bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial variation of the rain–snow temperature threshold across the Northern Hemisphere
Authors: Jennings Keith S. , Winchell Taylor S. , Livneh Ben , Molotch Noah P. 
Published: March 2018

AbstractDespite the importance of precipitation phase to global hydroclimate simulations, many land surface models use spatially uniform air temperature thresholds to partition rain and snow. Here we show, through the analysis of a 29-year observational dataset (n = 17.8 million), that the air temperature at which rain and snow fall in equal frequency varies significantly across the Northern Hemisphere, averaging 1.0 °C and ranging from –0.4 to 2.4 °C for 95% of the stations. Continental climates generally exhibit the warmest rain–snow thresholds and maritime the coolest. Simulations show precipitation phase methods incorporating humidity perform better than air temperature-only methods, particularly at relative humidity values below saturation and air temperatures between 0.6 and 3.4 °C. We also present the first continuous Northern Hemisphere map of rain–snow thresholds, underlining the spatial variability of precipitation phase partitioning. These results suggest precipitation phase could be better predicted using humidity and air temperature in large-scale land surface model runs.
Improving imputation in disease-relevant regions: lessons from cystic fibrosis
Authors: Panjwani Naim , Xiao Bowei , Xu Lizhen , Gong Jiafen , Keenan Katherine , Lin Fan , He Gengming , Baskurt Zeynep , Kim Sangook , Zhang Lin , Esmaeili Mohsen , Blackman Scott , Scherer Stephen W. , Corvol Harriet , Drumm Mitchell , Knowles Michael , Cutting Garry , Rommens Johanna M. , Sun Lei , Strug Lisa J. 
Published: March 2018

AbstractDoes genotype imputation with public reference panels identify variants contributing to disease? Genotype imputation using the 1000 Genomes Project (1KG; 2504 individuals) displayed poor coverage at the causal cystic fibrosis (CF) transmembrane conductance regulator (CFTR) locus for the International CF Gene Modifier Consortium. Imputation with the larger Haplotype Reference Consortium (HRC; 32,470 individuals) displayed improved coverage but low sensitivity of variants clinically relevant for CF. A hybrid reference that combined whole genome sequencing (WGS) from 101 CF individuals with the 1KG imputed a greater number of single-nucleotide variants (SNVs) that would be analyzed in a genetic association study (r2 ≥ 0.3 and MAF ≥ 0.5%) than imputation with the HRC, while the HRC excelled in the lower frequency spectrum. Using the 1KG or HRC as reference panels missed the most common CF-causing variants or displayed low imputation accuracy. Designs that incorporate population-specific WGS can improve imputation accuracy at disease-specific loci, while imputation using public data sets can omit disease-relevant genotypes.
Baseline mapping of Lassa fever virology, epidemiology and vaccine research and development
Authors: Hallam Hoai J. , Hallam Steven , Rodriguez Sergio E. , Barrett Alan D. T. , Beasley David W. C. , Chua Arlene , Ksiazek Thomas G. , Milligan Gregg N. , Sathiyamoorthy Vaseeharan , Reece Lisa M. 
Published: March 2018

AbstractLassa fever (LF) is a zoonotic disease associated with acute and potentially fatal hemorrhagic illness caused by the Lassa virus (LASV), a member of the family Arenaviridae. It is generally assumed that a single infection with LASV will produce life-long protective immunity. This suggests that protective immunity induced by vaccination is an achievable goal and that cell-mediated immunity may play a more important role in protection, at least following natural infection. Seropositive individuals in endemic regions have been shown to have LASV-specific T cells recognizing epitopes for nucleocapsid protein (NP) and glycoprotein precursor (GPC), suggesting that these will be important vaccine immunogens. The role of neutralizing antibodies in protective immunity is still equivocal as recent studies suggest a role for neutralizing antibodies. There is extensive genetic heterogeneity among LASV strains that is of concern in the development of assays to detect and identify all four LASV lineages. Furthermore, the gene disparity may complicate the synthesis of effective vaccines that will provide protection across multiple lineages. Non-human primate models of LASV infection are considered the gold standard for recapitulation of human LF. The most promising vaccine candidates to date are the ML29 (a live attenuated reassortant of Mopeia and LASV), vesicular stomatitis virus (VSV) and vaccinia-vectored platforms based on their ability to induce protection following single doses, high rates of survival following challenge, and the use of live virus platforms. To date no LASV vaccine candidates have undergone clinical evaluation.
Plasmon induced modification of silicon nanocrystals photoluminescence in presence of gold nanostripes
Authors: Dyakov S. A. , Zhigunov D. M. , Marinins A. , Shalygina O. A. , Vabishchevich P. P. , Shcherbakov M. R. , Presnov D. E. , Fedyanin A. A. , Kashkarov P. K. , Popov S. , Gippius N. A. , Tikhodeev S. G. 
Published: March 2018

