Interface Management for SKA Telescope Manager

The Square Kilometre Array (SKA) project is currently in the Pre-construction Phase. During this phase, the telescope subsystems are being designed. The Telescope Manager (TM) is a supervisory control and monitoring subsystem in each of the two radio telescopes of the SKA (SKA1-Low and SKA1-Mid). The TM interfaces with a number of diverse telescope subsystems. Interaction between TM and these subsystems is a major source of requirements for the TM. Careful management of TM external interfaces is therefore important. This discussion is a case study of TM interface management. Firstly, how system architectural design aspects like separation of concerns in the control hierarchy reduce telescope complexity with regards to interfaces is discussed. Secondly, the standardisation approach for monitoring and control interfaces to facilitate early elicitation of interface requirements for the TM, and to manage the diversity of interfacing subsystems is discussed. Thirdly, the relations between interface definition and requirements analysis activities, using SysML representations as an example is discussed

Testing Target Independence of the `Proton Spin' Effect in Semi-Inclusive Deep Inelastic Scattering

A natural consequence of the composite operator propagator-vertex description of deep inelastic scattering developed by the authors is that the anomalous suppression observed in the flavour singlet contribution to the first moment of the polarised proton structure function $g_1^p$ (the `proton spin' problem) is not a special property of the proton structure but is a target independent effect which can be related to an anomalous suppression in the QCD topological susceptibility. In this paper, it is shown how this target independent mechanism can be tested in semi-inclusive deep inelastic scattering in which a pion or D meson carrying a large target energy fraction $z$ is detected in the target fragmentation region.Comment: 23 pages, TeX, includes 11 ps figure

A Test of Target Independence of the `Proton Spin' Effect in Semi-Inclusive Deep Inelastic Scattering

The target-independent suppression mechanism proposed as an explanation of the EMC-SMC `proton spin' effect is reviewed and compared to current experimental data. According to this proposal, the anomalous suppression observed in the first moment of the polarised proton structure function g_1^p is not a special property of the proton structure, but reflects an anomalously small value of the first moment of the QCD topological susceptibility. It is shown how this mechanism can be tested in semi-inclusive DIS processes in which a pion or D meson carrying a large target energy fraction z is detected in the target fragmentation region

Muscle MRI in Patients with Oculopharyngeal Muscular Dystrophy: A Longitudinal Study

Background and ObjectivesOculopharyngeal muscular dystrophy (OPMD) is a rare progressive neuromuscular disease. MRI is one of the techniques that is used in neuromuscular disorders to evaluate muscle alterations. The aim of this study was to describe the pattern of fatty infiltration of orofacial and leg muscles using quantitative muscle MRI in a large national cohort and to determine whether MRI can be used as an imaging biomarker of disease progression in OPMD.MethodsPatients with OPMD (18 years or older) were invited from the national neuromuscular database or by their treating physicians and were examined twice with an interval of 20 months, with quantitative MRI of orofacial and leg muscles to assess fatty infiltration which were compared with clinical measures.ResultsIn 43 patients with genetically confirmed OPMD, the muscles that were affected most severely were the tongue (mean fat fraction: 37.0%, SD 16.6), adductor magnus (31.9%; 27.1), and soleus (27.9%; 21.5) muscles. The rectus femoris and tibialis anterior muscles were least severely affected (mean fat fractions: 6.8%; SD 4.7, 7.5%; 5.9). Eleven of 14 significant correlations were found between fat fraction and a clinical task in the corresponding muscles (r = -0.312 to -0.769, CI = -0.874 to -0.005). At follow-up, fat fractions had increased significantly in 17 of the 26 muscles: mean 1.7% in the upper leg muscles (CI = 0.8-2.4), 1.7% (1.0-2.3) in the lower leg muscles, and 1.9% (0.6-3.3) in the orofacial muscles (p < 0.05). The largest increase was seen for the soleus (3.8%, CI = 2.5-5.1). Correlations were found between disease duration and repeat length vs increased fat fraction in 7 leg muscles (r = 0.323 to -0.412, p < 0.05).DiscussionAccording to quantitative muscle MRI, the tongue, adductor magnus and soleus show the largest fat infiltration levels in patients with OPMD. Fat fractions increased in several orofacial and leg muscles over 20 months, with the largest fat fraction increase seen in the soleus. This study supports that this technique is sensitive enough to show worsening in fat fractions of orofacial and leg muscles and therefore a responsive biomarker for future clinical trials

