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The three‐dimensionally preserved Haliestes dasos from the Silurian (Wenlock) Lagerstätte is the most complete fossil sea spider and the oldest unambiguous pycnogonid known from the fossil record. The discovery of two new specimens to add to the holotype reveals new features including proximal annulations of the appendages and segmentation of the trunk end, critical details for comparison with pycnogonids from the Devonian (Emsian) Hunsrück Slate and for the interpretation of the evolutionary significance of Palaeozoic genera. There is some evidence of sexual dimorphism. Haliestes dasos was nektobenthic and its morphology indicates an unusual mode of feeding compared with living pycnogonids. The new morphological features of H. dasos are closely similar to those in Palaeoisopus problematicus from the Hunsrück Slate and it clearly belongs, together with that species, in stem Pycnogonida and not the crown group. [ABSTRACT FROM AUTHOR]

The first Silurian trilobite known with soft parts preserved, a Dalmanites species, is described from the Herefordshire Lagerstätte. Biramous appendages and much of the alimentary system are evident. High‐fidelity three‐dimensional preservation reveals a novel arrangement of the exopod, in which successive filaments are connected by a presumed membrane. This morphology explains a misinterpretation of the exopod as supporting spiral structures, originally reported nearly 150 years ago. Comparison with other trilobite limbs indicates that the exopod morphology of Dalmanites is present in other members of Phacopida. The function of the exopod is considered to be primarily respiratory. [ABSTRACT FROM AUTHOR]

Most Palaeozoic brittle stars lack the fused arm ossicles (vertebrae) that facilitate the remarkable mode of walking that characterizes living forms. Here we describe a stem ophiuroid from the Herefordshire Lagerstätte (Silurian, Wenlock Series), which is exceptional in preserving the body cavity uncompacted and the long tube feet. We assign the specimen to the order Oegophiurida. The morphology of the arms and attitude of the specimen suggest that locomotion may have been achieved by arm propulsion combined with podial walking. This ophiuroid increases the diversity of echinoderm higher taxa with preserved soft parts represented in the Herefordshire Lagerstätte. [ABSTRACT FROM AUTHOR]

It has often been suggested that the productivity of an ecosystem affects the number of species that it can support. Despite decades of study, the nature, extent, and underlying mechanisms of this relationship are unclear. One suggested mechanism is the "more individuals" hypothesis (MIH). This proposes that productivity controls the number of individuals in the ecosystem, and that more individuals can be divided into a greater number of species before their population size is sufficiently small for each to be at substantial risk of extinction. Here, we test this hypothesis using REvoSim: an individual‐based eco‐evolutionary system that simulates the evolution and speciation of populations over geological time, allowing phenomena occurring over timescales that cannot be easily observed in the real world to be evaluated. The individual‐based nature of this system allows us to remove assumptions about the nature of speciation and extinction that previous models have had to make. Many of the predictions of the MIH are supported in our simulations: Rare species are more likely to undergo extinction than common species, and species richness scales with productivity. However, we also find support for relationships that contradict the predictions of the strict MIH: species population size scales with productivity, and species extinction risk is better predicted by relative than absolute species population size, apparently due to increased competition when total community abundance is higher. Furthermore, we show that the scaling of species richness with productivity depends upon the ability of species to partition niche space. Consequently, we suggest that the MIH is applicable only to ecosystems in which niche partitioning has not been halted by species saturation. Some hypotheses regarding patterns of biodiversity implicitly or explicitly overlook niche theory in favor of neutral explanations, as has historically been the case with the MIH. Our simulations demonstrate that niche theory exerts a control on the applicability of the MIH and thus needs to be accounted for in macroecology. [ABSTRACT FROM AUTHOR]

Spray pyrolysis technique was applied to deposit two sets of ultra‐thin layers of tin dioxide (SnO2). For the first and second sets, 0.01 and 0.05 molar precursor solutions were prepared, respectively. In both sets, utilizing the X‐ray reflectivity (XRR) technique, the effect of precursor concentration (PC) and precursor volume (PV) on the layer structure are investigated. The layer thickness of the samples, in each set, is a PV‐dependent parameter. For the same PV, samples with higher PC have a larger thickness and higher density. The electron density profiles deduced from XRR data analyses establish a link between measured values of sheet resistance and electron densities. The samples with higher PV and PC show less sheet resistance. The quantum size effect was utilized to show that the surface roughness for layers of more than almost 200 Å of samples in set two plays no role in the layer conductivity. Meanwhile, the same effect explains, adequately, the role of the surface roughness in the resistivity of the ultra‐thin layers in Set 1. [ABSTRACT FROM AUTHOR]

X‐ray free‐electron lasers (X‐FELs) present new opportunities to study ultrafast lattice dynamics in complex materials. While the unprecedented source brilliance enables high fidelity measurement of structural dynamics, it also raises experimental challenges related to the understanding and control of beam‐induced irreversible structural changes in samples that can ultimately impact the interpretation of experimental results. This is also important for designing reliable high performance X‐ray optical components. In this work, X‐FEL beam‐induced lattice alterations are investigated by measuring the shot‐to‐shot evolution of near‐Bragg coherent scattering from a single crystalline germanium sample. It is shown that X‐ray photon correlation analysis of sequential speckle patterns measurements can be used to monitor the nature and extent of lattice rearrangements. Abrupt, irreversible changes are observed following intermittent high‐fluence monochromatic X‐ray pulses, thus revealing the existence of a threshold response to X‐FEL pulse intensity. [ABSTRACT FROM AUTHOR]

