bluuebunny/crossref_metadata_2025_split huggingface dataset:
Legionella SBT applied directly to respiratory samples as a rapid molecular epidemiological tool
Authors: Quero Sara , Párraga-Niño Noemí , Sabria Miquel , Barrabeig Irene , Sala Maria Rosa , Jané Mireia , Mateu Lourdes , Sopena Nieves , Pedro-Botet Maria Luisa , Garcia-Nuñez Marian 
Published: January 2019

AbstractLegionnaires’ disease (LD) is an atypical pneumonia caused by the inhalation of Legionella. The methods used for the diagnosis of LD are direct culture of respiratory samples and urinary antigen detection. However, the sensitivity of culture is low, and the urinary antigen test is specific only for L. pneumophila sg1. Moreover, as no isolates are obtained, epidemiological studies cannot be performed. The implementation of Nested-sequence-based typing (Nested-SBT) makes it possible to carry out epidemiological studies while also confirming LD, especially in cases caused by non-sg 1. Sixty-two respiratory samples from patients with Legionella clinically confirmed by positive urinary antigen tests were cultured and tested by Nested-SBT, following the European Study Group for Legionella Infections (ESGLI) protocol. Only 2/62 (3.2%) respiratory samples were culture-positive. Amplification and sequencing of Nested-SBT genes were successfully performed in 57/62 samples (91.9%). The seven target genes were characterised in 39/57 (68.4%) respiratory samples, and the complete sequence type (ST) was obtained. The mip gene was the most frequently amplified and sequenced. Nested-SBT is a useful method for epidemiological studies in culture-negative samples, achieving a 28.7-fold improvement over the results of culture studies and reducing the time needed to obtain molecular epidemiological results.
Experimental Demonstration on Quantum Sensitivity to Available Information in Decision Making
Authors: Lee Joong-Sung , Bang Jeongho , Lee Jinhyoung , Lee Kwang-Geol 
Published: January 2019

AbstractWe present an experimental illustration on the quantum sensitivity of decision making machinery. In the decision making process, we consider the role of available information, say hint, whether it influences the optimal choices. To the end, we consider a machinery method of decision making in a probabilistic way. Our main result shows that in decision making process our quantum machine is more highly sensitive than its classical counterpart to the hints we categorize into “good” and “poor”. This quantum feature originates from the quantum superposition involved in the decision making process. We also show that the quantum sensitivity persists before the quantum superposition is completely destroyed.
Gut microbiota-mediated Gene-Environment interaction in the TashT mouse model of Hirschsprung disease
Authors: Touré Aboubacrine Mahamane , Landry Mathieu , Souchkova Ouliana , Kembel Steven W. , Pilon Nicolas 
Published: January 2019

AbstractBased on the bilateral relationship between the gut microbiota and formation/function of the enteric nervous system (ENS), we sought to determine whether antibiotics-induced dysbiosis might impact the expressivity of genetically-induced ENS abnormalities. To address this, we took advantage of the TashT mouse model of Hirschsprung disease, in which colonic aganglionosis and hypoganglionosis are both much more severe in males. These defects result into two male-biased colon motility phenotypes: either megacolon that is lethal around weaning age or chronic constipation in adults, the latter being also associated with an increased proportion of nitrergic neurons in the distal ENS. Induction of dysbiosis using a cocktail of broad-spectrum antibiotics specifically impacted the colonic ENS of TashTTg/Tg mice in a stage-dependent manner. It further decreased the neuronal density at post-weaning age and differentially modulated the otherwise increased proportion of nitrergic neurons, which appeared normalized around weaning age and further increased at post-weaning age. These changes delayed the development of megacolon around weaning age but led to premature onset of severe constipation later on. Finally, local inhibition of nitric oxide signaling improved motility and prevented death by megacolon. We thus conclude that exposure to antibiotics can negatively influence the expressivity of a genetically-induced enteric neuropathy.
Optimal composition of the poly(triarylamine)-based polymer composite to maximize photorefractive performance
Authors: Masumura Kento , Nakanishi Ikumi , Van Thi Khuat Khanh , Kinashi Kenji , Sakai Wataru , Tsutsumi Naoto 
Published: January 2019

