bluuebunny/crossref_metadata_2025_split huggingface dataset:
EXTL3-interacting endometriosis-specific serum factors induce colony formation of endometrial stromal cells
Authors: Aints Alar , Mölder Signe , Salumets Andres 
Published: August 2019

AbstractEndometriosis is a benign chronic condition characterized by the existence of endometrial-like stroma and glandular tissue in extrauterine locations. The molecular mechanisms of its pathogenesis have not been elucidated. We have studied the role of EXTL3 (exostosin-like 3) in endometriosis and found that it is expressed in endometrial tissue as well as endometriosis lesions. We have found that serum from endometriosis patients contains a factor or factors, which interact with EXTL3 resulting in strongly increased colony formation in regenerating cell culture. We also found increased anti-EXTL3 antibodies in endometriosis patients’ sera. EXTL3 is an N-acetyl glucosamine (GlcNAc) transferase, performing a key step in heparan sulfate (HS) glucosaminoglycan synthesis. Many viruses replicate in regenerating epithelial cells and use HS as a receptor for cell entry. We measured antibody titres to viruses, which use HS as a receptor for cell entry, and found rarely increased titres for these viruses in endometriosis sera, whereas titres to viruses using other receptors were equally distributed in study groups. The data indicate that perturbation of HS metabolism is associated with endometriosis.
Cardiac MLC2 kinase is localized to the Z-disc and interacts with α-actinin2
Authors: X. Cai Lawrence , Tanada Yohei , D. Bello Gregory , C. Fleming James , F. Alkassis Fariz , Ladd Thomas , Golde Todd , Koh Jin , Chen Sixue , Kasahara Hideko 
Published: August 2019

AbstractCardiac contractility is enhanced by phosphorylation of myosin light chain 2 (MLC2) by cardiac-specific MLC kinase (cMLCK), located at the neck region of myosin heavy chain. In normal mouse and human hearts, the level of phosphorylation is maintained relatively constant, at around 30–40% of total MLC2, likely by well-balanced phosphorylation and phosphatase-dependent dephosphorylation. Overexpression of cMLCK promotes sarcomere organization, while the loss of cMLCK leads to cardiac atrophy in vitro and in vivo. In this study, we showed that cMLCK is predominantly expressed at the Z-disc with additional diffuse cytosolic expression in normal adult mouse and human hearts. cMLCK interacts with the Z-disc protein, α-actinin2, with a high-affinity kinetic value of 13.4 ± 0.1 nM through the N-terminus region of cMLCK unique to cardiac-isoform. cMLCK mutant deficient for interacting with α-actinin2 did not promote sarcomeric organization and reduced cardiomyocyte cell size. In contrast, a cMLCK kinase-deficient mutant showed effects similar to wild-type cMLCK on sarcomeric organization and cardiomyocyte cell size. Our results suggest that cMLCK plays a role in sarcomere organization, likely distinct from its role in phosphorylating MLC2, both of which will contribute to the enhancement of cardiac contractility.
Possible transport evidence for three-dimensional topological superconductivity in doped β-PdBi2
Authors: Kolapo Ayo , Li Tingxin , Hosur Pavan , Miller John H. 
Published: August 2019

AbstractInterest in topological states of matter burgeoned over a decade ago with the theoretical prediction and experimental detection of topological insulators, especially in bulk three-dimensional insulators that can be tuned out of it by doping. Their superconducting counterpart, the fully-gapped three-dimensional time-reversal-invariant topological superconductors, have evaded discovery in bulk intrinsic superconductors so far. The recently discovered topological metal β-PdBi2 is a unique candidate for tunable bulk topological superconductivity because of its intrinsic superconductivity and spin-orbit-coupling. In this work, we provide experimental transport signatures consistent with fully-gapped 3D time-reversal-invariant topological superconductivity in K-doped β-PdBi2. In particular, we find signatures of odd-parity bulk superconductivity via upper-critical field and magnetization measurements— odd-parity pairing can be argued, given the band structure of β-PdBi2, to result in 3D topological superconductivity. In addition, Andreev spectroscopy reveals surface states protected by time-reversal symmetry which might be possible evidence of Majorana surface states (Majorana cone). Moreover, we find that the undoped bulk system is a trivial superconductor. Thus, we discover β-PdBi2 as a unique bulk material that, on doping, can potentially undergo an unprecedented topological quantum phase transition in the superconducting state.
Loan maturity aggregation in interbank lending networks obscures mesoscale structure and economic functions
Authors: Van Soom Marnix , van den Heuvel Milan , Ryckebusch Jan , Schoors Koen 
Published: August 2019

