bluuebunny/crossref_metadata_2025_split huggingface dataset:
Angiostrongylus mackerrasae and A. cantonensis (Nematoda: Metastrongyloidea) belong to same genetic lineage: evidence from mitochondrial protein-coding genes
Authors: Song S.-L. , Yong H.-S. , Eamsobhana P. 
Published: July 2017

AbstractAngiostrongylus mackerrasae is a parasitic nematode of rats found in Australia. When first reported, it was referred to as A. cantonensis. Recent molecular studies, including the mitochondrial genome, indicate that it is highly similar to A. cantonensis. These studies did not include A. malaysiensis, another member of the A. cantonensis species complex, for comparison. The present study examined the genetic distance and phylogenetic relationship between the component taxa (A. cantonensis, A. mackerrasae and A. malaysiensis) of the A. cantonensis species complex, based on the 12 protein-coding genes (PCGs) of their mitochondrial genome. Both the nucleotide and amino acid sequences were analysed. Angiostrongylus mackerrasae and A. cantonensis are members of the same genetic lineage and both are genetically distinct from A. malaysiensis. The genetic distance based on concatenated nucleotide sequences of 12 mt-PCGs between A. mackerrasae and A. cantonensis from Thailand is p = 1.73%, while that between the Thai and Chinese taxa of A. cantonensis is p = 3.52%; the genetic distance between A. mackerrasae and A. cantonensis from China is p = 3.70%. The results indicate that A. mackerrasae and A. cantonensis belong to the same genetic lineage, and that A. mackerrasae may be conspecific with A. cantonensis. It remains to be resolved whether A. mackerrasae is conspecific with A. cantonensis or undergoing incipient speciation.
Optimising the use of otowicks in otitis externa
Authors: Bola S , Rashid M , Hickey S 
Published: July 2017

AbstractObjective:Otowicks are used to treat otitis externa with significant ear canal oedema. This study investigates how well drops penetrate through to reach the deep canal and whether it is safe to leave otowicks in the canal for more than 2 days.Methods:Sterile otowicks were inserted into mock ear canals and vertically over pseudomonas-seeded agar plates whilst gentamicin or ciprofloxacin drops were administered. The time taken for drops to penetrate through the otowick was recorded. Separately, pseudomonas-seeded otowicks were treated with saline or antibacterial drops. The penetrating drops were observed for bacterial growth on sterile agar.Results:It took six drops before penetration occurred for both antibiotics. When sterile saline drops were applied to bacterially contaminated otowicks, the penetrating drops displayed bacterial growth on agar, indicating that pseudomonas penetrated through the otowick. However, when antibiotic drops were applied, penetrating drops showed no bacterial growth on the corresponding agar plate.Conclusion:Bacteria can penetrate otowicks but this is prevented by continuous application of antibacterial ear drops. Ear wicks need priming with six drops before starting a regimen, so that the initial dose is fully absorbed.
Disentangling environmental and spatial effects on phylogenetic structure of angiosperm tree communities in China
Authors: Qian Hong , Chen Shengbin , Zhang Jin-Long 
Published: July 2017

AbstractNiche-based and neutrality-based theories are two major classes of theories explaining the assembly mechanisms of local communities. Both theories have been frequently used to explain species diversity and composition in local communities but their relative importance remains unclear. Here, we analyzed 57 assemblages of angiosperm trees in 0.1-ha forest plots across China to examine the effects of environmental heterogeneity (relevant to niche-based processes) and spatial contingency (relevant to neutrality-based processes) on phylogenetic structure of angiosperm tree assemblages distributed across a wide range of environment and space. Phylogenetic structure was quantified with six phylogenetic metrics (i.e., phylogenetic diversity, mean pairwise distance, mean nearest taxon distance, and the standardized effect sizes of these three metrics), which emphasize on different depths of evolutionary histories and account for different degrees of species richness effects. Our results showed that the variation in phylogenetic metrics explained independently by environmental variables was on average much greater than that explained independently by spatial structure, and the vast majority of the variation in phylogenetic metrics was explained by spatially structured environmental variables. We conclude that niche-based processes have played a more important role than neutrality-based processes in driving phylogenetic structure of angiosperm tree species in forest communities in China.
Spectral characteristics of cotton seeds treated by a dielectric barrier discharge plasma
Authors: Wang Xing-Quan , Zhou Ren-Wu , Groot Gerard de , Bazaka Kateryna , Murphy Anthony B. , Ostrikov Kostya 
Published: July 2017

