bluuebunny/crossref_metadata_2025 huggingface dataset:
In vivo multimodality imaging of miRNA-16 iron nanoparticle reversing drug resistance to chemotherapy in a mouse gastric cancer model
Authors: Sun Zhongchan , Song Xinxing , Li Xiujuan , Su Tao , Qi Shun , Qiao Ruirui , Wang Fu , Huan Yi , Yang Weidong , Wang Jing , Nie Yongzhan , Wu Kaichun , Gao Mingyuan , Cao Feng
Published: September 2014

Iron nanoparticles loading miRNA-16 reverse drug resistance to chemotherapyin vivo.
A novel CdS photocatalyst based on magnetic fly ash cenospheres as the carrier: performance and mechanism
Authors: He Ming , Lu Ziyang , Zhou Weichao , Chen Tingting , Shi Weidong , Che Guangbo , Huo Pengwei , Zhu Zhi , Zhao Xiaoxu , Yan Yongsheng
Published: September 2014

Easily recycled CdS photocatalysts loaded on magnetic fly ash cenospheres were fabricated, and the role of free radicals in the photocatalytic degradation of danofloxacin mesylate was discussed in detail.
A simple one pot synthesis of cubic Cu5FeS4
Authors: Kumar Prashant , Gusain Meenakshi , Kumar Pandian Senthil , Uma Sitharaman , Nagarajan Rajamani
Published: September 2014

Cubic Cu5FeS4, obtained from a simple refluxing reaction of CuCl, FeCl3 and thiourea in ethylene glycol, showed an optical band gap of 1.25 eV. It can be used as a UV-visible radiation absorber in photovoltaic cells.
Fabrication of quasi-cubic Fe3O4@rGO composite via a colloid electrostatic self-assembly process for supercapacitors
Authors: Liu Tiezhu , Zhang Xudong , Li Baojun , Ding Jie , Liu Yushan , Li Ge , Meng Xianghe , Cai Qiang , Zhang Jianmin
Published: September 2014

Superior behavior for supercapacitors highlight the potential applications of CFGC in energy storage issues.
Enhanced cycling stability of silicon anode by in situ polymerization of poly(aniline-co-pyrrole)
Authors: Wang Qingtao , Li Ruirong , Yu Dong , Zhou Xiaozhong , Li Jian , Lei Ziqiang
Published: September 2014

Poly(aniline-co-pyrrole)-encapsulated Si nanoparticles composite anode material were prepared by an in situ chemical oxidation polymerization method.
Highly transparent and flexible silica/cellulose films with a low coefficient of thermal expansion
Authors: Wu Yuehan , Zhang Xingzhong , Li Bin , Liu Shilin
Published: September 2014

Highly transparent and flexible silica/cellulose films with low thermal expansion coefficients have been prepared by thein situsynthesis of silica in cellulose scaffolds using Na2SiO3as a precursor.
Efficiency enhancement of mono-Si solar cell with CdO nanotip antireflection and down-conversion layer
Authors: Feng Wuliang , Liu Jie , Yu Xibin
Published: September 2014

A composite CdO nanotips/mono-Si solar cell achieved a 14% improvement in power conversion efficiency compared with the control that lacked CdO nanotips.
Synthesis of heterocycle-tethered acylbenzofurans and benzodifurans from odorless and recyclable organoseleno polystyrene resin
Authors: Wang Yuguang , Zhu Bingchun , Xu Qing , Zhu Qing , Yu Lei
Published: September 2014

Recyclable organoseleno resin-supported solid-phase synthesis (SPS) provided a quick access to heterocycle-tethered acylbenzofurans and benzodifurans in satisfactory overall yields and purities after multiple step reactions.
Electrochemical detection of adenine and guanine using a self-assembled copper(ii)–thiophenyl-azo-imidazole complex monolayer modified gold electrode
Authors: Barman Koushik , Jasimuddin Sk
Published: September 2014

A self-assembled copper(ii)–thiophenyl-azo-imidazole complex monolayer modified gold electrode exhibits an excellent electrochemical sensing ability towards adenine and guanine at physiological pH.
A facile template-free approach for the solid-phase synthesis of CoS2 nanocrystals and their enhanced storage energy in supercapacitors
Authors: Ji Ying , Liu Xiaoyang , Liu Wei , Wang Ying , Zhang Hongdan , Yang Min , Wang Xiaofeng , Zhao Xudong , Feng Shouhua
Published: September 2014

Porous CoS2 is synthesized by a modified molten-salt synthesis approach with a specific capacitance as high as 654 F g−1.
Functionalized single walled carbon nanotubes facilitate efficient differentiation of neuroblastoma cells in vitro
Authors: Kishore Abhinoy , Biswas Kaushiki , N Vijaykameswara Rao , Shunmugam Raja , Sarma Jayasri Das
Published: September 2014

Single-walled carbon nanotubes (SWNTs) have been increasingly used as scaffolds for neuronal growth and differentiation.
Evaluation of the effectiveness of conceptual change texts in the REACT strategy
Authors: Ültay Neslihan , Durukan Ümmü Gülsüm , Ültay Eser
Published: September 2014

