bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chemical dispersants enhance the activity of oil- and gas condensate-degrading marine bacteria
Authors: Tremblay Julien , Yergeau Etienne , Fortin Nathalie , Cobanli Susan , Elias Miria , King Thomas L , Lee Kenneth , Greer Charles W 
Published: August 2017

Abstract
Application of chemical dispersants to oil spills in the marine environment is a common practice to disperse oil into the water column and stimulate oil biodegradation by increasing its bioavailability to indigenous bacteria capable of naturally metabolizing hydrocarbons. In the context of a spill event, the biodegradation of crude oil and gas condensate off eastern Canada is an essential component of a response strategy. In laboratory experiments, we simulated conditions similar to an oil spill with and without the addition of chemical dispersant under both winter and summer conditions and evaluated the natural attenuation potential for hydrocarbons in near-surface sea water from the vicinity of crude oil and natural gas production facilities off eastern Canada. Chemical analyses were performed to determine hydrocarbon degradation rates, and metagenome binning combined with metatranscriptomics was used to reconstruct abundant bacterial genomes and estimate their oil degradation gene abundance and activity. Our results show important and rapid structural shifts in microbial populations in all three different oil production sites examined following exposure to oil, oil with dispersant and dispersant alone. We found that the addition of dispersant to crude oil enhanced oil degradation rates and favored the abundance and expression of oil-degrading genes from a Thalassolituus sp. (that is, metagenome bin) that harbors multiple alkane hydroxylase (alkB) gene copies. We propose that this member of the Oceanospirillales group would be an important oil degrader when oil spills are treated with dispersant.
Feathermoss and epiphytic Nostoc cooperate differently: expanding the spectrum of plant–cyanobacteria symbiosis
Authors: Warshan Denis , Espinoza Josh L , Stuart Rhona K , Richter R Alexander , Kim Sea-Yong , Shapiro Nicole , Woyke Tanja , C Kyrpides Nikos , Barry Kerrie , Singan Vasanth , Lindquist Erika , Ansong Charles , Purvine Samuel O , M Brewer Heather , Weyman Philip D , Dupont Christopher L , Rasmussen Ulla 
Published: August 2017

Abstract
Dinitrogen (N2)-fixation by cyanobacteria in symbiosis with feathermosses is the primary pathway of biological nitrogen (N) input into boreal forests. Despite its significance, little is known about the cyanobacterial gene repertoire and regulatory rewiring needed for the establishment and maintenance of the symbiosis. To determine gene acquisitions and regulatory changes allowing cyanobacteria to form and maintain this symbiosis, we compared genomically closely related symbiotic-competent and -incompetent Nostoc strains using a proteogenomics approach and an experimental set up allowing for controlled chemical and physical contact between partners. Thirty-two gene families were found only in the genomes of symbiotic strains, including some never before associated with cyanobacterial symbiosis. We identified conserved orthologs that were differentially expressed in symbiotic strains, including protein families involved in chemotaxis and motility, NO regulation, sulfate/phosphate transport, and glycosyl-modifying and oxidative stress-mediating exoenzymes. The physical moss–cyanobacteria epiphytic symbiosis is distinct from other cyanobacteria–plant symbioses, with Nostoc retaining motility, and lacking modulation of N2-fixation, photosynthesis, GS-GOGAT cycle and heterocyst formation. The results expand our knowledge base of plant–cyanobacterial symbioses, provide a model of information and material exchange in this ecologically significant symbiosis, and suggest new currencies, namely nitric oxide and aliphatic sulfonates, may be involved in establishing and maintaining the cyanobacteria–feathermoss symbiosis.
ROCKII inhibition promotes the maturation of human pancreatic beta-like cells
Authors: Ghazizadeh Zaniar , Kao Der-I , Amin Sadaf , Cook Brandoch , Rao Sahana , Zhou Ting , Zhang Tuo , Xiang Zhaoying , Kenyon Reyn , Kaymakcalan Omer , Liu Chengyang , Evans Todd , Chen Shuibing 
Published: August 2017

