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1.
Cell ; 173(7): 1593-1608.e20, 2018 06 14.
Artículo en Inglés | MEDLINE | ID: mdl-29906446

RESUMEN

Proliferating cells known as neoblasts include pluripotent stem cells (PSCs) that sustain tissue homeostasis and regeneration of lost body parts in planarians. However, the lack of markers to prospectively identify and isolate these adult PSCs has significantly hampered their characterization. We used single-cell RNA sequencing (scRNA-seq) and single-cell transplantation to address this long-standing issue. Large-scale scRNA-seq of sorted neoblasts unveiled a novel subtype of neoblast (Nb2) characterized by high levels of PIWI-1 mRNA and protein and marked by a conserved cell-surface protein-coding gene, tetraspanin 1 (tspan-1). tspan-1-positive cells survived sub-lethal irradiation, underwent clonal expansion to repopulate whole animals, and when purified with an anti-TSPAN-1 antibody, rescued the viability of lethally irradiated animals after single-cell transplantation. The first prospective isolation of an adult PSC bridges a conceptual dichotomy between functionally and molecularly defined neoblasts, shedding light on mechanisms governing in vivo pluripotency and a source of regeneration in animals. VIDEO ABSTRACT.


Asunto(s)
Proteínas Argonautas/metabolismo , Proteínas del Helminto/metabolismo , Planarias/fisiología , Tetraspaninas/metabolismo , Animales , Proteínas Argonautas/antagonistas & inhibidores , Proteínas Argonautas/genética , Ciclo Celular/efectos de la radiación , Regulación de la Expresión Génica , Proteínas del Helminto/antagonistas & inhibidores , Proteínas del Helminto/genética , Células Madre Pluripotentes/citología , Células Madre Pluripotentes/metabolismo , Células Madre Pluripotentes/trasplante , Análisis de Componente Principal , Interferencia de ARN , ARN Bicatenario/metabolismo , ARN de Helminto/química , ARN de Helminto/aislamiento & purificación , ARN de Helminto/metabolismo , Regeneración/genética , Análisis de Secuencia de ARN , Análisis de la Célula Individual , Tetraspaninas/genética , Irradiación Corporal Total
2.
Nat Immunol ; 19(6): 547-560, 2018 06.
Artículo en Inglés | MEDLINE | ID: mdl-29777223

RESUMEN

The adaptor CARD9 functions downstream of C-type lectin receptors (CLRs) for the sensing of microbial infection, which leads to responses by the TH1 and TH17 subsets of helper T cells. The single-nucleotide polymorphism rs4077515 at CARD9 in the human genome, which results in the substitution S12N (CARD9S12N), is associated with several autoimmune diseases. However, the function of CARD9S12N has remained unknown. Here we generated CARD9S12N knock-in mice and found that CARD9S12N facilitated the induction of type 2 immune responses after engagement of CLRs. Mechanistically, CARD9S12N mediated CLR-induced activation of the non-canonical transcription factor NF-κB subunit RelB, which initiated production of the cytokine IL-5 in alveolar macrophages for the recruitment of eosinophils to drive TH2 cell-mediated allergic responses. We identified the homozygous CARD9 mutation encoding S12N in patients with allergic bronchopulmonary aspergillosis and revealed activation of RelB and production of IL-5 in peripheral blood mononuclear cells from these patients. Our study provides genetic and functional evidence demonstrating that CARD9S12N can turn alveolar macrophages into IL-5-producing cells and facilitates TH2 cell-mediated pathologic responses.


Asunto(s)
Aspergilosis Broncopulmonar Alérgica/inmunología , Proteínas Adaptadoras de Señalización CARD/inmunología , Interleucina-5/biosíntesis , Macrófagos Alveolares/inmunología , Células Th2/inmunología , Animales , Aspergilosis Broncopulmonar Alérgica/genética , Proteínas Adaptadoras de Señalización CARD/genética , Humanos , Interleucina-5/inmunología , Macrófagos Alveolares/metabolismo , Ratones , Polimorfismo de Nucleótido Simple , Transducción de Señal/inmunología
3.
Cell ; 162(6): 1391-403, 2015 Sep 10.
Artículo en Inglés | MEDLINE | ID: mdl-26359990

