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At least 811 records · Page 45

A selective splicing variant of hepcidin mRNA in hepatocellular carcinoma cell lines

Hepcidin is a main regulator of iron metabolism, of which abnormal expression affects intestinal absorption and reticuloendothelial sequestration of iron by interacting with ferroportin. It is also noted that abnormal iron accumulation is one of the key factors to facilitate promotion and progression of cancer including hepatoma. By RT-PCR/agarose gel electrophoresis of hepcidin mRNA in a hepatocellular carcinoma cell line HLF, a smaller mRNA band was shown in addition to the wild-type hepcidin mRNA. From sequencing analysis, this additional band was a selective splicing variant of hepcidin mRNA lacking exon 2 of HAMP gene, producing the transcript that encodes truncated peptide lacking 20 amino acids at the middle of preprohepcidin. In the present study, we used the digital PCR, because such a small amount of variant mRNA was difficult to quantitate by the conventional RT-PCR amplification. Among seven hepatoma-derived cell lines, six cell lines have significant copy numbers of this variant mRNA, but not in one cell line. In the transient transfection analysis of variant-type hepcidin cDNA, truncated preprohepcidin has a different character comparing with native preprohepcidin: its product is insensitive to digestion, and secreted into the medium as a whole preprohepcidin form without maturation. Loss or reduction of function of HAMP gene by aberrantly splicing may be a suitable phenomenon to obtain the proliferating advantage of hepatoma cells. - Highlights: • An aberrant splicing variant of hepcidin mRNA lacking exon 2 of HAMP gene. • Absolute quantification of hepcidin mRNA by digital PCR amplification. • Hepatoma-derived cell lines have significant copies of variant-type hepcidin mRNA. • Truncated preprohepcidin is secreted from cells without posttranslational cleavage.

60 APPLIED LIFE SCIENCES↗

Computing the binding affinity of a ligand buried deep inside a protein with the hybrid steered molecular dynamics

Computing the ligand-protein binding affinity (or the Gibbs free energy) with chemical accuracy has long been a challenge for which many methods/approaches have been developed and refined with various successful applications. False positives and, even more harmful, false negatives have been and still are a common occurrence in practical applications. Inevitable in all approaches are the errors in the force field parameters we obtain from quantum mechanical computation and/or empirical fittings for the intra- and inter-molecular interactions. These errors propagate to the final results of the computed binding affinities even if we were able to perfectly implement the statistical mechanics of all the processes relevant to a given problem. And they are actually amplified to various degrees even in the mature, sophisticated computational approaches. In particular, the free energy perturbation (alchemical) approaches amplify the errors in the force field parameters because they rely on extracting the small differences between similarly large numbers. In this paper, we develop a hybrid steered molecular dynamics (hSMD) approach to the difficult binding problems of a ligand buried deep inside a protein. Sampling the transition along a physical (not alchemical) dissociation path of opening up the binding cavity- -pulling out the ligand- -closing back the cavity, we can avoid the problem of error amplifications by not relying on small differences between similar numbers. We tested this new form of hSMD on retinol inside cellular retinol-binding protein 1 and three cases of a ligand (a benzylacetate, a 2-nitrothiophene, and a benzene) inside a T4 lysozyme L99A/M102Q(H) double mutant. In all cases, we obtained binding free energies in close agreement with the experimentally measured values. This indicates that the force field parameters we employed are accurate and that hSMD (a brute force, unsophisticated approach) is free from the problem of error amplification suffered by many sophisticated approaches in the literature.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Necrostatin-7 suppresses RANK-NFATc1 signaling and attenuates macrophage to osteoclast differentiation

