bluuebunny/crossref_metadata_2025_split huggingface dataset:
Methylation-dependent regulation of HIF-1α stability restricts retinal and tumour angiogenesis
Authors: Kim Yunho , Nam Hye Jin , Lee Junyeop , Park Do Young , Kim Chan , Yu Young Suk , Kim Dongha , Park Se Won , Bhin Jinhyuk , Hwang Daehee , Lee Ho , Koh Gou Young , Baek Sung Hee 
Published: January 2016

AbstractHypoxia-inducible factor-1α (HIF-1α) mediates hypoxic responses and regulates gene expression involved in angiogenesis, invasion and metabolism. Among the various HIF-1α posttranslational modifications, HIF-1α methylation and its physiological role have not yet been elucidated. Here we show that HIF-1α is methylated by SET7/9 methyltransferase, and that lysine-specific demethylase 1 reverses its methylation. The functional consequence of HIF-1α methylation is the modulation of HIF-1α stability primarily in the nucleus, independent of its proline hydroxylation, during long-term hypoxic and normoxic conditions. Knock-in mice bearing a methylation-defective Hif1aKA/KA allele exhibit enhanced retinal angiogenesis and tumour vascularization via HIF-1α stabilization. Importantly, S28Y and R30Q mutations of HIF-1α, found in human cancers, are involved in the altered HIF-1α stability. Together, these results demonstrate a role for HIF-1α methylation in regulating protein stability, thereby modulating biological output including retinal and tumour angiogenesis, with therapeutic implications in human cancer.
Whole-genome sequencing expands diagnostic utility and improves clinical management in paediatric medicine
Authors: Stavropoulos Dimitri J , Merico Daniele , Jobling Rebekah , Bowdin Sarah , Monfared Nasim , Thiruvahindrapuram Bhooma , Nalpathamkalam Thomas , Pellecchia Giovanna , Yuen Ryan K C , Szego Michael J , Hayeems Robin Z , Shaul Randi Zlotnik , Brudno Michael , Girdea Marta , Frey Brendan , Alipanahi Babak , Ahmed Sohnee , Babul-Hirji Riyana , Porras Ramses Badilla , Carter Melissa T , Chad Lauren , Chaudhry Ayeshah , Chitayat David , Doust Soghra Jougheh , Cytrynbaum Cheryl , Dupuis Lucie , Ejaz Resham , Fishman Leona , Guerin Andrea , Hashemi Bita , Helal Mayada , Hewson Stacy , Inbar-Feigenberg Michal , Kannu Peter , Karp Natalya , Kim Raymond H , Kronick Jonathan , Liston Eriskay , MacDonald Heather , Mercimek-Mahmutoglu Saadet , Mendoza-Londono Roberto , Nasr Enas , Nimmo Graeme , Parkinson Nicole , Quercia Nada , Raiman Julian , Roifman Maian , Schulze Andreas , Shugar Andrea , Shuman Cheryl , Sinajon Pierre , Siriwardena Komudi , Weksberg Rosanna , Yoon Grace , Carew Chris , Erickson Raith , Leach Richard A , Klein Robert , Ray Peter N , Meyn M Stephen , Scherer Stephen W , Cohn Ronald D , Marshall Christian R 
Published: January 2016

AbstractThe standard of care for first-tier clinical investigation of the aetiology of congenital malformations and neurodevelopmental disorders is chromosome microarray analysis (CMA) for copy-number variations (CNVs), often followed by gene(s)-specific sequencing searching for smaller insertion–deletions (indels) and single-nucleotide variant (SNV) mutations. Whole-genome sequencing (WGS) has the potential to capture all classes of genetic variation in one experiment; however, the diagnostic yield for mutation detection of WGS compared to CMA, and other tests, needs to be established. In a prospective study we utilised WGS and comprehensive medical annotation to assess 100 patients referred to a paediatric genetics service and compared the diagnostic yield versus standard genetic testing. WGS identified genetic variants meeting clinical diagnostic criteria in 34% of cases, representing a fourfold increase in diagnostic rate over CMA (8%; P value=1.42E−05) alone and more than twofold increase in CMA plus targeted gene sequencing (13%; P value=0.0009). WGS identified all rare clinically significant CNVs that were detected by CMA. In 26 patients, WGS revealed indel and missense mutations presenting in a dominant (63%) or a recessive (37%) manner. We found four subjects with mutations in at least two genes associated with distinct genetic disorders, including two cases harbouring a pathogenic CNV and SNV. When considering medically actionable secondary findings in addition to primary WGS findings, 38% of patients would benefit from genetic counselling. Clinical implementation of WGS as a primary test will provide a higher diagnostic yield than conventional genetic testing and potentially reduce the time required to reach a genetic diagnosis.
Variations in the buccal-lingual alveolar bone thickness of impacted mandibular third molar: our classification and treatment perspectives
Authors: Ge Jing , Zheng Jia-Wei , Yang Chi , Qian Wen-Tao 
Published: January 2016