X‐ray speckle visibility spectroscopy using X‐ray free‐electron lasers has long been proposed as a probe of fast dynamics in noncrystalline materials. In this paper, numerical modeling is presented to show how the data interpretation of visibility spectroscopy can be impacted by the nonidealities of real‐life X‐ray detectors. Using simulated detector data, this work provides a detailed analysis of the systematic errors of several contrast extraction algorithms in the context of low‐count‐rate X‐ray speckle visibility spectroscopy and their origins are discussed. Here, it was found that the finite detector charge cloud and pixel size lead to an unavoidable 'degeneracy' in photon position determination, and that the contrasts extracted using different algorithms can all be corrected by a simple linear model. The results suggest that experimental calibration of the correction coefficient at the count rate of interest is possible and essential. This allows computationally lightweight algorithms to be implemented for on‐the‐fly analysis. [ABSTRACT FROM AUTHOR]

Macroevolutionary processes dictate the generation and loss of biodiversity. Understanding them is a key challenge when interrogating the earth–life system in deep time. Model‐based approaches can reveal important macroevolutionary patterns and generate hypotheses on the underlying processes. Here we present and document a novel model called REvoSim (Rapid Evolutionary Simulator) coupled with a software implementation of this model. The latter is available here as both source code (C++/Qt, GNU General Public License) and as distributables for a variety of operating systems. REvoSim is an individual‐based model with a strong focus on computational efficiency. It can simulate populations of 105–107 digital organisms over geological timescales on a typical desktop computer, and incorporates spatial and temporal environmental variation, recombinant reproduction, mutation and dispersal. Whilst microevolutionary processes drive the model, macroevolutionary phenomena such as speciation and extinction emerge. We present results and analysis of the model focusing on validation, and note a number potential applications. REvoSim can serve as a multipurpose platform for studying both macro and microevolution, and bridges this divide. It will be continually developed by the authors to expand its capabilities and hence its utility. [ABSTRACT FROM AUTHOR]

We report results from a long‐term experiment in which additional nitrogen has been deposited on a peat bog in central Scotland for over 14 years, in three different forms: as ammonia (NH3) gas, as ammonium (NH4+) solution, or as nitrate (NO3-) solution. The automated experiment was designed to apply nitrogen in such a way that mimics real‐world nitrogen deposition. Background nitrogen deposition at the site was 0.8 g N m−2 year−1).Observations of cover for 46 species were made. We analysed the change in six common species in relation to nitrogen dose and form. The responses differed among species and nitrogen forms, but five out of the six species declined, and NH3 produced the biggest change in cover per unit of nitrogen addition. The exception was the graminoid sedge Eriophorum vaginatum, which increased dramatically in the NH3 treatment. Multivariate analyses identified responses to nitrogen dose across treatments which were consistent with the univariate results.We surmised that the larger experimental response to nitrogen observed in the NH3 treatment (cf. the NH4+ and NO3- treatments) was because of the higher nitrogen concentrations at the vegetation surface produced by dry deposition. NH4+ and NO3- were sprayed in solution, but much of this will enter the peat porewater, and be further diluted. Because NH3 deposits directly to the leaf, it stays contained within the small volume of water on and in the leaf, producing a high internal concentration of nitrogen ions.Synthesis. Consistent trends with nitrogen were discernible across species. All species showed a decline with NH3 treatment, except for Eriophorum vaginatum which increased. In the absence of phosphorous and potassium (PK), all species declined with NH4+ and NO3-, except for Calluna vulgaris and Hypnum jutlandicum. The effect of PK was not consistent across species. Per unit of nitrogen deposited, NH3 generally had a larger impact on vegetation composition than NH4+ or NO3-. However, the actual deposition rate of NH3 on UK peat bogs is lower than the other forms. In the case of the most common species of the peat‐forming genus Sphagnum, we estimate that NH4+ deposition has the largest impact, followed by NO3- and NH3. [ABSTRACT FROM AUTHOR]

Objective: To test the hypothesis that benign prostatic hyperplasia (BPH) robotic surgery with aquablation would have a more pronounced benefit in certain patient subgroups, such as men with more challenging anatomies (e.g. large prostates, large middle lobes) and men with moderate BPH. Methods: We conducted prespecified and post hoc exploratory subgroup analyses from a double‐blind, multicentre prospective randomized controlled trial that compared transurethral resection of the prostate (TURP) using either standard electrocautery vs surgery using robotic waterjet (aquablation) to determine whether certain baseline factors predicted more marked responses after aquablation as compared with TURP. The primary efficacy endpoint was reduction in International Prostate Symptom Score (IPSS) at 6 months. The primary safety endpoint was the occurrence of Clavien–Dindo persistent grade 1 or grade ≥2 surgical complications. Results: For men with larger prostates (50–80 g), the mean IPSS reduction was four points greater after aquablation than after TURP (P = 0.001), a larger difference than the overall result (1.8 points; P = 0.135). Similarly, the primary safety endpoint difference (20% vs 46% [26% difference]; P = 0.008) was greater for men with large prostate compared with the overall result (26% vs 42% [16% difference]; P = 0.015). Postoperative anejaculation was also less common after aquablation compared with TURP in sexually active men with large prostates (2% vs 41%; P < 0.001) vs the overall results (10% vs 36%; P < 0.001). Exploratory analysis showed larger IPSS changes after aquablation in men with enlarged middle lobes, men with severe middle lobe obstruction, men with a low baseline maximum urinary flow rate, and men with elevated (>100) post‐void residual urine volume. Conclusions: In men with moderate‐to‐severe lower urinary tract symptoms attributable to BPH and larger, more complex prostates, aquablation was associated with both superior symptom score improvements and a superior safety profile, with a significantly lower rate of postoperative anejaculation. The standardized, robotically executed, surgical approach with aquablation may overcome the increased outcome variability in more complex anatomy, resulting in superior symptom score reduction. [ABSTRACT FROM AUTHOR]

