Lipidomic profiling in Crohn's disease: abnormalities in phosphatidylinositols, with preservation of ceramide, phosphatidylcholine and phosphatidylserine composition.

Crohn's disease is a chronic inflammatory condition largely affecting the terminal ileum and large bowel. A contributing cause is the failure of an adequate acute inflammatory response as a result of impaired secretion of pro-inflammatory cytokines by macrophages. This defective secretion arises from aberrant vesicle trafficking, misdirecting the cytokines to lysosomal degradation. Aberrant intestinal permeability is also well-established in Crohn's disease. Both the disordered vesicle trafficking and increased bowel permeability could result from abnormal lipid composition. We thus measured the sphingo- and phospholipid composition of macrophages, using mass spectrometry and stable isotope labelling approaches. Stimulation of macrophages with heat-killed Escherichia coli resulted in three main changes; a significant reduction in the amount of individual ceramide species, an altered composition of phosphatidylcholine, and an increased rate of phosphatidylcholine synthesis in macrophages. These changes were observed in macrophages from both healthy control individuals and patients with Crohn's disease. The only difference detected between control and Crohn's disease macrophages was a reduced proportion of newly-synthesised phosphatidylinositol 16:0/18:1 over a defined time period. Shotgun lipidomics analysis of macroscopically non-inflamed ileal biopsies showed a significant decrease in this same lipid species with overall preservation of sphingolipid, phospholipid and cholesterol composition

The Bloom Clock for Causality Testing

Testing for causality between events in distributed executions is a fundamental problem. Vector clocks solve this problem but do not scale well. The probabilistic Bloom clock can determine causality between events with lower space, time, and message-space overhead than vector clock; however, predictions suffer from false positives. We give the protocol for the Bloom clock based on Counting Bloom filters and study its properties including the probabilities of a positive outcome and a false positive. We show the results of extensive experiments to determine how these above probabilities vary as a function of the Bloom timestamps of the two events being tested, and to determine the accuracy, precision, and false positive rate of a slice of the execution containing events in the temporal proximity of each other. Based on these experiments, we make recommendations for the setting of the Bloom clock parameters. We postulate the causality spread hypothesis from the application's perspective to indicate whether Bloom clocks will be suitable for correct predictions with high confidence. The Bloom clock design can serve as a viable space-, time-, and message-space-efficient alternative to vector clocks if false positives can be tolerated by an application

Managing affect in learners' questions in undergraduate science

This is the author's accepted manuscript. The final published article is available from the link below. Copyright @ 2012 Society for Research into Higher Education.This article aims to position students' classroom questioning within the literature surrounding affect and its impact on learning. The article consists of two main sections. First, the act of questioning is discussed in order to highlight how affect shapes the process of questioning, and a four-part genesis to question-asking that we call CARE is described: the construction, asking, reception and evaluation of a learner's question. This work is contextualised through studies in science education and through our work with university students in undergraduate chemistry, although conducted in the firm belief that it has more general application. The second section focuses on teaching strategies to encourage and manage learners' questions, based here upon the conviction that university students in this case learn through questioning, and that an inquiry-based environment promotes better learning than a simple ‘transmission’ setting. Seven teaching strategies developed from the authors' work are described, where university teachers ‘scaffold’ learning through supporting learners' questions, and working with these to structure and organise the content and the shape of their teaching. The article concludes with a summary of the main issues, highlighting the impact of the affective dimension of learning through questioning, and a discussion of the implications for future research

Adjunctive liraglutide treatment in patients with persistent or recurrent type 2 diabetes after metabolic surgery (GRAVITAS): a randomised, double-blind, placebo-controlled trial

