Thiol density dependent classical potential for methyl-thiol on a Au(111) surface

A new classical potential for methyl-thiol on a Au(111) surface has been developed using density functional theory electronic structure calculations. Energy surfaces between methyl-thiol and a gold surface were investigated in terms of symmetry sites and thiol density. Geometrical optimization was employed over all the configurations while minimum energy and thiol height were determined. Finally, a new interatomic potential has been generated as a function of thiol density, and applications to coarse-grained simulations are presented

A simple qualitative approach for mapping regional landslide susceptibility in the Faroe Islands

The Faroe Islands in the North Atlantic Ocean are highly susceptible to landslides. Following recent landslide incidents, Jarðfeingi (Faroese Earth and Energy Directorate) has pointed out, that the risk of human lives or of property being lost or affected by landslides may be increasing. This paper aims at presenting and testing a simple qualitative approach for mapping regional landslide susceptibility in the Faroe Islands, using few key parameters. The susceptibility model holds information about both landslide initiation areas and runout zones. Landslide initiation areas are determined from slope angle thresholds (25°–40°) and soil cover data, while runout zones are delineated using the angle of reach approach taking into account the presence/absence of geological benches in the runout path, which has not been considered in earlier studies. Data input is obtained from a landslide database containing 67 debris flows throughout the Faroe Islands. Angle of reach values differ significantly with the presence/absence of geological benches in the runout path. Two values of angle of reach, 21.5° and 27.6°, are used for calculating runout zones. The landslide susceptibility model is tested in a study area at the town of Klaksvík in the northern part of the Faroe Islands. A map validation comparing predicted susceptibility zones with a validation-dataset of 87 actual landslides in the study area reveal that 69% and 92%, respectively, of actual landslide initiation areas and runout zones are correctly predicted. Moreover 87% of the actual landslides are included in the overall predicted landslide susceptibility areas

A soil moisture and temperature network for SMOS validation in Western Denmark

The Soil Moisture and Ocean Salinity Mission (SMOS) acquires surface soil moisture data of global coverage every three days. Product validation for a range of climate and environmental conditions across continents is a crucial step. For this purpose, a soil moisture and soil temperature sensor network was established in the Skjern River Catchment, Denmark. The objectives of this article are to describe a method to implement a network suited for SMOS validation, and to present sample data collected by the network to verify the approach. The design phase included (1) selection of a single SMOS pixel (44 × 44 km), which is representative of the land surface conditions of the catchment and with minimal impact from open water (2) arrangement of three network clusters along the precipitation gradient, and (3) distribution of the stations according to respective fractions of classes representing the prevailing environmental conditions. Overall, measured moisture and temperature patterns could be related to the respective land cover and soil conditions. Texture-dependency of the 0–5 cm soil moisture measurements was demonstrated. Regional differences in 0–5 cm soil moisture, temperature and precipitation between the north-east and south-west were found to be small. A first comparison between the 0–5 cm network averages and the SMOS soil moisture (level 2) product is in range with worldwide validation results, showing comparable trends for SMOS retrieved soil moisture (<i>R</i><sup>2</sup> of 0.49) as well as initial soil moisture and temperature from ECMWF used in the retrieval algorithm (<i>R</i><sup>2</sup> of 0.67 and 0.97, respectively). While retrieved/initial SMOS soil moisture indicate significant under-/overestimation of the network data (biases of −0.092/0.057 m<sup>3</sup> m<sup>−3</sup>), the initial temperature is in good agreement (bias of −0.2 °C). Based on these findings, the network performs according to expectations and proves to be well-suited for its purpose. The discrepancies between network and SMOS soil moisture will be subject of subsequent studies

Determination of PCR efficiency in chelex-100 purified clinical samples and comparison of real-time quantitative PCR and conventional PCR for detection of Chlamydia pneumoniae

BACKGROUND: Chlamydia pneumoniae infection has been detected by serological methods, but PCR is gaining more interest. A number of different PCR assays have been developed and some are used in combination with serology for diagnosis. Real-time PCR could be an attractive new PCR method; therefore it must be evaluated and compared to conventional PCR methods. RESULTS: We compared the performance of a newly developed real-time PCR with a conventional PCR method for detection of C. pneumoniae. The PCR methods were tested on reference samples containing C. pneumoniae DNA and on 136 nasopharyngeal samples from patients with a chronic cough. We found the same detection limit for the two methods and that clinical performance was equal for the real-time PCR and for the conventional PCR method, although only three samples tested positive. To investigate whether the low prevalence of C. pneumoniae among patients with a chronic cough was caused by suboptimal PCR efficiency in the samples, PCR efficiency was determined based on the real-time PCR. Seventeen of twenty randomly selected clinical samples had a similar PCR efficiency to samples containing pure genomic C. pneumoniae DNA. CONCLUSIONS: These results indicate that the performance of real-time PCR is comparable to that of conventional PCR, but that needs to be confirmed further. Real-time PCR can be used to investigate the PCR efficiency which gives a rough estimate of how well the real-time PCR assay works in a specific sample type. Suboptimal PCR efficiency of PCR is not a likely explanation for the low positivity rate of C. pneumoniae in patients with a chronic cough

Initial experiments to assess short-term survival of discarded plaice (Pleuronectes platessa) caught in trammel nets during winter season

European plaice (Pleuronectes platessa) is a key species in commercial fisheries in the North Sea, Skagerrak, Kattegat, and Baltic Sea. The reformed European Union Common Fisheries Policy includes the possibility of exemptions from the landing obligation for “species for which scientific evidence demonstrates high survival rates”. Discard survival from set-net fisheries is poorly studied. Trials were conducted on two commercial fishing vessels over seven trips from November to February 2017–2018 in the Baltic Sea. The nylon trammel nets had a nominal bar size for the inner/outer wall of 75/350 mm and 85/400 mm. Soaking time was 23–47 h, water depth 7–18 m, and deck temperature was − 0.1–6.0 ◦C. Following commercial practice, the trammel nets were hauled back onto the vessel, after which netting and fish passed through a net hauler onto a steel sorting table where the entire fish catch were manually untangled by the fishers and plaice collected by scientists. We used a storage system for housing the captured fish inside fishing harbours during observations. Catch-damage-index (CDI) and Reflex Action Mortality Predictor (RAMP) scores were used to assess fish condition immediately after capture and at the end of observation periods. All plaice below 40 cm were sampled with a total number of 118 individuals from 13 fleets (several nets joined together). The fish were assessed for short-term survival for 4–10 days with full survival (100%). The majority of fish exhibited no reflex impairments. Minor bruises, fraying, and net marks were frequently observed on captured fish. The overall condition of the fish did not change during observation periods