Optimal sampling and analysis methods for clinical diagnostics of vaginal microbiome

Next-generation sequencing-based microbiological analysis is a complex way to profile vaginal microbiome samples since each step affects the results gained. Methodologies for sample collection lack golden standards. We compared Puritan DNA/RNA swab (PS) and Copan FLOQ swab (CS) and provided consistent and reliable microbiome profiles analyzed by 16S rRNA gene sequencing. We collected two consecutive vaginal samples utilizing PS with room temperature storing and CS with instant freezing from 26 women. Variable region 4 of bacterial 16S rRNA gene was amplified with single PCR by custom-designed dual-indexed primers and sequenced with Illumina MiSeq system. Read quality control, operational taxonomic unit tables, and alpha and beta diversities analysis were performed, and community richness, diversity, and evenness were evaluated and compared between the two samplings and tests. Nineteen sample pairs produced detectable, intact DNA during the extraction protocol and/or further microbial profiles. Alpha bacterial diversity indices were independent on the collection protocol. No significant statistical differences were found in the measured beta diversity metrics between the collection methods. Of the women, 43% had Lactobacillus-dominated vaginal microbiome profile despite of collection method. Previously reported important vaginal microbiome phyla Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria, and Proteobacteria were present in the sample set although their relative abundances varied among individuals. PS and CS enable constant vaginal microbiota sampling. The PS method with no need for instant freezing is suitable for on-site collections at clinics. Furthermore, it seems to be possible to take two samples instead of one with constant microbiological results.Peer reviewe

Relative Humidity on Mars: New Results From the Phoenix TECP Sensor

In situ measurements of relative humidity (RH) on Mars have only been performed by the Phoenix (PHX) and Mars Science Laboratory (MSL) missions. Here we present results of our recalibration of the PHX thermal and electrical conductivity probe (TECP) RH sensor. This recalibration was conducted using a TECP engineering model subjected to the full range of environmental conditions at the PHX landing site in the Michigan Mars Environmental Chamber. The experiments focused on the warmest and driest conditions (daytime) because they were not covered in the original calibration (Zent et al., 2010, https://doi.org/10.1029/2009JE003420) and previous recalibration (Zent et al., 2016, https://doi.org/10.1002/2015JE004933). In nighttime conditions, our results are in excellent agreement with the previous 2016 recalibration, while in daytime conditions, our results show larger water vapor pressure values. We obtain vapor pressure values in the range ~0.005–1.4 Pa, while Zent et al. (2016, https://doi.org/10.1002/2015JE004933) obtain values in the range ~0.004–0.4 Pa. Our higher daytime values are in better agreement with independent estimates from the ground by the PHX Surface Stereo Imager instrument and from orbit by Compact Reconnaissance Imaging Spectrometer for Mars. Our results imply larger day‐to‐night ratios of water vapor pressure at PHX compared to MSL, suggesting a stronger atmosphere‐regolith interchange in the Martian arctic than at lower latitudes. Further, they indicate that brine formation at the PHX landing site via deliquescence can be achieved only temporarily between midnight and 6 a.m. on a few sols. The results from our recalibration are important because they shed light on the near‐surface humidity environment on Mars.Key PointsWe have recalibrated the relative humidity sensor of the Mars Phoenix landerWe obtain water vapor pressure values in the range ~0.005–1.4 Pa, while in previous recalibrations, values in the range ~0.004–0.4 PaOur results show a two‐order‐of‐magnitude diurnal variation of water vapor pressure, suggesting a strong atmosphere‐regolith interchangePlain Language SummaryWe present our recalibration of Phoenix’s humidity sensor. This recalibration was conducted with a copy of the sensor subjected to the environmental conditions at the Phoenix landing site. Our experiments focus on the warmest and driest conditions because they were not covered in previous calibrations. Our recalibration shows daytime water content values one order of magnitude larger than those in the previous calibration. At nighttime conditions, our results are in excellent agreement with the previous calibration. Our higher daytime values are in better agreement with independent estimates from the ground, and from orbit. Our results imply larger diurnal variations of water content at Phoenix compared to Curiosity, suggesting a stronger atmosphere‐soil interchange in the Martian arctic than at lower latitudes. Further, they indicate that environmental conditions favorable for the formation of saline solutions (brine) are only achieved temporarily between midnight and 6 a.m. on a few Martian days. The results from our recalibration are important because measurements of humidity on the Martian surface are needed to shed light on the local and global water cycle of Mars, and so far, only the Phoenix mission in the arctic region and the Curiosity rover at equatorial latitudes have performed such measurements.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/153252/1/jgre21230.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/153252/2/jgre21230_am.pd

