Multi-armed bandits, Thomson sampling and unsupervised machine learning in phylogenetic graph search.

A phylogenetic graph search relies on a large number of highly parameterized search procedures (e.g. branch-swapping, perturbation, simulated annealing, genetic algorithm). These procedures vary in effectiveness over datasets and at alternative points in analytical pipelines. The multi-armed bandit problem is applied to phylogenetic graph searching to more effectively utilize these procedures. Thompson sampling is applied to a collection of search and optimization "bandits" to favour productive search strategies over those that are less successful. This adaptive random sampling strategy is shown to be more effective in producing heuristically optimal phylogenetic graphs and more time efficient than existing uniform probability randomized search strategies. The strategy acts as a form of unsupervised machine learning that can be applied to a diversity of phylogenetic datasets without prior knowledge of their properties.

PhylogeneticGraph (PhyG) a new phylogenetic graph search and optimization program.

We present Phylogenetic Graph (PhyG), an open-source, phylogenetic search tool for diverse data types and graphs, including softwired and hardwired networks, in addition to trees. This allows for analysis of horizontal transfer and hybridization scenarios, as well as the necessary vertical inheritance of trees. PhyG is the successor to POY5 in performing combined data tree-alignment with enhancements in heuristic optimality (up to 7% in example data) and execution time (up to a factor of 200). Input data may exhibit a practically unlimited number of character states in qualitative or sequence (aligned and unaligned) types. Novel graph construction and refinement algorithms have been implemented and integrated into a variety of search procedures. Currently, PhyG implements parsimony and No-Common-Mechanism Likelihood optimization.

The Modified Reactive Strength Index Is a Valid Measure of Lower-Body Explosiveness in Male and Female High School Athletes.

ABSTRACT: Witte, BC, Schouten, TC, Westphal, JA, VanZile, AW, Jones, DD, Widenhoefer, TL, Dobbs, WC, Jagim, AR, Luedke, JA, and Almonroeder, TG. The modified reactive strength index is a valid measure of lower-body explosiveness in male and female high school athletes. J Strength Cond Res XX(X): 000-000, 2024-The modified reactive strength index (mRSI) is a commonly used metric to quantify lower-body explosiveness during countermovement jump (CMJ) performance. However, few studies have attempted to examine its validity as a measure of explosiveness, particularly among high school athletes. The purpose of this study was to examine the validity of the mRSI as a measure of lower-body explosiveness among a relatively large sample of male and female high school athletes from various sports. As part of this study, male (n = 132) and female (n = 43) high school athletes performed CMJs, while ground reaction forces were recorded using a force platform. The vertical ground reaction force data collected during the CMJs were used to derive the following variables: peak force (PF), peak power, time to PF, time to take-off, peak rate of force development, and the mRSI. Principal component analysis was applied and reduced these variables into 2 components related to "force" and "speed." The mRSI loaded on both the force (loading = 0.82) and speed (loading = -0.46) components, indicating that it incorporates elements of both force and speed, although it loaded more strongly on the force component than the speed component. The observed pattern of cross-loading suggests that the mRSI is generally a valid measure of lower-body explosiveness for male and female high school athletes.

Comprehensive Species Sampling and Sophisticated Algorithmic Approaches Refute the Monophyly of Arachnida.

Deciphering the evolutionary relationships of Chelicerata (arachnids, horseshoe crabs, and allied taxa) has proven notoriously difficult, due to their ancient rapid radiation and the incidence of elevated evolutionary rates in several lineages. Although conflicting hypotheses prevail in morphological and molecular data sets alike, the monophyly of Arachnida is nearly universally accepted, despite historical lack of support in molecular data sets. Some phylotranscriptomic analyses have recovered arachnid monophyly, but these did not sample all living orders, whereas analyses including all orders have failed to recover Arachnida. To understand this conflict, we assembled a data set of 506 high-quality genomes and transcriptomes, sampling all living orders of Chelicerata with high occupancy and rigorous approaches to orthology inference. Our analyses consistently recovered the nested placement of horseshoe crabs within a paraphyletic Arachnida. This result was insensitive to variation in evolutionary rates of genes, complexity of the substitution models, and alternative algorithmic approaches to species tree inference. Investigation of sources of systematic bias showed that genes and sites that recover arachnid monophyly are enriched in noise and exhibit low information content. To test the impact of morphological data, we generated a 514-taxon morphological data matrix of extant and fossil Chelicerata, analyzed in tandem with the molecular matrix. Combined analyses recovered the clade Merostomata (the marine orders Xiphosura, Eurypterida, and Chasmataspidida), but merostomates appeared nested within Arachnida. Our results suggest that morphological convergence resulting from adaptations to life in terrestrial habitats has driven the historical perception of arachnid monophyly, paralleling the history of numerous other invertebrate terrestrial groups.

