bluuebunny/crossref_metadata_2025 huggingface dataset:
4′-O-substitutions determine selectivity of aminoglycoside antibiotics
Authors: Perez-Fernandez Déborah , Shcherbakov Dmitri , Matt Tanja , Leong Ng Chyan , Kudyba Iwona , Duscha Stefan , Boukari Heithem , Patak Rashmi , Dubbaka Srinivas Reddy , Lang Kathrin , Meyer Martin , Akbergenov Rashid , Freihofer Pietro , Vaddi Swapna , Thommes Pia , Ramakrishnan V. , Vasella Andrea , Böttger Erik C.
Published: January 2014

Clinical use of 2-deoxystreptamine aminoglycoside antibiotics, which target the bacterial ribosome, is compromised by adverse effects related to limited drug selectivity. Here we present a series of 4′,6′-O-acetal and 4′-O-ether modifications on glucopyranosyl ring I of aminoglycosides. Chemical modifications were guided by measuring interactions between the compounds synthesized and ribosomes harbouring single point mutations in the drug-binding site, resulting in aminoglycosides that interact poorly with the drug-binding pocket of eukaryotic mitochondrial or cytosolic ribosomes. Yet, these compounds largely retain their inhibitory activity for bacterial ribosomes and show antibacterial activity. Our data indicate that 4′-O-substituted aminoglycosides possess increased selectivity towards bacterial ribosomes and little activity for any of the human drug-binding pockets.
Dike intrusions during rifting episodes obey scaling relationships similar to earthquakes
Authors: L. Passarelli , E. Rivalta , A. Shuler
Published: January 2014

As continental rifts evolve towards mid-ocean ridges, strain is accommodated by repeated episodes of faulting and magmatism. Discrete rifting episodes have been observed along two subaerial divergent plate boundaries, the Krafla segment of the Northern Volcanic Rift Zone in Iceland and the Manda-Hararo segment of the Red Sea Rift in Ethiopia. In both cases, the initial and largest dike intrusion was followed by a series of smaller intrusions. By performing a statistical analysis of these rifting episodes, we demonstrate that dike intrusions obey scaling relationships similar to earthquakes. We find that the dimensions of dike intrusions obey a power law analogous to the Gutenberg-Richter relation and the long-term release of geodetic moment is governed by a relationship consistent with the Omori law. Due to the effects of magma supply, the timing of secondary dike intrusions differs from that of the aftershocks. This work provides evidence of self-similarity in the rifting process.
New strategy to construct single-ion magnets: a unique Dy@Zn6 cluster exhibiting slow magnetic relaxation
Authors: Xiong Gang , Qin Xiang-Yang , Shi Peng-Fei , Hou Yin-Ling , Cui Jian-Zhong , Zhao Bin
Published: January 2014

A unique mononuclear dysprosium ion encapsulated inside a diamagnetic Zn6 cage exhibits a single-ion magnet behavior.
Achieving single domain relaxor-PT crystals by high temperature poling
Authors: Li Fei , Wang Linghang , Jin Li , Xu Zhuo , Zhang Shujun
Published: January 2014

Single domain relaxor-PT crystals are important from both fundamental and application viewpoints.
Recent advances in secondary ion mass spectrometry of solid acid catalysts: large zeolite crystals under bombardment
Authors: Hofmann Jan P. , Rohnke Marcus , Weckhuysen Bert M.
Published: January 2014

Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) is used for the characterization of heterogeneous catalysts. Large zeolite ZSM-5 crystals are discussed as a showcase system for solid acid catalysts and studied in high-resolution mass spectrometry, imaging, and sputter-depth profiling modes.
Dispersion corrected DFT approaches for anharmonic vibrational frequency calculations: nucleobases and their dimers
Authors: Fornaro Teresa , Biczysko Malgorzata , Monti Susanna , Barone Vincenzo
Published: January 2014

Toward a comprehensive and robust computational protocol for simulation of fully anharmonic vibrational (IR) spectra of nucleic acid base complexes and their adsorption on solid supports (organic/inorganic).
Extinction and extra-high depolarized light scattering spectra of gold nanorods with improved purity and dimension tunability: direct and inverse problems
Authors: Khlebtsov Boris N. , Khanadeev Vitaly A. , Khlebtsov Nikolai G.
Published: January 2014

High pure binary-surfactant gold nanorods demonstrate unprecedented depolarization ratio IVH/IVV approaching the theoretical limit 75%. The nanorod parameters can be retrieved from the extinction and depolarization spectra.
Synthesis of the phase pure Ba3Si6O12N2:Eu2+ green phosphor and its application in high color rendition white LEDs
Authors: Li Wanyuan , Xie Rong-Jun , Zhou Tianliang , Liu Lihong , Zhu Yuejin
Published: January 2014

A phase pure green Ba3Si6O12N2:Eu2+ phosphor (left) was successfully synthesized by controlling the Si/Ba and O/Ba of the starting materials, and it has great potential to prepare high CRI (Ra > 90) white LEDs (right).
Novel “3-D spacer” all fibre piezoelectric textiles for energy harvesting applications
Authors: Soin Navneet , Shah Tahir H. , Anand Subhash C. , Geng Junfeng , Pornwannachai Wiwat , Mandal Pranab , Reid David , Sharma Surbhi , Hadimani Ravi L. , Bayramol Derman Vatansever , Siores Elias
Published: January 2014

