bluuebunny/crossref_metadata_2025 huggingface dataset:
Elastically cooperative activated barrier hopping theory of relaxation in viscous fluids. I. General formulation and application to hard sphere fluids
Authors: Mirigian Stephen , Schweizer Kenneth S.
Published: May 2014

We generalize the force-level nonlinear Langevin equation theory of single particle hopping to include collective effects associated with long range elastic distortion of the liquid. The activated alpha relaxation event is of a mixed spatial character, involving two distinct, but inter-related, local and collective barriers. There are no divergences at volume fractions below jamming or temperatures above zero Kelvin. The ideas are first developed and implemented analytically and numerically in the context of hard sphere fluids. In an intermediate volume fraction crossover regime, the local cage process is dominant in a manner consistent with an apparent Arrhenius behavior. The super-Arrhenius collective barrier is more strongly dependent on volume fraction, dominates the highly viscous regime, and is well described by a nonsingular law below jamming. The increase of the collective barrier is determined by the amplitude of thermal density fluctuations, dynamic shear modulus or transient localization length, and a growing microscopic jump length. Alpha relaxation time calculations are in good agreement with recent experiments and simulations on dense fluids and suspensions of hard spheres. Comparisons of the theory with elastic models and entropy crisis ideas are explored. The present work provides a foundation for constructing a quasi-universal, fit-parameter-free theory for relaxation in thermal molecular liquids over 14 orders of magnitude in time.
Measurements of high-energy radiation generation from laser-wakefield accelerated electron beams
Authors: Schumaker W. , Sarri G. , Vargas M. , Zhao Z. , Behm K. , Chvykov V. , Dromey B. , Hou B. , Maksimchuk A. , Nees J. , Yanovsky V. , Zepf M. , Thomas A. G. R. , Krushelnick K.
Published: May 2014

Using high-energy (∼0.5 GeV) electron beams generated by laser wakefield acceleration (LWFA), bremsstrahlung radiation was created by interacting these beams with various solid targets. Secondary processes generate high-energy electrons, positrons, and neutrons, which can be measured shot-to-shot using magnetic spectrometers, short half-life activation, and Compton scattering. Presented here are proof-of-principle results from a high-resolution, high-energy gamma-ray spectrometer capable of single-shot operation, and high repetition rate activation diagnostics. We describe the techniques used in these measurements and their potential applications in diagnosing LWFA electron beams and measuring high-energy radiation from laser-plasma interactions.
Edge-states ferromagnetism of WS2 nanosheets
Authors: Huo Nengjie , Li Yan , Kang Jun , Li Renxiong , Xia Qinglin , Li Jingbo
Published: May 2014

The multilayer WS2 nanosheets prepared from WO3 nanowires exhibit strong ferromagnetic behavior with saturation magnetization (MS) of 0.0058 emu/g and coercive field (HC) of 92 Oe at room temperature. By decreasing the temperature down to 3 K the Hc is increased up to 1115 Oe, revealing the existence of long-range magnetic ordering. Density functional theory spin-polarized calculations predict that strong ferromagnetic moments in WS2 nanosheets are attributed to the zigzag edge sulphur S and tungsten W atoms. Our findings also suggest that the WS2 nanosheets with a high density of edge spins could be used to fabricate spintronics devices, which are circuits utilizing the spin of the electron to process and store information.
Coherence penalty functional: A simple method for adding decoherence in Ehrenfest dynamics
Authors: Akimov Alexey V. , Long Run , Prezhdo Oleg V.
Published: May 2014

We present a new semiclassical approach for description of decoherence in electronically non-adiabatic molecular dynamics. The method is formulated on the grounds of the Ehrenfest dynamics and the Meyer-Miller-Thoss-Stock mapping of the time-dependent Schrödinger equation onto a fully classical Hamiltonian representation. We introduce a coherence penalty functional (CPF) that accounts for decoherence effects by randomizing the wavefunction phase and penalizing development of coherences in regions of strong non-adiabatic coupling. The performance of the method is demonstrated with several model and realistic systems. Compared to other semiclassical methods tested, the CPF method eliminates artificial interference and improves agreement with the fully quantum calculations on the models. When applied to study electron transfer dynamics in the nanoscale systems, the method shows an improved accuracy of the predicted time scales. The simplicity and high computational efficiency of the CPF approach make it a perfect practical candidate for applications in realistic systems.
The influence of low-level pre-stressing on resonant magnetoelectric coupling in Terfenol-D/PZT/Terfenol-D laminated composite structure
Authors: Chen Zhengxin , Su Yu
Published: May 2014

