DNA methylation modulates epigenetic regulation in colorectal cancer diagnosis, prognosis and precision medicine.

Colorectal cancer (CRC) is a multifaceted disease influenced by the interplay of genetic and environmental factors. The clinical heterogeneity of CRC cannot be attributed exclusively to genetic diversity and environmental exposures, and epigenetic markers, especially DNA methylation, play a critical role as key molecular markers of cancer. This review compiles a comprehensive body of evidence underscoring the significant involvement of DNA methylation modifications in the pathogenesis of CRC. Moreover, this review explores the potential utility of DNA methylation in cancer diagnosis, prognostics, assessment of disease activity, and prediction of drug responses. Recognizing the impact of DNA methylation will enhance the ability to identify distinct CRC subtypes, paving the way for personalized treatment strategies and advancing precision medicine in the management of CRC.

Effect of carboxymethyl chitosan on the storage stability of rice dough during frozen storage.

In this study, we aimed to determine the effect of carboxymethyl chitosan (CMCh) and carboxymethyl cellulose sodium (CMCNa) on the quality of frozen rice dough. We used a variety of methods to conduct a thorough investigation of frozen rice dough, including nuclear magnetic resonance (NMR), scanning electron microscopy (SEM), Fourier transform infrared (FT-IR) spectroscopy, size exclusion high-performance liquid chromatography (SE-HPLC), X-ray diffraction (X-RD), differential scanning calorimetry (DSC), and rapid visco analyzer (RVA). Our findings showed that frozen storage caused significant damage to the texture of rice dough, and this damage was reduced by the inclusion of CMCh, which led to a gradual change in the orderly structure of proteins. The degree of cross-linking between CMCh-B (DS:1; 0.5 %, 1 %, and 1.5 %) and the large protein polymer was significantly higher than that between CMCh-A (DS:0.8; 0.5 %, 1 %, and 1.5 %) and CMCNa (DS:1; 1 %), which decreased the ability of bound water to become free water. This resulted in the increase of tan δ, which effectively delayed the structural transformation of frozen rice dough. Furthermore, the introduction of CMCh delayed the immediate order of starch and crystal structure modifications, altering the thermal properties and pasting qualities of the frozen rice dough. Therefore, 1.5 % CMCh-B showed the best protective effect on frozen rice dough.

Macroscopic on­site quality evaluation of biopsy specimens to improve the diagnostic accuracy of endoscopic ultrasound­guided fine needle aspiration using a 22­gauge needle for solid lesions: A single­center retrospective study.

The present study aimed to evaluate the clinical value of macroscopic on-site evaluation (MOSE) of solid masses by endoscopic ultrasound (EUS)-guided fine needle aspiration (FNA) using a standard 22-gauge needle and to explore the cut-off length of macroscopic visible core (MVC) required to obtain an accurate histopathological diagnosis. In total, 119 patients who satisfied the inclusion and exclusion criteria and underwent EUS-FNA were divided into conventional FNA and FNA combined with MOSE groups. In the MOSE group, the presence of MVC was examined and its total length measured, after which the pathological results of FNA were compared with the final diagnosis. The diagnostic sensitivity, specificity, accuracy, positive predictive value (PPV) and negative predictive value (NPV) of FNA in the two groups were calculated and the effect of MOSE on the FNA result was analyzed. The MOSE group had a higher diagnostic sensitivity (75.0% vs. 89.8%; P=0.038) and accuracy (74.5% vs. 90.6%; P=0.026). MVC was observed in 98.4% (63/64) of patients in the MOSE group. The median length of MVC was 15 mm. The optimal cut-off length of MVC for obtaining an accurate histological diagnosis was 13 mm, with a sensitivity of 90.2%. No statistically significant significance was observed in the specificity, PPV and NPV between the groups. Thus, MOSE helps to improve the diagnostic ability of FNA for solid masses and may be a useful alternative to assess the adequacy of puncture specimens in units where rapid on-site evaluation cannot be performed.

The enhanced expression of genes encoding diguanylate cyclases under cold stress contributes to the adhesion and biofilm formation of Shewanella putrefaciens WS13.

