Genome sequencing of domestic animals and advances in quantitative genetics have enable new approaches in animal breeding. This course will talk about recent advances in the area of quantitative genetics and genomics and the aplications in beef cattle breeding. The course will have the contribution of especialists in different areas. Provide the principles of quantitative genetics aplied to genome selection and genomics, so the students can understand a contribute to the development of this new area. Luiz de Queiroz College of Agriculture (ESALQ) Piracicaba campus The U.S. Beef Industry: Structure and Current Genetic Selection Programs; Priors in the Bayesian Alphabet; Developing Genomic Predictions: Training and Evaluation; Additive genomic relationship matrix and GBLUP; Haplotype-based models: BayesIM; Interpreting “genomic correlations” and pleiotropy; Tour of Genomics Center; Population structure in admixed populations; Reproducing kernel Hilbert spaces regression; GO enrichment analysis; MeSH enrichment analysis; GO / MeSH enrichment analysis in Bioconductor Luiz Lehmann Coutinho, Gerson Barreto Mour_o 75 LZT5869 4 University of Sao Paulo,Universidade de Campinas and Universidade Estadual Paulista Student participation and Exam. http://pt.esalq.usp.br/

The joint development of areas such as discrete mathematics, probability, operational research and computer theory is continuous and relevant. The solution of theoretical and applied problems in these areas can be given in terms of a probabilistic modeling that arises from physics as well as the analysis of engineering systems or areas such as economics, biology, engineering, neuroscience. The tools used in such modeling include Markov chains, martingales, stochastic optimization, coupling and combinatorics. Introduce and apply probability topics such as Markov chains, coupling and Poisson approaches through concrete examples such as those from the stochastic models for information theory, engineering, combinatorics, biology, neuroscience and other areas of application of Probability and Stochastic Processes. Institute of Mathematics ans Statistics (IME) São Paulo main campus 1. Discrete Probability Models; 2. Markov chains; 3. Recurrence and ergodicity; 4. Coupling and limiting behavior; 5. Martingales; 6. Renewal processes; 7. Contemporary Topics: Variable Range, Poisson Approximations, Reliability Theory, and Queue Theory Fabio Prates Machado, Luiz Renato Goncalves Fontes, Miguel Natalio Abadi 50 MAE5703 8 The evaluation will consist of the score’s average of tests and lists of exercises. https://www.ime.usp.br/en

Exploratory data analysis and computational techiques are fundamental to understand modern modern statistical methods. Introduce modern techniques of data analysis with concomitant using of computer. Using statistical packages. Institute of Mathematics ans Statistics (IME) São Paulo main campus 1. Exploratory data analysis (univariate and multivariate): position measurements, dispersion, asymmetry, robust measures, bivariate measures, association between variables, outliers identification, processing variables, graphics. 2. Linear Regression Models, Regression Tough and Smoothing Methods. 3. Stochastic Simulation: inversion methods, rejection, composition and resampling methods. 4. Numerical Optimization: Newton-Raphson, scoring, quasi-Newton. 5. EM Algorithm. 6. “Bootstrap” and “Jacknife”. 7. Monte Carlo methods and Gaussian quadratures Denise Aparecida Botter, Eduardo Jordao Neves, Anatoli Iambartsev 40 MAE5704 8 Tests, Lists of exercises and seminars https://www.ime.usp.br/en

