Disentangling basal and accumulated body mass for cross‐population comparisons

Measures of human body mass confound 1) well‐established population differences in body form and 2) exposure to obesogenic environments, posing challenges for using body mass index (BMI) in cross‐population studies of body form, energy reserves, and obesity‐linked disease risk. We propose a method for decomposing population BMI by estimating basal BMI (bBMI) among young adults living in extremely poor, rural households where excess body mass accumulation is uncommon. We test this method with nationally representative, cross‐sectional Demographic and Health Surveys (DHS) collected from 69,916 rural women (20–24 years) in 47 low‐income countries. Predicting BMI by household wealth, we estimate country‐level bBMI as the average BMI of young women (20–24 years) living in rural households with total assets <400 USD per capita. Above 400 USD per capita, BMI increases with both wealth and age. Below this point, BMI hits a baseline floor showing little effect of either age or wealth. Between‐country variation in bBMI (range of 4.3 kg m^?2) is reliable across decades and age groups (R² = 0.83–0.88). Country‐level estimates of bBMI show no relation to diabetes prevalence or country‐level GDP (R² < 0.05), supporting its independence from excess body mass. Residual BMI (average BMI minus bBMI) shows better fit with both country‐level GDP (R² = 0.55 vs. 0.40) and diabetes prevalence (R² = 0.23 vs. 0.17) than does conventional BMI. This method produces reliable estimates of bBMI across a wide range of nationally representative samples, providing a new approach to investigating population variation in body mass. Am J Phys Anthropol 153:542–550, 2014. © 2013 Wiley Periodicals, Inc.     

Tests of Independence and Zero Correlations Among P Random Variables

Suppose it is desired to determine whether there is an association between any pair of p random variables. A common approach is to test H₀ : R = I, where R is the usual population correlation matrix. A closely related approach is to test H₀ : R_pb = I, where R_pb is the matrix of percentage bend correlations. In so far as type I errors are a concern, at a minimum any test of H₀ should have a type I error probability close to the nominal level when all pairs of random variables are independent. Currently, the Gupta-Rathie method is relatively successful at controlling the probability of a type I error when testing H₀: R = I, but as illustrated in this paper, it can fail when sampling from nonnormal distributions. The main goal in this paper is to describe a new test of H₀: R_pb = I that continues to give reasonable control over the probability of a type I error in the situations where the Gupta-Rathie method fails. Even under normality, the new method has advantages when the sample size is small relative to p. Moreover, when there is dependence, but all correlations are equal to zero, the new method continues to give good control over the probability of a type I error while the Gupta-Rathie method does not. The paper also reports simulation results on a bootstrap confidence interval for the percentage bend correlation.     

Formulas for the Computation of the WILCOXON Test and other Rank Statistics

A simple program for the computation of the WILCOXON test is introduced, which is suitable for implementation on a programmable desk computer. The allocation of ranks R_i is not necessary (see BERCHTOLD, 1979). In an analogous manner any ranks respectively rank sums also can be calculated, so that any test criterion or statistical estimate called rank statistic, may be completely constituted by computer programs without explicitely ranging of values.     

Misprescription and misuse of one‐tailed tests

One‐tailed statistical tests are often used in ecology, animal behaviour and in most other fields in the biological and social sciences. Here we review the frequency of their use in the 1989 and 2005 volumes of two journals (Animal Behaviour and Oecologia), their advantages and disadvantages, the extensive erroneous advice on them in both older and modern statistics texts and their utility in certain narrow areas of applied research. Of those articles with data sets susceptible to one‐tailed tests, at least 24% in Animal Behaviour and at least 13% in Oecologia used one‐tailed tests at least once. They were used 35% more frequently with nonparametric methods than with parametric ones and about twice as often in 1989 as in 2005. Debate in the psychological literature of the 1950s established the logical criterion that one‐tailed tests should be restricted to situations where there is interest only in results in one direction. ‘Interest’ should be defined; however, in terms of collective or societal interest and not by the individual investigator. By this ‘collective interest’ criterion, all uses of one‐tailed tests in the journals surveyed seem invalid. In his book Nonparametric Statistics, S. Siegel unrelentingly suggested the use of one‐tailed tests whenever the investigator predicts the direction of a result. That work has been a major proximate source of confusion on this issue, but so are most recent statistics textbooks. The utility of one‐tailed tests in research aimed at obtaining regulatory approval of new drugs and new pesticides is briefly described, to exemplify the narrow range of research situations where such tests can be appropriate. These situations are characterized by null hypotheses stating that the difference or effect size does not exceed, or is at least as great as, some ‘amount of practical interest’. One‐tailed tests rarely should be used for basic or applied research in ecology, animal behaviour or any other science.     

