bluuebunny/crossref_metadata_2025 huggingface dataset:
Missense-depleted regions in population exomes implicate ras superfamily nucleotide-binding protein alteration in patients with brain malformation
Authors: Ge Xiaoyan , Gong Henry , Dumas Kevin , Litwin Jessica , Phillips Joanna J , Waisfisz Quinten , Weiss Marjan M , Hendriks Yvonne , Stuurman Kyra E , Nelson Stanley F , Grody Wayne W , Lee Hane , Kwok Pui-Yan , Shieh Joseph T C
Published: October 2016

Genomic sequence interpretation can miss clinically relevant missense variants for several reasons. Rare missense variants are numerous in the exome and difficult to prioritise. Affected genes may also not have existing disease association. To improve variant prioritisation, we leverage population exome data to identify intragenic missense-depleted regions (MDRs) genome-wide that may be important in disease. We then use missense depletion analyses to help prioritise undiagnosed disease exome variants. We demonstrate application of this strategy to identify a novel gene association for human brain malformation. We identified de novo missense variants that affect the GDP/GTP-binding site of ARF1 in three unrelated patients. Corresponding functional analysis suggests ARF1 GDP/GTP-activation is affected by the specific missense mutations associated with heterotopia. These findings expand the genetic pathway underpinning neurologic disease that classically includes FLNA. ARF1 along with ARFGEF2 add further evidence implicating ARF/GEFs in the brain. Using functional ontology, top MDR-containing genes were highly enriched for nucleotide-binding function, suggesting these may be candidates for human disease. Routine consideration of MDR in the interpretation of exome data for rare diseases may help identify strong genetic factors for many severe conditions, infertility/reduction in reproductive capability, and embryonic conditions contributing to preterm loss.
Integrated analysis of microRNA and mRNA expression profiles highlights the complex and dynamic behavior of toosendanin-induced liver injury in mice
Authors: Lu Xiaoyan , Ji Cai , Tong Wei , Lian Xueping , Wu Ying , Fan Xiaohui , Gao Yue
Published: October 2016

Triterpenoid Toosendanin (TSN) exhibits a plenty of pharmacological effects in human and great values in agriculture. However, the hepatotoxicity caused by TSN or Melia-family plants containing TSN used in traditional Chinese medicine has been reported and the mechanisms of TSN-induced liver injury (TILI) still remain largely unknown. In this study, the dose- and time-dependent effects of TSN on mice liver were investigated by an integrated microRNA-mRNA approach as well as the general toxicological assessments. As the results, the dose- and time-dependent liver injury and alterations in global microRNA and mRNA expressions were detected. Particularly, 9-days 80 mg/kg TSN exposure caused most serious liver injury in mice and the hepatic adaptation to TILI was unexpectedly observed after 21-days 80 mg/kg TSN administration. Based on the pathway analysis of the intersections between predicted targets of differentially expressed microRNAs and differentially expressed mRNAs at three time points, it revealed that TILI may be caused by glutathione depletion, mitochondrial dysfunction and lipid dysmetabolism, ultimately leading to hepatocytes necrosis in liver, while liver regeneration may play an important role in the hepatic adaptation to TILI. Our results demonstrated that the integrated microRNA−mRNA approach could provide new insight into the complex and dynamic behavior of TILI.
The Impact of Li Grain Size on Coulombic Efficiency in Li Batteries
Authors: Mehdi B. Layla , Stevens Andrew , Qian Jiangfeng , Park Chiwoo , Xu Wu , Henderson Wesley A. , Zhang Ji-Guang , Mueller Karl T. , Browning Nigel D.
Published: October 2016

One of the most promising means to increase the energy density of state-of-the-art lithium Li-ion batteries is to replace the graphite anode with a Li metal anode. While the direct use of Li metal may be highly advantageous, at present its practical application is limited by issues related to dendrite growth and low Coulombic efficiency, CE. Here operando electrochemical scanning transmission electron microscopy (STEM) is used to directly image the deposition/stripping of Li at the anode-electrolyte interface in a Li-based battery. A non-aqueous electrolyte containing small amounts of H2O as an additive results in remarkably different deposition/stripping properties as compared to the “dry” electrolyte when operated under identical electrochemical conditions. The electrolyte with the additive deposits more Li during the first cycle, with the grain sizes of the Li deposits being significantly larger and more variable. The stripping of the Li upon discharge is also more complete, i.e., there is a higher cycling CE. This suggests that larger grain sizes are indicative of better performance by leading to more uniform Li deposition and an overall decrease in the formation of Li dendrites and side reactions with electrolyte components, thus potentially paving the way for the direct use of Li metal in battery technologies.
Room-temperature near-infrared up-conversion lasing in single-crystal Er-Y chloride silicate nanowires
Authors: Ye Rui , Xu Chao , Wang Xingjun , Cui Jishi , Zhou Zhiping
Published: October 2016

Near-infrared up-conversion lasing in erbium(Er)-yttrium(Y) chloride silicate nanowires was demonstrated when pumped by 1476 nm laser at room temperature. The emission covers a very wide wavelength range (400–1000 nm). A clear threshold for 985 nm peak was observed at a launched average pump power of approximately 7 mW. Above threshold, the intensity increases linearly when turning up the pump power. The full width at half maximum at 985 nm decreases from 1.25 nm to 0.25 nm when reducing the measurement temperature from 30 K to 7 K, which is the narrowest linewidth of 980 nm micro-lasers to date. Our demonstration presents a possible novel method of utilizing up-conversion mechanism in Er-Y nanowire to achieve tunable near-infrared laser, which breaks new ground in the exploration of nanoscale optoelectronic devices operating at near-infrared wavelength.
Rapid genomic changes in allopolyploids of Carassius auratus red var. (♀) × Megalobrama amblycephala (♂)
Authors: Qin Qinbo , Lai Zhengfa , Cao Liu , Xiao Qiong , Wang YuDe , Liu Shaojun
Published: October 2016

