bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lifetime-preserving reference models for characterizing spreading dynamics on temporal networks
Authors: Li Mingwu , Rao Vikyath D. , Gernat Tim , Dankowicz Harry 
Published: January 2018

AbstractTo study how a certain network feature affects processes occurring on a temporal network, one often compares properties of the original network against those of a randomized reference model that lacks the feature in question. The randomly permuted times (PT) reference model is widely used to probe how temporal features affect spreading dynamics on temporal networks. However, PT implicitly assumes that edges and nodes are continuously active during the network sampling period – an assumption that does not always hold in real networks. We systematically analyze a recently-proposed restriction of PT that preserves node lifetimes (PTN), and a similar restriction (PTE) that also preserves edge lifetimes. We use PT, PTN, and PTE to characterize spreading dynamics on (i) synthetic networks with heterogeneous edge lifespans and tunable burstiness, and (ii) four real-world networks, including two in which nodes enter and leave the network dynamically. We find that predictions of spreading speed can change considerably with the choice of reference model. Moreover, the degree of disparity in the predictions reflects the extent of node/edge turnover, highlighting the importance of using lifetime-preserving reference models when nodes or edges are not continuously present in the network.
Evaluation of the effects of space allowance on measures of animal welfare in laboratory mice
Authors: Bailoo Jeremy D. , Murphy Eimear , Varholick Justin A. , Novak Janja , Palme Rupert , Würbel Hanno 
Published: January 2018

AbstractWe studied how space allowance affects measures of animal welfare in mice by systematically varying group size and cage type across three levels each in both males and females of two strains of mice (C57BL/6ByJ and BALB/cByJ; n = 216 cages, a total of 1152 mice). This allowed us to disentangle the effects of total floor area, group size, stocking density, and individual space allocation on a broad range of measures of welfare, including growth (food and water intake, body mass); stress physiology (glucocorticoid metabolites in faecal boli); emotionality (open field behaviour); brain function (recurrent perseveration in a two-choice guessing task); and home-cage behaviour (activity, stereotypic behaviour). While increasing group size was associated with a decrease in food and water intake in general, and more specifically with increased attrition due to escalated aggression in male BALB mice, no other consistent effects of any aspect of space allowance were found with respect to the measures studied here. Our results indicate that within the range of conditions commonly found in laboratory mouse housing, space allowance as such has little impact on measures of welfare, except for group size which may be a risk factor for escalating aggression in males of some strains.
Functionalisation of Detonation Nanodiamond for Monodispersed, Soluble DNA-Nanodiamond Conjugates Using Mixed Silane Bead-Assisted Sonication Disintegration
Authors: Edgington Robert , Spillane Katelyn M. , Papageorgiou George , Wray William , Ishiwata Hitoshi , Labarca Mariana , Leal-Ortiz Sergio , Reid Gordon , Webb Martin , Foord John , Melosh Nicholas , Schaefer Andreas T. 
Published: January 2018

AbstractNanodiamonds have many attractive properties that make them suitable for a range of biological applications, but their practical use has been limited because nanodiamond conjugates tend to aggregate in solution during or after functionalisation. Here we demonstrate the production of DNA-detonation nanodiamond (DNA-DND) conjugates with high dispersion and solubility using an ultrasonic, mixed-silanization chemistry protocol based on the in situ Bead-Assisted Sonication Disintegration (BASD) silanization method. We use two silanes to achieve these properties: (1) 3-(trihydroxysilyl)propyl methylphosphonate (THPMP); a negatively charged silane that imparts high zeta potential and solubility in solution; and (2) (3-aminopropyl)triethoxysilane (APTES); a commonly used functional silane that contributes an amino group for subsequent bioconjugation. We target these amino groups for covalent conjugation to thiolated, single-stranded DNA oligomers using the heterobifunctional crosslinker sulfosuccinimidyl 4-(N-maleimidomethyl)cyclohexane-1-carboxylate (Sulfo-SMCC). The resulting DNA-DND conjugates are the smallest reported to date, as determined by Dynamic Light Scattering (DLS) and Atomic Force Microscopy (AFM). The functionalisation method we describe is versatile and can be used to produce a wide variety of soluble DND-biomolecule conjugates.
The high concentration of progesterone is harmful for endometrial receptivity and decidualization
Authors: Liang Yu-Xiang , Liu Li , Jin Zhi-Yong , Liang Xiao-Huan , Fu Yong-Sheng , Gu Xiao-Wei , Yang Zeng-Ming 
Published: January 2018

