Experiments with the Site Frequency Spectrum

Evaluating the likelihood function of parameters in highly-structured population genetic models from extant deoxyribonucleic acid (DNA) sequences is computationally prohibitive. In such cases, one may approximately infer the parameters from summary statistics of the data such as the site-frequency-spectrum (SFS) or its linear combinations. Such methods are known as approximate likelihood or Bayesian computations. Using a controlled lumped Markov chain and computational commutative algebraic methods, we compute the exact likelihood of the SFS and many classical linear combinations of it at a non-recombining locus that is neutrally evolving under the infinitely-many-sites mutation model. Using a partially ordered graph of coalescent experiments around the SFS, we provide a decision-theoretic framework for approximate sufficiency. We also extend a family of classical hypothesis tests of standard neutrality at a non-recombining locus based on the SFS to a more powerful version that conditions on the topological information provided by the SFS.     

Evaluation of a simple preservative for bacteriological tests on urine

A urine preservative containing NaCl and polyvinyl-pyrrolidone has been in general use at this hospital for three years. It enables the specimen to be held at room temperature for 48 hours or more without appreciable change in the content of viable bacteria. The results of bacteriological tests performed on 2452 preserved urine specimens are compared with those from a control series examined before the method was introduced. A marked improvement in accuracy is demonstrated. The preservative can be very easily and cheaply prepared in any laboratory.     

Study of normal and cancerous urine using photoacoustic spectroscopy

Photoacoustic spectroscopy (PAS) is a valuable technique, increasingly applied in clinical and biological analysis. Light absorption properties of urine and body tissue can be obtained more easily by the PAS technique because of its high sensitivity, than by the conventional optical techniques. By observing their absorption properties it is possible to diagnose some diseases and in this study we have used PAS to assess cancerous changes in urine and tissue. Three groups were studied: normal individuals; patients with cancer; and patients with cancer and subsequent inflammation; and the characteristic light absorption peaks obtained for a certain band (240–420 nm). These results were compared with the clinical diagnosis and proved consistent and reliable for the diagnosis of urinary tract cancer subsequently confirmed by operation. This method will probably be a useful tool for the early clinical diagnosis of cancer of the urinary system.     

尿液作为新型生物标志物来源的探索

机体各种变化是生物标志物研究的核心内容.因为机体固有的稳态调控机制,在血液中早期产生的变化容易被清除.而在尿液中不存在稳态调控机制,允许容纳更多的变化因素存在.尤其在疾病发生的早期阶段,从尿液中更有可能发现新型的早期生物标志物.在尿液生物标志物研究中,亦应当考虑药物的影响.使用尿液生物标志物研究路线图,能够有效规避各种影响因素对于尿液生物标志物研究的干扰;同时,结合膜处理新技术,有利于经济、高效地大规模收集尿液样本,促进尿液生物标志物的大规模研究.另外,本文介绍了最容易在尿液中体现出变化的肾脏疾病生物标志物的研究进展.尿液生物标志物的研究,将赋予人类在疾病预防、诊断、治疗及预后监测等诸多方面实现更多进步的可能性.     

ChromoWheel: a new spin on eukaryotic chromosome visualization

ChromoWheel is an Internet browser application for generating whole-genome illustrations. It can be used to depict chromosomes, genes and relations between chromosomal loci. The circular layout of chromosomes is advantageous for showing relationships between different chromosomes, as the connecting line never crosses over a chromosome. All graphical image components are in the vector-based format Scalable Vector Graphics, which are highly scaleable and admit user interaction. ChromoWheel can either be run with user-provided data in the generic SFS format, or as a browser front-end for precompiled genomic data.     

Application of genetic algorithms and constructive neural networks for the analysis of microarray cancer data

Background

Extracting relevant information from microarray data is a very complex task due to the characteristics of the data sets, as they comprise a large number of features while few samples are generally available. In this sense, feature selection is a very important aspect of the analysis helping in the tasks of identifying relevant genes and also for maximizing predictive information.

