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1.
bioRxiv ; 2024 Mar 13.
Artículo en Inglés | MEDLINE | ID: mdl-38496513

RESUMEN

The spread of infectious diseases is shaped by spatial and temporal aspects, such as host population structure or changes in the transmission rate or number of infected individuals over time. These spatiotemporal dynamics are imprinted in the genome of pathogens and can be recovered from those genomes using phylodynamics methods. However, phylodynamic methods typically quantify either the temporal or spatial transmission dynamics, which leads to unclear biases, as one can potentially not be inferred without the other. Here, we address this challenge by introducing a structured coalescent skyline approach, MASCOT-Skyline that allows us to jointly infer spatial and temporal transmission dynamics of infectious diseases using Markov chain Monte Carlo inference. To do so, we model the effective population size dynamics in different locations using a non-parametric function, allowing us to approximate a range of population size dynamics. We show, using a range of different viral outbreak datasets, potential issues with phylogeographic methods. We then use these viral datasets to motivate simulations of outbreaks that illuminate the nature of biases present in the different phylogeographic methods. We show that spatial and temporal dynamics should be modeled jointly even if one seeks to recover just one of the two. Further, we showcase conditions under which we can expect phylogeographic analyses to be biased, particularly different subsampling approaches, as well as provide recommendations of when we can expect them to perform well. We implemented MASCOT-Skyline as part of the open-source software package MASCOT for the Bayesian phylodynamics platform BEAST2.

2.
Prev Vet Med ; 226: 106165, 2024 Mar 04.
Artículo en Inglés | MEDLINE | ID: mdl-38503655

RESUMEN

Target trial emulation applies design principles from randomised controlled trials to the analysis of observational data for causal inference and is increasingly used within human epidemiology. Using anonymised veterinary clinical data from the VetCompass Programme, this study applied the target trial emulation framework to determine whether surgical (compared to non-surgical) management for cranial cruciate ligament (CCL) rupture in dogs causes improved short- and long-term lameness and analgesia outcomes. The emulated target trial included dogs diagnosed with CCL rupture between January 1, 2019 and December 31, 2019 within the VetCompass database. Inclusion in the emulated trial required dogs aged ≥ 1.5 and < 12 years, first diagnosed with unilateral CCL rupture during 2019 and with no prior history of contralateral ligament rupture or stifle surgery. Dogs were retrospectively observed to have surgical or non-surgical management. Informed from a directed acyclic graph derived from expert opinion, data on the following variables were collected: age, breed, bodyweight, neuter status, insurance status, non-orthopaedic comorbidities, orthopaedic comorbidities and veterinary group. Inverse probability of treatment weighting (IPTW) was used to adjust for confounding, with weights calculated based on a binary logistic regression exposure model. Censored dogs were accounted for in the IPTW analysis using inverse probability of censoring weighting (IPCW). The IPCWs were combined with IPTWs and used to weight each dog's contribution to binary logistic regression outcome models. Standardized mean differences (SMD) examined the balance of covariate distribution between treatment groups. The emulated trial included 615 surgical CCL rupture cases and 200 non-surgical cases. The risk difference for short-term lameness in surgically managed cases (compared with non-surgically managed cases) was -25.7% (95% confidence interval (CI) -36.7% to -15.9%) and the risk difference for long-term lameness -31.7% (95% CI -37.9% to -18.1%). The study demonstrated the application of the target trial framework to veterinary observational data. The findings show that surgical management causes a reduction in short- and long-term lameness compared with non-surgical management in dogs.

3.
BMJ Open ; 14(1): e076354, 2024 01 17.
Artículo en Inglés | MEDLINE | ID: mdl-38233051

RESUMEN

OBJECTIVE: Dose shortages delayed access to COVID-19 vaccination. We aim to characterise inequality in two-dose vaccination by sociodemographic group across Brazil. DESIGN: This is a cross-sectional study. SETTING: We used data retrieved from the Brazilian Ministry of Health databases published between 17 January 2021 and 6 September 2021. METHODS: We assessed geographical inequalities in full vaccination coverage and dose by age, sex, race and socioeconomic status. We developed a Campaign Optimality Index to characterise inequality in vaccination access due to premature vaccination towards younger populations before older and vulnerable populations were fully vaccinated. Generalised linear regression was used to investigate the risk of death and hospitalisation by age group, socioeconomic status and vaccination coverage. RESULTS: Vaccination coverage is higher in the wealthier South and Southeast. Men, people of colour and low-income groups were more likely to be only partially vaccinated due to missing or delaying a second dose. Vaccination started prematurely for age groups under 50 years which may have hindered uptake in older age groups. Vaccination coverage was associated with a lower risk of death, especially in older age groups (ORs 9.7 to 29.0, 95% CI 9. 4 to 29.9). Risk of hospitalisation was greater in areas with higher vaccination rates due to higher access to care and reporting. CONCLUSIONS: Vaccination inequality persists between states, age and demographic groups despite increasing uptake. The association between hospitalisation rates and vaccination is attributed to preferential delivery to areas of greater transmission and access to healthcare.


