Fun in facets: A flexible new tool for population genomics in R.

The landscape of analytical tools for population genomics continues to evolve. However, these tools are scattered across programming languages, making them largely inaccessible for many biologists. In this issue of Molecular Ecology Resources, Hemstrom and Jones, 2022 (Mol Ecol Resour; 962) introduce a new R package, snpR. This package combines a large number of existing analyses, to provide a one-stop shop for population genomics. F-statistics, admixture analyses, effective population size inferences, genome-wide association studies (GWAS), and parentage analyses are all implemented natively within the package. A variety of third-party software can also be run without leaving the R environment. The authors pay particular attention to data structure - avoiding redundancy - and allowing analyses to be run across multiple sample or single-nucleotide polymorphism (SNP) groupings. Because of its great accessibility and wide range of analyses, snpR has the potential to become a favourite within the Molecular Ecology community.

Dispersal Reduction: Causes, Genomic Mechanisms, and Evolutionary Consequences.

Recent biological analyses suggest that reductions in dispersal ability have been key drivers of diversification across numerous lineages. We synthesise emerging data to highlight similarities regarding the causes and consequences of dispersal reduction across taxa and ecosystems, as well as the diverse genomic mechanisms underpinning these shifts. Natural selection has acted on standing genetic variation within taxa to drive often rapid - and in some cases parallel - losses of dispersal, and ultimately speciation. Such shifts can thus represent an important nexus between adaptive and neutral diversification processes, with substantial evolutionary consequences. Recognition of the links between these concepts that are emerging from different fields, taxa and ecosystems is transforming our understanding of the fascinating role of dispersal reduction in the formation of biodiversity.

The discrimination of geoforensic trace material from close proximity locations by organic profiling using HPLC and plant wax marker analysis by GC.

There is a need to develop a wider empirical research base to expand the scope for utilising the organic fraction of soil in forensic geoscience, and to demonstrate the capability of the analytical techniques used in forensic geoscience to discriminate samples at close proximity locations. The determination of wax markers from soil samples by GC analysis has been used extensively in court and is known to be effective in discriminating samples from different land use types. A new HPLC method for the analysis of the organic fraction of forensic sediment samples has also been shown recently to add value in conjunction with existing inorganic techniques for the discrimination of samples derived from close proximity locations. This study compares the ability of these two organic techniques to discriminate samples derived from close proximity locations and finds the GC technique to provide good discrimination at this scale, providing quantification of known compounds, whilst the HPLC technique offered a shorter and simpler sample preparation method and provided very good discrimination between groups of samples of different provenance in most cases. The use of both data sets together gave further improved accuracy rates in some cases, suggesting that a combined organic approach can provide added benefits in certain case scenarios and crime reconstruction contexts.

Deaths in Incorrectly Identified Low-Surgical-Risk Patients.

BACKGROUND: The American Society of Anesthesiologists (ASA) physical classification system was developed for assessing anaesthetic risk, but is often also used to estimate surgical death risk. Patients with low ASA grades (ASA 1 or 2) are expected to have better surgical outcomes than patients with higher ASA grades (ASA ≥ 4). This study examined the course to death in patients classified as ASA 1 or 2 was examined, to investigate possible factors in unexpected deaths, in addition to evaluating the use of ASA grades by clinicians. METHODS: Patient data from the national surgical mortality audit of Australian hospitals were examined. The patient group was listed as ASA grade 1 or 2 by surgeons. Patients over 60 or under 20 were excluded in the final analysis, as were cases from New South Wales due to data not being available. A total of 357 cases were examined. Assessor summaries of the cases were examined, and ASA score reassessed to determine accuracy. RESULTS: More than 95% (n = 339) of cases listed as ASA 1 or 2 were found to have an incorrectly low grade, with 17.6% (n = 63) of cases listed as "expected" deaths. CONCLUSION: ASA grades appear to be misunderstood in the reporting of patient surgical risk. Many patient summaries list patients with severe systemic disease or expected deaths as ASA 1 or 2, contrary to the intended use of this classification system. Improved education on the use of the ASA grading system would be beneficial to clinicians.

The identification of markers for Geoforensic HPLC profiling at close proximity sites.

Soil is a highly transferable source of trace physical material that is both persistent in the environment and varied in composition. This inherent variability can provide useful information to determine the geographical origin of a questioned sample or when comparing and excluding samples, since the composition of soil is dependent on geographical factors such as climate, bedrock geology and land use. Previous studies have limited forensic relevance due to the requirement for large sample amounts and unrealistic differences between the land use and geographical location of the sample sites. In addition the philosophical differences between the disciplines of earth sciences, for which most analytical techniques have been designed, and forensic sciences, particularly with regard to sample preparation and data interpretation have not been fully considered. This study presents an enhanced technique for the analysis of organic components of geoforensic samples by improving the sample preparation and data analysis strategies used in previous research into the analysis of soil samples by high performance liquid chromatography (HPLC). This study provides two alternative sets of marker peaks to generate HPLC profiles which allow both easy visual comparison of samples and the correct assignment of 100% of the samples to their location of origin when discriminating between locations of interest in multivariate statistical analyses. This technique thereby offers an independent form of analysis that is complementary to inorganic geoforensic techniques and offers an easily accessible method for discriminating between close proximity forensically relevant locations.

