bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of the Effects of Conjunctivochalasis Excision on Tear Stability and Contrast Sensitivity
Authors: Qiu Weiqiang , Zhang Mingzhou , Xu Ting , Liu Ziyuan , Lv Huibin , Wang Wei , Li Xuemin 
Published: November 2016

AbstractConjunctivochalasis (CCh) disrupts tear flow and damages tear film stability. This study sought to evaluate the tear stability and contrast sensitivity of patients with CCh on whom CCh excision was performed. The study included 39 eyes from 39 patients; all patients had eyes with grade 2 or 3 CCh, underwent CCh excision, and were evaluated before and three months after the surgery. The evaluated variables included the ocular surface disease index (OSDI), the tear break-up time (TBUT), corneal fluorescein staining, corneal surface irregularity, Schirmer’s I test, the tear meniscus area (TMA), and contrast sensitivity. A follow-up of three months was achieved in 36 eyes for 36 patients. All parameters improved significantly after surgery (p < 0.05), except Schirmer’s I test, thus suggesting that CCh excision is an effective method for reconstructing the lower tear meniscus and improving both tear film stability and corneal surface irregularity. The results further demonstrated a simultaneous increase in contrast sensitivity after surgery.
Isotope effect in superconducting n-doped SrTiO3
Authors: Stucky A. , Scheerer G. W. , Ren Z. , Jaccard D. , Poumirol J.-M. , Barreteau C. , Giannini E. , van der Marel D. 
Published: November 2016

AbstractWe report the influence on the superconducting critical temperature Tc in doped SrTiO3 of the substitution of the natural 16O atoms by the heavier isotope 18O. We observe that for a wide range of doping this substitution causes a strong (~50%) enhancement of Tc. Also the magnetic critical field Hc2 is increased by a factor ~2. Such a strong impact on Tc and Hc2, with a sign opposite to conventional superconductors, is unprecedented. The observed effect could be the consequence of strong coupling of the doped electrons to lattice vibrations (phonons), a notion which finds support in numerous optical and photo-emission studies. The unusually large size of the observed isotope effect supports a recent model for superconductivity in these materials based on strong coupling to the ferroelectric soft modes of SrTiO3.
Autophagy is required for PDAC glutamine metabolism
Authors: Seo Ju-Won , Choi Jungwon , Lee So-Yeon , Sung Suhyun , Yoo Hyun Ju , Kang Min-Ji , Cheong Heesun , Son Jaekyoung 
Published: November 2016

AbstractMacroautophagy (autophagy) is believed to maintain energy homeostasis by degrading unnecessary cellular components and molecules. Its implication in regulating cancer metabolism recently started to be uncovered. However, the precise roles of autophagy in cancer metabolism are still unclear. Here, we show that autophagy plays a critical role in glutamine metabolism, which is required for tumor survival. Pancreatic ductal adenocarcinoma (PDAC) cells require both autophagy and typical glutamine transporters to maintain intracellular glutamine levels. Glutamine deprivation, but not that of glucose, led to the activation of macropinocytosis-associated autophagy through TFEB induction and translocation into the nucleus. In contrast, glutamine uptake increased as a compensatory response to decreased intracellular glutamine levels upon autophagy inhibition. Moreover, autophagy inhibition and glutamine deprivation did not induce cell death, while glutamine deprivation dramatically activated apoptotic cell death upon autophagy inhibition. Interestingly, the addition of α-ketoglutarate significantly rescued the apoptotic cell death caused by the combination of the inhibition of autophagy with glutamine deprivation. Our data suggest that macropinocytosis-associated autophagy is a critical process providing glutamine for anaplerosis of the TCA cycle in PDAC. Thus, targeting both autophagy and glutamine metabolism to completely block glutamine supply may provide new therapeutic approaches to treat refractory tumors.
Transition steps in peroxide reduction and a molecular switch for peroxide robustness of prokaryotic peroxiredoxins
Authors: Kamariah Neelagandan , Sek Mun Foong , Eisenhaber Birgit , Eisenhaber Frank , Grüber Gerhard 
Published: November 2016

