bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling Oil Recovery for Mixed Macro- and Micro-Pore Carbonate Grainstones
Authors: Xu Ye , Li Qiuzi , King Hubert E. 
Published: August 2017

AbstractIn general, modeling oil-recovery is a challenging problem involving detailed fluid flow calculations with required structural details that challenge current experimental resolution. Recent laboratory experiments on mixed micro- and macro-pore suggest that there is a systematic relationship between remaining oil saturation (ROS) and the fraction of micro-pores. Working with experimental measurements of the pores obtained from X-ray tomography and mercury intrusion capillary pressure porosimetry, we define a digital rock model exemplifying the key structural elements of these carbonate grainstones. We then test two fluid-flow models: invasion percolation model and effective medium model. Although invasion percolation identifies the important impact of macro-pore percolation on permeability, it does not describe the dependence of ROS on micro-pore percentage. We thus modified the effective medium model by introducing a single-parameter descriptor, reff. Oil from pores r ≥ reff is fully removed, while for the remaining pores with r < reff, their contribution is scaled by (r/reff)2. Applying this straightforward physics to pore size distributions for the mixed-pore grainstones reproduces the experimental ROS dependence.
A Plasmodium plasma membrane reporter reveals membrane dynamics by live-cell microscopy
Authors: Burda Paul-Christian , Schaffner Marco , Kaiser Gesine , Roques Magali , Zuber Benoît , Heussler Volker T. 
Published: August 2017

AbstractDuring asexual replication within the Anopheles mosquito and their vertebrate host, Plasmodium parasites depend on the generation of a massive amount of new plasma membrane to produce thousands of daughter parasites. How the parasite plasma membrane (PPM) is formed has mostly been studied by electron microscopy, which does not allow an insight into the dynamics of this process. We generated a Plasmodium berghei reporter parasite line by GFP-tagging of a non-essential PPM-localized protein, and followed plasma membrane development in living parasites through the entire Plasmodium life cycle. By generating double-fluorescent parasites in which the PPM is visualized in combination with the parasite endoplasmic reticulum, we show that membrane contact sites are formed between both membrane systems during oocyst and liver stage development that might be used to deliver lipids to the dramatically expanding PPM. In conclusion, we have established a powerful tool to follow PPM development in living parasites, which promises to greatly expand our knowledge of membrane biology in the Plasmodium parasite.
Large and accessible conductivity of charged domain walls in lithium niobate
Authors: Werner Christoph S. , Herr Simon J. , Buse Karsten , Sturman Boris , Soergel Elisabeth , Razzaghi Cina , Breunig Ingo 
Published: August 2017

AbstractFerroelectric domain walls are interfaces between areas of a material that exhibits different directions of spontaneous polarization. The properties of domain walls can be very different from those of the undisturbed material. Metallic-like conductivity of charged domain walls (CDWs) in nominally insulating ferroelectrics was predicted in 1973 and detected recently. This important effect is still in its infancy: The electric currents are still smaller than expected, the access to the conductivity at CDWs is hampered by contact barriers, and stability is low because of sophisticated domain structures or proximity of the Curie point. Here, we report on large, accessible, and stable conductivity at CDWs in lithium niobate (LN) crystals – a vital material for photonics. Our results mark a breakthrough: Increase of conductivity at CDWs by more than 13 orders of magnitude compared to that of the bulk, access to the effect via ohmic and diode-like contacts, and high stability for temperatures T ≤ 70 °C are demonstrated. A promising and now realistic prospect is to combine CDW functionalities with linear and nonlinear optical phenomena. Our findings allow new generations of adaptive-optical elements, of electrically controlled integrated-optical chips for quantum photonics, and of advanced LN-semiconductor hybrid optoelectronic devices.
Fundamental and experimental aspects of diffraction for characterizing dislocations by electron channeling contrast imaging in scanning electron microscope
Authors: Kriaa H. , Guitton A. , Maloufi N. 
Published: August 2017