The resonant magnetoelectric coupling behavior in a Terfenol-D/PZT/Terfenol-D laminated composite structure is experimentally studied with specific interest in the dependence on the pre-applied low-level mechanical stress up to 1.25 MPa. A laminated composite consisting of two Terfenol-D plates and one transversely polarized sandwiched-in PZT plate is fabricated in lab followed by pre-stressing along the direction of length, width, and thickness, respectively. It is observed that resonant magnetoelectric coupling develops in such pre-stressed composite when magnetically excited in each of the orthogonal directions, and the longitudinal mode of principle vibration can be confirmed. The action of pre-stresses generally elevates the frequency of resonance through the ΔE effect in Terfenol-D. In the meanwhile, the increased pre-stress lowers the value of the resonance magnetoelectric coefficient. This is partly attributed to the decrease of the effective quality factor of the structure along the increase of pre-stress, and partly attributed to the piezomagnetic coefficient of Terfenol-D, which either decreases or remains constant depending on the magnetizing state. In addition to the resonant behaviors, the tunability of the magnetoelectric coefficient of the pre-stressed structure is examined at fixed excitation frequency. For the structure excited in the length or width direction, the magnetoelectric coupling can reach the maximum at an optimal bias field. When excited in thickness, however, the magnetoelectric coupling becomes very weak, and the value of the coefficient increases monotonically with the pre-stresses. The increase of the pre-stress causes degradation of the maximum magnetoelectric coefficient for the structure when excited in length or width direction. This observation can be explained via the upshift of the resonance frequency of the structure caused by increased pre-stresses. Alternatively, it can be viewed as the consequence of the change in the maximum piezomagnetic coefficient of Terfenol-D, which is observed to decrease upon the increase of pre-stresses.
Electron-phonon coupling enhanced by the FeSe/SrTiO3 interface
Authors: Li B. , Xing Z. W. , Huang G. Q. , Xing D. Y.
Published: May 2014

The electronic structure, phonon dispersions, and electron-phonon (EP) coupling in Fe2Se2/SrTiO3 (FeSe/STO) thinnest films are studied based on the first-principles calculations. It is found that the FeSe/STO interface with lattice strain leads to a change of band structures and a significant enhancement of the EP coupling, the latter being close related to interface-induced ferroelectric phonons coupled to electrons on the FeSe monolayer. In the FeSe/STO system, Tc of phonon-induced superconductivity is estimated to be much greater than that in the bulk FeSe, but still well below the experimental value of an FeSe monolayer on the STO substrate, indicating that the electron-phonon mechanism alone cannot explain its high Tc.
A continuum model with a percolation threshold and tunneling-assisted interfacial conductivity for carbon nanotube-based nanocomposites
Authors: Wang Yang , Weng George J. , Meguid Shaker A. , Hamouda Abdel Magid
Published: May 2014

A continuum model that possesses several desirable features of the electrical conduction process in carbon-nanotube (CNT) based nanocomposites is developed. Three basic elements are included: (i) percolation threshold, (ii) interface effects, and (iii) tunneling-assisted interfacial conductivity. We approach the first one through the selection of an effective medium theory. We approach the second one by the introduction of a diminishing layer of interface with an interfacial conductivity to build a "thinly coated" CNT. The third one is introduced through the observation that interface conductivity can be enhanced by electron tunneling which in turn can be facilitated with the formation of CNT networks. We treat this last issue in a continuum fashion by taking the network formation as a statistical process that can be represented by Cauchy's probability density function. The outcome is a simple and yet widely useful model that can simultaneously capture all these fundamental characteristics. It is demonstrated that, without considering the interface effect, the predicted conductivity would be too high, and that, without accounting for the additional contribution from the tunneling-assisted interfacial conductivity, the predicted conductivity beyond the percolation threshold would be too low. It is with the consideration of all three elements that the theory can fully account for the experimentally measured data. We further use the developed model to demonstrate that, despite the anisotropy of the intrinsic CNT conductivity, it is its axial component along the CNT direction that dominates the overall conductivity. This theory is also proved that, even with a totally insulating matrix, it is still capable of delivering non-zero conductivity beyond the percolation threshold.
Thickness dependent metal-insulator transition and dimensional crossover for weak localization in Si0.02Zn0.98O thin films grown by pulsed laser deposition
Authors: Das Amit K. , Ajimsha R. S. , Kukreja L. M.
Published: May 2014

Metal to insulator transition was observed in Si0.02Zn0.98O (SZO) films, grown by pulsed laser deposition on sapphire substrates, as the thicknesses of the films were reduced from ∼40 to 15 nm. The SZO film with thickness of ∼40 nm showed typical metallic behavior in temperature dependent resistivity measurements. On the contrary, the SZO film with thickness of ∼15 nm was found to exhibit strong localization where the transport at low temperature was dominated by variable range hopping conduction. In the intermediate thickness regime, quantum corrections were important and a dimensional crossover from 3D to 2D weak localization occurred in the SZO film with thickness of 20 nm.
Enhanced absorption of monolayer MoS2 with resonant back reflector
Authors: Liu Jiang-Tao , Wang Tong-Biao , Li Xiao-Jing , Liu Nian-Hua
Published: May 2014

The optical absorption of monolayer MoS2 on top of one-dimensional photonic crystal (1DPC) or metal films with spacer layers is theoretically investigated by extracting the permittivity of monolayer MoS2 from existing experimental results [K. F. Mak et al., Phys. Rev. Lett. 105, 136805 (2010)]. The absorption of graphene with 1DPC across a broad spectral range is substantially enhanced because of the photonic localization at the optical micro-cavity on top of the 1DPC or metal films. The absorption of monolayer MoS2 can be tuned by varying either the distance between the monolayer MoS2 and the back reflector or the thickness of the cover layers.
Octahedral spherical hohlraum and its laser arrangement for inertial fusion
Authors: Lan Ke , He Xian-Tu , Liu Jie , Zheng Wudi , Lai Dongxian
Published: May 2014