To better understand genomic changes in the early generations after polyploidisation, we examined the chromosomal consequences of genomic merger in allotetraploid hybrids (4 nF1) (AABB, 4n = 148) of Carassius auratus red var. (RCC) (AA, 2n = 100) (♀) × Megalobrama amblycephala (BSB) (BB, 2n = 48) (♂). Complete loss of the paternal 5S rDNA sequence and the expected number of maternal chromosomal loci were found in 4 nF1, suggesting directional genomic changes occurred in the first generations after polyploidisation. Recent studies have reported instability of newly established allotetraploid genomes. To assess this in the newly formed 4 nF1 genome, we performed fluorescence in situ hybridisation on an allotetraploid gynogenetic hybrid (4 nG) (AABB, 4n = 148) and an allopentaploid hybrid (5 nH) (AABBB, 5n = 172) from 4 nF1 (♀) × BSB (♂) with 5S rDNA gene and centromere probes from RCC, the original diploid parent. The expected numbers of maternal chromosomal loci were found in 4 nG, while chromosomal locus deletions and chromosome recombinations were detected in 5 nH. These observations suggest that abnormal meiosis did not lead to obvious genomic changes in the newly established allotetraploid genomes, but hybridisation with the original diploid parent resulted in obvious genomic changes in the newly established allotetraploid genomes, as was found for the maternal genome.
Dissection of brassinosteroid-regulated proteins in rice embryos during germination by quantitative proteomics
Authors: Li Qian-Feng , Xiong Min , Xu Peng , Huang Li-Chun , Zhang Chang-Quan , Liu Qiao-Quan
Published: October 2016

Brassinosteroids (BRs), essential plant-specific steroidal hormones, function in a wide spectrum of plant growth and development events, including seed germination. Rice is not only a monocotyledonous model plant but also one of the most important staple food crops of human beings. Rice seed germination is a decisive event for the next-generation of plant growth and successful seed germination is critical for rice yield. However, little is known about the molecular mechanisms on how BR modulates seed germination in rice. In the present study, we used isobaric tags for relative and absolute quantification (iTRAQ) based proteomic approach to study BR-regulated proteome during the early stage of seed germination. The results showed that more than 800 BR-responsive proteins were identified, including 88 reliable target proteins responsive to stimuli of both BR-deficiency and BR-insensitivity. Moreover, 90% of the 88 target proteins shared a similar expression change pattern. Gene ontology and string analysis indicated that ribosomal structural proteins, as well as proteins involved in protein biosynthesis and carbohydrate metabolisms were highly clustered. These findings not only enrich BR-regulated protein database in rice seeds, but also allow us to gain novel insights into the molecular mechanism of BR regulated seed germination.
GDF11 improves tubular regeneration after acute kidney injury in elderly mice
Authors: Zhang Ying , Li Qinggang , Liu Dong , Huang Qi , Cai Guangyan , Cui Shaoyuan , Sun Xuefeng , Chen Xiangmei
Published: October 2016

The GDF11 expression pattern and its effect on organ regeneration after acute injury in the elderly population are highly controversial topics. In our study, GDF11/8 expression increased after kidney ischemia–reperfusion injury (IRI), and the relatively lower level of GDF11/8 in the kidneys of aged mice was associated with a loss of proliferative capacity and a decline in renal repair, compared to young mice. In vivo, GDF11 supplementation in aged mice increased vimentin and Pax2 expression in the kidneys as well as the percentage of 5-ethynyl-2′-deoxyuridine (EdU)-positive proximal tubular epithelial cells. GDF11 improved the renal repair, recovery of renal function, and survival of elderly mice at 72 h after IRI. Moreover, the addition of recombinant GDF11 to primary renal epithelial cells increased proliferation, migration, and dedifferentiation by upregulating the ERK1/2 pathway in vitro. Our study indicates that GDF11/8 in the kidney decreases with age and that GDF11 can increase tubular cell dedifferentiation and proliferation as well as improve tubular regeneration after acute kidney injury (AKI) in old mice.
Genes implicated in thiopurine-induced toxicity: Comparing TPMT enzyme activity with clinical phenotype and exome data in a paediatric IBD cohort
Authors: Coelho Tracy , Andreoletti Gaia , Ashton James J. , Batra Akshay , Afzal Nadeem Ahmad , Gao Yifang , Williams Anthony P. , Beattie Robert M. , Ennis Sarah
Published: October 2016

