bluuebunny/crossref_metadata_2025_split huggingface dataset:
From coherent shocklets to giant collective incoherent shock waves in nonlocal turbulent flows
Authors: Xu G. , Vocke D. , Faccio D. , Garnier J. , Roger T. , Trillo S. , Picozzi A. 
Published: September 2015

AbstractUnderstanding turbulent flows arising from random dispersive waves that interact strongly through nonlinearities is a challenging issue in physics. Here we report the observation of a characteristic transition: strengthening the nonlocal character of the nonlinear response drives the system from a fully turbulent regime, featuring a sea of coherent small-scale dispersive shock waves (shocklets) towards the unexpected emergence of a giant collective incoherent shock wave. The front of such global incoherent shock carries most of the stochastic fluctuations and is responsible for a peculiar folding of the local spectrum. Nonlinear optics experiments performed in a solution of graphene nano-flakes clearly highlight this remarkable transition. Our observations shed new light on the role of long-range interactions in strongly nonlinear wave systems operating far from thermodynamic equilibrium, which reveals analogies with, for example, gravitational systems, and establishes a new scenario that can be common to many turbulent flows in photonic quantum fluids, hydrodynamics and Bose–Einstein condensates.
Involvement of a eukaryotic-like ubiquitin-related modifier in the proteasome pathway of the archaeon Sulfolobus acidocaldarius
Authors: Anjum Rana S. , Bray Sian M. , Blackwood John K. , Kilkenny Mairi L. , Coelho Matthew A. , Foster Benjamin M. , Li Shurong , Howard Julie A. , Pellegrini Luca , Albers Sonja-Verena , Deery Michael J. , Robinson Nicholas P. 
Published: September 2015

AbstractIn eukaryotes, the covalent attachment of ubiquitin chains directs substrates to the proteasome for degradation. Recently, ubiquitin-like modifications have also been described in the archaeal domain of life. It has subsequently been hypothesized that ubiquitin-like proteasomal degradation might also operate in these microbes, since all archaeal species utilize homologues of the eukaryotic proteasome. Here we perform a structural and biochemical analysis of a ubiquitin-like modification pathway in the archaeon Sulfolobus acidocaldarius. We reveal that this modifier is homologous to the eukaryotic ubiquitin-related modifier Urm1, considered to be a close evolutionary relative of the progenitor of all ubiquitin-like proteins. Furthermore we demonstrate that urmylated substrates are recognized and processed by the archaeal proteasome, by virtue of a direct interaction with the modifier. Thus, the regulation of protein stability by Urm1 and the proteasome in archaea is likely representative of an ancient pathway from which eukaryotic ubiquitin-mediated proteolysis has evolved.
Ambipolar solution-processed hybrid perovskite phototransistors
Authors: Li Feng , Ma Chun , Wang Hong , Hu Weijin , Yu Weili , Sheikh Arif D. , Wu Tom 
Published: September 2015

AbstractOrganolead halide perovskites have attracted substantial attention because of their excellent physical properties, which enable them to serve as the active material in emerging hybrid solid-state solar cells. Here we investigate the phototransistors based on hybrid perovskite films and provide direct evidence for their superior carrier transport property with ambipolar characteristics. The field-effect mobilities for triiodide perovskites at room temperature are measured as 0.18 (0.17) cm2V−1s−1for holes (electrons), which increase to 1.24 (1.01) cm2V−1s−1for mixed-halide perovskites. The photoresponsivity of our hybrid perovskite devices reaches 320 A W−1, which is among the largest values reported for phototransistors. Importantly, the phototransistors exhibit an ultrafast photoresponse speed of less than 10 μs. The solution-based process and excellent device performance strongly underscore hybrid perovskites as promising material candidates for photoelectronic applications.
Very low embryonic crude oil exposures cause lasting cardiac defects in salmon and herring
Authors: Incardona John P. , Carls Mark G. , Holland Larry , Linbo Tiffany L. , Baldwin David H. , Myers Mark S. , Peck Karen A. , Tagal Mark , Rice Stanley D. , Scholz Nathaniel L. 
Published: September 2015

