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Antigen epitope identification is a critical step in the vaccine development process and is a momentous cornerstone for the development of safe and efficient epitope vaccines. In particular, vaccine design is difficult when the function of the protein encoded by the pathogen is unknown. The genome of Tilapia lake virus (TiLV), an emerging virus from fish, encodes protein functions that have not been elucidated, resulting in a lag and uncertainty in vaccine development. Here, we propose a feasible strategy for emerging viral disease epitope vaccine development using TiLV. We determined the targets of specific antibodies in serum from a TiLV survivor by panning a Ph.D.-12 phage library, and we identified a mimotope, TYTTRMHITLPI, referred to as Pep3, which provided protection against TiLV after prime-boost vaccination; its immune protection rate was 57.6%. Based on amino acid sequence alignment and structure analysis of the target protein from TiLV, we further identified a protective antigenic site (399TYTTRNEDFLPT410) which is located on TiLV segment 1 (S1). The epitope vaccine with keyhole limpet hemocyanin (KLH-S1399-410) corresponding to the mimotope induced the tilapia to produce a durable and effective antibody response after immunization, and the antibody depletion test confirmed that the specific antibody against S1399-410 was necessary to neutralize TiLV. Surprisingly, the challenge studies in tilapia demonstrated that the epitope vaccine elicited a robust protective response against TiLV challenge, and the survival rate reached 81.8%. In conclusion, this study revealed a concept for screening antigen epitopes of emerging viral diseases, providing promising approaches for development and evaluation of protective epitope vaccines against viral diseases. IMPORTANCE Antigen epitope determination is an important cornerstone for developing efficient vaccines. In this study, we attempted to explore a novel approach for epitope discovery of TiLV, which is a new virus in fish. We investigated the immunogenicity and protective efficacy of all antigenic sites (mimotopes) identified in serum of primary TiLV survivors by using a Ph.D.-12 phage library. We also recognized and identified the natural epitope of TiLV by bioinformatics, evaluated the immunogenicity and protective effect of this antigenic site by immunization, and revealed 2 amino acid residues that play important roles in this epitope. Both Pep3 and S1399-410 (a natural epitope identified by Pep3) elicited antibody titers in tilapia, but S1399-410 was more prominent. Antibody depletion studies showed that anti-S1399-410-specific antibodies were essential for neutralizing TiLV. Our study demonstrated a model for combining experimental and computational screens to identify antigen epitopes, which is attractive for epitope-based vaccine development. [ABSTRACT FROM AUTHOR]

Consider Dirichlet problems of Laplace's equation in a bounded simply‐connected domain S$$ S $$, and use the null field equation (NFE) of Green's representation formulation, where the source nodes Q$$ Q $$ are located on a pseudo‐boundary ΓR$$ {\Gamma}_R $$ outside S$$ S $$ but not close to its boundary Γ(=∂S)$$ \Gamma \kern0.3em \left(=\partial S\right) $$. Simple algorithms are proposed in this article by using the central rule for the NFE, and the normal derivatives uν$$ {u}_{\nu } $$ of the solutions on the boundary Γ(=∂S)$$ \Gamma \kern0.3em \left(=\partial S\right) $$ can be easily obtained. These algorithms are called the discrete null field equation method (DNFEM) because the collocation equations are, indeed, the direct discrete form of the NFE. The bounds of the condition number are like those by the method of fundamental solutions (MFS) yielding the exponential growth as the number of unknowns increases. One trouble of the DNFEM is the near singularity of integrations for the solutions in boundary layers in Green's representation formulation. The traditional BEM also suffers from the same trouble. To deal with the near singularity, quadrature by expansions and the sinh transformation are often used. To handle this trouble, however, we develop two kinds of new techniques: (I) the interpolation techniques by Taylor's formulas with piecewise q$$ q $$‐degree polynomials and the Fourier series, and (II) the mini‐rules of integrals, such as the mini‐Simpson's and the mini‐Gaussian rules. Error analysis is made for technique I to achieve optimal convergence rates. Numerical experiments are carried out for disk domains to support the theoretical analysis made. The numerical performance of the DNFEM is excellent for disk domains to compete with the MFS. The errors with O(10−4)$$ O\left(1{0}^{-4}\right) $$ can be obtained by combination algorithms, which are satisfactory for most engineering problems. In summary, the new simple DNFEM is based on the NFE, which is different from the boundary element method (BEM). The theoretical basis in error and stability has been established in this article. One trouble in seeking the numerical solutions in boundary layers has been handled well; this is also an important contribution to the BEM. Besides, numerical experiments are encouraging. Hence the DNFEM is promising, and it may become a new boundary method for scientific/engineering computing. [ABSTRACT FROM AUTHOR]

The free-surface flows with particles are widely found in chemical engineering, and numerical modeling is a strong computing tool for in-depth understanding of the local and macrocharacteristics. In this study, a discrete element method-volume-of-fluid (DEM-VOF) model is extended to turbulent free-surface flows with particles, by means of Reynolds stress model. Also, we adopt a novel virtual dual-grid porosity model to calculate the fluid porosity. The simulated results of single particle sedimentation, the falling of sinking particles, and the floating of buoyant particles agree well to analytical and literatures, which validate the proposed DEM-VOF model. Furthermore, the DEM-VOF model developed in this paper is applied to the simulation of free surface flow with particles in solid-liquid mixing system for the first time. It is found that elliptical-head vessel is preferred to a flat-bottomed vessel for solid-liquid mixing by comparing the simulation results of four different stirred tanks, which agrees well to the related content of the book Handbook of Industrial Mixing (Paul, E. L.; Atiemo-Obeng, V. A.; Kresta, S. M. Eds.; John Wiley & Sons, 2004). [ABSTRACT FROM AUTHOR]

