Computational analysis of the Phanerochaete chrysosporium v2.0 genome database and mass spectrometry identiWcation of peptides in ligninolytic cultures reveal complex mixtures of secreted proteins

Treesearch

Amber Vanden Wymelenberg; Patrick Minges; Grzegorz Sabat; Diego Martinez; Andrea Aerts; Asaf Salamov; Igor Grigoriev; Harris Shapiro; Nik Putnam; Paula Belinky; Carlos Dosoretz; Jill Gaskell; Phil Kersten; Dan Cullen

2006-01-01

The white-rot basidiomycete Phanerochaete chrysosporium employs extracellular enzymes to completely degrade the major polymers of wood: cellulose, hemicellulose, and lignin. Analysis of a total of 10,048 v2.1 gene models predicts 769 secreted proteins, a substantial increase over the 268 models identified in the earlier database (v1.0). Within the v2.1 ‘computational...

Metagenomic analysis of microbial consortia enriched from compost: new insights into the role of Actinobacteria in lignocellulose decomposition.

PubMed

Wang, Cheng; Dong, Da; Wang, Haoshu; Müller, Karin; Qin, Yong; Wang, Hailong; Wu, Weixiang

2016-01-01

Compost habitats sustain a vast ensemble of microbes specializing in the degradation of lignocellulosic plant materials and are thus important both for their roles in the global carbon cycle and as potential sources of biochemical catalysts for advanced biofuels production. Studies have revealed substantial diversity in compost microbiomes, yet how this diversity relates to functions and even to the genes encoding lignocellulolytic enzymes remains obscure. Here, we used a metagenomic analysis of the rice straw-adapted (RSA) microbial consortia enriched from compost ecosystems to decipher the systematic and functional contexts within such a distinctive microbiome. Analyses of the 16S pyrotag library and 5 Gbp of metagenomic sequence showed that the phylum Actinobacteria was the predominant group among the Bacteria in the RSA consortia, followed by Proteobacteria, Firmicutes, Chloroflexi, and Bacteroidetes. The CAZymes profile revealed that CAZyme genes in the RSA consortia were also widely distributed within these bacterial phyla. Strikingly, about 46.1 % of CAZyme genes were from actinomycetal communities, which harbored a substantially expanded catalog of the cellobiohydrolase, β-glucosidase, acetyl xylan esterase, arabinofuranosidase, pectin lyase, and ligninase genes. Among these communities, a variety of previously unrecognized species was found, which reveals a greater ecological functional diversity of thermophilic Actinobacteria than previously assumed. These data underline the pivotal role of thermophilic Actinobacteria in lignocellulose biodegradation processes in the compost habitat. Besides revealing a new benchmark for microbial enzymatic deconstruction of lignocelluloses, the results suggest that actinomycetes found in compost ecosystems are potential candidates for mining efficient lignocellulosic enzymes in the biofuel industry.

Substantial equivalence analysis in fruits from three Theobroma species through chemical composition and protein profiling.

PubMed

Pérez-Mora, Walter; Jorrin-Novo, Jesús V; Melgarejo, Luz Marina

2018-02-01

Substantial equivalence studies were performed in three Theobroma spp., cacao, bicolor and grandiflorum through chemical composition analysis and protein profiling of fruit (pulp juice and seeds). Principal component analysis of sugar, organic acid, and phenol content in pulp juice revealed equivalence among the three species, with differences in some of the compounds that may result in different organoleptic properties. Proteins were extracted from seeds and pulp juice, resolved by two dimensional electrophoresis and major spots subjected to mass spectrometry analysis and identification. The protein profile, as revealed by principal component analysis, was variable among the three species in both seed and pulp, with qualitative and quantitative differences in some of protein species. The functional grouping of the identified proteins correlated with the biological role of each organ. Some of the identified proteins are of interest, being minimally discussed, including vicilin, a protease inhibitor, and a flavonol synthase/flavanone 3-hydroxylase. Theobroma grandiflorum and Theobroma bicolor are endemic Amazonian plants that are poorly traded at the local level. As close relatives of Theobroma cacao, they may provide a good alternative for human consumption and industrial purposes. In this regard, we performed equivalence studies by conducting a comparative biochemical and proteomics analysis of the fruit, pulp juice and seeds of these three species. The results indicated equivalent chemical compositions and variable protein profiles with some differences in the content of the specific compounds or protein species that may result in variable organoleptic properties between the species and can be exploited for traceability purposes. Copyright © 2017 Elsevier Ltd. All rights reserved.

Host genetic determinants of microbiota-dependent nutrition revealed by genome-wide analysis of Drosophila melanogaster

PubMed Central

Dobson, Adam J.; Chaston, John M.; Newell, Peter D.; Donahue, Leanne; Hermann, Sara L.; Sannino, David R.; Westmiller, Stephanie; Wong, Adam C.-N.; Clark, Andrew G.; Lazzaro, Brian P.; Douglas, Angela E.

2015-01-01

Animals bear communities of gut microorganisms with substantial effects on animal nutrition, but the host genetic basis of these effects is unknown. Here, we use Drosophila to demonstrate substantial among-genotype variation in the effects of eliminating the gut microbiota on five host nutritional indices (weight, and protein, lipid, glucose and glycogen contents); this includes variation in both the magnitude and direction of microbiota-dependent effects. Genome-wide associations to identify the genetic basis of the microbiota-dependent variation reveal polymorphisms in largely non-overlapping sets of genes associated with variation in the nutritional traits, including strong representation of conserved genes functioning in signaling. Key genes identified by the GWA study are validated by loss-of-function mutations that altered microbiota-dependent nutritional effects. We conclude that the microbiota interacts with the animal at multiple points in the signaling and regulatory networks that determine animal nutrition. These interactions with the microbiota are likely conserved across animals, including humans. PMID:25692519

Using carbonized low-cost materials for removal of chemicals of environmental concern from water.

PubMed

Weidemann, Eva; Niinipuu, Mirva; Fick, Jerker; Jansson, Stina

2018-06-01

Adsorption on low-cost biochars would increase the affordability and availability of water treatment in, for example, developing countries. The aim of this study was to identify the precursor materials and hydrochar surface properties that yield efficient removal of compounds of environmental concern (CEC). We determined the adsorption kinetics of a mixture containing ten CECs (octhilinone, triclosan, trimethoprim, sulfamethoxasole, ciprofloxacin, diclofenac, paracetamol, diphenhydramine, fluconazole, and bisphenol A) to hydrochars prepared from agricultural waste (including tomato- and olive-press wastes, rice husks, and horse manure). The surface characteristics of the hydrochars were evaluated via diffuse reflectance infrared spectroscopy (DRIFTS), X-ray photoelectron spectroscopy (XPS), and N 2 -adsorption. Kinetic adsorption tests revealed that removal efficiencies varied substantially among different materials. Similarly, surface analysis revealed differences among the studied hydrochars and the degree of changes that the materials undergo during carbonization. According to the DRIFTS data, compared with the least efficient adsorbent materials, the most efficient hydrochars underwent more substantial changes during carbonization.

Combination of pharmacotherapy and psychotherapy in the treatment of chronic depression: A systematic review and meta-analysis

PubMed Central

2012-01-01

Background Chronic depression represents a substantial portion of depressive disorders and is associated with severe consequences. This review examined whether the combination of pharmacological treatments and psychotherapy is associated with higher effectiveness than pharmacotherapy alone via meta-analysis; and identified possible treatment effect modifiers via meta-regression-analysis. Methods A systematic search was conducted in the following databases: Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, EMBASE, ISI Web of Science, BIOSIS, PsycINFO, and CINAHL. Primary efficacy outcome was a response to treatment; primary acceptance outcome was dropping out of the study. Only randomized controlled trials were considered. Results We identified 8 studies with a total of 9 relevant comparisons. Our analysis revealed small, but statistically not significant effects of combined therapies on outcomes directly related to depression (BR = 1.20) with substantial heterogeneity between studies (I² = 67%). Three treatment effect modifiers were identified: target disorders, the type of psychotherapy and the type of pharmacotherapy. Small but statistically significant effects of combined therapies on quality of life (SMD = 0.18) were revealed. No differences in acceptance rates and the long-term effects between combined treatments and pure pharmacological interventions were observed. Conclusions This systematic review could not provide clear evidence for the combination of pharmacotherapy and psychotherapy. However, due to the small amount of primary studies further research is needed for a conclusive decision. PMID:22694751

Gene Expression Architecture of Mouse Dorsal and Tail Skin Reveals Functional Differences in Inflammation and Cancer | Office of Cancer Genomics

Cancer.gov

Inherited germline polymorphisms can cause gene expression levels in normal tissues to differ substantially between individuals. We present an analysis of the genetic architecture of normal adult skin from 470 genetically unique mice, demonstrating the effect of germline variants, skin tissue location, and perturbation by exogenous inflammation or tumorigenesis on gene signaling pathways.

Toward DSM-V: An Item Response Theory Analysis of the Diagnostic Process for DSM-IV Alcohol Abuse and Dependence in Adolescents

ERIC Educational Resources Information Center

Gelhorn, Heather; Hartman, Christie; Sakai, Joseph; Stallings, Michael; Young, Susan; Rhee, So Hyun; Corley, Robin; Hewitt, John; Hopger, Christian; Crowley, Thomas D.

2008-01-01

Clinical interviews of approximately 5,587 adolescents revealed that DSM-IV diagnostic categories were found to be different in terms of the severity of alcohol use disorders (AUDs). However, a substantial inconsistency and overlap was found in severity of AUDs across categories. The need for an alternative diagnostic algorithm which considers all…

S. pombe Uba1-Ubc15 Structure Reveals a Novel Regulatory Mechanism of Ubiquitin E2 Activity.

PubMed

Lv, Zongyang; Rickman, Kimberly A; Yuan, Lingmin; Williams, Katelyn; Selvam, Shanmugam Panneer; Woosley, Alec N; Howe, Philip H; Ogretmen, Besim; Smogorzewska, Agata; Olsen, Shaun K

2017-02-16

Ubiquitin (Ub) E1 initiates the Ub conjugation cascade by activating and transferring Ub to tens of different E2s. How Ub E1 cooperates with E2s that differ substantially in their predicted E1-interacting residues is unknown. Here, we report the structure of S. pombe Uba1 in complex with Ubc15, a Ub E2 with intrinsically low E1-E2 Ub thioester transfer activity. The structure reveals a distinct Ubc15 binding mode that substantially alters the network of interactions at the E1-E2 interface compared to the only other available Ub E1-E2 structure. Structure-function analysis reveals that the intrinsically low activity of Ubc15 largely results from the presence of an acidic residue at its N-terminal region. Notably, Ub E2 N termini are serine/threonine rich in many other Ub E2s, leading us to hypothesize that phosphorylation of these sites may serve as a novel negative regulatory mechanism of Ub E2 activity, which we demonstrate biochemically and in cell-based assays. Copyright © 2017 Elsevier Inc. All rights reserved.

A pattern recognition approach to transistor array parameter variance

NASA Astrophysics Data System (ADS)

da F. Costa, Luciano; Silva, Filipi N.; Comin, Cesar H.

2018-06-01

The properties of semiconductor devices, including bipolar junction transistors (BJTs), are known to vary substantially in terms of their parameters. In this work, an experimental approach, including pattern recognition concepts and methods such as principal component analysis (PCA) and linear discriminant analysis (LDA), was used to experimentally investigate the variation among BJTs belonging to integrated circuits known as transistor arrays. It was shown that a good deal of the devices variance can be captured using only two PCA axes. It was also verified that, though substantially small variation of parameters is observed for BJT from the same array, larger variation arises between BJTs from distinct arrays, suggesting the consideration of device characteristics in more critical analog designs. As a consequence of its supervised nature, LDA was able to provide a substantial separation of the BJT into clusters, corresponding to each transistor array. In addition, the LDA mapping into two dimensions revealed a clear relationship between the considered measurements. Interestingly, a specific mapping suggested by the PCA, involving the total harmonic distortion variation expressed in terms of the average voltage gain, yielded an even better separation between the transistor array clusters. All in all, this work yielded interesting results from both semiconductor engineering and pattern recognition perspectives.

Public Policy and Economic Efficiency in Ontario's Electricity Market: 2002 to 2011

NASA Astrophysics Data System (ADS)

Olmstead, Derek E. H.

A competitive wholesale electricity market began operation in Ontario in 2002. The institutional features and development process are described, and the outcomes associated with certain features are assessed. First, a six-equation model of the market is specified and estimated. The results are used to undertake analysis of the province's renewable energy program. The impacts of the program on consumers' and producers' surplus, as well as the resulting degree of carbon dioxide (CO2) emission-abatement, are estimated. These results are used to infer the per-unit cost of CO 2 abatement resulting from the program. Under the assumption that the renewable-fuelled energy displaces coal-fuelled energy from the market, the estimated cost is approximately 93/tonne of CO2; under the alternative assumption that natural gas-fuelled generation is displaced, the estimated cost is 207/tonne of CO2. Comparison to costs observed in other markets and jurisdictions reveals the program to cost approximately one order of magnitude greater than elsewhere. It is concluded that Ontario pays substantially more for emission abatement than is necessary or, alternatively, that Ontario achieves substantially less abatement than is feasible for each dollar of economic resources expended. Second, the market model is also used to assess the treatment of electricity exports with respect to the so-called global adjustment charge. The analysis reveals that the current practise of exempting exports from the charge is not socially optimal from a total surplus-maximisation standpoint. That objective would be achieved if global adjustment was allocated to exports at approximately 32% of the rate at which it is applied to Ontario-based consumers, a result consistent with a Ramsey-type inverse elasticity rule. Third, the forward market unbiasedness hypothesis is assessed in the context of the market for financial transmission rights (FTR). Issues related to left-censoring of payouts at $0 and overlapping observations are dealt with. The analysis reveals little evidence in favour of the hypothesis, but finds less biasedness in long-term rights as compared to short-term rights. Analysis of bidder behaviour reveals greater levels of participation in auctions of FTRs that link Ontario to similarly competitive neighbouring jurisdictions as opposed to non-competitive jurisdictions.

Mini-BRU/BIPS foil bearing development

NASA Technical Reports Server (NTRS)

Dobler, F. X.; Miller, L. J.

1978-01-01

The analysis revealed the failure agent to be a combination of poor teflon coating adhesion, a decrease in bearing sway space and, possibly, lack of flushing flow through the bearing. A change in Teflon coating vendors provided substantially improved coating quality and surface finish. The sway space was increased and the cooling bleed flow was adjusted to flush the bearing. These changes were included in a test conducted in the WHL from 6 April to 22 May 1978 which resulted in the completion of 1006.9 hours of operation at temperature and load. Post-test inspection revealed the bearings to be in excellent condition and capable of completing a much longer test.

Investigation into diagnostic agreement using automated computer-assisted histopathology pattern recognition image analysis.

PubMed

Webster, Joshua D; Michalowski, Aleksandra M; Dwyer, Jennifer E; Corps, Kara N; Wei, Bih-Rong; Juopperi, Tarja; Hoover, Shelley B; Simpson, R Mark

2012-01-01

The extent to which histopathology pattern recognition image analysis (PRIA) agrees with microscopic assessment has not been established. Thus, a commercial PRIA platform was evaluated in two applications using whole-slide images. Substantial agreement, lacking significant constant or proportional errors, between PRIA and manual morphometric image segmentation was obtained for pulmonary metastatic cancer areas (Passing/Bablok regression). Bland-Altman analysis indicated heteroscedastic measurements and tendency toward increasing variance with increasing tumor burden, but no significant trend in mean bias. The average between-methods percent tumor content difference was -0.64. Analysis of between-methods measurement differences relative to the percent tumor magnitude revealed that method disagreement had an impact primarily in the smallest measurements (tumor burden <3%). Regression-based 95% limits of agreement indicated substantial agreement for method interchangeability. Repeated measures revealed concordance correlation of >0.988, indicating high reproducibility for both methods, yet PRIA reproducibility was superior (C.V.: PRIA = 7.4, manual = 17.1). Evaluation of PRIA on morphologically complex teratomas led to diagnostic agreement with pathologist assessments of pluripotency on subsets of teratomas. Accommodation of the diversity of teratoma histologic features frequently resulted in detrimental trade-offs, increasing PRIA error elsewhere in images. PRIA error was nonrandom and influenced by variations in histomorphology. File-size limitations encountered while training algorithms and consequences of spectral image processing dominance contributed to diagnostic inaccuracies experienced for some teratomas. PRIA appeared better suited for tissues with limited phenotypic diversity. Technical improvements may enhance diagnostic agreement, and consistent pathologist input will benefit further development and application of PRIA.

1/f model for long-time memory of the ocean surface temperature

NASA Astrophysics Data System (ADS)

Fraedrich, Klaus; Luksch, Ute; Blender, Richard

2004-09-01

The 1/f spectrum of the ocean surface temperature in the Atlantic and Pacific midlatitudes is explained by a simple vertical diffusion model with a shallow mixed layer on top of a deep ocean. The model is forced at the air-sea interface with the total surface heat flux from a 1000 year climate simulation. The analysis reveals the role of ocean advection and substantiates estimates of internal thermal diffusivities.

Reframing Financial Sector Identity: Options For Reducing Mexican Drug Cartel Economic Power

DTIC Science & Technology

2012-01-18

shows an organization listed by OFAC in 2011, the Cifuentes Villa Crime Organization, associated with the Sinaloa cartel. In this case , the diagram...respect to bulk cash smuggling and the overall scale of the issue. The most egregious case in banking history highlights the volume possible with a...fiscal regulations, with substantial failure of internal controls and policy at Wachovia.33 14  Further analysis of the Wachovia case reveals a

Evidence for presumable feline origin of sporadic G6P[9] rotaviruses in humans.

PubMed

Pietsch, Corinna; Liebert, Uwe G

2018-05-31

Species A rotaviruses are highly diverse and impose a substantial burden to human and animal health. Interspecies transmission between livestock, domestic animals and humans is commonly observed, but spread of animal-like rotaviruses within the human population is limited. During the continued monitoring of rotavirus strains in Germany, an unusual G6P[9] rotavirus strain was detected in feces of a child. The complete rotavirus coding sequences revealed a unique G6-P[9]-I2-R2-C2-M2-A3-N2-T3-E2-H3 genotype constellation. The virus was phylogenetically related to feline G3P[9] strains and other human G6P[9] rotaviruses of presumable zoonotic origin. Analysis of primer binding sites of G6 specific genotyping revealed further evidence of a G6P[9] feline reservoir. Moreover, substantial deficits of conventional semi-nested PCR genotyping approaches in detecting contemporary G6P[9] were revealed. Rotavirus strain GER29-14 most likely resulted from a direct or recent interspecies transmission from a cat to human. Further studies could assess nucleic acid sequences and genotype constellations of feline rotavirus to confirm the likely feline origin of sporadic human G6P[9] strains. Copyright © 2018 Elsevier B.V. All rights reserved.

SIMS analysis of extended impact features on LDEF experiment

NASA Technical Reports Server (NTRS)

Amari, S.; Foote, J.; Jessberger, E. K.; Simon, C.; Stadermann, F. J.; Swan, P.; Walker, R.; Zinner, E.

1991-01-01

Discussed here are the first Secondary Ion Mass Spectroscopy (SIMS) analysis of projectile material deposited in extended impact features on Ge wafers from the trailing edge. Although most capture cells lost their plastic film covers, they contain extended impact features that apparently were produced by high velocity impacts when the plastic foils were still intact. Detailed optical scanning of all bare capture cells from the trailing edge revealed more than 100 impacts. Fifty-eight were selected by scanning electron microscope (SEM) inspection as prime candidates for SIMS analysis. Preliminary SIMS measurements were made on 15 impacts. More than half showed substantial enhancements of Mg, Al, Si, Ca, and Fe in the impact region, indicating micrometeorites as the projectiles.

Peptidomic analysis reveals proteolytic activity of kefir microorganisms on bovine milk proteins

PubMed Central

Dallas, David C.; Citerne, Florine; Tian, Tian; Silva, Vitor L. M.; Kalanetra, Karen M.; Frese, Steven A.; Robinson, Randall C.; Mills, David A.; Barile, Daniela

2015-01-01

Scope The microorganisms that make up kefir grains are well known for lactose fermentation, but the extent to which they hydrolyze and consume milk proteins remains poorly understood. Peptidomics technologies were used to examine the proteolytic activity of kefir grains on bovine milk proteins. Methods and results Gel electrophoresis revealed substantial digestion of milk proteins by kefir grains, with mass spectrometric analysis showing the release of 609 protein fragments and alteration of the abundance of >1,500 peptides that derived from 27 milk proteins. Kefir contained 25 peptides identified from the literature as having biological activity, including those with antihypertensive, antimicrobial, immunomodulatory, opioid and anti-oxidative functions. 16S rRNA and shotgun metagenomic sequencing identified the principle taxa in the culture as Lactobacillus species. Conclusion The model kefir sample contained thousands of protein fragments released in part by kefir microorganisms and in part by native milk proteases. PMID:26616950

Genetic variability in environmental isolates of Legionella pneumophila from Comunidad Valenciana (Spain).

PubMed

Coscollá, Mireia; Gosalbes, María José; Catalán, Vicente; González-Candelas, Fernando

2006-06-01

Legionella pneumophila is associated to recurrent outbreaks in several Comunidad Valenciana (Spain) localities, especially in Alcoi, where social and climatic conditions seem to provide an excellent environment for bacterial growth. We have analysed the nucleotide sequences of three loci from 25 environmental isolates from Alcoi and nearby locations sampled over 3 years. The analysis of these isolates has revealed a substantial level of genetic variation, with consistent patterns of variability across loci, and comparable to that found in a large, European-wide sampling of clinical isolates. Among the tree loci studied, fliC showed the highest level of nucleotide diversity. The analysis of isolates sampled in different years revealed a clear differentiation, with samples from 2001 being significantly distinct from those obtained in 2002 and 2003. Furthermore, although linkage disequilibrium measures indicate a clonal nature for population structure in this sample, the presence of some recombination events cannot be ruled out.

[HYGIENIC ASSESSMENT OF NUTRITION IN VEGETARIANS AND PEOPLE WITH MIXED FEEDING].

PubMed

Yunatskaya, T A; Turchaninova, N S; Kostina, N N

2015-01-01

There was performed a comparative analysis of the actual nutrition of inhabitants of the city of Omsk with mixed feeding (n = 50), and representatives of different types of vegetarians: raw food diet (n = 12), veganism (n = 14), lacto-ovo vegetarians (n = 14). There were revealed differences in consumption of food and food substances in persons with different types of food. There was established insufficient energy value, reduced intake of protein, fats, carbohydrates, vitamin B12 in the diet of vegans and raw foodists. There was determined the availability of vitamin B12 by the analysis of this substance in the blood serum by mean of standard chemiluminescent immunoassay. Vitamin B12 deficiency was revealed in vegans and raw foodists. There were substantiated such basic directions ofelimination of the deficit of nutrients and calories in the diet of vegetarians as the careful planning and assortment of products, as well as the use of vitamin-mineral complexes.

Peptidomic analysis reveals proteolytic activity of kefir microorganisms on bovine milk proteins.

PubMed

Dallas, David C; Citerne, Florine; Tian, Tian; Silva, Vitor L M; Kalanetra, Karen M; Frese, Steven A; Robinson, Randall C; Mills, David A; Barile, Daniela

2016-04-15

The microorganisms that make up kefir grains are well known for lactose fermentation, but the extent to which they hydrolyze and consume milk proteins remains poorly understood. Peptidomics technologies were used to examine the proteolytic activity of kefir grains on bovine milk proteins. Gel electrophoresis revealed substantial digestion of milk proteins by kefir grains, with mass spectrometric analysis showing the release of 609 protein fragments and alteration of the abundance of >1500 peptides that derived from 27 milk proteins. Kefir contained 25 peptides identified from the literature as having biological activity, including those with antihypertensive, antimicrobial, immunomodulatory, opioid and anti-oxidative functions. 16S rRNA and shotgun metagenomic sequencing identified the principle taxa in the culture as Lactobacillus species. The model kefir sample contained thousands of protein fragments released in part by kefir microorganisms and in part by native milk proteases. Copyright © 2015 Elsevier Ltd. All rights reserved.

Production of Secondary Metabolites in Extreme Environments: Food- and Airborne Wallemia spp. Produce Toxic Metabolites at Hypersaline Conditions

PubMed Central

Frisvad, Jens C.; Kocev, Dragi; Džeroski, Sašo; Gunde-Cimerman, Nina

2016-01-01

The food- and airborne fungal genus Wallemia comprises seven xerophilic and halophilic species: W. sebi, W. mellicola, W. canadensis, W. tropicalis, W. muriae, W. hederae and W. ichthyophaga. All listed species are adapted to low water activity and can contaminate food preserved with high amounts of salt or sugar. In relation to food safety, the effect of high salt and sugar concentrations on the production of secondary metabolites by this toxigenic fungus was investigated. The secondary metabolite profiles of 30 strains of the listed species were examined using general growth media, known to support the production of secondary metabolites, supplemented with different concentrations of NaCl, glucose and MgCl2. In more than two hundred extracts approximately one hundred different compounds were detected using high-performance liquid chromatography-diode array detection (HPLC-DAD). Although the genome data analysis of W. mellicola (previously W. sebi sensu lato) and W. ichthyophaga revealed a low number of secondary metabolites clusters, a substantial number of secondary metabolites were detected at different conditions. Machine learning analysis of the obtained dataset showed that NaCl has higher influence on the production of secondary metabolites than other tested solutes. Mass spectrometric analysis of selected extracts revealed that NaCl in the medium affects the production of some compounds with substantial biological activities (wallimidione, walleminol, walleminone, UCA 1064-A and UCA 1064-B). In particular an increase in NaCl concentration from 5% to 15% in the growth media increased the production of the toxic metabolites wallimidione, walleminol and walleminone. PMID:28036382

Acinetobacter lactucae sp. nov., isolated from iceberg lettuce (Asteraceae: Lactuca sativa).

PubMed

Rooney, Alejandro P; Dunlap, Christopher A; Flor-Weiler, Lina B

2016-09-01

Strain NRRL B-41902T and three closely related strains were isolated from iceberg lettuce. The strain was found to consist of strictly aerobic, Gram-stain-negative rods that formed cocci in late stationary phase. 16S rRNA gene sequence analysis showed that strain NRRL B-41902T was most closely related to species within the genera Acinetobacter, and that a grouping of it and the three other closely related strains was most closely related to the type strain of Acinetobacter pittii, which was also confirmed through a phylogenomic analysis. Moreover, in silico DNA-DNA hybridization analysis revealed a substantial amount of genomic divergence (39.1 %) between strain NRRL B-41902T and the type strain of A. pittii, which is expected if the strains represent distinct species. Further phenotypic analysis revealed that strain NRRL B-41902T was able to utilize a combination of l-serine, citraconic acid and citramalic acid, which differentiated it from other, closely related Acinetobacter species. Therefore, strain NRRL B-41902T (=CCUG 68785T) is proposed as the type strain of a novel species, Acinetobacter lactucae sp. nov.

The Value of Training: Analysis of DAU’s Requirements Management Training Results

DTIC Science & Technology

2015-04-01

test outcomes. According to Kim and Wilson (2010), “there can be substantial effects of pretest on posttest , especially when the duration between them...determine whether one group might be better prepared for the advanced concepts course. The DAU faculty compares pre-test data to post-test data to...this assumption, however. The means of the group scores on the pre-test varied only between 49.5 and 53.7. An ANOVA test on the groups revealed no

Alteration of Sedimentary Clasts in Martian Meteorite Northwest Africa 7034

NASA Technical Reports Server (NTRS)

McCubbin, F. M.; Tartese, R.; Santos, A. R.; Domokos, G.; Muttik, N.; Szabo, T.; Vazquez, J.; Boyce, J. W.; Keller, L. P.; Jerolmack, D. J.;

Human neural stem cell-derived cultures in three-dimensional substrates form spontaneously functional neuronal networks.

PubMed

Smith, Imogen; Silveirinha, Vasco; Stein, Jason L; de la Torre-Ubieta, Luis; Farrimond, Jonathan A; Williamson, Elizabeth M; Whalley, Benjamin J

2017-04-01

Differentiated human neural stem cells were cultured in an inert three-dimensional (3D) scaffold and, unlike two-dimensional (2D) but otherwise comparable monolayer cultures, formed spontaneously active, functional neuronal networks that responded reproducibly and predictably to conventional pharmacological treatments to reveal functional, glutamatergic synapses. Immunocytochemical and electron microscopy analysis revealed a neuronal and glial population, where markers of neuronal maturity were observed in the former. Oligonucleotide microarray analysis revealed substantial differences in gene expression conferred by culturing in a 3D vs a 2D environment. Notable and numerous differences were seen in genes coding for neuronal function, the extracellular matrix and cytoskeleton. In addition to producing functional networks, differentiated human neural stem cells grown in inert scaffolds offer several significant advantages over conventional 2D monolayers. These advantages include cost savings and improved physiological relevance, which make them better suited for use in the pharmacological and toxicological assays required for development of stem cell-based treatments and the reduction of animal use in medical research. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

Instructor and peer bullying in college students: Distinct typologies based on Latent Class Analysis.

PubMed

Marraccini, Marisa E; Brick, Leslie Ann D; Weyandt, Lisa L

2018-03-22

Although bullying is traditionally considered within the context of primary and secondary school, recent evidence suggests that bullying continues into college and workplace settings. Participants/Method: Latent class analysis (LCA) was employed to classify college bullying involvement typologies among 325 college students attending a northeastern university. Four classes concerning bullying involvement were revealed: Non-involved (36%); Instructor victim (30%); Peer bully-victim (22%); and Peer bully-victim/ Instructor victim (12%). Findings from this study, which classified college bullying experiences by incorporating both peer and instructor (teacher and professor) bullying, add substantially to the literature by providing insight into patterns of relatively unexplored bullying behaviors.

The Ardipithecus ramidus skull and its implications for hominid origins.

PubMed

Suwa, Gen; Asfaw, Berhane; Kono, Reiko T; Kubo, Daisuke; Lovejoy, C Owen; White, Tim D

2009-10-02

The highly fragmented and distorted skull of the adult skeleton ARA-VP-6/500 includes most of the dentition and preserves substantial parts of the face, vault, and base. Anatomical comparisons and micro-computed tomography-based analysis of this and other remains reveal pre-Australopithecus hominid craniofacial morphology and structure. The Ardipithecus ramidus skull exhibits a small endocranial capacity (300 to 350 cubic centimeters), small cranial size relative to body size, considerable midfacial projection, and a lack of modern African ape-like extreme lower facial prognathism. Its short posterior cranial base differs from that of both Pan troglodytes and P. paniscus. Ar. ramidus lacks the broad, anteriorly situated zygomaxillary facial skeleton developed in later Australopithecus. This combination of features is apparently shared by Sahelanthropus, showing that the Mio-Pliocene hominid cranium differed substantially from those of both extant apes and Australopithecus.

Time-series analysis of ruminant foetal wastage at a slaughterhouse in North Central Nigeria between 2001 and 2012.

PubMed

Alhaji, Nma B; Odetokun, Ismail A; Shittu, Aminu; Onyango, Joshua; Chafe, Umar M; Abubakar, Muhammed S; Muraina, Issa A; Fasina, Folorunso O; Lee, Hu Suk

2015-12-15

In developing countries, foetal wastage from slaughtered ruminants and the associated economic losses appear to be substantial. However, only a limited number of studies have comprehensively evaluated these trends. In the current study, secondary (retrospective) and primary data were collected and evaluated to estimate the prevalence of foetal wastage from cattle, sheep and goats slaughtered at an abattoir in Minna, Nigeria, over a 12-year period (January 2001-December 2012). Time-series modelling revealed substantial differences in the rate of foetal wastage amongst the slaughtered species, with more lambs having been wasted than calves or kids. Seasonal effects seem to influence rates of foetal wastage and certain months in the year appear to be associated with higher odds of foetal wastage. Improved management systems are suggested to reduce the risk of foetal losses.

Children's Family Drawings as Expressions of Attachment Representations Across Cultures: Possibilities and Limitations.

PubMed

Gernhardt, Ariane; Keller, Heidi; Rübeling, Hartmut

2016-07-01

The present study explored the cross-cultural appropriateness of children's family drawings as a measure for attachment quality. The sample consisted of 63 children aged 6 years from two diverse ecosocial contexts: middle-class families from Berlin, Germany (n = 32) and rural farming families from small villages around Kumbo, Cameroon (n = 31). The analysis of drawings with two classical attachment procedures, the Checklist of Drawing Signs (Kaplan & Main, 1986) and the Global Rating Scales (Fury, 1996), revealed substantial cultural differences. The results thus substantiated children's drawings as important cultural documents. Implications of the findings, however, are discussed in consideration of culture-specific conceptions of attachment relationships as indicated by cultural variations in mother's socialization goals. © 2016 The Authors. Child Development © 2016 Society for Research in Child Development, Inc.

Sleep duration and obesity in children: A systematic review and meta-analysis of prospective cohort studies.

PubMed

Li, Lian; Zhang, Shuang; Huang, Yubei; Chen, Kexin

2017-04-01

Childhood obesity is a major public problem worldwide, and sleep duration may be associated with childhood obesity. We conducted a systematic review and meta-analysis of prospective cohort studies to estimate the associations between sleep duration and obesity/body mass index (BMI) in children. PubMed, Embase and the Cochrane Library were searched. For the meta-analysis, the pooled relative risk (RR) and 95% confidence intervals (CI) were estimated to reveal the association between short sleep duration and obesity. For the review, the outcomes focused on BMI change or subsequent BMI status. A total of 12 studies (15 populations) met the criteria for inclusion in the meta-analysis. Short sleep duration was significantly associated with obesity (RR: 1.45; 95% CI: 1.14-1.85). After excluding two cohorts that substantially affected the heterogeneity, the pooled results remained significant (RR: 1.30; 95% CI: 1.20-1.42), and the association was not substantially altered in the subgroup analysis. In addition, we summarised 24 studies that met the criteria for our review of the relationship between sleeping and BMI. The present meta-analysis indicated that short sleep duration increased the risk of childhood obesity. Public health efforts that encourage children to have sufficient sleep time may be important in combating obesity. © 2017 Paediatrics and Child Health Division (The Royal Australasian College of Physicians).

Reveal Salmonella 2.0 test for detection of Salmonella spp. in foods and environmental samples. Performance Tested Method 960801.

PubMed

Hoerner, Rebecca; Feldpausch, Jill; Gray, R Lucas; Curry, Stephanie; Islam, Zahidul; Goldy, Tim; Klein, Frank; Tadese, Theodros; Rice, Jennifer; Mozola, Mark

2011-01-01

Reveal Salmonella 2.0 is an improved version of the original Reveal Salmonella lateral flow immunoassay and is applicable to the detection of Salmonella enterica serogroups A-E in a variety of food and environmental samples. A Performance Tested Method validation study was conducted to compare performance of the Reveal 2.0 method with that of the U.S. Department of Agriculture-Food Safety and Inspection Service or U.S. Food and Drug Administration/Bacteriological Analytical Manual reference culture methods for detection of Salmonella spp. in chicken carcass rinse, raw ground turkey, raw ground beef, hot dogs, raw shrimp, a ready-to-eat meal product, dry pet food, ice cream, spinach, cantaloupe, peanut butter, stainless steel surface, and sprout irrigation water. In a total of 17 trials performed internally and four trials performed in an independent laboratory, there were no statistically significant differences in performance of the Reveal 2.0 and reference culture procedures as determined by Chi-square analysis, with the exception of one trial with stainless steel surface and one trial with sprout irrigation water where there were significantly more positive results by the Reveal 2.0 method. Considering all data generated in testing food samples using enrichment procedures specifically designed for the Reveal method, overall sensitivity of the Reveal method relative to the reference culture methods was 99%. In testing environmental samples, sensitivity of the Reveal method relative to the reference culture method was 164%. For select foods, use of the Reveal test in conjunction with reference method enrichment resulted in overall sensitivity of 92%. There were no unconfirmed positive results on uninoculated control samples in any trials for specificity of 100%. In inclusivity testing, 102 different Salmonella serovars belonging to serogroups A-E were tested and 99 were consistently positive in the Reveal test. In exclusivity testing of 33 strains of non-salmonellae representing 14 genera, 32 were negative when tested with Reveal following nonselective enrichment, and the remaining strain was found to be substantially inhibited by the enrichment media used with the Reveal method. Results of ruggedness testing showed that the Reveal test produces accurate results even with substantial deviation in sample volume or device development time.

Clinical laboratory urine analysis: comparison of the UriSed automated microscopic analyzer and the manual microscopy.

PubMed

Ma, Junlong; Wang, Chengbin; Yue, Jiaxin; Li, Mianyang; Zhang, Hongrui; Ma, Xiaojing; Li, Xincui; Xue, Dandan; Qing, Xiaoyan; Wang, Shengjiang; Xiang, Daijun; Cong, Yulong

2013-01-01

Several automated urine sediment analyzers have been introduced to clinical laboratories. Automated microscopic pattern recognition is a new technique for urine particle analysis. We evaluated the analytical and diagnostic performance of the UriSed automated microscopic analyzer and compared with manual microscopy for urine sediment analysis. Precision, linearity, carry-over, and method comparison were carried out. A total of 600 urine samples sent for urinalysis were assessed using the UriSed automated microscopic analyzer and manual microscopy. Within-run and between-run precision of the UriSed for red blood cells (RBC) and white blood cells (WBC) were acceptable at all levels (CV < 20%). Within-run and between-run imprecision of the UriSed testing for cast, squamous epithelial cells (EPI), and bacteria (BAC) were good at middle level and high level (CV < 20%). The linearity analysis revealed substantial agreement between the measured value and the theoretical value of the UriSed for RBC, WBC, cast, EPI, and BAC (r > 0.95). There was no carry-over. RBC, WBC, and squamous epithelial cells with sensitivities and specificities were more than 80% in this study. There is substantial agreement between the UriSed automated microscopic analyzer and the manual microscopy methods. The UriSed provides for a rapid turnaround time.

Neighborhood-level social processes and substantiated cases of child maltreatment.

PubMed

Molnar, Beth E; Goerge, Robert M; Gilsanz, Paola; Hill, Andrea; Subramanian, S V; Holton, John K; Duncan, Dustin T; Beatriz, Elizabeth D; Beardslee, William R

2016-01-01

Child maltreatment is a preventable public health problem. Research has demonstrated that neighborhood structural factors (e.g. poverty, crime) can influence the proportion of a neighborhood's children who are victims of maltreatment. A newer strategy is the identification of potentially modifiable social processes at the neighborhood level that can also influence maltreatment. Toward this end, this study examines neighborhood-level data (maltreatment cases substantiated by Illinois' child protection agency, 1995-2005, social processes measured by the Project on Human Development in Chicago Neighborhoods, U.S. Census data, proportions of neighborhoods on public assistance, and crime data) that were linked across clusters of contiguous, relatively homogenous Chicago, IL census tracts with respect to racial/ethnic and socioeconomic composition. Our analysis-an ecological-level, repeated cross-sectional design utilizing random-intercept logit models-with a sensitivity analysis using spatial models to control for spatial autocorrelation-revealed consistent associations between neighborhood social processes and maltreatment. Neighborhoods higher in collective efficacy, intergenerational closure, and social networks, and lower in disorder had lower proportions of neglect, physical abuse, and sexual abuse substantiated cases, controlling for differences in structural factors. Higher collective efficacy and social network size also predicted a lower proportion of substance-exposed infants. This research indicates that strategies to mobilize neighborhood-level protective factors may decrease child maltreatment more effectively than individual and family-focused efforts alone. Copyright © 2015 Elsevier Ltd. All rights reserved.

Reporting on Suicide Between 1819 and 1944.

PubMed

Arendt, Florian

2018-04-05

Suicide rates increased substantially in many countries during the 19th century. Little is known about news coverage on suicide in this period and its relationship to suicide rates. To test whether there was a covariation between the quantity of reporting and suicide rates and whether the press relied on sensational reporting. A content analysis of Austrian news coverage between 1819 and 1944 was conducted and compared with contemporary findings. There were similar corresponding troughs and peaks in both time series, indicative of covariation. The analysis revealed that variations in the quantity of reporting predicted the following year's suicide rates, a pattern consistent with a long-term Werther effect. Conversely, suicide rates did not predict future values of the quantity of reporting. Furthermore, the press substantially overrepresented "vivid" firearm suicides compared with other more "pallid" methods such as drowning, indicative of sensational reporting. The causal order of the quantity of reporting and suicide rates should be interpreted with caution. The press may have contributed to the establishment of suicide as a mass phenomenon in the 19th century. The contemporary comparison is indicative of temporal stability.

DFT-assisted spectroscopic characterization of pyrazosulfuron-ethyl: FT-Raman, FTIR and UV-vis studies of a sulfonyl urea herbicide

NASA Astrophysics Data System (ADS)

Monicka, J. Clemy; James, C.

2014-10-01

Raman and IR spectra of pyrazosulfuron-ethyl have been reported here, and it is shown that the spectra has been fully interpreted in terms of assigning normal modes to the various spectral features by using density functional theory calculations. The Raman bands observed for PY in solid phase are characteristic for the carbonyl group, Csbnd C, Csbnd H and Nsbnd H stretching and deformation vibrations. The dimer structure of PY was optimized, including the Nsbnd H…N and Csbnd H…O intermolecular interactions. Stability of the molecule arising from hyperconjugative interactions leading to its bioactivity and charge delocalization have been analyzed using natural bond orbital analysis. Spectral analysis reveals the substantial effect of non-bonding interaction, conjugation and induction effects in the molecule which in turn influences the bioactivity of the compound. Red shifting of (∼94 cm-1) Nsbnd H stretching band substantiates the presence of strong Nsbnd H…N intramolecular hydrogen bonding in the molecule. The aromatic behavior of pyrimidine and pyrazole ring has been calculated using the HOMA method.

Peptidome analysis of amniotic fluid from pregnancies with preeclampsia.

PubMed

Qian, Yating; Zhang, Lei; Rui, Can; Ding, Hongjuan; Mao, Pengyuan; Ruan, Hongjie; Jia, Ruizhe

2017-11-01

Preeclampsia (PE), a life‑threatening, complicated pregnancy‑associated disease, has recently become a research focus in obstetrics. However, the peptidome of the amniotic fluid in PE patients has rarely been investigated. The present study used peptidomic profiling to perform a comparative analysis of human amniotic fluid between normal and PE pregnancies. Centrifugal ultrafiltration and liquid chromatography‑tandem mass spectrometry (LC‑MS/MS) was combined with isotopomeric dimethyl labels to gain a deeper understanding of the role of proteins and the peptidome in the onset of PE. Following ultrafiltration and LC‑MS/MS, 352 peptides were identified. Of these, 23 peptides were observed to be significantly differentially expressed (6 downregulated and 17 upregulated; P<0.05). Using Gene Ontology and Blastp analyses, the functions and biological activities of these 23 peptides were identified and revealed to include autophagy, signal transduction, receptor activity, enzymatic activity and nucleic acid binding. In addition, a bibliographic search revealed that some of the identified peptides, including Titin, are crucial to the pathogenesis underlying PE. The present study identified 23 peptides expressed at significantly different levels in the amniotic fluid of PE and normal pregnancies. A comprehensive peptidome analysis is more efficient than a simple biomarker analysis at revealing deficiencies and improving the detection rate in diseases. These analyses therefore provide a substantial advantage in applications aimed at the discovery of disease‑specific biomarkers.

Limits to Cloud Susceptibility

NASA Technical Reports Server (NTRS)

Coakley, James A., Jr.

2002-01-01

1-kilometer AVHRR observations of ship tracks in low-level clouds off the west coast of the U S. were used to determine limits for the degree to which clouds might be altered by increases in anthropogenic aerosols. Hundreds of tracks were analyzed to determine whether the changes in droplet radii, visible optical depths, and cloud top altitudes that result from the influx of particles from underlying ships were consistent with expectations based on simple models for the indirect effect of aerosols. The models predict substantial increases in sunlight reflected by polluted clouds due to the increases in droplet numbers and cloud liquid water that result from the elevated particle concentrations. Contrary to the model predictions, the analysis of ship tracks revealed a 15-20% reduction in liquid water for the polluted clouds. Studies performed with a large-eddy cloud simulation model suggested that the shortfall in cloud liquid water found in the satellite observations might be attributed to the restriction that the 1-kilometer pixels be completely covered by either polluted or unpolluted cloud. The simulation model revealed that a substantial fraction of the indirect effect is caused by a horizontal redistribution of cloud water in the polluted clouds. Cloud-free gaps in polluted clouds fill in with cloud water while the cloud-free gaps in the surrounding unpolluted clouds remain cloud-free. By limiting the analysis to only overcast pixels, the current study failed to account for the gap-filling predicted by the simulation model. This finding and an analysis of the spatial variability of marine stratus suggest new ways to analyze ship tracks to determine the limit to which particle pollution will alter the amount of sunlight reflected by clouds.

Experimental evaluation of the certification-trail method

NASA Technical Reports Server (NTRS)

Sullivan, Gregory F.; Wilson, Dwight S.; Masson, Gerald M.; Itoh, Mamoru; Smith, Warren W.; Kay, Jonathan S.

1993-01-01

Certification trails are a recently introduced and promising approach to fault-detection and fault-tolerance. A comprehensive attempt to assess experimentally the performance and overall value of the method is reported. The method is applied to algorithms for the following problems: huffman tree, shortest path, minimum spanning tree, sorting, and convex hull. Our results reveal many cases in which an approach using certification-trails allows for significantly faster overall program execution time than a basic time redundancy-approach. Algorithms for the answer-validation problem for abstract data types were also examined. This kind of problem provides a basis for applying the certification-trail method to wide classes of algorithms. Answer-validation solutions for two types of priority queues were implemented and analyzed. In both cases, the algorithm which performs answer-validation is substantially faster than the original algorithm for computing the answer. Next, a probabilistic model and analysis which enables comparison between the certification-trail method and the time-redundancy approach were presented. The analysis reveals some substantial and sometimes surprising advantages for ther certification-trail method. Finally, the work our group performed on the design and implementation of fault injection testbeds for experimental analysis of the certification trail technique is discussed. This work employs two distinct methodologies, software fault injection (modification of instruction, data, and stack segments of programs on a Sun Sparcstation ELC and on an IBM 386 PC) and hardware fault injection (control, address, and data lines of a Motorola MC68000-based target system pulsed at logical zero/one values). Our results indicate the viability of the certification trail technique. It is also believed that the tools developed provide a solid base for additional exploration.

Comparative Proteomic and Nutritional Composition Analysis of Independent Transgenic Pigeon Pea Seeds Harboring cry1AcF and cry2Aa Genes and Their Nontransgenic Counterparts.

PubMed

Mishra, Pragya; Singh, Shweta; Rathinam, Maniraj; Nandiganti, Muralimohan; Ram Kumar, Nikhil; Thangaraj, Arulprakash; Thimmegowda, Vinutha; Krishnan, Veda; Mishra, Vagish; Jain, Neha; Rai, Vandna; Pattanayak, Debasis; Sreevathsa, Rohini

2017-02-22

Safety assessment of genetically modified plants is an important aspect prior to deregulation. Demonstration of substantial equivalence of the transgenics compared to their nontransgenic counterparts can be performed using different techniques at various molecular levels. The present study is a first-ever comprehensive evaluation of pigeon pea transgenics harboring two independent cry genes, cry2Aa and cry1AcF. The absence of unintended effects in the transgenic seed components was demonstrated by proteome and nutritional composition profiling. Analysis revealed that no significant differences were found in the various nutritional compositional analyses performed. Additionally, 2-DGE-based proteome analysis of the transgenic and nontransgenic seed protein revealed that there were no major changes in the protein profile, although a minor fold change in the expression of a few proteins was observed. Furthermore, the study also demonstrated that neither the integration of T-DNA nor the expression of the cry genes resulted in the production of unintended effects in the form of new toxins or allergens.

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations.

