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525 results for “amplification”
data for the paper "Role of Vertical Mixing in the Upper Ocean in the Seasonal Variation of Arctic Amplification" in 2nd round peer review
<p>Here are all data for the paper "Role of Vertical Mixing in the Upper Ocean in the Seasonal Variation of Arctic Amplification", which is still during its peer review period. </p>
Transient amplification enhances the persistence of tropicalising coral assemblages in marginal high latitude environments
<p>Predicting the viability of species exposed to increasing climatic stress requires an appreciation for the mechanisms underpinning the success or failure of marginal populations. Rather than traditional metrics of long-term population performance, here we illustrate that short-term (<em>i.e.</em>, transient) demographic characteristics, including measures of resistance, recovery, and compensation, are fundamental in the poleward range expansion of hard corals, facilitating the establishment of coral populations at higher latitudes. Through the annual census of tropical and subtropical <em>Acropora</em> spp. colonies in Japan between 2017-2019, we show how enhanced transient amplification (<em>i.e.</em>, short-term increases in population growth following disturbance) supports the persistence of coral assemblages within more variable high-latitude environments. The transient dynamics of both the tropical and subtropical assemblages were strongly influenced by their corresponding recruitment patterns. However, we demonstrate that variation in colony survival and fragmentation patterns between the two assemblages determines their relative capacities for transient amplification. This latitudinal variation in the transient dynamics of <em>Acropora</em> spp. assemblages emphasises that coral populations can possess the demographic plasticity necessary for exploiting more variable, marginal conditions.</p>
A fast machine-learning-guided primer design pipeline for selective whole genome amplification
<p>Addressing many of the major outstanding questions in the fields of microbial evolution and pathogenesis will require analyses of populations of microbial genomes. Although population genomic studies provide the analytical resolution to investigate evolutionary and mechanistic processes at fine spatial and temporal scales – precisely the scales at which these processes occur – microbial population genomic research is currently hindered by the practicalities of obtaining sufficient quantities of the relatively pure microbial genomic DNA necessary for next-generation sequencing. Here we present swga2.0, an optimized and parallelized pipeline to design selective whole genome amplification (SWGA) primer sets. Unlike previous methods, swga2.0 incorporates active and machine learning methods to evaluate the amplification efficacy of individual primers and primer sets. Additionally, swga2.0 optimizes primer set search and evaluates strategies, including parallelization at each stage of the pipeline, to dramatically decrease program runtime from weeks to minutes. Here we describe the swga2.0 pipeline, including the empirical data used to identify primer and primer set characteristics, that improve amplification performance. Additionally, we evaluated the novel swga2.0 pipeline by designing primers sets that successfully amplify <em>Prevotella melaninogenica</em>, an important component of the lung microbiome in cystic fibrosis patients, from samples dominated by human DNA.</p>
Melanopsin-mediated amplification of cone signals in the human visual cortex
<p>The ambient daylight variation is coded by melanopsin photoreceptors and their luxotonic activity increases towards midday when colour temperatures are cooler, and irradiances are higher. Although melanopsin and cone photoresponses can be mediated via separate pathways, the connectivity of melanopsin cells across all levels of the retina enables them to modify cone signals. The downstream effects of melanopsin-cone interactions on human vision are however, incompletely understood. Here, we determined how the change in daytime melanopsin activation affects the human cone pathway signals in the visual cortex. A 5-primary silent-substitution method was developed to evaluate the dependence of cone-mediated signals on melanopsin activation by spectrally tuning the lights and stabilising the rhodopsin activation under a constant cone photometric luminance. The retinal (white noise electroretinogram, wnERG) and cortical responses (visual evoked potential, wnVEP) were simultaneously recorded with the photoreceptor-directed lights in 10 observers. By increasing the melanopsin activation, a reverse response pattern was observed with cone signals being supressed in the retina by 27% (p=0.03) and subsequently amplified by 16% (p=0.01) as they reach the cortex. We infer that melanopsin activity can amplify cone signals at sites distal to retinal bipolar cells to cause a decrease in the psychophysical Weber fraction for cone vision.</p>
Data from: Affordable de novo generation of fish mitogenomes using amplification-free enrichment of mitochondrial DNA and deep sequencing of long fragments
<p>Biomonitoring surveys from environmental DNA make use of metabarcoding tools to describe the community composition. These studies match their sequencing results against public genomic databases to identify the species. However, mitochondrial genomic reference data are yet incomplete, only a few genes may be available, or the suitability of existing sequence data is suboptimal for species-level resolution. Here we present a dedicated and cost-effective workflow with no DNA amplification for generating complete fish mitogenomes for the purpose of strengthening fish mitochondrial databases. Two different long-fragment sequencing approaches using Oxford Nanopore sequencing coupled with mitochondrial DNA enrichment were used. One where the enrichment is achieved by preferential isolation of mitochondria followed by DNA extraction and nuclear DNA depletion ('mitoenrichment'). A second enrichment approach takes advantage of the CRISPR-Cas9 targeted scission on previously dephosphorylated DNA ('targeted mitosequencing'). The sequencing results varied between tissue, species, and integrity of the DNA. The mitoenrichment method yielded 0.17-12.33 % of sequences on target and a mean coverage ranging from 74.9 to 805-fold. The targeted mitosequencing experiment from native genomic DNA yielded 1.83-55 % of sequences on target and a 38 to 2123-fold mean coverage. This produced complete the mitogenome of species with homopolymeric regions, tandem repeats, and gene rearrangements. We demonstrate that deep sequencing of long fragments of native fish DNA is possible and can be achieved with low computational resources in a cost-effective manner, opening the discovery of mitogenomes of non-model or understudied fish taxa to a broad range of laboratories worldwide.</p>
Figure 1 in Diagnostic accuracy of loop-mediated isothermal amplification (LAMP) for screening patients with imported malaria in a non-endemic setting
Figure 1. Study flow chart.
