bluuebunny/crossref_metadata_2025_split huggingface dataset:
The transcriptional coactivator CmMBF1c is required for waterlogging tolerance in Chrysanthemum morifolium
Authors: Zhao Nan , Li Chuanwei , Yan Yajun , Wang Haibin , Wang Likai , Jiang Jiafu , Chen Sumei , Chen Fadi 
Published: September 2022

Abstract
Waterlogging is one of the most serious abiotic stressors affecting Chrysanthemum morifolium during its lifespan. However, the molecular mechanisms underlying the waterlogging tolerance of chrysanthemum remain unclear. In this study, we discovered that the transcriptional coactivator MULTIPROTEIN BRIDGING FACTOR 1c (CmMBF1c) was significantly induced by waterlogging stress in chrysanthemums. Promoter sequence analysis and transient dual-luciferase assay using chrysanthemum protoplasts showed that the waterlogging-tolerant cultivar ‘Nannongxuefeng’ carried more response elements involved in waterlogging and hypoxia stress compared with the waterlogging-sensitive cultivar ‘Qinglu’, conferring on ‘Nannongxuefeng’ a stronger hypoxia responsive activity and higher CmMBF1c expression under waterlogging conditions. Subcellular localization and transcriptional activity assays showed that CmMBF1c protein was localized to the nucleus and had no transcriptional activation activity. Overexpression of CmMBF1c in ‘Qinglu’ enhanced its waterlogging tolerance by promoting its reactive oxygen species (ROS) scavenging ability and maintaining low ROS levels. However, RNAi-mediated knockdown of CmMBF1c in cultivar ‘Nannongxuefeng’ resulted in the opposite tendency. Yeast two-hybrid screening and tobacco bimolecular fluorescence complementation assays revealed that CmHRE2, a pivotal regulator of hypoxia response, could interact with CmMBF1c. In summary, this study demonstrates that CmMBF1c improves chrysanthemum waterlogging tolerance by regulating its ROS signaling pathway and interacting with CmHRE2. These findings together offer, to our knowledge, new mechanistic insights into chrysanthemum waterlogging tolerance and provide a rational foundation for future research on the genetic improvement of horticultural crops for waterlogging stress tolerance.
Chromosome-level genome assembly and resequencing of camphor tree (Cinnamomum camphora) provides insight into phylogeny and diversification of terpenoid and triglyceride biosynthesis of Cinnamomum
Authors: Wang Xin-Dong , Xu Chun-Yan , Zheng Yong-Jie , Wu Yan-Fang , Zhang Yue-Ting , Zhang Ting , Xiong Zhen-Yu , Yang Hai-Kuan , Li Jiang , Fu Chao , Qiu Feng-Ying , Dai Xiao-Ying , Liu Xin-Liang , He Xiao-San , Zhou Song-Song , Li Sheng-Xing , Fu Tao , Xie Han , Chen Yan-Ling , Zhang Qian-Qian , Wang Hong-Qi , Wang Yang-Dong , Zhou Cheng , Jiang Xiang-Mei 
Published: September 2022

Abstract
Cinnamomum species attract attentions owing to their scents, medicinal properties, and ambiguous relationship in the phylogenetic tree. Here, we report a high-quality genome assembly of Cinnamomum camphora, based on which two whole-genome duplication (WGD) events were detected in the C. camphora genome: one was shared with Magnoliales, and the other was unique to Lauraceae. Phylogenetic analyses illustrated that Lauraceae species formed a compact sister clade to the eudicots. We then performed whole-genome resequencing on 24 Cinnamomum species native to China, and the results showed that the topology of Cinnamomum species was not entirely consistent with morphological classification. The rise and molecular basis of chemodiversity in Cinnamomum were also fascinating issues. In this study, six chemotypes were classified and six main terpenoids were identified as major contributors of chemodiversity in C. camphora by the principal component analysis. Through in vitro assays and subcellular localization analyses, we identified two key terpene synthase (TPS) genes (CcTPS16 and CcTPS54), the products of which were characterized to catalyze the biosynthesis of two uppermost volatiles (i.e. 1,8-cineole and (iso)nerolidol), respectively, and meditate the generation of two chemotypes by transcriptional regulation and compartmentalization. Additionally, the pathway of medium-chain triglyceride (MCT) biosynthesis in Lauraceae was investigated for the first time. Synteny analysis suggested that the divergent synthesis of MCT and long-chain triglyceride (LCT) in Lauraceae kernels was probably controlled by specific medium-chain fatty acyl-ACP thioesterase (FatB), type-B lysophosphatidic acid acyltransferase (type-B LPAAT), and diacylglycerol acyltransferase 2b (DGAT 2b) isoforms during co-evolution with retentions or deletions in the genome.
An approach for multi-patch surface modification with a curve constraint satisfying convergentG1 continuity
Authors: Luong Quang-Phap , Nam Jong-Ho , Le Tat-Hien 
Published: September 2022

