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  1. A popular line of recent research incorporates ML advice in the design of online algorithms to improve their performance in typical instances. These papers treat the ML algorithm as a blackbox, and redesign online algorithms to take advantage of ML predictions. In this paper, we ask the complementary question: can we redesign ML algorithms to provide better predictions for online algorithms? We explore this question in the context of the classic rent-or-buy problem, and show that incorporating optimization benchmarks directly in ML loss functions leads to significantly better performance, while maintaining a worst-case adversarial result when the advice is completely wrong. We support this finding both through theoretical bounds and numerical simulations, and posit that “learning for optimization” is a fertile area for future research.
    Free, publicly-accessible full text available July 1, 2023
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  3. Free, publicly-accessible full text available February 24, 2023
  4. The motion of cells orthogonal to the direction of main flow is of importance in natural and engineered systems. The lateral movement of red blood cells (RBCs) distal to sudden expansion is considered to influence the formation and progression of thrombosis in venous valves, aortic aneurysms, and blood-circulating devices and is also a determining parameter for cell separation applications in flow-focusing microfluidic devices. Although it is known that the unique geometry of venous valves alters the blood flow patterns and cell distribution in venous valve sinuses, the interactions between fluid flow and RBCs have not been elucidated. Here, using a dilute cell suspension in an in vitro microfluidic model of a venous valve, we quantified the spatial distribution of RBCs by microscopy and image analysis, and using micro-particle image velocimetry and 3D computational fluid dynamics simulations, we analyzed the complex flow patterns. The results show that the local hematocrit in the valve pockets is spatially heterogeneous and is significantly different from the feed hematocrit. Above a threshold shear rate, the inertial separation of streamlines and lift forces contribute to an uneven distribution of RBCs in the vortices, the entrapment of RBCs in the vortices, and non-monotonic wall shear stresses inmore »the valve pockets. Our experimental and computational characterization provides insights into the complex interactions between fluid flow, RBC distribution, and wall shear rates in venous valve mimics, which is of relevance to understanding the pathophysiology of thrombosis and improving cell separation efficiency.

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    Free, publicly-accessible full text available March 3, 2023
  5. The DNA-binding protein H-NS is a pleiotropic gene regulator in gram-negative bacteria. Through its capacity to sense temperature and other environmental factors, H-NS allows pathogens like Salmonella to adapt their gene expression to their presence inside or outside warm-blooded hosts. To investigate how this sensing mechanism may have evolved to fit different bacterial lifestyles, we compared H-NS orthologs from bacteria that infect humans, plants, and insects, and from bacteria that live on a deep-sea hypothermal vent. The combination of biophysical characterization, high-resolution proton-less nuclear magnetic resonance spectroscopy, and molecular simulations revealed, at an atomistic level, how the same general mechanism was adapted to specific habitats and lifestyles. In particular, we demonstrate how environment-sensing characteristics arise from specifically positioned intra- or intermolecular electrostatic interactions. Our integrative approach clarified the exact modus operandi for H-NS-mediated environmental sensing and suggested that this sensing mechanism resulted from the exaptation of an ancestral protein feature.
  6. Abstract Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating various subsystems and scales remain siloed by different software tools. For example, each tool must be executed through a distinct interface. To help investigators find and use simulation tools, we developed BioSimulators (https://biosimulators.org), a central registry of the capabilities of simulation tools and consistent Python, command-line and containerized interfaces to each version of each tool. The foundation of BioSimulators is standards, such as CellML, SBML, SED-ML and the COMBINE archive format, and validation tools for simulation projects and simulation tools that ensure these standards are used consistently. To help modelers find tools for particular projects, we have also used the registry to develop recommendation services. We anticipate that BioSimulators will help modelers exchange, reproduce, and combine simulations.
    Free, publicly-accessible full text available May 7, 2023
  7. In both biological and engineered systems, functioning at peak power output for prolonged periods of time requires thermoregulation. Here, we report a soft hydrogel-based actuator that can maintain stable body temperatures via autonomic perspiration. Using multimaterial stereolithography, we three-dimensionally print finger-like fluidic elastomer actuators having a poly- N -isopropylacrylamide (PNIPAm) body capped with a microporous (~200 micrometers) polyacrylamide (PAAm) dorsal layer. The chemomechanical response of these hydrogel materials is such that, at low temperatures (<30°C), the pores are sufficiently closed to allow for pressurization and actuation, whereas at elevated temperatures (>30°C), the pores dilate to enable localized perspiration in the hydraulic actuator. Such sweating actuators exhibit a 600% enhancement in cooling rate (i.e., 39.1°C minute −1 ) over similar non-sweating devices. Combining multiple finger actuators into a single device yields soft robotic grippers capable of both mechanically and thermally manipulating various heated objects. The measured thermoregulatory performance of these sweating actuators (~107 watts kilogram −1 ) greatly exceeds the evaporative cooling capacity found in the best animal systems (~35 watts kilogram −1 ) at the cost of a temporary decrease in actuation efficiency.
  8. Abstract

    Intestinal stem cells are non-quiescent, dividing epithelial cells that rapidly differentiate into progenitor cells of the absorptive and secretory cell lineages. The kinetics of this process is rapid such that the epithelium is replaced weekly. To determine how the transcriptome and proteome keep pace with rapid differentiation, we developed a new cell sorting method to purify mouse colon epithelial cells. Here we show that alternative mRNA splicing and polyadenylation dominate changes in the transcriptome as stem cells differentiate into progenitors. In contrast, as progenitors differentiate into mature cell types, changes in mRNA levels dominate the transcriptome. RNA processing targets regulators of cell cycle, RNA, cell adhesion, SUMOylation, and Wnt and Notch signaling. Additionally, global proteome profiling detected >2,800 proteins and revealed RNA:protein patterns of abundance and correlation. Paired together, these data highlight new potentials for autocrine and feedback regulation and provide new insights into cell state transitions in the crypt.

  9. Abstract

    Candida glabratais a human commensal and an opportunistic human fungal pathogen. It is more closely related to the model yeastSaccharomyces cerevisiaethan otherCandida spp. Compared withS.cerevisiae,C.glabrataexhibits higher innate tolerance to various environmental stressors, including hyperthermal stress. Here we investigate the molecular mechanisms ofC.glabrataadaptation to heat stress via adaptive laboratory evolution. We show that all parallel evolved populations readily adapt to hyperthermal challenge (from 47 °C to 50 °C) and exhibit convergence in evolved phenotypes with extensive cross-tolerance to various other environmental stressors such as oxidants, acids, and alcohols. Genome resequencing identified fixation of mutations inCgSTE11in all parallel evolved populations. TheCgSTE11homolog inS.cerevisiaeplays crucial roles in various mitogen-activated protein kinase (MAPK) signaling pathways, but its role is less understood inC.glabrata. Subsequent verification confirmed thatCgSTE11is important in hyperthermal tolerance and the observed extensive cross-tolerance to other environmental stressors. These results support the hypothesis thatCgSTE11mediates cross-talks between MAPK signaling pathways inC.glabratain response to environmental challenges.