University of Delaware Open Access Articles

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The University of Delaware Open Access Articles collection consists of scholarly articles written by University of Delaware-affiliated authors. These articles were added in compliance with the University of Delaware Open Access policy passed unanimously by the Faculty Senate April 6, 2015.

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Now showing 1 - 20 of 343
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    Non-minimal quartic inflation in supersymmetric SO(10)
    (Elsevier Science, 2016-12-16) Leontaris, George K.; Okada, Nobuchika; Shafi, Qaisar; George K. Leontaris, Nobuchika Okada, Qaisar Shafi; Shafi, Qaisar
    We describe how quartic (λφ4) inflation with non-minimal coupling to gravity is realized in realistic supersymmetric SO(10)models. In a well-motivated example the 16 −16Higgs multiplets, which break SO(10)to SU(5)and yield masses for the right-handed neutrinos, provide the inflaton field φ. Thus, leptogenesis is a natural outcome in this class of SO(10)models. Moreover, the adjoint (45-plet) Higgs also acquires a GUT scale value during inflation so that the monopole problem is evaded. The scalar spectral index nsis in good agreement with the observations and r, the tensor to scalar ratio, is predicted for realistic values of GUT parameters to be of order 10−3–10−2.
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    Protein Ontology (PRO): enhancing and scaling up the representation of protein entities
    (Oxford University Press, 2016-11-28) Natale, Darren A.; Arighi, Cecilia N.; Blake, Judith A.; Bona, Jonathan; Chen, Chuming; Chen, Sheng-Chih; Christie, Karen R.; Cowart, Julie; D’Eustachio, Peter; Diehl, Alexander D.; Drabkin, Harold J.; Duncan, William D.; Huang, Hongzhan; Ren, Jia; Ross, Karen; Ruttenberg, Alan; Shamovsky, Veronica; Smith, Barry; Wang, Qinghua; Zhang, Jian; El-Sayed, Abdelrahman; Wu, Cathy H.; Darren A. Natale, Cecilia N. Arighi, Judith A. Blake, Jonathan Bona, Chuming Chen, Sheng-Chih Chen, Karen R. Christie, Julie Cowart, Peter D’Eustachio, Alexander D. Diehl, Harold J. Drabkin, William D. Duncan, Hongzhan Huang, Jia Ren, Karen Ross, Alan Ruttenberg, Veronica Shamovsky, Barry Smith, Qinghua Wang, Jian Zhang, Abdelrahman El-Sayed and Cathy H. Wu; Arighi, Cecilia N.; Chen, Chuming; Chen, Sheng-Chih; Cowart, Julie; Huang, Hongzhan; Ren, Jia; Wang, Qinghua; Wu, Cathy H.
    The Protein Ontology (PRO; http://purl.obolibrary. org/obo/pr) formally defines and describes taxonspecific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and proteincontaining complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translationalmodification reference. We illustrate its use in facilitating an alignment between PRO and Reactome protein entities. We also address issues of scalability, describing our first steps into the use of text mining to identify protein-related entities, the large-scale import of proteoform information from expert curated resources, and our ability to dynamically generate PRO terms. Web views for individual terms are now more informative about closely-related terms, including for example an interactive multiple sequence alignment. Finally, we describe recent improvement in semantic utility, with PRO now represented in OWL and as a SPARQL endpoint. These developments will further support the anticipated growth of PRO and facilitate discoverability of and allow aggregation of data relating to protein entities.
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    Random sampling and model competition for guaranteed multiple consensus sets estimation
    (Sage Publications Inc., 2017-01-02) Li, Jing; Yang, Tao; Yu, Jingyi; Jing Li, Tao Yang and Jingyi Yu; Yu, Jingyi
    Robust extraction of consensus sets from noisy data is a fundamental problem in robot vision. Existing multimodel estimation algorithms have shown success on large consensus sets estimations. One remaining challenge is to extract small consensus sets in cluttered multimodel data set. In this article, we present an effective multimodel extraction method to solve this challenge. Our technique is based on smallest consensus set random sampling, which we prove can guarantee to extract all consensus sets larger than the smallest set from input data. We then develop an efficient model competition scheme that iteratively removes redundant and incorrect model samplings. Extensive experiments on both synthetic data and real data with high percentage of outliers and multimodel intersections demonstrate the superiority of our method.
