Genotypic Resistance Tests Sequences Reveal the Role of Marginalized Populations in HIV-1 Transmission in Switzerland.

Targeting hard-to-reach/marginalized populations is essential for preventing HIV-transmission. A unique opportunity to identify such populations in Switzerland is provided by a database of all genotypic-resistance-tests from Switzerland, including both sequences from the Swiss HIV Cohort Study (SHCS) and non-cohort sequences. A phylogenetic tree was built using 11,127 SHCS and 2,875 Swiss non-SHCS sequences. Demographics were imputed for non-SHCS patients using a phylogenetic proximity approach. Factors associated with non-cohort outbreaks were determined using logistic regression. Non-B subtype (univariable odds-ratio (OR): 1.9; 95% confidence interval (CI): 1.8-2.1), female gender (OR: 1.6; 95% CI: 1.4-1.7), black ethnicity (OR: 1.9; 95% CI: 1.7-2.1) and heterosexual transmission group (OR:1.8; 95% CI: 1.6-2.0), were all associated with underrepresentation in the SHCS. We found 344 purely non-SHCS transmission clusters, however, these outbreaks were small (median 2, maximum 7 patients) with a strong overlap with the SHCS'. 65% of non-SHCS sequences were part of clusters composed of >= 50% SHCS sequences. Our data suggests that marginalized-populations are underrepresented in the SHCS. However, the limited size of outbreaks among non-SHCS patients in-care implies that no major HIV outbreak in Switzerland was missed by the SHCS surveillance. This study demonstrates the potential of sequence data to assess and extend the scope of infectious-disease surveillance.

(Figure 1) Silicoflagellates at DSDP Hole 69-504

Diverse and abundant late Miocene to Pleistocene silicoflagellates at DSDP Site 504 can be correlated by tropical biostratigraphic zones and relative paleotemperature values to eastern tropical Pacific reference site DSDP 503A farther to the west. Early Pliocene assemblages, which were poorly known until now, are present and can be correlated locally between DSDP Holes 504, 503A, and 495, using species events associated with the new Dictyocha pulchella Subzone and Dictyocha angulata Subzone. Silicoflagellate relative paleotemperature values show major warming at 4.7 to 5.0 Ma (Cores 45-48), 3.4 to 3.8 Ma (Cores 32-33), 1.5 to 1.7 Ma (Cores 12-16), and 0.5 to 0.8 Ma (Cores 3-6). Major coolings occurred at 5.0 to 5.1 Ma (Core 51), 3.9 to 4.4 Ma (Cores 38-44), and 1.0 to 1.3 Ma (Cores 8-10). The appearance of Dictyocha longa is proposed to replace the asperoid/fibuloid ratio reversal as the bottom of the Dictyocha fibula Zone, because the non-evolutionary ratio reverses several times in the upper Miocene of Hole 503A, and at least once in Hole 504. Three new Pliocene silicoflagellates are defined: Dictyocha concinna Bukry, n. sp., D. helix Bukry, n. sp., and D. tamarae Bukry, n. sp.

