Detection of curved lines with B-COSFIRE filters: A case study on crack delineation

The detection of curvilinear structures is an important step for various computer vision applications, ranging from medical image analysis for segmentation of blood vessels, to remote sensing for the identification of roads and rivers, and to biometrics and robotics, among others. %The visual system of the brain has remarkable abilities to detect curvilinear structures in noisy images. This is a nontrivial task especially for the detection of thin or incomplete curvilinear structures surrounded with noise. We propose a general purpose curvilinear structure detector that uses the brain-inspired trainable B-COSFIRE filters. It consists of four main steps, namely nonlinear filtering with B-COSFIRE, thinning with non-maximum suppression, hysteresis thresholding and morphological closing. We demonstrate its effectiveness on a data set of noisy images with cracked pavements, where we achieve state-of-the-art results (F-measure=0.865). The proposed method can be employed in any computer vision methodology that requires the delineation of curvilinear and elongated structures.Comment: Accepted at Computer Analysis of Images and Patterns (CAIP) 201

Extending colonic mucosal microbiome analysis - Assessment of colonic lavage as a proxy for endoscopic colonic biopsies

This study was supported through GI Research funds and MRC Grant Ref: MR/M00533X/1 to GH.Peer reviewedPublisher PD

Data Descriptor: Systematic, continental scale temporal monitoring of marine pelagic microbiota by the Australian Marine Microbial Biodiversity Initiative

© 2018 Author(s). Sustained observations of microbial dynamics are rare, especially in southern hemisphere waters. The Australian Marine Microbial Biodiversity Initiative (AMMBI) provides methodologically standardized, continental scale, temporal phylogenetic amplicon sequencing data describing Bacteria, Archaea and microbial Eukarya assemblages. Sequence data is linked to extensive physical, biological and chemical oceanographic contextual information. Samples are collected monthly to seasonally from multiple depths at seven sites: Darwin Harbour (Northern Territory), Yongala (Queensland), North Stradbroke Island (Queensland), Port Hacking (New South Wales), Maria Island (Tasmania), Kangaroo Island (South Australia), Rottnest Island (Western Australia). These sites span ~30° of latitude and ~38° longitude, range from tropical to cold temperate zones, and are influenced by both local and globally significant oceanographic and climatic features. All sequence datasets are provided in both raw and processed fashion. Currently 952 samples are publically available for bacteria and archaea which include 88,951,761 bacterial (72,435 unique) and 70,463,079 archaeal (24,205 unique) 16 S rRNA v1-3 gene sequences, and 388 samples are available for eukaryotes which include 39,801,050 (78,463 unique) 18 S rRNA v4 gene sequences

Post-Translational Inhibition of IP-10 Secretion in IEC by Probiotic Bacteria: Impact on Chronic Inflammation

Peer reviewedPublisher PD

Internet-based randomised controlled trials for the evaluation of complementary and alternative medicines: probiotics in spondyloarthropathy

<b>Background</b> The clinical effectiveness of complementary and alternative medicines (CAMs) is widely debated because of a lack of clinical trials. The internet may provide an effective and economical approach for undertaking randomised controlled trials (RCTs) of low-risk interventions. We investigated whether the internet could be used to perform an internet-based RCT of a CAM fulfilling the revised CONSORT (Consolidated Standards of Reporting Trials) statement quality checklist for reporting of RCTs. A secondary aim was to examine the effect of probiotics compared to placebo in terms of well-being over 12 weeks.<p></p> <b>Methods</b> People aged ≥18 years with confirmed spondyloarthropathy living in the United Kingdom with internet access were invited to participate in an internet-based RCT of probiotic compared to placebo for improving well-being and bowel symptoms. The intervention was a probiotic containing 4 strains of live bacteria or identical placebo taken by mouth daily for 3 months. The primary outcome measure was the performance of the trial according to the revised CONSORT statement.<p></p> <b>Results</b> 147 people were randomised into the trial. The internet-based trial of the CAM fulfilled the revised CONSORT statement such as efficient blinding, allocation concealment, intention to treat analysis and flow of participants through the trial. Recruitment of the required number of participants was completed in 19 months. Sixty-five percent (96/147) completed the entire 3 months of the trial. The trial was low cost and demonstrated that in an intention to treat analysis, probiotics did not improve well-being or bowel symptoms.<p></p> <b>Conclusion</b> The internet-based RCT proved to be a successful and economical method for examining this CAM intervention. Recruitment, adherence and completion rate were all similar to those reported with conventional RCTs but at a fraction of the cost. Internet-based RCTs can fulfil all the criteria of the revised CONSORT statement and are an appropriate method for studying low-risk interventions

