59 research outputs found

    Automated 4D analysis of dendritic spine morphology: applications to stimulus-induced spine remodeling and pharmacological rescue in a disease model

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    Uncovering the mechanisms that regulate dendritic spine morphology has been limited, in part, by the lack of efficient and unbiased methods for analyzing spines. Here, we describe an automated 3D spine morphometry method and its application to spine remodeling in live neurons and spine abnormalities in a disease model. We anticipate that this approach will advance studies of synapse structure and function in brain development, plasticity, and disease

    Immune interference in effectiveness of influenza and COVID-19 vaccination

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    Vaccines are known to function as the most effective interventional therapeutics for controlling infectious diseases, including polio, smallpox, rabies, tuberculosis, influenza and SARS-CoV-2. Smallpox has been eliminated completely and polio is almost extinct because of vaccines. Rabies vaccines and Bacille Calmette-Guérin (BCG) vaccines could effectively protect humans against respective infections. However, both influenza vaccines and COVID-19 vaccines are unable to eliminate these two infectious diseases of their highly variable antigenic sites in viral proteins. Vaccine effectiveness (VE) could be negatively influenced (i.e., interfered with) by immune imprinting of previous infections or vaccinations, and repeated vaccinations could interfere with VE against infections due to mismatch between vaccine strains and endemic viral strains. Moreover, VE could also be interfered with when more than one kind of vaccine is administrated concomitantly (i.e., co-administrated), suggesting that the VE could be modulated by the vaccine-induced immunity. In this review, we revisit the evidence that support the interfered VE result from immune imprinting or repeated vaccinations in influenza and COVID-19 vaccine, and the interference in co-administration of these two types of vaccines is also discussed. Regarding the development of next-generation COVID-19 vaccines, the researchers should focus on the induction of cross-reactive T-cell responses and naive B-cell responses to overcome negative effects from the immune system itself. The strategy of co-administrating influenza and COVID-19 vaccine needs to be considered more carefully and more clinical data is needed to verify this strategy to be safe and immunogenic

    Soil Bacterial Function Associated With Stylo (Legume) and Bahiagrass (Grass) Is Affected More Strongly by Soil Chemical Property Than by Bacterial Community Composition

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    Soil microbes are driver of nutrient cycling, with microbial function affected by community composition and soil chemical property. Legume and grass are ubiquitous in many ecosystems, however, their differential effects on microbial function are less understood. Here we constructed compartmented rhizobox planted with stylo (Stylosanthes guianensis, legume) or bahiagrass (Paspalum natatum, grass) to compare their influences on bacterial function and to investigate the determinant of bacterial function. Soils in root compartment and in near (0–5 mm from root compartment) or far (10–15 mm from root compartment) rhizosphere were sampled. Soil chemical properties, bacterial community composition and function were characterized. Results indicate that plant species and distance significantly affected bacterial function. The activities of beta-xylosidase, nitrate reductase and phosphomonoesterase were higher in stylo soil than in bahiagrass soil, while leucine-aminopeptidase activity and nosZ abundance were vice versa. Rhizosphere effect was obvious for the activities of beta-glucosidase, beta-xylosidase, chitinase, and the abundances of AOB-amoA, nirS, nosZ. Statistical analysis revealed that soil chemical property was significantly associated with bacterial function, with a higher coefficient than bacterial community composition. These data suggest that stylo and bahiagrass differentially affect bacterial function, which is affected more strongly by soil chemical property than by community composition

    Genome-wide analysis of the TIFY family and function of CaTIFY7 and CaTIFY10b under cold stress in pepper (Capsicum annuum L.)

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    TIFY [TIF(F/Y)XG] proteins are a plant particular transcription factor family that regulates plant stress responses. Therefore, to fill this gap, we investigated CaTIFY genes in pepper. Gene structure and conserved motifs of the pepper TIFY gene family were systematically analyzed using sequence alignment analysis, Cis-acting element analysis, transcriptomic data, and RT-qPCR analysis, and their expression patterns were further analyzed using Virus-Induced Gene Silencing (VIGS) and cold stress reactive oxygen species (ROS) response. We identified 16 CaTIFY genes in pepper, which were dispersed among seven subgroups (JAZI, JAZII, JAZIII, PPD, TIFY, and ZIM/ZML). Several CaTIFY members had stress-related harmonic-responsive elements, and four (CaTIFY7, CaTIFY10b, CaTIFY1b, and CaTIFY6b) had low-temperature-responsive elements. Transcriptomic data and RT-qPCR analysis revealed that the TIFY genes in pepper displayed different expression patterns in the roots, stems, leaves, flower fruits, and seeds. In particular, CaTIFY7 was highly expressed in young leaves, and CaTIFY10b was highly expressed in roots. CaTIFYs participated in the regulation of several different abiotic stresses and CaTIFY7 and CaTIFY10b were significantly induced by cold stress. Additionally, Virus-Induced Gene Silencing (targeting CaTIFY7 and CaTIFY10b) resulted in plants that were sensitive to cold stress. Conversely, overexpression of CaTIFY7 and CaTIFY10b enhanced plant cold tolerance by promoting the expression of genes related to cold stress and the ROS response. CaTIFY7 and CaTIFY10b interacted with themselves and CaTIFY7 also interacted with CaTIFY10b in the yeast two-hybrid (Y2H) system. Our data provide a basis for further analysis of the role of pepper TIFY genes in cold-stress responses in the future

