bluuebunny/crossref_metadata_2025 huggingface dataset:
The classical and theoretical simulation for dominant radiated frequencies of plasma nanowire in presence of a long monopole antenna with long wavelength radiation
Authors: Safari S. , Jazi B.
Published: May 2017

A theoretical model based on the classical theory for the simulation of scattering phenomena of long wavelength electromagnetic waves from plasma nanowires is investigated. A line source as a monopole antenna radiator is considered, which radiates with frequency ω in the vicinity of plasma nanowires parallel to the nanowire axis. A mathematical relation for resonance frequency is obtained. It is shown that in the resonance situation, plasma nanowires represent most of the response to the presence of electromagnetic waves. Mathematical computations are done for both the cold and warm approximations of plasma cases. The diagrams of the variation of resonance frequency versus the variation of temperature, geometrical dimension, and carrier density of plasma nanowires are presented. Also, a mathematical relation for subsidiary resonance frequency with considering two line sources with opposite charge is offered. The diagrams of subsidiary resonance frequency versus the variation of temperature, geometrical dimension, and carrier density of plasma nanowires are presented. It is shown that the presented model provides a color diagnostic system for the determination of size, the number, and distribution of nanowires immersed in a fluid based on their temperature and geometrical dimension.
3-wave mixing Josephson dipole element
Authors: Frattini N. E. , Vool U. , Shankar S. , Narla A. , Sliwa K. M. , Devoret M. H.
Published: May 2017

Parametric conversion and amplification based on three-wave mixing are powerful primitives for efficient quantum operations. For superconducting qubits, such operations can be realized with a quadrupole Josephson junction element, the Josephson Ring Modulator, which behaves as a loss-less three-wave mixer. However, combining multiple quadrupole elements is a difficult task so it would be advantageous to have a three-wave dipole element that could be tessellated for increased power handling and/or information throughput. Here, we present a dipole circuit element with third-order nonlinearity, which implements three-wave mixing. Experimental results for a non-degenerate amplifier based on the proposed third-order nonlinearity are reported.
Modeling quasi-ballistic transient thermal transport with spatially sinusoidal heating: A McKelvey-Shockley flux approach
Authors: Abarbanel Daniel , Maassen Jesse
Published: May 2017

Ballistic phonon effects, arising on length scales comparable to the mean-free-path, result in non-diffusive heat flow and alter the thermal properties of materials. Simple theoretical models that accurately capture non-diffusive transport physics are valuable for experimental analysis, technology design, and providing physical insight. In this work, we utilize and extend the McKelvey-Shockley (McK-S) flux method, a simple and accurate framework, to investigate ballistic effects in transient phonon transport submitted to a spatially sinusoidal heating profile, simulating a transient thermal grating. We begin by extending a previous McK-S formulation to include inelastic scattering, then obtain an analytical solution in the single phonon energy case (gray approximation), and after show how this approach can readily support a full phonon dispersion and mean-free-path distribution. The results agree with experimental data and compare very well to solutions of the phonon Boltzmann transport equation in the diffusive and weakly quasi-ballistic transport regimes. We discuss the role of ballistic and non-equilibrium physics, and show that inelastic scattering is key to retrieving the heat equation solution in the diffusive limit. Overall the McK-S flux method, which takes the form of a diffusion-like equation, proves to be a simple and accurate framework that is applicable from the ballistic to diffusive transport regime.
Flexoelectric characterization of BaTiO3-0.08Bi(Zn1/2Ti1/2)O3
Authors: Huang Shujin , Kim Taeyang , Hou Dong , Cann David , Jones Jacob L. , Jiang Xiaoning
Published: May 2017

Flexoelectricity, the linear coupling between the strain gradient and the induced electric polarization, has been widely studied as a substitution for piezoelectricity among ceramic lead-free materials. Its potential in micro/nano-scale sensing has especially gained attention, outweighing the performance of cutting edge lead-based piezoelectric materials. In this letter, the flexoelectric coefficient of lead-free ceramic BaTiO3-0.08Bi(Zn1/2Ti1/2)O3 (BT-8BZT) was investigated in the transverse mode. The thermal dependence of flexoelectricity in BT-8BZT was investigated at temperatures ranging from 25 °C to 200 °C, and the results were compared with those of BaxSr1-xTiO3 (BST) ceramics. The effective μ12 of BT-8BZT is ∼25 μC/m at room temperature and can remain as high as ∼13 μC/m at 200 °C. This result suggests that BT-8BZT can be effectively used for micro/nano-sensing within a broad range of temperatures.
Evidence of terbium and oxygen co-segregation in annealed AlN:Tb
Authors: Angadi V. C. , Benz F. , Tischer I. , Thonke K. , Aoki T. , Walther T.
Published: May 2017

Analytical scanning transmission electron microscopy has been applied to study aluminium nitride (AlN) doped with terbium (Tb) and annealed at 800 °C. The correlation of the maps of Tb and oxygen (O) from electron energy-loss spectrum (EELS) imaging proves that these two elements co-segregate, replacing aluminium (Al) and nitrogen (N) atoms, respectively. This agrees well with modelling which predicted the existence of Tb–O complexes needed to fit all lines in the rather complicated cathodoluminescence emission spectrum of the sample.
Optimal pre- and post-selections of weak measurements for precision parameter estimation
Authors: Liu Xiong , Qiu Xiaodong , Xie Linguo , Luo Lan , Li Zhaoxue , Zhang Zhiyou , Du Jinglei
Published: May 2017

