bluuebunny/crossref_metadata_2025 huggingface dataset:
Correlation correction to configuration interaction singles from coupled cluster perturbation theory
Authors: Byrd Jason N. , Lotrich Victor F. , Bartlett Rodney J.
Published: June 2014

A new state specific correlation correction to configuration interaction singles (CIS) excitation energies is presented using coupled cluster perturbation theory (CCPT). General expressions for CIS-CCPT are derived and expanded explicitly to first-order in the wavefunction and second-order in the energy. By virtue of the nature of CCPT this method is a priori size extensive and incorporates infinite-order effects into the wavefunction. This results in a balanced singles space excited state theory that at second-order is an improvement over the ubiquitous CIS(D) method and comparable in quality to equation of motion coupled cluster (EOM-CC). A modest test set composed of the first four excited states from nine small organic molecules was used to quantify the accuracy and consistency of the CIS-CCPT2 excitation energies and density of states. We find that CIS-CCPT2 has a standard deviation error of 0.18 eV for excitation energies and 0.14 eV for density of states compared to EOM-CC, a factor of two better than CIS(D) with a significant reduction in the maximum deviation as well.
Atomic and electronic structure of the ferroelectric BaTiO3/Ge(001) interface
Authors: Fredrickson Kurt D. , Ponath Patrick , Posadas Agham B. , McCartney Martha R. , Aoki Toshihiro , Smith David J. , Demkov Alexander A.
Published: June 2014

In this study, we demonstrate the epitaxial growth of BaTiO3 on Ge(001) by molecular beam epitaxy using a thin Zintl template buffer layer. A combination of density functional theory, atomic-resolution electron microscopy and in situ photoemission spectroscopy is used to investigate the electronic properties and atomic structure of the BaTiO3/Ge interface. Aberration-corrected scanning transmission electron micrographs reveal that the Ge(001) 2 × 1 surface reconstruction remains intact during the subsequent BaTiO3 growth, thereby enabling a choice to be made between several theoretically predicted interface structures. The measured valence band offset of 2.7 eV matches well with the theoretical value of 2.5 eV based on the model structure for an in-plane-polarized interface. The agreement between the calculated and measured band offsets, which are highly sensitive to the detailed atomic arrangement, indicates that the most likely BaTiO3/Ge(001) interface structure has been identified.
An informatics based analysis of the impact of isotope substitution on phonon modes in graphene
Authors: Broderick Scott , Ray Upamanyu , Srinivasan Srikant , Rajan Krishna , Balasubramanian Ganesh
Published: June 2014

It is shown by informatics that the high frequency short ranged modes exert a significant influence in impeding thermal transport through isotope substituted graphene nanoribbons. Using eigenvalue decomposition methods, we have extracted features in the phonon density of states spectra that reveal correlations between isotope substitution and phonon modes. This study also provides a data driven computational framework for the linking of materials chemistry and transport properties in 2D systems.
Electron transport in carbon nanotube/RbAg4I5 film composite nanostructures modulated by optical field
Authors: Zhang Guowei , Wei Jinquan , Zhu Jia-Lin , Zhang Wei , Sun Jia-Lin
Published: June 2014

We explore the transport properties of mixed ionic-electronic conductors made of carbon nanotube/RbAg4I5 film composite nanostructures in the presence of optical fields. The formation of ion-electron bound states (IEBSs) due to Coulomb interactions results in significant conductance decrease. The wavelength-dependent and power-dependent dynamic responses show that the effect of photo-induced dissociation of IEBSs is pronounced in the visible region and negligible in near-infrared region. Our results lead to a deeper understanding of the impact of ion-electron interactions (IEIs) on transport and are expected to open up a way for designing new-type photodetectors based on IEIs.
The size effect and plastic deformation mechanism transition in the nanolayered polycrystalline metallic multilayers
Authors: Zhu Yaxin , Li Zhenhuan , Huang Minsheng
Published: June 2014

The strength and deformation mechanisms of the nanolayered polycrystalline metallic multilayers (NPMMs) are investigated via molecular dynamics simulation, with special attentions to the coupling effect of grain size and layer thickness. The results indicate that the strength of multilayers does not always increases sensitively with the decrease of layer thickness or grain size, and the smaller one of them governs substantially the size effect on the strength. Due to the constraint of GBs and phase interface to gilding dislocations, there are several possible deformation mechanisms, which can govern the strength of NPMMs, including the confined partial dislocation slip, confined extended dislocation slip, and confined grain boundary slip. With the increase or decrease of the characteristic size of multilayers (i.e., layer thickness or grain size), the dominant deformation mechanism changes from one to another, resulting in very intricate size effect on the strength of multilayers. The underlying reason of mechanism transition and its influence on the strength is carefully discussed and analyzed in this article.
Mechanism of multi-defect induced ferromagnetism in undoped rutile TiO2
Authors: Wang Hongxia , Zong Zhaocun , Yan Yu
Published: June 2014