RESUMEN

How metazoan mechanotransduction channels sense mechanical stimuli is not well understood. The NOMPC channel in the transient receptor potential (TRP) family, a mechanotransduction channel for Drosophila touch sensation and hearing, contains 29 Ankyrin repeats (ARs) that associate with microtubules. These ARs have been postulated to act as a tether that conveys force to the channel. Here, we report that these N-terminal ARs form a cytoplasmic domain essential for NOMPC mechanogating in vitro, mechanosensitivity of touch receptor neurons in vivo, and touch-induced behaviors of Drosophila larvae. Duplicating the ARs elongates the filaments that tether NOMPC to microtubules in mechanosensory neurons. Moreover, microtubule association is required for NOMPC mechanogating. Importantly, transferring the NOMPC ARs to mechanoinsensitive voltage-gated potassium channels confers mechanosensitivity to the chimeric channels. These experiments strongly support a tether mechanism of mechanogating for the NOMPC channel, providing insights into the basis of mechanosensitivity of mechanotransduction channels.


Asunto(s)
Proteínas de Drosophila/química , Proteínas de Drosophila/metabolismo , Drosophila/metabolismo , Mecanotransducción Celular , Canales de Potencial de Receptor Transitorio/química , Canales de Potencial de Receptor Transitorio/metabolismo , Animales , Drosophila/citología , Drosophila/crecimiento & desarrollo , Canal de Potasio Kv.1.2/metabolismo , Larva/citología , Larva/metabolismo , Microtúbulos/metabolismo , Estructura Terciaria de Proteína , Tacto
4.
Nat Methods ; 20(6): 824-835, 2023 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-37069271

RESUMEN

BigNeuron is an open community bench-testing platform with the goal of setting open standards for accurate and fast automatic neuron tracing. We gathered a diverse set of image volumes across several species that is representative of the data obtained in many neuroscience laboratories interested in neuron tracing. Here, we report generated gold standard manual annotations for a subset of the available imaging datasets and quantified tracing quality for 35 automatic tracing algorithms. The goal of generating such a hand-curated diverse dataset is to advance the development of tracing algorithms and enable generalizable benchmarking. Together with image quality features, we pooled the data in an interactive web application that enables users and developers to perform principal component analysis, t-distributed stochastic neighbor embedding, correlation and clustering, visualization of imaging and tracing data, and benchmarking of automatic tracing algorithms in user-defined data subsets. The image quality metrics explain most of the variance in the data, followed by neuromorphological features related to neuron size. We observed that diverse algorithms can provide complementary information to obtain accurate results and developed a method to iteratively combine methods and generate consensus reconstructions. The consensus trees obtained provide estimates of the neuron structure ground truth that typically outperform single algorithms in noisy datasets. However, specific algorithms may outperform the consensus tree strategy in specific imaging conditions. Finally, to aid users in predicting the most accurate automatic tracing results without manual annotations for comparison, we used support vector machine regression to predict reconstruction quality given an image volume and a set of automatic tracings.


Asunto(s)
Benchmarking , Microscopía , Microscopía/métodos , Imagenología Tridimensional/métodos , Neuronas/fisiología , Algoritmos
5.
Proc Natl Acad Sci U S A ; 120(3): e2217759120, 2023 01 17.
Artículo en Inglés | MEDLINE | ID: mdl-36626563

RESUMEN

Tau aggregates are a hallmark of multiple neurodegenerative diseases and can contain RNAs and RNA-binding proteins, including serine/arginine repetitive matrix protein 2 (SRRM2) and pinin (PNN). However, how these nuclear proteins mislocalize and their influence on the prion-like propagation of tau aggregates is unknown. We demonstrate that polyserine repeats in SRRM2 and PNN are necessary and sufficient for recruitment to tau aggregates. Moreover, we show tau aggregates preferentially grow in association with endogenous cytoplasmic assemblies-mitotic interchromatin granules and cytoplasmic speckles (CSs)-which contain SRRM2 and PNN. Polyserine overexpression in cells nucleates assemblies that are sites of tau aggregate growth. Further, modulating the levels of polyserine-containing proteins results in a corresponding change in tau aggregation. These findings define a specific protein motif, and cellular condensates, that promote tau aggregate propagation. As CSs form in induced pluripotent stem cell (iPSC) derived neurons under inflammatory or hyperosmolar stress, they may affect tau aggregate propagation in neurodegenerative disease.