This study aimed to investigate the effect of conceptual change text (CCT) in the REACT strategy for students' conceptions of solutions. A quasi-experimental method was used in the study. The study was carried out in the spring term of the 2012–2013 academic year with 61 freshmen students (aged 18–20 years) studying in the Elementary Education Department. To gather data, the solutions concept test (SCT) was used as a pretest (PrT) and posttest (PoT) and clinical interviews were used to increase the validity of the data obtained from SCT. In the experimental and control groups, the REACT strategy was used as the teaching strategy. In the experimental group, the REACT strategy was enriched with CCTs. Three CCTs were used for the experimental group. According to the findings, there was a significant difference between the experimental and control groups' PrT and PoT results. The REACT strategy was found to be successful at dealing with the alternative conceptions in solution chemistry. However, no significant difference was found between the groups' PoT results. On the other hand, qualitative analyses showed that the CCTs were slightly effective in remediation of alternative conceptions in solution chemistry. This suggests that we may need to use more than one intervention model to effectively remedy the alternative conceptions in solution chemistry. This study may be helpful for diagnosing alternative conceptions and guide researchers to remedy them. Hence, CCTs can be designed for other chemistry topics for implementation in schools.
The spatial-temporal characteristics of type I collagen-based extracellular matrix
Authors: Jones Christopher Allen Rucksack , Liang Long , Lin Daniel , Jiao Yang , Sun Bo
Published: September 2014

Type I collagen abounds in mammalian extracellular matrix (ECM) and is crucial to many biophysical processes.
Supercritical solvothermal preparation of a ZnxCd1−xS visible photocatalyst with enhanced activity
Authors: Zhong Jiahui , Zhang Ya , Hu Changqun , Hou Rujing , Yin Haibo , Li Hexing , Huo Yuning
Published: September 2014

A ZnxCd1−xS solid solution in uniform nanoparticles prepared using a supercritical solvothermal route achieved high photocatalytic activity and durability.
Upconversion luminescence nanoparticles-based lateral flow immunochromatographic assay for cephalexin detection
Authors: Liu Chunyan , Ma Wei , Gao Zhenyu , Huang Jiayi , Hou Yi , Xu Chuanlai , Yang Wensheng , Gao Mingyuan
Published: September 2014

Upconversion luminescence core–shell nanoparticles were used as antibody labels in a lateral flow immunochromatographic assay for the sensitive detection of cephalexin.
Optimisation of manufacturing parameters for inkjet‐printed and photonically sintered metallic nanoparticle UHF RFID tags
Authors: Ren Y. , Virkki J. , Sydänheimo L. , Ukkonen L.
Published: September 2014

Inkjet printing and photonic sintering parameters for silver and copper nanoparticle inks on flexible polyimide and environmentally friendly cardboard substrates have been studied. The results were utilised to manufacture prototype passive ultra‐high frequency (UHF) radio‐frequency identification (RFID) tag antennas. The manufactured tags showed peak read ranges of 2.9–5.5 m.
New experimental methodology, setup and LabView program for accurate absolute thermoelectric power and electrical resistivity measurements between 25 and 1600 K: Application to pure copper, platinum, tungsten, and nickel at very high temperatures
Authors: Abadlia L. , Gasser F. , Khalouk K. , Mayoufi M. , Gasser J. G.
Published: September 2014

In this paper we describe an experimental setup designed to measure simultaneously and very accurately the resistivity and the absolute thermoelectric power, also called absolute thermopower or absolute Seebeck coefficient, of solid and liquid conductors/semiconductors over a wide range of temperatures (room temperature to 1600 K in present work). A careful analysis of the existing experimental data allowed us to extend the absolute thermoelectric power scale of platinum to the range 0-1800 K with two new polynomial expressions. The experimental device is controlled by a LabView program. A detailed description of the accurate dynamic measurement methodology is given in this paper. We measure the absolute thermoelectric power and the electrical resistivity and deduce with a good accuracy the thermal conductivity using the relations between the three electronic transport coefficients, going beyond the classical Wiedemann-Franz law. We use this experimental setup and methodology to give new very accurate results for pure copper, platinum, and nickel especially at very high temperatures. But resistivity and absolute thermopower measurement can be more than an objective in itself. Resistivity characterizes the bulk of a material while absolute thermoelectric power characterizes the material at the point where the electrical contact is established with a couple of metallic elements (forming a thermocouple). In a forthcoming paper we will show that the measurement of resistivity and absolute thermoelectric power characterizes advantageously the (change of) phase, probably as well as DSC (if not better), since the change of phases can be easily followed during several hours/days at constant temperature.
Constriction model of actomyosin ring for cytokinesis by fission yeast using a two-state sliding filament mechanism
Authors: Jung Yong-Woon , Mascagni Michael
Published: September 2014