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    Seasonal control of Petermann Gletscher ice-shelf melt by the ocean’s response to sea-ice cover in Nares Strait
    (Cambridge University Press, 2017-02-02) Shroyer, E. L.; Padman, L.; Samelson, R. M.; Münchow, A.; Stearns, L. A.; E. L. SHROYER, L. PADMAN, R. M. SAMELSON, A. MÜNCHOW, L. A. STEARNS; Münchow, A
    Petermann Gletscher drains ∼4% of the Greenland ice sheet (GrIS) area, with ∼80% of its mass loss occurring by basal melting of its ice shelf. We use a high-resolution coupled ocean and sea-ice model with a thermodynamic glacial ice shelf to diagnose ocean-controlled seasonality in basal melting of the Petermann ice shelf. Basal melt rates increase by ∼20% in summer due to a seasonal shift in ocean circulation within Nares Strait that is associated with the transition from landfast sea ice to mobile sea ice. Under landfast ice, cold near-surface waters are maintained on the eastern side of the strait and within Petermann Fjord, reducing basal melt and insulating the ice shelf. Under mobile sea ice, warm waters are upwelled on the eastern side of the strait and, mediated by local instabilities and eddies, enter Petermann Fjord, enhancing basal melt down to depths of 200 m. The transition between these states occurs rapidly, and seasonal changes within Nares Strait are conveyed into the fjord within the same season. These results suggest that long-term changes in the length of the landfast sea-ice season will substantially alter the structure of Petermann ice shelf and its contribution to GrIS mass loss.
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    SoilGrids250m: Global gridded soil information based on machine learning
    (PLOS (Public Library of Science), 2017-02-16) Heng, Tomislav; Mendes de Jesus, Jorge; Heuvelink, Gerard B. M.; Ruiperez Gonzalez, Maria; Kilibarda, Milan; Blagotić, Aleksandar; Shangguan, Wei; Wright, Marvin N.; Geng, Xiaoyuan; Bauer-Marschallinger, Bernhard; Guevara, Mario Antonio; Vargas, Rodrigo; MacMillan, Robert A.; Batjes, Niels H.; Leenaars, Johan G. B.; Ribeiro, Eloi; Wheeler, Ichsani; Mantel, Stephan; Kempen, Bas; Tomislav Hengl, Jorge Mendes de Jesus, Gerard B. M. Heuvelink, Maria Ruiperez Gonzalez, Milan Kilibarda, Aleksandar Blagotić, Wei Shangguan, Marvin N. Wright, Xiaoyuan Geng, Bernhard Bauer-Marschallinger, Mario Antonio Guevara, Rodrigo Vargas, Robert A. MacMillan, Niels H. Batjes, Johan G. B. Leenaars, Eloi Ribeiro, Ichsani Wheeler, Stephan Mantel, Bas Kempen; Guevara, Mario Antonio; Vargas, Rodrigo
    This paper describes the technical development and accuracy assessment of the most recent and improved version of the SoilGrids system at 250m resolution (June 2016 update). SoilGrids provides global predictions for standard numeric soil properties (organic carbon, bulk density, Cation Exchange Capacity (CEC), pH, soil texture fractions and coarse fragments) at seven standard depths (0, 5, 15, 30, 60, 100 and 200 cm), in addition to predictions of depth to bedrock and distribution of soil classes based on the World Reference Base (WRB) and USDA classification systems (ca. 280 raster layers in total). Predictions were based on ca. 150,000 soil profiles used for training and a stack of 158 remote sensing-based soil covariates (primarily derived from MODIS land products, SRTM DEM derivatives, climatic images and global landform and lithology maps), which were used to fit an ensemble of machine learning methodsÐrandom forest and gradient boosting and/or multinomial logistic regressionÐas implemented in the R packages ranger, xgboost, nnet and caret. The results of 10±fold cross-validation show that the ensemble models explain between 56% (coarse fragments) and 83% (pH) of variation with an overall average of 61%. Improvements in the relative accuracy considering the amount of variation explained, in comparison to the previous version of SoilGrids at 1 km spatial resolution, range from 60 to 230%. Improvements can be attributed to: (1) the use of machine learning instead of linear regression, (2) to considerable investments in preparing finer resolution covariate layers and (3) to insertion of additional soil profiles. Further development of SoilGrids could include refinement of methods to incorporate input uncertainties and derivation of posterior probability distributions (per pixel), and further automation of spatial modeling so that soil maps can be generated for potentially hundreds of soil variables. Another area of future research is the development of methods for multiscale merging of SoilGrids predictions with local and/or national gridded soil products (e.g. up to 50 m spatial resolution) so that increasingly more accurate, complete and consistent global soil information can be produced. SoilGrids are available under the Open Data Base License.