High quality of SARS-CoV-2 molecular diagnostics in a diverse laboratory landscape through supported benchmark testing and External Quality Assessment

A two-step strategy combining assisted benchmark testing (entry controls) and External Quality Assessments (EQAs) with blinded simulated clinical specimens to enhance and maintain the quality of nucleic acid amplification testing was developed. This strategy was successfully applied to 71 diagnostic laboratories in The Netherlands when upscaling the national diagnostic capacity during the SARS-CoV-2 pandemic. The availability of benchmark testing in combination with advice for improvement substantially enhanced the quality of the laboratory testing procedures for SARS-CoV-2 detection. The three subsequent EQA rounds demonstrated high quality testing with regard to specificity (99.6% correctly identified) and sensitivity (93.3% correctly identified). Even with the implementation of novel assays, changing workflows using diverse equipment and a high degree of assay heterogeneity, the overall high quality was maintained using this two-step strategy. We show that in contrast to the limited value of Cq value for absolute proxies of viral load, these Cq values can, in combination with metadata on strategies and techniques, provide valuable information for laboratories to improve their procedures. In conclusion, our two-step strategy (preparation phase followed by a series of EQAs) is a rapid and flexible system capable of scaling, improving, and maintaining high quality diagnostics even in a rapidly evolving (e.g. pandemic) situation.</p

High quality of SARS-CoV-2 molecular diagnostics in a diverse laboratory landscape through supported benchmark testing and External Quality Assessment

A two-step strategy combining assisted benchmark testing (entry controls) and External Quality Assessments (EQAs) with blinded simulated clinical specimens to enhance and maintain the quality of nucleic acid amplification testing was developed. This strategy was successfully applied to 71 diagnostic laboratories in The Netherlands when upscaling the national diagnostic capacity during the SARS-CoV-2 pandemic. The availability of benchmark testing in combination with advice for improvement substantially enhanced the quality of the laboratory testing procedures for SARS-CoV-2 detection. The three subsequent EQA rounds demonstrated high quality testing with regard to specificity (99.6% correctly identified) and sensitivity (93.3% correctly identified). Even with the implementation of novel assays, changing workflows using diverse equipment and a high degree of assay heterogeneity, the overall high quality was maintained using this two-step strategy. We show that in contrast to the limited value of Cq value for absolute proxies of viral load, these Cq values can, in combination with metadata on strategies and techniques, provide valuable information for laboratories to improve their procedures. In conclusion, our two-step strategy (preparation phase followed by a series of EQAs) is a rapid and flexible system capable of scaling, improving, and maintaining high quality diagnostics even in a rapidly evolving (e.g. pandemic) situation.</p

Treatment-Free Remission Outcomes in a <i>BCR::ABL1</i> Digital PCR Selected Clinical Cohort of CML Patients

Approximately 40%–60% of patients reaching a stable deep molecular response during TKI treatment will maintain a state of remission after TKI discontinuation, denoted as treatment-free remission (TFR). Depth of molecular response assessed by BCR::ABL1 digital PCR prior to TKI discontinuation has demonstrated its significance as a reliable predictive parameter for TFR. A clinically applicable prediction cutoff of 0.0023%IS has been established and externally validated. In this study, BCR::ABL1 digital PCR, as most sensitive and stable assay of its kind, was investigated as a TFR prediction tool in the Netherlands, and evaluated for its predictive value to stop TKI treatment below the aforementioned cutoff. The primary endpoint of molecular recurrence (MolR, BCR::ABL1 &gt; 0.1%IS) at 12 months was prospectively assessed. Overall, 67 discontinued patients below the set BCR::ABL1 digital PCR cutoff were included. The overall MolR probability was 50% (95% CI, 36%–62%). In 38 patients treated for more than 6 years as commonly recommended as desirable treatment duration before TFR attempt, the MolR probability dropped to 36% (95% CI, 18%–50%). Patients attempting an early TKI discontinuation (treated for less than 6 years) had a high MolR probability of 76% (95% CI, 65%–89%). BCR::ABL1 digital PCR was successfully used in Dutch clinical practice. Our study indicates that in patients with a low BCR::ABL1 digital PCR result, a total TKI treatment duration of six or more years remains associated with a lower MolR rate and should generally be pursued. In patients treated for more than 6 years, BCR::ABL1 digital PCR was capable to identify stop candidates with a higher probability of TFR success.</p

