• Diffuse intrinsic pontine glioma (DIPG) is a fatal childhood brainstem tumor for which radiation is the only treatment. (thecurestartsnow.org)
  • In this project, OMICs data for patients with the brain cancer diffuse intrinsic pontine glioma (DIPG) was analyzed using an Elsevier biology knowledge graph and complementary software to develop a molecular disease model. (brighttalk.com)
  • In addition, several intrinsic and extrinsic noise sources are present during the recordings, affecting the signal-to-noise ratio of the measured voltages. (hindawi.com)
  • This model has the potential to address the different sources of variability that are relevant to transcriptional and translational processes at the molecular level, namely, intrinsic noise due to the stochastic nature of the birth and deaths processes involved in chemical reactions, and extrinsic noise arising from the cell-to-cell variation of kinetic parameters associated with these processes. (warwick.ac.uk)
  • Biological macromolecules function in highly crowded cellular environments. (elifesciences.org)
  • I am interested in understanding the functional nature of macromolecules, with a special focus on their evolutionary relationships and their interactions in biological systems. (about.me)
  • I am interested in studying rheological properties polymers and biopolymers and applying mathematical techniques, statistical mechanics and molecular modeling to study the properties of biological and synthetic macromolecules. (cmich.edu)
  • Transport properties (diffusivities, self -assembly and the intrinsic viscosities) of macromolecules using computational techniques. (cmich.edu)
  • I develop and use computational tools for the analysis of biological sequences and structures. (about.me)
  • Indeed, an important open problem is finding appropriate computational models that scale well for both the simulation and formal analysis of biological processes. (bio.net)
  • A central challenge in computational modelling of dynamic biological systems is parameter inference from experimental time course measurements. (warwick.ac.uk)
  • We have proposed the general and specific biological functions of IMs relying on existing computational, psychological and neuroscientific views and evidence on them. (cnr.it)
  • We develop a computational model for the hematopoietic erythroid-myeloid lineage decision, which is determined by a genetic switch involving the genes PU.1 and GATA-1. (lu.se)
  • Citation: Chickarmane V, Enver T, Peterson C (2009) Computational Modeling of the Hematopoietic Erythroid-Myeloid Switch Reveals Insights into Cooperativity, Priming, and Irreversibility. (lu.se)
  • Despite its simplicity, the theta model offers enough complexity in its dynamics that it has been used for a wide range of theoretical neuroscience research as well as in research beyond biology, such as in artificial intelligence. (wikipedia.org)
  • Motivated by the need to tune the dynamics and improve the robustness of gene circuits, biological engineers have proposed various designs that mimic natural molecular feedback control mechanisms. (nature.com)
  • Using molecular dynamics simulations of a comprehensive atomistic model cytoplasm we found that protein-protein interactions may destabilize native protein structures, whereas metabolite interactions may induce more compact states due to electrostatic screening. (elifesciences.org)
  • Since its 3.3 release, Modelica offers the possibility to specify models of dynamical systems with multiple modes having different DAE-based dynamics. (merl.com)
  • Apologies for multiple copies - changes on topic list and special issue] First International Workshop on Hybrid Systems and Biology Newcasle upon Tyne, UK, September 3, 2012 Colocated with CONCUR 2012 http://hsb2012.units.it/ The goal of systems biology is to provide a system-level understanding of biological systems by unveiling their structure, dynamics and control methods. (bio.net)
  • Logiaco, L., Abbott, L.F. and Escola, S. (2021) Thalamic Control of Cortical Dynamics in a Model of Flexible Motor Sequencing. (columbia.edu)
  • My main focus are protein structure and intrinsic disorder, their interactions mediated by linear motifs and their evolution as modeled by substitution matrices. (about.me)
  • Stability in biological matrices was either intrinsic to the peptide or engineered via the introduction of non-natural amino acids and nonpeptidic bonds. (nih.gov)
  • The model shows that some proteins have a much less rigid structure in cells than they do in isolation, whilst others are able to work together more closely to carry out certain tasks. (elifesciences.org)
