Detection of Chlamydia psittaci DNA in avian clinical samples by polymerase chain reaction

A polymerase chain reaction (PCR) assay was developed to detect Chlamydia psittaci DNA in faeces and tissue samples from avian species. Primers were designed to amplify a 264 bp product derived from part of the 5' non-translated region and part of the coding region of the ompA gene which encodes the major outer membrane protein. Amplified sequences were confirmed by Southern hybridization using an internal probe. The sensitivity of the combined assay was found to be between 60 to 600 fg of chlamydial DNA (approximately 6 to 60 genome copies). The specificity of the assay was confirmed since PCR product was not obtained from samples containing several serotypes of C. trachomatis, strains of C. pneumoniae, the type strain of C. pecorum, nor from samples containing microorganisms commonly found in the avian gut flora. In this study, 404 avian faeces and 141 avian tissue samples received by the Central Veterinary Laboratory over a 6 month period were analysed by PCR, antigen detection ELISA and where possible, cell culture isolation. PCR performed favourably compared with ELISA and cell culture, or with ELISA alone. The PCR assay was especially suited to the detection of C. psittaci DNA in avian faeces samples. The test was also useful when applied to tissue samples from small contact birds associated with a case of human psittacosis where ELISA results were negative and chlamydial isolation was a less favourable method due to the need for rapid diagnosis.

Isolation from a sheep of an attaching and effacing Escherichia coli O115:H- with a novel combination of virulence factors

Attaching and effacing (AE) lesions were observed in the caecum, proximal colon and rectum of one of four lambs experimentally inoculated at 6 weeks. of age with Escherichia coli O157:H7. However, the attached bacteria did not immunostain with O157-specific antiserum. Subsequent bacteriological analysis of samples from this animal yielded two E. coli O115:H- strains, one from the colon (CO) and one from the rectum (RC), and those bacteria forming the AE lesions were shown to be of the O115 serogroup by immunostaining. The O115:H(-)isolates formed microcolonies and attaching and effacing lesions, as demonstrated by the fluorescence actin staining test, on HEp-2 tissue culture cells. Both isolates were confirmed by PCR to encode the epsilon (epsilon) subtype of intimin. Supernates of both O115:H- isolates induced cytopathic effects on Vero cell monolayers, and PCR analysis verified that both isolates encoded EAST1, CNF1 and CNF2 toxins but not Shiga-like toxins. Both isolates harboured similar sized plasmids but-PCR analysis indicated that only one of the O115:H- isolates (CO) possessed the plasmid-associated virulence determinants ehxA and etpD. Neither strain possessed the espP, katP or bfpA plasmid-associated virulence determinants. These E. coli O115:H- strains exhibited a novel combination of virulence determinants and are the first isolates found to possess both CNF1 and CNF2.

Isolation of recombinant antibodies against EspA and intimin of Escherichia coli O157:H7

Intimin, Tir, and EspA proteins are expressed by attaching-effacing Escherichia coli, which include enteropathogenic and enterohemorrhagic E. coli pathotypes. EspA proteins are part of the type three secretion system needle complex that delivers Tir to the host epithelial cell, while surface arrayed intimin docks the bacterium to the translocated Tir. This intimate attachment leads to attaching and effacing lesions. Recombinant forms of these effector proteins from enterohemorrhagic E. coli O157:H7 were produced by using E. coli expression vectors. Binding of intimin and Tir fragments in enzyme-linked immunosorbent assay (ELISAs) demonstrated the interaction of intimin fragments containing the C-terminal 282 or 188 amino acids to a Tir fragment containing amino acid residues 258 to 361. Recombinant intimin and EspA proteins were used to elicit immune responses in rabbits and immune phage-display antibody libraries were produced. Screening of these immune libraries by conventional phage-antibody panning and colony filter screening produced a panel of antibodies with specificity for EspA or intimin. Antibodies recognizing different C-terminal epitopes on intimin bound specifically to the gamma intimin of O157:H7 and not to other classes of intimin. Antibodies recognizing EspA from E. coli O157 also recognized the protein from the eae-deficient O157 mutant DM3 and from E. coli O111. Anti-intimin antibodies were also produced as fusion proteins coupled to the reporter molecule alkaline phosphatase, allowing the one-step detection of gamma intimin. The isolated recombinant monoclonal antibodies were functional in a range of assay formats, including ELISA, Western blotting, and dot blots, thus demonstrating their diagnostic potential.

