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| 5. |
- Chen, DS, et al.
(författare)
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Single cell atlas for 11 non-model mammals, reptiles and birds
- 2021
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Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 12:1, s. 7083-
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Tidskriftsartikel (refereegranskat)abstract
- The availability of viral entry factors is a prerequisite for the cross-species transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Large-scale single-cell screening of animal cells could reveal the expression patterns of viral entry genes in different hosts. However, such exploration for SARS-CoV-2 remains limited. Here, we perform single-nucleus RNA sequencing for 11 non-model species, including pets (cat, dog, hamster, and lizard), livestock (goat and rabbit), poultry (duck and pigeon), and wildlife (pangolin, tiger, and deer), and investigated the co-expression of ACE2 and TMPRSS2. Furthermore, cross-species analysis of the lung cell atlas of the studied mammals, reptiles, and birds reveals core developmental programs, critical connectomes, and conserved regulatory circuits among these evolutionarily distant species. Overall, our work provides a compendium of gene expression profiles for non-model animals, which could be employed to identify potential SARS-CoV-2 target cells and putative zoonotic reservoirs.
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| 6. |
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| 7. |
- Zhen, XM, et al.
(författare)
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Socioeconomic Factors Contributing to Antibiotic Resistance in China: A Panel Data Analysis
- 2021
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Ingår i: Antibiotics (Basel, Switzerland). - : MDPI AG. - 2079-6382. ; 10:8
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Tidskriftsartikel (refereegranskat)abstract
- The relationship between socioeconomic factors and antibiotic resistance (ABR) prevalence remains a knowledge gap in China. In this study, our aim was to examine the association between ABR prevalence and socioeconomic factors across 30 provinces in mainland China. We used two measures of level of ABR: the proportion of methicillin-resistant Staphylococcus aureus (MRSA), third-generation cephalosporin-resistant Escherichia coli (3GCREC), and third-generation cephalosporin-resistant Klebsiella pneumoniae (3GCRKP), and the aggregate resistance. The data of ABR prevalence, education, gross domestic product (GDP) per capita, out-of-pocket (OOP) health expenditure, physician density, hospital bed density, and public toilet density during 2014 and 2018 in 30 provinces in mainland China were included. We examined the association between ABR prevalence and potential contributing socioeconomic factors using panel data modeling. In addition, we explored this relationship in the eastern, central, and western economic zones. Our results indicated that GDP per capita was significantly positively correlated with ABR in mainland China and the eastern economic zone; however, significantly positive associations did not exist in the central and western economic zones. Surprisingly, both higher GDP per capita and higher OOP health expenditure were associated with a higher level of MRSA, but a lower level of 3GCREC; higher physician density was associated with a lower level of MRSA, but a higher level of 3GCREC. In addition, ABR prevalence presented a decline trend during 2014 and 2018. Our study showed the potential associ-ations between resistance and GDP per capita, OOP health expenditure, physician density. It high-lights that the social and economic determinants can be of importance in tacking the development and spread of ABR in mainland China.
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| 8. |
- Abudurexiti, A, et al.
(författare)
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Taxonomy of the order Bunyavirales: update 2019
- 2019
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Ingår i: Archives of virology. - : Springer Science and Business Media LLC. - 1432-8798 .- 0304-8608. ; 164:7, s. 1949-1965
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Tidskriftsartikel (refereegranskat)
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| 9. |
- Akbarian, S, et al.
(författare)
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The PsychENCODE project
- 2015
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Ingår i: Nature neuroscience. - : Springer Science and Business Media LLC. - 1546-1726 .- 1097-6256. ; 18:12, s. 1707-1712
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Tidskriftsartikel (refereegranskat)
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| 13. |
- Deng, XM, et al.
(författare)
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The involvement of multiple protease-antiprotease systems and gut origin sepsis in zymosan-associated endothelial barrier injury and multiple organ dysfunction in rats
- 2001
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Ingår i: Shock. - 1540-0514. ; 16:4, s. 298-303
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Tidskriftsartikel (refereegranskat)abstract
- Multiple organ dysfunction syndrome is a dominant cause of mortality in the intensive care unit. Experimentally, a condition similar to the multiple organ dysfunction syndrome can be induced by the intraperitoneal injection of sterile zymosan. In the present study we investigate potential alterations in multiple organ functions, endothelial permeability, and antiproteinases after intraperitoneal injection of zymosan at various doses. Zymosan-induced generalized inflammation lead to endothelial barrier injury in multiple organs/tissues, a decrease in systemic arterial pressure, impaired organ function and gut defence function, and consumption of protease inhibitors, particularly the consumption of alpha (2) antiplasmin. Endothelial barrier injury appears to present a dose- and organ-dependent pattern in multiple organs/tissues, and the increase in endothelial barrier permeability occurred prior to organ dysfunction. Zymosan induced the development of multiple organ dysfunction syndrome, probably initiating multiple protease-antiprotease systems, particularly the fibrinolytic system, leading to endothelial barrier injury, tissue edema, parenchymal cell damage, and eventual organ dysfunction, potentially augmented by a secondary bacterial infection.
