bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comprehensive epigenome and transcriptome analysis of carbon reserve remobilization in indica and japonica rice stems under moderate soil drying
Authors: Wang Guanqun , Li Xiaozheng , Li Yongqiang , Ye Nenghui , Li Haoxuan , Zhang Jianhua 
Published: October 2020

Abstract
Moderate soil drying (MD) imposed at the post-anthesis stage significantly improves carbon reserve remobilization in rice stems, increasing grain yield. However, the methylome and transcriptome profiles of carbon reserve remobilization under MD are obscure in indica and japonica rice stems. Here, we generated whole-genome single-base resolution maps of the DNA methylome in indica and japonica rice stems. DNA methylation levels were higher in indica than in japonica and positively correlated with genome size. MD treatment had a weak impact on the changes in methylation levels in indica. Moreover, the number of differentially methylated regions was much lower in indica, indicating the existence of cultivar-specific methylation patterns in response to MD during grain filling. The gene encoding β-glucosidase 1, involved in the starch degradation process, was hypomethylated and up-regulated in indica, resulting in improved starch to sucrose conversion under MD treatment. Additionally, increased expression of MYBS1 transactivated the expression of AMYC2/OsAMY2A in both indica and japonica, leading to enhanced starch degradation under MD. In contrast, down-regulated expression of MYB30 resulted in increased expression of BMY5 in both cultivars. Our findings decode the dynamics of DNA methylation in indica and japonica rice stems and propose candidate genes for improving carbon reserve remobilization.
Natural polymorphisms in a pair of NSP2 homoeologs can cause loss of nodulation in peanut
Authors: Peng Ze , Chen Huiqiong , Tan Lubin , Shu Hongmei , Varshney Rajeev K , Zhou Zhekai , Zhao Zifan , Luo Ziliang , Chitikineni Annapurna , Wang Liping , Maku James , López Yolanda , Gallo Maria , Zhou Hai , Wang Jianping 
Published: October 2020

Abstract
Microbial symbiosis in legumes is achieved through nitrogen-fixing root nodules, and these are important for sustainable agriculture. The molecular mechanisms underlying development of root nodules in polyploid legume crops are largely understudied. Through map-based cloning and QTL-seq approaches, we identified a pair of homoeologous GRAS transcription factor genes, Nodulation Signaling Pathway 2 (AhNSP2-B07 or Nb) and AhNSP2-A08 (Na), controlling nodulation in cultivated peanut (Arachis hypogaea L.), an allotetraploid legume crop, which exhibited non-Mendelian and Mendelian inheritance, respectively. The segregation of nodulation in the progeny of Nananbnb genotypes followed a 3:1 Mendelian ratio, in contrast to the 5:3~1:1 non-Mendelian ratio for nanaNbnb genotypes. Additionally, a much higher frequency of the nb allele (13%) than the na allele (4%) exists in the peanut germplasm collection, suggesting that Nb is less essential than Na in nodule organogenesis. Our findings reveal the genetic basis of naturally occurred non-nodulating peanut plants, which can be potentially used for nitrogen fixation improvement in peanut. Furthermore, the results have implications for and provide insights into the evolution of homoeologous genes in allopolyploid species.
Potassium content diminishes in infected cells ofMedicago truncatulanodules due to the mislocation of channels MtAKT1 and MtSKOR/GORK
Authors: Fedorova Elena E , Coba de la Peña Teodoro , Lara-Dampier Victoria , Trifonova Natalia A , Kulikova Olga , Pueyo José J , Lucas M Mercedes 
Published: October 2020

AbstractRhizobia establish a symbiotic relationship with legumes that results in the formation of root nodules, where bacteria encapsulated by a membrane of plant origin (symbiosomes), convert atmospheric nitrogen into ammonia. Nodules are more sensitive to ionic stresses than the host plant itself. We hypothesize that such a high vulnerability might be due to defects in ion balance in the infected tissue. Low temperature SEM (LTSEM) and X-ray microanalysis of Medicago truncatula nodules revealed a potassium (K+) decrease in symbiosomes and vacuoles during the life span of infected cells. To clarify K+ homeostasis in the nodule, we performed phylogenetic and gene expression analyses, and confocal and electron microscopy localization of two key plant Shaker K+ channels, AKT1 and SKOR/GORK. Phylogenetic analyses showed that the genome of some legume species, including the Medicago genus, contained one SKOR/GORK and one AKT1 gene copy, while other species contained more than one copy of each gene. Localization studies revealed mistargeting and partial depletion of both channels from the plasma membrane of M. truncatula mature nodule-infected cells that might compromise ion transport. We propose that root nodule-infected cells have defects in K+ balance due to mislocation of some plant ion channels, as compared with non-infected cells. The putative consequences are discussed.
Search for dormant black holes in ellipsoidal variables I. Revisiting the expected amplitudes of the photometric modulation
Authors: Gomel Roy , Faigler Simchon , Mazeh Tsevi 
Published: October 2020

