bluuebunny/crossref_metadata_2025 huggingface dataset:
Tailoring of polarization in electron blocking layer for electron confinement and hole injection in ultraviolet light-emitting diodes
Authors: Lu Yu-Hsuan , Fu Yi-Keng , Huang Shyh-Jer , Su Yan-Kuin , Wang Kang L. , Pilkuhn Manfred H. , Chu Mu-Tao
Published: March 2014

The influence of the AlGaN electron blocking layer (EBL) with graded aluminum composition on electron confinement and hole injection in AlGaN-based ultraviolet light-emitting diodes (LEDs) are investigated. The light output power of LED with graded AlGaN EBL was markedly improved, comparing to LED with conventional EBL. In experimental results, a high increment of 86.7% can be obtained in light output power. Simulation analysis shows that via proper modification of the barrier profile from the last barrier of the active region to EBL, not only the elimination of electron overflow to p-type layer can be achieved but also the hole injection into the active region can be enhanced, compared to a conventional LED structure. The dominant factor to the performance improvement is shown to be the modulation of polarization field by the graded Al composition in EBL.
Investigation of cation distribution, electrical, magnetic properties and their correlation in Mn2-xCo2xNi1-xO4 films
Authors: Wu Jing , Huang Zhiming , Zhou Wei , Ouyang Cheng , Hou Yun , Gao Yanqing , Chen Ren , Chu Junhao
Published: March 2014

X-ray photoelectron spectroscopy was performed on Mn2-xCo2xNi1-xO4 (x = 0.2, 0.4, 0.5, 0.6, and 0.8) series spinel films to determine their cation distributions. The results show that both Ni and Co ions exhibit bivalence, while Mn ions exhibit coexisting multivalence. The hopping frequency ν0 of each sample was obtained by combining cation distribution results and electrical measurement data. Analysis of the divergence at Neel temperature between field cooling and zero-field cooling magnetization curves revealed that the ferromagnetic coupling between octahedral site ions first leads to spontaneous magnetization at TC, after which a second spontaneous magnetization arises from the antiferromagnetic couple between tetrahedral and octahedral sites at a lower temperature TN. The correlation between hopping conductivity and magnetic transition temperature is discussed. We propose that the strength of the ferromagnetic couple between octahedral sites is subject to the product term of Nc(1 − c)ν0, which determines the ferromagnetic transition temperature (TC) of the system. Our results provide an avenue to understand the origin of magnetic interaction in small-polaron hopping semiconductors.
Many body effect induced energy gap in an optically pumped graphene system
Authors: Wei X. F. , Wang W. Y. , Long M. S. , Gong Y. P. , Liu L. W.
Published: March 2014

We develop a simple way to investigate the energy gap induced by many body effect in optically pumped graphene at different carrier densities. The exchange self-energy and energy dispersions are obtained analytically at the long wave limit. An energy gap depending on the carrier density is observed at the Dirac point. The energy gap induced by many body effect lies in the microwave range which is in accordance with the experimental measurements. Our theoretical results indicate that the exchange interaction via Coulomb interaction can be a mechanism to create an energy gap in optically pumped graphene.
Influence of gadolinium doping on the structure and defects of ceria under fuel cell operating temperature
Authors: Acharya S. A. , Gaikwad V. M. , Sathe V. , Kulkarni S. K.
Published: March 2014

Correlation between atomic positional shift, oxygen vacancy defects, and oxide ion conductivity in doped ceria system has been established in the gadolinium doped ceria system from X-ray diffraction (XRD) and Raman spectroscopy study at operating temperature (300–600 °C) of Intermediate Temperature Solid Oxide Fuel Cell (IT-SOFC). High temperature XRD data are used to quantify atomic positional shift from mean position with temperature. The Raman spectroscopy study shows additional vibration modes related to ordering of defect spaces (GdCe′−Vo••)* and (2GdCe′−Vo••)x generated due to association of oxygen vacancies and reduced cerium or dopant cations site (Gd3+), which disappear at 450 °C; indicating oxygen vacancies dissociation from the defect complex. The experimental evidences of cation-anion positional shifting and oxygen vacancies dissociation from defect complex in the IT-SOFC operating temperature are discussed to correlate with activation energy for ionic conductivity.
Fabrications of insulator-protected nanometer-sized electrode gaps
Authors: Arima Akihide , Tsutsui Makusu , Morikawa Takanori , Yokota Kazumichi , Taniguchi Masateru
Published: March 2014

We developed SiO2-coated mechanically controllable break junctions for accurate tunneling current measurements in an ionic solution. By breaking the junction, we created dielectric-protected Au nanoprobes with nanometer separation. We demonstrated that the insulator protection was capable to suppress the ionic contribution to the charge transport through the electrode gap, thereby enabled reliable characterizations of liquid-mediated exponential decay of the tunneling conductance in an electrolyte solution. From this, we found distinct roles of charge points such as molecular dipoles and ion species on the tunneling decay constant, which was attributed to local structures of molecules and ions in the confined space between the sensing electrodes. The device described here would provide improved biomolecular sensing capability of tunneling current sensors.
Fundamental piezoresistive coefficients of p-type single crystalline 3C-SiC
Authors: Phan Hoang-Phuong , Viet Dao Dzung , Tanner Philip , Wang Li , Nguyen Nam-Trung , Zhu Yong , Dimitrijev Sima
Published: March 2014