We developed a model describing the structure and contractile mechanism of the actomyosin ring in fission yeast, Schizosaccharomyces pombe. The proposed ring includes actin, myosin, and α-actinin, and is organized into a structure similar to that of muscle sarcomeres. This structure justifies the use of the sliding-filament mechanism developed by Huxley and Hill, but it is probably less organized relative to that of muscle sarcomeres. Ring contraction tension was generated via the same fundamental mechanism used to generate muscle tension, but some physicochemical parameters were adjusted to be consistent with the proposed ring structure. Simulations allowed an estimate of ring constriction tension that reproduced the observed ring constriction velocity using a physiologically possible, self-consistent set of parameters. Proposed molecular-level properties responsible for the thousand-fold slower constriction velocity of the ring relative to that of muscle sarcomeres include fewer myosin molecules involved, a less organized contractile configuration, a low α-actinin concentration, and a high resistance membrane tension. Ring constriction velocity is demonstrated as an exponential function of time despite a near linear appearance. We proposed a hypothesis to explain why excess myosin heads inhibit constriction velocity rather than enhance it. The model revealed how myosin concentration and elastic resistance tension are balanced during cytokinesis in S. pombe.
Calculating hydrodynamic interactions for membrane-embedded objects
Authors: Noruzifar Ehsan , Camley Brian A. , Brown Frank L. H.
Published: September 2014

A recently introduced numerical scheme for calculating self-diffusion coefficients of solid objects embedded in lipid bilayer membranes is extended to enable calculation of hydrodynamic interactions between multiple objects. The method is used to validate recent analytical predictions by Oppenheimer and Diamant [Biophys. J. 96, 3041 2009] related to the coupled diffusion of membrane embedded proteins and is shown to converge to known near-field lubrication results as objects closely approach one another; however, the present methodology also applies outside of the limiting regimes where analytical results are available. Multiple different examples involving pairs of disk-like objects with various constraints imposed on their relative motions demonstrate the importance of hydrodynamic interactions in the dynamics of proteins and lipid domains on membrane surfaces. It is demonstrated that the relative change in self-diffusion of a membrane embedded object upon perturbation by a similar proximal solid object displays a maximum for object sizes comparable to the Saffman-Delbrück length of the membrane.
Area-preserving maps models of gyroaveraged E×B chaotic transport
Authors: da Fonseca J. D. , del-Castillo-Negrete D. , Caldas I. L.
Published: September 2014

Discrete maps have been extensively used to model 2-dimensional chaotic transport in plasmas and fluids. Here we focus on area-preserving maps describing finite Larmor radius (FLR) effects on E × B chaotic transport in magnetized plasmas with zonal flows perturbed by electrostatic drift waves. FLR effects are included by gyro-averaging the Hamiltonians of the maps which, depending on the zonal flow profile, can have monotonic or non-monotonic frequencies. In the limit of zero Larmor radius, the monotonic frequency map reduces to the standard Chirikov-Taylor map, and in the case of non-monotonic frequency, the map reduces to the standard nontwist map. We show that in both cases FLR leads to chaos suppression, changes in the stability of fixed points, and robustness of transport barriers. FLR effects are also responsible for changes in the phase space topology and zonal flow bifurcations. Dynamical systems methods based on the counting of recurrences times are used to quantify the dependence on the Larmor radius of the threshold for the destruction of transport barriers.
Simulation of one-dimensional evolution of wind waves in a deep water
Authors: Chalikov Dmitry , Babanin Alexander V.
Published: September 2014

A direct wave model based on the one-dimensional nonlinear equations for potential waves is used for simulation of wave field development under the action of energy input, dissipation, and nonlinear wave-wave interaction. The equations are written in conformal surface-fitted nonstationary coordinate system. New schemes for calculating the input and dissipation of wave energy are implemented. The wind input is calculated on the basis of the parameterization developed through the coupled modeling of waves and turbulent boundary layer. The wave dissipation algorithm, introduced to prevent wave breaking instability, is based on highly selective smoothing of the wave surface and surface potential. The integration is performed in Fourier domain with the number of modes M = 2048, broad enough to reproduce the energy downshifting. As the initial conditions, the wave field is assigned as train of Stokes waves with steepness ak = 0.15 at nondimensional wavenumber k = 512. Under the action of nonlinearity and energy input the spectrum starts to grow. This growth is followed by the downshifting. The total time of integration is equal to 7203 initial wave periods. During this time the energy increased by 1111 times. Peak of the spectrum gradually shifts from wavenumber nondimensional k = 512 down to k = 10. Significant wave height increases 33 times, while the peak period increases 51 times. Rates of the peak downshift and wave energy evolution are in good agreement with the JONSWAP formulation.
On the local electronic and atomic structure of Ce1−xPrxO2−δ epitaxial films on Si
Authors: Niu Gang , Schubert Markus Andreas , d'Acapito Francesco , Zoellner Marvin Hartwig , Schroeder Thomas , Boscherini Federico
Published: September 2014

