Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 20 de 253
Filter
1.
J Org Chem ; 89(17): 12533-12539, 2024 Sep 06.
Article in English | MEDLINE | ID: mdl-39166869

ABSTRACT

With the combination of the N-heterocyclic carbene-PdCl2-1-methylimidazole complex and Cu2O, we succeeded in the first example of double direct C-H bond arylation reactions between thiophenes and aryl chlorides, giving the desired 2,5-diarylated thiophenes in moderate to high yields under suitable conditions, consistent with the density functional theory calculations.

2.
Cell ; 2024 Aug 26.
Article in English | MEDLINE | ID: mdl-39197449

ABSTRACT

The protein import motor in chloroplasts plays a pivotal role in their biogenesis and homeostasis by driving the translocation of preproteins into chloroplasts. While the Ycf2-FtsHi complex serves as the import motor in land plants, its evolutionary conservation, specialization, and mechanisms across photosynthetic organisms are largely unexplored. Here, we isolated and determined the cryogenic electron microscopy (cryo-EM) structures of the native Ycf2-FtsHi complex from Chlamydomonas reinhardtii, uncovering a complex composed of up to 19 subunits, including multiple green-algae-specific components. The heterohexameric AAA+ ATPase motor module is tilted, potentially facilitating preprotein handover from the translocon at the inner chloroplast membrane (TIC) complex. Preprotein interacts with Ycf2-FtsHi and enhances its ATPase activity in vitro. Integrating Ycf2-FtsHi and translocon at the outer chloroplast membrane (TOC)-TIC supercomplex structures reveals insights into their physical and functional interplay during preprotein translocation. By comparing these findings with those from land plants, our study establishes a structural foundation for understanding the assembly, function, evolutionary conservation, and diversity of chloroplast protein import motors.

3.
Cell ; 2024 Aug 21.
Article in English | MEDLINE | ID: mdl-39197452

ABSTRACT

Chloroplast proteins are imported via the translocon at the outer chloroplast membrane (TOC)-translocon at the inner chloroplast membrane (TIC) supercomplex, driven by an ATPase motor. The Ycf2-FtsHi complex has been identified as the chloroplast import motor. However, its assembly and cooperation with the TIC complex during preprotein translocation remain unclear. Here, we present the structures of the Ycf2-FtsHi and TIC complexes from Arabidopsis and an ultracomplex formed between them from Pisum. The Ycf2-FtsHi structure reveals a heterohexameric AAA+ ATPase motor module with characteristic features. Four previously uncharacterized components of Ycf2-FtsHi were identified, which aid in complex assembly and anchoring of the motor module at a tilted angle relative to the membrane. When considering the structures of the TIC complex and the TIC-Ycf2-FtsHi ultracomplex together, it becomes evident that the tilted motor module of Ycf2-FtsHi enables its close contact with the TIC complex, thereby facilitating efficient preprotein translocation. Our study provides valuable structural insights into the chloroplast protein import process in land plants.

