keyword
https://read.qxmd.com/read/38547104/the-effect-of-cooperator-recognition-on-competition-among-clones-in-spatially-structured-microbial-communities
#21
JOURNAL ARTICLE
Adrienna Bingham, Aparajita Sur, Leah B Shaw, Helen A Murphy
In spatially structured microbial communities, clonal growth of stationary cells passively generates clusters of related individuals. This can lead to stable cooperation without the need for recognition mechanisms. However, recent research suggests that some biofilm-forming microbes may have mechanisms of kin recognition. To explore this unexpected observation, we studied the effects of different types of cooperation in a microbial colony using spatially explicit, agent-based simulations of two interacting strains...
2024: PloS One
https://read.qxmd.com/read/38547090/optimized-treatment-parameter-by-computer-simulation-for-high-intensity-focused-ultrasound-treatment-of-uterine-adenomyosis-short-term-and-long-term-results
#22
JOURNAL ARTICLE
Jae Seok Bae, Jae Young Lee, Hyun Hoon Chung, Maria Lee, Myung Jae Jeon, Hoon Kim, Hee Seung Kim, Kidong Kim, Chang-Soon Lee, Keonho Son, Joon Koo Han
This study aimed to investigate the efficacy and safety of using optimized parameters obtained by computer simulation for ultrasound-guided high-intensity focused ultrasound (HIFU) treatment of uterine adenomyosis in comparison with conventional parameters. We retrospectively assessed a single-institution, prospective study that was registered at Clinical Research Information Service (CRiS) of Republic of Korea (KCT0003586). Sixty-six female participants (median age: 44 years) with focal uterine adenomyosis were prospectively enrolled...
2024: PloS One
https://read.qxmd.com/read/38547079/developing-medical-simulations-for-opioid-overdose-response-training-a-qualitative-analysis-of-narratives-from-responders-to-overdoses
#23
JOURNAL ARTICLE
G Franklin Edwards, Cassandra Mierisch, Brock Mutcheson, Allison Strauss, Keel Coleman, Kimberly Horn, Sarah Henrickson Parker
Medical simulation offers a controlled environment for studying challenging clinical care situations that are difficult to observe directly. Overdose education and naloxone distribution (OEND) programs aim to train potential rescuers in responding to opioid overdoses, but assessing rescuer performance in real-life situations before emergency medical services arrive is exceedingly complex. There is an opportunity to incorporate individuals with firsthand experience in treating out-of-hospital overdoses into the development of simulation scenarios...
2024: PloS One
https://read.qxmd.com/read/38547060/substrate-recruitment-via-eif2%C3%AE-enhances-catalytic-efficiency-of-a-holophosphatase-that-terminates-the-integrated-stress-response
#24
JOURNAL ARTICLE
Yahui Yan, Maithili Shetty, Heather P Harding, Ginto George, Alisa Zyryanova, Katherine Labbé, Amirhossein Mafi, Qi Hao, Carmela Sidrauski, David Ron
Dephosphorylation of pSer51 of the α subunit of translation initiation factor 2 (eIF2αP ) terminates signaling in the integrated stress response (ISR). A trimeric mammalian holophosphatase comprised of a protein phosphatase 1 (PP1) catalytic subunit, the conserved C-terminally located ~70 amino acid core of a substrate-specific regulatory subunit (PPP1R15A/GADD34 or PPP1R15B/CReP) and G-actin (an essential cofactor) efficiently dephosphorylate eIF2αP in vitro. Unlike their viral or invertebrate counterparts, with whom they share the conserved 70 residue core, the mammalian PPP1R15s are large proteins of more than 600 residues...
April 2, 2024: Proceedings of the National Academy of Sciences of the United States of America
https://read.qxmd.com/read/38547059/mechanical-quenching-phenomenon-in-diamond
#25
JOURNAL ARTICLE
Zhengping Su, Yu Duan, Yusong Tian, Shukuan Guo, Penghui Li, Lin Wang, Yeqiang Bu, Anmin Nie, Hongtao Wang, Yongjun Tian, Wei Yang
The structure of dislocation cores, the fundamental knowledge on crystal plasticity, remains largely unexplored in covalent crystals. Here, we conducted atomically resolved characterizations of dislocation core structures in a plastically deformed diamond anvil cell tip that was unloaded from an exceptionally high pressure of 360 GPa. Our observations unveiled a series of nonequilibrium dislocation cores that deviate from the commonly accepted "five-seven-membered ring" dislocation core model found in FCC-structured covalent crystals...
