bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unnecessary antibiotic prescribing in pediatric ambulatory care visits for bronchitis and bronchiolitis in the United States, 2006–2015
Authors: Snyder Rachel L. , King Laura M. , Hersh Adam L. , Fleming-Dutra Katherine E. 
Published: October 2020

AbstractAntibiotics are not indicated for the treatment of bronchitis and bronchiolitis. Using a nationally representative database from 2006–2015, we found that antibiotics were prescribed in 58% of outpatient visits for bronchitis and bronchiolitis in children, serving as a possible baseline for the expanded HEDIS 2020 measure regarding antibiotic prescribing for bronchitis.
Patterns of older Australians’ engagement in health-promoting activities: a latent profile analysis
Authors: Pettigrew Simone , Dana Liyuwork Mitiku , Jongenelis Michelle I. , Jackson Ben 
Published: October 2020

AbstractBeing active in later life is key to remaining physically and mentally healthy, and health in turn influences individuals’ ability to remain active. Activity prevalence figures can disguise the existence of clusters of older people who are very active due to regular participation in multiple categories of activity versus those who are sedentary. The aim of this study was to conduct segmentation analyses based on retired seniors’ engagement in various activities (walking, active sport/exercise, gardening and volunteering) to identify groups characterised by varying patterns of participation. The sample comprised 746 Western Australians aged 60+ years (range 60–95 years, average age 71.66 years, standard deviation = 6.57), 61 per cent of whom were female. Using latent profile analysis, four distinct segments emerged. Those respondents classified as belonging to the most active group exhibited moderate to high levels of participation across all four forms of activity, and tended to be older and more educated than other respondents. Those allocated to the least active group had very low levels of participation across most of the assessed activities and the least favourable physical and mental health scores. Overall, the results indicate the existence of highly divergent segments within the older population in terms of participation across various combinations of health-promoting activities. Segment membership appears to be more closely associated with physical and psychological factors than socio-demographic characteristics.
The split of a fricative merger due to dialect contact and societal changes: A sociophonetic study on Andalusian Spanish read-speech
Authors: Regan Brendan 
Published: October 2020

AbstractIn line with a growing body of literature suggesting that mergers are reversible given the adequate dialect contact and social context, the present study examines the phonetic split of the Andalusian Spanish merger of ceceo into the Castilian Spanish feature of distinción. Specifically, the study analyzes 19,420 coronal fricatives produced by 80 Western Andalusian speakers from the city of Huelva and the nearby town of Lepe using a reading passage and wordlist. The analyses find that leaders of this change are younger speakers, women, those with more educational attainment, those of service and professional occupations, and those from Huelva. The implications are that large-scale societal changes have allowed for the split of the ceceo merger into distinción in both speech communities, albeit at different rates of change due to their unique socioeconomic histories, demonstrating that a split is possible given the right social context.
Dynamiques à l’œuvre dans le nivellement des voyelles nasales à Marseille
Authors: Courdès-Murphy Léa , Eychenne Julien 
Published: October 2020

RESUMELa réalisation des voyelles nasales constitue l’un des traits les plus saillants de la phonologie des variétés méridionales, ces voyelles étant généralement réalisées comme des voyelles orales ou partiellement nasalisées suivies d’un appendice nasal. S’il existe un certain nombre d’études qui ont documenté la variation sociale, certains paramètres linguistiques ou encore l’influence du substrat occitan dans la genèse de ces voyelles dans le Midi, les dynamiques à l’œuvre dans le nivellement de ces voyelles vers des réalisations plus proches du français septentrional sont encore assez mal comprises. À partir d’une étude statistique détaillée basée sur un corpus de 22 locuteurs enregistrés à Marseille, le principal centre urbain de la moitié sud de la France, nous montrons l’importance de plusieurs facteurs socio-situationnels (tâche, âge, sexe et positionnement attitudinal vis-à-vis de l’accent méridional), ainsi que de plusieurs facteurs linguistiques (timbre de la voyelle, position dans le mot, contexte droit et fréquence lexicale du mot hôte).
Chinggis Khan Defeated: Plano Carpini, Jūzjānī and the Symbolic Origins of the Mongol Empire
Authors: BERGER SIMON 
Published: October 2020

