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1.
Immunol Rev ; 321(1): 128-142, 2024 Jan.
Article in English | MEDLINE | ID: mdl-37553793

ABSTRACT

Immunogenic cell death (ICD) is one of the 12 distinct cell death forms, which can trigger immune system to fight against cancer cells. During ICD, a number of cellular changes occur that can stimulate an immune response, including the release of molecules called damage-associated molecular patterns (DAMPs), signaling to immune cells to recognize and attack cancer cells. By virtue of their pivotal role in immune surveillance, ICD-based drug development has been a new approach to explore novel therapeutic combinations and personalized strategies in cancer therapy. Several small molecules and microbes can induce ICD-relevant signals and cause cancer cell death. In this review, we highlighted the role of microbe-mediate ICD in cancer immunotherapy and described the mechanisms through which microbes might serve as ICD inducers in cancer treatment. We also discussed current attempts to combine microbes with chemotherapy regimens or immune checkpoint inhibitors (ICIs) in the treatment of cancer patients. We surmise that manipulation of microbes may guide personalized therapeutic interventions to facilitate anticancer immune response.


Subject(s)
Antineoplastic Agents , Neoplasms , Humans , Immunogenic Cell Death , Antineoplastic Agents/therapeutic use , Cell Death , Immunotherapy
2.
Bioinformatics ; 40(2)2024 02 01.
Article in English | MEDLINE | ID: mdl-38290765

ABSTRACT

SUMMARY: Single-cell multi-omics technologies provide a unique platform for characterizing cell states and reconstructing developmental process by simultaneously quantifying and integrating molecular signatures across various modalities, including genome, transcriptome, epigenome, and other omics layers. However, there is still an urgent unmet need for novel computational tools in this nascent field, which are critical for both effective and efficient interrogation of functionality across different omics modalities. Scbean represents a user-friendly Python library, designed to seamlessly incorporate a diverse array of models for the examination of single-cell data, encompassing both paired and unpaired multi-omics data. The library offers uniform and straightforward interfaces for tasks, such as dimensionality reduction, batch effect elimination, cell label transfer from well-annotated scRNA-seq data to scATAC-seq data, and the identification of spatially variable genes. Moreover, Scbean's models are engineered to harness the computational power of GPU acceleration through Tensorflow, rendering them capable of effortlessly handling datasets comprising millions of cells. AVAILABILITY AND IMPLEMENTATION: Scbean is released on the Python Package Index (PyPI) (https://pypi.org/project/scbean/) and GitHub (https://github.com/jhu99/scbean) under the MIT license. The documentation and example code can be found at https://scbean.readthedocs.io/en/latest/.


Subject(s)
Multiomics , Software , Genome , Transcriptome , Single-Cell Analysis , Data Analysis
3.
Plant Physiol ; 2024 May 14.
Article in English | MEDLINE | ID: mdl-38743633

ABSTRACT

The cultivated apple (Malus domestica Borkh.) is a cross-pollinated perennial fruit tree of great economic importance. Previous versions of apple reference genomes were unphased, fragmented, and lacked comprehensive insights into the highly heterozygous genome, which impeded genetic studies and breeding programs in apple. In this study, we assembled a haplotype-resolved telomere-to-telomere reference genome for the diploid apple cultivar Golden Delicious. Subsequently, we constructed a pangenome based on twelve assemblies from wild and cultivated apples to investigate different types of resistance gene analogs (RGAs). Our results revealed the dynamics of the gene gain and loss events during apple domestication. Compared with cultivated species, more gene families in wild species were significantly enriched in oxidative phosphorylation, pentose metabolic process, responses to salt, and abscisic acid biosynthesis process. Interestingly, our analyses demonstrated a higher prevalence of RGAs in cultivated apples than their wild relatives, partially attributed to segmental and tandem duplication events in certain RGAs classes. Other types of structural variations, mainly deletions and insertions, have affected the presence and absence of TIR-NB-ARC-LRR (TNL), NB-ARC-LRR (NL), and CC-NB-ARC-LRR (CNL) genes. Additionally, hybridization/introgression from wild species has also contributed to the expansion of resistance genes in domesticated apples. Our haplotype-resolved T2T genome and pangenome provide important resources for genetic studies of apples, emphasizing the need to study the evolutionary mechanisms of resistance genes in apple breeding programs.