Weak measurements, which offer a significant signal enhancement with pre- and post-selections, have proven to be powerful for precision metrology. However, the measured precision of the parameter of interest is always limited by the post-selection-induced probe loss, especially in the presence of technical noise. In this paper, we investigate the optimal pre- and post-selections of weak measurements for precision metrology in the presence of technical noise. While weak measurements apply more generally, we experimentally measure the spin splitting induced by the spin Hall effect of light (SHEL) to approach this issue. The highest measured precision of the spin splitting can be obtained with the post-selected state in the nonlinear intermediate regime. Surprisingly, the pre- and post-selections for the largest weak-value amplification are incapable of estimation of the spin splitting, since the amplified shift is independent of the spin splitting. Our results are not restricted to the SHEL and could be applied to other parameter estimations with weak measurements.
Vertically coupled double-microdisk lasers composed of InGaAs quantum dots-in-a-well active layers
Authors: Hsing J. Y. , Tzeng T. E. , Lay T. S. , Shih M. H.
Published: May 2017

We report the epitaxy, fabrication, and measurement of vertically coupled double-microdisk lasers using InGaAs quantum dots-in-a-well as the optical gain material. The bonding and anti-bonding photonic molecule laser modes are simultaneously observed at room temperature (T = 300 K). The optical coupling is confirmed by measuring the double disks for three different air gaps of 100 nm, 200 nm, and 480 nm, respectively. The coupling strengths for the photonic molecule bonding mode MB1,9 and anti-bonding mode MA1,9 between the adjacent microdisks are equal to 17.4 THz for 100 nm air gap, and 5.2 THz for 200 nm air gap, respectively. The refractive index sensing experiments show the lasing wavelength sensitivity of 60 nm/RIU for the vertically coupled double-microdisk laser of 100 nm air gap.
Monitoring of early catastrophic optical damage in laser diodes based on facet reflectivity measurement
Authors: Zhang S. Y. , Feng S. W. , Zhang Y. M. , An Z. F. , Yang H. W. , He X. , Wang X. , Qiao Y. B.
Published: May 2017

We propose a convenient, inexpensive technique to monitor the fast early stage of catastrophic optical damage (COD) in 808-nm high-power laser diodes (LDs). Using an optical system based on the 1550-nm laser diode illuminant and photodiode, we measured the facet reflectivity, which gives information about the surface morphology of the output facet with a temporal resolution of 2 ns, allowing us to trace the rapid early COD process in a transient, real-time mode. The formation of the detected 4-μm-long COD damaged area, which caused a local uneven surface at the output facet and a rapid drop in facet reflectivity at 1550 nm from 28% to 2%, was completed within 20–30 ns, 10 ns shorter than that in the longer-wavelength devices.
Lignin biopolymer based triboelectric nanogenerators
Authors: Bao Yukai , Wang Ruoxing , Lu Yunmei , Wu Wenzhuo
Published: May 2017

Ongoing research in triboelectric nanogenerators (TENGs) focuses on increasing power generation, but obstacles concerning economical and eco-friendly utilization of TENGs continue to prevail. Being the second most abundant biopolymer on earth, lignin offers a valuable opportunity for low-cost TENG applications in biomedical devices, benefitting from its biodegradability and biocompatibility. Here, we develop for the first time a lignin biopolymer based TENGs for harvesting mechanical energy in the environment, which shows great potential for self-powered biomedical devices among other applications and opens doors to new technologies that utilize otherwise wasted materials for economically feasible and ecologically friendly production of energy devices.
Direct laser writing of complex microtubes using femtosecond vortex beams
Authors: Yang Liang , Qian Dongdong , Xin Chen , Hu Zhijiang , Ji Shengyun , Wu Dong , Hu Yanlei , Li Jiawen , Huang Wenhao , Chu Jiaru
Published: May 2017

Microfabrication by using structured laser beams provides a rapid and facile way for creating some specific microstructures. As an important member in the structured beam category, optical vortices can be easily generated by a helical phase and focused into a geometry-tunable pattern by an objective. In this work, optical vortices with diverse intensity distributions, e.g., different sizes, geometries, and deflection angles, are generated by controlling the phase factors imprinted on optical vortices, including topological charge, fold number, and modulation depth, respectively. The focusing properties of the measured optical vortices in a high numerical aperture laser microfabrication system agree with the theoretical calculation by the Debye vectorial diffraction theory. Three dimensional complex microtubes are rapidly realized by simply scanning the optical vortices along a designed route in a photoresist. With this method, microtubes with controlled diameters, polygonal geometry, winding edges, and even 3D spiral microtubes are facilely achieved.
Pressure-induced elastic anomaly in a polyamorphous metallic glass
Authors: Zeng Qiaoshi , Zeng Zhidan , Lou Hongbo , Kono Yoshio , Zhang Bo , Kenney-Benson Curtis , Park Changyong , Mao Wendy L.
Published: May 2017