PubMed

Mallick, Swapan; Li, Heng; Lipson, Mark; Mathieson, Iain; Gymrek, Melissa; Racimo, Fernando; Zhao, Mengyao; Chennagiri, Niru; Nordenfelt, Susanne; Tandon, Arti; Skoglund, Pontus; Lazaridis, Iosif; Sankararaman, Sriram; Fu, Qiaomei; Rohland, Nadin; Renaud, Gabriel; Erlich, Yaniv; Willems, Thomas; Gallo, Carla; Spence, Jeffrey P; Song, Yun S; Poletti, Giovanni; Balloux, Francois; van Driem, George; de Knijff, Peter; Romero, Irene Gallego; Jha, Aashish R; Behar, Doron M; Bravi, Claudio M; Capelli, Cristian; Hervig, Tor; Moreno-Estrada, Andres; Posukh, Olga L; Balanovska, Elena; Balanovsky, Oleg; Karachanak-Yankova, Sena; Sahakyan, Hovhannes; Toncheva, Draga; Yepiskoposyan, Levon; Tyler-Smith, Chris; Xue, Yali; Abdullah, M Syafiq; Ruiz-Linares, Andres; Beall, Cynthia M; Di Rienzo, Anna; Jeong, Choongwon; Starikovskaya, Elena B; Metspalu, Ene; Parik, Jüri; Villems, Richard; Henn, Brenna M; Hodoglugil, Ugur; Mahley, Robert; Sajantila, Antti; Stamatoyannopoulos, George; Wee, Joseph T S; Khusainova, Rita; Khusnutdinova, Elza; Litvinov, Sergey; Ayodo, George; Comas, David; Hammer, Michael F; Kivisild, Toomas; Klitz, William; Winkler, Cheryl A; Labuda, Damian; Bamshad, Michael; Jorde, Lynn B; Tishkoff, Sarah A; Watkins, W Scott; Metspalu, Mait; Dryomov, Stanislav; Sukernik, Rem; Singh, Lalji; Thangaraj, Kumarasamy; Pääbo, Svante; Kelso, Janet; Patterson, Nick; Reich, David

2016-10-13

Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioural modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non-Africans.

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

PubMed Central

Mallick, Swapan; Li, Heng; Lipson, Mark; Mathieson, Iain; Gymrek, Melissa; Racimo, Fernando; Zhao, Mengyao; Chennagiri, Niru; Nordenfelt, Susanne; Tandon, Arti; Skoglund, Pontus; Lazaridis, Iosif; Sankararaman, Sriram; Fu, Qiaomei; Rohland, Nadin; Renaud, Gabriel; Erlich, Yaniv; Willems, Thomas; Gallo, Carla; Spence, Jeffrey P.; Song, Yun S.; Poletti, Giovanni; Balloux, Francois; van Driem, George; de Knijff, Peter; Romero, Irene Gallego; Jha, Aashish R.; Behar, Doron M.; Bravi, Claudio M.; Capelli, Cristian; Hervig, Tor; Moreno-Estrada, Andres; Posukh, Olga L.; Balanovska, Elena; Balanovsky, Oleg; Karachanak-Yankova, Sena; Sahakyan, Hovhannes; Toncheva, Draga; Yepiskoposyan, Levon; Tyler-Smith, Chris; Xue, Yali; Abdullah, M. Syafiq; Ruiz-Linares, Andres; Beall, Cynthia M.; Di Rienzo, Anna; Jeong, Choongwon; Starikovskaya, Elena B.; Metspalu, Ene; Parik, Jüri; Villems, Richard; Henn, Brenna M.; Hodoglugil, Ugur; Mahley, Robert; Sajantila, Antti; Stamatoyannopoulos, George; Wee, Joseph T. S.; Khusainova, Rita; Khusnutdinova, Elza; Litvinov, Sergey; Ayodo, George; Comas, David; Hammer, Michael; Kivisild, Toomas; Klitz, William; Winkler, Cheryl; Labuda, Damian; Bamshad, Michael; Jorde, Lynn B.; Tishkoff, Sarah A.; Watkins, W. Scott; Metspalu, Mait; Dryomov, Stanislav; Sukernik, Rem; Singh, Lalji; Thangaraj, Kumarasamy; Pääbo, Svante; Kelso, Janet; Patterson, Nick; Reich, David

2016-01-01

We report the Simons Genome Diversity Project (SGDP) dataset: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioral modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that in other non-Africans. PMID:27654912

Space station integrated propulsion and fluid systems study

NASA Technical Reports Server (NTRS)

Bicknell, B.; Wilson, S.; Dennis, M.; Shepard, D.; Rossier, R.

1988-01-01

The program study was performed in two tasks: Task 1 addressed propulsion systems and Task 2 addressed all fluid systems associated with the Space Station elements, which also included propulsion and pressurant systems. Program results indicated a substantial reduction in life cycle costs through integrating the oxygen/hydrogen propulsion system with the environmental control and life support system, and through supplying nitrogen in a cryogenic gaseous supercritical or subcritical liquid state. A water sensitivity analysis showed that increasing the food water content would substantially increase the amount of water available for propulsion use and in all cases, the implementation of the BOSCH CO2 reduction process would reduce overall life cycle costs to the station and minimize risk. An investigation of fluid systems and associated requirements revealed a delicate balance between the individual propulsion and fluid systems across work packages and a strong interdependence between all other fluid systems.

'They never talked to me about... ': Perspectives on aged care resident transfer to emergency departments.

PubMed

Arendts, Glenn; Popescu, Aurora; Howting, Denise; Quine, Susan; Howard, Kirsten

2015-06-01

To explore perspectives of three groups concerning transfers from aged care facilities to emergency departments. We sought to reveal factors influencing transfer decisions; how active each group was in making decisions; and to what extent groups ceded decision-making to others. Semi-structured interviews of 11 residents, 14 relatives and 17 staff with content analysis of interview transcripts. The three groups substantially differed in their involvement with initiating, and attitudes towards, transfer. Residents were least likely to be involved in the decision, yet most likely to support transfer. Staff felt conflicted between their desire to provide optimal treatment for one ill resident, and their obligations to other residents under care. Staff perspectives were largely consistent with published data, but we describe new results for other informant groups. Group expectations and preferences differ substantially. Service delivery to meet all preferences presents a challenge for health service design. © 2013 ACOTA.

Decelerated genome evolution in modern vertebrates revealed by analysis of multiple lancelet genomes

PubMed Central

Huang, Shengfeng; Chen, Zelin; Yan, Xinyu; Yu, Ting; Huang, Guangrui; Yan, Qingyu; Pontarotti, Pierre Antoine; Zhao, Hongchen; Li, Jie; Yang, Ping; Wang, Ruihua; Li, Rui; Tao, Xin; Deng, Ting; Wang, Yiquan; Li, Guang; Zhang, Qiujin; Zhou, Sisi; You, Leiming; Yuan, Shaochun; Fu, Yonggui; Wu, Fenfang; Dong, Meiling; Chen, Shangwu; Xu, Anlong

2014-01-01

Vertebrates diverged from other chordates ~500 Myr ago and experienced successful innovations and adaptations, but the genomic basis underlying vertebrate origins are not fully understood. Here we suggest, through comparison with multiple lancelet (amphioxus) genomes, that ancient vertebrates experienced high rates of protein evolution, genome rearrangement and domain shuffling and that these rates greatly slowed down after the divergence of jawed and jawless vertebrates. Compared with lancelets, modern vertebrates retain, at least relatively, less protein diversity, fewer nucleotide polymorphisms, domain combinations and conserved non-coding elements (CNE). Modern vertebrates also lost substantial transposable element (TE) diversity, whereas lancelets preserve high TE diversity that includes even the long-sought RAG transposon. Lancelets also exhibit rapid gene turnover, pervasive transcription, fastest exon shuffling in metazoans and substantial TE methylation not observed in other invertebrates. These new lancelet genome sequences provide new insights into the chordate ancestral state and the vertebrate evolution. PMID:25523484

Decelerated genome evolution in modern vertebrates revealed by analysis of multiple lancelet genomes.

PubMed

Huang, Shengfeng; Chen, Zelin; Yan, Xinyu; Yu, Ting; Huang, Guangrui; Yan, Qingyu; Pontarotti, Pierre Antoine; Zhao, Hongchen; Li, Jie; Yang, Ping; Wang, Ruihua; Li, Rui; Tao, Xin; Deng, Ting; Wang, Yiquan; Li, Guang; Zhang, Qiujin; Zhou, Sisi; You, Leiming; Yuan, Shaochun; Fu, Yonggui; Wu, Fenfang; Dong, Meiling; Chen, Shangwu; Xu, Anlong

2014-12-19

Vertebrates diverged from other chordates ~500 Myr ago and experienced successful innovations and adaptations, but the genomic basis underlying vertebrate origins are not fully understood. Here we suggest, through comparison with multiple lancelet (amphioxus) genomes, that ancient vertebrates experienced high rates of protein evolution, genome rearrangement and domain shuffling and that these rates greatly slowed down after the divergence of jawed and jawless vertebrates. Compared with lancelets, modern vertebrates retain, at least relatively, less protein diversity, fewer nucleotide polymorphisms, domain combinations and conserved non-coding elements (CNE). Modern vertebrates also lost substantial transposable element (TE) diversity, whereas lancelets preserve high TE diversity that includes even the long-sought RAG transposon. Lancelets also exhibit rapid gene turnover, pervasive transcription, fastest exon shuffling in metazoans and substantial TE methylation not observed in other invertebrates. These new lancelet genome sequences provide new insights into the chordate ancestral state and the vertebrate evolution.

Race and Older Mothers’ Differentiation: A Sequential Quantitative and Qualitative Analysis

PubMed Central

Sechrist, Jori; Suitor, J. Jill; Riffin, Catherine; Taylor-Watson, Kadari; Pillemer, Karl

2011-01-01

The goal of this paper is to demonstrate a process by which qualitative and quantitative approaches are combined to reveal patterns in the data that are unlikely to be detected and confirmed by either method alone. Specifically, we take a sequential approach to combining qualitative and quantitative data to explore race differences in how mothers differentiate among their adult children. We began with a standard multivariate analysis examining race differences in mothers’ differentiation among their adult children regarding emotional closeness and confiding. Finding no race differences in this analysis, we conducted an in-depth comparison of the Black and White mothers’ narratives to determine whether there were underlying patterns that we had been unable to detect in our first analysis. Using this method, we found that Black mothers were substantially more likely than White mothers to emphasize interpersonal relationships within the family when describing differences among their children. In our final step, we developed a measure of familism based on the qualitative data and conducted a multivariate analysis to confirm the patterns revealed by the in-depth comparison of the mother’s narratives. We conclude that using such a sequential mixed methods approach to data analysis has the potential to shed new light on complex family relations. PMID:21967639

Computational neuroanatomy of speech production.

PubMed

Hickok, Gregory

2012-01-05

Speech production has been studied predominantly from within two traditions, psycholinguistics and motor control. These traditions have rarely interacted, and the resulting chasm between these approaches seems to reflect a level of analysis difference: whereas motor control is concerned with lower-level articulatory control, psycholinguistics focuses on higher-level linguistic processing. However, closer examination of both approaches reveals a substantial convergence of ideas. The goal of this article is to integrate psycholinguistic and motor control approaches to speech production. The result of this synthesis is a neuroanatomically grounded, hierarchical state feedback control model of speech production.

Characterizing Urban Turbulence Under Haze Pollution: Insights into Temperature-Humidity Dissimilarity

NASA Astrophysics Data System (ADS)

Guo, Xiaofeng; Sun, Yele; Miao, Shiguang

2016-03-01

We present a description of urban boundary-layer turbulence characteristics under conditions of severe haze pollution, an emerging issue of interest to air-pollution-relevant investigations. Comparative analysis between clean and hazy episodes reveals their remarkable difference in atmospheric stability. A stability signature is then identified in temperature-humidity de-correlation and dissimilarity. Such a signature is noteworthy, because the accuracy of a reliable parametrization of the heat-to-moisture transport efficiency is substantiated in unstable and stable conditions rather than in near-neutral conditions.

[Complex hygiene evaluation of the influence of exogenous and endogenous factors on the occurance of urolithiasis in the children of the Primorye Territory].

PubMed

Koval'chuk, V K; Luchaninova, V N; Koldaev, V M

2005-01-01

The paper presents the results of a study of the influence of 43 exogenous and 14 endogenous factors on the occurrence of urolithiasis in children with regional features of the Primorye Territory being kept in mind. Multidimensional mathematical analysis was used to reveal continuous and intermittent risk factors of this disease. The authors show it necessary to take into account the findings in substantiating measures for primary prevention of urolithiasis among the children of the Primorye Territory.

Silylene-diethynyl-arylene polymers having liquid crystalline properties

DOEpatents

Barton, Thomas J.; Ding, Yiwei

1993-09-07

The present invention provides linear organosilicon polymers including diethynyl-(substituted)arylene units, and a process for their preparation. These novel polymers possess useful properties including electrical conductivity, liquid crystallinity, and/or photoluminescence. These polymers possess good solubility in organic solvents. A preferred example is produced according to the following reaction scheme. ##STR1## These polymers can be solvent-cast to yield excellent films and can also be pulled into fibers from concentrated solutions. All possess substantial crystallinity as revealed by DSC analysis and observation through a polarizing microscope, and possess liquid crystalline properties.

Synergy between (13)C-metabolic flux analysis and flux balance analysis for understanding metabolic adaptation to anaerobiosis in E. coli.

PubMed

Chen, Xuewen; Alonso, Ana P; Allen, Doug K; Reed, Jennifer L; Shachar-Hill, Yair

2011-01-01

Genome-based Flux Balance Analysis (FBA) and steady-state isotopic-labeling-based Metabolic Flux Analysis (MFA) are complimentary approaches to predicting and measuring the operation and regulation of metabolic networks. Here, genome-derived models of Escherichia coli (E. coli) metabolism were used for FBA and ¹³C-MFA analyses of aerobic and anaerobic growths of wild-type E. coli (K-12 MG1655) cells. Validated MFA flux maps reveal that the fraction of maintenance ATP consumption in total ATP production is about 14% higher under anaerobic (51.1%) than aerobic conditions (37.2%). FBA revealed that an increased ATP utilization is consumed by ATP synthase to secrete protons from fermentation. The TCA cycle is shown to be incomplete in aerobically growing cells and submaximal growth is due to limited oxidative phosphorylation. An FBA was successful in predicting product secretion rates in aerobic culture if both glucose and oxygen uptake measurement were constrained, but the most-frequently predicted values of internal fluxes yielded from sampling the feasible space differ substantially from MFA-derived fluxes. © 2010 Elsevier Inc. All rights reserved.

Hurricane Katrina-linked environmental injustice: race, class, and place differentials in attitudes.

PubMed

Adeola, Francis O; Picou, J Steven

2017-04-01

Claims of environmental injustice, human neglect, and racism dominated the popular and academic literature after Hurricane Katrina struck the United States in August 2005. A systematic analysis of environmental injustice from the perspective of the survivors remains scanty or nonexistent. This paper presents, therefore, a systematic empirical analysis of the key determinants of Katrina-induced environmental injustice attitudes among survivors in severely affected parishes (counties) in Louisiana and Mississippi three years into the recovery process. Statistical models based on a random sample of survivors were estimated, with the results revealing significant predictors such as age, children in household under 18, education, homeownership, and race. The results further indicate that African-Americans were more likely to perceive environmental injustice following Katrina than their white counterparts. Indeed, the investigation reveals that there are substantial racial gaps in measures of environmental injustice. The theoretical, methodological, and applied policy implications of these findings are discussed. © 2017 The Author(s). Disasters © Overseas Development Institute, 2017.

Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity

PubMed Central

Pope, Welkin H; Bowman, Charles A; Russell, Daniel A; Jacobs-Sera, Deborah; Asai, David J; Cresawn, Steven G; Jacobs, William R; Hendrix, Roger W; Lawrence, Jeffrey G; Hatfull, Graham F; Abbazia, Patrick; Ababio, Amma; Adam, Naazneen

2015-01-01

The bacteriophage population is large, dynamic, ancient, and genetically diverse. Limited genomic information shows that phage genomes are mosaic, and the genetic architecture of phage populations remains ill-defined. To understand the population structure of phages infecting a single host strain, we isolated, sequenced, and compared 627 phages of Mycobacterium smegmatis. Their genetic diversity is considerable, and there are 28 distinct genomic types (clusters) with related nucleotide sequences. However, amino acid sequence comparisons show pervasive genomic mosaicism, and quantification of inter-cluster and intra-cluster relatedness reveals a continuum of genetic diversity, albeit with uneven representation of different phages. Furthermore, rarefaction analysis shows that the mycobacteriophage population is not closed, and there is a constant influx of genes from other sources. Phage isolation and analysis was performed by a large consortium of academic institutions, illustrating the substantial benefits of a disseminated, structured program involving large numbers of freshman undergraduates in scientific discovery. DOI: http://dx.doi.org/10.7554/eLife.06416.001 PMID:25919952

School attributes, household characteristics, and demand for schooling: A case study of rural Peru

NASA Astrophysics Data System (ADS)

Ilon, Lynn; Moock, Peter

1991-12-01

Educational expansion, long a goal of many LDCs, has become a difficult policy to pursue. Growing populations, shrinking national incomes and higher marginal costs of schooling as schooling reaches more rural dwellers have caused policy makers to take a hard look at factors which influence educational demand and expansion. This paper examines the case of Peru where rural areas have yet to attain the nearly universal enrollment of urban areas. The study examines 2500 rural households to explore reasons why children do not attend school, drop out of school, and begin school at later ages. The study finds that the monetary costs of schools (fees and other costs) have a substantial influence on parental decisions regarding school attendance and continuation. Sensitivity analysis reveals that mother's education has a bearing on their children's educational participation, particularly in low-income households. Sensitivity analysis also reveals that school attendance of low income and female children are most strongly affected by simulated changes in school fees.

Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity.

PubMed

Pope, Welkin H; Bowman, Charles A; Russell, Daniel A; Jacobs-Sera, Deborah; Asai, David J; Cresawn, Steven G; Jacobs, William R; Hendrix, Roger W; Lawrence, Jeffrey G; Hatfull, Graham F

2015-04-28

The bacteriophage population is large, dynamic, ancient, and genetically diverse. Limited genomic information shows that phage genomes are mosaic, and the genetic architecture of phage populations remains ill-defined. To understand the population structure of phages infecting a single host strain, we isolated, sequenced, and compared 627 phages of Mycobacterium smegmatis. Their genetic diversity is considerable, and there are 28 distinct genomic types (clusters) with related nucleotide sequences. However, amino acid sequence comparisons show pervasive genomic mosaicism, and quantification of inter-cluster and intra-cluster relatedness reveals a continuum of genetic diversity, albeit with uneven representation of different phages. Furthermore, rarefaction analysis shows that the mycobacteriophage population is not closed, and there is a constant influx of genes from other sources. Phage isolation and analysis was performed by a large consortium of academic institutions, illustrating the substantial benefits of a disseminated, structured program involving large numbers of freshman undergraduates in scientific discovery.

Driver gene classification reveals a substantial overrepresentation of tumor suppressors among very large chromatin-regulating proteins.

PubMed

Waks, Zeev; Weissbrod, Omer; Carmeli, Boaz; Norel, Raquel; Utro, Filippo; Goldschmidt, Yaara

2016-12-23

Compiling a comprehensive list of cancer driver genes is imperative for oncology diagnostics and drug development. While driver genes are typically discovered by analysis of tumor genomes, infrequently mutated driver genes often evade detection due to limited sample sizes. Here, we address sample size limitations by integrating tumor genomics data with a wide spectrum of gene-specific properties to search for rare drivers, functionally classify them, and detect features characteristic of driver genes. We show that our approach, CAnceR geNe similarity-based Annotator and Finder (CARNAF), enables detection of potentially novel drivers that eluded over a dozen pan-cancer/multi-tumor type studies. In particular, feature analysis reveals a highly concentrated pool of known and putative tumor suppressors among the <1% of genes that encode very large, chromatin-regulating proteins. Thus, our study highlights the need for deeper characterization of very large, epigenetic regulators in the context of cancer causality.

The dead end of domestic violence: spotlight on children's narratives during forensic investigations following domestic homicide.

PubMed

Katz, Carmit

2014-12-01

The current study provides an in-depth exploration of the narratives of children who witnessed their father killing their mother. This exploration was conducted using a thematic analysis of the children's forensic interviews based on seven investigative interviews that were conducted with children following the domestic homicide. Investigative interviews were selected for study only for substantiated cases and only if the children disclosed the domestic homicide. All of the investigative interviews were conducted within 24h of the domestic homicide. Thematic analysis revealed the following four key categories: the domestic homicide as the dead end of domestic violence, what I did when daddy killed mommy, that one time that daddy killed mommy, and mommy will feel better and will go back home. The discussion examines the multiple layers of this phenomenon as revealed in the children's narratives and its consequences for professionals within the legal and clinical contexts. Copyright © 2014 Elsevier Ltd. All rights reserved.

Fault Tree Analysis.

PubMed

McElroy, Lisa M; Khorzad, Rebeca; Rowe, Theresa A; Abecassis, Zachary A; Apley, Daniel W; Barnard, Cynthia; Holl, Jane L

The purpose of this study was to use fault tree analysis to evaluate the adequacy of quality reporting programs in identifying root causes of postoperative bloodstream infection (BSI). A systematic review of the literature was used to construct a fault tree to evaluate 3 postoperative BSI reporting programs: National Surgical Quality Improvement Program (NSQIP), Centers for Medicare and Medicaid Services (CMS), and The Joint Commission (JC). The literature review revealed 699 eligible publications, 90 of which were used to create the fault tree containing 105 faults. A total of 14 identified faults are currently mandated for reporting to NSQIP, 5 to CMS, and 3 to JC; 2 or more programs require 4 identified faults. The fault tree identifies numerous contributing faults to postoperative BSI and reveals substantial variation in the requirements and ability of national quality data reporting programs to capture these potential faults. Efforts to prevent postoperative BSI require more comprehensive data collection to identify the root causes and develop high-reliability improvement strategies.

Vlasov analysis of microbunching instability for magnetized beams

DOE PAGES

Tsai, C. -Y.; Derbenev, Ya. S.; Douglas, D.; ...

2017-05-19

For a high-brightness electron beam with low energy and high bunch charge traversing a recirculation beamline, coherent synchrotron radiation and space charge effect may result in the microbunching instability (MBI). Both tracking simulation and Vlasov analysis for an early design of Circulator Cooler Ring for the Jefferson Lab Electron Ion Collider reveal significant MBI. It is envisioned these could be substantially suppressed by using a magnetized beam. In this work, we extend the existing Vlasov analysis, originally developed for a non-magnetized beam, to the description of transport of a magnetized beam including relevant collective effects. As a result, the newmore » formulation will be further employed to confirm prediction of microbunching suppression for a magnetized beam transport in a recirculating machine design.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuypers, Marshall A.; Lambert, Gregory Joseph; Moore, Thomas W.

Chronic infection with Hepatitis C virus (HCV) results in cirrhosis, liver cancer and death. As the nations largest provider of care for HCV, US Veterans Health Administration (VHA) invests extensive resources in the diagnosis and treatment of the disease. This report documents modeling and analysis of HCV treatment dynamics performed for the VHA aimed at improving service delivery efficiency. System dynamics modeling of disease treatment demonstrated the benefits of early detection and the role of comorbidities in disease progress and patient mortality. Preliminary modeling showed that adherence to rigorous treatment protocols is a primary determinant of treatment success. In depthmore » meta-analysis revealed correlations of adherence and various psycho-social factors. This initial meta-analysis indicates areas where substantial improvement in patient outcomes can potentially result from VA programs which incorporate these factors into their design.« less

Palynology in coal systems analysis-The key to floras, climate, and stratigraphy of coal-forming environments

USGS Publications Warehouse

Nichols, D.J.

2005-01-01

Palynology can be effectively used in coal systems analysis to understand the nature of ancient coal-forming peat mires. Pollen and spores preserved in coal effectively reveal the floristic composition of mires, which differed substantially through geologic time, and contribute to determination of depositional environment and paleo- climate. Such applications are most effective when integrated with paleobotanical and coal-petrographic data. Examples of previous studies of Miocene, Carboniferous, and Paleogene coal beds illustrate the methods and results. Palynological age determinations and correlations of deposits are also important in coal systems analysis to establish stratigraphic setting. Application to studies of coalbed methane generation shows potential because certain kinds of pollen are associated with gas-prone lithotypes. ??2005 Geological Society of America.

Network Analysis: Applications for the Developing Brain

PubMed Central

Chu-Shore, Catherine J.; Kramer, Mark A.; Bianchi, Matt T.; Caviness, Verne S.; Cash, Sydney S.

2011-01-01

Development of the human brain follows a complex trajectory of age-specific anatomical and physiological changes. The application of network analysis provides an illuminating perspective on the dynamic interregional and global properties of this intricate and complex system. Here, we provide a critical synopsis of methods of network analysis with a focus on developing brain networks. After discussing basic concepts and approaches to network analysis, we explore the primary events of anatomical cortical development from gestation through adolescence. Upon this framework, we describe early work revealing the evolution of age-specific functional brain networks in normal neurodevelopment. Finally, we review how these relationships can be altered in disease and perhaps even rectified with treatment. While this method of description and inquiry remains in early form, there is already substantial evidence that the application of network models and analysis to understanding normal and abnormal human neural development holds tremendous promise for future discovery. PMID:21303762

Phylogenetic analysis of nitrite, nitric oxide, and nitrous oxide respiratory enzymes reveal a complex evolutionary history for denitrification.

PubMed

Jones, Christopher M; Stres, Blaz; Rosenquist, Magnus; Hallin, Sara

2008-09-01

Denitrification is a facultative respiratory pathway in which nitrite (NO2(-)), nitric oxide (NO), and nitrous oxide (N2O) are successively reduced to nitrogen gas (N(2)), effectively closing the nitrogen cycle. The ability to denitrify is widely dispersed among prokaryotes, and this polyphyletic distribution has raised the possibility of horizontal gene transfer (HGT) having a substantial role in the evolution of denitrification. Comparisons of 16S rRNA and denitrification gene phylogenies in recent studies support this possibility; however, these results remain speculative as they are based on visual comparisons of phylogenies from partial sequences. We reanalyzed publicly available nirS, nirK, norB, and nosZ partial sequences using Bayesian and maximum likelihood phylogenetic inference. Concomitant analysis of denitrification genes with 16S rRNA sequences from the same organisms showed substantial differences between the trees, which were supported by examining the posterior probability of monophyletic constraints at different taxonomic levels. Although these differences suggest HGT of denitrification genes, the presence of structural variants for nirK, norB, and nosZ makes it difficult to determine HGT from other evolutionary events. Additional analysis using phylogenetic networks and likelihood ratio tests of phylogenies based on full-length sequences retrieved from genomes also revealed significant differences in tree topologies among denitrification and 16S rRNA gene phylogenies, with the exception of the nosZ gene phylogeny within the data set of the nirK-harboring genomes. However, inspection of codon usage and G + C content plots from complete genomes gave no evidence for recent HGT. Instead, the close proximity of denitrification gene copies in the genomes of several denitrifying bacteria suggests duplication. Although HGT cannot be ruled out as a factor in the evolution of denitrification genes, our analysis suggests that other phenomena, such gene duplication/divergence and lineage sorting, may have differently influenced the evolution of each denitrification gene.

Downsizing of a provincial department of health--causes and implications for fiscal policy.

PubMed

Blecher, Mark

2002-06-01

To analyse the financial basis for downsizing of a provincial health department and suggest implications for fiscal policy. Analysis of relevant departmental, provincial and national financing and expenditure trends from 1995/96 to 2002/03. Western Cape (WC) Department of Health (DOH). Downsizing involving 9,282 health workers (27.9%) and closure of 3,601 hospital beds (24.4%) over 5 years. Total aggregate provincial transfers (all provinces) remained fairly constant in real terms. The WC's share decreased from 11.8% in 1996/97 to 9.8% in 2002/03. This was offset by the DOH's share of the WC budget increasing from 25.6% to 29.6%, mainly because of an increase in national health conditional grants. The net effect of financing changes was that the DOH's allocation in real terms was similar in 2002/03 and 1995/96, which suggests that financing changes are not the major cause of downsizing. Expenditure analysis revealed a 39.7% real rise in the average cost of health personnel. Substantial interprovincial inequities remain. The major cause of downsizing was wage growth, particularly following the 1996 wage agreement. Disjointed fiscal and wage policy has affected health services. Simultaneous application of policies of fiscal constraint, redistribution and substantial real wage growth has resulted in substantial downsizing with limited inroads into inequities. Inequities will continue to call for further redistribution, reduction in conditional grants and downsizing, much of which could have been avoided if fiscal and wage policy choices had been optimal.

Evolutionary Meta-Analysis of Association Studies Reveals Ancient Constraints Affecting Disease Marker Discovery

PubMed Central

Dudley, Joel T.; Chen, Rong; Sanderford, Maxwell; Butte, Atul J.; Kumar, Sudhir

2012-01-01

Genome-wide disease association studies contrast genetic variation between disease cohorts and healthy populations to discover single nucleotide polymorphisms (SNPs) and other genetic markers revealing underlying genetic architectures of human diseases. Despite scores of efforts over the past decade, many reproducible genetic variants that explain substantial proportions of the heritable risk of common human diseases remain undiscovered. We have conducted a multispecies genomic analysis of 5,831 putative human risk variants for more than 230 disease phenotypes reported in 2,021 studies. We find that the current approaches show a propensity for discovering disease-associated SNPs (dSNPs) at conserved genomic positions because the effect size (odds ratio) and allelic P value of genetic association of an SNP relates strongly to the evolutionary conservation of their genomic position. We propose a new measure for ranking SNPs that integrates evolutionary conservation scores and the P value (E-rank). Using published data from a large case-control study, we demonstrate that E-rank method prioritizes SNPs with a greater likelihood of bona fide and reproducible genetic disease associations, many of which may explain greater proportions of genetic variance. Therefore, long-term evolutionary histories of genomic positions offer key practical utility in reassessing data from existing disease association studies, and in the design and analysis of future studies aimed at revealing the genetic basis of common human diseases. PMID:22389448

Changes in the genetic structure of Atlantic salmon populations over four decades reveal substantial impacts of stocking and potential resiliency

PubMed Central

Perrier, Charles; Guyomard, René; Bagliniere, Jean-Luc; Nikolic, Natacha; Evanno, Guillaume

2013-01-01

While the stocking of captive-bred fish has been occurring for decades and has had substantial immediate genetic and evolutionary impacts on wild populations, its long-term consequences have only been weakly investigated. Here, we conducted a spatiotemporal analysis of 1428 Atlantic salmon sampled from 1965 to 2006 in 25 populations throughout France to investigate the influence of stocking on the neutral genetic structure in wild Atlantic salmon (Salmo salar) populations. On the basis of the analysis of 11 microsatellite loci, we found that the overall genetic structure among populations dramatically decreased over the period studied. Admixture rates among populations were highly variable, ranging from a nearly undetectable contribution from donor stocks to total replacement of the native gene pool, suggesting extremely variable impacts of stocking. Depending on population, admixture rates either increased, remained stable, or decreased in samples collected between 1998 and 2006 compared to samples from 1965 to 1987, suggesting either rising, long-lasting or short-term impacts of stocking. We discuss the potential mechanisms contributing to this variability, including the reduced fitness of stocked fish and persistence of wild locally adapted individuals. PMID:23919174

Risky Sexual Behavior and Substance Use among Adolescents: A Meta-analysis

PubMed Central

Ritchwood, Tiarney D.; Ford, Haley; DeCoster, Jamie; Sutton, Marnie; Lochman, John E.

2015-01-01

This study presents the results of a meta-analysis of the association between substance use and risky sexual behavior among adolescents. 87 studies fit the inclusion criteria, containing a total of 104 independent effect sizes that incorporated more than 120,000 participants. The overall effect size for the relationship between substance use and risky sexual behavior was in the small to moderate range (r = .22, CI = .18, .26). Further analyses indicated that the effect sizes did not substantially vary across the type of substance use, but did substantially vary across the type of risky sexual behavior being assessed. Specifically, mean effect sizes were smallest for studies examining unprotected sex (r = .15, CI = .10, .20), followed by studies examining number of sexual partners (r = .25, CI = .21, .30), those examining composite measures of risky sexual behavior (r = .38, CI = .27, .48), and those examining sex with an intravenous drug user (r = .53, CI = .45, .60). Furthermore, our results revealed that the relationship between drug use and risky sexual behavior is moderated by several variables, including sex, ethnicity, sexuality, age, sample type, and level of measurement. Implications and future directions are discussed. PMID:25825550

GPs' Perceptions of Cardiovascular Risk and Views on Patient Compliance: A Qualitative Interview Study.

PubMed

Barfoed, Benedicte Lind; Jarbøl, Dorte Ejg; Paulsen, Maja Skov; Christensen, Palle Mark; Halvorsen, Peder Andreas; Nielsen, Jesper Bo; Søndergaard, Jens

2015-01-01

Objective. General practitioners' (GPs') perception of risk is a cornerstone of preventive care. The aims of this interview study were to explore GPs' professional and personal attitudes and experiences regarding treatment with lipid-lowering drugs and their views on patient compliance. Methods. The material was drawn from semistructured qualitative interviews. We sampled GPs purposively from ten selected practices, ensuring diversity of demographic, professional, and personal characteristics. The GPs were encouraged to describe examples from their own practices and reflect on them and were informed that the focus was their personal attitudes and experiences. Systematic text condensation was applied for analysis in order to uncover the concepts and themes. Results. The analysis revealed the following 3 main themes: (1) use of cardiovascular guidelines and risk assessment tools, (2) strategies for managing patient compliance, and (3) GPs' own risk management. There were substantial differences in the attitudes concerning all three themes. Conclusions. The substantial differences in the GPs' personal and professional risk perceptions may be a key to understanding why GPs do not always follow cardiovascular guidelines. The impact on daily clinical practice, personal consultation style, and patient behaviour with regard to prevention is worth studying further.

GPs' Perceptions of Cardiovascular Risk and Views on Patient Compliance: A Qualitative Interview Study

PubMed Central

Barfoed, Benedicte Lind; Jarbøl, Dorte Ejg; Paulsen, Maja Skov; Christensen, Palle Mark; Halvorsen, Peder Andreas; Nielsen, Jesper Bo; Søndergaard, Jens

2015-01-01

Objective. General practitioners' (GPs') perception of risk is a cornerstone of preventive care. The aims of this interview study were to explore GPs' professional and personal attitudes and experiences regarding treatment with lipid-lowering drugs and their views on patient compliance. Methods. The material was drawn from semistructured qualitative interviews. We sampled GPs purposively from ten selected practices, ensuring diversity of demographic, professional, and personal characteristics. The GPs were encouraged to describe examples from their own practices and reflect on them and were informed that the focus was their personal attitudes and experiences. Systematic text condensation was applied for analysis in order to uncover the concepts and themes. Results. The analysis revealed the following 3 main themes: (1) use of cardiovascular guidelines and risk assessment tools, (2) strategies for managing patient compliance, and (3) GPs' own risk management. There were substantial differences in the attitudes concerning all three themes. Conclusions. The substantial differences in the GPs' personal and professional risk perceptions may be a key to understanding why GPs do not always follow cardiovascular guidelines. The impact on daily clinical practice, personal consultation style, and patient behaviour with regard to prevention is worth studying further. PMID:26495143

High-resolution analysis of locomotor activity rhythms in disconnected, a visual-system mutant of Drosophila melanogaster.

PubMed

Dowse, H B; Dushay, M S; Hall, J C; Ringo, J M

1989-07-01

Free-running locomotor activity and eclosion rhythms of Drosophila melanogaster, mutant at the disconnected (disco) locus, are substantially different from the wild-type phenotype. Initial periodogram analysis revealed little or no rhythmicity (Dushay et al., 1989). We have reanalyzed the locomotor activity data using high-resolution signal analysis (maximum-entropy spectral analysis, or MESA). These analyses, corroborated by autocorrelograms, uncovered significant residual circadian rhythmicity and strong ultradian rhythms in most of the animals tested. In this regard the disco mutants are much like flies expressing mutant alleles of the period gene, as well as wild-type flies reared throughout life in constant darkness. We hypothesize that light normally triggers the coupling of multiple ultradian oscillators into a functional circadian clock and that this process is disrupted in disco flies as a result of the neural lesion.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tsai, C. -Y.; Derbenev, Ya. S.; Douglas, D.

For a high-brightness electron beam with low energy and high bunch charge traversing a recirculation beamline, coherent synchrotron radiation and space charge effect may result in the microbunching instability (MBI). Both tracking simulation and Vlasov analysis for an early design of Circulator Cooler Ring for the Jefferson Lab Electron Ion Collider reveal significant MBI. It is envisioned these could be substantially suppressed by using a magnetized beam. In this work, we extend the existing Vlasov analysis, originally developed for a non-magnetized beam, to the description of transport of a magnetized beam including relevant collective effects. As a result, the newmore » formulation will be further employed to confirm prediction of microbunching suppression for a magnetized beam transport in a recirculating machine design.« less

The use of available potential energy to evaluate the impact of satellite data on numerical model analysis during FGGE

NASA Technical Reports Server (NTRS)

Horn, Lyle H.; Koehler, Thomas L.; Whittaker, Linda M.

1988-01-01

To evaluate the effect of the FGGE satellite observing system, the following two data sets were compared by examining the available potential energy (APE) and extratropical cyclone activity within the entire global domain during the first Special Observing Period: (1) the complete FGGE IIIb set, which incorporates satellite soundings, and (2) a NOSAT set which incorporates only conventional data. The time series of the daily total APEs indicate that NOSAT values are larger than the FGGE values, although in the Northern Hemisphere the differences are negligible. Analyses of cyclone scale features revealed only minor differences between the Northern Hemisphere FGGE and NOSAT analyses. On the other hand, substantial differences were revealed in the two Southern Hemisphere analyses, where the satellite soundings apparently add detail to the FGGE set.

Communication-related affective, behavioral, and cognitive reactions in speakers with spasmodic dysphonia.

PubMed

Watts, Christopher R; Vanryckeghem, Martine

2017-12-01

To investigate the self-perceived affective, behavioral, and cognitive reactions associated with communication of speakers with spasmodic dysphonia as a function of employment status. Prospective cross-sectional investigation. 148 Participants with spasmodic dysphonia (SD) completed an adapted version of the Behavior Assessment Battery (BAB-Voice), a multidimensional assessment of self-perceived reactions to communication. The BAB-Voice consisted of four subtests: the Speech Situation Checklist for A) Emotional Reaction (SSC-ER) and B) Speech Disruption (SSC-SD), C) the Behavior Checklist (BCL), and D) the Communication Attitude Test for Adults (BigCAT). Participants were assigned to groups based on employment status (working versus retired). Descriptive comparison of the BAB-Voice in speakers with SD to previously published non-dysphonic speaker data revealed substantially higher scores associated with SD across all four subtests. Multivariate Analysis of Variance (MANOVA) revealed no significantly different BAB-Voice subtest scores as a function of SD group status (working vs. retired). BAB-Voice scores revealed that speakers with SD experienced substantial impact of their voice disorder on communication attitude, coping behaviors, and affective reactions in speaking situations as reflected in their high BAB scores. These impacts do not appear to be influenced by work status, as speakers with SD who were employed or retired experienced similar levels of affective and behavioral reactions in various speaking situations and cognitive responses. These findings are consistent with previously published pilot data. The specificity of items assessed by means of the BAB-Voice may inform the clinician of valid patient-centered treatment goals which target the impairment extended beyond the physiological dimension. 2b.

CscoreTool: fast Hi-C compartment analysis at high resolution.

PubMed

Zheng, Xiaobin; Zheng, Yixian

2018-05-01

The genome-wide chromosome conformation capture (Hi-C) has revealed that the eukaryotic genome can be partitioned into A and B compartments that have distinctive chromatin and transcription features. Current Principle Component Analyses (PCA)-based method for the A/B compartment prediction based on Hi-C data requires substantial CPU time and memory. We report the development of a method, CscoreTool, which enables fast and memory-efficient determination of A/B compartments at high resolution even in datasets with low sequencing depth. https://github.com/scoutzxb/CscoreTool. xzheng@carnegiescience.edu. Supplementary data are available at Bioinformatics online.

Acquisition and analysis of coastal ground-truth data for correlation with ERTS-1 imagery. [surface radiance data for Santa Monica Bay and Santa Barbara Channel

NASA Technical Reports Server (NTRS)

Anikouchine, W. A. (Principal Investigator)

1973-01-01

The author has identified the following significant results. Radiance profiles drawn along cruise tracks have been examined for use in correlating digital radiance levels with ground truth data. Preliminary examination results are encouraging. Adding weighted levels from the 4 MSS bands appears to enhance specular surface reflections while rendering sensor noise white. Comparing each band signature to the added specular signature ought to enhance non-specular effects caused by ocean turbidity. Preliminary examination of radiance profiles and ground truth turbidity measurements revealed substantial correlation.

Exercise training reinstates cortico-cortical sensorimotor functional connectivity following striatal lesioning: Development and application of a subregional-level analytic toolbox for perfusion autoradiographs of the rat brain

NASA Astrophysics Data System (ADS)

Peng, Yu-Hao; Heintz, Ryan; Wang, Zhuo; Guo, Yumei; Myers, Kalisa; Scremin, Oscar; Maarek, Jean-Michel; Holschneider, Daniel

2014-12-01

Current rodent connectome projects are revealing brain structural connectivity with unprecedented resolution and completeness. How subregional structural connectivity relates to subregional functional interactions is an emerging research topic. We describe a method for standardized, mesoscopic-level data sampling from autoradiographic coronal sections of the rat brain, and for correlation-based analysis and intuitive display of cortico-cortical functional connectivity (FC) on a flattened cortical map. A graphic user interface “Cx-2D” allows for the display of significant correlations of individual regions-of-interest, as well as graph theoretical metrics across the cortex. Cx-2D was tested on an autoradiographic data set of cerebral blood flow (CBF) of rats that had undergone bilateral striatal lesions, followed by 4 weeks of aerobic exercise training or no exercise. Effects of lesioning and exercise on cortico-cortical FC were examined during a locomotor challenge in this rat model of Parkinsonism. Subregional FC analysis revealed a rich functional reorganization of the brain in response to lesioning and exercise that was not apparent in a standard analysis focused on CBF of isolated brain regions. Lesioned rats showed diminished degree centrality of lateral primary motor cortex, as well as neighboring somatosensory cortex--changes that were substantially reversed in lesioned rats following exercise training. Seed analysis revealed that exercise increased positive correlations in motor and somatosensory cortex, with little effect in non-sensorimotor regions such as visual, auditory, and piriform cortex. The current analysis revealed that exercise partially reinstated sensorimotor FC lost following dopaminergic deafferentation. Cx-2D allows for standardized data sampling from images of brain slices, as well as analysis and display of cortico-cortical FC in the rat cerebral cortex with potential applications in a variety of autoradiographic and histologic studies.

Global geometric morphometric analyses of the human pelvis reveal substantial neutral population history effects, even across sexes.

PubMed

Betti, Lia; von Cramon-Taubadel, Noreen; Manica, Andrea; Lycett, Stephen J

2013-01-01

Recent applications of population genetic models to human craniodental traits have revealed a strong neutral component to patterns of global variation. However, little work has been undertaken to determine whether neutral processes might also be influencing the postcranium, perhaps due to substantial evidence for selection and plastic environmental responses in these regions. Recent work has provided evidence for neutral effects in the pelvis, but has been limited in regard to shape data (small numbers of linear measurements) and restricted only to males. Here, we use geometric morphometric methods to examine population variation in the human os coxae (pelvic bone) in both males and females. Neutrality is examined via apportionment of variance patterns and fit to an Out-of-Africa serial founder effect model, which is known to structure neutral genetic patterns. Moreover, we compare males and females directly, and the true versus false pelvis, in order to examine potential obstetrical effects. Our results indicate evidence for substantial neutral population history effects on pelvic shape variation. They also reveal evidence for the effect of obstetrical constraints, but these affect males and females to equivalent extents. Our results do not deny an important role for selection in regard to specific aspects of human pelvic variation, especially in terms of features associated with body size and proportions. However, our analyses demonstrate that at a global level, the shape of the os coxae reveals substantial evidence for neutral variation. Our analyses thus indicate that population variation in the human pelvis might be used to address important questions concerning population history, just as the human cranium has done.

Global Geometric Morphometric Analyses of the Human Pelvis Reveal Substantial Neutral Population History Effects, Even across Sexes

PubMed Central

Betti, Lia; von Cramon-Taubadel, Noreen; Manica, Andrea; Lycett, Stephen J.

2013-01-01

Recent applications of population genetic models to human craniodental traits have revealed a strong neutral component to patterns of global variation. However, little work has been undertaken to determine whether neutral processes might also be influencing the postcranium, perhaps due to substantial evidence for selection and plastic environmental responses in these regions. Recent work has provided evidence for neutral effects in the pelvis, but has been limited in regard to shape data (small numbers of linear measurements) and restricted only to males. Here, we use geometric morphometric methods to examine population variation in the human os coxae (pelvic bone) in both males and females. Neutrality is examined via apportionment of variance patterns and fit to an Out-of-Africa serial founder effect model, which is known to structure neutral genetic patterns. Moreover, we compare males and females directly, and the true versus false pelvis, in order to examine potential obstetrical effects. Our results indicate evidence for substantial neutral population history effects on pelvic shape variation. They also reveal evidence for the effect of obstetrical constraints, but these affect males and females to equivalent extents. Our results do not deny an important role for selection in regard to specific aspects of human pelvic variation, especially in terms of features associated with body size and proportions. However, our analyses demonstrate that at a global level, the shape of the os coxae reveals substantial evidence for neutral variation. Our analyses thus indicate that population variation in the human pelvis might be used to address important questions concerning population history, just as the human cranium has done. PMID:23409086

Enhanced forensic discrimination of pollutants by position-specific isotope analysis using isotope ratio monitoring by (13)C nuclear magnetic resonance spectrometry.

PubMed

Julien, Maxime; Nun, Pierrick; Höhener, Patrick; Parinet, Julien; Robins, Richard J; Remaud, Gérald S

2016-01-15

In forensic environmental investigations the main issue concerns the inference of the original source of the pollutant for determining the liable party. Isotope measurements in geochemistry, combined with complimentary techniques for contaminant identification, have contributed significantly to source determination at polluted sites. In this work we have determined the intramolecular (13)C profiles of several molecules well-known as pollutants. By giving additional analytical parameters, position-specific isotope analysis performed by isotope ratio monitoring by (13)C nuclear magnetic resonance (irm-(13)C NMR) spectrometry gives new information to help in answering the major question: what is the origin of the detected contaminant? We have shown that isotope profiling of the core of a molecule reveals both the raw materials and the process used in its manufacture. It also can reveal processes occurring between the contamination site 'source' and the sampling site. Thus, irm-(13)C NMR is shown to be a very good complement to compound-specific isotope analysis currently performed by mass spectrometry for assessing polluted sites involving substantial spills of pollutant. Copyright © 2015 Elsevier B.V. All rights reserved.

Acute Hepatopancreatic Necrosis Disease (AHPND) related microRNAs in Litopenaeus vannamei infected with AHPND-causing strain of Vibrio parahemolyticus.

PubMed

Zheng, Zhihong; Aweya, Jude Juventus; Wang, Fan; Yao, Defu; Lun, Jingsheng; Li, Shengkang; Ma, Hongyu; Zhang, Yueling

2018-05-08

Acute hepatopancreatic necrosis disease (AHPND) has emerged as a major debilitating disease that causes massive shrimp death resulting in substantial economic losses in shrimp aquaculture. Given that several diseases and infections have been associated with microRNAs (miRNAs), we conducted a comparative transcriptomic analysis using the AHPND (VA) and non-AHPND (VN) strains of Vibrio parahemolyticus to identify miRNAs potentially involved in AHPND pathogenesis in Litopenaeus vannamei. A total of 83 miRNAs (47 upregulated and 36 downregulated) were significantly differentially expressed between the VA and VN challenged groups, while 222 target genes of these miRNAs were predicted. Functional enrichment analysis revealed that the miRNAs target genes were involved in multiple biological processes including metabolic pathways, amoebiasis, Vibrio cholerae infection etc. Finally, interaction network and qPCR (Real-time Quantitative PCR) analysis of 12 potential key AHPND-related miRNAs and their predicted target genes, revealed their possible involvement in modulating several immune-related processes in the pathogenesis of AHPND. We have shown using comparative transcriptomic analysis, miRNAs and their target genes that are responsive to AHPND V. parahemolyticus infection in shrimp, therefore suggesting their possible role in defense response to AHPND V. parahemolyticus infection.

