The role of clay minerals in the preservation of Precambrian organic-walled microfossils.

Precambrian organic-walled microfossils (OWMs) are primarily preserved in mudstones and shales that are low in total organic carbon (TOC). Recent work suggests that high TOC may hinder OWM preservation, perhaps because it interferes with chemical interactions involving certain clay minerals that inhibit the decay of microorganisms. To test if clay mineralogy controls OWM preservation, and if TOC moderates the effect of clay minerals, we compared OWM preservational quality (measured by pitting on fossil surfaces and the deterioration of wall margins) to TOC, total clay, and specific clay mineral concentrations in 78 shale samples from 11 lithologic units ranging in age from ca. 1650 to 650 million years ago. We found that the probability of finding well-preserved microfossils positively correlates with total clay concentrations and confirmed that it negatively correlates with TOC concentrations. However, we found no evidence that TOC influences the effect of clay mineral concentrations on OWM preservation, supporting an independent role of both factors on preservation. Within the total clay fraction, well-preserved microfossils are more likely to occur in shales with high illite concentrations and low berthierine/chamosite concentrations; however, the magnitude of their effect on preservation is small. Therefore, there is little evidence that bulk clay chemistry is important in OWM preservation. Instead, we propose that OWM preservation is largely regulated by physical properties that isolate organic remains from microbial degradation such as food scarcity (low TOC) and low sediment permeability (high total clay content): low TOC increases the diffusive distances between potential carbon sources and heterotrophic microbes (or their degradative enzymes), while high clay concentrations reduce sediment pore space, thereby limiting the diffusion of oxidants and degradative enzymes to the sites of decay.

Whole blood interleukin-2 release test to detect and characterize rare circulating gluten-specific T cell responses in coeliac disease.

Whole blood cytokine release assays (CRA) assessing cellular immunity to gluten could simplify the diagnosis and monitoring of coeliac disease (CD). We aimed to determine the effectiveness of electrochemiluminescence CRA to detect responses to immunodominant gliadin peptides. HLA-DQ2·5+ CD adults (cohort 1, n = 6; cohort 2, n = 12) and unaffected controls (cohort 3, n = 9) were enrolled. Cohort 1 had 3-day gluten challenge (GC). Blood was collected at baseline, and for cohort 1 also at 3 h, 6 h and 6 days after commencing 3-day GC. Gliadin peptide-stimulated proliferation, interferon (IFN)-γ enzyme-linked immunospot (ELISPOT) and 14- and 3-plex electrochemiluminescence CRA were performed. Poisson distribution analysis was used to estimate responding cell frequencies. In cohort 1, interleukin (IL)-2 dominated the gliadin peptide-stimulated cytokine release profile in whole blood. GC caused systemic IL-2 release acutely and increased gliadin peptide-stimulated IFN-γ ELISPOT and whole blood CRA responses. Whole blood CRA after GC was dominated by IL-2, but also included IFN-γ, C-X-C motif chemokine ligand 10/IFN-γ-induced protein 10 (CXCL10/IP-10), CXCL9/monokine induced by IFN-γ (MIG), IL-10, chemokine (C-C motif) ligand 3/macrophage inflammatory protein 1-alpha (CCL3/MIP-1α), TNF-α and IL-8/CXCL8. In cohorts 2 and 3, gliadin peptide-stimulated whole blood IL-2 release was 100% specific and 92% sensitive for CD patients on a gluten-free diet; the estimated frequency of cells in CD blood secreting IL-2 to α-gliadin peptide was 0·5 to 11 per ml. Whole blood IL-2 release successfully mapped human leucocyte antigen (HLA)-DQ2·5-restricted epitopes in an α-gliadin peptide library using CD blood before and after GC. Whole blood IL-2 release assay using electrochemiluminescence is a sensitive test for rare gliadin-specific T cells in CD, and could aid in monitoring and diagnosis. Larger studies and validation with tetramer-based assays are warranted.

Topological features without a lattice in Rashba spin-orbit coupled atoms.

