Optimal estimation of initial concentrations and emission sources with 4D-Var for air pollution prediction in a 2D transport model.

Attributing sources of air pollution events by deploying an efficient observational network is an important and interesting problem in air quality control and forecast studies, but it is very challenging. In order to estimate the sensitivities of pollution events to emission sources, a comprehensive framework is built based on a horizontal 2-dimensional transport model and its adjoint in solving this problem. In an analysis of an idealized air pollution event of PM2.5 over the region of North China, an objective function is defined to optimally estimate the initial concentrations and emission sources through a series of minimization procedures. Results by means of the 4-dimensional variational approach show that, with the optimal initial conditions and emission sources, the model can successfully forecast the pollution event in a few days. The optimal observing network based on sensitivity analysis takes only one third of the cost but greatly retains predictability skill compared to the full-grid observing system, while nearly no predictability skill is detectable if the same number of observational sites is randomly deployed. We evaluate air pollution predictability in the point of focusing on to what degree the root mean square errors between the modeled concentration and the targeted air pollution are limited by the optimal observational network. Results show that air pollution predictability in association with the optimal observational network is limited in the time scales about 6 days. With the high efficiency and in an economic fashion, such a sensitivity-based optimal observing system holds promise for accurately predicting an air pollution event in the targeted area once the adjoint and variational procedure of a realistic atmosphere model including transport and chemical processes is performed.

Inertial particle segregation by turbulence.

We study collections of heavy and light small spherical particles initially well mixed with each other, subjected to linear (Stokes) drag force and gravity, and falling through a fluid turbulence. We introduce the segregation power spectrum, which we use to define the segregation length scale. Kinematic simulation predicts that the turbulence can segregate heavy and light falling particles and leads to a well-defined segregation length scale. The properties of this length scale and of the segregation power spectrum used to define it are discussed and, where possible, explained.

Homologous chromosome pairing in Drosophila melanogaster proceeds through multiple independent initiations.

The dynamics by which homologous chromosomes pair is currently unknown. Here, we use fluorescence in situ hybridization in combination with three-dimensional optical microscopy to show that homologous pairing of the somatic chromosome arm 2L in Drosophila occurs by independent initiation of pairing at discrete loci rather than by a processive zippering of sites along the length of chromosome. By evaluating the pairing frequencies of 11 loci on chromosome arm 2L over several timepoints during Drosophila embryonic development, we show that all 11 loci are paired very early in Drosophila development, within 13 h after egg deposition. To elucidate whether such pairing occurs by directed or undirected motion, we analyzed the pairing kinetics of histone loci during nuclear cycle 14. By measuring changes of nuclear length and correlating these changes with progression of time during cycle 14, we were able to express the pairing frequency and distance between homologous loci as a function of time. Comparing the experimentally determined dynamics of pairing to simulations based on previously proposed models of pairing motion, we show that the observed pairing kinetics are most consistent with a constrained random walk model and not consistent with a directed motion model. Thus, we conclude that simple random contacts through diffusion could suffice to allow pairing of homologous sites.

Deconstructing the nucleus: global architecture from local interactions.

Recent advances in fluorescence in situ hybridization and three-dimensional microscopy have revealed a high degree of large-scale order in the nucleus, indicating that the position of each gene within the nucleus is not random. As with any other biological phenomenon, this large-scale organization must ultimately be specified by molecular interactions. Biochemical and molecular investigations have revealed a small set of local molecular-scale interactions that can be used together in a combinatorial fashion to establish a global large-scale nuclear architecture.

Perturbation of nuclear architecture by long-distance chromosome interactions.

SUMMARY: Position-effect variegation (PEV) describes the stochastic transcriptional silencing of a gene positioned adjacent to heterochromatin. Using FISH, we have tested whether variegated expression of the eye-color gene brown in Drosophila is influenced by its nuclear localization. In embryonic nuclei, a heterochromatic insertion at the brown locus is always spatially isolated from other heterochromatin. However, during larval development this insertion physically associates with other heterochromatic regions on the same chromosome in a stochastic manner. These observations indicate that the brown gene is silenced by specific contact with centromeric heterochromatin. Moreover, they provide direct evidence for long-range chromosome interactions and their impact on three-dimensional nuclear architecture, while providing a cohesive explanation for the phenomenon of PEV.

