bluuebunny/crossref_metadata_2025_split huggingface dataset:
The multikinase inhibitor Sorafenib enhances glycolysis and synergizes with glycolysis blockade for cancer cell killing
Authors: Tesori Valentina , Piscaglia Anna Chiara , Samengo Daniela , Barba Marta , Bernardini Camilla , Scatena Roberto , Pontoglio Alessandro , Castellini Laura , Spelbrink Johannes N. , Maulucci Giuseppe , Puglisi Maria Ausiliatrice , Pani Giovambattista , Gasbarrini Antonio 
Published: March 2015

AbstractAlthough the only effective drug against primary hepatocarcinoma, the multikinase inhibitor Sorafenib (SFB) usually fails to eradicate liver cancer. Since SFB targets mitochondria, cell metabolic reprogramming may underlie intrinsic tumor resistance. To characterize cancer cell metabolic response to SFB, we measured oxygen consumption, generation of reactive oxygen species (ROS) and ATP content in rat LCSC (Liver Cancer Stem Cells) -2 cells exposed to the drug. Genome wide analysis of gene expression was performed by Affymetrix technology. SFB cytotoxicity was evaluated by multiple assays in the presence or absence of metabolic inhibitors, or in cells genetically depleted of mitochondria. We found that low concentrations (2.5–5 μM) of SFB had a relatively modest effect on LCSC-2 or 293 T cell growth, but damaged mitochondria and increased intracellular ROS. Gene expression profiling of SFB-treated cells was consistent with a shift toward aerobic glycolysis and, accordingly, SFB cytotoxicity was dramatically increased by glucose withdrawal or the glycolytic inhibitor 2-DG. Under metabolic stress, activation of the AMP dependent Protein Kinase (AMPK), but not ROS blockade, protected cells from death. We conclude that mitochondrial damage and ROS drive cell killing by SFB, while glycolytic cell reprogramming may represent a resistance strategy potentially targetable by combination therapies.
The Relationship between Dietary Protein Consumption and Risk of Fracture: a subgroup and dose-response meta-analysis of prospective cohort studies
Authors: Wu Ai-Min , Sun Xiao-Lei , Lv Qing-Bo , Zhou Yong , Xia Dong-Dong , Xu Hua-Zi , Huang Qi-Shan , Chi Yong-Long 
Published: March 2015

AbstractIt is still debate of the relationship between the dietary protein consumption and risk of fracture. We searched Medline and Embase to assess the effects of dietary protein consumption on risk of fracture. Twelve prospective cohort studies with 407,104 participants were included, higher total protein consumption may be decrease 11% risk of hip fractures, with adj. RR of 0.89 (0.82, 0.97), no significant difference was found for total protein and risk of all fractures and limb fracture; for animal protein consumption and risk of all fractures and hip fracture, with adj.RR of 0.79 (032, 1.96) and 1.04 (0.70, 1.54); for vegetable protein consumption and risk of all fractures, hip fracture and limb fractures with adj.RR of 0.77 (0.52, 1.12), 1.00 (0.53, 1.91) and 0.94 (0.40, 2.22), the subgroup of vegetable protein consumption and risk of all fractures of postmenopausal women with adj.RR of 0.78(0.52,1.16). Dose-response meta-analysis the relationship of total/animal/vegetable protein and hip fracture was consistent to the results of forest plot, the line of total protein and hip fracture was below the Y = 1.0 line. This meta-analysis showed that total dietary protein consumption may be decrease the risk of hip fracture, but not for animal or vegetable protein.
Preparation of Hollow CuO@SiO2 Spheres and Its Catalytic Performances for the NO + CO and CO Oxidation
Authors: Niu Xiaoyu , Zhao Tieying , Yuan Fulong , Zhu Yujun 
Published: March 2015

AbstractThe hollow CuO@SiO2spheres with a mean diameter of 240 nm and a thin shell layer of about 30 nm in thickness was synthesized using an inorganic SiO2shell coating on the surface of Cu@C composite that was prepared by a two-step hydrothermal method. The obtained hollow CuO@SiO2spheres were characterized by ICP-AES, nitrogen adsorption-desorption, SEM, TEM, XRD, H2-TPR, CO-TPR, CO-TPD and NO-TPD. The results revealed that the hollow CuO@SiO2spheres consist of CuO uniformly inserted into SiO2layer. The CuO@SiO2sample exhibits particular catalytic activities for CO oxidation and NO + CO reactions compared with CuO supported on SiO2(CuO/SiO2). The higher catalytic activity is attributed to the special hollow shell structure that possesses much more highly dispersed CuO nanocluster that can be easy toward the CO and NO adsorption and the oxidation of CO on its surface.
Trace phase formation, crystallization kinetics and crystallographic evolution of a lithium disilicate glass probed by synchrotron XRD technique
Authors: Huang Saifang , Huang Zhaohui , Gao Wei , Cao Peng 
Published: March 2015

