bluuebunny/crossref_metadata_2025_split huggingface dataset:
THE MAKING OF CHRONICLES AND THE MAKING OF ENGLAND: THE ANGLO-SAXON CHRONICLES AFTER ALFREDProthero Lecture
Authors: Stafford Pauline 
Published: November 2017

ABSTRACTBetweenc. 900 and the mid-twelfth century, a series of Old English vernacular chronicles were produced, growing out of the text produced at the court of King Alfred. These chronicles are collectively known as ‘the Anglo-Saxon Chronicle’. They have long been accorded fundamental status in the English national story. No others have shaped our view of the origins of England between the fifth and eleventh centuries to the same extent. They provide between them the only continuous narrative of this period. They are the story that has made England. This paper deals with the relationship between that story, these texts and England: how they have been read and edited – made – in the context of the English national story since the sixteenth century; but also their relationship to, the part they may have played in, the original making of the English kingdom. The focus is on developments during the tenth and eleventh centuries, when a political unit more or less equivalent to the England we now know emerged. It is argued that these texts were the ideological possession and expression of the southern English elite, especially of bishops and archbishops, at this critical period of kingdom-making. Special attention is given to their possible role in the incorporation of Northumbria into that kingdom. These chronicles were made by scribes a millennium ago, and to some extent have been reworked by modern editors from the sixteenth century on. They are daunting in their complexity. The differences between them are as important as the common ground they share. Understanding the making of these foundational texts has its own light to shed on the making of England.
Strong laser field control of fragment spatial distributions from a photodissociation reaction
Authors: Corrales María E. , de Nalda Rebeca , Bañares Luis 
Published: November 2017

AbstractThe notion that strong laser light can intervene and modify the dynamical processes of matter has been demonstrated and exploited both in gas and condensed phases. The central objective of laser control schemes has been the modification of branching ratios in chemical processes, under the philosophy that conveniently tailored light can steer the dynamics of a chemical mechanism towards desired targets. Less explored is the role that strong laser control can play on chemical stereodynamics, i.e. the angular distribution of the products of a chemical reaction in space. This work demonstrates for the case of methyl iodide that when a molecular bond breaking process takes place in the presence of an intense infrared laser field, its stereodynamics is profoundly affected, and that the intensity of this laser field can be used as an external knob to control it.
Structural basis for high-affinity actin binding revealed by a β-III-spectrin SCA5 missense mutation
Authors: Avery Adam W. , Fealey Michael E. , Wang Fengbin , Orlova Albina , Thompson Andrew R. , Thomas David D. , Hays Thomas S. , Egelman Edward H. 
Published: November 2017

AbstractSpinocerebellar ataxia type 5 (SCA5) is a neurodegenerative disease caused by mutations in the cytoskeletal protein β-III-spectrin. Previously, a SCA5 mutation resulting in a leucine-to-proline substitution (L253P) in the actin-binding domain (ABD) was shown to cause a 1000-fold increase in actin-binding affinity. However, the structural basis for this increase is unknown. Here, we report a 6.9 Å cryo-EM structure of F-actin complexed with the L253P ABD. This structure, along with co-sedimentation and pulsed-EPR measurements, demonstrates that high-affinity binding caused by the CH2-localized mutation is due to opening of the two CH domains. This enables CH1 to bind actin aided by an unstructured N-terminal region that becomes α-helical upon binding. This helix is required for association with actin as truncation eliminates binding. Collectively, these results shed light on the mechanism by which β-III-spectrin, and likely similar actin-binding proteins, interact with actin, and how this mechanism can be perturbed to cause disease.
Acetylated histone variant H2A.Z is involved in the activation of neo-enhancers in prostate cancer
Authors: Valdés-Mora Fátima , Gould Cathryn M. , Colino-Sanguino Yolanda , Qu Wenjia , Song Jenny Z. , Taylor Kylie M. , Buske Fabian A. , Statham Aaron L. , Nair Shalima S. , Armstrong Nicola J. , Kench James G. , Lee Kenneth M. L. , Horvath Lisa G. , Qiu Minru , Ilinykh Alexei , Yeo-Teh Nicole S. , Gallego-Ortega David , Stirzaker Clare , Clark Susan J. 
Published: November 2017