Based on first-principles calculations, the coexistence of Ti vacancies (VTi) and O vacancies (VO) is first considered to study the origin of the ferromagnetic ordering in undoped rutile TiO2. The calculations show that VO can induce local magnetic moments in TiO2, however, the ferromagnetic (FM) exchange interaction of two VO is not strong enough to induce room-temperature (RT) ferromagnetism on their own in undoped TiO2. The FM coupling between two VTi is about four times stronger than that between two VO. More importantly, the FM coupling between two VTi is further enhanced after VO is introduced. Our results indicate that the electrons induced by VO mediate the long-range FM exchange interaction between two distant VTi. This maybe the ferromagnetism mechanism in undoped TiO2: VTi produce local moments while the electrons induced by VO mediated the long-range FM exchange interaction. The results are in excellent agreement with the experimental evidences that VO alone cannot induce RT ferromagnetism while VO can promote the ferromagnetic ordering in undoped TiO2.
Thermal transport in folded zigzag and armchair graphene nanoribbons
Authors: Zhang Huisheng , Zhou Tong , Xie Guofeng , Cao Juexian , Yang Zhongqin
Published: June 2014

Thermal conductivities of graphene nanoribbons (GNRs) and carbon nanotubes (CNTs) are systematically investigated by employing nonequilibrium molecular dynamics. It is found that with the same size, the thermal conductivity of armchair GNR (AGNR) is smaller than that of zigzag CNT, while thermal conductivity of zigzag GNR (ZGNR) is larger than that of armchair CNT. The phonon participation ratios and local vibrational densities of states of GNRs (CNTs) demonstrate that the edges of the ZGNR are beneficial to the heat transport, while the edges of the AGNR are completely opposite. All these results are very helpful for us to understand the thermal transport mechanism in carbon-based nanostructures.
Extreme enhancement and reduction of the dielectric response of polymer nanoparticulate composites via interphasial charges
Authors: Lopez-Pamies Oscar , Goudarzi Taha , Meddeb Amira B. , Ounaies Zoubeida
Published: June 2014

An analytical solution is constructed for the homogenized (i.e., macroscopic) dielectric response of particulate composites comprising a random distribution of particles bonded to a matrix material through interphases of finite size that contain space charges. By accounting for interphasial charges, the solution is able to describe and explain both the extreme enhancement and the reduction of the dielectric response typically exhibited by emerging polymer nanoparticulate composites. More generally, the solution reveals that judicious manipulation of interphasial charges provides a promising path forward for the design of materials with exceptional dielectric properties.
Room-temperature electroluminescence from Ge/Ge1-xSnx/Ge diodes on Si substrates
Authors: Du Wei , Zhou Yiyin , Ghetmiri Seyed A. , Mosleh Aboozar , Conley Benjamin R. , Nazzal Amjad , Soref Richard A. , Sun Greg , Tolle John , Margetis Joe , Naseem Hameed A. , Yu Shui-Qing
Published: June 2014

Double heterostructure Ge/Ge1-xSnx/Ge light-emitting diodes (LEDs) with 6% and 8% Sn were grown on Si substrates using chemical vapor deposition. The electroluminescence emission spectra from the fabricated LEDs were investigated at room-temperature under different injection levels. The observed emission peaks at 0.645 eV and 0.601 eV are attributed to the direct bandgap transition of the Ge0.94Sn0.06 and Ge0.92Sn0.08 layers, respectively. Moreover, the integrated emission intensity increases as the Sn composition increases under the same injection condition.
Bilayer graphene quantum dot defined by topgates
Authors: Müller André , Kaestner Bernd , Hohls Frank , Weimann Thomas , Pierz Klaus , Schumacher Hans W.
Published: June 2014

We investigate the application of nanoscale topgates on exfoliated bilayer graphene to define quantum dot devices. At temperatures below 500 mK, the conductance underneath the grounded gates is suppressed, which we attribute to nearest neighbour hopping and strain-induced piezoelectric fields. The gate-layout can thus be used to define resistive regions by tuning into the corresponding temperature range. We use this method to define a quantum dot structure in bilayer graphene showing Coulomb blockade oscillations consistent with the gate layout.
Amorphization and recrystallization of single-crystalline hydrogen titanate nanowires by N+ ion irradiation
Authors: Behera Akshaya K. , Facsko Stefan , Bandyopadyay Malay K. , Das Siddhartha , Chatterjee Shyamal
Published: June 2014

We report on the phase transformation of hydrogen titanate (H2Ti3O7) nanowires induced by 50 keV N+ ion irradiation at room temperature with fluences of 1 × 1015 ions/cm2 and 1 × 1016 ions/cm2, respectively. Using transmission electron microscopy, the internal structure of the ion irradiated nanowires is analyzed. At low fluence, a transformation from crystalline H2Ti3O7 to amorphous TiO2 is observed. However, at higher fluence, a remarkable crystalline-amorphous TiO2 core-shell structure is formed. At this higher fluence, the recrystallization occurs in the core of the nanowire and the outer layer remains amorphous. The phase transformation and formation of core-shell structure are explained using the thermal spike model, radiation enhanced diffusion, and classical theory of nucleation and growth under non-equilibrium thermodynamics. X-ray photoelectron spectroscopy and Raman scattering reveal further insight into the structure of the nanowires before and after ion irradiation.
Stochastic dislocation kinetics and fractal structures in deforming metals probed by acoustic emission and surface topography measurements
Authors: Vinogradov A. , Yasnikov I. S. , Estrin Y.
Published: June 2014