Using “3D-spacer” technology, we have knitted 80% β-phase PVDF with Ag/PA66 fibres to demonstrate all fibre piezoelectric power generators. The 3D structure provides a power density of 1.10–5.10 μW cm−2at applied impacts of 0.02–0.10 MPa.
Hydrodeoxygenation of vanillin as a bio-oil model over carbonaceous microspheres-supported Pd catalysts in the aqueous phase and Pickering emulsions
Authors: Zhu Zhibin , Tan Hongyi , Wang Jin , Yu Shuzhen , Zhou Kebin
Published: January 2014

Amphiphilic carbonaceous microspheres-supported Pd catalysts are effective in hydrodeoxygenation of vanillin in aqueous phase and Pickering emulsions.
Micro-sublimation separation of boron in rock samples for isotopic measurement by MC-ICPMS
Authors: Pi Ju-lien , You Chen-Feng , Chung Chuan-Hsiung
Published: January 2014

The technique of micro-sublimation for boron (B) separation in silicates has been evaluated carefully.
Phase transformation and enhanced photocatalytic activity of S-doped Ag2O/TiO2 heterostructured nanobelts
Authors: Zhou W. J. , Leng Y. H. , Hou D. M. , Li H. D. , Li L. G. , Li G. Q. , Liu H. , Chen S. W.
Published: January 2014

Ag2O/Ag2S2O7/TiO2 heterostructured photocatalysts with enhanced and stable photocatalytic activity under both ultraviolet and visible light irradiation were obtained by the S-doping of Ag2O/TiO2.
Porous Pd nanoparticles with high photothermal conversion efficiency for efficient ablation of cancer cells
Authors: Xiao Jia-Wen , Fan Shi-Xuan , Wang Feng , Sun Ling-Dong , Zheng Xiao-Yu , Yan Chun-Hua
Published: January 2014

Pd NPs with a porous structure exhibit enhanced near infrared (NIR) absorption and enhanced photothermal effect compared to Pd nanocubes with a similar size, and show very high efficacy in photothermal ablation of HeLa cells.
1-Dimensional AgVO3 nanowires hybrid with 2-dimensional graphene nanosheets to create 3-dimensional composite aerogels and their improved electrochemical properties
Authors: Liang Liying , Xu Yimeng , Lei Yong , Liu Haimei
Published: January 2014

3D porous AgVO3 nanowires/graphene composite aerogels show high electrical conductivity, high mechanical flexibility, and good electrochemical performance for lithium ion storage.
Recent progress on asymmetric organocatalytic construction of chiral cyclohexenone skeletons
Authors: Yang Xin , Wang Jun , Li Pengfei
Published: January 2014

Chiral cyclohex-2-enones are important intermediates in synthetic chemistry as well as in the life science industries. In this focus review, recent advances in the organocatalytic asymmetric synthesis of chiral cyclohex-2-enone skeletons are summarized. The reaction mechanisms are also briefly discussed.
Direct sp3 C–H acroleination of N-aryl-tetrahydroisoquinolines by merging photoredox catalysis with nucleophilic catalysis
Authors: Feng Zhu-Jia , Xuan Jun , Xia Xu-Dong , Ding Wei , Guo Wei , Chen Jia-Rong , Zou You-Quan , Lu Liang-Qiu , Xiao Wen-Jing
Published: January 2014

Sequence catalysis merging photoredox catalysis (PC) and nucleophilic catalysis (NC) has been realized for the direct sp3 C–H acroleination of N-aryl-tetrahydroisoquinoline (THIQ), affording products in 50–91% yields.
NHC-catalyzed oxidative cyclization reaction for the synthesis of 3-substituted phthalides
Authors: Youn So Won , Song Hyoung Sub , Park Jong Hyub
Published: January 2014

An efficient NHC-catalyzed domino oxidation/oxa-Michael addition reaction of 2-alkenylbenzaldehydes has been developed to afford 3-substituted phthalides bearing a C3-stereogenic center with a broad substrate scope and wide functional group tolerance.
Catalytic materials for the hydrogenolysis of glycerol to 1,3-propanediol
Authors: Nakagawa Yoshinao , Tamura Masazumi , Tomishige Keiichi
Published: January 2014

The combinations of Pt–W and Ir–Re can catalyze the hydrogenolysis of glycerol to 1,3-propanediol in high selectivity.
A metallic carbon allotrope with superhardness: a first-principles prediction
Authors: Bu Hongxia , Zhao Mingwen , Dong Wenzheng , Lu Shuangwen , Wang Xiaopeng
Published: January 2014

From first-principles calculations, a novel carbon material with superhardness and metallicity is proposed and a possible endothermic transition is evaluated.
Calcium mediated formation of phosphorylcholine-based polyplexes for efficient knockdown of epidermal growth factor receptors (EGFR) in HeLa cells
Authors: Ahmed Marya , Ishihara Kazuhiko , Narain Ravin
Published: January 2014

Calcium mediated complexation of siRNA with phosphorylcholine based polymers for efficient gene knockdown in HeLa cells in the presence and absence of serum.
Room temperature biological quantum random walk in phycocyanin nanowires
Authors: Eisenberg Ido , Yochelis Shira , Ben-Harosh Roy , David Liron , Faust Adam , Even-Dar Naama , Taha Hesham , Haegel Nancy M. , Adir Noam , Keren Nir , Paltiel Yossi
Published: January 2014

