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1.
Nat Commun ; 15(1): 3928, 2024 May 09.
Artículo en Inglés | MEDLINE | ID: mdl-38724489

RESUMEN

Improving activity and stability of Ruthenium (Ru)-based catalysts in acidic environments is eager to replace more expensive Iridium (Ir)-based materials as practical anode catalyst for proton-exchange membrane water electrolyzers (PEMWEs). Here, a bicontinuous nanoreactor composed of multiscale defective RuO2 nanomonomers (MD-RuO2-BN) is conceived and confirmed by three-dimensional tomograph reconstruction technology. The unique bicontinuous nanoreactor structure provides abundant active sites and rapid mass transfer capability through a cavity confinement effect. Besides, existing vacancies and grain boundaries endow MD-RuO2-BN with generous low-coordination Ru atoms and weakened Ru-O interaction, inhibiting the oxidation of lattice oxygen and dissolution of high-valence Ru. Consequently, in acidic media, the electron- and micro-structure synchronously optimized MD-RuO2-BN achieves hyper water oxidation activity (196 mV @ 10 mA cm-2) and an ultralow degradation rate of 1.2 mV h-1. A homemade PEMWE using MD-RuO2-BN as anode also conveys high water splitting performance (1.64 V @ 1 A cm-2). Theoretical calculations and in-situ Raman spectra further unveil the electronic structure of MD-RuO2-BN and the mechanism of water oxidation processes, rationalizing the enhanced performance by the synergistic effect of multiscale defects and protected active Ru sites.

2.
RSC Adv ; 14(21): 15021-15030, 2024 May 02.
Artículo en Inglés | MEDLINE | ID: mdl-38720985

RESUMEN

In this work, gallic acid was successfully grafted onto quaternary aminated chitosan to prepare a high efficiency cationic flocculant. The mechanism of flocculation and different influencing factors were studied in detail. The prepared flocculant only needs 60 mg L-1 to achieve a 98.7% and 94.5% removal rate on methyl blue (MB) and Congo red (CR), respectively. The high removal rate (93.2%) of a CR-MB mixed dye also confirms the universality of flocculation. In addition, kaolin as a simulated suspended solid was removed at a rate of 97% in the experiment at a dosage of 3 mg L-1. A zeta potential test showed that it worked best when the potential of the flocculation system was zero; this was because an electrostatic balance was reached between the flocculant and pollutant. Importantly, the three-functional molecules can provide more possibilities to form hydrogen bonds with water molecules, which is conducive to the stretching of flocculant molecular chains in salt water. The flocculant maintained a high stability in four different salt environments and has a positive industrial application significance. Furthermore, the flocculation experiment of the actual wastewater of the printing and dyeing plant found that the dye wastewater changed obviously from turbidity to clarification, which proved the practical application potential of the flocculant. This work provides a feasible idea for the preparation of bio-based flocculants.

3.
Brief Bioinform ; 25(3)2024 Mar 27.
Artículo en Inglés | MEDLINE | ID: mdl-38701410

RESUMEN

Potentially pathogenic or probiotic microbes can be identified by comparing their abundance levels between healthy and diseased populations, or more broadly, by linking microbiome composition with clinical phenotypes or environmental factors. However, in microbiome studies, feature tables provide relative rather than absolute abundance of each feature in each sample, as the microbial loads of the samples and the ratios of sequencing depth to microbial load are both unknown and subject to considerable variation. Moreover, microbiome abundance data are count-valued, often over-dispersed and contain a substantial proportion of zeros. To carry out differential abundance analysis while addressing these challenges, we introduce mbDecoda, a model-based approach for debiased analysis of sparse compositions of microbiomes. mbDecoda employs a zero-inflated negative binomial model, linking mean abundance to the variable of interest through a log link function, and it accommodates the adjustment for confounding factors. To efficiently obtain maximum likelihood estimates of model parameters, an Expectation Maximization algorithm is developed. A minimum coverage interval approach is then proposed to rectify compositional bias, enabling accurate and reliable absolute abundance analysis. Through extensive simulation studies and analysis of real-world microbiome datasets, we demonstrate that mbDecoda compares favorably with state-of-the-art methods in terms of effectiveness, robustness and reproducibility.


