bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel Trichoderma asperellum strain DQ-1 promotes tomato growth and induces resistance to gray mold caused by Botrytis cinerea
Authors: Wang Rui , Chen Di , Khan Raja Asad Ali , Cui Jia , Hou Jumei , Liu Tong 
Published: November 2021

ABSTRACT
Gray mold caused by Botrytis cinerea is a major cause of economic losses during tomato production. In this study, we obtained 23 Trichoderma strains from tomato rhizosphere soil and their inhibitory effects on B. cinerea and the promoting effects on tomato growth were determined. Among them, the inhibition rate of strain DQ-1 on B. cinerea was 88.56%; compared with the control group, after treatment with strain DQ-1, the seeds germination rate and root length of tomato increased by 5.55 and 37.86%. The induced disease resistance of strain DQ-1 was evaluated by pot experiments. The disease incidence (DI) and disease severity index (DSI) of tomato pre-inoculated with strain DQ-1 and then inoculated with B. cinerea were reduced by 38 and 64% compared with the control. Furthermore, we detected the expression levels of tomato disease resistance related genes PR2 and TPX, ethylene pathway related genes ETR1 and CTR1 and jasmonic acid pathway related genes LOX1 and PAL in challenging and non-challenging inoculation treatments. The results showed that the tomato treated with strain DQ-1 triggered the system acquired resistance (SAR) and induced systemic resistance (ISR) pathway, thereby enhancing the disease resistance of tomato. Then the strain DQ-1 was identified as Trichoderma asperellum based on morphological characteristics and phylogenetic information. This study suggests that the novel T. asperellum strain DQ-1 can be a potential candidate for the biological control of gray mold in tomato.
Diversity of non-Saccharomycesyeasts of grape berry surfaces from representative Cabernet Sauvignon vineyards in Henan Province, China
Authors: Zhang Junjie , Shang Yimin , Chen Jinyong , Brunel Brigitte , Peng Shanshan , Li Shuo , Wang Entao 
Published: November 2021

ABSTRACTNon-Saccharomyces yeasts are important players during winemaking and may come from grapes grown in vineyards. To study the diversity of non-Saccharomyces yeasts on grape berry surfaces, 433 strains were isolated from different Cabernet Sauvignon vineyards grown in Henan Province. Our results demonstrated that these strains were classified into 16 morphotypes according to their growth morphology on Wallerstein Laboratory agar medium, and were identified as seven species from four genera—Hanseniaspora opuntiae, Hanseniaspora vineae, Hanseniaspora uvarum, Pichia occidentalis, Pichia kluyveri, Issatchenkia terricola and Saturnispora diversa—based on a series of molecular biological experiments. Hanseniaspora opuntiae was obtained from all sampling sites except Changyuan County, while Pichia kluyveri and Saturnispora diversa were only found in sites of Zhengzhou Grape Resource Garden and Minquan County, respectively. The site Minquan was home of the greatest species richness, while only one single species (Hanseniaspora opuntiae) was detected at NAPA winery from Zhengzhou or at Anyang County. Finally, this study suggested that the geographic distribution and diversity of non-Saccharomyces yeast populations on Cabernet Sauvignon grape berries were likely to be determined by a combination of grape varieties and environmental factors.
Keeping the host alive – lessons from obligate intracellular bacterial pathogens
Authors: Loterio Robson Kriiger , Zamboni Dario S , Newton Hayley J 
Published: November 2021

ABSTRACTMammals have evolved sophisticated host cell death signaling pathways as an important immune mechanism to recognize and eliminate cell intruders before they establish their replicative niche. However, intracellular bacterial pathogens that have co-evolved with their host have developed a multitude of tactics to counteract this defense strategy to facilitate their survival and replication. This requires manipulation of pro-death and pro-survival host signaling pathways during infection. Obligate intracellular bacterial pathogens are organisms that absolutely require an eukaryotic host to survive and replicate, and therefore they have developed virulence factors to prevent diverse forms of host cell death and conserve their replicative niche. This review encapsulates our current understanding of these host–pathogen interactions by exploring the most relevant findings of Anaplasma spp., Chlamydia spp., Rickettsia spp. and Coxiella burnetii modulating host cell death pathways. A detailed comprehension of the molecular mechanisms through which these obligate intracellular pathogens manipulate regulated host cell death will not only increase the current understanding of these difficult-to-study pathogens but also provide insights into new tools to study regulated cell death and the development of new therapeutic approaches to control infection.
Covariance Generalized Linear Models: An Approach for Quantifying Uncertainty in Tree Stem Taper Modeling
Authors: Fiorentin Luan Demarco , Bonat Wagner Hugo , Pelissari Allan Libanio , Machado Sebastião do Amaral , Téo Saulo Jorge 
Published: November 2021

