Rhesus macaque brain morphometry: A methodological comparison of voxel-wise approaches

Voxel-based morphometry studies have become increasingly common in human neuroimaging over the past several years; however, few studies have utilized this method to study morphometry changes in non-human primates. Here we describe the application of voxel-wise morphometry methods to the rhesus macaque (Macaca mulatta) using the 112RM-SL template and priors (McLaren et al. (2009) [42]) and as an illustrative example we describe age-associated changes in grey matter morphometry. Specifically, we evaluated the unified segmentation routine implemented using Statistical Parametric Mapping (SPM) software and the FMRIB’s Automated Segmentation Tool (FAST) in the FMRIB Software Library (FSL); the effect of varying the smoothing kernel; and the effect of the normalization routine. We found that when studying non-human primates, brain images need less smoothing than in human studies, 2–4 mm FWHM. Using flow field deformations (DARTEL) improved inter-subject alignment leading to results that were more likely due to morphometry differences as opposed to registration differences.     

Animal signals: Ethological and games-theory approaches are not incompatible

Recent authors have contrasted the ‘traditional ethological approach’ to the study of animal signals with that derived from games theory. It is argued here that the ‘traditonal ethological approach’ they portray is not in keeping with main stream of ethological research on animal signals. In particular, it has not been generally assumed that the evolution of animal signals was based on selection for mutual benefit of actor and reactor, nor that signals carry precise information of what the actor will do next. A synthesis of the ethological and games-theory approaches is possible. It is suggested that many threat displays may signal ‘Will stay, but attack if provoked’ or ‘Will stay, but will flee if provoked’, and that the subsequent behaviour of the displaying bird depends in part on that of the reactor.     

Biotinylated anisomycin: a comparison of classical and "click" chemistry approaches

Two approaches to the synthesis of biotinylated derivatives of the stress-activated protein kinase (SAPK) pathway activator anisomycin have been investigated. Attachment of the biotin moiety to the central core was achieved either through the use of a classical displacement reaction on alpha-halo carbonyl derivatives of biotin or through a copper(I)-catalyzed 1,3-dipolar Huisgen cycloaddition ("click") coupling of biotinylated azides to propargyl-marked analogues of anisomycin. In each case, the resultant N-linked molecular probes were found to be active in SAPK pathway immunoblot assays, while their O-linked counterparts were inactive. However, in sharp contrast to the classical coupling approach which results in low coupling yields, the aqueous "click" coupling process was found to deliver high yields of biotinylated probes, making it the conjugation method of choice. A survey of the available methods for the addition of a propargyl marker onto a range of chemical functionalities strongly suggests that this copper(I)-catalyzed 1,3-dipolar Huisgen cycloaddition approach to biotinylation may be generally applied.     

Risk assessment for developing gliomas: a comparison of two cytogenetic approaches

Chromosome instability (CIN) measured as chromosome aberrations has long been suggested as a cancer susceptibility biomarker. Conventional cytogenetic end-points are now being improved by combining molecular methods, which increases the sensitivity, specificity, and precision of the assay. In this study we examined both spontaneous and gamma-ray induced CIN in lymphocyte cultures from 51 previously untreated glioma patients and 51 age-, sex- and ethnicity-matched controls. CIN was assessed using two parallel methods: (1) the mutagen sensitivity (MS) assay and (2) the multicolor fluorescence in situ hybridization (FISH) assay. The frequency of spontaneous breaks was significantly higher in glioma patients (mean+/-S.D., 2.12+/-1.07) than in controls (1.24+/-0.86, P<0.001) when using the FISH assay but not the MS assay (0.019+/-0.02 and 0.019+/-0.01, respectively; P=0.915). Similarly, the frequency of induced chromatid breaks was significantly higher using the FISH assay (3.39+/-1.72) but not the MS assay (0.42+/-0.16) in the patients versus controls (2.08+/-1.18 and 0.37+/-0.15, respectively; P<0.001 and P=0.10, respectively). By using the median number of breaks in the controls as the cutoff value, we observed an odds ratio (ORs) of 5.13 (95% CI=2.23-12.1) for spontaneous and 4.86 (95% CI=2.08-11.4) for induced CIN using the FISH assay, whereas the ORs were 1.32 (95% CI=0.49-3.58) and 1.28 (95% CI=0.59-2.80) for spontaneous and induced CIN using the MS assay. There was also a significant increase in the frequency of hyperdiploid cells in the glioma cases which could only be detected using the FISH assay (OR=4.0, 95% CL=0.9-17.0). By combining both methods an estimated risk of 7.0 (95% CI=1.7-25.6) was observed. There was no correlation between the breaks detected by the two methods suggesting that each method is a measure of a different event. The results indicate that using the multicolor FISH assay for detection of CIN in peripheral blood lymphocytes in glioma patients is a more useful marker for risk assessment.     