The orientation dependence of the piezoresistive effect of p-type single crystalline 3C-SiC thin film grown on a (100)Si wafer was characterized. The longitudinal, transverse gauge factors in [100] orientation, and longitudinal gauge factor in [110] orientation were found to be 5.8, −5.2, and 30.3, respectively. The fundamental piezoresistive coefficients π11, π12, and π44 of p-type 3C-SiC were obtained to be 1.5 × 10−11 Pa−1, −1.4 × 10−11 Pa−1, and 18.1 × 10−11 Pa−1, respectively. From these coefficients, the piezoresistive effect in any crystallographic orientation in p-type single crystalline 3C-SiC can be estimated, which is very valuable in designing micro-mechanical sensors.
Increase of the grating coupler bandwidth with a graphene overlay
Authors: Cheng Zhenzhou , Li Zhen , Xu Ke , Tsang Hon Ki
Published: March 2014

We present theoretical and experimental results that demonstrate an increase in the grating bandwidth by placing a graphene on the chip. A focusing subwavelength grating with coupling efficiency of −4.3 dB and 1 dB bandwidth of ∼60 nm was demonstrated. After a graphene sheet was transferred onto the chip, the maximum 1 dB bandwidth was increased to ∼72 nm. Experimental results are consistent with the calculated graphene induced waveguide refractive index and dispersion changes, and the bandwidth improvement may be attributed to the reduction of grating dispersion. This study may be of interest for graphene-on-silicon photonic integrated circuit applications.
Electric current-driven migration of electrically neutral particles in liquids
Authors: Zhang Xinfang , Qin Rongshan
Published: March 2014

We design and experimentally demonstrate a migration of electrically neutral particles in liquids driven by electric current according to the discrepancies of their electrical conductivities. A force from electric current to electrically neutral particles has been identified to drive the particles toward the lateral surface from the centre of suspension via three distinguishable zones, namely, pushing, trapping, and expelling zones. The driving force can overtake gravity in practical cases. The property of the force is found neither similar to that of the force in electromagnetophoresis nor similar to that of the electromigration force in terms of direction and magnitude. An expression for the force at the pushing zone has been developed based on the numerical calculation of the thermodynamics of suspension fluids. The excellent agreement between numerical calculations and experimental data demonstrates that our calculation provides fundamental and predictive insight into particles separation from the liquids. Therefore, it is possible to use the force in many engineering applications such as separation of particles according to the differences of their electrical conductivities.
Soybean
SAT1
(
Symbiotic Ammonium Transporter 1
) encodes a bHLH transcription factor involved in nodule growth and NH
4
+
transport
Authors: Chiasson David M. , Loughlin Patrick C. , Mazurkiewicz Danielle , Mohammadidehcheshmeh Manijeh , Fedorova Elena E. , Okamoto Mamoru , McLean Elizabeth , Glass Anthony D. M. , Smith Sally E. , Bisseling Ton , Tyerman Stephen D. , Day David A. , Kaiser Brent N.
Published: March 2014

Significance

The legume/rhizobia symbiosis involves a root-based exchange of bacterial fixed nitrogen for plant-derived photosynthetic carbon. The exchange takes place within the legume root nodule, which is a specialized root tissue that develops in response to plant and bacterial signal exchange. The bacteria reside within plant cells inside the nodule. In this study, we explore the activity of a membrane-bound soybean transcription factor,
Glycine max
basic–helix-loop–helix membrane 1, which is important for soybean nodule growth and is linked to the activity of a unique class of ammonium channels and to signaling cascades influencing a nodule circadian clock.
Is Kashmiri passive really a passive?
Authors: Srishti Richa , Bhat Shahid
Published: March 2014

The present paper explores passives in Kashmiri, a Northwestern Dardic language of the Indo-Aryan family. Though Kashmiri has some special features like V-2 phenomenon, pronominal clitics etc. it has an analytic passive construction like its Indo-Aryan counterparts. The internal argument surfaces as the subject of the passive, where the participial/infinitival verbal form -nI is added to the verb root followed by a periphrastic auxiliary yun ‘to come’ in perfective form. The agent of the action is in the form of athi or zaryi (by/through) and is preferably omitted. This optionality casts a doubt on its status – whether it is an adjunct or an argument. The promotion of the internal argument to the subject position is another key issue. The present paper investigates the above issues and claims that the Kashmiri passive construction is also a kind of ACTIVE-Passive and not really passive as in English. It is argued that in Kashmiri passives, the underlying subject remains an active subject and the underlying object does not become the surface subject. To prove this claim, some tests based on anaphora binding, pronominal co-reference, control, etc. are applied.
Middles in the syntax
Authors: Chandra Pritha
Published: March 2014

It is well-known that while some languages mark middles and passives similarly, some others mark them differently. Researchers opine that this difference may ensue from the loci of middle generation; they can be generated either in the lexicon or in the syntax. I present some problems with the two-modular approach and propose a syntactic analysis for all middles, with the differences emanating from the choice of the non-active voice head. Languages like Hindi-Urdu which choose a middle non-active voice head fail to project a higher aspectual head hosting an external argument. The truncated structure makes the middles different from passives, in both morphological form and syntactic behavior.
Markedness and syncretism in Kashmiri differential argument encoding
Authors: Manetta Emily
Published: March 2014

