bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mechanisms responsible for increased circulating levels of galectin-3 in cardiomyopathy and heart failure
Authors: Nguyen My-Nhan , Su Yidan , Vizi Donna , Fang Lu , Ellims Andris H. , Zhao Wei-Bo , Kiriazis Helen , Gao Xiao-Ming , Sadoshima Junichi , Taylor Andrew J. , McMullen Julie R. , Dart Anthony M. , Kaye David M. , Du Xiao-Jun 
Published: May 2018

AbstractGalectin-3 is a biomarker of heart disease. However, it remains unknown whether increase in galectin-3 levels is dependent on aetiology or disease-associated conditions and whether diseased heart releases galectin-3 into the circulation. We explored these questions in mouse models of heart disease and in patients with cardiomyopathy. All mouse models (dilated cardiomyopathy, DCM; fibrotic cardiomyopathy, ischemia-reperfusion, I/R; treatment with β-adrenergic agonist isoproterenol) showed multi-fold increases in cardiac galectin-3 expression and preserved renal function. In mice with fibrotic cardiomyopathy, I/R or isoproterenol treatment, plasma galectin-3 levels and density of cardiac inflammatory cells were elevated. These models also exhibited parallel changes in cardiac and plasma galectin-3 levels and presence of trans-cardiac galectin-3 gradient, indicating cardiac release of galectin-3. DCM mice showed no change in circulating galectin-3 levels nor trans-cardiac galectin-3 gradient or myocardial inflammatory infiltration despite a 50-fold increase in cardiac galectin-3 content. In patients with hypertrophic cardiomyopathy or DCM, plasma galectin-3 increased only in those with renal dysfunction and a trans-cardiac galectin-3 gradient was not present. Collectively, this study documents the aetiology-dependency and diverse mechanisms of increment in circulating galectin-3 levels. Our findings highlight cardiac inflammation and enhanced β-adrenoceptor activation in mediating elevated galectin-3 levels via cardiac release in the mechanism.
Improved fermentation efficiency of S. cerevisiae by changing glycolytic metabolic pathways with plasma agitation
Authors: Recek Nina , Zhou Renwu , Zhou Rusen , Te’o Valentino Setoa Junior , Speight Robert E. , Mozetič Miran , Vesel Alenka , Cvelbar Uros , Bazaka Kateryna , Ostrikov Kostya 
Published: May 2018

AbstractProduction of ethanol by the yeast Saccharomyces cerevisiae is a process of global importance. In these processes, productivities and yields are pushed to their maximum possible values leading to cellular stress. Transient and lasting enhancements in tolerance and performance have been obtained by genetic engineering, forced evolution, and exposure to moderate levels of chemical and/or physical stimuli, yet the drawbacks of these methods include cost, and multi-step, complex and lengthy treatment protocols. Here, plasma agitation is shown to rapidly induce desirable phenotypic changes in S. cerevisiae after a single treatment, resulting in improved conversion of glucose to ethanol. With a complex environment rich in energetic electrons, highly-reactive chemical species, photons, and gas flow effects, plasma treatment simultaneously mimics exposure to multiple environmental stressors. A single treatment of up to 10 minutes performed using an atmospheric pressure plasma jet was sufficient to induce changes in cell membrane structure, and increased hexokinase 2 activity and secondary metabolite production. These results suggest that plasma treatment is a promising strategy that can contribute to improving metabolic activity in industrial microbial strains, and thus the practicality and economics of industrial fermentations.
Improved thermoelectric performance of solid solution Cu4Sn7.5S16 through isoelectronic substitution of Se for S
Authors: Cui Jiaolin , He Tongtong , Han Zhongkang , Liu Xianglian , Du Zhengliang 
Published: May 2018

