A hybrid adaptive MCMC algorithm in function spaces

The preconditioned Crank-Nicolson (pCN) method is a Markov Chain Monte Carlo (MCMC) scheme, specifically designed to perform Bayesian inferences in function spaces. Unlike many standard MCMC algorithms, the pCN method can preserve the sampling efficiency under the mesh refinement, a property referred to as being dimension independent. In this work we consider an adaptive strategy to further improve the efficiency of pCN. In particular we develop a hybrid adaptive MCMC method: the algorithm performs an adaptive Metropolis scheme in a chosen finite dimensional subspace, and a standard pCN algorithm in the complement space of the chosen subspace. We show that the proposed algorithm satisfies certain important ergodicity conditions. Finally with numerical examples we demonstrate that the proposed method has competitive performance with existing adaptive algorithms.Comment: arXiv admin note: text overlap with arXiv:1511.0583

Amyopathic Dermatomyositis May Be on the Spectrum of Autoinflammatory Disease: A Clinical Review

Systemic autoinflammatory diseases (SAIDs) are distinct from autoimmune diseases. The former primarily results from abnormal innate immune response and genetic testing is crucial for disease diagnosis. Similar cutaneous involvement is a main feature for both SAID and dermatomyositis (DM), so they can be confused with each other. A literature search of PubMed and MEDLINE was conducted for relevant articles. The similarities and differences between these two types of diseases were analyzed. We found phenotypic similarities between these two types of disorders. Accumulating data supports a major role of the innate immune system and a similar cytokine profile. Molecular testing using an autoinflammatory disease gene panel may help identify SAID patients from the DM population and may offer therapeutic benefit using interleukin-1 (IL-1) inhibitors. A subset of DM, notably amyopathic dermatomyositis in the absence of autoantibodies may be on the spectrum of autoinflammatory disease

Over-expression of eukaryotic translation initiation factor 4 gamma 1 correlates with tumor progression and poor prognosis in nasopharyngeal carcinoma

<p>Abstract</p> <p>Background</p> <p>The aim of the present study was to analyze the expression of eukaryotic translation initiation factor 4 gamma 1 (<it>EIF4G1</it>) in nasopharyngeal carcinoma (NPC) and its correlation with clinicopathologic features, including patients' survival time.</p> <p>Methods</p> <p>Using real-time PCR, we detected the expression of <it>EIF4G1 </it>in normal nasopharyngeal tissues, immortalized nasopharyngeal epithelial cell lines NP69, NPC tissues and cell lines. <it>EIF4G1 </it>protein expression in NPC tissues was examined using immunohistochemistry. Survival analysis was performed using Kaplan-Meier method. The effect of <it>EIF4G1 </it>on cell invasion and tumorigenesis were investigated.</p> <p>Results</p> <p>The expression levels of <it>EIF4G1 </it>mRNA were significantly greater in NPC tissues and cell lines than those in the normal nasopharyngeal tissues and NP69 cells (<it>P </it>< 0.001). Immunohistochemical analysis revealed that the expression of <it>EIF4G1 </it>protein was higher in NPC tissues than that in the nasopharyngeal tissues (<it>P </it>< 0.001). In addition, the levels of <it>EIF4G1 </it>protein in tumors were positively correlated with tumor T classification (<it>P </it>= 0.039), lymph node involvement (N classification, <it>P </it>= 0.008), and the clinical stages (<it>P </it>= 0.003) of NPC patients. Patients with higher <it>EIF4G</it>1 expression had shorter overall survival time (<it>P </it>= 0.019). Multivariate analysis showed that <it>EIF4G1 </it>expression was an independent prognostic indicator for the overall survival of NPC patients. Using shRNA to knock down the expression of <it>EIF4G1 </it>not only markedly inhibited cell cycle progression, proliferation, migration, invasion, and colony formation, but also dramatically suppressed <it>in vivo </it>xenograft tumor growth.</p> <p>Conclusion</p> <p>Our data suggest that <it>EIF4G1 </it>can serve as a biomarker for the prognosis of NPC patients.</p

An approximate empirical Bayesian method for large-scale linear-Gaussian inverse problems