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| 19. |
- Rahnev, D, et al.
(författare)
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The Confidence Database
- 2020
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Ingår i: Nature human behaviour. - : Springer Science and Business Media LLC. - 2397-3374. ; 4:3, s. 317-325
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Tidskriftsartikel (refereegranskat)
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| 20. |
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| 21. |
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| 22. |
- Yuen, RKC, et al.
(författare)
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Genome-wide characteristics of de novo mutations in autism
- 2016
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Ingår i: NPJ genomic medicine. - : Springer Science and Business Media LLC. - 2056-7944. ; 1, s. 160271-1602710
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Tidskriftsartikel (refereegranskat)abstract
- De novo mutations (DNMs) are important in autism spectrum disorder (ASD), but so far analyses have mainly been on the ~1.5% of the genome encoding genes. Here, we performed whole-genome sequencing (WGS) of 200 ASD parent–child trios and characterised germline and somatic DNMs. We confirmed that the majority of germline DNMs (75.6%) originated from the father, and these increased significantly with paternal age only (P=4.2×10−10). However, when clustered DNMs (those within 20 kb) were found in ASD, not only did they mostly originate from the mother (P=7.7×10−13), but they could also be found adjacent to de novo copy number variations where the mutation rate was significantly elevated (P=2.4×10−24). By comparing with DNMs detected in controls, we found a significant enrichment of predicted damaging DNMs in ASD cases (P=8.0×10−9; odds ratio=1.84), of which 15.6% (P=4.3×10−3) and 22.5% (P=7.0×10−5) were non-coding or genic non-coding, respectively. The non-coding elements most enriched for DNM were untranslated regions of genes, regulatory sequences involved in exon-skipping and DNase I hypersensitive regions. Using microarrays and a novel outlier detection test, we also found aberrant methylation profiles in 2/185 (1.1%) of ASD cases. These same individuals carried independently identified DNMs in the ASD-risk and epigenetic genes DNMT3A and ADNP. Our data begins to characterize different genome-wide DNMs, and highlight the contribution of non-coding variants, to the aetiology of ASD.
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| 23. |
- Yusuf, D, et al.
(författare)
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The transcription factor encyclopedia
- 2012
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Ingår i: Genome biology. - : Springer Science and Business Media LLC. - 1474-760X .- 1465-6906. ; 13:3, s. R24-
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Tidskriftsartikel (refereegranskat)
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| 24. |
- Zhen, XM, et al.
(författare)
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Clinical and Economic Burden of Carbapenem-Resistant Infection or Colonization Caused by Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii: A Multicenter Study in China
- 2020
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Ingår i: Antibiotics (Basel, Switzerland). - : MDPI AG. - 2079-6382. ; 9:8
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Tidskriftsartikel (refereegranskat)abstract
- Background: Carbapenem resistant Klebsiella pneumoniae (CRKP), Pseudomonas aeruginosa (CRPA), and Acinetobacter baumannii (CRAB) pose significant threats to public health. However, the clinical and economic impacts of CRKP, CRPA, and CRAB remain largely uninvestigated in China. This study aimed to examine the clinical and economic burden of CRKP, CRPA, and CRAB compared with carbapenem susceptible cases in China. Method: We conducted a retrospective and multicenter study among inpatients hospitalized at four tertiary hospitals between 2013 and 2015 who had K. pneumoniae, P. aeruginosa, and A. baumannii positive clinical samples. Propensity score matching (PSM) was used to balance the impact of potential confounding variables, including age, sex, insurance, number of diagnosis, comorbidities (disease diagnosis, and Charlson comorbidity index), admission to intensive care unit, and surgeries. The main indicators included economic costs, length of stay (LOS), and mortality rate. Results: We included 12,022 inpatients infected or colonized with K. pneumoniae, P. aeruginosa, and A. baumannii between 2013 and 2015, including 831 with CRKP and 4328 with carbapenem susceptible K. pneumoniae (CSKP), 1244 with CRPA and 2674 with carbapenem susceptible P. aeruginosa (CSPA), 1665 with CRAB and 1280 with carbapenem susceptible A. baumannii (CSAB). After PSM, 822 pairs, 1155 pairs, and 682 pairs, respectively were generated. Compared with carbapenem-susceptible cases, those with CRKP, CRPA, and CRAB were associated with statistically significantly increased total hospital cost ($14,252, p < 0.0001; $4605, p < 0.0001; $7277, p < 0.0001) and excess LOS (13.2 days, p < 0.0001; 5.4 days, p = 0.0003; 15.8 days, p = 0.0004). In addition, there were statistically significantly differences in hospital mortality rate between CRKP and CSKP, and CRAB and CSAB group (2.94%, p = 0.024; 4.03%, p = 0.03); however, the difference between CRPA and CSPA group was marginal significant (2.03%, p = 0.052). Conclusion: It highlights the clinical and economic impact of CRKP, CRPA, and CRAB to justify more resources for implementing antibiotic stewardship practices to improve clinical outcomes and to reduce economic costs.
