bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effects of diffuse ionized gas and spatial resolution on metallicity gradients: TYPHOON two-dimensional spectrophotometry of M83
Authors: Poetrodjojo Henry , D’Agostino Joshua J , Groves Brent , Kewley Lisa , Ho I-Ting , Rich Jeff , Madore Barry F , Seibert Mark 
Published: May 2019

Abstract
We present a systematic study of the diffuse ionized gas (DIG) in M83 and its effects on the measurement of metallicity gradients at varying resolution scales. Using spectrophotometric data cubes of M83 obtained at the 2.5m duPont telescope at Las Campanas Observatory as part of the TYPHOON programme, we separate the H ii regions from the DIG using the [S ii]/H α ratio, HIIphot (H ii-finding algorithm), and the H α surface brightness. We find that the contribution to the overall H α luminosity is approximately equal for the H ii and DIG regions. The data is then rebinned to simulate low-resolution observations at varying resolution scales from 41 pc up to 1005 pc. Metallicity gradients are measured using five different metallicity diagnostics at each resolution. We find that all metallicity diagnostics used are affected by the inclusion of DIG to varying degrees. We discuss the reasons why the metallicity gradients are significantly affected by DIG using the H ii dominance and emission line ratio radial profiles. We find that applying the [S ii]/H α cut will provide a closer estimate of the true metallicity gradient up to a resolution of 1005 pc for all metallicity diagnostics used in this study.
Do AGN triggering mechanisms vary with radio power? – I. Optical morphologies of radio-intermediate HERGs
Authors: Pierce J C S , Tadhunter C N , Ramos Almeida C , Bessiere P S , Rose M 
Published: May 2019

ABSTRACT
Active galactic nuclei (AGNs) with intermediate radio powers are capable of driving multiphase outflows in galaxy bulges, and are also more common than their high-radio-power counterparts. In-depth characterization of the typical host galaxies and likely triggering mechanisms for this population is therefore required in order to better understand the role of radio AGN feedback in galaxy evolution. Here, we use deep optical imaging data to study the detailed host morphologies of a complete sample of 30 local radio AGNs with high-excitation optical emission (HERG) spectra and intermediate radio powers [ z < 0.1; 22.5 < log($L_{\rm 1.4GHz}$) < 24.0 W Hz-1]. The fraction of hosts with morphological signatures of mergers and interactions is greatly reduced compared to the 2Jy radio-powerful galaxies [log($L_{\rm 1.4GHz}$) > 25.0 W Hz-1] with strong optical emission lines: 53 ± 9 per cent compared with 94 ± 4 per cent. In addition, the most radio-powerful half of the sample has a higher frequency of morphological disturbance than the least radio-powerful half (67 ± 12 per cent and 40 ± 13 per cent, respectively), including the eight most highly disturbed galaxies. This suggests that the importance of triggering nuclear activity in high-excitation radio galaxies (HERGs) through mergers and interactions reduces with radio power. Both visual inspection and detailed light profile modelling reveal a mixed population of early-type and late-type morphologies, contrary to the massive elliptical galaxy hosts of radio-powerful AGNs. The prevalence of late-type hosts could suggest that triggering via secular, disc-based processes has increased importance for HERGs with lower radio powers (e.g. disc instabilities and large-scale bars).
iMKT: the integrative McDonald and Kreitman test
Authors: Murga-Moreno Jesús , Coronado-Zamora Marta , Hervas Sergi , Casillas Sònia , Barbadilla Antonio 
Published: May 2019

AbstractThe McDonald and Kreitman test (MKT) is one of the most powerful and widely used methods to detect and quantify recurrent natural selection using DNA sequence data. Here we present iMKT (acronym for integrative McDonald and Kreitman test), a novel web-based service performing four distinct MKT types. It allows the detection and estimation of four different selection regimes −adaptive, neutral, strongly deleterious and weakly deleterious− acting on any genomic sequence. iMKT can analyze both user's own population genomic data and pre-loaded Drosophila melanogaster and human sequences of protein-coding genes obtained from the largest population genomic datasets to date. Advanced options in the website allow testing complex hypotheses such as the application example showed here: do genes located in high recombination regions undergo higher rates of adaptation? We aim that iMKT will become a reference site tool for the study of evolutionary adaptation in massive population genomics datasets, especially in Drosophila and humans. iMKT is a free resource online at https://imkt.uab.cat.
“Not Without My Daughter”: EU Asylum Law, Gender, and the Separation of Refugee Families
Authors: Bastaki Jinan 
Published: May 2019

