搜索结果：Current research in structural biology

In this paper, we propose and study several inverse problems of determining unknown parameters in nonlocal nonlinear coupled PDE systems, including the potentials, nonlinear interaction functions and time-fractional orders. In these coupled systems, we enforce non-negativity of the solutions, aligning with realistic scenarios in biology and ecology. There are several salient features of our inverse problem study: the drastic reduction in measurement/observation data due to averaging effects, the nonlinear coupling between multiple equations, and the nonlocality arising from fractional-type derivatives. These factors present significant challenges to our inverse problem, and such inverse problems have never been explored in previous literature. To address these challenges, we develop new and effective schemes. Our approach involves properly controlling the injection of different source terms to obtain multiple sets of mean flux data. This allows us to achieve unique identifiability results and accurately determine the unknown parameters. Finally, we establish a connection between our study and practical applications in biology, further highlighting the relevance of our work in real-

Understanding the biological mechanisms of disease is crucial for medicine, and in particular, for drug discovery. AI-powered analysis of genome-scale biological data holds great potential in this regard. The increasing availability of single-cell RNA sequencing data has enabled the development of large foundation models for disease biology. However, existing foundation models only modestly improve over task-specific models in downstream applications. Here, we explored two avenues for improving single-cell foundation models. First, we scaled the pre-training data to a diverse collection of 116 million cells, which is larger than those used by previous models. Second, we leveraged the availability of large-scale biological annotations as a form of supervision during pre-training. We trained the \model family of models comprising six transformer-based state-of-the-art single-cell foundation models with 70 million, 160 million, and 400 million parameters. We vetted our models on several downstream evaluation tasks, including identifying the underlying disease state of held-out donors not seen during training, distinguishing between diseased and healthy cells for disease conditions and

Structural biology aims at characterizing the structural and dynamic properties of biological macromolecules at atomic details. Gaining insight into three dimensional structures of biomolecules and their interactions is critical for understanding the vast majority of cellular processes, with direct applications in health and food sciences. Since 2010, the WeNMR project (www.wenmr.eu) has implemented numerous web-based services to facilitate the use of advanced computational tools by researchers in the field, using the high throughput computing infrastructure provided by EGI. These services have been further developed in subsequent initiatives under H2020 projects and are now operating as Thematic Services in the European Open Science Cloud (EOSC) portal (www.eosc-portal.eu), sending >12 millions of jobs and using around 4000 CPU-years per year. Here we review 10 years of successful e-infrastructure solutions serving a large worldwide community of over 23,000 users to date, providing them with user-friendly, web-based solutions that run complex workflows in structural biology. The current set of active WeNMR portals are described, together with the complex backend machinery that

Gait abnormality detection is critical for the early discovery and progressive tracking of musculoskeletal and neurological disorders, such as Parkinson's and Cerebral Palsy. Especially, analyzing the foot-floor contacts during walking provides important insights into gait patterns, such as contact area, contact force, and contact time, enabling gait abnormality detection through these measurements. Existing studies use various sensing devices to capture such information, including cameras, wearables, and force plates. However, the former two lack force-related information, making it difficult to identify the causes of gait health issues, while the latter has limited coverage of the walking path. In this study, we leverage footstep-induced structural vibrations to infer foot-floor contact profiles and detect gait abnormalities. The main challenge lies in modeling the complex force transfer mechanism between the foot and the floor surfaces, leading to difficulty in reconstructing the force and contact profile during foot-floor interaction using structural vibrations. To overcome the challenge, we first characterize the floor vibration for each contact type (e.g., heel, midfoot, and