AbstractA holographic display system requires the external diffraction efficiency to be greater than 10% and four orders of magnitude of sensitivity for practical usage. To achieve such requirements, the photorefractive (PR) performance of PR composite based on poly[bis(2,4,6-trimethylpheneyl)amine] (PTAA) has been investigated. In the present report, the change of the content of PTAA as a photoconductive polymer, (2,4,6-trimethylphenyl)diphenylamine (TAA) as a photoconductive plasticizer, and second trap agent bathophenanthroline (BPhen) reasonably optimized the PR response time and external diffraction efficiency. High sensitivity of 1851 cm2 J−1 with response time of 494 μs and external diffraction efficiency of 23.9% were achieved at 532 nm and 60 V μm−1 by reducing the content of PTAA and increasing the contents of TAA and BPhen. Decreasing the amount of PTAA and increasing the contents of TAA and BPhen lowered the absorption coefficient, resulting in the high external diffraction efficiency. The narrower distribution of the electronic density of states (DOS) for PTAA/TAA (43.5/20 and 33.5/30) also contributed to the shorter PR response time of hundreds of microseconds.
Development of a peptide-siRNA nanocomplex targeting NF- κB for efficient cartilage delivery
Authors: Yan Huimin , Duan Xin , Pan Hua , Akk Antonina , Sandell Linda J. , Wickline Samuel A. , Rai Muhammad Farooq , Pham Christine T. N. 
Published: January 2019

AbstractDelivery of therapeutic small interfering RNAs (siRNAs) in an effective dose to articular cartilage is very challenging as the cartilage dense extracellular matrix renders the chondrocytes inaccessible, even to intra-articular injections. Herein, we used a self-assembling peptidic nanoparticle (NP) platform featuring a cell penetrating peptide complexed to NF-κB p65 siRNA. We show that it efficiently and deeply penetrated human cartilage to deliver its siRNA cargo up to a depth of at least 700 μm. To simulate osteoarthritis in vitro, human articular cartilage explants were placed in culture and treated with IL-1β, a cytokine with known cartilage catabolic and pro-inflammatory effects. Exposure of peptide-siRNA NP to cartilage explants markedly suppressed p65 activation, an effect that persisted up to 3 weeks after an initial 48 h exposure to NP and in the presence of continuous IL-1β stimulation. Suppression of IL-1β-induced p65 activity attenuated chondrocyte apoptosis and maintained cartilage homeostasis. These findings confirm our previous in vivo studies in a murine model of post-traumatic osteoarthritis and suggest that the ability of peptide-siRNA NP to specifically modulate NF-κB pathway, a central regulator of the inflammatory responses in chondrocytes, may potentially mitigate the progression of cartilage degeneration.
Copepod manipulation of oil droplet size distribution
Authors: Uttieri Marco , Nihongi Ai , Hinow Peter , Motschman Jeffrey , Jiang Houshuo , Alcaraz Miquel , Strickler J. Rudi 
Published: January 2019

AbstractOil spills are one of the most dangerous sources of pollution in aquatic ecosystems. Owing to their pivotal position in the food web, pelagic copepods can provide crucial intermediary transferring oil between trophic levels. In this study we show that the calanoidParacartia granican actively modify the size-spectrum of oil droplets. Direct manipulation through the movement of the feeding appendages and egestion work in concert, splitting larger droplets (Ø = 16 µm) into smaller ones (Ø = 4–8 µm). The copepod-driven change in droplet size distribution can increase the availability of oil droplets to organisms feeding on smaller particles, sustaining the transfer of petrochemical compounds among different compartments. These results raise the curtain on complex small-scale interactions which can promote the understanding of oil spills fate in aquatic ecosystems.
The bacterial MrpORP is a novel Mrp/NBP35 protein involved in iron-sulfur biogenesis
Authors: Pardoux Romain , Fiévet Anouchka , Carreira Cíntia , Brochier-Armanet Céline , Valette Odile , Dermoun Zorah , Py Béatrice , Dolla Alain , Pauleta Sofia R. , Aubert Corinne 
Published: January 2019

AbstractDespite recent advances in understanding the biogenesis of iron-sulfur (Fe-S) proteins, most studies focused on aerobic bacteria as model organisms. Accordingly, multiple players have been proposed to participate in the Fe-S delivery step to apo-target proteins, but critical gaps exist in the knowledge of Fe-S proteins biogenesis in anaerobic organisms. Mrp/NBP35 ATP-binding proteins are a subclass of the soluble P-loop containing nucleoside triphosphate hydrolase superfamily (P-loop NTPase) known to bind and transfer Fe-S clusters in vitro. Here, we report investigations of a novel atypical two-domain Mrp/NBP35 ATP-binding protein named MrpORP associating a P-loop NTPase domain with a dinitrogenase iron-molybdenum cofactor biosynthesis domain (Di-Nase). Characterization of full length MrpORP, as well as of its two domains, showed that both domains bind Fe-S clusters. We provide in vitro evidence that the P-loop NTPase domain of the MrpORP can efficiently transfer its Fe-S cluster to apo-target proteins of the ORange Protein (ORP) complex, suggesting that this novel protein is involved in the maturation of these Fe-S proteins. Last, we showed for the first time, by fluorescence microscopy imaging a polar localization of a Mrp/NBP35 protein.
Can enzyme proximity accelerate cascade reactions?
Authors: Kuzmak Andrij , Carmali Sheiliza , von Lieres Eric , Russell Alan J. , Kondrat Svyatoslav 
Published: January 2019