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| 25. |
- Zhen, XM, et al.
(författare)
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Clinical and economic impact of methicillin-resistant Staphylococcus aureus: a multicentre study in China
- 2020
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Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 10:1, s. 3900-
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Tidskriftsartikel (refereegranskat)abstract
- Methicillin-resistant Staphylococcus aureus (MRSA) has become a serious threat to global health. In China, the proportion of S. aureus isolates that were MRSA was 44.6% in 2014. The clinical and economic impact of MRSA in China remains largely uninvestigated. This study aims to compare the differences in hospital costs, length of hospital stay, and hospital mortality rate between MRSA and methicillin-susceptible S. aureus (MSSA) colonization or infection and between MRSA cases and those without an S. aureus infection. A retrospective and multicentre study was conducted in four tertiary hospitals in China between 2013 and 2015. Inpatient characteristics and hospital costs were collected from electronic medical records. We conducted propensity score matching (PSM) to eliminate selection bias by balancing the potential confounding variables between the two groups. The main indicators included hospital costs, length of hospital stay, and hospital mortality rate. A total of 1,335 inpatients with MRSA, 1,397 with MSSA, and 33,606 without an S. aureus infection were included. PSM obtained 954 and 1,313 pairs between the MRSA and MSSA groups and between the MRSA and S. aureus-free groups, respectively. After PSM, MRSA colonization or infection is associated with an increased total hospital cost ranging from $3,220 to $9,606, an excess length of hospital stay of 6 days–14 days, and an attributable hospital mortality rate of 0–3.58%. Between the MRSA and MSSA groups, MRSA colonization or infection was significantly associated with a higher total hospital cost and longer length of hospital stay among survivors but not among non-survivors; however, there were no differences in the hospital mortality rate between these two groups. Between the MRSA and the S. aureus-free groups, MRSA colonization or infection was significantly associated with an increased total hospital cost, a prolonged length of hospital stay and a higher hospital mortality rate among both survivors and non-survivors. It is critical to quantify the clinical and economic impact of MRSA to justify resource allocation for the development of strategies to improve clinical outcomes and to reduce the economic burden.
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| 26. |
- Zhen, XM, et al.
(författare)
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Clinical and Economic Impact of Third-Generation Cephalosporin-Resistant Infection or Colonization Caused by Escherichia coli and Klebsiella pneumoniae: A Multicenter Study in China
- 2020
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Ingår i: International journal of environmental research and public health. - : MDPI AG. - 1660-4601. ; 17:24
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Tidskriftsartikel (refereegranskat)abstract
- Quantifying economic and clinical outcomes for interventions could help to reduce third-generation cephalosporin resistance and Escherichia coli or Klebsiella pneumoniae. We aimed to compare the differences in clinical and economic burden between third-generation cephalosporin-resistant E. coli (3GCREC) and third-generation cephalosporin-susceptible E. coli (3GCSEC) cases, and between third-generation cephalosporin-resistant K. pneumoniae (3GCRKP) and third-generation cephalosporin-susceptible K. pneumoniae (3GCSKP) cases. A retrospective and multicenter study was conducted. We collected data from electronic medical records for patients who had clinical samples positive for E. coli or K. pneumoniae isolates during 2013 and 2015. Propensity score matching (PSM) was conducted to minimize the impact of potential confounding variables, including age, sex, insurance, number of diagnoses, Charlson comorbidity index, admission to intensive care unit, surgery, and comorbidities. We also repeated the PSM including length of stay (LOS) before culture. The main indicators included economic costs, LOS and hospital mortality. The proportions of 3GCREC and 3GCRKP in the sampled hospitals were 44.3% and 32.5%, respectively. In the two PSM methods, 1804 pairs and 1521 pairs were generated, and 1815 pairs and 1617 pairs were obtained, respectively. Compared with susceptible cases, those with 3GCREC and 3GCRKP were associated with significantly increased total hospital cost and excess LOS. Inpatients with 3GCRKP were significantly associated with higher hospital mortality compared with 3GCSKP cases, however, there was no significant difference between 3GCREC and 3GCSEC cases. Cost reduction and outcome improvement could be achieved through a preventative approach in terms of both antimicrobial stewardship and preventing the transmission of organisms.
