Computational Sciences (United States)

The design of regulatory elements is pivotal in gene and cell therapy, where DNA sequences are engineered to drive elevated and cell-type specific expression. However, the systematic assessment of synthetic DNA sequences without robust metrics and easy-to-use software remains challenging. Here, we introduce Polygraph, a Python framework that evaluates synthetic DNA elements, based on features like diversity, motif and k-mer composition, similarity to endogenous sequences, and screening with predictive and foundational models. Polygraph is the first instrument for assessing synthetic regulatory sequences, enabling faster progress in therapeutic interventions and improving our understanding of gene regulatory mechanisms.

We explore the limitations of traditional crossentropy loss in a hierarchical multi-label classification setting and introduce a novel loss function. This function is designed to integrate hierarchical constraints directly into the training process. By incorporating such constraints into the loss, our approach slightly improves the logical consistency of predictions in structured domains. We demonstrate the efficacy of our approach through experiments on primary site and histology classification by using electronic pathology reports. These results show that our proposed hierarchical loss function enhances the model's ability to produce predictions that are logically consistent with the natural data hierarchies, and it slightly improves predictive accuracy. Our framework may be extended to other hierarchical domains, however the performance gains are context specific.

TEAD (transcriptional enhanced associate domain) transcription factors (TEAD1-4) serve as the primary effectors of the Hippo signaling pathway in various cancers. Targeted therapy leads to the emergence of resistance and the underlying mechanism of resistance to TEAD inhibition in cancers is less characterized. We uncover that upregulation of the AP-1 (activator protein-1) transcription factors, along with restored YAP (yes-associated protein) and TEAD activity, drives resistance to GNE-7883, a pan-TEAD inhibitor. Acute GNE-7883 treatment abrogates YAP-TEAD binding and attenuates FOSL1 (FOS like 1) activity. TEAD inhibitor resistant cells restore YAP and TEAD chromatin occupancy, acquire additional FOSL1 binding and exhibit increased MAPK (mitogen-activated protein kinase) pathway activity. FOSL1 is required for the chromatin binding of YAP and TEAD. This study describes a clinically relevant interplay between the Hippo and MAPK pathway and highlights the key role of MAPK pathway inhibitors in mitigating resistance to TEAD inhibition in Hippo pathway dependent cancers.

Metabolic fluxes are the rates of life-sustaining chemical reactions within a cell and metabolites are the components. Determining the changes in these fluxes is crucial to understanding diseases with metabolic causes and consequences. Kinetic flux profiling (KFP) is a method for estimating flux that utilizes data from isotope tracing experiments. In these experiments, the isotope-labeled nutrient is metabolized through a pathway and integrated into the downstream metabolite pools. Measurements of proportion labeled for each metabolite in the pathway are taken at multiple time points and used to fit an ordinary differential equations model with fluxes as parameters. We begin by generalizing the process of converting diagrams of metabolic pathways into mathematical models composed of differential equations and algebraic constraints. The scaled differential equations for proportions of unlabeled metabolite contain parameters related to the metabolic fluxes in the pathway. We investigate flux parameter identifiability given data collected only at the steady state of the differential equation. Next, we give criteria for valid parameter estimations in the case of a large separation of timescales with fast–slow analysis. Bayesian parameter estimation on simulated data from KFP experiments containing both irreversible and reversible reactions illustrates the accuracy and reliability of flux estimations. These analyses provide constraints that serve as guidelines for the design of KFP experiments to estimate metabolic fluxes.

Data visualization tools are important tools for making health decisions based on large amounts of data. However, very few comparisons of data visualization tools have been done in the context of health-related research. This paper compares commonly available visualization tools from the perspective of a dashboard developer in the context of scientific health research using real-world data and to provide general suggestions for dashboard developers’ future visualization efforts in health-related scientific discoveries. We evaluated four commonly available visualization tools (Tableau, Spotfire, PowerBI, and R Shiny). Each tool was evaluated on visualization outcomes (comparing the generated outputs of tables, scatterplots, correlation plots, treemaps, heatmaps, and geographic maps), usability, Cloud compatibility, analytic integration, and a few other factors. All tools generated comparable visualization outcomes in our tests and were equally usable with the exception of R Shiny which is not recommended for users with limited coding experience. Every tool except R Shiny supports connections to PostgreSQL, gSheets, and Athena without additional configurations. All tools support integration with R and Python; however, PowerBI requires some additional configuration. Every tool is capable of data pre-processing and supports data transformation, null detection and outlier detection. Each tool has its own unique advantages and limitations.

