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

DeCiFering the elusive cancer cell fraction in tumor heterogeneity and evolution

The cancer cell fraction (CCF), or proportion of cancerous cells in a tumor containing a single-nucleotide variant (SNV), is a fundamental statistic used to quantify tumor heterogeneity and evolution. Existing CCF estimation methods from bulk DNA sequencing data assume that every cell with an SNV contains the same number of copies of the SNV. This assumption is unrealistic in tumors with copy-number aberrations that alter SNV multiplicities. Furthermore, the CCF does not account for SNV losses due to copy-number aberrations, confounding downstream phylogenetic analyses. We introduce DeCiFer, an algorithm that overcomes these limitations by clustering SNVs using a novel statistic, the descendant cell fraction (DCF). The DCF quantifies both the prevalence of an SNV at the present time and its past evolutionary history using an evolutionary model that allows mutation losses. We show that DeCiFer yields more parsimonious reconstructions of tumor evolution than previously reported for 49 prostate cancer samples

The copy-number tree mixture deconvolution problem and applications to multi-sample bulk sequencing tumor data

Cancer is an evolutionary process driven by somatic mutation. This process can be represented as a phylogenetic tree. Constructing such a phylogenetic tree from genome sequencing data is a challenging task due to the mutational complexity of cancer and the fact that nearly all cancer sequencing is of bulk tissue, measuring a super-position of somatic mutations present in different cells. We study the problem of reconstructing tumor phylogenies from copy number aberrations (CNAs) measured in bulk-sequencing data. We introduce the Copy-Number Tree Mixture Deconvolution (CNTMD) problem, which aims to find the phylogenetic tree with the fewest number of CNAs that explain the copy number data from multiple samples of a tumor. CNTMD generalizes two approaches that have been researched intensively in recent years: deconvolution/factorization algorithms that aim to infer the number and proportions of clones in a mixed tumor sample; and phylogenetic models of copy number evolution that model the dependencies between copy number events that affect the same genomic loci. We design an algorithm for solving the CNTMD problem and apply the algorithm to both simulated and real data. On simulated data, we find that our algorithm outperforms existing approaches that perform either deconvolution or phylogenetic tree construction under the assumption of a single tumor clone per sample. On real data, we analyze multiple samples from a prostate cancer patient, identifying clones within these samples and a phylogenetic tree that relates these clones and their differing proportions across samples. This phylogenetic tree provides a higher-resolution view of copy number evolution of this cancer than published analyses

Modeling and Optimization of Hybrid Fenton and Ultrasound Process for Crystal Violet Degradation Using AI Techniques

\ua9 2023 by the authors. This study conducts a comprehensive investigation to optimize the degradation of crystal violet (CV) dye using the Fenton process. The main objective is to improve the efficiency of the Fenton process by optimizing various physicochemical factors such as the Fe2+ concentration, H2O2 concentration, and pH of the solution. The results obtained show that the optimal dosages of Fe2+ and H2O2 giving a maximum CV degradation (99%) are 0.2 and 3.13 mM, respectively. The optimal solution pH for CV degradation is 3. The investigation of the type of acid for pH adjustment revealed that sulfuric acid is the most effective one, providing 100% yield, followed by phosphoric acid, hydrochloric acid, and nitric acid. Furthermore, the examination of sulfuric acid concentration shows that an optimal concentration of 0.1 M is the most effective for CV degradation. On the other hand, an increase in the initial concentration of the dye leads to a reduction in the hydroxyl radicals formed (HO•), which negatively impacts CV degradation. A concentration of 10 mg/L of CV gives complete degradation of dye within 30 min following the reaction. Increasing the solution temperature and stirring speed have a negative effect on dye degradation. Moreover, the combination of ultrasound with the Fenton process resulted in a slight enhancement in the CV degradation, with an optimal stirring speed of 300 rpm. Notably, the study incorporates the use of Gaussian process regression (GPR) modeling in conjunction with the Improved Grey Wolf Optimization (IGWO) algorithm to accurately predict the optimal degradation conditions. This research, through its rigorous investigation and advanced modeling techniques, offers invaluable insights and guidelines for optimizing the Fenton process in the context of CV degradation, thereby achieving the twin goals of cost reduction and environmental impact minimization

Formulation and Characterization of Double Emulsions W/O/W Stabilized by Two Natural Polymers with Two Manufacturing Processes (Comparative Study)