The pronominal clitic system in Kashmiri takes the form of set of verbal suffixes conditioned by the case of the coreferent DP. This system interacts in unexpected ways with differential argument encoding (DAE) in Kashmiri, in which the case-marking of objects in non-perfective aspects is dependent on a person hierarchy. I will follow in spirit Aissen’s (2003) approach to DAE as adapted to Kashmiri in Sharma (2001), however I will argue that the particulars of the Kashmiri clitic system force us to adopt an account couched not in the syntax, but in the post-syntactic component of the grammar. Keine and Müller (2008) propose that DAE is a phenomenon of the morphology-syntax interface, employing harmonic alignment of scales within framework of Distributed Morphology (Halle & Marantz 1993, 1994). I argue here that an otherwise mysterious set of clitic syncretisms in Kashmiri, including the overlap in the marking of ergative subjects and accusative objects, find explanation if we consider Kashmiri DAE not as an instance of differential marking in the narrow syntax, but instead as a as a non-zero/non-zero alternation resulting from the interaction of morphological processes and a system of optimization at the morphology-syntax interface.
Ergativity and the object-oriented representation of verb meaning
Authors: Benz Anton
Published: March 2014

There is an interesting parallelism between the representation of one- place and two-place operations in object-oriented programming and case marking in ergative languages. The object-oriented approach has proven to be highly suc- cessful in computational system design and analysis. One of its peculiarities is to define operations within the class of the objects which are their main arguments. More specifically, operations that correspond to intransitive verbs are encoded in the class which corresponds to the subject NP, and operations that correspond to transitive verbs are encoded in the class that corresponds to the NP of the direct object. In ergative languages these NPs are marked by absolutive case. We discuss a number of semantic phenomena related to ergativity that show that conceptual representation of word meaning follows the object-oriented paradigm.
Object-orientation and the semantics of verbs
Authors: Schalley Andrea C.
Published: March 2014

The paper introduces a decompositional approach to verbal semantics that is object-oriented in nature and based on the Unified Modeling Language (UML), the de-facto standard formalism for object-oriented software design and analysis. In addition to laying out the very rich semantic structure of verbal meaning and its object-oriented modeling, the paper focuses on the advantages a semantic representation along the lines of the UML provides, in particular looking at the multi-layered architecture of UML and its implications for verbal meaning. Other semantic phenomena and problems (such as metaphors, questions of classifications of verbal meaning, or selectional restrictions) will be touched on and discussed in the light of an object-oriented, UML-based approach to verbal meaning.
Phases in verbal semantics
Authors: Engerer Volkmar
Published: March 2014

The following article deals with phasal verbs, i.e., verbs referring to a special phase of an entire event. Thus, for instance, start refers to the beginning of an event whereas stop and finish focus on an event’s final phase. After a general introduction, I shall show in Section 1.2 that there is a direct line from medieval thinking about event phases to recent semantic theories as they have been developed since the 1960s or so onward. Three influential modern theories are discussed in the second section, namely: (1) Jackendoff’s account of the cognitive mechanism used to delimit events and their initial and final sub-phases; (2) Pustejovsky’s theory of the interaction of phasal verbs with their complements; and (3) Partee and Bennett’s analysis of phasal verbs within their interval semantics. In the main Section 3 I try to integrate these approaches to the semantics of phasal verbs within a more elaborate and comprehensive model for the semantic description of phasal verbs. The discussion will show that a coherent and descriptively adequate analysis of phasal verbs is possible and that phasal verbs must be recognized as constituting a grammatical class at least in the languages discussed here.
The ‘say, do’ verb in Nyulnyul, Warrwa, and other Nyulnyulan languages is monosemic
Authors: McGregor William B.
Published: March 2014

A well-known feature of many Australian Aboriginal languages is that the same verb form can mean either ‘say’ or ‘do’ (Rumsey 1990; Dixon 2002: 121). The received story is that this represents a polysemic verb with two distinct though not unrelated meanings. Few linguists, however, have presented arguments for this position. An exception is Knight (2004), who presents a set of arguments couched within the theoretical and methodological framework of Natural Semantic Metalanguage (NSM) that the inflecting verb -MA in Bunuba (Bunuban, Kimberley) is polysemous. Many of these arguments apply to other Australian languages, including languages of the nearby Nyulnyulan family. In this paper I focus on the two Nyulnyulan languages that I have studied most intensively, Nyulnyul (Western Nyulnyulan) and Warrwa (Eastern Nyulnyulan), and discuss the range of meanings and uses of the inflecting verb -J(I) ~ -D(I). These include the senses ‘say’, ‘do’, ‘think’, among a number of more specific senses. I present arguments for a radically monosemic account (e.g., Ruhl 1989; McGregor 1997) of this verb in its lexical uses, arguing in the process that the type of evidence adduced by Knight (2004) does not in fact argue for polysemy. I argue, that is, that a single core meaning is associated with the inflecting verb -J(I) ~ -D(I), and the senses ‘say’ and ‘do’ represent contextual senses or interpretations engendered by the context of use. A consequence of my approach is that the semantic meaning of lexical verbs is more abstract than often thought; indeed, it is so abstract that it is impossible to distinguish between the semantics of lexical and grammatical items in terms of the degree of abstraction.
Predicate classes
Authors: Oehl Peter
Published: March 2014

