bluuebunny/crossref_metadata_2025_split huggingface dataset:
Acoustic meta-atom with experimentally verified maximum Willis coupling
Authors: Melnikov Anton , Chiang Yan Kei , Quan Li , Oberst Sebastian , Alù Andrea , Marburg Steffen , Powell David 
Published: July 2019

AbstractAcoustic metamaterials are structures with exotic acoustic properties, with promising applications in acoustic beam steering, focusing, impedance matching, absorption and isolation. Recent work has shown that the efficiency of many acoustic metamaterials can be enhanced by controlling an additional parameter known as Willis coupling, which is analogous to bianisotropy in electromagnetic metamaterials. The magnitude of Willis coupling in a passive acoustic meta-atom has been shown theoretically to have an upper limit, however the feasibility of reaching this limit has not been experimentally investigated. Here we introduce a meta-atom with Willis coupling which closely approaches this theoretical limit, that is much simpler and less prone to thermo-viscous losses than previously reported structures. We perform two-dimensional experiments to measure the strong Willis coupling, supported by numerical calculations. Our meta-atom geometry is readily modeled analytically, enabling the strength of Willis coupling and its peak frequency to be easily controlled.
Pooled library screening with multiplexed Cpf1 library
Authors: Liu Jintan , Srinivasan Sanjana , Li Chieh-Yuan , Ho I-Lin , Rose Johnathon , Shaheen MennatAllah , Wang Gang , Yao Wantong , Deem Angela , Bristow Chris , Hart Traver , Draetta Giulio 
Published: July 2019

AbstractCapitalizing on the inherent multiplexing capability of AsCpf1, we developed a multiplexed, high-throughput screening strategy that minimizes library size without sacrificing gene targeting efficiency. We demonstrated that AsCpf1 can be used for functional genomics screenings and that an AsCpf1-based multiplexed library performs similarly as compared to currently available monocistronic CRISPR/Cas9 libraries, with only one vector required for each gene. We construct the smallest whole-genome CRISPR knock-out library, Mini-human, for the human genome (n = 17,032 constructs targeting 16,977 protein-coding genes), which performs favorably compared to conventional Cas9 libraries.
Reactivity of shape-controlled crystals and metadynamics simulations locate the weak spots of alumina in water
Authors: Réocreux R. , Girel É. , Clabaut P. , Tuel A. , Besson M. , Chaumonnot A. , Cabiac A. , Sautet P. , Michel C. 
Published: July 2019

AbstractThe kinetic stability of any material in water relies on the presence of surface weak spots responsible for chemical weathering by hydrolysis. Being able to identify the atomistic nature of these sites and the first steps of transformation is therefore critical to master the decomposition processes. This is the challenge that we tackle here: combining experimental and modeling studies we investigate the stability of alumina in water. Exploring the reactivity of shape-controlled crystals, we identify experimentally a specific facet as the location of the weak spots. Using biasedab initiomolecular dynamics, we recognize this weak spot as a surface exposed tetra-coordinated Al atom and further provide a detailed mechanism of the first steps of hydrolysis. This understanding is of great importance to heterogeneous catalysis where alumina is a major support. Furthermore, it paves the way to atomistic understanding of interfacial reactions, at the crossroad of a variety of fields of research.
Label-free neuroimaging in vivo using synchronous angular scanning microscopy with single-scattering accumulation algorithm
Authors: Kim Moonseok , Jo Yonghyeon , Hong Jin Hee , Kim Suhyun , Yoon Seokchan , Song Kyung-Deok , Kang Sungsam , Lee Byunghak , Kim Guang Hoon , Park Hae-Chul , Choi Wonshik 
Published: July 2019

AbstractLabel-free in vivo imaging is crucial for elucidating the underlying mechanisms of many important biological systems in their most native states. However, the applicability of existing modalities has been limited to either superficial layers or early developmental stages due to tissue turbidity. Here, we report a synchronous angular scanning microscope for the rapid interferometric recording of the time-gated reflection matrix, which is a unique matrix characterizing full light-specimen interaction. By applying single scattering accumulation algorithm to the recorded matrix, we removed both high-order sample-induced aberrations and multiple scattering noise with the effective aberration correction speed of 10,000 modes/s. We demonstrated in vivo imaging of whole neural network throughout the hindbrain of the larval zebrafish at a matured stage where physical dissection used to be required for conventional imaging. Our method will expand the scope of applications for optical imaging, where fully non-invasive interrogation of living specimens is critical.
Active protection of a superconducting qubit with an interferometric Josephson isolator
Authors: Abdo Baleegh , Bronn Nicholas T. , Jinka Oblesh , Olivadese Salvatore , Córcoles Antonio D. , Adiga Vivekananda P. , Brink Markus , Lake Russell E. , Wu Xian , Pappas David P. , Chow Jerry M. 
Published: July 2019

