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The Journal of Physical Chemistry... Jun 2024Synaptic transistors have been proposed to implement neuron activation functions of neural networks (NNs). While promising to enable compact, fast, inexpensive, and...
Synaptic transistors have been proposed to implement neuron activation functions of neural networks (NNs). While promising to enable compact, fast, inexpensive, and energy-efficient dedicated NN circuits, they also have limitations compared to digital NNs (realized as codes for digital processors), including shape choices of the activation function using particular types of transistor implementation, and instabilities due to noise and other factors present in analog circuits. We present a computational study of the effects of these factors on NN performance and find that, while accuracy competitive with traditional NNs can be realized for many applications, there is high sensitivity to the instability in the shape of the activation function, suggesting that, when highly accurate NNs are required, high-precision circuitry should be developed beyond what has been reported for synaptic transistors to date.
PubMed: 38941557
DOI: 10.1021/acs.jpclett.4c01413 -
Bioinformatics (Oxford, England) Jun 2024One of the core problems in the analysis of protein tandem mass spectrometry data is the peptide assignment problem: determining, for each observed spectrum, the peptide...
MOTIVATION
One of the core problems in the analysis of protein tandem mass spectrometry data is the peptide assignment problem: determining, for each observed spectrum, the peptide sequence that was responsible for generating the spectrum. Two primary classes of methods are used to solve this problem: database search and de novo peptide sequencing. State-of-the-art methods for de novo sequencing use machine learning methods, whereas most database search engines use hand-designed score functions to evaluate the quality of a match between an observed spectrum and a candidate peptide from the database. We hypothesized that machine learning models for de novo sequencing implicitly learn a score function that captures the relationship between peptides and spectra, and thus may be re-purposed as a score function for database search. Because this score function is trained from massive amounts of mass spectrometry data, it could potentially outperform existing, hand-designed database search tools.
RESULTS
To test this hypothesis, we re-engineered Casanovo, which has been shown to provide state-of-the-art de novo sequencing capabilities, to assign scores to given peptide-spectrum pairs. We then evaluated the statistical power of this Casanovo score function, Casanovo-DB, to detect peptides on a benchmark of three mass spectrometry runs from three different species. In addition, we show that re-scoring with the Percolator post-processor benefits Casanovo-DB more than other score functions, further increasing the number of detected peptides.
Topics: Databases, Protein; Peptides; Machine Learning; Mass Spectrometry; Algorithms; Sequence Analysis, Protein; Tandem Mass Spectrometry
PubMed: 38940129
DOI: 10.1093/bioinformatics/btae218 -
Scientific Data Jun 2024Bladder cancer is one of the leading causes of cancer-related mortality in the urinary system. Understanding genomic information is important in the treatment and...
Bladder cancer is one of the leading causes of cancer-related mortality in the urinary system. Understanding genomic information is important in the treatment and prognosis of bladder cancer, but the current method used to identify mutations is time-consuming and labor-intensive. There are now many novel and convenient ways to predict cancerous genomics from pathological slides. However, the publicly available datasets are limited, especially for Asian populations. In this study, we developed a dataset consisting of 75 Asian cases of bladder cancers and 112 Whole-Slide Images with one to two images obtained for each patient. This dataset provides information on the most frequently and clinically significant mutated genes derived by whole-exome sequencing in these patients. This dataset will facilitate exploration and development of novel diagnostic and therapeutic technologies for bladder cancer.
Topics: Humans; Asian People; Exome Sequencing; Genomics; Mutation; Urinary Bladder Neoplasms
PubMed: 38937479
DOI: 10.1038/s41597-024-03526-3 -
JMIR Bioinformatics and Biotechnology May 2024Genetic data are widely considered inherently identifiable. However, genetic data sets come in many shapes and sizes, and the feasibility of privacy attacks depends on... (Review)
Review
BACKGROUND
Genetic data are widely considered inherently identifiable. However, genetic data sets come in many shapes and sizes, and the feasibility of privacy attacks depends on their specific content. Assessing the reidentification risk of genetic data is complex, yet there is a lack of guidelines or recommendations that support data processors in performing such an evaluation.
OBJECTIVE
This study aims to gain a comprehensive understanding of the privacy vulnerabilities of genetic data and create a summary that can guide data processors in assessing the privacy risk of genetic data sets.
METHODS
We conducted a 2-step search, in which we first identified 21 reviews published between 2017 and 2023 on the topic of genomic privacy and then analyzed all references cited in the reviews (n=1645) to identify 42 unique original research studies that demonstrate a privacy attack on genetic data. We then evaluated the type and components of genetic data exploited for these attacks as well as the effort and resources needed for their implementation and their probability of success.
