Assessing environmental toxins by human population effects

1982 ◽  
Vol 60 (7) ◽  
pp. 1053-1056
Author(s):  
R. E. M. Lees
Keyword(s):  
Human Population ◽  
Epidemiologic Methods ◽  
Environmental Toxins ◽  
Epidemiological Surveillance ◽  
Human Populations ◽  
Effect Relationship ◽  
Confounding Variables ◽  
Disease Associations ◽  
The Impact ◽  
Population Effects

The impact of toxins on the health of human populations can only be accurately assessed by epidemiologic methods. The investigation of toxin–disease associations in human populations and the accurate interpretation of data are often very difficult because of the existence of multiple confounding variables and the unrepresentativeness of sample or study populations.Factors influencing the deduction of cause and effect relationship rather than simple association are discussed, as is the need for continued development of epidemiological surveillance techniques.

scholarly journals High Seropositivity Rate of Neutralizing Antibodies to Astrovirus VA1 in Human Populations

mSphere ◽  
2021 ◽  
Author(s):  
Andrew B. Janowski ◽  
Macee C. Owen ◽  
Holly Dudley ◽  
Tomás López ◽  
Rafaela Espinosa ◽  
...  
Keyword(s):  
Neutralizing Antibodies ◽  
Human Population ◽  
Emerging Disease ◽  
Human Populations ◽  
Human Pathogens ◽  
Seropositivity Rate ◽  
Disease Associations

Astroviruses are human pathogens with emerging disease associations, including the recent recognition of their capacity to cause meningoencephalitis. Astrovirus VA1 is the most commonly identified astrovirus genotype from cases of human encephalitis, but it is unknown what percentage of the human population has neutralizing antibodies to VA1.

Super-volcanic eruptions and impacts on hominin evolution

2021 ◽  
Author(s):  
James Cole ◽  
Rob Hosfield
Keyword(s):  
Human Evolution ◽  
Human Population ◽  
Indian Subcontinent ◽  
Volcanic Eruptions ◽  
Climatic Conditions ◽  
Human Populations ◽  
Local Conditions ◽  
Climatic Cycles ◽  
Hominin Evolution ◽  
The Impact

<p>The impact of super volcanic eruptions (Volcanic Explosivity Index 7-8+) on human evolution is a topic that has invited much debate and controversy (Ambrose 1998, Petraglia et al. 2007, 2012; Clarkson et al., 2020), and has typically focused on the impacts on human populations within the last 100-200kya (e.g. Groucutt 2020). What is less well understood is whether there is any clear evidence to show how super-volcanic eruptions, and their subsequent impacts on paleo-environments and climates, may have influenced hominin evolution over the last c. 5mya. Previous studies using first and last hominin appearance dates have suggested that orbitally-induced climatic cycles (eccentricity, obliquity and precession) may play a role in hominin speciation events, but that only obliquity shows any significant relationship with extinction events (Grove 2012a). Firth and Cole (2015) subsequently suggested that selected super-eruptions may have acted as critical enhancers to particular orbital forcing events.</p><p> </p><p>This paper revisits the Firth and Cole (2015) study and presents a comparison of super volcanic eruptions against first and last hominin appearance dates; orbitally induced climatic cycles; global temperature (measured using the LR04 Benthic Stack – Lisiecki and Raymo 2005); and broad technological behavioural changes in order to assess to what extent such eruptions may have impacted, either directly or indirectly, on human evolution at different temporal and geographic scales. Such large eruptive events certainly do seem to disrupt climatic conditions for significant periods of time at a generational level (Harris 2008). Where data is fine grained enough, volcanic activity also seems to impact on human population dispersals, through push and pull factors, and drive changes in the behavioural record (e.g. Groucutt 2020). However, at the broad evolutionary scale, volcanic eruptions do not seem to lead to a significant turnover of hominin species (at least in regard to the resolution of the data currently available). Therefore, we suggest that future work should seek to bring these two perspectives of scale together to better understand super volcanoes in terms of the complex interplay of changing local conditions and their impacts on the broader global picture of human evolution.</p><p> </p><p> </p><p>References:</p><p>Ambrose, S.H., 1998. Late Pleistocene human population bottlenecks, volcanic winter, and differentiation of modern humans. Journal of Human Evolution. 34, 623–651.</p><p>Clarkson, C. et al. 2020. Human occupation of northern India spans the Toba super-eruption ~74,000 years ago. Nature Communications 11: 961.</p><p>Firth C.R. and Cole J. 2015: A review of super-volcano eruptions and their impact on hominin evolution. INQUA XIX Congress: Japan, July.</p><p>Groucutt, H. 2020. Volcanism and human prehistory in Arabia. Journal of Volcanology and Geothermal Research 402: 107003.</p><p>Harris, B. 2008. The potential impact of super-volcanic eruptions on the Earth’s atmosphere. Weather 63 (8): 221 – 225.</p><p>Petraglia, M.D., et al.,  2007. Middle Paleolithic assemblages from the Indian subcontinent before and after the Toba super-eruption. Science 317, 114–116.</p><p>Petraglia, M.D., Korisettar, R., Pal, J.N., 2012. The Toba volcanic super-eruption of 74,000 years ago: climate change, environments, and evolving humans. Quaternary International. 258, 1–4.</p>