AbstractConceptual shape design plays a critical role in determining the appearance and functionality of a product. Currently, computer-aided design systems can represent a complex shape through multiple surface patches; however, the methods used for multi-patch surface modification are still limited and counterintuitive. There is an ongoing need for more intuitive and efficient surface modification tools that allow designers to directly control shape changes through specific constraints while maintaining surface quality. In this paper, we propose an intuitive modification approach based on the designer’s activity to interactively manipulate a multi-patch surface with an arbitrary curve constraint with tangent continuity (G1) across connected B-spline patches. The advantages of the curve and surface superposition were used to change the shape of the surface. The first step was a shape-control mechanism that used shape functions to control the deformation of a superposed surface. A fine-tuning step was followed to ensure the aesthetic requirements and quality of the surface by achieving convergent G1 continuity in a linear manner. The efficiency and practicality of the proposed approach have been verified using application examples. The proposed approach can be applied to modify surfaces used in the design of a complex geometric model.
Structural design with dynamic constraints using weighted chaos game optimization
Authors: Goodarzimehr Vahid , Talatahari Siamak , Shojaee Saeed , Hamzehei-Javaran Saleh , Sareh Pooya 
Published: September 2022

Abstract
The chaos game optimization (CGO) algorithm is a recently developed metaheuristic inspired by chaos theory and fractal configurations. In CGO, possible optimal solutions are defined as seeds and the searching process is performed using some simple equations. In this paper, weighted chaos game optimization (WCGO) is proposed and implemented to optimize engineering structures with dynamic constraints. In this method, an inertia weight coefficient based on the minimum and maximum values ​​of the objective function is introduced to create a better balance between exploration and exploitation during the searching process. By applying the inertia weight coefficient to the seeds, their positions can be controlled accurately. To evaluate the performance of WCGO, a wide range of mathematical benchmark functions, as well as several structural design optimization problems under dynamic constraints, are computationally investigated using the new algorithm. In order to demonstrate the efficiency and robustness of WCGO, its results have been compared with those obtained by some conventional methods from the literature. Additionally, a Friedman rank test is conducted to perform a statistical study on the performance of the considered algorithms. The findings indicate that WCGO performs better than its rivals in solving these structural optimization problems with dynamic constraints.
The incidental finding of xanthogranulomatous cholecystitis: a report of 10 cases
Authors: Alotaibi Abdulrahman Muaod , Almasoudi Eid , Ahmed Hassan , Alzwaihiri Abubakr 
Published: September 2022

Abstract
There is insufficient clinical knowledge about xanthogranulomatous cholecystitis (XGC) due to biased reporting. This study aims to investigate the incidence of XGC and evaluate the clinical outcome regarding operative time, rate of conversion and intraoperative or postoperative complications. We included 1141 patients who underwent surgery for gallbladder disease between January 2019 and December 2021. Of 1141 patients who underwent cholecystectomy, XGC was seen in 10 (0.87%). The average age is 47 (24–81 years old) with a male to female ratio of 3:2. Biliary pancreatitis and obstructive jaundice are seen in two patients who did ERCP and stenting before surgery. One patient presented with a 4 cm necrotizing soft-tissue granuloma. The BMI was high, with class I obesity in five patients. Symptoms last from 1 to 12 weeks. One patient was only diagnosed preoperatively as XGC. Four out of 10 (40%) required more than 72 h of hospitalization. All patients underwent elective sitting surgery, with eight successfully managed by laparoscopy and one converted to open. The average operative time was 90 min (43–193 min), and a postoperative drain was inserted in four patients. The median follow-up is after 24 months (11–30 months), with no postoperative collection, bleeding, complication or readmission. XGC is a rare benign entity requiring no further action upon incidental discovery. Surgical resection is the cornerstone of management, with the laparoscopic approach considered feasible and safe. Four out of 10 patients might need more than 3 days of hospitalization. In the presence of mass, the frozen section can help guide the management.
Jet from the enigmatic high-latitude star BP Psc and evolutionary status of its driving source
Authors: Potravnov Ilya S , Khovritchev M Yu , Artemenko S A , Shakhovskoy D N 
Published: September 2022