The aim of our study was to assess the utility of next generation sequencing (NGS) for predicting toxicity and clinical response to thiopurine drugs in paediatric patients with inflammatory bowel disease. Exome data for 100 patients were assessed against biochemically measured TPMT enzyme activity, clinical response and adverse effects. The TPMT gene and a panel of 15 other genes implicated in thiopurine toxicity were analysed using a gene based statistical test (SKAT-O test). Nine patients out of 100 (Crohn’s disease- 67, ulcerative colitis- 23 and IBDU-10) had known TPMT mutations associated with deficient enzyme activity. A novel and a highly pathogenic TPMT variant not detectable through standard genotyping, was identified through NGS in an individual intolerant to thiopurines. Of the 14 patients intolerant to thiopurines, NGS identified deleterious TPMT variants in 5 individuals whereas the biochemical test identified 8 individuals as intolerant (sensitivity 35.7% and 57.14%; specificity 93.75% and 50% respectively). SKAT-O test identified a significant association between MOCOS gene and TPMT activity (p = 0.0015), not previously reported. Although NGS has the ability to detect rare or novel variants not otherwise identified through standard genotyping, it demonstrates no clear advantage over the biochemical test in predicting toxicity in our modest cohort.
Correction: Corrigendum: A load of mice to hypergravity causes AMPKα repression with liver injury, which is overcome by preconditioning loads via Nrf2
Authors: Lee Sang Gil , Lee Chan Gyu , Wu Hong Min , Oh Choong Sik , Chung So Won , Kim Sang Geon
Published: October 2016

Scientific Reports 5: Article number: 15643; published online: 23 October 2015; updated: 05 October 2016
Cold tolerance and silencing of three cold-tolerance genes of overwintering Chinese white pine larvae
Authors: Wang Juan , Zhang Ran-Ran , Gao Guan-Qun , Ma Ming-Yuan , Chen Hui
Published: October 2016

The values of physiological indices and the enzymes activities involved in the overwintering stage were studied in D. armandi larvae in each month from October 2014 to March 2015. The sorbitol, trehalose and glycerol values initially tended to increase as the ambient temperature decreased, before declining until the end of the winter. The activities of four enzymes (SOD, CAT, LDH and AchE) decreased, whereas POD, PK and MDH showed opposite trends in activity. Other enzyme activities (those of TPS, SDH and GLK) were low during the overwintering period and later increased and stabilized during spring. In this study, a polymerase chain reaction (PCR) genes of SDH, TPS and GLK was utilized to identify DarmSDH, DarmTPS and DarmGLK in D. armandi. They were found to be abundantly expressed during the overwintering stage by quantitative real-time PCR (qRT-PCR) analyses; by contrast, these three genes showed higher expression levels in December 2014 than in May 2015. The qRT-PCR results demonstrated that the reduction of mRNA expression levels was significant in DarmSDH-, DarmTPS- and DarmGLK-dsRNA-treated D. armandi compared with water-injected and non-injected controls. The mortality responses at low temperature were also increased in the dsRNA-treated D. armandi compared with the controls.
Preserved implicit mentalizing in schizophrenia despite poor explicit performance: evidence from eye tracking
Authors: Roux Paul , Smith Pauline , Passerieux Christine , Ramus Franck
Published: October 2016

Schizophrenia has been characterized by an impaired mentalizing. It has been suggested that distinguishing implicit from explicit processes is crucial in social cognition, and only the latter might be affected in schizophrenia. Two other questions remain open: (1) Is schizophrenia characterized by an hypo- or hyper attribution of intentions? (2) Is it characterized by a deficit in the attribution of intention or of contingency? To test these three questions, spontaneous mentalizing was tested in 29 individuals with schizophrenia and 29 control subjects using the Frith-Happé animations, while eye movements were recorded. Explicit mentalizing was measured from participants’ verbal descriptions and was contrasted with implicit mentalizing measured through eye tracking. As a group, patients made less accurate and less intentional descriptions of the goal-directed and theory of mind animations. No group differences were found in the attribution of contingency. Eye tracking results revealed that patients and controls showed a similar modulation of eye movements in response to the mental states displayed in the Frith-Happé animations. To conclude, in this paradigm, participants with schizophrenia showed a dissociation between explicit and implicit mentalizing, with a decrease in the explicit attribution of intentions, whereas their eye movements suggested a preserved implicit perception of intentions.
Novel population of small tumour-initiating stem cells in the ovaries of women with borderline ovarian cancer
Authors: Virant-Klun Irma , Stimpfel Martin
Published: October 2016

Small stem cells with diameters of up to 5 μm previously isolated from adult human ovaries indicated pluripotency and germinal lineage, especially primordial germ cells, and developed into primitive oocyte-like cells in vitro. Here, we show that a comparable population of small stem cells can be found in the ovarian tissue of women with borderline ovarian cancer, which, in contrast to small stem cells in “healthy” ovaries, formed spontaneous tumour-like structures and expressed some markers related to pluripotency and germinal lineage. The gene expression profile of these small putative cancer stem cells differed from similar cells sorted from “healthy” ovaries by 132 upregulated and 97 downregulated genes, including some important forkhead box and homeobox genes related to transcription regulation, developmental processes, embryogenesis, and ovarian cancer. These putative cancer stem cells are suggested to be a novel population of ovarian tumour-initiating cells in humans.
Racemic drug resolution: a comprehensive guide
Authors: Mane Sachin
Published: October 2016

The human body is amazingly chirally selective, and consequently enantiopure drugs are essential for treating disease. Nowadays, market approval of enantiopure drugs has increased exponentially whereas it has tremendously decreased for racemic and achiral drugs.
Condensation of anthranilic acids with pyridines to furnish pyridoquinazolones via pyridine dearomatization
Authors: Yang Yajun , Zhu Cuiju , Zhang Min , Huang Shijun , Lin Jingjing , Pan Xiandao , Su Weiping
Published: October 2016

The unprecedented carbodiimide-mediated condensation between pyridines and anthranilic acids at room temperature has been developed for pyridoquinazolones.
The catalytic effect of TiO2 nanosheets on extracellular electron transfer of Shewanella loihica PV-4
Authors: Yin Tao , Li Hui , Su Lin , Liu Shuo , Yuan Chunwei , Fu Degang
Published: October 2016

