bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving the Quantum Yields of Perylene Diimide Aggregates by Increasing Molecular Hydrophobicity in Polar Media
Authors: Xu Xiaoyu , Austin Ashli , Mylon Steven E. , Plenge Jürgen , Szarko Jodi M. 
Published: June 2017

AbstractHere we report the quantum yield of four aggregated perylene diimide (PDI) species that vary by the length of the branched side chains attached at the N,N’ imide positions. The PDI molecules were dissolved in binary water:methanol solvents as a means to vary the solvent polarity and control the degree of aggregation in solution. By performing spectroscopy, kinetics, and light scattering experiments, the nature of the molecular interactions in the solutions was determined. The maximum quantum yield of the aggregated molecules increased from 0.04 for the shortest chain molecule (B2) to 0.20 for the largest chain molecule (B13). The higher quantum yield of B13 compared with B2 correlates well with an increase in the fluorescence lifetime. The monomer emission lifetime was 4.8 ns whereas a lifetime as high as 21.2 ns was measured for the B13 aggregate fluorescence. A shorter sub‐nanosecond lifetime was also measured for suspended colloids in B5, B9, and B13. The enhanced quantum yield is attributed to an increase of disorder in the B13 aggregates. As the polarity of the solution increases, the hydrophobic effect further enhances the disorder, and, therefore, the quantum yields in these particles.
Mouse Model of Burn Wound and Infection: Thermal (Hot Air) Lesion‐Induced Immunosuppression
Authors: Calum Henrik , Høiby Niels , Moser Claus 
Published: June 2017

AbstractThe immunosuppression induced by thermal injury renders the burned victim susceptible to infection. A mouse model was developed to examine the immunosuppression, which was possible to induce even at a minor thermal insult of 6% total body surface area. After induction of the burn (48 hr) a depression of leukocytes in the peripheral blood was found of the burned mice. This depression was due to a reduction in the polymorphonuclear cells. The burned mice were not able to clear a Pseudomonas aeruginosa wound infection, since the infection spread to the blood as compared to mice only infected with P. aeruginosa subcutaneously. The burn model offers an opportunity to study infections under these conditions. The present model can also be used to examine new antibiotics and immune therapy. Our animal model resembling the clinical situation is useful in developing new treatments of burn wound victims. © 2017 by John Wiley & Sons, Inc.
A Fast, Easy, and Customizable Eight‐Color Flow Cytometric Method for Analysis of the Cellular Content of Bronchoalveolar Lavage Fluid in the Mouse
Authors: Daubeuf François , Becker Julien , Aguilar‐Pimentel Juan Antonio , Ebel Claudine , Hrabě de Angelis Martin , Hérault Yann , Frossard Nelly 
Published: June 2017

AbstractThe cell composition of bronchoalveolar lavage fluid (BAL) is an important indicator of airway inflammation. It is commonly determined by cytocentrifuging leukocytes on slides, then staining, identifying, and counting them as eosinophils, neutrophils, macrophages, or lymphocytes according to morphological criteria under light microscopy, where it is not always easy to distinguish macrophages from lymphocytes. We describe here a one‐step, easy‐to‐use, and easy‐to‐customize 8‐color flow cytometric method for performing differential cell count and comparing it to morphological counts on stained cytospins. This method identifies BAL cells by a simultaneous one‐step immunolabeling procedure using antibodies to identify T cells, B cells, neutrophils, eosinophils, and macrophages. Morphological analysis of flow‐sorted cell subsets is used to validate this protocol. An important advantage of this basic flow cytometry protocol is the ability to customize it by the addition of antibodies to study receptor expression at leukocyte cell surfaces and identify subclasses of inflammatory cells as needed. © 2017 by John Wiley & Sons, Inc.
Monitoring Pathogen‐Induced Sickness in Mice and Rats
Authors: Kolmogorova Daria , Murray Emma , Ismail Nafissa 
Published: June 2017

