bluuebunny/crossref_metadata_2025 huggingface dataset:
Sample storage conditions significantly influence faecal microbiome profiles
Authors: Choo Jocelyn M , Leong Lex EX , Rogers Geraint B
Published: November 2015

Sequencing-based studies of the human faecal microbiota are increasingly common. Appropriate storage of sample material is essential to avoid the introduction of post-collection bias in microbial community composition. Rapid freezing to −80 °C is commonly considered to be best-practice. However, this is not feasible in many studies, particularly those involving sample collection in participants’ homes. We determined the extent to which a range of stabilisation and storage strategies maintained the composition of faecal microbial community structure relative to freezing to −80 °C. Refrigeration at 4 °C, storage at ambient temperature and the use of several common preservative buffers (RNAlater, OMNIgene.GUT, Tris-EDTA) were assessed relative to freezing. Following 72 hours of storage, faecal microbial composition was assessed by 16 S rRNA amplicon sequencing. Refrigeration was associated with no significant alteration in faecal microbiota diversity or composition. However, samples stored using other conditions showed substantial divergence compared to −80 °C control samples. Aside from refrigeration, the use of OMNIgene.GUT resulted in the least alteration, while the greatest change was seen in samples stored in Tris-EDTA buffer. The commercially available OMNIgene.GUT kit may provide an important alternative where refrigeration and cold chain transportation is not available.
Silver nanowires decorated with silver nanoparticles for low-haze flexible transparent conductive films
Authors: Menamparambath Mini Mol , Muhammed Ajmal C. , Kim Kwang Hee , Yang Daejin , Roh Jongwook , Park Hyeon Cheol , Kwak Chan , Choi Jae-Young , Baik Seunghyun
Published: November 2015

Silver nanowires have attracted much attention for use in flexible transparent conductive films (TCFs) due to their low sheet resistance and flexibility. However, the haze was too high for replacing indium-tin-oxide in high-quality display devices. Herein, we report flexible TCFs, which were prepared using a scalable bar-coating method, with a low sheet resistance (24.1 Ω/sq at 96.4% transmittance) and a haze (1.04%) that is comparable to that of indium-tin-oxide TCFs. To decrease the haze and maintain a low sheet resistance, small diameter silver nanowires (~20 nm) were functionalized with low-temperature surface-sintering silver nanoparticles (~5 nm) using bifunctional cysteamine. The silver nanowire-nanoparticle ink stability was excellent. The sheet resistance of the TCFs was decreased by 29.5% (from 34.2 to 24.1 Ω/sq) due to the functionalization at a low curing temperature of 85 °C. The TCFs were highly flexible and maintained their stability for more than 2 months and 10,000 bending cycles after coating with a protective layer.
Universal Quake Statistics: From Compressed Nanocrystals to Earthquakes
Authors: Uhl Jonathan T. , Pathak Shivesh , Schorlemmer Danijel , Liu Xin , Swindeman Ryan , Brinkman Braden A. W. , LeBlanc Michael , Tsekenis Georgios , Friedman Nir , Behringer Robert , Denisov Dmitry , Schall Peter , Gu Xiaojun , Wright Wendelin J. , Hufnagel Todd , Jennings Andrew , Greer Julia R. , Liaw P. K. , Becker Thorsten , Dresen Georg , Dahmen Karin A.
Published: November 2015

Slowly-compressed single crystals, bulk metallic glasses (BMGs), rocks, granular materials and the earth all deform via intermittent slips or “quakes”. We find that although these systems span 12 decades in length scale, they all show the same scaling behavior for their slip size distributions and other statistical properties. Remarkably, the size distributions follow the same power law multiplied with the same exponential cutoff. The cutoff grows with applied force for materials spanning length scales from nanometers to kilometers. The tuneability of the cutoff with stress reflects “tuned critical” behavior, rather than self-organized criticality (SOC), which would imply stress-independence. A simple mean field model for avalanches of slipping weak spots explains the agreement across scales. It predicts the observed slip-size distributions and the observed stress-dependent cutoff function. The results enable extrapolations from one scale to another and from one force to another, across different materials and structures, from nanocrystals to earthquakes.
Role of Integrin β4 in Lung Endothelial Cell Inflammatory Responses to Mechanical Stress
Authors: Chen Weiguo , Epshtein Yulia , Ni Xiuquin , Dull Randal O. , Cress Anne E. , Garcia Joe G.N. , Jacobson Jeffrey R.
Published: November 2015

Simvastatin, an HMG-CoA reductase inhibitor, has lung vascular-protective effects that are associated with decreased agonist-induced integrin β4 (ITGB4) tyrosine phosphorylation. Accordingly, we hypothesized that endothelial cell (EC) protection by simvastatin is dependent on these effects and sought to further characterize the functional role of ITGB4 as a mediator of EC protection in the setting of excessive mechanical stretch at levels relevant to ventilator-induced lung injury (VILI). Initially, early ITGB4 tyrosine phosphorylation was confirmed in human pulmonary artery EC subjected to excessive cyclic stretch (18% CS). EC overexpression of mutant ITGB4 with specific tyrosines mutated to phenylalanine (Y1440, Y1526 Y1640, or Y1422) resulted in significantly attenuated CS-induced cytokine expression (IL6, IL-8, MCP-1 and RANTES). In addition, EC overexpression of ITGB4 constructs with specific structural deletions also resulted in significantly attenuated CS-induced inflammatory cytokine expression compared to overexpression of wildtype ITGB4. Finally, mice expressing a mutant ITGB4 lacking a cytoplasmic signaling domain were found to have attenuated lung injury after VILI-challenge (VT = 40 ml/kg, 4 h). Our results provide mechanistic insights into the anti-inflammatory properties of statins and may ultimately lead to novel strategies targeted at ITGB4 signaling to treat VILI.
Biocompatible fluorescent supramolecular nanofibrous hydrogel for long-term cell tracking and tumor imaging applications
Authors: Wang Huaimin , Mao Duo , Wang Youzhi , Wang Kai , Yi Xiaoyong , Kong Deling , Yang Zhimou , Liu Qian , Ding Dan
Published: November 2015