  • communicating and validating the models resulting from 3D structural studies on peptides, proteins, nucleic acids, and other molecules that act as ligands and co-factors. (europa.eu)
  • The concept is demonstrated for a simultaneous immunoassay for three model proteins (human, rabbit, and mouse IgGs). (cdc.gov)
  • Computations have been performed on random coil and wormlike models of linear chain polymers, star polymers, hyperbranched polymers, dendrimers, cyclodextrins, ssDNA and proteins and their interactions with and without functionalized carbon nanotubes. (cmich.edu)
  • The biological function of proteins is often related to large-scale domain motions, which are induced or suppressed by the binding of a substrate or due to cosolvents. (lu.se)
  • Domain motions can be related to soft hinges, flexible linker regions or -as in the case of intrinsic unfolded proteins- be native to the unfolded protein structure. (lu.se)
  • 2D POLIM was also applied to explore the aggregation state of proteins in the biological system. (lu.se)
  • This work is a first step towards physically realistic in silico whole-cell models that connect molecular with cellular biology. (elifesciences.org)
  • Rakesh, L, Interaction between sucrose, N-acetylcysteine and taurine in controlling insulin effects and energy shifts in body with and without the presence of diabetic drug Avandia: Molecular modeling study, J. Nanomedicine (in press), 2009. (cmich.edu)
  • The molecular basis for this effect has not been clearly established, despite its potential importance for a wide range of applications of agarose gels, including their use as biological tissue models in magnetic resonance imaging. (lu.se)
  • The magnetic relaxation mechanism invoked here, where spin relaxation is induced directly by molecular exchange, also provides a molecular basis for understanding the water 1H relaxation behavior that governs the intrinsic magnetic resonance image contrast in biological tissue. (lu.se)
  • The intrinsic multi-scale nature of these systems, both in space, in organization levels, and in time, makes extremely difficult to model all of them in a uniform way, e.g. by means of differential equations or discrete stochastic processes. (bio.net)
  • For each region, model parameters describing the expected value and signal-dependent variance of each interaction under a normal-lognormal distribution were learned using stochastic gradient descent. (nih.gov)
  • This model does not take into account spa- had contact with probable SARS patients, suspension of tial and stochastic processes of SARS transmission. (cdc.gov)
  • This model suggested new possible interactions between molecules inside cells that cannot currently be studied in real cells. (elifesciences.org)
  • Its state depends on the interactions among its previous states, its intrinsic properties, and the synaptic input it receives. (sciweavers.org)
  • To account for bias intrinsic to all 3C-based methods, as well as to 5C specifically, we developed a probabilistic model that simultaneously captures the non-biological contribution of specific primers and the distance-dependent background level of non-specific chromatin interactions (Imakaev et al. (nih.gov)
  • Considering the essential ligand-enzyme interactions, a pharmacophore model was built and applied in the virtual screening of a modified ZINC database. (uni-wuerzburg.de)
  • The main aim of this thesis was to investigate potential ecological constraints on this biological recovery, ranging from interactions between individuals to ecosystem-level processes, using a model stream system that has been extensively studied for over 40 years. (bl.uk)
  • I used a combination of long-term survey data and experiments, both in the field and the laboratory, to provide evidence that the lag in recovery of acidified aquatic communities is due to intrinsic resistance to re-colonisation by acid-sensitive species, as a result of both direct and indirect interactions between predators and prey. (bl.uk)
  • Dynamical models based upon known interactions between these master genes, such as mutual antagonism and autoregulation, fail to make the system bistable, a desired feature for robust lineage determination. (lu.se)
  • Hybrid modeling techniques, combining discrete and continuous processes, are gaining more and more attention in systems biology, and they have been applied to successfully capture the behavior of several biological complex systems, ranging from genetic networks, biochemical reactions, signaling pathways and cardiac tissues electrophysiology. (bio.net)
