A new long-term sampling approach to viruses on surfaces

The importance of virus disease outbreaks and its prevention is of growing public concern but our understanding of virus transmission routes is limited by adequate sampling strategies. While conventional swabbing methods provide merely a microbial snapshot, an ideal sampling strategy would allow reliable collection of viral genomic data over longer time periods. This study has evaluated a new, paper-based sticker approach for collection of reliable viral genomic data over longer time periods up to 14 days and after implementation of different hygiene measures. In contrast to swabbing methods, which sample viral load present on a surface at a given time, the paper-based stickers are attached to the surface area of interest and collect viruses that would have otherwise been transferred onto that surface. The major advantage of one-side adhesive stickers is that they are permanently attachable to a variety of surfaces. Initial results demonstrate that stickers permit stable recovery characteristics, even at low virus titers. Stickers also allow reliable virus detection after implementation of routine hygiene measures and over longer periods up to 14 days. Overall, results for this new sticker approach for virus genomic data collection are encouraging, but further studies are required to confirm anticipated benefits over a range of virus types.

Sea lice (Lepeophtherius salmonis) detection and quantification around aquaculture installations using environmental DNA

The naturally occurring ectoparasite salmon lice (Lepeophtherirus salmonis) poses a great challenge for the salmon farming industry, as well as for wild salmonids in the Northern hemisphere. To better control the infestation pressure and protect the production, there is a need to provide fish farmers with sensitive and efficient tools for rapid early detection and monitoring of the parasitic load. This can be achieved by targeting L. salmonis DNA in environmental samples. Here, we developed and tested a new L. salmonis specific DNA-based assay (qPCR assay) for detection and quantification from seawater samples using an analytical pipeline compatible with the Environmental Sample Processor (ESP) for autonomous water sample analysis of gene targets. Specificity of the L. salmonis qPCR assay was demonstrated through in-silico DNA analyses covering sequences of different L. salmonis isolates. Seawater was spiked with known numbers of nauplii and copepodite free-swimming (planktonic) stages of L. salmonis to investigate the relationship with the number of marker gene copies (MGC). Finally, field samples collected at different times of the year in the vicinity of a salmon production farm in Western Norway were analyzed for L. salmonis detection and quantification. The assay specificity was high and a high correlation between MGC and planktonic stages of L. salmonis was established in the laboratory conditions. In the field, L. salmonis DNA was consequently detected, but with MGC number below that expected for one copepodite or nauplii. We concluded that only L. salmonis tissue or eDNA residues were detected. This novel study opens for a fully automatized L. salmonis DNA quantification using ESP robotic to monitor the parasitic load, but the challenge remains the adequate sampling of a volume of seawater sufficiently large to be representative of outbreaks and load around fish farms.

Gastrointestinal Manifestations in Systemic Mastocytosis: The Need of a Multidisciplinary Approach

Mastocytosis represents a heterogeneous group of neoplastic mast cell disorders. The basic classification into a skin-limited disease and a systemic form with multi-organ involvement remains valid. Systemic mastocytosis is a disease often hard to diagnose, characterized by different symptoms originating from either the release of mast cell mediators or organ damage due to mast cell infiltration. Gastrointestinal symptoms represent one of the major causes of morbidity, being present in 60–80% of patients. A high index of suspicion by clinicians and pathologists is required to reach the diagnosis. Gastrointestinal mastocytosis can be a challenging diagnosis, as symptoms simulate other more common gastrointestinal diseases. The endoscopic appearance is generally unremarkable or nonspecific and gastrointestinal mast cell infiltration can be focal and subtle, requiring an adequate sampling with multiple biopsies by the endoscopists. Special stains, such as CD117, tryptase, and CD25, should be performed in order not to miss the gastrointestinal mast cell infiltrate. A proper patient’s workup requires a multidisciplinary approach including gastroenterologists, endoscopists, hematologists, oncologists, and pathologists. The aim of this review is to analyze the clinicopathological features of gastrointestinal involvement in systemic mastocytosis, focusing on the relevance of a multidisciplinary approach.