4.
AIDS Res Ther ; 21(1): 53, 2024 Aug 10.
Article in English | MEDLINE | ID: mdl-39127636

ABSTRACT

BACKGROUND: China braces for coronavirus disease 2019 (COVID-19) surge after adjusting the "zero COVID" strategy. We aimed to evaluate and compare the prevalence of clinical symptoms of the Omicron variant infection among people living with HIV (PLWH) and HIV-free people. METHODS: A cross-sectional study was conducted in Wuchang District, Wuhan, Hubei Province, in December 2022 by a self-administered online survey during the Omicron wave. Participants aged ≥ 18 years with confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnosis were recruited. PLWH managed by the local healthcare system were recruited, while HIV-free people were recruited by sending out online surveys through WeChat. We compared the prevalence of clinical symptoms of COVID-19 between PLWH and HIV-free people, and factors associated with symptom occurrence among PLWH were accessed. RESULTS: Total, 687 PLWH and 1222 HIV-free people were enrolled. After adjusting sex, age, body mass index, comorbidities and COVID-19 vaccination status, the prevalences of all symptoms, including higher degree and long duration of fever (aOR 0.51, 95%CI 0·42 - 0·61; aOR 0.52, 95%CI 0·43 - 0·63), were significantly lower among PLWH than among HIV-free people. Among PLWH, CD4+ T lymphocyte count (CD4 count) between 350 ~ 499 cells/µL and detectable HIV viral load (HIV-VL) were associated with significantly decreased risks of fever (aOR 0·63, 95%CI 0·40 - 0·97; aOR 0·56, 95%CI 0·33 - 0·94), headache (aOR 0·61, 95%CI 0·41 - 0·91; aOR 0·55, 95%CI 0·34 - 0·92) and muscle soreness (aOR 0·57, 95%CI 0·39 - 0·84; aOR 0·57, 95%CI 0·39 - 0·84). No apparent association between the symptoms prevalence and three/four doses of inactivated COVID-19 vaccination among PLWH was observed; both males and older age were associated with significantly decreased risks of nasal congestion/runny nose (aOR 0·52, 95%CI 0·32 - 0·82; aOR 0·97, 95%CI 0·96 - 0·99) and headache (aOR 0·58, 95%CI 0·36 - 0·92; aOR 0·96, 95%CI 0·95 - 0·98); older age was associated with significantly decreased risks of higher degree of fever (aOR 0·97, 95%CI 0·95 - 0·98). CONCLUSIONS: PLWH have significantly milder symptoms of the Omicron variant infection than HIV-free people. PLWH who are male, older, have low CD4 count, and detectable HIV-VL have reduced occurrence of COVID-19 symptoms. However, continuous monitoring should be conducted among PLWH during the COVID-19 pandemic.


Subject(s)
COVID-19 , HIV Infections , SARS-CoV-2 , Humans , COVID-19/epidemiology , Cross-Sectional Studies , Male , Female , Adult , Middle Aged , SARS-CoV-2/immunology , HIV Infections/epidemiology , HIV Infections/complications , HIV Infections/immunology , HIV Infections/virology , China/epidemiology , Prevalence , Young Adult , Aged , CD4 Lymphocyte Count
5.
Mediators Inflamm ; 2024: 8828367, 2024.
Article in English | MEDLINE | ID: mdl-39144184

ABSTRACT

Background: Bladder cancer (BC) is one of the most common malignancies of the urogenital system. This study assessed the nucleotide-binding oligomerization domain and leucine-rich repeat and pyrin domain-containing protein 3 (NLRP3) in BC as well as the effects of cryptotanshinone on changes in BC malignant behaviors and NLRP3 expression under a lipopolysaccharide (LPS)-induced inflammatory microenvironment. Methods: BC tissue specimens from 62 patients were collected for immunohistochemical detection of NLRP3 protein. BC and normal urothelial cell lines were cultured for the detection of NLRP3 mRNA and protein. Then, BC cells were pretreated with LPS to mimic the inflammatory tumor microenvironment. Next, these cells were incubated with a low or high dose of cryptotanshinone to assess its effects on tumor cell malignant behaviors as well as transfected with NLRP3 cDNA to confirm the role of NLRP3 in BC cells in vitro. Results: High NLRP3 expression was associated with larger tumor diameters (>2 cm), muscle invasion, and metastasis. The levels of NLRP3 mRNA and protein were greater in BC cells than in normal urothelial cells. LPS pretreatment significantly promoted NLRP3 and inflammatory cytokine expression in BC cells, and induced cell viability, migration, and invasion. However, cryptotanshinone was able to reduce the LPS-induced increase of NLRP3 and inflammatory cytokine expression as well as the BC cell malignant progression. NLRP3 overexpression using NLRP3 cDNA further promoted BC cell malignant progression after LPS stimulation and reversed cryptotanshinone-reduced LPS-induced BC cell malignant behaviors. Conclusion: NLRP3 might possess oncogenic activity in BC, and the antitumor activity of cryptotanshinone in BC in vitro might be related to its inhibition of NLRP3 expression.


