Low Latency and Sparse Computing Spiking Neural Networks With Self-Driven Adaptive Threshold Plasticity.

Spiking neural networks (SNNs) have captivated the attention worldwide owing to their compelling advantages in low power consumption, high biological plausibility, and strong robustness. However, the intrinsic latency associated with SNNs during inference poses a significant challenge, impeding their further development and application. This latency is caused by the need for spiking neurons to collect electrical stimuli and generate spikes only when their membrane potential exceeds a firing threshold. Considering the firing threshold plays a crucial role in SNN performance, this article proposes a self-driven adaptive threshold plasticity (SATP) mechanism, wherein neurons autonomously adjust the firing thresholds based on their individual state information using unsupervised learning rules, of which the adjustment is triggered by their own firing events. SATP is based on the principle of maximizing the information contained in the output spike rate distribution of each neuron. This article derives the mathematical expression of SATP and provides extensive experimental results, demonstrating that SATP effectively reduces SNN inference latency, further reduces the computation density while improving computational accuracy, so that SATP facilitates SNN models to be with low latency, sparse computing, and high accuracy.

Generic Repeat Finder: A High-Sensitivity Tool for Genome-Wide De Novo Repeat Detection.

Comprehensive and accurate annotation of the repeatome, including transposons, is critical for deepening our understanding of repeat origins, biogenesis, regulatory mechanisms, and roles. Here, we developed Generic Repeat Finder (GRF), a tool for genome-wide repeat detection based on fast, exhaustive numerical calculation algorithms integrated with optimized dynamic programming strategies. GRF sensitively identifies terminal inverted repeats (TIRs), terminal direct repeats (TDRs), and interspersed repeats that bear both inverted and direct repeats. GRF also detects DNA or RNA transposable elements characterized by these repeats in plant and animal genomes. For TIRs and TDRs, GRF identifies spacers in the middle and mismatches/insertions or deletions in terminal repeats, showing their alignment or base-pairing information. GRF helps improve the annotation for various DNA transposons and retrotransposons, such as miniature inverted-repeat transposable elements (MITEs), long terminal repeat (LTR) retrotransposons, and non-LTR retrotransposons, including long interspersed nuclear elements and short interspersed nuclear elements in plants. We used GRF to perform TIR/TDR, interspersed-repeat, and MITE detection in several species, including Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), and mouse (Mus musculus). As a generic bioinformatics tool in repeat finding implemented as a parallelized C++ program, GRF was faster and more sensitive than the existing inverted repeat/MITE detection tools based on numerical approaches (i.e. detectIR and detectMITE) in Arabidopsis and mouse. GRF is more sensitive than Inverted Repeat Finder in TIR detection, LTR_FINDER in short TDR detection (≤1,000 nt), and phRAIDER in interspersed repeat detection in Arabidopsis and rice. GRF is an open source available from Github.

JNSViewer-A JavaScript-based Nucleotide Sequence Viewer for DNA/RNA secondary structures.

Many tools are available for visualizing RNA or DNA secondary structures, but there is scarce implementation in JavaScript that provides seamless integration with the increasingly popular web computational platforms. We have developed JNSViewer, a highly interactive web service, which is bundled with several popular tools for DNA/RNA secondary structure prediction and can provide precise and interactive correspondence among nucleotides, dot-bracket data, secondary structure graphs, and genic annotations. In JNSViewer, users can perform RNA secondary structure predictions with different programs and settings, add customized genic annotations in GFF format to structure graphs, search for specific linear motifs, and extract relevant structure graphs of sub-sequences. JNSViewer also allows users to choose a transcript or specific segment of Arabidopsis thaliana genome sequences and predict the corresponding secondary structure. Popular genome browsers (i.e., JBrowse and BrowserGenome) were integrated into JNSViewer to provide powerful visualizations of chromosomal locations, genic annotations, and secondary structures. In addition, we used StructureFold with default settings to predict some RNA structures for Arabidopsis by incorporating in vivo high-throughput RNA structure profiling data and stored the results in our web server, which might be a useful resource for RNA secondary structure studies in plants. JNSViewer is available at http://bioinfolab.miamioh.edu/jnsviewer/index.html.

mirPRo-a novel standalone program for differential expression and variation analysis of miRNAs.

Being involved in many important biological processes, miRNAs can regulate gene expression by targeting mRNAs to facilitate their degradation or translational inhibition. Many miRNA sequencing studies reveal that miRNA variations such as isomiRs and "arm switching" are biologically relevant. However, existing standalone tools usually do not provide comprehensive, detailed information on miRNA variations. To deepen our understanding of miRNA variability, we developed a new standalone tool called "mirPRo" to quantify known miRNAs and predict novel miRNAs. Compared with the most widely used standalone program, miRDeep2, mirPRo offers several new functions including read cataloging based on genome annotation, optional seed region check, miRNA family expression quantification, isomiR identification and categorization, and "arm switching" detection. Our comparative data analyses using three datasets from mouse, human and chicken demonstrate that mirPRo is more accurate than miRDeep2 by avoiding over-counting of sequence reads and by implementing different approaches in adapter trimming, mapping and quantification. mirPRo is an open-source standalone program (https://sourceforge.net/projects/mirpro/).