AbstractNowadays Field Emission Gun-Scanning Electron Microscopes provide detailed crystallographic information with high spatial and angular resolutions, and allow direct observation of crystalline defects, such as dislocations, through an attractive technique called Electron Channeling Contrast Imaging (ECCI). Dislocations play a crucial role in the properties of materials and ECCI has naturally emerged as an adapted tool for characterizing defects in bulk specimen. Nevertheless, fine control of the channeling conditions is absolutely required to get strong dislocation contrast for achieving comprehensive analysis. In this work, experiment-assisted fundamental aspects of the origin of dislocation contrast are studied. Experimentally, the potential of ECCI is explored in several dislocation configurations in Interstitial-Free steel (Fe − 1% Si) used as a model material. Full interpretations of dislocation contrast in (g, −g) and its evolution along the Kikuchi band are shown. Furthermore, a dislocation dipole is observed and fully characterized for the first time in an SEM.
Lipoxygenase in singlet oxygen generation as a response to wounding: in vivo imaging in Arabidopsis thaliana
Authors: Prasad Ankush , Sedlářová Michaela , Kale Ravindra Sonajirao , Pospíšil Pavel 
Published: August 2017

AbstractWounding, one of the most intensive stresses influencing plants ontogeny and lifespan, can be induced by herbivory as well as by physical factors. Reactive oxygen species play indispensable role both in the local and systemic defense reactions which enable “reprogramming” of metabolic pathways to set new boundaries and physiological equilibrium suitable for survival. In our current study, we provide experimental evidence on the formation of singlet oxygen (1O2) after wounding of Arabidopsis leaves. It is shown that 1O2 is formed by triplet-triplet energy transfer from triplet carbonyls to molecular oxygen. Using lipoxygenase inhibitor catechol, it is demonstrated that lipid peroxidation is initiated by lipoxygenase. Suppression of 1O2 formation in lox2 mutant which lacks chloroplast lipoxygenase indicates that lipoxygenase localized in chloroplast is predominantly responsible for 1O2 formation. Interestingly, 1O2 formation is solely restricted to chloroplasts localized at the wounding site. Data presented in this study might provide novel insight into wound-induced signaling in the local defense reaction.
An efficient eco advanced oxidation process for phenol mineralization using a 2D/3D nanocomposite photocatalyst and visible light irradiations
Authors: Al-Kandari H. , Abdullah A. M. , Ahmad Yahia H. , Al-Kandari S. , AlQaradawi Siham Y. , Mohamed A. M. 
Published: August 2017

AbstractNanocomposites (CNTi) with different mass ratios of carbon nitride (C3N4) and TiO2 nanoparticles were prepared hydrothermally. Different characterization techniques were used including X-ray diffraction (XRD), UV-Vis diffuse reflectance spectroscopy (DRS), X-ray photoelectron spectroscopy (XPS), transmission electron spectroscopy (TEM) and Brunauer-Emmett-Teller (BET). UV-Vis DRS demonstrated that the CNTi nanocomposites exhibited absorption in the visible light range. A sun light - simulated photoexcitation source was used to study the kinetics of phenol degradation and its intermediates in presence of the as-prepared nanocomposite photocatalysts. These results were compared with studies when TiO2 nanoparticles were used in the presence and absence of H2O2 and/or O3. The photodegradation of phenol was evaluated spectrophotometrically and using the total organic carbon (TOC) measurements. It was observed that the photocatalytic activity of the CNTi nanocomposites was significantly higher than that of TiO2 nanoparticles. Additionally, spectrophotometry and TOC analyses confirmed that degraded phenol was completely mineralized to CO2 and H2O with the use of CNTi nanocomposites, which was not the case for TiO2 where several intermediates were formed. Furthermore, when H2O2 and O3 were simultaneously present, the 0.1% g-C3N4/TiO2 nanocomposite showed the highest phenol degradation rate and the degradation percentage was greater than 91.4% within 30 min.
Comparison of vaginal microbiota sampling techniques: cytobrush versus swab
Authors: Mitra Anita , MacIntyre David A. , Mahajan Vishakha , Lee Yun S. , Smith Ann , Marchesi Julian R. , Lyons Deirdre , Bennett Phillip R. , Kyrgiou Maria 
Published: August 2017

