bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sentimental politics or structural injustice? The ambivalence of emotions for political responsibility
Authors: Head Naomi 
Published: May 2020

AbstractStories and representations of suffering are frequently central to attempts to arouse our emotions and initiate political action. Yet, the evocation of emotion and, in particular, empathy, remains politically ambivalent. It does not necessarily lead to the acknowledgement of political responsibility or to actions to address the historically-constituted roots of contemporary structural injustices. Moving beyond the legal, moral, and institutional boundaries of political responsibility, this article argues for greater recognition of its affective dimensions. In particular, it differentiates between a sentimental politics and testimonial empathy to better understand the affective dynamics of political responsibility. While the former finds close company with pity and a lack of acknowledged political responsibility, the latter offers an ethical–political orientation towards radical reflexivity and social transformation, situating experiences of injustice within wider networks of power, privilege, and agency. Drawing on the work of feminist, cultural, and social theorists, the article offers a critical conceptualisation of testimonial empathy and its limits. The article illustrates the insights offered by re-thinking political responsibility in terms of testimonial empathy through a close reading of a historical account of structural injustice – slavery in the United States – as written in Harriet A. Jacobs’ 1861 slave narrative.
Self-maintenance vs. goal attainment: drivers of mortality anxiety in organized civil society
Authors: Bolleyer Nicole , Correa Patricia 
Published: May 2020

AbstractWhen do membership-based civil society organizations such as interest groups, political parties or service-oriented organizations consider their existence under threat? Distinguishing pressures of organizational self-maintenance from functional pressures of goal attainment, which all voluntary membership organizations – irrespective of their political or societal functions - need to reconcile, we propose a framework theorizing distinct categories of drivers of mortality anxiety in organized civil society. To test our hypotheses, we apply ordered logistic regression analysis to new data covering regionally and nationally active interest groups, service-oriented organizations and parties in Germany, Norway, Switzerland and the UK. We find that factors enhancing intraorganizational resilience thereby facilitating self-maintenance as well as exposure to different representation challenges complicating goal attainment have significant effects on mortality anxiety experienced by interest groups, political parties and service-oriented organizations alike – the former reducing, the latter enhancing it. Stressing the importance of a stable, durable organizational infrastructure with loyal and involved members to operate in increasingly volatile and diverse environments, our findings highlight the on-going importance of ‘traditional’ (sometimes considered ‘outdated’) organization-building.
Broad Consistency Between Observed and Simulated Trends in Sea Surface Temperature Patterns
Authors: Olonscheck Dirk , Rugenstein Maria , Marotzke Jochem 
Published: May 2020

AbstractUsing seven single‐model ensembles and the two multimodel ensembles CMIP5 and CMIP6, we show that observed and simulated trends in sea surface temperature (SST) patterns are globally consistent when accounting for internal variability. Some individual ensemble members simulate trends in large‐scale SST patterns that closely resemble the observed ones. Observed regional trends that lie at the outer edge of the models' internal variability range allow two nonexclusive interpretations: (a) Observed trends are unusual realizations of the Earth's possible behavior and/or (b) the models are systematically biased but large internal variability leads to some good matches with the observations. The existing range of multidecadal SST trends is influenced more strongly by large internal variability than by differences in the model formulation or the observational data sets.
A Census of Magnetospheric Electrons From Several eV to 30 keV
Authors: Walsh Brian M. , Hull Arthur J. , Agapitov Oleksiy , Mozer Forrest S. , Li Haimeng 
Published: May 2020

AbstractA survey of electrons with energies between ∼1 eV and 30 keV was conducted using measurements from the THEMIS spacecraft over radial distances between 3 and 12 Earth radii. Two distinct populations are observed, one with a peak energy near 10 eV and one at approximately 1 keV. These populations are present 88% of the time in the magnetosphere. The warm population (∼10 eV) is generally more dense (∼1 cm−3) and extends across the dayside. These warm electron characteristics are similar to the ion warm plasma cloak. The hot distribution (∼1 keV) peaks in number density (∼0.2 cm−3) near midnight and into the morning sector. Since the populations are transported through different evolutionary paths, there are spatial regions within the magnetosphere where the density ratio of the populations (warm to hot, nw/nh) is much larger or smaller than unity. At L shells greater than ∼6, near midnight and into the dawn sector, the density of the hot population is close to a factor of 10 larger than the warm populations. In other regions, the warm electron population is typically slightly more dense (∼2×) than the hot population.
A Model Investigation of the Influences of the South‐East Madagascar Current on the South‐East Madagascar Bloom
Authors: Dilmahamod A. F. , Penven P. , Aguiar‐González B. , Reason C. J. C. , Hermes J. C. 
Published: May 2020

