Scholarly Works, Chemical Engineering

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  • Bayesian-optimization-assisted discovery of stereoselective aluminum complexes for ring-opening polymerization of racemic lactide
    Wang, Xiaoqian; Huang, Yang; Xie, Xiaoyu; Liu, Yan; Huo, Ziyu; Lin, Maverick; Xin, Hongliang; Tong, Rong (Nature Research, 2023-06-20)
    Stereoselective ring-opening polymerization catalysts are used to produce degradable stereoregular poly(lactic acids) with thermal and mechanical properties that are superior to those of atactic polymers. However, the process of discovering highly stereoselective catalysts is still largely empirical.We aim to develop an integrated computational and experimental framework for efficient, predictive catalyst selection and optimization. As a proof of principle, we have developed a Bayesian optimization workflow on a subset of literature results for stereoselective lactide ring-opening polymerization, and using the algorithm, we identify multiple new Al complexes that catalyze either isoselective or heteroselective polymerization. In addition, feature attribution analysis uncovers mechanistically meaningful ligand descriptors, such as percent buried volume (%Vbur) and the highest occupied molecular orbital energy (Eₕₒₘₒ), that can access quantitative and predictivemodels for catalyst development.
  • Profiling renal dysfunction using Raman chemometric urinalysis, with special reference to COVID19, lupus nephritis, and diabetic nephropathy
    Robertson, John L.; Issa, Amr Sayed; Gomez, Mariana; Sullivan, Kathleen; Senger, Ryan S. (Knowledge Enterprise Journals, 2023-09-30)
    Background: Many systemic and urinary tract diseases alter renal structure and function, including changing the composition of urine. While routine urinalysis (physical properties, sediment evaluation, urine chemistry analytes) is useful in screening, it has limitations on separating disease processes, structural changes, and functional abnormalities. Likewise, while many individual ‘biomarkers’ have been used to screen for disease, they have not met with widespread clinical adoption. The recent COVID19 Pandemic and the recognition of post-acute sequelae SARS-CoV-2 infection (PASC) have highlighted the need for rapid, scalable, economical, and accurate screening tools for managing disease. Aims: Validate a Raman spectroscopy-based screening technology for urine analysis that could be used for recognition and quantification of systemic and renal effects of acute and PASC COVID19 disease. Methods: One hundred ten (110) urine specimens were obtained from consented adults diagnosed with COVID19 disease by RT-PCR and/or proximate (household) contact With RT-PCR-confirmed COVID19 disease. Samples were analyzed using Raman chemometric urinalysis, a technology that detects hundreds of discrete chemicals in urine and applies computational comparison-machine learning to detect COVID19-associated molecular patterns (‘fingerprints’). Results: When compared with the urine multimolecular ‘fingerprints’ of healthy individuals and patients with known systemic diseases (diabetes mellitus, lupus) that alter renal structure and function, patients with acute and PASC COVID19 had unique ‘fingerprints’ indicative of alterations in renal function (i.e. – infection altered urine composition). Differences in disease severity (mild to severe) were reflected by different ‘fingerprints’ in urine. Roughly 20% of hospitalized patients developed a degree of renal dysfunction (decrements in eGFR) that were correlated with distinct changes in urine fingerprints. Conclusion: Raman chemometric urinalysis may be a useful tool in management of patients with COVID19 disease, particularly in detecting patients with evolving renal dysfunction for whom there should be attention to medication use and renal health restoration/preservation.
  • Decreasing the Energy of Evaporation Using Interfacial Water: Is This Useful for Solar Evaporation Efficiency?
    Ducker, William A. (American Chemical Society, 2023-04)
    Evaporation of water using solar power is an economical and environmentally friendly method for purification of aqueous solutions. It has been suggested that intermediate states can be used to lower the enthalpy of evaporation of water and therefore to increase the efficiency of evaporation that uses absorption of sunlight. However, the relevant quantity is the enthalpy of evaporation from bulk water to bulk vapor, which is fixed for a given temperature and pressure. The formation of an intermediate state does not alter the enthalpy of the overall process.