Self ordered phycocyanin nanowires as building blocks for future quantum nano-devices.
The role of size and coating in Au nanoparticles incorporated into bi-component polymeric thin-film transistors
Authors: Mosciatti Thomas , Orgiu Emanuele , Raimondo Corinna , Samorì Paolo
Published: January 2014

We correlate the effect of size and coating of Au nanoparticles blended with P3HT on the electronic properties of the multicomponent OTFT.
Encapsulation and selectivity of sulfate with a furan-based hexaazamacrocyclic receptor in water
Authors: Rhaman Md Mhahabubur , Ahmed Lucky , Wang Jing , Powell Douglas R. , Leszczynski Jerzy , Hossain Md. Alamgir
Published: January 2014

A furan-based hexaazamacrocycle encapsulates a sulfate anion in its cavity showing strong affinity and selectivity for sulfate in water.
Bifunctional ferrocene-based squaramide-phosphine as an organocatalyst for highly enantioselective intramolecular Morita–Baylis–Hillman reaction
Authors: Zhang Xiaorui , Ma Pengfei , Zhang Dongxu , Lei Yang , Zhang Shengyong , Jiang Ru , Chen Weiping
Published: January 2014

Ferrocene is an excellent scaffold for organocatalysts. Bifunctional ferrocene-based phosphine (RC,SFc)-1 shows high enantioselectivity in the intramolecular Morita–Baylis–Hillman reaction of 7-aryl-7-oxo-5-heptenals.
Differential functions of calpain 1 during epithelial cell death and adipocyte differentiation in mammary gland involution
Authors: Arnandis Teresa , Ferrer-Vicens Ivan , Torres Luis , García Concha , Garcia-Trevijano Elena R. , Zaragoza Rosa , Viña Juan R.
Published: January 2014

Calpains become activated in the mammary gland early during weaning, cleaving several proteins located mainly in the cell membrane, but also in other organelles such as lysosomes, mitochondria and nuclei. By immunofluorescence and Western blot analysis, we have demonstrated the nuclear translocation of calpain-1 and calpain-2, together with the cleavage of several cytoplasmic nucleoporins in epithelial cells of the lobulo-alveolar compartment. In vivo and in vitro calpain inhibition prevented this nucleoporin degradation. In addition, calpain-1 was also present in the nucleus of non-epithelial mammary tissue cells, concomitant with adipocyte re-differentiation. Calpain-1 was internalized within nuclei and found to be present in the nuclear chromatin-enriched fraction, associated with histone H3. Furthermore, we have demonstrated, both in vivo and in vitro, the cleavage of the N-terminal residue of histone H3 by calpain-1. Calpain-1 co-localized with both H3K4me3 (histone H3 trimethylated at Lys4) and H3K27me3 (histone H3 trimethylated at Lys27) at the nuclear periphery, a bivalent epigenetic signal essential for cell differentiation. Using ChIP assays we could confirm the presence of calpain-1 in the promoters of key genes expressed in adipose tissue, such as Cebpa (CCAAT/enhancer-binding protein α) and Lep (leptin). The results of the present study highlight a dual role for calpain-1 in the weaned gland after the pregnancy/lactation cycle, controlling programmed cell death and participating in the epigenetic programme during adipocyte differentiation.
Managing Technological Change in the Digital Age: The Role of Architectural Frames
Authors: Henfridsson Ola , Mathiassen Lars , Svahn Fredrik
Published: January 2014

Inspired by Herbert Simon's notion of nearly decomposable systems, researchers have examined modularity as a powerful approach to manage technological change in product innovation. We articulate this approach as the hierarchy-of-parts architecture and explain how it emphasizes decomposition of a design into loosely coupled parts and subsequent aggregation of these into an industrial product. To realize the scale benefits of modularity, firms successively freeze design specifications before production and therefore only allow limited windows of functionality design and redesign. This makes it difficult to take advantage of the increased speed by which digitized products can be developed and modified. To address this problem, we draw on Christopher Alexander's notion of design patterns to introduce a complementary approach to manage technological change that is resilient to digital technology. We articulate this approach as the network-of-patterns architecture and explain how it emphasizes generalization of ideas into patterns and subsequent specialization of patterns for different design purposes. In response to the increased digitization of industrial products, we demonstrate the value of complementing hierarchy-of-parts thinking with network-of-patterns thinking through a case study of infotainment architecture at an automaker. As a result, we contribute to the literature on managing products in the digital age: we highlight the properties of digital technology that increase the speed by which digitized products can be redesigned; we offer the notion of architectural frames and propose hierarchy-of-parts and network-of-patterns as frames to support innovation of digitized products; and, we outline an agenda for future research that reconsiders the work of Simon and Alexander as well as their followers to address key challenges in innovating digitized products.
Perspective: Crystal structure prediction at high pressures
Authors: Wang Yanchao , Ma Yanming
Published: January 2014

Crystal structure prediction at high pressures unbiased by any prior known structure information has recently become a topic of considerable interest. We here present a short overview of recently developed structure prediction methods and propose current challenges for crystal structure prediction. We focus on first-principles crystal structure prediction at high pressures, paying particular attention to novel high pressure structures uncovered by efficient structure prediction methods. Finally, a brief perspective on the outstanding issues that remain to be solved and some directions for future structure prediction researches at high pressure are presented and discussed.
Tracer diffusion inside fibrinogen layers
Authors: Cieśla Michał , Gudowska-Nowak Ewa , Sagués Francesc , Sokolov Igor M.
Published: January 2014

