bluuebunny/crossref_metadata_2025 huggingface dataset:
Collaboration in Complex Systems: Multilevel Network Analysis for Community-Based Obesity Prevention Interventions
Authors: McGlashan Jaimie , de la Haye Kayla , Wang Peng , Allender Steven
Published: August 2019

Community-based systems interventions represent a promising, but complex approach to the prevention of childhood obesity. Existing studies suggest that the implementation of multiple actions by engaged community leaders (steering committees) is of critical importance to influence a complex system. This study explores two key components of systems interventions: (1) steering committees; and (2) causal loop diagrams (CLDs), used to map the complex community-level drivers of obesity. The interactions between two components create an entangled, complex process difficult to measure, and methods to analyse the dependencies between these two components in community-based systems interventions are limited. This study employs multilevel statistical models from social network analysis to explore the complex interdependencies between steering committee collaboration and their actions in the CLD. Steering committee members from two communities engaged in obesity prevention interventions reported on their collaborative relationships with each other, and where their actions are situated in a locally developed CLD. A multilevel exponential random graph model (MERGM) was developed for each community to explore the structural configurations of the collaboration network, actions in the CLD, and cross-level interactions. The models showed the tendency for reciprocated and transitive collaboration among committee members, as well as some evidence of more complex multilevel configurations that may indicate integrated solutions and collective action. The use of multilevel network analysis represents a step toward unpacking the complexities inherent in community-based systems interventions for obesity prevention.
No single, stable 3D representation can explain pointing biases in a spatial updating task
Authors: Vuong Jenny , Fitzgibbon Andrew W. , Glennerster Andrew
Published: August 2019

People are able to keep track of objects as they navigate through space, even when objects are out of sight. This requires some kind of representation of the scene and of the observer’s location but the form this might take is debated. We tested the accuracy and reliability of observers’ estimates of the visual direction of previously-viewed targets. Participants viewed four objects from one location, with binocular vision and small head movements then, without any further sight of the targets, they walked to another location and pointed towards them. All conditions were tested in an immersive virtual environment and some were also carried out in a real scene. Participants made large, consistent pointing errors that are poorly explained by any stable 3D representation. Any explanation based on a 3D representation would have to posit a different layout of the remembered scene depending on the orientation of the obscuring wall at the moment the participant points. Our data show that the mechanisms for updating visual direction of unseen targets are not based on a stable 3D model of the scene, even a distorted one.
Drug-induced Stress Granule Formation Protects Sensory Hair Cells in Mouse Cochlear Explants During Ototoxicity
Authors: Gonçalves Ana Cláudia , Towers Emily R. , Haq Naila , Porco John A. , Pelletier Jerry , Dawson Sally J. , Gale Jonathan E.
Published: August 2019

Stress granules regulate RNA translation during cellular stress, a mechanism that is generally presumed to be protective, since stress granule dysregulation caused by mutation or ageing is associated with neurodegenerative disease. Here, we investigate whether pharmacological manipulation of the stress granule pathway in the auditory organ, the cochlea, affects the survival of sensory hair cells during aminoglycoside ototoxicity, a common cause of acquired hearing loss. We show that hydroxamate (-)-9, a silvestrol analogue that inhibits eIF4A, induces stress granule formation in both an auditory cell line and ex-vivo cochlear cultures and that it prevents ototoxin-induced hair-cell death. In contrast, preventing stress granule formation using the small molecule inhibitor ISRIB increases hair-cell death. Furthermore, we provide the first evidence of stress granule formation in mammalian hair cells in-vivo triggered by aminoglycoside treatment. Our results demonstrate that pharmacological induction of stress granules enhances cell survival in native-tissue, in a clinically-relevant context. This establishes stress granules as a viable therapeutic target not only for hearing loss but also other neurodegenerative diseases.
Probing the solution structure of the E. coli multidrug transporter MdfA using DEER distance measurements with nitroxide and Gd(III) spin labels
Authors: Yardeni Eliane H. , Bahrenberg Thorsten , Stein Richard A. , Mishra Smriti , Zomot Elia , Graham Bim , Tuck Kellie L. , Huber Thomas , Bibi Eitan , Mchaourab Hassane S. , Goldfarb Daniella
Published: August 2019