Biocompatible peptide-based supramolecular hydrogel has recently emerged as a new and promising system for biomedical applications. In this work, Rhodamine B is employed as a new capping group of self-assembling peptide, which not only provides the driving force for supramolecular nanofibrous hydrogel formation, but also endows the hydrogel with intrinsic fluroescence signal, allowing for various bioimaging applications. The fluorescent peptide nanofibrous hydrogel can be formed via disulfide bond reduction. After dilution of the hydrogel with aqueous solution, the fluorescent nanofiber suspension can be obtained. The resultant nanofibers are able to be internalized by the cancer cells and effectively track the HeLa cells for as long as 7 passages. Using a tumor-bearing mouse model, it is also demonstrated that the fluorescent supramolecular nanofibers can serve as an efficient probe for tumor imaging in a high-contrast manner.
Selective interlayer ferromagnetic coupling between the Cu spins in YBa2Cu3O7−x grown on top of La0.7Ca0.3MnO3
Authors: Huang S. W. , Wray L. Andrew , Jeng Horng-Tay , Tra V. T. , Lee J. M. , Langner M. C. , Chen J. M. , Roy S. , Chu Y. H. , Schoenlein R. W. , Chuang Y.-D. , Lin J.-Y.
Published: November 2015

Studies to date on ferromagnet/d-wave superconductor heterostructures focus mainly on the effects at or near the interfaces while the response of bulk properties to heterostructuring is overlooked. Here we use resonant soft x-ray scattering spectroscopy to reveal a novelc-axis ferromagnetic coupling between the in-plane Cu spins in YBa2Cu3O7−x(YBCO) superconductor when it is grown on top of ferromagnetic La0.7Ca0.3MnO3(LCMO) manganite layer. This coupling, present in both normal and superconducting states of YBCO, is sensitive to the interfacial termination such that it is only observed in bilayers with MnO2but not with La0.7Ca0.3O interfacial termination. Such contrasting behaviors, we propose, are due to distinct energetic of CuO chain and CuO2plane at the La0.7Ca0.3O and MnO2terminated interfaces respectively, therefore influencing the transfer of spin-polarized electrons from manganite to cuprate differently. Our findings suggest that the superconducting/ferromagnetic bilayers with proper interfacial engineering can be good candidates for searching the theorized Fulde-Ferrel-Larkin-Ovchinnikov (FFLO) state in cuprates and studying the competing quantum orders in highly correlated electron systems.
Optogenetic stimulation reveals distinct modulatory properties of thalamostriatal vs corticostriatal glutamatergic inputs to fast-spiking interneurons
Authors: Sciamanna Giuseppe , Ponterio Giulia , Mandolesi Georgia , Bonsi Paola , Pisani Antonio
Published: November 2015

Parvalbumin-containing fast-spiking interneurons (FSIs) exert a powerful feed-forward GABAergic inhibition on striatal medium spiny neurons (MSNs), playing a critical role in timing striatal output. However, how glutamatergic inputs modulate their firing activity is still unexplored. Here, by means of a combined optogenetic and electrophysiological approach, we provide evidence for a differential modulation of cortico- vs thalamo-striatal synaptic inputs to FSIs in transgenic mice carrying light-gated ion channels channelrhodopsin-2 (ChR2) in glutamatergic fibers. Corticostriatal synapses show a postsynaptic facilitation, whereas thalamostriatal synapses present a postsynaptic depression. Moreover, thalamostriatal synapses exhibit more prominent AMPA-mediated currents than corticostriatal synapses and an increased release probability. Furthermore, during current-evoked firing activity, simultaneous corticostriatal stimulation increases bursting activity. Conversely, thalamostriatal fiber activation shifts the canonical burst-pause activity to a more prolonged, regular firing pattern. However, this change in firing pattern was accompanied by a significant rise in the frequency of membrane potential oscillations. Notably, the responses to thalamic stimulation were fully abolished by blocking metabotropic glutamate 1 (mGlu1) receptor subtype, whereas both acetylcholine and dopamine receptor antagonists were ineffective. Our findings demonstrate that cortical and thalamic glutamatergic input differently modulate FSIs firing activity through specific intrinsic and synaptic properties, exerting a powerful influence on striatal outputs.
High spectral response of self-driven GaN-based detectors by controlling the contact barrier height
Authors: Sun Xiaojuan , Li Dabing , Li Zhiming , Song Hang , Jiang Hong , Chen Yiren , Miao Guoqing , Zhang Zhiwei
Published: November 2015

