bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gynoecy instability in cucumber (Cucumis sativus L.) is due to unequal crossover at the copy number variation-dependent Femaleness (F) locus
Authors: Li Zheng , Han Yonghua , Niu Huanhuan , Wang Yuhui , Jiang Biao , Weng Yiqun 
Published: March 2020

AbstractCucumber,Cucumis sativusis an important vegetable crop, and gynoecy has played a critical role in yield increase of hybrid cucumber production. Cucumber has a unique genetic system for gynoecious sex expression, which is determined by the copy number variation (CNV)-based, dominant, and dosage-dependentfemaleness(F) locus. However, this gynoecy expression system seems unstable since monecious plants could often be found inF-dependent gynoecious cucumber inbreds. We hypothesized that gynoecy instability (gynoecy loss) may be due to unequal crossing over (UCO) during meiosis among repeat units of the CNV. In this study, using high throughput genome resequencing, fiber-FISH and genomic qPCR analyses, we first confirmed and refined the structure of theFlocus, which was a CNV of a 30.2-kb tandem repeat. Gynoecious plants contained three genes:CsACS1,CsACS1G, andCsMYB, of whichCsACS1Gis a duplication ofCsACS1but with a recombinant distal promoter that may contribute to gynoecy sex expression. In two large populations from self-pollinated gynoecious inbred lines, ‘gynoecy loss’ mutants were identified with similar mutation rates (~0.12%). We show that these monecious mutants have lostCsACS1G. In addition, we identified gynoecious lines in natural populations that carry two copies ofCSACS1G. We proposed a model to explain gynoecy instability inF-dependent cucumbers, which is caused by UCO amongCSACS1/Gunits during meiosis. The findings present a convincing case that the phenotypic variation of an economically important trait is associated with the dynamic changes of copy numbers at theFlocus. This work also has important implications in cucumber breeding.
A roadmap for research in octoploid strawberry
Authors: Whitaker Vance M. , Knapp Steven J. , Hardigan Michael A. , Edger Patrick P. , Slovin Janet P. , Bassil Nahla V. , Hytönen Timo , Mackenzie Kathryn K. , Lee Seonghee , Jung Sook , Main Dorrie , Barbey Christopher R. , Verma Sujeet 
Published: March 2020

AbstractThe cultivated strawberry (Fragaria × ananassa) is an allo-octoploid species, originating nearly 300 years ago from wild progenitors from the Americas. Since that time the strawberry has become the most widely cultivated fruit crop in the world, universally appealing due to its sensory qualities and health benefits. The recent publication of the first high-quality chromosome-scale octoploid strawberry genome (cv. Camarosa) is enabling rapid advances in genetics, stimulating scientific debate and provoking new research questions. In this forward-looking review we propose avenues of research toward new biological insights and applications to agriculture. Among these are the origins of the genome, characterization of genetic variants, and big data approaches to breeding. Key areas of research in molecular biology will include the control of flowering, fruit development, fruit quality, and plant–pathogen interactions. In order to realize this potential as a global community, investments in genome resources must be continually augmented.
PyWRKY26 and PybHLH3 cotargeted the PyMYB114 promoter to regulate anthocyanin biosynthesis and transport in red-skinned pears
Authors: Li Chuang , Wu Jun , Hu Kang-Di , Wei Shu-Wei , Sun Hong-Ye , Hu Lan-Ying , Han Zhuo , Yao Gai-Fang , Zhang Hua 
Published: March 2020

