Analysis of the antigen combining site: Correlations between length and sequence composition of the hypervariable loops and the nature of the antigen

It has long been suggested that the overall shape of the antigen combining site (ACS) of antibodies is correlated with the nature of the antigen. For example, deep pockets are characteristic of antibodies that bind haptens, grooves indicate peptide binders, while antibodies that bind to proteins have relatively flat combining sites. In. 1996, MacCallum, Martin and Thornton used a fractal shape descriptor and showed a strong correlation of the shape of the binding region with the general nature of the antigen. However, the shape of the ACS is determined primarily by the lengths of the six complementarity-determining regions (CDRs). Here, we make a direct correlation between the lengths of the CDRs and the nature of the antigen. In addition, we show significant differences in the residue composition of the CDRs of antibodies that bind to different antigen classes. As well as helping us to understand the process of antigen recognition, autoimmune disease and cross-reactivity these results are of direct application in the design of antibody phage libraries and modification of affinity. (C) 2003 Elsevier Science Ltd. All rights reserved.

Another look at the relative importance of sectors and regions in determining property returns

This paper re-examines the relative importance of sector and regional effects in determining property returns. Using the largest property database currently available in the world, we decompose the returns on individual properties into a national effect, common to all properties, and a number of sector and regional factors. However, unlike previous studies, we categorise the individual property data into an ever-increasing number of property-types and regions, from a simple 3-by-3 classification, up to a 10 by 63 sector/region classification. In this way we can test the impact that a finer classification has on the sector and regional effects. We confirm the earlier findings of previous studies that sector-specific effects have a greater influence on property returns than regional effects. We also find that the impact of the sector effect is robust across different classifications of sectors and regions. Nonetheless, the more refined sector and regional partitions uncover some interesting sector and regional differences, which were obscured in previous studies. All of which has important implications for property portfolio construction and analysis.

The relative importance of sectors v's regions in determining property returns

A number of studies have investigated the benefits of sector versus regional diversification within a real estate portfolio without explicitly quantify the relative benefits of one against the other. This paper corrects this omission by adopting the approach of Heston and Rouwenhorst (1994) and Beckers, Connor and Curds (1996) on a sample of 187 property data points using annual data over the period 1981-1995. The general conclusion of which is the sector diversification explains on average 22% of the variability of property returns compared with 8% for administratively defined regions. A result in line with previous work. Implying that sector diversification should be the first level of analysis in constructing and managing the real estate portfolio. However, unlike previous work functionally defined regions provide less of an explanation of regional diversification than administrative regions. Which may be down to the weak definition of economic regions employed in this study.

Numerical conformal mapping and mesh generation for polygonal and multiply-connected regions

Details are given of a boundary-fitted mesh generation method for use in modelling free surface flow and water quality. A numerical method has been developed for generating conformal meshes for curvilinear polygonal and multiply-connected regions. The method is based on the Cauchy-Riemann conditions for the analytic function and is able to map a curvilinear polygonal region directly onto a regular polygonal region, with horizontal and vertical sides. A set of equations have been derived for determining the lengths of these sides and the least-squares method has been used in solving the equations. Several numerical examples are presented to illustrate the method.

The latitudinal effect of corotating interaction regions on galactic cosmic rays

The response of galactic cosmic rays (GCRs) to an isolated enhancement of the non-axisymmetric component of the solar open magnetic field between June and November 1996 is investigated by using a combination of solar observations and numerical modelling of the interplanetary medium. The most obvious coronal hole visible from Earth at the time had little shielding effect on the flux of GCRs, as measured at Earth by neutron monitors. It is found that the evolution of the corotating interaction regions generated by a less obvious coronal hole was the principal controlling factor. Moreover, we demonstrate the imprint of the latitudinal and longitudinal evolution of that coronal hole on the variation of GCRs. The latitudinal extent of this solar minimum corotating interaction region had a determining, but local, shielding effect on GCRs, confirming previous modelling results.

