LIS–lnterlink—connecting laboratory information systems to remote primary health–care centres via the Internet

A pilot study was performed to evaluate the feasibility of using the Internet to securely deliver patient laboratory results, and the system has subsequently gone into routine use in Poland. The system went from design to pilot and then to live implementation within a four-month period, resulting in the LIS-Interlink software product. Test results are retrieved at regular intervals from the BioLinkTM LIS (Laboratory Information System), encrypted and transferred to a secure area on the Web server. The primary health-care centres dial into the Internet using a local-cell service provided by Polish Telecom (TP), obtain a TCP/IP address using the TP DHCP server, and perform HTTP ‘get’ and ‘post’ operations to obtain the files by secure handshaking. The data are then automatically inserted into a local SQL database (with optional printing of incoming reports)for cumulative reporting and searching functions. The local database is fully multi-user and can be accessed from different clinics within the centres by a variety of networking protocols

Pretransitional behavior in a water-DDAB-5CB microemulsion close to the demixing transition. Evidence for intermicellar attraction mediated by paranematic fluctuations

We present a study of a water-in-oil microemulsion in which surfactant coated water nanodroplets are dispersed in the isotropic phase of the thermotropic liquid crystal 5CB. As the temperature is lowered below the isotropic to nematic phase transition of pure 5CB, the system displays a demixing transition leading to a coexistence of a droplet rich isotropic phase with a droplet poor nematic. The transition is anticipated, in the high T side, by increasing pretransitional fluctuations in 5CB molecular orientation and in the nanodroplet concentration. The observed phase behavior supports the notion that the nanosized droplets, while large enough for their statistical behavior to be probed via light scattering, are also small enough to act as impurities, disturbing the local orientational ordering of the liquid crystal and thus experiencing pretransitional attractive interaction mediated by paranematic fluctuations. The pretransitional behavior, together with the topology of the phase diagram, can be understood on the basis of a diluted Lebwohl-Lasher model which describes the nanodroplets simply as holes in the liquid crystal.Comment: 64 pages, 16 figures, J. Chem. Phys. in pres

Soil as an Extended Composite Phenotype of the Microbial Metagenome

We use a unique set of terrestrial experiments to demonstrate how soil management practises result in emergence of distinct associations between physical structure and biological functions. These associations have a significant effect on the flux, resilience and efficiency of nutrient delivery to plants (including water). Physical structure determining the air-water balance in soil as well as transport rates is influenced by nutrient and physical interventions. Contrasting emergent soil structures exert selective pressures upon the microbiome metagenome. These selective pressures are associated with the quality of organic carbon inputs, the prevalence of anaerobic microsites and delivery of nutrients to microorganisms attached to soil surfaces. This variety results in distinctive gene assemblages characterising each state. The nature of the interactions provide evidence that soil behaves as an extended composite phenotype of the resident microbiome, responsive to the input and turnover of plant-derived organic carbon. We provide new evidence supporting the theory that soil-microbe systems are self-organising states with organic carbon acting as a critical determining parameter. This perspective leads us to propose carbon flux, rather than soil organic carbon content as the critical factor in soil systems, and we present evidence to support this view

Significant structural evolution of a long-term fallow soil in response to agricultural management practices requires at least 10 years after conversion at the aggregate level

Agricultural practices can have significant effects on the physical and biological properties of soil. The aim of this study was to understand how the physical structure of a compromised soil, arising from long-term bare-fallow management, was modified by adopting different field management practices. We hypothesised that changing agricultural practice from bare-fallow to arable or grassland would influence the modification of pore structure via an increase in porosity, pore connectivity, and a more homogenous distribution of pore sizes; and that this change exerts a rapid development of soil structure following conversion. Soil aggregates (< 2 mm) collected in successive years from field plots subjected to three contrasting managements were studied; viz. bare-fallow, bare-fallow converted to arable, and bare-fallow converted to grassland. Soil structure was assessed by X-ray Computed Tomography on the aggregates at 1.5 µm resolution, capturing detail relevant to soil biophysical processes. The grassland system increased porosity, diversity of pore sizes, pore-connectivity and pore-surface density significantly over the decade following conversion. However, measured at this resolution, the development of most of these metrics of soil structure required approximately 10 years post-conversion to show a significant effect. The arable system did not influence soil structural development significantly. Only the pore size distribution was modified in grassland in a shorter time frame (2 years post-conversion). Hence development of the soil structural characteristics appears to require at least a decadal timescale following conversion to grassland

The LONI QC System: A Semi-Automated, Web-Based and Freely-Available Environment for the Comprehensive Quality Control of Neuroimaging Data.