April 2, 2024: Proceedings of the National Academy of Sciences of the United States of America
https://read.qxmd.com/read/38547028/self-consistent-field-approach-for-the-variational-quantum-eigensolver-orbital-optimization-goes-adaptive
#26
JOURNAL ARTICLE
Aaron Fitzpatrick, Anton Nykänen, N Walter Talarico, Alessandro Lunghi, Sabrina Maniscalco, Guillermo García-Pérez, Stefan Knecht
We present a self-consistent field (SCF) approach within the adaptive derivative-assembled problem-tailored ansatz variational quantum eigensolver (ADAPT-VQE) framework for efficient quantum simulations of chemical systems on near-term quantum computers. To this end, our ADAPT-VQE-SCF approach combines the idea of generating an ansatz with a small number of parameters, resulting in shallow-depth quantum circuits with a direct minimization of an energy expression that is correct to second order with respect to changes in the molecular orbital basis...
March 28, 2024: Journal of Physical Chemistry. A
https://read.qxmd.com/read/38547014/operando-nuclear-magnetic-resonance-nmr-studies-of-a-trickle-bed-reactor-using-d-t2-correlations
#27
JOURNAL ARTICLE
Amy Sparks, Lynn Gladden, Colin Brennan, Mick Mantle
Catalytic conversions in fine-chemical and pharmaceutical production are increasingly performed in trickle-bed rectors. Optimisation of these processes is usually based on end of pipe measurement made at specific residence times. This process is both time-consuming and the data sometimes challenging to interpret. In the present work, operando nuclear magnetic resonance (NMR) techniques both at the scale of the whole bed (global) and spatially resolved within the bed (local) are used to gain new insights into the catalytic conversion process under reaction conditions...
March 27, 2024: Chimia
https://read.qxmd.com/read/38546997/adaptive-neural-cooperative-control-of-multirobot-systems-with-input-quantization
#28
JOURNAL ARTICLE
Tiedong Ma, Feng Hu, Xiaojie Su, Chao Shen, Xiaoyu Ma
This article develops the adaptive neural cooperative control scheme for a group of mobile robots with a limited sensing range in presence of input quantization by a dynamic surface control technique. First, to make the controller design feasible, the original robotic system is transformed into a new fully actuated system using a transverse function. Then, taking into consideration the effects of a hysteresis quantizer, an adaptive neural cooperative controller is developed based on the universal approximation property of the radial basis function neural networks and the connectivity preservation strategy...
March 28, 2024: IEEE Transactions on Cybernetics
https://read.qxmd.com/read/38546996/tackling-noisy-labels-with-network-parameter-additive-decomposition
#29
JOURNAL ARTICLE
Jingyi Wang, Xiaobo Xia, Long Lan, Xinghao Wu, Jun Yu, Wenjing Yang, Bo Han, Tongliang Liu
Given data with noisy labels, over-parameterized deep networks suffer overfitting mislabeled data, resulting in poor generalization. The memorization effect of deep networks shows that although the networks have the ability to memorize all noisy data, they would first memorize clean training data, and then gradually memorize mislabeled training data. A simple and effective method that exploits the memorization effect to combat noisy labels is early stopping. However, early stopping cannot distinguish the memorization of clean data and mislabeled data, resulting in the network still inevitably overfitting mislabeled data in the early training stage...
March 28, 2024: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://read.qxmd.com/read/38546995/impact-of-background-foreground-and-manipulated-object-rendering-on-egocentric-depth-perception-in-virtual-and-augmented-indoor-environments
#30
JOURNAL ARTICLE
Matthew McQuaigue, Kalpathi Subramanian, Paula Goolkasian, Zachary Wartell
This research investigated how the similarity of the rendering parameters of background and foreground objects affected egocentric depth perception in indoor virtual and augmented environments. We refer to the similarity of the rendering parameters as visual 'congruence'. Study participants manipulated the depth of a sphere to match the depth of a designated target peg. In the first experiment, the sphere and peg were both virtual, while in the second experiment, the sphere is virtual and the peg is real. In both experiments, depth perception accuracy was found to depend on the levels of realism and congruence between the sphere, pegs, and background...
