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Alm E, Broberg EK, Connor T, Hodcroft EB, Komissarov AB, Maurer-Stroh S, Melidou A, Neher RA, O'Toole Á, Pereyaslov D. Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020. Euro Surveill 2020; 25:2001410. [PMID: 32794443 PMCID: PMC7427299 DOI: 10.2807/1560-7917.es.2020.25.32.2001410] [Citation(s) in RCA: 143] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 08/11/2020] [Indexed: 02/01/2023] Open
Abstract
We show the distribution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three genomic nomenclature systems to all sequence data from the World Health Organization European Region available until 10 July 2020. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation, compare the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2.
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5 |
143 |
2
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Nakayama T, Kosugi T, Gersch M, Connor T, Sanchez-Lozada LG, Lanaspa MA, Roncal C, Perez-Pozo SE, Johnson RJ, Nakagawa T. Dietary fructose causes tubulointerstitial injury in the normal rat kidney. Am J Physiol Renal Physiol 2010; 298:F712-20. [PMID: 20071464 DOI: 10.1152/ajprenal.00433.2009] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Recent studies suggest that the metabolic syndrome is associated with renal disease. We previously reported that a high-fructose diet, but not a high-glucose diet, can induce metabolic syndrome and accelerate chronic renal disease in rats. We now examined the effects of a high-fructose diet on normal rat kidneys. Three groups of Sprague-Dawley rats were pair fed a special diet containing 60% fructose, 60% glucose, or control standard rat chow for 6 wk, and then histological studies were performed. The effect of fructose to induce cell proliferation in cultured proximal tubular cells was also performed. Fructose diet, but not glucose diet, significantly increased kidney weight by 6 wk. The primary finding was tubular hyperplasia and proliferation involving all segments of the proximal tubules while glomerular changes were not observed. This is the same site where the fructose transporters (GLUT2 and -5) as well as the key enzyme in fructose metabolism (ketohexokinase) were expressed. Consistently, fructose also induced proliferation of rat proximal tubular cells in culture. In vivo, tubular proliferation was also associated with focal tubular injury, with type III collagen deposition in the interstitium, an increase in alpha-smooth muscle actin positive myofibroblasts, and an increase in macrophage infiltration. In conclusion, a high-fructose diet induces cell proliferation and hyperplasia in proximal tubules, perhaps via a direct metabolic effect. The effect is independent of total energy intake and is associated with focal tubulointerstitial injury. These studies may provide a mechanism by which metabolic syndrome causes renal disease.
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Research Support, N.I.H., Extramural |
15 |
135 |
3
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Petrovska L, Mather AE, AbuOun M, Branchu P, Harris SR, Connor T, Hopkins KL, Underwood A, Lettini AA, Page A, Bagnall M, Wain J, Parkhill J, Dougan G, Davies R, Kingsley RA. Microevolution of Monophasic Salmonella Typhimurium during Epidemic, United Kingdom, 2005-2010. Emerg Infect Dis 2016; 22:617-24. [PMID: 26982594 PMCID: PMC4806966 DOI: 10.3201/eid2204.150531] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Microevolution resulted in considerable genotypic variation. Microevolution associated with emergence and expansion of new epidemic clones of
bacterial pathogens holds the key to epidemiologic success. To determine
microevolution associated with monophasic Salmonella Typhimurium
during an epidemic, we performed comparative whole-genome sequencing and phylogenomic
analysis of isolates from the United Kingdom and Italy during 2005–2012. These
isolates formed a single clade distinct from recent monophasic epidemic clones
previously described from North America and Spain. The UK monophasic epidemic clones
showed a novel genomic island encoding resistance to heavy metals and a composite
transposon encoding antimicrobial drug resistance genes not present in other
Salmonella Typhimurium isolates, which may have contributed to
epidemiologic success. A remarkable amount of genotypic variation accumulated during
clonal expansion that occurred during the epidemic, including multiple independent
acquisitions of a novel prophage carrying the sopE gene and multiple
deletion events affecting the phase II flagellin locus. This high level of
microevolution may affect antigenicity, pathogenicity, and transmission.
