bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sgr B2 hard X-ray emission with INTEGRAL after 2009: still detectable?
Authors: Kuznetsova Ekaterina , Krivonos Roman , Lutovinov Alexander , Clavel Maïca 
Published: October 2021

ABSTRACT
The molecular cloud Sgr B2 is a natural Compton mirror in the Central Molecular Zone. It is believed that the observed fading of the Sgr B2 X-ray emission in continuum and the Fe Kα 6.4 keV line indicates past X-ray flare activity of the supermassive black hole Sgr A⋆. Sgr B2 was investigated by the INTEGRAL observatory in the hard X-ray in 2003–2009, showing clear decay of its hard X-ray emission. In this work, we present a long-term time evolution of the Sgr B2 hard X-ray continuum after 2009, associated with the hard X-ray source IGR J17475−2822 as observed by INTEGRAL. The 30–80 keV sky maps, obtained in 2009–2019, demonstrate a significant excess spatially consistent with IGR J17475−2822. The observed 2003–2019 light curve of IGR J17475−2822 is characterized by a linear decrease by a factor of ∼2 until 2011, after which it reaches a constant level of ∼1 mCrab. The source spectrum above 17 keV is consistent with a power-law model with Γ = 1.4 and a high-energy cut-off at ∼43 keV. The Sgr B2 residual emission after ∼2011 shows a good correspondence with models of X-ray emission due to the irradiation of the molecular gas by hard X-rays and low-energy cosmic ray ions. We discuss the possible origin of the residual Sgr B2 emission after 2011 within these models, including theoretically predicted multiply scattered emission.
Polycyclic aromatic hydrocarbons and the ionized gas in galaxies with active nuclei
Authors: Silva-Ribeiro A , Krabbe A C , Canelo C M , Monteiro A F , Sales Dinalva A , Hernandez-Jimenez J A , Andrade D P P 
Published: October 2021

ABSTRACT
We present a study for a sample of galaxies with active nuclei to characterize the main type of PAH molecules present in these objects and the local physical conditions of their irradiating sources, as well as the characteristics of the residing ionized gas, by combining optical and infrared data. Photoionization models were built with the cloudy code to reproduce optical emission line ratios in combination with PAH intensity ratios. We find that the species containing 10−82 carbon atoms are the most abundant in the sample. We suggest that family of species with only two or three fused rings of and a nitrogen hanging, such as small aromatic amides are important targets worthy of consideration in future experimental/theoretical as well as observational studies. We find that the AGN photoionization models reproduce most of the observational data in the log (6.2/11.3) versus log ([${\rm N\, {\small II}}$] λ6584/H α) diagram with the optical to X-ray spectral index of αox = −1.4. The flux of small PAH, as well as the flux of ionized PAHs and PANH, decrease as the logarithm of the ionization parameter (log U) increases. The 6.2/11.3 PAH intensity ratio presents an anti correlation between the oxygen abundance and log U.Finally, we found that the ionization degree of PAH species increases with the decreasing of the 11.3/7.7 ratio and the log U, in agreement with the models proposed by Draine & Li.
Convergent Loss of Chemoreceptors across Independent Origins of Slave-Making in Ants
Authors: Jongepier Evelien , Séguret Alice , Labutin Anton , Feldmeyer Barbara , Gstöttl Claudia , Foitzik Susanne , Heinze Jürgen , Bornberg-Bauer Erich 
Published: October 2021

Abstract
The evolution of an obligate parasitic lifestyle often leads to the reduction of morphological and physiological traits, which may be accompanied by loss of genes and functions. Slave-making ants are social parasites that exploit the work force of closely related ant species for social behaviors such as brood care and foraging. Recent divergence between these social parasites and their hosts enables comparative studies of gene family evolution. We sequenced the genomes of eight ant species, representing three independent origins of ant slavery. During the evolution of eusociality, chemoreceptor genes multiplied due to the importance of chemical communication in insect societies. We investigated the evolutionary fate of these chemoreceptors and found that slave-making ant genomes harbored only half as many gustatory receptors as their hosts’, potentially mirroring the outsourcing of foraging tasks to host workers. In addition, parasites had fewer odorant receptors and their loss shows striking patterns of convergence across independent origins of parasitism, in particular in orthologs often implicated in sociality like the 9-exon odorant receptors. These convergent losses represent a rare case of convergent molecular evolution at the level of individual genes. Thus, evolution can operate in a way that is both repeatable and reversible when independent ant lineages lose important social traits during the transition to a parasitic lifestyle.
Hypoxia-inducible factor-1β is essential for upregulation of the hypoxia-induced FLT1 gene in placental trophoblasts
Authors: Sasagawa Tadashi , Nagamatsu Takeshi , Yanagisawa Manami , Fujii Tomoyuki , Shibuya Masabumi 
Published: October 2021

