Communicating geomorphology: global challenges for the twenty-first century

The British Society for Geomorphology (BSG), established as the British Geomorphological Research Group (BGRG) in 1960, is considering how best to represent geomorphology and geomorphologists in the light of recent changes in the nature of communication. These changes provide the BSG and other academic societies with challenges and opportunities. Seven drivers of communication change are outlined: the changing position of geomorphology in higher education, the nature of academic interaction, the means of communication available, a transformation in the nature of geomorphological research, changes in funding support, the government role in resource allocation, and developments in quantifying international research impact. Challenges arising from changing communications are identified as occurring beyond the `academy', in the nature of publication within the `academy', and associated with meetings of the `academy'. Although national societies now have to contemplate significantly different purposes to provide for their members than in the twentieth century, there are opportunities available that cannot be fulfilled by international organizations alone. Copyright (c) 2013 John Wiley & Sons, Ltd.

CISNE-P: a global scheduling oriented to NOW environments

In this work, we present an integral scheduling system for non-dedicated clusters, termed CISNE-P, which ensures the performance required by the local applications, while simultaneously allocating cluster resources to parallel jobs. Our approach solves the problem efficiently by using a social contract technique. This kind of technique is based on reserving computational resources, preserving a predetermined response time to local users. CISNE-P is a middleware which includes both a previously developed space-sharing job scheduler and a dynamic coscheduling system, a time sharing scheduling component. The experimentation performed in a Linux cluster shows that these two scheduler components are complementary and a good coordination improves global performance significantly. We also compare two different CISNE-P implementations: one developed inside the kernel, and the other entirely implemented in the user space.

Global Diversity Lines-A Five-Continent Reference Panel of Sequenced Drosophila melanogaster Strains.

Reference collections of multiple Drosophila lines with accumulating collections of "omics" data have proven especially valuable for the study of population genetics and complex trait genetics. Here we present a description of a resource collection of 84 strains of Drosophila melanogaster whose genome sequences were obtained after 12 generations of full-sib inbreeding. The initial rationale for this resource was to foster development of a systems biology platform for modeling metabolic regulation by the use of natural polymorphisms as perturbations. As reference lines, they are amenable to repeated phenotypic measurements, and already a large collection of metabolic traits have been assayed. Another key feature of these strains is their widespread geographic origin, coming from Beijing, Ithaca, Netherlands, Tasmania, and Zimbabwe. After obtaining 12.5× coverage of paired-end Illumina sequence reads, SNP and indel calls were made with the GATK platform. Thorough quality control was enabled by deep sequencing one line to >100×, and single-nucleotide polymorphisms and indels were validated using ddRAD-sequencing as an orthogonal platform. In addition, a series of preliminary population genetic tests were performed with these single-nucleotide polymorphism data for assessment of data quality. We found 83 segregating inversions among the lines, and as expected these were especially abundant in the African sample. We anticipate that this will make a useful addition to the set of reference D. melanogaster strains, thanks to its geographic structuring and unusually high level of genetic diversity.

Duration and compliance with antidepressant treatment in immigrant and native-born populations in Spain: a four year follow-up descriptive study

Background: Non-compliance with antidepressant treatment continues to be a complex problem in mental health care. In immigrant populations non-compliance is one of several barriers to adequate management of mental illness; some data suggest greater difficulties in adhering to pharmacological treatment in these groups and an increased risk of therapeutic failure. The aim of this study is to assess differences in the duration and compliance with antidepressant treatment among immigrants and natives in a Spanish health region. Methods: Population-based (n = 206,603), retrospective cohort study including all subjects prescribed ADT between 2007 and 2009 and recorded in the national pharmacy claims database. Compliance was considered adequate when the duration was longer than 4 months and when patients withdrew more than 80% of the packs required. Results: 5334 subjects (8.5% of them being immigrants) initiated ADT. Half of the immigrants abandoned treatment during the second month (median for natives = 3 months). Of the immigrants who continued, only 29.5% presented good compliance (compared with 38.8% in natives). The estimated risk of abandoning/ending treatment in the immigrant group compared with the native group, adjusted for age and sex, was 1.28 (95%CI 1.16-1.42). Conclusions: In the region under study, immigrants of all origins present higher percentages of early discontinuation of ADT and lower median treatment durations than the native population. Although this is a complex, multifactor situation, the finding of differences between natives and immigrants in the same region suggests the need to investigate the causes in greater depth and to introduce new strategies and interventions in this population group.

