Inverse sampling of controls in a matched case control study

A method of inverse sampling of controls in a matched case-control study is described in which, for each case, controls are sampled until a discordant set is achieved. For a binary exposure, inverse sampling is used to determine the number of controls for each case. When most individuals in a population have the same exposure, standard case-control sampling may result in many case-control sets being concordant with respect to exposure and thus uninformative in the conditional logistic analysis. The method using inverse control sampling is proposed as a solution to this problem in situations when it is practically feasible. In many circumstances, inverse control sampling is found to offer improved statistical efficiency relative to a comparable study with a fixed number of controls per case.     

The small angle light scattering of biological cells. Theoretical considerations

The light scattered by living biological cells (assumed homogeneous spheres with a relative refractive index, m = 1.05) at small angles has been calculated by the Hodkinson approximation and the more rigorous Mie theory. Both methods predict that relative volume distributions may be estimated from low angle scattering measurements on each cell in a population. Under conditions of short wavelength illumination or strong absorption, absolute volume information may also be obtained.     

The causes and consequences of variation in offspring size: a case study using Daphnia

Offspring size can have large and direct fitness implications, but we still do not have a complete understanding of what causes offspring size to vary. Daphnia (water fleas) generally produce fewer and larger offspring when food is limited. Here, we use a mathematical model to show that this could be explained by either: (1) an advantage of producing larger eggs when food is limited; or (2) a lower boundary on egg volume (below which eggs do not have sufficient resources to be viable), that is similar in volume to the evolutionarily stable egg volume predicted by standard clutch size models. We tested the first possibilities experimentally by placing offspring from mothers kept at two food treatments (high and low - leading to relatively small and large eggs respectively) into two food treatments (same as maternal treatments, in a fully factorial design) and measuring their fitness (reproduction, age at maturity, and size at maturity). We also tested survival under starvation conditions of offspring produced from mothers at low and high food treatments. We found that (larger) offspring produced by low-food mothers actually had lower fitness as they took longer to reproduce, regardless of their current food treatment. Additionally, we found no survival advantage to being born of a food-stressed mother. Consequently, our results do not support the hypothesis that there is an advantage to producing larger eggs when food is limited. In contrast, data from the literature support the importance of a lower boundary on egg size.     

Ecological consequences of biological invasions: three invertebrate case studies in the north-eastern Baltic Sea

Population dynamics and ecological impacts of the cirriped Balanus improvisus, the polychaete Marenzelleria neglecta and the cladoceran Cercopagis pengoi were investigated in the north-eastern Baltic Sea. After an increase during the first decade of invasion, the density of M. neglecta and C. pengoi declined afterwards. The studied abiotic environmental variables did not explain the interannual variability in the seasonal cycles of M. neglecta and C. pengoi indicating that the species are at their initial phase of invasion. The population dynamics of B. improvisus was best described by water temperature. B. improvisus promoted the growth of the green alga Enteromorpha intestinalis. M. neglecta enhanced the content of sediment chlorophyll a and reduced growth and survival of the polychaete Hediste diversicolor and growth of the amphipod Monoporeia affinis. Concurrent with the invasion of C. pengoi the abundance of small-sized cladocerans declined, especially above the thermocline. C. pengoi had become an important food for nine-spined stickleback, bleak, herring and smelt.     

Statistical issues and methods for meta-analysis of microarray data: a case study in prostate cancer

With the proliferation of related microarray studies by independent groups, a natural step in the analysis of these gene expression data is to combine the results across these studies. However, this raises a variety of issues in the analysis of such data. In this article, we discuss the statistical issues of combining data from multiple gene expression studies. This leads to more complications than those in standard meta-analyses, including different experimental platforms, duplicate spots and complex data structures. We illustrate these ideas using data from four prostate cancer profiling studies. In addition, we develop a simple approach for assessing differential expression using the LASSO method. A combination of the results and the pathway databases are then used to generate candidate biological pathways for cancer.     

Statistical convenience vs biological insight: consequences of data transformation for the analysis of fitness variation in heterogeneous environments

In plants, more favourable environmental conditions can lead to dramatic increases in both mean fitness and variance in fitness. This results in data that violate the equality-of-variance assumption of anova, a problem that most empiricists would address by log-transforming fitness values. Using heuristic data sets and simple simulations, we show that anova on log-transformed fitness consistently fails to match the outcome of selection in a heterogeneous environment or its sensitivity to environmental frequency. Only anova based on relative fitness within environments accurately predicts the sensitivity of genotype selection to the frequency of alternative environments. Parallel analyses of variance based on absolute fitness and relative fitness can bracket the expected success of alternative genotypes under hard and soft selection, respectively. For example, for Sinapis arvensis growing in full sun and partial shade treatments, families achieving high fitness in the best environment are favoured under hard selection, whereas soft selection favours different families that achieve consistently good performance across environments. Based on these findings, we recommend that log-transformation of fitness should no longer be standard practice in ecological genetics studies. Weighted anova is a preferable method for dealing with unequal variances, and investigators should also make greater use of techniques such as quantile regression or resampling to describe and evaluate fitness variation across heterogeneous environments.     