AbstractCu-Sn-S family of compounds have been considered as very competitive thermoelectric candidates in recent years due to their abundance and eco-friendliness. The first-principles calculation reveals that the density of states (DOS) increases in the vicinity of the Fermi level (Ef) upon an incorporation of Se in the Cu4Sn7.5S16−xSe
x
(x = 0–2.0) system, which indicates the occurrence of resonant states. Besides, the formation of Cu(Sn)-Se network upon the occupation of Se in S site reduces the Debye temperature from 395 K for Cu4Sn7S16 (x = 0) to 180.8 K for Cu4Sn7.5S16−xSe
x
(x = 1.0). Although the point defects mainly impact the phonon scattering, an electron-phonon interaction also bears significance in the increase in phonon scattering and the further reducion of lattice thermal conductivity at high temperatures. As a consequence, the resultant TE figure of merit (ZT) reaches 0.5 at 873 K, which is 25% higher compared to 0.4 for Cu4Sn7.5S16.
PhosContext2vec: a distributed representation of residue-level sequence contexts and its application to general and kinase-specific phosphorylation site prediction
Authors: Xu Ying , Song Jiangning , Wilson Campbell , Whisstock James C. 
Published: May 2018

AbstractPhosphorylation is the most important type of protein post-translational modification. Accordingly, reliable identification of kinase-mediated phosphorylation has important implications for functional annotation of phosphorylated substrates and characterization of cellular signalling pathways. The local sequence context surrounding potential phosphorylation sites is considered to harbour the most relevant information for phosphorylation site prediction models. However, currently there is a lack of condensed vector representation for this important contextual information, despite the presence of varying residue-level features that can be constructed from sequence homology profiles, structural information, and physicochemical properties. To address this issue, we present PhosContext2vec which is a distributed representation of residue-level sequence contexts for potential phosphorylation sites and demonstrate its application in both general and kinase-specific phosphorylation site predictions. Benchmarking experiments indicate that PhosContext2vec could achieve promising predictive performance compared with several other existing methods for phosphorylation site prediction. We envisage that PhosContext2vec, as a new sequence context representation, can be used in combination with other informative residue-level features to improve the classification performance in a number of related bioinformatics tasks that require appropriate residue-level feature vector representation and extraction. The web server of PhosContext2vec is publicly available at http://phoscontext2vec.erc.monash.edu/.
Spatially organizing biochemistry: choosing a strategy to translate synthetic biology to the factory
Authors: Jakobson Christopher M. , Tullman-Ercek Danielle , Mangan Niall M. 
Published: May 2018

AbstractNatural biochemical systems are ubiquitously organized both in space and time. Engineering the spatial organization of biochemistry has emerged as a key theme of synthetic biology, with numerous technologies promising improved biosynthetic pathway performance. One strategy, however, may produce disparate results for different biosynthetic pathways. We use a spatially resolved kinetic model to explore this fundamental design choice in systems and synthetic biology. We predict that two example biosynthetic pathways have distinct optimal organization strategies that vary based on pathway-dependent and cell-extrinsic factors. Moreover, we demonstrate that the optimal design varies as a function of kinetic and biophysical properties, as well as culture conditions. Our results suggest that organizing biosynthesis has the potential to substantially improve performance, but that choosing the appropriate strategy is key. The flexible design-space analysis we propose can be adapted to diverse biosynthetic pathways, and lays a foundation to rationally choose organization strategies for biosynthesis.
A Judgement Bias Test to Assess Affective State and Potential Therapeutics in a Rat Model of Chemotherapy-Induced Mucositis
Authors: George Rebecca P. , Barker Timothy H. , Lymn Kerry A. , Bigatton Dylan A. , Howarth Gordon S. , Whittaker Alexandra L. 
Published: May 2018

AbstractChemotherapy-induced mucositis is an extremely painful condition that occurs in 40–60% of patients undergoing chemotherapy. As mucositis currently has no effective treatment, and due to the self-limiting nature of the condition, the major treatment aims are to manage symptoms and limit pain with significance placed on improving patient quality of life. Rodent models are frequently used in mucositis research. These investigations typically assess pathological outcomes, yet fail to include a measure of affective state; the key therapeutic goal. Assessment of cognitive biases is a novel approach to determining the affective state of animals. Consequently, this study aimed to validate a cognitive bias test through a judgement bias paradigm to measure affective state in a rat model of chemotherapy-induced intestinal mucositis. Rats with intestinal mucositis demonstrated a negative affective state, which was partially ameliorated by analgesic administration, whilst healthy rats showed an optimistic response. This study concluded that the judgement bias test was able to evaluate the emotional state of rats with chemotherapy-induced mucositis. These findings provide a foundation for future refinement to the experimental design associated with the animal model that will expedite successful transitioning of novel therapeutics to clinical practice, and also improve humane endpoint implementation.
Naturally occurring a loss of a giant plasmid from Mycobacterium ulcerans subsp. shinshuense makes it non-pathogenic
Authors: Nakanaga Kazue , Ogura Yoshitoshi , Toyoda Atsushi , Yoshida Mitsunori , Fukano Hanako , Fujiwara Nagatoshi , Miyamoto Yuji , Nakata Noboru , Kazumi Yuko , Maeda Shinji , Ooka Tadasuke , Goto Masamichi , Tanigawa Kazunari , Mitarai Satoshi , Suzuki Koichi , Ishii Norihisa , Ato Manabu , Hayashi Tetsuya , Hoshino Yoshihiko 
Published: May 2018

