Multiple filtration and approximate pattern matching

Given a text of lengthn and a query of lengthq, we present an algorithm for finding all locations ofm-tuples in the text and in the query that differ by at mostk mismatches. This problem is motivated by the dot-matrix constructions for sequence comparison and optimal oligonucleotide probe selection routinely used in molecular biology. In the caseq=m the problem coincides with the classicalapproximate string matching with k mismatches problem. We present a new approach to this problem based on multiple hashing, which may have advantages over some sophisticated and theoretically efficient methods that have been proposed. This paper describes a two-stage process. The first stage (multiple filtration) uses a new technique to preselect roughly similarm-tuples. The second stage compares thesem-tuples using an accurate method. We demonstrate the advantages of multiple filtration in comparison with other techniques for approximate pattern matching.This research was supported in part by the National Science Foundation under Grant No. DMS 90-05833 and the National Institute of Health under Grant No. GM-36230.     

Oxygen concentration in milk of healthy and mastitic cows and implications of low oxygen tension for the killing of Staphylococcus aureus by bovine neutrophils

The partial pressure of O2 in milk from normal cows and from cows with mastitis was measured and the concentrations of O2 calculated. Oxygen levels of milk from normal cows were similar to those in venous plasma, but inflammation of the mammary gland led to a dramatic drop in O2 concentration to less than 10% of control values. Intracellular survival of Staphylococcus aureus strain M60 in bovine neutrophils was greater under anaerobic than aerobic conditions. The implications of low O2 concentrations in milk from infected mammary glands for the bactericidal activity of bovine neutrophils is discussed.     

Current practices of preoperative bowel preparation among North American colorectal surgeons

In North America, the rate of infections following colorectal surgery decreased after the introduction of oral antibiotic bowel preparation against colonic microflora. Eight hundred eight board-certified colorectal surgeons were surveyed for their current bowel preparation practices before elective procedures. The 471 responders (58%) all use mechanical preparation: oral polyethylene glycol solution (70.9% of the respondents), oral sodium phosphate solution with or without bisacodyl (28.4%), and "traditional" methods of dietary restriction, cathartics, and enemas (28.4%). Most surgeons (86.5%) add oral and parenteral antibiotics to the regimen; 11.5% add only parenteral antibiotics, 1.1% add only oral antibiotics, and 0.9% add no antibiotics. Generally (77.8% of cases), oral neomycin and erythromycin or metronidazole are combined with a perioperative parenteral antibiotic. Most individuals start the preparation as outpatients the day before surgery, and the parenteral drugs are added to the regimen 1-2 hours before the procedure. The use of outpatient bowel preparation is increasing; however, patient selection is critical, and education is needed to reduce the rate of complications.     

Grafting of methyl methacrylate on isoprene rubber

Methyl methacrylate has been grafted on artificial isoprene rubber (IR) latex, with use of redox initiation. The properties of latices containing up to 40 phr

1 Parts per hundred parts of rubber.

methyl methacrylate (MMA) as well as solid products containing up to 80 phr of this compound were studied. Compared with ungrafted IR latex with the same solids content, the grafted IR latices had a lower viscosity, owing to their particle size being larger. Vulcanised films obtained from the grafted latices showed a considerably higher modulus, particularly at large deformations, than those based on IR or blends of IR with polymethyl methacrylate. by incorporation of certain reinforcing white fillers in the MMA-grafted IR latices, a further increase in the modulus of the latex films was effected.     

Light-induced variation in phenolic levels in foliage of rain-forest plants

Levels of phenolic secondary metabolites in the leaves of four west African rain-forest plants,Acacia pennata, Cynometra leonensis, Diopyros thomasii, andTrema guineensis, were correlated with incident light intensity at both the inter- and intraindividual level. Enhanced phenolic levels under high light intensity appeared to be due to production of both polyphenolics (condensed and hydrolyzable tannins) and simple phenolics. InTrema guineensis, where it is possible to separate leaves in terms of both their age and the light incident upon them, condensed tannin production progressed differently during the development of sun and shade leaves, suggesting continuing production of new oligomers in the former but not in the latter. The results of this study suggest that the production of phenolics in relation to variation in incident light is a finely tuned process, which must be explained in terms of plant physiology and intermediate metabolism rather than in terms of resource allocation or a direct response to herbivory.     

