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Bioinformatics (Oxford, England) Feb 2019General-purpose processors can now contain many dozens of processor cores and support hundreds of simultaneous threads of execution. To make best use of these threads,...
MOTIVATION
General-purpose processors can now contain many dozens of processor cores and support hundreds of simultaneous threads of execution. To make best use of these threads, genomics software must contend with new and subtle computer architecture issues. We discuss some of these and propose methods for improving thread scaling in tools that analyze each read independently, such as read aligners.
RESULTS
We implement these methods in new versions of Bowtie, Bowtie 2 and HISAT. We greatly improve thread scaling in many scenarios, including on the recent Intel Xeon Phi architecture. We also highlight how bottlenecks are exacerbated by variable-record-length file formats like FASTQ and suggest changes that enable superior scaling.
AVAILABILITY AND IMPLEMENTATION
Experiments for this study: https://github.com/BenLangmead/bowtie-scaling.
BOWTIE
http://bowtie-bio.sourceforge.net.
BOWTIE 2
http://bowtie-bio.sourceforge.net/bowtie2.
HISAT
http://www.ccb.jhu.edu/software/hisat.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
Topics: Algorithms; Computer Systems; Genomics; Software
PubMed: 30020410
DOI: 10.1093/bioinformatics/bty648 -
Sensors (Basel, Switzerland) Oct 2022For a small satellite, the processor onboard the attitude determination and control system (ADCS) is required to monitor, communicate, and control all the sensors and...
For a small satellite, the processor onboard the attitude determination and control system (ADCS) is required to monitor, communicate, and control all the sensors and actuators. In addition, the processor is required to consistently communicate with the satellite bus. Consequently, the processor is unable to ensure all the sensors and actuators will immediately respond to the data acquisition request, which leads to asynchronous data problems. The extended Kalman filter (EKF) is commonly used in the attitude determination process, but it assumes fully synchronous data. The asynchronous data problem would greatly degrade the attitude determination accuracy by EKF. To minimize the attitude estimation accuracy loss due to asynchronous data while ensuring a reasonable computational complexity for small satellite applications, this paper proposes the simplex-back-propagation Kalman filter (SBPKF). The proposed SBPKF incorporates the time delay, gyro instability, and navigation error into both the measurement and covariance estimation during the Kalman update process. The performance of SBPKF has been compared with EKF, modified adaptive EKF (MAEKF), and moving-covariance Kalman filter (MC-KF). Simulation results show that the attitude estimation error of SBPKF is at least 30% better than EKF and MC-KF. In addition, the SBPKF's computational complexity is 17% lower than MAEKF and 29% lower than MC-KF.
PubMed: 36298321
DOI: 10.3390/s22207970 -
Journal of Healthcare Engineering 2022With the development of science and technology of the times, the level of medical care is constantly improving. For patients transferred from ICU, the intelligent... (Review)
Review
Safety Influencing Factors and Management Countermeasures of Patients Transferred from ICU in Transition Period Based on Intelligent Processor Three-Dimensional Quality Model.
With the development of science and technology of the times, the level of medical care is constantly improving. For patients transferred from ICU, the intelligent processor 3D quality model technology has gradually played an important role in clinical treatment and has become a new type of attention. In order to understand the implementation status of transitional care and the feelings of transitional care for patients transferred from ICU and understand the views of transitional care-related department doctors on transitional patient care and the role that the intelligent processor three-dimensional quality model can play, this article passed a review of the city ICU transferred patients from a hospital that conducted related investigations, reviewed related literature, conducted interviews with professionals, etc., collected relevant information, constructed case templates, and created a clinical research model using comprehensive quantitative and qualitative analysis methods. The results of the study found that, after treatment, patients transferred from the ICU based on the intelligent processor's three-dimensional quality model have higher physical activity than patients treated by other methods, the ratio is more than 20%, and the postoperative recovery efficiency of patients is higher than 15% and more. This shows that the three-dimensional quality model based on the intelligent processor can improve the important role in the transition period of patients transferred from ICU.
Topics: Humans; Intensive Care Units
PubMed: 35126898
DOI: 10.1155/2022/1455830 -
Medicines (Basel, Switzerland) Sep 2020Consumers are concerned about the use of synthetic additives in foods and this has forced food processors to find ways to produce food products without the use of these...
Consumers are concerned about the use of synthetic additives in foods and this has forced food processors to find ways to produce food products without the use of these additives [...].
PubMed: 32937755
DOI: 10.3390/medicines7090058 -
Sensors (Basel, Switzerland) Apr 2022This paper proposes a high-speed continuous wavelet transform (CWT) processor to analyze vital signals extracted from a frequency-modulated continuous wave (FMCW) radar...