The pressure-induced transitions discovered in metallic glasses (MGs) have attracted considerable research interest offering an exciting opportunity to study polyamorphism in densely packed systems. Despite the large body of work on these systems, the elastic properties of the MGs during polyamorphic transitions remain unclear. Here, using an in situ high-pressure ultrasonic sound velocity technique integrated with x-ray radiography and x-ray diffraction in a Paris-Edinburgh cell, we accurately determined both the compressional and shear wave velocities of a polyamorphous Ce68Al10Cu20Co2 MG up to 5.8 GPa. We observed elastic anomalies of a MG with minima (at ∼1.5 GPa) in the sound velocities, bulk modulus, and Poisson's ratio during its polyamorphic transition. This behavior was discussed in comparison to the elastic anomalies of silica glass and crystalline Ce.
Germanium oxidation occurs by diffusion of oxygen network interstitials
Authors: Li H. , Robertson J.
Published: May 2017

Density functional modeling is used to show that germanium oxidation occurs by the diffusion of network oxygens across the film as peroxyl bridges, not by molecular O2 interstitials (O2*). The smaller O bond angle of GeO2 leads to lower order rings in the amorphous GeO2 network than in SiO2. This leads to narrower interstitial diffusion channels, and less dilation of the interstitial volume around the transition state. This raises the migration barrier of O2* in GeO2, so that the overall diffusion energy of O2* in GeO2 is now higher than that of a network O interstitial. The low formation energy of the O vacancy in GeO2 leads to GeO2 being O-poor very near the Ge/GeO2 interface, but the lower overall diffusion energy of the O network interstitial than the vacancy leads to the network interstitial dominating diffusion.
Viral and cellular mRNA-specific activators harness PABP and eIF4G to promote translation initiation downstream of cap binding
Authors: Smith Richard W. P. , Anderson Ross C. , Larralde Osmany , Smith Joel W. S. , Gorgoni Barbara , Richardson William A. , Malik Poonam , Graham Sheila V. , Gray Nicola K.
Published: May 2017

Significance

The majority of genes are controlled at the level of mRNA translation, with accurate regulation being critical to cellular function and health. The repression or activation of subsets of mRNAs, so-called “mRNA-specific” regulation, is often mediated by RNA-binding proteins. However, the mechanisms underlying mRNA-specific activation have only been determined in a very few cases. Here, we uncover a mechanism of mRNA-specific activation used by viral and cellular proteins, which share no sequence similarity, suggesting that it may represent a widespread mechanism. Importantly, in so doing, we also expand our knowledge of how two key translation factors, poly(A)-binding protein (PABP) and eukaryotic initiation factor 4G (eIF4G), function during translation initiation, showing they have pleiotropic effects on small ribosomal subunit recruitment.
Disparate foundations of scientists’ policy positions on contentious biomedical research
Authors: Edelmann Achim , Moody James , Light Ryan
Published: May 2017

Significance

What drives scientists’ public support for contentious policy issues? We examined associations between peer exposure and academic specialization on public declarations about research involving potentially pandemic pathogens. Although we found significant peer associations for everyone, they are strongest among the opposition. Conversely, specializing in fields directly related to gain-of-function research predicts support better than specializing in fields related to epidemic risks predicts opposition. These findings suggest that different social processes, rooted in differing social networks and expertise, underlie support or opposition. Identifying the sources of policy support might help parties better understand the different, but legitimate, foundations of each other’s positions, providing additional information to inform decision making and thereby help to maintain science’s role as an objective arbiter for policy.
The impact of Last Glacial climate variability in west-European loess revealed by radiocarbon dating of fossil earthworm granules
Authors: Moine Olivier , Antoine Pierre , Hatté Christine , Landais Amaëlle , Mathieu Jérôme , Prud’homme Charlotte , Rousseau Denis-Didier
Published: May 2017

Significance

Last Glacial millennial-timescale warming phases well-recorded in Greenland ice cores are relevant across the Northern Hemisphere. However, dating limitations in loess deposits inhibited characterizing their impact on the European Great Plain. Here, the radiocarbon dating of a large set of earthworm calcite granule samples from the Nussloch reference loess sequence (Rhine Valley, Germany) led to a straightforward chronological distinction of all soil horizons. Resulting correlations with Greenland interstadials between 50 and 20 ka also revealed more complex climate dynamics than interpreted from Greenland δ
18
O records. This study is a fundamental contribution to understanding links between mid- and high-latitude climate changes and their spatial and temporal impact on paleoenvironments and prehistoric population settlement in Europe.
Early 20th-century Arctic warming intensified by Pacific and Atlantic multidecadal variability
Authors: Tokinaga Hiroki , Xie Shang-Ping , Mukougawa Hitoshi
Published: May 2017

Significance

Arctic amplification is a robust feature of climate response to global warming, with large impacts on ecosystems and societies. A long-standing mystery is that a pronounced Arctic warming occurred during the early 20th century when the rate of interdecadal change in radiative forcing was much weaker than at present. Here, using observations and model experiments, we show that the combined effect of internally generated Pacific and Atlantic interdecadal variabilities intensified the Arctic land warming in the early 20th century. The synchronized Pacific–Atlantic warming drastically alters planetary-scale atmospheric circulations over the Northern Hemisphere that transport warm air into the Arctic. Our results highlight the importance of regional sea surface temperature changes for Arctic climate and constrain model projections in this important region.
miR-183/96 plays a pivotal regulatory role in mouse photoreceptor maturation and maintenance
Authors: Xiang Lue , Chen Xue-Jiao , Wu Kun-Chao , Zhang Chang-Jun , Zhou Gao-Hui , Lv Ji-Neng , Sun Lan-Fang , Cheng Fei-Fei , Cai Xue-Bi , Jin Zi-Bing
Published: May 2017

