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PubMed2026

TCRspec: A Recognition Interface-Informed Multimodal Method for TCR-pMHC Specificity Prediction.

Specific recognition between T-cell receptors (TCRs) and peptide-major histocompatibility complexes (pMHCs) is central to adaptive immunity, yet accurate prediction of TCR-pMHC specificity remains challenging. Existing models mainly rely on sequence features or isolated molecular structures, limiting their ability to capture interface-level determinants within the ternary recognition complex. Here, we constructed the multimodal TCR-pMHC ternary complex (MM-TCR) data set, integrating paired TCR-pMHC sequences, V/J gene annotations, and modeled TCR-pMHC complex structures refined by short molecular dynamics-based relaxation. Based on MM-TCR, we developed TCRspec, an interpretable multimodal framework combining sequence embeddings, gene-usage features, and complex-level structural representations. Under a stringent CD-HIT TCR-cluster-disjoint split, TCRspec achieved an average AUROC of 0.896 and AUPRC of 0.882 across seven antigen-specific test data sets, outperforming representative baseline models. Cross-validation and ablation analyses confirmed the contribution of ternary complex structural information and MD-refined structures. In independent OOD peptide-TCR systems, TCRspec retained discriminative performance and identified model-inferred peptide positions associated with TCR recognition, providing a structure-informed framework for TCR specificity prediction.

Receptors, Antigen, T-Cell↗
PubMedDate not supplied

[Chronic renal failure: predictors of good adjustment to disease and treatment].

N = 109 patients with chronic renal failure were studied referring to somatic, psychological and social parameters, which are often discussed in psychonephrology. N = 25 of the patients were in the status of compensated retention, n = 43 were undergoing hemodialysis and n = 41 lived after transplantation. At the same time the treating physicians were asked to judge different criterias referring to the adaptation of the patients to the disease and treatment. Using a discriminant analysis, we were successful in predicting the quality of adaption in 75-85% using the patient variables. The results show, that each of the three treatment groups is to be considered separately, although some variables seem to have a generally strong prediction power: Serum level of Calcium, psychosomatic complaints and the extent of depressive disorder. Some aspects for further prospective studies and for the practical treatment are shown.

Adaptation, Psychological↗
PubMed2002

Functional adaptation of cancellous bone in human proximal femur predicted by trabecular surface remodeling simulation toward uniform stress state.

Two-dimensional simulation of trabecular surface remodeling was conducted for a human proximal femur to investigate the structural change of cancellous bone toward a uniform stress state. Considering that a local mechanical stimulus plays an important role in cellular activities in bone remodeling, local stress nonuniformity was assumed to drive trabecular structural change to seek a uniform stress state. A large-scale pixel-based finite element model was used to simulate structural changes of individual trabeculae over the entire bone. As a result, the initial structure of trabeculae changed from isotropic to anisotropic due to trabecular microstructural changes caused by surface remodeling according to the mechanical environment in the proximal femur. Under a single-loading condition, it was shown that the apparent structural property evaluated by fabric ellipses corresponded to the apparent stress state in cancellous bone. As is observed in the actual bone, a distributed trabecular structure was obtained under a multiple-loading condition. Through these studies, it was concluded that trabecular surface remodeling toward a local uniform stress state at the trabecular level could naturally bring about functional adaptation phenomenon at the apparent tissue level. The proposed simulation model would be capable of providing insight into the hierarchical mechanism of trabecular surface remodeling at the microstructural level up to the apparent tissue level.

Adaptation, Biological↗
PubMed1992

Adaptation and change in gastroenterology.

Predicting the future is a chancy business. In line with other medical specialties, gastroenterology will be subject to rapid and profound changes in the coming decades and will have to adapt and renew its approach to the way medicine will be practised. The pressures to change will be in several areas. Global demographic, political and economic factors will become more intrusive and rapid communication will end isolationism. Developing EC structures and regulations are likely to increase mobility of medical staff and uniformity in the standards of training and practice. Rapid technological advances will have to be reconciled with finite resources and the ever increasing expectations of our aging population.