Systematic benchmark of ancient DNA read mapping

2021 ◽  
Author(s):  
Adrien Oliva ◽  
Raymond Tobler ◽  
Alan Cooper ◽  
Bastien Llamas ◽  
Yassine Souilmi
Keyword(s):  
Ancient Dna ◽  
Dna Sequences ◽  
Population Genetic ◽  
Reference Genome ◽  
Population Data ◽  
Human Populations ◽  
Current Standard ◽  
Read Mapping ◽  
Reference Bias ◽  
The Impact

Abstract The current standard practice for assembling individual genomes involves mapping millions of short DNA sequences (also known as DNA ‘reads’) against a pre-constructed reference genome. Mapping vast amounts of short reads in a timely manner is a computationally challenging task that inevitably produces artefacts, including biases against alleles not found in the reference genome. This reference bias and other mapping artefacts are expected to be exacerbated in ancient DNA (aDNA) studies, which rely on the analysis of low quantities of damaged and very short DNA fragments (~30–80 bp). Nevertheless, the current gold-standard mapping strategies for aDNA studies have effectively remained unchanged for nearly a decade, during which time new software has emerged. In this study, we used simulated aDNA reads from three different human populations to benchmark the performance of 30 distinct mapping strategies implemented across four different read mapping software—BWA-aln, BWA-mem, NovoAlign and Bowtie2—and quantified the impact of reference bias in downstream population genetic analyses. We show that specific NovoAlign, BWA-aln and BWA-mem parameterizations achieve high mapping precision with low levels of reference bias, particularly after filtering out reads with low mapping qualities. However, unbiased NovoAlign results required the use of an IUPAC reference genome. While relevant only to aDNA projects where reference population data are available, the benefit of using an IUPAC reference demonstrates the value of incorporating population genetic information into the aDNA mapping process, echoing recent results based on graph genome representations.

scholarly journals The impact of huts on physiological stress: a refinement in post-transport housing of male guineapigs (Cavia porcellus)

2012 ◽  
Vol 46 (3) ◽  
pp. 220-224 ◽  
Author(s):  
Sherry L Walters ◽  
Cristobal Jose Torres-Urbano ◽  
Lee Chichester ◽  
Robert E Rose
Keyword(s):  
Animal Welfare ◽  
Physiological Stress ◽  
Cortisol Concentration ◽  
Experimental Science ◽  
Housing Environment ◽  
Confounding Variables ◽  
Animal Use ◽  
Acclimatization Period ◽  
The Impact ◽  
The Ideal