Asunto(s)
Algoritmos , Microbiota , Humanos , Análisis de Datos
4.
Nat Commun ; 15(1): 3698, 2024 May 01.
Artículo en Inglés | MEDLINE | ID: mdl-38693102

RESUMEN

Mouse models of autosomal dominant polycystic kidney disease (ADPKD) show that intact primary cilia are required for cyst growth following the inactivation of polycystin-1. The signaling pathways underlying this process, termed cilia-dependent cyst activation (CDCA), remain unknown. Using translating ribosome affinity purification RNASeq on mouse kidneys with polycystin-1 and cilia inactivation before cyst formation, we identify the differential 'CDCA pattern' translatome specifically dysregulated in kidney tubule cells destined to form cysts. From this, Glis2 emerges as a candidate functional effector of polycystin signaling and CDCA. In vitro changes in Glis2 expression mirror the polycystin- and cilia-dependent changes observed in kidney tissue, validating Glis2 as a cell culture-based indicator of polycystin function related to cyst formation. Inactivation of Glis2 suppresses polycystic kidney disease in mouse models of ADPKD, and pharmacological targeting of Glis2 with antisense oligonucleotides slows disease progression. Glis2 transcript and protein is a functional target of CDCA and a potential therapeutic target for treating ADPKD.


Asunto(s)
Cilios , Modelos Animales de Enfermedad , Riñón Poliquístico Autosómico Dominante , Transducción de Señal , Canales Catiónicos TRPP , Animales , Humanos , Masculino , Ratones , Cilios/metabolismo , Riñón/metabolismo , Riñón/patología , Ratones Endogámicos C57BL , Ratones Noqueados , Oligonucleótidos Antisentido/farmacología , Enfermedades Renales Poliquísticas/metabolismo , Enfermedades Renales Poliquísticas/genética , Enfermedades Renales Poliquísticas/patología , Riñón Poliquístico Autosómico Dominante/metabolismo , Riñón Poliquístico Autosómico Dominante/genética , Riñón Poliquístico Autosómico Dominante/patología , Riñón Poliquístico Autosómico Dominante/tratamiento farmacológico , Canales Catiónicos TRPP/metabolismo , Canales Catiónicos TRPP/genética
5.
Hum Vaccin Immunother ; 20(1): 2337161, 2024 Dec 31.
Artículo en Inglés | MEDLINE | ID: mdl-38566539

RESUMEN

The epidemiological and clinical aspects of Human Papillomavirus (HPV) infection in women have been extensively studied. However, there is a lack of information regarding HPV characteristics in males. In this study, we conducted a retrospective and observational study of 3737 consecutive male individuals attending outpatient clinics of Guangdong Women and Children Hospital from 2012 to 2023 in Guangzhou, South China, to determine the age- and genotype-specific prevalence of HPV in men. The results showed the overall prevalence of HPV among men was 42.15% (1575/3737), with variations ranging from 29.55% to 81.31% across distinct diagnostic populations. Low-risk HPV6 (15.47%), HPV11 (8.94%), and high-risk HPV52 (5.51%) were the most common types. The annual HPV prevalence decreased significantly (Z = -3.882, p < .001), ranging from 31.44% to 52.90%. 28.77% (1075/3737) of men manifested infection with a singular HPV type, predominantly identified as a low-risk type. The age-specific distribution of HPV infections revealed distinctive peaks in the < 25 y age group (47.60%, 208/437) and the 40-44 y age group (44.51%, 154/346). Notably, the positive rate of Chlamydia trachomatis was significantly higher among HPV-positive individuals in comparison to HPV-negatives (16.14% vs. 11.25%, p < .05). Our findings reveal a substantial prevalence of HPV infection among outpatient men in Guangzhou, South China. It is recommended to consider the inclusion of HPV vaccination for adolescent males in national immunization schedules, once an adequate supply of vaccines is accessible.