Foraging behavior of ants: Theoretical considerations

This paper describes models of behavior for two ant species recruiting to very different sorts of resource. One species, Solenopsis geminata, recruits to sugar solution. The other, Pogonomyrmex occidentalis, recruits to patches of seeds. The models clarify the assumptions entering into the theoretical analysis of these behaviors and point to measurements that should be made for their experimental analysis.Both models assume that the colony gains energy when a forager gets a load of resource. Energy is lost during the trip to a patch of resource in a manner dependent upon the current physical conditions of the environment. The only factor counterbalancing an ever increasing net energy gain when the recruitment rates are increased is interference among workers at a patch. As the rate of recruitment is elevated this interference decreases the efficiency with which the resource can be used and, thus, sets an optimum at some intermediate rate of recruitment.The limitation of considerations in this paper to energetic efficiency is discussed and justified in terms of components of fitness and ant physiology. It is found that several qualitative predictions can be experimentally tested, but that quantitative predictions require fine measurement of metabolic costs to individual foragers and of complicated gains to the colony as a whole. Both models can be differentiated experimentally from corresponding time minimization models.     

Matrix-level co-occurrence metrics are sensitive to sampling grain: a case study in species-rich shrublands

Plant Ecology - As ecological patterns are scale dependent, making decisions about sampling design critical. In the context of community assembly, many metrics have been developed to quantify...     

Photosynthetic consequences of phenotypic plasticity in response to submergence: Rumex palustris as a case study

Survival and growth of terrestrial plants is negatively affected by complete submergence. This is mainly the result of hampered gas exchange between plants and their environment, since gas diffusion is severely reduced in water compared with air, resulting in O2 deficits which limit aerobic respiration. The continuation of photosynthesis could probably alleviate submergence-stress in terrestrial plants, but its potential under water will be limited as the availability of CO2 is hampered. Several submerged terrestrial plant species, however, express plastic responses of the shoot which may reduce gas diffusion resistance and enhance benefits from underwater photosynthesis. In particular, the plasticity of the flooding-tolerant terrestrial species Rumex palustris turned out to be remarkable, making it a model species suitable for the study of these responses. During submergence, the morphology and anatomy of newly developed leaves changed: 'aquatic' leaves were thinner and had thinner cuticles. As a consequence, internal O2 concentrations and underwater CO2 assimilation rates were higher at the prevailing low CO2 concentrations in water. Compared with heterophyllous amphibious plant species, underwater photosynthesis rates of terrestrial plants may be very limited, but the effects of underwater photosynthesis on underwater survival are impressive. A combination of recently published data allowed quantification of the magnitude of the acclimation response in this species. Gas diffusion resistance in terrestrial leaves underwater was about 15,000 times higher than in air. Strikingly, acclimation to submergence reduced this factor to 400, indicating that acclimated leaves of R. palustris had an approximately 40 times lower gas diffusion resistance than non-acclimated ones.     

Acyl glucuronide reactivity in perspective: biological consequences

The metabolic conjugation of exogenous and endogenous carboxylic acid substrates with endogenous glucuronic acid, mediated by the uridine diphosphoglucuronosyl transferase (UGT) superfamily of enzymes, leads to the formation of acyl glucuronide metabolites. Since the late 1970s, acyl glucuronides have been increasingly identified as reactive electrophilic metabolites, capable of undergoing three reactions: intramolecular rearrangement, hydrolysis, and intermolecular reactions with proteins leading to covalent drug-protein adducts. This essential dogma has been accepted for over a decade. The key question proposed by researchers, and now the pharmaceutical industry, is: does or can the covalent modification of endogenous proteins, mediated by reactive acyl glucuronide metabolites, lead to adverse drug reactions, perhaps idiosyncratic in nature? This review evaluates the evidence for acyl glucuronide-derived perturbation of homeostasis, particularly that which might result from the covalent modification of endogenous proteins and other macromolecules. Because of the availability of acyl glucuronides for test tube/in vitro experiments, there is now a substantial literature documenting their rearrangement, hydrolysis and covalent modification of proteins in vitro. It is certain from in vitro experiments that serum albumin, dipeptidyl peptidase IV, tubulin and UGTs are covalently modified by acyl glucuronides. However, these in vitro experiments have been specifically designed to amplify any interference with a biological process in order to find biological effects. The in vivo situation is not at all clear. Certainly it must be concluded that all humans taking carboxylate drugs that form reactive acyl glucuronides will form covalent drug-protein adducts, and it must also be concluded that this in itself is normally benign. However, there is enough in vivo evidence implicating acyl glucuronides, which, when backed up by in vivo circumstantial and documented in vitro evidence, supports the view that reactive acyl glucuronides may initiate toxicity/immune responses. In summary, though acyl glucuronide-derived covalent modification of endogenous macromolecules is well-defined, the work ahead needs to provide detailed links between such modification and its possible biological consequences.     

