bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fibrin glue as a local drug-delivery system for bacteriophage PA5
Authors: Rubalskii Evgenii , Ruemke Stefan , Salmoukas Christina , Aleshkin Andrey , Bochkareva Svetlana , Modin Evgeny , Mashaqi Bakr , Boyle Erin C. , Boethig Dietmar , Rubalsky Maxim , Zulkarneev Eldar , Kuehn Christian , Haverich Axel 
Published: February 2019

AbstractFibrin glue has been used clinically for decades in a wide variety of surgical specialties and is now being investigated as a medium for local, prolonged drug delivery. Effective local delivery of antibacterial substances is important perioperatively in patients with implanted medical devices or postoperatively for deep wounds. However, prolonged local application of antibiotics is often not possible or simply inadequate. Biofilm formation and antibiotic resistance are also major obstacles to antibacterial therapy. In this paper we test the biocompatibility of bacteriophages incorporated within fibrin glue, track the release of bacteriophages from fibrin scaffolds, and measure the antibacterial activity of released bacteriophages. Fibrin glue polymerized in the presence of the PA5 bacteriophage released high titers of bacteriophages during 11 days of incubation in liquid medium. Released PA5 bacteriophages were effective in killing Pseudomonas aeruginosa PA01. Overall, our results show that fibrin glue can be used for sustained delivery of bacteriophages and this strategy holds promise for many antibacterial applications.
Improving solutions by embedding larger subproblems in a D-Wave quantum annealer
Authors: Okada Shuntaro , Ohzeki Masayuki , Terabe Masayoshi , Taguchi Shinichiro 
Published: February 2019

AbstractQuantum annealing is a heuristic algorithm that solves combinatorial optimization problems, and D-Wave Systems Inc. has developed hardware implementation of this algorithm. However, in general, we cannot embed all the logical variables of a large-scale problem, since the number of available qubits is limited. In order to handle a large problem, has been proposed as a method for partitioning the original large problem into subproblems that are embeddable in the D-Wave quantum annealer, and it then iteratively optimizes the subproblems using the quantum annealer. Multiple logical variables in the subproblem are simultaneously updated in this iterative solver, and using this approach we expect to obtain better solutions than can be obtained by conventional local search algorithms. Although embedding of large subproblems is essential for improving the accuracy of solutions in this scheme, the size of the subproblems are small in since the subproblems are basically embedded by using an embedding of a complete graph even for sparse problem graphs. This means that the resource of the D-Wave quantum annealer is not exploited efficiently. In this paper, we propose a fast algorithm for embedding larger subproblems, and we show that better solutions are obtained efficiently by embedding larger subproblems.
Propagation and self-healing properties of Bessel-Gaussian beam carrying orbital angular momentum in an underwater environment
Authors: Zhao Shengmei , Zhang Wenhao , Wang Le , Li Wei , Gong Longyan , Cheng Weiwen , Chen Hanwu , Gruska Jozef 
Published: February 2019

AbstractIn this paper, we report on experimental demonstration of the propagation and self-healing property of Bessel-Gaussian (BG) beam carrying orbital angular momentum (OAM) in an underwater environment. Especially, the effects of topological charge, temperature gradient, and salinity on the transmission and self-reconstruction of BG beam in underwater turbulence are analyzed. The results show that the detection probabilities both for propagation and self-healing greatly decrease with temperature gradient, and gradually decrease with salinity. BG beam has a self-healing property in the underwater environment when the obstruction is quite small. The detection probability greatly decreases with obstruction size, while it gradually decreases with salinity fluctuations for different obstruction sizes. For the same blockage ratio, the smaller topological charge of BG beam is, the better self-healing characteristics the BG beam has.
Litter removal reduced soil nitrogen mineralization in repeated freeze-thaw cycles
Authors: Yang Yulian , Zhang Li , Wei Xinyu , Chen Ya , Yang Wanqin , Tan Bo , Yue Kai , Ni Xiangyin , Wu Fuzhong 
Published: February 2019