Shewanella putrefaciens is a special spoilage bacterium of seafood during cold storage, which is easy to form biofilm and bring serious hazard to the seafood quality. Life cycle of biofilm starts after bacterial adhesion, which is essential for the formation and development of biofilm. As a ubiquitous second messenger in bacteria, c-di-GMP regulates the conversion between bacterial planktonic state and biofilm state. In this study, the adhesion and biofilm formation of S. putrefaciens WS13 under 4°C were compared to those under 30°C. Atom force microscope and scanning electron microscope were used to study the bacterial adhesion. Biofilm was analyzed by Fourier transform infrared spectroscopy, Bradford assay and phenol-sulfuric acid method. High-performance liquid chromatographic-tandem mass spectrometric and quantitative real-time PCR were applied to study c-di-GMP level and genes encoding diguanylate cyclases in cells, respectively. Results showed that the swarming mobility of S. putrefaciens WS13 was weaker under 4°C, however, the adhesive force under 4°C was 4-5 times higher than that under 30°C. Biofilm biomass, extracellular polysaccharides and extracellular proteins were 2.5 times, 3 times, and 1.6 times more than those under 30°C, respectively, but biofilm composition formed under both temperatures were similar. c-di-GMP level in S. putrefaciens WS13 under 30°C was no more than half of that in the corresponding growth stage under 4°C. Quantitative real-time PCR analysis also showed that the expression of genes encoding diguanylate cyclases were significantly enhanced under 4°C than that under 30°C. S. putrefaciens WS13 adapted to the cold stress by enhancing the expression of genes encoding diguanylate cyclases to promote bacterial adhesion and biofilm formation. This study provides a theoretical foundation for the research on the cold adaptation mechanism of specific spoilage bacteria of seafood based on c-di-GMP, and also provides a new idea to control seafood quality from the perspective of microbial molecular biology.

Treatment of Infertile Women with Unilateral Tubal Occlusion Diagnosed by Hysterosalpingography: The Role of Intrauterine Insemination.

The optimal assisted reproductive treatment strategy for infertile women with unilateral tubal obstruction remains uncertain. To investigate the role of intrauterine insemination (IUI) in the treatment of infertile women with unilateral tubal occlusion, the data of 148 couples were retrospectively collected and analyzed. Seventy-eight infertile women with unilateral occlusion diagnosed by hysterosalpingography (HSG) were categorized as the study group and 70 others with unexplained infertility as the control group. The study group was divided into a proximal occlusion subgroup and a mid-distal occlusion subgroup for further analysis. The main outcomes, namely the clinical pregnancy rate (CPR), ongoing pregnancy rate (OPR), and live birth rate (LBR) per cycle, were analyzed. Our results showed a tendency of lower CPR, OPR, and LBR in the study group than in the control group, without statistical significance. Further investigations revealed that the unilateral proximal occlusion subgroup had similar CPR, OPR, and LBR as the control group, while the unilateral mid-distal occlusion subgroup had significantly lower CPR (5.1% vs. 20.0%, P=0.035), OPR (5.1% vs. 20.0%, P=0.035), and LBR (5.1% vs. 20.0%, P=0.035) than the control group. In conclusion, the clinical outcomes of IUI were worse in patients with unilateral tubal occlusion than in those with unexplained infertility. This might be primarily caused by the worse outcome of patients with unilateral mid-distal tubal occlusion instead of proximal occlusion.

Systematic variational method for statistical nonlinear state and parameter estimation.

In statistical data assimilation one evaluates the conditional expected values, conditioned on measurements, of interesting quantities on the path of a model through observation and prediction windows. This often requires working with very high dimensional integrals in the discrete time descriptions of the observations and model dynamics, which become functional integrals in the continuous-time limit. Two familiar methods for performing these integrals include (1) Monte Carlo calculations and (2) variational approximations using the method of Laplace plus perturbative corrections to the dominant contributions. We attend here to aspects of the Laplace approximation and develop an annealing method for locating the variational path satisfying the Euler-Lagrange equations that comprises the major contribution to the integrals. This begins with the identification of the minimum action path starting with a situation where the model dynamics is totally unresolved in state space, and the consistent minimum of the variational problem is known. We then proceed to slowly increase the model resolution, seeking to remain in the basin of the minimum action path, until a path that gives the dominant contribution to the integral is identified. After a discussion of some general issues, we give examples of the assimilation process for some simple, instructive models from the geophysical literature. Then we explore a slightly richer model of the same type with two distinct time scales. This is followed by a model characterizing the biophysics of individual neurons.

Estimating the biophysical properties of neurons with intracellular calcium dynamics.

We investigate the dynamics of a conductance-based neuron model coupled to a model of intracellular calcium uptake and release by the endoplasmic reticulum. The intracellular calcium dynamics occur on a time scale that is orders of magnitude slower than voltage spiking behavior. Coupling these mechanisms sets the stage for the appearance of chaotic dynamics, which we observe within certain ranges of model parameter values. We then explore the question of whether one can, using observed voltage data alone, estimate the states and parameters of the voltage plus calcium (V+Ca) dynamics model. We find the answer is negative. Indeed, we show that voltage plus another observed quantity must be known to allow the estimation to be accurate. We show that observing both the voltage time course V(t) and the intracellular Ca time course will permit accurate estimation, and from the estimated model state, accurate prediction after observations are completed. This sets the stage for how one will be able to use a more detailed model of V+Ca dynamics in neuron activity in the analysis of experimental data on individual neurons as well as functional networks in which the nodes (neurons) have these biophysical properties.