bluuebunny/crossref_metadata_2025_split huggingface dataset:
Versatile functions of RNA m6A machinery on chromatin
Authors: Song Tanjing , Lv Suli , Li Neng , Zhao Xuefeng , Ma Xianyun , Yan Yingying , Wang Weixia , Sun Lidong 
Published: February 2022

Abstract
m6A, a conserved and abundant modification on RNA, regulates RNA processing and function. RNA m6A machinery, including writers, erasers, and readers of m6A, is indispensable for m6A installation and function. Intriguingly, recent studies have revealed that m6A machinery can be recruited to chromatin by pleiotropic factors, including nascent RNA, transcription factors, regulatory RNA, histone modifications, and epigenetic machinery. Consequently, recruitment of m6A machinery can directly regulate chromatin biology, such as transcription, DNA damage repair, and DNA recombination beyond installation of m6A on nascent mRNA. Here, we discuss recent evidence showing that m6A machinery is targeted to chromatin and the direct biological consequences along with the underlying mechanisms.
A rare case report of pigment gallstones and a concomitant gastric gastrointestinal stromal tumour
Authors: Pillay Yagan 
Published: February 2022

Abstract
Gastric gastrointestinal stromal tumours (GISTs) with cholelithiasis in the English literature are quite rare with a few published case reports. Their concurrent surgical management has also been debated as the clinical symptoms are often ascribed to one of the pathologies. All case reports to date have reported on cholesterol cholelithiasis. We would like to present a first case report of pigment cholelithiasis and a gastric GIST and their concurrent laparoscopically management. This was facilitated due to the patient’s request to deal with both pathologies as well as the nebular signs concerning the symptoms that she presented with. We were able to undertake the dual surgeries without compromising her oncological outcomes.
The profit petroleum-sharing arrangement: legal complications of profit petroleum-sharing provisions of the Kurdistan Region production sharing contracts
Authors: Salih Rdhwan S 
Published: February 2022

Abstract
The method for sharing the profit petroleum between the host State and the contractor is one of the major topics in Production Sharing Contracts (PSCs). Profit petroleum generally can be split between a contractor and the host State based on fixed shares or the sliding scale method. This study has the principal aim of critically analysing and arguing the provisions of the Kurdistan Region utilized PSCs regarding profit petroleum-sharing arrangement in order to ascertain its legal complications. This study also aims to seek some alternatives that can be useful and adopted by the Kurdistan Regional Government (KRG) to make more profit and reduce the burden on the government. The Study has clarified that the KRG’s Model PSC and most of its PSCs have adopted the R-factor formula for sharing of profit petroleum that derives from the Kurdistan Region Oil and Gas Law No (22) of 2007. The adopted R-factor is not an appropriate method and its calculation and the contractor percentage share of profit petroleum varies in the signed PSCs. On the other hand, a number of the KRG’s PSCs, contrary to the stipulated R-factor formula in the Kurdistan Region Oil and Gas Law 2007, have adopted different formulas. Finally, the study propounds numerous recommendations for the Kurdistan Region to minimize legal contentions relating to the profit petroleum-sharing arrangement of the Kurdistan Region.
The Class II KNOX family members KNAT3 and KNAT7 redundantly participate in Arabidopsis seed coat mucilage biosynthesis
Authors: Zhang Yuanyuan , Yin Qi , Qin Wenqi , Gao Han , Du Jinge , Chen Jiajun , Li Huiling , Zhou Gongke , Wu Hong , Wu Ai-Min 
Published: February 2022

Abstract
The production of Arabidopsis seed mucilage involves complex polysaccharide biosynthetic pathways and developmental processes in seed epidermal cells. Although the polysaccharide components of Arabidopsis seed mucilage have been identified, their regulatory mechanism requires further investigation. Here, we show that Class II KNOX gene family members KNAT3 and KNAT7 play an essential role in regulating mucilage production in the early developmental stages of Arabidopsis seeds. Double mutant knat3knat7 resulted in defective seed mucilage production and columellae formation, whereas knat3 showed a normal phenotype compared with wild type, and the mucilage thickness in knat7 was slightly disturbed. Rhamnogalacturonan I (RG-I) and its biosynthetic substrates galacturonic acid and rhamnose were reduced in both the adherent and soluble mucilage of knat3knat7. Comparative transcriptome analysis on whole seeds suggested that polysaccharide, glucosinolate and anthocyanin biosynthetic pathways were specifically repressed in knat3knat7. Transient co-expression of KNAT3 and KNAT7 with promoter regions of candidate genes in Arabidopsis protoplasts revealed that both KNAT3 and KNAT7 act as positive regulators of the RG-I biosynthetic gene MUCILAGE-MODIFIED 4 (MUM4, AT1G53500). Collectively, our results demonstrate that KNAT3 and KNAT7 are multifunctional transcription factors in secondary cell wall development and redundantly modulate mucilage biosynthesis in Arabidopsis seeds.
Nitrogen deficiency- and sucrose-induced anthocyanin biosynthesis is modulated by HISTONE DEACETYLASE15 in Arabidopsis
Authors: Liao Hong-Sheng , Yang Chien-Chih , Hsieh Ming-Hsiun 
Published: February 2022

