bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide DNA methylation reprogramming in response to inorganic arsenic links inhibition of CTCF binding, DNMT expression and cellular transformation
Authors: Rea Matthew , Eckstein Meredith , Eleazer Rebekah , Smith Caroline , Fondufe-Mittendorf Yvonne N. 
Published: February 2017

AbstractChronic low dose inorganic arsenic (iAs) exposure leads to changes in gene expression and epithelial-to-mesenchymal transformation. During this transformation, cells adopt a fibroblast-like phenotype accompanied by profound gene expression changes. While many mechanisms have been implicated in this transformation, studies that focus on the role of epigenetic alterations in this process are just emerging. DNA methylation controls gene expression in physiologic and pathologic states. Several studies show alterations in DNA methylation patterns in iAs-mediated pathogenesis, but these studies focused on single genes. We present a comprehensive genome-wide DNA methylation analysis using methyl-sequencing to measure changes between normal and iAs-transformed cells. Additionally, these differential methylation changes correlated positively with changes in gene expression and alternative splicing. Interestingly, most of these differentially methylated genes function in cell adhesion and communication pathways. To gain insight into how genomic DNA methylation patterns are regulated during iAs-mediated carcinogenesis, we show that iAs probably targets CTCF binding at the promoter of DNA methyltransferases, regulating their expression. These findings reveal how CTCF binding regulates DNA methyltransferase to reprogram the methylome in response to an environmental toxin.
High density lipoprotein (HDL) particles from end-stage renal disease patients are defective in promoting reverse cholesterol transport
Authors: Anderson Josephine L.C. , Gautier Thomas , Nijstad Niels , Tölle Markus , Schuchardt Mirjam , van der Giet Markus , Tietge Uwe J.F. 
Published: February 2017

AbstractAtherosclerotic cardiovascular disease (CVD) represents the largest cause of mortality in end-stage renal disease (ESRD). CVD in ESRD is not explained by classical CVD risk factors such as HDL cholesterol mass levels making functional alterations of lipoproteins conceivable. HDL functions in atheroprotection by promoting reverse cholesterol transport (RCT), comprising cholesterol efflux from macrophage foam cells, uptake into hepatocytes and final excretion into the feces. ESRD-HDL (n = 15) were compared to healthy control HDL (n = 15) for their capacity to promote in vitro (i) cholesterol efflux from THP-1 macrophage foam cells and (ii) SR-BI-mediated selective uptake into ldla[SR-BI] cells as well as (iii) in vivo RCT. Compared with HDL from controls, ESRD-HDL displayed a significant reduction in mediating cholesterol efflux (p < 0.001) and SR-BI-mediated selective uptake (p < 0.01), two key steps in RCT. Consistently, also the in vivo capacity of ESRD-HDL to promote RCT when infused into wild-type mice was significantly impaired (p < 0.01). In vitro oxidation of HDL from healthy controls with hypochloric acid was able to fully mimic the impaired biological activities of ESRD-HDL. In conclusion, we demonstrate that HDL from ESRD patients is dysfunctional in key steps as well as overall RCT, likely due to oxidative modification.
Cellular prion protein is present in mitochondria of healthy mice
Authors: Faris Robert , Moore Roger A. , Ward Anne , Race Brent , Dorward David W. , Hollister Jason R. , Fischer Elizabeth R. , Priola Suzette A. 
Published: February 2017

AbstractCellular prion protein (PrPC) is a mammalian glycoprotein which is usually found anchored to the plasma membrane via a glycophosphatidylinositol (GPI) anchor. PrPC misfolds to a pathogenic isoform PrPSc, the causative agent of neurodegenerative prion diseases. The precise function of PrPC remains elusive but may depend upon its cellular localization. Here we show that PrPC is present in brain mitochondria from 6–12 week old wild-type and transgenic mice in the absence of disease. Mitochondrial PrPC was fully processed with mature N-linked glycans and did not require the GPI anchor for localization. Protease treatment of purified mitochondria suggested that mitochondrial PrPC exists as a transmembrane isoform with the C-terminus facing the mitochondrial matrix and the N-terminus facing the intermembrane space. Taken together, our data suggest that PrPC can be found in mitochondria in the absence of disease, old age, mutation, or overexpression and that PrPC may affect mitochondrial function.
Cell-free measurements of brightness of fluorescently labeled antibodies
Authors: Zhou Haiying , Tourkakis George , Shi Dennis , Kim David M. , Zhang Hairong , Du Tommy , Eades William C. , Berezin Mikhail Y. 
Published: February 2017

