bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of TBK1 complexes required for the phosphorylation of IRF3 and the production of interferon β
Authors: Bakshi Siddharth , Taylor Jordan , Strickson Sam , McCartney Thomas , Cohen Philip
Published: February 2017

The double-stranded RNA mimetic poly(I:C) and lipopolysaccharide (LPS) activate Toll-like receptors 3 (TLR3) and TLR4, respectively, triggering the activation of TANK (TRAF family member-associated NF-κB activator)-binding kinase 1 (TBK1) complexes, the phosphorylation of interferon regulatory factor 3 (IRF3) and transcription of the interferon β (IFNβ) gene. Here, we demonstrate that the TANK–TBK1 and optineurin (OPTN)–TBK1 complexes control this pathway. The poly(I:C)- or LPS-stimulated phosphorylation of IRF3 at Ser396 and production of IFNβ were greatly reduced in bone marrow-derived macrophages (BMDMs) from TANK knockout (KO) mice crossed to knockin mice expressing the ubiquitin-binding-defective OPTN[D477N] mutant. In contrast, IRF3 phosphorylation and IFNβ production were not reduced significantly in BMDM from OPTN[D477N] knockin mice and only reduced partially in TANK KO BMDM. The TLR3/TLR4-dependent phosphorylation of IRF3 and IFNβ gene transcription were not decreased in macrophages from OPTN[D477N] crossed to mice deficient in IκB kinase ε, a TANK-binding kinase related to TBK1. In contrast with the OPTN–TBK1 complex, TBK1 associated with OPTN[D477N] did not undergo phosphorylation at Ser172 in response to poly(I:C) or LPS, indicating that the interaction of ubiquitin chains with OPTN is required to activate OPTN–TBK1 in BMDM. The phosphorylation of IRF3 and IFNβ production induced by Sendai virus infection were unimpaired in BMDM from TANK KO × OPTN[D477N] mice, suggesting that other/additional TBK1 complexes control the RIG-I-like receptor-dependent production of IFNβ. Finally, we present evidence that, in human HACAT cells, the poly(I:C)-dependent phosphorylation of TBK1 at Ser172 involves a novel TBK1-activating kinase(s).
Computational approaches forde novodesign and redesign of metal-binding sites on proteins
Authors: Akcapinar Gunseli Bayram , Sezerman Osman Ugur
Published: February 2017

Metal ions play pivotal roles in protein structure, function and stability. The functional and structural diversity of proteins in nature expanded with the incorporation of metal ions or clusters in proteins. Approximately one-third of these proteins in the databases contain metal ions. Many biological and chemical processes in nature involve metal ion-binding proteins, aka metalloproteins. Many cellular reactions that underpin life require metalloproteins. Most of the remarkable, complex chemical transformations are catalysed by metalloenzymes. Realization of the importance of metal-binding sites in a variety of cellular events led to the advancement of various computational methods for their prediction and characterization. Furthermore, as structural and functional knowledgebase about metalloproteins is expanding with advances in computational and experimental fields, the focus of the research is now shifting towards de novo design and redesign of metalloproteins to extend nature’s own diversity beyond its limits. In this review, we will focus on the computational toolbox for prediction of metal ion-binding sites, de novo metalloprotein design and redesign. We will also give examples of tailor-made artificial metalloproteins designed with the computational toolbox.
En route to precision medicine through the integration of biological sex into pharmacogenomics
Authors: Gaignebet Lea , Kararigas Georgios
Published: February 2017

Frequently, pharmacomechanisms are not fully elucidated. Therefore, drug use is linked to an elevated interindividual diversity of effects, whether therapeutic or adverse, and the role of biological sex has as yet unrecognized and underestimated consequences. A pharmacogenomic approach could contribute towards the development of an adapted therapy for each male and female patient, considering also other fundamental features, such as age and ethnicity. This would represent a crucial step towards precision medicine and could be translated into clinical routine. In the present review, we consider recent results from pharmacogenomics and the role of sex in studies that are relevant to cardiovascular therapy. We focus on genome-wide analyses, because they have obvious advantages compared with targeted single-candidate gene studies. For instance, genome-wide approaches do not necessarily depend on prior knowledge of precise molecular mechanisms of drug action. Such studies can lead to findings that can be classified into three categories: first, effects occurring in the pharmacokinetic properties of the drug, e.g. through metabolic and transporter differences; second, a pharmacodynamic or drug target-related effect; and last diverse adverse effects. We conclude that the interaction of sex with genetic determinants of drug response has barely been tested in large, unbiased, pharmacogenomic studies. We put forward the theory that, to contribute towards the realization of precision medicine, it will be necessary to incorporate sex into pharmacogenomics.
Optimal control for networked control systems with disturbances: a delta operator approach
Authors: Yuan Yuan , Yuan Huanhuan , Wang Zidong , Guo Lei , Yang Hongjiu
Published: February 2017

