Deccan volcanism at the Cretaceous-Tertiary boundary

The accuracy with which one can claim that Deccan trap volcanism occurred at the Cretaceous-Tertiary boundary (KTB) over a very short time interval is of key importance in deciding whether a volcanic origin of the KTB events should be taken seriously. In the two years since paleomagnetic, paleontological and geodynamic evidence was published, further data have become available and the case now appears to be well constrained. The Ar-40/Ar-39 results from six labs have yielded some 24 reliable plateau ages that narrow the age range to 65 to 69 Ma. Moreover, it appears that a significant part of this range results from inter-lab spread and possible minor alteration. Paleontology demonstrates that volcanism started in the Maestrichtian, more precisely in the A. mayaroensis zone. Paleomagnetism shows that volcanism spanned only 3 chrons and only one correlation remains possible, that of the main central reversed chron with 29R. Therefore, whereas Ar-40/Ar-39 is able only to restrict the duration of volcanism to some 4 Ma, paleomagnetism restricts it to 0.5 Ma. Using some geochemical indicators such as C-13 as proxy, it is suggested that volcanism actually consists of a few shorter events of unequal magnitude. Extrusion rates may be as high as 100 cu km/yr and fissure lengths as long as several 100 km. Such a scenario appears to be at least as successful as others in accounting for most anomalies observed at the KTB. Particularly important are Iridium and other platinum group elements (PGE) profiles, Sr-87/Sr-86, C-13, 0-18, other exotic geochemical signatures, spherules, soot, shocked minerals, selective and stepwise extinctions. The environmental impact of CO2 possibly released during explosive phases of volcanism, and SO2 released during effusive phases, and the ability of volcanism to ensure worldwide distribution of KTB products are now all addressed. In conclusion, the case for a causal link between internal hotspot activity, birth of the Reunion hotspot itself as the Deccan and KTB events appears to rest on an increasingly stronger basis

Degradation of AB25 dye in liquid medium by atmospheric pressure non-thermal plasma and plasma combination with photocatalyst TiO2

In this work, degradation of the anthraquinonic dye Acid Blue 25 by non-thermal plasma at atmospheric pressure with and without photocatalyst is investigated. Titanium dioxide (TiO2) is used as a photocatalyst. The dye degradation by plasma in the presence of TiO2 is investigated as a function of TiO2 concentration, dye concentration and pH. The degradation rate is higher in acidic solutions with pH of 2 to 4.3, especially at pH 2, and decreases to 0.38 mg L-1 min(-1) with the increase of pH from 2 to 5.65. A similar effect is observed in basic media, where a higher degradation rate is found at pH = 10.3. The degradation rate increases in the presence of TiO2 compared to the discharge without photocatalysis. The results show that the degradation of the dye increases in the presence of TiO2 until the catalyst load reaches 0.5 g L-1 after which the suppression of AB25 degradation is observed. The results indicate that the tested advanced oxidation processes are very effective for the degradation of AB25 in aqueous solutions

Comparative genomics of Burkholderia multivorans, a ubiquitous pathogen with a highly conserved genomic structure

The natural environment serves as a reservoir of opportunistic pathogens. A well-established method for studying the epidemiology of such opportunists is multilocus sequence typing, which in many cases has defined strains predisposed to causing infection. Burkholderia multivorans is an important pathogen in people with cystic fibrosis (CF) and its epidemiology suggests that strains are acquired from non-human sources such as the natural environment. This raises the central question of whether the isolation source (CF or environment) or the multilocus sequence type (ST) of B. multivorans better predicts their genomic content and functionality. We identified four pairs of B. multivorans isolates, representing distinct STs and consisting of one CF and one environmental isolate each. All genomes were sequenced using the PacBio SMRT sequencing technology, which resulted in eight high-quality B. multivorans genome assemblies. The present study demonstrated that the genomic structure of the examined B. multivorans STs is highly conserved and that the B. multivorans genomic lineages are defined by their ST. Orthologous protein families were not uniformly distributed among chromosomes, with core orthologs being enriched on the primary chromosome and ST-specific orthologs being enriched on the second and third chromosome. The ST-specific orthologs were enriched in genes involved in defense mechanisms and secondary metabolism, corroborating the strain-specificity of these virulence characteristics. Finally, the same B. multivorans genomic lineages occur in both CF and environmental samples and on different continents, demonstrating their ubiquity and evolutionary persistence