We investigate the obstructed motion of tracer (test) particles in crowded environments by carrying simulations of two-dimensional Gaussian random walk in model fibrinogen monolayers of different orientational ordering. The fibrinogen molecules are significantly anisotropic and therefore they can form structures where orientational ordering, similar to the one observed in nematic liquid crystals, appears. The work focuses on the dependence between level of the orientational order (degree of environmental crowding) of fibrinogen molecules inside a layer and non-Fickian character of the diffusion process of spherical tracer particles moving within the domain. It is shown that in general particles motion is subdiffusive and strongly anisotropic, and its characteristic features significantly change with the orientational order parameter, concentration of fibrinogens, and radius of a diffusing probe.
Cascading and local-field effects in non-linear optics revisited: A quantum-field picture based on exchange of photons
Authors: Bennett Kochise , Mukamel Shaul
Published: January 2014

The semi-classical theory of radiation-matter coupling misses local-field effects that may alter the pulse time-ordering and cascading that leads to the generation of new signals. These are then introduced macroscopically by solving Maxwell's equations. This procedure is convenient and intuitive but ad hoc. We show that both effects emerge naturally by including coupling to quantum modes of the radiation field that are initially in the vacuum state to second order. This approach is systematic and suggests a more general class of corrections that only arise in a QED framework. In the semi-classical theory, which only includes classical field modes, the susceptibility of a collection of N non-interacting molecules is additive and scales as N. Second-order coupling to a vacuum mode generates an effective retarded interaction that leads to cascading and local field effects both of which scale as N2.
Trajectory surface hopping study of the O(3P) + C2H2 reaction dynamics: Effect of collision energy on the extent of intersystem crossing
Authors: Rajak Karunamoy , Maiti Biswajit
Published: January 2014

Intersystem crossing (ISC) dynamics plays an important role in determining the product branching in the O(3P) + C2H2 reaction despite the necessarily small spin-orbit coupling constant values. In this study we investigate the effect of collision energy on the extent of the contribution of a spin non-conserving route through ISC dynamics to the product distributions at the initial collision energies 8.2, 9.5, and 13.1 kcal/mol. A direct dynamics trajectory surface hopping method is employed with potential energy surfaces generated at the unrestricted B3LYP/6-31G(d,p) level of theory to perform nonadiabatic dynamics. To make our calculation simpler, nonadibatic transitions were only considered at the triplet-singlet intersections. At the crossing points, Landau-Zener transition probabilities were calculated using spin-orbit coupling constant values computed at the same geometry. The Landau-Zener model for the title reaction is validated against a more rigorous Tully's fewest switches method and found to be working reasonably well as expected because of weak spin-orbit coupling. We have compared our results with the recent crossed molecular beam experiments and observed a very good agreement with respect to the primary product branching ratios. Our calculation revealed that there is no noticeable effect of the initial collision energy on the overall product distributions that corroborates the recent experimental findings. Our calculation indicates, however, that the extent of intersystem crossing contributions varies significantly with collision energy, needed to be verified, experimentally.
Communication: State mixing by spin-orbit coupling in the anionic chloroiodine dissociations
Authors: Xia L. , Wang X.-D. , Xuan C.-J. , Zeng X.-J. , Li H.-K. , Tian S. X. , Pan Y. , Lau K.-C.
Published: January 2014

Three spin-orbit states, 12Π1/2, 22Π3/2, and 22Π1/2, of chloroiodine anion (ICl−) formed by low-energy electron attachment in the Franck-Condon region are associated with the dissociative limits of I− (1S0) and Cl (2P3/2) or Cl* (2P1/2) fragments. Within the adiabatic scheme, the presumptive Π-symmetry of the fragment angular distributions is dramatically changed to be the Π-Σ mixing symmetry, due to the significant spin-orbit interaction effect on the electronic state couplings of ICl−. The present experimental approach also enables us to separate the contributions of different electronic states from the mixed states, providing a crucial method for quantitatively evaluating the configuration-interaction wavefunctions.
Dependence of adsorption-induced structural transition on framework structure of porous coordination polymers
Authors: Numaguchi Ryohei , Tanaka Hideki , Watanabe Satoshi , Miyahara Minoru T.
Published: January 2014

Porous coordination polymers (PCPs) with soft frameworks show a gate phenomenon consisting of an abrupt structural transition induced by adsorption of guest molecules. To understand the dependence of the gating behavior on the host framework structure, we conduct grand canonical Monte Carlo simulations and a free-energy analysis of a simplified model of a stacked-layer PCP. The interlayer width of the rigid layers composing the simplified model can be changed by guest adsorption and by varying the initial interlayer width h0, which is controlled by the length of pillars between the layers. We introduce three types of gating behavior, one-step gating, filling and gating, and double gating, which depend on three parameters: the initial interlayer width h0; the interaction parameter ɛss, which determines the host–guest framework interaction as well as the inter-framework interaction; and the elastic modulus of the framework, which depends on the stiffness of the pillars. We show that the one-step gating and the filling and gating behaviors depend strongly on h0 rather than on ɛss, and thus a transformation from filling and gating to double gating can be achieved by reducing the stiffness of the host framework. This study should be a guideline for controlling the gating pressure of PCPs by modifying their chemical components.
The solvation radius of silicate melts based on the solubility of noble gases and scaled particle theory
Authors: Ottonello Giulio , Richet Pascal
Published: January 2014

