bluuebunny/crossref_metadata_2025_split huggingface dataset:
The impact of wheat cultivar mixtures on virulence dynamics in Zymoseptoria tritici populations persists after interseason sexual reproduction
Authors: Orellana‐Torrejon Carolina , Vidal Tiphaine , Saint‐Jean Sébastien , Suffert Frédéric 
Published: April 2022

AbstractThis study follows on from a previous study showing that binary mixtures of wheat cultivars affect the evolution of Zymoseptoria tritici populations within a field epidemic from the beginning (t1) to the end (t2) of a growing season. Here, we focused on the impact of interseason sexual reproduction on this evolution. We studied mixtures of susceptible and resistant cultivars (carrying Stb16q, a recently broken‐down resistance gene) in proportions of 0.25, 0.5 and 0.75, and their pure stands. We determined the virulence status of 1440 ascospore‐derived strains collected from each cultivar residue by phenotyping on seedlings. Virulence frequencies in the ascospore‐derived population were lower in mixtures than in pure stands of the resistant cultivar, especially in the susceptible cultivar residues, as at t2, revealing that the impact of mixtures persisted until the next epidemic season (t3). Surprisingly, after sexual reproduction the avirulence frequencies on the resistant cultivar residues increased in mixtures where the proportion of the susceptible cultivar was higher. Our findings highlight two epidemiological processes: selection within the pathogen population between t1 and t2 driven by asexual cross‐contamination between cultivars (previous study) and sexual crosses between avirulent and virulent strains between t2 and t3 driven by changes in the probabilities of physical encounters (this study). Mixtures therefore appear to be a promising strategy for the deployment of qualitative resistances, not only to limit the intensity of Septoria tritici blotch epidemics, but also to reduce the erosion of resistances by managing evolution of the pathogen population at a pluriannual scale.
A first insight into the clinical manifestation of posttraumatic stress disorder in dementia: a systematic literature review
Authors: van Dongen Dorien H.E. , Havermans Demi , Deckers Kay , Olff Miranda , Verhey Frans , Sobczak Sjacko 
Published: April 2022

AbstractPosttraumatic stress disorder (PTSD) is a prevalent disorder worldwide and often co‐occurs in dementia. Both have a major impact on disease burden and quality of life. PTSD may be difficult to recognize in dementia and a structured diagnostic method is lacking. In order to get insight into the clinical diagnostics of PTSD in dementia, this systematic literature review evaluates the clinical presentation of PTSD and other relevant symptoms in people with dementia. PubMed, PsycINFO, Embase, and CINAHL were searched for all publications through 30 December 2021. Articles were included which met the following criteria: (i) description of at least one case with a current diagnosis of dementia and co‐morbid PTSD; (ii) clinical presentation of symptoms being adequately described; (iii) no difference being made between chronic PTSD, PTSD with re‐activation, and delayed onset PTSD. Of the 947 identified abstracts, 13 papers met the inclusion criteria and were included (describing 30 cases). Based on our rating, only one case completely fulfilled the DSM‐5 criteria of PTSD. Avoidance was only described in three cases. Most commonly described symptoms were irritability and anger (E1, 9%), persistent negative emotional state (D4, 9%), and sleep disturbances (E6, 8%). In 93% of the case reports, other symptoms were also described, i.e. memory problems (58%), screaming (33.3%), and wandering (22.2%). People with dementia who have experienced a traumatic event seem to present, based on our rating method, with insufficient symptoms to meet all criteria for a PTSD DSM‐5 diagnosis. The DSM‐5 core symptom of avoidance was absent in most of the cases. Clinical presentation consists mainly of symptoms of irritability, anger, persistent negative emotional state, and sleep disturbances, often accompanied by other symptoms. These findings suggest that older people with dementia may have other symptom presentations than people without dementia.
Season of birth and vulnerability to the pathology of Alzheimer's disease: an in vivo positron emission tomography study
Authors: Yasuno Fumihiko , Minami Hiroyuki ,   Alzheimer's Disease Neuroimaging Initiative
Published: April 2022