Asunto(s)
Vacunas contra la COVID-19 , COVID-19 , Masculino , Femenino , Humanos , Anciano , Persona de Mediana Edad , Factores Socioeconómicos , Brasil/epidemiología , Estudios Transversales , Factores Sociodemográficos , COVID-19/epidemiología , COVID-19/prevención & control , Vacunación , Programas de Inmunización
4.
PLoS Comput Biol ; 19(9): e1011492, 2023 09.
Artículo en Inglés | MEDLINE | ID: mdl-37721947

RESUMEN

China had conducted some of the most stringent public health measures to control the spread of successive SARS-CoV-2 variants. However, the effectiveness of these measures and their impacts on the associated disease burden have rarely been quantitatively assessed at the national level. To address this gap, we developed a stochastic age-stratified metapopulation model that incorporates testing, contact tracing and isolation, based on 419 million travel movements among 366 Chinese cities. The study period for this model began from September 2022. The COVID-19 disease burden was evaluated, considering 8 types of underlying health conditions in the Chinese population. We identified the marginal effects between the testing speed and reduction in the epidemic duration. The findings suggest that assuming a vaccine coverage of 89%, the Omicron-like wave could be suppressed by 3-day interval population-level testing (PLT), while it would become endemic with 4-day interval PLT, and without testing, it would result in an epidemic. PLT conducted every 3 days would not only eliminate infections but also keep hospital bed occupancy at less than 29.46% (95% CI, 22.73-38.68%) of capacity for respiratory illness and ICU bed occupancy at less than 58.94% (95% CI, 45.70-76.90%) during an outbreak. Furthermore, the underlying health conditions would lead to an extra 2.35 (95% CI, 1.89-2.92) million hospital admissions and 0.16 (95% CI, 0.13-0.2) million ICU admissions. Our study provides insights into health preparedness to balance the disease burden and sustainability for a country with a population of billions.


Asunto(s)
COVID-19 , Epidemias , Humanos , COVID-19/epidemiología , COVID-19/prevención & control , SARS-CoV-2 , Salud Pública , Epidemias/prevención & control , China/epidemiología
5.
Proc Natl Acad Sci U S A ; 120(33): e2305403120, 2023 08 15.
Artículo en Inglés | MEDLINE | ID: mdl-37549270

RESUMEN

Continually emerging SARS-CoV-2 variants of concern that can evade immune defenses are driving recurrent epidemic waves of COVID-19 globally. However, the impact of measures to contain the virus and their effect on lineage diversity dynamics are poorly understood. Here, we jointly analyzed international travel, public health and social measures (PHSM), COVID-19 vaccine rollout, SARS-CoV-2 lineage diversity, and the case growth rate (GR) from March 2020 to September 2022 across 63 countries. We showed that despite worldwide vaccine rollout, PHSM are effective in mitigating epidemic waves and lineage diversity. An increase of 10,000 monthly travelers in a single country-to-country route between endemic countries corresponds to a 5.5% (95% CI: 2.9 to 8.2%) rise in local lineage diversity. After accounting for PHSM, natural immunity from previous infections, and waning immunity, we discovered a negative association between the GR of cases and adjusted vaccine coverage (AVC). We also observed a complex relationship between lineage diversity and vaccine rollout. Specifically, we found a significant negative association between lineage diversity and AVC at both low and high levels but not significant at the medium level. Our study deepens the understanding of population immunity and lineage dynamics for future pandemic preparedness and responsiveness.


Asunto(s)
COVID-19 , SARS-CoV-2 , Humanos , SARS-CoV-2/genética , Vacunas contra la COVID-19 , Salud Pública , COVID-19/epidemiología , COVID-19/prevención & control , Vacunación , Pandemias/prevención & control
6.
Ann Neurol ; 93(1): 88-102, 2023 01.
Artículo en Inglés | MEDLINE | ID: mdl-36261315

RESUMEN

OBJECTIVE: The objective of this study was to assess the impact of treatment with dexamethasone, remdesivir or both on neurological complications in acute coronavirus diease 2019 (COVID-19). METHODS: We used observational data from the International Severe Acute and emerging Respiratory Infection Consortium World Health Organization (WHO) Clinical Characterization Protocol, United Kingdom. Hospital inpatients aged ≥18 years with laboratory-confirmed severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) infection admitted between January 31, 2020, and June 29, 2021, were included. Treatment allocation was non-blinded and performed by reporting clinicians. A propensity scoring methodology was used to minimize confounding. Treatment with remdesivir, dexamethasone, or both was assessed against the standard of care. The primary outcome was a neurological complication occurring at the point of death, discharge, or resolution of the COVID-19 clinical episode. RESULTS: Out of 89,297 hospital inpatients, 64,088 had severe COVID-19 and 25,209 had non-hypoxic COVID-19. Neurological complications developed in 4.8% and 4.5%, respectively. In both groups, neurological complications were associated with increased mortality, intensive care unit (ICU) admission, worse self-care on discharge, and time to recovery. In patients with severe COVID-19, treatment with dexamethasone (n = 21,129), remdesivir (n = 1,428), and both combined (n = 10,846) were associated with a lower frequency of neurological complications: OR = 0.76 (95% confidence interval [CI] = 0.69-0.83), OR = 0.69 (95% CI = 0.51-0.90), and OR = 0.54 (95% CI = 0.47-0.61), respectively. In patients with non-hypoxic COVID-19, dexamethasone (n = 2,580) was associated with less neurological complications (OR = 0.78, 95% CI = 0.62-0.97), whereas the dexamethasone/remdesivir combination (n = 460) showed a similar trend (OR = 0.63, 95% CI = 0.31-1.15). INTERPRETATION: Treatment with dexamethasone, remdesivir, or both in patients hospitalized with COVID-19 was associated with a lower frequency of neurological complications in an additive manner, such that the greatest benefit was observed in patients who received both drugs together. ANN NEUROL 2023;93:88-102.