Sedimentology and age determinations on core PS2813-1

Die Rekonstruktion des Einflusses von Strömungen und glazialmarinen Prozessen auf das Sedimentationsgeschehen am Kontinentalhang der Antarktischen Halbinsel im westlichen Weddellmeer basiert auf sedimentologischen und geophysikalischen Daten eines Kolbenlotkerns. Der Sedimentkern wurde während des Fahrtabschnitts ANT-XIV/3 mit dem FS "Polarstern" aus einer mächtigen Levee-Struktur eines Rinnen-Rückensystems gewonnen. Es wurden sedimentologische sowie sedimentphysikalische Untersuchungen an dem Kernmaterial durchgeführt. Die texturellen Änderungen im Kern und die Variationen der gemessenen Parameter ermöglichen eine lithofazielle Gliederung und stratigraphische Einstufung der Sedimentabfolge. Die untersuchten Sedimente umfassen den Zeitraum der vier letzten Klimazyklen bis heute und repräsentieren die Ablagerungsbedingungen von mehr als 340 000 Jahren. Vier Faziestypen wurden unterschieden, die sowohl glaziale als auch interglaziale Ablagerungsräume charakterisieren. (1) Die überwiegend groblaminierten Sedimentabfolgen wurden der Laminitfazies zugeordnet. Unter glazialen Umweltbedingungen kam es infolge schwacher Bodenströmungen zur Ablagerung feinkörniger, laminierter, strömungsbetonter Sedimente. (2) Strukturlose, sehr homogene Sedimentabfolgen des Kems beschreiben einen weiteren, den Kaltzeiten zugeordneten, Faziestyp, der durch geringe Variationen in den Sedimenteigenschaften charakterisiert ist. (3) Kernabschnitte, die weitgehend strukturlos sind bzw. leichte Bioturbationen und relativ viel eistransportiertes Material aufweisen, wurden als IRD-Fazies bezeichnet. Sie repräsentiert den Übergang vom Glazial zum Interglazial, in dem sich das Schelfeis und die Meereisbeckung zurückzogen. In den Sedimenten kam es infolge der gesteigerten Kalbungsrate zur Anreicherung der Eisfracht. (4) Die relativ biogenreichen, hellen Ablagerungen wurden der interglazialzeitlichen Karbonatfazies zugeteilt. Der signifikant erhöhte Anteil planktischer Foraminiferen weist auf eine gesteigerte Bioproduktivität im Oberflächenwasser hin, die aus verstärkten jahreszeitlichen Schwankungen der Meereisbedeckung resultiert. Die betrachteten Sedimentationsprozesse, wie biologische Produktivität, Umlagerungsprozesse durch Meeresströmungen, gravitativer Sedimenttransport und Eistransport, sind das Abbild komplexer Wechselwirkungen aus Meeresspiegelschwankungen, Änderungen ozeanographischer Bedingungen und der Vereisungsdynamik. Das Sedimentationsgeschehen im Untersuchungsgebiet wurde folglich durch die Variationen der vorherrschenden Umweltbedingungen bestimmt. Im Glazial kam es unter einer geschlossenen Meereisbedeckung zur Ablagerung feinkörniger, geschichteter Sedimente. Vorwiegend Turbiditströmungen kontrollierten das Sedimentationsgeschehen innerhalb des betrachteten Rinnen-Rückensystems. Unter dem Einfluß der Coriolis-Kraft und wahrscheinlich einer Konturströmung wurden die suspendierten, feinkörnigen Partikel aus dem zentralen Bereich der Rinne verdriftet und über dem nördlichen Uferwall abgelagert. Höherenergetische gravitative Prozesse beeinflußten das Sedimentationsgeschehen episodisch und sind durch gut sortierte Ablagerungen mit erhöhten Gehalten im Mittel- bis Grobsiltbereich dokumentiert. Höhere Sedimentationsraten in den Glazialen trugen verstärkt zur Bildung des Uferwalls bei. Die Ablagerungen der ebenfalls glazialzeitlichen homogenen Fazies belegen unterschiedliche Ablagerungsbedingungen und eine Verschiebung der dominierenden Prozesse. Während des Übergangs vom Glazial zum Interglazial nahm die Bodenwasserbildungsrate durch das Aufschwimmen des Schelfeises zu, wodurch die Strömungsintensität gesteigert wurde. Eine verstärkte Eisbergaktivität wird durch die Anreichung des IRD-Materials dokumentiert. Während interglazialer Zeiten ermöglichten offen-marine Bedingungen im Südsommer eine leicht erhöhte biologische Produktivität, so daß der Ablagerungsraum durch die Sedimentation biogener Komponenten verstärkt beeinflußt wurde.

(Tables 1-2) Composition of red coloured tills from Schobuell, Schleswig-Holstein and Møn Island, Denmark

The stratigraphic position of the glacially transported 'Scholle' (large-size erratic block) at Schobüll near Husum (Schleswig-Holstein) is now considered to be Devonian rather than 'Rotliegendes'. The 'Scholle', consisting of red clay and dolomite, is overlain by red-colored till without any flint but with up to 90% carbonate clasts (containing 15% dolomite), which indicates an eastern Baltic origin. The relationship of the 'Scholle' with the glacial till also points to an eastern Baltic origin for it, with up to 1 000 km transport distance.

