bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tunable transmission of quantum Hall edge channels with full degeneracy lifting in split-gated graphene devices
Authors: Zimmermann Katrin , Jordan Anna , Gay Frédéric , Watanabe Kenji , Taniguchi Takashi , Han Zheng , Bouchiat Vincent , Sellier Hermann , Sacépé Benjamin 
Published: April 2017

AbstractCharge carriers in the quantum Hall regime propagate via one-dimensional conducting channels that form along the edges of a two-dimensional electron gas. Controlling their transmission through a gate-tunable constriction, also called quantum point contact, is fundamental for many coherent transport experiments. However, in graphene, tailoring a constriction with electrostatic gates remains challenging due to the formation of p–n junctions below gate electrodes along which electron and hole edge channels co-propagate and mix, short circuiting the constriction. Here we show that this electron–hole mixing is drastically reduced in high-mobility graphene van der Waals heterostructures thanks to the full degeneracy lifting of the Landau levels, enabling quantum point contact operation with full channel pinch-off. We demonstrate gate-tunable selective transmission of integer and fractional quantum Hall edge channels through the quantum point contact. This gate control of edge channels opens the door to quantum Hall interferometry and electron quantum optics experiments in the integer and fractional quantum Hall regimes of graphene.
Nanoscale interface confinement of ultrafast spin transfer torque driving non-uniform spin dynamics
Authors: Razdolski Ilya , Alekhin Alexandr , Ilin Nikita , Meyburg Jan P. , Roddatis Vladimir , Diesing Detlef , Bovensiepen Uwe , Melnikov Alexey 
Published: April 2017

AbstractSpintronics had a widespread impact over the past decades due to transferring information by spin rather than electric currents. Its further development requires miniaturization and reduction of characteristic timescales of spin dynamics combining the sub-nanometre spatial and femtosecond temporal ranges. These demands shift the focus of interest towards the fundamental open question of the interaction of femtosecond spin current (SC) pulses with a ferromagnet (FM). The spatio-temporal properties of the impulsive spin transfer torque exerted by ultrashort SC pulses on the FM open the time domain for probing non-uniform magnetization dynamics. Here we employ laser-generated ultrashort SC pulses for driving ultrafast spin dynamics in FM and analysing its transient local source. Transverse spins injected into FM excite inhomogeneous high-frequency spin dynamics up to 0.6 THz, indicating that the perturbation of the FM magnetization is confined to 2 nm.
Single-molecule electrical contacts on silicon electrodes under ambient conditions
Authors: Aragonès Albert C. , Darwish Nadim , Ciampi Simone , Sanz Fausto , Gooding J. Justin , Díez-Pérez Ismael 
Published: April 2017

AbstractThe ultimate goal in molecular electronics is to use individual molecules as the active electronic component of a real-world sturdy device. For this concept to become reality, it will require the field of single-molecule electronics to shift towards the semiconducting platform of the current microelectronics industry. Here, we report silicon-based single-molecule contacts that are mechanically and electrically stable under ambient conditions. The single-molecule contacts are prepared on silicon electrodes using the scanning tunnelling microscopy break-junction approach using a top metallic probe. The molecular wires show remarkable current–voltage reproducibility, as compared to an open silicon/nano-gap/metal junction, with current rectification ratios exceeding 4,000 when a low-doped silicon is used. The extension of the single-molecule junction approach to a silicon substrate contributes to the next level of miniaturization of electronic components and it is anticipated it will pave the way to a new class of robust single-molecule circuits.
The microbiome of glaciers and ice sheets
Authors: Anesio Alexandre M. , Lutz Stefanie , Chrismas Nathan A. M. , Benning Liane G. 
Published: April 2017