Asunto(s)
Alanina , Antivirales , Tratamiento Farmacológico de COVID-19 , COVID-19 , Dexametasona , Adolescente , Adulto , Humanos , Alanina/uso terapéutico , Antivirales/efectos adversos , COVID-19/complicaciones , Dexametasona/uso terapéutico , SARS-CoV-2
7.
Nutrients ; 14(21)2022 Nov 04.
Artículo en Inglés | MEDLINE | ID: mdl-36364926

RESUMEN

Ascophyllum nodosum and Fucus vesiculosus both contain unique polyphenols called phlorotannins. Phlorotannins reportedly possess various pharmacological activities. A previous study reported that the activity of phlorotannin is strongly correlated with the normalization of metabolic function, and phlorotannins are extremely promising nutrients for use in the treatment of metabolic syndrome. To date, no study has explored the antihyperlipidemic effects of phlorotannins from A. nodosum and F. vesiculosus in animal models. Therefore, in the present study, we investigated the effects of phlorotannins using a rat model of high-energy diet (HED)-induced hyperlipidemia. The results showed that the rats that were fed an HED and treated with phlorotannin-rich extract from A. nodosum and F. vesiculosus had significantly lower serum fasting blood sugar (FBS), aspartate aminotransferase (AST), alanine aminotransferase (ALT), total cholesterol (TC), triacylglyceride (TG) and free fatty acids (FFAs) levels and hepatic TG level and had higher serum insulin, high-density lipoprotein cholesterol (HDL-C) levels and lipase activity in their fat tissues than in the case with the rats that were fed the HED alone. A histopathological analysis revealed that phlorotannin-rich extract could significantly reduce the size of adipocytes around the epididymis. In addition, the rats treated with phlorotannin-rich extract had significantly lowered interleukin 6 (IL-6) and tumor necrosis factor alpha (TNF-α) levels and increased superoxide dismutase (SOD) and glutathione peroxidase (GPX) activities than did those in the HED group. These results suggested that the phlorotannin-rich extract stimulated lipid metabolism and may have promoted lipase activity in rats with HED-induced hyperlipidemia. Our results indicated that A. nodosum and F. vesiculosus, marine algae typically used as health foods, have strong antihyperlipidemic effects and may, therefore, be useful for preventing atherosclerosis. These algae may be incorporated into antihyperlipidemia pharmaceuticals and functional foods.


Asunto(s)
Ascophyllum , Fucus , Hiperlipidemias , Enfermedades Metabólicas , Masculino , Ratas , Animales , Ascophyllum/metabolismo , Metabolismo de los Lípidos , Hiperlipidemias/tratamiento farmacológico , Hiperlipidemias/etiología , Enfermedades Metabólicas/tratamiento farmacológico , Extractos Vegetales/uso terapéutico , Inflamación/tratamiento farmacológico , Dieta , Lipasa/metabolismo , Hipolipemiantes/uso terapéutico , Colesterol/metabolismo
8.
Front Nutr ; 9: 814315, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-35495912

RESUMEN

With increased age, the appetite, chewing, swallowing, and digestive ability gradually decrease. Previous studies have shown that poor oral health is associated with an inadequate intake of macro and micronutrients and malnutrition. Therefore, improving the diet of elderly people and promoting nutrient absorption will help to improve the quality of life for elderly people. However, few studies have predicted their oral ability based on different food textures and other factors. The purpose of this study was to explore the correlation between oral assessment and texture parameters of high-protein black soybean koji products in elderly people in a nursing home. We used cross-sectional study design for seventy-nine residents aged 65 years and older were recruited. Three different texture of cookies, including normal cookie hardness (1.4 × 105 N/m2), minced cookie hardness (4.4 × 104 N/m2), and pureed cookie hardness (1.4 × 104 N/m2) were provided to participants to test the oral status. An oral assessment scale was used by a dentist to evaluate the oral status of the elderly participants. Different cookie textures showed a significant positive correlation with pronunciation (r = 0.237, p < 0.05), face (r = 0.371, p < 0.01), tongue (r = 0.362, p < 0.01), pharynx (r = 0.256, p < 0.05), swallowing (r = 0.272, p < 0.05), breathing (r = 0.315, p < 0.01), and the total oral score (r = 0.339, p < 0.01). We also used the high-protein black soybean koji products combined with elderly people's comprehensions in a predictive model that had a moderately high correlation to predict the oral status in the elderly group (r = 0.612). We concluded that the high-protein black soybean koji product was associated with the oral ability of elderly people in a nursing home in Taiwan. Our findings indicated that elderly people could immediately understand the correct food texture.

