Identifying the preferred subset of enzymatic profiles in nonlinear kinetic metabolic models via multiobjective global optimization and pareto filters

Optimization models in metabolic engineering and systems biology focus typically on optimizing a unique criterion, usually the synthesis rate of a metabolite of interest or the rate of growth. Connectivity and non-linear regulatory effects, however, make it necessary to consider multiple objectives in order to identify useful strategies that balance out different metabolic issues. This is a fundamental aspect, as optimization of maximum yield in a given condition may involve unrealistic values in other key processes. Due to the difficulties associated with detailed non-linear models, analysis using stoichiometric descriptions and linear optimization methods have become rather popular in systems biology. However, despite being useful, these approaches fail in capturing the intrinsic nonlinear nature of the underlying metabolic systems and the regulatory signals involved. Targeting more complex biological systems requires the application of global optimization methods to non-linear representations. In this work we address the multi-objective global optimization of metabolic networks that are described by a special class of models based on the power-law formalism: the generalized mass action (GMA) representation. Our goal is to develop global optimization methods capable of efficiently dealing with several biological criteria simultaneously. In order to overcome the numerical difficulties of dealing with multiple criteria in the optimization, we propose a heuristic approach based on the epsilon constraint method that reduces the computational burden of generating a set of Pareto optimal alternatives, each achieving a unique combination of objectives values. To facilitate the post-optimal analysis of these solutions and narrow down their number prior to being tested in the laboratory, we explore the use of Pareto filters that identify the preferred subset of enzymatic profiles. We demonstrate the usefulness of our approach by means of a case study that optimizes the ethanol production in the fermentation of Saccharomyces cerevisiae.

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).

Condicionants sociològics de la planificació lingüística en un context global i multicultural

La complexitat de la conformació de les societats actuals provoca l’aparició de reptes nous que s’afegeixen a l’emergència de realitats ja existents i no resoltes. Això fa que s’hagin d’analitzar amb mirada i perspectives noves problemes, qüestions i polítiques que es creien resolts o, com a mínim, superats. Obliga, alhora, a repensar les estratègies i també a repensarnos com a societat. La política lingüística, i la planificació que n’és la resultant, no pot quedar al marge d’aquestes reflexions perquè actua en —i per a— una població i en —i per a— una societat determinada, i l’una i l’altra estan en plena transformació i canvi. Els diversos contextos socials actuals en els quals —i per als quals— es prenen les decisions lingüístiques contenen condicionants característics que s’afegeixen i interactuen amb els preexistents. Uns i altres, amb diferents graus d’intensitat, les influencien. Aquest article s’aproxima a alguns d’aquests elements i a aquest context divers, global i local que els dota d’especificitat.

Cardiovascular disease and the changing face of global public health : a focus on low and middle income countries

Eighty percent of the global 17 million deaths due to cardiovascular disease (CVD) occur in low and middle income countries (LMICs). The burden of CVD and other noncommunicable diseases (NCDs) is expected to markedly increase because of the global aging of the population and increasing exposure to detrimental lifestyle-related risk in LMICs. Interventions to reduce four main risks related to modifiable behaviors (tobacco use, unhealthy diet, low physical activity and excess alcohol consumption) are key elements for effective primary prevention of the four main NCDs (CVD, cancer, diabetes and chronic pulmonary disease). These behaviors are best improved through structural interventions (e.g., clean air policy, taxes on cigarettes, new recipes for processed foods with reduced salt and fat, urban shaping to improve mobility, etc.). In addition, health systems in LMICs should be reoriented to deliver integrated cost-effective treatment to persons at high risk at the primary health care level. The full implementation of a small number of highly cost effective, affordable and scalable interventions ("best buys") is likely to be the necessary and sufficient ingredient for curbing NCDs in LMICs. NCDs are both a cause and a consequence of poverty. It is therefore important to frame NCD prevention and control within the broader context of social determinants and development agenda. The recent emphasis on NCDs at a number of health and economic forums (including the September 2011 High Level Meeting on NCDs at the United Nations) provides a new opportunity to move the NCD agenda forward in LMICs.