4.
Proc Natl Acad Sci U S A ; 119(45): e2204986119, 2022 Nov 08.
Article in English | MEDLINE | ID: mdl-36322766

ABSTRACT

The modern Pacific Ocean hosts the largest oxygen-deficient zones (ODZs), where oxygen concentrations are so low that nitrate is used to respire organic matter. The history of the ODZs may offer key insights into ocean deoxygenation under future global warming. In a 12-My record from the southeastern Pacific, we observe a >10‰ increase in foraminifera-bound nitrogen isotopes (15N/14N) since the late Miocene (8 to 9 Mya), indicating large ODZs expansion. Coinciding with this change, we find a major increase in the nutrient content of the ocean, reconstructed from phosphorus and iron measurements of hydrothermal sediments at the same site. Whereas global warming studies cast seawater oxygen concentrations as mainly dependent on climate and ocean circulation, our findings indicate that modern ODZs are underpinned by historically high concentrations of seawater phosphate.


Subject(s)
Foraminifera , Seawater , Oceans and Seas , Pacific Ocean , Oxygen/analysis , Nutrients
5.
BMC Med ; 22(1): 9, 2024 01 09.
Article in English | MEDLINE | ID: mdl-38191387

ABSTRACT

BACKGROUND: Due to the abundant usage of chemotherapy in young triple-negative breast cancer (TNBC) patients, the unbiased prognostic value of BRCA1-related biomarkers in this population remains unclear. In addition, whether BRCA1-related biomarkers modify the well-established prognostic value of stromal tumor-infiltrating lymphocytes (sTILs) is unknown. This study aimed to compare the outcomes of young, node-negative, chemotherapy-naïve TNBC patients according to BRCA1 status, taking sTILs into account. METHODS: We included 485 Dutch women diagnosed with node-negative TNBC under age 40 between 1989 and 2000. During this period, these women were considered low-risk and did not receive chemotherapy. BRCA1 status, including pathogenic germline BRCA1 mutation (gBRCA1m), somatic BRCA1 mutation (sBRCA1m), and tumor BRCA1 promoter methylation (BRCA1-PM), was assessed using DNA from formalin-fixed paraffin-embedded tissue. sTILs were assessed according to the international guideline. Patients' outcomes were compared using Cox regression and competing risk models. RESULTS: Among the 399 patients with BRCA1 status, 26.3% had a gBRCA1m, 5.3% had a sBRCA1m, 36.6% had tumor BRCA1-PM, and 31.8% had BRCA1-non-altered tumors. Compared to BRCA1-non-alteration, gBRCA1m was associated with worse overall survival (OS) from the fourth year after diagnosis (adjusted HR, 2.11; 95% CI, 1.18-3.75), and this association attenuated after adjustment for second primary tumors. Every 10% sTIL increment was associated with 16% higher OS (adjusted HR, 0.84; 95% CI, 0.78-0.90) in gBRCA1m, sBRCA1m, or BRCA1-non-altered patients and 31% higher OS in tumor BRCA1-PM patients. Among the 66 patients with tumor BRCA1-PM and ≥ 50% sTILs, we observed excellent 15-year OS (97.0%; 95% CI, 92.9-100%). Conversely, among the 61 patients with gBRCA1m and < 50% sTILs, we observed poor 15-year OS (50.8%; 95% CI, 39.7-65.0%). Furthermore, gBRCA1m was associated with higher (adjusted subdistribution HR, 4.04; 95% CI, 2.29-7.13) and tumor BRCA1-PM with lower (adjusted subdistribution HR, 0.42; 95% CI, 0.19-0.95) incidence of second primary tumors, compared to BRCA1-non-alteration. CONCLUSIONS: Although both gBRCA1m and tumor BRCA1-PM alter BRCA1 gene transcription, they are associated with different outcomes in young, node-negative, chemotherapy-naïve TNBC patients. By combining sTILs and BRCA1 status for risk classification, we were able to identify potential subgroups in this population to intensify and optimize adjuvant treatment.


