bluuebunny/crossref_metadata_2025_split huggingface dataset:
Involvement of the SAGA and TFIID coactivator complexes in transcriptional dysregulation caused by the separation of core and tail Mediator modules
Authors: Saleh Moustafa M , Hundley Heather A , Zentner Gabriel E 
Published: November 2022

Abstract
Regulation of RNA polymerase II transcription requires the concerted efforts of several multisubunit coactivator complexes, which interact with the RNA polymerase II preinitiation complex to stimulate transcription. We previously showed that separation of the Mediator core from Mediator’s tail module results in modest overactivation of genes annotated as highly dependent on TFIID for expression. However, it is unclear if other coactivators are involved in this phenomenon. Here, we show that the overactivation of certain genes by Mediator core/tail separation is blunted by disruption of the Spt-Ada-Gcn5-Acetyl transferase complex through the removal of its structural Spt20 subunit, though this downregulation does not appear to completely depend on reduced Spt-Ada-Gcn5-Acetyl transferase association with the genome. Consistent with the enrichment of TFIID-dependent genes among genes overactivated by Mediator core/tail separation, depletion of the essential TFIID subunit Taf13 suppressed the overactivation of these genes when Med16 was simultaneously removed. As with Spt-Ada-Gcn5-Acetyl transferase, this effect did not appear to be fully dependent on the reduced genomic association of TFIID. Given that the observed changes in gene expression could not be clearly linked to alterations in Spt-Ada-Gcn5-Acetyl transferase or TFIID occupancy, our data may suggest that the Mediator core/tail connection is important for the modulation of Spt-Ada-Gcn5-Acetyl transferase and/or TFIID conformation and/or function at target genes.
Rupture properties of the 2020Mw 6.8 Calama (northern Chile) intraslab earthquake. Comparison with similar intraslab events in the region
Authors: Herrera Carlos , Pastén-Araya Francisco , Cabrera Leoncio , Potin Bertrand , Rivera Efraín , Ruiz Sergio , Madariaga Raúl , Contreras-Reyes Eduardo 
Published: November 2022

SUMMARYWe study the 2020 Mw 6.8 Calama earthquake sequence that occurred within the subducting oceanic Nazca plate. The main shock is modelled via waveform inversion using a dynamic rupture model, while detection and location techniques are used to better characterize its aftershock sequence. We analyse the local seismotectonic and thermal context of the subducting Nazca plate to understand the trigger mechanism of this earthquake and how it compares with other significant earthquakes in the vicinity. The stress drop and the related dynamic rupture parameters of the Calama main shock are similar to those of the nearby 2007 Mw 6.8 Michilla and 2015Mw 6.7 Jujuy intraslab earthquakes, which occurred to the west (trenchwards) and to the east (under the backarc) of the Calama earthquake, respectively. The sequences of these three events were located using a 3-D tomographic velocity model. While the Michilla earthquake sequence occurred within the oceanic crust at temperatures of ∼250 °C, the Calama sequence occurred within the upper lithospheric mantle at ∼350 °C and exhibited a smaller aftershock productivity than Michilla. Additionally, the 3-D tomographic model shows intermediate VP/VS ratios (1.72–1.76) in the region of the Calama earthquake. This indicates a less hydrated environment that could be responsible for the smaller aftershock productivity of the Calama earthquake.
Making peace in the English civil wars
Authors: White William 
Published: November 2022

Abstract
This article argues that peacemaking became a central strand of political debate and practice in England during the 1640s. The traumatic experiences of civil war and the failure of elite politicians to negotiate a swift settlement forced English people to think more than ever before about how peace could be achieved and preserved. Those outside the usual spheres of political decision-making now offered themselves up as mediators between king and parliament and publicized their own schemes for national reconciliation. At the same time, the article shows how those most committed to the Parliamentarian or Royalist cause sought to present themselves as peacemakers. It argues that a crucial issue in these public debates about peace was whether a lasting settlement was more likely to be achieved through negotiation or through a decisive military victory for one side.
Macrophage-mediated immune response aggravates hearing disfunction caused by the disorder of mitochondrial dynamics in cochlear hair cells
Authors: Zhang Yuan , Fu Xiaolong , Li Yiyuan , Li Wen , Hong Guodong , Guo Siwei , Xiao Yu , Liu Ziyi , Ding Shuqin , Bi Xiuli , Ye Fanglei , Jin Jin , Chai Renjie 
Published: November 2022