9.
J Cachexia Sarcopenia Muscle ; 13(1): 515-531, 2022 02.
Artículo en Inglés | MEDLINE | ID: mdl-34766473

RESUMEN

BACKGROUND: Age-related muscle dysfunctions are common disorders resulting in poor quality of life in the elderly. Probiotic supplementation is a potential strategy for preventing age-related sarcopenia as evidence suggests that probiotics can enhance muscle function via the gut-muscle axis. However, the effects and mechanisms of probiotics in age-related sarcopenia are currently unknown. In this study, we examined the effects of Lactobacillus casei Shirota (LcS), a probiotic previously reported to improve muscle function in young adult mice. METHODS: We administered LcS (1 × 108 or 1 × 109  CFU/mouse/day) by oral gavage to senescence-accelerated mouse prone-8 mice for 12 weeks (16- to 28-week-old). Sixteen-week-old and 28-week-old SMAP8 mice were included as non-aged and aged controls, respectively. Muscle condition was evaluated using dual-energy X-ray absorptiometry for muscle mass, holding impulse and grip strength tests for muscle strength, and oxygen consumption rate, gene expressions of mitochondrial biogenesis, and mitochondrial number assays for mitochondria function. Inflammatory cytokines were determined using enzyme-linked immunosorbent assay. Gas chromatography-mass spectrometry was utilized to measure the short-chain fatty acid levels. The gut microbiota was analysed based on the data of 16S rRNA gene sequencing of mouse stool. RESULTS: The LcS supplementation reduced age-related declines in muscle mass (>94.6%, P < 0.04), strength (>66% in holding impulse and >96.3% in grip strength, P < 0.05), and mitochondrial function (P < 0.05). The concentration of short-chain fatty acids (acetic, isobutyric, butyric, penic, and hexanoic acid) was recovered by LcS (>65.9% in the mice given high dose of LcS, P < 0.05) in the aged mice, and LcS attenuated age-related increases in inflammation (P < 0.05) and reactive oxygen species (>89.4%, P < 0.001). The high dose of LcS supplementation was also associated with distinct microbiota composition as indicated by the separation of groups in the beta-diversity analysis (P = 0.027). LcS supplementation altered predicted bacterial functions based on the gut microbiota. Apoptosis (P = 0.026), p53 signalling (P = 0.017), and non-homologous end-joining (P = 0.031) were significantly reduced, whereas DNA repair and recombination proteins (P = 0.043), RNA polymerase (P = 0.008), and aminoacyl-tRNA biosynthesis (P = 0.003) were increased. Finally, the genera enriched by high-dose LcS [linear discriminant analysis (LDA) score > 2.0] were positively correlated with healthy muscle and physiological condition (P < 0.05), while the genera enriched in aged control mice (LDA score > 2.0) were negatively associated with healthy muscle and physiological condition (P < 0.05). CONCLUSIONS: Lactobacillus casei Shirota represents an active modulator that regulates the onset and progression of age-related muscle impairment potentially via the gut-muscle axis.


Asunto(s)
Probióticos , Sarcopenia , Animales , Ratones , Músculos , Probióticos/uso terapéutico , Calidad de Vida , ARN Ribosómico 16S/genética , Sarcopenia/terapia
10.
Microb Genom ; 7(11)2021 11.
Artículo en Inglés | MEDLINE | ID: mdl-34812717

RESUMEN

Staphylococcus aureus is a major bacterial pathogen in humans, and a dominant cause of severe bloodstream infections. Globally, antimicrobial resistance (AMR) in S. aureus remains challenging. While human risk factors for infection have been defined, contradictory evidence exists for the role of bacterial genomic variation in S. aureus disease. To investigate the contribution of bacterial lineage and genomic variation to the development of bloodstream infection, we undertook a genome-wide association study comparing bacteria from 1017 individuals with bacteraemia to 984 adults with asymptomatic S. aureus nasal carriage. Within 984 carriage isolates, we also compared healthcare-associated (HA) carriage with community-associated (CA) carriage. All major global lineages were represented in both bacteraemia and carriage, with no evidence for different infection rates. However, kmers tagging trimethoprim resistance-conferring mutation F99Y in dfrB were significantly associated with bacteraemia-vs-carriage (P=10-8.9-10-9.3). Pooling variation within genes, bacteraemia-vs-carriage was associated with the presence of mecA (HMP=10-5.3) as well as the presence of SCCmec (HMP=10-4.4). Among S. aureus carriers, no lineages were associated with HA-vs-CA carriage. However, we found a novel signal of HA-vs-CA carriage in the foldase protein prsA, where kmers representing conserved sequence allele were associated with CA carriage (P=10-7.1-10-19.4), while in gyrA, a ciprofloxacin resistance-conferring mutation, L84S, was associated with HA carriage (P=10-7.2). In an extensive study of S. aureus bacteraemia and nasal carriage in the UK, we found strong evidence that all S. aureus lineages are equally capable of causing bloodstream infection, and of being carried in the healthcare environment. Genomic variation in the foldase protein prsA is a novel genomic marker of healthcare origin in S. aureus but was not associated with bacteraemia. AMR determinants were associated with both bacteraemia and healthcare-associated carriage, suggesting that AMR increases the propensity not only to survive in healthcare environments, but also to cause invasive disease.