Topological order can be found in a wide range of physical systems, from crystalline solids, photonic meta-materials and even atmospheric waves to optomechanic, acoustic and atomic systems. Topological systems are a robust foundation for creating quantized channels for transporting electrical current, light, and atmospheric disturbances. These topological effects are quantified in terms of integer-valued 'invariants', such as the Chern number, applicable to the quantum Hall effect, or the [Formula: see text] invariant suitable for topological insulators. Here, we report the engineering of Rashba spin-orbit coupling for a cold atomic gas giving non-trivial topology, without the underlying crystalline structure that conventionally yields integer Chern numbers. We validated our procedure by spectroscopically measuring both branches of the Rashba dispersion relation which touch at a single Dirac point. We then measured the quantum geometry underlying the dispersion relation using matter-wave interferometry to implement a form of quantum state tomography, giving a Berry's phase with magnitude π. This implies that opening a gap at the Dirac point would give two dispersions (bands) each with half-integer Chern number, potentially implying new forms of topological transport.

Realization of a deeply subwavelength adiabatic optical lattice.

We propose and describe our realization of a deeply subwavelength optical lattice for ultracold neutral atoms using N resonantly Raman-coupled internal degrees of freedom. Although counterpropagating lasers with wavelength λ provided two-photon Raman coupling, the resultant lattice period was λ/2N, an N-fold reduction as compared to the conventional λ/2 lattice period. We experimentally demonstrated this lattice built from the three F = 1 Zeeman states of a 87Rb Bose-Einstein condensate, and generated a lattice with a λ/6 = 132 nm period from λ = 790 nm lasers. Lastly, we show that adding an additional rf-coupling field converts this lattice into a superlattice with N wells uniformly spaced within the original λ/2 unit cell.

Serum cytokines elevated during gluten-mediated cytokine release in coeliac disease.

Cytokines have been extensively studied in coeliac disease, but cytokine release related to exposure to gluten and associated symptoms has only recently been described. Prominent, early elevations in serum interleukin (IL)-2 after gluten support a central role for T cell activation in the clinical reactions to gluten in coeliac disease. The aim of this study was to establish a quantitative hierarchy of serum cytokines and their relation to symptoms in patients with coeliac disease during gluten-mediated cytokine release reactions. Sera were analyzed from coeliac disease patients on a gluten free-diet (n = 25) and from a parallel cohort of healthy volunteers (n = 25) who underwent an unmasked gluten challenge. Sera were collected at baseline and 2, 4 and 6 h after consuming 10 g vital wheat gluten flour; 187 cytokines were assessed. Confirmatory analyses were performed by high-sensitivity electrochemiluminescence immunoassay. Cytokine elevations were correlated with symptoms. Cytokine release following gluten challenge in coeliac disease patients included significant elevations of IL-2, chemokine (C-C motif) ligand 20 (CCL20), IL-6, chemokine (C-X-C motif) ligand (CXCL)9, CXCL8, interferon (IFN)-γ, IL-10, IL-22, IL-17A, tumour necrosis factor (TNF)-α, CCL2 and amphiregulin. IL-2 and IL-17A were earliest to rise. Peak levels of cytokines were generally at 4 h. IL-2 increased most (median 57-fold), then CCL20 (median 10-fold). Cytokine changes were strongly correlated with one another, and the most severely symptomatic patients had the highest elevations. Early elevations of IL-2, IL-17A, IL-22 and IFN-γ after gluten in patients with coeliac disease implicates rapidly activated T cells as their probable source. Cytokine release after gluten could aid in monitoring experimental treatments and support diagnosis.

Ex-vivo whole blood secretion of interferon (IFN)-γ and IFN-γ-inducible protein-10 measured by enzyme-linked immunosorbent assay are as sensitive as IFN-γ enzyme-linked immunospot for the detection of gluten-reactive T cells in human leucocyte antigen (HLA)-DQ2·5(+) -associated coeliac disease.

