Towards an Achievable Performance for the Loop Nests

Numerous code optimization techniques, including loop nest optimizations, have been developed over the last four decades. Loop optimization techniques transform loop nests to improve the performance of the code on a target architecture, including exposing parallelism. Finding and evaluating an optimal, semantic-preserving sequence of transformations is a complex problem. The sequence is guided using heuristics and/or analytical models and there is no way of knowing how close it gets to optimal performance or if there is any headroom for improvement. This paper makes two contributions. First, it uses a comparative analysis of loop optimizations/transformations across multiple compilers to determine how much headroom may exist for each compiler. And second, it presents an approach to characterize the loop nests based on their hardware performance counter values and a Machine Learning approach that predicts which compiler will generate the fastest code for a loop nest. The prediction is made for both auto-vectorized, serial compilation and for auto-parallelization. The results show that the headroom for state-of-the-art compilers ranges from 1.10x to 1.42x for the serial code and from 1.30x to 1.71x for the auto-parallelized code. These results are based on the Machine Learning predictions.Comment: Accepted at the 31st International Workshop on Languages and Compilers for Parallel Computing (LCPC 2018

Prognostic value of nuclear morphometry in patients with TNM stage T1 ovarian clear cell adenocarcinoma

In 40 patients with TNM stage T1 ovarian clear cell adenocarcinoma, we used nuclear morphometry to study the relations among morphometric variables, clinical prognostic factors and outcome. The presence of one or more giant nuclear cells was positively associated with death (OR = 10.6, P = 0.02) and tended to be associated with disease recurrence (OR = 5.1, P = 0.07). Nuclear irregularity (expressed in terms of the nuclear roundness factor) was positively associated with both death (OR = 8.6, P = 0.02) and disease recurrence (OR = 8.2, P = 0.02). A combination of giant nuclear cell presence or nuclear irregularity proved to be a useful prognostic indicator, with a sensitivity and specificity of 83% and 71% in the prediction of death, and 75% and 71% in the prediction of disease recurrence. Patients' age and substage were of no prognostic value. We conclude that the nuclear morphometric characteristics, especially the presence of giant nuclear cells and nuclear irregularity, may be useful in predicting outcome in patients with early stage ovarian clear cell adenocarcinoma. © 1999 Cancer Research Campaig

The Impact of NOD2 Variants on Fecal Microbiota in Crohn's Disease and Controls Without Gastrointestinal Disease.

BACKGROUND/AIMS: Current models of Crohn's disease (CD) describe an inappropriate immune response to gut microbiota in genetically susceptible individuals. NOD2 variants are strongly associated with development of CD, and NOD2 is part of the innate immune response to bacteria. This study aimed to identify differences in fecal microbiota in CD patients and non-IBD controls stratified by NOD2 genotype. METHODS: Patients with CD and non-IBD controls of known NOD2 genotype were identified from patients in previous UK IBD genetics studies and the Cambridge bioresource (genotyped/phenotyped volunteers). Individuals with known CD-associated NOD2 mutations were matched to those with wild-type genotype. We obtained fecal samples from patients in clinical remission with low fecal calprotectin (<250 µg/g) and controls without gastrointestinal disease. After extracting DNA, the V1-2 region of 16S rRNA genes were polymerase chain reaction (PCR)-amplified and sequenced. Analysis was undertaken using the mothur package. Volatile organic compounds (VOC) were also measured. RESULTS: Ninety-one individuals were in the primary analysis (37 CD, 30 bioresource controls, and 24 household controls). Comparing CD with nonIBD controls, there were reductions in bacterial diversity, Ruminococcaceae, Rikenellaceae, and Christensenellaceae and an increase in Enterobacteriaceae. No significant differences could be identified in microbiota by NOD2 genotype, but fecal butanoic acid was higher in Crohn's patients carrying NOD2 mutations. CONCLUSIONS: In this well-controlled study of NOD2 genotype and fecal microbiota, we identified no significant genotype-microbiota associations. This suggests that the changes associated with NOD2 genotype might only be seen at the mucosal level, or that environmental factors and prior inflammation are the predominant determinant of the observed dysbiosis in gut microbiota.Funding was supported by CORE, the Digestive Diseases Foundation and the Wellcome Trust [grant number 097943 to NAK, 093885 to CAL and 098051 to Alan W Walker and Julian Parkhill . Dr. Walker receives core funding support from the Scottish Government Rural and Environmental Science and Analysis Service (RESAS). We also acknowledge the NIHR Biomedical Research Centre awards to Addenbrooke’s Hospital/University of Cambridge School of Clinical Medicine and acknowledge the NIHR Newcastle Biomedical Research Centre

Continuity and change?: Exploring reactions to a guided self-management intervention in a randomised controlled trial for IBS with reference to prior experience of managing a long term condition

Self-care interventions are promoted as effective strategies for improving the quality of life and health outcomes for individuals with long-term health conditions. Outcome measures used in evaluations using Randomised Controlled Trials (RCTs) are not designed to consider patients' prior management strategies and experience of illness. Yet the experience of illness literature suggests that adjusting to living with chronic illness, together with broader contextual influences, are likely to be relevant to understanding responses to self-management initiatives. Using group and individual interview data we attempt to illuminate the transposition of IBS from a condition unsatisfactorily managed by medicine to one successfully managed within the life worlds of individuals. If routine embedding of complex interventions depends on the accomplishment of integration and workability in patients' everyday lives then the design and evaluation of such interventions should view participation as part of a process of continuity as well as change. Responses to formal self-management can be extended beyond psychological and other quantitatively measured outcomes. A useful addendum to trial outcomes for self-management education is an understanding of change as being inextricably linked to people's previous attempts to, and experience of, managing long-term conditions. We suggest that the benefits of understanding the prior experience of managing illness and contact with health services include the acceptability and workability of complex interventions in patients' everyday lives

