bluuebunny/crossref_metadata_2025_split huggingface dataset:
A MODAL TRANSLATION FOR DUAL-INTUITIONISTIC LOGIC
Authors: SHRAMKO YAROSLAV 
Published: February 2016

AbstractWe construct four binary consequence systems axiomatizing entailment relations between formulas of classical, intuitionistic, dual-intuitionistic and modal (S4) logics, respectively. It is shown that the intuitionistic consequence system is embeddable in the modal (S4) one by the usual modal translation prefixing □ to every subformula of the translated formula. An analogous modal translation of dual-intuitionistic formulas then consists of prefixing ◊ to every subformula of the translated formula. The philosophical importance of this result is briefly discussed.
Affinity purification-mass spectrometry analysis of bcl-2 interactome identified SLIRP as a novel interacting protein
Authors: Trisciuoglio D , Desideri M , Farini V , De Luca T , Di Martile M , Tupone M G , Urbani A , D'Aguanno S , Del Bufalo D 
Published: February 2016

AbstractMembers of the bcl-2 protein family share regions of sequence similarity, the bcl-2 homology (BH) domains. Bcl-2, the most studied member of this family, has four BH domains, BH1–4, and has a critical role in resistance to antineoplastic drugs by regulating the mitochondrial apoptotic pathway. Moreover, it is also involved in other relevant cellular processes such as tumor progression, angiogenesis and autophagy. Deciphering the network of bcl-2-interacting factors should provide a critical advance in understanding the different functions of bcl-2. Here, we characterized bcl-2 interactome by mass spectrometry in human lung adenocarcinoma cells. In silico functional analysis associated most part of the identified proteins to mitochondrial functions. Among them we identified SRA stem–loop interacting RNA-binding protein, SLIRP, a mitochondrial protein with a relevant role in regulating mitochondrial messenger RNA (mRNA) homeostasis. We validated bcl-2/SLIRP interaction by immunoprecipitation and immunofluorescence experiments in cancer cell lines from different histotypes. We showed that, although SLIRP is not involved in mediating bcl-2 ability to protect from apoptosis and oxidative damage, bcl-2 binds and stabilizes SLIRP protein and regulates mitochondrial mRNA levels. Moreover, we demonstrated that the BH4 domain of bcl-2 has a role in maintaining this binding.
Structural simulation of adenosine phosphate via plumbagin and zoledronic acid competitively targets JNK/Erk to synergistically attenuate osteoclastogenesis in a breast cancer model
Authors: Qiao H , Wang T-y , Yu Z-f , Han X-g , Liu X-q , Wang Y-g , Fan Q-m , Qin A , Tang T-t 
Published: February 2016

AbstractThe treatment of breast cancer-induced osteolysis remains a challenge in clinical settings. Here, we explored the effect and mechanism of combined treatment with zoledronic acid (ZA) and plumbagin (PL), a widely investigated component derived fromPlumbago zeylanica, against breast cancer-induced osteoclastogenesis. We found that the combined treatment with PL and ZA suppressed cell viability of precursor osteoclasts and synergistically inhibited MDA-MB-231-induced osteoclast formation (combination index=0.28) with the abrogation of recombinant mouse receptor activator of nuclear factor-κB ligand (RANKL)-induced activation of NF-κB/MAPK (nuclear factor-κB/mitogen-activated protein kinase) pathways. Molecular docking suggested a putative binding area within c-Jun N-terminal kinase/extracellular signal-regulated kinase (JNK/Erk) protease active sites through the structural mimicking of adenosine phosphate (ANP) by the spatial combination of PL with ZA. A homogeneous time-resolved fluorescence assay further illustrated the direct competitiveness of the dual drugs against ANP docking to phosphorylated JNK/Erk, contributing to the inhibited downstream expression of c-Jun/c-Fos/NFATc-1 (nuclear factor of activated T cells, cytoplasmic, calcineurin-dependent 1). Then,in vivotesting demonstrated that the combined administration of PL and ZA attenuated breast cancer growth in the bone microenvironment. Additionally, these molecules prevented the destruction of proximal tibia, with significant reduction of tartrate-resistant acid phosphatase (TRAcP)-positive osteoclast cells and potentiation of apoptotic cancer cells, to a greater extent when combined than when the drugs were applied independently. Altogether, the combination treatment with PL and ZA could significantly and synergistically suppress osteoclastogenesis and inhibit tumorigenesis bothin vitroandin vivoby simulating the spatial structure of ANP to inhibit competitively phosphorylation of c-Jun N-terminal kinase/extracellular signal-regulated kinase (JNK/Erk).
Coupled RNA-SIP and metatranscriptomics of active chemolithoautotrophic communities at a deep-sea hydrothermal vent
Authors: Fortunato Caroline S , Huber Julie A 
Published: February 2016