AbstractIn addition to their antioxidant function, the eukaryotic peroxiredoxins (Prxs) facilitate peroxide-mediated signaling by undergoing controlled inactivation by peroxide-driven over-oxidation. In general, the bacterial enzyme lacks this controlled inactivation mechanism, making it more resistant to high H2O2 concentrations. During peroxide reduction, the active site alternates between reduced, fully folded (FF), and oxidized, locally unfolded (LU) conformations. Here we present novel insights into the divergence of bacterial and human Prxs in robustness and sensitivity to inactivation, respectively. Structural details provide new insights into sub-steps during the catalysis of peroxide reduction, enabling the transition from an FF to a LU conformation. Complementary to mutational and enzymatic results, these data unravel the essential role of the C-terminal tail of bacterial Prxs to act as a molecular switch, mediating the transition from an FF to a LU state. In addition, we propose that the C-terminal tail has influence on the propensity of the disulphide bond formation, indicating that as a consequence on the robustness and sensitivity to over-oxidation. Finally, a physical linkage between the catalytic site, the C-terminal tail and the oligomer interface is described.
Lévy random walks on multiplex networks
Authors: Guo Quantong , Cozzo Emanuele , Zheng Zhiming , Moreno Yamir 
Published: November 2016

AbstractRandom walks constitute a fundamental mechanism for many dynamics taking place on complex networks. Besides, as a more realistic description of our society, multiplex networks have been receiving a growing interest, as well as the dynamical processes that occur on top of them. Here, inspired by one specific model of random walks that seems to be ubiquitous across many scientific fields, the Lévy flight, we study a new navigation strategy on top of multiplex networks. Capitalizing on spectral graph and stochastic matrix theories, we derive analytical expressions for the mean first passage time and the average time to reach a node on these networks. Moreover, we also explore the efficiency of Lévy random walks, which we found to be very different as compared to the single layer scenario, accounting for the structure and dynamics inherent to the multiplex network. Finally, by comparing with some other important random walk processes defined on multiplex networks, we find that in some region of the parameters, a Lévy random walk is the most efficient strategy. Our results give us a deeper understanding of Lévy random walks and show the importance of considering the topological structure of multiplex networks when trying to find efficient navigation strategies.
Droplet Merging on a Lab-on-a-Chip Platform by Uniform Magnetic Fields
Authors: Varma V. B. , Ray A. , Wang Z. M. , Wang Z. P. , Ramanujan R. V. 
Published: November 2016

AbstractDroplet microfluidics offers a range of Lab-on-a-chip (LoC) applications. However, wireless and programmable manipulation of such droplets is a challenge. We address this challenge by experimental and modelling studies of uniform magnetic field induced merging of ferrofluid based droplets. Control of droplet velocity and merging was achieved through uniform magnetic field and flow rate ratio. Conditions for droplet merging with respect to droplet velocity were studied. Merging and mixing of colour dye + magnetite composite droplets was demonstrated. Our experimental and numerical results are in good agreement. These studies are useful for wireless and programmable droplet merging as well as mixing relevant to biosensing, bioassay, microfluidic-based synthesis, reaction kinetics, and magnetochemistry.
Temporally-coherent terawatt attosecond XFEL synchronized with a few cycle laser
Authors: Kumar Sandeep , Parc Yong Woon , Landsman Alexandra S. , Kim Dong Eon 
Published: November 2016

AbstractAttosecond metrology using laser-based high-order harmonics has been significantly advanced and applied to various studies of electron dynamics in atoms, molecules and solids. Laser-based high-order harmonics have a limitation of low power and photon energies. There is, however, a great demand for even higher power and photon energy. Here, we propose a scheme for a terawatt attosecond (TW-as) X-ray pulse in X-ray free-electron laser controlled by a few cycle IR pulse, where one dominant current spike in an electron bunch is used repeatedly to amplify a seeded radiation to a terawatt level. This scheme is relatively simple, compact, straightforward, and also produces a temporally and spectrally clean pulse. The viability of this scheme is demonstrated in simulations using Pohang accelerator laboratory (PAL)-XFEL beam parameters.
Scattering of nanowire surface plasmons coupled to quantum dots with azimuthal angle difference
Authors: Kuo Po-Chen , Chen Guang-Yin , Chen Yueh-Nan 
Published: November 2016

