Methods and processes for development of a CONSORT extension for reporting pilot randomized controlled trials

Peer reviewed

Molecular diversity, cultivation, and improved detection by fluorescent in situ hybridization of a dominant group of human gut bacteria related to Roseburia spp. or Eubacterium rectale

Peer reviewed

Molecular diversity, cultivation, and improved detection by fluorescent in situ hybridization of a dominant group of human gut bacteria related to Roseburia spp. or Eubacterium rectale

Peer reviewed

On the autonomous norm on the group of Hamiltonian diffeomorphisms of the torus

27 pages, 6 figures

Bernice E. Cullinan with a group of children reading around a table

Inscription: Verso: Bernice E. Cullinan, president, International Reading Association, surrounded by children reading magazines, New York.

Group of jr. high school students

Inscriptions: Verso: [stamped] Credit must be given to Freda Leinwand from Monkmeyer Press Photo Service.

Molecular epidemiology of sexually transmitted human papillomavirus in a self referred group of women in Ireland

Background: Human papillomavirus (HPV) causes cervical cancer and external genital warts. The purpose of this study is to document the genotype distribution of HPV in females aged between 18 and 34 who self-referred to an STI clinic with visible external genital warts (EGW). Scrapings were taken from visible external genital warts (EGW). These scrapings were analysed by PCR for the presence of HPV DNA. Positive samples were then genotyped by means of a commercially available assay (LiPA). A comparison of genotyping results determined by the LiPA assay and direct amplicon DNA sequencing was also performed. Results: Ninety-two patients out of 105 samples (88%) had detectable levels of HPV DNA. The majority of individuals with EGW (66%) showed the presence of two or more genotypes. The most common HPV genotypes present in the study population were HPV-6, HPV-11, HPV-16, HPV-18, HPV-33 and HPV-53. Potential effects of vaccination on HPV molecular epidemiology indicate that 40% of the patients could have been protected from the high risk genotypes HPV-16 and HPV-18.Conclusion: This is the first report of the molecular epidemiology of external genital warts in women aged between 18 and 34 from Ireland based on results from a LiPA assay. The study shows that most individuals are infected with multiple genotypes including those with high oncogenic potential and that the newly available HPV vaccines could have a significant impact on prevalence of the most common HPV genotypes in this study population.

Paleoecology, Diagenesis and Biological Affinity of Tetradiids in the Upper Ordovician (Sandbian) Black River Group of the Kingston Area, Ontario, Canada

Tetradiids are a group of colonial, tubular fossils that occur globally in Middle to Upper Ordovician strata. Tetradiids were first described as a type of tabulate coral; however, based on their four-fold symmetry, division, and presence of a central-sparry canal, they were recently reinterpreted as a florideophyte rhodophyte algae, a reinterpretation that is tested in this thesis. This study focused on understanding the affinity and taphonomy of this order of fossil. Research was conducted by stratigraphic and petrographic analyses of the Black River Group in the Kingston, Ontario region. Tetradiid occurrences were divided into fragment or colonial, with three morphologies of tetradiids described (Tetradium, Phytopsis and Paratetradium). Morphology is specific to depositional environment, with compact Tetradium consistently within ooid grainstones and open branching Phytopsis and chained Paratetradium consistently within mudstones. Two types of patch reefs were recognized: a Paratetradium bioherm, and a Paratetradium, Phytopsis, stromatolite bioherm. The presence of bioherms implies that tetradiids were capable of hypercalcifying. Preservation styles of tetradiids were investigated, and were compared to brachiopods, echinoderms, mollusks, and ooids. Tetradiids were preferentially preserved as molds and demonstrated complete dissolution of skeletal material. Rare specimens, however, demonstrated preserved horizontal partitions, central plates, and a double wall. Skeletal molds were filled with either calcite spar, mud or encrusted by a cryptomicrobial colony. Both calcitic and aragonitic ooids were discovered. The co-occurrence of aragonitic ooids, aragonitic crytodontids, and the evolution of aragonitic, hypercalcifying tetradiids is interpreted as representing the geochemical favoring of aragonite and HMC in a time of global calcite seas. The geochemical favoring of aragonite is interpreted to be independent to global Mg: Ca ratios, but was the result of increased saturation levels and temperature driven by high atmospheric pCO2. Based on the presence of epitheca, tabulae, septa, and the commonality of growth forms, tetradiids are interpreted as an order of Cnidaria. The evolution of an aragonitic skeleton in tetradiids is interpreted to be the result of de novo acquisition of a skeleton from an unmineralized clade.

Calculation of electric field strengths at a sharp edge

Sharp edges were first used for field ionisation mass spectrometry by Beckey. Although Cross and Robertson found that etched metal foils were more effective than razor blades for field ionisation, blades are very convenient for determination of field ionisation mass spectra, as reported by Robertson and Viney. The electric field at the vertex of a sharp edge can be calculated by the method of the conformal transformation. Here we give some equations for the field deduced with the assumption that the edge surface can be approximated by a hyperbola. We also compare two hyperbolae with radii of curvature at the vertex of 500 Angstrom and 1000 Angstrom with the profile of a commercial carbon-steel razor blade.

Molecular characterization of human T cell leukemia virus type 1 subtypes in a group of infected individuals diagnosed in Portugal and Spain

Over the past decade, Portugal and Spain received large numbers of immigrants from HTLV-1 endemic areas. Our aim was to investigate the diversity of subtypes circulating in these two countries and the introduction of new variants. We performed a molecular analysis of HTLV-1 strains in patients diagnosed since 1998. LTR and env proviral sequences from 26 individuals were analyzed to generate phylogenetic trees along with reference HTLV-1 subtypes from several geographic origins. Epidemiological and clinical data were recorded. Most subjects were immigrants (57.7%) from South America and Africa. All isolates belonged to the cosmopolitan A subtype. Most carried the transcontinental subgroup A, but five subjects carried subgroup D and one carried subgroup C, previously unreported in Europe. HTLV strains showed separate clusters linked to the patients' geographic origin. Although subjects with HTLV-1 infection tend not to be engaged in high-risk practices, silent dissemination of a broad diversity of HTLV-1 viruses may still occur.

Observations of turbulence within the surf and swash zone of a field-scale sandy laboratory beach

Current coastal-evolution models generally lack the ability to accurately predict bed level change in shallow (<~2 m) water, which is, at least partly, due to the preclusion of the effect of surface-induced turbulence on sand suspension and transport. As a first step to remedy this situation, we investigated the vertical structure of turbulence in the surf and swash zone using measurements collected under random shoaling and plunging waves on a steep (initially 1:15) field-scale sandy laboratory beach. Seaward of the swash zone, turbulence was measured with a vertical array of three Acoustic Doppler Velocimeters (ADVs), while in the swash zone two vertically spaced acoustic doppler velocimeter profilers (Vectrino profilers) were applied. The vertical turbulence structure evolves from bottom-dominated to approximately vertically uniform with an increase in the fraction of breaking waves to ~ 50%. In the swash zone, the turbulence is predominantly bottom-induced during the backwash and shows a homogeneous turbulence profile during uprush. We further find that the instantaneous turbulence kinetic energy is phase-coupled with the short-wave orbital motion under the plunging breakers, with higher levels shortly after the reversal from offshore to onshore motion (i.e. wavefront).