bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hikarchaeia demonstrate an intermediate stage in the methanogen-to-halophile transition
Authors: Martijn Joran , Schön Max E. , Lind Anders E. , Vosseberg Julian , Williams Tom A. , Spang Anja , Ettema Thijs J. G. 
Published: October 2020

AbstractHalobacteria (henceforth: Haloarchaea) are predominantly aerobic halophiles that are thought to have evolved from anaerobic methanogens. This remarkable transformation most likely involved an extensive influx of bacterial genes. Whether it entailed a single massive transfer event or a gradual stream of transfers remains a matter of debate. To address this, genomes that descend from methanogen-to-halophile intermediates are necessary. Here, we present five such near-complete genomes of Marine Group IV archaea (Hikarchaeia), the closest known relatives of Haloarchaea. Their inclusion in gene tree-aware ancestral reconstructions reveals an intermediate stage that had already lost a large number of genes, including nearly all of those involved in methanogenesis and the Wood-Ljungdahl pathway. In contrast, the last Haloarchaea common ancestor gained a large number of genes and expanded its aerobic respiration and salt/UV resistance gene repertoire. Our results suggest that complex and gradual patterns of gain and loss shaped the methanogen-to-halophile transition.
Molecular mechanisms underlying the extreme mechanical anisotropy of the flaviviral exoribonuclease-resistant RNAs (xrRNAs)
Authors: Niu Xiaolin , Liu Qiuhan , Xu Zhonghe , Chen Zhifeng , Xu Linghui , Xu Lilei , Li Jinghong , Fang Xianyang 
Published: October 2020

AbstractMechanical anisotropy is an essential property for many biomolecules to assume their structures, functions and applications, however, the mechanisms for their direction-dependent mechanical responses remain elusive. Herein, by using a single-molecule nanopore sensing technique, we explore the mechanisms of directional mechanical stability of the xrRNA1 RNA from ZIKA virus (ZIKV), which forms a complex ring-like architecture. We reveal extreme mechanical anisotropy in ZIKV xrRNA1 which highly depends on Mg2+ and the key tertiary interactions. The absence of Mg2+ and disruption of the key tertiary interactions strongly affect the structural integrity and attenuate mechanical anisotropy. The significance of ring structures in RNA mechanical anisotropy is further supported by steered molecular dynamics simulations in combination with force distribution analysis. We anticipate the ring structures can be used as key elements to build RNA-based nanostructures with controllable mechanical anisotropy for biomaterial and biomedical applications.
Crbn modulates calcium influx by regulating Orai1 during efferocytosis
Authors: Moon Hyunji , Min Chanhyuk , Kim Gayoung , Kim Deokhwan , Kim Kwanhyeong , Lee Sang-Ah , Moon Byeongjin , Yang Susumin , Lee Juyeon , Yang Seung-Joo , Cho Steve K. , Lee Gwangrog , Lee Chang Sup , Park Chul-Seung , Park Daeho 
Published: October 2020

AbstractCalcium flux regulating intracellular calcium levels is essential and modulated for efficient efferocytosis. However, the molecular mechanism by which calcium flux is modulated during efferocytosis remains elusive. Here, we report that Orai1, a Crbn substrate, is upregulated via its attenuated interaction with Crbn during efferocytosis, which increases calcium influx into phagocytes and thereby promotes efferocytosis. We found that Crbn deficiency promoted phagocytosis of apoptotic cells, which resulted from facilitated phagocytic cup closure and was nullified by a CRAC channel inhibitor. In addition, Orai1 associated with Crbn, resulting in ubiquitination and proteasomal degradation of Orai1 and alteration of SOCE-mediated calcium influx. The association of Orai1 with Crbn was attenuated during efferocytosis, leading to reduced ubiquitination of Orai1 and consequently upregulation of Orai1 and calcium influx. Collectively, our study reveals a regulatory mechanism by which calcium influx is modulated by a Crbn-Orai1 axis to facilitate efferocytosis.
Proline rich 11 (PRR11) overexpression amplifies PI3K signaling and promotes antiestrogen resistance in breast cancer
Authors: Lee Kyung-min , Guerrero-Zotano Angel L. , Servetto Alberto , Sudhan Dhivya R. , Lin Chang-Ching , Formisano Luigi , Jansen Valerie M. , González-Ericsson Paula , Sanders Melinda E. , Stricker Thomas P. , Raj Ganesh , Dean Kevin M. , Fiolka Reto , Cantley Lewis C. , Hanker Ariella B. , Arteaga Carlos L. 
Published: October 2020