AbstractNonreciprocal microwave devices play critical roles in high-fidelity, quantum-nondemolition (QND) measurement schemes. They impose unidirectional routing of readout signals and protect the quantum systems from unwanted noise originated by the output chain. However, cryogenic circulators and isolators are disadvantageous in scalable superconducting architectures because they use magnetic materials and strong magnetic fields. Here, we realize an active isolator formed by coupling two nondegenerate Josephson mixers in an interferometric scheme and driving them with phase-shifted, same-frequency pumps. By incorporating our Josephson-based isolator into a superconducting qubit setup, we demonstrate fast, high-fidelity, QND measurements of the qubit while providing 20 dB of protection within a bandwidth of 10 MHz against amplified noise reflected off the Josephson amplifier in the output chain. A moderate reduction of 35% is observed in T2E when the Josephson-based isolator is turned on. Such a moderate degradation can be mitigated by minimizing heat dissipation in the pump lines.
Electronic-reconstruction-enhanced hydrogen evolution catalysis in oxide polymorphs
Authors: Li Yangyang , Yu Zhi Gen , Wang Ling , Weng Yakui , Tang Chi Sin , Yin Xinmao , Han Kun , Wu Haijun , Yu Xiaojiang , Wong Lai Mun , Wan Dongyang , Wang Xiao Renshaw , Chai Jianwei , Zhang Yong-Wei , Wang Shijie , Wang John , Wee Andrew T. S. , Breese Mark B. H. , Pennycook Stephen J. , Venkatesan Thirumalai , Dong Shuai , Xue Jun Min , Chen Jingsheng 
Published: July 2019

AbstractTransition metal oxides exhibit strong structure-property correlations, which has been extensively investigated and utilized for achieving efficient oxygen electrocatalysts. However, high-performance oxide-based electrocatalysts for hydrogen evolution are quite limited, and the mechanism still remains elusive. Here we demonstrate the strong correlations between the electronic structure and hydrogen electrocatalytic activity within a single oxide system Ti2O3. Taking advantage of the epitaxial stabilization, the polymorphism of Ti2O3 is extended by stabilizing bulk-absent polymorphs in the film-form. Electronic reconstructions are realized in the bulk-absent Ti2O3 polymorphs, which are further correlated to their electrocatalytic activity. We identify that smaller charge-transfer energy leads to a substantial enhancement in the electrocatalytic efficiency with stronger hybridization of Ti 3d and O 2p orbitals. Our study highlights the importance of the electronic structures on the hydrogen evolution activity of oxide electrocatalysts, and also provides a strategy to achieve efficient oxide-based hydrogen electrocatalysts by epitaxial stabilization of bulk-absent polymorphs.
From self-organization in relativistic electron bunches to coherent synchrotron light: observation using a photonic time-stretch digitizer
Authors: Bielawski Serge , Blomley Edmund , Brosi Miriam , Bründermann Erik , Burkard Eva , Evain Clément , Funkner Stefan , Hiller Nicole , Nasse Michael J. , Niehues Gudrun , Roussel Eléonore , Schedler Manuel , Schönfeldt Patrik , Steinmann Johannes L. , Szwaj Christophe , Walther Sophie , Müller Anke-Susanne 
Published: July 2019

AbstractIn recent and future synchrotron radiation facilities, relativistic electron bunches with increasingly high charge density are needed for producing brilliant light at various wavelengths, from X-rays to terahertz. In such conditions, interaction of electron bunches with their own emitted electromagnetic fields leads to instabilities and spontaneous formation of complex spatial structures. Understanding these instabilities is therefore key in most electron accelerators. However, investigations suffer from the lack of non-destructive recording tools for electron bunch shapes. In storage rings, most studies thus focus on the resulting emitted radiation. Here, we present measurements of the electric field in the immediate vicinity of the electron bunch in a storage ring, over many turns. For recording the ultrafast electric field, we designed a photonic time-stretch analog-to-digital converter with terasamples/second acquisition rate. We could thus observe the predicted link between spontaneous pattern formation and giant bursts of coherent synchrotron radiation in a storage ring.
VCF2CNA: A tool for efficiently detecting copy-number alterations in VCF genotype data and tumor purity
Authors: Putnam Daniel K. , Ma Xiaotu , Rice Stephen V. , Liu Yu , Newman Scott , Zhang Jinghui , Chen Xiang 
Published: July 2019

