Novel high-resolution characterization of ancient DNA reveals C > U-type base modification events as the sole cause of post mortem miscoding lesions

Ancient DNA (aDNA) research has long depended on the power of PCR to amplify trace amounts of surviving genetic material from preserved specimens. While PCR permits specific loci to be targeted and amplified, in many ways it can be intrinsically unsuited to damaged and degraded aDNA templates. PCR amplification of aDNA can produce highly-skewed distributions with significant contributions from miscoding lesion damage and non-authentic sequence artefacts. As traditional PCR-based approaches have been unable to fully resolve the molecular nature of aDNA damage over many years, we have developed a novel single primer extension (SPEX)-based approach to generate more accurate sequence information. SPEX targets selected template strands at defined loci and can generate a quantifiable redundancy of coverage; providing new insights into the molecular nature of aDNA damage and fragmentation. SPEX sequence data reveals inherent limitations in both traditional and metagenomic PCR-based approaches to aDNA, which can make current damage analyses and correct genotyping of ancient specimens problematic. In contrast to previous aDNA studies, SPEX provides strong quantitative evidence that C U-type base modifications are the sole cause of authentic endogenous damage-derived miscoding lesions. This new approach could allow ancient specimens to be genotyped with unprecedented accuracy.

Dietary prebiotics: current status and new definition

In November 2008, a group of scientists met at the 6th Meeting of the International Scientific Association of Probiotics and Prebiotics (ISAPP) in London, Ontario, Canada, to discuss the functionality of prebiotics. As a result of this, it was concluded that the prebiotic field is currently dominated by gastrointestinal events. However, in the future, it may be the case that other mixed microbial ecosystems may be modulated by a prebiotic approach, such as the oral cavity, skin and the urogenital tract. Therefore, a decision was taken to build upon the current prebiotic status and define a niche for ‘dietary prebiotics’. This review is co-authored by the working group of ISAPP scientists and sets the background for defining a dietary prebiotic as ‘‘a selectively fermented ingredient that results in specific changes in the composition and/or activity of the gastrointestinal microbiota, thus conferring benefit(s) upon host health’’.

The link between the Barents Sea and ENSO events simulated by NEMO model

An analysis of observational data in the Barents Sea along a meridian at 33°30' E between 70°30' and 72°30' N has reported a negative correlation between El Niño/La Niña Southern Oscillation (ENSO) events and water temperature in the top 200 m: the temperature drops about 0.5 °C during warm ENSO events while during cold ENSO events the top 200 m layer of the Barents Sea is warmer. Results from 1 and 1/4-degree global NEMO models show a similar response for the whole Barents Sea. During the strong warm ENSO event in 1997–1998 an anomalous anticyclonic atmospheric circulation over the Barents Sea enhances heat loses, as well as substantially influencing the Barents Sea inflow from the North Atlantic, via changes in ocean currents. Under normal conditions along the Scandinavian peninsula there is a warm current entering the Barents Sea from the North Atlantic, however after the 1997–1998 event this current is weakened. During 1997–1998 the model annual mean temperature in the Barents Sea is decreased by about 0.8 °C, also resulting in a higher sea ice volume. In contrast during the cold ENSO events in 1999–2000 and 2007–2008, the model shows a lower sea ice volume, and higher annual mean temperatures in the upper layer of the Barents Sea of about 0.7 °C. An analysis of model data shows that the strength of the Atlantic inflow in the Barents Sea is the main cause of heat content variability, and is forced by changing pressure and winds in the North Atlantic. However, surface heat-exchange with the atmosphere provides the means by which the Barents sea heat budget relaxes to normal in the subsequent year after the ENSO events.