Developing a predictive modelling capacity for a climate change-vulnerable blanket bog habitat: Assessing 1961-1990 baseline relationships

Aim: Understanding the spatial distribution of high priority habitats and developing predictive models using climate and environmental variables to replicate these distributions are desirable conservation goals. The aim of this study was to model and elucidate the contributions of climate and topography to the distribution of a priority blanket bog habitat in Ireland, and to examine how this might inform the development of a climate change predictive capacity for peat-lands in Ireland. Methods: Ten climatic and two topographic variables were recorded for grid cells with a spatial resolution of 1010 km, covering 87% of the mainland land surface of Ireland. Presence-absence data were matched to these variables and generalised linear models (GLMs) fitted to identify the main climatic and terrain predictor variables for occurrence of the habitat. Candidate predictor variables were screened for collinearity, and the accuracy of the final fitted GLM was evaluated using fourfold cross-validation based on the area under the curve (AUC) derived from a receiver operating characteristic (ROC) plot. The GLM predicted habitat occurrence probability maps were mapped against the actual distributions using GIS techniques. Results: Despite the apparent parsimony of the initial GLM using only climatic variables, further testing indicated collinearity among temperature and precipitation variables for example. Subsequent elimination of the collinear variables and inclusion of elevation data produced an excellent performance based on the AUC scores of the final GLM. Mean annual temperature and total mean annual precipitation in combination with elevation range were the most powerful explanatory variable group among those explored for the presence of blanket bog habitat. Main conclusions: The results confirm that this habitat distribution in general can be modelled well using the non-collinear climatic and terrain variables tested at the grid resolution used. Mapping the GLM-predicted distribution to the observed distribution produced useful results in replicating the projected occurrence of the habitat distribution over an extensive area. The methods developed will usefully inform future climate change predictive modelling for Irelan

Rapid growth rates of syndepositional marine aragonite cements in steep marginal slope deposits, Bahamas and Belize

Growth rates of marine botryoidal aragonite cements from steep (35-45[degree]) marginal slope deposits in the Bahamas and Belize have been determined by accelerator mass spectrometer radiocarbon dating of samples taken at the base and top of individual botryoids. The pore-filling cements, which range from approximately 11,000-13,000 years old, grew at average rates of 8-10mm/100 yr with maximum rates > 25mm/100 yr. Radiocarbon dating of coexisting skeletal components indicates that cementation was syndepositional. Microsampling transects across individual botryoids for stable-isotope analyses show little variation in [delta][sup 31]C and [delta][sup 18]O, supporting the conclusion that cementation was extremely rapid. Although the cements show a progressive depletion in isotopic composition of approximately 1[per thousand]([delta][sup 13]C) and 2[per thousand]([delta][sup 18]O) from 13 ka to 11 ka, the average variation ([delta][sub 1]) within individual pore-filling cements, ranging in size 2 mm to 32 mm (bottom to top), was 0.11[per thousand]([delta][sup 13]C) and 0.14[per thousand]([delta][sup 18]O). Results of this study provide the first quantitative data on growth rates of marine carbonate cements in a marginal slope environment. The data indicate that marginal slope deposits may lithify within several tens of years and suggest that geologically instantaneous cementation may be critical in stabilizing steep carbonate slope deposits at or above angles of repose