AbstractProgesterone is required for the establishment and maintenance of mammalian pregnancy and widely used for conservative treatment of luteal phase deficiency in clinics. However, there are limited solid evidences available for the optimal timing and dose of progesterone therapy, especially for the possible adverse effects on implantation and decidualization when progesterone is administrated empirically. In our study, mouse models were used to examine effects of excess progesterone on embryo implantation and decidualization. Our data indicate that excess progesterone is not only harmful for mouse implantation, but also impairs mouse decidualization. In excess progesterone-treated mice, the impaired LIF/STAT3 pathway and dysregulated endoplasmic reticulum stress may lead to the inhibition of embryo implantation and decidualization. It is possible that the decrease in birth weight of excess progesterone-treated mice is due to a compromised embryo implantation and decidualization. Furthermore, excess progesterone compromises in vitro decidualization of human endometrial stromal cells.
The effect of differentiation and TGFβ on mitochondrial respiration and mitochondrial enzyme abundance in cultured primary human skeletal muscle cells
Authors: Hoffmann Christoph , Höckele Selina , Kappler Lisa , Hrabĕ de Angelis Martin , Häring Hans-Ulrich , Weigert Cora 
Published: January 2018

AbstractMeasuring mitochondrial respiration in cultured cells is a valuable tool to investigate the influence of physiological and disease-related factors on cellular metabolism; however, the details of the experimental workflow greatly influence the informative value of the results. Working with primary cells and cell types capable of differentiation can be particularly challenging. We present a streamlined workflow optimised for investigation of primary human skeletal muscle cells. We applied the workflow to differentiated and undifferentiated cells and we investigated the effect of TGFβ1 treatment. Differentiation of myoblasts to myotubes increased mitochondrial respiration and abundance of mitochondrial enzymes and mitochondrial marker proteins. Differentiation also induced qualitative changes in mitochondrial protein composition and respiration. TGFβ1 reduced complex IV protein MTCO1 abundance in both myoblasts and myotubes. In myoblasts, spare electron transport system (ETS) capacity was reduced due to a reduction in maximal oxygen consumption. In TGFβ1-treated myotubes, the reduction in spare ETS capacity is mainly a consequence of increased oxidative phosphorylation capacity and complex III protein UQCRC2. Taken together, our data shows that it is important to monitor muscle cell differentiation when mitochondrial function is studied. Our workflow is not only sensitive enough to detect physiological-sized differences, but also adequate to form mechanistic hypotheses.
Chaotic universe model
Authors: Aydiner Ekrem 
Published: January 2018

AbstractIn this study, we consider nonlinear interactions between components such as dark energy, dark matter, matter and radiation in the framework of the Friedman-Robertson-Walker space-time and propose a simple interaction model based on the time evolution of the densities of these components. By using this model we show that these interactions can be given by Lotka-Volterra type equations. We numerically solve these coupling equations and show that interaction dynamics between dark energy-dark matter-matter or dark energy-dark matter-matter-radiation has a strange attractor for 0 > w
de
>−1, w
dm
≥ 0, w
m
≥ 0 and w
r
≥ 0 values. These strange attractors with the positive Lyapunov exponent clearly show that chaotic dynamics appears in the time evolution of the densities. These results provide that the time evolution of the universe is chaotic. The present model may have potential to solve some of the cosmological problems such as the singularity, cosmic coincidence, big crunch, big rip, horizon, oscillation, the emergence of the galaxies, matter distribution and large-scale organization of the universe. The model also connects between dynamics of the competing species in biological systems and dynamics of the time evolution of the universe and offers a new perspective and a new different scenario for the universe evolution.
Functionalized Sugarcane Bagasse for U(VI) Adsorption from Acid and Alkaline Conditions
Authors: Su Shouzheng , Liu Qi , Liu Jingyuan , Zhang Hongsen , Li Rumin , Jing Xiaoyan , Wang Jun 
Published: January 2018