Hsp90 inhibition induces both protein-specific and global changes in the ubiquitinome.

Inhibition of the essential chaperone Hsp90 with drugs causes a global perturbation of protein folding and the depletion of direct substrates of Hsp90, also called clients. Ubiquitination and proteasomal degradation play a key role in cellular stress responses, but the impact of Hsp90 inhibition on the ubiquitinome has not been characterized on a global scale. We used stable isotope labeling and antibody-based peptide enrichment to quantify more than 1500 protein sites modified with a Gly-Gly motif, the remnant of ubiquitination, in human T-cells treated with an Hsp90 inhibitor. We observed rapid changes in GlyGly-modification sites, with strong increases for some Hsp90 clients but also decreases for a majority of cellular proteins. A comparison with changes in total protein levels and protein synthesis and decay rates from a previous study revealed a complex picture with different regulatory patterns observed for different protein families. Overall the data support the notion that for Hsp90 clients GlyGly-modification correlates with targeting by the ubiquitin-proteasome system and decay, while for other proteins levels of GlyGly-modification appear to be mainly influenced by their synthesis rates. Therefore a correct interpretation of changes in ubiquitination requires knowledge of multiple parameters. Data are available via ProteomeXchange with identifier PXD001549. BIOLOGICAL SIGNIFICANCE: Proteostasis, i.e. the capacity of the cell to maintain proper synthesis and maturation of proteins, is a fundamental biological process and its perturbations have far-reaching medical implications e.g. in cancer or neurodegenerative diseases. Hsp90 is an essential chaperone responsible for the correct maturation and stability of a number of key proteins. Inhibition of Hsp90 triggers a global stress response caused by accumulation of misfolded chains, which have to be either refolded or eliminated by protein degradation pathways such as the Ubiquitin-Proteasome System (UPS). We present the first global assessment of the changes in the ubiquitinome, the subset of ubiquitin-modified proteins, following Hsp90 inhibition in human T-cells. The results provide clues on how cells respond to a specific proteostasis challenge. Furthermore, our data also suggest that basal ubiquitination levels for most proteins are influenced by synthesis rates. This has broad significance as it implies that a proper interpretation of data on ubiquitination levels necessitates simultaneous knowledge of other parameters.

Acetylation of cell wall is required for structural integrity of the leaf surface and exerts a global impact on plant stress responses.

The epidermis on leaves protects plants from pathogen invasion and provides a waterproof barrier. It consists of a layer of cells that is surrounded by thick cell walls, which are partially impregnated by highly hydrophobic cuticular components. We show that the Arabidopsis T-DNA insertion mutants of REDUCED WALL ACETYLATION 2 (rwa2), previously identified as having reduced O-acetylation of both pectins and hemicelluloses, exhibit pleiotrophic phenotype on the leaf surface. The cuticle layer appeared diffused and was significantly thicker and underneath cell wall layer was interspersed with electron-dense deposits. A large number of trichomes were collapsed and surface permeability of the leaves was enhanced in rwa2 as compared to the wild type. A massive reprogramming of the transcriptome was observed in rwa2 as compared to the wild type, including a coordinated up-regulation of genes involved in responses to abiotic stress, particularly detoxification of reactive oxygen species and defense against microbial pathogens (e.g., lipid transfer proteins, peroxidases). In accordance, peroxidase activities were found to be elevated in rwa2 as compared to the wild type. These results indicate that cell wall acetylation is essential for maintaining the structural integrity of leaf epidermis, and that reduction of cell wall acetylation leads to global stress responses in Arabidopsis.

