Memory loss can prevent chaos in games dynamics.

Recent studies have raised concerns on the inevitability of chaos in congestion games with large learning rates. We further investigate this phenomenon by exploring the learning dynamics in simple two-resource congestion games, where a continuum of agents learns according to a simplified experience-weighted attraction algorithm. The model is characterized by three key parameters: a population intensity of choice (learning rate), a discount factor (recency bias or exploration parameter), and the cost function asymmetry.

The role of the ecological scaffold in the origin and maintenance of whole-group trait altruism in microbial populations.

Background: Kin and multilevel selection provide explanations for the existence of altruism based on traits or processes that enhance the inclusive fitness of an altruist individual. Kin selection is often based on individual-level traits, such as the ability to recognize other altruists, whereas multilevel selection requires a metapopulation structure and dispersal process. These theories are unified by the general principle that altruism can be fixed by positive selection provided the benefit of altruism is preferentially conferred to other altruists.

Why are whales big? Genes behind ocean giants.

Gigantism is prevalent in animals, but it has never reached more extreme levels than in aquatic mammals such as whales, dolphins, and porpoises. A new study by Silva et al. has uncovered five genes underlying this gigantism, a phenotype with important connections to aging and cancer suppression in long-lived animals.

The gastrointestinal antibiotic resistome in pediatric leukemia and lymphoma patients.

Introduction: Most children with leukemia and lymphoma experience febrile neutropenia. These are treated with empiric antibiotics that include β-lactams and/or vancomycin. These are often administered for extended periods, and the effect on the resistome is unknown.

Evolution of the connectivity and indispensability of a transferable gene: the simplicity hypothesis.

Background: The number of interactions between a transferable gene or its protein product and genes or gene products native to its microbial host is referred to as connectivity. Such interactions impact the tendency of the gene to be retained by evolution following horizontal gene transfer (HGT) into a microbial population. The complexity hypothesis posits that the protein product of a transferable gene with lower connectivity is more likely to function in a way that is beneficial to a new microbial host compared to the protein product of a transferable gene with higher connectivity.

Community-level evolutionary processes: Linking community genetics with replicator-interactor theory.

Understanding community-level selection using Lewontin's criteria requires both community-level inheritance and community-level heritability, and in the discipline of community and ecosystem genetics, these are often conflated. While there are existing studies that show the possibility of both, these studies impose community-level inheritance as a product of the experimental design. For this reason, these experiments provide only weak support for the existence of community-level selection in nature.

Successful Dietary Therapy in Paediatric Crohn's Disease is Associated with Shifts in Bacterial Dysbiosis and Inflammatory Metabotype Towards Healthy Controls.

Background And Aims: Nutritional therapy with the Crohn's Disease Exclusion Diet + Partial Enteral Nutrition [CDED+PEN] or Exclusive Enteral Nutrition [EEN] induces remission and reduces inflammation in mild-to-moderate paediatric Crohn's disease [CD]. We aimed to assess if reaching remission with nutritional therapy is mediated by correcting compositional or functional dysbiosis.

Methods: We assessed metagenome sequences, short chain fatty acids [SCFA] and bile acids [BA] in 54 paediatric CD patients reaching remission after nutritional therapy [with CDED + PEN or EEN] [NCT01728870], compared to 26 paediatric healthy controls.

Antibiotic and antifungal use in pediatric leukemia and lymphoma patients are associated with increasing opportunistic pathogens and decreasing bacteria responsible for activities that enhance colonic defense.

Due to decreased immunity, both antibiotics and antifungals are regularly used in pediatric hematologic-cancer patients as a means to prevent severe infections and febrile neutropenia. The general effect of antibiotics on the human gut microbiome is profound, yielding decreased diversity and changes in community structure. However, the specific effect on pediatric oncology patients is not well-studied.

Ten simple rules for succeeding as an underrepresented STEM undergraduate.

Undergraduate students from underrepresented backgrounds (e.g., Black, Indigenous, and people of color [BIPOC], members of the Deaf community, people with disabilities, members of the 2SLGBTQIA+ community, from low-income backgrounds, or underrepresented genders) continue to face exclusion and marginalization in higher education.

Novel Application of Survival Models for Predicting Microbial Community Transitions with Variable Selection for Environmental DNA.

Survival analysis is a prolific statistical tool in medicine for inferring risk and time to disease-related events. However, it is underutilized in microbiome research to predict microbial community-mediated events, partly due to the sparsity and high-dimensional nature of the data. We advance the application of Cox proportional hazards (Cox PH) survival models to environmental DNA (eDNA) data with feature selection suitable for filtering irrelevant and redundant taxonomic variables.

Evolution of Amino Acid Propensities under Stability-Mediated Epistasis.

Site-specific amino acid preferences are influenced by the genetic background of the protein. The preferences for resident amino acids are expected to, on average, increase over time because of replacements at other sites-a nonadaptive phenomenon referred to as the "evolutionary Stokes shift." Alternatively, decreases in resident amino acid propensity have recently been viewed as evidence of adaptations to external environmental changes.

Shifts in amino acid preferences as proteins evolve: A synthesis of experimental and theoretical work.

Amino acid preferences vary across sites and time. While variation across sites is widely accepted, the extent and frequency of temporal shifts are contentious. Our understanding of the drivers of amino acid preference change is incomplete: To what extent are temporal shifts driven by adaptive versus nonadaptive evolutionary processes? We review phenomena that cause preferences to vary (e.

Gut bacterial gene changes following pegaspargase treatment in pediatric patients with acute lymphoblastic leukemia.

Treatment of pediatric acute lymphoblastic leukemia (ALL) with pegaspargase exploits ALL cells dependency on asparagine. Pegaspargase depletes asparagine, consequentially affecting aspartate, glutamine and glutamate. The gut as a confounding source of these amino acids (AAs) and the role of gut microbiome metabolism of AAs has not been examined.

