Bias toward codons that match the tRNA pool is robustly associated with high gene expression in diverse organisms, suggesting that codon optimization could be used in a reverse ecology framework to identify ecologically relevant genes. This study finds that this is indeed the case for 329 species of budding yeasts, suggesting that codon optimization harbors information about the metabolic ecology of microbial eukaryotes.

Species distribution models aim at linking species spatial distribution to the environment. They can highlight the ecological preferences of species and thus predict which species are likely to be present in a given environment. These models are used in many scenarios such as conservation plans or monitoring of invasive species. The choice of model and the environmental data used have a strong impact on the model’s ability to capture important information. Specificaly, state-of-the-art models generally use a punctual environment and do not take into account the environmental context or neighbourhood. Here we present a species distribution model based on a convolutional neural network that allows the use of large scale data such as spatialized environmental data including the environmental neighbourhood in addition to the punctual environment. We highlight the interests and limitations of this method as well as the importance of the environmental context in learning about species distributions.

Background

To investigate the effects of short-term exposure to sulfur dioxide (SO₂) and carbon monoxide (CO) in the central and southern China areas on ischemic heart disease (IHD) and non-accidental deaths.

Background

While lactation is a physiological process requiring high energy demand to fulfill the nutrient requirements of the mother and the breastfeeding child, many factors affecting maternal nutrient intake can lead to nutritional deficits. Previous studies in Ethiopia have reported the prevalence of maternal and child undernutrition and related complications. However, qualitative studies exploring potential barriers to utilizing available nutrition interventions are limited. This study, therefore, sought to qualitatively explore barriers hindering the uptake of nutrition services among lactating mothers from rural communities in Tigray, northern Ethiopia.

Background

The influence of the safety and security of environments on early childhood development (ECD) has been under-explored. Although housing might be linked to ECD by affecting a child’s health and a parent’s ability to provide adequate care, only a few studies have examined this factor. We hypothesized that housing environment is associated with ECD in sub-Saharan Africa (SSA).

In a cross-sectional analysis of nationally representative survey data from 20 countries, Yaqing Gao and colleagues investigate associations between housing environment and cognitive and social development in children.

Introduction

HIV self-testing (HIV-ST) is an effective means of improving HIV testing rates. Low- and middle-income countries (LMIC) are taking steps to include HIV-ST into their national HIV/AIDS programs but very few reviews have focused on implementation in LMIC. We performed a scoping review to describe and synthesize existing literature on implementation outcomes of HIV-ST in LMIC.

Karyotype, including chromosome number and morphology, has been observed even before DNA was identified as the primary genetic material. Although chromosomal changes are thought to play an important role in speciation, we have not reached a consensus on how rapidly karyotype can evolve and whether a particular karyotype is favored. This can be attributed partly to the lack of good probabilistic models for karyotype evolution. This contrasts with DNA sequence evolution, for which many established probabilistic models are available. Such probabilistic models have contributed to the understanding of rates and driving forces of DNA sequence evolution. Here, we built a probabilistic model including both chromosome and arm numbers. Using this model, we could demonstrate differences in the tempo and mode in karyotype evolution between two fish taxonomic groups and possible roles of karyotype in speciation and extinction. The use of our model in diverse taxa will lead to a better understanding of the evolutionary trends and functional roles of karyotypes.

Aedes aegypti and Aedes albopictus are species of mosquitoes responsible for the transmission of several arboviruses that cause infections worldwide. However, there are still no effective and safe vaccines or medications to prevent or treat arboviruses transmitted by these vectors, except for yellow fever. Moreover, current methodologies for monitoring and controlling A. aegypti and A. albopictus are not fully effective, as evidenced by the increasing cases of the arbovirus transmitted by these mosquitoes or have incompatible costs with the socioeconomic conditions of a large number of people. Thus, the traps tested in this study can be used as more effective and economical tools for monitoring A. aegypti and A. albopictus, since they are made with low cost material and they showed high efficiency in the capture of eggs, evidenced by the high values of ovitraps positive index and eggs density index, besides that one of the models captured Aedes spp. adults in both regions where they were tested. Therefore, the traps have potential for reducing Aedes spp. eggs and adults in the environment and sensibility for determining the local infestation index, which can be reconciled with official government strategies for more accurate vector monitoring actions.

Background

Unsafe disposal of children’s stool makes children susceptible to fecal-oral diseases and children remain vulnerable till the stools of all children are disposed of safely. There is a paucity of data on spatial distribution and factors associated with unsafe child stool disposal in Ethiopia. Previous estimates, however, do not include information regarding individual and community-level factors associated with unsafe child stool disposal. Hence, the current study aimed (i) to explore the spatial distribution and (ii) to identify factors associated with unsafe child stool disposal in Ethiopia.

Worldwide, ecosystems are collapsing or in danger of collapse, but the precise causes of these collapses are often unknown. Observational and experimental evidence shows that all ecosystems are characterized by strong interactions between and among species, and that these webs of interactions can be important contributors to the preservation of ecosystem diversity. But many of the interactions–such as those involving pathogenic microorganisms and the chemical defenses that are mounted by their prey–are not easily identified and analyzed in ecosystems that may have hundreds or thousands of species. Here we use our equal-area-annulus analytical method to examine census data from over three million trees in forest plots from around the world. We show how the method can be used to flag pairs and groups of species that exhibit unusual levels of interaction and that are likely on further investigation to yield information about their causative mechanisms. We give a detailed example showing how some of these interactions can be traced to defense mechanisms that are possessed by one of the tree species. We explore how our method can be used to identify the between-species interactions that play the largest roles in the maintenance of ecosystems and their diversity.

The mysterious ’neuston’ ecosystem at the ocean’s surface includes keystone organisms like the golden seaweed Sargassum that makes up the Sargasso Sea, floating barnacles, snails, nudibranchs, and cnidarians; this Essay explores threats to its wellbeing and the importance of further research.

Background

Internal hospital crises and disasters (IHCDs) are events that disrupt the routine functioning of a hospital while threatening the well-being of patients and staff. IHCDs may cause hospital closure, evacuations of patients and loss of healthcare capacity. The consequences may be ruinous for local communities. Although IHCDs occur with regularity, information on the frequency and types of these events is scarcely published in the medical literature. However, gray literature and popular media reports are widely available. We therefore conducted a scoping review of these literature sources to identify and characterize the IHCDs that occurred in Dutch hospitals from 2000 to 2020. The aim is to develop a systematic understanding of the frequency of the various types of IHCDs occurring in a prosperous nation such as the Netherlands.

Background

Clean water is an essential part of human healthy life and wellbeing. More recently, rapid population growth, high illiteracy rate, lack of sustainable development, and climate change; faces a global challenge in developing countries. The discontinuity of drinking water supply forces households either to use unsafe water storage materials or to use water from unsafe sources. The present study aimed to identify the determinants of water source types, use, quality of water, and sanitation perception of physical parameters among urban households in North-West Ethiopia.

This Essay hypothesizes that when human presence protects wild animals from their natural predators, this predator shield decouples commonly associated traits, resulting in a new range of coping phenotypes, dubbed “preactive.”

Background

Paracoccidioidomycosis (PCM) is a systemic and endemic fungal infection in Latin American, mainly in Brazil. The majority of PCM cases occur in large areas in Brazil, comprising the South, Southeast and Midwest regions, with the latter demonstrating a higher incidence of the species Paracoccidioides lutzii.

Paracoccidioides spp. complex and P. lutzii are etiological agents of paracoccidioidomycosis (PCM), one of the most important systemic mycosis of Latin America. This study aimed to describe the molecular epidemiology associated with clinical and serological data of Paracoccidiodes spp. in the Mato Grosso do Sul, located in the Midwest region, Brazil. Thus, for the first time in this state, the clinical Paracoccidioides species were molecularly identified. Previous findings have frequently been misinterpreted as proving that P. lutzii predominates in this region. In fact, we observed that this state differs from others in the Midwest, presenting a higher proportion of PCM cases due to P. brasiliensis sensu stricto (S1). In addition, we described the first report of P. restrepiensis (PS3) occurrence in the Brazilian Midwest region. Then, we presented an update on the occurrence of Paracoccidioides species in the Midwest region from Brazil. On the other hand, our results do not demonstrate clinical and epidemiological differences between Paracoccidioides spp. Nevertheless, this study reinforces that other researches should be carried out in order to evaluate an association of clinical manifestations and epidemiology with Paracoccidioides species.

