bluuebunny/crossref_metadata_2025_split huggingface dataset:
Herbarium specimens reveal substantial and unexpected variation in phenological sensitivity across the eastern United States
Authors: Park Daniel S. , Breckheimer Ian , Williams Alex C. , Law Edith , Ellison Aaron M. , Davis Charles C. 
Published: November 2018

Phenology is a key biological trait that can determine an organism's survival and provides one of the clearest indicators of the effects of recent climatic change. Long time-series observations of plant phenology collected at continental scales could clarify latitudinal and regional patterns of plant responses and illuminate drivers of that variation, but few such datasets exist. Here, we use the web toolCrowdCurioto crowdsource phenological data from over 7000 herbarium specimens representing 30 diverse flowering plant species distributed across the eastern United States. Our results, spanning 120 years and generated from over 2000 crowdsourcers, illustrate numerous aspects of continental-scale plant reproductive phenology. First, they support prior studies that found plant reproductive phenology significantly advances in response to warming, especially for early-flowering species. Second, they reveal that fruiting in populations from warmer, lower latitudes is significantly more phenologically sensitive to temperature than that for populations from colder, higher-latitude regions. Last, we found that variation in phenological sensitivities to climate within species between regions was of similar magnitude to variation between species. Overall, our results suggest that phenological responses to anthropogenic climate change will be heterogeneous within communities and across regions, with large amounts of regional variability driven by local adaptation, phenotypic plasticity and differences in species assemblages. As millions of imaged herbarium specimens become available online, they will play an increasingly critical role in revealing large-scale patterns within assemblages and across continents that ultimately can improve forecasts of the impacts of climatic change on the structure and function of ecosystems.This article is part of the theme issue ‘Biological collections for understanding biodiversity in the Anthropocene’.
A novel proof of concept for capturing the diversity of endophytic fungi preserved in herbarium specimens
Authors: Daru Barnabas H. , Bowman Elizabeth A. , Pfister Donald H. , Arnold A. Elizabeth 
Published: November 2018

Herbarium specimens represent important records of morphological and genetic diversity of plants that inform questions relevant to global change, including species distributions, phenology and functional traits. It is increasingly appreciated that plant microbiomes can influence these aspects of plant biology, but little is known regarding the historic distribution of microbes associated with plants collected in the pre-molecular age. If microbiomes can be observed reliably in herbarium specimens, researchers will gain a new lens with which to examine microbial ecology, evolution, species interactions. Here, we describe a method for accessing historical plant microbiomes from preserved herbarium specimens, providing a proof of concept using two plant taxa from the imperiled boreal biome (Andromeda polifoliaandLedum palustresubsp. groenlandicum,Ericaceae). We focus on fungal endophytes, which occur within symptomless plant tissues such as leaves. Through a three-part approach (i.e. culturing, cloning and next-generation amplicon sequencing via the Illumina MiSeq platform, with extensive controls), we examined endophyte communities in dried, pressed leaves that had been processed as regular herbarium specimens and stored at room temperature in a herbarium for four years.We retrieved only one endophyte in culture, but cloning and especially the MiSeq analysis revealed a rich community of foliar endophytes. The phylogenetic distribution and diversity of endophyte assemblages, especially among the Ascomycota, resemble endophyte communities from fresh plants collected in the boreal biome. We could distinguish communities of endophytes in each plant species and differentiate likely endophytes from fungi that could be surface contaminants. Taxa found by cloning were observed in the larger MiSeq dataset, but species richness was greater when subsets of the same tissues were evaluated with the MiSeq approach. Our findings provide a proof of concept for capturing endophyte DNA from herbarium specimens, supporting the importance of herbarium records as roadmaps for understanding the dynamics of plant-associated microbial biodiversity in the Anthropocene.This article is part of the theme issue ‘Biological collections for understanding biodiversity in the Anthropocene’.
Programmed His bundle pacing - a novel maneuver for the diagnosis of His bundle capture
Authors: Jastrzębski Marek , Moskal Paweł , Bednarek Agnieszka , Kiełbasa Grzegorz , Vijayaraman Pugazhendhi , Czarnecka Danuta 
Published: November 2018