ABSTRACT
Ellipsoidal variables present light-curve modulations caused by stellar distortion, induced by tidal interaction with their companions. An analytical approximated model of the ellipsoidal modulation is given as a discrete Fourier series by Morris & Naftilan. Based on numerical simulations using the phoebe code, we present here updated amplitudes of the first three harmonics of the model. The expected amplitudes are given as a function of the mass ratio and inclination of the binary system and the fillout factor of the primary – the ratio between the stellar radius and that of its Roche lobe. The corrections can get up to 30 per cent relative to the Morris & Naftilan model for fillout factors close to unity. The updated model can be instrumental in searching for short-period binaries with compact-object secondaries in large data sets of photometric light curves. As shown in one OGLE light-curve example, the minimum mass ratio can be obtained by using only the amplitudes of the three harmonics and an estimation of the stellar temperature. High enough amplitudes can help to identify binaries with mass ratios larger than unity, some of which might have compact companions.
The value of the Hubble–Lemaître constant queried by Type Ia supernovae: a journey from the Calán-Tololo Project to the Carnegie Supernova Program
Authors: Hamuy Mario , Cartier Régis , Contreras Carlos , Suntzeff Nicholas B 
Published: October 2020

ABSTRACT
We assess the robustness of the two highest rungs of the ‘cosmic distance ladder’ for Type Ia supernovae and the determination of the Hubble–Lemaître constant. In this analysis, we hold fixed Rung 1 as the distance to the LMC determined to 1 per cent using detached eclipsing binary stars. For Rung 2, we analyse two methods, the TRGB and Cepheid distances for the luminosity calibration of Type Ia supernovae in nearby galaxies. For Rung 3, we analyse various modern digital supernova samples in the Hubble flow, such as the Calán-Tololo, CfA, CSP, and Supercal data sets. This metadata analysis demonstrates that the TRGB calibration yields smaller H0 values than the Cepheid calibration, a direct consequence of the systematic difference in the distance moduli calibrated from these two methods. Selecting the three most independent possible methodologies/bandpasses (B, V, J), we obtain H0 = 69.9 ± 0.8 and H0= 73.5 ± 0.7 $\, \rm km\, s^{-1} \, Mpc^{-1}$from the TRGB and Cepheid calibrations, respectively. Adding in quadrature the systematic uncertainty in the TRGB and Cepheid methods of 1.1 and 1.0 $\, \rm km\, s^{-1} \, Mpc^{-1}$, respectively, this subset reveals a significant 2.0σ systematic difference in the calibration of Rung 2. If Rung 1 and Rung 2 are held fixed, the different formalisms developed for standardizing the supernova peak magnitudes yield consistent results, with a standard deviation of 1.5 $\, \rm km\, s^{-1} \, Mpc^{-1}$, that is, Type Ia supernovae are able to anchor Rung 3 with 2 per cent precision. This study demonstrates that Type Ia supernovae have provided a remarkably robust calibration of R3 for over 25 yr.
Identification of AKARI infrared sources by the Deep HSC Optical Survey: construction of a new band-merged catalogue in the North Ecliptic Pole Wide field
Authors: Kim Seong Jin , Oi Nagisa , Goto Tomotsugu , Ikeda Hiroyuki , Ho Simon C-C , Shim Hyunjin , Toba Yoshiki , Hwang Ho Seong , Hashimoto Tetsuya , Barrufet Laia , Malkan Matthew , Kim Helen K , Huang Ting-Chi , Matsuhara Hideo , Miyaji Takamitsu , Pearson Chris , Serjeant Stephen , Santos Daryl Joe D , Kim Eunbin , Pollo Agnieszka , Jeong Woong-Seob , Wang Ting-Wen , Momose Rieko , Takagi Toshinobu 
Published: October 2020

