A technique to detect and to quantify fasciocutaneous blood vessels in small laboratory animals ex vivo

PURPOSE: A microangiographical technique is described, which allows visualization of small and capillary blood vessels and quantification of fasciocutaneous blood vessels by means of digital computer analysis in very small laboratory animals. MATERIALS AND METHODS: The left carotid artery of 20 nu/nu mice was cannulated (26 gauge) and a mixture of gelatin, bariumsulfate, and green ink was injected according to standardized protocol. Fasciocutaneous blood vessels were visualized by digital mammography and analyzed for vessel length and vessel surface area as standardized units [SU] by computer program. RESULTS: With the described microangiography method, fasciocutaneous blood vessels down to capillary size level can be clearly visualized. Regions of interest (ROIs) can be defined and the containing vascular network quantified. Comparable results may be obtained by calculating the microvascular area index (MAI) and the microvascular length index (MLI), related to the ROIs size. Identical ROIs showed a high reproducibility for measured [SU] < 0.01 +/- 0.0012%. CONCLUSION: Combining microsurgical techniques, pharmacological knowledge, and modern digital image technology, we were able to visualize small and capillary blood vessels even in small laboratory animals. By using our own computer analytical program, quantification of vessels was reliable, highly reproducible, and fast.

A MULTILEVEL MODEL TO ADDRESS BATCH EFFECTS IN COPY NUMBER ESTIMATION USING SNP ARRAYS

Submicroscopic changes in chromosomal DNA copy number dosage are common and have been implicated in many heritable diseases and cancers. Recent high-throughput technologies have a resolution that permits the detection of segmental changes in DNA copy number that span thousands of basepairs across the genome. Genome-wide association studies (GWAS) may simultaneously screen for copy number-phenotype and SNP-phenotype associations as part of the analytic strategy. However, genome-wide array analyses are particularly susceptible to batch effects as the logistics of preparing DNA and processing thousands of arrays often involves multiple laboratories and technicians, or changes over calendar time to the reagents and laboratory equipment. Failure to adjust for batch effects can lead to incorrect inference and requires inefficient post-hoc quality control procedures that exclude regions that are associated with batch. Our work extends previous model-based approaches for copy number estimation by explicitly modeling batch effects and using shrinkage to improve locus-specific estimates of copy number uncertainty. Key features of this approach include the use of diallelic genotype calls from experimental data to estimate batch- and locus-specific parameters of background and signal without the requirement of training data. We illustrate these ideas using a study of bipolar disease and a study of chromosome 21 trisomy. The former has batch effects that dominate much of the observed variation in quantile-normalized intensities, while the latter illustrates the robustness of our approach to datasets where as many as 25% of the samples have altered copy number. Locus-specific estimates of copy number can be plotted on the copy-number scale to investigate mosaicism and guide the choice of appropriate downstream approaches for smoothing the copy number as a function of physical position. The software is open source and implemented in the R package CRLMM available at Bioconductor (http:www.bioconductor.org).

Validation of candidate smear microscopy quality indicators, extracted from tuberculosis laboratory registers

SETTING: Kinshasa Province, Democratic Republic of Congo. OBJECTIVE: To identify and validate register-based indicators of acid-fast bacilli (AFB) microscopy quality. DESIGN: Selection of laboratories based on reliability and variation in routine smear rechecking results. Calculation of relative sensitivity (RS) compared to recheckers and its correlation coefficient (R) with candidate indicators based on a fully probabilistic analysis incorporating vague prior information using WinBUGS. RESULTS: The proportion of positive follow-up smears correlated well (median R 0.81, 95% credibility interval [CI] 0.58-0.93), and the proportion of first smear-positive cases fairly (median R 0.70, 95% CI 0.38-0.89) with RS. The proportions of both positive suspect and low positive case smears showed poor correlations (median R 0.27 and -0.22, respectively, with ranges including zero). CONCLUSIONS: The proportion of positives in follow-up smears is the most promising indicator of AFB smear sensitivity, while the proportion of positive suspects may be more indicative of accessibility and suspect selection. Both can be obtained from simple reports, and should be used for internal and external monitoring and as guidance for supervision. As proportion of low positive suspect smears and consistency within case series are more difficult to interpret, they should be used only on-site by laboratory professionals. All indicators require more research to define their optimal range in various settings.