Abstract
Anthocyanin accumulation is a hallmark response to nitrogen (N) deficiency in Arabidopsis. Although the regulation of anthocyanin biosynthesis has been extensively studied, the roles of chromatin modification in this process are largely unknown. In this study we show that anthocyanin accumulation induced by N deficiency is modulated by HISTONE DEACETYLASE15 (HDA15) in Arabidopsis seedlings. The hda15-1 T-DNA insertion mutant accumulated more anthocyanins than the wild-type when the N supply was limited, and this was caused by up-regulation of anthocyanin biosynthetic and regulatory genes in the mutant. The up-regulated genes also had increased levels of histone acetylation in the mutant. The accumulation of anthocyanins induced by sucrose and methyl jasmonate, but not that induced by H2O2 and phosphate starvation, was also greater in the hda15-1 mutant. While sucrose increased histone acetylation in the hda15-1 mutant in genes in a similar manner to that caused by N deficiency, methyl jasmonate only enhanced histone acetylation in the genes involved in anthocyanin biosynthesis. Our results suggest that different stresses act through distinct regulatory modules to activate anthocyanin biosynthesis, and that HDA15-mediated histone modification modulates the expression of anthocyanin biosynthetic and regulatory genes to avoid overaccumulation in response to N deficiency and other stresses.
Transcription factor OsSGL is a regulator of starch synthesis and grain quality in rice
Authors: Liu Zhenming , Jiang Shun , Jiang Lingli , Li Wanjing , Tang Yuqin , He Wei , Wang Manling , Xing Junjie , Cui Yanchun , Lin Qinlu , Yu Feng , Wang Long 
Published: February 2022

Abstract
Starch biosynthesis during rice endosperm development is important for grain quality, as it influences grain size and physico-chemical properties, which together determine rice eating quality. Cereal starch biosynthetic pathways have been comprehensively investigated; however, their regulation, especially by transcriptional repressors remains largely unknown. Here, we identified a DUF1645 domain-containing protein, STRESS_tolerance and GRAIN_LENGTH (OsSGL), that participates in regulating rice starch biosynthesis. Overexpression of OsSGL reduced total starch and amylose content in the endosperm compared with the wild type. Chromatin immunoprecipitation sequencing and RNA-seq analyses indicated that OsSGL targets the transcriptional activity of several starch and sucrose metabolism genes. In addition, ChIP-qPCR, yeast one-hybrid, EMSA and dual-luciferase assays demonstrated that OsSGL directly inhibits the expression of SUCROSE SYNTHASE 1 (OsSUS1) in the endosperm. Furthermore, OsSUS1 interacts with OsSGL to release its transcriptional repression ability. Unexpectedly, our results also show that knock down and mutation of OsSGL disrupts the starch biosynthetic pathway, causing lower starch and amylose content. Therefore, our findings demonstrate that accurate control of OsSGL homeostasis is essential for starch synthesis and grain quality. In addition, we revealed the molecular mechanism of OsSGL in regulating starch biosynthesis-related genes, which are required for grain quality.
TRIPTYCHON-LIKE regulates aspects of both fruit flavor and color in citrus
Authors: He Jiaxian , Xu Yuantao , Huang Ding , Fu Jialing , Liu Ziang , Wang Lun , Zhang Yin , Xu Rangwei , Li Li , Deng Xiuxin , Xu Qiang 
Published: February 2022

