Biogeochemical parameters and processes in waters and bottom sediments of the Chukchi Sea

Study of biogeochemical processes in waters and sediments of the Chukchi Sea in August 2004 revealed atypical maxima of biogenic element (N, P, and Si) concentrations and rate of microbial sulfate reduction in the surface layer (0-3 cm) of marine sediments. The C/N/P ratio in organic matter (OM) of this layer does not fit the Redfield-Richards stoichiometric model. Specific features of biogeochemical processes in the sea are likely related to the complex dynamics of water, high primary produc¬tivity (110-1400 mg C/m**2/day), low depth of the basin (<50 m for 60% of the water area), reduced food chain due to low population of zooplankton, high density of zoobenthos (up to 4230 g/m**2), and high activity of microbial processes. Drastic decrease in concentrations of biogenic elements, iodine, total alkalinity, and population of microorganisms beneath the 0-3 cm layer testify to large-scale OM decay at the water-seafloor barrier. Our original experimental data support high annual rate of OM mineralization at the bottom of the Chukchi Sea.

Radionuclide measurements in sediments and water of the Kara Sea

In this report, the results of a 2000-2001 radiogeoecological investigation are presented for the region of the Ob and Yenisei estuaries and the adjacent Kara Sea. In order to study the behaviour and migration of Cs, Sr and Pu radionuclides in a river - sea system experimental research on the distribution of these radionuclides in the water column and surface sediments has been carried out. In addition, the role of suspended and dissolved organic matter on the behaviour of radionuclides in water solutions has been studied. The 137Cs and 239,240Pu concentrations in the upper 0-2cm layer of the sediments varied between 1,4 and 50,0 Bq/kg, with a mean of 12,4 Bq/kg, and between 0,065-1,96 Bq/kg, with a mean of 0,62 Bq/kg, respectively. There is a direct relationship of a specific radioactivity of 137Cs and 239,240Pu in the sediments and the content of clay fraction. The 137Cs, 90Sr and 239,240Pu concentrations in the water samples varied between 0,4 and 7,0 Bq/m**3 (mean of 3,6 Bq/m**3), 0,4 and 9,7 Bq/m**3 (mean of 3,3 Bq/m**3), and 0,01-0,3 Bq/m**3 (mean of 0,02 Bq/m**3), respectively. In the water samples the concentration of the water-soluble species l37Cs increases with increasing salinity, whereas the concentration of the 90Sr-radionuclide decreases with increasing salinity. This may be related to the physico-chemical behaviour of these radionuclides in water solutions and the influence of several sources on radioactive pollution in this basin. In sea water the suspended matter may absorb up to 10% 137Cs, 90Sr and 239,240Pu, in river water samples these values may reach 15-30%. More than 50% 90Sr and 239,240Pu is able to form complexes with dissolved organic matter. This effect is smaller in saline water. The comparison of the data of 137Cs radioactivity in the surface sediments in 1995 and 2000-2001 showed that the level of radioactivity has decreased.

samExploreR: exploring reproducibility and robustness of RNA-seq results based on SAM files

MOTIVATION: Data from RNA-seq experiments provide us with many new possibilities to gain insights into biological and disease mechanisms of cellular functioning. However, the reproducibility and robustness of RNA-seq data analysis results is often unclear. This is in part attributed to the two counter acting goals of (a) a cost efficient and (b) an optimal experimental design leading to a compromise, e.g., in the sequencing depth of experiments.

RESULTS: We introduce an R package called samExploreR that allows the subsampling (m out of n bootstraping) of short-reads based on SAM files facilitating the investigation of sequencing depth related questions for the experimental design. Overall, this provides a systematic way for exploring the reproducibility and robustness of general RNA-seq studies. We exemplify the usage of samExploreR by studying the influence of the sequencing depth and the annotation on the identification of differentially expressed genes.

AVAILABILITY: Availability: samExploreR is available as an R package from Bioconductor (after acceptance of the paper, download link: http://www.bio-complexity.com/samExploreR_1.0.0.tar.gz).

Systematic evaluation of patient-reported outcome (PRO) protocol content and reporting in UK cancer clinical trials: the EPiC study protocol

Introduction Emerging evidence suggests that patient-reported outcome (PRO)-specific information may be omitted in trial protocols and that PRO results are poorly reported, limiting the use of PRO data to inform cancer care. This study aims to evaluate the standards of PRO-specific content in UK cancer trial protocols and their arising publications and to highlight examples of best-practice PRO protocol content and reporting where they occur. The objective of this study is to determine if these early findings are generalisable to UK cancer trials, and if so, how best we can bring about future improvements in clinical trials methodology to enhance the way PROs are assessed, managed and reported. Hypothesis: Trials in which the primary end point is based on a PRO will have more complete PRO protocol and publication components than trials in which PROs are secondary end points.