AbstractMitochondrial dynamics is essential for maintaining the physiological function of the mitochondrial network, and its disorders lead to a variety of diseases. Our previous study identified mitochondrial dynamics controlled anti-tumor immune responses and anxiety symptoms. However, how mitochondrial dynamics affects auditory function in the inner ear remains unclear. Here, we show that the deficiency of FAM73a or FAM73b, two mitochondrial outer membrane proteins that mediate mitochondrial fusion, leads to outer hair cells (HCs) damage and progressive hearing loss in FVB/N mice. Abnormal mitochondrial fusion causes elevated oxidative stress and apoptosis of HCs in the early stage. Thereafter, the activation of macrophages and CD4+ T cell is found in the mutant mice with the increased expression of the inflammatory cytokines IL-12 and IFN-γ compared with control mice. Strikingly, a dramatically decreased number of macrophages by Clophosome®-A-Clodronate Liposomes treatment alleviates the hearing loss of mutant mice. Collectively, our finding highlights that FAM73a or FAM73b deficiency affects HCs survival by disturbing the mitochondrial function, and the subsequent immune response in the cochleae worsens the damage of HCs.
Therapeutic Applications of Garlic and Turmeric for the Diabetic Wound Healing in Mice
Authors: Farooq Muhammad A , Ali Shaukat , Sulayman Rida , Hassan Ali , Tahir Hafiz M , Shahzad Hafsa , Fiaz Umaima , Mughal Tafail A , Liaqat Irfana , Mumtaz Samaira , Nauroze Tooba , Mumtaz Shumaila 
Published: November 2022

Abstract
Diabetes is involved in delayed wound healing that can be cured by natural products such as garlic, turmeric, and fibroin extracts. Alloxan monohydrate is used for inducing diabetes in mice. The percent wound contraction of garlic (150 mg/ml), turmeric (100 mg/ml), and fibroin (50 mg/ml), individually and in combinations garlic (150 mg/ml) + fibroin (50 mg/ml), turmeric (100 mg/ml) + fibroin (50 mg/ml), garlic (150 mg/ml) + turmeric (100 mg/ml), and garlic (150 mg/ml) + turmeric (100 mg/ml) + fibroin (50 mg/ml) was checked by evaluating the healing time, % wound contraction and histological analysis. The serum level of MMPs (MMP 2, MMP7, MMP 9), pro-inflammatory cytokines (TNF-α, IL-6, IL-8), and TIMPs were evaluated. With the combination of three extracts (Ga+Tu+Fi) garlic (150 mg/ml), turmeric (100 mg/ml) and fibroin (50 mg/ml), wounds healed in 12 days and had 97.3 ± 2.2% wound contraction. While the positive control (polyfax) and diabetic control (saline) wounds healed in 17- and 19-days with wound contraction of 96.7 ± 1.4% and 96.3 ± 1.1%, respectively. Histological analysis showed that the combination of Ga+Tu+Fi exhibited an increase in the growth of collagen fibers, fibroblasts number, and keratinocytes, and lessened inflammation of blood vessels. The combination of Ga+Tu+Fi significantly alleviated the serum concentration of TNF-α (14.2 ± 0.7 pg/ml), IL-6 (10.0 ± 1.0 pg/ml), IL-8 (16.0 ± 1.5 pg/ml), MMP2 (228.0 ± 18.1 pg/ml), MMP7 (271.0 ± 9.9 pg/ml), and MMP9 (141.0 ± 5.3 pg/ml) to diabetic control. The level of TIMPs (193.0 ± 9.1 pg/ml) was increased significantly with respect to diabetic control. We conclude that the combination of these biomaterials possessed high regenerative and healing capabilities and can be an effective remedy in the healing of chronic wounds in diabetic patients.
In-plane-dominated vibration characteristics of piezoelectric thick circular plates based on higher-order plate theories
Authors: Ji Ming , Wu Yi-Chuang , Ma Chien-Ching 
Published: November 2022

