Search Results (12)

Several studies have shown that microsatellite changes can be profiled in urine for the detection of bladder cancer. The use of microsatellite analysis (MSA) for bladder cancer detection requires a comprehensive analysis of as many as 15 to 20 markers, based on the amplification and interpretations of many individual MSA markers, and it can be technically challenging. Here, to develop fast, more efficient, standardized, and less costly MSA for the detection of bladder cancer, we developed three multiplex-polymerase-chain-reaction-(PCR)-based MSA assays, all of which were analyzed via a genetic analyzer. First, we selected 16 MSA markers based on 9 selected publications. Based on samples from Johns Hopkins University (the JHU sample, the first set sample), we developed an MSA based on triplet, three-tube-based multiplex PCR (a Triplet MSA assay). The discovery, validation, and translation of biomarkers for the early detection of cancer are the primary focuses of the Early Detection Research Network (EDRN), an initiative of the National Cancer Institute (NCI). A prospective study sponsored by the EDRN was undertaken to determine the efficacy of a novel set of MSA markers for the early detection of bladder cancer. This work and data analysis were performed through a collaboration between academics and industry partners. In the current study, we undertook a re-analysis of the primary data from the Compass study to enhance the predictive power of the dataset in bladder cancer diagnosis. Using a four-stage pipeline of modern machine learning techniques, including outlier removal with a nonlinear model, correcting for majority/minority class imbalance, feature engineering, and the use of a model-derived variable importance measure to select predictors, we were able to increase the utility of the original dataset to predict the occurrence of bladder cancer. The results of this analysis showed an increase in accuracy (85%), sensitivity (82%), and specificity (83%) compared to the original analysis. The re-analysis of the EDRN study results using machine learning statistical analysis proved to achieve an appropriate level of accuracy, sensitivity, and specificity to support the use of the MSA for bladder cancer detection and monitoring. This assay can be a significant addition to the tools urologists use to both detect primary bladder cancers and monitor recurrent bladder cancer. Full article

Prolonged and excessive use of antibiotics has resulted in the development of antimicrobial resistance (AMR), which is considered an emerging global challenge that warrants a deeper understanding of the antibiotic-resistant gene elements (ARGEs/resistomes) involved in its rapid dissemination. Currently, advanced molecular methods such as high-throughput quantitative polymerase chain reaction (HT-qPCR) and shotgun metagenomic sequencing (SMS) are commonly applied for the surveillance and monitoring of AMR in the environment. Although both methods are considered complementary to each other, there are some appreciable differences that we wish to highlight in this communication. We compared both these approaches to map the ARGEs in the coastal sediments of Kuwait. The study area represents an excellent model as it receives recurrent emergency waste and other anthropogenic contaminants. The HT-qPCR identified about 100 ARGs, 5 integrons, and 18 MGEs (total—122). These ARGs coded for resistance against the drug classes of beta-lactams > aminoglycoside > tetracycline, macrolide lincosamide streptogramin B (MLSB) > phenicol > trimethoprim, quinolone, and sulfonamide. The SMS picked a greater number of ARGs (402), plasmid sequences (1567), and integrons (168). Based on the evidence, we feel the SMS is a better method to undertake ARG assessment to fulfil the WHO mandate of “One Health Approach.” This manuscript is a useful resource for environmental scientists involved in AMR monitoring. Full article

Quantum Markov chains (QMCs) and open quantum random walks (OQRWs) represent different quantum extensions of the classical Markov chain framework. QMCs stand as a more profound layer within the realm of Markovian dynamics. The exploration of both QMCs and OQRWs has been a predominant focus over the past decade. Recently, a significant connection between QMCs and OQRWs has been forged, yielding valuable applications. This bridge is particularly impactful when studying QMCs on tree structures, where it intersects with the realm of phase transitions in models naturally arising from quantum statistical mechanics. Furthermore, it aids in elucidating statistical properties, such as recurrence and clustering. The objective of this paper centers around delving into the intricate structure of QMCs on Cayley trees in relation to OQRWs. The foundational elements of this class of QMCs are built upon using classical probability measures that encompass the hierarchical nature of Cayley trees. This exploration unveils the pivotal role that the dynamics of OQRWs play in shaping the behavior of the Markov chains under consideration. Moreover, the analysis extends to their classical counterparts. The findings are further underscored by the examination of notable examples, contributing to a comprehensive understanding of the outcomes. Full article