  • Theoretical models and resources are now available - for example Ian Hacking's "looping effect" and Sally Haslanger's "discursive constructions" - that provide principled grounds for understanding social categories as both independently real and as the products of contingent social histories. (degruyter.com)
  • These models were to be be based on the two important experimental tachniques, protein crystallography and NMR, or be the result of theoretical modelling calculations. (europa.eu)
  • We investigate these issues not only with models (see below) but also with a theoretical approach and empirical experiments. (cnr.it)
  • The theta model, or Ermentrout-Kopell canonical model, is a biological neuron model originally developed to mathematically describe neurons in the animal Aplysia. (wikipedia.org)
  • We did a systematic review (PROSPERO CRD42023393345) of peer-reviewed articles reporting historical outbreaks, modelling studies, and epidemiological parameters focused on Marburg virus disease. (bvsalud.org)
  • When reported in host susceptibility - the intrinsic and that are not strongly associated with epidemiological studies, these tu- extrinsic factors that have an impact host susceptibility include the follow- mour sites are also noted in some on variable response to carcinogens: ing. (who.int)
  • These factors are included in Hodgkin-Huxley (HH) model, which describes the ionic mechanisms involved in the generation of an action potential. (sciweavers.org)
  • These mechanisms are normally difficult to harness experimentally due to the intrinsic complexity of the associated biological systems. (nccr-must.ch)
  • While these implementations provided a general framework to robustly regulate in vivo biological processes, an alternative implementation is desirable, in order to improve the robustness of synthetic biological processes and specifically the cell-free reaction platform. (nature.com)
  • Proton coupled electron transfers (PCET) are central in biological processes such as photosynthesis and in the respiratory chain, where they mediate long-range charge transfers. (nccr-must.ch)
  • We extract intrinsic layered material parameters of the articular cartilage using a triphasic model. (who.int)
  • We present a model consisting of two coupled vector fields controlled by magnetization parameters, and we address the contrast problem to the question of the classification of quadrics in four dimension. (lip6.fr)
  • Several MIPD approaches have been suggested to predict dosing strategies, including regression, reinforcement learning (RL) and pharmacokinetic and pharmacodynamic (PKPD) modelling. (bvsalud.org)
  • The model is particularly well-suited to describe neural bursting, which is characterized by periodic transitions between rapid oscillations in the membrane potential followed by quiescence. (wikipedia.org)
  • In contrast, other biophysically accurate neural models such as the Hodgkin-Huxley model and Morris-Lecar model consist of multiple variables that cannot be solved analytically, requiring numerical integration to solve. (wikipedia.org)
  • The purpose of this work was to assess various noise sources that affect extracellular recordings and to create model systems in which novel micropipette neural amplifier designs can be tested. (hindawi.com)
  • According to our model, the major noise sources which influence the signal to noise ratio are the intrinsic noise of the neural amplifier and the thermal noise from distributed pipette resistance. (hindawi.com)
  • This paper proposes training of an artificial neural network to identify and model the physiological properties of a biological neuron, and mimic its input-output mapping. (sciweavers.org)
  • Chung, S. and Abbott, L.F. (2021) Neural Population Geometry: An Approach for Understanding Biological and Artificial Neural Networks. (columbia.edu)
  • A single biological neuron is able to perform complex computations that are highly nonlinear in nature, adaptive, and superior to the perceptron model. (sciweavers.org)
  • Standard algorithms of Effective Algebraic Geometry are used, although special improve- ments permit to bypass the intrinsic high level of complexity of the formal computations. (lip6.fr)
  • Photoacoustic imaging works from the platform of the intrinsic absorption properties of the targeted biological tissue. (photonics.com)
  • Photoacoustic imaging, a fascinating technique relying on ultrasound generation upon the absorption of a light pulse, has been developed to overcome this issue, enabling to probe optical absorption contrast at large depths in biological tissue. (fresnel.fr)
  • Metal halide perovskites have the advantage of strong light absorption, long charge-carrier diffusion lengths, and low intrinsic surface recombination. (lu.se)
