Non-phenotypic tests to detect and characterize antibiotic resistance mechanisms in Enterobacteriaceae

In the past 2 decades, we have observed a rapid increase of infections due to multidrug-resistant Enterobacteriaceae. Regrettably, these isolates possess genes encoding for extended-spectrum β-lactamases (e.g., blaCTX-M, blaTEM, blaSHV) or plasmid-mediated AmpCs (e.g., blaCMY) that confer resistance to last-generation cephalosporins. Furthermore, other resistance traits against quinolones (e.g., mutations in gyrA and parC, qnr elements) and aminoglycosides (e.g., aminoglycosides modifying enzymes and 16S rRNA methylases) are also frequently co-associated. Even more concerning is the rapid increase of Enterobacteriaceae carrying genes conferring resistance to carbapenems (e.g., blaKPC, blaNDM). Therefore, the spread of these pathogens puts in peril our antibiotic options. Unfortunately, standard microbiological procedures require several days to isolate the responsible pathogen and to provide correct antimicrobial susceptibility test results. This delay impacts the rapid implementation of adequate antimicrobial treatment and infection control countermeasures. Thus, there is emerging interest in the early and more sensitive detection of resistance mechanisms. Modern non-phenotypic tests are promising in this respect, and hence, can influence both clinical outcome and healthcare costs. In this review, we present a summary of the most advanced methods (e.g., next-generation DNA sequencing, multiplex PCRs, real-time PCRs, microarrays, MALDI-TOF MS, and PCR/ESI MS) presently available for the rapid detection of antibiotic resistance genes in Enterobacteriaceae. Taking into account speed, manageability, accuracy, versatility, and costs, the possible settings of application (research, clinic, and epidemiology) of these methods and their superiority against standard phenotypic methods are discussed.

Studies to localize and characterize the isoform specific functional differences between cardiac and skeletal troponin C

Thin filament regulation of muscle contraction is a calcium dependent process mediated by the Tn complex. Calcium is released into the sarcomere and is bound by TnC. The subsequent conformation change in TnC is thought to begin a cascade of events that result in the activation of the actin-myosin ATPase. While the general events of this cascade are known, the molecular mechanisms of this signal transduction event are not. Recombinant DNA techniques, physiological and biochemical studies have been used to localize and characterize the structural domains of TnC that play a role in the calcium dependent signal transduction event that serves to trigger muscle contraction. The strategy exploited the observed functional differences between the isoforms of TnC to map regions of functional significance to the proteins. Chimeric cardiac-skeletal TnC proteins were generated to localize the domains of TnC that are required for maximal function in the myofibrilar ATPase assay. Characterization of these regions has yielded information concerning the molecular mechanism of muscle contraction. ^

Evaluating gillnetting protocols to characterize lacustrine fish communities

Ecological research and monitoring of lacustrine ecosystems often requires a whole-lake assessment of fish communities. Gillnet sampling offers an efficient means of estimating abundance, biomass and fish community composition. However the choice of gillnet sampling protocol may influence lake characterization via physical properties of the nets and allocation of sampling effort between littoral, benthic and pelagic habitats. This paper compares two commonly used, whole-lake sampling protocols applied across 17 prealpine, subalpine and alpine European lakes ranging widely in size, depth and altitude to determine their relative strength for research and management applications. Effort-corrected estimates of abundance, biomass and species richness were correlated between the protocols and both distinguished the trout-dominated alpine communities from subalpine and prealpine lakes dominated by whitefish and perch. A considerable amount of variance remained unexplained between the two protocols however, which seemed to correspond with differences in the proportion of effort among benthic and pelagic habitats. We suggest that both the European standard (CEN) and vertical (VERT) netting protocols are suitable for assessing ecological status and monitoring changes in lake fish communities through time. However the details of each protocol should be kept in mind when comparing fish communities between lakes. Mesh sizes used in CEN nets produce a more even size frequency distribution, suggesting that this protocol is most appropriate for assessing size structure of fish assemblages. The high proportion of netting effort in benthic habitats shallower than 70 m depth under the CEN protocol means that, particularly in larger lakes, outcomes will be disproportionately influenced by the ecological condition of this habitat. The VERT protocol presumably provides a more accurate estimate of whole-lake CPUE and community composition because effort, in terms of net area, is more evenly distributed across the entire volume of the lake. This is particularly important in large and deep lakes where pelagic habitats occupy a high proportion of the lake volume.