T cell cytokine release assays are used to diagnose infectious diseases, but not autoimmune or allergic disease. Coeliac disease (CD) is a common T cell-mediated disease diagnosed by the presence of gluten-dependent intestinal inflammation and serology. Many patients cannot be diagnosed with CD because they reduce dietary gluten before medical workup. Oral gluten challenge in CD patients treated with gluten-free diet (GFD) mobilizes gluten-reactive T cells measurable by interferon (IFN)-γ enzyme-linked immunospot (ELISPOT) or major histocompatibility complex (MHC) class II tetramers. Immunodominant peptides are quite consistent in the 90% of patients who possess HLA-DQ2·5. We aimed to develop whole blood assays to detect gluten-specific T cells. Blood was collected before and after gluten challenge from GFD donors confirmed to have CD (n = 27, all HLA-DQ2·5(+) ), GFD donors confirmed not to have CD (n = 6 HLA-DQ2·5(+) , 11 HLA-DQ2·5(-) ) and donors with CD not following GFD (n = 4, all HLA-DQ2·5(+) ). Plasma IFN-γ and IFN-γ inducible protein-10 (IP-10) were measured by enzyme-linked immunosorbent assay (ELISA) after whole blood incubation with peptides or gliadin, and correlated with IFN-γ ELISPOT. No T cell assay could distinguish between CD patients and controls prior to gluten challenge, but after gluten challenge the whole blood IFN-γ ELISA and the ELISPOT were both 85% sensitive and 100% specific for HLA-DQ2·5(+) CD patients; the whole blood IP-10 ELISA was 94% sensitive and 100% specific. We conclude that whole blood cytokine release assays are sensitive and specific for detection of gluten-reactive T cells in CD; further clinical studies addressing the utility of these tests in patients with an uncertain diagnosis of CD is warranted.

A scripted control system for autonomous hardware-timed experiments.

We present the labscript suite, an open-source experiment control system for automating shot-based experiments and their analysis. Experiments are composed as Python code, which is used to produce low-level hardware instructions. They are queued up and executed on the hardware in real time, synchronized by a pseudoclock. Experiment parameters are manipulated graphically, and analysis routines are run as new data are acquired. With this system, we can easily automate exploration of parameter spaces, including closed-loop optimization.

A versatile high resolution objective for imaging quantum gases.

We present a high resolution objective lens made entirely from catalog singlets that has a numerical aperture of 0.36. It corrects for aberrations introduced by a glass window and has a long working distance of 35 mm, making it suitable for imaging objects within a vacuum system. This offers simple high resolution imaging for many in the quantum gas community. The objective achieves a resolution of 1.3 µm at the design wavelength of 780 nm, and a diffraction-limited field of view of 360 µm when imaging through a 5 mm thick window. Images of a resolution target and a pinhole show quantitative agreement with the simulated lens performance. The objective is suitable for diffraction-limited monochromatic imaging on the D2 line of all the alkalis by changing only the aperture diameter, retaining numerical apertures above 0.32. The design corrects for window thicknesses of up to 15 mm if the singlet spacings are modified.

Dissecting the T-cell response to hordeins in coeliac disease can develop barley with reduced immunotoxicity.

BACKGROUND: Wheat, rye and barley prolamins are toxic to patients with coeliac disease. Barley is diploid with pure inbred cultivars available, and is attractive for genetic approaches to detoxification. AIM: To identify barley hordein fractions which activated the interferon-γ (IFN-γ) secreting peripheral blood T-cells from coeliac volunteers, and compare immunotoxicity of hordeins from experimental barley lines. METHODS: To reactivate a T-cell response to hordein, volunteers underwent a 3-day oral barley challenge. Peripheral blood mononuclear cells (PBMC) were isolated from twenty-one HLA DQ2(+) patients with confirmed coeliac disease. IFN-γ ELISpot assays enumerated T-cells activated by purified prolamins and positive controls. RESULTS: Hordein-specific T-cells were induced by oral barley challenge. All prolamin fractions were immunotoxic, but D- and C-hordeins were most active. Barley lines lacking B- and C-hordeins had a 5-fold reduced hordein-content, and immunotoxicity of hordein extracts were reduced 20-fold compared with wild-type barley. CONCLUSIONS: In vivo oral barley challenge offers a convenient and rapid approach to test the immunotoxicity of small amounts of purified hordeins using fresh T-cells from patients in high throughput overnight assays. Barley lines that did not accumulate B- and C-hordeins were viable, yet had substantially reduced immunotoxicity. Creation of hordein-free barley may therefore be possible.

