Linear-in-the-parameters oblique least squares (LOLS) provides more accurate estimates of density-dependent survival

Survival is a fundamental demographic component and the importance of its accurate estimation goes beyond the traditional estimation of life expectancy. The evolutionary stability of isomorphic biphasic life-cycles and the occurrence of its different ploidy phases at uneven abundances are hypothesized to be driven by differences in survival rates between haploids and diploids. We monitored Gracilaria chilensis, a commercially exploited red alga with an isomorphic biphasic life-cycle, having found density-dependent survival with competition and Allee effects. While estimating the linear-in-the-parameters survival function, all model I regression methods (i.e, vertical least squares) provided biased line-fits rendering them inappropriate for studies about ecology, evolution or population management. Hence, we developed an iterative two-step non-linear model II regression (i.e, oblique least squares), which provided improved line-fits and estimates of survival function parameters, while robust to the data aspects that usually turn the regression methods numerically unstable

A survey of UK medical schools' arrangements for early patient contact

Background: Many U.K. medical schools have patient contact in the first two years of the undergraduate course. Aim: To compare the purposes and organization of early patient contact in UK medical schools and to relate these arrangements to the schools' curricular objectives. Methods: A telephone survey of lead educators in UK medicals schools. Categories of contact were plotted against phases of the course to discern patterns of organisation. Results: The quantity of contact varies considerably (four to 65 days). There is a pattern, with learning objectives around the social context of health and illness preceding skills based work and integrated clinical knowledge for practice coming later. Schools fall into three categories: close adherence to the preclinical/clinical split, with limited early contact acting as an introduction to social aspects of health; provision of substantial patient contact to maximize the integration of knowledge and skills; and transitional, with limited clinical goals. General practice provides between one third and one half of early patient contact. Conclusions: Arrangements meet the objectives set by each school and reflect differing educational philosophies. Change is toward more early contact. There appears to be no national guidance which supports a minimum quantity of patient contact or specific educational purpose in the early years of U.K. basic medical training

Geocoding rural addresses in a community contaminated by PFOA: a comparison of methods

BACKGROUND: Location is often an important component of exposure assessment, and positional errors in geocoding may result in exposure misclassification. In rural areas, successful geocoding to a street address is limited by rural route boxes. Communities have assigned physical street addresses to rural route boxes as part of E911 readdressing projects for improved emergency response. Our study compared automated and E911 methods for recovering and geocoding valid street addresses and assessed the impact of positional errors on exposure classification. METHODS: The current study is a secondary analysis of existing data that included 135 addresses self-reported by participants of a rural community study who were exposed via public drinking water to perfluorooctanoate (PFOA) released from a DuPont facility in Parkersburg, West Virginia. We converted pre-E911 to post-E911 addresses using two methods: automated ZP4 address-correction software with the U.S. Postal Service LACS database and E911 data provided by Wood County, West Virginia. Addresses were geocoded using TeleAtlas, an online commercial service, and ArcView with StreetMap Premium North America NAVTEQ 2008 enhanced street dataset. We calculated positional errors using GPS measurements collected at each address and assessed exposure based on geocoded location in relation to public water pipes. RESULTS: The county E911 data converted 89% of the eligible addresses compared to 35% by ZP4 LACS. ArcView/NAVTEQ geocoded more addresses (n = 130) and with smaller median distance between geocodes and GPS coordinates (39 meters) than TeleAtlas (n = 85, 188 meters). Without E911 address conversion, 25% of the geocodes would have been more than 1000 meters from the true location. Positional errors in TeleAtlas geocoding resulted in exposure misclassification of seven addresses whereas ArcView/NAVTEQ methods did not misclassify any addresses. CONCLUSIONS: Although the study was limited by small numbers, our results suggest that the use of county E911 data in rural areas increases the rate of successful geocoding. Furthermore, positional accuracy of rural addresses in the study area appears to vary by geocoding method. In a large epidemiological study investigating the health effects of PFOA-contaminated public drinking water, this could potentially result in exposure misclassification if addresses are incorrectly geocoded to a street segment not serviced by public water