AbstractBackgroundDuring permanent non-selective (ns) His bundle (HB) pacing, it is crucial to confirm HB capture / exclude that only right ventricle (RV)-myocardial septal pacing is present. Because the effective refractory period (ERP) of the working myocardium is different than the ERP of the HB, we hypothesized that it should be possible to differentiate ns-HB capture from RV-myocardial capture using programmed extra-stimulus technique.MethodsIn consecutive patients during HB pacemaker implantation, programmed HB pacing was delivered from the screwed-in HB pacing lead. Premature beats were introduced at 10 ms steps during intrinsic rhythm and also after a drive train of 600 ms. The longest coupling interval that resulted in an abrupt change of QRS morphology was considered equal to ERP of HB or RV-myocardium.ResultsProgrammed HB pacing was performed from 50 different sites in 32 patients. In 34/36 cases of ns-HB pacing, the RV-myocardial ERP was shorter than HB ERP (271.8±38 ms vs 353.0±30 ms, p < 0.0001). Programmed HB pacing using a drive train resulted in a typical abrupt change of paced QRS morphology: from ns-HB to RV-myocardial QRS (34/36 cases) or to selective HB QRS (2/36 cases). Programmed HB pacing delivered during supraventricular rhythm resulted in obtaining selective HB QRS in 20/34 and RV-myocardial QRS in 14/34 of the ns-HB cases. In RV-myocardial only pacing cases (“false ns-HB pacing”, n=14), such responses were not observed – the QRS morphology remained stable. Therefore, the PHB pacing correctly diagnosed all ns-HB cases and all RV-myocardial pacing cases.ConclusionsA novel maneuver for the diagnosis of HB capture, based on the differences in ERP between HB and myocardium was formulated, assessed and found as diagnostically valuable. This method is unique in enabling to visualize selective HB QRS in patients with otherwise obligatory ns-HB pacing (RV-myocardial capture threshold < HB capture threshold).What this study addsProgrammed His bundle pacing – a novel and straightforward method for unquestionable diagnosis of His bundle capture during non-selective pacing was developed and assessed.A method for visualization of selective HB capture QRS in patients with obligatory non-selective pacing (myocardial capture threshold < His bundle capture threshold) was discovered and physiology behind it explained.
Prediction-error signals to violated expectations about person identity and head orientation are doubly-dissociated across the dorsal and ventral visual streams
Authors: Robinson Jonathan E. , Woods Will , Leung Sumie , Kaufman Jordy , Breakspear Michael , Young Andrew W. , Johnston Patrick J. 
Published: November 2018

AbstractPredictive coding theories of perception suggest the importance of constantly updated internal models of the world in predicting future sensory inputs. One implication of such models is that cortical regions whose function is to resolve particular stimulus attributes should also signal prediction violations with respect to those same stimulus attributes. Previously, through carefully designed experiments, we have demonstrated early-mid latency EEG/MEG prediction-error signals in the dorsal visual stream to violated expectations about stimulus orientation/trajectory, with localisations consistent with cortical areas processing motion and orientation. Here we extend those methods to simultaneously investigate the predictive processes in both dorsal and ventral visual streams. In this MEG study we employed a contextual trajectory paradigm that builds expectations using a series of image presentations. We created expectations about both face orientation and identity, either of which can subsequently be violated. Crucially this paradigm allows us to parametrically test double dissociations between these different types of violations. The study identified double dissociations across the type of violation in the dorsal and ventral visual streams, such that the right fusiform gyrus showed greater evidence of prediction-error signals to Identity violations than to Orientation violations, whereas the left angular gyrus and postcentral gyrus showed the opposite pattern of results. Our results suggest comparable processes for error checking and context updating in high-level expectations instantiated across both perceptual streams. Perceptual prediction-error signalling is initiated in regions associated with the processing of different stimulus properties.Significance StatementVisual processing occurs along ‘what’ and ‘where’ information streams that run, respectively along the ventral and dorsal surface of the posterior brain. Predictive coding models of perception imply prediction-error detection processes that are instantiated at the level where particular stimulus attributes are parsed. This implies that, for instance, when considering face stimuli, signals arising through violated expectations about the person identity of the stimulus should localise to the ventral stream, whereas signals arising through violated expectations about head orientation should localise to the dorsal stream. We test this in a magnetoencephalography source localisation study. The analysis confirmed that prediction-error signals to identity versus head-orientation occur with similar latency, but activate doubly-dissociated brain regions along ventral and dorsal processing streams.
Cryo-EM structure of adenovirus type 3 fibre with desmoglein 2 shows a novel mode of receptor engagement
Authors: Vassal-Stermann Emilie , Effantin Gregory , Zubieta Chloe , Burmeister Wim , Iseni Frédéric , Wang Hongjie , Lieber André , Schoehn Guy , Fender Pascal 
Published: November 2018