ABSTRACT
Numerous engineering applications exist for the piezoelectric effect, which results from the electromechanical coupling between electrical and mechanical fields. In-plane vibrations of piezoelectric plates’ resonance frequencies and associated mode shapes have been thoroughly investigated. However, analytical solutions for in-plane-dominated vibrations of thick piezoelectric circular plates are limited. In this paper, higher-order plate theories for the in-plane-dominated vibration characteristics of piezoelectric circular thick plates under fully clamped and completely free boundary conditions are presented. The resonant frequencies and associated mode shapes were investigated based on two higher-order plate theories: second-order shear deformation plate theory and third-order shear deformation plate theory, as well as simplified third-order linear piezoelectric theory. Hamilton's principle was applied to derive equations of motion and boundary conditions. In the theoretical analysis, the resonant frequencies, associated mode shapes and distribution of electric displacements for various radius-to-thickness ratios were calculated. The numerical results obtained by the finite element method were compared with those obtained from theoretical analysis. Excellent agreement was found between the theoretical and numerical results for the thick piezoelectric circular plates.
Antiovarian cancer mechanism of esculetin: inducing G0/G1 arrest and apoptosis via JAK2/STAT3 signalling pathway
Authors: Yin Wen , Fu Xu , Chang Wenwen , Han Li , Meng Jiahao , Cao Aijia , Ren Xiaomin , Fan Zhongxiong , Zhou Suqin 
Published: November 2022

Abstract

Objectives
Esculetin is a coumarin derivative, which is extracted from the dried barks of fraxinus chinensis Roxb. Although it is reported esculetin possesses multiple pharmacological activities, its associated regulatory mechanism on ovarian cancer isn’t well investigated.

Methods
Cytotoxicity is evaluated by MTT, clonogenic and living/dead cells staining assays. Migration and invasion effects are investigated by wound healing, and transwell assays. The effect of cell cycle and apoptosis are analyzed by flow cytometry and western blotting. Mitochondrial membrane potential and intracellular reactive oxygen species (ROS) is assessed by fluorescence microscope. Analysis of animal experiments are carried out by various pathological section assays.

Key findings
Esculetin exerts an anti- ovarian cancer effect. It is found that apoptosis induction is promoted by the accumulation of excessive ROS and inhibition of JAK2/STAT3 signalling pathway. In addition, exposure to esculetin leads to the cell viability reduction, migration and invasion capability decrease and G0/G1 phase cell cycle arrest induced by down-regulating downstream targets of STAT3. In vivo experimental results also indicate esculetin can inhibit tumour growth of mice.

Conclusions
Our study provides some strong evidences to support esculetin as a potential anti-cancer agent in ovarian cancer.
Unusual twisting of a reconstructed FDP tendon of the little finger after spontaneous attrition rupture on the hamate bone: a case report
Authors: Mousa Samar , Shirley Rebecca 
Published: November 2022

Abstract
We describe a case of attrition rupture of flexor digitorum profundus tendon of the right little finger in a 64-year-old lady caused by a prominent hook of hamate. The tendon was reconstructed primarily by palmaris longus tendon graft and was complicated by tendon graft twisting by scar tissue, resulting in the inability to fully extend the finger.
Mouse Phenome Database: towards a more FAIR-compliant and TRUST-worthy data repository and tool suite for phenotypes and genotypes
Authors: Bogue Molly A , Ball Robyn L , Philip Vivek M , Walton David O , Dunn Matthew H , Kolishovski Georgi , Lamoureux Anna , Gerring Matthew , Liang Hongping , Emerson Jake , Stearns Tim , He Hao , Mukherjee Gaurab , Bluis John , Desai Sejal , Sundberg Beth , Kadakkuzha Beena , Kunde-Ramamoorthy Govindarajan , Chesler Elissa J 
Published: November 2022

Abstract
The Mouse Phenome Database (MPD; https://phenome.jax.org; RRID:SCR_003212), supported by the US National Institutes of Health, is a Biomedical Data Repository listed in the Trans-NIH Biomedical Informatics Coordinating Committee registry. As an increasingly FAIR-compliant and TRUST-worthy data repository, MPD accepts phenotype and genotype data from mouse experiments and curates, organizes, integrates, archives, and distributes those data using community standards. Data are accompanied by rich metadata, including widely used ontologies and detailed protocols. Data are from all over the world and represent genetic, behavioral, morphological, and physiological disease-related characteristics in mice at baseline or those exposed to drugs or other treatments. MPD houses data from over 6000 strains and populations, representing many reproducible strain types and heterogenous populations such as the Diversity Outbred where each mouse is unique but can be genotyped throughout the genome. A suite of analysis tools is available to aggregate, visualize, and analyze these data within and across studies and populations in an increasingly traceable and reproducible manner. We have refined existing resources and developed new tools to continue to provide users with access to consistent, high-quality data that has translational relevance in a modernized infrastructure that enables interaction with a suite of bioinformatics analytic and data services.
QTLbase2: an enhanced catalog of human quantitative trait loci on extensive molecular phenotypes
Authors: Huang Dandan , Feng Xiangling , Yang Hongxi , Wang Jianhua , Zhang Wenwen , Fan Xutong , Dong Xiaobao , Chen Kexin , Yu Ying , Ma Xin , Yi Xianfu , Li Mulin Jun 
Published: November 2022