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Research Support, Non-U.S. Gov't |
9 |
129 |
4
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Perpetuo MD, Valdivieso M, Heilbrun LK, Nelson RS, Connor T, Bodey GP. Natural history study of gallbladder cancer: a review of 36 years experience at M. D. Anderson Hospital and Tumor Institute. Cancer 1978; 42:330-5. [PMID: 667804 DOI: 10.1002/1097-0142(197807)42:1<330::aid-cncr2820420150>3.0.co;2-f] [Citation(s) in RCA: 125] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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47 |
125 |
5
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Lin JW, Tang C, Wei HC, Du B, Chen C, Wang M, Zhou Y, Yu MX, Cheng L, Kuivanen S, Ogando NS, Levanov L, Zhao Y, Li CL, Zhou R, Li Z, Zhang Y, Sun K, Wang C, Chen L, Xiao X, Zheng X, Chen SS, Zhou Z, Yang R, Zhang D, Xu M, Song J, Wang D, Li Y, Lei S, Zeng W, Yang Q, He P, Zhang Y, Zhou L, Cao L, Luo F, Liu H, Wang L, Ye F, Zhang M, Li M, Fan W, Li X, Li K, Ke B, Xu J, Yang H, He S, Pan M, Yan Y, Zha Y, Jiang L, Yu C, Liu Y, Xu Z, Li Q, Jiang Y, Sun J, Hong W, Wei H, Lu G, Vapalahti O, Luo Y, Wei Y, Connor T, Tan W, Snijder EJ, Smura T, Li W, Geng J, Ying B, Chen L. Genomic monitoring of SARS-CoV-2 uncovers an Nsp1 deletion variant that modulates type I interferon response. Cell Host Microbe 2021; 29:489-502.e8. [PMID: 33548198 PMCID: PMC7846228 DOI: 10.1016/j.chom.2021.01.015] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/07/2021] [Accepted: 01/26/2021] [Indexed: 02/05/2023]
Abstract
The SARS-CoV-2 virus, the causative agent of COVID-19, is undergoing constant mutation. Here, we utilized an integrative approach combining epidemiology, virus genome sequencing, clinical phenotyping, and experimental validation to locate mutations of clinical importance. We identified 35 recurrent variants, some of which are associated with clinical phenotypes related to severity. One variant, containing a deletion in the Nsp1-coding region (Δ500-532), was found in more than 20% of our sequenced samples and associates with higher RT-PCR cycle thresholds and lower serum IFN-β levels of infected patients. Deletion variants in this locus were found in 37 countries worldwide, and viruses isolated from clinical samples or engineered by reverse genetics with related deletions in Nsp1 also induce lower IFN-β responses in infected Calu-3 cells. Taken together, our virologic surveillance characterizes recurrent genetic diversity and identified mutations in Nsp1 of biological and clinical importance, which collectively may aid molecular diagnostics and drug design.
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87 |
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Hill V, Du Plessis L, Peacock TP, Aggarwal D, Colquhoun R, Carabelli AM, Ellaby N, Gallagher E, Groves N, Jackson B, McCrone JT, O’Toole Á, Price A, Sanderson T, Scher E, Southgate J, Volz E, Barclay WS, Barrett JC, Chand M, Connor T, Goodfellow I, Gupta RK, Harrison EM, Loman N, Myers R, Robertson DL, Pybus OG, Rambaut A. The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK. Virus Evol 2022; 8:veac080. [PMID: 36533153 PMCID: PMC9752794 DOI: 10.1093/ve/veac080] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 07/28/2022] [Accepted: 08/25/2022] [Indexed: 01/06/2023] Open
Abstract
The first SARS-CoV-2 variant of concern (VOC) to be designated was lineage B.1.1.7, later labelled by the World Health Organization as Alpha. Originating in early autumn but discovered in December 2020, it spread rapidly and caused large waves of infections worldwide. The Alpha variant is notable for being defined by a long ancestral phylogenetic branch with an increased evolutionary rate, along which only two sequences have been sampled. Alpha genomes comprise a well-supported monophyletic clade within which the evolutionary rate is typical of SARS-CoV-2. The Alpha epidemic continued to grow despite the continued restrictions on social mixing across the UK and the imposition of new restrictions, in particular, the English national lockdown in November 2020. While these interventions succeeded in reducing the absolute number of cases, the impact of these non-pharmaceutical interventions was predominantly to drive the decline of the SARS-CoV-2 lineages that preceded Alpha. We investigate the only two sampled sequences that fall on the branch ancestral to Alpha. We find that one is likely to be a true intermediate sequence, providing information about the order of mutational events that led to Alpha. We explore alternate hypotheses that can explain how Alpha acquired a large number of mutations yet remained largely unobserved in a region of high genomic surveillance: an under-sampled geographical location, a non-human animal population, or a chronically infected individual. We conclude that the latter provides the best explanation of the observed behaviour and dynamics of the variant, although the individual need not be immunocompromised, as persistently infected immunocompetent hosts also display a higher within-host rate of evolution. Finally, we compare the ancestral branches and mutation profiles of other VOCs and find that Delta appears to be an outlier both in terms of the genomic locations of its defining mutations and a lack of the rapid evolutionary rate on its ancestral branch. As new variants, such as Omicron, continue to evolve (potentially through similar mechanisms), it remains important to investigate the origins of other variants to identify ways to potentially disrupt their evolution and emergence.