Hetero-metallic trinuclear nickel(II)–cadmium(II) complexes of a salicylaldimine ligand with thiocyanate, cyanate and azide ions: isolation of a pair of polymorphs with thiocyanate ion

Four new trinuclear hetero-metallic nickel(II)-cadmium(II) complexes [(NiL)(2)Cd(NCS)(2)] (1A and 1B), [(NiL)(2)Cd(NCO)(2)] (2) and [(NiL)(2)Cd(N-3)(2)] (3) have been synthesized using [NiL] as a so-called "ligand complex" (where H2L = N,N'-bis(salicylidene)-1,3-propanediamine) and structurally characterized. Crystal structure analyses reveal that all four complexes contain a trinuclear moiety in which two square planar [NiL] units are bonded to a central cadmium(II) ion through double phenoxido bridges. The Cd(II) is in a six-coordinate distorted octahedral environment being bonded additionally to two mutually cis nitrogen atoms of terminal thiocyanate (in 1A and 1B), cyanate (in 2) and azide (in 3). Complexes 1A and 1B have the same molecular formula but crystallize in very different monoclinic unit cells and can be considered as polymorphs. On the other hand, the two isoelectronic complexes 2 and 3 are indeed isomorphous and crystallize only in one form. Their conformation is similar to that observed in 1A.

Nonlinear error dynamics for cycled data assimilation methods

We investigate the error dynamics for cycled data assimilation systems, such that the inverse problem of state determination is solved at tk, k = 1, 2, 3, ..., with a first guess given by the state propagated via a dynamical system model from time tk − 1 to time tk. In particular, for nonlinear dynamical systems that are Lipschitz continuous with respect to their initial states, we provide deterministic estimates for the development of the error ||ek|| := ||x(a)k − x(t)k|| between the estimated state x(a) and the true state x(t) over time. Clearly, observation error of size δ > 0 leads to an estimation error in every assimilation step. These errors can accumulate, if they are not (a) controlled in the reconstruction and (b) damped by the dynamical system under consideration. A data assimilation method is called stable, if the error in the estimate is bounded in time by some constant C. The key task of this work is to provide estimates for the error ||ek||, depending on the size δ of the observation error, the reconstruction operator Rα, the observation operator H and the Lipschitz constants K(1) and K(2) on the lower and higher modes of controlling the damping behaviour of the dynamics. We show that systems can be stabilized by choosing α sufficiently small, but the bound C will then depend on the data error δ in the form c||Rα||δ with some constant c. Since ||Rα|| → ∞ for α → 0, the constant might be large. Numerical examples for this behaviour in the nonlinear case are provided using a (low-dimensional) Lorenz '63 system.

Intermittently-visual tracking experiments reveal the roles of error-correction and predictive mechanisms in the human visual-motor control system

Prediction mechanism is necessary for human visual motion to compensate a delay of sensory-motor system. In a previous study, “proactive control” was discussed as one example of predictive function of human beings, in which motion of hands preceded the virtual moving target in visual tracking experiments. To study the roles of the positional-error correction mechanism and the prediction mechanism, we carried out an intermittently-visual tracking experiment where a circular orbit is segmented into the target-visible regions and the target-invisible regions. Main results found in this research were following. A rhythmic component appeared in the tracer velocity when the target velocity was relatively high. The period of the rhythm in the brain obtained from environmental stimuli is shortened more than 10%. The shortening of the period of rhythm in the brain accelerates the hand motion as soon as the visual information is cut-off, and causes the precedence of hand motion to the target motion. Although the precedence of the hand in the blind region is reset by the environmental information when the target enters the visible region, the hand motion precedes the target in average when the predictive mechanism dominates the error-corrective mechanism.