We expand the utility of Natural Language Processing (NLP), backtracking through metabarcodes, utilizing papers that may not mention our subject of interest, C. neoformans, in a departure from usual text analysis methods. We confirm that C. neoformans is associated with decomposing wood which is reinforced by the inferred literature studied here on C. neoformans and its close congeneric relatives. This work demonstrates the potential utility of pairing NLP with single-locus metagenetic data for the study of Neglected Tropical Diseases. While the results of this article are largely confirmatory, we present a novel method to study the ecological niches of rare pathogens that leverages the immense amount of data available to researchers in the NCBI Sequence Read Archive (SRA) combined with a text-mining analysis based on Natural Language Processing. We demonstrate that text processing, noun identification, and verb identification can play an important role in analyzing a large corpus of documents together with metagenetic data. Forging this connection requires access to all of the available ecological 18S ribosomal RNA and Internal Transcribed Spacer NCBI SRA datasets. These datasets use metabarcoding to query taxonomic diversity in eukaryotic organisms, and in the case of the Internal Transcribed Spacer, they specifically target Fungi. The presence of specific species is inferred when diagnostic 18S or ITS gene region sequences are found in the SRA data. We searched for C. neoformans in all 18S and ITS datasets available and gathered all associated journal articles that either cite the SRA data accessions or are cited in the SRA data accessions. Published metagenetic data often have associated metadata including: latitude and longitude, temperature, and other physical characteristics describing the conditions in which the metagenetic sample was collected. These metadata are not always presented in consistent formats, so harmonizing study methods may be needed to appropriately compare metagenetic data as commonly required in metanalysis studies. We present an analysis which takes as input articles associated with SRA datasets that were found to contain evidence of C. neoformans. We apply NLP methods to this corpus of articles to describe the niche of C. neoformans. Our results reinforce the current understanding of C. neoformans’s niche, indicating the pertinence of employing an NLP analysis to identify the niche of an organism. This approach could further the description of virtually any other organism that routinely appears in metagenetic surveys, especially pathogens, whose ecological niches are unknown or poorly understood.

Nanopore technology was used for sequencing CHIKV complete genomes. Phylogenetic and epidemiological approaches were used to explore the recent spatio-temporal evolution and spread of the CHIKV-ECSA genotype in Midwest Brazil as well as in the Americas.

Epidemiological data revealed a reduction in the number of reported cases over 2018–2020, likely as a consequence of a gradual accumulation of herd-immunity. Phylogeographic reconstructions revealed that at least two independent introductions of the ECSA lineage occurred in MT from a dispersion event originating in the northeastern region and suggest that the midwestern Brazilian region appears to have acted as a source of virus transmission towards Paraguay, a bordering South American country.

Our results show a complex dynamic of transmission between epidemic seasons and suggest a possible role of Brazil as a source for international dispersion of the CHIKV-ECSA genotype to other countries in the Americas.

Since its introduction into Brazil in 2014, chikungunya virus (CHIKV) has presented sustained transmission, although much is unknown about its circulation in the midwestern states. Here, using a combined strategy of a mobile sequencing mission through this region, with genomic and epidemiological analysis we generated 24 novel partial and near complete CHIKV genome sequences by means of portable nanopore sequencing of chikungunya virus isolates obtained directly from clinical samples. Our findings reinforce that continued genomic surveillance strategies are needed to assist in the monitoring and understanding of arbovirus epidemics, which might help to attenuate public health impact of infectious diseases.

Background

Current intensive care unit (ICU) sedation guidelines recommend strategies using non-benzodiazepine sedatives. This survey was undertaken to explore inhaled ICU sedation practice in France.

Globally, more than 1 billion residents live in urban slums, where inadequate sanitation increases the spread of pathogens and their animal hosts. Leptospirosis is a globally distributed bacterial disease, and in urban areas the bacteria is spread by brown rats. Humans become infected upon exposure to water or soil/mud that was contaminated with the urine of infected rats. In four urban slums in the city of Salvador, Brazil, we used a range of individual, socioeconomic, and environmental variables to understand how they influence to one another and define o leptospirosis exposure in residents. Poverty and sanitation influenced the degree to which residents were exposed to sewer water and mud. Further, we found that while residents tried to improve the physical environment near their household, living in an area with poor sanitation mean that their infection risk remained high. This work highlight the importance of socioeconomic and environmental factors in determining disease risk, and suggests that governmental interventions should focus on improving sanitation changes in the poorest parts of the community.

Many motile cells navigate in complex environments along concentration gradients of signaling molecules. This chemotaxis has been studied extensively both experimentally and theoretically, yet mostly for idealized conditions of perfect chemical gradients. But under physiological conditions, concentration fields are subject to distortions, e.g., by turbulent flows in the ocean. Pioneering experiments suggest that in species with external fertilization, chemotaxis of sperm cells towards the egg may even work better at an optimal flow strength compared to conditions of still water. Yet to date, the mechanistic cause for this optimum is not known. We present a general theory of chemotactic navigation in external flow. We characterize how external flow distorts concentration fields into long filaments, and show how chemotaxing cells can subsequently ‘surf’ along these filaments towards a chemoattractant source. Stronger flows make concentration filaments longer, but also thinner; together, these two counter-acting effects set an optimal flow strength. Beyond fertilization of marine invertebrates, we believe that ‘surfing along concentration filaments’ could be a more general paradigm, relevant also for the ecology of marine bacteria feeding on organic marine snow in the ocean, or chemotaxis inside multi-cellular organisms with internal flows.

Background

Demand for family planning met/satisfied with modern contraceptive methods (mDFPS) has been proposed to track progress in Family Planning (FP) programs for Sustainable Development Goals. This study measured mDFPS among married women of reproductive age (MWRA) in Kenya to identify which groups were not being reached by FP programs.

Objective

To examine whether proximity and density of public open spaces, public parks, street connectivity, and serious and violent crimes were associated with Body Mass Index (BMI) and Waist Circumference (WC) within and across levels of urbanicity, sex and socioeconomic status (SES) in Jamaica, a small island developing state (SIDS).

CRISPR-based gene drive is an emerging genetic engineering technology that enables engineered genetic variants, which are usually designed to be harmful to the organism carrying them, to be spread rapidly in populations. Although this technology is promising for controlling disease vectors and invasive species, there is a considerable risk that a gene drive could unintentionally spillover from the target population, where it was deployed, to non-target populations. We develop mathematical models of gene-drive dynamics that incorporate migration between target and non-target populations to investigate the possibility of effectively applying a gene drive in the target population while limiting its spillover to non-target populations (‘differential targeting’). We observe that the feasibility of differential targeting depends on the gene-drive design specification, as well as on the migration rates between the populations. Even when differential targeting is possible, as migration increases, the possibility for differential targeting disappears. We find that differential targeting can be effective for low migration rates, and that it is sensitive to the design of the gene drive under high migration rates. We suggest that differential targeting could be used, in combination with other mitigation measures, as an additional safeguard to limit gene drive spillovers.

Background

Crimean-Congo haemorrhagic fever (CCHF) is a widespread tick-borne viral disease caused by the Crimean-Congo haemorrhagic fever virus (CCHFV). CCHFV has been implicated in severe viral haemorrhagic fever outbreaks. During the summer of 2016, the first two cases with genotype III (Africa 3) were reported in Spain. The first objective of our study was to determine the presence of CCHFV among patients with febrile illness during the spring and summer periods in 2017 and 2018. Finally, we perform a phylogenetic analysis to determine the genotype of the virus.

Crimean Congo hemorrhagic fever (CCHF) is a widespread tick-borne viral disease caused by a Nairovirus of the Bunyaviridae family. CCHFV has been considered to be one of the eight priority emergent pathogens for the last 3 years by the World Health Organization (WHO), requiring urgent attention in Research, Development and Innovation (R&D&I) because of its epidemic potential in the near future In this study, we describe a new circulation of European genotype V CCHFV in Spain. Moreover, this study suggests that CCHFV is an identifiable cause of febrile illness of unknown origin in Spain. Thus, CCHF could be suspected in patients with fever, liver damage, and/or haemorrhagic disorders, particularly in people with risk activities who present in the spring or summer.

Humans and many other hosts establish a diverse community of beneficial microbes anew each generation, but what determines the success of the assembly process remains poorly understood. This study develops ecological theory that reveals the rules underlying the assembly of such host-associated microbiota.

Background

Gut colonization by ESBL-producing Enterobacteriaceae (ESBL-PE) is widespread and is promoted by antibiotic exposure. Higher fecal abundance of ESBL-PE promotes the dissemination of the bacteria in the environment and is associated with increased risk of infection. Ceftriaxone and temocillin are commonly used antibiotics with a different activity on gut flora. Their impact on fecal abundance of ESBL-producing Enterobacteriaceae has not been studied. The objective of this study was to compare the propensity of ceftriaxone and temocillin to modify the abundance of ESBL-producing Escherichia coli in feces of colonized mice.

We have inherited our genomes from our parents, who, in turn, inherited their genomes from their parents, etc. Hence, a comparison between genomes of present day individuals reveals genetic population structure due to the varying levels of genetic relatedness among the individuals. We have utilized over 18,000 Finnish samples to characterize the fine-scale genetic population structure in Finland starting from a binary East-West division and ending up with 10 Finnish source populations. Furthermore, we have applied the resulting ancestry information to generate records of how the population structure has evolved each year between 1923 and 1987 in 12 geographical regions of Finland. For example, the war-related evacuation of Karelians from Southeast Finland to other parts of the country show up as a clear, sudden increase in the Evacuated ancestry elsewhere in Finland between 1939 and 1945. Additionally, different regions of Finland show very different levels of genetic mixing in 1900s, from little mixed regions like Ostrobothnia to highly mixed regions like Southwestern Finland. To distribute the results among general public, we provide an interactive website for browsing the municipality and region-level genetic ancestry profiles at https://geneviz.aalto.fi/genetic_ancestry_finland/

Background

A diverse and abundant gut microbiome can improve cancer patients’ treatment response; however, the effect of pelvic chemoradiotherapy (CRT) on gut diversity and composition is unclear. The purpose of this prospective study was to identify changes in the diversity and composition of the gut microbiome during and after pelvic CRT.

