BayesAge: A maximum likelihood algorithm to predict epigenetic age.

Introduction: DNA methylation, specifically the formation of 5-methylcytosine at the C5 position of cytosine, undergoes reproducible changes as organisms age, establishing it as a significant biomarker in aging studies. Epigenetic clocks, which integrate methylation patterns to predict age, often employ linear models based on penalized regression, yet they encounter challenges in handling missing data, count-based bisulfite sequence data, and interpretation. Methods: To address these limitations, we introduce BayesAge, an extension of the scAge methodology originally designed for single-cell DNA methylation analysis. BayesAge employs maximum likelihood estimation (MLE) for age inference, models count data using binomial distributions, and incorporates LOWESS smoothing to capture non-linear methylation-age dynamics. This approach is tailored for bulk bisulfite sequencing datasets. Results: BayesAge demonstrates superior performance compared to scAge. Notably, its age residuals exhibit no age association, offering a less biased representation of epigenetic age variation across populations. Furthermore, BayesAge facilitates the estimation of error bounds on age inference. When applied to down-sampled data, BayesAge achieves a higher coefficient of determination between predicted and actual ages compared to both scAge and penalized regression. Discussion: BayesAge presents a promising advancement in epigenetic age prediction, addressing key challenges encountered by existing models. By integrating robust statistical techniques and tailored methodologies for count-based data, BayesAge offers improved accuracy and interpretability in predicting age from bulk bisulfite sequencing datasets. Its ability to estimate error bounds enhances the reliability of age inference, thereby contributing to a more comprehensive understanding of epigenetic aging processes.

Harnessing Biomaterials to Amplify Immunity in Aged Mice through T Memory Stem Cells.

The durability of a protective immune response generated by a vaccine depends on its ability to induce long-term T cell immunity, which tends to decline in aging populations. The longest protection appears to arise from T memory stem cells (TMSCs) that confer high expandability and effector functions when challenged. Here we engineered artificial antigen presenting cells (aAPC) with optimized size, stiffness and activation signals to induce human and mouse CD8+ TMSCs in vitro. This platform was optimized as a vaccine booster of TMSCs (Vax-T) with prolonged release of small-molecule blockade of the glycogen synthase kinase-3ß together with target antigens. By using SARS-CoV-2 antigen as a model, we show that a single injection of Vax-T induces durable antigen-specific CD8+ TMSCs in young and aged mice, and generates humoral responses at a level stronger than or similar to soluble vaccines. This Vax-T approach can boost long-term immunity to fight infectious diseases, cancer, and other diseases.

Nuclear induction line shape: Non-Markovian diffusion with boundaries.

The dynamics of viscoelastic fluids are governed by a memory function, essential yet challenging to compute, especially when diffusion faces boundary restrictions. We propose a computational method that captures memory effects by analyzing the time-correlation function of the pressure tensor, a viscosity indicator, through the Stokes-Einstein equation's analytic continuation into the Laplace domain. We integrate this equation with molecular dynamics simulations to derive necessary parameters. Our approach computes nuclear magnetic resonance (NMR) line shapes using a generalized diffusion coefficient, accounting for temperature and confinement geometry. This method directly links the memory function with thermal transport parameters, facilitating accurate NMR signal computation for non-Markovian fluids in confined geometries.

Dual-Signal Chemical Exchange Saturation Transfer (Dusi-CEST): An Efficient Strategy for Visualizing Drug Delivery Monitoring in Living Cells.

We report a dual-signal chemical exchange saturation transfer (Dusi-CEST) strategy for drug delivery and detection in living cells. The two signals can be detected by operators in complex environments. This strategy is demonstrated on a cucurbit[6]uril (CB[6]) nanoparticle probe, as an example. The CB[6] probe is equipped with two kinds of hydrophobic cavities: one is found inside CB[6] itself, whereas the other exists inside the nanoparticle. When the probe is dispersed in aqueous solution as part of a hyperpolarized 129Xe NMR experiment, two signals appear at two different chemical shifts (100 and 200 ppm). These two resonances correspond to the NMR signals of 129Xe in the two different cavities. Upon loading with hydrophobic drugs, such as paclitaxel, for intracellular drug delivery, the two resonances undergo significant changes upon drug loading and cargo release, giving rise to a metric enabling the assessment of drug delivery success. The simultaneous change of Dusi-CEST likes a mobile phone that can receive both LTE and Wi-Fi signals, which can help reduce the occurrence of false positives and false negatives in complex biological environments and help improve the accuracy and sensitivity of single-shot detection.

