bluuebunny/crossref_metadata_2025_split huggingface dataset:
Determination of individual contact interfaces in carbon nanotube network-based transistors
Authors: Yoon Jinsu , Lim Meehyun , Choi Bongsik , Kim Dong Myong , Kim Dae Hwan , Kim Sungho , Choi Sung-Jin 
Published: July 2017

AbstractCarbon nanotubes (CNTs) used as semiconducting channels induce high mobility, thermal conductivity, mechanical flexibility, and chemical stability in field-effect, thin-film transistors (TFTs). However, the contact interfaces in CNT-TFTs have contact resistances that are difficult to reduce; this contact resistance can eventually limit the overall performance of CNT-TFTs. The contact interface between the source/drain electrodes and CNTs, especially for those CNT-TFTs in which the channel comprises randomly networked CNTs, plays a particularly dominant role in determining the performance and degree of variability in CNT-TFTs. However, no studies have reported a determination method that individually extracts each contact resistance at the source/drain electrodes. The present work presents an efficient method for directly determining the contact interfaces in CNT-TFTs by extracting each contact resistance produced at the source (R
S
) and drain (R
D
) electrodes. Moreover, we comprehensively simulated the randomly networked CNTs using an in-depth Monte-Carlo method, which provides an efficient method for visualizing the uniformity of a CNT network with various controllable CNT parameters. The proposed method provides guidance and a means for optimizing the design of the CNT network channel in CNT-TFTs and additional insights into improving the performance of CNT-TFTs.
Plasticity in the Oxidative Folding Pathway of the High Affinity Nerita Versicolor Carboxypeptidase Inhibitor (NvCI)
Authors: Esperante Sebastián A. , Covaleda Giovanni , Trejo Sebastián A. , Bronsoms Sílvia , Aviles Francesc X. , Ventura Salvador 
Published: July 2017

AbstractNerita Versicolor carboxypeptidase inhibitor (NvCI) is the strongest inhibitor reported so far for the M14A subfamily of carboxypeptidases. It comprises 53 residues and a protein fold composed of a two-stranded antiparallel β sheet connected by three loops and stabilized by three disulfide bridges. Here we report the oxidative folding and reductive unfolding pathways of NvCI. Much debate has gone on whether protein conformational folding guides disulfide bond formation or instead they are disulfide bonds that favour the arrangement of local or global structural elements. We show here that for NvCI both possibilities apply. Under physiological conditions, this protein folds trough a funnelled pathway involving a network of kinetically connected native-like intermediates, all sharing the disulfide bond connecting the two β-strands. In contrast, under denaturing conditions, the folding of NvCI is under thermodynamic control and follows a “trial and error” mechanism, in which an initial quasi-stochastic population of intermediates rearrange their disulfide bonds to attain the stable native topology. Despite their striking mechanistic differences, the efficiency of both folding routes is similar. The present study illustrates thus a surprising plasticity in the folding of this extremely stable small disulfide-rich inhibitor and provides the basis for its redesign for biomedical applications.
A method for validating Rent’s rule for technological and biological networks
Authors: Alcalde Cuesta Fernando , González Sequeiros Pablo , Lozano Rojo Álvaro 
Published: July 2017

AbstractRent’s rule is empirical power law introduced in an effort to describe and optimize the wiring complexity of computer logic graphs. It is known that brain and neuronal networks also obey Rent’s rule, which is consistent with the idea that wiring costs play a fundamental role in brain evolution and development. Here we propose a method to validate this power law for a certain range of network partitions. This method is based on the bifurcation phenomenon that appears when the network is subjected to random alterations preserving its degree distribution. It has been tested on a set of VLSI circuits and real networks, including biological and technological ones. We also analyzed the effect of different types of random alterations on the Rentian scaling in order to test the influence of the degree distribution. There are network architectures quite sensitive to these randomization procedures with significant increases in the values of the Rent exponents.
Sub-nanometer surface chemistry and orbital hybridization in lanthanum-doped ceria nano-catalysts revealed by 3D electron microscopy
Authors: Collins Sean M. , Fernandez-Garcia Susana , Calvino José J. , Midgley Paul A. 
Published: July 2017

