269 research outputs found
Effect of Extracellular pH on Selectin Adhesion: Theory and Experiment
AbstractSelectins mediate circulatory leukocyte trafficking to sites of inflammation and trauma, and the extracellular microenvironments at these sites often become acidic. In this study, we investigated the influence of slightly acidic pH on the binding dynamics of selectins (P-, L-, and E-selectin) to P-selectin glycoprotein ligand-1 (PSGL-1) via computational modeling (molecular dynamics) and experimental rolling assays under shear in vitro. The P-selectin/PSGL-1 binding is strengthened at acidic pH, as evidenced by the formation of a new hydrogen bond (seen computationally) and the observed decrease in the rolling velocities of model cells. In the case of L-selectin/PSGL-1 binding dynamics, the binding strength and frequency increase at acidic pH, as indicated by the greater cell-rolling flux of neutrophils and slower rolling velocities of L-selectin-coated microspheres, respectively. The cell flux is most likely due to an increased population of L-selectin in the high-affinity conformation as pH decreases, whereas the velocities are due to increased L-selectin/PSGL-1 contacts. In contrast to P- and L-selectin, the E-selectin/PSGL-1 binding does not exhibit significant changes at acidic pH levels, as shown both experimentally and computationally
Matrix Assisted Laser Desorption Ionization-Time-of-Flight mass spectrometry identification of Mycobacterium bovis in Bovinae.
In this study, Matrix Assisted Laser Desorption Ionization-Time-of-Flight (MALDITOF) mass spectrometry was used to identify Mycobacterium bovis from cattle and buffalo tissue isolates from the North and South regions of Brazil, grown in solid medium and previously identified by Polymerase Chain Reaction (PCR) based on Region of Difference 4 (RD4), sequencing and spoligotyping. For this purpose, the protein extraction protocol and the mass spectra reference database were optimized for the identification of 80 clinical isolates of mycobacteria. As a result of this optimization, it was possible to identify and differentiate M. bovis from other members of the Mycobacterium tuberculosis complex with 100% specificity, 90.91% sensitivity and 91.25% reliability. MALDI-TOF MS methodology described herein provides successful identification of M. bovis within bovine/bubaline clinical samples, demonstrating its usefulness for bovine tuberculosis diagnosis in the future
Epidemiological Study of Mycobacterium bovis Infection in Buffalo and Cattle in Amazonas, Brazil.
Bovine Tuberculosis (BTB) is an endemic disease in about one hundred countries, affecting the economy causing a decrease in productivity, condemnation of meat, and damaging the credibility on international trade. Additionally, Mycobacterium bovis the major causative agent for BTB can also infect humans causing a variety of clinical presentations. The aim of this study was to determine BTB prevalence and the main risk factors for theMycobacterium bovis prevalence in cattle and buffalos in Amazonas State, Brazil. Tissue samples from 151 animals (45 buffalo and 106 cattle from five herds with buffalo only, 22 herds with cattle only, and 12 herds with buffalo and cattle) were obtained from slaughterhouses under State Veterinary Inspection. M. bovis were isolated on Stonebrink medium. The positive cultures were confirmed by polymerase chain reaction (PCR) testing. The apparent herd and animal prevalence rates were 56.4 and 5.40%, respectively. Regarding animal species, the apparent prevalence rates were 3% in cattle and 11.8% in buffalo. Generalized Linear Mixed Models (GLMM) with random effect were used to assess the association with risk factors on the prevalence. Species (buffalo), herds size (>100 animals) and the presence of both species (buffalo and cattle) in the herd were the major risk factors for the infection by Mycobacterium bovis in the region. The findings reveal an urgent need for evidence-based effective intervention to reduce BTB prevalence in cattle and buffalo and prevent its spread to the human population. Studies are needed to understand why buffalo are more likely to be infected by M. bovis than cattle in Amazon. Recommendations for zoning, use of data from the inspection services to generate information regarding BTB focus, adoption of epidemiological tools, and discouragement of practices that promote the mixing of cattle and buffalo, were made
Ab initio van der Waals interactions in simulations of water alter structure from mainly tetrahedral to high-density-like
The structure of liquid water at ambient conditions is studied in ab initio
