Damp Buildings: Associated Fungi and How to Find Them

The number of buildings experiencing humidity problems and fungal growth appears to be increasing as energy-saving measures and changes in construction practices and climate become more common. Determining the cause of the problem and documenting the type and extent of fungal growth are complex processes involving both building physics and indoor mycology. New detection and identification methods have been introduced, and new fungal species have been added to the list of building-related fungi. However, the lack of standardised procedures and general knowledge hampers the effort to resolve the problems and advocate for an effective renovation plan. This review provides a framework for building inspections on current sampling methods and detection techniques for building-related fungi. The review also contains tables with fungal species that have been identified on commonly used building materials in Europe and North America (e.g., gypsum wallboard, oriented strand board (OSB), concrete and mineral wool). The most reported building-associated fungi across all materials are Penicillium chrysogenum and Aspergillus versicolor. Chaetomium globosum is common on all organic materials, whereas Aspergillus niger is common on all inorganic materials.

Effect of Sampling Method on Detection of the Equine Uterine Microbiome during Estrus

Bacterial endometritis is among the most common causes of subfertility in mares. It has a major economic impact on the equine breeding industry. The sensitivity of detecting uterine microbes using culture-based methods, irrespective of the sample collection method, double-guarded endometrial swab, endometrial biopsy, or uterine low-volume lavage (LVL), is low. Therefore, equine bacterial endometritis often goes undiagnosed. Sixteen individual mares were enrolled, and an endometrial sample was obtained using each method from all mares. After trimming, quality control and decontamination, 3824 amplicon sequence variants were detected in the dataset. We found using 16S rRNA sequencing that the equine uterus harbors a distinct resident microbiome during estrus. All three sampling methods used yielded similar results in composition as well as relative abundance at phyla (Proteobacteria, Firmicutes, and Bacteroidota) and genus (Klebsiella, Mycoplasma, and Aeromonas) levels. A significant difference was found in alpha diversity (Chao1) between LVL and endometrial biopsy, suggesting that LVL is superior at detecting the low-abundant (rare) taxa. These new data could pave the way for innovative treatment methods for endometrial disease and subfertility in mares. This, in turn, could lead to more judicious antimicrobial use in the equine breeding industry.

Detection and quantification of bacterial species DNA in bovine digital dermatitis lesions in swabs and fine-needle aspiration versus biopsies

Digital Dermatitis (DD) is a polymicrobial disease characterized by ulcerative lesions on the heel bulb of cattle and for which, despite being reported almost 50 years ago, information on the causative agent is still lacking. Tissue biopsies are regularly collected to identify bacterial presence-absence and their relative abundance in the microbiome, with sufficient evidence for the high abundance of species of Treponema spp. and other anaerobes in lesions. However, it is unclear what the potential of less-invasive sampling methods is for bacterial detection and quantification. This study aimed to test whether less-invasive sampling techniques, such as swabs and fine-needle aspiration (FNA), can be a convenient alternative to tissue biopsies in detecting and quantifying seven DD-associated bacteria in active, ulcerative DD lesions by qPCR. Twenty-two M2 DD lesions were collected using corresponding swabs, aspirates, and biopsies from dairy cows. Presence/absence and quantities of Treponema phagedenis, Treponema medium, Treponema pedis, Porphryromonas levii, Bacteroides pyogenes, Fusobacterium necrophorum, and Fusobacterium mortiferum were correlated, and Bland-Altman plot, McNemar's test, and Cohen's kappa coefficient were used to calculate the agreement among the methods. The quantities of all species were larger in swabs and smaller in aspirates compared to biopsies; however, the differences in bacterial enumeration observed between biopsies and swabs were smaller than in biopsies and aspirates. A strong correlation was observed between the quantity of T. pedis, T. medium, P. levii, and F. mortiferum in biopsies, swabs, and FNA. Yet, T. phagedenis presented the smallest difference between biopsies and swabs, followed by T. pedis and T. medium. In conclusion, swabs, aspirates, and biopsies were equal in their capacity to detect Treponema species based on the good agreement for bacteria presence/absence, with a more limited agreement for the other anaerobes, which were more often present in M2 lesions swabs by qPCR. Bacterial numbers were higher in swabs and lower in aspirates compared to biopsies, with the amounts of treponemes in swabs being closer to biopsies than in aspirates to biopsies. Therefore, aspirates were less suitable for bacterial quantification in DD lesions compared to the other methods.

