Subregion Products Research Articles

Machine Learning Model Stability for Sub-Regional Classification of Barossa Valley Shiraz Wine Using A-TEEM Spectroscopy.

With a view to maintaining the reputation of wine-producing regions among consumers, minimising economic losses caused by wine fraud, and achieving the purpose of data-driven terroir classification, the use of an absorbance-transmission and fluorescence excitation-emission matrix (A-TEEM) technique has shown great potential based on the molecular fingerprinting of a sample. The effects of changes in wine composition due to ageing and the stability of A-TEEM models over time had not been addressed, however, and the classification of wine blends required investigation. Thus, A-TEEM data were combined with an extreme gradient boosting discriminant analysis (XGBDA) algorithm to build classification models based on a range of Shiraz research wines (n = 217) from five Barossa Valley sub-regions over four vintages that had aged in bottle for several years. This spectral fingerprinting and machine learning approach revealed a 100% class prediction accuracy based on cross-validation (CV) model results for vintage year and 98.8% for unknown sample prediction accuracy when splitting the wine samples into training and test sets to obtain the classification models. The modelling and prediction of sub-regional production area showed a class CV prediction accuracy of 99.5% and an unknown sample prediction accuracy of 93.8% when modelling with the split dataset. Inputting a sub-set of the current A-TEEM data into the models generated previously for these Barossa sub-region wines yielded a 100% accurate prediction of vintage year for 2018-2020 wines, 92% accuracy for sub-region for 2018 wines, and 91% accuracy for sub-region using 2021 wine spectral data that were not included in the original modelling. Satisfactory results were also obtained from the modelling and prediction of blended samples for the vintages and sub-regions, which is of significance when considering the practice of wine blending.

Ecosystem spatial structure revealed by integrated survey data

Integrated marine survey series such as PELGAS provide comprehensive geo-referenced data over large sea areas in major ecosystem components with defined biological resolution and spatio-temporal sampling scale. These data enable to develop product at different levels of biological organization and spatial scale that are useful for ecosystem integrated assessments. Using the PELGAS integrated data series, we applied a generic procedure made of several steps to identify and map ecologically coherent ecosystem spatial units in the Bay of Biscay. First, the data were interpolated on a common spatial grid and organized as a time series of matrices containing at each time the variables as columns and the grid cell values as rows. The multi-table analysis method known as Multi-Factor Analysis (MFA) was then applied on the series of matrices, thus separating in the analysis the spatial from the temporal variability. Grouping the spatial grid cells based on their relative positions in the MFA space resulted in mapping ecosystem spatial entities based on common spatial patterns across ecosystem components. The result of the analysis is a map of ecosystem seascapes that are consistent over the years together with a map of their inter-annual variability. The ecosystem sub-units were in agreement with sub-regional production systems in the Bay of Biscay. This study thus highlights the possibility to characterize and monitor ecosystem spatial structure and develop indicators thereof for their use in ecosystem assessments. Also, it highlights the importance of identifying spatial limits of production systems for ecosystem description, assessment and management.

The use of electron probe microanalysis and laser ablation-inductively coupled plasma-mass spectrometry for the investigation of 8th–14th century plant ash glasses from the Middle East

This is the first broad survey using major, minor and trace element analyses of 8th–15th AD plant ash glass from the Middle East across a 2000mile area stretching from Egypt to northern Iran. This was part of the ancient Silk Road that extended from the Middle East, through central Asia to China. Up to now, some compositional distinctions have been identified for such glasses mainly using major and minor element oxides and radiogenic isotopes. Our new trace element characterisation is for such glasses, mainly found in selected cosmopolitan hubs, including one where there is archaeological evidence for primary glass making. It provides not only far clearer provenance definitions for regional centres of production, in the Levant, northern Syria and in Iraq and Iran, but also for sub-regional zones of production. This fingerprinting is provided by trace elements associated with the primary glass making raw materials used: ashed halophytic plants and sands. Even more surprising is a correlation between some of the sub-regional production hubs and the types of glass vessels with diagnostic decoration apparently manufactured in or near the cosmopolitan hubs where the glass was found such as colourless cut and engraved vessels (in Iraq and Iran) and trail-decorated vessels (in the Levant). This therefore provides evidence for centres of specialisation. Our trace element characterisation provides a new way of defining the Silk Road by characterising the glass that was traded or exchanged along it. Taken together this data provides a new decentralised model for ancient glass production.