Abstract
Placental hypoxia and increased levels of maternal blood anti-angiogenic protein, soluble fms-like tyrosine kinase-1 (sFLT1), are associated with the pathogenesis of pre-eclampsia. We have demonstrated that hypoxia-inducible factor (HIF)-2α mediates the upregulation of the hypoxia-induced FLT1 gene in trophoblasts and their cell lines. Here, we investigated the involvement of HIF-1β, which acts as a dimerization partner for HIF-α, in the upregulation of the FLT1 gene via hypoxia. We confirmed the interactions between HIF-1β and HIF-2α in the nuclei of BeWo, JAR and JEG-3 cells under hypoxia via co-immunoprecipitation. We found that hypoxia-induced upregulation of the FLT1 gene in BeWo cells and secretion of sFLT1 in human primary trophoblasts were significantly reduced by siRNAs targeting HIF-1β. Moreover, the upregulation of the FLT1 gene in BeWo cells induced by dimethyloxaloylglycine (DMOG) was also inhibited by silencing either HIF-2α or HIF-1β mRNA. It was recently shown that DNA demethylation increases both basal and hypoxia-induced expression levels of the FLT1 gene in three trophoblast-derived cell lines. In the demethylated BeWo cells, siRNAs targeting HIF-2α and HIF-1β suppressed the further increase in the expression levels of the FLT1 gene due to hypoxia or treatment with DMOG. However, luciferase reporter assays and bisulfite sequencing revealed that a hypoxia response element (−966 to −962) of the FLT1 gene is not involved in hypoxia or DMOG-induced upregulation of the FLT1 gene. These findings suggest that HIF-1β is essential for the elevated production of sFLT1 in the hypoxic trophoblasts and that the HIF-2α/HIF-1β complex may be a crucial therapeutic target for pre-eclampsia.
What Is Cosmopsychism?
Authors: Ganeri Jonardon , Shani Itay 
Published: October 2021

Abstract
With the deepening crisis of physicalism and the decline in its status as a sustainable research programme, philosophers of mind have begun to investigate the alternative idea—now commonly designated panpsychism—that consciousness is a fundamental feature of nature, and that the mental states, properties, and events exhibited by human beings are metaphysically grounded in the conscious actuality of reality’s most basic entities. Cosmopsychism is the thesis that the cosmos as a whole displays psychological properties, cosmopsychological properties as we might call them, and that the mental states of human beings, and indeed human beings themselves as individual subjects of experience, are metaphysically grounded in the cosmopsychological properties of the cosmos. Richly sophisticated varieties of cosmopsychism can be found in the ancient Sanskrit classics, the Upaniṣads, and more particularly in those Vedānta philosophers who provide interpretations of these texts. The papers in this issue are explorations of the connections and explanatory potential between contemporary work on cosmopsychism and arguments from the Sanskrit tradition.
The Playful Self-Involution of Divine Consciousness: Sri Aurobindo’s Evolutionary Cosmopsychism and His Response to the Individuation Problem
Authors: Medhananda Swami 
Published: October 2021

AbstractThis article argues that the Indian philosopher-mystic Sri Aurobindo (1872–1950) espoused a sophisticated form of cosmopsychism that has great contemporary relevance. After first discussing Aurobindo’s prescient reflections on the “central problem of consciousness” and his arguments against materialist reductionism, I explain how he developed a panentheistic philosophy of “realistic Adwaita” on the basis of his own spiritual experiences and his intensive study of the Vedāntic scriptures. He derived from this realistic Advaita philosophy a highly original doctrine of evolutionary cosmopsychism, according to which the Divine Saccidānanda is “involved” in everything in the universe and gradually manifests itself at each stage of the evolutionary process from matter to life to mind, and ultimately, to Supermind—the final stage that is yet to come, upon the attainment of which we will attain knowledge of our true divine nature as Saccidānanda. I then reconstruct Aurobindo’s novel solution to the individuation problem, according to which the Divine Saccidānanda individuates into various distinct consciousnesses by playfully limiting itself through a process of “exclusive concentration.” Finally, I highlight the continued relevance of Aurobindo’s evolutionary cosmopsychism by bringing him into conversation with Itay Shani, a contemporary proponent of cosmopsychism.
A Buddhist Response to the Quality-Combination Problem for Panpsychism
Authors: Chadha Monima 
Published: October 2021