This study deals with the optimal control problem for a class of delta‐domain networked control systems (NCSs) subjected to both matched and unmatched disturbances. In the presence of the disturbances, the so‐called ‐optimum is proposed to quantify the control performance. The purpose of the addressed problem is to design the optimal control strategy such that the cost function is minimised over the finite‐/infinite‐horizon under the network‐induced constraints. In virtue of the dynamic programming method, sufficient conditions are established to guarantee the existence of the desired control strategies, and the controller parameters are designed. For the obtained optimal control strategy, an upper bound for the ‐optimum is provided explicitly, and convex optimisation algorithms are given to compute such upper bound. Both simulation and experimental results are provided to illustrate the usefulness and applicability of the proposed methods.
Co‐simulation of distributed control system based on JADE for smart distribution networks with distributed generations
Authors: Duan Yilong , Luo Longfu , Li Yong , Cao Yijia , Rehtanz Christian , Küch Markus
Published: February 2017

The distributed system and multi‐agent system (MAS) enable the effective and efficient management of complex distribution network. How to realise the co‐simulation with a large number of controllers for these systems is being a hot issue. In this study, the characteristics of the simulation environment, which is suitable for the distributed control system, are discussed, and a new co‐simulation method based on Java agent development framework (JADE) is proposed. It fits for the simulation of distributed system and MAS, and can simulate the physical and the communication models concurrently. After the introduction of co‐simulation environment, the modelling methods of distributed controllers are described in detail. Finally, a comprehensive evaluation on the distributed protection algorithm is carried out by means of the co‐simulation, and the effectiveness of the proposed co‐simulation environment is validated.
Efficient local optimisation‐based approach for non‐convex and non‐smooth source localisation problems
Authors: Yao Zhiqiang , Huang Jinfeng , Wang Shiguo , Ruby Rukhsana
Published: February 2017

This study proposes a novel approach to solve the source localisation problem with noisy range measurements. Since the objective function of the range‐based least square problem is non‐convex and non‐smooth, it is challenging to achieve an accurate estimation. Unlike previous methods that took non‐convexity property of the objective function into account, this approach addresses the problem considering the non‐smoothness property of the objective function. The problem is solved by a two‐stage local optimisation technique which is based on a smooth non‐convex approximation of the original objective function. First, the least square method is utilised to obtain a coarse estimation of the problem. Then, the estimation is refined by the trust region method which converges quadratically. Simulation results are presented to show that the proposed approach outperforms other existing methods in terms of the mean squared localisation error and convergence speed.
Erratum: “Excellence R Us”: university research and the fetishisation of excellence
Authors: Moore Samuel , Neylon Cameron , Paul Eve Martin , O’Donnell Daniel Paul , Pattinson Damian
Published: February 2017

Correction to: Palgrave Communications (2017) 3 Article number: 16105 doi: 10.1057/palcomms.2016.105; Published 19 January 2017; Updated 7 February 2017 Previously the spelling of Martin Paul Eve’s institution in the Author Information section was given as “Birckbeck, University of London, UK ”. This has now been corrected to “Birkbeck, University of London, UK”.
Time slicing in 3D momentum imaging of the hydrogen molecular ion photo-fragmentation
Authors: Kaya N. , Kaya G. , Pham F. V. , Strohaber J. , Kolomenskii A. A. , Schuessler H. A.
Published: February 2017

Photo-fragmentation of the hydrogen molecular ion was investigated with 800 nm, 50 fs laser pulses by employing a time slicing 3D imaging technique that enables the simultaneous measurement of all three momentum components which are linearly related with the pixel position and slicing time. This is done for each individual product particle arriving at the detector. This mode of detection allows us to directly measure the three-dimensional fragment momentum vector distribution without having to rely on mathematical reconstruction methods, which additionally require the investigated system to be cylindrically symmetric. We experimentally reconstruct the laser-induced photo-fragmentation of the hydrogen molecular ion. In previous experiments, neutral molecules were used as a target, but in this work, performed with molecular ions, the initial vibrational level populations are well-defined after electron bombardment, which facilitates the interpretation. We show that the employed time-slicing technique allows us to register the fragment momentum distribution that reflects the initial molecular states with greater detail, revealing features that were concealed in the full time-integrated distribution on the detector.
Gamma-ray CT from incomplete projections for two-phase pipe flow
Authors: Xin S. , Wang H. X.
Published: February 2017

A low-energy low-dose γ-ray computed tomography (CT) system used in the gas-liquid two-phase pipe flow measurement has been studied at Tianjin University in recent years. The γ-ray CT system, having a third-generation X-ray CT scanning configuration, is comprised of one 300mCi 241Am source and 17 CdZnTe detector units and achieves a spatial image resolution of about 7 mm. It is primarily intended to measure the two-phase pipe flow and provide improvement suggestions for industrial CT system. Recently we improve the design for image reconstruction from incomplete projection to optimize the scanning parameters and reduce the radiation dose. First, tomographic problem from incomplete projections is briefly described. Next, a system structure and a hardware circuit design are listed and explained, especially on time parameter setting of the pulse shaper. And then a detailed system analysis is provided in Section II, mainly focusing on spatial resolution, temporal resolution, system noise, and imaging algorithm. Finally, we carry on necessary static and dynamic experiments in a full scan (360°) and two sets of partial scan reconstruction tests to determine the feasibility of this γ-ray CT system for reconstructing the images from insufficient projections. And based on an A-variable algebraic reconstruction technique method, a specially designed algorithm, we evaluate the system performance and noise level of this CT system working quantitatively and qualitatively. Results of dynamic test indicate that the acceptable results can be acquired using a multi-source γ-ray CT system with the same parameters when the flow rate is less than 0.04 m/s and the imaging speed is slower than 33 frames/s.
Temporal correlations and structural memory effects in break junction measurements
Authors: Magyarkuti A. , Lauritzen K. P. , Balogh Z. , Nyáry A. , Mészáros G. , Makk P. , Solomon G. C. , Halbritter A.
Published: February 2017