AbstractThis article aims to clarify an obscure passage in Plano Carpini's text, and subsequently in C. de Bridia's one, referring to a crushing defeat of Chinggis Khan, which has so far not been identified with certainty. The record of such a defeat is found in identical terms under the pen of Jūzjānī, and it actually appears that this strange narrative follows the pattern of the Mongol myth of origin, which is also common to the myths of the Türks, of the Kimeks and others. Here the argument is made that these accounts written outside the Mongol territory are therefore not only the result of confusion and distortion, contrary to what has long been thought. They testify to the existence of a legend of Chinggis Khan, built in an imperial propaganda effort directed at all the nomadic subjects of the Mongol Empire, and which placed the birth of the empire and the story of the origins contained in the myth on the same symbolic level.
Holocene Interactions Between Glacier Retreat, Sea Ice Formation, and Atlantic Water Advection at the Inner Northeast Greenland Continental Shelf
Authors: Syring Nicole , Lloyd Jeremy M. , Stein Ruediger , Fahl Kirsten , Roberts Dave H. , Callard Louise , O'Cofaigh Colm 
Published: October 2020

AbstractDuring the past four decades significant decrease in Arctic sea ice and a dramatic ice mass loss of the Greenland Ice Sheet (GIS) has been coincident with global warming and an increase in atmospheric CO2. In Northeast Greenland significant mass loss from the outlet glaciers Nioghalvfjerdsbræ (79NG) and Zachariæ Isstrøm (ZI) and intensive seasonal breakup of the local Norske Øer Ice Barrier (NØIB) have also been observed since 2000. In order to better understand the processes driving these modern changes, studies of paleoclimate records are important and of major societal relevance. A multiproxy study including organic‐biogeochemical and micropaleontological proxies was carried out on a marine sediment core recovered directly in front of 79NG. Data from Core PS100/270 evidenced a strong inflow of warm recirculating Atlantic Water across the Northeast Greenland shelf from the early Holocene between ~10 and 7.5 ka. An overall high in phytoplankton productivity occurred within a stable sea ice margin regime, accompanied by 79NG retreat most probably triggered by peak solar insolation and changes in the local ocean circulation. Enhanced basal melt of the underside of 79NG at ~7.5 ka then led to the total disintegration of the ice shelf. The released freshwater would have driven water column stratification and promoted the formation of the local landfast ice barrier, which is shown by lowered biomarker values and foraminifera abundances toward the end of the early Holocene. Near perennial sea ice conditions with short summers and 79NG retreat to the inner fjord then prevailed from ~7.5 to ~0.8 ka.
Relationships between nitrogen cycling microbial community abundance and composition reveal the indirect effect of soil pH on oak decline
Authors: Scarlett K , Denman S , Clark D R , Forster J , Vanguelova E , Brown N , Whitby C 
Published: October 2020

Abstract
Tree decline is a global concern and the primary cause is often unknown. Complex interactions between fluctuations in nitrogen (N) and acidifying compounds have been proposed as factors causing nutrient imbalances and decreasing stress tolerance of oak trees. Microorganisms are crucial in regulating soil N available to plants, yet little is known about the relationships between soil N-cycling and tree health. Here, we combined high-throughput sequencing and qPCR analysis of key nitrification and denitrification genes with soil chemical analyses to characterise ammonia-oxidising bacteria (AOB), archaea (AOA) and denitrifying communities in soils associated with symptomatic (declining) and asymptomatic (apparently healthy) oak trees (Quercus robur and Q. petraea) in the United Kingdom. Asymptomatic trees were associated with a higher abundance of AOB that is driven positively by soil pH. No relationship was found between AOA abundance and tree health. However, AOA abundance was driven by lower concentrations of NH4+, further supporting the idea of AOA favouring lower soil NH4+ concentrations. Denitrifier abundance was influenced primarily by soil C:N ratio, and correlations with AOB regardless of tree health. These findings indicate that amelioration of soil acidification by balancing C:N may affect AOB abundance driving N transformations, reducing stress on declining oak trees.
BioID-based proteomic analysis of the Bid interactome identifies novel proteins involved in cell-cycle-dependent apoptotic priming
Authors: Pedley Robert , King Louise E. , Mallikarjun Venkatesh , Wang Pengbo , Swift Joe , Brennan Keith , Gilmore Andrew P. 
Published: October 2020