AbstractX-ray diffraction technique using a laboratory radiation has generally shown limitation in detectability. In this work, we investigated the in situ high-temperature crystallization of a lithium disilicate glass-ceramic in the SiO2–Li2O–CaO–P2O5–ZrO2 system with the aid of synchrotron radiation. The formation of lithium metasilicate and other intermediate phases in trace amount was successfully observed by synchrotron X-ray diffraction (SXRD). The crystallization mechanism in this glass was thus intrinsically revised to be the co-nucleation of lithium metasilicate and disilicate, instead of the nucleation of lithium disilicate only. The phase content, crystallite size and crystallographic evolutions of Li2Si2O5 in the glass-ceramic as a function of annealing temperature were studied by performing Rietveld refinements. It is found that the growth of Li2Si2O5 is constrained by Li2SiO3 phase at 580–700°C. The relationship between the crystallographic evolution and phase transition was discussed, suggesting a common phenomenon of structural response of Li2Si2O5 along its c axis to other silicon-related phases during glass crystallization.
Does left-handedness confer resistance to spatial bias?
Authors: Bareham Corinne A. , Bekinschtein Tristan A. , Scott Sophie K. , Manly Tom 
Published: March 2015

AbstractWe recently demonstrated that drowsiness, indexed using EEG, was associated with left-inattention in a group of 26 healthy right-handers. This has been linked to alertness-related modulation of spatial bias in left neglect patients and the greater persistence of left, compared with right, neglect following injury. Despite handedness being among the most overt aspects of human lateralization, studies of this healthy analogue of left neglect have only been conducted with predominantly or exclusively right-handed individuals. Here, with a group of 26 healthy non-right-handers we demonstrate that, unlike right-handers who showed a rightward shift in attention with drowsiness, non-right-handers showed the opposite pattern on an auditory spatial localization task. The current results are the first indication that factors linked to handedness can affect the development and extremity of spatial biases, potentially conferring resilience to clinical symptoms in non-right-handers and, given that 90% of us are right-handed, why left neglect is disproportionately persistent.
Enhancer-promoter interaction facilitated by transiently forming G-quadruplexes
Authors: Hegyi Hedi 
Published: March 2015

AbstractG-quadruplexes are guanine-rich nucleic acid sequences capable of forming a four-stranded structure through Hoogsteen hydrogen bonding. G-quadruplexes are highly concentrated near promoters and transcription start sites suggesting a role in gene regulation. They are less often found on the template than non-template strand where they either inhibit or enhance transcription, respectively. However, their potential role in enhancers and other distal regulatory elements has not been assessed yet. Here we show that DNAse hypersensitive (DHS) cis-regulatory elements are also enriched in Gs and their G-content correlate with that of their respective promoters. Besides local G4s, the distal cis regions may form G-quadruplexes together with the promoters, each contributing half a G4. This model is supported more for the non-template strand and we hypothesised that the G4 forming capability of the promoter and the enhancer non-template strand could facilitate their binding together and making the DHS regions accessible for the transcription factory.
Error-based Extraction of States and Energy Landscapes from Experimental Single-Molecule Time-Series
Authors: Taylor J. Nicholas , Li Chun-Biu , Cooper David R. , Landes Christy F. , Komatsuzaki Tamiki 
Published: March 2015

AbstractCharacterization of states, the essential components of the underlying energy landscapes, is one of the most intriguing subjects in single-molecule (SM) experiments due to the existence of noise inherent to the measurements. Here we present a method to extract the underlying state sequences from experimental SM time-series. Taking into account empirical error and the finite sampling of the time-series, the method extracts a steady-state network which provides an approximation of the underlying effective free energy landscape. The core of the method is the application of rate-distortion theory from information theory, allowing the individual data points to be assigned to multiple states simultaneously. We demonstrate the method's proficiency in its application to simulated trajectories as well as to experimental SM fluorescence resonance energy transfer (FRET) trajectories obtained from isolated agonist binding domains of the AMPA receptor, an ionotropic glutamate receptor that is prevalent in the central nervous system.
Rsite: a computational method to identify the functional sites of noncoding RNAs
Authors: Zeng Pan , Li Jianwei , Ma Wei , Cui Qinghua 
Published: March 2015

