bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular heterogeneity in major urinary proteins of Mus musculus subspecies: potential candidates involved in speciation
Authors: Hurst Jane L. , Beynon Robert J. , Armstrong Stuart D. , Davidson Amanda J. , Roberts Sarah A. , Gómez-Baena Guadalupe , Smadja Carole M. , Ganem Guila 
Published: March 2017

AbstractWhen hybridisation carries a cost, natural selection is predicted to favour evolution of traits that allow assortative mating (reinforcement). Incipient speciation between the two European house mouse subspecies,Mus musculus domesticusandM.m.musculus, sharing a hybrid zone, provides an opportunity to understand evolution of assortative mating at a molecular level. Mouse urine odours allow subspecific mate discrimination, with assortative preferences evident in the hybrid zone but not in allopatry. Here we assess the potential of MUPs (major urinary proteins) as candidates for signal divergence by comparing MUP expression in urine samples from the Danish hybrid zone border (contact) and from allopatric populations. Mass spectrometric characterisation identified novel MUPs in both subspecies involving mostly new combinations of amino acid changes previously observed inM.m.domesticus. The subspecies expressed distinct MUP signatures, with most MUPs expressed by only one subspecies. Expression of at least eight MUPs showed significant subspecies divergence both in allopatry and contact zone. Another seven MUPs showed divergence in expression between the subspecies only in the contact zone, consistent with divergence by reinforcement. These proteins are candidates for the semiochemical barrier to hybridisation, providing an opportunity to characterise the nature and evolution of a putative species recognition signal.
Quantum Capacitance of a Topological Insulator-Ferromagnet Interface
Authors: Siu Zhuo Bin , Chowdhury Debashree , Jalil Mansoor B. A. , Basu Banasri 
Published: March 2017

AbstractWe study the quantum capacitance in a topological insulator thin film system magnetized in the in-plane direction in the presence of an out-of-plane magnetic field and hexagonal warping. To first order, the modification in quantum capacitance due to hexagonal warping compared to the clean case, where both the in-plane magnetization and hexagonal warping are absent, is always negative, and increases in magnitude monotonically with the energy difference from the charge neutrality point. In contrast, the change in the quantum capacitance due to in-plane magnetization oscillates with the energy in general, except when a certain relation between the inter-surface coupling, out of plane Zeeman energy splitting and magnetic field strength is satisfied. In this special case, the quantum capacitance remains unchanged by the in-plane magnetization for all energies.
Brilliant petawatt gamma-ray pulse generation in quantum electrodynamic laser-plasma interaction
Authors: Chang H. X. , Qiao B. , Huang T. W. , Xu Z. , Zhou C. T. , Gu Y. Q. , Yan X. Q. , Zepf M. , He X. T. 
Published: March 2017

AbstractWe show a new resonance acceleration scheme for generating ultradense relativistic electron bunches in helical motions and hence emitting brilliant vortical γ-ray pulses in the quantum electrodynamic (QED) regime of circularly-polarized (CP) laser-plasma interactions. Here the combined effects of the radiation reaction recoil force and the self-generated magnetic fields result in not only trapping of a great amount of electrons in laser-produced plasma channel, but also significant broadening of the resonance bandwidth between laser frequency and that of electron betatron oscillation in the channel, which eventually leads to formation of the ultradense electron bunch under resonant helical motion in CP laser fields. Three-dimensional PIC simulations show that a brilliant γ-ray pulse with unprecedented power of 6.7 PW and peak brightness of 1025 photons/s/mm2 /mrad2 /0.1% BW (at 15 MeV) is emitted at laser intensity of 1.9 × 1023 W/cm2.
Effect of prolonged freezing of semen on exosome recovery and biologic activity
Authors: Welch Jennifer L. , Madison Marisa N. , Margolick Joseph B. , Galvin Shannon , Gupta Phalguni , Martínez-Maza Otoniel , Dash Chandravanu , Okeoma Chioma M. 
Published: March 2017

