Formaldehyde over the central Pacific during PEM-Tropics B

Formaldehyde, CH2O, mixing ratios are reported for the central Pacific troposphere from a series of 41 flights, which took place in March-April 1999 as part of the NASA Pacific Exploratory Mission (PEM) -Tropics B mission. Ambient CH2O was collected in aqueous media and quantified using an enzyme-derivatization fluorescence technique. Primary calibration was performed using aqueous standards and known flow rates. Occasionally, CH2O gas standard additions to ambient air were performed as a secondary calibration. Analytical blanks were determined by replacing ambient air with pure air. The estimated precision was ±30 pptv and the estimated accuracy was the sum of ±30 parts per trillion by volume (pptv) ±15% of the measured value. Approximately 25% of the observations were less than the instrumental detection limit of 50 pptv, and 85% of these occurred above 6 km. CH2O mixing ratios decreased with altitude; for example, near the equator the median value in the lowest 2 km was 275 pptv, decreased to 150 pptv by 6 km and was below 100 pptv above 8 km. Between 130 and 170 W and below 1km, a small variation of CH2O mixing ratio with latitude was noted as near-surface median mixing ratios decreased near the equator (275 pptv) and were greater on either side (375 pptv). A marked decrease in near-surface CH2O (200 pptv) was noted south of 23° S on two flights. Between 3° and 23° S, median CH2O mixing ratios were lower in the eastern tropical Pacific than in the western or central Pacific; nominal differences were >100 pptv near the surface to ∼100 pptv at midaltitude to ∼50 pptv at high altitude. Off the coast of Central America and Mexico, mixing ratios as high as 1200 pptv were observed in plumes that originated to the east over land. CH2O observations were consistently higher than the results from a point model constrained by other photochemical species and meteorological parameters. Regardless of latitude or longitude, agreement was best at altitudes above 4 km where the difference between measured and modeled CH2O medians was less than 50 pptv. Below 2 km the model median was approximately 150 pptv less than the measured median. Copyright 2001 by the American Geophysical Union

Fourier-transform infrared spectroscopy for typing of vancomycin-resistant Enterococcus faecium: performance analysis and outbreak investigation.

Vancomycin-resistant Enterococci, mainly Enterococcus faecium (VREfm), are causing nosocomial infections and outbreaks. Bacterial typing methods are used to assist in outbreak investigations. Most of them, especially genotypic methods like multi-locus sequence typing (MLST), whole genome sequencing (WGS), or pulsed-field gel electrophoresis, are quite expensive and time-consuming. Fourier-transform infrared (FT-IR) spectroscopy assesses the biochemical composition of bacteria, such as carboxyl groups in polysaccharides. It is an affordable technique and has a faster turnaround time. Thus, the aim of this study was to evaluate FT-IR spectroscopy for VREfm outbreak investigations. Basic performance requirements like reproducibility and the effects of incubation time were assessed in distinct sample sets. After determining a FT-IR spectroscopy cut-off range, the clustering agreement between FT-IR and WGS within a retrospective (n: 92 isolates) and a prospective outbreak (n: 15 isolates) was investigated. For WGS an average nucleotide identity (ANI) cut-off score of 0.999 was used. Basic performance analysis showed reproducible results. Moreover, FT-IR spectroscopy readouts showed a high agreement with WGS-ANI analysis in clinical outbreak investigations (V-measure 0.772 for the retrospective and 1.000 for the prospective outbreak). FT-IR spectroscopy had a higher discriminatory power than MLST in the outbreak investigations. After determining cut-off values to achieve optimal resolution, FT-IR spectroscopy is a promising technique to assist in outbreak investigation as an affordable, easy-to-use tool with a turnaround time of less than one day. IMPORTANCE Vancomycin-resistant Enterococci, mainly Enterococcus faecium (VREfm), are a frequent cause of nosocomial outbreaks. Several bacterial typing methods are used to track transmissions and investigate outbreaks, whereby genome-based techniques are used as a gold standard. Current methods are either expensive, time-consuming, or both. Additionally, often, specifically trained staff needs to be available. This study provides insight into the use of Fourier-transform infrared (FT-IR) spectroscopy, an affordable, easy-to-use tool with a short turnaround time as a typing method for VREfm. By assessing clinical samples, this work demonstrates promising results for species discrimination and reproducibility. FT-IR spectrosopy shows a high level of agreement in the analysis of VREfm outbreaks in comparison with whole genome sequencing-based methods

