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Aging Jun 2024A deep understanding of the biological mechanisms of lung cancer offers more precise treatment options for patients. In our study, we integrated data from the Gene...
A deep understanding of the biological mechanisms of lung cancer offers more precise treatment options for patients. In our study, we integrated data from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) to investigate lung adenocarcinoma. Analyzing 538 lung cancer samples and 31 normal samples, we focused on 3076 autophagy-related genes. Using Seurat, dplyr, tidyverse, and ggplot2, we conducted single-cell data analysis, assessing the quality and performing Principal Component Analysis (PCA) and t-SNE analyses. Differential analysis of TCGA data using the "Limma" package, followed by immune infiltration analysis using the CIBERSORT algorithm, led us to identify seven key genes. These genes underwent further scrutiny through consensus clustering and gene set variation analysis (GSVA). We developed a prognostic model using Lasso Cox regression and multivariable Cox analysis, which was then validated with a nomogram, predicting survival rates for lung adenocarcinoma. The model's accuracy and universality were corroborated by ROC curves. Additionally, we explored the relationship between immune checkpoint genes and immune cell infiltration and identified two key genes, HLA-DQB1 and OLR1. This highlighted their potential as therapeutic targets. Our comprehensive approach sheds light on the molecular landscape of lung adenocarcinoma and offers insights into potential treatment strategies, emphasizing the importance of integrating single-cell and genomic data in cancer research.
PubMed: 38942606
DOI: 10.18632/aging.205973 -
RMD Open Jun 2024Fibromyalgia (FM) is a complex disorder with widespread pain and emotional distress, posing diagnostic challenges. FM patients show altered cognitive and emotional...
BACKGROUND
Fibromyalgia (FM) is a complex disorder with widespread pain and emotional distress, posing diagnostic challenges. FM patients show altered cognitive and emotional processing, with a preferential allocation of attention to pain-related information. This attentional bias towards pain cues can impair cognitive functions such as inhibitory control, affecting patients' ability to manage and express emotions. Sentiment analysis using large language models (LLMs) can provide insights by detecting nuances in pain expression. This study investigated whether open-source LLM-driven sentiment analysis could aid FM diagnosis.
METHODS
40 patients with FM, according to the 2016 American College of Rheumatology Criteria and 40 non-FM chronic pain controls referred to rheumatology clinics, were enrolled. Transcribed responses to questions on pain and sleep were machine translated to English and analysed by the LLM Mistral-7B-Instruct-v0.2 using prompt engineering targeting FM-associated language nuances for pain expression ('prompt-engineered') or an approach without this targeting ('ablated'). Accuracy, precision, recall, specificity and area under the receiver operating characteristic curve (AUROC) were calculated using rheumatologist diagnosis as ground truth.
RESULTS
The prompt-engineered approach demonstrated accuracy of 0.87, precision of 0.92, recall of 0.84, specificity of 0.82 and AUROC of 0.86 for distinguishing FM. In comparison, the ablated approach had an accuracy of 0.76, precision of 0.75, recall of 0.77, specificity of 0.75 and AUROC of 0.76. The accuracy was superior to the ablated approach (McNemar's test p<0.001).
CONCLUSION
This proof-of-concept study suggests LLM-driven sentiment analysis, especially with prompt engineering, may facilitate FM diagnosis by detecting subtle differences in pain expression. Further validation is warranted, particularly the inclusion of secondary FM patients.
Topics: Humans; Fibromyalgia; Female; Middle Aged; Male; Adult; ROC Curve; Natural Language Processing; Language; Emotions; Aged; Chronic Pain
PubMed: 38942593
DOI: 10.1136/rmdopen-2024-004367 -
Drug Metabolism and Disposition: the... Jun 2024Recently, we have proposed simple methodology to derive clearance and rate constant equations, independent of differential equations, based on Kirchhoff's Laws, a common...
