| 1. |
- Callaway, EM, et al.
(author)
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A multimodal cell census and atlas of the mammalian primary motor cortex
- 2021
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In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 598:7879, s. 86-102
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Journal article (peer-reviewed)abstract
- Here we report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcriptomes, morphological and electrophysiological properties and cellular resolution input–output mapping, integrated through cross-modal computational analysis. Our results advance the collective knowledge and understanding of brain cell-type organization1–5. First, our study reveals a unified molecular genetic landscape of cortical cell types that integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a consensus taxonomy of transcriptomic types and their hierarchical organization that is conserved from mouse to marmoset and human. Third, in situ single-cell transcriptomics provides a spatially resolved cell-type atlas of the motor cortex. Fourth, cross-modal analysis provides compelling evidence for the transcriptomic, epigenomic and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types. We further present an extensive genetic toolset for targeting glutamatergic neuron types towards linking their molecular and developmental identity to their circuit function. Together, our results establish a unifying and mechanistic framework of neuronal cell-type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties.
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| 2. |
- Ngo, Son Tung, et al.
(author)
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Distal Hydrophobic Loop Modulates the Copper Active Site and Reaction of AA13 Polysaccharide Monooxygenases
- 2022
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In: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 126:39, s. 7567-7578
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Journal article (peer-reviewed)abstract
- Polysaccharide monooxygenases (PMOs) use a type-2 copper center to activate O2 for the selective hydroxylation of one of the two C-H bonds of glycosidic linkages. Our electron paramagnetic resonance (EPR) analysis and molecular dynamics (MD) simulations suggest the unprecedented dynamic roles of the loop containing the residue G89 (G89 loop) on the active site structure and reaction cycle of starch-active PMOs (AA13 PMOs). In the Cu(II) state, the G89 loop could switch between an open and closed conformation, which is associated with the binding and dissociation of an aqueous ligand in the distal site, respectively. The conformation of the G89 loop influences the positioning of the copper center on the preferred substrate of AA13 PMOs. The dissociation of the distal ligand results in the bending of the T-shaped core of the Cu(II) active site, which could help facilitate its reduction to the active Cu(I) state. In the Cu(I) state, the G89 loop is in the closed conformation with a confined copper center, which could allow for efficient O2 binding. In addition, the G89 loop remains in the closed conformation in the Cu(II)-superoxo intermediate, which could prevent off-pathway superoxide release via exchange with the distal aqueous ligand. Finally, at the end of the reaction cycle, aqueous ligand binding to the distal site could switch the G89 loop to the open conformation and facilitate product release.
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| 3. |
- Pham, Thi Anh Mai, et al.
(author)
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Evaluation of screening algorithms to detect rectal colonization with carbapenemase-producing Enterobacterales in a resource-limited setting
- 2024
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In: JAC - Antimicrobial Resistance. - : OXFORD UNIV PRESS. - 2632-1823. ; 6:3
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Journal article (peer-reviewed)abstract
- Objectives To improve and rationalize the detection of carbapenemase-producing Enterobacterales (CPE) in rectal swabs in a high-prevalence and resource-constrained setting, addressing surveillance challenges typically encountered in laboratories with limited resources.Methods A point prevalence survey (PPS) was conducted on 15 August 2022, in a provincial children's hospital in northern Vietnam. Rectal swab samples of all admitted children were collected and plated on a selective medium for carbapenem-resistant Enterobacterales (CRE). Species identification and antimicrobial susceptibility testing (AST) were performed by MALDI-TOF, and VITEK2 XL and interpreted according to CLSI breakpoints (2022). Carbapenemases were detected by the carbapenem inactivation method (CIM) and quantitative real-time PCR (qRT-PCR).Results Rectal swab samples were obtained from 376 patients. Of 178 isolates growing on the CRE screening agar, 140 isolates were confirmed as Enterobacterales of which 118 (84.3%) isolates were resistant to meropenem and/or ertapenem. CIM and PCR showed that 90/118 (76.3%) were carbapenemase producers. Overall, 83/367 (22.6%) were colonized by CPE. Klebsiella pneumoniae, Escherichia coli and Enterobacter cloacae complex were the most common CPE detected, with NDM as the predominant carbapenemase (78/90; 86.7%). Phenotypic resistance to meropenem was the best predictor of CPE production (sensitivity 85.6%, specificity 100%) compared with ertapenem resistance (95.6% sensitivity, 36% specificity). CIM was 100% concordant with PCR in detecting carbapenemases.Conclusions These findings underscore the effectiveness of meropenem resistance as a robust indicator of the production of carbapenemases and the reliability of the CIM method to detect such carbapenemases in resource-limited settings where the performance of molecular methods is not possible.
