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Article ; Online: Children's exposure to indoor and outdoor black carbon and particulate matter air pollution at school in Rwanda, Central-East Africa

Egide Kalisa / Vincent Kuuire / Matthew Adams

Environmental Advances, Vol 11, Iss , Pp 100334- (2023)

2023

Abstract: Schoolchildren are a high-risk population, and their exposure to air pollution at school has been documented in high-income countries. As a result, school siting policies to protect children from air pollution have been established in those countries. ... ...

Abstract	Schoolchildren are a high-risk population, and their exposure to air pollution at school has been documented in high-income countries. As a result, school siting policies to protect children from air pollution have been established in those countries. Such policies are, however, non-existent in Africa where the air pollution problem is growing and gravely under-studied due to the lack of funding to install reliable ground-level monitoring networks and lack of air quality standards. The present study, the first of its kind to be conducted in Africa, measured Black Carbon (BC) and its related sources: fossil fuels (BCff) and biomass burning (BCbb). BC and fine particles (PM2.5) were measured simultaneously indoors and outdoors at schools over a 12-month period in Rwanda. The annual concentrations of BC in classrooms (8.15 µg/m3) and outdoor schoolyards (9.22 µg/m3) were higher than simultaneous concentrations recorded at Kigali urban background site (7.78 μg m3). The annual mean PM2.5 concentrations in classrooms and outdoor school were more than eight times higher than the World Health Organization's safe limits. The results demonstrated a more than two-fold increase in the concentrations of BCff during drop-off hours compared to off-peak hours, indicating the dominant contribution of vehicles queuing on the school premises. However, higher indoor than outdoor BC levels were recorded in some instances, 2 hours after an outdoor peak during drop-off times. The exposure peaks inside the classrooms were more pronounced for BC than PM2.5.The highest reduction of 24% and 19% were observed for BCff during weekends and school holidays in classrooms compared to regular days. No reduction was observed for BCbb concentrations. This study shows that BC and PM2.5 levels are considerably higher in schoolyards, and that further investigation of air pollution exposure at schools is warranted in Africa to promote improved drop-off/pick-up behaviors at and around school environments.
Keywords	School air pollution ; Indoor and outdoor air pollution ; Drop-off and pick up times ; Africa ; Environmental sciences ; GE1-350
Subject code	333
Language	English
Publishing date	2023-04-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Assessing the accuracy of long-term air pollution estimates produced with temporally adjusted short-term observations from unstructured sampling

Chastko, Karl / Matthew Adams

Journal of environmental management. 2019 June 15, v. 240

2019

Abstract: More commonly air pollution observations are obtained with unstructured monitoring, where either a research grade monitor or low-cost sensor is irregularly relocated throughout the study area. This unstructured data is commonly observed in community ... ...

