Comparison of methods for the identification of coagulase-negative staphylococci

Coagulase-negative staphylococci (CNS) species identification is still difficult for most clinical laboratories. The scheme proposed by Kloos and Schleifer and modified by Bannerman is the reference method used for the identification of staphylococcal species and subspecies; however, this method is relatively laborious for routine use since it requires the utilization of a large number of biochemical tests. The objective of the present study was to compare four methods, i.e., the reference method, the API Staph system (bioMérieux) and two methods modified from the reference method in our laboratory (simplified method and disk method), in the identification of 100 CNS strains. Compared to the reference method, the simplified method and disk method correctly identified 100 and 99% of the CNS species, respectively, while this rate was 84% for the API Staph system. Inaccurate identification by the API Staph method was observed for Staphylococcus epidermidis (2.2%), S. hominis (25%), S. haemolyticus (37.5%), and S. warneri (47.1%). The simplified method using the simple identification scheme proposed in the present study was found to be efficient for all strains tested, with 100% sensitivity and specificity and proved to be available alternative for the identification of staphylococci, offering, higher reliability and lower cost than the currently available commercial systems. This method would be very useful in clinical microbiology laboratory, especially in places with limited resources.

Identification of an immunogenic protein of Giardia lamblia using monoclonal antibodies generated from infected mice

The humoral immune response plays an important role in the clearance of Giardia lamblia. However, our knowledge about the specific antigens of G. lamblia that induce a protective immune response is limited. The purpose of this study was to identify and characterise the immunogenic proteins of G. lamblia in a mouse model. We generated monoclonal antibodies (moAbs) specific to G. lamblia (1B10, 2C9.D11, 3C10.E5, 3D10, 5G8.B5, 5F4, 4C7, 3C5 and 3C6) by fusing splenocytes derived from infected mice. Most of these moAbs recognised a band of ± 71 kDa (5G8 protein) and this protein was also recognised by serum from the infected mice. We found that the moAbs recognised conformational epitopes of the 5G8 protein and that this antigen is expressed on the cell surface and inside trophozoites. Additionally, antibodies specific to the 5G8 protein induced strong agglutination (> 70-90%) of trophozoites. We have thus identified a highly immunogenic antigen of G. lamblia that is recognised by the immune system of infected mice. In summary, this study describes the identification and partial characterisation of an immunogenic protein of G. lamblia. Additionally, we generated a panel of moAbs specific for this protein that will be useful for the biochemical and immunological characterisation of this immunologically interesting Giardia molecule.

The identification and differentiation of the Candida parapsilosis complex species by polymerase chain reaction-restriction fragment length polymorphism of the internal transcribed spacer region of the rDNA

Currently, it is accepted that there are three species that were formerly grouped under Candida parapsilosis: C. para- psilosis sensu stricto, Candida orthopsilosis, andCandida metapsilosis. In fact, the antifungal susceptibility profiles and distinct virulence attributes demonstrate the differences in these nosocomial pathogens. An accurate, fast, and economical identification of fungal species has been the main goal in mycology. In the present study, we searched sequences that were available in the GenBank database in order to identify the complete sequence for the internal transcribed spacer (ITS)1-5.8S-ITS2 region, which is comprised of the forward and reverse primers ITS1 and ITS4. Subsequently, an in silico polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was performed to differentiate the C. parapsilosis complex species. Ninety-eight clinical isolates from patients with fungaemia were submitted for analysis, where 59 isolates were identified as C. parapsilosis sensu stricto, 37 were identified as C. orthopsilosis, and two were identified as C. metapsilosis. PCR-RFLP quickly and accurately identified C. parapsilosis complex species, making this method an alternative and routine identification system for use in clinical mycology laboratories.

Identification of reference genes for expression analysis by real-time quantitative PCR in drought-stressed soybean

The objective of this work was to validate, by quantitative PCR in real time (RT-qPCR), genes to be used as reference in studies of gene expression in soybean in drought-stressed trials. Four genes commonly used in soybean were evaluated: Gmβ-actin, GmGAPDH, GmLectin and GmRNAr18S. Total RNA was extracted from six samples: three from roots in a hydroponic system with different drought intensities (0, 25, 50, 75 and 100 minutes of water stress), and three from leaves of plants grown in sand with different soil moistures (15, 5 and 2.5% gravimetric humidity). The raw cycle threshold (Ct) data were analyzed, and the efficiency of each primer was calculated for an overall analysis of the Ct range among the different samples. The GeNorm application was used to evaluate the best reference gene, according to its stability. The GmGAPDH was the least stable gene, with the highest mean values of expression stability (M), and the most stable genes, with the lowest M values, were the Gmβ-actin and GmRNAr18S, when both root and leaves samples were tested. These genes can be used in RT-qPCR as reference gene for expression analysis.