We demonstrate that the fractal dimension (FD) of the dislocation population in a deforming material is an important quantitative characteristic of the evolution of the dislocation structure. Thus, we show that peaking of FD signifies a nearing loss of uniformity of plastic flow and the onset of strain localization. Two techniques were employed to determine FD: (i) inspection of surface morphology of the deforming crystal by white light interferometry and (ii) monitoring of acoustic emission (AE) during uniaxial tensile deformation. A connection between the AE characteristics and the fractal dimension determined from surface topography measurements was established. As a common platform for the two methods, the dislocation density evolution in the bulk was used. The relations found made it possible to identify the occurrence of a peak in the median frequency of AE as a harbinger of plastic instability leading to necking. It is suggested that access to the fractal dimension provided by AE measurements and by surface topography analysis makes these techniques important tools for monitoring the evolution of the dislocation structure during plastic deformation—both as stand-alone methods and especially when used in tandem.
Forages for feedstocks of biorefineries in temperate environments: review of lignin research in bioenergy crops and some insight into Miscanthus studies
Authors: Dwiyanti Maria S. , Stewart J. Ryan , Yamada Toshihiko
Published: June 2014

Rhizomatous and perennial warm-season C4 grasses such as Miscanthus spp. and switchgrass (Panicum virgatum) are potential bioenergy crops for temperate regions. However, lignin in Miscanthus and switchgrass inhibits the cellulose digestion process during bioethanol production. One of the targets for improvement of forages from feedstocks to bioenergy crops is to develop a cost-efficient biorefinery process through lignin content manipulation. Numerous reports have shown that RNAi suppression of lignin-biosynthesis pathway genes can increase biomass fermentable sugar yields for biofuel production. These studies have also reported that RNAi suppression of cell-wall lignin biosynthesis can decrease biomass yield and resistance to biotic stress in the transgenic plants. Transcriptome and metabolome approaches can be used to clarify the networks and pathways of lignin biosynthesis to facilitate the identification of appropriate target genes for transformation. However, whole-genome sequencing of the forage species, which provides much-needed genomic information, is limited. Germplasm of natural, low-lignin mutants also plays a role in identification of genetic regulation of lignin content and this would be useful breeding material. Molecular markers have been developed and utilised to accelerate identification of quantitative trait loci/genes for traits relating to the biorefinery process. All of these studies will serve as basic information for supporting genetic improvement through classical breeding or genetic transformation, and offer the opportunity to develop cultivars which have enhanced biomass and are cost-efficient for biorefinery process.
Effect of superstimulation protocols on nuclear maturation and distribution of lipid droplets in bovine oocytes
Authors: Dadarwal D. , Honparkhe M. , Dias F. C. F. , Alce T. , Lessard C. , Singh J.
Published: June 2014

Our objective was to study the effect of superstimulation protocols on nuclear maturation of the oocyte and the distribution of lipid droplets in the ooplasm. Heifers (n = 4 each group) during the luteal phase were either treated with FSH for 4 days (Short FSH), FSH for 4 days followed by 84 h of gonadotropin free period (FSH Starvation) or for 7 days (Long FSH) starting from the day of wave emergence. In all groups, LH was given 24 h after induced luteolysis (penultimate day of FSH) and cumulus–oocyte complexes were collected 24 h later. Oocytes were stained for nuclear maturation (Lamin/chromatin) and lipid droplets (Nile red). The Long FSH group had a greater proportion of mature oocytes (metaphase II) compared with heifers in the Short FSH and FSH Starvation groups (59/100 vs 5/23 and 2/25, respectively; P < 0.01). On average across all groups, oocytes contained 22 pL of lipids (3.3% of ooplasm volume) distributed as 3000 droplets. Average volume of individual lipid droplets was higher in the FSH Starvation (11.5 ± 1.5 10–3 pL, P = 0.03) compared with the Short and Long FSH groups (7.2 ± 0.6 10–3 and 8.0 ± 0.8 10–3 pL, respectively). In conclusion, both FSH Starvation and Short FSH treatments yielded a lower proportion of mature oocytes compared with the Long FSH treatment. Furthermore, FSH starvation led to an accumulation of larger lipid droplets in the ooplasm, indicating atresia. Our results indicate that a longer superstimulation period in beef cattle yields higher numbers and better-quality oocytes.
Free-radical production after post-thaw incubation of ram spermatozoa is related to decreased in vivo fertility
Authors: Del Olmo Enrique , Bisbal Alfonso , García-Álvarez Olga , Maroto-Morales Alejandro , Ramón Manuel , Jiménez-Rabadán Pilar , Anel-López Luis , Soler Ana J. , Garde J. Julián , Fernández-Santos María R.
Published: June 2014

The aim of the present study was to evaluate the effect of sperm reactive oxygen species (ROS) production and DNA changes on male fertility. For that purpose, six rams with significantly different pregnancy rates were used; these were classified as having high fertility, i.e. 59.4% average pregnancy rate, or low fertility, i.e. 23.1% average pregnancy rate. Sperm quality was assessed after a two-step process of sample thawing followed by an incubation of 2 h, either in the freezing extender (37°C) or after dilution in synthetic oviductal fluid (SOF; 38°C, 5%CO2). Sperm viability (YO-PRO-1), ROS production (5-(and-6)-chloromethyl-2′,7′-dichlorodihydrofluorescein acetyl ester (CM-H2DCFDA)) and undamaged chromatin (sperm chromatin structure assay, terminal deoxynucleotidyl transferase-mediated dUTP nick-end labelling, chromomycin A3) were evaluated by flow cytometry. Although no significant differences in sperm viability were observed, our results showed increased ROS production during incubation in the freezing extender as well as in SOF medium. Comparison between fertility groups showed significant differences in ROS production after 2 h of incubation for the two treatments. Regarding DNA integrity, our results showed no significant differences either between treatments and incubation times or fertility groups. Linear regression analysis showed that ROS production determined by CM-H2DCFDA was a good indicator parameter for in vivo male fertility of SOF-incubated samples, yielding a fair correlation between both parameters (r = –0.92). These results indicate that detection of ROS production by CM-H2DCFDA and flow cytometry after 2 h of incubation in SOF could be a useful procedure for predicting fertility of ram spermatozoa.
The role of right-wing authoritarianism, sexism and culture of honour in rape myths acceptance / El papel del autoritarismo de derechas, del sexismo y de la cultura del honor en la aceptación de los mitos sobre la violación
Authors: Canto Jesús M. , Perles Fabiola , Martín Jesús San
Published: June 2014