RESULTS
From our literature review, we derived 9 nonmutually exclusive features of genetic data that are both inherent to any genetic data set and informative about privacy risk: biological modality, experimental assay, data format or level of processing, germline versus somatic variation content, content of single nucleotide polymorphisms, short tandem repeats, aggregated sample measures, structural variants, and rare single nucleotide variants.
CONCLUSIONS
On the basis of our literature review, the evaluation of these 9 features covers the great majority of privacy-critical aspects of genetic data and thus provides a foundation and guidance for assessing genetic data risk.
PubMed: 38935957
DOI: 10.2196/54332 -
The Journal of Chemical Physics Jun 2024We report an implementation of the McMurchie-Davidson (MD) algorithm for 3-center and 4-center 2-particle integrals over Gaussian atomic orbitals (AOs) with low and high...
We report an implementation of the McMurchie-Davidson (MD) algorithm for 3-center and 4-center 2-particle integrals over Gaussian atomic orbitals (AOs) with low and high angular momenta l and varying degrees of contraction for graphical processing units (GPUs). This work builds upon our recent implementation of a matrix form of the MD algorithm that is efficient for GPU evaluation of 4-center 2-particle integrals over Gaussian AOs of high angular momenta (l ≥ 4) [A. Asadchev and E. F. Valeev, J. Phys. Chem. A 127, 10889-10895 (2023)]. The use of unconventional data layouts and three variants of the MD algorithm allow for the evaluation of integrals with double precision and sustained performance between 25% and 70% of the theoretical hardware peak. Performance assessment includes integrals over AOs with l ≤ 6 (a higher l is supported). Preliminary implementation of the Hartree-Fock exchange operator is presented and assessed for computations with up to a quadruple-zeta basis and more than 20 000 AOs. The corresponding C++ code is part of the experimental open-source LibintX library available at https://github.com/ValeevGroup/libintx.
PubMed: 38934632
DOI: 10.1063/5.0217001 -
Journal of Personalized Medicine Jun 2024The early reliable detection and quantification of autoantibodies play an important role in autoimmune disease diagnosis and in disease-course monitoring. New...
BACKGROUND
The early reliable detection and quantification of autoantibodies play an important role in autoimmune disease diagnosis and in disease-course monitoring. New technologies, such as the multiplexed determination of autoantibodies, have recently been introduced and are being adopted more frequently. The aim of this study was to evaluate the ability of a new microdot array-based multiparametric assay (ZENIT AMiDot CTD panel, A. Menarini Diagnostics, Firenze, Italy) to correctly classify patients with autoimmune rheumatic diseases (ARDs) and compare it to a fluorescence enzyme immunoassay (FEIA) for the detection of anti-ENAs.
METHODS
The study included 69 consecutive samples from patients with ARDs that were analyzed using two different methods (FEIA and AMiDot) to detect anti-CENP B and six anti-ENA antibodies: anti-Scl-70, anti-SSB/La, anti-Jo-1, anti-U1-RNP, anti-Ro52, and anti-Ro60. The control group sera came from sixty-eight blood donors. Tests were run on the automated slide processor ZENIT FLOW, and then the slides were imaged and analyzed using ZENIT fast.
RESULTS
Since the samples were selected for at least one antibody positivity with an ARD diagnosis, we did not calculate clinical sensitivity but only specificity, which was 98.53%, ranging from 90% for anti-SSB/La antibodies to 100% for anti-CENP B ones. Mean agreement among the methods assessed by Cohen's kappa was 0.816 ± 0.240.
CONCLUSIONS
The assay demonstrated good clinical performance and may be considered a valuable aid in detecting ARD patients, offering an alternative to methods such as FEIA which are largely in use today.
PubMed: 38929828
DOI: 10.3390/jpm14060607 -
Scientific Reports Jun 2024In traditional von Neumann computing architecture, the efficiency of the system is often hindered by the data transmission bottleneck between the processor and memory. A...
In traditional von Neumann computing architecture, the efficiency of the system is often hindered by the data transmission bottleneck between the processor and memory. A prevalent approach to mitigate this limitation is the use of non-volatile memory for in-memory computing, with spin-orbit torque (SOT) magnetic random-access memory (MRAM) being a leading area of research. In this study, we numerically demonstrate that a precise combination of damping-like and field-like spin-orbit torques can facilitate precessional magnetization switching. This mechanism enables the binary memristivity of magnetic tunnel junctions (MTJs) through the modulation of the amplitude and width of input current pulses. Building on this foundation, we have developed a scheme for a reconfigurable spintronic logic gate capable of directly implementing Boolean functions such as AND, OR, and XOR. This work is anticipated to leverage the sub-nanosecond dynamics of SOT-MRAM cells, potentially catalyzing further experimental developments in spintronic devices for in-memory computing.
