bluuebunny/crossref_metadata_2025_split huggingface dataset:
Taxonomic dissimilarity in patterns of interception and establishment of alien arthropods, nematodes and pathogens affecting woody plants in Europe
Authors: Eschen René , Roques Alain , Santini Alberto 
Published: October 2014

AbstractAimThe number and impact of alien tree pests and pathogens increase in many countries as a result of international trade, despite phytosanitary measures aimed at preventing their introduction. We compared patterns in interceptions and establishments of alien arthropod pests and pathogens of woody plants in Europe.LocationEuropean Union.MethodsEstablishment data were extracted from the DAISIE and FORTHREATS databases and updated. Interception records (1995–2010) were obtained from the European and Mediterranean Plant Protection Organisation.ResultsThe rate of establishment increased, independently of host plant type, whether the species in the host genus are tropical or temperate, or whether invertebrates or pathogens, but interceptions were made on few host genera. There were large differences in the identities of the intercepted and established pests on species level, but similarities on higher taxonomic levels for arthropods and pathogens.Main ConclusionsDifferences between interceptions and establishments may result from the inspection focus on regulated organisms; while most established species were never regulated and especially pathogens are hard to detect. We suggest using molecular techniques to detect pathogens in asymptomatic plants and that pest risk analysis target potentially harmful organisms at a higher taxonomic level to cover more, potentially unknown pests in groups that have become established.
Contribution of the motor system to the perception of reachable space: an fMRI study
Authors: Bartolo Angela , Coello Yann , Edwards Martin G. , Delepoulle Samuel , Endo Satoshi , Wing Alan M. 
Published: October 2014

AbstractThe present functional magnetic resonance imaging (fMRI) study investigates the neural correlates of reachability judgements. In a block design experiment, 14 healthy participants judged whether a visual target presented at different distances in a virtual environment display was reachable or not with the right hand. In two control tasks, they judged the colour or the relative position of the visual target according to flankers. Contrasting the activations registered in the reachability judgement task and in the control tasks, we found activations in the frontal structures, and in the bilateral inferior and superior parietal lobe, including the precuneus, and the bilateral cerebellum. This fronto‐parietal network including the cerebellum overlaps with the brain network usually activated during actual motor production and motor imagery. In a following event‐related design experiment, we contrasted brain activations when targets were rated as ‘reachable’ with those when they were rated as ‘unreachable’. We found activations in the left premotor cortex, the bilateral frontal structures, and the left middle temporal gyrus. At a lower threshold, we also found activations in the left motor cortex, and in the bilateral cerebellum. Given that reaction time increased with target distance in reachable space, we performed a subsequent parametric analysis that revealed a related increase of activity in the fronto‐parietal network including the cerebellum. Unreachable targets did not show similar activation, and particularly in regions associated to motor production and motor imagery. Taken together, these results suggest that dynamical motor representations used to determine what is reachable are also part of the perceptual process leading to the distinct representation of peripersonal and extrapersonal spaces.
Interaural attention modulates outer hair cell function
Authors: Srinivasan Sridhar , Keil Andreas , Stratis Kyle , Osborne Aaron F. , Cerwonka Colin , Wong Jennifer , Rieger Brenda L. , Polcz Valerie , Smith David W. 
Published: October 2014