Asunto(s)
Enfermedad de Alzheimer , Enfermedades Neurodegenerativas , Tauopatías , Humanos , Proteínas tau/genética , Proteínas tau/metabolismo , Tauopatías/metabolismo , Péptidos , Enfermedad de Alzheimer/metabolismo
6.
Brief Bioinform ; 24(2)2023 03 19.
Artículo en Inglés | MEDLINE | ID: mdl-36907658

RESUMEN

The adaptive immune response to foreign antigens is initiated by T-cell receptor (TCR) recognition on the antigens. Recent experimental advances have enabled the generation of a large amount of TCR data and their cognate antigenic targets, allowing machine learning models to predict the binding specificity of TCRs. In this work, we present TEINet, a deep learning framework that utilizes transfer learning to address this prediction problem. TEINet employs two separately pretrained encoders to transform TCR and epitope sequences into numerical vectors, which are subsequently fed into a fully connected neural network to predict their binding specificities. A major challenge for binding specificity prediction is the lack of a unified approach to sampling negative data. Here, we first assess the current negative sampling approaches comprehensively and suggest that the Unified Epitope is the most suitable one. Subsequently, we compare TEINet with three baseline methods and observe that TEINet achieves an average AUROC of 0.760, which outperforms baseline methods by 6.4-26%. Furthermore, we investigate the impacts of the pretraining step and notice that excessive pretraining may lower its transferability to the final prediction task. Our results and analysis show that TEINet can make an accurate prediction using only the TCR sequence (CDR3$\beta $) and the epitope sequence, providing novel insights to understand the interactions between TCRs and epitopes.


Asunto(s)
Aprendizaje Profundo , Epítopos de Linfocito T , Receptores de Antígenos de Linfocitos T , Unión Proteica
7.
Rev Med Virol ; 34(1): e2503, 2024 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-38282397

RESUMEN

The diverse and severe nature of neurological manifestations associated with coronavirus disease 2019 (Covid-19) has garnered increasing attention. Exploring the potential to decrease neurological complications in Covid-19 patients involves targeting the mammalian target of rapamycin (mTOR) pathway as a therapeutic strategy. The mTOR pathway, widely recognised for its central role in essential cellular processes like synthesising proteins, facilitating autophagy, and modulating immune responses, has implications in various neurological disorders. Drawing parallels between these disorders and the observed neurological complications in Covid-19, we present a comprehensive review on the current understanding of mTOR signalling in the context of severe acute respiratory syndrome coronavirus 2 infection and neuroinflammation.


Asunto(s)
COVID-19 , Enfermedades del Sistema Nervioso , Serina-Treonina Quinasas TOR , Humanos , COVID-19/complicaciones , Enfermedades del Sistema Nervioso/etiología , Transducción de Señal , Serina-Treonina Quinasas TOR/metabolismo
8.
Nature ; 572(7767): 101-105, 2019 08.
Artículo en Inglés | MEDLINE | ID: mdl-31367031

RESUMEN

The discovery of superconducting and insulating states in magic-angle twisted bilayer graphene (MATBG)1,2 has ignited considerable interest in understanding the nature of electronic interactions in this chemically pristine material. The transport properties of MATBG as a function of doping are similar to those of high-transition-temperature copper oxides and other unconventional superconductors1-3, which suggests that MATBG may be a highly interacting system. However, to our knowledge, there is no direct experimental evidence of strong many-body correlations in MATBG. Here we present high-resolution spectroscopic measurements, obtained using a scanning tunnelling microscope, that provide such evidence as a function of carrier density. MATBG displays unusual spectroscopic characteristics that can be attributed to electron-electron interactions over a wide range of doping levels, including those at which superconductivity emerges in this system. We show that our measurements cannot be explained with a mean-field approach for modelling electron-electron interactions in MATBG. The breakdown of a mean-field approach when applied to other correlated superconductors, such as copper oxides, has long inspired the study of the highly correlated Hubbard model3. We show that a phenomenological extended-Hubbard-model cluster calculation, which is motivated by the nearly localized nature of the relevant electronic states of MATBG, produces spectroscopic features that are similar to those that we observed experimentally. Our findings demonstrate the critical role of many-body correlations in understanding the properties of MATBG.