Pedogenesis and carbon sequestration in transformed agricultural soils of Sicily

The increasing atmospheric CO2 concentration is a consequence of human activities leading to severe environmental deteriorations. Techniques are thus needed to sequester and reduce atmospheric carbon. One of the proposed techniques is the transformation or construction of new soils into which more organic carbon can be sequestered and CO2 be consumed by increased weathering. By using a chronosequence of new and transformed soils on crushed limestone (0–48 years) in a Mediterranean area (Sicily), we tried to quantify the amount of organic carbon that could be additionally sequestered and to derive the corresponding rates. A further aim was to trace chemical weathering and related CO2 consumption and the evolution of macropores that are relevant for water infiltration and plant nutrition. Owing to the irrigation of the table grape cultivation, the transformed soils developed fast. After about 48 years, the organic C stocks were near 12 kg m−2. The average org. C sequestration rates varied between 68 and 288 g m−2 yr−1. The C accumulation rates in the transformed soils are very high at the beginning and tend to decrease over (modelled) longer time scales. Over these 48 years, a substantial amount of carbonate was leached and reprecipitated as secondary carbonates. The proportion of secondary carbonates on the total inorganic carbon was up to 50%. Main mineralogical changes included the formation of interstratified clay minerals, the decrease of mica and increase of chloritic components as well as goethite. The atmospheric CO2 consumption due to silicate weathering was in the range of about 44–72 g C m−2 yr−1. Due to the high variability, the contribution of chemical weathering to CO2 consumption represents only an estimate. When summing up organic C sequestration and CO2 consumption by silicate weathering, rates in the order of 110–360 g C m−2 yr−1 are obtained. These are very high values. We estimated that high sequestration and CO2 consumption rates are maintained for about 50–100 years after soil transformation. The macropore volume decreased over the observed time span to half (from roughly 10 to 5 %). The transformation of soils may even amend their characteristics and increase agricultural production. Due to the relatively sandy character, enough macropores were present and no substantial compaction of the soils occurred. However, great caution has to be taken as such measures can trigger deterioration of both soil ecosystem services and soil quality

Project PathoPig—A practical approach to strengthen post mortem analyses and early detection of pig diseases and zoonoses

Post mortem examinations are important for early detection and diagnosis of animal diseases and zoonoses. Over the last ten years, the number of necropsies in livestock has decreased considerably in Switzerland. To counteract this decline, the Federal Food Safety and Veterinary Office (FSVO) launched a project in 2014 called PathoPig. The aim is to evaluate the significance of pathologic-anatomical examinations for early detection of pig diseases and to investigate the impact of the findings on the improvement of pig health. Pig producers can participate if at least one of the following criteria is fulfilled: high morbidity and/or high mortality, unusual clinical signs, recurrent problems of unknown aetiology resistant to therapy or increased use of antimicrobials. Accordingly, the veterinarian examines the herd, fills in a standardised anamnesis protocol and submits one to three pigs representing the health problem to a designated pathology laboratory. After post mortem examination, the veterinarian offers specific recommendations to the farmer. Three to six months later, the Swiss Pig Health Service (SPHS) follows up the success of the veterinary recommendations. In 2014, 371 farms submitted pigs for PathoPig. In 84% of these cases, a conclusive diagnosis was obtained. In 56% of the cases, gastrointestinal problems were determined, most often (44%) caused by pathogenic Escherichia coli. In more than 80% of the cases, the animal health status could be improved considerably after the veterinary consultation. Increased post mortem examinations allowed more specific therapeutic treatments and management recommendations. Additionally, an improvement of collaboration between diagnostic laboratories, veterinarians and producers was achieved, thereby strengthening disease awareness and early detection of pig diseases and zoonoses in Switzerland

