Distance-weighted Sinkhorn loss for Alzheimer's disease classification.

Traditional loss functions such as cross-entropy loss often quantify the penalty for each mis-classified training sample without adequately considering its distance from the ground truth class distribution in the feature space. Intuitively, the larger this distance is, the higher the penalty should be. With this observation, we propose a penalty called distance-weighted Sinkhorn (DWS) loss. For each mis-classified training sample (with predicted label A and true label B), its contribution to the DWS loss positively correlates to the distance the training sample needs to travel to reach the ground truth distribution of all the A samples. We apply the DWS framework with a neural network to classify different stages of Alzheimer's disease. Our empirical results demonstrate that the DWS framework outperforms the traditional neural network loss functions and is comparable or better to traditional machine learning methods, highlighting its potential in biomedical informatics and data science.

QOT: Efficient Computation of Sample Level Distance Matrix from Single-Cell Omics Data through Quantized Optimal Transport.

Single-cell technologies have emerged as a transformative technology enabling high-dimensional characterization of cell populations at an unprecedented scale. The data's innate complexity and voluminous nature pose significant computational and analytical challenges, especially in comparative studies delineating cellular architectures across various biological conditions (i.e., generation of sample level distance matrices). Optimal Transport (OT) is a mathematical tool that captures the intrinsic structure of data geometrically and has been applied to many bioinformatics tasks. In this paper, we propose QOT (Quantized Optimal Transport), a new method enables efficient computation of sample level distance matrix from large-scale single-cell omics data through a quantization step. We apply our algorithm to real-world single-cell genomics and pathomics datasets, aiming to extrapolate cell-level insights to inform sample level categorizations. Our empirical study shows that QOT outperforms OT-based algorithms in terms of accuracy and robustness when obtaining a distance matrix at the sample level from high throughput single-cell measures. Moreover, the sample level distance matrix could be used in downstream analysis (i.e. uncover the trajectory of disease progression), highlighting its usage in biomedical informatics and data science.

Impacts of artificial reef on community structure and functional traits of macrobenthos near Furong Island, Shandong, China.

To evaluate the ecological restoration effect of artificial reefs and explore the impacts of artificial reefs age on the structure and functional traits of the macrobenthos community, two artificial reef areas with different reef ages in the coastal waters of Furong Island, Laizhou Bay were investigated in May, August, and October 2019. A total of 120 macrobenthos species were identified in the three seasons, including 72 species in the control area, 74 species in the artificial reef with short age (1 year), and 80 species in the artificial reef with greater age (4-5 years). Nihonotrypaea harmandi was the dominant species in all areas. The biomass, abundance, Shannon diversity index, Margalef species richness index of macrobenthos communities were all in order of reef area with greater age > reef area with lower age > control area, and the biomass and abundance in the reef area with greater age were significantly higher than those in the other two areas. The composition and relative abundance of functional traits of macrobenthos communities in the reef area and the control area were different. However, the dominant categories of traits in different areas were consistent, including deposit-feeder, burrower, medium body size, medium life span, high body flexibility and infauna. The composition and relative abundance of functional traits of macrobenthos communities in the reef area and the control area were different mainly in feeding mode, habitat, and body size. The relative abundance of smaller individuals (1-3 cm) and suspension feeders in the reef area was higher than those in the control area, while predator abundance was lower, and such effect became more pronounced with increasing reef age. The reef area was significantly higher than the control area in functional diversity, but without significant difference in functional redundancy. The results of abundance/biomass comparison curve and marine biotic index showed that the benthic ecological quality in the study area was good. The macrobenthos community was slightly disturbed after 1 year of reef construction, while the conservation effect of macrobenthic resources and the benthic ecological quality were significantly improved after 4-5 years of reef placement.

Pathogenesis and treatment of Sjogren's syndrome: Review and update.

Sjogren's syndrome (SS) is a chronic autoimmune disease accompanied by multiple lesions. The main manifestations include dryness of the mouth and eyes, along with systemic complications (e.g., pulmonary disease, kidney injury, and lymphoma). In this review, we highlight that IFNs, Th17 cell-related cytokines (IL-17 and IL-23), and B cell-related cytokines (TNF and BAFF) are crucial for the pathogenesis of SS. We also summarize the advances in experimental treatment strategies, including targeting Treg/Th17, mesenchymal stem cell treatment, targeting BAFF, inhibiting JAK pathway, et al. Similar to that of SLE, RA, and MS, biotherapeutic strategies of SS consist of neutralizing antibodies and inflammation-related receptor blockers targeting proinflammatory signaling pathways. However, clinical research on SS therapy is comparatively rare. Moreover, the differences in the curative effects of immunotherapies among SS and other autoimmune diseases are not fully understood. We emphasize that targeted drugs, low-side-effect drugs, and combination therapies should be the focus of future research.

