bluuebunny/crossref_metadata_2025_split huggingface dataset:
iMiRNA-SSF: Improving the Identification of MicroRNA Precursors by Combining Negative Sets with Different Distributions
Authors: Chen Junjie , Wang Xiaolong , Liu Bin 
Published: January 2016

AbstractThe identification of microRNA precursors (pre-miRNAs) helps in understanding regulator in biological processes. The performance of computational predictors depends on their training sets, in which the negative sets play an important role. In this regard, we investigated the influence of benchmark datasets on the predictive performance of computational predictors in the field of miRNA identification and found that the negative samples have significant impact on the predictive results of various methods. We constructed a new benchmark set with different data distributions of negative samples. Trained with this high quality benchmark dataset, a new computational predictor called iMiRNA-SSF was proposed, which employed various features extracted from RNA sequences. Experimental results showed that iMiRNA-SSF outperforms three state-of-the-art computational methods. For practical applications, a web-server of iMiRNA-SSF was established at the website http://bioinformatics.hitsz.edu.cn/iMiRNA-SSF/.
Signaling through NOD-2 and TLR-4 Bolsters the T cell Priming Capability of Dendritic cells by Inducing Autophagy
Authors: Khan Nargis , Vidyarthi Aurobind , Pahari Susanta , Negi Shikha , Aqdas Mohammad , Nadeem Sajid , Agnihotri Tapan , Agrewala Javed N. 
Published: January 2016

AbstractT cells play a cardinal role in mediating protection against intracellular pathogens like Mycobacterium tuberculosis (Mtb). It is important to understand the factors that govern the T cell response; thereby can modulate its activity. Dendritic cells (DCs) are the major player in initiation and augmentation of T cell response. Targeting DCs to induce their optimum maturation and activation can lead to a better T cell response. Interestingly, we observed that combinatorial signaling of DCs through NOD-2 and TLR-4 fortified better yield of IL-12p40/70, IL-6 and IFN-γ and upregulated the expression of CD40, CD80 and CD86 costimulatory molecules. Further, we noticed improved phagocytic capabilities of DCs. Furthermore, NOD-2 and TLR-4 induced autophagy in DCs, which enhanced the activation of T cells. This study signifies that NOD-2 and TLR-4 exhibit synergism in invigorating the activity of DCs. Consequently, this strategy may have significant immunotherapeutic potential in bolstering the function of DCs and thus improving the immunity against pathogens.
Molecular mechanism of peptide editing in the tapasin–MHC I complex
Authors: Fisette Olivier , Wingbermühle Sebastian , Tampé Robert , Schäfer Lars V. 
Published: January 2016

AbstractImmune recognition of infected or malignantly transformed cells relies on antigenic peptides exposed at the cell surface by major histocompatibility complex class I (MHC I) molecules. Selection and loading of peptides onto MHC I is orchestrated by the peptide-loading complex (PLC), a multiprotein assembly whose structure has not yet been resolved. Tapasin, a central component of the PLC, stabilises MHC I and catalyses the exchange of low-affinity against high-affinity, immunodominant peptides. Up to now, the molecular basis of this peptide editing mechanism remained elusive. Here, using all-atom molecular dynamics (MD) simulations, we unravel the atomic details of how tapasin and antigen peptides act on the MHC I binding groove. Force distribution analysis reveals an intriguing molecular tug-of-war mechanism: only high-affinity peptides can exert sufficiently large forces to close the binding groove, thus overcoming the opposite forces exerted by tapasin to open it. Tapasin therefore accelerates the release of low-affinity peptides until a high-affinity antigen binds, promoting subsequent PLC break-down. Fluctuation and entropy analyses show how tapasin chaperones MHC I by stabilising it in a peptide-receptive conformation. Our results explain previous experiments and mark a key step towards a better understanding of adaptive immunity.
The Ebola Virus matrix protein, VP40, requires phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) for extensive oligomerization at the plasma membrane and viral egress
Authors: Johnson Kristen A. , Taghon Geoffrey J. F. , Scott Jordan L. , Stahelin Robert V. 
Published: January 2016