Surgical treatment and rehabilitation of medial Hoffa fracture fixed by locking plate and additional screws: A retrospective cohort study.

PURPOSE: Hoffa fracture fixed by only using a single plate or lag screws might be not strong enough to achieve direct stability. The goal of this study is to determine the functional outcome of the surgical treatment and rehabilitation of medial Hoffa fracture by a locking plate combined with cannulated or lag screws. METHODS: A total of 13 patients suffering isolated medical Hoffa fractures were identified during the study period (2005.February-2013.February) and retrospectively analyzed. All the fractures were treated by open reduction via the medial approach, and internal fixation by a locking plate combined with cannulated or lag screws. Early active rehabilitation including tele-rehabilitation for rural patients with restricted weight bearing was instituted after the surgical treatment. The radiological and functional outcome analysis was performed by using Knee Society Score (KSS), the range of movement (ROM), and the stability of fixation of the patients during 24 month follow-up. RESULTS: The bone union of medial Hoffa fractures was achieved in all patients. The articular surface of medial femoral condyle was anatomically reduced. There was no loss of reduction and fixation. All patients achieved satisfactory knee joint function and regained their walking ability with good clinical results through early postsurgical rehabilitation. Ten patients (77%) had 0°-130° range of motion with full extension; two patients (15%) had 0°-115° range of motion; one patient (8%) had 0°-110° range of motion. The KSS of all the patients were more than 80, and the scores of seven patients (54%) were more than 85. CONCLUSION: Fixation with a locking plate and cannulated or lag screws for medial Hoffa fracture seemed to be effective and reliable for achieving anatomical reduction, and gave satisfactory functional results when coupled with aggressive rehabilitation.

Surgical treatment of lateral Hoffa fracture with a locking plate through the lateral approach.

OBJECTIVES: The goal of this study is to determine the efficacy of the surgical treatment of lateral Hoffa fracture with a locking plate and cannulated or lag screws through the lateral approach. MATERIALS AND METHODS: A total of 12 isolated lateral Hoffa fractures were identified during the study period (February 2005 to February 2010). All fractures were treated by open reduction through the lateral approach. Internal fixation was performed with a contoured locking plate and cannulated or lag screws introduced from the non-weight-bearing area of the cartilage surface of the lateral femoral condyle. Radiological and functional outcome analysis was performed using Knee Society scores. RESULTS: Bony union of Hoffa fracture was achieved in all patients. The articular surface of lateral femoral condyle was anatomically reduced. There was no loss of reduction and fixation. Functional outcome of knee measurements showed a continuous significant improvement over the follow-up period. CONCLUSION: Fixation with a locking plate and cannulated or lag screws for lateral Hoffa fracture seemed to be effective and reliable. The lateral approach had advantages for reduction and fixation of lateral Hoffa fracture during operation.

Impact of release characteristics of sinomenine hydrochloride dosage forms on its pharmacokinetics in beagle dogs.

AIM: To investigate the effect of release behavior of sustained-release dosage forms of sinomenine hydrochloride (SM.HCl) on its pharmacokinetics in beagle dogs. METHODS: The in vitro release behavior of two SM.HCl dosage forms, including commercial 12-h sustained-release tablets and 24-h sustained-release pellets prepared in our laboratory, was examined. The two dosage forms were orally administrated to beagle dogs, and then the in vivo SM.HCl pharmacokinetics was investigated and compared. RESULTS: The optimal SM.HCl sustained-release formulation was achieved by mixing slow- and rapid-release pellets (9:1, w/w). The SM.HCl release profiles of the sustained-release pellets were scarcely influenced by the pH of the dissolution medium. Release from the 12-h sustained-release tablets was markedly quicker than that from the 24-h sustained-release pellets, the cumulative release up to 12-h was 99.9% vs 68.7%. From a pharmacokinetic standpoint, the 24-h SM.HCl sustained-release pellets had longer tmax and lower Cmax compared to the 12-h sustained-release tablets, the tmax being 2.67+/-0.52 h vs 9.83+/-0.98 h and the Cmax being 1 334.45+/-368.76 ng/mL vs 893.12+/-292.55 ng/mL, respectively. However, the AUC(0-tn) of two SM.HCl dosage forms was comparable and both preparations were statistically bioequivalent. Furthermore, the two preparations had good correlations between SM.HCl percentage absorption in vivo and the cumulative percentage release in vitro. CONCLUSION: The in vitro release properties of the dosage forms strongly affect their pharmacokinetic behavior in vivo. Therefore, managing the in vitro release behavior of dosage forms is a promising strategy for obtaining the optimal in vivo pharmacokinetic characteristics and safe therapeutic drug concentration-time curves.