Longitudinal investigation of the role of temperament and stressful life events in childhood anxiety

The current study investigated the longitudinal relationships between BI, life events, and anxiety in a sample of 102 behaviourally inhibited (BI) and 100 uninhibited (BUI) children aged 3 to 4 years. Children’s parents completed questionnaires on BI, stressful life events, and anxiety symptoms, and were administered a diagnostic interview three times in a 5-year period. In line with our hypotheses, negative life events, and negative behaviour- dependent life events (i.e. life events that are related to the children’s own behaviours) in particular, and the impact of negative life events, were predictive of increases in subsequent anxiety symptoms, the likelihood of having an anxiety disorder, and increased number of anxiety diagnoses over the five year follow-up period. Experiencing more positive, behaviour-independent life events decreased the risk of being diagnosed with an anxiety disorder. Furthermore, differences were found in life events between BI and BUI children. That is, BI children experienced fewer positive and specifically positive behaviour-dependent life events, and the impact of these positive life events was also lower in BI children than in BUI children. However, BI did not interact with life events in the prediction of anxiety problems as hypothesized. Therefore, this study seems to indicate that BI and life events act as additive risk factors in the development of anxiety problems.

On the clustering of winter storm loss events over Germany

During the last decades, several windstorm series hit Europe leading to large aggregated losses. Such storm series are examples of serial clustering of extreme cyclones, presenting a considerable risk for the insurance industry. Clustering of events and return periods of storm series for Germany are quantified based on potential losses using empirical models. Two reanalysis data sets and observations from German weather stations are considered for 30 winters. Histograms of events exceeding selected return levels (1-, 2- and 5-year) are derived. Return periods of historical storm series are estimated based on the Poisson and the negative binomial distributions. Over 4000 years of general circulation model (GCM) simulations forced with current climate conditions are analysed to provide a better assessment of historical return periods. Estimations differ between distributions, for example 40 to 65 years for the 1990 series. For such less frequent series, estimates obtained with the Poisson distribution clearly deviate from empirical data. The negative binomial distribution provides better estimates, even though a sensitivity to return level and data set is identified. The consideration of GCM data permits a strong reduction of uncertainties. The present results support the importance of considering explicitly clustering of losses for an adequate risk assessment for economical applications.

Periodic auroral events at the high-latitude convection reversal in the 16 MLT region

Combined optical and radar observations of two breakup-like auroral events near the polar cap boundary, within 74–76° MLAT and 1210 – 1240 UT (roughly 1540 – 1610 MLT) on 9 Jan. 1989 are reported. A two-component structure of the auroral phenomenon is indicated, with a local intensification of the pre-existing arc as well as a separate, tailward moving discrete auroral event on the poleward side of the background aurora, close to the reversal between well-defined zones of sunward and tailward ion flows. The all-sky TV observations do not indicate a connection between the two components, which also show different optical spectral composition. The 16 MLT background arc is located on sunward convecting field lines, as opposed to the 12–14 MLT auroral emission observed on this day. Although the magnetospheric plasma source (s) of the 16 MLT events are not easily identified from these ground-based data alone, it is suggested that the lower and higher latitude components, may map to the plasma sheet boundary layer and along open field lines to the magnetopause boundary, respectively. The events occur at the time of enhancements of westward ionospheric ion flow and corresponding eastward electrojet current south of 74° MLAT. Thus, they seem to be very significant events, involving periodic (10 min period), tailward moving filaments of field-aligned current/discrete auroral emission at the 16 MLT polar cap boundary.

The ionospheric signatures of flux transfer events and solar wind dynamic pressure changes

