Methods for Change Points Detection and Model Selection in State-Space Models

This dissertation first proposes a novel online algorithm for the sequential detection of change points in state-space models. The algorithm is designed to take advantage of the theoretical distribution of the ratio of observation and evolution variance estimators. The algorithm is computationally fast, and can be used for large and streaming data, and is sensitive to changes in model parameters (including observation and evolution variances), as well as model structure. We consider change point detection in a sequential way, when observations are received one by one, or in batches, with a (possibly soft) restart after each detected change point. We provide the theoretical foundation of the algorithm and study its performance in two concrete state-space models which are frequently used to model the growth of epidemics over time: an auto-regressive AR(1) process, and a non-linear dynamical system (SEIR). We illustrate the performance of the algorithm with simulation studies and with an analysis on real Covid-19 datasets. We then extend the study to the theoretical results on the quotient of the variance ratios between two models and design a novel algorithm for state-space model comparison. The algorithm is reliable, and efficient and can help to reduce the computational resources required. Its performance is evaluated through simulation studies on three state-space models: AR(1), AR(3), and SEIR model. The algorithm is also used for model selection using Covid-19 data, and also takes a step further by combining the detected change point with the model selection process. Overall, this dissertation contributes to the field of change point detection and model selection in state-space models and provides useful tools for analyzing and modeling epidemic growth.</p

Differential expression and correlation of immunoregulation related piRNA in rheumatoid arthritis

BackgroundAlthough PIWI-interacting RNAs (piRNAs) have recently been associated with germline development and many human diseases, their expression pattern and relationship in autoimmune diseases remain indistinct. This study aimed to investigate the presence and correlation of piRNAs in rheumatoid arthritis (RA).MethodsWe first analyzed the expression profile of piRNAs using small RNA sequencing in peripheral leukocytes of three new-onset untreated RA patients and three healthy controls (HCs). We then selected piRNAs related to immunoregulation by bioinformatics analysis and verified them in 42 new-onset RA patients and 81 HCs by RT-qPCR. Furthermore, a receiver operating characteristic curve was generated to quantify the diagnostic performance of these piRNAs. A correlation analysis was conducted to observe the link between piRNA expression and RA clinical characteristics.ResultsA total of 15 upregulated and 9 downregulated piRNAs among 1,565 known piRNAs were identified in peripheral leukocytes of RA patients. Dysregulated piRNAs were enriched in numerous pathways related to immunity. After selection and validation, two immunoregulation piRNAs (piR-hsa-27620 and piR-hsa-27124) were significantly elevated in RA patients and have good abilities to distinguish patients from controls, which have the potential to serve as biomarkers. PIWI and other proteins implicated in the piRNA pathway were also associated with RA

Effects of brine- and NaCl- fermented carrots on lipid metabolism and gut microbiota in high-fat diet-fed mice

This study investigated the alterations in the phytochemical components and the antioxidant abilities of brine- and NaCl-fermented carrots and their effects on the lipid metabolism and microbial community in high-fat diet (HFD)-fed mice. Results showed that brine-fermentation significantly improved the contents of total dietary fiber, total phenols and β-carotene by 57 %, 48 % and 117 %, respectively. Fermented carrots possessed a higher level of antioxidant activities (P < 0.05). Furthermore, fermented carrot attenuated the increase in body weight, alleviated liver injury and oxidative stress but also promoted the lipid metabolism and reduced fatty acid accumulation in vivo, which were correlated with the total phenols and dietary fiber contents. Further investigation demonstrated that fermented carrots can attenuate HFD-induced lipid accumulation through the AMPK pathway and restoring the gut microbiota in HFD mice. Overall, fermented carrots can modulate the lipid accumulation in the HFD mice through the AMPK pathway and the microbiota community

Maternal polyunsaturated fatty acids and allergic disease development in the offspring

To the Editor,The increasing global prevalence of allergic diseases makes it imperative to identify modifiable risk factors for allergic disease development. Maternal antenatal plasma fatty acid composition has been proposed as a risk factor of infant allergic disease.1, 2 Polyunsaturated fatty acids (PUFAs) are key components of cell membranes and influence immune cell function by regulating membrane fluidity, intracellular signaling, and gene expression.3 They can be classified into n-3 and n-6 PUFAs, which are linked to production of anti-inflammatory and pro-inflammatory molecules, respectively.3 The fetoplacental unit lacks the desaturase enzymes required to synthesize long chain PUFAs so that, during pregnancy, the fetus is dependent on transplacental supply of PUFAs from the mothe