bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diversity in D-genome synthetic hexaploid wheat association panel for seedling emergence traits under salinity stress
Authors: Khan Zeeshan , Qazi Javaria , Rasheed Awais , Mujeeb-Kazi Abdul 
Published: June 2016

AbstractSeedling emergence is the preliminary factor defining wheat adaptability and stability under salt stress. This study was led to assess the salinity tolerance amongst 226 synthetic hexaploid wheats (SHWs) evaluated against two check cultivars, the tolerant ‘S-24’ and the susceptible ‘PBW-343’ at three sodium chloride treatments (0, 100 and 200 mM). Highly significant and positive correlation was observed between germination % and germination index (r = 0.85), and between seedling height and weight (r = 0.85). All four traits across three treatments were transformed into the salt tolerance trait index and salt tolerance index (STI). STI had significant positive correlation with all four parameters indicating reliability of this index for ranking the tolerance levels. STI-based 20 best performing genotypes were known as being promising candidates for wheat breeding. Local tolerant check was amongst the top three tolerant accessions. Two SHWs, AUS30288 {Croc_1/Aegilops squarrosa (466)} and AUS34444 {Ceta/Ae. squarrosa (872)} outperformed S-24 with STI of 61.8 and 55.7, respectively. SHW with same durum parents were included in tolerant and susceptible categories indicating that tolerance is contributed by the Ae. squarrosa syn. tauschii parent of SHWs. In conclusion, this baseline study revealed that continuous variation in the seedling emergence traits under salt stress is a conduit towards implementing genome-wide association studies. Likewise, new diversity has implications in development of salt tolerance germplasm after genetic dissection permitting unique Ae. squarrosa accessional diversity validation to target SHW donors for breeding.
Long noncoding RNA NRON contributes to HIV-1 latency by specifically inducing tat protein degradation
Authors: Li Jun , Chen Cancan , Ma Xiancai , Geng Guannan , Liu Bingfeng , Zhang Yijun , Zhang Shaoyang , Zhong Fudi , Liu Chao , Yin Yue , Cai Weiping , Zhang Hui 
Published: June 2016

AbstractLong noncoding RNAs (lncRNAs) play multiple key regulatory roles in various cellular pathways. However, their functions in HIV-1 latent infection remain largely unknown. Here we show that a lncRNA named NRON, which is highly expressed in resting CD4+ T lymphocytes, could be involved in HIV-1 latency by specifically inducing Tat protein degradation. Our results suggest that NRON lncRNA potently suppresses the viral transcription by decreasing the cellular abundance of viral transactivator protein Tat. NRON directly links Tat to the ubiquitin/proteasome components including CUL4B and PSMD11, thus facilitating Tat degradation. Depletion of NRON, especially in combination with a histone deacetylase (HDAC) inhibitor, significantly reactivates the viral production from the HIV-1-latently infected primary CD4+ T lymphocytes. Our data indicate that lncRNAs play a role in HIV-1 latency and their manipulation could be a novel approach for developing latency-reversing agents.
Discovery of relict subglacial lakes and their geometry and mechanism of drainage
Authors: Livingstone Stephen J. , Utting Daniel J. , Ruffell Alastair , Clark Chris D. , Pawley Steven , Atkinson Nigel , Fowler Andrew C. 
Published: June 2016

AbstractRecent proxy measurements reveal that subglacial lakes beneath modern ice sheets periodically store and release large volumes of water, providing an important but poorly understood influence on contemporary ice dynamics and mass balance. This is because direct observations of how lake drainage initiates and proceeds are lacking. Here we present physical evidence of the mechanism and geometry of lake drainage from the discovery of relict subglacial lakes formed during the last glaciation in Canada. These palaeo-subglacial lakes comprised shallow (<10 m) lenses of water perched behind ridges orientated transverse to ice flow. We show that lakes periodically drained through channels incised into bed substrate (canals). Canals sometimes trend into eskers that represent the depositional imprint of the last high-magnitude lake outburst. The subglacial lakes and channels are preserved on top of glacial lineations, indicating long-term re-organization of the subglacial drainage system and coupling to ice flow.
An experimental test of noncontextuality without unphysical idealizations
Authors: Mazurek Michael D. , Pusey Matthew F. , Kunjwal Ravi , Resch Kevin J. , Spekkens Robert W. 
Published: June 2016

