Article
Biochemistry & Molecular Biology
Alexandra Semchenkova, Elena Zerkalenkova, Irina Demina, Svetlana Kashpor, Egor Volchkov, Elena Zakharova, Sergey Larin, Yulia Olshanskaya, Galina Novichkova, Alexey Maschan, Michael Maschan, Alexander Popov
Summary: Mixed-phenotype acute leukemia (MPAL) is a rare and heterogeneous form of acute leukemia characterized by cross-lineage antigen expression. It is important to sort and examine doubtful cell populations and leukemic blasts, and search for similar genetic aberrations to avoid misdiagnosis. In this study, monocytic cells that had minor immunophenotypic abnormalities were found to share the same gene rearrangements with dominant leukemic populations, confirming the same leukemic origin. This approach can identify implicit cases of MPAL and guide appropriate clinical management for patients.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Virology
Steven Adamou, Adam Vanarsdall, David C. Johnson
Summary: Research shows that PRV and HSV US9 proteins primarily function in the cytoplasm of neurons, promoting virus assembly and cytoplasmic sorting. Mutants lacking these proteins exhibit defects in virus assembly and cytoplasmic sorting, as well as reduced quantities of infectious virus in neurons and cell culture supernatants.
Article
Multidisciplinary Sciences
Sudeep Banjade, Lu Zhu, Jeffrey R. Jorgensen, Sho W. Suzuki, Scott D. Emr
Summary: This study investigates the mechanism of action of ESCRTs in yeast vacuoles, finding that multivalent interactions between ESCRT-0 and polyubiquitin are critical for substrate recognition and proposing that self-assembly of early ESCRTs induces condensation and assembly on membranes.
Article
Engineering, Biomedical
Yuyang Xie, Peijun Qin, Tianruo Guo, Amr Al Abed, Nigel H. Lovell, David Tsai
Summary: A computational toolkit was developed to create nerve stimulation models and study fiber responses under different electrode arrangements and stimulation waveforms. The toolkit allows bi-directional transfer of results and provides an agile and efficient design method for improving the design of intrafascicular implants.
JOURNAL OF NEURAL ENGINEERING
(2023)
Article
Cell Biology
Francesca Casciaro, Silvia Zia, Mattia Forcato, Manuela Zavatti, Francesca Beretti, Emma Bertucci, Andrea Zattoni, Pierluigi Reschiglian, Francesco Alviano, Laura Bonsi, Matilde Yung Follo, Marco Demaria, Barbara Roda, Tullia Maraldi
Summary: This study utilized Celector® technology to classify and characterize hAFSCs, uncovering deep intra-population differences and validating their impact on stemness properties. The results suggest the importance of selecting cellular fractions with the highest potential for use in regenerative medicine.
Article
Physics, Fluids & Plasmas
Sara Sadat, Veradi Isfahani, Keivan Aghababaei Samani
Summary: Social physics is a mathematical study that examines how the flow of ideas can influence individual behavior. This paper introduces the use of exploration and imitation processes to achieve this goal, employing a new type of imitation where the imitant strategy moves towards the role model strategy. The study finds that by combining exploration and soft imitation, the width of the strategy distribution function becomes stationary, and this model can be applied to complex networks.
Article
Cell Biology
Leonid Olender, Roshina Thapa, Roi Gazit
Summary: In this study, the researchers propose using CD34/CD150 instead of the traditional CD34/Fc gamma R approach to separate sub-populations in the LK compartment. They re-analyzed single-cell RNA-Seq data and confirmed their findings through independent FACS analysis. The newly-obtained LK sub-populations showed comparable differentiation potential to the classical ones.
Article
Clinical Neurology
Tsun-Haw Toh, Nur Adilah Abdul-Aziz, Mohd Azly Yahya, Khean-Jin Goh, Ee-Chin Loh, David Paul Capelle, Nortina Shahrizaila
Summary: The study aimed to develop a simple model based on clinical and NMUS parameters to predict ALS disease progression, with good discriminatory ability and sensitivity/specificity in differentiating fast progressors using a score of 3. This model has the potential to serve as a surrogate biomarker for disease progression in ALS patients.
CLINICAL NEUROPHYSIOLOGY
(2021)
Article
Agriculture, Dairy & Animal Science
K. C. Horvath, A. N. Brocious, E. K. Miller-Cushon
Summary: The study aimed to investigate the impact of including molasses-based liquid feed in a mixed diet on feed sorting behavior in calves. Results showed calves preferred starter over hay and the addition of molasses slightly reduced sorting post-weaning. There was no significant difference in intake or daily gain among different feed presentation treatments.