9.
BMC Genomics ; 25(1): 431, 2024 May 01.
Artículo en Inglés | MEDLINE | ID: mdl-38693480

RESUMEN

Ophthalmic manifestations have recently been observed in acute and post-acute complications of COVID-19 caused by SARS-CoV-2 infection. Our precious study has shown that host RNA editing is linked to RNA viral infection, yet ocular adenosine to inosine (A-to-I) RNA editing during SARS-CoV-2 infection remains uninvestigated in COVID-19. Herein we used an epitranscriptomic pipeline to analyze 37 samples and investigate A-to-I editing associated with SARS-CoV-2 infection, in five ocular tissue types including the conjunctiva, limbus, cornea, sclera, and retinal organoids. Our results revealed dramatically altered A-to-I RNA editing across the five ocular tissues. Notably, the transcriptome-wide average level of RNA editing was increased in the cornea but generally decreased in the other four ocular tissues. Functional enrichment analysis showed that differential RNA editing (DRE) was mainly in genes related to ubiquitin-dependent protein catabolic process, transcriptional regulation, and RNA splicing. In addition to tissue-specific RNA editing found in each tissue, common RNA editing was observed across different tissues, especially in the innate antiviral immune gene MAVS and the E3 ubiquitin-protein ligase MDM2. Analysis in retinal organoids further revealed highly dynamic RNA editing alterations over time during SARS-CoV-2 infection. Our study thus suggested the potential role played by RNA editing in ophthalmic manifestations of COVID-19, and highlighted its potential transcriptome impact, especially on innate immunity.


Asunto(s)
COVID-19 , Edición de ARN , SARS-CoV-2 , Humanos , COVID-19/genética , COVID-19/virología , SARS-CoV-2/genética , Adenosina/metabolismo , Inosina/metabolismo , Inosina/genética , Transcriptoma , Ojo/metabolismo , Ojo/virología
10.
Curr Issues Mol Biol ; 46(3): 2701-2712, 2024 Mar 21.
Artículo en Inglés | MEDLINE | ID: mdl-38534786

RESUMEN

Inflammation and collagen-degrading enzymes' overexpression promote collagen decomposition, which affects the structural integrity of the extracellular matrix. The polysaccharide and peptide extracts of the green alga Caulerpa microphysa (C. microphysa) have been proven to have anti-inflammatory, wound healing, and antioxidant effects in vivo and in vitro. However, the biological properties of the non-water-soluble components of C. microphysa are still unknown. In the present study, we demonstrated the higher effective anti-inflammatory functions of C. microphysa ethyl acetate (EA) extract than water extract up to 16-30% in LPS-induced HaCaT cells, including reducing the production of interleukin (IL)-1ß, IL-6, IL-8, and tumor necrosis factor-α (TNF-α). Furthermore, the excellent collagen homeostasis effects from C. microphysa were proven by suppressing the matrix metalloproteinase-1 (MMP-1) secretion, enhancing type 1 procollagen and collagen expressions dose-dependently in WS1 cells. Moreover, using UHPLC-QTOF-MS analysis, four terpenoids, siphonaxanthin, caulerpenyne, caulerpal A, and caulerpal B, were identified and may be involved in the superior collagen homeostasis and anti-inflammatory effects of the C. microphysa EA extract.

