MetaboLab - advanced NMR data processing and analysis for metabolomics

Background\ud Despite wide-spread use of Nuclear Magnetic Resonance (NMR) in metabolomics for the analysis of biological samples there is a lack of graphically driven, publicly available software to process large one and two-dimensional NMR data sets for statistical analysis.\ud \ud Results\ud Here we present MetaboLab, a MATLAB based software package that facilitates NMR data processing by providing automated algorithms for processing series of spectra in a reproducible fashion. A graphical user interface provides easy access to all steps of data processing via a script builder to generate MATLAB scripts, providing an option to alter code manually. The analysis of two-dimensional spectra (1H,13C-HSQC spectra) is facilitated by the use of a spectral library derived from publicly available databases which can be extended readily. The software allows to display specific metabolites in small regions of interest where signals can be picked. To facilitate the analysis of series of two-dimensional spectra, different spectra can be overlaid and assignments can be transferred between spectra. The software includes mechanisms to account for overlapping signals by highlighting neighboring and ambiguous assignments.\ud \ud Conclusions\ud The MetaboLab software is an integrated software package for NMR data processing and analysis, closely linked to the previously developed NMRLab software. It includes tools for batch processing and gives access to a wealth of algorithms available in the MATLAB framework. Algorithms within MetaboLab help to optimize the flow of metabolomics data preparation for statistical analysis. The combination of an intuitive graphical user interface along with advanced data processing algorithms facilitates the use of MetaboLab in a broader metabolomics context.\ud \u

The International Mass Loading Service

The International Mass Loading Service computes four loadings: a) atmospheric pressure loading; b) land water storage loading; c) oceanic tidal loading; and d) non-tidal oceanic loading. The service provides to users the mass loading time series in three forms: 1) pre-computed time series for a list of 849 space geodesy stations; 2) pre-computed time series on the global 1deg x 1deg grid; and 3) on-demand Internet service for a list of stations and a time range specified by the user. The loading displacements are provided for the time period from 1979.01.01 through present, updated on an hourly basis, and have latencies 8-20 hours.Comment: 8 pages, 3 figures, to appear in the Proceedings of the Reference Frames for Applications in Geosciences Simposium, held in Luxemboug in October 201

The Availability and Consistency of Dengue Surveillance Data Provided Online by the World Health Organization

Background: The use of high quality disease surveillance data has become increasingly important for public health action against new threats. In response, countries have developed a wide range of disease surveillance systems enabled by technological advancements. The heterogeneity and complexity of country data systems have caused a growing need for international organizations such as the World Health Organization (WHO) to coordinate the standardization, integration, and dissemination of country disease data at the global level for research and policy. The availability and consistency of currently available disease surveillance data at the global level are unclear. We investigated this for dengue surveillance data provided online by the WHO. Methods and Findings: We extracted all dengue surveillance data provided online by WHO Headquarters and Regional Offices (RO’s). We assessed the availability and consistency of these data by comparing indicators within and between sources. We also assessed the consistency of dengue data provided online by two example countries (Brazil and Indonesia). Data were available from WHO for 100 countries since 1955 representing a total of 23 million dengue cases and 82 thousand deaths ever reported to WHO. The availability of data on DengueNet and some RO’s declined dramatically after 2005. Consistency was lacking between sources (84% across all indicators representing a discrepancy of almost half a million cases). Within sources, data at high spatial resolution were often incomplete. Conclusions: The decline of publicly available, integrated dengue surveillance data at the global level will limit opportunities for research, policy, and advocacy. A new financial and operational framework will be necessary for innovation and for the continued availability of integrated country disease data at the global level

Trap selectivity and the effects of altering gear design in the South African rock lobster Jasus lalandii commercial fishery