AbstractMycobacterium ulcerans is the causative agent of Buruli ulcer (BU), a WHO-defined neglected tropical disease. All Japanese BU causative isolates have shown distinct differences from the prototype and are categorized as M. ulcerans subspecies shinshuense. During repeated sub-culture, we found that some M. shinshuense colonies were non-pigmented whereas others were pigmented. Whole genome sequence analysis revealed that non-pigmented colonies did not harbor a giant plasmid, which encodes elements needed for mycolactone toxin biosynthesis. Moreover, mycolactone was not detected in sterile filtrates of non-pigmented colonies. Mice inoculated with suspensions of pigmented colonies died within 5 weeks whereas those infected with suspensions of non-pigmented colonies had significantly prolonged survival (>8 weeks). This study suggests that mycolactone is a critical M. shinshuense virulence factor and that the lack of a mycolactone-producing giant plasmid makes the strain non-pathogenic. We made an avirulent mycolactone-deletion mutant strain directly from the virulent original.
Repeated administration of alpha-galactosylceramide ameliorates experimental lupus nephritis in mice
Authors: Uchida Takahiro , Nakashima Hiroyuki , Yamagata Akira , Ito Seigo , Ishikiriyama Takuya , Nakashima Masahiro , Seki Shuhji , Kumagai Hiroo , Oshima Naoki 
Published: May 2018

AbstractLupus nephritis is a crucial complication of systemic lupus erythematosus. In this study, we investigated the roles of mouse natural killer T (NKT) cells in lupus nephritis. From 24 weeks of age, NZB/NZW F1 mice were injected with alpha-galactosylceramide (α-GalCer) or vehicle once a week for four weeks. In the α-GalCer group, the levels of proteinuria and blood urea nitrogen were significantly lower than those in the vehicle group. The histological evaluation showed a decrease in glomerular immune complex deposits and an alleviation of podocyte injury. The proportion of NKT cells in the mononuclear cell (MNC) fraction in the α-GalCer group was significantly decreased in the liver, kidney, and spleen. The proliferation and cytokine production in α-GalCer-stimulated liver MNCs were markedly diminished in the α-GalCer group (anergy). The IFN-γ production in liver MNCs stimulated by concanavalin A or an anti-CD3 antibody did not differ between the two groups, whereas the IL-4 production was significantly lower in the α-GalCer group. In addition, the IgM production in CpG-oligodeoxynucleotide-stimulated spleen MNCs was significantly lower in the α-GalCer group. These results suggest that α-GalCer suppressed Th2 immune responses in NKT cells and B cell function, thereby slowing the progression of lupus nephritis.
Injectable cartilaginous template transformed BMSCs into vascularized bone
Authors: Feng Xiaoke , Li Zhiye , Wei Jianhua , Feng Zhihong , Wu Wei , Zhao Yimin 
Published: May 2018