Abstract
Abhidharma Buddhist philosophy presents a version of what is now often called “panprotopsychism.” The most pressing group of problems for the Abhidharma panprotopsychism, like all other panpsychist views, is what Seager calls “the combination problem.” There are at least three versions of the problem: the subject-combination problem; the quality-combination problem; and the structure-combination problem. I begin with the Abhidharma Buddhist version of panprotopsychism and its account of conscious experience. The main focus of this paper is to show that Abhidharma panprotopsychist account of conscious experience solves the quality-combination problem. In the last and closing Section, I look at other versions of the combination problem, primarily the subject-combination problem and the structural problem and provide a sketch of the Abhidharma Buddhist response to these.
Pol3Base: a resource for decoding the interactome, expression, evolution, epitranscriptome and disease variations of Pol III-transcribed ncRNAs
Authors: Cai Li , Xuan Jiajia , Lin Qiao , Wang Junhao , Liu Shurong , Xie Fangzhou , Zheng Lingling , Li Bin , Qu Lianghu , Yang Jianhua 
Published: October 2021

AbstractRNA polymerase III (Pol III) transcribes hundreds of non-coding RNA genes (ncRNAs), which involve in a variety of cellular processes. However, the expression, functions, regulatory networks and evolution of these Pol III-transcribed ncRNAs are still largely unknown. In this study, we developed a novel resource, Pol3Base (http://rna.sysu.edu.cn/pol3base/), to decode the interactome, expression, evolution, epitranscriptome and disease variations of Pol III-transcribed ncRNAs. The current release of Pol3Base includes thousands of regulatory relationships between ∼79 000 ncRNAs and transcription factors by mining 56 ChIP-seq datasets. By integrating CLIP-seq datasets, we deciphered the interactions of these ncRNAs with &gt;240 RNA binding proteins. Moreover, Pol3Base contains ∼9700 RNA modifications located within thousands of Pol III-transcribed ncRNAs. Importantly, we characterized expression profiles of ncRNAs in &gt;70 tissues and 28 different tumor types. In addition, by comparing these ncRNAs from human and mouse, we revealed about 4000 evolutionary conserved ncRNAs. We also identified ∼11 403 tRNA-derived small RNAs (tsRNAs) in 32 different tumor types. Finally, by analyzing somatic mutation data, we investigated the mutation map of these ncRNAs to help uncover their potential roles in diverse diseases. This resource will help expand our understanding of potential functions and regulatory networks of Pol III-transcribed ncRNAs.
Factorbook: an updated catalog of transcription factor motifs and candidate regulatory motif sites
Authors: Pratt Henry E , Andrews Gregory R , Phalke Nishigandha , Huey Jack D , Purcaro Michael J , van der Velde Arjan , Moore Jill E , Weng Zhiping 
Published: October 2021

AbstractThe human genome contains ∼2000 transcriptional regulatory proteins, including ∼1600 DNA-binding transcription factors (TFs) recognizing characteristic sequence motifs to exert regulatory effects on gene expression. The binding specificities of these factors have been profiled both in vitro, using techniques such as HT-SELEX, and in vivo, using techniques including ChIP-seq. We previously developed Factorbook, a TF-centric database of annotations, motifs, and integrative analyses based on ChIP-seq data from Phase II of the ENCODE Project. Here we present an update to Factorbook which significantly expands the breadth of cell type and TF coverage. The update includes an expanded motif catalog derived from thousands of ENCODE Phase II and III ChIP-seq experiments and HT-SELEX experiments; this motif catalog is integrated with the ENCODE registry of candidate cis-regulatory elements to annotate a comprehensive collection of genome-wide candidate TF binding sites. The database also offers novel tools for applying the motif models within machine learning frameworks and using these models for integrative analysis, including annotation of variants and disease and trait heritability. Factorbook is publicly available at www.factorbook.org; we will continue to expand the resource as ENCODE Phase IV data are released.
Functional asymmetry and chemical reactivity of CsoR family persulfide sensors
Authors: Fakhoury Joseph N , Zhang Yifan , Edmonds Katherine A , Bringas Mauro , Luebke Justin L , Gonzalez-Gutierrez Giovanni , Capdevila Daiana A , Giedroc David P 
Published: October 2021