Many ecosystems are exposed to rapidly changing environmental conditions, from global warming to overuse of antibiotics in medicine and agriculture. Therefore, there is great interest in elucidating the factors that affect the ability of ecosystems to adapt to these changes. While many such factors have been recently investigated, the effect of interactions within a community on its ability to adapt remains largely unexplored. In this work, we focus on the effect of positive interactions, in the form of cooperation between individual or different species, on the ability of communities to adapt to new environments. Using simulations and theoretical analysis, we find that positive interactions significantly reduce the probability of survival of cooperative communities in changing environments, elevating the risk of populations’ extinction. Furthermore, we suggest that the need for an adaptable solution of cooperation could have played a part in the circumstances leading to the transition between unicellular and multicellular life.

Background

Snake venom composition is dictated by various ecological and environmental factors, and can exhibit dramatic variation across geographically disparate populations of the same species. This molecular diversity can undermine the efficacy of snakebite treatments, as antivenoms produced against venom from one population may fail to neutralise others. India is the world’s snakebite hotspot, with 58,000 fatalities and 140,000 morbidities occurring annually. Spectacled cobra (Naja naja) and Russell’s viper (Daboia russelii) are known to cause the majority of these envenomations, in part due to their near country-wide distributions. However, the impact of differing ecologies and environment on their venom compositions has not been comprehensively studied.

Annually, India is burdened by the highest number of snake envenomations across the globe, with over 58,000 fatalities and three times the number of morbidities, predominantly affecting the rural agrarian communities. The spectacled cobra (Naja naja) and Russell’s viper (Daboia russelii) are responsible for the vast majority of envenomations in the country, in part, due to their near country-wide distributions. In this study, we unveil the astounding differences in venom composition of N. naja from six different biogeographical zones across the country (>6000 km). We provide a comprehensive account of their disparate venom proteomic profiles, biochemical and pharmacological effects, and the associated potencies. Our study uncovers alarming differences in the efficacy of the marketed polyvalent antivenoms in neutralising these venoms, thereby, emphasising the pressing need to develop dose-efficacious and pan-India effective antivenoms for the treatment of snakebites in the country. This study also highlights the significant influence of ecology and diverse environments on the venom variability, insinuating the necessity for innovating cost-effective and pan-India efficacious solutions to safeguard the lives, limbs and livelihoods of India’s two hundred thousand annual snakebite victims.

Background

Household environment condition is an important predictor of morbidity of the household members. Without forming a healthy household environment, creating a healthy population is not possible. In this background, this study assesses the impact of change in household environment conditions on morbidity.

The mousetrap-like mandibles of trap-jaw ants are a functional innovation capable of record-breaking acceleration. This study uses phylogenomics, X-ray microtomography and high-speed videography to reveal that they evolved multiple times around the world through a pathway of incremental steps.

This study shows how an important agricultural pest, the western corn rootworm, integrates nutrients (sugars) and plant defense compounds (benzoxazinoids) to navigate the maize rhizosphere and feed on the most nutritious roots.

The etiological agents of malaria are protozoa of the genus Plasmodium that are transmitted to humans and other vertebrate hosts by mosquitoes. In the Atlantic Forest in Southeastern and Southern Brazil, human infections by simian Plasmodium species have been detected, showing that in certain situations malaria can be transmitted zoonotically in this region. Anopheles cruzii, a sylvatic mosquito, is considered the main vector of malaria parasites in the Atlantic Forest. The fact that this species can feed on humans and monkeys reinforces the hypothesis of zoonotic transmission. Here we present a new mathematical model to explain the dynamics of zoonotic transmission of malaria in the Atlantic Forest. Simulations performed with the model showed that the prevalence of human cases and the basic reproduction number for malaria can be strongly influenced by variations in the abundance of An. cruzii and the frequency with which these mosquitoes move between the ground and the forest canopy to feed on humans and monkeys, respectively. The proposed model contributes to a better understanding of the dynamics of malaria transmission in the Atlantic Forest.

Background

Water quality monitoring at the dialysis units (DU) is essential to ensure an appropriate dialysis fluid quality and guarantee an optimal and safe dialysis treatment to patients. This paper aims to evaluate the effectiveness, economic and organizational impact of automation, digitalization and remote water quality monitoring, through a New Water Technology (NWT) at a hospital DU to produce dialysis water, compared to a Conventional Water Technology (CWT).

Background

Schistosoma constitutes a major public health problem and developmental challenges in the majority of developing and subtropical regions. The World Health Organization has set guidelines for the control and elimination of schistosomiasis. Ethiopia is providing school-based Mass Drug Administration (MDA) at the study areas of the Abbey and Didessa Valleys of western Ethiopian since 2015. Moreover, mass treatment was already done in the same villages 30 years ago. However, the current Schistosoma mansoni infection status among humans and snails in the study areas is not known. Hence, the present study aims to determine the current status.

Background

Schistosomiasis is a parasitic disease caused by trematode worms of the genus Schistosoma and belongs to the neglected tropical diseases. The disease has been reported in 78 countries, with around 290.8 million people in need of treatment in 2018. Schistosomiasis is predominantly considered a rural disease with a subsequent focus of research and control activities in rural settings. Over the past decades, occurrence and even expansion of schistosomiasis foci in peri-urban and urban settings have increasingly been observed. Rural–urban migration in low- and middle-income countries and subsequent rapid and unplanned urbanization are thought to explain these observations. Fifty-five percent (55%) of the world population is already estimated to live in urban areas, with a projected increase to 68% by 2050. In light of rapid urbanization and the efforts to control morbidity and ultimately achieve elimination of schistosomiasis, it is important to deepen our understanding of the occurrence, prevalence, and transmission of schistosomiasis in urban and peri-urban settings. A systematic literature review looking at urban and peri-urban schistosomiasis was therefore carried out as a first step to address the research and mapping gap.

Schistosomiasis is an infectious parasitic disease and one of the 20 diseases considered by the World Health Organization as a neglected tropical disease. It is typically associated with poor environmental and sanitary conditions, primarily affecting rural communities. However, with the currently observed rapid urbanization and predicted two-thirds of the world population living in urban areas by 2050, concerns are raised about a spread of schistosomiasis to urban and peri-urban areas. At the same time, there seems to be little knowledge of the extent of schistososomiasis in urban areas. In light of the efforts to control morbidity and ultimately achieve elimination of schistosomiasis as well as reaching Sustainable Development Goals 3 “achieve health for all” and 11 “make human settlements inclusive, safe, resilient, and sustainable,” this systematic literature review was conducted to address the existing research and mapping gaps and to contribute to the understanding of the burden of schistosomiasis in areas that have not, as yet, been the focus of control efforts and mass drug administration programs. The review suggests that rapid and unorganized urbanization and resulting poor living conditions in urban and peri-urban areas may lead to new disease foci and thereby increase the overall disease burden. Research and policy implications are discussed.

Globalization has led to the spread of pathogens through increased human movement. Microbiologists track epidemics of these pathogens by cataloguing geographic diversity in the genes that encode for variant surface antigens (VSA). Here, we developed a computational approach to explore the evolution of specific DNA sequences of the major VSA gene of the human malaria parasite, Plasmodium falciparum. First, we tested the method by comparing DNA sequences of these genes from P. falciparum to those of Plasmodium species that infect chimpanzees and gorillas. We showed that it could distinguish DNA signatures specific to each species. Next, we asked whether our method could detect geographic signatures within these genes by analyzing a global collection of P. falciparum isolates from 23 locations in 10 countries. The important outcome of our work was the ability to identify geographic signatures specific to countries and continents that were consistent with the “out of Africa” origin of P. falciparum. We can now identify malaria parasites from countries within Africa, South America, and Asia/Oceania using a diverse region of VSA genes without having to sequence and assemble whole parasite genomes. This methodology has potential applications in malaria surveillance to track parasites as they move around the world.

Background

Intestinal parasitic infections are still a serious public health problem in poor and developing countries like Ethiopia. Local epidemiological data is crucial to design and monitor prevention and control strategies. This study aimed to determine the prevalence of intestinal parasite infections and associated risk factors among patients requested for stool examination at Jimma health center, Southwest, Ethiopia.

