bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phonon laser in the coupled vector cavity optomechanics
Authors: Wang Bao , Xiong Hao , Jia Xiao , Wu Ying 
Published: January 2018

AbstractWe presented a method to control the intensity of a phonon-laser mode (the vibrational excitations of a mechanical mode) by adjusting the polarization of the pump light based on the experimentally achievable parameters, which provides an additional degree of freedom to control the phonon laser action. Due to orthogonally polarized modes of cavity, the polarization behavior of light field which describes it’s vector nature is introduced to control phonon laser action in our scheme. Compared with the traditional phonon laser scheme, polarization-related phonon laser in the coupled vector cavity optomechanics can be effectively controlled without changing other parameters of the device. This result provides an useful approach for acquiring polarization-related phonon laser by on-chip optical device.
Accelerated proteomic visualization of individual predatory venoms of Conus purpurascens reveals separately evolved predation-evoked venom cabals
Authors: Himaya S. W. A. , Marí Frank , Lewis Richard J. 
Published: January 2018

AbstractCone snail venoms have separately evolved for predation and defense. Despite remarkable inter- and intra-species variability, defined sets of synergistic venom peptides (cabals) are considered essential for prey capture by cone snails. To better understand the role of predatory cabals in cone snails, we used a high-throughput proteomic data mining and visualisation approach. Using this approach, the relationship between the predatory venom peptides from nine C. purpurascens was systematically analysed. Surprisingly, potentially synergistic levels of κ-PVIIA and δ-PVIA were only identified in five of nine specimens. In contrast, the remaining four specimens lacked significant levels of these known excitotoxins and instead contained high levels of the muscle nAChR blockers ψ-PIIIE and αA-PIVA. Interestingly, one of nine specimens expressed both cabals, suggesting that these sub-groups might represent inter-breeding sub-species of C. purpurascens. High throughput cluster analysis also revealed these two cabals clustered with distinct groups of venom peptides that are presently uncharacterised. This is the first report showing that the cone snails of the same species can deploy two separate and distinct predatory cabals for prey capture and shows that the cabals deployed by this species can be more complex than presently realized. Our semi-automated proteomic analysis facilitates the deconvolution of complex venoms to identify co-evolved families of peptides and help unravel their evolutionary relationships in complex venoms.
Correlation of Gli1 and HER2 expression in gastric cancer: Identification of novel target
Authors: Shao Xinyu , Kuai Xiaoyi , Pang Zhi , Zhang Liping , Wu Longyun , Xu Lijuan , Zhou Chunli 
Published: January 2018

AbstractHER2 becomes the standard of care for guiding adjuvant treatment of gastric cancer with trastuzumab in recent years. However, the usage of this target agent is still limited because of the resistance to trastuzumab or the negative expression of HER2 in tumor tissues. The Gli1 and HER2 both play an important role in the pathogenesis of gastric cancer. However, the correlation of them is still unclear. Here we found Gli1 and HER2 are highly expressed in gastric cancer tissues, and they are positively related. Next, we found Gli1 positive patients live a shorter survival time no matter HER2 positive or negative. Furthermore, univariate and multivariate analysis revealed that venous invasion, HER2 expression, Gli1 expression were independent prognostic factors for the survival time in gastric cancer. In addition, suppressing the expression level of Gli1 can decrease the cell viability and migration ability in cells and subcutaneous tumors. Finally, we found that HER2 may regulate Gli1 by Akt–mTOR–p70S6K pathway. Inhibit of HER2 and SMO have synergistic effect on reduction of cell viability. In conclusion, Gli1 is a favorable prognostic indicator in gastric cancer. As a novel target, Gli1 worth further study, especially in Her2-targeted therapy-resistant cancers.
Computational Investigation of Environment-Noise Interaction in Single-Cell Organisms: The Merit of Expression Stochasticity Depends on the Quality of Environmental Fluctuations
Authors: Lück Anja , Klimmasch Lukas , Großmann Peter , Germerodt Sebastian , Kaleta Christoph 
Published: January 2018