AbstractExosomes are important vehicles of intercellular communication that shape host responses to physiologic, tumorigenic, and pathogenic conditions. The composition and function of exosomes are dynamic and depends on the state and condition of the cellular source. In prior work, we found that semen exosomes (SE) from healthy donors who do not use illicit drugs potently inhibit HIV-1. Following semen donation, specimens are either used immediately or frozen for use at a later time. It has been shown that short-term freezing of semen has no effect on SE-mediated HIV-1 inhibition. However, the effect of illicit drugs and prolonged freezing on SE bioactivity is unknown. Here, we show preservation of SE physical properties, (morphology, concentration, intensity/size) irrespective of illicit drug use or duration of semen freezing. Interestingly, illicit drugs and prolonged freezing decreased the levels of SE-bound CD63/CD9 and acetylcholinesterase activity respectively. Furthermore, we show differential effects of illicit drug use and prolonged freezing on SE-mediated HIV-1 inhibition. Our results highlight the importance of the source of SE and condition of semen storage on SE content and function. In-depth evaluation of donor drug-use and duration of semen storage on SE cargo and bioactivity will advance our understanding of SE composition and function.
Superposition-free comparison and clustering of antibody binding sites: implications for the prediction of the nature of their antigen
Authors: Di Rienzo Lorenzo , Milanetti Edoardo , Lepore Rosalba , Olimpieri Pier Paolo , Tramontano Anna 
Published: March 2017

AbstractWe describe here a superposition free method for comparing the surfaces of antibody binding sites based on the Zernike moments and show that they can be used to quickly compare and cluster sets of antibodies. The clusters provide information about the nature of the bound antigen that, when combined with a method for predicting the number of direct antibody antigen contacts, allows the discrimination between protein and non-protein binding antibodies with an accuracy of 76%. This is of relevance in several aspects of antibody science, for example to select the framework to be used for a combinatorial antibody library.
Solitary perturbations in the steep boundary of magnetized toroidal plasma
Authors: Lee J. E. , Yun G. S. , Lee W. , Kim M. H. , Choi M. , Lee J. , Kim M. , Park H. K. , Bak J. G. , Ko W. H. , Park Y. S. 
Published: March 2017

AbstractSolitary perturbations (SPs) localized both poloidally and radially are detected within ~100 μs before the partial collapse of the high pressure gradient boundary region (called pedestal) of magnetized toroidal plasma in the KSTAR tokamak device. The SP develops with a low toroidal mode number (typically unity) in the pedestal ingrained with quasi-stable edge-localized mode (QSM) which commonly appears during the inter-collapse period. The SPs have smaller mode pitch and different (often opposite) rotation velocity compared to the QSMs. Similar solitary perturbations are also frequently observed before the onset of complete pedestal collapse, suggesting a strong connection between the SP generation and the pedestal collapse.
A role of the SAM domain in EphA2 receptor activation
Authors: Shi Xiaojun , Hapiak Vera , Zheng Ji , Muller-Greven Jeannine , Bowman Deanna , Lingerak Ryan , Buck Matthias , Wang Bing-Cheng , Smith Adam W. 
Published: March 2017

AbstractAmong the 20 subfamilies of protein receptor tyrosine kinases (RTKs), Eph receptors are unique in possessing a sterile alpha motif (SAM domain) at their C-terminal ends. However, the functions of SAM domains in Eph receptors remain elusive. Here we report on a combined cell biology and quantitative fluorescence study to investigate the role of the SAM domain in EphA2 function. We observed elevated tyrosine autophosphorylation levels upon deletion of the EphA2 SAM domain (EphA2ΔS) in DU145 and PC3 prostate cancer cells and a skin tumor cell line derived from EphA1/A2 knockout mice. These results suggest that SAM domain deletion induced constitutive activation of EphA2 kinase activity. In order to explain these effects, we applied fluorescence correlation spectroscopy to investigate the lateral molecular organization of EphA2. Our results indicate that SAM domain deletion (EphA2ΔS-GFP) increases oligomerization compared to the full length receptor (EphA2FL-GFP). Stimulation with ephrinA1, a ligand for EphA2, induced further oligomerization and activation of EphA2FL-GFP. The SAM domain deletion mutant, EphA2ΔS-GFP, also underwent further oligomerization upon ephrinA1 stimulation, but the oligomers were larger than those observed for EphA2FL-GFP. Based on these results, we conclude that the EphA2 SAM domain inhibits kinase activity by reducing receptor oligomerization.
Alizarin Red S for Online Pyrophosphate Detection Identified by a Rapid Screening Method
Authors: Fischbach Jens , Loh Qiuting , Bier Frank F. , Lim Theam Soon , Frohme Marcus , Glökler Jörn 
Published: March 2017