A recent publication [K. Lan et al., Phys. Plasmas 21, 010704 (2014)] proposed a spherical hohlraum with six laser entrance holes of octahedral symmetry at a specific hohlraum-to-capsule radius ratio of 5.14 for inertial fusion study, which has robust high symmetry during the capsule implosion and superiority on low backscatter without supplementary technology. This paper extends the previous one by studying the laser arrangement and constraints of octahedral hohlraum in detail. As a result, it has serious beam crossing at θL≤45°, and θL=50° to 60° is proposed as the optimum candidate range for the golden octahedral hohlraum, here θL is the opening angle that the laser quad beam makes with the Laser Entrance Hole (LEH) normal direction. In addition, the design of the LEH azimuthal angle should avoid laser spot overlapping on hohlraum wall and laser beam transferring outside hohlraum from a neighbor LEH. The octahedral hohlraums are flexible and can be applicable to diverse inertial fusion drive approaches. This paper also applies the octahedral hohlraum to the recent proposed hybrid indirect-direct drive approach.
Low temperature electrical and photo-responsive properties of MoSe2
Authors: Fan Chao , Yue Qu , Yang Juehan , Wei Zhongming , Yang Shengxue , Li Jingbo
Published: May 2014

MoSe2 was fabricated by a facile hydrothermal method, and a simple device based on it was prepared to investigate the low temperature electrical and photo-responsive (PR) properties. PR current of MoSe2 under 650 nm red illumination is 2.55 × 10−5 A and remains approximately at low temperatures, which demonstrates its fine PR property. As the temperature became lower, electrical conductivity of MoSe2 first decreased from 300 to 43 K and then increased at temperatures from 43 to 13 K. Mechanisms of such electrical and PR phenomenon were proposed. Our findings revealed potential method to adjust band gap of transition metal dichalcogenides and demonstrated their potential applications under special environment.
Study of the one dimensional electron gas arrays confined by steps in vicinal GaN/AlGaN heterointerfaces
Authors: Li Huijie , Zhao Guijuan , Liu Guipeng , Wei Hongyuan , Jiao Chunmei , Yang Shaoyan , Wang Lianshan , Zhu Qinsheng
Published: May 2014

One dimensional electron gas (1DEG) arrays in vicinal GaN/AlGaN heterostructures have been studied. The steps at the interface would lead to the lateral barriers and limit the electron movement perpendicular to such steps. Through a self-consistent Schrödinger-Poisson approach, the electron energy levels and wave functions were calculated. It was found that when the total electron density was increased, the lateral barriers were lowered due to the screening effects by the electrons, and the electron gas became more two-dimension like. The calculated 1DEG densities were compared to the experimental values and good agreements were found. Moreover, we found that a higher doping density is more beneficial to form 1-D like electron gas arrays.
An improved gravitational search algorithm for optimal placement and sizing of renewable distributed generation units in a distribution system for power quality enhancement
Authors: Fazliana Abdul Kadir Aida , Mohamed Azah , Shareef Hussain , Asrul Ibrahim Ahmad , Khatib Tamer , Elmenreich Wilfried
Published: May 2014

Distributed generation (DG) is an important element to be considered in distribution planning since it plays a major role in stability and power quality improvement. This paper presents a new method for determining optimal sizing and placement of DG in a distribution system. A multi-objective function is formed to minimize the total losses, average total voltage harmonic distortion, and voltage deviation in the distribution system. The improved gravitational search algorithm (IGSA) is proposed as an optimization techniques and its performance is compared with other optimization techniques such as particle swarm optimization (PSO) and GSA. The load flow algorithm from MATPOWER and harmonic load flow was integrated in MATLAB environment to solve the proposed multi-objective function. Finally, the proposed algorithm is tested on the radial 69-bus distribution system with three case studies. The results show that the IGSA performs better than PSO and GSA by giving the best fitness value and the fastest average elapsed time.
Near-infrared electroluminescence from light-emitting devices based on Nd-doped TiO2/p+-Si heterostructures
Authors: Yang Yang , Lv Chunyan , Zhu Chen , Li Si , Ma Xiangyang , Yang Deren
Published: May 2014

We report on near-infrared (NIR) electroluminescence (EL) from the light-emitting devices based on Nd-doped TiO2/p+-Si heterostructures. NIR emissions peaking at ∼910, 1090, and 1370 nm, originated from intra-4f transitions in Nd3+ ions, can be activated by a forward bias voltage as low as ∼5 V. Such NIR EL is triggered by the energy transferred from TiO2 host to Nd3+ ions. It is found that the coexistence of anatase and rutile phases in the TiO2 host enables the device to exhibit pronounced Nd-related EL without concurrent emission from the TiO2 host itself, quite other than the case of existing only anatase phase in TiO2 host. We tentatively suggest that the anatase/rutile interface states play important role in the energy transfer from TiO2 host to Nd3+ ions.
Uncooled resonant infrared detector based on aluminum nitride piezoelectric film through charge generations and lattice absorptions
Authors: Ang W. C. , Kropelnicki P. , Zhu Y. , Randles A. B. , Gu Y. A. , Leong K. C. , Tan C. S.
Published: May 2014