TiO2 nanosheets accelerate the extracellular electron transfer rate of Shewanella loihica PV-4.
Quantitative ionization energies and work functions of aqueous solutions
Authors: Olivieri Giorgia , Goel Alok , Kleibert Armin , Cvetko Dean , Brown Matthew A.
Published: October 2016

Redefining how ionization energies are determined from aqueous solutions: correcting for the electrochemical potential of the solution.
Temperature dependence of acoustic vibrations of CdSe and CdSe–CdS core–shell nanocrystals measured by low-frequency Raman spectroscopy
Authors: Mork A. Jolene , Lee Elizabeth M. Y. , Tisdale William A.
Published: October 2016

Low-temperature Raman spectroscopy reveals inhomogeneous broadening, surprisingly large frequency shifts, and the origin of higher harmonic peaks in core–shell nanocrystals.
Reactive oxygen species generating systems meeting challenges of photodynamic cancer therapy
Authors: Zhou Zijian , Song Jibin , Nie Liming , Chen Xiaoyuan
Published: October 2016

Summary of advanced strategies to generate reactive oxygen species (ROS) through both photodynamic and non-photodynamic procedures for cancer therapy.
Synthesis of a new class of silsesquioxanes with alkynyl and germyl functionality
Authors: Rzonsowska M. , Dudziec B. , Marciniec B.
Published: October 2016

Novel kinds of cubic monosubstituted silsesquioxanes bearing alkynyl and germyl functionality in one molecule were synthesized by germylative coupling reaction.
Characteristic single glucosinolates from Moringa oleifera: Induction of detoxifying enzymes and lack of genotoxic activity in various model systems
Authors: Förster Nadja , Mewis Inga , Glatt Hansruedi , Haack Michael , Brigelius-Flohé Regina , Schreiner Monika , Ulrichs Christian
Published: October 2016

Leaves ofMoringa oleiferaare used by tribes as biological cancer medicine.
Synthesis, crystal growth and characterization of di-valine maleic – a new nonlinear optical material
Authors: Adhikari Soma , Kar Tanusree , Seth Saikat Kumar
Published: October 2016

A new NLO material namely di-valine maleic (VM) was synthesized and characterized by X-ray diffraction analysis. The SHG efficiency of VM was investigated and dipole moment, polarizability, first order hyperpolarizability were calculated by DFT method.
Enhancement of optical gain characteristics of quantum dot films by optimization of organic ligands
Authors: Malak Sidney T. , Lafalce Evan , Jung Jaehan , Lin Chun Hao , Smith Marcus J. , Yoon Young Jun , Lin Zhiqun , Vardeny Z. Valy , Tsukruk Vladimir V.
Published: October 2016

Proper selection of the quantum dot ligand allows for controllable enhancement of optical gain characteristics (threshold, magnitude, and stability) in quantum dot films.
Design and validation of a large-format transition edge sensor array magnetic shielding system for space application
Authors: Bergen A. , van Weers H. J. , Bruineman C. , Dhallé M. M. J. , Krooshoop H. J. G. , ter Brake H. J. M. , Ravensberg K. , Jackson B. D. , Wafelbakker C. K.
Published: October 2016

The paper describes the development and the experimental validation of a cryogenic magnetic shielding system for transition edge sensor based space detector arrays. The system consists of an outer mu-metal shield and an inner superconducting niobium shield. First, a basic comparison is made between thin-walled mu-metal and superconducting shields, giving an off-axis expression for the field inside a cup-shaped superconductor as a function of the transverse external field. Starting from these preliminary analytical considerations, the design of an adequate and realistic shielding configuration for future space flight applications (either X-IFU [D. Barret et al., e-print arXiv:1308.6784 [astro-ph.IM] (2013)] or SAFARI [B. Jackson et al., IEEE Trans. Terahertz Sci. Technol. 2, 12 (2012)]) is described in more detail. The numerical design and verification tools (static and dynamic finite element method (FEM) models) are discussed together with their required input, i.e., the magnetic-field dependent permeability data. Next, the actual manufacturing of the shields is described, including a method to create a superconducting joint between the two superconducting shield elements that avoid flux penetration through the seam. The final part of the paper presents the experimental verification of the model predictions and the validation of the shield’s performance. The shields were cooled through the superconducting transition temperature of niobium in zero applied magnetic field (<10 nT) or in a DC field with magnitude ∼100 μT, applied either along the system’s symmetry axis or perpendicular to it. After cool-down, DC trapped flux profiles were measured along the shield axis with a flux-gate magnetometer and the attenuation of externally applied AC fields (100 μT, 0.1 Hz, both axial and transverse) was verified along this axis with superconducting quantum interference device magnetometers. The system’s measured on-axis shielding factor is greater than 106, well exceeding the requirement of the envisaged missions. Following field-cooling in an axial field of 85 μT, the residual internal DC field normal to the detector plane is less than 1 μT. The trapped field patterns are compared to the predictions of the dynamic FEM model, which describes them well in the region where the internal field exceeds 6 μT.
Spall fracture in additive manufactured Ti-6Al-4V
Authors: Jones D. R. , Fensin S. J. , Dippo O. , Beal R. A. , Livescu V. , Martinez D. T. , Trujillo C. P. , Florando J. N. , Kumar M. , Gray G. T.
Published: October 2016

