bluuebunny/crossref_metadata_2025_split huggingface dataset:
Aortic wrapping is life-saving in high-risk acute aortic dissection and intramural haematoma
Authors: Carrel Thierry , Sromicki Juri , Schmiady Martin , Aser Raed , Ouda Ahmed , Vogt Paul Robert 
Published: October 2022

Abstract
Aortic wrapping is a controversial repair in patients presenting with acute type A aortic dissection or intramural haematoma, but this method may be a potential alternative to medical treatment or conventional repair in patients aged &gt;80 years and in those presenting with prohibitive co-morbidities such as stroke, circulatory collapse, full oral anticoagulation with the last generation drugs. We report on 5 high-risk and/or patients over 80 years who received external aortic wrapping with or without cardiopulmonary bypass during the last 18 months. All survived the procedure and could be extubated early postoperatively. No patient remained on the intensive care longer than 2 days and all were discharged without additional complications. Postoperative radiological control was acceptable and no patient had any new aortic event up to 18 months postoperatively.
Association between averaged intraoperative nociceptive response index and postoperative complications after lung resection surgery
Authors: Okamoto Takuma , Matsuki Yuka , Ogata Hiroki , Okutani Hiroai , Ueki Ryusuke , Kariya Nobutaka , Tatara Tsuneo , Hirose Munetaka 
Published: October 2022

Abstract

OBJECTIVES
Since postoperative complications, defined as Clavien–Dindo grade ≥II, correlate with long-term survival after lung resection surgery in patients with primary lung cancer, identification of intraoperative risk factors for postoperative complications is crucial for better perioperative management. In the present study, we investigated the possible association between intraoperative variables for use in anaesthetic management and Clavien–Dindo grade ≥II.

METHODS
In this multi-institutional observational study, consecutive adult patients undergoing video-assisted thoracic surgery for primary lung cancer under general anaesthesia from March 2019 to April 2021 were enrolled. All patients were divided into 2 groups with Clavien–Dindo grade &lt;II and ≥II. Uni- and multivariable analyses were performed to identify intraoperative risk factors.

RESULTS
After univariable analysis between patients with Clavien–Dindo grade &lt;II (n = 415) and ≥II (n = 121), multivariable analysis revealed higher averaged nociceptive response (NR) index during surgery (mean NR), male sex, lower body mass index, longer duration of surgery, higher blood loss and lower urine volume, as independent risk factors for postoperative complications. In sensitivity analysis, based on the cut-off value of mean NR for postoperative complications, all patients were divided into high and low mean NR groups. The incidence of postoperative complications was significantly higher in patients with high mean NR (n = 332) than in patients with low mean NR (n = 204; P &lt; 0.001).

CONCLUSIONS
Higher mean NR, as intraoperative variables for use in anaesthetic management, is associated with the higher incidence of postoperative complications after primary lung cancer surgery.
Rational Origins of Revisionist War
Authors: Jordan Richard 
Published: October 2022

Abstract
The rise of China has returned attention to the links between power transitions and war. In this literature, three different causal mechanisms can be confused. This essay disentangles them. Power transitions can lead to three kinds of war: preventive, accidental, and revisionist. Formal models tend to study the first, in which a declining state tries to delay or prevent a rival’s ascent. However, major wars during great power transitions are usually initiated by the rising state, not the declining one. To describe these historical cases, less formal theories, especially neorealism and neoclassical realism, focus on accidental and revisionist wars, but these theories tend to fall back on nonrational mechanisms to connect changing power to the risk of conflict. This leaves a theoretical gap: Why would a rising, rational actor deliberately choose conflict, i.e., start a revisionist war? To suggest an answer, this essay demonstrates how a simple change in standard bargaining models—incorporating a nonzero probability of indecisive war—can ground realist intuitions on rationalist foundations. It further shows how this change leads immediately to an intuitive, formal definition of stability that aligns naturally with existing informal work. Then, contrary to existing realist theory, it shows why the rigorous analysis of realist assumptions leads to a nonmonotonic relationship between the offense/defense balance and war. It thus uses realism to inform and potentially redirect formal scholarship; it also uses formal scholarship to sharpen the logical foundations of realism and, in so doing, derive novel empirical predictions. The essay concludes by applying this synthesis to the rise of China today and indicating directions for deepening the formal/realist synthesis.
Power-Sharing: The Need to Explore the “Who” and the “Where”
Authors: Walsh Dawn 
Published: October 2022