AbstractAcetylation of the histone variant H2A.Z (H2A.Zac) occurs at active promoters and is associated with oncogene activation in prostate cancer, but its role in enhancer function is still poorly understood. Here we show that H2A.Zac containing nucleosomes are commonly redistributed to neo-enhancers in cancer resulting in a concomitant gain of chromatin accessibility and ectopic gene expression. Notably incorporation of acetylated H2A.Z nucleosomes is a pre-requisite for activation of Androgen receptor (AR) associated enhancers. H2A.Zac nucleosome occupancy is rapidly remodeled to flank the AR sites to initiate the formation of nucleosome-free regions and the production of AR-enhancer RNAs upon androgen treatment. Remarkably higher levels of global H2A.Zac correlate with poorer prognosis. Altogether these data demonstrate the novel contribution of H2A.Zac in activation of newly formed enhancers in prostate cancer.
Competition between crystal and fibril formation in molecular mutations of amyloidogenic peptides
Authors: Reynolds Nicholas P. , Adamcik Jozef , Berryman Joshua T. , Handschin Stephan , Zanjani Ali Asghar Hakami , Li Wen , Liu Kun , Zhang Afang , Mezzenga Raffaele 
Published: November 2017

AbstractAmyloidogenic model peptides are invaluable for investigating assembly mechanisms in disease related amyloids and in protein folding. During aggregation, such peptides can undergo bifurcation leading to fibrils or crystals, however the mechanisms of fibril-to-crystal conversion are unclear. We navigate herein the energy landscape of amyloidogenic peptides by studying a homologous series of hexapeptides found in animal, human and disease related proteins. We observe fibril-to-crystal conversion occurring within single aggregates via untwisting of twisted ribbon fibrils possessing saddle-like curvature and cross-sectional aspect ratios approaching unity. Changing sequence, pH or concentration shifts the growth towards larger aspect ratio species assembling into stable helical ribbons possessing mean-curvature. By comparing atomistic calculations of desolvation energies for association of peptides we parameterise a kinetic model, providing a physical explanation of fibril-to-crystal interconversion. These results shed light on the self-assembly of amyloidogenic peptides, suggesting amyloid crystals, not fibrils, represent the ground state of the protein folding energy landscape.
The effect of artificial selection on phenotypic plasticity in maize
Authors: Gage Joseph L. , Jarquin Diego , Romay Cinta , Lorenz Aaron , Buckler Edward S. , Kaeppler Shawn , Alkhalifah Naser , Bohn Martin , Campbell Darwin A. , Edwards Jode , Ertl David , Flint-Garcia Sherry , Gardiner Jack , Good Byron , Hirsch Candice N. , Holland Jim , Hooker David C. , Knoll Joseph , Kolkman Judith , Kruger Greg , Lauter Nick , Lawrence-Dill Carolyn J. , Lee Elizabeth , Lynch Jonathan , Murray Seth C. , Nelson Rebecca , Petzoldt Jane , Rocheford Torbert , Schnable James , Schnable Patrick S. , Scully Brian , Smith Margaret , Springer Nathan M. , Srinivasan Srikant , Walton Renee , Weldekidan Teclemariam , Wisser Randall J. , Xu Wenwei , Yu Jianming , de Leon Natalia 
Published: November 2017

AbstractRemarkable productivity has been achieved in crop species through artificial selection and adaptation to modern agronomic practices. Whether intensive selection has changed the ability of improved cultivars to maintain high productivity across variable environments is unknown. Understanding the genetic control of phenotypic plasticity and genotype by environment (G × E) interaction will enhance crop performance predictions across diverse environments. Here we use data generated from the Genomes to Fields (G2F) Maize G × E project to assess the effect of selection on G × E variation and characterize polymorphisms associated with plasticity. Genomic regions putatively selected during modern temperate maize breeding explain less variability for yield G × E than unselected regions, indicating that improvement by breeding may have reduced G × E of modern temperate cultivars. Trends in genomic position of variants associated with stability reveal fewer genic associations and enrichment of variants 0–5000 base pairs upstream of genes, hypothetically due to control of plasticity by short-range regulatory elements.
The effect of genetic variation on promoter usage and enhancer activity
Authors: Garieri Marco , Delaneau Olivier , Santoni Federico , Fish Richard J. , Mull David , Carninci Piero , Dermitzakis Emmanouil T. , Antonarakis Stylianos E. , Fort Alexandre 
Published: November 2017