The generation of flow and current vortices in the dayside auroral ionosphere has been predicted for two processes ocurring at the dayside magnetopause. The first of these mechanisms is time-dependent magnetic reconnection, in “flux transfer events” (FTEs); the second is the action of solar wind dynamic pressure changes. The ionospheric flow signature of an FTE should be a twin vortex, with the mean flow velocity in the central region of the pattern equal to the velocity of the pattern as a whole. On the other hand, a pulse of enhanced or reduced dynamic pressure is also expected to produce a twin vortex, but with the central plasma flow being generally different in speed from, and almost orthogonal to, the motion of the whole pattern. In this paper, we make use of this distinction to discuss recent observations of vortical flow patterns in the dayside auroral ionosphere in terms of one or other of the proposed mechanisms. We conclude that some of the observations reported are consistent only with the predicted signature of FTEs. We then evaluate the dimensions of the open flux tubes required to explain some recent simultaneous radar and auroral observations and infer that they are typically 300 km in north–south extent but up to 2000 km in longitudinal extent (i.e., roughly 5 hours of MLT). Hence these observations suggest that recent theories of FTEs which invoke time-varying reconnection at an elongated neutral line may be correct. We also present some simultaneous observations of the interplanetary magnetic field (IMF) and solar wind dynamic pressure (observed using the IMP8 satellite) and the ionospheric flow (observed using the EISCAT radar) which are also only consistent with the FTE model. We estimate that for continuously southward IMF ( ≈ 5 nT) these FTEs contribute about 30 kV to the mean total transpolar voltage (∼30%).

Midday auroral breakup events and related energy and momentum transfer from the magnetosheath

Combined observations by meridian-scanning photometers, all-sky auroral TV camera and the EISCAT radar permitted a detailed analysis of the temporal and spatial development of the midday auroral breakup phenomenon and the related ionospheric ion flow pattern within the 71°–75° invariant latitude radar field of view. The radar data revealed dominating northward and westward ion drifts, of magnitudes close to the corresponding velocities of the discrete, transient auroral forms, during the two different events reported here, characterized by IMF |BY/BZ| < 1 and > 2, respectively (IMF BZ between −8 and −3 nT and BY > 0). The spatial scales of the discrete optical events were ∼50 km in latitude by ∼500 km in longitude, and their lifetimes were less than 10 min. Electric potential enhancements with peak values in the 30–50 kV range are inferred along the discrete arc in the IMF |BY/BZ| < 1 case from the optical data and across the latitudinal extent of the radar field of view in the |BY/BZ| > 2 case. Joule heat dissipation rates in the maximum phase of the discrete structures of ∼ 100 ergs cm−2 s−1 (0.1 W m−2) are estimated from the photometer intensities and the ion drift data. These observations combined with the additional characteristics of the events, documented here and in several recent studies (i.e., their quasi-periodic nature, their motion pattern relative to the persistent cusp or cleft auroral arc, the strong relationship with the interplanetary magnetic field and the associated ion drift/E field events and ground magnetic signatures), are considered to be strong evidence in favour of a transient, intermittent reconnection process at the dayside magnetopause and associated energy and momentum transfer to the ionosphere in the polar cusp and cleft regions. The filamentary spatial structure and the spectral characteristics of the optical signature indicate associated localized ˜1-kV potential drops between the magnetopause and the ionosphere during the most intense auroral events. The duration of the events compares well with the predicted characteristic times of momentum transfer to the ionosphere associated with the flux transfer event-related current tubes. It is suggested that, after this 2–10 min interval, the sheath particles can no longer reach the ionosphere down the open flux tube, due to the subsequent super-Alfvénic flow along the magnetopause, conductivities are lower and much less momentum is extracted from the solar wind by the ionosphere. The recurrence time (3–15 min) and the local time distribution (∼0900–1500 MLT) of the dayside auroral breakup events, combined with the above information, indicate the important roles of transient magnetopause reconnection and the polar cusp and cleft regions in the transfer of momentum and energy between the solar wind and the magnetosphere.

Ionospheric ion upwelling in the wake of flux transfer events at the dayside magnetopause