The method of fundamental solutions (MFS) was first used by Kupradze in 1963 [21] . Since then, there have appeared numerous reports of the MFS. Most of the existing analysis for the MFS are confined to Dirichlet problems on disk domains. It seems to exist no analysis for Neumann problems. This paper is devoted to Neumann problems in non-disk domains, and the new stability analysis and the error analysis are made. The bounds for both condition numbers and errors are derived in detail. The optimal convergence rates in L 2 and H 1 norms in S are achieved, and the condition number grows exponentially as the number of fundamental functions increases. To reduce the huge condition numbers, the truncated singular value decomposition (TSVD) may be solicited. Numerical experiments are provided to support the analysis made. The analysis for Neumann problems in this paper is intriguing due to its distinct features. [ABSTRACT FROM AUTHOR]

Objective: The purpose of this study was to evaluate the frequency of RASSF1A hypermethylation in patients with acute myeloid leukemia (AML), in an attempt to modify the current molecular model for disease prognosis. Materials and methods: Aberrant RASSF1A promoter methylation levels were assessed in 226 newly diagnosed non-M3 AML patients and 30 apparently healthy controls, by quantitative methylation-specific polymerase chain reaction. Meanwhile, RASSF1A mRNA levels were detected by real-time quantitative polymerase chain reaction. Furthermore, hematological characteristics, cytogenetic abnormalities, and genetic aberrations were assessed. Finally, associations of RASSF1A hypermethylation with clinical outcomes were evaluated. Results: RASSF1A hypermethylation was observed in 23.0% of patients with non-M3 AML (52/226), but not in controls. Meanwhile, hypermethylation of the RASSF1A promoter was significantly associated with ASXL1 mutation. Furthermore, the log-rank test revealed that RASSF1A hypermethylation indicated decreased relapse-free survival (RFS) and overall survival (OS) in patients with non-M3 AML (P=0.012 and P=0.014, respectively). In multivariate analysis, RASSF1A hypermethylation was an independent prognostic factor for RFS (P=0.040), but not for OS (P=0.060). Conclusion: Hypermethylation of the RASSF1A promoter is associated with ASXL1 mutation in non-M3 AML patients, likely indicating poor outcome. These findings provide a molecular basis for stratified diagnosis and prognostic evaluation. [ABSTRACT FROM AUTHOR]

By driving a 3D transmon with microwave fields, we generate an effective avoided energy-level crossing. Then we chirpmicrowave frequency, which is equivalent to driving the system through the avoided energy-level crossing by sweeping the avoided crossing. A double-passage chirp produces Landau-Zener-Stückelberg-Majorana (LZSM) interference that agree well with the numerical results, especially with the initial state being an eigen-energy state in the center of an avoided level crossing. A time-resolved state tomography measurement is performed in the evolution of LZSM interference, showing an experimental evidence for the dynamical evolution of quantum state. Our method is fully applicable to other quantum systems that contain no intrinsic avoided level crossing, providing an alternative approach for quantum control and quantum simulation. [ABSTRACT FROM AUTHOR]

The biexciton cascade process in self-assembled quantum dots (QDs) provides an ideal system for realizing deterministic entangled photon-pair sources, which are essential to quantum information science. The entangled photon pairs have recently been generated in experiments after eliminating the fine-structure splitting (FSS) of excitons using a number of different methods. Thus far, however, QD-based sources of entangled photons have not been scalable because the wavelengths of QDs differ from dot to dot. Here, we propose a wavelength-tunable entangled photon emitter mounted on a three-dimensional stressor, in which the FSS and exciton energy can be tuned independently, thereby enabling photon entanglement between dissimilar QDs. We confirm these results via atomistic pseudopotential calculations. This provides a first step towards future realization of scalable entangled photon generators for quantum information applications. [ABSTRACT FROM AUTHOR]

Cryogenic autolysis is a typical phenomenon of abnormal metabolism in Volvariella volvacea. Recent studies have identified 20 significantly upregulated genes via high-throughput sequencing of the mRNAs expressed in the mycelia of V. volvacea after cold exposure. Among these significantly upregulated genes, 15 annotated genes were used for functional annotation cluster analysis. Our results showed that the cyclin-like F-box domain (FBDC) formed the functional cluster with the lowest P-value. We also observed a significant expansion of FBDC families in V. volvacea. Among these, the FBDC3 family displayed the maximal gene expansion in V. volvacea. Gene expression profiling analysis revealed only one FBDC gene in V. volvacea (FBDV1) that was significantly up-regulated, which is located in the FBDC3 family. Comparative genomics analysis revealed the homologous sequences of FBDV1 with high similarity were clustered on the same scaffold. However, FBDV1 was located far from these clusters, indicating the divergence of duplicated genes. Relative time estimation and rate test provided evidence for the divergence of FBDV1 after recent duplications. Real-time RT-PCR analysis confirmed that the expression of the FBDV1 was significantly up-regulated (P, 0.001) after cold-treatment of V. volvacea for 4 h. These observations suggest that the FBDV1 is involved in the cryogenic autolysis of V. volvacea. [ABSTRACT FROM AUTHOR]

The influence of coupling to the fluid field is neglected in the classic fluid mechanics theory. United Lagrangian-Eulerian method is used to solve the fluid-structure interaction (FSI) problem of the nonviscous and incompressible fluid flow around an elastic box plate taking into account the influence of deformation of the elastic plate. In this approach, each material is described in its preferred reference frame. Fluid flows are given in Eulerian coordinates whereas the elastic body is treated in a Lagrangian framework. The coupling between the fluid and elastic body domains is kinematic and dynamic conditions at the body surface. The kinematic and dynamic conditions are given in Eulerian and Lagrangian coordinates. The dynamic equation of the elastic box plate is expressed combining the dynamic conditions at the interface. The knowledge of both dynamic and static deformations, static pressure and velocity distributions is given by using the Taylor expansions method. The effect of plate deformation is taken into account for the obtained solutions. [ABSTRACT FROM AUTHOR]

