Likelihood-Based Tests of Species Tree Hypotheses.

Likelihood-based tests of phylogenetic trees are a foundation of modern systematics. Over the past decade, an enormous wealth and diversity of model-based approaches have been developed for phylogenetic inference of both gene trees and species trees. However, while many techniques exist for conducting formal likelihood-based tests of gene trees, such frameworks are comparatively underdeveloped and underutilized for testing species tree hypotheses. To date, widely used tests of tree topology are designed to assess the fit of classical models of molecular sequence data and individual gene trees and thus are not readily applicable to the problem of species tree inference. To address this issue, we derive several analogous likelihood-based approaches for testing topologies using modern species tree models and heuristic algorithms that use gene tree topologies as input for maximum likelihood estimation under the multispecies coalescent. For the purpose of comparing support for species trees, these tests leverage the statistical procedures of their original gene tree-based counterparts that have an extended history for testing phylogenetic hypotheses at a single locus. We discuss and demonstrate a number of applications, limitations, and important considerations of these tests using simulated and empirical phylogenomic data sets that include both bifurcating topologies and reticulate network models of species relationships. Finally, we introduce the open-source R package SpeciesTopoTestR (SpeciesTopology Tests in R) that includes a suite of functions for conducting formal likelihood-based tests of species topologies given a set of input gene tree topologies.

Aspirin and cancer treatment: systematic reviews and meta-analyses of evidence: for and against.

Aspirin as a possible treatment of cancer has been of increasing interest for over 50 years, but the balance of the risks and benefits remains a point of contention. We summarise the valid published evidence 'for' and 'against' the use of aspirin as a cancer treatment and we present what we believe are relevant ethical implications. Reasons for aspirin include the benefits of aspirin taken by patients with cancer upon relevant biological cancer mechanisms. These explain the observed reductions in metastatic cancer and vascular complications in cancer patients. Meta-analyses of 118 observational studies of mortality in cancer patients give evidence consistent with reductions of about 20% in mortality associated with aspirin use. Reasons against aspirin use include increased risk of a gastrointestinal bleed though there appears to be no valid evidence that aspirin is responsible for fatal gastrointestinal bleeding. Few trials have been reported and there are inconsistencies in the results. In conclusion, given the relative safety and the favourable effects of aspirin, its use in cancer seems justified, and ethical implications of this imply that cancer patients should be informed of the present evidence and encouraged to raise the topic with their healthcare team.

Efficient pulse sequence design framework for high-dimensional MR fingerprinting scans using systematic error index.

PURPOSE: For effective optimization of MR fingerprinting (MRF) pulse sequences, estimating and minimizing errors from actual scan conditions are crucial. Although virtual-scan simulations offer an approximation to these errors, their computational demands become expensive for high-dimensional MRF frameworks, where interactions between more than two tissue properties are considered. This complexity makes sequence optimization impractical. We introduce a new mathematical model, the systematic error index (SEI), to address the scalability challenges for high-dimensional MRF sequence design. METHODS: By eliminating the need to perform dictionary matching, the SEI model approximates quantification errors with low computational costs. The SEI model was validated in comparison with virtual-scan simulations. The SEI model was further applied to optimize three high-dimensional MRF sequences that quantify two to four tissue properties. The optimized scans were examined in simulations and healthy subjects. RESULTS: The proposed SEI model closely approximated the virtual-scan simulation outcomes while achieving hundred- to thousand-times acceleration in the computational speed. In both simulation and in vivo experiments, the optimized MRF sequences yield higher measurement accuracy with fewer undersampling artifacts at shorter scan times than the heuristically designed sequences. CONCLUSION: We developed an efficient method for estimating real-world errors in MRF scans with high computational efficiency. Our results illustrate that the SEI model could approximate errors both qualitatively and quantitatively. We also proved the practicality of the SEI model of optimizing sequences for high-dimensional MRF frameworks with manageable computational power. The optimized high-dimensional MRF scans exhibited enhanced robustness against undersampling and system imperfections with faster scan times.

Robust phylogenetic regression.

