bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distinct co-expression networks using multi-omic data reveal novel interventional targets in HPV-positive and negative head-and-neck squamous cell cancer
Authors: Costa Raquel L. , Boroni Mariana , Soares Marcelo A. 
Published: October 2018

AbstractThe human papillomavirus (HPV) is present in a significant fraction of head-and-neck squamous cell cancer (HNSCC). The main goal of this study was to identify distinct co-expression patterns between HPV+ and HPV− HNSCC and to provide insights into potential regulatory mechanisms/effects within the analyzed networks. We selected cases deposited in The Cancer Genome Atlas database comprising data of gene expression, methylation profiles and mutational patterns, in addition to clinical information. The intersection among differentially expressed and differentially methylated genes showed the negative correlations between the levels of methylation and expression, suggesting that these genes have their expression levels regulated by methylation alteration patterns in their promoter. Weighted correlation network analysis was used to identify co-expression modules and a systematic approach was applied to refine them and identify key regulatory elements integrating results from the other omics. Three distinct co-expression modules were associated with HPV status and molecular signatures. Validation using independent studies reporting biological experimental data converged for the most significant genes in all modules. This study provides insights into complex genetic and epigenetic particularities in the development and progression of HNSCC according to HPV status, and contribute to unveiling specific genes/pathways as novel therapeutic targets in HNSCC.
Circulating metabolic biomarkers of renal function in diabetic and non-diabetic populations
Authors: Barrios Clara , Zierer Jonas , Würtz Peter , Haller Toomas , Metspalu Andres , Gieger Christian , Thorand Barbara , Meisinger Christa , Waldenberger Melanie , Raitakari Olli , Lehtimäki Terho , Otero Sol , Rodríguez Eva , Pedro-Botet Juan , Kähönen Mika , Ala-Korpela Mika , Kastenmüller Gabi , Spector Tim D. , Pascual Julio , Menni Cristina 
Published: October 2018

AbstractUsing targeted NMR spectroscopy of 227 fasting serum metabolic traits, we searched for novel metabolic signatures of renal function in 926 type 2 diabetics (T2D) and 4838 non-diabetic individuals from four independent cohorts. We furthermore investigated longitudinal changes of metabolic measures and renal function and associations with other T2D microvascular complications. 142 traits correlated with glomerular filtration rate (eGFR) after adjusting for confounders and multiple testing: 59 in diabetics, 109 in non-diabetics with 26 overlapping. The amino acids glycine and phenylalanine and the energy metabolites citrate and glycerol were negatively associated with eGFR in all the cohorts, while alanine, valine and pyruvate depicted opposite association in diabetics (positive) and non-diabetics (negative). Moreover, in all cohorts, the triglyceride content of different lipoprotein subclasses showed a negative association with eGFR, while cholesterol, cholesterol esters (CE), and phospholipids in HDL were associated with better renal function. In contrast, phospholipids and CEs in LDL showed positive associations with eGFR only in T2D, while phospholipid content in HDL was positively associated with eGFR both cross-sectionally and longitudinally only in non-diabetics. In conclusion, we provide a wide list of kidney function–associated metabolic traits and identified novel metabolic differences between diabetic and non-diabetic kidney disease.
Identification of reference genes for RT-qPCR data normalization in Gammarus fossarum (Crustacea Amphipoda)
Authors: Mehennaoui Kahina , Legay Sylvain , Serchi Tommaso , Guérold François , Giamberini Laure , Gutleb Arno C. , Cambier Sébastien 
Published: October 2018

AbstractGene expression profiling via RT-qPCR is a robust technique increasingly used in ecotoxicology. Determination and validation of optimal reference genes is a requirement for initiating RT-qPCR experiments. To our best knowledge, this study is the first attempt of identifying a set of reference genes for the freshwater crustacean Gammarus fossarum. Six candidate genes (Actin, TUB, UB, SDH, Clathrin and GAPDH) were tested in order to determine the most stable ones in different stress conditions and to increase the robustness of RT-qPCR data. SDH and Clathrin appeared as the most stable ones. A validation was performed using G. fossarum samples exposed for 15 days to AgNO3, silver nanoparticles (AgNPs) 40 nm and gold nanoparticles (AuNPs) 40 nm. Effects on HSP90 were evaluated and data normalized using Clathrin and SDH. A down-regulation of HSP90 was observed when G. fossarum were exposed to AuNPs 40 nm whereas no effects were observed when G. fossarum were exposed to AgNPs 40 nm. This study highlights the importance of the preliminary determination of suitable reference genes for RT-qPCR experiments. Additionally, this study allowed, for the first time, the determination of a set of valuable genes that can be used in other RT-qPCR studies using G. fossarum as model organism.
Fine-tuning carbapenem resistance by reducing porin permeability of bacteria activated in the selection process of conjugation
Authors: Kong Hoi-Kuan , Pan Qing , Lo Wai-U. , Liu Xuan , Law Carmen O. K. , Chan Ting-fung , Ho Pak-Leung , Lau Terrence Chi-Kong 
Published: October 2018