molecular dynamics simulations using van der Waals (vdW) density-functional
theory, i.e. using the new exchange-correlation functionals optPBE-vdW and
vdW-DF2. Inclusion of the more isotropic vdW interactions counteracts highly
directional hydrogen-bonds, which are enhanced by standard functionals. This
brings about a softening of the microscopic structure of water, as seen from
the broadening of angular distribution functions and, in particular, from the
much lower and broader first peak in the oxygen-oxygen pair-correlation
function (PCF), indicating loss of structure in the outer solvation shells. In
combination with softer non-local correlation terms, as in the new
parameterization of vdW-DF, inclusion of vdW interactions is shown to shift the
balance of resulting structures from open tetrahedral to more close-packed. The
resulting O-O PCF shows some resemblance with experiment for high-density water
(A. K. Soper and M. A. Ricci, Phys. Rev. Lett., 84:2881, 2000), but not
directly with experiment for ambient water. However, an O-O PCF consisting of a
linear combination of 70% from vdW-DF2 and 30% from experiment on low-density
liquid water reproduces near-quantitatively the experimental O-O PCF for
ambient water, indicating consistency with a two-liquid model with fluctuations
between high- and low-density regions
Transparent bionanocomposites with improved properties prepared from acetylated bacterial cellulose and poly(lactic acid) through a simple approach
The preparation and characterization of biocomposite materials with improved properties based on poly(lactic acid) (PLA) and bacterial cellulose, and, for comparative purposes, vegetal cellulose fibers, both in their pristine form or after acetylation, is reported. The composite materials were obtained through the simple and green mechanical compounding of a PLA matrix and bacterial cellulose nanofibrils (or vegetable fibers), and were characterized by TGA, DSC, tensile assays, DMA, SEM and water uptake. The bionanocomposites obtained from PLA and acetylated bacterial cellulose were particularly interesting, given the considerable improvement in thermal and mechanical properties, as evidenced by the significant increase in both elastic and Young moduli, and in the tensile strength (increments of about 100, 40 and 25%, respectively) at very low nanofiller loadings (up to 6%). These nanocomposites also showed low hygroscopicity and considerable transparency, features reported here for the first time.FCT - PTDC/QUI/68472/2006FCT - SFRH/BPD/63250/2009FCT - L. C. T/ E. T.FCT-CAPES 2009FCT - National Program for Scientific Re-equipmentRede/1509/RME/2005REEQ/515/CTM/200
Genetic Diversity and Potential Paths of Transmission of Mycobacterium bovis in the Amazon: the Discovery of M. bovis Lineage Lb1 Circulating in South America.
S66: A Well-balanced Database of Benchmark Interaction Energies Relevant to Biomolecular Structures
With numerous new quantum chemistry methods being developed in recent years and the promise of even more new methods to be developed in the near future, it is clearly critical that highly accurate, well-balanced, reference data for many different atomic and molecular properties be available for the parametrization and validation of these methods. One area of research that is of particular importance in many areas of chemistry, biology, and material science is the study of noncovalent interactions. Because these interactions are often strongly influenced by correlation effects, it is necessary to use computationally expensive high-order wave function methods to describe them accurately. Here, we present a large new database of interaction energies calculated using an accurate CCSD(T)/CBS scheme. Data are presented for 66 molecular complexes, at their reference equilibrium geometries and at 8 points systematically exploring their dissociation curves; in total, the database contains 594 points: 66 at equilibrium geometries, and 528 in dissociation curves. The data set is designed to cover the most common types of noncovalent interactions in biomolecules, while keeping a balanced representation of dispersion and electrostatic contributions. The data set is therefore well suited for testing and development of methods applicable to bioorganic systems. In addition to the benchmark CCSD(T) results, we also provide decompositions of the interaction energies by means of DFT-SAPT calculations. The data set was used to test several correlated QM methods, including those parametrized specifically for noncovalent interactions. Among these, the SCS-MI-CCSD method outperforms all other tested methods, with a root-mean-square error of 0.08 kcal/mol for the S66 data set