Abstract
Power-sharing provisions have been included in many peace agreements intended to end intra-state violent conflict, including, for example, in Northern Ireland, Bosnia, Sudan, and Lebanon. Power-sharing has been subject to extensive scholarly examination. Many of these examinations focus on the impact of power-sharing on peace, often defined as the non-recurrence of violent conflict. However, the results of these examinations have not generated a consensus as to the value of power-sharing as a conflict management tool. This lack of consensus highlights a need to more clearly understand the effects of power-sharing. To fully comprehend the role of power-sharing, we must move away from simply asking if it is associated with the reoccurrence of violence and explore the paths through which it can contribute to different outcomes of interest, for example, group relations or stable government. Both Hartzell and Mehler (2019) and Keil and McCulloch (2021) seek to address this current weakness in our understanding of power-sharing, albeit in quite different ways. These books show that by paying closer attention to the impact of power-sharing on different outcomes, including a focus on the mechanisms that link its different power-sharing provisions to specific outcomes, we can develop a fundamentally deeper understanding of power-sharing.
Giving Suggestions: Using Quantity Requests to Increase Donations
Authors: Moon Alice , VanEpps Eric M 
Published: October 2022

Abstract
Across seven studies (N = 9,028), we provide evidence that quantity requests, wherein people consider multiple choice options of how much to donate (e.g., $5, $10, or $15), increase contributions compared to open-ended requests. Specifically, quantity requests encourage greater donations (study 1), even when respondents can passively choose not to donate (study 2) and even when the donation is directed toward a less popular cause (study 3). This increase in donations holds for quantity requests that start with both lower (e.g., $1) or higher (e.g., $10) donation amount options (study 4). Quantity requests also outperform other requests with multiple nonquantity donation options (e.g., multiple options of when to donate or to which charity branch to direct a donation; study 5). We offer evidence that quantity requests are effective because they simplify donation decisions by communicating normative donation magnitudes (studies 6 and 7). This clarified norm of donation magnitude boosts donation rates, which in turn leads to greater total donations. Our findings offer new conceptual insights into how quantity requests increase contributions as well as practical implications for charitable organizations to optimize contributions by leveraging the use of quantity requests.
Using genomic prediction with crop growth models enables the prediction of associated traits in wheat
Authors: Jighly Abdulqader , Thayalakumaran Thabo , O’Leary Garry J , Kant Surya , Panozzo Joe , Aggarwal Rajat , Hessel David , Forrest Kerrie L , Technow Frank , Tibbits Josquin F G , Totir Radu , Hayden Matthew J , Munkvold Jesse , Daetwyler Hans D 
Published: October 2022

AbstractCrop growth models (CGM) can predict the performance of a cultivar in untested environments by sampling genotype-specific parameters. As they cannot predict the performance of new cultivars, it has been proposed to integrate CGMs with whole genome prediction (WGP) to combine the benefits of both models. Here, we used a CGM–WGP model to predict the performance of new wheat (Triticum aestivum) genotypes. The CGM was designed to predict phenology, nitrogen, and biomass traits. The CGM–WGP model simulated more heritable GSPs compared with the CGM and gave smaller errors for the observed phenotypes. The WGP model performed better when predicting yield, grain number, and grain protein content, but showed comparable performance to the CGM–WGP model for heading and physiological maturity dates. However, the CGM–WGP model was able to predict unobserved traits (for which there were no phenotypic records in the reference population). The CGM–WGP model also showed superior performance when predicting unrelated individuals that clustered separately from the reference population. Our results demonstrate new advantages for CGM–WGP modelling and suggest future efforts should focus on calibrating CGM–WGP models using high-throughput phenotypic measures that are cheaper and less laborious to collect.
A New Auto-RPA-Fluorescence Detection Platform for SARS-CoV-2
Authors: Tian Jing , Chen Biao , Zhang Bin , Li Tantan , Liang Zhiqiang , Guo Yujin , Jiao Huping , Liang Fenghong , Xiang Longquan , Lin Fanzhong , Ren Ruiwen , Liu Qingbin 
Published: October 2022