Calcifediol versus vitamin D3 effects on gait speed and trunk sway in young postmenopausal women: a double-blind randomized controlled trial

UNLABELLED In this double-blind RCT, 4-month treatment with calcifediol compared with vitamin D3 improved gait speed by 18 % among young postmenopausal women. Consistently, change in 25(OH)D blood levels over time were significantly correlated with improvement in gait speed in these women. No effect could be demonstrated for trunk sway. INTRODUCTION The aim of this study is to test the effect of calcifediol compared with vitamin D3 on gait speed and trunk sway. METHODS Twenty healthy postmenopausal women with an average 25(OH)D level of 13.2 ng/ml (SD = ±3.9) and a mean age of 61.5 years (SD = ±7.2) were randomized to either 20 μg of calcifediol or 20 μg (800 IU) of vitamin D3 per day in a double-blind manner. At baseline and at 4 months of follow-up, the same physiotherapist blinded to treatment allocation tested 8-m gait speed and a body sway test battery (Sway star pitch and roll angle plus velocity while walking 8 m, and standing on both legs on a hard and soft surface). All analyses adjusted for baseline measurement, age, and body mass index. RESULTS Mean 25(OH)D levels increased to 69.3 ng/ml (SD = ±9.5) in the calcifediol group and to 30.5 ng/ml (SD = ±5.0) in the vitamin D3 group (p < 0.0001). Women receiving calcifediol compared with vitamin D3 had an 18 % greater improvement in gait speed at 4-month follow-up (p = 0.046) adjusting for baseline gait speed, age, and body mass index. Also, change in gait speed was significantly correlated with change in serum 25(OH)D concentrations (r = 0.5; p = 0.04). Across three tests of trunk sway, there were no consistent differences between groups and no significant correlation between change in 25(OH)D serum concentrations and change in trunk sway. CONCLUSIONS Calcifediol improved gait speed in early postmenopausal women compared with vitamin D3 and change in 25(OH)D level was moderately correlated with improvement in gait speed. A benefit on trunk sway could not be demonstrated

Adverse pregnancy and neonatal outcomes associated with <i>Neisseria gonorrhoeae:</i> systematic review and meta-analysis.

ObjectiveTo examine associations between Neisseria gonorrhoeae (NG) infection during pregnancy and the risk of preterm birth, spontaneous abortion, premature rupture of membranes, perinatal mortality, low birth weight and ophthalmia neonatorum.Data sourcesWe searched Medline, EMBASE, the Cochrane Library and Cumulative Index to Nursing and Allied Health Literature for studies published between 1948 and 14 January 2020.MethodsStudies were included if they reported testing for NG during pregnancy and compared pregnancy, perinatal and/or neonatal outcomes between women with and without NG. Two reviewers independently assessed papers for inclusion and extracted data. Risk of bias was assessed using established checklists for each study design. Summary ORs with 95% CIs were generated using random effects models for both crude and, where available, adjusted associations.ResultsWe identified 2593 records and included 30 in meta-analyses. Women with NG were more likely to experience preterm birth (OR 1.55, 95% CI 1.21 to 1.99, n=18 studies); premature rupture of membranes (OR 1.41, 95% CI 1.02 to 1.92, n=9); perinatal mortality (OR 2.16, 95% CI 1.35 to 3.46, n=9); low birth weight (OR 1.66, 95% CI 1.12 to 2.48, n=8) and ophthalmia neonatorum (OR 4.21, 95% CI 1.36 to 13.04, n=6). Summary adjusted ORs were, for preterm birth 1.90 (95% CI 1.14 to 3.19, n=5) and for low birth weight 1.48 (95% CI 0.79 to 2.77, n=4). In studies with a multivariable analysis, age was the variable most commonly adjusted for. NG was more strongly associated with preterm birth in low-income and middle-income countries (OR 2.21, 95% CI 1.40 to 3.48, n=7) than in high-income countries (OR 1.38, 95% CI 1.04 to 1.83, n=11).ConclusionsNG is associated with a number of adverse pregnancy and newborn outcomes. Further research should be done to determine the role of NG in different perinatal mortality outcomes because interventions that reduce mortality will have the greatest impact on reducing the burden of disease in low-income and middle-income countries.Prospero registration numberCRD42016050962

