bluuebunny/crossref_metadata_2025_split huggingface dataset:
Swiss needle cast tolerance in British Columbia’s coastal Douglas-fir breeding population
Authors: Montwé David , Elder Bryan , Socha Peter , Wyatt Jessica , Noshad David , Feau Nicolas , Hamelin Richard , Stoehr Michael , Ehlting Jürgen 
Published: June 2020

Abstract
Substantial growth losses in Douglas-fir can be the result of Swiss needle cast, a foliar disease caused by the fungus Nothophaeocryptopus gaeumannii. Although the disease is native to western North America, it is expected to become increasingly problematic in regions where climates become warmer in winter and wetter in spring, such as in coastal British Columbia (BC), Canada. Previous research suggests that tolerance to this disease is under partial genetic control. We therefore aim to screen for tolerance and resistance to the disease in the tree breeding population of coastal Douglas-fir (Pseudotsuga menziesii var. menziesii) in BC. We evaluated if early screening for resistance or tolerance to this disease is possible. We worked with 32 families grown for 18-years on two full-sibling genetic field trial sites representing different climates. We assessed &gt;900 trees for disease signs and symptoms from 2017 to 2019. Needle retention was assessed in the field. In the laboratory, the proportion of stomata occluded with pseudothecia was measured, deoxyribonucleic acid (DNA) was extracted, and the proportion of fungal DNA in the needles was assessed using quantitative polymerase chain reaction. Strong differences were observed among families for needle retention, stomatal occlusion and fungal load. The milder and wetter site closer to the coast was generally more severely affected. Families showed rank changes between the two sites for all response variables. Higher needle retention was correlated with increased tree volume. No correlation was found between the proportion of stomata occluded with pseudothecia, fungal DNA load and needle retention. These results indicate that a more complex pathology is involved in causing needle loss. We conclude that screening for Swiss needle cast tolerance in the coastal BC Douglas-fir breeding population is possible if needle retention can be assessed and that area-specific deployment strategies may be needed given family rank changes in different environments.
Physics-based simulation of sequences with multiple main shocks in Central Italy
Authors: Console Rodolfo , Murru Maura , Vannoli Paola , Carluccio Roberto , Taroni Matteo , Falcone Giuseppe 
Published: June 2020

SUMMARYThe application of a physics-based earthquake simulator to Central Italy allowed the compilation of a synthetic seismic catalogue spanning 100 000 yr, containing more than 300 000 M ≥ 4.0 simulated earthquakes, without the limitations that real catalogues suffer in terms of completeness, homogeneity and time duration. The seismogenic model upon which we applied the simulator code was derived from version 3.2.1 of the Database of Individual Seismogenic Sources (DISS; http://diss.rm.ingv.it/diss/), selecting, and modifying where appropriate, all the fault systems that are recognized in the portion of Central Italy considered in this study, with a total of 54 faults. Besides tectonic stress loading and static stress transfer as in the previous versions, the physical model on which the latest version of our simulation algorithm is based also includes the Rate and State constitutive law that helps to reproduce Omori's law. One further improvement in our code was also the introduction of trapezoidal-shaped faults that perform better than known faults. The resulting synthetic seismic catalogue exhibits typical magnitude, space and time features which are comparable to those in real observations. These features include the total seismic moment rate, the earthquake magnitude distribution, and the short- and medium-term earthquake clustering. A typical aspect of the observed seismicity in Central Italy, as well as across the whole Italian landmass and elsewhere, is the occurrence of earthquake sequences characterized by multiple main shocks of similar magnitude. These sequences are different from the usual earthquake clusters and aftershock sequences, since they have at least two main shocks of similar magnitude. Therefore, special attention was devoted to verifying whether the simulated catalogue includes this notable aspect. For this purpose, we developed a computer code especially for this work to count the number of multiple events contained in a seismic catalogue under a quantitative definition. We found that the last version of the simulator code produces a slightly larger number of multiple events than the previous versions, but not as large as in the real catalogue. A possible reason for this drawback is the lack of components such as pore-pressure changes due to fluid-diffusion in the adopted physical model.
Data- and model-domain up/down wave separation for reverse-time migration with free-surface multiples
Authors: Guo Peng , Guan Huimin , McMechan George A 
Published: June 2020