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McCrone JT, Hill V, Bajaj S, Pena RE, Lambert BC, Inward R, Bhatt S, Volz E, Ruis C, Dellicour S, Baele G, Zarebski AE, Sadilek A, Wu N, Schneider A, Ji X, Raghwani J, Jackson B, Colquhoun R, O'Toole Á, Peacock TP, Twohig K, Thelwall S, Dabrera G, Myers R, Faria NR, Huber C, Bogoch II, Khan K, du Plessis L, Barrett JC, Aanensen DM, Barclay WS, Chand M, Connor T, Loman NJ, Suchard MA, Pybus OG, Rambaut A, Kraemer MUG. Context-specific emergence and growth of the SARS-CoV-2 Delta variant. Nature 2022; 610:154-160. [PMID: 35952712 PMCID: PMC9534748 DOI: 10.1038/s41586-022-05200-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 08/05/2022] [Indexed: 02/01/2023]
Abstract
The SARS-CoV-2 Delta (Pango lineage B.1.617.2) variant of concern spread globally, causing resurgences of COVID-19 worldwide1,2. The emergence of the Delta variant in the UK occurred on the background of a heterogeneous landscape of immunity and relaxation of non-pharmaceutical interventions. Here we analyse 52,992 SARS-CoV-2 genomes from England together with 93,649 genomes from the rest of the world to reconstruct the emergence of Delta and quantify its introduction to and regional dissemination across England in the context of changing travel and social restrictions. Using analysis of human movement, contact tracing and virus genomic data, we find that the geographic focus of the expansion of Delta shifted from India to a more global pattern in early May 2021. In England, Delta lineages were introduced more than 1,000 times and spread nationally as non-pharmaceutical interventions were relaxed. We find that hotel quarantine for travellers reduced onward transmission from importations; however, the transmission chains that later dominated the Delta wave in England were seeded before travel restrictions were introduced. Increasing inter-regional travel within England drove the nationwide dissemination of Delta, with some cities receiving more than 2,000 observable lineage introductions from elsewhere. Subsequently, increased levels of local population mixing-and not the number of importations-were associated with the faster relative spread of Delta. The invasion dynamics of Delta depended on spatial heterogeneity in contact patterns, and our findings will inform optimal spatial interventions to reduce the transmission of current and future variants of concern, such as Omicron (Pango lineage B.1.1.529).
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Research Support, N.I.H., Extramural |
3 |
63 |
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Zhang J, Hull V, Ouyang Z, He L, Connor T, Yang H, Huang J, Zhou S, Zhang Z, Zhou C, Zhang H, Liu J. Modeling activity patterns of wildlife using time-series analysis. Ecol Evol 2017; 7:2575-2584. [PMID: 28428848 PMCID: PMC5395454 DOI: 10.1002/ece3.2873] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 02/09/2017] [Accepted: 02/10/2017] [Indexed: 11/17/2022] Open
Abstract
The study of wildlife activity patterns is an effective approach to understanding fundamental ecological and evolutionary processes. However, traditional statistical approaches used to conduct quantitative analysis have thus far had limited success in revealing underlying mechanisms driving activity patterns. Here, we combine wavelet analysis, a type of frequency‐based time‐series analysis, with high‐resolution activity data from accelerometers embedded in GPS collars to explore the effects of internal states (e.g., pregnancy) and external factors (e.g., seasonal dynamics of resources and weather) on activity patterns of the endangered giant panda (Ailuropoda melanoleuca). Giant pandas exhibited higher frequency cycles during the winter when resources (e.g., water and forage) were relatively poor, as well as during spring, which includes the giant panda's mating season. During the summer and autumn when resources were abundant, pandas exhibited a regular activity pattern with activity peaks every 24 hr. A pregnant individual showed distinct differences in her activity pattern from other giant pandas for several months following parturition. These results indicate that animals adjust activity cycles to adapt to seasonal variation of the resources and unique physiological periods. Wavelet coherency analysis also verified the synchronization of giant panda activity level with air temperature and solar radiation at the 24‐hr band. Our study also shows that wavelet analysis is an effective tool for analyzing high‐resolution activity pattern data and its relationship to internal and external states, an approach that has the potential to inform wildlife conservation and management across species.