AbstractSince the 2007–2009 financial crisis, substantial academic effort has been dedicated to improving our understanding of interbank lending networks (ILNs). Because of data limitations or by choice, the literature largely lacks multiple loan maturities. We employ a complete interbank loan contract dataset to investigate whether maturity details are informative of the network structure. Applying the layered stochastic block model of Peixoto (2015) and other tools from network science on a time series of bilateral loans with multiple maturity layers in the Russian ILN, we find that collapsing all such layers consistently obscures mesoscale structure. The optimal maturity granularity lies between completely collapsing and completely separating the maturity layers and depends on the development phase of the interbank market, with a more developed market requiring more layers for optimal description. Closer inspection of the inferred maturity bins associated with the optimal maturity granularity reveals specific economic functions, from liquidity intermediation to financing. Collapsing a network with multiple underlying maturity layers or extracting one such layer, common in economic research, is therefore not only an incomplete representation of the ILN’s mesoscale structure, but also conceals existing economic functions. This holds important insights and opportunities for theoretical and empirical studies on interbank market functioning, contagion, stability, and on the desirable level of regulatory data disclosure.
Fabrication of hierarchical core/shell MgCo2O4@MnO2 nanowall arrays on Ni-foam as high–rate electrodes for asymmetric supercapacitors
Authors: Xu Jiasheng , Wang Lin 
Published: August 2019

AbstractDesign and fabrication of a hierarchical core/shell MgCo2O4@MnO2 nanowall arrays on Ni-foam by a facile two-step hydrothermal method. The electrochemical measurements prove these composites with MnO2 definitely offer better supercapacitive performance of the MgCo2O4 electrode material. The nanowall structure provides more active sites and charge transfer during the Faradic reaction. The MgCo2O4@MnO2 nanowall shows an excellent electrochemical performance (852.5 F g−1 at 1 A g−1). The asymmetric supercapacitor is composed of the MgCo2O4@MnO2 nanowall and the activated carbon (AC). The energy densities of the asymmetric supercapacitor device can keep up 67.2 Wh·kg−1 at 5760.0 W·kg−1. The MgCo2O4@MnO2 nanowall shows excellent supercapacitive performance and has a great potential for more research and application in the asymmetric supercapacitor devices field.
A trade-off for covalent and intercalation binding modes: a case study for Copper (II) ions and singly modified DNA nucleoside
Authors: Mouesca Jean-Marie , Ahouari Hania , Dantu Sarath Chandra , Sicoli Giuseppe 
Published: August 2019

AbstractSelective binding to nucleic acids and, more generally, to biopolymers, very often requires at a minimum the presence of specific functionalities and precise spatial arrangement. DNA can fold into defined 3D structures upon binding to metal centers and/or lanthanides. Binding efficiency can be boosted by modified nucleosides incorporated into DNA sequences. In this work the high selectivity of modified nucleosides towards copper (II) ions, when used in the monomeric form, is unexpectedly and drastically reduced upon being covalently attached to the DNA sequence in single-site scenario. Surprisingly, such selectivity is partially retained upon non-covalent (i.e. intercalation) mixture formed by native DNA duplex and a nucleoside in the monomeric form. Exploiting the electron spin properties of such different and rich binding mode scenarios, 1D/2D pulsed EPR experiments have been used and tailored to differentiate among the different modes. An unusual correlation of dispersion of hyperfine couplings and strength of the binding mode(s) is described.
Decellularized liver scaffolds promote liver regeneration after partial hepatectomy
Authors: Shimoda Hirofumi , Yagi Hiroshi , Higashi Hisanobu , Tajima Kazuki , Kuroda Kohei , Abe Yuta , Kitago Minoru , Shinoda Masahiro , Kitagawa Yuko 
Published: August 2019