AbstractWe identified Alizarin Red S and other well known fluorescent dyes useful for the online detection of pyrophosphate in enzymatic assays, including the loop mediated isothermal amplification (LAMP) and polymerase chain reaction (PCR) assays. An iterative screening was used for a selected set of compounds to first secure enzyme compatibility, evaluate inorganic pyrophosphate sensitivity in the presence of manganese as quencher and optimize conditions for an online detection. Of the selected dyes, the inexpensive alizarin red S was found to selectively detect pyrophosphate under LAMP and PCR conditions and is superior with respect to its defined red-shifted spectrum, long shelf life and low toxicity. In addition, the newly identified properties may also be useful in other enzymatic assays which do not generate nucleic acids but are based on inorganic pyrophosphate. Finally, we propose that our screening method may provide a blueprint for rapid screening of compounds for detecting inorganic pyrophosphate.
Isolation and characterization of the E. coli membrane protein production strain Mutant56(DE3)
Authors: Baumgarten Thomas , Schlegel Susan , Wagner Samuel , Löw Mirjam , Eriksson Jonas , Bonde Ida , Herrgård Markus J. , Heipieper Hermann J. , Nørholm Morten H. H. , Slotboom Dirk Jan , de Gier Jan-Willem 
Published: March 2017

AbstractMembrane protein production is usually toxic to E. coli. However, using genetic screens strains can be isolated in which the toxicity of membrane protein production is reduced, thereby improving production yields. Best known examples are the C41(DE3) and C43(DE3) strains, which are both derived from the T7 RNA polymerase (P)-based BL21(DE3) protein production strain. In C41(DE3) and C43(DE3) mutations lowering t7rnap expression levels result in strongly reduced T7 RNAP accumulation levels. As a consequence membrane protein production stress is alleviated in the C41(DE3) and C43(DE3) strains, thereby increasing membrane protein yields. Here, we isolated Mutant56(DE3) from BL21(DE3) using a genetic screen designed to isolate BL21(DE3)-derived strains with mutations alleviating membrane protein production stress other than the ones in C41(DE3) and C43(DE3). The defining mutation of Mutant56(DE3) changes one amino acid in its T7 RNAP, which weakens the binding of the T7 RNAP to the T7 promoter governing target gene expression rather than lowering T7 RNAP levels. For most membrane proteins tested yields in Mutant56(DE3) were considerably higher than in C41(DE3) and C43(DE3). Thus, the isolation of Mutant56(DE3) shows that the evolution of BL21(DE3) can be promoted towards further enhanced membrane protein production.
Absence of a gestational diabetes phenotype in the LepRdb/+ mouse is independent of control strain, diet, misty allele, or parity
Authors: Plows Jasmine F. , Yu XinYang , Broadhurst Ric , Vickers Mark H. , Tong Chao , Zhang Hua , Qi HongBo , Stanley Joanna L. , Baker Philip N. 
Published: March 2017

AbstractTreatment options for gestational diabetes (GDM) are limited. In order to better understand mechanisms and improve treatments, appropriate animal models of GDM are crucial. Heterozygous db mice (db/+) present with glucose intolerance, insulin resistance, and increased weight gain during, but not prior to, pregnancy. This makes them an ideal model for GDM. However, several recent studies have reported an absence of GDM phenotype in their colony. We investigated several hypotheses for why the phenotype may be absent, with the aim of re-establishing it and preventing further resources being wasted on an ineffective model. Experiments were carried out across two laboratories in two countries (New Zealand and China), and were designed to assess type of control strain, diet, presence of the misty allele, and parity as potential contributors to the lost phenotype. While hyperleptinemia and pre-pregnancy weight gain were present in all db/+mice across the four studies, we found no consistent evidence of glucose intolerance or insulin resistance during pregnancy. In conclusion, we were unable to acquire the GDM phenotype in any of our experiments, and we recommend researchers do not use the db/+ mouse as a model of GDM unless they are certain the phenotype remains in their colony.
Effect of decomposition and organic residues on resistivity of copper films fabricated via low-temperature sintering of complex particle mixed dispersions
Authors: Yong Yingqiong , Nguyen Mai Thanh , Tsukamoto Hiroki , Matsubara Masaki , Liao Ying-Chih , Yonezawa Tetsu 
Published: March 2017