A Tropospheric Assessment of the ERA-40, NCEP, and JRA-25 Global Reanalyses in the Polar Regions

The reliability of the global reanalyses in the polar regions is investigated. The overview stems from an April 2006 Scientific Committee on Antarctic Research (SCAR) workshop on the performance of global reanalyses in high latitudes held at the British Antarctic Survey. Overall, the skill is much higher in the Arctic than the Antarctic, where the reanalyses are only reliable in the summer months prior to the modern satellite era. In the Antarctic, large circulation differences between the reanalyses are found primarily before 1979, when vast quantities of satellite sounding data started to be assimilated. Specifically for ERA-40, this data discontinuity creates a marked jump in Antarctic snow accumulation, especially at high elevations. In the Arctic, the largest differences are related to the reanalyses depiction of clouds and their associated radiation impacts; ERA-40 captures the cloud variability much better than NCEP1 and JRA-25, but the ERA-40 and JRA-25 clouds are too optically thin for shortwave radiation. To further contrast the reanalyses skill, cyclone tracking results are presented. In the Southern Hemisphere, cyclonic activity is markedly different between the reanalyses, where there are few matched cyclones prior to 1979. In comparison, only some of the weaker cyclones are not matched in the Northern Hemisphere from 1958-2001, again indicating the superior skill in this hemisphere. Although this manuscript focuses on deficiencies in the reanalyses, it is important to note that they are a powerful tool for climate studies in both polar regions when used with a recognition of their limitations.

Chemical composition observed over the mid-Atlantic and the detection of pollution signatures far from source regions

The atmospheric composition of the central North Atlantic region has been sampled using the FAAM BAe146 instrumented aircraft during the Intercontinental Transport of Ozone and Precursors (ITOP) campaign, part of the wider International Consortium for Atmospheric Research on Transport and Transformation (ICARTT). This paper presents an overview of the ITOP campaign. Between late July and early August 2004, twelve flights comprising 72 hours of measurement were made in a region from approximately 20 to 40°W and 33 to 47°N centered on Faial Island, Azores, ranging in altitude from 50 to 9000 m. The vertical profiles of O3 and CO are consistent with previous observations made in this region during 1997 and our knowledge of the seasonal cycles within the region. A cluster analysis technique is used to partition the data set into air mass types with distinct chemical signatures. Six clusters provide a suitable balance between cluster generality and specificity. The clusters are labeled as biomass burning, low level outflow, upper level outflow, moist lower troposphere, marine and upper troposphere. During this summer, boreal forest fire emissions from Alaska and northern Canada were found to provide a major perturbation of tropospheric composition in CO, PAN, organic compounds and aerosol. Anthropogenic influenced air from the continental boundary layer of the USA was clearly observed running above the marine boundary layer right across the mid-Atlantic, retaining high pollution levels in VOCs and sulfate aerosol. Upper level outflow events were found to have far lower sulfate aerosol, resulting from washout on ascent, but much higher PAN associated with the colder temperatures. Lagrangian links with flights of other aircraft over the USA and Europe show that such signatures are maintained many days downwind of emission regions. Some other features of the data set are highlighted, including the strong perturbations to many VOCs and OVOCs in this remote region.

Tripleclouds: an efficient method for representing horizontal cloud inhomogeneity in 1D radiation schemes by using three regions at each height

Radiation schemes in general circulation models currently make a number of simplifications when accounting for clouds, one of the most important being the removal of horizontal inhomogeneity. A new scheme is presented that attempts to account for the neglected inhomogeneity by using two regions of cloud in each vertical level of the model as opposed to one. One of these regions is used to represent the optically thinner cloud in the level, and the other represents the optically thicker cloud. So, along with the clear-sky region, the scheme has three regions in each model level and is referred to as “Tripleclouds.” In addition, the scheme has the capability to represent arbitrary vertical overlap between the three regions in pairs of adjacent levels. This scheme is implemented in the Edwards–Slingo radiation code and tested on 250 h of data from 12 different days. The data are derived from cloud retrievals using radar, lidar, and a microwave radiometer at Chilbolton, southern United Kingdom. When the data are grouped into periods equivalent in size to general circulation model grid boxes, the shortwave plane-parallel albedo bias is found to be 8%, while the corresponding bias is found to be less than 1% using Tripleclouds. Similar results are found for the longwave biases. Tripleclouds is then compared to a more conventional method of accounting for inhomogeneity that multiplies optical depths by a constant scaling factor, and Tripleclouds is seen to improve on this method both in terms of top-of-atmosphere radiative flux biases and internal heating rates.

A study of the sensitivity of ocean overturning circulation and climate to freshwater input in different regions of the North Atlantic

The Atlantic meridional overturning circulation (AMOC) is an important component of the climate system. Models indicate that the AMOC can be perturbed by freshwater forcing in the North Atlantic. Using an ocean-atmosphere general circulation model, we investigate the dependence of such a perturbation of the AMOC, and the consequent climate change, on the region of freshwater forcing. A wide range of changes in AMOC strength is found after 100 years of freshwater forcing. The largest changes in AMOC strength occur when the regions of deepwater formation in the model are forced directly, although reductions in deepwater formation in one area may be compensated by enhanced formation elsewhere. North Atlantic average surface air temperatures correlate linearly with the AMOC decline, but warming may occur in localised regions, notably over Greenland and where deepwater formation is enhanced. This brings into question the representativeness of temperature changes inferred from Greenland ice-core records.