11.
Lancet ; 402 Suppl 1: S97, 2023 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-37997144

RESUMEN

BACKGROUND: The increasing prevalence of type 2 diabetes in working-age people imposes a substantial societal burden. Although physical activity is crucial for diabetes management, limited evidence exists to inform optimal strategies for promoting physical activity in this population. We aimed to determine and compare the effectiveness of interventions for increasing physical activity level in working-age people with diabetes. METHODS: In this systematic review and meta-analysis, we searched Web of Science, the Cochrane Library, Medline, Embase, PsycINFO, ClinicalTrials.gov, and ICTRP for papers published between Jan 1, 1931, and June 30, 2022, in English. Search terms included "physical activity", "diabetes", and "randomised controlled trial". We included trials reporting the effects of interventions on physical activity level (objectively or subjectively measured) in people with type 2 diabetes aged 18-60 years. Two independent reviewers conducted summary data extraction and quality assessment. We used pairwise random-effects, frequentist network meta-analyses, and meta-regression to obtain pooled effects. Heterogeneity was evaluated using I2 statistic. The risk of bias and certainty of evidence were assessed using the Cochrane risk-of-bias 2 tool and the Grading of Recommendations Assessment, Development, and Evaluation. This study is registered with PROSPERO (CRD42022323165). FINDINGS: We identified 52 trials (6257 participants) from 21 countries (32 Asia, ten North America, eight Europe, one Australia, one Africa). The overall risk of bias was classified as "some concerns" for included studies. Four types of interventions (structured exercise training, physical activity education, psychological intervention, physical activity education plus psychological intervention) were identified. Compared with control groups, the interventions showed significant effects in objectively measured (standardised mean difference 0·77, 95% CI 0·27-1·27, low certainty), subjectively measured (0·88, 0·40-1·35, very low certainty), and overall physical activity (0·82, 0·48-1·16, moderate certainty). Physical activity education exerted large effect in overall physical activity compared with control groups. Psychological intervention exerted large effects in overall physical activity compared with other interventions. Heterogeneity was high (I2=96-97%). Intervention setting (p=0·04) and facilitator (p=0·03) showed effects on heterogeneity. INTERPRETATION: Psychologically modelled education might be the most beneficial way of promoting physical activity. Intervention setting and facilitator type should be considered when designing interventions for improving physical activity level in working-age people with type 2 diabetes. Limitations of this review include restriction to the English language and considerable heterogeneity between studies. FUNDING: King's-China Scholarship Council PhD Scholarship (202108440151).


Asunto(s)
Diabetes Mellitus Tipo 2 , Humanos , Diabetes Mellitus Tipo 2/terapia , Ejercicio Físico , África , Asia , Australia
12.
J Neuroinflammation ; 21(1): 88, 2024 Apr 10.
Artículo en Inglés | MEDLINE | ID: mdl-38600569

RESUMEN

BACKGROUND: Mechanical softening of the glial scar region regulates axonal regeneration to impede neurological recovery in central nervous system (CNS) injury. Microglia, a crucial cellular component of the glial scar, facilitate neuronal survival and neurological recovery after spinal cord injury (SCI). However, the critical mechanical characterization of injured spinal cord that harmonizes neuroprotective function of microglia remains poorly understood. METHODS: Spinal cord tissue stiffness was assessed using atomic force microscopy (AFM) in a mouse model of crush injury. Pharmacological depletion of microglia using PLX5622 was used to explore the effect of microglia on mechanical characterization. Conditional knockout of Fascin-1 in microglia (Fascin-1 CKO) alone or in combination with inhibition of myosin activity was performed to delve into relevant mechanisms of microglia regulating mechanical signal. Immunofluorescence staining was performed to evaluate the related protein levels, inflammatory cells, and neuron survival after SCI. The Basso mouse scale score was calculated to assess functional recovery. RESULTS: Spinal cord tissue significantly softens after SCI. Microglia depletion or Fascin-1 knockout in microglia limits tissue softening and alters mechanical characterization, which leads to increased tissue pathology and impaired functional recovery. Mechanistically, Fascin-1 inhibits myosin activation to promote microglial migration and control mechanical characterization after SCI. CONCLUSIONS: We reveal that Fascin-1 limits myosin activity to regulate mechanical characterization after SCI, and this mechanical signal should be considered in future approaches for the treatment of CNS diseases.


Asunto(s)
Proteínas de Microfilamentos , Microglía , Traumatismos de la Médula Espinal , Animales , Ratones , Proteínas Portadoras , Gliosis/metabolismo , Proteínas de Microfilamentos/metabolismo , Microglía/metabolismo , Médula Espinal/patología , Traumatismos de la Médula Espinal/patología
13.
Small ; : e2311967, 2024 May 07.
Artículo en Inglés | MEDLINE | ID: mdl-38712482

