New horizons in mouse immunoinformatics:reliable in silico prediction of mouse class I histocompatibility major complex peptide binding affinity

Quantitative structure–activity relationship (QSAR) analysis is a main cornerstone of modern informatic disciplines. Predictive computational models, based on QSAR technology, of peptide-major histocompatibility complex (MHC) binding affinity have now become a vital component of modern day computational immunovaccinology. Historically, such approaches have been built around semi-qualitative, classification methods, but these are now giving way to quantitative regression methods. The additive method, an established immunoinformatics technique for the quantitative prediction of peptide–protein affinity, was used here to identify the sequence dependence of peptide binding specificity for three mouse class I MHC alleles: H2–Db, H2–Kb and H2–Kk. As we show, in terms of reliability the resulting models represent a significant advance on existing methods. They can be used for the accurate prediction of T-cell epitopes and are freely available online (http://www.jenner.ac.uk/MHCPred).

Horizons régionaux et variations océaniennes des territoires français

« L’identité régionale […] repose sur une réalité concrète : la mer est aussi réelle que vous et moi […]. Je ne fais que constater qu’elle forge le caractère de cette planète, qu’elle est une source majeure de notre subsistance et que nous l’avons tous en partage, où que nous soyons en Océanie. Mais au-delà des épreuves quotidiennes, la mer nous lie les uns aux autres. Elle est source de sagesse infinie. La mer est notre métaphore la plus puissante. L’océan est en nous. » (Hau’Ofa, 2015 [1997] : 55-56). Souvent présentés de manière séparée, les territoires français dans le Pacifique Sud, objets de ce dossier, possèdent cependant des horizons régionaux intéressants qui mettent en exergue la variété des écosystèmes politiques de l’espace océanien1. Les facettes multidimensionnelles des évolutions humaines montrent une « mer d’îles » océaniennes en mouvement, selon l’intellectuel tongien Epeli Hau’Ofa (2008 [1993]). Sa pensée alimente la formation d’une identité régionale océanienne, à p... « Regional identity […] has been constructed on a foundation of concrete reality. That the sea is as real as you and I […], that it shapes the character of this planet, that it is a major source of our sustenance, that it is something that we all share in common wherever we are in Oceania – all of these are statements of fact. Yet beyond that level of everyday experience, the sea is our pathway to each other and to everyone else, the sea is our endless saga, the sea is our most powerful metaphor, the ocean is in us. » (Hau’Ofa, 2015 [1997]: 55-56). Often conceived of as separate entities, French overseas territories in the South Pacific, as the subject of this special issue, nevertheless possess interesting regional horizons, which highlight the variety of political ecosystems of Oceania. The multidimensional facets of human evolution show an Oceanian “Sea of Islands” in constant movement, according to the Tongan intellectual Epeli Hau’Ofa (2008 [1993]). His philosophy contributes to...

Model specification and forecasting foreign exchange rates with vector autoregressions

This study examines the forecasting accuracy of alternative vector autoregressive models each in a seven-variable system that comprises in turn of daily, weekly and monthly foreign exchange (FX) spot rates. The vector autoregressions (VARs) are in non-stationary, stationary and error-correction forms and are estimated using OLS. The imposition of Bayesian priors in the OLS estimations also allowed us to obtain another set of results. We find that there is some tendency for the Bayesian estimation method to generate superior forecast measures relatively to the OLS method. This result holds whether or not the data sets contain outliers. Also, the best forecasts under the non-stationary specification outperformed those of the stationary and error-correction specifications, particularly at long forecast horizons, while the best forecasts under the stationary and error-correction specifications are generally similar. The findings for the OLS forecasts are consistent with recent simulation results. The predictive ability of the VARs is very weak.

Introduction

Professional Encounters in TESOL investigates the developing discourses of English Language teachers in a variety of international contexts. By analysing how professional development takes place through participation in professional discourse, the chapters shed light on what teachers do and why they do it. The book is organised in four sections, reflecting the stages in an English language teacher's career: 'Starting Out' focuses on initial teacher training, 'Becoming Experienced' looks inside their classroom, 'New Horizons' shifts the perspective to the professional development of experienced teachers, and 'Passing on Knowledge' investigates the discourses of experienced teachers as they contribute to the professional development of their peers. Each section is followed by reflections on the chapters written by a teacher from an international context at the particular stage in their professional development reflected in the section. The book should have particular appeal to all those working in the area of teacher development and will also be of interest to practising teachers.

The sedimentology and diagenesis of the Pendleside limestone group in the Craven Basin of Northern England. Available in 2 volumes.