AbstractThe resectable liver volume is strictly limited and this reduces the number of patients who may be treated. Recently, “tissue/organ decellularization”, a new approach in bioengineering, has been investigated for its ability to produce a native organ scaffold by removing all the viable cells. Such a scaffold may support the repair of damaged or injured tissue. The purpose of this study was to evaluate the potential contribution of liver scaffolds to hepatic regeneration after hepatectomy. We sutured the partial liver scaffolds onto the surfaces of partially hepatectomized porcine livers and assessed their therapeutic potential by immune histological analysis at various time points. Animals were sacrificed after surgery and the implanted scaffolds were evaluated for the infiltration of various types of cells. Immune histochemical study showed that blood vessel-like structures, covered with CD31 positive endothelial cells and ALB positive cells, were present in all parts of the scaffolds at days 10 and 28. Blood inflow was observed in some of these ductal structures. More interestingly, CK19 and EpCAM positive cells appeared at day 10. These results suggest that the implantation of a decellularized organ scaffold could promote structural reorganization after liver resection.
Role of Oxidized Lipids in Permeation of H2O2 Through a Lipid Membrane: Molecular Mechanism of an Inhibitor to Promoter Switch
Authors: Ouchi Yuya , Unoura Kei , Nabika Hideki 
Published: August 2019

AbstractH2O2 permeation through a cell membrane significantly affects living organisms, and permeation is controlled by the physico-chemical nature of lipids and other membrane components. We investigated the molecular relationship between H2O2 permeation and lipid membrane structure using three oxidized lipids. POVPC and PazePC act as intra- and inter-molecular permeation promoters, respectively; however, their underlying mechanisms were different. The former changed the partition equilibrium, while the latter changed the permeation pathway. PoxnoPC inhibited permeation under our experimental conditions via an intra-molecular configuration change. Thus, both intra- and inter-molecular processes were found to control the role of oxidized lipids as inhibitors and promoters towards H2O2 permeation with different mechanisms depending on structure and composition. Here, we identified two independent H2O2 permeation routes: (i) permeation through lipid membrane with increased partition coefficient by intra-molecular configurational change and (ii) diffusion through pores (water channels) formed by inter-molecular configurational change of oxidized lipids. We provide new insight into how biological cells control permeation of molecules through intra- and inter-molecular configurational changes in the lipid membrane. Thus, by employing a rational design for both oxidized lipids and other components, the permeation behaviour of H2O2 and other ions and molecules through a lipid membrane could be controlled.
An incremental training method with automated, extendable maze for training spatial behavioral tasks in rodents
Authors: Holleman Esther , Mąka Jan , Schröder Tim , Battaglia Francesco 
Published: August 2019

AbstractWe present a training procedure and maze equipped with sensors and automated feeders for training spatial behavioral tasks in rodents. The maze can be transformed from an enclosed box to a maze of variable dimensions. The modularity of the protocol and setup makes it highly flexible and suitable for training a wide variety of spatial tasks, and facilitates incremental training stages of increasing maze size for more efficient learning. The apparatus, in its software and hardware, is able to adapt to animal performance, adjusting task challenges and difficulty. Two different methods of automatic behavioral scoring are evaluated against manual methods. Sensors embedded in the maze provide information regarding the order of reward locations visited and the time between the activation of the cue via the nose-poke and the activation of the reward location sensors. The distributions of these reaction times differ between correct and incorrect trials, providing an index of behavior and motivation. The automated maze system allows the trainer to operate and monitor the task away from the experimental set-up, minimizing human interference and improving the reproducibility of the experiment. We show that our method succeeds in training a binary forced-choice task in rats.
Evaluation of hepatitis C viral RNA persistence in HIV-infected patients with long-term sustained virological response by droplet digital PCR
Authors: Frías Mario , Rivero-Juárez Antonio , Téllez Francisco , Palacios Rosario , Jiménez-Arranz Álvaro , Pineda Juan A. , Merino Dolores , Gómez-Vidal María Amparo , Pérez-Camacho Inés , Camacho Ángela , Rivero Antonio 
Published: August 2019

