bluuebunny/crossref_metadata_2025_split huggingface dataset:
Next‐Gen Sequencing‐Based Mapping and Identification of Ethyl Methanesulfonate‐Induced Mutations in Arabidopsis thaliana
Authors: Zhang Xue‐Cheng , Millet Yves , Ausubel Frederick M. , Borowsky Mark 
Published: October 2014

AbstractForward genetic analysis using ethyl methanesulfonate (EMS) mutagenesis has proven to be a powerful tool in biological research, but identification and cloning of causal mutations by conventional genetic mapping approaches is a painstaking process. Recent advances in next‐gen sequencing have greatly invigorated the process of identifying EMS‐induced mutations corresponding to a specific phenotype in model genetic hosts, including the plant Arabidopsis thaliana and the nematode Caenorhabditis elegans. Next‐gen sequencing of bulked F2 mutant recombinants produces a wealth of high‐resolution genetic data, provides enhanced delimitation of the genomic location of mutations, and greatly reduces hands‐on time while maintaining high accuracy and reproducibility. In this unit, a detailed procedure to simultaneously map and identify EMS mutations in Arabidopsis is described. Curr. Protoc. Mol. Biol. 108:7.18.1‐7.18.16. © 2014 by John Wiley & Sons, Inc.
Protein Synthesis Using a Reconstituted Cell‐Free System
Authors: Tuckey Corinna , Asahara Haruichi , Zhou Ying , Chong Shaorong 
Published: October 2014

AbstractMost cell‐free protein‐synthesis systems are based on cell extracts, which often contain undesirable activities. Reconstituted systems, by contrast, are composed of a defined number of purified and recombinant components with minimal nuclease and protease activities. This unit describes the use of a particular commercial reconstituted system, PURExpress. This system allows in vitro synthesis of proteins from mRNA and circular and linear DNA templates, as well as co‐translational labeling of proteins. Unique to this system, all recombinant protein components of the system are His‐tagged, allowing purification of the synthesized untagged protein by removing the rest of the system's components. Newly synthesized proteins can often be visible on an SDS‐PAGE gel and directly assayed for their functions without labeling and purification. Certain components of the system, such as ribosomes or release factors, can be omitted for specific applications. Such “delta” versions of the system are well suited for studies of bacterial translation, assays of ribosome function, incorporation of unnatural amino acids, and ribosome display of protein libraries. Curr. Protoc. Mol. Biol. 108:16.31.1‐16.31.22. © 2014 by John Wiley & Sons, Inc.
Genome‐Wide Analysis of Nucleosome Positions, Occupancy, and Accessibility in Yeast: Nucleosome Mapping, High‐Resolution Histone ChIP, and NCAM
Authors: Rodriguez Jairo , McKnight Jeffrey N. , Tsukiyama Toshio 
Published: October 2014

AbstractBecause histones bind DNA very tightly, the location on DNA and the level of occupancy of a given DNA sequence by nucleosomes can profoundly affect accessibility of non‐histone proteins to chromatin, affecting virtually all DNA‐dependent processes, such as transcription, DNA repair, DNA replication and recombination. Therefore, it is often necessary to determine positions and occupancy of nucleosomes to understand how DNA‐dependent processes are regulated. Recent technological advances made such analyses feasible on a genome‐wide scale at high resolution. In addition, we have recently developed a method to measure nuclease accessibility of nucleosomes on a global scale. This unit describes methods to map nucleosome positions, to determine nucleosome density, and to determine nuclease accessibility of nucleosomes using deep sequencing. Curr. Protoc. Mol. Biol. 108:21.28.1‐21.28.16. © 2014 by John Wiley & Sons, Inc.
Confocal Microscopy for High‐Resolution and High‐Content Analysis of the Cell Cycle
Authors: Furia Laura , Pelicci Piergiuseppe , Faretta Mario 
Published: October 2014

