Article
Polymer Science
Tommy Yunpu Zhao, Max Meirow, Akalanka Tennakoon, Xun Wu, Alexander L. L. Paterson, Long Qi, Anne M. M. LaPointe, Jessica V. V. Lamb, Takeshi Kobayashi, Massimiliano Delferro, Aaron D. D. Sadow, Wenyu Huang, Erik Luijten, Frederic A. Perras
Summary: Chemical polymer upcycling by processive catalysts is a promising strategy for plastic waste remediation, which can produce high-value products with minimal energy input. By using a novel processive catalyst with a mesoporous SiO(2) shell/Pt nanoparticle/SiO2 core architecture, we found that the deconstruction of polyolefins occurs within narrow pores and involves a dehydrogenation-rehydrogenation cycle. The porous architecture enables the catalyst to perform multiple successive cleavages to the same polymer chain, and the extent of processivity is strongly correlated with the length of the pores.
Article
Physics, Multidisciplinary
Ling Liu, Yingqi Tian, Xuanye Yang, Chungen Liu
Summary: Characterizing the free energy landscape of water ionization is a challenging task. This study employs nanosecond timescale metadynamics simulations with classical nuclei enhanced by atomic neural network potentials to obtain convergent free energy surfaces. The results show good reproduction of the equilibrium constant and ionization rate constant. The character of the transition state reveals a concerted but asynchronous mechanism for the triple-proton transfer process. The conditional ensemble average analyses establish the presence of a dual-presolvation mechanism, which promotes water dissociation through local electric field fluctuations.
PHYSICAL REVIEW LETTERS
(2023)
Article
Biochemistry & Molecular Biology
Atsuhiro Tomita, Takashi Daiho, Tsukasa Kusakizako, Keitaro Yamashita, Satoshi Ogasawara, Takeshi Murata, Tomohiro Nishizawa, Osamu Nureki
Summary: The study elucidates the structure of ATP13A2 and its coupling mechanism between polyamine binding and dephosphorylation, providing a new theoretical basis for neuroprotective therapy. Polyamine is mainly recognized and bound through filling the luminal tunnel and electrostatic interactions, while the anchoring of the N-terminal domain stabilizes the conformation to facilitate the activation transition of the ATPase.
Article
Dentistry, Oral Surgery & Medicine
D. G. Moussa, R. W. Kung, J. S. Tse, W. L. Siqueira
Summary: Dental caries remains a widespread chronic disease worldwide. Researchers have developed customized proteinaceous coatings to control bacterial attachment and biofilm formation on dental enamel. By synthesizing bioactive proteins/peptides, they improved the antibiofilm efficacy and immobilization capacity on enamel. This translational approach shows promise in preventing dental caries.
JOURNAL OF DENTAL RESEARCH
(2023)
Article
Microbiology
Xiu-Juan Wang, Nan Zhang, Zhao-Jie Teng, Peng Wang, Wei-Peng Zhang, Xiu-Lan Chen, Yu-Zhong Zhang, Yin Chen, Hui-Hui Fu, Chun-Yang Li
Summary: Dimethylsulfide (DMS) and dimethylsulfoxide (DMSO) are important components in the global sulfur cycle, with SAR11 and MRC bacteria playing crucial roles in the oxidation of DMS to DMSO. The Tmm enzyme from these bacteria is proposed to have a catalytic mechanism involving a reductive and oxidative half-reaction, with FAD and NADPH molecules being essential for the process. By understanding this mechanism, researchers gain insight into how marine bacteria convert DMS into DMSO, contributing to a better understanding of the global sulfur cycle.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Pharmacology & Pharmacy
Alessandro Ratti, Enrico M. A. Fassi, Fabio Forlani, Matteo Mori, Federica Villa, Francesca Cappitelli, Jacopo Sgrignani, Gabriella Roda, Andrea Cavalli, Stefania Villa, Giovanni Grazioso
Summary: Bacterial biofilm is a major cause of persistent infection and antibiotic resistance. This study investigates the antibiofilm properties and mode of action of ellagic acid (EA), a natural polyphenol. The researchers propose that EA disrupts the bacterial redox homeostasis mediated by the NADH:quinone oxidoreductase enzyme WrbA, leading to its antibiofilm activity. These findings provide new insights into the potential use of EA for treating biofilm-related infections.
Article
Multidisciplinary Sciences
Mubashir Hassan, Sara Zahid, Hany Alashwal, Andrzej Kloczkowski, Ahmed A. Moustafa
Summary: Proteins like TNFR1 and MADD play crucial roles in activating downstream signaling pathways, leading to neuronal cell death and Alzheimer's disease. Common residues such as Asp400, Arg58, and Arg59 mediate the activation of these pathways, with aspartic acid and arginine playing key roles in these interactions. The interaction of death domains in TNFR1 and MADD can lead to conformational changes and activation of mediator proteins in cellular signaling pathways, making them potential pharmacological targets for Alzheimer's disease treatment.