Hydrogen evolution reaction (HER) from water through electrocatalysis using cost-effective materials to replace precious Pt catalysts holds great promise for clean energy technologies. In this work we developed a highly active and stable catalyst containing Co doped earth abundant iron pyrite FeS2 nanosheets hybridized with carbon nanotubes (Fe1-xCoxS2/CNT hybrid catalysts) for HER in acidic solutions. The pyrite phase of Fe1-xCoxS2/CNT was characterized by powder X-ray diffraction and absorption spectroscopy. Electrochemical measurements showed a low overpotential of ~0.12 V at 20 mA/cm², small Tafel slope of ~46 mV/decade, and long-term durability over 40 h of HER operation using bulk quantities of Fe0.9Co0.1S29/CNT hybrid catalysts at high loadings (~7 mg/cm²). Density functional theory calculation revealed that the origin of high catalytic activity stemmed from a large reduction of the kinetic energy barrier of H atom adsorption on FeS2 surface upon Co doping in the iron pyrite structure. It is also found that the high HER catalytic activity of Fe0.9Co0.1S2 hinges on the hybridization with CNTs to impart strong heteroatomic interactions between CNT and Fe0.9Co0.1S2. This work produces the most active HER catalyst based on iron pyrite, suggesting a scalable, low cost, and highly efficient catalyst for hydrogen generation. [ABSTRACT FROM AUTHOR]

We report the observation of quantum stochastic synchronization (QSS) in a dissipative quantum system-a moderately damped current-biased Josephson junction. We show that when the junction is biased subcritically by a combination of a constant current and a small sinusoidal modulation signal, forced phase synchronization between the otherwise random, incoherent quantum tunneling and the signal may arise as a consequence of the interplay between quantum fluctuation and the weak periodic drive. It is found that optimal synchronization occurs at a signal frequency fQSS that is comparable to the quantum tunneling rate. We also find a phenomenon called "modulation induced suppression of quantum noise": for signal frequency well below fQSS, the power spectral density of escape time distribution of the junction could be reduced substantially from the floor level of the unmodulated system. Furthermore, we demonstrate that the application of a small signal with proper phase can suppress the average tunneling rate and enhance the stability of the metastable system. Our experimental results agree well with the numerical calculations without the use of adjustable parameters. [ABSTRACT FROM AUTHOR]

We show that the combination of spin-orbit coupling and in-plane Zeeman field in a two-dimensional degenerate Fermi gas can lead to a larger parameter region for Fulbe-Ferrell-Larkin-Ovchinnikov (FFLO) phases than that using spin-imbalanced Fermi gases. The resulting FFLO superfluids are also more stable due to the enhanced energy difference between FFLO and conventional Bardeen-Cooper-Schrieffer (BCS) excited states. We clarify the crucial role of the symmetry of Fermi surface on the formation of finite momentum pairing. The phase diagram for FFLO superfluids is obtained in the BCS-BEC crossover region and possible experimental observations of FFLO phases are discussed. [ABSTRACT FROM AUTHOR]

Consider the method of fundamental solutions (MFS) for 2D Laplace's equation in a bounded simply connected domain S$$ S $$. In the standard MFS, the source nodes are located on a closed contour outside the domain boundary Γ(=∂S)$$ \Gamma \left(=\partial S\right) $$, which is called pseudo‐boundary. For circular, elliptic, and general closed pseudo‐boundaries, analysis and computation have been studied extensively. New locations of source nodes are proposed along two pseudo radial‐lines outside Γ$$ \Gamma $$. Numerical results are very encouraging and promising. Since the success of the MFS mainly depends on stability, our efforts are focused on deriving the lower and upper bounds of condition number (Cond). The study finds stability properties of new Vandermonde‐wise matrices on nodes xi∈[a,b]$$ {x}_i\in \left[a,b\right] $$ with 0

Pseudo- or secondary achalasia may mimic primary achalasia upon radiological examination and may be difficult to diagnose. It is usually due to a cancer or metastases involving the gastroesophageal junction. We present the case of a 53-year-old woman with recent onset of dysphagia, and with typical findings suggesting primary achalasia. We found a 4-cm mediastinal tumor invading the lower esophagus, which was proven to be a metastasis from a lung carcinoma. The patient was treated with surgery, chemotherapy and radiotherapy. In patients with a new onset of achalasia symptoms, keeping in mind the possibility of an underlying cancer is important. [ABSTRACT FROM AUTHOR]

We develop an effective model to describe the statistical properties of exciton fine structure splitting (FSS) and polarization angle in quantum dot ensembles (QDEs) using only a few symmetry-related parameters. The connection between the effective model and the random matrix theory is established. Such effective model is verified both theoretically and experimentally using several rather different types of QDEs, each of which contains hundreds to thousands of QDs. The model naturally addresses three fundamental issues regarding the FSS and polarization angels of QDEs, which are frequently encountered in both theories and experiments. The answers to these fundamental questions yield an approach to characterize the optical properties of QDEs. Potential applications of the effective model are also discussed. [ABSTRACT FROM AUTHOR]