The local electronic and atomic structure of (111)-oriented, single crystalline mixed Ce1−xPrxO2−δ (x = 0, 0.1 and 0.6) epitaxial thin films on silicon substrates have been investigated in view of engineering redox properties of complex oxide films. Non-destructive X-ray absorption near edge structure reveals that Pr shows only +3 valence and Ce shows only nominal +4 valence in mixed oxides. Extended x-ray absorption fine structure (EXAFS) studies were performed at K edges of Ce and Pr using a specially designed monochromator system for high energy measurements. They demonstrate that the fluorite lattice of ceria (CeO2) is almost not perturbed for x = 0.1 sample, while higher Pr concentration (x = 0.6) not only generates a higher disorder level (thus more disordered oxygen) but also causes a significant reduction of Ce–O interatomic distances. The valence states of the cations were also examined by techniques operating in highly reducing environments: scanning transmission electron microscopy-electron energy loss spectroscopy and X-ray photoemission spectroscopy; in these reducing environments, evidence for the presence of Ce3+ was clearly found for the higher Pr concentration. Thus, the introduction of Pr3+ into CeO2 strongly enhances the oxygen exchange properties of CeO2. This improved oxygen mobility properties of CeO2 are attributed to the lattice disorder induced by Pr mixing in the CeO2 fluorite lattice, as demonstrated by EXAFS measurements. Thus, a comprehensive picture of the modifications of the atomic and electronic structure of Ce1−xPrxO2−δ epitaxial films and their relation is obtained.
A versatile optical junction using photonic band-gap guidance and self collimation
Authors: Gupta Man Mohan , Medhekar Sarang
Published: September 2014

We show that it is possible to design two photonic crystal (PC) structures such that an optical beam of desired wavelength gets guided within the line defect of the first structure (photonic band gap guidance) and the same beam gets guided in the second structure by self-collimation. Using two dimensional simulation of a design made of the combination of these two structures, we propose an optical junction that allows for crossing of two optical signals of same wavelength and same polarization with very low crosstalk. Moreover, the junction can be operated at number of frequencies in a wide range. Crossing of multiple beams with very low cross talk is also possible. The proposed junction should be important in future integrated photonic circuits.
Effect of the quantum well thickness on the performance of InGaN photovoltaic cells
Authors: Redaelli L. , Mukhtarova A. , Valdueza-Felip S. , Ajay A. , Bougerol C. , Himwas C. , Faure-Vincent J. , Durand C. , Eymery J. , Monroy E.
Published: September 2014

We report on the influence of the quantum well thickness on the effective band gap and conversion efficiency of In0.12Ga0.88N/GaN multiple quantum well solar cells. The band-to-band transition can be redshifted from 395 to 474 nm by increasing the well thickness from 1.3 to 5.4 nm, as demonstrated by cathodoluminescence measurements. However, the redshift of the absorption edge is much less pronounced in absorption: in thicker wells, transitions to higher energy levels dominate. Besides, partial strain relaxation in thicker wells leads to the formation of defects, hence degrading the overall solar cell performance.
Physical origin of nanograting formation on fused silica with femtosecond pulses
Authors: Liang Feng , Vallée Réal
Published: September 2014

We present a comprehensive analysis of physical evolution of nanograting formation based on an experiment performed with femtosecond pulses focused under moderate focusing conditions and where pulse energy is slowly increased as the focused beam is moved along the sample surface. The results demonstrate that nanograting inscription is initiated at the location of the maximum plasma density and evolves through local intensity side lobes, whose locations are self-regulated in a closed feedback loop, in agreement with the plasmonic model.
Pseudo-square AlGaN/GaN quantum wells for terahertz absorption
Authors: Beeler M. , Bougerol C. , Bellet-Amalric E. , Monroy E.
Published: September 2014

THz intersubband transitions are reported down to 160 μm within AlGaN/GaN heterostructures following a 4-layer quantum well design. In such a geometry, the compensation of the polarization-induced internal electric field is obtained through creating a gradual increase in polarization field throughout the quantum “trough” generated by three low-Al-content layers. The intersubband transitions show tunable absorption with respect to doping level as well as geometrical variations which can be regulated from 53 to 160 μm. They also exhibit tunnel-friendly designs which can be easily integrated into existing intersubband device architectures.
Characterization of external resistance effect and performance optimization in unipolar-type SiOx-based resistive switching memory
Authors: Zhou Fei , Chang Yao-Feng , Byun Kwangsub , Fowler Burt , Lee Jack C.
Published: September 2014

SiOx-based resistive random access memory devices with metal-insulator-metal structure are compared to metal-insulator-semiconductor structures, and the effects of external resistance on device performance are characterized. The different reset behaviors are explained as a positive feedback mechanism involving a sudden voltage decrease across the external series resistance when the reset process commences. By varying external resistance, we observe a constant threshold voltage (2.46 V) for the reset process that is possibly due to a voltage-triggered switching mechanism. Our experimental results not only clarify the reset mechanism but also provide insights on optimization of external resistance for programing reliability and operating speed.
Critical route for coherent perfect absorption in a Fano resonance plasmonic system
Authors: Kang Ming , Chong Y. D. , Wang Hui-Tian , Zhu Weiren , Premaratne Malin
Published: September 2014

We develop a method for realizing coherent perfect absorption in thin metamaterial systems, based on the coupled-mode theory of Fano resonance. Coherent perfect absorption refers to the complete absorption of symmetric plane waves incident on opposite sides of the system, due to critical coupling into the dissipative degrees of freedom. Using the reflection and transmission spectra measured on a limited number of samples, our theory predicts the precise frequency and metamaterial parameter values required to achieve coherent perfect absorption. The coupled-mode theory and the design method are found to agree well with full-wave numerical simulations of a subwavelength-thickness metamaterial surface with a pair of bright and dark plasmonic modes.
Fabrication of rigid microstructures with thiol-ene-based soft lithography for continuous-flow cell lysis
Authors: Burke Jeffrey M. , Pandit Kunal R. , Goertz John P. , White Ian M.
Published: September 2014