AbstractOrganisms need to adapt to changing environments and they do so by using a broad spectrum of strategies. These strategies include finding the right balance between expressing genes before or when they are needed, and adjusting the degree of noise inherent in gene expression. We investigated the interplay between different nutritional environments and the inhabiting organisms’ metabolic and genetic adaptations by applying an evolutionary algorithm to an agent-based model of a concise bacterial metabolism. Our results show that constant environments and rapidly fluctuating environments produce similar adaptations in the organisms, making the predictability of the environment a major factor in determining optimal adaptation. We show that exploitation of expression noise occurs only in some types of fluctuating environment and is strongly dependent on the quality and availability of nutrients: stochasticity is generally detrimental in fluctuating environments and beneficial only at equal periods of nutrient availability and above a threshold environmental richness. Moreover, depending on the availability and nutritional value of nutrients, nutrient-dependent and stochastic expression are both strategies used to deal with environmental changes. Overall, we comprehensively characterize the interplay between the quality and periodicity of an environment and the resulting optimal deterministic and stochastic regulation strategies of nutrient-catabolizing pathways.
A Complex Network Approach for the Estimation of the Energy Demand of Electric Mobility
Authors: Mureddu Mario , Facchini Angelo , Scala Antonio , Caldarelli Guido , Damiano Alfonso 
Published: January 2018

AbstractWe study how renewable energy impacts regional infrastructures considering the full deployment of electric mobility at that scale. We use the Sardinia Island in Italy as a paradigmatic case study of a semi-closed system both by energy and mobility point of view. Human mobility patterns are estimated by means of census data listing the mobility dynamics of about 700,000 vehicles, the energy demand is estimated by modeling the charging behavior of electric vehicle owners. Here we show that current renewable energy production of Sardinia is able to sustain the commuter mobility even in the theoretical case of a full switch from internal combustion vehicles to electric ones. Centrality measures from network theory on the reconstructed network of commuter trips allows to identify the most important areas (hubs) involved in regional mobility. The analysis of the expected energy flows reveals long-range effects on infrastructures outside metropolitan areas and points out that the most relevant unbalances are caused by spatial segregation between production and consumption areas. Finally, results suggest the adoption of planning actions supporting the installation of renewable energy plants in areas mostly involved by the commuting mobility, avoiding spatial segregation between consumption and generation areas.
The Microwell-mesh: A high-throughput 3D prostate cancer spheroid and drug-testing platform
Authors: Mosaad E. O. , Chambers K. F. , Futrega K. , Clements J. A. , Doran M. R. 
Published: January 2018

AbstractTreatment following early diagnosis of Prostate cancer (PCa) is increasingly successful, whilst the treatment of advanced and metastatic PCa remains challenging. A major limitation in the development of new therapies is the prediction of drug efficacy using in vitro models. Classic in vitro 2-dimensional (2D) cell monolayer cultures are hypersensitive to anti-cancer drugs. As a result, there has been a surge in the development of platforms that enable three dimensional (3D) cultures thought to better replicate natural physiology and better predict drug efficacy. A deficiency associated with most 3D culture systems is that their complexity reduces the number of replicates and combination therapies that can be feasibly evaluated. Herein, we describe the use of a microwell platform that utilises a nylon mesh to retain 3D micro-tumours in discrete microwells; termed the Microwell-mesh. The Microwell-mesh enables the manufacture of ~150 micro-tumours per well in a 48-well plate, and response to anti-tumour drugs can be readily quantified. Our results demonstrate that 3D micro-tumours, unlike 2D monolayers, are not hypersensitive to Docetaxel or Abiraterone Acetate, providing a superior platform for the evaluation of sequential drug treatment. In summary, the Microwell-mesh provides an efficient 3D micro-tumour platform for single and sequential drug screening.
Complex Formation via Hydrogen bonding between Rhodamine B and Montmorillonite in Aqueous Solution
Authors: Fang Yanfen , Zhou Ao , Yang Wei , Araya Tirusew , Huang Yingping , Zhao Ping , Johnson David , Wang Jianzhu , Ren Zhiyong Jason 
Published: January 2018

