Characterization of Rotavirus Strains Detected in Windhoek, Namibia during 1998-1999

Background. Namibia, located on the southwestern coast of southern Africa, is characterized by vast deserts, limited fresh water, and low population density. Mortality estimates among children <5 of age are 63 deaths per 1000 live-births, with diarrheal diseases contributing to 3% of these deaths. Data on the burden of rotavirus disease and circulating serotypes in Namibia are currently not available. Materials and methods. From May 1998 through December 1999, 815 stool specimens were collected from children <5 years of age who attended the Windhoek State Hospital, Windhoek, Namibia, for diarrhea. Specimens were screened for the presence of rotavirus antigens. Rotavirus-positive specimens were further analyzed to determine electropherotype, subgroup (SG) specificity, and G and P genotypes. Results. Rotavirus was detected in 113 (13.8%) of 815 specimens, with the majority of infections occurring in children <18 months of age. Strains bearing 1 long electropherotype, SGII, and G1P[8] or G1P[6] specificity predominated during the 20-month study period. In addition to the typical winter rotavirus season, a peak in rotavirus infection was also observed during the summer. Conclusions. Serotypes G1P[8], G1P[6], G1P[4], and G2P[4] were found throughout the study period, predominantly in children <18 months of age. The observed summer rotavirus peak coincided with increased rainfall in Namibia and an increase in the diversity of detected serotypes. During the October to December 1999 peak, 2 G9P[6] strains and 1 G8P[4] strain were identified. Expanded and updated information on prevalence of rotavirus infection, circulating serotypes, and burden of disease will be required to enable local government to make decisions on the implementation of rotavirus vaccination in Namibi

Rotavirus genetic diversity, disease association, and temporal change in hospitalized rural Kenyan children

Background. The effectiveness of rotavirus vaccines will be dependent on the immunity conferred against prevalent and emergent variants causing severe diarrheal disease. Longitudinal surveillance of disease-causing strains is a prerequisite to intervention. Methods. Molecular characterization was conducted on rotavirus-positive stool samples from children admitted with diarrhea to a rural district hospital during 2002-2004. Extracted viral RNA was separated by polyacrylamide gel electrophoresis, and rotavirus VP4 (P types) and VP7 (G types) specificities were determined. Results. Among 558 investigated cases, the predominant genotype was P[8]G1 (42%), followed by P[8]G9 (15%), P[4]G8 (7%), P[6]G8 (6%), and P[8]G8 (4%), with 10% mixed strains. Overall, there were 6 different P types and 7 G types. No association was identified between genotype and child age, sex, or severity of diarrhea. The P and G genotypes and polyacrylamide gel electropherotypes showed significant temporal variation in frequency: P[8]G1 decreased from 51% (95% confidence interval [CI], 43%-58%) in 2002 to 30% (95% CI, 24%-37%) in 2004, and P[4]G8 increased from 2% (95% CI, 0%-5%) in 2002 to 13% (95% CI, 9%-19%). Quarterly data revealed seasonally endemic and emergence and/or decay patterns. Conclusions. Our study of rotavirus strains causing severe diarrhea in rural Kenyan children showed a predominance of P[8]G1 and confirms the importance of G8 and G9 strains in sub-Saharan Africa. Considerable genetic diversity of rotavirus strains was observed, including substantial mixed and unusual types, coupled with significant temporal strain variation and emergence. These results warn of variable vaccine efficacy and the need for long-term surveillance of circulating rotavirus genotypes

Bimodal Phase Diagram of the Superfluid Density in LaAlO3/SrTiO3 Revealed by an Interfacial Waveguide Resonator

We explore the superconducting phase diagram of the two-dimensional electron system at the LaAlO3/SrTiO3 interface by monitoring the frequencies of the cavity modes of a coplanar waveguide resonator fabricated in the interface itself. We determine the phase diagram of the superconducting transition as a function of temperature and electrostatic gating, finding that both the superfluid density and the transition temperature follow a dome shape, but that the two are not monotonically related. The ground state of this 2DES is interpreted as a Josephson junction array, where a transition from long- to short-range order occurs as a function of the electronic doping. The synergy between correlated oxides and superconducting circuits is revealed to be a promising route to investigate these exotic compounds, complementary to standard magneto-transport measurements.Comment: 5 pages, 4 figures and 10 pages of supplementary materia

