bluuebunny/crossref_metadata_2025_split huggingface dataset:
A predictive structural model for bulk metallic glasses
Authors: Laws K. J. , Miracle D. B. , Ferry M. 
Published: September 2015

AbstractGreat progress has been made in understanding the atomic structure of metallic glasses, but there is still no clear connection between atomic structure and glass-forming ability. Here we give new insights into perhaps the most important question in the field of amorphous metals: how can glass-forming ability be predicted from atomic structure? We give a new approach to modelling metallic glass atomic structures by solving three long-standing problems: we discover a new family of structural defects that discourage glass formation; we impose efficient local packing around all atoms simultaneously; and we enforce structural self-consistency. Fewer than a dozen binary structures satisfy these constraints, but extra degrees of freedom in structures with three or more different atom sizes significantly expand the number of relatively stable, ‘bulk’ metallic glasses. The present work gives a new approach towards achieving the long-sought goal of a predictive capability for bulk metallic glasses.
dNP2 is a blood–brain barrier-permeable peptide enabling ctCTLA-4 protein delivery to ameliorate experimental autoimmune encephalomyelitis
Authors: Lim Sangho , Kim Won-Ju , Kim Yeon-Ho , Lee Sohee , Koo Ja-Hyun , Lee Jung-Ah , Yoon Heeseok , Kim Do-Hyun , Park Hong-Jai , Kim Hye-Mi , Lee Hong-Gyun , Yun Kim Ji , Lee Jae-Ung , Hun Shin Jae , Kyun Kim Lark , Doh Junsang , Kim Hongtae , Lee Sang-Kyou , Bothwell Alfred L. M. , Suh Minah , Choi Je-Min 
Published: September 2015

AbstractCentral nervous system (CNS)-infiltrating effector T cells play critical roles in the development and progression of multiple sclerosis (MS). However, current drugs for MS are very limited due to the difficulty of delivering drugs into the CNS. Here we identify a cell-permeable peptide, dNP2, which efficiently delivers proteins into mouse and human T cells, as well as various tissues. Moreover, it enters the brain tissue and resident cells through blood vessels by penetrating the tightly organized blood–brain barrier. The dNP2-conjugated cytoplasmic domain of cytotoxic T-lymphocyte antigen 4 (dNP2-ctCTLA-4) negatively regulates activated T cells and shows inhibitory effects on experimental autoimmune encephalomyelitis in both preventive and therapeutic mouse models, resulting in the reduction of demyelination and CNS-infiltrating T helper 1 and T helper 17 cells. Thus, this study demonstrates that dNP2 is a blood–brain barrier-permeable peptide and dNP2-ctCTLA-4 could be an effective agent for treating CNS inflammatory diseases such as MS.
The fatty acid elongase Bond is essential for Drosophila sex pheromone synthesis and male fertility
Authors: Ng Wan Chin , Chin Jacqueline S. R. , Tan Kah Junn , Yew Joanne Y. 
Published: September 2015

AbstractInsects use a spectacular variety of chemical signals to guide their social behaviours. How such chemical diversity arises is a long-standing problem in evolutionary biology. Here we describe the contribution of the fatty acid elongase Bond to both pheromone diversity and male fertility inDrosophila. Genetic manipulation and mass spectrometry analysis reveal that the loss ofbondeliminates the male sex pheromone (3R,11Z,19Z)-3-acetoxy-11,19-octacosadien-1-ol (CH503). Unexpectedly, silencingbondexpression severely suppresses male fertility and the fertility of conspecific rivals. These deficits are rescued on ectopic expression ofbondin the male reproductive system. A comparative analysis across sixDrosophilaspecies shows that the gain of a novel transcription initiation site is correlated withbondexpression in the ejaculatory bulb, a primary site of male pheromone production. Taken together, these results indicate that modification ofcis-regulatory elements and subsequent changes in gene expression pattern is one mechanism by which pheromone diversity arises.
Autoantibody Profiling of Glioma Serum Samples to Identify Biomarkers Using Human Proteome Arrays
Authors: Syed Parvez , Gupta Shabarni , Choudhary Saket , Pandala Narendra Goud , Atak Apurva , Richharia Annie , KP Manubhai , Zhu Heng , Epari Sridhar , Noronha Santosh B. , Moiyadi Aliasgar , Srivastava Sanjeeva 
Published: September 2015