Abstract
A natural dependence among diameters measured within-tree is expected in taper data due to the hierarchical structure. The aim of this paper was to introduce the covariance generalized linear model (CGLM) framework in the context of forest biometrics for Pinus taeda stem form modeling. The CGLMs are based on marginal specification, which requires a definition of the mean and covariance components. The tree stem mean profiles were modeled by a nonlinear segmented model. The covariance matrix was built considering four strategies of linear combinations of known matrices, which expressed the variance or correlations among observations. The first strategy modeled only the variance of the diameters over the stem as a function of covariates, the second modeled correlation among observations, the third was defined based on a random walk model, the fourth was based on a structure similar to a mixed-effect model with a marginal specification, and the fourth was a traditional mixed-effect model. Mean squared error and bias showed that the approaches were similar for describing the mean profile for fitting and validation dataset. However, uncertainties expressed by confidence intervals of the relative diameters were significant and related to the matrix covariance structures of the CGLMs.
Adjoint envelope tomography for scattering and absorption using radiative transfer theory
Authors: Zhang Tuo , Sens-Schönfelder Christoph 
Published: November 2021

SUMMARY
To investigate the small-scale elastic structure of the subsurface at length scales below the resolution limits of waveform tomography, envelopes of high-frequency scattered seismic waveforms have been used with a variety of approaches. However, a rigorous framework for the iterative inversion of seismogram envelopes to image heterogeneity and high-frequency attenuation comparable to full waveform inversion (FWI) is missing. We present the mathematical framework for an iterative full envelope inversion using forward and adjoint simulations of the radiative transfer equations, in full analogy to FWI that is based on the wave equation. The forward and adjoint problems are solved by modelling 2-D multiple non-isotropic scattering in a random elastic medium with spatially variable heterogeneity and attenuation using the Monte Carlo method. Sensitivity kernels are derived for the squared difference between the full observed and modelled envelopes which is iteratively minimized with the L-BFGS method. We apply this algorithm in numerical tests in the acoustic approximation and show that it is possible to image the spatial distribution of small-scale heterogeneity and attenuation in iterative inversions. Our analysis shows that the relative importance of scattering and attenuation anomalies needs to be considered when the model resolution is assessed. The inversions confirm that the early coda is important for imaging the distribution of heterogeneity while later coda waves are more sensitive to intrinsic attenuation and we show that this dependency can be used to cope with the trade-off that exists between both material properties.
O-GlcNAcylation increases PYGL activity by promoting phosphorylation
Authors: Chen Yan-Fang , Zhu Jing-Jing , Li Jing , Ye Xin-Shan 
Published: November 2021

Abstract
O-GlcNAcylation is a post-translational modification that links metabolism with signal transduction. High O-GlcNAcylation appears to be a general characteristic of cancer cells. It promotes the invasion, metastasis, proliferation and survival of tumor cells, and alters many metabolic pathways. Glycogen metabolism increases in a wide variety of tumors, suggesting that it is an important aspect of cancer pathophysiology. Herein we focused on the O-GlcNAcylation of liver glycogen phosphorylase (PYGL)—an important catabolism enzyme in the glycogen metabolism pathway. PYGL expressed in both HEK 293T and HCT116 was modified by O-GlcNAc. And both PYGL O-GlcNAcylation and phosphorylation of Ser15 (pSer15) were decreased under glucose and insulin, whereas increased under glucagon and Na2S2O4 (hypoxia) conditions. Then, we identified the major O-GlcNAcylation site to be Ser430, and demonstrated that pSer15 and Ser430 O-GlcNAcylation were mutually reinforced. Lastly, we found that Ser430 O-GlcNAcylation was fundamental for PYGL activity. Thus, O-GlcNAcylation of PYGL positively regulated pSer15 and therefore its enzymatic activity. Our results provided another molecular insight into the intricate post-translational regulation network of PYGL.
Mini-thoracotomy and full-sternotomy approach for reoperative mitral valve surgery after a previous sternotomy
Authors: Kwon Yelee , Park Sung Jun , Kim Ho Jin , Kim Joon Bum , Jung Sung-Ho , Choo Suk Jung , Lee Jae Won 
Published: November 2021

