The COVID-19 pandemic provides an urgent example where a gap exists between availability of state-of-the-art diagnostics and current needs. As assay protocols and primer sequences become widely ...known, many laboratories perform diagnostic tests using methods such as RT-PCR or reverse transcription loop mediated isothermal amplification (RT-LAMP). Here, we report an RT-LAMP isothermal assay for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus and demonstrate the assay on clinical samples using a simple and accessible point-of-care (POC) instrument. We characterized the assay by dipping swabs into synthetic nasal fluid spiked with the virus, moving the swab to viral transport medium (VTM), and sampling a volume of the VTM to perform the RT-LAMP assay without an RNA extraction kit. The assay has a limit of detection (LOD) of 50 RNA copies per μL in the VTM solution within 30 min. We further demonstrate our assay by detecting SARS-CoV-2 viruses from 20 clinical samples. Finally, we demonstrate a portable and real-time POC device to detect SARS-CoV-2 from VTM samples using an additively manufactured three-dimensional cartridge and a smartphone-based reader. The POC system was tested using 10 clinical samples, and was able to detect SARS-CoV-2 from these clinical samples by distinguishing positive samples from negative samples after 30 min. The POC tests are in complete agreement with RT-PCR controls. This work demonstrates an alternative pathway for SARS-CoV-2 diagnostics that does not require conventional laboratory infrastructure, in settings where diagnosis is required at the point of sample collection.
Scale is a fundamental geographic concept, and a substantial literature exists discussing the various roles that scale plays in different geographical contexts. Relatively little work exists, though, ...that provides a means of measuring the geographic scale over which different processes operate. Here we demonstrate how geographically weighted regression (GWR) can be adapted to provide such measures. GWR explores the potential spatial nonstationarity of relationships and provides a measure of the spatial scale at which processes operate through the determination of an optimal bandwidth. Classical GWR assumes that all of the processes being modeled operate at the same spatial scale, however. The work here relaxes this assumption by allowing different processes to operate at different spatial scales. This is achieved by deriving an optimal bandwidth vector in which each element indicates the spatial scale at which a particular process takes place. This new version of GWR is termed multiscale geographically weighted regression (MGWR), which is similar in intent to Bayesian nonseparable spatially varying coefficients (SVC) models, although potentially providing a more flexible and scalable framework in which to examine multiscale processes. Model calibration and bandwidth vector selection in MGWR are conducted using a back-fitting algorithm. We compare the performance of GWR and MGWR by applying both frameworks to two simulated data sets with known properties and to an empirical data set on Irish famine. Results indicate that MGWR not only is superior in replicating parameter surfaces with different levels of spatial heterogeneity but provides valuable information on the scale at which different processes operate.
Geographically Weighted Regression (GWR) has been broadly used in various fields to model spatially non-stationary relationships. Multi-scale Geographically Weighted Regression (MGWR) is a recent ...advancement to the classic GWR model. MGWR is superior in capturing multi-scale processes over the traditional single-scale GWR model by using different bandwidths for each covariate. However, the multiscale property of MGWR brings additional computation costs. The calibration process of MGWR involves iterative back-fitting under the additive model (AM) framework. Currently, MGWR can only be applied on small datasets within a tolerable time and is prohibitively time-consuming to run with moderately large datasets (greater than 5,000 observations). In this paper, we propose a parallel implementation that has crucial computational improvements to the MGWR calibration. This improved computational method reduces both memory footprint and runtime to allow MGWR modelling to be applied to moderate-to-large datasets (up to 100,000 observations). These improvements are integrated into the mgwr python package and the MGWR 2.0 software, both of which are freely available to download.
Mouse embryonic stem (ES) cells grown in serum exhibit greater heterogeneity in morphology and expression of pluripotency factors than ES cells cultured in defined medium with inhibitors of two ...kinases (Mek and GSK3), a condition known as “2i” postulated to establish a naive ground state. We show that the transcriptome and epigenome profiles of serum- and 2i-grown ES cells are distinct. 2i-treated cells exhibit lower expression of lineage-affiliated genes, reduced prevalence at promoters of the repressive histone modification H3K27me3, and fewer bivalent domains, which are thought to mark genes poised for either up- or downregulation. Nonetheless, serum- and 2i-grown ES cells have similar differentiation potential. Precocious transcription of developmental genes in 2i is restrained by RNA polymerase II promoter-proximal pausing. These findings suggest that transcriptional potentiation and a permissive chromatin context characterize the ground state and that exit from it may not require a metastable intermediate or multilineage priming.
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▸ High-resolution genome-wide transcriptome and epigenome of naive pluripotency ▸ Reduced H3K27me3 at promoters and fewer bivalent domains in naive ES cells ▸ Reduced lineage priming and increased RNA polymerase II pausing in the naive state ▸ Naive ES cells show no delay in differentiation
Ground state pluripotency is characterized by a permissive chromatin context, but gene expression is not promiscuous due to the high prevalence of promoter-proximal pausing of transcription.