Methods

Due to its simplicity and speed, Stepwise Forward Selection (SFS) is a widely used feature selection technique. In this work, we carry a comparative study of SFS and Genetic Algorithms (GA) as general frameworks for the analysis of microarray data with the aim of identifying group of genes with high predictive capability and biological relevance. Six standard and machine learning-based techniques (Linear Discriminant Analysis (LDA), Support Vector Machines (SVM), Naive Bayes (NB), C-MANTEC Constructive Neural Network, K-Nearest Neighbors (kNN) and Multilayer perceptron (MLP)) are used within both frameworks using six free-public datasets for the task of predicting cancer outcome.

Results

Better cancer outcome prediction results were obtained using the GA framework noting that this approach, in comparison to the SFS one, leads to a larger selection set, uses a large number of comparison between genetic profiles and thus it is computationally more intensive. Also the GA framework permitted to obtain a set of genes that can be considered to be more biologically relevant. Regarding the different classifiers used standard feedforward neural networks (MLP), LDA and SVM lead to similar and best results, while C-MANTEC and k-NN followed closely but with a lower accuracy. Further, C-MANTEC, MLP and LDA permitted to obtain a more limited set of genes in comparison to SVM, NB and kNN, and in particular C-MANTEC resulted in the most robust classifier in terms of changes in the parameter settings.

Conclusions

This study shows that if prediction accuracy is the objective, the GA-based approach lead to better results respect to the SFS approach, independently of the classifier used. Regarding classifiers, even if C-MANTEC did not achieve the best overall results, the performance was competitive with a very robust behaviour in terms of the parameters of the algorithm, and thus it can be considered as a candidate technique for future studies.

     

Perfusion-induced redox differences in cytochrome c oxidase: ATR/FT-IR spectroscopy

Attenuated total reflection (ATR) spectroscopy brings an added dimension to studies of structural changes of cytochrome c oxidase (CcO) because it enables the recording of reaction-induced infrared difference spectra under a wide variety of controlled conditions (e.g. pH and chemical composition), without relying on light or potentiometric changes to trigger the reaction. We have used the ATR method to record vibrational difference spectra of CcO with reduction induced by flow-exchange of the aqueous buffer. Films of CcO prepared from Rhodobacter sphaeroides and beef heart mitochondria by reconstitution with lipid were adhered to the internal reflection element of the ATR device and retained their full functionality as evidenced by visible spectroscopy and time-resolved vibrational spectroscopy. These results demonstrate that the technique of perfusion-induced Fourier-transform infrared difference spectroscopy can be successfully applied to a large, complex enzyme, such as CcO, with sufficient signal/noise to probe vibrational changes in individual residues of the enzyme under various conditions.     

Investigation of a wide spectrum of inherited metabolic disorders by 13C NMR spectroscopy

High-resolution (1)H NMR spectroscopy of body fluids has proved to be very useful in diagnostics of inherited metabolic diseases, whereas (13)C NMR remains almost unexploited. In this paper the application of (13)C NMR spectroscopy of fivefold concentrated urine samples for diagnosis of selected metabolic diseases is reported. Various marker metabolites were identified in test urine samples from 33 patients suffering from 10 different diseases, providing information which could be crucial for their diagnoses. Spectra were accumulated for 2 h or overnight when using spectrometers operating at 9.4 or 4.7 T magnetic fields, respectively. Interpretation of the measurement results was based on a comparison of the peak positions in the measured spectrum with reference data. The paper contains a table with (13)C NMR chemical shifts of 73 standard compounds. The method can be applied individually or as an auxiliary technique to (1)H NMR or any other analytical method.     

Hypokalemic metabolic alkalosis caused by surreptitious vomiting: report of four cases.

Four women, aged 22 to 40 years, presented with severe hypokalemia and metabolic alkalosis. Three had related neuromuscular symptoms. All four patients denied vomiting or diuretic ingestion, and a diagnosis of Bartter''s syndrome was entertained. A diagnosis of surreptitious vomiting was suspected from the characteristic urine electrolyte pattern: high values for sodium and potassium, and a chloride concentration of less than 5 mmol/l. Three patients excreted sodium and potassium primarily with bicarbonate and had an alkaline urine; the fourth patient excreted these cations primarily with an organic anion and had an acid urine (pH 5.5). Since self-induced vomiting may be a common method of weight reduction in young women, recognition of this characteristic urine electrolyte pattern will assist in the rapid diagnosis of hypokalemia and metabolic alkalosis of obscure cause.     