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    Structural Analysis of Human Cofilin 2/Filamentous Actin Assemblies: Atomic-Resolution Insights from Magic Angle Spinning NMR Spectroscopy
    (Nature Publishing Group, 2017-03-17) Yehl, Jenna; Kudryashova, Elena; Reisler, Emil; Kudryashov, Dmitri; Polenova, Tatyana; Jenna Yehl, Elena Kudryashova, Emil Reisler, Dmitri Kudryashov & Tatyana Polenova; Polenova, Tatyana
    Cellular actin dynamics is an essential element of numerous cellular processes, such as cell motility, cell division and endocytosis. Actin’s involvement in these processes is mediated by many actinbinding proteins, among which the cofilin family plays unique and essential role in accelerating actin treadmilling in filamentous actin (F-actin) in a nucleotide-state dependent manner. Cofilin preferentially interacts with older filaments by recognizing time-dependent changes in F-actin structure associated with the hydrolysis of ATP and release of inorganic phosphate (Pi) from the nucleotide cleft of actin. The structure of cofilin on F-actin and the details of the intermolecular interface remain poorly understood at atomic resolution. Here we report atomic-level characterization by magic angle spinning (MAS) NMR of the muscle isoform of human cofilin 2 (CFL2) bound to F-actin. We demonstrate that resonance assignments for the majority of atoms are readily accomplished and we derive the intermolecular interface between CFL2 and F-actin. The MAS NMR approach reported here establishes the foundation for atomic-resolution characterization of a broad range of actin-associated proteins bound to F-actin.
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    The database of the PREDICTS (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems) project
    (Wiley-Blackwell, 2016-12-16) Hudson, Lawrence N.; Newbold, Tim; Contu, Sara; Hill, Samantha L. L.; Lysenko, Igor; De Palma, Adriana; Phillips, Helen R. P.; McCarthy, Jennifer L.; McCarthy, Kyle P.; McCarthy, Jennifer L.; McCarthy, Kyle P.
    The PREDICTS project—Projecting Responses of Ecological Diversity In Changing Terrestrial Systems (—has collated from published studies a large, reasonably representative database of comparable samples of biodiversity from multiple sites that differ in the nature or intensity of human impacts relating to land use. We have used this evidence base to develop global and regional statistical models of how local biodiversity responds to these measures. We describe and make freely available this 2016 release of the database, containing more than 3.2 million records sampled at over 26,000 locations and representing over 47,000 species. We outline how the database can help in answering a range of questions in ecology and conservation biology. To our knowledge, this is the largest and most geographically and taxonomically representative database of spatial comparisons of biodiversity that has been collated to date; it will be useful to researchers and international efforts wishing to model and understand the global status of biodiversity.
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    ThermoAlign: a genome-aware primer design tool for tiled amplicon resequencing
    (Nature Publishing Group, 2017-03-16) Francis, Felix; Dumas, Michael D.; Wisser, Randall J.; Felix Francis, Michael D. Dumas & Randall J. Wisser; Francis, Felix; Dumas, Michael D.; Wisser, Randall J.
    Isolating and sequencing specific regions in a genome is a cornerstone of molecular biology. This has been facilitated by computationally encoding the thermodynamics of DNA hybridization for automated design of hybridization and priming oligonucleotides. However, the repetitive composition of genomes challenges the identification of target-specific oligonucleotides, which limits genetics and genomics research on many species. Here, a tool called ThermoAlign was developed that ensures the design of target-specific primer pairs for DNA amplification. This is achieved by evaluating the thermodynamics of hybridization for full-length oligonucleotide-template alignments — thermoalignments — across the genome to identify primers predicted to bind specifically to the target site. For amplificationbased resequencing of regions that cannot be amplified by a single primer pair, a directed graph analysis method is used to identify minimum amplicon tiling paths. Laboratory validation by standard and long-range polymerase chain reaction and amplicon resequencing with maize, one of the most repetitive genomes sequenced to date (≈85% repeat content), demonstrated the specificity-by-design functionality of ThermoAlign. ThermoAlign is released under an open source license and bundled in a dependency-free container for wide distribution. It is anticipated that this tool will facilitate multiple applications in genetics and genomics and be useful in the workflow of high-throughput targeted resequencing studies.