AbstractThe highly efficient removal of uranium from mine tailings effluent, radioactive wastewater and enrichment from seawater is of great significance for the development of nuclear industry. In this work, we prepared an efficient U(VI) adsorbent by EDTA modified sugarcane bagasse (MESB) with a simple process. The prepared adsorbent preserves high adsorptive capacity for UO22+ (pH 3.0) and uranyl complexes, such as UO2(OH)+, (UO2)2(OH)22+ and (UO2)3(OH)5+ (pH 4.0 and pH 5.0) and good repeatability in acidic environment. The maximum adsorption capacity for U(VI) at pH 3.0, 4.0 and 5.0 is 578.0, 925.9 and 1394.1 mg/g and the adsorption capacity loss is only 7% after five cycles. With the pH from 3.0 to 5.0, the inhibitive effects of Na+ and K+ decreased but increased of Mg2+ and Ca2+. MESB also exhibits good adsorption for [UO2(CO3)3]4− at pH 8.3 from 10 mg/L to 3.3 μg/L. Moreover, MESB could effectively extract U(VI) from simulated seawater in the presence of other metals ions. This work provided a general and efficient uranyl enriched material for nuclear industry.
Label-Free, High Resolution, Multi-Modal Light Microscopy for Discrimination of Live Stem Cell Differentiation Status
Authors: Zhang Jing , Moradi Emilia , Somekh Michael G. , Mather Melissa L. 
Published: January 2018

AbstractA label-free microscopy method for assessing the differentiation status of stem cells is presented with potential application for characterization of therapeutic stem cell populations. The microscopy system is capable of characterizing live cells based on the use of evanescent wave microscopy and quantitative phase contrast (QPC) microscopy. The capability of the microscopy system is demonstrated by studying the differentiation of live immortalised neonatal mouse neural stem cells over a 15 day time course. Metrics extracted from microscope images are assessed and images compared with results from endpoint immuno-staining studies to illustrate the system’s performance. Results demonstrate the potential of the microscopy system as a valuable tool for cell biologists to readily identify the differentiation status of unlabelled live cells.
Robust fabrication of thin film polyamide-TiO2 nanocomposite membranes with enhanced thermal stability and anti-biofouling propensity
Authors: Khorshidi Behnam , Biswas Ishita , Ghosh Tanushree , Thundat Thomas , Sadrzadeh Mohtada 
Published: January 2018

AbstractThe development of nano-enabled composite materials has led to a paradigm shift in the manufacture of high-performance nanocomposite membranes with enhanced permeation, thermo-mechanical, and antibacterial properties. The major challenges to the successful incorporation of nanoparticles (NPs) to polymer films are the severe aggregation of the NPs and the weak compatibility of NPs with polymers. These two phenomena lead to the formation of non-selective voids at the interface of the polymer and NPs, which adversely affect the separation performance of the membrane. To overcome these challenges, we have developed a new method for the fabrication of robust TFN reverse osmosis membranes. This approach relies on the simultaneous synthesis and surface functionalization of TiO2 NPs in an organic solvent (heptane) via biphasic solvothermal reaction. The resulting stable suspension of the TiO2 NPs in heptane was then utilized in the interfacial (in-situ) polymerization reaction where the NPs were entrapped within the matrix of the polyamide (PA) membrane. TiO2 NPs of 10 nm were effectively incorporated into the thin PA layer and improved the thermal stability and anti-biofouling properties of the resulting TFN membranes. These features make our synthesized membranes potential candidates for applications where the treatment of high-temperature streams containing biomaterials is desirable.
Validation and optimization of the Systemic Inflammation-Based modified Glasgow Prognostic Score in predicting postoperative outcome of inflammatory bowel disease: preliminary data
Authors: Zhao Chenyan , Ding Chao , Xie Tingbin , Zhang Tenghui , Dai Xujie , Wei Yao , Li Yi , Gong Jianfeng , Zhu Weiming 
Published: January 2018

AbstractSystemic Inflammation-Based modified Glasgow Prognostic Score (mGPS) was developed as an objective tool to grade state of inflammation. However, the association between mGPS and postoperative complications for inflammatory bowel disease (IBD) patients was still unknown. In our study, 270 IBD patients [Crohn’s disease (CD), n = 186; Ulcerative colitis (UC), n = 84] from January 2013 and January 2016 who underwent elective bowel resection were retrospectively analyzed, and, the levels of preoperative C-reactive protein (CRP) and albumin were included as parameters of mGPS. The incidence of overall postoperative complications was 44.81% (121/270), including 46.77% (87/186) of CD and 40.48% (34/84) of UC. According to multivariate analysis, mGPS (CD: OR = 3.47, p = 0.003; UC: OR = 3.28, p = 0.019) was independently associated with an increased risk of postoperative complications. Patients with a higher mGPS also suffered longer postoperative stay and increased SSIs (both p < 0.05). Combining mGPS with neutrophil ratio improved its prognostic value with a better area under the curve (AUC), using receiver operating characteristic (ROC) method. Then we confirmed that mGPS was associated with postoperative complications in IBD patients undergoing elective bowel resection and the addition of neutrophil ratio enhanced its prognostic value.
The PEG-responding desiccome of the alder microsymbiont Frankia alni
Authors: Ghedira Kais , Harigua-Souiai Emna , Ben Hamda Cherif , Fournier Pascale , Pujic Petar , Guesmi Sihem , Guizani Ikram , Miotello Guylaine , Armengaud Jean , Normand Philippe , Sghaier Haïtham 
Published: January 2018