Background Many patients with type 2 diabetes do not achieve sustained diabetes remission after metabolic (bariatric) surgery for the treatment of obesity. Liraglutide, a glucagon-like peptide-1 analogue, improves glycaemic control and reduces bodyweight in patients with type 2 diabetes. Our aim was to assess the safety and efficacy of liraglutide 1·8 mg in patients with persistent or recurrent type 2 diabetes after metabolic surgery. Methods In the GRAVITAS randomised double-blind, placebo-controlled trial, we enrolled adults who had undergone Roux-en-Y gastric bypass or vertical sleeve gastrectomy and had persistent or recurrent type 2 diabetes with HbA1c levels higher than 48 mmol/mol (6·5%) at least 1 year after surgery from five hospitals in London, UK. Participants were randomly assigned (2:1) via a computer-generated sequence to either subcutaneous liraglutide 1·8 mg once daily or placebo, both given together with a reduced-calorie diet, aiming for a 500 kcal per day deficit from baseline energy intake, and increased physical activity. The primary outcome was the change in HbA1c from baseline to the end of the study period at 26 weeks, assessed in patients who completed the trial. Safety was assessed in the safety analysis population, consisting of all participants who received either liraglutide or placebo. This trial is registered with EudraCT, number 2014-003923-23, and the ISRCTN registry, number ISRCTN13643081. Findings Between Jan 29, 2016, and May 2, 2018, we assigned 80 patients to receive either liraglutide (n=53) or placebo (n=27). 71 (89%) participants completed the study and were included in the principal complete-cases analysis. In a multivariable linear regression analysis, with baseline HbA1c levels and surgery type as covariates, liraglutide treatment was associated with a difference of −13·3 mmol/mol (−1·22%, 95% CI −19·7 to −7·0; p=0·0001) in HbA1c change from baseline to 26 weeks, compared with placebo. Type of surgery had no significant effect on the outcome. 24 (45%) of 53 patients assigned to liraglutide and 11 (41%) of 27 assigned to placebo reported adverse effects: these were mainly gastrointestinal and in line with previous experience with liraglutide. There was one death during the study in a patient assigned to the placebo group, which was considered unrelated to study treatment. Interpretation These findings support the use of adjunctive liraglutide treatment in patients with persistent or recurrent type 2 diabetes after metabolic surgery

Renal obstructive dysplasia: Ultrasound diagnosis and therapeutic implications

57 cases of renal obstructive dysplasia (defined as the abnormal development of nephronic and ductal structures due to in utero obstruction of the urinary tract) were evaluated in terms of sonographic findings, renal and other associated anomalies, and current status of the child. More than one-third of the cases had bilateral disease and although not uniformly fatal bilateral involvement was associated with significant morbidity and mortality. In 12 of the 33 cases with unilateral dysplasia there was an association with contralateral renal problems including ureteropelvic junction obstruction, vesicoureteral reflux and aplasia. Almost one-half of the cases had congenital anomalies, these included VACTERL association, congenital heart disease, cranial abnormalities and gastrointestinal malformations. Fifteen stillborns and 12 of the patients with bilateral involvement and four with unilateral involvement have died. Four patients are on dialysis (two with bilateral involvement and two with unilateral renal obstructive dysplasia). Only one-quarter are otherwise normal. More serious problems are reported in this mixed age population of patients with obstructive renal dysplasia than has been identified in previous studies. Management decisions of the fetus and child must be based on this new age-expanded population.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/46696/1/247_2005_Article_BF02018623.pd

Model Convolution: A Computational Approach to Digital Image Interpretation

Digital fluorescence microscopy is commonly used to track individual proteins and their dynamics in living cells. However, extracting molecule-specific information from fluorescence images is often limited by the noise and blur intrinsic to the cell and the imaging system. Here we discuss a method called “model-convolution,” which uses experimentally measured noise and blur to simulate the process of imaging fluorescent proteins whose spatial distribution cannot be resolved. We then compare model-convolution to the more standard approach of experimental deconvolution. In some circumstances, standard experimental deconvolution approaches fail to yield the correct underlying fluorophore distribution. In these situations, model-convolution removes the uncertainty associated with deconvolution and therefore allows direct statistical comparison of experimental and theoretical data. Thus, if there are structural constraints on molecular organization, the model-convolution method better utilizes information gathered via fluorescence microscopy, and naturally integrates experiment and theory

Exploring health systems research and its influence on policy processes in low income countries