AbstractRed pear is favored because of its bright appearance and abundant anthocyanins. Anthocyanin biosynthesis is controlled by transcription factors (TFs) forming regulatory complexes. In red-skinned pears, the WRKY TFs have a significant relationship with anthocyanin biosynthesis, but the molecular mechanism of the WRKY TFs involved in regulating color formation in red-skinned pear is unclear. In this study, the TFs PyWRKY31 and PyWRKY26 were screened as candidate genes for controlling anthocyanin biosynthesis by transcriptome data and bioinformatics analysis. The effect of anthocyanin accumulations after cotransformation of PyWRKY31 or PyWRKY26 with its partners PyMYB10, PyMYB114, and PybHLH3 was verified in tobacco leaves and strawberry receptacles by a transient expression system. RT-qPCR analysis and a dual-luciferase reporter system further confirmed that this cotransformation activated the expression of PyDFR, PyANS, and PyUFGT in anthocyanin biosynthesis and PyGST in anthocyanin transport instead of the PyABC transporter and PyAVP. Furthermore, the cotransformed PyWRKY26 and PybHLH3 could bind to the PyMYB114 promoter, and PyWRKY26 directly activated the transcription of PyMYB114. In addition, the TF PyWRKY26 could interact with PybHLH3, as confirmed by firefly luciferase complementation and yeast two-hybrid (Y2H) assays. These results showed that the interaction of PyWRKY26 and PybHLH3 could cotarget the PyMYB114 promoter, which resulted in anthocyanin accumulation in red-skinned pear. This study further strengthened the understanding of the regulatory mechanism of anthocyanin accumulation and contributed to improving the appearance of red-skinned pears.
Portal of Juglandaceae: A comprehensive platform for Juglandaceae study
Authors: Guo Wenlei , Chen Junhao , Li Jian , Huang Jianqin , Wang Zhengjia , Lim Kean-Jin 
Published: March 2020

AbstractJuglandaceae species are plants of great economic value and have been cultivated, domesticated, and utilized by human society for a long time. Their edible, nutrient-rich nuts and tough, durable wood have attracted the attention of botanists and breeders. With the advent of the genomics era, genome sequencing of the Juglandaceae family has been greatly accelerated, and a large amount of data has been generated. In this paper, we introduce the Portal of Juglandaceae (PJU), a tool to bring all these data together. The PJU contains genomes, gene-coding sequences, protein sequences, various types of annotation information, expression data, and miRNA data, which are configured with BLAST, JBrowse, and our self-developed synteny analysis tool. The PJU has a user-friendly and straightforward interface that performs a variety of query tasks with a few simple operations. In the future, we hope that the PJU will serve as a hub for the study of the Juglandaceae family.
An update on the arsenal: mining resistance genes for disease management of Brassica crops in the genomic era
Authors: Lv Honghao , Fang Zhiyuan , Yang Limei , Zhang Yangyong , Wang Yong 
Published: March 2020

AbstractBrassicaspecies include many economically important crops that provide nutrition and health-promoting substances to humans worldwide. However, as with all crops, their production is constantly threatened by emerging viral, bacterial, and fungal diseases, whose incidence has increased in recent years. Traditional methods of control are often costly, present limited effectiveness, and cause environmental damage; instead, the ideal approach is to mine and utilize the resistance genes of theBrassicacrop hosts themselves. Fortunately, the development of genomics, molecular genetics, and biological techniques enables us to rapidly discover and apply resistance (R) genes. Herein, the R genes identified inBrassicacrops are summarized, including their mapping and cloning, possible molecular mechanisms, and application in resistance breeding. Future perspectives concerning how to accurately discover additional R gene resources and efficiently utilize these genes in the genomic era are also discussed.
Perspectives of CRISPR/Cas-mediated cis-engineering in horticulture: unlocking the neglected potential for crop improvement
Authors: Li Qiang , Sapkota Manoj , van der Knaap Esther 
Published: March 2020

AbstractDirected breeding of horticultural crops is essential for increasing yield, nutritional content, and consumer-valued characteristics such as shape and color of the produce. However, limited genetic diversity restricts the amount of crop improvement that can be achieved through conventional breeding approaches. Natural genetic changes in cis-regulatory regions of genes play important roles in shaping phenotypic diversity by altering their expression. Utilization of CRISPR/Cas editing in crop species can accelerate crop improvement through the introduction of genetic variation in a targeted manner. The advent of CRISPR/Cas-mediated cis-regulatory region engineering (cis-engineering) provides a more refined method for modulating gene expression and creating phenotypic diversity to benefit crop improvement. Here, we focus on the current applications of CRISPR/Cas-mediated cis-engineering in horticultural crops. We describe strategies and limitations for its use in crop improvement, including de novo cis-regulatory element (CRE) discovery, precise genome editing, and transgene-free genome editing. In addition, we discuss the challenges and prospects regarding current technologies and achievements. CRISPR/Cas-mediated cis-engineering is a critical tool for generating horticultural crops that are better able to adapt to climate change and providing food for an increasing world population.
Identification of Key Components in Colon Adenocarcinoma Using Transcriptome to Interactome Multilayer Framework
Authors: Pournoor Ehsan , Mousavian Zaynab , Dalini Abbas Nowzari , Masoudi-Nejad Ali 
Published: March 2020