Small‐angle X‐ray photon correlation spectroscopy (XPCS) measurements spanning delay times from 826 ns to 52.8 s were performed using a photon‐counting pixel array detector with a dynamic range of 0–3 (2 bits). Fine resolution and a wide dynamic range of time scales was achieved by combining two modes of operation of the detector: (i) continuous mode, where data acquisition and data readout are performed in parallel with a frame acquisition time of 19.36 µs, and (ii) burst mode, where 12 frames are acquired with frame integration times of either 2.56 µs frame−1 or 826 ns frame−1 followed by 3.49 ms or 1.16 ms, respectively, for readout. The applicability of the detector for performing multi‐speckle XPCS was demonstrated by measuring the Brownian dynamics of 10 nm‐radius gold and 57 nm‐radius silica colloids in water at room temperature. In addition, the capability of the detector to faithfully record one‐ and two‐photon counts was examined by comparing the statistical distribution of photon counts with expected probabilities from the negative binomial distribution. It was found that in burst mode the ratio of 2 s to 1 s is markedly smaller than predicted and that this is attributable to pixel‐response dead‐time. [ABSTRACT FROM AUTHOR]

Objective: Interpersonal psychotherapy (IPT) has demonstrated efficacy for the treatment of depression, yet little is known about its therapeutic mechanisms. As a specific treatment, IPT has been shown to directly reduce depressive symptoms, although it is unclear whether these reductions occur via interpersonal changes. Within IPT, the potential role of the working alliance, a common factor, as a predictor of depression and interpersonal changes is also unclear. Method: Participants were 147 depressed persons living with HIV in rural communities of 28 U.S. states enrolled in a randomized clinical trial. Seventy‐five patients received up to 9 sessions of telephone‐administered IPT (tele‐IPT) plus standard care and 72 patients received standard care only. Two models were tested; one included treatment condition (tele‐IPT vs. control) and another included the working alliance as independent variables. Results: The first model found an indirect effect whereby tele‐IPT reduced depression via decreased social avoidance. There was a direct effect between tele‐IPT and reduced depression. In the second model, the working alliance influenced depressive symptom relief via reductions in social avoidance. Both goal and task working alliance subscales were indirectly associated with reductions in depressive symptoms, also through reductions in social avoidance. There were no direct effects involving the working alliance. Tele‐IPT's influence on depressive symptom reduction was primarily through a direct effect, whereas the influence of working alliance depression was almost entirely via an indirect effect through interpersonal problems. Conclusion: Study findings have implications for IPT when intervening with depressed rural people living with HIV/AIDS over the telephone. [ABSTRACT FROM AUTHOR]

ABSTRACT The Late Jurassic to Early Cretaceous interval represents a time of environmental upheaval and cataclysmic events, combined with disruptions to terrestrial and marine ecosystems. Historically, the Jurassic/ Cretaceous ( J/ K) boundary was classified as one of eight mass extinctions. However, more recent research has largely overturned this view, revealing a much more complex pattern of biotic and abiotic dynamics than has previously been appreciated. Here, we present a synthesis of our current knowledge of Late Jurassic-Early Cretaceous events, focusing particularly on events closest to the J/ K boundary. We find evidence for a combination of short-term catastrophic events, large-scale tectonic processes and environmental perturbations, and major clade interactions that led to a seemingly dramatic faunal and ecological turnover in both the marine and terrestrial realms. This is coupled with a great reduction in global biodiversity which might in part be explained by poor sampling. Very few groups appear to have been entirely resilient to this J/ K boundary 'event', which hints at a 'cascade model' of ecosystem changes driving faunal dynamics. Within terrestrial ecosystems, larger, more-specialised organisms, such as saurischian dinosaurs, appear to have suffered the most. Medium-sized tetanuran theropods declined, and were replaced by larger-bodied groups, and basal eusauropods were replaced by neosauropod faunas. The ascent of paravian theropods is emphasised by escalated competition with contemporary pterosaur groups, culminating in the explosive radiation of birds, although the timing of this is obfuscated by biases in sampling. Smaller, more ecologically diverse terrestrial non-archosaurs, such as lissamphibians and mammaliaforms, were comparatively resilient to extinctions, instead documenting the origination of many extant groups around the J/ K boundary. In the marine realm, extinctions were focused on low-latitude, shallow marine shelf-dwelling faunas, corresponding to a significant eustatic sea-level fall in the latest Jurassic. More mobile and ecologically plastic marine groups, such as ichthyosaurs, survived the boundary relatively unscathed. High rates of extinction and turnover in other macropredaceous marine groups, including plesiosaurs, are accompanied by the origin of most major lineages of extant sharks. Groups which occupied both marine and terrestrial ecosystems, including crocodylomorphs, document a selective extinction in shallow marine forms, whereas turtles appear to have diversified. These patterns suggest that different extinction selectivity and ecological processes were operating between marine and terrestrial ecosystems, which were ultimately important in determining the fates of many key groups, as well as the origins of many major extant lineages. We identify a series of potential abiotic candidates for driving these patterns, including multiple bolide impacts, several episodes of flood basalt eruptions, dramatic climate change, and major disruptions to oceanic systems. The J/ K transition therefore, although not a mass extinction, represents an important transitional period in the co-evolutionary history of life on Earth. [ABSTRACT FROM AUTHOR]

