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Non-coding RNA Jan 2022Micro-RNAs (miRNAs) are a class of non-coding RNAs (ncRNAs) that act as post-transcriptional regulators of gene expression. Since their discovery in 1993, they have been... (Review)
Review
Micro-RNAs (miRNAs) are a class of non-coding RNAs (ncRNAs) that act as post-transcriptional regulators of gene expression. Since their discovery in 1993, they have been the subject of deep study due to their involvement in many important biological processes. Compared with other ncRNAs, miRNAs are generated from devoted transcriptional units which are processed by a specific set of endonucleases. The contribution of structural biology methods for understanding miRNA biogenesis and function has been essential for the dissection of their roles in cell biology and human disease. In this review, we summarize the application of structural biology for the characterization of the molecular players involved in miRNA biogenesis (processors and effectors), starting from the X-ray crystallography methods to the more recent cryo-electron microscopy protocols.
PubMed: 35202084
DOI: 10.3390/ncrna8010010 -
IScience Jan 2022Biological visual system can efficiently handle optical information within the retina and visual cortex of the brain, which suggests an alternative approach for the... (Review)
Review
Biological visual system can efficiently handle optical information within the retina and visual cortex of the brain, which suggests an alternative approach for the upgrading of the current low-intelligence, large energy consumption, and complex circuitry of the artificial vision system for high-performance edge computing applications. In recent years, retinomorphic machine vision based on the integration of optoelectronic image sensors and processors has been regarded as a promising candidate to improve this phenomenon. This novel intelligent machine vision technology can perform information preprocessing near or even within the sensor in the front end, thereby reducing the transmission of redundant raw data and improving the efficiency of the back-end processor for high-level computing tasks. In this contribution, we try to present a comprehensive review on the recent progress achieved in this emergent field.
PubMed: 35072015
DOI: 10.1016/j.isci.2021.103729 -
Brain Communications 2022Early implantable epilepsy therapy devices provided open-loop electrical stimulation without brain sensing, computing, or an interface for synchronized behavioural...
Early implantable epilepsy therapy devices provided open-loop electrical stimulation without brain sensing, computing, or an interface for synchronized behavioural inputs from patients. Recent epilepsy stimulation devices provide brain sensing but have not yet developed analytics for accurately tracking and quantifying behaviour and seizures. Here we describe a distributed brain co-processor providing an intuitive bi-directional interface between patient, implanted neural stimulation and sensing device, and local and distributed computing resources. Automated analysis of continuous streaming electrophysiology is synchronized with patient reports using a handheld device and integrated with distributed cloud computing resources for quantifying seizures, interictal epileptiform spikes and patient symptoms during therapeutic electrical brain stimulation. The classification algorithms for interictal epileptiform spikes and seizures were developed and parameterized using long-term ambulatory data from nine humans and eight canines with epilepsy, and then implemented prospectively in out-of-sample testing in two pet canines and four humans with drug-resistant epilepsy living in their natural environments. Accurate seizure diaries are needed as the primary clinical outcome measure of epilepsy therapy and to guide brain-stimulation optimization. The brain co-processor system described here enables tracking interictal epileptiform spikes, seizures and correlation with patient behavioural reports. In the future, correlation of spikes and seizures with behaviour will allow more detailed investigation of the clinical impact of spikes and seizures on patients.
PubMed: 35755635
DOI: 10.1093/braincomms/fcac115 -
The Journal of Histochemistry and... Jun 2021We evaluate the consequences of processing alcohol-fixed tissue in a processor previously used for formalin-fixed tissue. Biospecimens fixed in PAXgene Tissue Fixative...
We evaluate the consequences of processing alcohol-fixed tissue in a processor previously used for formalin-fixed tissue. Biospecimens fixed in PAXgene Tissue Fixative were cut into three pieces then processed in a flushed tissue processor previously used for formalin-fixed, paraffin-embedded (FFPE) blocks (neutral buffered formalin [NBF]), a formalin-free system (NBF), or left unprocessed. Histomorphology and immunohistochemistry were compared using hematoxylin/eosin staining and antibodies for MLH-1, Ki-67, and CK-7. Nucleic acid was extracted using the PAXgene Tissue RNA/DNA kits and an FFPE RNA extraction kit. RNA integrity was assessed using RNA integrity number (RIN), reverse transcription polymerase chain reaction (RT-PCR) (four amplicons), and quantitative RT-PCR (three genes). For DNA, multiplex PCR, quantitative PCR, DNA integrity number, and gel electrophoresis were used. Compared with NBF, RNA from NBF blocks had 88% lower yield and poorer purity; average RIN reduced from 5.0 to 3.8, amplicon length was 408 base pairs shorter, and Cq numbers were 1.9-2.4 higher. Using the FFPE extraction kit rescued yield and purity, but RIN further declined by 1.1 units. Differences between NBF and NBF in respect of DNA, histomorphology, and immunohistochemistry were either non-existent or small in magnitude. Formalin contamination of a tissue processor and its reagents therefore critically reduce RNA yield and integrity. We discuss the available options users can adopt to ameliorate this problem.
