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1.
CJC Open ; 6(6): 798-804, 2024 Jun.
Article in English | MEDLINE | ID: mdl-39022171

ABSTRACT

Background: Inaccurate blood pressure (BP) classification results in inappropriate treatment. We tested whether machine learning (ML), using routine clinical data, can serve as a reliable alternative to ambulatory BP monitoring (ABPM) in classifying BP status. Methods: This study employed a multicentre approach involving 3 derivation cohorts from Glasgow, Gdansk, and Birmingham, and a fourth independent evaluation cohort. ML models were trained using office BP, ABPM, and clinical, laboratory, and demographic data, collected from patients referred for hypertension assessment. Seven ML algorithms were trained to classify patients into 5 groups, named as follows: Normal/Target; Hypertension-Masked; Normal/Target-White-Coat (WC); Hypertension-WC; and Hypertension. The 10-year cardiovascular outcomes and 27-year all-cause mortality risks were calculated for the ML-derived groups using the Cox proportional hazards model. Results: Overall, extreme gradient boosting (using XGBoost open source software) showed the highest area under the receiver operating characteristic curve of 0.85-0.88 across derivation cohorts, Glasgow (n = 923; 43% female; age 50.7 ± 16.3 years), Gdansk (n = 709; 46% female; age 54.4 ± 13 years), and Birmingham (n = 1222; 56% female; age 55.7 ± 14 years). But accuracy (0.57-0.72) and F1 (harmonic mean of precision and recall) scores (0.57-0.69) were low across the 3 patient cohorts. The evaluation cohort (n = 6213; 51% female; age 51.2 ± 10.8 years) indicated elevated 10-year risks of composite cardiovascular events in the Normal/Target-WC and the Hypertension-WC groups, with heightened 27-year all-cause mortality observed in all groups, except the Hypertension-Masked group, compared to the Normal/Target group. Conclusions: ML has limited potential in accurate BP classification when ABPM is unavailable. Larger studies including diverse patient groups and different resource settings are warranted.


Contexte: Les erreurs dans la classification des valeurs de la pression artérielle (PA) entraînent une inadéquation du traitement. Nous avons tâché de déterminer si l'apprentissage machine, à l'aide de données cliniques routinières, constituait une solution de rechange fiable à la surveillance ambulatoire de la PA pour définir le statut de la PA. Méthodologie: Cette étude a utilisé une approche multicentrique incluant trois cohortes de dérivation de Glasgow, Gdansk et Birmingham, et une quatrième cohorte d'évaluation indépendante. Les modèles d'apprentissage machine ont été développés en analysant les données démographiques, les valeurs de la PA mesurée au cabinet, les données relatives à la surveillance ambulatoire de la PA et aux épreuves de laboratoire recueillies auprès de patients adressés pour une évaluation de l'hypertension. Sept algorithmes d'apprentissage machine ont été appliqués pour classer les patients en cinq groupes : Normale/Cible; Hypertension-Masquée; Normal/Cible-Blouse blanche; Hypertension-Blouse blanche; Hypertension. Les événements cardiovasculaires sur 10 ans et le risque de mortalité toutes causes confondues sur 27 ans ont été calculés dans les groupes dérivés de l'apprentissage machine à l'aide d'un modèle de risques proportionnels de Cox. Résultats: D'une manière générale, l'amplification de gradient extrême (à l'aide du logiciel ouvert XGBoost) a mis en évidence l'aire sous la courbe de la fonction d'efficacité du récepteur (courbe ROC pour Receiver Operating Characteristic) la plus haute, soit 0,85 à 0,88, pour toutes les cohortes de dérivation : Glasgow (n = 923; 43 % de femmes; âge : 50,7 ± 16,3 ans); Gdansk (n = 709; 46 % de femmes; âge : 54,4 ± 13 ans); Birmingham (n = 1 222; 56 % de femmes; âge : 55,7 ± 14 ans). La précision (0,57 ­ 0,72) et le score F1 (moyenne harmonique de la précision et du rappel) (0,57 ­ 0,69) ont été faibles dans les trois cohortes de patients. La cohorte d'évaluation (n = 6 213; 51 % de femmes; âge : 51,2 ± 10,8 ans) a indiqué un risque d'événements cardiovasculaires composites sur 10 ans élevé dans les groupes Normale/Cible-Blouse blanche et Hypertension-Blouse blanche, tandis qu'une hausse de la mortalité toutes causes confondues sur 27 ans a été observée dans tous les groupes, sauf dans le groupe Hypertension-Masquée, comparativement au groupe Normale/Cible. Conclusions: Le potentiel d'exactitude de la classification de la PA à l'aide de l'apprentissage machine lorsque la surveillance ambulatoire de la PA n'est pas possible est limité. Des études de plus grande envergure portant sur des groupes de patients et des niveaux de ressources diversifiés s'imposent.