Non-axial bone fracture but not depression as a risk factor for coeliac disease.

Screening for coeliac disease is confined to subgroups at greater risk for the disease, including type 1 diabetes mellitus, autoimmune thyroid disease and family members of affected individuals. This study examined the hypothesis that patients taking antidepressants or presenting with fractures could represent new subgroups at higher risk for coeliac disease. A total of 105 and 199 consecutive patients presenting to hospital taking antidepressants and/or with a fracture was screened with IgA tissue transglutaminase and had their IgA serum levels quantified. Patients with positive serology were offered further diagnostic and management follow up. No patients taking antidepressants had positive serology. Seven with fractures had elevated titres of IgA tissue transglutaminase. All of these patients had presented with non-axial fractures, representing a prevalence of 5.2% (95% confidence interval: 1.4-8.9%). Uptake of further investigation and management was poor. Patients presenting with non-axial fractures may be a subgroup in whom coeliac screening may be indicated. There needs to be greater awareness of atypical presentations of coeliac disease.

Systematic review: The evidence base for long-term management of coeliac disease.

BACKGROUND: While gluten-free diet is an effective treatment for coeliac disease, the need for and goals of long-term management of patients are poorly defined. AIM: To review systematically the complications and associations of coeliac disease, to identify potential risk factors, to define ways of assessing risk factors and to provide a strategy for management. METHODS: Review of medical literature from 1975. RESULTS: There is an increasing list of potential complications and/or conditions associated with coeliac disease, in particular, autoimmune disease, malignancy and bone disease. Risk factors that may predict or influence long-term outcomes include genetic susceptibility, environmental factors predominantly gluten ingestion, persistent small intestinal inflammation/injury and nutritional deficiencies. Genotyping of patients is yet to have an established clinical role in long-term management. Assessment of adherence to the gluten-free diet largely relies upon skilled dietary history, but the ultimate test is duodenal histopathology, which is the only currently established means of assessing healing. Symptoms, serology or other non-invasive means are poor predictors of healing and the likelihood of complications. CONCLUSION: Evidence (albeit limited) that adherence to a gluten-free diet and mucosal healing prevent and/or ameliorate complications indicates that a planned long-term strategy for follow-up is essential.

Coeliac disease: current approach and future prospects.

Public anxiety over gluten has fuelled widespread demand for gluten-free food, yet coeliac disease remains significantly underdiagnosed and some confusion remains regarding optimal diagnostic practices. Small bowel histology is the gold standard for diagnosis. High-quality commercial enzyme-linked immunosorbent assays for transglutaminase immunoglobulin A and deamidated gliadin immunoglobulin A and G are sensitive tools for screening, but almost 10% of coeliac disease is seronegative and serological testing is unreliable in the very young, in people already following a gluten-reduced diet, and those using immunosuppressive medications. HLA DQA and DQB genotyping to show that alleles encoding HLA DQ2 and DQ8 are absent virtually excludes coeliac disease. Confirming histological remission reduces the risks of later complications, such as osteoporosis and cancer. Monitoring remission by serology is unreliable. Because gluten is an exogenous antigen and the small intestine is readily accessible, the immunopathogenesis of coeliac disease is better understood than other strongly major histocompatibility complex class II-associated diseases, such as type 1 diabetes mellitus. Therapeutic targets have been identified and drugs are under development to supplement or even replace gluten-free diet. With greater awareness and non-dietary therapeutics, diagnosis and treatment of coeliac disease will be increasingly prominent in medical practice.

Antagonists and non-toxic variants of the dominant wheat gliadin T cell epitope in coeliac disease.