Integromics network meta-analysis on cardiac aging offers robust multi-layer modular signatures and reveals micronome synergism.

PubMed

Dimitrakopoulou, Konstantina; Vrahatis, Aristidis G; Bezerianos, Anastasios

2015-03-04

The avalanche of integromics and panomics approaches shifted the deciphering of aging mechanisms from single molecular entities to communities of them. In this orientation, we explore the cardiac aging mechanisms - risk factor for multiple cardiovascular diseases - by capturing the micronome synergism and detecting longevity signatures in the form of communities (modules). For this, we developed a meta-analysis scheme that integrates transcriptome expression data from multiple cardiac-specific independent studies in mouse and human along with proteome and micronome interaction data in the form of multiple independent weighted networks. Modularization of each weighted network produced modules, which in turn were further analyzed so as to define consensus modules across datasets that change substantially during lifespan. Also, we established a metric that determines - from the modular perspective - the synergism of microRNA-microRNA interactions as defined by significantly functionally associated targets. The meta-analysis provided 40 consensus integromics modules across mouse datasets and revealed microRNA relations with substantial collective action during aging. Three modules were reproducible, based on homology, when mapped against human-derived modules. The respective homologs mainly represent NADH dehydrogenases, ATP synthases, cytochrome oxidases, Ras GTPases and ribosomal proteins. Among various observations, we corroborate to the involvement of miR-34a (included in consensus modules) as proposed recently; yet we report that has no synergistic effect. Moving forward, we determined its age-related neighborhood in which HCN3, a known heart pacemaker channel, was included. Also, miR-125a-5p/-351, miR-200c/-429, miR-106b/-17, miR-363/-92b, miR-181b/-181d, miR-19a/-19b, let-7d/-7f, miR-18a/-18b, miR-128/-27b and miR-106a/-291a-3p pairs exhibited significant synergy and their association to aging and/or cardiovascular diseases is supported in many cases by a disease database and previous studies. On the contrary, we suggest that miR-22 has not substantial impact on heart longevity as proposed recently. We revised several proteins and microRNAs recently implicated in cardiac aging and proposed for the first time modules as signatures. The integromics meta-analysis approach can serve as an efficient subvening signature tool for more-oriented better-designed experiments. It can also promote the combinational multi-target microRNA therapy of age-related cardiovascular diseases along the continuum from prevention to detection, diagnosis, treatment and outcome.

Crossing the front: contrasting storm-forced dispersal dynamics revealed by biological, geological and genetic analysis of beach-cast kelp.

PubMed

Waters, Jonathan M; King, Tania M; Fraser, Ceridwen I; Craw, Dave

2018-03-01

The subtropical front (STF) generally represents a substantial oceanographic barrier to dispersal between cold-sub-Antarctic and warm-temperate water masses. Recent studies have suggested that storm events can drastically influence marine dispersal and patterns. Here we analyse biological and geological dispersal driven by two major, contrasting storm events in southern New Zealand, 2017. We integrate biological and physical data to show that a severe southerly system in July 2017 disrupted this barrier by promoting movement of substantial numbers of southern sub-Antarctic Durvillaea kelp rafts across the STF, to make landfall in mainland NZ. By contrast, a less intense easterly storm (Cyclone Cook, April 2017) resulted in more moderate dispersal distances, with minimal dispersal between the sub-Antarctic and mainland New Zealand. These quantitative analyses of approximately 200 freshly beach-cast kelp specimens indicate that storm intensity and wind direction can strongly influence marine dispersal and landfall outcomes. © 2018 The Author(s).

Multifractal detrended fluctuation analysis to characterize phase couplings in seahorse (Hippocampus kuda) feeding clicks.

PubMed

Haris, K; Chakraborty, Bishwajit; Menezes, A; Sreepada, R A; Fernandes, W A

2014-10-01

Nonlinear phenomena in animal vocalizations fundamentally includes known features, namely, frequency jump, subharmonics, biphonation, and deterministic chaos. In the present study, the multifractal detrended fluctuation analysis (MFDFA) has been employed to characterize the phase couplings revealed in the feeding clicks of Hippocampus kuda yellow seahorse. The fluctuation function Fq(s), generalized Hurst exponent h(q), multifractal scaling exponent τ(q), and the multifractal spectrum f(α) calculated in the procedure followed were analyzed to comprehend the underlying nonlinearities in the seahorse clicks. The analyses carried out reveal long-range power-law correlation properties in the data, substantiating the multifractal behavior. The resulting h(q) spectrum exhibits a distinct characteristic pattern in relation to the seahorse sex and size, and reveals a spectral blind spot in the data that was not possible to detect by conventional spectral analyses. The corresponding multifractal spectrum related width parameter Δh(q) is well clustered, defining the individual seahorse clicks. The highest degree of multifractality is evident in the 18 cm male seahorse, signifying greater heterogeneity. A further comparison between the seahorse body size and weight (wet) with respect to the width parameter Δh(q) and the second-order Hurst exponent h(q=2) underscores the versatility of MFDFA as a robust statistical tool to analyze bioacoustic observations.

Full genome sequence of Rocio virus reveal substantial variations from the prototype Rocio virus SPH 34675 sequence.

PubMed

Setoh, Yin Xiang; Amarilla, Alberto A; Peng, Nias Y; Slonchak, Andrii; Periasamy, Parthiban; Figueiredo, Luiz T M; Aquino, Victor H; Khromykh, Alexander A

2018-01-01

Rocio virus (ROCV) is an arbovirus belonging to the genus Flavivirus, family Flaviviridae. We present an updated sequence of ROCV strain SPH 34675 (GenBank: AY632542.4), the only available full genome sequence prior to this study. Using next-generation sequencing of the entire genome, we reveal substantial sequence variation from the prototype sequence, with 30 nucleotide differences amounting to 14 amino acid changes, as well as significant changes to predicted 3'UTR RNA structures. Our results present an updated and corrected sequence of a potential emerging human-virulent flavivirus uniquely indigenous to Brazil (GenBank: MF461639).

Label-Free Raman Imaging to Monitor Breast Tumor Signatures

NASA Astrophysics Data System (ADS)

Ciubuc, John

Methods built on Raman spectroscopy have shown major potential in describing and discriminating between malignant and benign specimens. Accurate, real-time medical diagnosis benefits in substantial improvements through this vibrational optical method. Not only is acquisition of data possible in milliseconds and analysis in minutes, Raman allows concurrent detection and monitoring of all biological components. Besides validating a significant Raman signature distinction between non-tumorigenic (MCF-10A) and tumorigenic (MCF-7) breast epithelial cells, this study reveals a label-free method to assess overexpression of epidermal growth factor receptors (EGFR) in tumor cells. EGFR overexpression sires Raman features associated with phosphorylated threonine and serine, and modifications of DNA/RNA characteristics. Investigations by gel electrophoresis reveal EGF induction of phosphorylated Akt, agreeing with the Raman results. The analysis presented is a vital step toward Raman-based evaluation of EGF receptors in breast cancer cells. With the goal of clinically applying Raman-guided methods for diagnosis of breast tumors, the current results lay the basis for proving label-free optical alternatives in making prognosis of the disease.

Phenotypic factor analysis of psychopathology reveals a new body-related transdiagnostic factor.

PubMed

Pezzoli, Patrizia; Antfolk, Jan; Santtila, Pekka

2017-01-01

Comorbidity challenges the notion of mental disorders as discrete categories. An increasing body of literature shows that symptoms cut across traditional diagnostic boundaries and interact in shaping the latent structure of psychopathology. Using exploratory and confirmatory factor analysis, we reveal the latent sources of covariation among nine measures of psychopathological functioning in a population-based sample of 13024 Finnish twins and their siblings. By implementing unidimensional, multidimensional, second-order, and bifactor models, we illustrate the relationships between observed variables, specific, and general latent factors. We also provide the first investigation to date of measurement invariance of the bifactor model of psychopathology across gender and age groups. Our main result is the identification of a distinct "Body" factor, alongside the previously identified Internalizing and Externalizing factors. We also report relevant cross-disorder associations, especially between body-related psychopathology and trait anger, as well as substantial sex and age differences in observed and latent means. The findings expand the meta-structure of psychopathology, with implications for empirical and clinical practice, and demonstrate shared mechanisms underlying attitudes towards nutrition, self-image, sexuality and anger, with gender- and age-specific features.

No rationale for 1 variable per 10 events criterion for binary logistic regression analysis.

PubMed

van Smeden, Maarten; de Groot, Joris A H; Moons, Karel G M; Collins, Gary S; Altman, Douglas G; Eijkemans, Marinus J C; Reitsma, Johannes B

2016-11-24

Ten events per variable (EPV) is a widely advocated minimal criterion for sample size considerations in logistic regression analysis. Of three previous simulation studies that examined this minimal EPV criterion only one supports the use of a minimum of 10 EPV. In this paper, we examine the reasons for substantial differences between these extensive simulation studies. The current study uses Monte Carlo simulations to evaluate small sample bias, coverage of confidence intervals and mean square error of logit coefficients. Logistic regression models fitted by maximum likelihood and a modified estimation procedure, known as Firth's correction, are compared. The results show that besides EPV, the problems associated with low EPV depend on other factors such as the total sample size. It is also demonstrated that simulation results can be dominated by even a few simulated data sets for which the prediction of the outcome by the covariates is perfect ('separation'). We reveal that different approaches for identifying and handling separation leads to substantially different simulation results. We further show that Firth's correction can be used to improve the accuracy of regression coefficients and alleviate the problems associated with separation. The current evidence supporting EPV rules for binary logistic regression is weak. Given our findings, there is an urgent need for new research to provide guidance for supporting sample size considerations for binary logistic regression analysis.

Uncoupling the Effects of Abscisic Acid on Plant Growth and Water Relations. Analysis of sto1/nced3, an Abscisic Acid-Deficient but Salt Stress-Tolerant Mutant in Arabidopsis1

PubMed Central

Ruggiero, Bruno; Koiwa, Hisashi; Manabe, Yuzuki; Quist, Tanya M.; Inan, Gunsu; Saccardo, Franco; Joly, Robert J.; Hasegawa, Paul M.; Bressan, Ray A.; Maggio, Albino

2004-01-01

We have identified a T-DNA insertion mutation of Arabidopsis (ecotype C24), named sto1 (salt tolerant), that results in enhanced germination on both ionic (NaCl) and nonionic (sorbitol) hyperosmotic media. sto1 plants were more tolerant in vitro than wild type to Na+ and K+ both for germination and subsequent growth but were hypersensitive to Li+. Postgermination growth of the sto1 plants on sorbitol was not improved. Analysis of the amino acid sequence revealed that STO1 encodes a 9-cis-epoxicarotenoid dioxygenase (similar to 9-cis-epoxicarotenoid dioxygenase GB:AAF26356 [Phaseolus vulgaris] and to NCED3 GB:AB020817 [Arabidopsis]), a key enzyme in the abscisic acid (ABA) biosynthetic pathway. STO1 transcript abundance was substantially reduced in mutant plants. Mutant sto1 plants were unable to accumulate ABA following a hyperosmotic stress, although their basal ABA level was only moderately altered. Either complementation of the sto1 with the native gene from the wild-type genome or supplementation of ABA to the growth medium restored the wild-type phenotype. Improved growth of sto1 mutant plants on NaCl, but not sorbitol, medium was associated with a reduction in both NaCl-induced expression of the ICK1 gene and ethylene accumulation. Osmotic adjustment of sto1 plants was substantially reduced compared to wild-type plants under conditions where sto1 plants grew faster. The sto1 mutation has revealed that reduced ABA can lead to more rapid growth during hyperionic stress by a signal pathway that apparently is at least partially independent of signals that mediate nonionic osmotic responses. PMID:15466233

Seeding and Establishment of Legionella pneumophila in Hospitals: Implications for Genomic Investigations of Nosocomial Legionnaires' Disease.

PubMed

David, Sophia; Afshar, Baharak; Mentasti, Massimo; Ginevra, Christophe; Podglajen, Isabelle; Harris, Simon R; Chalker, Victoria J; Jarraud, Sophie; Harrison, Timothy G; Parkhill, Julian

2017-05-01

Legionnaires' disease is an important cause of hospital-acquired pneumonia and is caused by infection with the bacterium Legionella. Because current typing methods often fail to resolve the infection source in possible nosocomial cases, we aimed to determine whether whole-genome sequencing (WGS) could be used to support or refute suspected links between cases and hospitals. We focused on cases involving a major nosocomial-associated strain, L. pneumophila sequence type (ST) 1. WGS data from 229 L. pneumophila ST1 isolates were analyzed, including 99 isolates from the water systems of 17 hospitals and 42 clinical isolates from patients with confirmed or suspected hospital-acquired infections, as well as isolates obtained from or associated with community-acquired sources of Legionnaires' disease. Phylogenetic analysis demonstrated that all hospitals from which multiple isolates were obtained have been colonized by 1 or more distinct ST1 populations. However, deep sampling of 1 hospital also revealed the existence of substantial diversity and ward-specific microevolution within the population. Across all hospitals, suspected links with cases were supported with WGS, although the degree of support was dependent on the depth of environmental sampling and available contextual information. Finally, phylogeographic analysis revealed that hospitals have been seeded with L. pneumophila via both local and international spread of ST1. WGS can be used to support or refute suspected links between hospitals and Legionnaires' disease cases. However, deep hospital sampling is frequently required due to the potential coexistence of multiple populations, existence of substantial diversity, and similarity of hospital isolates to local populations. © The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America.

SPICE Work Package 3: Modelling the Effects of Stratospheric Aerosol Geoengineering

NASA Astrophysics Data System (ADS)

Driscoll, Simon

2015-04-01

This talk presents the results of the SPICE Work Package 3. There is an obvious need for methods to verify the accuracy of geoengineering given no observations of a geoengineering programme. Accordingly, model ability in reproducing the observed dynamical response to volcanic eruptions is discussed using analysis of CMIP5 data and different configurations of the HadGEM2 model. With the HadGEM2-L60 model shown to be substantially better in reproducing the observed dynamical response to volcanic eruptions, simulations of GeoMIP's G4 scenario are performed. Simulated impacts of geoengineering are described, and asymmetries between the immediate onset and immediate cessation ('termination') of geoengineering are analysed. Whilst a rapid large increase in stratospheric sulphate aerosols (such as from volcanic eruptions) can cause substantial damage, most volcanic eruptions in general are not catastrophic. One may therefore suspect that an 'equal but opposite' change in radiative forcing from termination may therefore not be catastrophic, if the climatic response is simulated to be symmetric. HadGEM2 simulations reveal a substantially more rapid change in variables such as near-surface temperature and precipitation following termination than the onset, indicating that termination may be substantially more damaging and even catastrophic. Some suggestions for hemispherically asymmetric geoengineering have been proposed as a way to reduce Northern Hemisphere sea ice, for example, with lesser impacts on the rest of the climate. However, HadGEM2 simulations are performed and observations analysed following volcanic eruptions. Both indicate substantial averse consequences from hemispherically asymmetric loading of stratospheric loading on precipitation in the Sahelian region - a vulnerable region where drought has caused hundreds of thousands of deaths and created millions of refugees in the past.

Hybrid approach combining chemometrics and likelihood ratio framework for reporting the evidential value of spectra.

PubMed

Martyna, Agnieszka; Zadora, Grzegorz; Neocleous, Tereza; Michalska, Aleksandra; Dean, Nema

2016-08-10

Many chemometric tools are invaluable and have proven effective in data mining and substantial dimensionality reduction of highly multivariate data. This becomes vital for interpreting various physicochemical data due to rapid development of advanced analytical techniques, delivering much information in a single measurement run. This concerns especially spectra, which are frequently used as the subject of comparative analysis in e.g. forensic sciences. In the presented study the microtraces collected from the scenarios of hit-and-run accidents were analysed. Plastic containers and automotive plastics (e.g. bumpers, headlamp lenses) were subjected to Fourier transform infrared spectrometry and car paints were analysed using Raman spectroscopy. In the forensic context analytical results must be interpreted and reported according to the standards of the interpretation schemes acknowledged in forensic sciences using the likelihood ratio approach. However, for proper construction of LR models for highly multivariate data, such as spectra, chemometric tools must be employed for substantial data compression. Conversion from classical feature representation to distance representation was proposed for revealing hidden data peculiarities and linear discriminant analysis was further applied for minimising the within-sample variability while maximising the between-sample variability. Both techniques enabled substantial reduction of data dimensionality. Univariate and multivariate likelihood ratio models were proposed for such data. It was shown that the combination of chemometric tools and the likelihood ratio approach is capable of solving the comparison problem of highly multivariate and correlated data after proper extraction of the most relevant features and variance information hidden in the data structure. Copyright © 2016 Elsevier B.V. All rights reserved.

Dissecting the phyloepidemiology of Trypanosoma cruzi I (TcI) in Brazil by the use of high resolution genetic markers.

PubMed

Roman, Fabiola; das Chagas Xavier, Samanta; Messenger, Louisa A; Pavan, Márcio G; Miles, Michael A; Jansen, Ana María; Yeo, Matthew

2018-05-01

Trypanosoma cruzi, the causal agent of Chagas disease, is monophyletic but genetically heterogeneous. It is currently represented by six genetic lineages (Discrete Typing Units, DTUs) designated TcI-TcVI. TcI is the most geographically widespread and genetically heterogeneous lineage, this as is evidenced by a wide range of genetic markers applied to isolates spanning a vast geographic range in Latin America. In total, 78 TcI isolated from hosts and vectors distributed in 5 different biomes of Brazil, were analyzed using 6 nuclear housekeeping genes, 25 microsatellite loci and one mitochondrial marker. Nuclear markers reveal substantial genetic diversity, significant gene flow between biomes, incongruence in phylogenies, and haplotypic analysis indicative of intra-DTU genetic exchange. Phylogenetic reconstructions based on mitochondrial and nuclear loci were incongruent, and consistent with introgression. Structure analysis of microsatellite data reveals that, amongst biomes, the Amazon is the most genetically diverse and experiences the lowest level of gene flow. Investigation of population structure based on the host species/genus, indicated that Didelphis marsupialis might play a role as the main disperser of TcI. The present work considers a large TcI sample from different hosts and vectors spanning multiple ecologically diverse biomes in Brazil. Importantly, we combine fast and slow evolving markers to contribute to the epizootiological understanding of TcI in five distinct Brazilian biomes. This constitutes the first instance in which MLST analysis was combined with the use of MLMT and maxicircle markers to evaluate the genetic diversity of TcI isolates in Brazil. Our results demonstrate the existence of substantial genetic diversity and the occurrence of introgression events. We provide evidence of genetic exchange in TcI isolates from Brazil and of the relative isolation of TcI in the Amazon biome. We observe the absence of strict associations with TcI genotypes to geographic areas and/or host species.

Dissecting the phyloepidemiology of Trypanosoma cruzi I (TcI) in Brazil by the use of high resolution genetic markers

PubMed Central

das Chagas Xavier, Samanta; Messenger, Louisa A.; Pavan, Márcio G.; Miles, Michael A.; Jansen, Ana María; Yeo, Matthew

2018-01-01

Background Trypanosoma cruzi, the causal agent of Chagas disease, is monophyletic but genetically heterogeneous. It is currently represented by six genetic lineages (Discrete Typing Units, DTUs) designated TcI-TcVI. TcI is the most geographically widespread and genetically heterogeneous lineage, this as is evidenced by a wide range of genetic markers applied to isolates spanning a vast geographic range in Latin America. Methodology/Principal findings In total, 78 TcI isolated from hosts and vectors distributed in 5 different biomes of Brazil, were analyzed using 6 nuclear housekeeping genes, 25 microsatellite loci and one mitochondrial marker. Nuclear markers reveal substantial genetic diversity, significant gene flow between biomes, incongruence in phylogenies, and haplotypic analysis indicative of intra-DTU genetic exchange. Phylogenetic reconstructions based on mitochondrial and nuclear loci were incongruent, and consistent with introgression. Structure analysis of microsatellite data reveals that, amongst biomes, the Amazon is the most genetically diverse and experiences the lowest level of gene flow. Investigation of population structure based on the host species/genus, indicated that Didelphis marsupialis might play a role as the main disperser of TcI. Conclusions/Significance The present work considers a large TcI sample from different hosts and vectors spanning multiple ecologically diverse biomes in Brazil. Importantly, we combine fast and slow evolving markers to contribute to the epizootiological understanding of TcI in five distinct Brazilian biomes. This constitutes the first instance in which MLST analysis was combined with the use of MLMT and maxicircle markers to evaluate the genetic diversity of TcI isolates in Brazil. Our results demonstrate the existence of substantial genetic diversity and the occurrence of introgression events. We provide evidence of genetic exchange in TcI isolates from Brazil and of the relative isolation of TcI in the Amazon biome. We observe the absence of strict associations with TcI genotypes to geographic areas and/or host species. PMID:29782493

Engineering Adipose-like Tissue in vitro and in vivo Utilizing Human Bone Marrow and Adipose-derived Mesenchymal Stem Cells with Silk Fibroin 3D Scaffolds

PubMed Central

Mauney, Joshua R; Nguyen, Trang; Gillen, Kelly; Kirker-Head, Carl; Gimble, Jeffrey M.; Kaplan, David L.

2009-01-01

Biomaterials derived from silk fibrion prepared by aqueous (AB) and organic (HFIP) solvent based processes, along with collagen (COL) and poly-lactic acid (PLA) based scaffolds were studied in vitro and in vivo for their utility in adipose tissue engineering strategies. For in vitro studies, human bone marrow and adipose-derived mesenchymal stem cells (hMSCs and hASCs) were seeded on the various biomaterials and cultured for 21 days in the presence of adipogenic stimulants (AD) or maintained as noninduced controls. Alamar Blue analysis revealed each biomaterial supported initial attachment of hMSCs and hASCs to similar levels for all matrices except COL in which higher levels were observed. hASCs and hMSCs cultured on all biomaterials in the presence of AD showed significant upregulation of adipogenic mRNA transcript levels (LPL, GLUT4, FABP4, PPARγ, adipsin, ACS) to similar extents when compared to noninduced controls. Similarly Oil-Red O analysis of hASC or hMSC-seeded scaffolds displayed substantial amounts of lipid accumulating adipocytes following cultivation with AD. The data revealed AB and HFIP scaffolds supported similar extents of lipid accumulating cells while PLA and COL scaffolds qualitatively displayed lower and higher extents by comparison, respectively. Following a 4 week implantation period in a rat muscle pouch defect model, both AB and HFIP scaffolds supported in vivo adipogenesis either alone or seeded with hASCs or hMSCs as assessed by Oil-Red O analysis, however the presence of exogenous cell sources substantially increased the extent and frequency of adipogenesis observed. In contrast, COL and PLA scaffolds underwent rapid scaffold degradation and were irretrievable following the implantation period. The results suggest that macroporous 3D AB and HFIP silk fibroin scaffolds offer an important platform for cell-based adipose tissue engineering applications, and in particular, provide longer-term structural integrity to promote the maintenance of soft tissue in vivo. PMID:17765303

From attitude formation to behavioral response in organ donation: using marketing to increase consent rates.

PubMed

Aldridge, Alicia; Guy, Bonnie; Roggenkamp, Susan

2003-01-01

This article presents a theoretical analysis of attitude formation and the relationship to stated behavioral intentions as it relates to the decision to donate organs. This analysis reveals the presence of three distinct paths to behavior of potential donors, groups differing in their involvement with organ donation. Promotional objectives and campaign strategies designed to influence attitudes and behaviors should differ according to the behavioral path in operation and the involvement of the audience. Mass media campaigns are likely to reach high involvement groups only. Therefore, personal selling, underutilized in previous donation campaigns, should be brought into the donation strategy to appeal to low involvement groups. By recognizing differences in audience involvement and implementing different strategies, overall donation rates could substantially increase.

From damage to discovery via virtual unwrapping: Reading the scroll from En-Gedi

PubMed Central

Seales, William Brent; Parker, Clifford Seth; Segal, Michael; Tov, Emanuel; Shor, Pnina; Porath, Yosef

2016-01-01

Computer imaging techniques are commonly used to preserve and share readable manuscripts, but capturing writing locked away in ancient, deteriorated documents poses an entirely different challenge. This software pipeline—referred to as “virtual unwrapping”—allows textual artifacts to be read completely and noninvasively. The systematic digital analysis of the extremely fragile En-Gedi scroll (the oldest Pentateuchal scroll in Hebrew outside of the Dead Sea Scrolls) reveals the writing hidden on its untouchable, disintegrating sheets. Our approach for recovering substantial ink-based text from a damaged object results in readable columns at such high quality that serious critical textual analysis can occur. Hence, this work creates a new pathway for subsequent textual discoveries buried within the confines of damaged materials. PMID:27679821

Cultural prototypes and dimensions of honor.

PubMed

Cross, Susan E; Uskul, Ayse K; Gerçek-Swing, Berna; Sunbay, Zeynep; Alözkan, Cansu; Günsoy, Ceren; Ataca, Bilge; Karakitapoglu-Aygün, Zahide

2014-02-01

Research evidence and theoretical accounts of honor point to differing definitions of the construct in differing cultural contexts. The current studies address the question "What is honor?" using a prototype approach in Turkey and the Northern United States. Studies 1a/1b revealed substantial differences in the specific features generated by members of the two groups, but Studies 2 and 3 revealed cultural similarities in the underlying dimensions of self-respect, moral behavior, and social status/respect. Ratings of the centrality and personal importance of these factors were similar across the two groups, but their association with other relevant constructs differed. The tripartite nature of honor uncovered in these studies helps observers and researchers alike understand how diverse responses to situations can be attributed to honor. Inclusion of a prototype analysis into the literature on honor cultures can provide enhanced coverage of the concept that may lead to testable hypotheses and new theoretical developments.

Comprehensive Lipidome-Wide Profiling Reveals Dynamic Changes of Tea Lipids during Manufacturing Process of Black Tea.

PubMed

Li, Jia; Hua, Jinjie; Zhou, Qinghua; Dong, Chunwang; Wang, Jinjin; Deng, Yuliang; Yuan, Haibo; Jiang, Yongwen

2017-11-22

As important biomolecules in Camellia sinensis L., lipids undergo substantial changes during black tea manufacture, which is considered to contribute to tea sensory quality. However, limited by analytical capacity, detailed lipid composition and its dynamic changes during black tea manufacture remain unclear. Herein, we performed tea lipidome profiling using high resolution liquid chromatography coupled to mass spectrometry (LC-MS), which allows simultaneous and robust analysis of 192 individual lipid species in black tea, covering 17 (sub)classes. Furthermore, dynamic changes of tea lipids during black tea manufacture were investigated. Significant alterations of lipid pattern were revealed, involved with chlorophyll degradation, metabolic pathways of glycoglycerolipids, and other extraplastidial membrane lipids. To our knowledge, this report presented most comprehensive coverage of lipid species in black tea. This study provides a global and in-depth metabolic map of tea lipidome during black tea manufacture.

A rare case of mosaic 45,X/47,XX,+13 in 28-year-old women with secondary amenorrhoea: A case report and literature review

PubMed Central

Kumar, Mohit; Lal, Vandana; Chapadgaonkar, Shilpa; Bhattacharya, Saurabh Kumar

2014-01-01

In the present paper we report an extremely rare case of mosaicism of 45,X/47,XX,+13 in a 28-year-old women. The patient was referred for cytogenetic evaluation for secondary amenorrhoea. The patient was found to have some mild characteristic features of Turner syndrome such as wide carrying angle and short stature. Ultrasound examination revealed the presence of a small sized uterus and bilateral streak ovaries. G-banded chromosome analysis revealed a mosaic female karyotype involving two different cell lines. One cell line (72% of analysed metaphases) presented monosomy of X while the remaining 28% of cells showed trisomy of chromosome 13. Fluorescence in situ hybridization (FISH) with locus specific probe for trisomy 13 and CEP X for monosomy X substantiated the results obtained from karyotyping. PMID:26925371

ALMA Reveals a Compact Starburst Around a Hidden QSO at z˜5

NASA Astrophysics Data System (ADS)

Gilli, R.; Norman, C. A.; Vignali, C.

2015-12-01

We present ALMA 1.3mm observations of XID403, an SMG at z=4.75 in the Chandra Deep Field South hosting a heavily obscured, Compton-thick QSO. The ALMA data show that the dust heated by star formation is distributed within ˜0.9 kpc from the nucleus (effective radius). The SFR and dust temperature obtained from the Herschel+ALMA far-IR SED, reveal a warm and compact starburst with surface density of 200 M⊙ yr-1 kpc-2. Our analysis suggest that, besides the mass, SFR and gas consumption timescale, objects like XID403 have also the right size to be the progenitors of the compact quiescent massive galaxies seen at z˜3. It is finally shown that the density of the gas co-spatial with the dust provides a substantial contribution to the absorbing column density towards the QSO as measured from the X-rays.

Population genetic structure of critically endangered salamander (Hynobius amjiensis) in China: recommendations for conservation.

PubMed

Yang, J; Chen, C S; Chen, S H; Ding, P; Fan, Z Y; Lu, Y W; Yu, L P; Lin, H D

2016-06-10

Amji's salamander (Hynobius amjiensis) is a critically endangered species (IUCN Red List), which is endemic to mainland China. In the present study, five haplotypes were genotyped for the mtDNA cyt b gene in 45 specimens from three populations. Relatively low levels of haplotype diversity (h = 0.524) and nucleotide diversity (π = 0.00532) were detected. Analyses of the phylogenic structure of H. amjiensis showed no evidence of major geographic partitions or substantial barriers to historical gene flow throughout the species' range. Two major phylogenetic haplotype groups were revealed, and were estimated to have diverged about 1.262 million years ago. Mismatch distribution analysis, neutrality tests, and Bayesian skyline plots revealed no evidence of dramatic changes in the effective population size. According to the SAMOVA and STRUCTURE analyses, H. amjiensis should be regarded as two different management units.

Evaluating the Policies that Lead to Substantial Tuition Variation at Public Land-Grant Universities

ERIC Educational Resources Information Center

Burgess, Brent

2011-01-01

The aim of this study is to evaluate the current state of, and the causes for, the substantial variation in the tuition rates of America's land-grant universities. This aim was pursued with the objective of trying to identify consistent and revealing policies and external characteristics related to the high level of variation that exists among…

Canada's Physical Activity Guide: examining print-based material for motivating physical activity in the workplace.

PubMed

Plotnikoff, Ronald C; Todosijczuk, Ivan; Johnson, Steven T; Karunamuni, Nandini

2012-01-01

The authors conducted a secondary analysis on 202 adults from the Physical Activity Workplace Study. The aim of this analysis was to examine demographic characteristics associated with reading Canada's Physical Activity Guide (CPAG), being motivated by the guide, and whether participants in the Physical Activity Workplace Study who read the CPAG increased their physical activity levels over 1 year. Results revealed that less than 50% of participants read the full version of CPAG, and less than 10% were motivated by it. The CPAG also appears to be more appealing to and effective for women than for men. Although the CPAG had some influence in increasing mild physical activity levels in a workplace sample, there was also a decrease in physical activity levels among some members of the group. Overall, the effectiveness of CPAG was not substantial, and the findings of this analysis could help guide future targeted intervention materials and programs.

High-Throughput Single-Cell RNA Sequencing and Data Analysis.

PubMed

Sagar; Herman, Josip Stefan; Pospisilik, John Andrew; Grün, Dominic

2018-01-01

Understanding biological systems at a single cell resolution may reveal several novel insights which remain masked by the conventional population-based techniques providing an average readout of the behavior of cells. Single-cell transcriptome sequencing holds the potential to identify novel cell types and characterize the cellular composition of any organ or tissue in health and disease. Here, we describe a customized high-throughput protocol for single-cell RNA-sequencing (scRNA-seq) combining flow cytometry and a nanoliter-scale robotic system. Since scRNA-seq requires amplification of a low amount of endogenous cellular RNA, leading to substantial technical noise in the dataset, downstream data filtering and analysis require special care. Therefore, we also briefly describe in-house state-of-the-art data analysis algorithms developed to identify cellular subpopulations including rare cell types as well as to derive lineage trees by ordering the identified subpopulations of cells along the inferred differentiation trajectories.

Different autosomes evolved into sex chromosomes in the sister genera of Salix and Populus

PubMed Central

Hou, Jing; Ye, Ning; Zhang, Defang; Chen, Yingnan; Fang, Lecheng; Dai, Xiaogang; Yin, Tongming

2015-01-01

Willows (Salix) and poplars (Populus) are dioecious plants in Salicaceae family. Sex chromosome in poplar genome was consistently reported to be associated with chromosome XIX. In contrast to poplar, this study revealed that chromosome XV was sex chromosome in willow. Previous studies revealed that both ZZ/ZW and XX/XY sex-determining systems could be present in some species of Populus. In this study, sex of S. suchowensis was found to be determined by the ZW system in which the female was the heterogametic gender. Gene syntenic and collinear comparisons revealed macrosynteny between sex chromosomes and the corresponding autosomes between these two lineages. By contrast, no syntenic segments were found to be shared between poplar's and willow's sex chromosomes. Syntenic analysis also revealed substantial chromosome rearrangements between willow's alternate sex chromatids. Since willow and poplar originate from a common ancestor, we proposed that evolution of autosomes into sex chromosomes in these two lineages occurred after their divergence. Results of this study indicate that sex chromosomes in Salicaceae are still at the early stage of evolutionary divergence. Additionally, this study provided valuable information for better understanding the genetics and evolution of sex chromosome in dioecious plants. PMID:25766834

Communication‐related affective, behavioral, and cognitive reactions in speakers with spasmodic dysphonia

PubMed Central

Vanryckeghem, Martine

2017-01-01

Objectives To investigate the self‐perceived affective, behavioral, and cognitive reactions associated with communication of speakers with spasmodic dysphonia as a function of employment status. Study Design Prospective cross‐sectional investigation Methods 148 Participants with spasmodic dysphonia (SD) completed an adapted version of the Behavior Assessment Battery (BAB‐Voice), a multidimensional assessment of self‐perceived reactions to communication. The BAB‐Voice consisted of four subtests: the Speech Situation Checklist for A) Emotional Reaction (SSC‐ER) and B) Speech Disruption (SSC‐SD), C) the Behavior Checklist (BCL), and D) the Communication Attitude Test for Adults (BigCAT). Participants were assigned to groups based on employment status (working versus retired). Results Descriptive comparison of the BAB‐Voice in speakers with SD to previously published non‐dysphonic speaker data revealed substantially higher scores associated with SD across all four subtests. Multivariate Analysis of Variance (MANOVA) revealed no significantly different BAB‐Voice subtest scores as a function of SD group status (working vs. retired). Conclusions BAB‐Voice scores revealed that speakers with SD experienced substantial impact of their voice disorder on communication attitude, coping behaviors, and affective reactions in speaking situations as reflected in their high BAB scores. These impacts do not appear to be influenced by work status, as speakers with SD who were employed or retired experienced similar levels of affective and behavioral reactions in various speaking situations and cognitive responses. These findings are consistent with previously published pilot data. The specificity of items assessed by means of the BAB‐Voice may inform the clinician of valid patient‐centered treatment goals which target the impairment extended beyond the physiological dimension. Level of Evidence 2b PMID:29299525

Cluster Analysis to Identify Possible Subgroups in Tinnitus Patients.

PubMed

van den Berge, Minke J C; Free, Rolien H; Arnold, Rosemarie; de Kleine, Emile; Hofman, Rutger; van Dijk, J Marc C; van Dijk, Pim

2017-01-01

In tinnitus treatment, there is a tendency to shift from a "one size fits all" to a more individual, patient-tailored approach. Insight in the heterogeneity of the tinnitus spectrum might improve the management of tinnitus patients in terms of choice of treatment and identification of patients with severe mental distress. The goal of this study was to identify subgroups in a large group of tinnitus patients. Data were collected from patients with severe tinnitus complaints visiting our tertiary referral tinnitus care group at the University Medical Center Groningen. Patient-reported and physician-reported variables were collected during their visit to our clinic. Cluster analyses were used to characterize subgroups. For the selection of the right variables to enter in the cluster analysis, two approaches were used: (1) variable reduction with principle component analysis and (2) variable selection based on expert opinion. Various variables of 1,783 tinnitus patients were included in the analyses. Cluster analysis (1) included 976 patients and resulted in a four-cluster solution. The effect of external influences was the most discriminative between the groups, or clusters, of patients. The "silhouette measure" of the cluster outcome was low (0.2), indicating a "no substantial" cluster structure. Cluster analysis (2) included 761 patients and resulted in a three-cluster solution, comparable to the first analysis. Again, a "no substantial" cluster structure was found (0.2). Two cluster analyses on a large database of tinnitus patients revealed that clusters of patients are mostly formed by a different response of external influences on their disease. However, both cluster outcomes based on this dataset showed a poor stability, suggesting that our tinnitus population comprises a continuum rather than a number of clearly defined subgroups.

Diversity of Fusarium head blight populations and trichothecene toxin types reveals regional differences in pathogen composition and temporal dynamics

USDA-ARS?s Scientific Manuscript database

Analyses of genetic diversity, trichothecene genotype composition, and population structure were conducted using 4,086 Fusarium graminearum isolates collected from wheat in eight Canadian provinces over a three year period between 2005 and 2007. The results revealed substantial regional differences ...

Protecting the fabric of society? Heterosexual views on the usefulness of the anti-gay laws in Barbados, Guyana and Trinidad and Tobago

PubMed Central

Jackman, Mahalia

2017-01-01

Abstract This study evaluated the extent to which people living in Barbados, Guyana and Trinidad and Tobago believe that the anti-gay laws currently in place: (1) reflect moral standards; (2) stop the spread of homosexuality; (3) are important from a public health perspective; and (4) protect young people from abuse. Analysis reveals that demographics, religion, interpersonal contact and beliefs about the origin of homosexuality all influenced an individual’s views on the usefulness of the anti-gay laws in these states, but the significance of their impacts varied substantially across the arguments. PMID:27447435

Technical efficiency in the use of health care resources: a comparison of OECD countries.

PubMed

Retzlaff-Roberts, Donna; Chang, Cyril F; Rubin, Rose M

2004-07-01

Our paper analyzes technical efficiency in the production of aggregate health outcomes of reduced infant mortality and increased life expectancy, using Organization for Economic Cooperation and Development (OECD) health data. Application of data envelopment analysis (DEA) reveals that some countries achieve relative efficiency advantages, including those with good health outcomes (Japan, Sweden, Norway, and Canada) and those with modest health outcomes (Mexico and Turkey). We conclude the USA may learn from countries more economical in their allocation of healthcare resources that more is not necessarily better. Specifically, we find that the USA can substantially reduce inputs while maintaining the current level of life expectancy.

Single-crystal EPR spectra of the first alternating bimetallic chain compound MnCu(obp)(H2O)3·H2O (obp=oxamido bis(n,n‧-propionato))

NASA Astrophysics Data System (ADS)

Gatteschi, Dante; Zanchini, Claudia; Kahn, Olivier; Pei, Yu

1989-08-01

Single-crystal EPR spectra of the heterobimetallic alternating double-chain compound MnCu(obp) (H 2O) 3·H 2O (obp=oxamido bis (N,N'-propionato)) were recorded in the 300-20 K range. Analysis of the spectra indicate a substantially dipolar-determined linewidth with enhancement of the secular term of the second moment due to spin diffusion effects. The anisotropic shifts in the resonance field observed in low-temperature spectra revealed that interchain interactions are relevant in determining the preferred spin orientations.

Satisfied IUD acceptors as family planning motivators in Sri Lanka.

PubMed

Fisher, A A; de Silva, V

1986-01-01

In this study, government midwives were teamed with currently satisfied IUD acceptors to strengthen field motivational and recruitment efforts. The objective was to increase the number of new IUD acceptors. In the experimental study areas, a total of 3,019 new IUD acceptors were recruited. Time series regression analysis revealed a significant difference between the experimental and comparison areas that was over and above what might be expected on the basis of the past history of differences between these two areas. These and other findings suggest that teaming currently satisfied acceptors with government field-workers can have a substantial impact on the recruitment of new family planning users.

A cut above the rest? Private anthropometrics in marriage markets.

PubMed

Wilson, Nicholas; Janicki, Martha

2016-12-01

A large body of economic research suggests that publicly observable anthropometric characteristics affect labor and marriage market outcomes. Private anthropometrics may not affect these outcomes. We examine male circumcision in marriage markets in Zambia. Our analysis reveals substantial variation across local marriage markets in circumcision prevalence relative to preference for circumcised partners, as well as excess aggregate demand for circumcised males. Regression estimates suggest a marriage market premium of approximately one-half to one year of additional schooling for matching with a partner of preferred anthropometric type in a local marriage market with excess demand for that anthropometric characteristic. Copyright © 2016 Elsevier B.V. All rights reserved.

Nonlinear damping for vibration isolation of microsystems using shear thickening fluid

NASA Astrophysics Data System (ADS)

Iyer, S. S.; Vedad-Ghavami, R.; Lee, H.; Liger, M.; Kavehpour, H. P.; Candler, R. N.

2013-06-01

This work reports the measurement and analysis of nonlinear damping of micro-scale actuators immersed in shear thickening fluids (STFs). A power-law damping term is added to the linear second-order model to account for the shear-dependent viscosity of the fluid. This nonlinear model is substantiated by measurements of oscillatory motion of a torsional microactuator. At high actuation forces, the vibration velocity amplitude saturates. The model accurately predicts the nonlinear damping characteristics of the STF using a power-law index extracted from independent rheology experiments. This result reveals the potential to use STFs as adaptive, passive dampers for vibration isolation of microelectromechanical systems.

Orthorhombic-tetragonal phase coexistence and enhanced piezo-response at room temperature in Zr, Sn, and Hf modified BaTiO{sub 3}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kalyani, Ajay Kumar; Brajesh, Kumar; Ranjan, Rajeev, E-mail: rajeev@materials.iisc.ernet.in

2014-06-23

The effect of Zr, Hf, and Sn in BaTiO{sub 3} has been investigated at close composition intervals in the dilute concentration limit. Detailed structural analysis by x-ray and neutron powder diffraction revealed that merely 2 mol. % of Zr, Sn, and Hf stabilizes a coexistence of orthorhombic (Amm2) and tetragonal (P4mm) phases at room temperature. As a consequence, all the three systems show substantial enhancement in the longitudinal piezoelectric coefficient (d{sub 33}), with Sn modification exhibiting the highest value ∼425 pC/N.

A Road Less Traveled By: Exploring a Decade of Ellman Chemistry

PubMed Central

Shelat, Anang A.; Guy, R. Kiplin

2009-01-01

The Ellman group has been one of the most influential in the development and widespread adoption of combinatorial chemistry techniques for biomedical research. Their work has included substantial methodological development for library synthesis with a particular focus on new scaffolds rationally targeted to biomolecules of interest and biologically relevant natural products. Herein we analyze a representative set of libraries from this group with respect to their biological and biomedical relevance in comparison to existing drugs and probe compounds. This analysis reveals that the Ellman group has not only provided new methodologies to the community but also provided libraries with unique potential for further biological study. PMID:18343129

IARC use of oxidative stress as key mode of action characteristic for facilitating cancer classification: Glyphosate case example illustrating a lack of robustness in interpretative implementation.

PubMed

Bus, James S

2017-06-01

The International Agency for Research on Cancer (IARC) has formulated 10 key characteristics of human carcinogens to incorporate mechanistic data into cancer hazard classifications. The analysis used glyphosate as a case example to examine the robustness of IARC's determination of oxidative stress as "strong" evidence supporting a plausible cancer mechanism in humans. The IARC analysis primarily relied on 14 human/mammalian studies; 19 non-mammalian studies were uninformative of human cancer given the broad spectrum of test species and extensive use of formulations and aquatic testing. The mammalian studies had substantial experimental limitations for informing cancer mechanism including use of: single doses and time points; cytotoxic/toxic test doses; tissues not identified as potential cancer targets; glyphosate formulations or mixtures; technically limited oxidative stress biomarkers. The doses were many orders of magnitude higher than human exposures determined in human biomonitoring studies. The glyphosate case example reveals that the IARC evaluation fell substantially short of "strong" supporting evidence of oxidative stress as a plausible human cancer mechanism, and suggests that other IARC monographs relying on the 10 key characteristics approach should be similarly examined for a lack of robust data integration fundamental to reasonable mode of action evaluations. Copyright © 2017 Elsevier Inc. All rights reserved.

A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning

PubMed Central

Valouev, Anton; Ichikawa, Jeffrey; Tonthat, Thaisan; Stuart, Jeremy; Ranade, Swati; Peckham, Heather; Zeng, Kathy; Malek, Joel A.; Costa, Gina; McKernan, Kevin; Sidow, Arend; Fire, Andrew; Johnson, Steven M.

2008-01-01

Using the massively parallel technique of sequencing by oligonucleotide ligation and detection (SOLiD; Applied Biosystems), we have assessed the in vivo positions of more than 44 million putative nucleosome cores in the multicellular genetic model organism Caenorhabditis elegans. These analyses provide a global view of the chromatin architecture of a multicellular animal at extremely high density and resolution. While we observe some degree of reproducible positioning throughout the genome in our mixed stage population of animals, we note that the major chromatin feature in the worm is a diversity of allowed nucleosome positions at the vast majority of individual loci. While absolute positioning of nucleosomes can vary substantially, relative positioning of nucleosomes (in a repeated array structure likely to be maintained at least in part by steric constraints) appears to be a significant property of chromatin structure. The high density of nucleosomal reads enabled a substantial extension of previous analysis describing the usage of individual oligonucleotide sequences along the span of the nucleosome core and linker. We release this data set, via the UCSC Genome Browser, as a resource for the high-resolution analysis of chromatin conformation and DNA accessibility at individual loci within the C. elegans genome. PMID:18477713

Genomic Analysis of Phylotype I Strain EP1 Reveals Substantial Divergence from Other Strains in the Ralstonia solanacearum Species Complex

PubMed Central

Li, Peng; Wang, Dechen; Yan, Jinli; Zhou, Jianuan; Deng, Yinyue; Jiang, Zide; Cao, Bihao; He, Zifu; Zhang, Lianhui

2016-01-01

Ralstonia solanacearum species complex is a devastating group of phytopathogens with an unusually wide host range and broad geographical distribution. R. solanacearum isolates may differ considerably in various properties including host range and pathogenicity, but the underlying genetic bases remain vague. Here, we conducted the genome sequencing of strain EP1 isolated from Guangdong Province of China, which belongs to phylotype I and is highly virulent to a range of solanaceous crops. Its complete genome contains a 3.95-Mb chromosome and a 2.05-Mb mega-plasmid, which is considerably bigger than reported genomes of other R. solanacearum strains. Both the chromosome and the mega-plasmid have essential house-keeping genes and many virulence genes. Comparative analysis of strain EP1 with other 3 phylotype I and 3 phylotype II, III, IV strains unveiled substantial genome rearrangements, insertions and deletions. Genome sequences are relatively conserved among the 4 phylotype I strains, but more divergent among strains of different phylotypes. Moreover, the strains exhibited considerable variations in their key virulence genes, including those encoding secretion systems and type III effectors. Our results provide valuable information for further elucidation of the genetic basis of diversified virulences and host range of R. solanacearum species. PMID:27833603

What Can We Learn about Mental Health Needs from Tweets Mentioning Dementia on World Alzheimer’s Day?

