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Normalization is a critical step in quantitative analyses of biological processes. Recent works show that cross-platform integration and normalization enable machine learning (ML) training on RNA microarray and RNA-seq data, but no independent datasets were used in their studies. Therefore, it is unclear how to improve ML modelling performance on independent RNA array and RNA-seq based datasets. Inspired by the house-keeping genes that are commonly used in experimental biology, this study tests the hypothesis that non-differentially expressed genes (NDEG) may improve normalization of transcriptomic data and subsequently cross-platform modelling performance of ML models. Microarray and RNA-seq datasets of the TCGA breast cancer were used as independent training and test datasets, respectively, to classify the molecular subtypes of breast cancer. NDEG (p>0.85) and differentially expressed genes (DEG, p<0.05) were selected based on the p values of ANOVA analysis and used for subsequent data normalization and classification, respectively. Models trained based on data from one platform were used for testing on the other platform. Our data show that NDEG and DEG gene selection could effectively improve the model classification performance. Normalization methods based on parametric statistical analysis were inferior to those based on nonparametric statistics. In this study, the LOG_QN and LOG_QNZ normalization methods combined with the neural network classification model seem to achieve better performance. Therefore, NDEG-based normalization appears useful for cross-platform testing on completely independent datasets. However, more studies are required to examine whether NDEG-based normalization can improve ML classification performance in other datasets and other omic data types.more » « lessFree, publicly-accessible full text available January 24, 2026
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Siegel (Ed.)Intestinal microbiota confers susceptibility to diet-induced obesity yet many probiotic species that synthesize tryptophan (trp) actually attenuate this effect, however the underlying mechanisms are unclear. We monocolonized germ-free (GF) mice with a widely consumed probiotic Lacticaseibacillus rhamnosus GG (LGG) under trp-free or -sufficient dietary conditions. We obtained untargeted metabolomics from the mouse feces and serum using liquid chromatography-mass spectrometry and obtained intestinal transcriptomic profiles via bulk-RNA sequencing. When comparing LGG-monocolonized mice with GF mice, we found a synergy between LGG and dietary trp in markedly promoting the transcriptome of fatty acid metabolism and -oxidation. Upregulation was specific and was not observed in transcriptomes of trp-fed conventional mice and mice monocolonized with Ruminococcus gnavus. Metabolomics showed that fecal and serum metabolites were also modified by LGG-host-trp interaction. We developed an R-Script based MEtabolome-TRanscriptome Correlation Analysis (METRCA) algorithm and uncovered LGG- and trp-dependent metabolites that were positively or negatively correlated with fatty acid metabolism and -oxidation gene networks. This high throughput metabolome-transcriptome correlation strategy can be used in similar investigations to reveal potential interactions between specific metabolites and functional or disease-related transcriptomic networks.more » « lessFree, publicly-accessible full text available April 1, 2025
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Kaestner Pack (Ed.)BACKGROUND & AIMS: Lacticaseibacillus rhamnosus GG (LGG) is the world’s most consumed probiotic species but its mechanism of action on intestinal permeability and differentiation as well as its interactions with an essential source of signaling metabolites, dietary tryptophan, are incompletely studied. METHODS: Untargeted metabolomic and transcriptomic analysis were performed for LGG mono-colonized germ-free (GF) mice fed with tryptophan (trp)-free or -sufficient diets. LGG-derived metabolites were profiled in vitro under anaerobic and aerobic conditions. Multiomic correlations were performed using a newly developed metabolome-transcriptome correlating bioinformatic algorism. Newly uncovered gut barrier-modulating metabolites whose abundances are regulated by LGG and dietary trp were functionally tested in Trans-Epithelial Electrical Resistance (TEER) assay, mouse enteroid, and dextran sulfate sodium (DSS) experimental colitis. The contribution of trp-methylnicotinamide (MNA) pathway to barrier protection is delineated at specific tight junction (TJ) proteins and enterocyte-promoting factors with gain and loss of function approaches. RESULTS: LGG, strictly in the presence of dietary trp, promotes the enterocyte program and the expression of multiple TJ genes, particularly Ocln. Fecal and serum metabolites that are synergistically stimulated by LGG and dietary trp are identified. Functional evaluations revealed a novel LGG-stimulated trp-dependent Vitamin B3 metabolism pathway, with MNA unexpectedly being the most robust barrier-protective metabolite in vitro and in vivo. Reduced serum MNA is significantly associated with increased disease activity in IBD patients. Exogenous MNA enhances gut barrier in homeostasis and robustly promotes colonic healing in DSS colitis. MNA is sufficient to promote intestinal epithelial Ocln and RNF43, a master inhibitor of Wnt pathway. Blocking trp or Vitamin B3 absorption abolishes barrier recovery in vivo. CONCLUSIONS: Our study uncovers a novel LGG-regulated dietary trp-dependent production of MNA that protects gut barrier against colitis.more » « lessFree, publicly-accessible full text available April 1, 2025
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Abstract 2D van der Waals (vdW) magnets open landmark horizons in the development of innovative spintronic device architectures. However, their fabrication with large scale poses challenges due to high synthesis temperatures (>500 °C) and difficulties in integrating them with standard complementary metal‐oxide semiconductor (CMOS) technology on amorphous substrates such as silicon oxide (SiO2) and silicon nitride (SiN
