Ejection and impact angles of saltating particles measured with a high-speed camera

3D and 2D trajectory data of sand grains saltating over a bed are presented from highspeed camera measurements. They were obtained at Zingst peninsula and in laboratory using a wind tunnel. Trajectories, calculated with a Runge-Kutta procedure, using values of the mean wind profile and the air flow were fitted to the measured ones. The trajectory with the lowest RMSE against the measured one was used to estimate the grain diameter of the saltating grain. Also ejection and impact angle, ejection and impact speed of the grain were determined. The results confirm earlier findings that ejection angles decreases with increasing grain diameter. Ejection angles between 57° and 27° for fine (63-200 μm) and middle (200-630 μm) ejecta and between 38° and 20° for coarse grains (630-2000 μm) were found. The impact angle β increases with increasing grain diameter. Impact angles between 8° and 15° for fine impactors and between 12° and 36° for middle and coarse grains were found. Additionally the ratio between the mean ejection angle α and mean impact angle β, which decrease with increasing grain diameter (Rice et al., 1995), could be confirmed. The ration between the ejection speed ue and impact speed ui was found nearly the same for all determined grain sizes, but the grains ejected from the bed had an average speed of one order of magnitude less than the impact speed

Influence of grape rot on the contents of sulfur binding compounds in wine after automated optical grape sorting

In the last years, climate change has played an important role in some wine growing regions because of the increasing hazard of different kinds of bunch rot. Botrytis cinerea is the most important kind of rot on grapes. Beside sensory effects, this rot can influence the content of yeast nutrients, e.g. thiamine, in the must and thus affect the alcoholic fermentation. To get insight into the influence of Botrytis cinerea on the content of sulfur binding compounds formed during the fermentation process in wine, tons of grapes from the Mosel valley were sorted by an automated optical grape sorter, an innovative possibility of grape sorting, in 2011. Wine samples before sulfurisation of the four sorting fractions, namely control (unsorted berries), free-run (juice from opened berries), positive (healthy, intact berries) and negative (rotten berries) were analysed for the sulfur-binding compounds acetaldehyde, pyruvic acid, 2-oxoglutaric acid and for bound sulfur dioxide. The results show that acetaldehyde concentrations were not affected by rot, while pyruvic acid and 2-oxoglutaric acid levels were significantly higher in the negative fractions and lower in the positive fractions. Accordingly, bound sulfur levels were significantly higher in wines from the negative fraction. In conclusion, it could be shown that fractionation of the berries can efficiently help to reduce sulfur binding compounds in wine and thus reduce the addition of sulfur dioxide

Immobilisation of glycosidases from commercial preparation on magnetic beads: Part 2: Aroma enhancement in wine using immobilised glycosidases

Most of the terpenes in wines are conjugated to various sugars, representing a significant reservoir of aromatic precursors. To promote the release of these terpenes, certain enzymes, such as β-glucosidase, α-arabinosidase and α-rhamnosidase, are necessary. A simple and cost-effective procedure for the immobilisation of multiple glycosidase activities (β-D-glucopyranosidase, α-L-arabinofuranosidase, α-L-rhamnopyranosidase and β-D-xylopyranosidase) from commercial Aspergillus niger preparation onto magnetic beads as carriers was developed as reported in Part 1 (Ferner et al. 2016).The aim of this work was to analyse a possible application of this immobilised biocatalyst due to its well-known advantages over soluble enzyme preparations – that is, control of the reaction process and preparation of enzyme-free products. Volatile compounds were analysed by gas chromatography (mass spectrometric detection). After the treatment of the model wine with different glycosides and white wine with immobilised glycosidases, the amount of free terpenes was significantly increased with respect to that of the control wine.The results of this study are of considerable interest for possible future applications of immobilised enzymes in the wine-making industry

Corrigendum to "Comparing the influence of net and gross anthropogenic land-use and land-cover changes on the carbon cycle in the MPI-ESM (vol 11, pg 4817, 2014)"