This Letter demonstrates an aluminum nitride (AlN) based uncooled resonant infrared (IR) detector utilizing the photo-sensitive and piezoelectric properties of polycrystalline AlN. The AlN Lamb wave mode resonator is found responsive to IR illuminations by showing a decrease in the S21 magnitude instead of a resonant frequency shift. A −0.08 dB shift of S21 magnitude was observed for an IR incident power of 647 nW, which translates to a responsivity of 124 kdB/W. Photoresponse is proposed for the IR sensing mechanism through additional charge carriers generation rather than thermal effects.
Genetic diversity and biogeography of the boab Adansonia gregorii (Malvaceae: Bombacoideae)
Authors: Bell Karen L. , Rangan Haripriya , Fowler Rachael , Kull Christian A. , Pettigrew J. D. , Vickers Claudia E. , Murphy Daniel J.
Published: May 2014

The Kimberley region of Western Australia is recognised for its high biodiversity and many endemic species, including the charismatic boab tree, Adansonia gregorii F.Muell. (Malvaceae: Bombacoideae). In order to assess the effects of biogeographic barriers on A. gregorii, we examined the genetic diversity and population structure of the tree species across its range in the Kimberley and adjacent areas to the east. Genetic variation at six microsatellite loci in 220 individuals from the entire species range was examined. Five weakly divergent populations, separated by west–east and coast–inland divides, were distinguished using spatial principal components analysis. However, the predominant pattern was low geographic structure and high gene flow. Coalescent analysis detected a population bottleneck and significant gene flow across these inferred biogeographic divides. Climate cycles and coastline changes following the last glacial maximum are implicated in decreases in ancient A. gregorii population size. Of all the potential gene flow vectors, various macropod species and humans are the most likely.
Chiral Bicyclic Guanidine-Catalysed Conjugate Addition of α-Fluoro-β-Ketoesters to Cyclic Enones
Authors: Jing Zhenzhong , Liu Jin , Chin Kek Foo , Chen Wenchao , Tan Choon-Hong , Jiang Zhiyong
Published: May 2014

By utilising a chiral bicyclic guanidine as catalyst and triethylamine as additive, the first asymmetric Michael addition of α-fluoro-β-ketoesters to various cyclic enones has been successfully developed, affording a variety of Michael adducts with potential synthetic utilities with satisfactory stereoselectivity (up to 94 % ee and 4.3 : 1 dr).
Protein deubiquitination during oocyte maturation influences sperm function during fertilisation, antipolyspermy defense and embryo development
Authors: Yi Young-Joo , Sutovsky Miriam , Song Won-Hee , Sutovsky Peter
Published: May 2014

Ubiquitination is a covalent post-translational modification of proteins by the chaperone protein ubiquitin. Upon docking to the 26S proteasome, ubiquitin is released from the substrate protein by deubiquitinating enzymes (DUBs). We hypothesised that specific inhibitors of two closely related oocyte DUBs, namely inhibitors of the ubiquitin C-terminal hydrolases (UCH) UCHL1 (L1 inhibitor) and UCHL3 (L3 inhibitor), would alter porcine oocyte maturation and influence sperm function and embryo development. Aberrant cortical granule (CG) migration and meiotic spindle defects were observed in oocytes matured with the L1 or L3 inhibitor. Embryo development was delayed or blocked in oocytes matured with the general DUB inhibitor PR-619. Aggresomes, the cellular stress-inducible aggregates of ubiquitinated proteins, formed in oocytes matured with L1 inhibitor or PR-619, a likely consequence of impaired protein turnover. Proteomic analysis identified the major vault protein (MVP) as the most prominent protein accumulated in oocytes matured with PR-619, suggesting that the inhibition of deubiquitination altered the turnover of MVP. The mitophagy/autophagy of sperm-contributed mitochondria inside the fertilised oocytes was hindered by DUB inhibitors. It is concluded that DUB inhibitors alter porcine oocyte maturation, fertilisation and preimplantation embryo development. By regulating the turnover of oocyte proteins and mono-ubiquitin regeneration, the DUBs may promote the acquisition of developmental competence during oocyte maturation.
Validation of Krathom (Mitragyna speciosa Korth.) Dependence Scale (KDS): A Dependence Screen for Internationally Emerging Psychoactive Substance
Authors: Saingam Darika , Assanangkornchai Sawitri , Geater Alan F. , Lerkiatbundit Sanguan
Published: May 2014

Background

Krathom ( Mitragyna speciosa Korth.) is the most commonly used illicit substance in Thailand, and its use has become widespread internationally. Studies on krathom dependence and its health impact are scarce, as there has been no instrument to measure its dependence syndrome and classify krathom users. This study aimed to develop and explore the factor structure, reliability, and validity of a Krathom Dependence Scale (KDS).

Methods

This study comprised 2 phases. First, cross-sectional surveys were conducted with 523 (Phase I) and 595 (Phase II) male villagers aged >25 years who were regular, occasional, ex-, or nonusers of krathom. Scale construction was based on the qualitative results from users and previous literature. Exploratory factor analysis (EFA) using maximum likelihood extraction with oblimin rotation was conducted in Phase I and confirmatory factor analysis (CFA) in Phase II to confirm the construct of the scale. Internal consistency of the KDS was assessed using Cronbach's alpha coefficient. Discriminative validity was examined by checking its ability to differentiate between regular and occasional users and patterns of krathom use and its concurrent validity by comparing its levels of score with the Fagerstrom Test for Nicotine Dependence (FTND). The KDS contains 16 items on a 0–3 (never–always) rating scale, making a total score of 0–48.