AbstractThe 1989 Exxon Valdez disaster exposed embryos of pink salmon and Pacific herring to crude oil in shoreline spawning habitats throughout Prince William Sound, Alaska. The herring fishery collapsed four years later. The role of the spill, if any, in this decline remains one of the most controversial unanswered questions in modern natural resource injury assessment. Crude oil disrupts excitation-contraction coupling in fish heart muscle cells and we show here that salmon and herring exposed as embryos to trace levels of crude oil grow into juveniles with abnormal hearts and reduced cardiorespiratory function, the latter a key determinant of individual survival and population recruitment. Oil exposure during cardiogenesis led to specific defects in the outflow tract and compact myocardium and a hypertrophic response in spongy myocardium, evident in juveniles 7 to 9 months after exposure. The thresholds for developmental cardiotoxicity were remarkably low, suggesting the scale of the Exxon Valdez impact in shoreline spawning habitats was much greater than previously appreciated. Moreover, an irreversible loss of cardiac fitness and consequent increases in delayed mortality in oil-exposed cohorts may have been important contributors to the delayed decline of pink salmon and herring stocks in Prince William Sound.
A whole-genome RNAi screen uncovers a novel role for human potassium channels in cell killing by the parasite Entamoeba histolytica
Authors: Marie Chelsea , Verkerke Hans P. , Theodorescu Dan , Petri William A. 
Published: September 2015

AbstractThe parasite Entamoeba histolytica kills human cells resulting in ulceration, inflammation and invasion of the colonic epithelium. We used the cytotoxic properties of ameba to select a genome-wide RNAi library to reveal novel host factors that control susceptibility to amebic killing. We identified 281 candidate susceptibility genes and bioinformatics analyses revealed that ion transporters were significantly enriched among susceptibility genes. Potassium (K+) channels were the most common transporter identified. Their importance was further supported by colon biopsy of humans with amebiasis that demonstrated suppressed K+ channel expression. Inhibition of human K+ channels by genetic silencing, pharmacologic inhibitors and with excess K+ protected diverse cell types from E. histolytica-induced death. Contact with E. histolytica parasites triggered K+ channel activation and K+ efflux by intestinal epithelial cells, which preceded cell killing. Specific inhibition of Ca2+-dependent K+ channels was highly effective in preventing amebic cytotoxicity in intestinal epithelial cells and macrophages. Blockade of K+ efflux also inhibited caspase-1 activation, IL-1β secretion and pyroptotic death in THP-1 macrophages. We concluded that K+ channels are host mediators of amebic cytotoxicity in multiple cells types and of inflammasome activation in macrophages.
Friend or foe: differential responses of rice to invasion by mutualistic or pathogenic fungi revealed by RNAseq and metabolite profiling
Authors: Xu Xi-Hui , Wang Chen , Li Shu-Xian , Su Zhen-Zhu , Zhou Hui-Na , Mao Li-Juan , Feng Xiao-Xiao , Liu Ping-Ping , Chen Xia , Hugh Snyder John , Kubicek Christian P. , Zhang Chu-Long , Lin Fu-Cheng 
Published: September 2015

AbstractThe rice endophyte Harpophora oryzae shares a common pathogenic ancestor with the rice blast fungus Magnaporthe oryzae. Direct comparison of the interactions between a single plant species and two closely-related (1) pathogenic and (2) mutualistic fungi species can improve our understanding of the evolution of the interactions between plants and fungi that lead to either mutualistic or pathogenic interactions. Differences in the metabolome and transcriptome of rice in response to challenge by H. or M. oryzae were investigated with GC-MS, RNA-seq and qRT-PCR. Levels of metabolites of the shikimate and lignin biosynthesis pathways increased continuously in the M. oryzae-challenged rice roots (Mo-roots); these pathways were initially induced, but then suppressed, in the H. oryzae-challenged rice roots (Ho-roots). Compared to control samples, concentrations of sucrose and maltose were reduced in the Ho-roots and Mo-roots. The expression of most genes encoding enzymes involved in glycolysis and the TCA cycle were suppressed in the Ho-roots, but enhanced in the Mo-roots. The suppressed glycolysis in Ho-roots would result in the accumulation of glucose and fructose which was not detected in the Mo-roots. A novel co-evolution pattern of fungi-host interaction is proposed which highlights the importance of plant host in the evolution of fungal symbioses.
Non-radiative relaxation of photoexcited chlorophylls: theoretical and experimental study
Authors: Bricker William P. , Shenai Prathamesh M. , Ghosh Avishek , Liu Zhengtang , Enriquez Miriam Grace M. , Lambrev Petar H. , Tan Howe-Siang , Lo Cynthia S. , Tretiak Sergei , Fernandez-Alberti Sebastian , Zhao Yang 
Published: September 2015

