bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-quality de novo assembly of the Eucommia ulmoides haploid genome provides new insights into evolution and rubber biosynthesis
Authors: Li Yun , Wei Hairong , Yang Jun , Du Kang , Li Jiang , Zhang Ying , Qiu Tong , Liu Zhao , Ren Yongyu , Song Lianjun , Kang Xiangyang 
Published: November 2020

AbstractWe report the acquisition of a high-quality haploid chromosome-scale genome assembly for the first time in a tree species,Eucommia ulmoides, which is known for its rubber biosynthesis and medicinal applications. The assembly was obtained by applying PacBio and Hi–C technologies to a haploid that we specifically generated. Compared to the initial genome release, this one has significantly improved assembly quality. The scaffold N50 (53.15 MB) increased 28-fold, and the repetitive sequence content (520 Mb) increased by 158.24 Mb, whereas the number of gaps decreased from 104,772 to 128. A total of 92.87% of the 26,001 predicted protein-coding genes identified with multiple strategies were anchored to the 17 chromosomes. A new whole-genome duplication event was superimposed on the earlier γ paleohexaploidization event, and the expansion of long terminal repeats contributed greatly to the evolution of the genome. The more primitive rubber biosynthesis of this species, as opposed to that inHevea brasiliensis, relies on the methylerythritol-phosphate pathway rather than the mevalonate pathway to synthesize isoprenyl diphosphate, as the MEP pathway operates predominantly intrans-polyisoprene-containing leaves and central peels. Chlorogenic acid biosynthesis pathway enzymes were preferentially expressed in leaves rather than in bark. This assembly with higher sequence contiguity can foster not only studies on genome structure and evolution, gene mapping, epigenetic analysis and functional genomics but also efforts to improveE. ulmoidesfor industrial and medical uses through genetic engineering.
Small-scale alpine topography at low latitudes and high altitudes: refuge areas of the genus Chrysanthemum and its allies
Authors: Chen Xi , Wang Haibin , Yang Xiaodong , Jiang Jiafu , Ren Guopeng , Wang Zijuan , Dong Xiaodong , Chen Fadi 
Published: November 2020

AbstractCultivated chrysanthemum (Chrysanthemum morifoliumRamat.) is an economically important ornamental plant species grown worldwide. However, the origin of the genusChrysanthemumremains unclear. This study was conducted in the Hengduan Mountains, Yunnan Province. We took advantage of a special geographic region where the southernmost species ofAjaniaand the highest altitude population ofChrysanthemum indicumcoexist to investigate their evolutionary origins. Diversity analysis of 9 populations of 5 species that came from 3 genera was carried out based on morphological traits and SRAP markers. Furthermore, topographical and ecological analyses and surveys of the vegetation communities in the plots were carried out for correlation analysis, and past data were used to reconstruct the ancient topography and vegetation to estimate the migration path and divergence time. We found thatChrysanthemumandAjaniawere closely related based on the smooth transition states among marginal female florets and their common pollination system. The genetic relationship betweenPhaeostigmaandChrysanthemumwas relatively distant, andAjaniawas between them. Low light intensity and relatively humid habitats may be driving the elongation and evolution of marginal female florets. We found thatChrysanthemumand related genera were largely restricted to stony topographies at an altitude of ~3000 m.a.s.l. and in specialized alpine coniferous (Pinus) and broad-leaved (Quercus) mixed forest marginal communities. These stony topographies have become ecological islands of refuge for these species in the current interglacial period. The Hengduan Mountains play a key role in the evolution, divergence, and survival ofChrysanthemumand its allies.
The apple REFPOP—a reference population for genomics-assisted breeding in apple
Authors: Jung Michaela , Roth Morgane , Aranzana Maria José , Auwerkerken Annemarie , Bink Marco , Denancé Caroline , Dujak Christian , Durel Charles-Eric , Font i Forcada Carolina , Cantin Celia M. , Guerra Walter , Howard Nicholas P. , Keller Beat , Lewandowski Mariusz , Ordidge Matthew , Rymenants Marijn , Sanin Nadia , Studer Bruno , Zurawicz Edward , Laurens François , Patocchi Andrea , Muranty Hélène 
Published: November 2020