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    Unique genetic responses revealed in RNAseq of the spleen of chickens stimulated with lipopolysaccharide and short-term heat
    (PLoS (Public Library of Science), 2017-02-06) Van Goor, Angelica; Ashwell, Chris M.; Persia, Michael E.; Rothschild, Max F.; Schmidt, Carl J.; Lamont, Susan J.; Angelica Van Goor, Chris M. Ashwell, Michael E. Persia, Max F. Rothschild, Carl J. Schmidt, Susan J. Lamont; Schmidt, Carl J.
    Climate change and disease have large negative impacts on poultry production, but little is known about the interactions of responses to these stressors in chickens. Fayoumi (heat and disease resistant) and broiler (heat and disease susceptible) chicken lines were stimulated at 22 days of age, using a 2x2x2 factorial design including: breed (Fayoumi or broiler), inflammatory stimulus (lipopolysaccharide (LPS) or saline), and temperature (35ÊC or 25ÊC). Transcriptional changes in spleens were analyzed using RNA-sequencing on the Illumina HiSeq 2500. Thirty-two individual cDNA libraries were sequenced (four per treatment) and an average of 22 million reads were generated per library. Stimulation with LPS induced more differentially expressed genes (DEG, log2 fold change 2 and FDR 0.05) in the broiler (N = 283) than the Fayoumi (N = 85), whereas heat treatment resulted in fewer DEG in broiler (N = 22) compared to Fayoumi (N = 107). The double stimulus of LPS+heat induced the largest numbers of changes in gene expression, for which broiler had 567 DEG and Fayoumi had 1471 DEG of which 399 were shared between breeds. Further analysis of DEG revealed pathways impacted by these stressors such as Remodelling of Epithelial Adherens Junctions due to heat stress, Granulocyte Adhesion and Diapedesis due to LPS, and Hepatic Fibrosis/Hepatic Stellate Cell Activation due to LPS+heat. The genes and pathways identified provide deeper understanding of the response to the applied stressors and may serve as biomarkers for genetic selection for heat and disease tolerant chickens.
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    Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce
    (Nature Publishing Group, 2017-04-12) Reyes-Chin-Wo, Sebastian; Wang, Zhiwen; Yang, Xinhua; Kozik, Alexander; Arikit, Siwaret; Song, Chi; Xia, Liangfeng; Froenicke, Lutz; Lavelle, Dean O.; Truco, Marı´a-Jose´; Xia, Rui; Zhu, Shilin; Xu, Chunyan; Xu, Huaqin; Xu, Xun; Cox, Kyle; Korf, Ian; Meyers, Blake C.; Michelmore, Richard W.; Sebastian Reyes-Chin-Wo, Zhiwen Wang, Xinhua Yang, Alexander Kozik, Siwaret Arikit, Chi Song, Liangfeng Xia, Lutz Froenicke, Dean O. Lavelle, Marı´a-Jose´ Truco, Rui Xia, Shilin Zhu, Chunyan Xu, Huaqin Xu, Xun Xu, Kyle Cox, Ian Korf, Blake C. Meyers & Richard W. Michelmore; Arikit, Siwaret; Meyers, Blake C
    Lettuce (Lactuca sativa) is a major crop and a member of the large, highly successful Compositae family of flowering plants. Here we present a reference assembly for the species and family. This was generated using whole-genome shotgun Illumina reads plus in vitro proximity ligation data to create large superscaffolds; it was validated genetically and superscaffolds were oriented in genetic bins ordered along nine chromosomal pseudomolecules. We identify several genomic features that may have contributed to the success of the family, including genes encoding Cycloidea-like transcription factors, kinases, enzymes involved in rubber biosynthesis and disease resistance proteins that are expanded in the genome. We characterize 21 novel microRNAs, one of which may trigger phasiRNAs from numerous kinase transcripts. We provide evidence for a whole-genome triplication event specific but basal to the Compositae. We detect 26% of the genome in triplicated regions containing 30% of all genes that are enriched for regulatory sequences and depleted for genes involved in defence.
