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At least 91 records · Page 5Linked to original sources
PubMed2026

Non-invasive strategy for gastric cancer detection: Integration of cell-free DNA fragmentomics and protein biomarkers.

Gastric cancer (GC) ranks as the fifth most common cancer worldwide, however, accurate and non-invasive diagnostic modalities for GC remain limited. Cell-free DNA (cfDNA) fragmentomics has emerged as a promising tool for cancer cell detection. Here we develop a gastric cancer detection model, named GaFraD model. The GaFraD model uses four cfDNA fragmentomics features, including fragment size ratio (FSR), copy number variation (CNV), 9-bp end motif (Motif), and fragment size at transcription start sites (TF). This model achieves an area under the receiver-operating characteristic curve (AUC) of 0.970 (95% CI: 0.944 - 0.990), a sensitivity of 95.0% and a specificity of 80.9%. By combining the GaFraD model and conventional protein biomarkers CA19-9 and PG-I/PG-II, the CONFIRM model was generated. The CONFIRM model attained an AUC of 0.986 (95% CI: 0.966 - 1.000), a sensitivity of 95.0% and a specificity of 95.6% in detecting GC. Moreover, the CONFIRM model achieved remarkable performance (AUC = 0.983, sensitivity 95.6%, specificity 94.2%) in distinguishing patients with early-stage GC from controls. Our work showed the high discriminatory power in distinguishing GC patients from controls, indicating the clinical potential of using cfDNA fragmentomics combined with protein biomarkers for non-invasive GC detection. The results of the study provide a new avenue for early, accurate, and non-invasive clinical diagnosis of GC.

Cell-free DNA↗
PubMed1992

Motor-pattern-generating networks in invertebrates: modeling our way toward understanding.

Motor-pattern-generating networks in invertebrates have been the objects of intensive study to determine the origin and modulation of rhythmic neural activity. In some pattern generators, intrinsically bursting neurons drive activity throughout the network. In most pattern generators, however, rhythmicity arises from the interplay between intrinsic membrane properties and synaptic interaction. Reciprocal inhibitory synapses between neurons are thought to be crucial for generating oscillation in these networks, but a fundamental understanding of how such network oscillators work remains elusive. Progress towards this goal has come from attempts to combine computational modeling approaches with conventional physiological analysis.

Animals↗
PubMed1975

Generations and aging: a longitudinal study.

This study is a longitudinal investigation of the relationship between age and subjective outlook. Over the years, a number of theoretical positions have been introduced to either account for or to minimize age differences in attitudes, values and beliefs. The author has organized these theories of aging into three basic sociological fremeworks or models: the "generations" model, the "age status" model and the "illusion of differences" model. Using a relatively simple methodological desihn, hypotheses derived from these models were tested through secondary analysis of survey data. Strong support was found for the "generations" hypothesis, weak support for the "age status" hypothesis, and no support at all for the "illusion of differences" hypothesis.

Adult↗
PubMed2026

Artificial Intelligence for Natural Products Discovery and Development.

Natural products (NPs) remain a cornerstone of modern drug discovery, offering stereochemical complexity and diverse bioactivities that precisely modulate therapeutic targets, refined through billions of years of evolution. However, their research has long been hindered by inefficient, empirical workflows, high resource consumption, structural complexity, and the "multicomponent, multi-target" nature of their mechanisms. The exponential growth of genomic, metabolomic, and spectral data has overwhelmed conventional analytical methods, exposing critical bottlenecks in handling high-dimensional, heterogeneous datasets that exceed human interpretive capacity. Artificial intelligence (AI) is emerging as a transformative paradigm to address these challenges, integrating multi-omics and chemical data to shift NP research from fragmented empiricism toward mechanism-driven, precision-oriented development. By leveraging deep learning architectures- including graph neural networks, Transformers, and diffusion-based generative models-AI enables systematic decoding of NP biosynthesis, automated structure elucidation, rational target identification, knowledge extraction from vast unstructured scientific literature, and de novo molecular design. This review comprehensively surveys recent advances in AI applications across the full NP discovery and development pipeline, encompassing genome mining, structure-based and ligand-based virtual screening, multimodal structural characterization, lead optimization, and biosynthetic pathway engineering. We further examine the emerging roles of protein-centric, molecule- centric, and multimodal foundation models, as well as large language models, in bridging genotype-to-chemotype gaps and unlocking unstructured scientific knowledge. Finally, we discuss critical challenges including data scarcity, representational limitations for complex stereochemistry, physical plausibility in generative models, and the urgent need for experimental validation, while outlining future directions toward autonomous experimentation, closed-loop optimization, and human-AI collaborative discovery.

