Recent Developments in Species Sensitivity Distribution Modeling.

The species sensitivity distribution (SSD) is a statistical approach that is used to estimate either the concentration of a chemical that is hazardous to no more than x% of all species (the HCx) or the proportion of species potentially affected by a given concentration of a chemical. Despite a significant body of published research and critical reviews over the past 20 yr aimed at improving the methodology, the fundamentals remain unchanged. Although there have been some recent suggestions for improvements to SSD methods in the literature, in general, few of these suggestions have been formally adopted. Furthermore, critics of the approach can rightly point to the fact that differences in technical implementation can lead to marked differences in results, thereby undermining confidence in SSD approaches. Despite the limitations, SSDs remain a practical tool and, until a demonstrably better inferential framework is available, developments and enhancements to conventional SSD practice will and should continue. We therefore believe the time has come for the scientific community to decide how it wants SSD methods to evolve. The present study summarizes the current status of, and elaborates on several recent developments for, SSD methods, specifically, model averaging, multimodality, and software development. We also consider future directions with respect to the use of SSDs, with the ultimate aim of helping to facilitate greater international collaboration and, potentially, greater harmonization of SSD methods. Environ Toxicol Chem 2021;40:293-308. © 2020 SETAC.

A spatial regression model for the disaggregation of areal unit based data to high-resolution grids with application to vaccination coverage mapping.

The growing demand for spatially detailed data to advance the Sustainable Development Goals agenda of 'leaving no one behind' has resulted in a shift in focus from aggregate national and province-based metrics to small areas and high-resolution grids in the health and development arena. Vaccination coverage is customarily measured through aggregate-level statistics, which mask fine-scale heterogeneities and 'coldspots' of low coverage. This paper develops a methodology for high-resolution mapping of vaccination coverage using areal data in settings where point-referenced survey data are inaccessible. The proposed methodology is a binomial spatial regression model with a logit link and a combination of covariate data and random effects modelling two levels of spatial autocorrelation in the linear predictor. The principal aspect of the model is the melding of the misaligned areal data and the prediction grid points using the regression component and each of the conditional autoregressive and the Gaussian spatial process random effects. The Bayesian model is fitted using the INLA-SPDE approach. We demonstrate the predictive ability of the model using simulated data sets. The results obtained indicate a good predictive performance by the model, with correlations of between 0.66 and 0.98 obtained at the grid level between true and predicted values. The methodology is applied to predicting the coverage of measles and diphtheria-tetanus-pertussis vaccinations at 5 × 5 km2 in Afghanistan and Pakistan using subnational Demographic and Health Surveys data. The predicted maps are used to highlight vaccination coldspots and assess progress towards coverage targets to facilitate the implementation of more geographically precise interventions. The proposed methodology can be readily applied to wider disaggregation problems in related contexts, including mapping other health and development indicators.

Spatial association of nest construction by brown trout Salmo trutta.

Spawning patterns in female brown trout Salmo trutta were examined by documenting the construction of nests in a small stream and later excavating them to recover progeny. The maternal provenance of nests was determined by genetic typing of embryos using microsatellite markers. Seventy-two nests, for which position and date of construction were known, were made by 59 individuals. Position and date of construction were known for a further 35 nests, comprising 11 Atlantic salmon Salmo salar nests and 24 nests which contained few or no progeny. Salmo trutta showed a behavioural preference for spawning near (≤ 1 m) prior nests; nests made by different individuals tended to accumulate in a spatial sequence that progressed upstream. The directionality of the association between prior and new nests suggests that later spawners use the residual depressions created by previous spawners as the first element of their own nests.

RadCon: phylogenetic tree comparison and consensus.

SUMMARY: RadCon is a Macintosh program for manipulating and analysing phylogenetic trees. The program can determine the Cladistic Information Content of individual trees, the stability of leaves across a set of bootstrap trees, produce the strict basic Reduced Cladistic Consensus profile of a set of trees and convert a set of trees into its matrix representation for supertree construction. AVAILABILITY: The program is free and available at http://taxonomy.zoology.gla.ac.uk/ approximately jthorley/radcon/radcon.html.

A chain is no stronger than its weakest link: double decay analysis of phylogenetic hypotheses.