Methodological and technological advances in EPR spectroscopy have enabled novel insight into the structural and dynamic aspects of integral membrane proteins. In addition to an extensive toolkit of EPR methods, multiple spin labels have been developed and utilized, among them Gd(III)-chelates which offer high sensitivity at high magnetic fields. Here, we applied a dual labeling approach, employing nitroxide and Gd(III) spin labels, in conjunction with Q-band and W-band double electron-electron resonance (DEER) measurements to characterize the solution structure of the detergent-solubilized multidrug transporter MdfA from E. coli. Our results identify highly flexible regions of MdfA, which may play an important role in its functional dynamics. Comparison of distance distribution of spin label pairs on the periplasm with those calculated using inward- and outward-facing crystal structures of MdfA, show that in detergent micelles, the protein adopts a predominantly outward-facing conformation, although more closed than the crystal structure. The cytoplasmic pairs suggest a small preference to the outward-facing crystal structure, with a somewhat more open conformation than the crystal structure. Parallel DEER measurements with the two types of labels led to similar distance distributions, demonstrating the feasibility of using W-band spectroscopy with a Gd(III) label for investigation of the structural dynamics of membrane proteins.
Image-based Classification of Tumor Type and Growth Rate using Machine Learning: a preclinical study
Authors: Tang Tien T. , Zawaski Janice A. , Francis Kathleen N. , Qutub Amina A. , Gaber M. Waleed
Published: August 2019

Medical images such as magnetic resonance (MR) imaging provide valuable information for cancer detection, diagnosis, and prognosis. In addition to the anatomical information these images provide, machine learning can identify texture features from these images to further personalize treatment. This study aims to evaluate the use of texture features derived from T1-weighted post contrast scans to classify different types of brain tumors and predict tumor growth rate in a preclinical mouse model. To optimize prediction models this study uses varying gray-level co-occurrence matrix (GLCM) sizes, tumor region selection and different machine learning models. Using a random forest classification model with a GLCM of size 512 resulted in 92%, 91%, and 92% specificity, and 89%, 85%, and 73% sensitivity for GL261 (mouse glioma), U87 (human glioma) and Daoy (human medulloblastoma), respectively. A tenfold cross-validation of the classifier resulted in 84% accuracy when using the entire tumor volume for feature extraction and 74% accuracy for the central tumor region. A two-layer feedforward neural network using the same features is able to predict tumor growth with 16% mean squared error. Broadly applicable, these predictive models can use standard medical images to classify tumor type and predict tumor growth, with model performance, varying as a function of GLCM size, tumor region, and tumor type.
Survival of HIV/HCV co-infected patients before introduction of HCV direct acting antivirals (DAA)
Authors: Dold L. , Schwarze-Zander C. , Boesecke C. , Mohr R. , Langhans B. , Wasmuth J.-C. , Strassburg C. P. , Rockstroh J. K. , Spengler U.
Published: August 2019

HIV/HCV infection is supposed to substantially reduce survival as compared to HIV mono-infection. Here, we compared longtime-survival and causes of death in a cohort of HIV- and HIV/HCV-co-infected patients on combined antiretroviral therapy (cART), before introduction of HCV direct acting antivirals (DAA). 322 Caucasian patients with HIV (n = 176) and HIV/HCV-infection (n = 146) were enrolled into this study. All patients were recruited between 2003 and 2004 and followed until 01.01.2014. We compared overall survival between the two groups by the Kaplan-Meyer method and identified independent factors associated with long-time survival by conditional Cox regression analysis. In total 46 (14.3%) patients died during the observation period (HIV infection: n = 23 (13.1%), HIV/HCV infection: n = 23 (15.8%) but overall-survival did not differ significantly between HIV/HCV-infected and HIV mono-infected patients (p = 0.619). Survival was substantially better in patients with complete suppression of HIV replication below the level of detection than in those with residual viremia (p = 0.001). Age (p = 0.008), γ-glutamyltranspeptidase (p < 0.0001) and bilirubin (p = 0.008) were significant predictors of survival irrespective from HCV co-infection. Complete repression of HIV replication on cART is the key factor determining survival both in HIV- and HIV/HCV-co-infected patients, while HCV co-infection and therapy without DAAs seem to affect survival to a lesser extent. Thus, patients with HIV/HCV co-infection require particularly intensive cART.
Circulating but not faecal short-chain fatty acids are related to insulin sensitivity, lipolysis and GLP-1 concentrations in humans
Authors: Müller Mattea , Hernández Manuel A. González , Goossens Gijs H. , Reijnders Dorien , Holst Jens J. , Jocken Johan W. E. , van Eijk Hans , Canfora Emanuel E. , Blaak Ellen E.
Published: August 2019

