Rapid and robust assembly and decoding of molecular tags with DNA-based nanopore signatures

Molecular tagging is an approach to labeling physical objects using DNA or other molecules that can be used when methods such as RFID tags and QR codes are unsuitable. No molecular tagging method exists that is inexpensive, fast and reliable to decode, and usable in minimal resource environments to create or read tags. To address this, we present Porcupine, an end-user molecular tagging system featuring DNA-based tags readable within seconds using a portable nanopore device. Porcupine’s digital bits are represented by the presence or absence of distinct DNA strands, called molecular bits (molbits). We classify molbits directly from raw nanopore signal, avoiding basecalling. To extend shelf life, decrease readout time, and make tags robust to environmental contamination, molbits are prepared for readout during tag assembly and can be stabilized by dehydration. The result is an extensible, real-time, high accuracy tagging system that includes an approach to developing highly separable barcodes.

Porcupine: Rapid and robust tagging of physical objects using nanopore-orthogonal DNA strands

Molecular tagging is an approach to labeling physical objects using DNA or other molecules that can be used in cases where methods like RFID tags and QR codes are not suitable. No molecular tagging method exists that is inexpensive, fast and reliable to decode, and usable outside a lab setting to create or read tags. To address this, we present Porcupine, an end-user molecular tagging system that features DNA-based tags readable within seconds using a portable nanopore device. Porcupine’s digital bits are represented by the presence or absence of distinct, nanopore-orthogonal DNA strands, which we call molecular bits (molbits). We classify molbits directly from the raw nanopore signal, avoiding basecalling. To extend the tag’s shelf life, decrease readout time, and make tags robust to environmental contamination, molbits are prepared for readout during tag assembly and can be stabilized by dehydration. The result is an extensible, real time, high accuracy tagging system that includes a novel approach to developing nanopore-orthogonal barcodes.One sentence summaryPorcupine lets end-users label physical objects with custom DNA tags, without requiring a lab to create or read tags, and offers rapid readout using nanopore sequencing.

Switching and partially switching the hypercube while maintaining perfect state transfer

A graph is said to exhibit perfect state transfer (PST) if one of its corresponding Hamiltonian matrices, which are based on the vertex-edge structure of the graph, gives rise to PST in a quantum information-theoretic context, namely with respect to inter-qubit interactions of a quantum system. We perform various perturbations to the hypercube graph---a graph that is known to exhibit PST---to create graphs that maintain many of the same properties of the hypercube, including PST as well as the distance for which PST occurs. We show that the sensitivity with respect to readout time errors remains unaffected for the vertices involved in PST. We give motivation for when these perturbations may be physically desirable or even necessary.

Precision in a rush: trade-offs between reproducibility and steepness of the hunchback expression pattern

Fly development amazes us by the precision and reproducibility of gene expression, especially since the initial expression patterns are established during very short nuclear cycles. Recent live imaging of hunchback promoter dynamics shows a stable steep binary expression pattern established within the three minute interphase of nuclear cycle 11. Considering expression models of different complexity, we explore the trade-o between the ability of a regulatory system to produce a steep boundary and minimize expression variability between different nuclei. We show how a limited readout time imposed by short developmental cycles affects the gene’s ability to read positional information along the embryo’s anterior posterior axis and express reliably. Comparing our theoretical results to real-time monitoring of the hunchback transcription dynamics in live flies, we discuss possible regulatory strategies, suggesting an important role for additional binding sites, gradients or non-equilibrium binding and modified transcription factor search strategies.

Airborne measurements of CO₂ column concentrations made with a pulsed IPDA lidar using a multiple-wavelength-locked laser and HgCdTe APD detector