AbstractApoptotic priming controls the commitment of cells to apoptosis by determining how close they lie to mitochondrial permeabilisation. Variations in priming are important for how both healthy and cancer cells respond to chemotherapeutic agents, but how it is dynamically coordinated by Bcl-2 proteins remains unclear. The Bcl-2 family protein Bid is phosphorylated when cells enter mitosis, increasing apoptotic priming and sensitivity to antimitotic drugs. Here, we report an unbiased proximity biotinylation (BioID) screen to identify regulators of apoptotic priming in mitosis, using Bid as bait. The screen primarily identified proteins outside of the canonical Bid interactome. Specifically, we found that voltage-dependent anion-selective channel protein 2 (VDAC2) was required for Bid phosphorylation-dependent changes in apoptotic priming during mitosis. These results highlight the importance of the wider Bcl-2 family interactome in regulating the temporal control of apoptotic priming.
Metastable alloying structures in MAPbI3−xClx crystals
Authors: Qiao Wen-Cheng , Yang Jianming , Dong Wei , Yang Guang , Bao Qinye , Huang Rong , Wang Xue Lu , Yao Ye-Feng 
Published: October 2020

AbstractChlorine incorporation engineering has been widely used in optoelectronic devices based on methylammonium lead iodide (MAPbI3) perovskites. However, the characteristics of I/Cl alloying structures in MAPbI3−xClx mixed-halide perovskites and their influences on the optoelectronic properties have been issues of a long-standing controversy. Here, we present a detailed study of the I/Cl alloying structures in MAPbI3−xClx (x = 0.0 to 0.3) single crystals. We found that a small amount of Cl can substitute for the iodide of the PbI3 inorganic lattice, leading to a phase transition from the tetragonal to cubic phase and anomalous cation dynamics evolution. Analyses based on time-dependent X-ray diffraction, 207Pb NMR, and 2H NMR indicate that the alloying structures of the MAPbI3−xClx crystals are metastable and decompose over time. In addition, the photocurrent response measurement of MAPbI3−xClx proved a close correlation between the alloying structures and photoelectric properties of the material. This work sheds light on the essential understanding of the I/Cl alloying structure and provides a plausible explanation for the controversy regarding the role of chloride ions in optoelectronic devices.
Orbital climate variability on the northeastern Tibetan Plateau across the Eocene–Oligocene transition
Authors: Ao Hong , Dupont-Nivet Guillaume , Rohling Eelco J. , Zhang Peng , Ladant Jean-Baptiste , Roberts Andrew P. , Licht Alexis , Liu Qingsong , Liu Zhonghui , Dekkers Mark J. , Coxall Helen K. , Jin Zhangdong , Huang Chunju , Xiao Guoqiao , Poulsen Christopher J. , Barbolini Natasha , Meijer Niels , Sun Qiang , Qiang Xiaoke , Yao Jiao , An Zhisheng 
Published: October 2020

AbstractThe first major build-up of Antarctic glaciation occurred in two consecutive stages across the Eocene–Oligocene transition (EOT): the EOT-1 cooling event at ~34.1–33.9 Ma and the Oi-1 glaciation event at ~33.8–33.6 Ma. Detailed orbital-scale terrestrial environmental responses to these events remain poorly known. Here we present magnetic and geochemical climate records from the northeastern Tibetan Plateau margin that are dated precisely from ~35.5 to 31 Ma by combined magneto- and astro-chronology. These records suggest a hydroclimate transition at ~33.7 Ma from eccentricity dominated cycles to oscillations paced by a combination of eccentricity, obliquity, and precession, and confirm that major Asian aridification and cooling occurred at Oi-1. We conclude that this terrestrial orbital response transition coincided with a similar transition in the marine benthic δ18O record for global ice volume and deep-sea temperature variations. The dramatic reorganization of the Asian climate system coincident with Oi-1 was, thus, a response to coeval atmospheric CO2 decline and continental-scale Antarctic glaciation.
DIALib-QC an assessment tool for spectral libraries in data-independent acquisition proteomics
Authors: Midha Mukul K. , Campbell David S. , Kapil Charu , Kusebauch Ulrike , Hoopmann Michael R. , Bader Samuel L. , Moritz Robert L. 
Published: October 2020

AbstractData-independent acquisition (DIA) mass spectrometry, also known as Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH), is a popular label-free proteomics strategy to comprehensively quantify peptides/proteins utilizing mass spectral libraries to decipher inherently multiplexed spectra collected linearly across a mass range. Although there are many spectral libraries produced worldwide, the quality control of these libraries is lacking. We present the DIALib-QC (DIA library quality control) software tool for the systematic evaluation of a library’s characteristics, completeness and correctness across 62 parameters of compliance, and further provide the option to improve its quality. We demonstrate its utility in assessing and repairing spectral libraries for correctness, accuracy and sensitivity.
The protein translation machinery is expressed for maximal efficiency in Escherichia coli
Authors: Hu Xiao-Pan , Dourado Hugo , Schubert Peter , Lercher Martin J. 
Published: October 2020

