Assessing the Reliability of Amplified RNA Used in Microarrays

A certain minimal amount of RNA from biological samples is necessary to perform a microarray experiment with suitable replication. In some cases, the amount of RNA available is insufficient, necessitating RNA amplification prior to target synthesis. However, there is some uncertainty about the reliability of targets that have been generated from amplified RNA, because of nonlinearity and preferential amplification. This current work develops a straightforward strategy to assess the reliability of microarray data obtained from amplified RNA. The tabular method we developed, which utilises a Down-Up-Missing-Below (DUMB) classification scheme, shows that microarrays generated with amplified RNA targets are reliable within constraints. There was an increase in false negatives because of the need for increased filtering. Furthermore, this analysis method is generic and can be broadly applied to evaluate all microarray data. A copy of the Microsoft Excel spreadsheet is available upon request from Edward Bearden.     

Mathematical correlation between biomaterial and cellular parameters--critical reflection of statistics

For mathematical modelling of the biomaterial-cell contact, it is necessary to find both parameters characterizing physical and chemical properties of the material surface and also such describing the reaction of the adhering cells. Only those material and cell parameters that correlate with each other are applicable to model this contact mathematically. Only few papers are dealing with this special problem. The aim of this paper is to present results of physical/chemical and biological investigations made on differently modified rough titanium implant surfaces in order to find out only the correlating parameters. Furthermore we discuss several ways to apply statistical methods to the correlation problem. Only few ones of all investigated parameters both on material and on cellular side were applicable for correlation. For example we found in our studies that fractal structure parameter topothesy has influence on the spreading behaviour of the osteoblastic cells. However the value of the correlation coefficient and its statistical significance heavily depend on the method of averaging the available data. Especially the biological data (spreading area) were afflicted with relatively high error up to 30%. Averaging of this data masks the true facts. That is why the correlation coefficient considerably decreases if the biological parameters are not averaged. On the other hand, the statistical reliability increases due to the higher number of investigated cases. Critical error discussion is necessary in statistical correlation between material and biological parameters. Often the results are heavily influenced by the statistical handling of data, especially if only few data are available. May be that new unconventional methods like bootstrap method can show a way out of this dilemma.     

Reliability of stereotactic biopsy. A model to test the value of diagnoses obtained from small fragments of nervous system tumors

Because of the variability of the structural features of cerebral tumors, the characteristics observed in biopsy samples may not be representative of the whole neoplasm. The reliability of cerebral stereotactic biopsy is therefore greatly debated. In order to test the value of diagnoses based on biopsy samples, the authors compared histological and cytological data obtained from a small fragment of a tumor with the definitive diagnosis obtained from surgical or necropsy specimens. An analysis of 64 cases is reported, where a correct diagnosis from the biopsy sample was achieved in 92.2% of the cases. Neuroglial tumors were more difficult to characterize than other types of intracranial tumors, with an accuracy of 81.5%.     

Reconstructing DNA copy number by joint segmentation of multiple sequences

ABSTRACT: BACKGROUND: Variations in DNA copy number carry information on the modalities of genome evolution and mis-regulation of DNA replication in cancer cells. Their study can help localize tumor suppressor genes, distinguish different populations of cancerous cells, and identify genomic variations responsible for disease phenotypes. A number of different high throughput technologies can be used to identify copy number variable sites, and the literature documents multiple effective algorithms. We focus here on the specific problem of detecting regions where variation in copy number is relatively common in the sample at hand. This problem encompasses the cases of copy number polymorphisms, related samples, technical replicates, and cancerous sub-populations from the same individual. RESULTS: We present a segmentation method named generalized fused lasso (GFL) to reconstruct copy number variant regions, that is based on penalized estimation and is capable of processing multiple signals jointly. Our approach is computationally very attractive and leads to sensitivity and specificity levels comparable to those of state-of-the-art specialized methodologies. We illustrate its applicability with simulated and real data sets. CONCLUSIONS: The flexibility of our framework makes it applicable to data obtained with a wide range of technology. Its versatility and speed make GFL particularly useful in the initial screening stages of large data sets.     