AbstractValidation of imaging contrast agents, such as fluorescently labeled imaging antibodies, has been recognized as a critical challenge in clinical and preclinical studies. As the number of applications for imaging antibodies grows, these materials are increasingly being subjected to careful scrutiny. Antibody fluorescent brightness is one of the key parameters that is of critical importance. Direct measurements of the brightness with common spectroscopy methods are challenging, because the fluorescent properties of the imaging antibodies are highly sensitive to the methods of conjugation, degree of labeling, and contamination with free dyes. Traditional methods rely on cell-based assays that lack reproducibility and accuracy. In this manuscript, we present a novel and general approach for measuring the brightness using antibody-avid polystyrene beads and flow cytometry. As compared to a cell-based method, the described technique is rapid, quantitative, and highly reproducible. The proposed method requires less than ten microgram of sample and is applicable for optimizing synthetic conjugation procedures, testing commercial imaging antibodies, and performing high-throughput validation of conjugation procedures.
Piezoelectric scattering limited mobility of hybrid organic-inorganic perovskites CH3NH3PbI3
Authors: Lu Ying-Bo , Kong Xianghua , Chen Xiaobin , Cooke David G. , Guo Hong 
Published: February 2017

AbstractCarrier mobility is one of the most important parameters for semiconducting materials and their use in optoelectronic devices. Here we report a systematic first principles analysis of the acoustic phonon scattering mechanism that limits the mobility of CH3NH3PbI3 (MAPbI3) perovskites. Due to the unique hybrid organic-inorganic structure, the mechanical, electronic and transport properties are dominated by the same factor, i.e. the weak interatomic bond and the easy rotation of methylammonium (MA) molecules under strain. Both factors make MAPbI3 soft. Rotation of MA molecule induces a transverse shift between Pb and I atoms, resulting in a very low deformation potential and a strong piezoelectricity in MAPbI3. Hence the carrier mobility of pristine MAPbI3 is limited by the piezoelectric scattering, which is consistent to the form of its temperature dependence. Our calculations suggest that in the pristine limit, a high mobility of about several thousand cm2 V−1 S−1 is expected for MAPbI3.
Size-dependent cellular uptake mechanism and cytotoxicity toward calcium oxalate on Vero cells
Authors: Sun Xin-Yuan , Gan Qiong-Zhi , Ouyang Jian-Ming 
Published: February 2017

AbstractUrinary crystals with various sizes are present in healthy individuals and patients with kidney stone; however, the cellular uptake mechanism of calcium oxalate of various sizes has not been elucidated. This study aims to compare the internalization of nano-/micron-sized (50 nm, 100 nm, and 1 μm) calcium oxalate monohydrate (COM) and dihydrate (COD) crystals in African green monkey renal epithelial (Vero) cells. The internalization and adhesion of COM and COD crystals to Vero cells were enhanced with decreasing crystal size. Cell death rate was positively related to the amount of adhered and internalized crystals and exhibited higher correlation with internalization than that with adhesion. Vero cells mainly internalized nano-sized COM and COD crystals through clathrin-mediated pathways as well as micron-sized crystals through macropinocytosis. The internalized COM and COD crystals were distributed in the lysosomes and destroyed lysosomal integrity to some extent. The results of this study indicated that the size of crystal affected cellular uptake mechanism, and may provide an enlightenment for finding potential inhibitors of crystal uptake, thereby decreasing cell injury and the occurrence of kidney stones.
In Vitro and In Vivo Study of the Gastrointestinal Absorption and Metabolisation of Hymenocardine, a Cyclopeptide Alkaloid
Authors: Tuenter Emmy , Bijttebier Sebastiaan , Foubert Kenn , Breynaert Annelies , Apers Sandra , Hermans Nina , Pieters Luc 
Published: February 2017