AbstractProtein synthesis is the most expensive process in fast-growing bacteria. Experimentally observed growth rate dependencies of the translation machinery form the basis of powerful phenomenological growth laws; however, a quantitative theory on the basis of biochemical and biophysical constraints is lacking. Here, we show that the growth rate-dependence of the concentrations of ribosomes, tRNAs, mRNA, and elongation factors observed in Escherichia coli can be predicted accurately from a minimization of cellular costs in a mechanistic model of protein translation. The model is constrained only by the physicochemical properties of the molecules and has no adjustable parameters. The costs of individual components (made of protein and RNA parts) can be approximated through molecular masses, which correlate strongly with alternative cost measures such as the molecules’ carbon content or the requirement of energy or enzymes for their biosynthesis. Analogous cost minimization approaches may facilitate similar quantitative insights also for other cellular subsystems.
Reversible multicolor chromism in layered formamidinium metal halide perovskites
Authors: Rosales Bryan A. , Mundt Laura E. , Allen Taylor G. , Moore David T. , Prince Kevin J. , Wolden Colin A. , Rumbles Garry , Schelhas Laura T. , Wheeler Lance M. 
Published: October 2020

AbstractMetal halide perovskites feature crystalline-like electronic band structures and liquid-like physical properties. The crystal–liquid duality enables optoelectronic devices with unprecedented performance and a unique opportunity to chemically manipulate the structure with low energy input. In this work, we leverage the low formation energy of metal halide perovskites to demonstrate multicolor reversible chromism. We synthesized layered Ruddlesden-Popper FAn+1PbnX3n+1(FA = formamidinium, X = I, Br;n = number of layers = 1, 2, 3 … ∞) and reversibly tune the dimensionality (n) by modulating the strength and number of H-bonds in the system. H-bonding was controlled by exposure to solvent vapor (solvatochromism) or temperature change (thermochromism), which shuttles FAX salt pairs between the FAn+1PbnX3n+1domains and adjacent FAX “reservoir” domains. Unlike traditional chromic materials that only offer a single-color transition, FAn+1PbnX3n+1films reversibly switch between multiple colors including yellow, orange, red, brown, and white/colorless. Each colored phase exhibits distinct optoelectronic properties characteristic of 2D superlattice materials with tunable quantum well thickness.
Multivalent interactions drive nucleosome binding and efficient chromatin deacetylation by SIRT6
Authors: Liu Wallace H. , Zheng Jie , Feldman Jessica L. , Klein Mark A. , Kuznetsov Vyacheslav I. , Peterson Craig L. , Griffin Patrick R. , Denu John M. 
Published: October 2020

AbstractThe protein deacetylase SIRT6 maintains cellular homeostasis through multiple pathways that include the deacetylation of histone H3 and repression of transcription. Prior work suggests that SIRT6 is associated with chromatin and can substantially reduce global levels of H3 acetylation, but how SIRT6 is able to accomplish this feat is unknown. Here, we describe an exquisitely tight interaction between SIRT6 and nucleosome core particles, in which a 2:1 enzyme:nucleosome complex assembles via asymmetric binding with distinct affinities. While both SIRT6 molecules associate with the acidic patch on the nucleosome, we find that the intrinsically disordered SIRT6 C-terminus promotes binding at the higher affinity site through recognition of nucleosomal DNA. Together, multivalent interactions couple productive binding to efficient deacetylation of histones on endogenous chromatin. Unique among histone deacetylases, SIRT6 possesses the intrinsic capacity to tightly interact with nucleosomes for efficient activity.
Analysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry
Authors: Stützer Alexandra , Welp Luisa M. , Raabe Monika , Sachsenberg Timo , Kappert Christin , Wulf Alexander , Lau Andy M. , David Stefan-Sebastian , Chernev Aleksandar , Kramer Katharina , Politis Argyris , Kohlbacher Oliver , Fischle Wolfgang , Urlaub Henning 
Published: October 2020

