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PubMedDate not supplied

A deep model of the incidence of dental caries on proximal surfaces.

As a component of an analysis of the benefits of alternative frequencies of bitewing radiographs to detect dental caries, the authors developed and validated a model to generate an individual's probability distribution for new carious lesions in a year. The model postulates two sources of variability in caries incidence--differences in individuals' underlying caries susceptibilities and a random component. The model is used to examine the nature of caries risk over time. The large random fluctuations in an individual's caries susceptibility from year to year, combined with the random nature of caries attack, makes it difficult to predict future caries experience from the individual's caries experience in the recent past. By modeling the process giving rise to observed incidence data rather than focusing directly on the observed data, i.e., by developing a deep rather than a surface model, the authors have elucidated underlying disease dynamics and provided a basis for generalizing from the particular data used to develop the model.

Adolescent↗
PubMed2025

APNet, an explainable sparse deep learning model to discover differentially active drivers of severe COVID-19.

MOTIVATION: Computational analyses of bulk and single-cell omics provide translational insights into complex diseases, such as COVID-19, by revealing molecules, cellular phenotypes, and signalling patterns that contribute to unfavourable clinical outcomes. Current in silico approaches dovetail differential abundance, biostatistics, and machine learning, but often overlook nonlinear proteomic dynamics, like post-translational modifications, and provide limited biological interpretability beyond feature ranking. RESULTS: We introduce APNet, a novel computational pipeline that combines differential activity analysis based on SJARACNe co-expression networks with PASNet, a biologically informed sparse deep learning model, to perform explainable predictions for COVID-19 severity. The APNet driver-pathway network ingests SJARACNe co-regulation and classification weights to aid result interpretation and hypothesis generation. APNet outperforms alternative models in patient classification across three COVID-19 proteomic datasets, identifying predictive drivers and pathways, including some confirmed in single-cell omics and highlighting under-explored biomarker circuitries in COVID-19. AVAILABILITY AND IMPLEMENTATION: APNet's R, Python scripts, and Cytoscape methodologies are available at https://github.com/BiodataAnalysisGroup/APNet.

COVID-19↗
PubMed1985

Responses of neurons in the cat's superior colliculus to acoustic stimuli. II. A model of interaural intensity sensitivity.

Most neurons in the deep and intermediate layers of the superior colliculus (SC) that respond to acoustic stimuli are sensitive to interaural intensity disparities (IIDs). We examine a model for the generation of sensitivity to IIDs that depends upon temporal coincidence of the inputs from each ear at a given binaural neuron. Because the neural response latency decreases with increasing stimulus intensity, IIDs affect the relative timing of arrival of the inputs. If this model were true, the neurons sensitive to IIDs should also respond to interaural time differences (ITDs) of isointensive stimuli, provided that the magnitude of the delays reflect the neural latency-intensity relationship. For both major classes of binaural cells in the SC, namely those that exhibit binaural inhibition (BI) and binaural facilitation (BF), our results support the model in that the detection of IIDs is largely due to their sensitivity to the temporal overlap of inputs from each ear. The shapes of the IID and ITD functions for each class are similar. The summation of inputs includes inhibitory as well as facilitatory interactions. Estimates of the durations of the subliminal excitatory events in BF cells using the model indicate that they are relatively short (1-4 ms), whereas the durations of the inhibitory processes in BI cells are much longer. The model specifies a common neuronal mechanism for comparison of interaural disparities of time and intensity and does not separate the processing of IIDs and ITDs, as the classic duplex theory suggests. The model provides a physiological explanation for certain features of the psychophysical phenomenon of time-intensity trading. It is also consistent with recent experiments that have shown that the auditory system is sensitive to behaviorally significant ITDs of high-frequency complex signals. The model applies only to the processing of transient stimuli and does not address neural sensitivity to IIDs of continuous high-frequency tones.

Animals↗
PubMedDate not supplied

[Is the implantation of hinged knee joint prostheses still justifiable today? 15 years' experience using the Blauth knee joint prosthesis].