The realizations of spin-orbit coupling in cold atoms lead to a burst of research activities in the searching of topological matters in ultracold atom systems. Recent theoretical predictions show that topological Fulde- Ferrell-Larkin-Ovchinnikov (FFLO) superfluids can be realized with appropriate spin-orbit coupling and in-plane Zeeman fields. In this work, a comprehensive understanding of the pairing symmetry, phase diagram, and the edge modes in this topological matter are presented. The center of mass momentum of the Cooper pairs plays the role of renormalizing the in-plane Zeeman fields and chemical potential. The in-plane Zeeman fields also induce asymmetry to the effective p-wave pairing, apart from a small fraction of higher orbital components. As a result, the phase diagram is composed by different phases, which are determined by the Fermi surface topology and band gap width of the superfluids. Especially, the gapped and gapless topological FFLO phases have totally different finite size effects. These features show that the spin orbit coupled cold atoms provide an important platform in realizing topological matters which may not be materialized with solids. [ABSTRACT FROM AUTHOR]

DiGeorge syndrome critical region gene 8 (DGCR8) is the RNAbinding partner protein of the nuclease Drosha. DGCR8 and Drosha recognize and cleave primary transcripts of microRNAs (pri-miRNAs) in the maturation of canonical microRNAs (miRNAs) in animals. We previously reported that human, frog, and starfish DGCR8 bind heme when expressed in Escherichia coli and that Fe (III) heme activates apoDGCR8 in reconstituted pri-miRNA processing assays. However, the physiological relevance of heme in miRNA maturation has not been clear. Here, we present a live-cell pri-miRNA processing assay that produces robust signals and faithfully indicates DGCR8 and Drosha activities. We demonstrate that all known heme-binding-deficient DGCR8 mutants are defective in pri-miRNA processing in HeLa cells. DGCR8 contains a previously uncharacterized heme-binding motif, "IPCL," that is also required for its activity. Heme availability and biosynthesis in HeLa cells positively affect primiRNA processing and production of mature miRNA. These results establish an essential function for heme in pri-miRNA processing in mammalian cells. Our study suggests that abnormal heme biosynthesis and degradation may contribute to diseases via miRNAmediated gene regulation networks. [ABSTRACT FROM AUTHOR]

Silicon's sensitivity to corrosion has hindered its use in photoanode applications. We found that deposition of a ~2-nanometer nickel film on n-type silicon (n-Si) with its native oxide affords a high-performance metal-insulator-semiconductor photoanode for photoelectrochemical (PEC) water oxidation in both aqueous potassium hydroxide (KOH, pH = 14) and aqueous borate buffer (pH = 9.5) solutions. The Ni film acted as a surface protection layer against corrosion and as a nonprecious metal electrocatalyst for oxygen evolution. In 1 M aqueous KOH, the Ni/n-Si photoanodes exhibited high PEC activity with a low onset potential (~1.07 volts versus reversible hydrogen electrode), high photocurrent density, and durability. The electrode showed no sign of decay after ~80 hours of continuous PEC water oxidation in a mixed lithium borate-potassium borate electrolyte. The high photovoltage was attributed to a high built-in potential in a metal-insulatorsemiconductor- like device with an ultrathin, incomplete screening Ni/NiOx layer from the electrolyte. [ABSTRACT FROM AUTHOR]

Highly active, durable, and cost-effective electrocatalysts for water oxidation to evolve oxygen gas hold a key to a range of renewable energy solutions, including water-splitting and rechargeable metal-air batteries. Here, we report the synthesis of ultrathin nickel–iron layered double hydroxide (NiFe-LDH) nanoplates on mildly oxidized multiwalled carbon nanotubes (CNTs). Incorporation of Fe into the nickel hydroxide induced the formation of NiFe-LDH. The crystalline NiFe-LDH phase in nanoplate form is found to be highly active for oxygen evolution reaction in alkaline solutions. For NiFe-LDH grown on a network of CNTs, the resulting NiFe-LDH/CNT complex exhibits higher electrocatalytic activity and stability for oxygen evolution than commercial precious metal Ir catalysts. [ABSTRACT FROM AUTHOR]

This study explores the boundary methods for the two-dimensional homogeneous Stokes equations and investigates the particular solutions (PS) satisfying the Stokes equations. Smooth solutions for the Stokes equations are provided by explicit fundamental solutions (FS) and PS in this study, and singular corner solutions are also provided from linear elastostatics given in Li et al. ([Eng. Anal. Bound. Elem. 34 (2009), 533-648, 2009). A new singularity model with an interior crack is proposed and solved by the collocation Trefftz method (CTM). The proposed method achieves highly accurate solutions with the first leading coefficient having 10 significant digits. These solutions may be used as a benchmark for testing results obtained by other numerical methods. Error bounds are derived for the CTM solutions using the PS. For a general corner, the exponent ν k in r [ABSTRACT FROM AUTHOR]

Spin-orbit coupled semiconductor nanowires with Zeeman splitting in proximity contact with bulk s-wave superconductivity have recently been proposed as a promising platform for realizing Majorana fermions. However, in this setup the chemical potential of the nanowire is generally pinned by the Fermi surface of the superconductor. This makes the tuning of the chemical potential by external electrical gates, a crucial requirement for unambiguous detection of Majorana fermions, very challenging in experiments. Here we show that a tunable topological superconducting regime supporting Majorana fermions can be realized in semiconductor nanowires using uniaxial stress. For «-type nanowires the uniaxial stress tunes the effective chemical potential, while for p-type systems the effective pairing may also be modified by stress, thus significantly enhancing the topological minigap. We show that the required stress, of the order of 0.1%, is within current experimental reach using conventional piezocrystals. [ABSTRACT FROM AUTHOR]