Immunoreactivity to MIB-1 in breast cancer: methodological assessment and comparison with other proliferation indices

The recent availability of the monoclonal antibody MIB-1 (which is able to detect the human nuclear cell proliferation-associated antigen Ki-67 even on formalin-fixed, paraffin-embedded sections, microwave-treated and routinely processed for immunohistochemistry) could open new avenues for validation of the clinical role of tumour cell proliferation on large, consecutive and unselected series of human tumours. However, the routine use of such a marker requires a methodological standardization as well as the comparative assessment of some technical and biological aspects. The MIB-1 index was determined in parallel samples from 50 consecutive invasive breast carcinomas processed with different fixatives for different times. The median values of MIB-1 indices following 2, 6 and 24 h of formalin fixation were similar (29.4%, 30.6% and 29.7%, respectively) and consistent with those reported in the literature; squared linear regression coefficients were 0.99. The median values of MIB-1 indices were markedly lower in Bouin-fixed, paraffin-embedded, and in frozen samples (20.0% and 19.8%, respectively), with a poor correlation coefficient with the values detected following formalin fixation ( R ²=0.456). Moderate and poor correlations were observed between Ki-67 index and MIB-1 detected on frozen ( r _s, 0.78) or formalin-fixed, paraffin-embedded samples ( r _s, 0.47) and a minimal concordance was observed between TLI and MIB-1 or Ki-67 ( r _s, 0.25 and 0.22, respectively). Our results indicate interference of the fixative type on immunoreactivity to MIB-1 and also suggest that Ki-67 and MIB-1 reacted with different epitopes of the same antigen.     

Cell cycle target validation: approaches and successes

Evasion of the checks and balances that govern the human cell division cycle lies at the heart of all proliferative diseases. Because of the astonishing variety of ways that cancer cells manage to achieve growth advantages over normally proliferating cells, it can be expected that pharmacological reinstatement of cell cycle progression control should also be achievable in a multitude of ways. Very few cell cycle targets have so far been exploited for the discovery of mechanism-based anticancer drugs; even fewer targets have yielded actual or experimental clinical drugs. Here, we discuss the approaches that have been and are beginning to be used to identify and validate molecular targets whose pharmacological modulation holds the promise of nongenotoxic and inherently selective cancer therapy. We discuss an approach based on using the genetically amenable organism Drosophila melanogaster as a model for the identification of cell cycle targets, particularly those involved in the processes of mitosis.     

Biomarker discovery and validation: technologies and integrative approaches

The emerging field of biomarkers has applications in the diagnosis, staging, prognosis and monitoring of disease progression, as well as in the monitoring of clinical responses to a therapeutic intervention and the development and delivery of personalized treatments to reduce attrition in clinical trials. Moreover, biomarkers have a positive impact on health economics. The word "biomarker" has been used extensively across therapeutic areas and many disciplines, and its nature takes into consideration clinical, physiological, biochemical, developmental, morphological and molecular measures. In drug trials, biomarkers have been proposed for use in efficacy determination and patient population stratification, in deducing pharmacokinetic-pharmacodynamic relationships and in safety monitoring. The interfacing and integration of different technologies for data collection and analysis are pivotal to biomarker identification, characterization, validation and application. "Integrative functional informatics" represents a novel direction in such technology integration.     

Multisensory integration: methodological approaches and emerging principles in the human brain.

Understanding the conditions under which the brain integrates the different sensory streams and the mechanisms supporting this phenomenon is now a question at the forefront of neuroscience. In this paper, we discuss the opportunities for investigating these multisensory processes using modern imaging techniques, the nature of the information obtainable from each method and their benefits and limitations. Despite considerable variability in terms of paradigm design and analysis, some consistent findings are beginning to emerge. The detection of brain activity in human neuroimaging studies that resembles multisensory integration responses at the cellular level in other species, suggests similar crossmodal binding mechanisms may be operational in the human brain. These mechanisms appear to be distributed across distinct neuronal networks that vary depending on the nature of the shared information between different sensory cues. For example, differing extents of correspondence in time, space or content seem to reliably bias the involvement of different integrative networks which code for these cues. A combination of data obtained from haemodynamic and electromagnetic methods, which offer high spatial or temporal resolution respectively, are providing converging evidence of multisensory interactions at both "early" and "late" stages of processing--suggesting a cascade of synergistic processes operating in parallel at different levels of the cortex.     