Modern comparative biology owes much to phylogenetic regression. At its conception, this technique sparked a revolution that armed biologists with phylogenetic comparative methods (PCMs) for disentangling evolutionary correlations from those arising from hierarchical phylogenetic relationships. Over the past few decades, the phylogenetic regression framework has become a paradigm of modern comparative biology that has been widely embraced as a remedy for shared ancestry. However, recent evidence has sown doubt over the efficacy of phylogenetic regression, and PCMs more generally, with the suggestion that many of these methods fail to provide an adequate defense against unreplicated evolution-the primary justification for using them in the first place. Importantly, some of the most compelling examples of biological innovation in nature result from abrupt lineage-specific evolutionary shifts, which current regression models are largely ill-equipped to deal with. Here we explore a solution to this problem by applying robust linear regression to comparative trait data. We formally introduce robust phylogenetic regression to the PCM toolkit with linear estimators that are less sensitive to model violations than the standard least-squares estimator, while still retaining high power to detect true trait associations. Our analyses also highlight an ingenuity of the original algorithm for phylogenetic regression based on independent contrasts, whereby robust estimators are particularly effective. Collectively, we find that robust estimators hold promise for improving tests of trait associations and offer a path forward in scenarios where classical approaches may fail. Our study joins recent arguments for increased vigilance against unreplicated evolution and a better understanding of evolutionary model performance in challenging-yet biologically important-settings.

Comparative analyses of the banded alder borer (Rosalia funebris) and Asian longhorned beetle (Anoplophora glabripennis) genomes reveal significant differences in genome architecture and gene content among these and other Cerambycidae.

Rosalia funebris (RFUNE; Cerambycidae), the banded alder borer, is a longhorn beetle whose larvae feed on the wood of various economically and ecologically significant trees in western North America. Adults are short-lived and not known to consume plant material substantially. We sequenced, assembled and annotated the RFUNE genome using HiFi and RNASeq data. We documented genome architecture and gene content, focusing on genes putatively involved in plant feeding (phytophagy). Comparisons were made to the well-studied genome of the Asian longhorned beetle (AGLAB; Anoplophora glabripennis) and other Cerambycidae. The 814 Mb RFUNE genome assembly was distributed across 42 contigs, with an N50 of 30.18 Mb. Repetitive sequences comprised 60.27 % of the genome, and 99.0 % of expected single-copy orthologous genes were fully assembled. We identified 12657 genes, fewer than in the four other species studied, and 46.4 % fewer than for Aromia moschata (same subfamily as RFUNE). Of the 7258 orthogroups shared between RFUNE and AGLAB, 1461 had more copies in AGLAB and 1023 had more copies in RFUNE. We identified 240 genes in RFUNE that putatively arose via horizontal transfer events. The RFUNE genome encoded substantially fewer putative plant cell wall degrading enzymes than AGLAB, which may relate to the longer-lived plant-feeding adults of the latter species. The RFUNE genome provides new insights into cerambycid genome architecture and gene content and provides a new vantage point from which to study the evolution and genomic basis of phytophagy in beetles.

The genome of the invasive and broadly polyphagous Diaprepes root weevil, Diaprepes abbreviatus (Coleoptera), reveals an arsenal of putative polysaccharide-degrading enzymes.

The Diaprepes root weevil (DRW), Diaprepes abbreviatus, is a broadly polyphagous invasive pest of agriculture in the southern United States and the Caribbean. Its genome was sequenced, assembled, and annotated to study genomic correlates of specialized plant-feeding and invasiveness and to facilitate the development of new methods for DRW control. The 1.69 Gb D. abbreviatus genome assembly was distributed across 653 contigs, with an N50 of 7.8 Mb and the largest contig of 62 Mb. Most of the genome was comprised of repetitive sequences, with 66.17% in transposable elements, 5.75% in macrosatellites, and 2.06% in microsatellites. Most expected orthologous genes were present and fully assembled, with 99.5% of BUSCO genes present and 1.5% duplicated. One hundred and nine contigs (27.19 Mb) were identified as putative fragments of the X and Y sex chromosomes, and homology assessment with other beetle X chromosomes indicated a possible sex chromosome turnover event. Genome annotation identified 18,412 genes, including 43 putative horizontally transferred (HT) loci. Notably, 258 genes were identified from gene families known to encode plant cell wall degrading enzymes and invertases, including carbohydrate esterases, polysaccharide lyases, and glycoside hydrolases (GH). GH genes were unusually numerous, with 239 putative genes representing 19 GH families. Interestingly, several other beetle species with large numbers of GH genes are (like D. abbreviatus) successful invasive pests of agriculture or forestry.

Once daily cediranib and weekly paclitaxel to prevent malignant bowel obstruction in at-risk patients with platinum-resistant ovarian cancer (CEBOC): a single-arm, phase II safety trial.