AbstractVP40 is one of eight proteins encoded by the Ebola Virus (EBOV) and serves as the primary matrix protein, forming virus like particles (VLPs) from mammalian cells without the need for other EBOV proteins. While VP40 is required for viral assembly and budding from host cells during infection, the mechanisms that target VP40 to the plasma membrane are not well understood. Phosphatidylserine is required for VP40 plasma membrane binding, VP40 hexamer formation and VLP egress, However, PS also becomes exposed on the outer membrane leaflet at sites of VP40 budding, raising the question of how VP40 maintains an interaction with the plasma membrane inner leaflet when PS is flipped to the opposite side. To address this question, cellular and in vitro assays were employed to determine if phosphoinositides are important for efficient VP40 localization to the plasma membrane. Cellular studies demonstrated that PI(4,5)P2 was an important component of VP40 assembly at the plasma membrane and subsequent virus like particle formation. Additionally, PI(4,5)P2 was required for formation of extensive oligomers of VP40, suggesting PS and PI(4,5)P2 have different roles in VP40 assembly where PS regulates formation of hexamers from VP40 dimers and PI(4,5)P2 stabilizes and/or induces extensive VP40 oligomerization at the plasma membrane.
Nanoscale mapping of plasmon and exciton in ZnO tetrapods coupled with Au nanoparticles
Authors: Bertoni Giovanni , Fabbri Filippo , Villani Marco , Lazzarini Laura , Turner Stuart , Van Tendeloo Gustaaf , Calestani Davide , Gradečak Silvija , Zappettini Andrea , Salviati Giancarlo 
Published: January 2016

AbstractMetallic nanoparticles can be used to enhance optical absorption or emission in semiconductors, thanks to a strong interaction of collective excitations of free charges (plasmons) with electromagnetic fields. Herein we present direct imaging at the nanoscale of plasmon-exciton coupling in Au/ZnO nanostructures by combining scanning transmission electron energy loss and cathodoluminescence spectroscopy and mapping. The Au nanoparticles (~30 nm in diameter) are grown in-situ on ZnO nanotetrapods by means of a photochemical process without the need of binding agents or capping molecules, resulting in clean interfaces. Interestingly, the Au plasmon resonance is localized at the Au/vacuum interface, rather than presenting an isotropic distribution around the nanoparticle. On the contrary, a localization of the ZnO signal has been observed inside the Au nanoparticle, as also confirmed by numerical simulations.
APN1 is a functional receptor of Cry1Ac but not Cry2Ab in Helicoverpa zea
Authors: Wei Jizhen , Zhang Min , Liang Gemei , Wu Kongming , Guo Yuyuan , Ni Xinzhi , Li Xianchun 
Published: January 2016

AbstractLepidopteran midgut aminopeptidases N (APNs) are phylogenetically divided into eight clusters, designated as APN1–8. Although APN1 has been implicated as one of the receptors for Cry1Ac in several species, its potential role in the mode of action of Cry2Ab has not been functionally determined so far. To test whether APN1 also acts as one of the receptors for Cry1Ac in Helicoverpa zea and even for Cry2Ab in this species, we conducted a gain of function analysis by heterologously expressing H. zea APN1 (HzAPN1) in the midgut and fat body cell lines of H. zea and the ovarian cell line of Spodoptera frugiperda (Sf9) and a loss of function analysis by RNAi (RNA interference) silencing of the endogenous APN1 in the three cell lines using the HzAPN1 double strand RNA (dsRNA). Heterologous expression of HzAPN1 significantly increased the susceptibility of the three cell lines to Cry1Ac, but had no effects on their susceptibility to Cry2Ab. Knocking down of the endogenous APN1 made the three cell lines resistant to Cry1Ac, but didn’t change cell lines susceptibility to Cry2Ab. The findings from this study demonstrate that HzAPN1 is a functional receptor of Cry1Ac, but not Cry2Ab.
Dioscorea bulbifera polysaccharide and cyclophosphamide combination enhances anti-cervical cancer effect and attenuates immunosuppression and oxidative stress in mice
Authors: Cui Hongxia , Li Ting , Wang Liping , Su Yan , Xian Cory J. 
Published: January 2016

