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Article ; Online: Effect of Force Field Resolution on Membrane Mechanical Response and Mechanoporation Damage under Deformation Simulations.

Vo, Anh T N / Murphy, Michael A / Phan, Phong K / Prabhu, Raj K / Stone, Tonya W

2023 Volume 66, Issue 4, Page(s) 865–875

Abstract: Damage induced by transient disruption and mechanoporation in an intact cell membrane is a vital nanoscale biomechanical mechanism that critically affects cell viability. To complement experimental studies of mechanical membrane damage and disruption, ... ...

Abstract	Damage induced by transient disruption and mechanoporation in an intact cell membrane is a vital nanoscale biomechanical mechanism that critically affects cell viability. To complement experimental studies of mechanical membrane damage and disruption, molecular dynamics (MD) simulations have been performed at different force field resolutions, each of which follows different parameterization strategies and thus may influence the properties and dynamics of membrane systems. Therefore, the current study performed tensile deformation MD simulations of bilayer membranes using all-atom (AA), united-atom (UA), and coarse-grained Martini (CG-M) models to investigate how the damage biomechanics differs across atomistic and coarse-grained (CG) simulations. The mechanical response and mechanoporation damage were qualitatively similar but quantitatively different in the three models, including some progressive changes based on the coarse-graining level. The membranes yielded and reached ultimate strength at similar strains; however, the coarser systems exhibited lower average yield stresses and failure strains. The average failure strain in the UA model was approximately 7% lower than the AA, and the CG-M was 20% lower than UA and 27% lower than AA. The CG systems also nucleated a higher number of pores and larger pores, which resulted in higher damage during the deformation process. Overall, the study provides insight on the impact of force field-a critical factor in modeling biomolecular systems and their interactions-in inspecting membrane mechanosensitive responses and serves as a reference for justifying the appropriate force field for future studies of more complex membranes and more diverse biomolecular assemblies.
MeSH term(s)	Molecular Dynamics Simulation ; Cell Membrane/chemistry ; Lipid Bilayers/chemistry ; Biomechanical Phenomena ; Tensile Strength ; Stress, Mechanical
Chemical Substances	Lipid Bilayers
Language	English
Publishing date	2023-04-04
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1193057-3
ISSN	1559-0305 ; 1073-6085
ISSN (online)	1559-0305
ISSN	1073-6085
DOI	10.1007/s12033-023-00726-x
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Book ; Online: UIT-Saviors at MEDVQA-GI 2023

Thai, Triet M. / Vo, Anh T. / Tieu, Hao K. / Bui, Linh N. P. / Nguyen, Thien T. B.

Improving Multimodal Learning with Image Enhancement for Gastrointestinal Visual Question Answering

2023

Abstract: In recent years, artificial intelligence has played an important role in medicine and disease diagnosis, with many applications to be mentioned, one of which is Medical Visual Question Answering (MedVQA). By combining computer vision and natural language ...

Abstract	In recent years, artificial intelligence has played an important role in medicine and disease diagnosis, with many applications to be mentioned, one of which is Medical Visual Question Answering (MedVQA). By combining computer vision and natural language processing, MedVQA systems can assist experts in extracting relevant information from medical image based on a given question and providing precise diagnostic answers. The ImageCLEFmed-MEDVQA-GI-2023 challenge carried out visual question answering task in the gastrointestinal domain, which includes gastroscopy and colonoscopy images. Our team approached Task 1 of the challenge by proposing a multimodal learning method with image enhancement to improve the VQA performance on gastrointestinal images. The multimodal architecture is set up with BERT encoder and different pre-trained vision models based on convolutional neural network (CNN) and Transformer architecture for features extraction from question and endoscopy image. The result of this study highlights the dominance of Transformer-based vision models over the CNNs and demonstrates the effectiveness of the image enhancement process, with six out of the eight vision models achieving better F1-Score. Our best method, which takes advantages of BERT+BEiT fusion and image enhancement, achieves up to 87.25% accuracy and 91.85% F1-Score on the development test set, while also producing good result on the private test set with accuracy of 82.01%. Comment: ImageCLEF2023
Keywords	Computer Science - Computer Vision and Pattern Recognition ; Computer Science - Human-Computer Interaction
Subject code	006
Publishing date	2023-07-06
Publishing country	us
Document type	Book ; Online
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Article ; Online: Oxidation of Hydrogen Sulfide to Polysulfide and Thiosulfate by a Carbon Nanozyme: Therapeutic Implications with an Emphasis on Down Syndrome.