Microbial-derived short-chain fatty acids (SCFA) acetate, propionate and butyrate may provide a link between gut microbiota and whole-body insulin sensitivity (IS). In this cross-sectional study (160 participants, 64% male, BMI: 19.2–41.0 kg/m2, normal or impaired glucose metabolism), associations between SCFA (faecal and fasting circulating) and circulating metabolites, substrate oxidation and IS were investigated. In a subgroup (n = 93), IS was determined using a hyperinsulinemic-euglycemic clamp. Data were analyzed using multiple linear regression analysis adjusted for sex, age and BMI. Fasting circulating acetate, propionate and butyrate concentrations were positively associated with fasting GLP-1 concentrations. Additionally, circulating SCFA were negatively related to whole-body lipolysis (glycerol), triacylglycerols and free fatty acids levels (standardized (std) β adjusted (adj) −0.190, P = 0.023; std β adj −0.202, P = 0.010; std β adj −0.306, P = 0.001, respectively). Circulating acetate and propionate were, respectively, negatively and positively correlated with IS (M-value: std β adj −0.294, P < 0.001; std β adj 0.161, P = 0.033, respectively). We show that circulating rather than faecal SCFA were associated with GLP-1 concentrations, whole-body lipolysis and peripheral IS in humans. Therefore, circulating SCFA are more directly linked to metabolic health, which indicates the need to measure circulating SCFA in human prebiotic/probiotic intervention studies as a biomarker/mediator of effects on host metabolism.
Diamond-inclusion system recording old deep lithosphere conditions at Udachnaya (Siberia)
Authors: Nestola Fabrizio , Zaffiro Gabriele , Mazzucchelli Mattia L. , Nimis Paolo , Andreozzi Giovanni B. , Periotto Benedetta , Princivalle Francesco , Lenaz Davide , Secco Luciano , Pasqualetto Leonardo , Logvinova Alla M. , Sobolev Nikolay V. , Lorenzetti Alessandra , Harris Jeffrey W.
Published: August 2019

Diamonds and their inclusions are unique fragments of deep Earth, which provide rare samples from inaccessible portions of our planet. Inclusion-free diamonds cannot provide information on depth of formation, which could be crucial to understand how the carbon cycle operated in the past. Inclusions in diamonds, which remain uncorrupted over geological times, may instead provide direct records of deep Earth’s evolution. Here, we applied elastic geothermobarometry to a diamond-magnesiochromite (mchr) host-inclusion pair from the Udachnaya kimberlite (Siberia, Russia), one of the most important sources of natural diamonds. By combining X-ray diffraction and Fourier-transform infrared spectroscopy data with a new elastic model, we obtained entrapment conditions,Ptrap = 6.5(2) GPa andTtrap = 1125(32)–1140(33) °C, for the mchr inclusion. These conditions fall on a ca. 35 mW/m2geotherm and are colder than the great majority of mantle xenoliths from similar depth in the same kimberlite. Our results indicate that cold cratonic conditions persisted for billions of years to at least 200 km in the local lithosphere. The composition of the mchr also indicates that at this depth the lithosphere was, at least locally, ultra-depleted at the time of diamond formation, as opposed to the melt-metasomatized, enriched composition of most xenoliths.
EXTL3-interacting endometriosis-specific serum factors induce colony formation of endometrial stromal cells
Authors: Aints Alar , Mölder Signe , Salumets Andres
Published: August 2019

Endometriosis 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

Cardiac 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

Interest 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

Since 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

Design 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

Selective 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

The 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

H2O2 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

We 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

Several 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

The 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

Studies 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

While 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

Environmental 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

γ-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.
Direct Rubidium-Strontium Dating of Hydrocarbon Charge Using Small Authigenic Illitic Clay Aliquots from the Silurian Bituminous Sandstone in the Tarim Basin, NW China
Authors: Li Shaojie , Wang Xuan-Ce , Li Chao-Feng , Wilde Simon A. , Zhang Youyu , Golding Suzanne D. , Liu Keyu , Zhang Yuxiang
Published: August 2019