AbstractCoherent scatterings of surface plasmons coupled to quantun dots have attracted great attention in plasmonics. Recently, an experiment has shown that the quantum dots located nearby a nanowire can be separated not only in distance, but also an angle ϕ along the cylindrical direction. Here, by using the real-space Hamiltonian and the transfer matrix method, we analytically obtain the transmission/reflection spectra of nanowire surface plasmons coupled to quantum dots with an azimuthal angle difference. We find that the scattering spectra can show completely different features due to different positions and azimuthal angles of the quantum dots. When additionally coupling a cavity to the dots, we obtain the Fano-like line shape in the transmission and reflection spectra due to the interference between the localized and delocalized modes.
Novel recombinant papillomavirus genomes expressing selectable genes
Authors: Van Doorslaer Koenraad , Porter Samuel , McKinney Caleb , Stepp Wesley H. , McBride Alison A. 
Published: November 2016

AbstractPapillomaviruses infect and replicate in keratinocytes, but viral proteins are initially expressed at low levels and there is no effective and quantitative method to determine the efficiency of infection on a cell-to-cell basis. Here we describe human papillomavirus (HPV) genomes that express marker proteins (antibiotic resistance genes and Green Fluorescent Protein), and can be used to elucidate early stages in HPV infection of primary keratinocytes. To generate these recombinant genomes, the late region of the oncogenic HPV18 genome was replaced by CpG free marker genes. Insertion of these exogenous genes did not affect early replication, and had only minimal effects on early viral transcription. When introduced into primary keratinocytes, the recombinant marker genomes gave rise to drug-resistant keratinocyte colonies and cell lines, which maintained the extrachromosomal recombinant genome long-term. Furthermore, the HPV18 “marker” genomes could be packaged into viral particles (quasivirions) and used to infect primary human keratinocytes in culture. This resulted in the outgrowth of drug-resistant keratinocyte colonies containing replicating HPV18 genomes. In summary, we describe HPV18 marker genomes that can be used to quantitatively investigate many aspects of the viral life cycle.
Phenology and Growth dynamics of Avicennia marina in the Central Red Sea
Authors: Almahasheer Hanan , Duarte Carlos M. , Irigoien Xabier 
Published: November 2016

AbstractThe formation of nodes, stem elongation and the phenology of stunted Avicennia marina was examined in the Central Red Sea, where Avicennia marina is at the limit of its distribution range and submitted to extremely arid conditions with salinity above 38 psu and water temperature as high as 35° C. The annual node production was rather uniform among locations averaging 9.59 node y−1, which resulted in a plastocron interval, the interval in between production of two consecutive nodes along a stem, of 38 days. However, the internodal length varied significantly between locations, resulting in growth differences possibly reflecting the environmental conditions of locations. The reproductive cycle lasted for approximately 12 months, and was characterized by peak flowering and propagule development in November and January. These phenological observations provide a starting point for research and restoration programs on the ecology of mangroves in the Central Red Sea, while the plastochrone index reported here would allow calculations of the growth and production of the species from simple morphological measurements.
New Genome-Wide Algorithm Identifies Novel In-Vivo Expressed Mycobacterium Tuberculosis Antigens Inducing Human T-Cell Responses with Classical and Unconventional Cytokine Profiles
Authors: Coppola Mariateresa , van Meijgaarden Krista E. , Franken Kees L. M. C. , Commandeur Susanna , Dolganov Gregory , Kramnik Igor , Schoolnik Gary K. , Comas Inaki , Lund Ole , Prins Corine , van den Eeden Susan J. F. , Korsvold Gro E. , Oftung Fredrik , Geluk Annemieke , Ottenhoff Tom H. M. 
Published: November 2016

AbstractNew strategies are needed to develop better tools to control TB, including identification of novel antigens for vaccination. Such Mtb antigens must be expressed during Mtb infection in the major target organ, the lung, and must be capable of eliciting human immune responses. Using genome-wide transcriptomics of Mtb infected lungs we developed data sets and methods to identify IVE-TB (in-vivo expressed Mtb) antigens expressed in the lung. Quantitative expression analysis of 2,068 Mtb genes from the predicted first operons identified the most upregulated IVE-TB genes during in-vivo pulmonary infection. By further analysing high-level conservation among whole-genome sequenced Mtb-complex strains (n = 219) and algorithms predicting HLA-class-Ia and II presented epitopes, we selected the most promising IVE-TB candidate antigens. Several of these were recognized by T-cells from in-vitro Mtb-PPD and ESAT6/CFP10-positive donors by proliferation and multi-cytokine production. This was validated in an independent cohort of latently Mtb-infected individuals. Significant T-cell responses were observed in the absence of IFN-γ-production. Collectively, the results underscore the power of our novel antigen discovery approach in identifying Mtb antigens, including those that induce unconventional T-cell responses, which may provide important novel tools for TB vaccination and biomarker profiling. Our generic approach is applicable to other infectious diseases.
A peptidoglycan recognition protein acts in whitefly (Bemisia tabaci) immunity and involves in Begomovirus acquisition
Authors: Wang Zhi-Zhi , Shi Min , Huang Yi-Cun , Wang Xiao-Wei , Stanley David , Chen Xue-Xin 
Published: November 2016

