bluuebunny/crossref_metadata_2025_split huggingface dataset:
The regulation of sequence specific NF-κB DNA binding and transcription by IKKβ phosphorylation of NF-κB p50 at serine 80
Authors: Smith Emma L , Somma Domenico , Kerrigan David , McIntyre Zoe , Cole John J , Liang Kai Ling , Kiely Patrick A , Keeshan Karen , Carmody Ruaidhrí J 
Published: October 2019

AbstractPhosphorylation of the NF-κB transcription factor is an important regulatory mechanism for the control of transcription. Here we identify serine 80 (S80) as a phosphorylation site on the p50 subunit of NF-κB, and IKKβ as a p50 kinase. Transcriptomic analysis of cells expressing a p50 S80A mutant reveals a critical role for S80 in selectively regulating the TNFα inducible expression of a subset of NF-κB target genes including pro-inflammatory cytokines and chemokines. S80 phosphorylation regulates the binding of p50 to NF-κB binding (κB) sites in a sequence specific manner. Specifically, phosphorylation of S80 reduces the binding of p50 at κB sites with an adenine at the −1 position. Our analyses demonstrate that p50 S80 phosphorylation predominantly regulates transcription through the p50:p65 heterodimer, where S80 phosphorylation acts in trans to limit the NF-κB mediated transcription of pro-inflammatory genes. The regulation of a functional class of pro-inflammatory genes by the interaction of S80 phosphorylated p50 with a specific κB sequence describes a novel mechanism for the control of cytokine-induced transcriptional responses.
Star-PAP controlled alternative polyadenylation coupled poly(A) tail length regulates protein expression in hypertrophic heart
Authors: Sudheesh A P , Mohan Nimmy , Francis Nimmy , Laishram Rakesh S , Anderson Richard A 
Published: October 2019

AbstractAlternative polyadenylation (APA)-mediated 3′-untranslated region (UTR) shortening is known to increase protein expression due to the loss of miRNA regulatory sites. Yet, mRNAs with longer 3′-UTR also show enhanced protein expression. Here, we identify a mechanism by which longer transcripts generated by the distal-most APA site leads to increased protein expression compared to the shorter transcripts and the longer transcripts are positioned to regulate heart failure (HF). A Star-PAP target gene, NQO1 has three poly(A) sites (PA-sites) at the terminal exon on the pre-mRNA. Star-PAP selects the distal-most site that results in the expression of the longest isoform. We show that the NQO1 distal-specific mRNA isoform accounts for the majority of cellular NQO1 protein. Star-PAP control of the distal-specific isoform is stimulated by oxidative stress and the toxin dioxin. The longest NQO1 transcript has increased poly(A) tail (PA-tail) length that accounts for the difference in translation potentials of the three NQO1 isoforms. This mechanism is involved in the regulation of cardiac hypertrophy (CH), an antecedent condition to HF where NQO1 downregulation stems from the loss of the distal-specific transcript. The loss of NQO1 during hypertrophy was rescued by ectopic expression of the distal- but not the proximal- or middle-specific NQO1 mRNA isoforms in the presence of Star-PAP expression, and reverses molecular events of hypertrophy in cardiomyocytes.
KnockTF: a comprehensive human gene expression profile database with knockdown/knockout of transcription factors
Authors: Feng Chenchen , Song Chao , Liu Yuejuan , Qian Fengcui , Gao Yu , Ning Ziyu , Wang Qiuyu , Jiang Yong , Li Yanyu , Li Meng , Chen Jiaxin , Zhang Jian , Li Chunquan 
Published: October 2019