AbstractNonradiative relaxation of high-energy excited states to the lowest excited state in chlorophylls marks the first step in the process of photosynthesis. We perform ultrafast transient absorption spectroscopy measurements, that reveal this internal conversion dynamics to be slightly slower in chlorophyll B than in chlorophyll A. Modeling this process with non-adiabatic excited state molecular dynamics simulations uncovers a critical role played by the different side groups in the two molecules in governing the intramolecular redistribution of excited state wavefunction, leading, in turn, to different time-scales. Even given smaller electron-vibrational couplings compared to common organic conjugated chromophores, these molecules are able to efficiently dissipate about 1 eV of electronic energy into heat on the timescale of around 200 fs. This is achieved via selective participation of specific atomic groups and complex global migration of the wavefunction from the outer to inner ring, which may have important implications for biological light-harvesting function.
RNA sequencing provides exquisite insight into the manipulation of the alveolar macrophage by tubercle bacilli
Authors: Nalpas Nicolas C. , Magee David A. , Conlon Kevin M. , Browne John A. , Healy Claire , McLoughlin Kirsten E. , Rue-Albrecht Kévin , McGettigan Paul A. , Killick Kate E. , Gormley Eamonn , Gordon Stephen V. , MacHugh David E. 
Published: September 2015

AbstractMycobacterium bovis, the agent of bovine tuberculosis, causes an estimated $3 billion annual losses to global agriculture due, in part, to the limitations of current diagnostics. Development of next-generation diagnostics requires a greater understanding of the interaction between the pathogen and the bovine host. Therefore, to explore the early response of the alveolar macrophage to infection, we report the first application of RNA-sequencing to define, in exquisite detail, the transcriptomes ofM. bovis-infected and non-infected alveolar macrophages from ten calves at 2, 6, 24 and 48 hours post-infection. Differentially expressed sense genes were detected at these time points that revealed enrichment of innate immune signalling functions and transcriptional suppression of host defence mechanisms (e.g., lysosome maturation). We also detected differentially expressed natural antisense transcripts, which may play a role in subverting innate immune mechanisms following infection. Furthermore, we report differential expression of novel bovine genes, some of which have immune-related functions based on orthology with human proteins. This is the first in-depth transcriptomics investigation of the alveolar macrophage response to the early stages ofM. bovisinfection and reveals complex patterns of gene expression and regulation that underlie the immunomodulatory mechanisms used byM. bovisto evade host defence mechanisms.
Natural Killer Cells-Produced IFN-γ Improves Bone Marrow-Derived Hepatocytes Regeneration in Murine Liver Failure Model
Authors: Li Lu , Zeng Zhutian , Qi Ziping , Wang Xin , Gao Xiang , Wei Haiming , Sun Rui , Tian Zhigang 
Published: September 2015

AbstractBone-marrow transplantation (BMT) can repopulate the liver through BM-derived hepatocyte (BMDH) generation, although the underlying mechanism remains unclear. Using fumarylacetoacetate hydrolase–deficient (Fah−/−) mice as a liver-failure model, we confirmed that BMDHs were generated by fusion of BM-derived CD11b+F4/80+myelomonocytes with resident Fah−/− hepatocytes. Hepatic NK cells became activated during BMDH generation and were the major IFN-γ producers. Indeed, both NK cells and IFN-γ were required for BMDH generation since WT, but not NK-, IFN-γ–, or IFN-γR1–deficient BM transplantation successfully generated BMDHs and rescued survival in Fah−/− hosts. BM-derived myelomonocytes were determined to be the IFN-γ–responding cells. The IFN-γ–IFN-γR interaction contributed to the myelomonocyte–hepatocyte fusion process, as most of the CD11b+ BMDHs in mixed BM chimeric Fah−/− hosts transplanted with a 1:1 ratio of CD45.1+ WT and CD45.2+Ifngr1−/− BM cells were of CD45.1+ WT origin. Confirming these findings in vitro, IFN-γ dose-dependently promoted the fusion of GFP+ myelomonocytes with Fah−/− hepatocytes due to a direct effect on myelomonocytes; similar results were observed using activated NK cells. In conclusion, BMDH generation requires NK cells to facilitate myelomonocyte–hepatocyte fusion in an IFN-γ–dependent manner, providing new insights for treating severe liver failure.
Links between fear of humans, stress and survival support a non-random distribution of birds among urban and rural habitats
Authors: Rebolo-Ifrán Natalia , Carrete Martina , Sanz-Aguilar Ana , Rodríguez-Martínez Sol , Cabezas Sonia , Marchant Tracy A. , Bortolotti Gary R. , Tella José L. 
Published: September 2015