ABSTRACT
The North Ecliptic Pole field is a natural deep-field location for many satellite observations. It has been targeted many times since it was surveyed by the AKARI space telescope with its unique wavelength coverage from the near- to mid-infrared (mid-IR). Many follow-up observations have been carried out, making this field one of the most frequently observed areas with a variety of facilities, accumulating abundant panchromatic data from the X-ray to the radio wavelength range. Recently, a deep optical survey with the Hyper Suprime-Cam (HSC) at the Subaru telescope covered the NEP-Wide (NEPW) field, which enabled us to identify faint sources in the near- and mid-IR bands, and to improve the photometric redshift (photo-z) estimation. In this work, we present newly identified AKARI sources by the HSC survey, along with multiband photometry for 91 861 AKARI sources observed over the NEPW field. We release a new band-merged catalogue combining various photometric data from the GALEX UV to submillimetre (sub-mm) bands (e.g. Herschel/SPIRE, JCMT/SCUBA-2). About ∼20 000 AKARI sources are newly matched to the HSC data, most of which seem to be faint galaxies in the near- to mid-infrared AKARI bands. This catalogue is motivating a variety of current research, and will be increasingly useful as recently launched (eROSITA/ART-XC) and future space missions (such as JWST, Euclid, and SPHEREx) plan to take deep observations in the NEP field.
Histone sumoylation promotes Set3 histone-deacetylase complex-mediated transcriptional regulation
Authors: Ryu Hong-Yeoul , Zhao Dejian , Li Jianhui , Su Dan , Hochstrasser Mark 
Published: October 2020

Abstract
Histones are substrates of the SUMO (small ubiquitin-like modifier) conjugation pathway. Several reports suggest histone sumoylation affects transcription negatively, but paradoxically, our genome-wide analysis shows the modification concentrated at many active genes. We find that trans-tail regulation of histone-H2B ubiquitylation and H3K4 di-methylation potentiates subsequent histone sumoylation. Consistent with the known control of the Set3 histone deacetylase complex (HDAC) by H3K4 di-methylation, histone sumoylation directly recruits the Set3 complex to both protein-coding and noncoding RNA (ncRNA) genes via a SUMO-interacting motif in the HDAC Cpr1 subunit. The altered gene expression profile caused by reducing histone sumoylation matches well to the profile in cells lacking Set3. Histone H2B sumoylation and the Set3 HDAC coordinately suppress cryptic ncRNA transcription initiation internal to mRNA genes. Our results reveal an elaborate co-transcriptional histone crosstalk pathway involving the consecutive ubiquitylation, methylation, sumoylation and deacetylation of histones, which maintains transcriptional fidelity by suppressing spurious transcription.
PTRF/cavin-1 remodels phospholipid metabolism to promote tumor proliferation and suppress immune responses in glioblastoma by stabilizing cPLA2
Authors: Yi Kaikai , Zhan Qi , Wang Qixue , Tan Yanli , Fang Chuan , Wang Yunfei , Zhou Junhu , Yang Chao , Li Yansheng , Kang Chunsheng 
Published: October 2020

Abstract

Background
Metabolism remodeling is a hallmark of glioblastoma (GBM) that regulates tumor proliferation and the immune microenvironment. Previous studies have reported that increased polymerase 1 and transcript release factor (PTRF) levels are associated with a worse prognosis in glioma patients. However, the biological role and the molecular mechanism of PTRF in GBM metabolism remain unclear.

Methods
The relationship between PTRF and lipid metabolism in GBM was detected by nontargeted metabolomics profiling and subsequent lipidomics analysis. Western blotting, quantitative real-time PCR, and immunoprecipitation were conducted to explore the molecular mechanism of PTRF in lipid metabolism. A sequence of in vitro and in vivo experiments (both xenograft tumor and intracranial tumor mouse models) were used to detect the tumor-specific impacts of PTRF.

Results
Here, we show that PTRF triggers a cytoplasmic phospholipase A2 (cPLA2)–mediated phospholipid remodeling pathway that promotes GBM tumor proliferation and suppresses tumor immune responses. Research in primary cell lines from GBM patients revealed that cells overexpressing PTRF show increased cPLA2 activity—resulting from increased protein stability—and exhibit remodeled phospholipid composition. Subsequent experiments revealed that PTRF overexpression alters the endocytosis capacity and energy metabolism of GBM cells. Finally, in GBM xenograft and intracranial tumor mouse models, we showed that inhibiting cPLA2 activity blocks tumor proliferation and prevents PTRF-induced reduction in CD8+ tumor-infiltrating lymphocytes.