Abstract	More commonly air pollution observations are obtained with unstructured monitoring, where either a research grade monitor or low-cost sensor is irregularly relocated throughout the study area. This unstructured data is commonly observed in community science programs. Often the objective is to apply these data to estimate a long-term concentration, which is achieved using a temporal adjustment to correct for the irregular sampling. Temporal adjustments leverage information from a stationary continuous reference monitor, in combination with short-term monitoring data, to estimate long-term pollutant concentrations. We assess the performance of temporal adjustment approaches to predict long-term pollutant concentrations using data representing unstructured sampling. A series of monitoring campaigns are simulated from air pollution data obtained from regulatory monitoring networks in four different cities (Paris, France; Taipei, Taiwan; Toronto, Canada; and Vancouver, Canada) for eight different pollutants (CO, NO, NOx, NO2, O3, PM10, PM2.5, and SO2). These simulated campaigns have randomized monitoring locations and sampling times to simulate the irregular nature of crowd sourced or mobile monitoring data. The number of consecutive samples reported, and selection of the reference monitor used to adjust observations, are varied in this study. The accuracy of estimates is assessed by comparing the estimated long-term concentration to the observed long-term concentration from the complete regulatory monitoring dataset. This study found that a common temporal adjustment applied in research performed significantly worse than other adjustments including a Naïve Temporal Approach where no data adjustment occurred. Increasing the sample size improved the accuracy of estimates, which showed decreasing benefit with increased sample lengths. Lastly, controlling for land use conditions of the reference monitor did not consistently improve the long-term estimates, which suggests that land use pairing of mobile and reference monitors does not significantly influence the predictive power of temporal adjustment approaches. Temporal adjustments can reduce the error in long-term concentration estimates of air pollution using incomplete data, but this benefit cannot be assumed across all approaches, pollutants or sampling programs.
Keywords	air pollution ; carbon monoxide ; cities ; data collection ; land use ; monitoring ; nitric oxide ; nitrogen dioxide ; ozone ; particulates ; pollutants ; sulfur dioxide ; Canada ; France ; Taiwan
Language	English
Dates of publication	2019-0615
Size	p. 249-258.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	184882-3
ISSN	1095-8630 ; 0301-4797
ISSN (online)	1095-8630
ISSN	0301-4797
DOI	10.1016/j.jenvman.2019.03.108
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Urban forest fragments as unexpected sanctuaries for the rare endemic ghost butterfly from the Atlantic forest

Antonio C. deAndrade / William Medeiros / Matthew Adams

Ecology and Evolution, Vol 9, Iss 18, Pp 10767-

2019 Volume 10776

Abstract: Abstract Anthropogenic land expansion, particularly urbanization, is pervasive, dramatically modifies the environment and is a major threat to wildlife with its associated environmental stressors. Urban remnant vegetation can help mitigate these impacts ... ...

Abstract	Abstract Anthropogenic land expansion, particularly urbanization, is pervasive, dramatically modifies the environment and is a major threat to wildlife with its associated environmental stressors. Urban remnant vegetation can help mitigate these impacts and could be vital for species unable to survive in harsh urban environments. Although resembling nonurban habitats, urban vegetation remnants are subject to additional environmental stresses. Here, we evaluate the occurrence and density of the endemic ghost butterfly (Morpho epistrophus nikolajewna) that was once common, in the highly fragmented Atlantic forest of NE Brazil. We tested whether this butterfly would be found at lower densities in urban forest fragments of contrasting sizes as opposed to rural ones, given the number of environmental stressors found in urban areas. We surveyed 14 forest fragments (range 2.8 to over 3,000 ha) of semideciduous Atlantic forest in rural and urban locations using transect based distance sampling. The ghost butterflies showed strong seasonality; flying only from April to June. They were only identified in an urban fragment (515 ha), with an estimate of 720 individuals and a density 1.4 ind/ha. All forest fragments had experienced some level of logging in the past, which might have had an effect in the butterfly population. Nevertheless, rural forest fragments were subject to increased particulate matter concentrations, associated to biomass burning that we suggest might have had a more influential role driving the collapse of rural populations. Our findings show the importance of urban forest remnants to sustain population of this endangered species.
Keywords	agricultural practices ; Allee effect ; extinction ; forest‐dependent species ; insect communities ; pollution ; Ecology ; QH540-549.5
Language	English
Publishing date	2019-09-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
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Article ; Online: Wildlife Response to Wildfire in a Northern New York Jack Pine Barrens

Hannah Cave / Matthew Adams / Tristan Jaeger / Taylor Peet / Lloyd Staats / Danielle Garneau / Mark Lesser

Forests, Vol 12, Iss 676, p

2021 Volume 676

Abstract: Natural disturbances are an integral part of forested ecosystem function and successional pathways. In many forested ecosystems, wildfires are critical to shaping composition and structure, which, in turn, has major implications for wildlife usage and ... ...

