Peptide binding prediction for the human class II MHC allele HLA-DP2:a molecular docking approach

MHC class II proteins bind oligopeptide fragments derived from proteolysis of pathogen antigens, presenting them at the cell surface for recognition by CD4+ T cells. Human MHC class II alleles are grouped into three loci: HLA-DP, HLA-DQ and HLA-DR. In contrast to HLA-DR and HLA-DQ, HLA-DP proteins have not been studied extensively, as they have been viewed as less important in immune responses than DRs and DQs. However, it is now known that HLA-DP alleles are associated with many autoimmune diseases. Quite recently, the X-ray structure of the HLA-DP2 molecule (DPA*0103, DPB1*0201) in complex with a self-peptide derived from the HLA-DR a-chain has been determined. In the present study, we applied a validated molecular docking protocol to a library of 247 modelled peptide-DP2 complexes, seeking to assess the contribution made by each of the 20 naturally occurred amino acids at each of the nine binding core peptide positions and the four flanking residues (two on both sides).

Statnote 33:the intra-class correlation coefficient

The intra-class correlation coefficient (ICC or ri) is a method of measuring correlation when the data are paired and therefore, should be used when experimental units are organised into groups. A useful analogy is with the unpaired or paired ‘t’ test to compare the differences between the means of two groups. In studies of reproducibility, there may actually be little difference between the ICC and Pearson’s ‘r’ for ‘true’ repeated measurements. If, however, there is a systematic change in the measurements made on the first compared with the second occasion, then the ICC will be significantly less than ‘r’, and less confidence would be placed in the reproducibility of the results.

The church of England and the working class in Birmingham, 1861-1905

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The social construction of sleep and work in the British print news media

This article presents a sociological study of sleep issues in the British print news media, with particular focus on the relationship between sleep, work and the changing demands of ‘flexible capitalism’. Drawing on over 1000 newspaper articles from 1984 to 2005, we explore how and why sleep is framed or constructed in terms of continuity and change (in British working life and work cultures) and, equally, viewed as a neglected component of our social lives which is too easily sacrificed to the demands of the 24/7 society, long hours culture and the struggle to create a harmonious work-life balance. This is particularly the case for certain British work cultures in which sleep has conflicting and contrasting associations. Finally, we reflect on the broader class-based discourses and debates that arise from certain workers having their sleep patterns increasingly scrutinized and regulated, and the role of the media in any ensuing sleep/work ‘crisis’.

The relationship between parental perceptions of diabetes and glycaemic control

Aim: To measure the relationship between perceived child competence, parental self-efficacy, and children's glycaemic control. Methods: Cross-sectional outpatient based questionnaire survey of 78 parents of children aged 6-12 years with insulin dependent diabetes mellitus, diagnosed for at least one year. Parental perceptions of their child's competence were assessed, together with parental perceptions of their own self-efficacy in managing their child's diabetes. Glycaemic control was assessed by the average annual HbA 1C level. Results: The response rate was 64.5% (51 parents); 82% were mothers and the socioeconomic class and ethnicity spread was representative of the general population. The mean age of the children was 10 years and duration of diabetes 4.4 years. Poorer glycaemic control was associated with higher perceived child competence, together with lower perceived age of responsibility, lower perceived seriousness, and less frequent blood tests. Higher parental self-efficacy and higher perceived child competence predicted a higher level of normalisation, as did lower perceived seriousness, a lower perceived parental responsibility for management, and a less protective style of parenting. Conclusion: Parents' perceptions of their children's diabetes are significantly related to glycaemic control; however, those who appear more competent at managing diabetes may overestimate their child's capabilities, leading to poorer glycaemic control.

Alzheimer's disease: size class frequency distribution of senile plaques: do they indicate when a brain tissue was affected?