AbstractBreeding of apple is a long-term and costly process due to the time and space requirements for screening selection candidates. Genomics-assisted breeding utilizes genomic and phenotypic information to increase the selection efficiency in breeding programs, and measurements of phenotypes in different environments can facilitate the application of the approach under various climatic conditions. Here we present an apple reference population: the apple REFPOP, a large collection formed of 534 genotypes planted in six European countries, as a unique tool to accelerate apple breeding. The population consisted of 269 accessions and 265 progeny from 27 parental combinations, representing the diversity in cultivated apple and current European breeding material, respectively. A high-density genome-wide dataset of 303,239 SNPs was produced as a combined output of two SNP arrays of different densities using marker imputation with an imputation accuracy of 0.95. Based on the genotypic data, linkage disequilibrium was low and population structure was weak. Two well-studied phenological traits of horticultural importance were measured. We found marker–trait associations in several previously identified genomic regions and maximum predictive abilities of 0.57 and 0.75 for floral emergence and harvest date, respectively. With decreasing SNP density, the detection of significant marker–trait associations varied depending on trait architecture. Regardless of the trait, 10,000 SNPs sufficed to maximize genomic prediction ability. We confirm the suitability of the apple REFPOP design for genomics-assisted breeding, especially for breeding programs using related germplasm, and emphasize the advantages of a coordinated and multinational effort for customizing apple breeding methods in the genomics era.
Accumulation of mutations in genes associated with sexual reproduction contributed to the domestication of a vegetatively propagated staple crop, enset
Authors: Tesfamicael Kiflu Gebramicael , Gebre Endale , March Timothy J. , Sznajder Beata , Mather Diane E. , Rodríguez López Carlos Marcelino 
Published: November 2020

AbstractEnset (Ensete ventricosum(Welw.) Cheesman) is a drought tolerant, vegetatively propagated crop that was domesticated in Ethiopia. It is a staple food for more than 20 million people in Ethiopia. Despite its current importance and immense potential, enset is among the most genetically understudied and underexploited food crops. We collected 230 enset wild and cultivated accessions across the main enset producing regions in Ethiopia and applied amplified fragment length polymorphism (AFLP) and genotype by sequencing (GBS) analyses to these accessions. Wild and cultivated accessions were clearly separated from each other, with 89 genes found to harbour SNPs that separated wild from cultivated accessions. Among these, 17 genes are thought to be involved in flower initiation and seed development. Among cultivated accessions, differentiation was mostly associated with geographical location and with proximity to wild populations. Our results indicate that vegetative propagation of elite clones has favoured capacity for vegetative growth at the expense of capacity for sexual reproduction. This is consistent with previous reports that cultivated enset tends to produce non-viable seeds and flowers less frequently than wild enset.
Perception of unrelated microbe-associated molecular patterns triggers conserved yet variable physiological and transcriptional changes in Brassica rapa ssp. pekinensis
Authors: Kim Wanhui , Prokchorchik Maxim , Tian Yonghua , Kim Seulgi , Jeon Hyelim , Segonzac Cécile 
Published: November 2020

Abstract
Pattern-triggered immunity (PTI) includes the different transcriptional and physiological responses that enable plants to ward off microbial invasion. Surface-localized pattern-recognition receptors (PRRs) recognize conserved microbe-associated molecular patterns (MAMPs) and initiate a branched signaling cascade that culminate in an effective restriction of pathogen growth. In the model species Arabidopsis thaliana, early PTI events triggered by different PRRs are broadly conserved although their nature or intensity is dependent on the origin and features of the detected MAMP. In order to provide a functional basis for disease resistance in leafy vegetable crops, we surveyed the conservation of PTI events in Brassica rapa ssp. pekinensis. We identified the PRR homologs present in B. rapa genome and found that only one of the two copies of the bacterial Elongation factor-Tu receptor (EFR) might function. We also characterized the extent and unexpected specificity of the transcriptional changes occurring when B. rapa seedlings are treated with two unrelated MAMPs, the bacterial flagellin flg22 peptide and the fungal cell wall component chitin. Finally, using a MAMP-induced protection assay, we could show that bacterial and fungal MAMPs elicit a robust immunity in B. rapa, despite significant differences in the kinetic and amplitude of the early signaling events. Our data support the relevance of PTI for crop protection and highlight specific functional target for disease resistance breeding in Brassica crops.
Extracellular Histones Inhibit Fibrinolysis through Noncovalent and Covalent Interactions with Fibrin
Authors: Locke Matthew , Longstaff Colin 
Published: November 2020