The concept of natural resources remains vague and loose. Thus, there is a tenuous limit between what is still natural resource and what is already transformed by mankind to some extent. I the same way, a mere classification of renewable and exhaustible resources is insufficient to promote a satisfactory comprehension about this subject. Hence, before analysing natural resources themselves, it is necessary to undertake a conceptual revision that strengthens the accuracy of definitions towards their empirical correspondent objects – Mature the conceptual background about natural resources under a geographical perspective through which social and natural dimensions merge. – Comprehend the complex relationship between natural resources and human development. – Develop analysis skills by building links between conceptual background and Brazil´s natural resources. Faculty of Philosophy, Languages and Human Sciences (FFLCH) São Paulo main campus 1 – The concept of natural resource and its derivations Introduction 1.1 Some complementary issues 1.2 Renewable x exhaustible resources: a false antagonism 1.3 Renewable or Inexhaustible? 1.4 Difference between renewable and naturally recyclable resources: the case of water 1.5 Difference between renewable and reproductive resource Conclusions Activities 2 – The richness of resources in Brazil: natural premises Introduction 2.1 Geographical positioning and climate features 2.2 Tectonic: the architecture of territory and water concentration 2.3 Macro-structures: cratons, sedimentary basins and orogenic belts 2.4 Macro-sculptures: highlands, plains and depressions 2.5 Biodiversity: the result of combination of the landscape components Conclusions Activities 3 – Natural resources and territorial organisation Introduction 3.1 Global scale 3.2 Continental scale: Latin America 3.3 National scale: Egypt 3.4 Regional scale: Amazon 3.5 Local scale: coastal areas 3.6 Other examples 3.7 Territorial configuration beyond natural resources 3.8 The influence of natural conditions over the urbanisation of S_o Paulo State Activities 4 – Energy: an essential knowledge Introduction 4.1 Brief historic of use 4.2 Useful concepts: energy, force, work 4.3 Types of energy and possibilities of conversions 4.4 Potency and efficiency 4.5 Energy losses and rational use Conclusions Our vital virtual energy Activities EMPIRICAL LESSONS 5 _ Non-renewable minerals for energy generation Introduction 5.1 Hydrocarbons – Petrol – Natural gas – Shale gas – Coal 5.2 Uranium Activities 6 – Minerais (non-renewables, renewables and inexhaustibles) for other uses Introduction 6.1 Impacts and restoration 6.2 Raw material for construction – Aggregates, Stones, Sands, Clays, Chalk – Aggregates from rejects (non-naturals) 6.3 Other minerals (non-metallics) – Evaporites: salt and gypsum – Barite 6.4 Soils – Conservation of soils 6.5 Agrochemicals and natural resources 6.6 Ferrous metallic minerals – Iron ore – Other ferrous metallic minerals 6.7 Non-ferrous metallic minerals – Aluminium ore – Copper ore – Other non-ferrous metallic minerals Activities 7 – Renewable and reproductive natural resources: biomass Introduction 7.1 Biomass for food production – Agriculture – Livestock – Aquaculture and mariculture 7.2 Biomass for energy production – Modern biomass – Traditional and other biomasses 7.3 Biomass for other uses – Silviculture – Timber from deforestation – Other biomasses 7.4 Biomass related to environment preservation – Protected areas – Sustainable ways to produce biomass – The milestone of biodiversity and bio-piracy Conclusions Activities 8 – Water resources: a special chapter Introduction 8.1 Definition and essential information – Atmospheric waters – Superficial, fresh and liquid waters – Underground fresh water 8.2 Water uses – Non-energy uses – Energy uses 8.3 Desalination of ocean water 8.4 The Brazilian paradox 8.5 San Peter: wanted alive or dead 8.6 S_o Francisco river transposition 8.7 Perspectives Activities 9 – Natural resources for non-traditional or alternative energy production Introduction 9.1 Sun energy – Transformation of Sun energy into thermo-energy – Transformation of Sun energy into electrical energy 9.2 Wind energy 9.3 Geothermal energy – Transformation of geothermal energy into electricity – Geothermal energy in Brazil 9.4 Alternative hydraulic energy – Tidal energy – Wave energy – Water flow energy 9.5 Hydrogen (H2) Conclusion Activities Luis Antonio Bittar Venturi 42 FLG5144 8 Fieldworks may have alterations due to logistic issues All demanded activities during the course will be assessed. The final mark will be composed by the average marks of: exercises (E), seminars (S), fieldwork repo https://www.google.com.br/url?sa=t&rct=j&q=&esrc=s&source=web&cd=10&ved=0ahUKEwi3paLQ9tzYAhXBE5AKHdAvBDkQFghfMAk&url=http%3A%2F%2Fwww.ru.nl%2Fpublish%2Fpages%2F798477%2Fstudent_guide_fflch.pdf&usg=AOvVaw1Cv-BPFTbngDpr4qVjQBud