If students are to successfully grapple with authentic, complex biological problems as scientists and citizens, they need practice solving such problems during their undergraduate years. Physics education researchers have investigated student problem solving for the last three decades. Although physics and biology problems differ in structure and content, the instructional purposes align closely: explaining patterns and processes in the natural world and making predictions about physical and biological systems. In this paper, we discuss how research-supported approaches developed by physics education researchers can be adopted by biologists to enhance student problem-solving skills. First, we compare the problems that biology students are typically asked to solve with authentic, complex problems. We then describe the development of research-validated physics curricula emphasizing process skills in problem solving. We show that solving authentic, complex biology problems requires many of the same skills that practicing physicists and biologists use in representing problems, seeking relationships, making predictions, and verifying or checking solutions. We assert that acquiring these

Systems biology relies on mathematical models that often involve complex and intractable likelihood functions, posing challenges for efficient inference and model selection. Generative models, such as normalizing flows, have shown remarkable ability in approximating complex distributions in various domains. However, their application in systems biology for approximating intractable likelihood functions remains unexplored. Here, we elucidate a framework for leveraging normalizing flows to approximate complex likelihood functions inherent to systems biology models. By using normalizing flows in the Simulation-based inference setting, we demonstrate a method that not only approximates a likelihood function but also allows for model inference in the model selection setting. We showcase the effectiveness of this approach on real-world systems biology problems, providing practical guidance for implementation and highlighting its advantages over traditional computational methods.

The central dogma of molecular biology, formulated more than five decades ago, compartmentalized information exchange in the cell into the DNA, RNA and protein domains. This formalization has served as an implicit thematic distinguisher for cell biological research ever since. However, a clear account of the distribution of research across this formalization over time does not exist. Abstracts of >3.5 million publications focusing on the cell from 1975 to 2011 were analyzed for the frequency of 100 single-word DNA-, RNA- and protein-centric search terms and amalgamated to produce domain- and subdomain-specific trends. A preponderance of protein- over DNA- and in turn over RNA-centric terms as a percentage of the total word count is evident until the early 1990s, at which point the trends for protein and DNA begin to coalesce while RNA percentages remain relatively unchanged. This term-based census provides a yearly snapshot of the distribution of research interests across the three domains of the central dogma of molecular biology. A frequency chart of the most dominantly-studied elements of the periodic table is provided as an addendum.

In a recent paper, Wilmes et al. demonstrated a qualitative integration of omics data streams to gain a mechanistic understanding of cyclosporine A toxicity. One of their major conclusions was that cyclosporine A strongly activates the nuclear factor (erythroid-derived 2)-like 2 pathway (Nrf2) in renal proximal tubular epithelial cells exposed in vitro. We pursue here the analysis of those data with a quantitative integration of omics data with a differential equation model of the Nrf2 pathway. That was done in two steps: (i) Modeling the in vitro pharmacokinetics of cyclosporine A (exchange between cells, culture medium and vial walls) with a minimal distribution model. (ii) Modeling the time course of omics markers in response to cyclosporine A exposure at the cell level with a coupled PK-systems biology model. Posterior statistical distributions of the parameter values were obtained by Markov chain Monte Carlo sampling. Data were well simulated, and the known in vitro toxic effect EC50 was well matched by model predictions. The integration of in vitro pharmacokinetics and systems biology modeling gives us a quantitative insight into mechanisms of cyclosporine A oxidative-stress

A number of models in mathematical epidemiology have been developed to account for control measures such as vaccination or quarantine. However, COVID-19 has brought unprecedented social distancing measures, with a challenge on how to include these in a manner that can explain the data but avoid overfitting in parameter inference. We here develop a simple time-dependent model, where social distancing effects are introduced analogous to coarse-grained models of gene expression control in systems biology. We apply our approach to understand drastic differences in COVID-19 infection and fatality counts, observed between Hubei (Wuhan) and other Mainland China provinces. We find that these unintuitive data may be explained through an interplay of differences in transmissibility, effective protection, and detection efficiencies between Hubei and other provinces. More generally, our results demonstrate that regional differences may drastically shape infection outbursts. The obtained results demonstrate the applicability of our developed method to extract key infection parameters directly from publically available data so that it can be globally applied to outbreaks of COVID-19 in a number