Reliability of Computation in the Cerebellum

The mossy fiber-granule cell-parallel fiber-Purkinje cell system of the cerebellar cortex is investigated from the viewpoint of reliability of computation. It is shown that the effects of variability in the inputs to a Purkinje cell can be reduced by having a large number of parallel fibers whose activities are statistically independent. The mossy fiber-granule cell relay is shown to be capable of performing the required function of transforming the activity in a small number of mossy fibers into activity in a much larger number of parallel fibers, while ensuring that there is little correlation between the activities of individual parallel fibers. The effects of variability in the outputs of Purkinje cells may be reduced by redundancy and convergence schemes, as evidenced by the geometrical pattern of parallel fibers and Purkinje cells and the convergence of these cells onto their target neurons.     

Reporting the Reliability of Accelerometer Data with and without Missing Values

Objectives

Participants with complete accelerometer data often represent a low proportion of the total sample and, in some cases, may be distinguishable from participants with incomplete data. Because traditional reliability methods characterize the consistency of complete data, little is known about reliability properties for an entire sample. This study employed Generalizability theory to report an index of reliability characterizing complete (7 days) and observable (1 to 7 days) accelerometer data.

Design

Cross-sectional.

Methods

Accelerometer data from the Study of Early Child Care and Youth Development were analyzed in this study. Missing value analyses were conducted to describe the pattern and mechanism of missing data. Generalizability coefficients were derived from variance components to report reliability parameters for complete data and also for the entire observable sample. Analyses were conducted separately by age (9, 11, 12, and 15 yrs) and daily wear time criteria (6, 8, 10, and 12 hrs).

Results

Participants with complete data were limited (<34%) and, most often, data were not considered to be missing completely at random. Across conditions, reliability coefficients for complete data were between 0.74 and 0.87. Relatively lower reliability properties were found across all observable data, ranging from 0.52 to 0.67. Sample variability increased with longer wear time criteria, but decreased with advanced age.

Conclusions

A reliability coefficient that includes all participants, not just those with complete data, provides a global perspective of reliability that could be used to further understand group level associations between activity and health outcomes.     

A Geodata Production System: To allow people to stay at home or follow medical equipments in the hospitals

ObjectivesThe well-being of people depends in part on the sense of freedom, and one aspect is certainly the possibility for people to remain at home. However, there is a need for “following” the movements and, if possible, the activity of the person. The problem is that very few home systems make it possible to have these data at a reasonable price, and at an acceptable reliability level. We offer a simple to use, reliable and energy self-sufficient person location system. People are the first “targets”, but objects could be involved.Material and methodsThe system is described and their performance analyzed in real conditions of use. The positioning algorithms are explained and the practical implementations described.ResultsFirst results on the activity of a person at home are presented as well as some tracks on the type of data processing that could be considered.The simplicity of deployment is shown and the usefulness of the available data is discussed in the context of home care of an elderly person as well as the monitoring of hospital equipment.ConclusionOur approach provides simplicity of implementation and very high reliability in real time, without aiming for high accuracy in all cases. Conceptually taking into account the high variability of indoor radio measurements makes it possible to significantly increase the reliability of the geo-data produced. Moreover, we will mention two real deployments and the associated performances obtained, carried out in order to follow the behavior of an old autonomous man living alone at home, and in another hand to follow the stretchers of the emergency department of a French hospital.     

Further Assessment of Rosette Inhibition Test in Clinical Organ Transplantation

The rosette inhibition test was used in the clinical management of organ allografts to estimate the amount of immunosuppressive drugs necessary to prevent rejection. In patients surviving more than three months renal function appeared to be better than in a similar group of patients managed without the test. It is suggested that this was due to a reduction in the number of clinical or subclinical rejection episodes. On the other hand, the test indicates that in many cases the level of immunosuppression should be much higher, and if this advice is followed the patients become increasingly exposed to the risk of infection. In other words, those patients with good renal function remained well, whereas those who might otherwise have rejected their kidney and survived had in fact died of sepsis.     

