Estimation of Two-Stage Ditch Excavation Volume Using LiDAR Data

Drainage ditches are a major pathway for sediment, nutrients, and pesticides to enter stream systems, which threaten environmental and human health. Unlike trapezoidal ditches, two-stage ditches have a vegetated bench that acts as a floodplain, which helps to prevent erosion and to increase the processing of nutrients to improve water quality. Converting a trapezoidal ditch to a two-stage ditch is expensive, due to the large volumes of soil that need to be excavated. Since ditch geometries vary significantly and surveying each potential site by hand would be time consuming and expensive, a tool based upon online Light Detection and Ranging (LiDAR) data would be useful to estimate the volume. The excavation volume for two ditches was calculated using two methods: the LiDAR digital elevation model, gridded to 3 m resolution, and a ground survey using an RTK GPS unit. ArcGIS was used to create profiles of the trapezoidal streams. Hypothetical two-stage cross-sections were created by calculating the bankfull depth, based on the drainage area, and the width, using a three to one bench slope. OriginPro was used to find the difference between the area under the two-stage cross-section and the original trapezoidal cross-section. The estimated volume differed between the two methods. While the LiDAR based volume of one ditch was within 16.9% of the RTK GPS based volume, the other ditch’s volumes varied by 22.5%. This suggests that using the LiDAR DEM may not provide sufficient accuracy for this estimate, although it could provide a rough cost estimate without time-consuming surveys

Targeted exhaled breath analysis for detection of Pseudomonas aeruginosa in cystic fibrosis patients

Background Pseudomonas aeruginosa (PA) is an important respiratory pathogen for cystic fibrosis (CF) patients. Routine microbiology surveillance is time-consuming, and is best performed on expectorated sputum. As alternative, volatile organic compounds (VOCs) may be indicative of PA colonisation. In this study, we aimed to identify VOCs associated with PA in literature and perform targeted exhaled breath analysis to recognize PA positive CF patients non-invasively. Methods This study consisted of 1) a literature review to select VOCs of interest, and 2) a cross-sectional CF study. Definitions used: A) PA positive, PA culture at visit/chronically; B) PA free, no PA culture in ≥12 months. Exhaled VOCs were identified via quadrupole MS. The primary endpoint was the area under the receiver operating characteristics curve (AUROCC) of individual VOCs as well as combined VOCs against PA culture. Results 241 VOCs were identified in literature, of which 56 were further evaluated, and 13 could be detected in exhaled breath in our cohort. Exhaled breath of 25 pediatric and 28 adult CF patients, PA positive (n=16) and free (n=28) was available. 3/13 VOCs were significantly (p<0.05) different between PA groups in children; none were in adults. Notably, a composite model based on 5 or 1 VOC(s) showed an AUROCC of 0.86 (CI 0.71–1.0) and 0.87 (CI 0.72–1.0) for adults and children, respectively. Conclusions Targeted VOC analysis appears to discriminate children and adults with and without PA positive cultures with clinically acceptable sensitivity values

Sarcoma classification by DNA methylation profiling

Sarcomas are malignant soft tissue and bone tumours affecting adults, adolescents and children. They represent a morphologically heterogeneous class of tumours and some entities lack defining histopathological features. Therefore, the diagnosis of sarcomas is burdened with a high inter-observer variability and misclassification rate. Here, we demonstrate classification of soft tissue and bone tumours using a machine learning classifier algorithm based on array-generated DNA methylation data. This sarcoma classifier is trained using a dataset of 1077 methylation profiles from comprehensively pre-characterized cases comprising 62 tumour methylation classes constituting a broad range of soft tissue and bone sarcoma subtypes across the entire age spectrum. The performance is validated in a cohort of 428 sarcomatous tumours, of which 322 cases were classified by the sarcoma classifier. Our results demonstrate the potential of the DNA methylation-based sarcoma classification for research and future diagnostic applications

Diagnosis of primary ciliary dyskinesia: summary of the ERS Task Force report

Key points Primary ciliary dyskinesia (PCD) is a genetically and clinically heterogeneous disease characterised by abnormal motile ciliary function. There is no “gold standard” diagnostic test for PCD. The European Respiratory Society (ERS) Task Force Guidelines for diagnosing PCD recommend that patients should be referred for diagnostic testing if they have several of the following features: persistent wet cough; situs anomalies; congenital cardiac defects; persistent rhinitis; chronic middle ear disease with or without hearing loss; or a history, in term infants, of neonatal upper and lower respiratory symptoms or neonatal intensive care admission. The ERS Task Force recommends that patients should be investigated in a specialist PCD centre with access to a range of complementary tests: nasal nitric oxide, high-speed video microscopy analysis and transmission electron microscopy. Additional tests including immunofluorescence labelling of ciliary proteins and genetic testing may also help determine the diagnosis. Educational aims This article is intended for primary and secondary care physicians interested in primary ciliary dyskinesia (PCD), i.e. those who identify patients for testing, and those involved in diagnosing and managing PCD patients. It aims: to inform readers about the new European Respiratory Society Task Force Guidelines for diagnosing patients with PCD to enable primary and secondary care physicians to: identify patients who need diagnostic testing; understand the diagnostic tests that their patients will undergo, the results of the tests and their limitations; and ensure that appropriate care is subsequently delivered