Abstract
The chemolithoautotrophic microbial community of the rocky subseafloor potentially provides a large amount of organic carbon to the deep ocean, yet our understanding of the activity and metabolic complexity of subseafloor organisms remains poorly described. A combination of metagenomic, metatranscriptomic, and RNA stable isotope probing (RNA-SIP) analyses were used to identify the metabolic potential, expression patterns, and active autotrophic bacteria and archaea and their pathways present in low-temperature hydrothermal fluids from Axial Seamount, an active submarine volcano. Metagenomic and metatranscriptomic results showed the presence of genes and transcripts for sulfur, hydrogen, and ammonium oxidation, oxygen respiration, denitrification, and methanogenesis, as well as multiple carbon fixation pathways. In RNA-SIP experiments across a range of temperatures under reducing conditions, the enriched 13C fractions showed differences in taxonomic and functional diversity. At 30 °C and 55 °C, Epsilonproteobacteria were dominant, oxidizing hydrogen and primarily reducing nitrate. Methanogenic archaea were also present at 55 °C, and were the only autotrophs present at 80 °C. Correspondingly, the predominant CO2 fixation pathways changed from the reductive tricarboxylic acid (rTCA) cycle to the reductive acetyl-CoA pathway with increasing temperature. By coupling RNA-SIP with meta-omics, this study demonstrates the presence and activity of distinct chemolithoautotrophic communities across a thermal gradient of a deep-sea hydrothermal vent.
Approaching a universal scaling relationship between fracture stiffness and fluid flow
Authors: Pyrak-Nolte Laura J. , Nolte David D. 
Published: February 2016

AbstractA goal of subsurface geophysical monitoring is the detection and characterization of fracture alterations that affect the hydraulic integrity of a site. Achievement of this goal requires a link between the mechanical and hydraulic properties of a fracture. Here we present a scaling relationship between fluid flow and fracture-specific stiffness that approaches universality. Fracture-specific stiffness is a mechanical property dependent on fracture geometry that can be monitored remotely using seismic techniques. A Monte Carlo numerical approach demonstrates that a scaling relationship exists between flow and stiffness for fractures with strongly correlated aperture distributions, and continues to hold for fractures deformed by applied stress and by chemical erosion as well. This new scaling relationship provides a foundation for simulating changes in fracture behaviour as a function of stress or depth in the Earth and will aid risk assessment of the hydraulic integrity of subsurface sites.
Tyrosine kinase-mediated axial motility of basal cells revealed by intravital imaging
Authors: Roy Jeremy , Kim Bongki , Hill Eric , Visconti Pablo , Krapf Dario , Vinegoni Claudio , Weissleder Ralph , Brown Dennis , Breton Sylvie 
Published: February 2016

AbstractEpithelial cells are generally considered to be static relative to their neighbours. Basal cells in pseudostratified epithelia display a single long cytoplasmic process that can cross the tight junction barrier to reach the lumen. Usingin vivomicroscopy to visualize the epididymis, a model system for the study of pseudostratified epithelia, we report here the surprising discovery that these basal cell projections—which we call axiopodia—periodically extend and retract over time. We found that axiopodia extensions and retractions follow an oscillatory pattern. This movement, which we refer to as periodic axial motility (PAM), is controlled by c-Src and MEK1/2–ERK1/2. Therapeutic inhibition of tyrosine kinase activity induces a retraction of these projections. Such unexpected cell motility may reflect a novel mechanism by which specialized epithelial cells sample the luminal environment.
Loss of UBE3A from TH-expressing neurons suppresses GABA co-release and enhances VTA-NAc optical self-stimulation
Authors: Berrios Janet , Stamatakis Alice M. , Kantak Pranish A. , McElligott Zoe A. , Judson Matthew C. , Aita Megumi , Rougie Marie , Stuber Garret D. , Philpot Benjamin D. 
Published: February 2016