Results

Phase I EFA revealed a single-factor solution for the scale, which was confirmed by the CFA in Phase II, with an alpha coefficient of .98. The KDS discriminates regular from occasional users reasonably well and is highly correlated with the FTND score. Two cutoffs were suggested: 34/35 for distinguishing moderate from high dependence and 13/14 for low from moderate.

Conclusions

The KDS appears to capture key theoretical constructs and correlates with indices of drug dependence by standard criteria. It should be useful in early intervention for those with krathom use disorders in community and primary care settings.
Vanishing configurations in network dynamics with asynchronous updates
Authors: Dinwoodie Ian
Published: May 2014

We consider Boolean dynamics for biological networks where stochasticity is introduced through asynchronous updates. An exact method is given for finding states which can reach a steady state with positive probability, and a method is given for finding states which cannot reach other steady states. These methods are based on computational commutative algebra. The algorithms are applied to dynamics of a cell survival network to determine node assignments that exclude termination in a cancerous state.
Transcription regulation during stable elongation by a reversible halt of RNA polymerase II
Authors: Kaminski Tim Patrick , Siebrasse Jan Peter , Kubitscheck Ulrich
Published: May 2014

Regulation of RNA polymerase II (RNAPII) during transcription is essential for controlling gene expression. Here we report that the transcriptional activity of RNAPII at the Balbiani ring 2.1 gene could be halted during stable elongation in salivary gland cells of Chironomus tentans larvae for extended time periods in a regulated manner. The transcription halt was triggered by heat shock and affected all RNAPII independently of their position in the gene. During the halt, incomplete transcripts and RNAPII remained at the transcription site, the phosphorylation state of RNAPII was unaltered, and the transcription bubbles remained open. The transcription of halted transcripts was resumed upon relief of the heat shock. The observed mechanism allows cells to interrupt transcription for extended time periods and rapidly reactivate it without the need to reinitiate transcription of the complete gene. Our results suggest a so-far-unknown level of transcriptional control in eukaryotic cells.
The Spirit’s Work of Transformation: Part 2
Authors: Raith Charles
Published: May 2014

This chapter continues the discussion of Chapter 4 regarding the believer’s life of grace. Both Aquinas and Calvin interpret the “I” of 7:14–25 as the graced Apostle Paul, but they provide different accounts of Paul’s struggle. I analyze Aquinas’s and Calvin’s descriptions of the Apostle Paul’s “flesh” and “spirit” and then unfold the portraits of Paul’s moral life that emerge from their commentaries on 7:14–25. Aquinas’s account supports his belief that justification transforms a believer into a just person even while the just believer continues to struggle with the flesh. Calvin’s account demonstrates why he is convinced that both believers and their works remain condemnable in se. To stand before God as just, then, requires for Calvin a justice extra nos.
Simultaneous Structure in Phonology
Authors: Ladd D. Robert
Published: May 2014

The chapters of this book are free-standing but closely linked pieces on the shortcomings of one-dimensional idealizations of language. Theories of both phonology and syntax rely heavily on the assumption that the objects they are modelling are formally strings of elements. Many well-known linguistic phenomena make problems for this assumption (e.g. vowel harmony, ablaut morphology, pitch features both tonal and intonational), and many attempts have been made to incorporate these troublesome characteristics into our models (e.g. autosegmental phonology), but much theoretical effort in linguistics continues to be directed toward accounting for properties of strings. The chapters assembled here deal with various aspects of the problematical non-sequential phenomena. The topics covered include distinctive features, systematic phonetics, the definition of ‘prosody’, aspects of vocal paralinguistic communication and ‘gradience’, and duality of patterning. Each chapter reviews a wide range of relevant literature, generally going back to the beginnings of modern linguistics in the early twentieth century.
Why Ethics is Hard
Authors: Chappell Sophie Grace
Published: May 2014

The thesis of this chapter is that one thing that ethics is centrally about is phenomenal contents, experience, and it’s hard to talk about experience. Much important ethical knowledge is knowledge ‘what it’s like’ of the key scenarios and interactions of human life; such knowledge can be communicated, for example, by poetry and drama. In having such experiences, either in real life or at second-hand through art, we can gain moral knowledge, rather as Mary the colour scientist can gain knowledge of colours; such knowledge is a real cognitive gain, but it is not knowledge of the propositional kind that philosophers have usually focused on.
The Deconstructed Church
Authors: Marti Gerardo , Ganiel Gladys
Published: May 2014