AbstractOptical fluorescence microscopy offers a wide range of technological solutions to address many questions in biomedical research. Spatial resolution has been greatly improved by the use of confocal microscopes, providing a 3‐D analysis of the intracellular space. Automation has contributed to make confocal analysis available for high‐content image cytometry studies. However, the storage, browsing, and analysis of the amount of data generated can challenge the feasibility of such studies. Presented in this chapter is a multistep acquisition and analysis protocol that can bypass such difficulties by an analysis‐driven data collection. Cell‐cycle analysis of low‐resolution data can be employed to select cell populations of interest that can then be imaged at extremely high resolution and subjected to high‐content analysis.Curr. Protoc. Cytom. 70:7.42.1‐7.42.14. © 2014 by John Wiley & Sons, Inc.
Assessing WRF model parameter sensitivity: A case study with 5 day summer precipitation forecasting in the Greater Beijing Area
Authors: Di Zhenhua , Duan Qingyun , Gong Wei , Wang Chen , Gan Yanjun , Quan Jiping , Li Jianduo , Miao Chiyuan , Ye Aizhong , Tong Charles 
Published: October 2014

AbstractA global sensitivity analysis method was used to identify the parameters of the Weather Research and Forecasting (WRF) model that exert the most influence on precipitation forecasting. Twenty‐three adjustable parameters were selected from seven physical components of the WRF model. The sensitivity was evaluated based on skill scores calculated over nine 5 day precipitation forecasts during the summer seasons from 2008 to 2010 in the Greater Beijing Area in China. We found that eight parameters are more sensitive than others. Storm type seems to have no impact on the list of sensitive parameters but does influence the degree of sensitivity. We also examined the physical interpretation of parameter sensitivity. This analysis is useful for further optimization of the WRF model parameters to improve precipitation forecasting.
Modeling the evolution of climate‐sensitive Arctic subsea permafrost in regions of extensive gas expulsion at the West Yamal shelf
Authors: Portnov Alexey , Mienert Jurgen , Serov Pavel 
Published: October 2014

AbstractThawing subsea permafrost controls methane release from the Russian Arctic shelf having a considerable impact on the climate‐sensitive Arctic environment. Expulsions of methane from shallow Russian Arctic shelf areas may continue to rise in response to intense degradation of relict subsea permafrost. Here we show modeling of the permafrost evolution from the Late Pleistocene to present time at the West Yamal shelf. Modeling results suggest a highly dynamic permafrost system that directly responds to even minor variations of lower and upper boundary conditions, e.g., geothermal heat flux from below and/or bottom water temperature changes from above permafrost. Scenarios of permafrost evolution show a potentially nearest landward modern extent of the permafrost at the West Yamal shelf limited by ~17 m isobaths, whereas its farthest seaward extent coincides with ~100 m isobaths. The model also predicts seaward tapering of relict permafrost with a maximal thickness of 275–390 m near the shoreline. Previous field observations detected extensive emissions of free gas into the water column at the transition zone between today's shallow water permafrost (<20 m) and deeper water nonpermafrost areas (>20 m). The model adapts well to corresponding heat flux and ocean temperature data, providing crucial information about the modern permafrost conditions. It shows current locations of upper and lower permafrost boundaries and evidences for possible release of methane from the seabed to the hydrosphere in a warming Arctic.
Rizatriptan
Authors: Diao Xingxing 
Published: October 2014

