There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality.

Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

I and i

http://www.klinikaikozpont.u-szeged.hu/pedia/images/pdf/CME_TEL/Full-Text/25.pdf

The Hallmarks of Aging

This study describes and validates a new method for metagenomic biomarker discovery by way of class comparison, tests of biological consistency and effect size estimation. This addresses the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities, which is a central problem to the study of metagenomics. We extensively validate our method on several microbiomes and a convenient online interface for the method is provided at http://huttenhower.sph.harvard.edu/lefse/.

/pdf/metagenomic-biomarker-discovery-and-explanation-x530ilzkca.pdf

Metagenomic biomarker discovery and explanation

We have catalogued the protein kinase complement of the human genome (the "kinome") using public and proprietary genomic, complementary DNA, and expressed sequence tag (EST) sequences. This provides a starting point for comprehensive analysis of protein phosphorylation in normal and disease states, as well as a detailed view of the current state of human genome analysis through a focus on one large gene family. We identify 518 putative protein kinase genes, of which 71 have not previously been reported or described as kinases, and we extend or correct the protein sequences of 56 more kinases. New genes include members of well-studied families as well as previously unidentified families, some of which are conserved in model organisms. Classification and comparison with model organism kinomes identified orthologous groups and highlighted expansions specific to human and other lineages. We also identified 106 protein kinase pseudogenes. Chromosomal mapping revealed several small clusters of kinase genes and revealed that 244 kinases map to disease loci or cancer amplicons.

http://science.sciencemag.org/content/sci/298/5600/1912.full.pdf

The Protein Kinase Complement of the Human Genome

An expert panel was convened in October 2013 by the International Scientific Association for Probiotics and Prebiotics (ISAPP) to discuss the field of probiotics. It is now 13 years since the definition of probiotics and 12 years after guidelines were published for regulators, scientists and industry by the Food and Agriculture Organization of the United Nations and the WHO (FAO/WHO). The FAO/WHO definition of a probiotic--"live microorganisms which when administered in adequate amounts confer a health benefit on the host"--was reinforced as relevant and sufficiently accommodating for current and anticipated applications. However, inconsistencies between the FAO/WHO Expert Consultation Report and the FAO/WHO Guidelines were clarified to take into account advances in science and applications. A more precise use of the term 'probiotic' will be useful to guide clinicians and consumers in differentiating the diverse products on the market. This document represents the conclusions of the ISAPP consensus meeting on the appropriate use and scope of the term probiotic.

/pdf/expert-consensus-document-the-international-scientific-1zd5d1fmxy.pdf

Expert consensus document. The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic

Primary Biliary Cirrhosis associated with Coeliac Disease.

Performance of a modified abdominopelvic CT protocol reconstructed using full iterative reconstruction (IR) was assessed for imaging patients presenting with acute abdominal symptoms. Fifty-seven patients (17 male, 40 female; mean age of 56.5 ± 8 years) were prospectively studied. Low-dose (LD) and conventional-dose (CD) CTs were contemporaneously acquired between November 2015 and March 2016. The LD and CD protocols imparted radiation exposures approximating 10–20% and 80–90% those of routine abdominopelvic CT, respectively. The LD images were reconstructed with model-based iterative reconstruction (MBIR), and CD images with hybrid IR (40% adaptive statistical iterative reconstruction (ASIR)). Image quality was assessed quantitatively and qualitatively. Independent clinical interpretations were performed with a 6-week delay between reviews. A 74.7% mean radiation dose reduction was achieved: LD effective dose (ED) 2.38 ± 1.78 mSv (size-specific dose estimate (SSDE) 3.77 ± 1.97 mGy); CD ED 7.04 ± 4.89 mSv (SSDE 10.74 ± 5.5 mGy). LD-MBIR images had significantly lower objective and subjective image noise compared with CD-ASIR (p < 0.0001). Noise reduction for LD-MBIR studies was greater for patients with BMI < 25 kg/m2 than those with BMI ≥ 25 kg/m2 (5.36 ± 3.2 Hounsfield units (HU) vs. 4.05 ± 3.1 HU, p < 0.0001). CD-ASIR studies had significantly better contrast resolution, and diagnostic acceptability (p < 0.0001 for all). LD-MBIR studies had significantly lower streak artifact (p < 0.0001). There was no difference in sensitivity for primary findings between the low-dose and conventional protocols with the exception of one case of enteritis. Low-dose abdominopelvic CT performed with MBIR is a feasible radiation dose reduction strategy for imaging patients presenting with acute abdominal pain.

Low-dose CT imaging of the acute abdomen using model-based iterative reconstruction: a prospective study

Anti-TNF therapy for Crohn's disease: a perspective (infliximab is not the drug we have been waiting for)

Early metastasis contributes to the very poor prognosis of esophageal carcinoma. The recent immunohistochemical finding that invasive esophageal carcinomas express elevated levels of urokinase (uPA) and urokinase receptor (uPA-R) in vivo suggest that the plasminogen activation system may contribute to metastasis in esophageal cancer. The aim of our study was to functionally investigate, at the molecular level, the relative contribution of uPA and uPA-R to the invasiveness of esophageal cancer cells in vitro. The three esophageal cancer cell lines, OC1-3, generated in our laboratory, were analyzed for uPA and uPA-R expression by RT-PCR, immunoenzymatic staining, and quantitative ELISA. Invasiveness of all cell lines was quantified as percentage cellular invasiveness in a standardized Matrigel in vitro assay. OC1 and OC3, which were found to coexpress both uPA and uPA-R, displayed stronger invasiveness (44% and 32.5% respectively) relative to OC2 (19%) which expressed uPA-R but was negative for uPA. Transfection of OC2 cells with the uPA cDNA resulted in two variants, OC2.uPA1 and OC2.uPA2, stably expressing functional uPA. Both transfectants exhibited enhanced invasiveness (60% and 50% respectively) relative to the parent uPA-negative OC2 cells (19%). Antisense oligonucleotide inhibition of either uPA or uPA-R expression resulted in a similar, marked reduction in invasiveness of esophageal tumor cells which normally coexpress both molecules (OC1, OC3 and the uPA-expressing OC2-transfectant clones). Neither antisense treatment altered the basal invasiveness of OC2, which expresses uPA-R but not uPA. In conclusion, coexpression of uPA with its receptor, uPA-R, is required for functional involvement of the urokinase system in invasion by esophageal carcinoma cells. Our results suggest that these synergistic mediators of invasiveness are quantitatively major contributors to the invasiveness of esophageal carcinoma.

Invasion by esophageal cancer cells: functional contribution of the urokinase plasminogen activation system, and inhibition by antisense oligonucleotides to urokinase or urokinase receptor.

Fergus Shanahan

Papers

Primary Biliary Cirrhosis associated with Coeliac Disease.

Low-dose CT imaging of the acute abdomen using model-based iterative reconstruction: a prospective study

Anti-TNF therapy for Crohn's disease: a perspective (infliximab is not the drug we have been waiting for)

Invasion by esophageal cancer cells: functional contribution of the urokinase plasminogen activation system, and inhibition by antisense oligonucleotides to urokinase or urokinase receptor.

Odd forms of inflammatory bowel disease: What can they tell us?