AbstractGlaciers and ice sheets, like other biomes, occupy a significant area of the planet and harbour biological communities with distinct interactions and feedbacks with their physical and chemical environment. In the case of the glacial biome, the biological processes are dominated almost exclusively by microbial communities. Habitats on glaciers and ice sheets with enough liquid water to sustain microbial activity include snow, surface ice, cryoconite holes, englacial systems and the interface between ice and overridden rock/soil. There is a remarkable similarity between the different specific glacial habitats across glaciers and ice sheets worldwide, particularly regarding their main primary producers and ecosystem engineers. At the surface, cyanobacteria dominate the carbon production in aquatic/sediment systems such as cryoconite holes, while eukaryotic Zygnematales and Chlamydomonadales dominate ice surfaces and snow dynamics, respectively. Microbially driven chemolithotrophic processes associated with sulphur and iron cycle and C transformations in subglacial ecosystems provide the basis for chemical transformations at the rock interface under the ice that underpin an important mechanism for the delivery of nutrients to downstream ecosystems. In this review, we focus on the main ecosystem engineers of glaciers and ice sheets and how they interact with their chemical and physical environment. We then discuss the implications of this microbial activity on the icy microbiome to the biogeochemistry of downstream ecosystems.
Mycobacterium tuberculosis Lineage Distribution in Xinjiang and Gansu Provinces, China
Authors: Chen Haixia , He Li , Huang Hairong , Shi Chengmin , Ni Xumin , Dai Guangming , Ma Liang , Li Weimin 
Published: April 2017

AbstractMycobacterium tuberculosis (M. tuberculosis) genotyping has dramatically improved the understanding of the epidemiology of tuberculosis (TB). In this study, 187 M. tuberculosis isolates from Xinjiang Uygur Autonomous Region (Xinjiang) and Gansu province in China were genotyped using large sequence polymorphisms (LSPs) and variable number tandem repeats (VNTR). Ten isolates, which represent major nodes of VNTR-based minimum spanning tree, were selected and subsequently subjected to multi-locus sequence analyses (MLSA) that include 82 genes. Based on a robust lineage assignment, we tested the association between lineages and clinical characteristics by logistic regression. There are three major lineages of M. tuberculosis prevalent in Xinjiang, viz. the East Asian Lineage 2 (42.1%; 56/133), the Euro-American Lineage 4 (33.1%; 44/133), and the Indian and East African Lineage 3 (24.8%; 33/133); two lineages prevalent in Gansu province, which are the Lineage 2 (87%; 47/54) and the Lineage 4 (13%; 7/54). The topological structures of the MLSA-based phylogeny support the LSP-based identification of M. tuberculosis lineages. The statistical results suggest an association between the Lineage 2 and the hemoptysis/bloody sputum symptom, fever in Uygur patients. The pathogenicity of the Lineage 2 remains to be further investigated.
Agarose Spot as a Comparative Method for in situ Analysis of Simultaneous Chemotactic Responses to Multiple Chemokines
Authors: Ahmed Mohaned , Basheer Haneen A. , Ayuso Jose M. , Ahmet Djevdet , Mazzini Marco , Patel Roshan , Shnyder Steven D. , Vinader Victoria , Afarinkia Kamyar 
Published: April 2017

AbstractWe describe a novel protocol to quantitatively and simultaneously compare the chemotactic responses of cells towards different chemokines. In this protocol, droplets of agarose gel containing different chemokines are applied onto the surface of a Petri dish, and then immersed under culture medium in which cells are suspended. As chemokine molecules diffuse away from the spot, a transient chemoattractant gradient is established across the spots. Cells expressing the corresponding cognate chemokine receptors migrate against this gradient by crawling under the agarose spots towards their centre. We show that this migration is chemokine-specific; meaning that only cells that express the cognate chemokine cell surface receptor, migrate under the spot containing its corresponding chemokine ligand. Furthermore, we show that migration under the agarose spot can be modulated by selective small molecule antagonists present in the cell culture medium.
Identification and Characterization of Differentially-Regulated Type IVb Pilin Genes Necessary for Predation in Obligate Bacterial Predators
Authors: Avidan Ofir , Petrenko Margarita , Becker René , Beck Sebastian , Linscheid Michael , Pietrokovski Shmuel , Jurkevitch Edouard 
Published: April 2017