Quantifying, controlling, and monitoring image quality is an essential prerequisite for ensuring the validity and reproducibility of many types of neuroimaging data analyses. Implementation of quality control (QC) procedures is the key to ensuring that neuroimaging data are of high-quality and their validity in the subsequent analyses. We introduce the QC system of the Laboratory of Neuro Imaging (LONI): a web-based system featuring a workflow for the assessment of various modality and contrast brain imaging data. The design allows users to anonymously upload imaging data to the LONI-QC system. It then computes an exhaustive set of QC metrics which aids users to perform a standardized QC by generating a range of scalar and vector statistics. These procedures are performed in parallel using a large compute cluster. Finally, the system offers an automated QC procedure for structural MRI, which can flag each QC metric as being 'good' or 'bad.' Validation using various sets of data acquired from a single scanner and from multiple sites demonstrated the reproducibility of our QC metrics, and the sensitivity and specificity of the proposed Auto QC to 'bad' quality images in comparison to visual inspection. To the best of our knowledge, LONI-QC is the first online QC system that uniquely supports the variety of functionality where we compute numerous QC metrics and perform visual/automated image QC of multi-contrast and multi-modal brain imaging data. The LONI-QC system has been used to assess the quality of large neuroimaging datasets acquired as part of various multi-site studies such as the Transforming Research and Clinical Knowledge in Traumatic Brain Injury (TRACK-TBI) Study and the Alzheimer's Disease Neuroimaging Initiative (ADNI). LONI-QC's functionality is freely available to users worldwide and its adoption by imaging researchers is likely to contribute substantially to upholding high standards of brain image data quality and to implementing these standards across the neuroimaging community

Damage function for historic paper. Part I: Fitness for use

Background In heritage science literature and in preventive conservation practice, damage functions are used to model material behaviour and specifically damage (unacceptable change), as a result of the presence of a stressor over time. For such functions to be of use in the context of collection management, it is important to define a range of parameters, such as who the stakeholders are (e.g. the public, curators, researchers), the mode of use (e.g. display, storage, manual handling), the long-term planning horizon (i.e. when in the future it is deemed acceptable for an item to become damaged or unfit for use), and what the threshold of damage is, i.e. extent of physical change assessed as damage. Results In this paper, we explore the threshold of fitness for use for archival and library paper documents used for display or reading in the context of access in reading rooms by the general public. Change is considered in the context of discolouration and mechanical deterioration such as tears and missing pieces: forms of physical deterioration that accumulate with time in libraries and archives. We also explore whether the threshold fitness for use is defined differently for objects perceived to be of different value, and for different modes of use. The data were collected in a series of fitness-for-use workshops carried out with readers/visitors in heritage institutions using principles of Design of Experiments. Conclusions The results show that when no particular value is pre-assigned to an archival or library document, missing pieces influenced readers/visitors’ subjective judgements of fitness-for-use to a greater extent than did discolouration and tears (which had little or no influence). This finding was most apparent in the display context in comparison to the reading room context. The finding also best applied when readers/visitors were not given a value scenario (in comparison to when they were asked to think about the document having personal or historic value). It can be estimated that, in general, items become unfit when text is evidently missing. However, if the visitor/reader is prompted to think of a document in terms of its historic value, then change in a document has little impact on fitness for use

Chandra Observations of G11.2-0.3: Implications for Pulsar Ages

We present Chandra X-ray Observatory imaging observations of the young Galactic supernova remnant G11.2-0.3. The image shows that the previously known young 65-ms X-ray pulsar is at position (J2000) RA 18h 11m 29.22s, DEC -19o 25' 27.''6, with 1 sigma error radius 0.''6. This is within 8'' of the geometric center of the shell. This provides strong confirming evidence that the system is younger, by a factor of ~12, than the characteristic age of the pulsar. The age discrepancy suggests that pulsar characteristic ages can be poor age estimators for young pulsars. Assuming conventional spin down with constant magnetic field and braking index, the most likely explanation for the age discrepancy in G11.2-0.3 is that the pulsar was born with a spin period of ~62 ms. The Chandra image also reveals, for the first time, the morphology of the pulsar wind nebula. The elongated hard-X-ray structure can be interpreted as either a jet or a Crab-like torus seen edge on. This adds to the growing list of highly aspherical pulsar wind nebulae and argues that such structures are common around young pulsars.Comment: 16 pages, 3 figures, Accepted for publication in ApJ. For a full resolution version of Fig 1, see http://www.physics.mcgill.ca/~vkaspi/G11.2-0.3/f1.ep