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Connor T, Hull V, Liu J. Telemetry research on elusive wildlife: A synthesis of studies on giant pandas. Integr Zool 2016; 11:295-307. [PMID: 26940046 DOI: 10.1111/1749-4877.12197] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Telemetry studies that track animals through space and time can lead to advances in scientific understanding that are vital in conservation efforts. For example, telemetry studies of the giant panda (Ailuropoda melanoleuca) have shed light on many aspects of panda biology, but small sample sizes in each separate study make it difficult to draw broad conclusions. To overcome this problem we conducted the first synthesis of all 5 panda telemetry studies conducted to date. Using these data we investigated patterns in 6 main topics: home range, space-use interactions, core areas, movement patterns, seasonal migration and natal dispersal. We found that panda home range sizes do not vary between 2 main mountain ranges (Qionglai and Qinling), as was previously believed. Our results also suggest that female pandas increase their movement in the mating season: a behavior typically attributed only to males. We found and summarized telemetry and genetic evidence for female natal dispersal in the giant panda. Our synthesis highlights the need for additional research relating panda behavior to human disturbance factors, and can aid future studies on giant pandas as well as other species.
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Review |
9 |
47 |
10
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Xu Z, Chen X, Liu J, Zhang Y, Chau S, Bhattarai N, Wang Y, Li Y, Connor T, Li Y. Impacts of irrigated agriculture on food-energy-water-CO 2 nexus across metacoupled systems. Nat Commun 2020; 11:5837. [PMID: 33203840 PMCID: PMC7672069 DOI: 10.1038/s41467-020-19520-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 10/09/2020] [Indexed: 11/16/2022] Open
Abstract
Irrigated agriculture has important implications for achieving the United Nations Sustainable Development Goals. However, there is a lack of systematic and quantitative analyses of its impacts on food–energy–water–CO2 nexus. Here we studied impacts of irrigated agriculture on food–energy–water–CO2 nexus across food sending systems (the North China Plain (NCP)), food receiving systems (the rest of China) and spillover systems (Hubei Province, affected by interactions between sending and receiving systems), using life cycle assessment, model scenarios, and the framework of metacoupling (socioeconomic-environmental interactions within and across borders). Results indicated that food supply from the NCP promoted food sustainability in the rest of China, but the NCP consumed over four times more water than its total annual renewable water, with large variations in food–energy–water–CO2 nexus across counties. Although Hubei Province was seldom directly involved in the food trade, it experienced substantial losses in water and land due to the construction of the South-to-North Water Transfer Project which aims to alleviate water shortages in the NCP. This study suggests the need to understand impacts of agriculture on food–energy–water–CO2 nexus in other parts of the world to achieve global sustainability. Local human activities can lead to cross-border environmental impacts through the food–energy–water–CO2 nexus. Here, the authors report wide variations in environmental impacts of irrigated agriculture across counties within the North China Plain under different environmental and socioeconomic scenarios.
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5 |
44 |
11
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Kosugi T, Heinig M, Nakayama T, Connor T, Yuzawa Y, Li Q, Hauswirth WW, Grant MB, Croker BP, Campbell-Thompson M, Zhang L, Atkinson MA, Segal MS, Nakagawa T. Lowering blood pressure blocks mesangiolysis and mesangial nodules, but not tubulointerstitial injury, in diabetic eNOS knockout mice. THE AMERICAN JOURNAL OF PATHOLOGY 2009; 174:1221-9. [PMID: 19246639 PMCID: PMC2671355 DOI: 10.2353/ajpath.2009.080605] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/22/2008] [Indexed: 01/18/2023]
Abstract
Recently, we and others reported that diabetic endothelial nitric oxide synthase knockout (eNOSKO) mice develop advanced glomerular lesions that include mesangiolysis and nodular lesions. Interestingly, insulin treatment lowered blood pressure and prevented renal lesions, raising the question as to whether these beneficial effects of insulin were due to its ability to lower either high glucose levels or high blood pressure. We, therefore, examined the effect of lowering blood pressure using hydralazine in this diabetic eNOSKO mouse model. Hydralazine treatment significantly blocked the development of mesangiolysis and microaneurysms, whereas tubulointerstitial injury was not prevented in these mice. Additionally, hydralazine did not reduce expression levels of either tubulointerstitial thrombospondin-1 or transforming growth factor-beta despite controlling blood pressure. On the other hand, the critical role of high glucose levels on the development of tubulointerstitial injury was suggested by the observation that serum glucose levels were correlated with tubulointerstitial injury, as well as with the expression levels of both transforming growth factor-beta and thrombospondin-1. Importantly, controlling blood glucose with insulin completely blocked tubulointerstitial injury in diabetic eNOSKO mice. These data suggest that glomerular injury is dependent on systemic blood pressure, whereas hyperglycemia may have a more important role in tubulointerstitial injury, possibly due to the stimulation of the thrombospondin-1-transforming growth factor-beta pathway in diabetic eNOSKO mice. This study could provide insights into the pathogenesis of advanced diabetic nephropathy in the presence of endothelial dysfunction.