Abstract

Rizatriptan is a 5‐HT agonist used to treat migraine headaches. The absorption and disposition of [
14
C]‐rizatriptan were investigated in healthy human male subjects. After a single oral 10‐mg dose administration, unchanged rizatriptan and its metabolites were excreted mainly in the urine (82% of the dose). Approximately 14% of rizatriptan dose was excreted in urine as intact parent drug. In a high‐dose study (60‐mg p.o.), five metabolites were identified in urine samples. They were rizatriptan‐
N
10
‐oxide, triazolomethyl‐indole‐3‐acetic acid, 6‐hydroxy‐rizatriptan, 6‐hydroxy‐rizatriptan sulfate, and
N
10
‐monodesmethyl‐rizatriptan. Urinary excretion of triazolomethyl‐indole‐3‐acetic acid accounted for 51% of the dose.
Systemic chemotherapy decreases brain glucose metabolism
Authors: Horky Laura L. , Gerbaudo Victor H. , Zaitsev Alexander , Plesniak Wen , Hainer Jon , Govindarajulu Usha , Kikinis Ron , Dietrich Jörg 
Published: October 2014

AbstractObjectiveCancer patients may experience neurologic adverse effects, such as alterations in neurocognitive function, as a consequence of chemotherapy. The mechanisms underlying such neurotoxic syndromes remain poorly understood. We here describe the temporal and regional effects of systemically administered platinum‐based chemotherapy on glucose metabolism in the brain of cancer patients.MethodsUsing sequential FDG‐PET/CT imaging prior to and after administration of chemotherapy, we retrospectively characterized the effects of intravenously administered chemotherapy on brain glucose metabolism in a total of 24 brain regions in a homogenous cohort of 10 patients with newly diagnosed non‐small‐cell lung cancer.ResultsSignificant alterations of glucose metabolism were found in response to chemotherapy in all gray matter structures, including cortical structures, deep nuclei, hippocampi, and cerebellum. Metabolic changes were also notable in frontotemporal white matter (WM) network systems, including the corpus callosum, subcortical, and periventricular WM tracts.InterpretationOur data demonstrate a decrease in glucose metabolism in both gray and white matter structures associated with chemotherapy. Among the affected regions are those relevant to the maintenance of brain plasticity and global neurologic function. This study potentially offers novel insights into the spatial and temporal effects of systemic chemotherapy on brain metabolism in cancer patients.
Reversed‐Polarity Synthesis of Diaryl Ketones through Palladium‐Catalyzed Direct Arylation of 2‐Aryl‐1,3‐dithianes
Authors: Yucel Baris , Walsh Patrick J. 
Published: October 2014

AbstractAn umpolung approach to the synthesis of diaryl ketones has been developed based on in situ generation of acyl anion equivalents and their catalytic arylation. This method entails the base‐promoted, palladium‐catalyzed direct C‐H arylation of 2‐aryl‐1,3‐dithianes with aryl bromides. Use of MN(SiMe3)2 (M=Li, Na) base results in reversible deprotonation of the weakly acidic dithiane. In the presence of a Pd(NiXantphos)‐based catalyst and aryl bromide, cross‐coupling of the metallated 2‐aryl‐1,3‐dithiane takes place under mild conditions (2 h at rt) with yields as high as 96 %. The resulting 2,2‐diaryl‐1,3‐dithianes were converted into diaryl ketones by either molecular iodine, N‐bromo succinimide (NBS) or Selectfluor in the presence of water. The dithiane arylation/hydrolysis can be performed in a one‐pot procedure to yield a variety of diaryl ketones in good to excellent yields. This method is suitable for rapid and large‐scale synthesis of diaryl ketones. A one‐pot preparation of anti‐cholesterol drug fenofibrate (TriCor®) has been achieved on 10.0 mmol scale in 86 % yield.magnified image
Leptin, adiponectin, and heart rate variability among police officers
Authors: Charles Luenda E. , Burchfiel Cecil M. , Sarkisian Khachatur , Li Shengqiao , Miller Diane B. , Gu Ja K. , Fekedulegn Desta , Violanti John M. , Andrew Michael E. 
Published: October 2014