AbstractAntibiotic resistance is an emerging public health issue. Plasmids are one of the popular carriers to disseminate resistance genes among pathogens. However, the response of plasmid-carrying bacteria to antibiotic treatment and how these bacteria evolve to increase their resistance remain elusive. In this study, we conjugated plasmid pNDM-HK to E. coli J53 recipient cells and selected survivors using different concentrations of the broad spectrum antibiotic meropenem. After selection, transconjugants conferred varying minimum inhibitory concentrations with respect to carbapenems. We sequenced and compared the transcriptomes of transconjugants that exhibited distinct carbapenem susceptibilities, and found that the loss of outer membrane proteins led to antibiotic resistance. Moreover, we identified a novel mutation, G63S, in transcription factor OmpR which moderates the expression of outer membrane proteins. The loss of porins was due to incapability of phosphorylation, which is essential for porin transcription and carbapenem resistance. We also characterized other genes that are regulated by ompR in this mutant, which contributed to bacterial antibiotic resistance. Overall, our studies suggest antibiotic pressure after conjugation might be an alternative pathway to promote antimicrobial resistance.
Toxic Effects of Size-tunable Gold Nanoparticles on Caenorhabditis elegans Development and Gene Regulation
Authors: Hu Chun-Chih , Wu Gong-Her , Lai Sheng-Feng , Muthaiyan Shanmugam Muniesh , Hwu Y. , Wagner Oliver I. , Yen Ta-Jen 
Published: October 2018

AbstractWe utilized size-tunable gold nanoparticles (Au NPs) to investigate the toxicogenomic responses of the model organism Caenorhabditis elegans. We demonstrated that the nematode C. elegans can uptake Au NPs coated with or without 11-mercaptoundecanoic acid (MUA), and Au NPs are detectable in worm intestines using X-ray microscopy and confocal optical microscopy. After Au NP exposure, C. elegans neurons grew shorter axons, which may have been related to the impeded worm locomotion behavior detected. Furthermore, we determined that MUA to Au ratios of 0.5, 1 and 3 reduced the worm population by more than 50% within 72 hours. In addition, these MUA to Au ratios reduced the worm body size, thrashing frequency (worm mobility) and brood size. MTT assays were employed to analyze the viability of cultured C. elegans primary neurons exposed to MUA-Au NPs. Increasing the MUA to Au ratios increasingly reduced neuronal survival. To understand how developmental changes (after MUA-Au NP treatment) are related to changes in gene expression, we employed DNA microarray assays and identified changes in gene expression (e.g., clec-174 (involved in cellular defense), cut-3 and fil-1 (both involved in body morphogenesis), dpy-14 (expressed in embryonic neurons), and mtl-1 (functions in metal detoxification and homeostasis)).
Facile lipase-catalyzed synthesis of a chocolate fat mimetic
Authors: Ghazani Saeed M. , Marangoni Alejandro G. 
Published: October 2018

