An object simulation model for modeling hypothetical disease epidemics – EpiFlex

Background  

EpiFlex is a flexible, easy to use computer model for a single computer, intended to be operated by one user who need not be an expert. Its purpose is to study in-silico the epidemic behavior of a wide variety of diseases, both known and theoretical, by simulating their spread at the level of individuals contracting and infecting others. To understand the system fully, this paper must be read together in conjunction with study of the software and its results. EpiFlex is evaluated using results from modeling influenza A epidemics and comparing them with a variety of field data sources and other types of modeling.     

Statistical practice in high-throughput screening data analysis

High-throughput screening is an early critical step in drug discovery. Its aim is to screen a large number of diverse chemical compounds to identify candidate 'hits' rapidly and accurately. Few statistical tools are currently available, however, to detect quality hits with a high degree of confidence. We examine statistical aspects of data preprocessing and hit identification for primary screens. We focus on concerns related to positional effects of wells within plates, choice of hit threshold and the importance of minimizing false-positive and false-negative rates. We argue that replicate measurements are needed to verify assumptions of current methods and to suggest data analysis strategies when assumptions are not met. The integration of replicates with robust statistical methods in primary screens will facilitate the discovery of reliable hits, ultimately improving the sensitivity and specificity of the screening process.     

Re-evaluation of the primary structure of Ralstonia eutropha phasin and implications for polyhydroxyalkanoic acid granule binding

Sequence analysis of several cDNAs encoding the phasin protein of Ralstonia eutropha indicated that the carboxyl terminus of the resulting derived protein sequence is different from that reported previously. This was confirmed by: (1) sequencing of the genomic DNA; (2) SDS-PAGE and peptide analysis of wild-type and recombinant phasin; and (3) mass spectrometry of wild-type phasin protein. The results have implications for the model proposed for the binding of this protein to polyhydroxyalkanoic acid granules in the bacterium.     

Receptor-ligand binding: 'catch' bonds finally caught

Leukocyte recruitment to sites of inflammation is initiated by the selectin family of adhesion receptors. Recent research reveals that P-selectin binding to its ligand exhibits 'catch' to 'slip' bond transition that may help explain the shear threshold phenomenon.     

An experimental investigation of the competitive displacement of a native gecko by an invading gecko: no role for parasites

On islands across the Pacific the invasion of the gecko Hemidactylusfrenatus has caused a decline in the abundance of a resident gecko, Lepidodactyluslugubris. In a previous study we demonstrated that the prevalence of the cestode Cylindrotaenia sp. is higher in the resident gecko on islands where it is sympatric with the invader than on islands where it occurs alone. In the present study we experimentally test whether the presence of the invading gecko causes an increase in parasites, particularly Cylindrotaenia sp., in the resident. In addition, we test whether the effect of the invader on parasite prevalence in the resident is mediated through an increase in corticosterone in the resident. Corticosterone is the primary glucocorticoid, or “stress” hormone in lizards, and chronic elevation in corticosterone may suppress some types of immune responses. After experimental manipulations of interspecific interactions (single vs. mixed species treatments) and intraspecific densities (high vs. low), we detected no difference in parasite prevalence or circulating corticosterone among the experimental treatments in either L. lugubris or H. frenatus. Circulating levels of corticosterone were higher in geckos␣sampled at night than geckos sampled during the day, indicating a circadian cycle in corticosterone levels in these nocturnal animals. Circulating levels of corticosterone were higher in experimental geckos than in geckos that had not been used in the experiment, and, in some groups, higher in geckos infected with cestodes than in uninfected geckos. Circulating levels of corticosterone did not differ between non-experimental H. frenatus and L. lugubris, but when geckos used in the experiment were compared, circulating levels of corticosterone were significantly higher in H.␣frenatus than in L. lugubris. Received: 17 March 1997 / Accepted: 5 December 1997     

Microspectroscopic fluorescence analysis with prism-based imaging spectrometers: review and current studies.