AbstractThe heterogeneity and poor prognosis associated with gliomas, makes biomarker identification imperative. Here, we report autoantibody signatures across various grades of glioma serum samples and sub-categories of glioblastoma multiforme using Human Proteome chips containing ~17000 full-length human proteins. The deduced sets of classifier proteins helped to distinguish Grade II, III and IV samples from the healthy subjects with 88, 89 and 94% sensitivity and 87, 100 and 73% specificity, respectively. Proteins namely, SNX1, EYA1, PQBP1 and IGHG1 showed dysregulation across various grades. Sub-classes of GBM, based on its proximity to the sub-ventricular zone, have been reported to have different prognostic outcomes. To this end, we identified dysregulation of NEDD9, a protein involved in cell migration, with probable prognostic potential. Another subcategory of patients where the IDH1 gene is mutated, are known to have better prognosis as compared to patients carrying the wild type gene. On a comparison of these two cohorts, we found STUB1 and YWHAH proteins dysregulated in Grade II glioma patients. In addition to common pathways associated with tumourigenesis, we found enrichment of immunoregulatory and cytoskeletal remodelling pathways, emphasizing the need to explore biochemical alterations arising due to autoimmune responses in glioma.
SENP2 regulates MMP13 expression in a bladder cancer cell line through SUMOylation of TBL1/TBLR1
Authors: Tan Mingyue , Gong Hua , Wang Jun , Tao Le , Xu Dongliang , Bao Erdun , Liu Zhihong , Qiu Jianxin 
Published: September 2015

AbstractBladder cancer (BC) is the most popular malignant urinary cancer in China. BC has the highest incidence and mortality among all genitourinary system tumors. Although the early-stage BC could be treated with advanced electron flexible systourethroscope, early metastasis of the BC occur frequently and often results in poor prognosis. Recently, we reported that small ubiquitin related modifier (SUMO)-specific protease 2 (SENP2) was downregulated in BC specimen. SENP2 appeared to inhibit migration and invasion of bladder cancer cells in vitro, through suppressing MMP13 in BC cells. However, the exact underlying mechanisms remain unknown. Here, we reported that SENP2 inhibited nuclear translocation of β-catenin, which targeted the promotor of MMP13 to activate MMP13 to enhance BC cell metastasis. WNT ligands induced TBL1/TBLR1 SUMOylation to form complexes with β-catenin to facilitate β-catenin nuclear translocation, which could be efficiently inhibited through suppression of SUMOylation of TBL1/TBLR1. Together, our data suggest that SENP2 inhibits MMP13 expression in BC cells through de-SUMOylation of TBL1/TBLR1, which inhibits nuclear translocation of β-catenin. Thus, SENP2 may be a promising therapeutic target for BC.
Promotion of regulatory T cell induction by immunomodulatory herbal medicine licorice and its two constituents
Authors: Guo Ao , He Dongming , Xu Hong-Bo , Geng Chang-An , Zhao Jian 
Published: September 2015

AbstractRegulatory T cells (Treg) play a critical role to control immune responses and to prevent autoimmunity, thus selective increase of Treg cells in vivo has broad therapeutic implications for autoimmune and inflammatory diseases. Licorice is a well-known herbal medicine used worldwide for over thousands of years and accumulating evidence has shown its immunomodulatory potential. However, it is not clear whether licorice could regulate the induction and function of Treg cells. Here we found licorice extract could promote Treg cell induction and then we used a rational approach to isolate its functional fractions and constituents. The results showed that two constituents, isoliquiritigenin and naringenin, promoted Treg cell induction both in vitro and in vivo. The effective fractions and two constituents of licorice also enhanced immune suppression of Treg cells and they further reduced severity of DSS-induced colitis in mice. This study suggested that promotion of regulatory T cell induction could be an underlying mechanism of the historically and widely used herbal medicine licorice, providing its two effective molecules against autoimmune and inflammatory diseases.
Hearing in slow-motion: Humans underestimate the speed of moving sounds
Authors: Senna Irene , Parise Cesare V. , Ernst Marc O. 
Published: September 2015

AbstractPerception can often be described as a statistically optimal inference process whereby noisy and incomplete sensory evidence is combined with prior knowledge about natural scene statistics. Previous evidence has shown that humans tend to underestimate the speed of unreliable moving visual stimuli. This finding has been interpreted in terms of a Bayesian prior favoring low speed, given that in natural visual scenes objects are mostly stationary or slowly-moving. Here we investigated whether an analogous tendency to underestimate speed also occurs in audition: even if the statistics of the visual environment seem to favor low speed, the statistics of the stimuli reaching the individual senses may differ across modalities, hence potentially leading to different priors. Here we observed a systematic bias for underestimating the speed of unreliable moving sounds. This finding suggests the existence of a slow-motion prior in audition, analogous to the one previously found in vision. The nervous system might encode the overall statistics of the world, rather than the specific properties of the signals reaching the individual senses.
Real-time and label-free analysis of binding thermodynamics of carbohydrate-protein interactions on unfixed cancer cell surfaces using a QCM biosensor
Authors: Li Xueming , Song Siyu , Shuai Qi , Pei Yihan , Aastrup Teodor , Pei Yuxin , Pei Zhichao 
Published: September 2015