Depression, anxiety and PTSD symptoms before and during the COVID-19 pandemic in the UK.

BACKGROUND: The impact of the coronavirus disease 2019 (COVID-19) pandemic on mental health is still being unravelled. It is important to identify which individuals are at greatest risk of worsening symptoms. This study aimed to examine changes in depression, anxiety and post-traumatic stress disorder (PTSD) symptoms using prospective and retrospective symptom change assessments, and to find and examine the effect of key risk factors. METHOD: Online questionnaires were administered to 34 465 individuals (aged 16 years or above) in April/May 2020 in the UK, recruited from existing cohorts or via social media. Around one-third (n = 12 718) of included participants had prior diagnoses of depression or anxiety and had completed pre-pandemic mental health assessments (between September 2018 and February 2020), allowing prospective investigation of symptom change. RESULTS: Prospective symptom analyses showed small decreases in depression (PHQ-9: -0.43 points) and anxiety [generalised anxiety disorder scale - 7 items (GAD)-7: -0.33 points] and increases in PTSD (PCL-6: 0.22 points). Conversely, retrospective symptom analyses demonstrated significant large increases (PHQ-9: 2.40; GAD-7 = 1.97), with 55% reported worsening mental health since the beginning of the pandemic on a global change rating. Across both prospective and retrospective measures of symptom change, worsening depression, anxiety and PTSD symptoms were associated with prior mental health diagnoses, female gender, young age and unemployed/student status. CONCLUSIONS: We highlight the effect of prior mental health diagnoses on worsening mental health during the pandemic and confirm previously reported sociodemographic risk factors. Discrepancies between prospective and retrospective measures of changes in mental health may be related to recall bias-related underestimation of prior symptom severity.

Much ado about nothing: inapplicable data as insertion-deletion events.

The treatment of inapplicable characters has proved especially vexing to systematists. Investigators have wrestled with alternative coding scenarios to capture both the presence and absence of a feature, and its variation when present, in a reasonable manner. Three basic issues have presented themselves: (i) impossible states at internal nodes; (ii) action at a distance among disparate parts of the tree; and (iii) "secondary" (i.e. aspect variation) characters overwhelming "primary" (i.e. character presence/absence) patterns in grouping taxa. Multiple methods have been proposed to deal with these issues in the context of standard character coding with varying levels of complexity. Here, I show that these issues can be dealt with in a direct fashion by treating presence/absence not as a character, but as insertion/deletion of a character with all its potential variation. This approach removes these three problems in simple, straightforward manner.

Parsimony optimization of phylogenetic networks.

An algorithm is described for the optimization of character data (e.g. qualitative, nucleic acid sequence) on softwired phylogenetic networks. The algorithm presented here is an extension of those developed for trees under the parsimony criterion and can form the basis for phylogenetic network search procedures. Although the problem is (in general) an NP-Hard optimization, the resolution-based algorithm we describe here capitalizes on the significant amount of shared structure in sub-graphs containing network edges, reducing the execution time and allowing for the analysis of empirical datasets.

Experimental examination of the phase transition of water on silica at 298 K.

