Codon volatility of hemagglutinin genes of H5N1 avian influenza viruses from different clades

Codon volatility is a method recently developed to estimate selective pressures on proteins on the basis of their synonymous codon usage. Volatility of a codon was defined as the fraction of single nucleotide substitutions that would be nonsynonymous. Higher volatility may indicate that the gene has been under more positive selection in the recent past. We analyzed volatility of hemagglutinin genes of H5N1 viruses in the recent outbreaks and observed differences in the volatility among viruses of different clades. The codon volatility of subclade 2.1 viruses from Indonesia was the lowest among all H5N1 clades and subclades. Time series analyses since the beginning of the epidemic in 2004 showed that codon volatility of subclade 2.1 has gradually decreased, while those of other major clades have been increasing. This may reflect differences in the recent evolution of these viruses.     

Evidence for positive selection on the E2 gene of bovine viral diarrhoea virus type 1

Despite the growing interest in the molecular epidemiology of pestivirus, there have been few attempts to determine which regions of the pestivirus genome are subject to positive selection, although this may be a key indicator of the nature of the interaction between host and virus. By using likelihood-based methods for phylogenetic inference, the positive selection pressure of BVDV-1 E2 gene were assessed and a site-by-site analysis of the d _N/d _S ratio was performed, to identify specific codons undergoing diversifying positive selection. The overall ω was 0.20, indicating that most sites were subject to strong purifying selection and five positively selected sites (886, 888, 905, 944, and 946) were identified. It is surprising to find that all the potential positively selected sites fall within the C-terminal of E2, and out of the N-terminal of E2 which is thought to be surface-exposed and therefore prime targets for host antibody response. In conclusion, these results suggest that selection favoring avoidance of antibody recognition has not been a major factor in the history of BVDV-1. Further analysis is necessary to see if amino acid substitutions in the BVDV-1 positively selected sites can lead to change of host tropism or\and escape from epitope-specific CD8 T-cell response.     

Improved, computer-generated system for pyocin typing of Pseudomonas aeruginosa.

We applied numerical clustering algorithms to the selection of a new indicator strain set for the pyocin typing of Pseudomonas aeruginosa. The new indicator set is composed of selected indicator strains from the sets described in 1966 by Gillies and Govan (J. Pathol. Bacteriol. 91:339-345) and in 1974 by Jones, Zakanycz, Thomas, and Farmer (Appl. Microbiol. 27:400-406) and is designated the G-F set. This indicator set consists of 14 indicator strains which typed 99.5% of 114 test cultures, has a high degree of discrimination (10 patterns encompass 50% of the test strains), and provides 62.3% reproducibility of the same typing pattern in duplicate tests done on different days. The G-F set of indicator strains provides slightly higher percentages of typable cultures than either of the other two sets, has greater discriminatory capability, and is more reproducible than they are. We recommend that the G-F set of indicator strains be used instead of the two other sets for pyocin typing of P. aeruginosa. We also tested a recently described overlay procedure for pyocin testing of P. aeruginosa and found it to be superior to previous methods in that it is easier to perform, it provides answers in only 24 h instead of 48 h, and it can be used to type mucoid strains (which previous techniques could not readily do). Thus, the application of numerical clustering algorithms and use of a revised typing procedure have produced an improved system for pyocin typing of P. aeruginosa. Similar procedures may be applicable to other typing systems.     

Human–Mouse Gene Identification by Comparative Evidence Integration and Evolutionary Analysis

The identification of genes in the human genome remains a challenge, as the actual predictions appear to disagree tremendously and vary dramatically on the basis of the specific gene-finding methodology used. Because the pattern of conservation in coding regions is expected to be different from intronic or intergenic regions, a comparative computational analysis can lead, in principle, to an improved computational identification of genes in the human genome by using a reference, such as mouse genome. However, this comparative methodology critically depends on three important factors: (1) the selection of the most appropriate reference genome. In particular, it is not clear whether the mouse is at the correct evolutionary distance from the human to provide sufficiently distinctive conservation levels in different genomic regions, (2) the selection of comparative features that provide the most benefit to gene recognition, and (3) the selection of evidence integration architecture that effectively interprets the comparative features. We address the first question by a novel evolutionary analysis that allows us to explicitly correlate the performance of the gene recognition system with the evolutionary distance (time) between the two genomes. Our simulation results indicate that there is a wide range of reference genomes at different evolutionary time points that appear to deliver reasonable comparative prediction of human genes. In particular, the evolutionary time between human and mouse generally falls in the region of good performance; however, better accuracy might be achieved with a reference genome further than mouse. To address the second question, we propose several natural comparative measures of conservation for identifying exons and exon boundaries. Finally, we experiment with Bayesian networks for the integration of comparative and compositional evidence.     