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    Effective biomedical document classification for identifying publications relevant to the mouse Gene Expression Database (GXD)
    (Oxford University Press., 2017-03-24) Jiang, Xiangying; Ringwald, Martin; Blake, Judith; Shatkay, Hagit; Xiangying Jiang, Martin Ringwald, Judith Blake and Hagit Shatkay; ; Jiang, Xiangying; Shatkay, Hagit
    The Gene Expression Database (GXD) is a comprehensive online database within the Mouse Genome Informatics resource, aiming to provide available information about endogenous gene expression during mouse development. The information stems primarily from many thousands of biomedical publications that database curators must go through and read. Given the very large number of biomedical papers published each year, automatic document classification plays an important role in biomedical research. Specifically, an effective and efficient document classifier is needed for supporting the GXD annotation workflow. We present here an effective yet relatively simple classification scheme, which uses readily available tools while employing feature selection, aiming to assist curators in identifying publications relevant to GXD. We examine the performance of our method over a large manually curated dataset, consisting of more than 25 000 PubMed abstracts, of which about half are curated as relevant to GXD while the other half as irrelevant to GXD. In addition to text from title-and-abstract, we also consider image captions, an important information source that we integrate into our method. We apply a captions-based classifier to a subset of about 3300 documents, for which the full text of the curated articles is available. The results demonstrate that our proposed approach is robust and effectively addresses the GXD document classification. Moreover, using information obtained from image captions clearly improves performance, compared to title and abstract alone, affirming the utility of image captions as a substantial evidence source for automatically determining the relevance of biomedical publications to a specific subject area.
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    Ecophysiological responses of juvenile summer and winter flounder to hypoxia: experimental and modeling analyses of effects on estuarine nursery quality
    (Inter-Research, 2006-11-07) Stierhoff, Kevin L.; Targett, Timothy E.; Miller, KerriLynn; Kevin L. Stierhoff, Timothy E. Targett, KerriLynn Miller; Stierhoff, Kevin L.; Targett, Timothy E.; Miller, KerriLynn
    Growth and feeding rates were measured in juvenile summer flounder Paralichthys dentatus and winter flounder Pseudopleuronectes americanus exposed to sub-lethal hypoxia (low dissolved oxygen, DO) over a range of temperatures, to determine its potential effects on nursery habitat quality for these 2 estuary-dependent flatfishes. Growth rates of both species were generally reduced as DO decreased, particularly at DO levels of 50 to 70% air saturation, and as temperature increased. Summer flounder were more tolerant of low DO than were winter flounder at both 20 and 25°C. At these temperatures, summer flounder growth was reduced by ~25% (compared to growth at normoxia [7.0 mg O2 l–1]) at 3.5 mg O2 l–1 and by 50 to 60% at 2.0 mg O2 l–1. In contrast, growth of winter flounder at 20°C was reduced by ~50% at both 3.5 and 5.0 mg O2 l–1, and growth was zero at 2.0 mg O2 l–1. At 25°C, winter flounder grew poorly in all DO treatments and lost weight at 2.0 mg O2 l–1. Summer flounder were also tested at 30°C. Growth was significantly reduced even at 5.0 mg O2 l–1, and was reduced by ~90% at 2.0 mg O2 l–1. A significant relationship between feeding rate and growth suggested reduced consumption to be a major cause of growth limitation under hypoxia. There was no evidence of growth acclimation for either species after 7 to 14 d exposure to hypoxia. The effect of hypoxia on growth of summer flounder was reduced at lower salinity (15 vs. 25‰) and was unaffected by the presence of a sand substrate. Similarity between modeled growth under hypoxic conditions, based on our laboratory results, and observed growth of summer flounder in a hypoxic estuarine tributary suggests growth limitation in the wild. These laboratory and field results demonstrate that even moderate hypoxia can adversely affect growth rates, and thus the quality of estuarine nursery habitats for juvenile flatfishes.
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    Experimental characterization of tensile properties of epoxy resin by using micro-fiber specimens
    (SAGE Publications, 2016) Misumi, Jun; Ganesh, Raja; Sockalingam, Subramani; Gillespie, John W. Jr.; Jun Misumi, Raja Ganesh, Subramani Sockalingam and John W Gillespie Jr.; Misumi, Jun; Ganesh, Raja; Sockalingam, Subramani; Gillespie, John W. Jr.
    In unidirectional carbon fiber reinforced plastic (CFRP) laminates, the distance between fibers can vary from submicron to micron length scales. The mechanical properties of the matrix at this length scale are not well understood. In this study, processing methods have been developed to produce high quality epoxy micro-fibers with diameters ranging from 100 to 150 um that are used for tensile testing. Five types of epoxy resin systems ranging from standard DGEBA to high-crosslink TGDDM and TGMAP epoxy systems have been characterized. Epoxy macroscopic specimens with film thickness of 3300 um exhibited brittle behavior (1.7 to 4.9% average failure strain) with DGEBA resin having the highest failure strain level. The epoxy micro-fiber specimens exhibited significant ductile behavior (20 to 42% average failure strain) with a distinct yield point being observed in all five resin systems. In addition, the ultimate stress of the highly cross-linked TGDDM epoxy fiber exceeded the bulk film properties by a factor of two and the energy absorption was over 50 times greater on average. The mechanism explaining the dramatic difference in properties are discussed and is based on size effects (the film volume is about 2000 times greater than the fiber volume within the gage sections) and surface defects. Based on the findings 3 presented in this paper, the microscale fiber test specimens are recommended and provide more realistic stress-strain response for describing the role of the matrix in composites at smaller length scales.
