bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of leaf microbiome composition of near‐isogenic maize lines differing in broad‐spectrum disease resistance
Authors: Wagner Maggie R. , Busby Posy E. , Balint‐Kurti Peter 
Published: October 2019

Summary
Plant genotype strongly affects disease resistance, and also influences the composition of the leaf microbiome. However, these processes have not been studied and linked in the microevolutionary context of breeding for improved disease resistance. We hypothesised that broad‐spectrum disease resistance alleles also affect colonisation by nonpathogenic symbionts.
Quantitative trait loci (QTL) conferring resistance to multiple fungal pathogens were introgressed into a disease‐susceptible maize inbred line. Bacterial and fungal leaf microbiomes of the resulting near‐isogenic lines were compared with the microbiome of the disease‐susceptible parent line at two time points in multiple fields.
Introgression of QTL from disease‐resistant lines strongly shifted the relative abundance of diverse fungal and bacterial taxa in both 3‐wk‐old and 7‐wk‐old plants. Nevertheless, the effects on overall community structure and diversity were minor and varied among fields and years. Contrary to our expectations, host genotype effects were not any stronger in fields with high disease pressure than in uninfected fields, and microbiome succession over time was similar in heavily infected and uninfected plants.
These results show that introgressed QTL can greatly improve broad‐spectrum disease resistance while having only limited and inconsistent pleiotropic effects on the leaf microbiome in maize.
Remorin interacting with PCaP1 impairs Turnip mosaic virus intercellular movement but is antagonised by VPg
Authors: Cheng Guangyuan , Yang Zongtao , Zhang Hai , Zhang Jisen , Xu Jingsheng 
Published: October 2019

Summary

Group 1 Remorins (REMs) are extensively involved in virus trafficking through plasmodesmata (PD). However, their roles in Potyvirus cell‐to‐cell movement are not known. The plasma membrane (PM)‐associated Ca2+ binding protein 1 (PCaP1) interacts with the P3N‐PIPO of Turnip mosaic virus (TuMV) and is required for TuMV cell‐to‐cell movement, but the underlying mechanism remains elusive.

The mutant plants with overexpression or knockout of REM1.2 were used to investigate its role in TuMV cell‐to‐cell movement. Arabidopsis thaliana complementary mutants of pcap1 were used to investigate the role of PCaP1 in TuMV cell‐to‐cell movement. Yeast‐two‐hybrid, bimolecular fluorescence complementation, co‐immunoprecipitation and RT‐qPCR assays were employed to investigate the underlying molecular mechanism.

The results show that TuMV‐P3N‐PIPO recruits PCaP1 to PD and the actin filament‐severing activity of PCaP1 is required for TuMV intercellular movement. REM1.2 negatively regulates the cell‐to‐cell movement of TuMV via competition with PCaP1 for binding actin filaments. As a counteractive response, TuMV mediates REM1.2 degradation via both 26S ubiquitin–proteasome and autophagy pathways through the interaction of VPg with REM1.2 to establish systemic infection in Arabidopsis.

This work unveils the actin cytoskeleton and PM nanodomain‐associated molecular events underlying the cell‐to‐cell movement of potyviruses.
Prevalence estimates of neurodevelopmental disorders in Japan: A community sample questionnaire study
Authors: Kita Yosuke , Ashizawa Fumiko , Inagaki Masumi 
Published: October 2019

AimPrevalence estimates of neurodevelopmental disorders have been calculated by questionnaire surveys scored by a single rater, which introduces inherent rater biases. The present study aimed to estimate the prevalence and comorbidity rates of four neurodevelopmental disorders based on both parent and teacher rating scales.MethodsWe performed a community sample survey recruiting 3852 children aged 6 to 9 years. Parents and teachers evaluated clinical conditions in children using questionnaire‐style scales. These scales with cut‐off values were used to estimate the prevalence and comorbidity rates of attention deficit hyperactive disorder, autism spectrum disorder, specific learning disorder (or developmental dyslexia), and developmental coordination disorder.ResultsThe prevalence estimates were separately confirmed according to the raters. Some estimates were higher than those in previous studies conducted in other countries. We also found a large disagreement between the parent and teacher rating scores. Moreover, the degree of agreement between two raters varied depending on the severity of the child's clinical condition.ConclusionThese estimates are the first findings based on evaluating children by two different raters. The prevalence and comorbidity estimates are informative for researchers and clinicians of pediatric neurology. The disagreements between two different raters raise questions about previous estimates of neurodevelopmental disorders.
Export promotion and intra‐industry reallocations
Authors: Sørensen Allan 
Published: October 2019

