Dispersal Ecology: Where Have All the Seeds Gone?

How effective are different animals at dispersing seeds? A new study has traced seeds sampled in faeces to their mother of origin and concluded that carnivorous mammals can be better dispersers than birds.     

Where Have All Their Lineages Gone? Cattle and Descent Among the Nuer

Evans-Pritchard's The Nuer not only served as the paradigm of "segmentary lineage systems," but it also inspired a wide range of ethnographic literature which contributed to the elaboration of "descent theory." The Nuer ethnography was reanalyzed many times and most recently it was declared that the "segmentary lineage system" constituted a "representational model" only, quite different from the actors' "operational rules" (Holy 1979a). Despite the remarkable insight that it proved in the formation of Nuer local groups and the mechanics of Nuer politics, Holy's analysis falls short of a satisfactory reinterpretation of the Nuer polity for those interested in comparison because it restricted itself to local groups and failed to tackle the Nuer concepts of buth, thok dwiel and mar, central to Evans-Pritchard's interpretation. By relegating lineages to the status of "representation," Holy further obscures the course of comparative analysis since he does not provide any criterion to discover when lineages belong to the "representational" or the "operational" levels. Using a different conceptual framework, it is demonstrated that the groups which Evans-Prit chard interpreted as lineages are not "representations" but are in fact defined around cattle. It is concluded that the Nuer simply did not have any lineages, segmentary or not.     

Where Have All the Parasites Gone? Modelling Early Malaria Parasite Sequestration Dynamics

Traditional approaches to measuring the level of malaria infection involve counting the proportion of parasite-infected red blood cells (iRBC) in circulating blood, known as parasitaemia. However, iRBC can also accumulate within the microvasculature of tissues and organs, a process called sequestration. Thus measurements of parasitemia do not necessarily reflect the total parasite burden (TPB). Recent experimental advances have allowed TPB measurements to be made in humans and experimental models. TPB is particularly important because it is the best current predictor of malaria disease severity and death in humans. Understanding the relationship between freely circulating iRBC versus tissue-sequestered iRBC is an important question in infection dynamics. The recent ability to experimentally measure the dynamics of iRBC in blood and tissue during murine malaria provides an exciting potential window into sequestration, but new modeling approaches are clearly required to understand these interactions. We present a model of malaria dynamics during early infection that incorporates iRBC that both circulate in the blood and sequester in tissue microvasculature. We explore the effect that perturbations to the system have on the ratio of the number of iRBC between these compartments, and consider which changes are most consistent with experimental data from mice. Using this model we predict an increase in the clearance rate of sequestered iRBCs around the time when mild symptoms become apparent, but a more pronounced increase in the rate of sequestration of iRBCs associated with the onset of severe malaria symptoms.     

Have the Harmful Effects of Introduced Rats on Islands been Exaggerated?

Introduced rats are now being eradicated from many islands. Increasingly, these eradications are contested by activists claiming moral, legal, cultural, historic or scientific reasons and poorly documented evidence of effects. We reviewed the global literature on the effects of rats on island flora and fauna. We then used New Zealand as a case study because of its four-decade history of rat eradications and many detailed and innovative studies of how rats affect native species. These include use of exclosures, local manipulations of rat populations, video surveillance, and measurements of responses following eradications. The most intensive studies have been on the Pacific rat (Rattus exulans), a small South-East Asian species spread by Polynesians throughout the Pacific. These and the more recently introduced Norway rat (R. norvegicus) and ship (roof) rat (R. rattus) suppress some forest plants, and are associated with extinctions or declines of flightless invertebrates, ground-dwelling reptiles, land birds, and burrowing seabirds. On islands off France, Norway rats are also implicated in declines of shrews. Globally, ship rats were associated with declines or extinctions of the largest number of indigenous vertebrate species (60), including small mammals such as deer mice and bats. Effects of rats on forest trees and seabird populations are sufficiently pervasive to affect ecosystem structure and function. However, the data are patchy. Deficiencies in our knowledge would be reduced by documenting distribution and abundance of indigenous species before and after eradications. Comprehensive measurements of the responses of indigenous species to rat eradications would enable the development of testable models of rat invasion effects.     