AbstractEvidence suggests the vaginal microbiota (VM) may influence risk of persistent Human Papillomavirus (HPV) infection and cervical carcinogenesis. Established cytology biobanks, typically collected with a cytobrush, constitute a unique resource to study such associations longitudinally. It is plausible that compared to rayon swabs; the most commonly used sampling devices, cytobrushes may disrupt biofilms leading to variation in VM composition. Cervico-vaginal samples were collected with cytobrush and rayon swabs from 30 women with high-grade cervical precancer. Quantitative PCR was used to compare bacterial load and Illumina MiSeq sequencing of the V1-V3 regions of the 16S rRNA gene used to compare VM composition. Cytobrushes collected a higher total bacterial load. Relative abundance of bacterial species was highly comparable between sampling devices (R2 = 0.993). However, in women with a Lactobacillus-depleted, high-diversity VM, significantly less correlation in relative species abundance was observed between devices when compared to those with a Lactobacillus species-dominant VM (p = 0.0049). Cytobrush and swab sampling provide a comparable VM composition. In a small proportion of cases the cytobrush was able to detect underlying high-diversity community structure, not realized with swab sampling. This study highlights the need to consider sampling devices as potential confounders when comparing multiple studies and datasets.
New insights into tenocyte-immune cell interplay in an in vitro model of inflammation
Authors: Stolk Meaghan , Klatte-Schulz Franka , Schmock Aysha , Minkwitz Susann , Wildemann Britt , Seifert Martina 
Published: August 2017

AbstractInflammation plays an important role in the development and resolution of tendon diseases, but underlying mechanisms are poorly understood. We therefore aimed to analyze the response of human tenocytes to inflammatory stimuli and to uncover their interplay with macrophages in vitro. Tenocytes from human ruptured supraspinatus tendons (n = 10) were treated for three days with a stimulation mixture derived from activated mononuclear cells isolated from healthy human peripheral blood. Significantly increased expression levels of selected adhesion- and human leukocyte antigen (HLA)-molecules, and enhanced interleukin (IL)-6 release were detected by flow cytometry. Tenocyte stimulation with the pro-inflammatory cytokines interferon gamma, tumor necrosis factor alpha and IL-1ß triggered similar changes in surface markers and enhanced the release of IL-6, IL-8 and monocyte chemoattractant protein 1 (MCP-1). In co-cultures of macrophages with pre-stimulated tenocytes, macrophages significantly increased CD80 expression, but simultaneously decreased HLA-DR-expression, which are both typical pro-inflammatory polarization markers. Co-cultures also released more IL-6, IL-8, MCP-1 than tenocyte-cultures alone. We demonstrate that tenocytes respond to inflammatory environments in vitro with altered surface marker and cytokine profiles and influence macrophage polarization. Importantly, all changes detected in direct co-cultures were also present in a transwell setting, implicating that communication between the cells involves soluble factors.
Skeletal Site-specific Changes in Bone Mass in a Genetic Mouse Model for Human 15q11-13 Duplication Seen in Autism
Authors: Lewis Kirsty E. , Sharan Kunal , Takumi Toru , Yadav Vijay K. 
Published: August 2017

AbstractChildren suffering from autism have been reported to have low bone mineral density and increased risk for fracture, yet the cellular origin of the bone phenotype remains unknown. Here we have utilized a mouse model of autism that duplicates 6.3 Mb region of chromosome 7 (Dp/+) corresponding to a region of chromosome 15q11-13, duplication of which is recurrent in humans to characterize the bone phenotype. Paternally inherited Dp/+ (patDp/+) mice showed expected increases in the gene expression in bone, normal postnatal growth and body weight acquisition compared to the littermate controls. Four weeks-old patDp/+ mice develop a low bone mass phenotype in the appendicular but not the axial skeleton compared to the littermate controls. This low bone mass in the mutant mice was secondary to a decrease in the number of osteoblasts and bone formation rate while the osteoclasts remained relatively unaffected. Further in vitro cell culture experiments and gene expression analysis revealed a major defect in the proliferation, differentiation and mineralization abilities of patDp/+ osteoblasts while osteoclast differentiation remained unchanged compared to controls. This study therefore characterizes the structural and cellular bone phenotype in a mouse model of autism that can be further utilized to investigate therapeutic avenues to treat bone fractures in children with autism.
Delineation of Tumor Habitats based on Dynamic Contrast Enhanced MRI
Authors: Chang Yu-Cherng Channing , Ackerstaff Ellen , Tschudi Yohann , Jimenez Bryan , Foltz Warren , Fisher Carl , Lilge Lothar , Cho HyungJoon , Carlin Sean , Gillies Robert J. , Balagurunathan Yoganand , Yechieli Raphael L. , Subhawong Ty , Turkbey Baris , Pollack Alan , Stoyanova Radka 
Published: August 2017