For solving Laplace's equation in circular domains with circular holes, the null field method (NFM) was developed by Chen and his research group (see Chen and Shen (2009)). In Li et al. (2012) the explicit algebraic equations of the NFM were provided, where some stability analysis was made. For the NFM, the conservative schemes were proposed in Lee et al. (2013), and the algorithm singularity was fully investigated in Lee et al., submitted to Engineering Analysis with Boundary Elements, (2013). To target the same problems, a new interior field method (IFM) is also proposed. Besides the NFM and the IFM, the collocation Trefftz method (CTM) and the boundary integral equation method (BIE) are two effective boundary methods. This paper is devoted to a further study on NFM and IFM for three goals. The first goal is to explore their intrinsic relations. Since there exists no error analysis for the NFM, the second goal is to drive error bounds of the numerical solutions. The third goal is to apply those methods to Laplace's equation in the domains with extremely small holes, which are called actually punctured disks. By NFM, IFM, BIE, and CTM, numerical experiments are carried out, and comparisons are provided. This paper provides an in-depth overview of four methods, the error analysis of the NFM, and the intriguing computation, which are essential for the boundary methods. [ABSTRACT FROM AUTHOR]

An atomistic pseudopotential calculation of the spin-flip time (T1) of electrons and holes mediated by acoustic phonons in self-assembled In1-xGaxAs/GaAs quantum dots at zero magnetic field is presented. At low magnetic field, the first-order process is suppressed, and the second-order process becomes dominant. It is found that the spin-phonon-interaction-induced spin relaxation time is 100-221 s for electrons, and 4.4-60 ms for holes at 4.2 K. The calculated hole-spin relaxation times are in good agreement with recent experiments, which suggests that the two-phonon process is one of the main relaxation mechanisms for hole-spin relaxation in the self-assembled quantum dots at zero field. The structural and alloy composition effects on the spin relaxation in the quantum dots are clarified. [ABSTRACT FROM AUTHOR]

For fixed s = 1 and any t1, t2 ∈ (0, 1/2) we prove that the double inequality Gs(t1a + (1 - t1)b, t1b + (1 - t1)a)A1-s(a, b) < P(a, b) < Gs(t2a + (1 - t2)b, t2b + (1 - t2)a)A1-s(a, b) holds for all a, b > 0 with a≠ b if and only if t1 = (1 - √ 1 - (2/p)2/s)/2 and t2 = (1 - 1/ v 3s)/2. Here, P(a, b), A(a, b) and G(a, b) denote the Seiffert, arithmetic, and geometric means of two positive numbers a and b, respectively [ABSTRACT FROM AUTHOR]

We investigate the BCS-BEC crossover in three-dimensional degenerate Fermi gases in the presence of spin-orbit coupling (SOC) and Zeeman field. We show that the superfluid order parameter destroyed by a large Zeeman field can be restored by the SOC. With increasing strengths of the Zeeman field, there is a series of topological quantum phase transitions from a nontopological superfluid state with fully gapped fermionic spectrum to a topological superfluid state with four topologically protected Fermi points (i.e., nodes in the quasiparticle excitation gap) and then to a second topological superfluid state with only two Fermi points. The quasiparticle excitations near the Fermi points realize the long-sought low-temperature analog of Weyl fermions of particle physics. We show that the topological phase transitions can be probed using the experimentally realized momentum-resolved photoemission spectroscopy. [ABSTRACT FROM AUTHOR]

Lung cancer is the leading cause of cancer-related death in the world. Non-small cell lung carcinomas (Non-SCLC) account for almost 80% of lung cancers, of which 40% were adenocarcinomas. For a better understanding of the molecular mechanisms behind the development and progression of lung cancer, particularly lung adenocarcinoma, we have used proteomics technology to search for candidate prognostic and therapeutic targets in pulmonary adenocarcinoma. The protein profile changes between human pulmonary adenocarcinoma tissue and paired surrounding normal tissue were analyzed using two-dimensional polyacrylamide gel electrophoresis (2-DE) based approach. Differentially expressed proteinspots were identified with ESI-Q-TOF MS/MS instruments. As a result, thirty two differentially expressed proteins (over 2-fold, p<0.05) were identified in pulmonary adenocarcinoma compared to normal tissues. Among them, two proteins (PKM2 and cofilin-1), significantly up-regulated in adenocarcinoma, were selected for detailed analysis. Immunohistochemical examination indicated that enhanced expression of PKM2 and cofilin-1 were correlated with the severity of epithelial dysplasia, as well as a relatively poor prognosis. Knockdown of PKM2 expression by RNA interference led to a significant suppression of cell growth and induction of apoptosis in pulmonary adenocarcinoma SPC-A1 cells in vitro, and tumor growth inhibition in vivo xenograft model (P<0.05). In addition, the shRNA expressing plasmid targeting cofilin-1 significantly inhibited tumor metastases and prolonged survival in LL/2 metastatic model. While additional works are needed to elucidate the biological significance and molecular mechanisms of these altered proteins identified in this study, PKM2 and cofilin-1 may serve as potential diagnostic and prognostic biomarkers, as well as therapeutic targets for pulmonary adenocarcinoma. [ABSTRACT FROM AUTHOR]

We numerically investigate, using the time evolving block decimation algorithm, the quantum transport of ultracold bosonic atoms in a double-well optical lattice through slow and periodic modulation of the lattice parameters (intra- and inter-well tunneling, chemical potential, etc.). The transport of atoms does not depend on the rate of change of the parameters (as along as the change is slow) and can distribute atoms in optical lattices at the quantized level without involving external forces. The transport of atoms depends on the atom filling in each double well and the interaction between atoms. In the strongly interacting region, the bosonic atoms share the same transport properties as noninteracting fermions with quantized transport at the half filling and no atom transport at the integer filling. In the weakly interacting region, the number of the transported atoms is proportional to the atom filling. We show the signature of the quantum transport from the momentum distribution of atoms that can be measured in the time-of-flight image. A semiclassical transport model is developed to explain the numerically observed transport of bosonic atoms in the noninteracting and strongly interacting limits. The scheme may serve as an quantized battery for atomtronics applications. [ABSTRACT FROM AUTHOR]