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    Poisoning of Ru/C by Homogeneous Brønsted Acids in Hydrodeoxygenation of 2,5-Dimethylfuran via Catalytic Transfer Hydrogenation
    (Elsevier, 2017) Gilkey, Matthew J.; Vlachos, Dionisios G.; Xu, Bingjun; Matthew J. Gilkey, Dionisios G. Vlachos, Bingjun Xu; Gilkey, Matthew J.; Vlachos, Dionisios G; Xu, Bingjun
    It has been proposed that the combination of metal and acid sites is critical for effective ring opening of biomass-derived furans to linear molecules, a reaction that holds promise for the production of renewable polymer precursors and alkanes. In this work, we use 2,5-dimethylfuran (DMF) as a model compound to investigate hydrogenolysis and hydrogenation pathways using a combination of H2SO4 and Ru-mediated catalytic transfer hydrogenation in 2-propanol. Acid-catalyzed hydrolytic ring opening of DMF to 2,5-hexanedione (HDN) occurs readily at 80 °C with a selectivity of 89% in 2-propanol. Over Ru/C, HDN is fully converted after only 2 h at 80 °C, forming a mixture of both ring-closed products (~68% total yield), i.e., 2,5-dimethyltetrahydrofuran (DMTHF) and 2,5-dimethyl-2,3-dihydrofuran (DMDHF), as well as ring opened products (~28% total yield), i.e., 2,5-hexanediol (2,5-HDL) and 2-hexanol (HOL). Rather than observing sequential hydrolysis/hydrogenation reactions, we observe severe suppression of metal chemistry when having both Ru/C and H2SO4 in the reaction system. While minor leaching of Ru occurs in the presence of mineral acids, X-ray photoelectron spectroscopy coupled with CO chemisorption studies suggest that the primary cause of the lack of Ru-mediated chemistry is poisoning by strongly adsorbed sulfate species. This hypothesis is supported by the observation of Ru-catalyzed chemistry when replacing H2SO4 with Nafion, a solid Brønsted acid, as sulfonic acid groups tethered to the polymer backbone cannot adsorb on the metal sites.
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    Preferences and concerns for care needs in advanced Parkinson's disease: a qualitative study of couples.
    (Wiley-Blackwell, 2016-08-29) Habermann, B.; Shin, J.; Habermann, B., & Shin, J.; Habermann, B.
    Aims and objectives: To explore how couples with Parkinson’s disease (PD) discuss their needs, concerns, and preferences at the advanced stages of illness. Background: The majority of care for people with PD is provided at home by family members. PD is characterized by a slow progressive decline with care needs often exceeding a decade. Design: A descriptive qualitative study with 14 couples. Methods: Data were collected on two occasions over a one month period utilizing semi‐structured interviews, with both individual and couple interviews. Data were analyzed thematically by the research team. Results: All participants discussed the strong desire to remain in their homes for as long as possible. For the people with PD, placement to long‐term facilities was not an option to be considered. For spouses, there was an acknowledgement there may come a time when they could no longer continue to provide care. Concerns regarding falls, choking, voice production, financial strain and need for prognostic information from providers were influences on what they believed the future would hold and the decisions they would need to make. Conclusions: The need for improved communication between providers and PD couples is evident. Interventions to support the couple in their discussions and decision making regarding remaining in the home or not, and options to support advanced care needs are required. Relevance to clinical practice: Nurses can help support decision making by providing tangible information regarding the advanced stages of PD including adequate prognostic information. Advanced PD 2 What does this article contribute to the wider global clinical community? >\Preferences for placement to long‐term care facilities are different among people with PD and their spouses. Beliefs about the future and decision making are influenced by concerns about physical complications including falls and choking and the need for prognostic information from health care providers. The need for improved communication between health care providers and PD couples is reported. Nursing interventions to support the couple in their discussions and decision making regarding placement and options to support advanced care needs are required.