AbstractVCF2CNA is a tool (Linux commandline or web-interface) for copy-number alteration (CNA) analysis and tumor purity estimation of paired tumor-normal VCF variant file formats. It operates on whole genome and whole exome datasets. To benchmark its performance, we applied it to 46 adult glioblastoma and 146 pediatric neuroblastoma samples sequenced by Illumina and Complete Genomics (CGI) platforms respectively. VCF2CNA was highly consistent with a state-of-the-art algorithm using raw sequencing data (mean F1-score = 0.994) in high-quality whole genome glioblastoma samples and was robust to uneven coverage introduced by library artifacts. In the whole genome neuroblastoma set, VCF2CNA identified MYCN high-level amplifications in 31 of 32 clinically validated samples compared to 15 found by CGI’s HMM-based CNA model. Moreover, VCF2CNA achieved highly consistent CNA profiles between WGS and WXS platforms (mean F1 score 0.97 on a set of 15 rhabdomyosarcoma samples). In addition, VCF2CNA provides accurate tumor purity estimates for samples with sufficient CNAs. These results suggest that VCF2CNA is an accurate, efficient and platform-independent tool for CNA and tumor purity analyses without accessing raw sequence data.
A Naturally Occurring Splice Variant of GGA1 Inhibits the Anterograde Post-Golgi Traffic of α2B-Adrenergic Receptor
Authors: Zhang Maoxiang , Xu Xin , Li Chunman , Huang Wei , Xu Nenggui , Wu Guangyu 
Published: July 2019

AbstractThe regulatory mechanisms of cell surface targeting of nascent G protein-coupled receptors (GPCRs) en route from the endoplasmic reticulum through the Golgi remain poorly understood. We have recently demonstrated that three Golgi-localized, γ-adaptin ear domain homology, ADP ribosylation factor-binding proteins (GGAs) mediate the post-Golgi export of α2B-adrenergic receptor (α2B-AR), a prototypic GPCR, and directly interact with the receptor. In particular, GGA1 interaction with α2B-AR is mediated via its hinge domain. Here we determined the role of a naturally occurring truncated form of GGA1 (GGA1t) which lacks the N-terminal portion of the hinge domain in α2B-AR trafficking and elucidated the underlying mechanisms. We demonstrated that both GGA1 and GGA1t were colocalized and mainly expressed at the Golgi. In marked contrast to GGA1, the expression of GGA1t significantly attenuated the cell surface export of newly synthesized α2B-AR from the Golgi and in parallel receptor-mediated signaling. Furthermore, we found that GGA1t formed homodimers and heterodimers with GGA1. More interestingly, GGA1t was unable to bind the cargo α2B-AR and to recruit clathrin onto the trans-Golgi network. These data provide evidence implicating that the truncated form of GGA1 behaviors as a dominant-negative regulator for the cell surface export of α2B-AR and this function of GGA1t is attributed to its abilities to dimerize with its wide type counterpart and to inhibit cargo interaction and clathrin recruitment to form specialized transport vesicles.
Chitosan promoting formononetin and calycosin accumulation in Astragalus membranaceus hairy root cultures via mitogen-activated protein kinase signaling cascades
Authors: Gai Qing-Yan , Jiao Jiao , Wang Xin , Liu Jing , Wang Zi-Ying , Fu Yu-Jie 
Published: July 2019

