Solving the riddle of codon usage preferences: a test for translational selection

Translational selection is responsible for the unequal usage of synonymous codons in protein coding genes in a wide variety of organisms. It is one of the most subtle and pervasive forces of molecular evolution, yet, establishing the underlying causes for its idiosyncratic behaviour across living kingdoms has proven elusive to researchers over the past 20 years. In this study, a statistical model for measuring translational selection in any given genome is developed, and the test is applied to 126 fully sequenced genomes, ranging from archaea to eukaryotes. It is shown that tRNA gene redundancy and genome size are interacting forces that ultimately determine the action of translational selection, and that an optimal genome size exists for which this kind of selection is maximal. Accordingly, genome size also presents upper and lower boundaries beyond which selection on codon usage is not possible. We propose a model where the coevolution of genome size and tRNA genes explains the observed patterns in translational selection in all living organisms. This model finally unifies our understanding of codon usage across prokaryotes and eukaryotes. Helicobacter pylori, Saccharomyces cerevisiae and Homo sapiens are codon usage paradigms that can be better understood under the proposed model

The age patterns of severe malaria syndromes in sub-Saharan Africa across a range of transmission intensities and seasonality settings

BACKGROUND: A greater understanding of the relationship between transmission intensity, seasonality and the age-pattern of malaria is needed to guide appropriate targeting of malaria interventions in different epidemiological settings. METHODS: A systematic literature review identified studies which reported the age of paediatric hospital admissions with cerebral malaria (CM), severe malarial anaemia (SMA), or respiratory distress (RD). Study sites were categorized into a 3 × 2 matrix of Plasmodium falciparum transmission intensity and seasonality. Probability distributions were fitted by maximum likelihood methods, and best fitting models were used to estimate median ages and to represent graphically the age-pattern of each outcome for each transmission category in the matrix. RESULTS: A shift in the burden of CM towards younger age groups was seen with increasing intensity of transmission, but this was not the case for SMA or RD. Sites with 'no marked seasonality' showed more evidence of skewed age-patterns compared to areas of 'marked seasonality' for all three severe malaria syndromes. CONCLUSIONS: Although the peak age of CM will increase as transmission intensity decreases in Africa, more than 75% of all paediatric hospital admissions of severe malaria are likely to remain in under five year olds in most epidemiological settings

Why caretakers bypass Primary Health Care facilities for child care - a case from rural Tanzania

<p>Abstract</p> <p>Background</p> <p>Research on health care utilization in low income countries suggests that patients frequently bypass PHC facilities in favour of higher-level hospitals - despite substantial additional time and financial costs. There are limited number of studies focusing on user's experiences at such facilities and reasons for bypassing them. This study aimed to identify factors associated with bypassing PHC facilities among caretakers seeking care for their underfive children and to explore experiences at such facilities among those who utilize them.</p> <p>Methods</p> <p>The study employed a mixed-method approach consisting of an interviewer administered questionnaires and in-depth interviews among selected care-takers seeking care for their underfive children at Korogwe and Muheza district hospitals in north-eastern Tanzania.</p> <p>Results</p> <p>The questionnaire survey included 560 caretakers. Of these 30 in-depth interviews were conducted. Fifty nine percent (206/348) of caretakers had not utilized their nearer PHC facilities during the index child's sickness episode. The reasons given for bypassing PHC facilities were lack of possibilities for diagnostic facilities (42.2%), lack of drugs (15.5%), closed health facility (10.2%), poor services (9.7%) and lack of skilled health workers (3.4%). In a regression model, the frequency of bypassing a PHC facility for child care increased significantly with decreasing travel time to the district hospital, shorter duration of symptoms and low disease severity.</p> <p>Findings from the in-depth interviews revealed how the lack of quality services at PHC facilities caused delays in accessing appropriate care and how the experiences of inadequate care caused users to lose trust in them.</p> <p>Conclusion</p> <p>The observation that people are willing to travel long distances to get better quality services calls for health policies that prioritize quality of care before quantity. In a situation with limited resources, utilizing available resources to improve quality of care at available facilities could be more appropriate for improving access to health care than increasing the number of facilities. This would also improve equity in health care access since the poor who can not afford travelling costs will then get access to quality services at their nearer PHC facilities.</p

Do social networks affect the use of residential aged care among older Australians?

Background: Older people's social networks with family and friends can affect residential aged care use. It remains unclear if there are differences in the effects of specific (with children, other relatives, friends and confidants) and total social networks upon use of low-level residential care and nursing homes. Methods: Data were drawn from the Australian Longitudinal Study of Ageing. Six waves of data from 1477 people aged ≥ 70 collected over nine years of follow-up were used. Multinomial logistic regressions of the effects of specific and total social networks on residential care use were carried out. Propensity scores were used in the analyses to adjust for differences in participant's health, demographic and lifestyle characteristics with respect to social networks. Results Higher scores for confidant networks were protective against nursing home use (odds ratio [OR] upper versus lower tertile of confidant networks = 0.50; 95%CI 0.33–0.75). Similarly, a significant effect of upper versus lower total network tertile on nursing home use was observed (OR = 0.62; 95%CI 0.43–0.90). Evidence of an effect of children networks on nursing home use was equivocal. Nursing home use was not predicted by other relatives or friends social networks. Use of lower-level residential care was unrelated to social networks of any type. Social networks of any type did not have a significant effect upon low-level residential care use. Discussion: Better confidant and total social networks predict nursing home use in a large cohort of older Australians. Policy needs to reflect the importance of these particular relationships in considering where older people want to live in the later years of life.Lynne C Giles, Gary FV Glonek, Mary A Luszcz and Gary R Andrew

