bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metal-induced aggregation of valine capped gold nanoparticles: An efficient and rapid approach for colorimetric detection of Pb2+ ions
Authors: Priyadarshini E. , Pradhan N. 
Published: August 2017

AbstractIn this study, we report a novel application of valine-capped gold nanoparticles for colorimetric and visual detection of lead ions. The –COO− group of the hydrophobic valine molecules present efficient electrostatic repulsion resulting in generation of stable, well-dispersed and size-controlled GNPs. The GNPs were highly selective for Pb2+ ions and showed visible colour change in the assay mixture on addition of solution containing lead ions. Interestingly, a decrease in the intensity of original SPR peak at 530 nm was observed, with concomitant appearance of a new peak at longer wavelength due to agglomerated GNPs. The free –COO− groups on GNP surface interacted with Pb2+ and ion-dependent chelation mechanism lead to cross-linking of particles and subsequent agglomeration. Binding of Pb2+ ions and valine-capped GNPs occur in a stochiometric ratio of 1:2. The GNPs displayed colorimetric sensing in the range of 0 to 100 ppm concentration with a very high selectivity towards lead even in the presence of other metal ions. The minimum detection limit (MDL) for Pb2+ was 30.5 µM. We anticipate that these valine-capped GNPs may be employed for lead detection in polluted water/wastewater through a cost-efficient, one-step assay protocol as it does not require additional functionalization with specific ligand molecules.
On the use of atomistic simulations to aid bulk metallic glasses structural elucidation with solid-state NMR
Authors: Ferreira Ary R. , Rino José P. 
Published: August 2017

AbstractSolid-state nuclear magnetic resonance (ssNMR) experimental 27Al metallic shifts reported in the literature for bulk metallic glasses (BMGs) were revisited in the light of state-of-the-art atomistic simulations. In a consistent way, the Gauge-Including Projector Augmented-Wave (GIPAW) method was applied in conjunction with classical molecular dynamics (CMD). A series of Zr-Cu-Al alloys with low Al concentrations were selected as case study systems, for which realistic CMD derived structural models were used for a short- and medium-range order mining. That initial procedure allowed the detection of trends describing changes on the microstructure of the material upon Al alloying, which in turn were used to guide GIPAW calculations with a set of abstract systems in the context of ssNMR. With essential precision and accuracy, the ab initio simulations also yielded valuable trends from the electronic structure point of view, which enabled an overview of the bonding nature of Al-centered clusters as well as its influence on the experimental ssNMR outcomes. The approach described in this work might promote the use of ssNMR spectroscopy in research on glassy metals. Moreover, the results presented demonstrate the possibility to expand the applications of this technique, with deeper insight into nuclear interactions and less speculative assignments.
Oxygen nanobubbles revert hypoxia by methylation programming
Authors: Bhandari Pushpak N. , Cui Yi , Elzey Bennett D. , Goergen Craig J. , Long Christopher M. , Irudayaraj Joseph 
Published: August 2017

AbstractTargeting the hypoxic tumor microenvironment has a broad impact in cancer epigenetics and therapeutics. Oxygen encapsulated nanosize carboxymethyl cellulosic nanobubbles were developed for mitigating the hypoxic regions of tumors to weaken the hypoxia-driven pathways and inhibit tumor growth. We show that 5-methylcytosine (5mC) hypomethylation in hypoxic regions of a tumor can be reverted to enhance cancer treatment by epigenetic regulation, using oxygen nanobubbles in the sub-100 nm size range, both, in vitro and in vivo. Oxygen nanobubbles were effective in significantly delaying tumor progression and improving survival rates in mice models. Further, significant hypermethylation was observed in promoter DNA region of BRCA1 due to oxygen nanobubble (ONB) treatment. The nanobubbles can also reprogram several hypoxia associated and tumor suppressor genes such as MAT2A and PDK-1, in addition to serving as an ultrasound contrast agent. Our approach to develop nanosized oxygen encapsulated bubbles as an ultrasound contrast agent for methylation reversal is expected to have a significant impact in epigenetic programming and to serve as an adjuvant to cancer treatment.
Quantitative proteomic characterization of lung-MSC and bone marrow-MSC using DIA-mass spectrometry
Authors: Rolandsson Enes Sara , Åhrman Emma , Palani Anitha , Hallgren Oskar , Bjermer Leif , Malmström Anders , Scheding Stefan , Malmström Johan , Westergren-Thorsson Gunilla 
Published: August 2017