We study Bayesian inference methods for solving linear inverse problems, focusing on hierarchical formulations where the prior or the likelihood function depend on unspecified hyperparameters. In practice, these hyperparameters are often determined via an empirical Bayesian method that maximizes the marginal likelihood function, i.e., the probability density of the data conditional on the hyperparameters. Evaluating the marginal likelihood, however, is computationally challenging for large-scale problems. In this work, we present a method to approximately evaluate marginal likelihood functions, based on a low-rank approximation of the update from the prior covariance to the posterior covariance. We show that this approximation is optimal in a minimax sense. Moreover, we provide an efficient algorithm to implement the proposed method, based on a combination of the randomized SVD and a spectral approximation method to compute square roots of the prior covariance matrix. Several numerical examples demonstrate good performance of the proposed method

Transcriptional patterns, biomarkers and pathways characterizing nasopharyngeal carcinoma of Southern China

<p>Abstract</p> <p>Background</p> <p>The pathogenesis of nasopharyngeal carcinoma (NPC) is a complicated process involving genetic predisposition, Epstein-Bar Virus infection, and genetic alterations. Although some oncogenes and tumor suppressor genes have been previously reported in NPC, a complete understanding of the pathogenesis of NPC in the context of global gene expression, transcriptional pathways and biomarker assessment remains to be elucidated.</p> <p>Methods</p> <p>Total RNA from 32 pathologically-confirmed cases of poorly-differentiated NPC was divided into pools inclusive of four consecutive specimens and each pool (T1 to T8) was co-hybridized with pooled RNA from 24 normal non-cancerous nasopharyngeal tissues (NP) to a human 8K cDNA array platform. The reliability of microarray data was validated for selected genes by semi-quantitative RT-PCR and immunohistochemistry.</p> <p>Results</p> <p>Stringent statistical filtering parameters identified 435 genes to be up-regulated and 257 genes to be down-regulated in NPC compared to NP. Seven up-regulated genes including CYC1, MIF, LAMB3, TUBB2, UBE2C and TRAP1 had been previously proposed as candidate common cancer biomarkers based on a previous extensive comparison among various cancers and normal tissues which did not, however, include NPC or NP. In addition, nine known oncogenes and tumor suppressor genes, MIF, BIRC5, PTTG1, ATM, FOXO1A, TGFBR2, PRKAR1A, KLF5 and PDCD4 were identified through the microarray literature-based annotation search engine MILANO, suggesting these genes may be specifically involved in the promotion of the malignant conversion of nasopharyngeal epithelium. Finally, we found that these differentially expressed genes were involved in apoptosis, MAPK, VEGF and B cell receptor signaling pathways and other functions associated with cell growth, signal transduction and immune system activation.</p> <p>Conclusion</p> <p>This study identified potential candidate biomarkers, oncogenes/tumor suppressor genes involved in several pathways relevant to the oncogenesis of NPC. This information may facilitate the determination of diagnostic and therapeutic targets for NPC as well as provide insights about the molecular pathogenesis of NPC.</p

An alternative method of Bakri balloon placement for postpartum hemorrhage after vaginal delivery

Objectives: We developed a new Bakri balloon tamponade (BBT) placement technique after vaginal delivery, which aimed to be faster without balloon slippage. This study compared the new method with standard placement of BBT in women with postpartum hemorrhage (PPH) after vaginal delivery. Material and methods: This study was undertaken of women who underwent vaginal delivery at the obstetrics and gynecology departments of the Hospital of Chengdu University of Traditional Chinese Medicine, Sichuan Provincial Hospital for Women and Children, and Si Chuan JINXIN Women and Children Hospital between January 2014 and December 2020. Women who underwent BBT for PPH were grouped according to placement method into the old-BBT group and the new-BBT group. Results: Of 20487 childbirths by vaginal delivery, 512 (2.50%) had PPH, 77 women underwent BBT (old-BBT n = 28, new-BBT n = 49). Background characteristics were similar except prothrombin time (PT, p &lt; 0.01) and activated partial thromboplastin time (APTT, p &lt; 0.004) were lower in the new-BBT group than the old-BBT group. The operation time was shorter in the new-BBT group (p &lt; 0.001) with less bleeding (p &lt; 0.003) and saline injection (p &lt; 0.001). A balloon slippage was less likely (p &lt; 0.008) and postoperative bleeding (p &lt; 0.01), transfusion rate (p &lt; 0.03), transfusion volume (p &lt; 0.002), and hospital stay was lower in the new-BBT group (p &lt; 0.015). Multivariate analysis suggested PT (OR = 0.039, 95% CI: 0.002–0.730, p &lt; 0.030), international normalized ratio (OR = 8.244, 95% CI: 3.807–17.850, p &lt; 0.009), and BBT method (OR = 5.200, 95% CI: 1.745-15.493, p &lt; 0.003), were associated with requiring a blood transfusion. Conclusions: This method of BBT placement reduced operation time, balloon slippage, bleeding, and hospital stay in women with PPH after vaginal delivery