Ambulatory Care↗
PubMed2005

Remodeling of blood vessels: responses of diameter and wall thickness to hemodynamic and metabolic stimuli.

Vascular functions, including tissue perfusion and peripheral resistance, reflect continuous structural adaptation (remodeling) of blood vessels in response to several stimuli. Here, a theoretical model is presented that relates the structural and functional properties of microvascular networks to the adaptive responses of individual segments to hemodynamic and metabolic stimuli. All vessels are assumed to respond, according to a common set of adaptation rules, to changes in wall shear stress, circumferential wall stress, and tissue metabolic status (indicated by partial pressure of oxygen). An increase in vessel diameter with increasing wall shear stress and an increase in wall mass with increased circumferential stress are needed to ensure stable vascular adaptation. The model allows quantitative predictions of the effects of changes in systemic hemodynamic conditions or local adaptation characteristics on vessel structure and on peripheral resistance. Predicted effects of driving pressure on the ratio of wall thickness to vessel diameter are consistent with experimental observations. In addition, peripheral resistance increases by approximately 65% for an increase in driving pressure from 50 to 150 mm Hg. Peripheral resistance is predicted to be markedly increased in response to a decrease in vascular sensitivity to wall shear stress, and to be decreased in response to increased tissue metabolic demand. This theoretical approach provides a framework for integrating available information on structural remodeling in the vascular system and predicting responses to changing conditions or altered vascular reactivity, as may occur in hypertension.

Adaptation, Physiological↗
PubMed2006

Adapting the Rx-Risk-V for mortality prediction in outpatient populations.

OBJECTIVES: We sought to operationalize, test, and validate an outpatient pharmacy-based case-mix adjuster. METHODS: Outpatients from the Department of Veterans Affairs (VA) prescribed a nonsteroidal anti-inflammatory drug (NSAID) or cyclooxygenase-2 selective drug during 2002 were identified. We updated and extended the Rx-Risk-V by adding 26 additional disease categories and mapping them to VA drug-class codes; derived empirical weights for each from a logistic model of 1-year mortality; adjusted for age, race and sex; and scored the weights into 1 measure of comorbidity. We compared the weighted score to the Deyo diagnosis-based comorbidity index and validated it in a national cohort of 260,321 outpatients with chronic heart failure (CHF). RESULTS: One-year mortality among the 724,270-outpatient NSAID cohort was 1.6% (n = 11,766). Using a baseline model of age, race, and gender (c-index = 0.716), we found that the Deyo measure improved the prediction of mortality (c-index = 0.765), and the pharmacy comorbidity score further improved the prediction (c-index = 0.782), an increase of 25.8%. Using both, we found further improvement (c-index = 0.792). Among the CHF cohort, 9.7% (n = 25,251) died within 1 year. Performance of the baseline model controlling for age, race, and gender (c index = 0.620) improved with addition of the pharmacy comorbidity score (c index = 0.689), compared with the addition of the Deyo measure (c index = 0.651), an increase of 55.1%. Together, they slightly improved prediction in CHF patients (c index = 0.695). CONCLUSIONS: The updated and extended Rx-Risk-V is useful for case-mix adjustment of mortality in an outpatient population.

Aged↗
PubMed1998

A model for geometric and mechanical adaptation of arteries to sustained hypertension.

This study aimed to model phenomenologically the dynamics of arterial wall remodeling under hypertensive conditions. Sustained hypertension was simulated by a step increase in blood pressure. The arterial wall was considered to be a thick-walled tube made of nonlinear elastic incompressible material. Remodeling rate equations were postulated for the evolution of the geometric dimensions of the hypertensive artery at the zero-stress state, as well as for one of the material constants in the constitutive equations. The driving stimuli for the geometric adaptation are the normalized deviations of wall stresses from their values under normotensive conditions. The geometric dimensions are modulated by the evolution of the deformed inner radius, which serves to restore the level of the flow-induced shear stresses at the arterial endothelium. Mechanical adaptation is driven by the difference between the area compliance under hypertensive and normotensive conditions. The predicted time course of the geometry and mechanical properties of arterial wall are in good qualitative agreement with published experimental findings. The model predicts that the geometric adaptation maintains the stress distribution in arterial wall to its control level, while the mechanical adaptation restores the normal arterial function under induced hypertension.