Asunto(s)
Bacteriemia , Infecciones Estafilocócicas , Adulto , Antibacterianos/farmacología , Antibacterianos/uso terapéutico , Bacteriemia/microbiología , Atención a la Salud , Farmacorresistencia Bacteriana/genética , Estudio de Asociación del Genoma Completo , Humanos , Infecciones Estafilocócicas/microbiología , Staphylococcus aureus
11.
Antioxidants (Basel) ; 10(11)2021 Nov 17.
Artículo en Inglés | MEDLINE | ID: mdl-34829694

RESUMEN

Oxidative stress plays a key role in the degeneration of dopaminergic neurons in Parkinson's disease (PD), which may be aggravated by concomitant PD-associated gut dysbiosis. Probiotics and prebiotics are therapeutically relevant to these conditions due to their antioxidant, anti-inflammatory, and gut microbiome modulation properties. However, the mechanisms by which probiotic/prebiotic supplementation affects antioxidant capacity and the gut microbiome in PD remains poorly characterized. In this study, we assessed the effects of a Lactobacillus salivarius AP-32 probiotic, a prebiotic (dried AP-32 culture medium supernatant), and a probiotic/prebiotic cocktail in rats with unilateral 6-hydroxydopamine (6-OHDA)-induced PD. The neuroprotective effects and levels of oxidative stress were evaluated after eight weeks of daily supplementation. Fecal microbiota composition was analyzed by fecal 16S rRNA gene sequencing. The supplements were associated with direct increases in host antioxidant enzyme activities and short-chain fatty acid production, protected dopaminergic neurons, and improved motor functions. The supplements also altered the fecal microbiota composition, and some specifically enriched commensal taxa correlated positively with superoxide dismutase, glutathione peroxidase, and catalase activity, indicating supplementation also promotes antioxidant activity via an indirect pathway. Therefore, L. salivarius AP-32 supplementation enhanced the activity of host antioxidant enzymes via direct and indirect modes of action in rats with 6-OHDA-induced PD.

12.
Antioxidants (Basel) ; 10(9)2021 Aug 28.
Artículo en Inglés | MEDLINE | ID: mdl-34573012

RESUMEN

Radiation resistance is a significant clinical problem in rectal cancer treatment, the mechanisms of which are poorly understood. NRF2 signalling is known to contribute to chemo/radioresistance in some cancers, but its role in therapeutic resistance in colorectal cancer (CRC) is unexplored. Using siRNA and CRiSPR/Cas9 isogenic CRC cell lines, we investigated the effect of the knockdown and upregulation of the NRF2 pathway on chemo-radiosensitivity. Poly (A) enriched RNA sequencing and geneset enrichment analysis (GSEA) were carried out on both sensitive and resistant cell models for mechanistic insights. Finally, a cohort of rectal patient samples was profiled to understand the clinical relevance of NRF2 signalling. Radioresistant cell lines were significantly radiosensitised by siRNA knockdown (SW1463, SER10 1.22, ANOVA p < 0.0001; HT55, SER10 1.17, ANOVA p < 0.01), but not the (already) radiosensitive HCT116. The constitutive activation of NRF2 via a CRISPR Cas9 NFE2L2 mutation, E79K, induced radioresistance in HCT116 (SER10 0.71, ANOVA, p < 0.0001). GSEA demonstrated significant opposing metabolic dependencies in NRF2 signalling, specifically, the downregulation of amino acid and protein synthesis with low levels of NRF2 and upregulation with over expression. In a clinical cohort of 127 rectal patients, using a validated mRNA signature, higher baseline NRF2 signalling was associated with incomplete responses to radiation higher final neoadjuvant rectal (NAR) score (OR 1.34, 95% C.I. 1.01-1.80, LRT p-value = 0.023), where high NAR indicates poor radiation response and poor long-term prognosis. This is the first demonstration of NRF2-mediated radiation resistance in colorectal cancer. NRF2 appears to regulate crucial metabolic pathways, which could be exploited for therapeutic interventions.