Recently, we have proposed simple methodology to derive clearance and rate constant equations, independent of differential equations, based on Kirchhoff's Laws, a common methodology from physics used to describe rate-defining processes either in series or parallel. Our approach has been challenged in three recent publications, two published in this journal, but notably what is lacking is that none evaluate experimental pharmacokinetic data. As reviewed here, manuscripts from our laboratory have evaluated published experimental data, demonstrating that the Kirchhoff's Laws approach explains (1) why all of the experimental perfused liver clearance data appear to fit the equation that was previously believed to be the well-stirred model, (2) why linear pharmacokinetic systemic bioavailability determinations can be greater than 1, (3) why renal clearance can be a function of drug input processes, and (4) why statistically different bioavailability measures may be found for urinary excretion versus systemic concentration measurements. Our most recent paper demonstrates (5) how the universally accepted steady-state clearance approach utilized by the field for the past 50 years leads to unrealistic outcomes concerning the relationship between liver-to-blood and hepatic availability , highlighting the potential for errors in pharmacokinetic evaluations based on differential equations. The Kirchhoff's Laws approach is applicable to all pharmacokinetic analyses of quality experimental data, those that were previously adequately explained with present pharmacokinetic theory, and those that were not The publications that have attempted to rebut our position do not address unexplained experimental data, and we show here why their analyses are not valid. The Kirchhoff's Laws approach to deriving clearance equations for linear systems in parallel or in series, independent of differential equations, successfully describes published pharmacokinetic data that has previously been unexplained. Three recent publications claim to refute our proposed methodology; these publications only make theoretical arguments, do not evaluate experimental data; never demonstrate that the Kirchhoff methodology provides incorrect interpretations of experimental pharmacokinetic data, including statistically significant data not explained by present pharmacokinetic theory. We demonstrate why these analyses are invalid.
PubMed: 38942444
DOI: 10.1124/dmd.124.001735 -
Jornal de Pediatria Jun 2024
Erratum to: "Cross-cultural adaptation, validity, and reliability of the Child and Adolescent Behavior Inventory (CABI) for use in Brazil" (Jornal de Pediatria 99 (2023) 413-422).
PubMed: 38942066
DOI: 10.1016/j.jped.2024.06.001 -
European Journal of Dentistry Jun 2024The proper closure of the access cavity between appointments during endodontic treatment is paramount and relies on temporary fillings. This systematic review evaluates...
The proper closure of the access cavity between appointments during endodontic treatment is paramount and relies on temporary fillings. This systematic review evaluates the effectiveness of zinc oxide-based materials and glass-ionomer cement (GIC) as temporary coronal sealers after root canal treatment in extracted human teeth. Three databases were searched to identify randomized clinical trials that examined the sealing properties of various temporary sealing materials using dyes or stains as indicators. A total of seven studies that fulfilled the eligibility criteria were critically analyzed. These indicated significant variations in the relative sealing ability of the coronal breach of endodontically treated teeth, either by zinc oxide or GIC-based materials. While GIC-based material (e.g., Fuji IX and Fuji II) exhibited superior sealing of single-rooted teeth, zinc oxide-based material (e.g., Cavit, Coltosol, Caviton) also showed promising attributes. Resin-modified GIC formulations displayed enhanced physical properties, yet challenges related to adhesive failure and shrinkage during polymerization were observed. Zinc oxide-based materials have demonstrated superior coronal sealing effectiveness over certain GIC in controlled settings. Their premixed nature ensures consistent application and hygroscopic properties improve cavity sealing. However, the focus on dye penetration tests for microleakage may not fully represent the risk of bacterial infiltration. Thus, studies are crucial for validating these findings in clinical contexts.
PubMed: 38942056
DOI: 10.1055/s-0044-1782695 -
Journal of Insect Science (Online) May 2024The electrical penetration graph (EPG) technique is the most powerful tool for studying the feeding behavior of pierce-sucking insects. However, calculating EPG...