  • Supramolecular Peptide Nanostructures Regulate Catalytic Efficiency and Selectivity
    Li, Zhao; Joshi, Soumil Y.; Wang, Yin; Deshmukh, Sanket A.; Matson, John B. (Wiley-V C H, 2023-05)
    We report three constitutionally isomeric tetrapeptides, each comprising one glutamic acid (E) residue, one histidine (H) residue, and two lysine (K-S) residues functionalized with side-chain hydrophobic S-aroylthiooxime (SATO) groups. Depending on the order of amino acids, these amphiphilic peptides self-assembled in aqueous solution into different nanostructures:nanoribbons, a mixture of nanotoroids and nanoribbons, or nanocoils. Each nanostructure catalyzed hydrolysis of a model substrate, with the nanocoils exhibiting the greatest rate enhancement and the highest enzymatic efficiency. Coarse-grained molecular dynamics simulations, analyzed with unsupervised machine learning, revealed clusters of H residues in hydrophobic pockets along the outer edge of the nanocoils, providing insight for the observed catalytic rate enhancement. Finally, all three supramolecular nanostructures catalyzed hydrolysis of the l-substrate only when a pair of enantiomeric Boc-l/d-Phe-ONp substrates were tested. This study highlights how subtle molecular-level changes can influence supramolecular nanostructures, and ultimately affect catalytic efficiency.
  • Elucidating the Effect of Ion Exchange Protocol on the Copper Exchange Efficacy, Copper Siting, and SCR activity in Cu-SSZ-13
    Koishybay, Aibolat; Umhey, Charles; Kuo, Chun-Te; Groden, Kyle; McEwen, Jean-Sabin; Karim, Ayman M.; Shantz, Daniel F. (Wiley-VCH, 2023-05)
    The influence of the copper ion exchange protocol on SCR activity of SSZ-13 is quantified. Using the same parent SSZ-13 zeolite, four exchange protocols are used to assess how exchange protocol impacts metal uptake and SCR activity. Large differences in the SCR activity, nearly 30 percentage points at 160 degrees C at constant copper content, are observed for different exchange protocols implying that different exchange protocols lead to different copper species. Hydrogen temperature programmed reduction on selected samples and infrared spectroscopy of CO binding corroborates this conclusion as the reactivity at 160 degrees C correlates with the intensity of the IR band at 2162 cm(-1). DFT-based calculations show that such an IR assignment is consistent with CO adsorbed on a Cu(I) cation within an eight-membered ring. This work shows that SCR activity can be influenced by the ion exchange process even when different protocols lead to the same metal loading. Perhaps most interesting, a protocol used to generate Cu-MOR for methane to methanol studies led to the most active catalyst both on a unit mass or unit mole copper basis. This points to a yet not recognized means to tailor catalyst activity as the open literature is silent on this issue.
  • Facile Implementation of Antimicrobial Coatings through Adhesive Films (Wraps) Demonstrated with Cuprous Oxide Coatings
    Behzadinasab, Saeed; Williams, Myra D.; Falkinham, Joseph O.; Ducker, William A. (MDPI, 2023-05-17)
    Antimicrobial coatings have a finite lifetime because of wear, depletion of the active ingredient, or surface contamination that produces a barrier between the pathogen and the active ingredient. The limited lifetime means that facile replacement is important. Here, we describe a generic method for rapidly applying and reapplying antimicrobial coatings to common-touch surfaces. The method is to deposit an antimicrobial coating on a generic adhesive film (wrap), and then to attach that modified wrap to the common-touch surface. In this scenario, the adhesion of the wrap and antimicrobial efficacy are separated and can be optimized independently. We demonstrate the fabrication of two antimicrobial wraps, both using cuprous oxide (Cu2O) as the active ingredient. The first uses polyurethane (PU) as the polymeric binder and the second uses polydopamine (PDA). Our antimicrobial PU/Cu2O and PDA/Cu2O wraps, respectively, kill >99.98% and >99.82% of the human pathogen, P. aeruginosa, in only 10 min, and each of them kill >99.99% of the bacterium in 20 min. These antimicrobial wraps can be removed and replaced on the same object in <1 min with no tools. Wraps are already frequently used by consumers to coat drawers or cars for aesthetic or protective purposes.