AbstractThe identification of genetic variants affecting gene expression, namely expression quantitative trait loci (eQTLs), has contributed to the understanding of mechanisms underlying human traits and diseases. The majority of these variants map in non-coding regulatory regions of the genome and their identification remains challenging. Here, we use natural genetic variation and CAGE transcriptomes from 154 EBV-transformed lymphoblastoid cell lines, derived from unrelated individuals, to map 5376 and 110 regulatory variants associated with promoter usage (puQTLs) and enhancer activity (eaQTLs), respectively. We characterize five categories of genes associated with puQTLs, distinguishing single from multi-promoter genes. Among multi-promoter genes, we find puQTL effects either specific to a single promoter or to multiple promoters with variable effect orientations. Regulatory variants associated with opposite effects on different mRNA isoforms suggest compensatory mechanisms occurring between alternative promoters. Our analyses identify differential promoter usage and modulation of enhancer activity as molecular mechanisms underlying eQTLs related to regulatory elements.
Multi-scale investigation of uranium attenuation by arsenic at an abandoned uranium mine, South Terras
Authors: Corkhill Claire L. , Crean Daniel E. , Bailey Daniel J. , Makepeace Carmen , Stennett Martin C. , Tappero Ryan , Grolimund Daniel , Hyatt Neil C. 
Published: November 2017

AbstractDetailed mineralogical analysis of soils from the UK’s historical uranium mine, South Terras, was performed to elucidate the mechanisms of uranium degradation and migration in the 86 years since abandonment. Soils were sampled from the surface (0–2 cm) and near-surface (25 cm) in two distinct areas of ore processing activities. Bulk soil analysis revealed the presence of high concentrations of uranium (<1690 p.p.m.), arsenic (1830 p.p.m.) and beryllium (~250 p.p.m.), suggesting pedogenic weathering of the country rock and ore extraction processes to be the mechanisms of uranium ore degradation. Micro-focus XRF analysis indicated the association of uranium with arsenic, phosphate and copper; µ-XRD data confirmed the presence of the uranyl-arsenate minerals metazeunerite (Cu(UO2)2(AsO4)2·8H2O) and metatorbernite (Cu(UO2)2(PO4)2·8H2O) to be ubiquitous. Our data are consistent with the solid solution of these two uranyl-mica minerals, not previously observed at uranium-contaminated sites. Crystallites of uranyl-mica minerals were observed to coat particles of jarosite and muscovite, suggesting that the mobility of uranium from degraded ores is attenuated by co-precipitation with arsenic and phosphate, which was not previously considered at this site.
Topological networks for quantum communication between distant qubits
Authors: Lang Nicolai , Büchler Hans Peter 
Published: November 2017

AbstractEfficient communication between qubits relies on robust networks, which allow for fast and coherent transfer of quantum information. It seems natural to harvest the remarkable properties of systems characterized by topological invariants to perform this task. Here, we show that a linear network of coupled bosonic degrees of freedom, characterized by topological bands, can be employed for the efficient exchange of quantum information over large distances. Important features of our setup are that it is robust against quenched disorder, all relevant operations can be performed by global variations of parameters, and the time required for communication between distant qubits approaches linear scaling with their distance. We demonstrate that our concept can be extended to an ensemble of qubits embedded in a two-dimensional network to allow for communication between all of them.
Salt stress-induced FERROCHELATASE 1 improves resistance to salt stress by limiting sodium accumulation in Arabidopsis thaliana
Authors: Zhao Wen Ting , Feng Sheng Jun , Li Hua , Faust Franziska , Kleine Tatjana , Li Long Na , Yang Zhi Min 
Published: November 2017