AbstractThe South‐East Madagascar Bloom, one of the most compelling biogeochemical features of the Indian Ocean, occurs sporadically during austral summer in the oligotrophic waters south‐east of Madagascar, where it can cover up to 1% of the global ocean surface area. Its spatial extension and its timing are highly variable. A high‐resolution biophysical model is used to investigate a previous hypothesis that the onset of a particular circulation of the South‐East Madagascar Current advects fresher and nutrient‐rich waters eastward, feeding the bloom. The model is able to reproduce an intermittent phytoplankton bloom with large spatial variability but in the subsurface layers, as well as the presence of an irregular retroflection of the South‐East Madagascar Current. The simulated bloom occurs within a shallow stratified mixed layer, with fresher waters at the surface, parallel to the water mass in an observed bloom. The model results suggest, from a nutrient flux analysis, that horizontal advection of low‐salinity nutrient‐rich Madagascan coastal waters can indeed trigger a phytoplankton bloom. The coupled model is also able to resolve a bloom that is atmospherically forced by cyclonic activity.
Time‐Dependent Crustal Accretion on the Southeast Indian Ridge Revealed by Malaysia Airlines Flight MH370 Search
Authors: Parnell‐Turner Ross , Sim Shi J. , Olive Jean‐Arthur 
Published: May 2020

AbstractOur understanding of oceanic crustal formation is mostly limited to observations of young crust formed in the past several million years, due to the thick sediments on older crust and the remote location of many spreading centers. Here we use 40 m‐resolution bathymetric data collected over hundreds of square kilometers during the search for Malaysia Airlines Flight 370 on the flank of the Southeast Indian Ridge, which provides a record of crustal accretion from 11–23 Ma. Spectra calculated from the data show a characteristic timescale of 300–400 kyr and no evidence for periodicity coinciding with glacial cycles. This characteristic timescale could be explained by fluctuations in melt supply and the amount of faulting, leading to variations in crustal thickness. We show that this timescale of variation is consistent with porosity waves observed in a two‐phase flow model, which persist over millions of years.
Cadmium Pollution From Zinc‐Smelters up to Fourfold Higher Than Expected in Western Europe in the 1980s as Revealed by Alpine Ice
Authors: Legrand M. , McConnell J. R. , Lestel L. , Preunkert S. , Arienzo M. , Chellman N. J. , Stohl A. , Eckhardt S. 
Published: May 2020

AbstractEstimates of past emission inventories suggest that toxic heavy metal pollution in Europe was highest in the mid‐1970s for lead and in the mid‐1960s for cadmium, but these previous estimates have not been compared to observations. Here, alpine ice‐cores were used to document cadmium and lead pollution in western Europe between 1890 and 2000. The ice‐core trends show that while lead pollution largely from leaded gasoline reached a maximum in ~1975 as expected, cadmium pollution primarily from zinc smelters peaked in the early‐1980s rather than in ~1965 and was up to fourfold higher than estimated after 1975. Comparisons between ice‐core trends, estimated past emissions, and state‐of‐the‐art atmospheric aerosol transport and deposition modeling suggest that the estimated decreases in cadmium emissions after 1970 were based on overly optimistic emissions reductions from the introduction of pollution control devices and other technological improvements.
Juno Observations of Heavy Ion Energization During Transient Dipolarizations in Jupiter Magnetotail
Authors: Artemyev A. V. , Clark G. , Mauk B. , Vogt M. F. , Zhang X.‐J. 
Published: May 2020

AbstractTransient magnetic reconnection and associated fast plasma flows led by dipolarization fronts play a crucial role in energetic particle acceleration in planetary magnetospheres. Despite large statistical observations on this phenomenon in the Earth's magnetotail, many important characteristics (e.g., mass or charge dependence of acceleration efficiency and acceleration scaling with the spatial scale of the system) of transient reconnection cannot be fully investigated with the limited parameter range of the Earth's magnetotail. The much larger Jovian magnetodisk, filled by a mixture of various heavy ions and protons, provides a unique opportunity for such investigations. In this study, we use recent Juno observations in Jupiter's magnetosphere to examine the properties of reconnection associated dipolarization fronts and charged particle acceleration. High‐energy fluxes of sulfur, oxygen, and hydrogen ions show clear mass‐dependent acceleration with energy ∼m1/3. We compare Juno observations with similar observations in the Earth's magnetotail and discuss possible mechanism for the observed ion acceleration.
Response of the Bay of Bengal to 3‐7‐Day Synoptic Oscillations During the Southwest Monsoon of 2019
Authors: Subrahmanyam Bulusu , Roman‐Stork Heather L. , Murty V. S. N. 
Published: May 2020