Infection by Ralstonia Species in Cystic Fibrosis Patients: Identification of R. pickettii and R. mannitolilytica by Polymerase Chain Reaction

The frequency of respiratory tract infections caused by Ralstonia species in persons with cystic fibrosis (CF) and the role of these species in CF pulmonary disease are not well documented. In part, this lack of documentation may be attributed to the difficulty in accurately identifying Ralstonia species; R. mannitolilytica and R. pickettii in particular may be misidentified as other closely related species, particularly those of the Burkholderia cepacia complex. We used polyphasic analyses to identify 42 Ralstonia isolates from sputum cultures from 38 CF patients. Several isolates that could not be identified to the species level may belong to novel Ralstonia species. We demonstrated chronic colonization by using genotyping of serial isolates recovered from the same patient. To facilitate identification of R. mannitolilytica and R. pickettii, we developed 16S ribosomal DNA-based polymerase chain reaction assays that allow sensitive and specific identification of these species

Phylogenetic surveillance of viral genetic diversity and the evolving molecular epidemiology of human immunodeficiency virus type 1

With ongoing generation of viral genetic diversity and increasing levels of migration, the global human immunodeficiency virus type 1 (HIV-1) epidemic is becoming increasingly heterogeneous. In this study, we investigate the epidemiological characteristics of 5,675 HIV-1 pol gene sequences sampled from distinct infections in the United Kingdom. These sequences were phylogenetically analyzed in conjunction with 976 complete-genome and 3,201 pol gene reference sequences sampled globally and representing the broad range of HIV-1 genetic diversity, allowing us to estimate the probable geographic origins of the various strains present in the United Kingdom. A statistical analysis of phylogenetic clustering in this data set identified several independent transmission chains within the United Kingdom involving recently introduced strains and indicated that strains more commonly associated with infections acquired heterosexually in East Africa are spreading among men who have sex with men. Coalescent approaches were also used and indicated that the transmission chains that we identify originated in the late 1980s to early 1990s. Similar changes in the epidemiological structuring of HIV epidemics are likely to be taking in place in other industrialized nations with large immigrant populations. The framework implemented here takes advantage of the vast amount of routinely generated HIV-1 sequence data and can provide epidemiological insights not readily obtainable through standard surveillance methods

Linguistics

Contains reports on four research projects.National Institutes of Health (Grant MH-13390-01U. S. Air Force (Electronic Systems Division) under Contract AF 19(628)-248

The domestication of the probiotic bacterium Lactobacillus acidophilus

Lactobacillus acidophilus is a Gram-positive lactic acid bacterium that has had widespread historical use in the dairy industry and more recently as a probiotic. Although L. acidophilus has been designated as safe for human consumption, increasing commercial regulation and clinical demands for probiotic validation has resulted in a need to understand its genetic diversity. By drawing on large, well-characterised collections of lactic acid bacteria, we examined L. acidophilus isolates spanning 92 years and including multiple strains in current commercial use. Analysis of the whole genome sequence data set (34 isolate genomes) demonstrated L. acidophilus was a low diversity, monophyletic species with commercial isolates essentially identical at the sequence level. Our results indicate that commercial use has domesticated L. acidophilus with genetically stable, invariant strains being consumed globally by the human population

Linguistics

Contains reports on four research projects.U. S. Air Force (Electronics Systems Division) under Contract AF 19(628)-2487Joint Services Electronics Programs (U.S. Army, U.S. Navy, and U.S. Air Force) under Contract DA 28-043-AMC-02536(E)National Science Foundation (Grant GK-835)National Institutes of Health (Grant 2 PO1 MH-04737-06)National Aeronautics and Space Administration (Grant NsG-496