AbstractComplexity of cascading interrelations between molecular cell components at different levels from genome to metabolome ordains a massive difficulty in comprehending biological happenings. However, considering these complications in the systematic modelings will result in realistic and reliable outputs. The multilayer networks approach is a relatively innovative concept that could be applied for multiple omics datasets as an integrative methodology to overcome heterogeneity difficulties. Herein, we employed the multilayer framework to rehabilitate colon adenocarcinoma network by observing co-expression correlations, regulatory relations, and physical binding interactions. Hub nodes in this three-layer network were selected using a heterogeneous random walk with random jump procedure. We exploited local composite modules around the hub nodes having high overlay with cancer-specific pathways, and investigated their genes showing a different expressional pattern in the tumor progression. These genes were examined for survival effects on the patient’s lifespan, and those with significant impacts were selected as potential candidate biomarkers. Results suggest that identified genes indicate noteworthy importance in the carcinogenesis of the colon.
Quasi-Static Pull-in: an Instability in Electrostatic Actuators
Authors: Al-Ghamdi M. S. , Khater M. E. , Abdel-Rahman E. M. , Nepomuceno E. G. 
Published: March 2020

AbstractWe identify a new instability in electrostatic actuators dubbed quasi-static pull-in. We report experimental evidence of the instability and study its characteristics in two types of micro actuators operating in ambient air. We found that the underlying mechanism is a fast-slow dynamic interaction between slowly-varying electrostatic excitation and fast resonator response that instigate large non-resonant oscillatory orbits and eventually disappears in a global Shilnikov bifurcation. Based on these findings, we formulate and present a new taxonomy of pull-in instabilities in electrostatic actuators.
Futile complete recanalization: patients characteristics and its time course
Authors: Kitano Takaya , Todo Kenichi , Yoshimura Shinichi , Uchida Kazutaka , Yamagami Hiroshi , Sakai Nobuyuki , Sakaguchi Manabu , Nakamura Hajime , Kishima Haruhiko , Mochizuki Hideki , Ezura Masayuki , Okada Yasushi , Kitagawa Kazuo , Kimura Kazumi , Sasaki Makoto , Tanahashi Norio , Toyoda Kazunori , Furui Eisuke , Matsumaru Yuji , Minematsu Kazuo , Morimoto Takeshi 
Published: March 2020

AbstractAs the goal of mechanical thrombectomy is shifting toward mTICI-3 rather than mTICI-2b, we sought to clarify the limitation of the effect of mTICI-3. A post-hoc analysis of a registry of large-vessel occlusion stroke from 46 centers was conducted. Among 2,420 registered patients, 725 patients with anterior circulation occlusion who achieved successful reperfusion were analyzed. We compared outcomes between patients with mTICI-3 and mTICI-2b, and investigated how the effect of mTICI-3 changed according to baseline characteristics and time course. The proportion of patients with favorable outcomes (mRS 0–2 at day 90) was higher among patients with mTICI-3 compared to those with mTICI-2b (adjusted OR, 2.10; 95% CI, 1.49–2.97). There was no heterogeneity in the effect of mTICI-3 with respect to age, neurological deficit, alteplase use, occluded vessels, or infarct size. mTICI-3 was associated with favorable outcomes when the puncture-to-reperfusion time was <80 minutes (adjusted OR, 2.28; 95% CI, 1.52–3.41), but not when the puncture-to-reperfusion time was ≥80 minutes. A significant heterogeneity was found in the effect of mTICI-3 reperfusion across the puncture-to-reperfusion time subgroups (P for interaction = 0.025). Until when operators should continue the procedure after mTICI-2b has been achieved, needs to be studied.
A Painless and Time-Saving Modified Technique for Simple Renal Cyst Treatment with Single-session Ethanol Sclerotherapy
Authors: Zhang Hao , Xiong Shi-hua , Jiang Xu-jing , Li Lin , Zhang Ya-yun , Lyu Fa-jin 
Published: March 2020