BackgroundThis study used positron emission tomography to examine whether the seasonal birth effect as an exogenic indicator of early life environmental factors influenced vulnerability to Alzheimer's disease (AD) pathology in the elderly.MethodsWe analysed datasets from the Alzheimer's Disease Neuroimaging Initiative, which included the data for 234 cognitively normal (CN) individuals and patients with mild cognitive impairment (MCI) (n = 114) and AD dementia (n = 38). As an index of amyloid β (Aβ)/tau accumulation, the 18F‐AV‐45‐ and 18F‐AV‐1451‐standardized uptake value ratios (SUVRs) were compared between groups of spring‐to‐summer births and fall‐to‐winter births by analysis of covariance. In addition, a multiple linear regression analysis was performed to determine whether the season of birth was a predictor of 18F‐AV‐45 and/or 18F‐AV‐1451 SUVRs, for which a difference was observed.ResultsSeasonal birth difference was a good predictor of 18F‐AV‐1451 SUVR. We found that participants with a fall‐to‐winter birth showed lower 18F‐AV‐1451 SUVRs than those with a spring‐to‐summer birth in both the CN and MCI/AD groups, after correcting for the effect of age, sex, years of education, and Alzheimer's Disease Assessment Scale cognitive subscale score, that could possibly affect tau accumulation.ConclusionsParticipants with a fall‐to‐winter birth showed less tau accumulation than those with a spring‐to‐summer birth after accounting for the factors that could affect tau accumulation. Our findings showed a vulnerability to tau pathology in participants with a fall‐to‐winter birth, which may be caused by perinatal or postnatal brain damage due to the risk factors associated with the cold season.
Interactive effects of allelopathy and arbuscular mycorrhizal fungi on the competition between the invasive species Bidens alba and its native congener Bidens biternata
Authors: Cheng Jun‐Kang , Cao Meng‐Yan , Yang Heng‐Rong , Yue Mao‐Feng , Xin Guo‐Rong , Chen Bao‐Ming 
Published: April 2022

AbstractAllelopathy is an invasion driver, and arbuscular mycorrhizal fungi (AMF) also play an important role in plant invasion. However, little is known about their interactive effects on plant invasion mechanisms. In this study, we have investigated the interactive effects of allelopathy and AMF on competition between the exotic invasive species, Bidens alba, and its native congener, Bidens biternata. A two‐factor (allelopathy, AMF) common garden experiment was conducted using sterilised soil with or without AMF inoculation and with or without activated carbon (AC) addition. The results showed that both AC and AMF had significant effects on the relative yield (RY) of invasive species and competitive aggressivity (AG) between invasive and native species. Both AC and AMF exerted interactive effects on the AG. Activated carbon significantly reduced AG (0.86 vs 0.15%) without AMF, while it had no significant effects on AG with AMF. Moreover, AC significantly reduced the mycorrhizal dependency of the native species (108.06% vs 23.62%) but did not affect the invasive species. The AMF increased the variety of organic compounds in the aqueous extracts of the rhizosphere soil of invasive species, regardless of the competition. Overall, allelopathy significantly increased the mycorrhizal dependency of the native species, while it promoted the competitive ability of the invader regardless of AMF inoculation. Conversely, AMF reduced the facilitation of allelopathy in the AG of the invasive species. These results suggest that AMF play a critical role in improving the resistance of the native species to the invader by mediating allelopathy.
Generalized Formulation for the Behavior of Geometrically Curved and Twisted Three-Dimensional Timoshenko Beams and Its Isogeometric Analysis Implementation
Authors: Yin Hao , Lale Erol , Cusatis Gianluca 
Published: April 2022

Abstract
This article presents a novel derivation for the governing equations of geometrically curved and twisted three-dimensional Timoshenko beams. The kinematic model of the beam was derived rigorously by adopting a parametric description of the axis of the beam, using the local Frenet–Serret reference system, and introducing the constraint of the beam cross ection planarity into the classical, first-order strain versus displacement relations for Cauchy’s continua. The resulting beam kinematic model includes a multiplicative term consisting of the inverse of the Jacobian of the beam axis curve. This term is not included in classical beam formulations available in the literature; its contribution vanishes exactly for straight beams and is negligible only for curved and twisted beams with slender geometry. Furthermore, to simplify the description of complex beam geometries, the governing equations were derived with reference to a generic position of the beam axis within the beam cross section. Finally, this study pursued the numerical implementation of the curved beam formulation within the conceptual framework of isogeometric analysis, which allows the exact description of the beam geometry. This avoids stress locking issues and the corresponding convergence problems encountered when classical straight beam finite elements are used to discretize the geometry of curved and twisted beams. Finally, this article presents the solution of several numerical examples to demonstrate the accuracy and effectiveness of the proposed theoretical formulation and numerical implementation.
Trophic Relations between Native Salvelinus malma Walb. and Introduced Oncorhynchus nerka Walb. in the Landlocked Lake Sevo, Kamchatka
Authors: Busarova O. Yu. , Esin E. V. , Markevich G. N. 
Published: April 2022