Dynamical systems modeling, particularly via systems of ordinary differential equations, has been used to effectively capture the temporal behavior of different biochemical components in signal transduction networks. Despite the recent advances in experimental measurements, including sensor development and '-omics' studies that have helped populate protein-protein interaction networks in great detail, modeling in systems biology lacks systematic methods to estimate kinetic parameters and quantify associated uncertainties. This is because of multiple reasons, including sparse and noisy experimental measurements, lack of detailed molecular mechanisms underlying the reactions, and missing biochemical interactions. Additionally, the inherent nonlinearities with respect to the states and parameters associated with the system of differential equations further compound the challenges of parameter estimation. In this study, we propose a comprehensive framework for Bayesian parameter estimation and complete quantification of the effects of uncertainties in the data and models. We apply these methods to a series of signaling models of increasing mathematical complexity. Systematic analysis o

The optimization-based damage detection and damage state digital twinning capabilities are examined here of a novel conditional-labeled generative adversarial network methodology. The framework outperforms current approaches for fault anomaly detection as no prior information is required for the health state of the system: a topic of high significance for real-world applications. Specifically, current artificial intelligence-based digital twinning approaches suffer from the uncertainty related to obtaining poor predictions when a low number of measurements is available, physics knowledge is missing, or when the damage state is unknown. To this end, an unsupervised framework is examined and validated rigorously on the benchmark structural health monitoring measurements of Z24 Bridge: a post-tensioned concrete highway bridge in Switzerland. In implementing the approach, firstly, different same damage-level measurements are used as inputs, while the model is forced to converge conditionally to two different damage states. Secondly, the process is repeated for a different group of measurements. Finally, the convergence scores are compared to identify which one belongs to a different da

With the completion of human genome mapping, the focus of scientists seeking to explain the biological complexity of living systems is shifting from analyzing the individual components (such as a particular gene or biochemical reaction) to understanding the set of interactions amongst the large number of components that results in the different functions of the organism. To this end, the area of systems biology attempts to achieve a "systems-level" description of biology by focusing on the network of interactions instead of the characteristics of its isolated parts. In this article, we briefly describe some of the emerging themes of research in "network" biology, looking at dynamical processes occurring at the two different length scales of within the cell and between cells, viz., the intra-cellular signaling network and the nervous system. We show that focusing on the systems-level aspects of these problems allows one to observe surprising and illuminating common themes amongst them.

Characterizing structural and dynamic properties of proteins and large macromolecular assemblies is crucial to understand the molecular mechanisms underlying biological functions. In the field of Structural Biology, no single method comprehensively reveals the behavior of biological systems across various spatio-temporal scales. Instead, we have a versatile toolkit of techniques, each contributing a piece to the overall puzzle. Integrative Structural Biology combines different techniques to create accurate and precise multi-scale models that expand our understanding of complex biological systems. This review outlines recent advancements in computational and experimental methods in Structural Biology, with special focus on recent Artificial Intelligence techniques, emphasizes integrative approaches that combine different types of data for precise spatio-temporal modeling, and provides an outlook into future directions of this field.

Quantitative computational models play an increasingly important role in modern biology. Such models typically involve many free parameters, and assigning their values is often a substantial obstacle to model development. Directly measuring \emph{in vivo} biochemical parameters is difficult, and collectively fitting them to other data often yields large parameter uncertainties. Nevertheless, in earlier work we showed in a growth-factor-signaling model that collective fitting could yield well-constrained predictions, even when it left individual parameters very poorly constrained. We also showed that the model had a `sloppy' spectrum of parameter sensitivities, with eigenvalues roughly evenly distributed over many decades. Here we use a collection of models from the literature to test whether such sloppy spectra are common in systems biology. Strikingly, we find that every model we examine has a sloppy spectrum of sensitivities. We also test several consequences of this sloppiness for building predictive models. In particular, sloppiness suggests that collective fits to even large amounts of ideal time-series data will often leave many parameters poorly constrained. Tests over our m

