Clustering of Th cell epitopes on exposed regions of HIV envelope despite defects in antibody activity

A long-standing question in the field of immunology concerns the factors that contribute to Th cell epitope immunodominance. For a number of viral membrane proteins, Th cell epitopes are localized to exposed protein surfaces, often overlapping with Ab binding sites. It has therefore been proposed that Abs on B cell surfaces selectively bind and protect exposed protein fragments during Ag processing, and that this interaction helps to shape the Th cell repertoire. While attractive in concept, this hypothesis has not been thoroughly tested. To test this hypothesis, we have compared Th cell peptide immunodominance in normal C57BL/6 mice with that in C57BL/6MT/MT mice (lacking normal B cell activity). Animals were first vaccinated with DNA constructs expressing one of three different HIV envelope proteins, after which the CD4 T cell response profiles were characterized toward overlapping peptides using an IFN- ELISPOT assay. We found a striking similarity between the peptide response profiles in the two mouse strains. Profiles also matched those of previous experiments in which different envelope vaccination regimens were used. Our results clearly demonstrate that normal Ab activity is not required for the establishment or maintenance of Th peptide immunodominance in the HIV envelope response. To explain the clustering of Th cell epitopes, we propose that localization of peptide on exposed envelope surfaces facilitates proteolytic activity and preferential peptide shuttling through the Ag processing pathway.

Measuring the vulnerability of sub-national regions in South Africa

A small but growing literature has been concerned about the economic (and
environmental) vulnerability on the level of countries. Less attention is paid to the economic vulnerability of different regions within countries. By focusing on the vulnerability of subnational regions, this paper contributes to the small literature on the “vulnerability of place”. They authors see the vulnerability of place as being due to vulnerability in various domains, such as economic vulnerability, vulnerability of environment, and governance, demographic and health fragilities. They use a subnational data set on 354 magisterial districts from South Africa, recognize the potential relevance of measuring vulnerability on a subnational level, and construct a Local Vulnerability Index for the various districts. They condition this index on district per capita income and term this a Vulnerability Intervention Index, interpreting this as an indicator of where higher income per capita, often seen in the literature as a measure of resilience, will in itself be unlikely to reduce vulnerability.

Automatic extraction of abnormal regions from lung images

A system that could automatically extract abnormal lung regions may assist expert radiologists in verifying lung tissue abnormalities. This paper presents an automated lung nodule detection system consisting of five components: acquisition, pre-processing, background removal, detection, and false positives reduction. The system employs a combination of an ensemble classification and clustering methods. The performance of the developed system is compared against some existing counterparts. Based 011 the experimental results, the proposed system achieved a sensitivity of 100% and a false-positives/slice of 0.67 for 30 tested CT images.

Palaeobiogeography and palaeogeographical implications of Permian marine bivalve faunas in Northeast Asia (Kolyma–Omolon and erkhoyansk–Okhotsk regions, northeastern Russia)

The paper considers the biogeography and palaeogeographic implications of the Permian marine bivalve faunas of Northeast Asia, with a focus on the dynamic relationships between biotic similarities and palaeogeographic distance through an interval of ca. 50 million years. A stage-by-stage time series analysis of the biotic similarities between two previously recognized biochores in Northeast Asia, the Kolyma–Omolon and Verkhoyan–Okhotsk provinces, has been carried out using both the Jaccard and Dice similarity indices based on the spatio-temporal distributions of 355 Permian marine bivalve species in Northeast Asia. The outcome of this analysis, combined with other empirical data and previously published tectonic, sedimentological and palaeontological information, suggests that (1) the bivalve faunas from these two provinces were distinctive from one another as two separate biochores throughout all but the earliest (Asselian) Permian stages and (2) the biotic similarities between the Verkhoyan–Okhotsk and Kolyma–Omolon provinces remained consistently low since Sakmarian, all falling well below the minimum threshold of the Jaccard index of 0.42 required for distinguishing marine biotic provinces. We interpret these below-threshold Jaccard biotic similarities as an indication of significant palaeogeographic separation between the Verkhoyan-Okhotsk and Kolyma–Omolon provinces, which is in turn considered to indicate rifting and seafloor spreading of the Omolon microcontinent and associated terranes and island arcs away from the North Asian craton, at least from the Sakmarian to the beginning of the Late Permian.
Palaeo-distance separation appears to be the primary and most significant biogeographic determinant in accounting for the differences in the spatial distribution of most Permian bivalve species in Northeast Asia. Several other variables also appear to have played a significant role, including regional climate conditions, ocean currents and merged island chains as geographic barriers. In particular, the relatively high biotic similarity between the Verkhoyan–Okhotsk and Kolyma–Omolon provinces during the Late Wuchiapingian and Changhsingian may have been related to the shallowing of the deep-water basins (Oimyakon, Ayan-Yuryakh, Balygychan and Sugoi basins) that had previously separated the two provinces and the flooding (submergence) of the Okhotsk–Taigonos volcanic arc system, thus allowing the invasion of lower latitude warm-water Palaeotethyan and even Gondwanan species into Northeast Asia.