The objective of this study was to investigate the prediction of the wetting characteristics obtained from the equilibrium adsorption analysis using the Zeta adsorption isotherm approach with an experimental study. Water vapor's adsorption and wetting characteristics on a hydroxylated and nano-polished silica substrate were studied in near-equilibrium conditions at temperatures near 298 K. Using a UV-visible interferometer, water vapor adsorbate film thicknesses were measured and converted into amount adsorbed per unit area. The current results show that the wetting transition occurred at an average subcooling value of 0.39 K, less than the predicted value of 0.49 K. All the different experimental observations showed growth of film thickness as a function of subcooling value with a maximum film thickness of 12.6 nm. The analysis of the results further showed that the maximum stable film was in a metastable state that then condensed in a dropwise manner, if perturbed by increasing the subcooling. The study further revealed that the adsorbate is unstable after transitioning. The solid surface energy calculated by including the near-equilibrium observations was comparable and close to that of the equilibrium studies, thus supporting solid surface energy as a material property.

Phylogenomic Resolution of Sea Spider Diversification through Integration of Multiple Data Classes.

Despite significant advances in invertebrate phylogenomics over the past decade, the higher-level phylogeny of Pycnogonida (sea spiders) remains elusive. Due to the inaccessibility of some small-bodied lineages, few phylogenetic studies have sampled all sea spider families. Previous efforts based on a handful of genes have yielded unstable tree topologies. Here, we inferred the relationships of 89 sea spider species using targeted capture of the mitochondrial genome, 56 conserved exons, 101 ultraconserved elements, and 3 nuclear ribosomal genes. We inferred molecular divergence times by integrating morphological data for fossil species to calibrate 15 nodes in the arthropod tree of life. This integration of data classes resolved the basal topology of sea spiders with high support. The enigmatic family Austrodecidae was resolved as the sister group to the remaining Pycnogonida and the small-bodied family Rhynchothoracidae as the sister group of the robust-bodied family Pycnogonidae. Molecular divergence time estimation recovered a basal divergence of crown group sea spiders in the Ordovician. Comparison of diversification dynamics with other marine invertebrate taxa that originated in the Paleozoic suggests that sea spiders and some crustacean groups exhibit resilience to mass extinction episodes, relative to mollusk and echinoderm lineages.

Antimicrobial therapies for prevention of recurrent acute exacerbations of COPD (AECOPD): beyond the guidelines.

BACKGROUND: Unfortunately, many COPD patients continue to exacerbate despite good adherence to GOLD Class D recommended therapy. Acute exacerbations lead to an increase in symptoms, decline in lung function and increased mortality rate. The purpose of this review is to do a literature search for any prophylactic anti-microbial treatment trials in GOLD class D patients who 'failed' recommended therapy and discuss the role of COPD phenotypes, lung and gut microbiota and co-morbidities in developing a tailored approach to anti-microbial therapies for high frequency exacerbators. MAIN TEXT: There is a paucity of large, well-conducted studies in the published literature to date. Factors such as single-centre, study design, lack of well-defined controls, insufficient patient numbers enrolled and short follow-up periods were significant limiting factors in numerous studies. One placebo-controlled study involving more than 1000 patients, who had 2 or more moderate exacerbations in the previous year, demonstrated a non-significant reduction in exacerbations of 19% with 5 day course of moxifloxacillin repeated at 8 week intervals. In Pseudomonas aeruginosa (Pa) colonised COPD patients, inhaled antimicrobial therapy using tobramycin, colistin and gentamicin resulted in significant reductions in exacerbation frequency. Viruses were found to frequently cause acute exacerbations in COPD (AECOPD), either as the primary infecting agent or as a co-factor. However, other, than the influenza vaccination, there were no trials of anti-viral therapies that resulted in a positive effect on reducing AECOPD. Identifying clinical phenotypes and co-existing conditions that impact on exacerbation frequency and severity is essential to provide individualised treatment with targeted therapies. The role of the lung and gut microbiome is increasingly recognised and identification of pathogenic bacteria will likely play an important role in personalised antimicrobial therapies. CONCLUSION: Antimicrobial therapeutic options in patients who continue to exacerbate despite adherence to guidelines-directed therapy are limited. Phenotyping patients, identification of co-existing conditions and assessment of the microbiome is key to individualising antimicrobial therapy. Given the impact of viruses on AECOPD, anti-viral therapeutic agents and targeted anti-viral vaccinations should be the focus of future research studies.

Phylogenetic supergraphs.