AbstractChitosan, behaving as a potent biotic elicitor, can induce plant defense response with the consequent enhancement in phytoalexin accumulation. Accordingly, chitosan elicitation was conducted to promote the production of two phytoalexins, i.e. formononetin and calycosin (also known as health-promoting isoflavones), in Astragalus membranaceus hairy root cultures (AMHRCs). Compared with control, 12.45- and 6.17-fold increases in the yields of formononetin (764.19 ± 50.81 μg/g DW) and calycosin (611.53 ± 42.22 μg/g DW) were obtained in 34 day-old AMHRCs treated by 100 mg/L of chitosan for 24 h, respectively. Moreover, chitosan elicitation could cause oxidative burst that would induce the expression of genes (MPK3 and MPK6) related to mitogen-activated protein kinase signaling (MAPK) cascades, which contributed to the transcriptional activation of pathogenesis-related genes (β-1,3-glucanase, Chitinase, and PR-1) and eight biosynthesis genes involved in the calycosin and formononetin pathway. Overall, the findings in this work not only highlight a feasible chitosan elicitation practice to enhance the in vitro production of two bioactive isoflavones for nutraceutical and food applications, but also contribute to understanding the phytoalexin biosynthesis in response to chitosan elicitation.
Evaluation of genetic susceptibility between systemic lupus erythematosus and GRB2 gene
Authors: Xu Meifeng , Liu Yan , Li Xiaoli , Cheng Chuantao , Liu Yale , Dong Wei , Du Shaoyi , Xiao Shengxiang 
Published: July 2019

AbstractMultiple lines of evidence have shown that systemic lupus erythematosus (SLE) is attributable to both genetic and environmental factors. The product of GRB2 is a key factor in the activation of B cells and has been reported to be significantly associated with SLE in European populations. In the study, we aimed to investigate the relationship between GRB2 and SLE. A total of 1,710 Han Chinese women comprising 567 SLE patients and 1,143 controls were recruited to genotype 20 selected tagging SNPs. We tested the potential association between 13 clinical variables of SLE and the significant polymorphisms related to SLE. The eQTL data were extracted from the GTEx database to examine the functional consequences of the targeted SNPs. A significant association signal was identified between rs36023980 and SLE in both genotypic and allelic analyses (OR = 0.61, P = 0.0003). Complement inhibition was shown to be significantly associated with the genotypes of SNP rs36023980 in SLE patients (Pgenotype = 0.003). Further stratification analyses showed that the genetic association signal of SNP rs36023980 on SLE could only be identified in cases with complement inhibition. SNP rs36023980 was also identified to be significantly associated with the expression of GRB2 in whole blood and sun-exposed skin. In conclusion, our findings confirm the results from the previous GWAS and are the first to report the association of GRB2 with SLE in Han Chinese population.
Changes in nuclear and cytoplasmic microRNA distribution in response to hypoxic stress
Authors: Turunen Tiia A. , Roberts Thomas C. , Laitinen Pia , Väänänen Mari-Anna , Korhonen Paula , Malm Tarja , Ylä-Herttuala Seppo , Turunen Mikko P. 
Published: July 2019

AbstractMicroRNAs (miRNAs) are small non-coding RNAs that have well-characterized roles in cytoplasmic gene regulation, where they act by binding to mRNA transcripts and inhibiting their translation (i.e. post-transcriptional gene silencing, PTGS). However, miRNAs have also been implicated in transcriptional gene regulation and alternative splicing, events that are restricted to the cell nucleus. Here we performed nuclear-cytoplasmic fractionation in a mouse endothelial cell line and characterized the localization of miRNAs in response to hypoxia using small RNA sequencing. A highly diverse population of abundant miRNA species was detected in the nucleus, of which the majority (56%) was found to be preferentially localized in one compartment or the other. Induction of hypoxia resulted in changes in miRNA levels in both nuclear and cytoplasmic compartments, with the majority of changes being restricted to one location and not the other. Notably, the classical hypoxamiR (miR-210-3p) was highly up-regulated in the nuclear compartment after hypoxic stimulus. These findings reveal a previously unappreciated level of molecular complexity in the physiological response occurring in ischemic tissue. Furthermore, widespread differential miRNA expression in the nucleus strongly suggests that these small RNAs are likely to perform extensive nuclear regulatory functions in the general case.
DNA damage induction during localized chronic exposure to an insoluble radioactive microparticle
Authors: Matsuya Yusuke , Satou Yukihiko , Hamada Nobuyuki , Date Hiroyuki , Ishikawa Masayori , Sato Tatsuhiko 
Published: July 2019