Wellbeing is currently seen as an avenue that shapes, happiness, productivity, environmental awareness, social inclusion, and justice; however, most countries presently adopting wellbeing measures are in the global north. Neglected Tropical Diseases (NTDs) significantly compromise populations’ health and well-being in the global south, causing undesirable effects on the personal, social, and economic capabilities of communities living in endemic regions. As countries work towards achieving the Sustainable Development Goals (SDGs), it is paramount that countries in the global south adopt wellbeing measures and, in doing so, capture the lived experiences of individuals experiencing inequities, particularly as these are shaped by NTDs. In sub-Saharan Africa (SSA), political and economic power manifests across different scales, determining human-environmental interaction, distribution of resources, and the transmission of infectious agents. This paper uses a political ecology of health approach to identify the political, economic, social and cultural factors that contribute to NTDs, which are among the world’s greatest global health problems. The vast majority of people bearing the burden of NTDs reside in low-income countries. Surprisingly, as the economies of the low-income countries improve to middle-income status, NTDs continue to thrive among sub-populations of low socioeconomic status because of the unequal distribution of economic gains. As a result, NTDs are found in environments characterized by poverty and income inequality, and other inequalities in access to health services, housing, safe water, and sanitation. This paper uses political ecology of health in the primarily biomedical field of NTDs to demonstrate that inequities are embedded within the broad political, socio-cultural, and economic systems that exacerbate NTD infection. The study recommends that NTD endemic countries in SSA formulate policies that enhance equity through capacity building and empowerment enhance population wellbeing.

The parasite Toxoplasma gondii is a worldwide-distributed pathogen, able to infect all warm-blooded animals. There are important differences in the clinical expression of the infection in direct relation with the parasite genetic profile. In some regions, the geographical structuration of its genetic diversity points towards a crucial role of human activities in some lineages introduction or sorting. Benin is a West African country with a history of extensive transcontinental exchanges. Our genetic study of Toxoplasma in Benin shows a surprisingly homogeneous and autochthonous diversity, which contrasts with previous studies from other West and Central African countries. In Benin, the absence of European Toxoplasma lineages may be explained by the extreme rarity of the house mouse (Mus musculus), a host species that was previously described as highly susceptible to the mouse-virulent African strains. Might Benin be the origin region for the Africa 1 lineage, our results suggest that Guinean Gulf coasts may be a starting point of this lineage towards South America, especially Brazil, during the slave trade. As a whole, the present study provides further insights into the recent evolutionary history of Toxoplasma gondii and its consequences on human and animal health.

Introduction

Visitation to parks and protected areas is a common COVID-19 coping strategy promoted by state and national public health officials and political leadership. Crowding and congestions in parks has been a perennial problem and the ability to socially distance within them is an unproven assumption. Is it possible to socially distance in a busy national park that has been designed to concentrate use?

Paragonimiasis is a lung disease caused by food-borne zoonotic trematodes of Paragonimus spp., multi-host parasites whose complex life cycle includes primary (snail), secondary (freshwater decapod crustacea), and mammalian definitive hosts. In Africa, paragonimiasis is a particularly neglected disease, where prevalence has likely been underestimated through under reporting and misdiagnosis as tuberculosis; and it remains the only human parasite without a fully known life-cycle. We present the first systematic review of paragonimiasis in Africa, including 143 publications. In human studies, we uncovered substantial recent transmission in Southeast Nigeria, and recent transmission also in Côte d’Ivoire and Cameroon in endemic foci; significantly higher prevalence of P. uterobilateralis than P. africanus; and evidence supporting the existence of P. africanus in Côte d’Ivoire. In freshwater crab intermediate hosts, prevalence and intensity of either P. uterobilateralis or P. africanus varied across genera and species, suggesting differences in susceptibility. Mapping revealed evidence of temporal stability at endemic foci in rainforest regions; and widespread outliers. Numerous reports of significant recent transmission, particularly in Southeast Nigeria should be heeded by the international NTD research community. Increased studies are urgently needed to ascertain the real distribution and diversity of Paragonimus species in Africa.

Mathematical models of population dynamics are an important tool to advance our understanding of ecosystems, which can be relevant for environmental, clinical, and industrial applications. One sanity check for such models is to virtually split a population into two with identical properties – allegorically, we paint half the individuals of the population in a different color. As we do not change the ecological situation, the outcome of the model should not change either; we call this feature clone consistency. We investigated the mathematical properties of clone-consistent models and deduced simple rules for their form. These rules allow to easily check clone consistency in existing models and ensure it when building new ones. The resulting framework can guide researchers in building models for specific ecosystems and in investigating general properties of ecosystems. We showcase our approach by applying it to models for bacterial communities causing urinary-tract infections. We further discuss that clone inconsistency, which occurs in several prominent models, reflects strong, often implicit, assumptions and it is important to check whether these are justified. Such assumptions may diminish the applicability of these models and the generality of results obtained with them.

Background

Despite ~90% of sickle cell disease (SCD) occurring in low-and middle-income countries (LMICs), the vast majority of people are not receiving evidence-based interventions (EBIs) to reduce SCD-related adverse outcomes and mortality, and data on implementation research outcomes (IROs) and SCD is limited. This study aims to synthesize available data on EBIs for SCD and assess IROs.

Understanding the status of biodiversity and its changing patterns is crucial for conservation management. Ecological assessment in deep-sea environments is challenging owning to the limited accessibility and visibility. Nevertheless, we can listen to underwater sounds to investigate the acoustic behaviors of marine animals. This study applied machine learning techniques to analyze underwater recordings transmitted from a deep seafloor observatory off northeastern Taiwan. In particular, our computational approach does not require preexisting labels in the procedure of model building. The model can automatically learn acoustic features and effectively separate sounds of marine mammals, fishes, and shipping activities with minimal supervision. The analysis of 2.5 years of audio data revealed that the studied continental shelf environment has a high diversity of sound-producing animals, and the community structure changes with diurnal, lunar, and seasonal cycles. The applied techniques also generated a database of environmental and anthropogenic sounds, which can facilitate future investigations on how human activities affect the acoustic environment and biodiversity. Our technique is entirely based on passive acoustics, which minimizes interference with animals. It also transforms audio recordings into highly interpretable ecological data, which can be useful for tracking changes in marine biodiversity.

Human T-cell lymphotropic virus type 1 distributed all over the world. Since 1988, serological screening has been included in routine blood screening in certain developed countries and regions such as American countries and some parts of Western Europe and East Asia. However, data from some highly populated countries such as China are still not available. We performed a 3-year large-scale blood screening survey to systematically characterize the prevalence of HTLV infection among blood donors in Guangdong province in south China during 2016–2018. In general, Guangdong was considered to be a low-prevalence region for HTLV-1 infection, but the prevalence is significantly higher in Shanwei, a coastal city of eastern Guangdong. Transcontinental and Japanese subtype lineages dominate the prevalence in Guangdong. Moreover, similar molecular characteristics of prevalent HTLV-1 sequences in Mainland China, Taiwan and Japan suggested a same origin of these viruses.

Background

Trait-based approaches have been used to demonstrate the responses of plant functional traits to environmental change may manifest both among- and/or within-species. However, how community-level foliar stoichiometric characteristic variations respond to aridity and salinity is still not well-known.

Introduction

Despite skilled attendance during childbirth has been linked with the reduction of maternal deaths, equality in accessing this safe childbirth care is highly needed to achieving universal maternal health coverage. However, little information is available regarding the extent of inequalities in accessing safe childbirth care in Tanzania. This study was performed to assess the current extent, trend, and potential contributors of poor-rich inequalities in accessing safe childbirth care among women in Tanzania.

Background

Oncomelania snails serve as the sole intermediate host for Schistosoma japonicum, one of the most important neglected tropical diseases in the world. Afforestation suppression of the Oncomelania hupensis snail has been a long-term effective national strategy to decrease snail density in China. Many previous studies have made clear that vegetation (biotic factors) and soil (abiotic factors) were the basic requirements for snail survival on beaches. Moreover, a lot of research on snail control has been focused on the specific influencing environmental factors for snail survival, such as the vegetation community structure, species composition, diversity index, and the physical and chemical properties of the soil. Most of the existing research has studied the influence of a single factor on snail population density. Conversely, there have been only a few studies focused on the food sources and food composition of the snails. The current research situation on snail control has indicated that the mechanisms underlying ecological snail control have not been systematically characterized. The question of whether biotic or abiotic factors were more important in influencing snail survival remains unclear. Afforestation on beaches has significantly suppressed snail density in China so far. In this study, we proposed that the reduction of snail density was not affected by a single factor but by the interactions of multiple related factors introduced by afforestation. Moreover, different biotic and abiotic factors have significantly different effects on snail control. Therefore the goal of this study was to evaluate the relative importance and interactions of related biotic and abiotic factors on snail density. Methods: Four major vegetation communities: Sedge, Reed, Artificial poplar (3 years of age) and Artificial poplar (5 years of age), on the beaches of the Yangtze River in China were selected for vegetation and snail surveys, as well as for soil sampling. Structural Equation Model (SEM) analysis was used to assess the interactions of biotic and abiotic factors in the context of snail ecology. The soil properties were considered as abiotic factors, while algae of Chlorophyta, Cyanophyta and Bacillariophyta phyla were considered to be biotic factors. In the path analysis, the total effect between the variables was the sum of the direct and indirect effects.