Abstract
CstR is a persulfide-sensing member of the functionally diverse copper-sensitive operon repressor (CsoR) superfamily. While CstR regulates the bacterial response to hydrogen sulfide (H2S) and more oxidized reactive sulfur species (RSS) in Gram-positive pathogens, other dithiol-containing CsoR proteins respond to host derived Cu(I) toxicity, sometimes in the same bacterial cytoplasm, but without regulatory crosstalk in cells. It is not clear what prevents this crosstalk, nor the extent to which RSS sensors exhibit specificity over other oxidants. Here, we report a sequence similarity network (SSN) analysis of the entire CsoR superfamily, which together with the first crystallographic structure of a CstR and comprehensive mass spectrometry-based kinetic profiling experiments, reveal new insights into the molecular basis of RSS specificity in CstRs. We find that the more N-terminal cysteine is the attacking Cys in CstR and is far more nucleophilic than in a CsoR. Moreover, our CstR crystal structure is markedly asymmetric and chemical reactivity experiments reveal the functional impact of this asymmetry. Substitution of the Asn wedge between the resolving and the attacking thiol with Ala significantly decreases asymmetry in the crystal structure and markedly impacts the distribution of species, despite adopting the same global structure as the parent repressor. Companion NMR, SAXS and molecular dynamics simulations reveal that the structural and functional asymmetry can be traced to fast internal dynamics of the tetramer. Furthermore, this asymmetry is preserved in all CstRs and with all oxidants tested, giving rise to markedly distinct distributions of crosslinked products. Our exploration of the sequence, structural, and kinetic features that determine oxidant-specificity suggest that the product distribution upon RSS exposure is determined by internal flexibility.
ImmReg: the regulon atlas of immune-related pathways across cancer types
Authors: Jiang Tiantongfei , Zhou Weiwei , Chang Zhenghong , Zou Haozhe , Bai Jing , Sun Qisen , Pan Tao , Xu Juan , Li Yongsheng , Li Xia 
Published: October 2021

Abstract
Immune system gene regulation perturbation has been found to be a major cause of the development of various types of cancer. Numbers of mechanisms contribute to gene expression regulation, thus, systematically identification of potential regulons of immune-related pathways is critical to cancer immunotherapy. Here, we comprehensively chart the landscape of transcription factors, microRNAs, RNA binding proteins and long noncoding RNAs regulation in 17 immune-related pathways across 33 cancers. The potential immunology regulons are likely to exhibit higher expressions in immune cells, show expression perturbations in cancer, and are significantly correlated with immune cell infiltrations. We also identify a panel of clinically relevant immunology regulons across cancers. Moreover, the regulon atlas of immune-related pathways helps prioritizing cancer-related genes (i.e. ETV7, miR-146a-5p, ZFP36 and HCP5). We further identified two molecular subtypes of glioma (cold and hot tumour phenotypes), which were characterized by differences in immune cell infiltrations, expression of checkpoints, and prognosis. Finally, we developed a user-friendly resource, ImmReg (http://bio-bigdata.hrbmu.edu.cn/ImmReg/), with multiple modules to visualize, browse, and download immunology regulation. Our study provides a comprehensive landscape of immunology regulons, which will shed light on future development of RNA-based cancer immunotherapies.
Epigenetic regulation of nuclear lamina-associated heterochromatin by HAT1 and the acetylation of newly synthesized histones
Authors: Popova Liudmila V , Nagarajan Prabakaran , Lovejoy Callie M , Sunkel Benjamin D , Gardner Miranda L , Wang Meng , Freitas Michael A , Stanton Benjamin Z , Parthun Mark R 
Published: October 2021