AbstractWe report on the results of theoretical and experimental studies of photoluminescense of silicon nanocrystals in the proximity to plasmonic modes of different types. In the studied samples, the type of plasmonic mode is determined by the filling ratio of a one-dimensional array of gold stripes which covers the thin film with silicon nanocrystals on a quartz substrate. We analyze the extinction, photoluminesce spectra and decay kinetics of silicon nanocrystals and show that the incident and emitted light is coupled to the corresponding plasmonic mode. We demonstrate the modification of the extinction and photoluminesce spectra under the transition from wide to narrow gold stripes. The experimental extinction and photoluminescense spectra are in good agreement with theoretical calculations performed by the rigorous coupled wave analysis. We study the contribution of individual silicon nanocrystals to the overall photoluminescense intensity, depending on their spacial position inside the structure.
Intrinsic Frequency Analysis and Fast Algorithms
Authors: Tavallali Peyman , Koorehdavoudi Hana , Krupa Joanna 
Published: March 2018

AbstractIntrinsic Frequency (IF) has recently been introduced as an ample signal processing method for analyzing carotid and aortic pulse pressure tracings. The IF method has also been introduced as an effective approach for the analysis of cardiovascular system dynamics. The physiological significance, convergence and accuracy of the IF algorithm has been established in prior works. In this paper, we show that the IF method could be derived by appropriate mathematical approximations from the Navier-Stokes and elasticity equations. We further introduce a fast algorithm for the IF method based on the mathematical analysis of this method. In particular, we demonstrate that the IF algorithm can be made faster, by a factor or more than 100 times, using a proper set of initial guesses based on the topology of the problem, fast analytical solution at each point iteration, and substituting the brute force algorithm with a pattern search method. Statistically, we observe that the algorithm presented in this article complies well with its brute-force counterpart. Furthermore, we will show that on a real dataset, the fast IF method can draw correlations between the extracted intrinsic frequency features and the infusion of certain drugs.
Late cornified envelope 1C (LCE1C), a transcriptional target of TAp63 phosphorylated at T46/T281, interacts with PRMT5
Authors: Yabuta Norikazu , Ota Chie , Sasakura Towa , Naito Yoko , Okuzaki Daisuke , Fukushima Kohshiro , Nojima Hiroshi 
Published: March 2018

Abstractp63, a transcriptional factor that belongs to the p53 family, regulates epidermal differentiation, stemness, cell death, tumorigenesis, metastasis, and senescence. However, its molecular mechanism remains elusive. We report here that TAp63 phosphorylated at T46/T281 specifically upregulates the late cornified envelope 1C (LCE1C) gene that is essential at a relatively late stage of epithelial development. We identified these phosphorylation sites during a search for the targets of Cyclin G-associated kinase (GAK) in vitro. LCE1C was drastically upregulated by doxycycline-dependent expression of Myc-TAp63 wild-type protein. Luciferase reporter assays using the promoter region of the LCE1C gene confirmed that the phosphorylations of TAp63-T46/T281 contributed to full transcriptional activation of the LCE1C gene. LCE1C interacted with protein arginine methyltransferase 5 (PRMT5) and translocated it from the nucleus to the cytoplasm. Mass spectrometry and co-immunoprecipitation identified importin-α as one of the association partners of LCE1C. In summary, we propose that the GAK_TAp63-pT46/pT281_LCE1C axis plays an important role in preventing the nuclear function of PRMT5.
Tidal and diel orchestration of behaviour and gene expression in an intertidal mollusc
Authors: Schnytzer Y. , Simon-Blecher N. , Li J. , Waldman Ben-Asher H. , Salmon-Divon M. , Achituv Y. , Hughes M. E. , Levy O. 
Published: March 2018