AbstractSelecting either buccal or lingual approach for the mandibular third molar surgical extraction has been an intense debate for years. The aim of this observational retrospective study was to classify the molar based on the proximity to the external cortical bone and analyze the position of inferior alveolar canal (IAC) of each type. Cone-beam CT (CBCT) data of 110 deeply impacted mandibular third molars from 91 consecutive patients were analyzed. A new classification based on the mean deduction value (MD) of buccal-lingual alveolar bone thickness was proposed: MD≥1 mm was classified as buccal position, 1 mm>MD>−1 mm was classified as central position, MD≤−1 mm was classified as lingual position. The study samples were distributed as: buccal position (1.8%) in 2 subjects, central position (10.9%) in 12 and lingual position (87.3%) in 96. Ninety-six molars (87.3%) contacted the IAC. The buccal and inferior IAC course were the most common types in impacted third molar, especially in lingually positioned ones. Our study suggested that amongst deeply impacted mandibular third molars, lingual position occupies the largest proportion, followed by the central and then the buccal type.
Cytokine levels contribute to the pathogenesis of minimal hepatic encephalopathy in patients with hepatocellular carcinoma via STAT3 activation
Authors: Wu Hao , Li Ning , Jin Ronghua , Meng Qinghua , Chen Peng , Zhao Guoxian , Wang Rui , Li Li , Li Wei 
Published: January 2016

AbstractHepatocellular carcinoma (HCC) patients were grouped according to the degree of encephalopathy, with healthy volunteers as controls. We investigated clinical presentation, protein and mRNA expression of 14 cytokines and activation of six STAT proteins, the downstream signaling mediators. Levels of all 14 cytokines were significantly elevated in HCC patients with clinical hepatic encephalopathy. Statistical analysis showed that levels of IL-1β, IL-6, IFNγ, IL-17α, IFNλ2 and IFNλ3 were correlated with minimal hepatic encephalopathy (MHE). Multivariate regression analysis identified serum IL-6, IFNλ3 and IL-17α as independent risk factors for MHE. Increased mRNA levels of IL-6 and IFNγ were associated with MHE. Among the STAT proteins examined, only STAT3 was elevated in MHE. Treatment with a STAT3 inhibitor protected neurons from cytokine-induced apoptosis in vitro. In conclusion, this study identified potential biomarkers for MHE in HCC. The cytokines investigated may induce neural apoptosis via STAT3 in the pathogenesis of MHE in HCC.
The Neurochemical and Microstructural Changes in the Brain of Systemic Lupus Erythematosus Patients: A Multimodal MRI Study
Authors: Zhang Zhiyan , Wang Yukai , Shen Zhiwei , Yang Zhongxian , Li Li , Chen Dongxiao , Yan Gen , Cheng Xiaofang , Shen Yuanyu , Tang Xiangyong , Hu Wei , Wu Renhua 
Published: January 2016

AbstractThe diagnosis and pathology of neuropsychiatric systemic lupus erythematosus (NPSLE) remains challenging. Herein, we used multimodal imaging to assess anatomical and functional changes in brains of SLE patients instead of a single MRI approach generally used in previous studies. Twenty-two NPSLE patients, 21 non-NPSLE patients and 20 healthy controls (HCs) underwent 3.0 T MRI with multivoxel magnetic resonance spectroscopy, T1-weighted volumetric images for voxel based morphometry (VBM) and diffusional kurtosis imaging (DKI) scans. While there were findings in other basal ganglia regions, the most consistent findings were observed in the posterior cingulate gyrus (PCG). The reduction of multiple metabolite concentration was observed in the PCG in the two patient groups and the NPSLE patients were more prominent. The two patient groups displayed lower diffusional kurtosis (MK) values in the bilateral PCG compared with HCs (p < 0.01) as assessed by DKI. Grey matter reduction in the PCG was observed in the NPSLE group using VBM. Positive correlations among cognitive function scores and imaging metrics in bilateral PCG were detected. Multimodal imaging is useful for evaluating SLE subjects and potentially determining disease pathology. Impairments of cognitive function in SLE patients may be interpreted by metabolic and microstructural changes in the PCG.
Quantification of the Metabolic State in Cell-Model of Parkinson’s Disease by Fluorescence Lifetime Imaging Microscopy
Authors: Chakraborty Sandeep , Nian Fang-Shin , Tsai Jin-Wu , Karmenyan Artashes , Chiou Arthur 
Published: January 2016