Abstract
Transcription factors (TFs) and their target genes have important functions in human diseases and biological processes. Gene expression profile analysis before and after knockdown or knockout is one of the most important strategies for obtaining target genes of TFs and exploring TF functions. Human gene expression profile datasets with TF knockdown and knockout are accumulating rapidly. Based on the urgent need to comprehensively and effectively collect and process these data, we developed KnockTF (http://www.licpathway.net/KnockTF/index.html), a comprehensive human gene expression profile database of TF knockdown and knockout. KnockTF provides a number of resources for human gene expression profile datasets associated with TF knockdown and knockout and annotates TFs and their target genes in a tissue/cell type-specific manner. The current version of KnockTF has 570 manually curated RNA-seq and microarray datasets associated with 308 TFs disrupted by different knockdown and knockout techniques and across multiple tissue/cell types. KnockTF collects upstream pathway information of TFs and functional annotation results of downstream target genes. It provides details about TFs binding to promoters, super-enhancers and typical enhancers of target genes. KnockTF constructs a TF-differentially expressed gene network and performs network analyses for genes of interest. KnockTF will help elucidate TF-related functions and potential biological effects.
MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis
Authors: Vallenet David , Calteau Alexandra , Dubois Mathieu , Amours Paul , Bazin Adelme , Beuvin Mylène , Burlot Laura , Bussell Xavier , Fouteau Stéphanie , Gautreau Guillaume , Lajus Aurélie , Langlois Jordan , Planel Rémi , Roche David , Rollin Johan , Rouy Zoe , Sabatet Valentin , Médigue Claudine 
Published: October 2019

Abstract
Large-scale genome sequencing and the increasingly massive use of high-throughput approaches produce a vast amount of new information that completely transforms our understanding of thousands of microbial species. However, despite the development of powerful bioinformatics approaches, full interpretation of the content of these genomes remains a difficult task. Launched in 2005, the MicroScope platform (https://www.genoscope.cns.fr/agc/microscope) has been under continuous development and provides analysis for prokaryotic genome projects together with metabolic network reconstruction and post-genomic experiments allowing users to improve the understanding of gene functions. Here we present new improvements of the MicroScope user interface for genome selection, navigation and expert gene annotation. Automatic functional annotation procedures of the platform have also been updated and we added several new tools for the functional annotation of genes and genomic regions. We finally focus on new tools and pipeline developed to perform comparative analyses on hundreds of genomes based on pangenome graphs. To date, MicroScope contains data for >11 800 microbial genomes, part of which are manually curated and maintained by microbiologists (>4500 personal accounts in September 2019). The platform enables collaborative work in a rich comparative genomic context and improves community-based curation efforts.
Large-scale multiferroic complex oxide epitaxy with magnetically switched polarization enabled by solution processing
Authors: Liu Cong , An Feng , Gharavi Paria S M , Lu Qinwen , Zha Junkun , Chen Chao , Wang Liming , Zhan Xiaozhi , Xu Zedong , Zhang Yuan , Qu Ke , Yao Junxiang , Ou Yun , Zhao Zhiming , Zhong Xiangli , Zhang Dongwen , Valanoor Nagarajan , Chen Lang , Zhu Tao , Chen Deyang , Zhai Xiaofang , Gao Peng , Jia Tingting , Xie Shuhong , Zhong Gaokuo , Li Jiangyu 
Published: October 2019

Abstract
Complex oxides with tunable structures have many fascinating properties, though high-quality complex oxide epitaxy with precisely controlled composition is still out of reach. Here we have successfully developed solution-based single-crystalline epitaxy for multiferroic (1-x)BiTi(1-y)/2FeyMg(1-y)/2O3–(x)CaTiO3 (BTFM–CTO) solid solution in large area, confirming its ferroelectricity at the atomic scale with strong spontaneous polarization. Careful compositional tuning leads to a bulk magnetization of 0.07 ± 0.035 μB/Fe at room temperature, enabling magnetically induced polarization switching exhibiting a large magnetoelectric coefficient of 2.7–3.0 × 10−7 s/m. This work demonstrates the great potential of solution processing in large-scale complex oxide epitaxy and establishes novel room-temperature magnetoelectric coupling in epitaxial BTFM–CTO film, making it possible to explore a much wider space of composition, phase, and structure that can be easily scaled up for industrial applications.
Orbital element distribution of invariant manifolds associated with Lyapunov family of periodic orbits around L1 and L2
Authors: Saito Masaya M 
Published: October 2019

