upregulation of hundreds of stress-responsive genes, including some involved in the antioxidant defense system, such as superoxide dismutase (SOD), glutathione peroxidase (GPX) and glutathione-S-transferase (GST). As a consequence of the increased UCP1 activity and increased expression of oxidative stress-responsive genes, the UCP1-overexpressing plants showed reduced ROS accumulation. These beneficial metabolic effects may be responsible for the better performance of UCP1-overexpressing lines in low pH, high salt, high osmolarity, low temperature, and oxidative stress conditions. Overexpression of UCP1 in the mitochondrial inner membrane induced increased uncoupling respiration, decreased ROS accumulation under abiotic stresses, and diminished cellular ATP content. These events may have triggered the expression of mitochondrial and stress-responsive genes in a coordinated manner. Because these metabolic alterations did not impair plant growth and development, UCP1 overexpression can potentially be used to create crops better adapted to abiotic stress conditions.

Aquatic Toxicity Of Dyes Before And After Photo-fenton Treatment.

This study evaluated the ecotoxicity of five dyes to freshwater organisms before and during their photo-Fenton degradation. EC50 (48h) of the five tested dyes ranged from of 6.9 to >1000mgL(-1) for Daphnia similis. In the chronic tests IC50 (72h) varied from 65 to >100mgL(-1) for Pseudokirchneriella subcapitata and IC50 (8 days) from 0.5 to 410mgL(-1) for Ceriodaphnia dubia. Toxicity tests revealed that although the applied treatment was effective for decolorization of the dye, the partial mineralization may be responsible for the presence of degradation products which can be either more toxic than the original dye, as is the case of Vat Green 3 and Reactive Black 5, lead to initially toxic products which may be further degraded to non toxic products (acid Orange 7 and Food Red 17), or generate non toxic products as in the case of Food Yellow 3. The results highlighted the importance of assessing both acute and chronic toxicity tests of treated sample before effluent discharge.

High Diagnostic Accuracy And Reproducibility Of Fine-needle Aspiration Cytology For Diagnosing Salivary Gland Tumors: Cytohistologic Correlation In 182 Cases.

The purpose of this study was to assess the efficacy and reproducibility of the cytologic diagnosis of salivary gland tumors (SGTs) using fine-needle aspiration cytology (FNAC). The study aimed to determine diagnostic accuracy, sensitivity, and specificity and to evaluate the extent of interobserver agreement. We retrospectively evaluated SGTs from the files of the Division of Pathology at the Clinics Hospital of São Paulo and Piracicaba Dental School between 2000 and 2006. We performed cytohistologic correlation in 182 SGTs. The sensitivity, specificity, positive predictive value, negative predictive value, and diagnostic accuracy were 94%, 100%, 100%, 100%, and 99%, respectively. The interobserver cytologic reproducibility showed significant statistical concordance (P < .0001). FNAC is an effective tool for performing a reliable preoperative diagnosis in SGTs and shows high diagnostic accuracy and consistent interobserver reproducibility. Further FNAC studies analyzing large samples of malignant SGTs and reactive salivary lesions are needed to confirm their accuracy.

A Putative Otu Domain-containing Protein 1 Deubiquitinating Enzyme Is Differentially Expressed In Thyroid Cancer And Identifies Less-aggressive Tumours.

This study aimed to identify novel biomarkers for thyroid carcinoma diagnosis and prognosis. We have constructed a human single-chain variable fragment (scFv) antibody library that was selected against tumour thyroid cells using the BRASIL method (biopanning and rapid analysis of selective interactive ligands) and phage display technology. One highly reactive clone, scFv-C1, with specific binding to papillary thyroid tumour proteins was confirmed by ELISA, which was further tested against a tissue microarray that comprised of 229 thyroid tissues, including: 110 carcinomas (38 papillary thyroid carcinomas (PTCs), 42 follicular carcinomas, 30 follicular variants of PTC), 18 normal thyroid tissues, 49 nodular goitres (NG) and 52 follicular adenomas. The scFv-C1 was able to distinguish carcinomas from benign lesions (P=0.0001) and reacted preferentially against T1 and T2 tumour stages (P=0.0108). We have further identified an OTU domain-containing protein 1, DUBA-7 deubiquitinating enzyme as the scFv-binding antigen using two-dimensional polyacrylamide gel electrophoresis and mass spectrometry. The strategy of screening and identifying a cell-surface-binding antibody against thyroid tissues was highly effective and resulted in a useful biomarker that recognises malignancy among thyroid nodules and may help identify lower-risk cases that can benefit from less-aggressive management.