AbstractRepeated freeze-thaw cycles (FTCs) can alter the relationships between plant litter and soil nitrogen (N) mineralization in subalpine ecosystems, but little information is available about the underlying mechanisms. Therefore, a controlled soil incubation experiment was carried out to study the effects of litter removal on soil N mineralization during FTCs, and the results indicated that FTCs promoted soil N mineralization more than the continuously frozen or nonfrozen condition did. Litter removal promoted soil ammonium N (NH4+-N) and dissolved organic N (DON) as well as the cumulative N mineralization (CNM) and ammonification, but it reduced the soil microbial biomass N (MBN) in the early stage of FTCs. With an increasing number of FTCs, litter removal significantly reduced the CNM but increased the soil MBN. The modified first-order kinetics model was verified under incubation conditions and predicted a lower soil N mineralization rate in FTCs with litter removal. In addition, the dominant factor impacting soil N mineralization was soil NO3−-N, and soil MBN had a greater influence on soil N mineralization when litter remained than when it was removed. These results further clarify the mechanism driving the effect of plant residues on soil N cycling.
The role of diffusion-driven pure climb creep on the rheology of bridgmanite under lower mantle conditions
Authors: Reali Riccardo , Van Orman James A. , Pigott Jeffrey S. , Jackson Jennifer M. , Boioli Francesca , Carrez Philippe , Cordier Patrick 
Published: February 2019

AbstractThe viscosity of Earth’s lower mantle is poorly constrained due to the lack of knowledge on some fundamental variables that affect the deformation behaviour of its main mineral phases. This study focuses on bridgmanite, the main lower mantle constituent, and assesses its rheology by developing an approach based on mineral physics. Following and revising the recent advances in this field, pure climb creep controlled by diffusion is identified as the key mechanism driving deformation in bridgmanite. The strain rates of this phase under lower mantle pressures, temperatures and stresses are thus calculated by constraining diffusion and implementing a creep theoretical model. The viscosity of MgSiO3 bridgmanite resulting from pure climb creep is consequently evaluated and compared with the viscosity profiles available from the literature. We show that the inferred variability of viscosity in these profiles can be fully accounted for with the chosen variables of our calculation, e.g., diffusion coefficients, vacancy concentrations and applied stresses. A refinement of these variables is advocated in order to further constrain viscosity and match the observables.
Carbide-free one-zone sulfurization method grows thin MoS2 layers on polycrystalline CVD diamond
Authors: Sojková Michaela , Siffalovic Peter , Babchenko Oleg , Vanko Gabriel , Dobročka Edmund , Hagara Jakub , Mrkyvkova Nada , Majková Eva , Ižák Tibor , Kromka Alexander , Hulman Martin 
Published: February 2019

AbstractThe last few decades faced on the fabrication of advanced engineering materials involving also different composites. Here, we report on the fabrication of few-layer molybdenum disulfide on top of thin polycrystalline diamond substrates with a high specific surface area. In the method, pre-deposited molybdenum coatings were sulfurized in a one-zone furnace at ambient pressure. As-prepared MoS2 layers were characterized by several techniques including grazing-incidence wide-angle X-ray scattering, atomic force microscopy, scanning electron microscopy, Raman spectroscopy and X-ray photoelectron spectroscopy. We found out that the initial thickness of Mo films determined the final c-axis crystallographic orientation of MoS2 layer as previously observed on other substrates. Even though it is well-known that Mo diffuses into diamond at elevated temperatures, the competing sulfurization applied effectively suppressed the diffusion and a chemical reaction between molybdenum and diamond. In particular, a Mo2C layer does not form at the interface between the Mo film and diamond substrate. The combination of diamond high specific surface area along with a controllable layer orientation might be attractive for applications, such as water splitting or water disinfection.
Towards calibration-invariant spectroscopy using deep learning
Authors: Chatzidakis M. , Botton G. A. 
Published: February 2019