Advances in the Diagnosis of Human Opisthorchiasis: Development of Opisthorchis viverrini Antigen Detection in Urine

Background

Many strategies to control opisthorchiasis have been employed in Thailand, but not in the other neighbouring countries. Specific control methods include mass drug administration (MDA) and health education to reduce raw fish consumption. These control efforts have greatly shifted the epidemiology of Opisthorchis viverrini (OV) infection over the last decade from presenting as densely concentrated "heavy" infections in single villages to widespread "light" OV infections distributed over wide geographical areas. Currently, the "gold standard" detection method for OV infection is formalin ethyl-acetate concentration technique (FECT), which has limited diagnostic sensitivity and diagnostic specificity for light OV infections, with OV eggs often confused with eggs of minute intestinal flukes (MIFs) in feces. In this study, we developed and evaluated the diagnostic performance of a monoclonal antibody-based enzyme-linked immunosorbent assay for the measurement of OV excretory-secretory (ES) antigens in urine (urine OV-ES assay) for the diagnosis of opisthorchiasis compared to the gold standard detection FECT method.

Methodology

We tested several methods for pre-treating urine samples prior to testing the diagnostic performance of the urine OV-ES assay. Using trichloroacetic acid (TCA) pre-treated urine, we compared detection and quantification of OV infection using the urine OV-ES assay versus FECT in OV-endemic areas in Northeastern Thailand. Receiver operating characteristic (ROC) curves were used to determine the diagnostic sensitivity and specificity of the urine OV-ES assay using TCA pre-treated urine, and to establish diagnostic positivity thresholds. The Positive Predictive Value as well as the likelihood of obtaining a positive test result (LR+) or a negative test result (LR-) were calculated for the established diagnostic positivity threshold. Diagnostic risks (Odds Ratios) were estimated using logistic regression.

Results

When urine samples were pre-treated with TCA prior to use in the urine OV-ES assay, the analytical sensitivity was significantly improved. Using TCA pre-treatment of urine, the urine OV-ES assay had a limit of detection (LoD) of 39 ng/ml compared to the LoD of 52 ng/mL reported for coprological antigen detection methods. Similarly, the urine OV-ES assay correlated significantly with intensity of OV infection as measured by FECT. The urine OV-ES assay was also able to detect 28 individuals as positive from the 63 (44.4%) individuals previously determined to be negative using FECT. The likelihood of a positive diagnosis of OV infection by urine OV-ES assay increased significantly with the intensity of OV infection as determined by FECT. With reference to FECT, the sensitivity and specificity of the urine OV-ES assay was 81% and 70%, respectively.

Conclusion

The detection of OV-infection by the urine OV-ES assay showed much greater diagnostic sensitivity and diagnostic specificity than the current "gold standard" FECT method for the detection and quantification of OV infection. Due to its ease-of-use, and noninvasive sample collection (urine), the urine OV-ES assay offers the potential to revolutionize the diagnosis of liver fluke infection and provide an effective tool for control and elimination of these tumorigenic parasites.     

Can the Site-Frequency Spectrum Distinguish Exponential Population Growth from Multiple-Merger Coalescents?

The ability of the site-frequency spectrum (SFS) to reflect the particularities of gene genealogies exhibiting multiple mergers of ancestral lines as opposed to those obtained in the presence of population growth is our focus. An excess of singletons is a well-known characteristic of both population growth and multiple mergers. Other aspects of the SFS, in particular, the weight of the right tail, are, however, affected in specific ways by the two model classes. Using an approximate likelihood method and minimum-distance statistics, our estimates of statistical power indicate that exponential and algebraic growth can indeed be distinguished from multiple-merger coalescents, even for moderate sample sizes, if the number of segregating sites is high enough. A normalized version of the SFS (nSFS) is also used as a summary statistic in an approximate Bayesian computation (ABC) approach. The results give further positive evidence as to the general eligibility of the SFS to distinguish between the different histories.     