AbstractObjectiveThe outbreak of COVID-19 caused by SARS-CoV-2 has led to a serious worldwide pandemic. Quantitative reverse transcription–polymerase chain reaction (qRT-PCR)–based methods were recommended for routine detection of SARS-CoV-2 RNA. Because the reaction time and analytical sensitivity of qRT-PCR limits the diagnosis of SARS-CoV-2, development of a quick process of SARS-CoV-2 detection technology with high analytical sensitivity remains urgent.MethodsWe combined isothermal amplification and fluorescence detection technology to develop a new auto-recombinase polymerase amplification (RPA)-fluorescence platform that could be used in the diagnosis of SARS-CoV-2.ResultsBy optimization of primers and probes, the RPA platform could detect SARS-CoV-2 nucleotides within 15 min. The limits of detection and specificity of the auto-RPA-fluorescence platform were 5 copies/µL and 100%, respectively. The accuracy of detection of the auto-RPA-fluorescence platform in the 16 positive samples was 100%.ConclusionThe RPA platform is a potential technology for the diagnosis of SARS-CoV-2 infection.
A parameterized view on the complexity of dependence and independence logic
Authors: Kontinen Juha , Meier Arne , Mahmood Yasir 
Published: October 2022

Abstract
In this paper, we investigate the parameterized complexity of model checking for Dependence and Independence logic, which are well studied logics in the area of Team Semantics. We start with a list of nine immediate parameterizations for this problem, namely the number of disjunctions (i.e. splits)/(free) variables/universal quantifiers, formula-size, the tree-width of the Gaifman graph of the input structure, the size of the universe/team and the arity of dependence atoms. We present a comprehensive picture of the parameterized complexity of model checking and obtain a division of the problem into tractable and various intractable degrees. Furthermore, we also consider the complexity of the most important variants (data and expression complexity) of the model checking problem by fixing parts of the input.
Mode and Tempo of 3D Genome Evolution in Drosophila
Authors: Torosin Nicole S , Golla Tirupathi Rao , Lawlor Matthew A , Cao Weihuan , Ellison Christopher E 
Published: October 2022

Abstract
Topologically associating domains (TADs) are thought to play an important role in preventing gene misexpression by spatially constraining enhancer–promoter contacts. The deleterious nature of gene misexpression implies that TADs should, therefore, be conserved among related species. Several early studies comparing chromosome conformation between species reported high levels of TAD conservation; however, more recent studies have questioned these results. Furthermore, recent work suggests that TAD reorganization is not associated with extensive changes in gene expression. Here, we investigate the evolutionary conservation of TADs among 11 species of Drosophila. We use Hi-C data to identify TADs in each species and employ a comparative phylogenetic approach to derive empirical estimates of the rate of TAD evolution. Surprisingly, we find that TADs evolve rapidly. However, we also find that the rate of evolution depends on the chromatin state of the TAD, with TADs enriched for developmentally regulated chromatin evolving significantly slower than TADs enriched for broadly expressed, active chromatin. We also find that, after controlling for differences in chromatin state, highly conserved TADs do not exhibit higher levels of gene expression constraint. These results suggest that, in general, most TADs evolve rapidly and their divergence is not associated with widespread changes in gene expression. However, higher levels of evolutionary conservation and gene expression constraints in TADs enriched for developmentally regulated chromatin suggest that these TAD subtypes may be more important for regulating gene expression, likely due to the larger number of long-distance enhancer–promoter contacts associated with developmental genes.
The chromatin remodeler RSC prevents ectopic CENP-A propagation into pericentromeric heterochromatin at the chromatin boundary
Authors: Tsunemine Satoru , Nakagawa Hiromi , Suzuki Yutaka , Murakami Yota 
Published: October 2022

Abstract
Centromeres of most eukaryotes consist of two distinct chromatin domains: a kinetochore domain, identified by the histone H3 variant, CENP-A, and a heterochromatic domain. How these two domains are separated is unclear. Here, we show that, in Schizosaccharomyces pombe, mutation of the chromatin remodeler RSC induced CENP-ACnp1 misloading at pericentromeric heterochromatin, resulting in the mis-assembly of kinetochore proteins and a defect in chromosome segregation. We find that RSC functions at the kinetochore boundary to prevent CENP-ACnp1 from spreading into neighbouring heterochromatin, where deacetylated histones provide an ideal environment for the spread of CENP-ACnp1. In addition, we show that RSC decompacts the chromatin structure at this boundary, and propose that this RSC-directed chromatin decompaction prevents mis-propagation of CENP-ACnp1 into pericentromeric heterochromatin. Our study provides an insight into how the distribution of distinct chromatin domains is established and maintained.
APE1 assembles biomolecular condensates to promote the ATR–Chk1 DNA damage response in nucleolus
Authors: Li Jia , Zhao Haichao , McMahon Anne , Yan Shan 
Published: October 2022