AbstractThe 17q23 amplicon is associated with poor outcome in ER+ breast cancers, but the causal genes to endocrine resistance in this amplicon are unclear. Here, we interrogate transcriptome data from primary breast tumors and find that among genes in 17q23, PRR11 is a key gene associated with a poor response to therapeutic estrogen suppression. PRR11 promotes estrogen-independent proliferation and confers endocrine resistance in ER+ breast cancers. Mechanistically, the proline-rich motif-mediated interaction of PRR11 with the p85α regulatory subunit of PI3K suppresses p85 homodimerization, thus enhancing insulin-stimulated binding of p110-p85α heterodimers to IRS1 and activation of PI3K. PRR11-amplified breast cancer cells rely on PIK3CA and are highly sensitive to PI3K inhibitors, suggesting that PRR11 amplification confers PI3K dependence. Finally, genetic and pharmacological inhibition of PI3K suppresses PRR11-mediated, estrogen-independent growth. These data suggest ER+/PRR11-amplified breast cancers as a novel subgroup of tumors that may benefit from treatment with PI3K inhibitors and antiestrogens.
Control of single-ligand chemistry on thiolated Au25 nanoclusters
Authors: Cao Yitao , Fung Victor , Yao Qiaofeng , Chen Tiankai , Zang Shuangquan , Jiang De-en , Xie Jianping 
Published: October 2020

AbstractDiverse methods have been developed to tailor the number of metal atoms in metal nanoclusters, but control of surface ligand number at a given cluster size is rare. Here we demonstrate that reversible addition and elimination of a single surface thiolate ligand (-SR) on gold nanoclusters can be realized, opening the door to precision ligand engineering on atomically precise nanoclusters. We find that oxidative etching of [Au25SR18]− nanoclusters adds an excess thiolate ligand and generates a new species, [Au25SR19]0. The addition reaction can be reversed by CO reduction of [Au25SR19]0, leading back to [Au25SR18]− and eliminating precisely one surface ligand. Intriguingly, we show that the ligand shell of Au25 nanoclusters becomes more fragile and rigid after ligand addition. This reversible addition/elimination reaction of a single surface ligand on gold nanoclusters shows potential to precisely control the number of surface ligands and to explore new ligand space at each nuclearity.
Electron tunneling at the molecularly thin 2D perovskite and graphene van der Waals interface
Authors: Leng Kai , Wang Lin , Shao Yan , Abdelwahab Ibrahim , Grinblat Gustavo , Verzhbitskiy Ivan , Li Runlai , Cai Yongqing , Chi Xiao , Fu Wei , Song Peng , Rusydi Andrivo , Eda Goki , Maier Stefan A. , Loh Kian Ping 
Published: October 2020

AbstractQuasi-two-dimensional perovskites have emerged as a new material platform for optoelectronics on account of its intrinsic stability. A major bottleneck to device performance is the high charge injection barrier caused by organic molecular layers on its basal plane, thus the best performing device currently relies on edge contact. Herein, by leveraging on van der Waals coupling and energy level matching between two-dimensional Ruddlesden-Popper perovskite and graphene, we show that the plane-contacted perovskite and graphene interface presents a lower barrier than gold for charge injection. Electron tunneling across the interface occurs via a gate-tunable, direct tunneling-to-field emission mechanism with increasing bias, and photoinduced charge transfer occurs at femtosecond timescale (~50 fs). Field effect transistors fabricated on molecularly thin Ruddlesden-Popper perovskite using graphene contact exhibit electron mobilities ranging from 0.1 to 0.018 cm2V−1s−1 between 1.7 to 200 K. Scanning tunneling spectroscopy studies reveal layer-dependent tunneling barrier and domain size on few-layered Ruddlesden-Popper perovskite.
Sequential generation of linear cluster states from a single photon emitter
Authors: Istrati D. , Pilnyak Y. , Loredo J. C. , Antón C. , Somaschi N. , Hilaire P. , Ollivier H. , Esmann M. , Cohen L. , Vidro L. , Millet C. , Lemaître A. , Sagnes I. , Harouri A. , Lanco L. , Senellart P. , Eisenberg H. S. 
Published: October 2020