(Table 1) Minor and trace element concentrations in interstitial waters from ODP Leg 166 sites

Concentrations of minor and trace elements (Li, Rb, Sr, Ba, Fe, and Mn) in interstitial water (IW) were found in samples collected during Ocean Drilling Program (ODP) Leg 166 from Sites 1005, 1006, and 1007 on the western flank of the Great Bahama Bank (GBB). Concentrations of Li range from near-seawater values immediately below the sediment/water interface to a maximum of 250 µM deep in Site 1007. Concentrations determined during shore-based studies are substantially lower than the shipboard data presented in the Leg 166 Initial Reports volume (range of 28-439 µM) because of broad-band interferences from high dissolved Sr concentrations in the shipboard analyses. Rubidium concentrations of 1.3-1.7 µM were measured in IW from Site 1006 when salinity was less than 40 psu. A maximum of 2.5 µM is reached downhole at a salinity of 50 psu. Shipboard and shore-based concentrations of Sr2+ are in excellent agreement and vary from 0.15 mM near the sediment water interface to 6.8 mM at depth. The latter represent the highest dissolved Sr2+ concentrations observed to date in sediments cored during the Deep Sea Drilling Project (DSDP) or ODP. Concentrations of Ba2+ span three orders of magnitude (0.1-227µM). Concentrations of Fe (<0.1-14 µM) and Mn (0.1-2 µM) exhibit substantially greater fluctuations than other constituents. The concentrations of minor and trace metals in pore fluids from the GBB transect sites are mediated principally by changes in pore-water properties resulting from early diagenesis of carbonates associated with microbial degradation of organic matter, and by the abundance of detrital materials that serve as a source of these elements. Downcore variations in the abundance of detrital matter reflect differences in carbonate production during various sea-level stands and are more evident at the more proximal Site 1005 than at the more pelagic Site 1006. The more continuous delivery of detrital matter deep in Site 1007 and throughout all of Site 1006 is reflected in a greater propensity to provide trace elements to solution. Concentrations of dissolved Li+ derive principally from (1) release during dissolution of biogenic carbonates and subsequent exclusion during recrystallization and (2) release from partial dissolution of Li-bearing detrital phases, especially ion-exchange reactions with clay minerals. A third but potentially less important source of Li+ is a high-salinity brine hypothesized to exist in Jurassic age (unsampled) sediments underlying those sampled during Leg 166. The source of dissolved Sr2+ is almost exclusively biogenic carbonate, particularly aragonite. Concentrations of dissolved Sr2+ and Ba2+ are mediated by the solubility of their sulfates. Barite and detrital minerals appear to be the more important source of dissolved Ba2+. Concentrations of Fe and Mn2+ in anoxic pore fluids are mediated by the relative insolubility of pyrite and incorporation into diagenetic carbonates. The principal sources of these elements are easily reduced Fe-Mn-rich phases including Fe-rich clays found in lateritic soils and aoelian dust.

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v. 1-7, Handelingen van het ... Congres van het Algemeen syndicaat van suikerfabrikanten op Java.

Rearrangement of 2-quinolyl- and 1-isoquinolylcarbenes to naphthylnitrenes

2-Quinolylcarbene 23 and 1-isoquinolylcarbene 33 are generated by flash vacuum thermolysis (FVT) of the corresponding triazolo[1,5-a]quinoline and triazolo[5,1-a]isoquinoline 19 and 29, as well as 2-(5-tetrazolyl)quinoline and 1-(5-tetrazolyl)isoquinoline 20 and 30, respectively. These carbenes rearrange to 1- and 2-naphthylnitrene 21 and 31, respectively, and the nitrenes are also generated by FVT of 1- and 2-naphthyl azides 18 and 28. The products of FVT of both the nitrene and carbene precursors are the 2- and 3-cyanoindenes 26 and 27 together with the nitrene dimers, viz. azonaphthalenes 25 and 35, and the H-abstraction products, aminonaphthalenes 24 and 34. All the azide, triazole, and tetrazole precursors yield 3-cyanoindene 26 as the principal ring contraction product under conditions of low FVT temperature (340-400 degreesC) and high pressure (1 Torr N-2 as carrier gas for the purpose of collisional deactivation). This ring contraction reaction is strongly subject to chemical activation, which caused extensive isomerization of 3-cyanoindene to 2-cyanoindene under conditions of low pressure (10(-3) Torr). 2-Cyanoindene is calculated to be ca. 1.7 kcal/mol below 3-cyanoindene in energy; accordingly, high-temperature FVT of these cyanoindenes always gives mixtures of the two compounds with the 2-cyano isomer dominating. Photolysis of trizolo[1,5-a]quinoline 19 and triazolo[5,1-a]isoquinoline 29 in Ar matrixes causes partial ring opening to the corresponding 2-diazomethylquinoline 19' and 1-diazomethylisoquinoline 29'. The photolysis of the former gives rise to a small amount of the cyclic ketenimine 22, the intermediate connecting 2-quinolylcarbene and 1-naphthylnitrene.