AbstractA cocoa butter equivalent (CBE) was synthesized enzymatically from readily available edible fats with fatty acid and triacylglycerol compositions that closely resemble the fat present in chocolate, cocoa butter. A commercially available immobilized fungal lipase, Lipozyme RM IM, was used as the reaction catalyst. Reaction parameters were a temperature of 65 °C, water activity of 0.11, a 4 h reaction time, and a substrate mass ratio of a commercial enzymatically synthesized shea stearin (SS) to palm mid-fraction (PMF) of 6:4 (w/w). Fractionation was also used after reaction completion to further approach the triacylglycerol composition of cocoa butter by removing trisaturated and unsaturated triacylglycerols. The yield of the triglyceride 1-palmitoyl-2-oleoyl, 3-stearoyl-glycerol (POS) produced was 57.7% (w/w). The amounts of 1,3-dipalmitoyl-2-oleoyl-glycerol (POP), (POS) and 1,3-stearoyl-2-oleoyl-glycerol (SOS) in the final CBE were 11.2%, 36.3%, and 34.8%, respectively. In comparison, the amounts of POP, POS and SOS in the cocoa butter used in this study were 15.2%, 38.2%, and 27.8%, respectively. No significant differences (P > 0.05) in melting point and enthalpy of fusion between CB and the CBE were observed. In comparison, a non-interesterified blend of SS and PMF (60:40 w/w) showed significantly (P < 0.05) higher melting point and lower enthalpy of fusion compared to CB. The crystal polymorphic form V of CB (β2-3L) was similar to that of CBE and SS/PMF (60:40 w/w). The solid fat content (SFC) vs. temperature profile of the CBE generally resembled that of CB, except that the CBE had significantly (P < 0.05) higher SFCs at 5, 10, 15, 20 and 25 °C compared to both CB and SS/PMF (60:40 w/w). Addition of 15% (w/w) CBE to CB did not cause any changes in physical properties (melting point, SFC and crystal polymorphic forms) of the CB. This study demonstrates the potential for synthesizing a CB-like CBE using a green, rapid, straightforward one step enzymatic conversion followed by fractionation from widely available edible fats.
Milk Fat Globule Membrane Supplementation in Formula-fed Rat Pups Improves Reflex Development and May Alter Brain Lipid Composition
Authors: Moukarzel Sara , Dyer Roger A. , Garcia Cyrielle , Wiedeman Alejandra M. , Boyce Guilaine , Weinberg Joanne , Keller Bernd O. , Elango Rajavel , Innis Sheila M. 
Published: October 2018

AbstractHuman milk contains nutritional, immunoprotective and developmental components that support optimal infant growth and development. The milk fat globule membrane (MFGM) is one unique component, comprised of a tri-layer of polar lipids, glycolipids, and proteins, that may be important for brain development. MFGM is not present in most infant formulas. We tested the effects of bovine MFGM supplementation on reflex development and on brain lipid and metabolite composition in rats using the “pup in a cup” model. From postnatal d5 to d18, rats received either formula supplemented with MFGM or a standard formula without MFGM; a group of mother-reared animals was used as reference/control condition. Body and brain weights did not differ between groups. MFGM supplementation reduced the gap in maturation age between mother-reared and standard formula-fed groups for the ear and eyelid twitch, negative geotaxis and cliff avoidance reflexes. Statistically significant differences in brain phospholipid and metabolite composition were found at d13 and/or d18 between mother-reared and standard formula-fed groups, including a higher phosphatidylcholine:phosphatidylethanolamine ratio, and higher phosphatidylserine, glycerol-3 phosphate, and glutamine in mother-reared compared to formula-fed pups. Adding MFGM to formula narrowed these differences. Our study demonstrates that addition of bovine MFGM to formula promotes reflex development and alters brain phospholipid and metabolite composition. Changes in brain lipid metabolism and their potential functional implications for neurodevelopment need to be further investigated in future studies.
A new look at weather-related health impacts through functional regression
Authors: Masselot Pierre , Chebana Fateh , Ouarda Taha B. M. J. , Bélanger Diane , St-Hilaire André , Gosselin Pierre 
Published: October 2018

AbstractA major challenge of climate change adaptation is to assess the effect of changing weather on human health. In spite of an increasing literature on the weather-related health subject, many aspect of the relationship are not known, limiting the predictive power of epidemiologic models. The present paper proposes new models to improve the performances of the currently used ones. The proposed models are based on functional data analysis (FDA), a statistical framework dealing with continuous curves instead of scalar time series. The models are applied to the temperature-related cardiovascular mortality issue in Montreal. By making use of the whole information available, the proposed models improve the prediction of cardiovascular mortality according to temperature. In addition, results shed new lights on the relationship by quantifying physiological adaptation effects. These results, not found with classical model, illustrate the potential of FDA approaches.
A Prognostic 5-lncRNA Expression Signature for Head and Neck Squamous Cell Carcinoma
Authors: Liu Guancheng , Zheng Jinyang , Zhuang Liming , Lv Yunxia , Zhu Gangcai , Pi Leiming , Wang Junchen , Chen Changhan , Li Zhexuan , Liu Jiangyi , Chen liangjuan , Cai Gengming , Zhang Xin 
Published: October 2018