Abstract
This study explores the initial configurations that lead to an eventual approach to a given planet, particularly Jupiter, using the invariant manifold of Lyapunov orbits around Lagrangian points L1 or L2. Reachability to the vicinity of planets would provide information on developing a process for capturing irregular satellites, which are small bodies orbiting around a giant planet with a high eccentricity that are considered to have been captured by the mother planet, rather than formed in situ. A region several times the Hill radius is often used for determining reachability, combined with checking the velocity of the planetesimal with respect to the mother planet. This kind of direct computation is inapplicable when the Hill sphere is widely open and its boundary cannot be clearly recognized. Here, we thus employ Lyapunov periodic orbits (LOs) as a formal definition of the vicinity of Jupiter and numerically track the orbital distribution of the invariant manifold of an LO while varying the Jacobi constant, CJ. Numerical tracking of the manifold is carried out directly via repeated Poincaré mapping of points initially allocated densely on a fragment of the manifold near the fixed points, with the assistance of multi-precision arithmetic using the Multiple Precision Floating-Point Reliable Library. The numerical computations show that the distribution of the semi-major axis of points on the manifolds is quite heavily tailed and that its median spans roughly 1–2 times the Jovian orbital radius. The invariant manifold provides a distribution profile of a that is similar to that obtained using a direct method.
The Desert at the End of Empire: An Environmental History of the Armenian Genocide*
Authors: Dolbee Samuel 
Published: October 2019

Abstract
In the contentious historiography of the Armenian genocide, the desert has been acknowledged by almost everyone as the endpoint of the deportations of hundreds of thousands of Ottoman Armenian citizens in 1915 and the years that followed. Those who use the term ‘genocide’ suggest that this action was tantamount to a death sentence, while those who oppose the term claim that the desert exculpates the Ottoman state. This article unpacks the meaning of the Jazira region — one of the arid regions to which Armenians were sent — and suggests how Ottoman officials used the desert to kill and Armenians used it to survive, mostly as part of nomadic groups among whom they were somewhere between slaves and family members. The desert even came to shape the humanitarian rescue campaign in the wake of the genocide and World War I, as organizations worked to remove Armenian children from the desert and, subsequently, to transform the desert itself by establishing Armenian agricultural colonies. Yet some Armenians stayed, and remain to this day in the Jazira calling themselves Armenian Muslims in honor of their heritage. The desert not only shaped Armenian suffering and survival. The marginal environment also incubated a population of imperial survivors, whose existence did not fit comfortably with post-Ottoman national divisions, or the historiographies influenced by them.
A lattice implementation of the η-invariant and effective action for chiral fermions on the lattice
Authors: Tatsumi Aoyama , Kikukawa Yoshio 
Published: October 2019

Abstract
We consider a lattice implementation of the $\eta$-invariant, using the complex phase of the determinant of the simplified domain-wall fermion, which couples to an interpolating 5D gauge field. We clarify the relation to the effective action for chiral Ginsparg–Wilson fermions. The integrability, which holds true for anomaly-free theories in the classical continuum limit, is not assured on a lattice with finite spacing. A lattice expression for the 5D Chern–Simons term is obtained.
Langland and the Reinvention of Array in Late-Medieval England
Authors: Galloway Andrew 
Published: October 2019

Abstract
Tradecraft lurks throughout the allegories of cloth-making in William Langland’s Piers Plowman, more fully and sympathetically expressed than scholars have realized. But in spite of the depth of lore there, the poem continually examines the problem of supervising such craft production and producers. Assessing this double perspective adds a distinctive chapter to understandings of how Piers Plowman invokes and requires wide economic and social contexts, specifically those focused on cloth production, a topic more amenable to ‘thing theory’ than the ‘costume rhetoric’ often applied to the presentations of array in Chaucer and other poets. All writers in the period were confronted with major changes in how clothing was made, sold, and worn, but Piers Plowman’s concerns differ significantly from contemporary writings both in how intricately the poem invokes the cloth industry yet how frequently it indicates the need for its punctilious governance (and that of craft and labour in general). Langland’s presentations of array offer not only an original and highly informed contribution to a central instance of late-medieval social and allegorical signification but also a contradictory response to its changing social, industrial, and institutional dimensions. Langland uses array and its making and remaking to affirm craft, process, and aesthetics in general while imagining new forms of governance, religious and political, that might contain its social and ethical disruptions.
International Financial Integration and Crisis Contagion
Authors: Devereux Michael B , Yu Changhua 
Published: October 2019