Adsorption of Xe and Ar on Quasicrystalline Al-Ni-Co

An interaction potential energy between and adsorbate (Xe and Ar) and the 10-fold Al-Ni-Co quasicrystal is computed by summing over all adsorbate-substrate interatomic interactions. The quasicrystal atoms' coordinates are obtained from LEED experiments and the Lennard-Jones parameters of Xe-Al, Xe-Ni and Xe-Co are found using semiempirical combining rules. The resulting potential energy function of position is highly corrugated. Monolayer adsorption of Xe and Ar on the quasicrystal surface is investigated in two cases: 1) in the limit of low coverage (Henry's law regime), and 2) at somewhat larger coverage, when interactions between adatoms are considered through the second virial coefficient, C_{AAS}. A comparison with adsorption on a flat surface indicates that the corrugation enhances the effect on Xe-Xe (Ar-Ar) interactions. The theoretical results for the low coverage adsorption regime are compared to experimental (LEED isobar) data.Comment: 12 pages, 8figure

Chemogenomic Profiling of Antileishmanial Efficacy and Resistance in the Related Kinetoplastid Parasite <i>Trypanosoma brucei</i>

The arsenal of drugs used to treat leishmaniasis, caused by Leishmania spp., is limited and beset by emergent resistance and toxicity. Our understanding of drug mode-of-action and potential routes to resistance is also limited. Forward genetic approaches have revolutionised our understanding of drug mode-of-action in the related kinetoplastid parasite, Trypanosoma brucei. Therefore, we screened our genome-scale T. brucei RNAi library for knockdowns that render cells resistant to the current anti-leishmanial drugs, sodium stibogluconate (antimonial), paromomycin, miltefosine and amphotericin-B. Identification of T. brucei orthologues of the known Leishmania antimonial and miltefosine plasma membrane transporters effectively validated our approach, while a cohort of 42 novel drug efficacy determinants provides new insights and serves as a resource

Cognitive Performance of Wild Eastern Gray Squirrels ( Sciurus carolinensis ) in Rural and Urban, Native, and Non-native Environments

Enhanced cognitive ability has been shown to impart fitness advantages to some species by facilitating establishment in new environments. However, the cause of such enhancement remains enigmatic. Enhanced cognitive ability may be an adaptation occurring during the establishment process in response to new environments or, alternatively, such ‘enhancement’ may merely reflect a species’ characteristic. Based on previous findings that have shown ‘enhanced’ cognitive ability (i.e., higher success rate in solving novel food-extraction problems or, ‘innovation’) in Eastern gray squirrels (Sciurus carolinensis), a successful mammalian invader and urban dweller, we used an intraspecific comparative paradigm to examine the cause of their ‘enhanced’ cognitive ability. We conducted a field study to compare cognitive performance of free-ranging squirrels residing in rural and urban habitats in native (United States) and non-native environments (United Kingdom). By using established tasks, we examined squirrels’ performance in easy and difficult, novel food-extraction problems (innovation), a motor memory recall test of the difficult problem, and a spatial learning task. We found that the four groups of squirrels showed comparable performance in most measures. However, we also found that the native urban squirrels showed: (1) higher success rate on the first visit for the difficult problem than the non-native urban squirrels; (2) some evidence for higher recall latency for the difficult problem after an extended period than the non-native rural squirrels; and (3) learning when encountering the same difficult problem. These results suggest that the previously reported ‘enhanced’ performance is likely to be a general characteristic and thus, a pre-adaptive phenotypic trait that brings fitness advantages to this species in a new environment. Despite this, some cognitive abilities in gray squirrels such as solving novel problems has undergone mild variation during the adaptive process in new environments

Emergence and Characterization of Serotype G9 Rotavirus Strains from Africa

Serotype G9 strains have been detected sporadically and in localized outbreaks in various African countries, including South Africa, Botswana, Malawi, Kenya, Cameroon, Nigeria, Ghana, Guinea-Bissau, Libya, and Mauritius. Serotype G9 strains were analyzed to investigate genogroup characteristics, including subgroup specificity, electropherotype, and P and G genotypes. In addition, the antigenic composition of the South African G9 strains was assessed. African G9 strains were associated with both DS-1-like characteristics and Wa-like characteristics, indicating the predisposition of G9 strains to frequently reassort. Despite these reassortment events, serotype G9 strains appear to maintain antigenic character in the outer capsid protein, as evident with the reaction of the South African G9 strains with the G9-specific monoclonal antibody F45:1. Phylogenetic analysis clustered African G9 strains geographically, regardless of genogroup characteristics, into 1 lineage (IIId). Two groups of G9 strains, originating in India and Japan, were identified in this lineage. Continuous surveillance of circulating rotavirus strains in Africa is vital to prepare for future vaccine implementation on a continent that clearly needs such preventative medicine

Search for polyoma-, herpes-, and bornaviruses in squirrels of the family Sciuridae