AbstractTumor heterogeneity can be elucidated by mapping subregions of the lesion with differential imaging characteristics, called habitats. Dynamic Contrast Enhanced (DCE-)MRI can depict the tumor microenvironments by identifying areas with variable perfusion and vascular permeability, since individual tumor habitats vary in the rate and magnitude of the contrast uptake and washout. Of particular interest is identifying areas of hypoxia, characterized by inadequate perfusion and hyper-permeable vasculature. An automatic procedure for delineation of tumor habitats from DCE-MRI was developed as a two-part process involving: (1) statistical testing in order to determine the number of the underlying habitats; and (2) an unsupervised pattern recognition technique to recover the temporal contrast patterns and locations of the associated habitats. The technique is examined on simulated data and DCE-MRI, obtained from prostate and brain pre-clinical cancer models, as well as clinical data from sarcoma and prostate cancer patients. The procedure successfully identified habitats previously associated with well-perfused, hypoxic and/or necrotic tumor compartments. Given the association of tumor hypoxia with more aggressive tumor phenotypes, the obtained in vivo information could impact management of cancer patients considerably.
Tolerant indirect reciprocity can boost social welfare through solidarity with unconditional cooperators in private monitoring
Authors: Okada Isamu , Sasaki Tatsuya , Nakai Yutaka 
Published: August 2017

AbstractIndirect reciprocity is an important mechanism for resolving social dilemmas. Previous studies explore several types of assessment rules that are evolutionarily stable for keeping cooperation regimes. However, little is known about the effects of private information on social systems. Most indirect reciprocity studies assume public monitoring in which individuals share a single assessment for each individual. Here, we consider a private monitoring system that loosens such an unnatural assumption. We explore the stable norms in the private system using an individual-based simulation. We have three main findings. First, narrow and unstable cooperation: cooperation in private monitoring becomes unstable and the restricted norms cannot maintain cooperative regimes while they can in public monitoring. Second, stable coexistence of discriminators and unconditional cooperators: under private monitoring, unconditional cooperation can play a role in keeping a high level of cooperation in tolerant norm situations. Finally, Pareto improvement: private monitoring can achieve a higher cooperation rate than does public monitoring.
FMNL2 and -3 regulate Golgi architecture and anterograde transport downstream of Cdc42
Authors: Kage Frieda , Steffen Anika , Ellinger Adolf , Ranftler Carmen , Gehre Christian , Brakebusch Cord , Pavelka Margit , Stradal Theresia , Rottner Klemens 
Published: August 2017

AbstractThe Rho-family small GTPase Cdc42 localizes at plasma membrane and Golgi complex and aside from protrusion and migration operates in vesicle trafficking, endo- and exocytosis as well as establishment and/or maintenance of cell polarity. The formin family members FMNL2 and -3 are actin assembly factors established to regulate cell edge protrusion during migration and invasion. Here we report these formins to additionally accumulate and function at the Golgi apparatus. As opposed to lamellipodia, Golgi targeting of these proteins required both their N-terminal myristoylation and the interaction with Cdc42. Moreover, Golgi association of FMNL2 or -3 induced a phalloidin-detectable actin meshwork around the Golgi. Importantly, functional interference with FMNL2/3 formins by RNAi or CRISPR/Cas9-mediated gene deletion invariably induced Golgi fragmentation in different cell lines. Furthermore, absence of these proteins led to enlargement of endosomes as well as defective maturation and/or sorting into late endosomes and lysosomes. In line with Cdc42 - recently established to regulate anterograde transport through the Golgi by cargo sorting and carrier formation - FMNL2/3 depletion also affected anterograde trafficking of VSV-G from the Golgi to the plasma membrane. Our data thus link FMNL2/3 formins to actin assembly-dependent functions of Cdc42 in anterograde transport through the Golgi apparatus.
Anesthetic Alterations of Collective Terahertz Oscillations in Tubulin Correlate with Clinical Potency: Implications for Anesthetic Action and Post-Operative Cognitive Dysfunction
Authors: Craddock Travis J. A. , Kurian Philip , Preto Jordane , Sahu Kamlesh , Hameroff Stuart R. , Klobukowski Mariusz , Tuszynski Jack A. 
Published: August 2017