  • International Workshop on Digital Twins for Smart Health
    Deng, Jun; Ding, Ying; Achenie, Luke; Liu, Jinwei; Pan, Shimei; Purushotham, Sanjay; Wu, Huanmei; Wang, Qi (ACM, 2023-05)
  • Customized blends of polypropylene for extrusion based additive manufacturing
    Das, Arit; Shanmugham, Nishanth; Bortner, Michael J. (Wiley, 2022-11)
    Filament-based material extrusion (MatEx) additive manufacturing has garnered great interest due to its simplicity, customizability, and cost-effectiveness. However, MatEx of semicrystalline polymers is still largely relegated to prototyping applications. Major issues involving volumetric shrinkage and warpage of the printed parts must be addressed in order to employ them for printing functional parts. Moreover, the crystallization behavior and rheology of the polymer are dependent on the MatEx processing conditions. In the current work, the printability of blends of isotactic polypropylene with a soft, low crystallinity propylene based homopolymer is evaluated. Addition of the homopolymer resulted in an increase in the crystallization window of the blends by similar to 6 degrees C that had a profound impact on the interlayer adhesion and residual stress state. The shear-dependent melt flow behavior inside the printing nozzle as well as the interlayer chain diffusion and interlayer welding on the print bed were investigated. Rheological characterizations also indicate sufficient dispersion and miscibility of the homopolymer in the neat polypropylene matrix. The incorporation of the homopolymer as an additive significantly improved the dimensional accuracy of the printed parts through better dissipation of the entrapped residual stresses during MatEx. Moreover, the degree of mechanical anisotropy of the parts was significantly lower than that obtained using many 3D printable grade polymers. The findings from this study can be leveraged in toolpath planning, process parameter optimization, and new feedstock development, highlighting current limitations as well as providing valuable insights into necessary processing modifications in order to enable MatEx of next generation semicrystalline polymers.
  • Multi-axis alignment of Rod-like cellulose nanocrystals in drying droplets
    Pritchard, Cailean Q.; Navarro, Fernando; Roman, Maren; Bortner, Michael J. (Elsevier, 2021-12)
    Hypothesis: Radial capillary flow in evaporating droplets carry suspended nanoparticles to its periphery where they are deposited and form a coffee-ring. Rod-like nanoparticles seeking to minimize their capillary energy will align with their long-axis parallel to the contact line. Particles exhibiting electrostatic repulsion, such as cellulose nanocrystals (CNCs), establish a competition between capillary flow-induced impingement against a growing coffee-ring and entropic minimization leading to enhanced particle mobility. Therefore, balancing these effects by manipulating the local particle concentration in drying droplets should result in deposition with a controlled orientation of CNCs. Experiments: The dynamic local order in aqueous suspensions of CNCs in evaporating sessile droplets was investigated through time-resolved polarized light microscopy. The spatial distribution of alignment in deposited CNCs was explored as a function of nanoparticle concentration, droplet volume, initial degree of anisotropy, and substrate hydrophobicity. Computational analysis of the rotational Péclet number during evaporation was also investigated to evaluate any effects of shear-induced alignment. Findings: Multiple modes of orientation were identified suggesting local control over CNC orientation and subsequent properties can be attained via droplet-based patterning methods. Specifically, high local particle concentrations led to tangential alignment and lower local particle concentrations resulted in new evidence for radial alignment near the center of dried droplets.
  • Encapsulation of PI3K Inhibitor LY294002 within Polymer Nanoparticles Using Ion Pairing Flash Nanoprecipitation
    Fergusson, Austin D.; Zhang, Rui; Riffle, Judy S.; Davis, Richey M. (MDPI, 2023-04-06)
    Flash nanoprecipitation (FNP) is a turbulent mixing process capable of reproducibly producing polymer nanoparticles loaded with active pharmaceutical ingredients (APIs). The nanoparticles produced with this method consist of a hydrophobic core surrounded by a hydrophilic corona. FNP produces nanoparticles with very high loading levels of nonionic hydrophobic APIs. However, hydrophobic compounds with ionizable groups are not as efficiently incorporated. To overcome this, ion pairing agents (IPs) can be incorporated into the FNP formulation to produce highly hydrophobic drug salts that efficiently precipitate during mixing. We demonstrate the encapsulation of the PI3K inhibitor, LY294002, within poly(ethylene glycol)-b-poly(D,L lactic acid) nanoparticles. We investigated how incorporating two hydrophobic IPs (palmitic acid (PA) and hexadecylphosphonic acid (HDPA)) during the FNP process affected the LY294002 loading and size of the resulting nanoparticles. The effect of organic solvent choice on the synthesis process was also examined. While the presence of either hydrophobic IP effectively increased the encapsulation of LY294002 during FNP, HDPA resulted in well-defined colloidally stable particles, while the PA resulted in ill-defined aggregates. The incorporation of hydrophobic IPs with FNP opens the door for the intravenous administration of APIs that were previously deemed unusable due to their hydrophobic nature.