AbstractCyclophosphamide (CTX) is commonly used in cancer chemotherapy, which causes immunosuppression and tissue oxidative stress at high doses. As potential protective agents, some polysaccharides were shown to have anti-tumor, anti-inflammatory and/or anti-oxidant properties. This study explored potential effects of oral treatment of Dioscorea bulbifera polysaccharides (DBLP at 100 or 150 mg/kg) in U14 cervical tumor-bearing mice treated with CTX (25 mg/kg). While CTX suppressed tumor growth (65.4% inhibition) and DBLP alone also inhibited tumor (25.6% at 100 mg/kg or 37.6% at 150 mg/kg), CTX+DBLP combination produced tumor inhibition rates of 5.6 (for 100 mg/kg DBLP) or 9% (for 150 mg/kg) higher than CTX alone. While tumor itself and CTX treatment reduced thymus and/or spleen/body weight indices, DBLP alone or CTX + DBLP combination attenuated this reduction. DBLP lowered peripheral blood T-cell subpopulation CD4+/CD8+ ratio and DBLP+CTX combination attenuated CTX effect in lifting CD4+/CD8+ ratio. Tumor itself and CTX treatment heightened oxidative stress (with decreased superoxide dismutase but increased lactate dehydrogenase and malondialdehyde levels in serum and tissues), which was attenuated by DBLP treatment and DBLP+CTX combination suppressed CTX-induced oxidative stress. Combination use of DBLP with CTX can potentially enhance CTX anti-tumor effect and can attenuate CTX-induced immunosuppression and oxidative stress in U14 cervical tumor-bearing mice.
Emergence of a super-synchronized mobbing state in a large population of coupled chemical oscillators
Authors: Ghoshal Gourab , Muñuzuri Alberto P. , Pérez-Mercader Juan 
Published: January 2016

AbstractOscillatory phenomena are ubiquitous in Nature. The ability of a large population of coupled oscillators to synchronize constitutes an important mechanism to express information and establish communication among members. To understand such phenomena, models and experimental realizations of globally coupled oscillators have proven to be invaluable in settings as varied as chemical, biological and physical systems. A variety of rich dynamical behavior has been uncovered, although usually in the context of a single state of synchronization or lack thereof. Through the experimental and numerical study of a large population of discrete chemical oscillators, here we report on the unexpected discovery of a new phenomenon revealing the existence of dynamically distinct synchronized states reflecting different degrees of communication. Specifically, we discover a novel large-amplitude super-synchronized state separated from the conventionally reported synchronized and quiescent states through an unusual sharp jump transition when sampling the strong coupling limit. Our results assume significance for further elucidating globally coherent phenomena, such as in neuropathologies, bacterial cell colonies, social systems and semiconductor lasers.
The effect of annealing on a 3D SnO2/graphene foam as an advanced lithium-ion battery anode
Authors: Tian Ran , Zhang Yangyang , Chen Zhihang , Duan Huanan , Xu Biyi , Guo Yiping , Kang Hongmei , Li Hua , Liu Hezhou 
Published: January 2016

Abstract3D annealed SnO2/graphene sheet foams (ASGFs) are synthesized by in situ self-assembly of graphene sheets prepared by mild chemical reduction. L-ascorbyl acid is used to effectively reduce the SnO2 nanoparticles/graphene oxide colloidal solution and form the 3D conductive graphene networks. The annealing treatment contributes to the formation of the Sn-O-C bonds between the SnO2 nanoparticles and the reduced graphene sheets, which improves the electrochemical performance of the foams. The ASGF has features of typical aerogels: low density (about 19 mg cm−3), smooth surface and porous structure. The ASGF anodes exhibit good specific capacity, excellent cycling stability and superior rate capability. The first reversible specific capacity is as high as 984.2 mAh g−1 at a specific current of 200 mA g−1. Even at the high specific current of 1000 mA g−1 after 150 cycles, the reversible specific capacity of ASGF is still as high as 533.7 mAh g−1, about twice as much as that of SGF (297.6 mAh g−1) after the same test. This synthesis method can be scaled up to prepare other metal oxides particles/ graphene sheet foams for high performance lithium-ion batteries, supercapacitors and catalysts, etc.
Locating single-point sources from arrival times containing large picking errors (LPEs): the virtual field optimization method (VFOM)
Authors: Li Xi-Bing , Wang Ze-Wei , Dong Long-Jun 
Published: January 2016