AbstractFerrochelatase-1 as a terminal enzyme of heme biosynthesis regulates many essential metabolic and physiological processes. Whether FC1 is involved in plant response to salt stress has not been described. This study shows that Arabidopsis overexpressing AtFC1 displays resistance to high salinity, whereas a T-DNA insertion knock-down mutant fc1 was more sensitive to salt stress than wild-type plants. AtFC1 conferred plant salt resistance by reducing Na+ concentration, enhancing K+ accumulation and preventing lysis of the cell membrane. Such observations were associated with the upregulation of SOS1, which encodes a plasma membrane Na+/H+ antiporter. AtFC1 overexpression led to a reduced expression of several well known salt stress-responsive genes such as NHX1 and AVP1, suggesting that AtFC1-regulated low concentration of Na+ in plants might not be through the mechanism for Na+ sequestration. To investigate the mechanism leading to the role of AtFC1 in mediating salt stress response in plants, a transcriptome of fc1 mutant plants under salt stress was profiled. Our data show that mutation of AtFC1 led to 490 specific genes up-regulated and 380 specific genes down-regulated in fc1 mutants under salt stress. Some of the genes are involved in salt-induced oxidative stress response, monovalent cation-proton (Na+/H+) exchange, and Na+ detoxification.
Epigenetic Transitions and Knotted Solitons in Stretched Chromatin
Authors: Michieletto D. , Orlandini E. , Marenduzzo D. 
Published: November 2017

AbstractThe spreading and regulation of epigenetic marks on chromosomes is crucial to establish and maintain cellular identity. Nonetheless, the dynamic mechanism leading to the establishment and maintenance of tissue-specific, epigenetic pattern is still poorly understood. In this work we propose, and investigate in silico, a possible experimental strategy to illuminate the interplay between 3D chromatin structure and epigenetic dynamics. We consider a set-up where a reconstituted chromatin fibre is stretched at its two ends (e.g., by laser tweezers), while epigenetic enzymes (writers) and chromatin-binding proteins (readers) are flooded into the system. We show that, by tuning the stretching force and the binding affinity of the readers for chromatin, the fibre undergoes a sharp transition between a stretched, epigenetically disordered, state and a crumpled, epigenetically coherent, one. We further investigate the case in which a knot is tied along the chromatin fibre, and find that the knotted segment enhances local epigenetic order, giving rise to “epigenetic solitons” which travel and diffuse along chromatin. Our results point to an intriguing coupling between 3D chromatin topology and epigenetic dynamics, which may be investigated via single molecule experiments.
Topographic effect on the phenology of Ficus pedunculosa var. mearnsii (Mearns fig) in its northern boundary distribution, Taiwan
Authors: Kuo Chu-Chia , Bain Anthony , Chiu Yu-Ting , Ho Yi-Chiao , Chen Wen-Hsuan , Chou Lien-Siang , Tzeng Hsy-Yu 
Published: November 2017

AbstractMearns fig grows at the edge of coastal vegetation on uplifted coral reefs, its population and mutualistic-pollinators are susceptible to the influence of extreme weather. To determine the phenology of Mearns fig and the effects of various weather events under small-scale topographic differences, phenology was conducted for 3 years and 7 months. Results showed that Mearns figs had multiple leaf and fig productions year-round. Topographic effects caused population in Frog Rock Trail and Jialeshuei, which are less than 10 km away from each other, to exhibit different phenological patterns after experiencing severe weather events. Northeast monsoons led the Jialeshuei population to show low amounts of leaves and figs in winter and the phenological production was also susceptible to disturbances by typhoons in summer. Fig reproduction in such environment was disadvantageous to maintain pollinators. Besides, topographic complex in microhabitat of Frog Rock Trail protected some individuals from these same events thus safeguard population’s survival. The phenology of Mearns fig would respond to the weather events sensitively, which serve as references for estimating the mutualism system, and as indicators of climate change.
Risk Factors and Molecular Features of Sequence Type (ST) 131 Extended-spectrum β-Lactamase-producing Escherichia coli in Community-onset Bacteremia
Authors: Kim Hyunsoo , Kim Young Ah , Park Yoon Soo , Choi Min Hyuk , Lee Gyeong In , Lee Kyungwon 
Published: November 2017