AbstractCold atmospheric plasma has recently emerged as a simple, low-cost and efficient physical method for inducing significant biological responses in seeds and plants without the use of traditional, potentially environmentally-hazardous chemicals, fungicides or hormones. While the beneficial effects of plasma treatment on seed germination, disease resistance and agricultural output have been reported, the mechanisms that underpin the observed biological responses are yet to be fully described. This study employs Fourier Transform Infrared (FTIR) spectroscopy and emission spectroscopy to capture chemical interactions between plasmas and seed surfaces with the aim to provide a more comprehensive account of plasma−seed interactions. FTIR spectroscopy of the seed surface confirms plasma-induced chemical etching of the surface. The etching facilitates permeation of water into the seed, which is confirmed by water uptake measurements. FTIR of exhaust and emission spectra of discharges show oxygen-containing species known for their ability to stimulate biochemical processes and deactivate pathogenic microorganisms. In addition, water gas, CO2, CO and molecules containing −C(CH3)3− moieties observed in FTIR spectra of the exhaust gas during plasma treatment may be partly responsible for the plasma chemical etching of seed surface through oxidizing the organic components of the seed coat.
Genome reconstruction in Cynara cardunculus taxa gains access to chromosome-scale DNA variation
Authors: Acquadro Alberto , Barchi Lorenzo , Portis Ezio , Mangino Giulio , Valentino Danila , Mauromicale Giovanni , Lanteri Sergio 
Published: July 2017

AbstractThe genome sequence of globe artichoke (Cynara cardunculus L. var. scolymus, 2n = 2x = 34) is now available for use. A survey of C. cardunculus genetic resources is essential for understanding the evolution of the species, carrying out genetic studies and for application of breeding strategies. We report on the resequencing analyses (~35×) of four globe artichoke genotypes, representative of the core varietal types, as well as a genotype of the related taxa cultivated cardoon. The genomes were reconstructed at a chromosomal scale and structurally/functionally annotated. Gene prediction indicated a similar number of genes, while distinctive variations in miRNAs and resistance gene analogues (RGAs) were detected. Overall, 23,5 M SNP/indel were discovered (range 6,34 M –14,50 M). The impact of some missense SNPs on the biological functions of genes involved in the biosynthesis of phenylpropanoid and sesquiterpene lactone secondary metabolites was predicted. The identified variants contribute to infer on globe artichoke domestication of the different varietal types, and represent key tools for dissecting the path from sequence variation to phenotype. The new genomic sequences are fully searchable through independent Jbrowse interfaces (www.artichokegenome.unito.it), which allow the analysis of collinearity and the discovery of genomic variants, thus representing a one-stop resource for C. cardunculus genomics.
Glucagon-like peptide-1 reduces pancreatic β-cell mass through hypothalamic neural pathways in high-fat diet-induced obese rats
Authors: Ando Hisae , Gotoh Koro , Fujiwara Kansuke , Anai Manabu , Chiba Seiichi , Masaki Takayuki , Kakuma Tetsuya , Shibata Hirotaka 
Published: July 2017

AbstractWe examined whether glucagon-like peptide-1 (GLP-1) affects β-cell mass and proliferation through neural pathways, from hepatic afferent nerves to pancreatic efferent nerves via the central nervous system, in high-fat diet (HFD)-induced obese rats. The effects of chronic administration of GLP-1 (7–36) and liraglutide, a GLP-1 receptor agonist, on pancreatic morphological alterations, c-fos expression and brain-derived neurotrophic factor (BDNF) content in the hypothalamus, and glucose metabolism were investigated in HFD-induced obese rats that underwent hepatic afferent vagotomy (VgX) and/or pancreatic efferent sympathectomy (SpX). Chronic GLP-1 (7–36) administration to HFD-induced obese rats elevated c-fos expression and BDNF content in the hypothalamus, followed by a reduction in pancreatic β-cell hyperplasia and insulin content, thus resulting in improved glucose tolerance. These responses were abolished by VgX and SpX. Moreover, administration of liraglutide similarly activated the hypothalamic neural pathways, thus resulting in a more profound amelioration of glucose tolerance than native GLP-1 (7–36). These data suggest that GLP-1 normalizes the obesity-induced compensatory increase in β-cell mass and glucose intolerance through a neuronal relay system consisting of hepatic afferent nerves, the hypothalamus, and pancreatic efferent nerves.
Imaging mass spectrometry and MS/MS molecular networking reveals chemical interactions among cuticular bacteria and pathogenic fungi associated with fungus-growing ants
Authors: Boya P. Cristopher A. , Fernández-Marín Hermógenes , Mejía Luis C. , Spadafora Carmenza , Dorrestein Pieter C. , Gutiérrez Marcelino 
Published: July 2017