AbstractMesenchymal stromal cells (MSC) are ideal candidates for cell therapies, due to their immune-regulatory and regenerative properties. We have previously reported that lung-derived MSC are tissue-resident cells with lung-specific properties compared to bone marrow-derived MSC. Assessing relevant molecular differences between lung-MSC and bone marrow-MSC is important, given that such differences may impact their behavior and potential therapeutic use. Here, we present an in-depth mass spectrometry (MS) based strategy to investigate the proteomes of lung-MSC and bone marrow-MSC. The MS-strategy relies on label free quantitative data-independent acquisition (DIA) analysis and targeted data analysis using a MSC specific spectral library. We identified several significantly differentially expressed proteins between lung-MSC and bone marrow-MSC within the cell layer (352 proteins) and in the conditioned medium (49 proteins). Bioinformatics analysis revealed differences in regulation of cell proliferation, which was functionally confirmed by decreasing proliferation rate through Cytochrome P450 stimulation. Our study reveals important differences within proteome and matrisome profiles between lung- and bone marrow-derived MSC that may influence their behavior and affect the clinical outcome when used for cell-therapy.
Large Thermal Motion in Halide Perovskites
Authors: Tyson T. A. , Gao W. , Chen Y.-S. , Ghose S. , Yan Y. 
Published: August 2017

AbstractSolar cells based on hybrid perovskites have shown high efficiency while possessing simple processing methods. To gain a fundamental understanding of their properties on an atomic level, we investigate single crystals of CH3NH3PbI3with a narrow transition (~5 K) near 327 K. Temperature dependent structural measurements reveal a persistent tetragonal structure with smooth changes in the atomic displacement parameters (ADPs) on crossing T*. We show that the ADPs for I ions yield extended flat regions in the potential wells consistent with the measured large thermal expansion parameter. Molecular dynamics simulations reveal that this material exhibits significant asymmetries in the Pb-I pair distribution functions. We also show that the intrinsically enhanced freedom of motion of the iodine atoms enables large deformations. This flexibility (softness) of the atomic structure results in highly localized atomic relaxation about defects and hence accounts for both the high carrier mobility as well as the structural instability.
Electrical performance of lightweight CNT-Cu composite wires impacted by surface and internal Cu spatial distribution
Authors: Sundaram Rajyashree , Yamada Takeo , Hata Kenji , Sekiguchi Atsuko 
Published: August 2017

AbstractWe report ultralong conducting lightweight multiwall carbon nanotube (MWCNT)-Cu composite wires with MWCNTs uniformly distributed in a continuous Cu matrix throughout. With a high MWCNT vol% (40–45%), the MWCNT-Cu wire density was 2/3rd that of Cu. Our composite wires show manufacturing potential because we used industrially compatible Cu electrodeposition protocols on commercial CNT wires. Further, we systematically varied Cu spatial distribution on the composite wire surface and bulk and measured the associated electrical performance, including resistivity (ρ), temperature dependence of resistance, and stability to current (measured as current carrying capacity, CCC in vacuum). We find that a continuous Cu matrix with homogeneous MWCNT distribution, i.e., maximum internal Cu filling within MWCNT wires, is critical to high overall electrical performances. Wires with maximum internal Cu filling exhibit (i) low room temperature ρ, 1/100th of the starting MWCNT wires, (ii) suppressed resistance-rise with temperature-increase and temperature coefficient of resistance (TCR) ½ that of Cu, and (iii) vacuum-CCC 28% higher than Cu. Further, the wires showed real-world applicability and were easily soldered into practical circuits. Hence, our MWCNT-Cu wires are promising lightweight alternatives to Cu wiring for weight-reducing applications. The low TCR is specifically advantageous for stable high-temperature operation, e.g., in motor windings.
Effects of short indels on protein structure and function in human genomes
Authors: Lin Maoxuan , Whitmire Sarah , Chen Jing , Farrel Alvin , Shi Xinghua , Guo Jun-tao 
Published: August 2017

