bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantification of Evaporation and Drainage Processes in Unsaturated Porous Media Using Magnetic Resonance Imaging
Authors: Ranzinger Florian , Hille‐Reichel Andrea , Zehe Erwin , Guthausen Gisela , Horn Harald 
Published: February 2020

AbstractThe water loss in packed beds was studied spatially and time‐resolved via magnetic resonance imaging on the pore scale. The packed beds were measured under water‐saturated and unsaturated conditions, while the magnetic resonance method allowed a quantitative differentiation between air, liquid, and solid phases exploring the native contrast of the named phases without additional contrast agents. Beside a qualitative image comparison, subsequent quantitative image processing allowed for a detailed spatially resolved determination of water distribution, the differentiation between water transport processes, and the quantification of liquid clusters in 3‐D. Results are presented for two packed beds that show significant differences in their evaporation and drainage dynamics, which are mainly determined by the physical properties of the packed beds. The water loss of the packed bed of 2–4 mm quartz particles reached a level below interpretability after 18.2 hr; meanwhile, a successive decrease of the largest liquid cluster volume from 82.5 to 0.7 mm3was observed. The water content of the packed bed of 2 mm glass spheres was still observable after 70.9 hr. During the experiment, no significant changes in the structure of the liquid clusters were measured. The current work displays the applicability of magnetic resonance imaging for pore‐scale investigations without the addition of contrast agents.
Spatio-temporal characterization of the antiviral activity of the XRN1-DCP1/2 aggregation against cytoplasmic RNA viruses to prevent cell death
Authors: Ng Chen Seng , Kasumba Dacquin M. , Fujita Takashi , Luo Honglin 
Published: February 2020

AbstractHost nucleases are implicated in antiviral response through the processing of pathogen-derived nucleic acids. Among many host RNases, decapping enzymes DCP1 and 2, and 5′→3′ exonuclease XRN1, which are components of the RNA decay machinery, have been extensively studied in prokaryotes, plants, and invertebrates but less so in mammalian systems. As a result, the implication of XRN1 and DCPs in viral replication, in particular, the spatio-temporal dynamics during RNA viral infections remains elusive. Here, we highlight that XRN1 and DCPs play a critical role in limiting several groups of RNA viral infections. This antiviral activity was not obvious in wild-type cells but clearly observed in type I interferon (IFN-I)-deficient cells. Mechanistically, infection with RNA viruses induced the enrichment of XRN1 and DCPs in viral replication complexes (vRCs), hence forming distinct cytoplasmic aggregates. These aggregates served as sites for direct interaction between XRN1, DCP1/2, and viral ribonucleoprotein that contains viral RNA (vRNA). Although these XRN1-DCP1/2-vRC-containing foci resemble antiviral stress granules (SGs) or P-body (PB), they did not colocalize with known SG markers and did not correlate with critical PB functions. Furthermore, the presence of 5′ mono- and 5′ triphosphate structures on vRNA was not required for the formation of XRN1-DCP1/2-vRC-containing foci. On the other hand, single-, double-stranded, and higher-ordered vRNA species play a role but are not deterministic for efficient formation of XRN1-DCP1/2 foci and consequent antiviral activity in a manner proportional to RNA length. These results highlight the mechanism behind the antiviral function of XRN1-DCP1/2 in RNA viral infections independent of IFN-I response, protein kinase R and PB function.
The COMET toolkit for composing customizable genetic programs in mammalian cells
Authors: Donahue Patrick S. , Draut Joseph W. , Muldoon Joseph J. , Edelstein Hailey I. , Bagheri Neda , Leonard Joshua N. 
Published: February 2020

AbstractEngineering mammalian cells to carry out sophisticated and customizable genetic programs requires a toolkit of multiple orthogonal and well-characterized transcription factors (TFs). To address this need, we develop the COmposable Mammalian Elements of Transcription (COMET)—an ensemble of TFs and promoters that enable the design and tuning of gene expression to an extent not, to the best of our knowledge, previously possible. COMET currently comprises 44 activating and 12 inhibitory zinc-finger TFs and 83 cognate promoters, combined in a framework that readily accommodates new parts. This system can tune gene expression over three orders of magnitude, provides chemically inducible control of TF activity, and enables single-layer Boolean logic. We also develop a mathematical model that provides mechanistic insights into COMET performance characteristics. Altogether, COMET enables the design and construction of customizable genetic programs in mammalian cells.
Quantum non-demolition measurement of a many-body Hamiltonian
Authors: Yang Dayou , Grankin Andrey , Sieberer Lukas M. , Vasilyev Denis V. , Zoller Peter 
Published: February 2020