Abstract
Deciphering the genetic basis of organoleptic traits is critical for improving the quality of fruits, which greatly shapes their appeal to consumers. Here, we characterize the citrus R3-MYB transcription factor TRIPTYCHON-LIKE (CitTRL), which is closely associated with the levels of citric acid, proanthocyanidins (PAs), and anthocyanins. Overexpression of CitTRL lowered acidity levels and PA contents in citrus calli as well as anthocyanin and PA contents in Arabidopsis leaves and seeds. CitTRL interacts with the two basic helix–loop–helix (bHLH) proteins CitbHLH1 and ANTHOCYANIN 1 (CitAN1) to regulate fruit quality. We show that CitTRL competes with the R2R3-MYB CitRuby1 for binding to CitbHLH1 or CitAN1, thereby repressing their activation of anthocyanin structural genes. CitTRL also competes with a second R2R3-MYB, CitPH4, for binding to CitAN1, thus altering the expression of the vacuolar proton-pump gene PH5 and Leucoanthocyanidin reductase, responsible for vacuolar acidification and proanthocyanidins biosynthesis, respectively. Moreover, CitPH4 activates CitTRL transcription, thus forming an activator–repressor loop to prevent the overaccumulation of citric acid and PAs. Overall, this study demonstrates that CitTRL acts as a repressor of the accumulation of citric acid, PAs, and anthocyanins by a cross-regulation mechanism. Our results provide an opportunity to simultaneously manipulate these key traits as a means to produce citrus fruits that are both visually and organoleptically appealing.
An Eddington ratio-driven origin for the LX − M* relation in quiescent and star-forming active galaxies
Authors: Carraro Rosamaria , Shankar Francesco , Allevato Viola , Rodighiero Giulia , Marsden Christopher , Arévalo Patricia , Delvecchio Ivan , Lapi Andrea 
Published: February 2022

ABSTRACT
A mild correlation exists in active galaxies between the mean black hole accretion, as traced by the mean X-ray luminosity &lt;LX&gt; and the host galaxy stellar mass M*, characterised by a normalization steadily decreasing with cosmic time and lower in more quiescent galaxies. We create comprehensive semi-empirical mock catalogues of active black holes to pin down which parameters control the shape and evolution of the &lt;LX&gt; − M* relation of X-ray-detected active galaxies. We find that the normalization of the &lt;LX&gt; − M* relation is largely independent of the fraction of active galaxies (the duty cycle), but strongly dependent on the mean Eddington ratio, when adopting a constant underlying MBH − M* relation as suggested by observational studies. The data point to a decreasing mean Eddington ratio with cosmic time and with galaxy stellar mass at fixed redshift. Our data can be reproduced by black holes and galaxies evolving on similar MBH − M* relations but progressively decreasing their average Eddington ratios, mean X-ray luminosities, and specific star formation rates, when moving from the starburst to the quiescent phase. Models consistent with the observed &lt;LX&gt; − M* relation and independent measurements of the mean Eddington ratios are characterised by MBH − M* relations lower than those derived from dynamically measured local black holes. Our results point to the &lt;LX&gt; − M* relation as a powerful diagnostic to: (1) probe black hole–galaxy scaling relations and the level of accretion on to black holes; (2) efficiently break the degeneracies between duty cycles and accretion rates in cosmological models of black holes.
Low-frequency observations of giant pulses from ordinary pulsars
Authors: Kazantsev A N , Basalaeva M Yu 
Published: February 2022

ABSTRACTWe present the results of an investigation of the giant radio pulse (GRP) generation rate from five radio pulsars (B0301+19, B0950+08, B1112+50, B1133+16, and B1237+25) and anomalous intensity pulse generation rate from B0809+74. All data used were obtained with the Large Phased Array radio telescope at the Pushchino Radio Astronomy Observatory at 111 MHz from 2012 to 2021. In addition to the analysis of the rate of generation of bright pulses, we analyse the distribution of bright pulses in the phase of the pulsar period and search for clusters of bright pulses – several bright pulses emitted in adjacent pulsar periods. It is found that pulsars B0301+19, B1112+50, B1133+16, and B1237+25 demonstrate different generation rates and generation of clusters. Pulsar B1112+50 generates GRP clusters more often than the other pulsars studied. The longest cluster of GRPs containing four single pulses is detected from this pulsar. GRPs from the pulsars studied are distributed along the longitudes of the main components of the average pulses of these pulsars. This distribution is 1.5–2 times narrower than the phase distribution of non-giant pulses. It is found that the distance between the components of the average GRP profile and the distance between the components of the average non-giant profile differ substantially for pulsars with multicomponent average profiles.
A statistical study of the optical spectral variability in gamma-ray blazars
Authors: Otero-Santos J , Acosta-Pulido J A , Becerra González J , Luashvili A , Castro Segura N , González-Martín O , Raiteri C M , Carnerero M I 
Published: February 2022