The course offers an introduction to programming logic and computational tools for the social sciences graduate students. The course focus on procedures to (1) gather (2) organize and (3) present social data. The course aims to develop programming skills for handling data with academic purposes. Notice that this is not a methods, data analysis or computational social science course. The course is divided in two parts. In the first part we focus on preparing the computational enviroment, getting used with the tools and developing programming literacy in R, Git, SQL, Markdown, and other languages required in class. In the second part we apply the skills acquired in the first part to handle big datasets, webscrapping and third party APIs, digital files management for textual analysis, graphs, maps and other topics of interest. This course aims to fill a gap _common among social science students- providing the training in data management and computational skills Faculty of Philosophy, Languages and Human Sciences (FFLCH) São Paulo main campus 1 – Basics of R Programming 2 – Data structures and data management in R 3 – Tables and graphs in R 4 _ R + SQL basics 5 – Git basics 6 – Markdown basics 7 – LaTex basics 8 – Webscraping 9 – Text, corpus and natural language processing 10 – Maps and GIS 11 – Networks and graphs Glauco Peres da Silva, Leonardo Sangali Barone 40 FLS6397 8 Weekly activities (50%) and a final project (50%). https://www.google.com.br/url?sa=t&rct=j&q=&esrc=s&source=web&cd=10&ved=0ahUKEwi3paLQ9tzYAhXBE5AKHdAvBDkQFghfMAk&url=http%3A%2F%2Fwww.ru.nl%2Fpublish%2Fpages%2F798477%2Fstudent_guide_fflch.pdf&usg=AOvVaw1Cv-BPFTbngDpr4qVjQBud

The course aims to introduce students to the main research paradigms in comparative political behavior; and, to advance training in doing original empirical research on political participation, voting, public opinion analysis, etc. in a comparative perspective. Faculty of Philosophy, Languages and Human Sciences (FFLCH) São Paulo main campus Students should have a background in statistical inference (for example, FLS 5028, or a similar course) and multivariate regression analysis (for example, FLS 6183, or a similar course). 1. Participation 2. Values, Issues and Ideological Orientations 3. Partisanship and Voting 4. Attitudes and Political Behavior 5. Representation 6. Performance and the Vote 7. Economic Crisis and Reform 8. Globalization and the Vote Lorena Guadalupe Barberia 40 FLS6403 8 Problem Sets and Quizzes 50% Final Paper 50% https://www.google.com.br/url?sa=t&rct=j&q=&esrc=s&source=web&cd=10&ved=0ahUKEwi3paLQ9tzYAhXBE5AKHdAvBDkQFghfMAk&url=http%3A%2F%2Fwww.ru.nl%2Fpublish%2Fpages%2F798477%2Fstudent_guide_fflch.pdf&usg=AOvVaw1Cv-BPFTbngDpr4qVjQBud

A knowledge of how life originated and evolved on Earth is of central importance in historical Sciences (Geology, Biologie, Astrobiologie). To obtain a general view of the interelated processes (geodynamic, climatic, oceanic, biological) involved in the evolution of the early Earth during the first 2.5 Ga of its history (Hadean, Archean, Early Proterozic). Institute of Geosciences (IGc) São Paulo main campus Less than 200 Ma after its formation, the Earth holds all the attributes of a modern Earth (core, protolithosphere, oceans and atmosphere). However, it will take nearly two billion years to shape terrestrial geodynamics and the major bio-geochemical cycles as we know them today. What happened between the two? When and how did the plate tectonics begin? How did life appear on Earth and in what environments? What are the first traces of life? Is there a link between crustal growth, the diversification of microbial life and the evolution of the composition of the atmosphere? Is oxygenation of the atmosphere and oceans of biological or abiotic origin? These are, among others, the questions we will address during this course, as follows: 1) 4.5-4.4 Ga, accretion and differentiation core-mantle, late veneer, formation of the Moon 2) 4.4-4.1 Ga, first zircons, first continents, first oceans 3) Early Earth geodynamics 4) Early Oceans 5) Early atmosphere 6) Early life Marly Babinski, Pascal Andre Marie Philippot 20 GMG5838 4 Oral presentation given by individual students on key scientific issues related to the evolution of the primitive Earth and early Life. A final written exam on http://www.igc.usp.br/index.php?id=101&L=2

