Datalog extension for nested relations

AbstractThe nested relational model allows relations that are not in first normal form. This paper gives an extension of Datalog rules for nested relations. In our approach, nested Datalog is a natural extension of Datalog introduced for the relational data model. A nested Datalog program has a hierarchical structure of rules and subprograms to manipulate relation values of nested relations. We introduce a new category of predicate symbols, the variable predicate symbols to refer to tuples of subrelations. The notion of soundness, safety and consistency is defined to avoid undesirable nested Datalog programs. The evaluation of nested Datalog is given in terms of the nested relational algebra. Finally, we relate the expressive power of nonrecursive nested Datalog to the power of nested relational algebra and safe nested tuple relational calculus

Investigation of the effects of food processing and matrix components on the analytical results of ELISA using an incurred gliadin reference material candidate

Disorders induced by cereal proteins (e.g. wheat allergy, celiac disease) are widespread in human population. Since their only effective treatment is the avoidance of the problematic proteins, patients have to be familiar with the composition of food products. For checking special foods produced for them, proper analytical methods are necessary. At the moment, in gluten analysis there are no reference methods and reference materials which model real food matrices. During the production and experimental utilisation of our previously developed reference material candidate, numerous questions emerged. As our model product is a real food matrix, interactions can be present between gluten proteins and other macro and micro components. Fat content of the baked cookies is almost 20%, which might affect the results of ELISA measurements. The detectable gluten content is significantly increasing after the defatting procedure, as a pre-treatment of samples. Moreover, baking is a common food processing step that might modify the structure of gluten proteins leading to denaturation and aggregation. In the soluble protein fraction the amount of low molecular weight proteins increases, while that of high molecular weight proteins decreases during the baking procedure

The transcription factor EGR2 is the molecular linchpin connecting STAT6 activation to the late, stable epigenomic program of alternative macrophage polarization

Macrophages polarize into functionally distinct subtypes while responding to microenvironmental cues. The identity of proximal transcription factors (TFs) downstream from the polarization signals are known, but their activity is typically transient, failing to explain the long-term, stable epigenomic programs developed. Here, we mapped the early and late epigenomic changes of interleukin-4 (IL-4)-induced alternative macrophage polarization. We identified the TF, early growth response 2 (EGR2), bridging the early transient and late stable gene expression program of polarization. EGR2 is a direct target of IL-4-activated STAT6, having broad action indispensable for 77% of the induced gene signature of alternative polarization, including its autoregulation and a robust, downstream TF cascade involving PPARG. Mechanistically, EGR2 binding results in chromatin opening and the recruitment of chromatin remodelers and RNA polymerase II. Egr2 induction is evolutionarily conserved during alternative polarization of mouse and human macrophages. In the context of tissue resident macrophages, Egr2 expression is most prominent in the lung of a variety of species. Thus, EGR2 is an example of an essential and evolutionarily conserved broad acting factor, linking transient polarization signals to stable epigenomic and transcriptional changes in macrophages

Expression of toll-like receptor -7 and -9 in B cell subsets from patients with primary Sjögren's syndrome

Introduction: Sjögren’s syndrome (SS) is a rheumatic autoimmune disease characterized by inflammation of exocrine glands. As autoantibodies are present in a majority of patients, B cells have been suggested to play an important role in onset and development of the disease. Toll-like receptors (TLRs) are pattern recognition receptors triggering innate immune responses. Since an increased expression of TLRs has been detected in other rheumatic diseases the purpose of this study was to explore TLRs in B cells of SS patients. Methods: The expression of TLR-7 and -9 in B cell subsets of 25 patients with primary SS (pSS) and 25 healthy controls was analysed in peripheral blood using flow cytometry and real time quantitative PCR. Results: We detected similar levels of CD19+ B cells in pSS patients and healthy controls. An increased number of naïve B cells, as well as fewer pre-switched memory B cells were found in pSS patients. No significant differences were observed in TLR-7 and -9 expression in B cells between pSS patients and healthy controls. Conclusion: This study shows that pSS patients have an alteration in the B cell subpopulation composition compared to controls, with less pre-switched memory B cells and more naïve B cells. We did not detect any significant disparities in TLR-7 and -9 expression between the two groups

Diagnosis and risk stratification in patients with anti-RNP autoimmunity

INTRODUCTION: Anti-RNP autoantibodies occur either in Mixed Connective Tissue Disease (MCTD) (with a frequently favorable prognosis), or in systemic lupus (SLE) cases with aggressive major organ disease. It is uncertain how to assess for the risk of severe disease in anti-RNP+ patients. METHODS: Following IRB-approved protocols, clinical data and blood was collected from patients with known or suspected anti-RNP autoimmunity and normal controls in a cohort study. Samples were screened for parameters of immune activation. Groups were compared based on clinical diagnoses, disease classification criteria, disease activity, and specific end-organ clinical manifestations. RESULTS: 97% of patients satisfying Alarcon-Segovia MCTD criteria also met SLICC SLE criteria, while 47% of the anti-RNP+ SLE patients also met MCTD criteria. Among SLICC SLE patients, MCTD criteria were associated with reduced rates of renal disease (Odds Ratio 4.3, 95% confidence interval 1.3–14.0), increased rates of Raynaud’s Phenomenon (OR 3.5, 95% c.i. 1.3–9.5), and increased serum BCMA, TACI, and TNFa levels. Circulating immune markers and markers of Type I Interferon activation were not effective at distinguishing clinical subgroups. CONCLUSIONS: Among anti-RNP patients, the question of MCTD versus SLE is not either/or: most MCTD patients also have lupus. MCTD classification criteria (but not a broad set of immune markers) distinguish a subset of SLE patients at reduced risk for renal disease