Human Population Research Articles

A whole-organism landscape of X-inactivation in humans.

As females are mosaic for X-inactivation, direct determination of X-linked allelic expression in bulk tissues is typically unfeasible. Using females that are non-mosaic (completely skewed) for X-inactivation (nmXCI) has proven a powerful and natural genetic system for profiling X-inactivation in humans. By combining allele-resolution data for one previously reported and two newly identified nmXCI females, we directly determined X-inactivation status of 380 X-linked genes across 30 normal tissues, including 198 genes for which XCI status is directly determined for the first time. Our findings represent a substantial advance in our understanding of human X-inactivation and will serve as a reference for dissecting the genetic origin of sex bias in human traits. In addition, our study reveals nmXCI as a common feature of the human female population, with profound consequences for the penetrance and expressivity of X-linked traits in humans.

BLOOD GLUCOSE ALTERATIONS AND ASSOCIATED RISK FACTORS IN RESIDENTS OF SOUTH MARANHÃO, BRAZIL

Elevated blood glucose (BG) levels are often linked to the metabolic syndrome known as Diabetes mellitus (DM), a chronic condition that progressively affects multiple organs and requires continuous monitoring in human population. Therefore, this study aims to analyze the glycemic profiles and associated risk factors in patients from a clinical analysis laboratory in São Raimundo das Mangabeiras, Maranhão, Brazil. We employed a retrospective, observational, and cross-sectional analysis of data from 200 randomly selected blood conducted on patients between January and December 2022. The dataset included information on sex, age, total cholesterol (TC), triglyceride, low-density lipoprotein (LDL), high-density lipoprotein (HDL), and creatinine. A total of 42 individuals (21%) exhibited values exceeding the recommended standard. Most individuals with high BG levels were over 60 years old (p<0.001) and had higher triglyceride levels than those with normal BG levels (p<0.001). Finally, our multiple regression model confirmed that individuals with altered BG levels were approximately four times more likely to have elevated triglyceride levels (p<0.03). Therefore, we confirmed that elderly individuals are more likely to exhibit altered BG levels and that this clinical condition is associated with increased triglyceride levels in the human population.

A Game-Theoretic Model of Optimal Clean Equipment Usage to Prevent Hepatitis C Among Injecting Drug Users

Hepatitis C is an infectious liver disease which contributes to an estimated 400,000 deaths each year. The disease is caused by the hepatitis C virus (HCV) and is spread by direct blood contact between infected and susceptible individuals. While the magnitude of its impact on human populations has prompted a growing body of scientific work, the current epidemiological models of HCV transmission among injecting drug users treat risk behaviors as fixed parameters rather than as outcomes of a dynamic, decision-making process. Our study addresses this gap by constructing a game-theoretic model to investigate the implications of voluntary participation in clean needle exchange programs on the spread of HCV among this high-risk population. Individual drug users weigh the (perceived) cost of clean equipment usage relative to the (perceived) cost of infection, as well as the strategies adopted by the rest of the population, and look for a selfishly optimal level of protection. We find that the spread of HCV in this population can theoretically be eliminated if individuals use sterile equipment approximately two-thirds of the time. Achieving this level of compliance, however, requires that the real and perceived costs of obtaining sterile equipment are essentially zero. Our study demonstrates a robust method for integrating game theory with epidemiological models to analyze voluntary health interventions. It provides a quantitative justification for public health policies that eliminate all barriers—both monetary and social—to comprehensive harm-reduction services.

Genome wide association study of vaginal microbiota genetic diversity in French women

Background The composition of the vaginal microbiota is known to be highly structured into five main community state types (CSTs) that are found in all human populations. Several associations between self-reported ethnicity and the type of community have been reported. Methods Analysing data from in 168 women from the PAPCLEAR cohort study in France, we perform a genome wide association studies (GWAS) looking for human genetic polymorphisms that may impact vaginal microbiota community composition. Results We show that Shannon diversity is the trait related to the vaginal microbiota that is best explained by the human genome. Furthermore, we identify two genomic regions associated with its variations. Conclusion This is one of the first GWAS to use microbial genetic data instead of symptoms to characterise the vaginal microbiota and our results call for more powered studies in terms of participants and genome coverage.