The aspectual interpretation of sentences is constrained by the truth conditions predicates impose on points of times or time intervals. Using data from English, Vendler (1967) established a classification of four verb types on these grounds, that has been widely accepted in linguistic theory. Various researchers, among them Dowty (1979) for English and Ehrich (1992) for German, have proposed finer grained classifications. This paper is very much in the spirit of these proposals. Our aim is a detailed model of the compositional lexical semantics of predicates that models the contrasts of verbal aspect by implicit temporal arguments in the logical characterisation, thereby yielding a concise classification. Punctual and durative predicates are distinct through having either points in time or intervals as implicit temporal arguments. Truth intervals of predicates can be closed or open resulting in the telicity or atelicity of a verb. It is argued that resultativity must, in addition, be introduced by a secondary predicate denoting a result. This predicate may also be implicit. If it is explicit, however, it has the status of a syntactic argument. Since the secondary predicate is subject to a truth interval of its own, the verbal aspect of resultatives must be more complex than that of nonresultatives. Moreover, transitive and intransitive resultatives combine diverse kinds of elementary predicates such as ACT, BECOME, CAUSE Predicating over elementary events, licensing different argument structures and yielding specific truth conditions on times. Finally, a classification of 15 kinds of predicates is established on the basis of compositional complexity.
Right Ventricular Reverse Remodeling after Pulmonary Endarterectomy: Magnetic Resonance Imaging and Clinical and Right Heart Catheterization Assessment
Authors: Berman Marius , Gopalan Deepa , Sharples Linda , Screaton Nick , Maccan Caroline , Sheares Karen , Pepke‐Zaba Joanna , Dunning John , Tsui Steven , Jenkins David P.
Published: March 2014

The objective of this study was to assess the effect of pulmonary endarterectomy (PEA) on right ventricular (RV) reverse remodeling using magnetic resonance imaging (MRI) and to correlate MRI findings with clinical and hemodynamic outcomes postsurgery. We performed a retrospective analysis in 72 patients undergoing PEA surgery in whom MRI and right heart catheterization (RHC) were performed preoperation and 3 months postoperation. RV volumes and mass were assessed by MRI. Continuous variables were expressed as means, changes were compared with a paired t test, and associations between the variables were explored using Pearson correlation coefficients. The mean age was 57 years, and 51% were male. Both RV end‐diastolic volume (EDV; 176–117 mL; P < 0.001) and RV end‐systolic volume (ESV; 129–64 mL; P < 0.001) reduced significantly following PEA. Preoperative pulmonary artery pressure (PAP) correlated moderately with ESV (r = 0.46, P < 0.001). Postoperatively, PAP correlated with EDV (r = 0.45, P < 0.001) and ESV (r = 0.44, P < 0.001). Moderate correlation was present between hemodynamic parameters: PAP, pulmonary vascular resistance, and right atrial pressure with pre‐ and postoperation end‐systolic and end‐diastolic RV mass (P < 0.001). RHC and MRI measurements of cardiac output and RV volumes were significantly different (P < 0.001). In conclusion, RV reverse remodeling, as measured by improvement in RV volumes and mass by MRI, was observed for 3 months in patients who underwent PEA surgery. This is the largest series of patients with pre‐ and post‐PEA MRI assessment so far reported. MRI detects changes in parameters reflecting cardiac remodeling and pulmonary clearance, but measurements are significantly different from those of RHC.
Accepting Inequality Deters Responsibility: How Power Distance Decreases Charitable Behavior
Authors: Winterich Karen Page , Zhang Yinlong
Published: March 2014

Could power distance, which is the extent that inequality is expected and accepted, explain why some countries and consumers are more likely to engage in prosocial behavior, including donations of both money and time? This research proposes that higher power distance results in weaker perceptions of responsibility to aid others, which decreases charitable behavior. Both correlational and causal evidence is provided in a series of five studies that examine country-level power distance as well as individual and temporarily salient power distance belief. Consistent with the mediating role of perceived responsibility, results reveal that uncontrollable needs and communal relationship norms are boundary conditions that overcome the negative effect of power distance on charitable behavior. These results explain differences in charitable giving across cultures and provide implications for nonprofit organizations soliciting donations.
Basin Hopping Graph: a computational framework to characterize RNA folding landscapes
Authors: Kucharík Marcel , Hofacker Ivo L. , Stadler Peter F. , Qin Jing
Published: March 2014

Motivation: RNA folding is a complicated kinetic process. The minimum free energy structure provides only a static view of the most stable conformational state of the system. It is insufficient to give detailed insights into the dynamic behavior of RNAs. A sufficiently sophisticated analysis of the folding free energy landscape, however, can provide the relevant information.

Results: We introduce the Basin Hopping Graph (BHG) as a novel coarse-grained model of folding landscapes. Each vertex of the BHG is a local minimum, which represents the corresponding basin in the landscape. Its edges connect basins when the direct transitions between them are ‘energetically favorable’. Edge weights endcode the corresponding saddle heights and thus measure the difficulties of these favorable transitions. BHGs can be approximated accurately and efficiently for RNA molecules well beyond the length range accessible to enumerative algorithms.

Availability and implementation: The algorithms described here are implemented in C++ as standalone programs. Its source code and supplemental material can be freely downloaded from http://www.tbi.univie.ac.at/bhg.html .