AbstractBdellovibrio bacteriovorus is an obligate predator of bacteria that grows and divides within the periplasm of its prey. Functions involved in the early steps of predation have been identified and characterized, but mediators of prey invasion are still poorly detailed. By combining omics data available for Bdellovibrio and like organisms (BALO’s), we identified 43 genes expressed in B. bacteriovorus during the early interaction with prey. These included genes in a tight adherence (TAD) operon encoding for two type IVb fimbriae-like pilin proteins (flp1 and flp2), and their processing and export machinery. Two additional flp genes (flp3 and flp4) were computationally identified at other locations along the chromosome, defining the largest and most diverse type IVb complement known in bacteria to date. Only flp1, flp2 and flp4 were expressed; their respective gene knock-outs resulted in a complete loss of the predatory ability without losing the ability to adhere to prey cells. Additionally, we further demonstrate differential regulation of the flp genes as the TAD operon of BALOs with different predatory strategies is controlled by a flagellar sigma factor FliA, while flp4 is not. Finally, we show that FliA, a known flagellar transcriptional regulator in other bacteria, is an essential Bdellovibrio gene.
Disease biomarker identification from gene network modules for metastasized breast cancer
Authors: Sharma Pooja , Bhattacharyya Dhruba K. , Kalita Jugal 
Published: April 2017

AbstractAdvancement in science has tended to improve treatment of fatal diseases such as cancer. A major concern in the area is the spread of cancerous cells, technically refered to as metastasis into other organs beyond the primary organ. Treatment in such a stage of cancer is extremely difficult and usually palliative only. In this study, we focus on finding gene-gene network modules which are functionally similar in nature in the case of breast cancer. These modules extracted during the disease progression stages are analyzed using p-value and their associated pathways. We also explore interesting patterns associated with the causal genes, viz., SCGB1D2, MET, CYP1B1 and MMP9 in terms of expression similarity and pathway contexts. We analyze the genes involved in both the stages– non metastasis and metastatsis and change in their expression values, their associated pathways and roles as the disease progresses from one stage to another. We discover three additional pathways viz., Glycerophospholipid metablism, h-Efp pathway and CARM1 and Regulation of Estrogen Receptor, which can be related to the metastasis phase of breast cancer. These new pathways can be further explored to identify their relevance during the progression of the disease.
Quiescence of adult oligodendrocyte precursor cells requires thyroid hormone and hypoxia to activate Runx1
Authors: Tokumoto Yasuhito , Tamaki Shinpei , Kabe Yasuaki , Takubo Keiyo , Suematsu Makoto 
Published: April 2017

AbstractThe adult mammalian central nervous system (CNS) contains a population of slowly dividing oligodendrocyte precursor cells (OPCs), i.e., adult OPCs, which supply new oligodendrocytes throughout the life of animal. While adult OPCs develop from rapidly dividing perinatal OPCs, the mechanisms underlying their quiescence remain unknown. Here, we show that perinatal rodent OPCs cultured with thyroid hormone (TH) under hypoxia become quiescent and acquire adult OPCs-like characteristics. The cyclin-dependent kinase inhibitor p15/INK4b plays crucial roles in the TH-dependent cell cycle deceleration in OPCs under hypoxia. Klf9 is a direct target of TH-dependent signaling. Under hypoxic conditions, hypoxia-inducible factors mediates runt-related transcription factor 1 activity to induce G1 arrest in OPCs through enhancing TH-dependent p15/INK4b expression. As adult OPCs display phenotypes of adult somatic stem cells in the CNS, the current results shed light on environmental requirements for the quiescence of adult somatic stem cells during their development from actively proliferating stem/progenitor cells.
Psiguajadials A–K: Unusual Psidium Meroterpenoids as Phosphodiesterase-4 Inhibitors from the Leaves of Psidium guajava
Authors: Tang Gui-Hua , Dong Zhen , Guo Yan-Qiong , Cheng Zhong-Bin , Zhou Chu-Jun , Yin Sheng 
Published: April 2017

AbstractBioassay-guided fractionation of the ethanolic extract of the leaves of Psidium guajava led to the isolation of 11 new Psidium meroterpenoids, psiguajadials A–K (1–11), along with 17 known ones (12–28). Their structures and absolute configurations were elucidated by spectroscopic methods and comparison of experimental and calculated ECD. Compounds 1 and 2 represent two unprecedented skeletons of 3,5-diformyl-benzyl phloroglucinol-coupled sesquiterpenoid, while 3 is the first example of Psidium meroterpenoids coupling via an oxepane ring. Putative biosynthetic pathways towards 1 and 2 are proposed. Compounds 1–13 and 16–26 exhibited moderate inhibitory activities against phosphodiesterase-4 (PDE4), a drug target for asthma and chronic obstructive pulmonary disease, with IC50 values in the range of 1.34–7.26 μM.
Structural and functional analysis of lysozyme after treatment with dielectric barrier discharge plasma and atmospheric pressure plasma jet
Authors: Choi Sooho , Attri Pankaj , Lee Inhwan , Oh Jeongmin , Yun Ji-Hye , Park Ji Hoon , Choi Eun Ha , Lee Weontae 
Published: April 2017

