A closer look at multiple-clone Plasmodium vivax infections: detection methods, prevalence and consequences

The naturally occurring clonal diversity among field isolates of the major human malaria parasite Plasmodium vivax remained unexplored until the early 1990s, when improved molecular methods allowed the use of blood samples obtained directly from patients, without prior in vitro culture, for genotyping purposes. Here we briefly review the molecular strategies currently used to detect genetically distinct clones in patient-derived P. vivax samples, present evidence that multiple-clone P. vivax infections are commonly detected in areas with different levels of malaria transmission and discuss possible evolutionary and epidemiological consequences of the competition between genetically distinct clones in natural human infections. We suggest that, when two or more genetically distinct clones are present in the same host, intra-host competition for limited resources may select for P. vivax traits that represent major public health challenges, such as increased virulence, increased transmissibility and antimalarial drug resistance.

Emergence and disappearance of a virulent clone of Haemophilus influenzae biogroup aegyptius, cause of Brazilian Purpuric Fever

Summary: In 1984, children presented to the emergency department of a hospital in the small town of Promissão, São Paulo State, Brazil, with an acute febrile illness that rapidly progressed to death. Local clinicians and public health officials recognized that these children had an unusual illness, which led to outbreak investigations conducted by Brazilian health officials in collaboration with the U.S. Centers for Disease Control and Prevention. The studies that followed are an excellent example of the coordinated and parallel studies that are used to investigate outbreaks of a new disease, which became known as Brazilian purpuric fever (BPF). In the first outbreak investigation, a case-control study confirmed an association between BPF and antecedent conjunctivitis but the etiology of the disease could not be determined. In a subsequent outbreak, children with BPF were found to have bacteremia caused by Haemophilus influenzae biogroup aegyptius (H. aegyptius), an organism previously known mainly to cause self-limited purulent conjunctivitis. Molecular characterization of blood and other isolates demonstrated the clonal nature of the H. aegyptius strains that caused BPF, which were genetically distant from the diverse strains that cause only conjunctivitis. This led to an intense effort to identify the factors causing the unusual invasiveness of the BPF clone, which has yet to definitively identify the virulence factor or factors involved. After a series of outbreaks and sporadic cases through 1993, no additional cases of BPF have been reported

Developmental Potential of Bovine Hand-Made Clone Embryos Reconstructed by Aggregation or Fusion with Distinct Cytoplasmic Volumes

Animal cloning has been associated with developmental abnormalities, with the level of heteroplasmy caused by the procedure being one of its potential limiting factors. The aim of this study was to determine the effect of the fusion of hemicytoplasts or aggregation of hemiembryos, varying the final cytoplasmic volume, on development and cell density of embryos produced by hand-made cloning (HMC), parthenogenesis or by in vitro fertilization (IVF). One or two enucleated hemicytoplasts were paired and fused with one skin somatic cell. Activated clone and zona-free parthenote embryos and hemiembryos were in vitro cultured in the well-of-the-well (WOW) system, being allocated to one of six experimental groups, on a per WOW basis: single clone or parthenote hemiembryos (1 x 50%); aggregation of two (2 x 50%), three (3 x 50%), or four (4 x 50%) clone or parthenote hemiembryos; single clone or parthenote embryos (1 x 100%); or aggregation of two clone or parthenote embryos (2 x 100%). Control zona-intact parthenote or IVF embryos were in vitro cultured in four-well dishes. Results indicated that the increase in the number of aggregated structures within each WOW was followed by a linear increase in cleavage, blastocyst rate, and cell density. The increase in cytoplasmic volume, either by fusion or by aggregation, had a positive effect on embryo development, supporting the establishment of pregnancies and the birth of a viable clone calf after transfer to recipients. However, embryo aggregation did not improve development on a hemicytoplast basis, except for the aggregation of two clone embryos.