Random-phase approximation and its applications in computational chemistry and materials science
The random-phase approximation (RPA) as an approach for computing the
electronic correlation energy is reviewed. After a brief account of its basic
concept and historical development, the paper is devoted to the theoretical
formulations of RPA, and its applications to realistic systems. With several
illustrating applications, we discuss the implications of RPA for computational
chemistry and materials science. The computational cost of RPA is also
addressed which is critical for its widespread use in future applications. In
addition, current correction schemes going beyond RPA and directions of further
development will be discussed.Comment: 25 pages, 11 figures, published online in J. Mater. Sci. (2012
Direct Simulation of a Solidification Benchmark Experiment
International audienceA solidification benchmark experiment is simulated using a three-dimensional cellular automaton-finite element solidification model. The experiment consists of a rectangular cavity containing a Sn-3 wt pct Pb alloy. The alloy is first melted and then solidified in the cavity. A dense array of thermocouples permits monitoring of temperatures in the cavity and in the heat exchangers surrounding the cavity. After solidification, the grain structure is revealed by metallography. X-ray radiography and inductively coupled plasma spectrometry are also conducted to access a distribution map of Pb, or macrosegregation map. The solidification model consists of solutions for heat, solute mass, and momentum conservations using the finite element method. It is coupled with a description of the development of grain structure using the cellular automaton method. A careful and direct comparison with experimental results is possible thanks to boundary conditions deduced from the temperature measurements, as well as a careful choice of the values of the material properties for simulation. Results show that the temperature maps and the macrosegregation map can only be approached with a three-dimensional simulation that includes the description of the grain structure
Rationale, study design, and analysis plan of the Alveolar Recruitment for ARDS Trial (ART): study protocol for a randomized controlled trial
BACKGROUND:
Acute respiratory distress syndrome (ARDS) is associated with high in-hospital mortality. Alveolar recruitment followed by ventilation at optimal titrated PEEP may reduce ventilator-induced lung injury and improve oxygenation in patients with ARDS, but the effects on mortality and other clinical outcomes remain unknown. This article reports the rationale, study design, and analysis plan of the Alveolar Recruitment for ARDS Trial (ART).
METHODS/DESIGN:
ART is a pragmatic, multicenter, randomized (concealed), controlled trial, which aims to determine if maximum stepwise alveolar recruitment associated with PEEP titration is able to increase 28-day survival in patients with ARDS compared to conventional treatment (ARDSNet strategy). We will enroll adult patients with ARDS of less than 72 h duration. The intervention group will receive an alveolar recruitment maneuver, with stepwise increases of PEEP achieving 45 cmH2O and peak pressure of 60 cmH2O, followed by ventilation with optimal PEEP titrated according to the static compliance of the respiratory system. In the control group, mechanical ventilation will follow a conventional protocol (ARDSNet). In both groups, we will use controlled volume mode with low tidal volumes (4 to 6 mL/kg of predicted body weight) and targeting plateau pressure 6430 cmH2O. The primary outcome is 28-day survival, and the secondary outcomes are: length of ICU stay; length of hospital stay; pneumothorax requiring chest tube during first 7 days; barotrauma during first 7 days; mechanical ventilation-free days from days 1 to 28; ICU, in-hospital, and 6-month survival. ART is an event-guided trial planned to last until 520 events (deaths within 28 days) are observed. These events allow detection of a hazard ratio of 0.75, with 90% power and two-tailed type I error of 5%. All analysis will follow the intention-to-treat principle.
DISCUSSION:
If the ART strategy with maximum recruitment and PEEP titration improves 28-day survival, this will represent a notable advance to the care of ARDS patients. Conversely, if the ART strategy is similar or inferior to the current evidence-based strategy (ARDSNet), this should also change current practice as many institutions routinely employ recruitment maneuvers and set PEEP levels according to some titration metho
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