Toward fully automated high-resolution electron tomography.

Electron tomography is a powerful tool in elucidating the three-dimensional architecture of large biological complexes and subcellular organelles. Its use can be expanded through the simplification of the tomographic procedure by automation of its tasks. In this paper, we describe our EMACT/EMCAT system, which automates both tomographic data collection and reconstruction.

Three-dimensional structural characterization of centrosomes from early Drosophila embryos.

An understanding of the mechanism and structure of microtubule (MT)-nucleating sites within the pericentriolar material (PCM) of the centrosome has been elusive. This is partly due to the difficulty in obtaining large quantities of centrosomes for analysis, as well as to the problem of attaining interpretable structural data with conventional EM techniques. We describe a protocol for isolating a large quantity of functional centrosomes from early Drosophila embryos. Using automated electron tomography, we have begun a three-dimensional structural characterization of these intact centrosomes with and without regrown MTs. Reconstructions of the centrosomes to approximately 6-8 nm resolution revealed no large structures at the minus ends of MTs, suggesting that if MT-nucleating material physically contacts the MTs, it must conform closely to the shape of the minus end. While many MTs originate near the centrioles, MT minus ends were found throughout the PCM, and even close to its outer boundary. The MTs criss-crossed the PCM, suggesting that nucleating sites are oriented in many different directions. Reconstructions of centrosomes without MTs suggest that there is a reorganization of the PCM upon MT regrowth; moreover, ring-like structures that have a similar diameter as MTs are apparent in the PCM of centrosomes without MTs, and may be MT-nucleating sites.

Candida detection system (CAND-TEC) to differentiate between Candida albicans colonization and disease.

Eighty-three serum specimens from 24 patients infected with Candida albicans were examined for circulating Candida protein antigens with the Candida Detection System (CAND-TEC; Ramco Laboratories, Inc., Houston, Tex.). The medical records of each patient were reviewed for clinical evidence of Candida colonization or disease, predisposing factors for infection, underlying illness, the presence of a contaminated indwelling venous catheter, intravenous amphotericin B therapy, and outcome. Forty-nine serum specimens with antigen titers of 1:2 or less were obtained either from colonized patients or at a time when disseminated disease was not yet clinically suspected. Except for five specimens from two colonized patients, one with a contaminated arterial line, the other specimens with titers of 1:8 or greater (n = 14) were obtained from patients who had been clinically diagnosed and treated for disseminated candidiasis. Serum specimens with titers of 1:4 were often from patients with deep-seated candidal infection but were not uniformly diagnostic; in this situation additional specimens should be tested for Candida antigen titers. Only 1 of 24 serum specimens from patients with no evidence of C. albicans infection had a Candida protein antigen titer of 1:8. With a 1:8 or greater titer as a criterion for dissemination, the sensitivity of the CAND-TEC system was 71%, with a specificity of 98%. If the 1:8 titer for the colonized patient with a contaminated arterial line is not considered a false-positive result, the CAND-TEC sensitivity was 83%. The latex agglutination assay appears to be a useful, rapid, and noninvasive means of laboratory diagnosis of systemic candidiasis. The recovery of C. albicans from at least three body sites may also be a useful predictor of disseminated disease.

Infective endocarditis due to penicillin-tolerant Streptococcus bovis.

Two Streptococcus bovis isolates obtained from patients with endocarditis were found to be tolerant to penicillin and other cell wall active agents. By time-kill analysis, penicillin and streptomycin acted synergistically against these strains. The existence of tolerant S. bovis strains should be considered when initially choosing antibiotics for the treatment of serious S. bovis infections.

Comparison of the detection of herpes simplex virus in direct clinical specimens with herpes simplex virus-specific DNA probes and monoclonal antibodies.