Contact:  qin@bioinf.uni-leipzig.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
DBatVir: the database of bat-associated viruses
Authors: Chen Lihong , Liu Bo , Yang Jian , Jin Qi
Published: March 2014

Emerging infectious diseases remain a significant threat to public health. Most emerging infectious disease agents in humans are of zoonotic origin. Bats are important reservoir hosts of many highly lethal zoonotic viruses and have been implicated in numerous emerging infectious disease events in recent years. It is essential to enhance our knowledge and understanding of the genetic diversity of the bat-associated viruses to prevent future outbreaks. To facilitate further research, we constructed the database of bat-associated viruses (DBatVir). Known viral sequences detected in bat samples were manually collected and curated, along with the related metadata, such as the sampling time, location, bat species and specimen type. Additional information concerning the bats, including common names, diet type, geographic distribution and phylogeny were integrated into the database to bridge the gap between virologists and zoologists. The database currently covers >4100 bat-associated animal viruses of 23 viral families detected from 196 bat species in 69 countries worldwide. It provides an overview and snapshot of the current research regarding bat-associated viruses, which is essential now that the field is rapidly expanding. With a user-friendly interface and integrated online bioinformatics tools, DBatVir provides a convenient and powerful platform for virologists and zoologists to analyze the virome diversity of bats, as well as for epidemiologists and public health researchers to monitor and track current and future bat-related infectious diseases.

Database URL: http://www.mgc.ac.cn/DBatVir/
Characteristics of hospital- and community-acquired meticillin-resistant Staphylococcus aureus in Tehran, Iran
Authors: Rahimi Fateh , Katouli Mohammad , Pourshafie Mohammad Reza
Published: March 2014

Staphylococcus aureusis a leading cause of hospital-acquired (HA) and community-acquired (CA) infections worldwide. Recently,S. aureusstrains resistant to meticillin (MRSA) have become established within both communities. We isolated 314 isolates of MRSA from hospitalized patients in a referral hospital (HA isolates) and 268 isolates from its outpatient clinic (CA isolates) in Tehran, Iran, between February 2008 and December 2010. These isolates were tested for their susceptibility to 17 antibiotics and typed using the PhPlate system. The diversity in the structures of staphylococcal cassette chromosomemec(SCCmec) elements andccrtypes was also detected using a multiplex-PCR assay and isolates were examined for the presence of different classes of prophages. Whilst all isolates were resistant to penicillin, the HA isolates were significantly more resistant to all other antibiotics tested than the CA isolates. Isolates carrying only SCCmectype III andccrtype 3 were dominant (91 %), but 20 % of the CA isolates belonging to less prevalent types carried only SCCmectypes IVa, c andccrtype 2. These isolates also carriedpvlgenes and contained SGA prophage type. Our results indicate that whilst the dominant clonal groups of HA- and CA-MRSA belong to SCCmectype III and carryccrtype 3 genes, several distinct but less prevalent types of CA-MRSA carrying SCCmectype IVa, c and type 2ccrare also found in Tehran. These strains carrypvlgenes and the SGA prophage type, a characteristic that might be used as a marker for detection of CA–MRSA in this country.
Proteomic and cellular views of Arthrospira sp. PCC 8005 adaptation to nitrogen depletion
Authors: Deschoenmaeker Frédéric , Facchini Raphaël , Leroy Baptiste , Badri Hanène , Zhang C.-C. , Wattiez Ruddy
Published: March 2014

Cyanobacteria are photosynthetic prokaryotes that play a crucial role in the Earth’s nitrogen and carbon cycles. Nitrogen availability is one of the most important factors in cyanobacterial growth. Interestingly, filamentous non-diazotrophic cyanobacteria, such asArthrospirasp. PCC 8005, have developed survival strategies that enable them to adapt to nitrogen deprivation. Metabolic studies recently demonstrated a substantial synthesis and accumulation of glycogen derived from amino acids during nitrogen starvation. Nevertheless, the regulatory mechanism of this adaptation is poorly understood. To the best of our knowledge, this study is the first proteomic and cellular analysis ofArthrospirasp. PCC 8005 under nitrogen depletion. Label-free differential proteomic analysis indicated the global carbon and nitrogen reprogramming of the cells during nitrogen depletion as characterized by an upregulation of glycogen synthesis and the use of endogenous nitrogen sources. The degradation of proteins and cyanophycin provided endogenous nitrogen when exogenous nitrogen was limited. Moreover, formamides, cyanates and urea were also potential endogenous nitrogen sources. The transporters of some amino acids and alternative nitrogen sources such as ammonium permease 1 were induced under nitrogen depletion. Intriguingly, althoughArthrospirais a non-diazotrophic cyanobacterium, we observed the upregulation of HetR and HglK proteins, which are involved in heterocyst differentiation. Moreover, after a long period without nitrate, only a few highly fluorescent cells in each trichome were observed, and they might be involved in the long-term survival mechanism of this non-diazotrophic cyanobacterium under nitrogen deprivation.
Epigenetic Modifications are Associated with Inter-species Gene Expression Variation in Primates
Authors: Zhou Xiang , Cain Carolyn E. , Myrthil Marsha , Lewellen Noah , Michelini Katelyn , Davenport Emily R. , Stephens Matthew , Pritchard Jonathan K. , Gilad Yoav
Published: March 2014