Synthesis and nootropic activity of some 2,3-dihydro-1H-isoindol-1-one derivatives structurally related with piracetam

Three 2,3‐dihydro‐1H‐isoindol‐1‐ones structurally related with piracetam (=2‐oxopyrrolidine‐1‐acetamide) have been synthesized and tested for their nootropic effects in the passive avoidance test in mice. Compounds (RS)‐ 2 , (R,R)‐ 3 , and (R,S)‐ 3 were obtained in good yields in only two steps starting from methyl dl ‐phthaloylalanine. Compound (RS)‐ 2 exhibited nootropic activity at lower doses than piracetam, used as reference drug, but it showed lower efficacy. Whereas diastereoisomers (R,R)‐ 3 and (R,S)‐ 3 were as potent as piracetam to revert amnesia induced by scopolamine, (R,S)‐ 3 showed lower efficacy than (R,R)‐ 3 . Only (R,R)‐ 3 showed myorelaxant effect at doses of 10 and 30 mg/kg; other compounds did not exhibit any anticonvulsant, sedative, myorelaxant, or impaired motor‐coordination effect in mice. These synthesized 2,3‐dihydro‐1H‐isoindol‐1‐one derivatives constitute a new kind of nootropic compounds.     

Modelling Hospitalization,Home-Based Care,and Individual Withdrawal for People Living with HIV/AIDS in High Prevalence Settings

In sub-Saharan Africa, the model of care for people who are living with HIV/AIDS has changed from hospital care to home-based care. In this paper, a mathematical model describing the dynamics of HIV transmission, hospitalization, and home-based care is constructed and analysed. The model reproduction number R _e is determined and discussed. The equilibria are determined and analysed in terms of R _e . It is shown that if R _e <1, the disease free equilibrium is both locally and globally asymptotically stable. The model has a unique endemic equilibrium and is locally asymptotically stable whenever R _e >1. Five cases arise in the discussion of R _e pertaining to intervention strategies. Numerical simulations are done to compare the impact of each strategy on the dynamics of HIV/AIDS. The model is fitted to the prevalence data estimates from UNAIDS on Zimbabwe. The implications of some key epidemiological parameters are investigated numerically. Projections are made to determine the possible long term trends of the prevalence of HIV in Zimbabwe.     

A mathematical model for malaria involving differential susceptibility,exposedness and infectivity of human host

The main purpose of this article is to formulate a deterministic mathematical model for the transmission of malaria that considers two host types in the human population. The first type is called “non-immune” comprising all humans who have never acquired immunity against malaria and the second type is called “semi-immune”. Non-immune are divided into susceptible, exposed and infectious and semi-immune are divided into susceptible, exposed, infectious and immune. We obtain an explicit formula for the reproductive number, R ₀ which is a function of the weight of the transmission semi-immune-mosquito-semi-immune, R _0a , and the weight of the transmission non-immune-mosquito-non-immune, R _0e . Then, we study the existence of endemic equilibria by using bifurcation analysis. We give a simple criterion when R ₀ crosses one for forward and backward bifurcation. We explore the possibility of a control for malaria through a specific sub-group such as non-immune or semi-immune or mosquitoes.     

Validation of a DNA methylation reference panel for the estimation of nucleated cells types in cord blood

Cord blood is widely used as surrogate tissue in epigenome-wide association studies of prenatal conditions. Cell type composition variation across samples can be an important confounder of epigenome-wide association studies in blood that constitute a mixture of cells. We evaluated a newly developed cord blood reference panel to impute cell type composition from DNA methylation levels, including nucleated red blood cells (nRBCs). We estimated cell type composition from 154 unique cord blood samples with available DNA methylation data as well as direct measurements of nucleated cell types. We observed high correlations between the estimated and measured composition for nRBCs (r = 0.92, R² = 0.85), lymphocytes (r = 0.77, R² = 0.58), and granulocytes (r = 0.72, R² = 0.52), and a moderate correlation for monocytes (r = 0.51, R² = 0.25) as well as relatively low root mean square errors from the residuals ranging from 1.4 to 5.4%. These results validate the use of the cord blood reference panel and highlight its utility and limitations for epidemiological studies.     