In this paper, polynomial recurrence bounds for a class of stochastic differential equations with a rotational symmetric gradient type drift and an additive Wiener process are established, as well as certain a priori moment inequalities for solutions. The key feature of this paper is that the approach does not use Lyapunov functions because it is not clear how to construct them. The method based on Dynkin’s (nonrandom) chain of equations is applied instead. Another key feature is that the asymptotic conditions on the potential near infinity are assumed as inequalities—which allows for more flexibility compared to a single limit at infinity, making it less restrictive. Full article

This paper shows that Harris recurrent Markov chains and processes can be characterized as the class of Markov chains and processes for which there exists a random time T at which the distribution of the chain or process does not depend on its initial condition. In particular, no independence assumptions concerning the post-T process or T play a role in the characterization. Since Harris chains and processes are known to contain infinite sequences of regeneration times exhibiting various independence properties, it follows that the existence of this single T implies the existence of infinitely many times at which regeneration occurs. Full article

Background: Tumor-infiltrating lymphocytes (TILs) have been used to predict the prognosis of solid tumors. In this study, we investigated which molecules in TILs play a role in the prognosis of patients with oral squamous cell carcinoma (OSCC). Methods: In a retrospective case-control study, we immunohistochemically evaluated the expression of CD3, CD8, CD45RO, Granzyme B, and the major histocompatibility complex class I chain-related molecule A (MICA) of the histocompatibility complex as predictors of prognosis in 33 patients with OSCC. The patients were classified as TILs^High or TILs^Low according to the number of TILs for each molecule in the central tumor (CT) and invasive margin (IM). Furthermore, MICA expression scores were determined based on the intensity of the staining. Results: CD45RO⁺/TIL in the nonrecurrent group were significantly higher than those in the recurrent group in the CT and IM areas (p < 0.05). The disease-free survival/overall survival rate of the CD45RO⁺/TILs^Low group in the CT and IM areas and the Granzyme B⁺/TILs^Low group in the IM area was significantly lower than that of the CD45RO⁺/TILs^High group and the Granzyme B⁺/TILs^High group, respectively (p < 0.05). Furthermore, the MICA expression score of tumors around the CD45RO⁺/TILs^High group was significantly higher than that of the CD45RO⁺/TILs^Low group (p < 0.05). Conclusions: A high ratio of CD45RO-expressing TILs was associated with a disease-free/overall survival improvement in OSCC patients. Furthermore, the number of TILs that express CD45RO was associated with the expression of MICA in tumors. These results suggest that CD45RO-expressing TILs are useful biomarkers for OSCC. Full article

Inflammatory bowel disease (IBD), comprising Crohn’s disease (CD) and ulcerative colitis (UC), is characterized as a chronic and recurrent inflammatory disease whose pathogenesis is still elusive. The gut microbiota exerts important and diverse effects on host physiology through maintaining immune balance and generating health-benefiting metabolites. Many studies have demonstrated that IBD is associated with disturbances in the composition and function of the gut microbiota. Both the abundance and diversity of gut microbiota are dramatically decreased in IBD patients. Furthermore, some particular classes of microbiota-derived metabolites, principally short-chain fatty acids, tryptophan, and its metabolites, and bile acids have also been implicated in the pathogenesis of IBD. In this review, we aim to define the disturbance of gut microbiota and the key classes of microbiota-derived metabolites in IBD pathogenesis. In addition, we also focus on scientific evidence on probiotics, not only on the molecular mechanisms underlying the beneficial effects of probiotics on IBD but also the challenges it faces in safe and appropriate application. Full article

African-American (AA) men are more than twice as likely to die of prostate cancer (PCa) than European American (EA) men. Previous in silico analysis revealed enrichment of altered lipid metabolic pathways in pan-cancer AA tumors. Here, we performed global unbiased lipidomics profiling on 48 matched localized PCa and benign adjacent tissues (30 AA, 24 ancestry-verified, and 18 EA, 8 ancestry verified) and quantified 429 lipids belonging to 14 lipid classes. Significant alterations in long chain polyunsaturated lipids were observed between PCa and benign adjacent tissues, low and high Gleason tumors, as well as associated with early biochemical recurrence, both in the entire cohort, and within AA patients. Alterations in cholesteryl esters, and phosphatidyl inositol classes of lipids delineated AA and EA PCa, while the levels of lipids belonging to triglycerides, phosphatidyl glycerol, phosphatidyl choline, phosphatidic acid, and cholesteryl esters distinguished AA and EA PCa patients with biochemical recurrence. These first-in-field results implicate lipid alterations as biological factors for prostate cancer disparities. Full article