AbstractHistones released into circulation as neutrophil extracellular traps are causally implicated in the pathogenesis of arterial, venous, and microvascular thrombosis by promoting coagulation and enhancing clot stability. Histones induce structural changes in fibrin rendering it stronger and resistant to fibrinolysis. The current study extends these observations by defining the antifibrinolytic mechanisms of histones in purified, plasma, and whole blood systems. Although histones stimulated plasminogen activation in solution, they inhibited plasmin as competitive substrates. Protection of fibrin from plasmin digestion is enhanced by covalent incorporation of histones into fibrin, catalyzed by activated transglutaminase, coagulation factor FXIII (FXIIIa). All histone subtypes (H1, H2A, H2B, H3, and H4) were crosslinked to fibrin. A distinct, noncovalent mechanism explains histone-accelerated lateral aggregation of fibrin protofibrils, resulting in thicker fibers with higher mass-to-length ratios and in turn hampered fibrinolysis. However, histones were less effective at delaying fibrinolysis in the absence of FXIIIa activity. Therapeutic doses of low-molecular-weight heparin (LMWH) prevented covalent but not noncovalent histone–fibrin interactions and neutralized the effects of histones on fibrinolysis. This suggests an additional antithrombotic mechanism for LMWH beyond anticoagulation. In conclusion, for the first time we report that histones are crosslinked to fibrin by FXIIIa and promote fibrinolytic resistance which can be overcome by FXIIIa inhibitors and histone-binding heparinoids. These findings provide a rationale for targeting the FXIII–histone–fibrin axis to destabilize fibrin and prevent potentially thrombotic fibrin networks.
Management of a Case of Aortic Valve Replacement with Left Ventricle Clot Removal Developing Acute Kidney Injury in Postoperative Period
Authors: Aggarwal Naresh Kumar , Bhoi Sushanta 
Published: November 2020

AbstractCardiac surgery associated-acute kidney injury (AKI) is a common and a serious complication of cardiac surgery requiring cardiopulmonary bypass and it is the second most common cause of AKI in intensive care unit. Recently, two consensus conferences have suggested new diagnostic criteria to define AKI and risk score to better identify patients who will develop AKI after cardiac surgery. In fact, prompt recognition of high-risk patients could allow a more aggressive management at a reversible stage of an incoming ARF. In this case report, we have discussed a case of 21-year-old patient with bicuspid aortic valve with severe aortic stenosis with ejection fraction 15% and left ventricle (LV) clot undergoing surgery for aortic valve replacement with LV clot removal. In the postoperative period, he developed AKI that was managed successfully by early intervention by slow low efficiency dialysis and diafiltration and hemodialysis and patient discharged successfully from hospital.
Enhanced Context Sensitive Flash Codes
Authors: Baruch Gilad , Klein Shmuel T , Shapira Dana 
Published: November 2020

Abstract
A major property of flash memory is that a 0-bit can be changed into a 1-bit, but the symmetric task of switching from a 1-bit to a zero may only be performed in blocks and is therefore often prohibited. This led to the development of rewriting codes using the same storage space more than once, subject to the constraint that 0-bits can be changed into 1-bits, but not vice versa. Context sensitive rewriting codes extend this idea by also incorporating information gathered from surrounding bits. Several new context sensitive rewriting codes are presented and analyzed, some of which are better than the state of the art for sparse input. Empirical simulations show a good match with the theoretical results.
The Effects of Temperature and Host Stage on Development Rate of Parasitoids of Giant WhiteflyAleurodicus dugesii(Hemiptera: Aleyrodidae)
Authors: Schoeller Erich N , Redak Richard A 
Published: November 2020