AbstractProtein–DNA interactions are key to the functionality and stability of the genome. Identification and mapping of protein–DNA interaction interfaces and sites is crucial for understanding DNA-dependent processes. Here, we present a workflow that allows mass spectrometric (MS) identification of proteins in direct contact with DNA in reconstituted and native chromatin after cross-linking by ultraviolet (UV) light. Our approach enables the determination of contact interfaces at amino-acid level. With the example of chromatin-associated protein SCML2 we show that our technique allows differentiation of nucleosome-binding interfaces in distinct states. By UV cross-linking of isolated nuclei we determined the cross-linking sites of several factors including chromatin-modifying enzymes, demonstrating that our workflow is not restricted to reconstituted materials. As our approach can distinguish between protein–RNA and DNA interactions in one single experiment, we project that it will be possible to obtain insights into chromatin and its regulation in the future.
Repair of G1 induced DNA double-strand breaks in S-G2/M by alternative NHEJ
Authors: Yu Wei , Lescale Chloé , Babin Loelia , Bedora-Faure Marie , Lenden-Hasse Hélène , Baron Ludivine , Demangel Caroline , Yelamos José , Brunet Erika , Deriano Ludovic 
Published: October 2020

AbstractThe alternative non-homologous end-joining (NHEJ) pathway promotes DNA double-strand break (DSB) repair in cells deficient for NHEJ or homologous recombination, suggesting that it operates at all stages of the cell cycle. Here, we use an approach in which DNA breaks can be induced in G1 cells and their repair tracked, enabling us to show that joining of DSBs is not functional in G1-arrested XRCC4-deficient cells. Cell cycle entry into S-G2/M restores DSB repair by Pol θ-dependent and PARP1-independent alternative NHEJ with repair products bearing kilo-base long DNA end resection, micro-homologies and chromosome translocations. We identify a synthetic lethal interaction between XRCC4 and Pol θ under conditions of G1 DSBs, associated with accumulation of unresolved DNA ends in S-G2/M. Collectively, our results support the conclusion that the repair of G1 DSBs progressing to S-G2/M by alternative NHEJ drives genomic instability and represent an attractive target for future DNA repair-based cancer therapies.
Structural basis for two metal-ion catalysis of DNA cleavage by Cas12i2
Authors: Huang Xue , Sun Wei , Cheng Zhi , Chen Minxuan , Li Xueyan , Wang Jiuyu , Sheng Gang , Gong Weimin , Wang Yanli 
Published: October 2020

AbstractTo understand how the RuvC catalytic domain of Class 2 Cas proteins cleaves DNA, it will be necessary to elucidate the structures of RuvC-containing Cas complexes in their catalytically competent states. Cas12i2 is a Class 2 type V-I CRISPR-Cas endonuclease that cleaves target dsDNA by an unknown mechanism. Here, we report structures of Cas12i2–crRNA–DNA complexes and a Cas12i2–crRNA complex. We reveal the mechanism of DNA recognition and cleavage by Cas12i2, and activation of the RuvC catalytic pocket induced by a conformational change of the Helical-II domain. The seed region (nucleotides 1–8) is dispensable for RuvC activation, but the duplex of the central spacer (nucleotides 9–15) is required. We captured the catalytic state of Cas12i2, with both metal ions and the ssDNA substrate bound in the RuvC catalytic pocket. Together, our studies provide significant insights into the DNA cleavage mechanism by RuvC-containing Cas proteins.
Whole blood immunophenotyping uncovers immature neutrophil-to-VD2 T-cell ratio as an early marker for severe COVID-19
Authors: Carissimo Guillaume , Xu Weili , Kwok Immanuel , Abdad Mohammad Yazid , Chan Yi-Hao , Fong Siew-Wai , Puan Kia Joo , Lee Cheryl Yi-Pin , Yeo Nicholas Kim-Wah , Amrun Siti Naqiah , Chee Rhonda Sin-Ling , How Wilson , Chan Stephrene , Fan Bingwen Eugene , Andiappan Anand Kumar , Lee Bernett , Rötzschke Olaf , Young Barnaby Edward , Leo Yee-Sin , Lye David Chien , Renia Laurent , Ng Lai Guan , Larbi Anis , Ng Lisa FP 
Published: October 2020

AbstractSARS-CoV-2 is the novel coronavirus responsible for the current COVID-19 pandemic. Severe complications are observed only in a small proportion of infected patients but the cellular mechanisms underlying this progression are still unknown. Comprehensive flow cytometry of whole blood samples from 54 COVID-19 patients reveals a dramatic increase in the number of immature neutrophils. This increase strongly correlates with disease severity and is associated with elevated IL-6 and IP-10 levels, two key players in the cytokine storm. The most pronounced decrease in cell counts is observed for CD8 T-cells and VD2 γδ T-cells, which both exhibit increased differentiation and activation. ROC analysis reveals that the count ratio of immature neutrophils to VD2 (or CD8) T-cells predicts pneumonia onset (0.9071) as well as hypoxia onset (0.8908) with high sensitivity and specificity. It would thus be a useful prognostic marker for preventive patient management and improved healthcare resource management.