Highlights: • Nec-7, but not Nec-1, inhibited osteoclast formation and function. • Nec-7 did not affect the M-CSF-supported survival of osteoclast precursor cells. • Nec-7 selectively attenuated RANK-NFATc1 axis and osteoclastic gene expression. • Forced overexpression of RANK restored osteoclastogenesis and NFATc1 amplification. Osteoclasts play a crucial role in osteolytic bone diseases, such as osteoporosis, rheumatoid arthritis, periodontitis, Paget's disease of bone and bone metastatic tumors. Therefore, controlling osteoclast differentiation and function has been considered a promising therapeutic strategy. Here, we show that necrostatin (Nec)-7, an inhibitor of programmed necrosis, strongly suppressed receptor activator of nuclear factor (NF)-κB ligand (RANKL)-induced osteoclastogenesis and bone resorption, without compromising macrophage colony-stimulating factor (M-CSF)-supported survival and growth of osteoclast precursor cells. Accordingly, Nec-7 significantly decreased the levels of RANKL-induced osteoclastogenic marker genes, such as cathepsin K. Mechanistically, Nec-7 neither affected MAPK nor NF-κB activation; however, it strongly inhibited the RANKL receptor (RANK) to nuclear factor of activated T cells c1 (NFATc1) signaling. Lentiviral expression of RANK in bone marrow-derived macrophages significantly restored osteoclastogenesis and NFATc1 amplification in Nec-7-treated cells. In this study, we revealed that Nec-7-sensitive pathways are crucially involved in osteoclast formation and function. Investigation of the molecular mechanism(s) through which Nec-7 inhibits RANK-NFATc1 signaling axis may lead to the development of new therapeutic strategies for bone disease.

60 APPLIED LIFE SCIENCES↗

Are media reports able to cause somatic symptoms attributed to WiFi radiation? An experimental test of the negative expectation hypothesis

People suffering from idiopathic environmental intolerance attributed to electromagnetic fields (IEI-EMF) experience numerous non-specific symptoms that they attribute to EMF. The cause of this condition remains vague and evidence shows that psychological rather than bioelectromagnetic mechanisms are at work. We hypothesized a role of media reports in the etiology of IEI-EMF and investigated how somatosensory perception is affected. 65 healthy participants were instructed that EMF exposure can lead to enhanced somatosensory perception. Participants were randomly assigned to watch either a television report on adverse health effects of EMF or a neutral report. During the following experiment, participants rated stimulus intensities of tactile (electric) stimuli while being exposed to a sham WiFi signal in 50% of the trials. Sham WiFi exposure led to increased intensity ratings of tactile stimuli in the WiFi film group, especially in participants with higher levels of somatosensory amplification. Participants of the WiFi group reported more anxiety concerning WiFi exposure than the Control group and tended to perceive themselves as being more sensitive to EMF after the experiment compared to before. Sensational media reports can facilitate enhanced perception of tactile stimuli in healthy participants. People tending to perceive bodily symptoms as intense, disturbing, and noxious seem most vulnerable. Receiving sensational media reports might sensitize people to develop a nocebo effect and thereby contribute to the development of IEI-EMF. By promoting catastrophizing thoughts and increasing symptom-focused attention, perception might more readily be enhanced and misattributed to EMF. - Highlights: • The etiology of idiopathic environmental intolerance attributed to electromagnetic fields (IEI-EMF) is unknown. • Expectations induced by sensational TV reports could be important in this context. • Watching a sensational movie on EM radiation enhances tactile sensitivity. • Especially vulnerable are persons with high levels of somatosensory amplification. • IEI-EMF might be caused by a nocebo effect.

54 ENVIRONMENTAL SCIENCES↗

Recovery of DNA from fired and unfired cartridge casings: comparison of two DNA collection methods