AbstractSurface chemical composition, electronic structure, and bonding characteristics determine catalytic activity but are not resolved for individual catalyst particles by conventional spectroscopy. In particular, the nano-scale three-dimensional distribution of aliovalent lanthanide dopants in ceria catalysts and their effect on the surface electronic structure remains unclear. Here, we reveal the surface segregation of dopant cations and oxygen vacancies and observe bonding changes in lanthanum-doped ceria catalyst particle aggregates with sub-nanometer precision using a new model-based spectroscopic tomography approach. These findings refine our understanding of the spatially varying electronic structure and bonding in ceria-based nanoparticle aggregates with aliovalent cation concentrations and identify new strategies for advancing high efficiency doped ceria nano-catalysts.
TALEN based HPV-E7 editing triggers necrotic cell death in cervical cancer cells
Authors: Shankar Sumitra , Prasad Deepti , Sanawar Rahul , Das Ani V. , Pillai M. Radhakrishna 
Published: July 2017

AbstractHuman Papillomavirus E7 and E6 oncoproteins have been considered as suitable candidate anti-viral targets since they cause malignant conversion in cervical cancers. Transcription Activator-Like Effector Nucleases (TALENs) are recent editing tools to knockout genes by inducing double stranded breaks at specific sites in the genome. In here, we have designed specific TALENs to target E7 and analyzed their efficiency in inducing cell death in cervical cancer cells. We found that designed TALENs could yield about 10–12% editing activity as observed from T7E1 and nuclease resistance assays. Down-regulation of E7 and E6 was further evident at the transcript as well as proteins levels indicating that the selected TALENs were effective. TALEN-mediated E7 editing led to cell death as ascertained by cell cycle and Annexin V assays. Annexin profiling suggested that cell death could be due to necrosis as observed by upregulation of necrotic markers such as LDH A, Rip-1, and Cyclophilin A. Necrosis appears to be a better therapeutic response as it could further activate pro-inflammatory cytokines to attract immune cells to eliminate HPV-integrated cells and therefore TALEN editing strategy has the potential to be a promising tool as an adjuvant therapy in cervical cancer along with surgery.
Metadiffusers: Deep-subwavelength sound diffusers
Authors: Jiménez Noé , Cox Trevor J. , Romero-García Vicent , Groby Jean-Philippe 
Published: July 2017

AbstractWe present deep-subwavelength diffusing surfaces based on acoustic metamaterials, namely metadiffusers. These sound diffusers are rigidly backed slotted panels, with each slit being loaded by an array of Helmholtz resonators. Strong dispersion is produced in the slits and slow sound conditions are induced. Thus, the effective thickness of the panel is lengthened introducing its quarter wavelength resonance in the deep-subwavelength regime. By tuning the geometry of the metamaterial, the reflection coefficient of the panel can be tailored to obtain either a custom reflection phase, moderate or even perfect absorption. Using these concepts, we present ultra-thin diffusers where the geometry of the metadiffuser has been tuned to obtain surfaces with spatially dependent reflection coefficients having uniform magnitude Fourier transforms. Various designs are presented where, quadratic residue, primitive root and ternary sequence diffusers are mimicked by metadiffusers whose thickness are 1/46 to 1/20 times the design wavelength, i.e., between about a twentieth and a tenth of the thickness of traditional designs. Finally, a broadband metadiffuser panel of 3 cm thick was designed using optimization methods for frequencies ranging from 250 Hz to 2 kHz.
Novel data analysis method for multicolour flow cytometry links variability of multiple markers on single cells to a clinical phenotype
Authors: Tinnevelt Gerjen H. , Kokla Marietta , Hilvering Bart , van Staveren Selma , Folcarelli Rita , Xue Luzheng , Bloem Andries C. , Koenderman Leo , Buydens Lutgarde M. C. , Jansen Jeroen J. 
Published: July 2017

AbstractMulticolour Flow Cytometry (MFC) produces multidimensional analytical data on the quantitative expression of multiple markers on single cells. This data contains invaluable biomedical information on (1) the marker expressions per cell, (2) the variation in such expression across cells, (3) the variability of cell marker expression across samples that (4) may vary systematically between cells collected from donors and patients. Current conventional and even advanced data analysis methods for MFC data explore only a subset of these levels. The Discriminant Analysis of MultiAspect CYtometry (DAMACY) we present here provides a comprehensive view on health and disease responses by integrating all four levels. We validate DAMACY by using three distinct datasets: in vivo response of neutrophils evoked by systemic endotoxin challenge, the clonal response of leukocytes in bone marrow of acute myeloid leukaemia (AML) patients, and the complex immune response in blood of asthmatics. DAMACY provided good accuracy 91–100% in the discrimination between health and disease, on par with literature values. Additionally, the method provides figures that give insight into the marker expression and cell variability for more in-depth interpretation, that can benefit both physicians and biomedical researchers to better diagnose and monitor diseases that are reflected by changes in blood leukocytes.
Evaluation of eLIFT for Non-invasive Assessment of Liver fibrosis and Cirrhosis in Patients with Chronic Hepatitis B Virus Infection
Authors: Li Qiang , Lu Chuan , Li Weixia , Huang Yuxian , Chen Liang 
Published: July 2017