Abstract

OBJECTIVES
Right mini-thoracotomy approach may enhance the visualization of mitral valve (MV) visualization during redo MV surgery, thereby minimizing the risk of reoperative median sternotomy. We described the clinical outcomes of redo MV surgery by mini-thoracotomy and full-sternotomy approach.

METHODS
Of 730 consecutive adult patients who underwent redo MV surgery between 2002 and 2018 at our institution, we identified 380 patients (age: 56.0 [14.8] years) after excluding those who underwent concomitant aortic valve or coronary artery surgeries.

RESULTS
The clinical outcomes in patients who underwent mini-thoracotomy (MINI group; n = 168) and full-sternotomy (STERN group; n = 218) were described. The early and overall mortality in the MINI group was 4.3% (7/162) and 17.3% (28/162), with the rates of early major complications as follows: low cardiac output syndrome, 5.6% (9/162); early stroke, 6.8% (11/162); new-onset dialysis, 6.2% (10/162); prolonged ventilation, 15.4% (25/162); and postoperative bleeding requiring exploration, 7.4% (12/162). In the STERN group, the early mortality was 11.0% (24/218), whereas the risk of low cardiac output syndrome, early stroke, new-onset dialysis, prolonged ventilation, and postoperative bleeding was 12.4% (27/218), 14.2% (31/218), 17.0% (37/218), 33.0% (72/218), and 10.1% (22/218), respectively. The duration of intensive care unit and hospital stay was 2.0 [range 1.0, 3.0] and 8.0 [6.0, 13.0], respectively, in the MINI group and 3.0 [2.0, 7.0] and 14.0 [8.0, 29.0], respectively, in the STERN group.

CONCLUSIONS
Mini-thoracotomy may be a viable alternative to conventional sternotomy for redo MV surgery.
A multi-scale/multi-physics model for the theoretical study of the vascular configuration of retinal capillary plexuses based on OCTA data
Authors: Chiaravalli Greta , Guidoboni Giovanna , Sacco Riccardo , Radell Jake , Harris Alon 
Published: November 2021

Abstract
The retinal tissue is highly metabolically active and is responsible for translating the visual stimuli into electrical signals to be delivered to the brain. A complex vascular structure ensures an adequate supply of blood and oxygen, which is essential for the function and survival of the retinal tissue. To date, a complete understanding of the configuration of the retinal vascular structures is still lacking. Optical coherence tomography angiography has made available a huge amount of imaging data regarding the main retinal capillary plexuses, namely the superficial capillary plexuses (SCP), intermediate capillary plexuses (ICP) and deep capillary plexuses (DCP). However, the interpretation of these data is still controversial. In particular, the question of whether the three capillary plexuses are connected in series or in parallel remains a matter of debate. In this work, we address this question by utilizing a multi-scale/multi-physics mathematical model to quantify the impact of the two hypothesized vascular configurations on retinal hemodynamics and oxygenation. The response to central retinal vein occlusion (CRVO) and intraocular pressure (IOP) elevation is also simulated depending on whether the capillary plexuses are connected in series or in parallel. The simulation results show the following: (i) in the in series configuration, the plexuses exhibit a differential response, with DCP and ICP experiencing larger pressure drops than SCP; and (ii) in the in parallel configuration, the blood flow redistributes uniformly in the three plexuses. The different vascular configurations show different responses also in terms of oxygen profiles: (i) in the in series configuration, the outer nuclear layer, outer plexiform layer and inner nuclear layer (INL) are those most affected by CRVO and IOP elevation; and (ii) in the in parallel configuration the INL and ganglion cell layer are those most affected. The in series results are consistent with studies on paracentral acute middle maculopathy, secondary to CRVO and with studies on IOP elevation, in which DCP and ICP and the retinal tissues surrounding them are those most affected by ischemia. These findings seem to suggest that the in series configuration better describes the physiology of the vascular retinal capillary network in health and disease.
A consistent quasi–second-order staggered scheme for the two-dimensional shallow water equations
Authors: Herbin Raphaèle , Latché Jean-Claude , Nasseri Youssouf , Therme Nicolas 
Published: November 2021