Abstract
When refugee families arrive in Europe and the children are over 18 years of age, in most cases, they are assessed separately for their asylum claim. Where applicants want to apply for family reunification, only spouses and minors who wish to be reunified with adult family members can automatically do so. This has caused problems for adult women who want to remain a part of their family or be reunified with family members in other European Union States. There is evidence that single women are more vulnerable to gender-based violence, whether in the refugee camps or on the dangerous journey from their homes to Europe, but that reason is not sufficient for family reunification. Through interviews with Arab women seeking to be reunified with their families, this article analyses the impact of the laws in the European Union, and specifically in Greece, on female asylum-seekers reaching the Greek island of Lesvos. It argues that the asylum laws have negative humanitarian consequences on asylum-seeking families, and because the act of seeking protection is different than other forms of migration, previous family structures should be recognised if the asylum-seeking woman so wishes, in order to ensure that these women are not made vulnerable.
Inclusiveness of Parental-Leave Benefits in Twenty-One European Countries: Measuring Social and Gender Inequalities in Leave Eligibility
Authors: Dobrotić Ivana , Blum Sonja 
Published: May 2019

AbstractThis article analyzes eligibility for parental-leave benefits in twenty-one European countries. It distinguishes four ideal-type approaches to how leave-related benefits are granted (in-)dependent of parents’ labor market position: universal parenthood model, selective parenthood model, universal adult-worker model, and selective adult-worker model. An eligibility index is created to measure the inclusiveness of parental-leave benefits, alongside the degree of (de-)gendered entitlements. The importance of employment-based benefits and gender-sensitive policies increased between 2006 and 2017. Eligibility criteria remained stable, but due to labor market trends, such as increasing precariousness, fewer parents may fulfill the conditions for employment-based benefits.
Accounting for Uncertainty in the Evolutionary Timescale of Green Plants Through Clock-Partitioning and Fossil Calibration Strategies
Authors: Nie Yuan , Foster Charles S P , Zhu Tianqi , Yao Ru , Duchêne David A , Ho Simon Y W , Zhong Bojian 
Published: May 2019

AbstractEstablishing an accurate evolutionary timescale for green plants (Viridiplantae) is essential to understanding their interaction and coevolution with the Earth’s climate and the many organisms that rely on green plants. Despite being the focus of numerous studies, the timing of the origin of green plants and the divergence of major clades within this group remain highly controversial. Here, we infer the evolutionary timescale of green plants by analyzing 81 protein-coding genes from 99 chloroplast genomes, using a core set of 21 fossil calibrations. We test the sensitivity of our divergence-time estimates to various components of Bayesian molecular dating, including the tree topology, clock models, clock-partitioning schemes, rate priors, and fossil calibrations. We find that the choice of clock model affects date estimation and that the independent-rates model provides a better fit to the data than the autocorrelated-rates model. Varying the rate prior and tree topology had little impact on age estimates, with far greater differences observed among calibration choices and clock-partitioning schemes. Our analyses yield date estimates ranging from the Paleoproterozoic to Mesoproterozoic for crown-group green plants, and from the Ediacaran to Middle Ordovician for crown-group land plants. We present divergence-time estimates of the major groups of green plants that take into account various sources of uncertainty. Our proposed timeline lays the foundation for further investigations into how green plants shaped the global climate and ecosystems, and how embryophytes became dominant in terrestrial environments.
Societal Poverty: A Relative and Relevant Measure
Authors: Jolliffe Dean , Prydz Espen Beer 
Published: May 2019

AbstractPoverty lines are typically higher in richer countries, and lower in poorer ones, reflecting the relative nature of national assessments of who is considered poor. In many high-income countries, poverty lines are explicitly relative, set as a share of mean or median income. Despite systematic variation in how countries define poverty, global poverty counts are based on fixed-value lines. To reflect national assessments of poverty in a global headcount of poverty, this paper proposes a societal poverty line. The proposed societal poverty line is derived from 699 harmonized national poverty lines, has an intercept of $1 per day and a relative gradient of 50 percent of median national income or consumption. The societal poverty line is more closely aligned with national definitions of poverty than other proposed relative lines. By this relative measure, societal poverty has fallen steadily since 1990, but at a much slower pace than absolute extreme poverty.
Brain Responsivity to Emotional Faces Differs in Alcoholic Men and Women
Authors: Oscar-Berman Marlene , Ruiz Susan Mosher , Marinkovic Ksenija , Valmas Mary M. , Harris Gordon J. , Sawyer Kayle S. 
Published: May 2019