Identification of flexural stiffness parameters of beams

A three degree of freedom model of the dynamic mass at the middle of a test sample, resembling a Stockbridge neutraliser, is introduced. This model is used to identify the hereby called equivalent complex cross section flexural stiffness (ECFS) of the beam element which is part of the whole test sample. This ECFS, once identified, gives the effective cross section flexural stiffness of the beam as well as its effective damping, measured as the loss factor of an equivalent viscoelastic beam. The beam element of the test sample may be of any complexity, such as a segment of stranded cable of the ACSR type. These data are important parameters for the design of overhead power transmission lines and other cable structures. A cost function is defined and used in the identification of the ECFS. An experiment, designed to measure the dynamic masses of two test samples, is described. Experimental and identified results are presented and discussed.

Identification of Flexural Stiffness Parameters of Beams

A three degree of freedom model of the dynamic mass at the middle of a test sample, resembling a Stockbridge neutraliser, is introduced. This model is used to identify the hereby called equivalent complex cross section flexural stiffness (ECFS) of the beam element which is part of the whole test sample. This ECFS, once identified, gives the effective cross section flexural stiffness of the beam as well as its effective damping, measured as the loss factor of an equivalent viscoelastic beam. The beam element of the test sample may be of any complexity, such as a segment of stranded cable of the ACSR type. These data are important parameters for the design of overhead power transmission lines and other cable structures. A cost function is defined and used in the identification of the ECFS. An experiment, designed to measure the dynamic masses of two test samples, is described. Experimental and identified results are presented and discussed.

Fuzzy expert system in the prediction of neonatal resuscitation

In view of the importance of anticipating the occurrence of critical situations in medicine, we propose the use of a fuzzy expert system to predict the need for advanced neonatal resuscitation efforts in the delivery room. This system relates the maternal medical, obstetric and neonatal characteristics to the clinical conditions of the newborn, providing a risk measurement of need of advanced neonatal resuscitation measures. It is structured as a fuzzy composition developed on the basis of the subjective perception of danger of nine neonatologists facing 61 antenatal and intrapartum clinical situations which provide a degree of association with the risk of occurrence of perinatal asphyxia. The resulting relational matrix describes the association between clinical factors and risk of perinatal asphyxia. Analyzing the inputs of the presence or absence of all 61 clinical factors, the system returns the rate of risk of perinatal asphyxia as output. A prospectively collected series of 304 cases of perinatal care was analyzed to ascertain system performance. The fuzzy expert system presented a sensitivity of 76.5% and specificity of 94.8% in the identification of the need for advanced neonatal resuscitation measures, considering a cut-off value of 5 on a scale ranging from 0 to 10. The area under the receiver operating characteristic curve was 0.93. The identification of risk situations plays an important role in the planning of health care. These preliminary results encourage us to develop further studies and to refine this model, which is intended to implement an auxiliary system able to help health care staff to make decisions in perinatal care.

Identification of anaerobic threshold using heart rate response during dynamic exercise

The objective of the present study was to characterize the heart rate (HR) patterns of healthy males using the autoregressive integrated moving average (ARIMA) model over a power range assumed to correspond to the anaerobic threshold (AT) during discontinuous dynamic exercise tests (DDET). Nine young (22.3 ± 1.57 years) and 9 middle-aged (MA) volunteers (43.2 ± 3.53 years) performed three DDET on a cycle ergometer. Protocol I: DDET in steps with progressive power increases of 10 W; protocol II: DDET using the same power values as protocol 1, but applied randomly; protocol III: continuous dynamic exercise protocol with ventilatory and metabolic measurements (10 W/min ramp power), for the measurement of ventilatory AT. HR was recorded and stored beat-to-beat during DDET, and analyzed using the ARIMA (protocols I and II). The DDET experiments showed that the median physical exercise workloads at which AT occurred were similar for protocols I and II, i.e., AT occurred between 75 W (116 bpm) and 85 W (116 bpm) for the young group and between 60 W (96 bpm) and 75 W (107 bpm) for group MA in protocols I and II, respectively; in two MA volunteers the ventilatory AT occurred at 90 W (108 bpm) and 95 W (111 bpm). This corresponded to the same power values of the positive trend in HR responses. The change in HR response using ARIMA models at submaximal dynamic exercise powers proved to be a promising approach for detecting AT in normal volunteers.

