Transport models for numerical forecast

The explosive growth of computing power, coupled with scientific and technological emphasis on a national scale, has led to significant major advances in operational numerical weather prediction (NWP) during the last two decades. There are about half a dozen major centers around the world running global NWP models operationally. Many more countries have operational hemispheric or limited-area models which provide weather forecasts. The global models typically have several hundred kilometer resolution, while the limited-area models usually have horizontal spacing of 50 to 100 km. Given the pace of burgeoning growth in this area, it seems warranted to occasionally take an overview of aspects of the field common to all modelers. Here, a brief look is taken at the nature of subgrid scale turbulence transport parameterization, and some of the difficulties pertaining thereto, with particular emphasis on operational NWP models

Mesoscale Simulation of Supercritical, Subcritical, and Transcritical Flow along Coastal Topography

A mesoscale atmospheric model is used to address the characteristics of stratified flow bounded by a side wall along a varying coastline. Initial Froude number values are varied through alteration of marine inversion strength, permitting examination of supercritical, subcritical, and transcritical flow regimes encountering several coastal configurations. Consistent with shallow water models, sharp drops in boundary layer depth and flow acceleration occur in flow rounding convex bends; however, significant flow response occurs in the stratified layer aloft, which is unexplained by conventional shallow water theory. The strongest flow acceleration occurs in the transcritical case while, regardless of inversion strength, the deformation of the isentropes aloft shows general structural similarity. Advection of horizontal momentum is an important component of the horizontal force balance. A simulation having several coastline bends exhibits a detached, oblique hydraulic jump upwind of a concave bend that strongly blocks the flow. For the single-bend case, a shallow water similarity theory for stratified flow provides qualitative, and partial quantitative, agreement with the mesoscale model, in the boundary layer and aloft. Horizontal structure functions for these similarity solutions satisfy a set of equivalent shallow water equations. This comparison provides a new perspective on previous shallow water models of supercritical flow around coastal bends and suggests that the existence of the supercritical flow response may depend more on the presence of a low-level jet than on a sharp boundary layer inversion

Satellite inventory of Minnesota forest resources

The methods and results of using Landsat Thematic Mapper (TM) data to classify and estimate the acreage of forest covertypes in northeastern Minnesota are described. Portions of six TM scenes covering five counties with a total area of 14,679 square miles were classified into six forest and five nonforest classes. The approach involved the integration of cluster sampling, image processing, and estimation. Using cluster sampling, 343 plots, each 88 acres in size, were photo interpreted and field mapped as a source of reference data for classifier training and calibration of the TM data classifications. Classification accuracies of up to 75 percent were achieved; most misclassification was between similar or related classes. An inverse method of calibration, based on the error rates obtained from the classifications of the cluster plots, was used to adjust the classification class proportions for classification errors. The resulting area estimates for total forest land in the five-county area were within 3 percent of the estimate made independently by the USDA Forest Service. Area estimates for conifer and hardwood forest types were within 0.8 and 6.0 percent respectively, of the Forest Service estimates. A trial of a second method of estimating the same classes as the Forest Service resulted in standard errors of 0.002 to 0.015. A study of the use of multidate TM data for change detection showed that forest canopy depletion, canopy increment, and no change could be identified with greater than 90 percent accuracy. The project results have been the basis for the Minnesota Department of Natural Resources and the Forest Service to define and begin to implement an annual system of forest inventory which utilizes Landsat TM data to detect changes in forest cover

Sparing effects of selenium and ascorbic acid on vitamin C and E in guinea pig tissues