AbstractInternational financial integration helps to diversify risk but also may spread crises across countries. We provide a quantitative analysis of this trade-off in a two-country general equilibrium model with collateral-constrained borrowing using a global solution method. Borrowing constraints bind occasionally, depending upon the state of the economy and levels of inherited debt. We examine different degrees of international financial integration, moving from financial autarky, to bond and equity market integration. Financial integration leads to a significant increase in global leverage, substantially escalates the probability of crises for any one country, and dramatically increases the degree of “contagion” across countries. Outside of crises, the impact of financial integration on macroeconomic aggregates is relatively small. But the impact of a crisis with integrated international financial markets is much less severe than that under financial market autarky. Thus, a trade-off emerges between the probability of crises and the severity of crises. Using a large cross-country database of financial crises in developing and developed economies over a forty-year period, we find evidence in support of the model.
Dissecting Characteristics Nonparametrically
Authors: Freyberger Joachim , Neuhierl Andreas , Weber Michael 
Published: October 2019

Abstract
We propose a nonparametric method to study which characteristics provide incremental information for the cross-section of expected returns. We use the adaptive group LASSO to select characteristics and to estimate how selected characteristics affect expected returns nonparametrically. Our method can handle a large number of characteristics and allows for a flexible functional form. Our implementation is insensitive to outliers. Many of the previously identified return predictors don’t provide incremental information for expected returns, and nonlinearities are important. We study our method’s properties in simulations and find large improvements in both model selection and prediction compared to alternative selection methods.
Authors have furnished an Internet Appendix, which is available on the Oxford University Press Web site next to the link to the final published paper online.
Fli1 deficiency induces endothelial adipsin expression, contributing to the onset of pulmonary arterial hypertension in systemic sclerosis
Authors: Miyagawa Takuya , Taniguchi Takashi , Saigusa Ryosuke , Fukayama Maiko , Takahashi Takehiro , Yamashita Takashi , Hirabayashi Megumi , Miura Shunsuke , Nakamura Kouki , Yoshizaki Ayumi , Sato Shinichi , Asano Yoshihide 
Published: October 2019

AbstractObjectivesAdipsin, or complement factor D, is a serine proteinase catalysing complement factor C3 breakdown, leading to the production of opsonin (C3b), membrane attack complex (C5b–C9) and anaphylatoxins (C3a and C5a). Since adipsin is potentially associated with pulmonary arterial hypertension in SSc, we investigated adipsin expression in dermal small vessels of SSc-involved skin, the mechanism regulating adipsin expression in endothelial cells, and the correlation of serum adipsin levels with SSc clinical symptoms.MethodsAdipsin expression was assessed by immunohistochemistry with skin sections of SSc and healthy subjects. mRNA levels of target genes and transcription factor binding to the ADIPSIN promoter were evaluated by quantitative reverse transcription PCR and chromatin immunoprecipitation, respectively. Serum adipsin levels were determined by enzyme-linked immunosorbent assay.ResultsAdipsin expression was remarkably increased in dermal small vessels of SSc-involved skin as compared with those of healthy control skin. Consistent with the notion that Fli1 deficiency induces SSc-like phenotypes in various types of cells, FLI1 siRNA enhanced adipsin expression at protein and mRNA levels and Fli1 bound to the ADIPSIN promoter in human dermal microvascular endothelial cells. Serum adipsin levels were significantly lower in diffuse cutaneous SSc patients than in limited cutaneous SSc patients and healthy controls, and were associated positively with elevated right ventricular systolic pressure and inversely with interstitial lung disease by multivariate regression analysis.ConclusionAdipsin is up-regulated at least partially by Fli1 deficiency in endothelial cells, potentially contributing to the development of pulmonary vascular involvement in SSc.
Amygdala activity to angry and fearful faces relates to bullying and victimization in adolescents
Authors: Swartz Johnna R , Carranza Angelica F , Knodt Annchen R 
Published: October 2019