AbstractThe satellite‐derived precipitation over central India (73–78°E, 20–25°N) during the 2019 southwest monsoon season reveals that high‐amplitude 3‐7‐day synoptic oscillations dominated the other intraseasonal oscillations and contributed to the excess seasonal monsoon rainfall. In this paper, we address the contribution of 3‐7‐day synoptic oscillations in atmospheric and oceanic parameters during the 2019 southwest monsoon season over the Bay of Bengal (BoB). Our study reveals that both satellite observations and the Nucleus for European Modeling of the Ocean (NEMO) model simulations show high‐amplitude 3‐7‐day synoptic scale events during the 2019 monsoon. The upper 300 m of the water column responds to the basin‐scale 3‐7‐day synoptic oscillations as revealed in the vertical structures of NEMO model simulated temperature, salinity, and currents in the BoB. The synoptic scale wind stress drives strong currents in the shallow mixed layer due to salinity stratification in the northern BoB. The northward propagation of the synoptic scale oscillations is evident across the BoB but is capped to the base of the mixed layer, above which the propagation is affected by wind stress and the spread of freshwater flux. The 3‐7‐day synoptic scale oscillations in NEMO sea surface height appear to be related to synoptic scale wind‐driven convergence and divergence of waters through mesoscale eddy circulations that in turn contribute to thermocline variability, rather than the temperature and salinity in the mixed layer.
Mechanoradicals in tensed tendon collagen as a source of oxidative stress
Authors: Zapp Christopher , Obarska-Kosinska Agnieszka , Rennekamp Benedikt , Kurth Markus , Hudson David M. , Mercadante Davide , Barayeu Uladzimir , Dick Tobias P. , Denysenkov Vasyl , Prisner Thomas , Bennati Marina , Daday Csaba , Kappl Reinhard , Gräter Frauke 
Published: May 2020

AbstractAs established nearly a century ago, mechanoradicals originate from homolytic bond scission in polymers. The existence, nature and biological relevance of mechanoradicals in proteins, instead, are unknown. We here show that mechanical stress on collagen produces radicals and subsequently reactive oxygen species, essential biological signaling molecules. Electron-paramagnetic resonance (EPR) spectroscopy of stretched rat tail tendon, atomistic molecular dynamics simulations and quantum-chemical calculations show that the radicals form by bond scission in the direct vicinity of crosslinks in collagen. Radicals migrate to adjacent clusters of aromatic residues and stabilize on oxidized tyrosyl radicals, giving rise to a distinct EPR spectrum consistent with a stable dihydroxyphenylalanine (DOPA) radical. The protein mechanoradicals, as a yet undiscovered source of oxidative stress, finally convert into hydrogen peroxide. Our study suggests collagen I to have evolved as a radical sponge against mechano-oxidative damage and proposes a mechanism for exercise-induced oxidative stress and redox-mediated pathophysiological processes.
Effect of sequence depth and length in long-read assembly of the maize inbred NC358
Authors: Ou Shujun , Liu Jianing , Chougule Kapeel M. , Fungtammasan Arkarachai , Seetharam Arun S. , Stein Joshua C. , Llaca Victor , Manchanda Nancy , Gilbert Amanda M. , Wei Sharon , Chin Chen-Shan , Hufnagel David E. , Pedersen Sarah , Snodgrass Samantha J. , Fengler Kevin , Woodhouse Margaret , Walenz Brian P. , Koren Sergey , Phillippy Adam M. , Hannigan Brett T. , Dawe R. Kelly , Hirsch Candice N. , Hufford Matthew B. , Ware Doreen 
Published: May 2020

AbstractImprovements in long-read data and scaffolding technologies have enabled rapid generation of reference-quality assemblies for complex genomes. Still, an assessment of critical sequence depth and read length is important for allocating limited resources. To this end, we have generated eight assemblies for the complex genome of the maize inbred line NC358 using PacBio datasets ranging from 20 to 75 × genomic depth and with N50 subread lengths of 11–21 kb. Assemblies with ≤30 × depth and N50 subread length of 11 kb are highly fragmented, with even low-copy genic regions showing degradation at 20 × depth. Distinct sequence-quality thresholds are observed for complete assembly of genes, transposable elements, and highly repetitive genomic features such as telomeres, heterochromatic knobs, and centromeres. In addition, we show high-quality optical maps can dramatically improve contiguity in even our most fragmented base assembly. This study provides a useful resource allocation reference to the community as long-read technologies continue to mature.
Btk SH2-kinase interface is critical for allosteric kinase activation and its targeting inhibits B-cell neoplasms
Authors: Duarte Daniel P. , Lamontanara Allan J. , La Sala Giuseppina , Jeong Sukyo , Sohn Yoo-Kyoung , Panjkovich Alejandro , Georgeon Sandrine , Kükenshöner Tim , Marcaida Maria J. , Pojer Florence , De Vivo Marco , Svergun Dmitri , Kim Hak-Sung , Dal Peraro Matteo , Hantschel Oliver 
Published: May 2020