Subject(s)
Lipopolysaccharides , NLR Family, Pyrin Domain-Containing 3 Protein , Phenanthrenes , Urinary Bladder Neoplasms , Humans , NLR Family, Pyrin Domain-Containing 3 Protein/metabolism , Urinary Bladder Neoplasms/metabolism , Urinary Bladder Neoplasms/drug therapy , Urinary Bladder Neoplasms/pathology , Phenanthrenes/pharmacology , Male , Cell Line, Tumor , Female , Middle Aged , Tumor Microenvironment/drug effects , Aged , Cell Movement/drug effects , Cell Survival/drug effects , Inflammation/metabolism
6.
Hum Pathol ; 152: 105650, 2024 Aug 24.
Article in English | MEDLINE | ID: mdl-39187207

ABSTRACT

Extranodal natural killer (NK)/T-cell lymphoma (ENKTL) is prevalent in the Asian population; however, little is known about its molecular characteristics. In this study, we examined the CD30 expression in ENKTLs and then performed whole exome sequencing on ten CD30+ ENKTL and CD30- ENKTL paired samples. CD30 was positive in 55.74% of the ENKTLs. Single nucleotide and insertion/deletion polymorphism analyses revealed that 53.41% of the somatic mutations in CD30+ ENKTLs were shared with CD30- ENKTLs, including mutations in SERPINA9, MEGF6, MUC6, and KDM5A. Frequently mutated genes were primarily associated with cell proliferation and migration, the tumor microenvironment, energy and metabolism, epigenetic modulators, vascular remodeling, and neurological function. PI3K-AKT, cAMP, cGMP-PKG, and AMPK pathways were enriched in both CD30+ and CD30- ENKTLs. Copy number variation analysis identified a unique set of genes in CD30+ ENKTLs, including T-cell receptor genes (TRBV6-1 and TRBV8), cell cycle-related genes (MYC and CCND3), immune-related genes (GPS2, IFNA14, TTC38, and CTSV), and a large number of ubiquitination-related genes (USP32, TRIM23, TRIM2, DUSP7, and UBE2QL1). BCL10 mutation was identified in 6/10 CD30+ ENKTLs and 7/10 CD30- ENKTLs. Immunohistochemical analysis revealed that the expression pattern of BCL10 in normal lymphoid tissues was similar to that of BCL2; however, its expression in ENKTL cells was significantly higher (67.92% vs. 16.98%), implying the potential application of BCL10 inhibitors for treating ENKTLs. These results provide new insights into the genetic characteristics of CD30+ and CD30- ENKTLs, and could facilitate the clinical development of novel therapies for ENKTL.

7.
Acta Pharmacol Sin ; 2024 Jun 11.
Article in English | MEDLINE | ID: mdl-38862816

ABSTRACT

Kv1.3 belongs to the voltage-gated potassium (Kv) channel family, which is widely expressed in the central nervous system and associated with a variety of neuropsychiatric disorders. Kv1.3 is highly expressed in the olfactory bulb and piriform cortex and involved in the process of odor perception and nutrient metabolism in animals. Previous studies have explored the function of Kv1.3 in olfactory bulb, while the role of Kv1.3 in piriform cortex was less known. In this study, we investigated the neuronal changes of piriform cortex and feeding behavior after smell stimulation, thus revealing a link between the olfactory sensation and body weight in Kv1.3 KO mice. Coronal slices including the anterior piriform cortex were prepared, whole-cell recording and Ca2+ imaging of pyramidal neurons were conducted. We showed that the firing frequency evoked by depolarization pulses and Ca2+ influx evoked by high K+ solution were significantly increased in pyramidal neurons of Kv1.3 knockout (KO) mice compared to WT mice. Western blotting and immunofluorescence analyses revealed that the downstream signaling molecules CaMKII and PKCα were activated in piriform cortex of Kv1.3 KO mice. Pyramidal neurons in Kv1.3 KO mice exhibited significantly reduced paired-pulse ratio and increased presynaptic Cav2.1 expression, proving that the presynaptic vesicle release might be elevated by Ca2+ influx. Using Golgi staining, we found significantly increased dendritic spine density of pyramidal neurons in Kv1.3 KO mice, supporting the stronger postsynaptic responses in these neurons. In olfactory recognition and feeding behavior tests, we showed that Kv1.3 conditional knockout or cannula injection of 5-(4-phenoxybutoxy) psoralen, a Kv1.3 channel blocker, in piriform cortex both elevated the olfactory recognition index and altered the feeding behavior in mice. In summary, Kv1.3 is a key molecule in regulating neuronal activity of the piriform cortex, which may lay a foundation for the treatment of diseases related to piriform cortex and olfactory detection.