AbstractHead and neck squamous cell carcinoma (HNSCC) is a common malignant cancer that accounts for 5–10% of all cancers. This study aimed to identify essential genes associated with the prognosis of HNSCC and construct a powerful prognostic model for the risk assessment of HNSCC. RNAseq expression profile data for the patients with HNSCC were obtained from the TCGA database (GEO). A total of 500 samples with full clinical following-up were randomly divided into a training set and a validation set. The training set was used to screen for differentially expressed lncRNAs. Single-factor survival analysis was performed to obtain lncRNAs that associated with prognosis. A robust likelihood-based survival model was constructed to identify the lncRNAs that are essential for the prognosis of HNSCC. A co-expression network between genes and lncRNAs was also constructed to identify lncRNAs co-expressed with genes to serve as the final signature lncRNAs for prognosis. Finally, the prognostic effect of the signature lncRNAs was tested by multi-factor survival analysis and a scoring model for the prognosis of HNSCC was constructed. Moreover, the results of the validation set and the relative expression levels of the signature lncRNAs in the tumour and the adjacent tissue were consistent with the results of the training set. The 5 lncRNAs were distributed among 3 expression modules. Further KEGG pathway enrichment analysis showed that these 3 co-expressed modules participate in different pathways, and many of these pathways are associated with the development and progression of disease. Therefore, we proposed that the 5 validated lncRNAs can be used to predict the prognosis of HNSCC patients and can be applied in postoperative treatment and follow-up.
The effects of environmental and genetic factors on the germination of basidiospores in the Cryptococcus gattii species complex
Authors: You Man , Xu Jianping 
Published: October 2018

AbstractNatural and artificial hybridization has been frequently reported among divergent lineages within and between the two closely related human pathogenic fungi Cryptococcus gattii species complex and Cryptococcus neoformans species complex. However, the biological effects of such hybridization are not well known. Here we used five strains of the C. neoformans species complex and twelve strains of the C. gattii species complex to investigate the potential effects of selected environmental and genetic factors on the germination of their basidiospores from 29 crosses. We found that the germination rates varied widely among crosses and environmental conditions, ranging from 0% to 98%. Overall, the two examined media showed relatively little difference on spore germination while temperature effects were notable, with the high temperature (37 °C) having an overall deleterious effect on spore germination. Within the C. gattii species complex, one intra-lineage VGIII × VGIII cross had the highest germination rates among all crosses at all six tested environmental conditions. Our analyses indicate significant genetic, environmental, and genotype-environment interaction effects on the germination of basidiospores within the C. gattii species complex.
Age, primary symptoms, and genotype characteristics of norovirus outbreaks in Shanghai schools in 2017
Authors: Wang Yuanping , Hao Lipeng , Pan Lifeng , Xue Caoyi , Liu Qing , Zhao Xuetao , Zhu Weiping 
Published: October 2018

AbstractSixty norovirus outbreaks that occurred in Pudong District, Shanghai in 2017 and affected 959 people were summarised. Of the outbreaks, 29 (48.3%), 27 (45.0%), and 4 (6.7%) occurred in kindergartens, primary schools, and middle schools, respectively. Although the total number of outbreaks peaked in March (13/60, 21.7%), outbreaks in kindergartens and primary schools peaked in April (6/29, 20.7%) and March (8/27, 29.6%), respectively. Primary schools had the highest median number of cases per outbreak (19) and the highest proportion of cases (54.6%). The male-to-female case ratio differed among school classifications, with the highest male case ratio (69.2%) occurring in middle schools. Primary symptoms also differed across the school classifications. Molecular virology analysis showed that a single viral strain caused each outbreak at each school. In turn, 50.6, 28.8, and 20.6% of cases were infected by GII.4, GII.2, and GII.17, respectively. Vomiting was seen in 98.2, 97.3, and 88.6% of the subjects infected with noroviruses GII.17, GII.4, and GII.2, respectively, and nausea in 73.6, 43.9, and 39.0%. In conclusion, noroviruses mainly affect primary school and kindergarten students. GII.4, GII.2, and GII.17 are the main epidemic strains in the local area, and the primary symptoms differed by age and genotype.
Deep echocardiography: data-efficient supervised and semi-supervised deep learning towards automated diagnosis of cardiac disease
Authors: Madani Ali , Ong Jia Rui , Tibrewal Anshul , Mofrad Mohammad R. K. 
Published: October 2018