The purpose of this work is to analyse how some ideological variables (ambivalent sexism, culture of honour, and right-wing authoritarianism) affect rape myths acceptance (RMA). Two hundred and fourteen university students (83 men and 131 women), mean age 20.39 years old, participated. The results show that there is a high correlation between RMA and hostile sexism, benevolent sexism, culture of honour, and right-wing authoritarianism. Hostile sexism and right-wing authoritarianism predict RMA in both male and female samples. Benevolent sexism predicts RMA in the female sample. In addition, in the male sample right-wing authoritarianism interacts with hostile sexism to predict RMA, while in the female sample right-wing authoritarianism interacts with benevolent sexism to predict RMA. These results show the close relationship existing between certain ideological variables and RMA.
Training load quantification in elite swimmers using a modified version of the training impulse method
Authors: García‐Ramos Amador , Feriche Belén , Calderón Carmen , Iglesias Xavier , Barrero Anna , Chaverri Diego , Schuller Thorsten , Rodríguez Ferran A.
Published: June 2014

Prior reports have described the limitations of quantifying internal training loads using hear rate (HR)‐based objective methods such as the training impulse (TRIMP) method, especially when high‐intensity interval exercises are performed. A weakness of the TRIMP method is that it does not discriminate between exercise and rest periods, expressing both states into a single mean intensity value that could lead to an underestimate of training loads. This study was designed to compare Banister's original TRIMP method (1991) and a modified calculation procedure (TRIMPc) based on the cumulative sum of partial TRIMP, and to determine how each model relates to the session rating of perceived exertion (s‐RPE), a HR‐independent training load indicator. Over four weeks, 17 elite swimmers completed 328 pool training sessions. Mean HR for the full duration of a session and partial values for each 50 m of swimming distance and rest period were recorded to calculate the classic TRIMP and the proposed variant (TRIMPc). The s‐RPE questionnaire was self‐administered 30 minutes after each training session. Both TRIMPc and TRIMP measures strongly correlated with s‐RPE scores (r = 0.724 and 0.702, respectively; P < 0.001). However, TRIMPc was ∼9% higher on average than TRIMP (117 ± 53 vs. 107 ± 47; P < 0.001), with proportionally greater inter‐method difference with increasing workload intensity. Therefore, TRIMPc appears to be a more accurate and appropriate procedure for quantifying training load, particularly when monitoring interval training sessions, since it allows weighting both exercise and recovery intervals separately for the corresponding HR‐derived intensity.
Evaluating information seeking and use in the changing virtual world: the emerging role of Google Analytics
Authors: CLARK D.J. , NICHOLAS David , JAMALI Hamid R.
Published: June 2014

The paper identifies changes that have occurred in the Web environment over the last decade which have gradually rendered server logs, once the preeminent source of intelligence on usage and information‐seeking behaviour, an ineffective, impractical, and uneconomic resource. It also looks at the implications of these changes for information professionals and publishers who have come to rely on this data to understand the behaviour of clients and customers in the virtual environment. Ubiquitous and expanding, Google Analytics generates statistics about a website's traffic and traffic sources, albeit from a marketers' perspective, is evaluated as a possible replacement; something which might plug the user knowledge gap which is worryingly opening up, or maybe even, put us in a better position overall. The paper is built on the knowledge and experience of evaluating server logs for more than a decade, mostly for publishers and libraries, and also on two recent projects where server log analysis was supplemented with Google Analytics.
Maturation of late Golgi cisternae into RabERAB11exocytic post-Golgi carriers visualized in vivo
Authors: Pantazopoulou Areti , Pinar Mario , Xiang Xin , Peñalva Miguel A.
Published: June 2014

The mechanism(s) by which proteins traverse and exit the Golgi are incompletely understood. Using Aspergillus nidulans hyphae, we show that late Golgi cisternae undergo changes in composition to gradually lose Golgi identity while acquiring post-Golgi RabERAB11identity. This behavior of late Golgi cisternae is consistent with the cisternal maturation model. Post-Golgi RabERAB11carriers travel to, and accumulate at, the apex, indicating that fusion is rate limiting for exocytosis. These carriers, which are loaded with kinesin, dynein, and MyoEMYO5, move on a microtubule-based bidirectional conveyor belt relaying them to actin, which ultimately focuses exocytosis at the apex. Dynein drags RabERAB11carriers away if engagement of MyoEMYO5to actin cables fails. Microtubules seemingly cooperating with F-actin capture can sustain secretion if MyoEMYO5is absent. Thus, filamentous fungal secretion involving post-Golgi carriers is remarkably similar, mechanistically, to the transport of melanosomes in melanocyte dendrites, even though melanosome biogenesis involves lysosomes rather than Golgi.
Mathematical model with spatially uniform regulation explains long-range bidirectional transport of early endosomes in fungal hyphae
Authors: Gou Jia , Edelstein-Keshet Leah , Allard Jun
Published: June 2014