OBJECTIVE: Cytotoxic chemotherapy for ovarian cancer can be augmented by co-administration of vascular endothelial growth factor inhibitors but these are contraindicated in patients with bowel obstruction due to the risk of gastrointestinal perforation. We evaluated the safety and feasibility of paclitaxel plus cediranib to treat patients with platinum-resistant ovarian cancer at risk of malignant bowel obstruction. METHODS: A phase II trial included eligible patients between March 2018 and February 2021, identified by clinical symptoms and radiographic risk factors for malignant bowel obstruction. Cediranib (20 mg/day) was added to paclitaxel (70 mg/m2/week) within 9 weeks of starting paclitaxel if pretreatment bowel symptoms had improved. The primary endpoint was the number of patients treated for ≥5 days with cediranib that were free of grade 3-5 gastrointestinal perforation or fistula. Secondary endpoints were hospitalization for bowel obstruction, grade ≥3 adverse events, treatment compliance assessed by relative dose intensity, objective response, progression-free survival, and overall survival. RESULTS: Thirty patients were recruited. Of these, 12 received paclitaxel alone and 17 received paclitaxel and cediranib in combination. One patient died before starting treatment. No patient developed a grade 3-5 gastrointestinal perforation or fistula (one sided 95% confidence interval (CI) upper limit 0.16). One patient required hospitalization for bowel obstruction but recovered with conservative management. The most common cediranib-related grade ≥3 adverse events were fatigue (3/17), diarrhorea (2/17), and hypomagnesemia (2/17). Relative dose intensity for paclitaxel was 90% (interquartile range (IQR) 85-100%; n=29) and for cediranib 88% (IQR 76-93%; n=17). The objective response in patients who received paclitaxel and cediranib was 65.0% (one complete and 10 partial responses). Median progression-free survival was 6.9 months (95% CI 4.4-11.5 months; n=17) and overall survival was 19.4 months (95% CI 10.1-20.4 months; n=17). Median follow-up was 12.4 months (8.9-not reached; n=17). CONCLUSIONS: The unexpectedly high withdrawal rate during paclitaxel alone, before introducing cediranib, meant we were unable to definitely conclude that paclitaxel plus cediranib did not cause gastrointestinal perforation or fistula. The regimen was however tolerated. TRIAL REGISTRATION NUMBER: EudraCT 2016-004618-93.

Fifty million years of beetle evolution along the Antarctic Polar Front.

Global cooling and glacial-interglacial cycles since Antarctica's isolation have been responsible for the diversification of the region's marine fauna. By contrast, these same Earth system processes are thought to have played little role terrestrially, other than driving widespread extinctions. Here, we show that on islands along the Antarctic Polar Front, paleoclimatic processes have been key to diversification of one of the world's most geographically isolated and unique groups of herbivorous beetles-Ectemnorhinini weevils. Combining phylogenomic, phylogenetic, and phylogeographic approaches, we demonstrate that these weevils colonized the sub-Antarctic islands from Africa at least 50 Ma ago and repeatedly dispersed among them. As the climate cooled from the mid-Miocene, diversification of the beetles accelerated, resulting in two species-rich clades. One of these clades specialized to feed on cryptogams, typical of the polar habitats that came to prevail under Miocene conditions yet remarkable as a food source for any beetle. This clade's most unusual representative is a marine weevil currently undergoing further speciation. The other clade retained the more common weevil habit of feeding on angiosperms, which likely survived glaciation in isolated refugia. Diversification of Ectemnorhinini weevils occurred in synchrony with many other Antarctic radiations, including penguins and notothenioid fishes, and coincided with major environmental changes. Our results thus indicate that geo-climatically driven diversification has progressed similarly for Antarctic marine and terrestrial organisms since the Miocene, potentially constituting a general biodiversity paradigm that should be sought broadly for the region's taxa.

Education and employment as young adults living with spina bifida transition to adulthood in the USA: A study of the National Spina Bifida Patient Registry.