AbstractDiabetes is linked to loss of pancreatic beta-cells. Pluripotent stem cells offer a valuable source of human beta-cells for basic studies of their biology and translational applications. However, the signalling pathways that regulate beta-cell development and functional maturation are not fully understood. Here we report a high content chemical screen, revealing that H1152, a ROCK inhibitor, promotes the robust generation of insulin-expressing cells from multiple hPSC lines. The insulin expressing cells obtained after H1152 treatment show increased expression of mature beta cell markers and improved glucose stimulated insulin secretion. Moreover, the H1152-treated beta-like cells show enhanced glucose stimulated insulin secretion and increased capacity to maintain glucose homeostasis after transplantation. Conditional gene knockdown reveals that inhibition of ROCKII promotes the generation and maturation of glucose-responding cells. This study provides a strategy to promote human beta-cell maturation and identifies an unexpected role for the ROCKII pathway in the development and maturation of beta-like cells.
JunB promotes Th17 cell identity and restrains alternative CD4+ T-cell programs during inflammation
Authors: Carr Tiffany M. , Wheaton Joshua D. , Houtz Geoffrey M. , Ciofani Maria 
Published: August 2017

AbstractT helper 17 (Th17) cell plasticity contributes to both immunity and autoimmunity; however, the factors that control lineage flexibility are mostly unknown. Here we show the activator protein-1 (AP-1) factor JunB is an essential regulator of Th17 cell identity. JunB activates expression of Th17 lineage-specifying genes and coordinately represses genes controlling Th1 and regulatory T-cell fate. JunB supports Th17 cell identity by regulating key AP-1 complex constituents. In particular, JunB limits the expression of the subset repressor IRF8, and impedes access of JunD to regulatory regions of alternative effector loci. Although dispensable for homeostatic Th17 cell development, JunB is required for induction and maintenance of Th17 effector responses in the inflammatory contexts of both acute infection and chronic autoimmunity in mice. Through regulatory network analysis, we show that JunB is a core regulator of global transcriptional programs that promote Th17 cell identity and restrict alternative CD4+ T-cell potential.
Temporal profiling of depression vulnerability in a preclinical model of sustained depression
Authors: Riga D. , Schmitz L. J. M. , Hoogendijk W. J. G. , Smit A. B. , Spijker S. 
Published: August 2017

AbstractMajor Depression is a prevalent mental disorder that is characterized by negative mood and reduced motivation, and frequently results in social withdrawal and memory-related deficits. Repeated stressors, such as adverse life events, increase the risk for development of the disorder. Consequently, individual variability in stress response greatly weighs on depression-vulnerability and -resilience. Here, we employed the social defeat-induced persistent stress (SDPS) paradigm to identify depression-prone individuals and to examine the temporal development of depression in the months following exposure to brief defeat stress. Male Wistar rats were socially defeated (5 defeat episodes) and single-housed for a prolonged period of time (~24 weeks). We assessed the emergence of a sustained depressive-like state by repeatedly evaluating social motivation (social approach avoidance) and spatial memory (object place recognition) in SDPS rats during the isolation period. Individual variability in the effects of SDPS yielded two extreme subpopulations: an SDPS-prone group that showed gradual affective and cognitive deterioration in terms of social approach and memory retention, and a SDPS-resilient group that did not develop this phenotype. Notably, in SDPS-prone individuals, the affective deficits preceded later cognitive impairments, providing a novel temporal profile of the development of pathology in this preclinical model of sustained depression.
The saliva microbiome profiles are minimally affected by collection method or DNA extraction protocols
Authors: Lim Yenkai , Totsika Makrina , Morrison Mark , Punyadeera Chamindie 
Published: August 2017

AbstractSaliva has attracted attention as a diagnostic fluid due to the association of oral microbiota with systemic diseases. However, the lack of standardised methods for saliva collection has led to the slow uptake of saliva in microbiome research. The aim of this study was to systematically evaluate the potential effects on salivary microbiome profiles using different methods of saliva collection, storage and gDNA extraction. Three types of saliva fractions were collected from healthy individuals with or without the gDNA stabilising buffer. Subsequently, three types of gDNA extraction methods were evaluated to determine the gDNA extraction efficiencies from saliva samples. The purity of total bacterial gDNA was evaluated using the ratio of human β-globin to bacterial 16S rRNA PCR while 16S rRNA gene amplicon sequencing was carried out to identify the bacterial profiles present in these samples. The quantity and quality of extracted gDNA were similar among all three gDNA extraction methods and there were no statistically significant differences in the bacterial profiles among different saliva fractions at the genus-level of taxonomic classification. In conclusion, saliva sampling, processing and gDNA preparation do not have major influence on microbiome profiles.
Differential diagnostic performance of acoustic radiation force impulse imaging in small (≤20 mm) breast cancers: Is it valuable?
Authors: Wang Si-Da , Wang Lei , Li Zhi-Xian , Wei Kang-Lai , Liao Xin-Hong , Chen Yuan-Yuan , Huang Xue 
Published: August 2017