We present a study on the spall strength of additive manufactured (AM) Ti-6Al-4V. Samples were obtained from two pieces of selective laser melted (SLM, a powder bed fusion technique) Ti-6Al-4V such that the response to dynamic tensile loading could be investigated as a function of the orientation between the build layers and the loading direction. A sample of wrought bar-stock Ti-6Al-4V was also tested to act as a baseline representing the traditionally manufactured material response. A single-stage light gas-gun was used to launch a thin flyer plate into the samples, generating a region of intense tensile stress on a plane normal to the impact direction. The rear free surface velocity time history of each sample was recorded with laser-based velocimetry to allow the spall strength to be calculated. The samples were also soft recovered to enable post-mortem characterization of the spall damage evolution. Results showed that when the tensile load was applied normal to the interfaces between the build layers caused by the SLM fabrication process the spall strength was drastically reduced, dropping to 60% of that of the wrought material. However, when loaded parallel to the AM build layer interfaces the spall strength was found to remain at 95% of the wrought control, suggesting that when loading normal to the AM layer interfaces, void nucleation is facilitated more readily due to weaknesses along these boundaries. Quasi-static testing of the same sample orientations revealed a much lower degree of anisotropy, demonstrating the importance of rate-dependent studies for damage evolution in AM materials.
The physics of pressure variation in microchannels within corotating or static discs
Authors: Guha Abhijit , Sengupta Sayantan
Published: October 2016

We formulate a comprehensive analysis for the radial pressure variation in flow through microchannels within corotating (or static) discs, which is important for its fundamental value and application potential in macrofluidic and microfluidic devices. The uniqueness and utility of the present approach emanate from our ability to describe the physics completely in terms of non-dimensional numbers and to determine quantitatively the separate roles of inertia, centrifugal force, Coriolis force, and viscous effects in the overall radial pressure difference (Δpio). It is established here that the aspect ratio (ratio of inter-disc spacing and disc radius) plays only a secondary role as an independent parameter, its major role being contained within a newly identified dynamic similarity number (Ds). For radial inflow, it is shown that the magnitude of Δpio decreases monotonically as the tangential speed ratio (γ) increases but exhibits a minima when Ds is varied. For radial outflow, it is shown that Δpio increases monotonically as the flow coefficient (ϕ) decreases but evinces a maxima when Ds is varied. It is further shown that for the radial inflow case, the minima in the magnitude of Δpio exist even when the rotational speed of the discs is reduced to zero (static discs). The demonstrated existence of these extrema (i.e., minima for radial inflow and maxima for radial outflow) creates the scope for device optimization.
Envelope equation for the linear and nonlinear propagation of an electron plasma wave, including the effects of Landau damping, trapping, plasma inhomogeneity, and the change in the state of wave
Authors: Bénisti Didier
Published: October 2016

This paper addresses the linear and nonlinear three-dimensional propagation of an electron wave in a collisionless plasma that may be inhomogeneous, nonstationary, anisotropic, and even weakly magnetized. The wave amplitude, together with any hydrodynamic quantity characterizing the plasma (density, temperature, etc.) is supposed to vary very little within one wavelength or one wave period. Hence, the geometrical optics limit is assumed, and the wave propagation is described by a first order differential equation. This equation explicitly accounts for three-dimensional effects, plasma inhomogeneity, Landau damping, and the collisionless dissipation and electron acceleration due to trapping. It is derived by mixing results obtained from a direct resolution of the Vlasov-Poisson system and from a variational formalism involving a nonlocal Lagrangian density. In a one-dimensional situation, abrupt transitions are predicted in the coefficients of the wave equation. They occur when the state of the electron plasma wave changes, from a linear wave to a wave with trapped electrons. In a three dimensional geometry, the transitions are smoother, especially as regards the nonlinear Landau damping rate, for which a very simple effective and accurate analytic expression is provided.
Observation of anisotropic distribution of microstructure in GaP/GaAs epitaxial layers
Authors: Kumar Ravi , Dixit V. K. , Ganguli Tapas , Mukherjee C. , Srivastava A. K. , Sharma T. K.
Published: October 2016

Anisotropic distribution of microstructure in GaP/GaAs epitaxial layers is investigated by performing high resolution x-ray diffraction (HRXRD) experiments for symmetric reflections at different azimuths. The observed anisotropy leads to the different values of lattice relaxation along the [011¯] and [01¯1¯] directions as revealed by the reciprocal space maps recorded at 0° and 90° azimuths for (42¯2¯) and (422¯) reflections. The anisotropic relaxation process causes large differences in the full width at half maximum of (400) diffraction peaks of omega scans along the [011¯] and [01¯1¯] directions. It therefore provides large differences in the values of microstructural parameters of the GaP epitaxial layer along the two in-plane orthogonal directions. A systematic Williamson-Hall analysis of HRXRD data confirms the presence of large anisotropy of lattice relaxation process along the [011¯] and [01¯1¯] directions. Due to the large lattice mismatch, the GaP/GaAs epilayer presented here possesses grain boundaries and the broadening of the HRXRD pattern is strongly affected by the anisotropy of microstructure and dislocations. The kinetics of dislocations is discussed where it is observed that the misfit strain is primarily relieved by 90° partial dislocations up to a certain thickness of epilayer and thereafter the nucleation of 60° perfect dislocations dominates the strain relaxation process. The effect of the anisotropic distribution of relaxation process is also seen in the surface topography of GaP epilayer as revealed by atomic force microscopy images. The origin of the anisotropic distribution of dislocations is explained by considering the Burgers vector network, and its consequences are also observed in the cross sectional transmission electron microscopy images.
Lattice Boltzmann simulation of separation phenomenon in a binary gaseous flow through a microchannel
Authors: Wang Liang , Xu Zimian , Guo Zhaoli
Published: October 2016