Transarterial Embolization of Simple Pulmonary Arteriovenous Malformations: Long-Term Outcomes of 0.018-Inch Coils versus Vascular Plugs.

PURPOSE: To compare the safety, effectiveness, and persistence rates of 0.018-inch coils with those of Amplatzer vascular plugs (AVPs; Abbott Vascular, Abbott Park, Illinois) for the treatment of pulmonary arteriovenous malformations (PAVMs) in response to a growing concern that 0.018-inch coil embolization would increase the long-term persistence rate. MATERIALS AND METHODS: This is a retrospective, single-center study of a database (2002-2020) of 633 PAVM embolizations. Complex PAVMs and those not embolized with 0.018-inch coils or plugs were excluded. PAVM embolization material was classified into 4 groups: (a) 0.018-inch nonfibered coils (NFCs), (b) 0.018-inch fibered coils (FCs), (c) NFCs and FCs, or (d) plugs. Persistence was defined as flow through the PAVM on digital subtraction angiography (DSA) or as <30% diameter reduction of the aneurysmal sac on unenhanced computed tomography (CT). Kaplan-Meier analysis and Cox regression were used to assess PAVM's persistence-free survival. RESULTS: A total of 312 PAVM embolizations with NFCs (43 PAVMs), FCs (127 PAVMs), NFCs and FCs (12 PAVMs), or plugs (130 PAVMs) in 109 patients (28% men; mean age = 49 years) were included. All PAVM embolizations were technically successful without any major adverse events. PAVM persistence-free survival rates at 10 years' follow-up were 40.8% versus 44.7% in the NFC and FC groups (P = .22) and 47.3% versus 81.0% in the 0.018-inch coil (NFC or FC) and plug groups (P < .0001), respectively. There were 0.43 (79/182) and 0.08 (10/130) re-embolization procedures per PAVM in the 0.018-inch coil and plug groups, respectively (P < .001). CONCLUSIONS: PAVM embolization with 0.018-inch coils was safe, but persistence rate with PAVM embolization was significantly higher than that with plugs, with no significant differences between FCs and NFCs.

Nuclear induction lineshape modeling via hybrid SDE and MD approach.

The temperature dependence of the nuclear free induction decay in the presence of a magnetic-field gradient was found to exhibit motional narrowing in gases upon heating, a behavior that is opposite to that observed in liquids. This has led to the revision of the theoretical framework to include a more detailed description of particle trajectories since decoherence mechanisms depend on histories. In the case of free diffusion and single components, the new model yields the correct temperature trends. The inclusion of boundaries in the current formalism is not straightforward. We present a hybrid SDE-MD (stochastic differential equation - molecular dynamics) approach whereby MD is used to compute an effective viscosity and the latter is fed to the SDE to predict the line shape. The theory is in agreement with the experiments. This two-scale approach, which bridges the gap between short (molecular collisions) and long (nuclear induction) timescales, paves the way for the modeling of complex environments with boundaries, mixtures of chemical species, and intermolecular potentials.

Conducting polymer-based scaffolds for neuronal tissue engineering.

Neuronal tissue engineering has immense potential for treating neurological disorders and facilitating nerve regeneration. Conducting polymers (CPs) have emerged as a promising class of materials owing to their unique electrical conductivity and biocompatibility. CPs, such as poly(3,4-ethylenedioxythiophene) (PEDOT), poly(3-hexylthiophene) (P3HT), polypyrrole (PPy), and polyaniline (PANi), have been extensively explored for their ability to provide electrical cues to neural cells. These polymers are widely used in various forms, including porous scaffolds, hydrogels, and nanofibers, and offer an ideal platform for promoting cell adhesion, differentiation, and axonal outgrowth. CP-based scaffolds can also serve as drug delivery systems, enabling localized and controlled release of neurotrophic factors and therapeutic agents to enhance neural regeneration and repair. CP-based scaffolds have demonstrated improved neural regeneration, both in vitro and in vivo, for treating spinal cord and peripheral nerve injuries. In this review, we discuss synthesis and scaffold processing methods for CPs and their applications in neuronal tissue regeneration. We focused on a detailed literature review of the central and peripheral nervous systems.