March 28, 2024: IEEE Transactions on Visualization and Computer Graphics
https://read.qxmd.com/read/38546993/robust-fine-grained-visual-recognition-with-neighbor-attention-label-correction
#31
JOURNAL ARTICLE
Shunan Mao, Shiliang Zhang
Existing deep learning methods for fine-grained visual recognition often rely on large-scale, well-annotated training data. Obtaining fine-grained annotations in the wild typically requires concentration and expertise, such as fine category annotation for species recognition, instance annotation for person re-identification (re-id) and dense annotation for segmentation, which inevitably leads to label noise. This paper aims to tackle label noise in deep model training for fine-grained visual recognition. We propose a Neighbor-Attention Label Correction (NALC) model to correct labels during the training stage...
March 28, 2024: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://read.qxmd.com/read/38546991/trainable-delays-in-time-delay-neural-networks-for-learning-delayed-dynamics
#32
JOURNAL ARTICLE
Xunbi A Ji, Gabor Orosz
In this article, the connection between time delay systems and time delay neural networks (TDNNs) is presented from a continuous-time perspective. TDNNs are utilized to learn the nonlinear dynamics of time delay systems from trajectory data. The concept of TDNN with trainable delay (TrTDNN) is established, and training algorithms are constructed for learning the time delays and the nonlinearities simultaneously. The proposed techniques are tested on learning the dynamics of autonomous systems from simulation data and on learning the delayed longitudinal dynamics of a connected automated vehicle (CAV) from real experimental data...
March 28, 2024: IEEE Transactions on Neural Networks and Learning Systems
https://read.qxmd.com/read/38546987/concatenated-nanopore-dna-codes
#33
JOURNAL ARTICLE
Adrian Vidal, V B Wijekoon, Emanuele Viterbo
In nanopore sequencers, single-stranded DNA molecules (or k-mers) enter a small opening in a membrane called a nanopore and modulate the ionic current through the pore, producing a channel output in the form of a noisy piecewise constant signal. An important problem in DNA-based data storage is finding a set of k-mers, i.e. a DNA code, that is robust against noisy sample duplication introduced by nanopore sequencers. Good DNA codes should contain as many k-mers as possible that produce distinguishable current signals (squiggles) as measured by the sequencer...
April 2024: IEEE Transactions on Nanobioscience
https://read.qxmd.com/read/38546977/multiscale-computational-framework-for-the-liquid-liquid-phase-separation-of-intrinsically-disordered-proteins
#34
JOURNAL ARTICLE
Kalindu S Fernando, Ghodsiehsadat Jahanmir, Ilona C Unarta, Ying Chau
The reversible assembly of intrinsically disordered proteins (IDPs) to form membraneless organelles (MLOs) is a fundamental process involved in the spatiotemporal regulation in living cells. MLOs formed via liquid-liquid phase separation (LLPS) serve as molecule-enhancing hubs to regulate cell functions. Owing to the complexity and dynamic nature of the protein assembly via a network of weak inter- and intra-molecular interactions, it is challenging to describe and predict the LLPS behavior. We have developed a multiscale computational model for IDPs, using the fused in sarcoma (FUS) protein and its variants as illustrative examples...
March 28, 2024: Langmuir: the ACS Journal of Surfaces and Colloids
https://read.qxmd.com/read/38546892/influence-of-degree-of-substitution-on-the-hydroxypropyl-%C3%AE-cyclodextrin-complexation-with-rifampicin-in-water-solution-a-molecular-simulation
#35
JOURNAL ARTICLE
Elena Alvira
CONTEXT: Hydroxypropyl-β-cyclodextrin (HPβCD) is one of the derivatized cyclodextrins most widely used as an excipient in the pharmaceutical industry, for its capacity to improve certain drugs properties. Different configurations of HPβCD are possible depending on the number and location of the 2-hydroxypropyl groups substituted on the glucose rings. Rifampicin has become the most commonly clinically used antibiotic against tuberculosis in recent years, despite its low solubility and variable bioavailability...