A population genetic analysis of the nematode Strongyloides stercoralis in Asia shows that human infection is not a zoonosis from dogs

Gut nematode worms are important parasites of people and other animals. The parasitic nematode Strongyloides stercoralis infects an estimated 600 million people worldwide and is one of the soil-transmitted helminthiases, a WHO-defined neglected tropical disease. It has long been suggested that human S. stercoralis infection may be a zoonosis from dogs. We investigated this by whole genome sequence analysis of S. stercoralis from sympatric human and dog populations in Asia. We find that human- and dog-derived S. stercoralis have genetically distinct nuclear genomes, but we also find evidence of rare cross-infection. Analysis of the S. stercoralis mitochondrial genome reveals evidence of historical introgression between human- and dog-derived parasites. Based on these data, we suggest that S. stercoralis was originally a parasite of canids, that began to infect humans when people domesticated dogs, since when human- and dog-derived parasites have differentiated, but have not become separate species.

The Anthropogenic Factor as a Driver of Ecosystem Changes

Abstract Throughout history of life, natural events have shaped ecosystems until the human species began to overwhelmingly conquer and exploit this planet. Humans are profoundly altering ecosystems and the natural course of evolution, posing a serious threat to the future of life on our planet. The term "anthropogenic factor" refers to the influence of human actions and population growth on ecosystem structure and dynamics. In light of this, ecosystems can be classified into two categories: (i) natural ecosystems, which remain unchanged by human intervention, and (ii) intervened ecosystems, which have been influenced by the anthropogenic factors. Intervened ecosystems can be further categorized into three types: human-altered ecosystems, human-engineered ecosystems, and urban ecosystems. There is another category of ecosystems, the disappeared ecosystems, whose disappearance may be due to natural catastrophe or human intervention. The disappearance of an ecosystem is a biological tragedy, but it can also represent a new opportunity for life. For the sustainability of the planet as a source of life and to ensure a future for our species in harmony with nature, we need to achieve a sustainable balance between the development and well-being of all human beings, the population growth, the use of the services provided by ecosystems and the preservation of wild nature.

MAPPING TRYPANOSOMIASIS HOTSPOTS: A GEOSPATIAL APPROACH TO DISEASE RISK ASSESSMENT IN YANKARI GAME RESERVE

Trypanosomiasis, a parasitic vector-borne disease, poses a serious threat to both animal and human populations, especially in areas where the convergence of vectors and their hosts is easy. The Yankari Game Reserve in northeastern Nigeria is poorly understood as an environment with complex dynamics of Trypanosomiasis transmission. Using geospatial techniques, this paper comprehensively conducted an epidemiological risk assessment and mapping of Trypanosomiasis in the Yankari Game Reserve. This was achieved through combining Geospatial tools and methods such as Geographic Information Systems (GIS), Remote Sensing, and Spatial Analysis. This way, acquired data sets were integrated and analysed to generate risk maps delineating areas of high Trypanosomiasis transmission potential. Results indicated a spatial heterogeneity in the distribution of tsetse flies and trypanosome infections within the Game Reserve – Yankari. Environmental variables, including elevation, vegetation cover and proximity to water bodies, are identified as important predictors of Trypanosomiasis risk. Risk map results provide invaluable insights that aid in focusing target interventions on curtailing and mitigating the spread of Trypanosomiasis in the Game Reserve Region. The study also demonstrated the versatility of geospatial tools and techniques in interpreting the epidemiology of Trypanosomiasis, as well as highlighting the relevance of integrating multidisciplinary approaches for disease management and surveillance in wildlife reserves. Notably, this will significantly improve our understanding of the dynamics of Trypanosomiasis transmission and enhance the decision-making process, thereby safeguarding the health of both animal and human populations within and beyond Yankari Game Reserve.