AbstractThe fungus-growing ant-microbe symbiosis is an ideal system to study chemistry-based microbial interactions due to the wealth of microbial interactions described, and the lack of information on the molecules involved therein. In this study, we employed a combination of MALDI imaging mass spectrometry (MALDI-IMS) and MS/MS molecular networking to study chemistry-based microbial interactions in this system. MALDI IMS was used to visualize the distribution of antimicrobials at the inhibition zone between bacteria associated to the ant Acromyrmex echinatior and the fungal pathogen Escovopsis sp. MS/MS molecular networking was used for the dereplication of compounds found at the inhibition zones. We identified the antibiotics actinomycins D, X2 and X0β, produced by the bacterium Streptomyces CBR38; and the macrolides elaiophylin, efomycin A and efomycin G, produced by the bacterium Streptomyces CBR53.These metabolites were found at the inhibition zones using MALDI IMS and were identified using MS/MS molecular networking. Additionally, three shearinines D, F, and J produced by the fungal pathogen Escovopsis TZ49 were detected. This is the first report of elaiophylins, actinomycin X0β and shearinines in the fungus-growing ant symbiotic system. These results suggest a secondary prophylactic use of these antibiotics by A. echinatior because of their permanent production by the bacteria.
Transdifferentiated Human Vascular Smooth Muscle Cells are a New Potential Cell Source for Endothelial Regeneration
Authors: Hong Xuechong , Margariti Andriana , Le Bras Alexandra , Jacquet Laureen , Kong Wei , Hu Yanhua , Xu Qingbo 
Published: July 2017

AbstractEndothelial dysfunction is widely implicated in cardiovascular pathological changes and development of vascular disease. In view of the fact that the spontaneous endothelial cell (EC) regeneration is a slow and insufficient process, it is of great interest to explore alternative cell sources capable of generating functional ECs. Vascular smooth muscle cell (SMC) composes the majority of the vascular wall and retains phenotypic plasticity in response to various stimuli. The aim of this study is to test the feasibility of the conversion of SMC into functional EC through the use of reprogramming factors. Human SMCs are first dedifferentiated for 4 days to achieve a vascular progenitor state expressing CD34, by introducing transcription factors OCT4, SOX2, KLF4 and c-MYC. These SMC-derived progenitors are then differentiated along the endothelial lineage. The SMC-converted ECs exhibit typical endothelial markers expression and endothelial functions in vitro, in vivo and in disease model. Further comprehensive analysis indicates that mesenchymal-to-epithelial transition is requisite to initiate SMCs reprogramming into vascular progenitors and that members of the Notch signalling pathway regulate further differentiation of the progenitors into endothelial lineage. Together, we provide the first evidence of the feasibility of the conversion of human SMCs towards endothelial lineage through an intermediate vascular progenitor state induced by reprogramming.
Protein-protein binding selectivity and network topology constrain global and local properties of interface binding networks
Authors: Holland David O. , Shapiro Benjamin H. , Xue Pei , Johnson Margaret E. 
Published: July 2017

AbstractProtein-protein interactions networks (PPINs) are known to share a highly conserved structure across all organisms. What is poorly understood, however, is the structure of the child interface interaction networks (IINs), which map the binding sites proteins use for each interaction. In this study we analyze four independently constructed IINs from yeast and humans and find a conserved structure of these networks with a unique topology distinct from the parent PPIN. Using an IIN sampling algorithm and a fitness function trained on the manually curated PPINs, we show that IIN topology can be mostly explained as a balance between limits on interface diversity and a need for physico-chemical binding complementarity. This complementarity must be optimized both for functional interactions and against mis-interactions, and this selectivity is encoded in the IIN motifs. To test whether the parent PPIN shapes IINs, we compared optimal IINs in biological PPINs versus random PPINs. We found that the hubs in biological networks allow for selective binding with minimal interfaces, suggesting that binding specificity is an additional pressure for a scale-free-like PPIN. We confirm through phylogenetic analysis that hub interfaces are strongly conserved and rewiring of interactions between proteins involved in endocytosis preserves interface binding selectivity.
Photonic Needles for Light Delivery in Deep Tissue-like Media
Authors: Fain Romy , Barbosa Felippe , Cardenas Jaime , Lipson Michal 
Published: July 2017