Derry, Paul J / Liopo, Anton V / Mouli, Karthik / McHugh, Emily A / Vo, Anh T T / McKelvey, Ann / Suva, Larry J / Wu, Gang / Gao, Yan / Olson, Kenneth R / Tour, James M / Kent, Thomas A

Advanced materials (Deerfield Beach, Fla.)

2023 Volume 36, Issue 10, Page(s) e2211241

Abstract: Hydrogen sulfide ( ... ...

Abstract	Hydrogen sulfide (H
MeSH term(s)	Humans ; Animals ; Mice ; Hydrogen Sulfide ; Thiosulfates/metabolism ; Carbon ; Down Syndrome/drug therapy ; Sulfides ; Oxidation-Reduction ; Polyethylene Glycols/metabolism
Chemical Substances	polysulfide (9080-49-3) ; Hydrogen Sulfide (YY9FVM7NSN) ; Thiosulfates ; Carbon (7440-44-0) ; Sulfides ; Polyethylene Glycols (3WJQ0SDW1A)
Language	English
Publishing date	2023-07-23
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1474949-X
ISSN	1521-4095 ; 0935-9648
ISSN (online)	1521-4095
ISSN	0935-9648
DOI	10.1002/adma.202211241
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Article ; Online: Assessing HIV and overdose risks for people who use drugs exposed to compulsory drug abstinence programs (CDAP): A systematic review and meta-analysis.

Vo, Anh T / Magana, Christopher / Hickman, Matthew / Borquez, Annick / Beletsky, Leo / Martin, Natasha K / Cepeda, Javier A

The International journal on drug policy

2021 Volume 96, Page(s) 103401

Abstract: Background: Evidence supports integrating drug use treatment, harm reduction, and HIV prevention services to address dual epidemics of drug use disorders and HIV. These dual epidemics have spurred a rise in legally-enforced compulsory drug abstinence ... ...

Abstract	Background: Evidence supports integrating drug use treatment, harm reduction, and HIV prevention services to address dual epidemics of drug use disorders and HIV. These dual epidemics have spurred a rise in legally-enforced compulsory drug abstinence programs (CDAP), despite limited evidence on its effectiveness. We conducted a systematic review and meta-analysis evaluating the association between CDAP exposure and HIV and overdose-related risk. Methods: We searched PubMed, EBSCOhost and Sociological Abstracts for studies that contained an individual-level association between CDAP exposure and related HIV or overdose risks, with no date restrictions. Meta-analyses were conducted on data abstracted from eligible studies, using pooled random-effects models and I-squared statistics. We assessed quality of the studies across 14 criteria for observational studies. Results: Out of 2,226 abstracts screened, we included 8 studies (5253 individuals/776 events) across China, Mexico, Thailand, Norway, and the United States. All but two were cross-sectional analyses, limiting strength of observed associations. In the two studies that reported association between CDAP and HIV seropositivity or receptive syringe sharing, findings were inconsistent and did not indicate that those with exposure to CDAP had increased odds of HIV or syringe sharing. However, we found the odds of experiencing non-fatal overdose in lifetime and in the last 6-12 months were 2.02 (95% CI 0.22 - 18.86, p = 0.16) to 3.67 times higher (95% CI 0.21 - 62.88, p = 0.39), respectively, among those with CDAP exposure than those without. Conclusion: Research assessing HIV risk associated with CDAP is scant and inconclusive, while evidence of robust associations between CDAP and overdose risk continues to mount. More rigorous, longitudinal studies are needed to evaluate the causal relationships between CDAP and these health outcomes. Aside from the growing evidence base on collateral harms, ethical considerations dictate that voluntary, evidence-based drug treatment should be prioritized to address the drivers of excess morbidity and mortality among people who use drugs.
MeSH term(s)	Cross-Sectional Studies ; Drug Overdose/epidemiology ; HIV Infections/epidemiology ; HIV Infections/prevention & control ; Humans ; Needle Sharing ; Pharmaceutical Preparations ; Substance Abuse, Intravenous
Chemical Substances	Pharmaceutical Preparations
Language	English
Publishing date	2021-08-11
Publishing country	Netherlands
Document type	Journal Article ; Meta-Analysis ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Systematic Review
ZDB-ID	2010000-0
ISSN	1873-4758 ; 0955-3959
ISSN (online)	1873-4758
ISSN	0955-3959
DOI	10.1016/j.drugpo.2021.103401
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Article ; Online: Pharmacologic improvement of CFTR function rapidly decreases sputum pathogen density, but lung infections generally persist.