In this work, we introduce a method for the soft-lithography-based fabrication of rigid microstructures and a new, simple bonding technique for use as a continuous-flow cell lysis device. While on-chip cell lysis techniques have been reported previously, these techniques generally require a long on-chip residence time, and thus cannot be performed in a rapid, continuous-flow manner. Microstructured microfluidic devices can perform mechanical lysis of cells, enabling continuous-flow lysis; however, rigid silicon-based devices require complex and expensive fabrication of each device, while polydimethylsiloxane (PMDS), the most common material used for soft lithography fabrication, is not rigid and expands under the pressures required, resulting in poor lysis performance. Here, we demonstrate the fabrication of microfluidic microstructures from off-stoichiometry thiol-ene (OSTE) polymer using soft-lithography replica molding combined with a post-assembly cure for easy bonding. With finite element simulations, we show that the rigid microstructures generate an energy dissipation rate of nearly 107, which is sufficient for continuous-flow cell lysis. Correspondingly, with the OSTE device we achieve lysis of highly deformable MDA-MB-231 breast cancer cells at a rate of 85%, while a comparable PDMS device leads to a lysis rate of only 40%.
Effect of calcium salt of fatty acids supplementation on performance of Malpura lambs
Authors: Bhatt R. S. , Sahoo A. , Shinde A. K. , Karim S. A.
Published: September 2014

Twenty-four Malpura lambs (28 days old) were distributed into three equal groups (four each from either sexes). They were fed ad libitum on three experimental diets containing graded levels of calcium salt of fatty acids (source: rice bran oil; Ca-FA) at 0 (T1), 20 (T2) and 40 (T3) g per kg of concentrate and dry roughage (Prosopis cineraria leaves) up to 6 months of age along with suckling of mother till weaning (3 months). Effect of Ca-FA supplementation on liveweight gain, feed and nutrient intake was not observed during pre-weaning (28–90 days), which however increased (P < 0.05) in T3 during post-weaning (90–180 days). There was an increase in organic matter intake and digestibility as well as metabolisable energy intake in Ca-FA-supplemented groups. Rumen ammonia-N and ciliate protozoa population was increased (P < 0.05) in T2 and T3 with a positive shift in rumen fermentation (increased propionate and decreased acetate). Blood biochemical analysis revealed effect of treatment and age (P < 0.05) for free fatty acids and cholesterol concentration. Ca-FA supplementation improved (P < 0.05) dressing percentage both at 2% and 4% CA-FA inclusions levels with no change in fat yield and composition. It is concluded that supplementation of Ca-FA prepared from industrial-grade rice bran oil in growing lamb rations improved gain, organic matter intake and digestibility during the post-weaning period and a linear response to the level of supplementation recommends Ca-FA at 40 g/kg for improved lamb performance.
Evaluation of dried stoned olive pomace as supplementation for lactating Holstein cattle: effect on milk production and quality
Authors: Zilio D. Meo , Bartocci S. , Di Giovanni S. , Servili M. , Chiariotti A. , Terramoccia S.
Published: September 2014

The aim of this study was to investigate the effect of using dried stoned olive pomace (DSOP) as a feed supplement for dairy cattle on productive performances and milk quality traits. Control (C) and experimental (E) diets were formulated and offered to lactating Italian Holstein cows placed into two groups (five cows each) that were homogenous for liveweight (630.8 vs 667.2 kg) and for the main physiological and productive traits. The E group received 1.181 kg on dry matter (DM) basis of DSOP as a part of the concentrates pool. The C group was fed an isoenergetic (0.90 milk forage units (FU) /kg DM) and isoprotein (161.4 g/kg DM crude protein (CP)) ration but without the inclusion of DSOP. DM intake was 21 kg/day and the experiment lasted 40 days. There were no significant effects of diet on cattle performance (liveweight and body condition score), milk yield and quality (fat, protein, lactose, urea) or coagulation traits (pH, r, K20, A30). The results showed that the inclusion of DSOP (5.61% of the total diet on DM basis) is not related to detrimental effects and could represent a valid supplement for dairy cattle.
Folding pathway of a multidomain protein depends on its topology of domain connectivity
Authors: Inanami Takashi , Terada Tomoki P. , Sasai Masaki
Published: September 2014

Significance

Theoretical and experimental efforts during the last two decades have revealed many important features of protein folding. However, these efforts have largely focused on single-domain proteins, and additional methods and concepts have been awaited to understand the rich variety of multidomain proteins. To understand the relationship between the topology and folding pathways of multidomain proteins, we developed an Ising-like structure-based model. Our simulated results showed that a dominant pathway is selected in an example protein, dihydrofolate reductase (DHFR), which prevents the rapid decrease in conformation entropy during the course of folding. However, in its circular permutant, for which the topological complexity of wild-type DHFR is resolved, two pathways coexist, resulting in a complex folding behavior.
Disruption of the immune-checkpoint
VISTA
gene imparts a proinflammatory phenotype with predisposition to the development of autoimmunity
Authors: Wang Li , Le Mercier Isabelle , Putra Juan , Chen Wenna , Liu Jun , Schenk Austin D. , Nowak Elizabeth C. , Suriawinata Arief A. , Li Jiannan , Noelle Randolph J.
Published: September 2014