Phylogenetic graph structures used in empirical and theoretical analysis have expanded beyond trees to more general directed acyclic graphs including networks and forests. Several methods to reconcile multiple such graphs are presented and discussed here, extending existing consensus and supertree techniques to form a set of phylogenetic supergraph methods. These graphs can be used as the summary of analytical results, or as heuristic initial graphs for further phylogenetic analysis.

Tracking the Fatigue Status after a Resistance Exercise through Different Parameters.

The purpose of the study was to investigate the sensitivity of back squat bar velocity, isometric mid-thigh pull, heart rate variability parameters, perceived recovery scale and step counts for tracking the muscular fatigue time-course (reduction in countermovement jump [CMJ] performance) after strenuous acute lower limb resistance exercise. Sixteen healthy men performed heart rate variability assessment, perceived recovery scale, CMJ, back squat bar velocity, isometric mid-thigh pull, and daily step counts before and 24 h, 48 h and 72 h post a strenuous acute lower limb resistance exercise (8×10 repetitions). The CMJ height decreased at 24 and 48 h after exercise session (p≤0.017), evidencing the muscular fatigue. The perceived recovery scale presented lower values compared to baseline until 72 h after exercise session (p<0.001 for all). The heart rate variability parameters and step counts were not significantly different across time. At 24 h post, only mean force of mid-thigh pull was decreased (p=0.044), while at 48 h post, only peak force of mid-thigh pull was decreased (p=0.020). On the last day (72 h), only bar velocity (mean) presented reduction (p=0.022). Therefore, the perceived recovery scale was the only variable sensible to tracking muscular fatigue, i. e. presenting a similar time-course to CMJ height.

Phylogenetic relationships of the Boana pulchella Group (Anura: Hylidae).

In this paper we present a phylogenetic analysis of the treefrogs of the Boana pulchella Group with the goals of (1) providing a rigorous test of its monophyly; (2) providing a test of relationships supported in previous studies; and (3) exploring the relationships of the several species not included in previous analyses. The analyses included>300 specimens of 37 of the 38 species currently included in the group, plus 36 outgroups, exemplars of the diversity of Boana and the other genera of the hylid tribe Cophomantini. The dataset included eight mitochondrial genes (12S, 16S, CytB, COI, ND1, tRNAIle, tRNALeu, and tRNAVal) and five nuclear genes (RHO, TYR, RAG-1, CXCR4, SIAH1). The phylogenetic analyses recover the monophyly of the B. pulchella Group with lower support than previous studies, as a result of the inclusion of the B. claresignata Group, which is recovered as its sister taxon. Within the B. pulchella Group, the inclusion of almost all species of the group had little impact on previous notions of its phylogeny, except for the rejection of the hypothesized B. polytaenia Clade (B. goiana and B. phaeopleura are nested in the clade here called the B. prasina Clade), which is redefined. Phylogenetic support is strong for five major clades, which collectively include all but three of the species sampled: the B. balzani Clade (B. aguilari, B. balzani, B. gladiator, B. melanopleura, B. palaestes), the redefined B. polytaenia Clade (B. botumirim, B. buriti, B. cipoensis, B. jaguariaivensis, B. leptolineata, B. polytaenia, B. stenocephala, and two undescribed species), the B. prasina Clade (B. bischoffi, B. caingua, B. cordobae, B. goiana, B. guentheri, B. marginata, B. phaeopleura, B. prasina, B. pulchella, and one undescribed species), the B. riojana Clade (B. callipleura, B. marianitae, B. riojana), and the B. semiguttata Clade (B. caipora, B. curupi, B. joaquini, B. poaju, B. semiguttata, B. stellae, and two undescribed species). The monophyly of the B. prasina + B. riojana Clades, and that of the B. polytaenia + B. semiguttata Clades are well-supported. The relationships among these two clades, the B. balzani Clade, B. ericae + B. freicanecae, and B. cambui (representing the deepest phylogenetic splits within the B. pulchella Group) are recovered with weak support. We discuss the phenotypic evidence supporting the monophyly of the B. pulchella Group, and the taxonomy of several species, identifying three new synonyms of Boana polytaenia, one new synonym of Boana goiana, and one new synonym of B. riojana.