Water vapor variability in the tropics and its links to dynamics and precipitation

The distribution and variability of water vapor and its links with radiative cooling and latent heating via precipitation are crucial to understanding feedbacks and processes operating within the climate system. Column-integrated water vapor (CWV) and additional variables from the European Centre for Medium-Range Weather Forecasts (ECMWF) 40-year reanalysis (ERA40) are utilized to quantify the spatial and temporal variability in tropical water vapor over the period 1979–2001. The moisture variability is partitioned between dynamical and thermodynamic influences and compared with variations in precipitation provided by the Climate Prediction Center Merged Analysis of Precipitation (CMAP) and the Global Precipitation Climatology Project (GPCP). The spatial distribution of CWV is strongly determined by thermodynamic constraints. Spatial variability in CWV is dominated by changes in the large-scale dynamics, in particular associated with the El Niño–Southern Oscillation (ENSO). Trends in CWV are also dominated by dynamics rather than thermodynamics over the period considered. However, increases in CWV associated with changes in temperature are significant over the equatorial east Pacific when analyzing interannual variability and over the north and northwest Pacific when analyzing trends. Significant positive trends in CWV tend to predominate over the oceans while negative trends in CWV are found over equatorial Africa and Brazil. Links between changes in CWV and vertical motion fields are identified over these regions and also the equatorial Atlantic. However, trends in precipitation are generally incoherent and show little association with the CWV trends. This may in part reflect the inadequacies of the precipitation data sets and reanalysis products when analyzing decadal variability. Though the dynamic component of CWV is a major factor in determining precipitation variability in the tropics, in some regions/seasons the thermodynamic component cancels its effect on precipitation variability.

Can the frequency of blocking be described by a red noise process?

The frequency of persistent atmospheric blocking events in the 40-yr ECMWF Re-Analysis (ERA-40) is compared with the blocking frequency produced by a simple first-order Markov model designed to predict the time evolution of a blocking index [defined by the meridional contrast of potential temperature on the 2-PVU surface (1 PVU ≡ 1 × 10−6 K m2 kg−1 s−1)]. With the observed spatial coherence built into the model, it is able to reproduce the main regions of blocking occurrence and the frequencies of sector blocking very well. This underlines the importance of the climatological background flow in determining the locations of high blocking occurrence as being the regions where the mean midlatitude meridional potential vorticity (PV) gradient is weak. However, when only persistent blocking episodes are considered, the model is unable to simulate the observed frequencies. It is proposed that this persistence beyond that given by a red noise model is due to the self-sustaining nature of the blocking phenomenon.

Spatial and temporal scale issues in determining biomass burning regimes in Bolivia and Peru

ATSR-2 active fire data from 1996 to 2000, TRMM VIRS fire counts from 1998 to 2000 and burn scars derived from SPOT VEGETATION ( the Global Burnt Area 2000 product) were mapped for Peru and Bolivia to analyse the spatial distribution of burning and its intra- and inter-annual variability. The fire season in the region mainly occurs between May and October; though some variation was found between the six broad habitat types analysed: desert, grassland, savanna, dry forest, moist forest and yungas (the forested valleys on the eastern slope of the Andes). Increased levels of burning were generally recorded in ATSR-2 and TRMM VIRS fire data in response to the 1997/1998 El Nino, but in some areas the El Nino effect was masked by the more marked influences of socio-economic change on land use and land cover. There were differences between the three global datasets: ATSR-2 under-recorded fires in ecosystems with low net primary productivities. This was because fires are set during the day in this region and, when fuel loads are low, burn out before the ATSR-2 overpass in the region which is between 02.45 h and 03.30 h. TRMM VIRS was able to detect these fires because its overpasses cover the entire diurnal range on a monthly basis. The GBA2000 product has significant errors of commission (particularly areas of shadow in the well-dissected eastern Andes) and omission (in the agricultural zone around Santa Cruz, Bolivia and in north-west Peru). Particular attention was paid to biomass burning in high-altitude grasslands, where fire is an important pastoral management technique. Fires and burn scars from Landsat Thematic Mapper (TM) and Enhanced Thematic Mapper (ETM) data for a range of years between 1987 and 2000 were mapped for areas around Parque Nacional Rio Abiseo (Peru) and Parque Nacional Carrasco (Bolivia). Burn scars mapped in the grasslands of these two areas indicate far more burning had taken place than either the fires or the burn scars derived from global datasets. Mean scar sizes are smaller and have a smaller range in size between years the in the study area in Peru (6.6-7.1 ha) than Bolivia (16.9-162.5 ha). Trends in biomass burning in the two highland areas can be explained in terms of the changing socio-economic environments and impacts of conservation. The mismatch between the spatial scale of biomass burning in the high-altitude grasslands and the sensors used to derive global fire products means that an entire component of the fire regime in the region studied is omitted, despite its importance in the farming systems on the Andes.