COVID-19 outbreak at a reception centre for asylum seekers in Espoo, Finland

Publisher Copyright: © 2021Background shared accommodation may increase the risk of SARS-CoV-2 transmission. In April 2020, an increasing number of asylum seekers at a reception centre in Espoo, Finland presented with COVID-19 despite earlier implementation of preventive measures. We decided to screen the entire population of the centre for SARS-CoV-2. Methods we offered nasopharyngeal swab collection and SARS-CoV-2 real-time polymerase chain reaction (RT-PCR) analysis to the centre's clients. Symptoms were recorded at the time of diagnostic sample collection using electronic forms and followed up for two weeks through phone interviews and a review of medical records. Findings 260 clients were screened. Of them, 96 (37%) were found positive for SARS-CoV-2 and isolated. The high attack rate prompted the local public health authority to set the other clients in quarantine for 14 days to prevent further spread. Of the positive cases, 61 (64%) reported having had symptoms at the time of the screening or one week prior. Of the 35 initially asymptomatic individuals, 12 developed symptoms during follow-up, while 23 (or 18% of all screened SARS-CoV-2 positive clients) remained asymptomatic. No widespread transmission of COVID-19 was detected after the quarantine was lifted. Interpretation in this large COVID-19 outbreak, voluntary mass screening provided valuable information about its extent and helped guide the public health response. Comprehensive quarantine and isolation measures were likely instrumental in containing the outbreak. Funding Finnish Institution for Health and Welfare, Finnish Immigration Agency, City of EspooPeer reviewe

Severe ulcerative proctitis, pyoderma gangrenosum, hidradenitis suppurativa and fever in a patient with a rare variant of the PSTPIP1 gene

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The diverse meteorology of Jezero crater over the first 250 sols of Perseverance on Mars

NASA’s Perseverance rover’s Mars Environmental Dynamics Analyzer is collecting data at Jezero crater, characterizing the physical processes in the lowest layer of the Martian atmosphere. Here we present measurements from the instrument’s first 250 sols of operation, revealing a spatially and temporally variable meteorology at Jezero. We find that temperature measurements at four heights capture the response of the atmospheric surface layer to multiple phenomena. We observe the transition from a stable night-time thermal inversion to a daytime, highly turbulent convective regime, with large vertical thermal gradients. Measurement of multiple daily optical depths suggests aerosol concentrations are higher in the morning than in the afternoon. Measured wind patterns are driven mainly by local topography, with a small contribution from regional winds. Daily and seasonal variability of relative humidity shows a complex hydrologic cycle. These observations suggest that changes in some local surface properties, such as surface albedo and thermal inertia, play an influential role. On a larger scale, surface pressure measurements show typical signatures of gravity waves and baroclinic eddies in a part of the seasonal cycle previously characterized as low wave activity. These observations, both combined and simultaneous, unveil the diversity of processes driving change on today’s Martian surface at Jezero crater.This work has been funded by the Spanish Ministry of Economy and Competitiveness, through the projects no. ESP2014-54256-C4- 1-R (also -2-R, -3-R and -4-R); Ministry of Science, Innovation and Universities, projects no. ESP2016-79612-C3-1-R (also -2-R and -3-R); Ministry of Science and Innovation/State Agency of Research (10.13039/501100011033), projects no. ESP2016-80320-C2-1-R, RTI2018-098728-B-C31 (also -C32 and -C33), RTI2018-099825-B-C31, PID2019-109467GB-I00 and PRE2020-092562; Instituto Nacional de Técnica Aeroespacial; Ministry of Science and Innovation’s Centre for the Development of Industrial Technology; Spanish State Research Agency (AEI) Project MDM-2017-0737 Unidad de Excelencia “María de Maeztu”—Centro de Astrobiología; Grupos Gobierno Vasco IT1366- 19; and European Research Council Consolidator Grant no 818602. The US co-authors performed their work under sponsorship from NASA’s Mars 2020 project, from the Game Changing Development programme within the Space Technology Mission Directorate and from the Human Exploration and Operations Directorate. Part of this research was carried out at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with the National Aeronautics and Space Administration (80NM0018D0004). G.M. acknowledges JPL funding from USRA Contract Number 1638782. A.G.F. is supported by the European Research Council, Consolidator Grant no. 818602.Peer ReviewedPostprint (published version