Subject(s)
Neoplasms, Second Primary , Triple Negative Breast Neoplasms , Humans , Female , Adult , Triple Negative Breast Neoplasms/drug therapy , Triple Negative Breast Neoplasms/genetics , Adjuvants, Immunologic , Ethnicity , Biomarkers , BRCA1 Protein/genetics
6.
Small ; : e2309940, 2024 Mar 27.
Article in English | MEDLINE | ID: mdl-38534030

ABSTRACT

Ferroptosis is an iron-dependent and lipid peroxides (LPO)-overloaded programmed damage cell death, induced by glutathione (GSH) depletion and glutathione peroxide 4 (GPX4) inactivation. However, the inadequacy of endogenous iron and reactive oxygen species (ROS) restricts the efficacy of ferroptosis. To overcome this obstacle, a near-infrared photo-responsive FeP@PEG NPs is fabricated. Exogenous iron pool can enhance the effect of ferroptosis via the depletion of GSH and further regulate GPX4 inactivation. Generation of ·OH derived from the Fenton reaction is proved by increased accumulation of lipid peroxides. The heat generated by photothermal therapy and ROS generated by photodynamic therapy can enhance cell apoptosis under near-infrared (NIR-808 nm) irradiation, as evidenced by mitochondrial dysfunction and further accumulation of lipid peroxide content. FeP@PEG NPs can significantly inhibit the growth of several types of cancer cells in vitro and in vivo, which is validated by theoretical and experimental results. Meanwhile, FeP@PEG NPs show excellent T2-weighted magnetic resonance imaging (MRI) property. In summary, the FeP-based nanotheranostic platform for enhanced phototherapy/ferroptosis/chemodynamic therapy provides a reliable opportunity for clinical cancer theranostics.

7.
Bioinformatics ; 39(1)2023 01 01.
Article in English | MEDLINE | ID: mdl-36622018

ABSTRACT

MOTIVATION: Single-cell multimodal assays allow us to simultaneously measure two different molecular features of the same cell, enabling new insights into cellular heterogeneity, cell development and diseases. However, most existing methods suffer from inaccurate dimensionality reduction for the joint-modality data, hindering their discovery of novel or rare cell subpopulations. RESULTS: Here, we present VIMCCA, a computational framework based on variational-assisted multi-view canonical correlation analysis to integrate paired multimodal single-cell data. Our statistical model uses a common latent variable to interpret the common source of variances in two different data modalities. Our approach jointly learns an inference model and two modality-specific non-linear models by leveraging variational inference and deep learning. We perform VIMCCA and compare it with 10 existing state-of-the-art algorithms on four paired multi-modal datasets sequenced by different protocols. Results demonstrate that VIMCCA facilitates integrating various types of joint-modality data, thus leading to more reliable and accurate downstream analysis. VIMCCA improves our ability to identify novel or rare cell subtypes compared to existing widely used methods. Besides, it can also facilitate inferring cell lineage based on joint-modality profiles. AVAILABILITY AND IMPLEMENTATION: The VIMCCA algorithm has been implemented in our toolkit package scbean (≥0.5.0), and its code has been archived at https://github.com/jhu99/scbean under MIT license. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Subject(s)
Algorithms , Models, Statistical , Cell Differentiation , Cell Lineage
8.
Mol Phylogenet Evol ; 194: 108042, 2024 May.
Article in English | MEDLINE | ID: mdl-38401812

ABSTRACT

Climate changes at larger scales have influenced dispersal and range shifts of many taxa in East Asia. The fascicularis species group of macaques is composed of four species and is widely distributed in Southeast and East Asia. However, its phylogeography and demographic histories are currently poorly understood. Herein, we assembled autosomal, mitogenome, and Y-chromosome data for 106 individuals, and combined them with 174 mtDNA dloop haplotypes of this species group, with particular focus on the demographic histories and dispersal routes of Macaca fuscata, M. cyclopis, and M. mulatta. The results showed: (1) three monophyletic clades for M. fuscata, M. cyclopis, and M. mulatta based on the multiple genomics analyses; (2) the disparate demographic trajectories of the three species after their split ∼1.0 Ma revealed that M. cyclopis and M. fuscata were derived from an ancestral M. mulatta population; (3) the speciation time of M. cyclopis was later than that of M. fuscata, and their divergence time occurred at the beginning of "Ryukyu Coral Sea Stage" (1.0-0.2 Ma) when the East China Sea land bridge was completely submerged by the sea level rose; and (4) the three parallel rivers (Nujiang, Lancangjiang, and Jinshajiang) of Southwestern China divided M. mulatta into Indian and Chinese genetic populations ∼200 kya. These results shed light on understanding not only the evolutionary history of the fascicularis species group but also the formation mechanism of faunal diversity in East Asia during the Pleistocene.