AbstractTo make precise the sense in which nature fails to respect classical physics, one requires a formal notion of classicality. Ideally, such a notion should be defined operationally, so that it can be subject to direct experimental test, and it should be applicable in a wide variety of experimental scenarios so that it can cover the breadth of phenomena thought to defy classical understanding. Bell’s notion of local causality fulfils the first criterion but not the second. The notion of noncontextuality fulfils the second criterion, but it is a long-standing question whether it can be made to fulfil the first. Previous attempts to test noncontextuality have all assumed idealizations that real experiments cannot achieve, namely noiseless measurements and exact operational equivalences. Here we show how to devise tests that are free of these idealizations. We perform a photonic implementation of one such test, ruling out noncontextual models with high confidence.
Stabilizing lithium metal using ionic liquids for long-lived batteries
Authors: Basile A. , Bhatt A. I. , O’Mullane A. P. 
Published: June 2016

AbstractSuppressing dendrite formation at lithium metal anodes during cycling is critical for the implementation of future lithium metal-based battery technology. Here we report that it can be achieved via the facile process of immersing the electrodes in ionic liquid electrolytes for a period of time before battery assembly. This creates a durable and lithium ion-permeable solid–electrolyte interphase that allows safe charge–discharge cycling of commercially applicable Li|electrolyte|LiFePO4 batteries for 1,000 cycles with Coulombic efficiencies >99.5%. The tailored solid–electrolyte interphase is prepared using a variety of electrolytes based on the N-propyl-N-methylpyrrolidinium bis(fluorosulfonyl)imide room temperature ionic liquid containing lithium salts. The formation is both time- and lithium salt-dependant, showing dynamic morphology changes, which when optimized prevent dendrite formation and consumption of electrolyte during cycling. This work illustrates that a simple, effective and industrially applicable lithium metal pretreatment process results in a commercially viable cycle life for a lithium metal battery.
The social contingency of momentary subjective well-being
Authors: Rutledge Robb B. , de Berker Archy O. , Espenhahn Svenja , Dayan Peter , Dolan Raymond J. 
Published: June 2016

AbstractAlthough social comparison is a known determinant of overall life satisfaction, it is not clear how it affects moment-to-moment variation in subjective emotional state. Using a novel social decision task combined with computational modelling, we show that a participant’s subjective emotional state reflects not only the impact of rewards they themselves receive, but also the rewards received by a social partner. Unequal outcomes, whether advantageous or disadvantageous, reduce average momentary happiness. Furthermore, the relative impacts of advantageous and disadvantageous inequality on momentary happiness at the individual level predict a subject’s generosity in a separate dictator game. These findings demonstrate a powerful social influence upon subjective emotional state, where emotional reactivity to inequality is strongly predictive of altruism in an independent task domain.
Cross-membranes orchestrate compartmentalization and morphogenesis in Streptomyces
Authors: Celler Katherine , Koning Roman I. , Willemse Joost , Koster Abraham J. , van Wezel Gilles P. 
Published: June 2016

AbstractFar from being simple unicellular entities, bacteria have complex social behaviour and organization, living in large populations, and some even as coherent, multicellular entities. The filamentous streptomycetes epitomize such multicellularity, growing as a syncytial mycelium with physiologically distinct hyphal compartments separated by infrequent cross-walls. The viability of mutants devoid of cell division, which can be propagated from fragments, suggests the presence of a different form of compartmentalization in the mycelium. Here we show that complex membranes, visualized by cryo-correlative light microscopy and electron tomography, fulfil this role. Membranes form small assemblies between the cell wall and cytoplasmic membrane, or, as evidenced by FRAP experiments, large protein-impermeable cross-membrane structures, which compartmentalize the multinucleoid mycelium. All areas containing cross-membrane structures are nucleoid-restricted zones, suggesting that the membrane assemblies may also act to protect nucleoids from cell-wall restructuring events. Our work reveals a novel mechanism of controlling compartmentalization and development in multicellular bacteria.
Spatial niche formation but not malignant progression is a driving force for intratumoural heterogeneity
Authors: Hoefflin Rouven , Lahrmann Bernd , Warsow Gregor , Hübschmann Daniel , Spath Cathleen , Walter Britta , Chen Xin , Hofer Luisa , Macher-Goeppinger Stephan , Tolstov Yanis , Korzeniewski Nina , Duensing Anette , Grüllich Carsten , Jäger Dirk , Perner Sven , Schönberg Gita , Nyarangi-Dix Joanne , Isaac Sanjay , Hatiboglu Gencay , Teber Dogu , Hadaschik Boris , Pahernik Sascha , Roth Wilfried , Eils Roland , Schlesner Matthias , Sültmann Holger , Hohenfellner Markus , Grabe Niels , Duensing Stefan 
Published: June 2016

