Entropy analysis of DNA code dynamics in human chromosomes

Deoxyribonucleic acid, or DNA, is the most fundamental aspect of life but present day scientific knowledge has merely scratched the surface of the problem posed by its decoding. While experimental methods provide insightful clues, the adoption of analysis tools supported by the formalism of mathematics will lead to a systematic and solid build-up of knowledge. This paper studies human DNA from the perspective of system dynamics. By associating entropy and the Fourier transform, several global properties of the code are revealed. The fractional order characteristics emerge as a natural consequence of the information content. These properties constitute a small piece of scientific knowledge that will support further efforts towards the final aim of establishing a comprehensive theory of the phenomena involved in life.

Global material analysis on phosphorus flows, supply horizon and impact assessment on phosphorus depletion

Different problems are daily discuss on environmental aspects such acid rain, eutrophication, global warming and an others problems. Rarely do we find some discussions about phosphorus problematic. Through the years the phosphorus as been a real problem and must be more discussed. On this thesis was done a global material flow analysis of phosphorus, based on data from the year 2004, the production of phosphate rock in that year was 18.9 million tones, almost this amount it was used as fertilizer on the soil and the plants only can uptake, on average, 20% of the input of fertilizer to grow up, the remainder is lost for the phosphorus soil. In the phosphorus soil there is equilibrium between the phosphorus available to uptake from the plants and the phosphorus associate with other compounds, this equilibrium depends of the kind of soil and is related with the soil pH. A reserve inventory was done and we have 15,000 million tones as reserve, the amount that is economical available. The reserve base is estimated in 47,000 million tones. The major reserves can be found in Morocco and Western Sahara, United Sates, China and South Africa. The reserve estimated in 2009 was 15,000 million tone of phosphate rock or 1,963 million tone of P. If every year the mined phosphate rock is around 22 Mt/yr (phosphorus production on 2008 USGS 2009), and each year the consumption of phosphorus increases because of the food demand, the reserves of phosphate rock will be finished in about 90 years, or maybe even less. About the value/impact assessment was done a qualitative analysis, if on the future we don’t have more phosphate rock to produce fertilizers, it is expected a drop on the crops yields, each depends of the kind of the soil and the impact on the humans feed and animal production will not be a relevant problem. We can recovery phosphorus from different waste streams such as ploughing crop residues back into the soil, Food processing plants and food retailers, Human and animal excreta, Meat and bone meal, Manure fibre, Sewage sludge and wastewater. Some of these examples are developed in the paper.

Dynamical analysis of the global warming

Global warming is a major concern nowadays. Weather conditions are changing, and it seems that human activity is one of the main causes. In fact, since the beginning of the industrial revolution, the burning of fossil fuels has increased the nonnatural emissions of carbon dioxide to the atmosphere. Carbon dioxide is a greenhouse gas that absorbs the infrared radiation produced by the reflection of the sunlight on the Earth’s surface, trapping the heat in the atmosphere. Global warming and the associated climate changes are being the subject of intensive research due to their major impact on social, economic, and health aspects of human life. This paper studies the global warming trend in the perspective of dynamical systems and fractional calculus, which is a new standpoint in this context. Worldwide distributed meteorological stations and temperature records for the last 100 years are analysed. It is shown that the application of Fourier transforms and power law trend lines leads to an assertive representation of the global warming dynamics and a simpler analysis of its characteristics.

Cluster analysis and segmentation of Global M&A transactions

A Work Project, presented as part of the requirements for the Award of a Masters Degree in Finance from the NOVA – School of Business and Economics

Analysis and optimization of the satellite-to-plane link of an aeronautical global system

En aquest projecte s’ha analitzat i optimitzat l’enllaç satèl·lit amb avió per a un sistema aeronàutic global. Aquest nou sistema anomenat ANTARES està dissenyat per a comunicar avions amb estacions base mitjançant un satèl·lit. Aquesta és una iniciativa on hi participen institucions oficials en l’aviació com ara l’ECAC i que és desenvolupat en una col·laboració europea d’universitats i empreses. El treball dut a terme en el projecte compren bàsicament tres aspectes. El disseny i anàlisi de la gestió de recursos. La idoneïtat d’utilitzar correcció d’errors en la capa d’enllaç i en cas que sigui necessària dissenyar una opció de codificació preliminar. Finalment, estudiar i analitzar l’efecte de la interferència co-canal en sistemes multifeix. Tots aquests temes són considerats només per al “forward link”. L’estructura que segueix el projecte és primer presentar les característiques globals del sistema, després centrar-se i analitzar els temes mencionats per a poder donar resultats i extreure conclusions.

