Linear Amplification Research Articles

RNA-based isothermal amplification technology and its clinical application in pathogen infection

Abstract It is very important to detect pathogenic bacteria, viruses, or fungi in a patient’s secretion or body fluid samples as soon as possible to determine the patient’s recovery. For certain pathogens, the amount of ribosomal RNA copies contained is often tens of thousands of times higher than the amount of DNA copies, so the detection of RNA has higher sensitivity. In addition, whether for DNA pathogens or RNA pathogens, the direct detection of ribonucleic acid transcribed by pathogens in vivo can distinguish active infection or past infection, can eliminate the influence of residual DNA of pathogens that have died in the lesions, and can also avoid excessive medical interventions for transient infections, which is of great significance in the field of infectious pathogen detection. Isothermal amplification technology played important roles in molecular diagnosis because of its significant advantages. Highly sensitive RNA detection can be achieved by both direct transcription amplification and indirect amplification based on reverse transcription. Direct transcription amplification technologies relies on reverse transcriptase and T7 RNA polymerase to achieve linear transcription amplification of RNA on one-step; while the indirect amplification technology depends on a reverse transcriptional process at the beginning of the reaction. Both methods have outstanding advantages in clinical application, and commercial kits and commercial all-in-one machines based on these principles have been put into clinical use. This review mainly introduces the clinical application of isothermal amplification technologies in the detection of RNA pathogens and the main difficulties faced at this stage. It is hoped to provide insightful ideas for the construction of pathogen RNA detection technology to meet the needs of point-of-care testing in the future.

Supporting multiple entanglement flows through a continuous-variable quantum repeater

Quantum repeaters are critical to the development of quantum networks, enabling rates of entanglement distribution beyond those attainable by direct transmission. We consider multiple continuous-variable, squeezed light-based entanglement flows through a repeater involving noiseless linear amplification and dual homodyne detection. By analyzing a single-repeater-enhanced channel model with asymmetric losses across the repeater, we determine optimal placements of the central repeater hub in a 4-user hub-and-spoke network such that the rate of each entanglement flow through the hub is enhanced.

Comparison of techniques for distillation of entanglement over a lossy channel

We analyze three quantum communication protocols that have been proposed in the literature and compare how well they communicate single-rail entanglement. We use specific metrics for output-state purity and probability of success and include the presence of imperfect photon source and detection components. We find that a distributed noiseless linear amplification (NLA) protocol with a relay point placed halfway between Alice and Bob outperforms NLA at Bob's end and a recently proposed purification protocol under most conditions, unless the distance is very small or the photon source component is very good.

An advanced and efficient asymmetric PCR method for microarray applications.

The sensitivity of a PCR based biochip assay relies on the efficiency of PCR amplicons in binding to the microarray spots. The essential factor determining the sensitivity is the amount of single stranded (ss) amplicons available for biochip hybridization. Asymmetric PCR can generate ss-amplicons depending on the ratio of primers used in the amplification process, but this process is often inefficient. We report a novel variant of PCR called the Asymmetric Exponential and Linear Amplification (AELA) which can overcome these issues and generate large amounts of single stranded amplicons. AELA-PCR introduces an amplification strategy that makes use of both exponential and linear amplification of the target nucleic acid. This is done by specifically designed primers and choice of adequate thermal profiles. In conventional PCR with a classical thermal profile, these specifically designed primers will work normally and contribute to an exponential increase of amplicons. A designed sequence extension of one of the primers and a very specific thermal profile, will result in a situation that the extended primer will be the only functional one for amplification, resulting in a linear phase of the amplification process. That is why during this step only one of the two strands of the target is amplified linearly and no longer exponentially. The result of the whole process is an amplification product enriched very strongly in one of the two single strands of the target. These adaptions in PCR are particularly favorable where the generation of ss-DNA/RNA is required. We demonstrate the higher biochip sensitivity of AELA-PCR compared to conventional amplification methods with an example of the Staphylococcus aureus detection on a DNA oligonucleotide microarray.

Stimulated-Raman-scattering amplification of attosecond XUV pulses with pulse-train pumps and application to local in-depth plasma-density measurement.