AbstractTo evaluate acoustic radiation force impulse (ARFI) inthe differential diagnosis of small (≤20 mm) solid breast lesions and identify the most efficient ARFI parameters. Conventional ultrasonography and ARFIwere performed in 120 patients with 121 small solid breast lesions. The area ratios (ARs) of the lesion on virtual touch tissue compared to B-mode were calculated. The shear wave velocity of the inner (SWVi) and boundary (SWVb) of the lesions and surrounding fatty tissue (SWVf) was measured. The ratio of SWVi to SWVf (SWVrat) was calculated. AR, SWVi, SWVb, and SWVrat were significantly larger in malignant lesions (all P < 0.001). A cutoff AR of 1.17 yielded the highest area under the receiver operating characteristic curveamong the various parameters (91.2% sensitivity, 85.9% specificity, 88.4% accuracy) for the differential diagnosis of small breast lesions, but this value did not significantly differ from SWVi (P = 0.1144). This AR cutoff indowngradingcategory 4a to category 3 would avoid 83.3% unnecessary biopsies, and improved diagnostic specificity up to 73.4% without decreasing sensitivity. AR and SWVi are efficient parameters for the differential diagnosis of small breast lesions, whichwill improve diagnostic specificity and reduce unnecessary biopsies.
Automatic Categorization and Scoring of Solid, Part-Solid and Non-Solid Pulmonary Nodules in CT Images with Convolutional Neural Network
Authors: Tu Xiaoguang , Xie Mei , Gao Jingjing , Ma Zheng , Chen Daiqiang , Wang Qingfeng , Finlayson Samuel G. , Ou Yangming , Cheng Jie-Zhi 
Published: August 2017

AbstractWe present a computer-aided diagnosis system (CADx) for the automatic categorization of solid, part-solid and non-solid nodules in pulmonary computerized tomography images using a Convolutional Neural Network (CNN). Provided with only a two-dimensional region of interest (ROI) surrounding each nodule, our CNN automatically reasons from image context to discover informative computational features. As a result, no image segmentation processing is needed for further analysis of nodule attenuation, allowing our system to avoid potential errors caused by inaccurate image processing. We implemented two computerized texture analysis schemes, classification and regression, to automatically categorize solid, part-solid and non-solid nodules in CT scans, with hierarchical features in each case learned directly by the CNN model. To show the effectiveness of our CNN-based CADx, an established method based on histogram analysis (HIST) was implemented for comparison. The experimental results show significant performance improvement by the CNN model over HIST in both classification and regression tasks, yielding nodule classification and rating performance concordant with those of practicing radiologists. Adoption of CNN-based CADx systems may reduce the inter-observer variation among screening radiologists and provide a quantitative reference for further nodule analysis.
Mass production of polymer nano-wires filled with metal nano-particles
Authors: Lomadze Nino , Kopyshev Alexey , Bargheer Matias , Wollgarten Markus , Santer Svetlana 
Published: August 2017