The Emerging Church Movement (ECM) is a creative, entrepreneurial, religious movement that strives to achieve social legitimacy and spiritual vitality by actively disassociating from its roots in conservative, evangelical Christianity and “deconstructing” contemporary expressions of Christianity. Emerging Christians see themselves as overturning outdated interpretations of the bible, transforming hierarchical religious institutions, and reorientating Christianity outside the walls of church buildings toward working among and serving others in the “real world.” Drawing on ethnographic observations from emerging congregations, pub churches, neo-monastic communities, conferences, online networks, in-depth interviews, and congregational surveys in the US, UK, and Ireland, this book provides a comprehensive social scientific analysis of the development and significance of the ECM. Emerging Christians are shaping a distinct religious orientation that encourages individualism, deep relationships with others, new ideas around the nature of truth, doubt, and God, and innovations in preaching, worship, Eucharist, and leadership. More than other expressions of Christianity, the ECM simultaneously reacts against modernity while drawing on distinctly modern conceptions of self and community to produce a form of religiosity well-suited to our era.
Introduction
Authors: Marti Gerardo , Ganiel Gladys
Published: May 2014

The Emerging Church Movement (ECM) is one of the most important reframings of religion within Western Christianity in the last two decades. The book argues that Emerging Christians share a religious orientation built on a continual practice of deconstruction by the religious institutional entrepreneurs who drive the movement. To introduce the movement the book provides four descriptive snapshots of various manifestations of the ECM: pub churches, Emerging Christian conferences, web-based networks, and neo-monastic communities. We outline the history of the ECM, emphasizing its evangelical roots yet locating it within wider religious trends. The “deconstructed churches” of the ECM represent religious communities with loose boundaries of belonging and belief (so that pluralism is not just tolerated, but celebrated as a positive religious value). At the same time, ECM “churches” encourage people to follow individualized religious paths. This religious individualization is complemented by a fierce relational ethic, a type of “cooperative egoism” that sustains community life within emerging congregations. The ECM therefore both reacts against modernity and draws on modern Western conceptions of the self and community to produce a form of spirituality that is well suited to our era.
Evol
and
ProDy
for bridging protein sequence evolution and structural dynamics
Authors: Bakan Ahmet , Dutta Anindita , Mao Wenzhi , Liu Ying , Chennubhotla Chakra , Lezon Timothy R. , Bahar Ivet
Published: May 2014

Correlations between sequence evolution and structural dynamics are of utmost importance in understanding the molecular mechanisms of function and their evolution. We have integrated Evol , a new package for fast and efficient comparative analysis of evolutionary patterns and conformational dynamics, into ProDy , a computational toolbox designed for inferring pro tein dyn amics from experimental and theoretical data. Using information-theoretic approaches, Evol coanalyzes conservation and coevolution profiles extracted from multiple sequence alignments of protein families with their inferred dynamics.

Availability and implementation:  ProDy and Evol are open-source and freely available under MIT License fromhttp://prody.csb.pitt.edu/.

Contact:  bahar@pitt.edu
Testing the robustness of data-poor assessment methods to uncertainty in catch and biology: a retrospective approach
Authors: Arnold Linsey M. , Heppell Selina S.
Published: May 2014

The quality and quantity of data affect the reliability of all stock assessments. Over time, we expect data to improve and assessment predictions to become more reliable. There is a potential for strong bias in estimates of sustainable yield if the available data are not a good representation of stock dynamics, particularly for catch-based data-poor methods that rely on limited information and assumptions about stock status. We retrospectively investigated the interaction of data quantity and quality through time using the “real-world” data for a stock as it progressed from data-poor to data-rich. For this analysis, we chose a currently data-rich and overfished stock with historical assessments representing both a data-poor and data-moderate state, the canary rockfish (Sebastes pinniger). We asked how changes in the catch history and biological parameters over time affected the estimates of sustainable yield and the overfishing limit (OFL) predicted by two data-poor assessment tools, depletion-corrected average catch (DCAC) and depletion-based stock reduction analysis (DB-SRA). We found that both of these methods underestimated the “true” OFL in simulations with catch error alone. While there was slightly less bias for DB-SRA than DCAC, increasing error in the catch led to a more rapid increase in the variance of the DB-SRA harvest limit (HL). Our retrospective analysis showed that the expectation for a more accurate HL estimate between the data-poor and data-moderate canary rockfish assessments does not come from an increase in the quantity or quality of the catch data alone; a decrease in the quality of the biological data between assessments had the greatest impact. By evaluating these methods with historical data, our retrospective approach highlighted the impact of change in data quality and quantity on HL estimates for a long-lived rockfish, and could be used to define the amount and type of error included in simulation studies that further evaluate data-poor methods.
Fatal Chagas Disease Among Solid-Organ Transplant Recipients in Colombia
Authors: Gómez-P Carlos Fernando , Mantilla-H Julio César , Rodriguez-Morales Alfonso J.
Published: May 2014

Chagas disease continues to cause substantial morbidity and mortality in endemic areas in Latin America. Although there have been some well documented successes in halting the transmission of Chagas disease through preventive interventions to decrease vector-borne and blood-transfusion cases, this parasitic infection continues to be transmitted through these routes in some areas as well through perinatal and foodborne routes. In addition, transmission through solid-organ transplantation has been described in nonendemic settings due to the increasing globalization of Chagas disease to the United States of America, Europe, and other areas. Because there has been a concomitant increase in the number of solid-organ transplantations performed in Latin American settings endemic for American trypanosomiasis, there is increasing concern for the potential reactivation of Trypanosoma cruzi in a previously infected recipient and as a result of aggressive immunosuppression; or via transmission from organs donated by a latently infection donor transplanted onto an uninfected recipient. In this study, we report 2 cases of Chagas disease reactivation in 2 solid-organ transplant recipients in Northeastern Colombia, and we discuss the implications for screening as a crucial strategy for preventing transmission in endemic settings.
Capital is Back: Wealth-Income Ratios in Rich Countries 1700–2010 *
Authors: Piketty Thomas , Zucman Gabriel
Published: May 2014