AbstractThe interaction between matter and electromagnetic radiation provides a rich understanding of what the matter is composed of and how it can be quantified using spectrometers. In many cases, however, the calibration of the spectrometer changes as a function of time (such as in electron spectrometers), or the absolute calibration may be different between different instruments. Calibration differences cause difficulties in comparing the absolute position of measured emission or absorption peaks between different instruments and even different measurements taken at different times on the same instrument. Present methods of avoiding this issue involve manual feature extraction of the original signal or qualitative analysis. Here we propose automated feature extraction using deep convolutional neural networks to determine the class of compound given only the shape of the spectrum. We classify three unique electronic environments of manganese (being relevant to many battery materials applications) in electron energy loss spectroscopy using 2001 spectra we collected in addition to testing on spectra from different instruments. We test a variety of commonly used neural network architectures found in the literature and propose a new fully convolutional architecture with improved translation-invariance which is immune to calibration differences.
Serotonin Transporter Deficiency is Associated with Dysbiosis and Changes in Metabolic Function of the Mouse Intestinal Microbiome
Authors: Singhal Megha , Turturice Benjamin A. , Manzella Christopher R. , Ranjan Ravi , Metwally Ahmed A. , Theorell Juliana , Huang Yue , Alrefai Waddah A. , Dudeja Pradeep K. , Finn Patricia W. , Perkins David L. , Gill Ravinder K. 
Published: February 2019

AbstractSerotonin transporter (SERT) plays a critical role in regulating extracellular availability of serotonin (5-HT) in the gut and brain. Mice with deletion of SERT develop metabolic syndrome as they age. Changes in the gut microbiota are being increasingly implicated in Metabolic Syndrome and Diabetes. To investigate the relationship between the gut microbiome and SERT, this study assessed the fecal and cecal microbiome profile of 11 to 12 week-old SERT+/+ and SERT−/− mice. Microbial DNA was isolated, processed for metagenomics shotgun sequencing, and taxonomic and functional profiles were assessed. 34 differentially abundant bacterial species were identified between SERT+/+ and SERT−/−. SERT−/− mice displayed higher abundances of Bacilli species including genera Lactobacillus, Streptococcus, Enterococcus, and Listeria. Furthermore, SERT−/− mice exhibited significantly lower abundances of Bifidobacterium species and Akkermansia muciniphilia. Bacterial community structure was altered in SERT−/− mice. Differential abundance of bacteria was correlated with changes in host gene expression. Bifidobacterium and Bacilli species exhibited significant associations with host genes involved in lipid metabolism pathways. Our results show that SERT deletion is associated with dysbiosis similar to that observed in obesity. This study contributes to the understanding as to how changes in gut microbiota are associated with metabolic phenotype seen in SERT deficiency.
Real-time imaging of senescence in tumors with DNA damage
Authors: Wang Ying , Liu Jun , Ma Xiaowei , Cui Chao , Deenik Philip R. , Henderson Paul K. P. , Sigler Ashton L. , Cui Lina 
Published: February 2019

AbstractDetection of cellular senescence is important not only in the study of senescence in various biological systems, but also in various practical applications such as image-guided surgical removal of senescent cells, as well as the monitoring of drug-responsiveness during cancer therapies. Due to the lack of suitable imaging probes for senescence detection, particularly in living subjects, we have developed an activatable near-infrared (NIR) molecular probe with far-red excitation, NIR emission, and high “turn-on” ratio upon senescence-associated β-galactosidase (SABG) activation. We present here the first successful demonstration of NIR imaging of DNA damage-induced senescence both in vitro and in human tumor xenograft models.
Positive and negative contexts predict duration of pig vocalisations
Authors: Friel Mary , Kunc Hansjoerg P. , Griffin Kym , Asher Lucy , Collins Lisa M. 
Published: February 2019

AbstractEmotions are mental states occurring in response to external and internal stimuli and thus form an integral part of an animal’s behaviour. Emotions can be mapped in two dimensions based on their arousal and valence. Whilst good indicators of arousal exist, clear indicators of emotional valence, particularly positive valence, are still rare. However, positively valenced emotions may play a crucial role in social interactions in many species and thus, an understanding of how emotional valence is expressed is needed. Vocalisations are a potential indicator of emotional valence as they can reflect the internal state of the caller. We experimentally manipulated valence, using positive and negative cognitive bias trials, to quantify changes in pig vocalisations. We found that grunts were shorter in positive trials than in negative trials. Interestingly, we did not find differences in the other measured acoustic parameters between the positive and negative contexts as reported in previous studies. These differences in results suggest that acoustic parameters may differ in their sensitivity as indicators of emotial valence. However, it is important to understand how similar contexts are, in terms of their valence, to be able to fully understand how and when acoustic parameters reflect emotional states.
High sensitivity detection of extracellular vesicles immune-captured from urine by conventional flow cytometry
Authors: Campos-Silva Carmen , Suárez Henar , Jara-Acevedo Ricardo , Linares-Espinós Estefanía , Martinez-Piñeiro Luis , Yáñez-Mó María , Valés-Gómez Mar 
Published: February 2019