We review data analysis techniques that can be used to study temporal correlations among conductance traces in break junction measurements. We show that temporal histograms are a simple but efficient tool to check the temporal homogeneity of the conductance traces, or to follow spontaneous or triggered temporal variations, like structural modifications in trained contacts, or the emergence of single-molecule signatures after molecule dosing. To statistically analyze the presence and the decay time of temporal correlations, we introduce shifted correlation plots. Finally, we demonstrate that correlations between the opening and subsequent closing traces may indicate structural memory effects in atomic-sized metallic and molecular junctions. Applying these methods on measured and simulated gold metallic contacts as a test system, we show that the surface diffusion induced flattening of the broken junctions helps to produce statistically independent conductance traces at room temperature, whereas at low temperature repeating tendencies are observed as long as the contacts are not closed to sufficiently high conductance setpoints. Applying opening-closing correlation analysis on Pt–CO–Pt single-molecule junctions, we demonstrate pronounced contact memory effects and recovery of the molecule for junctions breaking before atomic chains are formed. However, if chains are pulled the random relaxation of the chain and molecule after rupture prevents opening-closing correlations.
Transport coefficients and heat fluxes in non-equilibrium high-temperature flows with electronic excitation
Authors: Istomin V. A. , Kustova E. V.
Published: February 2017

The influence of electronic excitation on transport processes in non-equilibrium high-temperature ionized mixture flows is studied. Two five-component mixtures, N2/N2+/N/N+/e− and O2/O2+/O/O+/e−, are considered taking into account the electronic degrees of freedom for atomic species as well as the rotational-vibrational-electronic degrees of freedom for molecular species, both neutral and ionized. Using the modified Chapman-Enskog method, the transport coefficients (thermal conductivity, shear viscosity and bulk viscosity, diffusion and thermal diffusion) are calculated in the temperature range 500–50 000 K. Thermal conductivity and bulk viscosity coefficients are strongly affected by electronic states, especially for neutral atomic species. Shear viscosity, diffusion, and thermal diffusion coefficients are not sensible to electronic excitation if the size of excited states is assumed to be constant. The limits of applicability for the Stokes relation are discussed; at high temperatures, this relation is violated not only for molecular species but also for electronically excited atomic gases. Two test cases of strongly non-equilibrium flows behind plane shock waves corresponding to the spacecraft re-entry (Hermes and Fire II) are simulated numerically. Fluid-dynamic variables and heat fluxes are evaluated in gases with electronic excitation. In inviscid flows without chemical-radiative coupling, the flow-field is weakly affected by electronic states; however, in viscous flows, their influence can be more important, in particular, on the convective heat flux. The contribution of different dissipative processes to the heat transfer is evaluated as well as the effect of reaction rate coefficients. The competition of diffusion and heat conduction processes reduces the overall effect of electronic excitation on the convective heating, especially for the Fire II test case. It is shown that reliable models of chemical reaction rates are of great importance for accurate predictions of the fluid dynamic variables and heat fluxes.
Influence of structural evolution on energy storage properties in Bi0.5Na0.5TiO3-SrTiO3-NaNbO3 lead-free ferroelectric ceramics
Authors: Li Feng , Zhai Jiwei , Shen Bo , Liu Xing , Yang Ke , Zhang Yang , Li Peng , Liu Baihui , Zeng Huarong
Published: February 2017

Lead-free (1−x)(0.8Bi0.5Na0.5TiO3-0.2SrTiO3)-xNaNbO3 (x = 0–0.1, abbreviated as BNT-ST-xNN) ceramics were fabricated by a conventional sintering route with pure perovskite phase via XRD analysis. Raman spectrum was exploited in order to give an insight into the variation of local structural evolution. All compositions exhibited an obvious evolution of dielectric relaxation behaviors. Dielectric and ferroelectric properties clarified that a crossover from nonergodic to ergodic relaxor properties was obtained with the addition of NN content. A relatively large energy storage density was obtained WRec ∼ 0.74 J/cm3 at 7 kV/mm for x = 0.05 at room temperature. Particularly, the energy storage properties exhibited temperature (25–160 °C) and frequency stability (0.1–20 Hz) with WRec around 0.6 J/cm3 at 6 kV/mm for x = 0.05 within the ergodic region. Pulsed discharging current waveforms were measured under different electric fields to detect the energy storage density and discharging speed behavior. An illustration of the charge-discharge process for the nonergodic and ergodic relaxor was depicted in order to disclose the difference of energy storage properties in BNT-ST-xNN system, and it is believed that this concept can be a guideline for fixing a position when designing a new energy-storage system for BNT-based relaxor ferroelectric ceramics.
Doping-free white organic light-emitting diodes without blue molecular emitter: An unexplored approach to achieve high performance via exciplex emission
Authors: Luo Dongxiang , Xiao Ye , Hao Mingming , Zhao Yu , Yang Yibin , Gao Yuan , Liu Baiquan
Published: February 2017