2.
Ann Thorac Surg ; 2024 Jun 29.
Article in English | MEDLINE | ID: mdl-38950725

ABSTRACT

BACKGROUND: We determined the safety of early discharge after coronary artery bypass grafting (CABG) in patients with uncomplicated postoperative courses and compared outcomes with routine discharge in a national cohort. We identified preoperative factors associated with readmission after early discharge after CABG. METHODS: The Nationwide Readmissions Database was queried to identify patients undergoing CABG from January 2016 to December 2018. Patients were stratified based on length of stay (LOS) as early (≤4 days) vs routine (5-10 days) discharge. Patients were excluded with hospital courses indicative of complicated stays (emergent procedures, LOS >10 days, discharge to extended care facility or with home health, index hospitalization mortality). Propensity score matching was performed to compare outcomes between cohorts. Multivariable logistic regression models were used to identify factors associated with readmission after early discharge. RESULTS: During the study period, 91,861 patients underwent CABG with an uncomplicated postoperative course (∼20% of CABG population). Of these, 31% (28,790 of 91,861) were discharged early, and 69% (63,071 of 91,861) were routinely discharged. After propensity score matching, patients discharged early had lower readmission rates at 30 days, 90 days, and up to 1 year (P < .001 for all). The index hospitalization cost was lower with early discharge ($26,676 vs $32,859; P < .001). Early discharge was associated with a lower incidence of nosocomial infection at the index hospitalization (0.17% vs 0.81%, P < .001) and readmission from infection (14.5% vs 18%, P = .016). CONCLUSIONS: Early discharge after uncomplicated CABG can be considered in a highly selective patient population. Early-discharge patients are readmitted less frequently than matched routine-discharge patients, with a lower incidence of readmission from infection. Appropriate postdischarge processes to facilitate early discharge after CABG should be further pursued.

3.
Tissue Cell ; 90: 102467, 2024 Jul 09.
Article in English | MEDLINE | ID: mdl-39053130

ABSTRACT

This review article will cover the recent developments in the new evolving field of Purkinje bioengineering and the development of human Purkinje networks. Recent work has progressed to the point of a methodological and systematic process to bioengineer Purkinje networks. This involves the development of 3D models based on human anatomy, followed by the development of tunable biomaterials, and strategies to reprogram stem cells to Purkinje cells. Subsequently, the reprogrammed cells and the biomaterials are coupled to bioengineer Purkinje networks, which are then tested using a small animal injury model. In this article, we discuss this process as a whole and then each step separately. We then describe potential applications of bioengineered Purkinje networks and challenges in the field that need to be overcome to move this field forward. Although the field of Purkinje bioengineering is new and in a state of infancy, it holds tremendous potential, both for therapeutic applications and to develop tools that can be used for disease modeling.

4.
Neurol India ; 72(3): 615-619, 2024 May 01.
Article in English | MEDLINE | ID: mdl-39041982

ABSTRACT

BACKGROUND: Extraparenchymal neurocysticercosis (NCC) commonly presents with symptoms of raised intracranial pressure such as headache, nausea, vomiting, or delirium. Intraventricular NCC is frequently associated with obstructive hydrocephalus as well as recurrent inflammatory cascade leading to chronic meningitis. OBJECTIVE: The aim of this study was to report the novel use and benefit of B cell depleting therapy in a case of treatment-refractory cysticercal meningoencephalitis. CASE: In this article, we report about a young male with intraventricular NCC, who had recurrent meningitis (with encephalitis) and kept relapsing despite multiple cerebrospinal fluid diversion procedures, cysticidal therapy, and high-dose steroids. He finally showed clinical and radiological resolution with pulsed rituximab therapy. CONCLUSION: This off-label use of a monoclonal antibody against CD20 may be considered as a rescue therapy in steroid-refractory immune-mediated cysticercal meningitis.