AbstractExtracellular vesicles (EVs) provide an invaluable tool to analyse physiological processes because they transport, in biological fluids, biomolecules secreted from diverse tissues of an individual. EV biomarker detection requires highly sensitive techniques able to identify individual molecules. However, the lack of widespread, affordable methodologies for high-throughput EV analyses means that studies on biomarkers have not been done in large patient cohorts. To develop tools for EV analysis in biological samples, we evaluated here the critical parameters to optimise an assay based on immunocapture of EVs followed by flow cytometry. We describe a straightforward method for EV detection using general EV markers like the tetraspanins CD9, CD63 and CD81, that allowed highly sensitive detection of urinary EVs without prior enrichment. In proof-of-concept experiments, an epithelial marker enriched in carcinoma cells, EpCAM, was identified in EVs from cell lines and directly in urine samples. However, whereas EVs isolated from 5–10 ml of urine were required for western blot detection of EpCAM, only 500 μl of urine were sufficient to visualise EpCAM expression by flow cytometry. This method has the potential to allow any laboratory with access to conventional flow cytometry to identify surface markers on EVs, even non-abundant proteins, using minimally processed biological samples.
Understanding the role of distance, direction and cue salience in an associative model of landmark learning
Authors: Commins Sean , Fey Dirk 
Published: February 2019

AbstractNavigation and spatial memory relies on the ability to use and recall environmental landmarks relative to important locations. Such learning is thought to result from the strengthening of associations between the goal location and environmental cues. Factors that contribute to the strength of this association include cue stability, saliency and cue location. Here we combine an autoregressive random walk model, that describes goal-directed swimming behaviour, with an associative learning model to provide an integrated model of landmark learning, using the water maze task. The model allows for the contribution of each cue, the salience and the vector information provided (both distance and directional) to be separately analysed. The model suggests that direction and distance information are independent components and can influence searching patterns. Importantly, the model can also be used to simulate various experimental scenarios to understand what has been learnt in relation to the cues, thereby offering new insights into how animals navigate.
Dissecting quantitative resistance to Xanthomonas campestris pv. campestris in leaves of Brassica oleracea by QTL analysis
Authors: Iglesias-Bernabé Laura , Madloo Pari , Rodríguez Víctor Manuel , Francisco Marta , Soengas Pilar 
Published: February 2019

AbstractBlack rot, caused by the bacterium Xanthomonas campestris pv. campestris (Xcc), produces important economic losses in crops of Brassica oleracea worldwide. Resistance to race 1, the most virulent and widespread in B. oleracea, is under quantitative control. Knowledge about the genetics of this resistance would help in designing strategies to control initial stages of invasion and development of the disease. QTL analysis of the resistance in the BolTBDH mapping population was performed. Resistance was measured with five traits related to initial stages of the invasion, success of infection and spread of the pathogen. Four single-trait QTLs of resistance were found, from which one represent novel variation. After performing multi-trait QTL, we concluded that spread of Xcc is related to the size of the leaf. Individuals from the mapping population follow two different strategies to cope with the spread of the disease: reducing lesion size or maintain more area of the leaf photosynthetically active, being more tolerant to Xcc invasion. Mechanisms underlying variation for resistance may be related to different aspects of plant immunity, including the synthesis of glucosinolates and phenolics.
X-ray induced damage of B4C-coated bilayer materials under various irradiation conditions
Authors: Follath Rolf , Koyama Takahisa , Lipp Vladimir , Medvedev Nikita , Tono Kensuke , Ohashi Haruhiko , Patthey Luc , Yabashi Makina , Ziaja Beata 
Published: February 2019