PubMed Central

Yoon, Sunmoo

2017-01-01

Background Twitter can address the mental health challenges of dementia care. The aims of this study is to explore the contents and user interactions of tweets mentioning dementia to gain insights for dementia care. Methods We collected 35,260 tweets mentioning Alzheimer’s or dementia on World Alzheimer’s Day, September 21st in 2015. Topic modeling and social network analysis were applied to uncover content and structure of user communication. Results Global users generated keywords related to mental health and care including #psychology and #mental health. There were similarities and differences between the UK and the US in tweet content. The macro-level analysis uncovered substantial public interest on dementia. The meso-level network analysis revealed that top leaders of communities were spiritual organizations and traditional media. Conclusions The application of topic modeling and multi-level network analysis while incorporating visualization techniques can promote a global level understanding regarding public attention, interests, and insights regarding dementia care and mental health. PMID:27803262

Single-Pixel Optical Fluctuation Analysis of Calcium Channel Function in Active Zones of Motor Nerve Terminals

PubMed Central

Luo, Fujun; Dittrich, Markus; Stiles, Joel R.; Meriney, Stephen D.

2011-01-01

We used high-resolution fluorescence imaging and single-pixel optical fluctuation analysis to estimate the opening probability of individual voltage-gated calcium (Ca2+) channels during an action potential and the number of such Ca2+ channels within active zones of frog neuromuscular junctions. Analysis revealed ~36 Ca2+ channels within each active zone, similar to the number of docked synaptic vesicles but far less than the total number of transmembrane particles reported based on freeze-fracture analysis (~200–250). The probability that each channel opened during an action potential was only ~0.2. These results suggest why each active zone averages only one quantal release event during every other action potential, despite a substantial number of docked vesicles. With sparse Ca2+ channels and low opening probability, triggering of fusion for each vesicle is primarily controlled by Ca2+ influx through individual Ca2+ channels. In contrast, the entire synapse is highly reliable because it contains hundreds of active zones. PMID:21813687

Experimental and theoretical analysis of a rare nitrato bridged 3d-4f complex containing LaZn2 core synthesized from a Zn(II) metalloligand

NASA Astrophysics Data System (ADS)

Sreejith, S. S.; Mohan, Nithya; Kurup, M. R. Prathapachandra

2018-02-01

A trinulcear Zn2La Schiff base complex was synthesized using slow-solvent evaporation technique from a Zn(II) mononuclear metalloligand by 2:1 addition with La(NO3)3 salt. Single crystal XRD analysis revealed a rare nitrato bridged trinuclear entity which is seldom seen in these class of ligand systems. Qualitative and quantitative analysis of intermolecular interactions/short contacts were done using Hirshfeld surface and 2D finger print analysis. The thermally stable, blue luminescent compound exhibits internal heavy atom effect thereby quenching the emission intensity of the ligand. DFT calculations were performed on the compound to analyze frontier orbitals and also ESP plots were used to monitor nucleophilic/electrophilic regions on the compound and its implications on hydrogen bonding. A comparison of the bond orders and atomic charges on the trinuclear compound and the Zn(II) metalloligand precursor was performed to substantiate the formation of the trinuclear product through ligand exchange.

Comprehensive Proteomics Analysis of Laticifer Latex Reveals New Insights into Ethylene Stimulation of Natural Rubber Production.

PubMed

Wang, Xuchu; Wang, Dan; Sun, Yong; Yang, Qian; Chang, Lili; Wang, Limin; Meng, Xueru; Huang, Qixing; Jin, Xiang; Tong, Zheng

2015-09-08

Ethylene is a stimulant to increase natural rubber latex. After ethylene application, both fresh yield and dry matter of latex are substantially improved. Moreover, we found that ethylene improves the generation of small rubber particles. However, most genes involved in rubber biosynthesis are inhibited by exogenous ethylene. Therefore, we conducted a proteomics analysis of ethylene-stimulated rubber latex, and identified 287 abundant proteins as well as 143 ethylene responsive latex proteins (ERLPs) with mass spectrometry from the 2-DE and DIGE gels, respectively. In addition, more than 1,600 proteins, including 404 ERLPs, were identified by iTRAQ. Functional classification of ERLPs revealed that enzymes involved in post-translational modification, carbohydrate metabolism, hydrolase activity, and kinase activity were overrepresented. Some enzymes for rubber particle aggregation were inhibited to prolong latex flow, and thus finally improved latex production. Phosphoproteomics analysis identified 59 differential phosphoproteins; notably, specific isoforms of rubber elongation factor and small rubber particle protein that were phosphorylated mainly at serine residues. This post-translational modification and isoform-specific phosphorylation might be important for ethylene-stimulated latex production. These results not only deepen our understanding of the rubber latex proteome but also provide new insights into the use of ethylene to stimulate rubber latex production.

Metabolomic analysis reveals altered metabolic pathways in a rat model of gastric carcinogenesis.

PubMed

Gu, Jinping; Hu, Xiaomin; Shao, Wei; Ji, Tianhai; Yang, Wensheng; Zhuo, Huiqin; Jin, Zeyu; Huang, Huiying; Chen, Jiacheng; Huang, Caihua; Lin, Donghai

2016-09-13

Gastric cancer (GC) is one of the most malignant tumors with a poor prognosis. Alterations in metabolic pathways are inextricably linked to GC progression. However, the underlying molecular mechanisms remain elusive. We performed NMR-based metabolomic analysis of sera derived from a rat model of gastric carcinogenesis, revealed significantly altered metabolic pathways correlated with the progression of gastric carcinogenesis. Rats were histologically classified into four pathological groups (gastritis, GS; low-grade gastric dysplasia, LGD; high-grade gastric dysplasia, HGD; GC) and the normal control group (CON). The metabolic profiles of the five groups were clearly distinguished from each other. Furthermore, significant inter-metabolite correlations were extracted and used to reconstruct perturbed metabolic networks associated with the four pathological stages compared with the normal stage. Then, significantly altered metabolic pathways were identified by pathway analysis. Our results showed that oxidative stress-related metabolic pathways, choline phosphorylation and fatty acid degradation were continually disturbed during gastric carcinogenesis. Moreover, amino acid metabolism was perturbed dramatically in gastric dysplasia and GC. The GC stage showed more changed metabolite levels and more altered metabolic pathways. Two activated pathways (glycolysis; glycine, serine and threonine metabolism) substantially contributed to the metabolic alterations in GC. These results lay the basis for addressing the molecular mechanisms underlying gastric carcinogenesis and extend our understanding of GC progression.

From risky to safer home care: health care assistants striving to overcome a lack of training, supervision, and support.

PubMed

Swedberg, Lena; Chiriac, Eva Hammar; Törnkvist, Lena; Hylander, Ingrid

2013-05-23

Patients receiving home care are becoming increasingly dependent upon competent caregivers' 24-h availability due to their substantial care needs, often with advanced care and home care technology included. In Sweden, care is often carried out by municipality-employed paraprofessionals such as health care assistants (HC assistants) with limited or no health care training, performing advanced care without formal training or support. The aim of this study was to investigate the work experience of the HC assistants and to explore how they manage when delivering 24-h home care to patients with substantial care needs. Grounded theory methodology involving multiple data sources comprising interviews with HC assistants (n=19) and field observations in patients' homes was used to collect data and constant comparative analysis was used for analysis. The initial analysis revealed a number of barriers, competence gap; trapped in the home setting; poor supervision and unconnected to the patient care system, describing the risks associated with the situations of HC assistants working in home care, thus affecting their working conditions as well as the patient care. The core process identified was the HC assistants' strivings to combine safe home care with good working conditions by using compensatory processes. The four identified compensatory processes were: day-by-day learning; balancing relations with the patient; self-managing; and navigating the patient care system. By actively employing the compensatory processes, the HC assistants could be said to adopt an inclusive approach, by compensating for their own barriers as well as those of their colleagues' and taking overall responsibility for their workplace. In conclusion, the importance of supporting HC assistants in relation to their needs for training, supervision,and support from health care professionals must be addressed when organising 24-h home care to patients with substantial care needs in the future.

Caffeine content of beverages as consumed.

PubMed Central

Gilbert, R. M.; Marshman, J. A.; Schwieder, M.; Berg, R.

1976-01-01

Quantitative analysis of beverages prepared at home by staff of the Addiction Research Foundation revealed a lower and much more variable caffeine content of both tea and coffee than had been reported in earlier studies, most of which were based on analysis of laboratory-prepared beverages. Median caffeine concentration of 37 home-prepared samples of tea was 27 mg per cup (range, 8 to 91 mg); for 46 coffee samples the median concentration was 74 mg per cup (range, 29 to 176 mg). If tea and coffee as drunk contain less caffeine than generally supposed, the potency of caffeine may be greater than commonly realized, as may the relative caffeine content of certain commercial preparations, including chocolate and colas. The substantial variation in caffeine content emphasizes the need to establish actual caffeine intake in clinical, epidemiologic and experimental investigations of caffeine effects. PMID:1032351

Theory of Mind in Children With Specific Language Impairment: A Systematic Review and Meta-Analysis.

PubMed

Nilsson, Kristine Kahr; de López, Kristine Jensen

2016-01-01

The relation between language and theory of mind (ToM) has been debated for more than two decades. In a similar vein, ToM has been examined in children with specific language impairment (SLI), albeit with inconsistent results. This meta-analysis of 17 studies with 745 children between the ages of 4 and 12 found that children with SLI had substantially lower ToM performance compared to age-matched typically developing children (d = .98). This effect size was not moderated by age and gender. By revealing that children with SLI have ToM impairments, this finding emphasizes the need for further investigation into the developmental interface between language and ToM as well as the extended consequences of atypical language development. © 2015 The Authors. Child Development © 2015 Society for Research in Child Development, Inc.

Profile of the genes expressed in the human peripheral retina, macula, and retinal pigment epithelium determined through serial analysis of gene expression (SAGE)

PubMed Central

Sharon, Dror; Blackshaw, Seth; Cepko, Constance L.; Dryja, Thaddeus P.

2002-01-01

We used the serial analysis of gene expression (SAGE) technique to catalogue and measure the relative levels of expression of the genes expressed in the human peripheral retina, macula, and retinal pigment epithelium (RPE) from one or both of two humans, aged 88 and 44 years. The cone photoreceptor contribution to all transcription in the retina was found to be similar in the macula versus the retinal periphery, whereas the rod contribution was greater in the periphery versus the macula. Genes encoding structural proteins for axons were found to be expressed at higher levels in the macula versus the retinal periphery, probably reflecting the large proportion of ganglion cells in the central retina. In comparison with the younger eye, the peripheral retina of the older eye had a substantially higher proportion of mRNAs from genes encoding proteins involved in iron metabolism or protection against oxidative damage and a substantially lower proportion of mRNAs from genes encoding proteins involved in rod phototransduction. These differences may reflect the difference in age between the two donors or merely interindividual variation. The RPE library had numerous previously unencountered tags, suggesting that this cell type has a large, idiosyncratic repertoire of expressed genes. Comparison of these libraries with 100 reported nonocular SAGE libraries revealed 89 retina-specific or enriched genes expressed at substantial levels, of which 14 are known to cause a retinal disease and 53 are RPE-specific genes. We expect that these libraries will serve as a resource for understanding the relative expression levels of genes in the retina and the RPE and for identifying additional disease genes. PMID:11756676

Graded exposure in vivo in the treatment of pain-related fear: a replicated single-case experimental design in four patients with chronic low back pain.

PubMed

Vlaeyen, J W; de Jong, J; Geilen, M; Heuts, P H; van Breukelen, G

2001-02-01

The aim of this investigation was to examine the effectiveness of a graded exposure in vivo treatment with behavioural experiments as compared to usual graded activity in reducing pain-related fears, catastrophising and pain disability in chronic low back pain patients reporting substantial fear of movement/(re)injury. Included in the study were four consecutive CLBP patients who were referred for outpatient behavioural rehabilitation, and who reported substantial fear of movement/(re)injury (Tampa Scale for Kinesiophobia score>40). A replicated single-case cross-over design was used. After a no-treatment baseline measurement period, the patients were randomly assigned to one of two interventions. In intervention A, patients received the exposure first, followed by graded activity. In intervention B, the sequence of treatment modules was reversed. Sixty-three daily measures of pain-related cognitions and fears were recorded with visual analogue scales. Before and after the treatment, the following measures were taken: pain-related fear, pain catastrophising, pain control and pain disability. Using time series analysis on the daily measures of pain-related cognitions and fears, we found that improvements only occurred during the graded exposure in vivo, and not during the graded activity, irrespective of the treatment order. Analysis of the pre-post treatment differences also revealed that decreases in pain-related fear concurred with decreases in pain catastrophising and pain disability, and in half of the cases an increase in pain control. This study shows that the external validity of exposure in vivo also extends to the subgroup of chronic low back pain patients who report substantial fear of movement/(re)injury.

Genetic stability of genome-scale deoptimized RNA virus vaccine candidates under selective pressure

PubMed Central

Le Nouën, Cyril; McCarty, Thomas; Brown, Michael; Smith, Melissa Laird; Lleras, Roberto; Dolan, Michael A.; Mehedi, Masfique; Yang, Lijuan; Luongo, Cindy; Liang, Bo; Munir, Shirin; DiNapoli, Joshua M.; Mueller, Steffen; Wimmer, Eckard; Collins, Peter L.; Buchholz, Ursula J.

2017-01-01

Recoding viral genomes by numerous synonymous but suboptimal substitutions provides live attenuated vaccine candidates. These vaccine candidates should have a low risk of deattenuation because of the many changes involved. However, their genetic stability under selective pressure is largely unknown. We evaluated phenotypic reversion of deoptimized human respiratory syncytial virus (RSV) vaccine candidates in the context of strong selective pressure. Codon pair deoptimized (CPD) versions of RSV were attenuated and temperature-sensitive. During serial passage at progressively increasing temperature, a CPD RSV containing 2,692 synonymous mutations in 9 of 11 ORFs did not lose temperature sensitivity, remained genetically stable, and was restricted at temperatures of 34 °C/35 °C and above. However, a CPD RSV containing 1,378 synonymous mutations solely in the polymerase L ORF quickly lost substantial attenuation. Comprehensive sequence analysis of virus populations identified many different potentially deattenuating mutations in the L ORF as well as, surprisingly, many appearing in other ORFs. Phenotypic analysis revealed that either of two competing mutations in the virus transcription antitermination factor M2-1, outside of the CPD area, substantially reversed defective transcription of the CPD L gene and substantially restored virus fitness in vitro and in case of one of these two mutations, also in vivo. Paradoxically, the introduction into Min L of one mutation each in the M2-1, N, P, and L proteins resulted in a virus with increased attenuation in vivo but increased immunogenicity. Thus, in addition to providing insights on the adaptability of genome-scale deoptimized RNA viruses, stability studies can yield improved synthetic RNA virus vaccine candidates. PMID:28049853

A Twin Study of ADHD Symptoms in Early Adolescence: Hyperactivity-Impulsivity and Inattentiveness Show Substantial Genetic Overlap but Also Genetic Specificity

ERIC Educational Resources Information Center

Greven, Corina U.; Rijsdijk, Fruhling V.; Plomin, Robert

2011-01-01

A previous paper in this journal revealed substantial genetic overlap between the ADHD dimensions of hyperactivity-impulsivity and inattentiveness in a sample of 8-year old twins drawn from a UK-representative population sample. Four years later, when the twins were 12 years old, more than 5,500 pairs drawn from the same sample were rated again on…

Automated image alignment for 2D gel electrophoresis in a high-throughput proteomics pipeline.

PubMed

Dowsey, Andrew W; Dunn, Michael J; Yang, Guang-Zhong

2008-04-01

The quest for high-throughput proteomics has revealed a number of challenges in recent years. Whilst substantial improvements in automated protein separation with liquid chromatography and mass spectrometry (LC/MS), aka 'shotgun' proteomics, have been achieved, large-scale open initiatives such as the Human Proteome Organization (HUPO) Brain Proteome Project have shown that maximal proteome coverage is only possible when LC/MS is complemented by 2D gel electrophoresis (2-DE) studies. Moreover, both separation methods require automated alignment and differential analysis to relieve the bioinformatics bottleneck and so make high-throughput protein biomarker discovery a reality. The purpose of this article is to describe a fully automatic image alignment framework for the integration of 2-DE into a high-throughput differential expression proteomics pipeline. The proposed method is based on robust automated image normalization (RAIN) to circumvent the drawbacks of traditional approaches. These use symbolic representation at the very early stages of the analysis, which introduces persistent errors due to inaccuracies in modelling and alignment. In RAIN, a third-order volume-invariant B-spline model is incorporated into a multi-resolution schema to correct for geometric and expression inhomogeneity at multiple scales. The normalized images can then be compared directly in the image domain for quantitative differential analysis. Through evaluation against an existing state-of-the-art method on real and synthetically warped 2D gels, the proposed analysis framework demonstrates substantial improvements in matching accuracy and differential sensitivity. High-throughput analysis is established through an accelerated GPGPU (general purpose computation on graphics cards) implementation. Supplementary material, software and images used in the validation are available at http://www.proteomegrid.org/rain/.

Genetic Diversity and Association Studies in US Hispanic/Latino Populations: Applications in the Hispanic Community Health Study/Study of Latinos

PubMed Central

Conomos, Matthew P.; Laurie, Cecelia A.; Stilp, Adrienne M.; Gogarten, Stephanie M.; McHugh, Caitlin P.; Nelson, Sarah C.; Sofer, Tamar; Fernández-Rhodes, Lindsay; Justice, Anne E.; Graff, Mariaelisa; Young, Kristin L.; Seyerle, Amanda A.; Avery, Christy L.; Taylor, Kent D.; Rotter, Jerome I.; Talavera, Gregory A.; Daviglus, Martha L.; Wassertheil-Smoller, Sylvia; Schneiderman, Neil; Heiss, Gerardo; Kaplan, Robert C.; Franceschini, Nora; Reiner, Alex P.; Shaffer, John R.; Barr, R. Graham; Kerr, Kathleen F.; Browning, Sharon R.; Browning, Brian L.; Weir, Bruce S.; Avilés-Santa, M. Larissa; Papanicolaou, George J.; Lumley, Thomas; Szpiro, Adam A.; North, Kari E.; Rice, Ken; Thornton, Timothy A.; Laurie, Cathy C.

2016-01-01

US Hispanic/Latino individuals are diverse in genetic ancestry, culture, and environmental exposures. Here, we characterized and controlled for this diversity in genome-wide association studies (GWASs) for the Hispanic Community Health Study/Study of Latinos (HCHS/SOL). We simultaneously estimated population-structure principal components (PCs) robust to familial relatedness and pairwise kinship coefficients (KCs) robust to population structure, admixture, and Hardy-Weinberg departures. The PCs revealed substantial genetic differentiation within and among six self-identified background groups (Cuban, Dominican, Puerto Rican, Mexican, and Central and South American). To control for variation among groups, we developed a multi-dimensional clustering method to define a “genetic-analysis group” variable that retains many properties of self-identified background while achieving substantially greater genetic homogeneity within groups and including participants with non-specific self-identification. In GWASs of 22 biomedical traits, we used a linear mixed model (LMM) including pairwise empirical KCs to account for familial relatedness, PCs for ancestry, and genetic-analysis groups for additional group-associated effects. Including the genetic-analysis group as a covariate accounted for significant trait variation in 8 of 22 traits, even after we fit 20 PCs. Additionally, genetic-analysis groups had significant heterogeneity of residual variance for 20 of 22 traits, and modeling this heteroscedasticity within the LMM reduced genomic inflation for 19 traits. Furthermore, fitting an LMM that utilized a genetic-analysis group rather than a self-identified background group achieved higher power to detect previously reported associations. We expect that the methods applied here will be useful in other studies with multiple ethnic groups, admixture, and relatedness. PMID:26748518

Network Analysis of Rat Spatial Cognition: Behaviorally-Established Symmetry in a Physically Asymmetrical Environment

PubMed Central

Eilam, David; Portugali, Juval; Blumenfeld-Lieberthal, Efrat

2012-01-01

Background We set out to solve two inherent problems in the study of animal spatial cognition (i) What is a “place”?; and (ii) whether behaviors that are not revealed as differing by one methodology could be revealed as different when analyzed using a different approach. Methodology We applied network analysis to scrutinize spatial behavior of rats tested in either a symmetrical or asymmetrical layout of 4, 8, or 12 objects placed along the perimeter of a round arena. We considered locations as the units of the network (nodes), and passes between locations as the links within the network. Principal Findings While there were only minor activity differences between rats tested in the symmetrical or asymmetrical object layouts, network analysis revealed substantial differences. Viewing ‘location’ as a cluster of stopping coordinates, the key locations (large clusters of stopping coordinates) were at the objects in both layouts with 4 objects. However, in the asymmetrical layout with 4 objects, additional key locations were spaced by the rats between the objects, forming symmetry among the key locations. It was as if the rats had behaviorally imposed symmetry on the physically asymmetrical environment. Based on a previous finding that wayfinding is easier in symmetrical environments, we suggest that when the physical attributes of the environment were not symmetrical, the rats established a symmetric layout of key locations, thereby acquiring a more legible environment despite its complex physical structure. Conclusions and Significance The present study adds a behavioral definition for “location”, a term that so far has been mostly discussed according to its physical attributes or neurobiological correlates (e.g. - place and grid neurons). Moreover, network analysis enabled the assessment of the importance of a location, even when that location did not display any distinctive physical properties. PMID:22815808

Child-Staff Ratios in Early Childhood Education and Care Settings and Child Outcomes: A Systematic Review and Meta-Analysis.

PubMed

Perlman, Michal; Fletcher, Brooke; Falenchuk, Olesya; Brunsek, Ashley; McMullen, Evelyn; Shah, Prakesh S

2017-01-01

Child-staff ratios are a key quality indicator in early childhood education and care (ECEC) programs. Better ratios are believed to improve child outcomes by increasing opportunities for individual interactions and educational instruction from staff. The purpose of this systematic review, and where possible, meta-analysis, was to evaluate the association between child-staff ratios in preschool ECEC programs and children's outcomes. Searches of Medline, PsycINFO, ERIC, websites of large datasets and reference sections of all retrieved articles were conducted up to July 3, 2015. Cross-sectional or longitudinal studies that evaluated the relationship between child-staff ratios in ECEC classrooms serving preschool aged children and child outcomes were independently identified by two reviewers. Data were independently extracted from included studies by two raters and differences between raters were resolved by consensus. Searches revealed 29 eligible studies (31 samples). Child-staff ratios ranged from 5 to 14.5 preschool-aged children per adult with a mean of 8.65. All 29 studies were included in the systematic review. However, the only meta-analysis that could be conducted was based on three studies that explored associations between ratios and children's receptive language. Results of this meta-analysis were not significant. Results of the qualitative systematic review revealed few significant relationships between child-staff ratios and child outcomes construed broadly. Thus, the available literature reveal few, if any, relationships between child-staff ratios in preschool ECEC programs and children's developmental outcomes. Substantial heterogeneity in the assessment of ratios, outcomes measured, and statistics used to capture associations limited quantitative synthesis. Other methodological limitations of the research integrated in this synthesis are discussed.

Child-Staff Ratios in Early Childhood Education and Care Settings and Child Outcomes: A Systematic Review and Meta-Analysis

PubMed Central

Perlman, Michal; Fletcher, Brooke; Falenchuk, Olesya; Brunsek, Ashley; McMullen, Evelyn; Shah, Prakesh S.

2017-01-01

Child-staff ratios are a key quality indicator in early childhood education and care (ECEC) programs. Better ratios are believed to improve child outcomes by increasing opportunities for individual interactions and educational instruction from staff. The purpose of this systematic review, and where possible, meta-analysis, was to evaluate the association between child-staff ratios in preschool ECEC programs and children’s outcomes. Searches of Medline, PsycINFO, ERIC, websites of large datasets and reference sections of all retrieved articles were conducted up to July 3, 2015. Cross-sectional or longitudinal studies that evaluated the relationship between child-staff ratios in ECEC classrooms serving preschool aged children and child outcomes were independently identified by two reviewers. Data were independently extracted from included studies by two raters and differences between raters were resolved by consensus. Searches revealed 29 eligible studies (31 samples). Child-staff ratios ranged from 5 to 14.5 preschool-aged children per adult with a mean of 8.65. All 29 studies were included in the systematic review. However, the only meta-analysis that could be conducted was based on three studies that explored associations between ratios and children’s receptive language. Results of this meta-analysis were not significant. Results of the qualitative systematic review revealed few significant relationships between child-staff ratios and child outcomes construed broadly. Thus, the available literature reveal few, if any, relationships between child-staff ratios in preschool ECEC programs and children’s developmental outcomes. Substantial heterogeneity in the assessment of ratios, outcomes measured, and statistics used to capture associations limited quantitative synthesis. Other methodological limitations of the research integrated in this synthesis are discussed. PMID:28103288

Energy component analysis of π interactions.

PubMed

Sherrill, C David

2013-04-16

Fundamental features of biomolecules, such as their structure, solvation, and crystal packing and even the docking of drugs, rely on noncovalent interactions. Theory can help elucidate the nature of these interactions, and energy component analysis reveals the contributions from the various intermolecular forces: electrostatics, London dispersion terms, induction (polarization), and short-range exchange-repulsion. Symmetry-adapted perturbation theory (SAPT) provides one method for this type of analysis. In this Account, we show several examples of how SAPT provides insight into the nature of noncovalent π-interactions. In cation-π interactions, the cation strongly polarizes electrons in π-orbitals, leading to substantially attractive induction terms. This polarization is so important that a cation and a benzene attract each other when placed in the same plane, even though a consideration of the electrostatic interactions alone would suggest otherwise. SAPT analysis can also support an understanding of substituent effects in π-π interactions. Trends in face-to-face sandwich benzene dimers cannot be understood solely in terms of electrostatic effects, especially for multiply substituted dimers, but SAPT analysis demonstrates the importance of London dispersion forces. Moreover, detailed SAPT studies also reveal the critical importance of charge penetration effects in π-stacking interactions. These effects arise in cases with substantial orbital overlap, such as in π-stacking in DNA or in crystal structures of π-conjugated materials. These charge penetration effects lead to attractive electrostatic terms where a simpler analysis based on atom-centered charges, electrostatic potential plots, or even distributed multipole analysis would incorrectly predict repulsive electrostatics. SAPT analysis of sandwich benzene, benzene-pyridine, and pyridine dimers indicates that dipole/induced-dipole terms present in benzene-pyridine but not in benzene dimer are relatively unimportant. In general, a nitrogen heteroatom contracts the electron density, reducing the magnitude of both the London dispersion and the exchange-repulsion terms, but with an overall net increase in attraction. Finally, using recent advances in SAPT algorithms, researchers can now perform SAPT computations on systems with 200 atoms or more. We discuss a recent study of the intercalation complex of proflavine with a trinucleotide duplex of DNA. Here, London dispersion forces are the strongest contributors to binding, as is typical for π-π interactions. However, the electrostatic terms are larger than usual on a fractional basis, which likely results from the positive charge on the intercalator and its location between two electron-rich base pairs. These cation-π interactions also increase the induction term beyond those of typical noncovalent π-interactions.

Unsteady aerodynamic analysis of space shuttle vehicles. Part 4: Effect of control deflections on orbiter unsteady aerodynamics

NASA Technical Reports Server (NTRS)

Reding, J. P.; Ericsson, L. E.

1973-01-01

The unsteady aerodynamics of the 040A orbiter have been explored experimentally. The results substantiate earlier predictions of the unsteady flow boundaries for a 60 deg swept delta wing at zero yaw and with no controls deflected. The test revealed a previously unknown region of discontinuous yaw characteristics at transonic speeds. Oilflow results indicate that this is the result of a coupling between wing and fuselage flows via the separated region forward of the deflected elevon. In fact, the large leeward elevon deflections are shown to produce a multitude of nonlinear stability effects which sometimes involve hysteresis. Predictions of the unsteady flow boundaries are made for the current orbiter. They should carry a good degree of confidence due to the present substantiation of previous predictions for the 040A. It is proposed that the present experiments be extended to the current configuration to define control-induced effects. Every effort should be made to account for Reynolds number, roughness, and possible hot-wall effects on any future experiments.

IOTN - a tool to prioritize treatment need in children and plan Dental Health services.

PubMed

Sharma, Jaideep; Sharma, Ruchi Dhir

2014-03-01

The study aimed to evaluate the orthodontic treatment need in school going children in Moradabad, North India, to assess the malocclusion traits, concern towards Dental Health and individual aesthetic perception compared to orthodontist's opinion. 5232 children, aged 11-14 yrs formed the sample. The Dental Health Component (DHC) and Aesthetic Component (AC) were recorded as defined by Brook and Shaw, with slight modification for AC assessment. Statistical analysis revealed that only 12.5% children had no treatment need while 87.5% presented malocclusion with varying treatment needs. There was insignificant sex difference for aesthetic perception. Examiner graded children less attractive than children. Class I was the most common malocclusion and crowding was the most common malocclusion trait. High intra-examiner and substantial inter-examiner agreements were observed for DHC and substantial intra- examiner and moderate inter-examiner agreements for AC. It can be concluded from the present study that, IOTN is a reliable epidemiologic tool to benefit local health services in planning their budget, and improve focus of services by inducing greater uniformity and standardization in the assessment of Orthodontic treatment need.

Posttraumatic Stress Symptoms and Trajectories in Child Sexual Abuse Victims: An Analysis of Sex Differences Using the National Survey of Child and Adolescent Well-Being

PubMed Central

Koenen, Karestan C.; Jaffee, Sara R.

2011-01-01

Very few studies have prospectively examined sex differences in posttraumatic stress symptoms and symptom trajectories in youth victimized by childhood sexual abuse. This study addresses that question in a relatively large sample of children, drawn from the National Survey of Child and Adolescent Well-Being, who were between the ages of 8–16 years and who were reported to Child Protective Services for alleged sexual abuse. Sex differences were examined using t tests, logistic regression, and latent trajectory modeling. Results revealed that there were not sex differences in victims’ posttraumatic stress symptoms or trajectories. Whereas caseworkers substantiated girls’ abuse at higher rates than boys’ abuse and rated girls significantly higher than boys on level of harm, there were not sex differences in three more objective measures of abuse severity characteristics. Overall, higher caseworker ratings of harm predicted higher initial posttraumatic stress symptom levels, and substantiation status predicted shallower decreases in trauma symptoms over time. Implications for theory and intervention are discussed. PMID:19221872

Light-induced alterations of pineapple (Ananas comosus [L.] Merr.) juice volatiles during accelerated ageing and mass spectrometric studies into their precursors.

PubMed

Steingass, Christof Björn; Glock, Mona Pia; Lieb, Veronika Maria; Carle, Reinhold

2017-10-01

Alterations of volatiles during accelerated light-induced ageing of pineapple juice were assessed by HS-SPME-GC-MS in a non-targeted profiling analysis over a 16-week period. Multivariate statistics permitted to reveal substantial chemical markers generally describing the effect of light storage. Volatiles generated comprised phenylpropenes, carbonyls, 2-methylthiophene, toluene, and furfural, while concentrations of methyl and ethyl esters, terpenes, and furanones decreased. In addition, the qualitative composition of phenolic compounds and glycoside-bound volatiles in selected samples was characterized by HPLC-DAD-ESI-MS n as well as HR-ESI-MS. The fresh juice contained unique pineapple metabolites such as S-p-coumaryl, S-coniferyl, S-sinapylglutathione, and structurally related derivatives. Among others, the presence of p-coumaroyl, feruloyl, and caffeoylisocitrate as well as three 4-hydroxy-2,5-dimethyl-3(2H)-furanone glycosides in pineapples could be substantiated by the HR-ESI-MS experiment. Mass spectrometric assignments of selected metabolites are presented, and putative linkages between volatiles and their precursors are established. Copyright © 2017 Elsevier Ltd. All rights reserved.

Spontaneous quaternary and tertiary T-R transitions of human hemoglobin in molecular dynamics simulation.

PubMed

Hub, Jochen S; Kubitzki, Marcus B; de Groot, Bert L

2010-05-06

We present molecular dynamics simulations of unliganded human hemoglobin (Hb) A under physiological conditions, starting from the R, R2, and T state. The simulations were carried out with protonated and deprotonated HC3 histidines His(beta)146, and they sum up to a total length of 5.6 micros. We observe spontaneous and reproducible T-->R quaternary transitions of the Hb tetramer and tertiary transitions of the alpha and beta subunits, as detected from principal component projections, from an RMSD measure, and from rigid body rotation analysis. The simulations reveal a marked asymmetry between the alpha and beta subunits. Using the mutual information as correlation measure, we find that the beta subunits are substantially more strongly linked to the quaternary transition than the alpha subunits. In addition, the tertiary populations of the alpha and beta subunits differ substantially, with the beta subunits showing a tendency towards R, and the alpha subunits showing a tendency towards T. Based on the simulation results, we present a transition pathway for coupled quaternary and tertiary transitions between the R and T conformations of Hb.

Spontaneous Quaternary and Tertiary T-R Transitions of Human Hemoglobin in Molecular Dynamics Simulation

PubMed Central

de Groot, Bert L.

2010-01-01

We present molecular dynamics simulations of unliganded human hemoglobin (Hb) A under physiological conditions, starting from the R, R2, and T state. The simulations were carried out with protonated and deprotonated HC3 histidines His(β)146, and they sum up to a total length of 5.6µs. We observe spontaneous and reproducible T→R quaternary transitions of the Hb tetramer and tertiary transitions of the α and β subunits, as detected from principal component projections, from an RMSD measure, and from rigid body rotation analysis. The simulations reveal a marked asymmetry between the α and β subunits. Using the mutual information as correlation measure, we find that the β subunits are substantially more strongly linked to the quaternary transition than the α subunits. In addition, the tertiary populations of the α and β subunits differ substantially, with the β subunits showing a tendency towards R, and the α subunits showing a tendency towards T. Based on the simulation results, we present a transition pathway for coupled quaternary and tertiary transitions between the R and T conformations of Hb. PMID:20463873

Comparative Analysis of V-Akt Murine Thymoma Viral Oncogene Homolog 3 (AKT3) Gene between Cow and Buffalo Reveals Substantial Differences for Mastitis.

PubMed

Ullah, Farman; Bhattarai, Dinesh; Cheng, Zhangrui; Liang, Xianwei; Deng, Tingxian; Rehman, Zia Ur; Talpur, Hira Sajjad; Worku, Tesfaye; Brohi, Rahim Dad; Safdar, Muhammad; Ahmad, Muhammad Jamil; Salim, Mohammad; Khan, Momen; Ahmad, Hafiz Ishfaq; Zhang, Shujun

2018-01-01

AKT3 gene is a constituent of the serine/threonine protein kinase family and plays a crucial role in synthesis of milk fats and cholesterol by regulating activity of the sterol regulatory element binding protein (SREBP). AKT3 is highly conserved in mammals and its expression levels during the lactation periods of cattle are markedly increased. AKT3 is highly expressed in the intestine followed by mammary gland and it is also expressed in immune cells. It is involved in the TLR pathways as effectively as proinflammatory cytokines. The aims of this study were to investigate the sequences differences between buffalo and cow. Our results showed that there were substantial differences between buffalo and cow in some exons and noteworthy differences of the gene size in different regions. We also identified the important consensus sequence motifs, variation in 2000 upstream of ATG, substantial difference in the "3'UTR" region, and miRNA association in the buffalo sequences compared with the cow. In addition, genetic analyses, such as gene structure, phylogenetic tree, position of different motifs, and functional domains, were performed to establish their correlation with other species. This may indicate that a buffalo breed has potential resistance to disease, environment changes, and airborne microorganisms and some good production and reproductive traits.

The Influence of Training Phase on Error of Measurement in Jump Performance.

PubMed

Taylor, Kristie-Lee; Hopkins, Will G; Chapman, Dale W; Cronin, John B

2016-03-01

The purpose of this study was to calculate the coefficients of variation in jump performance for individual participants in multiple trials over time to determine the extent to which there are real differences in the error of measurement between participants. The effect of training phase on measurement error was also investigated. Six subjects participated in a resistance-training intervention for 12 wk with mean power from a countermovement jump measured 6 d/wk. Using a mixed-model meta-analysis, differences between subjects, within-subject changes between training phases, and the mean error values during different phases of training were examined. Small, substantial factor differences of 1.11 were observed between subjects; however, the finding was unclear based on the width of the confidence limits. The mean error was clearly higher during overload training than baseline training, by a factor of ×/÷ 1.3 (confidence limits 1.0-1.6). The random factor representing the interaction between subjects and training phases revealed further substantial differences of ×/÷ 1.2 (1.1-1.3), indicating that on average, the error of measurement in some subjects changes more than in others when overload training is introduced. The results from this study provide the first indication that within-subject variability in performance is substantially different between training phases and, possibly, different between individuals. The implications of these findings for monitoring individuals and estimating sample size are discussed.

Neighborhood-Level Social Processes and Substantiated Cases of Child Maltreatment

PubMed Central

Molnar, Beth E.; Goerge, Robert M.; Gilsanz, Paola; Hill, Andrea; Subramanian, SV; Holton, John K.; Duncan, Dustin T.; Beatriz, Elizabeth D.; Beardslee, William R.

2015-01-01

Child maltreatment is a preventable public health problem. Research has demonstrated that neighborhood structural factors (e.g. poverty, crime) can influence the proportion of a neighborhood’s children who are victims of maltreatment. A newer strategy is the identification of potentially modifiable social processes at the neighborhood level that can also influence maltreatment. Toward this end, this study examines neighborhood-level data (maltreatment cases substantiated by Illinois’ child protection agency, 1995–2005, social processes measured by the Project on Human Development in Chicago Neighborhoods, U.S. Census data, proportions of neighborhoods on public assistance, and crime data) that were linked across clusters of contiguous, relatively homogenous Chicago, IL census tracts with respect to racial/ethnic and socioeconomic composition. Our analysis—an ecological-level, repeated cross-sectional design utilizing random-intercept logit models— with a sensitivity analysis using spatial models to control for spatial autocorrelation – revealed consistent associations between neighborhood social processes and maltreatment. Neighborhoods higher in collective efficacy, intergenerational closure, and social networks, and lower in disorder had lower proportions of neglect, physical abuse, and sexual abuse substantiated cases, controlling for differences in structural factors. Higher collective efficacy and social network size also predicted a lower proportion of substance-exposed infants. This research indicates that strategies to mobilize neighborhood-level protective factors may decrease child maltreatment more effectively than individual and family-focused efforts alone. PMID:26684963

Comparative Analysis of V-Akt Murine Thymoma Viral Oncogene Homolog 3 (AKT3) Gene between Cow and Buffalo Reveals Substantial Differences for Mastitis

PubMed Central

Bhattarai, Dinesh; Cheng, Zhangrui; Liang, Xianwei; Deng, Tingxian; Rehman, Zia Ur; Talpur, Hira Sajjad; Worku, Tesfaye; Brohi, Rahim Dad; Safdar, Muhammad; Ahmad, Muhammad Jamil; Salim, Mohammad; Khan, Momen; Ahmad, Hafiz Ishfaq

2018-01-01

AKT3 gene is a constituent of the serine/threonine protein kinase family and plays a crucial role in synthesis of milk fats and cholesterol by regulating activity of the sterol regulatory element binding protein (SREBP). AKT3 is highly conserved in mammals and its expression levels during the lactation periods of cattle are markedly increased. AKT3 is highly expressed in the intestine followed by mammary gland and it is also expressed in immune cells. It is involved in the TLR pathways as effectively as proinflammatory cytokines. The aims of this study were to investigate the sequences differences between buffalo and cow. Our results showed that there were substantial differences between buffalo and cow in some exons and noteworthy differences of the gene size in different regions. We also identified the important consensus sequence motifs, variation in 2000 upstream of ATG, substantial difference in the “3′UTR” region, and miRNA association in the buffalo sequences compared with the cow. In addition, genetic analyses, such as gene structure, phylogenetic tree, position of different motifs, and functional domains, were performed to establish their correlation with other species. This may indicate that a buffalo breed has potential resistance to disease, environment changes, and airborne microorganisms and some good production and reproductive traits. PMID:29862252

Impact of the cation distribution homogeneity on the americium oxidation state in the U0.54Pu0.45Am0.01O2-x mixed oxide

NASA Astrophysics Data System (ADS)

Vauchy, Romain; Robisson, Anne-Charlotte; Martin, Philippe M.; Belin, Renaud C.; Aufore, Laurence; Scheinost, Andreas C.; Hodaj, Fiqiri

2015-01-01

The impact of the cation distribution homogeneity of the U0.54Pu0.45Am0.01O2-x mixed oxide on the americium oxidation state was studied by coupling X-ray diffraction (XRD), electron probe micro analysis (EPMA) and X-ray absorption spectroscopy (XAS). Oxygen-hypostoichiometric Am-bearing uranium-plutonium mixed oxide pellets were fabricated by two different co-milling based processes in order to obtain different cation distribution homogeneities. The americium was generated from β- decay of 241Pu. The XRD analysis of the obtained compounds did not reveal any structural difference between the samples. EPMA, however, revealed a high homogeneity in the cation distribution for one sample, and substantial heterogeneity of the U-Pu (so Am) distribution for the other. The difference in cation distribution was linked to a difference in Am chemistry as investigated by XAS, with Am being present at mixed +III/+IV oxidation state in the heterogeneous compound, whereas only Am(IV) was observed in the homogeneous compound. Previously reported discrepancies on Am oxidation states can hence be explained by cation distribution homogeneity effects.

The mutual causality analysis between the stock and futures markets

NASA Astrophysics Data System (ADS)

Yao, Can-Zhong; Lin, Qing-Wen

2017-07-01

In this paper we employ the conditional Granger causality model to estimate the information flow, and find that the improved model outperforms the Granger causality model in revealing the asymmetric correlation between stocks and futures in the Chinese market. First, we find that information flows estimated by Granger causality tests from futures to stocks are greater than those from stocks to futures. Additionally, average correlation coefficients capture some important characteristics between stock prices and information flows over time. Further, we find that direct information flows estimated by conditional Granger causality tests from stocks to futures are greater than those from futures to stocks. Besides, the substantial increases of information flows and direct information flows exhibit a certain degree of synchronism with the occurrences of important events. Finally, the comparative analysis with the asymmetric ratio and the bootstrap technique demonstrates the slight asymmetry of information flows and the significant asymmetry of direct information flows. It reveals that the information flows from futures to stocks are slightly greater than those in the reverse direction, while the direct information flows from stocks to futures are significantly greater than those in the reverse direction.

Lipid Profiling of the Arabidopsis Hypersensitive Response Reveals Specific Lipid Peroxidation and Fragmentation Processes: Biogenesis of Pimelic and Azelaic Acid1[C][W

PubMed Central

Zoeller, Maria; Stingl, Nadja; Krischke, Markus; Fekete, Agnes; Waller, Frank; Berger, Susanne; Mueller, Martin J.

2012-01-01

Lipid peroxidation (LPO) is induced by a variety of abiotic and biotic stresses. Although LPO is involved in diverse signaling processes, little is known about the oxidation mechanisms and major lipid targets. A systematic lipidomics analysis of LPO in the interaction of Arabidopsis (Arabidopsis thaliana) with Pseudomonas syringae revealed that LPO is predominantly confined to plastid lipids comprising galactolipid and triacylglyceride species and precedes programmed cell death. Singlet oxygen was identified as the major cause of lipid oxidation under basal conditions, while a 13-lipoxygenase (LOX2) and free radical-catalyzed lipid oxidation substantially contribute to the increase upon pathogen infection. Analysis of lox2 mutants revealed that LOX2 is essential for enzymatic membrane peroxidation but not for the pathogen-induced free jasmonate production. Despite massive oxidative modification of plastid lipids, levels of nonoxidized lipids dramatically increased after infection. Pathogen infection also induced an accumulation of fragmented lipids. Analysis of mutants defective in 9-lipoxygenases and LOX2 showed that galactolipid fragmentation is independent of LOXs. We provide strong in vivo evidence for a free radical-catalyzed galactolipid fragmentation mechanism responsible for the formation of the essential biotin precursor pimelic acid as well as of azelaic acid, which was previously postulated to prime the immune response of Arabidopsis. Our results suggest that azelaic acid is a general marker for LPO rather than a general immune signal. The proposed fragmentation mechanism rationalizes the pathogen-induced radical amplification and formation of electrophile signals such as phytoprostanes, malondialdehyde, and hexenal in plastids. PMID:22822212

Lipid profiling of the Arabidopsis hypersensitive response reveals specific lipid peroxidation and fragmentation processes: biogenesis of pimelic and azelaic acid.

PubMed

Zoeller, Maria; Stingl, Nadja; Krischke, Markus; Fekete, Agnes; Waller, Frank; Berger, Susanne; Mueller, Martin J

2012-09-01

Lipid peroxidation (LPO) is induced by a variety of abiotic and biotic stresses. Although LPO is involved in diverse signaling processes, little is known about the oxidation mechanisms and major lipid targets. A systematic lipidomics analysis of LPO in the interaction of Arabidopsis (Arabidopsis thaliana) with Pseudomonas syringae revealed that LPO is predominantly confined to plastid lipids comprising galactolipid and triacylglyceride species and precedes programmed cell death. Singlet oxygen was identified as the major cause of lipid oxidation under basal conditions, while a 13-lipoxygenase (LOX2) and free radical-catalyzed lipid oxidation substantially contribute to the increase upon pathogen infection. Analysis of lox2 mutants revealed that LOX2 is essential for enzymatic membrane peroxidation but not for the pathogen-induced free jasmonate production. Despite massive oxidative modification of plastid lipids, levels of nonoxidized lipids dramatically increased after infection. Pathogen infection also induced an accumulation of fragmented lipids. Analysis of mutants defective in 9-lipoxygenases and LOX2 showed that galactolipid fragmentation is independent of LOXs. We provide strong in vivo evidence for a free radical-catalyzed galactolipid fragmentation mechanism responsible for the formation of the essential biotin precursor pimelic acid as well as of azelaic acid, which was previously postulated to prime the immune response of Arabidopsis. Our results suggest that azelaic acid is a general marker for LPO rather than a general immune signal. The proposed fragmentation mechanism rationalizes the pathogen-induced radical amplification and formation of electrophile signals such as phytoprostanes, malondialdehyde, and hexenal in plastids.

Plasmodium vivax merozoite surface protein-3 alpha: a high-resolution marker for genetic diversity studies.

PubMed

Prajapati, Surendra Kumar; Joshi, Hema; Valecha, Neena

2010-06-01

Malaria, an ancient human infectious disease caused by five species of Plasmodium, among them Plasmodium vivax is the most widespread human malaria species and causes huge morbidity to its host. Identification of genetic marker to resolve higher genetic diversity for an ancient origin organism is a crucial task. We have analyzed genetic diversity of P. vivax field isolates using highly polymorphic antigen gene merozoite surface protein-3 alpha (msp-3 alpha) and assessed its suitability as high-resolution genetic marker for population genetic studies. 27 P. vivax field isolates collected during chloroquine therapeutic efficacy study at Chennai were analyzed for genetic diversity. PCR-RFLP was employed to assess the genetic variations using highly polymorphic antigen gene msp-3 alpha. We observed three distinct PCR alleles at msp-3 alpha, and among them allele A showed significantly high frequency (53%, chi2 = 8.22, p = 0.001). PCR-RFLP analysis revealed 14 and 17 distinct RFLP patterns for Hha1 and Alu1 enzymes respectively. Further, RFLP analysis revealed that allele A at msp-3 alpha is more diverse in the population compared with allele B and C. Combining Hha1 and Alu1 RFLP patterns revealed 21 distinct genotypes among 22 isolates reflects higher diversity resolution power of msp-3 alpha in the field isolates. P. vivax isolates from Chennai region revealed substantial amount of genetic diversity and comparison of allelic diversity with other antigen genes and microsatellites suggesting that msp-3 alpha could be a high-resolution marker for genetic diversity studies among P. vivax field isolates.