The ATP-bound form of the Escherichia coli DnaA replication initiator protein remodels the chromosomal origin of replication, oriC, to load the replicative helicase. The primary mechanism for regulating the activity of DnaA involves the Hda and β clamp proteins, which act together to dramatically stimulate the intrinsic DNA-dependent ATPase activity of DnaA via a process termed Regulatory Inactivation of DnaA. In addition to hyperinitiation, strains lacking hda function also exhibit cold sensitive growth at 30°C. Strains impaired for the other regulators of initiation (i.e., Δ seqA or Δ datA) fail to exhibit cold sensitivity. The goal of this study was to gain insight into why loss of hda function impedes growth. We used a genetic approach to isolate 9 suppressors of Δ hda cold sensitivity, and characterized the mechanistic basis by which these suppressors alleviated Δ hda cold sensitivity. Taken together, our results provide strong support for the view that the fundamental defect associated with Δ hda is diminished levels of DNA precursors, particularly dGTP and dATP. We discuss possible mechanisms by which the suppressors identified here may regulate dNTP pool size, as well as similarities in phenotypes between the Δ hda strain and hda+ strains exposed to the ribonucleotide reductase inhibitor hydroxyurea. [ABSTRACT FROM AUTHOR]

Telepsychology research has focused primarily on treatment efficacy, with far less attention devoted to how common factors relate to teletherapy outcomes. This research identified trajectories of depressive symptom relief in 105 older people living with HIV with elevated depressive symptoms enrolled in a randomized clinical trial testing two 12-session group teletherapies and compared common factors (e.g., therapeutic alliance and group cohesion) across depressive symptom trajectory groups. Growth mixture modelling of weekly depression scores identified three depressive symptom change groups: (1) 'early improvers' (31%) who reported reductions in depressive symptoms by Session 4; (2) 'delayed improvers' (16%) whose symptoms improved after Session 5 and (3) 'non-improvers' (53%). Therapeutic alliance was unrelated to treatment outcome group. Group cohesion was greater in early improvers than non-improvers. Group cohesion was unexpectedly lower, and group member similarity was greater in delayed improvers than non-improvers. Early improvers had been living with HIV/AIDS for fewer years than non-improvers. In group teletherapy, group cohesion and group member similarity are more important than client-therapist alliance. Copyright © 2015 John Wiley & Sons, Ltd. Key Practitioner Message In group teletherapy with older people living with HIV (OPLWHIV), three latent outcome trajectory groups emerged over the 12-week treatment period: (1) non-improvers (53%); (2) early improvers (31%) and (3) delayed improvers (16%)., In group teletherapy with OPLWHIV, group cohesion is a stronger predictor of depressive symptom relief than is client-therapist alliance., OPLWHIV in group teletherapy who do not respond to treatment until the latter therapy sessions can still experience depressive symptom relief comparable with early responders. [ABSTRACT FROM AUTHOR]

Coleoid cephalopod phylogeny is well studied via both molecular and morphological data, yet although some agreement has been reached (e.g. that extant Decapodiformes and Octopoda are monophyletic) many details remain poorly resolved. Fossil coleoids, for which much data exists, have hitherto not been incorporated into analyses. Their inclusion is highly desirable for the support of neontological phylogenies, to better reconstruct character-state histories, and to investigate the placement of the fossil groups themselves. In this study we present and analyse a morphological data matrix including both extinct and extant taxa. Homology assumptions in our data are discussed. Our results are presented both with and without the constraint of a monophyletic Decapodiformes imposed. When analysed with this constraint our results are strikingly congruent with those from molecular phylogeny, for instance placing Idiosepius in a basal position within Decapodiformes, and recovering Oegopsida and Bathyteuthoidea (although as grades). Our results support an Octopodiformes clade ('vampire squid' Vampyroteuthis as sister to Octopoda) and an octopodiform interpretation for most fossil coleoids. They suggest the fossil sister taxon to the octopods to be Plesioteuthididae. Most fossil higher taxa are supported, although many genera, especially within suborder Teudopseina, appear para- or polyphyletic. [ABSTRACT FROM AUTHOR]

The Vertically Integrated Photon Imaging Chip (VIPIC) was custom-designed for X-ray photon correlation spectroscopy, an application in which occupancy per pixel is low but high time resolution is needed. VIPIC operates in a sparsified streaming mode in which each detected photon is immediately read out as a time- and position-stamped event. This event stream can be fed directly to an autocorrelation engine or accumulated to form a conventional image. The detector only delivers non-zero data (sparsified readout), greatly reducing the communications overhead typical of conventional frame-oriented detectors such as charge-coupled devices or conventional hybrid pixel detectors. This feature allows continuous acquisition of data with timescales from microseconds to hours. In this work VIPIC has been used to measure X-ray photon correlation spectroscopy data on polystyrene latex nano-colliodal suspensions in glycerol and on colloidal suspensions of silica spheres in water. Relaxation times of the nano-colloids have been measured for different temperatures. These results demonstrate that VIPIC can operate continuously in the microsecond time frame, while at the same time probing longer timescales. [ABSTRACT FROM AUTHOR]

Extant aplacophorans, a group of shell-less vermiform molluscs, respire through appendages within or projecting from a posterior cavity. Respiratory structures differ between the subclasses Caudofoveata (ctenidia within the cavity) and Solenogastres (folds of the mantle itself). Acaenoplax hayae, a Silurian vermiform mollusc from the Herefordshire Lagerstätte, England, exhibits characteristics of both these groups. While recent work places it within the crown group Aplacophora, near the caudofoveates, initial observations suggested that its respiratory structures were closer to those of the solenogastres. Here, we present new reconstructions of the posterior of Acaenoplax prepared with the aim of resolving features obscured when prior studies were undertaken. These reconstructions detail a novel posterior architecture, not closely comparable to that of either extant aplacophoran group, in which respiratory projections arise from a membrane that partly encloses a central posterior cavity. The posterior membrane is flanked by small spherical projections; both membrane and spherical projections are apparently unique within the Aplacophora. The existence of this previously undocumented respiratory system underlines the diversity of the aplacophoran clade during the Palaeozoic. [ABSTRACT FROM AUTHOR]