Design of compact dual-mode photoelectric modulator with high process tolerance based on vanadium dioxide.

Opto-electro modulators with nanometer-scale footprint are indispensable in integrated photonic electronic circuits. Due to weak light-matter interactions and limits of micro-nano fabrication technology, it is challenging to shrink a modulator to subwavelength size. In recent years, hybrid modulators based on surface plasmons have been proposed to solve this problem. Although the introduced high lossy surface plasmons provide large modulation depth, the polarization selectivity limits its application. Toward this end, in this paper, we present a design of an ultra-compact vanadium oxide (VO2)-based plasmonic waveguide modulator for both transverse electric (TE) and transverse magnetic (TM) modes. The device consists of two silicon tapers and a silicon waveguide embedded with a VO2 wedge. When electrical signals put on the device change the phase of VO2 from a metal to an insulator, the output optical signals along the waveguide are significantly modulated. For a 1.5 µm length modulator operating at 1.55 µm wavelength, the extinction ratio is 11.62 dB for the TE mode and 8.86 dB for the TM mode, while the insertion loss is 4.31 dB for the TE mode and 4.12 dB for the TM mode. Furthermore, the proposed design has excellent tolerance for fabrication process error, which greatly increases the yield rate of products and indicates a promotable application prospect.

High fructose diet: A risk factor for immune system dysregulation.

Excessive intake of sweets is a predisposing factor for metabolic disorders, and fructose, as one of the major dietary sugars in the diet, has been shown to be a major cause of obesity, diabetes, and metabolic syndrome. These disorders are usually associated with immune dysfunction. Therefore, exploring the effects of a high fructose diet on the immune system may provide insight into the underlying mechanisms of these diseases. We synthesized the available evidence to suggest that excessive fructose intake disrupts the body's immune homeostasis by promoting immune cell metabolic rearrangements, alterations in gut microbial community structure, and intestinal barrier permeability. Indeed, not only does fructose itself affect immune system homeostasis, but its metabolites also have a profound influence. The metabolites from fructolysis are mainly produced in the small intestine and liver and subsequently enter the systemic circulation. Elevated levels of fructose metabolites, such as uric acid, FFAs, and lactate, are closely associated with oxidative stress and local tissue and organ inflammatory responses. In this review, we will focus on the link between fructose and inflammatory responses. In the meanwhile, we will also briefly summarize the studies of cancer development and immune escape mediated by fructose, as it might be beneficial for cancer immunotherapy.

Taxonomic and functional responses of macrofaunal assemblage provide insight into ecological impacts of bottom-based Manila clam aquaculture.

Understanding ecological impacts of bottom-based clam aquaculture can improve its management. In this study, taxonomic and functional macrofaunal assemblage were evaluated for two clam farms located in Laizhou Bay, China. Beta diversity and factors potentially regulating the dissimilarity of macrofauna were estimated. Both taxonomic and functional composition of macrofauna showed large differences between the clam farm and the control area. Functional dissimilarity within the clam farms was found to be nestedness and negatively correlated to local clam abundance. Additionally, the cultured clam enhanced the functional richness but made the macrofaunal assemblage more fragile against species or function loss. This effect would increase with clam abundance, which highlights the importance of identifying optimal clam culture intensity in developing a bottom-based clam aquaculture program.

Mannose Treatment: A Promising Novel Strategy to Suppress Inflammation.

High glucose and fructose intake have been proven to display pro-inflammatory roles during the progression of inflammatory diseases. However, mannose has been shown to be a special type of hexose that has immune regulatory functions. In this review, we trace the discovery process of the regulatory functions of mannose and summarize some past and recent studies showing the therapeutic functions of mannose in inflammatory diseases. We conclude that treatment with mannose can suppress inflammation by inducing regulatory T cells, suppressing effector T cells and inflammatory macrophages, and increasing anti-inflammatory gut microbiome. By summarizing all the important findings, we highlight that mannose treatment is a safe and promising novel strategy to suppress inflammatory diseases, including autoimmune disease and allergic disease.