AbstractA novel approach to the study of binding thermodynamics and kinetics of carbohydrate-protein interactions on unfixed cancer cell surfaces using a quartz crystal microbalance (QCM) biosensor was developed, in which binding events take place at the cell surface, more closely mimicking a biologically relevant environment. In this study, colon adenocarcinoma cells (KM-12) and ovary adenocarcinoma cells (SKOV-3) grew on the optimized polystyrene-coated biosensor chip without fixation. The association and dissociation between the cell surface carbohydrates and a range of lectins, including WGA, Con A, UEA-I, GS-II, PNA and SBA, were monitored in real time and without label for evaluation of cell surface glycosylation. Furthermore, the thermodynamic and kinetic parameters of the interaction between lectins and cell surface glycan were studied, providing detailed information about the interactions, such as the association rate constant, dissociation rate constant, affinity constant, as well as the changes of entropy, enthalpy and Gibbs free energy. This application provides an insight into the cell surface glycosylation and the complex molecular recognition on the intact cell surface, which may have impacts on disease diagnosis and drug discovery.
Monolithic III–V on Silicon Plasmonic Nanolaser Structure for Optical Interconnects
Authors: Li Ning , Liu Ke , Sorger Volker J. , Sadana Devendra K. 
Published: September 2015

AbstractMonolithic integration of III–V semiconductor lasers with Si circuits can reduce cost and enhance performance for optical interconnects dramatically. We propose and investigate plasmonic III–V nanolasers as monolithically integrated light source on Si chips due to many advantages. First, these III–V plasmonic light sources can be directly grown on Si substrates free of crystallographic defects due to the submicron cavity footprint (250 nm × 250 nm) being smaller than the average defect free region size of the heteroepitaxial III–V material on Si. Secondly, the small lateral and vertical dimensions facilitate process co-integration with Si complementary metal-oxide-semiconductor (CMOS) in the front end of the line. Thirdly, combining with monolithically integrated CMOS circuits with low device capacitance and parasitic capacitance, the nano-cavity optoelectronic devices consume orders of magnitude less power than the conventional lasers and reduce the energy consumption. Fourthly, the modulation bandwidth of the plasmonic light-sources is enhanced to significantly higher than conventional lasers due to enhanced photon state density and transition rate. In addition, we show that these device performance are very robust after taking into account the surface recombination and variations in device fabrication processes.
Conditional deletion of nonmuscle myosin II-A in mouse tongue epithelium results in squamous cell carcinoma
Authors: Anne Conti Mary , Saleh Anthony D. , Brinster Lauren R. , Cheng Hui , Chen Zhong , Cornelius Shaleeka , Liu Chengyu , Ma Xuefei , Van Waes Carter , Adelstein Robert S. 
Published: September 2015

AbstractTo investigate the contribution of nonmuscle myosin II-A (NM II-A) to early cardiac development we crossed Myh9 floxed mice and Nkx2.5 cre-recombinase mice. Nkx2.5 is expressed in the early heart (E7.5) and later in the tongue epithelium. Mice homozygous for deletion of NM II-A (ANkx/ANkx) are born at the expected ratio with normal hearts, but consistently develop an invasive squamous cell carcinoma (SCC) of the tongue (32/32 ANkx/ANkx) as early as E17.5. To assess reproducibility a second, independent line of Myh9 floxed mice derived from a different embryonic stem cell clone was tested. This second line also develops SCC indistinguishable from the first (15/15). In ANkx/ANkx mouse tongue epithelium, genetic deletion of NM II-A does not affect stabilization of TP53, unlike a previous report for SCC. We attribute the consistent, early formation of SCC with high penetrance to the role of NM II in maintaining mitotic stability during karyokinesis.
The glucocorticoid mometasone furoate is a novel FXR ligand that decreases inflammatory but not metabolic gene expression
Authors: Bijsmans Ingrid T. G. W. , Guercini Chiara , Ramos Pittol José M. , Omta Wienand , Milona Alexandra , Lelieveld Daphne , Egan David A. , Pellicciari Roberto , Gioiello Antimo , van Mil Saskia W. C. 
Published: September 2015