Atomic Structure Evolution of Pt–Co Binary Catalysts: Single Metal Sites versus Intermetallic Nanocrystals

Due to their exceptional catalytic properties for the oxygen reduction reaction (ORR) and other crucial electrochemical reactions, PtCo intermetallic nanoparticle (NP) and single atomic (SA) Pt metal site catalysts have received considerable attention. However, their formation mechanisms at the atomic level during high-temperature annealing processes remain elusive. Here, the thermally driven structure evolution of Pt–Co binary catalyst systems is investigated using advanced in situ electron microscopy, including PtCo intermetallic alloys and single Pt/Co metal sites. The pre-doping of CoN4 sites in carbon supports and the initial Pt NP sizes play essential roles in forming either Pt3Co intermetallics or single Pt/Co metal sites. Importantly, the initial Pt NP loadings against the carbon support are critical to whether alloying to L12-ordered Pt3Co NPs or atomizing to SA Pt sites at high temperatures. High Pt NP loadings (e.g., 20%) tend to lead to the formation of highly ordered Pt3Co intermetallic NPs with excellent activity and enhanced stability toward the ORR. In contrast, at a relatively low Pt loading (<6 wt%), the formation of single Pt sites in the form of PtC3N is thermodynamically favorable, in which a synergy between the PtC3N and the CoN4 sites could enhance the catalytic activity for the ORR, but showing insufficient stability

Impacts of conversion of cropland to grassland on the C-N-P stoichiometric dynamics of soil, microorganisms, and enzymes across China: A synthesis

In response to escalating land degradation, the conversion of cropland to grassland has emerged as a crucial mitigation strategy. This conversion has a significant influence on the stoichiometry of soil, microorganisms, and enzymes, specifically in relation to carbon (C), nitrogen (N), and phosphorus (P). A meta-analysis was conducted with 371 observations from 122 articles investigating the impacts of cropland to grassland conversion on the C-N-P stoichiometric dynamics of soils, microorganisms, and enzymes across China. The findings revealed that conversion significantly increased soil C:P (9.0%), soil N:P (5.6%), microbial C:N (15.5%), and notably, microbial C:P by 57.9%. This substantial increase in microbial C:P indicates that microbial communities are highly responsive to land use conversion. Contrastingly, the enzyme C:P ratio decreased by 19.8%, suggesting microbial adaptation to changing nutrient availability. The duration of conversion was positively correlated with soil C:P and N:P ratios, implying that relative P availability may decrease as conversion progresses. However, duration was negatively correlated with microbial C:P. Environmental factors such as clay content, mean annual temperature, and mean annual precipitation were positively correlated with microbial C:N and negatively correlated with microbial N:P, while soil pH was inversely correlated with microbial C:N. These results suggest the substantial influence of cropland to grassland conversion on soil, microbial, and enzyme stoichiometry, with particularly pronounced effects on microbial communities. The observed shifts in stoichiometric ratios suggest changes in nutrient cycling and availability following conversion. While these changes are primarily attributed to the land use conversion, we acknowledge that alterations in management practices, such as reduced fertilization, likely contribute to the observed stoichiometric shifts. Our findings emphasize the importance of considering both environmental factors and management practices when implementing grassland conversion initiatives