AbstractMicroseismic monitoring systems using local location techniques tend to be timely, automatic and stable. One basic requirement of these systems is the automatic picking of arrival times. However, arrival times generated by automated techniques always contain large picking errors (LPEs), which may make the location solution unreliable and cause the integrated system to be unstable. To overcome the LPE issue, we propose the virtual field optimization method (VFOM) for locating single-point sources. In contrast to existing approaches, the VFOM optimizes a continuous and virtually established objective function to search the space for the common intersection of the hyperboloids, which is determined by sensor pairs other than the least residual between the model-calculated and measured arrivals. The results of numerical examples and in-site blasts show that the VFOM can obtain more precise and stable solutions than traditional methods when the input data contain LPEs. Furthermore, we discuss the impact of LPEs on objective functions to determine the LPE-tolerant mechanism, velocity sensitivity and stopping criteria of the VFOM. The proposed method is also capable of locating acoustic sources using passive techniques such as passive sonar detection and acoustic emission.
A Viral mRNA Motif at the 3′-Untranslated Region that Confers Translatability in a Cell-Specific Manner. Implications for Virus Evolution
Authors: Garcia-Moreno Manuel , Sanz Miguel Angel , Carrasco Luis 
Published: January 2016

AbstractSindbis virus (SINV) mRNAs contain several motifs that participate in the regulation of their translation. We have discovered a motif at the 3′ untranslated region (UTR) of viral mRNAs, constituted by three repeated sequences, which is involved in the translation of both SINV genomic and subgenomic mRNAs in insect, but not in mammalian cells. These data illustrate for the first time that an element present at the 3′-UTR confers translatability to mRNAs from an animal virus in a cell-specific manner. Sequences located at the beginning of the 5′-UTR may also regulate SINV subgenomic mRNA translation in both cell lines in a context of infection. Moreover, a replicon derived from Sleeping disease virus, an alphavirus that have no known arthropod vector for transmission, is much more efficient in insect cells when the repeated sequences from SINV are inserted at its 3′-UTR, due to the enhanced translatability of its mRNAs. Thus, these findings provide a clue to understand, at the molecular level, the evolution of alphaviruses and their host range.
Common features in the unfolding and misfolding of PDZ domains and beyond: the modulatory effect of domain swapping and extra-elements
Authors: Murciano-Calles Javier , Güell-Bosch Jofre , Villegas Sandra , Martinez Jose C. 
Published: January 2016

AbstractPDZ domains are protein-protein interaction modules sharing the same structural arrangement. To discern whether they display common features in their unfolding/misfolding behaviour we have analyzed in this work the unfolding thermodynamics, together with the misfolding kinetics, of the PDZ fold using three archetypical examples: the second and third PDZ domains of the PSD95 protein and the Erbin PDZ domain. Results showed that all domains passed through a common intermediate, which populated upon unfolding and that this in turn drove the misfolding towards worm-like fibrillar structures. Thus, the unfolding/misfolding behaviour appears to be shared within these domains. We have also analyzed how this landscape can be modified upon the inclusion of extra-elements, as it is in the nNOS PDZ domain, or the organization of swapped species, as happens in the second PDZ domain of the ZO2 protein. Although the intermediates still formed upon thermal unfolding, the misfolding was prevented to varying degrees.
Presynaptic GABAB receptors reduce transmission at parabrachial synapses in the lateral central amygdala by inhibiting N-type calcium channels
Authors: Delaney A.J. , Crane J.W. 
Published: January 2016