The ideal animal model would contribute no confounding variables in experimental science. Variables affect experimental design resulting in increased animal use or repeated studies. We demonstrated a simple refinement which may reduce the number of animals used experimentally while simultaneously improving animal welfare. The objective of this study was to determine if the presence of a hut was an impact on physiological stress levels, as determined by faecal cortisol concentration, during a routine four-day acclimatization period of newly received male Hartley-Outbred guineapigs. We hypothesized that those animals provided with huts would have decreased physiological stress compared with animals not provided with huts. We examined this effect within both paired and single-housed animals. A between-subjects one-way analysis of variance revealed that pair-housed animals with a hut had significantly lower faecal cortisol concentration than pair-housed animals without a hut and the presence and absence of a hut had no significant impact on faecal cortisol concentration in single-housed animals. These findings show that presence of a hut is beneficial in reducing physiological stress when pair housing male guineapigs and does not appear to have an impact when single housing male guineapigs. In addition, we have shown that faecal cortisol, and therefore physiological stress, is still increasing on study day 4 suggesting a longer acclimatization period is necessary. A simple refinement in housing environment and acclimatization time can both reduce the number of animals used experimentally and improve animal welfare.

scholarly journals Association of body condition with lameness in dairy cattle: a single-farm longitudinal study

2021 ◽  
pp. 1-4
Author(s):  
Michaela Kranepuhl ◽  
Detlef May ◽  
Edna Hillmann ◽  
Lorenz Gygax
Keyword(s):  
Body Condition ◽  
Body Condition Score ◽  
Mixed Effects ◽  
Mixed Effects Models ◽  
Linear Mixed Effects Models ◽  
Linear Mixed Effects ◽  
Confounding Variables ◽  
Condition Score ◽  
The Impact ◽  
The Relationship

Abstract This research communication describes the relationship between the occurrence of lameness and body condition score (BCS) in a sample of 288 cows from a single farm that were repeatedly scored in the course of 9 months while controlling for confounding variables. The relationship between BCS and lameness was evaluated using generalised linear mixed-effects models. It was found that the proportion of lame cows was higher with decreasing but also with increasing BCS, increased with lactation number and decreased with time since the last claw trimming. This is likely to reflect the importance of sufficient body condition in the prevention of lameness but also raises the question of the impact of overcondition on lameness and the influence of claw trimming events on the assessment of lameness. A stronger focus on BCS might allow improved management of lameness that is still one of the major problems in housed cows.

scholarly journals Survival analysis of time to SARS-CoV-2 PCR negativisation to optimise PCR prescription in health workers: the Henares COVID-19 healthcare workers cohort study

2021 ◽  
pp. oemed-2020-106903
Author(s):  
Julio González Martin-Moro ◽  
Marta Chamorro Gómez ◽  
Galicia Dávila Fernández ◽  
Ana Elices Apellaniz ◽  
Ana Fernández Hortelano ◽  
...  
Keyword(s):  
Cohort Study ◽  
Healthcare Workers ◽  
Cox Regression ◽  
Health Workers ◽  
Upper Respiratory Tract ◽  
Rt Pcr ◽  
Kaplan Meier ◽  
Confounding Variables ◽  
The Impact ◽  
Associated Variables

ObjectivesReverse transcriptase PCR (RT-PCR) is considered the gold standard in diagnosing COVID-19. Infected healthcare workers do not go back to work until RT-PCR has demonstrated that the virus is no longer present in the upper respiratory tract. The aim of this study is to determine the most efficient time to perform RT-PCR prior to healthcare workers’ reincorporation.Materials and methodsThis is a cohort study of healthcare workers with RT-PCR-confirmed COVID-19. Data were collected using the medical charts of healthcare workers and completed with a telephone interview. Kaplan-Meier curves were used to determine the influence of several variables on the time to RT-PCR negativisation. The impact of the variables on survival was assessed using the Breslow test. A Cox regression model was developed including the associated variables.Results159 subjects with a positive RT-PCR out of 374 workers with suspected COVID-19 were included. The median time to negativisation was 25 days from symptom onset (IQR 20–35 days). Presence of IgG, dyspnoea, cough and throat pain were associated with significant longer time to negativisation. Cox logistic regression was used to adjust for confounding variables. Only dyspnoea and cough remained in the model as significant determinants of prolonged negativisation time. Adjusted HRs were 0.68 (0.48–096) for dyspnoea and 0.61 (0.42–0.88) for dry cough.ConclusionsRT-PCR during the first 3 weeks leads to a high percentage of positive results. In the presence of respiratory symptoms, negativisation took nearly 1 week more. Those who developed antibodies needed longer time to negativisate.

