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Biophysical Reviews - Bioinformatics is the application of computational, mathematical and statistical techniques to solve problems in biology and medicine. Bioinformatics programs developed for...     

Opportunities and strategies to further reduce animal use for Leptospira vaccine potency testing

Hamsters are routinely infected with virulent Leptospira for two purposes in the regulation of biologics: the performance of Codified potency tests and maintenance of challenge culture for the Codified potency tests. Options for reducing animal use in these processes were explored in a plenary lecture at the “International Workshop on Alternative Methods for Leptospira Vaccine Potency Testing: State of the Science and the Way Forward” held at the Center for Veterinary Biologics in September 2012. The use of validated in vitro potency assays such as those developed by the U.S. Department of Agriculture for Leptospira (L.) canicola, Leptospira grippotyphosa, Leptospira pomona, and Leptospira icterohaemorrhagiae rather than the Codified hamster vaccination–challenge assay was encouraged. Alternatives such as reduced animal numbers in the hamster vaccination–challenge testing were considered for problematic situations. Specifically, the merits of sharing challenge controls, reducing group sizes, and eliminating animals for concurrent challenge dose titration were assessed. Options for maintaining virulent, stable cultures without serial passage through hamsters or with decreased hamster use were also discussed. The maintenance of virulent Leptospira without the use of live animals is especially difficult since a reliable means to maintain virulence after multiple in vitro passages has not yet been identified.     

Group testing for case identification with correlated responses

This article examines group testing procedures where units within a group (or pool) may be correlated. The expected number of tests per unit (i.e., efficiency) of hierarchical- and matrix-based procedures is derived based on a class of models of exchangeable binary random variables. The effect on efficiency of the arrangement of correlated units within pools is then examined. In general, when correlated units are arranged in the same pool, the expected number of tests per unit decreases, sometimes substantially, relative to arrangements that ignore information about correlation.     

Relatedness estimation of captive Asian elephants (Elephas maximas) by DNA fingerprinting

DNA from eighteen Asian elephants of known relatedness from three North American zoos was fingerprinted with the hypervariable probe M13. Paternity of a calf of known pedigree was verified. Paternity assignment of a calf having two proposed sires was suggested, but could not be conclusively determined due to a unique fragment in the calf and the unavailability of one potential sire for testing. It was concluded that DNA fingerprinting with M13 could provide a reasonable first estimator of relatedness for first degree relatives (mean S = 0.63±.11) and for unrelated animals (mean S = 0.26±.11), but would be unreliable for the discrimination of intermediate degrees of relatedness. DNA fingerprinting can be efficiently used for paternity determination only when all potential sires can be tested. © 1994 Wiley-Liss, Inc.     

Paternity exclusion in primates: Two strategies

Two strategies for the use of polymorphic biochemical and serological markers in paternity testing problems in non-human primate groups, where pedigree information is incomplete, are discussed. The positive approach, of attempting to prove paternity, is shown to be impracticable given the levels of detectable genetic variation among primates. The more conventional approach of paternity exclusion is examined and found to be useful under certain conditions. This approach is illustrated using the published data on the levels of biochemical and serological variation in Macaca nemestrina.     

A tail strength measure for assessing the overall univariate significance in a dataset

We propose an overall measure of significance for a set of hypothesis tests. The 'tail strength' is a simple function of the p-values computed for each of the tests. This measure is useful, for example, in assessing the overall univariate strength of a large set of features in microarray and other genomic and biomedical studies. It also has a simple relationship to the false discovery rate of the collection of tests. We derive the asymptotic distribution of the tail strength measure, and illustrate its use on a number of real datasets.     

“It just becomes much more complicated”: Genetic counselors' views on genetics and prenatal testing

Many social scientists and commentators have expressed concerns about the acceleration of genetic medicine and testing in the last few decades. While there is a growing body of work on how patients and the lay public view the potential of genetic medicine, there remains relatively little social science research on the personal and professional views of master's-trained genetic counselors, a growing profession of clinicians who are often the key medical actors translating increasingly complex genetic information to patients. This study begins to fill in this lacuna by examining the perspectives of 26 genetic counselors in the USA on some of the central bioethical concerns raised by genetic testing, with a particular focus on prenatal testing. The study finds that while there is general enthusiasm for genetic medicine, and prenatal testing in particular, genetic counselors also have reflexive ambivalence, expressing both skepticism and concern about the usefulness and consequences of acquiring genetic information.     