AbstractThe variation in the biological function of proteins plays an important role in plasma medicine and sterilization. Several non-thermal plasma sources with different feeding gases are used worldwide for plasma treatment, including dielectric barrier discharge (DBD) and atmospheric-pressure plasma jet (APPJ) as the most commonly used sources. Therefore, in the present work, we used both DBD and APPJ plasma sources with N2 and air as feeding gases to evaluate the effects on the structural, thermodynamic, and activity changes of enzymes. In the current work, we used lysozyme as a model enzyme and verified the structural changes using circular dichroism (CD), fluorescence, and X-ray crystallography. In addition, we investigated the lysozyme thermodynamics using CD thermal analysis and changes in the B-factor from X-ray crystallography. The results showed that lysozyme activity decreased after the plasma treatment. From these analyses, we concluded that N2-feeding gas plasma disturbs the structure and activity of lysozyme more than Air feeding gas plasma in our experimental studies. This study provides novel fundamental information on the changes to enzymes upon plasma treatment, which has been absent from the literature until now.
Refractive index tomograms and dynamic membrane fluctuations of red blood cells from patients with diabetes mellitus
Authors: Lee SangYun , Park HyunJoo , Kim Kyoohyun , Sohn YongHak , Jang Seongsoo , Park YongKeun 
Published: April 2017

AbstractIn this paper, we present the optical characterisations of diabetic red blood cells (RBCs) in a non-invasive manner employing three-dimensional (3-D) quantitative phase imaging. By measuring 3-D refractive index tomograms and 2-D time-series phase images, the morphological (volume, surface area and sphericity), biochemical (haemoglobin concentration and content) and mechanical (membrane fluctuation) parameters were quantitatively retrieved at the individual cell level. With simultaneous measurements of individual cell properties, systematic correlative analyses on retrieved RBC parameters were also performed. Our measurements show there exist no statistically significant alterations in morphological and biochemical parameters of diabetic RBCs, compared to those of healthy (non-diabetic) RBCs. In contrast, membrane deformability of diabetic RBCs is significantly lower than that of healthy, non-diabetic RBCs. Interestingly, non-diabetic RBCs exhibit strong correlations between the elevated glycated haemoglobin in RBC cytoplasm and decreased cell deformability, whereas diabetic RBCs do not show correlations. Our observations strongly support the idea that slow and irreversible glycation of haemoglobin and membrane proteins of RBCs by hyperglycaemia significantly compromises RBC deformability in diabetic patients.
Chemical and Electrochemical Synthesis of Platinum Black
Authors: Stanca S. E. , Hänschke F. , Ihring A. , Zieger G. , Dellith J. , Kessler E. , Meyer H.-G. 
Published: April 2017

AbstractWe present electrochemical and chemical synthesis of platinum black at room temperature in aqueous and non-aqueous media. X-ray analysis established the purity and crystalline nature. The electron micrographs indicate that the nanostructures consist of platinum crystals that interconnect to form porous assemblies. Additionally, the electron micrographs of the platinum black thin layer, which was electrochemically deposited on different metallic and semiconductive substrates (aluminium, platinum, silver, gold, tin-cooper alloy, indium-tin-oxide, stainless steel, and copper), indicate that the substrate influences its porous features but not its absorbance characteristics. The platinum black exhibited a broad absorbance and low reflectance in the ultraviolet, visible, and infrared regions. These characteristics make this material suitable for use as a high-temperature resistant absorber layer for the fabrication of microelectronics.
Crispr/Cas9 Mediated Inactivation of Argonaute 2 Reveals its Differential Involvement in Antiviral Responses
Authors: Ludman Márta , Burgyán József , Fátyol Károly 
Published: April 2017