Significance

The polycistronic miR-183/96/182 cluster is highly expressed in various types of terminally differentiating sensory neurons, including photoreceptors. Although miR-182 single-knockout mice do not exhibit significant retinal architecture alterations in photoreceptors, deletion of miR-183 and miR-96 gives rise to severe defects in cone maturation. Long-term follow-up analysis reveals that miR-183/96 ablation results in progressive photoreceptor degeneration. Mechanistic studies demonstrate that miR-183 and miR-96 directly regulate the expression of the taurine transporter Slc6a6. The expression levels of photoreceptor-specific genes change in accordance with the knockdown or overexpression of Slc6a6 in vivo. In both cases, the mouse scotopic electroretinography responses are compromised. Our findings reveal that the epigenetic regulation of miR-183/96 via Slc6a6 is essential for mouse photoreceptor formation and functionalization.
The POTRA domains of Toc75 exhibit chaperone-like function to facilitate import into chloroplasts
Authors: O’Neil Patrick K. , Richardson Lynn G. L. , Paila Yamuna D. , Piszczek Grzegorz , Chakravarthy Srinivas , Noinaj Nicholas , Schnell Danny
Published: May 2017

Significance

Nearly all proteins found within chloroplasts are synthesized in the cytoplasm as preproteins and then imported and trafficked to their final destination. The initial steps in importation are orchestrated by the TOC complex, which includes Toc75, serving as the translocation channel, and Toc33 and Toc159, both containing GTPase domains, which help drive substrate selection and importation. Aside from the soluble domain of Toc33/34, structural information for the TOC complex is lacking, hindering our ability to form mechanistic models for function. Here we report a structure of Toc75 consisting of three tandem POTRA domains. Our findings indicate that the POTRA domains may help facilitate preprotein import by directly binding preproteins and orchestrating handoff to the TIC complex.
Antimalarials inhibit hematin crystallization by unique drug–surface site interactions
Authors: Olafson Katy N. , Nguyen Tam Q. , Rimer Jeffrey D. , Vekilov Peter G.
Published: May 2017

Significance

Approximately 3.2 billion people are at risk for malaria. The resistance of malaria parasites to current advanced multidrug treatments, recently recorded to spread out of Southeast Asia, has raised concerns of dire public health consequences. We demonstrate that antimalarial drugs suppress heme detoxification in the malaria parasites in a manner that is counter to the prevailing hypothesis in the field. We find that quinoline-class drugs work by specific interactions with β-hematin crystals, which are the by-product of heme detoxification within the digestive vacuole of the parasites. We also identify specific drug adsorption sites on crystal surfaces. These insights may potentially spur development of antimalarial drugs that overcome parasite resistance through a rational approach, far superior to currently used combinatorial methods.
Structural basis for ligand binding to an enzyme by a conformational selection pathway
Authors: Kovermann Michael , Grundström Christin , Sauer-Eriksson A. Elisabeth , Sauer Uwe H. , Wolf-Watz Magnus
Published: May 2017

Significance

Cellular chemical reactions are slow, and to make them compatible with biological life, enzymes have evolved to accelerate their associated rate constants. Enzymatic catalysis is a complex process where the increase of rate constants predominantly depends on a reduction of the free energy barrier for product formation. It is now established that transient, so-called high-energy, enzyme states are indispensable entities that contribute to lowering of free energy barriers. Such states are inherently difficult to study. Here, we have been able to arrest a catalytically indispensable high-energy state of the enzyme adenylate kinase. A detailed characterization of its structure, dynamics, and function has revealed several aspects that together increase the understanding of how enzymes can perform their spectacular function.
Contacts between the endoplasmic reticulum and other membranes in neurons
Authors: Wu Yumei , Whiteus Christina , Xu C. Shan , Hayworth Kenneth J. , Weinberg Richard J. , Hess Harald F. , De Camilli Pietro
Published: May 2017

Significance

The cytoplasm of eukaryotic cells is compartmentalized by intracellular membranes that define subcellular organelles. One of these organelles, the endoplasmic reticulum, forms a continuous network of tubules and cisternae that extends throughout all cell compartments, including neuronal dendrites and axons. This network communicates with most other organelles by vesicular transport, and also by contacts that do not lead to fusion but allow cross-talk between adjacent bilayers. Though these membrane contacts have previously been observed in neurons, their distribution and abundance has not been systematically analyzed. Here, we have carried out such analysis. Our studies reveal new aspects of the internal structure of neurons and provide a critical complement to information about interorganelle communication emerging from functional and biochemical studies.
Input timing for spatial processing is precisely tuned via constant synaptic delays and myelination patterns in the auditory brainstem
Authors: Stange-Marten Annette , Nabel Alisha L. , Sinclair James L. , Fischl Matthew , Alexandrova Olga , Wohlfrom Hilde , Kopp-Scheinpflug Conny , Pecka Michael , Grothe Benedikt
Published: May 2017