The existing solubility data on noble gases in high-temperature silicate melts have been analyzed in terms of Scaling Particle Theory coupled with an ab initio assessment of the electronic, dispersive, and repulsive energy terms based on the Polarized Continuum Model (PCM). After a preliminary analysis of the role of the contracted Gaussian basis sets and theory level in reproducing appropriate static dipole polarizabilities in a vacuum, we have shown that the procedure returns Henry's law constants consistent with the values experimentally observed in water and benzene at T = 25 °C and P = 1 bar for the first four elements of the series. The static dielectric constant (ɛ) of the investigated silicate melts and its optical counterpart (ɛ∞) were then resolved through the application of a modified form of the Clausius-Mossotti relation. Argon has been adopted as a probe to depict its high-T solubility in melts through an appropriate choice of the solvent diameter σs, along the guidelines already used in the past for simple media such as water or benzene. The σs obtained was consistent with a simple functional form based on the molecular volume of the solvent. The solubility calculations were then extended to He, Ne, and Kr, whose dispersive and repulsive coefficients are available from theory and we have shown that their ab initio Henry's constants at high T reproduce the observed increase with the static polarizability of the series element with reasonable accuracy. At room temperature (T = 25 °C) the calculated Henry's constants of He, Ne, Ar, and Kr in the various silicate media predict higher solubilities than simple extrapolations (i.e., Arrhenius plots) based on high-T experiments and give rise to smooth trends not appreciably affected by the static polarizabilities of the solutes. The present investigation opens new perspectives on a wider application of PCM theory which can be extended to materials of great industrial interest at the core of metallurgical processes, ceramurgy, and the glass industry.
Comparing thermal wave function methods for multi-configuration time-dependent Hartree simulations
Authors: Lorenz U. , Saalfrank P.
Published: January 2014

We compare two methods for creating stochastic temperature wave functions that can be used for Multi-Configuration Time-Dependent Hartree (MCTDH) simulations. In the first method, the MCTDH coefficients are chosen randomly, while the other method uses a single Hartree product of random single-particle functions (SPFs). We find that using random SPFs dramatically improves convergence for a model system for surface sticking.
Communication: Ab initio simulations of hydrogen-bonded ferroelectrics: Collective tunneling and the origin of geometrical isotope effects
Authors: Wikfeldt K. T. , Michaelides A.
Published: January 2014

Ab initio simulations that account for nuclear quantum effects have been used to examine the order-disorder transition in squaric acid, a prototypical H-bonded antiferroelectric crystal. Our simulations reproduce the >100 K difference in transition temperature observed upon deuteration as well as the strong geometrical isotope effect observed on intermolecular separations within the crystal. We find that collective transfer of protons along the H-bonding chains – facilitated by quantum mechanical tunneling – is critical to the order-disorder transition and the geometrical isotope effect. This sheds light on the origin of isotope effects and the importance of tunneling in squaric acid which likely extends to other H-bonded ferroelectrics.
Understanding the length dependence of molecular junction thermopower
Authors: Karlström Olov , Strange Mikkel , Solomon Gemma C.
Published: January 2014

Thermopower of molecular junctions is sensitive to details in the junction and may increase, decrease, or saturate with increasing chain length, depending on the system. Using McConnell's theory for exponentially suppressed transport together with a simple and easily interpretable tight binding model, we show how these different behaviors depend on the molecular backbone and its binding to the contacts. We distinguish between resonances from binding groups or undercoordinated electrode atoms, and those from the periodic backbone. It is demonstrated that while the former gives a length-independent contribution to the thermopower, possibly changing its sign, the latter determines its length dependence. This means that the question of which orbitals from the periodic chain that dominate the transport should not be inferred from the sign of the thermopower but from its length dependence. We find that the same molecular backbone can, in principle, show four qualitatively different thermopower trends depending on the binding group: It can be positive or negative for short chains, and it can either increase or decrease with length.
Genetic dissection of plexin signaling in vivo
Authors: Worzfeld Thomas , Swiercz Jakub M. , Sentürk Aycan , Genz Berit , Korostylev Alexander , Deng Suhua , Xia Jingjing , Hoshino Mikio , Epstein Jonathan A. , Chan Andrew M. , Vollmar Brigitte , Acker-Palmer Amparo , Kuner Rohini , Offermanns Stefan
Published: January 2014