AbstractAttachment of adenovirus (HAd) to host cell is a critical step of infection. This work reports the cryo-electron microscopy (cryo-EM) structure of a non-symmetrical complex smaller than 100kDa formed by the trimeric human adenovirus of type 3 fibre knob (HAd3K) and human desmoglein 2 (DSG2). The structure reveals a unique stoichiometry, shedding light to new adenovirus infection strategies and providing new insights for adenoviral vector development.
On-scalp MEG system utilizing an actively shielded array of optically-pumped magnetometers
Authors: Iivanainen Joonas , Zetter Rasmus , Grön Mikael , Hakkarainen Karoliina , Parkkonen Lauri 
Published: November 2018

AbstractThe spatial resolution of magnetoencephalography (MEG) can be increased from that of conventional SQUID-based systems by employing on-scalp sensor arrays of e.g. optically-pumped magnetometers (OPMs). However, OPMs reach sufficient sensitivity for neuromagnetic measurements only when operated in a very low absolute magnetic field of few nanoteslas or less, usually not reached in a typical magnetically shielded room constructed for SQUID-based MEG. Moreover, field drifts affect the calibration of OPMs. Static and dynamic control of the ambient field is thus necessary for good-quality neuromagnetic measurements with OPMs. Here, we describe an on-scalp MEG system that utilizes OPMs and external compensation coils that provide static and dynamic shielding against ambient fields.In a conventional two-layer magnetically shielded room, our coil system reduced the maximum remanent DC-field component within an 8-channel OPM array from 70 to less than 1 nT, enabling the sensors to operate in the sensitive spin exchange relaxation-free regime. When compensating field drifts below 4 Hz, a low-frequency shielding factor of 22 dB was achieved, which reduced the peak-to-peak drift from 1.3 to 0.4 nT and thereby the standard deviation of the sensor calibration from 1.6% to 0.4%. Without band-limiting the field that is compensated, a low-frequency shielding factor of 43 dB was achieved.We validated the system by measuring brain responses to electric stimulation of the median nerve. With dynamic shielding and digital interference suppression methods, single-trial somatosensory evoked responses could be detected. Our results advance the deployment of OPM-based on-scalp MEG in lighter magnetic shields.
The microbiota influences theDrosophila melanogasterlife history strategy
Authors: Walters Amber W. , Matthews Melinda K. , Hughes Rachel , Malcolm Jaanna , Rudman Seth , Newell Peter D. , Douglas Angela E. , Schmidt Paul S. , Chaston John M. 
Published: November 2018