In decay analyses the support for a particular split in most-parsimonious trees is its decay index, that is, the extra steps required of the shortest trees that do not include the split. By focusing solely on the support for splits, traditional decay analysis may provide an incomplete and potentially misleading summary of the support for phylogenetic relationships common to the most-parsimonious tree or trees. Here, we introduce double decay analysis, a new approach to assessing support for phylogenetic relationships. Double decay analysis is the determination of the decay indices of all n-taxon statements/partitions common to the most-parsimonious tree. The results of double decay analyses are presented in a partition table, but various approaches to graphical representation of the results, including the use of reduced consensus support trees, are also discussed. Double decay analysis provides a more comprehensive summary and facilitates a better understanding of the strengths and weaknesses of complex phylogenetic hypotheses than does traditional decay analysis. The limitations of traditional decay analyses and the utility of double decay analyses are illustrated with both contrived data and real data for sauropod dinosaurs.

Simplified microscopy for rapid detection of significant bacteriuria in random urine specimens.

Simplified urine microscopy, nitrite testing, and dipstick culture were compared with urine loop streak culture colony counts in 219 random voided specimens to determine the accuracy of the three rapid screening techniques. Nitrite testing resulted in 65% false negative results, which could not be significantly improved by incubation at 37 degrees C but which could be improved by adding nitrate substrate before incubation. Dipstick culture could not be quantitated until after 18 h of incubation. A new, simplified microscopy technique, using unspun, unstained urine, resulted in 4% false negative results and 4% false positive results in specimens containing over 10(5) organisms per ml and was the best method Centrifuges, Gram staining reagents, and counting chambers are not necessary for accurate microscopic screening of random urine specimens for the presence of bacteriuria by this technique, and the results are immediately available.

The prevalence of antibody-coated bacteria in urine.

The prevalence of urinary antibody-coated bacteria (ACB), suggesting renal bacteriuria, was studied in three groups of patients: inpatients whose physicians suspected urinary tract infections, asymptomatic outpatients with neurogenic bladders but without urethral catheters, and asymptomatic inpatients with indwelling urethral catheters. The prevalence of ACB was 67% of inpatients with positive cultures without catheters, 94% of patients with neurogenic bladders, and 36% of patients with urethral catheters. These results suggest a high prevalence of upper urinary tract involvement in patients with positive urine cultures, even if asymptomatic.

Peripheral blood lymphocyte response to acute infections in humans.

The response of subpopulations of peripheral venous blood lymphocytes to systemic bacterial or viral infections was studied. B-lymphocytes were defined by the presence of surface binding sites for mu chains, which were determined by immunofluorescent staining. T-lymphocytes were defined by the ability to form active sheep cell rosettes. Virus-infectible lymphocytes, which may represent activated T-lymphocytes, were defined by the ability to support virus replication. Patients with bacterial infections had an increase in the B-lymphocytes of peripheral venous blood, whereas patients with viral infections had an increase in T-lymphocytes as compared to controls. The number of virus-infectible lymphocytes was increased in patients with bacterial infections but not in patients with viral infections. These studies suggest that subpopulations of human peripheral blood lymphocytes vary in response to different types of infectious agents.

Tetanus and diphtheria antitoxin levels following a hospital-based adult immunization program.

A hospital-based program to immunize adults against tetanus unless specific contraindications to immunization are present has been in effect at Parkland Memorial Hospital since 1959. Adsorbed tetanus toxoid was used from 1959 to 1970, and was replaced at that time by adult type adsorbed combined tetanus/diphtheria toxoid. In the present survey, the titers of diphtheria and tetanus antitoxins were determined in sera from 97 adults admitted to the Medical Service. Titers of diphtheria antitoxin less than 0.0125 units per ml were found in only seven patients and less than 0.0125 units per ml of tetanus antitoxin in only 17 patients. This high prevalence of immunity especially to tetanus appears to reflect our practice of routine immunization of adults. Although the recommended frequency of tetanus boosters has recently been reduced for adults who have completed a full primary immunization series, susceptibility to diphtheria or tetanus or both is not uncommon among adults in the US. Unless contraindications are present, we therefore urge routine immunization of all adults seeking medical care and of all hospital personnel as a means of diminishing the risk of diphtheria and tetanus in those adult populations with a significant incidence of susceptibility to these diseases.

Passive transfer of antibodies of maternal origin from blood to cerebrospinal fluid in infants.

The demonstration that specific IgM antibodies are present in the serum of infants is useful in the diagnosis of several congenital infections. However, it is less certain whether the detection of antibodies in cerebrospinal fluid (c.s.f.) of infants indicates congenital infection of the central nervous system, because the origins of such antibodies have not been established. In the present study diphtheria and tetanus antitoxins of maternal origin have been detected both in the serum and in the c.s.f. of infants. These observations suggest that an important source of immunoglobulins in c.s.f. is passive transfer of antibodies from serum which should be considered in interpreting serological studies with c.s.f.