Enhancement of the antigen-presenting function of monocytes by cholesterol: possible relevance to inflammatory mechanisms in extrinsic allergic alveolitis and atherosclerosis.

Extrinsic allergic alveolitis (EAA) (synonym: hypersensitivity pneumonitis) is a hypersensitivity lung disease characterized by lymphocytic infiltrates in the pulmonary interstitial tissues. We have previously reported that the numbers of lymphocytes in bronchoalveolar lavage (BAL) samples in this disease correlate with levels of cholesterol and neutral lipid-laden 'foamy' macrophages. We have also reported that the macrophages express an increased density of MHC class II antigens (in particular HLA-DQ) which are known to be essential for antigen recognition by T lymphocytes. The aim of the present study was to explore whether cholesterol is capable of enhancing the antigen-presenting function of mononuclear phagocytes by modulating the expression of HLA-D region products. Incubation of purified monocytes from healthy volunteers with cholesterol in serum-free medium induced a significant increase in both the percentages of monocytes expressing HLA-DQ (P less than 0.02) and in the intensity of expression of the three HLA-D sub-region products, HLA-DQ, -DP and -DR (P less than 0.02, less than 0.01, less than 0.05, respectively). The cholesterol pre-incubated monocytes also exhibited enhanced antigen-presenting function (P less than 0.05), compared with controls pre-incubated without cholesterol. These findings indicate that increases in cholesterol in the extracellular milieu may augment antigen presentation by modulating the expression of HLA-D region products on antigen-presenting cells. Apart from EAA, this observation may also have relevance to inflammatory mechanisms in atherosclerosis, where 'foamy' macrophages also occur in association with hypercholesterolaemia.

Attracting and Retaining Investments in Uncertain Times: Singapore in South-east Asia

This paper takes a political economy approach in evaluating the state's role in investment promotion. Using the Asian financial crisis as an opportunity to study regulatory mechanisms, the paper examines both state-society relations as well as relations between Singapore and its neighbours, Indonesia and Malaysia. The difficult policies which Singapore enacted during the crisis-namely, a wage-cut as well as the drive to recruit foreign skilled labour in the midst of a depressed economy—cannot be understood except in terms of an institutional context involving agencies, interest-groups and segments of society and the state's continuing ideological work and, specifically, within an embedded autonomy position where the state was able to fend off lobbying efforts while at the same time using its position with the unions to push for wage-cuts and skilled foreign labour. Such embedding or nestedness was also apparent in Singapore's regional relations. The incorporation of the Riau islands in Indonesia in sub-regional production networks managed by Singapore led to consistent stances taken by Singapore and Indonesian regional authorities to protect investments, in the midst of inconsistent signals between the national governments of the two countries.

CHINA-ASEAN EXPORT RIVALRY IN THE US MARKET

In this paper, the degree of export rivalry or competition among China and ASEAN-4 (Malaysia, Singapore, Thailand and Indonesia) is examined using the shift-share methodology. Our results show that overall China was more competitive than ASEAN-4 in its exports to the US. China was more competitive in manufacturing exports whereas ASEAN-4 fared better in agricultural or primary exports. China's advantages in export growth and industry structure vis-à-vis ASEAN-4 were less pronounced before, than after, the onset of the Asian financial crisis, implying that the crisis has indeed affected ASEAN-4 more than China. It has been contended that China's advantage in manufacturing exports could have been accentuated by Hong Kong' production in South China, which has been counted in US trade statistics as China's exports to the US. After disentangling Hong Kong's production in China, the degree of rivalry between China and ASEAN-4 is significantly reduced. Our analysis points to the role of sub-regional production synergy in boosting a country''s export competitiveness.

Immunoelectron microscopic localization of MHC class 1 and 2 antigens on bile duct epithelial cells in patients with primary biliary cirrhosis.

