Optimization of testing protocols to screen for COVID-19: a multi-objective model.

In this paper we develop a new multi-objective simulated annealing (MOSA) algorithm to generate optimal testing protocols for infectious diseases, using the COVID-19 pandemic as our context. A SEIR (susceptible-exposed-infected-recovered) epidemiological model is embedded as the computational platform for our MOSA algorithm to optimize testing protocols for screening across three joint objectives: minimum cost of test materials, minimum total infections over the testing horizon, and minimum number of false negatives over the horizon. We demonstrate the application of this optimization tool to recommend screening protocols for K-12 school districts in the U.

Neurologic Conditions Associated with Cavus Foot Deformity.

The cavus foot deformity is an often less understood deformity within the spectrum of foot and ankle conditions. The hallmark concern is the possibility of an underlying neurologic or neuromuscular disorder. Although a proportion of these deformities are idiopathic, a significant majority do correlate with an underlying disorder.

Human genomic characterization of a novel locus-specific repetitive sequence.

A novel human chromosome locus-specific repetitive sequence was identified and characterized using arbitrary PCR. The repeat monomer consensus sequence is 100 bp long, and there are a minimum of 140 to 160 copies of the repetitive sequence per haploid human genome. The repetitive sequence is highly clustered on 20q12 within a 200- to 400-kb region.

Cycled primer extension: a method for DNA amplification and labeling from templates of unknown sequence.

A method has been developed for simultaneous radiolabeling and amplification of DNA hybridization probes. The method is termed cycled primer extension (CPE). CPE is a series of temperature-driven reactions in which template DNA is successively denatured and extended by a thermostable primer-dependent DNA polymerase.

Chromosomal mapping of the human CNP gene using a meiotic crossover DNA panel, PCR, and allele-specific probes.

The human 2',3'-cyclic nucleotide 3'-phosphohydrolase (CNP) gene is located on chromosome 17, as determined by PCR of somatic cell hybrid DNA panels and confirmed using a mouse-human hybrid containing only human chromosome 17. A polymorphic site (C, T) was previously described at nucleotide 1215 within the most 3' intron of the gene. Nested PCR primer pairs were designed to amplify across this site, and PCR products were hybridized to end-labeled allele-specific probes.

Variation in genomic Alu repeat density as a basis for rapid construction of low resolution physical maps of human chromosomes.

Human DNA restriction fragments containing high numbers of Alu repeat sequences can be preferentially detected in the presence of other human DNA restriction fragments in DNA from human: rodent somatic cell hybrids when the DNA is fragmented with enzymes that cleave mammalian DNA infrequently. This ability to lower the observed human DNA complexity allowed us to develop an approach to order rapidly somatic hybrid cell lines retaining overlapping human genomic domains. The ordering process also generates a relative physical map of the human fragments detected with Alu probe DNA.

An efficient technique for obtaining sequences flanking inserted retroviruses.

Genomic mapping studies frequently employ retrovirus-mediated transfer of dominant selectable markers to specific target chromosomes. DNA probes containing sequences adjacent to inserted proviruses are valuable mapping tools in such studies. We have implemented a strategy for amplification of chromosomal sequences flanking the 5' LTR of MoMuLV-based vectors.

Restriction fragment length polymorphism DNA analysis by the FBI Laboratory protocol using a simple, convenient hardware system.

Restriction fragment length polymorphism analysis of human deoxyribonucleic acid (DNA) using two probes, pYNH24 and CMM101, was performed on the BIOS Timeframe system following the Federal Bureau of Investigation (FBI) Laboratory protocol and some variations of it. Comparable results were obtained by the different methods used.

Morphological transformation of BALB/3T3 cells by various procarcinogens in the presence of a rat liver S-9 activation system.

An Aroclor-induced rat hepatic S-9 metabolic activation system was incorporated into the BALB/3T3 cell transformation assay to increase its sensitivity to a wide range of procarcinogens. S-9 was prepared from Aroclor 1254-induced (500 mg/kg) Fischer 344 rats. Cyclophosphamide, dimethylnitrosamine, 2-aminofluorene, and 2-naphthylamine were metabolized to reactive forms capable of inducing both dose-dependent toxicity and morphological transformation of BALB/3T3 cells.