How do aggregate wealth-to-income ratios evolve in the long run and why? We address this question using 1970–2010 national balance sheets recently compiled in the top eight developed economies. For the United States, United Kingdom, Germany, and France, we are able to extend our analysis as far back as 1700. We find in every country a gradual rise` of wealth-income ratios in recent decades, from about 200–300% in 1970 to 400–600% in 2010. In effect, today’s ratios appear to be returning to the high values observed in Europe in the eighteenth and nineteenth centuries (600–700%). This can be explained by a long-run asset price recovery (itself driven by changes in capital policies since the world wars) and by the slowdown of productivity and population growth, in line with the β=sg Harrod-Domar-Solow formula. That is, for a given net saving rate s = 10%, the long-run wealth-income ratio β is about 300% if g = 3% and 600% if g = 1.5%. Our results have implications for capital taxation and regulation and shed new light on the changing nature of wealth, the shape of the production function, and the rise of capital shares.
A Retrospective Feasibility Study of Salvage Pelvic Nodal Radiation in 6 Patients With Biochemical Failure Following Prostate Fossa Radiation
Authors: Symon Zvi , Ben-Bezalel Guy , Spieler Ben , Tsvang Lev , Alezra Dror , Berger Raanan , Dotan Zohar , Lawrence Yaacov R. , Goldstein Jeffrey
Published: May 2014

Purpose:

To evaluate salvage pelvic nodal radiation as an alternative to androgen deprivation therapy (ADT) in patients with biochemical failure and lymph node recurrence following salvage prostate fossa radiation.

Methods:

Six patients with biochemical failure and lymph node recurrence following prostate fossa radiation were treated with salvage pelvic nodal radiation therapy. A gross target volume was contoured using Choline PET/CT, CT, or MRI imaging. The clinical target volume included pelvic nodes. Avoidance structures were created using isodose lines from previous prostate fossa radiation plans. Radiation was delivered using IMRT or VMAT techniques. Failure was defined as a confirmed rise of prostate-specific antigen (PSA) over 0.2 ng/mL.

Results:

Four patients had presalvage PSA values <1 and 2 patients had PSAs >1. Dose to the clinical target volume was 54 to 60 Gy. The gross target volume dose was 60 to 73.6 Gy. One of the 2 patients with a high PSA received 6 months of concomitant ADT. Mean follow-up after RT for all patients was 24.9 months (range, 18.1 to 33.0 mo). All 5 patients with no ADT had significant PSA responses. PSA reduction was 80% (62% to 100%) of pre-RT PSA. At last follow-up, 2 patients with initial PSA<1 ng/mL remain free of biochemical progression at 33 and 20 months. Four patients have had PSA rise and meet criteria for failure. This included both patients with initial PSA values > 1. Duration of response before failure was 18.1 to 30.7 months. ADT for failure has been started in 1 patient. There was no grade ≥2 GI or GU toxicity.

Conclusions:

Salvage lymph node irradiation for patients with early biochemical recurrence and radiologic evidence of pelvic nodal metastases is well tolerated and associated with a durable biochemical response and may be an alternative to or may delay the need for ADT in some patients.
Reduced ribosomes of the apicoplast and mitochondrion of
Plasmodium
spp. and predicted interactions with antibiotics
Authors: Gupta Ankit , Shah Priyanka , Haider Afreen , Gupta Kirti , Siddiqi Mohammad Imran , Ralph Stuart A. , Habib Saman
Published: May 2014

Apicomplexan protists such as
Plasmodium
and
Toxoplasma
contain a mitochondrion and a relic plastid (apicoplast) that are sites of protein translation. Although there is emerging interest in the partitioning and function of translation factors that participate in apicoplast and mitochondrial peptide synthesis, the composition of organellar ribosomes remains to be elucidated. We carried out an analysis of the complement of core ribosomal protein subunits that are encoded by either the parasite organellar or nuclear genomes, accompanied by a survey of ribosome assembly factors for the apicoplast and mitochondrion. A cross-species comparison with other apicomplexan, algal and diatom species revealed compositional differences in apicomplexan organelle ribosomes and identified considerable reduction and divergence with ribosomes of bacteria or characterized organelle ribosomes from other organisms. We assembled structural models of sections of
Plasmodium falciparum
organellar ribosomes and predicted interactions with translation inhibitory antibiotics. Differences in predicted drug–ribosome interactions with some of the modelled structures suggested specificity of inhibition between the apicoplast and mitochondrion. Our results indicate that
Plasmodium
and
Toxoplasma
organellar ribosomes have a unique composition, resulting from the loss of several large and small subunit proteins accompanied by significant sequence and size divergences in parasite orthologues of ribosomal proteins.
First report of rhinosinusitis caused by Neoscytalidium dimidiatum in Iran
Authors: Bakhshizadeh Mandana , Hashemian Hamid Reza , Najafzadeh Mohammad Javad , Dolatabadi Somayeh , Zarrinfar Hossein
Published: May 2014