Topics: DNA; Fixatives; Formaldehyde; Humans; Immunohistochemistry; Polymerase Chain Reaction; RNA; Tissue Fixation
PubMed: 34010071
DOI: 10.1369/00221554211017859 -
Biosensors Apr 2022Correlation has a variety of applications that require signal processing. However, it is computationally intensive, and software correlators require high-performance...
Correlation has a variety of applications that require signal processing. However, it is computationally intensive, and software correlators require high-performance processors for real-time data analysis. This is a challenge for embedded devices because of the limitation of computing resources. Hardware correlators that use Field Programmable Gate Array (FPGA) technology can significantly boost computational power and bridge the gap between the need for high-performance computing and the limited processing power available in embedded devices. This paper presents a detailed FPGA-based correlator design at the register level along with the open-source Very High-Speed Integrated Circuit Hardware Description Language (VHDL) code. It includes base modules for linear and multi-tau correlators of varying sizes. Every module implements a simple and unified data interface for easy integration with standard and publicly available FPGA modules. Eighty-lag linear and multi-tau correlators were built for validation of the design. Three input data sets-constant signal, pulse signal, and sine signal-were used to test the accuracy of the correlators. The results from the FPGA correlators were compared against the outputs of equivalent software correlators and validated with the corresponding theoretical values. The FPGA correlators returned results identical to those from the software references for all tested data sets and were proven to be equivalent to their software counterparts. Their computation speed is at least 85,000 times faster than the software correlators running on a Xilinx MicroBlaze processor. The FPGA correlator can be easily implemented, especially on System on a Chip (SoC) integrated circuits that have processor cores and FPGA fabric. It is the ideal component for device-on-chip solutions in biosensing.
Topics: Computers; Signal Processing, Computer-Assisted; Software
PubMed: 35448296
DOI: 10.3390/bios12040236 -
Otology & Neurotology : Official... Dec 2023Bone-conduction hearing device (BCHD) uses natural sound transmission through bone and soft tissue, directly to the cochlea, via an external processor that captures and... (Comparative Study)
Comparative Study Observational Study
INTRODUCTION
Bone-conduction hearing device (BCHD) uses natural sound transmission through bone and soft tissue, directly to the cochlea, via an external processor that captures and processes sound, which is converted into mechanical vibrations. Key parameters, as maximum power output (MPO) and broader frequency range (FR), must be considered when indicating a BCHD because they can be decisive for speech recognition, especially under listening challenge conditions.
OBJECTIVES
Compare hearing performance and speech recognition in noise of two sound processors (SPs), with different features of MPO and FR, among BCHD users.
MATERIALS AND METHODS
This single-blinded, comparative, observational study evaluated 21 individuals Baha 4 system users with conductive or mixed hearing impairment. The free-field audiometry and speech recognition results were blindly collected under the following conditions: unaided, with Baha 5, and with Baha 6 Max SP.
RESULTS
In free-field audiometry, significant differences were observed between the SP at 0.25, 3, 4, 6, and 8 kHz, with Baha 6 Max outperforming Baha 5. The Baha 6 Max provided significantly better speech recognition than Baha 5 under all the speech in noise conditions evaluated. Separating the transcutaneous from the percutaneous users, Baha 6 Max Attract SP provided the best results and significantly lowered the free-field thresholds than Baha 5 Attract. The Baha 6 Max also significantly improved speech recognition in noise, among both Attract and Connect users.
CONCLUSION
The present study revealed that the greater MPO and broader FR of the Baha 6 Max device helped increase high-frequency gain and improved speech recognition in BCHD-experimented users.