ObjectivesPolice officers have a high prevalence of cardiovascular disease (CVD). Reduced heart rate variability (HRV) is known to increase CVD risk. Leptin and adiponectin may be related to CVD health. Therefore, our objective was to investigate the relationship between these variables and HRV.MethodsLeptin and adiponectin levels were measured in 388 officers from the Buffalo Cardio‐Metabolic Occupational Police Stress study. HRV was assessed according to methods published by the Task Force of the European Society of Cardiology and the North American Society of Pacing Electrophysiology for measurement and analysis of HRV. Mean values of high‐frequency (HF) and low‐frequency (LF) HRV were compared across tertiles of leptin and adiponectin using analysis of variance and analysis of covariance; trends were assessed using linear regression models.ResultsLeptin, but not adiponectin, was significantly and inversely associated with HRV. Body mass index (BMI) and percent body fat significantly modified the association between leptin and LF (but not HF) HRV. Among officers with BMI < 25 kg/m2, leptin was not significantly associated with HRV. However, among officers with BMI ≥ 25 kg/m2, leptin was inversely associated with HRV, after adjustment for age, gender, and race/ethnicity; HF HRV, P = 0.019 and LF HRV, P < 0.0001. Similarly, among officers with percent body fat ≥ 25.5%, leptin and LF HRV showed significant, inverse associations (adjusted P = 0.001).ConclusionsLeptin levels were inversely associated with LF HRV, especially among officers with increased adiposity. Increased leptin levels may be associated with CVD‐related health problems. Am. J. Hum. Biol. 27:184–191, 2015. © 2014 Wiley Periodicals, Inc.
School day and weekend patterns of physical activity in urban 11‐year‐olds: A cross‐cultural comparison
Authors: Jurak Gregor , Sorić Maroje , Starc Gregor , Kovač Marjeta , Mišigoj‐Duraković Marjeta , Borer Katarina , Strel Janko 
Published: October 2014

ObjectivesThis multi‐center study was conducted to objectively evaluate energy expenditure and physical activity (PA) patterns on school days and weekends in urban 11‐year‐olds.MethodsThe sample consisted of 241 children from three cities: Zagreb, Ljubljana (both in Central Europe) and Ann Arbor (United States). Energy expenditure and PA were assessed during two school days and two weekend days using a multiple‐sensor body monitor.ResultsDifferences between the cities were observed for all PA variables. The highest level of moderate to vigorous PA (MVPA) was noted in Ljubljana boys [284 (98) min/day] and the lowest in Zagreb girls [179 (95) min/day]. In Zagreb and Ljubljana, boys were more physically active than girls, while in Ann Arbor the opposite was observed. In contrast, no gender difference in sedentary behavior was observed in any of the cities. A decline in PA from school days to weekends was noted in all city groups in both genders. However, the magnitude of the reduction in daily energy expenditure differed between the cities, with the largest differences being observed in Ljubljana and the smallest in Ann Arbor. In all three city groups, the great majority of boys and girls achieved current recommendations of 60 min of MVPA either during school days or weekends.ConclusionsWeekends seem to be an appropriate target when promoting PA in 11‐year‐olds in all the cities included in the study. Increasing vigorous activity on weekends seems to be of particular importance in Zagreb and Ljubljana. Am. J. Hum. Biol. 27:192–200, 2015. © 2014 Wiley Periodicals, Inc.
Cousins, siblings, or copies: the genomics of recurrent Staphylococcus aureus infections in chronic rhinosinusitis
Authors: Drilling Amanda , Coombs Geoffrey W. , Tan Hui‐leen , Pearson Julie C. , Boase Samuel , Psaltis Alkis , Speck Peter , Vreugde Sarah , Wormald Peter‐John 
Published: October 2014