AbstractRecently, the easy Liver Fibrosis Test (eLIFT), a sum of points attributed to age, gender, gamma-glutamyl transpeptidase, aspartate transaminase, platelets, and prothrombin time, was developed for diagnosing advanced fibrosis and cirrhosis in chronic liver disease. We aimed to evaluate the performance of eLIFT to predict liver fibrosis and cirrhosis in patients with chronic hepatitis B (CHB). Histologic and laboratory data of 747 CHB patients were analyzed. The performance of eLIFT for diagnosing liver fibrosis and cirrhosis was compared with that of aspartate transaminase to platelet ratio index (APRI) and fibrosis index based on the 4 factors (FIB-4). To predict advanced fibrosis, the AUROC of eLIFT was comparable with that of APRI (0.66 vs 0.71, p = 0.095) and FIB-4 (0.66 vs 0.67, p = 0.612). To predict severe fibrosis, the AUROC of eLIFT was lower than that of APRI (0.65 vs 0.83, p < 0.001) and FIB-4 (0.65 vs 0.82, p < 0.001). To predict cirrhosis, the AUROC of eLIFT was also lower than that of APRI (0.64 vs 0.85, p = 0.001) and FIB-4 (0.64 vs 0.76, p = 0.033). The eLIFT is not a good non-invasive test for the diagnosis of liver fibrosis and cirrhosis in CHB patients.
Deviation of the typical AAA substrate-threading pore prevents fatal protein degradation in yeast Cdc48
Authors: Esaki Masatoshi , Islam Md. Tanvir , Tani Naoki , Ogura Teru 
Published: July 2017

AbstractYeast Cdc48 is a well-conserved, essential chaperone of ATPases associated with diverse cellular activity (AAA) proteins, which recognizes substrate proteins and modulates their conformations to carry out many cellular processes. However, the fundamental mechanisms underlying the diverse pivotal roles of Cdc48 remain unknown. Almost all AAA proteins form a ring-shaped structure with a conserved aromatic amino acid residue that is essential for proper function. The threading mechanism hypothesis suggests that this residue guides the intrusion of substrate proteins into a narrow pore of the AAA ring, thereby becoming unfolded. By contrast, the aromatic residue in one of the two AAA rings of Cdc48 has been eliminated through evolution. Here, we show that artificial retrieval of this aromatic residue in Cdc48 is lethal, and essential features to support the threading mechanism are required to exhibit the lethal phenotype. In particular, genetic and biochemical analyses of the Cdc48 lethal mutant strongly suggested that when in complex with the 20S proteasome, essential proteins are abnormally forced to thread through the Cdc48 pore to become degraded, which was not detected in wild-type Cdc48. Thus, the widely applicable threading model is less effective for wild-type Cdc48; rather, Cdc48 might function predominantly through an as-yet-undetermined mechanism.
Experimental investigation on preconditioned rate induced tipping in a thermoacoustic system
Authors: Tony J. , Subarna S , Syamkumar K. S. , Sudha G. , Akshay S. , Gopalakrishnan E. A. , Surovyatkina E. , Sujith R. I. 
Published: July 2017

AbstractMany systems found in nature are susceptible to tipping, where they can shift from one stable dynamical state to another. This shift in dynamics can be unfavorable in systems found in various fields ranging from ecology to finance. Hence, it is important to identify the factors that can lead to tipping in a physical system. Tipping can mainly be brought about by a change in parameter or due to the influence of external fluctuations. Further, the rate at which the parameter is varied also determines the final state that the system attains. Here, we show preconditioned rate induced tipping in experiments and in a theoretical model of a thermoacoustic system. We provide a specific initial condition (preconditioning) and vary the parameter at a rate higher than a critical rate to observe tipping. We find that the critical rate is a function of the initial condition. Our study is highly relevant because the parameters that dictate the asymptotic behavior of many physical systems are temporally dynamic.
RNA structure refinement using NMR solvent accessibility data
Authors: Hartlmüller Christoph , Günther Johannes C. , Wolter Antje C. , Wöhnert Jens , Sattler Michael , Madl Tobias 
Published: July 2017