For over 10 years, various studies have attempted to increase the recovery of DNA from ammunition by modifying the DNA collection, extraction, purification, and amplification procedures, with varying levels of success. This study focused on the “soaking” method of Montpetit & O’Donnell [1] and the “rinse-and-swab" method of Bille et al. [2]. First, testing for the presence of exogenous DNA, 210 boxed cartridges (brass, steel, and nickel-plated) from nine manufacturers were swabbed and DNA was extracted, concentrated, and quantified. Extracts that quantified > 0 ng/µL (44 of 210) were amplified and genotyped with GlobalFiler™. Of those, only one extract yielded two alleles indicating that the manufacturing and packaging of ammunition was virtually DNA free. Next, to obtain a baseline comparison of two DNA collection methods on a non-metallic substrate and identify a suitable number of cells to spot on cartridges, different DNA input amounts of primary human adult epidermal keratinocytes (HEKa) were tested. Thereafter, 300 brass and 300 nickel-plated, cartridges were spotted with HEKa cells containing ~5 ng of DNA, fired or unfired, and processed with either method. Finally, five methods representing hybrids of the soaking and rinse-and-swab methods were tested to determine if variations of those methods could be used to increase DNA yield and recovery. The results show that the soaking method consistently yielded more DNA than the rinse-and-swab method from a non-metallic substrate. However, the comparison study demonstrated that both methods performed comparably for cartridges. On average, the soaking method recovered 0.25 ng of DNA (5.1% recovery) and the rinse-and-swab method recovered 0.28 ng (5.8% recovery). However, average recoveries were significantly different among three analysts and considerable variation in yields were observed, possibly due to storage time. Furthermore, consistent with prior reports, the DNA recovered from brass casings was only 16% of that recovered from nickel-plated casings and the average yield of DNA from fired casings was reduced to 67% of unfired casings. Moreover, DNA extracts from brass or nickel-plated casings did not appear to contain amplification inhibitors and only 30/596 appeared severely degraded. Finally, both the published rinse-and-swab and soaking methods yielded more DNA than all modifications of the two methods. Overall, both methods yielded equivalent DNA quantities. Additionally, recovery of DNA from any given cartridge casing may be dependent on storage time as well as the skill, proficiency, and experience of the analyst and may reflect stochastic effects, particularly for casings containing low copy and/or degraded DNA.

59 BASIC BIOLOGICAL SCIENCES↗

Recent and planned hydrodynamic instability experiments on indirect-drive implosions on the National Ignition Facility

At National Ignition Facility (NIF), yield amplification due to alpha particle heating approached ~3 in the highest performing inertial confinement fusion (ICF) implosions, while yield amplification of ~15-30 is needed for ignition. Hydrodynamic instabilities are a major factor in degradation of implosions while understanding and mitigation of the instabilities are critical to achieving ignition. This article describes recent and planned hydrodynamic instability experiments with several focused platforms that have been developed to directly measure these instabilities in all phases of ICF implosions. Measurements of ripple-shock generation at OMEGA laser have indicated initial seeds for the instabilities in three ablators - plastic (CH), beryllium, and high-density carbon (HDC). Hydrodynamic Growth Radiography (HGR) platform was used to measure instability growth at the ablation front in the acceleration phase of implosions. This platform used pre-imposed 2-D perturbations for growth factor measurements at different perturbation wavelengths and was also used to measure growth of “native roughness” modulations, fill tubes, and capsule support membranes or “tents”. Also, in the acceleration phase several new experimental platforms have been or are being developed to measure instability growth at the ablator-ice interface. In the deceleration phase of implosions, “self-emission” and “self-backlighting” platforms were developed to measure perturbations near peak compression. This article reviews recent progress and results.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Concatenated analyses of phase space microbunching in high brightness electron beam transport

Microbunching instability (MBI) has been a challenging issue in high-brightness electron beam transport for modern accelerators. The existing theoretical formulation of MBI for recirculating accelerators is based on the single-pass analysis. For multi-pass recirculation or a long beam transport line, the intuitive way of quantifying MBI by successive multiplication of individual scalar amplification gains from subsections of a beamline was found to underestimate the effect. More thorough analyses based on concatenation of gain matrices, aimed to combine the density, energy, and transverse–longitudinal modulations for a general linear transport line, will be developed in this paper. Inclusion of such cross-plane microbunching structures in semi-analytical Vlasov analysis is a crucial step to systematically characterize phase space modulations for a beamline complex in terms of concatenating individual beamline segments. In this paper we outline the concept of gain matrix and develop a semi-analytical formulation to include the microbunching structures in the aforementioned phase space modulations. Moreover we investigate the phase space microbunching dynamics in an example lattice of the recirculating beamline, compare the semi-analytical calculation with particle tracking simulations, and find that the microbunching amplification calculated from multiplication of concatenated gain matrices can be considered as upper limit to the start-to-end gains.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Compact readout of large CLYC scintillators with silicon photomultipler arrays