High spectral response of self-driven GaN-based ultraviolet detectors with interdigitated finger geometries were realized using interdigitated Schottky and near-ohmic contacts. Ni/GaN/Cr, Ni/GaN/Ag and Ni/GaN/Ti/Al detectors were designed with zero bias responsivities proportional to the Schottky barrier difference between the interdigitated contacts of 0.037 A/W, 0.083 A/W and 0.104 A/W, respectively. Voltage-dependent photocurrent was studied, showing high gain under forward bias. Differences between the electron and hole mobility model and the hole trapping model were considered to be the main photocurrent gain mechanism. These detectors operate in photoconductive mode with large photocurrent gain and depletion mode with high speed and can extend GaN-based metal-semiconductor-metal detector applications.
Subthreshold depression is associated with impaired resting-state functional connectivity of the cognitive control network
Authors: Hwang J W , Egorova N , Yang X Q , Zhang W Y , Chen J , Yang X Y , Hu L J , Sun S , Tu Y , Kong J
Published: November 2015

Subthreshold depression (StD) is a prevalent condition associated with social morbidity and increased service utilization, as well as a high risk of developing into a major depressive disorder (MDD). The lack of well-defined diagnostic criteria for StD has limited research on this disorder, with very few brain-imaging studies examining the neurobiology of StD. Yet, identifying the neural pathology of StD has the potential to elucidate risk factors and prognostic markers for major depression and is crucial for developing tailored treatments for patients at mild stages of depression. We investigated resting-state functional connectivity (rs-FC) of the cognitive control network (CCN), known to be dysregulated in MDD, using the bilateral dorsolateral prefrontal cortex (DLPFC) as a seed, focusing on two cohorts of StD subjects (young and middle aged) as well as matched controls. Irrespective of age, we found a significant rs-FC decrease in the CCN of the StD subjects, compared with matched controls, particularly between the DLPFC and the brain regions associated with the representation of self and other mental states (temporo-parietal junction (TPJ) and precuneus), as well as salience detection and orienting (insula). The functional connectivity between the DLPFC and the left TPJ was also associated with depressive symptom scores measured by the Center for Epidemiologic Studies Depression Scale. This finding may shed light on the neural pathology of StD, leading to better understanding of mild stages of depression, its diagnosis and the development of new treatments.
Improved oxidation of aromatic and aliphatic hydrocarbons using rate enhancing variants of P450Bm3 in combination with decoy molecules
Authors: Munday Samuel D. , Shoji Osami , Watanabe Yoshihito , Wong Luet-Lok , Bell Stephen G.
Published: November 2015

The addition of perfluorinated fatty acids to the rate accelerating KT2 mutant of P450Bm3 resulted in the highly active oxidation of cyclohexane and benzenes whilst maintaining the product selectivity.
Mixed anionic surfactant-templated mesoporous silica nanoparticles for fluorescence detection of Fe3+
Authors: Gai Fangyuan , Zhou Tianlei , Chu Guang , Li Ye , Liu Yunling , Huo Qisheng , Akhtar Farid
Published: November 2015

This work demonstrates the design and synthesis of large pore mesoporous silica nanoparticles by using mixed anionic surfactants as soft templates to introduce amino group for Fe3+ fluorescent detection.
Tridentate Lewis acids with phenyl substituted 1,3,5-trisilacyclohexane backbones
Authors: Weisheim Eugen , Bücker Lisa , Neumann Beate , Stammler Hans-Georg , Mitzel Norbert W.
Published: November 2015

A new 1,3,5-trisilacyclohexane scaffold with axially orientated ethynyl groups provides opportunities to create new tridentate Lewis acids. Some examples of these Lewis acids have been synthesized.
Organosilane sulfonated graphene oxide in the Biginelli and Biginelli-like reactions
Authors: Safari Javad , Gandomi-Ravandi Soheila , Ashiri Samira
Published: November 2015

The acid functionalized SSi-GO was used as a highly active, selective and reusable catalyst to improve the formation of pyrimidinones.
Chromenes involving a two-photon absorbing moiety: photochromism via intramolecular resonance energy transfer
Authors: Bekere Laura , Lokshin Vladimir , Sigalov Mark , Gvishi Raz , Zhao Peng , Hagan David J. , Van Stryland Eric W. , Khodorkovsky Vladimir
Published: November 2015

A general approach toward the synthesis of molecular dyads involving the photoactive moieties connected by a non-conjugative link is described.
Divergent synthetic route to new cyclopenta[c]pyran iridoids: syntheses of jatamanin A, F, G and J, gastrolactone and nepetalactone
Authors: Sim Jaehoon , Yoon Inah , Yun Hwayoung , An Hongchan , Suh Young-Ger
Published: November 2015

Six natural iridoids including jatamanin A, F, G and J, gastrolactone and nepetalactone have been synthesized via the efficient transformation of a core cyclopenta[c]pyran intermediate.
Correction: Ylide formal [4 + 1] annulation
Authors: Zhu Chunyin , Ding Ya , Ye Long-Wu
Published: November 2015

Correction for ‘Ylide formal [4 + 1] annulation’ by Chunyin Zhu et al., Org. Biomol. Chem., 2015, 13, 2530–2536.
Expression of concern: A unifying mechanism for the rearrangement of vinyl allene oxide geometric isomers to cyclopentenones
Authors: Kelly Richard
Published: November 2015

Expression of concern for ‘A unifying mechanism for the rearrangement of vinyl allene oxide geometric isomers to cyclopentenones’ by Adán B. González-Pérez et al., Org. Biomol. Chem., 2014, 12, 7694–7701.
Facile hydrothermal synthesis and formation mechanisms of Bi2Te3, Sb2Te3 and Bi2Te3–Sb2Te3 nanowires
Authors: Feng Hongqing , Wu Chunyang , Zhang Peng , Mi Jianli , Dong Mingdong
Published: November 2015