AbstractThe last decade has seen an exponential expansion of interest in conjugating multiple enzymes of cascades in close proximity to each other, with the overarching goal being to accelerate the overall reaction rate. However, some evidence has emerged that there is no effect of proximity channeling on the reaction velocity of the popular GOx-HRP cascade, particularly in the presence of a competing enzyme (catalase). Herein, we rationalize these experimental results quantitatively. We show that, in general, proximity channeling can enhance reaction velocity in the presence of competing enzymes, but in steady state a significant enhancement can only be achieved for diffusion-limited reactions or at high concentrations of competing enzymes. We provide simple equations to estimate the effect of channeling quantitatively and demonstrate that proximity can have a more pronounced effect under crowding conditions in vivo, particularly that crowding can enhance the overall rates of channeled cascade reactions.
A role for miR-132 in learned safety
Authors: Ronovsky Marianne , Zambon Alice , Cicvaric Ana , Boehm Vincent , Hoesel Bastian , Moser Bernhard A. , Yang Jiaye , Schmid Johannes A. , Haubensak Wulf E. , Monje Francisco J. , Pollak Daniela D. 
Published: January 2019

AbstractLearned safety is a fear inhibitory mechanism, which regulates fear responses, promotes episodes of safety and generates positive affective states. Despite its potential as experimental model for several psychiatric illnesses, including post-traumatic stress disorder and depression, the molecular mechanisms of learned safety remain poorly understood, We here investigated the molecular mediators of learned safety, focusing on the characterization of miRNA expression in the basolateral amygdala (BLA). Comparing levels of 22 miRNAs in learned safety and learned fear trained mice, six safety-related miRNAs, including three members of the miR-132/-212 family, were identified. A gain-of-function approach based upon in-vivo transfection of a specific miRNA mimic, and miR-132/212 knock-out mice as loss-of-function tool were used in order to determine the relevance of miR-132 for learned safety at the behavioral and the neuronal functional levels. Using a designated bioinformatic approach, PTEN and GAT1 were identified as potential novel miR-132 target genes and further experimentally validated. We here firstly provide evidence for a regulation of amygdala miRNA expression in learned safety and propose miR-132 as signature molecule to be considered in future preclinical and translational approaches testing the transdiagnostic relevance of learned safety as intermediate phenotype in fear and stress-related disorders.
Immunoinformatic and systems biology approaches to predict and validate peptide vaccines against Epstein–Barr virus (EBV)
Authors: Ali Arif , Khan Abbas , Kaushik Aman Chandra , Wang Yanjie , Ali Syed Shujait , Junaid Muhammad , Saleem Shoaib , Cho William C. S. , Mao Xueying , Wei Dong-Qing 
Published: January 2019

AbstractEpstein–Barr virus (EBV), also known as human herpesvirus 4 (HHV-4), is a member of the Herpesviridae family and causes infectious mononucleosis, Burkitt’s lymphoma, and nasopharyngeal carcinoma. Even in the United States of America, the situation is alarming, as EBV affects 95% of the young population between 35 and 40 years of age. In this study, both linear and conformational B-cell epitopes as well as cytotoxic T-lymphocyte (CTL) epitopes were predicted by using the ElliPro and NetCTL.1.2 webservers for EBV proteins (GH, GL, GB, GN, GM, GP42 and GP350). Molecular modelling tools were used to predict the 3D coordinates of peptides, and these peptides were then docked against the MHC molecules to obtain peptide-MHC complexes. Studies of their post-docking interactions helped to select potential candidates for the development of peptide vaccines. Our results predicted a total of 58 T-cell epitopes of EBV; where the most potential were selected based on their TAP, MHC binding and C-terminal Cleavage score. The top most peptides were subjected to MD simulation and stability analysis. Validation of our predicted epitopes using a 0.45 µM concentration was carried out by using a systems biology approach. Our results suggest a panel of epitopes that could be used to immunize populations to protect against multiple diseases caused by EBV.
Fibrogenic Gene Expression in Hepatic Stellate Cells Induced by HCV and HIV Replication in a Three Cell Co-Culture Model System
Authors: Akil Abdellah , Endsley Mark , Shanmugam Saravanabalaji , Saldarriaga Omar , Somasunderam Anoma , Spratt Heidi , Stevenson Heather L. , Utay Netanya S. , Ferguson Monique , Yi MinKyung 
Published: January 2019