8.
Article in English | MEDLINE | ID: mdl-38941209

ABSTRACT

Knowledge graph reasoning (KGR), aiming to deduce new facts from existing facts based on mined logic rules underlying knowledge graphs (KGs), has become a fast-growing research direction. It has been proven to significantly benefit the usage of KGs in many AI applications, such as question answering, recommendation systems, and etc. According to the graph types, existing KGR models can be roughly divided into three categories, i.e., static models, temporal models, and multi-modal models. Early works in this domain mainly focus on static KGR, and recent works try to leverage the temporal and multi-modal information, which are more practical and closer to real-world. However, no survey papers and open-source repositories comprehensively summarize and discuss models in this important direction. To fill the gap, we conduct a first survey for knowledge graph reasoning tracing from static to temporal and then to multi-modal KGs. Concretely, the models are reviewed based on bi-level taxonomy, i.e., top-level (graph types) and base-level (techniques and scenarios). Besides, the performances, as well as datasets, are summarized and presented. Moreover, we point out the challenges and potential opportunities to enlighten the readers. The corresponding open-source repository is shared on GitHub https://github.com/LIANGKE23/Awesome-Knowledge-Graph-Reasoning.

9.
mSystems ; 9(7): e0060024, 2024 Jul 23.
Article in English | MEDLINE | ID: mdl-38888356

ABSTRACT

Locusta migratoria is an important phytophagous pest, and its gut microbial communities play an important role in cellulose degradation. In this study, the gut microbial and cellulose digestibility dynamics of Locusta migratoria were jointly analyzed using high-throughput sequencing and anthrone colorimetry. The results showed that the gut microbial diversity and cellulose digestibility across life stages were dynamically changing. The species richness of gut bacteria was significantly higher in eggs than in larvae and imago, the species richness and cellulose digestibility of gut bacteria were significantly higher in early larvae (first and second instars) than in late larvae (third to fifth instars), and the diversity of gut bacteria and cellulose digestibility were significantly higher in imago than in late larvae. There is a correlation between the dynamics of gut bacterial communities and cellulose digestibility. Enterobacter, Lactococcus, and Pseudomonas are the most abundant genera throughout all life stages. Six strains of highly efficient cellulolytic bacteria were screened, which were dominant gut bacteria. Carboxymethyl cellulase activity (CMCA) and filter paper activity (FPA) experiments revealed that Pseudomonas had the highest cellulase enzyme activity. This study provides a new way for the screening of cellulolytic bacteria and lays the foundation for developing insects with significant biomass into cellulose-degrading bioreactors. IMPORTANCE: Cellulose is the most abundant and cheapest renewable resource in nature, but its degradation is difficult, so finding efficient cellulose degradation methods is an urgent challenge. Locusta migratoria is a large group of agricultural pests, and the large number of microorganisms that inhabit their intestinal tracts play an important role in cellulose degradation. We analyzed the dynamics of Locusta migratoria gut microbial communities and cellulose digestibility using a combination of high-throughput sequencing technology and anthrone colorimetry. The results revealed that the gut microbial diversity and cellulose digestibility were dynamically changed at different life stages. In addition, we explored the intestinal bacterial community of Locusta migratoria across life stages and its correlation with cellulose digestibility. The dominant bacterial genera at different life stages of Locusta migratoria were uncovered and their carboxymethyl cellulase activity (CMCA) and filter paper activity (FPA) were determined. This study provides a new avenue for screening cellulolytic bacteria and lays the foundation for developing insects with significant biomass into cellulose-degrading bioreactors.


Subject(s)
Bacteria , Cellulose , Gastrointestinal Microbiome , Locusta migratoria , Animals , Cellulose/metabolism , Gastrointestinal Microbiome/physiology , Locusta migratoria/microbiology , Bacteria/metabolism , Bacteria/genetics , Bacteria/isolation & purification , Larva/microbiology , High-Throughput Nucleotide Sequencing , Digestion/physiology
10.
Heliyon ; 10(9): e30112, 2024 May 15.
Article in English | MEDLINE | ID: mdl-38737287

