<Emphasis Type="Italic">c</Emphasis>hip <Emphasis Type="Italic">a</Emphasis>rtifact <Emphasis Type="Italic">CORRECT</Emphasis>ion (caCORRECT): A Bioinformatics System for Quality Assurance of Genomics and Proteomics Array Data

Quality assurance of high throughput "-omics" data is a major concern for biomedical discovery and translational medicine, and is considered a top priority in bioinformatics and systems biology. Here, we report a web-based bioinformatics tool called caCORRECT for chip artifact detection, analysis, and CORRECTion, which removes systematic artifactual noises that are commonly observed in microarray gene expression data. Despite the development of major databases such as GEO arrayExpress, caArray, and the SMD to manage and distribute microarray data to the public, reproducibility has been questioned in many cases, including high-profile papers and datasets. Based on both archived and synthetic data, we have designed the caCORRECT to have several advanced features: (1) to uncover significant, correctable artifacts that affect reproducibility of experiments; (2) to improve the integrity and quality of public archives by removing artifacts; (3) to provide a universal quality score to aid users in their selection of suitable microarray data; and (4) to improve the true-positive rate of biomarker selection verified by test data. These features are expected to improve the reproducibility of Microarray study. caCORRECT is freely available at: http://caCORRECT.bme.gatech.edu.     

PCR-restriction fragment length polymorphism for rapid, low-cost identification of isoniazid-resistant Mycobacterium tuberculosis

PCR-restriction fragment length poymorphism (PCR-RFLP) is a simple, robust technique for the rapid identification of isoniazid-resistant Mycobacterium tuberculosis. One hundred consecutive isolates from a Vietnamese tuberculosis hospital were tested by MspA1I PCR-RFLP for the detection of isoniazid-resistant katG_315 mutants. The test had a sensitivity of 80% and a specificity of 100% against conventional phenotypic drug susceptibility testing. The positive and negative predictive values were 1 and 0.86, respectively. None of the discrepant isolates had mutant katG_315 codons by sequencing. The test is cheap (less than $1.50 per test), specific, and suitable for the rapid identification of isoniazid resistance in regions with a high prevalence of katG_315 mutants among isoniazid-resistant M. tuberculosis isolates.     

Evaluation of two rapid immunochromatographic assays for diagnosis of dengue among Vietnamese febrile patients

Results from two dengue rapid tests, the PanBio Duo cassette and the SD Bioline strip test, were compared to those of enzyme-linked immunosorbent assays (Focus Diagnostics) from sera of 200 Vietnamese febrile patients. The PanBio assay was superior, with sensitivity and specificity values for acute-phase serum samples of 54% and 70% (immunoglobulin M) and 70% and 88% (immunoglobulin G), respectively.     

Arsenic induces cardiac rhythm dysfunction and acylcarnitines metabolism perturbation in rats

Background: Arsenic has been shown to cause various diseases (such as blackfoot disease, cardiovascular diseases, bladder cancer and skin cancer) in many areas of the world. However, the effects of arsenic on cardiac rhythm functions still lack investigation.

Methods: In this study, different concentrations of arsenic were orally applied to Sprague Dawley rats in order to examine the relationship between arsenic and cardiovascular rhythm (i.e. long QT) via electrocardiography measurement. In addition, QT correction formulas were used to correct the QT interval. Linear regression analysis was used to examine the correlation between the QT interval and cardiac cycle length, corrected QT and heart rate. A metabolomic approach was applied to study carnitine-derived metabolites under arsenic exposure by using an ultra-performance liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC/Q-TOF MS) system.

Results: The present findings showed that exposure to arsenic causes QT and corrected (QTc) prolongation and heart rate declines. However, the linear correlation analysis showed that there is no significant correlation between cardiac cycle length and the QT interval in both the uncorrected QT and corrected QT. The expression of acylcarnitine metabolites can be used to discriminate the control and arsenic-treated groups.

Conclusions: This study provides information concerning the effect of arsenic at different concentrations on cardiac rhythm (such as QT, QTc, and heart rate) but not on cardiac cycle length. The metabolism of acylcarnitine metabolites can be a potential pathway for arsenic-induced cardiac rhythm dysfunction in rats.     

Multiple recombinant noroviruses in Japan

A total of 417 fecal specimens collected from sporadic pediatric cases of acute gastroenteritis in Japan from 2005 to 2006 were tested for noroviruses by RT-PCR. Noroviruses were detected in 44 of 417 (10.1%) fecal specimens tested. Of these, the GII/3 was the most predominant genotype with a prevalence rate of 56.8%, followed by 34% of the GII/4 and others. Phylogenetic analysis reveals that multiple recombinant noroviruses, which were both dependently and independently introduced from four different continents (Asia, America, Europe, and Oceania), emerged to cause acute gastroenteritis among Japanese children. Of these, "new variant" noroviruses suddenly emerged to become the leading strain in Japan for the first time. This report is also the first indication of the existence of multiple recombinant noroviruses co-circulating in Japan.     