Value of heartburn for diagnosing gastroesophageal reflux disease in severely obese patients

Objective : To evaluate the prevalence of gastroesophageal reflux disease (GERD) in severely obese patients and the association between symptoms and objective data of GERD in this population. Research Methods and Procedures : A total of 158 consecutive severely obese patients (BMI ≥ 40 kg/m²) were prospectively evaluated. Symptoms were evaluated by a structured clinical questionnaire. Objective assessment was made by ambulatory 24‐hour esophageal pH monitoring and endoscopy. GERD was defined by the presence of symptoms or complications (esophagitis). The clinical criterion defining GERD was the presence of at least two episodes of heartburn per week. Results : The mean age of the 138 patients subjected to complete study was 42.6 ± 10.2 years, with a BMI of 50.1 ± 6.9 kg/m² (range, 40.6 to 69.4 kg/m²); 78% were women. The prevalence of GERD evaluated by symptoms and/or esophagitis was 33.3% (46/138). Clinical criteria of GERD were present in 31/138 cases (22.5%), and 26 (18.8%) had esophagitis. In 69/138 patients (50%), pHmetry was abnormal. Fifty‐three patients with esophagitis and/or abnormal pHmetry were asymptomatic. The sensitivity of heartburn as a diagnostic criterion of GERD in patients with severe obesity was 29.3%, with a specificity of 85.7%. No significant association was observed between severe obesity grade and the prevalence of symptoms and/or objective data. Discussion : Asymptomatic gastroesophageal reflux (abnormal esophageal acid exposure and/or reflux esophagitis) is more common than symptomatic gastroesophageal reflux in severely obese patients. Increased BMI is not associated with a greater prevalence of GERD in these patients.     

Identifying non-invasible habitats for marine copepods using temperature-dependent <Emphasis Type="Italic">R</Emphasis><Subscript>0</Subscript>

If a non-indigenous species is to thrive and become invasive it must first persist under its new set of environmental conditions. Net reproductive rate (R ₀) represents the average number of female offspring produced by a female over its lifetime, and has been used as a metric of population persistence. We modeled R ₀ as a function of ambient water temperature (T) for the invasive marine calanoid copepod Pseudodiaptomus marinus, which is introduced to west coast of North America from East Asia by ship ballast water. The model was based on temperature-dependent stage-structured population dynamics given by a system of ordinary differential equations. We proposed a methodology to identify habitats that are non-invasible for P. marinus using the threshold of R ₀(T) < 1 in order to identify potentially invasible habitats. We parameterized the model using published data on P. marinus and applied R ₀(T) to identify the range of non-invasible habitats in a global scale based on sea surface temperature data. The model predictions matched the field evidence of species occurrences well.     

Wave intensity amplification and attenuation in non-linear flow: Implications for the calculation of local reflection coefficients

Local reflection coefficients (R) provide important insights into the influence of wave reflection on vascular haemodynamics. Using the relatively new time-domain method of wave intensity analysis, R has been calculated as the ratio of the peak intensities (R_PI) or areas (R_CI) of incident and reflected waves, or as the ratio of the changes in pressure caused by these waves (R_ΔP). While these methods have not yet been compared, it is likely that elastic non-linearities present in large arteries will lead to changes in the size of waves as they propagate and thus errors in the calculation of R_PI and R_CI. To test this proposition, R_PI, R_CI and R_ΔP were calculated in a non-linear computer model of a single vessel with various degrees of elastic non-linearity, determined by wave speed and pulse amplitude (ΔP₊), and a terminal admittance to produce reflections. Results obtained from this model demonstrated that under linear flow conditions (i.e. as ΔP₊→0), R_ΔP is equivalent to the square-root of R_PI and R_CI (denoted by R_PI^p and R_CI^p). However for non-linear flow, pressure-increasing (compression) waves undergo amplification while pressure-reducing (expansion) waves undergo attenuation as they propagate. Consequently, significant errors related to the degree of elastic non-linearity arise in R_PI and R_CI, and also R_PI^p and R_CI^p, with greater errors associated with larger reflections. Conversely, R_ΔP is unaffected by the degree of non-linearity and is thus more accurate than R_PI and R_CI.     