The size class frequency distribution of a sample of senile plaques (SP) was determined in a total of 20 brain regions from 5 elderly cases of Alzheimer's disease (AD). The purpose of the study was to determine whether a comparison of the frequency distributions could be used to determine the chronology of SP development in the AD brain. SP from 10 microns to a maximum diameter of 160 microns were present in the tissue and the size class frequency distributions were positively skewed. The frequency distributions varied between brain regions in: (1) the size class containing the mode, (2) the degree of positive skew, and (3) the ratio of large to small SP. In most patients the ratio of large to small SP was higher in the hippocampus or adjacent gyrus compared with temporal, parietal and frontal neocortex. If the diameter of a SP reflects its age in the tissue than the data suggest that SP formed earlier either in the hippocampus or adjacent gyrus compared with the other neocortical tissues. However, this conclusion rests on a number of assumptions including: (1) that SP diameter is directly related to age, (2) that SP development occurs at similar rates in different brain regions and (3) that, once formed, SP are not removed from the tissue by astrocytes.

Factors associated with degeneration of the thallus centre in foliose lichens

Degeneration of the older parts of foliose lichen thalli often lead to the formation of a space or 'window' in the centre of the colonies. The percentage of thalli of different size which exhibited 'windows' was studied in twenty saxicolous lichen populations in south Gwynedd, Wales. The proportion of thalli with 'windows' increased with thallus size. The size class at which 50% and 100% of thalli exhibited 'windows' varied between populations. Differences between populations were not correlated with distance from the sea, aspect, slope or porosity of the substrate or the total number of lichen species present. However, a higher percentage of smaller thalli had 'windows' on rock surfaces with a greater lichen cover. There were no significant differences in the levels of Ca, Mg, Cu or Zn in large (>4 cm) and small (<2 cm) Parmelia conspersa (Ehrh. ex Ach.) Ach. thalli or in the centres and marginal lobes of these thalli. The concentration of ribitol, arabitol and mannitol was significantly reduced in the centre of large thalli compared with the margin of large thalli and the centre of small thalli. However, carbohydrate levels were similar in the centre of large thalli and the margin of small thalli. The data suggest that loss of the thallus centre is a degenerative process related to thallus size. In the field, the formation of 'windows' may be related to the intensity of competition on a substrate. Central degeneration was not associated with a deficiency or an accumulation of Ca, Mg, Cu and Zn in the thallus centre. However, degeneration may be associated with a reduction in carbohydrates in the centre compared with the marginal lobes.

Vacuum spacetimes of embedding class two

Doubt is cast on the much quoted results of Yakupov that the torsion vector in embedding class two vacuum space-times is necessarily a gradient vector and that class 2 vacua of Petrov type III do not exist. The rst result is equivalent to the fact that the two second fundamental forms associated with the embedding necessarily commute and has been assumed in most later investigations of class 2 vacuum space-times. Yakupov stated the result without proof, but hinted that it followed purely algebraically from his identity: Rijkl Ckl = 0 where Cij is the commutator of the two second fundamental forms of the embedding.From Yakupov's identity, it is shown that the only class two vacua with non-zero commutator Cij must necessarily be of Petrov type III or N. Several examples are presented of non-commuting second fundamental forms that satisfy Yakupovs identity and the vacuum condition following from the Gauss equation; both Petrov type N and type III examples occur. Thus it appears unlikely that his results could follow purely algebraically. The results obtained so far do not constitute denite counter-examples to Yakupov's results as the non-commuting examples could turn out to be incompatible with the Codazzi and Ricci embedding equations. This question is currently being investigated.

The campaign to save Croxteth comprehensive: an ethnographic study of a protest movement