AIM: To describe the education and employment transition experience of young adults with spina bifida (YASB) and investigate factors associated with employment. METHOD: We queried education and employment data from the US National Spina Bifida Patient Registry from 2009 to 2019. We applied generalized estimating equations models to analyze sociodemographic and disease-related factors associated with employment. RESULTS: A total of 1909 participants (850 males, 1059 females) aged 18 to 26 years contributed 4379 annual visits. Nearly 84% had myelomeningocele and, at last visit, the median age was 21 years (mean 21 years 5 months, SD 2 years 10 months). A total of 41.8% had at least some post-high school education, and 23.9% were employed. In a multivariable regression model, employment was significantly associated with education level, lower extremity functional level, bowel continence, insurance, and history of non-shunt surgery. This large, national sample of YASB demonstrated low rates of post-secondary education attainment and employment and several potentially modifiable factors associated with employment. INTERPRETATION: Specific sociodemographic, medical, and functional factors associated with employment are important for clinicians to consider when facilitating transition for YASB into adulthood. Additional research is needed to understand the impact of cognitive functioning and social determinants of health on transition success in YASB. WHAT THIS PAPER ADDS: There were low education attainment and employment rates in a large sample of young adults with spina bifida. Specific sociodemographic, medical, and functional factors are associated with employment. Some employment-associated factors, such as continence and self-management skills, are modifiable.

Microchromosomes Exhibit Distinct Features of Vertebrate Chromosome Structure and Function with Underappreciated Ramifications for Genome Evolution.

Microchromosomes are common yet poorly understood components of many vertebrate genomes. Recent studies have revealed that microchromosomes contain a high density of genes and possess other distinct characteristics compared with macrochromosomes. Whether distinctive characteristics of microchromosomes extend to features of genome structure and organization, however, remains an open question. Here, we analyze Hi-C sequencing data from multiple vertebrate lineages and show that microchromosomes exhibit consistently high degrees of interchromosomal interaction (particularly with other microchromosomes), appear to be colocalized to a common central nuclear territory, and are comprised of a higher proportion of open chromatin than macrochromosomes. These findings highlight an unappreciated level of diversity in vertebrate genome structure and function, and raise important questions regarding the evolutionary origins and ramifications of microchromosomes and the genes that they house.

The origins and evolution of chromosomes, dosage compensation, and mechanisms underlying venom regulation in snakes.

Here we use a chromosome-level genome assembly of a prairie rattlesnake (Crotalus viridis), together with Hi-C, RNA-seq, and whole-genome resequencing data, to study key features of genome biology and evolution in reptiles. We identify the rattlesnake Z Chromosome, including the recombining pseudoautosomal region, and find evidence for partial dosage compensation driven by an evolutionary accumulation of a female-biased up-regulation mechanism. Comparative analyses with other amniotes provide new insight into the origins, structure, and function of reptile microchromosomes, which we demonstrate have markedly different structure and function compared to macrochromosomes. Snake microchromosomes are also enriched for venom genes, which we show have evolved through multiple tandem duplication events in multiple gene families. By overlaying chromatin structure information and gene expression data, we find evidence for venom gene-specific chromatin contact domains and identify how chromatin structure guides precise expression of multiple venom gene families. Further, we find evidence for venom gland-specific transcription factor activity and characterize a complement of mechanisms underlying venom production and regulation. Our findings reveal novel and fundamental features of reptile genome biology, provide insight into the regulation of snake venom, and broadly highlight the biological insight enabled by chromosome-level genome assemblies.

PhyloWGA: chromosome-aware phylogenetic interrogation of whole genome alignments.

SUMMARY: Here, we present PhyloWGA, an open source R package for conducting phylogenetic analysis and investigation of whole genome data. AVAILABILITYAND IMPLEMENTATION: Available at Github (https://github.com/radamsRHA/PhyloWGA). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Of Traits and Trees: Probabilistic Distances under Continuous Trait Models for Dissecting the Interplay among Phylogeny, Model, and Data.

Stochastic models of character trait evolution have become a cornerstone of evolutionary biology in an array of contexts. While probabilistic models have been used extensively for statistical inference, they have largely been ignored for the purpose of measuring distances between phylogeny-aware models. Recent contributions to the problem of phylogenetic distance computation have highlighted the importance of explicitly considering evolutionary model parameters and their impacts on molecular sequence data when quantifying dissimilarity between trees. By comparing two phylogenies in terms of their induced probability distributions that are functions of many model parameters, these distances can be more informative than traditional approaches that rely strictly on differences in topology or branch lengths alone. Currently, however, these approaches are designed for comparing models of nucleotide substitution and gene tree distributions, and thus, are unable to address other classes of traits and associated models that may be of interest to evolutionary biologists. Here, we expand the principles of probabilistic phylogenetic distances to compute tree distances under models of continuous trait evolution along a phylogeny. By explicitly considering both the degree of relatedness among species and the evolutionary processes that collectively give rise to character traits, these distances provide a foundation for comparing models and their predictions, and for quantifying the impacts of assuming one phylogenetic background over another while studying the evolution of a particular trait. We demonstrate the properties of these approaches using theory, simulations, and several empirical data sets that highlight potential uses of probabilistic distances in many scenarios. We also introduce an open-source R package named PRDATR for easy application by the scientific community for computing phylogenetic distances under models of character trait evolution.[Brownian motion; comparative methods; phylogeny; quantitative traits.].

