bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sample storage conditions significantly influence faecal microbiome profiles
Authors: Choo Jocelyn M , Leong Lex EX , Rogers Geraint B 
Published: November 2015

AbstractSequencing-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

AbstractSilver 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

AbstractSlowly-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

AbstractSimvastatin, 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

AbstractBiocompatible 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

AbstractStudies 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

AbstractParvalbumin-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

AbstractHigh 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

AbstractSubthreshold 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.
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.
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.
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

SignificanceOnline 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.
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.
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.