Multivariate analysis in biological anthropology: Some considerations

The relation between modern multivariate statistical analysis and common objectives in biological anthropology is discussed. Many formal statistical assumptions should be satisfied to fully justify multi-variate analysis, but rarely are. Their failure does not have as adverse an effect upon scientific research as some procedural errors in research design. These include the treatment of single specimens as if they are samples, and the failure to separate considerations of size and shape. The superiority of elaborate multivariate distances over simpler quantitative techniques, inferred from the former's consideration of trait intercorrelations, is unwarranted from both theoretical and practical aspects. Based on these points and several comparative examples of analyses, it is argued that simpler, non-statistical approaches such as those of the school of numerical taxonomy have much to offer primato-logical studies. Classic multivariate statistics, while useful for studying closely similar living populations, are considerably more limited in usefulness and significance for paleoanthropological studies.     

Sequence variation and the biological function of genes: methodological and biological considerations

Single nucleotide polymorphisms (SNPs) are expected to facilitate the chromosomal mapping and eventual cloning of genetic determinants of complex quantitative phenotypes. To date, more than 2.5 million non-redundant human SNPs have been reported in the public domain, of which approximately 100000 have been validated by either independent investigators or by independent methods. Equally impressive is the myriad of methods developed for allelic discrimination. Nevertheless, reports of successful applications of SNPs to genome-wide linkage analysis of both mono- and polygenic traits are rare and limited to a few model organisms, that provide affordable platforms to test both novel methodological and biological concepts at a whole-genome scale under conditions that can be reasonably controlled. Progress in the analysis of SNPs needs to be complemented by methods that allow the systematic elucidation of both primary and secondary phenotypes of genes. Importantly, observations made in one species may very well be of immediate applicability to other species including human. This is particularly true for conserved biological processes such as mitochondrial respiration and DNA repair.     

Taxonomy and biological control: Neoseiulus cucumeris (Acari: Phytoseiidae), a case study

The predatory mite Neoseiulus cucumeris (Oudemans) (Acari: Phytoseiidae) is an important biological control agent of thrips and other small pests worldwide. Yet, despite its economic importance, this species is poorly defined taxonomically and cannot be reliably separated from other species on the basis of morphology alone. Neoseiulus cucumeris has been reported from Australia, although considerable confusion exists as to whether the Australian material is actually N. cucumeris or a presumed endemic species, Neoseiulus bellinus (Womersley). A morphological investigation of N. bellinus and several geographical 'strains' of N. cucumeris demonstrated that: (i) N. bellinus is a distinct species, the males of which can be morphologically separated from those of N. cucumeris , using setal and cheliceral lengths and number of teeth on the fixed digit; and (ii) N. cucumeris , or a morphologically identical species, is present in Australia. Despite behavioural differences, there are no significant morphological differences between the 'strains' of N. cucumeris . Biosystematic research is a more reliable method of species separation, and such a method is suggested for future work with phytoseiid mites.     

Comparing biological classifications of freshwater phytoplankton: a case study from South China

The use of ecological classification systems is becoming more and more widely used when studying phytoplankton. Grouping phytoplankton species into ecologically coherent groups allow to reduce redundancy and in this way, to handle a minor number of biological variables when investigating the ecological status of aquatic ecosystems. Three ecological classifications are mostly used when freshwater phytoplankton is studied: functional groups or coda, morpho-functional groups (MFGs) and morphology-based functional groups (MBFGs). In this study, these three ecological classifications were comparatively used along with two taxonomic classifications based on species and genera to analyse phytoplankton response to environmental variability in three sub-tropical Chinese reservoirs. Canonical correspondence analysis was performed to compare the five mentioned biological classifications. When ecological classifications were used, the percentage of variance explained in the biological groups?Cenvironmental variables was higher than that explained by the taxonomic classifications. Coda and MFGs showed a very high degree of overlapping, but since coda are associated to very detailed environmental templates, this method was more helpful in explaining phytoplankton variability in relation to environmental factors.     