Stigmatization from Work-Related COVID-19 Exposure: A Systematic Review with Meta-Analysis

Stigmatization from work-related COVID-19 exposure has not been investigated in detail yet. Therefore, we systematically searched three databases: Medline, Embase, and PsychInfo (until October 2020), and performed a grey literature search (until February 2021). We identified 46 suitable articles from 24 quantitative and 11 qualitative studies, 6 systematic reviews, 3 study protocols and 1 intervention. The assessment of stigmatization varied widely, ranging from a single-item question to a 22-item questionnaire. Studies mostly considered perceived self-stigma (27 of 35 original studies) in healthcare workers (HCWs) or hospital-related jobs (29 of 35). All articles reported on stigmatization as a result of work-related COVID-19 exposure. However, most quantitative studies were characterized by convenience sampling (17 of 24), and all studies—also those with an adequate sampling design—were considered of low methodological quality. Therefore, it is not possible to determine prevalence of stigmatization in defined occupational groups. Nevertheless, the work-related stigmatization of occupational groups with or without suspected contact to COVID-19 is a relevant problem and increases the risk for depression (odds ratio (OR) = 1.74; 95% confidence interval CI 1.29–2.36) and anxiety (OR = 1.64; 95% CI 1.18–2.28). For promoting workers’ health, anti-stigma strategies and support should be implemented in the workplace.

High Efficiency Configuration Space Sampling -- probing the distribution of available states

Substantial acceleration of research and more efficient utilization of resources can be achieved in modelling investigated phenomena by identifying the limits of system's accessible states instead of tracing the trajectory of its evolution. The proposed strategy uses the Metropolis-Hastings Monte-Carlo sampling of the configuration space probability distribution coupled with physically-motivated prior probability distribution. We demonstrate this general idea by presenting a high performance method of generating configurations for lattice dynamics and other computational solid state physics calculations corresponding to non-zero temperatures. In contrast to the methods based on molecular dynamics, where only a small fraction of obtained data is used, the proposed scheme is distinguished by a considerably higher, reaching even 80%, acceptance ratio and much lower amount of computation required to obtain adequate sampling of the system in thermal equilibrium at non-zero temperature.

189 Fundamentals, Common Mistakes, and Graduate Education in Statistics

Experimental design and statistical data analyses are fundamental components of animal science research. Proper design of experiments and adequate sampling permits testing hypotheses raised by researchers and sets the stage for collecting required data and subsequent statistical analysis. When designing experiments, researchers should respect rules of randomization of treatments to avoid statistical bias and permit proper inference to be drawn. Use of sample sizes that result in adequate statistical power to identify the hypothesized differences among factor levels of interest is key and should be driven by formal processes determining such. Best practices for data collection should be performed to obtain high quality data by reducing collection (e.g., mislabeling, improper technique) and measurement errors. With sound data, appropriate and optimal statistical methods should be used to generate valid results. The statistical method deployed should be chosen based on assumptions about residuals (e.g., normality, correlation, and homogeneity) and on the type of data (e.g., quantitative continuous or categorical). The appropriate statistical model used should also be consistent with the experimental design to validate the respective test statistics. The science of statistics is changing rapidly. With the development of high-throughput technologies, the generation of large datasets, high performance and sophisticated models and the interest in Big Data, the training of animal science graduate students in data management and rigorous statistical analyses is more important than ever. In order to meet the demands of current trends, animal science graduate students must be trained in several complex statistical and computational skills to meet the challenges imposed by these complicated, sophisticated and nuanced analytical methods. The livestock production sector will benefit from improved training, use of advanced and appropriate experimental designs, and collection and analysis of quality data in research.

Placental Sampling for Understanding Viral Infections — A Simplified Protocol for the COVID-19 Pandemic

Objective The coronavirus disease 2019 (COVID-19) is a pandemic viral disease, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The impact of the disease among the obstetric population remains unclear, and the study of the placenta can provide valuable information. Adequate sampling of the placental tissue can help characterize the pathways of viral infections. Methods A protocol of placental sampling is proposed, aiming at guaranteeing representativity of the placenta and describing the adequate conservation of samples and their integrity for future analysis. The protocol is presented in its complete and simplified versions, allowing its implementation in different complexity settings. Results Sampling with the minimum possible interval from childbirth is the key for adequate sampling and storage. This protocol has already been implemented during the Zika virus outbreak. Conclusion A protocol for adequate sampling and storage of placental tissue is fundamental for adequate evaluation of viral infections on the placenta. During the COVID-19 pandemic, implementation of this protocol may help to elucidate critical aspects of the SARS-CoV-2 infection.