AbstractThe Farnesoid X receptor (FXR) regulates bile salt, glucose and cholesterol homeostasis by binding to DNA response elements, thereby activating gene expression (direct transactivation). FXR also inhibits the immune response via tethering to NF-κB (tethering transrepression). FXR activation therefore has therapeutic potential for liver and intestinal inflammatory diseases. We aim to identify and develop gene-selective FXR modulators, which repress inflammation, but do not interfere with its metabolic capacity. In a high-throughput reporter-based screen, mometasone furoate (MF) was identified as a compound that reduced NF-κB reporter activity in an FXR-dependent manner. MF reduced mRNA expression of pro-inflammatory cytokines and induction of direct FXR target genes in HepG2-GFP-FXR cells and intestinal organoids was minor. Computational studies disclosed three putative binding modes of the compound within the ligand binding domain of the receptor. Interestingly, mutation of W469A residue within the FXR ligand binding domain abrogated the decrease in NF-κB activity. Finally, we show that MF-bound FXR inhibits NF-κB subunit p65 recruitment to the DNA of pro-inflammatory genes CXCL2 and IL8. Although MF is not suitable as selective anti-inflammatory FXR ligand due to nanomolar affinity for the glucocorticoid receptor, we show that separation between metabolic and anti-inflammatory functions of FXR can be achieved.
Modulation of AMPA receptor mediated current by nicotinic acetylcholine receptor in layer I neurons of rat prefrontal cortex
Authors: Tang Bo , Luo Dong , Yang Jie , Xu Xiao-Yan , Zhu Bing-Lin , Wang Xue-Feng , Yan Zhen , Chen Guo-Jun 
Published: September 2015

AbstractLayer I neurons in the prefrontal cortex (PFC) exhibit extensive synaptic connections with deep layer neurons, implying their important role in the neural circuit. Study demonstrates that activation of nicotinic acetylcholine receptors (nAChRs) increases excitatory neurotransmission in this layer. Here we found that nicotine selectively increased the amplitude of AMPA receptor (AMPAR)-mediated current and AMPA/NMDA ratio, while without effect on NMDA receptor-mediated current. The augmentation of AMPAR current by nicotine was inhibited by a selective α7-nAChR antagonist methyllycaconitine (MLA) and intracellular calcium chelator BAPTA. In addition, nicotinic effect on mEPSC or paired-pulse ratio was also prevented by MLA. Moreover, an enhanced inward rectification of AMPAR current by nicotine suggested a functional role of calcium permeable and GluA1 containing AMPAR. Consistently, nicotine enhancement of AMPAR current was inhibited by a selective calcium-permeable AMPAR inhibitor IEM-1460. Finally, the intracellular inclusion of synthetic peptide designed to block GluA1 subunit of AMPAR at CAMKII, PKC or PKA phosphorylation site, as well as corresponding kinase inhibitor, blocked nicotinic augmentation of AMPA/NMDA ratio. These results have revealed that nicotine increases AMPAR current by modulating the phosphorylation state of GluA1 which is dependent on α7-nAChR and intracellular calcium.
Identification of novel mureidomycin analogues via rational activation of a cryptic gene cluster in Streptomyces roseosporus NRRL 15998
Authors: Jiang Lingjuan , Wang Lu , Zhang Jihui , Liu Hao , Hong Bin , Tan Huarong , Niu Guoqing 
Published: September 2015

AbstractAntimicrobial agents are urgently needed to tackle the growing threat of antibiotic-resistant pathogens. An important source of new antimicrobials is the large repertoire of cryptic gene clusters embedded in microbial genomes. Genome mining revealed a napsamycin/mureidomycin biosynthetic gene cluster in the chromosome of Streptomyces roseosporus NRRL 15998. The cryptic gene cluster was activated by constitutive expression of a foreign activator gene ssaA from sansanmycin biosynthetic gene cluster of Streptomyces sp. strain SS. Expression of the gene cluster was verified by RT-PCR analysis of key biosynthetic genes. The activated metabolites demonstrated potent inhibitory activity against the highly refractory pathogen Pseudomonas aeruginosa and characterization of the metabolites led to the discovery of eight acetylated mureidomycin analogues. To our surprise, constitutive expression of the native activator gene SSGG_02995, a ssaA homologue in S. roseosporus NRRL 15998, has no beneficial effect on mureidomycin stimulation. This study provides a new way to activate cryptic gene cluster for the acquisition of novel antibiotics and will accelerate the exploitation of prodigious natural products in Streptomyces.
Bell’s measure and implementing quantum Fourier transform with orbital angular momentum of classical light
Authors: Song Xinbing , Sun Yifan , Li Pengyun , Qin Hongwei , Zhang Xiangdong 
Published: September 2015