AbstractThe effects of rearing temperature and host stage parasitized on the development of three parasitoid species; Encarsia noyesi Hayat (Hymenoptera: Aphelinidae), Idioporus affinis LaSalle & Polaszek (Hymenoptera: Pteromalidae), and Entedononecremnus krauteri Zolnerowich & Rose (Hymenoptera: Eulophidae) were investigated. These parasitoids are part of the biological control program for the giant whitefly Aleurodicus dugesii Cockerell (Hemiptera: Aleyrodidae) in the United States. Temperature and host-dependent development was assessed for each species using the nonlinear Brière-1 model and simple linear regression to obtain critical thermal parameters. All three parasitoids successfully developed at constant temperatures ranging from 15°C to 30°C, which was narrower to their predicted thermal limits due to thermal constraints of A. dugesii. There were significant effects of both temperature and A. dugesii nymphal stage parasitized on immature parasitoid development times. All three parasitoid species’ development time decreased as nymphal stage age increased. Thermal tolerance limits and development times varied by parasitoid species. The results of these findings in the context of biological control potential are discussed.
Prior reconstruction of an isolated left vertebral artery for Stanford type A aortic dissection
Authors: Zuo Yi , Zhou Zheng-Chun , Ge Jian-Jun 
Published: November 2020

Abstract
Although isolated left vertebral artery is a supra-aortic trunk variant, it is not so rare. It may pose additional difficulties during total arch replacement surgeries. The aim of this study was to present our experience with prior reconstruction of isolated left vertebral artery by isolated left vertebral artery–left common carotid artery during total arch replacement combined with stented elephant trunk implantation.
Stable super-resolution of images: theoretical study
Authors: Eftekhari Armin , Bendory Tamir , Tang Gongguo 
Published: November 2020

Abstract
We study the ubiquitous super-resolution problem, in which one aims at localizing positive point sources in an image, blurred by the point spread function of the imaging device. To recover the point sources, we propose to solve a convex feasibility program, which simply finds a non-negative Borel measure that agrees with the observations collected by the imaging device. In the absence of imaging noise, we show that solving this convex program uniquely retrieves the point sources, provided that the imaging device collects enough observations. This result holds true if the point spread function of the imaging device can be decomposed into horizontal and vertical components and if the translations of these components form a Chebyshev system, i.e., a system of continuous functions that loosely behave like algebraic polynomials. Building upon the recent results for one-dimensional signals, we prove that this super-resolution algorithm is stable, in the generalized Wasserstein metric, to model mismatch (i.e., when the image is not sparse) and to additive imaging noise. In particular, the recovery error depends on the noise level and how well the image can be approximated with well-separated point sources. As an example, we verify these claims for the important case of a Gaussian point spread function. The proofs rely on the construction of novel interpolating polynomials—which are the main technical contribution of this paper—and partially resolve the question raised in Schiebinger et al. (2017, Inf. Inference, 7, 1–30) about the extension of the standard machinery to higher dimensions.
Super platforms, big data, and competition law: the Japanese approach in contrast with the USA and EU
Authors: Takigawa Toshiaki 
Published: November 2020

ABSTRACT
This article examines antitrust issues concerning digital platforms equipped with big data. Recent initiatives by the Japanese competition agency are highlighted, comparing them with those by the USA and EU competition authorities. First examined is whether competition among platforms would result in a select few super platforms with market power, concluding that AI with machine learning has augmented the power of super platforms with strong AI-capability, leading to increased importance of merger control over acquisitions by platforms. Next scrutinized is the argument for utility-regulation to be imposed on super platforms, concluding that wide support is limited to data portability, leaving competition law as the key tool for addressing super platforms, its core tool being the provision against exclusionary conduct, enforcement of which, initially, concerns whether to order super platforms to render their data accessible to their rivals. Passive refusal-to-share data needs to be scrutinized under the essential facility doctrine. Beyond passive refusal, platforms’ exclusionary conduct requires competition agencies to weigh the conduct’s exclusionary effects against its efficiency effects. Finally addressed is exploitative abuse, explaining its relation to consumer protection, concluding that competition law enforcement on exploitative abuse should be minimized, since it accompanies risk of over-enforcement.
Measuring What Matters: How the Laboratory Contributes Value in the Opioid Crisis
Authors: Warrington Jill S , Swanson Kathleen , Dodd Monique , Lo Sheng-Ying , Haghamad Aya , Duque Teofilo Borunda , Cook Bernard 
Published: November 2020