Subject(s)
Macaca fuscata , Macaca , Animals , Phylogeography , Phylogeny , Macaca fuscata/genetics , Macaca/genetics , Asia, Eastern , DNA, Mitochondrial/genetics , Genomics , Demography
9.
Cytokine ; 179: 156626, 2024 07.
Article in English | MEDLINE | ID: mdl-38678810

ABSTRACT

PURPOSE: To determine the antifungal, anti-inflammatory and neuroprotective effects of resveratrol (RES) in Aspergillus fumigatus (A. fumigatus) keratitis. METHODS: Cytotoxicity assay and Draize eye assay were performed to assess the toxicity of RES. The antifungal effect of RES was assessed by minimal inhibitory concentration, scanning or transmission electron microscopy, propidium iodide uptake assay, and Calcofluor white staining. Phosphorylation of p38 MAPK, mRNA and protein levels of Dectin-1 and related inflammatory factors were measured by qRT-PCR, ELISA and Western blot in vitro and in vivo. Clinical score, HE staining, plate count, and myeloperoxidase test were used to observe the progress of fungal keratitis. IF staining, qRT-PCR, and the Von Frey test were selected to assess the neuroprotective effects of RES. RESULTS: RES suppressed A. fumigatus hyphae growth and altered hyphae morphology in vitro. RES decreased the expression of Dectin-1, IL-1ß and TNF-α, as well as p38 MAPK phosphorylation expression, and also decreased clinical scores, reduced inflammatory cell infiltration and neutrophil activity, and decreased fungal load. RES also protected corneal basal nerve fibers, down-regulated mechanosensitivity thresholds, and increased the mRNA levels of CGRP and TRPV-1.. CONCLUSION: These evidences revealed that RES could exert antifungal effects on A. fumigatus and ameliorate FK through suppressing the Dectin-1/p38 MAPK pathway to down-regulate IL-1ß, IL-6, etc. expression and play protective effect on corneal nerves.


Subject(s)
Anti-Inflammatory Agents , Aspergillus fumigatus , Keratitis , Lectins, C-Type , Neuroprotective Agents , Resveratrol , p38 Mitogen-Activated Protein Kinases , Aspergillus fumigatus/drug effects , Lectins, C-Type/metabolism , Keratitis/drug therapy , Keratitis/metabolism , Keratitis/microbiology , Resveratrol/pharmacology , p38 Mitogen-Activated Protein Kinases/metabolism , Animals , Neuroprotective Agents/pharmacology , Anti-Inflammatory Agents/pharmacology , Mice , Aspergillosis/drug therapy , Aspergillosis/metabolism , Antifungal Agents/pharmacology , Male , Signal Transduction/drug effects , MAP Kinase Signaling System/drug effects , Cornea/drug effects , Cornea/metabolism
10.
Pharmacol Res ; 199: 107034, 2024 Jan.
Article in English | MEDLINE | ID: mdl-38070793

ABSTRACT

The incidence and mortality of lung cancer are on the rise worldwide. However, the benefit of clinical treatment in lung cancer is limited. Owning to important sources of drug development, natural products have received constant attention around the world. Main ingredient polysaccharides in natural products have been found to have various activities in pharmacological research. In recent years, more and more scientists are looking for the effects and mechanisms of different natural product polysaccharides on lung cancer. In this review, we focus on the following aspects: First, natural product polysaccharides have been discovered to directly suppress the growth of lung cancer cells, which can be effective in limiting tumor progression. Additionally, polysaccharides have been considered to enhance immune function, which can play a pivotal role in fighting lung cancer. Lastly, polysaccharides can improve the efficacy of drugs in lung cancer treatment by regulating the gut microbiota. Overall, the research of natural product polysaccharides in the treatment of lung cancer is a promising area that has the potential to lead to new clinical treatments. With better understanding, natural product polysaccharides have the potential to become important components of future lung cancer treatments.