Local effects and global impact in neurotoxicity and neurodegeneration: The Xi"an International Neurotoxicology Conference

'Neurotoxicity and Neurodegeneration: Local Effect and Global Impact' was the theme of the Xi"an International Neurotoxicology Conference (XINC), held in Xi"an, June 2011. The Conference was a joint event of the 13th Biennial Meeting of the International Neurotoxicology Association (INA-13) and the 11th International Symposium on Neurobehavioral Methods and Effects in Occupational and Environmental Health (NEUREOH-11) of the Scientific Committee on Neurotoxicology and...

Potential of local bio-geoengineering to mitigate dangerous temperature increases in a global warming scenario

Crops and forests are already responding to rising atmospheric carbon dioxide and air temperatures. Increasing atmospheric CO2 concentrations are expected to enhance plant photosynthesis. Nevertheless, after long-term exposure, plants acclimate and show a reduction in photosynthetic activity (i.e. down-regulation). If in the future the Earth"s temperature is allowed to rise further, plant ecosystems and food security will both face significant threats. The scientific community has recognized that an increase in global temperatures should remain below 2°C in order to combat climate change. All this evidence suggests that, in parallel with reductions in CO2 emissions, a more direct approach to mitigate global warming should be considered. We propose here that global warming could be partially mitigated directly through local bio-geoengineering approaches. For example, this could be done through the management of solar radiation at surface level, i.e. by increasing global albedo. Such an effect has been documented in the south-eastern part of Spain, where a significant surface air temperature trend of -0.3°C per decade has been observed due to a dramatic expansion of greenhouse horticulture.

El resultado global: una aproximación de la información contable a la realidad de los mercados

Un elemento novedoso que incorporan las cuentas anuales es el resultado global, como nuevo concepto de resultado (que incorpora el tradicional resultado neto más o menos los ajustes en patrimonio neto) en sintonía con la realidad de los mercados. En nuestro trabajo analizamos si la información derivada del resultado global, en el período 2009-2011 para las empresas del IBEX 35, añade más poder informativo al análisis de los estados financieros y en especial a las rentabilidades como indicadores de la realidad de los mercados.

El fútbol y el negocio del entretenimiento global. Los clubes como multinacionales del ocio

El artículo tiene como objetivo analizar el proceso de expansión internacional de los clubes más ricos del fútbol español durante la primera década del siglo XXI, Real Madrid y FC Barcelona. Después de que los clubes de la Premier League inglesa fueran los primeros en crear una estrategia de branding internacional, otras ligas y organizaciones deportivas han adoptado sus mismos sistemas de gestión empresarial. En España, el Real Madrid y el FC Barcelona son el ejemplo más evidente, por su número de fans en todo el mundo, por sus acuerdos internacionales en la comercialización de sus productos con otras organizaciones y por la presencia que tienen sus marcas en todo el mundo gracias a las inversiones de sus fundaciones en escuelas de fútbol en concepto de Responsabilidad Social Corporativa. Por eso, ambos clubes, Real Madrid y FC Barcelona, pueden calificarse de nuevas multinacionales del ocio.

Financial integration, capital misallocation and global imbalances

This paper shows that in a stylized model with two countries, characterized by different levels of financial development, the following facts can be replicated: 1) persistent current account surpluses and 2) high TFP growth in China. Under autarky, entrepreneurs in the emerging country overinvest in short-term projects and underinvest in long-term projects because short-term assets help them secure long-term investments in the presence of credit constraints. This creates an aggregate misallocation of capital. When financial markets integrate, entrepreneurs with long-term projects can have access to cheaper short-term assets abroad, which leaves them more resources to invest in their projects. This both reduces capital misallocations and generates capital outflows.