A comparison of two commercially available kits for rapid herpes simplex virus (HSV) detection directly in patient specimens was performed. The immunofluorescence assay (IFA) utilized monoclonal antibodies to HSV, and the DNA probe assay utilized three HSV sequences cloned into pBR322. A sample of 243 specimens received in viral transport medium were inoculated into MRC-5 tissue cultures. The remainder of the specimen was centrifuged, and the cellular pellet was examined by IFA and DNA probes. One hundred and sixty-two (66.7%) specimens were considered satisfactory for IFA and DNA probe testing, based on a criterion of observing greater than or equal to 2 intact cells per high-power field. Of the 162 specimens, 35 (21.6%) yielded HSV by culture. By IFA, the sensitivity of detecting HSV culture-positive specimens was 77.1%; specificity was 100%, positive predictive value was 100%, and negative predictive value was 93.3%. DNA probe sensitivity was 71.4%; specificity was 90.6%; positive predictive value was 67.6%; and negative predictive value was 92%. Forty-four (27.2%) of the 162 specimens exhibited nonspecific cytoplasmic staining with the DNA probe. IFA and DNA probe assays can be completed in 2 to 3 h, whereas the average time to culture positivity in this series was 2.2 days. Rapid HSV diagnosis can aid in timely and appropriate patient management.

TORCH serologies and specific IgM antibody determination in acquired and congenital infections.

Except for rubella testing, routine TORCH serology screens in prenatal care are of little use. Individual TORCH tests may, however, be useful based on the clinical presentation and history of the patient. The laboratory test of choice for diagnosing cytomegalovirus (CMV) and herpes simplex virus (HSV) infections is culture isolation for the virus. The presence for specific IgM antibodies in neonates is diagnostic of congenital infection. In adults, IgM antibody results should be interpreted along with the clinical findings and history of the patient. IgM antibodies may persist for months and even years and may be detected during reactivation of latent virus infections. Serum fractionation should always be performed in IgM antibody testing to avoid false positive results owing to rheumatoid factors and false negative results owing to competing levels of specific IgG antibodies. With a single serum specimen, specific IgM antibody detection may be helpful in differentiating between a recent versus past infection.

Serologic diagnosis of toxoplasmosis with emphasis on the detection of Toxoplasma-specific immunoglobulin M antibodies.

Commercially available kits were used for the detection of Toxoplasma-specific IgM antibodies. False positive IgM results were observed in whole sera containing Toxoplasma-specific antibodies together with rheumatoid factor when tested by immunofluorescence (IFA). False negative IgM results occurred in whole sera containing competing levels of Toxoplasma-specific IgG antibodies, as indicated by the IFA:IgM-M ratio. False positive and false negative IgM results often occurred when whole sera were tested. These false reactions were eliminated by fractioning IgM from IgG using the Isolab's IgM Isolation System. All five sera in this study with an IFA titer to Toxoplasma of greater than or equal to 1:16,384 also contained Toxoplasma-specific IgM antibodies. This suggests that sera with high titers to Toxoplasma should be tested for Toxoplasma-specific IgM antibodies.

Two coagulase-variant forms of Staphylococcus aureus isolated from blood cultures.

Two coagulase-variant forms of Staphylococcus aureus were isolated from blood cultures of a patient with infective endocarditis. The coagulase-positive isolate was hemolytic, whereas the coagulase-negative isolate was nonhemolytic. All other properties examined were identical in both strains. Since coagulase-negative S. aureus strains have been isolated from clinical specimens, laboratories should consider using a combination of other biological properties along with coagulase production for the identification of S. aureus.

Growth of coagulase-negative staphylococci on colistin-nalidixic acid agar and susceptibility to polymyxins.

Colistin-nalidixic acid agar, although recently recommended as a replacement for blood agar for primary plating of urine specimens ( Fung et al., J. Clin. Microbiol. 16:632-636, 1982), has also been reported to suppress the growth of some strains of staphylococci that are susceptible to colistin (polymyxin E). The susceptibility of 11 species of staphylococci to polymyxins was determined, and the ability of these species to grow on colistin-nalidixic acid agar was examined. Although the MICs for most of the strains tested were 8 micrograms/ml or less, only a few coagulase-negative staphylococci grew on or were inhibited by colistin-nalidixic acid agar. This descrepancy was explained by the antagonistic effects that medium components, such as physiological concentrations of magnesium and calcium and 5% sheep blood, had on the activity of polymyxin. Colistin-nalidixic acid agar is still recommended for routine urine processing; however, the poor growth of 13% of the Staphylococcus saprophyticus strains tested suggests that blood agar should be included in the primary plating battery of urine specimens obtained from female outpatients.