JOURNAL OF DAIRY SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Guo Li, Ya-Hui Zhou, Hong-Fu Li, Yuan-Ming Zhang
Summary: Despite the advantages of multi-parent populations (MPPs) in genetic dissection and crop breeding, it is challenging to detect small-effect quantitative trait loci (QTL) in certain MPP populations. To tackle this issue, a multi-locus linear mixed model method called mppQTL is proposed. The method involves two steps: genome-wide scanning using a single-locus linear mixed model, and multi-locus analysis using an expectation-maximization empirical Bayes algorithm. The new method shows improved power, reduced false positive rate, and more accurate estimation compared to existing methods, and it successfully identified additional known genes in real dataset analysis. This study provides an effective approach for detecting small-effect QTLs in any MPPs.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Computer Science, Artificial Intelligence
Zhiwen Cheng, Haohao Song, Tiezhu Chang, Jiquan Wang
Summary: Reducers play a crucial role in mechanical transmission field and reducing material consumption has significant economic and social benefits. This study proposes an improved mixed-coded hybrid firefly algorithm to solve the mixed-discrete SSCGR problem and the experimental results demonstrate that the proposed algorithm outperforms other improved algorithms in terms of solution quality.
EXPERT SYSTEMS WITH APPLICATIONS
(2022)
Article
Multidisciplinary Sciences
Julio Diaz Caballero, Rachel M. Wheatley, Natalia Kapel, Carla Lopez-Causape, Thomas van der Schalk, Angus Quinn, Liam P. Shaw, Lois Ogunlana, Claudia Recanatini, Basil Britto Xavier, Leen Timbermont, Jan Kluytmans, Alexey Ruzin, Mark Esser, Surbhi Malhotra-Kumar, Antonio Oliver, R. Craig MacLean
Summary: Here, the authors extensively characterized patients colonized with different strains of Pseudomonas aeruginosa to study the impact of within-host diversity on the development of antibiotic resistance. They found that mixed strain populations are common in this pathogen, and resistance rapidly evolves through selection for pre-existing resistant strains in patients colonized with multiple strains. In contrast, resistance sporadically evolves in patients colonized with a single strain due to selection for novel resistance mutations. Furthermore, the study suggests that within-host diversity can also lead to the loss of resistance in the absence of antibiotic treatment.
NATURE COMMUNICATIONS
(2023)
Article
Automation & Control Systems
Hien Le, Pouria Ramazi
Summary: In anti-coordination social contexts, individuals who are best responders tend to reach an equilibrium state, while imitators are more likely to experience perpetual fluctuations. Real-world populations often consist of a mixture of best responders and imitators, and research suggests that the population almost surely reaches an equilibrium if it is capable of admitting one.
IEEE TRANSACTIONS ON AUTOMATIC CONTROL
(2021)
Article
Mathematics, Applied
Carlos Jerez-Hanckes, Isabel A. Martinez avila, Irina Pettersson, Volodymyr Rybalko
Summary: The work focuses on the multiscale modeling of a nerve fascicle of myelinated axons. A rigorous derivation of a macroscopic bidomain model describing the behavior of the electric potential in the fascicle based on the FitzHugh-Nagumo membrane dynamics is presented. The approach is based on the combination of two-scale convergence machinery and the method of monotone operators.
NONLINEAR ANALYSIS-REAL WORLD APPLICATIONS
(2023)
Article
Mathematics, Applied
Qianming Ding, Ya Jia
Summary: This paper investigates the effects of ion channel blocks, temperature, and ion channel noise on the propagation of action potentials along a myelinated axon using an improved Hodgkin-Huxley chain network model. The study reveals minimum coupling intensity threshold and maximum tolerance temperature threshold in the chain network, which can be altered by ion channel blockage. The simulated optimum membrane size correlates with the area range of feline thalamocortical relay cells observed in biological experiments.
Article
Mechanics
Debasish Chaudhuri, Abhishek Dhar
Summary: By studying active Brownian particles within a harmonic trap, the exact time dependence of moments can be evaluated using a Laplace transform approach. The kurtosis of displacement is calculated, showing differences between active steady state properties and equilibrium Gaussian form. The kurtosis increases with activity to asymptotic saturation, but varies non-monotonically with trap-stiffness, capturing observed active-to-passive re-entrant behavior.
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT
(2021)
Article
Materials Science, Multidisciplinary
Amir Shee, Subhadip Ghosh, Debasish Chaudhuri
Summary: This study investigates the dynamics of a rigid filament in a motor protein assay under external loading, as well as the effects of motor protein activity and quantity on system stability. Through stability analysis and numerical simulations, it was found that the system exhibits different behaviors under different loading conditions, including transitions from stability to instability and the emergence of stable limit cycle oscillations.