AbstractRetrospective studies indicate that co-infection of hepatitis C virus (HCV) and human immunodeficiency virus (HIV) accelerates hepatic fibrosis progression. We have developed a co-culture system (MLH) comprising primary macrophages, hepatic stellate cells (HSC, LX-2), and hepatocytes (Huh-7), permissive for active replication of HCV and HIV, and assessed the effect of these viral infections on the phenotypic changes and fibrogenic gene expression in LX-2 cells. We detected distinct morphological changes in LX-2 cells within 24 hr post-infection with HCV, HIV or HCV/HIV in MLH co-cultures, with migration enhancement phenotypes. Human fibrosis microarrays conducted using LX-2 cell RNA derived from MLH co-culture conditions, with or without HCV and HIV infection, revealed novel insights regarding the roles of these viral infections on fibrogenic gene expression in LX-2 cells. We found that HIV mono-infection in MLH co-culture had no impact on fibrogenic gene expression in LX-2 cells. HCV infection of MLH co-culture resulted in upregulation (>1.9x) of five fibrogenic genes including CCL2, IL1A, IL1B, IL13RA2 and MMP1. These genes were upregulated by HCV/HIV co-infection but in a greater magnitude. Conclusion: Our results indicate that HIV-infected macrophages accelerate hepatic fibrosis during HCV/HIV co-infection by amplifying the expression of HCV-dependent fibrogenic genes in HSC.
Attenuation of murine sclerodermatous models by the selective S1P1 receptor modulator cenerimod
Authors: Kano Miyu , Kobayashi Tadahiro , Date Mutsumi , Tennichi Momoko , Hamaguchi Yasuhito , Strasser Daniel S , Takehara Kazuhiko , Matsushita Takashi 
Published: January 2019

AbstractSphingosine-1-phosphate (S1P), a lipid mediator, regulates lymphocyte migration between lymphoid tissue and blood. Furthermore, S1P participates in several physiological phenomena including angiogenesis, inflammation, immune regulation, and neurotransmitter release. Moreover, S1P/S1P receptor signaling involves in systemic sclerosis (SSc) pathogenesis. This study aimed to investigate whether the selective S1P1receptor modulator cenerimod attenuates murine sclerodermatous models. Cenerimod was orally administered to murine sclerodermatous chronic graft versus host disease (Scl-cGVHD) mice, either from day 0 to 42 or day 22 to 42 after bone marrow transplantation. Bleomycin-induced SSc model mice were administered cenerimod from day 0 to 28. Early cenerimod administration inhibited, and delayed cenerimod administration attenuated skin and lung fibrosis in Scl-cGVHD mice. Cenerimod suppressed the infiltration of CD4+T cells, CD8+T cells, and CD11b+cells into the inflamed skin of Scl-cGVHD mice as opposed to control mice. In contrast, cenerimod increased the frequency of regulatory T cells in the spleen and skin of Scl-cGVHD mice. Additionally, cenerimod attenuated the mRNA expression of extracellular matrix and fibrogenic cytokines in the skin. Furthermore, cenerimod attenuated bleomycin-induced fibrosis in the skin and lung. Hence, the selective S1P1receptor modulator cenerimod is a promising candidate for treating patients with SSc and Scl-cGVHD.
Reliable low-temperature die attach process using Ag/Sn/Ag sandwich structure for high-temperature semiconductor devices
Authors: Choi Jinseok , Choi Gab Soo , An Sung Jin 
Published: January 2019

AbstractA low-cost and eco-friendly die attach process for high temperatures should be developed owing to the expansion of the field of high-temperature applications, such as high-power and high-frequency semiconductors. Pb-based and Au-based systems have been used as conventional die attach materials for high-temperature devices. However, these materials exhibit environmental problems and are expensive. Here, we show that the die attach process using the backside metal of the Ag/Sn/Ag sandwich structure is successfully developed for the mass production of Si devices. It has a low-temperature bonding process (235 °C), a high remelting temperature (above 400 °C), and rapid bonding time (20 ms). In addition, it exhibits better properties than Au-12Ge and Pb-10Sn backside metals, which are conventional materials for the high-temperature die attach process. After the die bonding process, various reliability tests of Si devices with the Ag/Sn/Ag backside metal structure were performed.
The gut microbiota heterogeneity and assembly changes associated with the IBD
Authors: Sun Yang , Li Lianwei , Xia Yao , Li Wendy , Wang Kunhua , Wang Lan , Miao Yinglei , Ma Sam 
Published: January 2019