A vegetarian diet has been associated with a lower risk of coronary artery disease (CAD). Plasma triacylglycerols, ceramides, and phosphatidylcholines may improve prediction of recurrent coronary events. We sought to investigate effects of a lacto-ovo-vegetarian diet (VD) on plasma lipidome in CAD patients and simultaneously assess associations of plasma lipids with the extent of coronary atherosclerotic burden. We analyzed 214 plasma lipids within glycerolipid, sphingolipid, and sterol lipid classes using lipidomics from a randomized controlled, crossover trial comprising 31 CAD patients on standard medical therapy. Subjects completed a four-week intervention with VD and isocaloric meat diet (MD), separated by a four-week washout period. The VD increased levels of 11 triacylglycerols and lowered 7 triacylglycerols, 21 glycerophospholipids, cholesteryl ester (18:0), and ceramide (d18:1/16:0) compared with MD. VD increased triacylglycerols with long-chain polyunsaturated fatty acyls while decreased triacylglycerols with saturated fatty acyls, phosphatidylcholines, and sphingomyelins than MD. The Sullivan extent score (SES) exhibited on coronary angiograms were inversely associated with triacylglycerols with long-chain polyunsaturated fatty acyls. Phosphatidylcholines that were lower with VD were positively associated with SES and the total number of stenotic lesions. The VD favorably changed levels of several lipotoxic lipids that have previously been associated with increased risk of coronary events in CAD patients. Full article

Let $f:M\to M$ be a diffeomorphism of a finite dimension, smooth compact Riemannian manifold M. In this paper, we demonstrate that if a diffeomorphism f lies within the $C^1$ interior of the set of all chain recurrence class-topologically stable diffeomorphisms, then the chain recurrence class is hyperbolic. Full article

The current paper is devoted to the investigation of the general form of the energy–momentum pseudotensor (pEMT) and the corresponding superpotential for the wide class of theories. The only requirement for such a theory is the general covariance of the action without any restrictions on the order of derivatives of the independent variables in it or their transformation laws. As a result of the generalized Noether procedure, we obtain a recurrent chain of the equations, which allows one to express canonical pEMT as a divergence of the superpotential. The explicit expression for this superpotential is also given. We discuss the structure of the obtained expressions and the conditions for the derived pEMT conservation laws to be satisfied independently (fully or partially) by the equations of motion. Deformations of the superpotential form for theories with a change in the independent variables in action are also considered. We apply these results to some interesting particular cases: general relativity and its modifications, particularly mimetic gravity and Regge–Teitelboim embedding gravity. Full article

In 1950, Nash proposed a natural equilibrium solution concept for games hence called Nash equilibrium, and proved that all finite games have at least one. The proof is through a simple yet ingenious application of Brouwer’s (or, in another version Kakutani’s) fixed point theorem, the most sophisticated result in his era’s topology—in fact, recent algorithmic work has established that Nash equilibria are computationally equivalent to fixed points. In this paper, we propose a new class of universal non-equilibrium solution concepts arising from an important theorem in the topology of dynamical systems that was unavailable to Nash. This approach starts with both a game and a learning dynamics, defined over mixed strategies. The Nash equilibria are fixpoints of the dynamics, but the system behavior is captured by an object far more general than the Nash equilibrium that is known in dynamical systems theory as chain recurrent set. Informally, once we focus on this solution concept—this notion of “the outcome of the game”—every game behaves like a potential game with the dynamics converging to these states. In other words, unlike Nash equilibria, this solution concept is algorithmic in the sense that it has a constructive proof of existence. We characterize this solution for simple benchmark games under replicator dynamics, arguably the best known evolutionary dynamics in game theory. For (weighted) potential games, the new concept coincides with the fixpoints/equilibria of the dynamics. However, in (variants of) zero-sum games with fully mixed (i.e., interior) Nash equilibria, it covers the whole state space, as the dynamics satisfy specific information theoretic constants of motion. We discuss numerous novel computational, as well as structural, combinatorial questions raised by this chain recurrence conception of games. Full article