AbstractSickness behavior monitoring, a technique for examining the development of sickness symptomatology following infection, is necessary in experiments studying neurochemical and physiological changes associated with pathogen‐induced immune activation. However, the results of sickness behavior monitoring are difficult to reconcile due to inconsistencies in protocol methods and rater bias. The protocol described herein offers a non‐invasive and unbiased approach to assess the progression of pathogen‐induced sickness behaviors. This simple, straightforward method uses a five‐point scale to assess animals for the presence of four sickness behaviors (i.e., ‘“0” = no sickness behaviors; “4” = four sickness behaviors) at various time points following exposure to a pathogen. This approach removes the ambiguity and bias inherent to other methods of sickness behavior monitoring that rely on subjective ratings of severity for individual symptoms. This protocol has been successfully applied to male and female rodents injected intraperitoneally with lipopolysaccharide and polyinosinic:polycytidylic acid, and has been effective in pubertal and adult populations. Protocols for changes in body temperature and weight are also provided as physiological markers of sickness. © 2017 by John Wiley & Sons, Inc.
Water‐Medium Synthesis of Nucleoside 5′‐Polyphosphates
Authors: Depaix Anaïs , Peyrottes Suzanne , Roy Béatrice 
Published: June 2017

AbstractThis unit describes a one‐pot, two step synthesis of ribonucleoside 5′‐di‐ and 5′‐triphosphates, as well as their purification. The first step of the synthesis involves the activation of an unprotected ribonucleoside 5′‐monophosphate with 2‐chloro‐1,3‐dimethylimidazolinium hexafluorophosphate and imidazole, in a mixture of water/acetonitrile. The resulting phosphorimidazolate intermediate is then treated with inorganic phosphate or pyrophosphate to afford the corresponding nucleoside 5′‐di‐ or 5′‐triphosphates. The attractive features of this strategy include the absence of protecting groups on the starting material and convenient set up (i.e., use of water, non‐dry solvents and reagents, commercially available sodium salts). © 2017 by John Wiley & Sons, Inc.
Nucleobase Protection of Deoxyribo‐ and Ribonucleosides
Authors: Meher Geeta , Meher Nabin K. , Iyer Radhakrishnan P. 
Published: June 2017

AbstractOligonucleotides carrying a variety of chemical modifications including conjugates are finding increasing applications in therapeutics, diagnostics, functional genomics, proteomics, and as research tools in chemical and molecular biology. The successful synthesis of oligonucleotides primarily depends on the use of appropriately protected nucleoside building blocks including the exocyclic amino groups of the nucleobases, the hydroxyl groups at the 2′‐, 3′‐, and 5′‐positions of the sugar moieties, and the internucleotide phospho‐linkage. This unit is a thoroughly revised update of the previously published version and describes the recent development of various protecting groups that facilitate reliable oligonucleotide synthesis. In addition, various protecting groups for the imide/lactam function of thymine/uracil and guanine, respectively, are described to prevent irreversible nucleobase modifications that may occur in the presence of reagents used in oligonucleotide synthesis. © 2017 by John Wiley & Sons, Inc.
Engineered Polymerases with Altered Substrate Specificity: Expression and Purification
Authors: Nikoomanzar Ali , Dunn Matthew R. , Chaput John C. 
Published: June 2017

AbstractPolymerase engineering is making it possible to synthesize xeno‐nucleic acid polymers (XNAs) with diverse backbone structures and chemical functionality. The ability to copy genetic information back and forth between DNA and XNA has led to a new field of science known as synthetic genetics, which aims to study the genetic concepts of heredity and evolution in artificial genetic polymers. Since many of the polymerases needed to synthesize XNA polymers are not available commercially, researchers must express and purify these enzymes as recombinant proteins from E. coli. This unit details the steps needed to express, purify, and evaluate the activity of engineered polymerases with altered substrate recognition properties. The protocol requires 6 days to complete and will produce ∼20 mg of pure, nuclease‐free polymerase per liter of E. coli bacterial culture. © 2017 by John Wiley & Sons, Inc.
Influence of the production system on the surface properties of influenza A virus particles
Authors: Hämmerling Frank , Pieler Michael M. , Hennig René , Serve Anja , Rapp Erdmann , Wolff Michael W. , Reichl Udo , Hubbuch Jürgen 
Published: June 2017