Characterizing aging-related genetic and physiological determinants of spinal curvature

Background:Increased spinal curvature is one of the most recognizable aging traits in the human population. However, despite high prevalence, the etiology of this condition remains poorly understood.MethodsTo gain better insight into the physiological, biochemical, and genetic risk factors involved, we developed a novel machine learning method to automatically derive thoracic kyphosis and lumbar lordosis angles from dual-energy X-ray absorptiometry (DXA) scans in the UK Biobank Imaging cohort. We carry out genome-wide association and epidemiological association studies to identify genetic and physiological risk factors for both traits.ResultsIn 41,212 participants, we find that on average males and females gain 2.42° in kyphotic and 1.48° in lordotic angle per decade of life. Increased spinal curvature shows a strong association with decreased muscle mass and bone mineral density. Adiposity demonstrates opposing associations, with decreased kyphosis and increased lordosis. Using Mendelian randomization, we show that genes fundamental to the maintenance of musculoskeletal function (COL11A1, PTHLH, ETFA, TWIST1) and cellular homeostasis such as RNA transcription and DNA repair (RAD9A, MMS22L, HIF1A, RAB28) are likely involved in increased spinal curvature.ConclusionsOur findings reveal a complex interplay between genetics, musculoskeletal health, and age-related changes in spinal curvature, suggesting potential drivers of this universal aging trait.

The mutational landscape of SARS-CoV-2 provides new insight into viral evolution and fitness

Although vaccines and treatments have strengthened our ability to combat the COVID-19 pandemic, new variants of SARS-CoV-2 continue to emerge in human populations. Because the evolution of SARS-CoV-2 is driven by mutation, a better understanding of its mutation rate and spectrum could improve our ability to forecast the trajectory of the pandemic. Here, we use circular RNA consensus sequencing (CirSeq) to determine the mutation rate of six SARS-CoV-2 variants and perform a short-term evolution experiment to determine the impact of these mutations on viral fitness. Our analyses indicate that the SARS-CoV-2 genome mutates at a rate of ∼1.5 × 10−6/base per viral passage and that the spectrum is dominated by C → U transitions. Moreover, we find that the mutation rate is significantly reduced in regions that form base-pairing interactions and that mutations that affect these secondary structures are especially harmful to viral fitness. In this work, we show that the biased mutation spectrum of SARS-CoV-2 is likely a result of frequent cytidine deamination and that the secondary structure of the virus plays an important role in this process, providing new insight into the parameters that guide viral evolution and highlighting fundamental weaknesses of the virus that may be exploited for therapeutic purposes.

A Roadmap of Primary Pandemic Prevention Through Spillover Investigation.

Since the COVID-19 pandemic, attention and investment in pandemic preparedness have increased. Although there are many valiant plans around pandemic preparedness, they typically involve slowing the spread or mitigating the effects of a pathogen after it has already entered the human population. The task of stopping the pathogen from entering the human population in the first place, spillover prevention, remains a neglected area in discussions and planning for pandemic risk mitigation. Every spillover offers an opportunity to learn about an emerging public health threat and the conditions that aligned to enable spillover occurrence. In this article, we outline One Health approaches for use in spillover investigations, drawing from our experience investigating Hendra and Nipah virus spillovers. We present a roadmap for how findings from those investigations can lead to the development of interventions for spillover and ultimately pandemic prevention.

Occurrence and molecular detection of antibiotic-resistant genes in Escherichia coli isolated from drinking water in selected locations in southwestern Nigeria

Abstract The quality of water available for households’ use was investigated in some selected locations in Nigeria. A total of 180 water samples were analyzed. The antimicrobial susceptibility testing of the E. coli from the water samples were determined using standard microbiological protocols and detection of ESBL resistance genes. Microbiological mean total coliform count (TC) values obtained in both stored and source water in sampling locations were high ranging from (3.10 ± 1.46 c. f. u/100 mL to 156.80 ± 42.9 c.f. u/100 mL for stored water) and (0.50 ± 0.31 c. f. u/100 mL to 90.60 ± 38.05 c.f.u/100 mL for source water). Also, majority of the source waters were devoid of faecal coliform whereas the stored water had mean count values between 0.80 ± 0.70 c.f. u/100 mL and 64.30 ± 14.15 c.f.u/100 mL. Twenty-five E. coli isolates obtained from the water samples were resistant to most antibacterial used. However, four of the E. coli isolates were sensitive to cefotaxime. PCR revealed that eleven out of the twenty-five E. coli isolates (44%) screened for ESBL resistance genes had TEM genes while four of the isolates (16%) had SHV gene. This study concluded that drinking water could be a source of exposure to antibiotic—resistant E. coli which may pose a threat to human populations and their health in the study area.

