Multiplex T-RFLP allows for increased target number and specificity : detection of Salmonella enterica and six species of Listeria in a single test

A multiplex T-RFLP test was developed to detect and identify Salmonella enterica and all six species of Listeria inoculated into milk at minimal levels. Extensive in silico analysis was used to design a fifteen-primer, six-amplimer methodology and in vitro application showed target organism DNA, when amplified individually, yielded the predicted terminal restriction fragments (TRFs) following digestion. Non-target organisms were either not-amplified or yielded TRFs which did not interfere with target identification. Multiple target DNA analysis gave over 86% detection of total TRFs predicted, and this was improved to over 90% detection of total TRFs predicted when only two target DNA extracts were combined analysed. Co-inoculation of milk with five strains each of the target species of S. enterica and L. monocytogenes, along with five strains of the non-target species E. coli was followed by enrichment in SEL medium for M-TRFLP analysis. This allowed for detection of both target species in all samples, with detection of one S. enterica and two Listeria TRFs in all cases, and detection of a second S. enterica TRF in 91% of cases. This was from an initial inoculum of <5 cfu per 25 ml milk with a background of competing E. coli present, and gave a result from sampling of under 20 hours. The ability to increase target species number without loss of sensitivity means that extensive screening can be performed at reduced cost due to a reduction in the number of tests required

3,3′-{Ethane-1,2-diylbis[carbonylbis(azanediyl)]}dipyridinium tetra­chloridoplatinate(II)

In the crystal structure of the title compound, (C14H18N6O2)·[PtCl4], the cation and square-planar anion are located on special positions (on a twofold axis and an inversion centre, respectively). In the crystal structure, N—H⋯Cl hydrogen bonds lead to a staircase-like motif. The central ethane backbone of the cation is disordered over two positions of equal occupancy

Source attribution, prevalence and enumeration of Campylobacter spp. from retail liver

Funding Information: We thank Food Standards Agency, Scotland for funding this work.Peer reviewedPreprin

Fecal pollution in water from storm sewers and adjacent seashores in Natal, Rio Grande do Norte, Brazil

A study on the distribution patterns of enteropathogenic bacteria polluting the shoreline in Natal, Rio Grande do Norte, Brazil, was carried out based on 72 samples obtained from three storm sewers and adjoining beach locations, Praia do Meio (PM), Areia Preta (AP) and Ponta Negra (PN). From each location, 12 water samples were taken and analyzed for fecal coliforms (FC) and Escherichia coli. In AP, two (16.7%) of the seawater samples and five (41.7%) of the storm sewer samples yielded values above 1.1 × 107 FC/100 ml, whereas only one (8.3%) of the samples from PM reached this level. There was no correlation (p > 0.05) between rainfall indeces and FC values. A total of 64 E. coli isolates were obtained: 37 from the storm sewer samples and 27 from the seawater samples. Of these isolates, four (O143, two O112ac, and O124) were enteroinvasive and two (O111 and O125) were enteropathogenic. Resistance to antibiotics and to heavy metals was also analyzed. Almost 36% of the E. coli strains isolated were resistant to more than one antibiotic. All strains were resistant to zinc and copper at the highest concentration tested (250 μg/ml), and several (23.4%) were resistant to mercury at 50 μg/ml. Our results agreed with previous reports that antibiotic resistance is commonly associated with heavy-metal resistance in pathogens. [Int Microbiol 2004; 7(3):213–218

2-All­yloxy-5-nitro­benzoic acid

The mol­ecule of the title compound, C10H9NO5, is approximately planar, with the mean planes of the nitro, carboxyl and all­yloxy groups rotated by 8.1 (3), 7.9 (3) and 4.52 (18)°, respectively, from the plane of the benzene ring. Bond lengths in the aromatic ring are influenced by both electronic effects and strain induced by ortho-substitution. In the crystal structure, centrosymmetrically related mol­ecules are paired into dimers through strong O—H⋯O hydrogen bonds