Illitic clay is ubiquitous in clastic hydrocarbon reservoirs, and the host for several radiometric isotopes such as the potassium-argon (K-Ar) and rubidium-strontium (Rb-Sr) systems. This study applied the isotope-dilution thermal ionization mass spectrometry technique for small samples (3–4 mg) to conduct illite Rb-Sr isotope dating of five illitic clay samples from the Silurian bituminous sandstone (SBS) intersected by five drillholes in the Tarim Basin, NW China. The 87Rb/86Sr ratio of clays is fractionated mainly by the addition of Rb during the illitization of mixed-layer illite/smectite (I/S), which is the dominant clay species in the Tarim Basin samples. The subsample-scale Rb/Sr isotope values suggest that each subsample may contain I/S particles of slightly variable degrees of illitization. Three of the analyzed samples (H6, KQ1 and TZ67) generated Rb-Sr isochron ages of 141 ± 61 Ma, 332 ± 32 Ma and 235 ± 8 Ma (errors quoted at 2σ), respectively. These results are similar to the corresponding K-Ar ages (125 Ma, 389 Ma and 234 Ma). The isotopic ages are consistent with the timing of hydrocarbon charge which varies in different drillholes as constrained by basin modelling, indicating that a closed-system behavior is attained by the hydrocarbon charge that inhibits the illitization of I/S. The Rb-Sr isotope analyses of the other two samples (YM35-1 and Q1) that did not yield isochron ages suggest the conditions for producing isochrons were not satisfied, which may be caused by disturbance of the isotope system by a post-charge hydrothermal event. The outcomes of this study show the robust potential of Rb-Sr clay subsample geochronology for cross-checking isotopic ages yielded by other systems (e.g. K-Ar system) and constraining the timing of hydrocarbon charge.
Arterio-venous metabolomics exploration reveals major changes across liver and intestine in the obese Yucatan minipig
Authors: Poupin Nathalie , Tremblay-Franco Marie , Amiel Aurélien , Canlet Cécile , Rémond Didier , Debrauwer Laurent , Dardevet Dominique , Thiele Ines , Aurich Maike K. , Jourdan Fabien , Savary-Auzeloux Isabelle , Polakof Sergio
Published: August 2019

Blood circulation mainly aims at distributing the nutrients required for tissue metabolism and collecting safely the by-products of all tissues to be further metabolized or eliminated. The simultaneous study of arterial (A) and venous (V) specific metabolites therefore has appeared to be a more relevant approach to understand and study the metabolism of a given organ. We propose to implement this approach by applying a metabolomics (NMR) strategy on paired AV blood across the intestine and liver on high fat/high sugar (HFHS)-fed minipigs. Our objective was to unravel kinetically and sequentially the metabolic adaptations to early obesity/insulin resistance onset specifically on these two tissues. After two months of HFHS feeding our study of AV ratios of the metabolome highlighted three major features. First, the hepatic metabolism switched from carbohydrate to lipid utilization. Second, the energy demand of the intestine increased, resulting in an enhanced uptake of glutamine, glutamate, and the recruitment of novel energy substrates (choline and creatine). Third, the uptake of methionine and threonine was considered to be driven by an increased intestine turnover to cope with the new high-density diet. Finally, the unique combination of experimental data and modelling predictions suggested that HFHS feeding was associated with changes in tryptophan metabolism and fatty acid β-oxidation, which may play an important role in lipid hepatic accumulation and insulin sensitivity.
CVD graphene/Ge interface: morphological and electronic characterization of ripples
Authors: Mendoza Cesar D. , Figueroa Neileth S. , Maia da Costa Marcelo E. H. , Freire Fernando L.
Published: August 2019

