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Total 157 results found since Jan 2013.

DeepMHCI: An anchor position-aware deep interaction model for accurate MHC-I peptide binding affinity prediction
Bioinformatics. 2023 Sep 5:btad551. doi: 10.1093/bioinformatics/btad551. Online ahead of print.ABSTRACTMOTIVATION: Computationally predicting MHC-I peptide binding affinity is an important problem in immunological bioinformatics, which is also crucial for the identification of neoantigens for personalized therapeutic cancer vaccines. Recent cutting-edge deep learning-based methods for this problem cannot achieve satisfactory performance, especially for non-9-mer peptides. This is because such methods generate the input by simply concatenating the two given sequences: a peptide and (the pseudo sequence of) an MHC class I mo...
Source: Cancer Control - September 5, 2023 Category: Cancer & Oncology Authors: Wei Qu Ronghui You Hiroshi Mamitsuka Shanfeng Zhu Source Type: research

What does the historic settlement won by Henrietta Lacks ’s family mean for others?
Last week, the family of Henrietta Lacks settled its lawsuit against the huge biotechnology company Thermo Fisher Scientific over its claim that the company had been “unjustly enriched” by its use of her cells. Lacks was a Black woman who died of cervical cancer in 1951, soon after a doctor took a sample from her tumor without her knowledge or consent and created an immortal cell line, HeLa. No financial payments or other terms of the settlement were disclosed, and no judge ruled on the fundamentals of the unusual claim. But some have nevertheless hailed it as precedent setting. And the family ’ s la...
Source: Science of Aging Knowledge Environment - August 7, 2023 Category: Geriatrics Source Type: research

Fight Aging! Newsletter, July 17th 2023
In conclusion, the longevity-associated genotype of FLT1 may confer increased lifespan by protecting against mortality risk posed by hypertension. We suggest that FLT1 expression in individuals with longevity genotype boosts vascular endothelial resilience mechanisms to counteract hypertension-related stress in vital organs and tissues. Resistance Exercise Slows the Onset of Pathology in a Mouse Model of Alzheimer's Disease https://www.fightaging.org/archives/2023/07/resistance-exercise-slows-the-onset-of-pathology-in-a-mouse-model-of-alzheimers-disease/ With the caveat that mouse models of Alzheimer's...
Source: Fight Aging! - July 16, 2023 Category: Research Authors: Reason Tags: Newsletters Source Type: blogs

Steering and controlling evolution - from bioengineering to fighting pathogens
Nat Rev Genet. 2023 Jul 3. doi: 10.1038/s41576-023-00623-8. Online ahead of print.ABSTRACTControl interventions steer the evolution of molecules, viruses, microorganisms or other cells towards a desired outcome. Applications range from engineering biomolecules and synthetic organisms to drug, therapy and vaccine design against pathogens and cancer. In all these instances, a control system alters the eco-evolutionary trajectory of a target system, inducing new functions or suppressing escape evolution. Here, we synthesize the objectives, mechanisms and dynamics of eco-evolutionary control in different biological systems. We...
Source: Cancer Control - July 3, 2023 Category: Cancer & Oncology Authors: Michael L ässig Ville Mustonen Armita Nourmohammad Source Type: research

Building a Digital Immune System
Credit: Courtesy of Dr. Tomas Helikar. The power of computer code has been a longtime fascination for Tomas Helikar, Ph.D., a professor of biochemistry at the University of Nebraska-Lincoln (UNL). In college, when he learned he could use that power to help researchers better understand biology and improve human health, Dr. Helikar knew he’d found his ideal career. Since then, he’s built a successful team of scientists studying the ways we can use mathematical models in biomedical research, such as creating a digital replica of the immune system that could predict how a patient will react to infectious microorganisms ...
Source: Biomedical Beat Blog - National Institute of General Medical Sciences - June 28, 2023 Category: Research Authors: Chrissa Chverchko Tags: Being a Scientist Cells Tools and Techniques Bioinformatics Computational Biology Cool Tools/Techniques Modeling Profiles Source Type: blogs

Fight Aging! Newsletter, June 26th 2023
This study explored the association between different cooking fuel types and the risk of cancer and all-cause mortality among seniors constructing Cox regression models. Data were obtained by linking waves of 6, 7, and 8 of the Chinese Longitudinal Healthy Longevity Survey, which included a total of 7,269 participants who were 65 years old and over. Cooking fuels were categorized as either biomass, fossil, or clean fuels. And the effects of switching cooking fuels on death risk were also investigated using Cox regression models. The results indicate that, compared with the users of clean fuels, individuals using bio...
Source: Fight Aging! - June 25, 2023 Category: Research Authors: Reason Tags: Newsletters Source Type: blogs

Researching COVID to Enhance Recovery (RECOVER) adult study protocol: Rationale, objectives, and design
The objectives of the Researching COVID to Enhance Recovery (RECOVER) Multi-site Observational Study of PASC in Adults (RECOVER-Adult) are to: (1) characterize PASC prevalence; (2) characterize the symptoms, organ dysfunction, natural history, and distinct phenotypes of PASC; (3) identify demographic, social and clinical risk factors for PASC onset and recovery; and (4) define the biological mechanisms underlying PASC pathogenesis.METHODS: RECOVER-Adult is a combined prospective/retrospective cohort currently planned to enroll 14,880 adults aged ≥18 years. Eligible participants either must meet WHO criteria for suspected...
Source: Cancer Control - June 23, 2023 Category: Cancer & Oncology Authors: Leora I Horwitz Tanayott Thaweethai Shari B Brosnahan Mine S Cicek Megan L Fitzgerald Jason D Goldman Rachel Hess S L Hodder Vanessa L Jacoby Michael R Jordan Jerry A Krishnan Adeyinka O Laiyemo Torri D Metz Lauren Nichols Rachel E Patzer Anisha Sekar Nor Source Type: research