We present a scheme for amplifying an extreme-ultraviolet (XUV) seed isolated attosecond pulse via stimulated Raman scattering of a pulse-train pump. At sufficient seed and pump intensity, the amplification is nonlinear, and the amplitude of the seed pulse can reach that of the pump, one order of magnitude higher than the initial seed amplitude. In the linear amplification regime, we find that the spectral signature of the pump pulse train is imprinted on the spectrum of the amplified seed pulse. Since the spectral signature is imprinted with its frequency downshifted by the plasma frequency, it is possible to deduce the electron density in the region of interaction. This region can be of micrometer length scale longitudinally. By varying the delay between the seed and the pump, this scheme provides a local electron-density measurement inside solid-density plasmas that cannot be probed with optical frequencies, with micrometer resolution.

Small-Signal Analysis and Controller Design of Anode Power Supply for ECRH

The anode power supply is very important to the stability of the output wave power of the electron cyclotron resonance heating (ECRH) system. In order to improve the stability and anti-interference ability of the anode power supply, the small-signal analysis and controller design of the anode power supply are carried out in this article. First, the anode power supply is simplified and equivalent. Then, the LCC resonant circuit and the linear amplification circuit are established, respectively, for detailed analysis and research, and the small-signal models of these two parts are established. The transfer function of the whole system is obtained, the stability and rapidity of the anode power supply are analyzed, and the controller parameters are designed. Finally, the simulation model and prototype are built. The experimental results show that the system has better dynamic response ability and anti-interference ability after adding the controller.

Construction of an Entropy-Driven Dumbbell-Type DNAzyme Assembly Circuit for Lighting Up Uracil-DNA Glycosylase in Living Cells.

Sensitive monitoring of intracellular uracil-DNA glycosylase (UDG) in living cells is essential to understanding the DNA repair pathways and discovery of anticancer drugs. Herein, we demonstrate the construction of an entropy-driven dumbbell-type DNAzyme assembly circuit for lighting up UDG in living cells via the integration of entropy-driven DNA catalysis (EDC) with the DNAzyme biocatalyst. Target UDG excises the damaged uracil base, causing the breakage of detection probe and the release of trigger. The released trigger can initiate the downstream EDC reaction to form two catalytically active DNAzyme units. The resultant dual Mg2+-DNAzyme units serve as the signal transducers to cyclically cleave the fluorophore/quenched-modified reporters, generating an enhanced fluorescence signal. In contrast to the single-layered EDC method with a linear amplification, the proposed doublet EDC-DNAzyme strategy exhibits high signal gain and achieves a detection limit of 8.71 × 10-6 U/mL. Notably, this assay can be performed in one-step manner at room temperature without the requirement of strict temperature control and complicated reaction procedures, and it can further screen the UDG inhibitors, measure kinetic parameters, and discriminate cancer cells from normal cells. Moreover, this strategy can monitor intracellular UDG activity with improved signal gain, and it may be exploited for sensing and imaging of other types of DNA modifying enzymes with the integration of the corresponding detection substrate, providing a facile and robust approach for biological research studies and clinical diagnosis.

Identification and characterization of extrachromosomal circular DNA in alcohol induced osteonecrosis of femoral head.

Alcohol-induced osteonecrosis of the femoral head (AIONFH) is a complicated refractory bone disease seen in the clinic. The pathogenesis of AIONFH is still controversial. Extrachromosomal circular DNA (eccDNA) elements have been indicated ubiquitously exist in eukaryotic genomes. However, the characteristics and biological functions of eccDNAs remain unclear in AIONFH. In this study, eccDNAs from AIONFH samples (n = 7) and fracture of femoral neck samples as a control (n = 7) were purified by removing linear DNA and rolling circle amplification. High-throughput sequencing and bioinformatics analysis were performed to study the characterization and biofunction of eccDNAs. We identified more than 600,000 unique eccDNAs. The number of detected eccDNAs in AIONFH was less than that in the control, and eccDNA formation may be related to transcription or other characteristics of coding genes. The eccDNA lengths are mainly distributed between 0.1 kb and 1 kb, with a major peak in 0.358 kb. The bioinformatic analysis showed that 25 significant genes were detected, including MAP3K1, ADCY1, CACNA1S, and MACF1, which contributed to regulating bone formation. GO and KEGG analyses suggested that the related genes derived from exons mainly affected metabolic processes and signal transduction, and bone metabolism-related pathways, such as the MAPK pathway and TGF-β pathway, were enriched. EccDNAs in AIONFH are common and may play an important role in pathogenesis by regulating bone metabolism.