USDA regulatory guidelines and practices for veterinary Leptospira vaccine potency testing

Batch-release potency testing of leptospiral vaccines licensed by the United States Department of Agriculture (USDA) historically was conducted through animal vaccination-challenge models. The hamster vaccination-challenge assay was Codified in 1974 for bacterins containing Leptospira pomona, Leptospira icterohaemorrhagiae, and Leptospira canicola, and in 1975 for bacterins containing Leptospira grippotyphosa. In brief, 10 hamsters are vaccinated with a specified dilution of bacterin. After a holding period, the vaccinated hamsters, as well as nonvaccinated controls, are challenged with virulent Leptospira and observed for mortality. Eighty percent of vaccinated hamsters must survive in the face of a valid challenge. The high cost of the Codified tests, in terms of monetary expense and animal welfare, prompted the Center for Veterinary Biologics (CVB) to develop ELISA alternatives for them. Potency tests for other serogroups, such as Leptospira hardjo-bovis, that do not have Codified requirements for potency testing continue to be examined on a case-by-case basis.     

Use of a laser diffraction particle sizer for the measurement of mean diameter of multicellular tumor spheroids

Summary Increasing use is being made of tumor cell lines cultured as cell aggregates (generally referred to as multicellular spheroids) in in vitro radiosensitivity and/or chemosensitivity tests. Conventional procedures for the determination of mean spheroid diameters for the construction of growth delay curves employ a microscope-image analyzer. However, this approach can prove excessively time consuming when large numbers of samples have to be, measured. We have, therefore, been exploring the use of a Laser Diffraction Particle Sizer, the Malvern 2600 long bench model, for the measurement of mean spheroid diameter and size distribution. We report here a direct comparison between measurements carried out by the instrument and under the microscope. Also a comparison of growth curves for six cell lines constructed from measurements by the microscope and by the instrument. A number of factors that might affect the accuracy of spheroid diameter measurement by the instrument have been investigated: The effect of stirring to maintain the spheroids in suspension during measurement. Sampling error due to removal of a series of spheroid samples from culture flasks for measurement. Optimum number of scans to be carried out by the instrument to reach a constant value for mean diameter, and minimum SE of the mean. This research was supported by the Yorkshire Cancer Research Campaign, Horrogate HG1 5LQ, United Kingdom, and by the Hospital Research Fund, Cookridge Hospitatl, Leeds LS16 6QB, United Kingdom.     

Antibiotic and Disinfectant Resistance in Tap Water Strains – Insight into the Resistance of Environmental Bacteria

Although antibiotic-resistant bacteria (ARB) have been isolated from tap water worldwide, the knowledge of their resistance patterns is still scarce. Both horizontal and vertical gene transfer has been suggested to contribute to the resistance spread among tap water bacteria. In this study, ARB were isolated from finished water collected at two independent water treatment plants (WTPs) and tap water collected at several point-of-use taps during summer and winter sampling campaigns. A total of 24 strains were identified to genus or species level and subjected to antibiotic and disinfectant susceptibility testing. The investigated tap water ARB belonged to phyla Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes. The majority of the isolates proved multidrug resistant and resistant to chemical disinfectant. Neither seasonal nor WTP-dependent variabilities in antibiotic or disinfectant resistance were found. Antibiotics most effective against the investigated isolates included imipenem, tetracyclines, erythromycin, and least effective – aztreonam, cefotaxime, amoxicillin, and ceftazidime. The most resistant strains originate from Afipia sp. and Methylobacterium sp. Comparing resistance patterns of isolated tap water ARB with literature reports concerning the same genera or species confirms intra-genus or even intra-specific variabilities of environmental bacteria. Neither species-specific nor acquired resistance can be excluded.     

Improved two‐stage group sequential procedures for testing a secondary endpoint after the primary endpoint achieves significance

In two‐stage group sequential trials with a primary and a secondary endpoint, the overall type I error rate for the primary endpoint is often controlled by an α‐level boundary, such as an O'Brien‐Fleming or Pocock boundary. Following a hierarchical testing sequence, the secondary endpoint is tested only if the primary endpoint achieves statistical significance either at an interim analysis or at the final analysis. To control the type I error rate for the secondary endpoint, this is tested using a Bonferroni procedure or any α‐level group sequential method. In comparison with marginal testing, there is an overall power loss for the test of the secondary endpoint since a claim of a positive result depends on the significance of the primary endpoint in the hierarchical testing sequence. We propose two group sequential testing procedures with improved secondary power: the improved Bonferroni procedure and the improved Pocock procedure. The proposed procedures use the correlation between the interim and final statistics for the secondary endpoint while applying graphical approaches to transfer the significance level from the primary endpoint to the secondary endpoint. The procedures control the familywise error rate (FWER) strongly by construction and this is confirmed via simulation. We also compare the proposed procedures with other commonly used group sequential procedures in terms of control of the FWER and the power of rejecting the secondary hypothesis. An example is provided to illustrate the procedures.     