Distribution of triclosan-resistant genes in major pathogenic microorganisms revealed by metagenome and genome-wide analysis

PubMed Central

Khan, Raees; Roy, Nazish; Choi, Kihyuck

2018-01-01

The substantial use of triclosan (TCS) has been aimed to kill pathogenic bacteria, but TCS resistance seems to be prevalent in microbial species and limited knowledge exists about TCS resistance determinants in a majority of pathogenic bacteria. We aimed to evaluate the distribution of TCS resistance determinants in major pathogenic bacteria (N = 231) and to assess the enrichment of potentially pathogenic genera in TCS contaminated environments. A TCS-resistant gene (TRG) database was constructed and experimentally validated to predict TCS resistance in major pathogenic bacteria. Genome-wide in silico analysis was performed to define the distribution of TCS-resistant determinants in major pathogens. Microbiome analysis of TCS contaminated soil samples was also performed to investigate the abundance of TCS-resistant pathogens. We experimentally confirmed that TCS resistance could be accurately predicted using genome-wide in silico analysis against TRG database. Predicted TCS resistant phenotypes were observed in all of the tested bacterial strains (N = 17), and heterologous expression of selected TCS resistant genes from those strains conferred expected levels of TCS resistance in an alternative host Escherichia coli. Moreover, genome-wide analysis revealed that potential TCS resistance determinants were abundant among the majority of human-associated pathogens (79%) and soil-borne plant pathogenic bacteria (98%). These included a variety of enoyl-acyl carrier protein reductase (ENRs) homologues, AcrB efflux pumps, and ENR substitutions. FabI ENR, which is the only known effective target for TCS, was either co-localized with other TCS resistance determinants or had TCS resistance-associated substitutions. Furthermore, microbiome analysis revealed that pathogenic genera with intrinsic TCS-resistant determinants exist in TCS contaminated environments. We conclude that TCS may not be as effective against the majority of bacterial pathogens as previously presumed. Further, the excessive use of this biocide in natural environments may selectively enrich for not only TCS-resistant bacterial pathogens, but possibly for additional resistance to multiple antibiotics. PMID:29420585

Co-Inheritance Analysis within the Domains of Life Substantially Improves Network Inference by Phylogenetic Profiling

PubMed Central

Shin, Junha; Lee, Insuk

2015-01-01

Phylogenetic profiling, a network inference method based on gene inheritance profiles, has been widely used to construct functional gene networks in microbes. However, its utility for network inference in higher eukaryotes has been limited. An improved algorithm with an in-depth understanding of pathway evolution may overcome this limitation. In this study, we investigated the effects of taxonomic structures on co-inheritance analysis using 2,144 reference species in four query species: Escherichia coli, Saccharomyces cerevisiae, Arabidopsis thaliana, and Homo sapiens. We observed three clusters of reference species based on a principal component analysis of the phylogenetic profiles, which correspond to the three domains of life—Archaea, Bacteria, and Eukaryota—suggesting that pathways inherit primarily within specific domains or lower-ranked taxonomic groups during speciation. Hence, the co-inheritance pattern within a taxonomic group may be eroded by confounding inheritance patterns from irrelevant taxonomic groups. We demonstrated that co-inheritance analysis within domains substantially improved network inference not only in microbe species but also in the higher eukaryotes, including humans. Although we observed two sub-domain clusters of reference species within Eukaryota, co-inheritance analysis within these sub-domain taxonomic groups only marginally improved network inference. Therefore, we conclude that co-inheritance analysis within domains is the optimal approach to network inference with the given reference species. The construction of a series of human gene networks with increasing sample sizes of the reference species for each domain revealed that the size of the high-accuracy networks increased as additional reference species genomes were included, suggesting that within-domain co-inheritance analysis will continue to expand human gene networks as genomes of additional species are sequenced. Taken together, we propose that co-inheritance analysis within the domains of life will greatly potentiate the use of the expected onslaught of sequenced genomes in the study of molecular pathways in higher eukaryotes. PMID:26394049

Revealing barriers and facilitators to use a new genetic test: comparison of three user involvement methods.

PubMed

Rhebergen, Martijn D F; Visser, Maaike J; Verberk, Maarten M; Lenderink, Annet F; van Dijk, Frank J H; Kezic, Sanja; Hulshof, Carel T J

2012-10-01

We compared three common user involvement methods in revealing barriers and facilitators from intended users that might influence their use of a new genetic test. The study was part of the development of a new genetic test on the susceptibility to hand eczema for nurses. Eighty student nurses participated in five focus groups (n = 33), 15 interviews (n = 15) or questionnaires (n = 32). For each method, data were collected until saturation. We compared the mean number of items and relevant remarks that could influence the use of the genetic test obtained per method, divided by the number of participants in that method. Thematic content analysis was performed using MAXQDA software. The focus groups revealed 30 unique items compared to 29 in the interviews and 21 in the questionnaires. The interviews produced more items and relevant remarks per participant (1.9 and 8.4 pp) than focus groups (0.9 and 4.8 pp) or questionnaires (0.7 and 2.3 pp). All three involvement methods revealed relevant barriers and facilitators to use a new genetic test. Focus groups and interviews revealed substantially more items than questionnaires. Furthermore, this study suggests a preference for the use of interviews because the number of items per participant was higher than for focus groups and questionnaires. This conclusion may be valid for other genetic tests as well.

Kernel analysis of partial least squares (PLS) regression models.

PubMed

Shinzawa, Hideyuki; Ritthiruangdej, Pitiporn; Ozaki, Yukihiro

2011-05-01

An analytical technique based on kernel matrix representation is demonstrated to provide further chemically meaningful insight into partial least squares (PLS) regression models. The kernel matrix condenses essential information about scores derived from PLS or principal component analysis (PCA). Thus, it becomes possible to establish the proper interpretation of the scores. A PLS model for the total nitrogen (TN) content in multiple Thai fish sauces is built with a set of near-infrared (NIR) transmittance spectra of the fish sauce samples. The kernel analysis of the scores effectively reveals that the variation of the spectral feature induced by the change in protein content is substantially associated with the total water content and the protein hydration. Kernel analysis is also carried out on a set of time-dependent infrared (IR) spectra representing transient evaporation of ethanol from a binary mixture solution of ethanol and oleic acid. A PLS model to predict the elapsed time is built with the IR spectra and the kernel matrix is derived from the scores. The detailed analysis of the kernel matrix provides penetrating insight into the interaction between the ethanol and the oleic acid.

The decade 1989-1998 in Spanish psychology: an analysis of research in statistics, methodology, and psychometric theory.

PubMed

García-Pérez, M A

2001-11-01

This paper presents an analysis of research published in the decade 1989-1998 by Spanish faculty members in the areas of statistical methods, research methodology, and psychometric theory. Database search and direct correspondence with faculty members in Departments of Methodology across Spain rendered a list of 193 papers published in these broad areas by 82 faculty members. These and other faculty members had actually published 931 papers over the decade of analysis, but 738 of them addressed topics not appropriate for description in this report. Classification and analysis of these 193 papers revealed topics that have attracted the most interest (psychophysics, item response theory, analysis of variance, sequential analysis, and meta-analysis) as well as other topics that have received less attention (scaling, factor analysis, time series, and structural models). A significant number of papers also dealt with various methodological issues (software, algorithms, instrumentation, and techniques). A substantial part of this report is devoted to describing the issues addressed across these 193 papers--most of which are written in the Spanish language and published in Spanish journals--and some representative references are given.

Ethics Reporting in Biospecimen and Genetic Research: Current Practice and Suggestions for Changes

PubMed Central

Chin, William Wei Lim; Wieschowski, Susanne; Prokein, Jana; Illig, Thomas

2016-01-01

Modern approaches for research with human biospecimens employ a variety of substantially different types of ethics approval and informed consent. In most cases, standard ethics reporting such as “consent and approval was obtained” is no longer meaningful. A structured analysis of 120 biospecimen studies recently published in top journals revealed that more than 85% reported on consent and approval, but in more than 90% of cases, this reporting was insufficient and thus potentially misleading. Editorial policies, reporting guidelines, and material transfer agreements should include recommendations for meaningful ethics reporting in biospecimen research. Meaningful ethics reporting is possible without higher word counts and could support public trust as well as networked research. PMID:27483445

Silica in alkaline brines

USGS Publications Warehouse

Jones, B.F.; Rettig, S.L.; Eugster, H.P.

1967-01-01

Analysis of sodium carbonate-bicarbonate brines from closed basins in volcanic terranes of Oregon and Kenya reveals silica contents of up to 2700 parts per million at pH's higher than 10. These high concentrations of SiO 2 can be attributed to reaction of waters with silicates, and subsequent evaporative concentration accompanied by a rise in pH. Supersaturation with respect to amorphous silica may occur and persist for brines that are out of contact with silicate muds and undersaturated with respect to trona; correlation of SiO2 with concentration of Na and total CO2 support this interpretation. Addition of moredilute waters to alkaline brines may lower the pH and cause inorganic precipitation of substantial amounts of silica.

Tetrasomy and pentasomy of the X chromosome.

PubMed

Schoubben, Edith; Decaestecker, Karin; Quaegebeur, Koen; Danneels, Lode; Mortier, Geert; Cornette, Luc

2011-10-01

We describe a newborn girl with a life-threatening laryngomalacia and extreme hypotonia. Genetic analysis revealed the very rare genetic condition mosaicism of 48,XXXX and 49,XXXXX (50/50). We here state that the degree of early hypotonia constitutes an important early prognostic feature in this syndrome. The timely insertion of a gastrostomy is warranted in order to prevent aspiration. A karyotype is mandatory in female newborns with moderate to severe hypotonia in order to exclude polyploid mosaicism of the X chromosome. An 'overall prognosis' for 48,XXXX and 49,XXXXX girls is difficult to provide towards parents in line with a well-known, substantial variability in outcome for all polysomy X infants.

Urban adolescent high-risk sexual behavior: corroboration of focus group discussions through pile-sorting. The AIDS Youth Research Team.

PubMed

Stanton, B F; Aronson, R; Borgatti, S; Galbraith, J; Feigelman, S

1993-01-01

Risk activities for acquisition of the human immunodeficiency virus (HIV) remain prevalent among urban adolescents. While interdisciplinary approaches to examine the variables contributing to risk/protective behaviors have been promoted, strategies for such explorations require further formulation. Recently we employed focus group discussions to explore factors placing urban adolescents at risk for engaging in HIV risk behaviors. The focus group format enables substantial interaction on a topic in a limited time period, but does not always provide expression of the full range of behavioral options. In this study we investigated the use of pile-sorts for confirmation of impressions from focus group discussions among 57 urban youths aged 10-14. The pile-sorts revealed some support for most of the views expressed in the group discussions. However, the sorts revealed more variability in views than was expressed in the group discussions. Substantial gender and age-based differences in perceptions were revealed with potentially important intervention implications.

Bright monomeric photoactivatable red fluorescent protein for two-color super-resolution sptPALM of live cells.

PubMed

Subach, Fedor V; Patterson, George H; Renz, Malte; Lippincott-Schwartz, Jennifer; Verkhusha, Vladislav V

2010-05-12

Rapidly emerging techniques of super-resolution single-molecule microscopy of living cells rely on the continued development of genetically encoded photoactivatable fluorescent proteins. On the basis of monomeric TagRFP, we have developed a photoactivatable TagRFP protein that is initially dark but becomes red fluorescent after violet light irradiation. Compared to other monomeric dark-to-red photoactivatable proteins including PAmCherry, PATagRFP has substantially higher molecular brightness, better pH stability, substantially less sensitivity to blue light, and better photostability in both ensemble and single-molecule modes. Spectroscopic analysis suggests that PATagRFP photoactivation is a two-step photochemical process involving sequential one-photon absorbance by two distinct chromophore forms. True monomeric behavior, absence of green fluorescence, and single-molecule performance in live cells make PATagRFP an excellent protein tag for two-color imaging techniques, including conventional diffraction-limited photoactivation microscopy, super-resolution photoactivated localization microscopy (PALM), and single particle tracking PALM (sptPALM) of living cells. Two-color sptPALM imaging was demonstrated using several PATagRFP tagged transmembrane proteins together with PAGFP-tagged clathrin light chain. Analysis of the resulting sptPALM images revealed that single-molecule transmembrane proteins, which are internalized into a cell via endocytosis, colocalize in space and time with plasma membrane domains enriched in clathrin light-chain molecules.

Isolation and characterization of butachlor-catabolizing bacterial strain Stenotrophomonas acidaminiphila JS-1 from soil and assessment of its biodegradation potential.

PubMed

Dwivedi, S; Singh, B R; Al-Khedhairy, A A; Alarifi, S; Musarrat, J

2010-07-01

Isolation, characterization and assessment of butachlor-degrading potential of bacterial strain JS-1 in soil. Butachlor-degrading bacteria were isolated using enrichment culture technique. The morphological, biochemical and genetic characteristics based on 16S rDNA sequence homology and phylogenetic analysis confirmed the isolate as Stenotrophomonas acidaminiphila strain JS-1. The strain JS-1 exhibited substantial growth in M9 mineral salt medium supplemented with 3.2 mmol l(-1) butachlor, as a sole source of carbon and energy. The HPLC analysis revealed almost complete disappearance of butachlor within 20 days in soil at a rate constant of 0.17 day(-1) and half-life (t((1/2))) of 4.0 days, following the first-order rate kinetics. The strain JS-1 in stationary phase of culture also produced 21.0 microg ml(-1) of growth hormone indole acetic acid (IAA) in the presence of 500 microg ml(-1) of tryptophan. The IAA production was stimulated at lower concentrations of butachlor, whereas higher concentrations above 0.8 mmol l(-1) were found inhibitory. The isolate JS-1 characterized as Stenotrophomonas acidaminiphila was capable of utilizing butachlor as sole source of carbon and energy. Besides being an efficient butachlor degrader, it substantially produces IAA. The bacterial strain JS-1 has a potential for butachlor remediation with a distinctive auxiliary attribute of plant growth stimulation.

Adoption of robotics in a general surgery residency program: at what cost?

PubMed

Mehaffey, J Hunter; Michaels, Alex D; Mullen, Matthew G; Yount, Kenan W; Meneveau, Max O; Smith, Philip W; Friel, Charles M; Schirmer, Bruce D

2017-06-01

Robotic technology is increasingly being utilized by general surgeons. However, the impact of introducing robotics to surgical residency has not been examined. This study aims to assess the financial costs and training impact of introducing robotics at an academic general surgery residency program. All patients who underwent laparoscopic or robotic cholecystectomy, ventral hernia repair (VHR), and inguinal hernia repair (IHR) at our institution from 2011-2015 were identified. The effect of robotic surgery on laparoscopic case volume was assessed with linear regression analysis. Resident participation, operative time, hospital costs, and patient charges were also evaluated. We identified 2260 laparoscopic and 139 robotic operations. As the volume of robotic cases increased, the number of laparoscopic cases steadily decreased. Residents participated in all laparoscopic cases and 70% of robotic cases but operated from the robot console in only 21% of cases. Mean operative time was increased for robotic cholecystectomy (+22%), IHR (+55%), and VHR (+61%). Financial analysis revealed higher median hospital costs per case for robotic cholecystectomy (+$411), IHR (+$887), and VHR (+$1124) as well as substantial associated fixed costs. Introduction of robotic surgery had considerable negative impact on laparoscopic case volume and significantly decreased resident participation. Increased operative time and hospital costs are substantial. An institution must be cognizant of these effects when considering implementing robotics in departments with a general surgery residency program. Copyright © 2017 Elsevier Inc. All rights reserved.

HPTLC analysis of Scoparia dulcis Linn (Scrophulariaceae) and its larvicidal potential against dengue vector Aedes aegypti.

PubMed

Wankhar, Wankupar; Srinivasan, Sakthivel; Rathinasamy, Sheeladevi

2015-01-01

This study evaluates the larvicidal activity of Scoparia dulcis aqueous extract against dengue vector and determines its major chemical components. The extract was tested at various concentrations ranging from 0.1 to 2 mg/mL against Aedes aegypti larvae. The extracts displayed significant larvicidal efficacy against Ae. aegypt species after 24 h exposure revealing LC50 of 3.3835 (mg/mL) and LC90 of 5.7578 (mg/mL). Finger printing profile carried out by CAMAG automatic TLC sample applicator programmed through WIN CATS software revealed peaks with different Rf values for three different volumes injected: 16, 15 and 18 peaks were spotted for 3, 6 and 9 μL, respectively. Ascending order of Rf values was also ascertained for each peak recorded. This study clearly signifies that S. dulcis extract contains numerous compounds that are known to have larvicidal properties which clearly substantiates its efficacy on Ae. aegypti larvae.

Neotectonic activity and parameters of seismotectonic deformations of seismic belts in Northeast Asia

NASA Astrophysics Data System (ADS)

Imaeva, Lyudmila; Gusev, Georgy; Imaev, Valerii; Mel'nikova, Valentina

2017-10-01

The Arctic-Asian and Okhotsk-Chukotka seismic belts bordering the Kolyma-Chukotka crustal plate are the subject of our study aimed at reconstructing the stress-strain state of the crust and defining the types of seismotectonic deformation (STD) in the region. Based on the degrees of activity of geodynamic processes, the regional principles for ranking neotectonic structures were constrained, and the corresponding classes of the discussed neotectonic structures were substantiated. We analyzed the structural tectonic positions of the modern structures, their deep structure parameters, and the systems of active faults in the Laptev, Kharaulakh, Koryak, and Chukotka segments and Chersky seismotectonic zone, as well as the tectonic stress fields revealed by tectonophysical analysis of the Late Cenozoic faults and folds. From the earthquake focal mechanisms, the average seismotectonic strain tensors were estimated. Using the geological, geostructural, geophysical and GPS data, and corresponding average tensors, the directions of the principal stress axes were determined. A regularity in the changes of tectonic settings in the Northeast Arctic was revealed.

"I Treat Him as a Normal Patient": Unveiling the Normalization Coping Strategy Among Formal Caregivers of Persons With Dementia and Its Implications for Person-Centered Care.

PubMed

Bentwich, Miriam Ethel; Dickman, Nomy; Oberman, Amitai; Bokek-Cohen, Ya'arit

2017-11-01

Currently, 47 million people have dementia, worldwide, often requiring paid care by formal caregivers. Research regarding family caregivers suggests normalization as a model for coping with negative emotional outcomes in caring for a person with dementia (PWD). The study aims to explore whether normalization coping mechanism exists among formal caregivers, reveal differences in its application among cross-cultural caregivers, and examine how this coping mechanism may be related to implementing person-centered care for PWDs. Content analysis of interviews with 20 formal caregivers from three cultural groups (Jews born in Israel [JI], Arabs born in Israel [AI], Russian immigrants [RI]), attending to PWDs. We extracted five normalization modes, revealing AI caregivers had substantially more utterances of normalization expressions than their colleagues. The normalization modes most commonly expressed by AI caregivers relate to the personhood of PWDs. These normalization modes may enhance formal caregivers' ability to employ person-centered care.

Palynostratigraphy of the Upper Cretaceous and Paleogene Deposits in the South of Western Siberia by Example of Russkaya Polyana Boreholes, Omsk Trough

NASA Astrophysics Data System (ADS)

Lebedeva, N. K.; Kuz'mina, O. B.

2018-01-01

The detailed study of Boreholes 8, 10, and 2 in the Russkaya Polyana district (Omsk Trough) made it possible to reveal the complex structure of the Upper Cretaceous sediments formed in unstable conditions of the marginal part of the Western Siberian basin. The Pokur, Kuznetsovo, Ipatovo, Slavgorod, and Gan'kino formations were subjected to palynological analysis and substantiation of their Late Cretaceous age. Eight biostratigraphic units with dinocysts and five units with spores and pollen from the Albian to the Maastrichtian were identified. The joint application of biostratigraphic and magnetostratigraphic methods made it possible to reveal the stratigraphic breaks in the studied sedimentary stratum and to estimate their scope. The age of the Lower Lyulinvor Subformation was specified in the marginal part of the Omsk Trough. The ingression traces of the Western Siberian basin in the Albian were found for the first time in the considered region.

Functional wiring of the yeast kinome revealed by global analysis of genetic network motifs

PubMed Central

Sharifpoor, Sara; van Dyk, Dewald; Costanzo, Michael; Baryshnikova, Anastasia; Friesen, Helena; Douglas, Alison C.; Youn, Ji-Young; VanderSluis, Benjamin; Myers, Chad L.; Papp, Balázs; Boone, Charles; Andrews, Brenda J.

2012-01-01

A combinatorial genetic perturbation strategy was applied to interrogate the yeast kinome on a genome-wide scale. We assessed the global effects of gene overexpression or gene deletion to map an integrated genetic interaction network of synthetic dosage lethal (SDL) and loss-of-function genetic interactions (GIs) for 92 kinases, producing a meta-network of 8700 GIs enriched for pathways known to be regulated by cognate kinases. Kinases most sensitive to dosage perturbations had constitutive cell cycle or cell polarity functions under standard growth conditions. Condition-specific screens confirmed that the spectrum of kinase dosage interactions can be expanded substantially in activating conditions. An integrated network composed of systematic SDL, negative and positive loss-of-function GIs, and literature-curated kinase–substrate interactions revealed kinase-dependent regulatory motifs predictive of novel gene-specific phenotypes. Our study provides a valuable resource to unravel novel functional relationships and pathways regulated by kinases and outlines a general strategy for deciphering mutant phenotypes from large-scale GI networks. PMID:22282571

Personal space smoking restrictions among African Americans.

PubMed

King, Gary; Mallett, Robyn; Kozlowski, Lynn; Bendel, Robert B; Nahata, Sunny

2005-01-01

This paper investigates the association between implementing a personal space smoking restriction for the home or automobile, and various sociodemographic, social, behavioral, and attitudinal variables. Approximately 1000 African-American adults (aged >18 years) residing in non-institutionalized settings were randomly selected using a cross-sectional stratified cluster sample of ten U.S. congressional districts represented by African Americans. A 62.0% and 70.4% ban was found, respectively, on smoking in homes and cars. Multivariate analysis revealed that region, marital status, number of friends who smoked, beliefs about environmental tobacco smoke (ETS), and smoking status predicted home smoking bans, while age, number of children in household, number of friends who smoked, and beliefs about ETS and smoking status predicted car smoking bans. Results suggest that a substantial segment of African Americans have accepted and translated public policy concerns about ETS into practice and reveal other variables that could be targeted in future interventions to increase implementation of personal space smoking restrictions.

Single-Cell RNA-Sequencing Reveals a Continuous Spectrum of Differentiation in Hematopoietic Cells.

PubMed

Macaulay, Iain C; Svensson, Valentine; Labalette, Charlotte; Ferreira, Lauren; Hamey, Fiona; Voet, Thierry; Teichmann, Sarah A; Cvejic, Ana

2016-02-02

The transcriptional programs that govern hematopoiesis have been investigated primarily by population-level analysis of hematopoietic stem and progenitor cells, which cannot reveal the continuous nature of the differentiation process. Here we applied single-cell RNA-sequencing to a population of hematopoietic cells in zebrafish as they undergo thrombocyte lineage commitment. By reconstructing their developmental chronology computationally, we were able to place each cell along a continuum from stem cell to mature cell, refining the traditional lineage tree. The progression of cells along this continuum is characterized by a highly coordinated transcriptional program, displaying simultaneous suppression of genes involved in cell proliferation and ribosomal biogenesis as the expression of lineage specific genes increases. Within this program, there is substantial heterogeneity in the expression of the key lineage regulators. Overall, the total number of genes expressed, as well as the total mRNA content of the cell, decreases as the cells undergo lineage commitment. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Gene Expression Architecture of Mouse Dorsal and Tail Skin Reveals Functional Differences in Inflammation and Cancer.

PubMed

Quigley, David A; Kandyba, Eve; Huang, Phillips; Halliwill, Kyle D; Sjölund, Jonas; Pelorosso, Facundo; Wong, Christine E; Hirst, Gillian L; Wu, Di; Delrosario, Reyno; Kumar, Atul; Balmain, Allan

2016-07-26

Inherited germline polymorphisms can cause gene expression levels in normal tissues to differ substantially between individuals. We present an analysis of the genetic architecture of normal adult skin from 470 genetically unique mice, demonstrating the effect of germline variants, skin tissue location, and perturbation by exogenous inflammation or tumorigenesis on gene signaling pathways. Gene networks related to specific cell types and signaling pathways, including sonic hedgehog (Shh), Wnt, Lgr family stem cell markers, and keratins, differed at these tissue sites, suggesting mechanisms for the differential susceptibility of dorsal and tail skin to development of skin diseases and tumorigenesis. The Pten tumor suppressor gene network is rewired in premalignant tumors compared to normal tissue, but this response to perturbation is lost during malignant progression. We present a software package for expression quantitative trait loci (eQTL) network analysis and demonstrate how network analysis of whole tissues provides insights into interactions between cell compartments and signaling molecules. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Characterisation of two-stage ignition in diesel engine-relevant thermochemical conditions using direct numerical simulation

DOE PAGES

Krisman, Alex; Hawkes, Evatt R.; Talei, Mohsen; ...

2016-08-30

With the goal of providing a more detailed fundamental understanding of ignition processes in diesel engines, this study reports analysis of a direct numerical simulation (DNS) database. In the DNS, a pseudo turbulent mixing layer of dimethyl ether (DME) at 400 K and air at 900 K is simulated at a pressure of 40 atmospheres. At these conditions, DME exhibits a two-stage ignition and resides within the negative temperature coefficient (NTC) regime of ignition delay times, similar to diesel fuel. The analysis reveals a complex ignition process with several novel features. Autoignition occurs as a distributed, two-stage event. The high-temperaturemore » stage of ignition establishes edge flames that have a hybrid premixed/autoignition flame structure similar to that previously observed for lifted laminar flames at similar thermochemical conditions. In conclusion, a combustion mode analysis based on key radical species illustrates the multi-stage and multi-mode nature of the ignition process and highlights the substantial modelling challenge presented by diesel combustion.« less

SWOT analysis: strengths, weaknesses, opportunities and threats of the Israeli Smallpox Revaccination Program.

PubMed

Huerta, Michael; Balicer, Ran D; Leventhal, Alex

2003-01-01

During September 2002, Israel began its current revaccination program against smallpox, targeting previously vaccinated "first responders" among medical and emergency workers. In order to identify the potential strengths and weaknesses of this program and the conditions under which critical decisions were reached, we conducted a SWOT analysis of the current Israeli revaccination program, designed to identify its intrinsic strengths and weaknesses, as well as opportunities for its success and threats against it. SWOT analysis--a practical tool for the study of public health policy decisions and the social and political contexts in which they are reached--revealed clear and substantial strengths and weaknesses of the current smallpox revaccination program, intrinsic to the vaccine itself. A number of threats were identified that may jeopardize the success of the current program, chief among them the appearance of severe complications of vaccination. Our finding of a lack of a generation of knowledge on smallpox vaccination highlights the need for improved physician education and dissipation of misconceptions that are prevalent in the public today.

Cancer-Related Psychological Distress: A Concept Analysis.

PubMed

Gundelach, Amy; Henry, Barb

2016-12-01

Cancer-related psychological distress, as a concept, has limited research literature substantiation. Several studies report that patients with cancer suffer from significant psychological distress; however, the description of the concept of cancer-related psychological distress has not been clearly described. Theoretical work based on the concept is also unclear. This article is a report on the concept of cancer-related psychological distress to clarify the concept as separate from non-cancer-related psychological distress and promote the use of the term in nursing practice and research across the cancer trajectory. This article used a content analysis to examine the literature. The literature review for this article used CINAHL®, PsycINFO®, and PubMed to search publications from 1999-2016. Content analysis of the literature revealed that the term psychological distress was used often with regard to distress in patients with cancer, but the concept of cancer-related psychological distress was not clearly defined. Four attributes encompass the concept of cancer-related psychological distress.

Genome-wide analysis of gene expression of EMS-induced short fiber mutant Ligon lintless-y (liy) in cotton (Gossypium hirsutum L.).

PubMed

Naoumkina, Marina; Bechere, Efrem; Fang, David D; Thyssen, Gregory N; Florane, Christopher B

2017-07-01

In this work we describe a chemically-induced short fiber mutant cotton line, Ligon-lintless-y (li y ), which is controlled by a single recessive locus and affects multiple traits, including height of the plant, and length and maturity of fiber. An RNAseq analysis was used to evaluate global transcriptional changes during cotton fiber development at 3, 8 and 16days post anthesis. We found that 613, 2629 and 3397 genes were significantly down-regulated, while 2700, 477 and 3260 were significantly up-regulated in li y at 3, 8 and 16 DPA. Gene set enrichment analysis revealed that many metabolic pathways, including carbohydrate, cell wall, hormone metabolism and transport were substantially altered in li y developing fibers. We discuss perturbed expression of genes involved in signal transduction and biosynthesis of phytohormones, such as auxin, abscisic acid, gibberellin and ethylene. The results of this study provide new insights into transcriptional regulation of cotton fiber development. Published by Elsevier Inc.

A new rational-based optimal design strategy of ship structure based on multi-level analysis and super-element modeling method

NASA Astrophysics Data System (ADS)

Sun, Li; Wang, Deyu

2011-09-01

A new multi-level analysis method of introducing the super-element modeling method, derived from the multi-level analysis method first proposed by O. F. Hughes, has been proposed in this paper to solve the problem of high time cost in adopting a rational-based optimal design method for ship structural design. Furthermore, the method was verified by its effective application in optimization of the mid-ship section of a container ship. A full 3-D FEM model of a ship, suffering static and quasi-static loads, was used as the analyzing object for evaluating the structural performance of the mid-ship module, including static strength and buckling performance. Research results reveal that this new method could substantially reduce the computational cost of the rational-based optimization problem without decreasing its accuracy, which increases the feasibility and economic efficiency of using a rational-based optimal design method in ship structural design.

Geographic variation in sexual behavior can explain geospatial heterogeneity in the severity of the HIV epidemic in Malawi.

PubMed

Palk, Laurence; Blower, Sally

2018-02-09

In sub-Saharan Africa, where ~ 25 million individuals are infected with HIV and transmission is predominantly heterosexual, there is substantial geographic variation in the severity of epidemics. This variation has yet to be explained. Here, we propose that it is due to geographic variation in the size of the high-risk group (HRG): the group with a high number of sex partners. We test our hypothesis by conducting a geospatial analysis of data from Malawi, where ~ 13% of women and ~ 8% of men are infected with HIV. We used georeferenced HIV testing and behavioral data from ~ 14,000 participants of a nationally representative population-level survey: the 2010 Malawi Demographic and Health Survey (MDHS). We constructed gender-stratified epidemic surface prevalence (ESP) maps by spatially smoothing and interpolating the HIV testing data. We used the behavioral data to construct gender-stratified risk maps that reveal geographic variation in the size of the HRG. We tested our hypothesis by fitting gender-stratified spatial error regression (SER) models to the MDHS data. The ESP maps show considerable geographic variation in prevalence: 1-29% (women), 1-20% (men). Risk maps reveal substantial geographic variation in the size of the HRG: 0-40% (women), 16-58% (men). Prevalence and the size of the HRG are highest in urban centers. However, the majority of HIV-infected individuals (~75% of women, ~ 80% of men) live in rural areas, as does most of the HRG (~ 80% of women, ~ 85% of men). We identify a significant (P < 0.001) geospatial relationship linking the size of the HRG with prevalence: the greater the size, the higher the prevalence. SER models show HIV prevalence in women is expected to exceed the national average in districts where > 20% of women are in the HRG. Most importantly, the SER models show that geographic variation in the size of the HRG can explain a substantial proportion (73% for women, 67% for men) of the geographic variation in epidemic severity. Taken together, our results provide substantial support for our hypothesis. They provide a potential mechanistic explanation for the geographic variation in the severity of the HIV epidemic in Malawi and, potentially, in other countries in sub-Saharan Africa.

Aging effects on vertical graphene nanosheets and their thermal stability

NASA Astrophysics Data System (ADS)

Ghosh, S.; Polaki, S. R.; Ajikumar, P. K.; Krishna, N. G.; Kamruddin, M.

2018-03-01

The present study investigates environmental aging effects and thermal stability of vertical graphene nanosheets (VGN). Self-organized VGN is synthesized by plasma enhanced chemical vapor deposition and exposed to ambient conditions over 6-month period to examine its aging behavior. A systematic inspection is carried out on morphology, chemical structure, wettability and electrical property by scanning electron microscopy, Raman spectroscopy, X-ray photoelectron spectroscopy, water contact angle and four-probe resistivity measurements at regular intervals, respectively. Detailed microscopic and spectroscopic analysis substantiated the retention of graphitic quality and surface chemistry of VGN over the test period. An unchanged sheet resistance and hydrophobicity reveals its electrical and wetting stability over the time, respectively. Thermogravimetric analysis ensures an excellent thermal stability of VGN up to 575 °C in ambient atmosphere. These findings of long-term morphological, structural, wetting, electrical and thermal stability of VGN validate their potential utilization for the next-generation device applications.

Genome-wide network analysis of Wnt signaling in three pediatric cancers

NASA Astrophysics Data System (ADS)

Bao, Ju; Lee, Ho-Jin; Zheng, Jie J.

2013-10-01

Genomic structural alteration is common in pediatric cancers, and analysis of data generated by the Pediatric Cancer Genome Project reveals such tumor-related alterations in many Wnt signaling-associated genes. Most pediatric cancers are thought to arise within developing tissues that undergo substantial expansion during early organ formation, growth and maturation, and Wnt signaling plays an important role in this development. We examined three pediatric tumors--medullobastoma, early T-cell precursor acute lymphoblastic leukemia, and retinoblastoma--that show multiple genomic structural variations within Wnt signaling pathways. We mathematically modeled this pathway to investigate the effects of cancer-related structural variations on Wnt signaling. Surprisingly, we found that an outcome measure of canonical Wnt signaling was consistently similar in matched cancer cells and normal cells, even in the context of different cancers, different mutations, and different Wnt-related genes. Our results suggest that the cancer cells maintain a normal level of Wnt signaling by developing multiple mutations.

Genetic variation in IBD: progress, clues to pathogenesis and possible clinical utility

PubMed Central

Ye, Byong Duk; McGovern, Dermot P.B.

2016-01-01

Epidemiological and clinical studies have suggested that the pathogenesis of inflammatory bowel disease (IBD) is strongly influenced by genetic predisposition. Beyond the limitations of linkage analysis, multiple genome-wide association studies, their meta-analyses, and targeted genotyping array techniques have broadened our understanding of the genetic architecture of IBD. Currently, over 200 single nucleotide polymorphisms are known to be associated with susceptibility to IBD and through functional analysis of genes and loci, a substantial proportion of pathophysiologic mechanisms have been revealed. However, because only a modest fraction of predicted heritability can be explained by known genes/loci, additional strategies are needed including the identification of rare variants with large effect sizes to help explain the missing heritability. Considerable progress is also being made on applying outcomes of genetic research in diagnostics, classification, prognostics, and the development of new therapeutics of IBD. PMID:27156530

Local structural distortion and electrical transport properties of Bi(Ni 1/2Ti 1/2)O 3 perovskite under high pressure

DOE PAGES

Zhu, Jinlong; Yang, Liuxiang; Wang, Hsiu -Wen; ...

2015-12-16

Perovskite-structure materials generally exhibit local structural distortions that are distinct from long-range, average crystal structure. The characterization of such distortion is critical to understanding the structural and physical properties of materials. In this work, we combined Pair Distribution Function (PDF) technique with Raman spectroscopy and electrical resistivity measurement to study Bi(Ni 1/2Ti 1/2)O 3 perovskite under high pressure. PDF analysis reveals strong local structural distortion at ambient conditions. As pressure increases, the local structure distortions are substantially suppressed and eventually vanish around 4 GPa, leading to concurrent changes in the electronic band structure and anomalies in the electrical resistivity. Wemore » find, consistent with PDF analysis, Raman spectroscopy data suggest that the local structure changes to a higher ordered state at pressures above 4 GPa.« less

More emotional facial expressions during episodic than during semantic autobiographical retrieval.

PubMed

El Haj, Mohamad; Antoine, Pascal; Nandrino, Jean Louis

2016-04-01

There is a substantial body of research on the relationship between emotion and autobiographical memory. Using facial analysis software, our study addressed this relationship by investigating basic emotional facial expressions that may be detected during autobiographical recall. Participants were asked to retrieve 3 autobiographical memories, each of which was triggered by one of the following cue words: happy, sad, and city. The autobiographical recall was analyzed by a software for facial analysis that detects and classifies basic emotional expressions. Analyses showed that emotional cues triggered the corresponding basic facial expressions (i.e., happy facial expression for memories cued by happy). Furthermore, we dissociated episodic and semantic retrieval, observing more emotional facial expressions during episodic than during semantic retrieval, regardless of the emotional valence of cues. Our study provides insight into facial expressions that are associated with emotional autobiographical memory. It also highlights an ecological tool to reveal physiological changes that are associated with emotion and memory.

Local structural distortion and electrical transport properties of Bi(Ni1/2Ti1/2)O3 perovskite under high pressure.

PubMed

Zhu, Jinlong; Yang, Liuxiang; Wang, Hsiu-Wen; Zhang, Jianzhong; Yang, Wenge; Hong, Xinguo; Jin, Changqing; Zhao, Yusheng

2015-12-16

Perovskite-structure materials generally exhibit local structural distortions that are distinct from long-range, average crystal structure. The characterization of such distortion is critical to understanding the structural and physical properties of materials. In this work, we combined Pair Distribution Function (PDF) technique with Raman spectroscopy and electrical resistivity measurement to study Bi(Ni1/2Ti1/2)O3 perovskite under high pressure. PDF analysis reveals strong local structural distortion at ambient conditions. As pressure increases, the local structure distortions are substantially suppressed and eventually vanish around 4 GPa, leading to concurrent changes in the electronic band structure and anomalies in the electrical resistivity. Consistent with PDF analysis, Raman spectroscopy data suggest that the local structure changes to a higher ordered state at pressures above 4 GPa.

Inferring Biological Structures from Super-Resolution Single Molecule Images Using Generative Models

PubMed Central

Maji, Suvrajit; Bruchez, Marcel P.

2012-01-01

Localization-based super resolution imaging is presently limited by sampling requirements for dynamic measurements of biological structures. Generating an image requires serial acquisition of individual molecular positions at sufficient density to define a biological structure, increasing the acquisition time. Efficient analysis of biological structures from sparse localization data could substantially improve the dynamic imaging capabilities of these methods. Using a feature extraction technique called the Hough Transform simple biological structures are identified from both simulated and real localization data. We demonstrate that these generative models can efficiently infer biological structures in the data from far fewer localizations than are required for complete spatial sampling. Analysis at partial data densities revealed efficient recovery of clathrin vesicle size distributions and microtubule orientation angles with as little as 10% of the localization data. This approach significantly increases the temporal resolution for dynamic imaging and provides quantitatively useful biological information. PMID:22629348

Observations of Terrestrial Nightglow (Meinel Bands) at King

NASA Astrophysics Data System (ADS)

Won, Young-In; Cho, Young-Min; Lee, Bang Yong; Kim, Jhoon; Chung, Jong Kyun; Kim, Yong Ha

1999-12-01

A Fourier Transform Spectrometer was used to study upper mesospheric thermodynamic by observing the hydroxyl(OH) emission. Rocket-born and satellited-born photometers place the peak emission near 87 μm. The instrument was installed in February 1999 at King Sejong station (62.22 deg S,301.25 deg E), Antarctica and has been in routine operation since then. An intensive operational effort has resulted in a substantial data between April and June, 1999. A harmonic analysis was carried out to examine information on the tidal characteristics. The measured amplitudes of the 12-hour oscillation are in the range of 2.4-3.7 K, which are in resonable agreement with theoretical model outputs. The harmonic analysis also revealed 8-hour oscillation which is not expected from the traditional theoretical studies. In addition, the observed 8-hour oscillations are apparent and sometimes dominate the temperature variation in the upper mesosphere.

The role of reflection in the effects of community service on adolescent development: a meta-analysis.

PubMed

van Goethem, Anne; van Hoof, Anne; Orobio de Castro, Bram; Van Aken, Marcel; Hart, Daniel

2014-01-01

This meta-analysis assessed the effect of community service on adolescent development and the moderation of this effect by reflection, community service, and adolescent characteristics to explicate the mechanisms underlying community service effects. Random effects analyses, based on 49 studies (24,477 participants, 12-20 years old), revealed that community service had positive effects on academic, personal, social, and civic outcomes. Moderation analyses indicated that reflection was essential; the effect for studies that include reflection was substantial (mean ES = .41) while community service in the absence of reflection yielded negligible benefits (mean ES = .05). Effects increased when studies include more frequent reflection and community service, reflection on academic content, and older adolescents. These findings have implications for understanding and improving community service. © 2014 The Authors. Child Development © 2014 Society for Research in Child Development, Inc.

Influenza Vaccine Uptake, Hand Hygiene Practices, and Perceived Barriers in Decision Making.

PubMed

Stedman-Smith, Maggie; Kingsbury, Diana M; Dubois, Cathy L Z; Grey, Scott F

2017-01-01

The annual costs of influenza are in the billions of dollars, with employers bearing substantial burdens. Yet, influenza vaccine uptake is sub-optimal. A random survey was administered to employees at a Midwestern public university using mixed quantitative and qualitative methods to identify the rate, characteristics, and barriers of self-reported flu vaccine uptake during March-April of 2012. The lowest uptake was among adults, ages 18 to 49 (29.8%), even though they are included in universal recommendations. Multiple regression analysis adjusted for demographic confounders showed an increase in self-identified protective hand hygiene behavior among those who reported influenza vaccine uptake compared with those who did not. Qualitative thematic analysis revealed contextual accounts of why vaccine uptake was declined including structural, perceptual, and knowledge barriers. Implementation and evaluation of novel multicomponent worksite vaccine interventions tailored to reach young and middle-aged employees including utilization of risk communication is needed to facilitate increased uptake.

Biosensor for the detection of Listeria monocytogenes: emerging trends.

PubMed

Soni, Dharmendra Kumar; Ahmad, Rafiq; Dubey, Suresh Kumar

2018-05-23

The early detection of Listeria monocytogenes (L. monocytogenes) and understanding the disease burden is of paramount interest. The failure to detect pathogenic bacteria in the food industry may have terrible consequences, and poses deleterious effects on human health. Therefore, integration of methods to detect and trace the route of pathogens along the entire food supply network might facilitate elucidation of the main contamination sources. Recent research interest has been oriented towards the development of rapid and affordable pathogen detection tools/techniques. An innovative and new approach like biosensors has been quite promising in revealing the foodborne pathogens. In spite of the existing knowledge, advanced research is still needed to substantiate the expeditious nature and sensitivity of biosensors for rapid and in situ analysis of foodborne pathogens. This review summarizes recent developments in optical, piezoelectric, cell-based, and electrochemical biosensors for Listeria sp. detection in clinical diagnostics, food analysis, and environmental monitoring, and also lists their drawbacks and advantages.

In Vivo Noninvasive Analysis of Human Forearm Muscle Function and Fatigue: Applications to EVA Operations and Training Maneuvers

NASA Technical Reports Server (NTRS)

Fotedar, L. K.; Marshburn, T.; Quast, M. J.; Feeback, D. L.

1999-01-01

Forearm muscle fatigue is one of the major limiting factors affecting endurance during performance of deep-space extravehicular activity (EVA) by crew members. Magnetic resonance (MR) provides in vivo noninvasive analysis of tissue level metabolism and fluid exchange dynamics in exercised forearm muscles through the monitoring of proton magnetic resonance imaging (MRI) and phosphorus magnetic resonance spectroscopy (P-31-MRS) parameter variations. Using a space glove box and EVA simulation protocols, we conducted a preliminary MRS/MRI study in a small group of human test subjects during submaximal exercise and recovery and following exhaustive exercise. In assessing simulated EVA-related muscle fatigue and function, this pilot study revealed substantial changes in the MR image longitudinal relaxation times (T2) as an indicator of specific muscle activation and proton flux as well as changes in spectral phosphocreatine-to-phosphate (PCr/Pi) levels as a function of tissue bioenergetic potential.

Report explores Congress' science policy

NASA Astrophysics Data System (ADS)

Jones, Richard

Scientists interested in understanding how Congress develops science policy would find it useful to read a recent report by the Carnegie Commission on Science, Technology, and Government. “Science, Technology and Congress: Analysis and Advice from the Congressional Support Agencies” contains revealing insights about the often hard-pressed system that Congress uses to analyze science and technology issues.“Congress is on the front line of many battles over the directions of science and technology,” says the 70-page report. “The quality of congressional decisions on these issues often depends on the quality and usefulness of information and analysis made available to Congress.” The report describes the overwhelming amount of information received by members of Congress, few of whom have “substantial training or experience” in science and technology. Making this information understandable and useful is the role of the Office of Technology Assessment, the Congressional Research Service, the General Accounting Office, and the Congressional Budget Office.

Electronic properties of 8 - Pmmn borophene

DOE PAGES

Lopez-Bezanilla, Alejandro; Littlewood, Peter B.

2016-06-15

First-principles calculations on monolayer 8-Pmmn borophene are reported to reveal unprecedented electronic properties in a two-dimensional material. Based on a Born effective charge analysis, 8-Pmmn borophene is the first single-element-based monolayered material exhibiting two sublattices with substantial ionic features. We observed Dirac cones are actually formed by the p(z) orbitals of one of the inequivalent sublattices composed of uniquely four atoms, yielding an underlying hexagonal network topologically equivalent to distorted graphene. One significant physical outcome of this effect includes the possibility of converting metallic 8-Pmmn borophene into an indirect band gap semiconductor by means of external shear stress. Furthermore, themore » stability of the strained structures are supported by a phonon frequency analysis. The Dirac cones are sensitive to the formation of vacancies only in the inequivalent sublattice electronically active at the Fermi level.« less

National and International Security Applications of Cryogenic Detectors—Mostly Nuclear Safeguards

NASA Astrophysics Data System (ADS)

Rabin, Michael W.

2009-12-01

As with science, so with security—in both arenas, the extraordinary sensitivity of cryogenic sensors enables high-confidence detection and high-precision measurement even of the faintest signals. Science applications are more mature, but several national and international security applications have been identified where cryogenic detectors have high potential payoff. International safeguards and nuclear forensics are areas needing new technology and methods to boost speed, sensitivity, precision and accuracy. Successfully applied, improved nuclear materials analysis will help constrain nuclear materials diversion pathways and contribute to treaty verification. Cryogenic microcalorimeter detectors for X-ray, gamma-ray, neutron, and alpha-particle spectrometry are under development with these aims in mind. In each case the unsurpassed energy resolution of microcalorimeters reveals previously invisible spectral features of nuclear materials. Preliminary results of quantitative analysis indicate substantial improvements are still possible, but significant work will be required to fully understand the ultimate performance limits.

ENSO controls interannual fire activity in southeast Australia

NASA Astrophysics Data System (ADS)

Mariani, M.; Fletcher, M.-S.; Holz, A.; Nyman, P.

2016-10-01

El Niño-Southern Oscillation (ENSO) is the main mode controlling the variability in the ocean-atmosphere system in the South Pacific. While the ENSO influence on rainfall regimes in the South Pacific is well documented, its role in driving spatiotemporal trends in fire activity in this region has not been rigorously investigated. This is particularly the case for the highly flammable and densely populated southeast Australian sector, where ENSO is a major control over climatic variability. Here we conduct the first region-wide analysis of how ENSO controls fire activity in southeast Australia. We identify a significant relationship between ENSO and both fire frequency and area burnt. Critically, wavelet analyses reveal that despite substantial temporal variability in the ENSO system, ENSO exerts a persistent and significant influence on southeast Australian fire activity. Our analysis has direct application for developing robust predictive capacity for the increasingly important efforts at fire management.

29 CFR 1990.145 - Consideration of substantial new issues or substantial new evidence.

Code of Federal Regulations, 2010 CFR

2010-07-01

... substance any substantial new issues upon which the Secretary did not reach a conclusion in the rulemaking... or an Advance Notice of Proposed Rulemaking; (v) A detailed statement and analysis as to why the...

29 CFR 1990.145 - Consideration of substantial new issues or substantial new evidence.

Code of Federal Regulations, 2011 CFR

2011-07-01

... substance any substantial new issues upon which the Secretary did not reach a conclusion in the rulemaking... or an Advance Notice of Proposed Rulemaking; (v) A detailed statement and analysis as to why the...

E3 Value Stream Mapping How-to Guide

EPA Pesticide Factsheets

Presentations and PDFs on value stream mapping for various sectors, which can reveal substantial opportunities to reduce costs, enhance production flow, save time, reduce inventory, and improve environmental performance.