AbstractDespite the ongoing progress in nanotechnology and its applications, the development of strategies for connecting nano-scale systems to micro- or macroscale elements is hampered by the lack of structural components that have both, nano- and macroscale dimensions. The production of nano-scale wires with macroscale length is one of the most interesting challenges here. There are a lot of strategies to fabricate long nanoscopic stripes made of metals, polymers or ceramics but none is suitable for mass production of ordered and dense arrangements of wires at large numbers. In this paper, we report on a technique for producing arrays of ordered, flexible and free-standing polymer nano-wires filled with different types of nano-particles. The process utilizes the strong response of photosensitive polymer brushes to irradiation with UV-interference patterns, resulting in a substantial mass redistribution of the polymer material along with local rupturing of polymer chains. The chains can wind up in wires of nano-scale thickness and a length of up to several centimeters. When dispersing nano-particles within the film, the final arrangement is similar to a core-shell geometry with mainly nano-particles found in the core region and the polymer forming a dielectric jacket.
TLR4-Mediated Placental Pathology and Pregnancy Outcome in Experimental Malaria
Authors: Barboza Renato , Lima Flávia Afonso , Reis Aramys Silva , Murillo Oscar Javier , Peixoto Erika Paula Machado , Bandeira Carla Letícia , Fotoran Wesley Luzetti , Sardinha Luis Roberto , Wunderlich Gerhard , Bevilacqua Estela , Lima Maria Regina D’Império , Alvarez José Maria , Costa Fabio Trindade Maranhão , Gonçalves Lígia Antunes , Epiphanio Sabrina , Marinho Claudio Romero Farias 
Published: August 2017

AbstractMalaria-associate pregnancy has a significant impact on infant morbidity and mortality. The detrimental effects of malaria infection during pregnancy have been shown to correlate with immune activation in the placental tissue. Herein we sought to evaluate the effect of Toll-like receptors (TLRs) activation on placental malaria (PM) development by using the Plasmodium berghei NK65GFP infection model. We observed that activation of the innate immune system by parasites leads to PM due to local inflammation. We identified TLR4 activation as the main pathway involved in the inflammatory process in the placental tissue since the absence of functional TLR4 in mice leads to a decrease in the pro-inflammatory responses, which resulted in an improved pregnancy outcome. Additionally, a similar result was obtained when infected pregnant mice were treated with IAXO-101, a TLR4/CD14 blocker. Together, this study illustrates the importance of TLR4 signalling for the generation of the severe inflammatory response involved in PM pathogenesis. Therefore, our results implicate that TLR4 blockage could be a potential candidate for therapeutic interventions to reduce malaria-induced pathology both in the mother and the fetus.
In vivo therapeutic efficacy of frog skin-derived peptides against Pseudomonas aeruginosa-induced pulmonary infection
Authors: Chen Chen , Mangoni Maria Luisa , Di Y. Peter 
Published: August 2017

AbstractPseudomonas aeruginosa is an opportunistic and frequently drug-resistant pulmonary pathogen especially in cystic fibrosis sufferers. Recently, the frog skin-derived antimicrobial peptide (AMP) Esc(1–21) and its diastereomer Esc(1–21)-1c were found to possess potent in vitro antipseudomonal activity. Here, they were first shown to preserve the barrier integrity of airway epithelial cells better than the human AMP LL-37. Furthermore, Esc(1–21)-1c was more efficacious than Esc(1–21) and LL-37 in protecting host from pulmonary bacterial infection after a single intra-tracheal instillation at a very low dosage of 0.1 mg/kg. The protection was evidenced by 2-log reduction of lung bacterial burden and was accompanied by less leukocytes recruitment and attenuated inflammatory response. In addition, the diastereomer was more efficient in reducing the systemic dissemination of bacterial cells. Importantly, in contrast to what reported for other AMPs, the peptide was administered at 2 hours after bacterial challenge to better reflect the real life infectious conditions. To the best of our knowledge, this is also the first study investigating the effect of AMPs on airway-epithelia associated genes upon administration to infected lungs. Overall, our data highly support advanced preclinical studies for the development of Esc(1–21)-1c as an efficacious therapeutic alternative against pulmonary P. aeruginosa infections.
Nosema ceranae, Fipronil and their combination compromise honey bee reproduction via changes in male physiology
Authors: Kairo Guillaume , Biron David G. , Ben Abdelkader Faten , Bonnet Marc , Tchamitchian Sylvie , Cousin Marianne , Dussaubat Claudia , Benoit Boris , Kretzschmar André , Belzunces Luc P. , Brunet Jean-Luc 
Published: August 2017