AbstractMounting evidence suggests that auditory attention tasks may modulate the sensitivity of the cochlea by way of the corticofugal and the medial olivocochlear (MOC) efferent pathways. Here, we studied the extent to which a separate efferent tract, the ‘uncrossed’ MOC, which functionally connects the two ears, mediates inter‐aural selective attention. We compared distortion product otoacoustic emissions (DPOAEs) in one ear with binaurally presented primaries, using an intermodal target detection task in which participants were instructed to report the occurrence of brief target events (visual changes, tones). Three tasks were compared under identical physical stimulation: (i) report brief tones in the ear in which DPOAE responses were recorded; (ii) report brief tones presented to the contralateral, non‐recorded ear; and (iii) report brief phase shifts of a visual grating at fixation. Effects of attention were observed as parallel shifts in overall DPOAE contour level, with DPOAEs relatively higher in overall level when subjects ignored the auditory stimuli and attended to the visual stimulus, compared with both of the auditory‐attending conditions. Importantly, DPOAE levels were statistically lowest when attention was directed to the ipsilateral ear in which the DPOAE recordings were made. These data corroborate notions that top‐down mechanisms, via the corticofugal and medial efferent pathways, mediate cochlear responses during intermodal attention. New findings show attending to one ear can significantly alter the physiological response of the contralateral, unattended ear, probably through the uncrossed‐medial olivocochlear efferent fibers connecting the two ears.
Diving Into The Water: Cues Related to the Decision‐Making by an Egg Parasitoid Attacking Underwater Hosts
Authors: Kohmura Hiroaki , Hirayama Hiroyuki , Ueno Takatoshi 
Published: October 2014

AbstractAlthough adult parasitoids spend a majority of their lives above ground, females of several species must search for their host in the water or on the soil. Adult parasitoids above ground can use a variety of sensory cues to detect their hosts from a distance. However, their sensory cues can be impaired from volatile chemicals, and their visual stimuli can be decreased while submerging or burrowing in the water of soil during their search for their hosts. Searching underwater or underground would incur high foraging costs, that is, time and energy consumption and increase risk of drowning. Therefore, to reduce such costs and increase searching efficiency, the decision on where to start submerging or burrowing for attacking hosts is important for parasitoids. Furthermore, there are no studies that have examined the cues of submerging or burrowing parasitoids on their exploit for the decision to attack their hosts. We have examined the cues used by the egg parasitoid Tiphodytes gerriphagus attacking underwater hosts. We compared the searching behaviors of T. gerriphagus among four oviposition site conditions. The four sites investigated were oviposition site with both host adult chemical residues and presence of eggs, with only the presence of eggs, with only the host adult chemical residues, and without any cue. Our results indicated that T. gerriphagus more frequently contacted and submerged at oviposition sites with the adult residues rather than at oviposition sites without them. Nonetheless, the presence of underwater host eggs did not affect the host‐searching behavior. This suggests that T. gerriphagus decided to submerge at the oviposition site in response to the adult residues. Furthermore, our observation also suggested that T. gerriphagus has already detected that the adult residues might be volatile before contacting the oviposition site. Finally, we will discuss the exploitation patterns of host‐searching cue by parasitoids that need to submerge from the context of its reliability and detectability problems.
Acceptance rates for manuscripts submitted to veterinary peer‐reviewed journals in 2012
Authors: Lamb C. R. , Adams C. A. 
Published: October 2014

SummaryReasons for performing studyRelatively few journals publish their annual acceptance rate, although this figure is of scientific and academic interest.ObjectivesTo determine the acceptance rate for manuscripts submitted to veterinary peer‐reviewed journals during 2012 and to determine the proportions of submitted manuscripts that were accepted without revision, accepted after revision or rejected.Study designSelf‐reporting email questionnaireMethodsEditors of 118 peer‐reviewed journals listed in the Web of Science in the subject category veterinary sciences were invited by email to submit data pertinent to manuscripts submitted to their journal in 2012.ResultsData were received from 30 (26%) journals. Mean ± s.d. acceptance rate was 47 ± 15%. On average 3 ± 5% submitted manuscripts were accepted without revision, 44% ± 15% manuscripts were accepted after revision, 4 ± 4% manuscripts were withdrawn by authors, 46 ± 17% manuscripts were rejected and 3 ± 5% manuscripts were still pending at the end of the study period.ConclusionsWith so few manuscripts accepted without revision, prospective authors must expect to expend time and effort revising and resubmitting their manuscripts for publication. Although authors are frequently able to correct manuscript flaws identified by reviewers, the knowledge that less than half submitted manuscripts are accepted might help stimulate prospective authors to try to submit better quality manuscripts.
Balanced exploitation and coexistence of interacting, size‐structured, fish species
Authors: Law Richard , Plank Michael J. , Kolding Jeppe 
Published: October 2014