Nichols, David P / Morgan, Sarah J / Skalland, Michelle / Vo, Anh T / Van Dalfsen, Jill M / Singh, Sachinkumar Bp / Ni, Wendy / Hoffman, Lucas R / McGeer, Kailee / Heltshe, Sonya L / Clancy, John P / Rowe, Steven M / Jorth, Peter / Singh, Pradeep K

The Journal of clinical investigation

2023 Volume 133, Issue 10

Abstract: BackgroundLung infections are among the most consequential manifestations of cystic fibrosis (CF) and are associated with reduced lung function and shortened survival. Drugs called CF transmembrane conductance regulator (CFTR) modulators improve activity ...

Abstract	BackgroundLung infections are among the most consequential manifestations of cystic fibrosis (CF) and are associated with reduced lung function and shortened survival. Drugs called CF transmembrane conductance regulator (CFTR) modulators improve activity of dysfunctional CFTR channels, which is the physiological defect causing CF. However, it is unclear how improved CFTR activity affects CF lung infections.MethodsWe performed a prospective, multicenter, observational study to measure the effect of the newest and most effective CFTR modulator, elexacaftor/tezacaftor/ivacaftor (ETI), on CF lung infections. We studied sputum from 236 people with CF during their first 6 months of ETI using bacterial cultures, PCR, and sequencing.ResultsMean sputum densities of Staphylococcus aureus, Pseudomonas aeruginosa, Stenotrophomonas maltophilia, Achromobacter spp., and Burkholderia spp. decreased by 2-3 log10 CFU/mL after 1 month of ETI. However, most participants remained culture positive for the pathogens cultured from their sputum before starting ETI. In those becoming culture negative after ETI, the pathogens present before treatment were often still detectable by PCR months after sputum converted to culture negative. Sequence-based analyses confirmed large reductions in CF pathogen genera, but other bacteria detected in sputum were largely unchanged. ETI treatment increased average sputum bacterial diversity and produced consistent shifts in sputum bacterial composition. However, these changes were caused by ETI-mediated decreases in CF pathogen abundance rather than changes in other bacteria.ConclusionsTreatment with the most effective CFTR modulator currently available produced large and rapid reductions in traditional CF pathogens in sputum, but most participants remain infected with the pathogens present before modulator treatment.Trial RegistrationClinicalTrials.gov NCT04038047.FundingThe Cystic Fibrosis Foundation and the NIH.
MeSH term(s)	Humans ; Cystic Fibrosis/drug therapy ; Cystic Fibrosis/genetics ; Cystic Fibrosis/complications ; Cystic Fibrosis Transmembrane Conductance Regulator/genetics ; Sputum/microbiology ; Prospective Studies ; Pneumonia ; Bacteria ; Benzodioxoles/pharmacology ; Benzodioxoles/therapeutic use ; Lung ; Mutation
Chemical Substances	Cystic Fibrosis Transmembrane Conductance Regulator (126880-72-6) ; Benzodioxoles ; CFTR protein, human
Language	English
Publishing date	2023-05-15
Publishing country	United States
Document type	Observational Study ; Multicenter Study ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	3067-3
ISSN	1558-8238 ; 0021-9738
ISSN (online)	1558-8238
ISSN	0021-9738
DOI	10.1172/JCI167957
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Article ; Online: Genome Capture Sequencing Selectively Enriches Bacterial DNA and Enables Genome-Wide Measurement of Intrastrain Genetic Diversity in Human Infections.

Hayden, Hillary S / Joshi, Snehal / Radey, Matthew C / Vo, Anh T / Forsberg, Cara / Morgan, Sarah J / Waalkes, Adam / Holmes, Elizabeth A / Klee, Sara M / Emond, Mary J / Singh, Pradeep K / Salipante, Stephen J

mBio

2022 Volume 13, Issue 5, Page(s) e0142422

Abstract: Within-host evolution produces genetic diversity in bacterial strains that cause chronic human infections. However, the lack of facile methods to measure bacterial allelic variation in clinical samples has limited understanding of intrastrain diversity's ...