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    War or Peace? How the Subjective Perception of Great Power Interdependence Shapes Preemptive Defensive Aggression
    (Frontiers Media S.A, 2017-06-02) Jing, Yiming; Gries, Peter H.; Li, Yang; Stivers, Adam W.; Mifune, Nobuhiro; Kuhlman, D. M.; Bai, Liying; Yiming Jing, Peter H. Gries, Yang Li , Adam W. Stivers , Nobuhiro Mifune , D. M. Kuhlman and Liying Bai; Kuhlman, D. M.
    Why do great powers with benign intentions end up fighting each other in wars they do not seek? We utilize an incentivized, two-person “Preemptive Strike Game” (PSG) to explore how the subjective perception of great power interdependence shapes defensive aggression against persons from rival great powers. In Study 1, college students from the United States (N D 115), China (N D 106), and Japan (N D 99) made PSG decisions facing each other. This natural experiment revealed that Chinese and Japanese participants (a) made more preemptive attacks against each other and Americans than against their compatriots, and that (b) greater preexisting perceptions of bilateral competition increased intergroup attack rates. In Study 2, adult Americans (N D 127) watched real CNN expert interviews portraying United States–China economic interdependence as more positive or negative. This randomized experiment revealed that the more positive portrayal reduced preemptive American strikes against Chinese (but not Japanese), while the more negative portrayal amplified American anger about China’s rise, increasing preemptive attacks against Chinese. We also found, however, that preemptive strikes were primarily defensive and not offensive. Interventions to reduce defensive aggression and promote great power peace are discussed.
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    Functionalization and Dispersion of Carbon Nanomaterials Using an Environmentally Friendly Ultrasonicated Ozonolysis Process
    (Journal of Visualized Experiments (JoVE), 2017-05-30) Yeo, Eudora S. Y.; Mathys, Gary I.; Brack, Narelle; Thostenson, Erik T.; Rider, Andrew N.; Eudora S. Y. Yeo, Gary I. Mathys, Narelle Brack, Erik T. Thostenson, Andrew N. Rider; Thostenson, Erik T.
    Functionalization of carbon nanomaterials is often a critical step that facilitates their integration into larger material systems and devices. In the as-received form, carbon nanomaterials, such as carbon nanotubes (CNTs) or graphene nanoplatelets (GNPs), may contain large agglomerates. Both agglomerates and impurities will diminish the benefits of the unique electrical and mechanical properties offered when CNTs or GNPs are incorporated into polymers or composite material systems. Whilst a variety of methods exist to functionalize carbon nanomaterials and to create stable dispersions, many the processes use harsh chemicals, organic solvents, or surfactants, which are environmentally unfriendly and may increase the processing burden when isolating the nanomaterials for subsequent use. The current research details the use of an alternative, environmentally friendly technique for functionalizing CNTs and GNPs. It produces stable, aqueous dispersions free of harmful chemicals. Both CNTs and GNPs can be added to water at concentrations up to 5 g/L and can be recirculated through a high-powered ultrasonic cell. The simultaneous injection of ozone into the cell progressively oxidizes the carbon nanomaterials, and the combined ultrasonication breaks down agglomerates and immediately exposes fresh material for functionalization. The prepared dispersions are ideally suited for the deposition of thin films onto solid substrates using electrophoretic deposition (EPD). CNTs and GNPs from the aqueous dispersions can be readily used to coat carbon- and glass-reinforcing fibers using EPD for the preparation of hierarchical composite materials.
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    Band alignment and p-type doping of ZnSnN2
    (American Physical Society, 2017-05-31) Wang, Tianshi; Ni, Chaoying; Janotti, Anderson; Tianshi Wang, Chaoying Ni, and Anderson Janotti; Wang, Tianshi; Ni, Chaoying; Janotti, Anderson
    Composed of earth-abundant elements, ZnSnN2 is a promising semiconductor for photovoltaic and photoelectrochemical applications. However, basic properties such as the precise value of the band gap and the band alignment to other semiconductors are still unresolved. For instance, reported values for the band gap vary from 1.4 to 2.0 eV. In addition, doping in ZnSnN2 remains largely unexplored. Using density functional theory with the Heyd-Scuseria-Ernzerhof hybrid functional, we investigate the electronic structure of ZnSnN2, its band alignment to GaN and ZnO, and the possibility of p-type doping. We find that the position of the valence-band maximum of ZnSnN2 is 0.39 eV higher than that in GaN, yet the conduction-band minimum is close to that in ZnO, which suggests that achieving p-type conductivity is likely as in GaN, yet it may be difficult to control unintentional n-type conductivity as in ZnO. Among possible p-type dopants, we explore Li, Na, and K substituting on the Zn site. We show that while LiZn is a shallow acceptor, NaZn and KZn are deep acceptors, which we trace back to large local relaxations around the Na and K impurities due to the atomic size mismatches.