SCIENTIFIC REPORTS
(2021)
Article
Microbiology
Matthew P. Ostrowski, Sabina Leanti La Rosa, Benoit J. Kunath, Andrew Robertson, Gabriel Pereira, Live H. Hagen, Neha J. Varghese, Ling Qiu, Tianming Yao, Gabrielle Flint, James Li, Sean P. McDonald, Duna Buttner, Nicholas A. Pudlo, Matthew K. Schnizlein, Vincent B. Young, Harry Brumer, Thomas M. Schmidt, Nicolas Terrapon, Vincent Lombard, Bernard Henrissat, Bruce Hamaker, Emiley A. Eloe-Fadrosh, Ashootosh Tripathi, Phillip B. Pope, Eric C. Martens
Summary: Our study reveals the presence of a potential food chain involving the degradation of xanthan gum in the human gut microbiota. We found that a primary degrader in the family Ruminococcaceae cleaves the backbone of xanthan gum, releasing oligosaccharides that can be further processed by other enzymes. Some individuals harbor Bacteroides intestinalis, which is unable to consume polymeric xanthan gum but can grow on the oligosaccharide products generated by the Ruminococcaceae.
NATURE MICROBIOLOGY
(2022)
Article
Polymer Science
Amanda K. Pearce, Sam J. Parkinson, Irem Akar, Matthew J. Derry, Paul D. Topham, Robert T. Mathers, Vasilios G. Stavros, Rachel K. O'Reilly
Summary: Polymerization-induced self-assembly (PISA) is a versatile method for producing nanoparticles in situ. This work demonstrates the use of a maleimide-based fluorophore as a powerful probe to study PISA over time. The fluorophore exhibits diagnostic increases in fluorescence lifetime with the onset of self-assembly and the evolution of particle morphology. The maleimide-functionalized nanostructures can also be used as cell imaging agents.
Article
Biochemical Research Methods
Blake J. Rasor, Payal Chirania, Grant A. Rybnicky, Richard J. Giannone, Nancy L. Engle, Timothy J. Tschaplinski, Ashty S. Karim, Robert L. Hettich, Michael C. Jewett
Summary: Researchers investigated the complexity of proteins and metabolites in Escherichia coli cell-free reactions, revealing the impact of cold shock-like proteins and buffer composition on gene expression.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Shihao Yao, Qiuzi Yi, Boyuan Ma, Xiaoting Mao, Ye Chen, Min-Xin Guan, Xiaohui Cang
Summary: Through molecular dynamics simulations and sequence analysis, this study reveals a highly specific ADP binding site in the ADP/ATP carrier (AAC), explaining its unusually high substrate specificity and specific substrate selectivity for ADP. This finding provides new insights into the transport mechanism of AAC and other adenine nucleotide transporters, opening up new directions for further research.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Chemistry, Physical
Sicong Li, Priscila dos Santos Bury, Fanglu Huang, Junhong Guo, Guo Sun, Anna Reva, Chuan Huang, Xinyun Jian, Yuan Li, Jiahai Zhou, Zixin Deng, Finian J. Leeper, Peter F. Leadlay, Marcio V. B. Dias, Yuhui Sun
Summary: The study reveals the dideoxygenation process of intermediates JI-20A and JI-20B in gentamicin, starting with phosphorylation catalyzed by GenP and then modified by GenB3 and GenB4 to form gentamicin C complex. Insights into the catalytic mechanisms of GenB3 and GenB4 are provided through crystal structures and site-directed mutagenesis.
Article
Chemistry, Physical
Tingting Qin, Wenli Zhang, Yue Ma, Wei Zhang, Taowen Dong, Xianyu Chu, Tian Li, Zizhun Wang, Nailin Yue, Hongyan Liu, Lirong Zheng, Xiaofeng Fan, Xingyou Lang, Qing Jiang, Weitao Zheng
Summary: In this study, the interaction mechanism between bismuth (Bi) and alkali metal ions (Li+, Na+ and K+) in aqueous alkali-metal ion batteries (ARABs) was investigated using various experimental and theoretical methods. It was found that Bi exhibited high specific capacity for Na+ and K+ storage, but lower capacity for Li+ storage. The irreversibility of Li+ dealloying from Bi matrix due to large adsorption energy resulted in poor rate performance and cycling stability. The large volume expansion caused by the largest radius of K+ contributed to the poor cycling stability for K+ storage. Bi showed superior performance for Na+ storage due to the appropriate interaction strength between Bi and Na+.