AbstractIn an ideal quantum measurement, the wave function of a quantum system collapses to an eigenstate of the measured observable, and the corresponding eigenvalue determines the measurement outcome. If the observable commutes with the system Hamiltonian, repeated measurements yield the same result and thus minimally disturb the system. Seminal quantum optics experiments have achieved such quantum non-demolition (QND) measurements of systems with few degrees of freedom. In contrast, here we describe how the QND measurement of a complex many-body observable, the Hamiltonian of an interacting many-body system, can be implemented in a trapped-ion analog quantum simulator. Through a single-shot measurement, the many-body system is prepared in a narrow band of (highly excited) energy eigenstates, and potentially even a single eigenstate. Our QND scheme, which can be carried over to other platforms of quantum simulation, provides a framework to investigate experimentally fundamental aspects of equilibrium and non-equilibrium statistical physics including the eigenstate thermalization hypothesis and quantum fluctuation relations.
Strain-driven growth of ultra-long two-dimensional nano-channels
Authors: Zhu Chao , Yu Maolin , Zhou Jiadong , He Yongmin , Zeng Qingsheng , Deng Ya , Guo Shasha , Xu Mingquan , Shi Jinan , Zhou Wu , Sun Litao , Wang Lin , Hu Zhili , Zhang Zhuhua , Guo Wanlin , Liu Zheng 
Published: February 2020

AbstractLateral heterostructures of two-dimensional transition metal dichalcogenides (TMDs) have offered great opportunities in the engineering of monolayer electronics, catalysis and optoelectronics. To explore the full potential of these materials, developing methods to precisely control the spatial scale of the heterostructure region is crucial. Here, we report the synthesis of ultra-long MoS2 nano-channels with several micrometer length and 2–30 nanometer width within the MoSe2 monolayers, based on intrinsic grain boundaries (GBs). First-principles calculations disclose that the strain fields near the GBs not only lead to the preferred substitution of selenium by sulfur but also drive coherent extension of the MoS2 channel from the GBs. Such a strain-driven synthesis mechanism is further shown applicable to other topological defects. We also demonstrate that the spontaneous strain of MoS2 nano-channels can further improve the hydrogen production activity of GBs, paving the way for designing GB based high-efficient TMDs in the catalytic application.
An interactive ImageJ plugin for semi-automated image denoising in electron microscopy
Authors: Roels Joris , Vernaillen Frank , Kremer Anna , Gonçalves Amanda , Aelterman Jan , Luong Hiêp Q. , Goossens Bart , Philips Wilfried , Lippens Saskia , Saeys Yvan 
Published: February 2020

AbstractThe recent advent of 3D in electron microscopy (EM) has allowed for detection of nanometer resolution structures. This has caused an explosion in dataset size, necessitating the development of automated workflows. Moreover, large 3D EM datasets typically require hours to days to be acquired and accelerated imaging typically results in noisy data. Advanced denoising techniques can alleviate this, but tend to be less accessible to the community due to low-level programming environments, complex parameter tuning or a computational bottleneck. We present DenoisEM: an interactive and GPU accelerated denoising plugin for ImageJ that ensures fast parameter tuning and processing through parallel computing. Experimental results show that DenoisEM is one order of magnitude faster than related software and can accelerate data acquisition by a factor of 4 without significantly affecting data quality. Lastly, we show that image denoising benefits visualization and (semi-)automated segmentation and analysis of ultrastructure in various volume EM datasets.
Revisiting the pH-gated conformational switch on the activities of HisKA-family histidine kinases
Authors: Mideros-Mora Cristina , Miguel-Romero Laura , Felipe-Ruiz Alonso , Casino Patricia , Marina Alberto 
Published: February 2020