ABSTRACT

Background: The reasons for gastrointestinal bleeding among patients with acquired immune deficiency syndrome (AIDS) were complex. Here we present an unusual case of life-threatening gastrointestinal bleeding caused by a cytomegalovirus-induced duodenal ulcer in an AIDS patient. Case presentation: A 31-year-old male with AIDS was admitted on July 18, 2023, complaining of abdominal pain for 38 days and intermittent hematochezia for 12 days. During his hospitalization, gastrointestinal endoscopy attributed gastrointestinal bleeding to a giant duodenal ulcer. Furthermore, cytomegalovirus(CMV) infection was confirmed as the reason for the ulcer through metagenomic next-generation sequencing (mNGs), hematoxylin-eosin(HE) staining, and immunohistochemistry (IHC) staining for the biopsy tissue. The patient's gastrointestinal bleeding was stopped by interventional embolization. Following a 4-week course of anti-CMV treatment, the giant duodenal ulcer was cured. Conclusions: For AIDS patients with gastrointestinal bleeding, the CMV-induced gastrointestinal ulcer should be considered. Comprehensive mothods (mNGs, HE staining and IHC staining for biopsy tissue) were benefit for confirmed diagnosis. Beside anti-CMV treatment, the interventional embolization is a choice for hemostasis.

11.
Sci Rep ; 14(1): 8148, 2024 Apr 08.
Article in English | MEDLINE | ID: mdl-38584204

ABSTRACT

With the advent of Transformer-based convolutional neural networks, stereo matching algorithms have achieved state-of-the-art accuracy in disparity estimation. Nevertheless, this method requires much model inference time, which is the main reason limiting its application in many vision tasks and robots. Facing the trade-off problem between accuracy and efficiency, this paper proposes an efficient and accurate multi-level cascaded recurrent network, LMCR-Stereo. To recover the detailed information of stereo images more accurately, we first design a multi-level network to update the difference values in a coarse-to-fine recurrent iterative manner. Then, we propose a new pair of slow-fast multi-stage superposition inference structures to accommodate the differences between different scene data. Besides, to ensure better disparity estimation accuracy with faster model inference speed, we introduce a pair of adaptive and lightweight group correlation layers to reduce the impact of erroneous rectification and significantly improve model inference speed. The experimental results show that the proposed approach achieves a competitive disparity estimation accuracy with a faster model inference speed than the current state-of-the-art methods. Notably, the model inference speed of the proposed approach is improved by 46.0% and 50.4% in the SceneFlow test set and Middlebury benchmark, respectively.

12.
Article in English | MEDLINE | ID: mdl-38648135

ABSTRACT

Temporal graph learning aims to generate high-quality representations for graph-based tasks with dynamic information, which has recently garnered increasing attention. In contrast to static graphs, temporal graphs are typically organized as node interaction sequences over continuous time rather than an adjacency matrix. Most temporal graph learning methods model current interactions by incorporating historical neighborhood. However, such methods only consider first-order temporal information while disregarding crucial high-order structural information, resulting in suboptimal performance. To address this issue, we propose a self-supervised method called S2T for temporal graph learning, which extracts both temporal and structural information to learn more informative node representations. Notably, the initial node representations combine first-order temporal and high-order structural information differently to calculate two conditional intensities. An alignment loss is then introduced to optimize the node representations, narrowing the gap between the two intensities and making them more informative. Concretely, in addition to modeling temporal information using historical neighbor sequences, we further consider structural knowledge at both local and global levels. At the local level, we generate structural intensity by aggregating features from high-order neighbor sequences. At the global level, a global representation is generated based on all nodes to adjust the structural intensity according to the active statuses on different nodes. Extensive experiments demonstrate that the proposed model S2T achieves at most 10.13% performance improvement compared with the state-of-the-art competitors on several datasets.