Schistosomiasis is the second largest tropical parasitic disease in the world after malaria. By the end of 2018, the areas in which schistosomiasis is endemic in China are distributed across 12 provinces (municipality and autonomous region). Among these areas, 5 provinces, including Shanghai, Zhejiang, Fujian, Guangdong and Guangxi, have continued to consolidate achievements in schistosomiasis elimination. Sichuan Province has achieved transmission interruption and 6 provinces of Hunan, Hubei, Anhui, Jiangxi, Yunnan, Jiangsu have achieved transmission control. Oncomelania hupensis (Snail) is the only intermediate host for the parasite schistosomiasis japonicum, so snail control is an important measure to control the spread of schistosomiasis. So far, the area the snail inhabits in China is 3.63 billion m², with more than 95% of this distributed along the beaches of Yangtze River. Forestry schistosomiasis prevention projects has effectively reduced the snail habitat area and decreased snail population density through afforestation of these areas in China. However, the key factors that inhibit snail population growth by afforestation remain unclear. We propose to investigate the interactional relationship between biotic and abiotic factors introduced by afforestation on the distribution of the snail population. The results revealed that the number of soil algae is the important biological element determining snail distribution. Abiotic factors, such as soil properties indirectly impact on the snail population through a direct influence on soil algae. Of these, the pH value, water content, capillary porosity, bulk density interact with the algae content (Chlorophyta, Cyanophyta and Bacillariophyta) to decrease snail density through afforestation.

Background

Considerable progress towards the elimination of urogenital schistosomiasis was made by the Zanzibar Elimination of Schistosomiasis Transmission project from 2012 till 2016, when biannual praziquantel mass drug administration (MDA) alone or with additional snail control or behaviour change interventions were implemented. Annual MDA was continued in 2017 and 2018, but not in 2019, imposing a 16-month treatment gap. We monitored the Schistosoma haematobium prevalence from 2012 till 2020 and assessed recrudescence patterns with focus on 2020.

Schistosomiasis is a neglected tropical disease caused by parasitic blood flukes of the genus Schistosoma. On the Zanzibar islands, United Republic of Tanzania, interventions to eliminate urogenital schistosomiasis commenced in 2012. From 2012 to 2016, the population was treated biannually with praziquantel and, additionally, some areas received mollusciciding against the intermediate host snail, or educational measures for behavior change. Mass drug administration (MDA) with praziquantel was continued annually in 2017 and 2018, but not in 2019. As a result of the interventions, the overall S. haematobium prevalence was reduced to 0.4% in adults and 3.4% in schoolchildren in 2020. However, in some areas, the MDA gap in 2019 resulted in a considerable rebound of infections. The recrudescence in 2020 was particularly striking for boys aged 9–16 years. In general, in 2020, male participants had higher odds of infection than females. Adults living near to a natural freshwater body also showed an increased risk of S. haematobium infection. Future elimination efforts in Zanzibar should focus on re-intensifying elimination interventions, including MDA, snail control and behavior change in hotspot areas. In low-prevalence areas, the strategy might be adapted from MDA to targeted interventions, such as surveillance-response.

Understanding the ecology of sand flies is critical to developing control measures. An important ecologic adaptation of sand flies is their selective use of habitats as resting or breeding habitats. However, the basis for this preference is not fully understood. Here, we sought to understand the distribution of sand flies in three different habitats namely animal shed, human dwelling (houses indoors) and termite mound, and analyzed the chemical cues associated with these habitats. The study was conducted in Rabai village in Baringo County, Kenya, endemic for visceral and cutaneous leishmaniasis. By analyzing sand flies surveyed at different time points during the dry season, we found that sand fly abundance and diversity varied between the habitats. We collected and analyzed volatile organic compounds from represented substrates associated with these habitats and found commonality in some compounds previously known as attractants for sand flies across the habitats. These volatiles may contribute to the composition of sand flies in these habitats that can potentially be exploited in sand fly surveillance and control purposes.

Background

Lassa fever (LF) is one of the most devastating rodent-borne diseases in West Africa, causing thousands of deaths annually. The geographical expansion of LF is also a concern; cases were recently identified in Ghana and Benin. Previous ecological studies have suggested that high natural-host biodiversity reduces the likelihood of spillover transmission of rodent-borne diseases, by suppressing the activities of reservoir species. However, the association of biodiversity with the geographical expansion of LF has not been the subject of epidemiological studies.

Rodent diversity has been studied as a protective factor for rodent-borne diseases and rodent-related tick-borne diseases, such as hantavirus infection and Lyme diseases, in human population. The protective effect is called dilution effect and based on the ecological mechanism that the high diversity of rodent species could suppress the activities of reservoir rodents thereby reduce the likelihood of spillover transmission from rodents. However, the effect has been studied mostly for endemic diseases, and the effect on the geographical expansion of rodent-borne diseases has not been the subject of epidemiological studies. Considering that the dilution effect may also be applicable to the geographic expansion of rodent-borne infectious diseases in that a high rodent species diversity could decrease migration of infected rodents from the disease-endemic area, we examined the association between rodent species richness and the geographical expansion of Lassa fever (LF) in West African countries. Analyzing the regions without LF until 2007, the results showed that the region with lower number of rodent species showed higher risk of emerging LF cases from 2008 to 2017, implying the protective effect of higher rodent species richness on spatial expansion of LF. The results reinforce the importance of the ‘One Health’ approach by demonstrating that a high level of biodiversity could benefit human health.

Background

Tree-based intercropping (agroforestry) has been advocated to reduce adverse environmental impacts of conventional arable cropping. Modern agroforestry systems in the temperate zone are alley-cropping systems that combine rows of fast-growing trees with rows of arable crops. Soil microbial communities in these systems have been investigated intensively; however, molecular studies with high taxonomical resolution are scarce.

Background

Côte d’Ivoire has had 45 years of intervention for onchocerciasis by vector control (from 1975 to 1991), ivermectin mass drug administration (MDA) (from 1992 to 1994) and community directed treatment with ivermectin (CDTi) from 1995 to the present. We modeled onchocerciasis endemicity during two time periods that correspond to the scale up of vector control and ivermectin distribution, respectively. This analysis illustrates progress towards elimination during these periods, and it has identified potential hotspots areas that are at risk for ongoing transmission.

Côte d’Ivoire is endemic for onchocerciasis (also known as “river blindness”). This neglected tropical disease is transmitted by biting black flies that breed in fast flowing rivers. From 1975 to 1991, onchocerciasis control was based on weekly aerial spraying of the insecticide temephos, on black fly breeding sites. Vector control, however, was mostly focused on the northern and central parts of the country. From 1992 to present, mass treatment with ivermectin was implemented in all endemic areas, including forested regions in the south. Here we present the first geospatial estimates of onchocerciasis endemicity over time. Using the machine learning algorithm quantile regression forest, we implemented models to: identify important socio-demographic and environmental factors that correlate with onchocerciasis infection; predict the prevalence and density of infection in areas without ground-truth data; delineate remaining infection hotspots. Our results show that Côte d’Ivoire has made very significant progress in reducing infection parameters over time, and they may help to inform future interventions to achieve the goal of onchocerciasis elimination in Côte d’Ivoire.

Leishmaniasis is a neglected disease that is endemic in tropical and subtropical regions affecting up to 2 million people every year. Currently, there is concern about the effects of human-made environmental changes on the transmission of leishmaniasis due to increased exposure to the sand fly vector. In this paper, the authors explored changes in the distribution of sand flies and natural leishmania infection across communities located along the interoceanic highway that connects Peru and Brazil. The study found differences in sand fly species composition and abundance between and within sites as well as a lower sand fly diversity in communities with high human disturbance. Ten pools belonging to Lutzomyia shawi, Lu. carrerai carrerai, Lu. yuilli yuilli, Lu. hirsuta hirsuta, Lu. (Helcocyrtomyia) spp. and Lu. (Lutzomyia) spp. were found positive for Leishmania spp. The majority of these positive pools were collected from a single community and far from the highway. The information provided by this manuscript will serve as a baseline to assess the effects of human activities in the region and guide future surveillance and intervention strategies.

Objective

Health-related quality of life is impaired in idiopathic inflammatory myopathies. This study aimed to identify the main areas of the health-related quality of life environment domain that are affected in patients with myositis.

It is estimated that snakebite envenoming affects around 2.7 million people every year worldwide. In Brazil, snakebite is part of the Ministry of Health surveillance system and cases receive antivenom free of charge. With a vast territory and limited production of antivenom, there is need to identify higher risk areas for its distribution and to develop preventative actions. The objective of this study is to provide an overview of the epidemiological situation of snakebite envenoming in Brazil and explore possible environmental and socioeconomic factors related to snakebites. On the basis of this information, a flowchart tool to support decision-makers identify higher risk areas was created and applied in one state as an example. An average of 27,120 snakebite cases per year were reported in Brazil, with the highest number of cases and rates in the Legal Amazon Region. The multivariable statistics analysis showed association of snakebite with environmental factors (type of major habitat, tropical or non-tropical; temperature; precipitation; elevation) and socioeconomic (lower percentage of urbanization; lower GDP per capita); also, a weaker relation with forest loss, and with venomous snake richness. The tool created to support decision-makers was applied in the state of Rio Grande do Sul, with 4,227 reported snakebites during the period. According to this tool, the majority of municipalities in this state were considered as medium risk and 56/496 as high risk. Snakebite cases are distributed across the entire country; however, the highest concentration is in the Legal Amazon Region. This creates a complex situation both for better understanding of the association of environmental and socioeconomic factors with snakebites and for the distribution and maintenance of antivenom to remote areas.