AbstractThis study investigates the adsorption mechanism differences among four nitrogenous dyes, sulforhodamine G (SRG), uncharged/deprotonated rhodamine B (RhB), orange II (Or II) and methyl blue (MB) by montmorillonite (MMT). MMT adsorption capacity for cationic MB was three times that of uncharged RhB and anionic SRG, while anionic Or II was not absorbed. Colloidal MMT particles have two types of surfaces, basal and edge, that interact with nitrogenous dyes very differently. The surface acidity of MMT was characterized with the pyridine adsorption method using in-situ diffuse reflectance infrared Fourier transform spectroscopy (in-situ DRIFTS). Adsorption of cationic MB was compared with the adsorption of RhB. In-situ attenuated total reflectance Fourier transform infrared (in-situ ATR-FTIR) spectroscopy indicated that a nitrogen atom on RhB complexes with a metal hydroxyl on an MMT edge through a water bridge. The highly polar edge hydroxyl is important to hydrogen bond formation. Cation ion exchange and washing experiments, as well as studies on the effect of temperature, pH and ionic strength on adsorption further clarified the adsorption mechanism. Our results provide insights into the effects of molecular structure on the adsorption of nitrogenous dyes by clay and the role of edge surfaces in the adsorption process.
Giant electrocaloric effect in a wide temperature range in PbTiO3 nanoparticle with double-vortex domain structure
Authors: Ye C. , Wang J. B. , Li B. , Zhong X. L. 
Published: January 2018

AbstractElectrocaloric effect (ECE) has the potential applications in solid-state refrigeration with the features of high efficiency and environmentally friendly. Large adiabatic temperature change in a wide temperature range is needed for electrocaloric effect to meet the requirement of commercially application. In this work, giant electrocaloric effect is found in PbTiO3 nanoparticle with double-vortex domain structure in a wide temperature range by using phase field method, which the lowest and highest adiabatic temperature change (ΔT) is 7.2 K and 16.5 K, respectively. The influence of misfit strain on the ECE of PbTiO3 nanoparticle with the double-vortex domain structure is investigated, and results show that the compress misfit strain can enhance the ECE, but the tensile misfit strain reduces the ECE. This work reveals a way to obtain giant ECE of ferroelectric materials by domain engineering and strain engineering in a wide temperature range.
Magnetisation process in the rare earth tetraborides, NdB4 and HoB4
Authors: Brunt D. , Balakrishnan G. , Mayoh D. A. , Lees M. R. , Gorbunov D. , Qureshi N. , Petrenko O. A. 
Published: January 2018

AbstractA field-induced magnetisation process in the frustrated antiferromagnets is often much richer compared to the materials without competing interactions. The applied field tends to stabilise unusual spin configurations which frequently results in the appearance of magnetisation plateaux. Here we report a study into the field-induced magnetisation of the two frustrated rare earth tetraborides, HoB4and NdB4. NdB4shows a fractional magnetisation plateau occurring atM/Msat ≈ $$\tfrac{{\bf{1}}}{{\bf{5}}}$$15before saturating in a field of 33 kOe. On cooling down to 0.5 K the temperature dependent susceptibility of NdB4shows an unconventional transition where the system returns to the zero field antiferromagnetic state from a higher-temperature ferrimagnetic state. We are able to reconstruct the magnetic phase diagram of NdB4from the magnetisation, susceptibility and resistivity measurements for bothH $$\parallel $$∥ candH ⊥ c. For HoB4, the most interesting behaviour is found at the lowest temperature of 0.5 K, where the field dependent magnetisation demonstrates a new fractional$$\tfrac{{\bf{1}}}{{\bf{2}}}$$12-magnetisation plateau. Further insight into the relations between the exchange interactions and single ion effects is gained through high-field magnetisation measurements in both HoB4and NdB4.
Highly selective and sensitive macrocycle-based dinuclear foldamer for fluorometric and colorimetric sensing of citrate in water
Authors: Rhaman Md Mhahabubur , Hasan Mohammad H. , Alamgir Azmain , Xu Lihua , Powell Douglas R. , Wong Bryan M. , Tandon Ritesh , Hossain Md. Alamgir 
Published: January 2018