Steady-state global optimization of metabolic non-linear dynamic models through recasting into power-law canonical models

Background: Design of newly engineered microbial strains for biotechnological purposes would greatly benefit from the development of realistic mathematical models for the processes to be optimized. Such models can then be analyzed and, with the development and application of appropriate optimization techniques, one could identify the modifications that need to be made to the organism in order to achieve the desired biotechnological goal. As appropriate models to perform such an analysis are necessarily non-linear and typically non-convex, finding their global optimum is a challenging task. Canonical modeling techniques, such as Generalized Mass Action (GMA) models based on the power-law formalism, offer a possible solution to this problem because they have a mathematical structure that enables the development of specific algorithms for global optimization. Results: Based on the GMA canonical representation, we have developed in previous works a highly efficient optimization algorithm and a set of related strategies for understanding the evolution of adaptive responses in cellular metabolism. Here, we explore the possibility of recasting kinetic non-linear models into an equivalent GMA model, so that global optimization on the recast GMA model can be performed. With this technique, optimization is greatly facilitated and the results are transposable to the original non-linear problem. This procedure is straightforward for a particular class of non-linear models known as Saturable and Cooperative (SC) models that extend the power-law formalism to deal with saturation and cooperativity. Conclusions: Our results show that recasting non-linear kinetic models into GMA models is indeed an appropriate strategy that helps overcoming some of the numerical difficulties that arise during the global optimization task.

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).

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.

The effect of information and communication technology on global paper consumption

The objective of this thesis is to find out how information and communication technology affects the global consumption of printing and writing papers. Another objective is to find out, whether there are differences between paper grades in these effects. The empirical analysis is conducted by linear regression analysis using three sets of country-level panel data from 1990-2006. Data set of newsprint contains 95 countries, data set of uncoated woodfree paper 61 countries and data set of coated mechanical paper 42 countries. The material is based on paper consumption data of RISI’s Industry Statistics Database and on the information and communication technology data of GMID-database. Results indicate that number of Internet users has statistically significant negative effect on the consumption of newsprint and on the consumption of coated mechanical paper and number of mobile telephone users has positive effect on the consumptions of these papers. Results also indicate that information and communication technologies have only small effect on consumption of uncoated woodfree paper or no significant effect at all, but these results are more uncertain to some extent.

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.

Comparação da disponibilidade de radiação solar global e fotoperíodo entre as regiões vinícolas de Campo Belo do Sul-SC, Brasil e Pech Rouge, França

Realizaram-se a caracterização e a comparação da disponibilidade de radiação solar global e do fotoperíodo para o Planalto de Santa Catarina, representado por Campo Belo do Sul (latitude -28º00'00'', longitude -51º00'00'' e altitude de 950 metros), e para a região Mediterrânea do Sul da França, representada por Pech Rouge (latitude 43º08'35'', longitude 03º07'59'' altitude de 1,5 metro). Este estudo foi realizado para a fase de maturação das variedades de videira Chardonnay, Portan, Syrah, Viognier, Carignan, Grenache, Marselan, Mourvèdre e Cabernet Sauvignon. Foram também avaliadas as durações do fotoperíodo anual, do período noturno, da radiação solar global, da radiação solar e da insolação máxima no período de maturação, para ambas as localidades. As diferenças de comportamento fenológico e das posições geográficas dos dois locais promoveram diferenças quanto à disponibilidade e intensidade da radiação solar global, assim como do fotoperíodo. Apesar da uma maior transmissividade da atmosfera para Pech Rouge, o Planalto Catarinense apresentou maior disponibilidade e intensidade de radiação solar durante a fase de maturação da videira. Também, o acúmulo de horas de fotoperíodo foi superior no Planalto Catarinense do que em Pech Rouge. Estas diferenças de disponibilidade de radiação solar e fotoperíodo foram provenientes da menor duração da fase de maturação para Pech Rouge, da declinação solar em relação aos dois locais por ocasião da ocorrência desta fase e da diferença da camada atmosférica resultante da diferença de altitude.