AbstractBruton’s tyrosine kinase (Btk) is critical for B-cell maturation and activation. Btk loss-of-function mutations cause human X-linked agammaglobulinemia (XLA). In contrast, Btk signaling sustains growth of several B-cell neoplasms which may be treated with tyrosine kinase inhibitors (TKIs). Here, we uncovered the structural mechanism by which certain XLA mutations in the SH2 domain strongly perturb Btk activation. Using a combination of molecular dynamics (MD) simulations and small-angle X-ray scattering (SAXS), we discovered an allosteric interface between the SH2 and kinase domain required for Btk activation and to which multiple XLA mutations map. As allosteric interactions provide unique targeting opportunities, we developed an engineered repebody protein binding to the SH2 domain and able to disrupt the SH2-kinase interaction. The repebody prevents activation of wild-type and TKI-resistant Btk, inhibiting Btk-dependent signaling and proliferation of malignant B-cells. Therefore, the SH2-kinase interface is critical for Btk activation and a targetable site for allosteric inhibition.
The landscape of chromothripsis across adult cancer types
Authors: Voronina Natalia , Wong John K. L. , Hübschmann Daniel , Hlevnjak Mario , Uhrig Sebastian , Heilig Christoph E. , Horak Peter , Kreutzfeldt Simon , Mock Andreas , Stenzinger Albrecht , Hutter Barbara , Fröhlich Martina , Brors Benedikt , Jahn Arne , Klink Barbara , Gieldon Laura , Sieverling Lina , Feuerbach Lars , Chudasama Priya , Beck Katja , Kroiss Matthias , Heining Christoph , Möhrmann Lino , Fischer Andrea , Schröck Evelin , Glimm Hanno , Zapatka Marc , Lichter Peter , Fröhling Stefan , Ernst Aurélie 
Published: May 2020

AbstractChromothripsis is a recently identified mutational phenomenon, by which a presumably single catastrophic event generates extensive genomic rearrangements of one or a few chromosome(s). Considered as an early event in tumour development, this form of genome instability plays a prominent role in tumour onset. Chromothripsis prevalence might have been underestimated when using low-resolution methods, and pan-cancer studies based on sequencing are rare. Here we analyse chromothripsis in 28 tumour types covering all major adult cancers (634 tumours, 316 whole-genome and 318 whole-exome sequences). We show that chromothripsis affects a substantial proportion of human cancers, with a prevalence of 49% across all cases. Chromothripsis generates entity-specific genomic alterations driving tumour development, including clinically relevant druggable fusions. Chromothripsis is linked with specific telomere patterns and univocal mutational signatures in distinct tumour entities. Longitudinal analysis of chromothriptic patterns in 24 matched tumour pairs reveals insights in the clonal evolution of tumours with chromothripsis.
Par complex cluster formation mediated by phase separation
Authors: Liu Ziheng , Yang Ying , Gu Aihong , Xu Jiawen , Mao Ying , Lu Haojie , Hu Weiguo , Lei Qun-Ying , Li Zhouhua , Zhang Mingjie , Cai Yu , Wen Wenyu 
Published: May 2020

AbstractThe evolutionarily conserved Par3/Par6/aPKC complex regulates the polarity establishment of diverse cell types and distinct polarity-driven functions. However, how the Par complex is concentrated beneath the membrane to initiate cell polarization remains unclear. Here we show that the Par complex exhibits cell cycle-dependent condensation in Drosophila neuroblasts, driven by liquid–liquid phase separation. The open conformation of Par3 undergoes autonomous phase separation likely due to its NTD-mediated oligomerization. Par6, via C-terminal tail binding to Par3 PDZ3, can be enriched to Par3 condensates and in return dramatically promote Par3 phase separation. aPKC can also be concentrated to the Par3N/Par6 condensates as a client. Interestingly, activated aPKC can disperse the Par3/Par6 condensates via phosphorylation of Par3. Perturbations of Par3/Par6 phase separation impair the establishment of apical–basal polarity during neuroblast asymmetric divisions and lead to defective lineage development. We propose that phase separation may be a common mechanism for localized cortical condensation of cell polarity complexes.
Minimal lactazole scaffold for in vitro thiopeptide bioengineering
Authors: Vinogradov Alexander A. , Shimomura Morito , Goto Yuki , Ozaki Taro , Asamizu Shumpei , Sugai Yoshinori , Suga Hiroaki , Onaka Hiroyasu 
Published: May 2020