The current trap fishery for the West Coast rock lobster Jasus lalandii in South African waters results in the capture, sorting and release of large numbers of undersized animals. Once removed from the water, they are vulnerable to damage from numerous sources. Even sub-lethal injury may result in a considerable reduction to individual productivity through decreased growth or reproductive potential. Given that the J. lalandii resource is heavily depleted, such wastage may have severe repercussions for the sustainability of the fishery. In an attempt to reduce these losses, 20% of the fishing gear used by the rock lobster industry has been modified to include grids designed to allow undersized rock lobsters (mainly females) to escape the traps before they are hauled. The efficiency of this gear (and two alternatives) was assessed by comparison with standard commercial gear over a range of fishing grounds. Results indicated that, in comparison to standard commercial traps, none of the alternative trap designs would be beneficial to the fishery in the long term, provided that overnight sets remain the most common fishing method. SELECT models were used to evaluate the fishing properties of commercial and bottom-grid traps relative to those of control (fine-mesh) traps. The results indicated that, given the choice, a rock lobster would preferentially enter a commercial trap, followed by a control trap, with bottom-grid traps being the least attractive. This suggests some level of saturation of control traps, a possibility that is of particular concern because the control trap design is used in a fishery-independent monitoring survey.Keywords: escape gaps, Jasus lalandii, rock lobster, SELECT models, trap selectivityAfrican Journal of Marine Science 2002, 24: 37–4

Changes to regulations and the gear used in the South African commercial fishery for Jasus lalandii

Alterations to the operational fishing gear used in the South African west coast rock lobster Jasus lalandii fishery and their resultant impacts are investigated. The most important developments have been: (i) a change during the 1960s from hand-hauled hoopnets to winch-hauled traps, with a concomitant modification of vessels; (ii) the introduction of deck-grid sorters in 1975; (iii) an increase during 1984 of minimum mesh aperture from 62 to 100 mm (stretched), with a concomitant decrease in the length of the trap codend; (iv) a decrease in the minimum legal size during the early1990s; and (v) the introduction of bottom-grid traps in 1994. Most of these alterations have been driven by a tradeoff between the need for greater operational efficiency and concerns surrounding the issue of how best to deal with the problem of catching and releasing specimens smaller than the minimum legal size.Keywords: fishing gear, fishing regulations, Jasus lalandii, rock lobsterAfrican Journal of Marine Science 2002, 24: 365–36

Comparing the effectiveness of small-particle versus large-particle inhaled corticosteroid in COPD

Dirkje S Postma,1 Nicolas Roche,2 Gene Colice,3 Elliot Israel,4 Richard J Martin,5 Willem MC van Aalderen,6 Jonathan Grigg,7 Anne Burden,8 Elizabeth V Hillyer,8 Julie von Ziegenweidt,8 Gokul Gopalan,9 David Price8,10 1University of Groningen, Department of Pulmonary Medicine and Tuberculosis, University Medical Center Groningen, Groningen, the Netherlands; 2Respiratory and Intensive Care Medicine, Cochin Hospital Group, APHP, Paris-Descartes University (EA2511), Paris, France; 3Pulmonary, Critical Care and Respiratory Services, Washington Hospital Center and George Washington University School of Medicine, Washington DC, USA; 4Pulmonary and Critical Care Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; 5Department of Medicine, National Jewish Health, Denver, CO, USA; 6Dept of Pediatric Respiratory Medicine and Allergy, Emma Children's Hospital AMC, Amsterdam, the Netherlands; 7Blizard Institute, Queen Mary University London, London, UK; 8Research in Real Life, Ltd, Cambridge, UK; 9Respiratory, Global Scientific Affairs, Teva Pharmaceuticals, Frazer, PA, USA; 10Academic Primary Care, Division of Applied Health Sciences, University of Aberdeen, Aberdeen, UK Purpose: Small airway changes and dysfunction contribute importantly to airway obstruction in chronic obstructive pulmonary disease (COPD), which is currently treated with inhaled corticosteroids (ICS) and long-acting bronchodilators at Global initiative for Obstructive Lung Disease (GOLD) grades 2–4. This retrospective matched cohort analysis compared effectiveness of a representative small-particle ICS (extrafine beclomethasone) and larger-particle ICS (fluticasone) in primary care patients with COPD. Patients and methods: Smokers and ex-smokers with COPD ≥40 years old initiating or stepping-up their dose of extrafine beclomethasone or fluticasone were matched 1:1 for demographic characteristics, index prescription year, concomitant therapies, and disease severity during 1 baseline year. During 2 subsequent years, we evaluated treatment change and COPD exacerbations, defined as emergency care/hospitalization for COPD, acute oral corticosteroids, or antibiotics for lower respiratory tract infection. Results: Mean patient age was 67 years, 57%–60% being male. For both initiation (n=334:334) and step-up (n=189:189) patients, exacerbation rates were comparable between extrafine beclomethasone and fluticasone cohorts during the 2 year outcome period. Odds of treatment stability (no exacerbation or treatment change) were significantly greater for patients initiating extrafine beclomethasone compared with fluticasone (adjusted odds ratio 2.50; 95% confidence interval, 1.32–4.73). Median ICS dose exposure during 2 outcome years was significantly lower (P<0.001) for extrafine beclomethasone than fluticasone cohorts (315 µg/day versus 436 µg/day for initiation, 438 µg/day versus 534 µg/day for step-up patients). Conclusion: We observed that small-particle ICS at significantly lower doses had comparable effects on exacerbation rates as larger-particle ICS at higher doses, whereas initiation of small-particle ICS was associated with better odds of treatment stability during 2-years' follow-up. Keywords: COPD exacerbation, extrafine particle, matched cohort analysis, real life, small airway