13.
HIV Med ; 25(7): 794-804, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38515324

ABSTRACT

BACKGROUND: Opportunistic infections in the central nervous system (CNS) can be a serious threat to people living with HIV. Early aetiological diagnosis and targeted treatment are crucial but difficult. Metagenomic next-generation sequencing (mNGS) has significant advantages over traditional detection methods. However, differences in the cerebrospinal fluid (CSF) microbiome profiles of patients living with and without HIV with suspected CNS infections using mNGS and conventional testing methods have not yet been adequately evaluated. METHODS: We conducted a retrospective cohort study in the first hospital of Changsha between January 2019 and June 2022 to investigate the microbiomes detected using mNGS of the CSF of patients living with and without HIV with suspected CNS infections. The pathogens causing CNS infections were concurrently identified using both mNGS and traditional detection methods. The spectrum of pathogens identified was compared between the two groups. RESULTS: Overall, 173 patients (140 with and 33 without HIV) with suspected CNS infection were enrolled in our study. In total, 106 (75.7%) patients with and 16 (48.5%) patients without HIV tested positive with mNGS (p = 0.002). Among the enrolled patients, 71 (50.7%) with HIV and five (15.2%) without HIV tested positive for two or more pathogens (p < 0.001). Patients with HIV had significantly higher proportions of fungus (20.7% vs. 3.0%, p = 0.016) and DNA virus (59.3% vs. 21.2%, p < 0.001) than those without HIV. Epstein-Barr virus (33.6%) was the most commonly identified potential pathogen in the CSF of patients living with HIV using mNGS, followed by cytomegalovirus (20.7%) and torque teno virus (13.8%). The top three causative pathogens identified in patients without HIV were Streptococcus (18.2%), Epstein-Barr virus (12.1%), and Mycobacterium tuberculosis (9.1%). In total, 113 patients living with HIV were diagnosed as having CNS infections. The rate of pathogen detection in people living with HIV with a CNS infection was significantly higher with mNGS than with conventional methods (93.8% vs. 15.0%, p < 0.001). CONCLUSION: CSF microbiome profiles differ between patients living with and without HIV with suspected CNS infection. mNGS is a powerful tool for the diagnosis of CNS infection among people living with HIV, especially in those with mixed infections.


Subject(s)
Central Nervous System Infections , Cerebrospinal Fluid , HIV Infections , High-Throughput Nucleotide Sequencing , Metagenomics , Humans , Male , Retrospective Studies , Female , High-Throughput Nucleotide Sequencing/methods , Adult , Middle Aged , Central Nervous System Infections/cerebrospinal fluid , Central Nervous System Infections/microbiology , Central Nervous System Infections/diagnosis , Central Nervous System Infections/virology , HIV Infections/complications , HIV Infections/cerebrospinal fluid , Metagenomics/methods , Cerebrospinal Fluid/microbiology , Cerebrospinal Fluid/virology , Microbiota/genetics , AIDS-Related Opportunistic Infections/cerebrospinal fluid , AIDS-Related Opportunistic Infections/microbiology , AIDS-Related Opportunistic Infections/diagnosis
14.
Molecules ; 29(5)2024 Mar 06.
Article in English | MEDLINE | ID: mdl-38474689

ABSTRACT

Hollow silica spheres have been widely studied for drug delivery because of their excellent biosecurity and high porosity. However, difficulties with degradation in the tumor microenvironment (TME) and premature leaking during drug delivery limit their clinical applications. To alleviate these problems, herein, hollow organosilica spheres (HOS) were initially prepared using a "selective etching strategy" and loaded with a photothermal drug: new indocyanine green (IR820). Then, the Cu2+-tannic acid complex (Cu-TA) was deposited on the surface of the HOS, and a new nanoplatform named HOS@IR820@Cu-TA (HICT) was finally obtained. The deposition of Cu-TA can gate the pores of HOS completely to prevent the leakage of IR820 and significantly enhance the loading capacity of HOS. Once in the mildly acidic TME, the HOS and outer Cu-TA decompose quickly in response, resulting in the release of Cu2+ and IR820. The released Cu2+ can react with the endogenous glutathione (GSH) to consume it and produce Cu+, leading to the enhanced production of highly toxic ·OH through a Fenton-like reaction due to the overexpressed H2O2 in the TME. Meanwhile, the ·OH generation was remarkably enhanced by the NIR light-responsive photothermal effect of IR820. These collective properties of HICT enable it to be a smart nanomedicine for dually enhanced chemodynamic therapy through GSH depletions and NIR light-triggered photothermal effects.