A Molecular Dynamics Simulation Scenario for Studying Solvent-mediated Interactions of Polymers and Application to Thermoresponse of Poly (N-isopropylacrylamide) in Water

Studying equilibrium properties of polymers in solution by atomistic simulations is a challenging task as the available computation time is often not sufficient to ensure representative sampling of the phase space. One approach to tackle this problem is to create a simulation scenario which is simple enough to enable adequate sampling of equilibrium states while it retains the essential parts of the physics of the polymer in solution. In this work, we present and test such a scenario, which is designed for studying whether a given polymer will aggregate or dissolve in a given solvent. Two periodic polymer molecules are simulated in the explicit solvent. The distance d between the polymer chains lends itself as an order parameter so that advanced sampling techniques, such as umbrella sampling, can be applied easily. A state corresponding to dissolved polymers (large d) and a state corresponding to aggregated polymers (small d) can be defined. The scenario misses the intramolecular collapse of the single chain, but it retains full atomistic detail regarding the polymer-solvent and the intermolecular polymer-polymer interactions. Thethermoresponsive behavior of PNIPAM in water is studied with the new scenario, and it is shown that quantitative predictions of the experimental equilibrium data can be obtained after adjusting a single state-independent parameter in the force field.

P91 Phyllodes Tumours: Looking for Predictive Features from Multidisciplinary Assessments

Introduction The breast triple assessment enables rapid evaluation of breast abnormalities. Lesions are assessed via the assessments based on clinical examination, imaging and histological sampling. Fibroepithelial lesions (FELs) are amongst the most common breast lesions of uncertain malignant potential. They encompass a spectrum of entities ranging from benign fibroadenomas (FA) to malignant phyllodes tumours (PT), with contrasting clinical management approaches. Unfortunately, the distinction between various FELs is often difficult, despite recent diagnostic advances. This is especially so between FAs and PTs. Nevertheless, understanding how to prioritise key characteristics of PTs, both radiologically and histologically may ease this challenge. In our opinion, a multidisciplinary approach including radiological input is probably the most helpful in reaching an accurate diagnosis. Methods We, retrospectively studied data from breast lesions which were initially diagnosed pre-operatively as R3/B3 FELs, and those with a final diagnosis of PT on excision. 71 suitable cases were identified from 2009 to 2019. Information was extracted from reports made by specialists at the pre-operative and post-excision stages. Statistical analysis will be applied to quantify the significance of features evaluated. Results Preliminary results suggest diagnoses made by pathologists on pre-operative samples correlated well with the eventual final diagnosis made on post-operative specimens. Adequate sampling appears to be a significant factor in influencing the pre-operative core biopsy diagnosis. Conclusion We anticipate to acquire a comprehensive knowledge of various predictive features of PTs, and the correlation between the key radiological features, thereby allowing accurate pre-operative diagnosis of these interesting and challenging lesions.

Precipitation Retrievals from Passive Microwave Cross-Track Sensors: The Precipitation Retrieval and Profiling Scheme

The retrieval of precipitation (snowfall and rainfall) from satellite sensors on a global basis is essential in aiding our knowledge and understanding of the Earth System and for many societal applications. Measurements from surface-based instruments are essentially limited to populated regions, necessitating the use of satellite-based observations to provide estimates of precipitation across the whole of the Earth’s surface. The temporal and spatial variability of precipitation requires adequate sampling, especially at finer resolutions. It is, therefore, necessary to exploit all available data from precipitation-capable satellites to ensure the proper representation of precipitation. To date, the estimation of precipitation using passive microwave observations has been largely concentrated upon the conically scanning imaging instruments, with relatively few techniques exploiting the observations made from the cross-track sounders. This paper describes the development of the Precipitation Retrieval and Profiling Scheme (PRPS) to retrieve precipitation from cross-track sensors, together with its performance against surface radar data and other satellite precipitation retrievals.