Computational cluster validation for microarray data analysis: experimental assessment of Clest,Consensus Clustering,Figure of Merit,Gap Statistics and Model Explorer

Background  

Inferring cluster structure in microarray datasets is a fundamental task for the so-called -omic sciences. It is also a fundamental question in Statistics, Data Analysis and Classification, in particular with regard to the prediction of the number of clusters in a dataset, usually established via internal validation measures. Despite the wealth of internal measures available in the literature, new ones have been recently proposed, some of them specifically for microarray data.     

Nest-site selection by Common Black-Hawks in southwestern New Mexico

ABSTRACT.   Despite the interest of resource managers and conservationists in the status of Common Black-Hawk ( Buteogallus anthracinus ) populations in the southwestern United States, little is known about their nesting success and habitat requirements. Because such information is essential for effective population and habitat management, I examined the nesting success and nest-site selection of Common Black-Hawks in southwestern New Mexico during 2000 and 2001. Of the 37 nesting attempts in 21 territories, ≥1 young fledged from 25 nests (68%). Comparison of nest-sites and nonused sites suggested that breeding Common Black-Hawks selected nest-sites in areas with a sparser and shorter subcanopy tree layer and in trees with a smaller trunk diameter and a greater minimum crown diameter. These differences appear to be related to variation in forest ages within territories, with nonused sites having fewer, but older, canopy trees than nest-sites. Sites with younger, smaller subcanopy trees may provide forest structure for more effective foraging, whereas the characteristics of younger nest tree canopies may reduce the risk of nest predation or offer more protection from inclement weather. Due to the limited range of this species in the southwestern United States, efforts to encourage the establishment and maturation of riparian forests in Common Black-Hawk breeding areas could be important in sustaining available nesting habitat and, in turn, maintaining or expanding current population levels.     

In vitro studies during long term oral administration of specific transfer factor

153 patients suffering from recurrent pathologies, i.e. viral infections (keratitis, keratouveitis, genital and labial herpes) uveitis, cystitis, and candidiasis were treated with in vitro produced transfer factor (TF) specific for HSV-1/2, CMV and Candida albicans. The cell-mediated immunity of seropositive patients to HSV-1/2 and/or CMV viruses was assessed using the leucocyte migration inhibition test (LMT) and lymphocyte stimulation test (LST) in presence of the corresponding antigens, and the frequency of positive tests before, during and after TF administration was studied. The data were stratified per type of test, antigen and the recipients’ pathology, and statistically evaluated. For the LMT, a total of 960 tests were carried out for each antigen dilution, 3 different antigen dilutions were used per test. 240/960 tests (25.4%) were found positive during non-treatment or treatment with unspecific TF, whereas 147/346 tests (42.5%) were found positive when the antigen corresponding to the specificity of the TF administered to the patient was used (P<0.001). When the data were stratified following pathology, a significant increased incidence of positive tests during specific treatment was also observed (0.0001<P<0.05). In the LST (1174 tests), a significant increase of thymidine uptake was observed in the absence of antigen (control cultures), during treatment with both specific and unspecific TF, but also in the presence of antigen and/or autologous serum during specific TF administration (P<0.0001). TF administration also significantly increased the soluble HLA class I antigens level in 40 patients studied to this effect.