In many cellular contexts, cargo is transported bidirectionally along microtubule bundles by dynein and kinesin-family motors. Upstream factors influence how individual cargoes are locally regulated, as well as how long-range transport is regulated at the whole-cell scale. Although the details of local, single-cargo bidirectional switching have been extensively studied, it remains to be elucidated how this results in cell-scale spatial organization. Here we develop a mathematical model of early endosome transport in Ustilago maydis. We demonstrate that spatiotemporally uniform regulation, with constant transition rates, results in cargo dynamics that is consistent with experimental data, including data from motor mutants. We find that microtubule arrays can be symmetric in plus-end distribution but asymmetric in binding-site distribution in a manner that affects cargo dynamics and that cargo can travel past microtubule ends in microtubule bundles. Our model makes several testable predictions, including secondary features of dynein and cargo distributions.
“Protect Me”
Authors: Alvandi Roham
Published: June 2014

This chapter traces the evolution of Iran from a client to a partner of the United States, from the announcement of the British withdrawal from the Persian Gulf in 1968 to the end of Nixon’s first term as president in 1972. The shah successfully lobbied the Nixon administration to abandon a policy of balancing Iran and Saudi Arabia as the “twin pillars” of the Gulf and to instead embrace Iran’s regional primacy under the Nixon Doctrine. Drawing on Iranian sources, this chapter reveals that the shah’s actions during the 1969 Shatt al-Arab border crisis between Iran and Iraq nearly sparked a war between the two countries. It also details the Nixon administration’s illegal funneling of American arms to Pakistan via Iran during the 1971 Indo-Pakistan War.
Iran’s Secret War with Iraq
Authors: Alvandi Roham
Published: June 2014

Chapter abstract: In the first detailed history of the CIA’s covert operation in Iraqi Kurdistan from 1972 to 1975, this chapter examines how the shah used his partnership with Nixon and Kissinger to draw the United States into Iran’s secret war against Iraq in Kurdistan in 1972. The shah used the Americans to keep Mustafa Barzani’s Kurds fighting, in order to paralyze the Iraqi army and thereby neutralize the Iraqi threat to Iran’s oil-rich province of Khuzestan and Iranian shipping in the Shatt al-Arab and the Persian Gulf. When the shah defied Kissinger and signed the Algiers Agreement with Iraqi strongman Saddam Hussein in March 1975, whereby Iran abandoned the Kurds in exchange for Iraqi territorial concessions in the Shatt, Kissinger had no choice but to accept the shah’s decision as a fait accompli and to suffer subsequent domestic recriminations for having betrayed the Kurds.
An Overview of Aristotelian Logic as seen by Medieval Logicians
Authors: Parsons Terence
Published: June 2014

Categorical propositions include universal, particular, and singular affirmative and negative propositions. ‘Every S is P’ contradicts ‘Some S isn’t P’; ‘No S is P’ contradicts ‘Some S is P’, and ‘n is P’ contradicts ‘n isn’t P’. Universal affirmatives and negatives are contraries, so universal affirmatives are false – and particular negatives true -- if either of their terms are empty. It seems odd that ‘Some chimera isn’t a rock’ is true just because there aren’t any chimeras, but medieval logicians took this as a datum. ‘Some S is a P’ converts to ‘Some P is an S’; likewise for ‘No S is a P’ and ‘No P is an S’. ‘Every S is a P’ converts by limitation (entails) to ‘Some P is an S’. Aristotle’s syllogisms are presented. The term-prefix ‘non’, called infinite negation, does not make a proposition negative. Aristotle defines validity modally, but his theory is formal.
Expanding the Notation
Authors: Parsons Terence
Published: June 2014

Medieval logicians used complex sentences, so Linguish is extended. Adjectives can be substantivated and used as nouns. Intransitive verbs were held to need analysis into ‘is’ plus their present participles; they were substantivized too. Transitive verbs were treated the same, but their logical behavior differs because the participle of a transitive verb creates a grammatical role, the direct object of the verb. Such participles have relative supposition; I call them parasitic terms. They require additional logical rules. Complex terms such as ‘donkey seeing every horse’ are incorporated with additional grammatical rules and inference rules. Relative clauses allow for a great deal of logical complexity; they are included in the rules and semantics. Genitive constructions allow logicians to construct propositions with multiple denoting phrases: ‘Of some woman every daughter sees a donkey’. Demonstrative expressions are also covered, as are molecular propositions made with ‘and’, ‘or’, and ‘if’.
Some Illustrative Topics
Authors: Parsons Terence
Published: June 2014

De Morgan famously claimed that certain logical inferences involving relational expressions are non-syllogistic. It is possible to validate the inferences he had in mind using the rules of Linguish. (Some of these involve parasitic terms.) John Buridan espoused certain distinctive views on the natures of subjects and predicates, ideas that do not occur in modern logic. His views are expounded; many of them can be captured within Linguish. Others seem to be problematic. Some logicians after Buridan developed algorithms for determining from surface grammar which strings of expressions form complex terms, and which are sequences of independent terms. This is vital for logical analysis. Following Karger, these algorithms are formulated and examined.
Relatives (Anaphoric Words)
Authors: Parsons Terence
Published: June 2014