Genetic parameters for faecal egg count, packed-cell volume and body-weight in Santa Inês lambs

Worm infection is one of the main factors responsible for economic losses in sheep breeding in Brazil. Random regression analysis was used to estimate genetic parameters for the factors faecal egg-count (FEC), packed-cell volume (PCV) and body weight (BW) in Santa Inês lambs. Data from 119 female, offspring of nine rams, were collected between December, 2005 and December, 2006, from the experimental flock of Embrapa Tabuleiros Costeiros, the Brazilian Agricultural Research Corporation located in Frei Paulo, SE, Brazil. After weaning, females were drenched until the faecal egg count had dropped to zero. Two natural challenges were undertaken. FEC heritability was extremely variable, this increasing from 0.04 to 0.27 in the first challenge and from 0.01 to 0.52 during the second. PCV heritability peaks were 0.31 and 0.12 in the first and second challenges, respectively. In the second challenge, BW heritability was close to 0.90. The genetic correlations among these traits did not differ from zero. There is the possibility of increasing parasite resistance in Santa Inês by selecting those animals with lower FEC. Selection to increase resistance will not adversely affect lamb-growth, although lambs with a slow growth-rate may be more susceptible to infection

Differentiation of haploid and diploid fertilities in Gracilaria chilensis affect ploidy ratio

Background Algal isomorphic biphasic life cycles alternate between free-living diploid (tetrasporophytes) and haploid (dioicious gametophytes) phases and the hypotheses explaining their maintenance are still debated. Classic models state that conditional differentiation between phases is required for the evolutionary stability of biphasic life cycles while other authors proposed that the uneven ploidy abundances observed in the field are explained by their cytological differences in spore production. Results We monitored the state and fate of individuals of the red seaweed Gracilaria chilensis periodically for 3 years in five intertidal pools from two sites with distinct conditions. We tested for differentiation in fecundity and spore survival among the gametophyte males and females (haploids) and the tetrasporophytes (diploids). We tested for the influence of fecundity and spore survival on the observed uneven ploidy abundances in recruits. The probability of a frond becoming fecund was size-dependent, highest for the haploid males and lowest for the haploid females, with the diploids displaying intermediate probabilities. Fecund diploids released more tetraspores than carpospores released by the haploid females. Spore survival depended on ploidy and on the local density of co-habiting adult fronds. An advantage of diploid over haploid germlings was observed at very low and very high adult fronds densities. Conclusions Neither spore production nor spore survival determined the highly variable ploidy ratio within G. chilensis recruits. This result invalidates the hypothesis of natural cytological differences in spore production as the only driver of uneven field ploidy abundances in this species. Diploid spores (carpospores) survived better than haploid spores (tetraspores), especially in locations and time periods that were associated with the occurrence of strong biotic and abiotic stressors. We hypothesise that carpospore survival is higher due to support by their haploid female progenitors passing-on nutrients and chemical compounds improving survival under stressful conditions.AHE was supported by fellowships SFRH/BPD/63703/2009, SFRH/BPD/ 107878/2015 and UID/Multi/04326/2016 of the National Science Foundation FCT of Portugal.info:eu-repo/semantics/publishedVersio

Spatial heterogeneity of habitat suitability for Rift Valley fever occurrence in Tanzania: an ecological niche modelling approach