Abstract
With over 20 years of the opioid crisis, our collective response has evolved to address the ongoing needs related to the management of opioid use and opioid use disorder. There has been an increasing recognition of the need for standardized metrics to evaluate organizational management and stewardship. The clinical laboratory, with a wealth of objective and quantitative health information, is uniquely poised to support opioid stewardship and drive valuable metrics for opioid prescribing practices and opioid use disorder (OUD) management.
To identify laboratory-related insights that support these patient populations, a collection of 5 independent institutions, under the umbrella of the Clinical Laboratory 2.0 movement, developed and prioritized metrics. Using a structured expert panel review, laboratory experts from 5 institutions assessed possible metrics as to their relative importance, usability, feasibility, and scientific acceptability based on the National Quality Forum criteria.
A total of 37 metrics spanning the topics of pain and substance use disorder (SUD) management were developed with consideration of how laboratory insights can impact clinical care. Monitoring these metrics, in the form of summative reports, dashboards, or embedded in laboratory reports themselves may support the clinical care teams and health systems in addressing the opioid crisis. The clinical insights and standardized metrics derived from the clinical laboratory during the opioid crisis exemplifies the value proposition of clinical laboratories shifting into a more active role in the healthcare system. This increased participation by the clinical laboratories may improve patient safety and reduce healthcare costs related to OUD and pain management.
Retroperitoneal leiomyoma of gynecologic type: a case report and review of the litterature
Authors: Sabrine Derqaoui , Hafsa Elouazzani , Omar Mkira , Jahid Ahmed , Znati Kaoutar , Zakia Bernoussi , Zouaidia Fouad 
Published: November 2020

Abstract
Retroperitoneal leiomyomas are rare benign tumors with smooth muscle differentiation, with only ~1001 cases reported in the English literature to date. Because of its scarcity and non-specific presentation, the preoperative diagnosis might be challenging. On histology, these neoplasms share the same macroscopic, morphological and phenotypic features with uterine leiomyoma; thus, they are referred to as leiomyoma of gynecologic type. Herein, we describe a case of a voluminous retroperitoneal leiomyoma in a 51-year-old woman with a history of total hysterectomy to raise awareness about this condition, as its differential diagnosis might be challenging.
Reactive oxygen species coordinate the transcriptional responses to iron availability in Arabidopsis
Authors: von der Mark Claudia , Ivanov Rumen , Eutebach Monique , Maurino Veronica G , Bauer Petra , Brumbarova Tzvetina 
Published: November 2020

Abstract
Reactive oxygen species play a central role in the regulation of plant responses to environmental stress. Under prolonged iron (Fe) deficiency, increased levels of hydrogen peroxide (H2O2) initiate signaling events, resulting in the attenuation of Fe acquisition through the inhibition of FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (FIT). As this H2O2 increase occurs in a FIT-dependent manner, our aim was to understand the processes involved in maintaining H2O2 levels under prolonged Fe deficiency and the role of FIT. We identified the CAT2 gene, encoding one of the three Arabidopsis catalase isoforms, as regulated by FIT. CAT2 loss-of-function plants displayed severe susceptibility to Fe deficiency and greatly increased H2O2 levels in roots. Analysis of the Fe homeostasis transcription cascade revealed that H2O2 influences the gene expression of downstream regulators FIT, BHLH genes of group Ib, and POPEYE (PYE); however, H2O2 did not affect their upstream regulators, such as BHLH104 and ILR3. Our data shows that FIT and CAT2 participate in a regulatory loop between H2O2 and prolonged Fe deficiency.