AbstractThe selective detection of citrate anions is essential for various biological functions in living systems. A quantitative assessment of citrate is required for the diagnosis of various diseases in the human body; however, it is extremely challenging to develop efficient fluorescence and color-detecting molecular probes for sensing citrate in water. Herein, we report a macrocycle-based dinuclear foldamer (1) assembled with eosin Y (EY) that has been studied for anion binding by fluorescence and colorimetric techniques in water at neutral pH. Results from the fluorescence titrations reveal that the 1·EY ensemble strongly binds citrate anions, showing remarkable selectivity over a wide range of inorganic and carboxylate anions. The addition of citrate anions to the 1·EY adduct led to a large fluorescence enhancement, displaying a detectable color change under both visible and UV light in water up to 2 μmol. The biocompatibility of 1·EY as an intracellular carrier in a biological system was evaluated on primary human foreskin fibroblast (HF) cells, showing an excellent cell viability. The strong binding properties of the ensemble allow it to be used as a highly sensitive, detective probe for biologically relevant citrate anions in various applications.
Structural ensemble-based docking simulation and biophysical studies discovered new inhibitors of Hsp90 N-terminal domain
Authors: Kim Hyun-Hwi , Hyun Ja-Shil , Choi Joonhyeok , Choi Kwang-Eun , Jee Jun-Goo , Park Sung Jean 
Published: January 2018

AbstractHeat shock protein 90 (Hsp90) is one of the most abundant cellular proteins and plays a substantial role in the folding of client proteins. The inhibition of Hsp90 has been regarded as an attractive therapeutic strategy for treating cancer because many oncogenic kinases are Hsp90 client proteins. In this study, we report new inhibitors that directly bind to N-terminal ATP-binding pocket of Hsp90. Optimized structure-based virtual screening predicted candidate molecules, which was followed by confirmation using biophysical and cell-based assays. Among the reported crystal structures, we chose the two structures that show the most favourable early enrichments of true-positives in the receiver operating characteristic curve. Four molecules showed significant changes in the signals of 2D [1H,15N] correlation NMR spectroscopy. Differential scanning calorimetry analysis supported the results indicating direct binding. Quantified dissociation constant values of the molecules, determined by a series of 2D NMR experiments, lie in the range of 0.1–33 μM. Growth inhibition assay with breast and lung cancer cells confirmed the cellular activities of the molecules. Cheminformatics revealed that the molecules share limited chemical similarities with known inhibitors. Molecular dynamics simulations detailed the putative binding modes of the inhibitors.
The chemical armament of reef-building corals: inter- and intra-specific variation and the identification of an unusual actinoporin in Stylophora pistilata
Authors: Ben-Ari Hanit , Paz Moran , Sher Daniel 
Published: January 2018

AbstractCorals, like other cnidarians, are venomous animals that rely on stinging cells (nematocytes) and their toxins to catch prey and defend themselves against predators. However, little is known about the chemical arsenal employed by stony corals, despite their ecological importance. Here, we show large differences in the density of nematocysts and whole-body hemolytic activity between different species of reef-building corals. In the branched coral Stylophora pistillata, the tips of the branches exhibited a greater hemolytic activity than the bases. Hemolytic activity and nematocyst density were significantly lower in Stylophora that were maintained for close to a year in captivity compared to corals collected from the wild. A cysteine-containing actinoporin was identified in Stylophora following partial purification and tandem mass spectrometry. This toxin, named Δ-Pocilopotoxin-Spi1 (Δ-PCTX-Spi1) is the first hemolytic toxin to be partially isolated and characterized in true reef-building corals. Loss of hemolytic activity during chromatography suggests that this actinoporin is only one of potentially several hemolytic molecules. These results suggest that the capacity to employ offensive and defensive chemicals by corals is a dynamic trait within and between coral species, and provide a first step towards identifying the molecular components of the coral chemical armament.
Interference of chemical defence and sexual communication can shape the evolution of chemical signals
Authors: Pfeiffer Lisa , Ruther Joachim , Hofferberth John , Stökl Johannes 
Published: January 2018