In objection to knee hinge prostheses there is often mentioned a higher complication rate. An increased load impact on the bone-cement interface results from the close connection of tibial and femoral components. This is assumed to cause bad results, as reported from early artificial knee joint replacements, characterised by weight bearing axes and direct contact metal to metal. These are contrasted to long term results of the Blauth hinge prosthesis. The Blauth prosthesis is constructed according to the low friction principle without a weightbearing axis. A prospective multicentric long term follow-up study reports on 556 prostheses. 463 (83%) were controlled between 1 and 15 years after operation (average: 43 months). Aseptic loosenings had to be confirmed in 1.3% of the patients, deep infections in 2.6%. The survival analysis did not show an erratic deterioration in dependence of the observation period. After 10 years there is still a probability of 89% that a prosthesis does not show a deep infection or loosening. The efficiency of artificial knee joint replacement by hinge joints should therefore not be judged on the results of the first generation of these models.

Adult↗
PubMed2025

Deep learning guided programmable design of Escherichia coli core promoters from sequence architecture to strength control.

Core promoters are essential regulatory elements that control transcription initiation, but accurately predicting and designing their strength remains challenging due to complex sequence-function relationships and the limited generalizability of existing AI-based approaches. To address this, we developed a modular platform integrating rational library design, predictive modelling, and generative optimization into a closed-loop workflow for end-to-end core promoter engineering. Conserved and spacer region of core promoters exert distinct effects on transcriptional strength, with the former driving large-scale variation and the latter enabling finer gradation. Based on this insight, Mutation-Barcoding-Reverse Sequencing approach was used and constructed a synthetic promoter library comprising 112 955 variants with minimal redundancy and a 16 226-fold expression range. A Transformer-based model trained on this dataset achieved a Pearson correlation of 0.87 with experimentally measured promoter strengths. When combined with a conditional diffusion model, the system enabled de novo generation of promoter sequences with defined strengths, achieving a design-to-measurement correlation of 0.95 and maintaining high accuracy (R = 0.93) across varied sequence contexts. The designed promoters consistently preserved their intended strength gradients, demonstrating robust plug-and-play functionality. This work establishes a scalable and extensible platform (www.yudenglab.com) for deep learning-guided programmable design of Escherichia coli core promoters, enabling precise transcriptional control.

Promoter Regions, Genetic↗
PubMed2026

Peptide-phosphorodiamidate morpholino oligomer therapy for dysferlinopathy induces pseudoexon skipping and restoration of functional protein.

The dysferlinopathies are a spectrum of autosomal recessive muscle diseases caused by mutations in the dysferlin gene (DYSF). Clinical manifestations vary from asymptomatic hyperCKemia to severe muscle pathology and loss of muscle function. These are designated as limb-girdle muscular dystrophy type 2R (LGMDR2; formerly LGMD2B or Miyoshi myopathy). Among other functions, dysferlin is crucial for plasma membrane repair and maintenance of intracellular calcium homeostasis. In previous studies, we identified 2 independent point mutations deep within introns that cause aberrant DYSF mRNA splicing and the inclusion of pseudoexons within transcripts that diminish protein expression. In this study, we generated and characterized a mouse model for 1 of these mutations (within DYSF intron 44). In these mice, a segment of human DYSF DNA containing the mutant intronic sequence flanked by surrounding human exon sequences replaced the normal homologous mouse DNA. These mice exhibited aberrant Dysf pre-mRNA splicing, pseudoexon inclusion, loss of DYSF protein expression, and muscle pathology similar to that observed in patients. Using this model, we identified antisense oligonucleotides and a peptide-phosphorodiamidate morpholino oligomer that blocks the mouse Dysf pre-mRNA splicing complexes from binding the mutant pre-mRNA, thereby restoring nearly normal muscle pathology and function.

Animals↗
PubMed1989

Creation of realistic appearing simulated patient cases using the INTERNIST-1/QMR knowledge base and interrelationship properties of manifestations.