Border effects among Catalan dialects

In this study, we investigate which factors influence the linguistic distance of Catalan dialectal pronunciations from standard Catalan. We use pronunciations from three regions where the northwestern variety of the Catalan language is spoken (Catalonia, Aragon and Andorra). In contrast to Aragon, Catalan has an official status in both Catalonia and Andorra, which likely influences standardization. Because we are interested in the potentially large range of differences that standardization might promote, we examine 357 words in Catalan varieties and in particular their pronunciation distances with respect to the standard. In order to be sensitive to differences among the words, we fitted a generalized additive mixed-effects regression model to this data. This allows us to examine simultaneously the general (i.e. aggregate) patterns in pronunciation distance and to detect those words that diverge substantially from the general pattern. The results revealed higher pronunciation distances from standard Catalan in Aragon than in the other regions. Furthermore, speakers in Catalonia and Andorra, but not in Aragon, showed a clear standardization pattern, with younger speakers having dialectal pronunciations closer to the standard than older speakers. This clearly indicates the presence of a border effect within a single country with respect to word pronunciation distances. Since a great deal of scholarship focuses on single segment changes, we compare our analysis to the analysis of three segment changes that have been discussed in the literature on Catalan. This comparison revealed that the pattern observed at the word pronunciation level was supported by two of the three cases examined. As not all individual cases conform to the general pattern,

Adherence to a Mediterranean-like dietary pattern in children from eight European countries : the IDEFICS study

BACKGROUND: Despite documented benefits of a Mediterranean-like dietary pattern, there is a lack of knowledge about how children from different European countries compare with each other in relation to the adherence to this pattern. In response to this need, we calculated the Mediterranean diet score (MDS) in 2-9-year-old children from the Identification and prevention of dietary-and lifestyle-induced health effects in children and infants (IDEFICS) eight-country study. SUBJECTS AND METHODS: Using 24 h dietary recall data obtained during the IDEFICS study (n = 7940), an MDS score was calculated based on the age- and sex-specific population median intakes of six food groups (vegetables and legumes, fruit and nuts, cereal grains and potatoes, meat products and dairy products) and the ratio of unsaturated to saturated fats. For fish and seafood, which was consumed by 10% of the population, one point was given to consumers. The percentages of children with high MDS levels (43) were calculated and stratified by sex, age and by having at least one migrant parent or both native parents. Demographic (sex and age) and socioeconomic characteristics (parental education and income) of children showing high (43) vs low (<= 3) MDS levels were examined. RESULTS: The highest prevalence of children with MDS 43 was found among the Italian pre-school boys (55.9%) and the lowest among the Spanish school-aged girls (26.0%). Higher adherence to a Mediterranean-like dietary pattern was not associated with living in a Mediterranean country or in a highly educated or high-income family, although with some exceptions. Differences in adherence between boys and girls or age groups varied between countries without any general pattern. CONCLUSIONS: With the exception of Italian pre-schoolers, similar adherence levels to a Mediterranean-like dietary pattern have been observed among European children

Probiotic Bacteria Produce Conjugated Linoleic Acid Locally in the Gut That Targets Macrophage PPAR γ to Suppress Colitis

Inflammatory bowel disease (IBD) therapies are modestly successful and associated with significant side effects. Thus, the investigation of novel approaches to prevent colitis is important. Probiotic bacteria can produce immunoregulatory metabolites in vitro such as conjugated linoleic acid (CLA), a polyunsaturated fatty acid with potent anti-inflammatory effects. This study aimed to investigate the cellular and molecular mechanisms underlying the anti-inflammatory efficacy of probiotic bacteria using a mouse model of colitis. The immune modulatory mechanisms of VSL#3 probiotic bacteria and CLA were investigated in a mouse model of DSS colitis. Colonic specimens were collected for histopathology, gene expression and flow cytometry analyses. Immune cell subsets in the mesenteric lymph nodes (MLN), spleen, blood and colonic lamina propria cells were phenotypically and functionally characterized. Fecal samples and colonic contents were collected to determine the effect of VSL#3 and CLA on gut microbial diversity and CLA production. CLA and VSL#3 treatment ameliorated colitis and decreased colonic bacterial diversity, a finding that correlated with decreased gut pathology. Colonic CLA concentrations were increased in response to probiotic bacterial treatment, but without systemic distribution in blood. VSL#3 and CLA decreased macrophage accumulation in the MLN of mice with DSS colitis. The loss of PPAR γ in myeloid cells abrogated the protective effect of probiotic bacteria and CLA in mice with DSS colitis. Probiotic bacteria modulate gut microbial diversity and favor local production of CLA in the colon that targets myeloid cell PPAR γ to suppress colitis