Great Bay Coast Watch: A Citizen Water Monitoring Program Volunteer Water Quality Monitoring Manual, 2004

The Great Bay Coast Watch is citizen volunteers, working within the UNH Cooperative Extension/NH Sea Grant Program, protecting the long-term health and natural resources of New Hampshire’s coastal waters and estuarine systems through monitoring and education projects. The purpose of this document is to present step-by-step instructions for conducting water quality testing in support of the Great Bay Coast Watch (GBCW)

Diversity of O Antigens within the Genus Cronobacter: from Disorder to Order

Cronobacter species are Gram-negative opportunistic pathogens that can cause serious infections in neonates. The lipopolysaccharides (LPSs) that form part of the outer membrane of such bacteria are possibly related to the virulence of particular bacterial strains. However, currently there is no clear overview of O-antigen diversity within the various Cronobacter strains and links with virulence. In this study, we tested a total of 82 strains, covering each of the Cronobacter species. The nucleotide variability of the O-antigen gene cluster was determined by restriction fragment length polymorphism (RFLP) analysis. As a result, the 82 strains were distributed into 11 previously published serotypes and 6 new serotypes, each defined by its characteristic restriction profile. These new serotypes were confirmed using genomic analysis of strains available in public databases: GenBank and PubMLST Cronobacter. Laboratory strains were then tested using the current serotype-specific PCR probes. The results show that the current PCR probes did not always correspond to genomic O-antigen gene cluster variation. In addition, we analyzed the LPS phenotype of the reference strains of all distinguishable serotypes. The identified serotypes were compared with data from the literature and the MLST database (www.pubmlst.org/cronobacter/). Based on the findings, we systematically classified a total of 24 serotypes for the Cronobacter genus. Moreover, we evaluated the clinical history of these strains and show that Cronobacter sakazakii O2, O1, and O4, C. turicensis O1, and C. malonaticus O2 serotypes are particularly predominant in clinical cases

Opening the consultation: how is this achieved between patient and physiotherapist?

Patients often give their reason for seeking health assistance in the opening phase of a health consultation. This opening phase normally involves two parts: first, an opening solicitation spoken by the health professional followed by the patient’s reason for the visit. However, how this is accomplished in real-life physiotherapy consultations is not well understood. That is, there has been limited research that has focused on the detailed discursive practices and strategies physiotherapists and patients use to organise problem presentation within real-life consultations. The aim of this presentation is to address this by identifying the discursive practices and strategies that physiotherapists and patients use in the opening phase of an initial consultation

shape to color associations in non synesthetes evidence for emotional mediation

4 Shape Features: Curviness: Curved, angular Symmetry: Asymmetric, symmetric Closure: Open, intersecting-once, intersecting>1 # of Line-Segments: 2, 3, 8 line-segments 8 Hues: Red, Yellow, Green, Blue, Orange, Chartreuse, Cyan, Purple 4 Saturation/Lightness levels ("cuts"): Saturated, Light, Muted, Dark + 5 Achromatic Colors: White, Black, Light, Medium, & Dark Gray 1a 1c 2a 2c 3a 3c 4a 4c 5a 5c 6

A Fast Sextupole Probe for Snapback Measurement in the LHC Dipoles

In superconducting particle accelerators a fast change of the magnetic field occurs during the first few seconds after the start of an energy ramp. Standard magnetic measurements using a coil rotating at 1 Hz do not have the time resolution required to completely resolve this phase, usually called snapback. For this reason we have developed a new and fast system dedicated to sextupole measurements. The basic component consists of three Hall plates mounted on a ring. In an ideal case this arrangement compensates the main dipole field and produces a signal proportional to the sextupole only. Mechanical tolerances and differences in the sensitivity of the Hall plates are compensated by instrumentation amplifiers and an in situ fine adjustment of the probe orientation. Using this hybrid compensation technique we have measured sextupole variations in an LHC dipole prototype during snapback at a rate of 5 Hz. In this paper we present details on the device and the results of our measurements

TaxMan : a server to trim rRNA reference databases and inspect taxonomic coverage