Relatives are anaphoric words. Logicians agree that a pronoun may be replaced by its antecedent if the antecedent is singular; otherwise not. A “singulation” theory was developed according to which pronouns remain unchanged when their antecedents change; in ‘Every cat sees itself; Tabby is a cat; therefore Tabby sees itself’, ‘itself’ has ‘cat’ as antecedent in the premise and ‘Tabby’ in the conclusion. This theory can be formulated within Linguish, and it works well. A non-reflexive pronoun was held to have the same mode of supposition as its antecedent, and to supposit for the same things as its antecedent, or for the things its antecedent is verified for. These accounts did not work well. But the singulation theory works well applied to any pronoun that occurs within the scope of its antecedent. Burley’s worries about certain pronouns are discussed. The theory covers anaphoric uses of ‘same’ and ‘other’.
Ampliation and Restriction
Authors: Parsons Terence
Published: June 2014

Terms are ampliated by tense; in a past tense sentence the subject supposits for presently existing and formerly existing things signified by the term, and the predicate supposits for formerly existing things that it signifies. Similarly for the future. When a modal term modifies the copula, subjects supposit for all possible things that they signify; the predicate term depends on the modality. Semantic terminology ampliates terms; in ‘In any past tense sentence ‘dodo’ supposits for dodos’ the predicate term is ampliated to formerly existing dodos because of the semantical term ‘supposit’. When a sentence contains a word which pertains to the soul, terms signify merely possible things: ‘A bishop thinks about a golden mountain’. Intentional verbs affect their terms; an example is ‘I promise you a horse’ when no particular horse is promised. Some held that in such a context the word ‘horse’ is made to “appellate” the concept horse; this affects the sentence’s truth value.
Bargaining with a Rising India
Authors: Narlikar Amrita , Narlikar Aruna
Published: June 2014

The need to negotiate effectively with India is only growing as its power rises. Understanding the negotiation culture wherein India's bargaining behaviour is embedded forms a crucial step to facilitate this process. In the literature on international negotiation, experimental studies point to specific behavioural characteristics of Indian negotiators. Empirical analyses confirm these findings, and suggest that the sources of India's negotiation behaviour are deep-rooted and culture-specific, going beyond what standard explanations of interest group politics, partisan politics, and institutional politics would suggest. But there are very few works that trace these sources. Extensive anthropological and sociological studies remain confined to their own fields and do not develop their implications for foreign policy or negotiation. There is a conspicuous lack of works that attempt to unpack the ‘negotiating culture’ variable using literary sources. This book aims to fill these gaps. It focuses on India's negotiating traditions through the lens of the classical Sanskrit text, the Mahabharata, and investigates the continuities and changes in India's negotiation behaviour as a rising power.
Playing Hardball?
Authors: Narlikar Amrita , Narlikar Aruna
Published: June 2014

This chapter presents the intellectual puzzle that underlies the book: to what extent does India's bargaining behaviour, as a rising power, reflect cultural continuities? It offers a discussion on the methodology used. It highlights the importance of the culture variable as a route to understanding international negotiation, and further explains the logic that underlies our choice of the Mahabharata as a lens into India's bargaining traditions, norms, and beliefs. The chapter further provides a conceptualization of negotiation behaviour; the concepts introduced herein are used throughout the book. It presents a brief overview of the main characteristics that have come to be associated with India's negotiation style. It situates these characteristics within a debate on India's foreign policy and negotiation behaviour today that has perplexed and divided analysts. Finally, it outlines the structure of the book and discusses the contribution that this project makes to the existing literature.
Time
Authors: Narlikar Amrita , Narlikar Aruna
Published: June 2014

The Indian readiness to engage in prolonged negotiation derives at least partly from its bureaucratic and political culture. Interestingly, the willingness of Indian negotiators to bide their time in international bargaining predates India's rise to power, and is only partially driven by strategic considerations. Rather, speed is often regarded as haste and associated with a failure to follow due process. Both the existence of this long shadow of the future and the particular ways in which it is conceptualized and translated into the negotiation process need explaining. This chapter investigates how negotiators (in the Mahabharata and the present day) interpret the culture-specific notion of time, focusing on the extent to which references to the past are used and allowed to influence negotiations, and further the responsiveness of negotiators to time pressures and deadlines.
Setting the Stage*
Authors: Craigo-Snell Shannon
Published: June 2014

Chapter 1 introduces the field of performance studies and argues that Christian communities interpret Scripture in the performance of worship and Christian life. Performance is characterized as event, interaction, and doubleness. Using both the analysis of performance studies and the analogy between church and theatre, this chapter argues that Christians perform the Bible in several different senses: from performing a set script to performing a commandment to performing ourselves as people shaped by this text. All of these different kinds of performance are ways in which communities interpret the Bible. Christian communities interpret Scripture through embodied, communal performance of worship and life. This chapter also outlines a performative anthropology (human identity is formed in multidirectional interactions that include biology, culture, and relationships over time), a performative epistemology (we know in our whole selves, including body, emotion, intellect, and will), and a performative hermeneutic (Christians interpret Scripture in and through performance).
Striking the Set
Authors: Craigo-Snell Shannon
Published: June 2014

Finally, chapter 5 brings together Karl Barth and Peter Brook to consider the possible problems of theatrical and performative views of church, and to develop an understanding of emptiness as necessary to worship that longs for the Spirit of God. The performance of church occurs in hope of the Spirit. Our performances cannot control the Spirit, but rather help us to be open and attuned to the Spirit’s presence and movement. Through a discipline of emptiness, we clear away the No-Gods of our own creation, repent of our arrogance, and hope for something far more than our own strivings. We hope to be taken up, to be allowed in on the action, to participate in the movement of the Spirit.
Semi-parametric Selection Models for Potentially Non-ignorable Attrition in Panel Studies with Refreshment Samples
Authors: Si Yajuan , Reiter Jerome P. , Hillygus D. Sunshine
Published: June 2014