Compact readout of a large (5 x 5 x 5 cm 3) CLYC scintillator was demonstrated with a 8 x 8 array of 6mm silicon photomultipliers (SiPMs, specifically, a SensL ArrayJ-60035-64P) and an optimized amplification and summing circuit. Read out by the SiPM array, the crystal yielded an energy resolution of 5.5% at 662 keV and a figure of merit of 3.5, equivalent to the performance achieved with a 3-inch Hamamatsu R6233-100 PMT. To reduce channel count and avoid individual amplification of each SiPM in the array, the standard outputs of 16 SiPMs were passively summed then amplified. A current feedback amplifier was used for each channel to provide the required fast response time. The four amplified channels were then passively summed resulting in a single signal channel. A custom laboratory setup, based on the PSD8C ASIC, was used to capture the output and provide time-gated integration for PSD computation. We conclude the compact volume, low bias voltage, and reduced mass of the SiPM array readout are desirable for space and national security applications.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Design, construction, and performance of the GEM based radial time projection chamber for the BONuS12 experiment with CLAS12

Here, a new radial time projection chamber based on Gas Electron Multiplier amplification layers was developed for the BONuS12 experiment in Hall B at Jefferson Lab. This device represents a significant evolutionary development over similar devices constructed for previous experiments, including cylindrical amplification layers constructed from single continuous GEM foils with less than 1% dead area. Particular attention had been paid to producing excellent geometric uniformity of all electrodes, including the very thin metalized polyester film of the cylindrical cathode. This manuscript describes the design, construction, and performance of this new detector.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

A 24-channel ultra-low-noise preamplifier for dN/dx measurements with drift tube detectors

Cluster counting $(dN/dx)$ is a promising method to enhance particle identification for gaseous detectors, especially in next-generation collider experiments like the FCC-ee, where good $π/K$ separation over a broad momentum range is essential. However, its implementation in large-scale systems has been limited by the challenging requirements for high-resolution signal amplification and readout. This paper presents a 24-channel ultra-low-noise preamplifier board designed for drift tube detectors to enable $dN/dx$ measurements. The three-stage amplification topology employs SiGe transistors and integrates dedicated noise-minimization techniques, achieving a charge gain of 21.11 mV/fC from 0.3 fC to 50 fC, a bandwidth of 542 MHz, and a voltage gain of 47.8 dB. The measured voltage noise density is 0.35 nV/$\sqrt{\textrm{Hz}}$ , surpassing most of the state-of-the-art preamplifiers for gaseous and silicon detectors. Validation tests conducted on the sMDT chambers at the CERN Proton Synchrotron test beam facility demonstrate that the proposed design meets the stringent preamplifier requirements for implementing the $dN/dx$ method in drift-tube detector systems, achieving an equivalent noise charge of 0.14 fC and a signal-to-noise ratio of 73 when operated with a He:iC 4 H 10 (90:10) gas mixture. The design also shows promise for broader application in other gaseous or semiconductor detectors.

Drift tube detector↗

A facile route towards large area self-assembled nanoscale silver film morphologies and their applications towards metal enhanced fluorescence

Here, we present a facile method for fabricating nanostructured silver films containing a high density of nanoscopic gap features through a surface directed phenomenon utilizing nanoporous scaffolds rather than through traditional lithographic patterning processes. This method enables tunability of the silver film growth by simply adjusting the formulation and processing conditions of the nanoporous film prior to metallization. We further demonstrate that this process can produce nanoscopic gaps in thick (100 nm) silver films supporting localized surface plasmon resonance with large field amplification within the gaps while enabling launching of propagating surface plasmons within the silver grains. These enhanced fields provide metal enhanced fluorescence with enhancement factors as high as 21 times compared to glass, as well as enable visualization of single fluorophore emission. This work provides a low-cost rapid approach for producing novel nanostructures capable of broadband fluorescence amplification, with potential applications including plasmonic and fluorescence based optical sensing and imaging applications.