AbstractThere is an increasing demand for identifying the functional sites of noncoding RNAs (ncRNAs). Here we introduce a tertiary-structure based computational approach, Rsite, which first calculates the Euclidean distances between each nucleotide and all the other nucleotides in a RNA molecule and then determines the nucleotides that are the extreme points in the distance curve as the functional sites. By analyzing two ncRNAs, tRNA (Lys) and Diels-Alder ribozyme, we demonstrated the efficiency of Rsite. As a result, Rsite recognized all of the known functional sites of the two ncRNAs, suggesting that Rsite could be a potentially useful tool for discovering the functional sites of ncRNAs. The source codes and data sets of Rsite are available at http://www.cuilab.cn/rsite.
Choice of Flap Affects Fistula Rate after Salvage Laryngopharyngectomy
Authors: Kao Huang-Kai , Abdelrahman Mohamed , Chang Kai-Ping , Wu Chao-Min , Hung Shao-Yu , Shyu Victor Bong-Hang 
Published: March 2015

AbstractDue to the significant morbidity and mortality associated with pharyngocutaneous fistula in pharyngoesophageal reconstruction following cancer resection, the purpose of this retrospective study is to examine the selection of tubed skin flaps that impact anastomotic integrity. The flaps evaluated included radial forearm flap versus anterolateral thigh flap and fasciocutaneous anterolateral thigh flap versus chimeric anterolateral thigh flap. The outcome of interest is the incidence of pharyngocutaneous fistula. The radial forearm group had a significantly higher rate of fistula than the anterolateral thigh group (56.6% vs. 30.2%, p = 0.03). No significant difference in the incidence of fistula was demonstrated between fasciocutaneous and chimeric anterolateral thigh flap (36.8% vs. 25%, p = 0.51). The anastomotic integrity in pharyngoesopharyngeal reconstruction is affected by choice of skin flaps. Anterolateral thigh flap appears to be a viable option for pharyngoesophageal reconstruction. The more technical demand of the anterolateral thigh flap must be weighed against an easily harvested radial forearm flap.
Atomic picture of elastic deformation in a metallic glass
Authors: Wang X. D. , Aryal S. , Zhong C. , Ching W. Y. , Sheng H. W. , Zhang H. , Zhang D. X. , Cao Q. P. , Jiang J. Z. 
Published: March 2015

AbstractThe tensile behavior of a Ni60Nb40 metallic glass (MG) has been studied by using ab initio density functional theory (DFT) calculation with a large cell containing 1024 atoms (614 Ni and 410 Nb). We provide insight into how a super elastic limit can be achieved in a MG. Spatially inhomogeneous responses of single atoms and also major polyhedra are found to change greatly with increasing external stress when the strain is over 2%, causing the intrinsically viscoelastic behavior. We uncover the origin of the observed super elastic strain limit under tension (including linear and viscoelastic strains) in small-sized MG samples, mainly caused by inhomogeneous distribution of excess volumes in the form of newly formed subatomic cavities.
Characterization of macrophage - cancer cell crosstalk in estrogen receptor positive and triple-negative breast cancer
Authors: Hollmén Maija , Roudnicky Filip , Karaman Sinem , Detmar Michael 
Published: March 2015

AbstractTumor heterogeneity may broadly influence the activation of tumor-associated macrophages. We aimed to dissect how breast cancer cells of different molecular characteristics contribute to macrophage phenotype and function. Therefore, we performed whole transcriptome sequencing of human monocytes that were co-cultured with estrogen receptor positive (ER+) or triple-negative (TNBC) breast cancer cell lines and studied the biological responses related to the differential gene activation in both monocytes and cancer cells by pathway analysis. ER+ and TNBC cancer cell lines induced distinctly different macrophage phenotypes with different biological functions, cytokine and chemokine secretion and morphology. Conversely, ER+ and TNBC breast cancer cell lines were distinctly influenced by the presence of macrophages. ER+ cells demonstrated up-regulation of an acute phase inflammatory response, IL-17 signaling and antigen presentation pathway, whereas thioredoxin and vitamin D3 receptor pathways were down-regulated in the respective macrophages. The TNBC educated macrophages down-regulated citrulline metabolism and differentiated into M2-like macrophages with increased MMR protein expression and CCL2 secretion. These data demonstrate how different cancer cells educate the host cells to support tumor growth and might explain why high infiltration of macrophages in TNBC tumors associates with poor prognosis.
Flagellar Kinematics and Swimming of Algal Cells in Viscoelastic Fluids
Authors: Qin B. , Gopinath A. , Yang J. , Gollub J. P. , Arratia P. E. 
Published: March 2015