AbstractUrban endocrine ecology aims to understand how organisms cope with new sources of stress and maintain allostatic load to thrive in an increasingly urbanized world. Recent research efforts have yielded controversial results based on short-term measures of stress, without exploring its fitness effects. We measured feather corticosterone (CORTf, reflecting the duration and amplitude of glucocorticoid secretion over several weeks) and subsequent annual survival in urban and rural burrowing owls. This species shows high individual consistency in fear of humans (i.e., flight initiation distance, FID), allowing us to hypothesize that individuals distribute among habitats according to their tolerance to human disturbance. FIDs were shorter in urban than in rural birds, but CORTflevels did not differ, nor were correlated to FIDs. Survival was twice as high in urban as in rural birds and links with CORTfvaried between habitats: while a quadratic relationship supports stabilizing selection in urban birds, high predation rates may have masked CORTf-survival relationship in rural ones. These results evidence that urban life does not constitute an additional source of stress for urban individuals, as shown by their near identical CORTfvalues compared with rural conspecifics supporting the non-random distribution of individuals among habitats according to their behavioural phenotypes.
Water from air: an overlooked source of moisture in arid and semiarid regions
Authors: McHugh Theresa A. , Morrissey Ember M. , Reed Sasha C. , Hungate Bruce A. , Schwartz Egbert 
Published: September 2015

AbstractWater drives the functioning of Earth’s arid and semiarid lands. Drylands can obtain water from sources other than precipitation, yet little is known about how non-rainfall water inputs influence dryland communities and their activity. In particular, water vapor adsorption – movement of atmospheric water vapor into soil when soil air is drier than the overlying air – likely occurs often in drylands, yet its effects on ecosystem processes are not known. By adding 18O-enriched water vapor to the atmosphere of a closed system, we documented the conversion of water vapor to soil liquid water across a temperature range typical of arid ecosystems. This phenomenon rapidly increased soil moisture and stimulated microbial carbon (C) cycling and the flux of water vapor to soil had a stronger impact than temperature on microbial activity. In a semiarid grassland, we also observed that non-rainfall water inputs stimulated microbial activity and C cycling. Together these data suggest that, during rain-free periods, atmospheric moisture in drylands may significantly contribute to variation in soil water content, thereby influencing ecosystem processes. The simple physical process of adsorption of water vapor to soil particles, forming liquid water, represents an overlooked but potentially important contributor to C cycling in drylands.
Magnetic Field Triggered Multicycle Damage Sensing and Self Healing
Authors: Ahmed Anansa S. , Ramanujan R. V. 
Published: September 2015

AbstractMultifunctional materials inspired by biological structures have attracted great interest, e.g. for wearable/ flexible “skin” and smart coatings. A current challenge in this area is to develop an artificial material which mimics biological skin by simultaneously displaying color change on damage as well as self healing of the damaged region. Here we report, for the first time, the development of a damage sensing and self healing magnet-polymer composite (Magpol), which actively responds to an external magnetic field. We incorporated reversible sensing using mechanochromic molecules in a shape memory thermoplastic matrix. Exposure to an alternating magnetic field (AMF) triggers shape recovery and facilitates damage repair. Magpol exhibited a linear strain response upto 150% strain and complete recovery after healing. We have demonstrated the use of this concept in a reusable biomedical device i.e., coated guidewires. Our findings offer a new synergistic method to bestow multifunctionality for applications ranging from medical device coatings to adaptive wing structures.
Aquaporin-1 Deficiency Protects Against Myocardial Infarction by Reducing Both Edema and Apoptosis in Mice
Authors: Li Lihua , Weng Zhiyong , Yao Chenjuan , Song Yuanlin , Ma Tonghui 
Published: September 2015