Abstract
A central component of the epigenome is the pattern of histone post-translational modifications that play a critical role in the formation of specific chromatin states. Following DNA replication, nascent chromatin is a 1:1 mixture of parental and newly synthesized histones and the transfer of modification patterns from parental histones to new histones is a fundamental step in epigenetic inheritance. Here we report that loss of HAT1, which acetylates lysines 5 and 12 of newly synthesized histone H4 during replication-coupled chromatin assembly, results in the loss of accessibility of large domains of heterochromatin, termed HAT1-dependent Accessibility Domains (HADs). HADs are mega base-scale domains that comprise ∼10% of the mouse genome. HAT1 globally represses H3 K9 me3 levels and HADs correspond to the regions of the genome that display HAT1-dependent increases in H3 K9me3 peak density. HADs display a high degree of overlap with a subset of Lamin-Associated Domains (LADs). HAT1 is required to maintain nuclear structure and integrity. These results indicate that HAT1 and the acetylation of newly synthesized histones may be critical regulators of the epigenetic inheritance of heterochromatin and suggest a new mechanism for the epigenetic regulation of nuclear lamina-heterochromatin interactions.
Evaluation of severity of delayed graft function in kidney transplant recipients
Authors: Schrezenmeier Eva , Müller Mia , Friedersdorff Frank , Khadzhynov Dmytro , Halleck Fabian , Staeck Oliver , Dürr Michael , Zhang Kun , Eckardt Kai-Uwe , Budde Klemens , Lehner Lukas J 
Published: October 2021

ABSTRACT

Background
The most common definition of delayed graft function (DGF) relies on dialysis during the first week post-transplant and does not consider DGF severity. The impact of DGF severity on long-term graft outcome remains controversial.

Methods
We analysed 627 deceased-donor kidney transplant recipients (KTRs) transplanted in 2005–2015 at our centre for DGF severity, associated risk factors and long-term consequences of DGF.

Results
We found 349 (55.7%) KTRs with DGF, which were classified into four groups according to DGF duration (0–1, 2–7, 8–14, &gt;14 days) and were compared with KTR with no DGF. A longer duration of DGF was associated with progressive worsening of 10-year death-censored graft survival {no DGF: 88.3% [95% confidence interval (CI) 82.4–94.2]; 0–1 day: 81.3% [95% CI 68.2–94.4], 2–7 days: 61.5% [95% CI 43.1.1–79.9], 8–14 days: 66.6% [95% CI 47.4–85.8], &gt;14 days: 51.2% [95% CI 33–69.4]; P &lt; 0.001}. In kidneys with a Kidney Donor Profile Index (KDPI) ≥85%, all DGF severity groups demonstrated reduced graft survival. However, in the &lt;85% KDPI kidneys, only &gt;14 days DGF duration showed worse outcomes.

Conclusions
DGF had a duration-dependent effect on graft survival, which varied depending on the KDPI. Of note, 0- to 1-day DGF showed comparable results to no DGF in the whole cohort.
Global Implementation of Tobacco Demand Reduction Measures Specified in Framework Convention on Tobacco Control
Authors: Hiilamo Heikki , Glantz Stanton 
Published: October 2021

Abstract

Introduction
The world’s first global health treaty, WHO Framework Convention on Tobacco Control (FCTC) aims to reduce tobacco product demand by focusing on tobacco taxes, smoking bans, health warning labels, and tobacco advertising bans. Previous studies almost unanimously suggest that FCTC has prompted countries to implement more effective tobacco demand reduction policies.

Aims and Methods
By taking into account the pre-FCTC status, country income level, and state capacity we studied if ratifying FCTC was associated with tobacco demand reduction measures in 2018/2019. We used logistic regression to assess the association of FCTC ratification with adoption demand reduction measures, accounting for years since ratification, baseline status, and other covariates.

Results
Except for taxes, state of tobacco policy implementation before FCTC ratification did not predict adoption of FCTC policies. Time since FCTC ratification was associated with implementing smoking bans and pictorial HWLs. In contrast, while the tax rate prior to FCTC ratification was positively associated with increased taxes after FCTC ratification, time since FCTC ratification was marginally negatively associated with increases in tobacco taxes.

Conclusions
While the FCTC was followed by implementation of compliant demand reduction policies, there are still many parties that have not implemented the FCTC, particularly increasing taxes and ending tobacco advertising and promotions.

Implications
We assessed changes in tobacco demand reductions measures over 22 years in 193 countries. By using internal tobacco industry documents, we were able establish a baseline before the FCTC negotiations. Unlike previous studies, we included four tobacco demand reductions measures: tobacco taxes, smoking bans, health warning labels, and tobacco advertising ban. The limitation of the study is that we do not have data to describe if demand reduction measures are actually enforced or what their effect on tobacco consumption is.