36 MATERIALS SCIENCE↗

Actuator selection and placement for localized feedback flow control

The selection and placement of actuators and sensors to control compressible viscous flows is addressed by developing a novel methodology based upon the eigensystem structural sensitivity of the linearized evolution operator appropriate for linear feedback control. Forward and adjoint global modes are used to construct a space of possible perturbations to the linearized operator, which yields a small optimization problem for selecting the parameters that best achieve the control objective, including where they should be placed. The method is demonstrated by informing actuation to suppress amplification of the instabilities in boundary layer separation in a high-subsonic diffuser. Complete stabilization is observed in the separated shear layer for short downstream distances at modest Reynolds number. Higher Reynolds numbers and longer distances are expected to be more challenging to stabilize; here the control informed by the procedure still substantively suppresses amplification of instabilities. It is also demonstrated that more complex actuator–sensor selections may not yield superior controllers.

Mechanics↗

Analysis of scale-dependent kinetic and potential energy in sheared, stably stratified turbulence

Budgets of turbulent kinetic energy (TKE) and turbulent potential energy (TPE) at different scales $\ell$ in sheared, stably stratified turbulence are analysed using a filtering approach. Competing effects in the flow are considered, along with the physical mechanisms governing the energy fluxes between scales, and the budgets are used to analyse data from direct numerical simulation at buoyancy Reynolds number $Re_b=O(100)$ . The mean TKE exceeds the TPE by an order of magnitude at the large scales, with the difference reducing as $\ell$ is decreased. At larger scales, buoyancy is never observed to be positive, with buoyancy always converting TKE to TPE. As $\ell$ is decreased, the probability of locally convecting regions increases, though it remains small at scales down to the Ozmidov scale. The TKE and TPE fluxes between scales are both downscale on average, and their instantaneous values are correlated positively, but not strongly so, and this occurs due to the different physical mechanisms that govern these fluxes. Moreover, the contributions to these fluxes arising from the sub-grid fields are shown to be significant, in addition to the filtered scale contributions associated with the processes of strain self-amplification, vortex stretching and density gradient amplification. Probability density functions (PDFs) of the $Q,R$ invariants of the filtered velocity gradient are considered and show that as $\ell$ increases, the sheared-drop shape of the PDF becomes less pronounced and the PDF becomes more symmetric about $R=0$ .

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Diffusive shock re-acceleration

Here, we have performed two-dimensional hybrid simulations of non-relativistic collisionless shocks in the presence of pre-existing energetic particles (‘seeds’); such a study applies, for instance, to the re-acceleration of galactic cosmic rays (CRs) in supernova remnant (SNR) shocks and solar wind energetic particles in heliospheric shocks. Energetic particles can be effectively reflected and accelerated regardless of shock inclination via a process that we call diffusive shock re-acceleration. We determine that re-accelerated seeds can drive the streaming instability in the shock upstream and produce effective magnetic field amplification. This can later trigger the injection of thermal protons even at oblique shocks that ordinarily cannot inject thermal particles. We characterize the current in reflected seeds, finding that it tends to a universal value $J\simeq en_{\text{CR}}v_{\text{sh}}$ , where $en_{\text{CR}}$ is the seed charge density and $v_{\text{sh}}$ is the shock velocity. When applying our results to SNRs, we find that the re-acceleration of galactic CRs can excite the Bell instability to nonlinear levels in less than ${\sim}10~\text{yr}$ , thereby providing a minimum level of magnetic field amplification for any SNR shock. Finally, we discuss the relevance of diffusive shock re-acceleration also for other environments, such as heliospheric shocks, galactic superbubbles and clusters of galaxies.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

From Weibel seeds to dynamo beyond pair-plasmas

Bridging the spatiotemporal scales of magnetic seed field generation and subsequent dynamo amplification in the weakly collisional intracluster medium presents an extreme numerical challenge. We perform collisionless turbulence simulations with initially unmagnetised electrons that capture both magnetic seed generation via the electron Weibel instability and the ensuing dynamo amplification. Going beyond existing pair-plasma studies, we use an ion-to-electron mass ratio of 100 for which we find electron and ion dynamics are sufficiently decoupled. These simulations are enabled by the 10-moment collisionless fluid solver of Gkeyll, which evolves the full pressure tensor for all species. The electron heat-flux closure regulates pressure isotropisation and effectively sets the magnetic Reynolds number. We investigate how the strength of the closure influences the transition between a regime reminiscent of previous kinetic pair-plasma simulations and a regime exhibiting dynamo behaviour qualitatively similar to magnetohydrodynamics.