Asunto(s)
Infecciones por Papillomavirus , Neoplasias del Cuello Uterino , Humanos , Masculino , China/epidemiología , Genotipo , Papillomaviridae/genética , Infecciones por Papillomavirus/epidemiología , Infecciones por Papillomavirus/prevención & control , Prevalencia , Estudios Retrospectivos , Riesgo , Neoplasias del Cuello Uterino/prevención & control , Vacunación , Adulto Joven , Adulto
6.
J Cell Biol ; 223(6)2024 Jun 03.
Artículo en Inglés | MEDLINE | ID: mdl-38587486

RESUMEN

ß-Coronaviruses remodel host endomembranes to form double-membrane vesicles (DMVs) as replication organelles (ROs) that provide a shielded microenvironment for viral RNA synthesis in infected cells. DMVs are clustered, but the molecular underpinnings and pathophysiological functions remain unknown. Here, we reveal that host fragile X-related (FXR) family proteins (FXR1/FXR2/FMR1) are required for DMV clustering induced by expression of viral non-structural proteins (Nsps) Nsp3 and Nsp4. Depleting FXRs results in DMV dispersion in the cytoplasm. FXR1/2 and FMR1 are recruited to DMV sites via specific interaction with Nsp3. FXRs form condensates driven by liquid-liquid phase separation, which is required for DMV clustering. FXR1 liquid droplets concentrate Nsp3 and Nsp3-decorated liposomes in vitro. FXR droplets facilitate recruitment of translation machinery for efficient translation surrounding DMVs. In cells depleted of FXRs, SARS-CoV-2 replication is significantly attenuated. Thus, SARS-CoV-2 exploits host FXR proteins to cluster viral DMVs via phase separation for efficient viral replication.


Asunto(s)
COVID-19 , Proteína de la Discapacidad Intelectual del Síndrome del Cromosoma X Frágil , Liposomas , Proteínas de Unión al ARN , SARS-CoV-2 , Humanos , Proliferación Celular , Análisis por Conglomerados , COVID-19/metabolismo , COVID-19/virología , Citoplasma , Proteína de la Discapacidad Intelectual del Síndrome del Cromosoma X Frágil/metabolismo , Células HeLa , Liposomas/metabolismo , Orgánulos , Proteínas de Unión al ARN/metabolismo , Proteínas no Estructurales Virales/metabolismo
7.
Sci Rep ; 14(1): 8840, 2024 04 17.
Artículo en Inglés | MEDLINE | ID: mdl-38632467

RESUMEN

Lung adenocarcinoma (LUAD), a leading cause of cancer-related mortality worldwide, demands a deeper understanding of its molecular mechanisms and the identification of reliable biomarkers for better diagnosis and targeted therapy. Leveraging data from the Cancer Genome Atlas (TCGA), the Clinical Proteomic Tumor Analysis Consortium (CPTAC), and the Human Protein Atlas (HPA), we investigated the mRNA and protein expression profiles of TIMM17A and assessed its prognostic significance through Kaplan-Meier survival curves and Cox regression analysis. Through Gene Set Enrichment Analysis, we explored the regulatory mechanisms of TIMM17A in LUAD progression and demonstrated its role in modulating the proliferative capacity of A549 cells, a type of LUAD cell, via in vitro experiments. Our results indicate that TIMM17A is significantly upregulated in LUAD tissues, correlating with clinical staging, lymph node metastasis, overall survival, and progression-free survival, thereby establishing it as a critical independent prognostic factor. The construction of a nomogram model further enhances our ability to predict patient outcomes. Knockdown of TIMM17A inhibited the growth of LUAD cells. The potential of TIMM17A as a biomarker and therapeutic target for LUAD presents a promising pathway for improving patient diagnosis and treatment strategies.


Asunto(s)
Adenocarcinoma del Pulmón , Neoplasias Pulmonares , Proteínas del Complejo de Importación de Proteínas Precursoras Mitocondriales , Humanos , Adenocarcinoma del Pulmón/diagnóstico , Adenocarcinoma del Pulmón/genética , Adenocarcinoma del Pulmón/metabolismo , Neoplasias Pulmonares/diagnóstico , Neoplasias Pulmonares/genética , Neoplasias Pulmonares/metabolismo , Nomogramas , Pronóstico , Proteómica , Proteínas del Complejo de Importación de Proteínas Precursoras Mitocondriales/genética , Proteínas del Complejo de Importación de Proteínas Precursoras Mitocondriales/metabolismo , Regulación Neoplásica de la Expresión Génica , Biomarcadores de Tumor , Células A549
8.
J Am Stat Assoc ; 119(545): 202-216, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-38481466

