Spatial Pathomics Toolkit for Quantitative Analysis of Podocyte Nuclei with Histology and Spatial Transcriptomics Data in Renal Pathology

Podocytes, specialized epithelial cells that envelop the glomerular capillaries, play a pivotal role in maintaining renal health. The current description and quantification of features on pathology slides are limited, prompting the need for innovative solutions to comprehensively assess diverse phenotypic attributes within Whole Slide Images (WSIs). In particular, understanding the morphological characteristics of podocytes, terminally differentiated glomerular epithelial cells, is crucial for studying glomerular injury. This paper introduces the Spatial Pathomics Toolkit (SPT) and applies it to podocyte pathomics. The SPT consists of three main components: (1) instance object segmentation, enabling precise identification of podocyte nuclei; (2) pathomics feature generation, extracting a comprehensive array of quantitative features from the identified nuclei; and (3) robust statistical analyses, facilitating a comprehensive exploration of spatial relationships between morphological and spatial transcriptomics features.The SPT successfully extracted and analyzed morphological and textural features from podocyte nuclei, revealing a multitude of podocyte morphomic features through statistical analysis. Additionally, we demonstrated the SPT's ability to unravel spatial information inherent to podocyte distribution, shedding light on spatial patterns associated with glomerular injury. By disseminating the SPT, our goal is to provide the research community with a powerful and user-friendly resource that advances cellular spatial pathomics in renal pathology. The implementation and its complete source code of the toolkit are made openly accessible at https://github.com/hrlblab/spatial_pathomics

The impact of immunoglobulin G N-glycosylation level on COVID-19 outcome: evidence from a Mendelian randomization study

BackgroundThe coronavirus disease 2019 (COVID-19) pandemic has exerted a profound influence on humans. Increasing evidence shows that immune response is crucial in influencing the risk of infection and disease severity. Observational studies suggest an association between COVID‐19 and immunoglobulin G (IgG) N-glycosylation traits, but the causal relevance of these traits in COVID-19 susceptibility and severity remains controversial.MethodsWe conducted a two-sample Mendelian randomization (MR) analysis to explore the causal association between 77 IgG N-glycosylation traits and COVID-19 susceptibility, hospitalization, and severity using summary-level data from genome-wide association studies (GWAS) and applying multiple methods including inverse-variance weighting (IVW), MR Egger, and weighted median. We also used Cochran’s Q statistic and leave-one-out analysis to detect heterogeneity across each single nucleotide polymorphism (SNP). Additionally, we used the MR-Egger intercept test, MR-PRESSO global test, and PhenoScanner tool to detect and remove SNPs with horizontal pleiotropy and to ensure the reliability of our results.ResultsWe found significant causal associations between genetically predicted IgG N-glycosylation traits and COVID-19 susceptibility, hospitalization, and severity. Specifically, we observed reduced risk of COVID-19 with the genetically predicted increased IgG N-glycan trait IGP45 (OR = 0.95, 95% CI = 0.92–0.98; FDR = 0.019). IGP22 and IGP30 were associated with a higher risk of COVID-19 hospitalization and severity. Two (IGP2 and IGP77) and five (IGP10, IGP14, IGP34, IGP36, and IGP50) IgG N-glycosylation traits were causally associated with a decreased risk of COVID-19 hospitalization and severity, respectively. Sensitivity analyses did not identify any horizontal pleiotropy.ConclusionsOur study provides evidence that genetically elevated IgG N-glycosylation traits may have a causal effect on diverse COVID-19 outcomes. Our findings have potential implications for developing targeted interventions to improve COVID-19 outcomes by modulating IgG N-glycosylation levels

Achieving high strength-ductility properties of wire-arc additive manufactured Al-Mg-Sc aluminum alloy via friction stir processing post-treatment and high temperature aging treatment

In this study, the high strength-ductility properties of wire-arc additive manufactured (WAAM) Al-Mg-Sc aluminum alloy were achieved by friction stir processing post-treatment (FSPPT) and high temperature aging treatment (HTAT). The FSPPT significantly refined the microstructure and eliminated porosity defects, which the average grain size was about 2.4 ± 0.2 μm in stirring zone (SZ). There was no obvious growth in grain size after HTAT and the average grain size was about 2.7 ± 0.4 μm in SZ. Many fine secondary Al3(Sc,Zr) phases were precipitated. Compared to WAAM sample, the average ultimate tensile strength (UTS), yield strength (YS) and elongation (EL) of FSPPT + HTAT sample increased by 57.9%, 54.7% and 205.9%, respectively