Artificial intelligence↗
PubMed1977

An extended transition probability model of the variability of cell generation times.

The transition probability model of variability of cell generation times is extended so that the rate constant for the transition from the A-state to the B-phase of the cell cycle depends on on time which a particular all has already spent in the A-state. A specific time dependence of this rate constant is introduced. It is determined by the value of one constant which is then an additional parameter of the model. The corresponding cell population kinetics are calculated and compared to existing experimental evidence. The model accounts satisfactorily for the generation time distribution function and for the shortening of the G1 phase of binucleate cells. The time dependence of the transition probability is related to the cell kinetics of an hypothetical cell constituent. A possible relationship is proposed between the chemical parameters with the cell and the parameters of the cell population kinetics.

Animals↗
PubMed1992

A crystallographic molecular lattice builder applied to model lipid bilayers.

It is often desirable for noncrystallographers to generate graphical models of three-dimensional crystal structures based on published coordinates of the atoms that make up the crystallographic unit cells. This type of visualization is particularly important for small-molecule crystals, such as lipid crystals, where one may be interested in investigating interactions between the individual molecules in addition to their conformations. BILAYER BUILDER is a program that generates a portion of the entire crystal structure from the coordinates of the molecules in a single unit cell. It gives users of small desktop computers, such as the Apple Macintosh, the capability to generate and examine model crystal structures with a molecular graphics display program. BILAYER BUILDER stores the crystal coordinates in a Brookhaven Protein Data Bank file format for possible use in a variety of applications on many different computers. Initially, it was written for use with lipid crystals and bilayers but may be used for building an assortment of molecular crystals.

Computer Graphics↗
PubMed1992

Phase resetting and fixed-delay stimulation of a simple model of respiratory rhythm generation.

In a previous study (Lewis et al., 1990), the response of the respiratory rhythm to a perturbing stimulus was investigated using two different stimulus protocols: phase resetting and fixed-delay stimulation. The first protocol consists of measuring the effects of perturbing an oscillator at different phases of the cycle on the duration of the perturbed cycle. The resulting phase response curves (PRCs) can be used to characterize the properties of the oscillator (Winfree, 1980). A second protocol, fixed-delay stimulation, involves perturbing an oscillator at a fixed latency from the onset of the cycle, repeated every n-th cycle. If a single stimulus produces an effect that lasts longer than a single cycle, complicated responses can be expected from fixed-delay stimulation (Lewis et al., 1987). A simple three-phase model for respiratory rhythm generation based on a hypothesis by Richter and coworkers (1982, 1983, 1986) was investigated in the context of these experimental studies. Phase resetting and fixed-delay stimulation protocols were simulated in the model. PRCs of the model resemble those obtained experimentally: a phase-dependent prolongation or shortening of the inspiratory phase depending on the stimulus magnitude, and a slight prolongation of the expiratory phase. Stimuli delivered to the model repetitively during successive inspiratory periods at a fixed-delay produced various combinations of shortened and prolonged cycles, similar to those observed in the experiments. However, the marked increases in cycle duration observed in the experiments during, as well as after, stimulation were not evident in the model. These comparisons suggest that (1) PRCs may not be an adequate way to evaluate certain models of rhythmogenesis, and (2) to improve the present simplified formulation of the three-phase model of the respiratory oscillator, time-varying stimulus dependent effects should be incorporated.

Animals↗
PubMed1978

A model of quick phase generation in the vestibuloocular reflex.

The vestibuloocular relfex of the cat was studied during step and sinusoidal head velocity stimuli. A model is presented which simulates the observed slow phase and quick phase behavior. The model is constructed to be compatible with neurophysiological observations of the behavior of neurons in the pons. Emphasis is placed on the amplitude and timing of quick phases which are active orienting movements that drive the eyes into the direction of turning. It is proposed that quick phases, like saccades, are generated by a local feedback loop in the pons which rapidly drives the eyes to a point in the orbit specified by a vestibular signal. It is suggested that two internal signals specify the eye positions at which quick phases start and end. The statistics of the fluctuations of these signals was measured and correlation between them was discovered and incorporated in the model.

Animals↗
PubMed1992

Saccade-vergence interactions in humans.