  • Biological activity was shown via assessment of on-target effects, in vitro growth, proliferation, and apoptosis analysis. (thecurestartsnow.org)
  • In addition to biological tissues, these systems have potential applications for the assessment of bioengineered tissues, biomaterials with fine structures, or some engineering materials. (who.int)
  • The packages were intended to provide assessment of the intrinsic quality of the experimental data and the agreement between such data and the derived atomic models. (europa.eu)
  • Animal model for assessment of skin irritancy. (cdc.gov)
  • Parabolic bursting models are mathematical models that mimic parabolic bursting in real biological systems. (wikipedia.org)
  • Robustness against perturbations and uncertainties is fundamental to biological systems that continuously sense and respond to their environment. (nature.com)
  • This workshop aims at collecting scientists working in the area of hybrid modeling applied to systems biology, in order to discuss about current achieved goals, current challenges and future possible developments. (bio.net)
  • Topics of interest include, but are not limited to: - Hybrid models of biological systems (case studies of genetic, cellular networks, models of tissues, etc. (bio.net)
  • During recent years, the biotic ligand model (BLM) has been proposed as a tool to evaluate quantitatively the manner in which water chemistry affects the speciation and biological availability of metals in aquatic systems. (researchgate.net)
  • EMRM 2023 is devoted to the mathematical analysis of PDE models for multi-component systems and reactive mixtures. (wias-berlin.de)
  • We break the limit of energy funneling efficiency and propose an asymmetric three-dipole model, which is more applicable for multi-chromophore systems. (lu.se)
  • Achieving systematic, genome-scale perturbations within intact biological systems is important for elucidating gene function and epigenetic regulation. (cdc.gov)
  • Studies of model systems. (lu.se)
  • The data gleaned from multiple experiments demonstrate that chemical agents capable of interfering with intrinsic antioxidant pathways do, in fact, increase noise -induced hearing loss and produce extensive outer hair cell death. (cdc.gov)
  • Furthermore, we did a series of computer experiments to examine and improve the SFA model. (lu.se)
  • Those factors make the method time-consuming and, to date, difficult to use in applications requiring the capture of the dynamic changes of functional information in biological tissues. (photonics.com)
  • In this paper, we introduced two methods of ultrasound elastomicroscopy using water jet and osmosis loading for imaging the elasticity of biological soft tissues with high resolutions. (who.int)
  • Present address: Institut fu¨r Physikalische Chemie, Universita¨t Mu¨nster, gels and in biological tissues.12-14 If these ideas were correct, DE-48149 Mu¨nster, Germany. (lu.se)
  • Information, at the level the new system is able deliver, provides subcellular insights useful for the study of disease models, such as in cancer research. (photonics.com)
  • Extinction risk, however, is not randomly distributed among species but depends on intrinsic (i.e. life history traits) and extrinsic factors (e.g. habitat destruction). (nrm.se)
  • It depends on the biological matter (blood, cerebral matter, water. (lip6.fr)
  • Statistical criteria for the validation of protein models and associated data have been considerably tightened. (europa.eu)
  • Their groundbreaking knowledge graph pairs their proprietary protein and genome sequences with environmental and chemical data, revealing intricate biological networks. (astrobiology.com)
  • Basecamp's knowledge graph as a result has become a superior resource for protein design applications across the bioeconomy and for generative AI models. (astrobiology.com)
  • Colonies of some ant species are able to synchronize their activity to fall into coherent bursts, but models of this phenomenon have neglected the potential effects of intrinsic noise and interspecific differences in individual-level behaviour. (escholarship.org)
  • Mitochondrial dysfunction is a common factor to many human diseases, however the intrinsic means cells employ to survive and ultimately recover from mitochondrial perturbations are only beginning to be understood. (umassmed.edu)
  • We employ a parsimonious agent-based model to study whether such a competition may affect the popularity of different memes, the diversity of information we are exposed to and the fading of our collective interests for specific topics. (nature.com)