BACKGROUND: Coeliac disease (CD) is due to an inappropriate T cell mediated response to specific gluten peptides. Measured by interferon gamma (IFN-gamma) ELISPOT, about half of the gliadin specific T cells induced with in vivo wheat gluten exposure in HLA-DQ2+ CD are specific for an alpha/beta-gliadin peptide (p57-73 QE65; QLQPFPQPELPYPQPQS) that includes two overlapping T cell epitopes (PFPQPELPY and PQPELPYPQ). AIM: To define minimally substituted variants of p57-73 QE65 universally devoid of IFN-gamma stimulatory capacity but capable of antagonising IFN-gamma secretion from polyclonal T cells specific for p57-73 QE65. METHODS: Peripheral blood mononuclear cells collected from 75 HLA-DQ2+ CD patients after in vivo gluten challenge were used in overnight ELISPOT assays to screen 218 single or double substituted variants of p57-73 QE65 for cytokine stimulatory and antagonist activity. RESULTS: The region p60-71 (PFPQPELPYPQP) and especially p64-67 (PELP) was sensitive to substitution. Twelve substitutions in p64-67 stimulated no IFN-gamma ELISPOT response. Among 131 partial agonists identified, 45 produced statistically significant inhibition of IFN-gamma ELISPOT responses when cocultured in fivefold excess with p57-73 QE65 (n = 10). Four substituted variants of p57-73 QE65 were inactive by IFN-gamma ELISPOT but consistently antagonised IFN-gamma ELISPOT responses to p57-73 QE65, and also retained interleukin 10 stimulatory capacity similar to p57-73 QE65. CONCLUSIONS: Altered peptide ligands of p57-73 QE65, identified using polyclonal T cells from multiple HLA-DQ2+ CD donors, have properties in vitro that suggest that a single substitution to certain alpha/beta-gliadins could abolish their capacity to stimulate IFN-gamma from CD4 T cells and also have anti-inflammatory or protective effects in HLA-DQ2+ CD.

T cells in peripheral blood after gluten challenge in coeliac disease.

BACKGROUND: Current understanding of T cell epitopes in coeliac disease (CD) largely derives from intestinal T cell clones in vitro. T cell clones allow identification of gluten peptides that stimulate T cells but do not quantify their contribution to the overall gluten specific T cell response in individuals with CD when exposed to gluten in vivo. AIMS: To determine the contribution of a putative dominant T cell epitope to the overall gliadin T cell response in HLA-DQ2 CD in vivo. PATIENTS: HLA-DQ2+ individuals with CD and healthy controls. METHODS: Subjects consumed 20 g of gluten daily for three days. Interferon gamma (IFN-gamma) ELISPOT was performed using peripheral blood mononuclear cells (PBMC) to enumerate and characterise peptide and gliadin specific T cells before and after gluten challenge. RESULTS: In 50/59 CD subjects, irrespective of homo- or heterozygosity for HLA-DQ2, IFN-gamma ELISPOT responses for an optimal concentration of A-gliadin 57-73 Q-E65 were between 10 and 1500 per million PBMC, equivalent to a median 51% of the response for a "near optimal" concentration of deamidated gliadin. Whole deamidated gliadin and gliadin epitope specific T cells induced in peripheral blood expressed an intestinal homing integrin (alpha4beta7) and were HLA-DQ2 restricted. Peripheral blood T cells specific for A-gliadin 57-73 Q-E65 are rare in untreated CD but can be predictably induced two weeks after gluten exclusion. CONCLUSION: In vivo gluten challenge is a simple safe method that allows relevant T cells to be analysed and quantified in peripheral blood by ELISPOT, and should permit comprehensive high throughput mapping of gluten T cell epitopes in large numbers of individuals with CD.

Actuarial and actual analysis of surgical results: empirical validation.

This report validates the use of the Kaplan-Meier (actuarial) method of computing survival curves by comparing 12-year estimates published in 1978 with current assessments. It also contrasts cumulative incidence curves, referred to as "actual" analysis in the cardiac-related literature with Kaplan-Meier curves for thromboembolism and demonstrates that with the former estimate the percentage of events that will actually occur.

The STS National Database: current changes and challenges for the new millennium. Committee to Establish a National Database in Cardiothoracic Surgery, The Society of Thoracic Surgeons.