The effects of flux transfer events (FTE) on the dayside auroral ionosphere are studied, using a simple twin-vortex model of induced ionospheric plasma flow. It is shown that the predicted and observed velocities of these flows are sufficient to drive nonthermal plasma in the F region, not only within the newly opened flux tube of the FTE, but also on the closed, or "old" open, field lines around it. In fact, with the expected poleward neutral wind, the plasma is more highly nonthermal on the flanks of, but outside, the open flux tube: EISCAT observations indicate that plasma is indeed driven into nonthermal distributions in these regions. The nonthermal plasma is thereby subject to additional upforce due to the resulting ion temperature anisotropy and transient expansion due to Joule heating and also to ion accelerations associated with the FTE field aligned current system. Any upflows produced on closed field lines in the vicinity of the FTE are effectively bunched-up in the "wake" of the FTE. Observations from the AMPTE-UKS satellite at the magnetopause reveal ion upflows of energy ∼100 eV flowing out from the ionosphere on closed field lines which are only found in the wake of the FTE. Such flows are also only found shortly after two, out of all the FTEs observed by AMPTE-UKS. The outflow from the ionosphere is two orders of magnitude greater than predicted for the "classical" polar wind. It is shown that such ionospheric ion flows are only expected in association with FTEs on the magnetopause which are well removed from the sub-solar point-either towards dusk or, as in the UKS example discussed here, towards dawn. It is suggested that such ionospheric ions will only be observed if the center of the FTE open flux tube passes very close to the satellite. Consequently, we conclude the ion upflows presented here are probably driven by the second of two possible source FTEs and are observed at the satellite with a lag after the FTE which is less than their time-of-flight.

Evidence of resilience to past climate change in Southwest Asia: early farming communities and the 9.2 and 8.2 ka events

Climate change is often cited as a major factor in social change. The so-called 8.2 ka event was one of the most pronounced and abrupt Holocene cold and arid events. The 9.2 ka event was similar, albeit of a smaller magnitude. Both events affected the Northern Hemisphere climate and caused cooling and aridification in Southwest Asia. Yet, the impacts of the 8.2 and 9.2 ka events on early farming communities in this region are not well understood. Current hypotheses for an effect of the 8.2 ka event vary from large-scale site abandonment and migration (including the Neolithisation of Europe) to continuation of occupation and local adaptation, while impacts of the 9.2 ka have not previously been systematically studied. In this paper, we present a thorough assessment of available, quality-checked radiocarbon (14C) dates for sites from Southwest Asia covering the time interval between 9500 and 7500 cal BP, which we interpret in combination with archaeological evidence. In this way, the synchronicity between changes observed in the archaeological record and the rapid climate events is tested. It is shown that there is no evidence for a simultaneous and widespread collapse, large-scale site abandonment, or migration at the time of the events. However, there are indications for local adaptation. We conclude that early farming communities were resilient to the abrupt, severe climate changes at 9250 and 8200 cal BP.

Detecting regular sound changes in linguistics as events of concerted evolution

Background: Concerted evolution is normally used to describe parallel changes at different sites in a genome, but it is also observed in languages where a specific phoneme changes to the same other phoneme in many words in the lexicon—a phenomenon known as regular sound change. We develop a general statistical model that can detect concerted changes in aligned sequence data and apply it to study regular sound changes in the Turkic language family. Results: Linguistic evolution, unlike the genetic substitutional process, is dominated by events of concerted evolutionary change. Our model identified more than 70 historical events of regular sound change that occurred throughout the evolution of the Turkic language family, while simultaneously inferring a dated phylogenetic tree. Including regular sound changes yielded an approximately 4-fold improvement in the characterization of linguistic change over a simpler model of sporadic change, improved phylogenetic inference, and returned more reliable and plausible dates for events on the phylogenies. The historical timings of the concerted changes closely follow a Poisson process model, and the sound transition networks derived from our model mirror linguistic expectations. Conclusions: We demonstrate that a model with no prior knowledge of complex concerted or regular changes can nevertheless infer the historical timings and genealogical placements of events of concerted change from the signals left in contemporary data. Our model can be applied wherever discrete elements—such as genes, words, cultural trends, technologies, or morphological traits—can change in parallel within an organism or other evolving group.