AbstractPublicly funded/subsidized export promotion agencies reducing informational barriers to export and thus firm‐level fixed/sunk costs of exporting are present in most countries. This paper develops a two‐country one‐sector heterogeneous firms model with origin‐specific publicly funded export promotion agencies and shows how the public good nature of export‐relevant information and the ability to engage in global public affairs may rationalize the existence of such agencies. A novel finding of the model is that gains from export promotion are shared with the trade partner via intra‐industry reallocations.
A Full Bayesian Implementation of A Generalized Partial Credit Model with an Application to an International Disability Survey
Authors: Sahu Sujit K. , Bass Mark R. , Sabariego Carla , Cieza Alarcos , Fellinghauer Carolina S. , Chatterji Somnath 
Published: October 2019

SummaryGeneralized partial credit models (GPCMs) are ubiquitous in many applications in the health and medical sciences that use item response theory. Such polytomous item response models have a great many uses ranging from assessing and predicting an individual's latent trait to ordering the items to test the effectiveness of the test instrumentation. By implementing these models in a full Bayesian framework, computed through the use of Markov chain Monte Carlo methods implemented in the efficient STAN software package, the paper exploits the full inferential capability of GPCMs. The GPCMs include explanatory covariate effects which allow simultaneous estimation of regression and item parameters. The Bayesian methods for ranking the items by using the Fisher information criterion are implemented by using Markov chain Monte Carlo sampling. This allows us to propagate fully and to ascertain uncertainty in the inferences by calculating the posterior predictive distribution of the item-specific Fisher information criterion in a novel manner that has not been exploited in the literature before. Lastly, we propose a new Monte Carlo method for predicting the latent trait score of a new individual by approximating the relevant Bayesian predictive distribution. Data from a model disability survey carried out in Sri Lanka by the World Health Organization and the World Bank are used to illustrate the methods. The approaches proposed are shown to provide simultaneous model-based inference for all aspects of disability which can be explained by environmental and socio-economic factors.
Care providers' troubled conscience related to an implementation of a time management system in residential care for older people—a participatory action research study
Authors: Ericson Lidman Eva , Strandberg Gunilla 
Published: October 2019

BackgroundCare providers in residential care for older people often refer to time shortage, a problem that may generate troubled conscience.AimThe aim of the study was to describe a PAR process to assist care providers in municipal residential care for older people to constructively deal with their troubled conscience related to an implemented time management system.MethodThis intervention study was carried out with 14 care providers and their manager in residential care for older people with the support of participatory action research (PAR). The recorded PAR sessions were transcribed and compiled with inspiration from content analysis.Ethical considerationsThe participants were given oral and written information and gave their written informed consent.FindingsThe PAR process was found to empower the participants to form their own structure of the practical professional planning, adapted to the residents needs and to their daily work. In this process, participants used their troubled conscience as a driving force and as an asset.ConclusionInstead of launching change without any deeper information, it is important to carefully prepare, involve and inform those who are going to execute the change. Meeting places should be arranged wherein care providers have the opportunity to share and reflect on challenging situations that can generate troubled conscience, especially when comprehensive changes in their work are going to be implemented.
Semiparametric multiparameter regression survival modeling
Authors: Burke Kevin , Eriksson Frank , Pipper C. B. 
Published: October 2019