RESUMEN

In this paper, we study high-dimensional multivariate logistic regression models in which a common set of covariates is used to predict multiple binary outcomes simultaneously. Our work is primarily motivated from many biomedical studies with correlated multiple responses such as the cancer cell-line encyclopedia project. We assume that the underlying regression coefficient matrix is simultaneously low-rank and row-wise sparse. We propose an intuitively appealing selection and estimation framework based on marginal model likelihood, and we develop an efficient computational algorithm for inference. We establish a novel high-dimensional theory for this nonlinear multivariate regression. Our theory is general, allowing for potential correlations between the binary responses. We propose a new type of nuclear norm penalty using the smooth clipped absolute deviation, filling the gap in the related non-convex penalization literature. We theoretically demonstrate that the proposed approach improves estimation accuracy by considering multiple responses jointly through the proposed estimator when the underlying coefficient matrix is low-rank and row-wise sparse. In particular, we establish the non-asymptotic error bounds, and both rank and row support consistency of the proposed method. Moreover, we develop a consistent rule to simultaneously select the rank and row dimension of the coefficient matrix. Furthermore, we extend the proposed methods and theory to a joint Ising model, which accounts for the dependence relationships. In our analysis of both simulated data and the cancer cell line encyclopedia data, the proposed methods outperform the existing methods in better predicting responses.

9.
J Hum Genet ; 2024 Mar 25.
Artículo en Inglés | MEDLINE | ID: mdl-38528049

RESUMEN

Identification of pleiotropy at the single nucleotide polymorphism (SNP) level provides valuable insights into shared genetic signals among phenotypes. One approach to study these signals is through mediation analysis, which dissects the total effect of a SNP on the outcome into a direct effect and an indirect effect through a mediator. However, estimated effects from mediation analysis can be confounded by the genetic correlation between phenotypes, leading to inaccurate results. To address this confounding effect in the context of genetic mediation analysis, we propose a restricted-maximum-likelihood (REML)-based mediation analysis framework called REML-mediation, which can be applied to either individual-level or summary statistics data. Simulations demonstrated that REML-mediation provides unbiased estimates of the true cross-trait causal effect, assuming certain assumptions, albeit with a slightly inflated standard error compared to traditional linear regression. To validate the effectiveness of REML-mediation, we applied it to UK Biobank data and analyzed several mediator-outcome trait pairs along with their corresponding sets of pleiotropic SNPs. REML-mediation successfully identified and corrected for genetic confounding effects in these trait pairs, with correction magnitudes ranging from 7% to 39%. These findings highlight the presence of genetic confounding effects in cross-trait epidemiological studies and underscore the importance of accounting for them in data analysis.

10.
BMC Anesthesiol ; 24(1): 105, 2024 Mar 19.
Artículo en Inglés | MEDLINE | ID: mdl-38504189

RESUMEN

OBJECTIVE: Postoperative fasting following thoracoscopic surgery can cause intense thirst and oral discomfort. However, there is currently no research on ultraearly oral hydration (UEOH) in middle-aged or elderly patients after thoracoscopic surgery. The aim of this study was to investigate the effectiveness and safety of UEOH for improving oral discomfort after thoracoscopic surgery. METHODS: This single-center prospective double-blind randomized controlled trial was conducted from April 2022 to November 2023. A total of 64 middle-aged and elderly patients who underwent the first thoracoscopic surgery on the day were enrolled at our institution. Postoperatively, in the Postanesthesia Care Unit (PACU), patients were randomly assigned at a 1:1 ratio to either the UEOH group or the standard care (SC) group. The primary outcome was the patient's thirst score at 6 h after surgery. Secondary outcomes included the incidence of postoperative oral discomfort; pain scores; the occurrence of adverse reactions such as nausea, vomiting, regurgitation and aspiration; anxiety scores on the first postoperative day; the time to first flatus; and recovery satisfaction scores. RESULTS: The demographic and surgical characteristics were similar between the two groups. Patients in the UEOH group had lower thirst scores 6 h after surgery than did those in the SC group(16.1 ± 6.70 vs. 78.4 ± 8.42, P < 0.01). The incidence of postoperative oral discomfort (P < 0.01), anxiety scores on the first postoperative day (P<0.05), and time to first flatus (P<0.05) were better in the UEOH group. Additionally, the incidences of adverse reactions, such as postoperative nausea, vomiting, regurgitation and aspiration, were similar between the two groups (P>0.05). CONCLUSION: For middle-aged and elderly patients undergoing thoracoscopic surgery, the use of a modified UEOH protocol postoperatively can improve thirst and promote gastrointestinal recovery without increasing complications. TRIAL REGISTRATION: This single-center, prospective, RCT has completed the registration of the Chinese Clinical Trial Center at 07/12/2023 with the registration number ChiCTR2300078425.


