Recent Submissions

  • Computational modeling identifies multitargeted kinase inhibitors as effective therapies for metastatic, castration-resistant prostate cancer 

    Bello, Thomas; Paindelli, Claudia; Diaz-Gomez, Luis A.; Melchiorri, Anthony; Mikos, Antonios G.; (2021)
    Castration-resistant prostate cancer (CRPC) is an advanced subtype of prostate cancer with limited therapeutic options. Here, we applied a systems-based modeling approach called kinome regularization (KiR) to identify multitargeted kinase inhibitors (KIs) that abrogate CRPC growth. Two predicted KIs, PP121 and SC-1, suppressed CRPC growth in ...
  • BMP-treated human embryonic stem cells transcriptionally resemble amnion cells in the monkey embryo 

    Chhabra, Sapna; Warmflash, Aryeh (2021)
    Human embryonic stem cells (hESCs) possess an immense potential to generate clinically relevant cell types and unveil mechanisms underlying early human development. However, using hESCs for discovery or translation requires accurately identifying differentiated cell types through comparison with their in vivo counterparts. Here, we set out to determine ...
  • Design of organic structure directing agents to control the synthesis of zeolites for carbon capture and storage 

    Daeyaert, Frits; W. Deem, Michael (2019)
    We have de novo designed organic structure directing agents (OSDAs) for zeolites that have been predicted to be effective materials for carbon capture and storage. The zeolites were selected for their reduced parasitic energy when used as CO2 adsorbants in a pressure–temperature swing process in coal- or natural gas-fired power plants. Synthetically ...
  • Development of an integrated multimodal optical imaging system with real-time image analysis for the evaluation of oral premalignant lesions 

    Yang, Eric C.; Vohra, Imran S.; Badaoui, Hawraa; Schwarz, Richard A.; Cherry, Katelin D.; (2019)
    Oral premalignant lesions (OPLs), such as leukoplakia, are at risk of malignant transformation to oral cancer. Clinicians can elect to biopsy OPLs and assess them for dysplasia, a marker of increased risk. However, it is challenging to decide which OPLs need a biopsy and to select a biopsy site. We developed a multimodal optical imaging system (MMIS) ...
  • Emergent spatiotemporal population dynamics with cell-length control of synthetic microbial consortia 

    Winkle, James J.; Karamched, Bhargav R.; Bennett, Matthew R.; Ott, William; Josić, Krešimir (2021)
    The increased complexity of synthetic microbial biocircuits highlights the need for distributed cell functionality due to concomitant increases in metabolic and regulatory burdens imposed on single-strain topologies. Distributed systems, however, introduce additional challenges since consortium composition and spatiotemporal dynamics of constituent ...
  • Fabrication of optical components using a consumer-grade lithographic printer 

    Berglund, Gregory D.; Tkaczyk, Tomasz S.; Tkaczyk, Tomasz S. (2019)
    The ability to 3D print optical elements will greatly expand the accessibility of optical fabrication. Here, we report on two fabrication techniques for plano-convex lens files using a consumer-grade lithographic printer. Lenses were post-processed using a simple spin coating technique with the resin used in the printing process or by curing directly ...
  • A novel disorder involving dyshematopoiesis, inflammation, and HLH due to aberrant CDC42 function 

    Lam, Michael T.; Coppola, Simona; Krumbach, Oliver H.F.; Prencipe, Giusi; Insalaco, Antonella; (2019)
    Hemophagocytic lymphohistiocytosis (HLH) is characterized by immune dysregulation due to inadequate restraint of overactivated immune cells and is associated with a variable clinical spectrum having overlap with more common pathophysiologies. HLH is difficult to diagnose and can be part of inflammatory syndromes. Here, we identify a novel ...
  • 3D Ultrastructure of the Cochlear Outer Hair Cell Lateral Wall Revealed By Electron Tomography 

    Triffo, William Jeffrey; Palsdottir, Hildur; Song, Junha; Morgan, David Gene; McDonald, Kent L.; (2019)
    Outer Hair Cells (OHCs) in the mammalian cochlea display a unique type of voltage-induced mechanical movement termed electromotility, which amplifies auditory signals and contributes to the sensitivity and frequency selectivity of mammalian hearing. Electromotility occurs in the OHC lateral wall, but it is not fully understood how the supramolecular ...
  • Hypoxia Stimulates Synthesis of Neutrophil Gelatinase-Associated Lipocalin in Aortic Valve Disease 

    Swaminathan, Ganesh; Krishnamurthy, Varun K.; Sridhar, Swetha; Robson, Denise C.; Ning, Yao; (2019)
    Objective: Aortic valve disease is commonly found in the elderly population. It is characterized by dysregulated extracellular matrix remodeling followed by extensive microcalcification of the aortic valve and activation of valve interstitial cells. The mechanism behind these events are largely unknown. Studies have reported expression of hypoxia ...
  • Toward development of a large field-of-view cancer screening patch (CASP) to detect cervical intraepithelial neoplasia 

    Gawedzinski, John; Schmeler, Kathleen M.; Milbourne, Andrea; Ramalingam, Preetha; Moghaddam, Parnian A.; (2019)
    Cervical cancers are primarily diagnosed via colposcopy, in which the tissue is visually assessed by a clinician for abnormalities, followed by directed biopsies and histologic analysis of excised tissue. Optical biopsy technologies offer a less invasive method of imaging such that subcellular features can be resolved without removing tissue. These ...
  • Impedance scaling for gold and platinum microelectrodes 