Imaging the fate of histone Cse4 reveals de novo replacement in S phase and subsequent stable residence at centromeres

PubMed Central

Wisniewski, Jan; Hajj, Bassam; Chen, Jiji; Mizuguchi, Gaku; Xiao, Hua; Wei, Debbie; Dahan, Maxime; Wu, Carl

2014-01-01

The budding yeast centromere contains Cse4, a specialized histone H3 variant. Fluorescence pulse-chase analysis of an internally tagged Cse4 reveals that it is replaced with newly synthesized molecules in S phase, remaining stably associated with centromeres thereafter. In contrast, C-terminally-tagged Cse4 is functionally impaired, showing slow cell growth, cell lethality at elevated temperatures, and extra-centromeric nuclear accumulation. Recent studies using such strains gave conflicting findings regarding the centromeric abundance and cell cycle dynamics of Cse4. Our findings indicate that internally tagged Cse4 is a better reporter of the biology of this histone variant. Furthermore, the size of centromeric Cse4 clusters was precisely mapped with a new 3D-PALM method, revealing substantial compaction during anaphase. Cse4-specific chaperone Scm3 displays steady-state, stoichiometric co-localization with Cse4 at centromeres throughout the cell cycle, while undergoing exchange with a nuclear pool. These findings suggest that a stable Cse4 nucleosome is maintained by dynamic chaperone-in-residence Scm3. DOI: http://dx.doi.org/10.7554/eLife.02203.001 PMID:24844245

Determinants of elevated healthcare utilization in patients with COPD.

PubMed

Simon-Tuval, Tzahit; Scharf, Steven M; Maimon, Nimrod; Bernhard-Scharf, Barbara J; Reuveni, Haim; Tarasiuk, Ariel

2011-01-13

Chronic obstructive pulmonary disease (COPD) imparts a substantial economic burden on western health systems. Our objective was to analyze the determinants of elevated healthcare utilization among patients with COPD in a single-payer health system. Three-hundred eighty-nine adults with COPD were matched 1:3 to controls by age, gender and area of residency. Total healthcare cost 5 years prior recruitment and presence of comorbidities were obtained from a computerized database. Health related quality of life (HRQoL) indices were obtained using validated questionnaires among a subsample of 177 patients. Healthcare utilization was 3.4-fold higher among COPD patients compared with controls (p < 0.001). The "most-costly" upper 25% of COPD patients (n = 98) consumed 63% of all costs. Multivariate analysis revealed that independent determinants of being in the "most costly" group were (OR; 95% CI): age-adjusted Charlson Comorbidity Index (1.09; 1.01-1.2), history of: myocardial infarct (2.87; 1.5-5.5), congestive heart failure (3.52; 1.9-6.4), mild liver disease (3.83; 1.3-11.2) and diabetes (2.02; 1.1-3.6). Bivariate analysis revealed that cost increased as HRQoL declined and severity of airflow obstruction increased but these were not independent determinants in a multivariate analysis. Comorbidity burden determines elevated utilization for COPD patients. Decision makers should prioritize scarce health care resources to a better care management of the "most costly" patients.

Envisioning the Third Sector's Welfare Role: Critical Discourse Analysis of ‘Post-Devolution’ Public Policy in the UK 1998–2012

PubMed Central

Chaney, Paul; Wincott, Daniel

2014-01-01

Welfare state theory has struggled to come to terms with the role of the third sector. It has often categorized welfare states in terms of the pattern of interplay between state social policies and the structure of the labour market. Moreover, it has frequently offered an exclusive focus on state policy – thereby failing to substantially recognize the role of the formally organized third sector. This study offers a corrective view. Against the backdrop of the international shift to multi-level governance, it analyses the policy discourse of third sector involvement in welfare governance following devolution in the UK. It reveals the changing and contrasting ways in which post-devolution territorial politics envisions the sector's role as a welfare provider. The mixed methods analysis compares policy framing and the structural narratives associated with the development of the third sector across the four constituent polities of the UK since 1998. The findings reveal how devolution has introduced a new spatial policy dynamic. Whilst there are elements of continuity between polities – such as the increasing salience of the third sector in welfare provision – policy narratives also provide evidence of the territorialization of third sector policy. From a methodological standpoint, this underlines the distinctive and complementary role discourse-based analysis can play in understanding contemporary patterns and processes shaping welfare governance. PMID:25574063

Envisioning the Third Sector's Welfare Role: Critical Discourse Analysis of 'Post-Devolution' Public Policy in the UK 1998-2012.

PubMed

Chaney, Paul; Wincott, Daniel

2014-12-01

Welfare state theory has struggled to come to terms with the role of the third sector. It has often categorized welfare states in terms of the pattern of interplay between state social policies and the structure of the labour market. Moreover, it has frequently offered an exclusive focus on state policy - thereby failing to substantially recognize the role of the formally organized third sector. This study offers a corrective view. Against the backdrop of the international shift to multi-level governance, it analyses the policy discourse of third sector involvement in welfare governance following devolution in the UK. It reveals the changing and contrasting ways in which post-devolution territorial politics envisions the sector's role as a welfare provider. The mixed methods analysis compares policy framing and the structural narratives associated with the development of the third sector across the four constituent polities of the UK since 1998. The findings reveal how devolution has introduced a new spatial policy dynamic. Whilst there are elements of continuity between polities - such as the increasing salience of the third sector in welfare provision - policy narratives also provide evidence of the territorialization of third sector policy. From a methodological standpoint, this underlines the distinctive and complementary role discourse-based analysis can play in understanding contemporary patterns and processes shaping welfare governance.

Preparation of amorphous solid dispersions by rotary evaporation and KinetiSol Dispersing: approaches to enhance solubility of a poorly water-soluble gum extract.

PubMed

Bennett, Ryan C; Brough, Chris; Miller, Dave A; O'Donnell, Kevin P; Keen, Justin M; Hughey, Justin R; Williams, Robert O; McGinity, James W

2015-03-01

Acetyl-11-keto-β-boswellic acid (AKBA), a gum resin extract, possesses poor water-solubility that limits bioavailability and a high melting point making it difficult to successfully process into solid dispersions by fusion methods. The purpose of this study was to investigate solvent and thermal processing techniques for the preparation of amorphous solid dispersions (ASDs) exhibiting enhanced solubility, dissolution rates and bioavailability. Solid dispersions were successfully produced by rotary evaporation (RE) and KinetiSol® Dispersing (KSD). Solid state and chemical characterization revealed that ASD with good potency and purity were produced by both RE and KSD. Results of the RE studies demonstrated that AQOAT®-LF, AQOAT®-MF, Eudragit® L100-55 and Soluplus with the incorporation of dioctyl sulfosuccinate sodium provided substantial solubility enhancement. Non-sink dissolution analysis showed enhanced dissolution properties for KSD-processed solid dispersions in comparison to RE-processed solid dispersions. Variances in release performance were identified when different particle size fractions of KSD samples were analyzed. Selected RE samples varying in particle surface morphologies were placed under storage and exhibited crystalline growth following solid-state stability analysis at 12 months in comparison to stored KSD samples confirming amorphous instability for RE products. In vivo analysis of KSD-processed solid dispersions revealed significantly enhanced AKBA absorption in comparison to the neat, active substance.

Analysis of Four Automated Urinalysis Systems Compared to Reference Methods.

PubMed

Bartosova, Kamila; Kubicek, Zdenek; Franekova, Janka; Louzensky, Gustav; Lavrikova, Petra; Jabor, Antonin

2016-11-01

The aim of this study was to compare four automated urinalysis systems: the Iris iQ200 Sprint (Iris Diagnostics, U.S.A.) combined with the Arkray AUTION MAX AX 4030, Iris + AUTION, Arkray AU 4050 (Arkray Global Business, Inc., Japan), Dirui FUS 2000 (Dirui Industrial Co., P.R.C.), and Menarini sediMAX (Menarini, Italy). Urine concentrations of protein and glucose (Iris, Dirui) were compared using reference quantitative analysis on an Abbott Architect c16000. Leukocytes, erythrocytes, epithelia, and casts (Iris, Arkray, Diuri, Menarini) were compared to urine sediment under reference light microscopy, Leica DM2000 (Leica Microsystems GmbH, Germany) with calibrated FastRead plates (Biosigma S.r.l., Italy), using both native and stained preparations. Total protein and glucose levels were measured using the Iris + AUTION system with borderline trueness, while the Dirui analysis revealed worse performances for the protein and glucose measurements. True classifications of leukocytes and erythrocytes were above 85% and 72%, respectively. Kappa statistics revealed a nearly perfect evaluation of leukocytes for all tested systems; the erythrocyte evaluation was nearly perfect for the Iris, Dirui and Arkray analyzers and substantial for the Menarini analyzer. The epithelia identification was connected to high false negativity (above 15%) in the Iris, Arkray, and Menarini analyses. False-negative casts were above 70% for all tested systems. The use of automated urinalysis demonstrated some weaknesses and should be checked by experienced laboratory staff using light microscopy.

Analysis of plasma membrane Ca(2+)-ATPase expression in control and SV40-transformed human fibroblasts.

PubMed

Reisner, P D; Brandt, P C; Vanaman, T C

1997-01-01

It has been long known that neoplastic transformation is accompanied by a lowered requirement for extracellular Ca2+ for growth. The studies presented here demonstrate that human fibroblastic cell lines produce the two commonly found 'housekeeping' isoforms of the plasma membrane Ca(2+)-ATPase (PMCA), PMCA1b and 4b, and at the expression of both is demonstrably lower in cell lines neoplastically transformed by SV40 than in the corresponding parental cell lines. Western blot analyses of lysates from control (GM00037) and SV40-transformed (GM00637) skin fibroblasts revealed a 138 kDa PMCA whose level was significantly lower in the SV40-transformed cells relative to either total cellular protein or alpha-tubulin. Similar analyses of plasma membrane preparations from control WI-38) and SV40-transformed (WI-38VA13) lung fibroblasts revealed 3-4-fold lower levels of PMCA in the SV40-transformed cells. Competitive ELISAs performed on detergent solubilized plasma membrane preparations indicated at least 3-4-fold lower levels of PMCA in the SV40-transformed cell lines compared to controls. Reverse transcriptase coupled-PCR analyses showed that PMCA1b and PMCA4b were the only isoforms expressed in all four cell lines. The PMCA4b mRNA level detected by Northern analysis also was substantially lower in SV40 transformed skin fibroblasts than in non-transformed fibroblasts. Quantitative RT-PCR analyses showed levels of PMCA1b and 4b mRNAs to be 5 and 10-fold lower, respectively, in GM00637 than in GM00037 when the levels of PCR products were normalized to glyceraldehyde-3-phosphate dehydrogenase (G3PDH) mRNA. These results demonstrate that the expression of these distinct PMCA genes is substantially lower in SV40 transformed human skin and lung fibroblasts and may be coordinately regulated in these cells.

Transcriptome Analysis of Portunus trituberculatus in Response to Salinity Stress Provides Insights into the Molecular Basis of Osmoregulation

PubMed Central

Lv, Jianjian; Liu, Ping; Wang, Yu; Gao, Baoquan; Chen, Ping; Li, Jian

2013-01-01

Background The swimming crab, Portunus trituberculatus, which is naturally distributed in the coastal waters of Asia-Pacific countries, is an important farmed species in China. Salinity is one of the most important abiotic factors that influence not only the distribution and abundance of crustaceans, it is also an important factor for artificial propagation of the crab. To better understand the interaction between salinity stress and osmoregulation, we performed a transcriptome analysis in the gills of Portunus trituberculatus challenged with salinity stress, using the Illumina Deep Sequencing technology. Results We obtained 27,696,835, 28,268,353 and 33,901,271 qualified Illumina read pairs from low salinity challenged (LC), non-challenged (NC), and high salinity challenged (HC) Portunus trituberculatus cDNA libraries, respectively. The overall de novo assembly of cDNA sequence data generated 94,511 unigenes, with an average length of 644 bp. Comparative genomic analysis revealed that 1,705 genes differentially expressed in salinity stress compared to the controls, including 615 and 1,516 unigenes in NC vs LC and NC vs HC respectively. GO functional enrichment analysis results showed some differentially expressed genes were involved in crucial processes related to osmoregulation, such as ion transport processes, amino acid metabolism and synthesis processes, proteolysis process and chitin metabolic process. Conclusion This work represents the first report of the utilization of the next generation sequencing techniques for transcriptome analysis in Portunus trituberculatus and provides valuable information on salinity adaptation mechanism. Results reveal a substantial number of genes modified by salinity stress and a few important salinity acclimation pathways, which will serve as an invaluable resource for revealing the molecular basis of osmoregulation in Portunus trituberculatus. In addition, the most comprehensive sequences of transcripts reported in this study provide a rich source for identification of novel genes in the crab. PMID:24312639

Salinity-induced inhibition of growth in the aquatic pteridophyte Azolla microphylla primarily involves inhibition of photosynthetic components and signaling molecules as revealed by proteome analysis.

PubMed

Thagela, Preeti; Yadav, Ravindra Kumar; Mishra, Vagish; Dahuja, Anil; Ahmad, Altaf; Singh, Pawan Kumar; Tiwari, Budhi Sagar; Abraham, Gerard

2017-01-01

Salinity stress causes adverse physiological and biochemical changes in the growth and productivity of a plant. Azolla, a symbiotic pteridophyte and potent candidate for biofertilizer due to its nitrogen fixation ability, shows reduced growth and nitrogen fixation during saline stress. To better understand regulatory components involved in salinity-induced physiological changes, in the present study, Azolla microphylla plants were exposed to NaCl (6.74 and 8.61 ds/m) and growth, photochemical reactions of photosynthesis, ion accumulation, and changes in cellular proteome were studied. Maximum dry weight was accumulated in control and untreated plant while a substantial decrease in dry weight was observed in the plants exposed to salinity. Exposure of the organism to different concentrations of salt in hydroponic conditions resulted in differential level of Na + and K + ion accumulation. Comparative analysis of salinity-induced proteome changes in A. microphylla revealed 58 salt responsive proteins which were differentially expressed during the salt exposure. Moreover, 42 % spots among differentially expressed proteins were involved in different signaling events. The identified proteins are involved in photosynthesis, energy metabolism, amino acid biosynthesis, protein synthesis, and defense. Downregulation of these key metabolic proteins appears to inhibit the growth of A. microphylla in response to salinity. Altogether, the study revealed that in Azolla, increased salinity primarily affected signaling and photosynthesis that in turn leads to reduced biomass.

THE OPPORTUNISTIC PATHOGEN TOXOPLASMA GONDII DEPLOYS A DIVERSE LEGION OF INVASION AND SURVIVAL PROTEINS

PubMed Central

Zhou, Xing W.; Kafsack, Björn F. C.; Cole, Robert N.; Beckett, Phil; Shen, Rong F.; Carruthers, Vern B.

2006-01-01

Host cell invasion is an essential step during infection by Toxoplasma gondii, an intracellular protozoan that causes the severe opportunistic disease toxoplasmosis in humans. Recent evidence strongly suggests that proteins discharged from Toxoplasma apical secretory organelles (micronemes, dense granules, and rhoptries) play key roles in host cell invasion and survival during infection. However, to date, only a limited number of secretory proteins have been discovered and the full spectrum of effector molecules involved in parasite invasion and survival remains unknown. To address these issues, we analyzed a large cohort of freely released Toxoplasma secretory proteins using two complementary methodologies, 2-DE/MS and LC/ESI-MS-MS (MudPIT, shotgun proteomics). Visualization of Toxoplasma secretory products by 2-DE revealed ∼100 spots, most of which were successfully identified by protein microsequencing or MALDI-MS analysis. Many proteins were present in multiple species suggesting they are subjected to substantial posttranslational modification. Shotgun proteomic analysis of the secretory fraction revealed several additional products including novel putative adhesive proteins, proteases, and hypothetical secretory proteins similar to products expressed by other related parasites including Plasmodium, the etiologic agent of malaria. A subset of novel proteins were re-expressed as fusions to yellow fluorescent protein and this initial screen revealed shared and distinct localizations within secretory compartments of T. gondii tachyzoites. The findings provide a uniquely broad view of Toxoplasma secretory proteins that participate in parasite survival and pathogenesis during infection. PMID:16002397

META-ANALYSIS OF CYP2D6 METABOLIZER PHENOTYPE AND METOPROLOL PHARMACOKINETICS

PubMed Central

Blake, CM; Kharasch, ED; Schwab, M; Nagele, P

2013-01-01

Metoprolol, a commonly prescribed beta-blocker, is primarily metabolized by cytochrome P450 2D6 (CYP2D6), an enzyme with substantial genetic heterogeneity. Several smaller studies have shown that metoprolol pharmacokinetics is influenced by CYP2D6 genotype and metabolizer phenotype. To increase robustness of metoprolol pharmacokinetic estimates, a systematic review and meta-analysis of pharmacokinetic studies that administered a single oral dose of immediate release metoprolol was performed. Pooled analysis (n= 264) demonstrated differences in peak plasma metoprolol concentration, area under the concentration-time curve, elimination half-life, and apparent oral clearance that were 2.3-, 4.9-, 2.3-, and 5.9-fold between extensive and poor metabolizers, respectively, and 5.3-, 13-, 2.6-, and 15-fold between ultra-rapid and poor metabolizers (all p<0.001). Enantiomer-specific analysis revealed genotype-dependent enantio-selective metabolism, with nearly 40% greater R- vs S-metoprolol metabolism in ultra-rapid and extensive metabolizers. This study demonstrates a marked effect of CYP2D6 metabolizer phenotype on metoprolol pharmacokinetics and confirms enantiomer specific metabolism of metoprolol. PMID:23665868

Chemical information obtained from Auger depth profiles by means of advanced factor analysis (MLCFA)

NASA Astrophysics Data System (ADS)

De Volder, P.; Hoogewijs, R.; De Gryse, R.; Fiermans, L.; Vennik, J.

1993-01-01

The advanced multivariate statistical technique "maximum likelihood common factor analysis (MLCFA)" is shown to be superior to "principal component analysis (PCA)" for decomposing overlapping peaks into their individual component spectra of which neither the number of components nor the peak shape of the component spectra is known. An examination of the maximum resolving power of both techniques, MLCFA and PCA, by means of artificially created series of multicomponent spectra confirms this finding unambiguously. Substantial progress in the use of AES as a chemical-analysis technique is accomplished through the implementation of MLCFA. Chemical information from Auger depth profiles is extracted by investigating the variation of the line shape of the Auger signal as a function of the changing chemical state of the element. In particular, MLCFA combined with Auger depth profiling has been applied to problems related to steelcord-rubber tyre adhesion. MLCFA allows one to elucidate the precise nature of the interfacial layer of reaction products between natural rubber vulcanized on a thin brass layer. This study reveals many interesting chemical aspects of the oxi-sulfidation of brass undetectable with classical AES.

Economic conditions, hypertension, and cardiovascular disease: analysis of the Icelandic economic collapse.

PubMed

Birgisdóttir, Kristín Helga; Jónsson, Stefán Hrafn; Ásgeirsdóttir, Tinna Laufey

2017-12-01

Previous research has found a positive short-term relationship between the 2008 collapse and hypertension in Icelandic males. With Iceland's economy experiencing a phase of economic recovery, an opportunity to pursue a longer-term analysis of the collapse has emerged. Using data from a nationally representative sample, fixed-effect estimations and mediation analyses were performed to explore the relationship between the Icelandic economic collapse in 2008 and the longer-term impact on hypertension and cardiovascular health. A sensitivity analysis was carried out with pooled logit models estimated as well as an alternative dependent variable. Our attrition analysis revealed that results for cardiovascular diseases were affected by attrition, but not results from estimations on the relationship between the economic crisis and hypertension. When compared to the boom year 2007, our results point to an increased probability of Icelandic women having hypertension in the year 2012, when the Icelandic economy had recovered substantially from the economic collapse in 2008. This represents a deviation from pre-crisis trends, thus suggesting a true economic-recovery impact on hypertension.

Comparative genome and methylome analysis reveals restriction/modification system diversity in the gut commensal Bifidobacterium breve

PubMed Central

Bottacini, Francesca; Morrissey, Ruth; Roberts, Richard John; James, Kieran; van Breen, Justin; Egan, Muireann; Lambert, Jolanda; van Limpt, Kees; Knol, Jan; Motherway, Mary O’Connell; van Sinderen, Douwe

2018-01-01

Abstract Bifidobacterium breve represents one of the most abundant bifidobacterial species in the gastro-intestinal tract of breast-fed infants, where their presence is believed to exert beneficial effects. In the present study whole genome sequencing, employing the PacBio Single Molecule, Real-Time (SMRT) sequencing platform, combined with comparative genome analysis allowed the most extensive genetic investigation of this taxon. Our findings demonstrate that genes encoding Restriction/Modification (R/M) systems constitute a substantial part of the B. breve variable gene content (or variome). Using the methylome data generated by SMRT sequencing, combined with targeted Illumina bisulfite sequencing (BS-seq) and comparative genome analysis, we were able to detect methylation recognition motifs and assign these to identified B. breve R/M systems, where in several cases such assignments were confirmed by restriction analysis. Furthermore, we show that R/M systems typically impose a very significant barrier to genetic accessibility of B. breve strains, and that cloning of a methyltransferase-encoding gene may overcome such a barrier, thus allowing future functional investigations of members of this species. PMID:29294107

People--things and data--ideas: bipolar dimensions?

PubMed

Tay, Louis; Su, Rong; Rounds, James

2011-07-01

We examined a longstanding assumption in vocational psychology that people-things and data-ideas are bipolar dimensions. Two minimal criteria for bipolarity were proposed and examined across 3 studies: (a) The correlation between opposite interest types should be negative; (b) after correcting for systematic responding, the correlation should be greater than -.40. In Study 1, a meta-analysis using 26 interest inventories with a sample size of 1,008,253 participants showed that meta-analytic correlations between opposite RIASEC (realistic, investigative, artistic, social, enterprising, conventional) types ranged from -.03 to .18 (corrected meta-analytic correlations ranged from -.23 to -.06). In Study 2, structural equation models (SEMs) were fit to the Interest Finder (IF; Wall, Wise, & Baker, 1996) and the Interest Profiler (IP; Rounds, Smith, Hubert, Lewis, & Rivkin, 1999) with sample sizes of 13,939 and 1,061, respectively. The correlations of opposite RIASEC types were positive, ranging from .17 to .53. No corrected correlation met the criterion of -.40 except for investigative-enterprising (r = -.67). Nevertheless, a direct estimate of the correlation between data-ideas end poles using targeted factor rotation did not reveal bipolarity. Furthermore, bipolar SEMs fit substantially worse than a multiple-factor representation of vocational interests. In Study 3, a two-way clustering solution on IF and IP respondents and items revealed a substantial number of individuals with interests in both people and things. We discuss key theoretical, methodological, and practical implications such as the structure of vocational interests, interpretation and scoring of interest measures for career counseling, and expert RIASEC ratings of occupations.

Different Blood Cell-Derived Transcriptome Signatures in Cows Exposed to Vaccination Pre- or Postpartum

PubMed Central

Weikard, Rosemarie; Demasius, Wiebke; Hadlich, Frieder; Kühn, Christa

2015-01-01

Periparturient cows have been found to reveal immunosuppression, frequently associated with increased susceptibility to uterine and mammary infections. To improve understanding of the causes and molecular regulatory mechanisms accounting for this phenomenon around calving, we examined the effect of an antigen challenge on gene expression modulation on cows prior to (BC) or after calving (AC) using whole transcriptome sequencing (RNAseq). The transcriptome analysis of the cows’ blood identified a substantially higher number of loci affected in BC cows (2,235) in response to vaccination compared to AC cows (208) and revealed a divergent transcriptional profile specific for each group. In BC cows, a variety of loci involved in immune defense and cellular signaling processes were transcriptionally activated, whereas protein biosynthesis and posttranslational processes were tremendously impaired in response to vaccination. Furthermore, energy metabolism in the blood cells of BC cows was shifted from oxidative phosphorylation to the glycolytic system. In AC cows, the number and variety of regulated pathways involved in immunomodulation and maintenance of immnunocompetence are considerably lower after vaccination, and upregulation of arginine degradation was suggested as an immunosuppressive mechanism. Elevated transcript levels of erythrocyte-specific genes involved in gas exchange processes were a specific transcriptional signature in AC cows pointing to hematopoiesis activation. The divergent and substantially lower magnitude of transcriptional modulation in response to vaccination in AC cows provides evidence for a suppressed immune capacity of early lactating cows on the molecular level and demonstrates that an efficient immune response of cows is related to their physiological and metabolic status. PMID:26317664

Tissue-specific and pathogen-inducible expression of a fusion protein containing a Fusarium-specific antibody and a fungal chitinase protects wheat against Fusarium pathogens and mycotoxins.

PubMed

Cheng, Wei; Li, He-Ping; Zhang, Jing-Bo; Du, Hong-Jie; Wei, Qi-Yong; Huang, Tao; Yang, Peng; Kong, Xian-Wei; Liao, Yu-Cai

2015-06-01

Fusarium head blight (FHB) in wheat and other small grain cereals is a globally devastating disease caused by toxigenic Fusarium pathogens. Controlling FHB is a challenge because germplasm that is naturally resistant against these pathogens is inadequate. Current control measures rely on fungicides. Here, an antibody fusion comprised of the Fusarium spp.-specific recombinant antibody gene CWP2 derived from chicken, and the endochitinase gene Ech42 from the biocontrol fungus Trichoderma atroviride was introduced into the elite wheat cultivar Zhengmai9023 by particle bombardment. Expression of this fusion gene was regulated by the lemma/palea-specific promoter Lem2 derived from barley; its expression was confirmed as lemma/palea-specific in transgenic wheat. Single-floret inoculation of independent transgenic wheat lines of the T3 to T6 generations revealed significant resistance (type II) to fungal spreading, and natural infection assays in the field showed significant resistance (type I) to initial infection. Gas chromatography-mass spectrometry analysis revealed marked reduction of mycotoxins in the grains of the transgenic wheat lines. Progenies of crosses between the transgenic lines and the FHB-susceptible cultivar Huamai13 also showed significantly enhanced FHB resistance. Quantitative real-time PCR analysis revealed that the tissue-specific expression of the antibody fusion was induced by salicylic acid drenching and induced to a greater extent by F. graminearum infection. Histochemical analysis showed substantial restriction of mycelial growth in the lemma tissues of the transgenic plants. Thus, the combined tissue-specific and pathogen-inducible expression of this Fusarium-specific antibody fusion can effectively protect wheat against Fusarium pathogens and reduce mycotoxin content in grain. © 2014 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

Manganese- and 1-methyl-4-phenylpyridinium-induced neurotoxicity display differences in morphological, electrophysiological and genome-wide alterations: implications for idiopathic Parkinson's disease.

PubMed

Mythri, Rajeswara Babu; Raghunath, Narayana Reddy; Narwade, Santosh Chandrakant; Pandareesh, Mirazkar Dasharatha Rao; Sabitha, Kollarkandi Rajesh; Aiyaz, Mohamad; Chand, Bipin; Sule, Manas; Ghosh, Krittika; Kumar, Senthil; Shankarappa, Bhagyalakshmi; Soundararajan, Soundarya; Alladi, Phalguni Anand; Purushottam, Meera; Gayathri, Narayanappa; Deobagkar, Deepti Dileep; Laxmi, Thenkanidiyoor Rao; Srinivas Bharath, Muchukunte Mukunda

2017-11-01

Idiopathic Parkinson's disease and manganese-induced atypical parkinsonism are characterized by movement disorder and nigrostriatal pathology. Although clinical features, brain region involved and responsiveness to levodopa distinguish both, differences at the neuronal level are largely unknown. We studied the morphological, neurophysiological and molecular differences in dopaminergic neurons exposed to the Parkinson's disease toxin 1-methyl-4-phenylpyridinium ion (MPP + ) and manganese (Mn), followed by validation in the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine and Mn mouse models. Morphological analysis highlighted loss of neuronal processes in the MPP + and not the Mn model. Cellular network dynamics of dopaminergic neurons characterized by spike frequency and inter-spike intervals indicated major neuronal population (~ 93%) with slow discharge rates (0-5 Hz). While MPP + exposure suppressed the firing of these neurons, Mn neither suppressed nor elevated the neuronal activity. High-throughput transcriptomic analysis revealed up-regulation of 694 and 603 genes and down-regulation of 428 and 255 genes in the MPP + and Mn models respectively. Many differentially expressed genes were unique to either models and contributed to neuroinflammation, metabolic/mitochondrial function, apoptosis and nuclear function, synaptic plasticity, neurotransmission and cytoskeleton. Analysis of the Janus kinase-signal transducer and activator of transcription pathway with implications for neuritogenesis and neuronal proliferation revealed contrasting profile in both models. Genome-wide DNA methylomics revealed differences between both models and substantiated the epigenetic basis of the difference in the Janus kinase-signal transducer and activator of transcription pathway. We conclude that idiopathic Parkinson's disease and atypical parkinsonism have divergent neurotoxicological manifestation at the dopaminergic neuronal level with implications for pathobiology and evolution of novel therapeutics. Cover Image for this issue: doi. 10.1111/jnc.13821. © 2017 International Society for Neurochemistry.

Six uneventful pregnancy outcomes in an extended vascular Ehlers-Danlos syndrome family.

PubMed

Baas, Annette F; Spiering, Wilko; Moll, Frans L; Page-Christiaens, Lieve; Beenakkers, Ingrid C M; Dooijes, Dennis; Vonken, Evert-Jan P A; van der Smagt, Jasper J; Knoers, Nine V; Koenen, Steven V; van Herwaarden, Joost A; Sieswerda, Gertjan Tj

2017-02-01

Vascular Ehlers-Danlos Syndrome (vEDS) is caused by heterozygous mutations in COL3A1 and is characterized by fragile vasculature and hollow organs, with a high risk of catastrophic events at a young age. During pregnancy and delivery, maternal mortality rates up until 25% have been reported. However, recent pedigree analysis reported a substantial lower pregnancy-related mortality rate of 4.9%. Here, we describe an extended vEDS family with multiple uneventful pregnancy outcomes. In the proband, a 37-year-old woman, DNA-analysis because of an asymptomatic iliac artery dissection revealed a pathogenic mutation in COL3A1 (c.980G>A; p. Gly327Asp). She had had three uneventful vaginal deliveries. At the time of diagnosis, her 33-year-old niece was 25 weeks pregnant. She had had one uneventful vaginal delivery. Targeted DNA-analysis revealed that she was carrier of the COL3A1 mutation. Ultrasound detected an aneurysm in the abdominal aorta with likely a dissection. An uneventful elective cesarean section was performed at a gestational age of 37 weeks. The 40-year-old sister of our proband had had one uneventful vaginal delivery and an active pregnancy wish. Cascade DNA-screening showed her to carry the COL3A1 mutation. Computed Tomography Angiography (CTA) of her aorta revealed a type B dissection with the most proximal entry tear just below the superior mesenteric artery. Pregnancy was therefore discouraged. This familial case illustrates the complexity and challenges of reproductive decision-making in a potentially lethal condition as vEDS, and highlights the importance of a multidisciplinary approach. Moreover, it suggests that previous pregnancy-related risks of vEDS may be overestimated. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Knock-in mice harboring a Ca(2+) desensitizing mutation in cardiac troponin C develop early onset dilated cardiomyopathy.

PubMed

McConnell, Bradley K; Singh, Sonal; Fan, Qiying; Hernandez, Adriana; Portillo, Jesus P; Reiser, Peter J; Tikunova, Svetlana B

2015-01-01

The physiological consequences of aberrant Ca(2+) binding and exchange with cardiac myofilaments are not clearly understood. In order to examine the effect of decreasing Ca(2+) sensitivity of cTnC on cardiac function, we generated knock-in mice carrying a D73N mutation (not known to be associated with heart disease in human patients) in cTnC. The D73N mutation was engineered into the regulatory N-domain of cTnC in order to reduce Ca(2+) sensitivity of reconstituted thin filaments by increasing the rate of Ca(2+) dissociation. In addition, the D73N mutation drastically blunted the extent of Ca(2+) desensitization of reconstituted thin filaments induced by cTnI pseudo-phosphorylation. Compared to wild-type mice, heterozygous knock-in mice carrying the D73N mutation exhibited a substantially decreased Ca(2+) sensitivity of force development in skinned ventricular trabeculae. Kaplan-Meier survival analysis revealed that median survival time for knock-in mice was 12 weeks. Echocardiographic analysis revealed that knock-in mice exhibited increased left ventricular dimensions with thinner walls. Echocardiographic analysis also revealed that measures of systolic function, such as ejection fraction (EF) and fractional shortening (FS), were dramatically reduced in knock-in mice. In addition, knock-in mice displayed electrophysiological abnormalities, namely prolonged QRS and QT intervals. Furthermore, ventricular myocytes isolated from knock-in mice did not respond to β-adrenergic stimulation. Thus, knock-in mice developed pathological features similar to those observed in human patients with dilated cardiomyopathy (DCM). In conclusion, our results suggest that decreasing Ca(2+) sensitivity of the regulatory N-domain of cTnC is sufficient to trigger the development of DCM.

KIT mutations in Russian patients with mucosal melanoma.

PubMed

Abysheva, Svetlana N; Iyevleva, Aglaya G; Efimova, Nina V; Mokhina, Yulia B; Sabirova, Feruza A; Ivantsov, Alexandr O; Artemieva, Anna S; Togo, Alexandr V; Moiseyenko, Vladimir M; Matsko, Dmitry E; Imyanitov, Evgeny N

2011-12-01

A single institution series of 48 mucosal melanomas (MMs) has been analyzed for the presence of KIT mutations using high-resolution melting and sequencing of abnormally melted DNA fragments. The analysis of exons 9, 11, 13, and 17 has revealed eight of 48 (17%) nonsynonymous alterations, including zero of seven head and neck, six of 24 anorectal, one of 15 genitourinary, one of one gastric, and zero of one mediastinal MMs. Seven of these mutations were potentially associated with the tumor sensitivity to KIT tyrosine kinase inhibitors. One tumor harbored somatically acquired silent nucleotide substitution c.1383A>G (T461T). This study adds to the evidence that a substantial portion of MMs carry a therapeutically relevant mutation in the KIT oncogene.

The Oral Microbiota in Health and Disease: An Overview of Molecular Findings.

PubMed

Siqueira, José F; Rôças, Isabela N

2017-01-01

Culture-independent nucleic acid technologies have been extensively applied to the analysis of oral bacterial communities associated with healthy and diseased conditions. These methods have confirmed and substantially expanded the findings from culture studies to reveal the oral microbial inhabitants and candidate pathogens associated with the major oral diseases. Over 1000 bacterial distinct species-level taxa have been identified in the oral cavity and studies using next-generation DNA sequencing approaches indicate that the breadth of bacterial diversity may be even much larger. Nucleic acid technologies have also been helpful in profiling bacterial communities and identifying disease-related patterns. This chapter provides an overview of the diversity and taxonomy of oral bacteria associated with health and disease.

World Population Stabilization Unlikely This Century

PubMed Central

Gerland, Patrick; Raftery, Adrian E.; Ševcíková, Hana; Li, Nan; Gu, Danan; Spoorenberg, Thomas; Alkema, Leontine; Fosdick, Bailey K.; Chunn, Jennifer; Lalic, Nevena; Bay, Guiomar; Buettner, Thomas; Heilig, Gerhard K.; Wilmoth, John

2014-01-01

The United Nations recently released population projections based on data until 2012 and a Bayesian probabilistic methodology. Analysis of these data reveals that, contrary to previous literature, world population is unlikely to stop growing this century. There is an 80% probability that world population, now 7.2 billion, will increase to between 9.6 and 12.3 billion in 2100. This uncertainty is much smaller than the range from the traditional UN high and low variants. Much of the increase is expected to happen in Africa, in part due to higher fertility and a recent slowdown in the pace of fertility decline. Also, the ratio of working age people to older people is likely to decline substantially in all countries, even those that currently have young populations. PMID:25301627

Enhancing anaerobic digestion of complex organic waste with carbon-based conductive materials.

PubMed

Dang, Yan; Holmes, Dawn E; Zhao, Zhiqiang; Woodard, Trevor L; Zhang, Yaobin; Sun, Dezhi; Wang, Li-Ying; Nevin, Kelly P; Lovley, Derek R

2016-11-01

The aim of this work was to study the methanogenic metabolism of dog food, a food waste surrogate, in laboratory-scale reactors with different carbon-based conductive materials. Carbon cloth, carbon felt, and granular activated carbon all permitted higher organic loading rates and promoted faster recovery of soured reactors than the control reactors. Microbial community analysis revealed that specific and substantial enrichments of Sporanaerobacter and Methanosarcina were present on the carbon cloth surface. These results, and the known ability of Sporanaerobacter species to transfer electrons to elemental sulfur, suggest that Sporanaerobacter species can participate in direct interspecies electron transfer with Methanosarcina species when carbon cloth is available as an electron transfer mediator. Copyright © 2016 Elsevier Ltd. All rights reserved.

Radiation effect on rocket engine performance

NASA Technical Reports Server (NTRS)

Chiu, Huei-Huang; Kross, K. W.; Krebsbach, A. N.

1990-01-01

Critical problem areas involving the effect of radiation on the combustion of bipropellants are addressed by formulating a universal scaling law in combination with a radiation-enhanced vaporization combustion model. Numerical algorithms are developed and data pertaining to the Variable Thrust Engine (VTE) and the Space Shuttle Main Engine (SSME) are used to conduct parametric sensitivity studies to predict the principal intercoupling effects of radiation. The analysis reveals that low-enthalpy engines, such as the VTE, are vulnerable to a substantial performance setback due to radiative loss, whereas the performance of high-enthalpy engines such as the SSME are hardly affected over a broad range of engine operation. Combustion enhancement by radiative heating of the propellant has a significant impact on propellants with high absorptivity.

Transcriptomic analysis of the highly efficient oil-degrading bacterium Acinetobacter venetianus RAG-1 reveals genes important in dodecane uptake and utilization [Transcriptomic analysis of the marine oil-degrading bacterium Acinetobacter venetianus RAG-1 reveals genes important in dodecane uptake and utilization

DOE PAGES

Kothari, Ankita; Charrier, Marimikel; Wu, Yu -Wei; ...

2016-09-22

The hydrocarbonoclastic bacterium Acinetobacter venetianus RAG-1 has attracted substantial attention due to its powerful oil-degrading capabilities and its potential to play an important ecological role in the cleanup of alkanes. In this study, we compare the transcriptome of the strain RAG-1 grown in dodecane, the corresponding alkanol (dodecanol), and sodium acetate for the characterization of genes involved in dodecane uptake and utilization. Comparison of the transcriptional responses of RAG-1 grown on dodecane led to the identification of 1074 genes that were differentially expressed relative to sodium acetate. Of these, 622 genes were upregulated when grown in dodecane. The highly upregulatedmore » genes were involved in alkane catabolism, along with stress response. Our data suggest AlkMb to be primarily involved in dodecane oxidation. Transcriptional response of RAG-1 grown on dodecane relative to dodecanol also led to the identification of permease, outer membrane protein and thin fimbriae coding genes potentially involved in dodecane uptake. As a result, this study provides the first model for key genes involved in alkane uptake and metabolism in A. venetianus RAG-1.« less

"The casual cruelty of our prejudices": on Walter Lippmann's theory of stereotype and its "obliteration" in psychology and social science.

PubMed

Bottom, William P; Kong, Dejun Tony

2012-01-01

Reflecting on his wartime government service, Walter Lippmann (1922) developed a theory of policy formulation and error. Introducing the constructs of stereotype, mental model, blind spots, and the process of manufacturing consent, his theory prescribed interdisciplinary social science as a tool for enhancing policy making in business and government. Lippmann used his influence with the Rockefeller foundations, business leaders, Harvard and the University of Chicago to gain support for this program. Citation analysis of references to "stereotype" and Lippmann reveals the rapid spread of the concept across the social sciences and in public discourse paralleled by obliteration by incorporation of the wider theory in behavioral science. "Stereotype" is increasingly invoked in anthropology, economics, and sociology though Lippmann and his wider theory ceased being cited decades ago. In psychology, citations are increasing but content analysis revealed blind spots and misconceptions about the theory and prescription. Studies of heuristics, biases, and organizational decision substantiate Lippmann's theory of judgment and choice. But his model for social science failed to consider the bounded rationality and blind spots of its practitioners. Policy formulation today is supported by research from narrow disciplinary silos not interdisciplinary science that reflects an awareness of history. © 2012 Wiley Periodicals, Inc.

Substantial gaps in knowledge of Bordetella pertussis antibody and T cell epitopes relevant for natural immunity and vaccine efficacy

PubMed Central

Vaughan, Kerrie; Seymour, Emily; Peters, Bjoern; Sette, Alessandro

2016-01-01

The recent increase in whooping cough in vaccinated populations has been attributed to waning immunity associated with the acellular vaccine. The Immune Epitope Database (IEDB) is a repository of immune epitope data from the published literature and includes T cell and antibody epitopes for human pathogens. The IEDB conducted a review of the epitope literature, which revealed 300 Bordetella pertussis-related epitopes from 39 references. Epitope data are currently available for six virulence factors of B. pertussis: pertussis toxin, pertactin, fimbrial 2, fimbrial 3, adenylate cyclase and filamentous hemagglutinin. The majority of epitopes were defined for antibody reactivity; fewer T cell determinants were reported. Analysis of available protective correlates data revealed a number of candidate epitopes; however few are defined in humans and few have been shown to be protective. Moreover, there are a limited number of studies defining epitopes from natural infection versus whole cell or acellular/subunit vaccines. The relationship between epitope location and structural features, as well as antigenic drift (SNP analysis) was also investigated. We conclude that the cumulative data is yet insufficient to address many fundamental questions related to vaccine failure and this underscores the need for further investigation of B. pertussis immunity at the molecular level. PMID:24530743

Transcriptomic analysis of the highly efficient oil-degrading bacterium Acinetobacter venetianus RAG-1 reveals genes important in dodecane uptake and utilization [Transcriptomic analysis of the marine oil-degrading bacterium Acinetobacter venetianus RAG-1 reveals genes important in dodecane uptake and utilization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kothari, Ankita; Charrier, Marimikel; Wu, Yu -Wei

The hydrocarbonoclastic bacterium Acinetobacter venetianus RAG-1 has attracted substantial attention due to its powerful oil-degrading capabilities and its potential to play an important ecological role in the cleanup of alkanes. In this study, we compare the transcriptome of the strain RAG-1 grown in dodecane, the corresponding alkanol (dodecanol), and sodium acetate for the characterization of genes involved in dodecane uptake and utilization. Comparison of the transcriptional responses of RAG-1 grown on dodecane led to the identification of 1074 genes that were differentially expressed relative to sodium acetate. Of these, 622 genes were upregulated when grown in dodecane. The highly upregulatedmore » genes were involved in alkane catabolism, along with stress response. Our data suggest AlkMb to be primarily involved in dodecane oxidation. Transcriptional response of RAG-1 grown on dodecane relative to dodecanol also led to the identification of permease, outer membrane protein and thin fimbriae coding genes potentially involved in dodecane uptake. As a result, this study provides the first model for key genes involved in alkane uptake and metabolism in A. venetianus RAG-1.« less

Ion-beam irradiation, gene identification, and marker-assisted breeding in the development of low-cadmium rice.

PubMed

Ishikawa, Satoru; Ishimaru, Yasuhiro; Igura, Masato; Kuramata, Masato; Abe, Tadashi; Senoura, Takeshi; Hase, Yoshihiro; Arao, Tomohito; Nishizawa, Naoko K; Nakanishi, Hiromi

2012-11-20

Rice (Oryza sativa L.) grain is a major dietary source of cadmium (Cd), which is toxic to humans, but no practical technique exists to substantially reduce Cd contamination. Carbon ion-beam irradiation produced three rice mutants with <0.05 mg Cd⋅kg(-1) in the grain compared with a mean of 1.73 mg Cd⋅kg(-1) in the parent, Koshihikari. We identified the gene responsible for reduced Cd uptake and developed a strategy for marker-assisted selection of low-Cd cultivars. Sequence analysis revealed that these mutants have different mutations of the same gene (OsNRAMP5), which encodes a natural resistance-associated macrophage protein. Functional analysis revealed that the defective transporter protein encoded by the mutant osnramp5 greatly decreases Cd uptake by roots, resulting in decreased Cd in the straw and grain. In addition, we developed DNA markers to facilitate marker-assisted selection of cultivars carrying osnramp5. When grown in Cd-contaminated paddy fields, the mutants have nearly undetectable Cd in their grains and exhibit no agriculturally or economically adverse traits. Because mutants produced by ion-beam radiation are not transgenic plants, they are likely to be accepted by consumers and thus represent a practical choice for rice production worldwide.

Evaluation of genetic diversity of Panicum turgidum Forssk from Saudi Arabia.

PubMed

Assaeed, Abdulaziz M; Al-Faifi, Sulieman A; Migdadi, Hussein M; El-Bana, Magdy I; Al Qarawi, Abdulaziz A; Khan, Mohammad Altaf

2018-01-01

The genetic diversity of 177 accessions of Panicum turgidum Forssk, representing ten populations collected from four geographical regions in Saudi Arabia, was analyzed using amplified fragment length polymorphism (AFLP) markers. A set of four primer-pairs with two/three selective nucleotides scored 836 AFLP amplified fragments (putative loci/genome landmarks), all of which were polymorphic. Populations collected from the southern region of the country showed the highest genetic diversity parameters, whereas those collected from the central regions showed the lowest values. Analysis of molecular variance (AMOVA) revealed that 78% of the genetic variability was attributable to differences within populations. Pairwise values for population differentiation and genetic structure were statistically significant for all variances. The UPGMA dendrogram, validated by principal coordinate analysis-grouped accessions, corresponded to the geographical origin of the accessions. Mantel's test showed that there was a significant correlation between the genetic and geographical distances ( r  = 0.35, P  < 0.04). In summary, the AFLP assay demonstrated the existence of substantial genetic variation in P. turgidum . The relationship between the genetic diversity and geographical source of P. turgidum populations of Saudi Arabia, as revealed through this comprehensive study, will enable effective resource management and restoration of new areas without compromising adaptation and genetic diversity.

Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing.

PubMed

Zuo, Chunman; Blow, Matthew; Sreedasyam, Avinash; Kuo, Rita C; Ramamoorthy, Govindarajan Kunde; Torres-Jerez, Ivone; Li, Guifen; Wang, Mei; Dilworth, David; Barry, Kerrie; Udvardi, Michael; Schmutz, Jeremy; Tang, Yuhong; Xu, Ying

2018-01-01

Switchgrass ( Panicum virgatum L.) is an important bioenergy crop widely used for lignocellulosic research. While extensive transcriptomic analyses have been conducted on this species using short read-based sequencing techniques, very little has been reliably derived regarding alternatively spliced (AS) transcripts. We present an analysis of transcriptomes of six switchgrass tissue types pooled together, sequenced using Pacific Biosciences (PacBio) single-molecular long-read technology. Our analysis identified 105,419 unique transcripts covering 43,570 known genes and 8795 previously unknown genes. 45,168 are novel transcripts of known genes. A total of 60,096 AS transcripts are identified, 45,628 being novel. We have also predicted 1549 transcripts of genes involved in cell wall construction and remodeling, 639 being novel transcripts of known cell wall genes. Most of the predicted transcripts are validated against Illumina-based short reads. Specifically, 96% of the splice junction sites in all the unique transcripts are validated by at least five Illumina reads. Comparisons between genes derived from our identified transcripts and the current genome annotation revealed that among the gene set predicted by both analyses, 16,640 have different exon-intron structures. Overall, substantial amount of new information is derived from the PacBio RNA data regarding both the transcriptome and the genome of switchgrass.