Figure 10 in Pseudomonas aeruginosa associated pulmonary infections and in vitro amplification virulent rhamnolipid (rhlR) gene
Figure 10. Bands glowing closer to the ladder band with 750 bp are representing PCR products.
Figure 2. Showing P in Pseudomonas aeruginosa associated pulmonary infections and in vitro amplification virulent rhamnolipid (rhlR) gene
Figure 2. Showing P. aeruginosa Growth on Citrimide Agar Plates.
Figure 5 in Pseudomonas aeruginosa associated pulmonary infections and in vitro amplification virulent rhamnolipid (rhlR) gene
Figure 5. Shows production of Pyocyanin (Left) and Pyoverdin (Right) pigments in LB broth
Figure 3 in Pseudomonas aeruginosa associated pulmonary infections and in vitro amplification virulent rhamnolipid (rhlR) gene
Figure 3. Showing β-Hemolysis by P. aeruginosa in Blood Agar Test.
Figure 7 in Pseudomonas aeruginosa associated pulmonary infections and in vitro amplification virulent rhamnolipid (rhlR) gene
Figure 7. Resistance of P. aeruginosa having no inhibition zone around antibiotic disc
A power amplification dyad in seahorses
<p><span>Throughout evolution, organisms repeatedly developed elastic elements to power explosive body motions, overcoming ubiquitous limits on the power capacity of fast-contracting muscles. Seahorses evolved such a latch-mediated spring actuation (LaMSA) mechanism; however, it is unclear how this mechanism powers the two complementary functions necessary for feeding: rapidly swinging the head towards the prey, and sucking water into the mouth to entrain it. Here, we combine flow visualization and hydrodynamic modeling to estimate the net power required for accelerating the suction-feeding flows in 13 fish species. We show that the mass-specific power of suction feeding in seahorses is ~3 times higher than the maximum recorded from any vertebrate muscle, resulting in suction flows that are ~8 times faster than similar-sized fish. Using material testing, we reveal that the rapid contraction of the sternohyoideus tendon can release ~72% of the power needed to accelerate the water into the mouth. We conclude that the LaMSA system in seahorses is powered by two elastic elements, the sternohyoideus and epaxial tendons. These elements jointly actuate the coordinated acceleration of the head and the fluid in front of the mouth. These findings extend the known function, capacity, and design of LaMSA systems.</span></p>
Dataset - In-situ amplification of spin echoes within a kinetic inductance parametric amplifier
<p>Raw data and analysis for arXiv:2211.11333</p> <p> </p>
Primer sequences for H3N2 canine influenza virus full-length amplification, polymerase activity assay, and rescue
<p><span>Influenza A viruses in animal reservoirs repeatedly cross species barriers to infect humans. Once an animal-borne virus with novel antigenicity acquired the efficient human-to-human transmissibility, it will become epidemic in the population. Dogs are the closest animal companions to humans, and canine respiratory tract expresses both SAα2,3-(avian type) and α2,6-Gal (human type) receptors. However, the role of dogs in the ecology of influenza viruses is unclear. H3N2 avian influenza viruses were transmitted to dogs around 2006 and have formed stable lineages. The long-term epidemic of avian-origin H3N2 virus in canines offers the best models to investigate the effect of dogs on the evolution of influenza viruses. Here, we carried out a systematic and comparative identification of the biological characteristics of H3N2 canine influenza viruses (CIVs) isolated in worldwide</span> <span>over 10 years. We found that during the adaptation of H3N2 CIVs to dogs, H3N2 CIVs became to recognize the human-like SAα2,6-Gal receptor, gradually increased HA acid stability and replication ability in human airway epithelial cells, and acquired a 100% transmission rate via respiratory droplet in ferret model, which were essential hallmarks of being adapted to humans. We also identified that the frequency of substitutions related to human adaptation has gradually increased in H3N2 CIVs and determined four cumulative molecular changes responsible for the increased airborne transmission ability in ferrets. Our results suggested that canines may serve as an intermediate for the adaptation of avian influenza virus to humans. Continuous surveillance coordinated with risk assessment for CIVs is necessary.</span></p>