    Fan, Bo; Wolfrum, Bernhard; Robinson, Jacob T. (2021)
    Objective. Electrical measurement of the activity of individual neurons is a primary goal for many invasive neural electrodes. Making these ‘single unit’ measurements requires that we fabricate electrodes small enough so that only a few neurons contribute to the signal, but not so small that the impedance of the electrode creates overwhelming noise ...
  • Synthesis of precision antibody conjugates using proximity-induced chemistry 

    Cao, Yu J.; Yu, Chenfei; Wu, Kuan-Lin; Wang, Xuechun; Liu, Dong; (2021)
    Rationale: Therapeutic antibody conjugates allow for the specific delivery of cytotoxic agents or immune cells to tumors, thus enhancing the antitumor activity of these agents and minimizing adverse systemic effects. Most current antibody conjugates are prepared by nonspecific modification of antibody cysteine or lysine residues, inevitably resulting ...
  • Clinically translatable quantitative molecular photoacoustic imaging with liposome-encapsulated ICG J-aggregates 

    Wood, Cayla A.; Han, Sangheon; Kim, Chang Soo; Wen, Yunfei; Sampaio, Diego R. T.; (2021)
    Photoacoustic (PA) imaging is a functional and molecular imaging technique capable of high sensitivity and spatiotemporal resolution at depth. Widespread use of PA imaging, however, is limited by currently available contrast agents, which either lack PA-signal-generation ability for deep imaging or their absorbance spectra overlap with hemoglobin, ...
  • Quantification of Myxococcus xanthus Aggregation and Rippling Behaviors: Deep-Learning Transformation of Phase-Contrast into Fluorescence Microscopy Images 

    Zhang, Jiangguo; Comstock, Jessica A.; Cotter, Christopher R.; Murphy, Patrick A.; Nie, Weili; (2021)
    Myxococcus xanthus bacteria are a model system for understanding pattern formation and collective cell behaviors. When starving, cells aggregate into fruiting bodies to form metabolically inert spores. During predation, cells self-organize into traveling cell-density waves termed ripples. Both phase-contrast and fluorescence microscopy are used to ...
  • Radiometric and design model for the tunable light-guide image processing snapshot spectrometer (TuLIPSS) 

    Zheng, Desheng; Flynn, Christopher; Stoian, Razvan I.; Lu, Jiawei; Cao, Haimu; (2021)
    The tunable light-guide image processing snapshot spectrometer (TuLIPSS) is a novel remote sensing instrument that can capture a spectral image cube in a single snapshot. The optical modelling application for the absolute signal intensity on a single pixel of the sensor in TuLIPSS has been developed through a numerical simulation of the integral ...
  • Predicting stability of DNA bulge at mononucleotide microsatellite 

    Bae, Jin H; Zhang, David Yu; Systems, Synthetic, and Physical Biology (2021)
    Mononucleotide microsatellites are clinically and forensically crucial DNA sequences due to their high mutability and abundance in the human genome. As a mutagenic intermediate of an indel in a microsatellite and a consequence of probe hybridization after such mutagenesis, a bulge with structural degeneracy sliding within a microsatellite is formed. ...
  • Decoupling Lineage-Associated Genes in Acute Myeloid Leukemia Reveals Inflammatory and Metabolic Signatures Associated With Outcomes 

    Abbas, Hussein A.; Mohanty, Vakul; Wang, Ruiping; Huang, Yuefan; Liang, Shaoheng; (2021)
    Acute myeloid leukemia (AML) is a heterogeneous disease with variable responses to therapy. Cytogenetic and genomic features are used to classify AML patients into prognostic and treatment groups. However, these molecular characteristics harbor significant patient-to-patient variability and do not fully account for AML heterogeneity. RNA-based ...
  • Oncogene Concatenated Enriched Amplicon Nanopore Sequencing for rapid, accurate, and affordable somatic mutation detection 

    Thirunavukarasu, Deepak; Cheng, Lauren Y.; Song, Ping; Chen, Sherry X.; Borad, Mitesh J.; (2021)
    We develop the Oncogene Concatenated Enriched Amplicon Nanopore Sequencing (OCEANS) method, in which variants with low variant allele frequency (VAFs) are amplified and subsequently concatenated for Nanopore Sequencing. OCEANS allows accurate detection of somatic mutations with VAF limits of detection between 0.05 and 1%. We construct 4 distinct ...
  • Wearable wireless power systems for `ME-BIT' magnetoelectric-powered bio implants 

    Alrashdan, Fatima T.; Chen, Joshua C.; Singer, Amanda; Avants, Benjamin W.; Yang, Kaiyuan; (2021)
    Objective. Compared to biomedical devices with implanted batteries, wirelessly powered technologies can be longer-lasting, less invasive, safer, and can be miniaturized to access difficult-to-reach areas of the body. Magnetic fields are an attractive wireless power transfer modality for such bioelectronic applications because they suffer negligible ...
  • Multiple neuronal networks coordinate Hydra mechanosensory behavior 

    Badhiwala, Krishna N; Primack, Abby S; Juliano, Celina E; Robinson, Jacob T (2021)
    Hydra vulgaris is an emerging model organism for neuroscience due to its small size, transparency, genetic tractability, and regenerative nervous system; however, fundamental properties of its sensorimotor behaviors remain unknown. Here, we use microfluidic devices combined with fluorescent calcium imaging and surgical resectioning to study how the ...

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