Sexually transmitted infections, their treatment and urban change in colonial Leopoldville, 1910–1960

During the colonial period sexually transmitted infections (STIs) came to be recognised as a major public health problem in African cities. Thus, STI control and urban modernisation became deeply entangled as authorities redrew spatial and social boundaries to manage populations and their cross-cultural interaction. Public health measures, urban planning and policing were part of a coordinated effort to neutralise the potential impact of rapidly growing African urban migration on the Belgian Congo’s ‘model’ capital Leopoldville. While STI control was facilitated by new drugs (arsenicals, sulfonamides and antibiotics) to treat syphilis, chancroid, gonorrhoea and chlamydia (bacterial STIs), the effects of the 1929 economic crisis and urban social change illustrated the limits of colonial authority. Redesigning urban spaces and repressive measures to curb polygyny and prostitution operated in a parallel fashion with the expansion of health coverage, new treatments and awareness campaigns. To gain a better understanding of the evolution of STI incidence among African urban populations during the colonial period between 1910 and 1960, extensive archival records and secondary literature were consulted to assess the interplay between improved screening, diagnostic and therapeutic methods with demographic and social change. They show that STI rates, probably peaked during the pre-1929 period and apart from a short period in the early 1930s associated with mass screening, declined until becoming residual in the 1950s. Reflecting upon sanitary interventions and their broader dimensions, the article analyses the evolution of treatment regimes and their impact in the changing urban organisation and environment of the colony’s capital.publishersversionpublishe

Analytical expressions for the conductance noise measured with four circular contacts placed in a square array

In the ideal case, noise measurements with four contacts minimize the contribution of the contact interface. There is a need to characterize conductance noise and noise correction factors for the different geometries provided with four contacts, as already is the case for resistivity measurements with van der Pauw structures. Here, we calculate the noise correction factors for two geometries with a pair of sensors and a pair of current driver electrodes placed in a square array. The first geometry investigated is a very large film compared to the distance L between four circular electrodes, which are placed in a square array far away from the borders of the film. The second is a square-shaped conductive film with side length L and provided with four quarter-circle corner contacts with radius l. The effect of the conductance noise in the film can be observed between current free sensors in a four-point measurement or between current carrying drivers in a two-point measurement. Our analytical expressions are based on approximations to solve the integrals (J·)2dA and |J|4dA for the voltage noise measured across a pair of sensors, SVQ, and across the drivers, SVD, respectively. The first and second integrands represent the squared dot product of the current density and adjoint current density and the modulus of the current density to the fourth power, respectively. The current density J in the samples is due to the current I passing through the driver contacts. The calculated expressions are applicable to samples with thickness tl0.1L. Hence, the disturbances in the neighborhood of the sensors on J and of the drivers on are ignored. Noise correction factors for two- and four-point measurements are calculated for sensors on an equipotential (transversal noise) with the driver contacts on the diagonal of a square and for sensors next to each other on one side of the square with the drivers next to each other on the other side of the square (longitudinal noise). In all cases the noise between the sensors is smaller and less sensitive to the contact size 2l/L than the noise between the drivers. The ratio SVQ/SVD becomes smaller with smaller contact radius l. Smaller sensors give a better suppression of interface noise at the contacts. But overly low 2l/L values result in overly high resistance between the sensors and too strong a contribution of thermal noise at the sensors. Therefore, equations are derived to calculate the current level needed to observe 1/f conductance fluctuations on top of the thermal noise. The results from the calculated analytical expressions show good agreement with experimental results obtained from the noise in carbon sheet resistance and numerical results. Transversal noise measurements on a square sample with corner contacts are recommended to characterize the 1/f noise of the layer. This is due to the increased current densities in the sample compared to the open structure, which result in easier detection of the 1/f on top of the thermal noise. ©2007 American Institute of Physic