Introducing a new breed of wine yeast: interspecific hybridisation between a commercial Saccharomyces cerevisiae wine yeast and Saccharomyces mikatae

Interspecific hybrids are commonplace in agriculture and horticulture; bread wheat and grapefruit are but two examples. The benefits derived from interspecific hybridisation include the potential of generating advantageous transgressive phenotypes. This paper describes the generation of a new breed of wine yeast by interspecific hybridisation between a commercial Saccharomyces cerevisiae wine yeast strain and Saccharomyces mikatae, a species hitherto not associated with industrial fermentation environs. While commercially available wine yeast strains provide consistent and reliable fermentations, wines produced using single inocula are thought to lack the sensory complexity and rounded palate structure obtained from spontaneous fermentations. In contrast, interspecific yeast hybrids have the potential to deliver increased complexity to wine sensory properties and alternative wine styles through the formation of novel, and wider ranging, yeast volatile fermentation metabolite profiles, whilst maintaining the robustness of the wine yeast parent. Screening of newly generated hybrids from a cross between a S. cerevisiae wine yeast and S. mikatae (closely-related but ecologically distant members of the Saccharomyces sensu stricto clade), has identified progeny with robust fermentation properties and winemaking potential. Chemical analysis showed that, relative to the S. cerevisiae wine yeast parent, hybrids produced wines with different concentrations of volatile metabolites that are known to contribute to wine flavour and aroma, including flavour compounds associated with non-Saccharomyces species. The new S. cerevisiae x S. mikatae hybrids have the potential to produce complex wines akin to products of spontaneous fermentation while giving winemakers the safeguard of an inoculated ferment.Jennifer R. Bellon, Frank Schmid, Dimitra L. Capone, Barbara L. Dunn, Paul J. Chamber

ESBL displace: a protocol for an observational study to identify displacing Escherichia coli strain candidates from ESBL-colonized travel returners using phenotypic, genomic sequencing and metagenome analysis

Introduction: Invading extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-PE), non-ESBL E. coli, and other bacteria form a complex environment in the gut. The duration and dynamics of ESBL-PE colonization varies among individuals. Understanding the factors associated with colonization may lead to decolonization strategies. In this study, we aim to identify (i) single E. coli strains and (ii) microbiome networks that correlate with retention or decline of colonization, and (iii) pan-sensitive E. coli strains that potentially could be used to displace ESBL-PE during colonization. Methods and analysis: We recruit healthy travellers to Southeast Asia for a one-year prospective observational follow-up study. We collect and biobank stool, serum, and peripheral blood mononuclear cells (PBMCs) at predefined timepoints. Additional information is collected with questionnaires. We determine the colonization status with ESBL-PE and non-ESBL E. coli and quantify cell densities in stools and ratios over time. We characterize multiple single bacterial isolates per patient and timepoint using whole genome sequencing (WGS) and 16S/ITS amplicon-based and shotgun metagenomics. We determine phylogenetic relationships between isolates, antimicrobial resistance (AMR; phenotypic and genotypic), and virulence genes. We describe the bacterial and fungal stool microbiome alpha and beta diversity on 16S/ITS metagenomic data. We describe patterns in microbiome dynamics to identify features associated with protection or risk of ESBL-PE colonization. Ethics and dissemination: The study is registered (clinicaltrials.gov; NCT04764500 on 09/02/2019) and approved by the Ethics Committee (EKNZ project ID 2019-00044). We will present anonymized results at conferences and in scientific journals. Bacterial sequencing data will be shared via publicly accessible databases according to FAIR principles