  • Clearance of Biodegradable Polymer and Polyethylene Films from the Rumens of Holstein Bull Calves
    Galyon, Hailey; Vibostok, Samuel; Duncan, Jane; Ferreira, Gonzalo; Whittington, Abby; Havens, Kirk; McDevitt, Jason; Cockrum, Rebecca (MDPI, 2023-03-03)
    Due to the occurrence of plastic impaction in ruminants and its deleterious effects on health and production, it is necessary to determine the suitability of biodegradable polymers to replace polyethylene-based agricultural plastics, such as hay netting. The objectives of this study were to evaluate the clearance of a polyhydroxyalkanoate (PHA) and poly(butylene succinate-co-adipate) (PBSA) melt-blend polymer from the rumen when fed to cattle and subsequent animal health. Twelve Holstein bull calves were dosed with an encapsulated 13.6 g of PBSA:PHA (Blend), 13.6 g of low-density polyethylene (LDPE), or four empty gelatin capsules (Control) for 30 d. The feed intake, body weight, and body temperature were evaluated, and hemograms were run on d 0 and d 30. On d 31, calves were euthanized to evaluate gross rumen measurements and pathology, papillae length, and polymer residues in rumen contents. No calves presented any signs related to plastic impaction. The feed intake; body weight; rectal temperature; hematological parameters; gross rumen measurements and pathology; and rumen pH and temperature were not affected by treatments. Calves dosed with LDPE had 27 g of undegraded polymer retained in the rumen while Blend calves had only 2 g of fragmented polymers that were 10% of their original size. Agricultural plastics developed from PBSA:PHA may be a suitable alternative to LDPE-based products in the case of animal ingestion and may reduce the incidence of plastic impaction.
  • Mechanism and Efficacy of Cu2O-Treated Fabric
    Benmamoun, Zachary; Wyhopen, Trent; Li, You; Ducker, William A. (MDPI, 2022-11-16)
    Pathogenic bacteria can remain viable on fabrics for several days and therefore are a source of infection. Antimicrobial fabrics are a potential method of reducing such infections, and advances in antimicrobial fabrics can be enhanced by knowledge of how the fabric kills bacteria. Metal oxides have been considered and used as antimicrobial ingredients in self-sanitizing surfaces, including in clinical settings. In this work, we examine how the addition of cuprous oxide (Cu2O) particles to polypropylene fibers kills bacteria. First, we show that the addition of the Cu2O particles reduces the viability of common hospital pathogens, Staphylococcus aureus, Pseudomonas aeruginosa, and Streptococcus pneumoniae, by 99.9% after 30 min of contact with the treated polypropylene. Then, we demonstrate that the main killing effect is due to the drying of the bacteria onto the cuprous oxide particles. There is also a weaker effect due to free Cu+ ions that dissolve into the liquid. Other dissolved species were unimportant. Chelation of these Cu+ ions in soluble form or precipitation removes their antimicrobial activity.
  • Subpopulation-specific machine learning prognosis for underrepresented patients with double prioritized bias correction
    Afrose, Sharmin; Song, Wenjia; Nemeroff, Charles B.; Yao, Danfeng (Nature Research, 2022-09)
    Background: Many clinical datasets are intrinsically imbalanced, dominated by overwhelming majority groups. Off-the-shelf machine learning models that optimize the prognosis of majority patient types (e.g., healthy class) may cause substantial errors on the minority prediction class (e.g., disease class) and demographic subgroups (e.g., Black or young patients). In the typical one-machine-learning-model-fits-all paradigm, racial and age disparities are likely to exist, but unreported. In addition, some widely used whole-population metrics give misleading results. Methods: We design a double prioritized (DP) bias correction technique to mitigate representational biases in machine learning-based prognosis. Our method trains customized machine learning models for specific ethnicity or age groups, a substantial departure from the one-model-predicts-all convention. We compare with other sampling and reweighting techniques in mortality and cancer survivability prediction tasks. Results: We first provide empirical evidence showing various prediction deficiencies in a typical machine learning setting without bias correction. For example, missed death cases are 3.14 times higher than missed survival cases for mortality prediction. Then, we show DP consistently boosts the minority class recall for underrepresented groups, by up to 38.0%. DP also reduces relative disparities across race and age groups, e.g., up to 88.0% better than the 8 existing sampling solutions in terms of the relative disparity of minority class recall. Crossrace and cross-age-group evaluation also suggests the need for subpopulation-specific machine learning models. Conclusions: Biases exist in the widely accepted one-machine-learning-model-fits-all-population approach. We invent a bias correction method that produces specialized machine learning prognostication models for underrepresented racial and age groups. This technique may reduce potentially life-threatening prediction mistakes for minority populations.