AbstractMixtures of a copper complex and copper fine particles as copper-based metal-organic decomposition (MOD) dispersions have been demonstrated to be effective for low-temperature sintering of conductive copper film. However, the copper particle size effect on decomposition process of the dispersion during heating and the effect of organic residues on the resistivity have not been studied. In this study, the decomposition process of dispersions containing mixtures of a copper complex and copper particles with various sizes was studied. The effect of organic residues on the resistivity was also studied using thermogravimetric analysis. In addition, the choice of copper salts in the copper complex was also discussed. In this work, a low-resistivity sintered copper film (7 × 10−6 Ω·m) at a temperature as low as 100 °C was achieved without using any reductive gas.
Simultaneously measuring multiple protein interactions and their correlations in a cell by Protein-interactome Footprinting
Authors: Luo Si-Wei , Liang Zhi , Wu Jia-Rui 
Published: March 2017

AbstractQuantitatively detecting correlations of multiple protein-protein interactions (PPIs) in vivo is a big challenge. Here we introduce a novel method, termed Protein-interactome Footprinting (PiF), to simultaneously measure multiple PPIs in one cell. The principle of PiF is that each target physical PPI in the interactome is simultaneously transcoded into a specific DNA sequence based on dimerization of the target proteins fused with DNA-binding domains. The interaction intensity of each target protein is quantified as the copy number of the specific DNA sequences bound by each fusion protein dimers. Using PiF, we quantitatively reveal dynamic patterns of PPIs and their correlation network in E. coli two-component systems.
Configurational Molecular Glue: One Optically Active Polymer Attracts Two Oppositely Configured Optically Active Polymers
Authors: Tsuji Hideto , Noda Soma , Kimura Takayuki , Sobue Tadashi , Arakawa Yuki 
Published: March 2017

AbstractD-configured poly(D-lactic acid) (D-PLA) and poly(D-2-hydroxy-3-methylbutanoic acid) (D-P2H3MB) crystallized separately into their homo-crystallites when crystallized by precipitation or solvent evaporation, whereas incorporation of L-configured poly(L-2-hydroxybutanoic acid) (L-P2HB) in D-configured D-PLA and D-P2H3MB induced co-crystallization or ternary stereocomplex formation between D-configured D-PLA and D-P2H3MB and L-configured L-P2HB. However, incorporation of D-configured poly(D-2-hydroxybutanoic acid) (D-P2HB) in D-configured D-PLA and D-P2H3MB did not cause co-crystallization between D-configured D-PLA and D-P2H3MB and D-configured D-P2HB but separate crystallization of each polymer occurred. These findings strongly suggest that an optically active polymer (L-configured or D-configured polymer) like unsubstituted or substituted optically active poly(lactic acid)s can act as “a configurational or helical molecular glue” for two oppositely configured optically active polymers (two D-configured polymers or two L-configured polymers) to allow their co-crystallization. The increased degree of freedom in polymer combination is expected to assist to pave the way for designing polymeric composites having a wide variety of physical properties, biodegradation rate and behavior in the case of biodegradable polymers.
Strong coupling of diffraction coupled plasmons and optical waveguide modes in gold stripe-dielectric nanostructures at telecom wavelengths
Authors: Thomas Philip A. , Auton Gregory H. , Kundys Dmytro , Grigorenko Alexander N. , Kravets Vasyl G. 
Published: March 2017

AbstractWe propose a hybrid plasmonic device consisting of a planar dielectric waveguide covering a gold nanostripe array fabricated on a gold film and investigate its guiding properties at telecom wavelengths. The fundamental modes of a hybrid device and their dependence on the key geometric parameters are studied. A communication length of 250 μm was achieved for both the TM and TE guided modes at telecom wavelengths. Due to the difference between the TM and TE light propagation associated with the diffractive plasmon excitation, our waveguides provide polarization separation. Our results suggest a practical way of fabricating metal-nanostripes-dielectric waveguides that can be used as essential elements in optoelectronic circuits.
Identification of cardiac hemo-vascular precursors and their requirement of sphingosine-1-phosphate receptor 1 for heart development
Authors: Hu Yan , Belyea Brian C. , Li Minghong , Göthert Joachim R. , Gomez R. Ariel , Sequeira-Lopez Maria Luisa S. 
Published: March 2017

