Sampling of cardiovascular data; how often and how much?

Long-term measurement of cardiovascular variables by telemetry in laboratory animals has become indispensable in recent years. However, limited battery life and management of large volumes of recorded data are major drawbacks. These limitations can often be overcome by intermittent sampling of data. The question is, how much data does one need to collect to accurately reflect the underlying average value? To investigate this, 24-h continuous recordings of rabbit heart rate, arterial pressure, and integrated renal sympathetic nerve activity (RSNA) were resampled using a variety of protocols that differed with respect to the number of individual sampling periods used and the total amount of time that was sampled. The absolute percentage errors of estimates of the daily mean, standard deviation, and interquartile range were calculated for each sampling protocol. A similar analysis was repeated using arterial pressure data from rats. The results show that the number of sampling periods spread throughout the day had more effect than the total amount of data recorded. For example, just 2 h of total sampling time spread over 12 evenly spaced 10-min periods gave estimates of the daily mean of blood pressure and heart rate with <1% error and RSNA with <3% error. We show that accurate estimates of the daily mean of arterial pressure, heart rate, and RSNA can all be made using scheduled recording, and we recommend recording a minimum of 2 h/day spread over a number of periods throughout the day.     

Phylogenetic inference: how much evolutionary history is knowable?

In order to reconstruct phylogenetic trees from extremely dissimilar sequences it is necessary to estimate accurately the extent of sequence divergence. In this paper a new method of sequence analysis, Markov triple analysis, is developed for determining the relative frequencies of nucleotide substitutions within the three branches of a three-taxon dendrogram. Assuming that nucleotide sites are independently and identically distributed and assuming a Markov model for nucleotide (or protein) evolution, it is shown that the unique Markov matrices can be reconstructed given only the joint probability distribution relating three taxa. (In the much simpler case involving only two taxa and two character states, Markov matrices can also be reconstructed, provided symmetry assumptions are placed on the elements of the matrices.) The method is illustrated using sequence data from the combined first and second codon positions derived from complete human, mouse, and cow mitochondrial sequences.      

Proximate and ultimate causes: how come? and what for?

Proximate and ultimate causes in evolutionary biology have come to conflate two distinctions. The first is a distinction between immediate and historical causes. The second is between explanations of mechanism and adaptive function. Mayr emphasized the first distinction but many evolutionary biologists use proximate and ultimate causes to refer to the second. I recommend that ‘ultimate cause’ be abandoned as ambiguous.     

Comparative genomics of archaea: how much have we learned in six years,and what's next?

Archaea comprise one of the three distinct domains of life (with bacteria and eukaryotes). With 16 complete archaeal genomes sequenced to date, comparative genomics has revealed a conserved core of 313 genes that are represented in all sequenced archaeal genomes, plus a variable 'shell' that is prone to lineage-specific gene loss and horizontal gene exchange. The majority of archaeal genes have not been experimentally characterized, but novel functional pathways have been predicted.     

Ecological and evolutionary consequences of size‐selective harvesting: how much do we know?

Size-selective harvesting, where the large individuals of a particular species are preferentially taken, is common in both marine and terrestrial habitats. Preferential removal of larger individuals of a species has been shown to have a negative effect on its demography, life history and ecology, and empirical studies are increasingly documenting such impacts. But determining whether the observed changes represent evolutionary response or phenotypic plasticity remains a challenge. In addition, the problem is not recognized in most management plans for fish and marine invertebrates that still mandate a minimum size restriction. We use examples from both aquatic and terrestrial habitats to illustrate some of the biological consequences of size-selective harvesting and discuss possible future directions of research as well as changes in management policy needed to mitigate its negative biological impacts.     

Reconstructing routes of invasion using genetic data: why,how and so what?

Detailed knowledge about the geographical pathways followed by propagules from their source to the invading populations—referred to here as routes of invasion—provides information about the history of the invasion process and the origin and genetic composition of the invading populations. The reconstruction of invasion routes is required for defining and testing different hypotheses concerning the environmental and evolutionary factors responsible for biological invasions. In practical terms, it facilitates the design of strategies for controlling or preventing invasions. Most of our knowledge about the introduction routes of invasive species is derived from historical and observational data, which are often sparse, incomplete and, sometimes, misleading. In this context, population genetics has proved a useful approach for reconstructing routes of introduction, highlighting the complexity and the often counterintuitive nature of the true story. This approach has proved particularly useful since the recent development of new model‐based methods, such as approximate Bayesian computation, making it possible to make quantitative inferences in the complex evolutionary scenarios typically encountered in invasive species. In this review, we summarize some of the fundamental aspects of routes of invasion, explain why the reconstruction of these routes is useful for addressing both practical and theoretical questions, and comment on the various reconstruction methods available. Finally, we consider the main insights obtained to date from studies of invasion routes.     

Trypanosomes and mammalian sperm: one of a kind?