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16 |
37 |
12
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Xu Z, Tang Y, Connor T, Li D, Li Y, Liu J. Climate variability and trends at a national scale. Sci Rep 2017; 7:3258. [PMID: 28607387 PMCID: PMC5468283 DOI: 10.1038/s41598-017-03297-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 04/26/2017] [Indexed: 11/17/2022] Open
Abstract
Climate variability and trends have significant environmental and socioeconomic impacts. Global challenges such as food security, biodiversity loss, water scarcity and human health are affected by reference evapotranspiration, temperature, solar radiation, and precipitation together, but nonlinear dynamics of these four climatic factors have not been assessed simultaneously at the national scale. This leads to unclear climatic dynamics and limited applications. To address this knowledge gap, we analyzed the daily variability and trends of four climatic factors (reference evapotranspiration, temperature, solar radiation, and precipitation) in China simultaneously using high spatial resolution data from 1960 to 2013. The results indicate that the daily variability of climate system dynamics (quantified by multiplying fractal dimensions of the four climatic factors) in north China was higher than that in south China. For example, the climate system dynamics were more chaotic and with higher nonlinear variation in north China, most notably in Heilongjiang Province, the major grain base of China, posing threats to food security in the context of growing national population. Spatial distribution of variability varies among different climatic factors. Our study highlights the need for a more holistic study of climate variability and trends in other countries with multiple climate types to address challenges of sustainable development.
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Millar JR, Bengu N, Fillis R, Sprenger K, Ntlantsana V, Vieira VA, Khambati N, Archary M, Muenchhoff M, Groll A, Grayson N, Adamson J, Govender K, Dong K, Kiepiela P, Walker BD, Bonsall D, Connor T, Bull MJ, Nxele N, Roider J, Ismail N, Adland E, Puertas MC, Martinez-Picado J, Matthews PC, Ndung'u T, Goulder P. HIGH-FREQUENCY failure of combination antiretroviral therapy in paediatric HIV infection is associated with unmet maternal needs causing maternal NON-ADHERENCE. EClinicalMedicine 2020; 22:100344. [PMID: 32510047 PMCID: PMC7264978 DOI: 10.1016/j.eclinm.2020.100344] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Early combination antiretroviral therapy (cART) reduces the size of the viral reservoir in paediatric and adult HIV infection. Very early-treated children may have higher cure/remission potential. METHODS In an observational study of 151 in utero (IU)-infected infants in KwaZulu-Natal, South Africa, whose treatment adhered strictly to national guidelines, 76 infants diagnosed via point-of-care (PoC) testing initiated cART at a median of 26 h (IQR 18-38) and 75 infants diagnosed via standard-of-care (SoC) laboratory-based testing initiated cART at 10 days (IQR 8-13). We analysed mortality, time to suppression of viraemia, and maintenance of aviraemia over the first 2 years of life. FINDINGS Baseline plasma viral loads were low (median 8000 copies per mL), with 12% of infants having undetectable viraemia pre-cART initiation. However, barely one-third (37%) of children achieved suppression of viraemia by 6 months that was maintained to >12 months. 24% had died or were lost to follow up by 6 months. Infant mortality was 9.3%. The high-frequency virological failure in IU-infected infants was associated not with transmitted or acquired drug-resistant mutations but with cART non-adherence (plasma cART undetectable/subtherapeutic, p<0.0001) and with concurrent maternal cART failure (OR 15.0, 95%CI 5.6-39.6; p<0.0001). High-frequency virological failure was observed in PoC- and SoC-tested groups of children. INTERPRETATION The success of early infant testing and cART initiation strategies is severely limited by subsequent cART non-adherence in HIV-infected children. Although there are practical challenges to administering paediatric cART formulations, these are overcome by mothers who themselves are cART-adherent. These findings point to the ongoing obligation to address the unmet needs of the mothers. Eliminating the particular barriers preventing adequate treatment for these vulnerable women and infants need to be prioritised in order to achieve durable suppression of viraemia on cART, let alone HIV cure/remission, in HIV-infected children. FUNDING Wellcome Trust, National Institutes of Health.
