bluuebunny/crossref_metadata_2025_split huggingface dataset:
Energetic instability of passive states in thermodynamics
Authors: Sparaciari Carlo , Jennings David , Oppenheim Jonathan 
Published: November 2017

AbstractPassivity is a fundamental concept in thermodynamics that demands a quantum system’s energy cannot be lowered by any reversible, unitary process acting on the system. In the limit of many such systems, passivity leads in turn to the concept of complete passivity, thermal states and the emergence of a thermodynamic temperature. Here we only consider a single system and show that every passive state except the thermal state is unstable under a weaker form of reversibility. Indeed, we show that given a single copy of any athermal quantum state, an optimal amount of energy can be extracted from it when we utilise a machine that operates in a reversible cycle. This means that for individual systems, the only form of passivity that is stable under general reversible processes is complete passivity, and thus provides a physically motivated identification of thermal states when we are not operating in the thermodynamic limit.
Retarding oxidation of copper nanoparticles without electrical isolation and the size dependence of work function
Authors: Dabera G. Dinesha M.R. , Walker Marc , Sanchez Ana M. , Pereira H. Jessica , Beanland Richard , Hatton Ross A. 
Published: November 2017

AbstractCopper nanoparticles (CuNPs) are attractive as a low-cost alternative to their gold and silver analogues for numerous applications, although their potential has hardly been explored due to their higher susceptibility to oxidation in air. Here we show the unexpected findings of an investigation into the correlation between the air-stability of CuNPs and the structure of the thiolate capping ligand; of the eight different ligands screened, those with the shortest alkyl chain, –(CH2)2–, and a hydrophilic carboxylic acid end group are found to be the most effective at retarding oxidation in air. We also show that CuNPs are not etched by thiol solutions as previously reported, and address the important fundamental question of how the work function of small supported metal particles scales with particle size. Together these findings set the stage for greater utility of CuNPs for emerging electronic applications.
Partially native intermediates mediate misfolding of SOD1 in single-molecule folding trajectories
Authors: Sen Mojumdar Supratik , N. Scholl Zackary , Dee Derek R. , Rouleau Logan , Anand Uttam , Garen Craig , Woodside Michael T. 
Published: November 2017

AbstractPrion-like misfolding of superoxide dismutase 1 (SOD1) is associated with the disease ALS, but the mechanism of misfolding remains unclear, partly because misfolding is difficult to observe directly. Here we study the most misfolding-prone form of SOD1, reduced un-metallated monomers, using optical tweezers to measure unfolding and refolding of single molecules. We find that the folding is more complex than suspected, resolving numerous previously undetected intermediate states consistent with the formation of individual β-strands in the native structure. We identify a stable core of the protein that unfolds last and refolds first, and directly observe several distinct misfolded states that branch off from the native folding pathways at specific points after the formation of the stable core. Partially folded intermediates thus play a crucial role mediating between native and non-native folding. These results suggest an explanation for SOD1’s propensity for prion-like misfolding and point to possible targets for therapeutic intervention.
Thin single crystal perovskite solar cells to harvest below-bandgap light absorption
Authors: Chen Zhaolai , Dong Qingfeng , Liu Ye , Bao Chunxiong , Fang Yanjun , Lin Yun , Tang Shi , Wang Qi , Xiao Xun , Bai Yang , Deng Yehao , Huang Jinsong 
Published: November 2017

AbstractThe efficiency of perovskite solar cells has surged in the past few years, while the bandgaps of current perovskite materials for record efficiencies are much larger than the optimal value, which makes the efficiency far lower than the Shockley–Queisser efficiency limit. Here we show that utilizing the below-bandgap absorption of perovskite single crystals can narrow down their effective optical bandgap without changing the composition. Thin methylammonium lead triiodide single crystals with tuned thickness of tens of micrometers are directly grown on hole-transport-layer covered substrates by a hydrophobic interface confined lateral crystal growth method. The spectral response of the methylammonium lead triiodide single crystal solar cells is extended to 820 nm, 20 nm broader than the corresponding polycrystalline thin-film solar cells. The open-circuit voltage and fill factor are not sacrificed, resulting in an efficiency of 17.8% for single crystal perovskite solar cells.
Environmental conditions limit attractiveness of a complex sexual signal in the túngara frog
Authors: Halfwerk Wouter , Smit Judith A. H. , Loning Hugo , Lea Amanda M. , Geipel Inga , Ellers Jacintha , Ryan Michael J. 
Published: November 2017