AbstractWe demonstrate a new platform for minimally invasive, light delivery probes leveraging the maturing field of silicon photonics, enabling massively parallel fabrication of photonic structures. These Photonic Needles probes have sub-10 μm cross-sectional dimensions, lengths greater than 3 mm–surpassing 1000 to 1 aspect ratio, and are released completely into air without a substrate below. We show the Photonic Needles to be mechanically robust when inserted into 2% agarose. The propagation loss of these waveguides is low–on the order of 4 dB/cm.
Common variants of T-cells contribute differently to phenotypic variation in sarcoidosis
Authors: Rivera Natalia V. , Hagemann-Jensen Michael , Ferreira Manuel A. R. , Kullberg Susanna , Eklund Anders , Martin Nicholas G. , Padyukov Leonid , Grunewald Johan 
Published: July 2017

AbstractThe involvement of the immune system, particularly the role of T-cells, in sarcoidosis is unclear. The existence of higher CD4+ T-cells and increased CD4/CD8 ratio may indicate a pathogenic role of T-cells in the disease. In this study, we quantified the contribution of T-cells associated variants and of CD4/CD8 ratio in sarcoidosis phenotypes, Löfgren’s syndrome (LS) and non- Löfgren’s syndrome (non-LS). We employed a polygenic-based approach using genome-wide association studies results on relative levels of T-cells in healthy individuals to measure the genetic contribution of T-cells in sarcoidosis entities. Results revealed that the genetic architecture of LS is highly influenced by genetic variants associated with CD8+ T-cells and CD4/CD8 ratio, explaining up to 7.94% and 6.49% of LS variation, respectively; whereas, the genetic architecture of non-LS is minimally influenced by T-cells, explaining a phenotypic variation of <1%. Moreover, pleiotropy assessment between T-cells and LS/non-LS associated-variants led to the discovery of highly scored pathway maps that shared common factors related to antigen presentation and T-cell regulatory mechanisms. Differences in significant polygenic scores, presence of pleiotropy, and distinct genetic factors provide further insights on how genetic variants and genes associated with relative levels of T-cell subtypes contribute differently to sarcoidosis phenotypes.
An Amino Acid Signature Associated with Obesity Predicts 2-Year Risk of Hypertriglyceridemia in School-Age Children
Authors: Moran-Ramos Sofia , Ocampo-Medina Elvira , Gutierrez-Aguilar Ruth , Macías-Kauffer Luis , Villamil-Ramírez Hugo , López-Contreras Blanca E. , León-Mimila Paola , Vega-Badillo Joel , Gutierrez-Vidal Roxana , Villarruel-Vazquez Ricardo , Serrano-Carbajal Erandi , Del-Río-Navarro Blanca E , Huertas-Vázquez Adriana , Villarreal-Molina Teresa , Ibarra-Gonzalez Isabel , Vela-Amieva Marcela , Aguilar-Salinas Carlos A. , Canizales-Quinteros Samuel 
Published: July 2017

AbstractChildhood obesity is associated with a number of metabolic abnormalities leading to increased cardiovascular risk. Metabolites can be useful as early biomarkers and new targets to promote early intervention beginning in school age. Thus, we aimed to identify metabolomic profiles associated with obesity and obesity-related metabolic traits. We used data from the Obesity Research Study for Mexican children (ORSMEC) in Mexico City and included a case control (n = 1120), cross-sectional (n = 554) and a longitudinal study (n = 301) of 6–12-year-old children. Forty-two metabolites were measured using electrospray MS/MS and multivariate regression models were used to test associations of metabolomic profiles with anthropometric, clinical and biochemical parameters. Principal component analysis showed a serum amino acid signature composed of arginine, leucine/isoleucine, phenylalanine, tyrosine, valine and proline significantly associated with obesity (OR = 1.57; 95%CI 1.45–1.69,P = 3.84 × 10−31) and serum triglycerides (TG) (β = 0.067,P = 4.5 × 10−21). These associations were validated in the cross-sectional study (P < 0.0001). In the longitudinal cohort, the amino acid signature was associated with serum TG and with the risk of hypertriglyceridemia after 2 years (OR = 1.19; 95%CI 1.03-1.39,P = 0.016). This study shows that an amino acid signature significantly associated with childhood obesity, is an independent risk factor of future hypertriglyceridemia in children.
Fish oil supplementation to rats fed high-fat diet during pregnancy prevents development of impaired insulin sensitivity in male adult offspring
Authors: Albert Benjamin B. , Vickers Mark H. , Gray Clint , Reynolds Clare M. , Segovia Stephanie A. , Derraik José G. B. , Garg Manohar L. , Cameron-Smith David , Hofman Paul L. , Cutfield Wayne S. 
Published: July 2017