Gas separation of a binary gaseous mixture is one of the characteristic phenomena in the micro-scale flows that differ from the conventional size flows. In this work, the separation in binary gas mixture flows through a microchannel is investigated by the lattice Boltzmann method with a diffuse-bounce-back boundary condition, where the wall function approach with effective relaxation time is combined in consideration of the high Knudsen numbers. The separation degree and rate are measured in the He–Ar and Ne–Ar systems for different mole fractions, pressure ratios, and Knudsen numbers. The results show that the separation phenomenon in the He–Ar mixture is more obvious than that in the Ne–Ar mixture at the same mole fraction owing to the larger molecular mass ratio. In addition, the increase in the pressure ratio reduces the difference in the molecular velocities between the two species, and the separation phenomenon becomes weaker. However, the gas separation is reduced with an increase in the Knudsen number. This is because the resulting rarefaction effect reduces the interactions between the gas molecules of the two species and thus increases the difference in the molecular velocity.
Raman scattering and photoluminescence investigations of N doped ZnO thin films: Local vibrational modes and induced ferromagnetism
Authors: Jindal Kajal , Tomar Monika , Katiyar R. S. , Gupta Vinay
Published: October 2016

N doped ZnO (ZnO:N) thin films are prepared by pulsed laser deposition in an oxygen environment using ZnO:N targets with varying nitrogen doping concentrations (1%–10%). The impact of nitrogen incorporation on the microstructural properties of prepared ZnO:N thin films has been studied using Raman scattering. The Raman shift of E2(high) mode towards lower frequencies indicate the substitution of N at O lattice sites (NO). A local vibrational mode corresponding to Zn–N was observed at 480.3 cm−1 in N doped ZnO thin films and highlights the increased strength of the Zn–N bond in the ZnO lattice. Photoluminescence studies reveal the dominant near band edge emission peak in the ultraviolet region and the absence of deep level emission due to defects. The ZnO:N thin films are found to possess room temperature ferromagnetism. N is found to play a significant role in arising ferromagnetism in ZnO and possess a solubility limit of 8% for uniform and homogeneous atomic substitution in ZnO. The present study confirms the promising application of N doped ZnO (ZnO:N) thin films for room temperature spintronics applications.
Opto-acoustic effects in an array of carbon nanotubes
Authors: Zhukov Alexander V. , Bouffanais Roland , Konobeeva Natalia N. , Belonenko Mikhail B.
Published: October 2016

In this paper, we investigate the propagation of electromagnetic waves in a piezoelectric composite comprising carbon nanotubes and piezoelectric fibers. This hybrid medium is initially subjected to the effects of an extremely short optical pulse consisting of just two oscillations of the electric field. On the basis of Maxwell's equations and the wave equation for the displacement vector of the medium, we obtain an effective governing equation for the vector potential of the electromagnetic field, as well as the displacement vector for the media. The dependence of the pulse shape on the parameters of the problem was analyzed, thereby revealing a non-trivial interplay between the characteristics of the pulse dynamics and the electrically induced mechanical vibrations of the medium. The uncovered properties could potentially offer promising prospects for the development of new materials for the optoelectronics industry.
General theory of the plasmoid instability
Authors: Comisso L. , Lingam M. , Huang Y.-M. , Bhattacharjee A.
Published: October 2016

A general theory of the onset and development of the plasmoid instability is formulated by means of a principle of least time. The scaling relations for the final aspect ratio, transition time to rapid onset, growth rate, and number of plasmoids are derived and shown to depend on the initial perturbation amplitude (ŵ0), the characteristic rate of current sheet evolution (1/τ), and the Lundquist number (S). They are not simple power laws, and are proportional to Sατβ[ln f(S,τ,ŵ0)]σ. The detailed dynamics of the instability is also elucidated, and shown to comprise of a period of quiescence followed by sudden growth over a short time scale.
Black carbon solar absorption suppresses turbulence in the atmospheric boundary layer
Authors: Wilcox Eric M. , Thomas Rick M. , Praveen Puppala S. , Pistone Kristina , Bender Frida A.-M. , Ramanathan Veerabhadran
Published: October 2016

Significance

The cooling effect of aerosols on climate and the modification of clouds by aerosols have been widely debated, because quantifying their effects is important for constraining current climate change. Here we present measurements of turbulence from unmanned aerial vehicles. We find that absorption of sunlight by black carbon (BC) aerosols suppresses turbulence in the lower atmosphere, with important consequences for the environmental impacts of BC emissions from anthropogenic fossil fuel and biomass burning. A mechanism is proposed that links the suppressed turbulence to taller clouds. These results highlight the importance of understanding and observing the role of turbulence in studies of aerosol impacts on clouds. Suppressed turbulence also exacerbates the visibility and human health impacts of pollution.
Sustained antigen availability during germinal center initiation enhances antibody responses to vaccination
Authors: Tam Hok Hei , Melo Mariane B. , Kang Myungsun , Pelet Jeisa M. , Ruda Vera M. , Foley Maria H. , Hu Joyce K. , Kumari Sudha , Crampton Jordan , Baldeon Alexis D. , Sanders Rogier W. , Moore John P. , Crotty Shane , Langer Robert , Anderson Daniel G. , Chakraborty Arup K. , Irvine Darrell J.
Published: October 2016