In Science Journals.

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Systemic enhancement of antitumour immunity by peritumourally implanted immunomodulatory macroporous scaffolds.

A tumour microenvironment abundant in regulatory T (Treg) cells aids solid tumours to evade clearance by effector T cells. Systemic strategies to suppress Treg cells or to augment immunity can elicit autoimmune side effects, cytokine storms and other toxicities. Here we report the design, fabrication and therapeutic performance of a biodegradable macroporous scaffold, implanted peritumourally, that releases a small-molecule inhibitor of transforming growth factor ß to suppress Treg cells, chemokines to attract effector T cells and antibodies to stimulate them. In two mouse models of aggressive tumours, the implant boosted the recruitment and activation of effector T cells into the tumour and depleted it of Treg cells, which resulted in an 'immunological abscopal effect' on distant metastases and in the establishment of long-term memory that impeded tumour recurrence. We also show that the scaffold can be used to deliver tumour-antigen-specific T cells into the tumour. Peritumourally implanted immunomodulatory scaffolds may represent a general strategy to enhance T-cell immunity and avoid the toxicities of systemic therapies.

Intramyocardial hemorrhage drives fatty degeneration of infarcted myocardium.

Sudden blockage of arteries supplying the heart muscle contributes to millions of heart attacks (myocardial infarction, MI) around the world. Although re-opening these arteries (reperfusion) saves MI patients from immediate death, approximately 50% of these patients go on to develop chronic heart failure (CHF) and die within a 5-year period; however, why some patients accelerate towards CHF while others do not remains unclear. Here we show, using large animal models of reperfused MI, that intramyocardial hemorrhage - the most damaging form of reperfusion injury (evident in nearly 40% of reperfused ST-elevation MI patients) - drives delayed infarct healing and is centrally responsible for continuous fatty degeneration of the infarcted myocardium contributing to adverse remodeling of the heart. Specifically, we show that the fatty degeneration of the hemorrhagic MI zone stems from iron-induced macrophage activation, lipid peroxidation, foam cell formation, ceroid production, foam cell apoptosis and iron recycling. We also demonstrate that timely reduction of iron within the hemorrhagic MI zone reduces fatty infiltration and directs the heart towards favorable remodeling. Collectively, our findings elucidate why some, but not all, MIs are destined to CHF and help define a potential therapeutic strategy to mitigate post-MI CHF independent of MI size.

In Science Journals.

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Management of Pancreatico-duodenal arterio-venous malformation.

PURPOSE: To describe the interventional management and clinical outcome of pancreatico-duodenal arterio-venous malformations (PDAVMs). MATERIAL AND METHODS: Seven patients presenting a PDAVM (6 women, 1 male; mean age: 61) were retrospectively reviewed. Technical, clinical success and complications of embolization and surgical management of symptomatic PDAVMs were assessed. Technical success was defined as a complete occlusion of the PDAVM and clinical success as no clinical symptom or recurrence during follow-up. Patients with asymptomatic PDAVMs were followed clinically, by Doppler ultrasound and CT-angiography. RESULTS: Mean follow-up time was 69 months (15-180). Five symptomatic patients presented with upper gastrointestinal bleeding (n=3), ascites (n=1), and abdominal pain (n=1). Two patients were asymptomatic. The PDAVMs were classified as follow: Yakes I (1), IIIa (2), IIIb (3) and IV (1). Five symptomatic patients were treated with 9 embolization sessions with arterial approach (onyx®, glue, coils) in 7 and venous approach in 2 (plugs, coils, covered stents, STS foam and onyx®). Technical success of embolization was 60% (3/5). Devascularization was incomplete for 2 Yakes IIIB patients. Clinical success of embolization was estimated at 80% (4/5) as one patient required additional surgery (Whipple) because of persistent bleeding. One splenic vein thrombosis was treated successfully by mechanical thrombectomy and heparin. No recurrence occurred during follow-up. No progression was documented in asymptomatic patients. CONCLUSION: Embolization of symptomatic PDAVMs is effective and surgery should be performed in second intention. Complete devascularization is more difficult to obtain in Yakes III PDAVM.