Background

The community practice towards disposal of expired and unused medications in spite of its adverse impact have been widely neglected in many developing countries. The available guidelines in Tanzania focus on the disposal of expired medications and cosmetics in hospitals and community pharmacies only.

Background

The impact of large scale Mass Drug Adminstration (MDA) of ivermectin on active onchocerciasis transmission by Simulium damnosum, which transmits the parasite O. volvulus is of great importance for onchocerciasis control programmes. We investigated in the Mbam river system area, the impact of MDA of ivermectin on entomological indices and also verify if there are river system factors that could have favoured the transmission of onchocerciasis in this area and contribute to the persistence of disease. We compared three independent techniques to detect Onchocerca larvae in blackflies and also analyzed the river system within 9 months post-MDA of ivermectin.

The presence of parasite strains that respond sub-optimally to an approved drug, favourable breeding sites for the vector and infected individual in an area, will surely provide conditions for continuous and persistent transmission of a disease despite a long-term control intervention. We investigated the impact of ivermectin on entomological indices within 9 months following a large-scale MDA in the Mbam river drainage. The river system factors that could have favoured abundance vector breeding and contribute to the persistence of disease transmission were also examined within the study period. We observed vector abundance and high entomological indices throughout the study period following ivermectin MDA. We also observed high water discharge along the main river of the drainage basin in both the rainy and dry seasons and this is due to the presence of two dams constructed upstream at Bamendjing and Mape to regularize the course of river Sanaga in view of generating hydroelectric power at Edea. Factors favouring continuous and persistent disease transmission are present in this drainage basin despite over 20 years of annual IVM-MDA. There is need for alternative control strategy in order to accelerate the fight against onchocerciasis in the area.

Background

Studies from high income countries report that HIV-positive people have an impaired systolic and diastolic cardiac function compared to HIV-negative people. It is unclear if results can be translated directly to the Sub-Saharan Africa context. This study assesses electro- and echocardiographic characteristics in an urban African population, comparing HIV-positive people (treated and not yet treated) with HIV-negative controls.

Introduction

Dengue fever is the most prevalent arboviral disease in the Brazilian Amazon and places a major health, social and economic burden on the region. Its association with deforestation is largely unknown, yet the clearing of tropical rainforests has been linked to the emergence of several infectious diseases, including yellow fever and malaria. This study aimed to explore potential drivers of dengue emergence in the Brazilian Amazon with a focus on deforestation.

Plants and insects often use the same compounds for chemical communication, but little is known about the convergent evolution of such chemical signals. This study identifies a novel terpene synthase involved in production of an anti-aphrodisiac pheromone by the butterfly Heliconius melpomene. This enzyme is unrelated to other insect terpene synthases, providing evidence that the ability to synthesise terpenes has arisen multiple times independently within the insects.

The arms race between plants and pathogens is a complex process. To dissect the plant defense and pathogen virulence responses simultaneously, we used sorghum and Xanthomonas vasicola pv. holcicola, as a model pathosystem. We performed dual RNA-seq on infected sorghum with a range of disease phenotypes. Our characterization of this pathosystem demonstrates that genes related to the plant defense and pathogen virulence responses are most highly induced during a resistance interaction. We observed a similar pattern of escalation in Arabidopsis infected with Pseudomonas syringae. These observations support a conceptual model of fluidity between the different stages of plant immunity and pathogen virulence.

The environments in which organisms evolve typically fluctuate, in both predictable ways, such as daily, seasonal and annual changes in, for example, temperature and photoperiod, as well as in hard to predict ways, such as changes in the weather. Most laboratory evolution experiments evolve organisms in either constant environments, or environments that change predictably, such as by serial dilution into fresh media periodically. To investigate how unpredictable changes in the environment can affect an organism’s evolution, we designed a series of experiments where the environment alternated between two conditions, either predictably, or randomly, with different timescales of switching. We then evolved the budding yeast, Saccharomyces cerevisiae under these different conditions. We found that the both the switch rate and the order of the conditions influences adaptation, and that switching can both speed up and slow down adaptation. We also observed different adaptive outcomes between populations, both at the genetic and phenotypic level, even if populations spent the same amount of total time in the two different conditions, but that the order and/or switch rate differed. These data suggest that adaptive outcomes are dependent on the exact nature of the prevailing environmental conditions.

Background

Due to the influence of gender, race/genetics, age, lifestyle habits and geography on the references intervals (RIs), the Clinical and Laboratory Standards Institute (CLSI) recommends the determination of population-specific RIs. Ghana continues to depend on pre-established RIs from other countries which poses the risk of misdiagnoses and wrong treatment. This study presents the haemato-biochemical RIs from four eco-geographical zones in Ghana.

Background

The United Nations Sustainable Development Goals stress the importance of equitable partnerships in research and practice that integrate grass-roots knowledge, leadership, and expertise. However, priorities for health research in low-and-middle income countries are set almost exclusively by external parties and priorities, while end-users remain "researched on" not "researched with". This paper presents the first stage of a Community-Based Participatory Research-inspired project to engage communities and public-health end-users in setting a research agenda to improve health in their community.

Our resident microbiota can prevent diseases by making it harder for pathogens to grow and establish, a phenomenon called “colonization resistance.” Colonization resistance is one of the major benefits provided by human-associated microbiota and a viable alternative to the use of antibiotics for preventing or treating infections. Here we use a model of microbial interactions through production and consumption of metabolic compounds to assay invasion and colonization resistance. We systematically examine in simulations how interactions among resident members and those between residents and an invader impact colonization resistance and invasion outcomes. In our simulations, the common strategy of increasing the dosage of probiotics is often unsuccessful for augmenting a new species into a resident microbiota. Instead, we find that the net facilitation or inhibition between the resident members and the invader explains whether the community remains intact and whether the invader can establish. Our results suggest that a better understanding of microbial interactions can inform successful microbiota interventions.

Objective

To determine whether long term exposure to outdoor nitrogen dioxide (NO₂) is associated with all-cause or cause-specific mortality.

Yellow fever (YF) is a viral haemorrhagic fever found in tropical South America and Africa that affects both humans and non-human primates (NHPs). Despite a long-standing recognition of YF as a pathogen of significant public health concern, not much is known about why cases are reported in some years and not others, or what drives the strong seasonal trends that are observed in South America.

Using a combination of statistical techniques, the authors have looked at the relationship between different types of land-use, vegetation, climate, human and NHP and the reporting of YF across all of South America and both inter-annual and seasonally over the period 2003–2016. The authors have found that both are highly influenced by changes in vegetation, however the inter-annual is additional influenced by land-cover and the seasonal climatic factors.

The authors have found that the differing drivers of seasonal and inter-annual transmission, though both are predominantly shaped by changes in vegetation, highlighting the role of land-cover in influencing the inter-annual and climate the seasonal.

This research enhances our understanding of YF transmission in South America, describing the geographic and temporal distribution of cases in relation to vegetation, land-cover and climate. This research is of particular importance, given the recent large-scale outbreaks of YF across the continent, global YF vaccination shortages and the exportation of cases globally.

Natural environments often have many species competing for the same resources and frequently one species will out-compete others. This poses the fundamental question of how a diverse array of species can coexist in a resource-limited environment. Among other mechanisms, previous studies examined how interactions between species–like cooperation or predation–could lead to stable biodiversity. In this work we looked at this question from a different angle: we used computational models to examine the role that the environment itself might play in stabilizing species that compete with each other when in proximity. We modeled how species arrange themselves in space when the environment contains objects that alter the interfaces along which competing species meet. We found that these ‘structured’ environments can stabilize species coexistence, across a range of density of those objects and in a way that was robust to differing strengths of interspecies competition. Thus, in addition to biological factors and other forms of environmental variation, our work presents a potentially generic mechanism by which the physical structure of the environment can influence ecological outcomes and stabilize biodiversity.

Background

Urogenital schistosomiasis (UGS) caused by S. haematobium has enormous reproductive health consequences including infertility. Reproductive aged individuals are a neglected group and not included in control programs in Cameroon. This study investigated the prevalence and severity of S. haematobium infection in the context of gender and socio-economic structures that shape behaviour among reproductive aged individuals living in Tiko, a semi-urban setting, Cameroon.