The study describes isolation ofNeoscytalidium dimidiatumfrom a case of eosinophilic fungal rhinosinusitis (EFRS). The isolate was identified by routine mycological methods and confirmed by DNA sequencing of the internal transcribed spacer (ITS) region of rDNA. To our knowledge, this is the first report of its kind from Iran.
Inferring human population size and separation history from multiple genome sequences
Authors: Schiffels Stephan , Durbin Richard
Published: May 2014

The availability of complete human genome sequences from populations across the world has given rise to new population genetic inference methods that explicitly model their ancestral relationship under recombination and mutation. So far, application of these methods to evolutionary history more recent than 20-30 thousand years ago and to population separations has been limited. Here we present a new method that overcomes these shortcomings. The Multiple Sequentially Markovian Coalescent (MSMC) analyses the observed pattern of mutations in multiple individuals, focusing on the first coalescence between any two individuals. Results from applying MSMC to genome sequences from nine populations across the world suggest that the genetic separation of non-African ancestors from African Yoruban ancestors started long before 50,000 years ago, and give information about human population history as recently as 2,000 years ago, including the bottleneck in the peopling of the Americas, and separations within Africa, East Asia and Europe.
Sperm should evolve to make female meiosis fair
Authors: Brandvain Yaniv , Coop Graham
Published: May 2014

Genomic conflicts arise when an allele gains an evolutionary advantage at a cost to organismal fitness. Oögenesis is inherently susceptible to such conflicts because alleles compete for inclusion into the egg. Alleles that distort meiosis in their favor (i.e. meiotic drivers) often decrease organismal fitness, and therefore indirectly favor the evolution of mechanisms to suppress meiotic drive. In this light, many facets of oögenesis and gametogenesis have been interpreted as mechanisms of protection against genomic outlaws. That females of many animal species do not complete meiosis until after fertilization, appears to run counter to this interpretation, because this delay provides an opportunity for sperm-acting alleles to meddle with the outcome of female meiosis and help like alleles drive in heterozygous females. Contrary to this perceived danger, the population genetic theory presented herein suggests that, in fact, sperm nearly always evolve to increase the fairness of female meiosis in the face of genomic conflicts. These results are consistent with the apparent sperm dependence of the best characterized female meiotic drivers in animals. Rather than providing an opportunity for sperm collaboration in female meiotic drive, the ‘fertilization requirement’ indirectly protects females from meiotic drivers by providing sperm an opportunity to suppress drive.
Structure of the nisin leader peptidase NisP revealing a C-terminal autocleavage activity
Authors: Xu Yueyang , Li Xin , Li Ruiqing , Li Shanshan , Ni Hongqian , Wang Hui , Xu Haijin , Zhou Weihong , Saris Per E. J. , Yang Wen , Qiao Mingqiang , Rao Zihe
Published: May 2014

Nisin is a widely used antibacterial lantibiotic polypeptide produced byLactococcus lactis. NisP belongs to the subtilase family and functions in the last step of nisin maturation as the leader-peptide peptidase. Deletion of thenisPgene in LAC71 results in the production of a non-active precursor peptide with the leader peptide unremoved. Here, the 1.1 Å resolution crystal structure of NisP is reported. The structure shows similarity to other subtilases, which can bind varying numbers of Ca atoms. However, no calcium was found in this NisP structure, and the predicted calcium-chelating residues were placed so as to not allow NisP to bind a calcium ion in this conformation. Interestingly, a short peptide corresponding to its own 635–647 sequence was found to bind to the active site of NisP. Biochemical assays and native mass-spectrometric analysis confirmed that NisP possesses an auto-cleavage site between residues Arg647 and Ser648. Further, it was shown that NisP mutated at the auto-cleavage site (R647P/S648P) had full catalytic activity for nisin leader-peptide cleavage, although the C-terminal region of NisP was no longer cleaved. Expressing this mutant inL. lactisLAC71 did not affect the production of nisin but did decrease the proliferation rate of the bacteria, suggesting the biological significance of the C-terminal auto-cleavage of NisP.
A new three-dimensional coordination polymer of SrIIbased on dipicolinic acid, with different coordination environments for SrII
Authors: Soleimannejad Janet , Derikvand Zohreh , Koleiae Farzaneh
Published: May 2014

A three-dimensional coordination polymer of SrIIbased on dipicolinic acid (pydcH2) has been synthesized and characterized, namely poly[[diaquabis(μ3-6-carboxypyridine-2-carboxylato)bis(μ4-pyridine-2,6-dicarboxylato)tristrontium(II)] dihydrate], {[Sr3(C7H3NO4)2(C7H4NO4)2(H2O)2]·2H2O}n. The asymmetric unit consists of two unique SrIIcentres (one of them situated on an inversion centre), two independent pydc2−ligands, and one coordinated and one uncoordinated water molecule. The two independent SrIIcations are surrounded by water and dipicolinate molecules in distorted square-antiprism and distorted tricapped trigonal prismatic geometries. The dipicolinate ligands adopt μ3- and μ4-bridging modes, linking the alkaline earth metal centres into a three-dimensional coordination framework. One dipicolinate ligand is doubly deprotonated, while the other is singly deprotonated.