Abstract
Fish introductions are known to be dangerous due to the unexpected spread of diseases and disorganization of the food web. In 1986, the resident sockeye salmon Oncorhynchus nerka from Kronotskoye Lake was introduced into an isolated lake in Kamchatka inhabited by the native lacustrine Dolly Varden charr Salvelinus malma. Thirty years later, we analyzed the stomach content, stable isotope ratio and lipid fractions in muscles, as well as the parasite fauna of fish to assess the trophic relationships between the two species. It has been found that the sockeye salmon has occupied the planktivorous niche; no diversification into trophic forms depending on the number of gill rakers, like in the ancestral population, was detected. The indigenous benthivorous S. malma is represented by three trophic groups. Mature dwarf individuals, as well as the juveniles, mainly consume insect larvae on the lake slope; large fish feed on amphipods in the same habitats; and 10% of the large Dolly Varden switches to facultative piscivory. Predators die as a result of Diphyllobothrium sp. hyper invasion, which infects fish when feeding on the sockeye salmon. The diversity of parasite fauna is 3/4 poorer in the introduced sockeye in comparison with the donor population; part of the parasite species is obtained by the sockeye from the Dolly Varden.
Reliability and interpretation of the microstructural parameters determined by X-ray line profile analysis for nanostructured materials
Authors: Gubicza Jenő 
Published: April 2022

AbstractIn this overview, the applicability of X-ray diffraction line profile analysis (XLPA) for the characterization of the microstructure in nanostructured materials is overviewed. The dislocation densities obtained by whole pattern fitting and from the breadth of the diffraction peaks are compared. Both theoretical considerations and experimental evidences prove that the evaluation of the peak breadth solely is not suitable for the determination of the dislocation density. In addition, the microstructural parameters determined by XLPA were compared to the values obtained directly by microscopic methods. It was found that the ratio of the grain size obtained by microscopy and the crystallite size determined by XLPA decreases with the reduction of the grain size in nanomaterials, and below $$\sim $$
∼
20 nm, the two values agree within the experimental error. In addition, correlation between the microstructural parameters (e.g., crystallite size and dislocation density) determined by XLPA was not found. It was revealed that bottom–up processing methods can produce similarly high defect density in nanostructured materials as severe plastic deformation (SPD). The influence of stacking fault energy, melting point, and degree of alloying on the microstructure of nanomaterials is discussed in detail.
Yield of Echocardiography in Ischemic Stroke and Patients With Transient Ischemic Attack With Established Indications for Long‐Term Direct Oral Anticoagulant Therapy: A Cross‐Sectional Diagnostic Cohort Study
Authors: Meinel Thomas R. , Brignoli Kristina , Kielkopf Moritz , Clenin Leander , Beyeler Morin , Scutelnic Adrian , Siepen Bernhard , Mueller Madlaine , Goeldlin Martina , Seiffge David , Kaesmacher Johannes , Mujanovic Adnan , Belachew Nebiyat F. , Fischer Urs , Arnold Marcel , Gräni Christoph , Seiler Christian , Buffle Eric , Jung Simon 
Published: April 2022

Background
We aimed to determine the diagnostic yield of transthoracic (TTE) and transesophageal echocardiography (TEE) in patients with ischemic stroke and transient ischemic attack with established indications for direct oral anticoagulants before the index event.

Methods and Results

This was a retrospective cohort study of consecutive patients with preceding established indications for long‐term therapeutic direct oral anticoagulants presenting to a single comprehensive stroke center with ischemic stroke or transient ischemic attack. Choice of echocardiography modality was based on expert recommendations. The primary outcome was a composite of prespecified management‐relevant high‐risk findings adjudicated by an expert panel, based on TTE and TEE reports according to evidence‐based recommendations. Explorative analyses were performed to identify biomarkers associated with the primary outcome. Of 424 patients included (median [interquartile range] age, 78 [70–84] years; 175 [41%] women; National Institutes of Health Stroke Scale, 4 [1–12]; 67% atrial fibrillation), 292 (69%) underwent echocardiography, while 132 (31%) did not. Modality was TTE in 191 (45%) and TEE in 101 (24%). Median time from index event to echocardiography was 2 (1–3) days. TTE identified 26 of 191 (14%) patients with 35 management‐relevant pathologies. TEE identified 16 of 101(16%) patients with 20 management‐relevant pathologies. Most management‐relevant findings represented indicated coronary artery disease and valvular pathologies. In a further 3 of 191 (2%) patients with TTE and 4 of 101 (4%) patients with TEE, other relevant findings were identified. Variables associated with management‐relevant high‐risk pathologies included more severe stroke, diabetes, and laboratory biomarkers (NT‐proBNP [N‐terminal pro‐B‐type natriuretic peptide], C‐reactive protein,
d
‐dimer, and troponin levels).