Significance

Plexins, a family of transmembrane receptors for semaphorins, control diverse biological processes during mouse development. However, it is largely unknown through which signaling pathways they exert their functions in vivo. Using an allelic series of transgenic mice, we show that the GTPase activating protein domain of plexins constitutes their key signaling module during development, which is required for proper formation of the nervous, cardiovascular, and skeletal system. In contrast, development of the liver vasculature specifically depends on the activation of the small GTPase RhoA by the plexin family member Plexin-B2. This study uncovers the in vivo context-dependence and functional specificity of individual plexin-mediated signaling pathways during mouse development.
High-throughput combinatorial screening identifies drugs that cooperate with ibrutinib to kill activated B-cell–like diffuse large B-cell lymphoma cells
Authors: Mathews Griner Lesley A. , Guha Rajarshi , Shinn Paul , Young Ryan M. , Keller Jonathan M. , Liu Dongbo , Goldlust Ian S. , Yasgar Adam , McKnight Crystal , Boxer Matthew B. , Duveau Damien Y. , Jiang Jian-Kang , Michael Sam , Mierzwa Tim , Huang Wenwei , Walsh Martin J. , Mott Bryan T. , Patel Paresma , Leister William , Maloney David J. , Leclair Christopher A. , Rai Ganesha , Jadhav Ajit , Peyser Brian D. , Austin Christopher P. , Martin Scott E. , Simeonov Anton , Ferrer Marc , Staudt Louis M. , Thomas Craig J.
Published: January 2014

Significance

The treatment of cancer is highly reliant on drug combinations. Next-generation, targeted therapeutics are demonstrating interesting single-agent activities in clinical trials; however, the discovery of companion drugs through iterative clinical trial-and-error is not a tenable mechanism to prioritize clinically important combinations for these agents. Herein we describe the results of a large, high-throughput combination screen of the Bruton’s tyrosine kinase inhibitor ibrutinib versus a library of nearly 500 approved and investigational drugs. Multiple ibrutinib combinations were discovered through this study that can be prioritized for clinical examination.
Selective mRNA sequestration by OLIGOURIDYLATE-BINDING PROTEIN 1 contributes to translational control during hypoxia in
Arabidopsis
Authors: Sorenson Reed , Bailey-Serres Julia
Published: January 2014

Significance

Posttranscriptional mechanisms that regulate the localization, stability, and translation of individual mRNAs are important factors in fine-tuning gene expression. Under low oxygen conditions, cellular protein synthesis is rapidly reduced and highly selective until reoxygenation. Here, we show that the preferential translation of stress-induced mRNAs over abundant nonstress transcripts is associated with the selective sequestration of mRNAs into large granular cytoplasmic complexes. The aggregation involves an RNA-binding protein and principally affects the transcripts that are not upregulated by the stress. This mechanism provides a means for rapid oscillation of mRNA translational activity in response to a transient energy stress.
A note on derivations of Murray–von Neumann algebras
Authors: Kadison Richard V. , Liu Zhe
Published: January 2014

Significance

In this article, derivations of algebras of unbounded operators acting on a Hilbert space are discussed. Derivations appear as the generators of one-parameter groups that express the symmetries and dynamical evolution of quantum-mechanical systems. One can see this relation to derivations by examining Dirac's Program for a mathematical formulation of the fundamentals of quantum mechanics.
Critical role for IL-1β in DNA damage-induced mucositis
Authors: Kanarek Naama , Grivennikov Sergei I. , Leshets Michael , Lasry Audrey , Alkalay Irit , Horwitz Elad , Shaul Yoav D. , Stachler Matthew , Voronov Elena , Apte Ron N. , Pagano Michele , Pikarsky Eli , Karin Michael , Ghosh Sankar , Ben-Neriah Yinon
Published: January 2014

Significance

Deletion of the E3 β-TrCP in the mouse gut epithelium deregulates enterocyte cell cycle, induces a DNA damage response (DDR), and abolishes the epithelium barrier function, resulting in a lethal mucosal inflammation. Epithelial-derived IL-1β, likely induced by DDR independently of NF-κB, is a major culprit, and initiates the pathology by compromising epithelial tight junctions (TJs). Anti–IL-1β treatment secures the TJs and prevents the fulminant mucosal inflammation. IL-1β secretion accompanies human mucositis, a severe mucosal inflammatory reaction caused by chemoradiation therapy-induced DNA damage, which often results in treatment suspension. We propose that anti–IL-1β preventive treatment may ameliorate mucositis, as well as multiple disorders associated with epithelial barrier permeability, including burn injuries, head and neck trauma, alcoholic intoxication, and graft-vs.-host disease.
On the dephasing of genetic oscillators
Authors: Potoyan Davit A. , Wolynes Peter G.
Published: January 2014

Significance

Genetic oscillators are ubiquitous regulatory motifs in the molecular control circuits of living cells. Prominent examples include the cell cycle and cellular signaling. There are two primary sources of noise in these oscillators: the binary character of gene states and the low copy numbers of proteins. This molecular noise induces dephasing in oscillators in analogy to the way imperfections in clocks lead to disparities in time. We can study how these two distinct sources contribute to dephasing and how well it can be approximated by adding noise to a macroscopic model. Using the
NFκB
/
IκB
oscillator as an example, we find that gene noise leads to significant deviations from the often-used phenomenological models.
Using constellation pharmacology to define comprehensively a somatosensory neuronal subclass
Authors: Teichert Russell W. , Memon Tosifa , Aman Joseph W. , Olivera Baldomero M.
Published: January 2014

Significance

Change in the nervous system occurs in response to diverse inputs, both normal and pathological. Defining such changes is required for understanding normal nervous-system functions and pathologies—e.g., from learning and memory to intractable disease. A unique combination pharmacology strategy allows identification of distinct neuronal subclasses through their constant functional expression of a specific subset of signaling proteins. Phenotypic alterations in signaling for one specific neuronal subclass were tracked as a function of development. These alterations provide proof-of-principle that changes in individual types of neurons can be monitored as a function of learning, disease, or aging. Developing biomarkers and therapeutic interventions for intractable nervous-system pathologies will require simultaneously monitoring different neuronal subclasses for such changes early during disease progression.
Präteritumschwund und Diskursgrammatik
Authors: Abraham Werner , Conradie C. Jac
Published: January 2014