AbstractHistidine is a versatile residue playing key roles in enzyme catalysis thanks to the chemistry of its imidazole group that can serve as nucleophile, general acid or base depending on its protonation state. In bacteria, signal transduction relies on two-component systems (TCS) which comprise a sensor histidine kinase (HK) containing a phosphorylatable catalytic His with phosphotransfer and phosphatase activities over an effector response regulator. Recently, a pH-gated model has been postulated to regulate the phosphatase activity of HisKA HKs based on the pH-dependent rotamer switch of the phosphorylatable His. Here, we have revisited this model from a structural and functional perspective on HK853–RR468 and EnvZ–OmpR TCS, the prototypical HisKA HKs. We have found that the rotamer of His is not influenced by the environmental pH, ruling out a pH-gated model and confirming that the chemistry of the His is responsible for the decrease in the phosphatase activity at acidic pH.
Energy-level quantization and single-photon control of phase slips in YBa2Cu3O7–x nanowires
Authors: Lyatti M. , Wolff M. A. , Gundareva I. , Kruth M. , Ferrari S. , Dunin-Borkowski R. E. , Schuck C. 
Published: February 2020

AbstractSignificant progress has been made in superconducting quantum circuits. However new quantum devices that have longer decoherence times at higher temperatures are urgently required for quantum technologies. Superconducting nanowires with quantum phase slips are promising candidates for use in novel quantum devices. Here, we demonstrate YBa2Cu3O7-x nanowires with phase-slip dynamics and study their switching-current statistics at temperatures below 20 K. We apply theoretical models developed for Josephson junctions and show that our results provide strong evidence for energy-level quantization in the nanowires. The crossover temperature to the quantum regime of 12–13 K and the lifetime in the excited state exceeding 20 ms at 5.4 K are superior to those in conventional Josephson junctions. We also show how the absorption of a single photon changes the phase-slip and quantum state of a nanowire, which is important for the development of single-photon detectors with high operating temperature and superior temporal resolution.
Minimally disruptive optical control of protein tyrosine phosphatase 1B
Authors: Hongdusit Akarawin , Zwart Peter H. , Sankaran Banumathi , Fox Jerome M. 
Published: February 2020

AbstractProtein tyrosine phosphatases regulate a myriad of essential subcellular signaling events, yet they remain difficult to study in their native biophysical context. Here we develop a minimally disruptive optical approach to control protein tyrosine phosphatase 1B (PTP1B)—an important regulator of receptor tyrosine kinases and a therapeutic target for the treatment of diabetes, obesity, and cancer—and we use that approach to probe the intracellular function of this enzyme. Our conservative architecture for photocontrol, which consists of a protein-based light switch fused to an allosteric regulatory element, preserves the native structure, activity, and subcellular localization of PTP1B, affords changes in activity that match those elicited by post-translational modifications inside the cell, and permits experimental analyses of the molecular basis of optical modulation. Findings indicate, most strikingly, that small changes in the activity of PTP1B can cause large shifts in the phosphorylation states of its regulatory targets.
Real-time calibration with spectator qubits
Authors: Majumder Swarnadeep , Andreta de Castro Leonardo , Brown Kenneth R. 
Published: February 2020

AbstractAccurate control of quantum systems requires a precise measurement of the parameters that govern the dynamics, including control fields and interactions with the environment. Parameters will drift in time and experiments interleave protocols that perform parameter estimation, with protocols that measure the dynamics of interest. Here we specialize to a system made of qubits where the dynamics correspond to a quantum computation. We propose setting aside some qubits, which we call spectator qubits, to be measured periodically during the computation, to act as probes of the changing experimental and environmental parameters. By using control strategies that minimize the sensitivity of the qubits involved in the computation, we can acquire sufficient information from the spectator qubits to update our estimates of the parameters and improve our control. As a result, we can increase the length of experiments where the dynamics of the data qubits are highly reliable. In particular, we simulate how spectator qubits can keep the error level of operations on data qubits below a 10−4 threshold in two scenarios involving coherent errors: a classical magnetic field gradient dynamically decoupled with sequences of two or four π-pulses, and laser beam instability detected via crosstalk with neighboring atoms in an ion trap.
Machine-Learning Studies on Spin Models
Authors: Shiina Kenta , Mori Hiroyuki , Okabe Yutaka , Lee Hwee Kuan 
Published: February 2020