AbstractOrganismal life history traits are ideally adapted to local environments when an organism has a fitness advantage in one location relative to conspecifics from other geographies. Local adaptation has been best studied across, for example, latitudinal gradients, where organisms may tradeoff between investment in traits that maximize one, but not both, fitness components of somatic maintenance or reproductive output in the context of finite environmental resources. Latitudinal gradients in life history strategies are traditionally attributed to environmentally mediated selection on an animal’s genotype, without any consideration of the possible impact of associated microorganisms (‘microbiota’) on life history traits. Here we show that inDrosophila melanogaster, a key organism for studying local adaptation and life history strategies, associated microorganisms can drive life history variation. First, we reveal that an isogenic fly line reared with different bacteria vary the investment in early reproduction versus somatic maintenance, with little resultant variation in lifetime fitness. Next, we show that in wildDrosophilathe abundance of these same bacteria was correlated with the latitude and life history strategy of the flies, and bacterial abundance was driven at least in part by host genetic selection. Finally, by eliminating or manipulating the microbiota of fly lines collected across a latitudinal gradient, we reveal that host genotype contributes to latitude-specific life history traits independent of the microbiota; but that the microbiota can override these host genetic adaptations. Taken together, these findings establish the microbiota as an essential consideration in local adaptation and life history evolution.Significance statementExplanations of local adaptation have historically focused on how animal genotypes respond to environmental selection. Although the impact of variation in host life histories on the composition of the microbiota has been investigated for many associations, the scale and pattern of microbial effects on host life history strategy are largely unknown. Here we demonstrate in the fruit flyDrosophila melanogasterthat microbiota effects on host life history strategy in the laboratory are matched by patterns of microbiota composition in wild host populations. In particular, microbiota composition varies with latitude and the effects of the microbiota on life history traits are greater than host genetic adaptations. Together, these findings demonstrate that the microbiota plays an important role in local adaptation.
SKN-1/Nrf2 regulation of neuromuscular function in response to oxidative stress requires EGL-15/FGF Receptor and DAF-2/insulin Receptor signaling inCaenorhabditis elegans
Authors: Kim Sungjin , Sieburth Derek 
Published: November 2018

AbstractThe transcription factor Nrf2 plays a critical role in the organism wide-regulation of the antioxidant stress response. The Nrf2 homolog SKN-1 functions in the intestine cell non-autonomously to negatively regulate neuromuscular (NMJ) function inCaenorhabditis elegans. To identify additional molecules that mediate SKN-1 signaling to the NMJ, we performed a candidate screen for suppressors of aldicarb-resistance caused by acute treatment with the SKN-1 activator, arsenite. We identified two receptor tyrosine kinases, EGL-15 (fibroblast growth factor receptor, FGFR) and DAF-2 (insulin-like peptide receptor, IR) that are required for NMJ regulation in response to stress. Through double mutant analysis, we found that EGL-15 functions downstream of SKN-1 and SPHK-1 (sphingosine kinase), and that the EGL-15 ligand EGL-17 FGF and canonical EGL-15 effectors are required for oxidative stress-mediated regulation of NMJ function. DAF-2 also functions downstream of SKN-1, independently of DAF-16/FOXO, to regulate NMJ function. Through tissue-specific rescue experiments, we found that FGFR signaling functions primarily in the hypodermis, whereas IR signaling is required in multiple tissues. Our results support the idea that the regulation of NMJ function by SKN-1 occurs via a complex organism-wide signaling network involving RTK signaling in multiple tissues.
Border-ownership-dependent tilt aftereffect for shape defined by binocular disparity and motion parallax
Authors: Rideaux Reuben , Harrison William J 
Published: November 2018