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    Antibody-nanoparticle conjugates to enhance the sensitivity of ELISA-based detection methods
    (Public Library of Science (PLOS), 2017-05-11) Billingsley, Margaret M.; Riley, Rachel S.; Day, Emily S.; Margaret M. Billingsley, Rachel S. Riley, Emily S. Day; Billingsley, Margaret M.; Riley, Rachel S.; Day, Emily S.
    Accurate antigen detection is imperative for clinicians to diagnose disease, assess treatment success, and predict patient prognosis. The most common technique used for the detection of disease-associated biomarkers is the enzyme linked immunosorbent assay (ELISA). In an ELISA, primary antibodies are incubated with biological samples containing the biomarker of interest. Then, detectible secondary antibodies conjugated with horseradish peroxidase (HRP) bind the primary antibodies. Upon addition of a color-changing substrate, the samples provide a colorimetric signal that directly correlates to the targeted biomarker concentration. While ELISAs are effective for analyzing samples with high biomarker content, they lack the sensitivity required to analyze samples with low antigen levels. We hypothesized that the sensitivity of ELISAs could be enhanced by replacing freely delivered primary antibodies with antibody-nanoparticle conjugates that provide excess binding sites for detectible secondary antibodies, ultimately leading to increased signal. Here, we investigated the use of nanoshells (NS) decorated with antibodies specific to epidermal growth factor receptor (EGFR) as a model system (EGFR-NS). We incubated one healthy and two breast cancer cell lines, each expressing different levels of EGFR, with EGFR-NS, untargeted NS, or unconjugated EGFR antibodies, as well as detectable secondary antibodies. We found that EGFR-NS consistently increased signal intensity relative to unconjugated EGFR antibodies, with a substantial 13-fold enhancement from cells expressing high levels of EGFR. Additionally, 40x more unconjugated antibodies were required to detect EGFR compared to those conjugated to NS. Our results demonstrate that antibody-nanoparticle conjugates lower the detection limit of traditional ELISAs and support further investigation of this strategy with other antibodies and nanoparticles. Owing to their enhanced sensitivity, we anticipate that nanoparticle-modified ELISAs can be used to detect low levels of biomarkers found in various diseases, such as cancers, tuberculosis, and rheumatoid arthritis, and may ultimately enable earlier diagnosis, better prognostication, and improved treatment monitoring
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    Reckless Self-destructive Behavior and PTSD in Veterans: The Mediating Role of New Adverse Events
    (Wiley-Blackwell, 2017-06-23) Lusk, Joanna D.; Sadeh, Naomi; Wolf, Erika J.; Miller, Mark W.; Joanna D. Lusk, B.A., Naomi Sadeh, Ph.D., Erika J. Wolf, Ph.D., & Mark W. Miller, Ph.D.; Sadeh, Naomi
    The addition of self-destructive and reckless behavior as a symptom of posttraumatic stress disorder (PTSD) in DSM-5 has stimulated renewed interest in understanding relationships between these behaviors and trauma-related psychopathology. This study examined the relationship between reckless and self-destructive behaviors (RSDB), intervening exposure to new adverse events, and later PTSD severity in a sample of traumaexposed veterans. At baseline, participants were assessed for RSDB (past 5 years) and current PTSD severity (N = 222). PTSD severity was then reassessed approximately 4 years later (N = 148). Overall, RSDB were reported by 74.4% of the sample, with 61.3% engaging in multiple forms of RSDB. The most commonly endorsed behaviors included alcohol/drug abuse (42.8%), driving while intoxicated (29.4%), gambling (24.7%), and aggression (23.1%). There was a positive correlation between RSDB and PTSD severity at both the baseline (r = .16, p = .031) and follow-up assessment (r = .24, p = .005). Path models indicated that exposure to new adverse events fully mediated the effect of Time 1 RSDB on PTSD symptoms at Time 2 (indirect association: β = .05, p =.046). Results suggest that RSDB are common among trauma-exposed veterans and may perpetuate PTSD symptoms by increasing exposure to new adverse events.