AbstractPeptidoglycan recognition proteins (PGRPs) are multifunctional pattern recognition proteins. Here, we report that a PGRP gene,BtPGRP, encodes a PGRP from the whiteflyBemisia tabaci(MEAM1) that binds and kills bacteriain vitro. We analyzedBtPGRPtranscriptional profiling, and the distribution of the cognate protein within the midgut. Fungal infection and wasp parasitization induced expression ofBtPGRP. SilencingBtPGRPwith artificial media amended with dsRNA led to reduced expression of a gene encoding an antimicrobial peptide,B. tabaci c-type lysozyme. Begomovirusinfection also led to increased expression ofBtPGRP. We propose that BtPGRP has a potentialTomato yellow leaf curl virus(TYLCV) binding site because we detectedin vitrointeraction between BtPGRP and TYLCV by immunocapture PCR, and recorded the co-localization of TYLCV and BtPGRP in midguts. This work addresses a visible gap in understanding whitefly immunity and provides insight into how the whitefly immunity acts in complex mechanisms ofBegomovirustransmission among plants.
Functional and Structural Signatures of the Anterior Insula are associated with Risk-taking Tendency of Analgesic Decision-making
Authors: Lin Chia-Shu , Lin Hsiao-Han , Wu Shih-Yun 
Published: November 2016

AbstractIn a medical context, decision-making is associated with complicated assessment of gains, losses and uncertainty of outcomes. We here provide novel evidence about the brain mechanisms underlying decision-making of analgesic treatment. Thirty-six healthy participants were recruited and completed the Analgesic Decision-making Task (ADT), which quantified individual tendency of risk-taking (RPI), as the frequency of choosing a riskier option to relieve pain. All the participants received resting-state (rs) functional magnetic resonance imaging (MRI) and structural MRI. On rs-functional connectome, degree centrality (DC) of the bilateral anterior insula (aINS) was positively correlated with the RPI. The functional connectivity between the aINS, the nucleus accumbens and multiple brain regions, predominantly the medial frontal cortex, was positively correlated with the RPI. On structural signatures, the RPI was positively correlated with grey matter volume at the right aINS, and such an association was mediated by DC of the left aINS. Regression analyses revealed that both DC of the left aINS and participants’ imagined pain relief, as the utility of pain reduction, could predict the individual RPI. The findings suggest that the functional and structural brain signature of the aINS is associated with the individual differences of risk-taking tendency in the context of analgesic decision-making.
Improving Estimation of Fiber Orientations in Diffusion MRI Using Inter-Subject Information Sharing
Authors: Chen Geng , Zhang Pei , Li Ke , Wee Chong-Yaw , Wu Yafeng , Shen Dinggang , Yap Pew-Thian 
Published: November 2016

AbstractDiffusion magnetic resonance imaging is widely used to investigate diffusion patterns of water molecules in the human brain. It provides information that is useful for tracing axonal bundles and inferring brain connectivity. Diffusion axonal tracing, namely tractography, relies on local directional information provided by the orientation distribution functions (ODFs) estimated at each voxel. To accurately estimate ODFs, data of good signal-to-noise ratio and sufficient angular samples are desired. This is however not always available in practice. In this paper, we propose to improve ODF estimation by using inter-subject image correlation. Specifically, we demonstrate that diffusion-weighted images acquired from different subjects can be transformed to the space of a target subject to drastically increase the number of angular samples to improve ODF estimation. This is largely due to the incoherence of the angular samples generated when the diffusion signals are reoriented and warped to the target space. To reorient the diffusion signals, we propose a new spatial normalization method that directly acts on diffusion signals using local affine transforms. Experiments on both synthetic data and real data show that our method can reduce noise-induced artifacts, such as spurious ODF peaks, and yield more coherent orientations.
Autologous temporomandibular joint reconstruction independent of exogenous additives: a proof-of-concept study for guided self-generation
Authors: Wei Jiao , Herrler Tanja , Han Dong , Liu Kai , Huang Rulin , Guba Markus , Dai Chuanchang , Li Qingfeng 
Published: November 2016