AbstractRegeneration of alveolar bone for dental implant remains a major issue, partifcularly for patients suffering from severe bone adsorption and irregular socket trauma. Recapitulating embryological development is becoming an attractive approach for engineer organ or three-dimensional tissues from stem cells. In this study, we aimed to develop an injectable “cartilaginous” graft with adequate mechanical resistance and ideal bone remodelling potential. The cartilaginous graft was composed of a particulate decellularised cartilage matrix (PDCM), chondrogenically primed bone mesenchymal stem cell (BMSC) bricks (CB), and enriched platelet-rich plasma (P) gel. In immunodeficient mice, we found that angiogenesis occurred quickly inside PDCM-CB-P constructs after implantation, thereby improving tissue survival and bone formation. In rabbit tibia bone defects around implants, we confirmed that CBs not only transformed into bone tissue rapidly, but also significantly promoted bone remodelling and replacement of PDCM, thus realising osseointegration of dental implants within 3 months. In conclusion, CBs exhibited the potential for endochondral ossification in vivo, and application of a cartilaginous template composed of PDCM, CB, and P provided a minimally-invasive, “free material residual” approach to regenerate alveolar bone tissues in vivo. This method could have applications in peri-implant bone regeneration.
Role of TREM-1 in pulmonary tuberculosis patients- analysis of serum soluble TREM-1 levels
Authors: Feng Jia-Yih , Su Wei-Juin , Pan Sheng-Wei , Yeh Yi-Chen , Lin Yung-Yang , Chen Nien-Jung 
Published: May 2018

AbstractTriggering receptor expressed on myeloid cells 1 (TREM-1) amplifies inflammatory responses and is upregulated during sepsis and pulmonary infection. The association between serum soluble TREM-1 (sTREM-1) level and pulmonary tuberculosis (PTB) disease deserves investigation. In the present study, patients with PTB, latent TB infection (LTBI), and non-TB, non-LTBI subjects were prospectively enrolled and serum levels of sTREM-1, sTREM-2, and C-reactive protein (CRP) were measured. We correlated serum biomarkers and clinical presentations and treatment outcomes of PTB cases. We also utilized immunohistochemistry (IHC) to visualize TREM-1-expressing cells in lung tissues from PTB patients. A total of 86 PTB, 41 LTBI, and 20 non-TB, non-LTBI subjects were enrolled. Serum levels of sTREM-1 and CRP significantly increased in PTB patients; these higher serum levels were correlated with more advanced involvement in chest films and higher bacteria burden in sputum. In multivariate analysis, serum levels of sTREM-1 >260 pg/mL and CRP >2.6 mg/L were independent predictors for on-treatment mortality. Abundant TREM-1-expressing macrophages were identified in lung tissues from PTB samples. In conclusion, serum levels of sTREM-1 correlated with disease severity and treatment outcomes in PTB patients.
Bacterial Communities Changes during Food Waste Spoilage
Authors: Wu Shanghua , Xu Shengjun , Chen Xi , Sun Haishu , Hu Mingli , Bai Zhihui , Zhuang Guoqiang , Zhuang Xuliang 
Published: May 2018

AbstractFood waste is an important component of municipal solid waste worldwide. There are various ways to treat or utilize food waste, such as, biogas fermentation, animal feed, etc. but pathogens and mycotoxins that accumulate in the process of spoilage can present a health hazard. However, spoilage of food waste has not yet been studied, and there are no reports of the bacterial communities present in this waste. In this research, food waste was collected and placed at two different temperatures. We investigated the spoilage microbiota by using culture-independent methods and measured the possible mycotoxins may appear in the spoilage process. The results showed that lactic acid bacteria are the most important bacteria in the food waste community, regardless of the temperature. Few microbial pathogens and aflatoxins were found in the spoilage process. This suggests that if food waste is stored at a relatively low temperature and for a short duration, there will be less risk for utilization.
Categorical and Geographical Separation in Science
Authors: Sienkiewicz Julian , Soja Krzysztof , Hołyst Janusz A. , Sloot Peter M. A. 
Published: May 2018

AbstractWe study scientific collaboration at the level of universities. The scope of this study is to answer two fundamental questions: (i) can one indicate a category (i.e., a scientific discipline) that has the greatest impact on the rank of the university and (ii) do the best universities collaborate with the best ones only? Restricting ourselves to the 100 best universities from year 2009 we show how the number of publications in certain categories correlates with the university rank. Strikingly, the expected negative trend is not observed in all cases – for some categories even positive values are obtained. After applying Principal Component Analysis we observe clear categorical separation of scientific disciplines, dividing the papers into almost separate clusters connected to natural sciences, medicine and arts and humanities. Moreover, using complex networks analysis, we give hints that the scientific collaboration is still embedded in the physical space and the number of common papers decays with the geographical distance between them.
Dimethyl fumarate induces a persistent change in the composition of the innate and adaptive immune system in multiple sclerosis patients
Authors: Montes Diaz G. , Fraussen J. , Van Wijmeersch B. , Hupperts R. , Somers V. 
Published: May 2018