Changes in gene regulation level have long been thought to play an important role in evolution and speciation, especially in primates. Over the past decade, comparative genomic studies have revealed extensive inter-species differences in gene expression levels yet we know much less about the extent to which regulatory mechanisms differ between species. To begin addressing this gap, we performed a comparative epigenetic study in primate lymphoblastoid cell lines (LCLs), to query the contribution of RNA polymerase II (Pol II) and four histone modifications (H3K4me1, H3K4me3, H3K27ac, and H3K27me3) to inter-species variation in gene expression levels. We found that inter-species differences in mark enrichment near transcription start sites are significantly more often associated with inter-species differences in the corresponding gene expression level than expected by chance alone. Interestingly, we also found that first-order interactions among the histone marks and Pol II do not markedly contribute to the degree of association between the marks and inter-species variation in gene expression levels, suggesting that the marginal effects of the five marks dominate this contribution.
Structures ofLegionella pneumophilaNTPDase1 in complex with polyoxometallates
Authors: Zebisch Matthias , Krauss Michel , Schäfer Petra , Sträter Norbert
Published: March 2014

Nucleoside triphosphate diphosphohydrolases (NTPDases) are secreted or membrane-bound ectonucleotidases that hydrolyze the anhydride bonds of nucleoside triphosphates and nucleoside diphosphates. Mammalian cell-surface NTPDase enzymes are inhibited by various polyoxometallates. Here, the structures of NTPDase1 from the bacteriumLegionella pneumophila(LpNTPDase1) in complex with the dodecatungstate POM-1, decavanadate and octamolybdate/heptamolybdate are described. The metal clusters are bound at different sites but always in a highly ordered fashionviaelectrostatic interactions and hydrogen bonds. For octamolybdate, covalent interactions after oxygen ligand exchange by a serine and histidine side chain are also observed. The potential inhibitory mechanism and the use of the metal clusters as phasing tools for new NTPDase structures are discussed. The binding mode of a tartrate ion at the catalytic centre suggests novel strategies for the structure-based design of NTPDase inhibitors, and the observation of the enzyme in an intermediate open state contributes to our understanding of NTPDase enzyme dynamics.
The peptideZ-Aib-Aib-Aib-L-Ala-OtBu
Authors: Gessmann Renate , Brückner Hans , Petratos Kyriacos
Published: March 2014

The title peptide,N-benzyloxycarbonyl-α-aminoisobutyryl-α-aminoisobutyryl-α-aminoisobutyryl-L-alaninetert-butyl ester orZ-Aib-Aib-Aib-L-Ala-OtBu (Aib is α-aminoisobutyric acid,Zis benzyloxycarbonyl and OtBu indicates thetert-butyl ester), C27H42N4O7, is a left-handed helix with a right-handed conformation in the fourth residue, which is the only chiral residue. There are two 4→1 intramolecular hydrogen bonds in the structure. In the lattice, molecules are hydrogen bonded to form columns along thecaxis.
Tissue tropism and vertical transmission ofCoxiellainRhipicephalus sanguineusandRhipicephalus turanicusticks
Authors: Lalzar Itai , Friedmann Yael , Gottlieb Yuval
Published: March 2014

Arthropod symbionts present tissue tropism that corresponds to the nature of the association and the mode of transmission between host generations. In ticks, however, our knowledge of symbiont tissue tropism and function is limited. Here, we quantified and localized previously describedCoxiella‐like symbionts in several organs of the tickRhipicephalus turanicus. Quantitative polymerase chain reaction revealed high densities ofCoxiellain the female gonads, and both male and femaleMalpighian tubules. Using fluorescencein situhybridization and transmission electron microscopy, we further showed that in the gonads of bothRh. turanicusandRh. sanguineus,Coxielladoes not colonize the primary oocytes but is found later in young and mature oocytes in a specific distribution, suggesting controlled vertical transmission. This method revealed the presenceCoxiellain the distal part of theMalpighian tubules, suggesting a possible role in nitrogen metabolism. While testingRickettsiasymbionts, no specific tissue tropism was found, but a slightly higher densities in the tick gut. The low density ofRickettsiain the female ovaries suggests competition betweenRickettsiaandCoxiellafor vertical transmission. The described tissue distribution supports an obligatory role forCoxiellain ticks.
Identification of key nitrous oxide production pathways in aerobic partial nitrifying granules
Authors: Ishii Satoshi , Song Yanjun , Rathnayake Lashitha , Tumendelger Azzaya , Satoh Hisashi , Toyoda Sakae , Yoshida Naohiro , Okabe Satoshi
Published: March 2014

The identification of the key nitrous oxide (N2O) production pathways is important to establish a strategy to mitigate N2O emission. In this study, we combined real‐time gas‐monitoring analysis, 15N stable isotope analysis, denitrification functional gene transcriptome analysis and microscale N2O concentration measurements to identify the main N2O producers in a partial nitrification (PN) aerobic granule reactor, which was fed with ammonium and acetate. Our results suggest that heterotrophic denitrification was the main contributor to N2O production in our PN aerobic granule reactor. The heterotrophic denitrifiers were probably related to Rhodocyclales bacteria, although different types of bacteria were active in the initial and latter stages of the PN reaction cycles, most likely in response to the presence of acetate. Hydroxylamine oxidation and nitrifier denitrification occurred, but their contribution to N2O emission was relatively small (20–30%) compared with heterotrophic denitrification. Our approach can be useful to quantitatively examine the relative contributions of the three pathways (hydroxylamine oxidation, nitrifier denitrification and heterotrophic denitrification) to N2O emission in mixed microbial populations.
Social Trust Fosters an Ability to Help Those in Need: Jewish Refugees in the Nazi Era
Authors: Bjørnskov Christian
Published: March 2014