  • Patient-derived xenograft mouse models were used to assess plasma and brain tissue pharmacokinetics, pharmacodynamics, and overall survival (OS). (thecurestartsnow.org)
  • Relating in vitro to in vivo exposures with physiologically based tissue dosimetry and tissue response models. (cdc.gov)
  • lymphoid tissue, and digestive tract), which the animal model captures the It can be difficult to parse out concordance has often been ob- range of potential human response reasons for lack of tumour site con- served among different species after to the particular agent tested. (who.int)
  • We will first compile species-specific traits (intrinsic traits) from the literature that are relevant to extinction risks, for example dispersal, other reproductive or habitat characteristics. (nrm.se)
  • Second, we will model extinction risk based on both the species biological and ecological traits and the main threats (extrinsic traits) using a range of analytical techniques, including machine learning. (nrm.se)
  • Using Earth - with its trillion-plus species - as an analog for planetary-level genomic modeling elsewhere is a good way to learn how to do this - and we can start doing it right now. (astrobiology.com)
  • A two process model is envisaged: (a) initiation of reactive oxygen species by moderate noise exposure and (b) promotion of oxidative stress through disrupting intrinsic antioxidant defenses. (cdc.gov)
  • Pharmacophore modeling: Superpose pharmacophore elements to identify bioactive conformation. (cmich.edu)
  • This systematic review and the accompanying database provide a comprehensive overview of Marburg virus disease epidemiology and identify key knowledge gaps, contributing crucial information for mathematical models to support future Marburg virus disease epidemic responses. (bvsalud.org)
  • An cordance (i.e. lack of response or exposure to a given IARC Group 1 integral consideration for the devel- common responses between spe- human carcinogen (see Chapter 21, opment and use of these models is cies). (who.int)
  • A key challenge is the intrinsic interaction between different constituents with further effects such as heat conduction, electrostatic forces, and compressibility. (wias-berlin.de)
  • How biomolecules efficiently function in real biological environments with crowding and significant chemical and physical heterogeneity remains a fundamental question in biology ( Minton, 2001 ). (elifesciences.org)
  • The availability of multiple single cell data provides a unique opportunity to estimate such a model and explicitly quantify the sources of variation from experimental data. (warwick.ac.uk)
  • Etoposide-induced senescence model may help investigate the initiation of cellular senescence in chondrocytes, and provide a useful model to develop therapeutic approaches to target senescence in OA. (aging-us.com)
  • The predictions of our model are consistent with empirical data from Twitter , a popular microblogging platform. (nature.com)
  • We model the emergence of synchronized rhythms using an agent-based model informed by our empirical data. (escholarship.org)
  • Biology is suffused with rhythmic behaviour, and interacting biological oscillators often synchronize their rhythms with one another. (escholarship.org)
  • 1974. Biological handbooks: Biology data book. (cdc.gov)
  • However, most of these studies only discuss how to reduce the intrinsic noise of the amplifier. (hindawi.com)
  • However, the handling of such models by the current Modelica tools is not satisfactory, with mathematically sound models yielding exceptions at runtime. (merl.com)
  • Furthermore such models are often not easily amenable to formal analysis and simulation at the organ or even the cell level is frequently impractical. (bio.net)
  • Metal-peptide cations experience both electron and proton transfers upon photoexcitation, proving an amenable model system to study PCET. (nccr-must.ch)
  • What is wrong with these statements is that they define scientific positions that need to be backed up by models that demonstrate precisely how a knowledge of genes in the developing organism will lead to an understanding of the three-dimensional form of the human heart or limb or eye, the arrangement of leaves on a plant and the organs of the flower, or the wings of a fruit fly. (timeshighereducation.com)
  • In OA, while it has been shown to reduce the severity of the disease in the murine model [ 8 , 16 ], the senolytic UBX0101 failed to demonstrate clinical efficacy in humans. (aging-us.com)