This paper proposes a high-speed continuous wavelet transform (CWT) processor to analyze vital signals extracted from a frequency-modulated continuous wave (FMCW) radar sensor. The proposed CWT processor consists of a fast Fourier transform (FFT) module, complex multiplier module, and inverse FFT (IFFT) module. For high-throughput processing, the FFT and IFFT modules are designed with the pipeline FFT architecture of radix-2 single-path delay feedback (R2SDF) and mixed-radix multipath delay commutator (MRMDC) architecture, respectively. In addition, the IFFT module and the complex multiplier module perform a four-channel operation to reduce the processing time from repeated operations. Simultaneously, the MRMDC IFFT module minimizes the circuit area by reducing the number of non-trivial multipliers by using a mixed-radix algorithm. In addition, the proposed CWT processor can support variable lengths of 8, 16, 32, 64, 128, 256, 512, and 1024 to analyze various vital signals. The proposed CWT processor was implemented in a field-programmable gate array (FPGA) device and verified through the measurement of heartbeat and respiration from an FMCW radar sensor. Experimental results showed that the proposed CWT processor can reduce the processing time by 48.4-fold and 40.7-fold compared to MATLAB software with Intel i7 CPU. Moreover, it can be confirmed that the proposed CWT processor can reduce the processing time by 73.3% compared to previous FPGA-based implementations.
Topics: Algorithms; Fourier Analysis; Radar; Signal Processing, Computer-Assisted; Wavelet Analysis
PubMed: 35459058
DOI: 10.3390/s22083073 -
Nature Oct 2023Measurement has a special role in quantum theory: by collapsing the wavefunction, it can enable phenomena such as teleportation and thereby alter the 'arrow of time'...
Measurement has a special role in quantum theory: by collapsing the wavefunction, it can enable phenomena such as teleportation and thereby alter the 'arrow of time' that constrains unitary evolution. When integrated in many-body dynamics, measurements can lead to emergent patterns of quantum information in space-time that go beyond the established paradigms for characterizing phases, either in or out of equilibrium. For present-day noisy intermediate-scale quantum (NISQ) processors, the experimental realization of such physics can be problematic because of hardware limitations and the stochastic nature of quantum measurement. Here we address these experimental challenges and study measurement-induced quantum information phases on up to 70 superconducting qubits. By leveraging the interchangeability of space and time, we use a duality mapping to avoid mid-circuit measurement and access different manifestations of the underlying phases, from entanglement scaling to measurement-induced teleportation. We obtain finite-sized signatures of a phase transition with a decoding protocol that correlates the experimental measurement with classical simulation data. The phases display remarkably different sensitivity to noise, and we use this disparity to turn an inherent hardware limitation into a useful diagnostic. Our work demonstrates an approach to realizing measurement-induced physics at scales that are at the limits of current NISQ processors.
PubMed: 37853150
DOI: 10.1038/s41586-023-06505-7 -
BMC Pediatrics Feb 2020Lifelong healthy habits developed during childhood may prevent chronic diseases in adulthood. Interventions to promote these habits must begin early. The BONES (Beat... (Randomized Controlled Trial)
Randomized Controlled Trial
BACKGROUND
Lifelong healthy habits developed during childhood may prevent chronic diseases in adulthood. Interventions to promote these habits must begin early. The BONES (Beat Osteoporosis - Nourish and Exercise Skeletons) project assessed whether early elementary school children participating in a multifaceted health behavior change, after-school based intervention would improve bone quality and muscular strength and engage in more bone-strengthening behaviors.
METHODS
The 2-year BONES (B) intervention included bone-strengthening physical activity (85 min/week), educational materials (2 days/week), and daily calcium-rich snacks (380 mg calcium/day) delivered by after-school program leaders. BONES plus Parent (B + P) included an additional parent education component. From 1999 to 2004, n = 83 after-school programs (N = 1434 children aged 6-9 years) in Massachusetts and Rhode Island participated in a group randomized trial with two intervention arms (B only, n = 25 programs; B + P, n = 33) and a control arm (C, n = 25). Outcome measures (primary: bone quality (stiffness index of the calcaneus) and muscular strength (grip strength and vertical jump); secondary: bone-strengthening behaviors (calcium-rich food knowledge, preference, and intake; and physical activity level (metabolic equivalent time (MET) score, and weight-bearing factor (WBF) score)) were recorded at baseline, and after years one and two. Analyses followed an intent-to-treat protocol, and focused on individual subjects' trajectories along the three time points adjusting for baseline age and race via a mixed-effects regression framework. Analyses were performed with and without sex stratification.
RESULTS
Children in B + P increased bone stiffness compared to C (p = 0.05); No significant changes were observed in muscle strength, food knowledge, or vertical jump. Children in B + P showed significant improvement in their MET and WBF scores compared to C (p < 0.01) with a stronger effect in boys in both B and B + P (all p < 0.01).
CONCLUSION
After-school programs, coupled with parental engagement, serving early elementary school children are a potentially feasible platform to deliver bone-strengthening behaviors to prevent osteoporosis in adulthood, with some encouraging bone and physical activity outcomes.
TRIAL REGISTRATION
ClinicalTrials.gov NCT00065247. Retrospectively registered. First posted July 22, 2003.
Topics: Adult; Child; Exercise; Female; Health Behavior; Humans; Male; Massachusetts; Osteoporosis; Skeleton
PubMed: 32093625
DOI: 10.1186/s12887-020-1964-y -
Frontiers in Neuroscience 2020Spiking neural networks are well-suited for spatiotemporal feature detection and learning, and naturally involve dynamic delay mechanisms in the synapses, dendrites, and...