AbstractThe nocioceptive information carried by neurons of the pontine parabrachial nucleus to neurons of the lateral division of the central amydala (CeA-L) is thought to contribute to the affective components of pain and is required for the formation of conditioned-fear memories. Importantly, excitatory transmission between parabrachial axon terminals and CeA-L neurons can be inhibited by a number of presynaptic receptors linked to Gi/o-type G-proteins, including α2-adrenoceptors and GABAB receptors. While the intracellular signalling pathway responsible for α2-adrenoceptor inhibition of synaptic transmission at this synapse is known, the mechanism by which GABAB receptors inhibits transmission has not been determined. The present study demonstrates that activation of presynaptic GABAB receptors reduces excitatory transmission between parabrachial axon terminals and CeA-L neurons by inhibiting N-type calcium channels. While the involvement of Gβγ subunits in mediating the inhibitory effects of GABAB receptors on N-type calcium channels is unclear, this inhibition does not involve Gβγ-independent activation of pp60C-src tyrosine kinase. The results of this study further enhance our understanding of the modulation of the excitatory input from parabrachial axon terminals to CeA-L neurons and indicate that presynaptic GABAB receptors at this synapse could be valuable therapeutic targets for the treatment of fear- and pain-related disorders.
Characterization and putative post-translational regulation of α- and β-tubulin gene families in Salix arbutifolia
Authors: Rao Guodong , Zeng Yanfei , He Caiyun , Zhang Jianguo 
Published: January 2016

AbstractMicrotubules, which are composed of heterodimers of α-tubulin (TUA) and β-tubulin (TUB) proteins, are closely associated with cellulose microfibril deposition and play pivotal roles in plant secondary cell wall development. In the present study, we identified eight TUA and twenty TUB genes in willow (Salix arbutifolia). Quantitative real-time PCR analysis showed that the small number of TUA gene family members relative to that of TUBs was complemented by a higher transcript copy number for each TUA gene, which is essential to the maintenance of the tubulin 1:1 heterodimer assembly. In Salix, five of eight TUAs were determined to be unusual because these contained a C-terminal methionine acid, leucine acid, glutamic acid and glutamine acid, instead of the more typical tyrosine residue, which in turn generated the hypothesis of post-translational modifications (PTMs) that included deleucylation, demethiolation, deglutamynation and deaspartylation. These PTMs are responsible for the removal of additional amino acid residues from TUAs prior to detyrosination, which is the first step of C-terminal PTMs. The additional PTMs of the TUA gene family might be responsible for the formation of different tubulin heterodimers that may have diverse functions for the adaptation of the woody perennial growth for Salix.
Hippocampal harms, protection and recovery following regular cannabis use
Authors: Yücel M , Lorenzetti V , Suo C , Zalesky A , Fornito A , Takagi M J , Lubman D I , Solowij N 
Published: January 2016

AbstractShifting policies towards legalisation of cannabis for therapeutic and recreational use raise significant ethical issues for health-care providers seeking evidence-based recommendations. We investigated whether heavy cannabis use is associated with persistent harms to the hippocampus, if exposure to cannabidiol offers protection, and whether recovery occurs with abstinence. To do this, we assessed 111 participants: 74 long-term regular cannabis users (with an average of 15.4 years of use) and 37 non-user healthy controls. Cannabis users included subgroups of participants who were either exposed to Δ9-tetrahydrocannabinol (THC) but not to cannabidiol (CBD) or exposed to both, and former users with sustained abstinence. Participants underwent magnetic resonance imaging from which three measures of hippocampal integrity were assessed: (i) volume; (ii) fractional anisotropy; and (iii) N-acetylaspartate (NAA). Three curve-fitting models across the entire sample were tested for each measure to examine whether cannabis-related hippocampal harms are persistent, can be minimised (protected) by exposure to CBD or recovered through long-term abstinence. These analyses supported a protection and recovery model for hippocampal volume (P=0.003) and NAA (P=0.001). Further pairwise analyses showed that cannabis users had smaller hippocampal volumes relative to controls. Users not exposed to CBD had 11% reduced volumes and 15% lower NAA concentrations. Users exposed to CBD and former users did not differ from controls on any measure. Ongoing cannabis use is associated with harms to brain health, underpinned by chronic exposure to THC. However, such harms are minimised by CBD, and can be recovered with extended periods of abstinence.
The dangers of hazards
Authors: Berry Colin 
Published: January 2016

Abstract
Concerns about the quality and reproducibility of scientific papers have emphasised the uncertainty of observations in the biological sciences. Focussing on this problem in the types of science that often underlie regulations affecting population exposures has clear implications for regulatory studies. Recent comments on the IARC process of hazard identification in the field of carcinogenesis have identified problems in dealing with public information content and regulatory value of the Monograph system. What is the value of a system that does not clearly identify its methodology for defining a hazard and which does not provide realistic estimates of risk?