In this work, we propose a new deep learning-based scheme for solving high dimensional nonlinear backward stochastic differential equations (BSDEs). The idea is to reformulate the problem as a global optimization, where the local loss functions are included. Essentially, we approximate the unknown solution of a BSDE using a deep neural network and its gradient with automatic differentiation. The approximations are performed by globally minimizing the quadratic local loss function defined at each time step, which always includes the terminal condition. This kind of loss functions are obtained by iterating the Euler discretization of the time integrals with the terminal condition. Our formulation can prompt the stochastic gradient descent algorithm not only to take the accuracy at each time layer into account, but also converge to a good local minima. In order to demonstrate performances of our algorithm, several high-dimensional nonlinear BSDEs including pricing problems in finance are provided.

Abstract To reduce both time and labour for systematic review, much effort has been made on developing automated tools using artificial intelligence and machine learning in nearly two decades. Unfortunately, systematic review automation tools still face a serious problem of social acceptance. Previous studies identified lack of trust as one important adoption barrier for systematic review automation. However, further discussion about building trust was limited to building trusted evidence base by benchmarked large-scale evaluation. This study extended the previous discussions of the trustworthiness of systematic review automation. Through semi-structure interviews with regular systematic reviewers, we tried to not only get answers for to what extent human reviewers trust automated tools and why, but also reveal more measures of building trust from human reviewers’ points of view and the impact of such measures on the trust in and adoption of systematic review automation tools. We believe that the results of this study may also shed light on some new directions of systematic review automation research.

Preterm birth (PTB) is the leading cause of infant mortality and follows multiple biological pathways, many of which are poorly understood. Some PTBs result from medically indicated labor following complications from hypertension and/or diabetes, while many others are spontaneous with unknown causes. Previously, investigation of potential risk factors has been limited by lack of data on maternal medical history and the difficulty of classifying PTBs as indicated or spontaneous. Here, we leverage electronic health record (EHR) data (patient health information including demographics, diagnoses, and medications) and a supplemental curated pregnancy database to overcome these limitations. Novel associations may provide new insight into the pathophysiology of PTB as well as help identify individuals who would be at risk of PTB. We quantified associations between maternal diagnoses and preterm birth using logistic regression controlling for maternal age and socioeconomic factors within a University of California, San Francisco (UCSF), EHR cohort with 10,643 births ( nterm = 9692, nspontaneous_preterm = 449, nindicated_preterm = 418) and maternal pre-conception diagnosis phenotypes derived from International Classification of Diseases (ICD) 9 and 10 codes. Eighteen conditions significantly and robustly (False Discovery Rate (FDR)<0.05) associated with PTBs compared to term. We discovered known (hypertension, diabetes, and chronic kidney disease) and less established (blood, cardiac, gynecological, and liver conditions) associations. Type 1 diabetes was the most significant overall association (adjusted p = 1.6×10 -14 , adjusted OR = 7 (95% CI 5, 12)), and the odds ratios for the significant phenotypes ranged from 3 to 13. We further carried out analysis stratified by spontaneous vs. indicated PTB. No phenotypes significantly associated with spontaneous PTB; however, the results for indicated PTB largely recapitulated the phenotype associations with all PTBs. Our study underscores the limitations of approaches that combine indicated and spontaneous births together. When combined, significant associations were almost entirely driven by indicated PTBs, although our spontaneous and indicated groups were of a similar size. Investigating the spontaneous population has the potential to reveal new pathways and understanding of the heterogeneity of PTB.

While inverter-based DER (distributed energy resources) are instrumental to integrating renewable energy into the power grid, they reduce the grid's mechanical inertia, thereby increasing the risk of frequency instabilities. To compensate for frequency instability risks, the grid must also undergo a transformation to include digital technologies that allow for two-way communication between the utility and customers. The current and future state of the power grid allows for building a cleaner energy landscape. However, the grid may also become vulnerable to novel cyber threats. To preemptively protect the power grid against elaborate cyber-attacks, we propose to discover potential threats via reinforcement learning. In this work, the focus is on studying false data injection attacks that target the control logic of frequency controllers. We show that a reinforcement learning agent can successfully discover how to best inject false data into linear droop controllers.