The aim of this discipline is to present the students seminal papers of molecular biology. These papers will be analysed from a historical, methodological and scientific perspective. This discipline complements the basic knowledge acquired in regular disciplines of molecular biology. By discussing original articles, the students will analyze in depth the historical context and the methodologies used by the scientists that pave the way of molecular biology. This will ultimately give the students the tools to understand the basis of molecular biology and the development of scientific thought. Biomedical Sciences Institute (ICB) São Paulo main campus Every lecture will be followed by the discussion of an original article. The student will receive a questionnaire that will guide him/her through the reading of the paper, with the help of the instructors. Items to be discussed include the following topics: (1) Structure and function of DNA ; ( 2 ) RNA and the genetic code ; ( 3 ) Advent of genetic engineering and genomics. Carlos Eduardo Winter, Beny Spira 25 ICB5751 8 Written tests will be used to evaluate student progress during the course. https://ww2.icb.usp.br/ing/

Many fields of biological research have changed markedly over the past few years with the rise of high-throughput laboratory techniques such as microarrays, massive nucleic acid sequencing and proteomic technologies. These technical developments have brought forth not only a significant, and still ongoing, change in philosophical outlook, but have also transformed how work in certain fields is performed in the lab _ more specifically, the computer lab. Generation of huge data files that are only useful after extensive computational processing became a frequent task in many biological research groups. Proper training in basic computational concepts and tools that can greatly aid in such endeavors have thus become essential in order to extract all the information that many modern large-scale techniques of biological research can provide. This course’s goal is to provide intensive and advanced training in computer usage on the command-line interface (CLI) for large-scale data analysis. At the end of the course, students from biologically-oriented backgrounds should be able to use the CLI to view, edit, manipulate, and summarize large data files, successfully extracting biological information and insight from the high-throughput analyses that generated those files. Biomedical Sciences Institute (ICB) São Paulo main campus • Introduction to computers and the Unix family of operating systems. • Accessing the shell (Bash), locally or remotely, and Bash basics. • Getting help with man, info, apropos, and Internet search engines. • Moving around the directory tree; finding and executing programs; navigating/understanding the system (memory, disk space etc.). • System structure; file types; user and group permission model; Changing file access (owner, group, permissions). • Standard streams and redirection; piping. • Finding and manipulating files and directories (create, delete, move, copy, rename, append, concatenate etc.). • Describing and summarizing file content (wc, file); getting data into the system (wget, scp, ftp). • Creating, exploring, and sub-setting files. • Comparing, sorting, and editing files. • Compressing and decompressing data (tar, gz, zip etc.). • Basics of regular expressions. • Compiling third-party programs. • Automating the CLI with basic Bash scripting. Jo_o Marcelo Pereira Alves 10 ICB5765 4 The course is structured in short lectures intermingled with class activity sessions, in order to make the course as practice-oriented as possible. In order to better reflect everyday research practice, the most widespread file formats used in the field will also be introduced and used in as many practical examples as possible. The whole course, including exams, takes place in a computer lab. The use of the command-line environment of Unix-like operating systems (such as Mac OS X and Linux-based systems) will be intensively explored, in order to give students all the working knowledge necessary to run most bioinformatics tools and efficiently analyze their output. Avaliation Form: Final grade will be calculated as the weighted average of midterm exam (weight 2), final exam (weight 2), in-class quizzes (weight 1), and practical exercises (weight 3). A passing grade consists of 5.0 or higher final average and at least 75% attendance. Students with regular semester final grades between 3.0 and 4.9 and attendance above 75% can take a supplementary exam, in which case the second final grade will be the average of the final grade above and the supplementary exam. https://ww2.icb.usp.br/ing/