Being Global? La crisis y los museos virtuales en arte público y diseño urbano

Este trabajo surge de la experiencia desarrollada en Barcelona, Zaragoza y Lisboa de puesta en marcha de los respectivos sistemas de información del Arte Público de estas ciudades, así como del desarrollo de investigación posibilitado por los proyectos BHA2002- 00520;HUM2005-00420;HUM2006-12803-C02-01, HAR 2009-13989-C02-01, del Ministerior de Ciencia e Innvoción español y de los proyectos 2005SGR00150 y 2009SGR903 de la Generalitat de Catalunya, así como de los distintos convenios entre la Universidad y el Ayuntamiento de Barcelona. Sorprendentemente, en el panorama de la innovación internacional, son proyectos del sur de Europa los que plantean por primera vez un uso sistemático de Internet para el mejor conocimiento y difusión de esta parte del patrimonio que es el Arte Público de las ciudades, una historia escrita en bronce y piedra que forma parte de la herencia cultural, de las raíces identitarias y del orgullo de ciudad Sin embargo, la crisis internacional supone un frenazo importante a estos proyectos y a la posibilidad de desarrollar un Museo Virtual del Arte Público y el Diseño Urbano.

Calidad de vida global en personas con demencia

Objetivo: Evaluar la calidad de vida (CV) global en personas con demencia e investigar las variables asociadas con la percepción subjetiva de la CV. Pacientes y métodos: Se llevó a cabo un estudio transversal en seis centros de Barcelona y Tarragona. Un total de 99 personas con demencia leve-moderada que vivían en casa con un cuidador conocido completaron una entrevista cara-cara que incluía información sociodemográfica, percepción del estado de salud, un listado de problemas crónicos de salud, sintomatología depresiva, estado funcional, aspectos positivos, sentido de la vida y satisfacción con las relaciones personales. La CV global se evaluó con la pregunta global del World Health Organization Quality of Life-BREF. Resultados: El 40,6% de los entrevistados consideró su CV como buena/muy buena. Los análisis univariados de regresión logística ordinal y binaria no mostraron asociación entre CV con datos sociodemográficos, gravedad de la demencia ni estado funcional, pero sí con las otras variables de estudio. Los análisis multivariados de la regresión logística ordinal y binaria mostraron que una mejor percepción de salud y mayor satisfacción con las relaciones personales se asociaban con mejor CV. Asimismo, en el análisis multivariado de regresión logística ordinal, mejor CV se asoció con un menor número de síntomas depresivos, y en el análisis de regresión logística binaria, con disfrutar de la vida y menor gravedad de la demencia. Conclusiones: Personas con demencia leve-moderada pueden informar sobre su CV y estados subjetivos. Además de los aspectos relacionados con la salud, aspectos positivos y las relaciones personales deberían evaluarse sistemáticamente en esta población.

CTP in Transient Global Amnesia: A Single-Center Experience of 30 Patients.

BACKGROUND AND PURPOSE: Medial temporal lobe abnormalities on DWI and functional imaging are occasionally observed in patients with transient global amnesia. We used CTP to study these patients during or briefly after resolution of their amnesic syndrome. MATERIALS AND METHODS: From 2002 onward, patients satisfying clinical criteria for transient global amnesia who underwent CTP were included. Patients with additional clinical features suggesting transient ischemic attack or stroke and those with an ischemic lesion on subsequent DWI were excluded. If deemed necessary by the clinician, DWI was performed within 10 days. RESULTS: Thirty patients with transient global amnesia underwent CTP at a median latency of 5.9 hours (interquartile range, 4.3-9.7 hours) after symptom onset. All findings, except for those in 1 patient, were normal, including those in the 14 patients with well-imaged hippocampi. In the patient with abnormal findings, CTP and PWI showed hypoperfusion in both lentiform nuclei extending into the insulae, with normalization on the repeat CTP 6 days later. In 10 patients, DWI was performed at a median latency of 2 days (interquartile range, 0-9 days). Of these, 2 showed punctate hippocampal lesions, often seen in transient global amnesia. In 2 patients excluded because of mildly atypical transient global amnesia and ischemic lesions on subsequent DWI, acute CTP findings were also normal. CONCLUSIONS: Patients with transient global amnesia had normal CTP findings in the acute phase with the exception of 1 patient with transient hypoperfusion in both basal ganglia. If imaging is performed for typical and atypical transient global amnesia, DWI should be the preferred method.