Digital computing is nearing its physical limits as computing needs and energy consumption rapidly increase. Analogue-memory-based neuromorphic computing can be orders of magnitude more energy efficient at data-intensive tasks like deep neural networks, but has been limited by the inaccurate and unpredictable switching of analogue resistive memory. Filamentary resistive random access memory (RRAM) suffers from stochastic switching due to the random kinetic motion of discrete defects in the nanometer-sized filament. In this work, this stochasticity is overcome by incorporating a solid electrolyte interlayer, in this case, yttria-stabilized zirconia (YSZ), toward eliminating filaments. Filament-free, bulk-RRAM cells instead store analogue states using the bulk point defect concentration, yielding predictable switching because the statistical ensemble behavior of oxygen vacancy defects is deterministic even when individual defects are stochastic. Both experiments and modeling show bulk-RRAM devices using TiO2-X switching layers and YSZ electrolytes yield deterministic and linear analogue switching for efficient inference and training. Bulk-RRAM solves many outstanding issues with memristor unpredictability that have inhibited commercialization, and can, therefore, enable unprecedented new applications for energy-efficient neuromorphic computing. Beyond RRAM, this work shows how harnessing bulk point defects in ionic materials can be used to engineer deterministic nanoelectronic materials and devices.
The Oxford MinION, the first commercial nanopore sequencer, is also the first to implement molecule-by-molecule real-time selective sequencing or “Read Until”. As DNA transits a MinION nanopore, real-time pore current data can be accessed and analyzed to provide active feedback to that pore. Fragments of interest are sequenced by default, while DNA deemed non-informative is rejected by reversing the pore bias to eject the strand, providing a novel means of background depletion and/or target enrichment. In contrast to the previously published pattern-matching Read Until approach, our RUBRIC method is the first example of real-time selective sequencing where on-line basecalling enables alignment against conventional nucleic acid references to provide the basis for sequence/reject decisions. We evaluate RUBRIC performance across a range of optimizable parameters, apply it to mixed human/bacteria and CRISPR/Cas9-cut samples, and present a generalized model for estimating real-time selection performance as a function of sample composition and computing configuration.
Bartsch, Michael B.; Uhnak, Nicolas E.F.; Morrison, Samuel S.; Hara, Nathaniel J.'.; Edwards, Harrison; Grate, Jay
In ultralow Pu analyses, the gold standard is thermal ionization mass spectrometry (TIMS), which requires pure sources to achieve its performance. This purity is achieved through step-wise purifications. In this work single, anion-exchange beads were trapped in the tubing to allow for dynamic solution cycling over the surface of the beads to improve the rates of metal complex uptake. Here, rates of Pu sorption on single ~900 μm SIR-1200 and ~620 μm Reillex-HPQ beads were determined for single beads trapped in a tube with syringe pump driven dynamic solution cycling over the bead, improving sorption and desorption rates. A static control was used as a comparison. Using 238Pu to enable facile activity-based measurements, rates were determined by measuring the residual Pu after contact with beads using liquid scintillation analysis (LSA) for fixed periods of time. Syringe pump driven dynamic solution cycling results in ~5 and ~15-fold improvements in the sorption rates for SIR-1200 and Reillex-HPQ. Impacts on desorption were also examined.
Emerging sequencing technologies are allowing us to characterize environmental, clinical and laboratory samples with increasing speed and detail, including real-time analysis and interpretation of data. One example of this is being able to rapidly and accurately detect a wide range of pathogenic organisms, both in the clinic and the field. Genomes can have radically different GC content however, such that accurate sequence analysis can be challenging depending upon the technology used. Here, we have characterized the performance of the Oxford MinION nanopore sequencer for detection and evaluation of organisms with a range of genomic nucleotide bias. We have diagnosed the quality of base-calling across individual reads and discovered that the position within the read affects base-calling and quality scores. Finally, we have evaluated the performance of the current state-of-the-art neural network-based MinION basecaller, characterizing its behavior with respect to systemic errors as well as context- and sequence-specific errors. Overall, we present a detailed characterization the capabilities of the MinION in terms of generating high-accuracy sequence data from genomes with a wide range of nucleotide content. This study provides a framework for designing the appropriate experiments that are the likely to lead to accurate and rapid field-forward diagnostics.