AbstractActinorhizal plants are ecologically and economically important. Symbiosis with nitrogen-fixing bacteria allows these woody dicotyledonous plants to colonise soils under nitrogen deficiency, water-stress or other extreme conditions. However, proteins involved in xerotolerance of symbiotic microorganisms have yet to be identified. Here we characterise the polyethylene glycol (PEG)-responding desiccome from the most geographically widespread Gram-positive nitrogen-fixing plant symbiont, Frankia alni, by next-generation proteomics, taking advantage of a Q-Exactive HF tandem mass spectrometer equipped with an ultra-high-field Orbitrap analyser. A total of 2,052 proteins were detected and quantified. Under osmotic stress, PEG-grown F. alni cells increased the abundance of envelope-associated proteins like ABC transporters, mechano-sensitive ion channels and Clustered Regularly Interspaced Short Palindromic Repeats CRISPR-associated (cas) components. Conjointly, dispensable pathways, like nitrogen fixation, aerobic respiration and homologous recombination, were markedly down-regulated. Molecular modelling and docking simulations suggested that the PEG is acting on Frankia partly by filling the inner part of an up-regulated osmotic-stress large conductance mechanosensitive channel.
Analysis of the HIV-2 protease’s adaptation to various ligands: characterization of backbone asymmetry using a structural alphabet
Authors: Triki Dhoha , Cano Contreras Mario Enrique , Flatters Delphine , Visseaux Benoit , Descamps Diane , Camproux Anne-Claude , Regad Leslie 
Published: January 2018

AbstractThe HIV-2 protease (PR2) is a homodimer of 99 residues with asymmetric assembly and binding various ligands. We propose an exhaustive study of the local structural asymmetry between the two monomers of all available PR2 structures complexed with various inhibitors using a structural alphabet approach. On average, PR2 exhibits asymmetry in 31% of its positions—i.e., exhibiting different backbone local conformations in the two monomers. This asymmetry was observed all along its structure, particularly in the elbow and flap regions. We first differentiated structural asymmetry conserved in most PR2 structures from the one specific to some PR2. Then, we explored the origin of the detected asymmetry in PR2. We localized asymmetry that could be induced by PR2’s flexibility, allowing transition from the semi-open to closed conformations and the asymmetry potentially induced by ligand binding. This latter could be important for the PR2’s adaptation to diverse ligands. Our results highlighted some differences between asymmetry of PR2 bound to darunavir and amprenavir that could explain their differences of affinity. This knowledge is critical for a better description of PR2’s recognition and adaptation to various ligands and for a better understanding of the resistance of PR2 to most PR2 inhibitors, a major antiretroviral class.
Conformational Landscape of the PRKACA-DNAJB1 Chimeric Kinase, the Driver for Fibrolamellar Hepatocellular Carcinoma
Authors: Tomasini Michael D. , Wang Yingjie , Karamafrooz Adak , Li Geoffrey , Beuming Thijs , Gao Jiali , Taylor Susan S. , Veglia Gianluigi , Simon Sanford M. 
Published: January 2018

AbstractIn fibrolamellar hepatocellular carcinoma a single genetic deletion results in the fusion of the first exon of the heat shock protein 40, DNAJB1, which encodes the J domain, with exons 2–10 of the catalytic subunit of protein kinase A, PRKACA. This produces an enzymatically active chimeric protein J-PKAcα. We used molecular dynamics simulations and NMR to analyze the conformational landscape of native and chimeric kinase, and found an ensemble of conformations. These ranged from having the J-domain tucked under the large lobe of the kinase, similar to what was reported in the crystal structure, to others where the J-domain was dislodged from the core of the kinase and swinging free in solution. These simulated dislodged states were experimentally captured by NMR. Modeling of the different conformations revealed no obvious steric interactions of the J-domain with the rest of the RIIβ holoenzyme.
Competitive influence maximization and enhancement of synchronization in populations of non-identical Kuramoto oscillators
Authors: Brede Markus , Stella Massimo , Kalloniatis Alexander C. 
Published: January 2018

