bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plasmonic monolithic lithium niobate directional coupler switches
Authors: Thomaschewski Martin , Zenin Vladimir A. , Wolff Christian , Bozhevolnyi Sergey I. 
Published: February 2020

AbstractLithium niobate (LN) has been the material of choice for electro-optic modulators owing to its excellent physical properties. While conventional LN electro-optic modulators continue to be the workhorse of the modern optoelectronics, they are becoming progressively too bulky, expensive, and power-hungry to fully serve the needs of this industry. Here, we demonstrate plasmonic electro-optic directional coupler switches consisting of two closely spaced nm-thin gold nanostripes on LN substrates that guide both coupled electromagnetic modes and electrical signals that control their coupling, thereby enabling ultra-compact switching and modulation functionalities. Extreme confinement and good spatial overlap of both slow-plasmon modes and electrostatic fields created by the nanostripes allow us to achieve a 90% modulation depth with 20-μm-long switches characterized by a broadband electro-optic modulation efficiency of 0.3 V cm. Our monolithic LN plasmonic platform enables a wide range of cost-effective optical communication applications that demand μm-scale footprints, ultrafast operation and high environmental stability.
Bacterial adaptation is constrained in complex communities
Authors: Scheuerl Thomas , Hopkins Meirion , Nowell Reuben W. , Rivett Damian W. , Barraclough Timothy G. , Bell Thomas 
Published: February 2020

AbstractA major unresolved question is how bacteria living in complex communities respond to environmental changes. In communities, biotic interactions may either facilitate or constrain evolution depending on whether the interactions expand or contract the range of ecological opportunities. A fundamental challenge is to understand how the surrounding biotic community modifies evolutionary trajectories as species adapt to novel environmental conditions. Here we show that community context can dramatically alter evolutionary dynamics using a novel approach that ‘cages’ individual focal strains within complex communities. We find that evolution of focal bacterial strains depends on properties both of the focal strain and of the surrounding community. In particular, there is a stronger evolutionary response in low-diversity communities, and when the focal species have a larger genome and are initially poorly adapted. We see how community context affects resource usage and detect genetic changes involved in carbon metabolism and inter-specific interaction. The findings demonstrate that adaptation to new environmental conditions should be investigated in the context of interspecific interactions.
Weak functional group interactions revealed through metal-free active template rotaxane synthesis
Authors: Tian Chong , Fielden Stephen D. P. , Whitehead George F. S. , Vitorica-Yrezabal Iñigo J. , Leigh David A. 
Published: February 2020

AbstractModest functional group interactions can play important roles in molecular recognition, catalysis and self-assembly. However, weakly associated binding motifs are often difficult to characterize. Here, we report on the metal-free active template synthesis of [2]rotaxanes in one step, up to 95% yield and >100:1 rotaxane:axle selectivity, from primary amines, crown ethers and a range of C=O, C=S, S(=O)2 and P=O electrophiles. In addition to being a simple and effective route to a broad range of rotaxanes, the strategy enables 1:1 interactions of crown ethers with various functional groups to be characterized in solution and the solid state, several of which are too weak — or are disfavored compared to other binding modes — to be observed in typical host–guest complexes. The approach may be broadly applicable to the kinetic stabilization and characterization of other weak functional group interactions.
Mitigating coherent noise using Pauli conjugation
Authors: Cai Zhenyu , Xu Xiaosi , Benjamin Simon C. 
Published: February 2020

AbstractCoherent noise can be much more damaging than incoherent (probabilistic) noise in the context of quantum error correction. One solution is to use twirling to turn coherent noise into incoherent Pauli channels. In this Article, we show that some of the coherence of the noise channel can actually be used to improve its logical fidelity by simply sandwiching the noise with a chosen pair of Pauli gates, which we call Pauli conjugation. Using the optimal Pauli conjugation, we can achieve a higher logical fidelity than using twirling and doing nothing. We devise a way to search for the optimal Pauli conjugation scheme and apply it to Steane code, 9-qubit Shor code and distance-3 surface code under global coherent $$Z$$
Z
noise. The optimal conjugation schemes show improvement in logical fidelity over twirling while the weights of the conjugation gates we need to apply are lower than the average weight of the twirling gates. In our example noise and codes, the concatenated threshold obtained using conjugation is consistently higher than the twirling threshold and can be up to 1.5 times higher than the original threshold where no mitigation is applied. Our simulations show that Pauli conjugation can be robust against gate errors. With the help of logical twirling, the undesirable coherence in the noise channel can be removed and the advantages of conjugation over twirling can persist as we go to multiple rounds of quantum error correction.
Generation of a global synthetic tropical cyclone hazard dataset using STORM
Authors: Bloemendaal Nadia , Haigh Ivan D. , de Moel Hans , Muis Sanne , Haarsma Reindert J. , Aerts Jeroen C. J. H. 
Published: February 2020

