Correlation Between Animal and Mathematical Models for Prostate Cancer Progression

This work demonstrates that prostate tumour progression in vivo can be analysed by using solutions of a mathematical model supplemented by initial conditions chosen according to growth rates of cell lines in vitro. The mathematical model is investigated and solved numerically. Its numerical solutions are compared with experimental data from animal models. The numerical results confirm the experimental results with the growth rates in vivo

Applications of Machine Learning in Human Microbiome Studies: A Review on Feature Selection, Biomarker Identification, Disease Prediction and Treatment

The number of microbiome-related studies has notably increased the availability of data on human microbiome composition and function. These studies provide the essential material to deeply explore host-microbiome associations and their relation to the development and progression of various complex diseases. Improved data-analytical tools are needed to exploit all information from these biological datasets, taking into account the peculiarities of microbiome data, i.e., compositional, heterogeneous and sparse nature of these datasets. The possibility of predicting host-phenotypes based on taxonomy-informed feature selection to establish an association between microbiome and predict disease states is beneficial for personalized medicine. In this regard, machine learning (ML) provides new insights into the development of models that can be used to predict outputs, such as classification and prediction in microbiology, infer host phenotypes to predict diseases and use microbial communities to stratify patients by their characterization of state-specific microbial signatures. Here we review the state-of-the-art ML methods and respective software applied in human microbiome studies, performed as part of the COST Action ML4Microbiome activities. This scoping review focuses on the application of ML in microbiome studies related to association and clinical use for diagnostics, prognostics, and therapeutics. Although the data presented here is more related to the bacterial community, many algorithms could be applied in general, regardless of the feature type. This literature and software review covering this broad topic is aligned with the scoping review methodology. The manual identification of data sources has been complemented with: (1) automated publication search through digital libraries of the three major publishers using natural language processing (NLP) Toolkit, and (2) an automated identification of relevant software repositories on GitHub and ranking of the related research papers relying on learning to rank approach

Applications of Machine Learning in Human Microbiome Studies: A Review on Feature Selection, Biomarker Identification, Disease Prediction and Treatment

The number of microbiome-related studies has notably increased the availability of data on human microbiome composition and function. These studies provide the essential material to deeply explore host-microbiome associations and their relation to the development and progression of various complex diseases. Improved data-analytical tools are needed to exploit all information from these biological datasets, taking into account the peculiarities of microbiome data, i.e., compositional, heterogeneous and sparse nature of these datasets. The possibility of predicting host-phenotypes based on taxonomy-informed feature selection to establish an association between microbiome and predict disease states is beneficial for personalized medicine. In this regard, machine learning (ML) provides new insights into the development of models that can be used to predict outputs, such as classification and prediction in microbiology, infer host phenotypes to predict diseases and use microbial communities to stratify patients by their characterization of state-specific microbial signatures. Here we review the state-of-the-art ML methods and respective software applied in human microbiome studies, performed as part of the COST Action ML4Microbiome activities. This scoping review focuses on the application of ML in microbiome studies related to association and clinical use for diagnostics, prognostics, and therapeutics. Although the data presented here is more related to the bacterial community, many algorithms could be applied in general, regardless of the feature type. This literature and software review covering this broad topic is aligned with the scoping review methodology. The manual identification of data sources has been complemented with: (1) automated publication search through digital libraries of the three major publishers using natural language processing (NLP) Toolkit, and (2) an automated identification of relevant software repositories on GitHub and ranking of the related research papers relying on learning to rank approach

Mathematical Modeling of Autoimmune Diseases

The human organism is a very complex system. To be in good health, its components must function properly. One of the most important systems of an organism is the immune system. It protects the body from the harmful effects of various external and internal agents. Sometimes, however, the immune system starts attacking its own healthy cells, tissues and organs. Then autoimmune diseases arise. They are widespread in recent decades. There is evidence that often autoimmune responses occur due to viral infections. In this paper, a new mathematical model of a general autoimmune disease is proposed. It describes the interactions between viral particles and host cells. The model is formulated by using integro-differential equations of Boltzmann type. This approach is typical for the nonequilibrium statistical mechanics. A preliminary qualitative and quantitative analysis of the model is presented

An Unconditional Positivity-Preserving Difference Scheme for Models of Cancer Migration and Invasion

In this paper, we consider models of cancer migration and invasion, which consist of two nonlinear parabolic equations (one of the convection–diffusion reaction type and the other of the diffusion–reaction type) and an additional nonlinear ordinary differential equation. The unknowns represent concentrations or densities that cannot be negative. Widely used approximations, such as difference schemes, can produce negative solutions because of truncation errors and can become unstable. We propose a new difference scheme that guarantees the positivity of the numerical solution for arbitrary mesh step sizes. It has explicit and fast performance even for nonlinear reaction terms that consist of sums of positive and negative functions. The numerical examples illustrate the simplicity and efficiency of the method. A numerical simulation of a model of cancer migration is also discussed

