The Network for the Detection of Atmospheric Composition Change (NDACC) is an international global network of more than 90 stations making high-quality measurements of atmospheric composition that ...began official operations in 1991 after 5 years of planning. Apart from sonde measurements, all measurements in the network are performed by ground-based remote-sensing techniques. Originally named the Network for the Detection of Stratospheric Change (NDSC), the name of the network was changed to NDACC in 2005 to better reflect the expanded scope of its measurements. The primary goal of NDACC is to establish long-term databases for detecting changes and trends in the chemical and physical state of the atmosphere (mesosphere, stratosphere, and troposphere) and to assess the coupling of such changes with climate and air quality. NDACC's origins, station locations, organizational structure, and data archiving are described. NDACC is structured around categories of ground-based observational techniques (sonde, lidar, microwave radiometers, Fourier-transform infrared, UV-visible DOAS (differential optical absorption spectroscopy)-type, and Dobson-Brewer spectrometers, as well as spectral UV radiometers), timely cross-cutting themes (ozone, water vapour, measurement strategies, cross-network data integration), satellite measurement systems, and theory and analyses. Participation in NDACC requires compliance with strict measurement and data protocols to ensure that the network data are of high and consistent quality. To widen its scope, NDACC has established formal collaborative agreements with eight other cooperating networks and Global Atmosphere Watch (GAW). A brief history is provided, major accomplishments of NDACC during its first 25 years of operation are reviewed, and a forward-looking perspective is presented.
With increased involvement of genetic data in most epidemiological investigations, gene–environment (G × E) interactions now stand as a topic, which must be meticulously assessed and thoroughly ...understood. The level, mode, and outcomes of interactions between environmental factors and genetic traits have the capacity to modulate disease risk. These must, therefore, be carefully evaluated as they have the potential to offer novel insights on the “missing heritability problem”, reaching beyond our current limitations. First, we review a definition of G × E interactions. We then explore how concepts such as the early manifestation of the genetic components of a disease, the heterogeneity of complex traits, the clear definition of epidemiological strata, and the effect of varying physiological conditions can affect our capacity to detect (or miss) G × E interactions. Lastly, we discuss the shortfalls of regression models to study G × E interactions and how other methods such as the ReliefF algorithm, pattern recognition methods, or the LASSO (Least Absolute Shrinkage and Selection Operator) method can enable us to more adequately model G × E interactions. Overall, we present the elements to consider and a path to follow when studying genetic determinants of disease in order to uncover potential G × E interactions.
Rapid antigen tests hold much promise for use in the school environment. However, the performance of these tests in non-clinical settings and among one of the main target populations in ...schools-asymptomatic children-is unclear. To address this gap, we examined the positive and negative concordance between the BinaxNOW™ rapid SARS-CoV-2 antigen assay and an RT-PCR test among children at a community-based Covid-19 testing site.
We conducted rapid antigen (BinaxNOW™) and oral fluid RT-PCR (Curative Labs) tests on children presenting at a walk-up testing site in Los Angeles County from November 25, 2020 to December 9, 2020. Positive concordance was determined as the fraction of RT-PCR positive participants that were also antigen positive. Negative concordance was determined as the fraction of RT-PCR negative participants that were also antigen negative. Multivariate logistic regression models were used to examine the association between positive or negative concordance and participant age, race-ethnicity, sex at birth, symptoms and Ct values.
226 children tested positive on RT-PCR; 127 children or 56.2% (95% CI: 49.5% to 62.8%) of these also tested positive on the rapid antigen test. Positive concordance was higher among symptomatic children (64.4%; 95% CI: 53.4% to 74.4%) compared to asymptomatic children (51.1%; 95% CI: 42.5% to 59.7%). Positive concordance was negatively associated with Ct values and was 93.8% (95% CI: 69.8% to 99.8%) for children with Ct values less than or equal to 25. 548 children tested negative on RT-PCR; 539 or 98.4% (95% CI: 96.9% to 99.2%) of these also tested negative on the rapid antigen test. Negative concordance was higher among asymptomatic children.