AbstractMotivated reward-seeking behaviours are governed by dopaminergic ventral tegmental area projections to the nucleus accumbens. In addition to dopamine, these mesoaccumbal terminals co-release other neurotransmitters including glutamate and GABA, whose roles in regulating motivated behaviours are currently being investigated. Here we demonstrate that loss of the E3-ubiquitin ligase, UBE3A, from tyrosine hydroxylase-expressing neurons impairs mesoaccumbal, non-canonical GABA co-release and enhances reward-seeking behaviour measured by optical self-stimulation.
The mRNA-edited form of GABRA3 suppresses GABRA3-mediated Akt activation and breast cancer metastasis
Authors: Gumireddy Kiranmai , Li Anping , Kossenkov Andrew V. , Sakurai Masayuki , Yan Jinchun , Li Yan , Xu Hua , Wang Jian , Zhang Paul J. , Zhang Lin , Showe Louise C. , Nishikura Kazuko , Huang Qihong 
Published: February 2016

AbstractMetastasis is a critical event affecting breast cancer patient survival. To identify molecules contributing to the metastatic process, we analysed The Cancer Genome Atlas (TCGA) breast cancer data and identified 41 genes whose expression is inversely correlated with survival. Here we show that GABAA receptor alpha3 (Gabra3), normally exclusively expressed in adult brain, is also expressed in breast cancer, with high expression of Gabra3 being inversely correlated with breast cancer survival. We demonstrate that Gabra3 activates the AKT pathway to promote breast cancer cell migration, invasion and metastasis. Importantly, we find an A-to-I RNA-edited form of Gabra3 only in non-invasive breast cancers and show that edited Gabra3 suppresses breast cancer cell invasion and metastasis. A-to-I-edited Gabra3 has reduced cell surface expression and suppresses the activation of AKT required for cell migration and invasion. Our study demonstrates a significant role for mRNA-edited Gabra3 in breast cancer metastasis.
SIRT7-dependent deacetylation of the U3-55k protein controls pre-rRNA processing
Authors: Chen Sifan , Blank Maximilian Felix , Iyer Aishwarya , Huang Bingding , Wang Lin , Grummt Ingrid , Voit Renate 
Published: February 2016

AbstractSIRT7 is an NAD+-dependent protein deacetylase with important roles in ribosome biogenesis and cell proliferation. Previous studies have established that SIRT7 is associated with RNA polymerase I, interacts with pre-ribosomal RNA (rRNA) and promotes rRNA synthesis. Here we show that SIRT7 is also associated with small nucleolar RNP (snoRNPs) that are involved in pre-rRNA processing and rRNA maturation. Knockdown of SIRT7 impairs U3 snoRNA dependent early cleavage steps that are necessary for generation of 18S rRNA. Mechanistically, SIRT7 deacetylates U3-55k, a core component of the U3 snoRNP complex, and reversible acetylation of U3-55k modulates the association of U3-55k with U3 snoRNA. Deacetylation by SIRT7 enhances U3-55k binding to U3 snoRNA, which is a prerequisite for pre-rRNA processing. Under stress conditions, SIRT7 is released from nucleoli, leading to hyperacetylation of U3-55k and attenuation of pre-rRNA processing. The results reveal a multifaceted role of SIRT7 in ribosome biogenesis, regulating both transcription and processing of rRNA.
Cybermaterials: materials by design and accelerated insertion of materials
Authors: Xiong Wei , Olson Gregory B 
Published: February 2016

AbstractCybermaterials innovation entails an integration of Materials by Design and accelerated insertion of materials (AIM), which transfers studio ideation into industrial manufacturing. By assembling a hierarchical architecture of integrated computational materials design (ICMD) based on materials genomic fundamental databases, the ICMD mechanistic design models accelerate innovation. We here review progress in the development of linkage models of the process-structure–property-performance paradigm, as well as related design accelerating tools. Extending the materials development capability based on phase-level structural control requires more fundamental investment at the level of the Materials Genome, with focus on improving applicable parametric design models and constructing high-quality databases. Future opportunities in materials genomic research serving both Materials by Design and AIM are addressed.
Radiosensitisation of human colorectal cancer cells by ruthenium(II) arene anticancer complexes
Authors: Carter R , Westhorpe A , Romero MJ , Habtemariam A , Gallevo CR , Bark Y , Menezes N , Sadler PJ , Sharma RA 
Published: February 2016