AbstractThe motility of microorganisms is influenced greatly by their hydrodynamic interactions with the fluidic environment they inhabit. We show by direct experimental observation of the bi-flagellated alga Chlamydomonas reinhardtii that fluid elasticity and viscosity strongly influence the beating pattern - the gait - and thereby control the propulsion speed. The beating frequency and the wave speed characterizing the cyclical bending are both enhanced by fluid elasticity. Despite these enhancements, the net swimming speed of the alga is hindered for fluids that are sufficiently elastic. The origin of this complex response lies in the interplay between the elasticity-induced changes in the spatial and temporal aspects of the flagellar cycle and the buildup and subsequent relaxation of elastic stresses during the power and recovery strokes.
Trek1 contributes to maintaining nasal epithelial barrier integrity
Authors: Jiang Jing , Liu Jiang-Qi , Li Jing , Li Meng , Chen Hong-Bin , Yan Hao , Mo Li-Hua , Qiu Shu-Qi , Liu Zhi-Gang , Yang Ping-Chang 
Published: March 2015

AbstractEpithelial barrier integrity is critical to maintain the homeostasis in the body. The regulatory mechanism of the epithelial barrier function has not been fully understood. This study aims to elucidate the role of the TWIK-related potassium channel-1 (Trek1) in the regulation of the epithelial barrier function of the nasal mucosa. In this study, the levels of Trek1 were assessed by real time RT-PCR and Western blotting. The epithelial barrier function of the rat nasal epithelia was evaluated by the Ussing chamber system. The results showed that Trek1 was detected in the human and rat nasal epithelia, which were significantly lower in patients and rats with allergic rhinitis than that in healthy controls. Exposure to the signature T helper 2 cytokine, interleukin (IL)-4, markedly suppressed the expression of Trek1 in the nasal mucosa via up regulating the expression of the histone deacetylase (HDAC)1. The IL-4-induced rat nasal epithelial barrier dysfunction could be blocked by HDAC1 inhibitor (Trichostatin A), or sodium butyrate, or administration of Clostridium Butyricum. We conclude that Trek1 is critical to maintain the nasal epithelial barrier function.
Requirement of CHROMOMETHYLASE3 for somatic inheritance of the spontaneous tomato epimutation Colourless non-ripening
Authors: Chen Weiwei , Kong Junhua , Qin Cheng , Yu Sheng , Tan Jinjuan , Chen Yun-ru , Wu Chaoqun , Wang Hui , Shi Yan , Li Chunyang , Li Bin , Zhang Pengcheng , Wang Ying , Lai Tongfei , Yu Zhiming , Zhang Xian , Shi Nongnong , Wang Huizhong , Osman Toba , Liu Yule , Manning Kenneth , Jackson Stephen , Rolin Dominique , Zhong Silin , Seymour Graham B. , Gallusci Philippe , Hong Yiguo 
Published: March 2015

AbstractNaturally-occurring epimutants are rare and have mainly been described in plants. However how these mutants maintain their epigenetic marks and how they are inherited remain unknown. Here we report that CHROMOMETHYLASE3 (SlCMT3) and other methyltransferases are required for maintenance of a spontaneous epimutation and its cognate Colourless non-ripening (Cnr) phenotype in tomato. We screened a series of DNA methylation-related genes that could rescue the hypermethylated Cnr mutant. Silencing of the developmentally-regulated SlCMT3 gene results in increased expression of LeSPL-CNR, the gene encodes the SBP-box transcription factor residing at the Cnr locus and triggers Cnr fruits to ripen normally. Expression of other key ripening-genes was also up-regulated. Targeted and whole-genome bisulfite sequencing showed that the induced ripening of Cnr fruits is associated with reduction of methylation at CHG sites in a 286-bp region of the LeSPL-CNR promoter and a decrease of DNA methylation in differentially-methylated regions associated with the LeMADS-RIN binding sites. Our results indicate that there is likely a concerted effect of different methyltransferases at the Cnr locus and the plant-specific SlCMT3 is essential for sustaining Cnr epi-allele. Maintenance of DNA methylation dynamics is critical for the somatic stability of Cnr epimutation and for the inheritance of tomato non-ripening phenotype.
Single-carbon discrimination by selected peptides for individual detection of volatile organic compounds
Authors: Ju Soomi , Lee Ki-Young , Min Sun-Joon , Yoo Yong Kyoung , Hwang Kyo Seon , Kim Sang Kyung , Yi Hyunjung 
Published: March 2015

