Gut microbiota and immune mediation: a Mendelian randomization study on granulomatosis with polyangiitis

BackgroundThe gut microbiota plays a pivotal role in influencing various health outcomes, including immune-mediated conditions. Granulomatosis with Polyangiitis (GPA) is one such condition, and its potential associations with gut microbiota remain underexplored.MethodUsing a two-sample Mendelian randomization approach, we investigated the causal links between gut microbiota and GPA. We sourced our data from multiple cohorts and consortiums, including the MiBioGen consortium. Our study design incorporated both direct associations and mediation effects of immune traits on the relationship between gut microbiota and GPA.ResultsOur analysis revealed significant associations between 1 phylum, 1 family 9 genus microbiota taxa and GPA. Furthermore, we identified several immune cell traits that mediated the effects of gut microbiota on GPA. For instance, the family Defluviitaleaceae and genus Defluviitaleaceae UCG011 influenced GPA through CD11c in granulocytes. The mediation effect proportions further elucidated the complex dynamics between gut microbiota exposures, immune markers, and their combined influence on GPA.ConclusionOur findings underscore the intricate relationship between gut microbiota, immune markers, and GPA. The identified associations and mediation effects provide valuable insights into the potential therapeutic avenues targeting gut microbiota to manage GPA

Effects of fracturing fluid composition and other factors on improving the oil imbibition recovery of shale reservoir

Imbibition is an important mechanism of shale reservoir development. In exploring the factors affecting the enhanced recovery of shale reservoirs by imbibition, laboratory spontaneous and forced imbibition experiments were conducted using outcrop cores of shale reservoirs. The effects of imbibition agent composition, fracture, and pressure on imbibition are obtained in this work based on imbibition recovery test findings and imbibition theory. Results show that the imbibition curve includes three stages, namely, imbibition, transition, and stability. Among the components of compound fracking fluid, surfactants have the greatest impact, whereas emulsifiers have the least impact. Complex crack structures and high-temperature environments can improve imbibition recovery. Pressure is inversely proportional to imbibition recovery in the highly stress-sensitive shale reservoir. In addition, the throughput time of the imbibition agent has an optimal value in the shale reservoir. After the huff-n-puff time exceeds the optimal value, the imbibition agent should be replaced to continuously improve the imbibition effect. The research results can serve as a basis for enhancing oil recovery through imbibition.Document Type: Original articleCited as: Li, S., Ye, Z., Wang, J., Tang, L., Lai, N. Effects of fracturing fluid composition and other factors on improving the oil imbibition recovery of shale reservoir. Capillarity, 2023, 9(3): 45-54. https://doi.org/10.46690/capi.2023.12.0

Kernel mapping for mitigating nonlinear impairments in optical short-reach communications

Nonlinear impairments induced by the opto-electronic components are one of the fundamental performance-limiting factors in high-speed optical short-reach communications, significantly hindering capacity improvement. This paper proposes to employ a kernel mapping function to map the signals in a Hilbert space to its inner product in a reproducing kernel Hilbert space, which has been successfully demonstrated to mitigate nonlinear impairments in optical short-reach communication systems. The operation principle is derived. An intensity modulation/direct detection system with 1.5-mu m vertical cavity surface emitting laser and 10-km 7-core fiber achieving 540.68-Gbps (net-rate 505.31-Gbps) has been carried out. The experimental results reveal that the kernel mapping based schemes are able to realize comparable transmission performance as the Volterra filtering scheme even with a high order. (C) 2019 Optical Society of America under the terms of the OSA Open Access Publishing Agreemen

Experimental Demonstration of 503.61-Gbit/s DMT over 10-km 7-Core Fiber with 1.5-\mu m SM-VCSEL for Optical Interconnects

We experimentally demonstrate a net-rate 503.61-Gbit/s discrete multitone (DMT) transmission over 10-km 7-core fiber with 1.5-\mu m single mode VCSEL, where low-complexity kernelrecursive-least-squares algorithm is employed for nonlinear channel equalization.Comment: 3 pages, 44th European Conference on Optical Communication (ECOC 2018), Rome, Italy, 201