AbstractOver the past few decades, the world has seen substantial tropical cyclone (TC) damages, with the 2017 Hurricanes Harvey, Irma and Maria entering the top-5 costliest Atlantic hurricanes ever. Calculating TC risk at a global scale, however, has proven difficult given the limited temporal and spatial information on TCs across much of the global coastline. Here, we present a novel database on TC characteristics on a global scale using a newly developed synthetic resampling algorithm we call STORM (Synthetic Tropical cyclOne geneRation Model). STORM can be applied to any meteorological dataset to statistically resample and model TC tracks and intensities. We apply STORM to extracted TCs from 38 years of historical data from IBTrACS to statistically extend this dataset to 10,000 years of TC activity. We show that STORM preserves the TC statistics as found in the original dataset. The STORM dataset can be used for TC hazard assessments and risk modeling in TC-prone regions.
A multilayer and spatial description of the Erasmus mobility network
Authors: Gadár László , Kosztyán Zsolt T. , Telcs András , Abonyi János 
Published: February 2020

AbstractThe Erasmus Programme is the biggest collaboration network consisting of European Higher Education Institutions (HEIs). The flows of students, teachers and staff form directed and weighted networks that connect institutions, regions and countries. Here, we present a linked and manually verified dataset of this multiplex, multipartite, multi-labelled, spatial network. We enriched the network with institutional socio-economic data from the European Tertiary Education Register (ETER) and the Global Research Identifier Database (GRID). We geocoded the headquarters of institutions and characterised the attractiveness and quality of their environments based on Points of Interest (POI) data. The linked datasets provide relevant information to grasp a more comprehensive understanding of the mobility patterns and attractiveness of the institutions.
Morphological and Hemodynamic Risk Factors for Middle Cerebral Artery Aneurysm: a Case-Control Study of 190 Patients
Authors: Kaspera Wojciech , Ćmiel-Smorzyk Karolina , Wolański Wojciech , Kawlewska Edyta , Hebda Anna , Gzik Marek , Ładziński Piotr 
Published: February 2020

AbstractThis study analyzed morphometric and hemodynamic parameters of aneurysmal and non-aneurysmal middle cerebral artery (MCA) bifurcations and their relationship with optimal values derived from the principle of minimum work (PMW). The study included 96 patients with MCA aneurysm and 94 controls. Aneurysm patients presented with significantly higher values of the radius and cross-sectional area of the MCA trunk, angle between the post-bifurcation branches (α angle) and volume flow rate (VFR) and had significantly lower values of junction exponent and pulsatility index than the controls. The Φ1 and Φ2 angles (angles between the MCA trunk axis and the larger and smaller branch, respectively) and α angle in all groups were significantly larger than the optimal PMW-derived angles. The most important independent predictors of MCA aneurysm were junction exponent (odds ratio, OR = 0.42), α angle (OR = 1.07) and VFR (OR = 2.36). Development of cerebral aneurysms might be an independent effect of abnormalities in hemodynamic and morphometric factors. The risk of aneurysm increased proportionally to the deviation of morphometric parameters of the bifurcation from their optimal PMW-derived values. The role of bifurcation angle in aneurysm development needs to be explained in future research as the values of this parameter in both aneurysm patients and non-aneurysmal controls in were scattered considerably around the PMW-derived optimum.
Sox2 controls Schwann cell self-organization through fibronectin fibrillogenesis
Authors: Torres-Mejía Elen , Trümbach Dietrich , Kleeberger Charlotte , Dornseifer Ulf , Orschmann Tanja , Bäcker Theresa , Brenke Jara Kerstin , Hadian Kamyar , Wurst Wolfgang , López-Schier Hernán , Desbordes Sabrina C. 
Published: February 2020