Impact Analysis of Climate Change, Socioeconomic Development, and Hydropower Generation on Water Availability in the Chitral River Basin Using Water Evaluation and Planning (WEAP) Model

Water, energy, and food are three major issues of concern because of the rapid growth of the population and economy, which are exacerbated by climate change. The disparity between the availability and demand of water is largely driven by domestic and agricultural uses, and it is important to evaluate its impact on hydropower generation. This study aims to integrate climate change, socioeconomic development, and hydropower generation analysis using the water evaluation and planning model (WEAP). This study uses the CMIP6 model to make future projections under shared socioeconomic pathways (SSPs). This study examined the projections of water demand under different scenarios (SSP1-2.6, SSP2-4.5, and SSP5-8.5) using the MPI-ESM1-2HR climate change model. In the reference year 2000, domestic water demand stood at 15 MCM, escalating to 54 MCM under the SSP5-8.5 scenario. Concurrently, agricultural water demand, which was 93.72 MCM in 2000, is projected to surge to 197.35 MCM by 2050. Based on expected future changes in streamflow, the results show that Golen Gol’s hydropower potential varies with the effects of socioeconomic and climatic changes. However, the fluctuation in hydropower generation is more prominent during June and July, leading to an increase in hydropower in future scenarios. The study findings suggest that by 2050, the combination of population growth and agricultural expansion will substantially escalate water demand, posing risks to both the environment and human populations. Consequently, adopting enhanced irrigation methods, refining agricultural techniques, and erecting water conservation and retention infrastructures could effectively mitigate these challenges. To formulate sustainable water management strategies, it is advised to further utilize the integrated water–energy–food nexus approach, strengthened by merging WEAP with the energy modeling program Low Emissions Analysis Platform (LEAP) for hydropower generation.

Reading comprehension in L1 and L2 readers: neurocomputational mechanisms revealed through large language models

While evidence has accumulated to support the argument of shared computational mechanisms underlying language comprehension between humans and large language models (LLMs), few studies have examined this argument beyond native-speaker populations. This study examines whether and how alignment between LLMs and human brains captures the homogeneity and heterogeneity in both first-language (L1) and second-language (L2) readers. We recorded brain responses of L1 and L2 English readers of texts and assessed reading performance against individual difference factors. At the group level, the two groups displayed comparable model-brain alignment in widespread regions, with similar unique contributions from contextual embeddings. At the individual level, multiple regression models revealed the effects of linguistic abilities on alignment for both groups, but effects of attentional ability and language dominance status for L2 readers only. These findings provide evidence that LLMs serve as cognitively plausible models in characterizing homogeneity and heterogeneity in reading across human populations.

One Health policy communities’ perspectives on zoonoses risk factors and management: A multiple qualitative methods approach