AbstractSome of the largest improvements in clinical outcomes for patients with solid cancers observed over the past 3 decades have been from concurrent treatment with chemotherapy and radiotherapy (RT). The lethal effects of RT on cancer cells arise primarily from damage to DNA. Ruthenium (Ru) is a transition metal of the platinum group, with potentially less toxicity than platinum drugs. We postulated that ruthenium-arene complexes are radiosensitisers when used in combination with RT. We screened 14 ruthenium-arene complexes and identified AH54 and AH63 as supra-additive radiosensitisers by clonogenic survival assays and isobologram analyses. Both complexes displayed facial chirality. At clinically relevant doses of RT, radiosensitisation of cancer cells by AH54 and AH63 was p53-dependent. Radiation enhancement ratios for 5–10 micromolar drug concentrations ranged from 1.19 to 1.82. In p53-wildtype cells, both drugs induced significant G2 cell cycle arrest and apoptosis. Colorectal cancer cells deficient in DNA damage repair proteins, EME1 and MUS81, were significantly more sensitive to both agents. Both drugs were active in cancer cell lines displaying acquired resistance to oxaliplatin or cisplatin. Our findings broaden the potential scope for these drugs for use in cancer therapy, including combination with radiotherapy to treat colorectal cancer.
The local density of optical states of a metasurface
Authors: Lunnemann Per , Koenderink A. Femius 
Published: February 2016

AbstractWhile metamaterials are often desirable for near-field functions, such as perfect lensing, or cloaking, they are often quantified by their response to plane waves from the far field. Here, we present a theoretical analysis of the local density of states near lattices of discrete magnetic scatterers, i.e., the response to near field excitation by a point source. Based on a pointdipole theory using Ewald summation and an array scanning method, we can swiftly and semi-analytically evaluate the local density of states (LDOS) for magnetoelectric point sources in front of an infinite two-dimensional (2D) lattice composed of arbitrary magnetoelectric dipole scatterers. The method takes into account radiation damping as well as all retarded electrodynamic interactions in a self-consistent manner. We show that a lattice of magnetic scatterers evidences characteristic Drexhage oscillations. However, the oscillations are phase shifted relative to the electrically scattering lattice consistent with the difference expected for reflection off homogeneous magnetic respectively electric mirrors. Furthermore, we identify in which source-surface separation regimes the metasurface may be treated as a homogeneous interface and in which homogenization fails. A strong frequency and in-plane position dependence of the LDOS close to the lattice reveals coupling to guided modes supported by the lattice.
Diet-induced changes in maternal gut microbiota and metabolomic profiles influence programming of offspring obesity risk in rats
Authors: Paul Heather A. , Bomhof Marc R. , Vogel Hans J. , Reimer Raylene A. 
Published: February 2016

AbstractMaternal obesity and overnutrition during pregnancy and lactation can program an increased risk of obesity in offspring. In this context, improving maternal metabolism may help reduce the intergenerational transmission of obesity. Here we show that, in Sprague-Dawley rats, selectively altering obese maternal gut microbial composition with prebiotic treatment reduces maternal energy intake, decreases gestational weight gain and prevents increased adiposity in dams and their offspring. Maternal serum metabolomics analysis, along with satiety hormone and gut microbiota analysis, identified maternal metabolic signatures that could be implicated in programming offspring obesity risk and highlighted the potential influence of maternal gut microbiota on maternal and offspring metabolism. In particular, the metabolomic signature of insulin resistance in obese rats normalized when dams consumed the prebiotic. In summary, prebiotic intake during pregnancy and lactation improves maternal metabolism in diet-induced obese rats in a manner that attenuates the detrimental nutritional programming of offspring associated with maternal obesity. Overall, these findings contribute to our understanding of the maternal mechanisms influencing the developmental programming of offspring obesity and provide compelling pre-clinical evidence for a potential strategy to improve maternal and offspring metabolic outcomes in human pregnancy.
Changes of immunogenic profiles between a single dose and one booster influenza vaccination in hemodialysis patients – an 18-week, open-label trial
Authors: Chang Yu-Tzu , Wang Jen-Ren , Lin Meng-Te , Wu Chi-Jung , Tsai Ming-Song , Wen-Chi Chiang Lin , Shih Te-En , Kuo Te-Hui , Song Eing-Ju , Sung Junne-Ming 
Published: February 2016