Abstract	Within-host evolution produces genetic diversity in bacterial strains that cause chronic human infections. However, the lack of facile methods to measure bacterial allelic variation in clinical samples has limited understanding of intrastrain diversity's effects on disease. Here, we report a new method termed genome capture sequencing (GenCap-Seq) in which users inexpensively make hybridization probes from genomic DNA or PCR amplicons to selectively enrich and sequence targeted bacterial DNA from clinical samples containing abundant human or nontarget bacterial DNA. GenCap-Seq enables accurate measurement of allele frequencies over targeted regions and is scalable from specific genes to entire genomes, including the strain-specific accessory genome. The method is effective with samples in which target DNA is rare and inhibitory and DNA-degrading substances are abundant, including human sputum and feces. In proof-of-principle experiments, we used GenCap-Seq to investigate the responses of diversified Pseudomonas aeruginosa populations chronically infecting the lungs of people with cystic fibrosis to
MeSH term(s)	Humans ; DNA, Bacterial/genetics ; Pseudomonas aeruginosa/genetics ; Cystic Fibrosis/microbiology ; Genome, Bacterial ; Sequence Analysis, DNA ; Anti-Bacterial Agents/pharmacology ; Genetic Variation ; Pseudomonas Infections/microbiology
Chemical Substances	DNA, Bacterial ; Anti-Bacterial Agents
Language	English
Publishing date	2022-09-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2557172-2
ISSN	2150-7511 ; 2161-2129
ISSN (online)	2150-7511
ISSN	2161-2129
DOI	10.1128/mbio.01424-22
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Article: Minimally invasive mitral valve replacement and concomitant Cox-Maze IV procedure using radiofrequency energy in situs inversus totalis: A case report.

Pham, Chuong V / Nguyen, Dinh H / Vo, Anh T / Nguyen, Trang T / Phan, Ly H / Nguyen, Bac H

International journal of surgery case reports

2020 Volume 73, Page(s) 285–288

Abstract: Introduction: Situs inversus totalis (SIT) is an uncommon congenital condition characterized by total transposition of abdominal and thoracic viscera. Performing minimally invasive cardiac surgery on individuals with SIT requires different surgical ... ...

Abstract	Introduction: Situs inversus totalis (SIT) is an uncommon congenital condition characterized by total transposition of abdominal and thoracic viscera. Performing minimally invasive cardiac surgery on individuals with SIT requires different surgical planning because of the unfamiliar positions of the heart and great vessels. Presentation of case: A 52-year-old female was admitted to our center with palpitations and dyspnea on exertion. Chest X-ray showed dextrocardia. Echocardiography and chest computerized tomography (CT) revealed SIT with severe rheumatic mitral valve disease. Discussion: Pre-operative three-dimensional (3D) chest CT reconstruction was helpful in surgical planning and management of cardiopulmonary bypass (CPB). Mitral valve replacement and concomitant atrial fibrillation (AF) ablation using radiofrequency (RF) energy via left mini-thoracotomy was successfully performed on the patient. Conclusion: Minimally invasive approach can be safely and effectively employed in patients with SIT.
Language	English
Publishing date	2020-07-18
Publishing country	Netherlands
Document type	Case Reports
ISSN	2210-2612
ISSN	2210-2612
DOI	10.1016/j.ijscr.2020.07.053
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Article: Minimally invasive aortic valve reconstruction with autologous pericardium: how we do it.

Nguyen, Dinh H / Vo, Anh T / Nguyen, Trang T / Le, Khoi M / Truong, Binh Q / Nguyen, Bac H

Annals of cardiothoracic surgery

2019 Volume 8, Issue 3, Page(s) 444–446

Language	English
Publishing date	2019-06-12
Publishing country	China
Document type	Editorial
ZDB-ID	2713627-9
ISSN	2304-1021 ; 2225-319X
ISSN (online)	2304-1021
ISSN	2225-319X
DOI	10.21037/acs.2019.05.12
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Article ; Online: Infants with cystic fibrosis have altered fecal functional capacities with potential clinical and metabolic consequences.

Eng, Alexander / Hayden, Hillary S / Pope, Christopher E / Brittnacher, Mitchell J / Vo, Anh T / Weiss, Eli J / Hager, Kyle R / Leung, Daniel H / Heltshe, Sonya L / Raftery, Daniel / Miller, Samuel I / Hoffman, Lucas R / Borenstein, Elhanan

BMC microbiology

2021 Volume 21, Issue 1, Page(s) 247

Abstract: Background: Infants with cystic fibrosis (CF) suffer from gastrointestinal (GI) complications, including pancreatic insufficiency and intestinal inflammation, which have been associated with impaired nutrition and growth. Recent evidence identified ... ...