Abstract Zoonoses emergence and endemicity are serious global public health problems that disproportionately affect low-resource settings. One Health (OH) serves as a framework to understand the interconnection of zoonoses risk factors and incentivizes collaboration, coordination, and communication among sectors. However, OH encounters barriers related to power imbalances, gaps in coordination, and conflicts of interest among diverse communities of practice, which are groups that share a problem and domain of interest and engage in collective learning. This research aims to elucidate the mental models of policy communities, which are representations of the environment, and how humans explain and predict their surroundings to describe their perspectives on zoonoses’ risk factors and management. We used a multiple methods approach, including qualitative system dynamics and rapid qualitative methods (RQM), to describe the perspectives of policy communities regarding the drivers of zoonoses emergence and endemicity and the complexity of zoonoses management. Participants included national and sub-national policy makers and key informants integral to zoonoses programs in Peru, including representatives of human, animal, and environmental systems. We completed 77 semi-structured interviews from June 2023 to November 2023, and the final analytical sample included 75 interviews, excluding 2 incomplete interviews. Participants’ mental models were represented with synthesized systems dynamics diagrams. Main themes and quotes from the RQM added context to the diagrams and described participants’ perspectives regarding zoonoses management complexity. Representatives from animal, human, and environmental public organizations described a similar structural conceptualization of the risk factors related to pets, humans, wildlife, and livestock, identifying economic, social, and environmental risk factors linked to zoonoses emergence and endemicity. Central themes include: global structural economic and social forces; factors affecting biodiversity and natural reservoirs; environmental changes; medical and public health services; country economic factors; rural reliance on farming and limited funding; agricultural factors; and water, hygiene, and sanitation-responsive governance. The system dynamics diagrams illustrated interrelationships between pet, human, wildlife, and livestock populations. However, risk factors related to zoonoses affecting livestock were more prominently represented. Participants recognized the need to apply OH to address zoonoses; however, contextual factors, such as regional adaptation, were necessary in poor rural areas. The study’s results inform about value systems that guide political action and decision making among the diverse OH communities of practice. A similar application in high-income settings could identify differences in zoonoses’ risk factors that may not be related to rural vulnerability or poverty. Further research is needed to describe the interconnection of organizational factors associated with OH collaborations. One Health impact statement Zoonoses control and prevention require collaboration, communication, and coordination among disciplines, organizations, communities, and regions. In this context, policy communities with different perspectives and agendas require a shared understanding of the problem to align their interests for collaboration. One Health provides an adequate framework for context-specific analysis of the policy process, incentivizing the inclusion of various levels of government and sectors. Our study investigated policy communities’ perspectives on the drivers and consequences of zoonoses’ emergence and endemicity in a low-resource setting. We included policy makers and experts from national and sub-national Peruvian organizations in animal, environmental, and human systems. This study examines the existing policy process and narratives surrounding the prevention and control of zoonoses in Peru. It is the first step to understanding how systems could be efficient and effective in facilitating multisectoral collaboration and coordination while informing efforts to scale up One Health programs in low-resource settings.

Q&A with Ke Wang.

Q&A with Ke Wang.

Ancient environmental DNA indicates limited human impact on marine biodiversity in pre-industrial Iceland.

Human activities are affecting marine biodiversity globally by accelerating extinction rates, altering ecosystem conditions and changing community structures. These changes can only be understood through establishing the ecosystem state prior to significant anthropogenic impact and by disentangling the anthropogenic effect from natural climatic changes. Here, we reconstruct marine biodiversity in Iceland across three millennia (1315 BCE-1785 CE), encompassing periods of climatic fluctuation and human settlement, to explore the comparative effect of natural and anthropogenic forces on marine biodiversity. We performed 18S metabarcoding of ancient environmental DNA from two sediment cores collected from northern Icelandic shelf seas, integrating local climatic records, population estimates and zooarchaeological remains from published sources to estimate the influence of climatic and anthropogenic impacts. Against the backdrop of increasing human populations and marine exploitation, we observe no large-scale taxonomic shifts or anthropogenic biodiversity changes across the period. In contrast, we found a positive correlation between herring (Clupea harengus) detection rates and proxy-reconstructed sea surface temperature, suggesting a role for climate in shaping marine biodiversity. Overall, our data suggest that despite impacts on terrestrial ecosystems and the development of a substantial export fishery across the study period, Icelandic society may have had a limited effect on marine biodiversity.This article is part of the theme issue 'Shifting seas: understanding deep-time human impacts on marine ecosystems'.

Cybersecurity Challenges in Small and Medium Enterprises: A Scoping Review

Small and medium-sized enterprises (SMEs) are one of the most important engines to add to the global economy by providing financial benefits to the human population, in the form of businesses (90%) and employment ships (60%). With the increase in the ratio of cybercrimes, SMEs have been overlooked in terms of cybersecurity measures, leaving them unprepared to deal with the increasing frequency, sophistication, and destructiveness of cyber challenges. This scoping review is designed to address the various cybersecurity threats to SMEs and their possible overcome. In this review, various databases such as Google Scholar, IEEE, Elsevier, Science Direct, and Taylor & Francis online were utilized in exploring the reported literature, and searched under various terminologies, in combinations and separately. Overall, 30 research articles were found to be most relevant to the respective topic, from which 20 unique themes were identified and categorized in novel findings. A framework was proposed for this scoping review by performing data analysis, which led us to find 20 different types of cyber challenges in SMEs. These challenges were further standardized into four classes. In this review, the main challenges to attaining cybersecurity resilience in SMEs are found to be a lack of awareness, unsuitable guidelines for SMEs, limited cybersecurity Knowledge, and constrained financial resources.