Doping-free white organic light-emitting diodes (DF-WOLEDs) are promising for the low-cost commercialization because of their simplified device structures. However, DF-WOLEDs reported thus far in the literature are based on the use of blue single molecular emitters, whose processing can represent a crucial point in device manufacture. Herein, DF-WOLEDs without the blue single molecular emitter have been demonstrated by managing a blue exciplex system. For the single-molecular-emitter (orange or yellow emitter) DF-WOLEDs, (i) a color rendering index (CRI) of 81 at 1000 cd/m2 can be obtained, which is one of the highest for the single-molecular-emitter WOLEDs, or (ii) a high efficiency of 35.4 lm/W can be yielded. For the dual-molecular-emitter (yellow/red emitters) DF-WOLED, a high CRI of 85 and low correlated color temperature of 2376 K at 1000 cd/m2 have been simultaneously achieved, which has not been reported by previous DF-WOLEDs. Such presented findings may unlock an alternative avenue to the simplified but high-performance WOLEDs.
Highly oriented diamond (111) films synthesized by pulse bias-enhanced nucleation and epitaxial grain selection on a 3C-SiC/Si (111) substrate
Authors: Suto Takeru , Yaita Junya , Iwasaki Takayuki , Hatano Mutsuko
Published: February 2017

We report the synthesis of highly oriented diamond (HOD) (111) films on 3C-SiC/Si (111) substrates. Bias-enhanced nucleation (BEN) is a key process for the heteroepitaxial growth of HOD films. Conventional long nucleation periods have been found to lead to a polycrystalline diamond film on the 3C-SiC (111) surface. Here, we propose a method that combines brief BEN (<30 s), called pulse BEN, and epitaxial grain selection by oxidative etching. Smaller diamond nuclei with a higher spatial density on the substrate were formed by pulse BEN with a pulse duration of <30 s. We found that precisely controlling the pulse duration is important for obtaining a nucleation density that is sufficiently high to obtain the HOD films. By adding oxygen gas to the subsequent growth process, non-epitaxial nuclei were removed and epitaxial diamond grains selectively remained. There was no notable difference in the relative growth rate of [111] to [100] with and without oxygen, and the orientation improvement was observed on both the (100) and (111) substrates. This suggests that the mechanism of oxidative removal was not evolutionary selective growth, but etching of the non-epitaxial interfaces between the nuclei and the (111) substrate. Finally, the HOD (111) films covering the entire 3C-SiC surface were synthesized, and they exhibited distinct diffraction spots, indicating the formation of the oriented diamond.
Climate change is projected to have severe impacts on the frequency and intensity of peak electricity demand across the United States
Authors: Auffhammer Maximilian , Baylis Patrick , Hausman Catherine H.
Published: February 2017

Significance

The existing empirical literature on the impacts of climate change on the electricity sector has focused on changing electricity consumption patterns. In this paper, we show that incorporating impacts on the frequency and intensity of peak load consumption during hot days implies sizable required investments in peak generating capacity (or major advances in storage technology or the structure of electricity prices), which results in substantially larger impacts than those from just changes in overall consumption.
Cross-cultural regularities in the cognitive architecture of pride
Authors: Sznycer Daniel , Al-Shawaf Laith , Bereby-Meyer Yoella , Curry Oliver Scott , De Smet Delphine , Ermer Elsa , Kim Sangin , Kim Sunhwa , Li Norman P. , Lopez Seal Maria Florencia , McClung Jennifer , O Jiaqing , Ohtsubo Yohsuke , Quillien Tadeg , Schaub Max , Sell Aaron , van Leeuwen Florian , Cosmides Leda , Tooby John
Published: February 2017

Significance

Cross-cultural tests from 16 nations were performed to evaluate the hypothesis that the emotion of pride evolved to guide behavior to elicit valuation and respect from others. Ancestrally, enhanced evaluations would have led to increased assistance and deference from others. To incline choice, the pride system must compute for a potential action an anticipated pride intensity that tracks the magnitude of the approval or respect that the action would generate in the local audience. All tests demonstrated that pride intensities measured in each location closely track the magnitudes of others’ positive evaluations. Moreover, different cultures echo each other both in what causes pride and in what elicits positive evaluations, suggesting that the underlying valuation systems are universal.
Systematic identification of anti-interferon function on hepatitis C virus genome reveals p7 as an immune evasion protein
Authors: Qi Hangfei , Chu Virginia , Wu Nicholas C. , Chen Zugen , Truong Shawna , Brar Gurpreet , Su Sheng-Yao , Du Yushen , Arumugaswami Vaithilingaraja , Olson C. Anders , Chen Shu-Hua , Lin Chung-Yen , Wu Ting-Ting , Sun Ren
Published: February 2017