Segment Anything Model (SAM) for Digital Pathology: Assess Zero-shot Segmentation on Whole Slide Imaging

The segment anything model (SAM) was released as a foundation model for image segmentation. The promptable segmentation model was trained by over 1 billion masks on 11M licensed and privacy-respecting images. The model supports zero-shot image segmentation with various segmentation prompts (e.g., points, boxes, masks). It makes the SAM attractive for medical image analysis, especially for digital pathology where the training data are rare. In this study, we evaluate the zero-shot segmentation performance of SAM model on representative segmentation tasks on whole slide imaging (WSI), including (1) tumor segmentation, (2) non-tumor tissue segmentation, (3) cell nuclei segmentation. Core Results: The results suggest that the zero-shot SAM model achieves remarkable segmentation performance for large connected objects. However, it does not consistently achieve satisfying performance for dense instance object segmentation, even with 20 prompts (clicks/boxes) on each image. We also summarized the identified limitations for digital pathology: (1) image resolution, (2) multiple scales, (3) prompt selection, and (4) model fine-tuning. In the future, the few-shot fine-tuning with images from downstream pathological segmentation tasks might help the model to achieve better performance in dense object segmentation

Genomic data for 78 chickens from 14 populations

Background: Since the domestication of the red jungle fowls (Gallus gallus; dating back to~10 000 B.P.) in Asia, domestic chickens (Gallus gallus domesticus) have been subjected to the combined effects of natural selection and human-driven artificial selection; this has resulted in marked phenotypic diversity in a number of traits, including behavior, body composition, egg production, and skin color. Population genomic variations through diversifying selection have not been fully investigated. Findings: The whole genomes of 78 domestic chickens were sequenced to an average of 18-fold coverage for each bird. By combining this data with publicly available genomes of five wild red jungle fowls and eight Xishuangbanna game fowls, we conducted a comprehensive comparative genomics analysis of 91 chickens from 17 populations. After aligning ~21.30 gigabases (Gb) of high-quality data from each individual to the reference chicken genome, we identified ~6.44 million (M) single nucleotide polymorphisms (SNPs) for each population. These SNPs included 1.10 M novel SNPs in 17 populations that were absent in the current chicken dbSNP (Build 145) entries. Conclusions: The current data is important for population genetics and further studies in chickens and will serve as a valuable resource for investigating diversifying selection and candidate genes for selective breeding in chickens.Peer reviewedAnimal Scienc

Comparative transcriptomics of 5 high-altitude vertebrates and their low-altitude relatives

Abstract Background: Species living at high altitude are subject to strong selective pressures due to inhospitable environments (e.g., hypoxia, low temperature, high solar radiation, and lack of biological production), making these species valuable models for comparative analyses of local adaptation. Studies that have examined high-altitude adaptation have identified a vast array of rapidly evolving genes that characterize the dramatic phenotypic changes in high-altitude animals. However, how high-altitude environment shapes gene expression programs remains largely unknown. Findings: We generated a total of 910 Gb of high-quality RNA-seq data for 180 samples derived from 6 tissues of 5 agriculturally important high-altitude vertebrates (Tibetan chicken, Tibetan pig, Tibetan sheep, Tibetan goat, and yak) and their cross-fertile relatives living in geographically neighboring low-altitude regions. Of these, ∼75% reads could be aligned to their respective reference genomes, and on average ∼60% of annotated protein coding genes in each organism showed FPKM expression values greater than 0.5. We observed a general concordance in topological relationships between the nucleotide alignments and gene expression–based trees. Tissue and species accounted for markedly more variance than altitude based on either the expression or the alternative splicing patterns. Cross-species clustering analyses showed a tissue-dominated pattern of gene expression and a species-dominated pattern for alternative splicing. We also identified numerous differentially expressed genes that could potentially be involved in phenotypic divergence shaped by high-altitude adaptation. Conclusions: These data serve as a valuable resource for examining the convergence and divergence of gene expression changes between species as they adapt or acclimatize to high-altitude environments