This thesis is based on ethnographic research carried out on a Liverpool protest movement which occurred between November, 1980 and July,1983. The protest movement was waged by residents of the working class community of Croxteth Liverpool who wished to retain their state secondary school, Croxteth Comprehensive. The Liverpool City Council voted in favour of closing Croxteth Comprehensive in January, 1981 because of its declining roles. Residents began theIr campaign as soon as they became aware of intentions to close the school at the end of the previous year. The campaIgn itself went through a number of different phases, distinguishable accordIng to the groups of people involved, the strategy and tactics they employed, the ways in which they justified their campaign, and the goals they pursued. In July of 1982 the organisation which led the protest, the Croxteth Community Action Committee, took illegal possession of the school buildings and ran a pilot summer school project. In September of 1982 they opened the school doors for all secondary pupils on the council estate and began running classes, with the help of volunteer teachers. The school was run successfully in this way for the entire 1982/83 school year. By the end of this period the school was officially reinstated by a new Labour Party majorIty on the city council. This thesis presents a comprehensive account of the entire campaign, from its beginning to end. The campaign is analysed in a number of ways: by situating the closure itself in the economic and political conditions of Liverpool in the 1980s, by examining the relation of Croxteth Comprehensive to its community, by describing the conditions in which different groups of people contributed to the campaign and the changes it went through in its use of tactics, and through a close examination of the activities which took place inside the school during its year of occupation. A number of levels of analysis are used in the study. To explain the closure and the early forms of resistance which developed to oppose it, the structural location of the local government of Liverpool in the late 1970s and early 1980s is described. To explain the relationship of the school to its community, the formation of a group of activists and their leaders, and the resources available to the protestors for pursuing their aims, a single-group model of social action is used. To analyse the establishment of social routines and schooling practices within the school during its occupation, action-theoretica1 models are drawn upon., The chapters of literature review and concept analysis with which this thesis begins link these different levels theoretIcalIy through a model of actIon and its conditions. The theoretical framework employed is reviewed in the last chapter. It is one which could be used to study any social movement, and has applications to other social phenomena as well. Lastly various issues within the sociology of education are examined in light of the events which took place in Croxteth Comprehensive, especially the theory of community education.

The use of context in the classification of urban aerial imagery

Urban regions present some of the most challenging areas for the remote sensing community. Many different types of land cover have similar spectral responses, making them difficult to distinguish from one another. Traditional per-pixel classification techniques suffer particularly badly because they only use these spectral properties to determine a class, and no other properties of the image, such as context. This project presents the results of the classification of a deeply urban area of Dudley, West Midlands, using 4 methods: Supervised Maximum Likelihood, SMAP, ECHO and Unsupervised Maximum Likelihood. An accuracy assessment method is then developed to allow a fair representation of each procedure and a direct comparison between them. Subsequently, a classification procedure is developed that makes use of the context in the image, though a per-polygon classification. The imagery is broken up into a series of polygons extracted from the Marr-Hildreth zero-crossing edge detector. These polygons are then refined using a region-growing algorithm, and then classified according to the mean class of the fine polygons. The imagery produced by this technique is shown to be of better quality and of a higher accuracy than that of other conventional methods. Further refinements are suggested and examined to improve the aesthetic appearance of the imagery. Finally a comparison with the results produced from a previous study of the James Bridge catchment, in Darleston, West Midlands, is made, showing that the Polygon classified ATM imagery performs significantly better than the Maximum Likelihood classified videography used in the initial study, despite the presence of geometric correction errors.

White working-class neighbourhoods:common themes and policy suggestions

What does it mean to be white and working class in modern Britain? The Joseph Rowntree Foundation’s studies of traditionally white estates in Bradford, London, Coventry and Birmingham are part of a growing body of research into ‘white identities’. This paper: • identifies common findings from JRF research into traditionally white estates, in the context of other similar work; • suggests how issues of white identity can be better understood and makes recommendations for policy and practice. Key points: • Profound economic and social change has increased isolation and fear in traditionally white estates. Residents often claim that things were better in the past. • ‘Estatism’ refers to specific social dynamics associated with council estates and prejudice towards residents based on where they live. This can result in lowered self-esteem and reluctance to participate in community campaigns. • People on traditionally white estates often feel they are not listened to by outside agencies. Consultations can raise hopes but ultimately reinforce disengagement. Initiatives to ensure equality have become associated with political correctness (‘PC’). • White working-class people feel they are bound by values of hard work, reciprocity and support. They are frustrated by the closure and lack of access to community facilities. The social class system simultaneously disadvantages the working class while giving advantage to other classes. • There is a strong desire for allocation of resources to be fair, with a widespread perception that minorities are given preference. Blaming incomers for decline is common, with the target of blame differing between sites. Participants did not want to be considered racist and felt that labelling ideas as racist prevents discussion. Similarly, the term ‘PC’ can also be used to shut down debate. • Recommendations include community-twinning, new ways of accessing local authorities, involvement from the private sector in disadvantaged areas and local panels to define and develop the ‘Big Society’. Initiatives aimed solely at white working-class people are unlikely to be successful.