Capnocytophaga: a review of the literature.

Capnocytophaga species are normal mouth flora but can be opportunistic pathogens causing juvenile peridontitis and bacteremia in the compromised host. Indole-negative fusiforms isolated anaerobically or in the presence of increased CO2 can presumptively be identified as Capnocytophaga species.

Evaluation of the usefulness of counterimmunoelectrophoresis for diagnosis of Clostridium difficile-associated colitis in clinical specimens.

Results of counterimmunoelectrophoresis (CIE) were compared with those of isolation of Clostridium difficile and assay for cytotoxicity in HeLa cells. On the basis of 471 stool specimens, CIE exhibited a sensitivity of 38% and a specificity of 88% as compared with the cytotoxin assay. The predictive value of a reactive CIE results is low (17%), whereas the predictive value of a nonreactive CIE result is significant (96%) and therefore warrants its use as a screening test. In addition, stool filtrates may nonspecifically precipitate with the C. difficile antitoxin in the CIE test. Such nonspecific reactions may be identified by simultaneous electrophoresis against nonimmune serum.

Printcultures for postmortem microbiology.

A modified printculture method for postmortem bacteriology was compared to the traditional tissue homogenate inoculum method. The two methods were comparable in their recovery rate of bacterial isolates. However, printcultures is an easy and rapid method; thus, it is superior to the traditional technique for postmortem culture. Histologic examination of most postmortem lung specimens with no bacterial growth showed no evidence of pneumonia or bronchitis, suggesting that the lack of growth is a reliable indicator of no bacterial infection.

Primary culture media for routine urine processing.

It has been recommended that routine microbiological processing of urine specimens include quantitative plating onto blood agar medium along with a selective and differential agar such as MacConkey agar for gram-negative organisms. Few data have been published to justify this combination. To evaluate the validity of this recommendation 2,553 midstream, clean-voided urine samples were quantitatively plated onto blood agar, MacConkey agar, and colistin-nalidixic acid agar, which is a selective medium for gram-positive organisms. The amounts of growth on each of the three media were compared. Results indicated that the best medium combination was colistin-nalidixic acid agar and MacConkey agar. The use of colistin-nalidixic acid agar instead of blood agar increased the detection of significant growth of enterococci, lactobacilli, and Torulopsis glabrata.

Immunochemical analysis of streptococcal group A, B, and C carbohydrates, with emphasis on group A.

Streptococcal group A, B, and C carbohydrates were analyzed by counterimmunoelectrophoresis, immunoelectrophoresis, and inhibition of immunoprecipitation. Extracts of streptococci group A or C were shown by counterimmunoelectrophoresis to contain both anodic and cathodic migrating components. In immunoelectrophoresis, group A and C substances formed a continuous precipitation line stretching from the anode to the cathode, suggesting a heterogeneous population of molecules with immunochemical identity. This identity was confirmed by inhibition of immunoprecipitation, in which both anodic and cathodic immunoprecipitates were inhibited by the same constituent sugars: group A-anti-A was inhibited by N-acetylglucosamine, and group C-anti-C was inhibited by N-acetylgalactosamine. Extracts of group B showed only anodic migration in counterimmunoelectrophoresis and a narrow, anodic arc in immunoelectrophoresis. The group B-anti-B reaction was inhibited by rhamnose. Carbohydrates of variant strains of group A streptococci were also analyzed by the same methods. The results suggest that the heterogeneity of group A carbohydrate may have resulted from attachment of various amounts of N-acetylglucosamine to the polyrhamnose backbone.

Comparison of slide agglutination test (Phadebact) with counterimmunoelectrophoresis for detection of streptococcal group antigens.

Sera from mice infected with group B streptococci and culture supernatants of group B, A, and C streptococci were examined for the presence of group-specific antigens by the Phadebact slide agglutination (PSA) test and counterimmunoelectrophoresis (CIE). The results were correlated with the number of organisms present in the blood or in vitro cultures. The PSA test was slightly more sensitive than CIE.