Reliability-based evaluation of design code provisions for circular concrete-filled steel columns

This paper presents an investigation of design code provisions for steel-concrete composite columns. The study covers the national building codes of United States, Canada and Brazil, and the transnational EUROCODE. The study is based on experimental results of 93 axially loaded concrete-filled tubular steel columns. This includes 36 unpublished, full scale experimental results by the authors and 57 results from the literature. The error of resistance models is determined by comparing experimental results for ultimate loads with code-predicted column resistances. Regression analysis is used to describe the variation of model error with column slenderness and to describe model uncertainty. The paper shows that Canadian and European codes are able to predict mean column resistance, since resistance models of these codes present detailed formulations for concrete confinement by a steel tube. ANSI/AISC and Brazilian codes have limited allowance for concrete confinement, and become very conservative for short columns. Reliability analysis is used to evaluate the safety level of code provisions. Reliability analysis includes model error and other random problem parameters like steel and concrete strengths, and dead and live loads. Design code provisions are evaluated in terms of sufficient and uniform reliability criteria. Results show that the four design codes studied provide uniform reliability, with the Canadian code being best in achieving this goal. This is a result of a well balanced code, both in terms of load combinations and resistance model. The European code is less successful in providing uniform reliability, a consequence of the partial factors used in load combinations. The paper also shows that reliability indexes of columns designed according to European code can be as low as 2.2, which is quite below target reliability levels of EUROCODE. (C) 2009 Elsevier Ltd. All rights reserved.

Verification of a mixed high-order accurate DNS code for laminar turbulent transition by the method of manufactured solutions

This paper presents results on a verification test of a Direct Numerical Simulation code of mixed high-order of accuracy using the method of manufactured solutions (MMS). This test is based on the formulation of an analytical solution for the Navier-Stokes equations modified by the addition of a source term. The present numerical code was aimed at simulating the temporal evolution of instability waves in a plane Poiseuille flow. The governing equations were solved in a vorticity-velocity formulation for a two-dimensional incompressible flow. The code employed two different numerical schemes. One used mixed high-order compact and non-compact finite-differences from fourth-order to sixth-order of accuracy. The other scheme used spectral methods instead of finite-difference methods for the streamwise direction, which was periodic. In the present test, particular attention was paid to the boundary conditions of the physical problem of interest. Indeed, the verification procedure using MMS can be more demanding than the often used comparison with Linear Stability Theory. That is particularly because in the latter test no attention is paid to the nonlinear terms. For the present verification test, it was possible to manufacture an analytical solution that reproduced some aspects of an instability wave in a nonlinear stage. Although the results of the verification by MMS for this mixed-order numerical scheme had to be interpreted with care, the test was very useful as it gave confidence that the code was free of programming errors. Copyright (C) 2009 John Wiley & Sons, Ltd.

An estimate of biometric parameters in eucalyptus clone plantations in Southern Bahia: an application of the airborne laser scanning (ALS) technology

The application of airborne laser scanning (ALS) technologies in forest inventories has shown great potential to improve the efficiency of forest planning activities. Precise estimates, fast assessment and relatively low complexity can explain the good results in terms of efficiency. The evolution of GPS and inertial measurement technologies, as well as the observed lower assessment costs when these technologies are applied to large scale studies, can explain the increasing dissemination of ALS technologies. The observed good quality of results can be expressed by estimates of volumes and basal area with estimated error below the level of 8.4%, depending on the size of sampled area, the quantity of laser pulses per square meter and the number of control plots. This paper analyzes the potential of an ALS assessment to produce certain forest inventory statistics in plantations of cloned Eucalyptus spp with precision equal of superior to conventional methods. The statistics of interest in this case were: volume, basal area, mean height and dominant trees mean height. The ALS flight for data assessment covered two strips of approximately 2 by 20 Km, in which clouds of points were sampled in circular plots with a radius of 13 m. Plots were sampled in different parts of the strips to cover different stand ages. The clouds of points generated by the ALS assessment: overall height mean, standard error, five percentiles (height under which we can find 10%, 30%, 50%,70% and 90% of the ALS points above ground level in the cloud), and density of points above ground level in each percentile were calculated. The ALS statistics were used in regression models to estimate mean diameter, mean height, mean height of dominant trees, basal area and volume. Conventional forest inventory sample plots provided real data. For volume, an exploratory assessment involving different combinations of ALS statistics allowed for the definition of the most promising relationships and fitting tests based on well known forest biometric models. The models based on ALS statistics that produced the best results involved: the 30% percentile to estimate mean diameter (R(2)=0,88 and MQE%=0,0004); the 10% and 90% percentiles to estimate mean height (R(2)=0,94 and MQE%=0,0003); the 90% percentile to estimate dominant height (R(2)=0,96 and MQE%=0,0003); the 10% percentile and mean height of ALS points to estimate basal area (R(2)=0,92 and MQE%=0,0016); and, to estimate volume, age and the 30% and 90% percentiles (R(2)=0,95 MQE%=0,002). Among the tested forest biometric models, the best fits were provided by the modified Schumacher using age and the 90% percentile, modified Clutter using age, mean height of ALS points and the 70% percentile, and modified Buckman using age, mean height of ALS points and the 10% percentile.