Asunto(s)
Dolor Postoperatorio , Sed , Persona de Mediana Edad , Anciano , Humanos , Estudios Prospectivos , Flatulencia , Náusea y Vómito Posoperatorios/epidemiología , Náusea y Vómito Posoperatorios/prevención & control , Toracoscopía , Método Doble Ciego
11.
Hum Genomics ; 18(1): 25, 2024 Mar 14.
Artículo en Inglés | MEDLINE | ID: mdl-38486307

RESUMEN

With the development of next-generation sequencing technology, de novo variants (DNVs) with deleterious effects can be identified and investigated for their effects on birth defects such as congenital heart disease (CHD). However, statistical power is still limited for such studies because of the small sample size due to the high cost of recruiting and sequencing samples and the low occurrence of DNVs. DNV analysis is further complicated by genetic heterogeneity across diseased individuals. Therefore, it is critical to jointly analyze DNVs with other types of genomic/biological information to improve statistical power to identify genes associated with birth defects. In this review, we discuss the general workflow, recent developments in statistical methods, and future directions for DNV analysis.


Asunto(s)
Heterogeneidad Genética , Genómica , Humanos , Secuenciación de Nucleótidos de Alto Rendimiento , Tamaño de la Muestra , Flujo de Trabajo
12.
bioRxiv ; 2024 Feb 19.
Artículo en Inglés | MEDLINE | ID: mdl-38464054

RESUMEN

Alternative splicing is an important cellular process in eukaryotes, altering pre-mRNA to yield multiple protein isoforms from a single gene. However, our understanding of the impact of alternative splicing events on protein structures is currently constrained by a lack of sufficient protein structural data. To address this limitation, we employed AlphaFold 2, a cutting-edge protein structure prediction tool, to conduct a comprehensive analysis of alternative splicing for approximately 3,000 human genes, providing valuable insights into its impact on the protein structural. Our investigation employed state of the art high-performance computing infrastructure to systematically characterize structural features in alternatively spliced regions and identified changes in protein structure following alternative splicing events. Notably, we found that alternative splicing tends to alter the structure of residues primarily located in coils and beta-sheets. Our research highlighted a significant enrichment of loops and highly exposed residues within human alternatively spliced regions. Specifically, our examination of the Septin-9 protein revealed potential associations between loops and alternative splicing, providing insights into its evolutionary role. Furthermore, our analysis uncovered two missense mutations in the Tau protein that could influence alternative splicing, potentially contributing to the pathogenesis of Alzheimer's disease. In summary, our work, through a thorough statistical analysis of extensive protein structural data, sheds new light on the intricate relationship between alternative splicing, evolution, and human disease.

13.
Virulence ; 15(1): 2329569, 2024 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-38555521

RESUMEN

BACKGROUND: Enteroviruses (EV) are common and can cause severe diseases, particularly in young children. However, the information of EV infection in infants in China is limited due to the vast population size and extensive geographical area of the country. Here, we conducted a retrospective multicenter analysis of available EV data to assess the current epidemiological situation in the infant population in southern China. METHODS: The study enrolled infants with suspected EV infection from 34 hospitals across 12 cities in southern China between 2019 to 2022, and the confirmation of EV was done using RT-PCR and VP1 gene sequencing. RESULTS: Out of 1221 infants enrolled, 330 (27.03%) were confirmed as EV-infected. Of these, 260 (78.79%) were newborns aged 0-28 days. The EV belonged to three species: EV-B (80.61%), EV-A (11.82%), and human rhinovirus (7.58%). Newborns were more susceptible to EV-B than older infants (p < 0.001). Within EV-B, we identified 15 types, with coxsackievirus (CV) B3 (20.91%), echovirus (E) 11 (19.70%), and E18 (16.97%) being the most common. The predominant EV types changed across different years. EV infection in infants followed a seasonal pattern, with a higher incidence from May to August. Furthermore, perinatal mother-to-child EV transmission in 12 mother-newborn pairs were observed. CONCLUSION: Our study is the first to demonstrate the emergence and widespread circulation of EV-B species, mainly CVB3, E11, and E18, in southern China, primarily affecting young infants. This research provides valuable insights for future epidemic assessment, prediction, as well as the elimination of mother-to-child transmission.