AbstractMany networked systems have evolved to optimize performance of function. Much literature has considered optimization of networks by central planning, but investigations of network formation amongst agents connecting to achieve non-aligned goals are comparatively rare. Here we consider the dynamics of synchronization in populations of coupled non-identical oscillators and analyze adaptations in which individual nodes attempt to rewire network topology to optimize node-specific aims. We demonstrate that, even though individual nodes’ goals differ very widely, rewiring rules in which each node attempts to connect to the rest of the network in such a way as to maximize its influence on the system can enhance synchronization of the collective. The observed speed-up of consensus finding in this competitive dynamics might explain enhanced synchronization in real world systems and shed light on mechanisms for improved consensus finding in society.
SPARC expression is associated with hepatic injury in rodents and humans with non-alcoholic fatty liver disease
Authors: Mazzolini Guillermo , Atorrasagasti Catalina , Onorato Agostina , Peixoto Estanislao , Schlattjan Martin , Sowa Jan-Peter , Sydor Svenja , Gerken Guido , Canbay Ali 
Published: January 2018

AbstractMechanisms that control progression from simple steatosis to steato-hepatitis and fibrosis in patients with non-alcoholic fatty liver disease (NAFLD) are unknown. SPARC, a secreted matricellular protein, is over-expressed in the liver under chronic injury. Contribution of SPARC accumulation to disease severity is largely unknown in NAFLD. We assessed the hypothesis that SPARC is increased in livers with more necrosis and inflammation and could be associated with more fibrosis. qrt-PCR, immunohistochemistry, and ELISA were employed to localize and quantify changes in SPARC in 62 morbidly obese patients with NAFLD/NASH and in a mouse model of diet-induced-NASH. Results were correlated with the severity of NAFLD/NASH. In obese patients 2 subgroups were identified with either high SPARC expression (n = 16) or low SPARC expression (n = 46) in the liver, with a cutoff of 1.2 fold expression. High expression of SPARC paralleled hepatocellular damage and increased mRNA expression of pro-fibrogenic factors in the liver. In line with these findings, in the NASH animal model SPARC knockout mice were protected from inflammatory injury, and showed less inflammation and fibrosis. Hepatic SPARC expression is associated with liver injury and fibrogenic processes in NAFLD. SPARC has potential as preventive or therapeutic target in NAFLD patients.
Gene and MicroRNA Perturbations of Cellular Response to Pemetrexed Implicate Biological Networks and Enable Imputation of Response in Lung Adenocarcinoma
Authors: Gamazon Eric R. , Trendowski Matthew R. , Wen Yujia , Wing Claudia , Delaney Shannon M. , Huh Won , Wong Shan , Cox Nancy J. , Dolan M. Eileen 
Published: January 2018

AbstractPemetrexed is indicated for non-small cell lung carcinoma and mesothelioma, but often has limited efficacy due to drug resistance. To probe the molecular mechanisms underlying chemotherapeutic response, we performed mRNA and microRNA (miRNA) expression profiling of pemetrexed treated and untreated lymphoblastoid cell lines (LCLs) and applied a hierarchical Bayesian method. We identified genetic variation associated with gene expression in human lung tissue for the most significant differentially expressed genes (Benjamini-Hochberg [BH] adjusted p < 0.05) using the Genotype-Tissue Expression data and found evidence for their clinical relevance using integrated molecular profiling and lung adenocarcinoma survival data from The Cancer Genome Atlas project. We identified 39 miRNAs with significant differential expression (BH adjusted p < 0.05) in LCLs. We developed a gene expression based imputation model of drug sensitivity, quantified its prediction performance, and found a significant correlation of the imputed phenotype generated from expression data with survival time in lung adenocarcinoma patients. Differentially expressed genes (MTHFD2 and SUFU) that are putative targets of differentially expressed miRNAs also showed differential perturbation in A549 fusion lung tumor cells with further replication in A549 cells. Our study suggests pemetrexed may be used in combination with agents that target miRNAs to increase its cytotoxicity.