Nomenclature for congenital and paediatric cardiac disease: Historical perspectives and The International Pediatric and Congenital Cardiac Code

Clinicians working in the field of congenital and paediatric cardiology have long felt the need for a common diagnostic and therapeutic nomenclature and coding system with which to classify patients of all ages with congenital and acquired cardiac disease. A cohesive and comprehensive system of nomenclature, suitable for setting a global standard for multicentric analysis of outcomes and stratification of risk, has only recently emerged, namely, The International Paediatric and Congenital Cardiac Code. This review, will give an historical perspective on the development of systems of nomenclature in general, and specifically with respect to the diagnosis and treatment of patients with paediatric and congenital cardiac disease. Finally, current and future efforts to merge such systems into the paperless environment of the electronic health or patient record on a global scale are briefly explored. On October 6, 2000, The International Nomenclature Committee for Pediatric and Congenital Heart Disease was established. In January, 2005, the International Nomenclature Committee was constituted in Canada as The International Society for Nomenclature of Paediatric and Congenital Heart Disease. This International Society now has three working groups. The Nomenclature Working Group developed The International Paediatric and Congenital Cardiac Code and will continue to maintain, expand, update, and preserve this International Code. It will also provide ready access to the International Code for the global paediatric and congenital cardiology and cardiac surgery communities, related disciplines, the healthcare industry, and governmental agencies, both electronically and in published form. The Definitions Working Group will write definitions for the terms in the International Paediatric and Congenital Cardiac Code, building on the previously published definitions from the Nomenclature Working Group. The Archiving Working Group, also known as The Congenital Heart Archiving Research Team, will link images and videos to the International Paediatric and Congenital Cardiac Code. The images and videos will be acquired from cardiac morphologic specimens and imaging modalities such as echocardiography, angiography, computerized axial tomography and magnetic resonance imaging, as well as intraoperative images and videos. Efforts are ongoing to expand the usage of The International Paediatric and Congenital Cardiac Code to other areas of global healthcare. Collaborative efforts are under-way involving the leadership of The International Nomenclature Committee for Pediatric and Congenital Heart Disease and the representatives of the steering group responsible for the creation of the 11th revision of the International Classification of Diseases, administered by the World Health Organisation. Similar collaborative efforts are underway involving the leadership of The International Nomenclature Committee for Pediatric and Congenital Heart Disease and the International Health Terminology Standards Development Organisation, who are the owners of the Systematized Nomenclature of Medicine or ""SNOMED"". The International Paediatric and Congenital Cardiac Code was created by specialists in the field to name and classify paediatric and congenital cardiac disease and its treatment. It is a comprehensive code that can be freely downloaded from the internet (http://www.IPCCC.net) and is already in use worldwide, particularly for international comparisons of outcomes. The goal of this effort is to create strategies for stratification of risk and to improve healthcare for the individual patient. The collaboration with the World Heath Organization, the International Health Terminology Standards Development Organisation, and the healthcare Industry, will lead to further enhancement of the International Code, and to Its more universal use.

Genes that code for T cell signaling proteins establish transcriptional regulatory networks during thymus ontogeny

Gene expression profiling by cDNA microarrays during murine thymus ontogeny has contributed to dissecting the large-scale molecular genetics of T cell maturation. Gene profiling, although useful for characterizing the thymus developmental phases and identifying the differentially expressed genes, does not permit the determination of possible interactions between genes. In order to reconstruct genetic interactions, on RNA level, within thymocyte differentiation, a pair of microarrays containing a total of 1,576 cDNA sequences derived from the IMAGE MTB library was applied on samples of developing thymuses (14-17 days of gestation). The data were analyzed using the GeneNetwork program. Genes that were previously identified as differentially expressed during thymus ontogeny showed their relationships with several other genes. The present method provided the detection of gene nodes coding for proteins implicated in the calcium signaling pathway, such as Prrg2 and Stxbp3, and in protein transport toward the cell membrane, such as Gosr2. The results demonstrate the feasibility of reconstructing networks based on cDNA microarray gene expression determinations, contributing to a clearer understanding of the complex interactions between genes involved in thymus/thymocyte development.