AbstractWe consider a log‐linear model for survival data, where both the location and scale parameters depend on covariates, and the baseline hazard function is completely unspecified. This model provides the flexibility needed to capture many interesting features of survival data at a relatively low cost in model complexity. Estimation procedures are developed, and asymptotic properties of the resulting estimators are derived using empirical process theory. Finally, a resampling procedure is developed to estimate the limiting variances of the estimators. The finite sample properties of the estimators are investigated by way of a simulation study, and a practical application to lung cancer data is illustrated.
Concordance‐based estimation approaches for the optimal sufficient dimension reduction score
Authors: Wang Shao‐Hsuan , Chiang Chin‐Tsang 
Published: October 2019

AbstractTo characterize the dependence of a response on covariates of interest, a monotonic structure is linked to a multivariate polynomial transformation of the central subspace (CS) directions with unknown structural degree and dimension. Under a very general semiparametric model formulation, such a sufficient dimension reduction (SDR) score is shown to enjoy the existence, optimality, and uniqueness up to scale and location in the defined concordance probability function. In light of these properties and its single‐index representation, two types of concordance‐based generalized Bayesian information criteria are constructed to estimate the optimal SDR score and the maximum concordance index. The estimation criteria are further carried out by effective computational procedures. Generally speaking, the outer product of gradients estimation in the first approach has an advantage in computational efficiency and the parameterization system in the second approach greatly reduces the number of parameters in estimation. Different from most existing SDR approaches, only one CS direction is required to be continuous in the proposals. Moreover, the consistency of structural degree and dimension estimators and the asymptotic normality of the optimal SDR score and maximum concordance index estimators are established under some suitable conditions. The performance and practicality of our methodology are also investigated through simulations and empirical illustrations.
Combined multiple testing of multivariate survival times by censored empirical likelihood
Authors: Parkinson Judith H. 
Published: October 2019

AbstractIn each study testing the survival experience of one or more populations, one must not only choose an appropriate class of tests, but further an appropriate weight function. As the optimal choice depends on the true shape of the hazard ratio, one is often not capable of getting the best results with respect to a specific dataset. For the univariate case several methods were proposed to conquer this problem. However, most of the interesting datasets contain multivariate observations nowadays. In this work we propose a multivariate version of a method based on multiple constrained censored empirical likelihood where the constraints are formulated as linear functionals of the cumulative hazard functions. By considering the conditional hazards, we take the correlation between the components into account with the goal of obtaining a test that exhibits a high power irrespective of the shape of the hazard ratio under the alternative hypothesis.
Genomic evidence suggests Mesapamea remmi is an imaginary species (Lepidoptera: Noctuidae)
Authors: Sihvonen Pasi , Lee Kyung Min , Lundsten Karl‐Erik , Mutanen Marko 
Published: October 2019

AbstractTaxonomic status of the noctuid moth Mesapamea remmi Rezbanyai‐Reser (Lepidoptera) has remained controversial since its description in 1985. Based on morphology, it has been considered a valid species or a hybrid between Mesapamea secalis (Linnaeus) and Mesapamea didyma (Esper). We studied this case of uncertain identity by using traditional Sanger sequencing techniques (COI and seven nuclear genes) as well as double digest restriction‐site associated DNA (ddRAD) sequencing, which resulted in analyses including 9402 loci and 1 512 976 bp across the genome. Our analyses showed that genomic data do not support the hybrid hypothesis and that M. remmi is not separated genetically from M. secalis; both are clearly distinct from M. didyma. Reproductive organs of M. remmi males are unique and diagnosable, whereas females are teratological in the sense that ductus seminalis is missing and corpus bursae is malformed, the latter being connected directly to the ovipore. These data support the view that M. remmi is not a valid species and we consider M. remmi Rezbanyai‐Reser, 1985 to be a junior synonym of M. secalis (Linnaeus, 1758). We demonstrate that genomic approaches provide an efficient way to address various difficult and long‐standing taxonomic issues, in this case oversplitting of species.
FinDonor 10 000 study: a cohort to identify iron depletion and factors affecting it in Finnish blood donors
Authors: Lobier Muriel , Niittymäki Pia , Nikiforow Nina , Palokangas Elina , Larjo Antti , Mattila Pirkko , Castrén Johanna , Partanen Jukka , Arvas Mikko 
Published: October 2019