RESUMEN

Intracellular bacteria pose a great challenge to antimicrobial therapy due to various physiological barriers at both cellular and bacterial levels, which impede drug penetration and intracellular targeting, thereby fostering antibiotic resistance and yielding suboptimal treatment outcomes. Herein, a cascade-target bacterial-responsive drug delivery nanosystem, MM@SPE NPs, comprising a macrophage membrane (MM) shell and a core of SPE NPs. SPE NPs consist of phenylboronic acid-grafted dendritic mesoporous silica nanoparticles (SP NPs) encapsulated with epigallocatechin-3-gallate (EGCG), a non-antibiotic antibacterial component, via pH-sensitive boronic ester bonds are introduced. Upon administration, MM@SPE NPs actively home in on infected macrophages due to the homologous targeting properties of the MM shell, which is subsequently disrupted during cellular endocytosis. Within the cellular environment, SPE NPs expose and spontaneously accumulate around intracellular bacteria through their bacteria-targeting phenylboronic acid groups. The acidic bacterial microenvironment further triggers the breakage of boronic ester bonds between SP NPs and EGCG, allowing the bacterial-responsive release of EGCG for localized intracellular antibacterial effects. The efficacy of MM@SPE NPs in precisely eliminating intracellular bacteria is validated in two rat models of intracellular bacterial infections. This cascade-targeting responsive system offers new solutions for treating intracellular bacterial infections while minimizing the risk of drug resistance.

14.
Clin Exp Immunol ; 216(2): 200-210, 2024 Apr 23.
Artículo en Inglés | MEDLINE | ID: mdl-38290436

RESUMEN

Mucosal bile acid (BA) profile is still unestablished in diarrhea-predominant irritable bowel syndrome (IBS-D). The aim of this study was to explore colonic mucosal BAs and their associations with mucosal mast cell (MMC)-derived nerve growth factor (NGF) and bowel symptoms in IBS-D. Colonic mucosal biopsies from 36 IBS-D patients and 35 healthy controls (HCs) were obtained for targeted BA profiling. MMC count and the expression of NGF and tight junction proteins (TJPs) were examined. We found that colonic mucosal BA profile was altered in the IBS-D cohort. The proportion of primary BAs was significantly higher and that of secondary BAs was lower in IBS-D patients. According to the 90th percentile of total mucosal BA content of HCs, IBS-D patients were divided into BA-H (n = 7, 19.4%) and BA-L (n = 29, 80.6%) subgroups. BA-H patients showed significantly higher total mucosal BA content compared to BA-L subgroup and HCs. The mucosal content of 11 BA metabolites significantly increased in BA-H subgroup, e.g. cholic acid (CA) and taurocholic acid (TCA). Moreover, BA-H patients displayed significantly elevated MMC count and NGF expression, with decreased expression of TJPs (claudin-1, junctional adhesion molecule-A and zonula occludens-1). Correlation analyses revealed that mucosal TCA content positively correlated with MMC count, MMC-derived NGF levels, and abdominal pain while negatively correlated with TJP expression. In conclusion, IBS-D patients showed an altered BA profile in the colonic mucosa. Approximately 20% of them exhibit elevated mucosal BA content, which may be associated with MMC-derived NGF signaling and bowel symptoms.

15.
Brief Bioinform ; 23(4)2022 07 18.
Artículo en Inglés | MEDLINE | ID: mdl-35801503

RESUMEN

The advances of single-cell DNA sequencing (scDNA-seq) enable us to characterize the genetic heterogeneity of cancer cells. However, the high noise and low coverage of scDNA-seq impede the estimation of copy number variations (CNVs). In addition, existing tools suffer from intensive execution time and often fail on large datasets. Here, we propose SeCNV, an efficient method that leverages structural entropy, to profile the copy numbers. SeCNV adopts a local Gaussian kernel to construct a matrix, depth congruent map (DCM), capturing the similarities between any two bins along the genome. Then, SeCNV partitions the genome into segments by minimizing the structural entropy from the DCM. With the partition, SeCNV estimates the copy numbers within each segment for cells. We simulate nine datasets with various breakpoint distributions and amplitudes of noise to benchmark SeCNV. SeCNV achieves a robust performance, i.e. the F1-scores are higher than 0.95 for breakpoint detections, significantly outperforming state-of-the-art methods. SeCNV successfully processes large datasets (>50 000 cells) within 4 min, while other tools fail to finish within the time limit, i.e. 120 h. We apply SeCNV to single-nucleus sequencing datasets from two breast cancer patients and acoustic cell tagmentation sequencing datasets from eight breast cancer patients. SeCNV successfully reproduces the distinct subclones and infers tumor heterogeneity. SeCNV is available at https://github.com/deepomicslab/SeCNV.