Subject(s)
Biological Products , Gastrointestinal Microbiome , Lung Neoplasms , Humans , Lung Neoplasms/drug therapy , Biological Products/pharmacology , Biological Products/therapeutic use , Polysaccharides/pharmacology , Polysaccharides/therapeutic use
11.
Bioorg Med Chem Lett ; 99: 129619, 2024 Feb 01.
Article in English | MEDLINE | ID: mdl-38244939

ABSTRACT

Compared with single-targeted therapy, the design and synthesis of heterozygous molecules is still a significant challenge for the discovery of antitumor drugs. Quinone oxidoreductase-1 (NQO1) is a potential target for selective cancer therapy due to its overexpression in many cancer cells and its unique bioredox properties. Based on the principle of combinatorial drug design, we successfully synthesized a new hybrid molecules 13 with an indolequinone structure. We found that the synthesized compounds exhibited much higher cytotoxicity against the tested cancer cells than free drugs. Further mechanism studies confirmed that compound 13 induced cell apoptosis was achieved by regulating p53-dependent mitochondrial pathway and cell cycle arrest at the G0/G1 phase.


Subject(s)
Antineoplastic Agents , Indolequinones , Erlotinib Hydrochloride/pharmacology , Antineoplastic Agents/chemistry , Quinazolines/pharmacology , Apoptosis , Indolequinones/chemistry , Drug Screening Assays, Antitumor , Cell Line, Tumor , Cell Proliferation , Structure-Activity Relationship
12.
Bioorg Chem ; 142: 106952, 2024 01.
Article in English | MEDLINE | ID: mdl-37952486

ABSTRACT

PARP1 is a multifaceted component of DNA repair and chromatin remodeling, making it an effective therapeutic target for cancer therapy. The recently reported proteolytic targeting chimera (PROTAC) could effectively degrade PARP1 through the ubiquitin-proteasome pathway, expanding the therapeutic application of PARP1 blocking. In this study, a series of nitrogen heterocyclic PROTACs were designed and synthesized through ternary complex simulation analysis based on our previous work. Our efforts have resulted in a potent PARP1 degrader D6 (DC50 = 25.23 nM) with high selectivity due to nitrogen heterocyclic linker generating multiple interactions with the PARP1-CRBN PPI surface, specifically. Moreover, D6 exhibited strong cytotoxicity to triple negative breast cancer cell line MDA-MB-231 (IC50 = 1.04 µM). And the proteomic results showed that the antitumor mechanism of D6 was found that intensifies DNA damage by intercepting the CDC25C-CDK1 axis to halt cell cycle transition in triple-negative breast cancer cells. Furthermore, in vivo study, D6 showed a promising PK property with moderate oral absorption activity. And D6 could effectively inhibit tumor growth (TGI rate = 71.4 % at 40 mg/kg) without other signs of toxicity in MDA-MB-321 tumor-bearing mice. In summary, we have identified an original scaffold and potent PARP1 PROTAC that provided a novel intervention strategy for the treatment of triple-negative breast cancer.


Subject(s)
Triple Negative Breast Neoplasms , Humans , Mice , Animals , Triple Negative Breast Neoplasms/pathology , Proteomics , Cell Proliferation , Cell Cycle Checkpoints , Nitrogen , Cell Line, Tumor , cdc25 Phosphatases , Poly (ADP-Ribose) Polymerase-1 , CDC2 Protein Kinase
13.
BMC Pregnancy Childbirth ; 24(1): 424, 2024 Jun 13.
Article in English | MEDLINE | ID: mdl-38872116