The RAINY3D Code: The Treatment of Condensation in Nova Remnants during Nebular Phase

Classical nova remnants are important scenarios for improving the photoionization modeling. This work describes the pseudo-three-dimensional code RAINY3D, which drives the photoionization code Cloudy as a subroutine. Photoionization simulations of old nova remnants are also presented and discussed. In these simulations we analyze the effect of condensation in the remnant spectra. The condensed mass fraction affects the Balmer lines by a factor of greater than 4 when compared with homogeneous models, and this directly impacts the shell mass determination. The He II 4686/H beta ratio decreases by a factor of 10 in clumpy shells. These lines are also affected by the clump size and density distributions. The behavior of the strongest nebular line observed in nova remnants is also analyzed for heterogeneous shells. The gas diagnoses in novae ejecta are thought to be more accurate during the nebular phase, but we have determined that at this phase the matter distribution can strongly affect the derived shell physical properties and chemical abundances.

The DNA puff 4C expresses a salivary secretion protein in Trichosia pubescens (Diptera; Sciaridae)

DNA puffs are genomic regions of polytene chromosomes that undergo developmentally controlled DNA amplification and transcription in salivary glands of sciarid flies. Here, we tested the hypothesis that DNA puff genes code for salivary proteins in Trichosia pubescens. To do that, we generated antibodies against saliva and immunoscreened a cDNA library made from salivary glands. We isolated clones corresponding to DNA puff regions, including clone D-50 that contained the entire coding sequence of the previously isolated C4B1 gene from puff 4C. Indeed, we showed that puff 4C is a DNA puff region detecting its local transcription and its extra rounds of DNA incorporation compared to neighboring regions. We further confirmed D-50 clone identity in Western blots reacted with the anti-saliva anitiserum. We detected a recombinant protein expressed by this clone that had the expected size for a full-length product of the gene. We end with a discussion of the relationship between DNA puff genes and their products.

Plasmodium vivax: Microsatellite analysis of multiple-clone infections

We used mixtures of genomic DNA from two genetically distinct isolates from Brazil, 42M and 312M, to investigate how accurately 12-locus microsatellite typing describes the overall genetic diversity and characterizes multilocus haplotypes in multiple-clone Plasmodium vivax infections. We found varying PCR amplification efficiencies of microsatellite alleles; for example, from the same 1:1 mixture of 42M and 312M DNA we amplified predominantly 312M-type alleles at 10 loci and 42M-type alleles at 2 loci. All microsatellite alleles were accurately scored in 1:0.5 and 1:0.25 312M:42M DNA mixtures, even when minor peak heights did not meet previously suggested criteria for minor allele detection in multiple-clone infections. Relative proportions of major and minor alleles were unaffected by multiple displacement amplification of template DNA prior to PCR-based microsatellite typing. Although microsatellite typing may detect minor alleles in clone mixtures, amplification biases may lead to inaccurate assignment of predominant haplotypes in multiple-clone P. vivax infections. (C) 2008 Elsevier Inc. All rights reserved.

Spallation product distributions and neutron multiplicities for accelerator-driven system using the CRISP code

Neutron multiplicities for several targets and spallation products of proton-induced reactions in thin targets of interest to an accelerator-driven system obtained with the CRISP code have been reported. This code is a Monte Carlo calculation that simulates the intranuclear cascade and evaporationl fission competition processes. Results are compared with experimental data, and agreement between each other can be considered quite satisfactory in a very broad energy range of incitant particles and different targets.

ON AMINO ACID AND CODON ASSIGNMENT IN ALGEBRAIC MODELS FOR THE GENETIC CODE

We give a list of all possible schemes for performing amino acid and codon assignments in algebraic models for the genetic code, which are consistent with a few simple symmetry principles, in accordance with the spirit of the algebraic approach to the evolution of the genetic code proposed by Hornos and Hornos. Our results are complete in the sense of covering all the algebraic models that arise within this approach, whether based on Lie groups/Lie algebras, on Lie superalgebras or on finite groups.

Symmetry breaking in the genetic code: Finite groups

We investigate the possibility of interpreting the degeneracy of the genetic code, i.e., the feature that different codons (base triplets) of DNA are transcribed into the same amino acid, as the result of a symmetry breaking process, in the context of finite groups. In the first part of this paper, we give the complete list of all codon representations (64-dimensional irreducible representations) of simple finite groups and their satellites (central extensions and extensions by outer automorphisms). In the second part, we analyze the branching rules for the codon representations found in the first part by computational methods, using a software package for computational group theory. The final result is a complete classification of the possible schemes, based on finite simple groups, that reproduce the multiplet structure of the genetic code. (C) 2010 Elsevier Ltd. All rights reserved.