Conclusions
The PTRF-cPLA2 lipid remodeling pathway promotes tumor proliferation and suppresses immune responses in GBM. In addition, our findings highlight multiple new therapeutic targets for GBM.
Henri Lefebvre
Authors: Zieleniec Andy 
Published: October 2020

Henri Lefebvre is now established as one of the most important social theorists of the 20th century. Over a long life (b. 1901–d. 1991) he wrote and published prodigiously more than sixty books and several hundred articles on a range of issues and themes. His legacy and lasting impact not only includes being the most influential and seminal theorist on the reprioritization of space in social and critical analysis but also recognition for his contribution to the analysis of everyday life, modernity, the Right to the City, and the urban. He continues to influence and inspire research across a number of disciplines and fields; these include rural and regional studies, sociology, geography, politics, philosophy, and urban studies. Lefebvre’s commitment Marxism; his nondogmatic and humanist approach to the definition, discussion, extension, and application of key concepts; and his integration of those concepts into his various analyses of the rural and the city, of the state, of space and politics, and of modernity and everyday life led him to a conflicted relationship and at times marginalization within the structuralist-influenced French Academy and the Communist Party of France in which he was a member for thirty years. His anti-Stalinist stance and nonconformist opposition to the structural determinism prevalent within the party led to his expulsion, but throughout the 1960s, as professor of sociology at the University of Strasbourg and latterly at the new university at Nanterre, he became one of the most respected teachers and intellectuals inspiring and influencing the May 1968 student revolt. Lefebvre’s work after that, still influenced and committed to Marxist dialectics and critique, increasingly focused on the urban, the social production of space, everyday life, modernity, and the survival of capitalism. Of these his introduction of the concept of the right to the city and the social production of space have been immensely influential for a range of urban scholars and theorists and his work as a whole is being increasingly adopted, adapted, and extended by a variety of researchers of the city in a range of disciplines. The works selected below reflect Lefebvre’s long career and extensive corpus of work. However, only those books and articles that have been translated into English are included here. They represent his exegesis of Marxism and its application to a range of themes that were applied or are important for urban analysis. The secondary literature cited is organized thematically and while not comprehensive provides an overview of the expanding literature on, about, and applying Lefebvrian analysis.
Balancing Rights and Interests: Reconstructing the Asymmetry Thesis
Authors: Klatt Matthias 
Published: October 2020

Abstract
Dworkin, Schauer and others have argued that the last step of the proportionality test, ie balancing, is subject to a significant asymmetry. While we could balance interests against each other, we could not do so with rights, lest we destroy the unique normative status of rights. If this asymmetry exists, the applicability of balancing would be considerably limited. I analyse the asymmetry thesis and discuss its merits and weaknesses. I then demonstrate how we can accommodate the rationale behind the asymmetry thesis within the principles theory’s account of balancing. My article confirms that proportionality adjudication includes the balancing of rights and interests.
Possession and Damages for Tortious Interferences with Chattels
Authors: Rostill Luke 
Published: October 2020

Abstract
The common law has long maintained that, where a defendant has tortiously interfered with a chattel that was in the claimant’s possession at the time of the wrong, the claimant is, in general, to be presumed to be the ‘absolute and complete owner’ of the chattel. It is argued in this article that the rule lacks a satisfactory justificatory basis: the justification that has been endorsed by the courts is fatally flawed, and the main alternative justifications that have been advanced in the academic literature are also unsatisfactory. If an adequate foundation cannot be found, the rule should be abolished and, if it were to be abolished, there are, it is suggested, good reasons to introduce a similar, but importantly different, rule of presumption.
Labor in the Boardroom
Authors: Jäger Simon , Schoefer Benjamin , Heining Jörg 
Published: October 2020

AbstractWe estimate the wage effects of shared governance, or codetermination, in the form of a mandate of one-third of corporate board seats going to worker representatives. We study a reform in Germany that abruptly abolished this mandate for stock corporations incorporated after August 1994, while it locked the mandate for the slightly older cohorts. Our research design compares firm cohorts incorporated before the reform and after; in a robustness check we draw on the analogous difference in unaffected firm types (LLCs). We find no effects of board-level codetermination on wages and the wage structure, even in firms with particularly flexible wages. The degree of rent sharing and the labor share are also unaffected. We reject that disinvestment could have offset wage effects through the canonical hold-up channel, as shared governance, if anything, increases capital formation.
Deep phenotyping of synovial molecular signatures by integrative systems analysis in rheumatoid arthritis
Authors: Jung Seung Min , Park Kyung-Su , Kim Ki-Jo 
Published: October 2020