AbstractLactazole A is a cryptic thiopeptide from Streptomyces lactacystinaeus, encoded by a compact 9.8 kb biosynthetic gene cluster. Here, we establish a platform for in vitro biosynthesis of lactazole A, referred to as the FIT-Laz system, via a combination of the flexible in vitro translation (FIT) system with recombinantly produced lactazole biosynthetic enzymes. Systematic dissection of lactazole biosynthesis reveals remarkable substrate tolerance of the biosynthetic enzymes and leads to the development of the minimal lactazole scaffold, a construct requiring only 6 post-translational modifications for macrocyclization. Efficient assembly of such minimal thiopeptides with FIT-Laz opens access to diverse lactazole analogs with 10 consecutive mutations, 14- to 62-membered macrocycles, and 18 amino acid-long tail regions, as well as to hybrid thiopeptides containing non-proteinogenic amino acids. This work suggests that the minimal lactazole scaffold is amenable to extensive bioengineering and opens possibilities to explore untapped chemical space of thiopeptides.
Flexibility of intrinsically disordered degrons in AUX/IAA proteins reinforces auxin co-receptor assemblies
Authors: Niemeyer Michael , Moreno Castillo Elena , Ihling Christian H. , Iacobucci Claudio , Wilde Verona , Hellmuth Antje , Hoehenwarter Wolfgang , Samodelov Sophia L. , Zurbriggen Matias D. , Kastritis Panagiotis L. , Sinz Andrea , Calderón Villalobos Luz Irina A. 
Published: May 2020

AbstractCullin RING-type E3 ubiquitin ligases SCFTIR1/AFB1-5and their AUX/IAA targets perceive the phytohormone auxin. The F-box protein TIR1 binds a surface-exposed degron in AUX/IAAs promoting their ubiquitylation and rapid auxin-regulated proteasomal degradation. Here, by adopting biochemical, structural proteomics and in vivo approaches we unveil how flexibility in AUX/IAAs and regions in TIR1 affect their conformational ensemble allowing surface accessibility of degrons. We resolve TIR1·auxin·IAA7 and TIR1·auxin·IAA12 complex topology, and show that flexible intrinsically disordered regions (IDRs) in the degron’s vicinity, cooperatively position AUX/IAAs on TIR1. We identify essential residues at the TIR1 N- and C-termini, which provide non-native interaction interfaces with IDRs and the folded PB1 domain of AUX/IAAs. We thereby establish a role for IDRs in modulating auxin receptor assemblies. By securing AUX/IAAs on two opposite surfaces of TIR1, IDR diversity supports locally tailored positioning for targeted ubiquitylation, and might provide conformational flexibility for a multiplicity of functional states.
Structural basis of transmembrane coupling of the HIV-1 envelope glycoprotein
Authors: Piai Alessandro , Fu Qingshan , Cai Yongfei , Ghantous Fadi , Xiao Tianshu , Shaik Md Munan , Peng Hanqin , Rits-Volloch Sophia , Chen Wen , Seaman Michael S. , Chen Bing , Chou James J. 
Published: May 2020

AbstractThe prefusion conformation of HIV-1 envelope protein (Env) is recognized by most broadly neutralizing antibodies (bnAbs). Studies showed that alterations of its membrane-related components, including the transmembrane domain (TMD) and cytoplasmic tail (CT), can reshape the antigenic structure of the Env ectodomain. Using nuclear magnetic resonance (NMR) spectroscopy, we determine the structure of an Env segment encompassing the TMD and a large portion of the CT in bicelles. The structure reveals that the CT folds into amphipathic helices that wrap around the C-terminal end of the TMD, thereby forming a support baseplate for the rest of Env. NMR dynamics measurements provide evidences of dynamic coupling across the TMD between the ectodomain and CT. Pseudovirus-based neutralization assays suggest that CT-TMD interaction preferentially affects antigenic structure near the apex of the Env trimer. These results explain why the CT can modulate the Env antigenic properties and may facilitate HIV-1 Env-based vaccine design.