AbstractThe extracellular matrix is known to modulate cell adhesion and migration during tissue regeneration. However, the molecular mechanisms that fine-tune cells to extra-cellular matrix dynamics during regeneration of the peripheral nervous system remain poorly understood. Using the RSC96 Schwann cell line, we show that Sox2 directly controls fibronectin fibrillogenesis in Schwann cells in culture, to provide a highly oriented fibronectin matrix, which supports their organization and directional migration. We demonstrate that Sox2 regulates Schwann cell behaviour through the upregulation of multiple extracellular matrix and migration genes as well as the formation of focal adhesions during cell movement. We find that mouse primary sensory neurons and human induced pluripotent stem cell-derived motoneurons require the Sox2-dependent fibronectin matrix in order to migrate along the oriented Schwann cells. Direct loss of fibronectin in Schwann cells impairs their directional migration affecting the alignment of the axons in vitro. Furthermore, we show that Sox2 and fibronectin are co-expressed in proregenerative Schwann cells in vivo in a time-dependent manner during sciatic nerve regeneration. Taken together, our results provide new insights into the mechanisms by which Schwann cells regulate their own extracellular microenvironment in a Sox2-dependent manner to ensure the proper migration of neurons.
A role of metallothionein-3 in radiation-induced autophagy in glioma cells
Authors: Cho Young Hyun , Lee Seung-Hwan , Lee Sook-Jeong , Kim Ha Na , Koh Jae-Young 
Published: February 2020

AbstractAlthough metallothionein-3 (MT3), a brain-enriched form of metallothioneins, has been linked to Alzheimer’s disease, little is known regarding the role ofMT3in glioma. AsMT3plays a role in autophagy in astrocytes, here, we investigated its role in irradiated glioma cells. Irradiation increased autophagy flux in GL261 glioma cells as evidenced by increased levels of LC3-II but decreased levels of p62 (SQSTM1). Indicating that autophagy plays a cytoprotective role in glioma cell survival following irradiation, measures inhibiting autophagy flux at various steps decreased their clonogenic survival of irradiated GL261 as well as SF295 and U251 glioma cells. Knockdown ofMT3with siRNA in irradiated glioma cells induced arrested autophagy, and decreased cell survival. At the same time, the accumulation of labile zinc in lysosomes was markedly attenuated byMT3knockdown. Indicating that such zinc accumulation was important in autophagy flux, chelation of zinc with tetrakis-(2-pyridylmethyl)ethylenediamine (TPEN), induced arrested autophagy in and reduced survival of GL261 cells following irradiation. Suggesting a possible mechanism for arrested autophagy,MT3knockdown and zinc chelation were found to impair lysosomal acidification. Since autophagy flux plays a cytoprotective role in irradiated glioma cells, present results suggest thatMT3and zinc may be regarded as possible therapeutic targets to sensitize glioma cells to ionizing radiation therapy.
A cross-sectional study to characterize local HIV-1 dynamics in Washington, DC using next-generation sequencing
Authors: Gibson Keylie M. , Jair Kamwing , Castel Amanda D. , Bendall Matthew L. , Wilbourn Brittany , Jordan Jeanne A. , Crandall Keith A. , Pérez-Losada Marcos ,   the DC Cohort Executive Committee, Subramanian Thilakavathy , Binkley Jeffery , Taylor Rob , Rayeed Nabil , Akridge Cheryl , Purinton Stacey , Naughton Jeff , Rakhmanina Natella , D’Angelo Larry , Kharfen Michael , Wood Angela , Serlin Michael , Kumar Princy , Parenti David , Greenberg Alan , Monroe Anne , Happ Lindsey Powers , Jaurretche Maria , Peterson James , Wilcox Ronald D , Rana Sohail , Horberg Michael A , Fernández Ricardo , Hebou Annick , Dieffenbach Carl , Masur Henry , Bordon Jose , Teferi Gebeyehu , Benator Debra , Ruiz Maria Elena , Goldstein Deborah , Hardy David 
Published: February 2020