Subject(s)
Coordination Complexes , Nanoparticles , Neoplasms , Polyphenols , Humans , Hydrogen Peroxide , Drug Delivery Systems , Glutathione , Tumor Microenvironment , Cell Line, Tumor
15.
Brief Bioinform ; 25(2)2024 Jan 22.
Article in English | MEDLINE | ID: mdl-38493338

ABSTRACT

In recent years, there has been a growing trend in the realm of parallel clustering analysis for single-cell RNA-seq (scRNA) and single-cell Assay of Transposase Accessible Chromatin (scATAC) data. However, prevailing methods often treat these two data modalities as equals, neglecting the fact that the scRNA mode holds significantly richer information compared to the scATAC. This disregard hinders the model benefits from the insights derived from multiple modalities, compromising the overall clustering performance. To this end, we propose an effective multi-modal clustering model scEMC for parallel scRNA and Assay of Transposase Accessible Chromatin data. Concretely, we have devised a skip aggregation network to simultaneously learn global structural information among cells and integrate data from diverse modalities. To safeguard the quality of integrated cell representation against the influence stemming from sparse scATAC data, we connect the scRNA data with the aggregated representation via skip connection. Moreover, to effectively fit the real distribution of cells, we introduced a Zero Inflated Negative Binomial-based denoising autoencoder that accommodates corrupted data containing synthetic noise, concurrently integrating a joint optimization module that employs multiple losses. Extensive experiments serve to underscore the effectiveness of our model. This work contributes significantly to the ongoing exploration of cell subpopulations and tumor microenvironments, and the code of our work will be public at https://github.com/DayuHuu/scEMC.


Subject(s)
Chromatin , RNA, Small Cytoplasmic , Single-Cell Gene Expression Analysis , Cluster Analysis , Learning , RNA, Small Cytoplasmic/genetics , Transposases , Sequence Analysis, RNA , Gene Expression Profiling
17.
Nature ; 627(8004): 656-663, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38418883

ABSTRACT

Understanding the cellular processes that underlie early lung adenocarcinoma (LUAD) development is needed to devise intervention strategies1. Here we studied 246,102 single epithelial cells from 16 early-stage LUADs and 47 matched normal lung samples. Epithelial cells comprised diverse normal and cancer cell states, and diversity among cancer cells was strongly linked to LUAD-specific oncogenic drivers. KRAS mutant cancer cells showed distinct transcriptional features, reduced differentiation and low levels of aneuploidy. Non-malignant areas surrounding human LUAD samples were enriched with alveolar intermediate cells that displayed elevated KRT8 expression (termed KRT8+ alveolar intermediate cells (KACs) here), reduced differentiation, increased plasticity and driver KRAS mutations. Expression profiles of KACs were enriched in lung precancer cells and in LUAD cells and signified poor survival. In mice exposed to tobacco carcinogen, KACs emerged before lung tumours and persisted for months after cessation of carcinogen exposure. Moreover, they acquired Kras mutations and conveyed sensitivity to targeted KRAS inhibition in KAC-enriched organoids derived from alveolar type 2 (AT2) cells. Last, lineage-labelling of AT2 cells or KRT8+ cells following carcinogen exposure showed that KACs are possible intermediates in AT2-to-tumour cell transformation. This study provides new insights into epithelial cell states at the root of LUAD development, and such states could harbour potential targets for prevention or intervention.


Subject(s)
Adenocarcinoma of Lung , Cell Differentiation , Epithelial Cells , Lung Neoplasms , Animals , Humans , Mice , Adenocarcinoma of Lung/genetics , Adenocarcinoma of Lung/pathology , Alveolar Epithelial Cells/metabolism , Alveolar Epithelial Cells/pathology , Aneuploidy , Carcinogens/toxicity , Epithelial Cells/classification , Epithelial Cells/metabolism , Epithelial Cells/pathology , Lung Neoplasms/genetics , Lung Neoplasms/pathology , Mutation , Organoids/drug effects , Organoids/metabolism , Precancerous Conditions/metabolism , Proto-Oncogene Proteins p21(ras)/genetics , Proto-Oncogene Proteins p21(ras)/metabolism , Survival Rate , Tobacco Products/adverse effects , Tobacco Products/toxicity
18.
Front Reprod Health ; 6: 1335239, 2024.
Article in English | MEDLINE | ID: mdl-38375500