S. haematobium deposit its eggs in the urogenital organs which may cause genital ulcers and other lesions. When untreated the infection causes infertility, miscarriage, ectopic pregnancies, spontaneous abortions, prematurity, vulva nodules, genital and cervical lesions, increased risk of HIV and Human Papilloma Virus in women. These may lead to social consequences such as low self-esteem, depression and stigma. The disease burden has been neglected in males, with more emphasis on female genital schistosomiasis. Control programs have focused on school age children, often overlooking reproductive aged individuals who are potential reservoirs. A total of 509 reproductive aged individuals living in Tiko, a semi urban setting in the mount Cameroon area were screened. The overall prevalence of S. haematobium infection was 22.8%, with significantly higher rates in males (35.2%) than females (16.2%). Similarly, intensity of infection was significantly higher in males (p = 0.009), singles (p = 0.004) and younger age individuals (0.012). Younger age, gender type (male) and awareness of UGS were identified as key factors that increase the odd of infection. In this setting, younger adults and males represent important public health risk groups and potential reservoir sources of disease transmission in the area.

Objectives

Decision-makers are increasingly requesting economic analyses on transportation-related interventions, but health is often excluded as a determinant of value. We assess the health-related economic impact of bicycle infrastructure investments in three Canadian cities (Victoria, Kelowna and Halifax), comparing a baseline reference year (2016) with the future infrastructure build-out (2020).

The diversity of life on our planet has produced a remarkable variety of biological traits that characterize different species, and such traits are widely considered an alternative to taxonomy to increase our understanding of biodiversity and ecosystem functioning. This study presents an unbiased and fully reproducible framework to delineate trophic guilds in reef fishes.

Biological studies and experiments have provided many insights as to the complex nature of the criteria (objectives) that species may evaluate in decisions regarding inter-habitat landscape traversal. Those insights are often used to develop models for identifying paths or corridors potentially supporting inter-habitat movement to characterize habitat connectivity from the species’ perspective. However, typically only a small proportion of the alternative paths that may also support species movement and be important to habitat connectivity are identified. Thus, the computational challenge is to develop methods that can more completely characterize the set of paths/corridors that may support habitat connectivity. To address this challenge, a modeling framework that better integrates the objectives thought to influence inter-habitat movement is outlined, facilitating the identification of a broader set of paths reflecting the tradeoffs among the objectives. Through an application of the developed framework to model habitat connectivity for multiobjective amphibian movement in a wetland system, it is demonstrated that an extensive and diverse set of efficient inter-habitat paths can be identified. The capability to characterize these additional dimensions of habitat connectivity supporting species movement can provide researchers and practitioners with a means to develop more robust representations of complex biological systems.

Phylogeography studies past location and migration using information from current geographic locations of genetic sequences. For example, phylogeography can be used to reconstruct the history of geographical spread of an outbreak using the genetic sequences of the pathogen collected at different times and locations. Here, we investigate the effects of different model assumptions on phylogeographic inference. In particular, we examine the effects of the strategy used to collect samples. We show that sample collection biases can have a strong impact on the quality of phylogeographic reconstruction: geographically biased sampling scheme can be very detrimental for popular continuous phylogeography models. We consider different ways to counter these effects, from utilising alternative phylogeographic models, to the inclusion of partially informative samples (known cases without genetic sequences). While these strategies do alleviate the effects of sampling biases, they also lead to considerable additional computational burden. We also investigate the intrinsic differences of different phylogeographic models, and their effects on reconstructed patterns in different scenarios.

Zoonotic diseases are increasingly becoming an emerging public health threat, partially due to the risk of spillover events at the human-wildlife interface. This cross -sectional study was carried out among high-risk communities around forest fragments of Hoima District, Uganda, to describe activities that could lead to disease spillover in humans in order to inform public health practitioners of the potential risks at community level for preparedness and response efforts. The study also sought to gain an understanding of the community’s perception of the risk of zoonotic diseases, what activities could expose them to zoonoses, and whether the healthcare services are adequate to identify such diseases at community level. We found that most people were not aware of zoonotic diseases transmissible from wildlife to humans and this can partly be explained by lack of information filtering through to the grass root. It is important to note however, that the interaction between wildlife and humans, is largely driven by communities’ struggle to survive and meet their livelihood needs making it difficult to predict under what circumstances disease could emerge in the community. We need to remind ourselves that all major outbreaks have started at community level and well as the health experts are fast to diagnose the disease in question, some communities are hearing these diseases for the very first time. Quite often these outbreaks are putting the available alternative livelihood in question and demanding for quick unstainable changes that communities are quick to abandon once the outbreaks are over. We recommend that this is the time to invest in health education and create awareness about zoonotic diseases among communities at the human-wildlife interface. Health promotion and or livelihood-based intervention programs should use existing evidence and case studies implemented in collaboration with government agencies and partners.

Background

Anaemia is a significant public health problem in most South-Asian countries, causing increased maternal and child mortality and morbidity. This study aimed to estimate the prevalence of and factors associated with anaemia in women of reproductive age in Bangladesh, Maldives, and Nepal.

Malaria is one of the most important vector-borne diseases in the world. In Southeast Asia, the incidence of human malaria infections caused by simian malaria parasites that originate from macaques has been increasing in the last decade, possibly due to closer proximity between the macaque and human population as a result of deforestation. In Singapore, urbanization and change in land use have resulted in closer proximity and interactions between macaques and the general human population. In order to assess the risk of potential simian malaria zoonosis, 1039 macaques’ blood samples were screened in this study for simian malaria parasites. Our results showed that simian malaria parasites were only detected in macaques living deep in the forest within the military protected zone, while macaques living close to human habitations are malaria-free. This study illustrated a low risk of zoonotic transmission of simian malaria parasites to the general population in Singapore.

Background

Exposure to per- and polyfluoroalkyl substances (PFAS) is a public health issue globally. In Australia high concentrations of PFAS have been found in environments close to sites where Aqueous Film Forming Foams (AFFF) were historically used for firefighting activities. This has resulted in significant community concern about the potential long-term health effects of these chemicals.

Lyme disease is common in the northeastern United States, but rare in the southeast, even though the tick vector is found in both regions. This study shows that this is largely because the tick vectors attach abundantly to rodents (which are good hosts for the Lyme bacteria) in the north, and to lizards (which are relatively poor hosts for Lyme bacteria) in the south.

It is widely known that not all mosquito species serve as medically-important virus’ vectors. Even among the vectors, there are variations in their ability to transmit one virus or the other. Nonetheless, while the known primary vectors’ transmission efficiency is evident, the importance of confirming the ability of other potential vectors is indispensable when it comes to the threat of disease introduction to new areas. Japanese encephalitis is a mosquito-borne disease mainly circulating in Asia. However, pockets of infection have been detected outside this endemic area, where the primary mosquito vector (a Culex species) is almost nonexistent. One possibility is that the causal virus is carried by the invasive mosquito species (an Aedes species), originating from Asia, confirmed to adapt well in Europe and North America. Thus, a thorough evaluation will be needed to determine the competence of both the Culex and Aedes species to transmit Japanese encephalitis virus (JEV). Here, the authors found that although the difference in the transmission efficiency between the Culex and Aedes was significant, their competence as vector is evident. This research provides evidence of the possible relevance of the Aedes species in the distribution and spread of JE into new areas.

Background and aims

Hepatitis C virus (HCV) genotyping is a pivotal tool for epidemiological investigation, guiding management and antiviral treatment. Challenge existed in identifying subtypes of genotype-1 (G-1) and genotype (GT) of indeterminate. Recently, the Abbott HCV RealTime Genotype Plus RUO assay (HCV GT Plus) has been developed aiming to overcome the limitations. We aimed to evaluate the performance of the assay compared with 5’ UTR sequencing in clinical samples.

Helicobacter pylori, one of the most common bacterial pathogens colonizing humans, is the main agent responsible for stomach ulcers and cancer. Certain strain types are associated with increased risk of disease, however many factors contributing to disease outcome remain unknown. Prior work has documented genetic diversity among bacterial populations within single individuals, but the impact of this diversity for continued bacterial infection or disease progression remains understudied. In our analysis we examined both genetic and functional features of many stomach isolates from a single individual infected over six years. During these six years the subject shifted from having excess acid production and a duodenal ulcer to lower acid production from gastric atrophy. The 39 isolates form sub-populations based on gene sequence changes that accumulated in the different isolates. In addition to having distinguishing genetic features, these sub-populations also have differences in several bacterial properties, including cell shape, ability to activate immune responses, and colonization in a mouse model of infection. This apparent functional specialization suggests that the bacterial sub-populations may have adapted to distinct niches within the stomach during chronic infection.

Background

Since the founding of the China, the Chinese government, depending on the changing epidemiological situations over time, adopted different strategies to continue the progress towards elimination of schistosomiasis in the country. Although the changing pattern of schistosomiasis distribution in both time and space is well known and has been confirmed by numerous studies, the problem of how these patterns evolve under different control strategies is far from being understood. The purpose of this study is, therefore, to investigate the spatio-temporal change of the distribution of schistosomiasis with special reference to how these patterns evolve under different control strategies.

