The course aims to provide basic knowledge to understand physical concepts and methods currently applied to medicine. In particular, the student will be acquainted about some basic physical laws, useful to understand the physiological processes and will learn basic concepts useful in the proper use of the equipment used at work.
As prerequisite a basic knowledge of classical physics, algebra, Euclidean geometry and trigonometry are required.
Objective of the course is the acquisition of methods for the analysis of biological sequences and structures and the capability of searching in in biological databases (eg. Genes, sequences, functional domains). Starting from primary sequences of nucleic acids or proteins can hypothesize the function, evolutionary history and structure. The tools used to achieve these objectives are the public databases and the tools for the analysis and visualization of such kind of data.
Knowledge and understanding: Students will gain knowledge on methods for the analysis of biological sequences and for searching in biological databases. In particular students will be able to search on database of sequences and domains. Also, public databases available on NCBI will be presented together with software for the and the analysis and visualization of biological data. Finally, students will acquire the basic tools for the analysis of the transcriptome.
Applying knowledge and understanding: identify the appropriate tools to manipulate data and extract knowledge underlying; solve problems through the use of appropriate software in bioinformatics.
Making judgments: Through guided exercises, the students will acquire the basic skills necessary to deal with the analysis of new biological sequences, hypothesizing the function, study the transcriptome.
Communication skills: the student will acquire the necessary communication skills and expressive appropriateness in the use of technical language within the general framework of the analysis of biological data.
Learning skills: The course aims, as the goal, to provide students with the necessary basic theoretical methods and practices in order to address and solve problems concerning the analysis of biological data.
The course begins with basic knowledge of statistics, presenting methods for descriptive statistics of various kinds of data. The fundamental tests used in biomedical statistics will be presented. Key concepts of epidemiological methodology will be presented. At the end of the course the student will be able to understand statistical results reported in biomedical literature, and to use simple techniques for statistical analysis and presentation of results.
Physical quantities and their measurement - Physical quantities, units and systems of measurement, dimensional analysis. Measurements and uncertainties. Characteristics of measuring Instruments. Analytical and graphical representations. Scalar and vector quantities.
Elements of mechanics and concepts of Biomechanics - Kinematics. Circular and harmonic motion. Momentum. Principles of dynamics. Work. Energy. Power and efficiency. Statics. Elasticity. Physiological statics. Essential of bone fractures.
Basics of fluids and applications in biological systems – Density. Viscosity. Hydrostatic pressure. Fluid statics. Stevin’s law. Pascal’s principle. Archimede’s principle. Drip feed. Transfusion. Blood sample. Drainage. Dynamics of ideal fluids. Bernoulli's theorem. Aneurysm and stenosis. Real liquids. Poiseuille’s law. Hydraulic resistance and Reynold’s number. Sphygmomanometry.
Temperature measurement and thermoregulation – Temperature and heat. Temperature metrology. Temperature scales. Clinical thermometers. Heat capacity and Specific Heat. Thermal equilibrium. Change of phase and latent heat. Heat transfer mechanisms. Basal metabolic power.
Electrical and bioelectrical phenomena – Electrical charges and fields. Capacitors. Electrical current. Ohm's law. Elementary circuits. Joule effect. RC circuits. Pacemaker and defibrillator. Risks related to the use of electricity.
Waves and radiations. – Wave phenomena. Period and frequency. Amplitude and energy. Mechanical waves. Sound. Decibel. Phonendoscope. Ultrasonic waves. Electromagnetic waves. Electromagnetic spectrum. Eye and vision. Radiation for diagnostics and therapy. X ray imaging. Radioisotopes and nuclear medicine. Radiotherapy. Biological effects of ionizing radiation. Introduction to radiation protection dosimetry.
Introducion to relational Databases: • Data representation; • The Relational model; • Relational Algebra; • Database Design; • Access: Tables, queries, report, forms; • Examples and case studies. Biological and biomedical databases: - NCBI: The Entrez system. Methods for querying databases Gene, Nucleotide, Protein, PubMed, OMIM. - Special purpors databases: Protein Data Bank (PDB), Single Nucleotide Polymorphism DB (SNP), Gene Expression Omnibus (GEO), Genome, UCSC, ENSEMBL, Gene Ontologies DB, BioSystem Pathways, KEGG Patways, Patways Commons, Tarbase, Mirò, mirBase, Expressed Sequence Tag (EST).
Introduction to statistics:
Probability and statistical inference
D. Scannicchio - Fisica Biomedica - EdiSES, Napoli 2013
Pagano, Gauvreau. "Principles of biostatistics". Duxbury Press
Swinscow, Campbell. “Statistics at square one”, Wiley, 2009