AbstractIn this study, influenza A/Puerto Rico/8/34 H1N1 virus particles (VP) produced in adherent and suspension Madin Darby canine kidney cells were investigated with a broad analytical toolbox to obtain more information on the VP's surface properties potentially affecting their aggregation behavior. First, differences in aggregation behavior were revealed by VP size distributions obtained via differential centrifugal sedimentation and confirmed by dynamic light scattering. The VP produced in adherent cells showed increased levels of aggregation in a 20 mM NaCl 10 mM Tris‐HCl pH 7.4 low‐salt buffer. This included the formation of multimers (dimers up to pentamers), whereas VP produced in suspension cells displayed no tendency toward aggregate formation. To investigate the cause of these differences in aggregation behavior, the VP samples were compared based on their zeta potential, their surface hydrophobicity, their lipid composition, and the N‐glycosylation of their major VP surface protein hemagglutinin. The zeta potential and the hydrophobicity of the VP produced in the adherent cells was significantly decreased compared to the VP produced in the suspension cells. The lipid composition of both VP systems was approximately identical. The hemagglutinin of the VP produced in adherent cells included more of the larger N‐glycans, whereas the VP produced in suspension cells included more of the smaller N‐glycans. These results indicate that differences in the glycosylation of viral surface proteins should be monitored to characterize VP hydrophobicity and aggregation behavior, and to avoid aggregate formation and product losses in virus purification processes for vaccines and gene therapy.
Sensitivity analysis of the seismic demands of RC moment resisting frames to different aspects of ground motions
Authors: Kiani Jalal , Pezeshk Shahram 
Published: June 2017

SummaryA weight vector representing the relative importance of various characteristics of ground motions (GMs) and a conditioning intensity measure (IM) are required to be able to use the generalized conditional IM framework for the purpose of GM selection. An inappropriate weight vector may result in the biased distributions of some important characteristics of GMs and, consequently, the bias in the structural responses. This article aims to provide the analyst with the understanding of which properties of GMs are important in capturing the accurate structural responses, to specifically assign a suitable weight to them and to select an appropriate conditioning IM as well. To this end, 4 reinforced concrete buildings, located at the site in which the seismic hazard is dominated by shallow crustal earthquakes, are considered. The findings reveal that the appropriate weight vectors depend on the characteristics of the employed structural systems. In addition, the role played by each IM in capturing the true structural responses changes over different earthquake intensity levels implying that different weight vectors are required over different earthquake levels. Furthermore, this study shows that, even in case of shorter‐duration GMs from shallow events, GM duration should be incorporated in GM selection as it has effects on the peak‐based structural responses in the earthquake levels beyond the level of 2%‐in‐50‐years. Specifically, the findings reveal that in case of shallow events, unlike large magnitude earthquakes, the shorter the duration of GM the more rapid release of energy and, consequently, the larger the peak‐based structural responses.
Detecting genetic association through shortest paths in a bidirected graph
Authors: Ueki Masao , Kawasaki Yoshinori , Tamiya Gen ,   for Alzheimer's Disease Neuroimaging Initiative
Published: June 2017

ABSTRACTGenome‐wide association studies (GWASs) commonly use marginal association tests for each single‐nucleotide polymorphism (SNP). Because these tests treat SNPs as independent, their power will be suboptimal for detecting SNPs hidden by linkage disequilibrium (LD). One way to improve power is to use a multiple regression model. However, the large number of SNPs preclude simultaneous fitting with multiple regression, and subset regression is infeasible because of an exorbitant number of candidate subsets. We therefore propose a new method for detecting hidden SNPs having significant yet weak marginal association in a multiple regression model. Our method begins by constructing a bidirected graph locally around each SNP that demonstrates a moderately sized marginal association signal, thefocalSNPs. Vertexes correspond to SNPs, and adjacency between vertexes is defined by an LD measure. Subsequently, the method collects from each graph all shortest paths to the focal SNP. Finally, for each shortest path the method fits a multiple regression model to all the SNPs lying in the path and tests the significance of the regression coefficient corresponding to the terminal SNP in the path. Simulation studies show that the proposed method can detect susceptibility SNPs hidden by LD that go undetected with marginal association testing or with existing multivariate methods. When applied to real GWAS data from the Alzheimer's Disease Neuroimaging Initiative (ADNI), our method detected two groups of SNPs: one in a region containing theapolipoprotein E(APOE) gene, and another in a region close to thesemaphorin 5A(SEMA5A) gene.
Tumor‐Targeting Salmonella typhimurium A1‐R Promotes Tumoricidal CD8+ T Cell Tumor Infiltration and Arrests Growth and Metastasis in a Syngeneic Pancreatic‐Cancer Orthotopic Mouse Model
Authors: Murakami Takashi , Hiroshima Yukihiko , Zhang Yong , Zhao Ming , Kiyuna Tasuku , Hwang Ho Kyoung , Miyake Kentaro , Homma Yuki , Mori Ryutaro , Matsuyama Ryusei , Chishima Takashi , Ichikawa Yasushi , Tanaka Kuniya , Bouvet Michael , Endo Itaru , Hoffman Robert M. 
Published: June 2017