Variability of cytochrome b gene of mitochondrial DNA of pink salmon Oncorhynchus gorbuscha (Walbaum) from the rivers of the continental coast of the Sea of Okhotsk and Zavyalov Island

Data on the structure and variability of the nucleotide sequence of the cytochrome b (cytb) gene fragment of mitochondrial DNA (mtDNA) in pink salmon of adjacent generations from the rivers of the continental coast of the Sea of Okhotsk and Zavyalov Island were obtained. The differences between adjacent generations were discovered. By the marker studied, pink salmon of the even-year line are characterized by a high level of genetic variability. It is shown that reproductive isolation has led to accumulation of specific mutations of the mtDNA cytb gene in each line and, consequently, to their divergence. Analysis of the data showed that the share of intrapopulation genetic variability of northern Sea of Okhotsk pink salmon accounts for about 91%. The intergroup component that was calculated for adjacent generations of the species is relatively small and is 9%, which seems to be indicative of a relatively recent divergence of adjacent generations of salmon.     

Inferring gene regulatory networks from multiple microarray datasets

MOTIVATION: Microarray gene expression data has increasingly become the common data source that can provide insights into biological processes at a system-wide level. One of the major problems with microarrays is that a dataset consists of relatively few time points with respect to a large number of genes, which makes the problem of inferring gene regulatory network an ill-posed one. On the other hand, gene expression data generated by different groups worldwide are increasingly accumulated on many species and can be accessed from public databases or individual websites, although each experiment has only a limited number of time-points. RESULTS: This paper proposes a novel method to combine multiple time-course microarray datasets from different conditions for inferring gene regulatory networks. The proposed method is called GNR (Gene Network Reconstruction tool) which is based on linear programming and a decomposition procedure. The method theoretically ensures the derivation of the most consistent network structure with respect to all of the datasets, thereby not only significantly alleviating the problem of data scarcity but also remarkably improving the prediction reliability. We tested GNR using both simulated data and experimental data in yeast and Arabidopsis. The result demonstrates the effectiveness of GNR in terms of predicting new gene regulatory relationship in yeast and Arabidopsis. AVAILABILITY: The software is available from http://zhangorup.aporc.org/bioinfo/grninfer/, http://digbio.missouri.edu/grninfer/ and http://intelligent.eic.osaka-sandai.ac.jp or upon request from the authors.     

Reliability and validity of the physical disector method for estimating neuron number

The physical disector was proposed as an unbiased and efficient means to estimate neuron number; however, the validity and reliability of this method have been examined only infrequently. Estimates of neuron number in the dorsal root ganglia (DRG) of bullfrogs (Rana catesbeiana) were compared to nucleolar counts based on 3-dimensional reconstructions. Accuracy of disector estimates were not affected by size of the animal. Similarly, disector estimates were not systematically altered when area measurements were limited to cellular regions of the DRG versus inclusion of the entire cross-sectional area. However, the recommended protocol for applying the disector resulted in sampling errors that introduced considerable variability in repeated estimates of neuron number from a single ganglion. In addition to this lack of reliability, disector estimates were consistently lower than those obtained by means of a nucleolar counting method that was calibrated against 3-dimensional reconstructions of neuronal profiles. The systematic error of the disector method was greater when ganglia were cut parallel to the long axis of the DR than when they were cut perpendicular to this axis. Increasing the sample size beyond what was recommended increased the reliability of estimates obtained with the disector; however, the bias associated with the plane of section was not reduced. These results emphasize the need for empirical validation of methods used to estimate neuron number in the tissue to which they are to be applied. © 1996 John Wiley & Sons, Inc.     

抗冻蛋白应用于水稻悬浮细胞超低温保存的研究

AFP from winter flounder was utilized in cryopreservation of plant cells. During cryopreservation of rice suspension cells by two-step method, AFP at 0.01 mg/ml damaged the cells extremely. The data obtained at relatively high concentration, however, decreased the variability of survival rate. During vitrification of rice cells, AFP at 0.2 mg/ml enhanced the viability. However, high concentration AFP (> 5 mg/ml) decreased the recovery rate. Studies indicated that the results of application of AFP in cryopreservation were closely related to the concentration of cryoprotectant. The amount of ice crystal in environment, the concentration of AFP and cryoprotectant, and the composition of plasma membrane were several key factors affecting the results of AFP application. In mechanism analysis, the authors suggested that on one hand AFP can interact with ice crystal, which inhibits ice recrystallization and prevent the cells from devitrification. On the other hand, AFP also can interact with cell membrane, resulting in the ice growth around the plasma membrane.     