AbstractDeep learning and computer vision algorithms can deliver highly accurate and automated interpretation of medical imaging to augment and assist clinicians. However, medical imaging presents uniquely pertinent obstacles such as a lack of accessible data or a high-cost of annotation. To address this, we developed data-efficient deep learning classifiers for prediction tasks in cardiology. Using pipeline supervised models to focus relevant structures, we achieve an accuracy of 94.4% for 15-view still-image echocardiographic view classification and 91.2% accuracy for binary left ventricular hypertrophy classification. We then develop semi-supervised generative adversarial network models that can learn from both labeled and unlabeled data in a generalizable fashion. We achieve greater than 80% accuracy in view classification with only 4% of labeled data used in solely supervised techniques and achieve 92.3% accuracy for left ventricular hypertrophy classification. In exploring trade-offs between model type, resolution, data resources, and performance, we present a comprehensive analysis and improvements of efficient deep learning solutions for medical imaging assessment especially in cardiology.
Evolution of the flow field in decaying active regions
Authors: Strecker H. , Bello González N. 
Published: October 2018

Context. Fully fledged sunspots are known to be surrounded by a radial outflow called the moat flow.
Aims. We investigate the evolution of the horizontal flow field around sunspots during their decay, that is, from fully fledged to naked spots, after they loose the penumbra, to the remnant region after the spot has fully dissolved.
Methods. We analysed the extension and horizontal velocity of the flow field around eight sunspots using SDO/HMI Doppler maps. By assuming a radially symmetrical flow field, the applied analysis method determines the radial dependence of the azimuthally averaged flow field. For comparison, we studied the flow in supergranules using the same technique.
Results. All investigated, fully fledged sunspots are surrounded by a flow field whose horizontal velocity profile decreases continuously from 881 m s−1 at 1.1 Mm off the spot boundary, down to 199 m s−1 at a mean distance of 11.9 Mm to that boundary, in agreement with other studies. Once the penumbra is fully dissolved, however, the velocity profile of the flow changes: The horizontal velocity increases with increasing distance to the spot boundary until a maximum value of about 398 m s−1 is reached. Then, the horizontal velocity decreases for farther distances to the spot boundary. In supergranules, the horizontal velocity increases with increasing distance to their centre up to a mean maximum velocity of 355 m s−1. For larger distances, the horizontal velocity decreases. We thus find that the velocity profile of naked sunspots resembles that of supergranular flows. The evolution of the flow field around individual sunspots is influenced by the way the sunspot decays and by the interplay with the surrounding flow areas.
Conclusions. Observations of the flow around eight decaying sunspots suggest that as long as penumbrae are present, sunspots with their moat cell are embedded in network cells. The disappearance of the penumbra (and consequently the moat flow) and the competing surrounding supergranular cells, both have a significant role in the evolution of the flow field: The moat cell transforms into a supergranule, which hosts the remaining naked spot.
Unusually high magnetic fields in the coma of 67P/Churyumov-Gerasimenko during its high-activity phase
Authors: Goetz C. , Tsurutani B. T. , Henri P. , Volwerk M. , Behar E. , Edberg N. J. T. , Eriksson A. , Goldstein R. , Mokashi P. , Nilsson H. , Richter I. , Wellbrock A. , Glassmeier K. H. 
Published: October 2018

Aims. On July 3, 2015, an unprecedented increase in the magnetic field magnitude was measured by the Rosetta spacecraft orbiting comet 67P/Churyumov-Gerasimenko (67P). This increase was accompanied by large variations in magnetic field and ion and electron density and energy. To our knowledge, this unusual event marks the highest magnetic field ever measured in the plasma environment of a comet. Our goal here is to examine possible physical causes for this event, and to explain this reaction of the cometary plasma and magnetic field and its trigger.
Methods. We used observations from the entire Rosetta Plasma Consortium as well as energetic particle measurements from the Standard Radiation Monitor on board Rosetta to characterize the event. To provide context for the solar wind at the comet, observations at Earth were compared with simulations of the solar wind.
Results. We find that the unusual behavior of the plasma around 67P is of solar wind origin and is caused by the impact of an interplanetary coronal mass ejection, combined with a corotating interaction region. This causes the magnetic field to pile up and increase by a factor of six to about 300 nT compared to normal values of the enhanced magnetic field at a comet. This increase is only partially accompanied by an increase in plasma density and energy, indicating that the magnetic field is connected to different regions of the coma.