Despite the long history of Rift Valley fever (RVF) in Tanzania, extent of its suitable habitat in the country remains unclear. In this study we investigated potential effects of temperature, precipitation, elevation, soil type, livestock density, rainfall pattern, proximity to wild animals, protected areas and forest on the habitat suitability for RVF occurrence in Tanzania. Presence-only records of 193 RVF outbreak locations from 1930 to 2007 together with potential predictor variables were used to model and map the suitable habitats for RVF occurrence using ecological niche modelling. Ground-truthing of the model outputs was conducted by comparing the levels of RVF virus specific antibodies in cattle, sheep and goats sampled from locations in Tanzania that presented different predicted habitat suitability values. Habitat suitability values for RVF occurrence were higher in the northern and central-eastern regions of Tanzania than the rest of the regions in the country. Soil type and precipitation of the wettest quarter contributed equally to habitat suitability (32.4% each), followed by livestock density (25.9%) and rainfall pattern (9.3%). Ground-truthing of model outputs revealed that the odds of an animal being seropositive for RVFV when sampled from areas predicted to be most suitable for RVF occurrence were twice the odds of an animal sampled from areas least suitable for RVF occurrence (95% CI: 1.43, 2.76, p < 0.001). The regions in the northern and central-eastern Tanzania were more suitable for RVF occurrence than the rest of the regions in the country. The modelled suitable habitat is characterised by impermeable soils, moderate precipitation in the wettest quarter, high livestock density and a bimodal rainfall pattern. The findings of this study should provide guidance for the design of appropriate RVF surveillance, prevention and control strategies which target areas with these characteristics

Positive Selection Results in Frequent Reversible Amino Acid Replacements in the G Protein Gene of Human Respiratory Syncytial Virus

Human respiratory syncytial virus (HRSV) is the major cause of lower respiratory tract infections in children under 5 years of age and the elderly, causing annual disease outbreaks during the fall and winter. Multiple lineages of the HRSVA and HRSVB serotypes co-circulate within a single outbreak and display a strongly temporal pattern of genetic variation, with a replacement of dominant genotypes occurring during consecutive years. In the present study we utilized phylogenetic methods to detect and map sites subject to adaptive evolution in the G protein of HRSVA and HRSVB. A total of 29 and 23 amino acid sites were found to be putatively positively selected in HRSVA and HRSVB, respectively. Several of these sites defined genotypes and lineages within genotypes in both groups, and correlated well with epitopes previously described in group A. Remarkably, 18 of these positively selected tended to revert in time to a previous codon state, producing a “flip-flop” phylogenetic pattern. Such frequent evolutionary reversals in HRSV are indicative of a combination of frequent positive selection, reflecting the changing immune status of the human population, and a limited repertoire of functionally viable amino acids at specific amino acid sites

Nut production in Bertholletia excelsa across a logged forest mosaic: implications for multiple forest use

Although many examples of multiple-use forest management may be found in tropical smallholder systems, few studies provide empirical support for the integration of selective timber harvesting with non-timber forest product (NTFP) extraction. Brazil nut (Bertholletia excelsa, Lecythidaceae) is one of the world’s most economically-important NTFP species extracted almost entirely from natural forests across the Amazon Basin. An obligate out-crosser, Brazil nut flowers are pollinated by large-bodied bees, a process resulting in a hard round fruit that takes up to 14 months to mature. As many smallholders turn to the financial security provided by timber, Brazil nut fruits are increasingly being harvested in logged forests. We tested the influence of tree and stand-level covariates (distance to nearest cut stump and local logging intensity) on total nut production at the individual tree level in five recently logged Brazil nut concessions covering about 4000 ha of forest in Madre de Dios, Peru. Our field team accompanied Brazil nut harvesters during the traditional harvest period (January-April 2012 and January-April 2013) in order to collect data on fruit production. Three hundred and ninety-nine (approximately 80%) of the 499 trees included in this study were at least 100 m from the nearest cut stump, suggesting that concessionaires avoid logging near adult Brazil nut trees. Yet even for those trees on the edge of logging gaps, distance to nearest cut stump and local logging intensity did not have a statistically significant influence on Brazil nut production at the applied logging intensities (typically 1–2 timber trees removed per ha). In one concession where at least 4 trees ha-1 were removed, however, the logging intensity covariate resulted in a marginally significant (0.09) P value, highlighting a potential risk for a drop in nut production at higher intensities. While we do not suggest that logging activities should be completely avoided in Brazil nut rich forests, when a buffer zone cannot be observed, low logging intensities should be implemented. The sustainability of this integrated management system will ultimately depend on a complex series of socioeconomic and ecological interactions. Yet we submit that our study provides an important initial step in understanding the compatibility of timber harvesting with a high value NTFP, potentially allowing for diversification of forest use strategies in Amazonian Perù