The role of purifying selection in the origin and maintenance of complex function.

Fitness contribution alone should not be the criterion of 'function' in molecular biology and genomics. Disagreement over the use of 'function' in molecular biology and genomics is still with us, almost eight years after publicity surrounding the Encyclopedia of DNA Elements project claimed that 80.4% of the human genome comprises "functional elements".

Urine lipoarabinomannan for rapid tuberculosis diagnosis in HIV-infected adult outpatients in Khayelitsha.

Background: Decreasing tuberculosis (TB) mortality is constrained by diagnostic and treatment delays. The World Health Organization (WHO) recently actively recommended the point-of-care Alere Determine Lipoarabinomannan Ag assay (AlereLAM) to assist in the diagnosis of tuberculosis in specific HIV-infected outpatients.

Objectives: The primary objective of this study was to compare time to ambulatory TB treatment in HIV-infected adults with CD4 ≤ 100 cells/μL before and after ('primary comparison groups') availability of AlereLAM.

Synthesis of erythro- B13 enantiomers and stereospecific action of full set of B13-isomers in MCF7 breast carcinoma cells: Cellular metabolism and effects on sphingolipids.

B13 is an acid ceramidase (ACDase) inhibitor. The two chiral centers of this aromatic amido alcohol lead to four stereoisomers, yet we have little knowledge about its erythro- enantiomers, (1R, 2S) and (1S, 2R). In this paper, for the first time, the synthesis of two erythro- enantiomers is described, and the compounds are evaluated along with two threo- enantiomers, (1R, 2R) and (1S, 2S).

Investigating the gut microbial community and genes in children with differing levels of change in serum asparaginase activity during pegaspargase treatment for acute lymphoblastic leukemia.

Asparaginase (ASNase) is an effective treatment of pediatric acute lymphoblastic leukemia (ALL). Changes in ASNase activity may lead to suboptimal treatment and poorer outcomes. The gut microbiome produces metabolites that could impact ASNase therapy, however, remains uninvestigated.

Consequences of Stability-Induced Epistasis for Substitution Rates.

Do interactions between residues in a protein (i.e., epistasis) significantly alter evolutionary dynamics? If so, what consequences might they have on inference from traditional codon substitution models which assume site-independence for the sake of computational tractability? To investigate the effects of epistasis on substitution rates, we employed a mechanistic mutation-selection model in conjunction with a fitness framework derived from protein stability.

Re-evaluating the relationship between missing heritability and the microbiome.

Human genome-wide association studies (GWASs) have recurrently estimated lower heritability estimates than familial studies. Many explanations have been suggested to explain these lower estimates, including that a substantial proportion of genetic variation and gene-by-environment interactions are unmeasured in typical GWASs. The human microbiome is potentially related to both of these explanations, but it has been more commonly considered as a source of unmeasured genetic variation.

Modelling Free-Living and Particle-Associated Bacterial Assemblages across the Deep and Hypoxic Lower St. Lawrence Estuary.

The Estuary and Gulf of St. Lawrence (EGSL) in eastern Canada are among the largest and most productive coastal ecosystems in the world. Very little information on bacterial diversity exists, hampering our understanding of the relationships between bacterial community structure and biogeochemical function in the EGSL.

Role of 1-Deoxysphingolipids in docetaxel neurotoxicity.

A major dose-limiting side effect of docetaxel chemotherapy is peripheral neuropathy. Patients' symptoms include pain, numbness, tingling and burning sensations, and motor weakness in the extremities. The molecular mechanism is currently not understood, and there are no treatments available.

Bacterial Taxa and Functions Are Predictive of Sustained Remission Following Exclusive Enteral Nutrition in Pediatric Crohn's Disease.

Background: The gut microbiome is extensively involved in induction of remission in pediatric Crohn's disease (CD) patients by exclusive enteral nutrition (EEN). In this follow-up study of pediatric CD patients undergoing treatment with EEN, we employ machine learning models trained on baseline gut microbiome data to distinguish patients who achieved and sustained remission (SR) from those who did not achieve remission nor relapse (non-SR) by 24 weeks.

Methods: A total of 139 fecal samples were obtained from 22 patients (8-15 years of age) for up to 96 weeks.

The relationship between fecal bile acids and microbiome community structure in pediatric Crohn's disease.

Gut microbiome community structure is associated with Crohn's disease (CD) development and response to therapy. Bile acids (BAs) play a central role in modulating intestinal immune responses, and changes in gut bacterial communities can profoundly alter the intestinal BA pool. The liver synthesizes and conjugates primary bile acids (priBAs) that are then deconjugated, epimerized, and dehydroxylated by gut bacteria to produce secondary bile acids (secBAs).

A Phenotype-Genotype Codon Model for Detecting Adaptive Evolution.

A central objective in biology is to link adaptive evolution in a gene to structural and/or functional phenotypic novelties. Yet most analytic methods make inferences mainly from either phenotypic data or genetic data alone. A small number of models have been developed to infer correlations between the rate of molecular evolution and changes in a discrete or continuous life history trait.

Looking for Darwin in Genomic Sequences: Validity and Success Depends on the Relationship Between Model and Data.

Codon substitution models (CSMs) are commonly used to infer the history of natural section for a set of protein-coding sequences, often with the explicit goal of detecting the signature of positive Darwinian selection. However, the validity and success of CSMs used in conjunction with the maximum likelihood (ML) framework is sometimes challenged with claims that the approach might too often support false conclusions. In this chapter, we use a case study approach to identify four legitimate statistical difficulties associated with inference of evolutionary events using CSMs.