AbstractHymenocardine is a cyclopeptide alkaloid present in the root bark of Hymenocardia acida. In traditional African medicine, the leaves and roots of this plant are used to treat malaria, and moderate in vitro antiplasmodial activity has been reported for hymenocardine. However, in view of its peptide-like nature, potential metabolisation after oral ingestion has to be taken into account when considering in vivo experiments. In this study, the stability and small intestinal absorption of hymenocardine was assessed using an in vitro gastrointestinal dialysis model. In addition, potential liver metabolisation was investigated in vitro by incubation with a human S9 fraction. Moreover, hymenocardine was administered to rats per os, and blood and urine samples were collected until 48 and 24 h after oral administration, respectively. All samples resulting from these three experiments were analyzed by LC-MS. Analysis of the dialysate and retentate, obtained from the gastrointestinal dialysis model, indicated that hymenocardine is absorbed unchanged from the gastrointestinal tract, at least in part. After S9 metabolisation, several metabolites of hymenocardine could be identified, the major ones being formed by the reduction and/or the loss of an N-methyl group. The in vivo study confirmed that hymenocardine is absorbed from the gastrointestinal tract unchanged, since it could be identified in both rat plasma and urine, together with hymenocardinol, its reduction product.
Harnessing host ROS-generating machinery for the robust genome replication of a plant RNA virus
Authors: Hyodo Kiwamu , Hashimoto Kenji , Kuchitsu Kazuyuki , Suzuki Nobuhiro , Okuno Tetsuro 
Published: February 2017

Significance
Reactive oxygen species (ROS) production is induced by multiple environmental stresses in various organisms. In plants, ROS transduce local and systemic signaling for adaptation and tolerance to these stresses. Here we show that red clover necrotic mosaic virus (RCNMV), a plant positive-strand RNA [(+)RNA] virus, hijacks the host’s ROS-generating machinery during infection. An RCNMV replication protein associates with host ROS-generating machinery and triggers intracellular ROS bursts. These bursts are required for robust viral RNA replication. We further show that another (+)RNA virus, brome mosaic virus, also depends on ROS for replication. This study represents an example of diversion of a plant stress-resilience system for robust virus replication.
The nonreceptor tyrosine kinase c-Src attenuates SCF(β-TrCP) E3-ligase activity abrogating Taz proteasomal degradation
Authors: Shanzer Matan , Adler Julia , Ricardo-Lax Inna , Reuven Nina , Shaul Yosef 
Published: February 2017

Significance
Taz (transcriptional coactivator with PDZ-binding motif) and Yap (yes-associated protein), the Hippo pathway effector proteins regulating cell fate, organ size, and homeostasis, are targeted by the potent viral oncogene polyomavirus middle T antigen (PyMT). A key process of PyMT is the activation of Src, a cellular proto-oncogene. Remarkably, active Src prevents the Hippo pathway from enhancing Taz decay mediated by its E3-ubiquitin ligase SCF(β-TrCP). We resolved the underlying mechanism by demonstrating that Src inhibits β-TrCP. β-TrCP is a key cellular component regulating a wide range of cellular signaling in cell fate determination. Our discovery of a function of the well-studied Src tyrosine kinase in abrogating β-TrCP function is expected to have wide ramifications for cell fate determination, including in oncogenesis.
The dynamics of a recovering fish stock: Georges Bank herring
Authors: Melvin Gary D. , Stephenson Robert L. 
Published: February 2017

Abstract
Melvin, G. D., and Stephenson, R. L. 2007. The dynamics of a recovering fish stock: Georges Bank herring – ICES Journal of Marine Science, 64, 69–82. The decline and subsequent recovery of Georges Bank Atlantic herring (Clupea harengus) provides a rare opportunity to examine the dynamics of a recovering fish population. Moreover, the near absence of a commercial fishery on Georges Bank between 1978 and 1995 removes the confounding effects of exploitation during the recovery period. Herring abundance on Georges Bank increased and the distribution of adult spawning fish evolved from a few isolated locations to most of the northern fringe during the period 1983–1995. The distribution of recently hatched larvae also expanded in a manner consistent with progressive occupation of historical spawning grounds. Changes in the size composition and age structure of herring during the spawning season broadened from the dominance of a single age class to multiple year classes as the stock recovered and expanded. Growth, as reflected by length-at-age, decreased significantly and was correlated with the number of fish estimated to be in the stock. This and the observed difference in mean length and length at first spawning during the recovery provide strong evidence of density-dependent growth. In particular, there is a highly correlated (p<0.01) relationship between the number of 4+ herring in the stock at the start of the year and the mean length of herring aged 3 recruiting to the spawning stock in autumn of the same year. A mechanism based on an extended period of prespawning interaction is proposed to explain the density-dependence.
A post-processing technique to estimate the signal-to-noise ratio and remove echosounder background noise
Authors: De Robertis Alex , Higginbottom Ian 
Published: February 2017