Comprehensive landscape of the miRNA-regulated prognostic marker LAYN with immune infiltration and stemness in pan-cancer
CONCLUSION: This study elucidated the functional mechanisms of LAYN from a pan-cancer perspective and provided novel insights into cancer prognosis, metastasis, and immunotherapy. LAYN has the potential to become a new target of mRNA vaccines and molecular therapies in tumors.PMID:37335337 | DOI:10.1007/s00432-023-04986-7
Source: Cell Research - June 19, 2023 Category: Cytology Authors: Wang Jiawen Wang Jinfu Liu Jianyong Zhang Yaoguang Wang Jianye Source Type: research

Fight Aging! Newsletter, June 19th 2023
In conclusion, among Swedish middle-aged subjects, nearly two-thirds showed complete fatty degeneration of thymus on CT. Age-Related Dysfunction of Water Homeostasis https://www.fightaging.org/archives/2023/06/age-related-dysfunction-of-water-homeostasis/ Dehydration can be an issue in older people. As in every complex system in the body, the mechanisms by which hydration is regulated become dysfunctional with advancing age. Researchers here look at the brain region responsible for regulating some of the response to dehydration, cataloging altered gene expression in search of the more important mechani...
Source: Fight Aging! - June 18, 2023 Category: Research Authors: Reason Tags: Newsletters Source Type: blogs

Protocol for Classification Single-Cell PBMC Types from Pathological Samples Using Supervised Machine Learning
Methods Mol Biol. 2023;2673:53-67. doi: 10.1007/978-1-0716-3239-0_4.ABSTRACTPeripheral blood mononuclear cells (PBMC) are mixed subpopulations of blood cells composed of five cell types. PBMC are widely used in the study of the immune system, infectious diseases, cancer, and vaccine development. Single-cell transcriptomics (SCT) allows the labeling of cell types by gene expression patterns from biological samples. Classifying cells into cell types and states is essential for single-cell analyses, especially in the classification of diseases and the assessment of therapeutic interventions, and for many secondary analyses. M...
Source: Mol Biol Cell - May 31, 2023 Category: Molecular Biology Authors: Minjie Lyu Lin Xin Huan Jin Lou T Chitkushev Guanglan Zhang Derin B Keskin Vladimir Brusic Source Type: research

MITNet: a fusion transformer and convolutional neural network architecture approach for T-cell epitope prediction
Brief Bioinform. 2023 May 30:bbad202. doi: 10.1093/bib/bbad202. Online ahead of print.ABSTRACTClassifying epitopes is essential since they can be applied in various fields, including therapeutics, diagnostics and peptide-based vaccines. To determine the epitope or peptide against an antibody, epitope mapping with peptides is the most extensively used method. However, this method is more time-consuming and inefficient than using present methods. The ability to retrieve data on protein sequences through laboratory procedures has led to the development of computational models that predict epitope binding based on machine lear...
Source: Briefings in Bioinformatics - May 30, 2023 Category: Bioinformatics Authors: Jeremie Theddy Darmawan Jenq-Shiou Leu Cries Avian Nanda Rizqia Pradana Ratnasari Source Type: research

Fight Aging! Newsletter, April 24th 2023
In this study, researchers show that mice lacking a functional ATF4 gene show little to no loss of grip strength and treadmill performance into late life; it is quite an impressive effect size. Assessments of muscle biochemistry do show age-related declines, but to a lesser degree than the controls. How ATF4 knockout functions to produce this outcome is an interesting question. The researchers point out a range of possible downstream and upstream targets that have been implicated in the regulation of muscle growth, but it will clearly require further work to identify the important mechanisms involved. Aging slowly...
Source: Fight Aging! - April 23, 2023 Category: Research Authors: Reason Tags: Newsletters Source Type: blogs

Primary role of type I interferons for the induction of functionally optimal antigen-specific CD8 < sup > + < /sup > T cells in HIV infection
EBioMedicine. 2023 Apr 12;91:104557. doi: 10.1016/j.ebiom.2023.104557. Online ahead of print.ABSTRACTBACKGROUND: CD8+ T cells equipped with a full arsenal of antiviral effector functions are critical for effective immune control of HIV-1. It has nonetheless remained unclear how best to elicit such potent cellular immune responses in the context of immunotherapy or vaccination. HIV-2 has been associated with milder disease manifestations and more commonly elicits functionally replete virus-specific CD8+ T cell responses compared with HIV-1. We aimed to learn from this immunological dichotomy and to develop informed strategi...
Source: Cancer Control - April 14, 2023 Category: Cancer & Oncology Authors: Mariela P Cabral-Piccin Laura Papagno Xavier Lahaye Federico Perdomo-Celis Stevenn Volant Eoghann White Val érie Monceaux Sian Llewellyn-Lacey R émi Fromentin David A Price Nicolas Chomont Nicolas Manel Asier Saez-Cirion Victor Appay Source Type: research

Communication strategies to improve human papillomavirus (HPV) immunisation uptake among adolescents in sub-Saharan Africa: a systematic review and meta-analysis
Conclusion HPV vaccine communication is critical in ensuring that the community understands the importance of vaccination. The most effective communication strategies included those which educate the population about the HPV vaccine, facilitate decision-making on vaccine uptake and community ownership of the vaccination process immunisation. PROSPERO registration number CRD42021243683.
Source: BMJ Open - April 3, 2023 Category: General Medicine Authors: Oketch, S. Y., Ochomo, E. O., Orwa, J. A., Mayieka, L. M., Abdullahi, L. H. Tags: Open access, Communication Source Type: research