The Internist-1/Quick Medical Reference (QMR) knowledge base (KB) describes the clinical manifestations of some 600 diseases in the domain of internal medicine. This KB, while not representing deep causal modelling of disease processes, is nonetheless effective in providing medical diagnostic assistance through the QMR medical decision support system. One potential application of this extensive KB is the generation of simulated patient cases for use in educating health professionals. However, the "flat" KB is not adequate for this because the clinical manifestations used in the disease descriptions are not mutually independent. While it is theoretically possible to construct disease descriptions which embody pathophysiologic mechanisms of disease causality, it is not practical from the standpoint of resource utilization. Short of constructing a causal knowledge base, the authors herein describe the generation of realistic appearing simulated patient case data using existing information in the knowledge base. This existing information in the KB is in the form of properties which represent a shallow form of interrelationships of the manifestations. The authors conclude that this ability to generate simulated cases represents another view in which to look at an extensive knowledge base, as well as having application to constructing intelligent tutoring systems for health professionals in training.

Artificial Intelligence↗
PubMed2026

Machine Learning in Hyperlipidaemia Research: Screening and Experimental Insights into Lipid Metabolism Modulators.

Hyperlipidemia, characterized by elevated blood lipid levels, represents a major global health concern due to its strong association with cardiovascular disease, diabetes, and metabolic syndrome. While current therapies - such as statins, fibrates, bile acid sequestrants, and PCSK9 inhibitors - are effective in controlling hyperlipidemia, they are often associated with adverse effects, potential drug resistance, and suboptimal efficacy in certain patient populations. All of the above underscore the urgent need for safer and more effective therapeutic alternatives. Among the major molecular targets involved in the regulation of lipid metabolism are HMG-CoA reductase, PCSK9, peroxisome proliferator-activated receptors (PPARs), cholesteryl ester transfer protein (CETP), and nuclear receptors, including the liver X receptor (LXR) and farnesoid X receptor (FXR), which are also targets for future antihyperlipidemic drug development. Recent advancements in artificial intelligence (AI) and machine learning (ML) have significantly transformed and accelerated drug discovery by enabling the processing of vast amounts of genomic, proteomic, and chemical data. Furthermore, ML tools such as quantitative structure-activity relationship (QSAR) modelling, deep learning, random forest, and support vector machines (SVM) have proven predictive and effective in identifying novel lipid metabolism modulators, thereby enhancing the efficacy and accuracy of virtual screening. Meanwhile, molecular docking has become an integral part of structure-based drug design (SBDD), and software such as AutoDock, Glide, and GOLD have proven effective in generating accurate ligand-target docking models. Molecular docking, together with ML-based approaches, enables the identification of potent and selective drug candidates. Overall, the combination of ML and molecular docking offers an efficient and accurate platform for antihyperlipidemic drug discovery, helping to overcome the limitations of currently available therapeutic strategies.

HMG-CoA reductase↗
PubMed1986

Architecture of the masticatory apparatus in eastern raccoons (Procyon lotor lotor).

The structure and function of the masticatory apparatus of raccoons resemble those found in carnivores. In this study, the architecture of the skull, dentition, and masticatory apparatus is described, and a model is proposed that suggests a mechanism used by raccoons to reduce different foods. The model suggests that jaw movements are similar to those of cats, the posterior regions of the superficial and deep parts of the temporalis and the anterior region of the medial pterygoid generate horizontal jaw movements, and the anterior portions of the superficial and deep temporalis as well as portions of the masseteric complex generate vertical closing movement. The distributions of slow, fast fatigable, and fast fatigue-resistant fibers for the temporalis and masseteric complex are related to the possible actions of these muscles during mastication, as are the regional cross-sectional areas of the masticatory muscles.

Animals↗
PubMed2026

Unveiling tumor heterogeneity by single cell RNA-sequencing: From basic considerations to clinical applications.