Effects of Experimental Choices and Analysis Noise on Surveys of the “Rare Biosphere”

When planning a survey of 16S rRNA genes from a complex environment, investigators face many choices including which primers to use and how to taxonomically classify sequences. In this study, we explored how these choices affected a survey of microbial diversity in a sample taken from the aerobic basin of the activated sludge of a North Carolina wastewater treatment plant. We performed pyrosequencing reactions on PCR products generated from primers targeting the V1-V2, V6, and V6-V7 variable regions of the 16S rRNA gene. We compared these sequences to 16S rRNA gene sequences found in a whole-genome shotgun pyrosequencing run performed on the same sample. We found that sequences generated from primers targeting the V1-V2 variable region had the best match to the whole-genome shotgun reaction across a range of taxonomic classifications from phylum to family. Pronounced differences between primer sets, however, occurred in the “rare biosphere” involving taxa that we observed in fewer than 11 sequences. We also examined the results of analysis strategies comparing a classification scheme using a nearest-neighbor approach to directly classifying sequences with a naïve Bayesian algorithm. Again, we observed pronounced differences between these analysis schemes in infrequently observed taxa. We conclude that if a study is meant to probe the rare biosphere, both the experimental conditions and analysis choices will have a profound impact on the observed results.For nearly 3 decades, investigations of the distribution of microbes in complex environments have focused on the use of rRNA genes (1, 2, 4, 11, 16, 18, 19, 22, 24). Because the full-length 16S rRNA sequence can be obtained with paired-end reads via traditional Sanger sequencing, until recently most studies of the 16S rRNA gene captured most or nearly most of the 16S sequence length. New pyrosequencing technologies, however, have recently been introduced that greatly reduce the per base cost of sequencing but with shorter read lengths than traditional Sanger sequencing (17). This new approach has proven powerful, yielding a previously unobtainable view of rare taxa (7, 12-14, 25).The shorter reads produced by pyrosequencing require the choice of a particular region of the 16S rRNA gene to target for pyrosequencing as well as the choice of an algorithm to classify the taxonomy of the shorter reads. In their initial surveys of microbial diversity with pyrosequencing (12, 14, 25), Sogin and colleagues targeted the V6 variable region, in part because it is was small enough to be captured with the 100-bp reads of the pyrosequencing technology available at the time. Recently, the read length of 454 pyrosequencing machines has been increased to an average of ∼250 bp. This allows for more flexibility in primer design and opens up the possibility of targeting regions of the 16S rRNA gene other than V6. In recent work, Huse et al. took advantage of this new capability to compare the classifications made for the human gut microbiome with the V6 and longer V3 regions (13). Plotting the taxonomic abundance of these two sequence sets against each other yielded an excellent correlation (r² = 0.99), suggesting that the choice of which variable region to target makes little difference. In this report, we introduce a data set examining the performance of sets of primers targeting the V1-V2, V6, and V6-V7 regions. By using a sample for which we have also generated a whole-genome shotgun sequencing run with 250 bp reads, we were able to compare the observed 16S rRNA genes in samples with and without an initial PCR step targeting the 16S rRNA gene. Our results demonstrate that experimental choices such as which region of the 16S rRNA gene to sequence and which algorithm to use to classify taxa are much more likely to affect observations of the “rare biosphere” than more commonly observed taxa.     

Stress Reduction by Technology? An Experimental Study into the Effects of Brainmachines on Burnout and State Anxiety

Stress and burnout are widely acknowledged as major causes of societal and individual problems in the Western world. In order to reduce material and immaterial expenses, increased efforts are made to enhance relaxation and stress reduction. Based on neuropsychological findings, alternative ways have been explored, one of them being the application of so-called brain wave synchronizers, which are said to induce a relaxation response by entraining alpha brain-wave activity (8–13 Hz) through audiovisual stimulation. A double blind, quasi-experiment was conducted among employees at a Dutch addiction care center to investigate the possible effects of two distinct brainmachine programs on burnout and anxiety. Subjects in both conditions showed a significant, immediate decrease in state anxiety as assessed by Spielberger's State-Trait Anxiety Inventory (STAI) and reported a range of subjective effects. However, a long-term effect on burnout, as measured with Maslach's Burnout Inventory (MBI-NL), could not be established. A long-term effect on anxiety (STAI), as investigated by interrupted time-series measurement, could not be established either. These and other findings suggest that the major claims with respect to these machines cannot hold over time, although pleasant short-term effects do occur. Individual differences in baseline responsivity, the stable character of burnout dimensions, or the ill-defined nature of relaxation, or a combination of these, may account for these results.     

Two Decades of Research on Euthanasia from the Netherlands. What Have We Learnt and What Questions Remain?