Significance

Understanding how viruses interact with their hosts, especially the mechanisms that restrict virus replication, will provide a molecular basis for vaccine development. However, the search for restriction factors is oftentimes difficult if the virus has already evolved to counteract the restriction. Here, we describe a systematic approach to identify such restriction and counterrestriction mechanisms. We constructed a library of mutant hepatitis C viruses, where each mutant has a 15-nt stretch randomly inserted on the genome. We aimed to identify mutations that lose the anti-IFN function, but maintain replication capacity. We have identified p7 as an immune evasion protein and further characterize the antiviral function of IFI6-16 against hepatitus C virus (HCV) replication.
Selection maintains signaling function of a highly diverged intrinsically disordered region
Authors: Zarin Taraneh , Tsai Caressa N. , Nguyen Ba Alex N. , Moses Alan M.
Published: February 2017

Significance

Intrinsically disordered regions (IDRs) are widespread, have diverse functions, and are involved in human disease. Because standard sequence analysis methods identify little sequence homology in IDRs, it is not currently understood whether (or how) the functions of these protein regions are preserved over evolution. Here we show that orthologous IDRs can preserve regulatory functions despite near-complete sequence divergence. This suggests that natural selection maintains aggregate molecular properties in IDRs, which we propose to be quantitative traits. Consistent with this, we find signatures of stabilizing selection on the electrostatic properties of IDRs. Thus, in analogy to the rapid evolution of noncoding DNA in eukaryotic enhancers, divergence in primary amino acid sequence does not imply functional divergence in IDRs.
iPSCs and fibroblast subclones from the same fibroblast population contain comparable levels of sequence variations
Authors: Kwon Erika M. , Connelly John P. , Hansen Nancy F. , Donovan Frank X. , Winkler Thomas , Davis Brian W. , Alkadi Halah , Chandrasekharappa Settara C. , Dunbar Cynthia E. , Mullikin James C. , Liu Paul
Published: February 2017

Significance

One important unsolved question in the stem cell field is, do induced pluripotent stem cells (iPSCs) have more mutations than other cultured somatic cells because of the reprogramming process? In this work, we took a novel approach to interrogate the genome integrity of iPSCs by comparing mutational load of clonal fibroblast lines and iPSC lines derived from the same fibroblast parental cells. Whole exome sequencing demonstrates that iPSCs and clonal fibroblasts have comparable numbers of new mutations, as compared with their parental fibroblasts. Deep, targeted resequencing also shows that greater than 90% of these mutations are random, preexisting sequence variants in small subsets of the parental fibroblast population. Our data strongly suggest that reprogramming process is not mutagenic.
Northward extent of East Asian monsoon covaries with intensity on orbital and millennial timescales
Authors: Goldsmith Yonaton , Broecker Wallace S. , Xu Hai , Polissar Pratigya J. , deMenocal Peter B. , Porat Naomi , Lan Jianghu , Cheng Peng , Zhou Weijian , An Zhisheng
Published: February 2017

Significance

The magnitude, rate, and extent of past and future East Asian monsoon (EAM) rainfall fluctuations remain unresolved. Here, we present a rainfall reconstruction based on the surface area of a closed-basin lake located at the modern northwestern boundary of the EAM. Our record shows that fluctuations of EAM intensity and spatial extent covaried over the past 125 ka. This record contributes to the resolution of a current controversy concerning the response of the EAM to external climatic forcings. We propose that a substantial decrease in rainfall at 5.5 ka was a major factor leading to a large cultural collapse of the Early Neolithic culture in north China.
Conformational disruption of PI3Kδ regulation by immunodeficiency mutations in
PIK3CD
and
PIK3R1
Authors: Dornan Gillian L. , Siempelkamp Braden D. , Jenkins Meredith L. , Vadas Oscar , Lucas Carrie L. , Burke John E.
Published: February 2017

Significance

Activated PI3K Delta Syndrome (APDS) is a primary immunodeficiency disease caused by activating mutations in phosphoinositide 3-kinases (PI3Kδ). Activating mutations in either the p110δ catalytic or the p85α regulatory subunit of PI3Kδ result in APDS. Mutations in p85α leading to APDS are surprising, as other p85α-activating mutations are oncogenic when bound to the PI3Kα isoform. Using hydrogen–deuterium exchange mass spectrometry, we determined the molecular mechanisms by which APDS mutations in p110δ or p85α activate PI3Kδ and reveal why the p85α APDS2 mutant primarily activates PI3Kδ. All APDS mutants are potently inhibited by the PI3Kδ-specific inhibitor idelalisib. Together, the biophysical and biochemical data reveal insights into PI3Kδ regulation and provide a possible therapeutic strategy for treating patients with APDS.
Multiple functional self-association interfaces in plant TIR domains
Authors: Zhang Xiaoxiao , Bernoux Maud , Bentham Adam R. , Newman Toby E. , Ve Thomas , Casey Lachlan W. , Raaymakers Tom M. , Hu Jian , Croll Tristan I. , Schreiber Karl J. , Staskawicz Brian J. , Anderson Peter A. , Sohn Kee Hoon , Williams Simon J. , Dodds Peter N. , Kobe Bostjan
Published: February 2017

