A Unified Pre-training and Adaptation Framework for Combinatorial Optimization on Graphs

Combinatorial optimization (CO) on graphs is a classic topic that has been extensively studied across many scientific and industrial fields. Recently, solving CO problems on graphs through learning methods has attracted great attention. Advanced deep learning methods, e.g., graph neural networks (GNNs), have been used to effectively assist the process of solving COs. However, current frameworks based on GNNs are mainly designed for certain CO problems, thereby failing to consider their transferable and generalizable abilities among different COs on graphs. Moreover, simply using original graphs to model COs only captures the direct correlations among objects, which does not consider the mathematical logicality and properties of COs. In this paper, we propose a unified pre-training and adaptation framework for COs on graphs with the help of the maximum satisfiability (Max-SAT) problem. We first use Max-SAT to bridge different COs on graphs since they can be converted to Max-SAT problems represented by standard formulas and clauses with logical information. Then, we further design a pre-training and domain adaptation framework to extract the transferable and generalizable features so that different COs can benefit from them. In the pre-training stage, Max-SAT instances are generated to initialize the parameters of the model. In the fine-tuning stage, instances from CO and Max-SAT problems are used for adaptation so that the transferable ability can be further improved. Numerical experiments on several datasets show that features extracted by our framework exhibit superior transferability and Max-SAT can boost the ability to solve COs on graphs

Identification and characterization of nucleotide metabolism and neuroendocrine regulation-associated modification patterns in stomach adenocarcinoma with auxiliary prognostic assessment and immunotherapy response prediction

BackgroundThe significance of nucleotide metabolism and neuroendocrine in cellular immune response and cancer is becoming more well-established. However, the mechanisms underlying nucleotide metabolism and neuroendocrine involvement in stomach adenocarcinoma (STAD) remain unclear.MethodsFirst, a pan-cancer overview of nucleotide metabolism and neuroendocrine-related genes (NMNGs) was explored through the integration of expression profiles, prognostic values, mutation information, methylation levels, and pathway-regulation relationships. We next extensively assessed variations in prognosis and tumor microenvironment (TME) features across the various modification patterns, based on an extensive analysis of the NMNG modification patterns of 808 STAD samples based on 46 NMNGs. Utilizing principal component analysis methodologies, the NMNGscore was developed to measure NMNG alteration patterns of individual tumors.ResultsPan-cancer analysis shows that NMNGs mostly act as risk genes in multiple cancer types, especially in STAD. Based on the NMNGs we detected two different NMNG modification patterns in STAD. Both patterns showed distinct immune cell infiltration features and biological behavior, with NMNGcluster A exhibiting a worse prognosis and a larger amount of immune infiltration. Differentially expressed genes with prognostic relevance were used to classify the STAD samples into three genomic subgroups. Analysis of survival rates revealed that cluster B genes were associated with longer life expectancy than clusters A and C. Individual STAD patients’ NMNG alteration patterns were analyzed by analyzing their NMNGscore signatures. NMNGscore and immune cells showed a statistically significant adverse correlation with each other. Increased longevity, a higher incidence of mutations, and a better response to immunotherapy were associated with patients’ NMNG scores.ConclusionsOur findings provide a personalized prediction tool for prognosis and immunotherapy sensitivity in patients, as well as a promising knowledge of nucleotide metabolism and neuroendocrine in STAD

Risk factors for symptomatic rotator cuff tears: a retrospective case–control study

BackgroundThe incidence and diagnostic rate of rotator cuff tears (RCTs) have increased significantly. The purpose of this study was to investigate and analyze the risk factors for symptomatic RCTs to provide a basis for their prevention and treatment.MethodsWe retrospectively analyzed the relevant clinical indicators of 193 patients with RCTs and 161 patients without RCTs hospitalized with shoulder pain as the main complaint from January 1, 2017, to August 31, 2021. Univariate analysis and multivariate logistic regression analysis were used to analyze the differences in potential risk factors between the two groups.ResultsUnivariate analysis revealed that age (p < 0.001), body mass index (BMI) (p = 0.036), hypertension (p < 0.001), coronary heart disease (p = 0.028), history of shoulder trauma (p < 0.001), hyperlipidemia (p = 0.025), type III acromion (p = 0.012) and critical shoulder angle (CSA) (p < 0.001) increased the risk of RCTs. Multivariate logistic regression analysis revealed that age ≥ 60 years (OR = 2.61, 95% CI = 1.23 to 5.12), CSA ≥ 35° (OR = 4.24, 95% CI = 1.60 to 11.22), hypertension (OR = 2.34, 95% CI = 1.33 to 4.11) and history of shoulder trauma (OR = 5.20, 95% CI = 2.87 to 9.45) were independent risk factors for symptomatic RCTs.ConclusionThe results of this study showed that age ≥ 60 years, CSA ≥35°, hypertension and history of shoulder trauma are independent risk factors for symptomatic RCTs and can provide directions for further development of prevention and treatment strategies. Future studies need to clarify the mechanism underlying the association between these risk factors and symptomatic RCTs

Mechanisms of action and synergetic formulas of plant-based natural compounds from traditional Chinese medicine for managing osteoporosis: a literature review