Quantum scissors for noiseless linear amplification of polarization frequency hyper-encoded coherent state

Quantum scissor (QS) is a powerful tool to realize the optical truncation and noiseless linear amplification (NLA) of the Fock state. The hyper-encoding technology which encodes messages in two or more degrees of freedom of a photon is a promising tool for increasing the channel capacity of photons and has been widely used in quantum computing and quantum communication fields. Here, we propose the one-photon and three-photon QSs for the frequency-encoded and polarization frequency hyper-encoded coherent states, which can realize the one-order and three-order truncation and NLA of the coherent state, and preserve the encoded features of the photons. The quantum scissors for the hyper-encoded coherent state would introduce some unwanted disturb items with small probability. Our QSs can be extended to distill the hyper-encoded multi-spatial-mode entanglement. Our QSs have application potential in the future quantum information processing field.

A study on the effect of site response on California seismic hazard map assessment

Prior studies have repeatedly shown that probabilistic seismic hazard maps from several different countries predict higher shaking than that observed. Previous map assessments have not, however, considered the influence of site response on hazard. Seismologists have long acknowledged the influence of near-surface geology, in particular low-impedance sediment layers, on earthquake ground-motion at frequencies of engineering concern. Although the overall effects of site response are complex, modern ground-motion models (GMMs) account for site effects using terms based on VS30, the time-averaged shear-wave velocity in the upper 30 m of the Earth’s surface. In this study, we consider general implications of incorporating site terms from modern GMMs using site-specific VS30 as a proxy in probabilistic seismic hazard maps for California. At the long periods (1–5 s) that affect tall buildings, site terms amplify the mapped hazard by factors of 1–3 at many sites relative to maps calculated for the standard reference soft-rock site condition, VS30 = 760 m/s. However, at the short periods of ground-motion that are the main contributors to peak ground acceleration (PGA) and thus affect smaller structures, only negligible effects occur due to nonlinear deamplification of strong ground-motion at high frequencies. Nonlinear deamplification increases as the shaking level increases. For very strong shaking, deamplification can overcome the linear amplification, yielding net deamplification. We explore the implications of these results for the evaluation of hazard maps. Because site effects do not change the maps appreciably at short periods, we can exclude site response as an explanation for why the maps overpredict historically observed shaking as captured by the California Historical Intensity Mapping Project (CHIMP) dataset. The results are expected to be generalizable to regions that are comparable to California in terms of structure and seismicity rates. In low-to-moderate-seismicity regions where the hazard reflects weaker shaking, nonlinear site response is expected to be less important for the hazard.

A digitally controlled linear power supply for HALF fast orbit correctors

The fourth-generation synchrotron radiation source Hefei Advanced Light Facility (HALF) requires higher stability of the beam orbit. The corrector power supply with fast response and high stability can effectively reduce the latency of the Fast Orbit FeedBack (FOFB) system and improve the beam quality. In this paper, an FPGA-based, fully digitally controlled linear power supply based on H-bridge topology is proposed. Multiple buck circuits are cascaded as the front stage power supply, and the linear amplification of the H-bridge MOSFETs provides the power for the corrector load. The PI closed loop is calculated by the FPGA and finally drives the MOSFETs through the high precision Digital to Analog Converter (DAC) chip. As a result, the response bandwidth of the power supply can reach 5 kHz, and the long-term stability and current ripple are better than 20 ppm, which will improve the beam quality of HALF. The design can also be easily extended to other magnet power supply and fast power conversion technologies.