Postulations of flame spread mechanisms

An experimental study was conducted to explore the flame spread mechanism over thin solid fuel sheets. Flame spread rates over paper at various inclined angles were measured, and Schlieren photography was used to qualitatively assess heat transfer to the unburnt material in front of the pyrolysis zone. Two different types of flame spread were observed. One is te downward flame spread observed in the range of ?90 to ?30 deg from the horizontal. In this region, flame spread rate was almost constant with time, although it increased slightly with increasing angle. The other type of spread observed was the accelerative upward flame spread at angles of zero to 90 deg. Flame spread at angles from ?30 deg to zero seemed unsatable and increased by repetitive acceleration and deceleration In the range of inclined angles from ?90 to ?30 deg, heat transfer from the flame zone to the unburnt material seemed to take place mainly through the gas phase in the region 0.2 ～ 0.4 cm in front of the pyrolysis zone. In this case, the direction of the gas stream could be considered to oppose that of the flame spread. In the case of upward flame spread, the unburnt material in front of the pyrolysis zone seemed to be heated by convection of the bottom side, where the direction of the gas stream was obviously parallel with that of flame spread.     

Effects of copper status on neutrophil function, superoxide dismutase, and copper distribution in steers.

Twelve Holstein steers in a completely randomized block design were fed either a basal diet (concentrate:silage or hay at a DM ratio of 35:65) plus Cu sulfate at 20 ppm of Cu (Cu-supplemented diet) or a basal diet plus ammonium molybdate to obtain 10 ppm of Mo (Cu-depleting diet) on a DM basis in the whole diet for 8 mo. Supplemental Mo was utilized in the Cu-depleting diet to develop a Cu-deficient group. Molybdenum slowly accumulated in the liver in the group fed the Cu-depleting diet. Copper concentrations in the liver and polymorphonuclear neutrophils decreased in the Cu-deficient group compared with the Cu-sufficient group. Plasma Cu concentration did not change during the trial for the Cu-sufficient group. In the Cu-deficient group, plasma Cu concentrations increased during the first 3 mo of the trial, then declined, and remained unchanged for the last 5 mo. Superoxide dismutase activities in red blood cells, polymorphonuclear neutrophils, and whole blood decreased in the Cu-deficient group. Phagocytic capacity was not affected by Cu status, but killing capacity was decreased by low Cu status in the Cu-deficient group by the end of the trial. Glutathione peroxidase activity was unaffected by Cu status. Clinical symptoms of Cu-deficiency were not observed in this trial; there was no evidence of blood hemoglobin or BW gain difference between the two groups. In this study, Cu status affected its distribution in the tissues and related enzyme activities as well as bactericidal function of neutrophils.     

Structural Analysis of Cytochrome P450 105N1 Involved in the Biosynthesis of the Zincophore, Coelibactin

Coelibactin is a putative non-ribosomally synthesized peptide with predicted zincophore activity and which has been implicated in antibiotic regulation in Streptomyces coelicolor A3(2). The coelibactin biosynthetic pathway contains a stereo- and regio-specific monooxygenation step catalyzed by a cytochrome P450 enzyme (CYP105N1). We have determined the X-ray crystal structure of CYP105N1 at 2.9 Å and analyzed it in the context of the bacterial CYP105 family as a whole. The crystal structure reveals a channel between the α-helical domain and the β-sheet domain exposing the heme pocket and the long helix I to the solvent. This wide-open conformation of CYP105N1 may be related to the bulky substrate coelibactin. The ligand-free CYP105N1 structure has enough room in the substrate access channel to allow the coelibactin to enter into the active site. Analysis of typical siderophore ligands suggests that CYP105N1 may produce derivatives of coelibactin, which would then be able to chelate the zinc divalent cation.     

Epiregulin is a potent pan-ErbB ligand that preferentially activates heterodimeric receptor complexes

The ErbB signaling network consists of four transmembrane receptor tyrosine kinases and more than a dozen ligands sharing an epidermal growth factor (EGF) motif. The multiplicity of ErbB-specific ligands is incompletely understood in terms of signal specificity because all ErbB molecules signal through partially overlapping pathways. Here we addressed the action of epiregulin, a recently isolated ligand of ErbB-1. By employing a set of factor-dependent cell lines engineered to express individual ErbBs or their combinations, we found that epiregulin is the broadest specificity EGF-like ligand so far characterized: not only does it stimulate homodimers of both ErbB-1 and ErbB-4, it also activates all possible heterodimeric ErbB complexes. Consistent with its relaxed selectivity, epiregulin binds the various receptor combinations with an affinity that is approximately 100-fold lower than the affinity of ligands with more stringent selectivity, including EGF. Nevertheless, epiregulin's action upon most receptor combinations transmits a more potent mitogenic signal than does EGF. This remarkable discrepancy between binding affinity and bioactivity is permitted by a mechanism that prevents receptor down-regulation, and results in a weak, but prolonged, state of receptor activation.