AbstractAnesthesia blocks consciousness and memory while sparing non-conscious brain activities. While the exact mechanisms of anesthetic action are unknown, the Meyer-Overton correlation provides a link between anesthetic potency and solubility in a lipid-like, non-polar medium. Anesthetic action is also related to an anesthetic’s hydrophobicity, permanent dipole, and polarizability, and is accepted to occur in lipid-like, non-polar regions within brain proteins. Generally the protein target for anesthetics is assumed to be neuronal membrane receptors and ion channels, however new evidence points to critical effects on intra-neuronal microtubules, a target of interest due to their potential role in post-operative cognitive dysfunction (POCD). Here we use binding site predictions on tubulin, the protein subunit of microtubules, with molecular docking simulations, quantum chemistry calculations, and theoretical modeling of collective dipole interactions in tubulin to investigate the effect of a group of gases including anesthetics, non-anesthetics, and anesthetic/convulsants on tubulin dynamics. We found that these gases alter collective terahertz dipole oscillations in a manner that is correlated with their anesthetic potency. Understanding anesthetic action may help reveal brain mechanisms underlying consciousness, and minimize POCD in the choice and development of anesthetics used during surgeries for patients suffering from neurodegenerative conditions with compromised cytoskeletal microtubules.
Pathway-based expression profiling of benign prostatic hyperplasia and prostate cancer delineates an immunophilin molecule associated with cancer progression
Authors: Bhowal Ankur , Majumder Subhadipa , Ghosh Subarna , Basu Sanmitra , Sen Debrup , Roychowdhury Susanta , Sengupta Sanghamitra , Chatterji Urmi 
Published: August 2017

AbstractAberrant restoration of AR activity is linked with prostate tumor growth, therapeutic failures and development of castrate-resistant prostate cancer. Understanding the processes leading to AR-reactivation should provide the foundation for novel avenues of drug discovery. A differential gene expression study was conducted using biopsies from CaP and BPH patients to identify the components putatively responsible for reinstating AR activity in CaP. From the set of genes upregulated in CaP, FKBP52, an AR co-chaperone, was selected for further analysis. Expression of FKBP52 was positively correlated with that of c-Myc. The functional cross-talk between c-Myc and FKBP52 was established using c-Myc specific-siRNA to LNCaP cells that resulted in reduction of FKBP52. A non-canonical E-box sequence housing a putative c-Myc binding site was detected on the FKBP4 promoter using in silico search. LNCaP cells transfected with the FKBP52 promoter cloned in pGL3 basic showed increased luciferase activity which declined considerably when the promoter-construct was co-transfected with c-Myc specific-siRNA. ChIP-PCR confirmed the binding of c-Myc with the conserved E-box located in the FKBP52 promoter. c-Myc downregulation concomitantly affected expression of FGF8. Since expression of FGF8 is controlled by AR, our study unveiled a novel functional axis between c-Myc, AR and FGF8 operating through FKBP52.
Intermolecular base stacking mediates RNA-RNA interaction in a crystal structure of the RNA chaperone Hfq
Authors: Schulz Eike C. , Seiler Markus , Zuliani Cecilia , Voigt Franka , Rybin Vladimir , Pogenberg Vivian , Mücke Norbert , Wilmanns Matthias , Gibson Toby J. , Barabas Orsolya 
Published: August 2017

AbstractThe RNA-chaperone Hfq catalyses the annealing of bacterial small RNAs (sRNAs) with target mRNAs to regulate gene expression in response to environmental stimuli. Hfq acts on a diverse set of sRNA-mRNA pairs using a variety of different molecular mechanisms. Here, we present an unusual crystal structure showing two Hfq-RNA complexes interacting via their bound RNA molecules. The structure contains two Hfq6:A18 RNA assemblies positioned face-to-face, with the RNA molecules turned towards each other and connected via interdigitating base stacking interactions at the center. Biochemical data further confirm the observed interaction, and indicate that RNA-mediated contacts occur between Hfq-RNA complexes with various (ARN)X motif containing RNA sequences in vitro, including the stress response regulator OxyS and its target, fhlA. A systematic computational survey also shows that phylogenetically conserved (ARN)X motifs are present in a subset of sRNAs, some of which share similar modular architectures. We hypothesise that Hfq can co-opt RNA-RNA base stacking, an unanticipated structural trick, to promote the interaction of (ARN)X motif containing sRNAs with target mRNAs on a “speed-dating” fashion, thereby supporting their regulatory function.