AbstractRNA silencing constitutes an important antiviral mechanism in plants. Small RNA guided Argonaute proteins fulfill essential role in this process by acting as executors of viral restriction. Plants encode multiple Argonaute proteins of which several exhibit antiviral activities. A recent addition to this group is AGO2. Its involvement in antiviral responses is established predominantly by studies employing mutants of Arabidopsis thaliana. In the virological model plant, Nicotiana benthamiana, the contribution of AGO2 to antiviral immunity is much less certain due to the lack of appropriate genetic mutants. Previous studies employed various RNAi based tools to down-regulate AGO2 expression. However, these techniques have several disadvantages, especially in the context of antiviral RNA silencing. Here, we have utilized the CRISPR/Cas9 technology to inactivate the AGO2 gene of N. benthamiana. The ago2 plants exhibit differential sensitivities towards various viruses. AGO2 is a critical component of the plants’ immune responses against PVX, TuMV and TCV. In contrast, AGO2 deficiency does not significantly influence the progression of tombusvirus and CMV infections. In summary, our work provides unequivocal proof for the virus-specific antiviral role of AGO2 in a plant species other than A. thaliana for the first time.
Nontrivial nonradiating all-dielectric anapole
Authors: Nemkov Nikita A. , Stenishchev Ivan V. , Basharin Alexey A. 
Published: April 2017

AbstractDynamic anapole is a promising element for future nonradiating devices, such as cloaked sources and sensors, quantum emitters, and especially the sources for observing dynamic Aharonov-Bohm effect. However, the anapole response can be damped by the Joule losses. In this paper we theoretically propose and experimentally demonstrate a novel type of active all-dielectric source, which is in some sense, realizes the elementary anapole of Afanasiev, and study its radiative/nonradiative regimes in the microwave range.
Optimization of amino acid replacement costs by mutational pressure in bacterial genomes
Authors: Błażej Paweł , Mackiewicz Dorota , Grabińska Małgorzata , Wnętrzak Małgorzata , Mackiewicz Paweł 
Published: April 2017

AbstractMutations are considered a spontaneous and random process, which is important component of evolution because it generates genetic variation. On the other hand, mutations are deleterious leading to non-functional genes and energetically costly repairs. Therefore, one can expect that the mutational pressure is optimized to simultaneously generate genetic diversity and preserve genetic information. To check if empirical mutational pressures are optimized in these ways, we compared matrices of nucleotide mutation rates derived from bacterial genomes with their best possible alternatives that minimized or maximized costs of amino acid replacements associated with differences in their physicochemical properties (e.g. hydropathy and polarity). It should be noted that the studied empirical nucleotide substitution matrices and the costs of amino acid replacements are independent because these matrices were derived from sites free of selection on amino acid properties and the amino acid costs assumed only amino acid physicochemical properties without any information about mutation at the nucleotide level. Obtained results indicate that the empirical mutational matrices show a tendency to minimize costs of amino acid replacements. It implies that bacterial mutational pressures can evolve to decrease consequences of amino acid substitutions. However, the optimization is not full, which enables generation of some genetic variability.
Role of the Ion Channel Extracellular Collar in AMPA Receptor Gating
Authors: Yelshanskaya Maria V. , Mesbahi-Vasey Samaneh , Kurnikova Maria G. , Sobolevsky Alexander I. 
Published: April 2017

AbstractAMPA subtype ionotropic glutamate receptors mediate fast excitatory neurotransmission and are implicated in numerous neurological diseases. Ionic currents through AMPA receptor channels can be allosterically regulated via different sites on the receptor protein. We used site-directed mutagenesis and patch-clamp recordings to probe the ion channel extracellular collar, the binding region for noncompetitive allosteric inhibitors. We found position and substitution-dependent effects for introduced mutations at this region on AMPA receptor gating. The results of mutagenesis suggested that the transmembrane domains M1, M3 and M4, which contribute to the ion channel extracellular collar, undergo significant relative displacement during gating. We used molecular dynamics simulations to predict an AMPA receptor open state structure and rationalize the results of mutagenesis. We conclude that the ion channel extracellular collar plays a distinct role in gating and represents a hub for powerful allosteric modulation of AMPA receptor function that can be used for developing novel therapeutics.