Statistical considerations of optimal study design for human plasma proteomics and biomarker discovery

A mass spectrometry-based plasma biomarker discovery workflow was developed to facilitate biomarker discovery. Plasma from either healthy volunteers or patients with pancreatic cancer was 8-plex iTRAQ labeled, fractionated by 2-dimensional reversed phase chromatography and subjected to MALDI ToF/ToF mass spectrometry. Data were processed using a q-value based statistical approach to maximize protein quantification and identification. Technical (between duplicate samples) and biological variance (between and within individuals) were calculated and power analysis was thereby enabled. An a priori power analysis was carried out using samples from healthy volunteers to define sample sizes required for robust biomarker identification. The result was subsequently validated with a post hoc power analysis using a real clinical setting involving pancreatic cancer patients. This demonstrated that six samples per group (e.g., pre- vs post-treatment) may provide sufficient statistical power for most proteins with changes>2 fold. A reference standard allowed direct comparison of protein expression changes between multiple experiments. Analysis of patient plasma prior to treatment identified 29 proteins with significant changes within individual patient. Changes in Peroxiredoxin II levels were confirmed by Western blot. This q-value based statistical approach in combination with reference standard samples can be applied with confidence in the design and execution of clinical studies for predictive, prognostic, and/or pharmacodynamic biomarker discovery. The power analysis provides information required prior to study initiation.     

Statistical strategies for relating metabolomics and proteomics data: a real case study in nutrition research area

The current investigations were carried out in the context of a nutritional case study aiming at assessing the postnatal impact of maternal dietary protein restriction during pregnancy and lactation on rat offspring plasma metabolome and hypothalamic proteome. Although data generated by different ??Omics?? technologies are usually considered and analyzed separately, their interrelation may offer a valuable opportunity for assessing the emerging ??integrated biology?? concept. The overall strategy of analysis first investigated data pretreatment and variable selection for each dataset. Then, three multivariate analyses were applied to investigate the links between the abundance of metabolites and the expression of proteins collected on the same samples. Unfold principal component analysis and regularized canonical correlation analysis did not take into account the presence of groups of individuals related to the intervention study. On the contrary, the predictive MultiBlock Partial Least Squares method used this information. Regularized canonical correlation analysis appeared as a relevant approach to investigate of the relationships between the two datasets. However, in order to highlight the molecular compounds, proteins and metabolites, associated in interacting or common metabolic pathways for the experimental groups, MultiBlock partial least squares was the most appropriate method in the present nutritional case study.     

Tracking a fluctuating environment: a study of sampling

The problem of how animals keep track of unpredictable changes in the profitability of foraging sites was studied. An optimality model was used to predict the frequency with which a forager should sample a foraging site in which the probability of reward fluctuates randomly between high and low. The alternative foraging site is stable and offers an intermediate probability of reward. The model was tested with pigeons in a shuttle-box the two ends of which represented the two foraging sites. The pigeons succeeded in tracking the changes in the fluctuating site and the payoff attained was close to the optimum. Variations in the frequency of sampling between experimental treatments were in qualitative agreement with the model for some treatments but not others. The quantitative details of sampling behaviour were not as predicted by the optimality model, but many features could be accounted for by a mechanistic model of choice. The pigeons' choice rule, although different from that of the optimality model, is one that produces near-optimal payoffs under the conditions of this experiment.     

Dynamics of biological invasions and pathways over time: a case study of a temperate coastal sea

Coastal and regional sea ecosystems suffer from several human-induced stressors, including human mediated bioinvasions. The Baltic Sea is generally considered to be susceptible to invasions by non-indigenous species (NIS). Out of the total of 132 NIS and cryptogenic species recorded, 59% are currently established in at least one country surrounding the Baltic Sea. On average, each country currently hosts 27 such species with 15% of the established species being found in at least 50% of the countries. Benthic macroinvertebrates dominate, both among those recorded (48%) and established (59%) species. Shipping, deliberate stocking and natural spread of NIS previously introduced to the North Sea are the main introduction pathways, with considerable dynamics over time. Amongst the pathways responsible for the currently established species, shipping and natural spread strongly dominate. Substantial uncertainty in the information on introduction pathways (except for deliberate releases) hampers detailed analyses and poses major challenges for management. Spatio-temporal variability in the invasion dynamics reflects both the spatial differences in the main hydrographic conditions of the Baltic Sea as well as the availability of introduction pathways. We conclude that the Baltic Sea cannot be considered as a uniform waterbody in terms of the established introduced species and at least two major regions with differing hydrographic conditions and introduction pathways can be clearly distinguished. Due to the importance of natural spread of NIS from the North Sea, regional cooperation in bioinvasion management should be enhanced in the future.