Funded through the IHNS/E&HS investment area for FY16-18, the RAPIER LDRD sought to evaluate the potential benefits and applicability of the new Oxford MinION nanopore sequencer to pathogen diagnostic applications in biodefense, biosurveillance, and global/public health. The project had four primary objectives: 1) to investigate the performance of the MinION sequencer while building facility with its operation, 2) to develop microfluidic library prep automation facilitating the use of the MinION in field-forward or point-of-care applications, 3) to leverage CRISPR/Cas9 technology to enable targeted identification of bacterial pathogens, and 4) to capitalize on the real- time data output capabilities of the MinION to enable rapid sequence-based diagnostics. While the rapid evolution of the MinION sequencing technology during the course of the project posed a number of challenges and required a reassessment of initial project priorities, it also provided unique opportunities, notably culminating in our development of the RUBRIC real-time selective sequencing software.
Advances in molecular biology, microfluidics, and laboratory automation continue to expand the accessibility and applicability of these methods beyond the confines of conventional, centralized laboratory facilities and into point of use roles in clinical, military, forensic, and field-deployed applications. As a result, there is a growing need to adapt the unit operations of molecular biology (e.g., aliquoting, centrifuging, mixing, and thermal cycling) to compact, portable, low-power, and automation-ready formats. Here we present one such adaptation, the rotary zone thermal cycler (RZTC), a novel wheel-based device capable of cycling up to four different fixed-temperature blocks into contact with a stationary 4-microliter capillarybound sample to realize 1-3 second transitions with steady state heater power of less than 10 W. We demonstrate the utility of the RZTC for DNA amplification as part of a highly integrated rotary zone PCR (rzPCR) system that uses low-volume valves and syringe-based fluid handling to automate sample loading and unloading, thermal cycling, and between-run cleaning functionalities in a compact, modular form factor. In addition to characterizing the performance of the RZTC and the efficacy of different online cleaning protocols, we present preliminary results for rapid single-plex PCR, multiplex short tandem repeat (STR) amplification, and second strand cDNA synthesis.
Emerging infectious diseases present a profound threat to global health, economic development, and political stability, and therefore represent a significant national security concern for the United States. The increased prevalence of international travel and globalized trade further amplify the threat of infectious disease outbreaks of catastrophic effect. The key to containing and eradicating an outbreak before it goes global is rapid identification of index cases and initial clusters of affected individuals. This depends upon establishment of a biosurveillance network that effectively reaches infectious disease hotspots in even the most remote regions of the world and provides a network-integrated, location-appropriate diagnostic capability. At present, there are two critical needs which must be addressed in order to extend biosurveillance activities beyond centralized laboratory facilities: 1) A simple, reliable, and safe method for immediate stabilization of clinical specimens in the field; and 2) A flexible sample processing platform that enables in-field preparation of clinical specimens for rapid, on-site analysis using a variety of diagnostic assay platforms. These needs are not necessarily mutually exclusive; in fact, we propose that they are most efficiently addressed by a deployable sample processing platform that immediately stabilizes the information content of clinical specimens through transformation of the inherently unstable analytes of interest into stable equivalents that are appropriately formatted for downstream analysis. In order to address this problem, we have developed a sample processing pipeline and microfluidics-based platform modules enabling: 1) Extraction of total RNA from finger-stick quantities of human whole blood; and 2) Microscale synthesis of appropriately-formatted cDNA products that capture the information content of blood RNA in a stable form that supports pathogen detection and/or characterization via PCR and/or Second Generation Sequencing (SGS). Through this research we have discovered new, effective solutions for problems that thus far have hindered use of digital microfluidics (DMF) in biomedical applications. Our work reveals a clear path forward to fieldable, automated sample processing systems that will enable rapid, on-site identification of usual-suspect and novel pathogens in clinical specimens for improved biosurveillance.