astrophysical plasmas↗

Application of ATONA Amplifiers to the Measurement of Uranium Isotopic Ratios by Thermal Ionization Mass Spectrometry

Uranium isotopic composition can provide valuable information about the history and provenance of a nuclear material; therefore, uranium isotopic analyses are frequently made in the nuclear forensics, safeguards, and environmental monitoring communities. These measurements have always presented challenges due to the extreme variability in the relative abundance between the major ( 235 U, 238 U) and minor ( 233 U, 234 U, 236 U) isotopes of uranium. Here, the recently developed ATONA (Atto- to Nano-Amp) amplification system paired with Faraday cup detectors has a large dynamic range and low noise floor making it ideal for measuring uranium isotopic ratios in materials of both natural and anthropogenic origin. A wide variety of certified reference materials were analyzed to investigate the utility of the ATONA amplification system for determining uranium isotopic composition in samples ranging from depleted to highly enriched. The ATONA amplifiers provide nearly an order of magnitude improvement in external reproducibility over 10 11 Ω amplifiers when measuring the minor 234 U/ 238 U ratio in isotopically natural and depleted samples and when paired with a secondary electron multiplier can measure very low relative abundance uranium isotopes (i.e., 236 U).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Determining the Reliability of Measuring Mercury Cycling Gene Abundance with Correlations with Mercury and Methylmercury Concentrations

Methylmercury (MeHg) is a bioaccumulative toxic contaminant in many ecosystems but factors governing its production are poorly understood. Recent work has shown that the anaerobic microbial conversion of mercury (Hg) to MeHg requires the Hg-methylation genes hgcAB and that these genes can be used as biomarkers in PCR-based estimators of Hg-methylator abundance. In an effort to determine reliable methods for assessing hgcA abundance and diversity and linking it to MeHg concentrations, multiple approaches were compared including metagenomic shotgun sequencing, 16S rRNA gene pyrosequencing and cloning/sequencing hgcAB gene products. Hg-methylator abundance was also determined by quantitative hgcA qPCR amplification and metaproteomics for comparison to the above measurements. Samples from eight Hg-contaminated sites were examined over a range of total Hg (HgT; 0.03–14 mg kg-1 wet wt. soil) and MeHg (0.05–27 µg kg-1 wet wt. soil) concentrations. In the metagenome and amplicon sequencing of hgcAB diversity, the Deltaproteobacteria were the dominant Hg-methylators, while Firmicutes and methanogenic Archaea were typically ~50% less abundant. This was consistent with metaproteomics estimates where the Deltaproteobacteria were consistently higher. The 16S rRNA gene pyrosequencing did not have sufficient resolution to identify hgcAB+ species. Metagenomic and hgcAB results were similar for Hg-methylator diversity and showed a tractable relationship between Hg-methylating bacteria and soil Hg concentrations among similar environmental samples. However, clade-specific qPCR-based approaches for hgcA are only appropriate when comparing the abundance of a particular clade across various samples.

59 BASIC BIOLOGICAL SCIENCES↗

Experimental Study of the Detection Limit in Dual-Gate Biosensors Using Ultrathin Silicon Transistors

Dual-gate field-effect biosensors (bioFETs) with asymmetric gate capacitances were shown to surpass the Nernst limit of 59 mV/pH. However, previous studies have conflicting findings on the effect of the capacitive amplification scheme on the sensor detection limit, which is inversely proportional to the signal-to-noise ratio (SNR). In this paper, we present a systematic experimental investigation of the SNR using ultrathin silicon transistors. Our sensors operate at low voltage and feature asymmetric front and back oxide capacitances with asymmetry factors of 1.4 and 2.3. We demonstrate that in the dual-gate configuration, the response of our bioFETs to the pH change increases proportional to the asymmetry factor and indeed exceeds the Nernst limit. Further, our results reveal that the noise amplitude also increases in proportion to the asymmetry factor. We establish that the commensurate increase of the noise amplitude originates from the intrinsic low-frequency characteristic of the sensor noise, dominated by number fluctuation. Finally, these findings suggest that this capacitive signal amplification scheme does not improve the intrinsic detection limit of the dual-gate biosensors.

42 ENGINEERING↗