A classification of tasks for the systematic study of immune response using functional genomics data

A full understanding of the immune system and its responses to infection by different pathogens is important for the development of anti-parasitic vaccines. A growing number of large-scale experimental techniques, such as microarrays, are being used to gain a better understanding of the immune system. To analyse the data generated by these experiments, methods such as clustering are widely used. However, individual applications of these methods tend to analyse the experimental data without taking publicly available biological and immunological knowledge into account systematically and in an unbiased manner. To make best use of the experimental investment, to benefit from existing evidence, and to support the findings in the experimental data, available biological information should be included in the analysis in a systematic manner. In this review we present a classification of tasks that shows how experimental data produced by studies of the immune system can be placed in a broader biological context. Taking into account available evidence, the classification can be used to identify different ways of analysing the experimental data systematically. We have used the classification to identify alternative ways of analysing microarray data, and illustrate its application using studies of immune responses in mice to infection with the intestinal nematode parasites Trichuris muris and Heligmosomoides polygyrus

Bound states near a moving charge in a quantum plasma

It is investigated how the shielding of a moving point charge in a one-component fully degenerate fermion plasma affects the bound states near the charge at velocities smaller than the Fermi one. The shielding is accounted for by using the Lindhard dielectric function, and the resulting potential is substituted into the Schr\"odinger equation in order to obtain the energy levels. Their number and values are shown to be primarily determined by the value of the charge and the quantum plasma coupling parameter, while the main effect of the motion is to split certain energy levels. This provides a link between quantum plasma theory and possible measurements of spectra of ions passing through solids.Comment: Published in EPL, see http://epljournal.edpsciences.org/articles/epl/abs/2011/09/epl13478/epl13478.htm

ICES coordinated acoustic survey of ICES divisions IIIa, IVa, IVb AND Via (North) 2002 Results and long term trends

Six surveys were carried out during late June and July covering most of the continental shelf north of 54oN in the North Sea and to the west of Scotland to a northern limit of 62oN. The eastern edge of the survey area was bounded by the Norwegian and Danish, Swedish and German coasts, and to the west by the shelf edge between 200 and 400 m depth. The surveys are reported individually in the report of the planning group for herring surveys, and a combined report has been prepared from the data from all surveys. The combined survey results provide spatial distributions of herring abundance by number and biomass at age by statistical rectangle; and distributions of mean weight and fraction mature at age. The estimates of North Sea autumn spawning herring are consistent with previous years at 2.9 million tonnes and 17,200 million herring. The survey also shows two exceptional year classes of herring (the 1998 and 2000 year classes) in the North Sea, which is consistent with the observation of exceptionally large year classes observed in the MIK and IBTS surveys. The estimates of Western Baltic spring spawning herring SSB are 255,000 tonnes and 2.9 millions (Table 2) and show a large increase compared with the previous year. The Western Baltic survey produces a rather noisy signal but the indications are of a stock that is higher now than between 1996 to 2000. The West of Scotland survey estimates of 548,000 tonnes and 2,900 million and shows the high 1995 year class again this year. The 1998 year class now (3 ring) is also a large one. Total adult mortality shows much lower mortality than last year (0.1 compared to 0.5 ) but the mean mortality over the last 4 years has been 0.3: this is consistent with the 2002 assessment that the stock is lightly exploited. The overall time series of abundance by age from 1989 to 2002 are summarised by simple models describing the spatial distribution over time. The changes over time with latitude, longitude and area occupied are compared with changes in abundance

ICES coordinated acoustic survey of ICES divisions IIIa, IVa, IVb AND Via (North) 2002 Results and long term trends