Are clinical documents optimised for patient safety? A critical analysis of patient safety outcomes using the EDA error model

Iatrogenic errors and patient safety in clinical processes are an increasing concern. The quality of process information in hardcopy or electronic form can heavily influence clinical behaviour and decision making errors. Little work has been undertaken to assess the safety impact of clinical process planning documents guiding the clinical actions and decisions. This paper investigates the clinical process documents used in elective surgery and their impact on latent and active clinical errors. Eight clinicians from a large health trust underwent extensive semi- structured interviews to understand their use of clinical documents, and their perceived impact on errors and patient safety. Samples of the key types of document used were analysed. Theories of latent organisational and active errors from the literature were combined with the EDA semiotics model of behaviour and decision making to propose the EDA Error Model. This model enabled us to identify perceptual, evaluation, knowledge and action error types and approaches to reducing their causes. The EDA error model was then used to analyse sample documents and identify error sources and controls. Types of knowledge artefact structures used in the documents were identified and assessed in terms of safety impact. This approach was combined with analysis of the questionnaire findings using existing error knowledge from the literature. The results identified a number of document and knowledge artefact issues that give rise to latent and active errors and also issues concerning medical culture and teamwork together with recommendations for further work.

Isolation and characterization of an AINTEGUMENTA-like gene in different coconut (Cocos nucifera L.) varieties from Sri Lanka

Development of an efficient tissue culture protocol in coconut is hampered by numerous technical constraints. Thus a greater understanding of the fundamental aspects of embryogenesis is essential. The role of AINTEGUMENTA-like genes in embryogenesis has been elucidated not only in model plants but also in economically important crops. A coconut gene, CnANT, that encodes two APETALA2 (AP2) domains and a conserved linker region similar to those of the BABY BOOM transcription factor was cloned, characterized, and its tissue specific expression was examined. The full-length cDNA of 1,780 bp contains a 1,425-bp open reading frame that encodes a putative peptide of 474 amino acids. The genomic DNA sequence includes 2,317 bp and consists of nine exons interrupted by eight introns. The exon/intron organization of CnANT is similar to that of homologous genes in other plant species. Analysis of differential tissue expression by real-time polymerase chain reaction indicated that CnANT is expressed more highly in in vitro grown tissues than in other vegetative tissues. Sequence comparison of the genomic sequence of CnANT in different coconut varieties revealed one single nucleotide polymorphism and one indel in the first exon and first intron, respectively, which differentiate the Tall group of trees from Dwarfs. The indel sequence, which can be considered a simple sequence repeats marker, was successfully used to distinguish the Tall and Dwarf groups as well as to develop a marker system, which may be of value in the identification of parental varieties that are used in coconut breeding programs in Sri Lanka.

Growth rate and vertical propagation of the initial error in baroclinic models

The present study investigates the growth of error in baroclinic waves. It is found that stable or neutral waves are particularly sensitive to errors in the initial condition. Short stable waves are mainly sensitive to phase errors and the ultra long waves to amplitude errors. Analysis simulation experiments have indicated that the amplitudes of the very long waves become usually too small in the free atmosphere, due to the sparse and very irregular distribution of upper air observations. This also applies to the four-dimensional data assimilation experiments, since the amplitudes of the very long waves are usually underpredicted. The numerical experiments reported here show that if the very long waves have these kinds of amplitude errors in the upper troposphere or lower stratosphere the error is rapidly propagated (within a day or two) to the surface and to the lower troposphere.

Transition from an anti-phase error-correction-mode to a synchronization mode in the mutual hand tracking

Proactive motion in hand tracking and in finger bending, in which the body motion occurs prior to the reference signal, was reported by the preceding researchers when the target signals were shown to the subjects at relatively high speed or high frequencies. These phenomena indicate that the human sensory-motor system tends to choose an anticipatory mode rather than a reactive mode, when the target motion is relatively fast. The present research was undertaken to study what kind of mode appears in the sensory-motor system when two persons were asked to track the hand position of the partner with each other at various mean tracking frequency. The experimental results showed a transition from a mutual error-correction mode to a synchronization mode occurred in the same region of the tracking frequency with that of the transition from a reactive error-correction mode to a proactive anticipatory mode in the mechanical target tracking experiments. Present research indicated that synchronization of body motion occurred only when both of the pair subjects operated in a proactive anticipatory mode. We also presented mathematical models to explain the behavior of the error-correction mode and the synchronization mode.