AbstractThe effects of dimethyl fumarate (DMF) on the immune system in multiple sclerosis (MS) are not completely elucidated. In this study, an extensive immunophenotypic analysis of innate and adaptive immune cells of DMF-treated MS patients was performed. Peripheral blood immune cell phenotypes were determined using flow cytometry in a follow-up study of 12 MS patients before, after 3 and 12 months of DMF treatment and a cross-sectional study of 25 untreated and 64 DMF-treated MS patients. Direct effects of DMF on B cells were analyzed in vitro. After 12 months of DMF treatment, percentages of monocytes, natural killer cells, naive T and B cells and transitional B cells increased. Percentages of (effector) memory T cells, (non) class-switched memory B cells and double negative B cells decreased together with CD4+ T cells expressing interferon-γ (IFN-γ), granulocyte macrophage colony-stimulating factor (GM-CSF) and interleukin-17 (IL-17). DMF treatment was fully effective as of 6 months and directly induced apoptosis and decreased expression of costimulatory CD40, antigen presentation molecule MHCII and B cell activating factor receptor (BAFFR) on B cells. DMF induced a persistent change of the immune system of MS patients, directly induced apoptosis and reduced expression of functional markers on B cells.
Excitation and injury of adult ventricular cardiomyocytes by nano- to millisecond electric shocks
Authors: Semenov Iurii , Grigoryev Sergey , Neuber Johanna U. , Zemlin Christian W. , Pakhomova Olga N. , Casciola Maura , Pakhomov Andrei G. 
Published: May 2018

AbstractIntense electric shocks of nanosecond (ns) duration can become a new modality for more efficient but safer defibrillation. We extended strength-duration curves for excitation of cardiomyocytes down to 200 ns, and compared electroporative damage by proportionally more intense shocks of different duration. Enzymatically isolated murine, rabbit, and swine adult ventricular cardiomyocytes (VCM) were loaded with a Ca2+ indicator Fluo-4 or Fluo-5N and subjected to shocks of increasing amplitude until a Ca2+ transient was optically detected. Then, the voltage was increased 5-fold, and the electric cell injury was quantified by the uptake of a membrane permeability marker dye, propidium iodide. We established that: (1) Stimuli down to 200-ns duration can elicit Ca2+ transients, although repeated ns shocks often evoke abnormal responses, (2) Stimulation thresholds expectedly increase as the shock duration decreases, similarly for VCMs from different species, (3) Stimulation threshold energy is minimal for the shortest shocks, (4) VCM orientation with respect to the electric field does not affect the threshold for ns shocks, and (5) The shortest shocks cause the least electroporation injury. These findings support further exploration of ns defibrillation, although abnormal response patterns to repetitive ns stimuli are of a concern and require mechanistic analysis.
The degree of prevalence of similarity between outer tropical cyclone rainbands and squall lines
Authors: Yu Cheng-Ku , Lin Che-Yu , Cheng Lin-Wen , Luo Jhang-Shuo , Wu Chun-Chieh , Chen Ying 
Published: May 2018

AbstractTropical cyclone rainbands (TCRs) are not only one of the most striking and persistent features of tropical cyclones (TCs) but also one of the major causes for extreme floods as TCs approach or encounter the land area. TCRs have been traditionally considered as manifestations of atmospheric waves initiated near the eyewall or close to the TC center. However, the limited evidence from recent studies showed the possibility for TCRs to develop squall-line-like characteristics in the outer region of TCs. In this study, the degree of the prevalence for this similarity is explored by radar and surface observations from a large set of 50 outer TCRs associated with 22 TCs as they approached Taiwan. The results indicate that around 58% of outer TCRs are similar to squall lines. These outer TCRs are generally characterized by convective precipitation, an obvious convergence zone between the band-relative rear-to-front flow and front-to-rear flow at low levels, either frontward or rearward tilting updrafts, and a surface cold pool signature. The frequent similarity between the outer TCRs and squall lines documented provides important insights into the formation of organized, heavy precipitation associated with TCs.