Significance

Neural computation depends on precisely timed synaptic inputs, but the way that the timing of inputs is tuned to match postsynaptic processing requirements is not well understood. Here, we studied the same brainstem sound localization pathway in two species with dissimilar temporal processing requirements. Two factors that limit precise timing are synaptic delay and axonal conduction time. In gerbils, which depend on precise timing for sound localization, synaptic delays in fast conducting axons are stable across activity level, and axon myelination is adapted to minimize conduction delays. In mice, which do not depend on precise timing, these specializations are absent. Our results suggest that both axonal and synaptic properties are optimized to the specific functional requirements of neural computation, advancing our understanding of the mechanisms that optimize neural circuits.
Superresolution microscopy reveals the three-dimensional organization of meiotic chromosome axes in intact
Caenorhabditis elegans
tissue
Authors: Köhler Simone , Wojcik Michal , Xu Ke , Dernburg Abby F.
Published: May 2017

Significance

Meiosis is the essential cell division process that generates haploid gametes from diploid precursor cells. It relies on a dramatic reorganization of chromosomes around a central axis, which establishes a platform for homologous pairing and its subsequent stabilization by the formation of a proteinaceous structure, the synaptonemal complex, and by physical linkages resulting from crossover recombination events. Despite their central role in regulating key meiotic events, little is known about the organization of the chromosome axes. Here, we use superresolution microscopy, combined with CRISPR/Cas9 genome editing, to build a three-dimensional model of the synapsed chromosome axis. Our data link axis structure to its functions in synapsis and regulation of partner choice during meiotic double-strand break repair.
RNA-seq reveals conservation of function among the yolk sacs of human, mouse, and chicken
Authors: Cindrova-Davies Tereza , Jauniaux Eric , Elliot Michael G. , Gong Sungsam , Burton Graham J. , Charnock-Jones D. Stephen
Published: May 2017

Significance

The human yolk sac is often considered vestigial. Here, we report RNA-sequencing analysis of the human and murine yolk sacs and compare with that of the chicken. We relate the human RNA-sequencing data to coelomic fluid proteomic data. Conservation of transcripts across the species indicates the human secondary yolk sac likely performs key functions early in development, particularly uptake and processing of macro- and micronutrients, many of which are found in coelomic fluid. More generally, our findings shed light on evolutionary mechanisms giving rise to complex structures such as the placenta. We propose that although a choriovitelline placenta is never established physically in the human, the placental villi, exocoelomic cavity, and secondary yolk sac function together as a physiological equivalent.
Dating rice remains through phytolith carbon-14 study reveals domestication at the beginning of the Holocene
Authors: Zuo Xinxin , Lu Houyuan , Jiang Leping , Zhang Jianping , Yang Xiaoyan , Huan Xiujia , He Keyang , Wang Can , Wu Naiqin
Published: May 2017

Significance

When the domestication of rice began in its homeland, China, is an enduring and important issue of debate for researchers from many different disciplines. Reliable chronological and robust identification criteria for rice domestication are keys to understanding the issue. Here, we first use phytolith dating to constrain the initial occupation of Shangshan, an important site with early rice remains located in the Lower Yangtze region of China. We then identify the rice phytoliths of Shangshan as partly domesticated based on their morphological characteristics. The results indicate that rice domestication may have begun at Shangshan in the Lower Yangtze during the beginning of the Holocene.
Assessing human weaning practices with calcium isotopes in tooth enamel
Authors: Tacail Théo , Thivichon-Prince Béatrice , Martin Jeremy E. , Charles Cyril , Viriot Laurent , Balter Vincent
Published: May 2017

Significance

The practice of weaning, the dietary transition from exclusive breastfeeding to exclusive nonmilk food, is a key aspect of development and evolution of hominins, but its study in the fossil record is hampered by a lack of unambiguous biomarkers. Ca stable isotope ratios of skeletal remains are expected to bear information about milk consumption. Here we demonstrate that modern human tooth enamel records a temporal variation of Ca isotope compositions, which is related to breastfeeding duration. Ca isotopes could be used as a biomarker for reconstruction of weaning practices in past human and fossil hominin species.
Structure-guided evolution of antigenically distinct adeno-associated virus variants for immune evasion
Authors: Tse Longping Victor , Klinc Kelli A. , Madigan Victoria J. , Castellanos Rivera Ruth M. , Wells Lindsey F. , Havlik L. Patrick , Smith J. Kennon , Agbandje-McKenna Mavis , Asokan Aravind
Published: May 2017

Significance

Preexisting neutralizing antibodies (NAbs) against adeno-associated viruses (AAVs) pose a major, unresolved challenge that restricts patient enrollment in gene therapy clinical trials using recombinant AAV vectors. To tackle this problem, we developed a structure-guided approach to evolve AAV variants with altered antigenic footprints that cannot be recognized by preexisting antibodies. These proof-of-principle studies demonstrate that synthetic AAV variants can be evolved to evade neutralizing sera from different species—mice, nonhuman primates, and humans—without compromising yield and transduction efficiency or altering tropism. Our approach provides a roadmap for engineering any AAV strain to evade NAbs in prospective patients for human gene therapy.
Rifamycin action on RNA polymerase in antibiotic-tolerant
Mycobacterium tuberculosis
results in differentially detectable populations
Authors: Saito Kohta , Warrier Thulasi , Somersan-Karakaya Selin , Kaminski Lina , Mi Jianjie , Jiang Xiuju , Park Suna , Shigyo Kristi , Gold Ben , Roberts Julia , Weber Elaina , Jacobs William R. , Nathan Carl F.
Published: May 2017