Dimensions of impulsive behavior in adolescents: laboratory behavioral assessments

Impulsivity is a multifaceted construct that defines a range of maladaptive behavioral styles. The present research aimed to identify different dimensions of impulsive behavior in adolescents from a battery of laboratory behavioral assessments. In one analysis, correlations were examined between two self report and seven laboratory behavioral measures of impulsivity. The correlation between the two self report measures was high compared to correlations between the self report and laboratory behavioral measures. In a second analysis, a principal components analysis was performed with just the laboratory behavioral measures. Three behavioral dimensions were identified -- "impulsive decision-making", "impulsive inattention", and "impulsive disinhibition". These dimensions were further evaluated using the same sample with a confirmatory factor analysis, which did support the hypothesis that these are significant and independent dimensions of impulsivity. This research indicates there are at least three separate subtypes of impulsive behavior when using laboratory behavioral assessments with adolescent participants.

Diagnostic workup of patients with acute transverse myelitis: spectrum of clinical presentation, neuroimaging and laboratory findings

STUDY DESIGN: Retrospective 9-year survey. OBJECTIVES: Clinical presentation of acute myelitis syndromes is variable, and neuroimaging and laboratory findings are not specific enough to establish the diagnosis with certainty. We evaluated the spectrum clinical features and paraclinical findings encountered during diagnostic workup and aiding the diagnosis. SETTING: Department of Neurology, Inselspital Bern, Switzerland. MATERIAL: Charts and magnetic resonance imaging (MRI) of 63 patients discharged with the diagnosis of acute transverse myelitis. RESULTS: The diagnosis was supported by abnormal MRI and cerebrospinal fluid (CSF) findings in 52 patients (82.5%) and suspected in the remaining either because of a spinal cord MRI lesion suggestive of myelitis (n=5), or abnormal CSF findings (n=4), or electrophysiological evidence of a spinal cord dysfunction (n=2). Clinical impairment was mild (ASIA D) in the majority. All patients had sensory disturbances, whereas motor deficit and autonomic dysfunction were less frequent. Neurological levels were mainly located in cervical or thoracic dermatomes. Spinal cord lesions were visualized by MRI in 90.4% of the patients and distributed either in the cervical or thoracic cord, or both. Multiple lesions were present in more than half of the patients, and lateral, centromedullary and posterior locations were most common. A high percentage of multiple sclerosis (MS)-typical brain lesions and CSF findings suggested a substantial number of MS-related myelitis in our cohort. CONCLUSION: The diagnostic workup of acute myelitis discloses a broad spectrum of CSF or MRI findings, and may be associated with diagnostic uncertainty due to lack of specific CSF or MRI features, or pathological findings.

Is virtuality close enough to reality? A comparison of the effectiveness of simulations with traditional laboratory activities in a high school biology class

Some schools do not have ideal access to laboratory space and supplies. Computer simulations of laboratory activities can be a cost-effective way of presenting experiences to students, but are those simulations as effective at supplementing content concepts? This study compared the use of traditional lab activities illustrating the principles of cell respiration and photosynthesis in an introductory high school biology class with virtual simulations of the same activities. Additionally student results were analyzed to assess if student conceptual understanding was affected by the complexity of the simulation. Although all student groups posted average gain increases between the pre and post-tests coupled with positive effect sizes, students who completed the wet lab version of the activity consistently outperformed the students who completed the virtual simulation of the same activity. There was no significant difference between the use of more or less complex simulations. Students also tended to rate the wet lab experience higher on a motivation and interest inventory.