Asunto(s)
Infecciones por Enterovirus , Enterovirus , Femenino , Humanos , Lactante , Recién Nacido , China/epidemiología , Enterovirus/genética , Enterovirus Humano B/genética , Infecciones por Enterovirus/epidemiología , Genotipo , Transmisión Vertical de Enfermedad Infecciosa , Filogenia
14.
RSC Adv ; 14(15): 10191-10198, 2024 Mar 26.
Artículo en Inglés | MEDLINE | ID: mdl-38544940

RESUMEN

Aqueous zinc-ion batteries (AZIBs) employing mild aqueous electrolytes are recognized for their high safety, cost-effectiveness, and scalability, rendering them promising candidates for large-scale energy storage infrastructure. However, the practical viability of AZIBs is notably impeded by their limited capacity and cycling stability, primarily attributed to sluggish cathode kinetics during electrochemical charge-discharge processes. This study proposes a transition-metal ion intercalation chemistry approach to augment the Zn2+ (de)intercalation dynamics using copper ions as prototypes. Electrochemical assessments reveal that the incorporation of Cu2+ into the host MnO2 lattice (denoted as MnO2-Cu) not only enhances the capacity performance owing to the additional redox activity of Cu2+ but also facilitates the kinetics of Zn2+ ion transport during charge-discharge cycles. Remarkably, the resulting AZIB employing the MnO2-Cu cathode exhibits a superior capacity of 429.4 mA h g-1 (at 0.1 A g-1) and maintains 50% capacity retention after 50 cycles, surpassing both pristine MnO2 (146.8 mA h g-1) and non-transition-metal ion-intercalated MnO2 (MnO2-Na, 198.5 mA h g-1). Through comprehensive electrochemical kinetics investigations, we elucidate that intercalated Cu2+ ions serve as mediators for interlayer stabilization and redox centers within the MnO2 host, enhancing capacity and cycling performance. The successful outcomes of this study underscore the potential of transition-metal ion intercalation strategies in advancing the development of high-performance cathodes for AZIBs.

15.
Mol Psychiatry ; 2024 Mar 15.
Artículo en Inglés | MEDLINE | ID: mdl-38491344

RESUMEN

Persons diagnosed with schizophrenia (SCZ) or bipolar I disorder (BPI) are at high risk for self-injurious behavior, suicidal ideation, and suicidal behaviors (SB). Characterizing associations between diagnosed health problems, prior pharmacological treatments, and polygenic scores (PGS) has potential to inform risk stratification. We examined self-reported SB and ideation using the Columbia Suicide Severity Rating Scale (C-SSRS) among 3,942 SCZ and 5,414 BPI patients receiving care within the Veterans Health Administration (VHA). These cross-sectional data were integrated with electronic health records (EHRs), and compared across lifetime diagnoses, treatment histories, follow-up screenings, and mortality data. PGS were constructed using available genomic data for related traits. Genome-wide association studies were performed to identify and prioritize specific loci. Only 20% of the veterans who reported SB had a corroborating ICD-9/10 EHR code. Among those without prior SB, more than 20% reported new-onset SB at follow-up. SB were associated with a range of additional clinical diagnoses, and with treatment with specific classes of psychotropic medications (e.g., antidepressants, antipsychotics, etc.). PGS for externalizing behaviors, smoking initiation, suicide attempt, and major depressive disorder were associated with SB. The GWAS for SB yielded no significant loci. Among individuals with a diagnosed mental illness, self-reported SB were strongly associated with clinical variables across several EHR domains. Analyses point to sequelae of substance-related and psychiatric comorbidities as strong correlates of prior and subsequent SB. Nonetheless, past SB was frequently not documented in health records, underscoring the value of regular screening with direct, in-person assessments, especially among high-risk individuals.