Spiking neural networks are well-suited for spatiotemporal feature detection and learning, and naturally involve dynamic delay mechanisms in the synapses, dendrites, and axons. Dedicated delay neurons and axonal delay circuits have been considered when implementing such pattern recognition networks in dynamic neuromorphic processors. Inspired by an auditory feature detection circuit in crickets, featuring a delayed excitation by post-inhibitory rebound, we investigate disynaptic delay elements formed by inhibitory-excitatory pairs of dynamic synapses. We configured such disynaptic delay elements in the DYNAP-SE neuromorphic processor and characterized the distribution of delayed excitations resulting from device mismatch. Interestingly, we found that the disynaptic delay elements can be configured such that the timing and magnitude of the delayed excitation depend mainly on the efficacy of the inhibitory and excitatory synapses, respectively, and that a neuron with multiple delay elements can be tuned to respond selectively to a specific pattern. Furthermore, we present a network with one disynaptic delay element that mimics the auditory feature detection circuit of crickets, and we demonstrate how varying synaptic weights, input noise and processor temperature affect the circuit. Dynamic delay elements of this kind open up for synapse level temporal feature tuning with configurable delays of up to 100 ms.
PubMed: 32180698
DOI: 10.3389/fnins.2020.00150 -
Scientific Reports Jul 2021In this paper, we report for the first time overlimiting current near a nanochannel using all-atom molecular dynamics (MD) simulations. Here, the simulated system...
In this paper, we report for the first time overlimiting current near a nanochannel using all-atom molecular dynamics (MD) simulations. Here, the simulated system consists of a silicon nitride nanochannel integrated with two reservoirs. The reservoirs are filled with [Formula: see text] potassium chloride (KCl) solution. A total of [Formula: see text] million atoms are simulated with a total simulation time of [Formula: see text] over [Formula: see text] 30000 CPU hours using 128 core processors (Intel(R) E5-2670 2.6 GHz Processor). The origin of overlimiting current is found to be due to an increase in chloride ([Formula: see text]) ion concentration inside the nanochannel leading to an increase in ionic conductivity. Such effects are seen due to charge redistribution and focusing of the electric field near the interface of the nanochannel and source reservoir. Also, from the MD simulations, we observe that the earlier theoretical and experimental postulations of strong convective vortices resulting in overlimiting current are not the true origin for overlimiting current. Our study may open up new theories for the mechanism of overlimiting current near the nanochannel interconnect devices.
PubMed: 34312433
DOI: 10.1038/s41598-021-94477-x -
Frontiers in Neurology 2021To analyze intensity-latency functions of intraoperative auditory evoked brainstem responses (ABRs) to stimulation by the Vibrant Soundbridge (VSB) active middle ear...
OBJECTIVE
To analyze intensity-latency functions of intraoperative auditory evoked brainstem responses (ABRs) to stimulation by the Vibrant Soundbridge (VSB) active middle ear implant with respect to coupling efficiency, VSB evoked ABR thresholds, and coupling modality [oval window (OW) placement vs. Incus placement and vs. round window (RW) placement].
STUDY DESIGN
Exploratory study.
SETTING
Bi-centric study at tertiary referral centers.
PATIENTS
Twenty-four patients (10 female, 14 male, mean age: 58 years) who received a VSB.
OUTCOME MEASURES
Wave-V intensity-latency functions of intraoperative VSB evoked ABRs using a modified audio processor programmed to preoperative bone conduction thresholds for stimulation. Threshold level correction to coupling efficiency and ABR thresholds. Individual plots and exponential function fits.
RESULTS
After ABR threshold level correction, the latency functions could be aligned. A large variance of latencies was observed at individual threshold level. Wave-V latency was longest in the Incus placement subgroup (9.73 ms, SD: 1.04) as compared to OW placement subgroup (9.47 ms, SD: 1.05), with the shortest latency in the RW placement subgroup (8.99 ms, SD: 0.68). For increasing stimulation levels, the variance decreased with intensity-latency function slopes converging toward a steady-state (saturation) latency caused by saturation of audio processor (stimulation) gain. Latency saturation was reached at a stimulation level of 50 dB nHL for the OW placement subgroup, 35 dB nHL for the Incus placement subgroup, and 30 dB nHL for the RW placement subgroup. The latency and saturation results indicated decreased dynamic range for RW placement, i.e., reverse stimulation.
CONCLUSIONS
VSB evoked ABR wave-V intensity-latency function slopes were similar to acoustic stimulation at high stimulation levels with a shift toward longer latencies caused by audio processor signal delay. Saturation of latencies occurred for higher stimulation levels due to saturation of audio processor gain. Thus, the analysis of VSB evoked intensity-latency functions appears to allow for the objective assessment of a patient's individual dynamic range. This can further improve diagnostics as well as intraoperative and postoperative quality control.
PubMed: 35126279
DOI: 10.3389/fneur.2021.739906