Significance

The discovery of V domain-containing Ig suppressor of T-cell activation (VISTA) as a novel immune-checkpoint regulator comes at an exciting time, as the field of cancer immunotherapy has made significant progress owing to the clinical success of targeting immune-checkpoint proteins such as cytotoxic T lymphocyte-associated antigen 4 and programmed death 1 and ligand. Recent studies also show the promise of monoclonal antibody-mediated VISTA targeting for enhancing antitumor immunity in murine tumor models. The current study demonstrates the spectrum of immune alterations upon genetic disruption of VISTA in mice in the context of self-tolerance as well as immune response against neoantigen. These results enhance the understanding of the immune-regulatory role of VISTA and form the foundation for designing future clinical applications that target VISTA in treating human diseases.
An early sophisticated East Polynesian voyaging canoe discovered on New Zealand's coast
Authors: Johns Dilys A. , Irwin Geoffrey J. , Sung Yun K.
Published: September 2014

Significance

Conservation of a large section of an early, sophisticated sailing canoe recently discovered on the New Zealand coast provides an opportunity to study maritime technology directly associated with the colonization of East Polynesia. A sea turtle carved on its hull makes symbolic connections with ancestral Polynesian culture. We describe the artifact, identify and radiocarbon date construction materials, and reconstruct a likely form of the canoe in the context of archaeological and ethnohistoric information. The canoe is contemporary with early archaeological settlements around New Zealand and on-going voyaging between Polynesian islands.
Climate windows for Polynesian voyaging to New Zealand and Easter Island
Authors: Goodwin Ian D. , Browning Stuart A. , Anderson Atholl J.
Published: September 2014

Significance

South Pacific migration routes used in East Polynesian colonization (A.D. 800−1500) have been assumed to be commonly upwind, when based on an understanding of modern climate patterns. Instead, our novel paleowind field reconstructions at bidecadal resolution show that migration routes lay downwind from East Polynesia during known times of initial colonization of New Zealand and Easter Island. This finding is significant in showing that a windward seafaring capacity in Polynesian colonization voyaging was not essential, and that long-term temporal variation in sailing conditions due to the expansion of the tropics was important in shaping colonization histories. The paleoclimate reconstruction broadens colonization possibilities, and the method represents a new, globally applicable approach to understanding patterning in prehistoric maritime migration.
Designer substrate library for quantitative, predictive modeling of reaction performance
Authors: Bess Elizabeth N. , Bischoff Amanda J. , Sigman Matthew S.
Published: September 2014

Significance

Product distributions of chemical reactions are dictated by a myriad of interactions between molecular species. Identifying which of these features affects reaction selectivity is a key facet for mechanistically understanding a transformation. Such insight often facilitates optimization as well as indicates which types of substrates (substrate scope) are well suited to the method. Unfortunately, the assessment of impactful features is frequently a qualitative endeavor that would significantly benefit from quantitation. We demonstrate a robust method for developing a varied substrate scope library of ketones, identifying quantitative descriptors of mechanistic significance, and applying these descriptors to mathematically elucidate trends in enantioselective reaction outcomes of rhodium-catalyzed asymmetric transfer hydrogenation. The developed mathematical relationships were used to predict future outcomes of new ketone substrates.
On inference of causality for discrete state models in a multiscale context
Authors: Gerber Susanne , Horenko Illia
Published: September 2014

Significance

The presented framework is capable of parameter identification and optimal causality inference for discrete/Boolean-valued processes in a multiscale context, allowing us to understand such processes beyond the usual statistical assumptions of standard approaches. By applying this framework to appropriately coarse-grained molecular dynamics data it is demonstrated that the optimal causality of the considered process is localized in time and space. This offers new opportunities for applying localized parameterization tools from other areas in a molecular dynamics context, thus opening up new possibilities to bridge the gap toward long timescales in molecular dynamics simulations. The new methodology is expected to become very useful in various scientific fields (bioinformatics, geoscience) where large amounts of multiscale discrete/Boolean data have been accumulated.
Bacterial quorum sensing and metabolic slowing in a cooperative population
Authors: An Jae Hyung , Goo Eunhye , Kim Hongsup , Seo Young-Su , Hwang Ingyu
Published: September 2014

Significance

Quorum sensing (QS) is a coordinated gene-regulation system that controls bacterial social behaviors, such as virulence, motility, biofilm formation, and toxin production, in response to cell density. Acyl-homoserine lactone-mediated QS coordinates cooperativity between individual cells of many
Proteobacteria
species. QS may also control nutrient acquisition and help maintain the homeostatic primary metabolism of individuals in a cooperative population. Here, we show that QS restricts glucose uptake and slows primary metabolism of individual cells in crowded conditions. QS-deficient cells experienced serious physiological challenges under similar conditions, indicating that QS functions as a means to ensure efficient energy and resource utilization of individuals in crowded environments.
Transmembrane domain of surface-exposed outer membrane lipoprotein RcsF is threaded through the lumen of β-barrel proteins
Authors: Konovalova Anna , Perlman David H. , Cowles Charles E. , Silhavy Thomas J.
Published: September 2014