13.
Virus Evol ; 7(2): veab065, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-34532064

RESUMEN

Studies have shown that hepatitis C virus subtype 3a (HCV-3a) is likely to have been circulating in South Asia before its global spread. However, the time and route of this dissemination remain unclear. For the first time, we generated host and virus genome-wide data for more than 500 patients infected with HCV-3a from the UK, North America, Australia, and New Zealand. We used the host genomic data to infer the ancestry of the patients and used this information to investigate the epidemic history of HCV-3a. We observed that viruses from hosts of South Asian ancestry clustered together near the root of the tree, irrespective of the sampling country, and that they were more diverse than viruses from other host ancestries. We hypothesized that South Asian hosts are more likely to have been infected in South Asia and used the inferred host ancestries to distinguish between the location where the infection was acquired and where the sample was taken. Next, we inferred that three independent transmission events resulted in the spread of the virus from South Asia to the UK, North America, and Oceania. This initial spread happened during or soon after the end of World War II. This was subsequently followed by many independent transmissions between the UK, North America, and Oceania. Using both host and virus genomic information can be highly informative in studying the virus epidemic history, especially in the context of chronic infections where migration histories need to be accounted for.

14.
Int J Mol Sci ; 22(16)2021 Aug 17.
Artículo en Inglés | MEDLINE | ID: mdl-34445528

RESUMEN

Restenosis is a common vascular complication after balloon angioplasty. Catheter balloon inflation-induced transient ischemia (hypoxia) of local arterial tissues plays a pathological role in neointima formation. Phosphoglycerate kinase 1 (PGK1), an adenosine triphosphate (ATP)-generating glycolytic enzyme, has been reported to associate with cell survival and can be triggered under hypoxia. The purposes of this study were to investigate the possible role and regulation of PGK1 in vascular smooth muscle cells (VSMCs) and balloon-injured arteries under hypoxia. Neointimal hyperplasia was induced by a rat carotid artery injury model. The cellular functions and regulatory mechanisms of PGK1 in VSMCs were investigated using small interfering RNAs (siRNAs), chemical inhibitors, or anaerobic cultivation. Our data indicated that protein expression of PGK1 can be rapidly induced at a very early stage after balloon angioplasty, and the silencing PGK1-induced low cellular energy circumstance resulted in the suppressions of VSMC proliferation and migration. Moreover, the experimental results demonstrated that blockage of PDGF receptor-ß (PDGFRB) or its downstream pathway, the phosphoinositide 3-kinase (PI3K)-AKT-mammalian target of rapamycin (mTOR) axis, effectively reduced hypoxia-induced factor-1 (HIF-1α) and PGK1 expressions in VSMCs. In vivo study evidenced that PGK1 knockdown significantly reduced neointima hyperplasia. PGK1 was expressed at the early stage of neointimal formation, and suppressing PGK1 has a potential beneficial effect for preventing restenosis.


Asunto(s)
Angioplastia de Balón/efectos adversos , Traumatismos de las Arterias Carótidas/terapia , Músculo Liso Vascular/patología , Miocitos del Músculo Liso/patología , Neointima/patología , Fosfoglicerato Quinasa/metabolismo , Animales , Movimiento Celular , Células Cultivadas , Masculino , Músculo Liso Vascular/metabolismo , Miocitos del Músculo Liso/metabolismo , Neointima/etiología , Neointima/metabolismo , Fosfoglicerato Quinasa/genética , Ratas , Ratas Sprague-Dawley , Transducción de Señal
15.
Artículo en Inglés | MEDLINE | ID: mdl-34306155

RESUMEN

Balloon angioplasty-induced neointimal hyperplasia remains a clinical problem that must be resolved. The bioactivities of the Crossostephium chinense extract (CCE) have demonstrated potential in preventing the progression of restenosis. The present study evaluated whether CCE can suppress balloon angioplasty-induced neointima formation and elucidated its possible pharmacological mechanisms. A rat model of carotid arterial balloon angioplasty was established to evaluate the inhibitory effect of CCEs on neointimal hyperplasia. Two cell lines, A10 vascular smooth muscle cells (VSMCs) and RAW264.7 macrophages, were used to investigate the potential regulatory activities and pharmacological mechanisms of CCEs in cell proliferation and migration and in inflammation. Our in vitro results indicated that CCE3, the ethanolic extract of C. chinense, exerted the strongest growth inhibitory and antimigratory effects on VSMCs. CCE3 blocked the activation of focal adhesion kinase, platelet-derived growth factor receptor-ß (PDGFRB), and its downstream molecules (AKT and mTOR) and reduced the expression of matrix metalloproteinase-2. In addition, our findings revealed that CCE3 significantly increased the expression of miRNA-132, an inhibitory regulator of inflammation and restenosis, and suppressed the expression of inflammation-related molecules (inducible nitric oxide synthase, cyclooxygenase-2, interleukin- (IL-) 1ß, and IL-6). Our in vivo study results indicated that balloon injury-induced neointimal hyperplasia was inhibited by CCE3. CCE3 could reduce neointima formation in balloon-injured arteries, and this effect may be partially attributed to the CCE3-induced suppression of PDGFRB-mediated downstream pathways and inflammation-related molecules.