Summary of the Abrahamson and Gulerce NGA-SUB ground-motion model for subduction earthquakes

A set of region-specific ground-motion models (GMMs) for subduction zone earthquakes are developed based on the database compiled by the Pacific Earthquake Engineering Research Center (PEER) Next Generation Attenuation: Subduction project (NGA-SUB). The subset used to develop the GMMs includes 3914 recordings from 113 subduction interface earthquakes with magnitudes between 5 and 9.2 and 4850 recordings from 89 intraslab events with magnitudes between 5 and 7.8. The functional form of the global GMM accommodates the differences in the magnitude, distance, and depth scaling for interface and intraslab earthquakes. In addition to the global model, region-specific GMMs are developed for seven regions: Alaska, Cascadia, Central America, Japan, New Zealand, South America, and Taiwan. The magnitude scaling and the geometrical spreading parameters of the global model are used in all region-specific models, with the exception of the Taiwan region, which has a region-specific geometrical-spreading term. Four region-specific terms are included in the median GMM: the large distance (linear R) scaling, linear site amplification scaling (ln(VS30)), basin depth scaling (for Cascadia and Japan), and the constant term. The aleatory variability is also regionalized with larger aleatory variability at short periods for the Central America, Japan, and South America regions. Estimates of the epistemic uncertainty for the median and aleatory terms for each region are provided. The proposed global and region-specific GMMs are considered to be applicable to sites in the forearc region at distances up to 500 km, magnitudes of 5.0–9.5, and spectral periods from 0 to 10 s. The Cascadia-specific model is applicable to distances of 800 km including the backarc region.

Efficiency Enhancement of CMOS Power Amplifier for RF Applications

This paper presented a new structure for the CMOS power amplifiers as a more effective trend to amplify radio frequency (RF) signals compared to polar power amplifiers PA's by using envelope removal and restoration (EER) technique. Polar PA offers high-efficiency RF-modulated linear signal amplification. However, these amplifiers need high uniformity between the amplitude and phase of the modulated signals. The last translates promptly into higher energy consumption. Rather than deconstructing the quadrature signals into the combination of phase and amplitude signals, it is suggested that the CMOS quadrature power amplifier (QPA's) technique had been used to amplify RF signals immediately. The linearity, bandwidth, efficiency, and power consumption of the QPA's has been improved by separate amplitude and phase quadrature signals. The quadratic geometry architecture contains two bridges from modulated PA's that are able to treat negative or positive voltages, modulation, and RF-power bundling. The design of the new structure is compared with respect to parameters such as fundamental frequency, power gain, PAE, output power, technology or fabrication process, and number of stage transistors. Simulation results for PA's design using CMOS process show an effective quadrature model by a power-added-efficiency (PAE) of 78.413% at a maximum output power of 21.619dBm. The third intermodulation IDM3 is -49.2dBc at output power driven at frequency 2.4 GHz and input power greater than 20dBm. The amplitude and phase distortion has been obtained of 1.4 and 0.26 ᵒ/dB respectively at 50MHz of bandwidth for modulated signals.

Predicting Aided Outcome With Aided Word Recognition Scores Measured With Linear Amplification at Above-conversational Levels.

Many hearing aid (HA) users receive limited benefit from amplification, especially when trying to understand speech in noise, and they often report hearing-related residual activity limitations. Current HA fitting strategies are typically based on pure-tone hearing thresholds only, even though suprathreshold factors have been linked to aided outcomes. Furthermore, clinical measures of speech perception such as word recognition scores (WRSs) are performed without frequency-specific amplification, likely resulting in suboptimal speech audibility and thus inaccurate estimates of suprathreshold hearing abilities. Corresponding measures with frequency-specific amplification ("aided") would likely improve such estimates and enable more accurate aided outcome prediction. Here, we investigated potential links between either unaided WRSs or aided WRSs measured at several above-conversational levels and two established HA outcome measures: The Hearing-In-Noise Test (HINT) and the International Outcome Inventory for Hearing Aids (IOI-HA). Thirty-seven older individuals with bilateral hearing impairments participated. Two conditions were tested: unaided and aided, with all stimuli presented over headphones. In the unaided condition, the most comfortable level (MCL) for the presented speech stimuli, WRS at MCL+10 dB as well as uncomfortable levels (UCLs) for narrowband noise stimuli were measured. In the aided condition, all stimuli were individually amplified according to the "National Acoustic Laboratories-Revised, Profound" fitting rule. Aided WRSs were then measured using an Interacoustics Affinity system at three above-conversational levels, allowing for the maximum aided WRS as well as the presence of "rollover" in the performance-intensity function to be estimated. Multivariate data analyses were performed to examine the relations between the HINT (measured using a simulated HA with the NAL-RP amplification) or IOI-HA scores (for the participants' own HAs) and various potential predictors (age, pure-tone average hearing loss, unaided WRS, aided WRS, rollover presence [ROp], and UCL). Aided WRSs predicted the HINT scores better than any other predictor and were also the only significant predictor of the IOI-HA scores. In addition, UCL and ROp in the aided WRSs were significant predictors of the HINT scores and competed for variance in the statistical models. Neither age nor pure-tone average hearing loss could predict the two aided outcomes. Aided WRSs can predict HA outcome more effectively than unaided WRSs, age or pure-tone audiometry and could be relatively easily implemented in clinical settings. More research is necessary to better understand the relations between ROp, UCL and speech recognition at above-conversational levels.