We studied the distribution of class 1 and class 2 major histocompatibility complex (MHC) antigens on bile duct epithelial cells in liver from patients with primary biliary cirrhosis (PBC) by an immunohistochemical method using monoclonal antibodies to HLA-ABC products and HLA-D subregion products (HLA-DR, -DP, -DQ). By light microscopy, the expression of MHC class 1 antigens (HLA-ABC antigens) was enhanced in PBC compared with controls. While negligible staining of MHC class 2 antigens was detected on the bile duct in controls, de novo expression of MHC class 2 antigens, as well as the coexpression of HLA-DR, HLA-DQ, and HLA-DP antigens on the bile duct epithelial cells, was observed in PBC. By electron microscopy, HLA-ABC and HLA-DR antigens were present preferentially along the basolateral domain of the cell surface of the bile duct epithelial cells and on the membrane of the endoplasmic reticulum in the cytoplasm, suggesting that these MHC antigens are synthesized by the bile duct epithelial cells in PBC. The distribution of these MHC antigens on the basolateral surface of the bile duct epithelial cells, where they are easily accessible to immunocytes, supports the idea that MHC-restricted cytotoxic T lymphocytes are involved in the bile duct injury in PBC.

Relation between T cell number and epithelial HLA class II expression quantified by image analysis in normal and inflamed human gastric mucosa.

Epithelial expression of HLA class II determinants and the number of lamina propria and intraepithelial T cells were quantified in gastric body mucosa by means of paired immunofluorescence staining which was subjected to computerised image analysis. In normal mucosa, epithelial HLA-DR expression was virtually absent. A significantly increased expression was seen in simple chronic gastritis, most extensively in the isthmus zone, where a positive reaction was seen in 34% of the epithelial area when the gastritis was of low degree and in 85% when it was of moderate severity. The most extensive HLA-DR expression was found in moderate 'stump gastritis' 28 to 32 years after Billroth II resections. In these patients the epithelial area in the foveolar and isthmus zones showed 83% and 92% positive responses, respectively. The HLA subregion products were expressed in a differential manner (DR greater than DP greater than DQ). The number of both intraepithelial and lamina propria T cells increased significantly with increasing severity of gastritis, and the fraction of putative memory T cells was also raised. Correlation analyses showed a positive relation between the epithelial expression of HLA-DR and the intraepithelial as well as the lamina propria density of T cell. These results suggest a biological link between T cells, aberrant HLA-DR expression, and gastritis, although the pathogenic importance of this relation is unknown. Enhanced epithelial presentation of autoantigens or luminal antigens, or both leading to increased activation of T cells is one possible explanation.

Immunopathology of the placenta in pemphigoid gestationis and linear IgA disease.

We have investigated the immunopathology of the placenta in bullous diseases by studying the deposition of immune complexes and expression of MHC class II subregion products by immunohistological methods. Placentae from seven patients with pemphigoid gestationis (PG) and two patients with linear IgA disease were studied. In PG immune complexes containing IgGI and C3 were identified in six cases. In linear IgA disease IgAI containing immune complexes were found in both cases. Placentae from patients with PG showed aberrant expression of MHC Class II products. This was not seen in the placentae from patients with linear IgA disease. In PG there was incoordinate expression of the subregion products, DP and DR being more extensively and consistently expressed than DQ. These results and previous immunogenetic studies suggest that PG may be unique among organ specific autoimmune disease, the autoantibodies forming during an allogenic response rather than target cells behaving as antigen presenting cells.

Ｂ型慢性肝炎における肝組織中ＭＨＣ Ｃｌａｓｓ ＩＩ Ｓｕｂｒｅｇｉｏｎ Ｐｒｏｄｕｃｔｓの表出について

Ｂ型慢性肝炎における肝組織中ＭＨＣ Ｃｌａｓｓ ＩＩ Ｓｕｂｒｅｇｉｏｎ Ｐｒｏｄｕｃｔｓの表出について

Differential expression of epithelial MHC class II determinants (HLA-DR, -DP, and -DQ) and increased class I expression in inflamed salivary glands.

Sjogren’s syndrome (SS) affects salivary and lacrimal glands, causing xerostomia and keratoconjunivitis. An increased number of infiltrating leukocytes are present and the glandular tissue is gradually destroyed. Increased epithelial HLA-DR expression in salivary glands from SS patients has been reported (1,2,3), but the other MHC class II subregion products(HLA-DP and -DQ) and MHC class I determinants have not been studied.

Abnormal expression of class II MHC antigens in placentae from patients with pemphigoid gestationis: Analysis of class II MHC subregion product expression

Abnormal expression of class lI MHC antigens was consistently observed in an immunohistological study on placentae from patients with pemphigoid gestationis. The area affected in all the placentae was the chorionic villi adjacent to the maternal decidua. The villous stroma, and in some cases the chorionic fetal endothelium, had abnormal expression of class II MHC antigens. Monoclonal antibodies specific for the class II MHC subregion products (DR, DP and DQ) were used to analyse the class II MHC antigen expression. Differential expression of the class lI MHC subregion products was observed on the villous stroma and chorionic fetal endothelium; DR and DP were always expressed but DQ in some cases was heterogeneous. This abnormal expression of class II MHC antigens may reflect an immunological attack on the placenta in pemphigoid gestationis.