Evaluation of an EIA method for measuring serum levels of the estrogen metabolite 2-hydroxyestrone in adults

Two-hydroxyestrone (2OHE-1) and 16alpha-hydroxyestrone (16OHE-1) are two estrogen metabolites that may play important roles in the development or promotion of breast cancer. Our study assessed the reliability of a newly developed kit procedure for measuring 2OHE-1. Although under certain conditions the assay would not distinguish 2OHE-1 from estriol, or possibly 2-methoxyestrone, steroids such as 17beta-estradiol, estrone and 16OHE-1 should not interfere with the test. Our study evaluated the precision of this enzyme immunoassay (EIA) kit for measuring 2OHE-1 levels in serum obtained from healthy men and women. As a result of several replicate analyses of specimens obtained from 18 men and 20 women, we found that the within-run coefficients of variation (CVs) were approximately 20% and the among run CVs, 30%. Because the SD for the procedure is high, the limit of detection (LOD) was also high (130 ng/l). Nonetheless the assay could distinguish between 2OHE-1 levels in men (128 ng/l) and women (332 ng/l) because we performed a large number of analyses on each specimen. Improving the reproducibility of the assay would reduce the: 1. LOD; number of replicates needed to obtain reliable estimates of 2-OHE-1 levels; amount of time, effort, and cost for each analysis; and greatly improve the reliability of the method. Because the within-run variability is relatively smaller than the total variability (among run + within run), use of the assay for determining differences among groups could be justified only when measurements were made in a single run.     

The Conditions for Reliability of a Psychological Experiment

The problem of the reliability of a psychological experiment has assumed considerable significance in contemporary experimental psychology. This problem has been posed especially and studied in detail in bourgeois psychological techniques and testing. For this reason, theories on the criteria of the reliability of an investigation are usually connected with these areas of study. Furthermore, the approach to this problem, typical of bourgeois psychology, is also linked to these areas of psychology.     

Mouse inbred strain sequence information and yin-yang crosses for quantitative trait locus fine mapping

The shared ancestry of mouse inbred strains, together with the availability of sequence and phenotype information, is a resource that can be used to map quantitative trait loci (QTL). The difficulty in using only sequence information lies in the fact that in most instances the allelic state of the QTL cannot be unambiguously determined in a given strain. To overcome this difficulty, the performance of multiple crosses between various inbred strains has been proposed. Here we suggest and evaluate a general approach, which consists of crossing the two strains used initially to map the QTL and any new strain. We have termed these crosses "yin-yang," because they are complementary in nature as shown by the fact that the QTL will necessarily segregate in only one of the crosses. We used the publicly available SNP database of chromosome 16 to evaluate the mapping resolution achievable through this approach. Although on average the improvement of mapping resolution using only four inbred strains was relatively small (i.e., reduction of the QTL-containing interval by half at most), we found a great degree of variability among different regions of chromosome 16 with regard to mapping resolution. This suggests that with a large number of strains in hand, selecting a small number of strains may provide a significant contribution to the fine mapping of QTL.     

抗冻蛋白应用于水稻悬浮细胞超低温保存的研究

本文将鱼类抗冻蛋白应用于植物细胞的超低温保存。结果表明,在水稻悬浮细胞的两步法保存中,浓度为0.01mg/ml的抗冻蛋白具有特别的负作用,相对高浓度的抗冻蛋白则能减小细胞存活率的波动性。在玻璃化法保存中,浓度为0.2mg/ml的抗冻蛋白能改善保存效果,更高浓度的抗冻蛋白(>5mg/ml)反而会降低保存效果。环境冰晶量、抗冻蛋白浓度、低温保护剂浓度和细胞膜组成等是影响抗冻蛋白使用效果的几大因素。作者在机理分析中认为,一方面,抗冻蛋白能和冰晶作用,抑制重冰晶,防止去玻璃化;另一方面,抗冻蛋白也能和细胞膜作用,诱发膜表面冰晶形成。     

Reliability study of thermal quantitative sensory testing in healthy Chinese

Background: Test–retest reliability is important to establish for any diagnostic tool. The reliability of quantitative sensory testing (QST) in the trigeminal region has recently been described in Caucasians as well as differences in absolute thresholds and responses between Caucasians and Chinese. However, the test–retest reliability has not been determined in a Chinese population.