A facile and “green” glucose-assisted hydrothermal method is proposed to synthesize Bi2Te3, Sb2Te3 and Bi2Te3–Sb2Te3 nanowires.
Reactivities of platinum subnanocluster catalysts for the oxidation reaction of alcohols
Authors: Takahashi Masaki , Imaoka Takane , Yamamoto Kimihisa
Published: November 2015

The size-dependent catalytic activity for alcohol oxidation was investigated using the platinum subnanoclusters synthesized by the dendrimer template method.
Strained surface siloxanes as a source of synthetically important radicals
Authors: Ward Antony J. , Lesic Rebecca A. , Proschogo Nicholas , Masters Anthony F. , Maschmeyer Thomas
Published: November 2015

The calcination of pure amorphous silica at temperatures up to 850 °C results in the formation of strained siloxane rings which are capable of undergoing homolytic cleavage to generate radicals when in the presence of an appropriate substrate.
New insights in partial nitrification start-up revealed by a model based approach
Authors: Wu Jun , Yan Gang , Zhou Guojing , Xu Ting
Published: November 2015

Nitrite oxidizing bacteria washout condition achieved by model based approach.
Protein-modified hollow copper sulfide nanoparticles carrying indocyanine green for photothermal and photodynamic therapy
Authors: Han Lu , Zhang Yang , Chen Xu-Wei , Shu Yang , Wang Jian-Hua
Published: November 2015

Protein-modified hollow copper sulfide nanoparticles carrying indocyanine green (ICG) facilitate combined therapeutic effects including photothermal therapy of CuS nanocarriers and cytotoxic effects of photodynamic and photothermal therapy by ICG.
Increasing peak detectivity (D*) of In0.5Ga0.5As/GaAs quantum dot infrared photodetectors by up to two orders with high‐energy proton implantation
Authors: Upadhyay S. , Mandal A. , Ghadi H. , Pal D. , Basu A. , Subrahmanyam N.B.V. , Singh P. , Chakrabarti S.
Published: November 2015

In(Ga)As/GaAs‐based quantum dot infrared photodetectors (QDIPs) are among the most efficient devices for use in the mid‐ and long‐wavelength infrared regions, making them suitable for various defence and space applications. Considering previously reported results on In(Ga)As/GaAs QDIPs, a post‐growth method is investigated to improve QDIP characteristics using high‐energy proton implantation. It was found that implantation suppressed the field‐assisted tunnelling of dark current generation, which decreased the dark current density by three orders, whereas the peak detectivity (D*) in the implanted devices increased by up to two orders of magnitude, from 6.1 × 108 to 1.0 × 1010 cm‐Hz1/2/W at 77 K.
Strategy of active learning support vector machine for image retrieval
Authors: Qi Yali , Zhang Guoshan
Published: November 2015

This study proposes a new method for content‐based image retrieval by finding an optimal classifier. The optimal classifier is achieved by a new active learning support vector machine (SVM) which combines the model selection with the active learning. The unlabelled samples close to the boundary of the SVM classifier are selected based on the feature similarity for the active learning, and the adaptive regularisation is used to select the optimal model. The combination of model selection with active learning accelerates the convergence of the classifier. The new method can improve the image retrieval accuracy and reduce the time consumption. The experimental results show that the proposed method has a better performance with fewer samples and less time consumption for image retrieval.
Junction‐aware water flow approach for urban road network extraction
Authors: Shanmugam Leninisha , Kaliaperumal Vani
Published: November 2015

The highways now offer more and more complex road junctions composed of many surrounding roads, overlapping each other with high curvature. Traditional road detection methods are not adequate for the rapid development of cities with increased complexity of the road junction shape. The major challenges in road extraction are varying spectral reflectance, lane markings, obstacles with different sizes, of various shapes, and intersected roads. However, very few researchers have attempted handling overlapped roads with low curvature only. In this study, a water flow‐based semi‐automatic approach is proposed for extracting road network with various shapes of junctions (Y‐shaped with different acute angles), intersected and also for overlapped high curvilinear roads. Recognising the complex road junction is done with fewer automatically generated anchor points without human intervention, which detects the number of roads (branches) connected to that junction along the road's width, orientation and length with less computation time. Hence, from a manually selected seed point, the authors' algorithm can be automatically propagated throughout a whole road network with or without single lane or multiple lanes (lined, dotted or both). Experimental results show that this proposed approach can accurately and efficiently extract interconnected road network from QuickBird images with minimal seed points.
Adaptive interference cancellation using a sampled analogue signal processor
Authors: Rivet Francois , Veyrac Yoan , Deval Yann , Garrec Patrick
Published: November 2015

Radars are developed with the aim to process any type of signals even in the presence of interferences in a hostile context. The authors propose a circuit which can deal with any signal, whatever its frequency, its modulation scheme. This circuit is based on sampled analogue signal processor (SASP) performing a fast Fourier transform (FFT) using voltage samples. The idea is to process any radio frequency signal from 0 to 5 GHz using the FFT to obtain frequency shifting and filtering, presenting a new approach to reduce dramatically power consumption and thus address radar application such as FOPEN. The measurement results presented here on the SASP have been obtained with a 65 nm CMOS technology from STMicroelectronics. Further, the concept of an active interference‐cancelling system using the analogue signal processor in a feed‐forward loop is presented.
High current DC negative ion source for cyclotron
Authors: Etoh H. , Onai M. , Aoki Y. , Mitsubori H. , Arakawa Y. , Sakuraba J. , Kato T. , Mitsumoto T. , Hiasa T. , Yajima S. , Shibata T. , Hatayama A. , Okumura Y.
Published: November 2015