x ). Here, a seeded growth technique for crystallizing CrTe2films on amorphous SiNx /Si and SiO2/Si substrates with a low thermal budget is presented. This fabrication process optimizes large‐scale, granular atomic layers on amorphous substrates, yielding a substantial coercivity of 11.5 kilo‐oersted, attributed to weak intergranular exchange coupling. Field‐driven Néel‐type stripe domain dynamics explain the amplified coercivity. Moreover, the granular CrTe2devices on Si wafers display significantly enhanced magnetoresistance, more than doubling that of single‐crystalline counterparts. Current‐assisted magnetization switching, enabled by a substantial spin–orbit torque with a large spin Hall angle (85) and spin Hall conductivity (1.02 × 107ℏ/2e Ω⁻¹ m⁻¹), is also demonstrated. These observations underscore the proficiency in manipulating crystallinity within integrated 2D magnetic films on Si wafers, paving the way for large‐scale batch manufacturing of practical magnetoelectronic and spintronic devices, heralding a new era of technological innovation.Free, publicly-accessible full text available June 1, 2025 -
The analysis of non-metallic inclusions is crucial for the assessment of steel properties. Scanning electron microscopy (SEM) coupled with energy dispersive spectroscopy (EDS) is one of the most prominent methods for inclusion analysis. This study utilizes the output generated from SEM/EDS analysis to predict inclusion types from BSE images. Prediction models were generated using two different algorithms, Random Forest (RF) and convolutional neural networks (CNN), for comparison. For each method, three separate models were developed. Starting with a simple binary model to differentiate between inclusions and non-inclusions, then developing to more complex four and five class models. For the 4-class model, inclusions were split into oxides, sulfides, and oxy-sulfides, in addition to the non-inclusion class. The 5-class model included specific types of inclusions only, namely alumina, calcium aluminates, calcium sulfides, complex calcium-manganese sulfides, and oxy-sulfide inclusions. CNN achieved better accuracy for the binary (92%) and 4-class (78%) models, compared to RF (binary 87%, 4-class 75%). For the 5-class model, the results were similar, 60% accuracy for RF and 59% for CNN.more » « less
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Abstract Background Lactobacillus rhamnosus GG (LGG) is the most widely used probiotic, but the mechanisms underlying its beneficial effects remain unresolved. Previous studies typically inoculated LGG in hosts with established gut microbiota, limiting the understanding of specific impacts of LGG on host due to numerous interactions among LGG, commensal microbes, and the host. There has been a scarcity of studies that used gnotobiotic animals to elucidate LGG-host interaction, in particular for gaining specific insights about how it modifies the metabolome. To evaluate whether LGG affects the metabolite output of pathobionts, we inoculated with LGG gnotobiotic mice containing Propionibacterium acnes, Turicibacter sanguinis, and Staphylococcus aureus (PTS). Results 16S rRNA sequencing of fecal samples by Ion Torrent and MinION platforms showed colonization of germ-free mice by PTS or by PTS plus LGG (LTS). Although the body weights and feeding rates of mice remained similar between PTS and LTS groups, co-associating LGG with PTS led to a pronounced reduction in abundance of P. acnes in the gut. Addition of LGG or its secretome inhibited P. acnes growth in culture. After optimizing procedures for fecal metabolite extraction and metabolomic liquid chromatography-mass spectrometry analysis, unsupervised and supervised multivariate analyses revealed a distinct separation among fecal metabolites of PTS, LTS, and germ-free groups. Variables-important-in-projection scores showed that LGG colonization robustly diminished guanine, ornitihine, and sorbitol while significantly elevating acetylated amino acids, ribitol, indolelactic acid, and histamine. In addition, carnitine, betaine, and glutamate increased while thymidine, quinic acid and biotin were reduced in both PTS and LTS groups. Furthermore, LGG association reduced intestinal mucosal expression levels of inflammatory cytokines, such as IL-1α, IL-1β and TNF-α. Conclusions LGG co-association had a negative impact on colonization of P. acnes , and markedly altered the metabolic output and inflammatory response elicited by pathobionts.more » « less
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null (Ed.)ABSTRACT Microsporidia are a large phylum of obligate intracellular parasites. Approximately a dozen species of microsporidia infect humans, where they are responsible for a variety of diseases and occasionally death, especially in immunocompromised individuals. To better understand the impact of microsporidia on human cells, we infected human colonic Caco2 cells with Encephalitozoon intestinalis , and showed that these enterocyte cultures can be used to recapitulate the life cycle of the parasite, including the spread of infection with infective spores. Using transmission electron microscopy, we describe this lifecycle and demonstrate nuclear, mitochondrial and microvillar alterations by this pathogen. We also analyzed the transcriptome of infected cells to reveal host cell signaling alterations upon infection. These high-resolution imaging and transcriptional profiling analysis shed light on the impact of the microsporidial infection on its primary human target cell type. This article has an associated First Person interview with the first authors of the paper.more » « less
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ABSTRACT Although Wnt signaling is clearly important for the intestinal epithelial homeostasis, the relevance of various sources of Wnt ligands themselves remains incompletely understood. Blocking the release of Wnt in distinct stromal cell types suggests obligatory functions of several stromal cell sources and yields different observations. The physiological contribution of epithelial Wnt to tissue homeostasis remains unclear. We show here that blocking epithelial Wnts affects colonic Reg4+ epithelial cell differentiation and impairs colonic epithelial regeneration after injury in mice. Single-cell RNA analysis of intestinal stroma showed that the majority of Wnt-producing cells were contained in transgelin (Tagln+) and smooth muscle actin α2 (Acta2+) expressing populations. We genetically attenuated Wnt production from these stromal cells using Tagln-Cre and Acta2-CreER drivers, and found that blockage of Wnt release from either epithelium or Tagln+ and Acta2+ stromal cells impaired colonic epithelial healing after chemical-induced injury. Aggregated blockage of Wnt release from both epithelium and Tagln+ or Acta2+ stromal cells drastically diminished epithelial repair, increasing morbidity and mortality. These results from two uncharacterized stromal populations suggested that colonic recovery from colitis-like injury depends on multiple Wnt-producing sources.more » « less