AbstractInclusion of women in alcoholism research has shown that gender differences contribute to unique profiles of cognitive, emotional, and neuropsychological dysfunction. We employed functional magnetic resonance imaging (fMRI) of abstinent long-term alcoholics (21 women [ALCw] and 21 men [ALCm]) and demographically-similar nonalcoholic controls (21 women [NCw] and 21 men [NCm]) to explore how gender and alcoholism interact to influence emotional processing and memory. Participants completed a delayed match-to-sample emotional face memory fMRI task. While the results corroborated reports implicating amygdalar, superior temporal, and cerebellar involvement in emotional processing overall, the alcoholic participants showed hypoactivation of the left intraparietal sulcus to encoding the identity of the emotional face stimuli. The nonalcoholic participants demonstrated more reliable gender differences in neural responses to encoding the identity of the emotional faces than did the alcoholic group, and widespread neural responses to these stimuli were more pronounced in the NCw than in the NCm. By comparison, gender differences among ALC participants were either smaller or in the opposite direction (higher brain activation in ALCm than ALCw). Specifically, Group by Gender interaction effects indicated stronger responses to emotional faces by ALCm than ALCw in the left superior frontal gyrus and the right inferior frontal sulcus, while NCw had stronger responses than NCm. However, this pattern was inconsistent throughout the brain, with results suggesting the reverse direction of gender effects in the hippocampus and anterior cingulate cortex. Together, these findings demonstrated that gender plays a significant role in the profile of functional brain abnormalities observed in alcoholism.
Throughput and Resolution with a Next Generation Direct Electron Detector
Authors: Mendez Joshua H. , Mehrani Atousa , Randolph Peter , Stagg Scott 
Published: May 2019

AbstractDirect electron detectors (DEDs) have revolutionized cryo-electron microscopy by facilitating correction of beam-induced motion and radiation damage and by providing high-resolution image capture. A new generation of DEDs has been developed by Direct Electron, the DE64, that has good performance in both integrating and counting modes. Integrating mode is superior in throughput while counting mode is superior in image quality. We show that despite being ~10x slower in throughput, counting mode is superior in terms of reconstruction resolution per unit time of data collection.
Video-based motion-resilient reconstruction of 3D position for fNIRS and EEG head mounted probes
Authors: Jaffe-Dax Sagi , Bermano Amit H. , Erel Yotam , Emberson Lauren L. 
Published: May 2019

AbstractSignificanceWe propose a novel video-based, motion-resilient, and fast method for estimating the position of optodes on the scalp.AimMeasuring the exact placement of probes (e.g., electrodes, optodes) on a participant’s head is a notoriously difficult step in acquiring neuroimaging data from methods which rely on scalp recordings (e.g., EEG and fNIRS), and is particularly difficult for any clinical or developmental population. Existing methods of head measurements require the participant to remain still for a lengthy period of time, are laborious, and require extensive training. Therefore, a fast and motion-resilient method is required for estimating the scalp location of probes.ApproachWe propose an innovative video-based method for estimating the probes’ positions relative to the participant’s head, which is fast, motion-resilient, and automatic. Our method builds on capitalizing the advantages, and understanding the limitations, of cutting-edge computer vision and machine learning tool. We validate our method on 10 adult subjects and provide proof of feasibility with infant subjects.ResultsWe show that our method is both reliable and valid compared to existing state-of-the-art methods by estimating probe positions in a single measurement, and by tracking their translation and consistency across sessions. Finally, we show that our automatic method is able to estimate the position of probes on an infant head without lengthy offline procedures, a task which is considered challenging until now.ConclusionsOur proposed method allows, for the first time, the use of automated spatial co-registration methods on developmental and clinical populations, where lengthy, motion-sensitive measurement methods routinely fail.
The metabolic response ofPseudomonas taiwanensisto NADH dehydrogenase deficiency
Authors: Nies Salome C. , Dinger Robert , Chen Yan , Wordofa Gossa G. , Kristensen Mette , Schneider Konstantin , Büchs Jochen , Petzold Christopher J. , Keasling Jay D. , Blank Lars M. , Ebert Birgitta E. 
Published: May 2019