AbstractIntracellular endogenous fluorescent co-enzymes, reduced nicotinamide adenine dinucleotide (NADH) and flavin adenine dinucleotide (FAD), play a pivotal role in cellular metabolism; quantitative assessment of their presence in living cells can be exploited to monitor cellular energetics in Parkinson’s disease (PD), a neurodegenerative disorder. Here, we applied two-photon fluorescence lifetime imaging microscopy (2P-FLIM) to noninvasively measure the fluorescence lifetime components of NADH and FAD and their relative contributions in MPP+(1-methyl-4-phenylpyridinium) treated neuronal cells, derived from PC12 cells treated with nerve growth factor (NGF), to mimic PD conditions. A systematic FLIM data analysis showed a statistically significant (p < 0.001) decrease in the fluorescence lifetime of both free and protein-bound NADH, as well as free and protein-bound FAD in MPP+treated cells. On the relative contributions of the free and protein-bound NADH and FAD to the life time, however, both the free NADH contribution and the corresponding protein-bound FAD contribution increase significantly (p < 0.001) in MPP+treated cells, compared to control cells. These results, which indicate a shift in energy production in the MPP+treated cells from oxidative phosphorylation towards anaerobic glycolysis, can potentially be used as cellular metabolic metrics to assess the condition of PD at the cellular level.
Synthesis of Large-Area WS2 monolayers with Exceptional Photoluminescence
Authors: McCreary Kathleen M. , Hanbicki Aubrey T. , Jernigan Glenn G. , Culbertson James C. , Jonker Berend T. 
Published: January 2016

AbstractMonolayer WS2 offers great promise for use in optical devices due to its direct bandgap and high photoluminescence intensity. While fundamental investigations can be performed on exfoliated material, large-area and high quality materials are essential for implementation of technological applications. In this work, we synthesize monolayer WS2 under various controlled conditions and characterize the films using photoluminescence, Raman and x-ray photoelectron spectroscopies. We demonstrate that the introduction of hydrogen to the argon carrier gas dramatically improves the optical quality and increases the growth area of WS2, resulting in films exhibiting mm2 coverage. The addition of hydrogen more effectively reduces the WO3 precursor and protects against oxidative etching of the synthesized monolayers. The stoichiometric WS2 monolayers synthesized using Ar + H2 carrier gas exhibit superior optical characteristics, with photoluminescence emission full width half maximum (FWHM) values below 40 meV and emission intensities nearly an order of magnitude higher than films synthesized in a pure Ar environment.
Fractal density and singularity analysis of heat flow over ocean ridges
Authors: Qiuming Cheng 
Published: January 2016

AbstractPeak heat flow occurs at mid-ocean ridges and decreases with the age of the oceanic lithosphere. Several plate models, including the Parsons and Sclater (PSM) model, Global Depth and Heat (GDH1) model and Constant Heat flow Applied on the Bottom Lithospheric Isotherm (CHABLIS) model, have been used to predict heat flow in the ocean lithosphere. The discrepancy between the predicted and measured heat flow in the younger lithosphere (i.e. younger than 55 Myr) influenced by local hydrothermal circulation has been used to estimate hydrothermal heat flux and investigate hydrothermal processes. We can modify the cooling models by substituting the ordinary mass density of lithosphere by fractal density with singularity. This new model provides a modified solution to fit the observed heat flow data used in other models in the literature throughout the age range. This model significantly improves the results for prediction of heat flow that were obtained using the PSM, GDH1 and CHABLIS models. Furthermore, the heat flow model does not exhibit special characteristics around any particular age of lithosphere. This raises a fundamental question about the existence of a “sealing” age and accordingly the hydrothermal flux estimation based on the cooling models.
Texture analysis in gel electrophoresis images using an integrative kernel-based approach
Authors: Fernandez-Lozano Carlos , Seoane Jose A. , Gestal Marcos , Gaunt Tom R. , Dorado Julian , Pazos Alejandro , Campbell Colin 
Published: January 2016