AbstractLight states composed of multiple entangled photons—such as cluster states—are essential for developing and scaling-up quantum computing networks. Photonic cluster states can be obtained from single-photon sources and entangling gates, but so far this has only been done with probabilistic sources constrained to intrinsically low efficiencies, and an increasing hardware overhead. Here, we report the resource-efficient generation of polarization-encoded, individually-addressable photons in linear cluster states occupying a single spatial mode. We employ a single entangling-gate in a fiber loop configuration to sequentially entangle an ever-growing stream of photons originating from the currently most efficient single-photon source technology—a semiconductor quantum dot. With this apparatus, we demonstrate the generation of linear cluster states up to four photons in a single-mode fiber. The reported architecture can be programmed for linear-cluster states of any number of photons, that are required for photonic one-way quantum computing schemes.
Optimized design of single-cell RNA sequencing experiments for cell-type-specific eQTL analysis
Authors: Mandric Igor , Schwarz Tommer , Majumdar Arunabha , Hou Kangcheng , Briscoe Leah , Perez Richard , Subramaniam Meena , Hafemeister Christoph , Satija Rahul , Ye Chun Jimmie , Pasaniuc Bogdan , Halperin Eran 
Published: October 2020

AbstractSingle-cell RNA-sequencing (scRNA-Seq) is a compelling approach to directly and simultaneously measure cellular composition and state, which can otherwise only be estimated by applying deconvolution methods to bulk RNA-Seq estimates. However, it has not yet become a widely used tool in population-scale analyses, due to its prohibitively high cost. Here we show that given the same budget, the statistical power of cell-type-specific expression quantitative trait loci (eQTL) mapping can be increased through low-coverage per-cell sequencing of more samples rather than high-coverage sequencing of fewer samples. We use simulations starting from one of the largest available real single-cell RNA-Seq data from 120 individuals to also show that multiple experimental designs with different numbers of samples, cells per sample and reads per cell could have similar statistical power, and choosing an appropriate design can yield large cost savings especially when multiplexed workflows are considered. Finally, we provide a practical approach on selecting cost-effective designs for maximizing cell-type-specific eQTL power which is available in the form of a web tool.
Regioselective Markovnikov hydrodifluoroalkylation of alkenes using difluoroenoxysilanes
Authors: Hu Xiao-Si , He Jun-Xiong , Dong Su-Zhen , Zhao Qiu-Hua , Yu Jin-Sheng , Zhou Jian 
Published: October 2020

AbstractAlkene hydrodifluoroalkylation is a fruitful strategy for synthesizing difluoromethylated compounds that are interesting for developing new medicinal agents, agrochemicals, and advanced materials. Whereas the anti-Markovnikov hydrodifluoroalkylation to linear-type products is developed, employing radical-based processes, the Markovnikov synthesis of branched adducts remains unexplored. Herein, we describe acid-catalyzed processes involving carbocation intermediates as a promising strategy to secure the Markovnikov regioselectivity. Accordingly, the Markovnikov hydrodifluoroalkylation of mono-, di-, tri-, and tetrasubstituted alkenes using difluoroenoxysilanes, catalyzed by Mg(ClO4)2·6H2O, is achieved. This allows the diversity-oriented synthesis of α,α-difluoroketones with a quaternary or tertiary carbon at the β-position that are otherwise difficult to access. The method is applied to the modification of natural products and drug derivatives. The resulting α,α-difluorinated ketones could be converted to the corresponding α,α-difluorinated esters or alcohols, or organofluorine compounds featuring a CF2H or CF2CF2Ph moiety. Mechanistic studies support that Mg(ClO4)2·6H2O functions as a hidden Brønsted acid catalyst.
Engineered lactobacilli display anti-biofilm and growth suppressing activities against Pseudomonas aeruginosa
Authors: Chappell Todd C. , Nair Nikhil U. 
Published: October 2020