Abstract	Background: Infants with cystic fibrosis (CF) suffer from gastrointestinal (GI) complications, including pancreatic insufficiency and intestinal inflammation, which have been associated with impaired nutrition and growth. Recent evidence identified altered fecal microbiota taxonomic compositions in infants with CF relative to healthy infants that were characterized by differences in the abundances of taxa associated with GI health and nutrition. Furthermore, these taxonomic differences were more pronounced in low length infants with CF, suggesting a potential link to linear growth failure. We hypothesized that these differences would entail shifts in the microbiome's functional capacities that could contribute to inflammation and nutritional failure in infants with CF. Results: To test this hypothesis, we compared fecal microbial metagenomic content between healthy infants and infants with CF, supplemented with an analysis of fecal metabolomes in infants with CF. We identified notable differences in CF fecal microbial functional capacities, including metabolic and environmental response functions, compared to healthy infants that intensified during the first year of life. A machine learning-based longitudinal metagenomic age analysis of healthy and CF fecal metagenomic functional profiles further demonstrated that these differences are characterized by a CF-associated delay in the development of these functional capacities. Moreover, we found metagenomic differences in functions related to metabolism among infants with CF that were associated with diet and antibiotic exposure, and identified several taxa as potential drivers of these functional differences. An integrated metagenomic and metabolomic analysis further revealed that abundances of several fecal GI metabolites important for nutrient absorption, including three bile acids, correlated with specific microbes in infants with CF. Conclusions: Our results highlight several metagenomic and metabolomic factors, including bile acids and other microbial metabolites, that may impact nutrition, growth, and GI health in infants with CF. These factors could serve as promising avenues for novel microbiome-based therapeutics to improve health outcomes in these infants.
MeSH term(s)	Cystic Fibrosis/complications ; Cystic Fibrosis/microbiology ; Dysbiosis/complications ; Feces/microbiology ; Gastrointestinal Diseases/etiology ; Gastrointestinal Diseases/microbiology ; Gastrointestinal Diseases/physiopathology ; Humans ; Infant ; Longitudinal Studies ; Metabolome ; Metabolomics/methods ; Metagenome ; Prospective Studies
Language	English
Publishing date	2021-09-15
Publishing country	England
Document type	Journal Article ; Observational Study ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2041505-9
ISSN	1471-2180 ; 1471-2180
ISSN (online)	1471-2180
ISSN	1471-2180
DOI	10.1186/s12866-021-02305-z
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Article ; Online: Acute retrograde type A intramural hematoma treated with an endovascular approach.

Vo, Anh T / Le, Khoi M / Nguyen, Trang T / Vu, Thanh T / Vu, Thien T / Nguyen, Dinh H

Asian cardiovascular & thoracic annals

2018 Volume 26, Issue 4, Page(s) 308–310

Abstract: A 71-year-old woman was admitted with sudden onset of severe chest pain. Computed tomography demonstrated acute type A intramural hematoma with an entry tear in the first part of the descending aorta. The patient refused an operation. Endovascular repair ...

Abstract	A 71-year-old woman was admitted with sudden onset of severe chest pain. Computed tomography demonstrated acute type A intramural hematoma with an entry tear in the first part of the descending aorta. The patient refused an operation. Endovascular repair was performed to prevent conversion to a typical dissection of the ascending aorta. At the 1-year follow-up, computed tomography showed total resolution of the intramural hematoma.
MeSH term(s)	Acute Disease ; Aged ; Aneurysm, Dissecting/diagnostic imaging ; Aneurysm, Dissecting/surgery ; Aortic Aneurysm, Thoracic/diagnostic imaging ; Aortic Aneurysm, Thoracic/surgery ; Aortography/methods ; Blood Vessel Prosthesis Implantation ; Computed Tomography Angiography ; Endovascular Procedures ; Female ; Hematoma/diagnostic imaging ; Hematoma/surgery ; Humans ; Time Factors ; Treatment Outcome
Language	English
Publishing date	2018-03-27
Publishing country	England
Document type	Case Reports ; Journal Article
ZDB-ID	1400468-9
ISSN	1816-5370 ; 0218-4923
ISSN (online)	1816-5370
ISSN	0218-4923
DOI	10.1177/0218492318766791
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