SUMMARYSeismic data recorded using a marine acquisition geometry contain both upgoing reflections from subsurface structures and downgoing ghost waves reflected back from the free surface. In addition to the ambiguity of propagation directions in the data, using the two-way wave equation for wavefield extrapolation of seismic imaging generates backscattered/turned waves when there are strong velocity contrasts/gradients in the model, which further increases the wavefield complexity. For reverse-time migration (RTM) of free-surface multiples, apart from unwanted crosstalk between inconsistent orders of reflections, image artefacts can also be formed along with the true reflector images from the overlapping of up/downgoing waves in the data and in the extrapolated wavefield. We present a wave-equation-based, hybrid (data- and model-domain) wave separation workflow, with vector seismic data containing pressure- and vertical-component particle velocity from dual-sensor seismic acquisition, for removing image artefacts produced by the mixture of up/downgoing waves. For imaging with free-surface multiples, the wavefield extrapolated from downgoing ghost events (reflected from the free surface) in the recorded data act as an effective source wavefield for one-order-higher free-surface multiples. Therefore, only the downgoing waves in the data should be used as the source wavefield for RTM with multiples; the recorded upgoing waves in the seismograms will be used for extrapolation of the time-reversed receiver wavefield. We use finite-difference (FD) injection for up/down separation in the data domain, to extrapolate the down- and upgoing waves of the common-source gathers for source and receiver wavefield propagation, respectively. The model-domain separation decomposes the extrapolated wavefield into upgoing (backscattered) and downgoing (transmitted) components at each subsurface grid location, to remove false images produced by cross-correlating backscattered waves along unphysical paths. We combine FD injection with the model-domain wavefield separation, for separating the wavefield into up- and downgoing components for the recorded data and for the extrapolated wavefields. Numerical examples using a simple model, and the Sigsbee 2B model, demonstrate that the hybrid up/down separation approach can effectively produce seismic images of free-surface multiples with better resolution and fewer artefacts.
Longitudinal increases in somatic mosaicism of the expanded CTG repeat in myotonic dystrophy type 1 are associated with variation in age-at-onset
Authors: Morales Fernando , Vásquez Melissa , Corrales Eyleen , Vindas-Smith Rebeca , Santamaría-Ulloa Carolina , Zhang Baili , Sirito Mario , Estecio Marcos R , Krahe Ralf , Monckton Darren G 
Published: June 2020

Abstract
In myotonic dystrophy type 1 (DM1), somatic mosaicism of the (CTG)n repeat expansion is age-dependent, tissue-specific and expansion-biased. These features contribute toward variation in disease severity and confound genotype-to-phenotype analyses. To investigate how the (CTG)n repeat expansion changes over time, we collected three longitudinal blood DNA samples separated by 8–15 years and used small pool and single-molecule PCR in 43 DM1 patients. We used the lower boundary of the allele length distribution as the best estimate for the inherited progenitor allele length (ePAL), which is itself the best predictor of disease severity. Although in most patients the lower boundary of the allele length distribution was conserved over time, in many this estimate also increased with age, suggesting samples for research studies and clinical trials should be obtained as early as possible. As expected, the modal allele length increased over time, driven primarily by ePAL, age-at-sampling and the time interval. As expected, small expansions &lt;100 repeats did not expand as rapidly as larger alleles. However, the rate of expansion of very large alleles was not obviously proportionally higher. This may, at least in part, be a result of the allele length-dependent increase in large contractions that we also observed. We also determined that individual-specific variation in the increase of modal allele length over time not accounted for by ePAL, age-at-sampling and time was inversely associated with individual-specific variation in age-at-onset not accounted for by ePAL, further highlighting somatic expansion as a therapeutic target in DM1.
Modeling escape success in terrestrial predator–prey interactions
Authors: Wilson Robbie S , Pavlic Theodore P , Wheatley Rebecca , Niehaus Amanda C , Levy Ofir 
Published: June 2020

