Publications by authors named "Tianming Zhou"

Leveraging blackcurrant anthocyanin (BC) as an indicator and carboxymethyl cellulose (CMC), gum xanthan (GX), and citric acid (CA) as film fabricating materials, an innovative amine-responsive beef freshness intelligent film, known as CGC-BC, was successfully created. It was found that the physical characteristics, sensitivity to the biogenic amine reaction, and original color of the film were all highly influenced by the pH of the film-forming solutions. The film's freshness monitoring ability was assessed at 4, 25, and 35 °C, and various color changes were employed to monitor beef deterioration.

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The organization of mammalian genomes features a complex, multiscale three-dimensional (3D) architecture, whose functional significance remains elusive because of limited single-cell technologies that can concurrently profile genome organization and transcriptional activities. Here, we introduce genome architecture and gene expression by sequencing (GAGE-seq), a scalable, robust single-cell co-assay measuring 3D genome structure and transcriptome simultaneously within the same cell. Applied to mouse brain cortex and human bone marrow CD34 cells, GAGE-seq characterized the intricate relationships between 3D genome and gene expression, showing that multiscale 3D genome features inform cell-type-specific gene expression and link regulatory elements to target genes.

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Chinese sausage is a popular traditional Chinese meat product, but its high-fat content makes consumers hesitant. The purpose of this study is to compare the nutritional differences of Chinese sausages with different fermentation times (0, 10, 20, 30 d) and fat content (the initial content was 11.59% and 20.

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This study focused on the development and evaluation of a stable emulsion system using rice starch, protein isolates, and bran oil as food ingredients. This was performed using a one-factor-at-a-time (OFAT) experimental strategy, which was subsequently refined using response surface modeling (RSM), and the emulsion was then characterized. The resulting quadratic polynomial model effectively captured all the responses, with regression coefficients exceeding 0.

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Beta-carotene (β-C) is a natural phytochemical with good functions, but the strong hydrophobicity and acid-base instability limit its absorption in the intestine. A well-designed heat-induced myofibrillar protein (MP) transport system can improve the bioavailability of β-C, and temperature might have a significant impact on this process. This study utilized multispectral, surface plasmon resonance (SPR), and molecular dynamics simulation to investigate the effect of temperature on the interaction between β-C and MP.

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Article Synopsis
  • Lactic acid bacteria (LAB) struggle with protein and fat breakdown, which limits flavor in fermented sausages, whereas Bacillus has strong enzyme production for these processes.
  • A specific strain, Bacillus cereus DM423, was tested as a co-starter alongside Lactiplantibacillus plantarum HH-LP56, and it significantly enhanced the sausage's flavor without disrupting fermentation.
  • Analysis showed DM423 improved protein and fat hydrolysis and increased various flavor compounds, leading to the conclusion that this strain could be a valuable co-starter for better flavor development in sausages.
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The organization of mammalian genomes within the nucleus features a complex, multiscale three-dimensional (3D) architecture. The functional significance of these 3D genome features, however, remains largely elusive due to limited single-cell technologies that can concurrently profile genome organization and transcriptional activities. Here, we report GAGE-seq, a highly scalable, robust single-cell co-assay that simultaneously measures 3D genome structure and transcriptome within the same cell.

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This work compared the flavor evolution of normal-fat (NF) with that of low-fat (LF) Chinese sausage during natural fermentation. Higher degree of lipid oxidation occurred in NF sausages, resulting in its faster formation of stable volatile profiles. Faster formation of esters occurred in NF sausage in the initial 10 days, whereas prolonged fermentation reduced the level of ethyl lactate-M, ethyl heptanoate, ethyl hexanoate-D and ethyl pentanoate-D.

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Spatial transcriptomics can reveal spatially resolved gene expression of diverse cells in complex tissues. However, the development of computational methods that can use the unique properties of spatial transcriptome data to unveil cell identities remains a challenge. Here we introduce SPICEMIX, an interpretable method based on probabilistic, latent variable modeling for joint analysis of spatial information and gene expression from spatial transcriptome data.

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Single-cell Hi-C (scHi-C) technologies can probe three-dimensional (3D) genome structures in individual cells. However, existing scHi-C analysis methods are hindered by the data quality and complex 3D genome patterns. The lack of computational scalability and interpretability poses further challenges for large-scale analysis.

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Single-cell Hi-C (scHi-C) can identify cell-to-cell variability of three-dimensional (3D) chromatin organization, but the sparseness of measured interactions poses an analysis challenge. Here we report Higashi, an algorithm based on hypergraph representation learning that can incorporate the latent correlations among single cells to enhance overall imputation of contact maps. Higashi outperforms existing methods for embedding and imputation of scHi-C data and is able to identify multiscale 3D genome features in single cells, such as compartmentalization and TAD-like domain boundaries, allowing refined delineation of their cell-to-cell variability.

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The spatial organization of the genome in the cell nucleus is pivotal to cell function. However, how the 3D genome organization and its dynamics influence cellular phenotypes remains poorly understood. The very recent development of single-cell technologies for probing the 3D genome, especially single-cell Hi-C (scHi-C), has ushered in a new era of unveiling cell-to-cell variability of 3D genome features at an unprecedented resolution.

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Motivation: Neural networks have been widely used to analyze high-throughput microscopy images. However, the performance of neural networks can be significantly improved by encoding known invariance for particular tasks. Highly relevant to the goal of automated cell phenotyping from microscopy image data is rotation invariance.

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ComplexContact (http://raptorx2.uchicago.edu/ComplexContact/) is a web server for sequence-based interfacial residue-residue contact prediction of a putative protein complex.

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The Li3PO4 modified LiFePO4/C and Li4P2O7 modified LiFePO4/C cathode materials were synthesized by in-situ synthesis method, respectively. Phase compositions and microstructures of the products were characterized by X-ray powder diffraction (XRD), scanning electronic microscope (SEM). Results indicate that Li3PO4 and Li4P2O7 can sufficiently coat on the LiFePO4 surface and does not alter LiFePO4 crystal structure.

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Objective: To present the experience of nasal reconstruction with forehead flap.

Method: nasal reconstruction with forehead flap were applied in eight nasal carcinoma cases after operation and 5 nasal trauma cases with defects.

Result: These forehead flaps were alive in all patients, all incision healed in I stage, no post operative complications were found.

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Objective: To observe the immune modulatory and therapeutic effect of BCG polysaccharides nucleic acid (BCG-PSN) on patients with perennial allergic rhinitis.

Method: Sixty patients with perennial allergic rhinitis were randomly divided into two groups, 30 in the test group were treated with BCG-PSN plus ketotefen and 30 in the control group were treated with ketotefen respectively. All patients were followed up and assessed for 3 months, and the blood samples were collected before treatment and 3 months after treatment for measuring the blood IgA, IgG, IgM, IgE, CD3, CD4 and CD8.

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