A filament driven multi-cusp negative ion source has been developed for proton cyclotrons in medical applications. In Cs-free operation, continuous H− beam of 10 mA and D− beam of 3.3 mA were obtained stably at an arc-discharge power of 3 kW and 2.4 kW, respectively. In Cs-seeded operation, H− beam current reached 22 mA at a lower arc power of 2.6 kW with less co-extracted electron current. The optimum gas flow rate, which gives the highest H− current, was 15 sccm in the Cs-free operation, while it decreased to 4 sccm in the Cs-seeded operation. The relationship between H− production and the design/operating parameters has been also investigated by a numerical study with KEIO-MARC code, which gives a reasonable explanation to the experimental results of the H− current dependence on the arc power.
The snowflake divertor
Authors: Ryutov D. D. , Soukhanovskii V. A.
Published: November 2015

The snowflake magnetic configuration is characterized by the presence of two closely spaced poloidal field nulls that create a characteristic hexagonal (reminiscent of a snowflake) separatrix structure. The magnetic field properties and the plasma behaviour in the snowflake are determined by the simultaneous action of both nulls, this generating a lot of interesting physics, as well as providing a chance for improving divertor performance. Among potential beneficial effects of this geometry are: increased volume of a low poloidal field around the null, increased connection length, and the heat flux sharing between multiple divertor channels. The authors summarise experimental results obtained with the snowflake configuration on several tokamaks. Wherever possible, relation to the existing theoretical models is described.
Predicting the solid solubility limit in high-entropy alloys using the molecular orbital approach
Authors: Sheikh Saad , Klement Uta , Guo Sheng
Published: November 2015

High-entropy alloys (HEAs) are currently at the research frontier of metallic materials. Understanding the solid solubility limit in HEAs, such a highly concentrated multicomponent alloy system, is scientifically intriguing. It is also technically important to achieve desirable mechanical properties by controlling the formation of topologically or geometrically closed packed phases. Previous approaches to describe the solid solubilities in HEAs could not accurately locate the solubility limit and have to utilize at least two parameters. Here, we propose to use a single parameter, the average energy of d-orbital levels, Md, to predict the solid solubility limit in HEAs. It is found that Md can satisfactorily describe the solid solubilities in fcc structured HEAs containing 3 d transition metals, and also in bcc structured HEAs. This finding will greatly simplify the alloys design and lends more flexibility to control the mechanical properties of HEAs. When 4 d transition metals are alloyed, Md alone cannot describe the solid solubility limit in fcc structured HEAs, due to the large increase of the bond strength that can be gauged by the bond order, Bo. The potential opportunities and challenges with applying the molecular orbital approach to HEAs are discussed.
Surface roughness scattering effects on the ballisticity of Schottky barrier nanowire field effect transistors
Authors: Jung Hyo-Eun , Shin Mincheol
Published: November 2015

The surface roughness scattering effects on Schottky barrier (SB) silicon nanowire metal-oxide-semiconductor field effect transistors (MOSFETs) are investigated and compared to those of silicon nanowire MOSFETs with doped source and drain. In particular, the ballisticity of both types of devices is examined extensively as the root-mean-square (RMS) value of surface roughness, channel length, channel width (W), Schottky barrier height, and drain voltage are varied. It is found that the surface roughness scattering effectively raises the Schottky barrier height by δΦ̃B and the overall characteristics of the ballisticity of SB-MOSFETs are determined by δΦ̃B. Contrary to the case of MOSFETs with doped source and drain, the ballisticity shows little dependence on channel length and a linear decrease with RMS/W in SB-MOSFETs.
On the estimation of sound speed in two-dimensional Yukawa fluids
Authors: Semenov I. L. , Khrapak S. A. , Thomas H. M.
Published: November 2015

The longitudinal sound speed in two-dimensional Yukawa fluids is estimated using the conventional hydrodynamic expression supplemented by appropriate thermodynamic functions proposed recently by Khrapak et al. [Phys. Plasmas 22, 083706 (2015)]. In contrast to the existing approaches, such as quasi-localized charge approximation (QLCA) and molecular dynamics simulations, our model provides a relatively simple estimate for the sound speed over a wide range of parameters of interest. At strong coupling, our results are shown to be in good agreement with the results obtained using the QLCA approach and those derived from the phonon spectrum for the triangular lattice. On the other hand, our model is also expected to remain accurate at moderate values of the coupling strength. In addition, the obtained results are used to discuss the influence of the strong coupling effects on the adiabatic index of two-dimensional Yukawa fluids.
Grassland and forest understorey biomass emissions from prescribed fires in the south-eastern United States – RxCADRE 2012
Authors: Strand Tara , Gullett Brian , Urbanski Shawn , O'Neill Susan , Potter Brian , Aurell Johanna , Holder Amara , Larkin Narasimhan , Moore Mark , Rorig Miriam
Published: November 2015