Investigation of Linear Amplification Using Abasic Site-Containing Primers Coupled to Routine STR Typing for LT-DNA Analysis.

Obtaining a full short tandem repeat (STR) profile from a low template DNA (LT-DNA) still presents a challenge for conventional methods due to significant stochastic effects and polymerase slippage. A novel amplification method with a lower cost and higher accuracy is required to improve the DNA amount. Previous studies suggested that DNA polymerases without bypass activity could not perform processive DNA synthesis beyond abasic sites in vitro and our results showed a lack of bypass activity for Phusion, Pfu and KAPA DNA polymerases in this study. Based on this feature, we developed a novel linear amplification method, termed Linear Aamplification for double-stranded DNA using primers with abasic sites near 3′ end (abLAFD), to limit the replication error. The amplification efficiency was evaluated by qPCR analysis with a result of approximately a 130-fold increase in target DNA. In a LT-DNA analysis, the abLAFD method can be employed as a pre-PCR. Similar to nested PCRs, primer sets used for the abLAFD method were designed as external primers suitable for commercial multiplex STR amplification assays. The practical performance of the abLAFD method was evaluated by coupling it to a routine PP21 STR analysis using 50 pg and 25 pg DNA. Compared to reference profiles, all abLAFD profiles showed significantly recovered alleles, increased average peak height and heterozygote balance with a comparable stutter ratio. Altogether, our results support the theory that the abLAFD method is a promising strategy coupled to STR typing for forensic LT-DNA analysis.

Boundary-Layer Instabilities over a Cone–Cylinder–Flare Model at Mach 6

Computations are performed to investigate the convective and global boundary-layer instabilities over a sharp cone–cylinder–flare model at zero-degree angle of attack. The model geometry and the flow conditions are selected to match the experiments conducted in the Boeing/AFOSR Mach 6 Quiet Tunnel at Purdue University. The geometry consists of a nominally sharp 5 deg half-angle cone, followed by a cylindrical segment, and then a 10 deg flare. Additionally, flare half angles equal to 8 and 12 deg and nosetip radii equal to 0.1, 1, and 5 mm are studied. An axisymmetric separation bubble is generated as a result of the laminar shock–boundary-layer interaction in the cylinder–flare region. The comparison of the laminar flow solution and the schlieren images shows a remarkable agreement between the respective locations of both the boundary-layer edge and the reattachment shock. The linear amplification of first and second Mack mode instabilities that begin to amplify in the cone region are computed with a combination of the parabolized stability equations and the harmonic linearized Navier–Stokes equations. The predicted frequency spectra of the surface pressure fluctuations associated with both planar and oblique instability waves capture the distinct lobes within the disturbance amplification spectra measured with PCB® and Kulite sensors. To our knowledge, this represents the first successful comparison between convective instability analysis and measured surface pressure fluctuations for a hypersonic configuration with a separation bubble. Finally, the global instability analysis shows that the laminar flow becomes supercritical for flare half angles larger than 8 deg.