Altered Neural Correlate of the Self-Agency Experience in First-Episode Schizophrenia-Spectrum Patients: An fMRI Study

PubMed Central

Spaniel, Filip; Tintera, Jaroslav; Rydlo, Jan; Ibrahim, Ibrahim; Kasparek, Tomas; Horacek, Jiri; Zaytseva, Yuliya; Matejka, Martin; Fialova, Marketa; Slovakova, Andrea; Mikolas, Pavol; Melicher, Tomas; Görnerova, Natalie; Höschl, Cyril; Hajek, Tomas

2016-01-01

Background: The phenomenology of the clinical symptoms indicates that disturbance of the sense of self be a core marker of schizophrenia. Aims: To compare neural activity related to the self/other-agency judgment in patients with first-episode schizophrenia-spectrum disorders (FES, n = 35) and healthy controls (HC, n = 35). Method: A functional magnetic resonance imaging (fMRI) using motor task with temporal distortion of the visual feedback was employed. A task-related functional connectivity was analyzed with the use of independent component analysis (ICA). Results: (1) During self-agency experience, FES showed a deficit in cortical activation in medial frontal gyrus (BA 10) and posterior cingulate gyrus, (BA 31; P < .05, Family-Wise Error [FWE] corrected). (2) Pooled-sample task-related ICA revealed that the self/other-agency judgment was dependent upon anti-correlated default mode and central-executive networks (DMN/CEN) dynamic switching. This antagonistic mechanism was substantially impaired in FES during the task. Discussion: During self-agency experience, FES demonstrate deficit in engagement of cortical midline structures along with substantial attenuation of anti-correlated DMN/CEN activity underlying normal self/other-agency discriminative processes. PMID:26685867

Structural features of N-glycans linked to glycoproteins expressed in three kinds of water plants: Predominant occurrence of the plant complex type N-glycans bearing Lewis a epitope.

PubMed

Maeda, Megumi; Tani, Misato; Yoshiie, Takeo; Vavricka, Christopher J; Kimura, Yoshinobu

2016-11-29

The Japanese cedar pollen allergen (Cry j1) and the mountain cedar pollen allergen (Jun a1) are glycosylated with plant complex type N-glycans bearing Lewis a epitope(s) (Galβ1-3[Fucα1-4]GlcNAc-). The biological significance of Lewis a type plant N-glycans and their effects on the human immune system remain to be elucidated. Since a substantial amount of such plant specific N-glycans are required to evaluate immunological activity, we have searched for good plant-glycan sources to characterize Lewis a epitope-containing plant N-glycans. In this study, we have found that three water plants, Elodea nuttallii, Egeria densa, and Ceratophyllum demersum, produce glycoproteins bearing Lewis a units. Structural analysis of the N-glycans revealed that almost all glycoproteins expressed in these three water plants predominantly carry plant complex type N-glycans including the Lewis a type, suggesting that these water plants are good sources for preparation of Lewis a type plant N-glycans in substantial amounts. Copyright © 2016 Elsevier Ltd. All rights reserved.

Natural orifice translumenal endoscopic surgery: Progress in humans since white paper

PubMed Central

Santos, Byron F; Hungness, Eric S

2011-01-01

Since the first description of the concept of natural orifice translumenal endoscopic surgery (NOTES), a substantial number of clinical NOTES reports have appeared in the literature. This editorial reviews the available human data addressing research questions originally proposed by the white paper, including determining the optimal method of access for NOTES, developing safe methods of lumenal closure, suturing and anastomotic devices, advanced multitasking platforms, addressing the risk of infection, managing complications, addressing challenges with visualization, and training for NOTES procedures. An analysis of the literature reveals that so far transvaginal access and closure appear to be the most feasible techniques for NOTES, with a limited, but growing transgastric, transrectal, and transesophageal NOTES experience in humans. The theoretically increased risk of infection as a result of NOTES procedures has not been substantiated in transvaginal and transgastric procedures so far. Development of suturing and anastomotic devices and advanced platforms for NOTES has progressed slowly, with limited clinical data on their use so far. Data on the optimal management and incidence of intraoperative complications remain sparse, although possible factors contributing to complications are discussed. Finally, this editorial discusses the likely direction of future NOTES development and its possible role in clinical practice. PMID:21483624

Asymmetry of Reinforcement and Punishment in Human Choice

PubMed Central

Rasmussen, Erin B; Newland, M Christopher

2008-01-01

The hypothesis that a penny lost is valued more highly than a penny earned was tested in human choice. Five participants clicked a computer mouse under concurrent variable-interval schedules of monetary reinforcement. In the no-punishment condition, the schedules arranged monetary gain. In the punishment conditions, a schedule of monetary loss was superimposed on one response alternative. Deviations from generalized matching using the free parameters c (sensitivity to reinforcement) and log k (bias) were compared in the no-punishment and punishment conditions. The no-punishment conditions yielded values of log k that approximated zero for all participants, indicating no bias. In the punishment condition, values of log k deviated substantially from zero, revealing a 3-fold bias toward the unpunished alternative. Moreover, the c parameters were substantially smaller in punished conditions. The values for bias and sensitivity under punishment did not change significantly when the measure of net reinforcers (gains minus losses) was applied to the analysis. These results mean that punishment reduced the sensitivity of behavior to reinforcement and biased performance toward the unpunished alternative. We concluded that a single punisher subtracted more value than a single reinforcer added, indicating an asymmetry in the law of effect. PMID:18422016

Enhancement of stability of aqueous suspension of alumina nanoparticles by femtosecond laser irradiation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Seo, Youngsang; Ha, Jeonghong; Kim, Dongsik, E-mail: dskim87@postech.ac.kr

2015-09-21

In this work, we report substantially enhanced colloidal stability of aqueous nanoparticle suspensions by ultrashort laser pulse irradiation. A Ti:Sapphire femtosecond laser (wavelength: 800 nm; pulse duration: 50 fs at full width at half maximum) was used to modify the electrochemical properties of nanoparticle suspensions at laser fluences below the particle ablation threshold. The colloidal stability of the suspension was evaluated by zeta potential and dynamic light scattering (DLS). The DLS results along with the images from transmission electron microscopy revealed that the laser irradiation caused no distinct morphological change to the individual alumina particles, but a substantial portion of themore » clustered particles was fragmented by the laser pulses, decreasing the apparent size of the suspended particles. Also, X-ray photoelectron spectroscopy analysis indicates that the laser irradiation modified the surface chemistry of the alumina particles. The stabilizing capability of the proposed technique was turned out to be better than that of conventional ultrasonic treatments. The stability of the laser-treated sample with no added surfactant was maintained for up to 30 days, without requiring an additional homogenizing process such as magnetic stirring.« less

Geological dates and molecular rates: rapid divergence of rivers and their biotas.

PubMed

Waters, Jonathan M; Rowe, Diane L; Apte, Smita; King, Tania M; Wallis, Graham P; Anderson, Leigh; Norris, Richard J; Craw, Dave; Burridge, Christopher P

2007-04-01

We highlight a novel molecular clock calibration system based on geologically dated river reversal and river capture events. Changes in drainage pattern may effect vicariant isolation of freshwater taxa, and thus provide a predictive framework for associated phylogeographic study. As a case in point, New Zealand's Pelorus and Kaituna rivers became geologically isolated from the larger Wairau River system 70 to 130 kyr BP. We conducted mitochondrial DNA phylogeographic analyses of two unrelated freshwater-limited fish taxa native to these river systems (Gobiomorphus breviceps, n = 63; Galaxias divergens, n = 95). Phylogenetic analysis of combined control region and cytochrome b sequences yielded reciprocally monophyletic clades of Pelorus-Kaituna and Wairau haplotypes for each species. Calibrated rates of molecular change based on this freshwater vicariant event are substantially faster than traditionally accepted rates for fishes but consistent with other recent inferences based on geologically young calibration points. A survey of freshwater phylogeographic literature reveals numerous examples in which the ages of recent evolutionary events may have been substantially overestimated through the use of "accepted" calibrations. We recommend that--wherever possible--biologists should start to reassess the conclusions of such studies by using more appropriate molecular calibrations derived from recent geological events.

The Legacy of Episodic Climatic Events in Shaping Temperate, Broadleaf Forests

NASA Technical Reports Server (NTRS)

Pederson, Neil; Dyer, James M.; McEwan, Ryan W.; Hessl, Amy E.; Mock, Cary J.; Orwig, David A.; Rieder, Harald E.; Cook, Benjamin I.

2015-01-01

In humid, broadleaf-dominated forests where gap dynamics and partial canopy mortality appears to dominate the disturbance regime at local scales, paleoecological evidence shows alteration at regional-scales associated with climatic change. Yet, little evidence of these broad-scale events exists in extant forests. To evaluate the potential for the occurrence of large-scale disturbance, we used 76 tree-ring collections spanning approx. 840 000 sq km and 5327 tree recruitment dates spanning approx. 1.4 million sq km across the humid eastern United States. Rotated principal component analysis indicated a common growth pattern of a simultaneous reduction in competition in 22 populations across 61 000 km2. Growth-release analysis of these populations reveals an intense and coherent canopy disturbance from 1775 to 1780, peaking in 1776. The resulting time series of canopy disturbance is so poorly described by a Gaussian distribution that it can be described as ''heavy tailed,'' with most of the years from 1775 to 1780 comprising the heavy-tail portion of the distribution. Historical documents provide no evidence that hurricanes or ice storms triggered the 1775-1780 event. Instead, we identify a significant relationship between prior drought and years with elevated rates of disturbance with an intense drought occurring from 1772 to 1775. We further find that years with high rates of canopy disturbance have a propensity to create larger canopy gaps indicating repeated opportunities for rapid change in species composition beyond the landscape scale. Evidence of elevated, regional-scale disturbance reveals how rare events can potentially alter system trajectory: a substantial portion of old-growth forests examined here originated or were substantially altered more than two centuries ago following events lasting just a few years. Our recruitment data, comprised of at least 21 species and several shade-intolerant species, document a pulse of tree recruitment at the subcontinental scale during the late-1600s suggesting that this event was severe enough to open large canopy gaps. These disturbances and their climatic drivers support the hypothesis that punctuated, episodic, climatic events impart a legacy in broadleaf-dominated forests centuries after their occurrence. Given projections of future drought, these results also reveal the potential for abrupt, meso- to large-scale forest change in broadleaf-dominated forests over future decades.

IgG3 deficiency extends lifespan and attenuates progression of glomerulonephritis in MRL/lpr mice

PubMed Central

2012-01-01

Background Antibodies of the IgG3 subclass have been implicated in the pathogenesis of the spontaneous glomerulonephritis observed in mice of the MRL/MpJ-Tnfrsf6lpr (MRL/lpr) inbred strain which have been widely studied as a model of systemic lupus erythematosus We have produced IgG3-deficient (-/-) mice with the MRL/lpr genetic background to determine whether IgG3 antibodies are necessary for or at least contributory to MRL/lpr-associated nephritis. Results The gamma3 genotype (+/+ vs. +/- vs. -/-) did not appear to significantly affect serum titers of IgG auto-antibodies specific for double-stranded DNA (dsDNA) or α-actinin. However, while substantial serum titers of IgG3 auto-antibodies specific for double-stranded DNA (dsDNA) or α-actinin were seen in gamma3 +/+ mice, somewhat lower serum titers of these IgG3 auto-antibodies were found in gamma3 +/- mice, and gamma3 -/- mice exhibited baseline concentrations of these auto-antibodies. Analysis of immunoglobulins eluted from snap-frozen kidneys obtained from mice of all three gamma3 genotypes at ~18 weeks of age revealed much higher quantities of IgG in the kidneys from gamma3 +/+ than gamma3 -/- mice, and most IgG eluted from +/+ mice was IgG3. The serum creatinine levels in gamma3 +/+ mice substantially exceeded those of age-matched gamma3 -/- mice after ~21 weeks of age. Histopathological examination of kidneys from mice sacrificed at pre-determined ages also revealed more extensive glomerulosclerosis in gamma3 +/+ or +/- mice than in -/- mice beginning at 21 weeks of age. Survival analysis for IgG3-deficient and IgG3-producing MRL/lpr mice revealed that gamma3 -/- mice lived significantly longer (p = 0.0006) than either gamma3 +/- or +/+ mice. Spontaneous death appeared to be due to irreversible renal failure, because > 85% of glomeruli in kidneys from mice that died spontaneously were obliterated by glomerulosclerosis. Conclusions The available evidence suggests that IgG3 deficiency partially protects MRL/lpr mice against glomerulonephritis-associated morbidity and mortality by slowing or arresting the progression to glomerulosclerosis. Reviewers This article was reviewed by Pushpa Pandiyan, Irun Cohen, and Etienne Joly. PMID:22248284

Climate change and the macroeconomic structure in pre-industrial europe: new evidence from wavelet analysis.

PubMed

Pei, Qing; Zhang, David D; Li, Guodong; Lee, Harry F

2015-01-01

The relationship between climate change and the macroeconomy in pre-industrial Europe has attracted considerable attention in recent years. This study follows the combined paradigms of evolutionary economics and ecological economics, in which wavelet analysis (spectrum analysis and coherence analysis) is applied as the first attempt to examine the relationship between climate change and the macroeconomic structure in pre-industrial Europe in the frequency domain. Aside from confirming previous results, this study aims to further substantiate the association between climate change and macroeconomy by presenting new evidence obtained from the wavelet analysis. Our spectrum analysis shows a consistent and continuous frequency band of 60-80 years in the temperature, grain yield ratio, grain price, consumer price index, and real wage throughout the study period. Besides, coherence analysis shows that the macroeconomic structure is shaped more by climate change than population change. In addition, temperature is proven as a key climatic factor that influences the macroeconomic structure. The analysis reveals a unique frequency band of about 20 years (15-35 years) in the temperature in AD1600-1700, which could have contributed to the widespread economic crisis in pre-industrial Europe. Our findings may have indications in re-examining the Malthusian theory.

Climate Change and the Macroeconomic Structure in Pre-Industrial Europe: New Evidence from Wavelet Analysis

PubMed Central

Pei, Qing; Zhang, David D.; Li, Guodong; Lee, Harry F.

2015-01-01

The relationship between climate change and the macroeconomy in pre-industrial Europe has attracted considerable attention in recent years. This study follows the combined paradigms of evolutionary economics and ecological economics, in which wavelet analysis (spectrum analysis and coherence analysis) is applied as the first attempt to examine the relationship between climate change and the macroeconomic structure in pre-industrial Europe in the frequency domain. Aside from confirming previous results, this study aims to further substantiate the association between climate change and macroeconomy by presenting new evidence obtained from the wavelet analysis. Our spectrum analysis shows a consistent and continuous frequency band of 60–80 years in the temperature, grain yield ratio, grain price, consumer price index, and real wage throughout the study period. Besides, coherence analysis shows that the macroeconomic structure is shaped more by climate change than population change. In addition, temperature is proven as a key climatic factor that influences the macroeconomic structure. The analysis reveals a unique frequency band of about 20 years (15–35 years) in the temperature in AD1600-1700, which could have contributed to the widespread economic crisis in pre-industrial Europe. Our findings may have indications in re-examining the Malthusian theory. PMID:26039087

Hypothyroidism as a risk factor for open angle glaucoma: A systematic review and meta-analysis

PubMed Central

Liu, Yue; Zheng, Guangying

2017-01-01

Purpose The relationship between hypothyroidism and primary open angle glaucoma (POAG) has attracted intense interest recently, but the reported results have been controversial. This meta-analysis was carried out to determine the association between hypothyroidism and POAG. Methods The literature was identified from three databases (Web of Science, Embase, and PubMed). The meta-analyses were performed using random-effects models, with results reported as adjusted odds ratios (ORs) with 95% confidence intervals (CI 95%). Results A total of 11 studies meeting the inclusion criteria were included in the final meta-analysis. The pooled OR based on 11 risk estimates showed a statistically significant increased risk of POAG prevalence among individuals with hypothyroidism (OR = 1.64, 95% CI = 1.27–2.13). Substantial heterogeneity among these studies was detected (P < 0.001; I2 = 83.2%). Sub-group analysis revealed that the cohort studies and case–control studies showed a significant association between hypothyroidism and POAG, which was not observed in cross-sectional studies. There was no significant publication bias in this study. Conclusions The findings of this meta-analysis indicate that individuals with hypothyroidism have an increased risk of developing POAG. PMID:29069095

Myostatin-2 gene structure and polymorphism of the promoter and first intron in the marine fish Sparus aurata: evidence for DNA duplications and/or translocations.

PubMed

Nadjar-Boger, Elisabeth; Funkenstein, Bruria

2011-02-01

Myostatin (MSTN) is a member of the transforming growth factor-ß superfamily that functions as a negative regulator of skeletal muscle development and growth in mammals. Fish express at least two genes for MSTN: MSTN-1 and MSTN-2. To date, MSTN-2 promoters have been cloned only from salmonids and zebrafish. Here we described the cloning and sequence analysis of MSTN-2 gene and its 5' flanking region in the marine fish Sparus aurata (saMSTN-2). We demonstrate the existence of three alleles of the promoter and three alleles of the first intron. Sequence comparison of the promoter region in the three alleles revealed that although the sequences of the first 1050 bp upstream of the translation start site are almost identical in the three alleles, a substantial sequence divergence is seen further upstream. Careful sequence analysis of the region upstream of the first 1050 bp in the three alleles identified several elements that appear to be repeated in some or all sequences, at different positions. This suggests that the promoter region of saMSTN-2 has been subjected to various chromosomal rearrangements during the course of evolution, reflecting either insertion or deletion events. Screening of several genomic DNA collections indicated differences in allele frequency, with allele 'b' being the most abundant, followed by allele 'c', whereas allele 'a' is relatively rare. Sequence analysis of saMSTN-2 gene also revealed polymorphism in the first intron, identifying three alleles. The length difference in alleles '1R' and '2R' of the first intron is due to the presence of one or two copies of a repeated block of approximately 150 bp, located at the 5' end of the first intron. The third allele, '4R', has an additional insertion of 323 bp located 116 bp upstream of the 3' end of the first intron. Analysis of several DNA collections showed that the '2R' allele is the most common, followed by the '4R' allele, whereas the '1R' allele is relatively rare. Progeny analysis of a full-sib family showed a Mendelian mode of inheritance of the two genetic loci. No clear association was found between the two genetic markers and growth rate. These results show for the first time a substantial degree of polymorphism in both the promoter and first intron of MSTN-2 gene in a perciform fish species which points to chromosomal rearrangements that took place during evolution.

Metabolic changes in transgenic maize mature seeds over-expressing the Aspergillus niger phyA2.

PubMed

Rao, Jun; Yang, Litao; Guo, Jinchao; Quan, Sheng; Chen, Guihua; Zhao, Xiangxiang; Zhang, Dabing; Shi, Jianxin

2016-02-01

Non-targeted metabolomics analysis revealed only intended metabolic changes in transgenic maize over-expressing the Aspergillus niger phyA2. Genetically modified (GM) crops account for a large proportion of modern agriculture worldwide, raising increasingly the public concerns of safety. Generally, according to substantial equivalence principle, if a GM crop is demonstrated to be equivalently safe to its conventional species, it is supposed to be safe. In this study, taking the advantage of an established non-target metabolomic profiling platform based on the combination of UPLC-MS/MS with GC-MS, we compared the mature seed metabolic changes in transgenic maize over-expressing the Aspergillus niger phyA2 with its non-transgenic counterpart and other 14 conventional maize lines. In total, levels of nine out of identified 210 metabolites were significantly changed in transgenic maize as compared with its non-transgenic counterpart, and the number of significantly altered metabolites was reduced to only four when the natural variations were taken into consideration. Notably, those four metabolites were all associated with targeted engineering pathway. Our results indicated that although both intended and non-intended metabolic changes occurred in the mature seeds of this GM maize event, only intended metabolic pathway was found to be out of the range of the natural metabolic variation in the metabolome of the transgenic maize. Therefore, only when natural metabolic variation was taken into account, could non-targeted metabolomics provide reliable objective compositional substantial equivalence analysis on GM crops.

Evaluation of Three Protein-Extraction Methods for Proteome Analysis of Maize Leaf Midrib, a Compound Tissue Rich in Sclerenchyma Cells.

PubMed

Wang, Ning; Wu, Xiaolin; Ku, Lixia; Chen, Yanhui; Wang, Wei

2016-01-01

Leaf morphology is closely related to the growth and development of maize (Zea mays L.) plants and final kernel production. As an important part of the maize leaf, the midrib holds leaf blades in the aerial position for maximum sunlight capture. Leaf midribs of adult plants contain substantial sclerenchyma cells with heavily thickened and lignified secondary walls and have a high amount of phenolics, making protein extraction and proteome analysis difficult in leaf midrib tissue. In the present study, three protein-extraction methods that are commonly used in plant proteomics, i.e., phenol extraction, TCA/acetone extraction, and TCA/acetone/phenol extraction, were qualitatively and quantitatively evaluated based on 2DE maps and MS/MS analysis using the midribs of the 10th newly expanded leaves of maize plants. Microscopy revealed the existence of substantial amounts of sclerenchyma underneath maize midrib epidermises (particularly abaxial epidermises). The spot-number order obtained via 2DE mapping was as follows: phenol extraction (655) > TCA/acetone extraction (589) > TCA/acetone/phenol extraction (545). MS/MS analysis identified a total of 17 spots that exhibited 2-fold changes in abundance among the three methods (using phenol extraction as a control). Sixteen of the proteins identified were hydrophilic, with GRAVY values ranging from -0.026 to -0.487. For all three methods, we were able to obtain high-quality protein samples and good 2DE maps for the maize leaf midrib. However, phenol extraction produced a better 2DE map with greater resolution between spots, and TCA/acetone extraction produced higher protein yields. Thus, this paper includes a discussion regarding the possible reasons for differential protein extraction among the three methods. This study provides useful information that can be used to select suitable protein extraction methods for the proteome analysis of recalcitrant plant tissues that are rich in sclerenchyma cells.

Analytical Round Robin for Elastic-Plastic Analysis of Surface Cracked Plates: Phase I Results

NASA Technical Reports Server (NTRS)

Wells, D. N.; Allen, P. A.

2012-01-01

An analytical round robin for the elastic-plastic analysis of surface cracks in flat plates was conducted with 15 participants. Experimental results from a surface crack tension test in 2219-T8 aluminum plate provided the basis for the inter-laboratory study (ILS). The study proceeded in a blind fashion given that the analysis methodology was not specified to the participants, and key experimental results were withheld. This approach allowed the ILS to serve as a current measure of the state of the art for elastic-plastic fracture mechanics analysis. The analytical results and the associated methodologies were collected for comparison, and sources of variability were studied and isolated. The results of the study revealed that the J-integral analysis methodology using the domain integral method is robust, providing reliable J-integral values without being overly sensitive to modeling details. General modeling choices such as analysis code, model size (mesh density), crack tip meshing, or boundary conditions, were not found to be sources of significant variability. For analyses controlled only by far-field boundary conditions, the greatest source of variability in the J-integral assessment is introduced through the constitutive model. This variability can be substantially reduced by using crack mouth opening displacements to anchor the assessment. Conclusions provide recommendations for analysis standardization.

Metabolomics of dates (Phoenix dactylifera) reveals a highly dynamic ripening process accounting for major variation in fruit composition.

PubMed

Diboun, Ilhame; Mathew, Sweety; Al-Rayyashi, Maryam; Elrayess, Mohamed; Torres, Maria; Halama, Anna; Méret, Michaël; Mohney, Robert P; Karoly, Edward D; Malek, Joel; Suhre, Karsten

2015-12-16

Dates are tropical fruits with appreciable nutritional value. Previous attempts at global metabolic characterization of the date metabolome were constrained by small sample size and limited geographical sampling. In this study, two independent large cohorts of mature dates exhibiting substantial diversity in origin, varieties and fruit processing conditions were measured by metabolomics techniques in order to identify major determinants of the fruit metabolome. Multivariate analysis revealed a first principal component (PC1) significantly associated with the dates' countries of production. The availability of a smaller dataset featuring immature dates from different development stages served to build a model of the ripening process in dates, which helped reveal a strong ripening signature in PC1. Analysis revealed enrichment in the dry type of dates amongst fruits with early ripening profiles at one end of PC1 as oppose to an overrepresentation of the soft type of dates with late ripening profiles at the other end of PC1. Dry dates are typical to the North African region whilst soft dates are more popular in the Gulf region, which partly explains the observed association between PC1 and geography. Analysis of the loading values, expressing metabolite correlation levels with PC1, revealed enrichment patterns of a comprehensive range of metabolite classes along PC1. Three distinct metabolic phases corresponding to known stages of date ripening were observed: An early phase enriched in regulatory hormones, amines and polyamines, energy production, tannins, sucrose and anti-oxidant activity, a second phase with on-going phenylpropanoid secondary metabolism, gene expression and phospholipid metabolism and a late phase with marked sugar dehydration activity and degradation reactions leading to increased volatile synthesis. These data indicate the importance of date ripening as a main driver of variation in the date metabolome responsible for their diverse nutritional and economical values. The biochemistry of the ripening process in dates is consistent with other fruits but natural dryness may prevent degenerative senescence in dates following ripening. Based on the finding that mature dates present varying extents of ripening, our survey of the date metabolome essentially revealed snapshots of interchanging metabolic states during ripening empowering an in-depth characterization of underlying biology.

A data analysis framework for biomedical big data: Application on mesoderm differentiation of human pluripotent stem cells

PubMed Central

Karlsson, Alexander; Riveiro, Maria; Améen, Caroline; Åkesson, Karolina; Andersson, Christian X.; Sartipy, Peter; Synnergren, Jane

2017-01-01

The development of high-throughput biomolecular technologies has resulted in generation of vast omics data at an unprecedented rate. This is transforming biomedical research into a big data discipline, where the main challenges relate to the analysis and interpretation of data into new biological knowledge. The aim of this study was to develop a framework for biomedical big data analytics, and apply it for analyzing transcriptomics time series data from early differentiation of human pluripotent stem cells towards the mesoderm and cardiac lineages. To this end, transcriptome profiling by microarray was performed on differentiating human pluripotent stem cells sampled at eleven consecutive days. The gene expression data was analyzed using the five-stage analysis framework proposed in this study, including data preparation, exploratory data analysis, confirmatory analysis, biological knowledge discovery, and visualization of the results. Clustering analysis revealed several distinct expression profiles during differentiation. Genes with an early transient response were strongly related to embryonic- and mesendoderm development, for example CER1 and NODAL. Pluripotency genes, such as NANOG and SOX2, exhibited substantial downregulation shortly after onset of differentiation. Rapid induction of genes related to metal ion response, cardiac tissue development, and muscle contraction were observed around day five and six. Several transcription factors were identified as potential regulators of these processes, e.g. POU1F1, TCF4 and TBP for muscle contraction genes. Pathway analysis revealed temporal activity of several signaling pathways, for example the inhibition of WNT signaling on day 2 and its reactivation on day 4. This study provides a comprehensive characterization of biological events and key regulators of the early differentiation of human pluripotent stem cells towards the mesoderm and cardiac lineages. The proposed analysis framework can be used to structure data analysis in future research, both in stem cell differentiation, and more generally, in biomedical big data analytics. PMID:28654683

A data analysis framework for biomedical big data: Application on mesoderm differentiation of human pluripotent stem cells.

PubMed

Ulfenborg, Benjamin; Karlsson, Alexander; Riveiro, Maria; Améen, Caroline; Åkesson, Karolina; Andersson, Christian X; Sartipy, Peter; Synnergren, Jane

2017-01-01

The development of high-throughput biomolecular technologies has resulted in generation of vast omics data at an unprecedented rate. This is transforming biomedical research into a big data discipline, where the main challenges relate to the analysis and interpretation of data into new biological knowledge. The aim of this study was to develop a framework for biomedical big data analytics, and apply it for analyzing transcriptomics time series data from early differentiation of human pluripotent stem cells towards the mesoderm and cardiac lineages. To this end, transcriptome profiling by microarray was performed on differentiating human pluripotent stem cells sampled at eleven consecutive days. The gene expression data was analyzed using the five-stage analysis framework proposed in this study, including data preparation, exploratory data analysis, confirmatory analysis, biological knowledge discovery, and visualization of the results. Clustering analysis revealed several distinct expression profiles during differentiation. Genes with an early transient response were strongly related to embryonic- and mesendoderm development, for example CER1 and NODAL. Pluripotency genes, such as NANOG and SOX2, exhibited substantial downregulation shortly after onset of differentiation. Rapid induction of genes related to metal ion response, cardiac tissue development, and muscle contraction were observed around day five and six. Several transcription factors were identified as potential regulators of these processes, e.g. POU1F1, TCF4 and TBP for muscle contraction genes. Pathway analysis revealed temporal activity of several signaling pathways, for example the inhibition of WNT signaling on day 2 and its reactivation on day 4. This study provides a comprehensive characterization of biological events and key regulators of the early differentiation of human pluripotent stem cells towards the mesoderm and cardiac lineages. The proposed analysis framework can be used to structure data analysis in future research, both in stem cell differentiation, and more generally, in biomedical big data analytics.

GIS Modeling of Air Toxics Releases from TRI-Reporting and Non-TRI-Reporting Facilities: Impacts for Environmental Justice

PubMed Central

Dolinoy, Dana C.; Miranda, Marie Lynn

2004-01-01

The Toxics Release Inventory (TRI) requires facilities with 10 or more full-time employees that process > 25,000 pounds in aggregate or use > 10,000 pounds of any one TRI chemical to report releases annually. However, little is known about releases from non-TRI-reporting facilities, nor has attention been given to the very localized equity impacts associated with air toxics releases. Using geographic information systems and industrial source complex dispersion modeling, we developed methods for characterizing air releases from TRI-reporting as well as non-TRI-reporting facilities at four levels of geographic resolution. We characterized the spatial distribution and concentration of air releases from one representative industry in Durham County, North Carolina (USA). Inclusive modeling of all facilities rather than modeling of TRI sites alone significantly alters the magnitude and spatial distribution of modeled air concentrations. Modeling exposure receptors at more refined levels of geographic resolution reveals localized, neighborhood-level exposure hot spots that are not apparent at coarser geographic scales. Multivariate analysis indicates that inclusive facility modeling at fine levels of geographic resolution reveals exposure disparities by income and race. These new methods significantly enhance the ability to model air toxics, perform equity analysis, and clarify conflicts in the literature regarding environmental justice findings. This work has substantial implications for how to structure TRI reporting requirements, as well as methods and types of analysis that will successfully elucidate the spatial distribution of exposure potentials across geographic, income, and racial lines. PMID:15579419

Long-term growth decline in Toona ciliata in a moist tropical forest in Bangladesh: Impact of global warming

NASA Astrophysics Data System (ADS)

Rahman, Mizanur; Islam, Rofiqul; Islam, Mahmuda

2017-04-01

Tropical forests are carbon rich ecosystems and small changes in tropical forest tree growth substantially influence the global carbon cycle. Forest monitoring studies report inconsistent growth changes in tropical forest trees over the past decades. Most of the studies highlighted changes in the forest level carbon gain, neglecting the species-specific growth changes which ultimately determine community-level responses. Tree-ring analysis can provide historical data on species-specific tree growth with annual resolution. Such studies are inadequate in Bangladesh, which is one of the most climate sensitive regions in the tropics. In this study, we investigated long-term growth rates of Toona ciliata in a moist tropical forest of Bangladesh by using tree-ring analysis. We sampled 50 trees of varying size, obtained increment cores from these trees and measured tree-ring width. Analyses of growth patterns revealed size-dependent growth increments. After correcting for the effect of tree size on tree growth (ontogenetic changes) by two different methods we found declining growth rates in T. ciliata from 1960 to 2013. Standardized ring-width index (RWI) was strongly negatively correlated with annual mean and maximum temperatures suggesting that rising temperature might cause the observed growth decline in T. ciliata. Assuming that global temperatures will rise at the current rate, the observed growth decline is assumed to continue. The analysis of stable carbon and oxygen isotopes may reveal more insight on the physiological response of this species to future climatic changes.

Phosphoproteomic Analysis Identifies Focal Adhesion Kinase 2 (FAK2) as a Potential Therapeutic Target for Tamoxifen Resistance in Breast Cancer*

PubMed Central

Wu, Xinyan; Zahari, Muhammad Saddiq; Renuse, Santosh; Nirujogi, Raja Sekhar; Kim, Min-Sik; Manda, Srikanth S.; Stearns, Vered; Gabrielson, Edward; Sukumar, Saraswati; Pandey, Akhilesh

2015-01-01

Tamoxifen, an estrogen receptor-α (ER) antagonist, is an important agent for the treatment of breast cancer. However, this therapy is complicated by the fact that a substantial number of patients exhibit either de novo or acquired resistance. To characterize the signaling mechanisms underlying this resistance, we treated the MCF7 breast cancer cell line with tamoxifen for over six months and showed that this cell line acquired resistance to tamoxifen in vitro and in vivo. We performed SILAC-based quantitative phosphoproteomic profiling on the tamoxifen resistant and vehicle-treated sensitive cell lines to quantify the phosphorylation alterations associated with tamoxifen resistance. From >5600 unique phosphopeptides identified, 1529 peptides exhibited hyperphosphorylation and 409 peptides showed hypophosphorylation in the tamoxifen resistant cells. Gene set enrichment analysis revealed that focal adhesion pathway was one of the most enriched signaling pathways activated in tamoxifen resistant cells. Significantly, we showed that the focal adhesion kinase FAK2 was not only hyperphosphorylated but also transcriptionally up-regulated in tamoxifen resistant cells. FAK2 suppression by specific siRNA knockdown or a small molecule inhibitor repressed cellular proliferation in vitro and tumor formation in vivo. More importantly, our survival analysis revealed that high expression of FAK2 is significantly associated with shorter metastasis-free survival in estrogen receptor-positive breast cancer patients treated with tamoxifen. Our studies suggest that FAK2 is a potential therapeutic target for the management of hormone-refractory breast cancers. PMID:26330541

Gene Expression Analysis Reveals New Possible Mechanisms of Vancomycin-Induced Nephrotoxicity and Identifies Gene Markers Candidates

PubMed Central

Dieterich, Christine; Puey, Angela; Lyn, Sylvia; Swezey, Robert; Furimsky, Anna; Fairchild, David; Mirsalis, Jon C.; Ng, Hanna H.

2009-01-01

Vancomycin, one of few effective treatments against methicillin-resistant Staphylococcus aureus, is nephrotoxic. The goals of this study were to (1) gain insights into molecular mechanisms of nephrotoxicity at the genomic level, (2) evaluate gene markers of vancomycin-induced kidney injury, and (3) compare gene expression responses after iv and ip administration. Groups of six female BALB/c mice were treated with seven daily iv or ip doses of vancomycin (50, 200, and 400 mg/kg) or saline, and sacrificed on day 8. Clinical chemistry and histopathology demonstrated kidney injury at 400 mg/kg only. Hierarchical clustering analysis revealed that kidney gene expression profiles of all mice treated at 400 mg/kg clustered with those of mice administered 200 mg/kg iv. Transcriptional profiling might thus be more sensitive than current clinical markers for detecting kidney damage, though the profiles can differ with the route of administration. Analysis of transcripts whose expression was changed by at least twofold compared with vehicle saline after high iv and ip doses of vancomycin suggested the possibility of oxidative stress and mitochondrial damage in vancomycin-induced toxicity. In addition, our data showed changes in expression of several transcripts from the complement and inflammatory pathways. Such expression changes were confirmed by relative real-time reverse transcription–polymerase chain reaction. Finally, our results further substantiate the use of gene markers of kidney toxicity such as KIM-1/Havcr1, as indicators of renal injury. PMID:18930951

Gene expression analysis reveals new possible mechanisms of vancomycin-induced nephrotoxicity and identifies gene markers candidates.

PubMed

Dieterich, Christine; Puey, Angela; Lin, Sylvia; Lyn, Sylvia; Swezey, Robert; Furimsky, Anna; Fairchild, David; Mirsalis, Jon C; Ng, Hanna H

2009-01-01

Vancomycin, one of few effective treatments against methicillin-resistant Staphylococcus aureus, is nephrotoxic. The goals of this study were to (1) gain insights into molecular mechanisms of nephrotoxicity at the genomic level, (2) evaluate gene markers of vancomycin-induced kidney injury, and (3) compare gene expression responses after iv and ip administration. Groups of six female BALB/c mice were treated with seven daily iv or ip doses of vancomycin (50, 200, and 400 mg/kg) or saline, and sacrificed on day 8. Clinical chemistry and histopathology demonstrated kidney injury at 400 mg/kg only. Hierarchical clustering analysis revealed that kidney gene expression profiles of all mice treated at 400 mg/kg clustered with those of mice administered 200 mg/kg iv. Transcriptional profiling might thus be more sensitive than current clinical markers for detecting kidney damage, though the profiles can differ with the route of administration. Analysis of transcripts whose expression was changed by at least twofold compared with vehicle saline after high iv and ip doses of vancomycin suggested the possibility of oxidative stress and mitochondrial damage in vancomycin-induced toxicity. In addition, our data showed changes in expression of several transcripts from the complement and inflammatory pathways. Such expression changes were confirmed by relative real-time reverse transcription-polymerase chain reaction. Finally, our results further substantiate the use of gene markers of kidney toxicity such as KIM-1/Havcr1, as indicators of renal injury.

Epigenetic modification and inheritance in sexual reversal of fish.

PubMed

Shao, Changwei; Li, Qiye; Chen, Songlin; Zhang, Pei; Lian, Jinmin; Hu, Qiaomu; Sun, Bing; Jin, Lijun; Liu, Shanshan; Wang, Zongji; Zhao, Hongmei; Jin, Zonghui; Liang, Zhuo; Li, Yangzhen; Zheng, Qiumei; Zhang, Yong; Wang, Jun; Zhang, Guojie

2014-04-01

Environmental sex determination (ESD) occurs in divergent, phylogenetically unrelated taxa, and in some species, co-occurs with genetic sex determination (GSD) mechanisms. Although epigenetic regulation in response to environmental effects has long been proposed to be associated with ESD, a systemic analysis on epigenetic regulation of ESD is still lacking. Using half-smooth tongue sole (Cynoglossus semilaevis) as a model-a marine fish that has both ZW chromosomal GSD and temperature-dependent ESD-we investigated the role of DNA methylation in transition from GSD to ESD. Comparative analysis of the gonadal DNA methylomes of pseudomale, female, and normal male fish revealed that genes in the sex determination pathways are the major targets of substantial methylation modification during sexual reversal. Methylation modification in pseudomales is globally inherited in their ZW offspring, which can naturally develop into pseudomales without temperature incubation. Transcriptome analysis revealed that dosage compensation occurs in a restricted, methylated cytosine enriched Z chromosomal region in pseudomale testes, achieving equal expression level in normal male testes. In contrast, female-specific W chromosomal genes are suppressed in pseudomales by methylation regulation. We conclude that epigenetic regulation plays multiple crucial roles in sexual reversal of tongue sole fish. We also offer the first clues on the mechanisms behind gene dosage balancing in an organism that undergoes sexual reversal. Finally, we suggest a causal link between the bias sex chromosome assortment in the offspring of a pseudomale family and the transgenerational epigenetic inheritance of sexual reversal in tongue sole fish.

HIV populations are large and accumulate high genetic diversity in a nonlinear fashion.

PubMed

Maldarelli, Frank; Kearney, Mary; Palmer, Sarah; Stephens, Robert; Mican, JoAnn; Polis, Michael A; Davey, Richard T; Kovacs, Joseph; Shao, Wei; Rock-Kress, Diane; Metcalf, Julia A; Rehm, Catherine; Greer, Sarah E; Lucey, Daniel L; Danley, Kristen; Alter, Harvey; Mellors, John W; Coffin, John M

2013-09-01

HIV infection is characterized by rapid and error-prone viral replication resulting in genetically diverse virus populations. The rate of accumulation of diversity and the mechanisms involved are under intense study to provide useful information to understand immune evasion and the development of drug resistance. To characterize the development of viral diversity after infection, we carried out an in-depth analysis of single genome sequences of HIV pro-pol to assess diversity and divergence and to estimate replicating population sizes in a group of treatment-naive HIV-infected individuals sampled at single (n = 22) or multiple, longitudinal (n = 11) time points. Analysis of single genome sequences revealed nonlinear accumulation of sequence diversity during the course of infection. Diversity accumulated in recently infected individuals at rates 30-fold higher than in patients with chronic infection. Accumulation of synonymous changes accounted for most of the diversity during chronic infection. Accumulation of diversity resulted in population shifts, but the rates of change were low relative to estimated replication cycle times, consistent with relatively large population sizes. Analysis of changes in allele frequencies revealed effective population sizes that are substantially higher than previous estimates of approximately 1,000 infectious particles/infected individual. Taken together, these observations indicate that HIV populations are large, diverse, and slow to change in chronic infection and that the emergence of new mutations, including drug resistance mutations, is governed by both selection forces and drift.

Intrinsic disorder in transcription factors†

PubMed Central

Liu, Jiangang; Perumal, Narayanan B.; Oldfield, Christopher J.; Su, Eric W.; Uversky, Vladimir N.; Dunker, A. Keith

2008-01-01

Intrinsic disorder (ID) is highly abundant in eukaryotes, which reflect the greater need for disorder-associated signaling and transcriptional regulation in nucleated cells. Although several well-characterized examples of intrinsically disordered proteins in transcriptional regulation have been reported, no systematic analysis has been reported so far. To test for a general prevalence of intrinsic disorder in transcriptional regulation, we used the Predictor Of Natural Disorder Regions (PONDR) to analyze the abundance of intrinsic disorder in three transcription factor datasets and two control sets. This analysis revealed that from 94.13% to 82.63% of transcription factors posses extended regions of intrinsic disorder, relative to 54.51% and 18.64% of the proteins in two control datasets, which indicates the significant prevalence of intrinsic disorder in transcription factors. This propensity of transcription factors for intrinsic disorder was confirmed by cumulative distribution function analysis and charge-hydropathy plots. The amino acid composition analysis showed that all three transcription factor datasets were substantially depleted in order-promoting residues, and significantly enriched in disorder-promoting residues. Our analysis of the distribution of disorder within the transcription factor datasets revealed that: (a) The AT-hooks and basic regions of transcription factor DNA-binding domains are highly disordered; (b) The degree of disorder in transcription factor activation regions is much higher than that in DNA-binding domains; (c) The degree of disorder is significantly higher in eukaryotic transcription factors than in prokaryotic transcription factors; (d) The level of α-MoRFs (molecular recognition feature) prediction is much higher in transcription factors. Overall, our data reflected the fact that the eukaryotes with well-developed gene transcription machinery require transcription factor flexibility to be more efficient. PMID:16734424

Multiplexed immunohistochemistry, imaging, and quantitation: a review, with an assessment of Tyramide signal amplification, multispectral imaging and multiplex analysis.

PubMed

Stack, Edward C; Wang, Chichung; Roman, Kristin A; Hoyt, Clifford C

2014-11-01

Tissue sections offer the opportunity to understand a patient's condition, to make better prognostic evaluations and to select optimum treatments, as evidenced by the place pathology holds today in clinical practice. Yet, there is a wealth of information locked up in a tissue section that is only partially accessed, due mainly to the limitations of tools and methods. Often tissues are assessed primarily based on visual analysis of one or two proteins, or 2-3 DNA or RNA molecules. Even while analysis is still based on visual perception, image analysis is starting to address the variability of human perception. This is in contrast to measuring characteristics that are substantially out of reach of human perception, such as parameters revealed through co-expression, spatial relationships, heterogeneity, and low abundance molecules. What is not routinely accessed is the information revealed through simultaneous detection of multiple markers, the spatial relationships among cells and tissue in disease, and the heterogeneity now understood to be critical to developing effective therapeutic strategies. Our purpose here is to review and assess methods for multiplexed, quantitative, image analysis based approaches, using new multicolor immunohistochemistry methods, automated multispectral slide imaging, and advanced trainable pattern recognition software. A key aspect of our approach is presenting imagery in a workflow that engages the pathologist to utilize the strengths of human perception and judgment, while significantly expanding the range of metrics collectable from tissue sections and also provide a level of consistency and precision needed to support the complexities of personalized medicine. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Biomechanical analysis of fatigue-related foot injury mechanisms in athletes and recruits during intensive marching.

PubMed

Gefen, A

2002-05-01

An integrative analysis, comprising radiographic imaging of the foot, plantar pressure measurements, surface electromyography (EMG) and finite element (FE) modelling of the three-dimensional (3D) foot structure, was used to determine the effects of muscular fatigue induced by intensive athletic or military marching on the structural stability of the foot and on its internal stress state during the stance phase. The medial/lateral (M/L) tendency towards instability of the foot structure during marching in fatigue conditions was experimentally characterised by measuring the M/L deviations of the foot-ground centre of pressure (COP) and correlating these data with fatigue of specific lower-limb muscles, as demonstrated by the EMG spectra. The results demonstrated accelerated fatigue of the peroneus longus muscle in marching conditions (treadmill march of 2 km completed by four subjects at an approximately constant velocity of 8 km h-1). Severe fatigue of the peroneus longus is apparently the dominant cause of lack of foot stability, which was manifested by abnormal lateral deviations of the COP during the stance phase. Under these conditions, ankle sprain injuries are likely to occur. The EMG analysis further revealed substantial fatigue of the pre-tibial and triceps surae muscles during intensive marching (averaged decreases of 36% and 40% in the median frequency of their EMG signal spectra, respectively). Incorporation of this information into the 3D FE model of the foot resulted in a substantial rise in the levels of calcaneal and metatarsal stress concentrations, by 50% and 36%, respectively. This may point to the mechanism by which stress fractures develop and provide the biomechanical tools for future clinical investigations.

Analysis of the entire genomes of torque teno midi virus variants in chimpanzees: infrequent cross-species infection between humans and chimpanzees.

PubMed

Ninomiya, Masashi; Takahashi, Masaharu; Hoshino, Yu; Ichiyama, Koji; Simmonds, Peter; Okamoto, Hiroaki

2009-02-01

Humans are frequently infected with three anelloviruses which have circular DNA genomes of 3.6-3.9 kb [Torque teno virus (TTV)], 2.8-2.9 kb [Torque teno mini virus (TTMV)] and 3.2 kb [a recently discovered anellovirus named Torque teno midi virus (TTMDV)]. Unexpectedly, human TTMDV DNA was not detectable in any of 74 chimpanzees tested, although all but one tested positive for both human TTV and TTMV DNA. Using universal primers for anelloviruses, novel variants of TTMDV that are phylogenetically clearly separate from human TTMDV were identified from chimpanzees, and over the entire genome, three chimpanzee TTMDV variants differed by 17.9-20.3 % from each other and by 40.4-43.6 % from all 18 reported human TTMDVs. A newly developed PCR assay that uses chimpanzee TTMDV-specific primers revealed the high prevalence of chimpanzee TTMDV in chimpanzees (63/74, 85 %) but low prevalence in humans (1/100). While variants of TTV and TTMV from chimpanzees and humans were phylogenetically interspersed, those of TTMDV were monophyletic for each species, with sequence diversity of <33 and <20 % within the 18 human and three chimpanzee TTMDV variants, respectively. Maximum within-group divergence values for TTV and TTMV were 51 and 57 %, respectively; both of these values were substantially greater than the maximum divergence among TTMDV variants (44 %), consistent with a later evolutionary emergence of TTMDV. However, substantiation of this hypothesis will require further analysis of genetic diversity using an expanded dataset of TTMDV variants in humans and chimpanzees. Similarly, the underlying mechanism of observed infrequent cross-species infection of TTMDV between humans and chimpanzees deserves further analysis.

Engineering of a conditional allele reveals multiple roles of XRN2 in Caenorhabditis elegans development and substrate specificity in microRNA turnover.

PubMed

Miki, Takashi S; Rüegger, Stefan; Gaidatzis, Dimos; Stadler, Michael B; Großhans, Helge

2014-04-01

Although XRN2 proteins are highly conserved eukaryotic 5'→3' exonucleases, little is known about their function in animals. Here, we characterize Caenorhabditis elegans XRN2, which we find to be a broadly and constitutively expressed nuclear protein. An xrn-2 null mutation or loss of XRN2 catalytic activity causes a molting defect and early larval arrest. However, by generating a conditionally mutant xrn-2ts strain de novo through an approach that may be also applicable to other genes of interest, we reveal further functions in fertility, during embryogenesis and during additional larval stages. Consistent with the known role of XRN2 in controlling microRNA (miRNA) levels, we can demonstrate that loss of XRN2 activity stabilizes some rapidly decaying miRNAs. Surprisingly, however, other miRNAs continue to decay rapidly in xrn-2ts animals. Thus, XRN2 has unanticipated miRNA specificity in vivo, and its diverse developmental functions may relate to distinct substrates. Finally, our global analysis of miRNA stability during larval stage 1 reveals that miRNA passenger strands (miR*s) are substantially less stable than guide strands (miRs), supporting the notion that the former are mostly byproducts of biogenesis rather than a less abundant functional species.

