Management options for restoring estuarine dynamics and implications for ecosystems: a quantitative approach for the Southwest Delta in the Netherlands

The Delta Works, a series of dams and barriers constructed in the 1960's–1980's changed the estuarine landscape of the Rhine-Meuse-Scheldt delta (SW Netherlands) into more stagnant and disengaged freshwater, brackish water or saltwater lakes. The remaining tidal systems were adapted by building a storm surge barrier in the Oosterschelde and dike reinforcement works along the Westerschelde. The Delta Works brought protection against flooding, but at the same time resulted in environmental and socio-economic problems, such as degradation of ecological quality and ecosystem functioning, disruption of fish migration routes, water and sediment quality problems.In this study we explore in an integrated, quantitative way the consequences of a number of management options for the Southwest Delta and their implications for the occurrence and distribution of aquatic and estuarine habitats, considering the mutual coherence between the water basins. Five scenarios were evaluated using a 1D hydraulic, water quality and primary production numerical model and GIS habitat mapping. Scenarios vary from small-scale interventions, such as changes in day-to-day management of hydraulic infrastructures or creation of small inlets in dams, feasible in the short term, to restoration of an open delta by removing dams and barriers, as a long term potential. We evaluate the outcomes in relation to the restoration of estuarine dynamics, as this is in policy plans proposed as a generic solution for the current ecological and environmental problems. Net water flow rates show more complex patterns when connectivity between water basins is increased and when sluice management is less strict. Estuarine transition zones and fish migration routes are partly restored, but only fully develop when basins are in open connection with each other. Area of intertidal habitats, tidal flats and tidal marshes, increases in each scenario, ranging between 7 and 83%, 1–56%, and 8–100% respectively, depending on scenario. Large scale infrastructural adaptations are needed to restore estuarine dynamics at large scale.The use of a 1D numerical model allowed to quantify the effect of different management measures for all water basins simultaneously, but also has its limitations. The model does not resolve more complex processes such as vertical mixing and morphodynamic changes. This requires expert judgment and more detailed 3D modelling

Inter- and intrafractional 4D dose accumulation for evaluating ΔNTCP robustness in lung cancer.

BACKGROUND AND PURPOSE Model-based selection of proton therapy patients relies on a predefined reduction in normal tissue complication probability (NTCP) with respect to photon therapy. The decision is necessarily made based on the treatment plan, but NTCP can be affected when the delivered treatment deviates from the plan due to delivery inaccuracies. Especially for proton therapy of lung cancer, this can be important because of tissue density changes and, with pencil beam scanning, the interplay effect between the proton beam and breathing motion. MATERIALS AND METHODS In this work, we verified whether the expected benefit of proton therapy is retained despite delivery inaccuracies by reconstructing the delivered treatment using log-file based dose reconstruction and inter- and intrafractional accumulation. Additionally, the importance of two uncertain parameters for treatment reconstruction, namely deformable image registration (DIR) algorithm and α/β ratio, was assessed. RESULTS The expected benefit or proton therapy was confirmed in 97% of all studied cases, despite regular differences up to 2 percent point (p.p.) NTCP between the delivered and planned treatments. The choice of DIR algorithm affected NTCP up to 1.6 p.p., an order of magnitude higher than the effect of α/β ratio. CONCLUSION For the patient population and treatment technique employed, the predicted clinical benefit for patients selected for proton therapy was confirmed for 97.0 % percent of all cases, although the NTCP based proton selection was subject to 2 p.p. variations due to delivery inaccuracies

IEA BESTEST Multi-Zone Non-Airflow In-Depth Diagnostic Cases: Preprint

This paper documents a set of in-depth diagnostic test cases for multi-zone heat transfer models that do not include the heat and mass transfer effects of airflow between zones. The multi-zone non-airflow test cases represent an extension to IEA BESTEST (Judkoff and Neymark 1995a)

International Energy Agency Building Energy Simulation Test and Diagnostic Method (IEA BESTEST) Multi-Zone Non-Airflow In-Depth Diagnostic Cases: MZ320 -- MZ360

This report documents a set of diagnostic test cases for multi-zone heat transfer models. The methodology combines empirical validation, analytical verification, and comparative analysis techniques

IEA BESTEST Multi-Zone Non-Airflow In-Depth Diagnostic Cases: Preprint

This paper documents a set of in-depth diagnostic test cases for multi-zone heat transfer models that do not include the heat and mass transfer effects of airflow between zones. The multi-zone non-airflow test cases represent an extension to IEA BESTEST (Judkoff and Neymark 1995a)

Multipoint genome-wide linkage scan for nonword repetition in a multigenerational family further supports chromosome 13q as a locus for verbal trait disorders

Verbal trait disorders encompass a wide range of conditions and are marked by deficits in five domains that impair a person’s ability to communicate: speech, language, reading, spelling, and writing. Nonword repetition is a robust endophenotype for verbal trait disorders that is sensitive to cognitive processes critical to verbal development, including auditory processing, phonological working memory, and motor planning and programming. In the present study, we present a six-generation extended pedigree with a history of verbal trait disorders. Using genome-wide multipoint variance component linkage analysis of nonword repetition, we identified a region spanning chromosome 13q14–q21 with LOD = 4.45 between 52 and 55 cM, spanning approximately 5.5 Mb on chromosome 13. This region overlaps with SLI3, a locus implicated in reading disability in families with a history of specific language impairment. Our study of a large multigenerational family with verbal trait disorders further implicates the SLI3 region in verbal trait disorders. Future studies will further refine the specific causal genetic factors in this locus on chromosome 13q that contribute to language traits