AbstractPercutaneous puncture ethanol sclerotherapy is a simple, effective, minimally invasive, and inexpensive procedure to manage symptomatic simple renal cysts. We modified specific technical aspects to balance certain potential intraprocedural factors for ensuring minimal procedural pain and duration as well as maximal clinical therapeutic effects and evaluated the safety and efficacy of this modified technique. A total of 84 eligible patients underwent computed tomography-guided single-session ethanol sclerotherapy using the conventional (group A) or modified (group B) technique. In group B, the puncture route was modified from tansparenchymal to direct for reducing renal injury, and preinjection of low-dose intracystic lidocaine was used to control distending pain caused by ethanol injections; therefore, greater ethanol volumes could be injected for improving the resistance and contact of ethanol with the cyst wall, precluding the need for patient repositioning multiple times to decrease procedural duration. Visual analog scale score for pain and procedural time were significantly higher in group A than in group B. The complication rate was slightly higher in group A than in group B, but the success rate was comparable between the two groups. These results suggest that the modified technique is painless, time-saving, and injury-reducing and can thus improve medical care.
Theory of relaxor-ferroelectricity
Authors: Zhang Li-Li , Huang Yi-Neng 
Published: March 2020

AbstractRelaxor-ferroelectrics are fascinating and useful materials, but the mechanism of relaxor-ferroelectricity has been puzzling the scientific community for more than 65 years. Here, a theory of relaxor-ferroelectricity is presented based on 3-dimensional-extended-random-site-Ising-model along with Glauber-dynamics of pseudospins. We propose a new mean-field of pseudospin-strings to solve this kinetic model. The theoretical results show that, with decreasing pseudospin concentration, there are evolutions from normal-ferroelectrics to relaxor-ferroelectrics to paraelectrics, especially indicating by the crossovers from, (a) the sharp to diffuse change at the phase-transition temperature to disappearance in the whole temperature range of order-parameter, and (b) the power-law to Vogel-Fulcher-law to Arrhenius-relation of the average relaxation time. Particularly, the calculated local-order-parameter of the relaxor-ferroelectrics gives the polar-nano-regions appearing far above the diffuse-phase-transition and shows the quasi-fractal characteristic near and below the transition temperature. We also provide a new mechanism of Burns-transformation which stems from not only the polar-nano-regions but also the correlation-function between pseudospins, and put forward a definition of the canonical relaxor-ferroelectrics. The theory accounts for the main facts of relaxor-ferroelectricity, and in addition gives a good quantitative agreement with the experimental results of the order-parameter, specific-heat, high-frequency permittivity, and Burns-transformation of lead magnesium niobate, the canonical relaxor-ferroelectric.
Double-Stranded DNA and NETs Components in Relation to Clinical Outcome After ST-Elevation Myocardial Infarction
Authors: Langseth Miriam Sjåstad , Helseth Ragnhild , Ritschel Vibeke , Hansen Charlotte Holst , Andersen Geir Øystein , Eritsland Jan , Halvorsen Sigrun , Fagerland Morten Wang , Solheim Svein , Arnesen Harald , Seljeflot Ingebjørg , Opstad Trine Baur 
Published: March 2020

AbstractNeutrophil extracellular traps (NETs) have been implicated in atherothrombosis; however, their potential role as markers of risk is unclear. We investigated whether circulating NETs-related components associated with clinical outcome and hypercoagulability in ST-elevation myocardial infarction (STEMI). In this observational cohort study, STEMI patients admitted for PCI (n = 956) were followed for median 4.6 years, recording 190 events (reinfarction, unscheduled revascularization, stroke, heart failure hospitalization, or death). Serum drawn median 18 hours post-PCI was used to quantify double-stranded DNA (dsDNA) and the more specific NETs markers myeloperoxidase-DNA and citrullinated histone 3. Levels of the NETs markers did not differ significantly between groups with/without a primary composite endpoint. However, patients who died (n = 76) had higher dsDNA compared to survivors (p < 0.001). Above-median dsDNA was associated with an increased number of deaths (54 vs. 22, p < 0.001). dsDNA in the upper quartiles (Q) was associated with increased mortality (Q3 vs. Q1 + 2 adjusted HR: 1.89 [95% CI 1.03 to 3.49], p = 0.041 and Q4 vs. Q1 + 2 adjusted HR: 2.28 [95% CI 1.19 to 4.36], p = 0.013). dsDNA was weakly correlated with D-dimer (rs = 0.17, p < 0.001). dsDNA levels associated with increased all-cause mortality, yet weakly with hypercoagulability in STEMI patients. The prognostic significance of potentially NETs-related markers requires further exploration.
Synergy of combined free nitrous acid and Fenton technology in enhancing anaerobic digestion of actual sewage waste activated sludge
Authors: Karimi Razieh , Hallaji Seyed Mostafa , Siami Salar , Torabian Ali , Aminzadeh Behnoush , Eshtiaghi Nicky , Zahedi Soraya 
Published: March 2020