Significance

Most of the
Mycobacterium tuberculosis
(Mtb) bacilli in the sputum of most patients with tuberculosis studied to date do not grow on standard agar-based media but rather grow when diluted in liquid media of similar composition. Here, we describe a rigorously standardized and independently replicated method to generate and count these differentially detectable (DD) Mtb in culture. DD Mtb generation required the action of a rifamycin on RNA polymerase after induction of phenotypic tolerance. Generation of these cells in vitro led to identification of one drug that can kill them and should facilitate the discovery of others.
Feature reassembly in the acquisition of plural marking by Korean and Indonesian bilinguals
Authors: Lee Eunji , Lardiere Donna
Published: May 2017

This bidirectional study investigated the L2 acquisition of plural marking in L2 Indonesian by native Korean speakers and in L2 Korean by native Indonesian speakers. Indonesian and Korean are classifier languages with partially overlapping restrictions on how pluralization interacts with quantification, allowing us to test the acquisition of new L2 features vs. the preemption of L1 features that are not in the L2. We also examined how the contextual complexity of new L2 features impacts development. Seventy learners at three L2 Korean proficiency levels and 40 native controls participated in Experiment 1; 61 learners at three L2 Indonesian proficiency levels and 39 native controls participated in Experiment 2. All participants completed three tasks – a Sentence Completion Task, a Grammaticality Judgment Task and a Multiple-Choice Task. Whereas learners were largely able to overcome the difficulty of preemption, they were less successful in acquiring new L2 feature contrasts in more complex conditioning environments.
Processing DOM in relative clauses
Authors: Sagarra Nuria , Sánchez Liliana , Bel Aurora
Published: May 2017

Early heritage bilinguals have been repeatedly found to differ from late bilinguals and from monolinguals (e.g.,Montrul, 2008,2011). In the realm of Spanish Differential Object Marking (DOM), both early heritage bilinguals (Montrul et al., 2015) and late bilinguals (e.g.,Bowles & Montrul, 2008;Guijarro-Fuentes, 2012) exhibit difficulties. DOM in a complex structure such as relative clauses (RCs) provides an ideal setting to differentiate early from late bilinguals, but it has only been explored offline (Perpiñán & Moreno-Villar, 2013). This study fills this gap by examining the role of word order (SVO, OSV, OVS), optionality (obligatory vs. optional contexts), and saliency (bound vs. unbound morphology) on the processing of DOM in embedded RCs in Spanish, by Spanish monolinguals, and advanced early heritage and late bilinguals of Spanish. The results of a word-by-word non-cumulative self-paced reading task revealed that all participants were more accurate but were slower in subject than object RCs, and in OSV than OVS RCs. Slower RTs in subject RCs were due to the presence of DOM, and in OSV to interpreting OVS as SVO. Also, all participants were both more accurate as well as faster in obligatory than optional DOM, unbound than bound morphology, and masculine than feminine RC NPs. These findings reveal that processing difficulties in RCs result from the interaction of word order and DOM, and that processing DOM depends on both salience and, to a lesser extent, gender. Finally, this study shows that early heritage bilinguals are closer to monolinguals than late bilinguals in terms of morphosyntactic processing patterns.
Hungary's radical right 2.0
Authors: Karl Philipp
Published: May 2017

In the digital age, the Internet is an important factor in the emergence and success of political parties and social movements. Despite growing evidence that extremists of all stripes use the virtual world for their purposes, research on this topic still lacks a wide array of empirical data, case studies, and theoretical background. In particular, Facebook, as the most important social networking site, is a new tool for political parties and movements to mobilize followers. The article explores how the extreme-right party Jobbik uses this tool more successfully than other Hungarian parties or Western European extreme-right parties. Comparing the growth in followers highlights this success, and a look at how it generates likes helps to explain it. The article argues that Jobbik uses Facebook in a sophisticated way and suggests that this “likable” attitude helps to attract young and first-time voters.
Persistent mTORC1 signaling in cell senescence results from defects in amino acid and growth factor sensing
Authors: Carroll Bernadette , Nelson Glyn , Rabanal-Ruiz Yoana , Kucheryavenko Olena , Dunhill-Turner Natasha A. , Chesterman Charlotte C. , Zahari Qabil , Zhang Tong , Conduit Sarah E. , Mitchell Christina A. , Maddocks Oliver D.K. , Lovat Penny , von Zglinicki Thomas , Korolchuk Viktor I.
Published: May 2017

