bluuebunny/crossref_metadata_2025_split huggingface dataset:
Weaker plant-enemy interactions decrease tree seedling diversity with edge-effects in a fragmented tropical forest
Authors: Krishnadas Meghna , Bagchi Robert , Sridhara Sachin , Comita Liza S. 
Published: October 2018

AbstractIn fragmented forests, tree diversity declines near edges but the ecological processes underlying this loss of diversity remain poorly understood. Theory predicts that top-down regulation of seedling recruitment by insect herbivores and fungal pathogens contributes to maintaining tree diversity in forests, but it is unknown whether proximity to forest edges compromises these diversity-enhancing biotic interactions. Here we experimentally demonstrate that weakened activity of fungal pathogens and insect herbivores reduced seedling diversity, despite similar diversity of seed rain, during recruitment near forest edges in a human-modified tropical landscape. Only at sites farthest from forest edges (90–100 m) did the application of pesticides lower seedling diversity relative to control plots. Notably, lower seedling diversity corresponded with weaker density-dependent mortality attributable to insects and fungi during the seed-to-seedling transition. We provide mechanistic evidence that edge-effects can manifest as cryptic losses of crucial biotic interactions that maintain diversity.
Transcriptome analysis of extended-spectrum β-lactamase-producing Escherichia coli and methicillin-resistant Staphylococcus aureus exposed to cefotaxime
Authors: Brochmann P. R. , Hesketh A. , Jana B. , Brodersen G. H. , Guardabassi L. 
Published: October 2018

AbstractPrevious studies on bacterial response to antibiotics mainly focused on susceptible strains. Here we characterized the transcriptional responses of distinct cephalosporin-resistant bacteria of public health relevance to cefotaxime (CTX), a cephalosporin widely used in clinical practice. Adaptation to therapeutic concentrations of CTX (30 µg/ml) was investigated by RNA sequencing in mid-exponential phase cultures of a methicillin-resistant Staphylococcus aureus (MRSA) and two genetically diverse E. coli producing CTX-M-15 or CMY-2 β-lactamase following genome sequencing and annotation for each strain. MRSA showed the most notable adaptive changes in the transcriptome after exposure to CTX, mainly associated with cell envelope functions. This reprogramming coincided with a transient reduction in cell growth, which also occurred in the CMY-2-producing E. coli but not in the CTX-M-15-producing strain. Re-establishment of growth in the CMY-2 producer proceeded without any notable adaptive transcriptional response, while limited reprogramming of gene transcription was observed in the CTX-M-15 producer. Our data show that the transcriptional response of CTX-resistant bacteria to CTX depends on the bacterial species, level of resistance and resistance determinant involved. Gene products induced in the presence of CTX may play an essential role for bacterial survival during therapy and merit further investigation as possible targets for potentiating CTX.
The c-Jun and JunB transcription factors facilitate the transit of classical Hodgkin lymphoma tumour cells through G1
Authors: Zhang Jingxi , Wu Zuoqiao , Savin Anton , Yang Mihye , Hsu Ying-Han R. , Jantuan Eugeniu , Bacani Julinor T. C. , Ingham Robert J. 
Published: October 2018

AbstractClassical Hodgkin Lymphoma (cHL) is primarily a B cell lymphoid neoplasm and a member of the CD30–positive lymphomas. cHL and the other CD30–positive lymphomas are characterized by the elevated expression and/or constitutive activation of the activator protein-1 (AP-1) family transcription factors, c-Jun and JunB; however, the specific roles they play in the pathobiology of cHL are unclear. In this report we show that reducing either c-Jun or JunB expression with short-hairpin RNAs (shRNAs) reduced the growth of cHL cell lines in vitro and in vivo, primarily through impairing cell cycle transition through G1. We further investigated the effect of c-Jun and JunB knock-down on proliferation in another CD30–positive lymphoma, anaplastic lymphoma kinase-positive, anaplastic large cell lymphoma (ALK+ ALCL). We found that JunB knock-down in most ALK+ ALCL cell lines examined also resulted in reduced proliferation that was associated with a G0/G1 cell cycle defect. In contrast, c-Jun knock-down in multiple ALK+ ALCL cell lines had no effect on proliferation. In summary, this study directly establishes that both c-Jun and JunB play roles in promoting HRS cell proliferation. Furthermore, we demonstrate there are similarities and differences in c-Jun and JunB function between cHL and ALK+ ALCL.
Substantial diagnostic impact of blood culture independent molecular methods in bloodstream infections: Superior performance of PCR/ESI-MS
Authors: Makristathis Athanasios , Harrison Nicole , Ratzinger Franz , Kussmann Manuel , Selitsch Brigitte , Forstner Christina , Hirschl Alexander M. , Burgmann Heinz 
Published: October 2018