Improvement of P300-Based Brain-Computer Interfaces for Home Appliances Control by Data Balancing Techniques

The oddball paradigm used in P300-based brain-computer interfaces (BCIs) intrinsically poses the issue of data imbalance between target stimuli and nontarget stimuli. Data imbalance can cause overfitting problems and, consequently, poor classification performance. The purpose of this study is to improve BCI performance by solving this data imbalance problem with sampling techniques. The sampling techniques were applied to BCI data in 15 subjects controlling a door lock, 15 subjects an electric light, and 14 subjects a Bluetooth speaker. We explored two categories of sampling techniques: oversampling and undersampling. Oversampling techniques, including random oversampling, synthetic minority oversampling technique (SMOTE), borderline-SMOTE, support vector machine (SVM) SMOTE, and adaptive synthetic sampling, were used to increase the number of samples for the class of target stimuli. Undersampling techniques, including random undersampling, neighborhood cleaning rule, Tomek's links, and weighted undersampling bagging, were used to reduce the class size of nontarget stimuli. The over- or undersampled data were classified by an SVM classifier. Overall, some oversampling techniques improved BCI performance while undersampling techniques often degraded performance. Particularly, using borderline-SMOTE yielded the highest accuracy (87.27%) and information transfer rate (8.82 bpm) across all three appliances. Moreover, borderline-SMOTE led to performance improvement, especially for poor performers. A further analysis showed that borderline-SMOTE improved SVM by generating more support vectors within the target class and enlarging margins. However, there was no difference in the accuracy between borderline-SMOTE and the method of applying the weighted regularization parameter of the SVM. Our results suggest that although oversampling improves performance of P300-based BCIs, it is not just the effect of the oversampling techniques, but rather the effect of solving the data imbalance problem.

Evaluation of quenching methods for metabolite recovery in photoautotrophic Synechococcus sp. PCC 7002

The first step of many metabolomics studies is quenching, a technique vital for rapidly halting metabolism and ensuring that the metabolite profile remains unchanging during sample processing. The most widely used approach is to plunge the sample into prechilled cold methanol; however, this led to significant metabolite loss in Synecheococcus sp. PCC 7002. Here we describe our analysis of the impacts of cold methanol quenching on the model marine cyanobacterium Synechococcus sp. PCC 7002, as well as our brief investigation of alternative quenching methods. We tested several methods including cold methanol, cold saline, and two filtration approaches. Targeted central metabolites were extracted and metabolomic profiles were generated using liquid chromatography-tandem mass spectrometry (LC-MS/MS). The results indicate that cold methanol quenching induces dramatic metabolite leakage in Synechococcus, resulting in a majority of central metabolites being lost prior to extraction. Alternatively, usage of a chilled saline quenching solution mitigates metabolite leakage and improves sample recovery without sacrificing rapid quenching of cellular metabolism. Finally, we illustrate that metabolite leakage can be assessed, and subsequently accounted for, in order to determine absolute metabolite pool sizes; however, our results show that metabolite leakage is inconsistent across various metabolite pools and therefore must be determined for each individually measured metabolite.

Measuring the gut microbiome in birds: Comparison of faecal and cloacal sampling

The gut microbiomes of birds and other animals are increasingly being studied in ecological and evolutionary contexts. Numerous studies on birds and reptiles have made inferences about gut microbiota using cloacal sampling; however, it is not known whether the bacterial community of the cloaca provides an accurate representation of the gut microbiome. We examined the accuracy with which cloacal swabs and faecal samples measure the microbiota in three different parts of the gastrointestinal tract (ileum, caecum, and colon) using a case study on juvenile ostriches, Struthio camelus, and high-throughput 16S rRNA sequencing. We found that faeces were significantly better than cloacal swabs in representing the bacterial community of the colon. Cloacal samples had a higher abundance of Gammaproteobacteria and fewer Clostridia relative to the gut and faecal samples. However, both faecal and cloacal samples were poor representatives of the microbial communities in the caecum and ileum. Furthermore, the accuracy of each sampling method in measuring the abundance of different bacterial taxa was highly variable: Bacteroidetes was the most highly correlated phylum between all three gut sections and both methods, whereas Actinobacteria, for example, was only strongly correlated between faecal and colon samples. Based on our results, we recommend sampling faeces, whenever possible, as this sample type provides the most accurate assessment of the colon microbiome. The fact that neither sampling technique accurately portrayed the bacterial community of the ileum nor the caecum illustrates the difficulty in noninvasively monitoring gut bacteria located further up in the gastrointestinal tract. These results have important implications for the interpretation of avian gut microbiome studies.