The electrical penetration graph (EPG) technique is the most powerful tool for studying the feeding behavior of pierce-sucking insects. However, calculating EPG variables is often very time-consuming, and consequently, several software programs have been developed for the automatic calculation of EPG variables. Here we present a new user-friendly Excel Workbook that uses a standardized list of EPG variables and follows expert guidelines for calculating them. The program developed in Visual Basic for Applications (VBA) is a step up from the existing software and allows easy data analysis and interpretation. It also includes a novel option for dealing with the common problem of "truncated"-waveforms artificially terminated by the end of recording. The only requirement to run the program is Microsoft Excel software running under a PC environment. The Workbook was validated by calculating variables from EPG recordings of aphids and psyllids and the results obtained were compared with those of existing software such as the Sarria Workbook. Our EPG Workbook provides researchers with a reliable and standardized tool for the automatic calculation of up to 127 EPG variables from phloem-sap-sucking insects.
Topics: Animals; Software; Feeding Behavior; Aphids; Hemiptera
PubMed: 38942050
DOI: 10.1093/jisesa/ieae063 -
Cell Reports. Medicine Jun 2024Prior studies indicate no correlation between the gut microbes of healthy first-degree relatives (HFDRs) of patients with Crohn's disease (CD) and the development of CD....
Prior studies indicate no correlation between the gut microbes of healthy first-degree relatives (HFDRs) of patients with Crohn's disease (CD) and the development of CD. Here, we utilize HFDRs as controls to examine the microbiota and metabolome in individuals with active (CD-A) and quiescent (CD-R) CD, thereby minimizing the influence of genetic and environmental factors. When compared to non-relative controls, the use of HFDR controls identifies fewer differential taxa. Faecalibacterium, Dorea, and Fusicatenibacter are decreased in CD-R, independent of inflammation, and correlated with fecal short-chain fatty acids (SCFAs). Validation with a large multi-center cohort confirms decreased Faecalibacterium and other SCFA-producing genera in CD-R. Classification models based on these genera distinguish CD from healthy individuals and demonstrate superior diagnostic power than models constructed with markers identified using unrelated controls. Furthermore, these markers exhibited limited discriminatory capabilities for other diseases. Finally, our results are validated across multiple cohorts, underscoring their robustness and potential for diagnostic and therapeutic applications.
PubMed: 38942021
DOI: 10.1016/j.xcrm.2024.101624 -
EBioMedicine Jun 2024Drug development for atrial fibrillation (AF) has failed to yield new approved compounds. We sought to identify and prioritise potential druggable targets with support...
BACKGROUND
Drug development for atrial fibrillation (AF) has failed to yield new approved compounds. We sought to identify and prioritise potential druggable targets with support from human genetics, by integrating the available evidence with bioinformatics sources relevant for AF drug development.
METHODS
Genetic hits for AF and related traits were identified through structured search of MEDLINE. Genes derived from each paper were cross-referenced with the OpenTargets platform for drug interactions. Confirmation/validation was demonstrated through structured searches and review of evidence on MEDLINE and ClinialTrials.gov for each drug and its association with AF.
FINDINGS
613 unique drugs were identified, with 21 already included in AF Guidelines. Cardiovascular drugs from classes not currently used for AF (e.g. ranolazine and carperitide) and anti-inflammatory drugs (e.g. dexamethasone and mehylprednisolone) had evidence of potential benefit. Further targets were considered druggable but remain open for drug development.
INTERPRETATION
Our systematic approach, combining evidence from different bioinformatics platforms, identified drug repurposing opportunities and druggable targets for AF.
FUNDING
KK is supported by Barts Charity grant G-002089 and is mentored on the AFGen 2023-24 Fellowship funded by the AFGen NIH/NHLBI grant R01HL092577. RP is supported by the UCL BHF Research Accelerator AA/18/6/34223 and NIHR grant NIHR129463. AFS is supported by the BHF grants PG/18/5033837, PG/22/10989 and UCL BHF Accelerator AA/18/6/34223 as well as the UK Research and Innovation (UKRI) under the UK government's Horizon Europe funding guarantee EP/Z000211/1 and by the UKRI-NIHR grant MR/V033867/1 for the Multimorbidity Mechanism and Therapeutics Research Collaboration. AF is supported by UCL BHF Accelerator AA/18/6/34223. CF is supported by UCL BHF Accelerator AA/18/6/34223.