ABSTRACTThe present study determined the effect of the tumor‐targeting strain Salmonella typhimurium A1‐R (S. typhimurium A1‐R) on CD8+ tumor‐infiltrating lymphocytes (TILs) in a syngeneic pancreatic‐cancer orthotopic mouse model. The effect of tumor‐targeting S. typhimurium A1‐R on CD8+ TILs was determined on the Pan02 murine pancreatic‐adenocarcinoma implanted orthotopically in the pancreatic tail of C57BL/6 immunocompromised mice. Three weeks after orthotopic implantation, mice were randomized as follows G1: untreated control group (n = 8); and G2: S. typhimurium A1‐R‐treatment group (n = 8, 1 × 107 colony forming units [CFU]/body, iv, weekly, 3 weeks). On the 22nd day from initial treatment, all mice were sacrificed and tumors were harvested. The tumor‐volume ratio was defined as ratio of tumor volume on the 22nd day relative to the 1st day. The tumor volume ratio was significantly lower in the S. typhimurium A1‐R‐treated group (G2) (3.0 ± 2.8) than the untreated control (G1) (39.9 ± 30.7, P < 0.01). Hematoxylin and easin (H&E) staining on tumor sections was performed to evaluate tumor destruction which was classified according to the Evans grading system and found to be much greater in the S. typhimurium A1‐R‐treated mice (G2). Six mice in G1 had peritoneal dissemination, whereas no mice showed peritoneal dissemination in G2 (P < 0.01). Immunohistochemical staining with anti‐mouse CD8+ antibody was performed in order to detect TILs determined by calculating the average number of CD8+ cells in three high power fields (200×) in the treated and untreated tumors. The TIL score was significantly higher in G2 (133.5 ± 32.2) than G1 (45.1 ± 19.4, P < 0.001). The present study demonstrates that S. typhimurium A1‐R promotes CD8+ T cell infiltration and inhibition of tumor growth and metastasis. J. Cell. Biochem. 119: 634–639, 2018. © 2017 Wiley Periodicals, Inc.
d:x reflectance measurement for curved surface with integrating sphere
Authors: Yu Hsueh‐Ling , Young Richard , Liu Wen‐Chun , Hsiao Chin‐Chai 
Published: June 2017

AbstractAmbient contrast ratio (ACR) is a useful parameter to evaluate the quality of displays when used under diffuse lighting conditions. The methodology recommended by most documentary standards calculates the ACR of the display from d:x reflectance. Reflectance measurement of flat surfaces typically employs an integrating sphere and a flat white reference plate. However, the shape difference between the flat white standard and test curved sample causes changes to the amount of light illuminating their surfaces and thus gives measurement errors. Especially for concave test surfaces, the error is significant when the sample has small radius of curvature. To increase the measurement accuracy, this paper derives the correction factor to compensate the effect caused by shape difference between the reference plate and test curved sample. The associated uncertainty analysis is also discussed in this paper.
Characterizing the detection threshold for optical imaging in surgical oncology
Authors: Prince Andrew C. , Jani Aditi , Korb Melissa , Tipirneni Kiranya E. , Kasten Benjamin B. , Rosenthal Eben L. , Warram Jason M. 
Published: June 2017