Rapid antigen testing can successfully identify most COVID infections in children with viral load levels likely to be infectious. Serial rapid testing may help compensate for limited sensitivity in early infection.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Microbial communities drive geochemical cycles in soils. Relatively few studies have assessed the long-term impacts of different types of soil amendments under field conditions in long-term ...experiments. The response of soil microbial organisms in a Mollisol cultivated with maize for 35 years was examined. Treatments involved the use of N, P, and K fertilizers and two doses of straw residue in isolation or combined. Real-time PCR and Illumina MiSeq sequencing methods were used to characterize the microbial community. The results showed that addition of nitrogen fertilizers decreased soil pH, but this was mitigated when a high dose of straw was also incorporated. Long-term application of inorganic fertilizers was able to alter the abundance of functional soil microbial population. Application of inorganic N fertilizer resulted in distinctive changes on N-cycle microorganisms. Phosphate-solubilizing functional genes abundance was lower in plots with no phosphate fertilizer. Sequencing analysis showed that the presence or absence of N in the fertilizer mix is a key factor affecting bacterial community diversity of agricultural soil, and pH, total organic C, and total N show a high correlation with bacterial community composition. Nitrogen addition increased the N concentration in the soil, which could cause changes in the soil pH and change the soil bacterial community. Our findings proved that interaction of N fertilizer with other fertilizers can affect microbial communities.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Abstract
Background
Despite the generally accepted World Health Organization guidelines on semen analysis, an individual’s results can display significant variation when performed across time or in ...different laboratories. Semen parameters are in fact highly variable measures that can differ significantly between various analyses. Numerous researchers have discovered a wide range of semen parameters within each individual male, but only a few studies included the analysis of semen parameters variability in patients with infertility. The aim of this study was to evaluate the inter- and intra-individual variability of semen parameters in men of reproductive age with normozoospermia and those with oligozoospermia.
Methods
Five hundred and thirteen who provided ≥ 2 semen samples (798 samples in total) using an at-home mail-in kit over a period of about 2 years were enrolled in the study. Semen samples collection using Give Legacy at-home mail-in semen collection kit; semen analysis at a CLIA-certified laboratory.
Results
The degree of intra-subject variation across all semen parameters was lower in men with normozoospermia compared to men with oligozoospermia. Men with normozoospermia furthermore demonstrated a level of intra-subject variation that was lower than inter-subject variation across all measured parameters. No association was observed between intra-subject coefficients of variation in any of the semen parameters, including sperm concentration, sperm count, motile sperm count, total motility, progressive motility, the percentage of sperm with normal morphology, and the age, duration of abstinence, and BMI of the men.
Conclusion
The results of this observational study confirm the significant variability in semen parameters in men with normozoospermia and oligozoospermia, as measured from at-home semen collection kit samples. This further underscore the importance of securing multiple samples for analysis to provide a robust assessment of male fertility.
We detected the simian malaria parasites Plasmodium knowlesi, P. cynomolgi, P. inui, P. coatneyi, P. inui–like, and P. simiovale among forest fringe–living indigenous communities from various ...locations in Malaysia. Our findings underscore the importance of using molecular tools to identify newly emergent malaria parasites in humans.
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DOBA, IZUM, KILJ, NUK, ODKLJ, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
In light of climate change and growing numbers of people inhabiting riverine floodplains, worldwide demand for flood protection is increasing, typically through engineering approaches such as more ...and bigger levees. However, the well-documented “levee effect” of increased floodplain use following levee construction or enhancement often results in increased problems, especially when levees fail or are compromised by big flood events. Herein, we argue that there are also unintended socio-economic and ecological consequences of traditional engineering solutions that need to be better considered, communicated and weighed against alternative solutions. Socio-economic consequences include reduced aesthetic and recreational values as well as increased downstream flooding risk and reduced ecosystem services. Ecological consequences include hydraulic decoupling, loss of biodiversity and increased risk of contamination during flooding. In addition, beyond river losses of connectivity and natural riparian vegetation created by levees, changes in groundwater levels and increased greenhouse gas emissions are likely. Because flood protection requires huge financial investments and results in major and persistent changes to the landscape, more balanced decisions that involve all stakeholders and policymakers should be made in the future. This requires a transdisciplinary approach that considers alternative solutions such as green infrastructure and places emphasis on integrated flood management rather than on reliance on technical protection measures.