A simplified method to estimate Diphyllobothrium spp. infection in salmonids

Some fish parasites constitute severe management problems as they may cause mortality of their fish host or are important zoonoses of humans. Parasite assessments are therefore critical to keep track of infections. If conventional sampling techniques can be simplified, parasite assessments might be easier to obtain, less time-consuming and more extensive. In this study, we compare the assessed number of Diphyllobothrium spp. cysts (CYST) with the counted number of Diphyllobothrium spp. plerocercoid larvae recovered using a conventional digestive technique (LARV). The aim was to determine the potential of using CYST as a simplified methodology for assessing Diphyllobothrium spp. infection in salmonids. In total, 365 brown trout and 424 Arctic charr were sampled from nine lakes in subarctic Norway. Strong correlation, significant linear relationship and large amount of explained variation were found between log₁₀ CYST and log₁₀ LARV in both fish species. The method had a slight, but not significant tendency to work better in charr compared to trout. In addition, absolute difference between CYST and LARV increased at parasite intensities >100 indicating that the method has reduced functionality when estimating parasite intensity in heavily infected salmonid populations. However, overall, using this simplified and less time-consuming methodology, a good indication of Diphyllobothrium spp. intensity, abundance and prevalence was obtained. We suggest that this method provides a sound proxy of the Diphyllobothrium spp. burden and have the potential to be used in parasite assessment during fish monitoring and fisheries management surveys, particularly if the time and resources for detailed parasite studies are not available.

Reaching multi-nanosecond timescales in combined QM/MM molecular dynamics simulations through parallel horsetail sampling

We report an enhanced sampling technique that allows to reach the multi-nanosecond timescale in quantum mechanics/molecular mechanics molecular dynamics simulations. The proposed technique, called horsetail sampling, is a specific type of multiple molecular dynamics approach exhibiting high parallel efficiency. It couples a main simulation with a large number of shorter trajectories launched on independent processors at periodic time intervals. The technique is applied to study hydrogen peroxide at the water liquid-vapor interface, a system of considerable atmospheric relevance. A total simulation time of a little more than 6 ns has been attained for a total CPU time of 5.1 years representing only about 20 days of wall-clock time. The discussion of the results highlights the strong influence of the solvation effects at the interface on the structure and the electronic properties of the solute. © 2017 Wiley Periodicals, Inc.

Human as the Ultimate Wound Healing Model: Strategies for Studies Investigating the Dermal Lipidome

PURPOSE OF REVIEW

Educate the reader of the multiple roles undertaken by the human epidermal lipidome and the experimental techniques of measuring them.

RECENT FINDINGS

Damage to skin elicits a wound healing process that is capped by the recreation of the lipid barrier. In addition to barrier function, lipids also undertake an active signaling role during wound healing. Achievement of these multiple functions necessitates a significant complexity and diversity in the lipidome resulting in a composition that is unique to the human skin. As such, any attempts to delineate the function of the lipidome during the wound healing process in humans need to be addressed via studies undertaken in humans.

SUMMARY

The human cutaneous lipidome is unique and play a functionally significant role in maintaining barrier and regulating wound healing. Modern mass spectrometry and Raman spectroscopy based methods enable the investigation epidermal lipidome with respect to those functions.

Analysis of Uncertainty and Variability in Finite Element Computational Models for Biomedical Engineering: Characterization and Propagation

Computational modeling has become a powerful tool in biomedical engineering thanks to its potential to simulate coupled systems. However, real parameters are usually not accurately known, and variability is inherent in living organisms. To cope with this, probabilistic tools, statistical analysis and stochastic approaches have been used. This article aims to review the analysis of uncertainty and variability in the context of finite element modeling in biomedical engineering. Characterization techniques and propagation methods are presented, as well as examples of their applications in biomedical finite element simulations. Uncertainty propagation methods, both non-intrusive and intrusive, are described. Finally, pros and cons of the different approaches and their use in the scientific community are presented. This leads us to identify future directions for research and methodological development of uncertainty modeling in biomedical engineering.

Importance of accurate sampling techniques in microbiological diagnosis of endophthalmitis

BACKGROUND

Endophthalmitis is an ocular emergency and bacteria are the commonest aetiological agents of infectious endophthalmitis. Any delay in treatment will result in serious complications like complete loss of vision. Therefore, obtaining the most appropriate sample is of paramount importance for a microbiologist to identify the aetiological agents that help the ophthalmologist in planning treatment.

OBJECTIVE

[corrected] This study was undertaken to determine the intraocular specimen that is most likely to yield a positive culture on microbiological examination.

METHODS

From 60 cases, intraocular samples were collected in the operation theatre under anaesthesia. The samples obtained were aqueous humour and vitreous humour by vitreous tap, vitreous biopsy or pars plana vitrectomy. The specimens were processed within half an hour, first by inoculating onto culture media and then direct smear examination by Gram's Stain

RESULTS

Eighty samples were obtained from 60 cases of which the most were vitreous fluid (vitreous biopsy/tap + vitrectomy fluid), i.e., 75%. Culture was positive in 88% vitrectomy fluid as compared to 74% in vitreous tap/biopsy followed by 20% in aqueous fluid.

CONCLUSION

Vitrectomy fluid appears to be the best sample for culture from clinically diagnosed endophthalmitis cases.