Performance of Portuguese laboratories in Labquality/PNAEQ EQA schemes for N. gonorrhoeae and C. trachomatis nucleic acid detection

The National External Quality Assessment Program (PNAEQ) includes the National Health Institute Dr. Ricardo Jorge (INSA, IP), which is legally responsible for the promotion, organization and coordination of External Quality Assessment Laboratory programs. PNAEQ has been collaborating with the Finnish peer Labquality, since 2000. In 2013 a Consortium between the two entities was signed, seeking closer working relationships, and the promotion of research and development in the area of external quality assessment. The participation of laboratories in interlaboratory EQA schemes not only facilitates diagnosis, therapeutic monitorization, and quality assessment and guidance, but it also improves performance and increases the laboratory quality level, which will directly benefit the patient. Proficiency testing programs play a key role in the evaluation of clinical laboratories and of manufactured tests but, in the case of molecular biology testing, it is yet complicated to evaluate EQAS programs. The Chlamydia trachomatis and Neisseria gonorrhoeae nucleic acid detection EQA schemes were chosen for the evaluation of the performance of the Portuguese laboratories in the field of molecular biology. C. trachomatis and N. gonorrhoeae are responsible for urogenital infections causing cervicitis in women and urethritis in both men and women. Infections are mainly asymptomatic (~40% of men and ~70% of women for C. trachomatis, and ~10% of men and ~60% of women for N. gonorrhoeae). Therefore, most cases remain undetected and untreated, and can progress to serious complications, especially in women, such as pelvic inflammatory disease, tubal infertility and ectopic pregnancy, justifying the need for using very sensitive molecular biology methods for their screening and diagnosis

The GeoClaw software for depth-averaged flows with adaptive refinement

Many geophysical flow or wave propagation problems can be modeled with two-dimensional depth-averaged equations, of which the shallow water equations are the simplest example. We describe the GeoClaw software that has been designed to solve problems of this nature, consisting of open source Fortran programs together with Python tools for the user interface and flow visualization. This software uses high-resolution shock-capturing finite volume methods on logically rectangular grids, including latitude--longitude grids on the sphere. Dry states are handled automatically to model inundation. The code incorporates adaptive mesh refinement to allow the efficient solution of large-scale geophysical problems. Examples are given illustrating its use for modeling tsunamis, dam break problems, and storm surge. Documentation and download information is available at www.clawpack.org/geoclawComment: 18 pages, 11 figures, Animations and source code for some examples at http://www.clawpack.org/links/awr10 Significantly modified from original posting to incorporate suggestions of referee

Numerical modeling of two-phase gravitational granular flows with bottom topography

(A. Mangeney), [email protected] (J.-P. Vilotte). Summary. We study a depth-averaged model of gravity-driven mixtures of solid grains and fluid moving over variable basal surface. The particular application we are interested in is the numerical description of geophysical flows such as avalanches and debris flows, which typically contain both solid material and interstitial fluid. The depth-averaged mass and momentum equations for the solid and fluid components form a non-conservative system, where non-conservative terms involving the derivatives of the unknowns couple together the sets of equations of the two phases. The system can be shown to be hyperbolic at least when the difference of velocities of the two constituents is sufficiently small. We numerically solve the model equations in one dimension by a finite volume scheme based on a Roe-type Riemann solver. Well-balancing of topography source terms is obtained via a technique that includes these contributions into the wave structure of the Riemann solution

Changing Immunochemistry Platforms : Thyroid Function Test Comparison and Reference Intervals Based on Clinical Needs

Background: Diagnosis of thyroid dysfunction relies on thyroid stimulating hormone (TSH), free thyroxine (FT4), and free tri-iodothyronine (FT3) tests against valid reference intervals (Rls). We changed the immunoassay platform from Abbott Architect to Siemens Atellica and aimed to establish Atellica Rls based on laboratory information system (LIS) patient data. Methods: Atellica thyroid hormone immunoassays were verified against those of Architect. Real-life patient results were retrieved from LIS. A single result per patient dataset was used to establish the Rls by the indirect method. Results: Atellica and Architect assays correlated well but Atellica showed a positive bias between 13% and 53%, the largest for FT4. Variations of the Atellica assays were Conclusions: We verified thyroid hormone Rls for Atellica by the indirect method for the first time. Our model proved reliable for selecting results of presumably healthy individuals from LIS data. Critical review of the Rls with local endocrinologists is essential.Peer reviewe

Handling of hemolyzed serum samples in clinical chemistry laboratories: The Nordic hemolysis project