Change in Criteria for USP Dissolution Performance Verification Tests

The US Pharmacopeial Convention has been evaluating its performance verification tests (PVT) for several years. These tests help ensure the integrity of the US Pharmacopeia performance test when a dissolution procedure, as described in General Chapter Dissolution <711>, is relied upon to test a nonsolution orally administered dosage form. One result of the evaluation is a change in the PVT criterion from one based on individual tablet results to one based on the mean and variability of a set of tablets. This paper describes the new PVT and its criterion and how its acceptance limits are derived from results of a collaborative study, explains a two-stage option for the test, and presents operating characteristics.     

A New Neotropical Genus and Species of Odontocerinae (Trichoptera: Odontoceridae) from Southeastern Brazil

Anastomoneura gen. nov. and A. guahybae sp. nov. are described and illustrated based on adult male and female specimens from the Mantiqueira mountain range, Minas Gerais State. This is the third genus recorded of the family Odontoceridae from South America. The new genus is characterized by the forewing anastomosis of veins R₄ and R₅ and male genitalia with a unique, tubular, projection dorsad to the plates of tergite X.     

landscapemetrics: an open‐source R tool to calculate landscape metrics

Quantifying landscape characteristics and linking them to ecological processes is one of the central goals of landscape ecology. Landscape metrics are a widely used tool for the analysis of patch‐based, discrete land‐cover classes. Existing software to calculate landscape metrics has several constraints, such as being limited to a single platform, not being open‐source or involving a complicated integration into large workflows. We present landscapemetrics, an open‐source R package that overcomes many constraints of existing landscape metric software. The package includes an extensive collection of commonly used landscape metrics in a tidy workflow. To facilitate the integration into large workflows, landscapemetrics is based on a well‐established spatial framework in R. This allows pre‐processing of land‐cover maps or further statistical analysis without importing and exporting the data from and to different software environments. Additionally, the package provides many utility functions to visualize, extract, and sample landscape metrics. Lastly, we provide building‐blocks to motivate the development and integration of new metrics in the future. We demonstrate the usage and advantages of landscapemetrics by analysing the influence of different sampling schemes on the estimation of landscape metrics. In so doing, we demonstrate the many advantages of the package, especially its easy integration into large workflows. These new developments should help with the integration of landscape analysis in ecological research, given that ecologists are increasingly using R for the statistical analysis, modelling and visualization of spatial data.     

HOW CRITICAL IS THE CRITICAL N:P RATIO?1

The value of cellular N:P that corresponds to co‐limitation by N and P, the critical (R_crit) or optimum ratio, has been used to infer the competitive advantage of phytoplankton growing in P‐impoverished systems. Using a revised quota model, with a normalized quota function and capable of simulating surge transport, the interactions between the minimum P‐quota (PCo), the shape of the P‐quota–cell growth relationship (affected by constant KQP), and transport kinetics in affecting the utility of R_crit are considered. For a low PCo to endow an organism with a high R_crit over a wide range of growth rates, the P‐quota curve must be more hyperbolic (KQP low) rather than linear (KQP high). PCo and KQP also affect the half saturation constant for growth, KgP ; this and the capacity to transport nutrients at rates above those required to sustain steady‐state growth endows a competitive advantage. However, the kinetics of transport into the organism have a greater potential for affecting KgP than changing the kinetics of internal P usage. Thus, the value of R_crit is not a critical factor affecting competition except in extreme oligotrophic conditions. For competition between species, nutrient transport, accumulation, and resource utilization are all important. However, the efficiency of internal resource utilization is of lesser importance, and certainly not of greater importance, than resource acquisition. Multinutrient models intended to describe competition need to recognize these interactions; the traditional quota model is poorly equipped to do so.     