PubMed: 38926523
DOI: 10.1038/s41598-024-65634-9 -
Clinical Otolaryngology : Official... Jun 2024Although the Baha 5SP has been commercially available for six years, very few studies have been performed on the device's efficacy. The current study aims to evaluate...
INTRODUCTION
Although the Baha 5SP has been commercially available for six years, very few studies have been performed on the device's efficacy. The current study aims to evaluate the characteristics and audiological results in patients with severe-to-profound mixed hearing loss fitted with this superpower sound processor.
METHODS
This retrospective evaluation was conducted at a tertiary referral centre where a series of 82 adult patients with severe-to-profound mixed hearing loss were implanted with a percutaneous bone-anchored hearing system and fitted with a superpower sound processor between 2016 and 2019. Patients with incomplete or unreliable audiological data (n = 24) were excluded, resulting in 58 data sets for analysis. The main outcome measures were unaided and aided pure-tone thresholds and aided free-field speech perception in quiet.
RESULTS
The median unaided air conduction (AC) threshold averaged across 0.5, 1 and 2 kHz (PTA) of all patients was 75 dB hearing loss (HL); the median unaided AC averaged across 1, 2 and 4 kHz (PTA) was 84 dB HL. For bone conduction and direct bone conduction, the median PTA was 52 and 47 dB HL, respectively. With the superpower device, the median free-field speech reception threshold was 54 dB sound pressure level (SPL), and the median speech perception score at 65 dB SPL was 80%.
CONCLUSIONS
At least 75% of the patients reached a maximum phoneme score of 70%. For patients with lower scores, the superpower device still provides a substantial hearing benefit. This makes the superpower device particularly suitable for patients with severe-to-profound mixed hearing loss with a contraindication for conventional hearing aids and/or cochlear implants.
PubMed: 38926155
DOI: 10.1111/coa.14187 -
Life Sciences Jun 2024Caries and pulpitis remain a major global disease burden and affect the quality of life of patients. Odontoblasts are key players in the progression of caries and... (Review)
Review
Caries and pulpitis remain a major global disease burden and affect the quality of life of patients. Odontoblasts are key players in the progression of caries and pulpitis, not only secreting and mineralizing to form dentin, but also acting as a wall of defense to initiate immune defenses. Mitochondrion is an information processor for numerous cellular activities, and dysregulation of mitochondrion homeostasis not only affects cellular metabolism but also triggers a wide range of diseases. Elucidating mitochondrial homeostasis in odontoblasts can help deepen scholars' understanding of odontoblast-associated diseases. Articles on mitochondrial homeostasis in odontoblasts were evaluated for information pertinent to include in this narrative review. This narrative review focused on understanding the complex interplay between mitochondrial homeostasis in odontoblasts under physiological and pathological conditions. Furthermore, mitochondria-centered therapeutic strategies (including mitochondrial base editing, targeting platforms, and mitochondrial transplantation) were emphasized by resolving key genes that regulate mitochondrial function. Mitochondria are involved in odontoblast differentiation and function, and act as mitochondrial danger-associated molecular patterns (mtDAMPs) to mediate odontoblast pathological progression. Novel mitochondria-centered therapeutic strategies are particularly attractive as emerging therapeutic approaches for the maintenance of mitochondrial homeostasis. It is expected to probe key events of odontoblast differentiation and advance the clinical resolution of dentin formation and mineralization disorders and odontoblast-related diseases.
PubMed: 38917871
DOI: 10.1016/j.lfs.2024.122797 -
ACS Engineering Au Jun 2024We propose a numerical strategy based on dynamic load balancing (DLB) aimed at enhancing the computational efficiency of multiscale CFD simulation of reactive flows at...
We propose a numerical strategy based on dynamic load balancing (DLB) aimed at enhancing the computational efficiency of multiscale CFD simulation of reactive flows at catalyst surfaces. Our approach employs DLB combined with a hybrid parallelization technique, integrating both MPI and OpenMP protocols. This results in an optimized distribution of the computational load associated with the chemistry solution across processors, thereby minimizing computational overheads. Through assessments conducted on fixed and fluidized bed reactor simulations, we demonstrated a remarkable improvement of the parallel efficiency from 19 to 87% and from 19 to 91% for the fixed and fluidized bed, respectively. Owing to this improved parallel efficiency, we observe a significant computational speed-up of 1.9 and 2.1 in the fixed and fluidized bed reactor simulations, respectively, compared to simulations without DLB. All in all, the proposed approach is able to improve the computational efficiency of multiscale CFD simulations paving the way for a more efficient exploitation of high-performance computing resources and expanding the current boundaries of feasible simulations.
PubMed: 38911942
DOI: 10.1021/acsengineeringau.3c00066