J. Energy Resour. Technol.-Trans. ASME

Coal resource is abundant in China, while the reserves of natural gas and petroleum are limited. Due to the rapid increase in the number of automobiles, a competitive way to produce liquid fuels from coal is urgently needed in China. A so-called "coal topping process" is under development at the Institute of Process Engineering, Chinese Academy of Sciences, from which liquid products can be obtained by flash pyrolysis in an integrated circulating fluidized bed system. In order to achieve a high yield of liquid products from high volatile coal, controlling the residence time of coal particles and produced gas may be of importance for minimizing the degree of the secondary reactions; i.e., polymerization and cracking of the liquid products. Experiments of the flash pyrolysis of coal have been conducted in an entrained bed reactor which is especially designed to study the influence of the coal particle residence time on the product distribution. The results show that the gaseous, liquid, and solid product distribution, the gas compositions as well as the liquid compositions depend strongly on the gas and particle residence time.Coal resource is abundant in China, while the reserves of natural gas and petroleum are limited. Due to the rapid increase in the number of automobiles, a competitive way to produce liquid fuels from coal is urgently needed in China. A so-called "coal topping process" is under development at the Institute of Process Engineering, Chinese Academy of Sciences, from which liquid products can be obtained by flash pyrolysis in an integrated circulating fluidized bed system. In order to achieve a high yield of liquid products from high volatile coal, controlling the residence time of coal particles and produced gas may be of importance for minimizing the degree of the secondary reactions; i.e., polymerization and cracking of the liquid products. Experiments of the flash pyrolysis of coal have been conducted in an entrained bed reactor which is especially designed to study the influence of the coal particle residence time on the product distribution. The results show that the gaseous, liquid, and solid product distribution, the gas compositions as well as the liquid compositions depend strongly on the gas and particle residence time

Study on the solid solution temperature of achieving ultra-high strength in wire-arc additive manufactured Al-Zn-Mg-Cu aluminum alloy

Al-Zn-Mg-Cu aluminum alloys are typically heat-treatable aluminum alloys. The heat treatment has a significant effect on the microstructure and mechanical properties of Al-Zn-Mg-Cu alloy. In this study, the solid solution temperature of achieving ultra-high strength in wire-arc additive manufactured 7B55 aluminum alloy was systematically investigated. The results showed that the microstructure of the as-deposited 7B55 aluminum alloy was composed of equiaxed grains with an average grain size of 4.2 ± 0.5 μm. A large number of the second phases were continuously distributed along grain boundaries. The precipitated phases within grains were mainly composed of the larger η phases and the smaller η′ phases, and the amount of precipitated phases was fewer. The second phases distributed along grain boundaries gradually dissolved into α-Al matrix with the increase of solid solution temperature, resulting in a higher supersaturation of the α-Al matrix and more homogeneous distribution of alloy elements. Combined with the results of DSC analysis, the optimal solid solution temperature of the 7B55 aluminum alloy was determined to be 480 °C. After solid solution of 480 °C，the microstructure was still composed of equiaxed grains with an average grain size of 4.8 ± 0.4 μm. The size of the grain did not grow significantly. A larger number of nanoscale fine GP zones, η′ phases and secondary Al3(Sc,Zr) particles were precipitated within the grains during subsequently artificial aging process, resulting in a significant increase in tensile properties. The ultimate tensile strength (UTS), yield strength (YS) and elongation (EL) reached 621 MPa, 555 MPa and 5.73%, respectively, which was significantly higher than the strength level of WAAM aluminum alloy reported among all the existing literature

Genomic Analysis of the Chicken Infectious Anemia Virus in a Specific Pathogen-Free Chicken Population in China

The antibody to chicken infectious anemia virus (CIAV) was positive in a specific pathogen-free (SPF) chicken population by ELISA test in our previous inspection, indicating a possible infection with CIAV. In this study, blood samples collected from the SPF chickens were used to isolate CIAV by inoculating into MSB1 cells and PCR amplification. A CIAV strain (SD1403) was isolated and successfully identified. Three overlapping genomic fragments were obtained by PCR amplification and sequencing. The full genome sequence of the SD1403 strain was obtained by aligning the sequences. The genome of the SD1403 strain was 2293 bp with a nucleotide identity of 94.8% to 98.5% when compared with 30 referred CIAV strains. The viral proteins VP2 and VP3 were highly conserved, but VP1 was not relatively conserved. Both amino acids 139 and 144 of VP1 were glutamine, which was in accord with the low pathogenic characteristics. In this study, we first reported that CIAV exists in Chinese SPF chicken populations and may be an important reason why attenuated vaccine can be contaminated with CIAV

Robotic‐assisted bronchoscopy for the diagnosis of peripheral pulmonary lesions: A systematic review and meta‐analysis

Abstract Robotic‐assisted bronchoscopy (RAB) is a newly developed bronchoscopic technique for the diagnosis of peripheral pulmonary lesions (PPLs). The objective of this meta‐analysis was to analyze the diagnostic yield and safety of RAB in patients with PPLs. Five databases (PubMed, Embase, Web of Science, CENTRAL, and ClinicalTrials.gov) were searched from inception to April 2023. Two independent investigators screened retrieved articles, extracted data, and assessed the study quality. The pooled diagnostic yield and complication rate were estimated. Subgroup analysis was used to explore potential sources of heterogeneity. Publication bias was assessed using funnel plots and the Egger test. Sensitivity analysis was also conducted to assess the robustness of the synthesized results. A total of 725 lesions from 10 studies were included in this meta‐analysis. No publication bias was found. Overall, RAB had a pooled diagnostic yield of 80.4% (95% CI: 75.7%–85.1%). Lesion size of >30 mm, presence of a bronchus sign, and a concentric radial endobronchial ultrasound view were associated with a statistically significantly higher diagnostic yield. Heterogeneity exploration showed that studies using cryoprobes reported better yields than those without cryoprobes (90.0%, 95% CI: 83.2%–94.7% vs. 79.0%, 95% CI: 75.8%–82.2%, p < 0.01). The pooled complication rate was 3.0% (95% CI: 1.6%–4.4%). In conclusion, RAB is an effective and safe technique for PPLs diagnosis. Further high‐quality prospective studies still need to be conducted