Abstract	Natural disturbances are an integral part of forested ecosystem function and successional pathways. In many forested ecosystems, wildfires are critical to shaping composition and structure, which, in turn, has major implications for wildlife usage and behavior. In July 2018, a wildfire burned 225 ha of the Altona Flat Rock pine barrens in northern New York. This event presented the opportunity to study how wildlife respond to the immediate effects of disturbance in this unique habitat but also how that response would change through time as regeneration progressed. Game cameras were deployed from September 2018 to September 2020 at two reference (unburned) and two disturbed (burned) sites within the pine barrens. We analyzed total and seasonal occurrences, to determine how usage differed between disturbed and reference conditions, and with time since disturbance. Additionally, for coyote ( Canis latrans , Say), white-tailed deer ( Odocoileus virginianus , Zimmermann), and snowshoe hare ( Lepus americanus , Erxleben), we evaluated daily activity patterns and overlap to determine how predator–prey relationships differed between conditions, and with time since disturbance. Over 730 days, a total of 1048 wildlife occurrences were captured across 23 wildlife species. Fifty-seven percent of all occurrences were at reference sites with over 100 more occurrences than at disturbed sites; however, differences were most pronounced immediately following the fire and overall occurrences have grown more similar between the sites over time. Specifically, deer and hare were found more often at reference sites immediately following the fire, but shifted to using both conditions equally by the first growing season. Habitat overlap among sympatric prey (deer, hare) can be explained by understory regeneration increasing foraging opportunities and concealment cover in the disturbed condition, while predators (coyotes) tracked prey availability regardless of the habitat condition. This study provides wildlife management guidance on ...
Keywords	disturbance ; ecosystem recovery ; succession ; regeneration ; game cameras ; predator–prey ; Plant ecology ; QK900-989
Subject code	590 ; 333
Language	English
Publishing date	2021-05-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
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Article ; Online: Regulation of canonical Wnt signalling by the ciliopathy protein MKS1 and the E2 ubiquitin-conjugating enzyme UBE2E1

Katarzyna Szymanska / Karsten Boldt / Clare V Logan / Matthew Adams / Philip A Robinson / Marius Ueffing / Elton Zeqiraj / Gabrielle Wheway / Colin A Johnson

eLife, Vol

2022 Volume 11

Abstract: Primary ciliary defects cause a group of developmental conditions known as ciliopathies. Here, we provide mechanistic insight into ciliary ubiquitin processing in cells and for mouse model lacking the ciliary protein Mks1. In vivo loss of Mks1 sensitises ...

Abstract	Primary ciliary defects cause a group of developmental conditions known as ciliopathies. Here, we provide mechanistic insight into ciliary ubiquitin processing in cells and for mouse model lacking the ciliary protein Mks1. In vivo loss of Mks1 sensitises cells to proteasomal disruption, leading to abnormal accumulation of ubiquitinated proteins. We identified UBE2E1, an E2 ubiquitin-conjugating enzyme that polyubiquitinates β-catenin, and RNF34, an E3 ligase, as novel interactants of MKS1. UBE2E1 and MKS1 colocalised, and loss of UBE2E1 recapitulates the ciliary and Wnt signalling phenotypes observed during loss of MKS1. Levels of UBE2E1 and MKS1 are co-dependent and UBE2E1 mediates both regulatory and degradative ubiquitination of MKS1. We demonstrate that processing of phosphorylated β-catenin occurs at the ciliary base through the functional interaction between UBE2E1 and MKS1. These observations suggest that correct β-catenin levels are tightly regulated at the primary cilium by a ciliary-specific E2 (UBE2E1) and a regulatory substrate-adaptor (MKS1).
Keywords	MKS1 ; primary cilia ; Wnt signalling ; beta-catenin ; UBE2E1 ; ciliopathies ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
Subject code	570
Language	English
Publishing date	2022-02-01T00:00:00Z
Publisher	eLife Sciences Publications Ltd
Document type	Article ; Online
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Article ; Online: An In Silico Analysis of Malaria Pre-Erythrocytic-Stage Antigens Interpreting Worldwide Genetic Data to Suggest Vaccine Candidate Variants and Epitopes