No abstract available

Comparing the influence of net and gross anthropogenic land-use and land-cover changes on the carbon cycle in the MPI-ESM

Global vegetation models traditionally treat anthropogenic land-use and land-cover changes (LULCCs) only as the changes in vegetation cover seen from one year to the next (net transitions). This approach ignores subgrid-scale processes such as shifting cultivation which do not affect the net vegetation distribution but which have an impact on the carbon budget. The differences in the carbon stocks feed back on processes like wildfires and desert formation. The simulations for the Coupled Model Intercomparison Project Phase 5 (CMIP5) all describe LULCCs using the "Land-Use Harmonization Dataset''. Though this dataset describes such subgrid-scale processes (gross transitions), some of the CMIP5 models still use the traditional approach. Using JSBACH/CBALANCE - the land carbon component of the Max Planck Institute Earth System Model (MPI-ESM), this study demonstrates how this potentially leads to a severe underestimation of the carbon emissions from LULCCs. Using net transitions lowers the average land-use emissions from 1.44 to 0.90 Pg C yr(-1) (38 %) during the historical period (1850-2005) - a total lowering by 85 Pg C. The difference between the methods is smaller in the RCP scenarios (2006-2100) but in RCP2.6 and RCP8.5 still cumulates to 30-40 PgC (on average 0.3-0.4 Pg Cyr(-1) or 13-25 %). In RCP4.5 essentially no difference between the methods is found. Results from models using net transitions are furthermore found to be sensitive to model resolution

Validation of New Gene Variant Classification Methods:a Field-Test in Diagnostic Cardiogenetics

Background: In the molecular genetic diagnostics of Mendelian disorders, solutions are needed for the major challenge of dealing with the large number of variants of uncertain significance (VUSs) identified using next-generation sequencing (NGS). Recently, promising approaches using constraint metrics to calculate case excess scores (CE), etiological fractions (EF), and gnomAD-derived constraint scores have been reported that estimate the likelihood of rare variants in specific genes or regions that are pathogenic. Our objective is to study the usability of these constraint data into variant interpretation in a diagnostic setting, using our cardiomyopathy cohort. Methods and Results: Patients (N = 2002) referred for clinical genetic diagnostics underwent NGS testing of 55–61 genes associated with cardiomyopathies. Previously classified likely pathogenic (LP) and pathogenic (P) variants were used to validate the use of data from CE, EF, and gnomAD constraint analyses for (re)classification of associated variant types in specific cardiomyopathy subtype-related genes. The classifications corroborated in 94% (354/378) of cases. Next, we reclassified 23 unique VUSs to LP, increasing the diagnostic yield by 1.2%. In addition, 106 unique VUSs (5.3% of patients) were prioritized for co-segregation or functional analyses. Conclusions: Our analysis confirms that the use of constraint metrics data can improve variant interpretation, and we, therefore, recommend using constraint scores on other cohorts and disorders and its inclusion in variant interpretation protocols

Urine E-cadherin: A Marker for early detection of kidney injury in diabetic patients.

Diabetic nephropathy (DN) is the main reason for end-stage renal disease. Microalbuminuria as the non-invasive available diagnosis marker lacks specificity and gives high false positive rates. To identify and validate biomarkers for DN, we used in the present study urine samples from four patient groups: diabetes without nephropathy, diabetes with microalbuminuria, diabetes with macroalbuminuria and proteinuria without diabetes. For the longitudinal validation, we recruited 563 diabetic patients and collected 1363 urine samples with the clinical data during a follow-up of 6 years. Comparative urinary proteomics identified four proteins Apolipoprotein A-I (APOA1), Beta-2-microglobulin (B2M), E-cadherin (CDH1) and Lithostathine-1-alpha (REG1A), which differentiated with high statistical strength (p < 0.05) between DN patients and the other groups. Label-free mass spectrometric quantification of the candidates confirmed the discriminatory value of E-cadherin and Lithostathine-1-alpha (p < 0.05). Immunological validation highlighted E-cadherin as the only marker able to differentiate significantly between the different DN stages with an area under the curve (AUC) of 0.85 (95%-CI: [0.72, 0.97]). The analysis of the samples from the longitudinal study confirmed the prognostic value of E-cadherin, the critical increase in urinary E-cadherin level was measured 20 ± 12.5 months before the onset of microalbuminuria and correlated significantly (p < 0.05) with the glomerular filtration rate measured by estimated glomerular filtration rate (eGFR)