AbstractJoint defects are complex and difficult to reconstruct. By exploiting the body’s own regenerative capacity, we aimed to individually generate anatomically precise neo-tissue constructs for autologous joint reconstruction without using any exogenous additives. In a goat model, CT scans of the mandibular condyle including articular surface and a large portion of the ascending ramus were processed using computer-aided design and manufacturing. A corresponding hydroxylapatite negative mold was printed in 3D and temporarily embedded into the transition zone of costal periosteum and perichondrium. A demineralized bone matrix scaffold implanted on the contralateral side served as control. Neo-tissue constructs obtained by guided self-generation exhibited accurate configuration, robust vascularization, biomechanical stability, and function. After autologous replacement surgery, the constructs showed stable results with similar anatomical, histological, and functional findings compared to native controls. Further studies are required to assess long-term outcome and possible extensions to other further applications. The absence of exogenous cells, growth factors, and scaffolds may facilitate clinical translation of this approach.
Variations in abundance, diversity and community composition of airborne fungi in swine houses across seasons
Authors: Kumari Priyanka , Woo Cheolwoon , Yamamoto Naomichi , Choi Hong-Lim 
Published: November 2016

AbstractWe examined the abundance, diversity and community composition of airborne fungi in swine houses during winter and summer seasons by using quantitative PCR and Illumina HiSeq sequencing of ITS1 region. The abundance of airborne fungi varied significantly only between seasons, while fungal diversity varied significantly both within and between seasons, with both abundance and diversity peaked in winter. The fungal OTU composition was largely structured by the swine house unit and season as well as by their interactions. Of the measured microclimate variables, relative humidity, particulate matters (PMs), ammonia, and stocking density were significantly correlated with fungal OTU composition. The variation in beta diversity was higher within swine houses during summer, which indicates that the airborne fungal community composition was more heterogeneous in summer compared to winter. We also identified several potential allergen/pathogen related fungal genera in swine houses. The total relative abundance of potential allergen/pathogen related fungal genera varied between swine houses in both seasons, and showed positive correlation with PM2.5. Overall, our findings show that the abundance, diversity and composition of airborne fungi are highly variable in swine houses and to a large extent structured by indoor microclimate variables of swine houses.
Negative feedback regulation of ABA biosynthesis in peanut (Arachis hypogaea): a transcription factor complex inhibits AhNCED1 expression during water stress
Authors: Liu Shuai , Li Meijuan , Su Liangchen , Ge Kui , Li Limei , Li Xiaoyun , Liu Xu , Li Ling 
Published: November 2016

AbstractAbscisic acid (ABA), a key plant stress-signaling hormone, is produced in response to drought and counteracts the effects of this stress. The accumulation of ABA is controlled by the enzyme 9-cis-epoxycarotenoid dioxygenase (NCED). In Arabidopsis, NCED3 is regulated by a positive feedback mechanism by ABA. In this study in peanut (Arachis hypogaea), we demonstrate that ABA biosynthesis is also controlled by negative feedback regulation, mediated by the inhibitory effect on AhNCED1 transcription of a protein complex between transcription factors AhNAC2 and AhAREB1. AhNCED1 was significantly down-regulated after PEG treatment for 10 h, at which time ABA content reached a peak. A ChIP-qPCR assay confirmed AhAREB1 and AhNAC2 binding to the AhNCED1 promoter in response to ABA. Moreover, the interaction between AhAREB1 and AhNAC2, and a transient expression assay showed that the protein complex could negatively regulate the expression of AhNCED1. The results also demonstrated that AhAREB1 was the key factor in AhNCED1 feedback regulation, while AhNAC2 played a subsidiary role. ABA reduced the rate of AhAREB1 degradation and enhanced both the synthesis and degradation rate of the AhNAC2 protein. In summary, the AhAREB1/AhNAC2 protein complex functions as a negative feedback regulator of drought-induced ABA biosynthesis in peanut.