AbstractNMR spectroscopy is a powerful technique to study ribonucleic acids (RNAs) which are key players in a plethora of cellular processes. Although the NMR toolbox for structural studies of RNAs expanded during the last decades, they often remain challenging. Here, we show that solvent paramagnetic relaxation enhancements (sPRE) induced by the soluble, paramagnetic compound Gd(DTPA-BMA) provide a quantitative measure for RNA solvent accessibility and encode distance-to-surface information that correlates well with RNA structure and improves accuracy and convergence of RNA structure determination. Moreover, we show that sPRE data can be easily obtained for RNAs with any isotope labeling scheme and is advantageous regarding sample preparation, stability and recovery. sPRE data show a large dynamic range and reflect the global fold of the RNA suggesting that they are well suited to identify interaction surfaces, to score structural models and as restraints in RNA structure determination.
Can weather generation capture precipitation patterns across different climates, spatial scales and under data scarcity?
Authors: Breinl Korbinian , Di Baldassarre Giuliano , Girons Lopez Marc , Hagenlocher Michael , Vico Giulia , Rutgersson Anna 
Published: July 2017

AbstractStochastic weather generators can generate very long time series of weather patterns, which are indispensable in earth sciences, ecology and climate research. Yet, both their potential and limitations remain largely unclear because past research has typically focused on eclectic case studies at small spatial scales in temperate climates. In addition, stochastic multi-site algorithms are usually not publicly available, making the reproducibility of results difficult. To overcome these limitations, we investigated the performance of the reduced-complexity multi-site precipitation generator TripleM across three different climatic regions in the United States. By resampling observations, we investigated for the first time the performance of a multi-site precipitation generator as a function of the extent of the gauge network and the network density. The definition of the role of the network density provides new insights into the applicability in data-poor contexts. The performance was assessed using nine different statistical metrics with main focus on the inter-annual variability of precipitation and the lengths of dry and wet spells. Among our study regions, our results indicate a more accurate performance in wet temperate climates compared to drier climates. Performance deficits are more marked at larger spatial scales due to the increasing heterogeneity of climatic conditions.
Cryo-EM reconstruction of the Cafeteria roenbergensis virus capsid suggests novel assembly pathway for giant viruses
Authors: Xiao Chuan , Fischer Matthias G. , Bolotaulo Duer M. , Ulloa-Rondeau Nancy , Avila Gustavo A. , Suttle Curtis A. 
Published: July 2017

AbstractWhereas the protein composition and overall shape of several giant virus capsids have been described, the mechanism by which these large capsids assemble remains enigmatic. Here, we present a reconstruction of the capsid of Cafeteria roenbergensis virus (CroV), one of the largest viruses analyzed by cryo-electron microscopy (cryo-EM) to date. The CroV capsid has a diameter of 3,000 Å and a Triangulation number of 499. Unlike related mimiviruses, the CroV capsid is not decorated with glycosylated surface fibers, but features 30 Å-long surface protrusions that are formed by loops of the major capsid protein. Based on the orientation of capsomers in the cryo-EM reconstruction, we propose that the capsids of CroV and related giant viruses are assembled by a newly conceived assembly pathway that initiates at a five-fold vertex and continuously proceeds outwards in a spiraling fashion.
Colored and fluorescent nanofibrous silk as a physically transient chemosensor and vitamin deliverer
Authors: Min Kyungtaek , Kim Sookyoung , Kim Chang Gun , Kim Sunghwan 
Published: July 2017

AbstractBiodegradable and physically transient optics represent an emerging paradigm in healthcare devices by harnessing optically active system and obviating issues with chronic uses. Light emitting components that can efficiently interact with their environments have advantages of high sensitivity, visibility, and wireless operation. Here, we report a novel combination of silk biopolymer and optically active organic dyes resulting in versatile fluorescent silk nanofibers (FSNs). FSNs generated by the electrospinning method exhibit attractive functions of the doped organic dyes along with programming the system that physically disappear at prescribed time. Red-green-blue (RGB) fluorescent nanofibrous mats, eco-friendly and transient fluorescent chemosensors for acid vapor detection, and disposable membranes for nutrition delivery were successfully demonstrated using FSNs. These functions introduced using four water soluble dyes: rhodamine B, sodium fluorescein, stilbene 420, and riboflavin. The FSN with sodium fluorescein especially, showed a sensing capability for hazardous and volatile hydrochloric acid vapors. Delivering riboflavin (vitamin B2, an important nutrient for skin care) in the FSN to a biological tissue could be observed by tracing the fluorescence of riboflavin.
TRAIL regulatory receptors constrain human hepatic stellate cell apoptosis
Authors: Singh Harsimran D. , Otano Itziar , Rombouts Krista , Singh Kasha P. , Peppa Dimitra , Gill Upkar S. , Böttcher Katrin , Kennedy Patrick T. F. , Oben Jude , Pinzani Massimo , Walczak Henning , Fusai Giuseppe , Rosenberg William M. C. , Maini Mala K. 
Published: July 2017