AbstractIntertidal inhabitants are exposed to the 24-hour solar day, and the 12.4 hour rising and falling of the tides. One or both of these cycles govern intertidal organisms’ behaviour and physiology, yet little is known about the molecular clockworks of tidal rhythmicity. Here, we show that the limpet Cellana rota exhibits robust tidally rhythmic behaviour and gene expression. We assembled a de-novo transcriptome, identifying novel tidal, along with known circadian clock genes. Surprisingly, most of the putative circadian clock genes, lack a typical rhythmicity. We identified numerous tidally rhythmic genes and pathways commonly associated with the circadian clock. We show that not only is the behaviour of an intertidal organism in tune with the tides, but so too are many of its genes and pathways. These findings highlight the plasticity of biological timekeeping in nature, strengthening the growing notion that the role of ‘canonical’ circadian clock genes may be more fluid than previously thought, as exhibited in an organism which has evolved in an environment where tidal oscillations are the dominant driving force.
Complement C1q stimulates the progression of hepatocellular tumor through the activation of discoidin domain receptor 1
Authors: Lee Ji-Hyun , Poudel Barun , Ki Hyeon-Hui , Nepali Sarmila , Lee Young-Mi , Shin Jeon-Soo , Kim Dae-Ki 
Published: March 2018

AbstractC1q is known to perform several functions in addition to the role it plays in complement activation. C1q contains a collagen-like portion and DDR1 (discoidin domain receptor 1) is a well-known collagen receptor. Accordingly, we hypothesized C1q might be a novel ligand of DDR1. This study shows for the first time C1q directly induces the activation and upregulation of DDR1, and that this leads to enhanced migration and invasion of HepG2 cells. In addition, C1q was found to induce the activations of mitogen-activated protein kinases (MAPKs) and phosphoinositide 3-kinase (PI3K)/Akt signaling, and to increase the expressions of matrix metalloproteinases (MMP2 and 9). Our results reveal a relationship between C1q and DDR1 and suggest C1q-induced DDR1 activation signaling may be involved in the progression of hepatocellular carcinoma.
Identification of new inhibitors against human Great wall kinase using in silico approaches
Authors: Ammarah Ummi , Kumar Amit , Pal Rajesh , Bal Naresh C. , Misra Gauri 
Published: March 2018

AbstractMicrotubule associated serine/threonine kinase (MASTL) is an important Ser/Thr kinase belonging to the family of AGC kinases. It is the human orthologue of Greatwall kinase (Gwl) that plays a significant role in mitotic progression and cell cycle regulation. Upregulation of MASTL in various cancers and its association with poor patient survival establishes it as an important drug target in cancer therapy. Nevertheless, the target remains unexplored with the paucity of studies focused on identification of inhibitors against MASTL, which emphasizes the relevance of our present study. We explored various drug databases and performed virtual screening of compounds from both natural and synthetic sources. A list of promising compounds displaying high binding characteristics towards MASTL protein is reported. Among the natural compounds, we found a 6-hydroxynaphthalene derivative ZINC85597499 to display best binding energy value of −9.32 kcal/mol. While among synthetic compounds, a thieno-pyrimidinone based tricyclic derivative ZINC53845290 compound exhibited best binding affinity of value −7.85 kcal/mol. MASTL interactions with these two compounds were further explored using molecular dynamics simulations. Altogether, this study identifies potential inhibitors of human Gwl kinase from both natural and synthetic origin and calls for studying these compounds as potential drugs for cancer therapy.
Microbiome-metabolome signatures in mice genetically prone to develop dementia, fed a normal or fatty diet
Authors: Sanguinetti Elena , Collado Maria Carmen , Marrachelli Vannina G. , Monleon Daniel , Selma-Royo Marta , Pardo-Tendero Mercedes M. , Burchielli Silvia , Iozzo Patricia 
Published: March 2018

AbstractCognitive decline, obesity and gut dysfunction or microbial dysbiosis occur in association. Our aim was to identify gut microbiota-metabolomics signatures preceding dementia in genetically prone (3xtg) mice, with and without superimposed high-fat diet. We examined the composition and diversity of their gut microbiota, and serum and faecal metabolites. 3xtg mice showed brain hypometabolism typical of pre-demented stage, and lacked the physiological bacterial diversity between caecum and colon seen in controls. Cluster analyses revealed distinct profiles of microbiota, and serum and fecal metabolome across groups. Elevation in Firmicutes-to-Bacteroidetes abundance, and exclusive presence of Turicibacteraceae, Christensenellaceae, Anaeroplasmataceae and Ruminococcaceae, and lack of Bifidobacteriaceae, were also observed. Metabolome analysis revealed a deficiency in unsaturated fatty acids and choline, and an overabundance in ketone bodies, lactate, amino acids, TMA and TMAO in 3xtg mice, with additive effects of high-fat diet. These metabolic alterations were correlated with high prevalence of Enterococcaceae, Staphylococcus, Roseburia, Coprobacillus and Dorea, and low prevalence of S24.7, rc4.4 and Bifidobacterium, which in turn related to cognitive impairment and cerebral hypometabolism. Our results indicate an effect of transgenic background on gut microbiome-metabolome, enhanced by high-fat diet. The resulting profiles may precede overt cognitive impairment, suggesting their predictive or risk-stratifying potential.
The tobacco carcinogen NNK drives accumulation of DNMT1 at the GR promoter thereby reducing GR expression in untransformed lung fibroblasts
Authors: Taylor Kerryn M. , Wheeler Roxanne , Singh Nimisha , Vosloo Dalene , Ray David W. , Sommer Paula 
Published: March 2018