AbstractMany studies have determined that AQP1 plays an important role in edema formation and resolution in various tissues via water transport across the cell membrane. The aim of this research was to determine both if and how AQP1 is associated with cardiac ischemic injury, particularly the development of edema following myocardial infarction (MI). AQP1+/+ and AQP1−/− mice were used to create the MI model. Under physiological conditions, AQP1−/− mice develop normally; however, in the setting of MI, they exhibit cardioprotective properties, as shown by reduced cardiac infarct size determined via NBT staining, improved cardiac function determined via left ventricular catheter measurements, decreased AQP1-dependent myocardial edema determined via water content assays and decreased apoptosis determined via TUNEL analysis. Cardiac ischemia caused by hypoxia secondary to AQP1 deficiency stabilized the expression of HIF-1α in endothelial cells and subsequently decreased microvascular permeability, resulting in the development of edema. The AQP1-dependent myocardial edema and apoptosis contributed to the development of MI. AQP1 deficiency protected cardiac function from ischemic injury following MI. Furthermore, AQP1 deficiency reduced microvascular permeability via the stabilization of HIF-1α levels in endothelial cells and decreased cellular apoptosis following MI.
Electroporation of mammalian cells by nanosecond electric field oscillations and its inhibition by the electric field reversal
Authors: Gianulis Elena C. , Lee Jimo , Jiang Chunqi , Xiao Shu , Ibey Bennet L. , Pakhomov Andrei G. 
Published: September 2015

AbstractThe present study compared electroporation efficiency of bipolar and unipolar nanosecond electric field oscillations (NEFO). Bipolar NEFO was a damped sine wave with 140 ns first phase duration at 50% height; the peak amplitude of phases 2–4 decreased to 35%, 12% and 7% of the first phase. This waveform was rectified to produce unipolar NEFO by cutting off phases 2 and 4. Membrane permeabilization was quantified in CHO and GH3 cells by uptake of a membrane integrity marker dye YO-PRO-1 (YP) and by the membrane conductance increase measured by patch clamp. For treatments with 1–20 unipolar NEFO, at 9.6–24 kV/cm, 10 Hz, the rate and amount of YP uptake were consistently 2-3-fold higher than after bipolar NEFO treatments, despite delivering less energy. However, the threshold amplitude was about 7 kV/cm for both NEFO waveforms. A single 14.4 kV/cm unipolar NEFO caused a 1.5–2 times greater increase in membrane conductance (p < 0.05) than bipolar NEFO, along with a longer and less frequent recovery. The lower efficiency of bipolar NEFO was preserved in Ca2+-free conditions and thus cannot be explained by the reversal of electrophoretic flows of Ca2+. Instead, the data indicate that the electric field polarity reversals reduced the pore yield.
Thermal post-treatment alters nutrient release from a controlled-release fertilizer coated with a waterborne polymer
Authors: Zhou Zijun , Du Changwen , Li Ting , Shen Yazhen , Zhou Jianmin 
Published: September 2015

AbstractControlled-release fertilizers (CRF) use a controlled-release technology to enhance the nutrient use efficiency of crops. Many factors affect the release of nutrients from the waterborne polymer-coated CRF, but the effects of thermal post-treatments remain unclear. In this study, a waterborne polyacrylate-coated CRF was post-treated at different temperatures (30 °C, 60 °C and 80 °C) and durations (2, 4, 8, 12 and 24 h) after being developed in the Wurster fluidized bed. To characterize the polyacrylate membrane and hence to analyze the mechanism of nutrient release, Fourier transform mid-infrared spectroscopy, scanning electron microscopy and atomic force microscopy were employed. The nutrient-release model of CRF post-treated at 30 °C was the inverse “L” curve, but an increased duration of the post-treatment had no effect. The nutrient-release model was “S” curve and nutrient-release period was enhanced at higher post-treatment temperatures and increased post-treatment duration lengthened slowed nutrient release due to a more compact membrane and a smoother membrane surface as well as a promoted crosslinking action. CRF equipped with specified nutrient-release behaviors can be achieved by optimizing the thermal post-treatment parameters, which can contribute to the development and application of waterborne polymer-coated CRF and controlled-release technologies.