A simple method for defining malaria seasonality

BACKGROUND: There is currently no standard way of defining malaria seasonality, resulting in a wide range of definitions reported in the literature. Malaria cases show seasonal peaks in most endemic settings, and the choice and timing for optimal malaria control may vary by seasonality. A simple approach is presented to describe the seasonality of malaria, to aid localized policymaking and targeting of interventions. METHODS: A series of systematic literature reviews were undertaken to identify studies reporting on monthly data for full calendar years on clinical malaria, hospital admission with malaria and entomological inoculation rates (EIR). Sites were defined as having 'marked seasonality' if 75% or more of all episodes occurred in six or less months of the year. A 'concentrated period of malaria' was defined as the six consecutive months with the highest cumulative proportion of cases. A sensitivity analysis was performed based on a variety of cut-offs. RESULTS: Monthly data for full calendar years on clinical malaria, all hospital admissions with malaria, and entomological inoculation rates were available for 13, 18, and 11 sites respectively. Most sites showed year-round transmission with seasonal peaks for both clinical malaria and hospital admissions with malaria, with a few sites fitting the definition of 'marked seasonality'. For these sites, consistent results were observed when more than one outcome or more than one calendar year was available from the same site. The use of monthly EIR data was found to be of limited value when looking at seasonal variations of malaria transmission, particularly at low and medium intensity levels. CONCLUSION: The proposed definition discriminated well between studies with 'marked seasonality' and those with less seasonality. However, a poor fit was observed in sites with two seasonal peaks. Further work is needed to explore the applicability of this definition on a wide-scale, using routine health information system data where possible, to aid appropriate targeting of interventions

Body composition-derived BMI cut-offs for overweight and obesity in Indians and Creoles of Mauritius: comparison with Caucasians

Global estimates of overweight and obesity prevalence are based on the World Health Organisation (WHO) body mass index (BMI) cut-off values of 25 and 30 kg m⁻², respectively. To validate these BMI cut-offs for adiposity in the island population of Mauritius, we assessed the relationship between BMI and measured body fat mass in this population according to gender and ethnicity.Methods: In 175 young adult Mauritians (age 20-42 years) belonging to the two main ethnic groups—Indians (South Asian descent) and Creoles (African/Malagasy descent), body weight, height and waist circumference (WC) were measured, total body fat assessed by deuterium oxide (D2O) dilution and trunk (abdominal) fat by segmental bioimpedance analysis.Results: Compared to body fat% predicted from BMI using Caucasian-based equations, body fat% assessed by D2O dilution in Mauritians was higher by 3–5 units in Indian men and women as well as in Creole women, but not in Creole men. This gender-specific ethnic difference in body composition between Indians and Creoles is reflected in their BMI–Fat% relationships, as well as in their WC–Trunk Fat% relationships. Overall, WHO BMI cut-offs of 25 and 30 kg m⁻² for overweight and obesity, respectively, seem valid only for Creole men (~24 and 29.5, respectively), but not for Creole women whose BMI cut-offs are 2–4 units lower (21–22 for overweight; 27–28 for obese) nor for Indian men and women whose BMI cut-offs are 3–4 units lower (21–22 for overweight; 26–27 for obese).Conclusions: The use of BMI cut-off points for classifying overweight and obesity need to take into account both ethnicity and gender to avoid gross adiposity status misclassification in this population known to be at high risk for type-2 diabetes and cardiovascular diseases. This is particularly of importance in obesity prevention strategies both in clinical medicine and public health

Spectral Risk Measures and the Choice of Risk Aversion Function

UCD Geary Institute Discussion Papers often represent preliminary work and are circulated to encourage discussion. Citation of such a paper should account for its provisional character. A revised version may be available directly from the author. Any opinions expressed here are those of the author(s) and not those of UCD Geary Institute. Research published in this series may include views on policy, but the institute itself takes no institutional policy positions

Compact diode laser based light source with alternating dual-wavelength emission at 532 nm

Compact nonlinear frequency conversion of a Y-branch distributed Bragg reflector (DBR) diode laser for alternating dual-wavelength laser emission at 532 nm is presented for the very first time. The developed light source, realized on a 5 × 25 mm2 micro-optical bench, is based on single-pass second harmonic generation of a 1064 nm Y-branch DBR diode laser in a periodically poled lithium niobate waveguide crystal with superimposed poling periods. Phase-matching is obtained by intrinsic wavelength stabilization of the laser and wavelength tuning by implemented heater elements above the DBR gratings. Obtained optical output powers of 5.6 mW at 532.45 nm and 6.7 mW at 531.85 nm are limited by central lobe power contents of 52% available for waveguide coupling. With a spectral performance showing narrowband emission with spectral widths of 0.01 nm (0.4 cm−1) limited by the spectral resolution of the spectrum analyzer and a spectral spacing of 0.6 nm (20 cm−1), the developed light source is suitable for applications such as Raman spectroscopy and shifted excitation Raman difference spectroscopy (SERDS). Separate electrical contacts of the Y-branch diode laser enable alternating operation at both wavelengths