Panel studies typically suffer from attrition. Ignoring the attrition can result in biased inferences if the missing data are systematically related to outcomes of interest. Unfortunately, panel data alone cannot inform the extent of bias due to attrition. Many panel studies also include refreshment samples, which are data collected from a random sample of new individuals during the later waves of the panel. Refreshment samples offer information that can be utilized to correct for biases induced by non-ignorable attrition while reducing reliance on strong assumptions about the attrition process. We present a Bayesian approach to handle attrition in two-wave panels with one refreshment sample and many categorical survey variables. The approach includes (1) an additive non-ignorable selection model for the attrition process; and (2) a Dirichlet process mixture of multinomial distributions for the categorical survey variables. We present Markov chain Monte Carlo algorithms for sampling from the posterior distribution of model parameters and missing data. We apply the model to correct attrition bias in an analysis of data from the 2007–08 Associated Press/Yahoo News election panel study.
Clavibacter michiganensis subsp. michiganensis Vatr1 and Vatr2 Transcriptional Regulators Are Required for Virulence in Tomato
Authors: Savidor Alon , Chalupowicz Laura , Teper Doron , Gartemann Karl-Heinz , Eichenlaub Rudolf , Manulis-Sasson Shulamit , Barash Isaac , Sessa Guido
Published: June 2014

The plant pathogen Clavibacter michiganensis subsp. michiganensis is a gram-positive bacterium responsible for wilt and canker disease of tomato. Although disease development is well characterized and diagnosed, molecular mechanisms of C. michiganensis subsp. michiganensis virulence are poorly understood. Here, we identified and characterized two C. michiganensis subsp. michiganensis transcriptional regulators, Vatr1 and Vatr2, that are involved in pathogenicity of C. michiganensis subsp. michiganensis. Vatr1 and Vatr2 belong to TetR and MocR families of transcriptional regulators, respectively. Mutations in their corresponding genes caused attenuated virulence, with the Δvatr2 mutant showing a more dramatic effect than Δvatr1. Although both mutants grew well in vitro and reached a high titer in planta, they caused reduced wilting and canker development in infected plants compared with the wild-type bacterium. They also led to a reduced expression of the ethylene-synthesizing tomato enzyme ACC-oxidase compared with wild-type C. michiganensis subsp. michiganensis and to reduced ethylene production in the plant. Transcriptomic analysis of wild-type C. michiganensis subsp. michiganensis and the two mutants under infection-mimicking conditions revealed that Vatr1 and Vatr2 regulate expression of virulence factors, membrane and secreted proteins, and signal-transducing proteins. A 70% overlap between the sets of genes positively regulated by Vatr1 and Vatr2 suggests that these transcriptional regulators are on the same molecular pathway responsible for C. michiganensis subsp. michiganensis virulence.
Potential of Pseudomonas chlororaphis subsp. aurantiaca Strain Pcho10 as a Biocontrol Agent Against Fusarium graminearum
Authors: Hu Weiqun , Gao Qixun , Hamada Mohamed Sobhy , Dawood Dawood Hosni , Zheng Jingwu , Chen Yun , Ma Zhonghua
Published: June 2014

To develop an effective biocontrol strategy for management of Fusarium head blight on wheat caused by Fusarium graminearum, the bacterial biocontrol agent Pcho10 was selected from more than 1,476 wheat-head-associated bacterial strains according to its antagonistic activity in vitro. This strain was subsequently characterized as Pseudomonas chlororaphis subsp. aurantiaca based on 16S ribosomal DNA sequence analysis, assays of the BIOLOG microbial identification system, and unique pigment production. The major antifungal metabolite produced by Pcho10 was further identified as phenazine-1-carboxamide (PCN) on the basis of nuclear magnetic resonance data. The core PCN biosynthesis gene cluster in Pcho10 was cloned and sequenced. PCN showed strong inhibitory activity against F. graminearum conidial germination, mycelial growth, and deoxynivalenol production. Tests both under growth chamber conditions and in field trials showed that Pcho10 well colonized on the wheat head and effectively controlled the disease caused by F. graminearum. Results of this study indicate that P. chlororaphis subsp. aurantiaca Pcho10 has high potential to be developed as a biocontrol agent against F. graminearum. To our knowledge, this is the first report of the use of P. chlororaphis for the management of Fusarium head blight.
Lipoxygenase Activation in Peanut Seed Cultivars Resistant and Susceptible to Aspergillus parasiticus Colonization
Authors: Müller V. , Amé M. V. , Carrari V. , Gieco J. , Asis R.
Published: June 2014

Accumulative evidence indicates that the lipoxygenase (LOX) pathway plays a significant role in the Aspergillus–seed interaction, such as interfering with activities of endogenous fungal oxylipins or producing antimicrobial compounds and signaling molecules. In this study, we characterized the LOX pathway in peanut seed during Aspergillus parasiticus colonization in a model of two cultivars distinguished as resistant (‘PI337394’) and susceptible (‘Florman INTA’) to Aspergillus spp. infection and aflatoxin contamination. The LOX activity together with the content of LOX substrate and LOX products demonstrated the presence of a differential response mechanism to A. parasiticus infection between cultivars. Our findings suggest that this mechanism is under transcriptional control of previously identified (LOX 2 and LOX 3) and novel (LOX 4 and LOX 5) LOX genes. The results of this study support the role of these enzymes in defense during fungus infection in peanut seed.
Bifidobacterium faecale sp. nov., isolated from human faeces
Authors: Choi Jung-Hye , Lee Kyung Min , Lee Myung-Ki , Cha Chang-Jun , Kim Geun-Bae
Published: June 2014