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14
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Gunsolley JC, Tew JG, Connor T, Burmeister JA, Schenkein HA. Relationship between race and antibody reactive with periodontitis-associated bacteria. J Periodontal Res 1991; 26:59-63. [PMID: 1825335 DOI: 10.1111/j.1600-0765.1991.tb01627.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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34 |
30 |
15
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Yang H, Yang W, Zhang J, Connor T, Liu J. Revealing pathways from payments for ecosystem services to socioeconomic outcomes. SCIENCE ADVANCES 2018; 4:eaao6652. [PMID: 29750187 PMCID: PMC5943056 DOI: 10.1126/sciadv.aao6652] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 02/08/2018] [Indexed: 05/04/2023]
Abstract
Payments for ecosystem services (PES) programs have been widely implemented as a promising tool to conserve ecosystems while facilitating socioeconomic development. However, the underlying pathways (or processes) through which PES programs affect socioeconomic outcomes remain elusive, and existing literature provides little guidance to quantify them. By integrating linkages among PES programs, livelihood activities, and socioeconomic outcomes, we develop a framework to reveal pathways from PES programs to socioeconomic outcomes. We empirically demonstrate the framework's operationalization and uncover the pathways that lead to unexpected negative effects of two important PES programs on participating households' income. With improved understanding of the pathways (for example, the programs decreased income through reducing crop production), we provide recommendations to enhance the PES programs' outcomes in our demonstration site and beyond. Our study highlights the finding that elucidating the pathways from PES programs to their outcomes can help identify specific strategies to achieve ecosystem conservation and socioeconomic development simultaneously.
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Zhao Z, Cai M, Wang F, Winkler JA, Connor T, Chung MG, Zhang J, Yang H, Xu Z, Tang Y, Ouyang Z, Zhang H, Liu J. Synergies and tradeoffs among Sustainable Development Goals across boundaries in a metacoupled world. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 751:141749. [PMID: 32890805 DOI: 10.1016/j.scitotenv.2020.141749] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/15/2020] [Accepted: 08/15/2020] [Indexed: 06/11/2023]
Abstract
Synergies and tradeoffs among the United Nations Sustainable Development Goals (SDGs) within specific locations have been widely studied. However, there is little understanding of SDG synergies and tradeoffs across spatial/administrative boundaries although the world is increasingly interconnected and the United Nations aims to achieve SDGs everywhere by 2030. To fill such an important gap, we introduce a new theoretical framework and develop a general procedure of applying the framework to empirically evaluate SDG synergies and tradeoffs within and across boundaries, based on the concept of metacoupling. We work through our framework using the examples of tourism and panda loans between the globally important Wolong Nature Reserve for panda conservation and the rest of the world to evaluate their effects on six SDGs in Wolong and the other 66 panda reserves. Our analyses uncover a total of 17 synergies and two tradeoffs, of which 10 synergies and one tradeoff are internal to Wolong, while seven synergies and one tradeoff occur across reserve boundaries. Given the first empirical evidence about cross-boundary synergies and tradeoffs, it is our hope that this study provides a foundation for further research to reveal more SDG synergies and tradeoffs across boundaries worldwide. The findings will be essential to enhance SDG synergies and reduce tradeoffs across boundaries for achieving SDGs everywhere.
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Karlsson SL, Thomson N, Mutreja A, Connor T, Sur D, Ali M, Clemens J, Dougan G, Holmgren J, Lebens M. Retrospective Analysis of Serotype Switching of Vibrio cholerae O1 in a Cholera Endemic Region Shows It Is a Non-random Process. PLoS Negl Trop Dis 2016; 10:e0005044. [PMID: 27706170 PMCID: PMC5051702 DOI: 10.1371/journal.pntd.0005044] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 09/15/2016] [Indexed: 01/29/2023] Open
Abstract
Genomic data generated from clinical Vibrio cholerae O1 isolates collected over a five year period in an area of Kolkata, India with seasonal cholera outbreaks allowed a detailed genetic analysis of serotype switching that occurred from Ogawa to Inaba and back to Ogawa. The change from Ogawa to Inaba resulted from mutational disruption of the methyltransferase encoded by the wbeT gene. Re-emergence of the Ogawa serotype was found to result either from expansion of an already existing Ogawa clade or reversion of the mutation in an Inaba clade. Our data suggests that such transitions are not random events but rather driven by as yet unidentified selection mechanisms based on differences in the structure of the O1 antigen or in the serotype-determining wbeT gene.