AbstractAnnual influenza vaccination is recommended, but its efficacy in dialysis population is still controversial. Here we aimed to compare the dynamic changes of immune response between various influenza vaccination protocols in hemodialysis patients. A 18-week open label, non-randomized, controlled trial was conducted during 2011–2012. The efficacy between unvaccinated, one- and two-dose regimens were evaluated in 175 hemodialysis patients. Immunogenic profiles were assessed by hemagglutination-inhibition assays. At 3–9 weeks post-vaccination, antibody responses were similar between the one- and two-dose regimens, while the seroprotection rates (antibody titer ≥1:40) for influenza A were 55.6–82.5% in the adult (18–60 years) and 33.3–66.7% in the elderly (>60 years). Meanwhile, the seroprotection rates for influenza B were low (4.0–25.0%). By 18 weeks post-vaccination, the seroprotection rates for influenza A and B declined (0.0–33.3%) in both the adult and elderly receiving one- or two-dose regimens. Of dialysis patients, at most 2.4% developed moderate to severe adverse effects(myalgia and headache) after vaccination. In conclusion, the two-dose regimen could not improve immune responses than the one-dose regimen in hemodialysis patients; meanwhile the induced protective antibodies of both regimens could not be maintained for more than 4 months. Modification of current influenza vaccination strategy in dialysis population should be re-considered.
Induction of virulence factors in Giardia duodenalis independent of host attachment
Authors: Emery Samantha J. , Mirzaei Mehdi , Vuong Daniel , Pascovici Dana , Chick Joel M. , Lacey Ernest , Haynes Paul A. 
Published: February 2016

AbstractGiardia duodenalis is responsible for the majority of parasitic gastroenteritis in humans worldwide. Host-parasite interaction models in vitro provide insights into disease and virulence and help us to understand pathogenesis. Using HT-29 intestinal epithelial cells (IEC) as a model we have demonstrated that initial sensitisation by host secretions reduces proclivity for trophozoite attachment, while inducing virulence factors. Host soluble factors triggered up-regulation of membrane and secreted proteins, including Tenascins, Cathepsin-B precursor, cystatin and numerous Variant-specific Surface Proteins (VSPs). By comparison, host-cell attached trophozoites up-regulated intracellular pathways for ubiquitination, reactive oxygen species (ROS) detoxification and production of pyridoxal phosphate (PLP). We reason that these results demonstrate early pathogenesis in Giardia involves two independent host-parasite interactions. Motile trophozoites respond to soluble secreted signals, which deter attachment and induce expression of virulence factors. Trophozoites attached to host cells, in contrast, respond by up-regulating intracellular pathways involved in clearance of ROS, thus anticipating the host defence response.
Periodic Mesoporous Organosilica Nanocubes with Ultrahigh Surface Areas for Efficient CO2 Adsorption
Authors: Wei Yong , Li Xiaomin , Zhang Renyuan , Liu Yong , Wang Wenxing , Ling Yun , El-Toni Ahmed Mohamed , Zhao Dongyuan 
Published: February 2016

AbstractUltrahigh surface area single-crystals of periodic mesoporous organosilica (PMOs) with uniform cubic or truncated-cubic morphology and organic/inorganic components homogeneously distributed over the whole frameworks have successfully been prepared by a sol-gel surfactant-templating method. By tuning the porous feature and polymerization degree, the surface areas of the obtained PMO nanocubes can reach as high as 2370 m2/g, which is the highest for silica-based mesoporous materials. The ultrahigh surface area of the obtained PMO single crystals is mainly resulted from abundant micropores in the mesoporous frameworks. Furthermore, the diameter of the nanocubes can also be well controlled from 150 to 600 nm. The materials show ultrahigh CO2 adsorption capacity (up to 1.42 mmol/g at 273 K) which is much higher than other porous silica materials and comparable to some carbonaceous materials. The adsorption of CO2 into the PMO nanocubes is mainly in physical interaction, therefore the adsorption-desorption process is highly reversible and the adsorption capacity is much dependent on the surface area of the materials. Moreover, the selectivity is also very high (~11 times to N2) towards CO2 adsorption.
Drosophila screen connects nuclear transport genes to DPR pathology in c9ALS/FTD
Authors: Boeynaems Steven , Bogaert Elke , Michiels Emiel , Gijselinck Ilse , Sieben Anne , Jovičić Ana , De Baets Greet , Scheveneels Wendy , Steyaert Jolien , Cuijt Ivy , Verstrepen Kevin J. , Callaerts Patrick , Rousseau Frederic , Schymkowitz Joost , Cruts Marc , Van Broeckhoven Christine , Van Damme Philip , Gitler Aaron D. , Robberecht Wim , Van Den Bosch Ludo 
Published: February 2016

AbstractHexanucleotide repeat expansions in C9orf72 are the most common cause of amyotrophic lateral sclerosis (ALS) and frontotemporal degeneration (FTD) (c9ALS/FTD). Unconventional translation of these repeats produces dipeptide repeat proteins (DPRs) that may cause neurodegeneration. We performed a modifier screen in Drosophila and discovered a critical role for importins and exportins, Ran-GTP cycle regulators, nuclear pore components and arginine methylases in mediating DPR toxicity. These findings provide evidence for an important role for nucleocytoplasmic transport in the pathogenic mechanism of c9ALS/FTD.