© The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nucleic Acids Research 40 (2012): W82-W87, doi:10.1093/nar/gks418.Amplicon sequencing of the hypervariable regions of the small subunit ribosomal RNA gene is a widely accepted method for identifying the members of complex bacterial communities. Several rRNA gene sequence reference databases can be used to assign taxonomic names to the sequencing reads using BLAST, USEARCH, GAST or the RDP classifier. Next-generation sequencing methods produce ample reads, but they are short, currently ∼100–450 nt (depending on the technology), as compared to the full rRNA gene of ∼1550 nt. It is important, therefore, to select the right rRNA gene region for sequencing. The primers should amplify the species of interest and the hypervariable regions should differentiate their taxonomy. Here, we introduce TaxMan: a web-based tool that trims reference sequences based on user-selected primer pairs and returns an assessment of the primer specificity by taxa. It allows interactive plotting of taxa, both amplified and missed in silico by the primers used. Additionally, using the trimmed sequences improves the speed of sequence matching algorithms. The smaller database greatly improves run times (up to 98%) and memory usage, not only of similarity searching (BLAST), but also of chimera checking (UCHIME) and of clustering the reads (UCLUST). TaxMan is available at http://www.ibi.vu.nl/programs/taxmanwww/.University of Amsterdam under the research priority area ‘Oral Infections and Inflammation’ (to B.W.B.); National Science Foundation [NSF/BDI 0960626 to S.M.H.]; the European Union Seventh Framework Programme (FP7/ 2007-2013) under ANTIRESDEV grant agreement no 241446 (to E.Z.)

Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution

The standard approach to analyzing 16S tag sequence data, which relies on clustering reads by sequence similarity into Operational Taxonomic Units (OTUs), underexploits the accuracy of modern sequencing technology. We present a clustering-free approach to multi-sample Illumina datasets that can identify independent bacterial subpopulations regardless of the similarity of their 16S tag sequences. Using published data from a longitudinal time-series study of human tongue microbiota, we are able to resolve within standard 97% similarity OTUs up to 20 distinct subpopulations, all ecologically distinct but with 16S tags differing by as little as 1 nucleotide (99.2% similarity). A comparative analysis of oral communities of two cohabiting individuals reveals that most such subpopulations are shared between the two communities at 100% sequence identity, and that dynamical similarity between subpopulations in one host is strongly predictive of dynamical similarity between the same subpopulations in the other host. Our method can also be applied to samples collected in cross-sectional studies and can be used with the 454 sequencing platform. We discuss how the sub-OTU resolution of our approach can provide new insight into factors shaping community assembly.Comment: Updated to match the published version. 12 pages, 5 figures + supplement. Significantly revised for clarity, references added, results not change

A System for Series Magnetic Measurements of the LHC Main Quadrupoles

More than 400 twin aperture lattice quadrupoles are needed for the Large Hadron Collider (LHC) which is under construction at CERN. The main quadrupole is assembled with correction magnets in a common cryostat called the Short Straight Section (SSS). We plan to measure all SSS's in cold conditions with an unprecedented accuracy: integrated gradient of the field within 150 ppm, harmonics in a range of 1 to 5 ppm, magnetic axis of all elements within 0.1 mm and their field direction within 0.2 mrad. In this paper we describe the automatic measurement system that we have designed, built and calibrated. Based on the results obtained on the two first prototypes of the SSS's (SSS3 and SSS4) we show that this system meets all above requirements

2-Arachidonoylglycerol mobilizes myeloid cells and worsens heart function after acute myocardial infarction.

Myocardial infarction (MI) leads to an enhanced release of endocannabinoids and a massive accumulation of neutrophils and monocytes within the ischaemic myocardium. These myeloid cells originate from haematopoietic precursors in the bone marrow and are rapidly mobilized in response to MI. We aimed to determine whether endocannabinoid signalling is involved in myeloid cell mobilization and cardiac recruitment after ischaemia onset. Intravenous administration of endocannabinoid 2-arachidonoylglycerol (2-AG) into wild type (WT) C57BL6 mice induced a rapid increase of blood neutrophil and monocyte counts as measured by flow cytometry. This effect was blunted when using cannabinoid receptor 2 knockout mice. In response to MI induced in WT mice, the lipidomic analysis revealed significantly elevated plasma and cardiac levels of the endocannabinoid 2-AG 24 h after infarction, but no changes in anandamide, palmitoylethanolamide, and oleoylethanolamide. This was a consequence of an increased expression of 2-AG synthesizing enzyme diacylglycerol lipase and a decrease of metabolizing enzyme monoacylglycerol lipase (MAGL) in infarcted hearts, as determined by quantitative RT-PCR analysis. The opposite mRNA expression pattern was observed in bone marrow. Pharmacological blockade of MAGL with JZL184 and thus increased systemic 2-AG levels in WT mice subjected to MI resulted in elevated cardiac CXCL1, CXCL2, and MMP9 protein levels as well as higher cardiac neutrophil and monocyte counts 24 h after infarction compared with vehicle-treated mice. Increased post-MI inflammation in these mice led to an increased infarct size, an impaired ventricular scar formation assessed by histology and a worsened cardiac function in echocardiography evaluations up to 21 days. Likewise, JZL184-administration in a myocardial ischaemia-reperfusion model increased cardiac myeloid cell recruitment and resulted in a larger fibrotic scar size. These findings suggest that changes in endocannabinoid gradients due to altered tissue levels contribute to myeloid cell recruitment from the bone marrow to the infarcted heart, with crucial consequences on cardiac healing and function