Synthesis and Chemistry of Ammonioethenyl and Phosphonioethenyl Ligands in Zwitterionic Dirhenium Carbonyl Complexes.

New zwitterionic dirhenium carbonyl complexes containing ammonioethenyl and phosphonioethenyl ligands have been synthesized and studied. The reaction of Re2(CO)10 with C2H2 and Me3NO yielded the dirhenium complex Re2(CO)9(NMe3) (6) and the new zwitterionic complex Re2(CO)9[η1-E-2-CH═CH(NMe3)] (7). Compound 6 was characterized structurally and was found to have a NMe3 ligand in an equatorial coordination site cis to a long Re-Re single bond, Re-Re = 3.0938(2) Å. Compound 7 can be obtained from the reaction of 6 with ethyne (C2H2) formally by the insertion of ethyne into the Re-N bond to the NMe3 ligand. Compound 7 contains a 2-trimethylammonioethenyl ligand, -CH═CH(+NMe3), that is formally a zwitterion having a positive charge on the nitrogen atom and a negative charge on the terminal carbon atom. When coordinated to rhenium by the terminal ethenyl carbon atom, the negative charge on the -CH═CH(+NMe3) carbon atom is formally transferred to the rhenium atom. The reaction of Re2(CO)10 with C2H2 and NEt3 in the presence of Me3NO yielded the new dirhenium complex Re2(CO)9[η1-E-2-CH═CH(NEt3)] (8) together with some 6 and 7. Compound 8 is structurally similar to 7, but it contains a NEt3 group in the ammonioethenyl ligand in the place of the NMe3 group in 7. Reactions of 7 with PMePh2 and PPh3 yielded the zwitterionic 2-arylphosphonioethenyl-coordinated dirhenium carbonyl complexes, Re2(CO)9[η1-E-2-CH═CH(PPh2Me)] (9a) and Re2(CO)9[η1-E-2-CH═CH(PPh3)] (9b), and the zwitterionic 1-phosphonioethenyl ligand in the dirhenium carbonyl complexes, Re2(CO)9[η1-1-C(PPh2Me)(═CH2)] (10a), Re2(CO)8[µ-η2-1-C(PPh2Me)(═CH2)] (11a), and Re2(CO)8[[µ-η2-1-C(PPh3)(CH2)] (11b). Compound 10a was converted to 11a and the new compound Re2(CO)7(µ-H)[µ-η2-1-(CH2C)P(Ph)(Me)(o-C6H4)], (12) by decarbonylation using Me3NO. Compound 12 contains an ortho-metalated phenyl ring. The new products 6,7, 8, 9b, 10a, 11a, 11b and 12 were characterized structurally by single-crystal X-ray diffraction analyses.

Experiences of running a stratified medicine adaptive platform trial: Challenges and lessons learned from 10 years of the FOCUS4 trial in metastatic colorectal cancer.