BACKGROUND: The Society of Thoracic Surgeons (STS) established the National Database (NDB) for Cardiac Surgery in 1989. Since then it has grown to be the largest database of its kind in medicine. The NDB has been one of the pioneers in the analysis and reporting of risk-adjusted outcomes in cardiothoracic surgery. METHODS AND RESULTS: This report explains the numerous changes in the NDB and its structure that have occurred over the past 2 years. It highlights the benefits of these changes, both to the individual member participants and to the STS overall. Additionally, the vision changes to the NDB and reporting structure are identified. The individuals who have participated in this effort since 1989 are acknowledged, and the STS owes an enormous debt of gratitude to each of them. CONCLUSIONS: Because of their collective efforts, the goal to establish the STS NDB as a "gold standard" worldwide for process and outcomes analysis related to cardiothoracic surgery is becoming a reality.

In vivo antigen challenge in celiac disease identifies a single transglutaminase-modified peptide as the dominant A-gliadin T-cell epitope.

Celiac disease (CD) is an increasingly diagnosed enteropathy (prevalence, 1:200-1:300) that is induced by dietary exposure to wheat gliadins (as well as related proteins in rye and barley) and is strongly associated with HLA-DQ2 (alpha1*0501, beta1*0201), which is present in over 90% of CD patients. Because a variety of gliadin peptides have been identified as epitopes for gliadin-specific T-cell clones and as bioactive sequences in feeding studies and in ex vivo CD intestinal biopsy challenge, it has been unclear whether a 'dominant' T-cell epitope is associated with CD. Here, we used fresh peripheral blood lymphocytes from individual subjects undergoing short-term antigen challenge and tissue transglutaminase-treated, overlapping synthetic peptides spanning A-gliadin to demonstrate a transient, disease-specific, DQ2-restricted, CD4 T-cell response to a single dominant epitope. Optimal gamma interferon release in an ELISPOT assay was elicited by a 17-amino-acid peptide corresponding to the partially deamidated peptide of A-gliadin amino acids 57-73 (Q65E). Consistent with earlier reports indicating that host tissue transglutaminase modification of gliadin enhances gliadin-specific CD T-cell responses, tissue transglutaminase specifically deamidated Q65 in the peptide of A-gliadin amino acids 56-75. Discovery of this dominant epitope may allow development of antigen-specific immunotherapy for CD.

The use of micro-dose aprotinin with continuous infusion in coronary artery bypass surgery.

BACKGROUND: To evaluate the efficacy of aprotinin at a dose far less than standard. EXPERIMENTAL DESIGN: Retrospective, case-control study. SETTING: community-based, teaching hospital PATIENTS: one hundred one patients undergoing primary, non-emergent, coronary artery bypass during two, six-month periods were studied. INTERVENTIONS: during the first period aprotinin was not administered, and these patients served as controls (n = 52). During the second period all patients received aprotinin via a micro-dose regimen (n = 49). MEASURES: postoperative bleeding and blood product usage served as determinants of efficacy. RESULTS: A significant difference existed in postoperative bleeding with the mean thoracic drain outputs being reduced in the aprotinin group both at 6 hours (p = 0.0003) and in total (p = 0.0004). This was further supported by significantly higher hematocrits (p = 0.03) on the first postoperative day in patients receiving aprotinin. Likewise, there was a significant reduction in total blood product exposures (p = 0.04) and platelet usage (p = 0.02) in the aprotinin group with a tendency towards decreased red cell usage. Further, when all patients with a hematocrit < or =30% prior to bypass were excluded, the significant reduction in total blood product exposures persisted (p = 0.04), and there was a significant reduction in red cell usage (p = 0.04) with a trend towards decreased platelet usage (p = 0.06) in the aprotinin group. CONCLUSIONS: Micro-dose aprotinin significantly reduces postoperative bleeding and blood product usage in primary, non-emergent, CABG patients.

Inflammatory bowel disease.

IBD results from the interaction of genetic and environmental factors (e.g., smoking). Clinical suspicion is the key to diagnosis, which then rests on colonoscopy, histopathological examination of multiple biopsy specimens, small bowel barium radiology and faecal examination. The primary goal of treatment is remission--histological in ulcerative colitis and symptomatic in Crohn's disease. Treating active disease and maintaining remission require different approaches. For active disease, short term corticosteroids are the mainstay of treatment, while immunosuppressive drugs are important in chronically active disease. For maintenance, mesalazine-delivering drugs and immunosuppressive agents are efficacious in both ulcerative colitis and Crohn's disease; patients with Crohn's disease should not smoke.