Geographically regulated designs of incidence surveys can match the precision of classical survey designs whilst requiring smaller sample sizes: the case of snakebite envenoming in Sri Lanka

Background

Snakebite envenoming is a neglected tropical disease. Data from the worst affected countries are limited because conducting epidemiological surveys is challenging. We assessed the utility of inhibitory geostatistical design with close pairs (ICP) to estimate snakebite envenoming incidence.

Methods

The National Snakebite Survey (NSS) in Sri Lanka adopted a multistage cluster sampling design, based on population distribution, targeting 1% of the country’s population. Using a simulation-based study, we assessed predictive efficiency of ICP against a classical survey design at different fractions of the original sample size of the NSS. We also assessed travel distance, time taken to complete the survey, and sensitivity and specificity for detecting high-risk areas for snake envenoming, when using these methods.

Results

A classical survey design with 33% of the original NSS sample size was able to yield a similar predictive efficiency. ICP yielded the same at 25% of the NSS sample size, a 25% reduction in sample size compared with a classical survey design. ICP showed >80% sensitivity and specificity for detecting high-risk areas of envenoming when the sampling fraction was >20%. When ICP was adopted with 25% of the original NSS sample size, travel distance was reduced by >40% and time to conduct the survey was reduced by >75%.

Conclusions

This study showed that snakebite envenoming incidence can be estimated by adopting an ICP design with similar precision at a lower sample size than a classical design. This would substantially save resources and time taken to conduct epidemiological surveys and may be suited for low-resource settings.

STEM vs non-STEM differences in university teaching and research during the COVID-19 pandemic: the case of Sri Lanka

Purpose

This study aims to explore the differences between science, technology, engineering and mathematics (STEM) and non-STEM disciplines in terms of the changes to teaching and research practices caused by the COVID-19 pandemic.

Design/methodology/approach

The paper analyses survey responses collected between July and November 2020 from 241 academics (excluding library staff) from the five oldest state universities in Sri Lanka. The analysis focuses on the differences between STEM and non-STEM faculty using multiple linear regression to control for demographic characteristics such as age, gender and designation as well as university-specific factors.

Findings

The paper finds significant differences in the teaching practices of STEM and non-STEM academics, both in terms of preparation time for teaching and tools used for online delivery. Significant differences are also observed in research practices, with STEM faculty being significantly more likely to engage in research collaborations, obtain research funding and be involved in more research projects. The authors do not find any evidence of the pandemic having differential impacts on research productivity between the broad disciplines.

Originality/value

This research provides insights into the differences between STEM and non-STEM disciplines in online teaching and research practices adopted since the onset of the pandemic, which are important for formulating appropriate policy responses to mitigate the impact of the pandemic on both students and staff. The contribution is particularly significant for developing countries where the creation of a skilled workforce is a key driver of the development process.

Analysis of protein profile of tomato root infected with Fusarium oxysporum f. sp lycopersici

Fusarium wilt caused by Fusarium oxysporum f. sp lycopersici (Fol) is one of the main diseases affecting tomatoes. The BHRS 2,3 genotype of tomato is, however, resistant to this disease. A proteomic approach was used to understand the defense mechanisms of this genotype using the tomato root, the first tissue that interacts with the fungus, as a target. Protein was extracted and separated by two-dimensional electrophoresis followed by staining with Coomassie brilliant blue. The proteins were identified by MALDI-TOF/TOF mass spectrometry. A total of 22 proteins were identified, 21 of which showed differential expression with 12 proteins being upregulated and nine being downregulated. Plants responded to the pathogen with increased expression of pathogenesis-related proteins. We noted the induction of proteins involved in hypersensitivity reaction and other defense mechanisms. The expression of proteins of primary metabolism related to energy production, however, decreased, as did the expression of two proteins related to defense against abiotic stress. These results demonstrate the presence of important mechanisms for defense against Fol in the tomato genotype BHRS 2,3.