Smoke measurements were made during grass and forest understorey prescribed fires as part of a comprehensive programme to understand fire and smoke behaviour. Instruments deployed on the ground, airplane and tethered aerostat platforms characterised the smoke plumes through measurements of carbon dioxide (CO2), carbon monoxide (CO), methane (CH4) and particulate matter (PM), and measurements of optical properties. Distinctions were observed in aerial and ground-based measurements, with aerial measurements exhibiting smaller particle size distributions and PM emission factors, likely due to particle settling. Black carbon emission factors were similar for both burns and were highest during the initial flaming phase. On average, the particles from the forest fire were less light absorbing than those from the grass fires due to the longer duration of smouldering combustion in the forest biomass. CO and CH4 emission factors were over twice as high for the forest burn than for the grass burn, corresponding with a lower modified combustion efficiency and greater smouldering combustion. This dataset reveals the evolution of smoke emissions from two different commonly burned fuel types and demonstrates the complexity of emission factors.
The long-term impact of low-intensity surface fires on litter decomposition and enzyme activities in boreal coniferous forests
Authors: Köster Kajar , Berninger Frank , Heinonsalo Jussi , Lindén Aki , Köster Egle , Ilvesniemi Hannu , Pumpanen Jukka
Published: November 2015

In boreal forest ecosystems fire, fungi and bacteria, and their interactions, have a pronounced effect on soil carbon dynamics. In this study we measured enzymatic activities, litter decomposition rates, carbon stocks and fungal and microbial biomasses in a boreal subarctic coniferous forest on a four age classes of non-stand replacing fire chronosequence (2, 42, 60 and 152 years after the fire). The results show that microbial activity recovered slowly after fire and the decomposition of new litter was affected by the disturbance. The percent mass loss of Scots pine litter increased with time from the last fire. Slow litter decomposition during the first post-fire years accelerates soil organic matter accumulation that is essential for the recovery of soil biological activities. Fire reduced the enzymatic activity across all the enzyme types measured. Carbon-degrading, chitin-degrading and phosphorus-dissolving enzymes showed different responses with the time elapsed since the fire disturbance. Microbial and enzymatic activity took decades before recovering to the levels observed in old forest stands. Our study demonstrates that slower post-fire litter decomposition has a pronounced impact on the recovery of soil organic matter following forest fires in northern boreal coniferous forests.
Persistent states in vision break universality and time invariance
Authors: Wexler Mark , Duyck Marianne , Mamassian Pascal
Published: November 2015

Significance

Studies of perception usually measure overt variables—how sensory stimulation governs what is perceived. Here we show that perception is also governed by hidden variables that we call perceptual states. These hidden variables—two of which we study in this paper—can be inferred as systematic biases governing the perception of two families of ambiguous 3D stimuli. They vary widely across individuals, causing observers to often perceive the same stimulus in opposite ways. The variables change cumulatively over time and thus constitute a previously unknown type of perceptual memory. We document dynamics on time scales from minutes to months (the latter scale virtually unknown in perception), showing that aspects of the variables’ behavior can be modeled by random walks.
A cross-hazard analysis of terse message retransmission on Twitter
Authors: Sutton Jeannette , Gibson C. Ben , Phillips Nolan Edward , Spiro Emma S. , League Cedar , Johnson Britta , Fitzhugh Sean M. , Butts Carter T.
Published: November 2015

Significance

Online social networks (OSNs) enable time-resolved measurement of communication behavior during disasters, making it possible to probe the mechanisms by which messages are amplified or suppressed with precision unattainable by traditional data sources. To our knowledge, this research provides the first systematic study of the factors predicting the social amplification of risk communication in OSNs by examining the retransmission of official messages across five hazards. Our findings demonstrate the respective impacts of sender characteristics, message content, and message style in determining whether an official message will be passed on during an emergency, as well whether these vary across hazards. These results contribute to the evidence base for policies guiding the delivery by emergency management organizations of lifesaving information to the public.
Secondary PDZ domain-binding site on class B plexins enhances the affinity for PDZ–RhoGEF
Authors: Pascoe Heath G. , Gutowski Stephen , Chen Hua , Brautigam Chad A. , Chen Zhe , Sternweis Paul C. , Zhang Xuewu
Published: November 2015

Significance

Protein interactions mediated by modular domains, such as PDZ and SH2 domains, play critical roles in biology. The modules typically recognize a linear motif in their ligands, with a few residues in the motif determining the specificity. We report a crystal structure of the complex between the cytoplasmic region of PlexinB2 and the PDZ domain of PDZ–RhoGEF. The structure shows that, in addition to the PDZ/motif interaction, a secondary interface is formed between the three-dimensional domains of the two proteins. We further show that the secondary interface enhances the affinity between plexin and PDZ–RhoGEF and is important for plexin signaling. Our analyses suggest that secondary interface-mediated interactions may be a broadly used mechanism for modular domains to achieve high specificity.
Neurotrophic-priming of glucocorticoid receptor signaling is essential for neuronal plasticity to stress and antidepressant treatment
Authors: Arango-Lievano Margarita , Lambert W. Marcus , Bath Kevin G. , Garabedian Michael J. , Chao Moses V. , Jeanneteau Freddy
Published: November 2015

Significance

Stress-related disorders are prevalent worldwide, but the pathophysiology of these disorders and specific therapeutic targets remain elusive. Two hypothetical frameworks show great promise: decreased neurotrophic support and decreased responsiveness to glucocorticoids. Our study shows that the glucocorticoid receptor is a prominent target of the brain-derived neurotrophic factor (BDNF) signaling, which gives rise to unique functional attributes essential for the neuroplasticity to an antidepressant. We propose a unifying mechanism of BDNF-priming of glucocorticoid signaling, which provides new prospects for discovering innovative treatments for disorders featuring unpaired BDNF and glucocorticoid activities. Eliciting glucocorticoid receptor phosphorylation is an attractive means to confront resistance to antidepressants.
Ab initio optimization of phonon drag effect for lower-temperature thermoelectric energy conversion
Authors: Zhou Jiawei , Liao Bolin , Qiu Bo , Huberman Samuel , Esfarjani Keivan , Dresselhaus Mildred S. , Chen Gang
Published: November 2015