Objective: To provide novel information on the test–retest reliability of thermal QST in the trigeminal and spinal system in healthy Chinese.

Methods: Twenty healthy volunteers (10 women and 10 men) participated. Cold detection threshold (CDT), warm detection threshold (WDT), cold pain threshold (CPT), and heat pain threshold (HPT) were measured at two sites: the surface of the left hand and the left masseter. The testing was performed over three consecutive stimuli trials, three sessions conducted on one day and repeated one week later. Data were analyzed with intra-tester reliability test and four-way analysis of variance (ANOVA) for repeated measures.

Results: There was a tendency for the first trial in CDT (p?=?0.005), CPT (p?=?0.02), and HPT (p?p?=?0.003) and HPT (p?=?0.045) with higher sensitivity at the masseter muscle. There were significant gender differences with higher sensitivity in women for CPT (p?=?0.001) and HPT (p?=?0.001).

Conclusion: Test site and gender affect thermal thresholds substantially. The test–retest reliability of most thermal threshold measures were acceptable for assessing somatosensory function, however, innocuous thresholds appear to be associated with larger variability than noxious thresholds in a Chinese population.     

Reliability of telemetric electromyography and near-infrared spectroscopy during high-intensity resistance exercise

This study quantified the inter- and intra-test reliability of telemetric surface electromyography (EMG) and near infrared spectroscopy (NIRS) during resistance exercise. Twelve well-trained young men performed high-intensity back squat exercise (12 sets at 70–90% 1-repetition maximum) on two occasions, during which EMG and NIRS continuously monitored muscle activation and oxygenation of the thigh muscles. Intra-test reliability for EMG and NIRS variables was generally higher than inter-test reliability. EMG median frequency variables were generally more reliable than amplitude-based variables. The reliability of EMG measures was not related to the intensity or number of repetitions performed during the set. No notable differences were evident in the reliability of EMG between different agonist muscles. NIRS-derived measures of oxyhaemoglobin, deoxyhaemoglobin and tissue saturation index were generally more reliable during single-repetition sets than multiple-repetition sets at the same intensity. Tissue saturation index was the most reliable NIRS variable. Although the reliability of the EMG and NIRS measures varied across the exercise protocol, the precise causes of this variability are not yet understood. However, it is likely that biological variation during multi-joint isotonic resistance exercise may account for some of the variation in the observed results.     

Autosomal mutations and human spermatogenic failure

Infertility, defined as the inability to conceive after 1 year of unprotected intercourse, is a healthcare problem that has a worldwide impact. Male factors are involved in at least half of these cases of infertility. Despite 33 years of assisted reproductive activities, a considerable number of cases (25–30%) remain idiopathic. This situation can be explained by a poor understanding of the basic mechanisms driving male and female gametogenesis. Compared to multi-organ pathologies, only a few non-syndromic genetic causes of human infertility have been described so far, despite the fact that it is estimated that some infertility cases could be explained by genetic causes and that over 200 infertile or subfertile genetic mouse models have been described. So far, very little has been discovered in the field of human male reproductive genetics. Consequently, genetic tests proposed to infertile couples are limited, although worldwide efforts devoted to the field of human genetics of infertility are expected to provide new genetic tests in the near future. We present the requirements for performing informative genetics studies in the field of infertility, the techniques used and the results obtained so far. This article is part of a Special Issue entitled: Molecular Genetics of Human Reproductive Failure.     

Analysis of Coyote Mitochondrial DNA Genotype Frequencies: Estimation of the Effective Number of Alleles

A restriction-site survey of 327 coyotes (Canis latrans) from most parts of their North American range reveals 32 mitochondrial DNA (mtDNA) genotypes. The genotypes are not strongly partitioned in space, suggesting that there is high gene flow among coyote subpopulations. Consequently, each new geographic location added to the study has a decreasing probability of containing a mtDNA genotype that had not been previously discovered. This being the case, by using Monte Carlo sampling experiments, we can estimate the total number of genotypes that would be found if all possible localities were surveyed. This estimate of total genotypic variability agrees qualitatively with estimates based on theoretical considerations of the expected number of alleles in a stable population. We also predict effective population sizes from genotype data. The accuracy of these estimates is thought to be dependent on the fact that coyotes are not highly genetically structured, a situation which may apply to highly mobile species.