ABSTRACT Tensile stress-relaxation measurements have been performed on a series of cross-linked filled elastomers. The fillers are chosen to investigate the effect of the filler-filler and the filler-matrix interactions on the time dependence of the tensile relaxation modulus E(t) after UP and DOWN jumps. For the carbon black-filled sample (strong filler-elastomer interaction) E(t) decreases as log( t) when the strain ε is strictly larger than 0.2 and reached by UP jumps. For the silica-filled samples in the same conditions, and for all samples after a DOWN jump, including ε = 0.2, the experimental data can be fitted with a power law equation characterized by the exponent m. Thus, in all cases, |dE(t)/dt| scales as t−α with α ⩵ m + 1. Pertinence of the soft glassy rheology model for interpreting these results is examined. It is shown that α could be equivalent to the effective noise temperature x and related to the polymer chain mobility. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2014, 52, 647-656 [ABSTRACT FROM AUTHOR]

Wet deposition of nitrogen (N) occurs in oxidized (nitrate) and reduced (ammonium) forms. Whether one form drives vegetation change more than the other is widely debated, as field evidence has been lacking. We are manipulating N form in wet deposition to an ombrotrophic bog, Whim (Scottish Borders), and here report nine years of results. Ammonium and nitrate were provided in rainwater spray as NH4Cl or NaNO3 at 8, 24 or 56 kg N ha−1 yr−1, plus a rainwater only control, via an automated system coupled to site meteorology. Detrimental N effects were observed in sensitive nonvascular plant species, with higher cumulative N loads leading to more damage at lower annual doses. Cover responses to N addition, both in relation to form and dose, were species specific and mostly dependent on N dose. Some species were generally indifferent to N form and dose, while others were dose sensitive. Calluna vulgaris showed a preference for higher N doses as ammonium N and Hypnum jutlandicum for nitrate N. However, after 9 years, the magnitude of change from wet deposited N on overall species cover is small, indicating only a slow decline in key species. Nitrogen treatment effects on soil N availability were likewise small and rarely correlated with species cover. Ammonium caused most N accumulation and damage to sensitive species at lower N loads, but toxic effects also occurred with nitrate. However, because different species respond differently to N form, setting of ecosystem level critical loads by N form is challenging. We recommend implementing the lowest value of the critical load range where communities include sensitive nonvascular plants and where ammonium dominates wet deposition chemistry. In the context of parallel assessment at the same site, N treatments for wet deposition showed overall much smaller effects than corresponding inputs of dry deposition as ammonia. [ABSTRACT FROM AUTHOR]

The technique of speckle visibility spectroscopy has been employed for the measurement of dynamics using coherent X-ray scattering. It is shown that the X-ray contrast within a single exposure can be related to the relaxation time of the intermediate scattering function, and this methodology is applied to the diffusion of 72 nm-radius latex spheres in glycerol. Data were collected with exposure times as short as 2 ms by employing a resonant shutter. The weak scattering present for short exposures necessitated an analysis formalism based on the spatial correlation function of individual photon charge droplets on an area detector, rather than the usual methods employed for intensity correlations. It is demonstrated that this method gives good agreement between theory and experiment and thus holds promise for extending area-detector-based coherent scattering methods to the study of faster dynamics than previously obtainable. [ABSTRACT FROM AUTHOR]

The ATP-bound form of the Escherichia coli DnaA protein binds 'DnaA boxes' present in the origin of replication ( oriC) and operator sites of several genes, including dnaA, to co-ordinate their transcription with initiation of replication. The Hda protein, together with the β sliding clamp, stimulates the ATPase activity of DnaA via a process termed regulatory inactivation of DnaA (RIDA), to regulate the activity of DnaA in DNA replication. Here, we used the mutant dnaN159 strain, which expresses the β159 clamp protein, to gain insight into how the actions of Hda are co-ordinated with replication. Elevated expression of Hda impeded growth of the dnaN159 strain in a Pol II- and Pol IV-dependent manner, suggesting a role for Hda managing the actions of these Pols. In a wild-type strain, elevated levels of Hda conferred sensitivity to nitrofurazone, and suppressed the frequency of −1 frameshift mutations characteristic of Pol IV, while loss of hda conferred cold sensitivity. Using the dnaN159 strain, we identified 24 novel hda alleles, four of which supported E. coli viability despite their RIDA defect. Taken together, these findings suggest that although one or more Hda functions are essential for cell viability, RIDA may be dispensable. [ABSTRACT FROM AUTHOR]

The palaeoloricate 'polyplacophorans' are an extinct paraphyletic group of basal chiton-like organisms known primarily from their fossilized valves. Their phylogenetic placement remains contentious, but they are likely to include both stem-group Polyplacophora and stem-group Aplacophora. Candidates for the latter position include ' Helminthochiton' thraivensis from the Ordovician of Scotland, which we redescribe here through a combined optical and micro-CT (XMT) restudy of the type material. The 11 specimens in the type series are all articulated, presenting partial or complete valve series as well as mouldic preservation of the girdle armature; they demonstrate a vermiform body plan. The valves are typically palaeoloricate in aspect, but differ in detail from all existing palaeoloricate genera; we hence erect Phthipodochiton gen. nov. to contain the species. The most notable feature of the fossils is the spicular girdle; this is impersistently preserved, but demonstrably wraps entirely around the ventral surface of the animal, implying that a 'true' (i.e. polyplacophoran like) foot was absent, although we do not exclude the possibility of a narrow solenogastre-like median pedal groove having been present. Phthipodochiton thraivensis presents an apparent mosaic of aplacophoran and polyplacophoran features and as such will inform our understanding of the relationship between these groups of extant molluscs. An inference may also be drawn that at least some other palaeoloricates possessed an 'armoured aplacophoran' body plan, in contrast to the 'limpet-like' body plan of extant Polyplacophora. [ABSTRACT FROM AUTHOR]