Amed Ouattara / Ankit Dwivedi / Matthew Adams / Amadou Niangaly / Matthew B. Laurens / Myaing M. Nyunt / Christopher V. Plowe / Abdoulaye Djimde / Shannon Takala-Harrison / Joana C. Silva

Microorganisms, Vol 10, Iss 1090, p

2022 Volume 1090

Abstract: Failure to account for genetic diversity of antigens during vaccine design may lead to vaccine escape. To evaluate the vaccine escape potential of antigens used in vaccines currently in development or clinical testing, we surveyed the genetic diversity, ... ...

Abstract	Failure to account for genetic diversity of antigens during vaccine design may lead to vaccine escape. To evaluate the vaccine escape potential of antigens used in vaccines currently in development or clinical testing, we surveyed the genetic diversity, measured population differentiation, and performed in silico prediction and analysis of T-cell epitopes of ten such Plasmodium falciparum pre-erythrocytic-stage antigens using whole-genome sequence data from 1010 field isolates. Of these, 699 were collected in Africa (Burkina Faso, Cameroon, Guinea, Kenya, Malawi, Mali, and Tanzania), 69 in South America (Brazil, Colombia, French Guiana, and Peru), 59 in Oceania (Papua New Guinea), and 183 in Asia (Cambodia, Myanmar, and Thailand). Antigens surveyed include cell-traversal protein for ookinetes and sporozoites, circumsporozoite protein, liver-stage antigens 1 and 3, sporozoite surface proteins P36 and P52, sporozoite asparagine-rich protein-1, sporozoite microneme protein essential for cell traversal-2, and upregulated-in-infectious-sporozoite 3 and 4 proteins. The analyses showed that a limited number of these protein variants, when combined, would be representative of worldwide parasite populations. Moreover, predicted T-cell epitopes were identified that could be further explored for immunogenicity and protective efficacy. Findings can inform the rational design of a multivalent malaria vaccine.
Keywords	plasmodium ; liver-stage ; antigen ; polymorphism ; variants ; global diversity ; Biology (General) ; QH301-705.5
Subject code	616
Language	English
Publishing date	2022-05-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
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Article ; Online: Overprescription of antibiotics in patients with community-acquired pneumonia in the intensive care unit

Rorak Hooten / Jose Luis Marquez / Kady Goldlist / Rafael Urcis / Matthew Adams / Kathryn Matthias / David Nix / Mayar Al Mohajer

Avicenna Journal of Medicine, Vol 9, Iss 03, Pp 107-

2019 Volume 110

Abstract: Purpose: We aimed to assess factors associated with therapy failure in patients with community-acquired pneumonia in the intensive care unit (ICU). Methods: Electronic charts of patients with International Classification of Diseases, Ninth Revision, ... ...

Abstract	Purpose: We aimed to assess factors associated with therapy failure in patients with community-acquired pneumonia in the intensive care unit (ICU). Methods: Electronic charts of patients with International Classification of Diseases, Ninth Revision, codes of pneumonia who were admitted to the ICU at a tertiary academic medical center in Southern Arizona were reviewed. Results: Antipseudomonal coverage and anti-methicillin-resistant Staphylococcus aureus (MRSA) coverage were often prescribed (58.4% and 54.1%, respectively). Antipseudomonal coverage was rarely necessary as pseudomonal pneumonia was found in only one case (0.9%). Antipseudomonal and anti-MRSA coverage was not associated with improved outcomes. Conclusion: Overprescription of antibiotics in this population remains a significant problem. More work is needed to further limit unnecessary antibiotic use.
Keywords	antimicrobials ; incentive care unit ; outcomes ; overuse ; respiratory infection ; Medicine ; R
Language	English
Publishing date	2019-07-01T00:00:00Z
Publisher	Thieme Medical and Scientific Publishers Pvt. Ltd.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Artemether-lumefantrine efficacy among adults on antiretroviral therapy in Malawi