Graphene grown directly on germanium is a possible route for the integration of graphene into nanoelectronic devices as well as it is of great interest for materials science. The morphology of the interface between graphene and germanium influences the electronic properties and has not already been completely elucidated at atomic scale. In this work, we investigated the morphology of the single-layer graphene grown on Ge substrates with different crystallographic orientations. We determined the presence of sinusoidal ripples with a single propagation direction, zig-zag, and could arise due to compressive biaxial strain at the interface generated as a result of the opposite polarity of the thermal expansion coefficient of graphene and germanium. Local density of states measurements on the ripples showed a linear dispersion relation with the Dirac point slightly shifted with respect to the Fermi energy indicating that these out-of-plane deformations were n-doped, while the graphene regions between the highs were undoped.
A new, easily generated mouse model of diabetic kidney fibrosis
Authors: He Xiaolin , Zhang Tianzhou , Tolosa Monica , Goru Santosh Kumar , Chen Xiaolan , Misra Paraish S. , Robinson Lisa A. , Yuen Darren A.
Published: August 2019

Our understanding of diabetic kidney disease pathogenesis has been hampered by the lack of easily generated pre-clinical animal models that faithfully recapitulate critical features of human disease. While most standard animal models develop manifestations of early stage diabetic injury such as hyperfiltration and mesangial matrix expansion, only a select few develop key late stage features such as interstitial fibrosis and reduced glomerular filtration rate. An underlying theme in these late stage disease models has been the addition of renin-angiotensin system hyperactivation, an important contributor to human disease pathogenesis. Widespread use of these models has been limited, however, as they are either labour intensive to generate, or have been developed in the rat, preventing the use of the many powerful genetic tools developed for mice. Here we describe the Akita+/− Ren+/− mouse, a new, easily generated murine model of diabetic kidney disease that develops many features of late stage human injury, including not only hyperglycemia, hypertension, and albuminuria, but also reduced glomerular filtration rate, glomerulosclerosis, and interstitial fibrosis.
Proteasome dysfunction in alveolar type 2 epithelial cells is associated with acute respiratory distress syndrome
Authors: Sitaraman Sneha , Na Cheng-Lun , Yang Li , Filuta Alyssa , Bridges James P. , Weaver Timothy E.
Published: August 2019

Proteasomes are a critical component of quality control that regulate turnover of short-lived, unfolded, and misfolded proteins. Proteasome activity has been therapeutically targeted and considered as a treatment option for several chronic lung disorders including pulmonary fibrosis. Although pharmacologic inhibition of proteasome activity effectively prevents the transformation of fibroblasts to myofibroblasts, the effect on alveolar type 2 (AT2) epithelial cells is not clear. To address this knowledge gap, we generated a genetic model in which a proteasome subunit, RPT3, which promotes assembly of active 26S proteasome, was conditionally deleted in AT2 cells of mice. Partial deletion of RPT3 resulted in 26S proteasome dysfunction, leading to augmented cell stress and cell death. Acute loss of AT2 cells resulted in depletion of alveolar surfactant, disruption of the alveolar epithelial barrier and, ultimately, lethal acute respiratory distress syndrome (ARDS). This study underscores importance of proteasome function in maintenance of AT2 cell homeostasis and supports the need to further investigate the role of proteasome dysfunction in ARDS pathogenesis.
Prognosis of non-small-cell lung cancer in patients with idiopathic pulmonary fibrosis
Authors: Han SongYi , Lee Yeon Joo , Park Jong Sun , Cho Young-Jae , Yoon Ho Il , Lee Jae-Ho , Lee Choon-Taek , Chung Jin-Haeng , Lee Kyung Won , Lee Sang Hoon
Published: August 2019

The risk of lung cancer is higher in idiopathic pulmonary fibrosis (IPF) because both conditions share common risk factors. However, no standard treatment modality for LC in IPF exists due to rare incidence, poor prognosis, and acute exacerbation (AE) of IPF during treatment. We aimed to determine the efficacy of LC treatments and the prognosis in LC patients with IPF according to the LC stage and GAP (gender [G], age [A], and two physiology variables [P]) stage. From 2003 to 2016, 160 retrospectively enrolled patients were classified according to the LC clinical stage and GAP stage. The average (±standard deviation) patient age was 70.1 ± 8.2 years; the cohort predominantly comprised men (94.4%). In GAP stage I, surgery was significantly associated with better survival outcomes in LC. In contrast, no treatment modality yielded significant clinical improvement in GAP stage II/III. The incidences of AE in IPF and its mortality during treatment were 13.8% and 6.3%, respectively. AE occurred commonly in advanced GAP stage. Active treatment should be considered in GAP stage I. The performance status and LC stage should be considered when deciding about the necessity of surgery for patients in advanced GAP stage.