AbstractAlthough volatile organic compounds (VOCs) are becoming increasingly recognized as harmful agents and potential biomarkers, selective detection of the organic targets remains a tremendous challenge. Among the materials being investigated for target recognition, peptides are attractive candidates because of their chemical robustness, divergence and their homology to natural olfactory receptors. Using a combinatorial peptide library and either a graphitic surface or phenyl-terminated self-assembled monolayer as relevant target surfaces, we successfully selected three interesting peptides that differentiate a single carbon deviation among benzene and its analogues. The heterogeneity of the designed target surfaces provided peptides with varying affinity toward targeted molecules and generated a set of selective peptides that complemented each other. Microcantilever sensors conjugated with each peptide quantitated benzene, toluene and xylene to sub-ppm levels in real time. The selection of specific receptors for a group of volatile molecules will provide a strong foundation for general approach to individually monitoring VOCs.
The Glycan Role in the Glycopeptide Immunogenicity Revealed by Atomistic Simulations and Spectroscopic Experiments on the Multiple Sclerosis Biomarker CSF114(Glc)
Authors: Bruno Agostino , Scrima Mario , Novellino Ettore , D'Errico Gerardino , D'Ursi Anna Maria , Limongelli Vittorio 
Published: March 2015

AbstractGlycoproteins are often recognized as not-self molecules by antibodies triggering the onset of severe autoimmune diseases such as Multiple Sclerosis (MS). Thus, the development of antigen-mimicking biomarkers represents an attractive strategy for an early diagnosis of the disease. An example is the synthetic glycopeptide CSF114(Glc), which was designed and tested as MS biomarker and whose clinical application was limited by its reduced ability to detect autoantibodies in MS patients. In the attempt to improve the efficacy of CSF114(Glc), we have characterized all the events leading to the final binding of the biomarker to the autoantibody using atomistic simulations, ESR and NMR experiments. The glycosydic moiety plays a primary role in the whole process. In particular, in an environment mimicking that used in the clinical tests the glycopeptide assumes a α-helix structure that is functional for the interaction with the antibody. In this conformation CSF114(Glc) binds the monoclonal antibody mAb8-18C5 similarly to the myelin oligodendrocyte glycoprotein MOG, which is a known MS auto-antigen, thus explaining its diagnostic activity. Our study offers new molecular bases to design more effective biomarkers and provides a most valid protocol to investigate other systems where the environment effect is determinant for the biological activity.
Pushing the limit: Examining factors that affect anoxia tolerance in a single genotype of adult D. melanogaster
Authors: Benasayag-Meszaros Raquel , Risley Monica G. , Hernandez Priscilla , Fendrich Margo , Dawson-Scully Ken 
Published: March 2015

AbstractDrosophila melanogaster is a promiscuous species that inhabits a large range of harsh environments including flooded habitats and varying temperature changes. To survive these environments, fruit flies have adapted mechanisms of tolerance that allow them to thrive. During exposure to anoxic stress, fruit flies and other poikilotherms enter into a reversible, protective coma. This coma can be manipulated based on controlled environmental conditions inside the laboratory. Here we utilize a common laboratory raised strain of D. melanogaster to characterize adaptation abilities to better understand coma recovery and survival limitations. Our goal is to mimic the fly's natural environments (wet anoxia) and relate findings to a typical gas induced environment (dry anoxia) that is commonly used in a laboratory. Despite the abundance of research regarding acute and chronic anoxic exposure and cold stress, the literature is lacking evidence linking anoxic stress with variable environmental conditions such as animal age and stress duration. We present novel ways to assess coma recovery and survival using readily available laboratory tools. Our findings suggest that younger age, exposure to colder temperatures and wet environments increase resistance to anoxic stress.