Although the effects of atmospheric nitrogen deposition on species composition are relatively well known, the roles of the different forms of nitrogen, in particular gaseous ammonia ( NH3), have not been tested in the field. Since 2002, we have manipulated the form of N deposition to an ombrotrophic bog, Whim, on deep peat in southern Scotland, with low ambient N (wet + dry = 8 kg N ha−1 yr−1) and S (4 kg S ha−1 yr−1) deposition. A gradient of ammonia ( NH3, dry N), from 70 kg N ha−1 yr−1 down to background, 3-4 kg N ha−1 yr−1 was generated by free air release. Wet ammonium ( NH4+, wet N) was provided to replicate plots in a fine rainwater spray ( NH4 Cl at +8, +24, +56 kg N ha−1 yr−1). Automated treatments are coupled to meteorological conditions, in a globally unique, field experiment. Ammonia concentrations were converted to NH3- N deposition (kg N ha−1) using a site/vegetation specific parameterization. Within 3 years, exposure to relatively modest deposition of NH3, 20-56 kg NH3-N ha−1 yr−1 led to dramatic reductions in species cover, with almost total loss of Calluna vulgaris, Sphagnum capillifolium and Cladonia portentosa. These effects appear to result from direct foliar uptake and interaction with abiotic and biotic stresses, rather than via effects on the soil. Additional wet N by contrast, significantly increased Calluna cover after 5 years at the 56 kg N dose, but reduced cover of Sphagnum and Cladonia. Cover reductions caused by wet N were significantly different from and much smaller than those caused by equivalent dry N doses. The effects of gaseous NH3 described here, highlight the potential for ammonia to destroy acid heathland and peat bog ecosystems. Separating the effects of gaseous ammonia and wet ammonium deposition, for a peat bog, has significant implications for regulatory bodies and conservation agencies. [ABSTRACT FROM AUTHOR]

Summary 1. Atmospheric ammonia (NH3) is one of the main drivers for ecosystem changes world-wide, including biodiversity loss. Modelling its deposition to evaluate its impact on ecosystems has been the focus of many studies. For that, universal indicators are needed to determine and compare the early effects of NH3 across ecosystems. 2. We evaluate the effects of atmospheric NH3 in ecosystems using lichens, which are one of the most sensitive communities at the ecosystem level. Rather than measuring total diversity, we use a functional diversity approach because this is potentially a more universal tool. 3. We evaluated the spatial and temporal patterns of atmospheric NH3 concentrations ([NH3]atm) emitted from a point-source over a 1-year period in a cork oak Mediterranean woodland. We observed a temporal pattern of [NH3]atm, with maximum concentrations during autumn. 4. The distribution of lichen species was c. 90% explained by [NH3]atm. The tolerance of lichen species to atmospheric NH3, based on expert knowledge from literature, was tested for the first time against direct measurements of atmospheric NH3. Most species were well classified, with the exception of Lecanora albella and Chrysothrix candelaris, which were more tolerant than expected. Our updated lichen classification can be used to establish lichen functional groups that respond to atmospheric NH3, and these can be used in other Mediterranean countries. 5. Increasing [NH3]atm led to a complete replacement of oligotrophic by nitrophytic species within 65 m of the NH3 source. The geostatistical analysis of functional diversity variables yielded a spatial model with low non-spatial variance, indicating that these variables can cope robustly with high spatial variation in NH3. 6. Synthesis and applications. Our results support the use of functional diversity variables, such as a lichen diversity value, as accurate and robust indicators of the effects of atmospheric NH3 on ecosystems. The spatial modelling of these indicators can provide information with high spatial resolution about the effects of atmospheric NH3 around point- and diffuse sources. As this methodology is based on functional groups, it can be applied to monitor both the impact of atmospheric NH3 and the success of mitigation strategies. [ABSTRACT FROM AUTHOR]

The article presents a case study on the benefits of alternative scenarios for controlling the emissions of agricultural ammonia in Great Britain. It says that an impact pathway approach was used to assess the impact of ammonia emission reductions on ecosystem service delivery. According to the author, the ecosystem service-based valuation provides significant advantages and strengths to support a more holistic approach to the management of air quality. The article also discusses the effects of ammonia emissions on terrestrial and aquatic ecosystems.

This paper compares data on N fluxes compiled by Schulze and colleagues, with information available in the literature and publicly available open databases, and finds important discrepancies for a number of such fluxes for Europe (emissions, deposition, aerosol formation of compounds containing N) - exceeding a factor of two in several cases. A qualitative assessment of the uncertainties of the respective approaches indicates that these differences are beyond the uncertainty margins that can be reasonably attributed to the respective data.We conclude that the results should be used with caution, that agricultural application of N should still be considered to be the largest source of N released to the environment, and that this agricultural N affects soils more strongly than atmospheric deposition, at the European scale. [ABSTRACT FROM AUTHOR]

In this study we examined ecosystem respiration ( R) data from 104 sites belonging to FLUXNET, the global network of eddy covariance flux measurements. The goal was to identify the main factors involved in the variability of R: temporally and between sites as affected by climate, vegetation structure and plant functional type (PFT) (evergreen needleleaf, grasslands, etc.). We demonstrated that a model using only climate drivers as predictors of R failed to describe part of the temporal variability in the data and that the dependency on gross primary production (GPP) needed to be included as an additional driver of R. The maximum seasonal leaf area index (LAI) had an additional effect that explained the spatial variability of reference respiration (the respiration at reference temperature T=15 °C, without stimulation introduced by photosynthetic activity and without water limitations), with a statistically significant linear relationship ( r=0.52, P<0.001, n=104) even within each PFT. Besides LAI, we found that reference respiration may be explained partially by total soil carbon content (SoilC). For undisturbed temperate and boreal forests a negative control of total nitrogen deposition (N) on reference respiration was also identified. We developed a new semiempirical model incorporating abiotic factors (climate), recent productivity (daily GPP), general site productivity and canopy structure (LAI) which performed well in predicting the spatio-temporal variability of R, explaining >70% of the variance for most vegetation types. Exceptions include tropical and Mediterranean broadleaf forests and deciduous broadleaf forests. Part of the variability in respiration that could not be described by our model may be attributed to a series of factors, including phenology in deciduous broadleaf forests and management practices in grasslands and croplands. [ABSTRACT FROM AUTHOR]