Asunto(s)
Neoplasias de la Mama , Variaciones en el Número de Copia de ADN , Algoritmos , Neoplasias de la Mama/genética , Femenino , Genoma , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Humanos , Análisis de Secuencia de ADN/métodos
16.
Brief Bioinform ; 23(1)2022 01 17.
Artículo en Inglés | MEDLINE | ID: mdl-34929741

RESUMEN

Several factors, including advances in computational algorithms, the availability of high-performance computing hardware, and the assembly of large community-based databases, have led to the extensive application of Artificial Intelligence (AI) in the biomedical domain for nearly 20 years. AI algorithms have attained expert-level performance in cancer research. However, only a few AI-based applications have been approved for use in the real world. Whether AI will eventually be capable of replacing medical experts has been a hot topic. In this article, we first summarize the cancer research status using AI in the past two decades, including the consensus on the procedure of AI based on an ideal paradigm and current efforts of the expertise and domain knowledge. Next, the available data of AI process in the biomedical domain are surveyed. Then, we review the methods and applications of AI in cancer clinical research categorized by the data types including radiographic imaging, cancer genome, medical records, drug information and biomedical literatures. At last, we discuss challenges in moving AI from theoretical research to real-world cancer research applications and the perspectives toward the future realization of AI participating cancer treatment.


Asunto(s)
Inteligencia Artificial , Aprendizaje Profundo , Neoplasias , Algoritmos , Bases de Datos Factuales , Humanos , Neoplasias/genética , Proyectos de Investigación
17.
J Transl Med ; 22(1): 345, 2024 Apr 10.
Artículo en Inglés | MEDLINE | ID: mdl-38600566

RESUMEN

BACKGROUND: Hearing loss has been shown to be a risk factor for psychiatric disorders. In addition, long-term hearing loss is associated with increased hospitalization and mortality rates; however, the increased risk and duration of effect of hearing loss in combination with other chronic diseases on each psychiatric disorder are still not clearly defined. The purpose of this article is to clarify the risk of hearing loss for each disorder over time. METHODS: This was a retrospective cohort study, and a national health insurance research database in Taiwan was utilized. All (n = 1,949,101) Taiwanese residents who had a medical visit between 2000 and 2015 were included. Patients with hearing loss and a comparative retrospective cohort were analyzed. Every subject was tracked individually from their index date to identify the subjects who later received a diagnosis of a psychiatric disorder. The Kaplan‒Meier method was used to analyze the cumulative incidence of psychiatric disorders. Cox regression analysis was performed to identify the risk of psychiatric disorders. RESULTS: A total of 13,341 (15.42%) and 31,250 (9.03%) patients with and without hearing loss, respectively, were diagnosed with psychiatric disorders (P < 0.001). Multivariate analysis indicated that hearing loss significantly elevated the risk of psychiatric disorders (adjusted HR = 2.587, 95% CI 1.723-3.346, p < 0.001). CONCLUSION: Our findings indicate that patients with hearing loss are more likely to develop psychiatric disorders. Furthermore, the various psychiatric disorders are more likely to occur at different times. Our findings have important clinical implications, including a need for clinicians to implement early intervention for hearing loss and to pay close attention to patients' psychological status. Trial registration TSGHIRB No. E202216036.


Asunto(s)
Pérdida Auditiva , Trastornos Mentales , Humanos , Estudios de Cohortes , Pérdida Auditiva/complicaciones , Pérdida Auditiva/epidemiología , Incidencia , Trastornos Mentales/complicaciones , Trastornos Mentales/epidemiología , Factores de Riesgo , Taiwán/epidemiología
18.
Mol Syst Biol ; 19(2): e11300, 2023 02 10.
Artículo en Inglés | MEDLINE | ID: mdl-36573357