BACKGROUND: Fluorescence imaging spectroscopy is a powerful but under-utilized tool. This article gives perspective on the use of imaging spectroscopy, and provides two examples of imaging spectroscopy done with a prism-based system. The intent is to give insight into the power of imaging spectroscopy when used in combination with other imaging techniques. In particular, studies of intact coral photobleaching and beads designed to show energy transfer are reported. In the bead study, spectroscopic lifetime imaging was performed at each photobleaching step. RESULTS: Spectroscopic photobleaching of the hard coral, Montastrea annularis, revealed two spectral regions. A region in the red portion of the spectrum bleached rapidly while progressively increasing fluorescence was observed over a wide portion of the spectrum. This behavior is consistent with current theories for the role of fluorescent proteins in corals.Following a photobleaching study of beads designed to exhibit energy transfer with imaging spectroscopic fluorescence lifetime imaging microscopy (ISFLIM) allowed unambiguous assignment of fluorescence resonance energy transfer (FRET). The data in this experiment indicated that most of the commonly used markers of FRET would have been inconclusive. The ability of the ISFLIM to look at all regions of the spectrum, particularly the acceptor region, allowed FRET to be assigned. CONCLUSIONS: Fluorescence imaging spectroscopy is a rapidly advancing technology, uniquely suited to the flexible detection of dyes over a wide range of wavelengths.     

Preclinical studies of monoclonal antibodies for intravesical radioimmunotherapy of human bladder cancer

Eighty percent of bladder cancers present as superficial disease. Many are multifocal, and apparently successful treatment is frequently followed by recurrence. The use of monoclonal antibodies (MAbs) to target radiotherapy to these tumors offers great potential, especially since they can be administered directly into the bladder (intravesically) bypassing many of the side effects encountered to date with systemic MAb-based therapy. Implantation of human bladder cancer cell lines in the bladder wall of nude rats results in tumor formation, providing an excellent model to test this. Tumor size can be monitored by X-ray analysis after administration of urograffin. Comparative studies of two murine MAbs, BLCA-8, IgG3, and C1-137, IgG1, against malignant human bladder cancer cells have been performed. Radio-immunoconjugates produced with¹²⁵Iodine (¹²⁵I) have been used for biodistribution studies following administration directly into rat bladder. Radioiodinated intact MAbs or Fabs administered intravesically into nontumor bearing rats did not leak into the systemic circulation and were stable in urine for up to 100 h. Biodistribution studies carried out following intravesical administration of radio-immunoconjugates to tumor-bearing nude rats indicate better tumor uptake of C1-137 than BLCA-8. Further studies to test two-step intravesical administration of biotinylated MAb followed by radioiodinated streptavidin are in progress. Our studies indicate that the C1-137 MAb may have considerable potential for intravesical radioimmunotherapy of patients with superficial bladder tumors.     

Biotin analogs activate guanylate cyclase

Summary The sulfur atom in the vitamin biotin has previously been suggested to be essential in biotin's mechanism of action. In a series of investigations on structure-function relationships with biotin analogs not containing the sulfur atom, the biotin analogs, azabiotin, bisnorazabiotin, carbobiotin and isoazabiotin enhanced guanylate cyclase, an enzyme that has recently been demonstrated to be activated by biotin. These analogs increased guanylate cyclase activity two-fold in liver, cerebellum, heart, kidney and colon at 1 M concentrations. The ED₅₀ for stimulation of guanulate cyclase activity occurred at 0.1 M for each of the biotin analogs. These data indicate that the sulfur atom is not essential in biotin's activation of guanylate cyclase since these analogs do not contain the sulfur atom. Studies on the ring structure of biotin revealed that even compounds with a single 5-membered ring (2-imidazolidone) could augment guanylate cyclase activity. The guanylate cyclase co-factor manganese was not essential for the enhancement of guanylate cyclase by these agents but a maximal activation of this enzyme by these analogs could not be obtained without manganese present.     

Osteoclast cell-surface changes during the egg-laying cycle in Japanese quail

The medullary bone serves as a source of labile calcium mobilized during calcification of the egg shell in birds. Quantitative histological methods demonstrate that the numbers of medullary bone osteoclasts and nuclei per osteoclast remain unchanged during the egg cycle in the Japanese quail (Coturnix). Therefore, cyclic changes in bone resorption cannot be explained by modulations of osteoclasts from and into other bone cells, a mechanism previously suggested for certain species of birds. Rather, dramatic changes in osteoclast cell-surface features occur during the egg cycle, which might account for cyclic variations in resorptive activity. During egg shell calcification, osteoclasts with ruffled borders are closely apposed to bone surfaces; the cytoplasm is rich in vacuoles that contain mineral crystals and seem to derive from the ruffled border. At the completion of egg shell calcification, the ruffled borders and vacuoles move away from the bone surface, although the osteoclast remains attached to the bone along the filamentous or "clear" zone. Associated with the disappearance of the ruffled borders is the appearance of extensive interdigitated cell processes along the peripheral surface of the osteoclast away from the bone. These unusual structures, which may serve as a reservoir of membrane, largely disappear when ruffled borders and associated structures reappear. Therefore, in these hens, the osteoclasts modulate their cell surface rather than their population during the egg cycle.