This opinion piece seeks to define and contextualise educational terms that are used, and appear to be misused, in contemporary academic literature and practice. It aims to explore the concept that ...these three words, open, flexible, and distance, fall into the categories of policy, mode of learning, and models of delivery. In the context in which the globaleducational community across all sectors adapts to new forms of learning, it is essential that practitioners agree on the terminology. Words have definitions, but they also have technical meanings and daily, commonplace, uses that sometimes defy those dictionary definitions. Words sometimes become symbolic, they are adopted by a specific community to cover a range of “sins”, and this use serves to normalise or induct new users into that community. The ability to twist and bend definitions to suit a specific context, to appeal to policy makers or funders, relies on some malleability, some ambiguity, of definitions. In the context of Boyer’s definition of the integration of research (Boyer, 1997), the purpose of this piece is to enable colleagues to decide how to best define and deploy existing, and validate new terminology.
To monitor the incidence of Plasmodium knowlesi infections and determine whether other simian malaria parasites are being transmitted to humans, we examined 1,047 blood samples from patients with ...malaria at Kapit Hospital in Kapit, Malaysia, during June 24, 2013-December 31, 2017. Using nested PCR assays, we found 845 (80.6%) patients had either P. knowlesi monoinfection (n = 815) or co-infection with other Plasmodium species (n = 30). We noted the annual number of these zoonotic infections increased greatly in 2017 (n = 284). We identified 6 patients, 17-65 years of age, with P. cynomolgi and P. knowlesi co-infections, confirmed by phylogenetic analyses of the Plasmodium cytochrome c oxidase subunit 1 gene sequences. P. knowlesi continues to be a public health concern in the Kapit Division of Sarawak, Malaysian Borneo. In addition, another simian malaria parasite, P. cynomolgi, also is an emerging cause of malaria in humans.
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•We catalogued DNA repair mutations across the NCI-60, CCLE and TCGA datasets.•We reveal new gene-drug associations for 260 DNA repair genes across the NCI-60.•SLX4 mutations sensitize to ...topoisomerases and DNA synthesis inhibitors.•This study provides a database for DNA repair alterations in cancer.
Loss of function of DNA repair (DNAR) genes is associated with genomic instability and cancer predisposition; it also makes cancer cells reliant on a reduced set of DNAR pathways to resist DNA-targeted therapy, which remains the core of the anticancer armamentarium. Because the landscape of DNAR defects across numerous types of cancers and its relation with drug activity have not been systematically examined, we took advantage of the unique drug and genomic databases of the US National Cancer Institute cancer cell lines (the NCI-60) to characterize 260 DNAR genes with respect to deleterious mutations and expression down-regulation; 169 genes exhibited a total of 549 function-affecting alterations, with 39 of them scoring as putative knockouts across 31 cell lines. Those mutations were compared to tumor samples from 12 studies of The Cancer Genome Atlas (TCGA) and The Cancer Cell Line Encyclopedia (CCLE). Based on this compendium of alterations, we determined which DNAR genomic alterations predicted drug response for 20,195 compounds present in the NCI-60 drug database. Among 242 DNA damaging agents, 202 showed associations with at least one DNAR genomic signature. In addition to SLFN11, the Fanconi anemia-scaffolding gene SLX4 (FANCP/BTBD12) stood out among the genes most significantly related with DNA synthesis and topoisomerase inhibitors. Depletion and complementation experiments validated the causal relationship between SLX4 defects and sensitivity to raltitrexed and cytarabine in addition to camptothecin. Therefore, we propose new rational uses for existing anticancer drugs based on a comprehensive analysis of DNAR genomic parameters.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
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