AbstractIn this report, we analyse X-ray induced damage of B4C-coated bilayer materials under various irradiation geometries, following the conditions of our experiment performed at the free-electron-laser facility SACLA. We start with the discussion of structural damage in solids and damage threshold doses for the experimental system components: B4C, SiC, Mo and Si. Later, we analyze the irradiation of the experimentally tested coated bilayer systems under two different incidence conditions of a linearly polarized X-ray pulse: (i) grazing incidence, and (ii) normal incidence, in order to compare quantitatively the effect of the pulse incidence on the radiation tolerance of both systems. For that purpose, we propose a simple theoretical model utilizing properties of hard X-ray propagation and absorption in irradiated materials and of the following electron transport. With this model, we overcome the bottleneck problem of large spatial scales, inaccessible for any existing first-principle-based simulation tools due to their computational limitations for large systems. Predictions for damage thresholds obtained with the model agree well with the available experimental data. In particular, they confirm that two coatings tested: 15 nm B4C/20 nm Mo on silicon wafer and 15 nm B4C/50 nm SiC on silicon wafer can sustain X-ray irradiation at the fluences up to ~10 μJ/μm2, when exposed to linearly polarized 10 keV X-ray pulse at a grazing incidence angle of 3 mrad. Below we present the corresponding theoretical analysis. Potential applications of our approach for design and radiation tolerance tests of multilayer components within X-ray free-electron-laser optics are indicated.
Experimental Tracheal Replacement Using 3-dimensional Bioprinted Artificial Trachea with Autologous Epithelial Cells and Chondrocytes
Authors: Park Jae-Hyun , Yoon Jeong-Kee , Lee Jung Bok , Shin Young Min , Lee Kang-Woog , Bae Sang-Woo , Lee JunHee , Yu JunJie , Jung Cho-Rok , Youn Young-Nam , Kim Hwi-Yool , Kim Dae-Hyun 
Published: February 2019

AbstractVarious treatment methods for tracheal defects have been attempted, such as artificial implants, allografts, autogenous grafts, and tissue engineering; however, no perfect method has been established. We attempted to create an effective artificial trachea via a tissue engineering method using 3D bio-printing. A multi-layered scaffold was fabricated using a 3D printer. Polycaprolactone (PCL) and hydrogel were used with nasal epithelial and auricular cartilage cells in the printing process. An artificial trachea was transplanted into 15 rabbits and a PCL scaffold without the addition of cells was transplanted into 6 rabbits (controls). All animals were followed up with radiography, CT, and endoscopy at 3, 6, and 12 months. In the control group, 3 out of 6 rabbits died from respiratory symptoms. Surviving rabbits in control group had narrowed tracheas due to the formation of granulation tissue and absence of epithelium regeneration. In the experimental group, 13 of 15 animals survived, and the histologic examination confirmed the regeneration of epithelial cells. Neonatal cartilage was also confirmed at 6 and 12 months. Our artificial trachea was effective in the regeneration of respiratory epithelium, but not in cartilage regeneration. Additional studies are needed to promote cartilage regeneration and improve implant stability.
Silver diamine fluoride versus sodium fluoride for arresting dentine caries in children: a systematic review and meta-analysis
Authors: Trieu Alice , Mohamed Ahmed , Lynch Edward 
Published: February 2019

AbstractDental caries can compromise quality of life and is associated with demineralization of tooth structure by organic acids produced by microorganisms. This study systematically reviewed the dentine caries arrest capabilities of silver diamine fluoride (SDF) and sodium fluoride (NaF). A comprehensive search strategy was developed to identify the relevant publications in electronic databases and hand searched journals and reviews (to March 2018). By applying strict inclusion and exclusion criteria, only six papers (two randomized controlled trials, two follow-up articles and two secondary statistical analysis studies) were considered for full text qualitative and quantitative assessment. The included studies were critically appraised and statistically evaluated. Only four articles were considered for meta-analysis, as the other two were secondary analyses of included studies. When comparing the caries arrest lesions of SDF and NaF, SDF was found to be statistically more effective in dentine caries arrest of primary teeth during the 18 and 30 month clinical examinations. The weighted total effect size of the differences between SDF and NaF regarding arrested caries surfaces was calculated and showed nearly double the effectiveness of SDF to NaF at 30 months. Therefore, SDF is a more effective caries management reagent than NaF. Further clinical research is needed to consolidate the findings of this systematic review.