This work demonstrates that what is commonly called preterite decay in Upper German (PS; cf. German Präteritumschwund) is in fact a phenomenon common to a great number of European languages, all of which are in areal con-tact. However, the conclusion that this is a phenomenon arising under areal influence appears clearly mistaken — not only so because it would no more than postpone the search for the real trigger of this development. It will be shown, first, that the preterite loss in the languages under inspection comes in different states of completion. It will be seen that the loss of the preterite, under this perspective, German is by no means a completed process. Second, and what is more, it will be argued that the trigger for this decay of the synthetic preterite and its replacement by analytic preterite forms is the specific criteria under which oral (as opposed to written) communication is executed. Counter to the rich, existing literature on the topic, a number of parsing principles will be claimed to be responsible for this diachronic development yielding different results due to a different execution of these principles.
Mediating Criticism
Authors: Sell Roger D.
Published: January 2014

In the twentieth century, literature was under threat. Not only was there the challenge of new forms of oral and visual culture. Even literary education and literary criticism could sometimes actually distance novels, poems and plays from their potential audience. This is the trend which Roger D. Sell now seeks to reverse. Arguing that literature can still be a significant and democratic channel of human interactivity, he sees the most helpful role of teachers and critics as one of mediation. Through their own example they can encourage readers to empathize with otherness, to recognize the historical achievement of significant acts of writing, and to respond to literary authors’ own faith in communication itself. By way of illustration, he offers major re-assessments of five canonical figures (Vaughan, Fielding, Dickens, T.S. Eliot, and Frost), and of two fascinating twentieth-century writers who were somewhat misunderstood (the novelist William Gerhardie and the poet Andrew Young).
Introduction to Neurolinguistics
Authors: Ahlsén Elisabeth
Published: January 2014

This introduction to neurolinguistics is intended for anybody who wants to acquire a grounding in the field. It was written for students of linguistics and communication disorders, but students of psychology, neuroscience and other disciplines will also find it valuable. The introductory section presents the theories, models and frameworks underlying modern neurolinguistics. Then the neurolinguistic aspects of different components of language – phonology, morphology, lexical semantics, and semantics-pragmatics in communication – are discussed. The third section examines reading and writing, bilingualism, the evolution of language, and multimodality. The book also contains three resource chapters, one on techniques for investigating the brain, another on modeling brain functions, and a third that introduces the basic concepts of neuroanatomy and neurophysiology. This text provides an up-to-date linguistic perspective, with a special focus on semantics and pragmatics, evolutionary perspectives, neural network modeling and multimodality, areas that have been less central in earlier introductory works.
An Introduction to the Theory of Formal Languages and Automata
Authors: Levelt Willem J.M.
Published: January 2014

The present text is a re-edition of Volume I of Formal Grammars in Linguistics and Psycholinguistics, a three-volume work published in 1974. This volume is an entirely self-contained introduction to the theory of formal grammars and automata, which hasn’t lost any of its relevance. Of course, major new developments have seen the light since this introduction was first published, but it still provides the indispensible basic notions from which later work proceeded. The author’s reasons for writing this text are still relevant: an introduction that does not suppose an acquaintance with sophisticated mathematical theories and methods, that is intended specifically for linguists and psycholinguists (thus including such topics as learnability and probabilistic grammars), and that provides students of language with a reference text for the basic notions in the theory of formal grammars and automata, as they keep being referred to in linguistic and psycholinguistic publications; the subject index of this introduction can be used to find definitions of a wide range of technical terms. An appendix has been added with further references to some of the core new developments since this book originally appeared.
Stylistic Use of Phraseological Units in Discourse
Authors: Naciscione Anita
Published: January 2014

Stylistic Use of Phraseaological Units in Discourse received honourable mention of the ESSE Book Award 2012 in the field of English Language and Linguistics.

This interdisciplinary study presents the cutting-edge state of theoretical and applied research in the fascinating field of phraseology. The author elaborates key terminology and theoretical concepts of phraseology, while challenging some prevailing assumptions. Exploration of phraseological meaning across sentence boundaries is supported by ample textual illustrations of stylistic use ranging from Old English to Modern English. The book contains innovative research in the discourse-level features of phraseological units from a cognitive perspective, along with creative use of phraseological metaphor, metonymy and allusion, multimodal discourse included. The author argues for applied stylistics as a distinct area and the need to raise stylistic awareness among teachers and learners, translators, lexicographers and advertisers. The book offers an extensive glossary of key terms and a comprehensive bibliography.
Stylistic Use of Phraseological Units in Discourse is a skilfully revised and extensively expanded new edition of the author’s previously published 'Phraseological Units in Discourse: Towards Applied Stylistics' (2001).
An Introduction to Linguistic Typology
Authors: Velupillai Viveka
Published: January 2014