Background and ObjectivesThere is increasing evidence that frequent blood donation depletes the iron stores of some blood donors. The FinDonor 10 000 study was set up to study iron status and factors affecting iron stores in Finnish blood donors. In Finland, iron supplementation for at‐risk groups has been in place since the 1980s.Material and MethodsA total of 2584 blood donors (N = 8003 samples) were recruited into the study alongside standard donation at three donation sites in the capital region of Finland between 5/2015 and 12/2017. All participants were asked to fill out a questionnaire about their health and lifestyle. Blood samples were collected from the sample pouch of whole blood collection set, kept in cool temperature and processed centrally. Whole blood count, CRP, ferritin and sTFR were measured from the samples, and DNA was isolated for GWAS studies.ResultsParticipant demographics, albeit in general similar to the general blood donor population in Finland, indicated some bias towards older and more frequent donors. Participation in the study increased median donation frequency of the donors. Analysis of the effect of time lag from the sampling to the analysis and the time of day when sample was drawn revealed small but significant time‐dependent changes.ConclusionThe FinDonor cohort now provides us with tools to identify potential donor groups at increased risk of iron deficiency and factors explaining this risk. The increase in donation frequency during the study suggests that scientific projects can be used to increase the commitment of blood donors.
Calcium isotope evidence for environmental variability before and across the Cretaceous-Paleogene mass extinction
Authors: Linzmeier Benjamin J. , Jacobson Andrew D. , Sageman Bradley B. , Hurtgen Matthew T. , Ankney Meagan E. , Petersen Sierra V. , Tobin Thomas S. , Kitch Gabriella D. , Wang Jiuyuan 
Published: October 2019

Abstract
Carbon dioxide release during Deccan Traps volcanism and the Chicxulub impact likely contributed to the Cretaceous-Paleogene (K-Pg) mass extinction; however, the intensity and duration of CO2 input differed between the two events. Large and rapid addition of CO2 to seawater causes transient decreases in pH, [CO32–], and carbonate mineral saturation states. Compensating mechanisms, such as dissolution of seafloor sediment, reduced biomineralization, and silicate weathering, mitigate these effects by increasing the same parameters. The calcium isotope ratios (δ44/40Ca) of seawater and marine carbonates are hypothesized to respond to these perturbations through weathering/carbonate deposition flux imbalances and/or changes in fractionation between carbonate minerals and seawater. We used a high-precision thermal ionization mass spectrometry method to measure δ44/40Ca values of aragonitic bivalve and gastropod mollusk shells from the K-Pg interval of the López de Bertodano Formation on Seymour Island, Antarctica. Well-preserved shells spanning the late Maastrichtian (ca. 67 Ma) to early Danian (ca. 65.5 Ma) have δ44/40Ca values ranging from −1.89‰ to −1.57‰ (seawater [sw]). Shifts in δ44/40Ca inversely correlate with sedimentological indicators of saturation state. A negative excursion begins before and continues across the K-Pg boundary. According to a simple mass-balance model, neither input/output flux imbalances nor change in the globally integrated bulk carbonate fractionation factor can produce variations in seawater δ44/40Ca sufficient to explain the measured trends. The data are consistent with a dynamic molluscan Ca isotope fractionation factor sensitive to the carbonate geochemistry of seawater. The K-Pg extinction appears to have occurred during a period of carbonate saturation state variability caused by Deccan volcanism.
Fossil subduction recorded by quartz from the coesite stability field
Authors: Alvaro M. , Mazzucchelli M.L. , Angel R.J. , Murri M. , Campomenosi N. , Scambelluri M. , Nestola F. , Korsakov A. , Tomilenko A.A. , Marone F. , Morana M. 
Published: October 2019