<p>Abstract</p> <p>Background</p> <p>The interface between research and policymaking in low-income countries is highly complex. The ability of health systems research to influence policy processes in such settings face numerous challenges. Successful analysis of the research-policy interface in these settings requires understanding of contextual factors as well as key influences on the interface. <it>Future Health Systems (FHS): Innovations for Equity </it>is a consortium conducting research in six countries in Asia and Africa. One of the three cross-country research themes of the consortium is analysis of the relationship between research (evidence) and policy making, especially their impact on the poor; insights gained in the initial conceptual phase of FHS activities can inform the global knowledge pool on this subject.</p> <p>Discussion</p> <p>This paper provides a review of the research-policy interface in low-income countries and proposes a conceptual framework, followed by directions for empirical approaches. First, four developmental perspectives are considered: social institutional factors; virtual versus grassroots realities; science-society relationships; and construction of social arrangements. Building on these developmental perspectives three research-policy interface entry points are identified: 1. Recognizing policy as complex processes; 2. Engaging key stakeholders: decision-makers, providers, scientists, and communities; and 3. Enhancing accountability. A conceptual framework with three entry points to the research-policy interface – policy processes; stakeholder interests, values, and power; and accountability – within a context provided by four developmental perspectives is proposed. Potential empirical approaches to the research-policy interface are then reviewed. Finally, the value of such innovative empirical analysis is considered.</p> <p>Conclusion</p> <p>The purpose of this paper is to provide the background, conceptual framework, and key research directions for empirical activities focused on the research-policy interface in low income settings. The interface can be strengthened through such analysis leading to potential improvements in population health in low-income settings. Health system development cognizant of the myriad factors at the research-policy interface can form the basis for innovative future health systems.</p

Computer-assisted assessment of the Human Epidermal Growth Factor Receptor 2 immunohistochemical assay in imaged histologic sections using a membrane isolation algorithm and quantitative analysis of positive controls

<p>Abstract</p> <p>Background</p> <p>Breast cancers that overexpress the human epidermal growth factor receptor 2 (HER2) are eligible for effective biologically targeted therapies, such as trastuzumab. However, accurately determining HER2 overexpression, especially in immunohistochemically equivocal cases, remains a challenge. Manual analysis of HER2 expression is dependent on the assessment of membrane staining as well as comparisons with positive controls. In spite of the strides that have been made to standardize the assessment process, intra- and inter-observer discrepancies in scoring is not uncommon. In this manuscript we describe a pathologist assisted, computer-based continuous scoring approach for increasing the precision and reproducibility of assessing imaged breast tissue specimens.</p> <p>Methods</p> <p>Computer-assisted analysis on HER2 IHC is compared with manual scoring and fluorescence in situ hybridization results on a test set of 99 digitally imaged breast cancer cases enriched with equivocally scored (2+) cases. Image features are generated based on the staining profile of the positive control tissue and pixels delineated by a newly developed Membrane Isolation Algorithm. Evaluation of results was performed using Receiver Operator Characteristic (ROC) analysis.</p> <p>Results</p> <p>A computer-aided diagnostic approach has been developed using a membrane isolation algorithm and quantitative use of positive immunostaining controls. By incorporating internal positive controls into feature analysis a greater Area Under the Curve (AUC) in ROC analysis was achieved than feature analysis without positive controls. Evaluation of HER2 immunostaining that utilized membrane pixels, controls, and percent area stained showed significantly greater AUC than manual scoring, and significantly less false positive rate when used to evaluate immunohistochemically equivocal cases.</p> <p>Conclusion</p> <p>It has been shown that by incorporating both a membrane isolation algorithm and analysis of known positive controls a computer-assisted diagnostic algorithm was developed that can reproducibly score HER2 status in IHC stained clinical breast cancer specimens. For equivocal scoring cases, this approach performed better than standard manual evaluation as assessed by ROC analysis in our test samples. Finally, there exists potential for utilizing image-analysis techniques for improving HER2 scoring at the immunohistochemically equivocal range.</p

Improved Measurement of the Pseudoscalar Decay Constant fDsf_{D_{s}}

We present a new determination of the Ds decay constant, f_{Ds} using 5 million continuum charm events obtained with the CLEO II detector. Our value is derived from our new measured ratio of widths for Ds -> mu nu/Ds -> phi pi of 0.173+/- 0.021 +/- 0.031. Taking the branching ratio for Ds -> phi pi as (3.6 +/- 0.9)% from the PDG, we extract f_{Ds} = (280 +/- 17 +/- 25 +/- 34){MeV}. We compare this result with various model calculations.Comment: 23 page postscript file, postscript file also available through http://w4.lns.cornell.edu/public/CLN