SynopsisPrey species often modify their foraging and reproductive behaviors to avoid encounters with predators; yet once they are detected, survival depends on out-running, out-maneuvering, or fighting off the predator. Though predation attempts involve at least two individuals—namely, a predator and its prey—studies of escape performance typically measure a single trait (e.g., sprint speed) in the prey species only. Here, we develop a theoretical model in which the likelihood of escape is determined by the prey animal’s tactics (i.e., path trajectory) and its acceleration, top speed, agility, and deceleration relative to the performance capabilities of a predator. The model shows that acceleration, top speed, and agility are all important determinants of escape performance, and because speed and agility are biomechanically related to size, smaller prey with higher agility should force larger predators to run along curved paths that do not allow them to use their superior speeds. Our simulations provide clear predictions for the path and speed a prey animal should choose when escaping from predators of different sizes (thus, biomechanical constraints) and could be used to explore the dynamics between predators and prey.
Axisymmetric Diffeomorphisms and Ideal Fluids on Riemannian 3-Manifolds
Authors: Lichtenfelz Leandro , Misiołek Gerard , Preston Stephen C 
Published: June 2020

Abstract
We study the Riemannian geometry of 3D axisymmetric ideal fluids. We prove that the $L^2$ exponential map on the group of volume-preserving diffeomorphisms of a $3$-manifold is Fredholm along axisymmetric flows with sufficiently small swirl. Along the way, we define the notions of axisymmetric and swirl-free diffeomorphisms of any manifold with suitable symmetries and show that such diffeomorphisms form a totally geodesic submanifold of infinite $L^2$ diameter inside the space of volume-preserving diffeomorphisms whose diameter is known to be finite. As examples, we derive the axisymmetric Euler equations on $3$-manifolds equipped with each of Thurston’s eight model geometries.
Attenuated Interferon and Proinflammatory Response in SARS-CoV-2–Infected Human Dendritic Cells Is Associated With Viral Antagonism of STAT1 Phosphorylation
Authors: Yang Dong , Chu Hin , Hou Yuxin , Chai Yue , Shuai Huiping , Lee Andrew Chak-Yiu , Zhang Xi , Wang Yixin , Hu Bingjie , Huang Xiner , Yuen Terrence Tsz-Tai , Cai Jian-Piao , Zhou Jie , Yuan Shuofeng , Zhang Anna Jinxia , Chan Jasper Fuk-Woo , Yuen Kwok-Yung 
Published: June 2020

Abstract
Clinical manifestations of coronavirus disease 2019 (COVID-19) vary from asymptomatic virus shedding, nonspecific pharyngitis, to pneumonia with silent hypoxia and respiratory failure. Dendritic cells and macrophages are sentinel cells for innate and adaptive immunity that affect the pathogenesis of severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS). The interplay between SARS-CoV-2 and these cell types remains unknown. We investigated infection and host responses of monocyte-derived dendritic cells (moDCs) and macrophages (MDMs) infected by SARS-CoV-2. MoDCs and MDMs were permissive to SARS-CoV-2 infection and protein expression but did not support productive virus replication. Importantly, SARS-CoV-2 launched an attenuated interferon response in both cell types and triggered significant proinflammatory cytokine/chemokine expression in MDMs but not moDCs. Investigations suggested that this attenuated immune response to SARS-CoV-2 in moDCs was associated with viral antagonism of STAT1 phosphorylation. These findings may explain the mild and insidious course of COVID-19 until late deterioration.
Rethinking Heresy as a Category of Analysis
Authors: Shogimen Takashi 
Published: June 2020

AbstractThis article aims to rehabilitate and restore the concept of heresy in the analysis of “religion” in a broad sense. Heresy is largely considered as a paradigmatically Christian, pre-modern, and, by implication, useless concept for scholarly investigations into religious phenomena today. A re-examination of the medieval concept of heresy, particularly that of William of Ockham, reveals that pertinacity as a defining feature of heresy in the medieval sense indicates heresy is the observed failure to recognize the obligatory nature, not the truth, of what authority asserts. The medieval idea of heresy may thus be redefined as the interference with the sacred, because obligations that generate the sacred are at the heart of what Emile Durkheim called “religious phenomena.” The Durkheimian reconceptualization of the medieval idea of heresy serves to illuminate the mechanism of social exclusion in both religious and secular contexts.
Arthropod Infestation Levels on Mandarins in California
Authors: Cass Bodil N , Hack Lindsey M , Mueller Tobias G , Buckman Darian , Grafton-Cardwell Elizabeth E , Rosenheim Jay A 
Published: June 2020