Ecotoxicity impact assessment of laundry products: a comparison of USEtox and critical dilution volume approaches

Purpose  

There is an increasing interest in the assessment and comparison of the environmental impacts of consumer products. Schemes such as Grenelle de l’Environnement, currently under development in France, aim to assess and communicate the life cycle impacts of consumer products. Freshwater ecotoxicity is one of the impact categories under consideration. This paper presents the results of a comparison of USEtox and critical dilution volume (CDV) approaches for assessing laundry products.     

Semi-automated genetic analyses of soil microbial communities: comparison of T-RFLP and RISA based on descriptive and discriminative statistical approaches

Cultivation independent analyses of soil microbial community structures are frequently used to describe microbiological soil characteristics. This approach is based on direct extraction of total soil DNA followed by PCR amplification of selected marker genes and subsequent genetic fingerprint analyses. Semi-automated genetic fingerprinting techniques such as terminal restriction fragment length polymorphism (T-RFLP) and ribosomal intergenic spacer analysis (RISA) yield high-resolution patterns of highly diverse soil microbial communities and hold great potential for use in routine soil quality monitoring, when rapid high throughput screening for differences or changes is more important than phylogenetic identification of organisms affected. Our objective was to perform profound statistical analysis to evaluate the cultivation independent approach and the consistency of results from T-RFLP and RISA. As a model system, we used two different heavy metal treated soils from an open top chamber experiment. Bacterial T-RFLP and RISA profiles of 16S rDNA were converted into numeric data matrices in order to allow for detailed statistical analyses with cluster analysis, Mantel test statistics, Monte Carlo permutation tests and ANOVA. Analyses revealed that soil DNA-contents were significantly correlated with soil microbial biomass in our system. T-RFLP and RISA yielded highly consistent and correlating results and both allowed to distinguish the four treatments with equal significance. While RISA represents a fast and general fingerprinting method of moderate cost and labor intensity, T-RFLP is technically more demanding but offers the advantage of phylogenetic identification of detected soil microorganisms. Therefore, selection of either of these methods should be based on the specific research question under investigation.     

Statistical assessment of population variability: a methodological approach

We have implemented a multivariate statistical methodology to assess the degree and pattern of cranial variability in skeletal samples. Specifically, the method is designed to test whether variability in a skeletal sample exceeds "normal within-group variability" defined in the present instance as variability present among crania from a cemetery associated with a village. It involves comparing a covariance matrix derived from a sample of unknown composition to one representing "normal within-group variability." The method has been applied to two Plains Indian craniometric samples. The Leavenworth site (39CO9) represents the remnants of previously autonomous Arikara Indian villages devastated by epidemic diseases in the late 1700s. The Bad River 2 Phase is an archaeological designation grouping together closely related sites in the Bad-Cheyenne region of South Dakota dating from 1740-1795 AD. We were able to show substantial heterogeneity among crania from Leavenworth. District burial areas at Leavenworth account for some of the heterogeneity, supporting the notion that they represent an attempt to maintain former social distinctions. We were unable to differentiate among sites within the Bad River 2 Phase, suggesting that it is a valid biological unit.     

The system of flowering plants: synthesis of classical and molecular approaches

The proposed system of flowering plants (Angiospermae) is based on synthesis of cladistic researches from different authors, morphological data and "traditional" systematics as well. Classis Angiospermae is divided for 4 subclassis: Magloliidae, Liliidae, Rosidae and Asteridae. Thus, monocots belong to subclassis Liliidae, and so-called "dicots" to three other subclasses. Altogether there are 35 orders and 328 families of flowering plants in this system.     