AbstractSeveral studies have reported the persistence of HCV RNA in liver and/or peripheral blood mononuclear cells (PBMCs) in spite of undetectable viremia in patients who have achieved sustained virological response (SVR). This event, defined as occult HCV infection, remains controversial and low titers of persistent virus may be underestimated because it has not yet been analyzed by a highly sensitive test such as droplet digital PCR (ddPCR). This method provides an alternate ultra-sensitive detection technique for very low numbers of copies of viral RNA or DNA. The aim of this study was to evaluate the persistence of HCV in HIV-coinfected patients with long-term SVR using ddPCR. For each patient, the presence of HCV RNA in serum and PBMCs at baseline was determined by nested RT-ddPCR. Patients with HCV RNA in PBMCs at baseline were followed until the end of the study. One hundred and twenty-three patients were analyzed for persistence of HCV RNA in serum and PBMCs. Persistence of HCV was not found in serum in any patient. HCV RNA was detected in PBMCs in one patient (0.81%; 95% CI: 0.04–3.94) and resolved spontaneously during follow-up. Persistence of HCV RNA in PBMCs is not a common event in HIV/HCV co-infected patients with long-term SVR evaluated by RT-ddPCR.
Specific increase of Fusobacterium in the faecal microbiota of neonatal calves infected with Cryptosporidium parvum
Authors: Ichikawa-Seki Madoka , Motooka Daisuke , Kinami Aiko , Murakoshi Fumi , Takahashi Yoko , Aita Junya , Hayashi Kei , Tashibu Atsushi , Nakamura Shota , Iida Tetsuya , Horii Toshihiro , Nishikawa Yoshifumi 
Published: August 2019

AbstractThe faecal microbiota plays a critical role in host health, with alterations in the human faecal microbial composition associated with various conditions, particularly diarrhoeal diseases. However, little is known about microbial changes during cryptosporidiosis, one of the most important diarrhoeal diseases caused by protozoa in cattle. In this study, alterations in the faecal microbiota of neonatal calves as a result ofCryptosporidium parvuminfection were investigated on aC. parvum-positive farm. Comparisons were made among groups ofC. parvum-infected, rotavirus-infected, and the pathogen-negative calves. A specific increase in the abundance ofFusobacteriumwas observed in the faecal microbiota ofC. parvum-infected animals. Diarrhoea severity increased in accordance with the abundance ofC. parvumandFusobacterium. Moreover, the specific increase ofFusobacteriumappeared to be a universal feature ofC. parvuminfection, since neonatal calves from geographically separated areas showed the same result. These observations indicated that the growth ofFusobacteriummay be an important aggravating factor of cryptosporidiosis.
Exposure to graphene oxide sheets alters the expression of reference genes used for real-time RT-qPCR normalization
Authors: de Lázaro Irene , Kostarelos Kostas 
Published: August 2019

AbstractStudies unraveling the interactions between graphene oxide (GO) and the biological milieu, including cells and tissues, are multiplying quickly as the biomedical applications of this and other 2D materials continue to be explored. Many of such studies rely on real-time RT-qPCR as a powerful yet simple technique to assess gene expression. However, a systematic investigation of potential GO-induced changes in the expression of reference genes, crucial for appropriate qPCR data normalization, is still lacking. We aimed to cover this gap investigating the stability of the expression of ten candidate reference genes upon exposure to increasing, but subtoxic, GO concentrations, with two established algorithms (Bestkeeper and NormFinder). The study was performed in a human cancer cell line (MCF7) and in mouse, non-cancerous, primary cells (mouse embryonic fibroblasts, MEFs), to assess different behaviors between cell types. Both algorithms evidenced significant deviations in the expression of various reference genes. Ribosomal proteins scored among the most significantly dysregulated in both cell types. ACTB and GAPDH, the most frequent calibrators in real-time RT-qPCR, were also affected, although differences existed between cell lines. This study illustrates the need to validate reference genes for appropriate real-time RT-qPCR normalization, according to specific experimental conditions, when GO-cell interactions occur.
Ionizing Radiation induction of cholesterol biosynthesis in Lung tissue
Authors: Werner Erica , Alter Andrew , Deng Qiudong , Dammer Eric B. , Wang Ya , Yu David S. , Duong Duc M. , Seyfried Nicholas T. , Doetsch Paul W. 
Published: August 2019