ABSTRACT

This study investigates the clinical effects of the novel Traditional Chinese Medicine (TCM) topical wash used in combination with negative pressure irrigation and tadalafil for the treatment of vascular erectile dysfunction. Eighty-seven patients with vascular erectile dysfunction were divided into an observation group and a control group. The observation group was administered negative pressure irrigation (TCM) in combination with oral tadalafil for four weeks, and the control group was administered oral tadalafil for four weeks. The observation group included 21 patients with arterial erectile dysfunction and 22 with intravenous erectile dysfunction. After treatment, IIEF-5, EHS, GAD scores, PSV, EDV and RI in observation group were improved compared with those before treatment (P = 0.000, 0.000, 0.000, L0.000/R0.000, L0.000/R0.000, L0.003/R0.000). Erectile function (IIEF-5, EHS) was significantly improved compared with the control group (P = 0.008, 0.002). In the observation group, there were 21 cases of arterial erectile dysfunction and 22 cases of intravenous erectile dysfunction. After treatment, PSV of arterial ED improved significantly (P = L0.000/R0.000), but EDV did not decrease significantly (P = L0.084/R 0.098). In patients with venous ED, PSV increased (P = L0.026/R0.032) and EDV decreased significantly (P = L0.000/R0.000). These findings suggest that TCM negative pressure lavage combined with tadalafil improves the blood supply of the penile artery, relaxes smooth muscle, and improves the closing mechanism of venous vessels in patients with vascular erectile dysfunction, ultimately improving the erectile function.

19.
Article in English | MEDLINE | ID: mdl-38315591

ABSTRACT

Few-shot relation reasoning on knowledge graphs (FS-KGR) is an important and practical problem that aims to infer long-tail relations and has drawn increasing attention these years. Among all the proposed methods, self-supervised learning (SSL) methods, which effectively extract the hidden essential inductive patterns relying only on the support sets, have achieved promising performance. However, the existing SSL methods simply cut down connections between high-frequency and long-tail relations, which ignores the fact, i.e., the two kinds of information could be highly related to each other. Specifically, we observe that relations with similar contextual meanings, called aliasing relations (ARs), may have similar attributes. In other words, the ARs of the target long-tail relation could be in high-frequency, and leveraging such attributes can largely improve the reasoning performance. Based on the interesting observation above, we proposed a novel Self-supervised learning model by leveraging Aliasing Relations to assist FS-KGR, termed . Specifically, we propose a graph neural network (GNN)-based AR-assist module to encode the ARs. Besides, we further provide two fusion strategies, i.e., simple summation and learnable fusion, to fuse the generated representations, which contain extra abundant information underlying the ARs, into the self-supervised reasoning backbone for performance enhancement. Extensive experiments on three few-shot benchmarks demonstrate that achieves state-of-the-art (SOTA) performance compared with other methods in most cases.

20.
Small ; 20(26): e2311027, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38263719

ABSTRACT

Nanozyme-based metabolic regulation triggered by tumor-specific endogenous stimuli has emerged as a promising therapeutic strategy for tumors. The current efficacy, however, is constrained by the limited concentration of endogenous substrates and the metabolic plasticity of tumors. Consequently, the implementation of efficient metabolic regulation in tumor therapy is urgently needed. Herein, a versatile nanozyme-based nicotinamide adenine dinucleotide (NADH) circulating oxidation nanoreactor is reported. First, the synthesized cobalt-doped hollow carbon spheres (Co-HCS) possess NADH oxidase (NOX)-mimicking activity for the NADH oxidation to disrupt oxidative phosphorylation (OXPHOS) pathway of tumor cells. Second, the substrate-cycle manner of Co-HCS can be used for NADH circulating oxidation to overcome the limitation of substrate deficiency. Finally, 2-Deoxy-D-glucose (2-DG) and 6-aminonicotinamide (6-AN) are introduced to block glycolysis and pentose phosphate pathway (PPP), thus creating a versatile nanozyme-based NADH circulating oxidation nanoreactor (Co-HCS/D/A) for tumor therapy through triple cellular metabolism disruption. In vitro and in vivo results demonstrate that the designed nanoreactor not only enhances the catalytic efficiency but also disrupts the tumor metabolic homeostasis, leading to efficient therapy outcome. This study develops a novel NADH circulating oxidation nanoreactor for tumor therapy through triple cellular metabolism disruption, which addresses the limitations of current nanozyme-based metabolism regulation for tumor therapy.


Subject(s)
NAD , Oxidation-Reduction , NAD/metabolism , NAD/chemistry , Humans , Animals , Neoplasms/drug therapy , Neoplasms/metabolism , Cell Line, Tumor , Mice
SELECTION OF CITATIONS
SEARCH DETAIL