Abstract
Metamorphic rocks are the records of plate tectonic processes whose reconstruction relies on correct estimates of the pressures and temperatures (P-T) experienced by these rocks through time. Unlike chemical geothermobarometry, elastic geobarometry does not rely on chemical equilibrium between minerals, so it has the potential to provide information on overstepping of reaction boundaries and to identify other examples of non-equilibrium behavior in rocks. Here we introduce a method that exploits the anisotropy in elastic properties of minerals to determine the unique P and T of entrapment from a single inclusion in a mineral host. We apply it to preserved quartz inclusions in garnet from eclogite xenoliths hosted in Yakutian kimberlites (Russia). Our results demonstrate that quartz trapped in garnet can be preserved when the rock reaches the stability field of coesite (the high-pressure and high-temperature polymorph of quartz) at 3 GPa and 850 °C. This supports a metamorphic origin for these xenoliths and sheds light on the mechanisms of craton accretion from a subducted crustal protolith. Furthermore, we show that interpreting P and T conditions reached by a rock from the simple phase identification of key inclusion minerals can be misleading.
Focused fluid seepage related to variations in accretionary wedge structure, Hikurangi margin, New Zealand
Authors: Watson Sally J. , Mountjoy Joshu J. , Barnes Philip M. , Crutchley Gareth J. , Lamarche Geoffroy , Higgs Ben , Hillman Jess , Orpin Alan R. , Micallef Aaron , Neil Helen , Mitchell John , Pallentin Arne , Kane Tim , Woelz Susi , Bowden David , Rowden Ashley A. , Pecher Ingo A. 
Published: October 2019

AbstractHydrogeological processes influence the morphology, mechanical behavior, and evolution of subduction margins. Fluid supply, release, migration, and drainage control fluid pressure and collectively govern the stress state, which varies between accretionary and nonaccretionary systems. We compiled over a decade of published and unpublished acoustic data sets and seafloor observations to analyze the distribution of focused fluid expulsion along the Hikurangi margin, New Zealand. The spatial coverage and quality of our data are exceptional for subduction margins globally. We found that focused fluid seepage is widespread and varies south to north with changes in subduction setting, including: wedge morphology, convergence rate, seafloor roughness, and sediment thickness on the incoming Pacific plate. Overall, focused seepage manifests most commonly above the deforming backstop, is common on thrust ridges, and is largely absent from the frontal wedge despite ubiquitous hydrate occurrences. Focused seepage distribution may reflect spatial differences in shallow permeability architecture, while diffusive fluid flow and seepage at scales below detection limits are also likely. From the spatial coincidence of fluids with major thrust faults that disrupt gas hydrate stability, we surmise that focused seepage distribution may also reflect deeper drainage of the forearc, with implications for pore-pressure regime, fault mechanics, and critical wedge stability and morphology. Because a range of subduction styles is represented by 800 km of along-strike variability, our results may have implications for understanding subduction fluid flow and seepage globally.
Inherited terrane properties explain enigmatic post-collisional Himalayan-Tibetan evolution
Authors: Kelly Sean , Beaumont Christopher , Butler Jared P. 
Published: October 2019

AbstractObservations highlight the complex tectonic, magmatic, and geodynamic phases of the Cenozoic post-collisional evolution of the Himalayan-Tibetan orogen and show that these phases migrate erratically among terranes accreted to Asia prior to the Indian collision. This behavior contrasts sharply with the expected evolution of large, hot orogens formed by collision of lithospheres with laterally uniform properties. Motivated by this problem, we use two-dimensional numerical geodynamical model experiments to show that the enigmatic behavior of the Himalayan-Tibetan orogeny can result from crust-mantle decoupling, transport of crust relative to the mantle lithosphere, and diverse styles of lithospheric mantle delamination, which emerge self-consistently as phases in the evolution of the system. These model styles are explained by contrasting inherited mantle lithosphere properties of the Asian upper-plate accreted terranes. Deformation and lithospheric delamination preferentially localize in terranes with the most dense and weak mantle lithosphere, first in the Qiangtang and then in the Lhasa mantle lithospheres. The model results are shown to be consistent with 11 observed complexities in the evolution of the Himalayan-Tibetan orogen. The broad implication is that all large orogens containing previously accreted terranes are expected to have an idiosyncratic evolution determined by the properties of these terranes, and will be shown to deviate from predictions of uniform lithosphere models.