  • Focused Ultrasound Biofilm Ablation: Investigation of Histotripsy for the Treatment of Catheter-Associated Urinary Tract Infections (CAUTIs)
    Childers, Christopher; Edsall, Connor; Gannon, Jessica; Whittington, Abby R.; Muelenaer, Andre A.; Rao, Jayasimha; Vlaisavljevich, Eli (IEEE, 2021-09-01)
    Urinary catheters often become contaminated with biofilms, resulting in catheter-associated urinary tract infections (CAUTIs) that adversely affect patient outcomes. Histotripsy is a non-invasive focused ultrasound therapy previously developed for the non-invasive ablation of cancerous tumors and soft tissues. Histotripsy has also previously shown the ability to treat biofilms on glass slides and surgical meshes. Here, we investigate the potential of histotripsy for the treatment of CAUTIs for the first time in vitro. Clinically relevant catheter materials (Tygon, Silicone, and latex catheter mimics) and commonly used clinical catheters were tested to determine the feasibility of producing luminal histotripsy bubble clouds. A Pseudomonas aeruginosa (strain PA14) biofilm model was developed and tested to produce luminal biofilms in an in vitro Tygon catheter mimic. This model was treated with histotripsy to determine the ability to remove a luminal biofilm. Finally, the bactericidal effects of histotripsy were tested by treating PA14 suspended inside the Tygon catheter mimic. Results showed that histotripsy produced precise luminal cavitation within all tested catheter mimics and clinical catheters. Histotripsy treatment of a PA14 biofilm with histotripsy reduced luminal biofilm OD590 signal down to background levels. Further, the treatment of suspended PA14 in LB showed a 3.45±0.11 log10 reduction in CFU/mL after 6 histotripsy scans across the catheter mimics. Overall, the results of this study demonstrate the potential of histotripsy to provide a new modality for removing bacterial biofilms from catheter-based medical devices and suggest that additional work is warranted to investigate histotripsy for the treatment of CAUTIs and other biomaterial-associated infections.
  • Synthesis and Characterization of Silica-Tantala Microporous Membranes for Gas Separations Fabricated Using Chemical Vapor Deposition
    Lundin, Sean-Thomas B.; Wang, Hongsheng; Oyama, S. Ted (MDPI, 2022-09-16)
    Composite membranes consisting of microporous tantalum-doped silica layers supported on mesoporous alumina substrates were fabricated using chemical vapor deposition (CVD) in both thermal decomposition and counter-flow oxidative deposition modes. Tetraethyl orthosilicate (TEOS) was used as the silica precursor and tantalum (V) ethoxide (TaEO) as the tantalum source. Amounts of TaEO from 0 mol% to 40 mol% were used in the CVD gas mixture and high H2 permeances above 10−7 mol m−2 s−1 Pa−1 were obtained for all conditions. Close examination was made of the H2/CH4 and O2/CH4 selectivities due to the potential use of these membranes in methane reforming or partial oxidation of methane applications. Increasing deposition temperature correlated with increasing H2/CH4 selectivity at the expense of O2/CH4 selectivity, suggesting a need to optimize membrane synthesis for a specific selectivity. Measured at 400 °C, the highest H2/CH4 selectivity of 530 resulted from thermal CVD at 650 °C, whereas the highest O2/CH4 selectivity of 6 resulted from thermal CVD at 600 °C. The analysis of the membranes attempted by elemental analysis, X-ray photoelectron spectroscopy, and X-ray absorption near-edge spectroscopy revealed that Ta was undetectable because of instrumental limitations. However, the physical properties of the membranes indicated that the Ta must have been present at least at dopant levels. It was found that the pore size of the resultant membranes increased from 0.35 nm for pure Si to 0.37 nm for a membrane prepared with 40 mol% Ta. Similarly, an increase in Ta in the feed resulted in an increase in O2/CH4 selectivity at the expense of H2/CH4 selectivity. Additionally, it resulted in a decrease in hydrothermal stability, with the membranes prepared with higher Ta suffering greater permeance and selectivity declines during 96 h of exposure to 16 mol% H2O in Ar at 650 °C.