AbstractInsoluble radioactive microparticles emitted by the incident at the Fukushima nuclear power plant have drawn keen interests from the viewpoint of radiation protection. Cs-bearing particles have been assumed to adhere in the long term to trachea after aspirated into respiratory system, leading to heterogeneous dose distribution within healthy tissue around the particles. However, the biological effects posed by an insoluble radioactive particle remain unclear. Here, we show cumulative DNA damage in normal human lung cells proximal and distal to the particle (β-ray and γ-ray-dominant areas, respectively) under localized chronic exposure in comparison with uniform exposure. We put a Cs-bearing particle into a microcapillary tip and placed it onto a glass-base dish containing fibroblast or epithelial cells cultured in vitro. A Monte Carlo simulation with PHITS code provides the radial distribution of absorbed dose-rate around the particle, and subsequently we observed a significant change in nuclear γ-H2AX foci after 24 h or 48 h exposure to the particle. The nuclear foci in the cells distal to the particle increased even under low-dose-rate exposure compared with uniform exposure to 137Cs γ-rays, which was suppressed by a treatment with a scavenger of reactive oxygen species. In contrast, such focus formation was less manifested in the exposed cells proximal to the particle compared with uniform exposure. These data suggest that the localized exposure to a Cs-bearing particle leads to not only disadvantage to distal cells but also advantage to proximal cells. This study is the first to provide quantitative evaluation for the spatial distribution of DNA double strand breaks after the heterogeneous chronic exposure to a Cs-bearing particle in comparison with uniform Cs exposure.
Proteogenomic Analysis of Protein Sequence Alterations in Breast Cancer Cells
Authors: Lazar Iulia M. , Karcini Arba , Ahuja Shreya , Estrada-Palma Carly 
Published: July 2019

AbstractCancer evolves as a result of an accumulation of mutations and chromosomal aberrations. Developments in sequencing technologies have enabled the discovery and cataloguing of millions of such mutations. The identification of protein-level alterations, typically by using reversed-phase protein arrays or mass spectrometry, has lagged, however, behind gene and transcript-level observations. In this study, we report the use of mass spectrometry for detecting the presence of mutations-missense, indels and frame shifts-in MCF7 and SKBR3 breast cancer, and non-tumorigenic MCF10A cells. The mutations were identified by expanding the database search process of raw mass spectrometry files by including an in-house built database of mutated peptides (XMAn-v1) that complemented a minimally redundant, canonical database of Homo sapiens proteins. The work resulted in the identification of nearly 300 mutated peptide sequences, of which ~50 were characterized by quality tandem mass spectra. We describe the criteria that were used to select the mutated peptide sequences, evaluate the parameters that characterized these peptides, and assess the artifacts that could have led to false peptide identifications. Further, we discuss the functional domains and biological processes that may be impacted by the observed peptide alterations, and how protein-level detection can support the efforts of identifying cancer driving mutations and genes. Mass spectrometry data are available via ProteomeXchange with identifier PXD014458.
Extreme wet and dry conditions affected differently by greenhouse gases and aerosols
Authors: Sillmann Jana , Stjern Camilla W. , Myhre Gunnar , Samset Bjørn H. , Hodnebrog Øivind , Andrews Timothy , Boucher Olivier , Faluvegi Gregory , Forster Piers , Kasoar Matthew R. , Kharin Viatcheslav V. , Kirkevåg Alf , Lamarque Jean-Francois , Olivié Dirk J. L. , Richardson Thomas B. , Shindell Drew , Takemura Toshihiko , Voulgarakis Apostolos , Zwiers Francis W. 
Published: July 2019

AbstractGlobal warming due to greenhouse gases and atmospheric aerosols alter precipitation rates, but the influence on extreme precipitation by aerosols relative to greenhouse gases is still not well known. Here we use the simulations from the Precipitation Driver and Response Model Intercomparison Project that enable us to compare changes in mean and extreme precipitation due to greenhouse gases with those due to black carbon and sulfate aerosols, using indicators for dry extremes as well as for moderate and very extreme precipitation. Generally, we find that the more extreme a precipitation event is, the more pronounced is its response relative to global mean surface temperature change, both for aerosol and greenhouse gas changes. Black carbon (BC) stands out with distinct behavior and large differences between individual models. Dry days become more frequent with BC-induced warming compared to greenhouse gases, but so does the intensity and frequency of extreme precipitation. An increase in sulfate aerosols cools the surface and thereby the atmosphere, and thus induces a reduction in precipitation with a stronger effect on extreme than on mean precipitation. A better understanding and representation of these processes in models will provide knowledge for developing strategies for both climate change and air pollution mitigation.