Methods and analysis Completed National Institute for Health Research (NIHR) Portfolio Cancer clinical trials (all cancer specialities/age-groups) will be included if they contain a primary/secondary PRO end point. The NIHR portfolio includes cancer trials, supported by a range of funders, adjudged as high-quality clinical research studies. The sample will be drawn from studies completed between 31 December 2000 and 1 March 2014 (n=1141) to allow sufficient time for completion of the final trial report and publication. Two reviewers will then review the protocols and arising publications of included trials to: (1) determine the completeness of their PRO-specific protocol content; (2) determine the proportion and completeness of PRO reporting in UK Cancer trials and (3) model factors associated with PRO protocol and reporting completeness and with PRO reporting proportion.

Ethics and dissemination The study was approved by the ethics committee at University of Birmingham (ERN_15-0311). Trial findings will be disseminated via presentations at local, national and international conferences, peer-reviewed journals and social media including the CPROR twitter account and UOB departmental website (http://www.birmingham.ac.uk/cpro0r).

Development of a cargo screening process simulator: a first approach

The efficiency of current cargo screening processes at sea and air ports is largely unknown as few benchmarks exists against which they could be measured. Some manufacturers provide benchmarks for individual sensors but we found no benchmarks that take a holistic view of the overall screening procedures and no benchmarks that take operator variability into account. Just adding up resources and manpower used is not an effective way for assessing systems where human decision-making and operator compliance to rules play a vital role. Our aim is to develop a decision support tool (cargo-screening system simulator) that will map the right technology and manpower to the right commodity-threat combination in order to maximise detection rates. In this paper we present our ideas for developing such a system and highlight the research challenges we have identified. Then we introduce our first case study and report on the progress we have made so far.

Modelling and analysing cargo screening processes: a project outline

The efficiency of current cargo screening processes at sea and air ports is unknown as no benchmarks exists against which they could be measured. Some manufacturer benchmarks exist for individual sensors but we have not found any benchmarks that take a holistic view of the screening procedures assessing a combination of sensors and also taking operator variability into account. Just adding up resources and manpower used is not an effective way for assessing systems where human decision-making and operator compliance to rules play a vital role. For such systems more advanced assessment methods need to be used, taking into account that the cargo screening process is of a dynamic and stochastic nature. Our project aim is to develop a decision support tool (cargo-screening system simulator) that will map the right technology and manpower to the right commodity-threat combination in order to maximize detection rates. In this paper we present a project outline and highlight the research challenges we have identified so far. In addition we introduce our first case study, where we investigate the cargo screening process at the ferry port in Calais.

Multi-sensor Cloud and Aerosol Retrieval Simulator and Its Applications

Executing a cloud or aerosol physical properties retrieval algorithm from controlled synthetic data is an important step in retrieval algorithm development. Synthetic data can help answer questions about the sensitivity and performance of the algorithm or aid in determining how an existing retrieval algorithm may perform with a planned sensor. Synthetic data can also help in solving issues that may have surfaced in the retrieval results. Synthetic data become very important when other validation methods, such as field campaigns,are of limited scope. These tend to be of relatively short duration and often are costly. Ground stations have limited spatial coverage whilesynthetic data can cover large spatial and temporal scales and a wide variety of conditions at a low cost. In this work I develop an advanced cloud and aerosol retrieval simulator for the MODIS instrument, also known as Multi-sensor Cloud and Aerosol Retrieval Simulator (MCARS). In a close collaboration with the modeling community I have seamlessly combined the GEOS-5 global climate model with the DISORT radiative transfer code, widely used by the remote sensing community, with the observations from the MODIS instrument to create the simulator. With the MCARS simulator it was then possible to solve the long standing issue with the MODIS aerosol optical depth retrievals that had a low bias for smoke aerosols. MODIS aerosol retrieval did not account for effects of humidity on smoke aerosols. The MCARS simulator also revealed an issue that has not been recognized previously, namely,the value of fine mode fraction could create a linear dependence between retrieved aerosol optical depth and land surface reflectance. MCARS provided the ability to examine aerosol retrievals against “ground truth” for hundreds of thousands of simultaneous samples for an area covered by only three AERONET ground stations. Findings from MCARS are already being used to improve the performance of operational MODIS aerosol properties retrieval algorithms. The modeling community will use the MCARS data to create new parameterizations for aerosol properties as a function of properties of the atmospheric column and gain the ability to correct any assimilated retrieval data that may display similar dependencies in comparisons with ground measurements.

Análise exploratória de simulações sociais computacionais por meio de estatística multivariada e mapas auto-organizáveis.

Visando oferecer subsídios para a avaliação do Plano Territorial de Desenvolvimento Rural Sustentável do Ministério do Desenvolvimento Agrário este trabalho teve como objetivo a aplicação da análise de componentes principais, da análise de agrupamentos pelo método hierárquico aglomerativo e da rede neural do tipo Mapa Auto-Organizável de Kohonen na análise exploratória de resultados de simulações sociais computacionais do sistema socioterritorial ?Território Rural Sul "sergipano?. A metodologia basea-se na Sociologia da Ação Organizada e no método Soclab. As análises estatísticas mostraram que o sistema socioterritorial em questão tem estrutura simples e determinística, ou seja, apresenta um jogo social cooperativo com forte tendência à estabilidade mesmo com situações de interesses divergentes. A análise neural permitiu a caracterização das situações atípicas quando ocorrem a estabilidade do sistema social.