AbstractObligate aerobic organisms rely on a functional electron transport chain for energy generation and NADH oxidation. Because of this essential requirement, the genes of this pathway are likely constitutively and highly expressed to avoid a cofactor imbalance and energy shortage under fluctuating environmental conditions.We here investigated the essentiality of the three NADH dehydrogenases of the respiratory chain of the obligate aerobePseudomonas taiwanensisVLB120 and the impact of the knockouts of corresponding genes on its physiology and metabolism. While a mutant lacking all three NADH dehydrogenases seemed to be nonviable, the generated single or double knockout strains displayed none or only a marginal phenotype. Only the mutant deficient in both type 2 dehydrogenases showed a clear phenotype with biphasic growth behavior and strongly reduced growth rate in the second phase. In-depth analyses of the metabolism of the generated mutants including quantitative physiological experiments, transcript analysis, proteomics and enzyme activity assays revealed distinct responses to type II and type I dehydrogenase deletions. An overall high metabolic flexibility enablesP. taiwanensisto cope with the introduced genetic perturbations and maintain stable phenotypes by rerouting of metabolic fluxes.This metabolic adaptability has implications for biotechnological applications. While the phenotypic robustness is favorable in large-scale applications with inhomogeneous conditions, versatile redirecting of carbon fluxes upon genetic interventions can frustrate metabolic engineering efforts.ImportanceWhilePseudomonashas the capability for high metabolic activity and the provision of reduced redox cofactors important for biocatalytic applications, exploitation of this characteristic might be hindered by high, constitutive activity of and consequently competition with the NADH dehydrogenases of the respiratory chain. The in-depth analysis of NADH dehydrogenase mutants ofPseudomonas taiwanensisVLB120 presented here, provides insight into the phenotypic and metabolic response of this strain to these redox metabolism perturbations. The observed great metabolic flexibility needs to be taken into account for rational engineering of this promising biotechnological workhorse towards a host with controlled and efficient supply of redox cofactors for product synthesis.
An astrocytic basis of caloric restriction action on the brain plasticity
Authors: Plata Alex , Popov Alexander , Denisov Pavel , Bychkov Maxim , Brazhe Alexey , Lyukmanova Ekaterina , Lazareva Natalia , Verkhratsky Alexei , Semyanov Alexey 
Published: May 2019

AbstractOne month of calorically restricted diet (CR) induced morphological plasticity of astrocytes in the stratum (str.) radiatum of hippocampal CA1 in three-months old mice: the volume fraction of distal perisynaptic astrocytic processes increased whereas the number of gap-junction coupled astrocytes decreased. The uncoupling was not associated with a decrease in the expression of connexin 43. Uncoupling and morphological remodeling affected spontaneous Ca2+ activity in the astrocytic network: Ca2+ events became longer, whereas their spread was reduced. The change in the pattern of astrocytic Ca2+ activity may increase the spatial resolution of the information encoding in the astroglial network. Consistent with expanded synaptic enwrapping by the astroglial processes, the spillover of synaptically released K+ and glutamate was diminished after CR. However, no significant changes in the expression of astrocytic glutamate transporter (GLT-1/EAAT2) were observed, although the level of glutamine synthetase was decreased. Glutamate uptake is known to regulate the synaptic plasticity. Indeed, the magnitude of long-term potentiation (LTP) in the glutamatergic CA3-CA1 synapses was significantly enhanced after CR. Our findings highlight an astroglial basis for improved learning and memory reported in various species subjected to CR.
MobiLab – A Mobile Laboratory for On-Site Listening Experiments in Virtual Acoustic Environments
Authors: Pausch Florian , Fels Janina 
Published: May 2019