AbstractThis study analyzed the performance of different molecular technologies along with blood culture (BC) in the diagnosis of bloodstream infections (BSI) in patients from internal medicine wards - including intensive care units (ICUs) - and the emergency room. Patients with systemic inflammatory response syndrome were prospectively included. BCs and EDTA whole blood were obtained simultaneously. The latter was analyzed by PCR combined with electrospray ionization mass spectrometry (PCR/ESI-MS; IRIDICA BAC BSI assay, Abbott) and by SeptiFast (Roche). Cases were classified as BSI according to adapted European Centre for Disease Prevention and Control criteria. Out of 462 analyzed episodes, 193 with valid test results fulfilled the inclusion criteria and were further evaluated. Sixty-nine (35.8%) were classified as BSI. PCR/ESI-MS showed a significantly better overall performance than BC (p = 0.004) or SeptiFast (p = 0.034). Only in patients from the ICU the performance of SeptiFast was comparable to that of PCR/ESI-MS. Mainly due to the negative effect of antimicrobial pre-treatment on BC results, the cumulative performance of each of the molecular tests with BC was significantly higher than that of BC alone (p < 0.001). SeptiFast and in particular the broad-range pathogen detection system PCR/ESI-MS proved to be an essential addition to BC-based diagnostics in BSI.
Deep learning enables automated scoring of liver fibrosis stages
Authors: Yu Yang , Wang Jiahao , Ng Chan Way , Ma Yukun , Mo Shupei , Fong Eliza Li Shan , Xing Jiangwa , Song Ziwei , Xie Yufei , Si Ke , Wee Aileen , Welsch Roy E. , So Peter T. C. , Yu Hanry 
Published: October 2018

AbstractCurrent liver fibrosis scoring by computer-assisted image analytics is not fully automated as it requires manual preprocessing (segmentation and feature extraction) typically based on domain knowledge in liver pathology. Deep learning-based algorithms can potentially classify these images without the need for preprocessing through learning from a large dataset of images. We investigated the performance of classification models built using a deep learning-based algorithm pre-trained using multiple sources of images to score liver fibrosis and compared them against conventional non-deep learning-based algorithms - artificial neural networks (ANN), multinomial logistic regression (MLR), support vector machines (SVM) and random forests (RF). Automated feature classification and fibrosis scoring were achieved by using a transfer learning-based deep learning network, AlexNet-Convolutional Neural Networks (CNN), with balanced area under receiver operating characteristic (AUROC) values of up to 0.85–0.95 versus ANN (AUROC of up to 0.87–1.00), MLR (AUROC of up to 0.73–1.00), SVM (AUROC of up to 0.69–0.99) and RF (AUROC of up to 0.94–0.99). Results indicate that a deep learning-based algorithm with transfer learning enables the construction of a fully automated and accurate prediction model for scoring liver fibrosis stages that is comparable to other conventional non-deep learning-based algorithms that are not fully automated.
Postprandial glycaemia-lowering effect of a green tea cultivar Sunrouge and cultivar-specific metabolic profiling for determining bioactivity-related ingredients
Authors: Wasai Masafumi , Fujimura Yoshinori , Nonaka Haruna , Kitamura Ryo , Murata Motoki , Tachibana Hirofumi 
Published: October 2018