This clear and accessible introduction to linguistic typology covers all linguistic domains from phonology and morphology over parts-of-speech, the NP and the VP, to simple and complex clauses, pragmatics and language change. There is also a discussion on methodological issues in typology. This textbook is the first introduction that consistently applies the findings of the World Atlas of Language Structures, systematically includes pidgin and creole languages and devotes a section to sign languages in each chapter. All chapters contain numerous illustrative examples and specific feature maps. Keywords and exercises help review the main topics of each chapter. Appendices provide macro data for all the languages cited in the book as well as a list of web sites of typological interest. An extensive glossary gives at-a-glance definitions of the terms used in the book. This introduction is designed for students of courses with a focus on language diversity and typology, as well as typologically-oriented courses in morphology and syntax. The book will also serve as a guide for field linguists.
An Interdisciplinary Bibliography on Language, Gender and Sexuality (2000–2011)
Authors: Motschenbacher Heiko
Published: January 2014

This comprehensive, state-of-the-art bibliography documents the most recent research activity in the vibrant field of language, gender and sexuality. It provides experts in the field and students in tertiary education with access to language-centred resources on gender and sexuality and is, therefore, an ideal research companion. The main part of the bibliography lists 3,454 relevant publications (monographs, edited volumes, journal articles and contributions to edited volumes) that have been published within the period from 2000 to 2011. It unites work done in linguistics with that of neighbouring disciplines, covering studies dealing with a broad range of languages and cultures around the globe. Alphabetical listing and a keyword index facilitate finding relevant work by author and subject matter. The e-book version additionally enables users to search the entire document for specific terms. Sections on earlier bibliographies and general reference works on language, gender and sexuality complete the compilation.
Syntax
Authors: Givón T.
Published: January 2014

This new edition of Syntax: A functional-typological introduction is at many points radically revised. In the previous edition (1984) the author deliberately chose to de-emphasize the more formal aspects of syntactic structure, in favor of a more comprehensive treatment of the semantic and pragmatic correlates of syntactic structure. With hindsight the author now finds the de-emphasis of the formal properties a somewhat regrettable choice, since it creates the false impression that one could somehow be a functionalist without being at the same time a structuralist. To redress the balance, explicit treatment is given to the core formal properties of syntactic constructions, such as constituency and hierarchy (phrase structure), grammatical relations and relational control, clause union, finiteness and governed constructions.
At the same time, the cognitive and communicative underpinning of grammatical universals are further elucidated and underscored, and the interplay between grammar, cognition and neurology is outlined. Also the relevant typological database is expanded, now exploring in greater precision the bounds of syntactic diversity. Lastly, Syntax treats synchronic-typological diversity more explicitly as the dynamic by-product of diachronic development or grammaticalization. In so doing a parallel is drawn between linguistic diversity and diachrony on the one hand and biological diversity and evolution on the other. It is then suggested that — as in biology — synchronic universals of grammar are exercised and instantiated primarily as constraints on development, and are thus merely the apparent by-products of universal constraints on grammaticalization.
Reduction of endoplasmic reticulum stress attenuates the defects caused by Drosophila mitofusin depletion
Authors: Debattisti Valentina , Pendin Diana , Ziviani Elena , Daga Andrea , Scorrano Luca
Published: January 2014

Ablation of the mitochondrial fusion and endoplasmic reticulum (ER)–tethering protein Mfn2 causes ER stress, but whether this is just an epiphenomenon of mitochondrial dysfunction or a contributor to the phenotypes in mitofusin (Mfn)-depleted Drosophila melanogaster is unclear. In this paper, we show that reduction of ER dysfunction ameliorates the functional and developmental defects of flies lacking the single Mfn mitochondrial assembly regulatory factor (Marf). Ubiquitous or neuron- and muscle-specific Marf ablation was lethal, altering mitochondrial and ER morphology and triggering ER stress that was conversely absent in flies lacking the fusion protein optic atrophy 1. Expression of Mfn2 and ER stress reduction in flies lacking Marf corrected ER shape, attenuating the developmental and motor defects. Thus, ER stress is a targetable pathogenetic component of the phenotypes caused by Drosophila Mfn ablation.
KIF13B erects an endocytic scaffold
Authors: Short Ben
Published: January 2014

A kinesin motor promotes the endocytosis of the membrane receptor LRP1 by recruiting it to caveolae.
Light chain editors of anti-DNA receptors in human B cells
Authors: Kalinina Olga , Wang Yue , Sia Kevin , Radic Marko , Cazenave Pierre-André , Weigert Martin
Published: January 2014

Receptor editing is a mechanism of self-tolerance used in newly generated B cells. The expressed heavy (H) or light (L) chain of an autoreactive receptor is replaced by upstream V genes which eliminate or modify autoreactivity. Editing of anti-DNA receptors has been characterized in anti-DNA transgenic mouse models including 3H9, 3H9/56R, and their revertant 3H9GL. Certain L chains, termed editors, rescue anti-DNA B cells by neutralizing or modifying DNA binding of the H chain. This editing mechanism acts on the natural H chain repertoire; endogenous H chains with anti-DNA features are expressed primarily in combination with editor L chains. We ask whether a similar set of L chains exists in the human repertoire, and if so, do they edit H chains with anti-DNA signatures? We compared the protein sequences of mouse editors to all human L chains and found several human L chains similar to mouse editors. These L chains diminish or veto anti-DNA binding when expressed with anti-DNA H chains. The human H chains expressed with these L chains also have relatively high arginine (Arg) content in the H chain complementarity determining region (H3), suggesting that receptor editing plays a role in establishing tolerance to DNA in humans.