ABSTRACT

OBJECTIVE: To establish the population pharmacokinetics (PPK) of magnesium sulfate (MgSO4)in women with preeclampsia (PE), and to determine the key covariates having an effect in magnesium pharmacokinetics in Chinese PE. METHODS: Pregnant women with PE prescribed MgSO4 were enrolled in this prospective study from April 2021 to April 2023. On the initial day of administration, the patients were administered a loading dose of 5 g in conjunction with 10 g of magnesium sulfate as a maintenance dose. On the second day, only the maintenance dose was administration, and maternal blood samples were taken at 0, 4, 5, and 12 h after the second day's 10 g maintenance dose. The software Phoenix was used to estimate PPK parameters of MgSO4, such as clearance (CL) and volume of distribution (V), and to model PPK models with patient demographic, clinical, and laboratory covariates. RESULTS: A total of 199 blood samples were collected from 51 women with PE and PPK profiles were analyzed. The PPK of MgSO4 is consistent with to a one-compartment model. The base model adequately described the maternal serum magnesium concentrations after magnesium administration. The population parameter estimates were as follows: CL was 2.98 L/h, V was 25.07 L. The model predictions changed significantly with covariates (BMI, creatinine clearance, and furosemide). Furosemide statistically influences V. The creatinine clearance, BMI and furosemide jointly affects CL. Monte Carlo simulation results showed that a loading dose combined with a maintenance dose would need to be administered daily to achieve the therapeutic blood magnesium concentrations. For the non-furosemide group, the optimal dosing regimen was a 5 g loading dose combined with a 10 g maintenance dose of MgSO4. For the furosemide group, the optimal dosing regimen was a 2.5 g loading dose combined with a 10 g maintenance dose of MgSO4. CONCLUSIONS: The magnesium PPK model was successfully developed and evaluated in Chinese preeclampsia population, and the dose optimization of MgSO4 was completed through Monte Carlo simulation.


Subject(s)
Magnesium Sulfate , Pre-Eclampsia , Humans , Female , Magnesium Sulfate/administration & dosage , Magnesium Sulfate/pharmacokinetics , Pre-Eclampsia/drug therapy , Pre-Eclampsia/blood , Pregnancy , Adult , Prospective Studies , China , Young Adult , Dose-Response Relationship, Drug , East Asian People
14.
Sensors (Basel) ; 24(12)2024 Jun 08.
Article in English | MEDLINE | ID: mdl-38931517

ABSTRACT

This study integrates hollow microneedle arrays (HMNA) with a novel jellyfish-shaped electrochemical sensor for the detection of key biomarkers, including uric acid (UA), glucose, and pH, in artificial interstitial fluid. The jellyfish-shaped sensor displayed linear responses in detecting UA and glucose via differential pulse voltammetry (DPV) and chronoamperometry, respectively. Notably, the open circuit potential (OCP) of the system showed a linear variation with pH changes, validating its pH-sensing capability. The sensor system demonstrates exceptional electrochemical responsiveness within the physiological concentration ranges of these biomarkers in simulated epidermis sensing applications. The detection linear ranges of UA, glucose, and pH were 0~0.8 mM, 0~7 mM, and 4.0~8.0, respectively. These findings highlight the potential of the HMNA-integrated jellyfish-shaped sensors in real-world epidermal applications for comprehensive disease diagnosis and health monitoring.


Subject(s)
Biomarkers , Biosensing Techniques , Electrochemical Techniques , Extracellular Fluid , Needles , Extracellular Fluid/chemistry , Biomarkers/analysis , Biosensing Techniques/instrumentation , Biosensing Techniques/methods , Electrochemical Techniques/instrumentation , Electrochemical Techniques/methods , Hydrogen-Ion Concentration , Glucose/analysis , Uric Acid/analysis , Animals , Humans
15.
Neuroimage ; 274: 120089, 2023 07 01.
Article in English | MEDLINE | ID: mdl-37086875

ABSTRACT

To embrace big-data neuroimaging, harmonizing the site effect in resting-state functional magnetic resonance imaging (R-fMRI) data fusion is a fundamental challenge. A comprehensive evaluation of potentially effective harmonization strategies, particularly with specifically collected data, has been scarce, especially for R-fMRI metrics. Here, we comprehensively assess harmonization strategies from multiple perspectives, including tests on residual site effect, individual identification, test-retest reliability, and replicability of group-level statistical results, on widely used R-fMRI metrics across various datasets, including data obtained from participants with repetitive measures at different scanners. For individual identifiability (i.e., whether the same subject could be identified across R-fMRI data scanned across different sites), we found that, while most methods decreased site effects, the Subsampling Maximum-mean-distance based distribution shift correction Algorithm (SMA) and parametric unadjusted CovBat outperformed linear regression models, linear mixed models, ComBat series and invariant conditional variational auto-encoder in clustering accuracy. Test-retest reliability was better for SMA and parametric adjusted CovBat than unadjusted ComBat series and parametric unadjusted CovBat in the number of overlapped voxels. At the same time, SMA was superior to the latter in replicability in terms of the Dice coefficient and the scale of brain areas showing sex differences reproducibly observed across datasets. Furthermore, SMA better detected reproducible sex differences of ALFF under the site-sex confounded situation. Moreover, we designed experiments to identify the best target site features to optimize SMA identifiability, test-retest reliability, and stability. We noted both sample size and distribution of the target site matter and introduced a heuristic formula for selecting the target site. In addition to providing practical guidelines, this work can inform continuing improvements and innovations in harmonizing methodologies for big R-fMRI data.