Abstract
Multifunctional protein APE1/APEX1/HAP1/Ref-1 (designated as APE1) plays important roles in nuclease-mediated DNA repair and redox regulation in transcription. However, it is unclear how APE1 regulates the DNA damage response (DDR) pathways. Here we show that siRNA-mediated APE1-knockdown or APE1 inhibitor treatment attenuates the ATR–Chk1 DDR under stress conditions in multiple immortalized cell lines. Congruently, APE1 overexpression (APE1-OE) activates the ATR DDR under unperturbed conditions, which is independent of APE1 nuclease and redox functions. Structural and functional analysis reveals a direct requirement of the extreme N-terminal motif within APE1 in the assembly of distinct biomolecular condensates in vitro and DNA/RNA-independent activation of the ATR DDR. Overexpressed APE1 co-localizes with nucleolar NPM1 and assembles biomolecular condensates in nucleoli in cancer but not non-malignant cells, which recruits ATR and activator molecules TopBP1 and ETAA1. APE1 protein can directly activate ATR to phosphorylate its substrate Chk1 in in vitro kinase assays. W119R mutant of APE1 is deficient in nucleolar condensation, and is incapable of activating nucleolar ATR DDR in cells and ATR kinase in vitro. APE1-OE-induced nucleolar ATR DDR activation leads to compromised ribosomal RNA transcription and reduced cell viability. Taken together, we propose distinct mechanisms by which APE1 regulates ATR DDR pathways.
ChemPert: mapping between chemical perturbation and transcriptional response for non-cancer cells
Authors: Zheng Menglin , Okawa Satoshi , Bravo Miren , Chen Fei , Martínez-Chantar María-Luz , del Sol Antonio 
Published: October 2022

Abstract
Prior knowledge of perturbation data can significantly assist in inferring the relationship between chemical perturbations and their specific transcriptional response. However, current databases mostly contain cancer cell lines, which are unsuitable for the aforementioned inference in non-cancer cells, such as cells related to non-cancer disease, immunology and aging. Here, we present ChemPert (https://chempert.uni.lu/), a database consisting of 82 270 transcriptional signatures in response to 2566 unique perturbagens (drugs, small molecules and protein ligands) across 167 non-cancer cell types, as well as the protein targets of 57 818 perturbagens. In addition, we develop a computational tool that leverages the non-cancer cell datasets, which enables more accurate predictions of perturbation responses and drugs in non-cancer cells compared to those based onto cancer databases. In particular, ChemPert correctly predicted drug effects for treating hepatitis and novel drugs for osteoarthritis. The ChemPert web interface is user-friendly and allows easy access of the entire datasets and the computational tool, providing valuable resources for both experimental researchers who wish to find datasets relevant to their research and computational researchers who need comprehensive non-cancer perturbation transcriptomics datasets for developing novel algorithms. Overall, ChemPert will facilitate future in silico compound screening for non-cancer cells.
The novel type II toxin–antitoxin PacTA modulates Pseudomonas aeruginosa iron homeostasis by obstructing the DNA-binding activity of Fur
Authors: Song Yingjie , Zhang Siping , Ye Zirui , Song Yongyan , Chen Lin , Tong Aiping , He Yongxing , Bao Rui 
Published: October 2022

Abstract
Type II toxin–antitoxin (TA) systems are widely distributed in bacterial and archaeal genomes and are involved in diverse critical cellular functions such as defense against phages, biofilm formation, persistence, and virulence. GCN5-related N-acetyltransferase (GNAT) toxin, with an acetyltransferase activity-dependent mechanism of translation inhibition, represents a relatively new and expanding family of type II TA toxins. We here describe a group of GNAT-Xre TA modules widely distributed among Pseudomonas species. We investigated PacTA (one of its members encoded by PA3270/PA3269) from Pseudomonas aeruginosa and demonstrated that the PacT toxin positively regulates iron acquisition in P. aeruginosa. Notably, other than arresting translation through acetylating aminoacyl-tRNAs, PacT can directly bind to Fur, a key ferric uptake regulator, to attenuate its DNA-binding affinity and thus permit the expression of downstream iron-acquisition-related genes. We further showed that the expression of the pacTA locus is upregulated in response to iron starvation and the absence of PacT causes biofilm formation defect, thereby attenuating pathogenesis. Overall, these findings reveal a novel regulatory mechanism of GNAT toxin that controls iron-uptake-related genes and contributes to bacterial virulence.
The Protective Role of Non-Photochemical Quenching in PSII Photo-Susceptibility: A Case Study in the Field
Authors: Han Li-Jun , Fan Da-Yong , Wang Xiang-Ping , Xu Cheng-Yang , Xia Xin-Li , Chow Wah Soon 
Published: October 2022