Palaeontology was established as a science in the Victorian era, yet has roots that stretch deeper into the recesses of history. More than 2000 years ago, the Greek philosopher Aristotle deduced that fossil sea shells were once living organisms, and around 500ad Xenophanes used fossils to argue that many areas of land must have previously been submarine. In 1027, the Persian scholar Avicenna suggested that organisms were fossilized by petrifying fluids; this theory was accepted by most natural philosophers up until the eighteenth century Enlightenment, and even beyond. The late 1700s were notable for the work of Georges Cuvier who established the reality of extinction. This, coupled with advances in the recognition of faunal successions made by the canal engineer William Smith, laid the framework for the discipline that would become known as palaeontology. As the nineteenth century progressed, the scientific community became increasingly well organized. Most fossil workers were gentleman scientists and members of the clergy, who self-funded their studies in a new and exciting field. Many of the techniques used to study fossils today were developed during this ‘classical’ period. Perhaps the most fundamental of these is to expose a fossil by splitting the rock housing it, and then conduct investigations based upon the exposed surface ( Fig. 1 ). This approach has served the science well in the last two centuries, having been pivotal to innumerable advances in our understanding of the history of life. Nevertheless, there are many cases where splitting a rock in this way results in incomplete data recovery; those where the fossils are not flattened, but are preserved in three-dimensions. Even the ephemeral soft-tissues of organisms are occasionally preserved in a three-dimensional state, for example in the Herefordshire, La Voulte Sûr Rhone and Orsten ‘Fossil Lagerstätten’ (sites of exceptional fossil preservation). These rare and precious deposits provide a wealth of information about the history of life on Earth, and are perhaps our most important resource in the quest to understand the palaeobiology of extinct organisms. With the aid of twenty-first century technology, we can now make the most of these opportunities through the field of ‘virtual palaeontology’—computer-aided visualization of fossils. [ABSTRACT FROM AUTHOR]

Candida albicans Hsp70 Ssa1/2 proteins have been identified as cell wall binding partners for the antifungal cationic peptide Histatin 5 (Hst 5) in vivo. C. albicans Ssa2p plays a major role in binding and translocation of Hst 5 into fungal cells, as demonstrated by defective peptide uptake and killing in C. albicans SSA2 null mutants. Candidal Hsp70 proteins are classical chaperone proteins with two discrete functional domains consisting of peptide binding and ATP binding regions. Pull-down assays with full-length and truncated Ssa2 proteins found that the ATPase domain was required for Hst 5 binding. Further mapping of Ssa2p by limited digestion and peptide array analyses identified two discrete Hst 5-binding epitopes within the ATPase region. Expression of Ssa2p in C. albicans cells carrying mutations in the first epitope identified by thermolysin digestion (Ssa2128−132A3) significantly reduced intracellular transport and fungicidal activity of Hst 5, confirming its importance as a binding site for Hst 5 function in vivo. Since this Hst 5 binding site lies within the Ssa2p ATPase domain near the ATP-binding cleft, it is possible that ATP modulates Hst 5 binding to Ssa2p. Indeed, gel filtration assays demonstrated that although nucleotides are not required for Hst 5 binding, their presence improved binding affinity by 10-fold. Thus, C. albicans Ssa2p binds Hst 5 at a surface-localized epitope in a subunit of the ATPase domain; and this region is required for intracellular translocation and killing functions of Hst 5. [ABSTRACT FROM AUTHOR]

In a recent study, Magnani et al. report how atmospheric nitrogen deposition drives stand-lifetime net ecosystem productivity (NEPav) for midlatitude forests, with an extremely high C to N response (725 kg C kg−1 wet-deposited N for their European sites). We present here a re-analysis of these data, which suggests a much smaller C : N response for total N inputs. Accounting for dry, as well as wet N deposition reduces the C : N response to 177 : 1. However, if covariance with intersite climatological differences is accounted for, the actual C : N response in this dataset may be <70 : 1. We then use a model analysis of 22 European forest stands to simulate the findings of Magnani et al. Multisite regression of simulated NEPav vs. total N deposition reproduces a high C : N response (149 : 1). However, once the effects of intersite climatological differences are accounted for, the value is again found to be much smaller, pointing to a real C : N response of about 50–75 : 1. [ABSTRACT FROM AUTHOR]

Escherichia coli strains expressing the mutant β159-sliding clamp protein (containing both a G66E and a G174A substitution) are temperature sensitive for growth and display altered DNA polymerase (pol) usage. We selected for suppressors of the dnaN159 allele able to grow at 42°C, and identified four intragenic suppressor alleles. One of these alleles ( dnaN780) contained only the G66E substitution, while a second ( dnaN781) contained only the G174A substitution. Genetic characterization of isogenic E. coli strains expressing these alleles indicated that certain phenotypes were dependent upon only the G174A substitution, while others required both the G66E and G174A substitutions. In order to understand the individual contributions of the G66E and the G174A substitution to the dnaN159 phenotypes, we utilized biochemical approaches to characterize the purified mutant β159 (G66E and G174A), β780 (G66E) and β781 (G174A) clamp proteins. The G66E substitution conferred a more pronounced effect on pol IV replication than it did pol II or pol III, while the G174A substitution conferred a greater effect on pol III and pol IV than it did pol II. Taken together, these findings indicate that pol II, pol III and pol IV interact with distinct, albeit overlapping surfaces of the β clamp. [ABSTRACT FROM AUTHOR]