The proposed program includes experimental designs used in the agricultural experimentation whose structure requires special attention due to the methodology applied for the analysis of the obtianed data. Aims to provide a solid methodological basis for the use of models in the analysis of continuous data and in research, involving concepts of matrix algebra and statistical inference, teaching Hasse diagrams, linear models for incomplete data using the theory of mixed models, including the estimation techniques, checking of model fitting, diagnostics, inference and confidence intervals. Luiz de Queiroz College of Agriculture (ESALQ) Piracicaba campus Hasse Diagrams. Unbalanced cross-classifications. Split-plot experiments. Split-Block experiments. Incomplete block designs. Lattice squares. Groups of experiments. Groups of experiments with common treatments (augmented block). Introduction to mixed models. Sonia Maria de Stefano Piedade, Clarice Garcia Borges Demetrio, Taciana Villela Savian 25 LCE5872 8 Evaluation tests and Seminars http://pt.esalq.usp.br/

Systems analysis is a powerful way to explore and analyse the dynamics of interacting entities. In the case of crop health, systems approaches enable understanding the interaction between pests (plant pathogens and pests) and crops. Systems approaches also allow addressing the impact of the environment (e.g., physical: weather, social: human actions, economic, etc.) on these interactions. A broad context for plant health and its management can therefore be envisioned, including for example socio-economic context of production, trade, and policies. To introduce concepts and methods of systems analysis, and their application to the study, analysis, and management of crop health. Students will acquire a broadened understanding of the dynamics and the impact of plant diseases and pests on crop (agricultural) production, as well as on the environment, and on society and the economy. This will be achieved through systems approach techniques, including but not limited to, simulation modelling. Luiz de Queiroz College of Agriculture (ESALQ) Piracicaba campus This course considers crop health  the collective dynamics of diseases and pests as a whole in a crop. Crop health depends on production situations, that is to say, the set of inter-linked environmental, technical, social, and economical factors that determine the context where agricultural production takes place. Understanding the joint evolution of crop health and production situations is important for future plant health professionals. Brazil occupies a very important position in global agricultural and food trade. The course will introduce issues pertaining to global food and agricultural security, and to globalization, because of their implications for crop health. Systems analysis covers a range of techniques that enable exploring and understanding large and complex questions. One of the approaches of systems analysis, mechanistic simulation modelling, will in particular be used as a methodological backbone for the course. Simulation modelling will be introduced and explained in the course. 1  Context of agricultural production and crop health – Introduction to systems analysis and simulation – Examples of production situations and associated crop health syndromes – Illustration of shifts in production situations leading to crop health changes – Introduction to global agriculture, global crop health problems – Introduction to the effects of global changes on agriculture, crop health – Crop health and global food security – General strategies to manage crop health 2 _Systems analysis: introduction and application to crop health – Systems analysis: concepts and methods – Production levels, crop losses – Damage mechanisms caused by pests – Simulation modelling – Management of natural resources – Negative impacts of agriculture – Long-term disease and pest management Armando Bergamin Filho, Laetitia Willocquet, Serge Savary 30 LFT5890 2 The course will be held during 2 weeks in February: first week for classes and second week for practical activities. Presentation of a case study http://pt.esalq.usp.br/

Sterilization processes are performed in laboratories, hospitals and industries as the final processing step for preparation of safe critical materials and devices used in the Public Health sector and for pharmaceutical products, in order to preserve products and to ensure their expected shelf-life. A better understanding of sterilization processes (as the choice of sterilizing agent to be used, kinetic parameters determination and biological indicators application) can minimize misunderstandings related to contamination, production and/or processing of these pharmaceuticals devices. This course aims to present the basic concepts and parameters related to sterilization and validation processes, which are responsible to guarantee consistent sterility levels required for obtaining pharmaceutical and medical products. School of Pharmaceutical Sciences (FCF) São Paulo main campus 1. Introduction_- Concepts and application of sterilization. 2. Kinetic parameters: Decimal reduction time (D-value), Relative resistance (z-value), Sterility Assurance Level, Process equivalent time (F value), Q10 parameter and activation energy. 3. Biological and chemical Indicators: main characteristics, types, applications and relationship. 4. Sterilizing agents: Physical, chemical and gaseous agents. 5. Validation processes: definitions and legislation, qualification of installation, operating system qualification_and physical and biological validation. Practical: Application of biological indicators, determination of kinetic parameters Marina Ishii 13 FBT5736 6 Exercises and seminars. http://www.fcf.usp.br/english.php