Significance

Toll/interleukin-1 receptor/resistance protein (TIR) domains are present in plant and animal innate immunity receptors and appear to play a scaffold function in defense signaling. In both systems, self-association of TIR domains is crucial for their function. In plants, the TIR domain is associated with intracellular immunity receptors, known as nucleotide-binding oligomerization domain-like receptors (NLRs). Previous studies from several plant NLRs have identified two distinct interfaces that are required for TIR:TIR dimerization in different NLRs. We show that the two interfaces previously identified are both important for self-association and defense signaling of multiple TIR–NLR proteins. Collectively, this work suggests that there is a common mechanism of TIR domain self-association in signaling across the TIR–NLR class of receptor proteins.
Dynamics of SIV-specific CXCR5+ CD8 T cells during chronic SIV infection
Authors: Mylvaganam Geetha H. , Rios Daniel , Abdelaal Hadia M. , Iyer Smita , Tharp Gregory , Mavigner Maud , Hicks Sakeenah , Chahroudi Ann , Ahmed Rafi , Bosinger Steven E. , Williams Ifor R. , Skinner Pamela J. , Velu Vijayakumar , Amara Rama R.
Published: February 2017

Significance

Simian immunodeficiency virus (SIV)-specific follicular CD8 T cells represent a unique subset of antiviral CD8 T cells that rapidly expand during pathogenic SIV infection, localize within B-cell follicles, and contribute to control of chronic SIV replication. The potential for these cells to infiltrate sites of ongoing viral replication and viral persistence and the ability to induce these cells by vaccination provide a tremendous opportunity to develop and optimize therapeutic strategies to target and reduce the HIV reservoirs in lymphoid tissues.
An amidase is required for proper intercellular communication in the filamentous cyanobacteriumAnabaenasp. PCC 7120
Authors: Zheng Zhenggao , Omairi-Nasser Amin , Li Xiying , Dong Chunxia , Lin Yan , Haselkorn Robert , Zhao Jindong
Published: February 2017

Significance

The filamentous cyanobacteriumAnabaenahas become a widely studied model to determine the molecular mechanisms involved in establishing and maintaining the pattern of heterocyst differentiation in response to the removal of fixed nitrogen from the environment. Heterocysts develop from vegetative cells, usually spaced about 10 cells apart, converting an oxic cell capable of division into an anoxic factory for nitrogen fixation that does not divide. Genetic analysis to elucidate the mechanisms of intercellular material exchange between heterocysts and vegetative cells is in an early phase. Here we show that an amidase is involved in the function of channels that penetrate the rigid peptidoglycan walls that separate cells in the filaments.
Simultaneous interpreting and religious experience
Authors: Hokkanen Sari
Published: February 2017

In this paper, I discuss the volunteer simultaneous church interpreting I conduct as a professionally trained interpreter, using autoethnography as my methodological approach. The aim is to examine how my professional identity and my identity as a Pentecostal Christian coexist in this non-professional interpreting context. Pentecostalism emphasizes personal religious experience, defined as encountering God, making it a salient feature of the social context of the volunteer interpreting context. Therefore, I study spiritual and practical levels of preparation related to simultaneous interpreting at church. In addition, I examine the ways in which a personal religious experience, especially “hearing from God,” can take place while interpreting, which speaks of my active participation in the interpreted service. This paper thus highlights the dynamics of professional and non-professional interpreting as social contexts carrying meaning over to personal practice.
Child language brokering in private and public settings
Authors: Cirillo Letizia
Published: February 2017

This paper presents the results of a survey on child language brokering (CLB) conducted in junior high schools of Emilia Romagna (Northern Italy). Two questionnaires were drafted to investigate the perceptions of young brokers and their teachers on CLB-related issues. The responses gathered so far contribute to shed light on the who, where, when, and what of CLB in Italy, and generally confirm the results obtained by previous studies at both national and international levels. A comparison between the two sets of responses reveals brokers’ and teachers’ somehow different attitudes toward CLB, which deserve further investigation.
Seeing brokering in bright colours
Authors: Torresi Ira
Published: February 2017

A recurrent issue in child language brokering (CLB) research is how to best adjust ethnographic methodologies in order to collect data from young children. There are a number of practical considerations in addition to the necessary ethical aspects. Questionnaires and other methods relying on the written word may prove inadequate for first- and second-graders, and even for older bilingual or multilingual children who may not have the same level of literacy in all their languages. Methods relying on the spoken word, such as interviews, focus groups or participant observation, may prove similarly problematic when groups of respondents have mixed language proficiency levels. Artwork elicitation, on the contrary, can be an effective and inclusive way to collect qualitative data about young children’s feelings and perceptions about CLB. It has the potential to elicit visual narratives from large groups of children (e.g. entire classes or schools), while leaving them free to include aspects of the phenomenon being investigated that would otherwise be difficult for them to describe in words. This chapter explores primary school children’s experience of CLB as it emerges from artwork submitted for the “Budding translators” competition described by Antonini (this volume), and proposes an analysis that draws mainly on visual and social semiotics.
Discovery of a magnetic field in the δ Scuti F2m star ρ Pup
Authors: Neiner C. , Wade G. A. , Sikora J.
Published: February 2017