Processes driving intraseasonal displacements of the eastern edge of the warm pool: the contribution of westerly wind events

We investigate the processes responsible for the intraseasonal displacements of the eastern edge of the western Pacific warm pool (WPEE), which appear to play a role in the onset and development of El Niño events. We use 25 years of output from an ocean general circulation model experiment that is able to accurately capture the observed displacements of the WPEE, sea level anomalies, and upper ocean zonal currents at intraseasonal time scales in the western and central Pacific Ocean. Our results confirm that WPEE displacements driven by westerly wind events (WWEs) are largely controlled by zonal advection. This paper has also two novel findings: first, the zonal current anomalies responsible for the WPEE advection are driven primarily by local wind stress anomalies and not by intraseasonal wind-forced Kelvin waves as has been shown in most previous studies. Second, we find that intraseasonal WPEE fluctuations that are not related to WWEs are generally caused by intraseasonal variations in net heat flux, in contrast to interannual WPEE displacements that are largely driven by zonal advection. This study hence raises an interesting question: can surface heat flux-induced zonal WPEE motions contribute to El Niño–Southern Oscillation evolution, as WWEs have been shown to be able to do?

The impact of the abrupt 8.2 ka cold event on the Mesolithic population of western Scotland: a Bayesian chronological analysis using ‘activity events’ as a population proxy

The potential impact of the abrupt 8.2 ka cold event on human demography, settlement patterns and culture in Europe and the Near East has emerged as a key theme in current discussion and debate. We test whether this event had an impact on the Mesolithic population of western Scotland, a case study located within the North Atlantic region where the environmental impact of the 8.2 ka event is likely to have been the most severe. By undertaking a Bayesian analysis of the radiocarbon record and using the number of activity events as a proxy for the size of the human population, we find evidence for a dramatic reduction in the Mesolithic population synchronous with the 8.2 ka event. We interpret this as reflecting the demographic collapse of a low density population that lacked the capability to adapt to the rapid onset of new environmental conditions. This impact of the 8.2 ka event in the North Atlantic region lends credence to the possibility of a similar impact on populations in Continental Europe and the Near East.

A novel approach for distributed application scheduling based on prediction of communication events

The evolution of commodity computing lead to the possibility of efficient usage of interconnected machines to solve computationally-intensive tasks, which were previously solvable only by using expensive supercomputers. This, however, required new methods for process scheduling and distribution, considering the network latency, communication cost, heterogeneous environments and distributed computing constraints. An efficient distribution of processes over such environments requires an adequate scheduling strategy, as the cost of inefficient process allocation is unacceptably high. Therefore, a knowledge and prediction of application behavior is essential to perform effective scheduling. In this paper, we overview the evolution of scheduling approaches, focusing on distributed environments. We also evaluate the current approaches for process behavior extraction and prediction, aiming at selecting an adequate technique for online prediction of application execution. Based on this evaluation, we propose a novel model for application behavior prediction, considering chaotic properties of such behavior and the automatic detection of critical execution points. The proposed model is applied and evaluated for process scheduling in cluster and grid computing environments. The obtained results demonstrate that prediction of the process behavior is essential for efficient scheduling in large-scale and heterogeneous distributed environments, outperforming conventional scheduling policies by a factor of 10, and even more in some cases. Furthermore, the proposed approach proves to be efficient for online predictions due to its low computational cost and good precision. (C) 2009 Elsevier B.V. All rights reserved.

Bayesian analysis of extreme events with threshold estimation

The aim of this paper is to analyze extremal events using Generalized Pareto Distributions (GPD), considering explicitly the uncertainty about the threshold. Current practice empirically determines this quantity and proceeds by estimating the GPD parameters based on data beyond it, discarding all the information available be10w the threshold. We introduce a mixture model that combines a parametric form for the center and a GPD for the tail of the distributions and uses all observations for inference about the unknown parameters from both distributions, the threshold inc1uded. Prior distribution for the parameters are indirectly obtained through experts quantiles elicitation. Posterior inference is available through Markov Chain Monte Carlo (MCMC) methods. Simulations are carried out in order to analyze the performance of our proposed mode1 under a wide range of scenarios. Those scenarios approximate realistic situations found in the literature. We also apply the proposed model to a real dataset, Nasdaq 100, an index of the financiai market that presents many extreme events. Important issues such as predictive analysis and model selection are considered along with possible modeling extensions.