AbstractAccording to current evolutionary theory, insect pheromones can originate from extant precursor compounds being selected for information transfer. This is exemplified by females of the parasitoid wasp Leptopilina heterotoma whose defensive secretion consisting mainly of (−)-iridomyrmecin has evolved secondary functions as cue to avoid other females during host search and as female sex pheromone. To promote our understanding of pheromone evolution from defensive secretions we studied the chemical ecology of Leptopilina clavipes. We show here that L. clavipes also produces a defensive secretion that contains (−)-iridomyrmecin as major component and that females use it to detect and avoid host patches occupied by other females. However, the female sex pheromone of L. clavipes consists solely of cuticular hydrocarbons (CHCs) and males did not respond to female CHCs if presented in combination with the defensive secretion containing (−)-iridomyrmecin. This is in contrast to other species of Leptopilina, in which the iridoid compounds have no inhibiting effect or even function as sex pheromone triggering courtship behaviour. This indicates that Leptopilina species differ in the cost-benefit ratio for males searching for females, which might explain the strong divergence in the composition of the sex pheromone in the genus.
CRISPR/Cas9-mediated gene modification and gene knock out in the human-infective parasite Trichomonas vaginalis
Authors: Janssen Brian D. , Chen Yi-Pei , Molgora Brenda M. , Wang Shuqi E. , Simoes-Barbosa Augusto , Johnson Patricia J. 
Published: January 2018

AbstractThe sexually-transmitted parasite Trichomonas vaginalis infects ~1/4 billion people worldwide. Despite its prevalence and myriad adverse outcomes of infection, the mechanisms underlying T. vaginalis pathogenesis are poorly understood. Genetic manipulation of this single-celled eukaryote has been hindered by challenges presented by its complex, repetitive genome and inefficient methods for introducing DNA (i.e. transfection) into the parasite. Here, we have developed methods to increase transfection efficiency using nucleofection, with the goal of efficiently introducing multiple DNA elements into a single T. vaginalis cell. We then created DNA constructs required to express several components essential to drive CRISPR/Cas9-mediated DNA modification: guide RNA (gRNA), the Cas9 endonuclease, short oligonucleotides and large, linearized DNA templates. Using these technical advances, we have established CRISPR/Cas9-mediated repair of mutations in genes contained on circular DNA plasmids harbored by the parasite. We also engineered CRISPR/Cas9 directed homologous recombination to delete (i.e. knock out) two non-essential genes within the T. vaginalis genome. This first report of the use of the CRISPR/Cas9 system in T. vaginalis greatly expands the ability to manipulate the genome of this pathogen and sets the stage for testing of the role of specific genes in many biological processes.
Fourier Transform Infrared Microscopy Enables Guidance of Automated Mass Spectrometry Imaging to Predefined Tissue Morphologies
Authors: Rabe Jan-Hinrich , A. Sammour Denis , Schulz Sandra , Munteanu Bogdan , Ott Martina , Ochs Katharina , Hohenberger Peter , Marx Alexander , Platten Michael , Opitz Christiane A. , Ory Daniel S. , Hopf Carsten 
Published: January 2018

AbstractMultimodal imaging combines complementary platforms for spatially resolved tissue analysis that are poised for application in life science and personalized medicine. Unlike established clinical in vivo multimodality imaging, automated workflows for in-depth multimodal molecular ex vivo tissue analysis that combine the speed and ease of spectroscopic imaging with molecular details provided by mass spectrometry imaging (MSI) are lagging behind. Here, we present an integrated approach that utilizes non-destructive Fourier transform infrared (FTIR) microscopy and matrix assisted laser desorption/ionization (MALDI) MSI for analysing single-slide tissue specimen. We show that FTIR microscopy can automatically guide high-resolution MSI data acquisition and interpretation without requiring prior histopathological tissue annotation, thus circumventing potential human-annotation-bias while achieving >90% reductions of data load and acquisition time. We apply FTIR imaging as an upstream modality to improve accuracy of tissue-morphology detection and to retrieve diagnostic molecular signatures in an automated, unbiased and spatially aware manner. We show the general applicability of multimodal FTIR-guided MALDI-MSI by demonstrating precise tumor localization in mouse brain bearing glioma xenografts and in human primary gastrointestinal stromal tumors. Finally, the presented multimodal tissue analysis method allows for morphology-sensitive lipid signature retrieval from brains of mice suffering from lipidosis caused by Niemann-Pick type C disease.