Conclusions
In patients with established indications for long‐term direct oral anticoagulant therapy and stroke who received echocardiography, both TTE and TEE identified a relevant and similar proportion of management‐relevant high‐risk pathologies and predictive biomarkers could help to guide diagnostic workup in such patients.
Scaling Notebooks as Re-configurable Cloud Workflows
Authors: Wang Yuandou , Koulouzis Spiros , Bianchi Riccardo , Li Na , Shi Yifang , Timmermans Joris , Kissling W. Daniel , Zhao Zhiming 
Published: April 2022

AbstractLiterate computing environments, such as the Jupyter (i.e., Jupyter Notebooks, JupyterLab, and JupyterHub), have been widely used in scientific studies; they allow users to interactively develop scientific code, test algorithms, and describe the scientific narratives of the experiments in an integrated document. To scale up scientific analyses, many implemented Jupyter environment architectures encapsulate the whole Jupyter notebooks as reproducible units and autoscale them on dedicated remote infrastructures (e.g., highperformance computing and cloud computing environments). The existing solutions are still limited in many ways, e.g., 1) the workflow (or pipeline) is implicit in a notebook, and some steps can be generically used by different code and executed in parallel, but because of the tight cell structure, all steps in the Jupyter notebook have to be executed sequentially and lack of the flexibility of reusing the core code fragments, and 2) there are performance bottlenecks that need to improve the parallelism and scalability when handling extensive input data and complex computation.In this work, we focus on how to manage the workflow in a notebook seamlessly. We 1) encapsulate the reusable cells as RESTful services and containerize them as portal components, 2) provide a composition tool for describing workflow logic of those reusable components, and 3) automate the execution on remote cloud infrastructure. Empirically, we validate the solution's usability via a use case from the Ecology and Earth Science domain, illustrating the processing of massive Light Detection and Ranging (LiDAR) data. The demonstration and analysis show that our method is feasible, but that it needs further improvement, especially on integrating distributed workflow scheduling, automatic deployment, and execution to develop as a mature approach.
Changes in the Relationship between ENSO and the Winter Arctic Stratospheric Polar Vortex in Recent Decades
Authors: Zhang Ruhua , Zhou Wen , Tian Wenshou , Zhang Yue , Liu Zhenchen , Cheung Paxson K. Y. 
Published: April 2022

Abstract
The impact of El Niño–Southern Oscillation (ENSO) on the winter stratospheric polar vortex intensity (PVI) is re-examined, using JRA-55 datasets and the CESM2 model. Our results show that the negative correlation between ENSO and PVI has weakened in recent decades and is no longer statistically significant after the mid-1990s. This weakening ENSO–PVI relationship after the mid-1990s is associated with wave-1 fluxes entering the stratosphere; that is, the ENSO-induced increasing wave-1 fluxes are weaker after the mid-1990s than before the mid-1990s. Except for the Pacific–North America (PNA)-like wave train, the stratospheric wave flux changes are related to ENSO-induced geopotential height changes over East Asia. The ENSO-induced tropical zonal circulation anomalies are enhanced from the central Pacific to East Asia, leading to more substantial wave flux anomalies propagating westward from the central Pacific to East Asia and a more significant high center over Northeast Asia after the mid-1990s than before the mid-1990s. This ENSO-induced high center after the mid-1990s is out of phase with the climatological center of wave 1, leading to a relatively weaker increase in wave 1. Model results show that changes in the ENSO–PVI relationship and ENSO–Asia circulation are associated with changes in ENSO-related SST combined with global mean SST.