An ignored aspect of efforts to save Jewish citizens in occupied Europe during the Second World War is that large-scale rescue arguably constitutes a collective action problem. Due to Nazi occupation, no formal institutions contributed to solving this problem. Exploring the differences in rescue rates across all 30 occupied countries shows that the informal institution of social trust contributed to solving the collective action problem and strongly affected rescue rates.
Avoidance and Engagement: Issue Competition in Multiparty Systems
Authors: Green-Pedersen Christoffer , Mortensen Peter B.
Published: March 2014

A substantial literature claims that political parties compete over issues by selectively emphasizing favorable issues and avoiding issues emphasized by their opponents. In recent years, this understanding of issue competition has been challenged by empirical studies showing issue engagement to be the rule rather than the exception. To move the discussion beyond the descriptive question about degree of issue avoidance or issue engagement, this article offers a theoretical framework of issue competition that addresses central but hitherto neglected questions about which parties respond to which parties. The main implications of the theoretical framework are tested in a set of statistical time-series analyses of party interaction in Denmark covering more than 50 years, 24 major issues and 21 elections. These analyses offer support to the ideas that parties are more responsive to the issue agendas of parties from their own party family than to the issue agendas of non-family parties and that large mainstream parties are more responsive than niche parties to the common issue agenda of the other parties in the party system.
Symbolic Meta-Policy: (Not) Tackling Climate Change in the Transport Sector
Authors: Bache Ian , Reardon Louise , Bartle Ian , Marsden Greg , Flinders Matthew
Published: March 2014

This paper seeks to understand how the UK government's headline climate change targets are translated into action at the local level in the transport sector drawing on the findings of research in two English regions. In doing so, these headline targets are identified as a symbolic meta-policy that results in little action on the ground and which challenges established conceptions of policy implementation. Both the ‘meta’ and ‘symbolic’ aspects of the policy offer part of the explanation for the lack of substantive action on the ground. As a meta-policy, the headline targets across government require the elaboration of other policies at other levels such as targets for government departments and local authorities, but these are largely absent, leaving the meta-policy without teeth. Over time, these headline targets have developed into a symbolic policy, serving political goals but having little practical effectiveness.
Statistical Classification Methods for Estimating Ancestry Using Morphoscopic Traits,
Authors: Hefner Joseph T. , Ousley Stephen D.
Published: March 2014

Ancestry assessments using cranial morphoscopic traits currently rely on subjective trait lists and observer experience rather than empirical support. The trait list approach, which is untested, unverified, and in many respects unrefined, is relied upon because of tradition and subjective experience. Our objective was to examine the utility of frequently cited morphoscopic traits and to explore eleven appropriate and novel methods for classifying an unknown cranium into one of several reference groups. Based on these results, artificial neural networks (aNNs), OSSA, support vector machines, and random forest models showed mean classification accuracies of at least 85%. The aNNs had the highest overall classification rate (87.8%), and random forests show the smallest difference between the highest (90.4%) and lowest (76.5%) classification accuracies. The results of this research demonstrate that morphoscopic traits can be successfully used to assess ancestry without relying only on the experience of the observer.
Working below and above the line: the research–practice gap in diversity management
Authors: Kulik Carol T.
Published: March 2014

In HRM, a line can be drawn that distinguishes research on formal organisational programmes (above‐the‐line research) from research on organisational practices as they are experienced by employees (below‐the‐line research). Diversity management research has heavily emphasised below‐the‐line research using methodologies that measure employee perceptions of diversity management activities. This research demonstrates an impact of diversity management on employee reactions and identifies unit‐level factors (e.g. leader behaviour) that impact the effectiveness of diversity management activities. However, below‐the‐line research is not able to answer HR professionals' questions about which diversity management activities should be adopted when, and so a research–practice gap is developing. I explain how both academics and practitioners would benefit from more above‐the‐line research examining the impact of formal organisational diversity management activities as reported by senior managers or documented in organisational records.
Inhibition ofListeria monocytogenesandSalmonellaby Combinations of Oriental Mustard, Malic Acid, and EDTA
Authors: Olaimat Amin N. , Holley Richard A.
Published: March 2014