Mammalian target of rapamycin complex 1 (mTORC1) and cell senescence are intimately linked to each other and to organismal aging. Inhibition of mTORC1 is the best-known intervention to extend lifespan, and recent evidence suggests that clearance of senescent cells can also improve health and lifespan. Enhanced mTORC1 activity drives characteristic phenotypes of senescence, although the underlying mechanisms responsible for increased activity are not well understood. We have identified that in human fibroblasts rendered senescent by stress, replicative exhaustion, or oncogene activation, mTORC1 is constitutively active and resistant to serum and amino acid starvation. This is driven in part by depolarization of senescent cell plasma membrane, which leads to primary cilia defects and a resultant failure to inhibit growth factor signaling. Further, increased autophagy and high levels of intracellular amino acids may act to support mTORC1 activity in starvation conditions. Interventions to correct these phenotypes restore sensitivity to the mTORC1 signaling pathway and cause death, indicating that persistent signaling supports senescent cell survival.
Multi-omics analysis identifies ATF4 as a key regulator of the mitochondrial stress response in mammals
Authors: Quirós Pedro M. , Prado Miguel A. , Zamboni Nicola , D’Amico Davide , Williams Robert W. , Finley Daniel , Gygi Steven P. , Auwerx Johan
Published: May 2017

Mitochondrial stress activates a mitonuclear response to safeguard and repair mitochondrial function and to adapt cellular metabolism to stress. Using a multiomics approach in mammalian cells treated with four types of mitochondrial stressors, we identify activating transcription factor 4 (ATF4) as the main regulator of the stress response. Surprisingly, canonical mitochondrial unfolded protein response genes mediated by ATF5 are not activated. Instead, ATF4 activates the expression of cytoprotective genes, which reprogram cellular metabolism through activation of the integrated stress response (ISR). Mitochondrial stress promotes a local proteostatic response by reducing mitochondrial ribosomal proteins, inhibiting mitochondrial translation, and coupling the activation of the ISR with the attenuation of mitochondrial function. Through a trans–expression quantitative trait locus analysis, we provide genetic evidence supporting a role for Fh1 in the control of Atf4 expression in mammals. Using gene expression data from mice and humans with mitochondrial diseases, we show that the ATF4 pathway is activated in vivo upon mitochondrial stress. Our data illustrate the value of a multiomics approach to characterize complex cellular networks and provide a versatile resource to identify new regulators of mitochondrial-related diseases.
Fibroblast-adapted human CMV vaccines elicit predominantly conventional CD8 T cell responses in humans
Authors: Murray Susan E. , Nesterenko Pavlo A. , Vanarsdall Adam L. , Munks Michael W. , Smart Savannah M. , Veziroglu Eren M. , Sagario Lavinia C. , Lee Ronzo , Claas Frans H.J. , Doxiadis Ilias I.N. , McVoy Michael A. , Adler Stuart P. , Hill Ann B.
Published: May 2017

Cytomegalovirus (CMV)-based vaccines have shown remarkable efficacy in the rhesus macaque model of acquired immune deficiency syndrome, enabling 50% of vaccinated monkeys to clear a subsequent virulent simian immunodeficiency virus challenge. The protective vaccine elicited unconventional CD8 T cell responses that were entirely restricted by MHC II or the nonclassical MHC I molecule, MHC-E. These unconventional responses were only elicited by a fibroblast-adapted rhesus CMV vector with limited tissue tropism; a repaired vector with normal tropism elicited conventional responses. Testing whether these unusual protective CD8 T responses could be elicited in humans requires vaccinating human subjects with a fibroblast-adapted mutant of human CMV (HCMV). In this study, we describe the CD8 T cell responses of human subjects vaccinated with two fibroblast-adapted HCMV vaccines. Most responses were identified as conventional classically MHC I restricted, and we found no evidence for MHC II or HLA-E restriction. These results indicate that fibroblast adaptation alone is unlikely to explain the unconventional responses observed in macaques.
The Addition of Graphene and Magnetite Materials in TiO2/CuO Catalyst for Enhancing Photosonocatalytic Performance and Reusability
Authors: Taufik A , Muzaki A , Saleh R
Published: May 2017

In the present study, TiO2/CuO with the addition of graphene and magnetite materials were investigated as a catalyst for waste water removal through the photosonocatalytic process. TiO2/CuO/graphene and Fe3O4/TiO2/CuO/graphene were synthesized by using the sol-gel method. Their physical properties were characterized by using X-ray Diffraction, Fourier Transform Infra-red Spectroscopy, Thermogravimetric Analysis, Transmission Electron Microscope, and Breneur Emmet Teller (BET) surface area analyzer. The Photosonocatalytic activity was examined under visible light irradiation and 40 kHz ultrasound frequency with methyl orange (MO) as a model of organic pollutant. Compared to photocatalytic and sonocatalytic process, photosonocatalytic activity can improve the degradation process due to a synergistic effect between photocatalytic and sonocatalytic process at the same time. The addition of graphene materials can improve the charge carrier separation and prevent recombination electron and holes. Therefore, the photosonocatalytic performance increases significantly with the addition of graphene materials. The addition of magnetite materials is not only can enhance the photosonocatalytic performance but also can improve the separation process for reuse the catalyst. The photosonocatalytic mechanism was correlated with their physical properties and visible as well as ultrasound irradiation.
Model-based branching point detection in single-cell data by K-branches clustering
Authors: Chlis Nikolaos K , Wolf F Alexander , Theis Fabian J
Published: May 2017

Motivation

The identification of heterogeneities in cell populations by utilizing single-cell technologies such as single-cell RNA-Seq, enables inference of cellular development and lineage trees. Several methods have been proposed for such inference from high-dimensional single-cell data. They typically assign each cell to a branch in a differentiation trajectory. However, they commonly assume specific geometries such as tree-like developmental hierarchies and lack statistically sound methods to decide on the number of branching events.