AbstractBiofilms are an emerging target for new therapeutics in the effort to address the continued increase in resistance and tolerance to traditional antimicrobials. In particular, the distinct nature of the biofilm growth state often means that traditional antimcirobials, developed to combat planktonic cells, are ineffective. Biofilm treatments are designed to both reduce pathogen load at an infection site and decrease the development of resistance by rendering the embedded organisms more susceptible to treatment at lower antimicrobial concentrations. In this work, we developed a new antimicrobial treatment modality using engineered lactic acid bacteria (LAB). We first characterized the natural capacity of two lactobacilli, L. plantarum and L. rhamnosus, to inhibit P. aeruginosa growth, biofilm formation, and biofilm viability, which we found to be dependent upon the low pH generated during culture of the LAB. We further engineered these LAB to secrete enzymes known to degrade P. aeruginosa biofilms and show that our best performing engineered LAB, secreting a pathogen-derived enzyme (PelAh), degrades up to 85% of P. aeruginosa biofilm.
Bio-priming with a hypovirulent phytopathogenic fungus enhances the connection and strength of microbial interaction network in rapeseed
Authors: Qu Zheng , Zhao Huizhang , Zhang Hongxiang , Wang Qianqian , Yao Yao , Cheng Jiasen , Lin Yang , Xie Jiatao , Fu Yanping , Jiang Daohong 
Published: October 2020

AbstractPlant disease is one of the most important causes of crop losses worldwide. The effective control of plant disease is related to food security.Sclerotiniastem rot (SSR) caused bySclerotinia sclerotiorumleads to serious yield losses in rapeseed (Brassica napus) production. Hypovirulent strain DT-8 ofS. sclerotiorum, infected with Sclerotinia sclerotiorum hypovirulence-associated DNA virus 1 (SsHADV-1), has the potential to control SSR. In this study, we found rapeseed bio-priming with strain DT-8 could significantly decrease the disease severity of SSR and increase yield in the field. After bio-priming, strain DT-8 could be detected on the aerial part of the rapeseed plant. By 16S rRNA gene and internal transcribed spacer (ITS) sequencing technique, the microbiome on different parts of the SSR lesion on bioprimed and non-bioprimed rapeseed stem was determined. The results indicated that SSR and bio-priming treatment could influence the structure and composition of fungal and bacterial communities. Bio-priming treatment could reduce the total abundance of possible plant pathogens and enhance the connectivity and robustness of the interaction network at the genus level. This might be one of the mechanisms that rapeseed bioprimed with strain DT-8 had excellent tolerance on SSR. It might be another possible mechanism of biocontrol and will provide a theoretical guide for agricultural practical production.
Electrochemical drag effect on grain boundary motion in ionic ceramics
Authors: Vikrant K. S. N. , Rheinheimer Wolfgang , García R. Edwin 
Published: October 2020

AbstractThe effects of drag imposed by extrinsic ionic species and point defects on the grain boundary motion of ionic polycrystalline ceramics were quantified for the generality of electrical, chemical, or structural driving forces. In the absence of, or for small driving forces, the extended electrochemical grain boundary remains pinned and symmetrically distributed about the structural interface. As the grain boundary begins to move, charged defects accumulate unsymmetrically about the structural grain boundary core. Above the critical driving force for motion, grain boundaries progressively shed individual ionic species, from heavier to lighter, until they display no interfacial electrostatic charge and zero Schottky potential. Ionic p–n junction moving grain boundaries that induce a finite electrostatic potential difference across entire grains are identified for high velocity grains. The developed theory is demonstrated for Fe-doped SrTiO3. The increase in average Fe concentration and grain boundary crystallographic misorientation enhances grain boundary core segregation and results in thick space charge layers, which leads to a stronger drag force that reduces the velocity of the interface. The developed theory sets the stage to assess the effects of externally applied fields such as temperature, electromagnetic fields, and chemical stimuli to control the grain growth for developing textured, oriented microstructures desirable for a wide range of applications.
Dysfunction in superior frontal gyrus associated with diphasic dyskinesia in Parkinson’s disease
Authors: Shen Yu-Ting , Yuan Yong-Sheng , Wang Min , Zhi Yan , Wang Jian-Wei , Wang Li-Na , Ma Ke-Wei , Si Qian-Qian , Zhang Ke-Zhong 
Published: October 2020