AbstractWhile evidence supporting the notion that exposures to heavy ion radiation increase the risk for cancer and other disease development is accumulating, the underlying biological mechanisms remain poorly understood. To identify novel phenotypes that persist over time that may be related to increased disease development risk, we performed a quantitative global proteome analysis of immortalized human bronchial epithelial cells (HBEC3-KT) at day 7 post exposure to 0.5 Gy Fe ion (600 MeV/nucleon, Linear Energy Transfer (LET) = 175 keV/μm). The analysis revealed a significant increase in the expression of 4 enzymes of the cholesterol biosynthesis pathway. Elevated expression of enzymes of the cholesterol pathway was associated with increased cholesterol levels in irradiated cells and in lung tissue measured by a biochemical method and by filipin staining of cell-bound cholesterol. While a 1 Gy dose of Fe ion was sufficient to induce a robust response, a dose of 5 Gy X-rays was necessary to induce a similar cholesterol accumulation in HBEC3-KT cells. Radiation-increased cholesterol levels were reduced by treatment with inhibitors affecting the activity of enzymes in the biosynthesis pathway. To examine the implications of this finding for radiotherapy exposures, we screened a panel of lung cancer cell lines for cholesterol levels following exposure to X-rays. We identified a subset of cell lines that increased cholesterol levels in response to 5 Gy X-rays. Survival studies revealed that statin treatment is radioprotective, suggesting that cholesterol increases are associated with cytotoxicity. In summary, our findings uncovered a novel radiation-induced response, which may modify radiation treatment outcomes and contribute to risk for radiation–induced cardiovascular disease and carcinogenesis.
Environmental DNA size sorting and degradation experiment indicates the state of Daphnia magna mitochondrial and nuclear eDNA is subcellular
Authors: Moushomi Rashnat , Wilgar Gregory , Carvalho Gary , Creer Simon , Seymour Mathew 
Published: August 2019

AbstractEnvironmental DNA analysis has emerged as a key component of biodiversity and environmental monitoring. However, the state and fate of eDNA in natural environments is still poorly understood for many ecological systems. Here we assess the state and fate of eDNA derived from the water flea, Daphnia magna, using a full factorial mesocosm experiment. We measured the quantity and degradation of eDNA over a two month period across a range of filters differing in pore size (0, 0.2, 1 and 10 µm), which spans the range of eDNA source material including subcellular, cellular and tissue. We also used two primer sets targeting mitochondrial (COI) and nuclear (18S) genomic regions. Our findings demonstrated that eDNA was most prevalent in the effluent water, but also reliably detected on the 0.2 μm filter, suggesting subcellular material is the predominate state of eDNA. Temporal eDNA quantity dynamics followed an exponential decay function over the course of 6-17 days, demonstrating a predictable decline in eDNA concentration. Nuclear eDNA was more abundant than mitochondrial eDNA, which may be a result of greater primer affinity, or indicate greater availability of nuclear eDNA gene targets in the environment. In contrast to two previous size-sorting experiments, which utilizing fish eDNA, our findings suggest that the state of invertebrate eDNA is much smaller than previously suspected. Overall, our data suggest that the detection of eDNA greatly depends on our knowledge of the state and fate of eDNA, which differ among species, and likely across environmental conditions.
Definitive evidence of the presence of 24-methylenecycloartanyl ferulate and 24-methylenecycloartanyl caffeate in barley
Authors: Ito Junya , Sawada Kazue , Ogura Yusuke , Xinyi Fan , Rahmania Halida , Mohri Tomoyo , Kohyama Noriko , Kwon Eunsang , Eitsuka Takahiro , Hashimoto Hiroyuki , Kuwahara Shigefumi , Miyazawa Teruo , Nakagawa Kiyotaka 
Published: August 2019

Abstractγ-Oryzanol (OZ), which has a lot of beneficial effects, is a mixture of ferulic acid esters of triterpene alcohols (i.e., triterpene alcohol type of OZ (TTA-OZ)) and ferulic acid esters of plant sterols (i.e., plant sterol type of OZ (PS-OZ)). Although it has been reported that OZ is found in several kinds of cereal typified by rice, TTA-OZ (e.g., 24-methylenecycloartanyl ferulate (24MCA-FA)) has been believed to be characteristic to rice and has not been found in other cereals. In this study, we isolated a compound considered as a TTA-OZ (i.e., 24MCA-FA) from barley and determined the chemical structure using by HPLC-UV-MS, high-resolution MS, and NMR. Based on these results, we proved for the first time that barley certainly contains 24MCA-FA (i.e., TTA-OZ). During the isolation and purification of 24MCA-FA from barley, we found the prospect that a compound with similar properties to OZ (compound-X) might exist. To confirm this finding, the compound-X was also isolated, determined the chemical structure, and identified as a caffeic acid ester of 24-methylenecycloartanol (24MCA-CA), which has rarely been reported before. We also quantified these compounds in various species of barley cultivars and found for the first time the existence of 24MCA-FA and 24MCA-CA in various barley. Through these findings, it opens the possibility to use barley as a new source of 24MCA-FA and 24MCA-CA.