16.
bioRxiv ; 2024 Feb 27.
Artículo en Inglés | MEDLINE | ID: mdl-38464157

RESUMEN

Foundation Models (FMs) have made significant strides in both industrial and scientific domains. In this paper, we evaluate the performance of FMs in single-cell sequencing data analysis through comprehensive experiments across eight downstream tasks pertinent to single-cell data. By comparing ten different single-cell FMs with task-specific methods, we found that single-cell FMs may not consistently excel in all tasks than task-specific methods. However, the emergent abilities and the successful applications of cross-species/cross-modality transfer learning of FMs are promising. In addition, we present a systematic evaluation of the effects of hyper-parameters, initial settings, and stability for training single-cell FMs based on a proposed scEval framework, and provide guidelines for pre-training and fine-tuning. Our work summarizes the current state of single-cell FMs and points to their constraints and avenues for future development.

17.
Parasit Vectors ; 17(1): 106, 2024 Mar 04.
Artículo en Inglés | MEDLINE | ID: mdl-38439081

RESUMEN

BACKGROUND: Although whole-genome sequencing (WGS) is the preferred genotyping method for most genomic analyses, limitations are often experienced when studying genomes characterized by a high percentage of repetitive elements, high linkage, and recombination deserts. The Asian tiger mosquito (Aedes albopictus), for example, has a genome comprising up to 72% repetitive elements, and therefore we set out to develop a single-nucleotide polymorphism (SNP) chip to be more cost-effective. Aedes albopictus is an invasive species originating from Southeast Asia that has recently spread around the world and is a vector for many human diseases. Developing an accessible genotyping platform is essential in advancing biological control methods and understanding the population dynamics of this pest species, with significant implications for public health. METHODS: We designed a SNP chip for Ae. albopictus (Aealbo chip) based on approximately 2.7 million SNPs identified using WGS data from 819 worldwide samples. We validated the chip using laboratory single-pair crosses, comparing technical replicates, and comparing genotypes of samples genotyped by WGS and the SNP chip. We then used the chip for a population genomic analysis of 237 samples from 28 sites in the native range to evaluate its usefulness in describing patterns of genomic variation and tracing the origins of invasions. RESULTS: Probes on the Aealbo chip targeted 175,396 SNPs in coding and non-coding regions across all three chromosomes, with a density of 102 SNPs per 1 Mb window, and at least one SNP in each of the 17,461 protein-coding genes. Overall, 70% of the probes captured the genetic variation. Segregation analysis found that 98% of the SNPs followed expectations of single-copy Mendelian genes. Comparisons with WGS indicated that sites with genotype disagreements were mostly heterozygotes at loci with WGS read depth < 20, while there was near complete agreement with WGS read depths > 20, indicating that the chip more accurately detects heterozygotes than low-coverage WGS. Sample sizes did not affect the accuracy of the SNP chip genotype calls. Ancestry analyses identified four to five genetic clusters in the native range with various levels of admixture. CONCLUSIONS: The Aealbo chip is highly accurate, is concordant with genotypes from WGS with high sequence coverage, and may be more accurate than low-coverage WGS.


Asunto(s)
Aedes , Mosquitos Vectores , Humanos , Animales , Genotipo , Mosquitos Vectores/genética , Heterocigoto , Aedes/genética
18.
BMJ Open ; 14(3): e080998, 2024 Mar 05.
Artículo en Inglés | MEDLINE | ID: mdl-38448078