The attractive female body weight and female body dissatisfaction in 26 countries across 10 world regions : results of the international body project 1

This study reports results from the first International Body Project (IBP-I), which surveyed 7,434 individuals in 10 major world regions about body weight ideals and body dissatisfaction. Participants completed the female Contour Drawing Figure Rating Scale (CDFRS) and self-reported their exposure to Western and local media. Results indicated there were significant cross-regional differences in the ideal female figure and body dissatisfaction, but effect sizes were small across highsocioeconomic-status (SES) sites. Within cultures, heavier bodies were preferred in low-SES sites compared to high-SES sites in Malaysia and South Africa (ds = 1.94-2.49) but not in Austria. Participant age, body mass index (BMI), and Western media exposure predicted body weight ideals. BMI and Western media exposure predicted body dissatisfaction among women. Our results show that body dissatisfaction and desire for thinness is commonplace in high-SES settings across world regions, highlighting the need for international attention to this problem.

Identifying foldable regions in protein sequence from the hydrophobic signal

Structural genomics initiatives aim to elucidate representative 3D structures for the majority of protein families over the next decade, but many obstacles must be overcome. The correct design of constructs is extremely important since many proteins will be too large or contain unstructured regions and will not be amenable to crystallization. It is therefore essential to identify regions in protein sequences that are likely to be suitable for structural study. Scooby-Domain is a fast and simple method to identify globular domains in protein sequences. Domains are compact units of protein structure and their correct delineation will aid structural elucidation through a divide-and-conquer approach. Scooby-Domain predictions are based on the observed lengths and hydrophobicities of domains from proteins with known tertiary structure. The prediction method employs an A*-search to identify sequence regions that form a globular structure and those that are unstructured. On a test set of 173 proteins with consensus CATH and SCOP domain definitions, Scooby-Domain has a sensitivity of 50% and an accuracy of 29%, which is better than current state-of-the-art methods. The method does not rely on homology searches and, therefore, can identify previously unknown domains.

Chronic stress alters the density and morphology of microglia in a subset of stress-responsive brain regions

The current study, in parallel experiments, evaluated the impact of chronic psychological stress on physiological and behavioural measures, and on the activation status of microglia in 15 stress-responsive brain regions. Rats were subjected, for 14 days, to two 30 min sessions of restraint per day, applied at random times each day. In one experiment the effects of stress on sucrose preference, weight gain, core body temperature, and struggling behaviour during restraint, were determined. In the second experiment we used immunohistochemistry to investigate stress-induced changes in ionized calcium-binding adaptor molecule-1 (Iba1), a marker constitutively expressed by microglia, and major histocompatibility complex-II (MHC-II), a marker often expressed on activated microglia, in a total of 15 stress-responsive nuclei. We also investigated cellular proliferation in these regions using Ki67 immunolabelling, to check for the possibility of microglial proliferation. Collectively, the results we obtained showed that chronic stress induced a significant increase in anhedonia, a decrease in weight gain across the entire observation period, a significant elevation in core body temperature during restraint, and a progressive decrease in struggling behaviour within and over sessions. With regard to microglial activation, chronic stress induced a significant increase in the density of Iba1 immunolabelling (nine of 15 regions) and the number of Iba1-positive cells (eight of 15 regions). Within the regions that exhibited an increased number of Iba1-positive cells after chronic stress, we found no evidence of a between group difference in the number of MHC-II or Ki67 positive cells. In summary, these results clearly demonstrate that chronic stress selectively increases the number of microglia in certain stress-sensitive brain regions, and also causes a marked transition of microglia from a ramified-resting state to a non-resting state. These findings are consistent with the view that microglial activation could play an important role in controlling and/or adapting to stress.

Combining image regions and human activity for indirect object recognition in indoor wide-angle views

Traditional methods of object recognition are reliant on shape and so are very difficult to apply in cluttered, wideangle and low-detail views such as surveillance scenes. To address this, a method of indirect object recognition is proposed, where human activity is used to infer both the location and identity of objects. No shape analysis is necessary. The concept is dubbed 'interaction signatures', since the premise is that a human will interact with objects in ways characteristic of the function of that object - for example, a person sits in a chair and drinks from a cup. The human-centred approach means that recognition is possible in low-detail views and is largely invariant to the shape of objects within the same functional class. This paper implements a Bayesian network for classifying region patches with object labels, building upon our previous work in automatically segmenting and recognising a human's interactions with the objects. Experiments show that interaction signatures can successfully find and label objects in low-detail views and are equally effective at recognising test objects that differ markedly in appearance from the training objects.