This thesis describes the stratigraphy, sedimentology and diagenesis of the Pendleside Limestone (Asbian age), a sequence of limestones, shales and dolostones in the Clitheroe area of N. W. England. Field study of 19 measured sections indicates that it was deposited in a rhythmically subsiding basin (Craven Basin) because of movements on the Mid-Craven Fault which was active in Dinantian times. The sequence is up to 190m thick and consists mostly of distal turbidite deposits which have been reworked at horizons when sediment accumulation built up to the wave base. The original depositional fabric and mineralogy of the Pendleside Limestone Group has been extensively modified by diagenetic processes including cementation, authi­genesis, dolomitization and silicification. These processes have been studied using a wide variety of laboratory techniques. The carbonate cements of the PendIeside Limestone consist predominantly of ferroan calcite and non-ferroan calcite with microdolomite incIusions. The former is probably a stable replacement of original-high-magnesian calcite. Cementation was accompanied by the formation of authigenic albite and quartz. Much of the upper part of the Pendleside Limestone has been extensively dolomitized and chertified. Several distinct zones of dolomitization are found which increase in thickness and intensity towards the top of the Pendleside Limestone Group. The dolostone horizons correspond to coarser-grained lithologies deposited during periods of shallow water sedimentation. The composition of the dolomites changes from ferroan dolomite in the lower part of the Group to non-ferroan dolomite in the upper part. The low strontium and sodium content of the dolostones in association with the other evidence suggests that the dolomitization was brought about in an open system by the mixing of marine and fresh water in phreatic lens which were established at periodic intervals. The dolomitization was closely associated with chertification although this was initiated by the dissolution of siliceous spicules which provided the necessary source of silica.

The relationship of mineralization to petrology at Parys Mountain, Anglesey

The Lower Palaeozoic succession at Parys Mountain overlies a Precambrian basement (the Iona Series). This succession consists of Ordovician slates, overlain by, and in part interbedded with, Ordovician dacitic and rhyolitic volcanics, which in turn are unconformably overlain by Silurian slates. Both basement and Palaeozoic rocks have been deformed during Caledonian and Variscan orogenies. The resultant structure of Parys Mountain is interpreted as an east-north-easterly trending, single syncline overturned to the north. Many primary extrusive characters are retained by the volcanic rocks, despite the high degree of deformation. The lithologies and textures allow subdivision and interpretation of these rocks as dacite, lithic tuff, siliceous sinter, rhyolitic tuff, rhyolitic ignimbrite, rhyolitic tuff-lava, and rhyolitic lava. The results of 61 bulk chemical analyses are interpreted to show that the volcanism was of the orogenic calc-alkaline type from a continental margin/island arc environment. The magmas probably result from either partial melting of the crustal part of the oceanic lithosphere on a Benioff zone, or partial melting of the mantle, above a Benioff zone, under high load pressures and high water pressures. The mineral deposits are largely confined within the volcanic succession though some occur in the Ordovician and Silurian slates near to their contacts with the volcanics. The majority of the deposits form conformable lenses and tabular bodies, with subordinate deposits as veins and stockworks. The ore mineral assemblages are of chalcopyrite, galena, sphalerite, and pyrite. The general paragenetic sequence (73 sections) is pyrite--chalcopyrite--galena-sphalerite. The main mineralization episode is interpreted to be syngenetic, genetically related to the volcanism. The veins and stockworks probably result from Caledonian and Variscan remobilization of the primary mineralization. Trace element analyses (Cu, Zn, Pb, Ni, Co, Cd, Cr, Hg, Ba, Sr), on 350 specimens, detected anomalous concentrations of these elements around the mineralized zones, though some occur where no mineralization was found. The analyses also indicate a close relationship between the mineralization and the volcanic horizons, especially the siliceous sinter.

The palynology of the Plenmeller Coalfield and adjacent areas in Northern England

The samples collected in the present investigation from Featherstone, Plenmeller and adjacent areas in the North of England, yielded diverse, well preserved miospore assemblages with marked vertical variation, which compare fairly closely with those previously described from strata of the same age elsewhere. Six major Assemblages are recognised from coal and shale samples collected within Namurian and Westphalian A and B strata which have not previously been dated by miospore evidence. Oetailed comparisons are made with miospore assemblages previously described by several authors from similar stratigraphical horizons in Scotland, North England and. the Central Province. Formal taxonomic description is presented for 206 species belonging to 71 genera.tions 22 new types are described and one new combination is suggested.