Crystal structure of P450cin in a complex with its substrate, 1,8-cineole, a close structural homologue to D-camphor, the substrate for P450cam

Cytochrome P450cin catalyzes the monooxygenation of 1,8-cineole, which is structurally very similar to D-camphor, the substrate for the most thoroughly investigated cytochrome P450, cytochrome P450cam. Both 1,8-cineole and D-camphor are C-10 monoterpenes containing a single oxygen atom with very similar molecular volumes. The cytochrome P450cin-substrate complex crystal structure has been solved to 1.7 Angstrom resolution and compared with that of cytochrome P450cam. Despite the similarity in substrates, the active site of cytochrome P450cin is substantially different from that of cytochrome P450cam in that the B' helix, essential for substrate binding in many cytochrome P450s including cytochrome P450cam, is replaced by an ordered loop that results in substantial changes in active site topography. In addition, cytochrome P450cin does not have the conserved threonine, Thr252 in cytochrome P450cam, which is generally considered as an integral part of the proton shuttle machinery required for oxygen activation. Instead, the analogous residue in cytochrome P450cin is Asn242, which provides the only direct protein H-bonding interaction with the substrate. Cytochrome P450cin uses a flavodoxin-like redox partner to reduce the heme iron rather than the more traditional ferredoxin-like Fe2S2 redox partner used by cytochrome P450cam and many other bacterial P450s. It thus might be expected that the redox partner docking site of cytochrome P450cin would resemble that of cytochrome P450BM3, which also uses a flavodoxin-like redox partner. Nevertheless, the putative docking site topography more closely resembles cytochrome P450cam than cytochrome P450BM3.

Contribution of the collagen I alpha 1 and vitamin D receptor genes to the risk of hip fracture in elderly women

Context and Objective: Hip fracture is partially genetically determined. The present study was designed to examine the contributions of vitamin D receptor (VDR) and collagen I alpha 1 (COLIA1) genotypes to the liability to hip fracture in postmenopausal women. Design: The study was designed as a prospective population-based cohort investigation. Subjects: Six hundred seventy-seven postmenopausal women of Caucasian background, aged 70 +/- 7 yr (mean +/- SD), have been followed for up to 14 yr. Sixty-nine women had sustained a hip fracture during the period. Main Outcome: Atraumatic hip fractures were prospectively identified through radiologists' reports. Bone mineral density (BMD) at the hip and lumbar spine was measured by dual-energy x-ray absorptiometry. Genotypes: The TaqI and SpI COLIA1 polymorphisms of the VDR and COLIA1 genes were determined. Using the Single Nucleotide Polymorphism database, VDR TT, Tt, and tt genotypes were coded as TT, TC, and CC, whereas COLIA1 SS, Ss, and ss were coded as GG, GT, and TT. Results: Women with VDR CC genotype (16% prevalence) and COLIA1 TT genotype (5% prevalence) had an increased risk of hip fracture [odds ratio (OR) associated with CC, 2.6; 95% confidence interval (CI), 1.2-5.3; OR associated with TT, 3.8; 95% CI, 1.3-10.8] after adjustment for femoral neck BMD (OR, 3.4 per SD; 95% CI, 2.3-5.0) and age (OR, 1.4 per 5 yr; 95% CI, 1.1-1.7). Approximately 20 and 12% of the liability to hip fracture was attributable to the presence of the CC genotype and TT genotype, respectively. Conclusion: The VDR CC genotype and COLIA1 TT genotype were associated with increased hip fracture risk in Caucasian women, and this association was independent of BMD and age.

Development of an electrically tuneable Bragg grating filter in polymer optical fibre operating at 1.55 µm

We present a thorough study on the development of a polymer optical fibre-based tuneable filter utilizing an intra-core Bragg grating that is electrically tuneable, operating at 1.55 µm. The Bragg grating is made tuneable using a thin-film resistive heater deposited on the surface of the fibre. The polymer fibre was coated via the photochemical deposition of a Pd/Cu metallic layer with the procedure induced by VUV radiation at room temperature. The resulting device, when wavelength tuned via Joule heating, underwent a wavelength shift of 2 nm for a moderate input power of 160 mW, a wavelength to input power coefficient of -13.4 pm mW-1 and time constant of 1.7 s-1. A basic theoretical study verified that for this fibre type one can treat the device as a one-dimensional system. The model was extended to include the effect of input electrical power changes on the refractive index of the fibre and subsequently to changes in the Bragg wavelength of the grating, showing excellent agreement with the experimental measurements.