Significance Statement
In this study, changes in the ENSO–polar vortex relationship and the relevant mechanisms are analyzed from the perspective of the ENSO-induced East Asia circulation. The results can help us better understand and predict variations in the stratospheric polar vortex.
Bridgesite-(Ce), a new rare earth element sulfate, with a unique crystal structure, from Tynebottom Mine, Cumbria, United Kingdom
Authors: Rumsey Mike S. , Hawthorne Frank C. , Spratt John , Najorka Jens , Montgomery Wren 
Published: April 2022

AbstractBridgesite-(Ce), (IMA2019-034), was discovered at Tynebottom Mine, Cumbria, UK. It occurs as thin (1–2 μm) translucent blue crystals with a lath-like to acicular habit, aggregated into thin crusts and is associated mainly with brochantite, malachite, serpierite, devilline, gypsum, aragonite, jarosite, pyrite, lanthanite-(Ce) and undifferentiated iron oxyhydroxides, it is often intergrown with these other minerals. The lustre, hardness, cleavage and parting could not be determined, nor could density be measured due to crystal size. It has a pale blue streak and is brittle with a splintery fracture. Bridgesite-(Ce) is biaxial (–), shows no pleochroism and has refractive indices (white light): α = 1.526(2), β = 1.564(2), γ = 1.572(2) and 2V(calc) = 48.3°. The empirical formula calculated on the basis of 44 negative charges is Ca0.86REEΣ1.99Al0.07Cu5.95(SO4)3.99(SiO4)0.05(PO4)0.02(OH)11.52⋅8H2O. The idealised formula is CaCe2Cu6(SO4)4(OH)12⋅8H2O, requiring (wt.%): 3.91 CaO, 22.89 Ce2O3, 33.28 CuO, 22.33 SO3 and 17.59 H2O. Bridgesite-(Ce) is monoclinic, space group C2/m, a = 24.801(5), b = 6.3520(13), c = 11.245(2) Å, β = 114.51(3)°, V = 1611.9(6) Å and Z = 2. The five most intense X-ray diffraction peaks in the measured pattern are [d in Å (I, %) (hkl)]: 11.3 (100) (200), 6.391 (15) (201), 2.770 (8) (420), 3.194 (6) (402) and 4.858 (5) (310). The crystal structure was solved using single crystal data and refined to an R1 index of 5.86%. Bridgesite-(Ce) contains three distinct Cu sites containing Cu2+, two are coordinated octahedrally and one is square pyramidal. The octahedra form chains through edge sharing parallel to the b-axis which are linked by the square pyramid to form sheets oriented parallel to {100}. Sulfate tetrahedra decorate the sheets which are held together by interstitial REE3+, Ca2+ and hydrogen bonding. The structure is unique. Despite apparent similarity in chemical formula, bridgesite-(Ce) is not closely related to any other natural Cu-sulfate mineral. An FTIR absorption spectra is presented for reference purposes.
Whole-genome sequencing reveals complex genomic features underlying anti-CD19 CAR T-cell treatment failures in lymphoma
Authors: Jain Michael D. , Ziccheddu Bachisio , Coughlin Caroline A. , Faramand Rawan , Griswold Anthony J. , Reid Kayla M. , Menges Meghan , Zhang Yonghong , Cen Ling , Wang Xuefeng , Hussaini Mohammad , Landgren Ola , Davila Marco L. , Schatz Jonathan H. , Locke Frederick L. , Maura Francesco 
Published: April 2022

Abstract
CD19-directed chimeric antigen receptor (CAR-19) T cells are groundbreaking immunotherapies approved for use against large B-cell lymphomas. Although host inflammatory and tumor microenvironmental markers associate with efficacy and resistance, the tumor-intrinsic alterations underlying these phenomena remain undefined. CD19 mutations associate with resistance but are uncommon, and most patients with relapsed disease retain expression of the wild-type receptor, implicating other genomic mechanisms. We therefore leveraged the comprehensive resolution of whole-genome sequencing to assess 51 tumor samples from 49 patients with CAR-19–treated large B-cell lymphoma. We found that the pretreatment presence of complex structural variants, APOBEC mutational signatures, and genomic damage from reactive oxygen species predict CAR-19 resistance. In addition, the recurrent 3p21.31 chromosomal deletion containing the RHOA tumor suppressor was strongly enriched in patients for whom CAR T-cell therapy failed. Pretreatment reduced expression or monoallelic loss of CD19 did not affect responses, suggesting CAR-19 therapy success and resistance are related to multiple mechanisms. Our study showed that tumor-intrinsic genomic alterations are key among the complex interplay of factors that underlie CAR-19 efficacy and resistance for large B-cell lymphomas.