Abstract
A quasi–second-order scheme is developed to obtain approximate solutions of the two-dimensional shallow water equations (SWEs) with bathymetry. The scheme is based on a staggered finite volume space discretization: the scalar unknowns are located in the discretization cells while the vector unknowns are located on the edges of the mesh. A monotonic upwind-central scheme for conservation laws (MUSCL)-like interpolation for the discrete convection operators in the water height and momentum balance equations is performed in order to improve the accuracy of the scheme. The time discretization is performed either by a first-order segregated forward Euler scheme or by the second-order Heun scheme. Both schemes are shown to preserve the water height positivity under a Courants Friedrichs Lewy (CFL) condition and an important state equilibrium known as the lake at rest. Using some recent Lax–Wendroff type results for staggered grids, these schemes are shown to be LW-consistent with the weak formulation of the continuous equations, in the sense that if a sequence of approximate solutions is bounded and strongly converges to a limit, then this limit is a weak solution of the SWEs; besides, the forward Euler scheme is shown to be LW-consistent with a weak entropy inequality. Numerical results confirm the efficiency and accuracy of the schemes.
A New Family of Exceptional Rational Functions
Authors: Ding Zhiguo , Zieve Michael E 
Published: November 2021

AbstractFor each odd prime power $q$, we construct an infinite sequence of rational functions $f(X) \in{\mathbb{F}}_q(X)$, each of which is exceptional in the sense that for infinitely many $n$ the map $c \mapsto f(c)$ induces a bijection of ${\mathbb{P}}^1({\mathbb{F}}_{q^n})$. Moreover, each of our functions $f(X)$ is indecomposable in the sense that it cannot be written as the composition of lower-degree rational functions in ${\mathbb{F}}_q(X)$. These are the first known examples of wildly ramified indecomposable exceptional rational functions $f(X)$, other than linear changes of polynomials. In case $q$ is not a power of $3$, these are also the first known examples of indecomposable exceptional rational functions $f(X)$ over ${\mathbb{F}}_q$ which have non-solvable monodromy groups and have arbitrarily large degree.
Polarizations of Abelian Varieties Over Finite Fields via Canonical Liftings
Authors: Bergström Jonas , Karemaker Valentijn , Marseglia Stefano 
Published: November 2021

AbstractWe describe all polarizations for all abelian varieties over a finite field in a fixed isogeny class corresponding to a squarefree Weil polynomial, when one variety in the isogeny class admits a canonical lifting to characteristic zero, that is, a lifting for which the reduction morphism induces an isomorphism of endomorphism rings. Categorical equivalences between abelian varieties over finite fields and fractional ideals in étale algebras enable us to explicitly compute isomorphism classes of polarized abelian varieties satisfying some mild conditions. We also implement algorithms to perform these computations.
Complex Valued Analytic Torsion and Dynamical Zeta Function on Locally Symmetric Spaces
Authors: Shen Shu 
Published: November 2021

AbstractWe show that the Ruelle dynamical zeta function on a closed odd dimensional locally symmetric space twisted by an arbitrary flat vector bundle has a meromorphic extension to the whole complex plane and that its leading term in the Laurent series at the zero point is related to the regularised determinant of the flat Laplacian of Cappell–Miller. When the flat vector bundle is close to an acyclic and unitary one, we show that the dynamical zeta function is regular at the zero point and that its value is equal to the complex valued analytic torsion of Cappell–Miller. This generalises the author’s previous results for unitarily flat vector bundles as well as Müller and Spilioti’s results on hyperbolic manifolds.
Oral Vaccination Protects Against Severe Acute Respiratory Syndrome Coronavirus 2 in a Syrian Hamster Challenge Model
Authors: Johnson Susan , Martinez Clarissa I , Tedjakusuma Sarah N , Peinovich Nadine , Dora Emery G , Birch Sharla M , Kajon Adriana E , Werts Adam D , Tucker Sean N 
Published: November 2021