1. We recorded eye movements in four normal human subjects during refixations between targets calling for various combinations of saccades and vergence. We confirmed and extended prior observations of 1) transient changes in horizontal ocular alignment during both pure horizontal saccades (relative divergence followed by relative convergence) and pure vertical saccades (usually divergence for upward and convergence for downward saccades); 2) occasional, high-frequency (20-25 Hz), conjugate oscillations along the axis orthogonal to the main saccade; and 3) the speeding up of horizontal vergence by both horizontal and vertical saccades. 2. To interpret these findings, we developed a hypothesis for the generation of vergence to step changes in target depth, both with and without associated saccades. The essential features of this hypothesis are 1) the transient changes in horizontal ocular alignment during pure horizontal saccades reflect asymmetries in the mechanical properties of the lateral and medial rectus muscles causing adduction to lag abduction; 2) pure vergence movements in response to step changes in target depth are generated by a neural network that uses a desired change in vergence position as its input command and instantaneous vergence motor error (the difference between the desired change and the actual change in vergence) to drive vergence premoter neurons; and 3) the facilitation of horizontal vergence by saccades arises from nonlinear interactions in central premotor circuits. 3. The hypothetical network for generating pure vergence to step changes in target depth is analogous in structure to the local feedback model for the generation of saccades and has the same conceptual appeal. With the assumption of a single nonlinearity describing the relationship between a vergence motor error signal and the output of the neurons that generate promoter vergence velocity commands, this model generates pure vergence movements with peak velocity-amplitude relationships and trajectories that closely match those of experimental data. 4. Several types of models are proposed for the central, nonlinear interaction that occurs when saccades and vergence are combined. Common to all models is the idea that omnidirectional pause neurons (OPN), which are thought to gate activity for saccade burst neurons, also gate activity for saccade-related vergence. In one model we hypothesize the existence of a separate class of saccade-related vergence burst neurons, which generate premotor horizontal vergence commands but only during saccades. In a second model we hypothesize separate right eye and left eye saccadic burst neurons that receive not only conjugate, but also equal but oppositely directed vergence error signals.(ABSTRACT TRUNCATED AT 400 WORDS)

Adult↗
PubMed1992

Automatic search for model to simulate the differentiation of T lymphocytes within the thymus.

The differentiation of T Lymphocytes within the thymus is an important biological phenomenon during which these cell acquire their functions to further control the immune system. Numerous experiments under various conditions have been devised to understand the different mechanisms involved in this complex process. Nevertheless, interpretation of these experiments lead to still contradictory debatable hypotheses. Modelisation of this process through classical simulation methods cannot be envisaged because they are not adapted to modifications of the model structure, which is the point of interest. For these reasons, we proposed a new approach of automatic search for model. The program consists of four independent connected modules: The generator produces model, based on the rationale of formal grammars. Protocol and experimental data are stored in a set of experiments. The simulator using a protocol and a model provides simulated results. Finally, the supervisor by comparing simulated results and experimental data, adapts the model parameters to increase their fit and either chooses a new experiment to explore, or modifies the model structure. Change of the model structure is performed among still unexplored models according to their "promise" level, which is iteratively evaluated relatively to previously explored models through a proposed model distance. The generator is written in Prolog and the other modules in C++. The architecture of the program allows us to modify or complete a module without changing anything in the other modules. As a consequence, the proposed modeling approach conceived to study T lymphocyte differentiation within the thymus remains independent of this biological phenomenon and can be applied to other biological problems.

Cell Differentiation↗
PubMed1979

Influence of diastolic fibre orientation on the left ventricular power generation.

A mathematical model is described which in a simplified way, without directly taking into account the elastic properties of the heart wall, describes the EDV which corresponds to the experimental data. The model further describes the power generation of the left ventricle at high EDV. The volume density of power is expressed with a product of three factors (1) average density of the CE, (2) a factor which contains the inotropic properties of a single CE and (3) a form factor, which involves structural changes in the heart wall at various EDV.

Cardiac Volume↗
PubMed1992

Development of a rate adaptive pacemaker based on the maximum rate-of-rise of right ventricular pressure (RV dP/dtmax).

The maximum rate of rise of right ventricular pressure (RV dP/dtmax) may change in response to physiological stress and thereby provide an appropriate parameter upon which to base rate adaptive pacing. Initial feasibility testing was carried out in six patients using externally closed loop rate adaptive pacing with a pressure sensing lead (Model 6220) and an investigational VVI pulse generator (Medtronic, Model 2451). During exercise, maximum positive RV dP/dtmax increased from 223 +/- 55 to 405 +/- 181 mmHg.sec.1 (P less than 0.05). Based on these results, rate adaptive pulse generators using maximum positive RV dP/dt were implanted in 12 patients (Medtronic, Model 2503). Exercise treadmill testing in the VVI mode resulted in heart rates ranging from 69 +/- 6 beats/min at rest to 79 +/- 14 beats/min (n = 12; P greater than 0.05). In contrast, VVIR mode pacing rates ranged from 71 +/- 11 beats/min to 115 +/- 24 beats/min (n = 17; P less than 0.05). Holter recording showed heart rates ranging from 51 +/- 6 to 110 +/- 22 beats/min during activities of normal daily living (n = 9; P less than 0.05). Passive postural tilt resulted in rates of 69 +/- 8 beats/min in the supine position increasing to 74 +/- 14 beats/min with 60 degrees upright tilt (n = 16; P greater than 0.05). With up to 5-year follow-up data, there have been no late failures of pacing but one lead showed insulation failure with over- and undersensing after 4.5 years. A number of deficiencies were identified in the prototypes leading to modifications of a subsequent generation of rate responsive pacemaker based on RV dP/dtmax. These initial data demonstrate that rate adaptive pacing based on RV dP/dtmax responds in a physiological manner. This rate responsive system is of particular interest as it is based on a beat-to-beat parameter of cardiac mechanical function.