Series expansions of fundamental solutions are essential to algorithms and analysis of the null field method (NFM) and to analysis of the method of fundamental solutions (MFS). For linear elastostatics, new Fourier series expansions of FS are derived, directly from integration. The new expansions of the FS are simpler than those in Chen et al. (J Mech 26(3):393-401, ), thus facile to application in NFM and MFS. The new series expansions of FS in this paper are important to both theory and computation of linear elastostatics. Some computation of the MFS for linear elastostatics is provided, where the expansions of fundamental solutions are a basis tool in analysis. Numerical results of a simple example are reported, accompanied with error analysis. [ABSTRACT FROM AUTHOR]

Abstract: In this paper, the Trefftz method of fundamental solution (FS), called the method of fundamental solution (MFS), is used for biharmonic equations. The bounds of errors are derived for the MFS with Almansi’s fundamental solutions (denoted as the MAFS) in bounded simply connected domains. The exponential and polynomial convergence rates are obtained from highly and finitely smooth solutions, respectively. The stability analysis of the MAFS is also made for circular domains. Numerical experiments are carried out for both smooth and singularity problems. The numerical results coincide with the theoretical analysis made. When the particular solutions satisfying the biharmonic equation can be found, the method of particular solutions (MPS) is always superior to the MFS and the MAFS, based on numerical examples. However, if such singular particular solutions near the singular points do not exist, the local refinement of collocation nodes and the greedy adaptive techniques can be used for seeking better source points. Based on the computed results, the MFS using the greedy adaptive techniques may provide more accurate solutions for singularity problems. Moreover, the numerical solutions by the MAFS with Almansi’s FS are slightly better in accuracy and stability than those by the traditional MFS. Hence, the MAFS with the AFS is recommended for biharmonic equations due to its simplicity. [Copyright &y& Elsevier]

Chemotherapeutic drug resistance is a frequent cause of treatment failure in colon cancer patients. Several mechanisms have been implicated in drug resistance. However, they are not sufficient to exhaustively account for this resistance emergence. In this study, two-dimensional gel electrophoresis (2-DE) and the PDQuest software analysis were applied to compare the differential expression of irinotecan-resistance-associated protein in human colon adenocarcinoma LoVo cells and irinotecan-resistant LoVo cells (LoVo/irinotecan). The differential protein dots were excised and analysed by ESI-Q-TOF mass spectrometry (MS). Fifteen proteins were identified, including eight proteins with decreased expression and seven proteins with increased expression. The identified known proteins included those that function in diverse biological processes such as cellular transcription, cell apoptosis, electron transport/redox regulation, cell proliferation/differentiation and retinol metabolism pathways. Identification of such proteins could allow improved understanding of the mechanisms leading to the acquisition of chemoresistance. [ABSTRACT FROM AUTHOR]

Givetian, Frasnian and Famennian limestones from southern China contain microfossils generally regarded as calcified algae and cyanobacteria. These are present in 61 out of 253 sampled horizons in four sections from three widely spaced localities in Guangxi and southern Guizhou. Three of the sections sampled are Givetian-Frasnian-Famennian; one section is Frasnian-Famennian. They include reef and non-reef carbonates of shallow marine platform facies. The following taxa are identified with differing degrees of confidence, and placed in algae, cyanobacteria or microproblematica. Algae: Halysis, 'solenoporaceans', Vermiporella. Cyanobacteria: Bevocastria, Girvanella, Hedstroemia, Subtifloria. Microproblematica: ?Chabakovia, Garwoodia, ?Issinella, Izhella, Paraepiphyton, Rothpletzella, Shuguria, ?Stenophycus, Tharama, Wetheredella. As a whole, the abundance of algae, cyanobacteria and microproblematica increases by 34% from Givetian to Frasnian, and declines by 63% in the Famennian. This secular pattern of marked Famennian decrease does not support recognition of them as "disaster forms" in the immediate aftermath of late Frasnian extinction. Nonetheless, their survival into the Famennian could indicate tolerance of environmental stress, independence of changes in food supply, morphologic plasticity, and ability to occupy a range of habitats and depths. Uncertainties concerning the affinities of the problematic taxa hinder assessment of their significance. [ABSTRACT FROM AUTHOR]

Gong, Y.-M., Shi, G.R., Zhang, L.-J. & Weldon, E.A. 2009: Zoophycos composite ichnofabrics and tiers from the Permian neritic facies in South China and south-eastern Australia. Lethaia, Vol. 43, pp. 182–196. Zoophycos composite ichnofabrics (ZCI) comprising two or more suites of the same form of Zoophycos are widespread and densely distributed in Early and Middle Permian (Cisuralian–Guadalupian) neritic limestones (Qixia and Maokou Formations) of palaeotropical origin in the Laibin area, Guangxi, South China. Similar ZCI also occur in neritic greywackes of glaciomarine origin from the Middle Permian (Guadalupian) Westley Park Sandstone Member (Broughton Formation) in the southern Sydney Basin, south-eastern Australia. Zoophycos from both regions consists of planar spreite with major and minor lamellae and a cylindrical tunnel interpreted as a marginal tube and/or axial shaft. The cylindrical tunnel is herein considered to be an essential component of Zoophycos, and thus can be used to define and characterize the morphological variability of Zoophycos. It is suggested that the variation of spreite and major and minor lamellae originated from the different morphologies and migration manners of the cylindrical tunnel. The shallowest, shallow, middle and deepest Zoophycos tiers have been distinguished in ZCI on the basis of cross-cutting relationships, the soft-sediment deformation and the contrast in colour between Zoophycos and its host rock. The multiple tiers may represent the substrate consistency spectrum from a softground through a stiffground to a firmground. The different Zoophycos tiers may have been constructed by tracemakers of either different or the same taxonomic affinities in response to the gradual accretion and lithification of sediment layers on the seafloor. The tracemakers appeared to be very sensitive to neither climate nor lithology. The width of the planar spreiten of Zoophycos decreases slightly with the depth of tiering in ZCI. □ Composite ichnofabric, Permian, South China, south-eastern Australia, tier, Zoophycos . [ABSTRACT FROM AUTHOR]