Schistosomiasis japonica is one of the most serious parasitic diseases in China. The Chinese government has launched three different rounds of national schistosomiasis control programs since 1950s. The latest two are the World Bank Loan Project (WBLP) that ushered in chemotherapy as the main control approach, active from 1992 to 2001, and the integrated control strategy that took its place in 2005. In this study, we investigated changes in the dynamics of schistosomiasis transmission over space and time under these different control strategies. Based on spatio-temporal analyses of the schistosomiasis prevalence data at the village level during 1991–2014 in Guichi, Anhui Province, we built a dynamic model to evaluate the evolving pattern of prevalence. We found that the schistosomiasis prevalence generally showed a north-western shift over the study area during 1991–2005, while there was no such trend during 2006–2014. This global shifting trend disappeared after the effect of proximity to river was taken into account, but local change still existed which was possibly due to the transition between the two latest national control strategies. We conclude that proximity to River is still an important determinant for schistosomiasis prevalence and that although the integrated control strategy is more effective than the WBPL in reducing schistosomiasis prevalence, the disease would remain endemic for the long term without further improvements of the control program.

West Nile virus is a widely spread flavivirus, which is transmitted from birds to humans by mosquitoes. In humans, the virus can cause West Nile Fever (WNF) and in some cases, it affects the nervous system leading to severe symptoms that may result in death. Human cases have increased in Europe since the large-scale epidemic in 1996, being 2018 the year with the highest number of cases registered to date. We developed risk models based on 2017 cases, and predicted in 2018: 1) the occurrence of the disease; 2) the intensity of the outbreaks; and 3) the imminence of the cases. We identified favorable areas for the incidence of the virus in which environmental and human-related variables had an important role. The outbreaks began in the lower areas of large river basins and spread to higher areas, which highlights the importance of river basins in the propagation of outbreaks. Consequently, the early warning should be based on a basin scale.

Background

The possibility that onchocerciasis may cause epilepsy has been suggested for a long time, but thus far, an etiological link has not been universally accepted. The objective of this review is to critically appraise the relationship between Onchocerca volvulus and epilepsy and subsequently apply the Bradford Hill criteria to further evaluate the likelihood of a causal association.

There is growing epidemiological evidence that an infection with Onchocerca volvulus (the parasite causing onchocerciasis or river blindness) can trigger epilepsy, including nodding and Nakalanga syndromes. We studied the association between onchocerciasis and epilepsy using previously proposed criteria for causality and found strong arguments in favor of a causal relationship. The risk for children to develop epilepsy seems to be determined by the O. volvulus microfilarial load. However, the mechanism by which the O. volvulus parasite is able to trigger seizures remains to be elucidated. This form of epilepsy, called onchocerciasis-associated epilepsy (OAE), is an important public health problem in onchocerciasis-endemic regions with nonexistent or suboptimal onchocerciasis elimination programs. OAE is often characterized by sudden seizure onset in previously healthy children, between 3 to 18 years, without any other obvious cause of epilepsy. On the basis of the findings presented in this paper, it appears that onchocerciasis control may be able to prevent OAE. This further highlights the importance to eliminate onchocerciasis, particularly in areas with a high burden of epilepsy.

Background

This study aimed to establish a traumatic hemorrhagic shock (THS) model in swine and examine pathophysiological characteristics in a dry-heat environment.

Background

Exposure to air pollution, a leading contributor to the global burden of disease, can cause economic losses. Driven by clean air policies, the air quality in China, one of the most polluted countries, has improved rapidly since 2013. This has enabled a unique, quasi-experiment to assess the economic impact of air pollution empirically.

In this observational study, Tao Xue and colleagues explore associations between medical expenses and changes to clean air policies in China since 2013.

Objectives

Systematic mapping of the concept, content, and outcome of wilderness programs for childhood cancer survivors.

Objective

The answer to this article lies in: Does the financial activities of physical enterprises have an adverse impact on their main business? Is it conducive to the sustainable development of the national economy? However, when most scholars study the impact of environmental regulations on companies performance, they have not classified companies performance. This article will study the relationship between environmental regulations and performance levels based on the classification of companies performance, and then divide the nature of industry pollution, companies location and nature of property for in-depth research.

The research results confirmed the presence of both nutritional essential minerals and hazardous heavy metals in the birch sap. At the same time, the content of minerals and heavy metals was found to be very variable and the differences between their concentrations, recorded on the same day of collecting in several trees of the same age group, can be even several dozen times higher. Depending on the examined elements, the factors influencing their content vary. The age of the trees determines only the manganese content; daily sap volume significantly affects the content of manganese and copper, and date of collection differentiates the content of zinc, lead, nickel and cadmium.

The results may be interesting in the context of developing procedures for collecting birch sap for the purpose of obtaining raw material with beneficial nutritional values and a high level of health safety. For this reason, our recommendation for guaranteeing the health safety and high nutritional value of birch sap is to combine batches of raw material taken from as many trees as possible, and at the same time to publicize the fact that collecting birch sap from just one single tree may result in a raw material that is both dangerous and has no nutritional benefits.

Many neglected tropical diseases have reservoirs in wildlife. The effects of human activities on wildlife include changes in species abundance, community composition, and the transmission dynamics of parasites. Introduced species, especially black rats (Rattus rattus) are known to transmit zoonotic diseases among wildlife species and people. Leptospira, a water-borne bacterium that infects wildlife and people, is an important pathogen in the tropics, and in Madagascar, multiple strains and hosts have been identified. We tested how land use gradients in a forest-frontier agricultural system affect the composition of small mammal communities, and in turn the prevalence of Leptospira. We investigated 11 species of small mammals, including native rodents and tenrecs, as well as introduced rodents and shrews, in old growth forest, forest fragments, agricultural fields, and in a village. Leptospira prevalence and infection risk were highest in introduced species compared to native species and lower in forest fragments. The results highlight how the introduction of non-native species affects the variation in disease prevalence in small mammals, with potential consequences for spill-over to people.

The mitochondrial unfolded protein response (UPR^mt) is a cellular pathway that mediates recovery of damaged mitochondria. Mitigation of mitochondrial dysfunction is critical due to the essential nature of the organelle. The UPR^mt controls the expression of genes that help restore mitochondrial homeostasis via the bZIP transcription factor ATFS-1. The activation of the UPR^mt is associated not only with extended animal lifespan but also with increased host protection during infection with bacterial pathogens. Using a genetic screen to identify pathways that activate the UPR^mt, we recovered a novel reduction of function mutation in the mitochondrial ribosomal gene mrpl-2 that mediates protein translation in mitochondria. Interestingly, our isolated mrpl-2 mutant activates the UPR^mt and promotes longevity when fed a specific diet which is low in the metabolite vitamin B12. We find that impaired function of methionine synthase, an enzyme that uses vitamin B12 as a cofactor to convert homocysteine to methionine, genetically interacts with the isolated mrpl-2 mutant to activate the UPR^mt and extend lifespan. Our findings suggest that the lifespan-extending benefits of impaired mitochondrial translation and that of methionine restriction occur through a common mechanism that includes the activation of the UPR^mt.

Background & aim

Non-alcoholic steatohepatitis (NASH) is a severe form of non-alcoholic fatty liver disease (NAFLD) that is responsible for a growing fraction of cirrhosis and liver cancer cases worldwide. Changes in the gut microbiome have been implicated in NASH pathogenesis, but the lack of suitable murine models has been a barrier to progress. We have therefore characterized the microbiome in a well-validated murine NASH model to establish its value in modeling human disease.

Vibrio cholerae, is the causative agent of the diarrheal disease cholera, which infects millions of people worldwide. Despite intensive research, the environmental reservoir of V. cholerae is still unclear and under debate within the scientific community. Chironomids, an aquatic insect group that is closely related to mosquitoes, were reported to function as reservoirs of V. cholerae. Nevertheless, until now, there have been no reports regarding the presence of pandemic-causing V. cholerae O1/O139 serogroups in chironomids. By using molecular tools including metagenomic analyses of chironomids larval microbiomes, we provide here evidence for the first time, that chironomids harbor pandemic serogroups (O1/O139) of V. cholerae, which possess the cholera-toxin gene. Chironomid populations and V. cholerae demonstrate biannual peaks similar to the biannual peaks of cholera epidemics in the Bengal Delta region in India. Thus, we hypothesize that monitoring and controlling chironomid populations in endemic areas could be used as a tool for predicting and controlling the devastating cholera outbreaks.

Rabies, a fatal viral disease transmitted via the bite of an infected animal, causes over 59,000 human deaths each year. While domestic dogs are responsible for most human cases, wild animals, particularly carnivores and bats, play an essential role in rabies persistence. Several carnivore and bat species have been identified in the field and laboratory as important rabies reservoirs that can maintain different rabies variants. However, the role of many other carnivore and bat species remains unknown and additional insights are hampered by logistical and funding limitations of field and laboratory research. Using machine learning, we used information on known rabies reservoirs to forecast previously unidentified rabies reservoirs. Our models predicted 44 carnivore and 34 bat species that could already be serving as unrecognized rabies reservoirs or that have trait profiles suggesting their capacity to become reservoirs via future host shifting. In many cases, the distribution of these predicted reservoirs overlaps geographically with known reservoir ranges. Our findings can help understand rabies circulation in wildlife and is a first step to guide future epidemiological surveillance in neglected species.