AbstractAlthough the major green tea catechins can inhibit the activity of carbohydrate-hydrolyzing enzymes, there is a paucity of information describing the potential of other green tea ingredients and numerous green tea cultivars. Herein, we reveled that a green tea cultivar Sunrouge significantly suppressed the postprandial blood glucose level in mice. Unlike the most representative Japanese green tea cultivar, Yabukita, the suppression by Sunrouge was observed clearly during the initial period after oral dosing of starch. Sunrouge also strongly inhibited the carbohydrate-hydrolyzing enzymes α-glucosidase and α-amylase when compared with that of Yabukita and many other cultivars. Liquid chromatography–mass spectrometry (LC–MS)-based metabolic profiling (MP) of 42 Japanese green tea cultivars was performed. Multivariate statistical analysis enabled visualization of the differences among cultivars with respect to their ability to inhibit carbohydrate-hydrolyzing activities. Analysis of metabolites, contributing to the discrimination and prediction of the bioactivity of cultivars, showed that O-methylated catechins, epicatechin-3-O-(3-O-methyl) gallate (ECG3”Me) and epigallocatechin-3-O-(3-O-methyl) gallate (EGCG3”Me), were newly identified α-glucosidase inhibitors. Such ability was also observed in epigallocatechin-3-O-gallate (EGCG), epicatechin-3-O-gallate (ECG), delphinidin-3-O-glucoside and myricetin-3-O-glucoside. The amounts of these compounds in Sunrouge were higher than that in many other cultivars. These results suggest that Sunrouge has high potential for suppressing the elevation of the postprandial blood glucose level, and an MP approach may become a valuable strategy for evaluating the anti-hyperglycemic activity of green tea and for screening its active ingredients.
Phosphoinositide 3-kinase-delta could be a biomarker for eosinophilic nasal polyps
Authors: Kim Jong Seung , Jeong Jae Seok , Lee Kyung Bae , Kim So Ri , Choe Yeong Hun , Kwon Sam Hyun , Cho Seong Ho , Lee Yong Chul 
Published: October 2018

AbstractNasal polyps (NP) cause diverse clinical symptoms of chronic rhinosinusitis (CRS). Chronic inflammation of sinonasal mucosa is known to be crucial in NP formation. We aimed to define the implications of phosphoinositide 3-kinase (PI3K)-δ in nasal inflammation associated with NP by analyzing NP tissue obtained from CRS patients. Results showed that expression of p110δ, a regulatory subunit of PI3K-δ, in NP tissue was increased compared to control tissue. Increased p110δ expression was closely correlated with more severe CRS features. Interestingly, p110δ expression was increased in eosinophilic NP, which are closely related to more complicated clinical courses of the disease. Furthermore, CRS patients possessing NP with higher p110δ expression displayed more eosinophils in NP tissue and blood, higher levels of IL-5 in NP tissue, and more severe features of the disease. Therefore, PI3K-δ may contribute to the formation of NP, especially eosinophilic NP associated with more severe clinical presentations and radiological features.
Pay-off scarcity causes evolution of risk-aversion and extreme altruism
Authors: Evans R. M. L. 
Published: October 2018

AbstractAll organisms descend from populations with limited resources, so it is clear why evolution should select strategies that win resources at the expense of competitors. Less obvious is how altruistic behaviours evolve, whereby an individual helps others despite expense to itself. Modelling simple agents using evolutionary game theory, it is shown that steady states of extreme altruism can evolve when pay-offs are very rare compared with death. In these states, agents give away most of their wealth. A new theorem for general evolutionary models shows that, when pay-offs are rare, evolution no longer selects strategies to maximize income (average pay-off), but to minimize the risk of missing-out entirely on a rare resource. Principles revealed by the model are widely applicable, where the game represents rare life-changing events: disasters or gluts.
Acidity and Antioxidant Activity of Cold Brew Coffee
Authors: Rao Niny Z. , Fuller Megan 
Published: October 2018

AbstractThe acidity and antioxidant activity of cold brew coffee were investigated using light roast coffees from Brazil, two regions of Ethiopia, Columbia, Myanmar, and Mexico. The concentrations of three caffeoylquinic acid (CQA) isomers were also determined. Cold brew coffee chemistry was compared to that of hot brew coffee prepared with the same grind-to-coffee ratio. The pH values of the cold and hot brew samples were found to be comparable, ranging from 4.85 to 5.13. The hot brew coffees were found to have higher concentrations of total titratable acids, as well as higher antioxidant activity, than that of their cold brew counterparts. It was also noted that both the concentration of total titratable acids and antioxidant activity correlated poorly with total CQA concentration in hot brew coffee. This work suggests that the hot brew method tends to extract more non-deprotonated acids than the cold brew method. These acids may be responsible for the higher antioxidant activities observed in the hot brew coffee samples.
NF-κB p65 directs sex-specific neuroprotection in human neurons
Authors: Ruiz-Perera Lucia M. , Schneider Lennart , Windmöller Beatrice A. , Müller Janine , Greiner Johannes F. W. , Kaltschmidt Christian , Kaltschmidt Barbara 
Published: October 2018