Analysis of environmental DNA (eDNA) offers an unprecedented ability to accurately survey biodiversity from aquatic ecosystems. Although eDNA methods have been applied to myriad taxa, scientists are ...now moving away from proof-of-concept work, ultimately evaluating the limits and opportunities of this technology to detect and quantify abundance across organisms and environments. Important considerations enabling such methodology to be used for aquatic conservation contexts includes understanding both the effects of (1) the amount of eDNA released from focal taxa—sources, and (2) the removal of eDNA in the environment—sinks. I review publications on aquatic macroorganism eDNA that have evaluated or considered the effect of sources on signal detection (or quantification) and find few studies acknowledge, and fewer still evaluate, the impact of eDNA production on genomic signal recovery. In this review, I encourage readers to carefully consider source dynamics, and using previously published literature, dissect what roles biotic (e.g. life-history traits, species interactions including stressors) and abiotic (e.g. temperature, salinity) factors likely play in eDNA deposition and recovery, and how this impacts detection, abundance, biomass estimation, and ultimately informed signal interpretation. I further explore the physical sources of eDNA and propose other methods (spatial and temporal) and markers to assist in identifying eDNA origins in aquatic systems. Understanding how these parameters influence variation in eDNA sources will allow for a more comprehensive survey tool, and potentially give insights into environment-population responses.
In this study, targeted sequencing to screen 50 multidrug refractory multiple myeloma (rMM) patients was performed by using the Multiple Myeloma Mutation Panel. Patients were pretreated with both ...immunomodulatory drugs (IMiDs) and proteasome inhibitors (PIs), and 88%, 78%, and 68% were refractory to an IMiD, a PI, or both, respectively. The majority of patients had progressive (82%) or refractory (78%) disease immediately before sampling, with 43% being IMiD refractory and 46% being PI refractory in the most recent line of therapy. Compared with newly diagnosed MM, an increased prevalence of mutations in the Ras pathway genes KRAS, NRAS, and/or BRAF (72%), as well as TP53 (26%), CRBN (12%), and CRBN pathway genes (10%) was observed. Longitudinal analyses performed in 3 patients with CRBN mutations at time of IMiD resistance confirmed that these mutations were undetectable at earlier, IMiD-sensitive time points. Furthermore, the functional introduction of these mutations in MM cells conferred lenalidomide resistance in vitro. These data indicate a differential genetic landscape in rMM associated with drug response.
•The incidence of mutations within the MAPK pathway, the CRBN pathway, and TP53 is significantly increased in drug-refractory MM.•Mutations in CRBN might contribute to IMiD resistance in drug-refractory MM.
An Active Approach to Colloidal Self-Assembly Mallory, Stewart A; Valeriani, Chantal; Cacciuto, Angelo
Annual review of physical chemistry,
04/2018, Letnik:
69, Številka:
1
Journal Article
Recenzirano
Odprti dostop
In this review, we discuss recent advances in the self-assembly of self-propelled colloidal particles and highlight some of the most exciting results in this field, with a specific focus on dry ...active matter. We explore this phenomenology through the lens of the complexity of the colloidal building blocks. We begin by considering the behavior of isotropic spherical particles. We then discuss the case of amphiphilic and dipolar Janus particles. Finally, we show how the geometry of the colloids and/or the directionality of their interactions can be used to control the physical properties of the assembled active aggregates, and we suggest possible strategies for how to exploit activity as a tunable driving force for self-assembly. The unique properties of active colloids lend promise to the design of the next generation of functional, environment-sensing microstructures able to perform specific tasks in an autonomous and targeted manner.
EPDF and EPUB available Open Access under CC-BY-NC-ND licence.It is often claimed that the UK is unusually attached to its National Health Service, and the last decade has seen increasingly visible ...displays of gratitude and love. While social surveys of public attitudes measure how much Britain loves the NHS, this book mobilises new empirical research to ask how Britain love its NHS. Ellen A. Stewart offers timely critique of both the potential, and the dysfunctions, of Britain’s complex love affair with its healthcare system.
The surprising ability of thalidomide and its analogs to treat various hematologic malignancies is through the loss of two transcription factors.
Also see Reports by
Krönke
et al.
and
Lu
et al.
The ...55-year history of the drug thalidomide is Shakespearean in scope, awash in unintended consequences, tragedy, resilience, driven characters, and redemption. Indeed, the most notorious pharmaceutical of modern times comes replete with images of devastating birth defects still firmly embedded in the public consciousness. Less well known has been the resurgence in its use as a therapy to treat hematologic malignancy. On pages 305 and 301 of this issue,
Lu
et al.
(
1
) and
Krönke
et al.
(
2
), respectively, report that thalidomide and derivative compounds have a toxic effect on multiple myeloma by causing the degradation of two transcription factors, Ikaros and Aiolos. This loss halts myeloma growth while simultaneously altering immune cell function.
Understanding the Bone in Cancer Metastasis Fornetti, Jaime; Welm, Alana L; Stewart, Sheila A
Journal of bone and mineral research,
December 2018, Letnik:
33, Številka:
12
Journal Article
PDF