    Group DETR v2: Strong Object Detector with Encoder-Decoder Pretraining

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    We present a strong object detector with encoder-decoder pretraining and finetuning. Our method, called Group DETR v2, is built upon a vision transformer encoder ViT-Huge~\cite{dosovitskiy2020image}, a DETR variant DINO~\cite{zhang2022dino}, and an efficient DETR training method Group DETR~\cite{chen2022group}. The training process consists of self-supervised pretraining and finetuning a ViT-Huge encoder on ImageNet-1K, pretraining the detector on Object365, and finally finetuning it on COCO. Group DETR v2 achieves 64.5\textbf{64.5} mAP on COCO test-dev, and establishes a new SoTA on the COCO leaderboard https://paperswithcode.com/sota/object-detection-on-cocoComment: Tech report, 3 pages. We establishes a new SoTA (64.5 mAP) on the COCO test-de

    Abnormal Liver Function Tests Were Associated With Adverse Clinical Outcomes: An Observational Cohort Study of 2,912 Patients With COVID-19

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    Background and Aim: The impact of liver function test (LFTs) abnormality on adverse clinical outcomes in coronavirus disease 2019 (COVID-19) patients remains controversial. The aim of this study was to assess the impact of abnormal LFTs on clinical outcomes in a large cohort of hospitalized patients with COVID-19.Methods: We retrospectively collected data on 2,912 consecutive patients with COVID-19 who were admitted to a makeshift hospital in China between 5 February and 23 March 2020. The association between LFTs abnormalities (baseline and peak values) and clinical outcomes was measured by using Cox regression models.Results: On admission 1,414 patients (48.6%) had abnormal LFTs, with alanine aminotransferase (ALT), aspartate aminotransferase (AST), total bilirubin (TBIL), alkaline phosphatase (ALP), and gamma-glutamyltransferase (GGT) elevation in 662 (22.7%), 221 (7.6%), 52 (1.8%), 135 (4.6%), and 536 (18.5%) patients, respectively, and hypoalbuminemia in 737 (25.3%) patients. During a median 13 (IQR: 8–19) days of hospitalization, 61 patients (2.1%) died, 106 patients (3.6%) admitted to intensive care unit (ICU), and 75 patients (2.6%) required mechanical ventilation. After adjustment for confounders, baseline abnormal LFTs were independently associated with increased risks of mortality (adjusted HR 3.66, 95%CI 1.64–8.19, p = 0.002), ICU admission (adjusted HR 3.12 95%CI 1.86–5.23, p < 0.001), and mechanical ventilation (adjusted HR 3.00, 95%CI 1.63–5.52, p < 0.001), which was homogeneous across the severity of COVID-19 infection. Among the parameters of LTFs, the associations with the outcomes were more pronounced for AST and albumin abnormality. In contrast, ALT elevation was not significantly associated with those outcomes. Similar results were observed for peak values of LFTs during hospitalization.Conclusions: Abnormality of AST, albumin, TBIL, ALP, and GGT but not ALT were independently associated with adverse outcomes

    RUNX3 Mediates Suppression of Tumor Growth and Metastasis of Human CCRCC by Regulating Cyclin Related Proteins and TIMP-1

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    Here we presented that the expression of RUNX3 was significantly decreased in 75 cases of clear cell renal cell carcinoma (CCRCC) tissues (p<0.05). Enforced RUNX3 expression mediated 786-O cells to exhibit inhibition of growth, G1 cell-cycle arrest and metastasis in vitro, and to lost tumorigenicity in nude mouse model in vivo. RUNX3-induced growth suppression was found partially to regulate various proteins, including inhibition of cyclinD1, cyclinE, cdk2, cdk4 and p-Rb, but increase of p27Kip1, Rb and TIMP-1. Therefore, RUNX3 had the function of inhibiting the proliferative and metastatic abilities of CCRCC cells by regulating cyclins and TIMP1

    Finishing the euchromatic sequence of the human genome

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    The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead
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