Subject(s)
Brain , Connectome , Humans , Male , Female , Reproducibility of Results , Brain/diagnostic imaging , Brain/pathology , Magnetic Resonance Imaging/methods , Connectome/methods , Neuroimaging
16.
Neuroimage ; 265: 119775, 2023 01.
Article in English | MEDLINE | ID: mdl-36455761

ABSTRACT

Is the brain at rest during the so-called resting state? Ongoing experiences in the resting state vary in unobserved and uncontrolled ways across time, individuals, and populations. However, the role of self-generated thoughts in resting-state fMRI remains largely unexplored. In this study, we collected real-time self-generated thoughts during "resting-state" fMRI scans via the think-aloud method (i.e., think-aloud fMRI), which required participants to report whatever they were currently thinking. We first investigated brain activation patterns during a think-aloud condition and found that significantly activated brain areas included all brain regions required for speech. We then calculated the relationship between divergence in thought content and brain activation during think-aloud and found that divergence in thought content was associated with many brain regions. Finally, we explored the neural representation of self-generated thoughts by performing representational similarity analysis (RSA) at three neural scales: a voxel-wise whole-brain searchlight level, a region-level whole-brain analysis using the Schaefer 400-parcels, and at the systems level using the Yeo seven-networks. We found that "resting-state" self-generated thoughts were distributed across a wide range of brain regions involving all seven Yeo networks. This study highlights the value of considering ongoing experiences during resting-state fMRI and providing preliminary methodological support for think-aloud fMRI.


Subject(s)
Brain , Magnetic Resonance Imaging , Humans , Brain/diagnostic imaging , Brain/physiology , Cognition , Brain Mapping/methods , Speech
17.
J Am Chem Soc ; 145(34): 18800-18811, 2023 Aug 30.
Article in English | MEDLINE | ID: mdl-37590178

ABSTRACT

Supramolecular electronics provide an opportunity to introduce molecular assemblies into electronic devices through a combination of noncovalent interactions such as [π···π] and hydrogen-bonding interactions. The fidelity and dynamics of noncovalent interactions hold considerable promise when it comes to building devices with controllable and reproducible switching functions. Here, we demonstrate a strategy for building electronically robust switches by harnessing two different noncovalent interactions between a couple of pyridine derivatives. The single-supermolecule switch is turned ON when compressing the junction enabling [π···π] interactions to dominate the transport, while the switch is turned OFF by stretching the junction to form hydrogen-bonded dimers, leading to a dramatic decrease in conductance. The robustness and reproducibility of these single-supermolecule switches were achieved by modulating the junction with Ångström precision at frequencies of up to 190 Hz while obtaining high ON/OFF ratios of ∼600. The research presented herein opens up an avenue for designing robust bistable mechanoresponsive devices which will find applications in the building of integrated circuits for microelectromechanical systems.

18.
Hum Brain Mapp ; 44(17): 6245-6257, 2023 12 01.
Article in English | MEDLINE | ID: mdl-37837649

ABSTRACT

Rumination is closely linked to the onset and maintenance of major depressive disorder (MDD). Prior neuroimaging studies have identified the association between self-reported rumination trait and the functional coupling among a network of brain regions using resting-state functional magnetic resonance imaging (MRI). However, little is known about the underlying neural circuitry mechanism during active rumination in MDD. Degree centrality (DC) is a simple metric to denote network integration, which is critical for higher-order psychological processes such as rumination. During an MRI scan, individuals with MDD (N = 45) and healthy controls (HC, N = 46) completed a rumination state task. We examined the interaction effect between the group (MDD vs. HC) and condition (rumination vs. distraction) on vertex-wise DC. We further characterized the identified brain region's functional involvement with Neurosynth and BrainMap. Network-wise seed-based functional connectivity (FC) analysis was also conducted for the identified region of interest. Finally, exploratory correlation analysis was conducted between the identified region of interest's network FCs and self-reported in-scanner affect levels. We found that a left superior frontal gyrus (SFG) region, generally overlapped with the frontal eye field, showed a significant interaction effect. Further analysis revealed its involvement with executive functions. FCs between this region, the frontoparietal, and the dorsal attention network (DAN) also showed significant interaction effects. Furthermore, its FC to DAN during distraction showed a marginally significant negative association with in-scanner affect level at the baseline. Our results implicated an essential role of the left SFG in the rumination's underlying neural circuitry mechanism in MDD and provided novel evidence for the conceptualization of rumination in terms of impaired executive control.