Here we report on measurements made with an improved CO2 Sounder lidar during the ASCENDS 2014 and 2016 airborne campaigns. The changes made to the 2011 version of the lidar included incorporating a rapidly wavelength-tunable, step-locked seed laser in the transmitter, using a much more sensitive HgCdTe APD detector and using an analog digitizer with faster readout time in the receiver. We also improved the lidar's calibration approach and the XCO2 retrieval algorithm. The 2014 and 2016 flights were made over several types of topographic surfaces from 3 to 12 km aircraft altitudes in the continental US. The results are compared to the XCO2 values computed from an airborne in situ sensor during spiral-down maneuvers. The 2014 results show significantly better performance and include measurement of horizontal gradients in XCO2 made over the Midwestern US that agree with chemistry transport models. The results from the 2016 airborne lidar retrievals show precisions of ∼ 0.7 parts per million (ppm) with 1 s averaging over desert surfaces, which is an improvement of about 8 times compared to similar measurements made in 2011. Measurements in 2016 were also made over fresh snow surfaces that have lower surface reflectance at the laser wavelengths. The results from both campaigns showed that the mean values of XCO2 retrieved from the lidar consistently agreed with those based on the in situ sensor to within 1 ppm. The improved precision and accuracy demonstrated in the 2014 and 2016 flights should benefit future airborne science campaigns and advance the technique's readiness for a space-based instrument.

Tests and foreseen developments of fibered-OSLD gamma heating measurements in low-power reactors

In this paper are presented test measurements of a fibered-OSLD system performed during a dedicated experimental phase in EOLE zero-power reactor. The measurement setup consists of an OSLD crystal connected onto the extremity of an optical fiber and a laser stimulation system, manufactured by the CEA/LIST in Saclay. The OSL sensor is remotely stimulated via an optical fiber using a diode-pumped solid-state laser. The OSL light is collected and guided back along the same fiber to a photomultiplier tube. Results obtained using this system are compared to usual gamma heating measurement protocol using OSLD pellets. The presence of induced radio-luminescence in the OSLD during the irradiation was also observed and could be used to monitor the gamma flux. The feasibility of remote measurements is achieved, whereas further developments could be conducted to improve this technique since the readout procedure still requires to withdraw the OSLD off the gamma flux (hence from the core) on account of the dose rate (around a few Gy.h-1), and the readout time remains quite long for on-line applications. Several improvements are foreseen, and will be tested in the forthcoming years.

Nanophotonic rare-earth quantum memory with optically controlled retrieval

Optical quantum memories are essential elements in quantum networks for long-distance distribution of quantum entanglement. Scalable development of quantum network nodes requires on-chip qubit storage functionality with control of the readout time. We demonstrate a high-fidelity nanophotonic quantum memory based on a mesoscopic neodymium ensemble coupled to a photonic crystal cavity. The nanocavity enables >95% spin polarization for efficient initialization of the atomic frequency comb memory and time bin–selective readout through an enhanced optical Stark shift of the comb frequencies. Our solid-state memory is integrable with other chip-scale photon source and detector devices for multiplexed quantum and classical information processing at the network nodes.

Assessment of colorimetric amplification methods in a paper-based immunoassay for diagnosis of malaria

We have evaluated the impact of readout time and the ease-of-perception on accurate interpretation of colorimetric readouts in immunoassays.

Design and Analysis of High Frame Rate Capable Active Pixel Sensor by Using CNTFET Devices for Nanoelectronics

This paper presents a high frame rate capable Active Pixel Sensor (APS) using Carbon Nanotube Field Effect Transistor (CNTFET) instead of Complementary Metal Oxide Semiconductor (CMOS). Conventionally, the design of a single APS circuit is based on three transistors (3T) model. In order to achieve higher frame rate, one extra transistor with a column sensor circuit has been introduced in the proposed design to reduce the readout time. This study also concerns about the effect of transistor sizing, bias current, and moreover, the chiral vector of CNTFET. The power consumption and power delay product (PDP) are also investigated for specific sets of reset and row selector signal. Data for these studies were collected with the help of HSPICE software which were further plotted in OriginPro to analyze the optimal operation point of APS circuit. The bias current was also recorded for the readout transistor which is uniquely introduced in the proposed model for achieving better readout time. Hence, the main focus of this paper is to improve the frame rate by reducing the readout time. Results of the proposed CNTFET APS circuit are compared with the conventional CMOS APS circuit. The performance benchmarking shows that CNTFET APS cell significantly reduces readout time, PDP, and thus can achieve much higher frame rate than that of conventional CMOS APS cell.