AbstractIntratumoural heterogeneity (ITH) is a major cause of cancer-associated lethality. Extensive genomic ITH has previously been reported in clear cell renal cell carcinoma (ccRCC). Here we address the question whether ITH increases with malignant progression and can hence be exploited as a prognostic marker. Unexpectedly, precision quantitative image analysis reveals that the degree of functional ITH is virtually identical between primary ccRCCs of the lowest stage and advanced, metastatic tumours. Functional ITH was found to show a stage-independent topological pattern with peak proliferative and signalling activities almost exclusively in the tumour periphery. Exome sequencing of matching peripheral and central primary tumour specimens reveals various region-specific mutations. However, these mutations cannot directly explain the zonal pattern suggesting a role of microenvironmental factors in shaping functional ITH. In conclusion, our results indicate that ITH is an early and general characteristic of malignant growth rather than a consequence of malignant progression.
Extensive local adaptation within the chemosensory system following Drosophila melanogaster’s global expansion
Authors: Arguello J. Roman , Cardoso-Moreira Margarida , Grenier Jennifer K. , Gottipati Srikanth , Clark Andrew G. , Benton Richard 
Published: June 2016

AbstractHow organisms adapt to new environments is of fundamental biological interest, but poorly understood at the genetic level. Chemosensory systems provide attractive models to address this problem, because they lie between external environmental signals and internal physiological responses. To investigate how selection has shaped the well-characterized chemosensory system of Drosophila melanogaster, we have analysed genome-wide data from five diverse populations. By couching population genomic analyses of chemosensory protein families within parallel analyses of other large families, we demonstrate that chemosensory proteins are not outliers for adaptive divergence between species. However, chemosensory families often display the strongest genome-wide signals of recent selection within D. melanogaster. We show that recent adaptation has operated almost exclusively on standing variation, and that patterns of adaptive mutations predict diverse effects on protein function. Finally, we provide evidence that chemosensory proteins have experienced relaxed constraint, and argue that this has been important for their rapid adaptation over short timescales.
Mesoscale atmosphere ocean coupling enhances the transfer of wind energy into the ocean
Authors: Byrne D. , Münnich M. , Frenger I. , Gruber N. 
Published: June 2016

AbstractAlthough it is well established that the large-scale wind drives much of the world’s ocean circulation, the contribution of the wind energy input at mesoscales (10–200 km) remains poorly known. Here we use regional simulations with a coupled high-resolution atmosphere–ocean model of the South Atlantic, to show that mesoscale ocean features and, in particular, eddies can be energized by their thermodynamic interactions with the atmosphere. Owing to their sea-surface temperature anomalies affecting the wind field above them, the oceanic eddies in the presence of a large-scale wind gradient provide a mesoscale conduit for the transfer of energy into the ocean. Our simulations show that this pathway is responsible for up to 10% of the kinetic energy of the oceanic mesoscale eddy field in the South Atlantic. The conditions for this pathway to inject energy directly into the mesoscale prevail over much of the Southern Ocean north of the Polar Front.
Loss of OLFM4 promotes tumor migration through inducing interleukin-8 expression and predicts lymph node metastasis in early gastric cancer
Authors: Zhao J , Shu P , Duan F , Wang X , Min L , Shen Z , Ruan Y , Qin J , Sun Y , Qin X 
Published: June 2016