AbstractProtection of neurons against oxidative stress is crucial during neuronal development, maintenance and for treating neurodegenerative diseases. However, little is known about the molecular mechanisms underlying sex-specific maturation and survival of neurons. In the present study, we demonstrate NF-κB-p65 mediated neuroprotection in human glutamatergic neurons differentiated from inferior turbinate stem cells (ITSCs) in a sex-dependent manner. We successfully differentiated ITSCs into MAP-2+/NF200+/Synaptophysin+/vGlut2+-glutamatergic neurons in vitro and ex vivo and validated their functionality. TNF-α-dependent NF-κB-p65 activation was accompanied by significant neuroprotection against oxidative stress-induced neuronal death, which was surprisingly higher in neurons from female donors. Accordingly, sex-specific neuroprotection of female neurons was followed by an increased expression of special NF-κB target genes SOD2 and IGF2. Among these, SOD2 is a well known gene protecting cells against oxidative stress resulting in longevity. In addition, IGF2 is known to promote synapse formation and spine maturation, and it has antioxidant and neuroprotective effects against oxidative damage. In conclusion, we show that NF-κB-p65 is a key player in neuroprotection of human neurons, however the protective gene expression program beneath it differs between sexes. Our findings are in accordance with the increasing evidences pointing towards sex-specific differences in risk and severity of neurodegenerative diseases.
Genome sequence of the cauliflower mushroom Sparassis crispa (Hanabiratake) and its association with beneficial usage
Authors: Kiyama Ryoiti , Furutani Yoshiyuki , Kawaguchi Kayoko , Nakanishi Toshio 
Published: October 2018

AbstractSparassis crispa (Hanabiratake) is a widely used medicinal mushroom in traditional Chinese medicine because it contains materials with pharmacological activity. Here, we report its 39.0-Mb genome, encoding 13,157 predicted genes, obtained using next-generation sequencing along with RNA-seq mapping data. A phylogenetic analysis by comparison with 25 other fungal genomes revealed that S. crispa diverged from Postia placenta, a brown-rot fungus, 94 million years ago. Several features specific to the genome were found, including the A-mating type locus with the predicted genes for HD1 and HD2 heterodomain transcription factors, the mitochondrial intermediate peptidase (MIP), and the B-mating type locus with seven potential pheromone receptor genes and three potential pheromone precursor genes. To evaluate the benefits of the extract and chemicals from S. crispa, we adopted two approaches: (1) characterization of carbohydrate-active enzyme (CAZyme) genes and β-glucan synthase genes and the clusters of genes for the synthesis of second metabolites, such as terpenes, indoles and polyketides, and (2) identification of estrogenic activity in its mycelial extract. Two potential β-glucan synthase genes, ScrFKS1 and ScrFKS2, corresponding to types I and II, respectively, characteristic of Agaricomycetes mushrooms, were newly identified by the search for regions homologous to the reported features of β-glucan synthase genes; both contained the characteristic transmembrane regions and the regions homologous to the catalytic domain of the yeast β-glucan synthase gene FKS1. Rapid estrogenic cell-signaling and DNA microarray-based transcriptome analyses revealed the presence of a new category of chemicals with estrogenic activity, silent estrogens, in the extract. The elucidation of the S. crispa genome and its genes will expand the potential of this organism for medicinal and pharmacological purposes.
Evidence of natural Zika virus infection in neotropical non-human primates in Brazil
Authors: Terzian Ana Carolina B. , Zini Nathalia , Sacchetto Lívia , Rocha Rebeca Froes , Parra Maisa Carla Pereira , Del Sarto Juliana Lemos , Dias Ana Carolina Fialho , Coutinho Felipe , Rayra Jéssica , da Silva Rafael Alves , Costa Vivian Vasconcelos , Fernandes Natália Coelho Couto De Azevedo , Réssio Rodrigo , Díaz-Delgado Josué , Guerra Juliana , Cunha Mariana S. , Catão-Dias José Luiz , Bittar Cintia , Reis Andréia Francesli Negri , Santos Izalco Nuremberg Penha dos , Ferreira Andréia Cristina Marascalchi , Cruz Lilian Elisa Arão Antônio , Rahal Paula , Ullmann Leila , Malossi Camila , Araújo Jr João Pessoa de , Widen Steven , de Rezende Izabela Maurício , Mello Érica , Pacca Carolina Colombelli , Kroon Erna Geessien , Trindade Giliane , Drumond Betânia , Chiaravalloti-Neto Francisco , Vasilakis Nikos , Teixeira Mauro M. , Nogueira Maurício Lacerda 
Published: October 2018