Disposable platform for bacterial lysis and nucleic acid amplification based on a single USB-powered printed circuit board
<p>Recent advances in electronics and microfluidics have enabled several research groups to develop fully integrated, sample-to-result isothermal nucleic acid amplification test (NAAT) platforms for the point of care. However, high component counts and costs have limited translation of these platforms beyond the clinic to low-resource settings—including homes. Many NAATs include complex, multi-component heater electronics based on flex circuits or multiple printed circuit boards (PCBs) to support essential NAAT steps such as lysis, sample deactivation, and nucleic acid amplification. In contrast, current commercial assays for home use, such as those for pregnancy or ovulation that include electronics, typically have just one onboard PCB. This work describes a generalizable strategy to integrate all heaters and the electronics needed to control them onto a single low-cost, USB-powered PCB. We built a multiplexable disposable NAAT ("MD NAAT") platform that applies these principles, integrating small-area heaters that heat small regions to near-boiling (for pathogen lysis and deactivation) and large-area heaters (for amplification) on the same PCB. We show that both classes of heaters have high intra-board and inter-device reproducibility despite only heating a NAAT cartridge from below. We validated the small-area heaters by lysing methicillin-resistant <em>Staphylococcus</em> <em>aureus</em> (MRSA) cells and the large-area heaters by performing two types of isothermal NAATs (isothermal strand displacement amplification (iSDA) and loop-mediated isothermal amplification (LAMP)). These results demonstrate the merit of integrating NAAT heaters and control electronics onto a single printed circuit board and are a step toward translating NAATs to the home.</p>
Estimated site amplifications at DONET stations, 1D velocity models, and movies for seismic wave propagation in a local 1D models
<ul> <li>Site amplification factors of vertical (V) and horizontal (H) components at DONET stations at each frequency band (1-2, 2-4, 4-8, and 2-8 Hz)</li> <li>Anelastic attenuations are estimated during least square inversions for maximum S-wave amplitudes at DONET and F-net stations.</li> <li>Local 1D velocity structure models used in this study</li> <li>Animation movie of seismic wave propagation in local 1D models <ul> <li>Movies can be available using <a href="https://www.videolan.org/vlc/index.en_GB.html">the VLC media player</a></li> </ul> </li> </ul> <p>Details of the method and results were described in the paper:<br><span>Takemura, S.</span>, <span>Emoto, K.</span>, & <span>Yabe, S.</span> (<span>2024</span>). <span>Revisiting seismic energy of shallow tremors: Amplifications due to site and propagation path effects near the Nankai Trough</span>. <em>Journal of Geophysical Research: Solid Earth</em>, <span>129</span>, e2024JB029168. <a href="https://doi.org/10.1029/2024JB029168">https://doi.org/10.1029/2024JB029168</a></p>
A Study of ABT-414 in Participants With Newly Diagnosed Glioblastoma (GBM) With Epidermal Growth Factor Receptor (EGFR) Amplification
ClinicalTrials.gov study NCT02573324. IPD Sharing: YES. Countries: 28. Publications: 3.
Derazantinib in Subjects With FGFR2 Gene Fusion-, Mutation- or Amplification- Positive Inoperable or Advanced Intrahepatic Cholangiocarcinoma
ClinicalTrials.gov study NCT03230318. IPD Sharing: NO. Countries: 11. Publications: 1.
AZD1775 in Treating Patients With Advanced Refractory Solid Tumors With CCNE1 Amplification
ClinicalTrials.gov study NCT03253679. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Performance of Nucleic Acid Amplification Tests for the Detection of NG and CT
ClinicalTrials.gov study NCT02870101. IPD Sharing: Not stated. Countries: 1. Publications: 23.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
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