Optical and Radioisotope Indicator Dilution Measurements in Pulmonary Edema

The objective of this study was a validation of an optical multiple indicator dilution technique for measuring microvascular exchange parameters in edematous lungs by comparison to conventional radioisotope multiple indicator dilution methods. Six anesthetized dogs were studied at baseline and after alloxan infusion to increase capillary permeability. In addition, 11 isolated, perfused dog lungs were studied at baseline and after edema was created by increasing venous pressure or by infusing alloxan to increase vascular permeability. Increased capillary permeability from alloxan infusion led to increases in most but not all capillary exchange parameters as analyzed by mathematical models and measured by both optical and radioisotope methods. Increased vascular pressure led to increased edema but no significant increases in capillary exchange parameters. Two-way analysis of variance (ANOVA; variations in baseline versus pressure or alloxan and variation in optical versus radioisotope for each transport parameter derived from the mathematical models) indicated few significant differences in capillary exchange parameters between optical and radioisotope measures. Newman–Keuls multiple comparison tests did uncover some variations between a few of the group-mean values derived from optical and radioisotope methods. However, optical and radioisotope parameter measurements were highly correlated for all studies regardless of the mathematical model used for analysis.     

A wavelet-based data pre-processing analysis approach in mass spectrometry

Recently, mass spectrometry analysis has a become an effective and rapid approach in detecting early-stage cancer. To identify proteomic patterns in serum to discriminate cancer patients from normal individuals, machine-learning methods, such as feature selection and classification, have already been involved in the analysis of mass spectrometry (MS) data with some success. However, the performance of existing machine learning methods for MS data analysis still needs improving. The study in this paper proposes a wavelet-based pre-processing approach to MS data analysis. The approach applies wavelet-based transforms to MS data with the aim of de-noising the data that are potentially contaminated in acquisition. The effects of the selection of wavelet function and decomposition level on the de-noising performance have also been investigated in this study. Our comparative experimental results demonstrate that the proposed de-noising pre-processing approach has potentials to remove possible noise embedded in MS data, which can lead to improved performance for existing machine learning methods in cancer detection.     

Validation and application of an ascorbate oxidase biosensor for the rapid analysis of vitamin C in food and pharmaceutical samples

L-ascorbic acid occurs naturally in many foods and is frequently added to processed foods as an antioxidant. As the ascorbic acid content in food materials is an indicator of its freshness and nutritive value, rapid and accurate analysis of ascorbic acid is important. Conventional methods of ascorbic acid analysis have several disadvantages and a biosensor is a reliable alternative for rapid analysis of vitamin C in food and pharmaceutical samples. This paper deals with the use of a biosensor technique to analyse the ascorbic acid content in food and pharmaceutical samples and to compare it with the conventional methods of analysis such as high pressure liquid chromatography, titrimetry and spectrophotometric methods.     

Practicalities of localization in animal and human tumours.

Factors affecting the selection and application of localization methods for measuring tumours by NMR spectroscopy are considered, with particular regard to the S/N ratio and to contaminating signal from outside the volume of interest. Methods of assessing the performance of localization techniques are considered, and their importance for quantitative measurements and comparative studies is discussed.     

Controversies in the assessment of HER-2: more questions than answers

Human epidermal growth factor receptor 2 (HER-2) is over-expressed in 15% to 30% of breast cancers and is a poor prognostic marker in node-positive patients. HER-2 expression is an indicator of greater sensitivity to anthracycline-based chemotherapy and is the major criterion for selection for treatment with the anti-HER-2 antibody trastuzumab (Herceptin). Fluorescence in situ hybridization and immunohistochemistry (IHC) are the 2 most commonly used methods for detection of the gene and protein, respectively. Criticisms have been levied at the IHC method of identifying HER-2 overexpression but convenience and costs of this technique cannot be overlooked. Modifications to the IHC technique and scoring accommodate for many of the problems that derive from variables in preanalytical and analytic factors that influence results but standardization is currently impossible to attain. Deficiencies in fluorescence in situ hybridization assay also exist and alternative molecular methods of assay are explored in this review.     