Biosorption of Cadmium from Aqueous Solution by Shell Dust of the Fresh Water Snail Melanoides tuberculata

ABSTRACT The metal bioadsorption potential of shell dust of the freshwater snail Melanoides tuberculata (MTSD) was evaluated under laboratory conditions using cadmium as a model metal. As bioadsorbent, MTSD exhibited a biosorption capacity of 27.03 mg g^?1 at pH 6, indicating potential to remove cadmium from aqueous solution. The adsorption data fit more to the Langmuir (R² = 0.998) equation than the Freundlich (R² = 0.761) equation at equilibrium condition. The kinetics of biosorption followed the pseudo-second-order model (R² = 0.999) better than the Lagergren model (R² = 0.676), as was evident from the regression analysis. The presence of calcium ions appears to have facilitated ion exchange with cadmium along with the binding of different functional groups, as revealed through Fourier transform infrared (FT-IR) analysis. It is apparent from these observations that MTSD can act as low-cost and efficient bioadsorbent for cadmium bioremediation from aquatic habitats. Use of the shells of M. tuberculata for metal biosorption will promote the utility of a waste material of biological origin for bioremediation of heavy metals such as cadmium.     

Empirical Estimation of R 0 for Unknown Transmission Functions: The Case of Chronic Wasting Disease in Alberta

We consider the problem of estimating the basic reproduction number R ₀ from data on prevalence dynamics at the beginning of a disease outbreak. We derive discrete and continuous time models, some coefficients of which are to be fitted from data. We show that prevalence of the disease is sufficient to determine R ₀. We apply this method to chronic wasting disease spread in Alberta determining a range of possible R ₀ and their sensitivity to the probability of deer annual survival.     

A curious case of resistance to a new encounter pathogen: myrtle rust in Australia

Resistance genes (R genes) in plants mediate a highly specific response to microbial pathogens, often culminating in localized cell death. Such resistance is generally pathogen race specific and believed to be the result of evolutionary selection pressure. Where a host and pathogen do not share an evolutionary history, specific resistance is expected to be absent or rare. Puccinia psidii, the causal agent of myrtle rust, was recently introduced to Australia, a continent rich in myrtaceous taxa. Responses within species to this new pathogen range from full susceptibility to resistance. Using the myrtle rust case study, we examine models to account for the presence of resistance to new encounter pathogens, such as the retention of ancient R genes through prolonged ‘trench warfare’, pairing of resistance gene products and the guarding of host integrity.     

Paper chromatography of auxins and inhibitors in two Nicotiana species and their hybrid

Auxins and auxin inhibitors from tissue extracts of normal Nicotiana plants, Nicotiana glauca, N. langsdorffii and their hybrid (which spontaneously produces tumors) were separated by ascending paper chromatography with n-butanol-distilled water. An Avena curvature test was used for demonstrating growth-promoting and growth-inhibiting substances. IAA could be found in extracts of the parents and the hybrid (R_F 0.75). Hybrid tissue yielded the highest amount (37.1°), N. glauca tissue less (30.8°), and N. langsdorffii tissue the least amount (8.5°) of IAA. A second growth promoter (R_F 0.35) could be separated from the tissue extracts of the parents and the hybrid, but it showed only low activity in the Avena test. Three inhibitors were present in extracts from N. langsdorffii and the hybrid at R_F 0.25, 0.45, and 0.85, whereas N. glauca showed only two of them (R_F 0.25 and 0.85). The inhibitor with an R_F of 0.45 seemed to be identical with the acidic, benzene-insoluble “inhibitor β” of Bennet-Clark and Kefford (1953). The inhibitor (neutral, benzene-soluble) at R_F 0.85 could be found in some tissue extracts of the parents and the hybrid, but showed only little activity in the curvature tests. From neutral and from acidic plant extracts within a pH range of 4.4 to 5.8 a third inhibitor with an R_F of 0.25 could be separated. It seems that the high concentration of natural IAA in the hybrid is regulated by a variety of inhibitors with different specificities in the growth-regulating process. Nicotiana langsdorffii tissue has much less auxin but the same variety of inhibitors as the hybrid, whereas N. glauca tissue contains less auxin than the hybrid and only two of the three inhibitors found in N. langsdorffii and hybrid extracts.