A De-Embedding Method to Characterize Differential

This paper analyses the noise and gain measurement of microwave differential amplifiers using two passive baluns. A model of the baluns that includes potential losses and unbalances has been considered. This analysis allows to de-embed the actual performance of the differential device from the single-ended measurements of the two-port cascaded system and the baluns. The method has been validated with measured results from a fully-differential amplifier prototype.

Preliminary test to characterize the soundscape of the Plaza Mayor in Madrid

This paper is a first step of a research about the analysis of the richness of the existing sounds in the Plaza Mayor, due to the old and traditional shops and bars under its porticoes together with the huge daily affluence of people. In this paper we study the sound preferences of the salesmen and bar tenders at those traditional shops. These sound preferences include particular sounds, time of occurrence and date of specific annoying and pleasant sounds perceived at the square and the shops surrounding it. To carry out this study, several noise level measurements and socio-acoustic surveys were held. We will also try to correlate sound preferences and annoyance with noise levels of specific events existing at this particular square.

HERMES: Towards an Integrated Toolbox to Characterize Functional and Effective Brain Connectivity

The analysis of the interdependence between time series has become an important field of research in the last years, mainly as a result of advances in the characterization of dynamical systems from the signals they produce, the introduction of concepts such as generalized and phase synchronization and the application of information theory to time series analysis. In neurophysiology, different analytical tools stemming from these concepts have added to the ‘traditional’ set of linear methods, which includes the cross-correlation and the coherency function in the time and frequency domain, respectively, or more elaborated tools such as Granger Causality. This increase in the number of approaches to tackle the existence of functional (FC) or effective connectivity (EC) between two (or among many) neural networks, along with the mathematical complexity of the corresponding time series analysis tools, makes it desirable to arrange them into a unified-easy-to-use software package. The goal is to allow neuroscientists, neurophysiologists and researchers from related fields to easily access and make use of these analysis methods from a single integrated toolbox. Here we present HERMES (http://hermes.ctb.upm.es), a toolbox for the Matlab® environment (The Mathworks, Inc), which is designed to study functional and effective brain connectivity from neurophysiological data such as multivariate EEG and/or MEG records. It includes also visualization tools and statistical methods to address the problem of multiple comparisons. We believe that this toolbox will be very helpful to all the researchers working in the emerging field of brain connectivity analysis.

HERMES: towards an integrated toolbox to characterize functional and effective brain connectivity

The analysis of the interdependence between time series has become an important field of research in the last years, mainly as a result of advances in the characterization of dynamical systems from the signals they produce, the introduction of concepts such as generalized and phase synchronization and the application of information theory to time series analysis. In neurophysiology, different analytical tools stemming from these concepts have added to the ?traditional? set of linear methods, which includes the cross-correlation and the coherency function in the time and frequency domain, respectively, or more elaborated tools such as Granger Causality. This increase in the number of approaches to tackle the existence of functional (FC) or effective connectivity (EC) between two (or among many) neural networks, along with the mathematical complexity of the corresponding time series analysis tools, makes it desirable to arrange them into a unified, easy-to-use software package. The goal is to allow neuroscientists, neurophysiologists and researchers from related fields to easily access and make use of these analysis methods from a single integrated toolbox. Here we present HERMES (http://hermes.ctb.upm.es), a toolbox for the Matlab® environment (The Mathworks, Inc), which is designed to study functional and effective brain connectivity from neurophysiological data such as multivariate EEG and/or MEG records. It includes also visualization tools and statistical methods to address the problem of multiple comparisons. We believe that this toolbox will be very helpful to all the researchers working in the emerging field of brain connectivity analysis.

Compressibility as a means to detect and characterize globular protein states.

We report compressibility data on single-domain, globular proteins which suggest a general relationship between protein conformational transitions and delta kzeroS, the change in the partial specific adiabatic compressibility which accompanies the transition. Specifically, we find transitions between native and compact intermediate states to be accompanied by small increases in kzeroS of +(1-4) x 10(-6) cm3.g-1.bar-1 (1 bar = 100 kPa). By contrast, transitions between native and partially unfolded states are accompanied by small decreases in kzeroS of -(3-7) x 10(-6) cm3.g-1.bar-1, while native-to-fully unfolded transitions result in large decreases in kzeroS of -(18-20) x 10(-6) cm3.g-1.bar-1. Thus, for the single-domain, globular proteins studied here, changes in kzeroS correlate with the type of transition being monitored, independent of the specific protein. Consequently, kzeroS measurements may provide a convenient approach for detecting the existence of and for defining the nature of protein transitions, while also characterizing the hydration properties of individual protein states.