RESUMEN

Plasmid fitness is directed by two orthogonal processes-vertical transfer through cell division and horizontal transfer through conjugation. When considered individually, improvements in either mode of transfer can promote how well a plasmid spreads and persists. Together, however, the metabolic cost of conjugation could create a tradeoff that constrains plasmid evolution. Here, we present evidence for the presence, consequences, and molecular basis of a conjugation-growth tradeoff across 40 plasmids derived from clinical Escherichia coli pathogens. We discover that most plasmids operate below a conjugation efficiency threshold for major growth effects, indicating strong natural selection for vertical transfer. Below this threshold, E. coli demonstrates a remarkable growth tolerance to over four orders of magnitude change in conjugation efficiency. This tolerance fades as nutrients become scarce and horizontal transfer attracts a greater share of host resources. Our results provide insight into evolutionary constraints directing plasmid fitness and strategies to combat the spread of antibiotic resistance.


Asunto(s)
Escherichia coli , Transferencia de Gen Horizontal , Escherichia coli/genética , Plásmidos/genética , Farmacorresistencia Microbiana , Antibacterianos/farmacología
19.
J Med Virol ; 96(3): e29544, 2024 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-38511577

RESUMEN

The impact of SARS-CoV-2 infection shortly after vaccination on vaccine-induced immunity is unknown, which is also one of the concerns for some vaccinees during the pandemic. Here, based on a cohort of individuals who encountered BA.5 infection within 8 days after receiving the fourth dose of a bivalent mRNA vaccine, preceded by three doses of inactivated vaccines, we show that booster mRNA vaccination provided 48% protection efficacy against symptomatic infections. At Day 7 postvaccination, the level of neutralizing antibodies (Nabs) against WT and BA.5 strains in the uninfected group trended higher than those in the symptomatic infection group. Moreover, there were greater variations in Nabs levels and a significant decrease in virus-specific CD4+ T cell response observed in the symptomatic infection group. However, symptomatic BA.5 infection significantly increased Nab levels against XBB.1.9.1 and BA.5 (symptomatic > asymptomatic > uninfected group) at Day 10 and resulted in a more gradual decrease in Nabs against BA.5 compared to the uninfected group at Day 90. Our data suggest that BA.5 infection might hinder the early generation of Nabs and the recall of the CD4+ T cell response but strengthens the Nab and virus-specific T cell response in the later phase. Our data confirmed that infection can enhance host immunity regardless of the short interval between vaccination and infection and alleviate concerns about infections shortly after vaccination, which provides valuable guidance for developing future vaccine administration strategies.


Asunto(s)
Anticuerpos Neutralizantes , Vacunación , Humanos , Inmunización Secundaria , ARN Mensajero/genética , Vacunas Combinadas , Anticuerpos Antivirales
20.
Opt Express ; 32(8): 14133-14142, 2024 Apr 08.
Artículo en Inglés | MEDLINE | ID: mdl-38859367

RESUMEN

Compact efficient high-power continuous-wave Nd:YVO4 Raman lasers for selectable wavelengths within 559-603 nm are achieved by using KGW crystal for intracavity stimulated Raman scattering (SRS) and lithium triborate (LBO) crystal for intracavity sum frequency generation (SFG) and second harmonic generation (SHG). The LBO crystal with the cut angle in the XY plane for the type-I phase matching is used to perform intracavity SHG or SFG. Experimental results reveal that the participated Stokes lines include the internal vibration mode at 901 cm-1, the external vibrational mode at 209 cm-1, and the combination mode of the 901 cm-1 and 209 cm-1 Raman shifts. By tuning LBO temperature for attaining the maximum output power, the output spectrum reveals the triple peaks of 588.7, 595.7, and 603.1 nm with the intensity ratio of 10:4:1. Under this circumstance, the output power can reach the highest value of 10.8 W at a pump power of 40 W. Furthermore, the output spectrum can be simply concentrated on the single peaks among 588.7 (orange), 565.7 (yellow), and 559.1 nm (lime) by tuning LBO temperature to fulfill the selection of the critical phase matching. The output powers at a pump power of 40 W can be up to 8.0, 6.1, and 9.8 W for the single-peak emission at 588.7, 565.7, and 559.1 nm, respectively. Finally, a dual-peak emission of 565.7 and 572.3 nm with total output power of 5.2 W can be generated by tuning LBO temperature to match the SFG for 572.3 nm.

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