AbstractWith the recent developments in machine learning, Carrasquilla and Melko have proposed a paradigm that is complementary to the conventional approach for the study of spin models. As an alternative to investigating the thermal average of macroscopic physical quantities, they have used the spin configurations for the classification of the disordered and ordered phases of a phase transition through machine learning. We extend and generalize this method. We focus on the configuration of the long-range correlation function instead of the spin configuration itself, which enables us to provide the same treatment to multi-component systems and the systems with a vector order parameter. We analyze the Berezinskii-Kosterlitz-Thouless (BKT) transition with the same technique to classify three phases: the disordered, the BKT, and the ordered phases. We also present the classification of a model using the training data of a different model.
Validating a targeted next-generation sequencing assay and profiling somatic variants in Chinese non-small cell lung cancer patients
Authors: Jiang Ruirui , Zhang Bo , Teng Xiaodong , Hu Peizhen , Xu Sanpeng , Zheng Zuyu , Liu Rui , Tang Tingdong , Ye Feng 
Published: February 2020

AbstractNon-small cell lung cancer (NSCLC) is featured with complex genomic alterations. Molecular profiling of large cohort of NSCLC patients is thus a prerequisite for precision medicine. We first validated the detection performance of a next-generation sequencing (NGS) cancer hotspot panel, OncoAim, on formalin-fixed paraffin-embedded (FFPE) samples. We then utilized OncoAim to delineate the genomic aberrations in Chinese NSCLC patients. Overall detection performance was powerful for mutations with allele frequency (MAF) ≥ 5% at >500 × coverage depth, with >99% sensitivity, high specificity (positive predictive value > 99%), 94% accuracy and 96% repeatability. Profiling 422 NSCLC FFPE samples revealed that patient characteristics, including gender, age, lymphatic spread, histologic grade and histologic subtype were significantly associated with the mutation incidence of EGFR and TP53. Moreover, RTK signaling pathway activation was enriched in adenocarcinoma, while PI(3)K pathway activation, oxidative stress pathway activation, and TP53 pathway inhibition were more prevalent in squamous cell carcinoma. Additionally, novel co-existence (e.g., variants in BRAF and PTEN) and mutual-exclusiveness (e.g., alterations in EGFR and NFE2L2) were found. Finally, we revealed distinct mutation spectrum in TP53, as well as a previously undervalued PTEN aberration. Our findings could aid in improving diagnosis, prognosis and personalized therapeutic decisions of Chinese NSCLC patients.
Photosensitive nanocarriers for specific delivery of cargo into cells
Authors: Mena-Giraldo Pedro , Pérez-Buitrago Sandra , Londoño-Berrío Maritza , Ortiz-Trujillo Isabel C. , Hoyos-Palacio Lina M. , Orozco Jahir 
Published: February 2020

AbstractNanoencapsulation is a rapidly expanding technology to enclose cargo into inert material at the nanoscale size, which protects cargo from degradation, improves bioavailability and allows for controlled release. Encapsulation of drugs into functional nanocarriers enhances their specificity, targeting ability, efficiency, and effectiveness. Functionality may come from cell targeting biomolecules that direct nanocarriers to a specific cell or tissue. Delivery is usually mediated by diffusion and erosion mechanisms, but in some cases, this is not sufficient to reach the expected therapeutic effects. This work reports on the development of a new photoresponsive polymeric nanocarrier (PNc)-based nanobioconjugate (NBc) for specific photo-delivery of cargo into target cells. We readily synthesized the PNcs by modification of chitosan with ultraviolet (UV)-photosensitive azobenzene molecules, with Nile red and dofetilide as cargo models to prove the encapsulation/release concept. The PNcs were further functionalized with the cardiac targeting transmembrane peptide and efficiently internalized into cardiomyocytes, as a cell line model. Intracellular cargo-release was dramatically accelerated upon a very short UV-light irradiation time. Delivering cargo in a time-space controlled fashion by means of NBcs is a promising strategy to increase the intracellular cargo concentration, to decrease dose and cargo side effects, thereby improving the effectiveness of a therapeutic regime.
The Order-Disorder Continuum: Linking Predictions of Protein Structure and Disorder through Molecular Simulation
Authors: Hsu Claire C. , Buehler Markus J. , Tarakanova Anna 
Published: February 2020