Osteoporosis (OP) is a systemic skeletal disease prevalent in older adults, characterized by substantial bone loss and deterioration of microstructure, resulting in heightened bone fragility and risk of fracture. Traditional Chinese Medicine (TCM) herbs have been widely employed in OP treatment owing to their advantages, such as good tolerance, low toxicity, high efficiency, and minimal adverse reactions. Increasing evidence also reveals that many plant-based compounds (or secondary metabolites) from these TCM formulas, such as resveratrol, naringin, and ginsenoside, have demonstrated beneficial effects in reducing the risk of OP. Nonetheless, the comprehensive roles of these natural products in OP have not been thoroughly clarified, impeding the development of synergistic formulas for optimal OP treatment. In this review, we sum up the pathological mechanisms of OP based on evidence from basic and clinical research; emphasis is placed on the in vitro and preclinical in vivo evidence-based anti-OP mechanisms of TCM formulas and their chemically active plant constituents, especially their effects on imbalanced bone homeostasis regulated by osteoblasts (responsible for bone formation), osteoclasts (responsible for bone resorption), bone marrow mesenchymal stem cells as well as bone microstructure, angiogenesis, and immune system. Furthermore, we prospectively discuss the combinatory ingredients from natural products from these TCM formulas. Our goal is to improve comprehension of the pharmacological mechanisms of TCM formulas and their chemically active constituents, which could inform the development of new strategies for managing OP

A novel 25-ferroptosis-related gene signature for the prognosis of gliomas

BackgroundFerroptosis is closely associated with cancer and is of great importance in the immune evasion of cancer. However, the relationship between ferroptosis and glioma is unclear.MethodsWe downloaded the expression profiles and clinical data of glioma from the GlioVis database and obtained the expression profiles of ferroptosis genes. A ferroptosis-related gene signature was developed for the prognosis of gliomas.ResultsWe screened out prognostic ferroptosis genes, named ferroptosis-related genes, by the Cox regression method. Based on these genes, we used unsupervised clustering to obtain two different clusters; the principal component analysis algorithm was applied to determine the gene score of each patient, and then all the patients were classified into two subgroups. Results showed that there exist obvious differences in survival between different clusters and different gene score subgroups. The prognostic model constructed by the 25 ferroptosis-related genes was then evaluated to predict the clinicopathological features of immune activity in gliomas.ConclusionThe ferroptosis-related genes play an important role in the malignant process of gliomas, potentially contributing to the development of prognostic stratification and treatment strategies

Osteoporosis guidelines on TCM drug therapies: a systematic quality evaluation and content analysis

ObjectiveThe aims of this study were to evaluate the quality of osteoporosis guidelines on traditional Chinese medicine (TCM) drug therapies and to analyze the specific recommendations of these guidelines.MethodsWe systematically collected guidelines, evaluated the quality of the guidelines using the Appraisal of Guidelines Research and Evaluation (AGREE) II tool, and summarized the recommendations of TCM drug therapies using the Patient-Intervention-Comparator-Outcome (PICO) model as the analysis framework.Results and conclusionsA total of 20 guidelines were included. Overall quality evaluation results revealed that four guidelines were at level A, four at level B, and 12 at level C, whose quality needed to be improved in the domains of “stakeholder involvement”, “rigor of development”, “applicability” and “editorial independence”. Stratified analysis suggested that the post-2020 guidelines were significantly better than those published before 2020 in the domains of “scope and purpose”, “stakeholder involvement” and “editorial independence”. Guidelines with evidence systems were significantly better than those without evidence systems in terms of “stakeholder involvement”, “rigor of development”, “clarity of presentation” and “applicability”. The guidelines recommended TCM drug therapies for patients with osteopenia, osteoporosis and osteoporotic fracture. Recommended TCM drugs were mainly Chinese patent medicine alone or combined with Western medicine, with the outcome mainly focused on improving bone mineral density (BMD)

Infrared nanoscopy of Dirac plasmons at the graphene-SiO2 interface

We report on infrared (IR) nanoscopy of 2D plasmon excitations of Dirac fermions in graphene. This is achieved by confining mid-IR radiation at the apex of a nanoscale tip: an approach yielding two orders of magnitude increase in the value of in-plane component of incident wavevector q compared to free space propagation. At these high wavevectors, the Dirac plasmon is found to dramatically enhance the near-field interaction with mid-IR surface phonons of SiO2 substrate. Our data augmented by detailed modeling establish graphene as a new medium supporting plasmonic effects that can be controlled by gate voltage.Comment: 12 pages, 4 figure

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Value of miR-15b-5p combined with ultrasound imaging in early diagnosis of renal cell carcinoma

Renal cancer is one of the most common malignancies, and its incidence is increasing year by year, second only to prostate and bladder cancers. Therefore, early screening is of great significance to prevent and improve the prognosis of patients with renal cancer. Therefore, this study intends to observe the early diagnostic value of miR-15b-5p combined with Colour ultrasound imaging in renal cell carcinoma. In this study, the clinical samples of 76 patients with renal cell carcinoma diagnosed by pathology in our hospital from April 2020 to June 2022 were retrospectively collected as the research objects. Another 100 healthy people who underwent general physical examination in our hospital during the same period were selected to detect the expression level of miR-15b-5 in serum by RT-PCR together with the 76 experimental samples. Colour ultrasound imaging was used to detect the blood flow distribution around and inside the kidney of the patients with renal cancer, and the parameters were measured and compared with the gold standard for statistical analysis. The expression level of miR-15b-5 in renal cell carcinoma group was significantly higher than that in control group. Most of them showed renal hamartoma (40.79%). Benign renal tumors were mainly characterized by type I and II blood flow, while malignant renal tumors were characterized by type III and IV blood flow. Compared with the pathological gold standard, the diagnostic accuracy of ultrasound imaging was founded to be about 81.25%. Further ROC analysis showed that ultrasound imaging combined with miR-15b-5 detection could effectively improve the early screening value of renal cell carcinoma. We observed that miR-15b-5 has a specific expression level in the serum of patients with renal cell carcinoma, and its combination with ultrasound imaging can significantly improve the early detection of renal cell carcinoma. This approach is envisaged to be highly useful for, early diagnosis, intervention and management of patients with renal cell carcinoma