Topics: Humans; Bone Conduction; Hearing; Hearing Aids; Hearing Loss, Conductive; Speech; Speech Perception
PubMed: 37917961
DOI: 10.1097/MAO.0000000000004043 -
Sensors (Basel, Switzerland) Sep 2019It is widely recognized that nanoscience and nanotechnology and their subfields, such as nanophotonics, nanoelectronics, and nanomechanics, have had a tremendous impact... (Review)
Review
It is widely recognized that nanoscience and nanotechnology and their subfields, such as nanophotonics, nanoelectronics, and nanomechanics, have had a tremendous impact on recent advances in sensing, imaging, and communication, with notable developments, including novel transistors and processor architectures. For example, in addition to being supremely fast, optical and photonic components and devices are capable of operating across multiple orders of magnitude length, power, and spectral scales, encompassing the range from macroscopic device sizes and kW energies to atomic domains and single-photon energies. The extreme versatility of the associated electromagnetic phenomena and applications, both classical and quantum, are therefore highly appealing to the rapidly evolving computing and communication realms, where innovations in both hardware and software are necessary to meet the growing speed and memory requirements. Development of all-optical components, photonic chips, interconnects, and processors will bring the speed of light, photon coherence properties, field confinement and enhancement, information-carrying capacity, and the broad spectrum of light into the high-performance computing, the internet of things, and industries related to cloud, fog, and recently edge computing. Conversely, owing to their extraordinary properties, 0D, 1D, and 2D materials are being explored as a physical basis for the next generation of logic components and processors. Carbon nanotubes, for example, have been recently used to create a new processor beyond proof of principle. These developments, in conjunction with neuromorphic and quantum computing, are envisioned to maintain the growth of computing power beyond the projected plateau for silicon technology. We survey the qualitative figures of merit of technologies of current interest for the next generation computing with an emphasis on edge computing.
PubMed: 31546907
DOI: 10.3390/s19184048 -
Nature Jun 2023Quantum computing promises to offer substantial speed-ups over its classical counterpart for certain problems. However, the greatest impediment to realizing its full...
Quantum computing promises to offer substantial speed-ups over its classical counterpart for certain problems. However, the greatest impediment to realizing its full potential is noise that is inherent to these systems. The widely accepted solution to this challenge is the implementation of fault-tolerant quantum circuits, which is out of reach for current processors. Here we report experiments on a noisy 127-qubit processor and demonstrate the measurement of accurate expectation values for circuit volumes at a scale beyond brute-force classical computation. We argue that this represents evidence for the utility of quantum computing in a pre-fault-tolerant era. These experimental results are enabled by advances in the coherence and calibration of a superconducting processor at this scale and the ability to characterize and controllably manipulate noise across such a large device. We establish the accuracy of the measured expectation values by comparing them with the output of exactly verifiable circuits. In the regime of strong entanglement, the quantum computer provides correct results for which leading classical approximations such as pure-state-based 1D (matrix product states, MPS) and 2D (isometric tensor network states, isoTNS) tensor network methods break down. These experiments demonstrate a foundational tool for the realization of near-term quantum applications.
PubMed: 37316724
DOI: 10.1038/s41586-023-06096-3 -
Nature Communications Apr 2022Computational meta-optics brings a twist on the accelerating hardware with the benefits of ultrafast speed, ultra-low power consumption, and parallel information...
Computational meta-optics brings a twist on the accelerating hardware with the benefits of ultrafast speed, ultra-low power consumption, and parallel information processing in versatile applications. Recent advent of metasurfaces have enabled the full manipulation of electromagnetic waves within subwavelength scales, promising the multifunctional, high-throughput, compact and flat optical processors. In this trend, metasurfaces with nonlocality or multi-layer structures are proposed to perform analog optical computations based on Green's function or Fourier transform, intrinsically constrained by limited operations or large footprints/volume. Here, we showcase a Fourier-based metaprocessor to impart customized highly flexible transfer functions for analog computing upon our single-layer Huygens' metasurface. Basic mathematical operations, including differentiation and cross-correlation, are performed by directly modulating complex wavefronts in spatial Fourier domain, facilitating edge detection and pattern recognition of various image processing. Our work substantiates an ultracompact and powerful kernel processor, which could find important applications for optical analog computing and image processing.
Topics: Computers; Fourier Analysis; Image Processing, Computer-Assisted; Optics and Photonics
PubMed: 35449139
DOI: 10.1038/s41467-022-29732-4 -
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