Abstract
Deciphering the fine-scale molecular mechanisms that shape the genetic effects at disease-associated loci from genome-wide association studies (GWAS) remains challenging. The key avenue is to identify the essential molecular phenotypes that mediate the causal variant and disease under particular biological conditions. Therefore, integrating GWAS signals with context-specific quantitative trait loci (QTLs) (such as different tissue/cell types, disease states, and perturbations) from extensive molecular phenotypes would present important strategies for full understanding of disease genetics. Via persistent curation and systematic data processing of large-scale human molecular trait QTLs (xQTLs), we updated our previous QTLbase database (now QTLbase2, http://mulinlab.org/qtlbase) to comprehensively analyze and visualize context-specific QTLs across 22 molecular phenotypes and over 95 tissue/cell types. Overall, the resource features the following major updates and novel functions: (i) 960 more genome-wide QTL summary statistics from 146 independent studies; (ii) new data for 10 previously uncompiled QTL types; (iii) variant query scope expanded to fit 195 QTL datasets based on whole-genome sequencing; (iv) supports filtering and comparison of QTLs for different biological conditions, such as stimulation types and disease states; (v) a new linkage disequilibrium viewer to facilitate variant prioritization across tissue/cell types and QTL types.
A proto-telomere is elongated by telomerase in a shelterin-dependent manner in quiescent fission yeast cells
Authors: Vaurs Mélina , Audry Julien , Runge Kurt W , Géli Vincent , Coulon Stéphane 
Published: November 2022

Abstract
Telomere elongation is coupled with genome replication, raising the question of the repair of short telomeres in post-mitotic cells. We investigated the fate of a telomere-repeat capped end that mimics a single short telomere in quiescent fission yeast cells. We show that telomerase is able to elongate this single short telomere during quiescence despite the binding of Ku to the proto-telomere. While Taz1 and Rap1 repress telomerase in vegetative cells, both shelterin proteins are required for efficient telomere extension in quiescent cells, underscoring a distinct mode of telomerase control. We further show that Rad3ATR and Tel1ATM are redundantly required for telomere elongation in quiescence through the phosphorylation of Ccq1 and that Rif1 and its associated-PP1 phosphatases negatively regulate telomerase activity by opposing Ccq1 phosphorylation. The distinct mode of telomerase regulation in quiescent fission yeast cells may be relevant to that in human stem and progenitor cells.
Chromatin accessibility-based characterisation of brain gene regulatory networks in three distinct honey bee polyphenisms
Authors: Lowe Robert , Wojciechowski Marek , Ellis Nancy , Hurd Paul J 
Published: November 2022

Abstract
The honey bee genome has the capacity to produce three phenotypically distinct organisms (two diploid female castes: queen and worker, and a haploid male drone). Previous studies have implicated metabolic flux acting via epigenetic regulation in directing nutrition-driven phenotypic plasticity in the honey bee. However, the cis-acting DNA regulatory elements that establish tissue and polyphenism -specific epigenomes and gene expression programmes, remain unclear. Using a high resolution multiomic approach including assay for transposase-accessible chromatin by sequencing (ATAC-seq), RNA-seq and ChIP-seq, we produce the first genome-wide maps of the regulatory landscape across all three adult honey bee phenotypes identifying &gt; 5000 regulatory regions in queen, 7500 in worker and 6500 in drone, with the vast majority of these sites located within intronic regions. These regions are defined by positive enrichment of H3K27ac and depletion of H3K4me3 and show a positive correlation with gene expression. Using ATAC-seq footprinting we determine queen, worker and drone -specific transcription factor occupancy and uncover novel phenotype-specific regulatory networks identifying two key nuclear receptors that have previously been implicated in caste-determination and adult behavioural maturation in honey bees; ecdysone receptor and ultraspiracle. Collectively, this study provides novel insights into key gene regulatory networks that are associated with these distinct polyphenisms in the honey bee.
Underwater acoustic metamaterials
Authors: Dong Erqian , Cao Peizheng , Zhang Jinhu , Zhang Sai , Fang Nicholas X , Zhang Yu 
Published: November 2022