Sparse probability density function estimation using the minimum integrated square error

We develop a new sparse kernel density estimator using a forward constrained regression framework, within which the nonnegative and summing-to-unity constraints of the mixing weights can easily be satisfied. Our main contribution is to derive a recursive algorithm to select significant kernels one at time based on the minimum integrated square error (MISE) criterion for both the selection of kernels and the estimation of mixing weights. The proposed approach is simple to implement and the associated computational cost is very low. Specifically, the complexity of our algorithm is in the order of the number of training data N, which is much lower than the order of N2 offered by the best existing sparse kernel density estimators. Numerical examples are employed to demonstrate that the proposed approach is effective in constructing sparse kernel density estimators with comparable accuracy to those of the classical Parzen window estimate and other existing sparse kernel density estimators.

Analysis and compensation of power amplifier nonlinearity in MIMO transmit diversity systems

The nonlinearity of high-power amplifiers (HPAs) has a crucial effect on the performance of multiple-input-multiple-output (MIMO) systems. In this paper, we investigate the performance of MIMO orthogonal space-time block coding (OSTBC) systems in the presence of nonlinear HPAs. Specifically, we propose a constellation-based compensation method for HPA nonlinearity in the case with knowledge of the HPA parameters at the transmitter and receiver, where the constellation and decision regions of the distorted transmitted signal are derived in advance. Furthermore, in the scenario without knowledge of the HPA parameters, a sequential Monte Carlo (SMC)-based compensation method for the HPA nonlinearity is proposed, which first estimates the channel-gain matrix by means of the SMC method and then uses the SMC-based algorithm to detect the desired signal. The performance of the MIMO-OSTBC system under study is evaluated in terms of average symbol error probability (SEP), total degradation (TD) and system capacity, in uncorrelated Nakagami-m fading channels. Numerical and simulation results are provided and show the effects on performance of several system parameters, such as the parameters of the HPA model, output back-off (OBO) of nonlinear HPA, numbers of transmit and receive antennas, modulation order of quadrature amplitude modulation (QAM), and number of SMC samples. In particular, it is shown that the constellation-based compensation method can efficiently mitigate the effect of HPA nonlinearity with low complexity and that the SMC-based detection scheme is efficient to compensate for HPA nonlinearity in the case without knowledge of the HPA parameters.

Joint compensation of multiple RF impairments in MIMO STBC systems

In this paper, we propose a compensation method for the joint effect of high-power amplifier (HPA) nonlinearity, in-phase/quadrature-phase (I/Q) imbalance and crosstalk in multiple-input multiple-output (MIMO) orthogonal space-time block coding (OSTBC) systems. The performance of the MIMO OSTBC equipped with the proposed compensation mechanism is evaluated in terms of average symbol error probability and system capacity, in Rayleigh fading channels. Numerical results are provided and show the effects on performance of several system parameters, namely, the HPA parameters, image-leakage ratio, crosstalk, numbers of antennas, and phase-shift keying modulation order.

On the effect of power amplifier nonlinearity on MIMO transmit diversity systems

Nonlinearity of high-power amplifier (HPA) plays a crucial role in the performance of multiple-input multiple-output (MIMO) systems. In this paper, we investigate the performance of MIMO orthogonal space-time block coding (STBC) systems in the presence of nonlinear HPA. Specifically, we assess the impact of HPA nonlinearity on the average symbol error probability (SEP), total degradation (TD), and system capacity of orthogonal STBC in uncorrelated Nakagami-m fading channels. Numerical results are provided and show the effects of several system parameters, such as the output back-off (OBO) of nonlinear HPA, numbers of transmit and receive antennas, and modulation order of quadrature amplitude modulation (QAM), on performance.