The spatiotemporal distribution of human pathogens in ancient Eurasia.

Infectious diseases have had devastating effects on human populations throughout history, but important questions about their origins and past dynamics remain1. To create an archaeogenetic-based spatiotemporal map of human pathogens, we screened shotgun-sequencing data from 1,313 ancient humans covering 37,000 years of Eurasian history. We demonstrate the widespread presence of ancient bacterial, viral and parasite DNA, identifying 5,486 individual hits against 492 species from 136 genera. Among those hits, 3,384 involve known human pathogens2, many of which had not previously been identified in ancient human remains. Grouping the ancient microbial species according to their likely reservoir and type of transmission, we find that most groups are identified throughout the entire sampling period. Zoonotic pathogens are only detected fromaround 6,500 years ago, peaking roughly 5,000 years ago, coinciding with the widespread domestication of livestock3. Our findings provide direct evidence that this lifestyle change resulted in an increased infectious disease burden. They also indicate that the spread of these pathogens increased substantially during subsequent millennia, coinciding with the pastoralist migrations from the Eurasian Steppe4,5.

Bisphenol S Induced Transgenerational Lipid Accumulation by Triggering Intestine-to-Germline Histone H3K4me3 Modification in Caenorhabditis elegans.

Despite the widespread prevalence of BPS in human populations, its potential impacts on offspring and the underlying mechanisms remain poorly understood. In this study, we found that parental exposure to BPS at environmental doses induced lipid accumulation in Caenorhabditis elegans from one-generational parent (P0) to two-generational offspring (F2), even in the absence of BPS exposure in offspring. Mechanistically, BPS-induced transgenerational lipid accumulation was due to the activation of lipogenic genes (fat-5 and fat-7, encoding delta-9 desaturases) and the associated transcriptional regulators (sbp-1 and mdt-15). Knockdown of methyltransferase wdr-5.1 reversed BPS-induced transgenerational inheritance via inhibiting histone H3K4 trimethylation (H3K4me3). Interestingly, germline-specific wdr-5.1/H3K4me3, rather than intestinal, was identified as being responsible for transgenerational inheritance. Our study provides the first evidence elucidating the mechanisms through which environmentally relevant BPS exposure induces lipid accumulation and transmits this effect across generations.

The Impact of Shifts in Both Precipitation Pattern and Temperature Changes on River Discharge in Central Japan

Rivers play a crucial role in the hydrological cycle and serve as essential freshwater resources for both human populations and ecosystems. Climate change significantly alters precipitation patterns and river discharge variability. However, the impact of precipitation patterns (rainfall and snowfall) and air temperature on river discharge in coastal zones remains inadequately understood. This study focused on Toyama Prefecture, located along the Sea of Japan, as a representative coastal area. We analyzed over 30 years of datasets, including air temperature, precipitation, snowfall, and river discharge, to assess the effects of climate change on river discharge. Trends in hydroclimatic datasets were assessed using the rescaled adjusted partial sums (RAPS) method and the Mann–Kendall (MK) non-parametric test. Furthermore, a correlation analysis and the Structural Equation Model (SEM) were applied to construct a relationship between precipitation, temperature, and river discharge. Our findings indicated a significant increase in air temperature at a rate of 0.2 °C per decade, with notable warming observed in late winter (January and February) and early spring (March). The average river fluxes for the Jinzu, Oyabe, Kurobe, Shou, and Joganji rivers were 182.52 m3/s, 60.37 m3/s, 41.40 m3/s, 38.33 m3/s, and 18.72 m3/s, respectively. The tipping point for snowfall decline occurred in 1992, marked by an obvious decrease in snowfall depth. The SEM showed that, although rainfall dominated the changes in river discharge (loading = 0.94), the transition from solid (snow) to liquid (rain) precipitation may alter the river discharge regime. The percentage of flood occurrence increased from 19% (1940–1992) to 41% (1993–2020). These changes highlight the urgent need to raise awareness about the impacts of climate change on river floods and freshwater resources in global coastal regions.