Significance

In
Escherichia coli
, most outer membrane (OM) lipoproteins are thought to be soluble proteins that are simply tethered to the inner leaflet of this membrane by lipid moieties attached to the N terminus. Here we show that lipoprotein RcsF (regulator of capsule synthesis) adopts a transmembrane orientation with the lipidated N terminus on the cell surface and the folded C-terminal domain in the periplasm. The short, unstructured, polar linker domain spans the hydrophobic membrane by passing through the lumen of several different OM β-barrel proteins. This remarkable, interlocked structure is formed by the Bam complex, which folds and inserts all β-barrel proteins in the OM, suggesting that this assembly machine translocates the lipid moieties and then folds the β barrel around the RcsF linker.
The evolution of the Persian aspecto-modal suffix-ē, between the 10th and the 16th centuries
Authors: Lenepveu-Hotz Agnès
Published: September 2014

In New Persian, the aspecto-modal suffix-ēis a marker of counterfactuality and past habitual. It was frequently used in texts between the 10th and 16th centuries and did not disappear until the 18th century (earlier in some regions, depending on the dialect). However, in texts of the 15th century, -ēbegan to be replaced by the prefixmē-, which marks the concomitance, the present habitual, the frequentative-distributive and the continuative perfective. This article demonstrates that this replacement is not only morphological but that it also has a consequence for the reorganization of the aspectual and modal markings in New Persian: the replacement of-ēbymē-in all occurrences progressively leads to a loss of the marker’s first value of concomitance; it expresses all presents, concomitant and non-concomitant. The old unmarked present is marginalized and ends up expressing the subjunctive. This evolution is compared to the development described by different scholars about several unrelated languages.
Unity and diversity across Asian migrant Arabic pidgins in the Middle East
Authors: Bizri Fida
Published: September 2014

Several pidginized varieties of Arabic developed in the Middle East during the last 40 years between native Arabic-speaking employers and Asian migrants, who are mainly from the Indian subcontinent. This paper postulates the presence of a meta-category called Asian Migrant Arabic Pidgins (AMAP) under which would be grouped all the varieties attested from the Gulf area and from Lebanon, and it proposes to account for both unity and diversity between them in terms of a set of parameters where purely linguistic developments interact with contextual ones. The analysis of the social situation and of the available linguistic data shows that migrants’ mobility across the region is the major factor for homogenizing both native Arabic-speakers’ foreigner talk and migrants’ pidgin Arabic, thus validating the over-arching category of AMAP and proposing it as a useful framework for further studies of said data.
How nouns turn into adjectives
Authors: Van Goethem Kristel , De Smet Hendrik
Published: September 2014

This study focuses on French, English and Dutch adjectives that arise through debonding from N+N (and N+A) compounds or compound-like sequences (e.g. the adjectival uses of English ‘key’ and French clé “key”). Debonding is a type of degrammaticalization defined by Norde as “a composite change whereby a bound morpheme in a specific linguistic context becomes a free morpheme” (Norde, 2009: 186). We investigate for each of the three languages how the debonding process is impacted by three different factors: (1) the semantics of the noun subject to debonding, (2) the degree of prosodic and morphological cohesion of the sequence, (3) the presence of adjective inflection in the language. It is furthermore argued that in the case of Dutch, an additional process should be taken into account, that is the possibility of clipping of N+A compounds (e.g. stapel “lit. pile; madly in love” < stapelverliefd “lit. pile-in love; madly in love”).
Contrasting the syntax and semantics of negative causation
Authors: Enghels Renata , Roegiest Eugeen
Published: September 2014

The main objective of this study is to compare the structure of the factitive construction expressing negative causation withdejar/deixar(“to let”) in Ibero-Romance languages. It is generally accepted that Portuguese and Spanish exhibit a high degree of syntactic equivalence. However, the nature of the infinitive in the two languages is quite different, displaying more verbal characteristics in Portuguese than in Spanish. By means of a detailed empirical study, this article examines whether this structural difference has an effect on the syntax of the causatives withdeixaranddejar. Indeed, statistically the selection of the different complement types (finite clause vs. infinitive, with an anteposed or postposed causee) differs substantially in the two languages. A multifactorial analysis shows to what extent the degree of dynamicity of the main constituents, namely the causer, the causee and the caused event, determine the syntactic variation in the two languages and how this variation can be linked to the different grammatical status of the infinitive.
Benefaction proper and surrogation
Authors: Zúñiga Fernando
Published: September 2014

The semantic role of beneficiary is usually conceptualized in very general terms, typically without an intensive definition of what can constitute a benefit in the particular construction under study. Among those accounts that have proposed to discuss benefaction as related to the notion(s) of surrogation, substituting, and/or deputing, Kittilä (2005) proposes a distinction between recipients, beneficiaries, and recipient-beneficiaries based on the binary features [reception] and [substitutive benefaction]; the recipient includes only reception (and the beneficiary only substitutive benefaction), whereas both features are relevant with recipient-beneficiaries.