Textural and microstructural studies of zinc sulfide and associated phases in certain base metal deposits

A textural and microstructural study of a variety of zinc sulfide-containing ores has been undertaken, and the possible depositional and deformational controls of textural and microstructural development considered. Samples for the study were taken from both deformed and undeformed zinc ores of the Central U.S. Appalachians, and deformed zinc ores of the English Pennines. A variety of mineralogical techniques were employed, including transmitted and reflected light microscopy of etched and unetched material, transmission electron microscopy and electron microprobe analysis. For the Pennine zinc sulfides, spectroscopic, x-ray diffraction and fluid inclusion studies were also undertaken. Optical and electron optical examination of the Appalachian material confirmed the suitability of zinc sulfide for detailed study with such techniques. Growth and deformation-related microstructures could be distinguished from specimen-preparation induced artifacts. A deformationally-mduced lamelliform optical anisotropy is seen to be developed in areas hosting a dense planar microstructure of {111} twin- and slip-planes. The Pennine zinc sulfide texturally records a changing depositional environment. Thus, for example, delicately growth- zoned crystals are truncated and cross-cut by solution disconformities. Fluid inclusion studies indicate a highly saline (20-25 wt. % equiv. NaCl), low temperature (100-150°C.) fluid. Texturally, two varieties of zinc sulfide can be recognised; a widely developed, iron- banded variety, and a paragenetically early variety, banded due to horizons rich in crystal defects and microscopic inclusions. The zinc sulfide takes the form of a disordered 3C-polytype, with much of the disorder being deformational in origin. Twin- and slip-plane fabrics are developed . A deformation-related optical anisotropy is seen to overprint growth-related anisotropy, along with cuprian alteration of certain {111} deformation planes.

Genetic studies of Cu-Pb-Zn mineralisation in Triassic red beds of Western Europe

Continental red bed sequences are host, on a worldwide scale, to a characteristic style of mineralisation which is dominated by copper, lead, zinc, uranium and vanadium. This study examines the features of sediment-hosted ore deposits in the Permo-Triassic basins of Western Europe, with particular reference to the Cu-Pb-Zn-Ba mineralisation in the Cheshire Basin, northwest England, the Pb-Ba-F deposits of the Inner Moray Firth Basin, northeast Scotland, and the Pb-rich deposits of the Eifel and Oberpfalz regions, West Germany. The deposits occur primarily but not exclusively in fluvial and aeolian sandstones on the margins of deep, avolcanic sedimentary basins containing red beds, evaporites and occasionally hydrocarbons. The host sediments range in age from Permian to Rhaetian and often contain (or can be inferred to have originally contained) organic matter. Textural studies have shown that early diagenetic quartz overgrowths precede the main episode of sulphide deposition. Fluid inclusion and sulphur isotope data have significantly constrained the genetic hypotheses for the mineralisation and a model involving the expulsion of diagenetic fluids and basinal brines up the faulted margins of sedimentary basins is favoured. Consideration of the development of these sedimentary basins suggests that ore emplacement occurred during the tectonic stage of basin evolution or during basin inversion in the Tertiary. ð34S values for barite in the Cheshire Basin range from 13.8% to 19.3% and support the theory that the Upper Triassic evaporites were the principal sulphur source for the mineralisation and provided the means by which mineralising fluids became saline. In contrast, δ34S values for barite in the Inner Moray Firth Basin (mean δ34S = + 29%) are not consistent with simple derivation of sulphur from the evaporite horizons in the basin and it is likely that sulphur-rich Jurassic shales supplied the sulphur for the mineralisation at Elgin. Possible sources of sulphur for the mineralisation in West Germany include hydrothermal vein sulphides in the underlying Devonian sediments and evaporites in the overlying Muschelkalk. Textural studies of the deeply buried sandstones in the Cheshire Basin reveal widespread dissolution and replacement of detrital phases and support the theory that red bed diagenetic processes are responsible for the release of metals into pore fluids. The ore solutions are envisaged as being warm (60-150%C), saline (9-22 wt % equiv NaCl) fluids in which metals were transported as chloride complexes. The distribution of δ34S values for sulphides in the Cheshire Basin (-1.8% to + 16%), the Moray Firth Basin (-4.8% to + 27%) and the German Permo-Triassic Basins (-22.2% to -12.2%) preclude a magmatic source for the sulphides and support the contention that sulphide precipitation is thought to result principally from sulphate reduction processes, although a decrease in temperature of the ore fluid or reaction with carbonates may also be important. Methane is invoked as the principal reducing agent in the Cheshire Basin, whilst terrestrial organic debris and bacterial reduction processes are thought to have played a major part in the genesis of the German ore deposits.