Activities of Daily Living↗
PubMed2025

Biomarker-Based Nomogram to Predict Neoadjuvant Chemotherapy Response in Muscle-Invasive Bladder Cancer.

Background/Objectives: The aim of this study was to identify response prediction and prognostic biomarkers in muscle-invasive bladder cancer (MIBC) patients undergoing neoadjuvant chemotherapy (NAC). Methods: A retrospective multicentre study including 191 patients with MIBC who received NAC previous to radical cystectomy (RC) between 1996 and 2013. Gene expression patterns were analysed in 34 samples from transurethral resection of the bladder (TURB) using Illumina microarrays. The expression levels of 45 selected differentially expressed genes between responders and non-responders to NAC were validated by quantitative PCR in an independent cohort of 157 patients. Regression analysis was used to identify predictors of downstaging and relapse. A nomogram for predicting downstaging and relapse-including clinicopathological and gene expression variables-was developed. Results: The expression levels of 1352 transcripts differed between responders and non-responders to NAC. A nomogram based on the most predictive clinical variables (age, Tis (in situ), gender, history of NMIBC, and lymphadenopathy) and genes selected following the Akaike information criterion (AIC) (CBTB16, CHMP6, DDX54, CASP8, LOR, and PLEC) was then created. In addition, a three-gene expression prognostic model to predict tumour relapse was generated. This model was able to discriminate between two groups of patients with a significantly different probability of tumour relapse (HR: 2.11; CI: 1.16-3.83, p = 0.01). Conclusions: Our nomogram based on gene expression and clinical data is a useful tool to predict downstaging and tumour relapse after NAC in MIBC patients. Further validation is warranted.

bladder cancer↗
PubMed1977

A second order model of the optic generator potential and its relation to Stevens' power function.

The component PIII of the electroretinogram representing the optic generator potential was recorded after stimulation with short stimuli with different light intensity. It is shown that the impulse response function of a linear second order model with intensity-dependent coefficients can be well fit to the recordings. Two of its parameters, after logarithmic transformations, are linearly dependent on the luminance while the third parameter varies only within a small interval. It is therefore possible to describe the relation between PIII and luminance in a linearized second order model. Furthermore, both the type of the function relating the gain of the model to the luminance and its exponent are nearly identical with the psychophysic function relating luminance to subjective brightness. Further physiological implications are also considered.

Animals↗
PubMedDate not supplied

[Mechanism of early receptor potential generation and an electrical model of retinal rods in rats].

A passive electric model of the retinal rod can reproduce the changes of the ELP-waveform at temperatures within the range 10 degrees--45 degrees C. R2-component of the ERP is generated by the process with the time constant ca. 500 microseconds (37 degrees C) and activation energy 31 kcal/mol characteristic of metarhodopsin I--metarhodopsin II transition. R1 originates not later than at prelumirhodopsin--lumirhodopsin conversion. Charge displacements are 0.006 (R1) and 0.04 (R2) electronic charges per rhodopsin bleached. The model is used for determining membrane capacitance and resistance of the rat retinal rod.

Animals↗
PubMed1992

Bayesian methods and optimal experimental design for gene mapping by radiation hybrids.

Radiation hybrid mapping is a somatic cell technique for ordering human loci along a chromosome and estimating the physical distance between adjacent loci. The present paper considers a realistic model of fragment generation and retention. This model assumes that fragments are generated in the ancestral cell of a clone according to a Poisson breakage process along the chromosome. Once generated, fragments are independently retained in the clone with a common retention probability. Based on this and less restrictive models, statistical criteria such as minimum obligate breaks, maximum likelihood, and Bayesian posterior probabilities can be used to decide order. Distances can be estimated by either maximum likelihood or Bayesian posterior means. The model also permits rational design of radiation dose for optimal statistical precision. A brief examination of some real data illustrates our criteria and computational algorithms.

Algorithms↗