AbstractResearch in the last decades has pointed out negative effects of noise on cognitive processing and general health. Depending on the frequency and level of exposure as well as individual shielding potential, risk groups like children or elderly people may be particularly vulnerable to commonly known consequences including a reduced attention span, influencing the learning success during education, increased blood pressure and cardiovascular problems or sleep disturbances. To better understand the susceptibility to noise, specifically designed listening experiments in controlled laboratory environments are indispensable but might put high demands on older study participants whose travel expenses to test locations could increase due to reduced mobility. For children, organizational issues like insured transport and supervision during waiting periods, necessitating additional resources, need to be resolved. In order to facilitate practical and efficient study execution, we therefore implemented a mobile hearing laboratory by acoustically optimizing the interior of a caravan. All necessary technical facilities were integrated to perform listening experiments in virtual acoustic environments under controlled conditions directly on site, for example, in front of schools or senior residential centers. The design and construction of this laboratory are presented here and evaluated through acoustic measurements.
Checkpoint signaling and error correction require regulation of the MPS1 T-loop by PP2A-B56
Authors: Hayward Daniel , Bancroft James , Mangat Davinderpreet , Alfonso-Pérez Tatiana , Dugdale Sholto , McCarthy Julia , Barr Francis A. , Gruneberg Ulrike 
Published: May 2019

AbstractDuring mitosis, the formation of microtubule-kinetochore attachments is monitored by the serine/threonine kinase Mono-Polar Spindle 1 (MPS1). MPS1 is recruited to unattached kinetochores where it phosphorylates KNL1, BUB1 and MAD1 to initiate the spindle checkpoint. This arrests the cell cycle until all kinetochores have been stably captured by microtubules. MPS1 also contributes to the error correction process rectifying incorrect kinetochore attachments. MPS1 activity at kinetochores requires auto-phosphorylation at multiple sites including T676 in the activation segment or “T-loop”. We now demonstrate that a BUBR1-bound pool of PP2A-B56 regulates MPS1 T-loop autophosphorylation and hence activation status in mammalian cells. Overriding this regulation using phospho-mimetic mutations in the MPS1 T-loop to generate a constitutively active kinase results in a prolonged mitotic arrest with continuous turn-over of microtubule-kinetochore attachments. Dynamic regulation of MPS1 catalytic activity by kinetochore-localized PP2A-B56 is thus critical for controlled MPS1 activity and timely cell cycle progression.
Verify Hub Genes of expression profile in aortic dissection
Authors: Wang Weitie , Liu Qing , Wang Yong , Piao Hulin , Li Bo , Zhu Zhicheng , Li Dan , Wang Tiance , Xu Rihao , Liu Kexiang 
Published: May 2019

AbstractBackgroundTo assess the mRNAs expression profile and explore the hub mRNAs and potential molecular mechanisms in the pathogenesis of human thoracic aortic dissection (TAD). Methodology: mRNA microarray expression signatures of TAD tissues (n=6) and no TAD tissues (NT;n=6) were analyzed by Arraystar human mRNAs microarray. Real-time PCR (qRT-PCR) were used to validate the result of mRNAs microarray. Bioinformatic tools including gene ontology, and Kyoto Encyclopedia of Genes and Genomes pathway analysis were utilized. The protein-protein interaction networks were constructed based on data from the STRING database. Molecular Complex Detection (MCODE) and cytohubba analysis were used to infer the most hug gene and pathways. Results: The top 10 hub genes CDK1, CDC20, CCNB2, CCNB1, MAD2L1, AURKA, C3AR1, NCAPG,CXCL12 and ASPM were identified from the PPI network. Module analysis revealed that TAD was associated with cell cycle, oocyte meiosis, p53 signaling pathway, progesterone-mediated oocyte maturation. The qRT-PCR result showed that the expression of all hug genes was significantly increased in TAD samples (p < 0.05). Conclusions: These candidate genes could be used as potential diagnostic biomarkers and therapeutic targets of TAD.Author summaryMany basic characteristics underlying the establishment of aortic dissection have not been studied in detail. The presented work sought to understand the pathogenesis of human thoracic aortic dissection by employing bioinformatic tools to explore the hub mRNAs and potential molecular mechanisms of thoracic aortic dissection. Many pathway were thought to have relevant with this disease, but the most important pathway was not define. We used bio-mathematical analysis to explore the potential functions in thoracic aortic dissection and identified the hub genes and explored the intrinsic molecular mechanisms involved in thoracic aortic dissection between two microarray analysis. Finally, we indentified the cell cycle maybe the key pathway in thoracic aortic dissection.