A metrological approach to improve accuracy and reliability of ammonia measurements in ambient air

The environmental impacts of ammonia (NH$_3$) in ambient air have become more evident in the recent decades, leading to intensifying research in this field. A number of novel analytical techniques and monitoring instruments have been developed, and the quality and availability of reference gas mixtures used for the calibration of measuring instruments has also increased significantly. However, recent inter-comparison measurements show significant discrepancies, indicating that the majority of the newly developed devices and reference materials require further thorough validation. There is a clear need for more intensive metrological research focusing on quality assurance, intercomparability and validations. MetNH3 (Metrology for ammonia in ambient air) is a three-year project within the framework of the European Metrology Research Programme (EMRP), which aims to bring metrological traceability to ambient ammonia measurements in the 0.5–500 nmol mol$^{−1}$ amount fraction range. This is addressed by working in three areas: (1) improving accuracy and stability of static and dynamic reference gas mixtures, (2) developing an optical transfer standard and (3) establishing the link between high-accuracy metrological standards and field measurements. In this article we describe the concept, aims and first results of the project.EMRP MetNH3 (EURAMET

A metrological approach to improve accuracy and reliability of ammonia measurements in ambient air

The environmental impacts of ammonia (NH$_3$) in ambient air have become more evident in the recent decades, leading to intensifying research in this field. A number of novel analytical techniques and monitoring instruments have been developed, and the quality and availability of reference gas mixtures used for the calibration of measuring instruments has also increased significantly. However, recent inter-comparison measurements show significant discrepancies, indicating that the majority of the newly developed devices and reference materials require further thorough validation. There is a clear need for more intensive metrological research focusing on quality assurance, intercomparability and validations. MetNH3 (Metrology for ammonia in ambient air) is a three-year project within the framework of the European Metrology Research Programme (EMRP), which aims to bring metrological traceability to ambient ammonia measurements in the 0.5–500 nmol mol$^{−1}$ amount fraction range. This is addressed by working in three areas: (1) improving accuracy and stability of static and dynamic reference gas mixtures, (2) developing an optical transfer standard and (3) establishing the link between high-accuracy metrological standards and field measurements. In this article we describe the concept, aims and first results of the project.EMRP MetNH3 (EURAMET

Gene Ontology annotations and resources.

The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over the past year, the GOC has implemented several processes to increase the quantity, quality and specificity of GO annotations. First, the number of manual, literature-based annotations has grown at an increasing rate. Second, as a result of a new 'phylogenetic annotation' process, manually reviewed, homology-based annotations are becoming available for a broad range of species. Third, the quality of GO annotations has been improved through a streamlined process for, and automated quality checks of, GO annotations deposited by different annotation groups. Fourth, the consistency and correctness of the ontology itself has increased by using automated reasoning tools. Finally, the GO has been expanded not only to cover new areas of biology through focused interaction with experts, but also to capture greater specificity in all areas of the ontology using tools for adding new combinatorial terms. The GOC works closely with other ontology developers to support integrated use of terminologies. The GOC supports its user community through the use of e-mail lists, social media and web-based resources

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Background: A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging. Results: We conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2. Conclusions: The top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent. Keywords: Protein function prediction, Disease gene prioritizationpublishedVersio