NIPTeR:an R package for fast and accurate trisomy prediction in non-invasive prenatal testing

BACKGROUND: Various algorithms have been developed to predict fetal trisomies using cell-free DNA in non-invasive prenatal testing (NIPT). As basis for prediction, a control group of non-trisomy samples is needed. Prediction accuracy is dependent on the characteristics of this group and can be improved by reducing variability between samples and by ensuring the control group is representative for the sample analyzed.RESULTS: NIPTeR is an open-source R Package that enables fast NIPT analysis and simple but flexible workflow creation, including variation reduction, trisomy prediction algorithms and quality control. This broad range of functions allows users to account for variability in NIPT data, calculate control group statistics and predict the presence of trisomies.CONCLUSION: NIPTeR supports laboratories processing next-generation sequencing data for NIPT in assessing data quality and determining whether a fetal trisomy is present. NIPTeR is available under the GNU LGPL v3 license and can be freely downloaded from https://github.com/molgenis/NIPTeR or CRAN.</p

CoNVaDING:Single Exon Variation Detection in Targeted NGS Data

We have developed a tool for detecting single exon copy number variations (CNVs) in targeted next-generation sequencing data: CoNVaDING (Copy Number Variation Detection In Next-generation sequencing Gene panels). CoNVaDING includes a stringent quality control metric, that excludes or flags low quality exons. Since this quality control shows exactly which exons can be reliably analysed and which exons are in need of an alternative analysis method, CoNVaDING is not only useful for CNV detection in a research setting, but also in clinical diagnostics. During the validation phase, CoNVaDING detected all known CNVs in high quality targets in 320 samples analysed, giving 100% sensitivity and 99.998% specificity for 308,574 exons. CoNVaDING outperforms existing tools by exhibiting a higher sensitivity and specificity and by precisely identifying low-quality samples and regions. This article is protected by copyright. All rights reserved.</p

Diagnostic yield of targeted next generation sequencing in 2002 Dutch cardiomyopathy patients

BACKGROUND: Next-generation sequencing (NGS) is increasingly used for clinical evaluation of cardiomyopathy patients as it allows for simultaneous screening of multiple cardiomyopathy-associated genes. Adding copy number variant (CNV) analysis of NGS data is not routine yet and may contribute to the diagnostic yield. OBJECTIVES: Determine the diagnostic yield of our targeted NGS gene panel in routine clinical diagnostics of Dutch cardiomyopathy patients and explore the impact of exon CNVs on diagnostic yield. METHODS: Patients (N = 2002) referred for clinical genetic analysis underwent diagnostic testing of 55-61 genes associated with cardiomyopathies. Samples were analyzed and evaluated for single nucleotide variants (SNVs), indels and CNVs. CNVs identified in the NGS data and suspected of being pathogenic based on type, size and location were confirmed by additional molecular tests. RESULTS: A (likely) pathogenic (L)P variant was detected in 22.7% of patients, including 3 with CNVs and 25 where a variant was identified in a gene currently not associated with the patient's cardiomyopathy subtype. Only 15 out of 2002 patients (0.8%) were found to carry two (L)P variants. CONCLUSION: The yield of routine clinical diagnostics of cardiomyopathies was relatively low when compared to literature. This is likely due to the fact that our study reports the outcome of patients in daily routine diagnostics, therefore also including patients not fully fulfilling (subtype specific) cardiomyopathy criteria. This may also explain why (L)P variants were identified in genes not associated with the reported subtype. The added value of CNV analysis was shown to be limited but not negligible