Evaluating 35 Methods to Generate Structural Connectomes Using Pairwise Classification

There is no consensus on how to construct structural brain networks from diffusion MRI. How variations in pre-processing steps affect network reliability and its ability to distinguish subjects remains opaque. In this work, we address this issue by comparing 35 structural connectome-building pipelines. We vary diffusion reconstruction models, tractography algorithms and parcellations. Next, we classify structural connectome pairs as either belonging to the same individual or not. Connectome weights and eight topological derivative measures form our feature set. For experiments, we use three test-retest datasets from the Consortium for Reliability and Reproducibility (CoRR) comprised of a total of 105 individuals. We also compare pairwise classification results to a commonly used parametric test-retest measure, Intraclass Correlation Coefficient (ICC).Comment: Accepted for MICCAI 2017, 8 pages, 3 figure

Lower bounds for several online variants of bin packing

We consider several previously studied online variants of bin packing and prove new and improved lower bounds on the asymptotic competitive ratios for them. For that, we use a method of fully adaptive constructions. In particular, we improve the lower bound for the asymptotic competitive ratio of online square packing significantly, raising it from roughly 1.68 to above 1.75.Comment: WAOA 201

Structural subnetwork evolution across the life-span: rich-club, feeder, seeder

The impact of developmental and aging processes on brain connectivity and the connectome has been widely studied. Network theoretical measures and certain topological principles are computed from the entire brain, however there is a need to separate and understand the underlying subnetworks which contribute towards these observed holistic connectomic alterations. One organizational principle is the rich-club - a core subnetwork of brain regions that are strongly connected, forming a high-cost, high-capacity backbone that is critical for effective communication in the network. Investigations primarily focus on its alterations with disease and age. Here, we present a systematic analysis of not only the rich-club, but also other subnetworks derived from this backbone - namely feeder and seeder subnetworks. Our analysis is applied to structural connectomes in a normal cohort from a large, publicly available lifespan study. We demonstrate changes in rich-club membership with age alongside a shift in importance from 'peripheral' seeder to feeder subnetworks. Our results show a refinement within the rich-club structure (increase in transitivity and betweenness centrality), as well as increased efficiency in the feeder subnetwork and decreased measures of network integration and segregation in the seeder subnetwork. These results demonstrate the different developmental patterns when analyzing the connectome stratified according to its rich-club and the potential of utilizing this subnetwork analysis to reveal the evolution of brain architectural alterations across the life-span