服刑人员132例人格障碍筛查问卷调查

目的:了解人格障碍筛查问卷的初步诊断情况。方法:于2005-09/10选择广东省三水劳教所的服刑人员154人为调查对象,将人格障碍筛查问卷的软件中的106个检查条目制成“是”或“否”问卷进行调查。结果:发放问卷154份,回收问卷154份,有效问卷132份。132名服刑人员中未提示任何人格障碍和品行障碍的有10名(7.58%)。73名提示18岁前有品行障碍,提示有人格障碍的116名,99名存在2项以上人格障碍。结论:问卷结果提示的人格障碍和品行障碍有可能存在诊断过度的问题。对调查阳性者进行人格障碍临床半定式检测工具测试是下一步要进行的工作。     

L''incontinence urinaire chez la femme sportive nullipare. Enquête épidémiologique. À propos de 105 cas

One hundred and five nulliparous top-level young sportswomen (average age: 21.5 years) responded to an inquiry by means of questionnaire designed to investigate a possible relationship between urinary incontinence due to effort (UIE) and sports activities. Sixty-six sportswomen (62.8%) stated having UIE, which infrequently interfered with their normal sports activities; whereas 63 (60%) declared that they were coping with UIE on a daily basis. These two types of UIE are closely related. A comparative study on a similar population of 105 non-athletic women performed in parallel with this study showed that only 38 (34%) subjects declared having urinary incontinence, confirming therefore the influence of sport practice. Using the χ² and student's t-test, we investigated a relationship between UIE and different factors (age, duration of physical exercise, duration and type of sport practised, abdominal exercises, presence of acuneresis in children, presence of constipation). Only the presence of enuresis in children together with the presence of constipation led to statistically significant relationship. Being frustrated by taboos and considering the troubles as pathological, only a few sportswomen talked openly about this problem. Both information and effective control of the perineum could help prevent this condition. © 1998 Elsevier, Paris     

Degenerate‐disc Infection Study with Contaminant Control: Discussion on the Research Methods

Objective

The role of bacterial infection in the causation of disc degeneration and its consequences is controversial. The current evidence is limited to underpowered studies, with the majority of such studies having only an internal contaminant arm, and only one study having a control arm with a non‐degenerate disc population. The Degenerate‐disc Infection Study with Contaminant Control (DISC) study includes a control arm and an internal contaminant control to resolve these shortcomings.

Methods

The study is designed as a case‐control study: cases are patients undergoing surgery for degenerated disc pathology and controls are patients undergoing surgery for non‐degenerate pathology, such as trauma, scoliosis or tumor cases.

Results

This study is part of a multi‐centric trial involving six spine centers with 15 spine surgeons contributing. The DISC study methodology, rationale and controversies are presented here. The predominant issue is how to interpret contamination. We present our algorithm for the DISC study to address this. For disc samples that are positive concurrently with positive paraspinal tissue sample, the result will be interpreted as contamination. For positive disc samples with a negative paraspinal tissue culture result, the interpretation of this result will be infection. If cultures for both disc sample and paraspinal tissue sample are negative, then the result is interpreted as non‐infected. If the disc culture is negative but paraspinal tissue culture is positive, then it is treated as a contaminant.

Conclusions

Future large‐scale studies are required with a good control arm, a contamination arm, and histopathological correlations.     

Convergence of fMRI and ERP measures of emotional face processing in combat‐exposed U. S. military veterans

The late positive potential (LPP) and fMRI blood‐oxygen‐level dependent (BOLD) activity can provide complementary measures of the processing of affective and social stimuli. Separate lines of research using these measures have often employed the same stimuli, paradigms, and samples; however, there remains relatively little understanding of the way in which individual differences in one of these measures relates to the other, and all prior research has been conducted in psychiatrically healthy samples and using emotional scenes (not faces). Here, 32 combat‐exposed U. S. military veterans with varying levels of posttraumatic stress symptomatology viewed affective social stimuli (angry, fearful, and happy faces) and geometric shapes during separate EEG and fMRI BOLD recordings. Temporospatial principal component analysis was used to quantify the face‐elicited LPP in a data‐driven manner, prior to conducting whole‐brain correlations between resulting positivities and fMRI BOLD elicited by faces. Participants with larger positivities to fearful faces (> shapes) showed increased activation in the amygdala; larger positivities to angry and happy faces (> shapes) were associated with increased BOLD activation in the posterior fusiform gyrus and inferior temporal gyrus, respectively. Across all face types, larger positivities were associated with increased activation in the fusiform “face” area. Correlations using mean area amplitude LPPs showed an association with increased activation in the anterior insula for angry faces (> shapes). LPP‐BOLD associations were not moderated by PTSD. Findings provide the first evidence of correspondence between face‐elicited LPP and BOLD activation across a range of (normal to disordered) psychiatric health.