ρ Pup is a δ Scuti F2 pulsator, known to host a main radial mode as well as non-radial pulsations, with chemical peculiarities typical of evolved Am stars. We present a high-precision spectropolarimetric observations of this star, obtained with ESPaDOnS at the Canada–France–Hawaii Telescope in the frame of the BRITE spectropolarimetric survey. A magnetic field is clearly detected in ρ Pup, with a longitudinal field strength below 1 G. This makes ρ Pup the second known magnetic δ Scuti discovered, after HD 188774, and a possible cool evolved counterpart of the recently discovered ultraweakly magnetic Am family.
Commentary: Appropriate Use Criteria for Lumbar Degenerative Scoliosis: Developing Evidence-based Guidance for Complex Treatment Decisions
Authors: Glassman Steven D. , Berven Sigurd H. , Shaffrey Christopher I. , Mummaneni Praveen V. , Polly David W.
Published: February 2017

Lumbar degenerative scoliosis is a relatively common problem, and is being treated more frequently due to the confluence of an aging population and an increased capacity and willingness to manage difficult problems in older patients. Lumbar degenerative scoliosis is a complex pathology as it often involves the intersection of degenerative spinal stenosis and spinal deformity. While previous studies provide an indication that these patients may benefit from surgical treatment, the substantial variability in treatment underscores the opportunity for improvement. Optimizing treatment for lumbar degenerative scoliosis is critical as surgical intervention, while potentially providing substantial clinical benefit also entails measurable risk and significant expense. In light of these issues, evidence-based guidance generated through Appropriate Use Criteria (AUC) development offers the potential to improve both the quality and cost effectiveness of care.

The lumbar degenerative scoliosis AUC represents a significant step toward evidence-based treatment in spinal surgery. This is the first time that spine societies and industry partners have collaborated to support evidence development. The willingness of all involved to support a completely independent process underlines a commitment to trust the evidence. Subsequent studies may validate and/or refine the AUC recommendations, but the most important result is that the standard for evidence quality has been raised.
Love as a Disposition
Authors: Naar Hichem
Published: February 2017

This chapter proposes that the question “What is love?” be given an ontological treatment. Rather than asking whether love can be identified with a familiar mental phenomenon (desire, emotion, etc.), it suggests that we should first ask what kind of phenomenon love is, where a kind should here be understood as the most general category to which a given phenomenon belongs, an inquiry that is largely missing from contemporary discussions about love. After motivating this project, the chapter discusses and rejects a view according to which love is a certain kind of pattern or process, and then argues that love should be conceived of as a certain kind of state, namely a dispositional state.
The Argument from the Poverty of the Stimulus
Authors: Lasnik Howard , Lidz Jeffrey L.
Published: February 2017

This article explores what Noam Chomsky called ‘the argument from poverty of the stimulus’: the argument that our experience far underdetermines our knowledge and hence that our biological endowment is responsible for much of the derived state. It first frames the poverty of the stimulus argument either in terms of the set of sentences allowed by the grammar (its weak generative capacity) or the set of structures generated by the grammar (its strong generative capacity). It then considers the five steps to a poverty argument and goes on to discuss the possibility that children can learn via indirect negative evidence on the basis of Bayesian learning algorithms. It also examines structure dependence, polar interrogatives, and artificial phrase structure and concludes by explaining how Universal Grammar shapes the representation of all languages and enables learners to acquire the complex system of knowledge that undergirds the ability to produce and understand novel sentences.
First Language Acquisition
Authors: Guasti Maria-Teresa
Published: February 2017

Humans acquire language naturally, namely without specific instruction, by being exposed to it and by interacting with other human beings. According to the generativist enterprise, humans are endowed with a system of knowledge on the form of possible human languages (Universal Grammar). Evidence consistent with this assumption is provided in the chapter, by illustrating crucial phenomena ranging from the acquisition of phonology, to morphosyntax, syntax, formal semantics, and pragmatics. Infants’ brain organization is tuned to speech stimuli and presents left hemisphere specialization, from the first days of life, if not already in the mother’s womb. Infants set apart languages at two days of age, based on durational or rhythmic properties. Toddlers combine words by respecting the basic word order and are very sensitive to the hierarchical organization of sentences, both when it comes to the syntactic structure and when it comes to the interpretation of sentences.
A Null Theory of Creole Formation Based on Universal Grammar
Authors: Aboh Enoch , deGraff Michel
Published: February 2017

Creole languages are typically the linguistic side effects of the creation of global economies based on the forced migration and labor of enslaved Africans toiling in European colonies in the Americas. Section 1 addresses terminological and methodological preliminaries in Creole studies, including definitions of ‘Creole’ languages that contradict some of the fundamental assumptions in studies of Universal Grammar (UG). Section 2 evaluates Creole-formation hypotheses, including claims about the lesser grammatical complexity of Creoles and about an exceptional ‘Creole typology’ outside the scope of the Comparative Method in historical linguistics. Section 3 offers the sketch of a framework for a Null Theory of Creole Formation (NTC) that excludes sui generis stipulations about Creole formation and Creole languages and that is rooted in UG, as it applies to all languages. Section 4 concludes the paper with open-ended questions on the place of Creole formation within larger patterns of contact-induced language change.
Self-Locating Credences
Authors: Titelbaum Michael
Published: February 2017