Induction of mutagenesis and transformation in BALB/c-3T3 clone A31-1 cells by diverse chemical carcinogens.

BALB/c-3T3 cells were employed to examine the genotoxic potential of a variety of known chemical carcinogens. BALB/c-3T3 cells displayed a dose-dependent transformation response to a variety of carcinogens (polycyclic hydrocarbons, methylating agents, ethylating agents, aflatoxin B1 [AFB1], and 4-nitroquinoline-N-oxide [4-NQO]). When the ability of these compounds to induce mutagenesis to resistance to the cardiac glycoside ouabain (OUAR) was examined, we found the short chain alkylating agents to be particularly effective mutagens, causing biologic effects at doses below those necessary to induce a transformation response.

An interlaboratory evaluation of the Syrian hamster embryo cell transformation assay using eighteen coded chemicals.

Eighteen coded chemicals were evaluated in the Syrian hamster embryo (SHE) cell transformation assay in three different laboratories using the same basic experimental protocol with minor modifications. In addition, individual cell and serum sources were selected. Major factors influencing intra-and interlaboratory reproducibility were the source of cells and serum, the toxicity of the chemicals, and the dose-range selected for transformation evaluation.

A method for the amplification of chemically induced transformation in C3H/10T1/2 clone 8 cells: its use as a potential screening assay.

A method has been developed by which to amplify expression of phenotypic transformation of C3H/10T1/2 clone 8 mouse embryo cells not otherwise observed in the standard transformation assay. The expression of transformed foci was amplified by subcultivating chemically treated target cells after they had reached confluence and replating them at subconfluent cell densities. Conditions leading to the expression of the highest numbers of transformed foci include a) a cell seeding density for chemical treatment of 1 X 10(4) cells/dish, b) subculture 4 weeks after treatment, and c) replating cells at a density of 2 X 10(5) cells/-dish.

Chronic inhalation studies in mice. II. Effects of long-term exposure to 2R1 cigarette smoke on (C57BL/Cum x C3H/AnfCum)F1 mice.

Standardized exposure conditions with Kentucky reference 2R1 cigarettes were used to expose 2,053 (C57BL/Cum x C3H/AnfCum)F1 female mice (nose only) to fresh, whole cigarette smoke. In addition, 1,014 mice were sham-exposed, and 449 mice were held as shelf controls. The protocol entailed exposing mice to smoke (or sham-exposure) on a daily basis, 5 days/week, for 110 weeks and observing remaining mice until death.

Induction of immunotoxicity in mice by polyhalogenated biphenyls.

Acute administration of Aroclor-1254 (500 mg/kg) or 3,4,5,3',4',5'-hexabromobiphenyl (HBB) (2-6 mg/kg) IP, profoundly inhibited the plaque forming response to subsequent challenge with sheep erythrocytes in Ah locus positive (C57Bl/6N or B6C3F1N) mice. These studies showed: the immunotoxicity results paralleled enzyme induction results insofar as HBB was approximately 100 times more potent than Aroclor 1254; neither Aroclor nor HBB treatment caused significant induction in the Ah locus negative DBA/2N mice; when B6C3F1 mice were challenged with sheep red blood cells (SRBC) 6 or 16 weeks post Aroclor 1254 treatment, substantial recovery of a PFC response was observed; when these compounds were administered to older (76-week-old) (B6C3F1 mice, severe depression of a PFC response was observed. In contrast to its profound depression of a PFC response, Aroclor-1254 (up to 1250 mg/kg) caused slight increases in lymphocyte proliferation induced by either T or B cell mitogens.

Influence of various parameters on benzo(a)pyrene enhancement of adenovirus SA7 transformation of Syrian hamster embryo cells.

Several of the major variable factors in the Syrian hamster embryo/simian adenovirus SA7 (SHE/SA7) viral enhancement assay were identified and the effects of these parameters on assay sensitivity were assessed. The extent of dose-dependent cytotoxicity and enhancement of SA7 transformation of primary SHE target cells by benzo(a)pyrene was examined through analysis of data obtained from 37 assays performed over a 2-year period. The variables analyzed for contribution to assay sensitivity included the number of SA7-induced transformed SHE cell foci enumerated in ten replicate dishes in the negative control condition (background focus count) (range: 26-139); the age of the SHE cell cultures at the time of exposure to benzo(a)pyrene (range: 72-144 hr postseeding); and the source of the pregnant hamsters used to prepare the primary SHE cells (Wilmington colony vs Lakeview colony, Charles River Laboratories, Inc.