16.
Syst Biol ; 71(1): 121-138, 2021 12 16.
Artículo en Inglés | MEDLINE | ID: mdl-33989428

RESUMEN

In Bayesian phylogenetics, the coalescent process provides an informative framework for inferring changes in the effective size of a population from a phylogeny (or tree) of sequences sampled from that population. Popular coalescent inference approaches such as the Bayesian Skyline Plot, Skyride, and Skygrid all model these population size changes with a discontinuous, piecewise-constant function but then apply a smoothing prior to ensure that their posterior population size estimates transition gradually with time. These prior distributions implicitly encode extra population size information that is not available from the observed coalescent data or tree. Here, we present a novel statistic, $\Omega$, to quantify and disaggregate the relative contributions of the coalescent data and prior assumptions to the resulting posterior estimate precision. Our statistic also measures the additional mutual information introduced by such priors. Using $\Omega$ we show that, because it is surprisingly easy to overparametrize piecewise-constant population models, common smoothing priors can lead to overconfident and potentially misleading inference, even under robust experimental designs. We propose $\Omega$ as a useful tool for detecting when effective population size estimates are overly reliant on prior assumptions and for improving quantification of the uncertainty in those estimates.[Coalescent processes; effective population size; information theory; phylodynamics; prior assumptions; skyline plots.].


Asunto(s)
Modelos Genéticos , Teorema de Bayes , Filogenia , Densidad de Población
17.
Lancet Digit Health ; 3(6): e349-e359, 2021 06.
Artículo en Inglés | MEDLINE | ID: mdl-34045001

RESUMEN

BACKGROUND: Until broad vaccination coverage is reached and effective therapeutics are available, controlling population mobility (ie, changes in the spatial location of a population that affect the spread and distribution of pathogens) is one of the major interventions used to reduce transmission of SARS-CoV-2. However, population mobility differs across locations, which could reduce the effectiveness of pandemic control measures. Here we assess the extent to which socioeconomic factors are associated with reductions in population mobility during the COVID-19 pandemic, at both the city level in China and at the country level worldwide. METHODS: In this retrospective, observational study, we obtained anonymised daily mobile phone location data for 358 Chinese cities from Baidu, and for 121 countries from Google COVID-19 Community Mobility Reports. We assessed the intra-city movement intensity, inflow intensity, and outflow intensity of each Chinese city between Jan 25 (when the national emergency response was implemented) and Feb 18, 2020 (when population mobility was lowest) and compared these data to the corresponding lunar calendar period from the previous year (Feb 5 to March 1, 2019). Chinese cities were classified into four socioeconomic index (SEI) groups (high SEI, high-middle SEI, middle SEI, and low SEI) and the association between socioeconomic factors and changes in population mobility were assessed using univariate and multivariable linear regression. At the country level, we compared six types of mobility (residential, transit stations, workplaces, retail and recreation, parks, and groceries and pharmacies) 35 days after the implementation of the national emergency response in each country and compared these to data from the same day of the week in the baseline period (Jan 3 to Feb 6, 2020). We assessed associations between changes in the six types of mobility and the country's sociodemographic index using univariate and multivariable linear regression. FINDINGS: The reduction in intra-city movement intensity in China was stronger in cities with a higher SEI than in those with a lower SEI (r=-0·47, p<0·0001). However, reductions in inter-city movement flow (both inflow and outflow intensity) were not associated with SEI and were only associated with government control measures. In the country-level analysis, countries with higher sociodemographic and Universal Health Coverage indexes had greater reductions in population mobility (ie, in transit stations, workplaces, and retail and recreation) following national emergency declarations than those with lower sociodemographic and Universal Health Coverage indexes. A higher sociodemographic index showed a greater reduction in mobility in transit stations (r=-0·27, p=0·0028), workplaces (r=-0·34, p=0·0002), and areas retail and recreation (rxs=-0·30, p=0·0012) than those with a lower sociodemographic index. INTERPRETATION: Although COVID-19 outbreaks are more frequently reported in larger cities, our analysis shows that future policies should prioritise the reduction of risks in areas with a low socioeconomic level-eg, by providing financial assistance and improving public health messaging. However, our study design only allows us to assess associations, and a long-term study is needed to decipher causality. FUNDING: Chinese Ministry of Science and Technology, Research Council of Norway, Beijing Municipal Science & Technology Commission, Beijing Natural Science Foundation, Beijing Advanced Innovation Program for Land Surface Science, National Natural Science Foundation of China, China Association for Science and Technology.


Asunto(s)
COVID-19 , Dinámica Poblacional , Factores Socioeconómicos , Viaje , Adulto , Teléfono Celular , China , Ciudades , Salud Global , Humanos , Distanciamiento Físico , Dinámica Poblacional/tendencias , Vigilancia de la Población/métodos , Estudios Retrospectivos , SARS-CoV-2
18.
Front Aging Neurosci ; 13: 668775, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-34025392