AbstractAnimals choosing particular display sites often balance sexual and natural selection pressures. Here we assess how physical properties of display sites can alter this balance by influencing signal production and attractiveness of the túngara frog (Physalaemus pustulosus). Males that call from very shallow water bodies (few mm depth) benefit from reduced predation risk, but by manipulating water levels, we show that this comes at a cost of reduced attractiveness to females. Our data show that calling from shallower water reduces a male’s ability to float, limits the inflation of his vocal sac, and consequently reduces signal conspicuousness in terms of amplitude and complexity. Our results demonstrate that display site properties can set limits on signal production and attractiveness and may hence influence signal evolution. Signallers may shift between sites or engineer their display location, which can play a crucial role in signal divergence and speciation, particularly in a rapidly changing world.
Fine control of metal concentrations is necessary for cells to discern zinc from cobalt
Authors: Osman Deenah , Foster Andrew W. , Chen Junjun , Svedaite Kotryna , Steed Jonathan W. , Lurie-Luke Elena , Huggins Thomas G. , Robinson Nigel J. 
Published: November 2017

AbstractBacteria possess transcription factors whose DNA-binding activity is altered upon binding to specific metals, but metal binding is not specific in vitro. Here we show that tight regulation of buffered intracellular metal concentrations is a prerequisite for metal specificity of Zur, ZntR, RcnR and FrmR in Salmonella Typhimurium. In cells, at non-inhibitory elevated concentrations, Zur and ZntR, only respond to Zn(II), RcnR to cobalt and FrmR to formaldehyde. However, in vitro all these sensors bind non-cognate metals, which alters DNA binding. We model the responses of these sensors to intracellular-buffered concentrations of Co(II) and Zn(II) based upon determined abundances, metal affinities and DNA affinities of each apo- and metalated sensor. The cognate sensors are modelled to respond at the lowest concentrations of their cognate metal, explaining specificity. However, other sensors are modelled to respond at concentrations only slightly higher, and cobalt or Zn(II) shock triggers mal-responses that match these predictions. Thus, perfect metal specificity is fine-tuned to a narrow range of buffered intracellular metal concentrations.
Cytochrome b5 protects photoreceptors from light stress-induced lipid peroxidation and retinal degeneration
Authors: Chen Xinping , Hall Hana , Simpson Jeffrey P. , Leon-Salas Walter D. , Ready Donald F. , Weake Vikki M. 
Published: November 2017

AbstractLipid peroxides are generated by oxidative stress in cells, and contribute to ageing and neurodegenerative disease. The eye is at special risk for lipid peroxidation because photoreceptors possess amplified sensory membranes rich in peroxidation-susceptible polyunsaturated fatty acids. Light-induced lipid peroxidation in the retina contributes to retinal degeneration, and lipid peroxidation has been implicated in the progression of age-associated ocular diseases such as age-related macular degeneration (AMD). Here, we show that exposing Drosophila melanogaster to strong blue light induces oxidative stress including lipid peroxidation that results in retinal degeneration. Surprisingly, very young flies are resilient to this acute light stress, suggesting they possess endogenous neuroprotective mechanisms. While lipophilic antioxidants partially suppressed blue light-induced retinal degeneration in older flies, we find that overexpression of cytochrome b5 (Cyt-b5) completely suppressed both blue light-induced lipid peroxidation and retinal degeneration. Our data identify Cyt-b5 as a neuroprotective factor that targets light-induced oxidative damage, particularly lipid peroxidation. Cyt-b5 may function via supporting antioxidant recycling, thereby providing a strategy to prevent oxidative stress in ageing photoreceptors that would be synergistic with dietary antioxidant supplementation.
Crumbs, Moesin and Yurt regulate junctional stability and dynamics for a proper morphogenesis of the Drosophila pupal wing epithelium
Authors: Salis Pauline , Payre Francois , Valenti Philippe , Bazellieres Elsa , Le Bivic André , Mottola Giovanna 
Published: November 2017