Tumor heterogeneity-encompassing diverse cellular phenotypes, genomic alterations, and microenvironmental contexts-is a principal barrier to effective cancer therapy. Single-cell RNA sequencing (scRNA-seq) has transformed our ability to resolve this complexity by capturing transcriptomes at single-cell resolution. Here, we review the technical foundations required for high-quality scRNA-seq studies. We then trace the evolution of scRNA-seq platforms from manual micromanipulation to high-throughput systems, and describe the computational pipelines that enable reliable data interpretation. The application of scRNA-seq is exemplarily shown in the context of lung cancer, where single-cell profiling has revealed (i) the clonal and sub-clonal architecture of tumors, (ii) extensive remodeling of the immune microenvironment, iii) key mechanisms underlying resistance to targeted agents and immune-checkpoint blockade, and (iv) the dynamics of neo-antigen-specific T-cell responses. Integrating machine-learning techniques-such as deep-learning classifiers and graph-based models-with single-cell transcriptomic data has markedly sped up biomarker discovery, produced more accurate risk-stratification scores, and enabled the generation of patient-specific therapeutic predictions. We surveyed the major trial registry ClinicalTrials.gov and identified ∼380 ongoing or completed studies that explicitly incorporate scRNA-seq as a correlative or pharmacodynamic endpoint. Overall, the analysis shows that scRNA-seq becomes an increasingly important component of modern trials, providing high-resolution cellular and molecular readouts that complement conventional imaging and bulk-omics endpoints. While key challenges remain, ranging from costs, scalability and need for rigorous validation before routine clinical deployment, ongoing technological advances continue to expand the potential of scRNA-seq as a cornerstone of precision medicine.

Humans↗
PubMed2025

DiCARN-DNase: enhancing cell-to-cell Hi-C resolution using dilated cascading ResNet with self-attention and DNase-seq chromatin accessibility data.

MOTIVATION: The spatial organization of chromatin is fundamental to gene regulation and essential for proper cellular function. The Hi-C technique remains the leading method for unraveling 3D genome structures, but the limited availability of high-resolution (HR) Hi-C data poses significant challenges for comprehensive analysis. Deep learning models have been developed to predict HR Hi-C data from low-resolution counterparts. Early Convolutional Neural Network (CNN)-based models improved resolution but struggled with issues like blurring and capturing fine details. In contrast, Generative Adversarial Network (GAN)-based methods encountered difficulties in maintaining diversity and generalization. Additionally, most existing algorithms perform poorly in cross-cell line generalization, where a model trained on one cell type is used to enhance HR data in another cell type. RESULTS: In this work, we propose Dilated Cascading Residual Network (DiCARN) to overcome these challenges and improve Hi-C data resolution. DiCARN leverages dilated convolutions and cascading residuals to capture a broader context while preserving fine-grained genomic interactions. Additionally, we incorporate DNase-seq data into our model, providing a robust framework that demonstrates superior generalizability across cell lines in HR Hi-C data reconstruction. AVAILABILITY AND IMPLEMENTATION: DiCARN is publicly available at https://github.com/OluwadareLab/DiCARN.

Chromatin↗
PubMed1991

The influence of model parameter values on the prediction of skin surface temperature: II. Contact problems.

A model of heat transfer and temperature distribution in the skin and superficial tissues which is based on a finite difference numerical solution of the one-dimensional multilayer coupled bioheat equation is presented. The model is used to investigate the influence of the values chosen to represent the physiological and thermal properties of the tissues on the skin surface temperature after contact with an external medium. It was found that the skin blood flow and dermal conductivity were the main cutaneous parameters which influence the contact response, but in terms of normalized temperature the response was little influenced by cutaneous metabolic heat generation and deep dermal temperature. For contact with a good conductor, the transient behaviour was sensitive to the heat transfer coefficient on the outer surface and the thickness of the contact material, but insensitive to the conductivity of the material.

Humans↗
PubMed2025

Caenorhabditis diversity on Pohnpei, Micronesia, provides evidence that the Elegans Supergroup has its roots in the Americas and diversified in the Pacific en route to Asia.

The microscopic nematode Caenorhabditis elegans stands unrivaled as a model for developmental biology, neurobiology, and genetics, but fundamental aspects of its ecology, biogeography, and natural history remain unknown. Leveraging recent findings that place its center of diversity in the cool, high-elevation forests of Hawaii, we performed an intensive survey of the Caenorhabditis fauna of Pohnpei, a high island in Micronesia that is home to the largest patch of high-elevation forest between Hawaii and East Asia. We found nine species of Caenorhabditis, five of them new, but not C. elegans. Most species were limited to the hot lowlands but three spanned the elevational range and one was found only in the cloudforest. Using the distribution of Caenorhabditis nematodes among habitat patches - individual rotting fruits or flowers - we parameterized simple models that capture key aspects of the population biology of these animals. We generated transcriptomes for the new species and inferred a phylogeny for 70 species of Caenorhabditis, based on 2955 genes. This phylogeny allowed us to perform the first quantitative biogeographic analysis for the group. Our analysis suggests that the deep ancestors of the Elegans Supergroup of species lived in the Americas, and that the Supergroup's subsequent diversification occurred in Remote Oceania. The ancestors of the Supergroup gave rise to a diverse Oceanian fauna and ultimately to multiple lineages that moved into Asia, Africa, Australasia, and back into the Americas. Though biogeographic inferences are limited by the lack of information from key regions of the southwest Pacific, the data are consistent with a model of trans-Pacific migration, with the islands of Oceania serving as sources rather than sinks for biodiversity.