(3R,4S,5S,8S,10R,13R)-3-Hy­droxy­kaura-9(11),16-dien-18-oic acid

The title compound, C20H28O3, was isolated during our investigation into the chemical composition and pharmacological activity of Centipeda cunninghamii (DC.) A. Braun & Asch. (Asteraceae). The enanti­opure compound, a diterpene with a carbon skeleton, is composed of three six- and one five-membered rings in chair, twist-boat, half-chair and envelope conformations, respectively. Each mol­ecule makes one intra- and one inter­molecular O—H⋯O hydrogen bond in the crystal lattice, forming hydrogen-bonded chains along [010]. The absolute configuration of the compound was assigned on the basis of optical rotation measurements

From wormhole to time machine: Comments on Hawking's Chronology Protection Conjecture

The recent interest in ``time machines'' has been largely fueled by the apparent ease with which such systems may be formed in general relativity, given relatively benign initial conditions such as the existence of traversable wormholes or of infinite cosmic strings. This rather disturbing state of affairs has led Hawking to formulate his Chronology Protection Conjecture, whereby the formation of ``time machines'' is forbidden. This paper will use several simple examples to argue that the universe appears to exhibit a ``defense in depth'' strategy in this regard. For appropriate parameter regimes Casimir effects, wormhole disruption effects, and gravitational back reaction effects all contribute to the fight against time travel. Particular attention is paid to the role of the quantum gravity cutoff. For the class of model problems considered it is shown that the gravitational back reaction becomes large before the Planck scale quantum gravity cutoff is reached, thus supporting Hawking's conjecture.Comment: 43 pages,ReV_TeX,major revision

Colorectal cancer linkage on chromosomes 4q21, 8q13, 12q24, and 15q22

A substantial proportion of familial colorectal cancer (CRC) is not a consequence of known susceptibility loci, such as mismatch repair (MMR) genes, supporting the existence of additional loci. To identify novel CRC loci, we conducted a genome-wide linkage scan in 356 white families with no evidence of defective MMR (i.e., no loss of tumor expression of MMR proteins, no microsatellite instability (MSI)-high tumors, or no evidence of linkage to MMR genes). Families were ascertained via the Colon Cancer Family Registry multi-site NCI-supported consortium (Colon CFR), the City of Hope Comprehensive Cancer Center, and Memorial University of Newfoundland. A total of 1,612 individuals (average 5.0 per family including 2.2 affected) were genotyped using genome-wide single nucleotide polymorphism linkage arrays; parametric and non-parametric linkage analysis used MERLIN in a priori-defined family groups. Five lod scores greater than 3.0 were observed assuming heterogeneity. The greatest were among families with mean age of diagnosis less than 50 years at 4q21.1 (dominant HLOD = 4.51, α = 0.84, 145.40 cM, rs10518142) and among all families at 12q24.32 (dominant HLOD = 3.60, α = 0.48, 285.15 cM, rs952093). Among families with four or more affected individuals and among clinic-based families, a common peak was observed at 15q22.31 (101.40 cM, rs1477798; dominant HLOD = 3.07, α = 0.29; dominant HLOD = 3.03, α = 0.32, respectively). Analysis of families with only two affected individuals yielded a peak at 8q13.2 (recessive HLOD = 3.02, α = 0.51, 132.52 cM, rs1319036). These previously unreported linkage peaks demonstrate the continued utility of family-based data in complex traits and suggest that new CRC risk alleles remain to be elucidated. © 2012 Cicek et al

Regularizing Portfolio Optimization

The optimization of large portfolios displays an inherent instability to estimation error. This poses a fundamental problem, because solutions that are not stable under sample fluctuations may look optimal for a given sample, but are, in effect, very far from optimal with respect to the average risk. In this paper, we approach the problem from the point of view of statistical learning theory. The occurrence of the instability is intimately related to over-fitting which can be avoided using known regularization methods. We show how regularized portfolio optimization with the expected shortfall as a risk measure is related to support vector regression. The budget constraint dictates a modification. We present the resulting optimization problem and discuss the solution. The L2 norm of the weight vector is used as a regularizer, which corresponds to a diversification "pressure". This means that diversification, besides counteracting downward fluctuations in some assets by upward fluctuations in others, is also crucial because it improves the stability of the solution. The approach we provide here allows for the simultaneous treatment of optimization and diversification in one framework that enables the investor to trade-off between the two, depending on the size of the available data set