Article
Mechanics
Amir Shee, Debasish Chaudhuri
Summary: The motion of an active Brownian particle with speed fluctuations in d-dimensions is considered, along with translational and orientational diffusion, using an Ornstein-Uhlenbeck process for active speed generation. An exact time dependence evaluation of all relevant dynamical moments is conducted using a Laplace transform approach based on the Fokker-Planck equation method. Analytical predictions are compared with numerical simulations to analyze dynamical crossovers, demonstrating positive and negative deviations in kurtosis of displacement at intermediate times based on the dominance of speed and orientational fluctuations.
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT
(2022)
Article
Physics, Multidisciplinary
Subhashree Subhrasmita Khuntia, Abhishek Chaudhuri, Debasish Chaudhuri
Summary: Active walker models are effective in understanding the evolution of biological systems. This study proposes a simple model of a random walker, investigates the influence of the walker on its local environment and the subsequent motion of the walker. The study also explores the structural transitions of the walker's trajectory and the dynamics of the mean-squared displacement.
Article
Chemistry, Physical
Chitrak Karan, Debasish Chaudhuri
Summary: We study the motion of a bio-filament driven collectively by motor proteins that irreversibly attach to a substrate and undergo stochastic attachment-detachment with the filament, resulting in a directed force. By using analytical theory and numerical simulations, we investigate the dependence of the mean directed force and force correlations on the parameters of individual motor proteins. The effective Langevin description for the filament motion provides information on mean-squared displacement, asymptotic diffusion constant, and mobility, allowing the determination of an effective temperature. We further demonstrate how competition between motor protein extensions generates a self-load on the filament, which can be described in terms of the effective temperature and affects the filament motion.
Article
Physics, Fluids & Plasmas
Amir Shee, Debasish Chaudhuri
Summary: This study investigates the influence of active speed fluctuations on the dynamics of a one-dimensional active Brownian particle. Exact expressions for time-dependent dynamical moments are obtained using the Laplace transform of the Fokker-Planck equation. The results demonstrate multiple dynamical crossovers and dynamical anisotropy-induced subdiffusive scaling and changes in kurtosis. Numerical simulations also reveal two crossovers in the probability distribution of particle displacement, controlled by speed fluctuations and persistence.
Meeting Abstract
Biophysics
Amit Kumar, Pinaki Swain, Bela Mulder, Debasish Chaudhuri
BIOPHYSICAL JOURNAL
(2022)
Article
Chemistry, Physical
Subhadip Ghosh, Sashideep Gutti, Debasish Chaudhuri
Summary: This study focuses on the active force generation by an actin-myosin cortex coupled to a cell membrane, and its role in cell deformation, environmental response, motility, and division. Through the coupled evolution of fields, linear stability analysis, and numerical calculations, the researchers reveal the instability of a spherical membrane towards pattern formation, localized pulsation, and running pulsation between poles when activity overcomes stabilizing factors like surface tension and bending rigidity.
Article
Chemistry, Physical
Amir Shee, Nisha Gupta, Abhishek Chaudhuri, Debasish Chaudhuri
Summary: This study investigates the movement of an extensible semiflexible filament in two dimensions under the influence of motor proteins explicitly represented as active harmonic linkers. The filament undergoes a phase transition from an open chain to a spiral conformation, with reentrant behavior observed in both active extension and turnover processes. The orientational dynamics captures the rotation of spirals, with correlation time decaying with activity following a power law.
Article
Chemistry, Physical
Shubhendu Shekhar Khali, Dipanjan Chakraborty, Debasish Chaudhuri
Summary: The detailed numerical simulation study of a two-dimensional system interacting via the Weeks-Chandler-Anderson potential reveals a two-step melting process: continuous melting from solid to hexatic phase, followed by a first-order melting from hexatic to liquid phase. The solid-hexatic melting is consistent with the Berezinskii-Kosterlitz-Thouless-Halperin-Nelson-Young (BKTHNY) scenario while the hexatic-liquid melting displays defect-strings formed at the interfaces.
Article
Chemistry, Physical
Amir Shee, Abhishek Dhar, Debasish Chaudhuri
Article
Chemistry, Physical
Shubhendu Shekhar Khali, Dipanjan Chakraborty, Debasish Chaudhuri
Article
Chemistry, Physical
Biplab Bhattacherjee, Debasish Chaudhuri
Article
Chemistry, Physical
Pinaki Swain, Bela M. Mulder, Debasish Chaudhuri
Article
Physics, Fluids & Plasmas
Nisha Gupta, Abhishek Chaudhuri, Debasish Chaudhuri