Background Squirrels (family Sciuridae) are globally distributed members of the order Rodentia with wildlife occurrence in indigenous and non-indigenous regions (as invasive species) and frequent presence in zoological gardens and other holdings. Multiple species introductions, strong inter-species competition as well as the recent discovery of a novel zoonotic bornavirus resulted in increased research interest on squirrel pathogens. Therefore we aimed to test a variety of squirrel species for representatives of three virus families. Methods Several species of the squirrel subfamilies Sciurinae, Callosciurinae and Xerinae were tested for the presence of polyomaviruses (PyVs; family Polyomaviridae) and herpesviruses (HVs; family Herpesviridae), using generic nested polymerase chain reaction (PCR) with specificity for the PyV VP1 gene and the HV DNA polymerase (DPOL) gene, respectively. Selected animals were tested for the presence of bornaviruses (family Bornaviridae), using both a broad-range orthobornavirus- and a variegated squirrel bornavirus 1 (VSBV-1)-specific reverse transcription-quantitative PCR (RT-qPCR). Results In addition to previously detected bornavirus RNA-positive squirrels no more animals tested positive in this study, but four novel PyVs, four novel betaherpesviruses (BHVs) and six novel gammaherpesviruses (GHVs) were identified. For three PyVs, complete genomes could be amplified with long-distance PCR (LD-PCR). Splice sites of the PyV genomes were predicted in silico for large T antigen, small T antigen, and VP2 coding sequences, and experimentally confirmed in Vero and NIH/3T3 cells. Attempts to extend the HV DPOL sequences in upstream direction resulted in contiguous sequences of around 3.3 kilobase pairs for one BHV and two GHVs. Phylogenetic analysis allocated the novel squirrel PyVs to the genera Alpha- and Betapolyomavirus, the BHVs to the genus Muromegalovirus, and the GHVs to the genera Rhadinovirus and Macavirus. Conclusions This is the first report on molecular identification and sequence characterization of PyVs and HVs and the detection of bornavirus coinfections with PyVs or HVs in two squirrel species. Multiple detection of PyVs and HVs in certain squirrel species exclusively indicate their potential host association to a single squirrel species. The novel PyVs and HVs might serve for a better understanding of virus evolution in invading host species in the future

The Lick AGN Monitoring Project: Reverberation Mapping of Optical Hydrogen and Helium Recombination Lines

We have recently completed a 64-night spectroscopic monitoring campaign at the Lick Observatory 3-m Shane telescope with the aim of measuring the masses of the black holes in 12 nearby (z < 0.05) Seyfert 1 galaxies with expected masses in the range ~10^6-10^7M_sun and also the well-studied nearby active galactic nucleus (AGN) NGC 5548. Nine of the objects in the sample (including NGC 5548) showed optical variability of sufficient strength during the monitoring campaign to allow for a time lag to be measured between the continuum fluctuations and the response to these fluctuations in the broad Hbeta emission, which we have previously reported. We present here the light curves for the Halpha, Hgamma, HeII 4686, and HeI 5876 emission lines and the time lags for the emission-line responses relative to changes in the continuum flux. Combining each emission-line time lag with the measured width of the line in the variable part of the spectrum, we determine a virial mass of the central supermassive black hole from several independent emission lines. We find that the masses are generally consistent within the uncertainties. The time-lag response as a function of velocity across the Balmer line profiles is examined for six of the AGNs. Finally we compare several trends seen in the dataset against the predictions from photoionization calculations as presented by Korista & Goad. We confirm several of their predictions, including an increase in responsivity and a decrease in the mean time lag as the excitation and ionization level for the species increases. Further confirmation of photoionization predictions for broad-line gas behavior will require additional monitoring programs for these AGNs while they are in different luminosity states. [abridged]Comment: 37 pages, 18 figures and 15 tables, accepted for publication in the Astrophysical Journa

Improving the normalization of complex interventions : part 2 - validation of the NoMAD instrument for assessing implementation work based on normalization process theory (NPT)

Funding This study is funded by the Economic and Social Research Council Study [Grant Number RES-062-23-3274] which is gratefully acknowledged. This work was also partially supported by funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 733025, ImpleMentAll project. This content reflects only the author’s view and the European Commission is not responsible for any use that may be made of the information it contains.The Health Services Research Unit, University of Aberdeen, receives core funding from the Chief Scientist Office of the Scottish Government Health Directorates. CRV was funded by a Clinician Scientist award supported by the National Institute for Health Research during this independent research. Availability of data and materials The datasets generated and/or analysed during the current study are deposited on UK Datashare (record 852,387). Further information is available from the corresponding author on reasonable request.Peer reviewedPublisher PD