Flagellar-mediated motility is an indispensable function for cell types as evolutionarily distant as mammalian sperm and kinetoplastid parasites, a large group of flagellated protozoa that includes several important human pathogens. Despite the obvious importance of flagellar motility, little is known about the signalling processes that direct the frequency and wave shape of the flagellar beat, or those that provide the motile cell with the necessary environmental cues that enable it to aim its movement. Similarly, the energetics of the flagellar beat and the problem of a sufficient ATP supply along the entire length of the beating flagellum remain to be explored. Recent proteome projects studying the flagella of mammalian sperm and kinetoplastid parasites have provided important information and have indicated a surprising degree of similarities between the flagella of these two cell types.     

Obtaining data from randomised controlled trials: how much do we need for reliable and informative meta-analyses?

Many randomised controlled trials compare treatments that will produce only moderate differences in outcome, but these differences can be clinically important. However, they are difficult to assess reliably and require a large amount of randomised evidence. This can be achieved through large prospective randomised trials which will accrue future patients, the meta-analysis of results from randomised trials involving patients from the past, or--ideally--both. The techniques require that all possible biases are minimised, and in meta-analyses this can best be achieved by ensuring that all of the randomised evidence--both trials and participants in those trials--is included. The meta-analysis of individual patient data has been described as the gold standard for this approach. It will remove many of the problems associated with relying solely on published data and some of the problems arising from a reliance on aggregate data, and will also add to the analyses that can be performed. Such projects, however, require considerable time and effort.     

The evolution of noncoding DNA: how much junk, how much func?

Comparative sequence analysis on a genomic scale has opened the door for the systematic analysis of cis-acting regulatory DNA. It is now possible to begin to answer basic questions such as, how much meaningful noncoding sequence is in the genome? How strong is natural selection on functional noncoding sequences in different species? Two recent articles have capitalized on the comparative genomic approach in an attempt to answer these questions with surprising results.     

Actin in the nucleus: what form and what for?

Actin is an abundant protein in most nonmuscle cells. It has often been observed in isolated nuclei, yet cytoplasmic contamination was of course initially regarded as the most plausible origin. Numerous studies on nuclear actin appeared in the 1970s and 1980s, but the picture remained rather muddy. The viewpoint at that time was that actin-shown to move freely between cytoplasm and nucleus-was a mere "thermodynamic wanderer," transiently occupying the nucleus. More recently, evidence has been mounting that actin's presence in the nucleus is not simply governed by the laws of diffusion. The same holds true for the finding of various actin-related proteins in the nucleus, and the case for nuclear myosin, specifically myosin I, is now quite convincing. Moreover, the first intimations of functional roles of nuclear actin are now emerging. Here we examine the overall subject from cell biological and chemical perspectives. The major issue is no longer the presence of actin in the nucleus but rather its supramolecular organization, intranuclear locations, and, of course, functions. These issues interface with recent findings that reveal a surprisingly diverse repertoire of actin conformations and oligomer and polymer forms beyond monomeric G-actin and polymeric F-actin. We present ideas for advancing the nuclear actin field and call for a renewed attack on this major problem in cell biology.     

How to tell green from grey? Towards a methodological framework for evaluating the greening of national tax systems

In this paper, we evaluate four types of indicators that can be used for measuring the greening of a tax system: revenue-based indicators, single tax rates, aggregate tax-rate based indicators and the implicit tax rate on energy. We develop an evaluation framework, introducing two principal evaluation criteria: content validity and comprehensiveness, and four statistical criteria: data availability, comparison over time, international comparability and ease of aggregation. Additional analysis regarding the issue of weighting is carried out for the aggregate tax-rate based indicator. The theoretical and methodological evaluation is supplemented and validated empirically using recent data on the Belgian and Flemish tax system. Finally, conclusions are drawn with regard to the strengths and the weaknesses of the four types of indicators, and recommendations are made for further research.     

What kind of lamp for the cultivation of algae?

A method for quantitative evaluation of light sources from the point of their suitability for algal cultivation is described. Two parameters are used for the evaluation:

Towards diversity in genomics: The emergence of neurogenomics in Africa?

There is a high burden of mental and neurological disorders in Africa. Nevertheless, there appears to be an under-representation of African ancestry populations in large-scale genomic studies. Here, we evaluated the extent of under-representation of Africans in neurogenomic studies in the GWAS Catalog. We found 569 neurogenomic studies, of which 88.9% were exclusively focused on people with European ancestry and the remaining 11.1% having African ancestry cases included. In terms of population, only 1.2% of the total populations involved in these 569 GWAS studies were of African descent. Further, most of the individuals in the African ancestry category were identified to be African-Americans/Afro-Caribbeans, highlighting the huge under-representation of homogenous African populations in large-scale neurogenomic studies. Efforts geared at establishing strong collaborative ties with European/American researchers, maintaining freely accessible biobanks and establishing comprehensive African genome data repositories to track African genome variations are critical for propelling neurogenomics/precision medicine in Africa.