Jejunal epithelium of patients with coeliac disease shows enhanced expression of MHC class II subregion products.

We have previously shown that HLA class II molecules are expressed by small intestinal epithelial cells, both in control subjects with a normal mucosa (1) and in coeliac disease (CD) patients with total villous atrophy (2). CD is HLA-associated, and particularly related to DR3, DR7 (3) and DQ2 (A,5). It develops in genetically susceptible individuals because of gluten ingestion. Antigens of gluten may be presented by enterocytes to intraepithelial T cells as an initial step in the pathogenesis of CD. Class II-positive rat enterocytes have in fact been reported to perform antigen presentation (6). In this study we used a panel of monoclonal antibodies to better define the epithelial expression of class II subregion products in CD.

Class II MHC Subregion Products Are Differentially Expressed by Keratinocytes in Cutaneous Diseases

Class II MHC Subregion Products Are Differentially Expressed by Keratinocytes in Cutaneous Diseases

Expression of major histocompatibility complex class II subregion products by jejunal epithelium in patients with coeliac disease.

The MHC class II subregion products (HLA-DR), HLA-DP, and HLA-DQ) were located by immunofluorescence in serial sections of ethanol-fixed, paraffin-embedded jejunal mucosa from control subjects and patients with coeliac disease (CD). DR staining was seen in a granular luminal distribution and basolaterally on surface epithelial cells in both untreated and treated CD patients and in controls. In untreated CD the crypt epithelium was positive for DR almost to the bottom of the glands. This contrasted with virtually absent glandular DR staining in controls and weak staining including only the upper part of the crypts in 5 out of 11 treated patients. HLA-DP was present apically in the surface epithelium in all untreated patients, in 5 out of 11 treated patients, and in 4 out of 11 controls. HLA-DQ appeared only in three untreated patients and was restricted to patches of surface epithelium. The number of intraepithelial T lymphocytes per millimetre of surface epithelium was significantly higher in untreated than in treated CD patients or controls; it was also significantly higher in specimens with epithelial DP expression than in those without. This suggested that intraepithelial lymphocytes modulate epithelial class II expression.

Monoclonal antibodies to sheep MHC class II molecules recognize all HLA-D or subsets of HLA-D region products

Six murine monoclonal antibodies raised against sheep MHC class II molecules were analyzed for reactivity with HLA-D subregion products. All the antibodies with human peripheral blood lymphocytes, monocytes, and B-lymphoblastoid cell lines homozygous for various HLA-DR specificities, suggesting that the antibodies recognized nonpolymorphic determinants on HLA class II molecules. SDS-PAGE and two-dimensional NEPHGE/SDS-PAGE analyses of molecules immunoprecipitated from 35S-methionine-labeled, DR-homozygous B-lymphoblastoid cell lines showed that the monoclonal antibodies precipitated typical class II molecules (M r 32–34K and 25–29K). From comparison with antibodies of known HLA-D subregion specificity, two of the sheep antibodies appeared to react with the products of single HLA-D subregions, while another showed balanced reactivity with all HLA-D molecules. Antibody SBU.II 27–38 reacted exclusively with HLA-DQ molecules, antibody SBU.II 28-1 with HLA-DP molecules, and antibody SBU.II 49-1 with HLA-DR, -DQ, and -DP molecules. However, analysis of immunoprecipitates from surface-iodinated WT-49 cells (DR3 homozygous) using SBU.II 28-1 and the DP-specific monoclonal antibody B7/21, suggested that the two antibodies immunoprecipitated different α polypeptides. The two antibodies SBU.II 38-27 and 28-1 appear to be at least as specific as existing reagents, if not more so. As such, they are of value in their potential contribution to our understanding of the molecular characteristics and ultimately the functions of the HLA-DQ and -DP subregion products, as well as the identification/characterization of HLA-D equivalents in other species.

HLA-DP, DQ and DR gene expression in Graves' disease and normal thyroid epithelium.