AbstractBackgroundVaccines that are shelf stable and easy to administer are crucial to improve vaccine access and reduce severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission around the world.MethodsIn this study, we demonstrate that an oral, adenovirus-based vaccine candidate protects against SARS-CoV-2 in a Syrian hamster challenge model.ResultsHamsters administered 2 doses of VXA-CoV2-1 showed a reduction in weight loss and lung pathology and had completely eliminated infectious virus 5 days postchallenge. Oral immunization induced antispike immunoglobulin G, and neutralizing antibodies were induced upon oral immunization with the sera, demonstrating neutralizing activity.ConclusionsOverall, these data demonstrate the ability of oral vaccine candidate VXA-CoV2-1 to provide protection against SARS-CoV-2 disease.
Qur’anic Literacy as Women’s Empowerment: Cultivating Interpretive Authority at the Women’s Mosque of America
Authors: Ali Tazeen M 
Published: November 2021

AbstractThis study shows how the Women’s Mosque of America, an emergent women-only mosque in Los Angeles, is a useful locus to engage contemporary global debates about Islamic authority. In these debates, scholars of religion have not yet attended to the recent appearance of women-led mosques in the West, thereby overlooking American Muslim women as legitimate mediators of the Islamic tradition. This article takes seriously American Muslim women’s interventions in authority and analyzes the Women’s Mosque of America as a discursive space that arises from the genre of American Muslim feminist exegesis, which treats the Qur’an as an essentially gender-egalitarian text. Using a lived religions approach, I draw on a close reading of its inaugural sermon and ethnographic interviews with congregants to argue that the Women’s Mosque of America challenges hegemonic understandings of Islamic authority by advocating for English translations of the Qur’an and lay Muslims’ right to interpret scripture.
In vitro activity of a novel aminomethylcycline antibacterial (KBP-7072), a third-generation tetracycline, against clinical isolates with molecularly characterized tetracycline resistance mechanisms
Authors: Pfaller Michael A , Li Li , Liu Qingmei , Zhang Jay , Huband Michael D , Lindley Jill M , Mendes Rodrigo E 
Published: November 2021

Abstract

Objectives
This study evaluated the in vitro activity of KBP-7072 against 413 contemporary surveillance isolates, including subsets with known tetracycline resistance genes.

Materials
In total, 105 Klebsiella pneumoniae (51 tetracycline resistant), 103 Escherichia coli (52 tetracycline resistant), 103 Staphylococcus aureus (51 tetracycline resistant) and 102 Streptococcus pneumoniae (51 tetracycline resistant) isolates were included. These isolates were tested by broth microdilution using fresh media. CLSI/EUCAST breakpoints were applied, except for tigecycline and omadacycline, which used FDA criteria.

Results
KBP-7072 (MIC50, 0.06 mg/L), tigecycline (MIC50, 0.12 and 0.25 mg/L) and omadacycline (MIC50, 0.12 and 0.5 mg/L) showed similar MIC50s for tetracycline-susceptible and -resistant S. aureus. Other tetracycline comparators had their MIC50 increased 64- to 256-fold by tet. For S. pneumoniae, KBP-7072 (MIC50/90, ≤0.015/0.03 mg/L) showed the lowest MICs, which remained unchanged for tetracycline-susceptible or -resistant isolates [mostly tet(M)]. Similar MICs were observed for omadacycline (MIC50/90, 0.03–0.06/0.06 mg/L) and tigecycline (MIC50/90, 0.03/0.03 mg/L) in the S. pneumoniae population. Tetracycline-susceptible and -resistant E. coli [94.2% tet(A)/tet(B)], KBP-7072 (MIC90, 0.25 and 1 mg/L, respectively) and tigecycline (MIC90, 0.25 and 0.5 mg/L) showed similar MIC90s. KBP-7072 (MIC50/90, 0.25/0.5 mg/L) and tigecycline (MIC50/90, 0.5/0.5 mg/L) had the lowest MIC for tetracycline-susceptible K. pneumoniae. The MIC for KBP-7072 (MIC50/90, 1/4 mg/L) and tigecycline (MIC50/90, 1/2 mg/L) increased 2- to 8-fold for tetracycline-resistant K. pneumoniae, which mostly produced Tet(A).

Conclusions
KBP-7072 activity was minimally affected by the presence of acquired tetracycline genes.