AbstractDue to the spread of a single CTX-M-type extended-spectrum β-lactamase (ESBL) clone of sequence type (ST) 131, community-onset bacteremia caused by ESBL-producing Escherichia coli has increased dramatically. We evaluated the risk factors and molecular features of ESBL-producing E. coli ST131 clones isolated from Korean patients with community-onset bacteremia. We collected a total of 124 ESBL-producing E. coli isolates from blood in patients with community-onset bacteremia over a 2 year-period. Among 124 patients, the number of community-associated bacteremia cases was 57 (46%). ST131 strains accounted for 49.1% (28/57) of community-associated bacteremia cases and 44.8% (30/67) of healthcare-associated community-onset bacteremia cases. Among 58 ST131 strains, nine isolates were shown to harbor O16-H41, and 61.1% (30/49) of O25 had H30Rx. In a multivariate analysis, independent risk factors for acquisition of ST131 isolates over non-ST131 isolates were underlying diabetes mellitus and absence of prior chemotherapy history. The most common ESBL genotype was CTX-M-15 (46.0%), followed by CTX-M-14 (37.1%). A considerable proportion of community-onset ESBL-producing E. coli bacteremia was observed. ST131 clones appear to be associated with the spread of community-associated bacteremia exhibiting high antimicrobial resistance and highly virulent H30Rx traits, which could become a major public health concern in Korea.
Giant Slip Induced Anomalous Dewetting of an Ultrathin Film on a Viscous Sublayer
Authors: Xu Lin , Bandyopadhyay Dipankar , Reddy Puchalapalli Dinesh Sankar , Sharma Ashutosh , Joo Sang Woo 
Published: November 2017

AbstractA ‘giant’ slip dynamics was engineered to a highly confined interface of a dewetting polymethylmethacrylate (PMMA) ultrathin film by introducing a lubricating viscous polystyrene (PS) sublayer. The crossover of regimes from no-slip to giant-slip was engendered by tuning the viscosity and thickness of the sublayer. A long-range hole-rim interaction with increase in slippage on the PMMA-PS interface transformed the circular holes on the PMMA surface into the noncircular faceted ones. The extent of the slippage and the transition of the length scales from slip-dominated to no-slip regime were evaluated using a general linear stability analysis. The proposed formulation provided an analytical tool to evaluate the slippage effective at the soft and deformable liquid-liquid interfaces.
Microscopy as a statistical, Rényi-Ulam, half-lie game: a new heuristic search strategy to accelerate imaging
Authors: Drumm Daniel W. , Greentree Andrew D. 
Published: November 2017

AbstractFinding a fluorescent target in a biological environment is a common and pressing microscopy problem. This task is formally analogous to the canonical search problem. In ideal (noise-free, truthful) search problems, the well-known binary search is optimal. The case of half-lies, where one of two responses to a search query may be deceptive, introduces a richer, Rényi-Ulam problem and is particularly relevant to practical microscopy. We analyse microscopy in the contexts of Rényi-Ulam games and half-lies, developing a new family of heuristics. We show the cost of insisting on verification by positive result in search algorithms; for the zero-half-lie case bisectioning with verification incurs a 50% penalty in the average number of queries required. The optimal partitioning of search spaces directly following verification in the presence of random half-lies is determined. Trisectioning with verification is shown to be the most efficient heuristic of the family in a majority of cases.
Constitutive expression of NF-κB inducing kinase in regulatory T cells impairs suppressive function and promotes instability and pro-inflammatory cytokine production
Authors: Polesso Fanny , Sarker Minhazur , Anderson Arian , Parker David C. , Murray Susan E. 
Published: November 2017

AbstractCD4+Foxp3+ regulatory T cells (Tregs) are indispensable negative regulators of immune responses. To understand Treg biology in health and disease, it is critical to elucidate factors that affect Treg homeostasis and suppressive function. Tregs express several costimulatory TNF receptor family members that activate non-canonical NF-κB via accumulation of NF-κB inducing kinase (NIK). We previously showed that constitutive NIK expression in all T cells causes fatal multi-organ autoimmunity associated with hyperactive conventional T cell responses and poor Treg-mediated suppression. Here, we show that constitutive NIK expression that is restricted to Tregs via a Cre-inducible transgene causes an autoimmune syndrome. We found that constitutive NIK expression decreased expression of numerous Treg signature genes and microRNAs involved in Treg homeostasis and suppressive phenotype. NIK transgenic Tregs competed poorly with WT Tregs in vivo and produced pro-inflammatory cytokines upon stimulation. Lineage tracing experiments revealed accumulation of ex-Foxp3+ T cells in mice expressing NIK constitutively in Tregs, and these former Tregs produced copious IFNγ and IL-2. Our data indicate that under inflammatory conditions in which NIK is activated, Tregs may lose suppressive function and may actively contribute to inflammation.