A qualitative study of independent fast food vendors near secondary schools in disadvantaged Scottish neighbourhoods

Background: Preventing and reducing childhood and adolescent obesity is a growing priority in many countries. Recent UK data suggest that children in more deprived areas have higher rates of obesity and poorer diet quality than those in less deprived areas. As adolescents spend a large proportion of time in school, interventions to improve the food environment in and around schools are being considered. Nutrient standards for school meals are mandatory in the UK, but many secondary pupils purchase foods outside schools at break or lunchtime that may not meet these standards. Methods: Qualitative interviews were conducted with fast food shop managers to explore barriers to offering healthier menu options. Recruitment targeted independently-owned shops near secondary schools (pupils aged c.12-17) in low-income areas of three Scottish cities. Ten interviews were completed, recorded, and transcribed for analysis. An inductive qualitative approach was used to analyse the data in NVivo 10. Results: Five themes emerged from the data: pride in what is sold; individual autonomy and responsibility; customer demand; profit margin; and neighbourhood context. Interviewees consistently expressed pride in the foods they sold, most of which were homemade. They felt that healthy eating and general wellbeing are the responsibility of the individual and that offering what customers want to eat, not necessarily what they should eat, was the only way to stay in business. Most vendors felt they were struggling to maintain a profit, and that many aspects of the low-income neighbourhood context would make change difficult or impossible. Conclusions: Independent food shops in low-income areas face barriers to offering healthy food choices, and interventions and policies that target the food environment around schools should take the neighbourhood context into consideration

Differences in diversity and community composition of the shell microbiome of apparently healthy lobsters Homarus americanus across Atlantic Canada

Host-microbe dynamics are of increasing interest in marine research due to their role in host health and productivity. Changes in the shell microbiome of American lobsters have been associated with epizootic shell disease, a syndrome that is spreading northwards across the eastern U.S. and Canadian Atlantic coast. This study analyzed differences in alpha and beta diversity, as well as differentially abundant taxa, in the shell-associated bacterial community of apparently healthy lobsters from four lobster fishing areas (LFAs) in Atlantic Canada. Over 180 lobsters from New Brunswick, Nova Scotia and Prince Edward Island (PEI) were sampled during seven sampling events over four sampling months. The bacterial community was identified using novel PacBio long-read sequencing, while alpha and beta diversity parameters were analyzed using linear regression models and weighted UniFrac distances. The bacterial richness, diversity and evenness differed by sampling location, sampling month, and molt stage, but not by lobster sex or size, nor sampling depth. Similarly, based on LFA, sampling month, year and lobster molt stage, the shell microbiome differed in microbial community composition with up to 34 out of 162 taxa differing significantly in abundance between sampling groups. This large-scale microbial survey suggests that the shell microbial diversity of apparently healthy lobsters is influenced by spatial and temporal factors such as geographic location, as well as the length of time the carapace is exposed to the surrounding seawater

Long-read sequencing reveals the shell microbiome of apparently healthy American lobsters Homarus americanus from Atlantic Canada

The shell microbial community of lobsters—a key factor in the development of epizootic shell disease (ESD)—is still insufficiently researched in Atlantic Canada and many knowledge gaps remain. This study aimed to establish a baseline description and analysis of the shell microbiome of apparently healthy lobsters from four locations in the region. More than 180 lobster shell swab samples were collected from New Brunswick, Nova Scotia and Prince Edward Island (PEI). PacBio long-read 16S rDNA sequencing and bioinformatic analyses in QIIME2 identified the shell-associated bacteria. The shell microbiome of healthy lobsters consisted mainly of the bacterial classes Gammaproteobacteria, Saprospiria, Verrucomicrobiae, Alphaproteobacteria, Flavobacteriia, Acidimicrobiia and Planctomycetia. The microbial composition differed regionally and seasonally, with some classes showing decreased or increased relative abundances in the PEI samples as well as in the winter and spring samples in Nova Scotia. The core shell microbiome included potentially pathogenic as well as beneficial bacterial taxa, of which some were present only in certain regions. Bacterial taxa that have previously been associated with ESD were present on healthy lobsters in Atlantic Canada, but their frequency differed by location, sampling time, and moult stage. This study indicated that geographical and seasonal factors influenced the shell microbiome of apparently healthy lobsters more than host factors such as sex, size, and moult stage. Our results provide valuable reference microbial data from lobsters in a disease-free state