This paper proposes an alternative account (i) by defining benefaction proper in terms of a prototype related to possession (and thereby to reception) and a periphery, and (ii) by defining surrogation as a separate notion that can, but need not, coalesce with benefaction proper. Thus, the beneficiaries’ condition improves because they are relieved from having to carry out a given action themselves.
Sigma: Strain-level inference of genomes from metagenomic analysis for biosurveillance
Authors: Ahn Tae-Hyuk , Chai Juanjuan , Pan Chongle
Published: September 2014

Motivation: Metagenomic sequencing of clinical samples provides a promising technique for direct pathogen detection and characterization in biosurveillance. Taxonomic analysis at the strain level can be used to resolve serotypes of a pathogen in biosurveillance. Sigma was developed for strain-level identification and quantification of pathogens using their reference genomes based on metagenomic analysis.

Results: Sigma provides not only accurate strain-level inferences, but also three unique capabilities: (i) Sigma quantifies the statistical uncertainty of its inferences, which includes hypothesis testing of identified genomes and confidence interval estimation of their relative abundances; (ii) Sigma enables strain variant calling by assigning metagenomic reads to their most likely reference genomes; and (iii) Sigma supports parallel computing for fast analysis of large datasets. The algorithm performance was evaluated using simulated mock communities and fecal samples with spike-in pathogen strains.

Availability and Implementation: Sigma was implemented in C++ with source codes and binaries freely available at http://sigma.omicsbio.org .

Contact:  panc@ornl.gov

Supplementary information:  Supplementary data are available at Bioinformatics online.
IL-10 enhances the phenotype of M2 macrophages induced by IL-4 and confers the ability to increase eosinophil migration
Authors: Makita Naoyuki , Hizukuri Yoshiyuki , Yamashiro Kyoko , Murakawa Masao , Hayashi Yasuhiro
Published: September 2014

M2 macrophages have been subdivided into subtypes such as IL-4-induced M2a and IL-10-induced M2c in vitro. Although it was reported that IL-10 stimulation leads to an increase in IL-4Rα, the effect of IL-4 and IL-10 in combination with macrophage subtype differentiation remains unclear. Thus, we sought to clarify whether IL-10 enhanced the M2 phenotype induced by IL-4. In this study, we showed that IL-10 enhanced IL-4Rα expression in M-CSF-induced bone marrow-derived macrophages (BMDMs). Global gene expression analysis of M2 macrophages induced by IL-4, IL-10 or IL-4 + IL-10 showed that IL-10 enhanced gene expression of M2a markers induced by IL-4 in M-CSF-induced BMDMs. Moreover, IL-4 and IL-10 synergistically induced CCL24 (Eotaxin-2) production. Enhanced CCL24 expression was also observed in GM-CSF-induced BMDMs and zymosan-elicited, thioglycolate-elicited and naive peritoneal macrophages. CCL24 is a CCR3 agonist and an eosinophil chemoattractant. In vitro, IL-4 + IL-10-stimulated macrophages produced a large amount of CCL24 and increased eosinophil migration, which was inhibited by anti-CCL24 antibody. We also showed that IL-4 + IL-10-stimulated (but not IL-4 or IL-10 alone) macrophages transferred into the peritoneum of C57BL/6J mice increased eosinophil infiltration into the peritoneal cavity. These results demonstrate that IL-4 + IL-10-simulated macrophages have enhanced M2a macrophage-related gene expression, CCL24 production and eosinophil infiltration-inducing activity, thereby suggesting their contribution to eosinophil-related diseases.
Book of Kells
Authors: Farr Carol A.
Published: September 2014

The Book of Kells is a large format manuscript of the gospels, famed for the beauty and ingenuity of its decoration. One of the most renowned medieval manuscripts, its exact date and place of origin are unknown. Generally accepted to have been made in the late 8th or early 9th century, it is usually attributed to the monastery founded in 563 by the Irish holy man St. Columba on the island of Iona, off the west coast of Scotland. Written in bold Insular style scripts, it has a mixed Vulgate and Old Latin text typical of gospels associated with early medieval Ireland, but with some notable unique variants. It opens with accessory texts introducing the whole gospel book and prefatory texts proper to each gospel. Documents relating to lands of the Columban monastery at Kells were written on blank sides of several of these prefatory folios in the 11th and 12th centuries, providing evidence of its later medieval location. Some scholars attribute all or part of it to Kells, founded in the early 9th century after Viking attacks on Iona. The manuscript was removed from Kells during the religious and political turmoil of the 17th century and eventually sent to Dublin, where it was given to Trinity College Library. Today, as Manuscript 58, it remains at Trinity. One of Ireland’s most precious treasures, its visual art and historical aura are part of the modern Irish national self-image. It contains all types of Insular manuscript art: “beast” canon tables, four-symbols pages, full-page initials, an evangelist portrait, full-page pictures, one “cross-carpet” page, and thousands of decorated minor initials. Modern scholarship is mainly art-historical, with concentration on “word and image” and other interpretative studies. Efforts to determine the date of origin have receded from the contentious debates of the 20th century, as to a lesser extent have the arguments over its place of origin, with recognition of the general cultural unity of Ireland and the British Isles in the early Middle Ages and the fading of modern prejudices. Date and origin remain, however, unresolved important questions, with the absence of conclusive argument frustrating detailed contextual studies. Other questions, such as the number of artists and scribes who contributed to the manuscript and how often and by whom it was viewed, also remain without definitive answers. Despite the knowledge gaps, the Book of Kells remains one of the most discussed works of the early Middle Ages.