Ultrasensitive molecular building block for biothiol NMR detection at picomolar concentrations.

Magnetic resonance imaging (MRI) provides structural and functional information, but it did not probe chemistry. Chemical information could help improve specificity of detection. Herein, we introduce a general method based on a modular design to construct a molecular building block Xe probe to help image intracellular biothiols (glutathione (GSH), cysteine (Cys) and homocysteine (Hcy)), the abnormal content of which is related to various diseases. This molecular building block possesses a high signal-to-noise ratio and no background signal effects. Its detection threshold was 100 pM, which enabled detection of intracellular biothiols in live cells. The construction strategy can be easily extended to the detection of any other biomolecule or biomarker. This modular design strategy promotes efficiency of development of low-cost multifunctional probes that can be combined with other readout parameters, such as optical readouts, to complement 129Xe MRI to usher in new capabilities for molecular imaging.

Mapping Cell Viability Quantitatively and Independently From Cell Density in 3D Gels Noninvasively.

OBJECTIVE: In biomanufacturing there is a need for quantitative methods to map cell viability and density inside 3D bioreactors to assess health and proliferation over time. Recently, noninvasive MRI readouts of cell density have been achieved. However, the ratio of live to dead cells was not varied. Herein we present an approach for measuring the viability of cells embedded in a hydrogel independently from cell density to map cell number and health. METHODS: Independent quantification of cell viability and density was achieved by calibrating the 1H magnetization transfer- (MT) and diffusion-weighted NMR signals to samples of known cell density and viability using a multivariate approach. Maps of cell viability and density were generated by weighting NMR images by these parameters post-calibration. RESULTS: Using this method, the limits of detection (LODs) of total cell density and viable cell density were found to be 3.88 ×108 cells · mL -1· Hz -1/2 and 2.36 ×109 viable cells · mL -1· Hz -1/2 respectively. CONCLUSION: This mapping technique provides a noninvasive means of visualizing cell viability and number density within optically opaque bioreactors. SIGNIFICANCE: We anticipate that such nondestructive readouts will provide valuable feedback for monitoring and controlling cell populations in bioreactors.

Safety and Efficacy of Paclitaxel-Eluting Balloon Angioplasty for Dysfunctional Hemodialysis Access: A randomized trial Comparing with Angioplasty Alone.

PURPOSE: To assess whether angioplasty of hemodialysis access (HA) stenosis with a drug-coated balloon (DCB) would prevent restenosis in comparison with plain-balloon percutaneous transluminal angioplasty (PTA). MATERIALS AND METHODS: This prospective randomized clinical trial enrolled 120 patients with dysfunctional arteriovenous fistulae (n = 109) and grafts (n = 11), due to a ≥50% stenosis between March 2014 and April 2018. All patients underwent high-pressure balloon angioplasty and were then randomized to either DCB (n = 60) or PTA (n = 60). Patients were followed-up for 1 year, and angiography was performed 6 months after angioplasty. The primary endpoint was the late lumen loss (LLL) at 6 months. Secondary endpoints included other angiographic parameters at 6 months and HA failures, adverse event, and mortality at 12 months. Continuous variables were compared with a Student t-test, and Kaplan-Meier curves were used for freedom from HA failure and for mortality. RESULTS: LLL in the DCB and in the PTA group were 0.64 mm ± 1.20 and 1.13 mm ± 1.51, respectively (P = .082, adjusted P = .0498). DCB was associated with lower percentage stenosis (54.2% ± 19.3 vs 61.7% ± 18.2; P = .047) and binary restenosis ≥50% (56.5% vs 81.1%; P = .009) than PTA. The number of HA failures after 12 months was lower for DCB than for PTA (45% vs 66.7%; P = .017). Mortality at 12 months was 10% and 8.3% in the DCB and PTA groups, respectively (P = .75). CONCLUSIONS: Despite LLL improvement that failed to reach statistical significance, this study demonstrated decreased incidence and severity of restenosis with DCB compared with PTA to treat dysfunctional HA.

