Phyolin: Identifying a Linear Perfect Phylogeny in Single-Cell DNA Sequencing Data of Tumors

Cancer arises from an evolutionary process where somatic mutations occur and eventually give rise to clonal expansions. Modeling this evolutionary process as a phylogeny is useful for treatment decision-making as well as understanding evolutionary patterns across patients and cancer types. However, cancer phylogeny inference from single-cell DNA sequencing data of tumors is challenging due to limitations with sequencing technology and the complexity of the resulting problem. Therefore, as a first step some value might be obtained from correctly classifying the evolutionary process as either linear or branched. The biological implications of these two high-level patterns are different and understanding what cancer types and which patients have each of these trajectories could provide useful insight for both clinicians and researchers. Here, we introduce the Linear Perfect Phylogeny Flipping Problem as a means of testing a null model that the tree topology is linear and show that it is NP-hard. We develop Phyolin and, through both in silico experiments and real data application, show that it is an accurate, easy to use and a reasonably fast method for classifying an evolutionary trajectory as linear or branched

Mathematical Modeling Describing the Effect of Fishing and Dispersion on Hermaphrodite Population Dynamics

International audienceIn order to study the impact of fishing on a grouper population, we propose in this paper to model the dynamics of a grouper population in a fishing territory by using structured models. For that purpose, we have integrated the natural population growth, the fishing, the competition for shelter and the dispersion. The dispersion was considered as a consequence of the competition. First we prove, that the grouper stocks may be less sensitive to the removal of large male individuals if female population are totally protected. Second, we show that fishing does not disturb the demographic structure of the population. Finally, we prove that female selective fisheries have the potential of drastically reduce reproductive rates. We also prove that male fishing decreases competition and then increases the total population number

Complex Network Approaches for Epidemic Modeling: A Case Study of COVID-19

Since the SARS-CoV-2 outbreak, the importance of mathematical modeling as a tool for comprehending disease dynamics has been highlighted, with several mathematical modeling techniques being applied and developed to simulate and measure the impact of interventions aimed at controlling the spread of the disease and minimizing its burden. In this work, we applied complex network techniques to analyze a Susceptible-Exposed-Asymptomatic-Hospitalized-Recovered (SEAHR) model to describe COVID-19 transmission dynamics, using the Basque Country region of Spain as a case study. We compared two network modeling approaches: the Watts-Strogatz network and the Barabasi-Albert scale-free network. By applying immunization strategies on both networks, we demonstrate that targeted immunization yields superior results within a scale-free network due to its increased heterogeneity. Moreover, the basic reproduction number of the model is calculated, and sensitivity analysis is performed to determine the influence of the model parameters on the disease dynamics.Juan de la Cierva Formación grant FJC2021-046826-I

Phase II trial of temsirolimus for relapsed/refractory primary CNS lymphoma

Purpose: In this phase II study (NCT00942747), temsirolimus was tested in patients with relapsed or refractory primary CNS lymphoma (PCNSL). Patients and Methods: Immunocompetent adults with histologically confirmed PCNSL after experiencing high-dose methotrexate-based chemotherapy failure who were not eligible for or had experienced high-dose chemotherapy with autologous stem-cell transplant failure were included. The first cohort (n = 6) received 25 mg temsirolimus intravenously once per week. All consecutive patients received 75 mg intravenously once per week. Results: Thirty-seven eligible patients (median age, 70 years) were included whose median time since their last treatment was 3.9 months (range, 0.1 to 14.6 months). Complete response was seen in five patients (13.5%), complete response unconfirmed in three (8%), and partial response in 12 (32.4%) for an overall response rate of 54%. Median progression-free survival was 2.1 months (95% CI, 1.1 to 3.0 months). The most frequent Common Toxicity Criteria ≥ 3° adverse event was hyperglycemia in 11 (29.7%) patients, thrombocytopenia in eight (21.6%), infection in seven (19%), anemia in four (10.8%), and rash in three (8.1%). Fourteen blood/CSF pairs were collected in nine patients (10 pairs in five patients in the 25-mg cohort and four pairs in four patients in the 75-mg cohort). The mean maximum blood concentration was 292 ng/mL for temsirolimus and 37.2 ng/mL for its metabolite sirolimus in the 25-mg cohort and 484 ng/mL and 91.1 ng/mL, respectively, in the 75-mg cohort. Temsirolimus CSF concentration was 2 ng/mL in one patient in the 75-mg cohort; in all others, no drug was found in their CSF. Conclusion: Single-agent temsirolimus at a weekly dose of 75 mg was found to be active in relapsed/refractory patients with PCNSL; however, responses were usually short lived

13-Series resolvins mediate the leukocyte-platelet actions of atorvastatin and pravastatin in inflammatory arthritis

This work was supported by funding from the European Research Council under the European Union’s Horizon 2020 research and innovation program (Grant 677542), a Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (Grant 107613/Z/15/Z), and the Barts Charity (Grant MGU0343). This work was also funded, in part, by Medical Research Council Advance Course Masters (Grant MR/J015741/1). The authors declare no conflicts of interest

Formyl Peptide Receptor as a Novel Therapeutic Target for Anxiety-Related Disorders

Formyl peptide receptors (FPR) belong to a family of sensors of the immune system that detect microbe-associated molecules and inform various cellular and sensorial mechanisms to the presence of pathogens in the host. Here we demonstrate that Fpr2/3-deficient mice show a distinct profile of behaviour characterised by reduced anxiety in the marble burying and light-dark box paradigms, increased exploratory behaviour in an open-field, together with superior performance on a novel object recognition test. Pharmacological blockade with a formyl peptide receptor antagonist, Boc2, in wild type mice reproduced most of the behavioural changes observed in the Fpr2/3(-/-) mice, including a significant improvement in novel object discrimination and reduced anxiety in a light/dark shuttle test. These effects were associated with reduced FPR signalling in the gut as shown by the significant reduction in the levels of p-p38. Collectively, these findings suggest that homeostatic FPR signalling exerts a modulatory effect on anxiety-like behaviours. These findings thus suggest that therapies targeting FPRs may be a novel approach to ameliorate behavioural abnormalities present in neuropsychiatric disorders at the cognitive-emotional interface

Novel R-roscovitine NO-donor hybrid compounds as potential pro-resolution of inflammation agents

AbstractNeutrophils play a pivotal role in the pathophysiology of multiple human inflammatory diseases. Novel pharmacological strategies which drive neutrophils to undergo programmed cell death (apoptosis) have been shown to facilitate the resolution of inflammation. Both the cyclin-dependent kinase inhibitor (CDKi) R-roscovitine and nitric oxide (NO) have been shown to enhance apoptosis of neutrophils and possess pro-resolution of inflammation properties. In order to search for new multi-target pro-resolution derivatives, here we describe the design, synthesis and investigation of the biological potential of a small series of hybrid compounds obtained by conjugating R-roscovitine with two different NO-donor moieties (compounds 2, 9a, 9c). The synthesized compounds were tested as potential pro-resolution agents, with their ability to promote human neutrophil apoptosis evaluated. Both compound 9a and 9c showed an increased pro-apoptotic activity when compared with either R-roscovitine or structurally related compounds devoid of the ability to release NO (des-NO analogues). Inhibition of either NO-synthase or soluble guanylate cyclase did not affect the induction of apoptosis by the R-roscovitine derivatives, similar to that reported for other classes of NO-donors. In contrast the NO scavenger PTIO prevented the enhanced apoptosis seen with compound 9a over R-roscovitine. These data show that novel compounds such as CDKi–NO-donor hybrids may have additive pro-resolution of inflammation effects