Distribution of human immunodeficiency virus type 1 subtypes in the state of Amazonas, Brazil, and subtype C identification

Few studies have reported the molecular epidemiological characterization of HIV-1 in the Northern region of Brazil. The present study reports the molecular and epidemiological characterization of 31 HIV-1 isolates from blood donors from the State of Amazonas who donated blood between April 2006 and March 2007. Serum/plasma samples from all donors were screened for HIV antibodies by ELISA and the results confirmed by Western blot analysis. Genomic DNA was extracted from the buffy coat using the Super Quik-Gene-DNA Isolation kit. Nested PCR was performed on the env, gag, and pol regions of HIV-1 using the Gene Amp PCR System 9700. Sequencing reactions were performed using the inner PCR primers and the DYEnamic™ ET Dye Terminator Kit, and phylogenetic analysis was performed using the gag, pol, and env gene sequences. We collected samples from 31 blood donors who tested positive for HIV-1 in confirmatory experiments. The male:female ratio of blood donors was 3.4:1, and the mean age was 32.4 years (range: 19 to 61 years). Phylogenetic analysis showed that subtype B is the most prevalent among Northern Brazilian HIV-1-seropositive blood donors. One HIV-1 subtype C and one circulating recombinant form (CRF_BF) of HIV-1 were identified in the State of Amazonas. This is the first study showing the occurrence of a possible "homogenous" subtype C in this region of Brazil. This finding could contribute to a better characterization of the HIV-1 strains that circulate in the country.

Early detection of metabolic and energy disorders by thermal time series stochastic complexity analysis

Maintenance of thermal homeostasis in rats fed a high-fat diet (HFD) is associated with changes in their thermal balance. The thermodynamic relationship between heat dissipation and energy storage is altered by the ingestion of high-energy diet content. Observation of thermal registers of core temperature behavior, in humans and rodents, permits identification of some characteristics of time series, such as autoreference and stationarity that fit adequately to a stochastic analysis. To identify this change, we used, for the first time, a stochastic autoregressive model, the concepts of which match those associated with physiological systems involved and applied in male HFD rats compared with their appropriate standard food intake age-matched male controls (n=7 per group). By analyzing a recorded temperature time series, we were able to identify when thermal homeostasis would be affected by a new diet. The autoregressive time series model (AR model) was used to predict the occurrence of thermal homeostasis, and this model proved to be very effective in distinguishing such a physiological disorder. Thus, we infer from the results of our study that maximum entropy distribution as a means for stochastic characterization of temperature time series registers may be established as an important and early tool to aid in the diagnosis and prevention of metabolic diseases due to their ability to detect small variations in thermal profile.

Assessment of physiological potential of cucumber seeds using the software Seedling Vigor Imaging System® (SVIS®)

The software Seed Vigor Imaging System (SVIS®), has been successfully used to evaluate seed physiological potential by automated analyses of scanned seedlings. In this research, the efficiency of this system was compared to other tests accepted for assessing cucumber (Cucumis sativus L.) seed vigor of distinct seed lots of Supremo and Safira cultivars. Seeds were subjected to germination, traditional and saturated salt accelerated aging, seedling emergence, seedling length and SVIS analyses (determination of vigor indices and seedling growth uniformity, lengths of primary root, hypocotyl and whole seedlings). It was also determined whether the definition of seedling growth/uniformity ratios affects the sensitivity of the SVIS®. Results showed that analyses SVIS have provided consistent identification of seed lots performance, and have produced information comparable to those from recommended seed vigor tests, thus demonstrating a suitable sensitivity for a rapid and objective evaluation of physiological potential of cucumber seeds. Analyses of four-days-old cucumber seedlings using the SVIS® are more accurate and growth/uniformity does not affect the precision of results.