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Connor TA, Clark JM, Jayamohan J, Stewart M, McGoldrick A, Williams C, Seemungal BM, Smith R, Burek R, Gilchrist MD. Do equestrian helmets prevent concussion? A retrospective analysis of head injuries and helmet damage from real-world equestrian accidents. SPORTS MEDICINE-OPEN 2019; 5:19. [PMID: 31127396 PMCID: PMC6534639 DOI: 10.1186/s40798-019-0193-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 05/14/2019] [Indexed: 11/10/2022]
Abstract
OBJECTIVES To collect and analyse helmets from real-world equestrian accidents. To record reported head injuries associated with those accidents. To compare damage to helmets certified to different standards and the injuries associated with them. METHODS Two hundred sixteen equestrian helmets were collected in total. One hundred seventy-six helmets from amateur jockeys were collected via accident helmet return schemes in the UK and USA, while 40 helmets from professional jockeys were collected by The Irish Turf Club. All helmet damage was measured, and associated head injury was recorded. RESULTS Eighty-eight percent (189) of equestrian fall accidents returned an injury report of which 70% (139) reported a head injury. Fifty-four percent (75) of head injury cases had associated helmet damage while 46% had no helmet damage. Reported head injuries consisted of 91% (126) concussion, 4% (6) skull fractures, 1 (0.7%) subdural hematoma, 1 (0.7%) cerebral edema and 5 (3.6%) diffuse axonal injury (DAI). It is also shown that helmets certified to the most severe standard are overrepresented in this undamaged group (p <0.001). CONCLUSIONS It is clear that despite jockeys wearing a helmet, large proportions of concussion injuries still occur in the event of a jockey sustaining a fall. However, the data suggest it is likely that helmets reduce the severity of head injury as the occurrence of skull fracture is low. The proportion of undamaged helmets with an associated head injury suggests that many helmets may be too stiff relative to the surface they are impacting to reduce the risk of traumatic brain injury (TBI). It may be possible to improve helmet designs and certification tests to reduce the risk of head injury in low-severity impacts.
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Connor T, Viña A, Winkler JA, Hull V, Tang Y, Shortridge A, Yang H, Zhao Z, Wang F, Zhang J, Zhang Z, Zhou C, Bai W, Liu J. Interactive spatial scale effects on species distribution modeling: The case of the giant panda. Sci Rep 2019; 9:14563. [PMID: 31601927 PMCID: PMC6787011 DOI: 10.1038/s41598-019-50953-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 09/19/2019] [Indexed: 11/08/2022] Open
Abstract
Research has shown that varying spatial scale through the selection of the total extent of investigation and the grain size of environmental predictor variables has effects on species distribution model (SDM) results and accuracy, but there has been minimal investigation into the interactive effects of extent and grain. To do this, we used a consistently sampled range-wide dataset of giant panda occurrence across southwest China and modeled their habitat and distribution at 4 extents and 7 grain sizes. We found that increasing grain size reduced model accuracy at the smallest extent, but that increasing extent negated this effect. Increasing extent also generally increased model accuracy, but the models built at the second-largest (mountain range) extent were more accurate than those built at the largest, geographic range-wide extent. When predicting habitat suitability in the smallest nested extents (50 km2), we found that the models built at the next-largest extent (500 km2) were more accurate than the smallest-extent models but that further increases in extent resulted in large decreases in accuracy. Overall, this study highlights the impacts of the selection of spatial scale when evaluating species' habitat and distributions, and we suggest more explicit investigations of scale effects in future modeling efforts.
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Legator MS, Connor T, Stoeckel M. The detection of mutagenic substances in the urine and blood of man. Ann N Y Acad Sci 1975; 269:16-20. [PMID: 773237 DOI: 10.1111/j.1749-6632.1976.tb35133.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Xu Z, Chau SN, Ruzzenenti F, Connor T, Li Y, Tang Y, Li D, Gong M, Liu J. Evolution of multiple global virtual material flows. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 658:659-668. [PMID: 30580220 DOI: 10.1016/j.scitotenv.2018.12.169] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 12/11/2018] [Accepted: 12/11/2018] [Indexed: 05/12/2023]
Abstract
The world is connected through multiple flows of material, but a comprehensive assessment of their temporal dynamics and interactions is rare. To address this knowledge gap, we assessed the evolution and interactions of global flows of virtual water, energy, land, CO2, nitrogen as well as financial capital embodied in international trade from 1995 to 2008. We found that the volumes of all these flows, except for land flow, increased over time. Financial capital flows increased most (188.9%), followed by flows of CO2 (59.3%), energy (58.1%), water (50.7%) and nitrogen (10.5%), while land transfer decreased by 8.8%. Volumes of virtual material flows among distant countries were much higher than those among adjacent countries. The top five countries accounted for a surprisingly large proportion (47% to 80%) of total flow volumes. Different kinds of virtual material flows tended to enhance each other through synergistic effects, and CO2 and nitrogen flows tended to have stronger positive synergetic impacts on the other virtual material flows. Our results suggest that it is important to pay particular attention to such fast-growing material flows, promote cooperation between distant countries, and target countries with the largest flows to achieve global sustainable development goals.