The antimicrobial activities of oriental mustard extract alone or combined with malic acid and EDTA were investigated againstSalmonellaspp. orListeria monocytogenesat different temperatures. Five strainSalmonellaorL. monocytogenescocktails were separately inoculated in Brain Heart Infusion broth containing 0.5% (w/v) aqueous oriental mustard extract and incubated at 4 °C to 21 °C for 21 d. For inhibitor combination tests,Salmonella Typhimurium02:8423 andL. monocytogenes2–243 were individually inoculated in Mueller Hinton broth containing the mustard extract with either or both 0.2% (w/v) malic acid and 0.2% (w/v) EDTA and incubated at 10 °C or 21 °C for 10 to 14 d. Mustard extract inhibited growth of theL. monocytogenescocktail at 4 °C up to 21 d (2.3 log10CFU/mL inhibition) or at 10 °C for 7 d (2.4 log10CFU/mL inhibition).Salmonellaspp. viability was slightly, but significantly reduced by mustard extract at 4 °C by 21 d. Although hydrolysis of sinigrin in mustard extract by both pathogens was 2 to 6 times higher at 21 °C than at 4 °C to 10 °C, mustard was not inhibitory at 21 °C, perhaps because of the instability of its hydrolysis product (allyl isothiocyanate). At 21 °C, additive inhibitory effects of mustard extract with EDTA or malic acid led to undetectable levels ofS.TyphimuriumandL. monocytogenesby 7 d and 10 d, respectively. At 10 °C,S.Typhimuriumwas similarly susceptible, but combinations of antimicrobials were not more inhibitory toL. monocytogenesthan the individual agents.
Sub‐surface Property, Free‐entry Mineral Staking and Settler Colonialism in Canada
Authors: Hoogeveen Dawn
Published: March 2014

This article examines mineral rights and claim staking in northern Canada, with a focus on settler colonialism and how liberal understandings of property are embedded in the legal geography of the right to explore for minerals. The history of these legal systems is explained through the “free‐entry” principle understood as the right to stake a mineral claim without consulting with private landholders or Indigenous peoples. Free‐entry debate highlights how ideologies of property are assumed neutral through staking regulations. Based on an analysis of interviews with key informants involved in mining regulation, I analyze the geographic stratification of land into two categories, above and below the surface, as an avenue to understand how dominant ideologies of property reveal a critical site of contestation.
Retrospective evaluation of methotrexate elimination when co‐administered with proton pump inhibitors
Authors: Reeves David J. , Moore Elizabeth S. , Bascom Devon , Rensing Brandon
Published: March 2014

Aims

The aim was to assess potential interaction between methotrexate (MTX) and proton pump inhibitors (PPIs) in patients receiving high‐dose MTX.

Methods

Records of 56 adults receiving 201 cycles of MTX were reviewed to determine effects of PPI administration on MTX elimination. Repeated‐measures logistic regressions and Cox regressions were performed to evaluate the possible drug interaction.

Results

Despite a significant difference between those receiving a PPI and not receiving a PPI in median MTX levels at 24 (8.0 vs. 3.9 μmol l−1, respectively, P = 0.013) and 72 h after MTX administration (0.08 vs. 0.05 μmol l−1, respectively, P = 0.037), there was no difference between those receiving a PPI and not receiving a PPI in the proportion of patients experiencing delayed elimination at 24 (19.2% vs. 20.2%, respectively, P = 1.000) and 72 h (36.2% vs. 33.7%, respectively, P = 0.765). When data were analysed using Cox regression, controlling for multiple cycles of MTX per patient, PPI use was not a significant predictor of time to MTX < 0.1 μmol l−1. When the clustering effect of multiple cycles of MTX per patient was controlled for, co‐administration of PPIs was not a significant predictor of MTX level (P = 0.969). A comparison of patients with delayed elimination at any time point and those without delayed elimination indicated that PPI use was not a significant predictor of delayed elimination (P = 0.607).

Conclusions

This study does not support previous findings of a significant interaction between PPIs and MTX. Based on these results, the clinical significance of any potential interaction is likely to be small.
Pathophysiology of isoprostanes in the cardiovascular system: implications of isoprostane‐mediated thromboxane A2 receptor activation
Authors: Bauer Jochen , Ripperger Anne , Frantz Stefan , Ergün Süleyman , Schwedhelm Edzard , Benndorf Ralf A
Published: March 2014

Isoprostanes are free radical‐catalysed PG‐like products of unsaturated fatty acids, such as arachidonic acid, which are widely recognized as reliable markers of systemic lipid peroxidation and oxidative stress in vivo. Moreover, activation of enzymes, such as COX‐2, may contribute to isoprostane formation. Indeed, formation of isoprostanes is considerably increased in various diseases which have been linked to oxidative stress, such as cardiovascular disease (CVD), and may predict the atherosclerotic burden and the risk of cardiovascular complications in the latter patients. In addition, several isoprostanes may directly contribute to the functional consequences of oxidant stress via activation of the TxA2 prostanoid receptor (TP), for example, by affecting endothelial cell function and regeneration, vascular tone, haemostasis and ischaemia/reperfusion injury. In this context, experimental and clinical data suggest that selected isoprostanes may represent important alternative activators of the TP receptor when endogenous TxA2 levels are low, for example, in aspirin‐treated individuals with CVD. In this review, we will summarize the current understanding of isoprostane formation, biochemistry and (patho) physiology in the cardiovascular context.
Kinship and Nonrelative Foster Care: The Effect of Placement Type on Child Well‐Being
Authors: Font Sarah A.
Published: March 2014

This study uses a national sample of 1,215 children, ages 6–17, who spent some time in formal kinship or nonrelative foster care to identify the effect of placement type on academic achievement, behavior, and health. Several identification strategies are used to reduce selection bias, including ordinary least squares, change score models, propensity score weighting, and instrumental variables regression. The results consistently estimate a negative effect of kin placements on reading scores, but kin placements appear to have no effect on child health, and findings on children's math and cognitive skills test scores and behavioral problems are mixed. Estimated declines in both academic achievement and behavioral problems are concentrated among children who are lower functioning at baseline.