Linear modal instabilities around post-stall swept finite wings at low Reynolds numbers

Linear modal instabilities of flow over untapered wings with aspect ratios$AR=4$and 8, based on the NACA 0015 profile, have been investigated numerically over a range of angles of attack,$\alpha$, and angles of sweep,$\varLambda$, at chord Reynolds numbers$100\le Re\le 400$. Laminar base flows have been generated using direct numerical simulation and selective frequency damping, as appropriate. Several families of unstable three-dimensional linear global (TriGlobal) eigenmodes have been identified and their dependence on geometric parameters has been examined in detail at$Re=400$. The leading global mode A is associated with the peak recirculation in the three-dimensional laminar separation bubble formed on the wing and becomes unstable when recirculation reaches$\textit {O}(10\,\%)$. On unswept wings, this mode peaks in the midspan region of the wake and moves towards the wing tip with increasing$\varLambda$, following the displacement of peak recirculation; its linear amplification leads to wake unsteadiness. Additional amplified modes exist at nearly the same and higher frequencies compared to mode A. The critical$Re$has been identified and it is shown that amplification increases with increasing sweep, up to$\varLambda \approx 10^\circ$. At higher$\varLambda$, all global modes become less amplified and are ultimately stable at$\varLambda =30^\circ$. An increase in amplification of the leading mode with sweep was not observed over the$AR=4$wing, where tip vortex effects were shown to dominate.

Non-PCR Ultrasensitive Detection of Viral RNA by a Nanoprobe-Coupling Strategy: SARS-CoV-2 as an Example.

Developing efficient and highly sensitive diagnostic techniques for early detections of pathogenic viruses such as Severe Acute Respiratory Syndrome Coronavirus 2 (SARS‐CoV‐2) is vitally important for preventing its widespread. However, the conventional polymerase chain reaction (PCR)‐based detection features high complexity, excessive time‐consumption, and labor‐intensiveness, while viral protein‐based detections suffer from moderate sensitivity and specificity. Here, a non‐PCR but ultrasensitive viral RNA detection strategy is reported based on a facile nanoprobe‐coupling strategy without enzymatic amplification, wherein PCR‐induced bias and other shortcomings are successfully circumvented. This approach endows the viral RNA detection with ultra‐low background to maximum signal ratio in the linear signal amplification by using Au nanoparticles as reporters. The present strategy exhibits 100% specificity toward SARS‐CoV‐2 N gene, and ultrasensitive detection of as low as 52 cp mL−1 of SARS‐CoV‐2 N gene without pre‐PCR amplification. This approach presents a novel ultrasensitive tool for viral RNA detections for fighting against COVID‐19 and other types of pathogenic virus‐caused diseases.

Stability of flow in a channel with repeated flow-facing wedge-shaped protrusions

Motivated by an interest in inciting instabilities and mixing for heat transfer enhancement in ducts, flow in a channel with repeated wedge-shaped protrusions is considered for various blockage ratios (wedge height to duct height), pitch (distance between wedges) and wedge angles. The stability of the two-dimensional base flow and its dependence on the geometric parameters is elucidated through a global linear stability analysis. A linearly unstable two-dimensional mode was found, contrasting similar confined flow set-ups. However, the primary instability is a three-dimensional mode manifesting as counter-rotating streamwise vortices over the wedge tip. Analysis of the kinetic energy budget indicates a lift-up mechanism leading to instability, with the dominant energy gain of the global three-dimensional mode due to shear in the base flow. Structural sensitivity and receptivity of the instability to momentum forcing identifies the core of the instability and locations important for flow control. An endogeneity approach is used to show that the local perturbation pressure gradient component dominates the distribution of the local contribution to the growth rate of the linear global eigenmode in most cases considered, despite its net contribution being identically zero. Weakly nonlinear Stuart–Landau analysis reveals that the primary bifurcation is supercritical across all tested geometric parameter combinations. This is consistent with the finding of low linear transient growth amplifications at subcritical Reynolds numbers, being orders of magnitude lower than in similar channel flow set-ups.

Deterministic enhancement for bright-seeded Mach–Zehnder interferometer using low-noise feed-forward amplifiers

We propose to use low-noise feed-forward amplifiers (LFAs) to enhance the phase sensitivity of a bright-seeded Mach–Zehnder interferometer (MZI). LFAs are performed on the two arms inside the MZI, which are based entirely on linear optics, off-line squeezed ancillary states, and homodyne detectors. We demonstrate the necessity of LFA-based topology in achieving sensitivity improvement beyond the standard quantum limit, compared with the deterministic linear amplification scheme. Remarkably, we find that the LFA-based MZI is advantageous over the standard MZI in robustness against the internal losses of the interferometer.