\ua9 2024 by the authors.Four distinct types of multiple emulsions were synthesized using xanthan gum and pectin through two distinct manufacturing processes. The assessment encompassed the examination of morphology, stability, and rheological properties for the resulting water-in-oil-in-water (W/O/W) double emulsions. Formulations were meticulously crafted with emulsifiers that were compatible with varying compositions. Remarkably stable multiple emulsions were achieved with a 0.5 wt% xanthan concentration, demonstrating resilience for nearly two months across diverse storage temperatures. In contrast, multiple emulsions formulated with a higher pectin concentration (2.75 wt%) exhibited instability within a mere three days. All multiple emulsions displayed shear-thinning behavior, characterized by a decline in apparent viscosity with escalating shear rates. Comparatively, multiple emulsions incorporating xanthan gum showcased elevated viscosity at low shear rates in contrast to those formulated with pectin. These results underscore the pivotal role of the stepwise process over the direct approach and emphasize the direct correlation between biopolymer concentration and emulsion stability. This present investigation demonstrated the potential use of pectin and xanthan gum as stabilizers of multiple emulsions with potential application in the pharmaceutical industry for the formulation of topical dosage forms

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

An Introductory Guide to Aligning Networks Using SANA, the Simulated Annealing Network Aligner.

Sequence alignment has had an enormous impact on our understanding of biology, evolution, and disease. The alignment of biological networks holds similar promise. Biological networks generally model interactions between biomolecules such as proteins, genes, metabolites, or mRNAs. There is strong evidence that the network topology-the "structure" of the network-is correlated with the functions performed, so that network topology can be used to help predict or understand function. However, unlike sequence comparison and alignment-which is an essentially solved problem-network comparison and alignment is an NP-complete problem for which heuristic algorithms must be used.Here we introduce SANA, the Simulated Annealing Network Aligner. SANA is one of many algorithms proposed for the arena of biological network alignment. In the context of global network alignment, SANA stands out for its speed, memory efficiency, ease-of-use, and flexibility in the arena of producing alignments between two or more networks. SANA produces better alignments in minutes on a laptop than most other algorithms can produce in hours or days of CPU time on large server-class machines. We walk the user through how to use SANA for several types of biomolecular networks

Evaluating the Effectiveness of Coagulation–Flocculation Treatment Using Aluminum Sulfate on a Polluted Surface Water Source: A Year-Long Study

\ua9 2024 by the authors.Safeguarding drinking water is a major public health and environmental concern because it is essential to human life but may contain pollutants that can cause illness or harm the environment. Therefore, continuous research is necessary to improve water treatment methods and guarantee its quality. As part of this study, the effectiveness of coagulation–flocculation treatment using aluminum sulfate (Al2(SO4)3) was evaluated on a very polluted site. Samplings were taken almost every day for a month from the polluted site, and the samples were characterized by several physicochemical properties, such as hydrogen potential (pH), electrical conductivity, turbidity, organic matter, ammonium (NH+4), phosphate (PO43−), nitrate (NO3−), nitrite (NO2−), calcium (Ca2+), magnesium (Mg2+), total hardness (TH), chloride (Cl−), bicarbonate (HCO3−), sulfate (SO42−), iron (Fe3+), manganese (Mn2+), aluminum (Al3+), potassium (K+), sodium (Na+), complete alkalimetric titration (TAC), and dry residue (DR). Then, these samples were treated with Al2(SO4)3 using the jar test method, which is a common method to determine the optimal amount of coagulant to add to the water based on its physicochemical characteristics. A mathematical model had been previously created using the support vector machine method to predict the dose of coagulant according to the parameters of temperature, pH, TAC, conductivity, and turbidity. This Al2(SO4)3 treatment step was repeated at the end of each month for a year, and a second characterization of the physicochemical parameters was carried out in order to compare them with those of the raw water. The results showed a very effective elimination of the various pollutions, with a very high rate, thus demonstrating the effectiveness of the Al2(SO4)3. The physicochemical parameters measured after the treatment showed a significant reduction in the majority of the physicochemical parameters. These results demonstrated that the coagulation–flocculation treatment with Al2(SO4)3 was very effective in eliminating the various pollutions present in the raw water. They also stress the importance of continued research in the field of water treatment to improve the quality of drinking water and protect public health and the environment

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