AbstractInsertions and deletions (indels) represent the second most common type of genetic variations in human genomes. Indels can be deleterious and contribute to disease susceptibility as recent genome sequencing projects revealed a large number of indels in various cancer types. In this study, we investigated the possible effects of small coding indels on protein structure and function, and the baseline characteristics of indels in 2504 individuals of 26 populations from the 1000 Genomes Project. We found that each population has a distinct pattern in genes with small indels. Frameshift (FS) indels are enriched in olfactory receptor activity while non-frameshift (NFS) indels are enriched in transcription-related proteins. Structural analysis of NFS indels revealed that they predominantly adopt coil or disordered conformations, especially in proteins with transcription-related NFS indels. These results suggest that the annotated coding indels from the 1000 Genomes Project, while contributing to genetic variations and phenotypic diversity, generally do not affect the core protein structures and have no deleterious effect on essential biological processes. In addition, we found that a number of reference genome annotations might need to be updated due to the high prevalence of annotated homozygous indels in the general population.
Self-propelled ion gel at air-water interface
Authors: Furukawa Kazuaki , Teshima Tetsuhiko , Ueno Yuko 
Published: August 2017

AbstractWe report on a self-propelled gel using ionic liquid as a new type of self-propellant that generates a powerful and durable motion at an air-water interface. The gel is composed of 1-ethyl-3-methylimidazolium-bis(trifluoromethylsulfonyl)imide (EMIM-TFSI) and poly(vinylidene fluoride-co-hexafluoropropylene) (P(VDF-co-HFP)). A long rectangular ion gel piece placed on the interface shows rapid rotation motion with maximum frequency close to 10 Hz, corresponding to the velocity over 300 mms−1 at an outmost end of the piece. The rotation continues for ca. 102 s, followed by a reciprocating motion (<~103 s) and a nonlinear motion in long-time observations (>~103 s). The behaviours can be explained by the model considering elution of EMIM-TFSI to the air-water interface, rapid dissolution into water, and slow diffusion in an inhomogeneous polymer gel network. Because the self-propellants are promptly removed from the interface by dissolution, durable self-propelled motions are observed also at limited interface areas close in size to the gel pieces. A variety of motions are induced in such systems where the degree of freedom in motion is limited. As the ion gel possesses formability and processability, it is also advantageous for practical applications. We demonstrate that the gel does work as an engine.
Cerium oxide nanoparticles inhibit differentiation of neural stem cells
Authors: Gliga Anda R. , Edoff Karin , Caputo Fanny , Källman Thomas , Blom Hans , Karlsson Hanna L. , Ghibelli Lina , Traversa Enrico , Ceccatelli Sandra , Fadeel Bengt 
Published: August 2017

AbstractCerium oxide nanoparticles (nanoceria) display antioxidant properties and have shown cytoprotective effects both in vitro and in vivo. Here, we explored the effects of nanoceria on neural progenitor cells using the C17.2 murine cell line as a model. First, we assessed the effects of nanoceria versus samarium (Sm) doped nanoceria on cell viability in the presence of the prooxidant, DMNQ. Both particles were taken up by cells and nanoceria, but not Sm-doped nanoceria, elicited a temporary cytoprotective effect upon exposure to DMNQ. Next, we employed RNA sequencing to explore the transcriptional responses induced by nanoceria or Sm-doped nanoceria during neuronal differentiation. Detailed computational analyses showed that nanoceria altered pathways and networks relevant for neuronal development, leading us to hypothesize that nanoceria inhibits neuronal differentiation, and that nanoceria and Sm-doped nanoceria both interfere with cytoskeletal organization. We confirmed that nanoceria reduced neuron specific β3-tubulin expression, a marker of neuronal differentiation, and GFAP, a neuroglial marker. Furthermore, using super-resolution microscopy approaches, we could show that both particles interfered with cytoskeletal organization and altered the structure of neural growth cones. Taken together, these results reveal that nanoceria may impact on neuronal differentiation, suggesting that nanoceria could pose a developmental neurotoxicity hazard.
A novel mechanism of ERK1/2 regulation in smooth muscle involving acetylation of the ERK1/2 scaffold IQGAP1
Authors: Vetterkind Susanne , Lin Qian Qian , Morgan Kathleen G. 
Published: August 2017