Global tractography with embedded anatomical priors for quantitative connectivity analysis.

Tractography algorithms provide us with the ability to non-invasively reconstruct fiber pathways in the white matter (WM) by exploiting the directional information described with diffusion magnetic resonance. These methods could be divided into two major classes, local and global. Local methods reconstruct each fiber tract iteratively by considering only directional information at the voxel level and its neighborhood. Global methods, on the other hand, reconstruct all the fiber tracts of the whole brain simultaneously by solving a global energy minimization problem. The latter have shown improvements compared to previous techniques but these algorithms still suffer from an important shortcoming that is crucial in the context of brain connectivity analyses. As no anatomical priors are usually considered during the reconstruction process, the recovered fiber tracts are not guaranteed to connect cortical regions and, as a matter of fact, most of them stop prematurely in the WM; this violates important properties of neural connections, which are known to originate in the gray matter (GM) and develop in the WM. Hence, this shortcoming poses serious limitations for the use of these techniques for the assessment of the structural connectivity between brain regions and, de facto, it can potentially bias any subsequent analysis. Moreover, the estimated tracts are not quantitative, every fiber contributes with the same weight toward the predicted diffusion signal. In this work, we propose a novel approach for global tractography that is specifically designed for connectivity analysis applications which: (i) explicitly enforces anatomical priors of the tracts in the optimization and (ii) considers the effective contribution of each of them, i.e., volume, to the acquired diffusion magnetic resonance imaging (MRI) image. We evaluated our approach on both a realistic diffusion MRI phantom and in vivo data, and also compared its performance to existing tractography algorithms.

Global phylogenomic analysis of nonencapsulated Streptococcus pneumoniae reveals a deep-branching classic lineage that is distinct from multiple sporadic lineages.

The surrounding capsule of Streptococcus pneumoniae has been identified as a major virulence factor and is targeted by pneumococcal conjugate vaccines (PCV). However, nonencapsulated S. pneumoniae (non-Ec-Sp) have also been isolated globally, mainly in carriage studies. It is unknown if non-Ec-Sp evolve sporadically, if they have high antibiotic nonsusceptiblity rates and a unique, specific gene content. Here, whole-genome sequencing of 131 non-Ec-Sp isolates sourced from 17 different locations around the world was performed. Results revealed a deep-branching classic lineage that is distinct from multiple sporadic lineages. The sporadic lineages clustered with a previously sequenced, global collection of encapsulated S. pneumoniae (Ec-Sp) isolates while the classic lineage is comprised mainly of the frequently identified multilocus sequences types (STs) ST344 (n = 39) and ST448 (n = 40). All ST344 and nine ST448 isolates had high nonsusceptiblity rates to β-lactams and other antimicrobials. Analysis of the accessory genome reveals that the classic non-Ec-Sp contained an increased number of mobile elements, than Ec-Sp and sporadic non-Ec-Sp. Performing adherence assays to human epithelial cells for selected classic and sporadic non-Ec-Sp revealed that the presence of a integrative conjugative element (ICE) results in increased adherence to human epithelial cells (P = 0.005). In contrast, sporadic non-Ec-Sp lacking the ICE had greater growth in vitro possibly resulting in improved fitness. In conclusion, non-Ec-Sp isolates from the classic lineage have evolved separately. They have spread globally, are well adapted to nasopharyngeal carriage and are able to coexist with Ec-Sp. Due to continued use of PCV, non-Ec-Sp may become more prevalent.

The global report of trafficking in persons: analysis and results

L'Oficina de les Nacions Unides contra la Droga i el Delicte en el seu informe "Global Report on Trafficking in Persons" de 2012 recull que "l'explotació sexual és, amb gran diferència, la forma de tràfic de persones detectades amb més freqüència, concretament en xifres un total del 79 % dels casos. Enllaç a l'informe sencer: http://www.unodc.org/documents/data-and-analysis/glotip/Trafficking_in_Persons_2012_web.pdf

The TREAT-NMD DMD Global Database: Analysis of More than 7,000 Duchenne Muscular Dystrophy Mutations.