Abstract
Integrated pest management (IPM) guidelines for horticulture are typically established from years of experimental research and experience for a crop species. Ecoinformatics methods can help to quickly adapt these guidelines following major changes in growing practices. Citrus production in California is facing several major challenges, one of which is a shift away from sweet oranges [Citrus sinensis (L.) Osbeck Sapindales: Rutaceae] toward mandarins (including mostly cultivars of C. reticulata Blanco and C. clementina hort. ex Tanaka). In the absence of IPM guidelines for mandarins, growers are relying on pest information developed from oranges. We mined a database of management records from commercial growers and consultants to determine densities for four arthropod pests: cottony cushion scale (Icerya purchasi Maskell Hemiptera: Monophlebidae), citricola scale (Coccus pseudomagnoliarum Kuwana Hemiptera: Coccidae), European earwig (Forficula auricularia Linnaeus Dermaptera: Forficulidae), citrus red mite (Panonychus citri McGregor Acari: Tetranychidae), and a natural enemy, predatory mites in the genus Euseius (Congdon Acarina: Phytoseiidae). Densities of cottony cushion scale were approximately 10–40 times higher in the two most commonly grown mandarin species than in sweet oranges, suggesting this pest is reaching outbreak levels more often on mandarins. Densities of the other pests and predatory mites did not differ significantly across citrus species. This is a first step toward establishing IPM guidelines for mandarins for these pests; more research is needed to determine how arthropod densities relate to crop performance in mandarins.
A Laboratory Diet-Overlay Bioassay to Monitor Resistance in Lygus lineolaris (Hemiptera: Miridae) to Insecticides Commonly Used in the Mississippi Delta
Authors: Portilla Maribel 
Published: June 2020

Abstract
A laboratory, diet-overlay pesticide bioassay was developed using a susceptible population of the tarnished plant bug, Lygus lineolaris (Palisot de Beauvois), to study its susceptibility to neonicotinoid, sulfoxamine, organophosphate, and pyrethroid insecticides (thiamethoxam, sulfoxaflor, acephate, and permethrin, respectively). The diet-overlay bioassay was compared to the traditional glass-vial surface residue bioassay. We measured LC50 values by feeding tarnished plant bug adults known doses of insecticides dispensed on top of diet in a 10% solution of honey water for thiamethoxam and 10% acetone in water solutions for permethrin, acephate, and sulfoxaflor. Both the diet-overlay and glass-vial bioassays used dose-response (mortality) regression lines to calculate LC50 values for each insecticide at 6-, 24-, 48-, and 72-h post-exposure. Data variability from the glass-vial bioassay was higher for permethrin, sulfoxaflor, and thiamethoxam than the diet-overlay bioassay, for all evaluation times. In contrast, there was lower variability among replicates to acephate in the glass-vial assay compared to the diet-overlay assay. Control mortalities observed on diet-overlay bioassay were lower (0–5%) than those observed on the glass-vial bioassay (4–27%). The use of green beans, floral-foam, rolling glass vials, and insect handling made the existing standard method tedious to manipulate and difficult to handle large numbers of individuals. The nonautoclaved solid diet provides an opportunity to significantly reduce cost and variability associated with procedures of other bioassay methods. In general, the baseline data provide a basis for future comparison to determine changes in resistance over time.
Bayesian Inference of Multivariate Regression Models with Endogenous Markov Regime-Switching Parameters
Authors: Kim Young Min , Kang Kyu Ho 
Published: June 2020