A mathematical model of some viral-induced autoimmune diseases

Proponujemy nowy matematyczny model wirusowych chorób autoimmunologicznych który opisany jest dwuliniowym układem czterech równań różniczkowo-różniczkowych typu Boltzmanna. Prezentujemy wyniki liczbowe ilustrujące kilka typowych takich chorób. W szczególności szczególną uwagę poświęca się roli zdolności efektorowych komórek odpornościowych do niszczenia komórek docelowych do rozwoju chorób autoimmunologicznych. We consider a mathematical model of autoimmune disease. The model is described by a bilinear system of four integro-differential equations of Boltzmann type. We present numerical results illustrating several typical outcomes of autoimmune disease. In particular, special attention is devoted to the role of viral infections for development of autoimmune diseases

Numerical Versus Experimental Data for Prostate Tumour Growth

The goal of this paper is to solve mathematical model equations on solid tumour growth and compute their parameter values by applying growth rates of prostate cancer cell lines in vivo. For these computations, we investigate previously developed C3(1)/Tag transgenic models of prostate cancer. To make the computations fast, we have constructed an algorithm, which is based on small amounts of spatial grid-points and obtained a correspondence between the in vivo growth of tumours and the solutions of the model equations

An Unconditional Positivity-Preserving Difference Scheme for Models of Cancer Migration and Invasion

In this paper, we consider models of cancer migration and invasion, which consist of two nonlinear parabolic equations (one of the convection–diffusion reaction type and the other of the diffusion–reaction type) and an additional nonlinear ordinary differential equation. The unknowns represent concentrations or densities that cannot be negative. Widely used approximations, such as difference schemes, can produce negative solutions because of truncation errors and can become unstable. We propose a new difference scheme that guarantees the positivity of the numerical solution for arbitrary mesh step sizes. It has explicit and fast performance even for nonlinear reaction terms that consist of sums of positive and negative functions. The numerical examples illustrate the simplicity and efficiency of the method. A numerical simulation of a model of cancer migration is also discussed

Incremental anomaly identification in flight data analysis by adapted one-class SVM method

In our work we used the capability of one-class support vector machine (SVM) method to develop a novel one-class classification approach. Algorithm is designed and tested, aimed for fault detection in complex technological systems, such as aircraft. The main objective of this project was to create an algorithm responsible for collecting and analyzing the data since the launch of an aircraft engine. Data can be transferred from a variety of sensors that are responsible for the speed, oil temperature and etc. In order to provide high generalization level and sufficient learning data sets an incremental algorithm is considered. The proposed method analyzes both “positive”/“normal” and “negative”/ “abnormal” examples. However, overall model structure is based on one-class classification paradigm. Modified SVM-base outlier detection method is verified in comparison with several classifiers, including the traditional one-class SVM. This algorithm has been tested on real flight data from the Western European and Russia. The test results are presented in the final part of the article

The "GEnomics of Musculo Skeletal Traits TranslatiOnal NEtwork" : Origins, Rationale, Organization, and Prospects

Musculoskeletal research has been enriched in the past ten years with a great wealth of new discoveries arising from genome wide association studies (GWAS). In addition to the novel factors identified by GWAS, the advent of whole-genome and whole-exome sequencing efforts in family based studies has also identified new genes and pathways. However, the function and the mechanisms by which such genes influence clinical traits remain largely unknown. There is imperative need to bring multidisciplinary expertise together that will allow translating these genomic discoveries into useful clinical applications with the potential of improving patient care. Therefore "GEnomics of MusculoSkeletal traits TranslatiOnal NEtwork" (GEMSTONE) aims to set the ground for the: 1) functional characterization of discovered genes and pathways; 2) understanding of the correspondence between molecular and clinical assessments; and 3) implementation of novel methodological approaches. This research network is funded by The European Cooperation in Science and Technology (COST). GEMSTONE includes six working groups (WG), each with specific objectives: WG1-Study populations and expertise groups: creating, maintaining and updating an inventory of experts and resources (studies and datasets) participating in the network, helping to assemble focus groups defined by phenotype, functional and methodological expertise. WG2-Phenotyping: describe ways to decompose the phenotypes of the different functional studies into meaningful components that will aid the interpretation of identified biological pathways. WG3 Monogenic conditions - human KO models: makes an inventory of genes underlying musculoskeletal monogenic conditions that aids the assignment of genes to GWAS signals and prioritizing GWAS genes as candidates responsible for monogenic presentations, through biological plausibility. WG4 Functional investigations: creating a roadmap of genes and pathways to be prioritized for functional assessment in cell and organism models of the musculoskeletal system. WG5 Bioinformatics seeks the integration of the knowledge derived from the distinct efforts, with particular emphasis on systems biology and artificial intelligence applications. Finally, WG6 Translational outreach: makes a synopsis of the knowledge derived from the distinct efforts, allowing to prioritize factors within biological pathways, use refined disease trait definitions and/or improve study design of future investigations in a potential therapeutic context (e.g. clinical trials) for musculoskeletal diseases.Peer reviewe