AbstractAlterations in brain function in Parkinson’s disease (PD) patients with diphasic dyskinesia have not been investigated. We aimed to explore the alterations in regional brain function. Each of 53 levodopa (LD)-treated PD patients had two resting-state functional magnetic resonance imaging (rs-fMRI) scans in the same morning, before and after taking LD. The regional homogeneity (ReHo) approach was used to reveal local synchronization changes. Two-way factorial repeated measures analysis of covariance, with group as a between-subject factor and LD effect as a within-subject factor, was performed to explore the two main effects and interaction. Interactive analysis was used to show outcomes that combined disease status and LD effect. Spearman’s correlations were used to detect associations between interactive brain regions and severity of dyskinetic symptoms, assessed by the Unified Dyskinesia Rating Scale (UDyRS) scores, along with moderation analyses. There was no significant difference in the main group effect analysis. Significantly different clusters obtained from main LD effect analysis were in left caudate nucleus and putamen. ReHo values decreased in the caudate nucleus and increased in the putamen during the ON state after taking LD. Interaction between group and LD effect was found in left medial superior frontal gyrus (mSFG), where there were the lowest ReHo values, and was negatively correlated with UDyRS scores in the diphasic dyskinetic group during the ON state. The relationship was independent of LD dose. Abnormal local synchronization in the mSFG is closely associated with the development of diphasic dyskinesia in PD patients.
Macular vessel density and foveal avascular zone parameters in patients after acute primary angle closure determined by OCT angiography
Authors: Liu Kangcheng , Xu Huizhuo , Jiang Haibo , Wang Hua , Wang Pingbao , Xu Yi , Li Fangling , Xu Bei , Yao Xueyan , Zou Jing 
Published: October 2020

AbstractThis study analyzed the optical coherence tomography angiography (OCTA) macular parameters in primary angle-closure glaucoma (PACG) patients after acute primary angle closure (APAC) episodes. Thirty-three patients with 33 APAC eyes and 33 primary angle closure suspect (PACS) eyes and 33 age-matched normal subjects (controls) were enrolled. Macular vessel density (VD) in central, inner, outer and full regions and foveal avascular zone (FAZ) parameters (area, perimeter and circularity index) were compared between APAC, PACS, and control eyes. For resolved APAC eyes, the VD in each macular region was significantly lower than that in control eyes, with less central and inner macular VD than PACS eyes. The central macular VD was significantly lower in PACS eyes than in controls. There was no difference in FAZ area and perimeter between APAC, PACS, and control eyes. FAZ circularity was highest in control eyes, followed by PACS eyes, and lowest in APAC eyes. The AUC, sensitivity and specificity of FAZ circularity were 0.944, 93.9% and 84.8%, respectively, in APAC eyes and 0.881, 84.8% and 81.8%, respectively, in PACS eyes. Therefore, FAZ circularity had the best discrimination capability for detecting both APAC and PACS eyes. Macular assessment with OCTA could provide an accurate early-stage diagnostic tool for PACG.
Complex societies and the growth of the law
Authors: Katz Daniel Martin , Coupette Corinna , Beckedorf Janis , Hartung Dirk 
Published: October 2020

AbstractWhile many informal factors influence how people interact, modern societies rely upon law as a primary mechanism to formally control human behaviour. How legal rules impact societal development depends on the interplay between two types of actors: the people who create the rules and the people to which the rules potentially apply. We hypothesise that an increasingly diverse and interconnected society might create increasingly diverse and interconnected rules, and assert that legal networks provide a useful lens through which to observe the interaction between law and society. To evaluate these propositions, we present a novel and generalizable model of statutory materials as multidimensional, time-evolving document networks. Applying this model to the federal legislation of the United States and Germany, we find impressive expansion in the size and complexity of laws over the past two and a half decades. We investigate the sources of this development using methods from network science and natural language processing. To allow for cross-country comparisons over time, based on the explicit cross-references between legal rules, we algorithmically reorganise the legislative materials of the United States and Germany into cluster families that reflect legal topics. This reorganisation reveals that the main driver behind the growth of the law in both jurisdictions is the expansion of the welfare state, backed by an expansion of the tax state. Hence, our findings highlight the power of document network analysis for understanding the evolution of law and its relationship with society.