Invariance and restriction toward a limited set of self-antigens characterize neonatal IgM antibody repertoires and prevail in autoreactive repertoires of healthy adults.

Analysis of the reactivity of IgM with self-antigens in tissues by a quantitative immunoblotting technique showed striking invariance among newborns in the human and in the mouse. The self-reactive repertoire of IgM of adults was also markedly conserved; it comprised most anti-self reactivities that prevailed among neonates. Multivariate analysis confirmed the homogeneity of IgM repertoires of neonates toward self- and non-self-antigens. Multivariate analysis discriminated between newborn and adult repertoires for reactivity with two of five sources of self-proteins and with non-self-antigens. Our observations support the concept that naturally activated B lymphocytes are selected early in development and throughout life for reactivity with a restricted set of self-antigens.

Spectral BRDF-based determination of proper measurement geometries to characterize color shift of special effect coatings

A reduced set of measurement geometries allows the spectral reflectance of special effect coatings to be predicted for any other geometry. A physical model based on flake-related parameters has been used to determine nonredundant measurement geometries for the complete description of the spectral bidirectional reflectance distribution function (BRDF). The analysis of experimental spectral BRDF was carried out by means of principal component analysis. From this analysis, a set of nine measurement geometries was proposed to characterize special effect coatings. It was shown that, for two different special effect coatings, these geometries provide a good prediction of their complete color shift.

The use of simultaneous H-1 & P-31 magic angle spinning nuclear magnetic resonance measurements to characterize energy metabolism during the conversion of muscle to meat

In order to investigate the potential of magic angle spinning nuclear magnetic resonance (MAS NMR) in the elucidation of post-mortem metabolism in muscle biopsies, simultaneous H-1 and (31)p MAS NMR measurements were made continuously on postmortem (20 min to 24 h) muscle longissimus samples from rabbits. The animals had either been or not been given adrenaline (0.5 mg kg(-1) 4 h pre-slaughter) to deplete stores of muscle glycogen. The intracellular pH was calculated from H-1 spectra, and the post-mortem rate of formation of lactate was followed and quantified. Comparison of measurements made on muscle samples from rabbits treated with adrenaline with measurements made on muscle samples from untreated' rabbits revealed significant effects of adrenaline treatment on both pH (pH24 h = 6.42 vs. pH24 It = 5.60) and formation of lactate (16 mmol g(-1) vs. 65 mmol g(-1)). The P-31 NMR spectra were used to follow the rate of degradation of ATP and phosphocreatine. The present study clearly shows that MAS NMR has potential for the study of post-mortem energy metabolism.

Application of a generalized thermodynamic approach to characterize mesoporous materials

Equilibrium adsorption and desorption in mesoporous adsorbents is considered on the basis of rigorous thermodynamic analysis, in which the curvature-dependent solid-fluid potential and the compressibility of the adsorbed phase are accounted for. The compressibility of the adsorbed phase is considered for the first time in the literature in the framework of a rigorous thermodynamic approach. Our model is a further development of continuum thermodynamic approaches proposed by Derjaguin and Broekhoff and de Boer, and it is based on a reference isotherm of a non-porous material having the same chemical structure as that of the pore wall. In this improved thermodynamic model, we incorporated a prescription for transforming the solid-fluid potential exerted by the flat reference surface to the potential inside cylindrical and spherical pores. We relax the assumption that the adsorbed film density is constant and equal to that of the saturated liquid. Instead, the density of the adsorbed fluid is allowed to vary over the adsorbed film thickness and is calculated by an equation of state. As a result, the model is capable to describe the adsorption-desorption reversibility in cylindrical pores having diameter less than 2 nm. The generalized thermodynamic model may be applied to the pore size characterization of mesoporous materials instead of much more time-consuming molecular approaches. (c) 2005 Elsevier B.V. All rights reserved.