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Wang X, Huang J, Connor TA, Bai W, Zhang J, Wei W, Zhang Z, Liu D, Zhou C. Impact of livestock grazing on biodiversity and giant panda habitat. J Wildl Manage 2019. [DOI: 10.1002/jwmg.21743] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Weld KJ, Ames CD, Landman J, Morrissey K, Connor T, Hruby G, Allaf ME, Bhayani SB. EVALUATION OF INTRA-ABDOMINAL PRESSURES AND GAS EMBOLISM DURING LAPAROSCOPIC PARTIAL NEPHRECTOMY IN A PORCINE MODEL. J Urol 2005; 174:1457-9. [PMID: 16145470 DOI: 10.1097/01.ju.0000173010.96639.85] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE Gas embolization is a well documented complication of laparoscopic surgery. We evaluated the association of gas embolization with increased intra-abdominal pressure (IAP) in the porcine model during laparoscopic partial nephrectomy with real-time transesophageal echocardiography. MATERIALS AND METHODS Eight domestic pigs weighing 143 to 162 pounds underwent unilateral transperitoneal laparoscopic heminephrectomy with renal artery clamping with varied IAPs. The renal vein was not clamped, allowing the exposure of venous tributaries to the pneumoperitoneum. IAP was increased in 5 mm Hg increments in 4 pigs each by 1) insufflation pressure adjustment to a maximum of 30 mm Hg and 2) intermittent application of an argon beam coagulator (ABC) to the cut kidney surface. Transesophageal echocardiography was used to monitor embolism. RESULTS None of the 4 animals subjected to increased CO2 insufflation pressure (maximum 30 mm Hg) demonstrated gas embolization during partial nephrectomy. The ABC caused gas embolization during partial nephrectomy at an IAP of 30 to 50 mm Hg in 4 animals. The volume of embolized gas was 4 to 20 ml. None of the animals showed intraoperative hemodynamic compromise. CONCLUSIONS Gas embolization was not seen during laparoscopic partial nephrectomy with typical insufflation pressures. The ABC can rapidly increase IAP and cause argon embolization at IAPs greater than 30 mm Hg. Prophylactic maneuvers to prevent gas embolization, such as intra-abdominal venting or renal vein clamping, should be considered when applying the ABC.
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B'Hymer C, Connor T, Stinson D, Pretty J. Validation of an HPLC-MS/MS and wipe procedure for mitomycin C contamination. J Chromatogr Sci 2014; 53:619-24. [PMID: 25129062 DOI: 10.1093/chromsci/bmu095] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A high-performance liquid chromatography-tandem mass spectrometric (HPLC-MS/MS) method was developed for the determination of mitomycin C, an anticancer drug, from contamination on various surfaces. Mitomycin C is often used in various forms of intraperitoneal chemotherapy, and operating room healthcare worker exposure to this drug is possible. The surface testing method consisted of a wiping procedure utilizing a solution of 20/45/35 (v/v/v) of acetonitrile-isopropanol-water made 0.01 M in ammonium citrate (apparent pH 7.0). The wipe solutions were analyzed by means of HPLC-MS/MS using a reversed-phase gradient system and electrospray ionization in positive ion mode with a triple-quadrupole MS detector. Accuracy and precision of this method were demonstrated by a series of recovery studies of both spiked solutions and extracted wipes from various surfaces (stainless steel, vinyl and Formica(®)) spiked with known levels of mitomycin C. Recoveries of spiked solutions containing the analyte demonstrate mean recoveries (accuracy) ranged from 93 to 105%. Precision as measured by the relative standard deviation (% RSD) of multiple samples (n= 10) at each concentration level demonstrated values of 7.5% or less. The recoveries from spiked surfaces varied from 30 to 99%. The limit of detection for this methodology is ∼2 ng/100 cm(2) equivalent surface area, and the limit of quantitation is ∼6 ng/100 cm(2).
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