Significance

It has been well known that the phonon drag effect—an extra electrical current induced by phonon heat flow via electron–phonon interaction—can lead to unusually high Seebeck coefficient at low temperatures. However, its use for improving thermoelectric performance has been controversial. Here, using first principles calculations we examine the phonon drag with detailed mode-specific contributions and reveal that even in heavily doped silicon at room temperature, phonon drag can still be significant, which challenges the previous belief that phonon drag vanishes in heavily doped samples. A phonon filter is designed to spectrally decouple the phonon drag from the heat conduction. Our simulation explores the coupled electron phonon transport and uncovers the possibility of optimizing the phonon drag for better thermoelectrics.
Space station image captures a red tide ciliate bloom at high spectral and spatial resolution
Authors: Dierssen Heidi , McManus George B. , Chlus Adam , Qiu Dajun , Gao Bo-Cai , Lin Senjie
Published: November 2015

Significance

Many different types of plankton bloom in the coastal ocean. Some produce harmful toxins, whereas others are considered important contributors to primary production and ecosystem dynamics. Routine ocean color sensors can reveal a dense bloom or “red tide” from space but cannot differentiate types of plankton. The Hyperspectral Imager for the Coastal Ocean on the International Space Station allowed for new “hyperspectral” approaches to identify pigments and assess biophysical forcing associated with different blooms. Consistent with field and molecular observations, imagery revealed dense surface patches of
Mesodinium rubrum
, a ciliate that uses the chloroplasts from its cryptophyte algal prey to photosynthesize. For the first time, to our knowledge, the distribution and abundance were mapped based on the unique yellow fluorescence properties of its signature pigment phycoerythrin.
Compromising the phosphodependent regulation of the GABA
A
R β3 subunit reproduces the core phenotypes of autism spectrum disorders
Authors: Vien Thuy N. , Modgil Amit , Abramian Armen M. , Jurd Rachel , Walker Joshua , Brandon Nicholas J. , Terunuma Miho , Rudolph Uwe , Maguire Jamie , Davies Paul A. , Moss Stephen J.
Published: November 2015

Significance

Alterations in the efficacy of neuronal inhibition mediated by GABA
A
receptors (GABA
A
Rs) containing β3 subunits are continually implicated in autism spectrum disorders (ASDs). In vitro, the plasma membrane stability of GABA
A
Rs is potentiated via phosphorylation of serine residues 408 and 409 (S408/9) in the β3 subunit, an effect that is mimicked by their mutation to alanines. Here, we created a mouse in which S408/9 have been mutated to alanines (S408/9A). S408/9A mice exhibited altered dendritic spine structure, increased repetitive behavior, decreased social interaction, and an epileptic phenotype. Thus, mutation of S408/9 reproduces the core deficits seen in humans with ASDs. Collectively, our results suggest that alterations in phosphorylation and/or activity of β3-containing GABA
A
Rs may directly contribute to the pathophysiology of ASDs.
Effects of confinement on models of intracellular macromolecular dynamics
Authors: Chow Edmond , Skolnick Jeffrey
Published: November 2015

Significance

We use Brownian and Stokesian dynamics simulations to explore diffusion processes within an idealized biological cell. Although most studies assume processes occurring in an infinite medium, we focus on the effect that confinement within a cellular membrane may have on intracellular dynamics. One finding is that model proteins near the membrane tend to diffuse along the membrane; this may give additional time for signal transduction across the membrane to occur. We also observe more strongly correlated motions near the membrane than in the cell’s interior, potentially facilitating interactions between proteins there. Finally, we find that deep in the interior of the model cell, the confining effects of the finite size of a cell on the dynamics can be neglected.
Gourds and squashes (
Cucurbita
spp.) adapted to megafaunal extinction and ecological anachronism through domestication
Authors: Kistler Logan , Newsom Lee A. , Ryan Timothy M. , Clarke Andrew C. , Smith Bruce D. , Perry George H.
Published: November 2015

Significance

Squashes, pumpkins, and gourds belonging to the genus
Cucurbita
were domesticated on several occasions throughout the Americas, beginning around 10,000 years ago. The wild forms of these species are unpalatably bitter to humans and other extant mammals, but their seeds are present in mastodon dung deposits, demonstrating that they may have been dispersed by large-bodied herbivores undeterred by their bitterness. However,
Cucurbita
may have been poorly adapted to a landscape lacking these large dispersal partners. Our study proposes a link between the disappearance of megafaunal mammals from the landscape, the decline of wild
Cucurbita
populations, and, ultimately, the evolution of domesticated
Cucurbita
alongside human cultivators.
Post-conversion sialylation of prions in lymphoid tissues
Authors: Srivastava Saurabh , Makarava Natallia , Katorcha Elizaveta , Savtchenko Regina , Brossmer Reinhard , Baskakov Ilia V.
Published: November 2015

Significance

In mammals, sialic acids are the most abundant terminal residues on cell-surface glycans and comprise “self-associated molecular patterns,” which protect the host from inappropriate activation of multiple immune pathways. In a striking illustration of molecular mimicry, a number of microbial pathogens recruit host sialic acids to decorate their surfaces and hide from the same immune responses. Prions are proteinaceous infectious agents, not conventional pathogens. This study found that sialylation of prions is enhanced upon their colonization of secondary lymphoid organs, via extracellular host sialylation machinery. Thus, prions may use strategies similar to other pathogens to camouflage themselves from the immune system, facilitating host invasion.
Shifting the feeding of mice to the rest phase creates metabolic alterations, which, on their own, shift the peripheral circadian clocks by 12 hours
Authors: Mukherji Atish , Kobiita Ahmad , Chambon Pierre
Published: November 2015