Adaptation, Physiological↗
PubMed2006

Evolutionary neuropathology & congenital mental retardation: environmental cues predictive of maternal deprivation influence the fetus to minimize cerebral metabolism in order to express bioenergetic thrift.

This article will propose that humans have an adaptive vulnerability to certain forms of mental retardation, specifically, neuropathological disorders that cause decreased energy expenditure in the hippocampus and the cerebral cortex. This hypothesis will be analyzed in terms of the thrifty phenotype paradigm according to which adverse prenatal events can cause differential gene expression resulting in a phenotype that is better suited, metabolically, for a deprived environment. For example, a malnourished mother has an increased propensity to give birth to offspring that feature a "thrifty phenotype" which permits highly efficient calorie utilization, increased fat deposition and a sedentary nature. This article interprets several prenatal occurrences, including maternal malnourishment, low birth weight, multiparity, short birth interval, advanced maternal age and maternal stress--which are currently identified by the epidemiological literature as risk factors for neuropathology--to be environmental cues that communicate to the fetus that, because it will be neglected of maternal investment, developing a metabolically conservative brain will be the most effective ecological strategy. Success in hunting and foraging in mammals, primates and especially humans is known to be dependent on prolonged maternal investment. Low levels of maternal care are known to result in low survivorship of offspring, largely because the offspring are forced to subsist using simple, low-yield foraging strategies. A predictive, adaptive response, marked by cerebral hypometabolism, may produce a level of metabolic conservancy that mitigates the risks associated with low levels of maternal care. This article will suggest that certain, human neuropathological phenotypes would have been well suited for an ecological niche that closely resembled the less skill-intensive niche of our less encephalized, primate ancestors. The forms of congenital neuropathology discussed in this article do not cause damage to vital homeostatic systems; most simply decrease the size and energy expenditure of the cerebral cortex and the hippocampus, the two structures known to show plasticity during changes in ecological rigor in vertebrates. Also, many disorders that present comorbidly with neuropathology, such as tendency toward obesity, decrement in anabolic hormones, hypotonic musculature, up-regulation of the hypothalamic-pituitary-adrenal axis, and decreased thyroid output are associated with energy conservancy and the thrifty phenotype, further implicating neuropathology in an ecological strategy. Determining the relative impact of evolutionary causation on neuropathological disease should prove informative for medical and gene therapeutic treatment modalities. Furthermore, use of the maternal deprivation paradigm presented here may help researchers more precisely identify the risk factors that determine cognitive trajectory.

Animals↗
PubMed2002

Adaptation of movement endpoints to perturbations of visual feedback.

We investigated the extent to which humans can quickly adapt their goal-directed arm movements to perturbed feedback. We predicted that the magnitude of adaptation to a changed relationship between vision and kinesthesia would depend on the type of perturbation, being largest when the perturbation can be generalized within egocentric frames of reference. To test this prediction we asked subjects to align a real 5-cm cube so that they could feel, but not see, with a simulation that they saw via a mirror. Subjects made successive movements between target locations in a sequence of adaptation and test phases. During adaptation phases, subjects received continuous visual feedback about the position of the real cube. The feedback was either veridical or perturbed. The perturbations were consistent with either a uniform translation, a scaling or a rotation. The latter two were relative to a central position between all the targets. During test phases, subjects received no visual feedback. We compared test movement endpoints after perturbed feedback with ones after veridical feedback. We found about 40% adaptation to translation, 20% to scaling and 10% to rotation. This difference in magnitude is consistent with the ease with which the transformation can be generalized within egocentric frames of reference. Changing the task so that it required different arm postures did not change the magnitude of adaptation, so postural configuration of the arm does not appear to be critical. Nevertheless, transfer to the unexposed arm was incomplete for translations and rotations, though it was complete for scaling, suggesting that at least part of the adaptation is posture based. We conclude that the adaptation to different kinds of perturbations not only differs in extent but also involves different (egocentric) mechanisms.