AbstractWe examined whether maternal fish oil supplementation during pregnancy could prevent development of insulin resistance in adult male offspring of rat dams fed a high-fat diet. Time-mated Sprague-Dawley rat dams were randomised into four treatment groups: Con-Con, dams fed a control diet (fat: 15% kcal) and administered water by gavage; Con-FO, control diet with unoxidised fish oil by gavage; HF-Con, high-fat diet (fat: 45% kcal) and water by gavage; and HF-FO, high-fat diet and unoxidised fish oil by gavage. Dams were fed the allocated diet ad libitum during pregnancy and lactation, but daily gavage occurred only during pregnancy. After weaning, male offspring consumed a chow diet ad libitum until adulthood. Maternal high-fat diet led to increased food consumption, adiposity, systolic blood pressure, and triglycerides and plasma leptin in adult HF-Con offspring. HF-Con offspring also exhibited lower insulin sensitivity than Con-Con rats. Male offspring from HF-FO group were similar to HF-Con regarding food consumption and most metabolic parameters. However, insulin sensitivity in the HF-FO group was improved relative to the HF-Con offspring. Supplementation with unoxidised n-3 PUFA rich oils in the setting of a maternal obesogenic diet improved insulin sensitivity, but had no impact on body composition of adult male offspring.
RADseq provides evidence for parallel ecotypic divergence in the autotetraploid Cochlearia officinalis in Northern Norway
Authors: Brandrud Marie K. , Paun Ovidiu , Lorenzo Maria T. , Nordal Inger , Brysting Anne K. 
Published: July 2017

AbstractSpeciation encompasses a continuum over time from freely interbreeding populations to reproductively isolated species. Along this process, ecotypes – the result of local adaptation – may be on the road to new species. We investigated whether three autotetraploidCochlearia officinalisecotypes, adapted to different habitats (beach, estuary, spring), are genetically differentiated and result from parallel ecotypic divergence in two distinct geographical regions. We obtained genetic data from thousands of single nucleotide polymorphisms (SNPs) from restriction-site associated DNA sequencing (RADseq) and from six microsatellite markers for 12 populations to assess genetic divergence at ecotypic, geographic and population level. The genetic patterns support differentiation among ecotypes as suggested by morphology and ecology. The data fit a scenario where the ancestral beach ecotype has recurrently and polytopically given rise to the estuary and spring ecotypes. Several ecologically-relevant loci with consistent non-random segregating patterns are identified across the recurrent origins, in particular around genes related to salt stress. Despite being ecologically distinct, theCochleariaecotypes still represent an early stage in the process of speciation, as reproductive isolation has not (yet) developed. A sequenced annotated genome is needed to specifically target candidate genes underlying local adaptation.
A Novel Pathogen Capturing Device for Removal and Detection
Authors: Kim Gwangseong , Vinerean Horatiu , Gaitas Angelo 
Published: July 2017

AbstractA simple technique that employs an antibody coated polydimethylsiloxane tube is used for effective capturing of bloodborne and foodborne pathogens. By recirculating the entire sample through the antibody coated tube, accumulation of target pathogens is achieved, thereby delivering a higher concentration of pathogens in a small volume. The described method can provide an effective and economical solution to microbiology techniques that rely on enrichment, thereby expediting diagnostics. Using this method 80.3 ± 5.6% of Staphylococcus aureus with a starting concentration of ~107 CFU/mL and 95.4 ± 1.0% of Methicillin-resistant Staphylococcus aureus with starting concentration of ~104 CFU/mL were removed from 5 mL blood in a few hours. This concept was extended to live rats with an induced bloodstream S. aureus infection. A reduction of two orders of magnitude in the bacterial load of the rats was observed within a few hours. The same technique was used to capture a food pathogen, Salmonella typhimurium, with starting concentrations as low as ~100 CFU, from 100 or 250 mL of culture broth within similar timeframes as above. The feasibility for food pathogen testing applications was additionally confirmed by capturing and detecting S. typhimurium in ground chicken and ground beef.