Palaeohydrology of the Fazzan Basin and surrounding regions: The last 7 million years

We have integrated information on topography, geology and geomorphology with the results of targeted fieldwork in order to develop a chronology for the development of Lake Megafazzan, a giant lake that has periodically existed in the Fazzan Basin since the late Miocene. The development of the basin can be best understood by considering the main geological and geomorphological events that occurred thought Libya during this period and thus an overview of the palaeohydrology of all Libya is also presented. The origin of the Fazzan Basin appears to lie in the Late Miocene. At this time Libya was dominated by two large rivers systems that flowed into the Mediterranean Sea, the Sahabi River draining central and eastern Libya and the Wadi Nashu River draining much of western Libya. As the Miocene progressed the region become increasingly affected by volcanic activity on its northern and eastern margin that appears to have blocked the River Nashu in Late Miocene or early Messinian times forming a sizeable closed basin in the Fazzan within which proto-Lake Megafazzan would have developed during humid periods. The fall in base level associated with the Messinian desiccation of the Mediterranean Sea promoted down-cutting and extension of river systems throughout much of Libya. To the south of the proto Fazzan Basin the Sahabi River tributary know as Wadi Barjuj appears to have expanded its headwaters westwards. The channel now terminates at Al Haruj al Aswad. We interpret this as a suggestion that Wadi Barjuj was blocked by the progressive development of Al Haruj al Aswad. K/Ar dating of lava flows suggests that this occurred between 4 and 2 Ma. This event would have increased the size of the closed basin in the Fazzan by about half, producing a catchment close to its current size (-350,000 km(2)). The Fazzan Basin contains a wealth of Pleistocene to recent palaeolake sediment outcrops and shorelines. Dating of these features demonstrates evidence of lacustrine conditions during numerous interglacials spanning a period greater than 420 ka. The middle to late Pleistocene interglacials were humid enough to produce a giant lake of about 135,000 km(2) that we have called Lake Megafazzan. Later lake phases were smaller, the interglacials less humid, developing lakes of a few thousand square kilometres. In parallel with these palaeohydrological developments in the Fazzan Basin, change was occurring in other parts of Libya. The Lower Pliocene sea level rise caused sediments to infill much of the Messinian channel system. As this was occurring, subsidence in the Al Kufrah Basin caused expansion of the Al Kufrah River system at the expense of the River Sahabi. By the Pleistocene, the Al Kufrah River dominated the palaeohydrology of eastern Libya and had developed a very large inland delta in its northern reaches that exhibited a complex distributary channel network which at times fed substantial lakes in the Sirt Basin. At this time Libya was a veritable lake district during humid periods with about 10% of the country underwater. (C) 2008 Elsevier B.V. All rights reserved.

Determining nugget: sill ratios of standardized variograms from aerial photographs to krige sparse soil data

Maps of kriged soil properties for precision agriculture are often based on a variogram estimated from too few data because the costs of sampling and analysis are often prohibitive. If the variogram has been computed by the usual method of moments, it is likely to be unstable when there are fewer than 100 data. The scale of variation in soil properties should be investigated prior to sampling by computing a variogram from ancillary data, such as an aerial photograph of the bare soil. If the sampling interval suggested by this is large in relation to the size of the field there will be too few data to estimate a reliable variogram for kriging. Standardized variograms from aerial photographs can be used with standardized soil data that are sparse, provided the data are spatially structured and the nugget:sill ratio is similar to that of a reliable variogram of the property. The problem remains of how to set this ratio in the absence of an accurate variogram. Several methods of estimating the nugget:sill ratio for selected soil properties are proposed and evaluated. Standardized variograms with nugget:sill ratios set by these methods are more similar to those computed from intensive soil data than are variograms computed from sparse soil data. The results of cross-validation and mapping show that the standardized variograms provide more accurate estimates, and preserve the main patterns of variation better than those computed from sparse data.