Significance

We explored the effect of nontraditional vaccine dosing profiles on antibody titers of vaccines and discovered that certain dosing profiles demonstrate >10-fold higher antibody production than the traditional single-dose prime–boost method. We also present a computational model that captures the experimental results and provides a mechanistic understanding of the biology behind the effectiveness of our strategy. This work has clinical significance in vaccine design because it is a simple method to increase the efficacy of subunit vaccines, which may lead to the development of efficacious vaccines for diseases such as HIV.
Nonlinear two-dimensional terahertz photon echo and rotational spectroscopy in the gas phase
Authors: Lu Jian , Zhang Yaqing , Hwang Harold Y. , Ofori-Okai Benjamin K. , Fleischer Sharly , Nelson Keith A.
Published: October 2016

Significance

Molecular rotations of small molecules provide a useful testbed for examining light−matter interactions with quantum mechanical systems, but the methods of modern spectroscopy have been largely unavailable in the terahertz frequency range where most of the rotational states that are thermally populated at ordinary temperatures absorb light. Applying a pair of strong terahertz pulses, we excite molecular rotations coherently, interrogate thermally populated rotational states, manipulate the rotational motions nonlinearly, and observe connections between different rotational states spectroscopically. The method is applicable to polar molecules in flames and other reactive conditions, and it enables enhanced control over molecular motion with light.
Allelic barley MLA immune receptors recognize sequence-unrelated avirulence effectors of the powdery mildew pathogen
Authors: Lu Xunli , Kracher Barbara , Saur Isabel M. L. , Bauer Saskia , Ellwood Simon R. , Wise Roger , Yaeno Takashi , Maekawa Takaki , Schulze-Lefert Paul
Published: October 2016

Significance

Gene-for-gene immunity is frequently found in interactions between plants and host-adapted pathogens and reflects population-level diversification of immune receptors detecting matching pathogen effectors. We identified effector genes of a pathogenic powdery mildew fungus that are recognized by allelic variants of barley intracellular nucleotide-binding domain and leucine-rich repeat protein-type receptors. These pathogen effectors are phylogenetically unrelated, demonstrating that allelic immune receptors can evolve to recognize sequence-unrelated proteins. Conserved effector recognition in distantly related
Arabidopsis
indicates that the underlying mechanism is not restricted to monocotyledonous plants. Furthermore, our study reveals that the expression of a fungal avirulence effector alone is necessary and sufficient for allele-specific mildew resistance locus A receptor activation in planta
.
Mutational landscape of
EGFR-
,
MYC-
, and
Kras-
driven genetically engineered mouse models of lung adenocarcinoma
Authors: McFadden David G. , Politi Katerina , Bhutkar Arjun , Chen Frances K. , Song Xiaoling , Pirun Mono , Santiago Philip M. , Kim-Kiselak Caroline , Platt James T. , Lee Emily , Hodges Emily , Rosebrock Adam P. , Bronson Roderick T. , Socci Nicholas D. , Hannon Gregory J. , Jacks Tyler , Varmus Harold
Published: October 2016

Significance

Knowledge of oncogenic alterations that drive lung adenocarcinoma formation has enabled the development of genetically engineered mouse models that are increasingly being used to study the biology and therapeutic vulnerabilities of this disease. Given the importance of genomic alterations in these processes in human lung cancer, information on the mutational landscape of the mouse tumors is valuable for the design and interpretation of these experiments. In this study, we compared whole-exome sequencing data from lung adenocarcinomas induced by different lung adenocarcinoma-associated drivers. In contrast to their human counterparts, oncogene-driven lung adenocarcinomas in genetically engineered mouse models harbor few somatic mutations. These results have important implications for the use of these models to study tumor progression and response and resistance to therapy.
Intergenerational Analysis of Patronymic Transformations in the Quebec (Canada) Population Since the Seventeenth Century
Authors: Tremblay Marc
Published: October 2016

Surnames may undergo several transformations over time. Thus, patronymic distributions observed in a population at a given time may hide changes that occurred previously, the extent of which can be estimated with intergenerational data. Using a corpus of 5,100 deep-rooted ascending genealogies from the Quebec (Canada) population, this study compares contemporary surnames with those of founding ancestors in each paternal line and identifies various patronymic mutations occurring over multiple generations. On average, paternal lines go back eight generations. About one-third of all paternal lines presented at least one orthographic difference between the contemporary and the original surnames. Many surnames were transformed several times in a single paternal line, and some changes were different for a given surname along different lines. Most changes occurred among the first generations following that of the founding ancestors. Regional comparisons also show important variations.
PPARγ attenuates hypoxia‐induced hypertrophic transcriptional pathways in the heart
Authors: Chaudhry Abubakr , Carthan Kristal A. , Kang Bum‐Yong , Calvert John , Sutliff Roy L. , Michael Hart C.
Published: October 2016