AbstractIn Africa, Old World Primates are involved in the maintenance of sylvatic circulation of ZIKV. However, in Brazil, the hosts for the sylvatic cycle remain unknown. We hypothesized that free-living NHPs might play a role in urban/periurban ZIKV dynamics, thus we undertook an NHP ZIKV investigation in two cities in Brazil. We identified ZIKV-positive NHPs and sequences obtained were phylogenetically related to the American lineage of ZIKV. Additionally, we inoculated fourC.penicillatawith ZIKV and our results demonstrated that marmosets had a sustained viremia. The natural and experimental infection of NHPs with ZIKV, support the hypothesis that NHPs may be a vertebrate host in the maintainance of ZIKV transmission/circulation in urban tropical settings. Further studies are needed to understand the role they may play in maintaining the urban cycle of the ZIKV and how they may be a conduit in establishing an enzootic transmission cycle in tropical Latin America.
PVA-PDMS-Stearic acid composite nanofibrous mats with improved mechanical behavior for selective filtering applications
Authors: Perween Shama , Khan Ziyauddin , Singh Somendra , Ranjan Amit 
Published: October 2018

AbstractIn this work, we report a facile way to fabricate composite nanofibrous mats of polyvinyl alcohol (PVA), polydimethylsiloxane (PDMS), and stearic acid (SA) by employing the electrospinning-technique, with PDMS fraction ranging from 40w% to nearly 80w%. The results show that for a predetermined fraction of PVA and SA, incorporation of an optimal amount of PDMS is necessary for which the mats exhibit the best mechanical behavior. Beyond this optimal PDMS fraction, the mechanical properties of the composite mats deteriorate. This result has been attributed to the ability of the SA molecules to mediate binding between the PVA and PDMS long-chain molecules via van-der-Waals bonding. The morphological, structural, mechanical, and thermal characterizations respectively using SEM, XRD, DMA/tensile test, and DSC lend support to this explanation. By this method, it is possible to control the hydrophilicity/oleophilicity of the mats, and the mats show an excellent selective permeability to oil as compared to water and successfully filter water from a water-in-oil emulsion. Incorporation of SA not only serves to aid in electrospinning of a PDMS-rich nanofibrous mat with good mechanical strength and control over hydrophilicity/oleophilicity, but also has a potential use in fabricating sheets impregnated with phase change materials for thermal energy storage.
Roughness of surface decorated with randomly distributed pillars
Authors: Weroński Paweł 
Published: October 2018

AbstractWe have presented a quantitative analysis of roughness of planar surfaces decorated with randomly distributed, cylindrical pillars, disks, or cavities. We have described the roughness in terms of the surface power spectral density (PSD). First, we have derived a general equation for the PSD of such surfaces. Then, we have found the PSD for the special case of statistically isotropic, circular areas. We have demonstrated that the PSD provides quantitative information on the radius of the circular area, dimensions of the pillar, and surface coverage. We have also discussed the numerical method of extracting the parameters from experimental PSD data obtained from discrete Fourier transform of surface scanning measurements.
Legume plants may facilitate Zanthoxylum bungeanum tolerance to extreme rainfall
Authors: Li Zilong , Pan Kaiwen , Tariq Akash , Sun Feng , Wang Sizhong , Zhang Lin , Sun Xiaoming , Wu Xiaogang , Song Dagang 
Published: October 2018

AbstractA complete randomized design was implemented with two watering regimes (extreme rainfall and control) and three different plant combinations (Zanthoxylum bungeanum, Z. bungeanum + Capsicum annum, Z. bungeanum + Glycine max) in order to assess the morphological and physio-biochemical responses of focal and neighbor plants. The results indicated that, extreme rainfall had significantly negative impacts on Z. bungeanum in three intercropping systems. However, intercropping with G. max improved the transpiration rate (Tr) and stomatal conductance (Gs), raised leaf relative water content (LRWC), increased chlorophyll a (Chl a) and carotenoid (Car) content, and enhanced the superoxide dismutase activity (SOD) of Z. bungeanum. After recovery, the Z. bungeanum + G. max mixed culture significantly increased soil NO3−-N, improved the intercellular carbon dioxide concentration (Ci) and Tr, upregulated soluble sugar and proline, and enhanced hydrogen peroxidase activity (CAT). Moreover, the higher root biomass of G. max provided much more nitrogen for Z. bungeanum via the return of organic matter. However, intercropping with C. annum significantly increased active oxygen (ROS). Compared with neighboring species, in intercropping systems, G. max could have improved the tolerance of the focal species Z. bungeanum in response to extreme rainfall and its recovery after extreme rainfall.