scholarly journals Impact of Influenza A Virus Shutoff Proteins on Host Immune Responses

Vaccines ◽  
2021 ◽  
Vol 9 (6) ◽  
pp. 629
Author(s):  
Megan M. Dunagan ◽  
Kala Hardy ◽  
Toru Takimoto
Keyword(s):  
Immune Response ◽  
Immune Responses ◽  
Influenza A Virus ◽  
Influenza A ◽  
Human Populations ◽  
Lymphocyte Migration ◽  
Host Immune Responses ◽  
Mhc Molecules ◽  
The Impact

Influenza A virus (IAV) is a significant human pathogen that causes seasonal epidemics. Although various types of vaccines are available, IAVs still circulate among human populations, possibly due to their ability to circumvent host immune responses. IAV expresses two host shutoff proteins, PA-X and NS1, which antagonize the host innate immune response. By transcriptomic analysis, we previously showed that PA-X is a major contributor for general shutoff, while shutoff active NS1 specifically inhibits the expression of host cytokines, MHC molecules, and genes involved in innate immunity in cultured human cells. So far, the impact of these shutoff proteins in the acquired immune response in vivo has not been determined in detail. In this study, we analyzed the effects of PA-X and NS1 shutoff activities on immune response using recombinant influenza A/California/04/2009 viruses containing mutations affecting the expression of shutoff active PA-X and NS1 in a mouse model. Our data indicate that the virus without shutoff activities induced the strongest T and B cell responses. Both PA-X and NS1 reduced host immune responses, but shutoff active NS1 most effectively suppressed lymphocyte migration to the lungs, antibody production, and the generation of IAV specific CD4+ and CD8+ T cells. NS1 also prevented the generation of protective immunity against a heterologous virus challenge. These data indicate that shutoff active NS1 plays a major role in suppressing host immune responses against IAV infection.

scholarly journals Quantifying the impact of land degradation on crop production: the case of Senegal

Solid Earth ◽  
2016 ◽  
Vol 7 (1) ◽  
pp. 93-103 ◽  
Author(s):  
B. G. J. S. Sonneveld ◽  
M. A. Keyzer ◽  
D. Ndiaye
Keyword(s):  
Land Degradation ◽  
Crop Production ◽  
Crop Yields ◽  
Fertilizer Application ◽  
Yield Reduction ◽  
Sufficient Information ◽  
Persistent Problem ◽  
Confounding Variables ◽  
A Site ◽  
The Impact

Abstract. Land degradation has been a persistent problem in Senegal for more than a century and by now has become a serious impediment to long-term development. In this paper, we quantify the impact of land degradation on crop yields using the results of a nationwide land degradation assessment. For this, the study needs to address two issues. First, the land degradation assessment comprises qualitative expert judgements that have to be converted into more objective, quantitative terms. We propose a land degradation index and assess its plausibility. Second, observational data on soils, land use, and rainfall do not provide sufficient information to isolate the impact of land degradation. We, therefore, design a pseudo-experiment that for sites with otherwise similar circumstances compares the yield of a site with and one without land degradation. This pairing exercise is conducted under a gradual refining of the classification of circumstances, until a more or less stable response to land degradation is obtained. In this way, we hope to have controlled sufficiently for confounding variables that will bias the estimation of the impact of land degradation on crop yields. A small number of shared characteristics reveal tendencies of "severe" land degradation levels being associated with declining yields as compared to similar sites with "low" degradation levels. However, as we zoom in at more detail some exceptions come to the fore, in particular in areas without fertilizer application. Yet, our overall conclusion is that yield reduction is associated with higher levels of land degradation, irrespective of whether fertilizer is being applied or not.

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