AbstractCeramide, a bioactive lipid and signaling molecule associated with cardiovascular disease, is known to activate extracellular signal regulated kinases 1 and 2 (ERK1/2). Here, we determined that the effect of ceramide on ERK1/2 is mediated by ceramide signaling on an ERK scaffold protein, IQ motif containing GTPase activating protein 1 (IQGAP1). Experiments were performed with aortic smooth muscle cells using inhibitor screening, small interfering RNA (siRNA), immunoprecipitation (IP), immunoblots and bioinformatics. We report here that C6 ceramide increases serum-stimulated ERK1/2 activation in a manner dependent on the ERK1/2 scaffold IQGAP1. C6 ceramide increases IQGAP1 protein levels by preventing its cleavage. Bioinformatic analysis of the IQGAP1 amino acid sequence revealed potential cleavage sites for proteases of the proprotein convertase family that match the cleavage products. These potential cleavage sites overlap with known motifs for lysine acetylation. Deacetylase inhibitor treatment increased IQGAP1 acetylation and reduced IQGAP1 cleavage. These data are consistent with a model in which IQGAP1 cleavage is regulated by acetylation of the cleavage sites. Activation of ERK1/2 by ceramide, known to increase lysine acetylation, appears to be mediated by acetylation-dependent stabilization of IQGAP1. This novel mechanism could open new possibilities for therapeutic intervention in cardiovascular diseases.
Development of an ensemble Kalman filter data assimilation system for the Venusian atmosphere
Authors: Sugimoto Norihiko , Yamazaki Akira , Kouyama Toru , Kashimura Hiroki , Enomoto Takeshi , Takagi Masahiro 
Published: August 2017

AbstractThe size and mass of Venus is similar to those of the Earth; however, its atmospheric dynamics are considerably different and they are poorly understood due to limited observations and computational difficulties. Here, we developed a data assimilation system based on the local ensemble transform Kalman filter (LETKF) for a Venusian Atmospheric GCM for the Earth Simulator (VAFES), to make full use of the observational data. To examine the validity of the system, two datasets were assimilated separately into the VAFES forecasts forced with solar heating that excludes the diurnal component Qz; one was created from a VAFES run forced with solar heating that includes the diurnal component Qt, whereas the other was based on observations made by the Venus Monitoring Camera (VMC) onboard the Venus Express. The VAFES-LETKF system rapidly reduced the errors between the analysis and forecasts. In addition, the VAFES-LETKF system successfully reproduced the thermal tide excited by the diurnal component of solar heating, even though the second datasets only included horizontal winds at a single altitude on the dayside with a long interval of approximately one Earth day. This advanced system could be useful in the analysis of future datasets from the Venus Climate Orbiter ‘Akatsuki’.
Evolution of rubisco complex small subunit transit peptides from algae to plants
Authors: Razzak Md. Abdur , Lee Dong Wook , Yoo Yun-Joo , Hwang Inhwan 
Published: August 2017

AbstractChloroplasts evolved from a free-living cyanobacterium acquired by the ancestor of all photosynthetic eukaryotes, including algae and plants, through a single endosymbiotic event. During endosymbiotic conversion, the majority of genes in the endosymbiont were transferred to the host nucleus and many of the proteins encoded by these genes must therefore be transported into the chloroplast after translation in the cytosol. Chloroplast-targeted proteins contain a targeting signal, named the transit peptide (TP), at the N-terminus. However, the evolution of TPs is not well understood. In this study, TPs from RbcS (rubisco small subunit) were compared between lower and higher eukaryotes. Chlamydomonas reinhardtii RbcS (CrRbcS) TP was non-functional in Arabidopsis. However, inclusion of a critical sequence motif, FP-RK, from Arabidopsis thaliana RbcS (AtRbcS) TP allowed CrRbcS TP to deliver proteins into plant chloroplasts. The position of the FP-RK motif in CrRbcS TP was critical for function. The QMMVW sequence motif in CrRbcS TP was crucial for its transport activity in plants. CrRbcS TPs containing additional plant motifs remained functional in C. reinhardtii. These results suggest that TPs evolved by acquiring additional sequence motifs to support protein targeting to chloroplasts during evolution of land plants from algae.
A systematic analysis of the RNA-targeting potential of secreted bacterial effector proteins
Authors: Tawk Caroline , Sharan Malvika , Eulalio Ana , Vogel Jörg 
Published: August 2017