AbstractSmall cell lung cancer (SCLC) is a highly aggressive, predominantly cigarette smoke-induced tumour with poor prognosis. The glucocorticoid receptor (GR), a SCLC tumour suppressor gene, is typically reduced in SCLC. We now show that SCLC cells express high levels of DNA methyltransferase 1 (DNMT1) which accumulates at the GR promoter. DNMT1 expression is further increased by exposure to the tobacco carcinogen NNK. In the untransformed human lung fibroblast cell line, MRC-5, short term NNK treatment decreases GRα mRNA and protein expression due to accumulation of DNMT1 at the GR promoter. Long term NNK treatment results in persistently augmented DNMT1 levels with lowered GR levels. Long term exposure to NNK slows cell proliferation and induces DNA damage, while the GR antagonist RU486 stimulates proliferation and protects against DNA damage. Although both NNK and RU486 treatment increases methylation at the GR promoter, neither are sufficient to prevent senescence in this context. NNK exposure results in accumulation of DNMT1 at the GR promoter in untransformed lung cells mimicking SCLC cells, directly linking tobacco smoke exposure to silencing of the GR, an important step in SCLC carcinogenesis.
Direct synthesis and in situ characterization of monolayer parallelogrammic rhenium diselenide on gold foil
Authors: Jiang Shaolong , Hong Min , Wei Wei , Zhao Liyun , Zhang Na , Zhang Zhepeng , Yang Pengfei , Gao Nan , Zhou Xiebo , Xie Chunyu , Shi Jianping , Huan Yahuan , Tong Lianming , Zhao Jijun , Zhang Qing , Fu Qiang , Zhang Yanfeng 
Published: March 2018

AbstractRhenium diselenide (ReSe2) has recently garnered great research interest due to its distorted 1T structure, anisotropic physical properties, and applications in polarization-sensitive photodetectors. However, ReSe2 synthesized by chemical vapor deposition (CVD) is usually a multilayer/polycrystalline material containing numerous grain boundaries, thereby hindering its further applications. Here we describe the direct CVD growth of high-quality monolayer ReSe2 single crystals with a parallelogram shape arising from its anisotropic structure on a gold foil substrate. In particular, we use low-energy electron microscopy/diffraction combined with scanning tunneling microscopy/spectroscopy to determine the atomic-scale structure, domain orientation/boundaries, and band features of monolayer ReSe2 flakes grown directly on gold foils. This work may open new opportunities for the direct synthesis and in situ characterization of CVD-grown monolayer ReSe2.
Optimization of Preparation of Zeolite Y Dealuminate Catalysts for Glycerol Conversion to Glycerol Mono Laurate
Authors: Dwi Anggoro Didi , Buchori Luqman , Istadi Istadi , Fadhil R. P. , Antonio G. 
Published: March 2018

This Research has been done to analyze Zeolite Y CBV 712 as a catalyst. Zeolite Y CBV 712 was dealuminated by treating it with H2SO4 solution, with 3 – 8 M concentration at 40 – 60 oC. The dealumination treatment runs for 4 hours. Then, dealuminated zeolite was calcinated with a furnace for 3 hours with temperature range between 500 – 600 oC. Dealuminated zeolit Y then tested to synthesize Glycerol Mono Laurate (GML). By Analysis of Variance (ANOVA) analyze, indicated that the higher Glycerol Monolaurate yield, X2 factor is the most significance factor, indicating with high F-value (29.60768) and low P-value (0.001600). Objective function from this tests, is used to determine the optimum value between dealumination temperature (X1), acid concentration used (X2) and calcinating temperature (X3). The relation between each operating variables and the responses is shown in mathematical equation below :
[see formula in PDF]
The optimum condition obtained is 43.25oC for dealumination temperature, 5.45 M for acid concentration and 614oC for calcination temperature. According to the optimum condition obtained, the glycerol monolaurate yield obtained is 59.470%.
Mood Components in Cocoa and Chocolate: The Mood Pyramid
Authors: Tuenter Emmy , Foubert Kenn , Pieters Luc 
Published: March 2018