  • We describe the Framework for Integrated, Conceptual, and Systematic Microbial Ecology (FICSME), an experimental design framework for conducting process-focused microbial ecology studies that incorporates biological, chemical, and physical drivers of a microbial system into a conceptual model. (frontiersin.org)
  • The BLM is a mathematical model developed to measure, assess, and understand how the chemical properties of a waterbody can affect metallic contaminant speciation, bioavailability, and consequent toxicity, comprising an important tool in understanding and predicting metal toxicity in different waterbodies [8,10]. (researchgate.net)
  • The team at Basecamp has built partnerships with nature parks across 5 continents to collect biological & chemical data across more than 50% of global biomes to address the fundamental knowledge gap of us knowing less than 0.001% of our planet's biodiversity. (astrobiology.com)
  • While attempts to limit or halt acidifying emissions have been successful in reversing the chemical consequences of acidification, any corresponding biological recovery has been patchy at best. (bl.uk)
  • Through the establishment of a National Marine Biodiscovery Laboratory in Ireland we strive for a strong collaboration between marine biologists, taxonomists, microbiologists, and chemists to organize a biological and chemical repository of marine products. (universityofgalway.ie)
  • In: Threshold limit values for chemical substances and physical agents and biological exposure indices. (cdc.gov)
  • We propose an agent-based model to study the role of the limited attention of individual users in the diffusion process and in particular whether competition for our finite attention may affect meme popularity, diversity and lifetime. (nature.com)
  • Modeling and theory guide experimental implementation with well-defined operational predictability. (nature.com)
  • The internal model principle in control theory states, in essence, that the existence of an integrator in the control loop is necessary for the tight regulation of the variable of interest in the presence of constant disturbances or stimuli 12 . (nature.com)
  • Techniques and protocols for refining models against these and other data have been improved. (europa.eu)
  • Partner 2 concentrated on the general release of a new software package, REFMAC, for the refinement of models against X-ray data using maximum likelihood. (europa.eu)
  • the Deep RL model and the PKPD model individualise dosing regimens accounting also for additional variation using monitoring data. (bvsalud.org)
  • However, the Deep RL model focusses on control of the treatment response, while the PKPD model uses the data also to further the individualisation of predictions. (bvsalud.org)
  • We present a two-dimensional continuous-time Bayesian hierarchical model based on van Kampen's linear noise approximation. (warwick.ac.uk)
  • A model based on single funnel approximation (SFA) is applied to fit the 2D polarization portrait obtained from 2D POLIM measurements. (lu.se)
  • Therefore, our study aimed to generate models of chondrocyte senescence. (aging-us.com)
  • Only one study presented a mathematical model of Marburg virus transmission. (bvsalud.org)
  • The model consists of one variable that describes the membrane potential of a neuron along with an input current. (wikipedia.org)
  • The methods conventionally developed for validation of X-ray models have been extended to NMR. (europa.eu)
  • Using both C. elegans and mammalian models, we have significant progress in understanding the signal transduction mechanism as well its biological roles. (umassmed.edu)
  • This is mainly due to the limitations of quantitative predictive models for the latter case. (nature.com)
  • In this way, the intrinsic luminescence of the MLNPs serves as an internal standard in the quantitative immunoassay. (cdc.gov)
  • 2D POLIM in combination with the SFA model allows the quantitative characterization of EET efficiency. (lu.se)
  • An equivalent circuit of the glass micropipette and the noise model of this circuit, which accurately describe the various noise sources involved in extracellular recordings, have been developed. (hindawi.com)
  • Discussions of various biological noise sources as well as the electrode noise are largely lacking. (hindawi.com)
  • Noise resistant synchronization and collective rhythm switching in a model of animal group locomotion. (escholarship.org)
  • This simple model successfully generates synchronized group oscillations despite the addition of noise to ants' refractory periods. (escholarship.org)
  • We also find that adding noise reduces the likelihood that the model will spontaneously switch between distinct collective cycle frequencies. (escholarship.org)