Abstract
De Robertis, A., and Higginbottom, I. 2007. A post-processing technique to estimate the signal-to-noise ratio and remove echosounder background noise. – ICES Journal of Marine Science, 64: 1282–1291. A simple and effective post-processing technique to estimate echosounder background-noise levels and signal-to-noise ratios (SNRs) during active pinging is developed. Similar to other methods of noise estimation during active pinging, this method assumes that some portion of the sampled acoustic signal is dominated by background noise, with a negligible contribution from the backscattered transmit signal. If this assumption is met, the method will provide robust and accurate estimates of background noise equivalent to that measured by the receiver if the transmitter were disabled. It provides repeated noise estimates over short intervals of time without user intervention, which is beneficial in cases where background noise changes over time. In situations where background noise is dominant in a portion of the recorded signal, it is straightforward to make first-order corrections for the effects of noise and to estimate the SNR to evaluate the effects of background noise on acoustic measurements. Noise correction and signal-to-noise-based thresholds have the potential to improve inferences from acoustic measurements in lower signal-to-noise situations, such as when surveying from noisy vessels, using multifrequency techniques, surveying at longer ranges, and when working with weak acoustic targets such as invertebrates and fish lacking swimbladders.
Elevated CO2 and plant growth: cellular mechanisms and responses of whole plants
Authors: Taylor Gail , Ranasinghe Sananthanie , Bosac Creana , Gardner S.D.L. , Ferris Rachel 
Published: February 2017

Abstract
Much research has focused on the photosynthetic responses of plants to elevated CO2 , with less attention given to the post-photosynthetic events which may lead to changes in the growth of tissues, organs and whole plants. The aim of this review is to identify how plant growth is altered in elevated CO2 and to determine which growth processes or cellular mechanisms are sensitive to carbon supply.
For leaves, both the expansion of individual leaves and the initiation of leaf primordia are stimulated in elevated CO2. When lamina growth is promoted, this is usually associated with increased leaf cell expansion rather than increased leaf cell production. Using several clones of hybrid poplar (Populus euramericana, P. interamericana) two native herbs (Plantago media, Sanguisorba minor) and bean (Phaseolus vulgaris) we have identified the mechanism through which leaf cell expansion is promoted in elevated CO2. Changes in the water relations, turgor pressure (P) and yield turgor (Y) of growing leaves cannot explain increased cell expansion; this appears to occur because cell wall loosening is promoted, as suggested by three pieces of evidence. (i) The rate of decline of water potential (ψ) with time is accelerated when growing leaves are placed in psychrometers and allowed to relax, (ii) Instron-measured cell wall extensibility (WEX), is greater for leaves exposed to elevated CO2 and (iii) the activity of the putative wall loosening enzyme, XET is increased for leaves of P. vulgaris exposed to elevated CO2. Species differences do, however, exist; in the herb Lotus corniculatus small stimulations of leaf growth in elevated CO2 are due to increased leaf cell production and decreased cell size in elevated CO2. These results are discussed in relation to the concept of functional types.
There is evidence to suggest that both cell production and cell expansion are promoted in roots of plants exposed to elevated CO2. For native herbs (Anthyllis vulneraria, Lotus corniculatus, P. media and S. minor), increased root growth in elevated CO2 is due to increased cell elongation. In contrast to leaves, this appears to occur because both root cell turgor pressure (P) and root cell wall extensibility (WEX) are promoted by exposure of shoots to elevated CO2. In longer-term studies on root growth, the effects of additional carbon on the production of root primordia and root branching are of overriding importance, suggesting that carbon supply may influence some aspect of the cell cycle, when effects on the extension of individual roots may not be apparent.
An anisotropic minijets model for the GRB prompt emission
Authors: Barniol Duran R. , Leng M. , Giannios D. 
Published: February 2017