BACKGROUND: Selenium (Se), vitamin C and vitamin E function as antioxidants within the body. In this study, we investigated the effects of reduced dietary Se and L-ascorbic acid (AA) on vitamin C and α-tocopherol (AT) status in guinea pig tissues. METHODS: Male Hartley guinea pigs were orally dosed with a marginal amount of AA and fed a diet deficient (Se-D/MC), marginal (Se-M/MC) or normal (Se-N/MC) in Se. An additional diet group (Se-N/NC) was fed normal Se and dosed with a normal amount of AA. Guinea pigs were killed after 5 or 12 weeks on the experimental diets at 24 and 48 hours post AA dosing. RESULTS: Liver Se-dependent glutathione peroxidase activity was decreased (P < 0.05) in guinea pigs fed Se or AA restricted diets. Plasma total glutathione concentrations were unaffected (P > 0.05) by reduction in dietary Se or AA. All tissues examined showed a decrease (P < 0.05) in AA content in Se-N/MC compared to Se-N/NC guinea pigs. Kidney, testis, muscle and spleen showed a decreasing trend (P < 0.05) in AA content with decreasing Se in the diet. Dehydroascorbic acid concentrations were decreased (P < 0.05) in several tissues with reduction in dietary Se (heart and spleen) or AA (liver, heart, kidney, muscle and spleen). At week 12, combined dietary restriction of Se and AA decreased AT concentrations in most tissues. In addition, restriction of Se (liver, heart and spleen) and AA (liver, kidney and spleen) separately also reduced AT in tissues. CONCLUSION: Together, these data demonstrate sparing effects of Se and AA on vitamin C and AT in guinea pig tissues

Highlights of Coastal Waves 1996

Highlights of Coastal Waves 199

Sustained unresponsiveness to peanut in subjects who have completed peanut oral immunotherapy

Although peanut oral immunotherapy (OIT) has been conclusively shown to cause desensitization, it is currently unknown whether clinical protection persists after stopping therapy

Molecular Analysis of Integrated Human Papillomavirus 16 Sequences in the Cervical Cancer Cell Line SiHa

Human papillomavirus (HPV) 16 is frequently found integrated into cervical cancer cell genomes and these integrations are thought to play a role in tumorigenesis. To investigate the mechanisms of HPV integration and its effect on transcription and chromosomal sequence organization, we have cloned and analyzed the HPV16 integration from the cervical cancer cell line SiHa. Restriction analysis and Southern blotting indicated that approximately 95% of an HPV16 genome was integrated without gross rearrangement. Sequence analysis of the cellular-viral DNA junctions revealed that integration had occurred within the E2 and E4 ORFs where 251 bp of viral sequence was deleted. One viral terminus occurred within sequences of an Alu repeat and a 4-bp homology was present at the site of recombination. Using unique cellular flanking DNA probes, a 4.8-kb deletion of cellular sequences was detected at the site of viral integration. The chromosomal location of the viral integration and cellular deletion were mapped to chromosome 13 using a rodent × human somatic cell hybrid panel. Northern blot analysis using viral subgenomic and 3′ cellular probes revealed transcription from the 3′ portion of integrated HPV16 (E6, E7, E1) and flanking cellular sequences. The observation of viral-cell transcripts and chromosomal deletions associated with HPV integration may indicate that such events are part of a multistep mechanism leading to the development of cervical cancer

Organization and Chromosomal Specificity of Autosomal Homologs of Human Y Chromosome Repeated DNA

The human Y chromosome contains a group of repeated DNA elements, identified as 3.4-kilobase pair (kb) fragments in Hae III digests of male genomic DNA, which contain both Y-specific and non-Y-specific sequences. We have used these 3.4-kb Hae III Y fragments to explore the organizational properties and chromosomal distribution of the autosomal homologs of the non-Y-specific (NYS) 3.4-kb Hae III Y elements. Three distinct organizations, termed domains, have been identified and shown to have major concentrations on separate chromosomes. We have established that domain K is located on chromosome 15 and domain D on chromosome 16 and suggested that domain R is on chromosome 1. Our findings suggest that each domain is composed of a tandemly arrayed cluster of a regularly repeating unit containing two sets of repeated sequences: one that is homologous to the NYS 3.4-kb Hae III Y sequences and one that does not cross-react with the 3.4-kb Hae III Y repeats. Thus, these autosomal repeated DNA domains, like their Y chromosome counterparts, consist of a complex mixture of repeated DNA elements interspersed among each other in ways that lead to defined periodicities. Although each of the three identified autosomal domains cross-reacts with 3.4-kb Hae III Y fragments purified from genomic DNA, the length periodicities and sequence content of the autosomal domains are chromosome specific. The organizational properties and chromosomal distribution of these NYS 3.4-kb Hae III homologs seem inconsistent with stochastic mechanisms of sequence diffusion between chromosomes