Association Between Prehypertension, Metabolic And Inflammatory Markers, Decreased Adiponectin And Enhanced Insulinemia In Obese Subjects.

Obesity is associated with development of the cardiorenal metabolic syndrome, which is a constellation of risk factors, such as insulin resistance, inflammatory response, dyslipidemia, and high blood pressure that predispose affected individuals to well-characterized medical conditions such as diabetes, cardiovascular and kidney chronic disease. The study was designed to establish relationship between metabolic and inflammatory disorder, renal sodium retention and enhanced blood pressure in a group of obese subjects compared with age-matched, lean volunteers. The study was performed after 14 h overnight fast after and before OGTT in 13 lean (BMI 22.92 ± 2.03 kg/m(2)) and, 27 obese (BMI 36.15 ± 3.84 kg/m(2)) volunteers. Assessment of HOMA-IR and QUICKI index were calculated and circulating concentrations of TNF-α, IL-6 and C-reactive protein, measured by immunoassay. THE STUDY SHOWS THAT A HYPERINSULINEMIC (HI: 10.85 ± 4.09 μg/ml) subgroup of well-characterized metabolic syndrome bearers-obese subjects show higher glycemic and elevated blood pressure levels when compared to lean and normoinsulinemic (NI: 5.51 ± 1.18 μg/ml, P < 0.027) subjects. Here, the combination of hyperinsulinemia, higher HOMA-IR (HI: 2.19 ± 0.70 (n = 12) vs. LS: 0.83 ± 0.23 (n = 12) and NI: 0.98 ± 0.22 (n = 15), P < 0.0001) associated with lower QUICKI in HI obese when compared with LS and NI volunteers (P < 0.0001), suggests the occurrence of insulin resistance and a defect in insulin-stimulated peripheral action. Otherwise, the adiponectin measured in basal period was significantly enhanced in NI subjects when compared to HI groups (P < 0.04). The report also showed a similar insulin-mediated reduction of post-proximal urinary sodium excretion in lean (LS: 9.41 ± 0.68% vs. 6.38 ± 0.92%, P = 0.086), and normoinsulinemic (NI: 8.41 ± 0.72% vs. 5.66 ± 0.53%, P = 0.0025) and hyperinsulinemic obese subjects (HI: 8.82 ± 0.98% vs. 6.32 ± 0.67%, P = 0.0264), after oral glucose load, despite elevated insulinemic levels in hyperinsulinemic obeses. In conclusion, this study highlights the importance of adiponectin levels and dysfunctional inflammatory modulation associated with hyperinsulinemia and peripheral insulin resistance, high blood pressure, and renal dysfunction in a particular subgroup of obeses.

Mechanical Properties And Fracture Dynamics Of Silicene Membranes.

As graphene has become one of the most important materials, there is renewed interest in other similar structures. One example is silicene, the silicon analogue of graphene. It shares some of the remarkable graphene properties, such as the Dirac cone, but presents some distinct ones, such as a pronounced structural buckling. We have investigated, through density functional based tight-binding (DFTB), as well as reactive molecular dynamics (using ReaxFF), the mechanical properties of suspended single-layer silicene. We calculated the elastic constants, analyzed the fracture patterns and edge reconstructions. We also addressed the stress distributions, unbuckling mechanisms and the fracture dependence on the temperature. We analysed the differences due to distinct edge morphologies, namely zigzag and armchair.