ENERGY STORAGE MATERIALS
(2022)
Article
Chemistry, Medicinal
Parthiban Marimuthu, Suresh Gorle, Konda Reddy Karnati
Summary: This study employed multiple computational approaches to investigate the mechanistic basis of high-affinity inhibitors for the main protease of SARS-CoV-2, providing insights into potential anti-M-pro strategies.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Biochemistry & Molecular Biology
Alexis Bigo-Simon, Jennifer Rodon Fores, Miryam Criado-Gonzalez, Lucille Blandin, Jean-Yves Runser, Bernard Senger, Guillaume Fleith, Marc Schmutz, Rachel Schurhammer, Alain Chaumont, Pierre Schaaf, Jeirome Combet, Loi''c Jierry
Summary: Composite hydrogels composed of low-molecular-weight peptide self-assemblies and polysaccharides have attracted great interest as new biomaterials. In this study, the impact of hyaluronic acid (HA) on the enzyme-assisted self-assembly of Fmoc-FFY peptides was investigated. HA was found to induce the formation of bundled peptide nanofibers, and the presence of HA in the bundles was dynamic. Molecular dynamic simulations explained the attractive interaction between HA and the peptide fibers through hydrogen bonds. The presence of HA also led to the organization of the peptide nanofibers into a nematic phase and an ordered 2D hexagonal columnar phase.
Article
Engineering, Biomedical
Ali Kamali, Mohammad Sarabian, Kaveh Laksari
Summary: Elasticity imaging is a technique to discover the mechanical properties of tissues using deformation and force measurements. We use physics-informed neural networks (PINN) to simultaneously discover the distribution of elastic modulus and Poisson's ratio in linear elasticity problems. Our model is validated through experiments and simulations.
ACTA BIOMATERIALIA
(2023)
Correction
Engineering, Biomedical
Nicholas J. Cecchi, August G. Domel, Yuzhe Liu, Eli Rice, Rong Lu, Xianghao Zhan, Zhou Zhou, Samuel J. Raymond, Sohrab Sami, Heer Singh, India Rangel, Landon P. Watson, Svein Kleiven, Michael Zeineh, David B. Camarillo, Gerald Grant
ANNALS OF BIOMEDICAL ENGINEERING
(2023)
Article
Engineering, Multidisciplinary
Mohammad Hossein Naderi, Hessam Babaee
Summary: Stochastic reduced-order modeling based on time-dependent bases has been successful in capturing low-dimensional manifold from stochastic partial differential equations (SPDEs). A new adaptive sparse interpolation algorithm is proposed to enable stochastic ROMs to achieve computational efficiency for nonlinear SPDEs. The algorithm constructs a low-rank approximation for the SPDE using the DEIM method, and it does not require any offline computation, allowing it to adapt to transient changes on-the-fly. The algorithm achieves computational speedup by adaptive sampling of the state and random spaces, resulting in significant reduction in computational cost for various test cases.
COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING
(2023)
Article
Engineering, Biomedical
Nicholas J. Cecchi, Ashlyn A. Callan, Landon P. Watson, Yuzhe Liu, Xianghao Zhan, Ramanand V. Vegesna, Collin Pang, Enora Le Flao, Gerald A. Grant, Michael M. Zeineh, David B. Camarillo
Summary: This study evaluated the impact attenuation capabilities of a padded helmet shell cover in both laboratory and field settings. The results showed that the padded helmet shell cover effectively reduced the magnitude of angular head accelerations and brain injury risk metrics in laboratory tests. However, no significant differences in head impact magnitude were observed between wearing the padded helmet shell cover and not wearing it in field tests. This research supports the need for in vivo helmet research to validate laboratory testing results.
ANNALS OF BIOMEDICAL ENGINEERING
(2023)
Article
Clinical Neurology
Mahta Karimpoor, Marios Georgiadis, Moss Y. Zhao, Maged Goubran, Hossein Moein Taghavi, Brian D. Mills, Dean Tran, Nicole Mouchawar, Sohrab Sami, Max Wintermark, Gerald Grant, David B. Camarillo, Michael E. Moseley, Greg Zaharchuk, Michael M. Zeineh
Summary: Long-term exposure to head impacts in high-contact sports can lead to changes in cerebral blood flow, with an initial increase followed by a decrease over time. This study highlights the importance of understanding the relationship between sports and brain injury.
ANNALS OF NEUROLOGY
(2023)
Article
Clinical Neurology
Ali Kamali, Laurel A. Dieckhaus, Emily C. Peters, Collin A. Preszler, Russell S. Witte, Paulo W. Pires, Elizabeth B. Hutchinson, Kaveh Laksari
Summary: The study investigates the pathophysiological changes in mice's brain within the first 3 hours after traumatic brain injury (TBI) and subarachnoid hemorrhage (SAH) using multimodal imaging. The results show that both TBI and SAH result in decreased brain oxygenation and blood flow, but TBI can recover while SAH cannot. MRI scans also reveal hemorrhage, edema, reduced perfusion, and altered diffusivity in both injury models. These findings can inform future studies on improving long-term recovery.