BackgroundStaphylococcus aureus infection is known to play a role in recalcitrant chronic rhinosinusitis (CRS). However, it is unknown if recurrent S. aureus infections are caused by the same strain or are due to independent acquisitions of different strains.MethodsSamples were collected from patients with CRS from July 2011 to August 2012. S. aureus was isolated from mucosal swabs and tissue specimens from patients who underwent surgery during the study period, or from swabs of areas of purulence taken in the postoperative period under endoscopic guidance. Pulsed‐field gel electrophoresis was used to characterize S. aureus isolates.ResultsThirty‐four patients were included in the study; 79% showed persistence of the same S. aureus strain in their paranasal sinuses (p = 0.001; H1 ≠ 50%). Furthermore, a significantly high frequency of patients with known biofilm status were positive for S. aureus biofilm (p = 0.002; H1 ≠ 50%). When patients were stratified according to disease evolution postsurgery, certain strains appeared to be more commonly associated with symptom persistence.ConclusionThe same S. aureus strain appears to persist in the paranasal sinuses of CRS patients despite multiple courses of culture‐directed antibiotics. This suggests that conventional antimicrobial therapies in patients with CRS may not eliminate the organism. This may be partly explained by the formation of biofilms in the paranasal sinus region.
Experimental and Computational Studies on the Reactivity of a Terminal Thorium Imidometallocene towards Organic Azides and Diazoalkanes
Authors: Ren Wenshan , Zhou Enwei , Fang Bo , Hou Guohua , Zi Guofu , Fang De‐Cai , Walter Marc D. 
Published: October 2014

AbstractThe reaction of the base‐free terminal thorium imido complex [{η5‐1,2,4‐(Me3C)3C5H2}2ThN(p‐tolyl)] (1) with p‐azidotoluene yielded irreversibly the tetraazametallacyclopentene [{η5‐1,2,4‐(Me3C)3C5H2}2Th{N(p‐tolyl)NNN(p‐tolyl)}] (2), whereas the bridging imido complex [{[η5‐1,2,4‐(Me3C)3C5H2]Th(N3)2}2{μ‐N(p‐tolyl)}2][(n‐C4H9)4N]2 (3) was isolated from the reaction of 1 with [(n‐C4H9)4N]N3. Unexpectedly, upon the treatment of 1 with 9‐diazofluorene, the NN bond was cleaved, an N atom was transferred, and the η2‐diazenido iminato complex [{η5‐1,2,4‐(Me3C)3C5H2}2Th{η2‐[NN(p‐tolyl)]}{N(9‐C13H8)}] (4) was formed. In contrast, the reaction of 1 with Me3SiCHN2 gave the nitrilimido complex [{η5‐1,2,4‐(Me3C)3C5H2}2Th{NH(p‐tolyl)}{N2CSiMe3}] (5), which slowly converted into [{η5‐1,2,4‐(Me3C)3C5H2}{η5:κ‐N‐1,2‐(Me3C)2‐4‐CMe2(CH2NNCHSiMe3)C5H2}Th{NH(p‐tolyl)}] (6) by intramolecular CH bond activation. The experimental results are complemented by density functional theory (DFT) studies.
Self‐healing Ag/epoxy electrically conductive adhesive using encapsulated epoxy‐amine healing chemistry
Authors: Tao Yu , Chang Yu , Tao Yuxiao , Wu Haiping , Yang Zhenguo 
Published: October 2014

ABSTRACTIn this study, a dual‐microcapsule epoxy‐amine self‐healing concept is used for electrically conductive adhesives (ECAs). It provides the ECA samples with the ability to recover mechanical and electrical properties automatically. Epoxy and amine microcapsules were prepared and incorporated into silver/epoxy ECAs. The healing efficiency and bulk resistivity of the undamaged, damaged, and healed specimens were measured, respectively. The optimal loading of the epoxy and amine microcapsules is 6 wt % (weight ratio 1.05), and the bulk resistivity of the healed specimens is 3.4 × 10−3 Ω cm. © 2014 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2015, 132, 41483.
Mixed templates molecularly imprinted solid‐phase extraction for the detection of sulfonamides in fish farming water
Authors: Qin Shili , Su Liqiang , Wang Peng , Deng Sheng 
Published: October 2014