An agent's self-locating credences capture her opinions about who she is, where she is, and what time it is. Most authors agree that self-locating credences cannot be rationally updated simply by applying traditional Bayesian conditionalization. After explaining why this is, I catalog alternative updating schemes that have been proposed for self-locating credence. I separate those schemes into three broad approaches: ‘shifting schemes’, ‘stable base schemes’, and ‘demonstrative schemes’. Each approach solves particular problems but has its particular blindspots. I then suggest that the Sleeping Beauty Problem has generated so much controversy in the literature because it falls into the blindspots of all three types of updating schemes.
Probabilistic Causation
Authors: Hitchcock Christopher
Published: February 2017

This chapter will explore a variety of projects that aim to characterize causal concepts using probability. These are, somewhat arbitrarily, divided into four categories. First, a tradition within philosophy that has aimed to define, or at least constrain, causation in terms of conditional probability is discussed. Secondly, the use of causal Bayes nets to represent causal relations, to facilitate inferences from probabilities to causal relations, and to ‘identify’ causal quantities in probabilistic terms is discussed. Thirdly, efforts to measure causal strength in probabilistic terms are reviewed, with particular attention to the significance of these measures in the context of epidemiology. Finally, attempts are discussed to analyze the relation of ‘actual causation’ (sometimes called ‘singular causation’) using probability.
Islamic Law and Finance
Authors: Emon Anver M.
Published: February 2017

This essay provides a historiographic introduction to the literature on Islamic finance. It situates the financial practice in terms of foundational principles; historical legal doctrines as reapplied in a contemporary financial context; and an institutional, regulatory framework developed over the course of the twentieth century. The rise of Islamic finance occurs at the intersection of excessive surplus wealth from the 1970 oil boom and an increasingly deregulated global financial sector in the 1980s; as such, this essay conceptually situates the Islamic financial order within the broader turn to free-market ideologies and policies globally.
Debating Autonomous Weapon Systems, their Ethics, and their Regulation under International Law
Authors: Anderson Kenneth , Waxman Matthew C.
Published: February 2017

An international public debate over the law and ethics of autonomous weapon systems (AWS) has been underway since 2012, with those urging legal regulation of AWS under existing principles and requirements of the international law of armed conflict in argument with opponents who favour, instead, a preemptive international treaty ban on all such weapons. This chapter provides an introduction to this international debate, offering the main arguments on each side. These include disputes over defining an AWS, the morality and law of automated targeting and target selection by machine, and the interaction of humans and machines in the context of lethal weapons of war. Although the chapter concludes that a categorical ban on AWS is unjustified morally and legally—favouring the law of armed conflict’s existing case-by-case legal evaluation—it offers an exposition of arguments on each side of the AWS issue.
Leadership and the Politics of Development
Authors: Leftwich Adrian , Lyne De Ver Heather
Published: February 2017

This chapter focuses on the role of leadership in economic development. It first defines leadership as a collective political process, not simply or solely as a function of the attributes, traits, and activities of individuals in the tradition of the “great man/woman” of history. Second, the chapter locates leadership within a theoretical context about how economic and political development happens. Third, the chapter undertakes a political analysis of how actors—as agents (individual and collective)—interpret their interests and ideas, make choices, frame and strategize their activities, and encounter and interact with each other and their interests in the context of different structures of power.
Newton’s Optical Experiments and Theories
Authors: Shapiro Alan E.
Published: February 2017

This chapter describes Newton’s experimental and theoretical optical investigations. The discussions include his theory of color and the compound nature of white light; his interchanges with the critics of that theory; his methodological concern with certainty and hypotheses; his efforts to explain optical phenomena using a projectile or corpuscular theory of light; his quest to explain refraction and chromatic dispersion; his investigation of the colors of thin plates or the interference of light; his theory of the colors of natural bodies; his work on the colors of thick plates and the theory of fits; and his composition of the Opticks and investigation of diffraction.
Kant’s Foundations for Newtonian Science
Authors: Smith Sheldon R.
Published: February 2017

Throughout his career, Immanuel Kant was engaged rather closely with Newtonian science. Although Kant adopts many Newtonian principles, most obviously the Newtonian gravitational law, he is also critical of Newton for, among other things, not having provided “metaphysical foundations” for science. Kant’s own attempt to provide such foundations leads him to have a somewhat different picture of the physical world from Newton. This article describes why Kant thought that metaphysical foundations were required and some of the ways this requirement leads Kant toward non-Newtonian views. In particular, it compares and contrasts their views on the nature of matter, force, the laws of nature, and absolute space and absolute motion.
Word and Image in the English Renaissance
Authors: Preston Claire
Published: February 2017

The rich and expanding rhetorical universe of the English Renaissance annexed the expressive possibilities of painting and the plastic arts using a variety of figures and tropes. These—ekphrasis (intense description), blason (anatomizing description), paragone (the contest between the arts), and emblems and imprese (formal verbal-visual symbols)—allowed English writers to press the visual into the service of the verbal, creating powerful rhetorical tools and distinctive literary expression. This article describes the development of these verbal-visual tools from the late medieval period through the early seventeenth century by Italian art theorists and in the exemplary works of Sidney, Spenser, and Shakespeare.