AbstractThis paper examines some effects of exploitation on a simple ecosystem containing two interacting fish species, with life histories similar to mackerel (Scomber scombrus) and cod (Gadus morhua), using a dynamic, size‐spectrum model. Such models internalize body growth and mortality from predation, allowing bookkeeping of biomass at a detailed level of individual predation and growth and enabling scaling up to the mass balance of the ecosystem. Exploitation set independently for each species with knife‐edge, size‐at‐entry fishing can lead to collapse of cod. Exploitation to achieve a fixed ratio of yield to productivity across species can also lead to collapse of cod. However, harvesting balanced to the overall productivity of species in the exploited ecosystem exerts a strong force countering such collapse. If balancing across species is applied to a fishery with knife‐edge selection, size distributions are truncated, changing the structure of the system and reducing its resilience to perturbations. If balancing is applied on the basis of productivity at each body size as well as across species, there is less disruption to size‐structure, resilience is increased, and substantially greater biomass yields are possible. We note an identity between the body size at which productivity is maximized and the age at which cohort biomass is maximized. In our numerical results based on detailed bookkeeping of biomass, cohort biomass reaches its maximum at body masses <1 g, unlike standard yield‐per‐recruit models, where body growth and mortality are independent externalities, and cohort biomass is maximized at larger body sizes.
The crystal structure of isoniazid‐bound KatG catalase‐peroxidase from Synechococcus elongatus PCC7942
Authors: Kamachi Saori , Hirabayashi Kei , Tamoi Masahiro , Shigeoka Shigeru , Tada Toshiji , Wada Kei 
Published: October 2014

Isoniazid (INH) is one of the most effective antibiotics against tuberculosis. INH is a prodrug that is activated by KatG. Although extensive studies have been performed in order to understand the mechanism of KatG, even the binding site of INH in KatG remains controversial. In this study, we determined the crystal structure of KatG from Synechococcus elongatus PCC7942 (SeKatG) in a complex with INH at 2.12‐Å resolution. Three INH molecules were bound to the molecular surface. One INH molecule was bound at the entrance to the ε‐edge side of heme (designated site 1), another was bound at the entrance to the γ‐edge side of heme (site 2), and another was bound to the loop structures in front of the heme propionate side chain (site 3). All of the interactions between KatG and the bound INH seemed to be weak, being mediated mainly by van der Waals contacts. Structural comparisons revealed that the identity and configuration of the residues in site 1 were very similar among SeKatG, Burkholderia pseudomallei KatG, and Mycobacterium tuberculosis KatG. In contrast, sites 2 and 3 were structurally diverse among the three proteins. Thus, site 1 is probably the common KatG INH‐binding site. A static enzymatic analysis and thermal shift assay suggested that the INH‐activating reaction does not proceed in site 1, but rather that this site may function as an initial trapping site for the INH molecule.DatabaseThe atomic coordinates and structure factors have been deposited in the Protein Data Bank under the accession number 3WXO.
Novel insights into matrix pathobiology regulatory mechanisms in health and disease
Authors: Karamanos Nikos K. , Passi Alberto 
Published: October 2014

Matrix macromolecules exhibit leading roles in tissue properties, physiological processes, as well as the development and progression of several diseases. This thematic series covers emerging areas of research in the matrix macromolecule field and includes epigenetics, stem cells, microRNAs, as well as proteoglycan interactions with proteolytic enzymes. Current knowledge of these aspects will elucidate their regulatory mechanisms in pathophysiology and aid the design of novel pharmacological agents.Accompanied by a podcast, listen now. Or listen in iTunes
Isotopic discrimination and kinetic parameters of RubisCO from the marine bloom‐forming diatom, Skeletonema costatum
Authors: Boller A. J. , Thomas P. J. , Cavanaugh C. M. , Scott K. M. 
Published: October 2014