HLA class II antigen expression by human thyroid epithelium may influence the pathogenesis of autoimmune thyroid disease. HLA-DP, DQ and DR alpha chain-specific RNA probes and monoclonal antibodies specific for the three HLA-D subregion products were used to analyze class II antigen expression in thyroid epithelial cells from normal thyroid tissue and thyroid tissue obtained from patients with Graves' autoimmune thyroid disease. Class II alpha chain RNA transcripts, as well as immunoreactive protein representing all three HLA class II antigens, were detected in Graves' thyroid tissue, and the levels of class II antigen expression appeared to correlate with the degree of lymphocytic infiltration within the gland. Thyroid epithelial cells from normal thyroid glands contained low or absent levels of HLA class II alpha chain mRNA and contained no detectable immunoreactive HLA class II antigen. Thyroid cell monolayer cultures prepared from both Graves' disease and normal thyroid glands exhibited coordinate induction by lectin or human recombinant gamma interferon of HLA-DP, DQ and DR gene expression. These data demonstrate the potential for HLA-DP, DQ and DR antigen expression in thyroid epithelium, and imply a dose relationship between lymphocytic infiltration and coordinate transcription and translation of HLA class II genes.

HLA–D region epitopes associated with juvenile arthritis. recognition by alloreactive t cell clones and alloantisera

The HLA-D region antigens DR5 (w11,w12), DRw6 (w13,w14), DRw8, DRw52, and DQw1 have previously been shown to be increased in frequency in subsets of patients with juvenile arthritis. Since the HLA-D region is complex (composed of at least 3 subregions encoding multiple molecules, each in turn presenting multiple alloantigenic epitopes), we sought to clarify whether one strongly associated factor might explain the previous findings. To search for the pertinent HLA-D region stimulatory epitopes, alloreactive T cells were primed against DR5 and DRw6 haplotypes and cloned by limiting dilution. Three T cell clones and 1 alloantiserum met the criteria for significant association with juvenile arthritis on patient testing, including DR5, DRw6, and DRw8 haplotypes. Monoclonal antibody blocking revealed that all 4 recognized epitopes on DR subregion products. For 2 of the clones, the relative risks for JA (10.5 and 9.4) were higher than the risks with any other previously described typing reagents.

Keratinocyte Expression of MHC Class II Antigens in Allergic Sensitization and Challenge Reactions and in Irritant Contact Dermatitis

Keratinocytes expressed major histocompatibility complex class II antigens during the development of irritant contact dermatitis, and during the induction of contact hypersensitivity, as well as in established allergic contact dermatitis. A battery of anti-class II monoclonal antibodies, some of which are specific for class II subregion products (DP, DQ, DR), was used in an immunohistochemical study of the sequential changes in the allergic challenge reactions to dinitrochlorobenzene (DNCB) and nickel, the irritant response to anthralin, and the induction of sensitization to DNCB. The induction of keratinocyte class II expression paralleled the influx of Leu-3a+ T cells into the skin and had occurred by 24 or 48 h in each type of reaction. Differential expression of class II subregion products on keratinocytes was noted: DR was the most frequently expressed molecule, followed by DP and DQ, although in the irritant response, DP expression was not observed. The importance of these observations can be decided only by functional studies.

Phenotypic heterogeneity displayed by T-non Hodgkin's lymphoma (T-NHL) cells dispersed from diagnostic lymph node biopsies.

In this communication we present the results of the study of the surface antigen expression of cells dispersed from 19 fresh lymph node biopsies. All cases subsequently received a histological diagnosis of T-cell lymphoma (T-NHL). The monoclonal antibody (Mab) panel employed for surface staining of viable cells contained reagents reactive with the sheep red blood cell receptor (OKT11) and T3-receptor associated determinants (UCHT1, OKT3) and a range of surface antigens found on subsets of T-cells. These antibodies are characterized according to their CD group as allocated by the First and Second Monoclonal Antibody Workshops. Cells were also stained with Mabs reactive with MHC class II subregion products. All 19 cases displayed marked heterogeneity for both pan-T-cell and T-subset antigens. An observation which is significant in terms of the routine diagnosis of T-NHL and with regard to the rational classification of node-based tumours of T-cell origin. Unlike resting peripheral blood T-cells, MHC class II subregion products were expressed on most of the cases examined though Tu22, directed towards a monomorphic determinant of HLA-DQ, stained fewer cells than other antibodies. Aberrant expression of MHC class II on lymphoma cells may reflect the activation of the tumour population.