BACKGROUND: Complex innovative design trials are becoming increasingly common and offer potential for improving patient outcomes in a faster time frame. FOCUS4 was the first molecularly stratified trial in metastatic colorectal cancer and it remains one of the first umbrella trial designs to be launched globally. Here, we aim to describe lessons learned from delivery of the trial over the last 10 years. METHODS: FOCUS4 was a Phase II/III molecularly stratified umbrella trial testing the safety and efficacy of targeted therapies in metastatic colorectal cancer. It used adaptive statistical methodology to decide which sub-trial should close early, and new therapies were added as protocol amendments. Patients with newly diagnosed metastatic colorectal cancer were registered, and central laboratory testing was used to stratify their tumour into molecular subtypes. Following 16 weeks of first-line therapy, patients with stable or responding disease were eligible for randomisation into either a molecularly stratified sub-trial (FOCUS4-B, C or D) or non-stratified FOCUS4-N. The primary outcome for all studies was progression-free survival comparing the intervention with active monitoring/placebo. At the close of the trial, feedback was elicited from all investigators through surveys and interviews and consolidated into a series of recommendations and lessons learned for the delivery of similar future trials. RESULTS: Between January 2014 and October 2020, 1434 patients were registered from 88 UK hospitals. Of the 20 drug combinations that were explored for inclusion in the platform trial, three molecularly targeted sub-trials were activated: FOCUS4-D (February 2014-March 2016) evaluated AZD8931 in the BRAF-PIK3CA-RAS wildtype subgroup; FOCUS4-B (February 2016-July 2018) evaluated aspirin in the PIK3CA mutant subgroup and FOCUS4-C (June 2017-October 2020) evaluated adavosertib in the RAS+TP53 double mutant subgroup. FOCUS4-N was active throughout and evaluated capecitabine monotherapy versus a treatment break. A total of 361 (25%) registered patients were randomised into a sub-trial. Feedback on the experiences of delivery of FOCUS4 could be grouped into three main areas of challenge: funding/infrastructure, biomarker testing procedures and trial design efficiencies within which 20 recommendations are summarised. CONCLUSION: Adaptive stratified medicine platform studies are feasible in common cancers but present challenges. Our stakeholder feedback has helped to inform how these trial designs can succeed and answer multiple questions efficiently, providing resource is adequate.

Carbon monoxide exposures reported to the UK National Poisons Information Service: a 4-year study.

BACKGROUND: Unintentional carbon monoxide (CO) poisoning poses a public health challenge. The UK National Poisons Information Service (NPIS) provides advice to healthcare professionals via the online database, TOXBASE®, and a 24-hour telephone line. Our aim was to analyse all CO-related enquiries to the NPIS. METHODS: We analysed enquiries regarding unintentional CO exposure (1st July 2015-30th June 2019). Information on patient demographics, CO source and location, clinical features and poisoning severity was collected from telephone enquiries and TOXBASE accesses. RESULTS: 2970 unintentional non-fire-related CO exposures were reported. Exposures occurred commonly in the home (60%) with faulty boilers frequently implicated (27.4%). Although five fatalities were reported, 68.7% of patients experienced no or minor symptoms only (headache most frequently reported). Despite being the gold standard measurement, blood carboxyhaemoglobin concentration was only recorded in 25.6% patients, with no statistically significant correlation with severity. CONCLUSIONS: Unintentional CO exposures in the UK commonly occur in domestic settings and although are generally of low severity, fatalities continue to occur. Carboxyhaemoglobin measurement is important to confirm exposure but further work is required to assess its validity as a prognostic indicator in CO exposure. Public health policy should continue to focus on raising awareness of the dangers of CO.

Associations between mindfulness, posttraumatic stress disorder symptoms, and posttraumatic growth in police academy cadets: An exploratory study.

Mindfulness-based treatments have been increasingly noted in the professional literature as a possible means to reduce posttraumatic stress disorder (PTSD) symptoms and promote well-being, especially among law enforcement officers. Scant research, however, has been conducted to study dispositional mindfulness and health outcomes in police cadets. The current exploratory study examined the association between the various facets of dispositional mindfulness (i.e., observing, describing, acting with awareness, nonjudging, and nonreactivity) and PTSD symptoms, posttraumatic growth (PTG), and other variables, including world assumptions, in police cadets (N = 379). Consistent with findings from previous studies of experienced officers, the results indicate that (a) mindful nonjudging is a salient trait in police cadets, which uniquely predicted lower PTSD symptoms, ß = -.31, p < .001, and was related to lower levels of PTG, r = -.12, p = .025, and (b) mindful observing was related to higher levels of PTSD symptoms, r = .14, p = .009 and higher levels of PTG, r = .26, p < .001, in the present sample. In addition, the findings demonstrate that nonjudging is an important trait in police cadets regarding world assumptions such that nonjudging was a significant, unique predictor of world assumption facets, including controllability of events, ß = .15, p = .025, and trustworthiness and goodness of people, ß = .18, p = .004. Clinical implications, including the importance of understanding the association between mindful nonjudging and the shattering and rebuilding of worldviews and following trauma reactions, are discussed.

Snake Recombination Landscapes Are Concentrated in Functional Regions despite PRDM9.