AbstractObjectiveRA encompasses a complex, heterogeneous and dynamic group of diseases arising from molecular and cellular perturbations of synovial tissues. The aim of this study was to decipher this complexity using an integrative systems approach and provide novel insights for designing stratified treatments.MethodsAn RNA sequencing dataset of synovial tissues from 152 RA patients and 28 normal controls was imported and subjected to filtration of differentially expressed genes, functional enrichment and network analysis, non-negative matrix factorization, and key driver analysis. A naïve Bayes classifier was applied to the independent datasets to investigate the factors associated with treatment outcome.ResultsA matrix of 1241 upregulated differentially expressed genes from RA samples was classified into three subtypes (C1–C3) with distinct molecular and cellular signatures. C3 with prominent immune cells and proinflammatory signatures had a stronger association with the presence of ACPA and showed a better therapeutic response than C1 and C2, which were enriched with neutrophil and fibroblast signatures, respectively. C2 was more occupied by synovial fibroblasts of destructive phenotype and carried highly expressed key effector molecules of invasion and osteoclastogenesis. CXCR2, JAK3, FYN and LYN were identified as key driver genes in C1 and C3. HDAC, JUN, NFKB1, TNF and TP53 were key regulators modulating fibroblast aggressiveness in C2.ConclusionsDeep phenotyping of synovial heterogeneity captured comprehensive and discrete pathophysiological attributes of RA regarding clinical features and treatment response. This result could serve as a template for future studies to design stratified approaches for RA patients.
Evaluation of performance and carcass traits for a five-cohort All Heifer, No Cow beef production system demonstration herd
Authors: Harrison Meredith A , Arce-Cordero Jose A , Seidel George E , Archibeque Shawn L , Whittier Jack C , Rhoades Ryan D , Ahola Jason K 
Published: October 2020

Abstract
The All Heifer, No Cow (AHNC) beef production system is an alternative to conventional cow/calf production that involves insemination of nulliparous heifers with sexed semen to produce female calves that are early weaned at 3 mo of age. Dams are finished on a high-concentrate diet and harvested before reaching 30 mo of age. Objectives of this research were to document reproductive, feedyard, calf, and carcass performance of an AHNC herd; evaluate effects of carcass maturity on carcass quality; and determine if performance of initial cohorts (i.e., cohorts 1 and 2) differed from sustaining cohorts (i.e., cohorts 3–5). A total of 272 heifers were enrolled in the AHNC system via five annual cohorts. The system was initiated with 51 yearling, Angus-based heifers, and a replicate set (n = 56) was started 12 mo after. Heifers in cohorts 3 (n = 53), 4 (n = 56), and 5 (n = 56) were primarily offspring of prior cohorts (i.e., cohort 3 heifers born to cohort 1 females), but some were purchased to maintain inventory. Angus replacement heifers were purchased in cohorts 3 (n = 26), 4 (n = 26), and 5 (n = 28). Mean (±standard deviation) pregnancy rate at 30 d after fixed-time artificial insemination (AI) with sexed semen was 50.8% ± 9.4%, and 140-d pregnancy rate was 93.0% ± 1.5%. With AHNC, 61.0% ± 6.5% of females replaced themselves with a heifer. During finishing, average daily gain (ADG) was 1.9 ± 0.4 kg • d−1 and dry matter intake (DMI) was 14.9 ± 1.9 kg • d−1. Hot carcass weight (HCW) was 367 ± 35 kg. The USDA grading system classified 20.5% of all carcasses (n = 220) as C maturity (A00 = 100, B00 = 200, etc.), 62.4% ± 29.1% of carcasses as USDA Choice. USDA yield grade (YG) was 2.6 ± 0.7. Based on cohorts 1 and 2, there were no differences (P = 0.96) in Warner–Bratzler shear force values between A and B maturity vs. C maturity carcasses. Across all cohorts, there were no differences in USDA YG, marbling score (MA), and lean maturity between A and B maturity vs. C maturity carcasses; there were differences in age (P &lt; 0.001), bone maturity (P &lt; 0.001), and overall maturity (P &lt;0.001). A comparison of initial vs. sustaining cohorts showed that initial cohorts had lower (P &lt; 0.001) DMI, heavier (P &lt; 0.001) HCW, and more advanced (P &lt; 0.05) bone maturity. However, there were no differences for 30- and 140-d pregnancy rates, ADG, USDA YG, and MA between initial and sustaining cohorts. The AHNC beef production system can effectively produce female calves and quality carcasses for harvest.