Subject(s)
Neurocysticercosis , Humans , Male , Neurocysticercosis/complications , Neurocysticercosis/immunology , Rituximab/therapeutic use , Meningitis/immunology , Meningitis/drug therapy , Meningitis/therapy , B-Lymphocytes/immunology , Immunologic Factors/therapeutic use , Adult
5.
ACS Appl Mater Interfaces ; 16(29): 38711-38722, 2024 Jul 24.
Article in English | MEDLINE | ID: mdl-38995218

ABSTRACT

Two-dimensional (2D) van der Waals heterostructures combine the distinct properties of individual 2D materials, resulting in metamaterials, ideal for emergent electronic, optoelectronic, and spintronic phenomena. A significant challenge in harnessing these properties for future hybrid circuits is their large-scale realization and integration into graphene interconnects. In this work, we demonstrate the direct growth of molybdenum disulfide (MoS2) crystals on patterned graphene channels. By enhancing control over vapor transport through a confined space chemical vapor deposition growth technique, we achieve the preferential deposition of monolayer MoS2 crystals on monolayer graphene. Atomic resolution scanning transmission electron microscopy reveals the high structural integrity of the heterostructures. Through in-depth spectroscopic characterization, we unveil charge transfer in Graphene/MoS2, with MoS2 introducing p-type doping to graphene, as confirmed by our electrical measurements. Photoconductivity characterization shows that photoactive regions can be locally created in graphene channels covered by MoS2 layers. Time-resolved ultrafast transient absorption (TA) spectroscopy reveals accelerated charge decay kinetics in Graphene/MoS2 heterostructures compared to standalone MoS2 and upconversion for below band gap excitation conditions. Our proof-of-concept results pave the way for the direct growth of van der Waals heterostructure circuits with significant implications for ultrafast photoactive nanoelectronics and optospintronic applications.

6.
PLoS One ; 19(7): e0305710, 2024.
Article in English | MEDLINE | ID: mdl-38990850

ABSTRACT

There is an urgent unmet need for more targeted and effective treatments for advanced epithelial ovarian cancer (EOC). The emergence of drug resistance is a particular challenge, but small molecule covalent inhibitors have promise for difficult targets and appear less prone to resistance. Michael acceptors are covalent inhibitors that form bonds with cysteines or other nucleophilic residues in the target protein. However, many are categorized as pan-assay interference compounds (PAINS) and considered unsuitable as drugs due to their tendency to react non-specifically. Targeting RPN13/ADRM1-mediated substrate recognition and deubiquitination by the proteasome 19S Regulatory Particle (RP) is a promising treatment strategy. Early candidate RPN13 inhibitors (iRPN13) produced a toxic accumulation of very high molecular weight polyubiquitinated substrates, resulting in therapeutic activity in mice bearing liquid or solid tumor models, including ovarian cancer; however, they were not drug-like (PAINS) because of their central piperidone core. Up284 instead has a central spiro-carbon ring. We hypothesized that adding a guanidine moiety to the central ring nitrogen of Up284 would produce a compound, RA475, with improved drug-like properties and therapeutic activity in murine models of ovarian cancer. RA475 produced a rapid accumulation of high molecular polyubiquitinated proteins in cancer cell lines associated with apoptosis, similar to Up284 although it was 3-fold less cytotoxic. RA475 competed binding of biotinylated Up284 to RPN13. RA475 shows improved solubility and distinct pharmacodynamic properties compared to Up284. Specifically, tetraubiquitin firefly luciferase expressed in leg muscle was stabilized in mice more effectively upon IP treatment with RA475 than with Up284. However, pharmacologic analysis showed that RA475 was more rapidly cleared from the circulation, and less orally available than Up284. RA475 shows reduced ability to cross the blood-brain barrier and in vitro inhibition of HERG. Treatment of mice with RA475 profoundly inhibited the intraperitoneal growth of the ID8-luciferase ovarian tumor model. Likewise, RA475 treatment of immunocompetent mice inhibited the growth of spontaneous genetically-engineered peritoneal tumor, as did weekly cisplatin dosing. The combination of RA475 and cisplatin significantly extended survival compared to individual treatments, consistent with synergistic cytotoxicity in vitro. In sum, RA475 is a promising candidate covalent RPN13i with potential utility for treatment of patients with advanced EOC in combination with cisplatin.