JOURNAL OF NEUROIMAGING
(2023)
Article
Hospitality, Leisure, Sport & Tourism
Xianghao Zhan, Yiheng Li, Yuzhe Liu, Nicholas J. Cecchi, Samuel J. Raymond, Zhou Zhou, Hossein Vahid Alizadeh, Jesse Ruan, Saeed Barbat, Stephen Tiernan, Olivier Gevaert, Michael M. Zeineh, Gerald A. Grant, David B. Camarillo
Summary: This study investigated the spectral characteristics of different head impact types using kinematics classification. The machine-learning-based classifier showed high accuracy in classifying head impact types, and different types of impacts had different distributions of spectral densities in low- and high-frequency ranges. This research contributes to a better understanding of impact kinematics in different sports.
JOURNAL OF SPORT AND HEALTH SCIENCE
(2023)
Article
Chemistry, Multidisciplinary
Declan A. Patton, Reza Mohammadi, Peter Halldin, Svein Kleiven, Andrew S. McIntosh
Summary: Recent studies have shown that alpine helmets reduce the risk of focal injuries caused by radial impacts, likely due to current helmet standards that prioritize linear acceleration pass criteria. However, there is a need to evaluate their performance in more realistic snow impacts. This study developed a method to assess alpine helmets' performance for both radial and oblique impacts on snow surfaces, finding that snow sample collection time and the presence of a rotation-damping system significantly affect helmet performance.
APPLIED SCIENCES-BASEL
(2023)
Article
Biotechnology & Applied Microbiology
Xiaogai Li, Qiantailang Yuan, Natalia Lindgren, Qi Huang, Madelen Fahlstedt, Jonas Osth, Bengt Pipkorn, Lotta Jakobsson, Svein Kleiven
Summary: Finite element human body models (HBMs) are crucial for traffic safety, and developing reliable personalized HBMs is a challenging task. This study presents a new image registration-based mesh morphing method to generate personalized HBMs, which show comparable element quality to the baseline models. The method enables the comparison of HBMs and has superior geometry correction capabilities, facilitating personalized simulations.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Nicholas J. Cecchi, Hossein Vahid Alizadeh, Yuzhe Liu, David B. Camarillo
Summary: Concerns have been raised regarding the long-term effects of head impacts and concussions in American football. This study explores the potential of liquid shock absorbers in improving helmet safety performance. Results show that the liquid helmet model significantly reduces impact forces compared to existing helmet models and has lower brain strains. The findings suggest the promising ability of liquid shock absorbers in mitigating brain injury risk.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Article
Computer Science, Interdisciplinary Applications
Colin M. Huber, Declan A. Patton, Jalaj Maheshwari, Zhou Zhou, Svein Kleiven, Kristy B. Arbogast
Summary: Finite element (FE) modeling is used to examine the influence of repetitive head loading in sports on tissue level injury metrics. Controlled soccer headers were simulated in two directions using a human head FE model. The results showed that headers were associated with peak strains and stresses, but these values were below typical injury levels. This study provides quantitative data to understand the effects of repetitive loading on the brain.
COMPUTER METHODS IN BIOMECHANICS AND BIOMEDICAL ENGINEERING
(2023)
Article
Clinical Neurology
Maged Goubran, Brian David Mills, Marios Georgiadis, Mahta Karimpoor, Nicole Mouchawar, Sohrab Sami, Emily Larson Dennis, Carolyn Akers, Lex Mitchell, Brian Boldt, David Douglas, Phillip Scott Digiacomo, Jarrett Rosenberg, Gerald Grant, Max Wintermark, David Benjamin Camarillo, Michael Zeineh
Summary: This study investigated longitudinal changes in brain microstructure of high-contact (football) and low-contact (volleyball) collegiate athletes using advanced diffusion MRI. It found significant differences in microstructural metrics and tracts between football and volleyball players, especially in concussed football players. The findings suggest alterations in white matter development in football athletes due to concussive and repeated subconcussive impacts.
Meeting Abstract
Biophysics
Maryam Majdolhosseini, Zhou Zhou, Svein Kleiven, Alessandra Villa
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS
(2023)
Article
Energy & Fuels
Yinmin Liu, Hessam Babaee, Peyman Givi, Harsha K. Chelliah, Daniel Livescu, Arash G. Nouri
Summary: This study employs a local-sensitivity-analysis technique to generate new skeletal reaction models for methane combustion. Through calculating and analyzing the sensitivities, different levels of accuracy in reproducing the foundational fuel chemistry model (FFCM-1) results are suggested.