Six surveys were carried out during late June and July covering most of the continental shelf north of 54oN in the North Sea and to the west of Scotland to a northern limit of 62oN. The eastern edge of the survey area was bounded by the Norwegian and Danish, Swedish and German coasts, and to the west by the shelf edge between 200 and 400 m depth. The surveys are reported individually in the report of the planning group for herring surveys, and a combined report has been prepared from the data from all surveys. The combined survey results provide spatial distributions of herring abundance by number and biomass at age by statistical rectangle; and distributions of mean weight and fraction mature at age. The estimates of North Sea autumn spawning herring are consistent with previous years at 2.9 million tonnes and 17,200 million herring. The survey also shows two exceptional year classes of herring (the 1998 and 2000 year classes) in the North Sea, which is consistent with the observation of exceptionally large year classes observed in the MIK and IBTS surveys. The estimates of Western Baltic spring spawning herring SSB are 255,000 tonnes and 2.9 millions (Table 2) and show a large increase compared with the previous year. The Western Baltic survey produces a rather noisy signal but the indications are of a stock that is higher now than between 1996 to 2000. The West of Scotland survey estimates of 548,000 tonnes and 2,900 million and shows the high 1995 year class again this year. The 1998 year class now (3 ring) is also a large one. Total adult mortality shows much lower mortality than last year (0.1 compared to 0.5 ) but the mean mortality over the last 4 years has been 0.3: this is consistent with the 2002 assessment that the stock is lightly exploited. The overall time series of abundance by age from 1989 to 2002 are summarised by simple models describing the spatial distribution over time. The changes over time with latitude, longitude and area occupied are compared with changes in abundance

Impact of sea ice on air-sea CO2 exchange – A critical review of polar eddy covariance studies

Sparse in situ measurements and poor understanding of the impact of sea ice on air-sea gas exchange introduce large uncertainties to models of polar oceanic carbon uptake. The eddy covariance technique can be used to produce insightful air-sea gas exchange datasets in the presence of sea ice, but results differ between studies. We present a critical review of historical polar eddy covariance studies and can identify only five that present comparable flux datasets. Assessment of ancillary datasets, including sea-ice coverage and type and air-sea concentration gradient of carbon dioxide, used to interpret flux datasets (with a specific focus on their role in estimating and interpreting sea ice zone gas transfer velocities) identifies that standardised methodologies to characterise the flux footprint would be beneficial. In heterogeneous ice environments both ancillary data un�certainties and controls on gas exchange are notably complex. To address the poor understanding, we highlight how future efforts should focus on the collection of robust gas flux datasets within heterogeneous sea ice regions during key seasonal processes alongside consistent ancillary data with a full characterisation of their associated uncertainties

Modeling fiber-matrix splitting failure through a mesh-objective continuum-decohesive finite element method

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/106435/1/AIAA2013-1725.pd

Взаимовлияние валютного курса и платежного баланса в Украине

Цель статьи - выявить основные каналы взаимовлияния валютного курса и платежного баланса для определения наиболее подходящей модели валютного регулирования в Украине

Temporal dynamics of ikaite in experimental sea ice

Ikaite (CaCO3 · 6H2O) is a metastable phase of calcium carbonate that normally forms in a cold environment and/or under high pressure. Recently, ikaite crystals have been found in sea ice, and it has been suggested that their precipitation may play an important role in air-sea CO 2 exchange in ice-covered seas. Little is known, however, of the spatial and temporal dynamics of ikaite in sea ice. Here we present evidence for highly dynamic ikaite precipitation and dissolution in sea ice grown at an outdoor pool of the Sea-ice Environmental Research Facility (SERF) in Manitoba, Canada. During the experiment, ikaite precipitated in sea ice when temperatures were below -4 °C, creating three distinct zones of ikaite concentrations: (1) a millimeter-to-centimeter-thin surface layer containing frost flowers and brine skim with bulk ikaite concentrations of >2000 μmol kg-1, (2) an internal layer with ikaite concentrations of 200-400 μmol kg -1, and (3) a bottom layer with ikaite concentrations of <100 μmol kg-1. Snowfall events caused the sea ice to warm and ikaite crystals to dissolve. Manual removal of the snow cover allowed the sea ice to cool and brine salinities to increase, resulting in rapid ikaite precipitation. The observed ikaite concentrations were on the same order of magnitude as modeled by FREZCHEM, which further supports the notion that ikaite concentration in sea ice increases with decreasing temperature. Thus, varying snow conditions may play a key role in ikaite precipitation and dissolution in sea ice. This could have a major implication for CO2 exchange with the atmosphere and ocean that has not been accounted for previously