The neuropathology of the occipital cortex and its significance in the visual problems of patients with variant Creutzfeldt-Jakob disease (vCJD)

The occipital lobe is one of the cortical areas most affected by the pathology of variant Creutzfeldt-Jakob disease (vCJD). To understand the visual problems of vCJD patients, neuropathological changes were studied in striate (B17, V1) and extrastriate (B18, V2) regions of the occipital cortex in eleven cases of vCJD. No differences in the density of vacuoles or surviving neurons were observed in B17 and B18 but densities of glial cell nuclei and deposits of the protease resistant form of prion protein (PrPsc) were greater in B18. The density of PrPsc deposits in B17 was positively correlated with their density in B18. The density of the diffuse PrPsc deposits in B17 was negatively correlated with the density of the surviving neurons in B18. In B17 and B18, the vacuoles either exhibited density peaks in laminae II/III and V/VI or were more uniformly distributed across the laminae. Diffuse PrPsc deposits were most frequent in laminae II/III and florid PrPsc deposits more generally distributed. In B18, the surviving neurons were more consistently bimodally distributed and the glial cell nuclei most abundant in laminae V/VI compared with B17. Hence, both striate and extrastriate areas of the occipital cortex are affected by the pathology of vCJD, the pathological changes being most severe in B18. Neuronal degeneration in B18 may be associated with the development of diffuse PrPsc deposits in B17. These data suggest that the short cortico-cortical connections between B17 and B18 and the pathways to subcortical visual areas are compromised in vCJD. Pathological changes in striate and extrastriate regions of the occipital cortex may contribute to several of the visual problems identified in patients with vCJD including oculomotor and visuo-spatial function.

Density and spatial pattern of the neuropathological changes in the cerebellum in the prion disease variant Creutzfeldt-Jakob disease (vCJD)

The objective of this chapter is to quantify the neuropathology of the cerebellar cortex in cases of the prion disease variant Creutzfeldt-Jakob disease (vCJD). Hence, sequential sections of the cerebellum of 15 cases of vCJD were stained with H/E, or immunolabelled with a monoclonal antibody 12F10 against prion protein (PrP) and studied using quantitative techniques and spatial pattern analysis. A significant loss of Purkinje cells was evident in all cases. Densities of the vacuolation and the protease resistant form of prion protein (PrPSc) in the form of diffuse and florid plaques were greater in the granule cell layer (GL) than the molecular layer (ML). In the ML, vacuoles and PrPSc plaques, occurred in clusters which were regularly distributed along the folia, larger clusters of vacuoles and diffuse plaques being present in the GL. There was a negative spatial correlation between the vacuoles and the surviving Purkinje cells in the ML and a positive spatial correlation between the clusters of vacuoles and the diffuse PrPSc plaques in the ML and GL in five and six cases respectively. A canonical variate analysis (CVA) suggested a negative correlation between the densities of the vacuolation in the GL and the diffuse PrPSc plaques in the ML. The data suggest: 1) all laminae of the cerebellar cortex were affected by the pathology of vCJD, the GL more severely than the ML, 2) the pathology was topographically distributed especially in the Purkinje cell layer and GL, 3) pathological spread may occur in relation to a loop of anatomical projections connecting the cerebellum, thalamus, cerebral cortex, and pons, and 4) there are differences in the pathology of the cerebellum in vCJD compared with the M/M1 subtype of sporadic CJD (sCJD).

Temporal lobe pathology in neurodegenerative disease:a comparative study of eight disorders with special reference to the hippocampus

The temporal lobe is a major site of pathology in a number of neurodegenerative diseases. In this chapter, the densities of the characteristic pathological lesions in various regions of the temporal lobe were compared in eight neurodegenerative disorders, viz., Alzheimer’s disease (AD), Down’s syndrome (DS), dementia with Lewy bodies (DLB), Pick’s disease (PiD), corticobasal degeneration (CBD), progressive supranuclear palsy (PSP), sporadic Creutzfeldt-Jakob disease (sCJD), and neuronal intermediate filament inclusion disease (NIFID). Temporal lobe pathology was observed in all of these disorders most notably in AD, DS, PiD, sCJD, and NIFID. The regions of the temporal lobe affected by the pathology, however, varied between disorders. In AD and DS, the greatest densities of ?-amyloid (A?) deposits were recorded in cortical regions adjacent to the hippocampus (HC), DS exhibiting greater densities of A? deposits than AD. Similarly, in sCJD, greatest densities of prion protein (PrPsc) deposits were recorded in cortical areas of the temporal lobe. In AD and PiD, significant densities of neurofibrillary tangles (NFT) and Pick bodies (PB) respectively were present in sector CA1 of the HC while in CBD, the greatest densities of tau-immunoreactive neuronal cytoplasmic inclusions (NCI) were present in the parahippocampal gyrus (PHG). Particularly high densities of PB were present in the DG in PiD, whereas NFT in AD and Lewy bodies (LB) in DLB were usually absent in this region. These data confirm that the temporal lobe is an important site of pathology in the disorders studied regardless of their molecular ‘signature’. However, disorders differ in the extent to which the pathology spreads to affect the HC which may account for some of the observed differences in clinical dementia.