TheEscherichia coliβ sliding clamp is proposed to play an important role in regulating DNA polymerase traffic at the replication fork. As part of an ongoing effort to understand how organisms manage the actions of their multiple DNA polymerases, we examined the ability of several mutant forms of theβ clamp to function in DNA polymerase V- (pol V-) dependent translesion DNA synthesis (TLS)in vivo. Our results indicate that adnaN159strain, which expresses a temperature sensitive form of theβ clamp, was impaired for pol V-dependent TLS at the permissive temperature of 37°C. This defect was complemented by a plasmid that expressed near-physiological levels of the wild-type clamp. Using adnaN159mutant strain, together with various plasmids expressing mutant forms of the clamp, we determined that residues H148 through R152, which comprise a portion of a solvent exposed loop, as well as position P363, which is located in the C-terminal tail of theβ clamp, are critically important for pol V-dependent TLSin vivo. In contrast, these same residues appear to be less critical for pol III-dependent replication. Taken together, these findings indicate that: (i) theβ clamp plays an essential role in pol V-dependent TLSin vivoand (ii) pol III and pol V interact with non-identical surfaces of theβ clamp. [ABSTRACT FROM AUTHOR]

Acaenoplax hayae is a spinose worm-like animal from the Silurian Herefordshire Lagerstätte of England, a deposit that preserves high-fidelity soft-part morphology of invertebrates in three dimensions. Specimens have been serially ground and reconstructed by computer to their three-dimensional form. Acaenoplax bears serially repeated transverse ridges dorsally, each with an array of probably aragonitic spines inclined posteriorly. Oblique ventral lobe-rows correspond in position to the dorsal ridges. Aragonitic dorsal valves overlie every third ridge; the penultimate valve is absent leaving a total of seven. The anterior termination is disk-like, surrounding an antero-medial mouth. At the posterior termination there is a cavity between the posteriormost dorsal and a posteroventral valve, from which soft-part projections extend. Acaenoplax is interpreted as a creeping epibenthic animal that fed on sessile prey. It is an ‘aculiferan’ mollusc, combining unique autapomorphic structures with characters typical of the Polyplacophora and Aplacophora. Its morphology can be accommodated within both of the competing schemes of molluscan phylogeny, and its closest living relatives in both cases are aplacophorans. The highly serialized morphology of Acaenoplax is unique within the Mollusca, but the pattern it highlights is an attractive candidate for the primitive state of serial repetition within the phylum. [ABSTRACT FROM AUTHOR]

There are two contrasting hypotheses regarding the drivers of biomass‐distribution among trophic levels within ecosystems. Energetic or bottom–up models propose control by supply of energy, either from autotrophy or from the underlying trophic level. Dynamical or top–down models propose control by predators in the overlying trophic level. Although multiple approaches have been used to reconcile these hypotheses, they have rarely considered the evolutionary pressures created by different distributions of biomass. Here, we study the effects of these evolutionary processes using an agent‐based, spatially‐explicit, eco‐evolutionary model. We demonstrate that, when ecosystems are simple and predator–prey relationships between species are fixed and do not evolve, primary productivity limits the number of trophic levels. In this case, the abundance in the top trophic level is always limited by productivity. However, productivity‐limited trophic levels subject those below them to limitation by predation, and predation‐limited trophic levels allow trophic levels below them to grow until limited by productivity. These results match the expectations of the exploitation ecosystems hypothesis (EEH), which predicts the same pattern of alternating top–down and bottom–up control on trophic levels. When species are able to evolve to adaptively adjust their trophic levels, however, selection is liable to lead to collapse of the trophic pyramid through prey switching. Under these conditions, all trophic levels experience bottom–up control. When the evolution of prey switching is restricted, higher trophic levels are evolutionarily stable and the predictions of the EEH are once again met; the stability of long food chains is thus dependent on the difficulty associated with prey switching. These results suggest that, at least under the combinations of model parameters explored in this study, evolutionary limitation is key to maintaining trophic structure. [ABSTRACT FROM AUTHOR]

The global emission of ammonia (NH3) is about 54 Mt N. The major global sources arc excreta from domestic animals and fertilizers, but oceans, biomass burning and crops are also important. About 60% of the global NH3 emission is estimated to come from anthropogenic sources. NH3-N emissions are of the same order as the NOx-N emissions on both global and European scales. Emitted NH3 returns to the surface mainly in the form of dry deposition of NH3 and Wet deposition of ammonium (NH3). In countries with high NH4 emission densities, dry deposition of NH3 from local sources and wet deposition of NH3- from remote sources dominate the deposition. In countries with low NH3, emission densities only wet deposition of NH3- from remote sources dominates the deposition. Surface exchange of NH3, is essentially bi-directional, depending on the NH4 compensation point concentration of the vegetation and the airborne concentration. In general, the compensation point is larger for agricultural than semi-natural plants, and varies with plant growth stage. According to basic thermodynamics the leaf tissue or stomatal compensation point of NH3 doubles for each increase of 5 °C. However, exchange of NH3 does not only occur through the stomata, but it can also he deposited to leaf surfaces, as well as emitted back to the atmosphere from drying leaf surfaces. Atmospheric transport and deposition models can be used to interpolate NH3, concentrations and depositions in space and time, to calculate import/export balances and to estimate past or future situations. Adverse effects on sensitive ecosystems caused by high N deposition can he reduced by lowering the emissions and, to a limited extent, also by removing sources close to the ecosystem to be protected. [ABSTRACT FROM AUTHOR]

A letter to the editor is presented offering information on the role of agricultural ammonia emissions in increasing China's urban air pollution.