Wongani Nyangulu / Randy G. Mungwira / Titus H. Divala / Nginache Nampota-Nkomba / Osward M. Nyirenda / Andrea G. Buchwald / Jernelle Miller / Dominique E. Earland / Matthew Adams / Christopher V. Plowe / Terrie E. Taylor / Jane E. Mallewa / Joep J. van Oosterhout / Sunil Parikh / Matthew B. Laurens / Miriam K. Laufer / the TSCQ Study Team

Malaria Journal, Vol 22, Iss 1, Pp 1-

2023 Volume 8

Abstract: Abstract Background When people with human immunodeficiency virus (HIV) infection (PWH) develop malaria, they are at risk of poor anti-malarial treatment efficacy resulting from impairment in the immune response and/or drug-drug interactions that alter ... ...

Abstract	Abstract Background When people with human immunodeficiency virus (HIV) infection (PWH) develop malaria, they are at risk of poor anti-malarial treatment efficacy resulting from impairment in the immune response and/or drug-drug interactions that alter anti-malarial metabolism. The therapeutic efficacy of artemether-lumefantrine was evaluated in a cohort of PWH on antiretroviral therapy (ART) and included measurement of day 7 lumefantrine levels in a subset to evaluate for associations between lumefantrine exposure and treatment response. Methods Adults living with HIV (≥ 18 years), on ART for ≥ 6 months with undetectable HIV RNA viral load and CD4 count ≥ 250/mm3 were randomized to daily trimethoprim-sulfamethoxazole (TS), weekly chloroquine (CQ) or no prophylaxis. After diagnosis of uncomplicated Plasmodium falciparum malaria, a therapeutic efficacy monitoring was conducted with PCR-correction according to WHO guidelines. The plasma lumefantrine levels on day 7 in 100 episodes of uncomplicated malaria was measured. A frailty proportional hazards model with random effects models to account for clustering examined the relationship between participant characteristics and malaria treatment failure within 28 days. Pearson’s Chi—squared test was used to compare lumefantrine concentrations among patients with treatment failure and adequate clinical and parasitological response (ACPR). Results 411 malaria episodes were observed among 186 participants over 5 years. The unadjusted ACPR rate was 81% (95% CI 77–86). However, after PCR correction to exclude new infections, ACPR rate was 94% (95% CI 92–97). Increasing age and living in Ndirande were associated with decreased hazard of treatment failure. In this population of adults with HIV on ART, 54% (51/94) had levels below a previously defined optimal day 7 lumefantrine level of 200 ng/ml. This occurred more commonly among participants who were receiving an efavirenz-based ART compared to other ART regimens (OR 5.09 [95% CI 1.52–7.9]). Participants who experienced ...
Keywords	Arctic medicine. Tropical medicine ; RC955-962 ; Infectious and parasitic diseases ; RC109-216
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
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Article ; Online: Optimization of parasite DNA enrichment approaches to generate whole genome sequencing data for Plasmodium falciparum from low parasitaemia samples

Zalak Shah / Matthew Adams / Kara A. Moser / Biraj Shrestha / Emily M. Stucke / Miriam K. Laufer / David Serre / Joana C. Silva / Shannon Takala-Harrison

Malaria Journal, Vol 19, Iss 1, Pp 1-

2020 Volume 10

Abstract: Abstract Background Owing to the large amount of host DNA in clinical samples, generation of high-quality Plasmodium falciparum whole genome sequencing (WGS) data requires enrichment for parasite DNA. Enrichment is often achieved by leukocyte depletion ... ...