AbstractIn this study, actual swage waste activated sludge in batch reactors was employed to assess the synergistic effect of free nitrous acid and Fenton pre-treatments on enhancing methane production in the anaerobic digestion process. In addition to methane enhancement, the mechanisms driving the enhancement were also investigated via measuring enzymes activity and solubilisation of organic matter. This study revealed that the combined pre-treatments solubilised organic matter significantly more than the bioreactors pre-treated with individual FNA and Fenton. For understanding the influence of pre-treatments on solubilisation of organic matter, soluble protein, soluble polysaccharide and soluble chemical oxygen demand (SCOD) were measured before and after the treatments and it was shown that they respectively increased by 973%, 33% and 353% after the treatments. Protease and cellulase activity, as the key constituents of the microbial community in activated sludge, decreased considerably after the combined pre-treatments 42% and 32% respectively, which resulted in considerable methane enhancement. The results corroborate the synergy of the combined FNA and Fenton pre-treatment in degrading the organic and microbial constituents in waste activated sludge, paving the way for the big-scale implementation of these technologies.
Automatic optic nerve head localization and cup-to-disc ratio detection using state-of-the-art deep-learning architectures
Authors: Park Keunheung , Kim Jinmi , Lee Jiwoong 
Published: March 2020

AbstractComputer vision has greatly advanced recently. Since AlexNet was first introduced, many modified deep learning architectures have been developed and they are still evolving. However, there are few studies comparing these architectures in the field of ophthalmology. This study compared the performance of various state-of-the-art deep-learning architectures for detecting the optic nerve head and vertical cup-to-disc ratio in fundus images. Three different architectures were compared: YOLO V3, ResNet, and DenseNet. We compared various aspects of performance, which were not confined to the accuracy of detection but included, as well, the processing time, diagnostic performance, effect of the graphic processing unit (GPU), and image resolution. In general, as the input image resolution increased, the classification accuracy, localization error, and diagnostic performance all improved, but the optimal architecture differed depending on the resolution. The processing time was significantly accelerated with GPU assistance; even at the high resolution of 832 × 832, it was approximately 170 ms, which was at least 26 times slower without GPU. The choice of architecture may depend on the researcher’s purpose when balancing between speed and accuracy. This study provides a guideline to determine deep learning architecture, optimal image resolution, and the appropriate hardware.
Exploring the origins of crystallisation kinetics in hierarchical materials using in situ X-ray diffraction and pair distribution function analysis
Authors: Potter Matthew E. , Light Mark E. , Irving Daniel J. M. , Oakley Alice E. , Chapman Stephanie , Chater Philip , Cutts Geoff , Watts Andrew , Wharmby Michael , Vandegehuchte Bart D. , Schreiber Moritz W. , Raja Robert 
Published: March 2020

Novel in situ synchrotron total scattering measurements probe the assembly of primary building units into templated hierarchically porous aluminophosphate catalysts, providing unique insights to understanding crystallisation kinetics.
Offline method for experimental identification of load‐dependentsaturation of induction motor taking into account variation of inverse rotortime constant
Authors: Lipcak Ondrej , Bauer Jan 
Published: March 2020

Accurate knowledge of induction machine parameters has a direct impact on theoverall performance of field‐oriented control strategies. In the case of rotorflux oriented control, parameter mismatch causes a discrepancy in the estimatedrotor flux position and amplitude. Magnetising inductance is one of theparameters whose detuning has a direct impact on the setpoints of the controlloops and estimation of hardly or non‐measurable quantities. Conventional ironsaturation, which can be obtained by a standard no‐load test, is not the onlytype of saturation occurring in the machine. Depending on the rotor design, themagnetising inductance and the rotor leakage inductance may also stronglysaturate as a function of load and, thus, rotor current. Based on the authors’previous work, a new, improved experimental method for identifying theload‐dependent saturation of induction motor, which takes into account variationof the inverse rotor time constant, is proposed. Experimental results conductedon 12 kW motor show improved static and dynamic behaviour of the drive comparedto the constant parameter model.