AbstractWashington, DC continues to experience a generalized HIV-1 epidemic. We characterized the local phylodynamics of HIV-1 in DC using next-generation sequencing (NGS) data. Viral samples from 68 participants from 2016 through 2017 were sequenced and paired with epidemiological data. Phylogenetic and network inferences, drug resistant mutations (DRMs), subtypes and HIV-1 diversity estimations were completed. Haplotypes were reconstructed to infer transmission clusters. Phylodynamic inferences based on the HIV-1 polymerase (pol) and envelope genes (env) were compared. Higher HIV-1 diversity (n.s.) was seen in men who have sex with men, heterosexual, and male participants in DC. 54.0% of the participants contained at least one DRM. The 40–49 year-olds showed the highest prevalence of DRMs (22.9%). Phylogenetic analysis of pol and env sequences grouped 31.9–33.8% of the participants into clusters. HIV-TRACE grouped 2.9–12.8% of participants when using consensus sequences and 9.0–64.2% when using haplotypes. NGS allowed us to characterize the local phylodynamics of HIV-1 in DC more broadly and accurately, given a better representation of its diversity and dynamics. Reconstructed haplotypes provided novel and deeper phylodynamic insights, which led to networks linking a higher number of participants. Our understanding of the HIV-1 epidemic was expanded with the powerful coupling of HIV-1 NGS data with epidemiological data.
Two-phase wash to solve the ubiquitous contaminant-carryover problem in commercial nucleic-acid extraction kits
Authors: Jue Erik , Witters Daan , Ismagilov Rustem F. 
Published: February 2020

AbstractThe success of fundamental and applied nucleic acid (NA) research depends on NA purity, but obtaining pure NAs from raw, unprocessed samples is challenging. Purification using solid-phase NA extractions utilizes sequential additions of lysis and wash buffers followed by elution. The resulting eluent contains NAs and carryover of extraction buffers. Typically, these inhibitory buffers are heavily diluted by the reaction mix (e.g., 10x dilution is 1 µL eluent in 9 µL reaction mix), but in applications requiring high sensitivity (e.g., single-cell sequencing, pathogen diagnostics) it is desirable to use low dilutions (e.g., 2x) to maximize NA concentration. Here, we demonstrate pervasive carryover of inhibitory buffers into eluent when several commercial sample-preparation kits are used following manufacturer protocols. At low eluent dilution (2–2.5x) we observed significant reaction inhibition of polymerase chain reaction (PCR), loop-mediated isothermal amplification (LAMP), and reverse transcription (RT). We developed a two-phase wash (TPW) method by adding a wash buffer with low water solubility prior to the elution step. The TPW reduces carryover of extraction buffers, phase-separates from the eluent, and does not reduce NA yield (measured by digital PCR). We validated the TPW for silica columns and magnetic beads by demonstrating significant improvements in performance and reproducibility of qPCR, LAMP, and RT reactions.
Observation of diffraction contrast in scanning helium microscopy
Authors: Bergin M. , Lambrick S. M. , Sleath H. , Ward D. J. , Ellis J. , Jardine A. P. 
Published: February 2020

AbstractScanning helium microscopy is an emerging form of microscopy using thermal energy neutral helium atoms as the probe particle. The very low energy combined with lack of charge gives the technique great potential for studying delicate systems, and the possibility of several new forms of contrast. To date, neutral helium images have been dominated by topographic contrast, relating to the height and angle of the surface. Here we present data showing contrast resulting from specular reflection and diffraction of helium atoms from an atomic lattice of lithium fluoride. The signature for diffraction is evident by varying the scattering angle and observing sharp features in the scattered distribution. The data indicates the viability of the approach for imaging with diffraction contrast and suggests application to a wide variety of other locally crystalline materials.
Switchable crossed spin conductance in a graphene-based junction: The role of spin-orbit coupling
Authors: Beiranvand Razieh , Hamzehpour Hossein 
Published: February 2020

AbstractWe theoretically investigate the crossed spin conductance (CSC) of a graphene-based heterostructure consists of ferromagnet, Rashba spin-orbit and superconductor regions. Using Dirac Bogoliubov-de Gennes formalism in the ballistic regime, we show that in the presence of Rashba spin-orbit coupling there are an anomalous crossed Andreev reection and spin-ipped co-tunneling in the process of quantum transport. We demonstrate that the CSC can be reversed with respect to charge conductance by tuning the Rashba spin-orbit coupling which experimentally can be adjusted by the applied perpendicular electric field on the graphene sheet. This feature in addition to a long spin relaxation time of Dirac fermions in graphene proposes designing a device with a non-local spin switch which is crucial for spintronics circuits.
Culture modulates face scanning during dyadic social interactions
Authors: Haensel Jennifer X. , Danvers Matthew , Ishikawa Mitsuhiko , Itakura Shoji , Tucciarelli Raffaele , Smith Tim J. , Senju Atsushi 
Published: February 2020