  • Biomass Valorization to Bioenergy: Assessment of Biomass Residues' Availability and Bioenergy Potential in Nigeria
    Ezealigo, Uchechukwu Stella; Ezealigo, Blessing Nonye; Kemausuor, Francis; Achenie, Luke Ekem Kweku; Onwualu, Azikiwe Peter (MDPI, 2021-12)
    The bioenergy sector in Nigeria currently lacks a proper assessment of resource availability. In this study, we investigated the bioenergy potential of agricultural residues and municipal solid and liquid waste using data from 2008 to 2018, and we applied a computational and analytical approach with mild assumptions. The technical potential for the production of cellulosic ethanol and biogas was estimated from the available biomass. It was discovered that higher energy was generated from biogas than cellulosic ethanol for the same type of residue. The available crop residue technical potential of 84 Mt yielded cellulosic ethanol and biogas of 14,766 ML/yr (8 Mtoe) and 15,014 Mm(3)/yr (13 Mtoe), respectively. Biogas has diverse applications ranging from heat to electric power generation and therefore holds great potential in solving the current electricity crisis in Nigeria. It will also position the nation towards achieving the 7th sustainable development goal (SDG 7) on clean and affordable energy.
  • Alterations in the molecular composition of COVID-19 patient urine, detected using Raman spectroscopic/computational analysis
    Robertson, John L.; Senger, Ryan S.; Talty, Janine; Du, Pang; Sayed-Issa, Amr; Avellar, Maggie L.; Ngo, Lacy T.; Gomez de la Espriella, Mariana; Fazili, Tasaduq N.; Jackson-Akers, Jasmine Y.; Guruli, Georgi; Orlando, Giuseppe (PLOS, 2022-07-01)
    We developed and tested a method to detect COVID-19 disease, using urine specimens. The technology is based on Raman spectroscopy and computational analysis. It does not detect SARS-CoV-2 virus or viral components, but rather a urine ‘molecular fingerprint’, representing systemic metabolic, inflammatory, and immunologic reactions to infection. We analyzed voided urine specimens from 46 symptomatic COVID-19 patients with positive real time-polymerase chain reaction (RT-PCR) tests for infection or household contact with test-positive patients. We compared their urine Raman spectra with urine Raman spectra from healthy individuals (n = 185), peritoneal dialysis patients (n = 20), and patients with active bladder cancer (n = 17), collected between 2016–2018 (i.e., pre-COVID-19). We also compared all urine Raman spectra with urine specimens collected from healthy, fully vaccinated volunteers (n = 19) from July to September 2021. Disease severity (primarily respiratory) ranged among mild (n = 25), moderate (n = 14), and severe (n = 7). Seventy percent of patients sought evaluation within 14 days of onset. One severely affected patient was hospitalized, the remainder being managed with home/ambulatory care. Twenty patients had clinical pathology profiling. Seven of 20 patients had mildly elevated serum creatinine values (>0.9 mg/dl; range 0.9–1.34 mg/dl) and 6/7 of these patients also had estimated glomerular filtration rates (eGFR) <90 mL/min/1.73m2 (range 59–84 mL/min/1.73m2). We could not determine if any of these patients had antecedent clinical pathology abnormalities. Our technology (Raman Chemometric Urinalysis—Rametrix®) had an overall prediction accuracy of 97.6% for detecting complex, multimolecular fingerprints in urine associated with COVID-19 disease. The sensitivity of this model for detecting COVID-19 was 90.9%. The specificity was 98.8%, the positive predictive value was 93.0%, and the negative predictive value was 98.4%. In assessing severity, the method showed to be accurate in identifying symptoms as mild, moderate, or severe (random chance = 33%) based on the urine multimolecular fingerprint. Finally, a fingerprint of ‘Long COVID-19’ symptoms (defined as lasting longer than 30 days) was located in urine. Our methods were able to locate the presence of this fingerprint with 70.0% sensitivity and 98.7% specificity in leave-one-out cross-validation analysis. Further validation testing will include sampling more patients, examining correlations of disease severity and/or duration, and employing metabolomic analysis (Gas Chromatography–Mass Spectrometry [GC-MS], High Performance Liquid Chromatography [HPLC]) to identify individual components contributing to COVID-19 molecular fingerprints.