AbstractThe Crumbs (Crb) complex is a key epithelial determinant. To understand its role in morphogenesis, we examined its function in the Drosophila pupal wing, an epithelium undergoing hexagonal packing and formation of planar-oriented hairs. Crb distribution is dynamic, being stabilized to the subapical region just before hair formation. Lack of crb or stardust, but not DPatj, affects hexagonal packing and delays hair formation, without impairing epithelial polarities but with increased fluctuations in cell junctions and perimeter length, fragmentation of adherens junctions and the actomyosin cytoskeleton. Crb interacts with Moesin and Yurt, FERM proteins regulating the actomyosin network. We found that Moesin and Yurt distribution at the subapical region depends on Crb. In contrast to previous reports, yurt, but not moesin, mutants phenocopy crb junctional defects. Moreover, while unaffected in crb mutants, cell perimeter increases in yurt mutant cells and decreases in the absence of moesin function. Our data suggest that Crb coordinates proper hexagonal packing and hair formation, by modulating junction integrity via Yurt and stabilizing cell perimeter via both Yurt and Moesin. The Drosophila pupal wing thus appears as a useful system to investigate the functional diversification of the Crb complex during morphogenesis, independently of its role in polarity.
Vacuum level dependent photoluminescence in chemical vapor deposition-grown monolayer MoS
2
Authors: Sun Linfeng , Zhang Xiaoming , Liu Fucai , Shen Youde , Fan Xiaofeng , Zheng Shoujun , Thong John T. L. , Liu Zheng , Yang Shengyuan A. , Yang Hui Ying 
Published: November 2017

AbstractThe stronger photoluminescence (PL) in chemical vapor deposition (CVD) grown monolayer MoS2 has been attributed to its high crystal quality compared with that in mechanically exfoliated (ME) crystal, which is contrary to the cognition that the ME crystal usually have better crystal quality than that of CVD grown one and it is expected with a better optical quality. In this report, the reason of abnormally strong PL spectra in CVD grown monolayer crystal is systematically investigated by studying the in-situ opto-electrical exploration at various environments for both of CVD and ME samples. High resolution transmission electron microscopy is used to investigate their crystal qualities. The stronger PL in CVD grown crystal is due to the high p-doping effect of adsorbates induced rebalance of exciton/trion emission. The first principle calculations are carried out to explore the interaction between adsorbates in ambient and defects sites in MoS2, which is consistent to the experimental phenomenon and further confirm our proposed mechanisms.
Optimization of segmented thermoelectric generator using Taguchi and ANOVA techniques
Authors: Kishore Ravi Anant , Sanghadasa Mohan , Priya Shashank 
Published: November 2017

AbstractRecent studies have demonstrated that segmented thermoelectric generators (TEGs) can operate over large thermal gradient and thus provide better performance (reported efficiency up to 11%) as compared to traditional TEGs, comprising of single thermoelectric (TE) material. However, segmented TEGs are still in early stages of development due to the inherent complexity in their design optimization and manufacturability. In this study, we demonstrate physics based numerical techniques along with Analysis of variance (ANOVA) and Taguchi optimization method for optimizing the performance of segmented TEGs. We have considered comprehensive set of design parameters, such as geometrical dimensions of p-n legs, height of segmentation, hot-side temperature, and load resistance, in order to optimize output power and efficiency of segmented TEGs. Using the state-of-the-art TE material properties and appropriate statistical tools, we provide near-optimum TEG configuration with only 25 experiments as compared to 3125 experiments needed by the conventional optimization methods. The effect of environmental factors on the optimization of segmented TEGs is also studied. Taguchi results are validated against the results obtained using traditional full factorial optimization technique and a TEG configuration for simultaneous optimization of power and efficiency is obtained.
Impact of the crystal orientation of Fe-doped lithium niobate on photo-assisted proton exchange and chemical etching
Authors: Li Shaobei , Liang Guohong , Zan Zhitao , Shi Lihong , Yan Wenbo , Liang Chao , Li Feifei , Chen Lipin , Fan Bolin , Wang Xuliang , Jiang Xuju , Chen Hongjian 
Published: November 2017