Chemical enhancement of SA7 virus transformation of hamster embryo cells: evaluation by interlaboratory testing of diverse chemicals.

Twelve chemicals from diverse structural classes were tested under code for their capacity to enhance the transformation of Syrian hamster embryo cells by simian adenovirus SA7 in two independent laboratories. Pretreatment of hamster cells with eight of those chemicals (reserpine, dichlorvos, methapyrilene hydrochloride, benzidine dihydrochloride, diphenylhydantoin, cinnamyl anthranilate, 11-aminoundecanoic acid, and 4,4'-oxydianiline) produced repeatable enhancement of SA7 transformation at two or more consecutive dose levels, which constitutes clear evidence of enhancing activity in this assay. Both toxic and nontoxic doses of each of these chemicals caused enhancement of virus transformation.

Analysis of the interlaboratory and intralaboratory reproducibility of the enhancement of simian adenovirus SA7 transformation of Syrian hamster embryo cells by model carcinogenic and noncarcinogenic compounds.

The intralaboratory and interlaboratory reproducibility of a DNA virus (SA7) transformation enhancement assay was investigated using nine carcinogenic and noncarcinogenic compounds representing a variety of chemical classes. By the use of standardized procedures designed to limit assay variables, replicate assay data were collected in two independent laboratories and analyzed for concurrence. The carcinogens, 7,12-dimethylbenz(a)anthracene, benzo(a)pyrene, and N-methyl-N'-nitro-N-nitrosoguanidine yielded reproducible dose-dependent cytotoxicity and positive transformation effects (defined as statistically significant [p less than or equal to 0.

Induction of immunotoxicity by polycyclic hydrocarbons: role of the Ah locus.

We have employed the plaque forming cell (PFC) response to sheep erythrocytes as well as lymphocyte proliferation to study the induction of immunotoxicity in AHH-inducible (Ah Locus positive, C57BL/6N; B6C3F1) and AHH non-inducible (Ah Locus negative, DBA2/N) mice following administration of polycyclic aromatic hydrocarbons. When two potent carcinogenic polycyclic hydrocarbons which induce AHH activity, 3-methylcholanthrene (MCA) or 1,2,5,6-dibenzanthracene [DB(a,h)A] were administered IP, immunotoxicity was observed in both AHH-inducible and AHH non-inducible animals. However, the AHH-inducible animals appeared to be more sensitive, and substantial suppression of a PFC response toxicity could be induced with doses as low as 14 mg/kg methylcholanthrene.

Increased sister-chromatid exchange in bone-marrow cells of mice exposed to whole cigarette smoke.

Using defined cigarette smoke exposure conditions, BC3F1/Cum mice were exposed nose-only to two different types of whole cigarette smoke on a daily basis for 1 week and up to 46 weeks. The number of sister-chromatid exchanges (SCEs) per metaphase was determined in bone-marrow cells. Studies were scheduled so that all cytogenetic observations were made 2-3 days after the last smoke exposure.

Xeroderma pigmentosum fibroblasts are more sensitive to asbestos fibers than are normal human fibroblasts.

Xeroderma pigmentosum fibroblasts (XPF) are defective in the repair of certain DNA adducts. We show here that XPF cells are more sensitive to the toxic effects of chrysotile, amosite and crocidolite asbestos than are normal human fibroblasts (NF). XPF cells from different complementation groups have a sensitivity to chrysotile which parallels the degree of their DNA repair deficiency.

Aryl hydrocarbon hydroxylase inducibility among primary relatives of children with leukemia or solid tumors.

In mice, there is a correlation between genetically regulated levels of inducible aryl hydrocarbon hydroxylase (AHH) activity and the risk of polycyclic hydrocarbon-induced leukemia or solid tumors. Recent clinical studies suggest a relationship between high AHH activity and lung cancer associated with cigarette smoking (Kouri, R.E.