Optimizing Phylogenetic Supertrees Using Answer Set Programming

The supertree construction problem is about combining several phylogenetic trees with possibly conflicting information into a single tree that has all the leaves of the source trees as its leaves and the relationships between the leaves are as consistent with the source trees as possible. This leads to an optimization problem that is computationally challenging and typically heuristic methods, such as matrix representation with parsimony (MRP), are used. In this paper we consider the use of answer set programming to solve the supertree construction problem in terms of two alternative encodings. The first is based on an existing encoding of trees using substructures known as quartets, while the other novel encoding captures the relationships present in trees through direct projections. We use these encodings to compute a genus-level supertree for the family of cats (Felidae). Furthermore, we compare our results to recent supertrees obtained by the MRP method.Comment: To appear in Theory and Practice of Logic Programming (TPLP), Proceedings of ICLP 201

Effect of remdesivir post hospitalization for COVID-19 infection from the randomized SOLIDARITY Finland trial

We report the first long-term follow-up of a randomized trial (NCT04978259) addressing the effects of remdesivir on recovery (primary outcome) and other patient-important outcomes one year after hospitalization resulting from COVID-19. Of the 208 patients recruited from 11 Finnish hospitals, 198 survived, of whom 181 (92%) completed follow-up. At one year, self-reported recovery occurred in 85% in remdesivir and 86% in standard of care (SoC) (RR 0.94, 95% CI 0.47-1.90). We infer no convincing difference between remdesivir and SoC in quality of life or symptom outcomes (p > 0.05). Of the 21 potential long-COVID symptoms, patients reported moderate/major bother from fatigue (26%), joint pain (22%), and problems with memory (19%) and attention/concentration (18%). In conclusion, after a one-year follow-up of hospitalized patients, one in six reported they had not recovered well from COVID-19. Our results provide no convincing evidence of remdesivir benefit, but wide confidence intervals included possible benefit and harm.Peer reviewe

Traces of trauma – a multivariate pattern analysis of childhood trauma, brain structure and clinical phenotypes

Background: Childhood trauma (CT) is a major yet elusive psychiatric risk factor, whose multidimensional conceptualization and heterogeneous effects on brain morphology might demand advanced mathematical modeling. Therefore, we present an unsupervised machine learning approach to characterize the clinical and neuroanatomical complexity of CT in a larger, transdiagnostic context. Methods: We used a multicenter European cohort of 1076 female and male individuals (discovery: n = 649; replication: n = 427) comprising young, minimally medicated patients with clinical high-risk states for psychosis; patients with recent-onset depression or psychosis; and healthy volunteers. We employed multivariate sparse partial least squares analysis to detect parsimonious associations between combinations of items from the Childhood Trauma Questionnaire and gray matter volume and tested their generalizability via nested cross-validation as well as via external validation. We investigated the associations of these CT signatures with state (functioning, depressivity, quality of life), trait (personality), and sociodemographic levels. Results: We discovered signatures of age-dependent sexual abuse and sex-dependent physical and sexual abuse, as well as emotional trauma, which projected onto gray matter volume patterns in prefronto-cerebellar, limbic, and sensory networks. These signatures were associated with predominantly impaired clinical state- and trait-level phenotypes, while pointing toward an interaction between sexual abuse, age, urbanicity, and education. We validated the clinical profiles for all three CT signatures in the replication sample. Conclusions: Our results suggest distinct multilayered associations between partially age- and sex-dependent patterns of CT, distributed neuroanatomical networks, and clinical profiles. Hence, our study highlights how machine learning approaches can shape future, more fine-grained CT research

A New Tooth Wear–Based Dietary Analysis Method for Proboscidea (Mammalia)

<div><p>ABSTRACT</p><p>Dietary analyses of herbivorous mammals are important for paleoecological reconstruction. Several methods applicable to fossil teeth have been developed lately. The mesowear method based on wear-induced occlusal shape and relief of ungulate molars has proven to be a robust method for dietary analysis. In its original form it can only be used for selenodont, plagiolophodont, and ectolophodont ungulate molars, but the principle can be extended to other kinds of tooth morphology. We introduce a new method of dietary analysis for proboscideans similar to the mesowear method, based on angle measurements from worn dentin valleys reflecting the relief of enamel ridges. The enamel ridges should be heavily worn when the abrasiveness of diet increases, resulting in lower occlusal relief and larger angles. For testing this, we compared the mesowear angles with stable carbon isotope values from dental enamel from populations of extant and fossil species from localities from Kenya and India. This enables us to compare diet and tooth wear in proboscideans, because the stable carbon isotope ratios in tropical environments provide a reliable standard for assessing the relative amounts of C4 and C3 plants in diet, and most of the C4 plants are grasses, which should be reflected in the mesowear signal.</p><p>SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP</p></div

Alpha taxonomy of the Russian Permian procolophonoids

European Russia has been the source of many procolophonoid taxa from both the Permian and Triassic, and a Permian or− igin for the procolophonoid family Procolophonidae has been based on the Russian taxon Microphon exiguus. Recently, this taxon was reclassified as a seymouriamorph and, in its place, the taxa Nyctiphruretus, Suchonosaurus, and Kinelia from the Middle and Upper Permian of Russia were suggested as “procolophons”, using evolutionary−systematic classifi− cation methods. In recent phylogenies, however, Nyctiphruretus has been recovered as a non–procolophonoid para− reptile, whereas Kinelia and Suchonosaurus have never been included in a phylogenetic study. Re−examination indicates that Suchonosaurus is a member of the procolophonoid subfamily Procolophonidae based on the shape of the maxillary bone and the external naris, the laterally visible maxillary depression, and the number and type of maxillary teeth. Kinelia, on the other hand, is excluded from the Procolophonoidea because of its subpleurodont dental attachment and lack of any procolophonoid features. Thus, Suchonosaurus is the only confirmed Permian procolophonid from the Permian of Rus− sia. Additionally, re−examination of the holotype of Microphon exiguus confirms that it is identical to the seymouria− morph specimens recently included in the genus Microphon and that it lacks procolophonoid features. The earliest un− equivocal record of the subfamily Procolophonidae is confirmed from the Late Permian of Russia, making Russia the only region where, with certainty, both Permian and Triassic procolophonids have been discovered

The Origin and Early History of NOW as It Happened

The NOW database of fossil mammals came to be through a confluence of several initiatives spanning multiple decades. The first public version of NOW database was released in 1996 and the first Advisory BoardNOW Databaseadvisory board was established the year after. Originally, NOW stood for Neogene of the Old World but with the gradual expansion of the database the acronym was eventually reassigned to stand for New and Old Worlds. The structure of what would become NOW was originally cloned from the ETE databaseEvolution of Terrestrial Ecosystems (ETE) Database of the Smithsonian Institution and the first NOW version accessible over the internet was a node of the ETE databaseEvolution of Terrestrial Ecosystems (ETE) Database. The first standalone, online version of NOW was launched in 2005 and the first formal steering groupNOW Databasesteering group was established in 2009. During its existence, NOW has been funded, directly or indirectly, by several organizations but fundamentally it has always been an unfunded community effort, dependent on voluntary work by the participants.Peer reviewe