Subject(s)
Ovarian Neoplasms , Female , Animals , Humans , Ovarian Neoplasms/drug therapy , Ovarian Neoplasms/pathology , Ovarian Neoplasms/metabolism , Mice , Cell Line, Tumor , Antineoplastic Agents/pharmacology , Antineoplastic Agents/therapeutic use , Antineoplastic Agents/chemistry , Spiro Compounds/pharmacology , Spiro Compounds/therapeutic use , Spiro Compounds/chemistry , Xenograft Model Antitumor Assays , Carcinoma, Ovarian Epithelial/drug therapy , Guanidines/pharmacology , Guanidines/therapeutic use , Guanidines/chemistry , Intracellular Signaling Peptides and Proteins
8.
Front Microbiol ; 15: 1396116, 2024.
Article in English | MEDLINE | ID: mdl-39040911

ABSTRACT

Veterinary medications are constantly being used for the diagnosis, treatment, and prevention of diseases in livestock. However, untreated veterinary drug active compounds are interminably discharged into numerous water bodies and terrestrial ecosystems, during production procedures, improper disposal of empty containers, unused medication or animal feed, and treatment procedures. This exhaustive review describes the different pathways through which veterinary medications enter the environment, discussing the role of agricultural practices and improper disposal methods. The detrimental effects of veterinary drug compounds on aquatic and terrestrial ecosystems are elaborated with examples of specific veterinary drugs and their known impacts. This review also aims to detail the mechanisms by which microbes degrade veterinary drug compounds as well as highlighting successful case studies and recent advancements in microbe-based bioremediation. It also elaborates on microbial electrochemical technologies as an eco-friendly solution for removing pharmaceutical pollutants from wastewater. Lastly, we have summarized potential innovations and challenges in implementing bioremediation on a large scale under the section prospects and advancements in this field.

9.
Cureus ; 16(6): e61763, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38975486

ABSTRACT

The genitofemoral nerve (GFN) presents with a variable course in nearly half of the population. This variation can be seen in its availability, course, and branching. Here, a notable case during a cadaveric dissection revealed an unusually high bifurcation of the GFN on the left side, contrasting with the typical bifurcation observed on the right. This divergence was highlighted using colored markers to aid educational visualization, facilitating a comprehensive learning experience about the nerve's variability and its functional implications, such as the cremasteric reflex. Embryologically, these variations stem from the migratory paths of myotomes during development, influenced by extrinsic signals and growth factors. Despite the high incidence of anatomical variability, the muscular structure remains consistent, suggesting that the nerve's formation is more susceptible to developmental shifts than the muscles it innervates. Clinically, understanding GFN variations is crucial due to the nerve's involvement in conditions like genitofemoral neuropathy, which can arise from surgical procedures. Accurate knowledge of these variations aids in precise diagnostic and therapeutic interventions, reducing complications, and enhancing patient outcomes in lower abdominal and groin surgeries. However, further research is needed to elucidate the exact embryological and genetic underpinnings of these variations.

10.
bioRxiv ; 2024 May 22.
Article in English | MEDLINE | ID: mdl-38826407

ABSTRACT

The expansion of biobanks has significantly propelled genomic discoveries yet the sheer scale of data within these repositories poses formidable computational hurdles, particularly in handling extensive matrix operations required by prevailing statistical frameworks. In this work, we introduce computational optimizations to the SAIGE (Scalable and Accurate Implementation of Generalized Mixed Model) algorithm, notably employing a GPU-based distributed computing approach to tackle these challenges. We applied these optimizations to conduct a large-scale genome-wide association study (GWAS) across 2,068 phenotypes derived from electronic health records of 635,969 diverse participants from the Veterans Affairs (VA) Million Veteran Program (MVP). Our strategies enabled scaling up the analysis to over 6,000 nodes on the Department of Energy (DOE) Oak Ridge Leadership Computing Facility (OLCF) Summit High-Performance Computer (HPC), resulting in a 20-fold acceleration compared to the baseline model. We also provide a Docker container with our optimizations that was successfully used on multiple cloud infrastructures on UK Biobank and All of Us datasets where we showed significant time and cost benefits over the baseline SAIGE model.