Caenorhabditis↗
PubMed1987

Role of platelets in atherogenesis: relevance to coronary arterial restenosis after angioplasty.

There is now considerable evidence to suggest that some aspects of early lesion formation and later lesion growth are a reaction to injury. Hemodynamic factors are important in determining the site of injury and may produce injury directly. Injury can lead to atherogenesis in animal models as well as in humans. Superficial injury exposes the subendothelium, allowing platelet adhesion, which at high shear rates is dependent on vWF. Platelet adhesion and degranulation release PDGF, which stimulates smooth muscle cell proliferation, synthetic functions, and vasoconstriction. LDL stimulates smooth muscle cell growth as well as damages endothelium in some experimental systems. Thus, a link is provided between platelet and lipid involvement in atherosclerosis. Direct evidence for a role of platelets in atherogenesis comes from studies in which animals were treated to reduce platelet number or function or in which platelet function is genetically impaired (pigs with von Willebrand's disease). In these models, reduced platelet function is associated with less atherosclerosis. Deeper injury exposes collagen, with subsequent platelet aggregation, thrombin and fibrin generation. The role of reduced production of PGI2 and fibrinolytic agents following severe damage is unknown. Deep injury to the vessel occurs during plaque fissuring, the pathologic process underlying most cases of myocardial infarction, unstable angina, and some cases of sudden death. Angioplasty produces amelioration of many patients' symptoms and is safe. However, acute occlusion occurs occasionally, and restenosis in the first year occurs in some 30 percent of patients treated. Angioplasty damages the arterial wall, with endothelial denudation and intimal and medial splitting. Why does this, and plaque injury, by stimulating platelet deposition, not produce more restenosis? Changes in arterial anatomy are likely to be important: the increase in vessel diameter and in blood flow produce conditions less favorable for thrombotic or arteriosclerotic restenosis.

Angioplasty, Balloon↗
PubMed2026

[Applications and Challenges of Deep Learning in Human Genome Research].

In recent years, the advent of high-throughput omics technologies has fueled an explosive growth in human genomic data. Uncovering the latent functions within this vast data has become a significant challenge in functional genomics research. While traditional statistical methods have proved successful for analyzing smaller-scale datasets in the past, they exhibit clear limitations in analytical efficiency and integrating multi-dimensional data, struggling to meet the escalating demands of contemporary genomic analysis. The introduction of deep learning (DL) technologies offers a novel paradigm for this field. This review systematically examines the advances in applying deep learning to human genomics research. Studies demonstrate that when ample labeled data is available, discriminative DL computational methods-such as Convolutional Neural Networks (CNNs) and Long Short-Term Memory networks (LSTMs)-achieve high accuracy and efficiency in genomic variant discovery tasks. Furthermore, generative DL methods, particularly Large Language Models (LLMs) leveraging self-supervised pre-training strategies, effectively integrate complex genomic information and exhibit superior performance in functional genomic sequence annotation and gene regulation studies. This review also explores the application of LLMs in multi-omics data integration and prediction. Looking ahead, the continued accumulation of long-read sequencing and high-dimensional data is expected to enable DL technologies to integrate increasingly complex and heterogeneous genomic information, playing an increasingly crucial role in human genomics research.

Deep Learning↗
PubMed2024

Nanopore sequencing to detect A-to-I editing sites.