ABSTRACT
Blazars optical emission is generally dominated by relativistic jets, although the host galaxy, accretion disc, and broad-line region (BLR) may also contribute significantly. Disentangling their contributions has been challenging for years due to the dominance of the jet. To quantify the contributions to the spectral variability, we use the statistical technique for dimensionality reduction non-negative matrix factorization on a spectroscopic data set of 26 γ-ray blazars. This technique allows to model large numbers of spectra in terms of a reduced number of components. We use a priori knowledge to obtain components associated with meaningful physical processes. The sources are classified according to their optical spectrum as host-galaxy dominated BL Lac objects (BL Lacs), BL Lacs, or flat spectrum radio quasars (FSRQs). Host-galaxy sources show less variability, as expected, and bluer-when-brighter (BWB) trends, as the other BL Lacs. For FSRQs, more complicated colour-flux behaviours are observed: redder-when-brighter for low states saturating above a certain level and, in some cases, turning to BWB. We are able to reproduce the variability observed during 10 yr using only two to four components, depending on the type. The simplest scenario corresponds to host-galaxy blazars, whose spectra are reconstructed using the stellar population and a power law (PL) for the jet. BL Lac spectra are reproduced using from two to four PLs. Different components can be associated with acceleration/cooling processes taking place in the jet. The reconstruction of FSRQs also incorporates a QSO-like component to account for the BLR, plus a very steep PL, associated with the accretion disc.
Structure and kinematics of tidally limited satellite galaxies in LCDM
Authors: Errani Raphaël , Navarro Julio F , Ibata Rodrigo , Peñarrubia Jorge 
Published: February 2022

ABSTRACT
We use N-body simulations to model the tidal evolution of dark matter-dominated dwarf spheroidal galaxies embedded in cuspy Navarro-Frenk-White subhaloes. Tides gradually peel off stars and dark matter from a subhalo, trimming it down according to their initial binding energy. This process strips preferentially particles with long orbital times, and comes to an end when the remaining bound particles have crossing times shorter than a fraction of the orbital time at pericentre. The properties of the final stellar remnant thus depend on the energy distribution of stars in the progenitor subhalo, which in turn depends on the initial density profile and radial segregation of the initial stellar component. The stellar component may be completely dispersed if its energy distribution does not extend all the way to the subhalo potential minimum, although a bound dark remnant may remain. These results imply that ‘tidally limited’ galaxies, defined as systems whose stellar components have undergone substantial tidal mass-loss, neither converge to a unique structure nor follow a single tidal track. On the other hand, tidally limited dwarfs do have characteristic sizes and velocity dispersions that trace directly the characteristic radius (rmx) and circular velocity (Vmx) of the subhalo remnant. This result places strong upper limits on the size of satellites whose unusually low velocity dispersions are often ascribed to tidal effects. In particular, the large size of kinematically cold ‘feeble giant’ satellites like Crater 2 or Antlia 2 cannot be explained as due to tidal effects alone in the Lambda Cold Dark Matter scenario.
Using artificial intelligence and real galaxy images to constrain parameters in galaxy formation simulations
Authors: Macciò Andrea V , Ali-Dib Mohamad , Vulanovic Pavle , Al Noori Hind , Walter Fabian , Krieger Nico , Buck Tobias 
Published: February 2022

ABSTRACT
Cosmological galaxy formation simulations are still limited by their spatial/mass resolution and cannot model from first principles some of the processes, like star formation, that are key in driving galaxy evolution. As a consequence they still rely on a set of ’effective parameters’ that try to capture the scales and the physical processes that cannot be directly resolved in the simulation. In this study, we show that it is possible to use Machine Learning techniques applied to real and simulated images of galaxies to discriminate between different values of these parameters by making use of the full information content of an astronomical image instead of collapsing it into a limited set of values like size, or stellar/ gas masses. In this work, we apply our method to the NIHAO simulations and the THINGS and VLA-ANGST observations of H i maps in nearby galaxies to test the ability of different values of the star formation density threshold n to reproduce observed H i maps. We show that observations indicate the need for a high value of n ≳ 80 cm−3 (although the numerical value is model-dependent), which has important consequences for the dark matter distribution in galaxies. Our study shows that with innovative methods it is possible to take full advantage of the information content of galaxy images and compare simulations and observations in an interpretable, non-parametric, and quantitative manner.
Quantifying the Population-Level Effect of the COVID-19 Mass Vaccination Campaign in Israel: A Modeling Study
Authors: Somekh Ido , KhudaBukhsh Wasiur R , Root Elisabeth Dowling , Boker Lital Keinan , Rempala Grzegorz , Simões Eric A F , Somekh Eli 
Published: February 2022

Abstract

Background
Estimating real-world vaccine effectiveness is challenging as a variety of population factors can impact vaccine effectiveness. We aimed to assess the population-level reduction in cumulative severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cases, hospitalizations, and mortality due to the BNT162b2 mRNA coronavirus disease 2019 (COVID-19) vaccination campaign in Israel during January–February 2021.