AbstractInflammatory bowel disease (IBD) is an immunologically mediated disease and may be caused by abnormal immunological response to gut microbes. Although several studies on the ecological changes associated with IBD, such as community diversities, were reported, no previous studies have investigated the changes in the spatial heterogeneity and the mechanism of community assembly of the gut microbiota associated with IBD. In the present study, we first applied the Taylor’s power law extensions to compare the community spatial heterogeneity between the gut microbial communities of the IBD patients and those of the healthy individuals. We found that the community spatial heterogeneity of gut microbiota in IBD patients is slightly lower than in the healthy individuals. This finding suggests that IBD may lower the spatial heterogeneity of gut microbiota, possibly via lowering the abundance of dominant species. We further applied the neutral theory of biodiversity to comparatively investigate the community assembly and diversity maintenance of the gut microbiota with and without IBD, and our application suggested that deterministic factors such as host immunity should be dominant forces shaping gut microbiota assembly, and diseases such as IBD may not be strong enough to change the trend set by the deterministic host factors.
Alternative Face-on Thin Film Structure of Pentacene
Authors: Shioya Nobutaka , Murdey Richard , Nakao Kazuto , Yoshida Hiroyuki , Koganezawa Tomoyuki , Eda Kazuo , Shimoaka Takafumi , Hasegawa Takeshi 
Published: January 2019

AbstractPentacene attracts a great deal of attention as a basic material used in organic thin-film transistors for many years. Pentacene is known to form a highly ordered structure in a thin film, in which the molecular long axis aligns perpendicularly to the substrate surface, i.e., end-on orientation. On the other hand, the face-on oriented thin film, where the molecular plane is parallel to the substrate, has never been found on an inert substrate represented by SiO2. As a result, the face-on orientation has long been believed to be generated only on specific substrates such as a metal single crystal. In the present study, the face-on orientation grown on a SiO2 surface has first been identified by means of visible and infrared p-polarized multiple-angle incidence resolution spectrometry (pMAIRS) together with two-dimensional grazing incidence X-ray diffraction (2D-GIXD). The combination of the multiple techniques readily reveals that the face-on phase is definitely realized as the dominant component. The face-on film is obtained when the film growth is kinetically restricted to be prevented from transforming into the thermodynamically stable structure, i.e., the end-on orientation. This concept is useful for controlling the molecular orientation in general organic semiconductor thin films.
Investigation of multiple adsorption mechanisms for efficient removal of ofloxacin from water using lignin-based adsorbents
Authors: Gao Boqiang , Li Pei , Yang Ran , Li Aimin , Yang Hu 
Published: January 2019

AbstractTwo series of lignin (LN)-based adsorbents, namely, cross-linked lignin (LNEs) with different crosslinking densities and carboxymethyl cross-linked lignin (LNECs) with various degrees of carboxymethyl substitution, were prepared to remove ofloxacin (OFL), a popular fluoroquinolone (FQ) antibiotic, from water. LNEs and LNECs exhibited satisfactory performance in OFL adsorption. Both of them had high adsorption capacity (the maximum contribution of 0.828 mmol/g), good anti-interference to some inorganic salts, and efficient regeneration and reuse performance. The crosslinking density and degree of carboxymethyl substitution strongly affected the content and distribution of oxygen-containing groups in these LN-based adsorbents, which played important roles in OFL adsorption. The pH dependencies of the adsorption performance of LNEs and LNECs indicated the involvement of multiple adsorption mechanisms, including hydrogen bond, electrostatic attraction, π-π electron–donor–acceptor interactions, and negative charge-assisted hydrogen bond. Different mechanisms were dominant under various pH levels, in a near neutral pH, the synergistic effect of electrostatic attraction and π-π interaction allows LINEs and LINECs to reach maximum adsorption capacity. Five FQs with similar structures and their two sub structural analogs were compared in terms of adsorption behavior and electrostatic potential by density functional theory using quantum chemical calculation. FQs with secondary amino groups and low π electron cloud density readily bound to LN-based adsorbents. Hence, LNEs and LNECs were efficient and environment-friendly adsorbents.