Analyzing the type and frequency of patient-specific mutations that give rise to Duchenne muscular dystrophy (DMD) is an invaluable tool for diagnostics, basic scientific research, trial planning, and improved clinical care. Locus-specific databases allow for the collection, organization, storage, and analysis of genetic variants of disease. Here, we describe the development and analysis of the TREAT-NMD DMD Global database (http://umd.be/TREAT_DMD/). We analyzed genetic data for 7,149 DMD mutations held within the database. A total of 5,682 large mutations were observed (80% of total mutations), of which 4,894 (86%) were deletions (1 exon or larger) and 784 (14%) were duplications (1 exon or larger). There were 1,445 small mutations (smaller than 1 exon, 20% of all mutations), of which 358 (25%) were small deletions and 132 (9%) small insertions and 199 (14%) affected the splice sites. Point mutations totalled 756 (52% of small mutations) with 726 (50%) nonsense mutations and 30 (2%) missense mutations. Finally, 22 (0.3%) mid-intronic mutations were observed. In addition, mutations were identified within the database that would potentially benefit from novel genetic therapies for DMD including stop codon read-through therapies (10% of total mutations) and exon skipping therapy (80% of deletions and 55% of total mutations).

Global surveillance of cancer survival 1995-2009 : analysis of individual data for 25 676 887 patients from 279 population-based registries in 67 countries (CONCORD-2)

BACKGROUND: Worldwide data for cancer survival are scarce. We aimed to initiate worldwide surveillance of cancer survival by central analysis of population-based registry data, as a metric of the effectiveness of health systems, and to inform global policy on cancer control. METHODS: Individual tumour records were submitted by 279 population-based cancer registries in 67 countries for 25·7 million adults (age 15-99 years) and 75 000 children (age 0-14 years) diagnosed with cancer during 1995-2009 and followed up to Dec 31, 2009, or later. We looked at cancers of the stomach, colon, rectum, liver, lung, breast (women), cervix, ovary, and prostate in adults, and adult and childhood leukaemia. Standardised quality control procedures were applied; errors were corrected by the registry concerned. We estimated 5-year net survival, adjusted for background mortality in every country or region by age (single year), sex, and calendar year, and by race or ethnic origin in some countries. Estimates were age-standardised with the International Cancer Survival Standard weights. FINDINGS: 5-year survival from colon, rectal, and breast cancers has increased steadily in most developed countries. For patients diagnosed during 2005-09, survival for colon and rectal cancer reached 60% or more in 22 countries around the world; for breast cancer, 5-year survival rose to 85% or higher in 17 countries worldwide. Liver and lung cancer remain lethal in all nations: for both cancers, 5-year survival is below 20% everywhere in Europe, in the range 15-19% in North America, and as low as 7-9% in Mongolia and Thailand. Striking rises in 5-year survival from prostate cancer have occurred in many countries: survival rose by 10-20% between 1995-99 and 2005-09 in 22 countries in South America, Asia, and Europe, but survival still varies widely around the world, from less than 60% in Bulgaria and Thailand to 95% or more in Brazil, Puerto Rico, and the USA. For cervical cancer, national estimates of 5-year survival range from less than 50% to more than 70%; regional variations are much wider, and improvements between 1995-99 and 2005-09 have generally been slight. For women diagnosed with ovarian cancer in 2005-09, 5-year survival was 40% or higher only in Ecuador, the USA, and 17 countries in Asia and Europe. 5-year survival for stomach cancer in 2005-09 was high (54-58%) in Japan and South Korea, compared with less than 40% in other countries. By contrast, 5-year survival from adult leukaemia in Japan and South Korea (18-23%) is lower than in most other countries. 5-year survival from childhood acute lymphoblastic leukaemia is less than 60% in several countries, but as high as 90% in Canada and four European countries, which suggests major deficiencies in the management of a largely curable disease. INTERPRETATION: International comparison of survival trends reveals very wide differences that are likely to be attributable to differences in access to early diagnosis and optimum treatment. Continuous worldwide surveillance of cancer survival should become an indispensable source of information for cancer patients and researchers and a stimulus for politicians to improve health policy and health-care systems. FUNDING: Canadian Partnership Against Cancer (Toronto, Canada), Cancer Focus Northern Ireland (Belfast, UK), Cancer Institute New South Wales (Sydney, Australia), Cancer Research UK (London, UK), Centers for Disease Control and Prevention (Atlanta, GA, USA), Swiss Re (London, UK), Swiss Cancer Research foundation (Bern, Switzerland), Swiss Cancer League (Bern, Switzerland), and University of Kentucky (Lexington, KY, USA).