Chronic hypoxia‐induced pulmonary hypertension (PH) is characterized by increased pressure and resistance in the pulmonary vasculature and hypertrophy of the right ventricle (RV). The transcription factors, nuclear factor activated T‐cells (NFAT), and nuclear factor kappa‐light‐chain‐enhancer of activated B cells (NF‐κB/p65) contribute to RV hypertrophy (RVH). Because peroxisome proliferator‐activated receptor gamma (PPARγ) activation attenuates hypoxia‐induced PH and RVH, we hypothesized that PPARγ inhibits activation of RV hypertrophic transcriptional signaling mechanisms. C57BL/6J mice were exposed to normoxia (21% O2) or hypoxia (10% O2) for 21 days. During the final 10 days of exposure, selected mice were treated with the PPARγ ligand, pioglitazone. RV systolic pressure (RVSP) and RVH were measured, and NFATc2 and NF‐kB/p65 protein levels were measured in RV and LV nuclear and cytosolic fractions. Cardiomyocyte hypertrophy was assessed with wheatgerm agglutinin staining. NFAT activation was also examined with luciferase reporter mice and analysis of protein levels of selected transcriptional targets. Chronic‐hypoxia increased: (1) RVH, RVSP, and RV cardiomyocyte hypertrophy; (2) NFATc2 and NF‐κB activation in RV nuclear homogenates; (3) RV and LV NFAT luciferase activity; and (4) RV protein levels of brain natriuretic peptide (BNP) and β‐myosin heavy chain (β‐MyHC). Treatment with pioglitazone attenuated hypoxia‐induced increases in both RV and LV NFAT luciferase activity. Chronic hypoxia caused sustained RV NFATc2 and NF‐κB activation. Pioglitazone attenuated PH, RVH, cardiomyocyte hypertrophy, and activation of RV hypertrophic signaling and also attenuated LV NFAT activation. PPARγ favorably modulates signaling derangements in the heart as well as in the pulmonary vascular wall.
Vitamin D3: Preconcentration and Determination in Cereal Samples Using Ultrasonic‐Assisted Extraction and Microextraction Method
Authors: Kamankesh Marzieh , Mohammadi Abdorreza , Mollahosseini Afsaneh , Jazaeri Sahar , Shahdoostkhany Mehrnoosh
Published: October 2016

This research is the first analytical method to isolate and determine cholecalciferol (vitamin D3) in cereal samples. Ultrasonic‐assisted extraction followed by dispersive liquid‐liquid microextraction as a fast, reliable, and highly sensitive method was employed for the preconcentration step. High‐performance liquid chromatography allowed an efficient and considerably faster analysis. Alcoholic KOH solution was employed for accomplishing the fast and easy release of vitamin D3 from the wheat flour and bread matrix. Effective factors in the microextraction process were investigated and optimized with response surface methodology based on a central composite design. Under the best conditions, the calibration curves showed high levels of linearity (R2 > 0.999) for vitamin D3 in the range of 2–500 ng/g. The relative standard deviation for the seven analyses was 6.2%. The relative recoveries of vitamin D3 in spiked wheat flour and bread samples were 87–98%. The limit of detection and limit of quantitation were 0.7 and 2.1 ng/g, respectively. The method compared favorably with other methods for vitamin D3 analysis of various foods.
Temporal Dynamics of Botrytis cinerea and Sclerotinia sclerotiorum in Seed Alfalfa Fields of Southern Alberta, Canada
Authors: Reich J. , Chatterton S. , Johnson D.
Published: October 2016

Blossom blight of seed alfalfa (Medicago sativa L.), caused by the fungal pathogens Botrytis cinerea and Sclerotinia sclerotiorum, is a potentially devastating disease on the Canadian Prairies in moist growing seasons. Monitoring the airborne spore concentrations of these pathogens could facilitate disease forecasting in the region. Nineteen seed alfalfa fields in southern Alberta, Canada were assessed throughout the growing seasons of 2014 and 2015. Trace levels of blossom blight symptoms were found in both years; however, plated floret and pod samples indicated that, overall, B. cinerea increased over the growing season whereas S. sclerotiorum decreased. In both seasons, Burkard 7-day volumetric spore samplers collected daily aerosol samples, and weather stations recorded environmental variables in three fields. Conidia and ascospores collected were quantified each day with a real-time polymerase chain reaction assay. Spore quantification indicated that both B. cinerea and S. sclerotiorum numbers remained low in July and increased in August. Both species had multiple days with high spore discharge, with seasonal maxima of 21,137 conidia and 2,265 ascospores. Exploratory model development indicated that spore discharge of both fungi is associated with environmental stressors such as large changes in relative humidity or high temperatures on preceding days.
Mining Vavilov’s Treasure Chest of Wheat Diversity for Adult Plant Resistance to Puccinia triticina
Authors: Riaz Adnan , Athiyannan Naveenkumar , Periyannan Sambasivam , Afanasenko Olga , Mitrofanova Olga , Aitken Elizabeth A. B. , Lagudah Evans , Hickey Lee T.
Published: October 2016

Leaf rust (LR) caused by Puccinia triticina, is among the most important diseases of wheat (Triticum aestivum L.) crops globally. Deployment of cultivars incorporating genetic resistance, such as adult plant resistance (APR) or all-stage resistance, is considered the most sustainable control method. APR is preferred for durability because it places lower selection pressure on the pathogen and is often polygenic. In the search for new sources of APR, here we explored a diversity panel sourced from the N. I. Vavilov Institute of Plant Genetic Resources. Based on DNA marker screening, 83 of the 300 lines were deemed to carry known APR genes; namely, Lr34, Lr46, and Lr67. Interestingly, lines carrying Lr67 were mostly landraces from India and Pakistan, reconfirming the likely origin of the gene. Rapid phenotypic screening using a method that integrates assessment at both seedling and adult growth stages under accelerated growth conditions (i.e., constant light and controlled temperature) identified 50 lines carrying APR. Levels of APR corresponded well with phenotypes obtained in a field nursery inoculated using the same pathotype (R2 = 0.82). The second year of field testing, using a mixture of pathotypes with additional virulence for race-specific APR genes (Lr13 and Lr37), identified a subset of 13 lines that consistently displayed high levels of APR across years and pathotypes. These lines provide useful sources of resistance for future research. A strategy combining rapid generation advance coupled with phenotyping under controlled conditions could accelerate introgression of these potentially novel alleles into adapted genetic backgrounds.