This article frames the relation between biology and physics by characterizing the former as a subdiscipline rather than a special case of the latter. To do this, we posit biological physics as the science of living matter in contrast to classic biophysics, the study of organismal properties by physical techniques. At the scale of the individual cell, living matter is nonunitary, i.e., not composed of aggregated subunits, and has features (e.g., intracellular organizational arrangements and biomolecular condensates) that are unlike any materials of the nonliving world. In transiently or constitutively multicellular forms (social microorganisms, animals, plants), living matter sustains physical processes that are generic (shared with nonliving matter, e.g., subunit communication by molecular diffusion in cellular slime molds), biogeneric (analogous to nonliving matter but realized through cellular activities, e.g., subunit demixing in animal embryos) or nongeneric (pertaining to sui generis materials, e.g., budding of active solids in plants). This "forms of matter" perspective is philosophically situated in the dialectical materialism of Engels and Hessen and the multilevel physica

In most countries, basic research is supported by research councils that select, after peer review, the individuals or teams that are to receive funding. Unfortunately, the number of grants these research councils can allocate is not infinite and, in most cases, a minority of the researchers receive the majority of the funds. However, evidence as to whether this is an optimal way of distributing available funds is mixed. The purpose of this study is to measure the relation between the amount of funding provided to 12,720 researchers in Quebec over a fifteen year period (1998-2012) and their scientific output and impact from 2000 to 2013. Our results show that both in terms of the quantity of papers produced and of their scientific impact, the concentration of research funding in the hands of a so-called "elite" of researchers generally produces diminishing marginal returns. Also, we find that the most funded researchers do not stand out in terms of output and scientific impact.

Systems biology models are useful models of complex biological systems that may require a large amount of experimental data to fit each model's parameters or to approximate a likelihood function. These models range from a few to thousands of parameters depending on the complexity of the biological system modeled, potentially making the task of fitting parameters to the model difficult - especially when new experimental data cannot be gathered. We demonstrate a method that uses structural biology predictions to augment systems biology models to improve systems biology models' predictions without having to gather more experimental data. Additionally, we show how systems biology models' predictions can help evaluate novel structural biology hypotheses, which may also be expensive or infeasible to validate.

Accurate structural response prediction forms a main driver for structural health monitoring and control applications. This often requires the proposed model to adequately capture the underlying dynamics of complex structural systems. In this work, we utilize a learnable Extended Kalman Filter (EKF), named the Neural Extended Kalman Filter (Neural EKF) throughout this paper, for learning the latent evolution dynamics of complex physical systems. The Neural EKF is a generalized version of the conventional EKF, where the modeling of process dynamics and sensory observations can be parameterized by neural networks, therefore learned by end-to-end training. The method is implemented under the variational inference framework with the EKF conducting inference from sensing measurements. Typically, conventional variational inference models are parameterized by neural networks independent of the latent dynamics models. This characteristic makes the inference and reconstruction accuracy weakly based on the dynamics models and renders the associated training inadequate. In this work, we show that the structure imposed by the Neural EKF is beneficial to the learning process. We demonstrate the

Recent tumor genome sequencing confirmed that one tumor often consists of multiple cell subpopulations (clones) which bear different, but related, genetic profiles such as mutation and copy number variation profiles. Thus far, one tumor has been viewed as a whole entity in cancer functional studies. With the advances of genome sequencing and computational analysis, we are able to quantify and computationally dissect clones from tumors, and then conduct clone-based analysis. Emerging technologies such as single-cell genome sequencing and RNA-Seq could profile tumor clones. Thus, we should reconsider how to conduct cancer systems biology studies in the genome sequencing era. We will outline new directions for conducting cancer systems biology by considering that genome sequencing technology can be used for dissecting, quantifying and genetically characterizing clones from tumors. Topics discussed in Part 1 of this review include computationally quantifying of tumor subpopulations; clone-based network modeling, cancer hallmark-based networks and their high-order rewiring principles and the principles of cell survival networks of fast-growing clones.