11.
Bioresour Technol ; 406: 130976, 2024 Aug.
Article in English | MEDLINE | ID: mdl-38879056

ABSTRACT

This study aimed to understand the wastewater treatment and electricity generation performance besides the microbial communities of the integrated Hydroponics-Microbial Electrochemical Technology (iHydroMET) systems operated with water-saturated and water-unsaturated reactors. The organics removal was slightly higher in the water-unsaturated system (93 ± 4 %) than in the water-saturated system (87 ± 2 %). The total nitrogen removal and electric voltage were considerably higher in the water-saturated system (42 ± 5 %; 111 ± 8 V per reactor) than in the water-unsaturated system (18 ± 3 %; 95 ± 9 V per reactor). The enhanced organics and nitrogen removal and high voltage output in respective conditions were due to the dominance of polysaccharide-degrading aerobes (e.g., Pirellula), anammox bacteria (e.g., Anammoximicrobium), denitrifiers (e.g., Thauera and Rheinheimera), and electroactive microorganisms (e.g., Geobacter). The differential performance governed by distinct microbial communities under the tested conditions indicates that an appropriate balancing of water saturation and unsaturation in reactors is crucial to achieving optimum iHydroMET performance.


Subject(s)
Bacteria , Bioreactors , Nitrogen , Bioreactors/microbiology , Bacteria/metabolism , Hydroponics/methods , Wastewater/microbiology , Water Purification/methods , Electrochemical Techniques/methods , Electricity , Water/chemistry , Bioelectric Energy Sources/microbiology
12.
BJR Artif Intell ; 1(1): ubae006, 2024 Jan.
Article in English | MEDLINE | ID: mdl-38828430

ABSTRACT

Innovation in medical imaging artificial intelligence (AI)/machine learning (ML) demands extensive data collection, algorithmic advancements, and rigorous performance assessments encompassing aspects such as generalizability, uncertainty, bias, fairness, trustworthiness, and interpretability. Achieving widespread integration of AI/ML algorithms into diverse clinical tasks will demand a steadfast commitment to overcoming issues in model design, development, and performance assessment. The complexities of AI/ML clinical translation present substantial challenges, requiring engagement with relevant stakeholders, assessment of cost-effectiveness for user and patient benefit, timely dissemination of information relevant to robust functioning throughout the AI/ML lifecycle, consideration of regulatory compliance, and feedback loops for real-world performance evidence. This commentary addresses several hurdles for the development and adoption of AI/ML technologies in medical imaging. Comprehensive attention to these underlying and often subtle factors is critical not only for tackling the challenges but also for exploring novel opportunities for the advancement of AI in radiology.

13.
Article in English | MEDLINE | ID: mdl-38840395

ABSTRACT

OBJECTIVE: This review paper examines biotechnological methods for enhancing edible insects using enzymatic hydrolysis and fermentation. Evaluations involve improving functionality, analyzing consumer acceptability elements, guaranteeing safety and quality, negotiating regulatory frameworks, and suggesting field breakthroughs and applications. METHODS: Our method comprises a thorough literature analysis and academic database searches for edible insect enzymatic hydrolysis and fermentation investigations. Based on gaps in the literature, we investigate edible insect safety, consumer acceptability, and legal and regulatory issues. RESULTS: The results show biotechnological advances in enzymatic hydrolysis and fermentation for edible insect functioning. Sensory and cultural aspects affect consumer acceptability. To ensure edible insect product safety, hazards and pollutants are addressed. The legal analysis highlights compliance issues and possibilities. CONCLUSION: This review shows how enzymatic hydrolysis and fermentation improve edible insect functioning, safety, and nutrition. The review includes consumer acceptability dynamics, legal issues, and safety analysis.

14.
J Org Chem ; 2024 Jun 05.
Article in English | MEDLINE | ID: mdl-38836310

ABSTRACT

Photoactivatable (PA) rhodamine dyes are widely used in single-molecule tracking (SMT) and a variety of other fluorescence-based imaging modalities. One of the most commonly employed scaffolds uses a diazoketone to lock the rhodamine in the nonfluorescent closed form, which can be activated with 405 nm light. However, poor properties of previously reported dyes require significant washing, which can be resource- and cost-intensive, especially when performing microscopy in a large scale and high-throughput fashion. Here, we report improved diazoketorhodamines that perform exceptionally well in single-molecule tracking microscopy. We also report on the optimization of an improved synthetic method for further iteration and tailoring of diazoketorhodamines to the requirements of a specific user.