A novel strain, designated strain CU3-7T, was isolated from faeces of a two-week-old baby. The isolate was Gram-staining-positive, anaerobic and rod-shaped. Results from 16S rRNA gene sequence analysis revealed that strain CU3-7T was phylogenetically affiliated with members of the genus

Bifidobacterium

. Strain CU3-7T showed the highest level of sequence similarity with

Bifidobacterium adolescentis

KCTC 3216T (98.4 %), followed by

Bifidobacterium ruminantium

KCTC 3425T (97.9 %). Analysis of hsp60 sequences showed that strain CU3-7T was closely related to

B. adolescentis

KCTC 3216T (94.0 %) and

B. ruminantium

KCTC 3425T (92.5 %). The DNA–DNA hybridization values with the closely related strains were all below the cut-off value for species delineation, 17.0 % with

B. ruminantium

KCTC 3425T and 14.9 % with

B. adolescentis

KCTC 3216T. Fructose-6-phosphate phosphoketolase activity was detected. The predominant cellular fatty acids were C16 : 0 (27.7 %), C18 : 1ω9c (27.4 %) and C18 : 1ω9c dimethylacetate (15.5 %). The DNA G+C content was 58.6 mol%. On the basis of polyphasic taxonomy, strain CU3-7T should be classified as the type strain of a novel species within the genus

Bifidobacterium

, for which the name Bifidobacterium faecale sp. nov. is proposed ( = KACC 17904T = JCM 19861T).
Polyphasic taxonomic revision of the Ralstonia solanacearum species complex: proposal to emend the descriptions of Ralstonia solanacearum and Ralstonia syzygii and reclassify current R. syzygii strains as Ralstonia syzygii subsp. syzygii subsp. nov., R. solanacearum phylotype IV strains as Ralstonia syzygii subsp. indonesiensis subsp. nov., banana blood disease bacterium strains as Ralstonia syzygii subsp. celebesensis subsp. nov. and R. solanacearum phylotype I and III strains as Ralstonia
pseudosolanacearum sp. nov.
Authors: Safni Irda , Cleenwerck Ilse , De Vos Paul , Fegan Mark , Sly Lindsay , Kappler Ulrike
Published: June 2014

The Ralstonia solanacearum species complex has long been recognized as a group of phenotypically diverse strains that can be subdivided into four phylotypes. Using a polyphasic taxonomic approach on an extensive set of strains, this study provides evidence for a taxonomic and nomenclatural revision of members of this complex. Data obtained from phylogenetic analysis of 16S-23S rRNA ITS gene sequences, 16S–23S rRNA intergenic spacer (ITS) region sequences and partial endoglucanase (egl) gene sequences and DNA–DNA hybridizations demonstrate that the R. solanacearum species complex comprises three genospecies. One of these includes the type strain of

Ralstonia solanacearum

and consists of strains of

R. solanacearum

phylotype II only. The second genospecies includes the type strain of

Ralstonia syzygii

and contains only phylotype IV strains. This genospecies is subdivided into three distinct groups, namely

R. syzygii

, the causal agent of Sumatra disease on clove trees in Indonesia,

R. solanacearum

phylotype IV strains isolated from different host plants mostly from Indonesia, and strains of the blood disease bacterium (BDB), the causal agent of the banana blood disease, a bacterial wilt disease in Indonesia that affects bananas and plantains. The last genospecies is composed of

R. solanacearum

strains that belong to phylotypes I and III. As these genospecies are also supported by phenotypic data that allow the differentiation of the three genospecies, the following taxonomic proposals are made: emendation of the descriptions of

Ralstonia solanacearum

and

Ralstonia syzygii

and descriptions of Ralstonia syzygii subsp. nov. (type strain R 001T = LMG 10661T = DSM 7385T) for the current

R. syzygii

strains, Ralstonia syzygii subsp. indonesiensis subsp. nov. (type strain UQRS 464T = LMG 27703T = DSM 27478T) for the current

R. solanacearum

phylotype IV strains, Ralstonia syzygii subsp. celebesensis subsp. nov. (type strain UQRS 627T = LMG 27706T = DSM 27477T) for the BDB strains and Ralstonia pseudosolanacearum sp. nov. (type strain UQRS 461T = LMG 9673T = NCPPB 1029T) for the strains of

R. solanacearum

phylotypes I and III.
The overdue promise of short tandem repeat variation for heritability
Authors: Press Maximilian O. , Carlson Keisha D. , Queitsch Christine
Published: June 2014

Short tandem repeat (STR) variation has been proposed as a major explanatory factor in the heritability of complex traits in humans and model organisms. However, we still struggle to incorporate STR variation into genotype-phenotype maps. Here, we review the promise of STRs in contributing to complex trait heritability, and highlight the challenges that STRs pose due to their repetitive nature. We argue that STR variants are more likely than single nucleotide variants to have epistatic interactions, reiterate the need for targeted assays to accurately genotype STRs, and call for more appropriate statistical methods in detecting STR-phenotype associations. Lastly, somatic STR variation within individuals may serve as a read-out of disease susceptibility, and is thus potentially a valuable covariate for future association studies.