AbstractRecent studies have revealed significant cultural modulations on face scanning strategies, thereby challenging the notion of universality in face perception. Current findings are based on screen-based paradigms, which offer high degrees of experimental control, but lack critical characteristics common to social interactions (e.g., social presence, dynamic visual saliency), and complementary approaches are required. The current study used head-mounted eye tracking techniques to investigate the visual strategies for face scanning in British/Irish (in the UK) and Japanese adults (in Japan) who were engaged in dyadic social interactions with a local research assistant. We developed novel computational data pre-processing tools and data-driven analysis techniques based on Monte Carlo permutation testing. The results revealed significant cultural differences in face scanning during social interactions for the first time, with British/Irish participants showing increased mouth scanning and the Japanese group engaging in greater eye and central face looking. Both cultural groups further showed more face orienting during periods of listening relative to speaking, and during the introduction task compared to a storytelling game, thereby replicating previous studies testing Western populations. Altogether, these findings point to the significant role of postnatal social experience in specialised face perception and highlight the adaptive nature of the face processing system.
Mitochondrial toxicity and body shape changes during nucleos(t)ide analogues administration in patients with chronic hepatitis B
Authors: Madeddu Giordano , Fiore Vito , Melis Michela , Ortu Silvia , Mannu Franca , Muredda Alberto Augusto , Garrucciu Giovanni , Bandiera Franco , Zaru Salvatore , Bagella Paola , Calvisi Diego Francesco , Babudieri Sergio 
Published: February 2020

AbstractOur study purpose was to evaluate mitochondrial (mt)DNA and RNA in peripheral blood mononuclear cells (PBMCs) and body shape changes (BSC) in HBV-infected patients. mtDNA and mtRNA were measured in PBMCs. The presence of BSC was evaluated through a questionnaire and clinical evaluation. A total of 157 subjects were enrolled, of these 107 were HBV-infected patients, 54 receiving nucleoside analogues (NAs, Group A), 53 naive to antivirals (Group B) and 50 age-sex matched controls (Group C). All HBV-treated patients had negative HBV–DNA. Twenty (37,0%) received lamivudine + adefovir, 20 (37.0%) tenofovir, 2 (3.7%) lamivudine and 12 (22.2%) entecavir. Therapy median duration was 38 months (IQR 20–60) in NA-treated patients. Group A showed significantly higher mtDNA/nuclear (n) DNA ratio (p = 0.000008) compared to Group C and Group B (p = 0.002). Group B showed significantly higher mtDNA/nDNA ratio compared to Group C (p = 0.017). Group A and B had significantly lower mtRNA/nRNA ratio compared to Group C (p = 0.00003 and p = 0.00006, respectively). Tenofovir and entecavir showed less impact compared to lamivudine + adefovir. mtDNA/nDNA ratio positively (Rho = 0.34, p < 0.05) and mtRNA/nRNA ratio negatively (Rho = −0.34, p < 0.05) correlated with therapy duration. BSC were significantly more frequent in Group A [10/54 (18.5%)] compared to Group B [3/53 (5.6%, p = 0.04)] and Group C [0/50, (p = 0.0009)]. In conclusion, long-term NA therapy was associated both to mitochondrial toxicity and BSC, showing significant differences in mtDNA and mtRNA levels. Tenofovir and entecavir showed lower impact on alterations, compared to 1stgeneration NA.
Waste foundry sand/MgFe-layered double hydroxides composite material for efficient removal of Congo red dye from aqueous solution
Authors: Ahmed Dooraid N. , Naji Laith A. , Faisal Ayad A. H. , Al-Ansari Nadhir , Naushad Mu. 
Published: February 2020

AbstractWe aimed to obtain magnesium/iron (Mg/Fe)-layered double hydroxides (LDHs) nanoparticles-immobilized on waste foundry sand-a byproduct of the metal casting industry. XRD and FT-IR tests were applied to characterize the prepared sorbent. The results revealed that a new peak reflected LDHs nanoparticles. In addition, SEM-EDS mapping confirmed that the coating process was appropriate. Sorption tests for the interaction of this sorbent with an aqueous solution contaminated with Congo red dye revealed the efficacy of this material where the maximum adsorption capacity reached approximately 9127.08 mg/g. The pseudo-first-order and pseudo-second-order kinetic models helped to describe the sorption measurements, indicating that the physical and chemical forces governed the removal process.