AbstractThis study introduces a multivariate regression model with endogenous Markov regime-switching parameters, in which the regression disturbances and regime switches are allowed to be instantaneously correlated. For the estimation and model comparison, we develop a posterior sampling algorithm for the parameters, regimes, and marginal likelihood calculation. We demonstrate the reliability of the proposed method using simulation and empirical studies. The simulation study shows that neglecting the endogeneity leads to inaccurate parameter estimates, and that our marginal likelihood comparison chooses a correctly specified model. In the business cycle application, we find that the joint dynamics of the U.S. industrial production index (IPI) growth and unemployment rates are subject to three-state endogenous regime shifts. Another application to stock and bond return data suggests that negative shocks to the stock return seem to cause regime shifts from a low volatility state to a high volatility state of the financial markets. (JEL: C11, C53, E43, G12)
Primary hydatid cyst looked like renal cell carcinoma: case report
Authors: Mohamed Irzi , Tarik Mhanna , Mohammed Aynaou , Alaoui Wassim , Abdelghani Ouraghi , Ali Barki 
Published: June 2020

Abstract
Renal hydatid cyst is a rare disease comprising of about 2–3% of all locations. We present a case of renal hydatid disease in a 48-year-old female patient who presented with a history of left flank pain without fever or hematuria. Ultrasonography and computed tomography showed a 3-cm cystic lesion Bosniak IV occupying the mid-zone of the left kidney diagnosed as renal malignancy. Laparoscopic partial nephrectomy was performed, but the histopathological examination of the lesion revealed hydatid cysts. Isolated renal hydatid cyst is very rare, especially in developed countries and can be misdiagnosed as a renal cell carcinoma pre-operatively.
Queer Music in the Queen’s Hall: Teleny and Decadent Musical Geographies at the Fin de Siècle
Authors: Riddell Fraser 
Published: June 2020

Abstract
This article examines the significance of music and musical performance in Teleny, or the Reverse of the Medal (1893), an anonymous pornographic novel attributed by some scholars to Oscar Wilde. It draws upon historical material on late-Victorian concert venues, queer literary sub-cultures and sexology to illuminate the representation of musical spaces in the text. Teleny exists in two different versions: an English text, which is set in Paris, and a French text, which is set in London. The opening section of the article suggests that Teleny’s dynamic engagement with cosmopolitan cultural exchange between Paris and London is brought into sharper focus by situating the musical performances in the novel in the precise built environment of London’s Queen Hall. The second section explores the novel’s concern with queer geographies (the Orient, Eastern Europe) in the context of other texts that address music and homosexual identity in the period. The third section examines the significance of space in the novel’s presentation of musical listening, arguing that its focus on the materiality of sound and the haptic transmission of desire responds to sexological conceptions of embodied musical response by homosexual subjects. The significance of this sensory experience of listening is understood in the light of Sara Ahmed’s theorization of ‘queer phenomenology’. Finally, the article traces the significance of musical allusions to songs by Franz Schubert to show how they form part of the novel’s broader concerns with the spatial articulation of same-sex desire and the representation of queer urban geographies.
Human-like telomeres in Zostera marina reveal a mode of transition from the plant to the human telomeric sequences
Authors: Peska Vratislav , Mátl Martin , Mandáková Terezie , Vitales Daniel , Fajkus Petr , Fajkus Jiří , Garcia Sònia 
Published: June 2020

Abstract
A previous study describing the genome of Zostera marina, the most widespread seagrass in the Northern hemisphere, revealed some genomic signatures of adaptation to the aquatic environment such as the loss of stomatal genes, while other functions such as an algal-like cell wall composition were acquired. Beyond these, the genome structure and organization were comparable with those of the majority of plant genomes sequenced, except for one striking feature that went unnoticed at that time: the presence of human-like instead of the expected plant-type telomeric sequences. By using different experimental approaches including fluorescence in situ hybridization (FISH), genome skimming by next-generation sequencing (NGS), and analysis of non-coding transcriptome, we have confirmed its telomeric location in the chromosomes of Z. marina. We have also identified its telomerase RNA (TR) subunit, confirming the presence of the human-type telomeric sequence in the template region. Remarkably, this region was found to be very variable even in clades with a highly conserved telomeric sequence across their species. Based on this observation, we propose that alternative annealing preferences in the template borders can explain the transition between the plant and human telomeric sequences. The further identification of paralogues of TR in several plant genomes led us to the hypothesis that plants may retain an increased ability to change their telomeric sequence. We discuss the implications of this occurrence in the evolution of telomeres while introducing a mechanistic model for the transition from the plant to the human telomeric sequences.