AbstractIntrinsically disordered proteins (IDPs) and intrinsically disordered regions within proteins (IDRs) serve an increasingly expansive list of biological functions, including regulation of transcription and translation, protein phosphorylation, cellular signal transduction, as well as mechanical roles. The strong link between protein function and disorder motivates a deeper fundamental characterization of IDPs and IDRs for discovering new functions and relevant mechanisms. We review recent advances in experimental techniques that have improved identification of disordered regions in proteins. Yet, experimentally curated disorder information still does not currently scale to the level of experimentally determined structural information in folded protein databases, and disorder predictors rely on several different binary definitions of disorder. To link secondary structure prediction algorithms developed for folded proteins and protein disorder predictors, we conduct molecular dynamics simulations on representative proteins from the Protein Data Bank, comparing secondary structure and disorder predictions with simulation results. We find that structure predictor performance from neural networks can be leveraged for the identification of highly dynamic regions within molecules, linked to disorder. Low accuracy structure predictions suggest a lack of static structure for regions that disorder predictors fail to identify. While disorder databases continue to expand, secondary structure predictors and molecular simulations can improve disorder predictor performance, which aids discovery of novel functions of IDPs and IDRs. These observations provide a platform for the development of new, integrated structural databases and fusion of prediction tools toward protein disorder characterization in health and disease.
Highly Efficient Excitonic Recombination of Non-polar ($$11\overline{2}0$$) GaN Nanocrystals for Visible Light Emitter by Hydride Vapour Phase Epitaxy
Authors: Lee Moonsang , Lee Dongyun , Baik Hionsuck , Kim Heejin , Jeong Yesul , Yang Mino , Lee Hyun Uk , Hahm Myung Gwan , Kim Jaekyun 
Published: February 2020

AbstractWhile non-polar nanostructured-GaN crystals are considered as a prospective material for the realization of futuristic opto-electronic application, the formation of non-polar GaN nanocrystals (NCs) with highly efficient visible emission characteristics remain unquestionable up to now. Here, we report the oxygen-incorporated a-plane GaN NCs with highly visible illumination excitonic recombination characteristics. Epitaxially aligned a-plane NCs with average diameter of 100 nm were formed on r-plane sapphire substrates by hydride vapor phase epitaxy (HVPE), accompanied by the oxygen supply during the growth. X-ray photoemission spectroscopy measurements proved that the NCs exhibited Ga-O bonding in the materials, suggesting the formation of oxidized states in the bandgap. It was found that the NCs emitted the visible luminescence wavelength of 400‒500 nm and 680‒720 nm, which is attributed to the transition from oxygen-induced localized states. Furthermore, time-resolved photoluminescence studies revealed the significant suppression of the quantum confined Stark effect and highly efficient excitonic recombination within GaN NCs. Therefore, we believe that the HVPE non-polar GaN NCs can guide the simple and efficient way toward the nitride-based next-generation nano-photonic devices.
Differences in vegetative growth of two invasive hawkweeds at temperatures simulating invaded habitats at two altitudes
Authors: French Kris , Watts Eva 
Published: February 2020

AbstractHieracium pilosella and H. aurantiacum are invading alpine regions in New South Wales, Australia. In a glasshouse experiment we investigated germination and growth rates of these two species at temperatures simulating the altitudes where invasions are occurring from autumn to spring. We measured germination rates, growth rates and the development of stolons and ramets using seedlings and plantlets from established plants. Germination was low in H. aurantiacum and unaffected by altitude or seed age. H. pilosella showed site to site variability in germination but had greater germination. No species produced flower spikes. Both species grew rapidly and put at least twice as much biomass into roots compared to shoots. H. aurantiacum could begin to produce stolons after 27 days and seedlings grew a little larger than for H. pilosella. Hieracium aurantiacum put significantly more resources into ramets, allocating between 4–15% of biomass. H. pilosella produced 2.6 stolons month−1, in contrast to 9.8 stolons month−1 for H. aurantiacum. Furthermore, plantlets from established plants had vastly different growth rates. Plantlets of H. aurantiacum produced 2.1 leaves day−1 from late summer to winter where H. pilosella was 3 times slower for the same period but faster following winter. Both species were able to maintain strong growth over cooler months suggesting hawkweeds have the capacity for fast growth in the invaded range under high nutrients and lower competition. H. aurantiacum is likely to be a more effective invader than H. pilosella spreading through stolons and the development of weed mats.