Abstract
Acoustic metamaterials have been widely investigated over the past few decades and have realized acoustic parameters that are not achievable using conventional materials. After demonstrating that locally resonant acoustic metamaterials are capable of acting as subwavelength unit cells, researchers have evaluated the possibility of breaking the classical limitations of the material mass density and bulk modulus. Combined with theoretical analysis, additive manufacturing and engineering applications, acoustic metamaterials have demonstrated extraordinary capabilities, including negative refraction, cloaking, beam formation and super-resolution imaging. Owing to the complexity of impedance boundaries and mode transitions, there are still challenges in freely manipulating acoustic propagation in an underwater environment. This review summarizes the developments in underwater acoustic metamaterials over the past 20 years, which include underwater acoustic invisibility cloaking, underwater beam formation, underwater metasurfaces and phase engineering, underwater topological acoustics and underwater acoustic metamaterial absorbers. With the evolution of underwater metamaterials and the timeline of scientific advances, underwater acoustic metamaterials have demonstrated exciting applications in underwater resource development, target recognition, imaging, noise reduction, navigation and communication.
Electoral System
Authors: Fernandes Jorge M. 
Published: November 2022

Abstract
This chapter examines the Portuguese electoral system. Firstly, it unpacks its institutional building blocks by examining districts, magnitude, and the electoral formula. Secondly, it examines the historical roots of the electoral system to understand the incentives that led constitution-makers to choose particular electoral rules and regulations. Next, the chapter turns to the consequences of the electoral system. On the one hand, it examines the impact of within-system district magnitude variation for representation. On the other hand, it looks at legislators’ behavioural incentives in light of the electoral system. More specifically, the localism puzzle, that is, why legislators choose to engage in home service in the absence of institutional incentives. Lastly, the chapter looks at the institutional reforms (or lack thereof) of the Portuguese electoral system. The conclusion examines three lessons drawn from the impact of the electoral system on representation and democracy in Portugal.
Citizens and Politics: Support and Engagement
Authors: Magalhães Pedro C. 
Published: November 2022

Abstract
This chapter examines patterns and trends in public support for political authorities and the democratic regime in Portugal, as well regarding political engagement over the last two decades. Past assessments of the Portuguese case, particularly those based on social-scientific survey data, suggested that high levels of dissatisfaction with political authorities and low levels of political engagement have coexisted with a broad commitment towards democracy and its norms. Looking at data from the last two decades, this diagnosis seems to require some qualification. In spite of the large negative impact of the 2010–2013 economic crisis on specific support, the last few years—which coincided with a period of some economic recovery and the geringonça [government]—showed remarkably high levels of support for political authorities, a recovery that stands out against other countries that were similarly affected by the crisis. Furthermore, although electoral turnout has continued to decline, other forms of political participation have thrived, producing a convergence with levels found in established European democracies. Finally, there are signs that the commitment of the Portuguese to liberal democracy as a regime is exhibiting new signs of ambivalence, to which the strong emphasis on economic egalitarianism in political culture—and the perceived meagre achievements of Portuguese democracy in that respect—seem to be contributing.
Interest Groups, Business Associations, and Unions
Authors: Lisi Marco , Loureiro João 
Published: November 2022

Abstract
Interest groups are commonly defined as organizations that aim to influence public policies without contesting elections or taking government positions. These actors play an important role in terms of political representation and the policy-making process. This chapter explores the different dimensions of interest group politics in Portugal, a topic that has been largely understudied especially when compared with other Western democracies. The chapter begins with a review of the system of interest intermediation, which aims to frame the Portuguese case from both a theoretical and historical perspective. Thereafter, the chapter focuses on economic groups, i.e. business associations and trade unions, and examines two key dimensions in particular, namely organizational features and mobilization strategies. Lastly, the chapter discusses recent developments and the challenges ahead.