Using models of nucleotide evolution to build phylogenetic trees

Molecular phylogenetics and its applications are popular and useful tools for making comparative investigations in genetics; however, estimating phylogenetic trees is not always straightforward. Some phylogenetic estimators use an explicit model of nucleotide evolution to estimate evolutionary parameters such as branch lengths and tree topology. There are many models to choose from, and use of the optimal model for a particular data set is important to avoid a loss of power and accuracy in phylogenetic estimations. Here, we review some molecular evolutionary forces and the parameters included in some common models of evolution used to interpret resulting patterns of molecular variation. We present some statistical methods of selecting a particular model of nucleotide evolution, and provide an empirical example of model selection. Statistical model selection strikes a balance between the bias introduced by some models and the increased variance of parameter estimates that results from using other models.     

A powerful score test to detect positive selection in genome-wide scans

One of the surest signatures of recent positive selection is a local elevation of advantageous allele frequency and linkage disequilibrium (LD). We proposed to detect such hitchhiking effects by using extended stretches of homozygosity as a surrogate indicator of recent positive selection. An extended haplotype-based homozygosity score test (EHHST) was developed to detect excess homozygosity. The EHHST conditioned on existing LD and it tested the haplotype version of the Hardy–Weinberg equilibrium. Compared with existing popular tests, which usually lack clear distribution, the EHHST is asymptotically normal, which makes analysis and applications easier. In particular, the EHHST facilitates the computation of an asymptotic P-value instead of an empirical P-value, using simulations. We evaluated by simulation that the EHHST led to appropriate false-positive rates, and it had higher or similar power as the existing popular methods. The method was applied to HapMap Phase II data. We were able to replicate previous findings of strong positive selection in 17 autosome genomic regions out of 20 reported candidates. On the basis of high EHHST values and population differentiations, we identified 15 new candidate regions that could undergo recent selection.     

Renal blood flow in isolated kidneys measured with an electromagnetic flowmeter and by xenon-133 and krypton-85 wash-out techniques

Summary By use of an electromagnetic flowmeter and the inert gas desaturation method 43 comparative measurements of the blood flow were performed in 6 isolated dog kidneys. For the measurements by use of the latter method krypton-85 and xenon-133 were employed, for a fast, and respectively, a slow injection of the indicator into the renal artery. Calculation of the blood flow from the wash-out curves was made by use of the formulas advanced by Kety (1951) and by Zierler (1965).A good accordance was found between the flowmeter values and those obtained with the desaturation methods. Recirculation and resorption of indicator in fat tissue surrounding the kidney explain that previous examinations in kidneys in situ have resulted in very low perfusion values, when Zierler's formula has been applied. Extrapolation of the final slope to obtain the area of the curve may be a major source of error by calculation of the blood flow with Zierler's formula.     

儿童烧伤治疗及瘢痕防治策略的探讨

本文结合儿童生理特点,从儿童烧伤休克复苏补液的液体选择、晶体配方、输注方式;创面修复中敷料的选择、新型敷料的应用;深度烧伤创面手术时机和处理方法以及覆盖物的选择,多方位对儿童烧伤治疗进行阐述。同时,对烧伤瘢痕的预防措施,如压力疗法、激光治疗、支具应用;瘢痕的手术和非手术治疗的新进展;儿童瘢痕整形手术方法的选择;烧伤治疗全程康复措施和经验等作了分享和探讨,旨在为临床一线工作的医护人员提供参考依据。     

A review of physiological simulation models of intracranial pressure dynamics

This paper reviews the literature regarding the development, testing, and application of physiology-based computer simulation models of intracranial pressure dynamics. Detailed comparative information is provided in tabular format about the model variables and logic, any data collected, model testing and validation methods, and model results. Several syntheses are given that summarize the research carried out by influential research teams and researchers, review important findings, and discuss the methods employed, limitations, and opportunities for further research.     