Identification of the HLA-DM/HLA-DR interface

Human leukocyte antigen (HLA)-DM is a critical participant in antigen presentation that catalyzes the dissociation of the Class II-associated Invariant chain-derived Peptide (CLIP) from the major histocompatibility complex (MHC) Class II molecules. There is competition amongst peptides for access to an MHC Class II groove and it has been hypothesised that DM functions as a 'peptide editor' that catalyzes the replacement of one peptide for another within the groove. It is established that the DM catalyst interacts directly with the MHC Class II but the precise location of the interface is unknown. Here, we combine previously described mutational data with molecular docking and energy minimisation simulations to identify a putative interaction site of >4000A2 which agrees with known point mutational data for both the DR and DM molecule. The docked structure is validated by comparison with experimental data and previously determined properties of protein-protein interfaces. A possible dissociation mechanism is suggested by the presence of an acidic cluster near the N terminus of the bound peptide.

Feature LDA:a supervised topic model for automatic detection of web API documentations from the web

Web APIs have gained increasing popularity in recent Web service technology development owing to its simplicity of technology stack and the proliferation of mashups. However, efficiently discovering Web APIs and the relevant documentations on the Web is still a challenging task even with the best resources available on the Web. In this paper we cast the problem of detecting the Web API documentations as a text classification problem of classifying a given Web page as Web API associated or not. We propose a supervised generative topic model called feature latent Dirichlet allocation (feaLDA) which offers a generic probabilistic framework for automatic detection of Web APIs. feaLDA not only captures the correspondence between data and the associated class labels, but also provides a mechanism for incorporating side information such as labelled features automatically learned from data that can effectively help improving classification performance. Extensive experiments on our Web APIs documentation dataset shows that the feaLDA model outperforms three strong supervised baselines including naive Bayes, support vector machines, and the maximum entropy model, by over 3% in classification accuracy. In addition, feaLDA also gives superior performance when compared against other existing supervised topic models.

Development of areolae and growth of the peripheral prothallus in the crustose lichen Rhizocarpon geographicum:an image analysis study

Areolae of the crustose lichen Rhizocarpon geographicum (L.) DC., are present on the peripheral prothallus (marginal areolae) and also aggregate to form confluent masses in the centre of the thallus (central areolae). To determine the relationships between these areolae and whether growth of the peripheral prothallus is dependent on the marginal areolae, the density, morphology, and size frequency distributions of marginal areolae were measured in 23 thalli of R. geographicum in north Wales, UK using image analysis (Image J). Size and morphology of central areolae were also studied across the thallus. Marginal areolae were small, punctate, and occurred in clusters scattered over the peripheral prothallus while central areolae were larger and had a lobed structure. The size-class frequency distributions of the marginal and central areolae were fitted by power-law and log-normal models respectively. In 16 out of 23 thalli, central areolae close to the outer edge were larger and had a more complex lobed morphology than those towards the thallus centre. Neither mean width nor radial growth rate (RaGR) of the peripheral prothallus were correlated with density, diameter, or area fraction of marginal areolae. The data suggest central areolae may develop from marginal areolae as follows: (1) marginal areolae develop in clusters at the periphery and fuse to form central areolae, (2) central areolae grow exponentially, and (3) crowding of central areolae results in constriction and fragmentation. In addition, growth of the peripheral prothallus may be unrelated to the marginal areolae. © 2013 Springer Science+Business Media Dordrecht.