AbstractRelational bullying and victimization are common social experiences during adolescence, but relatively little functional magnetic resonance imaging (fMRI) research has examined the neural correlates of bullying and victimization in adolescents. The aim of the present study was to address this gap by examining the association between amygdala activity to angry and fearful faces and peer relational bullying and victimization in a community-based sample of adolescents. Participants included 49 adolescents, 12–15 years old, who underwent fMRI scanning while completing an emotional face matching task. Results indicated that interactions between amygdala activity to angry and fearful faces predicted self-reported relational bullying and victimization. Specifically, a combination of higher amygdala activity to angry faces and lower amygdala activity to fearful faces predicted more bullying behavior, whereas a combination of lower amygdala activity to angry faces and lower amygdala activity to fearful faces predicted less relational victimization. Exploratory whole-brain analyses also suggested that increased rostral anterior cingulate cortex activity to fearful faces was associated with less bullying. These results suggest that relational bullying and victimization are related to different patterns of neural activity to angry and fearful faces, which may help in understanding how patterns of social information processing predict these experiences.
Dopamine-Induced Dysconnectivity Between Salience Network and Auditory Cortex in Subjects With Psychotic-like Experiences: A Randomized Double-Blind Placebo-Controlled Study
Authors: Rössler Julian , Rössler Wulf , Seifritz Erich , Unterrassner Lui , Wyss Thomas , Haker Helene , Wotruba Diana 
Published: October 2019

Abstract
Dopamine is involved in the pathophysiology of schizophrenia. Disrupted salience processing by the salience network (SN) may be a central link between dysregulated dopamine function and psychotic symptoms. However, dopaminergic influence on the SN and its presumed influence on psychotic and subpsychotic symptoms or psychotic-like experiences in healthy individuals remain unclear. Therefore, we investigated dopamine-induced changes in functional connectivity of the right anterior insula (rAI), a central SN hub, and their association with psychotic-like experiences. We enrolled 54 healthy, right-handed male subjects in a randomized, double-blind, cross-sectional placebo-controlled experiment. Psychotic-like experiences were assessed using the revised Exceptional Experiences Questionnaire (PAGE-R). They then received either placebo (n = 32) or 200 mg L-DOPA (n = 33), a dopamine precursor, orally and underwent resting-state functional magnetic resonance imaging. In a seed-to-voxel approach, we analyzed dopamine-induced changes in functional connectivity of the rAI and assessed the relationship between functional connectivity changes and PAGE-R score. L-DOPA reduced functional connectivity between the rAI and the left auditory cortex planum polare. In the placebo group, we found a strong negative correlation between PAGE-R score and rAI to planum polare functional connectivity; in the L-DOPA group, there was a strong positive correlation between PAGE-R score and functional connectivity between rAI and planum polare. The PAGE-R score explained about 30% of the functional connectivity variation between rAI and planum polare in the two groups. Our findings suggest that psychotic-like experiences are associated with dopamine-induced disruption of auditory input to the SN, which may lead to aberrant attribution of salience.
Biphasic feature of placebo response in primary insomnia: pooled analysis of data from randomized controlled clinical trials of orexin receptor antagonists
Authors: He Dongmei , Jiang Binghu , Guo Zhiwei , Mu Qiwen , Mcclure Morgan A 
Published: October 2019

Abstract

Objectives
The placebo response to orexin receptor antagonists in primary insomnia is little-known. Our aim was, therefore, to conduct a systematic review of placebo-controlled randomized clinical trials to characterize placebo response.

Methods
We performed a comprehensive literature search for randomized, placebo-controlled, double-blind clinical trials evaluating the efficacy of orexin receptor antagonists addressing primary insomnia. To pool effect size estimates (Cohen’s d) of placebo and orexin receptor antagonists across trials for outcome measures, a meta-analysis was done according to the Cochrane guideline.

Results
The placebo response was significant and robust to improve the symptoms of insomnia in terms of objective and subjective measures, and the effects (0.70 ± 0.51) in subjective measures were smaller than that (1.10 ± 1.14) in objective measures (p = 0.027). The biphasic feature of placebo response showed an initial short-term increase of placebo effect and subsequent changeless long-term effect.

Conclusion
The biphasic feature of placebo response is clinically useful, and neuroimaging is essential to clarify the long-term mechanism in the future.