PubMed: 38941956
DOI: 10.1016/j.ebiom.2024.105194 -
Poultry Science Jun 2024Salmonella and Campylobacter are major foodborne pathogens that cause outbreaks associated with contaminated chicken liver. Proper cooking is necessary to avoid the risk...
Salmonella and Campylobacter are major foodborne pathogens that cause outbreaks associated with contaminated chicken liver. Proper cooking is necessary to avoid the risk of illness to consumers. This study tested the thermal inactivation of a 4-strain Salmonella cocktail and a 3-strain Campylobacter cocktail in chicken livers separately at temperatures ranging from 55.0 to 62.5°C. Inoculated livers were sealed in aluminum cells and immersed in a water bath. The decimal reduction time (D-values) of Salmonella in chicken livers were 9.01, 2.36, 0.82, and 0.23 min at 55.0, 57.5, 60.0, and 62.5°C, respectively. The D-values of Campylobacter ranged from 2.22 min at 55.0°C to 0.19 min at 60.0°C. Salmonella and Campylobacter had similar z-values in chicken livers of 4.8 and 4.6°C, respectively. Chicken livers can be heated to internal temperatures of 70.0 to 73.9°C for at least 1.6 to 0.2 s to achieve a 7-log reduction of Salmonella. Validation tests demonstrated that heating chicken livers to internal temperatures of 70.0 to 73.9°C for 2 to 0 s resulted in a reduction of Salmonella exceeding 7 logs. Collectively, these data show that Salmonella exhibits higher heat resistance than Campylobacter in chicken livers. Therefore, Salmonella could be considered as the target pathogen when designing thermal treatments or cooking instructions for liver products. These findings will aid in designing effective thermal processing for both industrial and home cooking to eliminate Salmonella and Campylobacter, ensuring consumer safety when consuming chicken liver products.
PubMed: 38941761
DOI: 10.1016/j.psj.2024.103961 -
Ultrasonics Sonochemistry Jun 2024Sonoporation is a non-invasive method that uses ultrasound for drug and gene delivery for therapeutic purposes. Here, both Finite Element Method (FEM) and Lattice...
Sonoporation is a non-invasive method that uses ultrasound for drug and gene delivery for therapeutic purposes. Here, both Finite Element Method (FEM) and Lattice Boltzmann Method (LBM) are applied to study the interaction physics of microbubble oscillation and collapse near flexible tissue. After validating the Finite Element Method with the nonlinear excited lipid-coated microbubble as well as the Lattice Boltzmann Method with experimental results, we have studied the behavior of a three-dimensional compressible microbubble in the vicinity of tissue. In the FEM phase, the oscillation microbubble with a lipid shell interacts with the boundary. The range of pressure and ultrasound frequency have been considered in the field of therapeutic applications of sonoporation. The viscoelastic and interfacial tension as the coating properties of the microbubble shell have been investigated. The presence of an elastic boundary increases the resonance frequency of the microbubble compared to that of a free microbubble. The increase in pressure leads to an expansion in the range of the microbubble's motion, the velocity induced in the fluid, and the shear stress on the boundary walls of tissue. An enhancement in the surface tension of the microbubble can influence fluid flow and reduce the shear stress on the boundary. The multi-pseudo-potential interaction LBM is used to reduce thermodynamic inconsistency and high-density ratio in a two-phase system for modeling the cavitation process. The three-dimensional shape of the microbubble during the collapse stages and the counter of pressure are displayed. There is a time difference between the occurrence of maximum velocity and pressure. All results in detail are presented in the article bodies.
PubMed: 38941703
DOI: 10.1016/j.ultsonch.2024.106972