Adaptation, Physiological↗
PubMed1998

A test of the acoustic adaptation hypothesis in four species of marmots.

Acoustic signals must be transmitted from a signaller to a receiver during which time they become modified. The acoustic adaptation hypothesis suggests that selection should shape the structure of long-distance signals to maximize transmission through different habitats. A specific prediction of the acoustic adaptation hypothesis is that long-distance signals of animals in their native habitat are expected to change less during transmission than non-native signals within that habitat. This prediction was tested using the alarm calls of four species of marmots that live in acoustically different habitats and produce species-specific, long-distance alarm vocalizations: yellow-bellied marmot, Marmota flaviventris; Olympic marmot, M. olympus; hoary marmot, M. caligata; and woodchuck, M. monax. By doing so, we evaluated the relative importance the acoustic environment plays on selecting for divergent marmot alarm calls. Representative alarm calls of the four species were broadcast and rerecorded in each species' habitat at four distances from a source. Rerecorded, and therefore degraded alarm calls, were compared to undegraded calls using spectrogram correlation. If each species' alarm call was transmitted with less overall degradation in its own environment, a significant interaction between species' habitat and species' call type would be expected. Transmission fidelity at each of four distances was treated as a multivariate response and differences among habitat and call type were tested in a two-way MANOVA. Although significant overall differences in the transmission properties of the habitats were found, and significant overall differences in the transmission properties of the call types were found, there was no significant interaction between habitat and call type. Thus, the evidence did not support the acoustic adaptation hypothesis for these marmot species. Factors other than maximizing long-distance transmission through the environment may be important in the evolution of species-specific marmot alarm calls. (c) 1998 The Association for the Study of Animal Behaviour.

Journal Article↗
PubMedDate not supplied

Tendon and ligament adaptation to exercise, immobilization, and remobilization.

This study provides a theoretical and computational basis for understanding and predicting how tendons and ligaments adapt to exercise, immobilization, and remobilization. In a previous study, we introduced a model that described the growth and development of tendons and ligaments. In this study, we use the same model to predict changes in the cross-sectional area, modulus, and strength of tendons and ligaments due to increased or decreased loading. The model predictions are consistent with the results of experimental exercise and immobilization studies performed by other investigators. These results suggest that the same fundamental principles guide both development and adaptation. A basic understanding of these principles can contribute both to prevention of tendon and ligament injuries and to more effective rehabilitation when injury does occur.

Achilles Tendon↗
PubMed2005

An empirical test of the mutational landscape model of adaptation using a single-stranded DNA virus.

The primary impediment to formulating a general theory for adaptive evolution has been the unknown distribution of fitness effects for new beneficial mutations. By applying extreme value theory, Gillespie circumvented this issue in his mutational landscape model for the adaptation of DNA sequences, and Orr recently extended Gillespie's model, generating testable predictions regarding the course of adaptive evolution. Here we provide the first empirical examination of this model, using a single-stranded DNA bacteriophage related to phiX174, and find that our data are consistent with Orr's predictions, provided that the model is adjusted to incorporate mutation bias. Orr's work suggests that there may be generalities in adaptive molecular evolution that transcend the biological details of a system, but we show that for the model to be useful as a predictive or inferential tool, some adjustments for the biology of the system will be necessary.

Adaptation, Biological↗
PubMed1987

Adaptive bone-remodeling theory applied to prosthetic-design analysis.

The subject of this article is the development and application of computer-simulation methods to predict stress-related adaptive bone remodeling, in accordance with 'Wolff's Law'. These models are based on the Finite Element Method (FEM) in combination with numerical formulations of adaptive bone-remodeling theories. In the adaptive remodeling models presented, the Strain Energy Density (SED) is used as a feed-back control variable to determine shape or bone density adaptations to alternative functional requirements, whereby homeostatic SED distribution is assumed as the remodeling objective. These models are applied to investigate the relation between 'stress shielding' and bone resorption in the femoral cortex around intramedullary prostheses, such as used in Total Hip Arthroplasty (THA). It is shown that the amount of bone resorption depends mainly on the rigidity and the bonding characteristics of the implant. Homeostatic SED can be obtained when the resorption process occurs at the periosteal surface, rather than inside the cortex, provided that the stem is adequately flexible.