AbstractWe perform Bell’s measurement for the non-separable correlation between polarization and orbital angular momentum from the same classical vortex beam. The violation of Bell’s inequality for such a non-separable classical correlation has been demonstrated experimentally. Based on the classical vortex beam and non-quantum entanglement between the polarization and the orbital angular momentum, the Hadamard gates and conditional phase gates have been designed. Furthermore, a quantum Fourier transform has been implemented experimentally.
Dimethyl adipimidate/Thin film Sample processing (DTS); A simple, low-cost and versatile nucleic acid extraction assay for downstream analysis
Authors: Shin Yong , Lim Swee Yin , Lee Tae Yoon , Park Mi Kyoung 
Published: September 2015

AbstractSample processing, especially that involving nucleic acid extraction, is a prerequisite step for the isolation of high quantities of relatively pure DNA for downstream analyses in many life science and biomedical engineering studies. However, existing methods still have major problems, including labor-intensive time-consuming methods and high costs, as well as requirements for a centrifuge and the complex fabrication of filters and membranes. Here, we first report a versatile Dimethyl adipimidate/Thin film based Sample processing (DTS) procedure without the limitations of existing methods. This procedure is useful for the extraction of DNA from a variety of sources, including 6 eukaryotic cells, 6 bacteria cells and 2 body fluids in a single step. Specifically, the DTS procedure does not require a centrifuge and has improved time efficiency (30 min), affordability and sensitivity in downstream analysis. We validated the DTS procedure for the extraction of DNA from human body fluids, as well as confirmed that the quality and quantity of the extracted DNA were sufficient to allow robust detection of genetic and epigenetic biomarkers in downstream analysis.
A nitrogen-vacancy spin based molecular structure microscope using multiplexed projection reconstruction
Authors: Lazariev Andrii , Balasubramanian Gopalakrishnan 
Published: September 2015

AbstractMethods and techniques to measure and image beyond the state-of-the-art have always been influential in propelling basic science and technology. Because current technologies are venturing into nanoscopic and molecular-scale fabrication, atomic-scale measurement techniques are inevitable. One such emerging sensing method uses the spins associated with nitrogen-vacancy (NV) defects in diamond. The uniqueness of this NV sensor is its atomic size and ability to perform precision sensing under ambient conditions conveniently using light and microwaves (MW). These advantages have unique applications in nanoscale sensing and imaging of magnetic fields from nuclear spins in single biomolecules. During the last few years, several encouraging results have emerged towards the realization of an NV spin-based molecular structure microscope. Here, we present a projection-reconstruction method that retrieves the three-dimensional structure of a single molecule from the nuclear spin noise signatures. We validate this method using numerical simulations and reconstruct the structure of a molecular phantom β-cyclodextrin, revealing the characteristic toroidal shape.
The Anti-fibrotic Effects and Mechanisms of MicroRNA-486-5p in Pulmonary Fibrosis
Authors: Ji Xiaoming , Wu Baiqun , Fan Jingjing , Han Ruhui , Luo Chen , Wang Ting , Yang Jingjin , Han Lei , Zhu Baoli , Wei Dong , Chen Jingyu , Ni Chunhui 
Published: September 2015

AbstractTo identify microRNAs (miRNAs, miRs) with potential roles in lung fibrogenesis, we performed genome-wide profiling of miRNA expression in lung tissues from a silica-induced mouse model of pulmonary fibrosis using microarrays. Seventeen miRNAs were selected for validation via qRT-PCR based on the fold changes between the silica and the control group. The dysregulation of five miRNAs, including miR-21, miR-455, miR-151-3p, miR-486-5p and miR-3107, were confirmed by qRT-PCRs in silica-induced mouse model of pulmonary fibrosis and were also confirmed in a bleomycin (BLM)-induced mouse lung fibrosis. Notably, miR-486-5p levels were decreased in the serum samples of patients with silicosis, as well as in the lung tissues of patients with silicosis and idiopathic pulmonary fibrosis (IPF). In addition, as determined by luciferase assays and Western blotting, SMAD2, a crucial mediator of pulmonary fibrosis, was identified to be one of target genes of miR-486-5p. To test the potential therapeutic significance of this miRNA, we overexpressed miR-486-5p in animal models. At day 28, miR-486-5p expression significantly decreased both the distribution and severity of lung lesions compared with the silica group (P < 0.01). In addition, miR-486-5p had a similar effect in the BLM group (P < 0.001). These results indicate that miR-486-5p may inhibit fibrosis.