AbstractThe cosmopolitan, bloom‐forming diatom, Skeletonema costatum, is a prominent primary producer in coastal oceans, fixing CO2 with ribulose 1,5‐bisphosphate carboxylase/oxygenase (RubisCO) that is phylogenetically distinct from terrestrial plant RubisCO. RubisCOs are subdivided into groups based on sequence similarity of their large subunits (IA–ID, II, and III). ID is present in several major oceanic primary producers, including diatoms such as S. costatum, coccolithophores, and some dinoflagellates, and differs substantially in amino acid sequence from the well‐studied IB enzymes present in most cyanobacteria and in green algae and plants. Despite this sequence divergence, and differences in isotopic discrimination apparent in other RubisCO enzymes, stable carbon isotope compositions of diatoms and other marine phytoplankton are generally interpreted assuming enzymatic isotopic discrimination similar to spinach RubisCO (IB). To interpret phytoplankton δ13C values, S. costatum RubisCO was characterized via sequence analysis, and measurement of its KCO2 and Vmax, and degree of isotopic discrimination. The sequence of this enzyme placed it among other diatom ID RubisCOs. Michaelis‐Menten parameters were similar to other ID enzymes (KCO2 = 48.9 ± 2.8 μm; Vmax = 165.1 ± 6.3 nmol min−1 mg−1). However, isotopic discrimination (ε = [12k/13k − 1] × 1000) was low (18.5‰; 17.0–19.9, 95% CI) when compared to IA and IB RubisCOs (22–29‰), though not as low as ID from coccolithophore, Emiliania huxleyi (11.1‰). Variability in ε‐values among RubisCOs from primary producers is likely reflected in δ13C values of oceanic biomass. Currently, δ13C variability is ascribed to physical or chemical factors (e.g. illumination, nutrient availability) and physiological responses to these factors (e.g. carbon‐concentrating mechanisms). Estimating the importance of these factors from δ13C measurements requires an accurate ε‐value, and a mass‐balance model using the ε‐value for S. costatum RubisCO is presented. Clearly, appropriate ε‐values must be included in interpreting δ13C values of environmental samples.
Stoichiometry and temperature sensitivity of methanogenesis and CO2 production from saturated polygonal tundra in Barrow, Alaska
Authors: Roy Chowdhury Taniya , Herndon Elizabeth M. , Phelps Tommy J. , Elias Dwayne A. , Gu Baohua , Liang Liyuan , Wullschleger Stan D. , Graham David E. 
Published: October 2014

AbstractArctic permafrost ecosystems store ~50% of global belowground carbon (C) that is vulnerable to increased microbial degradation with warmer active layer temperatures and thawing of the near surface permafrost. We used anoxic laboratory incubations to estimate anaerobic CO2 production and methanogenesis in active layer (organic and mineral soil horizons) and permafrost samples from center, ridge and trough positions of water‐saturated low‐centered polygon in Barrow Environmental Observatory, Barrow AK, USA. Methane (CH4) and CO2 production rates and concentrations were determined at −2, +4, or +8 °C for 60 day incubation period. Temporal dynamics of CO2 production and methanogenesis at −2 °C showed evidence of fundamentally different mechanisms of substrate limitation and inhibited microbial growth at soil water freezing points compared to warmer temperatures. Nonlinear regression better modeled the initial rates and estimates of Q10 values for CO2 that showed higher sensitivity in the organic‐rich soils of polygon center and trough than the relatively drier ridge soils. Methanogenesis generally exhibited a lag phase in the mineral soils that was significantly longer at −2 °C in all horizons. Such discontinuity in CH4 production between −2 °C and the elevated temperatures (+4 and +8 °C) indicated the insufficient representation of methanogenesis on the basis of Q10 values estimated from both linear and nonlinear models. Production rates for both CH4 and CO2 were substantially higher in organic horizons (20% to 40% wt. C) at all temperatures relative to mineral horizons (<20% wt. C). Permafrost horizon (~12% wt. C) produced ~5‐fold less CO2 than the active layer and negligible CH4. High concentrations of initial exchangeable Fe(II) and increasing accumulation rates signified the role of iron as terminal electron acceptors for anaerobic C degradation in the mineral horizons.
Will among‐population variation in seed traits improve the chance of species persistence under climate change?
Authors: Cochrane Anne , Yates Colin J. , Hoyle Gemma L. , Nicotra Adrienne B. 
Published: October 2014