Background: Exploring metabolic evolution is a way to understand metabolic complexity. The substrate transport of mitochondrial carrier family (MCF) influences direct metabolic activities, making it possible to understand indirectly metabolic evolution from the evolution of substrate transport of MCF. However, the evolutionary study of substrate transport of MCF does not mean that all the concrete structures of mitochondrial carriers (MCs) must first be gained. Results: Here we studied the alternation of MCF structure and potential correlated functions of MCF during metazoan evolution. The data analysis indicates that the types of substrates transported by MCF as a whole were maintained during metazoan evolution. However, the size of the substrates transported by members of MCs continuously diminished during the evolutionary process. We have found that the ratio of hydrophobic amino acids at specific helix-helix interfaces increases significantly during vertebrate evolution. Amino acid's spatial positioning and the calculating of packing values both indicate the increase in the number of hydrophobic amino acids would lead to a more "tight" structure of the TR domain, which is in agreement with the trend of diminishing size of substrates transported by MCs. In addition, there was a significant increase in the number of carriers of MCF during vertebrate evolution. Conclusions: We propose that the more "tight" TR structure generated by the increase of the hydrophobic amino acids at specific helix-helix interfaces during vertebrate evolution enhances the substrate selectivity of MCF, reflecting the evolutionary trajectory of MCF during metazoan evolution. [ABSTRACT FROM AUTHOR]

We consider systems of linear differential-algebraic equations of order ≥ 2 and present conditions under which there exist nonsingular transformations splitting the system into systems of linear ordinary differential equations of lower order and, possibly, an algebraic part. [ABSTRACT FROM AUTHOR]

Two types of pyrite framboids (PF, probably sulphate-reducing bacteria) have been found within the Zoophycos spreiten, hosted in the Guadalupian (Middle Permian) glaciomarine greywacke of the Westley Park Sandstone Member within the Broughton Formation from the southern Sydney Basin of southeastern Australia. They are composed of non-sheathed (PF1) and sheathed (PF2) sub-micron balls, respectively. Chemically, the sub-micron balls consist of iron, sulphur, carbon and oxygen. Both PF1 and PF2 occur in rhythmic alternation within the thick, light-grey and thin, dark-grey minor lamellae of Zoophycos spreiten. The framboids from the minor lamellae are highly abundant and occur in an orderly arrangement of equal density and in a good state of preservation. Within Zoophycos spreiten no homogeneous filling, fecal pellets, or any sign of re-exploitation of the minor lamellae have been recognized. No similar framboids have been observed outside Zoophycos spreiten. Therefore, the framboids are interpreted as the pyritized remains of microbial colonies within Zoophycos spreiten. The trace Zoophycos would be a multifunctional garden that may have been carefully constructed by the Zoophycos maker, where different microbial colonies were orderly and carefully planted and cultured within different minor lamellae. Further, it is proposed that the Zoophycos maker had a symbiotic relationship with microbial colonies on the mutual basis of food supply and redox conditions. The fact that the overlying spreiten cut the underlying ones indicates that the Zoophycos from the study area is of an upward construction. The rhythmic alternation of both the thick, light-grey and thin, dark-grey minor lamellae within Zoophycos spreiten may be suggestive of a gardening manner of the Zoophycos maker responding to the warm and cold changes, food supply in pulses and variations of sedimentation rate for planting and culturing microbial colonies under the conditions of a glaciomarine environment at the high latitudes. [ABSTRACT FROM AUTHOR]

Studies in vitro have established that free tryptophan induces tna operon expression by binding to the ribosome that has just completed synthesis of TnaC-tRNAPro, the peptidyl-tRNA precursor of the leader peptide of this operon. Tryptophan acts by inhibiting Release Factor 2-mediated cleavage of tl is peptidyl-tRNA at the tnaC stop codon. Here we analyze the ribosomal location of free tryptophan, the changes it produces in the ribosome, and the role of the nascent TnaC-tRNAPro peptide in facilitating tryptophan binding and induction. The positional changes of 23S rRNA nucleotides that occur during induction were detected by using methylation protection and binding/competition assays. The ribosome-TnaC-tRNAPro complexes analyzed were formed in vitro; they contained either wild-type TnaC-tRNAPro or its nonfunctional substitute, TnaC(W12R)-tRNAPro. Upon comparing these two peptidyl-tRNA-ribosome complexes, free tryptophan was found to block methylation of nucleotide A2572 of wild-type ribosome-TnaC-tRNAPro complexes but not of ribosome-TnaC(W12R)-tRNAPro complexes. Nucleotide A2572 is in the ribosomal peptidyl transferase center. Tryptophanol, a noninducing competitor of tryptophan, was ineffective in blocking A2572 methylation; however, it did reverse the protective effect of tryptophan. Free tryptophan inhibited puromycin cleavage of TnaC-tRNAPro; it also inhibited binding of the antibiotic sparsomycin. These effects were not observed with TnaC(W12R)-tRNAPro mutant complexes. These findings establish that Trp-12 of TnaC-tRNAPro is required for introducing specific changes in the peptidyl transferase center of the ribosome that activate free tryptophan binding, resulting in peptidyl transferase inhibition. Free tryptophan appears to act at or near the binding sites of several antibiotics in the peptidyl transferase center. [ABSTRACT FROM AUTHOR]