Subject(s)
Depressive Disorder, Major , Humans , Brain/diagnostic imaging , Prefrontal Cortex , Executive Function , Frontal Lobe , Magnetic Resonance Imaging , Brain Mapping
19.
Opt Express ; 31(23): 38077-38096, 2023 Nov 06.
Article in English | MEDLINE | ID: mdl-38017924

ABSTRACT

We propose an aperture division multispectral camera for Earth observation (EAMC) based on the Lagrange L1 point of the Earth-Moon system to measure the Earth's reflected solar radiation (RSR), quantify the effective radiative forcing (ERF) and establish the pixel-scale multispectral angular distribution model (ADM) of the Earth's radiance. The EAMC adopts the snapshot technique to provide multispectral images in the 360-920 nm wavelength, employing nine subsystems sharing a primary system. The camera can capture the entire Earth's two-dimensional morphology and spectral fingerprints at a 10 km spatial resolution, with all spectral images acquired concurrently on a single detector. The camera's optical system is designed and simulated, and the stray light is analyzed and suppressed. Simulation and analysis results show that the camera can obtain high-quality images of the Earth's disk with a 2.5° field of view (FOV). The stray light is suppressed to less than 0.05% of the observed multispectral Earth radiation. The novel EAMC provides a new way to generate climate-relevant knowledge from the perspective of global Earth observation and has great potential for other applications in space-based remote sensing spectral imaging.

20.
Cell Biol Int ; 47(3): 584-597, 2023 Mar.
Article in English | MEDLINE | ID: mdl-36378581

ABSTRACT

Amyloid-ß (Aß) is thought to be a critical pathologic factor of retinal pigment epithelium (RPE) degeneration in age-related macular degeneration (AMD). Aß induces inflammatory responses in RPE cells and recent studies demonstrate the N6-methyladenosine (m6A) regulatory role in RPE cell inflammation. m6A is a reversible epigenetic posttranslational modification, but its relationship with Aß-induced RPE degeneration is yet to be thoroughly investigated. The present study explored the role and mechanism of m6A in Aß-induced RPE degeneration model. This model was induced via intravitreally injecting oligomeric Aß and the morphology of its retina was analyzed. One of m6A demethylases, the fat mass and obesity-associated (FTO) gene expression, was assessed. An m6A-messenger RNA (mRNA) epitranscriptomic microarray was employed for further bioinformatic analyses. It was confirmed that Aß induced FTO upregulation within the RPE. Hypopigmentation alterations and structural disorganization were observed in Aß-treated eyes, and inhibition of FTO exacerbated retinal degeneration and RPE impairment. Moreover, the m6A-mRNA epitranscriptomic microarray suggested that protein kinase A (PKA) was a target of FTO, and the PKA/cyclic AMP-responsive element binding (CREB) signaling pathway was involved in Aß-induced RPE degeneration. m6A-RNA binding protein immunoprecipitation confirmed that FTO demethylated PKA within the RPE cells of Aß-treated eyes. Altered expression of PKA and its downstream targets (CREB and brain-derived neurotrophic factor) was confirmed by quantitative reverse-transcription polymerase chain reaction and Western blot analyses. Hence, this study's findings shed light on FTO-mediated m6A modification in Aß-induced RPE degeneration and indicate potential therapeutic targets for AMD.


Subject(s)
Macular Degeneration , Retina , Humans , Retina/metabolism , Macular Degeneration/metabolism , Amyloid beta-Peptides/metabolism , Signal Transduction , RNA, Messenger/metabolism , Obesity/metabolism , Epithelial Cells/metabolism , Retinal Pigments/metabolism , Alpha-Ketoglutarate-Dependent Dioxygenase FTO
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