AbstractPhoto-assisted proton-exchange (PAPE) is carried out on the +c- and y-surfaces of Fe-doped LiNbO3 crystals and the impact of the crystal orientation on the PAPE and the subsequent photo-assisted chemical etching (PACE) is investigated. The proton distributions and the morphologies of the proton-exchanged surfaces are studied by using Micro-FT-IR, Micro-Raman, optical and scanning electron microscopy. Through the PAPE process the proton-exchange can be confined in a specific region by an incident laser beam with fixed intensity profile. It is found that the y-surface is much more fragile than the +c-surface and that micro-cracks are easily generated on the y-surface during the PAPE process. Moreover, the range and number of these micro-cracks can be controlled by the experimental parameters of the PAPE process. The etching morphology of the y-surface shows apparent directional features along the c-axis of LiNbO3 crystal and the proton spatial distribution is found elongated along the c-axis. Both effects are attributed to the accumulation of photovoltaic charges at the two sides of the illumination area along the c-axis.
RNA-seq of serial kidney biopsies obtained during progression of chronic kidney disease from dogs with X-linked hereditary nephropathy
Authors: Chu Candice P. , Hokamp Jessica A. , Cianciolo Rachel E. , Dabney Alan R. , Brinkmeyer-Langford Candice , Lees George E. , Nabity Mary B. 
Published: November 2017

AbstractDogs with X-linked hereditary nephropathy (XLHN) have a glomerular basement membrane defect that leads to progressive juvenile-onset renal failure. Their disease is analogous to Alport syndrome in humans, and they also serve as a good model of progressive chronic kidney disease (CKD). However, the gene expression profile that affects progression in this disease has only been partially characterized. To help fill this gap, we used RNA sequencing to identify differentially expressed genes (DEGs), over-represented pathways, and upstream regulators that contribute to kidney disease progression. Total RNA from kidney biopsies was isolated at 3 clinical time points from 3 males with rapidly-progressing CKD, 3 males with slowly-progressing CKD, and 2 age-matched controls. We identified 70 DEGs by comparing rapid and slow groups at specific time points. Based on time course analysis, 1,947 DEGs were identified over the 3 time points revealing upregulation of inflammatory pathways: integrin signaling, T cell activation, and chemokine and cytokine signaling pathways. T cell infiltration was verified by immunohistochemistry. TGF-β1 was identified as the primary upstream regulator. These results provide new insights into the underlying molecular mechanisms of disease progression in XLHN, and the identified DEGs can be potential biomarkers and therapeutic targets translatable to all CKDs.
Preferential selection of Arginine at the lipid-water-interface of TRPV1 during vertebrate evolution correlates with its snorkeling behaviour and cholesterol interaction
Authors: Saha Somdatta , Ghosh Arijit , Tiwari Nikhil , Kumar Ashutosh , Kumar Abhishek , Goswami Chandan 
Published: November 2017

AbstractTRPV1 is a thermo-sensitive ion channel involved in neurosensory and other physiological functions. The trans-membrane helices of TRPV1 undergo quick and complex conformational changes governed by thermodynamic parameters and membrane components leading to channel opening. However, the molecular mechanisms underlying such events are poorly understood. Here we analysed the molecular evolution of TRPV1 at the lipid-water-interface region (LWI), typically defined as a layer of 6 Å thickness on each side of the membrane with less availability of free water. Amino acids demarcating the end of the trans-membrane helices are highly conserved. Residues present in the inner leaflet are more conserved and have been preferentially selected over others. Amino acids with snorkeling properties (Arginine and Tyrosine) undergo specific selection during the vertebrate evolution in a cholesterol-dependent and/or body temperature manner. Results suggest that H-bond formation between the OH- group of cholesterol and side chain of Arg557 or Arg575 at the inner leaflet is a critical parameter that can regulate channel functions. Different LWI mutants of TRPV1 have altered membrane localization and deficient colocalization with lipid raft markers. These findings may help to understand the lipid-protein interactions, and molecular basis of different neuronal functions. Such findings may have broad importance in the context of differential sensory responses, pathophysiologies, and application of pharmacological drugs such as anaesthetics acting on TRPVs.
Artificial controlled model of blood circulation system for adhesive evaluation
Authors: Jung Sang-Myung , Chung Goo Yong , Shin Hwa Sung 
Published: November 2017