Population Control Policies and Fertility Convergence

Rapid population growth in developing countries in the middle of the 20th century led to fears of a population explosion and motivated the inception of what effectively became a global population-control program. The initiative, propelled in its beginnings by intellectual elites in the United States, Sweden, and some developing countries, mobilized resources to enact policies aimed at reducing fertility by widening contraception provision and changing family-size norms. In the following five decades, fertility rates fell dramatically, with a majority of countries converging to a fertility rate just above two children per woman, despite large cross-country differences in economic variables such as GDP per capita, education levels, urbanization, and female labor force participation. The fast decline in fertility rates in developing economies stands in sharp contrast with the gradual decline experienced earlier by more mature economies. In this paper, we argue that population-control policies likely played a central role in the global decline in fertility rates in recent decades and can explain some patterns of that fertility decline that are not well accounted for by other socioeconomic factors.

CYP2E1 RsaI and 96-bp insertion genetic polymorphisms associated with risk for colorectal cancer

We investigated a possible association between alcoholism, cigarette smoking, obesity and CYP2E1 RsaI and 96-bp insertion genetic polymorphisms with risk for colorectal cancer (CRC). Patients with CRC (70 women and 61 men) were matched for gender and age to 206 healthy controls. The mean age of the two groups was 62 years. Meat intake, cigarette smoking and alcohol drinking were assessed using a specific frequency questionnaire. The body mass index was also calculated. DNA was extracted from peripheral blood; RsaI polymorphism genotypes were evaluated by PCR-RFLP and 96-bp insertion genetic polymorphisms were evaluated by specific primers. The distributions of CYP2E1 RsaI c1/c1, c1/c2 and c2/c2 genotypes were 90.2, 9.2 and 0.6%, respectively, in controls and 83.9, 13.7 and 2.4% in CRC cases. Allele c2 was associated with increased risk for CRC [odds ratio (OR) = 1.88, 95% confidence interval (95%CI) = 1.02-3.45]. The CYP2E1 RsaI c2/c2 genotype was associated with an increased risk for rectal cancer (OR = 3.23, 95%CI = 1.26-9.03). The 96-bp insertion was slightly more frequent in the CRC group (9.3 vs 11.4%, P = 0.19), especially in females (6.4 vs 11.5%, P = 0.34). Smoking, alcohol drinking or high intake of red meat and CYP2E1 polymorphisms were not associated with increased risk for CRC. The 96-bp insertion was marginally more frequent (P = 0.07) in undernourished CRC subjects. We concluded that the risk for CRC is higher among individuals with allele c2. The CYP2E1 RsaI c2/c2 genotype was associated with an increased risk for rectal cancer.

A comparative genomics strategy for targeted discovery of single-nucleotide polymorphisms and conserved-noncoding sequences in orphan crops

Completed genome sequences provide templates for the design of genome analysis tools in orphan species lacking sequence information. To demonstrate this principle, we designed 384 PCR primer pairs to conserved exonic regions flanking introns, using Sorghum/Pennisetum expressed sequence tag alignments to the Oryza genome. Conserved-intron scanning primers (CISPs) amplified single-copy loci at 37% to 80% success rates in taxa that sample much of the approximately 50-million years of Poaceae divergence. While the conserved nature of exons fostered cross-taxon amplification, the lesser evolutionary constraints on introns enhanced single-nucleotide polymorphism detection. For example, in eight rice (Oryza sativa) genotypes, polymorphism averaged 12.1 per kb in introns but only 3.6 per kb in exons. Curiously, among 124 CISPs evaluated across Oryza, Sorghum, Pennisetum, Cynodon, Eragrostis, Zea, Triticum, and Hordeum, 23 (18.5%) seemed to be subject to rigid intron size constraints that were independent of per-nucleotide DNA sequence variation. Furthermore, we identified 487 conserved-noncoding sequence motifs in 129 CISP loci. A large CISP set (6,062 primer pairs, amplifying introns from 1,676 genes) designed using an automated pipeline showed generally higher abundance in recombinogenic than in nonrecombinogenic regions of the rice genome, thus providing relatively even distribution along genetic maps. CISPs are an effective means to explore poorly characterized genomes for both DNA polymorphism and noncoding sequence conservation on a genome-wide or candidate gene basis, and also provide anchor points for comparative genomics across a diverse range of species.