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| 4. |
- Vu, Tung T., et al.
(author)
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Energy-Efficient Massive MIMO for Serving Multiple Federated Learning Groups
- 2021
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In: 2021 IEEE GLOBAL COMMUNICATIONS CONFERENCE (GLOBECOM). - : IEEE. - 9781728181042
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Conference paper (peer-reviewed)abstract
- With its privacy preservation and communication efficiency, federated learning (FL) has emerged as a learning framework that suits beyond SG and towards 6G systems. This work looks into a future scenario in which there are multiple groups with different learning purposes and participating in different FL processes. We give energy-efficient solutions to demonstrate that this scenario can be realistic. First, to ensure a stable operation of multiple FL processes over wireless channels, we propose to use a massive multiple-input multiple-output network to support the local and global FL training updates, and let the iterations of these FL processes be executed within the same large-scale coherence time. Then, we develop asynchronous and synchronous transmission protocols where these iterations are asynchronously and synchronously executed, respectively, using the downlink unicasting and conventional uplink transmission schemes. Zero-forcing processing is utilized for both uplink and downlink transmissions. Finally, we propose an algorithm that optimally allocates power and computation resources to save energy at both base station and user sides, while guaranteeing a given maximum execution time threshold of each FL iteration. Compared to the baseline schemes, the proposed algorithm significantly reduces the energy consumption, especially when the number of base station antennas is large.
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| 5. |
- Dinh, Canh T., et al.
(author)
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A New Look and Convergence Rate of Federated Multitask Learning With Laplacian Regularization
- 2023
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In: IEEE Transactions on Neural Networks and Learning Systems. - : IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC. - 2162-237X .- 2162-2388.
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Journal article (peer-reviewed)abstract
- Non-independent and identically distributed (non-IID) data distribution among clients is considered as the key factor that degrades the performance of federated learning (FL). Several approaches to handle non-IID data, such as personalized FL and federated multitask learning (FMTL), are of great interest to research communities. In this work, first, we formulate the FMTL problem using Laplacian regularization to explicitly leverage the relationships among the models of clients for multitask learning. Then, we introduce a new view of the FMTL problem, which, for the first time, shows that the formulated FMTL problem can be used for conventional FL and personalized FL. We also propose two algorithms FedU and decentralized FedU (dFedU) to solve the formulated FMTL problem in communication-centralized and decentralized schemes, respectively. Theoretically, we prove that the convergence rates of both algorithms achieve linear speedup for strongly convex and sublinear speedup of order 1/2 for nonconvex objectives. Experimentally, we show that our algorithms outperform the conventional algorithm FedAvg, FedProx, SCAFFOLD, and AFL in FL settings, MOCHA in FMTL settings, as well as pFedMe and Per-FedAvg in personalized FL settings.
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| 6. |
- Vu, Tung T., et al.
(author)
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Data Size-Aware Downlink Massive MIMO: A Session-Based Approach
- 2022
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In: IEEE Wireless Communications Letters. - : IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC. - 2162-2337 .- 2162-2345. ; 11:7, s. 1468-1472
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Journal article (peer-reviewed)abstract
- This letter considers the development of transmission strategies for the downlink of massive multiple-input multiple-output networks, with the objective of minimizing the completion time of the transmission. Specifically, we introduce a session-based scheme that splits time into sessions and allocates different rates in different sessions for the different users. In each session, one user is selected to complete its transmission and will not join subsequent sessions, which results in successively lower levels of interference when moving from one session to the next. An algorithm is developed to assign users and allocate transmit power that minimizes the completion time. Numerical results show that our proposed session-based scheme significantly outperforms conventional non-session-based schemes.
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