Flight of Rhyzopertha dominica (Coleoptera: Bostrichidae)-a Spatio-Temporal Analysis With Pheromone Trapping and Population Genetics.

The flight of the lesser grain borer, Rhyzopertha dominica (F.), near grain storages and at distances from them, was investigated to assess the potential of these beetles to infest grain and spread insecticide resistance genes. We caught R. dominica in pheromone-baited flight traps (and blank controls) set at storages, in fields away from storages, and in native vegetation across a 12-mo period. A functional set of highly polymorphic microsatellite markers was developed, enabling population genetic analyses on the trapped beetles. Pheromone-baited traps caught just as many R. dominica adults at least 1 km from grain storages as were caught adjacent to grain storages. Samples of beetles caught were genetically homogeneous across the study area (over 7,000 km2) in South Queensland, Australia. However, a change in genetic structure was detected at one bulk storage site. Subsequent analysis detected a heterozygous excess, which indicated a population bottleneck. Only a few beetles were caught during the winter months of June and July. To assess the mating status and potential fecundity of dispersing R. dominica females, we captured beetles as they left grain storages and quantified offspring production and life span in the laboratory. Nearly all (95%) of these dispersing females had mated and these produced an average of 242 offspring. We demonstrated that R. dominica populations in the study area display a high degree of connectivity and this is a result of the active dispersal of mated individuals of high potential fecundity.

High-resolution computed tomographic appearance of MALToma of the lung.

MALToma of the lung is rare and advances in molecular techniques have only recently allowed accurate diagnostic classification of the previously termed "pseudolymphomas" by demonstrating that many are monoclonal B-cell proliferations of MALT tissue and therefore true low-grade lymphomas. No significant previous contribution was found in the literature regarding the high-resolution CT appearance (HRCT) of these tumours. We describe the high-resolution CT appearances in five cases presenting to our institution from 1994 to 1997. The HRCT scans (1-mm sections at 10- to 15-mm intervals) were performed as the opacities seen radiographically were thought to be part of a diffuse lung process. In one patient a spiral sequence was performed through the main airway. Multifocal, ill-defined nodules containing air bronchograms were seen in four cases and focal lobar consolidation in one case. Interlobular septal thickening, centrilobular micronodules and bronchial wall thickening were seen in two cases. Mediastinal lymphadenopathy and pleural reaction do not appear to be characteristic features. The appearance of multifocal consolidation is similar to that seen in bronchoalveolar cell carcinoma and cryptogenic organising pneumonia.

Radiological features of papillary carcinoma of the breast.

Seventeen patients with papillary carcinoma of the breast were analysed with respect to the radiological findings by three experienced breast radiologists. The most frequent mammographic appearance of papillary tumours was of an ill-defined (70%) and lobulated (60%) mass and at ultrasound as a well-defined (76%), inhomogeneous (62%) and hypoechoic (92%) lesion. Histopathological subtypes of encysted papillary carcinoma, encysted papillary carcinoma with an invasive focus and invasive papillary carcinomas could not be predicted from the radiological features, although invasive tumours tended to be larger at presentation than the other subtypes.

Phrenic nerve pacing in two young quadriplegic ventilator-dependent patients.

Patients who survive high cervical injury are usually dependent on mechanical ventilation and tracheostomy if the lesion above C3 is complete. We report our experience with phrenic nerve pacing (PNP) to achieve ventilator-independence in two young quadriplegic patients. A diaphragm conditioning programme, and combination of low frequency electrophrenic stimulation within each inspiratory burst and low breathing frequency enabled both patients initially to achieve continuous 24 hour ventilation independent of mechanical ventilation. One patient reverted to overnight mechanical ventilation (six hours) after three years. PNP should be considered in ventilator dependent patients with high cervical injury to achieve independence and improve quality of life.

Plasma melatonin, luteinizing hormone, follicle-stimulating hormone, prolactin, and corticoids in two patients with pinealoma.

Plasma melatonin, LH, FSH, PRL, and corticoids were measured in two patients with pineal tumors. Plasma melatonin was not detectable (less than 7 pg/ml) in either patient while gonadotropin and cortisol levels were within the normal range. One patient exhibited low PRL levels and the other patient, a prepubertal boy, had elevated levels. The clinical value of the measurement of melatonin as a potential marker for all pineal tumors must be questioned.

Posterior fossa extradural haematoma.

A case of extradural haematoma of the posterior cranial fossa is presented and some of the pertinent literature reviewed. Suggestions are made which may enable the general surgeon and his staff looking after the patient in the acute phase to detect the presence of this lesion.