Adenosine-to-inosine (A-to-I) RNA editing, mediated by the ADAR family of enzymes, is pervasive in metazoans and functions as an important mechanism to diversify the proteome and control gene expression. Over the years, there have been multiple efforts to comprehensively map the editing landscape in different organisms and in different disease states. As inosine (I) is recognized largely as guanosine (G) by cellular machineries including the reverse transcriptase, editing sites can be detected as A-to-G changes during sequencing of complementary DNA (cDNA). However, such an approach is indirect and can be confounded by genomic single nucleotide polymorphisms (SNPs) and DNA mutations. Moreover, past studies rely primarily on the Illumina platform, which generates short sequencing reads that can be challenging to map. Recently, nanopore direct RNA sequencing has emerged as a powerful technology to address the issues. Here, we describe the use of the technology together with deep learning models that we have developed, named Dinopore (Detection of inosine with nanopore sequencing), to interrogate the A-to-I editome of any organism.

Inosine↗
PubMed1978

Neuronal mechanisms of the late N-wave induced in vitro in thin sections of the olfactory cortex of rats.

Experiments were done to elucidate properties of the late N-wave which was induced in vitro in thin sections of the olfactory cortex of the rat in response to stimulation of the lateral olfactory tract. The late N-wave decreased in size at a stimulation rate of more than once every 90 sec or at temperatures higher than 27 degrees C. The late N-wave was suppressed in the presence of GABA, picrotoxin or bicuculline or in the Cl-free medium. Penicillin or pentylenetetrazol, which blocked actions of GABA on the presynaptic potential, also suppressed the late N-wave. The late N-wave first appeared at postnatal ages of 18--25 days. The late N-wave reversed in polarity when recorded from the deep layers of the sections or from the cut surface of the sections. Single cells in the deep portions of the sections discharged during the late N-wave. Cells in the superficial layers fired just before or after the late N-wave. In order to explain these observations, a neuronal model for generation of the late N-wave was presented.

Action Potentials↗
PubMed1995

Susceptibility of different cell layers of the anterior and posterior part of the piriform cortex to electrical stimulation and kindling: comparison with the basolateral amygdala and "area tempestas".

Several lines of evidence suggest that the piriform cortex functions as a generator in the development and propagation of forebrain (limbic type) seizures, particularly in the kindling model of epilepsy. It is, however, not clear where, within the rather large piriform cortex region, the generator resides, and how much tissue is involved. Highly sensitive loci to chemical or electrical stimulation have been described both in the deep anterior and posterior parts of the piriform cortex. Furthermore, data from piriform cortex slice preparations indicated that epileptiform potentials originate in deep structures, particularly the endopiriform nucleus that underlies the piriform cortex. In the present study, in rats, we implanted stimulation and recording electrodes in various rostrocaudal locations of the piriform cortex and endopiriform nucleus, including the "area tempestas", i.e. a structure in the anterior part of the piriform cortex previously proposed to be critically involved in the generation of convulsive seizures of limbic origin. Within the piriform cortex, electrodes were aimed at different cellular layers of this structure. For comparison, additional animals received electrodes in different parts of the basolateral amygdala. A total of 19 different locations was obtained in this way. The susceptibility of these locations to electrical stimulation was characterized by determining the threshold for induction of afterdischarges. The afterdischarge threshold was lowest in layer III of the posterior piriform cortex and some locations in the endopiriform nucleus, whereas amygdala and "area tempestas" displayed higher values. In several animals, particularly those with electrodes in layer III of the posterior piriform cortex, spontaneous spiking was seen in prestimulation recordings, whereas this was never observed in recordings from the amygdala. Subsequent kindling by repeated stimulation of the various locations demonstrated marked differences in afterdischarge threshold reduction and kindling rate. The most marked decreases in afterdischarge threshold were seen in locations within layer III of the piriform cortex, whereas several other locations, including the "area tempestas", exhibited only moderate decreases or no decrease at all. In contrast to previous observations with only few locations in the piriform cortex region, the posterior piriform cortex was not in general slower to kindle than the anterior piriform cortex, although some locations in the posterior piriform cortex exhibited significantly lower kindling rates than the amygdala. The highest kindling rate was seen in the dorsal endopiriform nucleus.(ABSTRACT TRUNCATED AT 400 WORDS)

Amygdala↗