On a Special Feature of the Patel-Gupta Equivalence Test

For small variances level and power of the Patel-Gupta test show a somewhat irregular behaviour. This phenomenon is mathematically explained here.     

Anin vitro model for the biological evaluation of dental materials using human periodontal ligament cells

Anin vitro system is described which uses human diploid cells derived from the periodontal ligament. It simulates the clinical situation and is suitable for rapid cytotoxicity screening of dental materials. It can also be adapted to study various factors influencing biocompatibility.     

The Value of Human Testing of Pesticides

Recently, the issue of using human volunteers as subjects for studying the potential toxicity of pesticides has received public attention through the media and subsequently in the regulatory arena. The debate has focused on whether such studies are ethical per se and if data from these investigations should be used for regulatory decisions. The precipitating event that prompted the current debate was the enactment of the Food Quality Protection Act (FQPA) of 1996. The FQPA, which amended the two laws governing the regulation of pesticides in the United States, requires the Environmental Protection Agency to reassess all of the nearly 10,000 tolerances (maximum allowable residues in food) and exemptions from tolerances that were in place when the law went into effect. When reassessing tolerances the U.S. Environmental Protection Agency (USEPA) reviews the data, including toxicology, available on each pesticide to determine if they are adequate to allow the Agency to make the necessary safety finding. Historically, it had been considered acceptable to conduct and use data from studies of exposure to chemicals (including pesticides) of human volunteers if these studies were conducted according to specific criteria as outlined in the Helsinki Declaration and Common Rule. Now this philosophy is being challenged and the USEPA is faced with answering the question of whether pesticides should be viewed as different, from an ethical standpoint, from other chemicals, and how such data should be used in the risk assessment process. The following paper makes an argument for the use of human volunteer testing of pesticides applying the logic that, if one wants to protect humans from the potential harm that may occur from eating foods containing pesticides, one must use the best possible data available. There can be little doubt that the best data for predicting the toxicity of a chemical in humans is to obtain and use human data, as long as it is obtained in an ethical manner.     

A Problem of Equivalence in Clinical Trials

Several methods exist for testing the bioequivalence in bioavailability trials. In this article we propose a method for testing the equivalence of two drugs in clinical trials when the response variable is assumed to have a normal distribution. The null and alternative hypotheses are formulated in a nonconventional manner. Computing aspects for the power and sample size are discussed.     

假说检验和科学方法

本文的意图是让研究者审视研究方法,并在研究设计中充分使用假说检验,并在选择模式物种时充分理解其自然史.我们的总前提是,按照"强推论"(指假定拒绝某一假说而不是支持某一偏爱假说)的逻辑,科学能够进展得更快、更可观、更有确定性.我们强调并提供了符合逻辑的一系列步骤,即确定科学问题或确定具有未知生物学意义的问题;列出所有可靠的、能解释所观察现象的假说,每个假说列出其可检验的、可证明其无根据的预测;然后是符合预测检验的实验或研究设计.我们也强调,模式物种对于解决科学的理论问题以及得出推论是很重要的.本文所展示的不是新思想,只是提醒研究者要注意遵循的基本研究途径.     

A Quick,Onsite Test for Delineating Arsenic Contaminant Plumes in Soil

Dipping vats were used routinely in the southeastern U.S. in the early 1900s to eradicate the cattle fever tick. The legacy is many dip vat sites with arsenic (As)-contaminated soil and ground water. Assessing the extent of these As plumes can be time consuming and expensive. We describe a quicker and less expensive, onsite test for soil As. It is a modification of a commercially available test designed for As in water, taking about 10?min to complete, allowing large plume areas to be delineated in a single day. An As contaminant plume in Alachua County, FL, was delineated using the quick test. Soil samples taken from a large grid encompassing the plume were analyzed in the laboratory for As to confirm the results obtained with the quick test. The comparison showed that the quick test very accurately delineated the outer boundary of the plume as well as zones of higher As concentration within the plume.