Papillomavirus-Associated Focal Oral Hyperplasia in Wild and Captive Asian Lions (Panthera leo persica)

Four Asian lions (Panthera leo persica), two wild and two captive, were diagnosed with focal oral hyperplasia affecting the ventral surface of their tongues. Focal, flat, sessile lesions consisted of hyperplastic, stratified squamous epithelium. Koilocytotic atypia was evident in the upper layers of cells, some of which contained characteristic intranuclear papillomavirus particles visible by electron microscopy. In addition, large amphophilic cytoplasmic inclusions were evident in the koilocytes and were considered to be a product of the viral E4 gene. Papillomavirus group-specific antigens were detected by immunohistochemistry in the atypical cell nuclei. Conserved papillomavirus antigenic epitopes differed from epitopes found in cutaneous papillomavirus-induced lesions from domestic cats. An 8,000-base pair DNA fragment, linearized by Bam HI digestion, was detected by Southern blot hybridization probed with a mixed human papillomavirus genomic probe. Limited restriction endonuclease studies of DNA prepared using an oral hyperplastic lesion from an Asian lion indicate that this is a novel feline papillomavirus different from the domestic cat cutaneous papillomavirus. This new virus has been designated P1PV

Common genetic variants and risk for HPV persistence and progression to cervical cancer.

HPV infrequently persists and progresses to cervical cancer. We examined host genetic factors hypothesized to play a role in determining which subset of individuals infected with oncogenic human papillomavirus (HPV) have persistent infection and further develop cervical pre-cancer/cancer compared to the majority of infected individuals who will clear infection.We evaluated 7140 tag single nucleotide polymorphisms (SNPs) from 305 candidate genes hypothesized to be involved in DNA repair, viral infection and cell entry in 416 cervical intraepithelial neoplasia 3 (CIN3)/cancer cases, 356 HPV persistent women (median: 25 months), and 425 random controls (RC) from the 10,049 women Guanacaste Costa Rica Natural History study. We used logistic regression to compute odds ratios and p-trend for CIN3/cancer and HPV persistence in relation to SNP genotypes and haplotypes (adjusted for age). We obtained pathway and gene-level summary of associations by computing the adaptive combination of p-values. Genes/regions statistically significantly associated with CIN3/cancer included the viral infection and cell entry genes 2',5' oligoadenylate synthetase gene 3 (OAS3), sulfatase 1 (SULF1), and interferon gamma (IFNG); the DNA repair genes deoxyuridine triphosphate (DUT), dosage suppressor of mck 1 homolog (DMC1), and general transcription factor IIH, polypeptide 3 (GTF2H4); and the EVER1 and EVER2 genes (p<0.01). From each region, the single most significant SNPs associated with CIN3/cancer were OAS3 rs12302655, SULF1 rs4737999, IFNG rs11177074, DUT rs3784621, DMC1 rs5757133, GTF2H4 rs2894054, EVER1/EVER2 rs9893818 (p-trends</=0.001). SNPs for OAS3, SULF1, DUT, and GTF2H4 were associated with HPV persistence whereas IFNG and EVER1/EVER2 SNPs were associated with progression to CIN3/cancer. We note that the associations observed were less than two-fold. We identified variations DNA repair and viral binding and cell entry genes associated with CIN3/cancer. Our results require replication but suggest that different genes may be responsible for modulating risk in the two critical transition steps important for cervical carcinogenesis: HPV persistence and disease progression