ABSTRACT
BP Psc is an active late-type (sp:G9) star with unclear evolutionary status lying at high-galactic latitude b = −57°. It is also the source of the well collimated bipolar jet. We present results of the proper motion and radial velocity study of BP Psc outflow based on the archival Hα imaging with the GMOS camera at 8.1-m Gemini-North telescope as well as recent imaging and long-slit spectroscopy with the SCORPIO multimode focal reducer at 6-m BTA telescope of SAO RAS. The 3D kinematics of the jet revealed the full spatial velocity up to ∼140 km s−1 and allows us to estimate the distance to BP Psc system as D = 135 ± 40 pc. This distance leads to an estimation of the central source luminosity L* ≈ 1.2 L⊙, indicating that it is the ≈1.3M⊙ T Tauri star with an age t ≲ 7 Myrs. We measured the electron density of order Ne ∼ 102 cm−3 and mean ionization fraction f ≈ 0.04 within the jet knots and estimated upper limit of the mass-loss rate in NE lobe as $\dot{M}_{\rm out}\approx 1.2\cdot 10^{-8}{\rm M}_{\odot }\,{\rm yr}^{-1}$. The physical characteristics of the outflow are typical for the low-excitation YSO jets and consistent with the magnetocentrifugal mechanism of its launching and collimation. Prominent wiggling pattern revealed in Hα images allowed us to suppose the existence of a secondary substellar companion in a non-coplanar orbit and estimate its most plausible mass as Mp ≈ 30MJup. We conclude that BP Psc is one of the closest to the Sun young jet-driving systems and its origin is possibly related to the episode of star formation triggered by expanding supershells in second Galactic quadrant.
Searching for the next Galactic Luminous red nova
Authors: Addison Harry , Blagorodnova Nadejda , Groot Paul J , Erasmus Nicolas , Jones David , Mogawana Orapeleng 
Published: September 2022

ABSTRACT
Luminous red novae (LRNe) are astrophysical transients believed to be caused by the partial ejection of a binary star’s common envelope (CE) and the merger of its components. The formation of the CE is likely to occur during unstable mass transfer, initiated by a primary star which is evolving off the main sequence (a Hertzsprung gap star) and a lower mass companion. In agreement with observations, theoretical studies have shown that outflows from the pre-CE phase produce a detectable brightening of the progenitor system a few years before the ejection event. Based on these assumptions, we present a method to identify Galactic LRNe precursors, the resulting precursor candidates, and our follow-up analysis to uncover their nature. We begin by constructing a sample of progenitor systems, i.e. Hertzsprung gap stars, by statistically modelling the density of a colour magnitude diagram formed from ‘well behaved’ Gaia DR2 sources. Their time-domain evolution from the Zwicky Transient Facility (ZTF) survey is used to search for slowly brightening events, as pre-CE precursor candidates. The nature of the resulting candidates is further investigated using archival data and our own spectroscopic follow-up. Overall, we constructed a sample of ∼5.4 × 104 progenitor sources, from which 21 were identified as candidate LRNe precursors. Further analysis revealed 16 of our candidates to be Hα emitters, with their spectra often suggesting hotter (albeit moderately extincted) A-type or B-type stars. Because of their long-term variability in optical and mid-infrared wavelengths, we propose that many of our candidates are mass-transferring binaries with compact companions surrounded by dusty circumstellar discs or alternatively magnetically active stellar merger remnants.
Timing analysis of a sample of five cataclysmic variable candidates observed by the XMM–Newton satellite
Authors: Nucita A A , Lezzi S M , De Paolis F , Strafella F , Licchelli D , Franco A , Maiorano M 
Published: September 2022

ABSTRACT
Intermediate polars are a class of cataclysmic variables in which a white dwarf accretes material from a companion star. The intermediate polar nature confirmation usually derives from the detection of two periods in both X-ray and optical photometry. In this respect, the high-energy signal is often characterized by modulations on the white dwarf spin and the orbital period. However, noting that the periodograms may be characterized by strong features also at the synodic period and/or other sidebands, the timing analysis of the X-ray signal may offer the unique possibility to firmly discover an intermediate polar candidate. Here, we concentrate on a sample of five cataclysmic variable binary candidates: i.e. SAXJ1748.2-2808, 1RXS J211336.1 + 542226, CXOGC J174622.7-285218, CXOGC J174517.4-290650, and V381 Vel, listed in the IPHome catalogue. Our main aim is to confirm if they belong to the intermediate polar class or not. The results of our analysis show that we can safely assess the intermediate polar nature of all the considered sources, apart for the case of V381 Vel which instead behaves like a cataclysmic variable of the polar subclass. Moreover, the source SAXJ1748.2-2808, previously classified as an HMXB, appears to be, most likely, an intermediate polar variable.
The essential character of the neutrino mechanism of core-collapse supernova explosions
Authors: Wang Tianshu , Vartanyan David , Burrows Adam , Coleman Matthew S B 
Published: September 2022