AbstractEndoscopic surgery is increasingly used for early gastric cancer (EGC) treatment worldwide, and lymph node metastasis remains the most important risk factor for endoscopic surgery in EGC patients. Olfactomedin 4 (OLFM4) is mainly expressed in the digestive system and upregulated in several types of tumors. However, the role of OLFM4 in EGC has not been explored. We evaluated OLFM4 expression by immunohistochemical staining in 105 patients with EGC who underwent gastrectomy. The clinicopathological factors and OLFM4 expression were co-analyzed to predict lymph node metastasis in EGC. The metastatic mechanism of OLFM4 in gastric cancer was also investigated. We found that OLFM4 was upregulated in EGC tumor sections, and relatively low expression of OLFM4 was observed in patients with lymph node metastasis. OLFM4 expression as well as tumor size and differentiation were identified as independent factors, which could be co-analyzed to generate a better model for predicting lymph node metastasis in EGC patients. In vitro studies revealed that knockdown of OLFM4 promoted the migration of gastric cancer cells through activating the NF-κB/interleukin-8 axis. Negative correlation between OLFM4 and interleukin-8 expression was also observed in EGC tumor samples. Our study implies that OLFM4 expression is a potential predictor of lymph node metastasis in EGC, and combing OLFM4 with tumor size and differentiation could better stratify EGC patients with different risks of lymph node metastasis.
A Disposable paper breathalyzer with an alcohol sensing organic electrochemical transistor
Authors: Bihar Eloїse , Deng Yingxin , Miyake Takeo , Saadaoui Mohamed , Malliaras George G. , Rolandi Marco 
Published: June 2016

AbstractBreathalyzers estimate Blood Alcohol Content (BAC) from the concentration of ethanol in the breath. Breathalyzers are easy to use but are limited either by their high price and by environmental concerns, or by a short lifetime and the need for continuous recalibration. Here, we demonstrate a proof-of-concept disposable breathalyzer using an organic electrochemical transistor (OECT) modified with alcohol dehydrogenase (ADH) as the sensor. The OECT is made with the conducting polymer poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) and is printed on paper. ADH and its cofactor nicotinamide adenine dinucleotide (NAD+) are immobilized onto the OECT with an electrolyte gel. When the OECT-breathalyzer is exposed to ethanol vapor, the enzymatic reaction of ADH and ethanol transforms NAD+ into NADH, which causes a decrease in the OECT source drain current. In this fashion, the OECT-breathalyzer easily detects ethanol in the breath equivalent to BAC from 0.01% to 0.2%. The use of a printed OECT may contribute to the development of breathalyzers that are disposable, ecofriendly and integrated with wearable devices for real-time BAC monitoring.
Compressed Sensing Electron Tomography for Determining Biological Structure
Authors: Guay Matthew D. , Czaja Wojciech , Aronova Maria A. , Leapman Richard D. 
Published: June 2016

AbstractThere has been growing interest in applying compressed sensing (CS) theory and practice to reconstruct 3D volumes at the nanoscale from electron tomography datasets of inorganic materials, based on known sparsity in the structure of interest. Here we explore the application of CS for visualizing the 3D structure of biological specimens from tomographic tilt series acquired in the scanning transmission electron microscope (STEM). CS-ET reconstructions match or outperform commonly used alternative methods in full and undersampled tomogram recovery, but with less significant performance gains than observed for the imaging of inorganic materials. We propose that this disparity stems from the increased structural complexity of biological systems, as supported by theoretical CS sampling considerations and numerical results in simulated phantom datasets. A detailed analysis of the efficacy of CS-ET for undersampled recovery is therefore complicated by the structure of the object being imaged. The numerical nonlinear decoding process of CS shares strong connections with popular regularized least-squares methods and the use of such numerical recovery techniques for mitigating artifacts and denoising in reconstructions of fully sampled datasets remains advantageous. This article provides a link to the software that has been developed for CS-ET reconstruction of electron tomographic data sets.
A molecular determinant of phosphoinositide affinity in mammalian TRPV channels
Authors: Velisetty Phanindra , Borbiro Istvan , Kasimova Marina A. , Liu Luyu , Badheka Doreen , Carnevale Vincenzo , Rohacs Tibor 
Published: June 2016

AbstractPhosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] is an important cofactor for ion channels. Affinity for this lipid is a major determinant of channel inhibition by depletion of PI(4,5)P2 upon phospholipase C (PLC) activation. Little is known about what determines PI(4,5)P2 affinity in mammalian ion channels. Here we report that two members of the Transient Receptor Potential Vanilloid (TRPV) ion channel family, TRPV5 and TRPV6 lack a positively charged residue in the TM4-TM5 loop that was shown to interact with PI(4,5)P2 in TRPV1, which shows high affinity for this lipid. When this positively charged residue was introduced to either TRPV6 or TRPV5, they displayed markedly higher affinities for PI(4,5)P2, and were largely resistant to inhibition by PI(4,5)P2 depletion. Furthermore, Ca2+-induced inactivation of TRPV6 was essentially eliminated in the G488R mutant, showing the importance of PLC-mediated PI(4,5)P2 depletion in this process. Computational modeling shows that the introduced positive charge interacts with PI(4,5)P2 in TRPV6.
Optically induced metal-to-dielectric transition in Epsilon-Near-Zero metamaterials
Authors: Kaipurath R. M. , Pietrzyk M. , Caspani L. , Roger T. , Clerici M. , Rizza C. , Ciattoni A. , Di Falco A. , Faccio D. 
Published: June 2016

AbstractEpsilon-Near-Zero materials exhibit a transition in the real part of the dielectric permittivity from positive to negative value as a function of wavelength. Here we study metal-dielectric layered metamaterials in the homogenised regime (each layer has strongly subwavelength thickness) with zero real part of the permittivity in the near-infrared region. By optically pumping the metamaterial we experimentally show that close to the Epsilon-Near-Zero (ENZ) wavelength the permittivity exhibits a marked transition from metallic (negative permittivity) to dielectric (positive permittivity) as a function of the optical power. Remarkably, this transition is linear as a function of pump power and occurs on time scales of the order of the 100 fs pump pulse that need not be tuned to a specific wavelength. The linearity of the permittivity increase allows us to express the response of the metamaterial in terms of a standard third order optical nonlinearity: this shows a clear inversion of the roles of the real and imaginary parts in crossing the ENZ wavelength, further supporting an optically induced change in the physical behaviour of the metamaterial.
Hollow Cone Electron Imaging for Single Particle 3D Reconstruction of Proteins
Authors: Tsai Chun-Ying , Chang Yuan-Chih , Lobato Ivan , Van Dyck Dirk , Chen Fu-Rong 
Published: June 2016

AbstractThe main bottlenecks for high-resolution biological imaging in electron microscopy are radiation sensitivity and low contrast. The phase contrast at low spatial frequencies can be enhanced by using a large defocus but this strongly reduces the resolution. Recently, phase plates have been developed to enhance the contrast at small defocus but electrical charging remains a problem. Single particle cryo-electron microscopy is mostly used to minimize the radiation damage and to enhance the resolution of the 3D reconstructions but it requires averaging images of a massive number of individual particles. Here we present a new route to achieve the same goals by hollow cone dark field imaging using thermal diffuse scattered electrons giving about a 4 times contrast increase as compared to bright field imaging. We demonstrate the 3D reconstruction of a stained GroEL particle can yield about 13.5 Å resolution but using a strongly reduced number of images.
Magnetization and magneto-transport staircaselike behavior in layered perovskite Sr2CoO4 at low temperature
Authors: Li Qiuhang , Yuan Xueping , Xing Lei , Xu Mingxiang 
Published: June 2016

AbstractPolycrystalline layered perovskite Sr2CoO4 sample was synthesized by high temperature and high pressure method. The staircaselike behavior has been observed in the magnetization and resistivity versus field curves of Sr2CoO4 at low temperature. The main features of the steps can be obtained from the measured results: (i) the positions of the external magnetic field at which steps occur are varying in different measurement runs, (ii) the steps only appear at low temperature and disappear with a slight increase of the temperature, (iii) the steps are dependent on the temperature and field sweep rate. Based on the features of the magnetization and magneto-transport staircaselike behavior in Sr2CoO4, the unusual phenomenon can be ascribed to an avalanche of flipping domains in terms of the random field theory.