Background and ObjectivesOptical imaging to guide cancer resections is rapidly transitioning into the operating room. However, the sensitivity of this technique to detect subclinical disease is yet characterized. The purpose of this study was to determine the minimum range of cancer cells that can be detected by antibody‐based fluorescence imaging.Methods2LMP (breast), COLO‐205 (colon), MiaPaca‐2 (pancreas), and SCC‐1 (head and neck) cells incubated in vitro with cetuximab‐IRDye800CW (dose range 8.6‐86 nM) were implanted subcutaneously in mice (n = 3 mice, 5 tumors/mouse). Following incubation with 8.6 × 10−2 µM of cetuximab‐IRDye800CW in vitro, serial dilutions of each cell type (1 × 103–1 × 106) were implanted subcutaneously (n = 3, 5 tumors/mouse). Tumors were imaged with Pearl Impulse and Xenogen IVIS 100 imaging systems. Scatchard analysis was performed to determine receptor density and kinetics for each cell line.ResultsUnder conditions of minimal cetuximab‐IRDye800CW exposure to low cellular quantity, closed‐field fluorescence imaging theoretically detected a minimum of 4.2 × 104‐9.5 × 104 2LMP cells, 1.9 × 105‐4.5 × 105 MiaPaca‐2 cells, and 2.4 × 104‐6.7 × 104 SCC‐1 cells; COLO‐205 cells could not be identified. Higher EGFR‐mediated uptake of cetuximab correlated with sensitivity of detection.ConclusionThis study supports the clinical utility of cetuximab‐IRDye800CW to sensitively localize subclinical disease in the surgical setting.
Prescribed fire influences habitat selection of female eastern wild turkeys
Authors: Yeldell Nathan A. , Cohen Bradley S. , Prebyl Thomas J. , Collier Bret A. , Chamberlain Michael J. 
Published: June 2017

ABSTRACTPrescribed fire is widely used in southeastern pine (Pinus spp.) forests to maintain desirable forest conditions and provide early successional vegetation. However, it is unclear how fires applied just prior to and during the reproductive cycle of ground nesting Galliformes influence resource selection. We examined the short‐term influence of prescribed fire on habitat selection of female eastern wild turkeys (Meleagris gallopavo silvestris) throughout their reproductive cycle (Feb−Aug) at Kisatchie National Forest in west‐central Louisiana, USA during 2014 and 2015. Kisatchie was dominated (>60%) by pine stands managed with prescribed fire at a frequent (i.e., 1–3 yr) return interval. We captured 46 females and equipped them with backpack‐style global positioning system (GPS) transmitters programmed to collect relocation data hourly from 0600 to 2000 each day. We used distance‐based analysis to estimate selection or avoidance of vegetation communities relative to reproductive phenology of individual females. Hardwood and mixed‐pine hardwood vegetation communities were selected for before and after reproductive efforts; hardwood stands were avoided during brooding. While laying their first clutch of the reproductive period, females selected mature pines burned 0–5 months prior. Females avoided mature pine stands 2 growing seasons post‐burn prior to initiating their first nests. Females avoided mature pine stands 3 growing seasons post‐burn when brooding. Turkeys did not select for pine stands that had experienced ≥3 growing seasons post‐burn during any reproductive period, and may avoid these stands during pre‐nesting and brooding. Frequent fire return intervals maintain vegetation communities that females select at some point during the reproductive season in pine‐dominated landscapes. © 2017 The Wildlife Society.
Trends in sleep studies performed for Medicare beneficiaries
Authors: Chiao Whitney , Durr Megan L. 
Published: June 2017

Objectives/HypothesisTo quantify trends and characteristics of sleep studies performed for Medicare beneficiaries in the United States.Study DesignRetrospective longitudinal study of the Centers for Medicare and Medicaid Services' Part B National Summary Data and Medicare Provider Utilization and Payment Data from 2000 to 2014.MethodsSleep study data were analyzed according to type of study performed, total expenditure amount, provider specialty, and geographic location.ResultsIn 2014, 845,569 sleep studies were completed by 1.4% of Medicare beneficiaries for a total of $189 million. Since 2010, annual expenditures for sleep studies have declined, whereas the number of studies performed has increased by 9.1%. In 2014, polysomnography, split‐night polysomnography, and unattended home sleep studies accounted for 40%, 48%, and 12%, respectively, of total sleep studies. This represents a dramatic growth in the number of unattended sleep studies performed since 2000, when they represented only 0.9%. Pulmonologists, independent diagnostic testing facilities, and neurologists are the top specialties that bill for sleep studies. Sleep medicine is a growing specialty and ranked fifth among providers, whereas otolaryngologists ranked eighth.ConclusionsThe healthcare burden of administering sleep studies is substantial, although the annual cost is declining. Unattended sleep studies contribute to decreasing costs and should be considered for patients who meet the correct indications.Level of Evidence4. Laryngoscope, 127:2891–2896, 2017