Integration of renal and gastrointestinal function

In birds, the kidney does not independently regulate the composition of the extracellular fluid, as is the case for mammals. The urine of birds enters the cloaca and is moved by a reverse peristaltic action into the colon. In the colon, the urine comes in contact with an epithelium that modifies its composition. If the osmotic potential of the urine is significantly higher than that of the plasma, the urine will not be refluxed into the colon. The composition of the ureteral urine is sensed in the cloaca which in turn modulates the refluxing activity. It appears to be the large contraction waves of the colon that are modified by changes in the composition of the urine, although radiographic evidence indicates that the small contraction waves of the colon do the actual refluxing. It is necessary for the urine to be moved into the colon. This may be driven by the need to recover some, if not all, of the protein in the urine. This protein maintains uric acid in a colloidal suspension that prevents the formation of uric acid crystals which would block the renal tubules. Thus, the kidneys and lower gastrointestinal tract must function in concert in the regulation of the composition of the extracellular fluid.     

Analytical method for the determination of urinary 3-phenoxybenzoic acid in subjects occupationally exposed to pyrethroid insecticides

The determination of urinary 3-phenoxybenzoic acid enables exposure to pyrethroid insecticides to be evaluated. A method for the quantitative determination of this metabolite in urine is described. The compound and the internal standard (2-phenoxybenzoic acid) are derivatized with pentafluorobenzylbromide and transformed into pentafluorobenzyl esters, which are determined by gas chromatography with an intermediate polarity capillary column and an electron-capture detector. Before GC analysis, the urinary extracts are purified on LC-Si SPE columns. The proposed method has a detection limit of 0.5 μg/l and a mean recovery of 91.3%. The coefficient of variation of the analytical procedure, evaluated at a concentration of 24.96 μg/l, was 9.58%. Storage of the urine samples for 3 months at −18°C did not lead to significant changes in the concentration of analyte. The method was tested analysing the urine of a farm worker with symptoms of pyrethroid poisoning, occupationally exposed to esfenvalerate.     

A simple ballistocardiographic system for a medical cardiovascular physiology course

Ballistocardiography is an old, noninvasive technique used to record the movements of the body synchronous with the heartbeat due to left ventricular pump activity. Despite the fact that this technique to measure cardiac output has been superseded by more advanced and precise techniques, it is useful for teaching cardiac cycle physiology in an undergraduate practical course because of its noninvasive application in humans, clear physiological and physiopathological analysis, and practical approach to considering cardiac output issues. In the present report, a simple, low cost, easy-to-build ballistocardiography system is implemented together with a theoretical and practical session that includes Newton's laws, cardiac output, cardiac pump activity, anatomy and physiology of the vessel circulation, vectorial composition, and signal transduction, which makes cardiovascular physiology easy to understand and focuses on the study of cardiac output otherwise seen only with the help of computer simulation or echocardiography. The proposed system is able to record body displacement or force as ballistocardiography traces and its changes caused by different physiological factors. The ballistocardiography session was included in our medical physiology course six years ago with very high acceptance and approval rates from the students.     

Kidney function in the Spinifex hopping mouse, Notomys alexis

Notomys alexis (Spinifex hopping mouse) is found in the arid zone of Australia. The structure and function of the kidneys allow this species to conserve water. This study investigated the rate at which N. alexis can reduce urine volume and increase the concentration of electrolytes and solutes when water deprived. It also looked at the response to rehydration, following a period of water deprivation. The laboratory mouse, Mus musculus domesticus, was used for comparison. N. alexis is able to reduce urine volume and increase urine concentration more rapidly than M. m. domesticus when water deprived. This appears to occur prior to any measurable changes in plasma electrolyte concentrations and is not due to reductions in glomerular filtration rate. Gradual water deprivation over a period of 10 days allowed N. alexis to adjust so that urine composition was similar in many ways to animals that had ad libitum access to water, whereas M. m. domesticus required significant water supplementation to maintain body weight at 85% of initial body weight. Ability to concentrate urine rapidly is characteristic of a well-insulated renal medulla [Bankir, L., DeRouffignac, C., 1985. Urinary concentrating ability: insights from comparative anatomy. Am. J. Physiol. 249, R643-666]. However, a well-insulated medulla is normally associated with slow dilution of urine when animals are rehydrated. N. alexis was able to produce dilute urine very rapidly following rehydration of water deprived animals. Physiological control of renal function appears to be complex. Although M. m. domesticus is able to produce concentrated urine, it is unable to survive without free water and responds more slowly to water deprivation.     