Eye Lens Dosimetry in Interventional Radiology: Assessment With Dedicated Hp(3) Dosimeters.

PURPOSE: To quantify eye lens dose in interventional radiology and assess whether neck dosimeter is a good surrogate to evaluate eye lens dosimetry. METHODS: Radiation exposure was prospectively measured in 9 interventional radiologists between May and October 2017. Standard Hp(0,07) thermoluminescent dosimeters (TLDs) were worn at the neck outside the lead apron, and 2 dedicated eye lens Hp(3) TLDs were placed just above the eyes, one midline and another at the outer edge of the left eye. Correlations between eye lens and neck TLD doses were assessed with Pearson coefficient, and linear regression was used to predict eye lens dose from neck TLD values. RESULTS: Eye lens dose without eye protection was 0.18 ± 0.11 (mean ± standard deviation; 0.08-0.41) mSv per workday and 35.3 ± 6.6 mSv (16.3-82.9) annually (200 workdays/year). Five (56%) radiologists exceeded the 20 mSv annual eye lens dose limit. Eye lens doses from left and central TLDs were 12.46 ± 3.02 and 9.29 ± 3.38 mSv, respectively (P = .027). Mean eye lens (left and central) and neck TLD doses were 10.87 ± 2.67 and 16.56 ± 5.67 mSv, respectively (P = .008). Pearson correlation coefficient between both eye lens TLD and between mean eye lens TLD and neck TLD doses were 0.91 and 0.92, respectively. Average of eye lens dose was 0.0179 + (0.5971 × neck dose). CONCLUSION: Full-time interventional radiologists are likely to suffer from deterministic radiation effects to the eye lens, especially on the left side. Neck TLD significantly overestimates eye lens dose. However, eye lens doses are highly correlated with neck doses and may be predicted from the neck TLD values.

Damaged lung gas exchange function of discharged COVID-19 patients detected by hyperpolarized 129Xe MRI.

The recovery process of COVID-19 patients is unclear. Some recovered patients complain of continued shortness of breath. Vasculopathy has been reported in COVID-19, stressing the importance of probing pulmonary microstructure and function at the alveolar-capillary interface. While computed tomography (CT) detects structural abnormalities, little is known about the impact of disease on lung function. 129Xe magnetic resonance imaging (MRI) is a technique uniquely capable of assessing ventilation, microstructure, and gas exchange. Using 129Xe MRI, we found that COVID-19 patients show a higher rate of ventilation defects (5.9% versus 3.7%), unchanged microstructure, and longer gas-blood exchange time (43.5 ms versus 32.5 ms) compared with healthy individuals. These findings suggest that regional ventilation and alveolar airspace dimensions are relatively normal around the time of discharge, while gas-blood exchange function is diminished. This study establishes the feasibility of localized lung function measurements in COVID-19 patients and their potential usefulness as a supplement to structural imaging.

Augmenting T-cell responses to tumors by in situ nanomanufacturing.

Recent innovations in immunoregulatory treatments have demonstrated both the impressive potential and vital role of T cells in fighting cancer. These treatments come at a cost, with systemic side effects including life-threatening autoimmunity and immune dysregulation the norm. Here, we developed an approach to locally synthesize immune therapies and in this way, avoid systemic toxicity. Rather than just encapsulating cytokines, we endowed our nanoparticles with transcriptional and translational machinery to make cytokines locally, in situ, and on demand (activated by light). We demonstrated the capabilities of these particles in vitro and in vivo, in a mouse model of melanoma, and showed that tumor-infiltrating T cells were more highly activated in the context of these "microfactory" particles that make the synthetic cytokine.