RESUMEN

OBJECTIVE: Medication non-adherence to immunosuppressants threatens allograft survival and function maintenance among solid organ transplant (SOT) recipients. This study aimed to investigate the prevalence of immunosuppressant medication non-adherence and associated factors during the COVID-19 reopening period among Chinese SOT recipients. DESIGN: Cross-sectional study. SETTING: South-central China. POPULATION: Adult patients who received SOT with functioning graft. METHODS: Sociodemographic questionnaire and scales to measure physical activity, depression and medication non-adherence were used to collect data. Logistic regression analysis was conducted to identify factors associated with medication non-adherence. Mediation and moderated mediation analyses were performed to examine the potential mechanisms influencing medication behaviour during the pandemic reopening period using SPSS PROCESS macro 4.3 software. RESULTS: A total of 1121 participants were recruited and the prevalence of medication non-adherence was 36.3% in this study. Recipients who were men, had a higher monthly income, lived alone, had received transplantation for a minimum of 3 years, had received COVID-19 vaccination and experienced depressive symptoms exhibited an increased risk of non-adherence. Contrarily, those who engaged in high-intensity physical activity exhibited a decreased risk. Physical activity was negatively associated with medication non-adherence (r=-0.124, p<0.001) with depression fully mediating this relationship (B=-0.014, 95% CI: -0.032 to -0.003). COVID-19 vaccination significantly moderated the relationship between physical activity and depression (B=-0.303, 95% CI: -0.515 to -0.090). CONCLUSION: This study investigated the prevalence of medication non-adherence among SOT recipients during the COVID-19 reopening period in China, its associated factors and a potential mechanism. Depression fully mediated the association between physical activity and medication non-adherence, and COVID-19 vaccination moderated the relationship between physical activity and depression. These findings provide some insights for managing medication behaviour when confronting public health emergencies. However, relationships displayed in the moderated mediation model should be tracked after returning to normal life and other potential relationships should be explored to deeply understand medication non-adherent behaviour.


Asunto(s)
COVID-19 , Clorofluorocarburos de Etano , Trasplante de Órganos , Adulto , Masculino , Humanos , Femenino , Estudios Transversales , Vacunas contra la COVID-19 , COVID-19/epidemiología , Inmunosupresores/uso terapéutico , China/epidemiología
19.
IEEE J Biomed Health Inform ; 28(5): 3102-3113, 2024 May.
Artículo en Inglés | MEDLINE | ID: mdl-38483807

RESUMEN

The classification analysis of incomplete and imbalanced data is still a challenging task since these issues could negatively impact the training of classifiers, which were also found in our study on the physical fitness assessments of patients. And in fields such as healthcare, there are higher requirements for the accuracy of the generated imputation values. To train a high-performance classifier and pursue high accuracy, we attempted to resolve any potential negative impact by using a novel algorithmic approach based on the combination of multivariate imputation by chained equations and the ensemble learning method (MICEEN), which can solve the two problems simultaneously. We used multivariate imputation by chained equations to generate more accurate imputation values for the training set passed to ensemble learning to build a predictor. On the other hand, missing values were introduced into minority classes and used them to generate new samples belonging to the minority classes in order to balance the distribution of classes. On real-world datasets, we perform extensive experiments to assess our method and compare it to other state-of-the-art approaches. The advantages of the proposed method are demonstrated by experimental results for the benchmark datasets and self-collected datasets of physical fitness assessment of tumor patients with varying missing rates.


Asunto(s)
Algoritmos , Aprendizaje Automático , Humanos , Bases de Datos Factuales , Aptitud Física/fisiología , Análisis Multivariante
20.
Angew Chem Int Ed Engl ; 63(20): e202402171, 2024 May 13.
Artículo en Inglés | MEDLINE | ID: mdl-38494450

RESUMEN

Design the electrocatalysts without noble metal is still a challenge for oxygen evolution reaction (OER) in acid media. Herein, we reported the manganese (Mn) doping method to decrease the concentration of oxygen vacancy (VO) and form the Mn-O structure adjacent octahedral sites in spinel NiCo2O4-δ (NiMn1.5Co3O4-δ), which highly enhanced the activity and stability of spinel NiCo2O4-δ with a low overpotential (η) of 280 mV at j=10 mA cm-2 and long-term stability of 80 h in acid media. The isotopic labelling experiment based on differential electrochemical mass spectrometry (DEMS) clearly demonstrated the lattice oxygen in NiMn1.5Co3O4-δ is more stable due to strong Mn-O bond and shows synergetic adsorbate evolution mechanism (SAEM) for acid OER. Density functional theory (DFT) calculations reveal highly increased oxygen vacancy formation energy (EVO) of NiCo2O4-δ after Mn doping. More importantly, the highly hydrogen bonding between Mn-O and *OOH adsorbed on adjacent Co octahedral sites promote the formation of *OO from *OOH due to the greatly enhanced charge density of O in Mn substituted sites.

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