AbstractThe TRAIL pathway can mediate apoptosis of hepatic stellate cells to promote the resolution of liver fibrosis. However, TRAIL has the capacity to bind to regulatory receptors in addition to death-inducing receptors; their differential roles in liver fibrosis have not been investigated. Here we have dissected the contribution of regulatory TRAIL receptors to apoptosis resistance in primary human hepatic stellate cells (hHSC). hHSC isolated from healthy margins of liver resections from different donors expressed variable levels of TRAIL-R2/3/4 (but negligible TRAIL-R1) ex vivo and after activation. The apoptotic potential of TRAIL-R2 on hHSC was confirmed by lentiviral-mediated knockdown. A functional inhibitory role for TRAIL-R3/4 was revealed by shRNA knockdown and mAb blockade, showing that these regulatory receptors limit apoptosis of hHSC in response to both oligomerised TRAIL and NK cells. A close inverse ex vivo correlation between hHSC TRAIL-R4 expression and susceptibility to apoptosis underscored its central regulatory role. Our data provide the first demonstration of non-redundant functional roles for the regulatory TRAIL receptors (TRAIL-R3/4) in a physiological setting. The potential for these inhibitory TRAIL receptors to protect hHSC from apoptosis opens new avenues for prognostic and therapeutic approaches to the management of liver fibrosis.
Comparative study of Arabidopsis PBS1 and a wheat PBS1 homolog helps understand the mechanism of PBS1 functioning in innate immunity
Authors: Sun Jianhang , Huang Guozhong , Fan Fenggui , Wang Shuangfeng , Zhang Yingying , Han Yufang , Zou Yanmin , Lu Dongping 
Published: July 2017

AbstractArabidopsis AVRPPHB SUSCEPTIBLE1 (PBS1) serves as a “decoy” in activating RESISTANCE TO PSEUDOMONAS SYRINGAE5 (RPS5) upon cleavage by Pseudomonas phaseolicola B (AvrPphB), a Pseudomonas syringae effector. The SEMPH motif in PBS1 was thought to allow it to be distinguished by RPS5 from the closely related Arabidopsis kinases. However, the underlying mechanism is not fully understood. Here, we isolated and characterized a wheat PBS1 homolog, TaPBS1. Although this plasma membrane-localized kinase could be cleaved by AvrPphB and could associate with RPS5, it failed to trigger RPS5-mediated hypersensitive response (HR) in a transient assay. TaPBS1 harbors a STRPH motif. The association of RPS5 with TaPBS1 was weaker than with PBS1. Change of the STRPH motif to the SEMPH motif allowed TaPBS1 to trigger HR. However, the SEMPH motif is not required for association of PBS1 with RPS5. The difference between “SEMPH” and “STRPH” points to the importance of “EM” in PBS1. Furthermore we found that a negatively charged amino acid at the position of “E” in the SEMPH motif was required for recognition of PBS1 by RPS5. Additionally, both PBS1 and TaPBS1 undergo the flagellin-induced phosphorylation. Therefore, our work will help understand the mechanism of PBS1 functioning in plant innate immunity.
Electro-mechanical light modulator based on controlling the interaction of light with a metasurface
Authors: Cencillo-Abad Pablo , Ou Jun-Yu , Plum Eric , Zheludev Nikolay I. 
Published: July 2017

AbstractWe demonstrate a reflective light modulator, a dynamic Salisbury screen where modulation of light is achieved by moving a thin metamaterial absorber to control its interaction with the standing wave formed by the incident wave and its reflection on a mirror. Electrostatic actuation of the plasmonic metamaterial absorber’s position leads to a dynamic change of the Salisbury screen’s spectral response and 50% modulation of the reflected light intensity in the near infrared part of the spectrum. The proposed approach can also be used with other metasurfaces to control the changes they impose on the polarization, intensity, phase, spectrum and directional distribution of reflected light.