Abstract
In order to explain rapid light-curve variability without invoking a variable source, several authors have proposed ‘minijets’ that move relativistically relative to the main flow of the jet. Here, we consider the possibility that these minijets, instead of being isotropically distributed in the comoving frame of the jet, form primarily perpendicular to the direction of the flow, as the jet dissipates its energy at a large emission radius. This yields two robust features. First, the emission is significantly delayed compared with the isotropic case. This delay allows for the peak of the afterglow emission to appear while the source is still active, in contrast to the simplest isotropic model. Secondly, the flux decline after the source turns off is steeper than the isotropic case. We find that these two features are realized in gamma-ray bursts (GRBs). (1) The peak of most GeV light curves (ascribed to the external shock) appears during the prompt emission phase. (2) Many X-ray light curves exhibit a period of steep decay, which is faster than that predicted by the standard isotropic case. The gamma-ray generation mechanism in GRBs, and possibly in other relativistic flows, may therefore be anisotropic.
Changes in the activities of ornithine decarboxylase, putrescine N-methyltransferase and N-methylputrescine oxidase in tobacco roots in relation to nicotine biosynthesis
Authors: Mizusaki Shigenobu , Tanabe Yoko , Noguchi Masao , Tamaki Einosuke 
Published: February 2017

Abstract
Changes in ornithine decarboxylase, putrescine N-methyltransferase and N-methylputrescine oxidase activities in response to some treatments were investigated using hydroponically grown tobacco plants. Decapitation of shoots brought about marked elevation of the three enzyme activities, which reached their peaks 24 hr after decapitation, then declined. An excellent correlation was observed between the accumulation of nicotine and changes in the three root enzyme activities. Administration of IAA at 2.5 to 5 μconcentration significandy increased these enzyme activities in roots of decapitated plants but higher concentrations of IAA prevented the rise in enzyme activities promoted by decapitation. Nicotine strongly inhibited the rise in enzyme activities in roots of decapitated plants in all cases. The results suggest that these enzymes are under the control of a common regulatory system, in which auxin and nicotine are important components. Ornithine decarboxylase was present in all the plants examined, but putrescine N-methyltransferase and N-mediylputrescine oxidase were detected only in the roots of tobacco, Datura and Atropa plants.
The Application of Radiophotoluminescent Glass to Gamma Dosimetry in Mixed n-Gamma Fields
Authors: Croft S. , Weaver D.R. , Heffer P.J.H. 
Published: February 2017

Abstract
High Z radiophotoluminescent glass of British manufacture has been studied with a view to using it as a ? ray dosemeter in mixed n-? fields at ambient and elevated temperatures. Environments such as these are widespread amongst nuclear enginering, accident dosimetry and military application areas. The radiation response of the glass has been fully characterised and the results are presented. The photon response over the energy range 16 keV-7 MeV has been determined and interpreted within the framework of a simplified model. The neutron response from thermal energies to 15 MeV has been measured using reactor and accelerator based sources. The fast neutron response was found to be small, although the thermal neutron sensitivity is too high for most in-core applications without a thermal neutron shield. The results are also compared with new measurements of the neutron response of Toshiba FD7 glass over the energy range thermal - 2.2 MeV. The signal build-up and fade characteristics of the dosemeter at ambient temperatures and 100 oC are presented for irradiations carried out both at ambient and 100 oC. Acceptable stability is found at these elevated temperatures. The potential use of this high Z glass in tandem with low Z beryllium oxide dosemeters as a measure of gamma ray spectra is also discussed.
Thermoluminescence Dating of Pleistocene Travertine
Authors: Reddmann Th. , Schüttlekopf H. 
Published: February 2017

Abstract
We investigated the thermoluminescence characteristics of travertine samples from a deposit at Bad-Cannstatt, Stuttgart, South West Germany. This location is known as a prehistoric hunting place of homo erectus, whose age has been approximated to about 200,000 years. The calcite material has been found to show a high fraction of clay impurities. A pre-treatment using heavy liquid separation techniques resulted, however, in a good reproducibility of the TL signal. On the other hand, a high degree of spatial homogeneity of the U/Th distribution has been found. In addition 238U, 234U and 230Th concentrations were determined in the samples using radiochemical analysis. The derived isotope ratios and the paleodoses prove that a substantial fraction of the uranium must have been removed after deposition. A best fit method is used to correct for this loss and to derive ages for the material.