Results

We present K-Branches, a solution to the above problem by locally fitting half-lines to single-cell data, introducing a clustering algorithm similar to K-Means. These halflines are proxies for branches in the differentiation trajectory of cells. We propose a modified version of the GAP statistic for model selection, in order to decide on the number of lines that best describe the data locally. In this manner, we identify the location and number of subgroups of cells that are associated with branching events and full differentiation, respectively. We evaluate the performance of our method on single-cell RNA-Seq data describing the differentiation of myeloid progenitors during hematopoiesis, single-cell qPCR data of mouse blastocyst development, single-cell qPCR data of human myeloid monocytic leukemia and artificial data.

Availability and implementation

An R implementation of K-Branches is freely available at https://github.com/theislab/kbranches.

Supplementary information

Supplementary data are available at Bioinformatics online.
FunGAP: Fungal Genome Annotation Pipeline using evidence-based gene model evaluation
Authors: Min Byoungnam , Grigoriev Igor V , Choi In-Geol
Published: May 2017

Motivation

Successful genome analysis depends on the quality of gene prediction. Although fungal genome sequencing and assembly have become trivial, its annotation procedure has not been standardized yet.

Results

FunGAP predicts protein-coding genes in a fungal genome assembly. To attain high-quality gene models, this program runs multiple gene predictors, evaluates all predicted genes, and assembles gene models that are highly supported by homology to known sequences. To do this, we built a scoring function to estimate the congruency of each gene model based on known protein or domain homology.

Availability and implementation

FunGAP is written in Python script and is available in GitHub (https://github.com/CompSynBioLab-KoreaUniv/FunGAP). This software is freely available only for noncommercial users.

Supplementary information

Supplementary data are available at Bioinformatics online.
Integrative analysis of multiple genomic variables using a hierarchical Bayesian model
Authors: Schäfer Martin , Klein Hans-Ulrich , Schwender Holger
Published: May 2017

Motivation

Genes showing congruent differences in several genomic variables between two biological conditions are crucial to unravel causalities behind phenotypes of interest. Detecting such genes is important in biomedical research, e.g. when identifying genes responsible for cancer development. Small sample sizes common in next-generation sequencing studies are a key challenge, and there are still only very few statistical methods to analyze more than two genomic variables in an integrative, model-based way. Here, we present a novel bioinformatics approach to detect congruent differences between two biological conditions in a larger number of different measurements such as various epigenetic marks or mRNA transcript levels.

Results

We propose a coefficient quantifying the degree to which genes present consistent alterations in multiple (more than two) genomic variables when comparing samples presenting a condition of interest (e.g. cancer) to a reference group. A hierarchical Bayesian model is employed to assess uncertainty on a gene level, incorporating information on functional relationships between genes. We demonstrate the approach on different data sets containing RNA-seq gene transcripton and up to four ChIP-seq histone modification measurements. Both the coefficient-based ranking and the inference based on the model lead to a plausible prioritizing of candidate genes when analyzing multiple genomic variables.

Availability and implementation

BUGS code in the Supplement.

Supplementary information

Supplementary data are available at Bioinformatics online.
Glycan Reader is improved to recognize most sugar types and chemical modifications in the Protein Data Bank
Authors: Park Sang-Jun , Lee Jumin , Patel Dhilon S , Ma Hongjing , Lee Hui Sun , Jo Sunhwan , Im Wonpil
Published: May 2017

Motivation

Glycans play a central role in many essential biological processes. Glycan Reader was originally developed to simplify the reading of Protein Data Bank (PDB) files containing glycans through the automatic detection and annotation of sugars and glycosidic linkages between sugar units and to proteins, all based on atomic coordinates and connectivity information. Carbohydrates can have various chemical modifications at different positions, making their chemical space much diverse. Unfortunately, current PDB files do not provide exact annotations for most carbohydrate derivatives and more than 50% of PDB glycan chains have at least one carbohydrate derivative that could not be correctly recognized by the original Glycan Reader.

Results

Glycan Reader has been improved and now identifies most sugar types and chemical modifications (including various glycolipids) in the PDB, and both PDB and PDBx/mmCIF formats are supported. CHARMM-GUI Glycan Reader is updated to generate the simulation system and input of various glycoconjugates with most sugar types and chemical modifications. It also offers a new functionality to edit the glycan structures through addition/deletion/modification of glycosylation types, sugar types, chemical modifications, glycosidic linkages, and anomeric states. The simulation system and input files can be used for CHARMM, NAMD, GROMACS, AMBER, GENESIS, LAMMPS, Desmond, OpenMM, and CHARMM/OpenMM. Glycan Fragment Database in GlycanStructure.Org is also updated to provide an intuitive glycan sequence search tool for complex glycan structures with various chemical modifications in the PDB.

Availability and implementation

http://www.charmm-gui.org/input/glycan and http://www.glycanstructure.org.

Supplementary information

Supplementary data are available at Bioinformatics online.