AbstractCocoa and chocolate, prepared from cocoa beans that originate from the fruits of the cocoa tree Theobroma cacao, have a long-standing reputation as healthy food, including mood-enhancing effects. In spite of many clinical trials with chocolate, cocoa, or its constituents, the mechanisms of action on mood and cognition remain unclear. More in particular, it is still controversial which constituents may contribute to the psychopharmacological activities, ranging from the major cacao flavanols and methylxanthines to the minor amines, amides, and alkaloids. In this review a critical appraisal is made of recent studies on mood and cognition, with a special emphasis on analytical characterization of the test samples. It is concluded that the mood and cognition-enhancing effects of cocoa and chocolate can be ranked from more general activities associated with flavanols and methylxanthines, to more specific activities related to minor constituents such as salsolinol, with on top the orosensory properties of chocolate. Therefore, the “mood pyramid” of cocoa and chocolate is proposed as a new concept. To understand the role and interactions of the different major and minor constituents of cocoa, it is recommended that all test samples used in future in vitro, in vivo, or human studies should be phytochemically characterized in much more detail than is common practice today.
Current Management of Scaphoid Nonunion Based on the Biomechanical Study
Authors: Oka Kunihiro , Moritomo Hisao 
Published: March 2018

AbstractScaphoid nonunion causes abnormal wrist kinematics and typically leads to carpal collapse and subsequent degenerative arthritis of the wrist. However, the natural history, including carpal collapse and degenerative arthritis of scaphoid nonunion, may vary at different fracture locations. This article reviews recent biomechanical studies related to the natural history of scaphoid nonunion. In the distal-type fractures (type B2 in Herbert classification), where the fracture located distal to the scaphoid apex, the proximal scaphoid fragment and lunate, which are connected through the dorsal scapholunate interosseous ligament (DSLIL) and dorsal intercarpal ligament (DIC), extend together, and the distal fragment of the scaphoid flexes individually. Therefore, untreated type B2 fractures normally show the humpback deformity, resulting in dorsal intercalated segment instability deformity relatively earlier after the injury. In the proximal-type fractures (type B1), where the fracture is located proximal to the scaphoid apex, the connection between the distal fragment and lunate is preserved through the DSLIL and DIC so that the scaphoid–lunate complex remains stable and the carpal collapse is less severe than that in distal-type fractures. The fracture location relative to the apex of the dorsal scaphoid ridge is a reliable landmark in the determination of the natural history of scaphoid nonunion.
Interobserver Analysis of CEUS-Derived Perfusion in Fibrotic and Inflammatory Crohn’s Disease
Authors: Nylund Kim , Sævik Fredrik , Leh Sabine , Pfeffer Frank , Hausken Trygve , Gilja Odd 
Published: March 2018

Abstract
Aim To examine if there are perfusion differences in fibrotic versus inflammatory lesions in patients with Crohn’s disease (CD) and to assess the interobserver reliability of the analysis.
Materials and Methods 37 patients with Crohn’s disease were prospectively recruited. 20 were operated and 18 of them had fibrotic disease. 17 received and were mostly responsive to medical treatment (14/17). Each patient underwent clinical scoring and ultrasound (US) examination with high-frequency linear transducers and US contrast. The perfusion analysis was performed using exported DICOM videos with VueBox® (Bracco Suisse SA, Genève, Switzerland). The program fits the time-intensity data to a standardized curve, from which several parameters can be derived, such as amplitude-based peak enhancement (PE), total area under the curve (AUC), area under the curve during wash-in and wash-out (WiAUC and WoAUC), wash-in rate (WiR) and wash-out rate (WoR) and time-based rise time (RT), fall time (FT) and mean transit time (MTT).
Results There was a significant difference between the groups for the parameters PE (p = 0.032), WiAUC (p = 0.035) and WoR (p = 0.038). We found no significant difference for RT, MTT, FT, WiR, AUC and WoAUC. An interobserver analysis showed correlation between two observers for all the parameters (r = 0.66 – 0.92, p < 0.001), except MTT (r = 0.46, p = 0.129). Bland Altman analysis revealed a fixed bias for the parameters PE, WiAUC and RT.
Conclusion The amplitude-based parameters PE, WiAUC and WoR could potentially be used to separate fibrotic and inflammatory lesions in patients suffering from CD due to significant differences and low interobserver variability.