Braving the Storm: How Are Global Biofuel Policies Sustained Despite Being Contested? An Analysis of the Biofuel Discourses of the EU, Brazil and Mozambique

Considered as a remedy to multiple problems that our world is facing, biofuels are nowadays promoted on a global scale. Despite this globalised approach, however, biofuels are heavily contested. Not only the social implications of biofuels are disputed and uncertain, particularly in countries of the global South, but also their environmental and economic rationales. Given these huge controversies, policies promoting biofuels would seem difficult to maintain. Yet, support for them has been surprisingly well established on the political agendas. With the aim of understanding this puzzle, this study asks how the dominant approach to biofuels has been sustained on a global level. In order to answer this question, the meanings and assumptions in biofuel discourses are explored through the lens of Maarten Hajer’s “argumentative” discourse analysis. Based on the existence of a “partnership for sustainable bioenergy” between the EU, Brazil and Mozambique, the study takes these three locations as case studies. The analysis reveals that various discursive strategies, including a particular problem construction and the use of two main story-lines, have played an important role in ensuring the permanence of the global approach to biofuels. Moreover, while the discourse of critics against biofuels demonstrates that there is room for contestation, the analysis finds that the opponents’ discourse largely fails to target the most salient justification for biofuels. A more effective strategy for critics would therefore be to also question the problem constructions underpinning this main justification in the global discourse.

Wavelets in real-time paper web analysis

Online paper web analysis relies on traversing scanners that criss-cross on top of a rapidly moving paper web. The sensors embedded in the scanners measure many important quality variables of paper, such as basis weight, caliper and porosity. Most of these quantities are varying a lot and the measurements are noisy at many different scales. The zigzagging nature of scanning makes it difficult to separate machine direction (MD) and cross direction (CD) variability from one another. For improving the 2D resolution of the quality variables above, the paper quality control team at the Department of Mathematics and Physics at LUT has implemented efficient Kalman filtering based methods that currently use 2D Fourier series. Fourier series are global and therefore resolve local spatial detail on the paper web rather poorly. The target of the current thesis is to study alternative wavelet based representations as candidates to replace the Fourier basis for a higher resolution spatial reconstruction of these quality variables. The accuracy of wavelet compressed 2D web fields will be compared with corresponding truncated Fourier series based fields.

Un análisis optimista de la educación matemática en la formación de maestros de educación infantil = An optimistic analysis of mathematics education in training pre-school teachers

This article offers a panorama of mathematics training for future teachers at pre-school level in Spain. With this goal in mind, this article is structured infour sections: where we come from, where we are, where we’re going and where we want to go. It offers, in short, a brief analysis that shows the efforts made to ensure there is sufficient academic and scientific rigour in teachers’ studies at pre-school in general and students’ mathematics education in particular. Together with a description of the progress made in recent years, it also raises some questions for all those involved in training future teachers for this educational stage

Mathematics inspired by Darwin. Adaptive dynamics of dispersal and cooperation

In 1859, Charles Darwin published his theory of evolution by natural selection, the process occurring based on fitness benefits and fitness costs at the individual level. Traditionally, evolution has been investigated by biologists, but it has induced mathematical approaches, too. For example, adaptive dynamics has proven to be a very applicable framework to the purpose. Its core concept is the invasion fitness, the sign of which tells whether a mutant phenotype can invade the prevalent phenotype. In this thesis, four real-world applications on evolutionary questions are provided. Inspiration for the first two studies arose from a cold-adapted species, American pika. First, it is studied how the global climate change may affect the evolution of dispersal and viability of pika metapopulations. Based on the results gained here, it is shown that the evolution of dispersal can result in extinction and indeed, evolution of dispersalshould be incorporated into the viability analysis of species living in fragmented habitats. The second study is focused on the evolution of densitydependent dispersal in metapopulations with small habitat patches. It resulted a very surprising unintuitive evolutionary phenomenon, how a non-monotone density-dependent dispersal may evolve. Cooperation is surprisingly common in many levels of life, despite of its obvious vulnerability to selfish cheating. This motivated two applications. First, it is shown that density-dependent cooperative investment can evolve to have a qualitatively different, monotone or non-monotone, form depending on modelling details. The last study investigates the evolution of investing into two public-goods resources. The results suggest one general path by which labour division can arise via evolutionary branching. In addition to applications, two novel methodological derivations of fitness measures in structured metapopulations are given.