ABSTRACTHighly selective molecularly imprinted polymers (MIPs) that absorb sulfonamides (SAs) are prepared using two types of SAs as mixed templates, 2‐vinylpyridine as the functional monomer and ethylene glycol dimethacrylate as the crosslinker. The optimum combination of the mixed templates, their adsorption effect and the imprinting mechanism are evaluated based on SPE recoveries of a family of analytes, equilibrium binding, BET surface area analysis and UV. The results indicate that the mixed templates not only optimize the cavities of the MIPs but also improve the MIPs selectivity and adsorption capacity for the target analytes in aqueous solution. Therefore, MIPs are used for the quantitative analysis of SAs in fish farming water using off‐line SPE coupled to HPLC/DAD. The recovery and RSD were 84.16–101.19 and 1.98–7.10%, respectively. Four SAs analytes were detected in four types of water samples in the range of 8.49–74.60 ng L−1. © 2014 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2015, 132, 41491.
Characterization of cross‐linking depth for thin polymeric films using atomic force microscopy
Authors: Guo Qiuquan , Paliy Maxim , Kobe Brad , Trebicky Tomas , Suhan Natalie , Arsenault Gilles , Ferrari Lorenzo , Yang Jun 
Published: October 2014

ABSTRACTThin polymeric films made with various elastomers, like polyisoprene, and elastomer composites were prepared for characterization of cross‐linking depth in this study. Various cross‐linking methods have been applied to get mechanically stronger, more thermally stable and chemically resistant polymer coatings. However, there is no existing approach that could effectively characterize the degree or depth of cross‐linking for thin polymer films. The objective of this work is to use atomic force microscopy to characterize cross‐linking depth in a precise way. Hyperthermal hydrogen bombardment‐induced cross‐linking was employed as a cross‐linking method and the depth of cross‐linking was estimated via local change of the elastic modulus along the sample cross‐section with precise force measurement and high spatial resolution. It is found that the cross‐linking depth is closely related to the chemical composition of thin films. Understanding the depth of cross‐linking is vital for a broad range of applications. It is believed that the developed technique is also applicable for studying other cross‐linkable materials. © 2014 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2015, 132, 41493.
Spectroscopic analysis and catalytic application of biopolymer capped silver nanoparticle, an effective antimicrobial agent
Authors: Pramanik Nilkamal , Bhattacharyya Aditi , Kundu Patit Paban 
Published: October 2014

ABSTRACTMicrobial reduction of silver ion (conc. 1 mM AgNO3) was performed by Alkaliphilus oremlandii strain ohILAs in an alkaline pH 10. The synthesized silver nanoparticle was stabilized by poly(3‐hydroxybutyrate‐co‐3‐hydroxyvalerate) biopolymer which was also synthesized by the microbial culture of Alkaliphilus oremlandii strain ohILAs at pH8. The particle size and shape of the silver nanoparticles was studied by dynamic light scattering and under a transmission electron microscope and it was found that the particle size of polymer stabilized colloidal silver was comparatively lower (22–43nm) than that for the unstabilized one (63–93 nm). The stabilization of nanoparticles in polymer dispersed medium after around 60 days was confirmed from analysis of UV‐visible spectroscopy and scanning electron microscopy. The crystalline peaks as recorded with X‐ray's diffraction were observed at 2θ values of 38° and 43°, indicating the fcc crystalline structure of the silver nanoparticle. The antimicrobial activity of silver nanoparticles on gram‐negative bacteria strain (Escherichia coli XL1B) and gram‐positive strain (Lysinibacillus fusiformis) showed better performance by the solution of polymer stabilized nanoparticle than that for the non polymer stabilized one. The reduction of nitro group in p‐nitrophenol to p‐aminophenol was observed from the analysis of UV‐Visible spectroscopy in which, the shifting of absorption peak at 400 to 295 nm and the simultaneous regeneration of light brown color (λmax 410 nm) of silver nanoparticles confirmed the catalytic activity of silver nanomaterials. © 2014 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2015, 132, 41495.