Towards the clinical implementation of intensity-modulated proton therapy for thoracic indications with moderate motion:Robust optimised plan evaluation by means of patient and machine specific information

PURPOSE: Compared to volumetric modulated arc therapy (VMAT), clinical benefits are anticipated when treating thoracic tumours with intensity-modulated proton therapy (IMPT). However, the current concern of plan robustness as a result of motion hampers its wide clinical implementation. To define an optimal protocol to treat lung and oesophageal cancers, we present a comprehensive evaluation of IMPT planning strategies, based on patient 4DCTs and machine log files. MATERIALS AND METHODS: For ten lung and ten oesophageal cancer patients, a planning 4DCT and weekly repeated 4DCTs were collected. For these twenty patients, the CTV volume and motion were assessed based on the 4DCTs. In addition to clinical VMAT plans, layered rescanned 3D and 4D robust optimised IMPT plans (IMPT_3D and IMPT_4D respectively) were generated, and approved clinically, for all patients. The IMPT plans were then delivered in dry runs at our proton facility to obtain log files, and subsequently evaluated through our 4D robustness evaluation method (4DREM). With this method, for each evaluated plan, fourteen 4D accumulated scenario doses were obtained, representing 14 possible fractionated treatment courses. RESULTS: From VMAT to IMPT_3D, nominal Dmean(lungs-GTV) decreased 2.75 ± 0.56 GyRBE and 3.76 ± 0.92 GyRBE over all lung and oesophageal cancer patients, respectively. A more pronounced reduction was verified for Dmean(heart): 5.38 ± 7.36 GyRBE (lung cases) and 9.51 ± 2.25 GyRBE (oesophagus cases). Target coverage robustness of IMPT_3D was sufficient for 18/20 patients. Averaged dose in critical structures over all 4DREM scenarios changed only slightly for both IMPT_3D and IMPT_4D. Relative to IMPT_3D, no gain in IMPT_4D was observed. CONCLUSION: The dosimetric superiority of IMPT over VMAT has been established. For most thoracic tumours, our IMPT_3D planning protocol showed to be robust and clinically suitable. Nevertheless, accurate patient positioning and adapting to anatomical variations over the course of treatment remain compulsory

Comparison of seven commercial RT-PCR diagnostic kits for COVID-19

The final months of 2019 witnessed the emergence of a novel coronavirus in the human population. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has since spread across the globe and is posing a major burden on society. Measures taken to reduce its spread critically depend on timely and accurate identification of virus-infected individuals by the most sensitive and specific method available, i.e. real-time reverse transcriptase PCR (RT-PCR). Many commercial kits have recently become available, but their performance has not yet been independently assessed. The aim of this study was to compare basic analytical and clinical performance of selected RT-PCR kits from seven different manufacturers (Altona Diagnostics, BGI, CerTest Biotec, KH Medical, PrimerDesign, R-Biopharm AG, and Seegene). We used serial dilutions of viral RNA to establish PCR efficiency and estimate the 95 % limit of detection (LOD95). Furthermore, we ran a panel of SARS-CoV-2-positive clinical samples (n = 13) for a preliminary evaluation of clinical sensitivity. Finally, we used clinical samples positive for non-coronavirus respiratory viral infections (n = 6) and a panel of RNA from related human coronaviruses to evaluate assay specificity. PCR efficiency was ≥96 % for all assays and the estimated LOD95 varied within a 6-fold range. Using clinical samples, we observed some variations in detection rate between kits. Importantly, none of the assays showed cross-reactivity with other respiratory (corona)viruses, except as expected for the SARS-CoV-1 E-gene. We conclude that all RT-PCR kits assessed in this study may be used for routine diagnostics of COVID-19 in patients by experienced molecular diagnostic laboratories

International Energy Agency Building Energy Simulation Test and Diagnostic Method (IEA BESTEST): In-Depth Diagnostic Cases for Ground Coupled Heat Transfer Related to Slab-on-Grade Construction

This report documents a set of idealized in-depth diagnostic test cases for use in validating ground-coupled floor slab heat transfer models. These test cases represent an extension to IEA BESTEST

A genome-wide scan for common alleles affecting risk for autism

Although autism spectrum disorders (ASDs) have a substantial genetic basis, most of the known genetic risk has been traced to rare variants, principally copy number variants (CNVs). To identify common risk variation, the Autism Genome Project (AGP) Consortium genotyped 1558 rigorously defined ASD families for 1 million single-nucleotide polymorphisms (SNPs) and analyzed these SNP genotypes for association with ASD. In one of four primary association analyses, the association signal for marker rs4141463, located within MACROD2, crossed the genome-wide association significance threshold of P < 5 × 10−8. When a smaller replication sample was analyzed, the risk allele at rs4141463 was again over-transmitted; yet, consistent with the winner's curse, its effect size in the replication sample was much smaller; and, for the combined samples, the association signal barely fell below the P < 5 × 10−8 threshold. Exploratory analyses of phenotypic subtypes yielded no significant associations after correction for multiple testing. They did, however, yield strong signals within several genes, KIAA0564, PLD5, POU6F2, ST8SIA2 and TAF1C