Two decades of research on euthanasia in the Netherlands have resulted into clear insights in the frequency and characteristics of euthanasia and other medical end-of-life decisions in the Netherlands. These empirical studies have contributed to the quality of the public debate, and to the regulating and public control of euthanasia and physician-assisted suicide. No slippery slope seems to have occurred. Physicians seem to adhere to the criteria for due care in the large majority of cases. Further, it has been shown that the majority of physicians think that the euthanasia Act has improved their legal certainty and contributes to the carefulness of life-terminating acts. In 2005, eighty percent of the euthanasia cases were reported to the review committees. Thus, the transparency envisaged by the Act still does not extend to all cases. Unreported cases almost all involve the use of opioids, and are not considered to be euthanasia by physicians. More education and debate is needed to disentangle in these situations which acts should be regarded as euthanasia and which should not. Medical end-of-life decision-making is a crucial part of end-of-life care. It should therefore be given continuous attention in health care policy and medical training. Systematic periodic research is crucial for enhancing our understanding of end-of-life care in modern medicine, in which the pursuit of a good quality of dying is nowadays widely recognized as an important goal, in addition to the traditional goals such as curing diseases and prolonging life.     

Does the Future Affect the Present? The Effects of Future Weather on the Current Collection of Planted Crops and Wildlife in a Native Amazonian Society of Bolivia

Unlike neighboring disciplines, anthropology rarely studies how actual future events affect current behavior. Such studies could lay the groundwork for studies of ethno-forecasting. Psychologists argue that people forecast poorly, but some empirical work in cultural anthropology suggests that at least with weather, rural people might make reasonably accurate forecasts. Using data from a small-scale, pre-industrial rural society in the Bolivian Amazon, this study estimates the effects of future weather on the current collection of planted crops and wildlife. If actual future events affect current behavior, then this would suggest that people must forecast accurately. Longitudinal data covering 11 consecutive months (10/2002–8/2003, inclusive) from 311 women and 326 men ≥age 14 in 13 villages of a contemporary society of forager-farmers in Bolivia’s Amazon (Tsimane’) are used. Individual fixed-effect panel linear regressions are used to estimate the effect of future weather (mean hourly temperature and total daily rain) over the next 1–7 days from today on the probability of collecting wildlife (game, fish, and feral plants excluding firewood) and planted farm crops (annuals and perennials) today. Daily weather records come from a town next to the Tsimane’ territory and data on foraging and farming come from scans (behavioral spot observations) and surveys of study participants done during scans. Short-term future weather (≤3 days) affected the probability of collecting planted crops and wildlife today, although the effect was greater on the amount of planted crops harvested today than on the amount of wildlife collected today. Future weather beyond 3 days bore no significant association with the amount of planted crops harvested today nor with the amount of wildlife collected today. After controlling for future and past weather, today’s weather (mean hourly temperature, but not rain) affected the probability of collecting wildlife today, but today’s weather (temperature or rain) did not affect the probability of collecting planted crops today. The study supports prior work by anthropologists suggesting that rural people forecast accurately. If future weather affects the probability of harvesting planted crops and collecting wildlife today, then this suggests that Tsimane’ must forecast accurately. We discuss possible reasons for the finding. The study also supports growing evidence from rural areas of low-income nations that rural people tend to protect their food production and food consumption well against small idiosyncratic shocks or, in our case, against ordinary daily weather that is not extreme. However, the greater responsiveness of daily foraging output compared with daily farming output to today’s weather suggests that foraging might not protect food consumption as well as farming against adverse climate perturbations.     

The Ability of Different Imputation Methods to Preserve the Signi?cant Genes and Pathways in Cancer

Deciphering important genes and pathways from incomplete gene expression data could facilitate a better understanding of cancer. Different imputation methods can be applied to estimate the missing values. In our study, we evaluated various imputation methods for their performance in preserving signi?cant genes and pathways. In the ?rst step, 5% genes are considered in random for two types of ignorable and non-ignorable missingness mechanisms with various missing rates. Next,10 well-known imputation methods were applied to the complete datasets. The signi?cance analysis of microarrays(SAM) method was applied to detect the signi?cant genes in rectal and lung cancers to showcase the utility of imputation approaches in preserving signi?cant genes. To determine the impact of different imputation methods on the identi?cation of important genes, the chi-squared test was used to compare the proportions of overlaps between signi?cant genes detected from original data and those detected from the imputed datasets. Additionally, the signi?cant genes are tested for their enrichment in important pathways, using the Consensus Path DB. Our results showed that almost all the signi?cant genes and pathways of the original dataset can be detected in all imputed datasets, indicating that there is no signi?cant difference in the performance of various imputationmethods tested. The source code and selected datasets are available on http://pro?les.bs.ipm.ir/softwares/imputation_methods/.