15.
Cancers (Basel) ; 16(12)2024 Jun 07.
Article in English | MEDLINE | ID: mdl-38927874

ABSTRACT

In hormone receptor-positive/human epidermal growth factor receptor 2-negative (HR+/HER2-) metastatic breast cancer (MBC), cyclin-dependent kinase 4/6 inhibitors (CDK4/6is) have replaced endocrine therapy alone as the standard of care; however, several barriers to treatment initiation still exist. We assessed social determinants of health (SDOH) and other factors associated with the initiation of CDK4/6i for HR+/HER2- MBC in the Medicare population. Using a retrospective cohort design, patients aged ≥65 years and diagnosed during 2015-2017 were selected from the SEER-Medicare database. Time from MBC diagnosis to first CDK4/6i initiation was the study outcome. The effect of SDOH measures and other predictors on the outcome was assessed using the multivariable Fine and Gray hazard modeling. Of 752 eligible women, 352 (46.8%) initiated CDK4/6i after MBC diagnosis (median time to initiation: 27.9 months). In adjusted analysis, SDOH factors significantly associated with CDK4/6i initiation included high versus low median household income (HHI) (hazard ratio [HR] = 1.70; 95% CI = 1.03-2.81) and the percentage of population with high versus low Medicare-only coverage (HR = 1.54; 95% CI = 1.04-2.27). In summary, older Medicare patients with HR+/HER2- MBC residing in areas with high median HHI and a high proportion of Medicare-only coverage had higher rates of initiating CDK4/6i, suggesting inequitable access to these novel, effective treatments and a need for policy intervention.

16.
J Environ Manage ; 365: 121391, 2024 Aug.
Article in English | MEDLINE | ID: mdl-38905793

ABSTRACT

In many industrial processes a large amount of water with high salinity is co-produced whose treatment poses considerable challenges to the available technologies. The produced water (PW) from offshore operations is currently being discharged to sea without treatment for dissolved pollutants due to space limitations. A biofilter on the seabed adjacent to a production platform would negate all size restrictions, thus reducing the environmental impact of oil and gas production offshore. The moving bed biofilm reactor (MBBR) was investigated for PW treatment from different oilfields in the North Sea at 10 °C and 40 °C, corresponding to the sea and PW temperature, respectively. The six PW samples in study were characterized by high salinity and chemical oxygen demand with ecotoxic effects on marine algae S. pseudocostatum (0.4%

Subject(s)
Biofilms , Bioreactors , Temperature , Water Purification/methods , Salinity , Biological Oxygen Demand Analysis , Water Pollutants, Chemical
17.
J Heart Lung Transplant ; 43(8): 1199-1234, 2024 Aug.
Article in English | MEDLINE | ID: mdl-38878021

ABSTRACT

Life expectancy of patients with a durable, continuous-flow left ventricular assist device (CF-LVAD) continues to increase. Despite significant improvements in the delivery of care for patients with these devices, hemocompatability-related adverse events (HRAEs) are still a concern and contribute to significant morbility and mortality when they occur. As such, dissemination of current best evidence and practices is of critical importance. This ISHLT Consensus Statement is a summative assessment of the current literature on prevention and management of HRAEs through optimal management of oral anticoagulant and antiplatelet medications, parenteral anticoagulant medications, management of patients at high risk for HRAEs and those experiencing thrombotic or bleeding events, and device management outside of antithrombotic medications. This document is intended to assist clinicians caring for patients with a CF-LVAD provide the best care possible with respect to prevention and management of these events.


Subject(s)
Consensus , Heart-Assist Devices , Heart-Assist Devices/adverse effects , Humans , Anticoagulants/therapeutic use , Heart Failure/therapy , Heart Failure/surgery , Thrombosis/prevention & control , Thrombosis/etiology , Hemorrhage/prevention & control , Platelet Aggregation Inhibitors/therapeutic use
18.
Nat Commun ; 15(1): 5483, 2024 Jun 28.
Article in English | MEDLINE | ID: mdl-38942804

ABSTRACT

Dexamethasone is the standard of care for critically ill patients with COVID-19, but the mechanisms by which it decreases mortality and its immunological effects in this setting are not understood. Here we perform bulk and single-cell RNA sequencing of samples from the lower respiratory tract and blood, and assess plasma cytokine profiling to study the effects of dexamethasone on both systemic and pulmonary immune cell compartments. In blood samples, dexamethasone is associated with decreased expression of genes associated with T cell activation, including TNFSFR4 and IL21R. We also identify decreased expression of several immune pathways, including major histocompatibility complex-II signaling, selectin P ligand signaling, and T cell recruitment by intercellular adhesion molecule and integrin activation, suggesting these are potential mechanisms of the therapeutic benefit of steroids in COVID-19. We identify additional compartment- and cell- specific differences in the effect of dexamethasone that are reproducible in publicly available datasets, including steroid-resistant interferon pathway expression in the respiratory tract, which may be additional therapeutic targets. In summary, we demonstrate compartment-specific effects of dexamethasone in critically ill COVID-19 patients, providing mechanistic insights with potential therapeutic relevance. Our results highlight the importance of studying compartmentalized inflammation in critically ill patients.