Abstract	Abstract Background Owing to the large amount of host DNA in clinical samples, generation of high-quality Plasmodium falciparum whole genome sequencing (WGS) data requires enrichment for parasite DNA. Enrichment is often achieved by leukocyte depletion of infected blood prior to storage. However, leukocyte depletion is difficult in low-resource settings and limits analysis to prospectively-collected samples. As a result, approaches such as selective whole genome amplification (sWGA) are being used to enrich for parasite DNA. However, sWGA has had limited success in generating reliable sequencing data from low parasitaemia samples. In this study, enzymatic digestion with MspJI prior to sWGA and whole genome sequencing was evaluated to determine whether this approach improved genome coverage compared to sWGA alone. The potential of sWGA to cause amplification bias in polyclonal infections was also examined. Methods DNA extracted from laboratory-created dried blood spots was treated with a modification-dependent restriction endonuclease, MspJI, and filtered via vacuum filtration. Samples were then selectively amplified using a previously reported sWGA protocol and subjected to WGS. Genome coverage statistics were compared between the optimized sWGA approach and the previously reported sWGA approach performed in parallel. Differential amplification by sWGA was assessed by comparing WGS data generated from lab-created mixtures of parasite isolates, from the same geographical region, generated with or without sWGA. Results MspJI digestion did not enrich for parasite DNA. Samples that underwent vacuum filtration (without MspJI digestion) prior to sWGA had the highest parasite DNA concentration and displayed greater genome coverage compared to MspJI + sWGA and sWGA alone, particularly for low parasitaemia samples. The optimized sWGA (filtration + sWGA) approach was successfully used to generate WGS data from 218 non-leukocyte depleted field samples from Malawi. Sequences from lab-created mixtures of parasites did not ...
Keywords	Plasmodium falciparum ; Malaria ; Whole genome sequencing ; Selective whole genome amplification ; Vacuum filtration ; Arctic medicine. Tropical medicine ; RC955-962 ; Infectious and parasitic diseases ; RC109-216
Subject code	572
Language	English
Publishing date	2020-03-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Development of a Transformation Method for Metschnikowia borealis and other CUG-Serine Yeasts

Zachary B. Gordon / Maximillian P.M. Soltysiak / Christopher Leichthammer / Jasmine A. Therrien / Rebecca S. Meaney / Carolyn Lauzon / Matthew Adams / Dong Kyung Lee / Preetam Janakirama / Marc-André Lachance / Bogumil J. Karas

Genes, Vol 10, Iss 2, p

2019 Volume 78

Abstract: Yeasts belonging to the Metschnikowia genus are particularly interesting for the unusual formation of only two needle-shaped ascospores during their mating cycle. Presently, the meiotic process that can lead to only two spores from a diploid zygote is ... ...

Abstract	Yeasts belonging to the Metschnikowia genus are particularly interesting for the unusual formation of only two needle-shaped ascospores during their mating cycle. Presently, the meiotic process that can lead to only two spores from a diploid zygote is poorly understood. The expression of fluorescent nuclear proteins should allow the meiotic process to be visualized in vivo; however, no large-spored species of Metschnikowia has ever been transformed. Accordingly, we aimed to develop a transformation method for Metschnikowia borealis , a particularly large-spored species of Metschnikowia , with the goal of enabling the genetic manipulations required to study biological processes in detail. Genetic analyses confirmed that M. borealis , and many other Metschnikowia species, are CUG-Ser yeasts. Codon-optimized selectable markers lacking CUG codons were used to successfully transform M. borealis by electroporation and lithium acetate, and transformants appeared to be the result of random integration. Mating experiments confirmed that transformed-strains were capable of generating large asci and undergoing recombination. Finally, random integration was used to transform an additional 21 yeast strains, and all attempts successfully generated transformants. The results provide a simple method to transform many yeasts from an array of different clades and can be used to study or develop many species for various applications.
Keywords	genome engineering ; synthetic biology ; yeasts ; Metschnikowia ; genetic tools ; DNA delivery ; CUG-Ser ; Genetics ; QH426-470
Subject code	580
Language	English
Publishing date	2019-01-01T00:00:00Z
Publisher	MDPI AG
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