AbstractTexture information could be used in proteomics to improve the quality of the image analysis of proteins separated on a gel. In order to evaluate the best technique to identify relevant textures, we use several different kernel-based machine learning techniques to classify proteins in 2-DE images into spot and noise. We evaluate the classification accuracy of each of these techniques with proteins extracted from ten 2-DE images of different types of tissues and different experimental conditions. We found that the best classification model was FSMKL, a data integration method using multiple kernel learning, which achieved AUROC values above 95% while using a reduced number of features. This technique allows us to increment the interpretability of the complex combinations of textures and to weight the importance of each particular feature in the final model. In particular the Inverse Difference Moment exhibited the highest discriminating power. A higher value can be associated with an homogeneous structure as this feature describes the homogeneity; the larger the value, the more symmetric. The final model is performed by the combination of different groups of textural features. Here we demonstrated the feasibility of combining different groups of textures in 2-DE image analysis for spot detection.
Sublethal Dosage of Imidacloprid Reduces the Microglomerular Density of Honey Bee Mushroom Bodies
Authors: Peng Yi-Chan , Yang En-Cheng 
Published: January 2016

AbstractThe dramatic loss of honey bees is a major concern worldwide. Previous studies have indicated that neonicotinoid insecticides cause behavioural abnormalities and have proven that exposure to sublethal doses of imidacloprid during the larval stage decreases the olfactory learning ability of adults. The present study shows the effect of sublethal doses of imidacloprid on the neural development of the honey bee brain by immunolabelling synaptic units in the calyces of mushroom bodies. We found that the density of the synaptic units in the region of the calyces, which are responsible for olfactory and visual functions, decreased after being exposed to a sublethal dose of imidacloprid. This not only links a decrease in olfactory learning ability to abnormal neural connectivity but also provides evidence that imidacloprid damages the development of the nervous system in regions responsible for both olfaction and vision during the larval stage of the honey bee.
Host-associated coral reef microbes respond to the cumulative pressures of ocean warming and ocean acidification
Authors: Webster N. S. , Negri A. P. , Botté E. S. , Laffy P. W. , Flores F. , Noonan S. , Schmidt C. , Uthicke S. 
Published: January 2016

AbstractKey calcifying reef taxa are currently threatened by thermal stress associated with elevated sea surface temperatures (SST) and reduced calcification linked to ocean acidification (OA). Here we undertook an 8 week experimental exposure to near-future climate change conditions and explored the microbiome response of the corals Acropora millepora and Seriatopora hystrix, the crustose coralline algae Hydrolithon onkodes, the foraminifera Marginopora vertebralis and Heterostegina depressa and the sea urchin Echinometra sp. Microbial communities of all taxa were tolerant of elevated pCO2/reduced pH, exhibiting stable microbial communities between pH 8.1 (pCO2 479–499 μatm) and pH 7.9 (pCO2 738–835 μatm). In contrast, microbial communities of the CCA and foraminifera were sensitive to elevated seawater temperature, with a significant microbial shift involving loss of specific taxa and appearance of novel microbial groups occurring between 28 and 31 °C. An interactive effect between stressors was also identified, with distinct communities developing under different pCO2 conditions only evident at 31 °C. Microbiome analysis of key calcifying coral reef species under near-future climate conditions highlights the importance of assessing impacts from both increased SST and OA, as combinations of these global stressors can amplify microbial shifts which may have concomitant impacts for coral reef structure and function.
Crystal-Size Effects on Carbon Dioxide Capture of a Covalently Alkylamine-Tethered Metal-Organic Framework Constructed by a One-Step Self-Assembly
Authors: Kim Yun Kyeong , Hyun Sung-min , Lee Jae Hwa , Kim Tae Kyung , Moon Dohyun , Moon Hoi Ri 
Published: January 2016