Dipper discs not inclined towards edge-on orbits

The so-called dipper stars host circumstellar discs and have optical and infrared light curves that exhibit quasi-periodic or aperiodic dimming events consistent with extinction by transiting dusty structures orbiting in the inner disc. Most of the proposed mechanisms explaining the dips - i.e. occulting disc warps, vortices, and forming planetesimals - assume nearly edge-on viewing geometries. However, our analysis of the three known dippers with publicly available resolved sub-mm data reveals discs with a range of inclinations, most notably the face-on transition disc J1604-2130 (EPIC 204638512). This suggests that nearly edge-on viewing geometries are not a defining characteristic of the dippers and that additional models should be explored. If confirmed by further observations of more dippers, this would point to inner disc processes that regularly produce dusty structures far above the outer disc mid-plane in regions relevant to planet formation.Support comes from NSF grant AST-1208911 (MA), NASA grants NNX11AC33G (EG) and NNX15AC92G (JPW), ERC grant 279973 (MCW), Hubble Fellowship 51364 (AWM), and a Royal Society University Research Fellowship (GK)

Death of a tumor: targeting CCN in pancreatic cancer

The matricellular protein CCN2 (connective tissue growth factor, CTGF) has been previously implicated in tumorigenesis. In pancreatic cancer cells, CCN2 expression occurs downstream of ras/MEK/ERK. Direct evidence that CCN2 mediates tumor progression in pancreatic cancer has been lacking. An exciting recent report by Bennewith et al. (Cancer Res 69:775–784, 2009) has used shRNA knockdown of CCN2 to illustrate that CCN2 contributes to growth of pancreatic tumor cells, both in vitro and in vivo. This report briefly summarizes these findings

Thyroglossal duct cyst carcinoma with concurrent thyroid carcinoma: a case report

<p>Abstract</p> <p>Introduction</p> <p>Thyroglossal duct carcinoma is a very rare finding and its presentation is similar to that of a benign cyst, which is a relatively common developmental abnormality that may manifest as a midline, neck mass. In general the diagnosis of thyroglossal duct carcinoma is based on the pathologic examination of the mass, but needle aspiration cytology, ultrasound and computed tomography play a role in the differential diagnosis of malignancy.</p> <p>Case presentation</p> <p>A further case of thyroglossal duct carcinoma and concurrent thyroid carcinoma with locoregional lymph node metastases affecting a 40-year-old woman followed up for 4 years is presented and discussed.</p> <p>Conclusion</p> <p>Sistrunk's surgical technique must always be the initial treatment, but in case of carcinoma further surgery, that is, thyroidectomy with or without lymph node dissection, and treatment with radioactive iodine have to be considered according to the microscopic and clinical findings. Accurate pre-operative clinical and radiological evaluation should be performed in order to plan surgical strategy.</p

The impact of different DNA extraction kits and laboratories upon the assessment of human gut microbiota composition by 16S rRNA gene sequencing

Peer reviewedPublisher PD

Galaxy And Mass Assembly (GAMA): Understanding the wavelength dependence of galaxy structure with bulge-disc decompositions

With a large sample of bright, low-redshift galaxies with optical$-$near-IR imaging from the GAMA survey we use bulge-disc decompositions to understand the wavelength-dependent behavior of single-S\'ersic structural measurements. We denote the variation in single-S\'ersic index with wavelength as $\mathcal{N}$, likewise for effective radius we use $\mathcal{R}$. We find that most galaxies with a substantial disc, even those with no discernable bulge, display a high value of $\mathcal{N}$. The increase in S\'ersic index to longer wavelengths is therefore intrinsic to discs, apparently resulting from radial variations in stellar population and/or dust reddening. Similarly, low values of $\mathcal{R}$ ($<$ 1) are found to be ubiquitous, implying an element of universality in galaxy colour gradients. We also study how bulge and disc colour distributions vary with galaxy type. We find that, rather than all bulges being red and all discs being blue in absolute terms, both components become redder for galaxies with redder total colours. We even observe that bulges in bluer galaxies are typically bluer than discs in red galaxies, and that bulges and discs are closer in colour for fainter galaxies. Trends in total colour are therefore not solely due to the colour or flux dominance of the bulge or disc

Automatic Identification of Defects on Eggshell Through a Multispectral Vision System

The objective of this research was to develop an off-line artificial vision system to automatically detect defective eggshells, i.e., dirty or cracked eggshells, by employing multispectral images with the final purpose to adapt the system to an on-line grading machine. In particular, this work was focused to study the feasibility of identifying organic stains on brown eggshells (dirty eggshell), caused by blood, feathers, feces, etc., from natural stains, caused by deposits of pigments on the outer layer of clean eggshells. During the analysis a total of 384 eggs were evaluated (clean: 148, dirty: 236). Dirty samples were evaluated visually in order to classify them according to the kind of defect (blood, feathers, and white, clear or dark feces), and clean eggshells were classified on the basis of the colour of the natural stains (clear or dark). For each sample digital images were acquired by employing a Charged Coupled Device (CCD) camera endowed with 15 monochromatic filters (440-940 nm). A Matlab® function was developed in order to automate the process and analyze images, with the aim to classify samples as clean or dirty. The program was constituted by three major steps: first, the research of an opportune combination of monochromatic images in order to isolate the eggshell from the background; second, the detection of the dirt stains; third, the classification of the images samples into the dirty or clean group on the basis of geometric characteristics of the stains (area in pixel). The proposed classification algorithm was able to correctly classify near 98% of the samples with a very low processing time (0.05s). The robustness of the proposed classification was observed applying an external validation to a second set of samples (n = 178), obtaining similar percentage of correctly classified samples (97%)