Abstract
Calibrating with detailed 2D core-collapse supernova (CCSN) simulations, we derive a simple CCSN explosion condition based solely upon the terminal density profiles of state-of-the-art stellar evolution calculations of the progenitor massive stars. This condition captures the vast majority of the behaviour of the one hundred 2D state-of-the-art models we performed to gauge its usefulness. The goal is to predict, without resort to detailed simulation, the explodability of a given massive star. We find that the simple maximum fractional ram pressure jump discriminant we define works well ∼90 per cent of the time and we speculate on the origin of the few false positives and false negatives we witness. The maximum ram pressure jump generally occurs at the time of accretion of the silicon/oxygen interface, but not always. Our results depend upon the fidelity with which the current implementation of our code F ornax adheres to Nature and issues concerning the neutrino–matter interaction, the nuclear equation of state, the possible effects of neutrino oscillations, grid resolution, the possible role of rotation and magnetic fields, and the accuracy of the numerical algorithms employed remain to be resolved. Nevertheless, the explodability condition we obtain is simple to implement, shows promise that it might be further generalized while still employing data from only the unstable Chandrasekhar progenitors, and is a more credible and robust simple explosion predictor than can currently be found in the literature.
Comparative single-cell transcriptomes of dose and time dependent epithelial–mesenchymal spectrums
Authors: Panchy Nicholas , Watanabe Kazuhide , Takahashi Masataka , Willems Andrew , Hong Tian 
Published: September 2022

AbstractEpithelial–mesenchymal transition (EMT) is a cellular process involved in development and disease progression. Intermediate EMT states were observed in tumors and fibrotic tissues, but previous in vitro studies focused on time-dependent responses with single doses of signals; it was unclear whether single-cell transcriptomes support stable intermediates observed in diseases. Here, we performed single-cell RNA-sequencing with human mammary epithelial cells treated with multiple doses of TGF-β. We found that dose-dependent EMT harbors multiple intermediate states at nearly steady state. Comparisons of dose- and time-dependent EMT transcriptomes revealed that the dose-dependent data enable higher sensitivity to detect genes associated with EMT. We identified cell clusters unique to time-dependent EMT, reflecting cells en route to stable states. Combining dose- and time-dependent cell clusters gave rise to accurate prognosis for cancer patients. Our transcriptomic data and analyses uncover a stable EMT continuum at the single-cell resolution, and complementary information of two types of single-cell experiments.
Hepatitis C Virus Coinfection in People With Human Immunodeficiency Virus in Iran: A Systematic Review and Meta-Analysis
Authors: Razavi-Amoli Seyedeh-Kiana , Alipour Abbas 
Published: September 2022

AbstractBackgroundHepatitis C virus (HCV) coinfection is associated with higher mortality and morbidity in people with human immunodeficiency virus (PWH).MethodsWe aimed to characterize the epidemiology and factors associated with HCV coinfection among PWH in Iran. In this systematic review, we searched 3 English databases (MEDLINE, SCOPUS, Embase) and 2 Farsi databases (Scientific Information Database and Magiran) for studies that measured the prevalence of HCV coinfection among PWH, published between 2000 and January 1, 2021. We included studies with a minimum sample size of 5 PWH. Reviews, editorials, conference abstracts, theses, studies with no relevant data, and unclear serological assays were excluded.ResultsWe summarized the HCV coinfection prevalence by random-effect meta-analysis and assessed the sources of heterogeneity by a meta-regression model. Of the 858 records identified, 69 eligible studies with 12 996 PWH were included. Overall, HCV coinfection prevalence was 64% (95% confidence interval [CI], 58–69). The prevalence was higher among older (mean age ≥35 years) PWH (69%; 95% CI, 64–74) and PWH who inject drugs (77%; 95% CI, 71–82). Furthermore, we found that coinfection was higher among studies conducted between 2000 and 2014 (67%; 95% CI, 59–75) versus 2015–2020 (57%; 95% CI, 50–64).ConclusionsThe prevalence of HCV coinfection is high in Iranian PWH, with significant geographical variations. Hepatitis C virus screening and treatment among PWH are warranted to avoid the future burden of HCV-related liver damage, cancer, and mortality.
Sleep duration, plasma metabolites, and obesity and diabetes: a metabolome-wide association study in US women
Authors: Fritz Josef , Huang Tianyi , Depner Christopher M , Zeleznik Oana A , Cespedes Feliciano Elizabeth M , Li Wenjun , Stone Katie L , Manson JoAnn E , Clish Clary , Sofer Tamar , Schernhammer Eva , Rexrode Kathryn , Redline Susan , Wright Kenneth P , Vetter Céline 
Published: September 2022