Statistical Modeling of Distribution Patterns: A Markov Random Field Implementation and Its Application on Areas of Endemism.

A statistical framework to infer areas of endemism from geographic distributions is proposed. This novel method is based on hidden Markov random fields (HMRFs), a type of undirected graph model commonly used in computer vision. This framework assumes areas of endemism are the states of the hidden layer of the model, whereas taxon distributions are emitted values in the observed layer. Taxon distributions are associated to the observed layer through a clustering procedure based on the extent of overlap. Observations are emitted by the hidden layer according to a Gaussian distribution, whereas the joint distribution of the hidden layer follows a Potts model. State and parameter inference of the maximum a posteriori configuration is performed through a modified version of the expectation-maximization algorithm. The optimal number of areas of endemism in the data set is estimated through the pseudolikelihood information criterion, a model selection procedure that uses an approximation to likelihood. The performance of the new algorithm was assessed on simulated data, and compared with the most popular methods for delimitation of areas of endemism: biotic element analysis, parsimony analysis of endemism, and endemicity analysis. HMRFs efficiently recovered the true pattern across a wide range of uncertainty values. The performance was also examined on empirical data: South African weevils (Sciobius) and Central American ground beetles and funnel-web tarantulas (Carabidae and Dipluridae, respectively). HMRFs uncovered six areas of endemism from the weevil data set, whereas eight were estimated for the Central American arthropods (compared with 3-5 and 3-14 from the other methods, respectively).

Distance Wagner tree refinement as a heuristic approach to character-based initial tree construction.

The distance Wagner procedure of Farris (American Naturalist, 1972, 106, 645), in its original or random addition sequence form, is a rapid method of tree construction. The original formulation did not allow for refinement of tree hypotheses via common trajectory search operations (e.g. SPR, TBR). Here, the distance Wagner method is extended to allow for refinement of initial trees produced via the four-point condition (Mathematics and the Archeological and Historical Sciences, Edinburgh University Press, Edinburgh, 1974). The performance of the extended distance Wagner as a heuristic search procedure is evaluated with several unaligned sequences and combined source datasets within the parsimony framework. Distance Wagner both with and without refinement is shown to be a rapid and useful heuristic method to generate initial trees for further, character-based, analysis.

The phylogeny of Dendropsophini (Anura: Hylidae: Hylinae).

The relationships of the hyline tribe Dendropsophini remain poorly studied, with most published analyses dealing with few of the species groups of Dendropsophus. In order to test the monophyly of Dendropsophini, its genera, and the species groups currently recognized in Dendropsophus, we performed a total evidence phylogenetic analysis. The molecular dataset included sequences of three mitochondrial and five nuclear genes from 210 terminals, including 12 outgroup species, the two species of Xenohyla, and 93 of the 108 recognized species of Dendropsophus. The phenomic dataset includes 46 terminals, one per species (34 Dendropsophus, one Xenohyla, and 11 outgroup species). Our results corroborate the monophyly of Dendropsophini and the reciprocal monophyly of Dendropsophus and Xenohyla. Some species groups of Dendropsophus are paraphyletic (the D. microcephalus, D. minimus, and D. parviceps groups, and the D. rubicundulus clade). On the basis of our results, we recognize nine species groups; for three of them (D. leucophyllatus, D. microcephalus, and D. parviceps groups) we recognize some nominal clades to highlight specific morphology or relationships and facilitate species taxonomy. We further discuss the evolution of oviposition site selection, where our results show multiple instances of independent evolution of terrestrial egg clutches during the evolutionary history of Dendropsophus.

Efficient implied alignment.

BACKGROUND: Given a binary tree [Formula: see text] of n leaves, each leaf labeled by a string of length at most k, and a binary string alignment function ⊗, an implied alignment can be generated to describe the alignment of a dynamic homology for [Formula: see text]. This is done by first decorating each node of [Formula: see text] with an alignment context using ⊗, in a post-order traversal, then, during a subsequent pre-order traversal, inferring on which edges insertion and deletion events occurred using those internal node decorations. RESULTS: Previous descriptions of the implied alignment algorithm suggest a technique of "back-propagation" with time complexity [Formula: see text]. Here we describe an implied alignment algorithm with complexity [Formula: see text]. For well-behaved data, such as molecular sequences, the runtime approaches the best-case complexity of Ω(k∗n). CONCLUSIONS: The reduction in the time complexity of the algorithm dramatically improves both its utility in generating multiple sequence alignments and its heuristic utility.