Significance

Under homeostasis, peripheral circadian clocks (CCs) and metabolism are intimately linked, as pathologies occur on perturbation of their coupling. In mice, shifting the feeding time from the phase of activity (night) to the phase of rest (day) is known to act as a time cue for peripheral CCs, leading to a 12-hour shift of the time at which their CC components are expressed. However, the molecular mechanisms that underlie this shift are largely unknown. Here, we reveal both the origin and the identity of the metabolic signals that are generated on shifting eating to the rest phase and how these signals directly alter the expression of CC components to generate the shift that ultimately leads to metabolic syndrome-like pathology.
Shifting eating to the circadian rest phase misaligns the peripheral clocks with the master SCN clock and leads to a metabolic syndrome
Authors: Mukherji Atish , Kobiita Ahmad , Damara Manohar , Misra Nisha , Meziane Hamid , Champy Marie-France , Chambon Pierre
Published: November 2015

Significance

Mounting epidemiological and genetic evidence suggests that the disruption of circadian rhythms is at the origin of pathologies. It is known that people who are engaged in shift work and exhibit a shifted feeding schedule often develop a cohort of metabolic pathologies including diabetes, obesity, and metabolic syndrome. However, the molecular mechanisms that are at the origin of these pathologies are poorly understood. Using mice, we now revealed at the molecular level how metabolic alterations generated on shifting the eating schedule from the normal active phase to the rest phase creates a misalignment’ between the central and peripheral circadian clocks. Importantly, we demonstrate that this misalignment progressively induces a metabolic pathological syndrome similar to that observed in shift workers.
microRNA classifiers are powerful diagnostic/prognostic tools in
ALK-
,
EGFR-
, and
KRAS
-driven lung cancers
Authors: Gasparini Pierluigi , Cascione Luciano , Landi Lorenza , Carasi Stefania , Lovat Francesca , Tibaldi Carmelo , Alì Greta , D’Incecco Armida , Minuti Gabriele , Chella Antonio , Fontanini Gabriella , Fassan Matteo , Cappuzzo Federico , Croce Carlo M.
Published: November 2015

Significance

microRNA profiles of anaplastic lymphoma kinase (
ALK
)-driven non-small cell lung cancers (NSCLCs) are currently not available in publically accessible databases. Identifying translocated
ALK
, mutant EGF receptor, and mutant V-Ki-ras2 Kirsten rat sarcoma cases in NSCLC is of value for determining which patients are more likely to benefit from a targeted therapy, to explicate mechanisms underlying chemotherapy survival, and ultimately in new drug development. microRNA-based classifiers are newly developed prognostic and diagnostic tools that can improve and complement the current gold-standard techniques. These classifiers also potentially represent an engine for boosting research on the role of these microRNAs in response to commonly used chemotherapy regimens in NSCLC to maximize patient outcomes.
Oxidative stress–dependent phosphorylation activates ZNRF1 to induce neuronal/axonal degeneration
Authors: Wakatsuki Shuji , Furuno Akiko , Ohshima Makiko , Araki Toshiyuki
Published: November 2015

Oxidative stress is a well-known inducer of neuronal apoptosis and axonal degeneration. We previously showed that the E3 ubiquitin ligase ZNRF1 promotes Wallerian degeneration by degrading AKT to induce GSK3B activation. We now demonstrate that oxidative stress serves as an activator of the ubiquitin ligase activity of ZNRF1 by inducing epidermal growth factor receptor (EGFR)–mediated phosphorylation at the 103rd tyrosine residue and that the up-regulation of ZNRF1 activity by oxidative stress leads to neuronal apoptosis and Wallerian degeneration. We also show that nicotinamide adenine dinucleotide phosphate–reduced oxidase activity is required for the EGFR-dependent phosphorylation-induced activation of ZNRF1 and resultant AKT degradation via the ubiquitin proteasome system to induce Wallerian degeneration. These results indicate the pathophysiological significance of the EGFR–ZNRF1 pathway induced by oxidative stress in the regulation of neuronal apoptosis and Wallerian degeneration. A deeper understanding of the regulatory mechanism for ZNRF1 catalytic activity via phosphorylation will provide a potential therapeutic avenue for neurodegeneration.
Insulin–InsR signaling drives multipotent progenitor differentiation toward lymphoid lineages
Authors: Xia Pengyan , Wang Shuo , Du Ying , Huang Guanling , Satoh Takashi , Akira Shizuo , Fan Zusen
Published: November 2015

The lineage commitment of HSCs generates balanced myeloid and lymphoid populations in hematopoiesis. However, the underlying mechanisms that control this process remain largely unknown. Here, we show that insulin–insulin receptor (InsR) signaling is required for lineage commitment of multipotent progenitors (MPPs). Deletion of Insr in murine bone marrow causes skewed differentiation of MPPs to myeloid cells. mTOR acts as a downstream effector that modulates MPP differentiation. mTOR activates Stat3 by phosphorylation at serine 727 under insulin stimulation, which binds to the promoter of Ikaros, leading to its transcription priming. Our findings reveal that the insulin–InsR signaling drives MPP differentiation into lymphoid lineages in early lymphopoiesis, which is essential for maintaining a balanced immune system for an individual organism.