  • Cell-type-specific epigenomic variations associated with BRCA1 mutation in pre-cancer human breast tissues
    Hsieh, Yuan-Pang; Naler, Lynette B.; Ma, Sai; Lu, Chang (Oxford University Press, 2022-01-13)
    BRCA1 germline mutation carriers are predisposed to breast cancers. Epigenomic regulations have been known to strongly interact with genetic variations and potentially mediate biochemical cascades involved in tumorigenesis. Due to the cell-type specificity of epigenomic features, profiling of individual cell types is critical for understanding the molecular events in various cellular compartments within complex breast tissue. Here, we produced cell-type-specific profiles of genome-wide histone modifications including H3K27ac and H3K4me3 in basal, luminal progenitor, mature luminal and stromal cells extracted from a small pilot cohort of pre-cancer BRCA1 mutation carriers (BRCA1(mut/+)) and non-carriers (BRCA1(+/+)), using a low-input ChIP-seq technology that we developed. We discovered that basal and stromal cells present the most extensive epigenomic differences between mutation carriers (BRCA1(mut/+)) and non-carriers (BRCA1(+/+)), while luminal progenitor and mature luminal cells are relatively unchanged with the mutation. Furthermore, the epigenomic changes in basal cells due to BRCA1 mutation appear to facilitate their transformation into luminal progenitor cells. Taken together, epigenomic regulation plays an important role in the case of BRCA1 mutation for shaping the molecular landscape that facilitates tumorigenesis.
  • Epigenomic and transcriptomic analyses reveal differences between low-grade inflammation and severe exhaustion in LPS-challenged murine monocytes
    Naler, Lynette B.; Hsieh, Yuan-Pang; Geng, Shuo; Zhou, Zirui; Li, Liwu; Lu, Chang (Nature Portfolio, 2022-01-28)
    Emerging studies suggest that monocytes can be trained by bacterial endotoxin to adopt distinct memory states ranging from low-grade inflammation to immune exhaustion. While low-grade inflammation may contribute to the pathogenesis of chronic diseases, exhausted monocytes with pathogenic and immune-suppressive characteristics may underlie the pathogenesis of polymicrobial sepsis including COVID-19. However, detailed processes by which the dynamic adaption of monocytes occur remain poorly understood. Here we exposed murine bone-marrow derived monocytes to chronic lipopolysaccharide (LPS) stimulation at low-dose or high-dose, as well as a PBS control. The cells were profiled for genome-wide H3K27ac modification and gene expression. The gene expression of TRAM-deficient and IRAK-M-deficient monocytes with LPS exposure was also analyzed. We discover that low-grade inflammation preferentially utilizes the TRAM-dependent pathway of TLR4 signaling, and induces the expression of interferon response genes. In contrast, high dose LPS uniquely upregulates exhaustion signatures with metabolic and proliferative pathways. The extensive differences in the epigenomic landscape between low-dose and high-dose conditions suggest the importance of epigenetic regulations in driving differential responses. Our data provide potential targets for future mechanistic or therapeutic studies. Lynette Naler and Yuan-Pang Hsieh et al. evaluate epigenomic and transcriptomic differences in mouse bone marrow-derived macrophages following exposure to high or low doses of LPS. Their results suggest that both low- and high-grade inflammation involve TRAM-dependent pathways.
  • Coarse-grained molecular dynamics integrated with convolutional neural network for comparing shapes of temperature sensitive bottlebrushes
    Joshi, Soumil Y.; Singh, Samrendra; Deshmukh, Sanket A. (Nature Portfolio, 2022-03-18)
    Quantification of shape changes in nature-inspired soft material architectures of stimuli-sensitive polymers is critical for controlling their properties but is challenging due to their softness and flexibility. Here, we have computationally designed uniquely shaped bottlebrushes of a thermosensitive polymer, poly(N-isopropylacrylamide) (PNIPAM), by controlling the length of side chains along the backbone. Coarse-grained molecular dynamics simulations of solvated bottlebrushes were performed below and above the lower critical solution temperature of PNIPAM. Conventional analyses (free volume, asphericity, etc.) show that lengths of side chains and their immediate environments dictate the compactness and bending in these architectures. We further developed 100 unique convolutional neural network models that captured molecular-level features and generated a statistically significant quantification of the similarity between different shapes. Thus, our study provides insights into the shapes of complex architectures as well as a general method to analyze them. The shapes presented here may inspire the synthesis of new bottlebrushes.