Work-based physiological assessment of physically-demanding trades: a methodological overview

Technological advances, modified work practices, altered employment strategies, work-related injuries, and the rise in work-related litigation and compensation claims necessitate ongoing trade analysis research. Such research enables the identification and development of gender- and age-neutral skills, physiological attributes and employment standards required to satisfactorily perform critical trade tasks. This paper overviews a methodological approach which may be adopted when seeking to establish trade-specific physiological competencies for physically-demanding trades (occupations). A general template is presented for conducting a trade analyses within physically-demanding trades, such as those encountered within military or emergency service occupations. Two streams of analysis are recommended: the trade analysis and the task analysis. The former involves a progressive dissection of activities and skills into a series of specific tasks (elements), and results in a broad approximation of the types of trade duties, and the links between trade tasks. The latter, will lead to the determination of how a task is performed within a trade, and the physiological attributes required to satisfactorily perform that task. The approach described within this paper is designed to provide research outcomes which have high content, criterion-related and construct validities.     

Prostate cancer: risk assessment and diagnostic approaches

The successful treatment of prostate cancer relies on detection of the disease at its earliest stages. Although prostate-specific antigen (PSA)-based screening has been a significant advance in the early diagnosis of prostate cancer, identifying specific genetic alterations in a given family or patient will allow more appropriate screening for early disease. Mapping and identification of specific prostate cancer susceptibility genes is slowly becoming a reality. Other prostate cancer risks include a family history, race, and possibly serum markers such as insulin-like growth factor-I (IGF-I). Once a high-risk man is identified, transrectal ultrasound (TRUS)-guided biopsies are the standard to diagnose prostate cancer. Although TRUS is an advance over traditional digitally directed biopsies, it represents a random sampling of the prostate since most lesions cannot be visualized. Newer modalities such as ultrasound contrast agents, pattern recognition, and artificial neural networks (ANNs), applied to TRUS images, may improve diagnostic accuracy. If a man at risk for prostate cancer has undergone a negative TRUS biopsy, the decision for the need for additional biopsies is problematic. Use of PSA derivatives such as free and total PSA and the initial biopsy abnormalities such as atypia or high-grade prostatic intraepithelial neoplasia may define those patients in need of follow-up biopsy.     

Drug safety assessment in clinical trials: methodological challenges and opportunities

ABSTRACT: Randomized controlled trials are the principal means of establishing the efficacy of drugs. However pre-marketing trials are limited in size and duration and exclude high-risk populations. They have limited statistical power to detect rare but potentially serious adverse events in real-world patients. We summarize the principal methodological challenges in the reporting, analysis and interpretation of safety data in clinical trials using recent examples from systematic reviews. The principle challenges include the lack of an evidentiary gold standard, the limited statistical power of randomized controlled trials and resulting type 2 error, the lack of adequate ascertainment of adverse events and limited generalizability of safety trials that exclude high risk patients. We discuss potential solutions to these challenges. Evaluation of drug safety requires careful examination of data from heterogeneous sources. Meta-analyses of drug safety should include appropriate statistical methods and assess the optimal information size to avoid type 2 errors. They should evaluate outcome reporting biases and missing data to ensure reliable and accurate interpretation of findings. Regulatory and academic partnerships should be fostered to provide an independent and transparent evaluation of drug safety.     

An assessment of time-dependent effects of lead exposure in algerian mice (Mus spretus) using different methodological approaches

Time-dependent effects of lead (Pb) toxicity were studied in Algerian mice (Mus spretus) treated with Pb acetate via drinking water (1 g Pb acetate/L) for different periods of exposure (15, 45, and 90 d). End points included the determination of hepatic Pb concentration and the assessment of some morphophysiological, biochemical and cytogenetical parameters. A control group receiving distilled water was also monitored for comparative purposes. Hepatic Pb accumulation increased with the time of exposure and was significantly higher in treated mice when compared to controls. In association with significant body mass loss in Pb-exposed mice, for 15 and 45 d, a significant increase in the relative spleen mass was observed after 45 d of intoxication. Pb-exposed mice also showed significant decreases in red blood cells, hematocrit, and mean corpuscular hemoglobin. On the contrary, changes in plasma transferases (aspartate aminotransferase and alanine aminotransferase) and hepatic superoxide dismutase activities did not reach statistical significance. A significant increase in the frequency of micronucleated polychromatic bone marrow erythrocytes was also found in the 90-d-exposed mice, compared to nontreated mice and the other exposed groups. Exposure to Pb acetate resulted also in a slight time-dependent decrease of the polychromatic-normochromatic ratio. These results support the concept that a long-term chronic exposure to Pb induced alterations upon some morphophysiological and genetic parameters in Algerian mice.