AbstractShort and long sleep duration are associated with adverse metabolic outcomes, such as obesity and diabetes. We evaluated cross-sectional differences in metabolite levels between women with self-reported habitual short (&lt;7 h), medium (7–8 h), and long (≥9 h) sleep duration to delineate potential underlying biological mechanisms. In total, 210 metabolites were measured via liquid chromatography-mass spectrometry in 9207 women from the Nurses’ Health Study (NHS; N = 5027), the NHSII (N = 2368), and the Women’s Health Initiative (WHI; N = 2287). Twenty metabolites were consistently (i.e. praw &lt; .05 in ≥2 cohorts) and/or strongly (pFDR &lt; .05 in at least one cohort) associated with short sleep duration after multi-variable adjustment. Specifically, levels of two lysophosphatidylethanolamines, four lysophosphatidylcholines, hydroxyproline and phenylacetylglutamine were higher compared to medium sleep duration, while levels of one diacylglycerol and eleven triacylglycerols (TAGs; all with ≥3 double bonds) were lower. Moreover, enrichment analysis assessing associations of metabolites with short sleep based on biological categories demonstrated significantly increased acylcarnitine levels for short sleep. A metabolite score for short sleep duration based on 12 LASSO-regression selected metabolites was not significantly associated with prevalent and incident obesity and diabetes. Associations of single metabolites with long sleep duration were less robust. However, enrichment analysis demonstrated significant enrichment scores for four lipid classes, all of which (most markedly TAGs) were of opposite sign than the scores for short sleep. Habitual short sleep exhibits a signature on the human plasma metabolome which is different from medium and long sleep. However, we could not detect a direct link of this signature with obesity and diabetes risk.
Hour-to-hour variability of respiratory sleep indices and ambulatory blood pressure
Authors: Seah Shawn Jing-Sheng , Chiu Shi Ting , Thant As Tar , Chan Siew Pang , Ou Yi-Hui , Teo Yao Hao , Wong Serene , Koo Chieh-Yang , Barbé Ferran , Lee Chi-Hang 
Published: September 2022

Abstract

Study Objectives
Respiratory sleep indices are traditionally reported on the basis of the average total sleep time. The relationship between the hour-to-hour variability of these parameters and blood pressure (BP) has not been reported.

Methods
We evaluated the associations of the hour-to-hour variability of the apnea–hypopnea index (AHI), oxygen desaturation index (ODI), and lowest oxygen saturation with the 24-h ambulatory BP in patients with hypertension and newly diagnosed obstructive sleep apnea. A total of 147 patients underwent polysomnography, based on which obstructive sleep apnea was diagnosed in 106 patients; these patients underwent 24-h ambulatory BP monitoring within the next 30 days. Each polysomnogram was divided into hourly reports to calculate the variability of the respiratory sleep indices. Variability independent of the mean was considered the primary measure of variability.

Results
The median number of hourly polysomnogram reports was 7 (range, 4–8). The hour-to-hour variability of both AHI and ODI, but not of the lowest oxygen saturation, was correlated with the 24-h pulse pressure, 24-h systolic BP, and awake systolic BP (p &lt; 0.05 for all). The fully adjusted linear regression analysis indicated that the hour-to-hour variability of AHI and ODI remained associated with the 24-h pulse pressure (AHI: β coefficient, 0.264 [95% CI = 0.033–0.495], p = 0.026; ODI: β coefficient, 0.450 [95% CI = 0.174–0.726], p = 0.002).

Conclusions
The hour-to-hour variability of AHI and ODI is independently associated with the 24-h pulse pressure. Further investigations are warranted to evaluate the clinical relevance of this new-found association.