AbstractMany pathogenic bacteria utilize specialized secretion systems to deliver proteins called effectors into eukaryotic cells for manipulation of host pathways. The vast majority of known effector targets are host proteins, whereas a potential targeting of host nucleic acids remains little explored. There is only one family of effectors known to target DNA directly, and effectors binding host RNA are unknown. Here, we take a two-pronged approach to search for RNA-binding effectors, combining biocomputational prediction of RNA-binding domains (RBDs) in a newly assembled comprehensive dataset of bacterial secreted proteins, and experimental screening for RNA binding in mammalian cells. Only a small subset of effectors were predicted to carry an RBD, indicating that if RNA targeting was common, it would likely involve new types of RBDs. Our experimental evaluation of effectors with predicted RBDs further argues for a general paucity of RNA binding activities amongst bacterial effectors. We obtained evidence that PipB2 and Lpg2844, effector proteins of Salmonella and Legionella species, respectively, may harbor novel biochemical activities. Our study presenting the first systematic evaluation of the RNA-targeting potential of bacterial effectors offers a basis for discussion of whether or not host RNA is a prominent target of secreted bacterial proteins.
Mesohepatectomy Versus Extended Hemihepatectomies for Centrally Located Liver Tumors: A Meta-Analysis
Authors: Li Jianbo , Wang Chengdi , Song Jiulin , Chen Nan , Jiang Li , Yang Jiayin , Yan Lunan 
Published: August 2017

AbstractThe comparison of Mesohepatectomy (MH) with conventional extended hemihepatectomies (EH) for patients with centrally located liver tumors (CLLTs) were inconsistent. Our aims were to systemically compare MH with EH and to determine whether MH can achieve a similar clinical outcome as EH through this meta-analysis. PubMed/Medline, EMBASE, Web of Knowledge and Cochrane Library were searched updated to June 11, 2016. Blood loss and operation time favored MH in elder patients (mean difference [MD] for blood loss: −692.82 ml, 95% CI: −976.72 to −408.92 ml, P < 0.001; MD for operation time: −78.75 min, 95% CI: −107.66 to −49.81, P < 0.001). Morbidity rate (29.2%, 95% CI: 24.1 to 34.8%), mortality rate (2.0%, 95% CI: 1.2 to 3.3%) and overall survival (median OS 38.2 m, 95% CI: 34.0 to 42.8 m) of MH were comparable with those of EH. The low liver failure rate favored MH (odds ratio [OR]: 0.29, 95% CI: 0.09 to 0.88, P = 0.03). For MH, bile leakage was the most common surgical complication (MH vs. EH: 13.5% vs. 6.7%, P = 0.016), while for EH, it was wound infection (MH vs. EH: 6.9% vs. 15.7%, P < 0.001). Thus MH might be in general safe and feasible for treating CLLTs with a similar clinical outcome as EH.
Personalized Monitoring and Advance Warning System for Cardiac Arrhythmias
Authors: Kiranyaz Serkan , Ince Turker , Gabbouj Moncef 
Published: August 2017

AbstractEach year more than 7 million people die from cardiac arrhythmias. Yet no robust solution exists today to detect such heart anomalies right at the moment they occur. The purpose of this study was to design a personalized health monitoring system that can detect early occurrences of arrhythmias from an individual’s electrocardiogram (ECG) signal. We first modelled the common causes of arrhythmias in the signal domain as a degradation of normal ECG beats to abnormal beats. Using the degradation models, we performed abnormal beat synthesis which created potential abnormal beats from the average normal beat of the individual. Finally, a Convolutional Neural Network (CNN) was trained using real normal and synthesized abnormal beats. As a personalized classifier, the trained CNN can monitor ECG beats in real time for arrhythmia detection. Over 34 patients’ ECG records with a total of 63,341 ECG beats from the MIT-BIH arrhythmia benchmark database, we have shown that the probability of detecting one or more abnormal ECG beats among the first three occurrences is higher than 99.4% with a very low false-alarm rate.
A comparative study of the mechanical and thermal properties of defective ZrC, TiC and SiC
Authors: Jiang M. , Zheng J. W. , Xiao H. Y. , Liu Z. J. , Zu X. T. 
Published: August 2017

AbstractZrC and TiC have been proposed to be alternatives to SiC as fuel-cladding and structural materials in nuclear reactors due to their strong radiation tolerance and high thermal conductivity at high temperatures. To unravel how the presence of defects affects the thermo-physical properties under irradiation, first-principles calculations based on density function theory were carried out to investigate the mechanical and thermal properties of defective ZrC, TiC and SiC. As compared with the defective SiC, the ZrC and TiC always exhibit larger bulk modulus, smaller changes in the Young’s and shear moduli, as well as better ductility. The total thermal conductivity of ZrC and TiC are much larger than that of SiC, implying that under radiation environment the ZrC and TiC will exhibit superior heat conduction ability than the SiC. One disadvantage for ZrC and TiC is that their Debye temperatures are generally lower than that of SiC. These results suggest that further improving the Debye temperature of ZrC and TiC will be more beneficial for their applications as fuel-cladding and structural materials in nuclear reactors.