Collection and preservation of urinary proteins,using a fluff pulp diaper

Change is the most fundamental property of a biomarker. In contrast to the blood, which is under homeostatic controls, urine reflects changes in the body earlier and is more sensitive, thus making it a better biomarker source. Moreover, drawing blood from infants and toddlers is difficult and not tolerated well. For patients limited by language, communicating their chief complaint is difficult. Thus, monitoring biomarkers in urine can provide valuable clues for the diagnosis of diseases, especially pediatric diseases. Collecting urine from young children and some adult patients is more challenging than collecting it from healthy adults.Here, we propose a method that uses a fluff pulp diaper to collect urine. Urinary proteins are then eluted and adsorbed onto a piece of nitrocellulose membrane, which can be dried and stored in a vacuum bag. SDS-PAGE and LC-MS/MS analysis indicated that this method is reproducible, and similar proteins were identified as those obtained by an acetone precipitation method. With this simple and economical method, it is possible to collect and preserve urine samples from infants, toddlers, and patients with special needs, even for large-scale biomarker studies.     

Minor fatty acids of biological fluids of urogenital organs and their significance in the diagnosis of inflammatory processes

Minor lipid components (less than 1%), not occurring in the cells of mammals, have been detected in the profile of fatty acids (FA) in urine and vaginal fluid in females, as well as in ejaculate in males, by the method of gas chromatography and mass spectrometry. Their origin is supposedly attributed to microorganisms colonizing urogenital organs under normal conditions and in infectious pathology. Minor FA in the biological fluids of the urogenital tract (UGT) in man are compared with the FA composition of pure microbial cultures. The statistical analysis of FA concentrations in 500 specimens of UGT biological fluids indicates that lipid markers of microbial origin (in UGT inflammatory diseases) have a range of quantitative changes exceeding the limits of values characteristic of healthy persons and in a number of cases correlate with the diagnosis of the disease or the results of the bacteriological study. The reliability of the interpretation of the results of the marker analysis is confirmed by the difference in the composition of UGT microorganisms under normal conditions and in pathology, correlation with the clinical picture of pathological deviations, a decrease (to zero or normal values) in the concentration of the markers of pathogens as the result of treatment with antibiotics, as well as by the adequate composition of UGT microorganisms, determined by the marker method in comparison with the cultural biochemical method.     

Protein assay in the microgram range: modifications of the Hiraoka-Glick method

A method is described for the accurate estimation of protein samples ranging in size from 1 to 100 μg. It is based on fluorescence quenching of eosin Y by protein and modifies a method originally published by Hiraoka and Glick. The modified method is convenient to use. It is carried out with a stabilized reagent in cuvettes of standard size and permits the estimation of 5 μg or less of protein with precision of ± 9%. The measurements are shown to be sensitive to slight variations in ambient temperature and these contribute at least 3% to the error term shown. A graphical manner of presenting the data has been devised that provides a linear relationship over nearly 50-fold range of protein concentrations. Quenching is unaffected by presence of glucose or urea and partially inhibited by glycine or mercaptoethanol only if these are present in better than 100-fold excess over protein. Different proteins show different degrees of quenching and the method is thus most suitable for comparing quantitatively protein mixtures of similar composition. The modified method should be useful not only where microgram quantities of protein must be measured, but also with automated equipment or in cases where the Folin-Ciocalteau method cannot be employed due to presence of interfering substances.     

石制品研究中的定量分析方法:组合间对比

石制品组合间对比是石制品研究的关键一环,定量分析凭借其在复杂变量对比研究中具有的客观优势拓宽了石制品组合间对比的视野,与考古学思想、石制品组合内涵解读的深化具有相辅相成的关系。一般而言,定量分析方法分为图表法和统计法两类,主要包括三个基本步骤:选择对比组合,确定研究目标;根据研究目标提取变量;选择合适的定量分析方法。值得注意的是,考古学解释仍为石制品研究的重点,定量分析方法更多作为一种辅助手段,应用时需检验其有效性。