March 28, 2024: Journal of Molecular Modeling
https://read.qxmd.com/read/38546874/acetylation-of-c-myc-at-lysine-148-protects-neurons-after-ischemia
#36
JOURNAL ARTICLE
V V Guzenko, S S Bachurin, V A Dzreyan, A M Khaitin, Y N Kalyuzhnaya, S V Demyanenko
This study focuses on understanding the role of c-Myc, a cancer-associated transcription factor, in the penumbra following ischemic stroke. While its involvement in cell death and survival is recognized, its post-translational modifications, particularly acetylation, remain understudied in ischemia models. Investigating these modifications could have significant clinical implications for controlling c-Myc activity in the central nervous system. Although previous studies on c-Myc acetylation have been limited to non-neuronal cells, our research examines its expression in perifocal cells during stroke recovery to explore regulatory mechanisms via acetylation...
March 28, 2024: Neuromolecular Medicine
https://read.qxmd.com/read/38546840/physicochemical-compatibility-of-caffeine-citrate-and-caffeine-base-injections-with-parenteral-medications-used-in-neonatal-intensive-care-settings
#37
JOURNAL ARTICLE
D Thisuri N De Silva, Michael Petrovski, Tobias Strunk, Nabeelah Mukadam, Madhu Page-Sharp, Brioni R Moore, Kevin T Batty
PURPOSE: To investigate the physicochemical compatibility of caffeine citrate and caffeine base injections with 43 secondary intravenous (IV) drugs used in Neonatal Intensive Care Unit (NICU) settings. METHODS: Caffeine citrate (20 mg/mL or 10 mg/mL) or caffeine base injection (10 mg/mL) were mixed in a volume ratio of 1:1 with the secondary drug solution to simulate Y-site co-administration procedures in NICUs. Physical compatibility was evaluated based on visual observation for 2 h, against a black and white background and under polarised light, for changes in colour, precipitation, haze and evolution of gas...
March 28, 2024: European Journal of Clinical Pharmacology
https://read.qxmd.com/read/38546837/predicting-deamidation-and-isomerization-sites-in-therapeutic-antibodies-using-structure-based-in-silico-approaches
#38
JOURNAL ARTICLE
David Hoffmann, Joschka Bauer, Markus Kossner, Andrew Henry, Anne R Karow-Zwick, Giuseppe Licari
Asparagine (Asn) deamidation and aspartic acid (Asp) isomerization are common degradation pathways that affect the stability of therapeutic antibodies. These modifications can pose a significant challenge in the development of biopharmaceuticals. As such, the early engineering and selection of chemically stable monoclonal antibodies (mAbs) can substantially mitigate the risk of subsequent failure. In this study, we introduce a novel in silico approach for predicting deamidation and isomerization sites in therapeutic antibodies by analyzing the structural environment surrounding asparagine and aspartate residues...
2024: MAbs
https://read.qxmd.com/read/38546820/computational-investigation-of-the-covalent-inhibition-mechanism-of-bruton-s-tyrosine-kinase-by-ibrutinib
#39
JOURNAL ARTICLE
Angela M Barragan, Kyle Ghaby, Matthew P Pond, Benoît Roux
Covalent inhibitors represent a promising class of therapeutic compounds. Nonetheless, rationally designing covalent inhibitors to achieve a right balance between selectivity and reactivity remains extremely challenging. To better understand the covalent binding mechanism, a computational study is carried out using the irreversible covalent inhibitor of Bruton tyrosine kinase (BTK) ibrutinib as an example. A multi-μs classical molecular dynamics trajectory of the unlinked inhibitor is generated to explore the fluctuations of the compound associated with the kinase binding pocket...
March 28, 2024: Journal of Chemical Information and Modeling
https://read.qxmd.com/read/38546811/structure-based-multitargeted-docking-screening-pharmacokinetics-dft-and-dynamics-simulation-studies-reveal-mitoglitazone-as-a-potent-inhibitor-of-cellular-survival-and-stress-response-proteins-of-lung-cancer
#40
JOURNAL ARTICLE
Abdulkarim S Binshaya, Omar Saad Alkahtani, Fahad M Aldakheel, Ahmed Hjazi, Hassan H Almasoudi
Lung cancer is a disease in which lung cells grow abnormally and uncontrollably, and the cause of it is direct smoking, secondhand smoke, radon, asbestos, and certain chemicals. The worldwide leading cause of death is lung cancer, which is responsible for more than 1.8 million deaths yearly and is expected to rise to 2.2 million by 2030. The most common type of lung cancer is non-small cell lung cancer (NSCLC), which accounts for about 80% and small cell lung cancer (SCLC), which is more aggressive than NSCLC and is often diagnosed later and accounts for 20% of cases...
March 28, 2024: Medical Oncology
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