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| 29. |
- Zhen, XM, et al.
(författare)
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The Clinical and Economic Impact of Antibiotic Resistance in China: A Systematic Review and Meta-Analysis
- 2019
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Ingår i: Antibiotics (Basel, Switzerland). - : MDPI AG. - 2079-6382. ; 8:3
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Tidskriftsartikel (refereegranskat)abstract
- Antibiotic resistance (ABR) is one of the biggest threats to global health, especially in China. This study aims to analyze the published literature on the clinical and economic impact of ABR or multi-drug resistant (MDR) bacteria compared to susceptible bacteria or non-infection, in mainland China. English and Chinese databases were searched to identify relevant studies evaluating mortality, hospital stay, and hospital costs of ABR. A meta-analysis of mortality was performed using a random effects model. The costs were converted into 2015 United States (US) dollars. Of 13,693 studies identified, 44 eligible studies were included. Twenty-nine investigated the impact of ABR on hospital mortality, 37 were focused on hospital stay, and 21 on hospital costs. Patients with ABR were associated with a greater risk of overall mortality compared to those with susceptibility or those without infection (odds ratio: 2.67 and 3.29, 95% confidence interval: 2.18–3.26 and 1.71–6.33, p < 0.001 and p < 0.001, respectively). The extra mean total hospital stay and total hospital cost were reported, ranging from 3 to 46 days, and from US$238 to US$16,496, respectively. Our study indicates that ABR is associated with significantly higher mortality. Moreover, ABR is not always, but usually, associated with significantly longer hospital stay and higher hospital costs.
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| 30. |
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| 31. |
- Zhou, X, et al.
(författare)
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Alcohol consumption, blood DNA methylation and breast cancer: a Mendelian randomisation study
- 2022
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Ingår i: European journal of epidemiology. - : Springer Science and Business Media LLC. - 1573-7284 .- 0393-2990. ; 37:7, s. 701-712
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Tidskriftsartikel (refereegranskat)abstract
- Alcohol intake is thought to be a risk factor for breast cancer, but the causal relationship and carcinogenic mechanisms are not clear. We performed an up-to-date meta-analysis of prospective studies to assess observational association, and then conducted MR analysis to make causal inference based on the genetic predisposition to alcohol consumption (“drinks per week”) and pathological drinking behaviours (“alcohol use disorder” and “problematic alcohol use”), as well as genetically predicted DNA methylation at by alcohol-related CpG sites in blood. We found an observational dose–response association between alcohol intake and breast cancer incidence with an additional risk of 4% for per 10 g/day increase in alcohol consumption. Genetic predisposition to alcohol consumption (“drinks per week”) was not causally associated with breast cancer incidence at the OR of 1.01 (95% CI 0.84, 1.23), but problematic alcohol use (PAU) was linked to a higher breast cancer risk at the OR of 1.76 (95% CI 1.04, 2.99) when conditioning on alcohol consumption. Epigenetic MR analysis identified four CpG sites, cg03260624 near CDC7 gene, cg10816169 near ZNF318 gene, cg03345232 near RIN3 gene, and cg26312998 near RP11-867G23.13 gene, where genetically predicted epigenetic modifications were associated with an increased breast cancer incidence risk. Our findings re-affirmed that alcohol consumption is of high risk for breast cancer incidence even at a very low dose, and the pathogenic effect of alcohol on breast cancer could be due to pathological drinking behaviour and epigenetic modification at several CpG sites, which could be potential intervention targets for breast cancer prevention.
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| 34. |
- Niemi, MEK, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 35. |
- Kanai, M, et al.
(författare)
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- 2023
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swepub:Mat__t
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