Adaptation, Physiological↗
PubMed2001

Conformation-family Monte Carlo: a new method for crystal structure prediction.

A new global optimization method, Conformation-family Monte Carlo, has been developed recently for searching the conformational space of macromolecules. In the present paper, we adapted this method for prediction of crystal structures of organic molecules without assuming any symmetry constraints except the number of molecules in the unit cell. This method maintains a database of low energy structures that are clustered into families. The structures in this database are improved iteratively by a Metropolis-type Monte Carlo procedure together with energy minimization, in which the search is biased toward the regions of the lowest energy families. The Conformation-family Monte Carlo method is applied to a set of nine rigid and flexible organic molecules by using two popular force fields, AMBER and W99. The method performed well for the rigid molecules and reasonably well for the molecules with torsional degrees of freedom.

Crystallization↗
PubMed1997

What do tissues and cells know of mechanics?

Many tissues and cells adapt to their mechanical environment, i.e. the stresses and strains to which the tissues are exposed during daily activities. Simple mechanical explanations of such adaptation naturally provide appeal, yet fail to predict accurately tissue appearance and behaviour. Continuum mechanics, the field from which our concepts of stress and strain arise, assumes a solid continuous structure, an assumption that does not apply at cell level. Merely correlating a given stress or strain magnitude with tissue behaviour does not per se account for the time over which responses occur. Tissues undoubtedly 'temporally process' mechanical signals, responding to some portion of the mechanical environment, and ignoring others. Further, the deformation that cells experience will depend upon their nonrigid connections to the matrix, so that the strains in the tissue may not be those experienced by the cell (and those causing the adaptation). Relatively simple mechanical models incorporating temporal features may adequately predict tissue adaptation, but the noncontinuum nature of tissues suggests that such models cannot adequately explain either tissue adaptation or the responses leading to adaptation.

Adaptation, Physiological↗
PubMed1983

[Modeling adaptation of the membranes of the nodes of Ranvier of a nerve fiber to the action of a steady current as a result of sodium channel inactivation].

A modified version of the Hodgkin-Huxley model for the Ranvier node (Dodge model) was used to study an effect of the second order kinetics of the sodium channels' inactivation on impulse activity. Computations based on data obtained by Chiu and on those obtained by Kniffki et al. permitted suggesting that adaptation in amphibian nerve may be due to second order properties of the sodium inactivation system. Unlike potassium mechanism of adaptation the sodium mechanism predicts constancy or progressive decrease of spike amplitudes.

Action Potentials↗
PubMed2000

Diminishing returns of population size in the rate of RNA virus adaptation.

Whenever an asexual viral population evolves by adapting to new environmental conditions, beneficial mutations, the ultimate cause of adaptation, are randomly produced and then fixed in the population. The larger the population size and the higher the mutation rate, the more beneficial mutations can be produced per unit time. With the usually high mutation rate of RNA viruses and in a large enough population, several beneficial mutations could arise at the same time but in different genetic backgrounds, and if the virus is asexual, they will never be brought together through recombination. Thus, the best of these genotypes must outcompete each other on their way to fixation. This competition among beneficial mutations has the effect of slowing the overall rate of adaptation. This phenomenon is known as clonal interference. Clonal interference predicts a speed limit for adaptation as the population size increases. In the present report, by varying the size of evolving vesicular stomatitis virus populations, we found evidence clearly demonstrating this speed limit and thus indicating that clonal interference might be an important factor modulating the rate of adaptation to an in vitro cell system. Several evolutionary and epidemiological implications of the clonal interference model applied to RNA viruses are discussed.

Adaptation, Physiological↗