Under embargo until: 2020-07-09Hemolysis of blood samples is a pre-analytical challenge that often leads to sample rejection in medical laboratories [1]. Hemolysis occurs when blood cells break down and the intracellular contents leak into the surrounding fluid [2]. When hemolyzed blood samples are analyzed in medical laboratories, the content released from the blood cells can interfere with the measurement procedure, leading to erroneous results that may not reflect the patient’s clinical condition. How, and to what extent, hemolysis may affect test results depends on the analyte and the measurement method used [1]. Interference studies are performed to establish how much the various analytes, when measured by different methods, will be affected by hemolysis [3]. Based on the results, instrument-specific cut-off points are determined to prevent hemolysis from significantly affecting the clinical interpretation of laboratory results. Most instruments used in medical laboratories today can measure cell-free hemoglobin (Hb) in individual blood samples and transfer the result to the laboratory information system (LIS). These Hb results may be combined with predefined Hb cut-off points, enabling the laboratories to automatically reject or comment upon test results significantly affected by hemolysis [4]. Cut-off points for rejection of samples are commonly recommended by the manufacturers of in vitro diagnostic (IVD) analytical systems. The Clinical and Laboratory Standards Institute (CLSI) recommends that the laboratories verify the intended usefulness, strengths and limitations of manufacturer-derived cut-off points before they are implemented [5]. This is time and resource consuming for the laboratory, and may be difficult as manufacturers’ package inserts often lack information about experiment design and how the cut-off points were defined [6], [7], [8]. Consequently, many laboratories use the manufacturers’ cut-off points for hemolysis, without further verification studies [8]. The Nordic cooperation of External Quality Assurance (EQA) organizers, EQAnord, performed a large interference study in 2002 to obtain data on the effect of hemolysis on analytical performance on different clinical chemistry instruments [9]. The aims of the current study were (1) to obtain updated information about how hemolysis affects clinical chemistry test results on different instrument platforms, and (2) to obtain data on how test results from hemolyzed samples are reported in medical biochemistry hospital laboratories in the Nordic countries.publishedVersio

An acoustic-transport splitting method for the barotropic Baer-Nunziato two-phase flow model*

This work focuses on the numerical approximation of the barotropic Baer-Nunziato two-phase flow model. We propose a numerical scheme that relies on an operator splitting method corresponding to a separate treatment of the acoustic and the material transport phenomena. In the subsonic case, this also corresponds to a separate treatment of the fast and the slow propagation phenomena. This approach follows the lines of the implicit-explicit schemes developed in [8]. The operator splitting enable the use of time steps that are no longer constrained by the sound velocity thanks to an implicit treatment of the acoustic waves, while maintaining accuracy in the subsonic regime thanks to an explicit treatment of the material waves. In the present setting, a particular attention will be also given to the discretization of the non-conservative terms that figure in the two-phase model. We prove that the proposed numerical strategy is positivity preserving for the volume fractions and the partial masses. The scheme is tested against several one-dimensional test cases including flows featuring vanishing phases

Aggregated data from the same laboratories participating in two glucose external quality assessment schemes show that commutability and transfers of values to control materials are decisive for the biases found

Objectives We report the results of glucose measurements performed during one year by the same measurement procedures (MPs) in 58 Norwegian hospital laboratories using control materials provided by external quality assessment (EQA) schemes from two different providers. The providers used materials with presumed vs. verified commutability and transfers of values using reference material vs. using a highest-order reference MP. Methods Data from six Labquality and three Noklus glucose EQA surveys were aggregated for each MP (Abbott Alinity, Abbott Architect, Roche Cobas, and Siemens Advia) in each scheme. For each EQA result, percent difference from target value (% bias) was calculated. Median percent bias for each MP per scheme was then calculated. Results The median % biases observed for each MP in the Labquality scheme were significantly larger than those in the Noklus scheme, which uses verified commutable control materials and highest-order reference MP target values. The difference ranged from 1.2 (Roche Cobas, 2.9 vs. 1.7 %) to 4.4 percentage points (Siemens Advia, 3.2 % vs. −1.2 %). The order of bias size for the various MPs was different in the two schemes. In contrast to the Labquality scheme, the median % biases observed in the Noklus scheme for Abbott Alinity (−0.1 %), Abbott Architect (−0.5 %), and Siemens Advia (−1.2 %) were not significantly different from target value (p>0.756). Conclusions This study underlines the importance of using verified commutable EQA materials and target values traceable to reference MPs in EQA schemes designed for assessment of metrological traceability of laboratory results.publishedVersio

Efficient simulation of chromatographic separation processes

This work presents the development and testing of an efficient, high resolution algorithm developed for the solution of equilibrium and non-equilibrium chromatographic problems as a means of simultaneously producing high fidelity predictions with a minimal increase in computational cost. The method involves the coupling of a high-order WENO scheme, adapted for use on non-uniform grids, with a piecewise adaptive grid (PAG) method to reduce runtime while accurately resolving the sharp gradients observed in the processes under investigation. Application of the method to a series of benchmark chromatographic test cases, within which an increasing number of components are included over short and long spatial domains and containing shocks, shows that the method is able to accurately resolve the discontinuities and that the use of the PAG method results in a reduction in the CPU runtime of up to 90%, without degradation of the solution, relative to an equivalent uniform grid