Methods
A susceptible-infected-recovered/removed (SIR) model and a Dynamic Survival Analysis (DSA) statistical approach were used. Daily counts of individuals who tested positive and of vaccine doses administered, obtained from the Israeli Ministry of Health, were used to calibrate the model. The model was parameterized using values derived from a previous phase of the pandemic during which similar lockdown and other preventive measures were implemented in order to take into account the effect of these prevention measures on COVID-19 spread.

Results
Our model predicted for the total population a reduction of 648 585 SARS-CoV-2 cases (75% confidence interval [CI], 25 877–1 396 963) during the first 2 months of the vaccination campaign. The number of averted hospitalizations for moderate to severe conditions was 16 101 (75% CI, 2010–33 035), and reduction of death was estimated at 5123 (75% CI, 388–10 815) fatalities. Among children aged 0–19 years, we estimated a reduction of 163 436 (75% CI, 0–433 233) SARS-CoV-2 cases, which we consider to be an indirect effect of the vaccine.

Conclusions
Our results suggest that the rapid vaccination campaign prevented hundreds of thousands of new cases as well as thousands of hospitalizations and fatalities and has probably averted a major health care crisis.
Circulating Biomarkers for Therapeutic Monitoring of Anti-cancer Agents
Authors: Janse van Rensburg Helena J , Spiliopoulou Pavlina , Siu Lillian L 
Published: February 2022

Abstract
Circulating biomarkers have emerged as valuable surrogates for evaluating disease states in solid malignancies. Their relative ease of access and rapid turnover has bolstered clinical applications in monitoring treatment efficacy and cancer progression. In this review, the roles of various circulating biomarkers in monitoring treatment response are described. Non-specific markers of disease burden, tumor markers (eg CA 125, CEA, PSA, etc.), circulating tumor cells, nucleic acids, exosomes, and metabolomic arrays are highlighted. Specifically, the discovery of each of these markers is reviewed, with examples illustrating their use in influencing treatment decisions, and barriers to their application noted where these exist. Finally, opportunities for future work using these circulating biomarkers are discussed.
Survival and Incidence Patterns of Pancreatic Neuroendocrine Tumors Over the Last 2 Decades: A SEER Database Analysis
Authors: Sonbol Mohamad Bassam , Mazza Gina L , Mi Lanyu , Oliver Thomas , Starr Jason , Gudmundsdottir Hallbera , Cleary Sean P , Hobday Timothy , Halfdanarson Thorvardur R 
Published: February 2022

Abstract

Background
Pancreatic neuroendocrine tumors (pNETs) are rare cancers with outcomes determined by multiple factors including grade, stage, and clinical presentation. In this study, we aimed to determine the prognosis of patients with pNETs using a large population-based database.

Materials and Methods
In this population-based study, we identified patients with pNETs from the SEER 18 registry (2000-2016) using a combination of ICD-O-3 and histology codes. We calculated age-adjusted incidence rates using SEER*Stat 8.3.5. In addition, we analyzed overall survival (OS) using the Kaplan-Meier method, and investigated prognostic factors using a multivariable Cox proportional hazards model.

Results
A total of 8944 pNETs patients were identified. Annual incidence rates increased from 0.27 to 1.00 per 100 000. This was largely explained by an increase in number of patients diagnosed with localized disease in more recent years (2012-2016). Median OS was 68 months (95% CI [64, 73]) and 5-year OS rates in localized, regional, and metastatic disease were 83%, 67%, and 28%, respectively. There was a significant improvement in OS for patients diagnosed between 2009 and 2016 (median OS 85 months) compared with those diagnosed between 2000 and 2008 (median OS 46 months) (HR 0.66; 95% CI [0.62, 0.70]). This improvement in OS was consistent across all stages.

Conclusions and Relevance
This study shows a steady increase pNETs incidence with notable stage migration to earlier stages in recent years. This increase in incidence is accompanied by a significant improvement in survival across different disease stages.