AbstractSince there are several casualties due to uncontrolled bleeding resulting from simple injury to surgery, effective styptic or vessel adhesives are important; however, their development is limited by the lack of standardized systems to evaluate potential compounds. The current study outlines the development of an aorta styptic evaluation system, comprising of decellularized swine aorta tissue and a heart pump-mimicking system. Although the cells in the swine aorta were removed, the structural stability of the aorta was sustained due to the maintenance of the extracellular matrix. Using a control adhesive, Cyanoacrylate, the developed model was found to have similar adhesive efficacy to intact aorta. The circulatory-mimicking system was designed to mimic the beat rate and strength of blood-flow from the heart, which was necessary to evaluate the adherent efficacy. The decellularized aorta improves instabilities of intact tissues, which occurs on account of storage and origin, thereby allowing for a more standardized system. The system was able to simulate several symptoms of circulation, according to patient age and health, by adjusting pumping frequency and intensity. Therefore, this system can be used as a standardized evaluation system for screening adhesives. Further, it would also evaluate other medical devices, such as stent or medications.
Rational engineering of a native hyperthermostable lactonase into a broad spectrum phosphotriesterase
Authors: Jacquet Pauline , Hiblot Julien , Daudé David , Bergonzi Céline , Gotthard Guillaume , Armstrong Nicholas , Chabrière Eric , Elias Mikael 
Published: November 2017

AbstractThe redesign of enzyme active sites to alter their function or specificity is a difficult yet appealing challenge. Here we used a structure-based design approach to engineer the lactonase SsoPox from Sulfolobus solfataricus into a phosphotriesterase. The five best variants were characterized and their structure was solved. The most active variant, αsD6 (V27A-Y97W-L228M-W263M) demonstrates a large increase in catalytic efficiencies over the wild-type enzyme, with increases of 2,210-fold, 163-fold, 58-fold, 16-fold against methyl-parathion, malathion, ethyl-paraoxon, and methyl-paraoxon, respectively. Interestingly, the best mutants are also capable of degrading fensulfothion, which is reported to be an inhibitor for the wild-type enzyme, as well as others that are not substrates of the starting template or previously reported W263 mutants. The broad specificity of these engineered variants makes them promising candidates for the bioremediation of organophosphorus compounds. Analysis of their structures reveals that the increase in activity mainly occurs through the destabilization of the active site loop involved in substrate binding, and it has been observed that the level of disorder correlates with the width of the enzyme specificity spectrum. This finding supports the idea that active site conformational flexibility is essential to the acquisition of broader substrate specificity.
Territory holders and non-territory holders in Ayu fish coexist only in the population growth process due to hysteresis
Authors: Katsumata Yuki , Uehara Takashi , Ito Hiromu , Yoshimura Jin , Tainaka Kei-ichi , Ichinose Genki 
Published: November 2017

AbstractAyu fish form feeding territories during a non-breeding (growing) season. When the density of the fish increases, phases gradually change. In the early growing season, all fish can hold territories at low density. Once all territory sites are occupied, newcomers become floaters. As the density further increases, territory holders have to spend much more time in defending their own territory and lose the time to feed on algae. Eventually, all fish give up their own territories and then form a school. In contrast, when the density decreases, territories are directly reformed from the school. In short, ayu fish exhibit a different transition, called hysteresis, where the two transitions occur widely-apart from each other. The dynamics of this intrinsic phenomena has not been demonstrated in previous studies. We develop a rate equation to describe the population dynamics within territorial competition. Our model successfully reproduces territorial hysteresis and indicates that territory holders and floaters can coexist only in the process of population growth. Moreover, we also find that the two critical densities of territorial hysteresis are conspicuously different from each other when the increase of the density of floaters sharply influences (step-function-like) the territories.