Subject(s)
COVID-19 Drug Treatment , COVID-19 , Cytokines , Dexamethasone , Lung , SARS-CoV-2 , Dexamethasone/therapeutic use , Dexamethasone/pharmacology , Humans , COVID-19/immunology , COVID-19/virology , SARS-CoV-2/drug effects , Lung/drug effects , Lung/virology , Cytokines/metabolism , Cytokines/blood , Critical Illness , Male , Single-Cell Analysis , Female , Middle Aged , T-Lymphocytes/immunology , T-Lymphocytes/drug effects , T-Lymphocytes/metabolism , Aged , Lymphocyte Activation/drug effects
19.
bioRxiv ; 2024 Jun 13.
Article in English | MEDLINE | ID: mdl-38915643

ABSTRACT

HflX is known to rescue stalled ribosomes and is implicated in antibiotic resistance in several bacteria. Here we present several high-resolution cryo-EM structures of mycobacterial HflX in complex with the ribosome and its 50S subunit, with and without antibiotics. These structures reveal a distinct mechanism for HflX-mediated ribosome splitting and antibiotic resistance in mycobacteria. In addition to dissociating ribosome into two subunits, mycobacterial HflX mediates persistent disordering of multiple 23S rRNA helices to generate an inactive pool of 50S subunits. Mycobacterial HflX also acts as an anti-association factor by binding to pre-dissociated 50S subunits. A mycobacteria-specific insertion in HflX reaches further into the peptidyl transferase center. The position of this insertion overlaps with ribosome-bound macrolides or lincosamide class of antibiotics. The extended conformation of insertion seen in the absence of these antibiotics retracts and adjusts around the bound antibiotics instead of physically displacing them. It therefore likely imparts antibiotic resistance by sequestration of the antibiotic-bound inactive 50S subunits.

20.
HGG Adv ; 5(3): 100315, 2024 Jul 18.
Article in English | MEDLINE | ID: mdl-38845201

ABSTRACT

Deciphering the genetic basis of prostate-specific antigen (PSA) levels may improve their utility for prostate cancer (PCa) screening. Using genome-wide association study (GWAS) summary statistics from 95,768 PCa-free men, we conducted a transcriptome-wide association study (TWAS) to examine impacts of genetically predicted gene expression on PSA. Analyses identified 41 statistically significant (p < 0.05/12,192 = 4.10 × 10-6) associations in whole blood and 39 statistically significant (p < 0.05/13,844 = 3.61 × 10-6) associations in prostate tissue, with 18 genes associated in both tissues. Cross-tissue analyses identified 155 statistically significantly (p < 0.05/22,249 = 2.25 × 10-6) genes. Out of 173 unique PSA-associated genes across analyses, we replicated 151 (87.3%) in a TWAS of 209,318 PCa-free individuals from the Million Veteran Program. Based on conditional analyses, we found 20 genes (11 single tissue, nine cross-tissue) that were associated with PSA levels in the discovery TWAS that were not attributable to a lead variant from a GWAS. Ten of these 20 genes replicated, and two of the replicated genes had colocalization probability of >0.5: CCNA2 and HIST1H2BN. Six of the 20 identified genes are not known to impact PCa risk. Fine-mapping based on whole blood and prostate tissue revealed five protein-coding genes with evidence of causal relationships with PSA levels. Of these five genes, four exhibited evidence of colocalization and one was conditionally independent of previous GWAS findings. These results yield hypotheses that should be further explored to improve understanding of genetic factors underlying PSA levels.


Subject(s)
Genetic Predisposition to Disease , Genome-Wide Association Study , Prostate-Specific Antigen , Prostatic Neoplasms , Transcriptome , Humans , Male , Prostate-Specific Antigen/blood , Prostatic Neoplasms/genetics , Prostatic Neoplasms/blood , Gene Expression Profiling , Polymorphism, Single Nucleotide
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