ABSTRACTDiscerning objects from their surrounds (i.e., figure-ground segmentation) in a way that guides adaptive behaviours is a fundamental task of the brain. Neurophysiological work has revealed a class of cells in the macaque visual cortex that may be ideally suited to support this neural computation: border-ownership cells (Zhou, Friedman, & von der Heydt, 2000). These orientation-tuned cells appear to respond conditionally to the borders of objects. A behavioural correlate supporting the existence of these cells in humans was demonstrated using two-dimensional luminance defined objects (von der Heydt, Macuda, & Qiu, 2005). However, objects in our natural visual environments are often signalled by complex cues, such as motion and depth order. Thus, for border-ownership systems to effectively support figure-ground segmentation and object depth ordering, they must have access to information from multiple depth cues with strict depth order selectivity. Here we measure in humans (of both sexes) border-ownership-dependent tilt aftereffects after adapting to figures defined by either motion parallax or binocular disparity. We find that both depth cues produce a tilt aftereffect that is selective for figure-ground depth order. Further, we find the effects of adaptation are transferable between cues, suggesting that these systems may combine depth cues to reduce uncertainty (Bülthoff & Mallot, 1988). These results suggest that border-ownership mechanisms have strict depth order selectivity and access to multiple depth cues that are jointly encoded, providing compelling psychophysical support for their role in figure-ground segmentation in natural visual environments.SIGNIFICANCE STATEMENTSegmenting a visual object from its surrounds is a critical function that may be supported by “border-ownership” neural systems that conditionally respond to object borders. Psychophysical work indicates these systems are sensitive to objects defined by luminance contrast. To effectively support figure-ground segmentation, however, neural systems supporting border-ownership must have access to information from multiple depth cues and depth order selectivity. We measured border-ownership-dependent tilt aftereffects to figures defined by either motion parallax or binocular disparity and found aftereffects for both depth cues. These effects were transferable between cues, but selective for figure-ground depth order. Our results suggest that the neural systems supporting figure-ground segmentation have strict depth order selectivity and access to multiple depth cues that are jointly encoded.
Endoparasites and vector-borne pathogens in dogs from Greek islands: pathogen distribution and zoonotic implications
Authors: Diakou Anastasia , Di Cesare Angela , Morelli Simone , Colombo Mariasole , Halos Lenaig , Simonato Giulia , Tamvakis Androniki , Beugnet Frederic , Paoletti Barbara , Traversa Donato 
Published: November 2018

AbstractThe present study investigated the presence of endo- and ecto-parasites, and vector-borne pathogens, in dogs from four islands of Greece. A total of 200 owned and sheltered dogs were examined with different microscopic, serological and molecular methods.Of the examined dogs, 130 (65%) were positive for one or more parasites and/or vector-borne pathogens. The most common zoonotic intestinal helminths recorded were Ancylostomatidae (12.5%) andToxocara canis(3.5%). Ninety-three dogs (46.5%) seroreacted toRickettsia conorii. Twenty-two (11%) of them were also PCR positive and 7 (3.5%) showed corpuscoles suggestive ofRickettsiaspp. on the blood smears. Nineteen dogs (9.5%) were seropositive forEhrlichia canis, three of them being also PCR positive. Dogs positive forAnaplasma phagocytophilum-Anaplasma platys(1%),Dirofilaria immitis(0.5%) andBabesia canis(0.5%) were also found. Fleas and ticks were recorded in 53 (26.5%) and 50 (25%) dogs and all specimens were identified asCtenocephalides felis felisandRhipicephalus sanguineus sensu latu. Binary multiple univariate Generalized Linear Models were used to investigate factors and clinical signs related to the recorded positivity, while the association of specific signs with the pathogens was evaluated using tests of independence. Knowledge of occurrence and impact of zoonotic parasites and vector-borne pathogens in dog populations is crucial to prevent the infection in animals and people, and to control the risk of spreading of these pathogens in endemic and non-endemic areas.Author summaryBoth owned and sheltered dogs can harbor a variety of intestinal and extra-intestinal endoparasites, as well as vector-borne pathogens and ectoparasites, of zoonotic concern. Dog shelters and stray dogs are present in several touristic areas of Greece, including Sporades and Cyclades islands, where tourists often bring their pets with them, likely travelling from non-endemic to endemic areas. The present study has been carried out with the aim to evaluate the occurrence of the aforementioned pathogens. Data obtained showed that they are present in canine populations of Greece, with possibilities of infection for travelling dogs, which can also contribute to the spreading of zoonotic vector-borne diseases, introducing new pathogens in previously non-endemic areas. For these reasons, a constant monitoring of the epidemiological situation, improving control measures and correct diagnostic approaches are of primary importance for the prevention of canine and human infections, decreasing the spreading of potentially deadly pathogens.