Barriers to patient involvement in health service planning and evaluation: an exploratory study

OBJECTIVE: Patient involvement in health service planning and evaluation is considered important yet not widely practiced. This study explored stakeholder beliefs about patient participation in performance indicator selection to better understand hypothesized barriers. METHODS: Interviews with 30 cancer patients and health professionals from two teaching hospitals were analyzed qualitatively. RESULTS: All groups believed patients, not members of the public, should be involved in the selection of indicators. Ongoing, interactive methods such as committee involvement, rather than single, passive efforts such as surveys were preferred. Health professionals recommended patients assume a consultative, rather than decision-making role. Older patients agreed with this. CONCLUSION: Variable patient interest, health professional attitudes, and a lack of insight on appropriate methods may be limiting patient involvement in this, and other service planning and evaluation activities. More research is required to validate expressed views among the populations these stakeholders represent, and to establish effective methods for engaging patients. PRACTICE IMPLICATIONS: Efforts to encourage a change in health professional attitude may be required, along with dedicated organizational resources, coordinators and training. Methods to engage patients should involve deliberation, which can be achieved through modified Delphi panel or participatory research approaches.     

Cryptosporidium parvum oocyst viability and behaviour of the residual body during the excystation process

This study was conducted as a comparative evaluation of time-dependent changes in the viability of purified Cryptosporidium parvum oocysts by means of different excystation methods. Oocyst samples were 2 weeks to 12 months old and were treated with bile or sodium taurocholate, partly after pretreatment with hypochlorite. Pretreatment markedly enhanced the excystation of younger oocyst samples but did not increase excystation rates of 9 or 12-month-old oocysts. A cell culture-PCR assay was used as a second indicator for oocyst viability and was most consistent with excystation trials including oocyst pretreatment. In experiments aiming at the determination of the behaviour of the oocyst residual body during excystation, it could be demonstrated that it might be involved in this process.     

Tumoural vascularity as a prognostic factor in cancer patients: the evidence continues to grow

Accurate prognostic indicators would help in identifying patients at high risk for recurrence and death. Recent and previous studies indicate that intratumoural microvessel density (iMVD) of invasive breast carcinoma (a measure of tumour angiogenesis) is associated with aggressive tumour growth; iMVD may thus be a valuable prognostic indicator. Moreover, the bulk of accumulating data indicates that microvessel density in the area of most intense neovascularization in invasive breast carcinoma is an independent, significant and accurate prognostic indicator in predicting poorer survival. Such an indicator would be useful in the selection of high-risk patients with breast carcinoma for systemic adjuvant therapy. © 1998 John Wiley & Sons, Ltd.     

Comparative Evaluation of Pelvic Allograft Selection Methods

This paper presents a firsthand comparative evaluation of three different existing methods for selecting a suitable allograft from a bone storage bank. The three examined methods are manual selection, automatic volume-based registration, and automatic surface-based registration. Although the methods were originally published for different bones, they were adapted to be systematically applied on the same data set of hemi-pelvises. A thorough experiment was designed and applied in order to highlight the advantages and disadvantages of each method. The methods were applied on the whole pelvis and on smaller fragments, thus producing a realistic set of clinical scenarios. Clinically relevant criteria are used for the assessment such as surface distances and the quality of the junctions between the donor and the receptor. The obtained results showed that both automatic methods outperform the manual counterpart. Additional advantages of the surface-based method are in the lower computational time requirements and the greater contact surfaces where the donor meets the recipient.     

A Microspectrophotometric Technique for Determination of Respiration in Comparison to the Cartesian Diver Method. —Respiratory Activity of Rat Corpus Luteum Cells with Reference to Substrate

A comparative study of two microrespirometric methods, the classical standard-diver technique and a newly introduced spectrophotometric procedure, using hemoglobin as indicator of oxygen tension as well as donor of oxygen, has been performed on small samples of well-defined rat corpus luteum tissue. Oxygen consumption of this tissue was determined in absence of substrate as well as in the presence of oxalacetate and succinate, respectively. The accuracy of the two methods was equal though small differences in absolute values were found. Rapidity and simplicity of performance is considerably increased with the spectrophotometric procedure. Endogenous respiration was found to be approximately 1 μl O₂/mg dry weight × h, and in the presence of oxalacetate oxygen consumption was increased by 50 per cent. In the presence of succinate respiration was increased to about 10 μ O₂/mg dry weight × h.