AbstractThe cardiac endothelium plays a crucial role in the development of a functional heart. However, the precise identification of the endocardial precursors and the mechanisms they require for their role in heart morphogenesis are not well understood. Using in vivo and in vitro cell fate tracing concomitant with specific cell ablation and embryonic heart transplantation studies, we identified a unique set of precursors which possess hemogenic functions and express the stem cell leukemia (SCL) gene driven by its 5′ enhancer. These hemo-vascular precursors give rise to the endocardium, atrioventricular cushions and coronary vascular endothelium. Furthermore, deletion of the sphingosine-1-phosphate receptor 1 (S1P1) in these precursors leads to ventricular non-compaction cardiomyopathy, a poorly understood condition leading to heart failure and early mortality. Thus, we identified a distinctive population of hemo-vascular precursors which require S1P1 to exert their functions and are essential for cardiac morphogenesis.
Hyperspectral imaging using the single-pixel Fourier transform technique
Authors: Jin Senlin , Hui Wangwei , Wang Yunlong , Huang Kaicheng , Shi Qiushuai , Ying Cuifeng , Liu Dongqi , Ye Qing , Zhou Wenyuan , Tian Jianguo 
Published: March 2017

AbstractHyperspectral imaging technology is playing an increasingly important role in the fields of food analysis, medicine and biotechnology. To improve the speed of operation and increase the light throughput in a compact equipment structure, a Fourier transform hyperspectral imaging system based on a single-pixel technique is proposed in this study. Compared with current imaging spectrometry approaches, the proposed system has a wider spectral range (400–1100 nm), a better spectral resolution (1 nm) and requires fewer measurement data (a sample rate of 6.25%). The performance of this system was verified by its application to the non-destructive testing of potatoes.
First order reversal curves and intrinsic parameter determination for magnetic materials; limitations of hysteron-based approaches in correlated systems
Authors: Ruta Sergiu , Hovorka Ondrej , Huang Pin-Wei , Wang Kangkang , Ju Ganping , Chantrell Roy 
Published: March 2017

AbstractThe generic problem of extracting information on intrinsic particle properties from the whole class of interacting magnetic fine particle systems is a long standing and difficult inverse problem. As an example, the Switching Field Distribution (SFD) is an important quantity in the characterization of magnetic systems, and its determination in many technological applications, such as recording media, is especially challenging. Techniques such as the first order reversal curve (FORC) methods, were developed to extract the SFD from macroscopic measurements. However, all methods rely on separating the contributions to the measurements of the intrinsic SFD and the extrinsic effects of magnetostatic and exchange interactions. We investigate the underlying physics of the FORC method by applying it to the output predictions of a kinetic Monte-Carlo model with known input parameters. We show that the FORC method is valid only in cases of weak spatial correlation of the magnetisation and suggest a more general approach.
Veratridine produces distinct calcium response profiles in mouse Dorsal Root Ganglia neurons
Authors: Mohammed Zainab A. , Doran Ciara , Grundy David , Nassar Mohammed A. 
Published: March 2017

AbstractNociceptors are a subpopulation of dorsal root ganglia (DRG) neurons that detect noxious stimuli and signal pain. Veratridine (VTD) is a voltage-gated sodium channel (VGSC) modifier that is used as an “agonist” in functional screens for VGSC blockers. However, there is very little information on VTD response profiles in DRG neurons and how they relate to neuronal subtypes. Here we characterised VTD-induced calcium responses in cultured mouse DRG neurons. Our data shows that the heterogeneity of VTD responses reflects distinct subpopulations of sensory neurons. About 70% of DRG neurons respond to 30–100 μM VTD. We classified VTD responses into four profiles based upon their response shape. VTD response profiles differed in their frequency of occurrence and correlated with neuronal size. Furthermore, VTD response profiles correlated with responses to the algesic markers capsaicin, AITC and α, β-methylene ATP. Since VTD response profiles integrate the action of several classes of ion channels and exchangers, they could act as functional “reporters” for the constellation of ion channels/exchangers expressed in each sensory neuron. Therefore our findings are relevant to studies and screens using VTD to activate DRG neurons.