New fossils of Australopithecus anamensis from Kanapoi, West Turkana, Kenya (2012-2015).

Kanapoi, Kenya, has yielded the earliest evidence of the genus Australopithecus, Australopithecus anamensis. Renewed fieldwork from 2012 through 2015 yielded 18 new fossils attributable to this species. The new specimens include the second maxillary fragment known from a Kanapoi hominin and the first from a relatively young adult. The new maxilla has the distinctive rounded nasal aperture margin characteristic of A. anamensis. A second partial proximal tibia from the site is the first postcranial element from a small A. anamensis individual. A new partial mandible and complete mandibular dentition display distinctive Kanapoi hominin morphology, but the mandible displays a larger trigonid on its fourth premolar than any known so far. Two new complete sets of mandibular incisors are also notably large, especially the lateral ones, a distinctive feature of A. anamensis compared with Australopithecus afarensis. The new fossils also highlight the distinctive morphology of Kanapoi A. anamensis compared to later hominins.

Geochemical fractionation of hazardous elements in fresh and drilled weathered South African coal fly ashes.

The chemical reactions of dry-disposed ash dump, ingressed oxygen, carbon dioxide, and infiltrating rainwater affect mineralogical transformation, redistribution, and migration of chemical species. Composite samples of weathered coal fly ash taken at various depths and fresh coal fly ash were examined using organic petrographic, X-ray diffraction, X-ray fluorescence techniques, and successive extraction procedures. Results obtained show relative enrichment of glass, Al-Fe-oxides, calcite, and tridymite in the weathered CFA, but the fresh CFA is enriched in mullite, inertinite, maghemite, and ettringite. The enrichment of the weathered CFA in amorphous glass suggests higher reactivity when compared to fresh CFA. The evident depletion of soluble oxides in the weathered CFA is attributed to flushing of the soluble salts by percolating rainwater. Comparative enrichment of examined elements in water-soluble, exchangeable, reducible, and residual fractions of the weathered CFA is partly due to the slow release of adsorbed chemical species from the alumina-silicate matrix and diffusion from the deeper sections of the particles of coal fly ash. Sodium and potassium show enrichment in the oxidisable fraction of fresh CFA. The estimated mobility factor indicates mobility for Ca, Mg, Na, Se, Mo, and Sb and K, Sr, V, Cu, Cr, Se, and B in fresh and weathered CFAs, respectively.

Combined neurosurgical and orbital intervention for spheno-orbital meningiomas - the Manchester experience.

PURPOSE: Surgical resection of spheno-orbital meningioma (SOM) is challenging, requiring a multidisciplinary surgical approach. We present our experience of the surgical management of patients with SOM. METHODS: A retrospective analysis of patients with SOM who underwent joint neurosurgical and orbital surgical procedures between January 2000 and June 2017. Pre-operative clinical signs, indication for surgery, surgical complications and post-operative outcomes were recorded. RESULTS: Twenty-four operations were performed. Mean age was 49.5 years. Ninety-two percent of patients were female. Pre-operatively mean Snellen acuity vision was 6/12; 13 (54%) had an RAPD; 12 (50%) had reduced colour vision; 16 (67%) had a visual field defect. The majority (21 patients, 88%) had proptosis (average 4.5 mm ± 2.8 mm). The indication for surgery was evidence of visual dysfunction in 17 (71%), the remaining 7 (29%) had high risk of visual loss clinically or radiologically. Three-months post operatively, vision was stable in 13 (58%), improved in 6 (21%) and worse in 5 (17%). Average long-term follow-up was 82 months (1-220). Fourteen (58%) maintain improved or stable visual function. Four (17%) had reduced vision due to regrowth of the tumour at an average of 24 months. CONCLUSION: SOMs are very challenging to treat surgically. In this cohort the patients were predominantly young females with aggressive disease. Visual function was improved or stabilised in 79% of the patients.