AbstractAimSeed traits related to recruitment have direct relevance for plant fitness and persistence. Trait variation in time and among populations may increase species resilience and ultimately reduce the risk of extinction. However, patterns of among‐population variation in critical recruitment traits remain poorly known and are often disregarded when considering extinction risk under future climates.LocationGlobal.MethodsIn this paper we review and synthesize current knowledge about among‐population variation in physiological and morphological traits related to plant recruitment. We outline the consequences of that variation for species persistence under climate change, and discuss the implications for conservation, management and restoration.ResultsThe evaluated studies provide compelling evidence that among‐population variation in traits underpinning seedling emergence, growth and establishment is widespread. Contrary to expectations, environmental gradients do not appear to be reliable predictors of variation among populations and responses are often individualistic. Likewise, well‐established cross‐species patterns are not consistently reflected among populations within a species. As the pattern of this variation is unpredictable, we cannot make simple generalizations about how this variation is allocated across geographic ranges or the extent of environmental versus fixed genetic differences. Nor do these patterns clearly elucidate the potential for this variation to mitigate negative effects of climate change.Main conclusionsIf we ignore among‐population variation in seed traits, or assume it will follow simple environmental clines, we do so at our own peril. The consequences of such an approach are likely to include biased forecasts of future range dynamics, hindering identification of the genetic material most appropriate for conservation, restoration and management. Further research that integrates ecology and emerging evolutionary genetic techniques to identify the distribution of seed traits within foundation species and the mechanisms driving them is urgently required to guide the management and maintenance of systems in the face of rapidly changing climates.
An analysis of methodological and spatial differences in global cropping systems models and maps
Authors: Anderson Weston , You Liangzhi , Wood Stanley , Wood‐Sichra Ulrike , Wu Wenbin 
Published: October 2014

AbstractAimAgricultural practices have dramatically altered the land cover of the earth, but the spatial extent and intensity of these practices is often difficult to catalogue. Information on the distribution and performance of specific crops is often only available through national or subnational statistics. Recently, however, there have been multiple independent efforts to incorporate the detailed information available from statistical surveys with supplemental spatial information to produce a spatially explicit global dataset specific to individual crops. While these datasets provide decision makers with improved information on global cropping systems, the final global cropping maps differ substantially from one another. This study aims to explore and quantify systematic similarities and differences between four major global cropping systems products and the subsequent implications for analyses dependent on those models.LocationThis study was conducted at a global scale.MethodsEach global cropping systems model was assessed by latitude as a measure of biophysical plausibility and each pair of models was compared using a Gaussian filter to remove trivial spatial discrepancies. Model disagreement was explored in relation to the interdependent input data of each model pair with a particular focus on cropland extent. The influence of the observed model differences on subsequent analyses was demonstrated using model‐dependent estimates of the yield gap as an example.ResultsThe results of our analysis indicate that the choice of cropping systems model is non‐trivial: considerable differences exist between model‐specific estimates of the yield gap across nearly all climate zones and the average model difference exceeds the average estimated yield gap in certain regions. The differences in crop‐specific harvested area and yield products of each model are significant, and mostly result from differences in the input datasets and downscaling methodologies. In particular, the choice of dataset on cropland extent proved to be influential regardless of the downscaling process employed.Main conclusionsDiscrepancies in the final products of cropping systems models are currently poorly understood, but have implications for basic policy decisions relating to agricultural production and food security. The considerable disagreement between models serves as a reminder of the ongoing challenges to the creation of spatially explicit estimates of harvested area and yield based on crop statistics. Our analysis helps shed light on the importance of model choice by demonstrating the implications for further analyses that depend on cropping systems models, and works to overcome these challenges by characterizing model‐dependent differences in harvested area and yield.