AbstractThe honey bee is threatened by biological agents and pesticides that can act in combination to induce synergistic effects on its physiology and lifespan. The synergistic effects of a parasite/pesticide combination have been demonstrated on workers and queens, but no studies have been performed on drones despite their essential contribution to colony sustainability by providing semen diversity and quality. The effects of the Nosema ceranae/fipronil combination on the life traits and physiology of mature drones were examined following exposure under semi-field conditions. The results showed that the microsporidia alone induced moderate and localized effects in the midgut, whereas fipronil alone induced moderate and generalized effects. The parasite/insecticide combination drastically affected both physiology and survival, exhibiting an important and significant generalized action that could jeopardize mating success. In terms of fertility, semen was strongly impacted regardless of stressor, suggesting that drone reproductive functions are very sensitive to stress factors. These findings suggest that drone health and fertility impairment might contribute to poorly mated queens, leading to the storage of poor quality semen and poor spermathecae diversity. Thus, the queens failures observed in recent years might result from the continuous exposure of drones to multiple environmental stressors.
Tip-dated phylogeny of whirligig beetles reveals ancient lineage surviving on Madagascar
Authors: Gustafson Grey T. , Prokin Alexander A. , Bukontaite Rasa , Bergsten Johannes , Miller Kelly B. 
Published: August 2017

AbstractThe temporal origin of Madagascar’s extraordinary endemic diversity is debated. A preference for Cenozoic dispersal origins has replaced the classical view of Mesozoic vicariance in the wake of molecular dating. However, evidence of ancient origins is mounting from arthropod groups. Using phylogenetic ‘tip-dating’ analysis with fossils, we show that a whirligig beetle species,Heterogyrus milloti, inhabiting forest streams in southeastern Madagascar is the last survivor of a once dominant and widespread Mesozoic group. With a Late Triassic to Early Jurassic origin (226–187 Ma) it is the hitherto oldest dated endemic lineage of animal or plant on Madagascar. Island biotas’ sensitivity to extinction is well known, but islands can also provide refuge from continental extinction.Heterogyrus millotiis an irreplaceable link to the freshwater biota of the Mesozoic and serves as a reminder of what may be lost without critical conservation efforts on Madagascar.
Novel STAT binding elements mediate IL-6 regulation of MMP-1 and MMP-3
Authors: Cutler Samuel J. , Doecke James D. , Ghazawi Ibtisam , Yang Jinbo , Griffiths Lyn R. , Spring Kevin J. , Ralph Stephen J. , Mellick Albert S. 
Published: August 2017

AbstractDynamic remodelling of the extracellular matrix (ECM) is a key feature of cancer progression. Enzymes that modify the ECM, such as matrix metalloproteinases (MMPs), have long been recognised as important targets of anticancer therapy. Inflammatory cytokines are known to play a key role in regulating protease expression in cancer. Here we describe the identification of gamma-activated site (GA﻿S)-like, signal transducer and activator of transcription (STAT) binding elements (SBEs) within the proximal promoters of theMMP-1andMMP-3genes, which in association with AP-1 components (c-Fos or Jun), bind STAT-1 in ahomodimerlike complex (HDLC). We further demonstrate that MMP expression and binding of this complex to SBEs can either be enhanced by interleukin (IL)-6, or reduced by interferon gamma (IFN-γ), and that IL-6 regulation of MMPs is not STAT-3 dependent. Collectively, this data adds to existing understanding of the mechanism underlying cytokine regulation of MMP expression via STAT-1, and increases our understanding of the links between inflammation and malignancy in colon cancer.
Asymmetry of the temporal code for space by hippocampal place cells
Authors: Souza Bryan C. , Tort Adriano B. L. 
Published: August 2017

AbstractHippocampal place cells convey spatial information through spike frequency (“rate coding”) and spike timing relative to the theta phase (“temporal coding”). Whether rate and temporal coding are due to independent or related mechanisms has been the subject of wide debate. Here we show that the spike timing of place cells couples to theta phase before major increases in firing rate, anticipating the animal’s entrance into the classical, rate-based place field. In contrast, spikes rapidly decouple from theta as the animal leaves the place field and firing rate decreases. Therefore, temporal coding has strong asymmetry around the place field center. We further show that the dynamics of temporal coding along space evolves in three stages as the animal traverses the place field: phase coupling, sharp precession and phase decoupling. These results suggest that independent mechanisms may govern rate and temporal coding.