Meiotic recombination in vertebrates is concentrated in hotspots throughout the genome. The location and stability of hotspots have been linked to the presence or absence of PRDM9, leading to two primary models for hotspot evolution derived from mammals and birds. Species with PRDM9-directed recombination have rapid turnover of hotspots concentrated in intergenic regions (i.e., mammals), whereas hotspots in species lacking PRDM9 are concentrated in functional regions and have greater stability over time (i.e., birds). Snakes possess PRDM9, yet virtually nothing is known about snake recombination. Here, we examine the recombination landscape and test hypotheses about the roles of PRDM9 in rattlesnakes. We find substantial variation in recombination rate within and among snake chromosomes, and positive correlations between recombination rate and gene density, GC content, and genetic diversity. Like mammals, snakes appear to have a functional and active PRDM9, but rather than being directed away from genes, snake hotspots are concentrated in promoters and functional regions-a pattern previously associated only with species that lack a functional PRDM9. Snakes therefore provide a unique example of recombination landscapes in which PRDM9 is functional, yet recombination hotspots are associated with functional genic regions-a combination of features that defy existing paradigms for recombination landscapes in vertebrates. Our findings also provide evidence that high recombination rates are a shared feature of vertebrate microchromosomes. Our results challenge previous assumptions about the adaptive role of PRDM9 and highlight the diversity of recombination landscape features among vertebrate lineages.

Molecular subtype-specific efficacy of anti-EGFR therapy in colorectal cancer is dependent on the chemotherapy backbone.

BACKGROUND: Patient selection for addition of anti-EGFR therapy to chemotherapy for patients with RAS and BRAF wildtype metastatic colorectal cancer can still be optimised. Here we investigate the effect of anti-EGFR therapy on survival in different consensus molecular subtypes (CMSs) and stratified by primary tumour location. METHODS: Retrospective analyses, using the immunohistochemistry-based CMS classifier, were performed in the COIN (first-line oxaliplatin backbone with or without cetuximab) and PICCOLO trial (second-line irinotecan with or without panitumumab). Tumour tissue was available for 323 patients (20%) and 349 (41%), respectively. RESULTS: When using an irinotecan backbone, anti-EGFR therapy is effective in both CMS2/3 and CMS4 in left-sided primary tumours (progression-free survival (PFS): HR 0.44, 95% CI 0.26-0.75, P = 0.003 and HR 0.12, 95% CI 0.04-0.36, P < 0.001, respectively) and in CMS4 right-sided tumours (PFS HR 0.17, 95% CI 0.04-0.71, P = 0.02). Efficacy using an oxaliplatin backbone was restricted to left-sided CMS2/3 tumours (HR 0.57, 95% CI 0.36-0.96, P = 0.034). CONCLUSIONS: The subtype-specific efficacy of anti-EGFR therapy is dependent on the chemotherapy backbone. This may provide the possibility of subtype-specific treatment strategies for a more optimal use of anti-EGFR therapy.

Probabilistic Species Tree Distances: Implementing the Multispecies Coalescent to Compare Species Trees Within the Same Model-Based Framework Used to Estimate Them.

Despite the ubiquitous use of statistical models for phylogenomic and population genomic inferences, this model-based rigor is rarely applied to post hoc comparison of trees. In a recent study, Garba et al. derived new methods for measuring the distance between two gene trees computed as the difference in their site pattern probability distributions. Unlike traditional metrics that compare trees solely in terms of geometry, these measures consider gene trees and associated parameters as probabilistic models that can be compared using standard information theoretic approaches. Consequently, probabilistic measures of phylogenetic tree distance can be far more informative than simply comparisons of topology and/or branch lengths alone. However, in their current form, these distance measures are not suitable for the comparison of species tree models in the presence of gene tree heterogeneity. Here, we demonstrate an approach for how the theory of Garba et al. (2018), which is based on gene tree distances, can be extended naturally to the comparison of species tree models. Multispecies coalescent (MSC) models parameterize the discrete probability distribution of gene trees conditioned upon a species tree with a particular topology and set of divergence times (in coalescent units), and thus provide a framework for measuring distances between species tree models in terms of their corresponding gene tree topology probabilities. We describe the computation of probabilistic species tree distances in the context of standard MSC models, which assume complete genetic isolation postspeciation, as well as recent theoretical extensions to the MSC in the form of network-based MSC models that relax this assumption and permit hybridization among taxa. We demonstrate these metrics using simulations and empirical species tree estimates and discuss both the benefits and limitations of these approaches. We make our species tree distance approach available as an R package called pSTDistanceR, for open use by the community.