RESUMEN

Parkinson's disease (PD) is a neurodegenerative disease associated with progressive impairment of motor and non-motor functions in aging people. Overwhelming evidence indicate that mitochondrial dysfunction is a central factor in PD pathophysiology, which impairs energy metabolism. While, several other studies have shown probiotic supplementations to improve host energy metabolism, alleviate the disease progression, prevent gut microbiota dysbiosis and alter commensal bacterial metabolites. But, whether probiotic and/or prebiotic supplementation can affect energy metabolism and cause the impediment of PD progression remains poorly characterized. Therefore, we investigated 8-weeks supplementation effects of probiotic [Lactobacillus salivarius subsp. salicinius AP-32 (AP-32)], residual medium (RM) obtained from the AP-32 culture medium, and combination of AP-32 and RM (A-RM) on unilateral 6-hydroxydopamine (6-OHDA)-induced PD rats. We found that AP-32, RM and A-RM supplementation induced neuroprotective effects on dopaminergic neurons along with improved motor functions in PD rats. These effects were accompanied by significant increases in mitochondrial activities in the brain and muscle, antioxidative enzymes level in serum, and altered SCFAs profile in fecal samples. Importantly, the AP-32 supplement restored muscle mass along with improved motor function in PD rats, and produced the best results among the supplements. Our results demonstrate that probiotic AP-32 and A-RM supplementations can recover energy metabolism via increasing SCFAs producing and mitochondria function. This restoring of mitochondrial function in the brain and muscles with improved energy metabolism might additionally be potentiated by ROS suppression by the elevated generation of antioxidants, and which finally leads to facilitated recovery of 6-OHDA-induced motor deficit. Taken together, this work demonstrates that probiotic AP-32 supplementation could be a potential candidate for alternate treatment strategy to avert PD progression.

19.
BMJ Glob Health ; 6(4)2021 04.
Artículo en Inglés | MEDLINE | ID: mdl-33926892

RESUMEN

INTRODUCTION: Little evidence exists on the differential health effects of COVID-19 on disadvantaged population groups. Here we characterise the differential risk of hospitalisation and death in São Paulo state, Brazil, and show how vulnerability to COVID-19 is shaped by socioeconomic inequalities. METHODS: We conducted a cross-sectional study using hospitalised severe acute respiratory infections notified from March to August 2020 in the Sistema de Monitoramento Inteligente de São Paulo database. We examined the risk of hospitalisation and death by race and socioeconomic status using multiple data sets for individual-level and spatiotemporal analyses. We explained these inequalities according to differences in daily mobility from mobile phone data, teleworking behaviour and comorbidities. RESULTS: Throughout the study period, patients living in the 40% poorest areas were more likely to die when compared with patients living in the 5% wealthiest areas (OR: 1.60, 95% CI 1.48 to 1.74) and were more likely to be hospitalised between April and July 2020 (OR: 1.08, 95% CI 1.04 to 1.12). Black and Pardo individuals were more likely to be hospitalised when compared with White individuals (OR: 1.41, 95% CI 1.37 to 1.46; OR: 1.26, 95% CI 1.23 to 1.28, respectively), and were more likely to die (OR: 1.13, 95% CI 1.07 to 1.19; 1.07, 95% CI 1.04 to 1.10, respectively) between April and July 2020. Once hospitalised, patients treated in public hospitals were more likely to die than patients in private hospitals (OR: 1.40%, 95% CI 1.34% to 1.46%). Black individuals and those with low education attainment were more likely to have one or more comorbidities, respectively (OR: 1.29, 95% CI 1.19 to 1.39; 1.36, 95% CI 1.27 to 1.45). CONCLUSIONS: Low-income and Black and Pardo communities are more likely to die with COVID-19. This is associated with differential access to quality healthcare, ability to self-isolate and the higher prevalence of comorbidities.


Asunto(s)
COVID-19/etnología , COVID-19/mortalidad , Etnicidad/estadística & datos numéricos , Mortalidad Hospitalaria/etnología , Neumonía Viral , Áreas de Pobreza , Características de la Residencia/estadística & datos numéricos , Adulto , Anciano , Anciano de 80 o más Años , Brasil/epidemiología , Estudios Transversales , Femenino , Disparidades en el Estado de Salud , Humanos , Masculino , Persona de Mediana Edad , Pandemias , Neumonía Viral/epidemiología , SARS-CoV-2 , Estudios Seroepidemiológicos , Factores Socioeconómicos
20.
Sci Data ; 8(1): 73, 2021 03 04.
Artículo en Inglés | MEDLINE | ID: mdl-33664243

RESUMEN

Brazil has one of the fastest-growing COVID-19 epidemics worldwide. Non-pharmaceutical interventions (NPIs) have been adopted at the municipal level with asynchronous actions taken across 5,568 municipalities and the Federal District. This paper systematises the fragmented information on NPIs reporting on a novel dataset with survey responses from 4,027 mayors, covering 72.3% of all municipalities in the country. This dataset responds to the urgency to track and share findings on fragmented policies during the COVID-19 pandemic. Quantifying NPIs can help to assess the role of interventions in reducing transmission. We offer spatial and temporal details for a range of measures aimed at implementing social distancing and the dates when these measures were relaxed by local governments.


Asunto(s)
COVID-19/prevención & control , Control de Enfermedades Transmisibles/métodos , Brasil , COVID-19/transmisión , Ciudades , Humanos , Pandemias
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