Abstract
Non-photochemical quenching (NPQ) has been regarded as a safety valve to dissipate excess absorbed light energy not used for photochemistry. However, there exists no general consensus on the photoprotective role of NPQ. In the present study, we quantified the Photosystem II (PSII) photo-susceptibilities (mpi) in the presence of lincomycin, under red light given to five shade-acclimated tree species grown in the field. Photosynthetic energy partitioning theory was applied to investigate the relationships between mpi and each of the regulatory light-induced NPQ [Y(NPQ)], the quantum yield of the constitutive nonregulatory NPQ [Y(NO)] and the PSII photochemical yield in the light-adapted state [Y(PSII)] under different red irradiances. It was found that in the low to moderate irradiance range (50–800 μmol m–2 s–1) when the fraction of open reaction centers (qP) exceeded 0.4, mpi exhibited no association with Y(NPQ), Y(NO) and Y(PSII) across species. However, when qP &lt; 0.4 (1,500 μmol m–2 s–1), there existed positive relationships between mpi and Y(NPQ) or Y(NO) but a negative relationship between mpi and Y(PSII). It is postulated that both Y(NPQ) and Y(NO) contain protective and damage components and that using only Y(NPQ) or Y(NO) metrics to identify the photo-susceptibility of a species is a risk. It seems that qP regulates the balance of the two components for each of Y(NPQ) and Y(NO). Under strong irradiance, when both protective Y(NPQ) and Y(NO) are saturated/depressed, the forward electron flow [i.e. Y(PSII)] acts as the last defense to resist photoinhibition.
Factor of DNA methylation 1 affects woodland strawberry plant stature and organ size via DNA methylation
Authors: Zheng Guanghui , Hu Shaoqiang , Cheng Simin , Wang Liyang , Kan Lijun , Wang Zhengming , Xu Qiang , Liu Zhongchi , Kang Chunying 
Published: October 2022

Abstract
RNA-directed DNA methylation (RdDM) is an epigenetic process that directs silencing to specific genomic regions and loci. The biological functions of RdDM are not well studied in horticultural plants. Here, we isolated the ethyl methane-sulfonate-induced mutant reduced organ size (ros) producing small leaves, flowers, and fruits in woodland strawberry (Fragaria vesca) due to reduced cell numbers compared with that in the wild-type (WT). The candidate mutation causes a premature stop codon in FvH4_6g28780, which shares high similarity to Arabidopsis (Arabidopsis thaliana) Factor of DNA Methylation1 (FDM1) encoding an RdDM pathway component and was named FveFDM1. Consistently, the fvefdm1CR mutants generated by CRISPR/Cas9 also produced smaller organs. Overexpressing FveFDM1 in an Arabidopsis fdm1-1 fdm2-1 double mutant restored DNA methylation at the RdDM target loci. FveFDM1 acts in a protein complex with its homolog Involved in De Novo 2 (FveIDN2). Furthermore, whole-genome bisulfite sequencing revealed that DNA methylation, especially in the CHH context, was remarkably reduced throughout the genome in fvefdm1. Common and specific differentially expressed genes were identified in different tissues of fvefdm1 compared to in WT tissues. DNA methylation and expression levels of several gibberellic acid (GA) biosynthesis and cell cycle genes were validated. Moreover, the contents of GA and auxin were substantially reduced in the young leaves of fvefdm1 compared to in the WT. However, exogenous application of GA and auxin could not recover the organ size of fvefdm1. In addition, expression levels of FveFDM1, FveIDN2, Nuclear RNA Polymerase D1 (FveNRPD1), Domains Rearranged Methylase 2 (FveDRM2), and cell cycle genes were greatly induced by GA treatment. Overall, our work demonstrated the critical roles of FveFDM1 in plant growth and development via RdDM-mediated DNA methylation in horticultural crops.