Here we describe the development of a microarray-based mapping strategy to rapidly isolate deletion mutant genes. The presented approach is particularly useful for mapping mutant genes that are difficult to phenotype. This strategy uses masking bulk segregant analysis to mask unrelated deletions, thus allowing identification of target deletions by microarray hybridization of pooled genomic DNA from both WT and mutant F2 populations. Elemental profiling has proven to be a powerful tool for isolation of nutrient and toxic metal accumulation mutants in Arabidopsis. Using microarray mapping, a sodium overaccumulation mutant FN1148 was identified as having a 523-bp genomic deletion within the second exon and intron of the AtHKT1 gene. Further cosegregation, complementation, and comparative analyses among different salt-sensitive mutants confirmed that the deletion within the AtHKT1 gene is responsible for the sodium overaccumulation in shoots and leaf sodium sensitivity of the P41148 mutant. These results demonstrate that microarray-based cloning is an efficient and powerful tool to rapidly clone ion accumulation or other genetic deletion mutants that are otherwise difficult to phenotype for mapping, such as metabolic or cell signaling mutants. [ABSTRACT FROM AUTHOR]

Phytochelatin synthases (PCS) mediate cellular heavy-metal resistance in plants, fungi, and worms. However, phytochelatins (PCs) are generally considered to function as intracellular heavymetal detoxification mechanisms, and whether long-distance transport of PCs occurs during heavy-metal detoxification remains unknown. Here, wheat TaPCS1 cDNA expression was either targeted to Arabidopsis roots with the Arabidopsis alcohol dehydrogenase (Adh) promoter (Adh::TaPCS1/cad1-3) or ectopically expressed with the cauliflower mosaic virus 35S promoter (35S::TaPCS1/cad1-3) in the PC-deficient mutant cad1-3. Adh::TaPCS1/cadl-3 and 35S::TaPCS1/cad1-3 complemented the cadmium, mercury, and arsenic sensitivities of the cad1-3 mutant. Northern blot, RT-PCR, and Western blot analyses showed Adh promoter-driven TaPCS1 expression only in roots and thus demonstrated lack of long-distance TaPCS1 mRNA and protein transport in plants. Fluorescence HPLC analyses showed that under Cd[sup 2+] stress, no PCs were detectable in cad1-3. However, in Adh::TaPCS1/cad1-3 plants, PCs were detected in roots and in rosette leaves and stems. Inductively coupled plasma atomic emission spectrometer analyses showed that either root-specific or ectopic expression of TaPCS1 significantly enhanced long-distance Cd[sup 2+] transport into stems and rosette leaves. Unexpectedly, transgenic expression of TaPCS1 reduced Cd[sup 2+] accumulation in roots compared with cad1-3. The reduced Cd[sup 2+] accumulation in roots and enhanced root-to-shoot Cd[sup 2+] transport in transgenic plants were abrogated by L-buthionine sulfoximine. The presented findings show that (i) transgenic expression of TaPCS1 suppresses the heavy-metal sensitivity of cad1-3, (ii) PCs can be transported from roots to shoots, and (iii) transgenic expression of the TaPCSl gene increases long-distance root-to-shoot Cd[sup 2+] transport and reduces Cd[sup 2+] accumulation in roots. [ABSTRACT FROM AUTHOR]

A differentially expressed OsIM1 gene was isolated from rice salt-tolerant mutant M-20 by differential display. Sequence analysis revealed that the amino-acid sequence of OsIM1 showed 66% and 62% identity with PTOX from tomato (Capsicum annuum) and AtIM from Arabidopsis, both of which encoded chloroplast-orientated terminal oxidase. Comparison of the nucleotide sequence of the OsIM1 cDNA with its genomic sequence revealed that OsIM1 genomic DNA contained nine exons and eight introns. A pseudo-transcript (OsIM2), which probably resulted from the abnormal splicing of the OsIM1 pre-mRNA, was also identified. Southern-blot analysis showed that there existed only one copy of the OsIM1 gene in the rice genome. RFLP analysis located it on rice chromosome 3. The Northern blot revealed that OsIM1 was up-regulated by NaCl and ABA treatment. RT-PCR analysis indicated that OsIM1 and OsIM2 co-existed in the OsIM transcript pool, and the ratio of OsIM1/OsIM2 was differentially regulated by salt stress in the salt-sensitive variety and the salt-tolerant varieties. [ABSTRACT FROM AUTHOR]

Cardiovascular diseases remain the leading cause of death in the United States. Two factors associated with a decreased risk of developing cardiovascular disease are elevated HDL levels and sex -- specifically, a decreased risk is found in premenopausal women. HDL and estrogen stimulate eNOS and the production of nitric oxide, which has numerous protective effects in the vascular system including vasodilation, antiadhesion, and anti-inflammatory effects. We tested the hypothesis that HDL binds to its receptor, scavenger receptor class B type I (SR-BI), and delivers estrogen to eNOS, thereby stimulating the enzyme. HDL isolated from women stimulated eNOS, whereas HDL isolated from men had minimal activity. Studies with ovariectomized and ovariectomized/estrogen replacement mouse models demonstrated that HDL-associated estradiol stimulation of eNOS is SR-BI dependent. Furthermore, female HDL, but not male HDL, promoted the relaxation of muscle strips isolated from C57BL/6 mice but not SR-BI null mice. Finally, HDL isolated from premenopausal women or postmenopausal women receiving estradiol replacement therapy stimulated eNOS, whereas HDL isolated from postmenopausal women did not stimulate eNOS. We conclude that HDL-associated estrodial is capable of the stimulating eNOS. These studies establish a new paradigm for examining the cardiovascular effects of HDL and estrogen. [ABSTRACT FROM AUTHOR]