AbstractTo enhance the carbon dioxide (CO2) uptake of metal-organic frameworks (MOFs), amine functionalization of their pore surfaces has been studied extensively. In general, amine-functionalized MOFs have been synthesized via post-synthetic modifications. Herein, we introduce a one-step construction of a MOF ([(NiLethylamine)(BPDC)] = MOFNH2; [NiLethylamine]2+ = [Ni(C12H32N8)]2+; BPDC2− = 4,4‘-biphenyldicarboxylate) possessing covalently tethered alkylamine groups without post-synthetic modification. Two-amine groups per metal centre were introduced by this method. MOFNH2 showed enhanced CO2 uptake at elevated temperatures, attributed to active chemical interactions between the amine groups and the CO2 molecules. Due to the narrow channels of MOFNH2, the accessibility to the channel of CO2 is the limiting factor in its sorption behaviour. In this context, only crystal size reduction of MOFNH2 led to much faster and greater CO2 uptake at low pressures.
Unveiling Spatial Epidemiology of HIV with Mobile Phone Data
Authors: Brdar Sanja , Gavrić Katarina , Ćulibrk Dubravko , Crnojević Vladimir 
Published: January 2016

AbstractAn increasing amount of geo-referenced mobile phone data enables the identification of behavioral patterns, habits and movements of people. With this data, we can extract the knowledge potentially useful for many applications including the one tackled in this study - understanding spatial variation of epidemics. We explored the datasets collected by a cell phone service provider and linked them to spatial HIV prevalence rates estimated from publicly available surveys. For that purpose, 224 features were extracted from mobility and connectivity traces and related to the level of HIV epidemic in 50 Ivory Coast departments. By means of regression models, we evaluated predictive ability of extracted features. Several models predicted HIV prevalence that are highly correlated (>0.7) with actual values. Through contribution analysis we identified key elements that correlate with the rate of infections and could serve as a proxy for epidemic monitoring. Our findings indicate that night connectivity and activity, spatial area covered by users and overall migrations are strongly linked to HIV. By visualizing the communication and mobility flows, we strived to explain the spatial structure of epidemics. We discovered that strong ties and hubs in communication and mobility align with HIV hot spots.
A graphene oxide/amidoxime hydrogel for enhanced uranium capture
Authors: Wang Feihong , Li Hongpeng , Liu Qi , Li Zhanshuang , Li Rumin , Zhang Hongsen , Liu Lianhe , Emelchenko G. A. , Wang Jun 
Published: January 2016

AbstractThe efficient development of selective materials for the recovery of uranium from nuclear waste and seawater is necessary for their potential application in nuclear fuel and the mitigation of nuclear pollution. In this work, a graphene oxide/amidoxime hydrogel (AGH) exhibits a promising adsorption performance for uranium from various aqueous solutions, including simulated seawater. We show high adsorption capacities (Qm = 398.4 mg g−1) and high % removals at ppm or ppb levels in aqueous solutions for uranium species. In the presence of high concentrations of competitive ions such as Mg2+, Ca2+, Ba2+ and Sr2+, AGH displays an enhanced selectivity for uranium. For low uranium concentrations in simulated seawater, AGH binds uranium efficiently and selectively. The results presented here reveal that the AGH is a potential adsorbent for remediating nuclear industrial effluent and adsorbing uranium from seawater.
Down regulated lncRNA MEG3 eliminates mycobacteria in macrophages via autophagy
Authors: Pawar Kamlesh , Hanisch Carlos , Palma Vera Sergio Eliseo , Einspanier Ralf , Sharbati Soroush 
Published: January 2016

AbstractSmall non-coding RNA play a major part in host response to bacterial agents. However, the role of long non-coding RNA (lncRNA) in this context remains unknown. LncRNA regulate gene expression by acting e.g. as transcriptional coactivators, RNA decoys or microRNA sponges. They control development, differentiation and cellular processes such as autophagy in disease conditions. Here, we provide an insight into the role of lncRNA in mycobacterial infections. Human macrophages were infected with Mycobacterium bovis BCG and lncRNA expression was studied early post infection. For this purpose, lncRNA with known immune related functions were preselected and a lncRNA specific RT-qPCR protocol was established. In addition to expression-based prediction of lncRNA function, we assessed strategies for thorough normalisation of lncRNA. Arrayed quantification showed infection-dependent repression of several lncRNA including MEG3. Pathway analysis linked MEG3 to mTOR and PI3K-AKT signalling pointing to regulation of autophagy. Accordingly, IFN-γ induced autophagy in infected macrophages resulted in sustained MEG3 down regulation and lack of IFN-γ allowed for counter regulation of MEG3 by viable M. bovis BCG. Knockdown of MEG3 in macrophages resulted in induction of autophagy and enhanced eradication of intracellular M. bovis BCG.