A novel Tc-99m and fluorescence labeled peptide as a multimodal imaging agent for targeting angiogenesis in a murine hindlimb ischemia model.

PubMed

Hyoun Kim, Myoung; Kim, Seul-Gi; Guhn Kim, Chang; Kim, Dae-Weung

2017-03-01

The serine-aspartic acid-valine (SDV) peptide binds specifically to integrin αvβ3. We developed a Tc-99m and TAMRA labeled peptide, Tc-99m SDV-ECG-K-TAMRA for multimodal imaging of angiogenesis. Tc-99m SDV-ECG-K-TAMRA was prepared in high yield (>96%) and showed low cytotoxicity. Tc-99m tetrofosmin images 1 week after operation, revealed significantly decreased perfusion of the ischemic hindlimb, and the perfusion recovered gradually for 4 weeks. In contrast, Tc-99m SDV-ECG-K-TAMRA uptake was maximal 1 week after the operation (ischemic-to-non-ischemic uptake ratio =5.03±1.01) and decreased gradually. The ischemic-to-non-ischemic ratio of Tc-99m SDV-ECG-K-TAMRA and Tc-99m tetrofosmin was strongly negatively correlated (r =-0.94). A postmortem analysis revealed increased angiogenesis markers and uptake of Tc-99m SDV-ECG-K-TAMRA by ischemic tissue. Our in vivo and in vitro studies revealed substantial uptake of Tc-99m SDV-ECG-K-TAMRA by ischemic tissue. Tc-99m SDV-ECG-K-TAMRA could be a good candidate dual-modality imaging agent to assess angiogenesis. Copyright © 2016 Elsevier Ltd. All rights reserved.

Dynamic analysis of a 5-MW tripod offshore wind turbine by considering fluid-structure interaction

NASA Astrophysics Data System (ADS)

Zhang, Li-wei; Li, Xin

2017-10-01

Fixed offshore wind turbines usually have large underwater supporting structures. The fluid influences the dynamic characteristics of the structure system. The dynamic model of a 5-MW tripod offshore wind turbine considering the pile-soil system and fluid structure interaction (FSI) is established, and the structural modes in air and in water are obtained by use of ANSYS. By comparing low-order natural frequencies and mode shapes, the influence of sea water on the free vibration characteristics of offshore wind turbine is analyzed. On basis of the above work, seismic responses under excitation by El-Centro waves are calculated by the time-history analysis method. The results reveal that the dynamic responses such as the lateral displacement of the foundation and the section bending moment of the tubular piles increase substantially under the influence of the added-mass and hydrodynamic pressure of sea water. The method and conclusions presented in this paper can provide a theoretical reference for structure design and analysis of offshore wind turbines fixed in deep seawater.

Experimental and Theoretical Approaches for the Surface Interaction between Copper and Activated Sludge Microorganisms at Molecular Scale

NASA Astrophysics Data System (ADS)

Luo, Hong-Wei; Chen, Jie-Jie; Sheng, Guo-Ping; Su, Ji-Hu; Wei, Shi-Qiang; Yu, Han-Qing

2014-11-01

Interactions between metals and activated sludge microorganisms substantially affect the speciation, immobilization, transport, and bioavailability of trace heavy metals in biological wastewater treatment plants. In this study, the interaction of Cu(II), a typical heavy metal, onto activated sludge microorganisms was studied in-depth using a multi-technique approach. The complexing structure of Cu(II) on microbial surface was revealed by X-ray absorption fine structure (XAFS) and electron paramagnetic resonance (EPR) analysis. EPR spectra indicated that Cu(II) was held in inner-sphere surface complexes of octahedral coordination with tetragonal distortion of axial elongation. XAFS analysis further suggested that the surface complexation between Cu(II) and microbial cells was the distorted inner-sphere coordinated octahedra containing four short equatorial bonds and two elongated axial bonds. To further validate the results obtained from the XAFS and EPR analysis, density functional theory calculations were carried out to explore the structural geometry of the Cu complexes. These results are useful to better understand the speciation, immobilization, transport, and bioavailability of metals in biological wastewater treatment plants.

Scalable and cost-effective NGS genotyping in the cloud.

PubMed

Souilmi, Yassine; Lancaster, Alex K; Jung, Jae-Yoon; Rizzo, Ettore; Hawkins, Jared B; Powles, Ryan; Amzazi, Saaïd; Ghazal, Hassan; Tonellato, Peter J; Wall, Dennis P

2015-10-15

While next-generation sequencing (NGS) costs have plummeted in recent years, cost and complexity of computation remain substantial barriers to the use of NGS in routine clinical care. The clinical potential of NGS will not be realized until robust and routine whole genome sequencing data can be accurately rendered to medically actionable reports within a time window of hours and at scales of economy in the 10's of dollars. We take a step towards addressing this challenge, by using COSMOS, a cloud-enabled workflow management system, to develop GenomeKey, an NGS whole genome analysis workflow. COSMOS implements complex workflows making optimal use of high-performance compute clusters. Here we show that the Amazon Web Service (AWS) implementation of GenomeKey via COSMOS provides a fast, scalable, and cost-effective analysis of both public benchmarking and large-scale heterogeneous clinical NGS datasets. Our systematic benchmarking reveals important new insights and considerations to produce clinical turn-around of whole genome analysis optimization and workflow management including strategic batching of individual genomes and efficient cluster resource configuration.

It's all in the delivery! An analysis of instructional strategies from effective health education curricula.

PubMed

Herbert, Patrick C; Lohrmann, David K

2011-05-01

This study explores the relationship between instructional strategies and effective health education curricula. A content analysis of 10 health education curricula was conducted to determine if they include common instructional strategies for actively engaging students in acquisition of health skills. To be included, the curricula had to (1) be research-based and proven via empirical testing to positively influence the health behaviors and (2) address 1 of Centers for Disease Control and Prevention's 6 priority health risk behaviors. Content analysis revealed 5 active learning strategies incorporated to involve students in acquiring health skills. Role play, group cooperation, and small group discussion were found in all 10 curricula. To a lesser extent, interactive technology and team games were also included. When combined with previous research regarding the characteristics of effective teachers, it becomes clear that effective health education is delivered by teachers who employ a wide repertoire of active learning strategies while devoting substantial instructional time to those specific strategies that involve students in skills practice. © 2011, American School Health Association.

Principles for circadian orchestration of metabolic pathways.

PubMed

Thurley, Kevin; Herbst, Christopher; Wesener, Felix; Koller, Barbara; Wallach, Thomas; Maier, Bert; Kramer, Achim; Westermark, Pål O

2017-02-14

Circadian rhythms govern multiple aspects of animal metabolism. Transcriptome-, proteome- and metabolome-wide measurements have revealed widespread circadian rhythms in metabolism governed by a cellular genetic oscillator, the circadian core clock. However, it remains unclear if and under which conditions transcriptional rhythms cause rhythms in particular metabolites and metabolic fluxes. Here, we analyzed the circadian orchestration of metabolic pathways by direct measurement of enzyme activities, analysis of transcriptome data, and developing a theoretical method called circadian response analysis. Contrary to a common assumption, we found that pronounced rhythms in metabolic pathways are often favored by separation rather than alignment in the times of peak activity of key enzymes. This property holds true for a set of metabolic pathway motifs (e.g., linear chains and branching points) and also under the conditions of fast kinetics typical for metabolic reactions. By circadian response analysis of pathway motifs, we determined exact timing separation constraints on rhythmic enzyme activities that allow for substantial rhythms in pathway flux and metabolite concentrations. Direct measurements of circadian enzyme activities in mouse skeletal muscle confirmed that such timing separation occurs in vivo.

Principles for circadian orchestration of metabolic pathways

PubMed Central

Thurley, Kevin; Herbst, Christopher; Wesener, Felix; Koller, Barbara; Wallach, Thomas; Maier, Bert; Kramer, Achim

2017-01-01

Circadian rhythms govern multiple aspects of animal metabolism. Transcriptome-, proteome- and metabolome-wide measurements have revealed widespread circadian rhythms in metabolism governed by a cellular genetic oscillator, the circadian core clock. However, it remains unclear if and under which conditions transcriptional rhythms cause rhythms in particular metabolites and metabolic fluxes. Here, we analyzed the circadian orchestration of metabolic pathways by direct measurement of enzyme activities, analysis of transcriptome data, and developing a theoretical method called circadian response analysis. Contrary to a common assumption, we found that pronounced rhythms in metabolic pathways are often favored by separation rather than alignment in the times of peak activity of key enzymes. This property holds true for a set of metabolic pathway motifs (e.g., linear chains and branching points) and also under the conditions of fast kinetics typical for metabolic reactions. By circadian response analysis of pathway motifs, we determined exact timing separation constraints on rhythmic enzyme activities that allow for substantial rhythms in pathway flux and metabolite concentrations. Direct measurements of circadian enzyme activities in mouse skeletal muscle confirmed that such timing separation occurs in vivo. PMID:28159888

Flow sensing by pinniped whiskers

PubMed Central

Miersch, L.; Hanke, W.; Wieskotten, S.; Hanke, F. D.; Oeffner, J.; Leder, A.; Brede, M.; Witte, M.; Dehnhardt, G.

2011-01-01

Beside their haptic function, vibrissae of harbour seals (Phocidae) and California sea lions (Otariidae) both represent highly sensitive hydrodynamic receptor systems, although their vibrissal hair shafts differ considerably in structure. To quantify the sensory performance of both hair types, isolated single whiskers were used to measure vortex shedding frequencies produced in the wake of a cylinder immersed in a rotational flow tank. These measurements revealed that both whisker types were able to detect the vortex shedding frequency but differed considerably with respect to the signal-to-noise ratio (SNR). While the signal detected by sea lion whiskers was substantially corrupted by noise, harbour seal whiskers showed a higher SNR with largely reduced noise. However, further analysis revealed that in sea lion whiskers, each noise signal contained a dominant frequency suggested to function as a characteristic carrier signal. While in harbour seal whiskers the unique surface structure explains its high sensitivity, this more or less steady fundamental frequency might represent the mechanism underlying hydrodynamic reception in the fast swimming sea lion by being modulated in response to hydrodynamic stimuli impinging on the hair. PMID:21969689

Schlieren Measurements of Buoyancy Effects on Flow Transition in Low-Density Gas Jets

NASA Technical Reports Server (NTRS)

Pasumarthi, Kasyap S.; Agrawal, Ajay K.

2005-01-01

The transition from laminar to turbulent flow in helium jets discharged into air was studied using Rainbow Schlieren Deflectometry technique. In particular, the effects of buoyancy on jet oscillations and flow transition length were considered. Experiments to simulate microgravity were conducted in the 2.2s drop tower at NASA Glenn Research Center. The jet Reynolds numbers varied from 800 to1200 and the jet Richardson numbers ranged between 0.01 and 0.004. Schlieren images revealed substantial variations in the flow structure during the drop. Fast Fourier Transform (FFT) analysis of the data obtained in Earth gravity experiments revealed the existence of a discrete oscillating frequency in the transition region, which matched the frequency in the upstream laminar regime. In microgravity, the transition occurred farther downstream indicating laminarization of the jet in the absence of buoyancy. The amplitude of jet oscillations was reduced by up to an order of magnitude in microgravity. Results suggest that jet oscillations were buoyancy induced and that the brief microgravity period may not be sufficient for the oscillations to completely subside.

Structural evolution and growth mechanisms of RF-magnetron sputter-deposited hydroxyapatite thin films on the basis of unified principles

NASA Astrophysics Data System (ADS)

Ivanova, Anna A.; Surmeneva, Maria A.; Surmenev, Roman A.; Depla, Diederik

2017-12-01

The structural features of RF-magnetron sputter-deposited hydroxyapatite (HA) coatings are investigated in order to reveal the effect of the working gas composition and the sample position of the substrate relative to the target erosion zone. The film properties were observed to change as a result of bombardment with energetic ions. XRD analysis of the coated substrates indicates that with the increase of the ion-to-atom ratio, the fiber texture changes from a mixed (11 2 bar 2) + (0002) over (0002) orientation, finally reaching a (30 3 bar 0) out-of-plane orientation at high ion-to-atom ratios. TEM reveals that the microstructure of the HA coating consists of columnar grains and differs with the coating texture. The contribution of Ji/Ja to the development of microstructure and texture of the HA coating is schematically represented and discussed. The obtained results may contribute substantially to the progress of research into the development of HA coatings with tailored properties, and these coatings may be applied on the surfaces of metal implants used in bone surgery.

Two-sided block of a dual-topology F- channel.

PubMed

Turman, Daniel L; Nathanson, Jacob T; Stockbridge, Randy B; Street, Timothy O; Miller, Christopher

2015-05-05

The Fluc family is a set of small membrane proteins forming F(-)-specific electrodiffusive ion channels that rescue microorganisms from F(-) toxicity during exposure to weakly acidic environments. The functional channel is built as a dual-topology homodimer with twofold symmetry parallel to the membrane plane. Fluc channels are blocked by nanomolar-affinity fibronectin-domain monobodies originally selected from phage-display libraries. The unusual symmetrical antiparallel dimeric architecture of Flucs demands that the two chemically equivalent monobody-binding epitopes reside on opposite ends of the channel, a double-sided blocking situation that has never before presented itself in ion channel biophysics. However, it is not known if both sites can be simultaneously occupied, and if so, whether monobodies bind independently or cooperatively to their transmembrane epitopes. Here, we use direct monobody-binding assays and single-channel recordings of a Fluc channel homolog to reveal a novel trimolecular blocking behavior that reveals a doubly occupied blocked state. Kinetic analysis of single-channel recordings made with monobody on both sides of the membrane shows substantial negative cooperativity between the two blocking sites.

Novel genotype of Ehrlichia canis detected in samples of human blood bank donors in Costa Rica.

PubMed

Bouza-Mora, Laura; Dolz, Gaby; Solórzano-Morales, Antony; Romero-Zuñiga, Juan José; Salazar-Sánchez, Lizbeth; Labruna, Marcelo B; Aguiar, Daniel M

2017-01-01

This study focuses on the detection and identification of DNA and antibodies to Ehrlichia spp. in samples of blood bank donors in Costa Rica using molecular and serological techniques. Presence of Ehrlichia canis was determined in 10 (3.6%) out of 280 blood samples using polymerase chain reaction (PCR) targeting the ehrlichial dsb conserved gene. Analysis of the ehrlichial trp36 polymorphic gene in these 10 samples revealed substantial polymorphism among the E. canis genotypes, including divergent tandem repeat sequences. Nucleotide sequences of dsb and trp36 amplicons revealed a novel genotype of E. canis in blood bank donors from Costa Rica. Indirect immunofluorescence assay (IFA) detected antibodies in 35 (35%) of 100 serum samples evaluated. Thirty samples showed low endpoint titers (64-256) to E. canis, whereas five sera yielded high endpoint titers (1024-8192); these five samples were also E. canis-PCR positive. These findings represent the first report of the presence of E. canis in humans in Central America. Copyright © 2016 Elsevier GmbH. All rights reserved.

Job-related stress in psychiatric nurses in Japan caring for elderly patients with dementia.

PubMed

Yada, Hironori; Abe, Hiroshi; Lu, Xi; Wakizaki, Yuko; Omori, Hisamitsu; Matsuo, Hisae; Ishida, Yasushi; Katoh, Takahiko

2014-11-01

We investigated the specificity and structures of job-related stress in psychiatric dementia nurses (PDNs) caring for elderly patients with serious behavioral and psychological symptoms of dementia who required substantial assistance with activities of daily living, in order to obtain fundamental knowledge toward providing mental health care for these nurses. Subjects were 244 nurses [63 PDNs and 181 other psychiatric nurses (OPNs)] Analysis of covariance to examine the specificity of job-related stress in PDNs revealed physical workload and work environment to be more significant stressors, and irritability and anxiety to be more significant stress reactions in PDNs than in OPNs. An examination of PDNs' job-related stress structures established in a structural equation model with two stress reactions confirmed as specific outcomes for PDNs revealed a significant positive influence of work environment on irritability; utilization of techniques for anxiety and physical workload influenced both stress reactions. Our findings highlight the importance of reducing physical workload and environment and establishing a structure for nursing techniques in psychiatric dementia wards to improve the mental health of PDNs.

Two-dimensional H2 in Si: Raman scattering and modeling study

NASA Astrophysics Data System (ADS)

Melnikov, V. V.; Hiller, M.; Lavrov, E. V.

2018-03-01

Molecular hydrogen trapped within {111}-oriented platelets in silicon is studied by means of Raman scattering and first principles theory. The rotational transition S0(0 ) (J =0 →J =2 ) of para-H2 (nuclear spin I =0 ) at 353 cm-1 is used as a probe. We find that for temperatures below 100 K the S0(0 ) Raman line starts to broaden asymmetrically, which is interpreted as the onset of a phase transition from a state with a short-range order ("gaseous" or "liquid" phase) to a two-dimensional molecular crystal lying in the {111} plane of silicon. The shape of the S0(0 ) line at helium temperatures strongly depends on the relative content of ortho- (nuclear spin I =1 ) and para-H2 revealing the details of the intermolecular interaction. A comprehensive theoretical analysis based on ab initio calculations, molecular dynamics simulations, and rotational spectra modeling reveals that the phase transition to the crystalline state of the two-dimensional hydrogen does occur at temperatures substantially higher compared to those of bulk H2.

Purification and characterization of a novel thermostable mycelial lectin from Aspergillus terricola.

PubMed

Singh, Ram Sarup; Bhari, Ranjeeta; Kaur, Hemant Preet; Vig, Monika

2010-11-01

Lectin has been isolated from mycelia of Aspergillus terricola by single step purification on porcine stomach mucin-Sepharose 4B affinity column. Lectin could be effectively purified with 75% recovery and 4.47-fold increase in specific activity. Lectin migrated as a single band on SDS-PAGE with an apparent molecular mass of 32.5 kDa. Sugar inhibition assay revealed that the lectin did not strongly interact with most carbohydrates and their derivatives tested while strong binding affinity to D-glucose, D-sucrose, N-acetyl-D-galactosamine, asialofetuin, porcine stomach mucin, and bovine submaxillary mucin was indicated. Neuraminidase and protease treatment to erythrocytes enhanced lectin titre. Lectin activity was stable within the pH range of 7.0-10.5. A. terricola lectin displayed remarkable thermostability and remained unaffected upon incubation at 70 degrees C for 2.5 h. Lectin did not require metal ions for its activity. Incubation with denaturants (urea, thiourea, and guanidine-HCl) substantially reduced lectin activity. Carbohydrate analysis revealed that it is a glycoprotein with 9.76% total sugars.

Effects of moist- and dry-heat cooking on the meat quality, microstructure and sensory characteristics of native chicken meat.

PubMed

Chumngoen, Wanwisa; Chen, Chih-Feng; Tan, Fa-Jui

2018-01-01

This study investigates the effects of moist- (water-cooking; WC) and dry-heat (oven-cooking; OC) on the quality, microstructure and sensory characteristics of native chicken breast meat. The results revealed that OC meat had a significantly higher cooking time, cooking loss, and shear force values and lower L* values. Protein solubility decreased after cooking in both cooking methods; however, no statistical difference was observed between WC and OC meats, whereas collagen solubility and myofibrillar fragmentation index (MFI) increased after cooking and WC meat exhibited higher collagen solubility and MFI (P < 0.05). The fiber diameter and sarcomere length decreased substantially after cooking, and fibril shrinkage was noticeable in OC meat (P < 0.05). Descriptive sensory analysis revealed that WC meat exhibited a significantly higher moisture release and lower initial hardness, chewdown hardness and residual loose particles. A darker color and enhanced chickeny flavor were observed for OC meat. Based on the unique sensory and physicochemical characteristics in demand, producers should employ appropriate cooking methods to optimize native chicken meat quality. © 2017 Japanese Society of Animal Science.

GWA Mapping of Anthocyanin Accumulation Reveals Balancing Selection of MYB90 in Arabidopsis thaliana

PubMed Central

Bac-Molenaar, Johanna A.; Fradin, Emilie F.; Rienstra, Juriaan A.; Vreugdenhil, Dick; Keurentjes, Joost J. B.

2015-01-01

Induction of anthocyanin accumulation by osmotic stress was assessed in 360 accessions of Arabidopsis thaliana. A wide range of natural variation, with phenotypes ranging from green to completely red/purple rosettes, was observed. A genome wide association (GWA) mapping approach revealed that sequence diversity in a small 15 kb region on chromosome 1 explained 40% of the variation observed. Sequence and expression analyses of alleles of the candidate gene MYB90 identified a causal polymorphism at amino acid (AA) position 210 of this transcription factor of the anthocyanin biosynthesis pathway. This amino acid discriminates the two most frequent alleles of MYB90. Both alleles are present in a substantial part of the population, suggesting balancing selection between these two alleles. Analysis of the geographical origin of the studied accessions suggests that the macro climate is not the driving force behind positive or negative selection for anthocyanin accumulation. An important role for local climatic conditions is, therefore, suggested. This study emphasizes that GWA mapping is a powerful approach to identify alleles that are under balancing selection pressure in nature. PMID:26588092

Why do the biotechnology and the climate change debates hardly mix? Evidence from a global stakeholder survey.

PubMed

Aerni, Philipp

2013-05-25

Despite its potential to address climate change problems, the role of biotechnology is hardly ever touched upon in the global sustainability debate. We wanted to know why. For that purpose, we conducted a global online stakeholder survey on biotechnology and climate change. The relevant stakeholders and their representatives were selected by means of key informants that were familiar with either of the two debates. A self-assessment showed that a majority of respondents felt more familiar with the climate change than the biotechnology debate. Even though the survey results reveal that most respondents consider the potential of modern biotechnology to address climate change to be substantial, the policy network analysis revealed that one stakeholder who is not just considered to be relevant in both debates but also crucial in the formation of global public opinion, strongly rejects the view that biotechnology is a climate-friendly and therefore clean technology. This influential opposition seems to ensure that the biotechnology and the climate change debates do not mix. Copyright © 2012 Elsevier B.V. All rights reserved.

In silico serine β-lactamases analysis reveals a huge potential resistome in environmental and pathogenic species.

PubMed

Brandt, Christian; Braun, Sascha D; Stein, Claudia; Slickers, Peter; Ehricht, Ralf; Pletz, Mathias W; Makarewicz, Oliwia

2017-02-24

The secretion of antimicrobial compounds is an ancient mechanism with clear survival benefits for microbes competing with other microorganisms. Consequently, mechanisms that confer resistance are also ancient and may represent an underestimated reservoir in environmental bacteria. In this context, β-lactamases (BLs) are of great interest due to their long-term presence and diversification in the hospital environment, leading to the emergence of Gram-negative pathogens that are resistant to cephalosporins (extended spectrum BLs = ESBLs) and carbapenems (carbapenemases). In the current study, protein sequence databases were used to analyze BLs, and the results revealed a substantial number of unknown and functionally uncharacterized BLs in a multitude of environmental and pathogenic species. Together, these BLs represent an uncharacterized reservoir of potentially transferable resistance genes. Considering all available data, in silico approaches appear to more adequately reflect a given resistome than analyses of limited datasets. This approach leads to a more precise definition of BL clades and conserved motifs. Moreover, it may support the prediction of new resistance determinants and improve the tailored development of robust molecular diagnostics.

Microbial communities affecting albumen photography heritage: a methodological survey

NASA Astrophysics Data System (ADS)

Puškárová, Andrea; Bučková, Mária; Habalová, Božena; Kraková, Lucia; Maková, Alena; Pangallo, Domenico

2016-02-01

This study is one of the few investigations which analyze albumen prints, perhaps the most important photographic heritage of the late 19th and early 20th centuries. The chemical composition of photographic samples was assessed using Fourier-transform infrared spectroscopy and X-ray fluorescence. These two non-invasive techniques revealed the complex nature of albumen prints, which are composed of a mixture of proteins, cellulose and salts. Microbial sampling was performed using cellulose nitrate membranes which also permitted the trapped microflora to be observed with a scanning electron microscope. Microbial analysis was performed using the combination of culture-dependent (cultivation in different media, including one 3% NaCl) and culture-independent (bacterial and fungal cloning and sequencing) approaches. The isolated microorganisms were screened for their lipolytic, proteolytic, cellulolytic, catalase and peroxidase activities. The combination of the culture-dependent and -independent techniques together with enzymatic assays revealed a substantial microbial diversity with several deteriogen microorganisms from the genera Bacillus, Kocuria, Streptomyces and Geobacillus and the fungal strains Acrostalagmus luteoalbus, Bjerkandera adusta, Pleurotus pulmonarius and Trichothecium roseum.

Unbiased Protein Association Study on the Public Human Proteome Reveals Biological Connections between Co-Occurring Protein Pairs

PubMed Central

2017-01-01

Mass-spectrometry-based, high-throughput proteomics experiments produce large amounts of data. While typically acquired to answer specific biological questions, these data can also be reused in orthogonal ways to reveal new biological knowledge. We here present a novel method for such orthogonal data reuse of public proteomics data. Our method elucidates biological relationships between proteins based on the co-occurrence of these proteins across human experiments in the PRIDE database. The majority of the significantly co-occurring protein pairs that were detected by our method have been successfully mapped to existing biological knowledge. The validity of our novel method is substantiated by the extremely few pairs that can be mapped to existing knowledge based on random associations between the same set of proteins. Moreover, using literature searches and the STRING database, we were able to derive meaningful biological associations for unannotated protein pairs that were detected using our method, further illustrating that as-yet unknown associations present highly interesting targets for follow-up analysis. PMID:28480704

Structural Analysis of the Synaptic Protein Neuroligin and Its β-Neurexin Complex: Determinants for Folding and Cell Adhesion

PubMed Central

Fabrichny, Igor P.; Leone, Philippe; Sulzenbacher, Gerlind; Comoletti, Davide; Miller, Meghan T.; Taylor, Palmer; Bourne, Yves; Marchot, Pascale

2009-01-01

SUMMARY The neuroligins are postsynaptic cell adhesion proteins whose associations with presynaptic neurexins participate in synaptogenesis. Mutations in the neuroligin and neurexin genes appear to be associated with autism and mental retardation. The crystal structure of a neuroligin reveals features not found in its catalytically active relatives, such as the fully hydrophobic interface forming the functional neuroligin dimer; the conformations of surface loops surrounding the vestigial active center; the location of determinants that are critical for folding and processing; and the absence of a macromolecular dipole and presence of an electronegative, hydrophilic surface for neurexin binding. The structure of a β-neurexin-neuroligin complex reveals the precise orientation of the bound neurexin and, despite a limited resolution, provides substantial information on the Ca2+-dependent interactions network involved in trans-synaptic neurexin-neuroligin association. These structures exemplify how an α/β-hydrolase fold varies in surface topography to confer adhesion properties and provide templates for analyzing abnormal processing or recognition events associated with autism. PMID:18093521

Microbial communities affecting albumen photography heritage: a methodological survey.

PubMed

Puškárová, Andrea; Bučková, Mária; Habalová, Božena; Kraková, Lucia; Maková, Alena; Pangallo, Domenico

2016-02-11

This study is one of the few investigations which analyze albumen prints, perhaps the most important photographic heritage of the late 19(th) and early 20(th) centuries. The chemical composition of photographic samples was assessed using Fourier-transform infrared spectroscopy and X-ray fluorescence. These two non-invasive techniques revealed the complex nature of albumen prints, which are composed of a mixture of proteins, cellulose and salts. Microbial sampling was performed using cellulose nitrate membranes which also permitted the trapped microflora to be observed with a scanning electron microscope. Microbial analysis was performed using the combination of culture-dependent (cultivation in different media, including one 3% NaCl) and culture-independent (bacterial and fungal cloning and sequencing) approaches. The isolated microorganisms were screened for their lipolytic, proteolytic, cellulolytic, catalase and peroxidase activities. The combination of the culture-dependent and -independent techniques together with enzymatic assays revealed a substantial microbial diversity with several deteriogen microorganisms from the genera Bacillus, Kocuria, Streptomyces and Geobacillus and the fungal strains Acrostalagmus luteoalbus, Bjerkandera adusta, Pleurotus pulmonarius and Trichothecium roseum.

3D Lifetime Tomography Reveals How CdCl 2 Improves Recombination Throughout CdTe Solar Cells

DOE PAGES

Barnard, Edward S.; Ursprung, Benedikt; Colegrove, Eric; ...

2016-11-15

When using two-photon tomography, carrier lifetimes are mapped in polycrystalline CdTe photovoltaic devices. These 3D maps probe subsurface carrier dynamics that are inaccessible with traditional optical techniques. They reveal that CdCl 2 treatment of CdTe solar cells suppresses nonradiative recombination and enhances carrier lifetimes throughout the film with substantial improvements particularly near subsurface grain boundaries and the critical buried p-n junction.

Heterogeneity in Trajectories of Child Maltreatment Severity: A Two-Part Growth Mixture Model

PubMed Central

Yampolskaya, Svetlana; Greenbaum, Paul E.; Brown, C. Hendricks; Armstrong, Mary I.

2016-01-01

This study examined the trajectories of maltreatment severity and substantiation over a 24-month period among children (N = 82,396) with repeated maltreatment reports. Findings revealed two different longitudinal patterns. The first pattern, Elevated Severity, showed a higher level of maltreatment during the initial incident and increased maltreatment severity during subsequent incidents but the substantiation rates for this class decreased over time. The second pattern, Lowered Severity, showed a much lower level of severity, but the likelihood of substantiation increased over time. The Elevated Severity class was comprised of children with an elevated risk profile due to both individual and contextual risk factors including older age, female gender, caregivers’ substance use problems, and a higher number of previous maltreatment reports. Implications of the findings are discussed. PMID:26300381

Ethics of phase 1 oncology studies: reexamining the arguments and data.

PubMed

Agrawal, Manish; Emanuel, Ezekiel J

2003-08-27

Phase 1 oncology trials are critical to improving the treatment of cancer. Critics have raised 2 fundamental ethical challenges about phase 1 cancer research: the paucity of benefits with substantial risks and poor-quality informed consent. Despite 3 decades of controversy about phase 1 oncology research, there is little critical analysis of the arguments or of the data relevant to these questions. Existing but old data reveal that about 5% of patients in phase 1 trials experience shrinkage of their tumor, with a 0.5% mortality rate. In some notable cases, patients in phase 1 trials have been cured or sustained long-term remissions. Limited data suggest that patients in phase 1 trials may have better quality of life than comparable patients receiving supportive care. More important, the risks and benefits of phase 1 trials are not clearly worse than risk-benefit ratios used by the US Food and Drug Administration to approve chemotherapeutic agents for clinical use. The objections based on informed consent are deficiencies of disclosure, understanding, and voluntariness. The available data do not support the claim that disclosure is deficient. Although studies evaluating patient understanding have substantial methodological problems, they demonstrate that more than 70% of patients understand that they may not directly benefit even when they hope they will personally benefit. Finally, a closer look at issues of voluntariness reveals that patients with advanced cancer who participate in phase 1 research may have a different set of values than do critics and are not coerced. Overall, it appears that phase 1 oncology trials satisfy the requirement for a favorable risk-benefit ratio and that patients who enroll provide adequate informed consent.

Knowledge and psychosocial effects of the film super size me on young adults.

PubMed

Cottone, Ellen; Byrd-Bredbenner, Carol

2007-07-01

The prevalence of overweight and obesity has risen dramatically over the past 2 decades. Among the many contributing factors is increased consumption of fast foods. Mass media outlets have cited the potential of the film Super Size Me to alter this behavior. The purpose of this study was to determine the effect of this film on young adults' fast-food knowledge and psychosocial measures (ie, attitudes, self-efficacy, healthy weight locus of control, and stage of change) and evaluate the effectiveness of this film as a form of emotional arousal and consciousness-raising. A pretest-posttest follow-up control group design with random assignment was used. Young adults (n=135; 54% female) completed the pretest; approximately 10 days later viewed a film then completed the posttest; and about 9 days later completed the follow-up test. The experimental group (n=80) viewed Super Size Me. The control group (n=55) viewed an unrelated film. Unpaired t tests revealed that the study groups did not differ significantly (P>0.05) at pretest on any measure. Analysis of covariance, with pretest score as the covariate, revealed the experimental group scored substantially better than the control group at posttest on knowledge and nearly all psychosocial measures. In addition, the experimental group continued to score substantially higher than the control group at follow-up on knowledge, stage of change, and consciousness-raising and lower on external: chance health locus of control. Super Size Me represents a potentially powerful tool for nutrition education. Nutrition practitioners should consider using Super Size Me as a consciousness-raising and emotional arousal change process with patients in pre-action stages of change for reducing fast-food intake.

Reduction of microbial contamination and improvement of germination of sweet basil (Ocimum basilicum L.) seeds via surface dielectric barrier discharge

NASA Astrophysics Data System (ADS)

Ambrico, Paolo F.; Šimek, Milan; Morano, Massimo; De Miccolis Angelini, Rita M.; Minafra, Angelantonio; Trotti, Pasquale; Ambrico, Marianna; Prukner, Václav; Faretra, Francesco

2017-08-01

Naturally contaminated basil seeds were treated by a surface dielectric barrier discharge driven in the humid air by an amplitude modulated AC high voltage to avoid heat shock. In order to avoid direct contact of seeds with microdischarge filaments, the seeds to be treated were placed at sufficient distance from the surface discharge. After treatment, the seeds were analyzed in comparison with control samples for their microbial contamination as well as for the capability of germination and seedling growth. Moreover, chemical modification of seed surface was observed through the elemental energy dispersive x-ray analysis and wettability tests. We found that treatment applied at 20% duty cycle (effective discharge duration up to 20 s) significantly decreases microbial load without reducing the viability of the seeds. On the other side, seedling growth was considerably accelerated after the treatment, and biometric growth parameters of seedlings (total length, weight, leaf extension) considerably increased compared to the controls. Interestingly, scanning electron microscopy images taken for the different duration of treatment revealed that seed radicle micropylar regions underwent significant morphological changes while the coat was substantially undamaged. Inside the seed, the embryo seemed to be well preserved while the endosperm body was detached from the epithelial tegument. A total of 9 different genera of fungi were recovered from the analyzed seeds. Scanning electron microscopy images revealed that conidia were localized especially in the micropylar region, and after plasma treatment, most of them showed substantial damages. Therefore, the overall effect of the treatment of naturally contaminated seeds by reactive oxygen and nitrogen species produced by plasma and the consequent changes in surface chemistry and microbial load can significantly improve seed vigor.

Quantitative proteomic analysis of human testis reveals system-wide molecular and cellular pathways associated with non-obstructive azoospermia.

PubMed

Alikhani, Mehdi; Mirzaei, Mehdi; Sabbaghian, Marjan; Parsamatin, Pouria; Karamzadeh, Razieh; Adib, Samane; Sodeifi, Niloofar; Gilani, Mohammad Ali Sadighi; Zabet-Moghaddam, Masoud; Parker, Lindsay; Wu, Yunqi; Gupta, Vivek; Haynes, Paul A; Gourabi, Hamid; Baharvand, Hossein; Salekdeh, Ghasem Hosseini

2017-06-06

Male infertility accounts for half of the infertility problems experienced by couples. Azoospermia, having no measurable level of sperm in seminal fluid, is one of the known conditions resulting in male infertility. In order to elucidate the complex molecular mechanisms causing male azoospermia, label-free quantitative shotgun proteomics was carried out on testicular tissue specimens from patients with obstructive azoospermia and non-obstructive azoospermia, including maturation arrest (MA) and Sertoli cell only syndrome (SCOS). The abundance of 520 proteins was significantly changed across three groups of samples. We were able to identify several functional biological pathways enriched in azoospermia samples and confirm selected differentially abundant proteins, using multiple histological methods. The results revealed that cell cycle and proteolysis, and RNA splicing were the most significant biological processes impaired by the substantial suppression of proteins related to the aforementioned categories in SCOS tissues. In the MA patient testes, generation of precursor metabolites and energy as well as oxidation-reduction were the most significantly altered processes. Novel candidate proteins identified in this study include key transcription factors, many of which have not previously been shown to be associated with azoospermia. Our findings can provide substantial insights into the molecular regulation of spermatogenesis and human reproduction. The obtained data showed a drastic suppression of proteins involved in spliceosome, cell cycle and proteasome proteins, as well as energy and metabolic production in Sertoli cell only syndrome testis tissue, and to a lesser extent in maturation arrest samples. Moreover, we identified new transcription factors that are highly down-regulated in SCOS and MA patients, thus helping to understand the molecular complexity of spermatogenesis in male infertility. Our findings provide novel candidate protein targets associated with SCOS or MA azoospermia. Copyright © 2017 Elsevier B.V. All rights reserved.

Sapphire reinforced alumina matrix composites

NASA Technical Reports Server (NTRS)

Jaskowiak, Martha H.; Setlock, John A.

1994-01-01

Unidirectionally reinforced A1203 matrix composites have been fabricated by hot pressing. Approximately 30 volume % of either coated or uncoated sapphire fiber was used as reinforcement. Unstabilized ZrO2 was applied as the fiber coating. Composite mechanical behavior was analyzed both after fabrication and after additional heat treatment. The results of composite tensile tests were correlated with fiber-matrix interfacial shear strengths determined from fiber push-out tests. Substantially higher strength and greater fiber pull-out were observed for the coated fiber composites for all processing conditions studied. The coated fiber composites retained up to 95% and 87% of their as-fabricated strength when heat treated at 14000C for 8 or 24 hours, respectively. Electron microscopy analysis of the fracture surfaces revealed extensive fiber pull-out both before and after heat treatment.

Pesticides in ground water: Do atrazine metabolites matter?

USGS Publications Warehouse

Liu, S.; Yen, S.T.; Kolpin, D.W.

1996-01-01

Atrazine and atrazine-residue (atrazine + two metabolites - deethylatrazine and deisopropylatrazine) concentrations were examined to determine if consideration of these atrazine metabolites substantially adds to our understanding of the distribution of this pesticide in groundwater of the midcontinental United States. The mean of atrazine.residue concentrations was 53 percent greater than that of atrazine alone for those observations above the detection limit (> 0.05 μg/l). Furthermore, a censored regression analysis using atrazine-residue concentrations revealed significant factors not identified when only atrazine concentrations were used. Thus, knowledge of concentrations of these atrazine metabolites is required to obtain a true estimation of risk of using these aquifers as sources for drinking water, and such knowledge also provides information that ultimately may be important for future management policies designed to reduce atrazine concentrations in ground water.

Adolescent personality factors in self-ratings and peer nominations and their prediction of peer acceptance and peer rejection.

PubMed

Scholte, R H; van Aken, M A; van Lieshout, C F

1997-12-01

In this study, the robustness of the Big Five personality factors in adolescents' self-ratings and peer nominations was investigated. Data were obtained on 2,001 adolescents attending secondary school (885 girls; 1,116 boys; M age = 14.5 years). Exploratory and confirmatory factor analyses on the self-ratings confirmed the Big Five personality factors. In contrast, exploratory analysis on the peer nominations revealed five different factors: Aggression-Inattentiveness, Achievement-Withdrawal, Self-Confidence, Sociability, and Emotionality-Nervousness. It is suggested that peers evaluate group members not in terms of their personality but in terms of their group reputation. Peer evaluations contributed substantially to the prediction of peer acceptance and rejection; the Big Five personality factors based on self-ratings did not.

Multi-phase gas, clumping and non-thermal pressure in cluster outskirts via X-ray, SZ and lensing data

NASA Astrophysics Data System (ADS)

Morandi, Andrea

2017-09-01

We propose to study multitemperature structure, clumpy gas distribution and non-thermal pressure in the outskirts of a sample of galaxy clusters by means of Chandra X-ray, Sunyaev Zeldovich and lensing data. We propose to recover the X-ray spectroscopic temperatures close to the virial radius and compare them to the average (gas mass-weighted) temperature probed through SZ. Our preliminary analysis reveals compelling evidence of a substantial amounts of cold gas (T 0.8 keV) at subvirial temperature which coexists with the hot (>4 keV) thermal component of the intracluster medium (ICM). The proposed investigation has important implications for understanding the astrophysics of the ICM in the outer volumes and the CDM scenario, and it has crucial ramifications for the cosmology.

Gynogenic plant regeneration from unpollinated flower explants of Eragrostis tef (Zuccagni) Trotter.

PubMed

Gugsa, Likyelesh; Sarial, Ashok K; Lörz, Horst; Kumlehn, Jochen

2006-12-01

Tef [Eragrostis tef (Zucc.) Trotter] is the most important cereal in Ethiopia. In its wild relative E. mexicana, regeneration of six green plants resulted from culture of 121 non-pollinated immature pistils. In the allotetraploid crop species tef, however, only callus and root formation was obtained by this method. By contrast, immature spikelets and panicle segments of E. tef proved amenable to gynogenic plant regeneration. Upon step-wise optimization of the protocol, efficient plant formation was achieved in all three cultivars tested. In cv. DZ-01-196, culture of 1305 immature spikelets resulted in formation of 159 green plants. Flow cytometric analysis revealed (di)haploid, triploid, tetraploid and octoploid regenerants, from which the vast majority was tetraploid. Tef-breeding programs will likely benefit substantially from efficient generation of true-breeding plants.

A critical analysis of the numerical and analytical methods used in the construction of the lunar gravity potential model.

NASA Astrophysics Data System (ADS)

Tuckness, D. G.; Jost, B.

1995-08-01

Current knowledge of the lunar gravity field is presented. The various methods used in determining these gravity fields are investigated and analyzed. It will be shown that weaknesses exist in the current models of the lunar gravity field. The dominant part of this weakness is caused by the lack of lunar tracking data information (farside, polar areas), which makes modeling the total lunar potential difficult. Comparisons of the various lunar models reveal an agreement in the low-order coefficients of the Legendre polynomials expansions. However, substantial differences in the models can exist in the higher-order harmonics. The main purpose of this study is to assess today's lunar gravity field models for use in tomorrow's lunar mission designs and operations.

Studies on the Inhibition of Mild Steel Corrosion by Rauvolfia serpentina in Acid Media

NASA Astrophysics Data System (ADS)

Bothi Raja, P.; Sethuraman, M. G.

2010-07-01

Alkaloid extract of Rauvolfia serpentina was tested as corrosion inhibitor for mild steel in 1 M HCl and H2SO4 using weight loss method at three different temperatures, viz., 303, 313, and 323 K, potentiodynamic polarization, electrochemical impedance spectroscopy and scanning electron microscope (SEM) studies. It is evident from the results of this study that R. serpentina effectively inhibits the corrosion in both the acids through adsorption process following Tempkin adsorption isotherm. The protection efficiency increased with increase in inhibitor concentration and temperature. Free energy of adsorption calculated from the temperature studies also revealed the chemisorption. The mixed mode of action exhibited by the inhibitor was confirmed by the polarization studies while SEM analysis substantiated the formation of protective layer over the mild steel surface.

Preparation and some properties of Cu-Li alloys containing up to 20 at. % Li

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mendelsohn, M.; Krauss, A.R.; Gruen, D.M.

1985-01-01

Lithium strongly segregates to the surface of Cu-Li alloys, thus substantially lowering the Cu sputtering yield relative to pure Cu. Use of Cu-Li limiters or divertors in tokamaks can therefore be expected to be beneficial in limiting high-Z plasma impurity influx. A large scale (100-200g) method for the preparation of Cu-Li alloys is described. Analysis reveals that on solidification from the melt stratification occurs which leads to compositional inhomogeneity. The results are discussed in the light of the Cu-Li binary phase diagram and rationalized on the basis of large density differences between Cu and Cu-Li solid solutions. It is concludedmore » that obtaining homogeneous Cu-Li solid solutions is a nontrivial task.« less

System for Conservation of Specially Protected Natural Areas as Sustainable Urban Development Element

NASA Astrophysics Data System (ADS)

Kryakhtunov, A.; Pelymskaya, O.; Chernykh, E.

2017-11-01

The article is devoted to the problem of the conservation of specially protected natural territories. The research topic is especially interesting for urban areas that provide sustainable urban development. The authors consider the main aspects of the sustainable settlement development and substantiate the direct dependence of the evolution of territories in the implementation of urban development activities with the ecological framework of a city. The object of the study is a specially protected natural area located in Western Siberia in the city of Tyumen, the Tyumen region. As a result of the analysis, the main problems of preservation of the nature monument of regional importance were revealed as well as a set of measures and management decisions regarding the conservation of the forest park.

Dynamically assisted Schwinger effect beyond the spatially-uniform-field approximation

NASA Astrophysics Data System (ADS)

Aleksandrov, I. A.; Plunien, G.; Shabaev, V. M.

2018-06-01

We investigate the phenomenon of electron-positron pair production from vacuum in the presence of a strong electric field superimposed by a weak but fast varying pulse which substantially increases the total particle yield. We employ a nonperturbative numerical technique and perform the calculations beyond the spatially-uniform-field approximation, i.e., dipole approximation, taking into account the coordinate dependence of the fast component. The analysis of the main characteristics of the pair-production process (momentum spectra of particles and total amount of pairs) reveals a number of important features which are absent within the previously used approximation. In particular, the structure of the momentum distribution is modified both qualitatively and quantitatively, and the total number of pairs created as well as the enhancement factor due to dynamical assistance become significantly smaller.

Catalytic properties of an expressed and purified higher plant type zeta-carotene desaturase from Capsicum annuum.

PubMed

Breitenbach, J; Kuntz, M; Takaichi, S; Sandmann, G

1999-10-01

The zeta-carotene desaturase from Capsicum annuum (EC 1.14.99.-) was expressed in Escherichia coli, purified and characterized biochemically. The enzyme acts as a monomer with lipophilic quinones as cofactors. Km values for the substrate zeta-carotene or the intermediate neurosporene in the two-step desaturation reaction are almost identical. Product analysis showed that different lycopene isomers are formed, including substantial amounts of the all-trans form, together with 7,7',9,9'-tetracis prolycopene via the corresponding neurosporene isomers. The application of different geometric isomers as substrates revealed that the zeta-carotene desaturase has no preference for certain isomers and that the nature of the isomers formed during catalysis depends strictly on the isomeric composition of the substrate.

Influence of circumferential notch and fatigue crack on the mechanical integrity of biodegradable magnesium-based alloy in simulated body fluid.

PubMed

Bobby Kannan, M; Singh Raman, R K; Witte, F; Blawert, C; Dietzel, W

2011-02-01

Applications of magnesium alloys as biodegradable orthopaedic implants are critically dependent on the mechanical integrity of the implant during service. In this study, the mechanical integrity of an AZ91 magnesium alloy was studied using a constant extension rate tensile (CERT) method. The samples in two different geometries that is, circumferentially notched (CN), and circumferentially notched and fatigue cracked (CNFC), were tested in air and in simulated body fluid (SBF). The test results show that the mechanical integrity of the AZ91 magnesium alloy decreased substantially (∼50%) in both the CN and CNFC samples exposed to SBF. Fracture surface analysis revealed secondary cracks suggesting stress corrosion cracking susceptibility of the alloy in SBF. Copyright © 2010 Wiley Periodicals, Inc.

Narrative medicine in metastatic prostate cancer reveals ways to improve patient awareness & quality of care.

PubMed

Vincentis, Giuseppe De; Monari, Fabio; Baldari, Sergio; Salgarello, Matteo; Frantellizzi, Viviana; Salvi, Elisabetta; Reale, Luigi; Napolitano, Silvia; Conti, Giario; Cortesi, Enrico

2018-06-15

To describe the journey of patients with metastatic castration-resistant prostate cancer (mCRPC) in treatment with radium-223. A multiperspective analysis was performed using narrative medicine in four Italian centers. The substantial impact of mCRPC on quality of life through all phases of the disease was described. After an initial lack of awareness of the disease or denial of its effects, symptoms of pain, fatigue and side effects often led to sadness, fear and loneliness. The majority underwent radium-223 therapy positively, restoring their quality of life and routine activities. Using narrative medicine, the importance of a patient-centered approach in the pathway of care for patients with mCRPC through all the stages of the disease was highlighted.

Pregnancy-associated polyuria in familial renal glycosuria.

PubMed

Toka, Hakan R; Yang, Jun; Zera, Chloe A; Duffield, Jeremy S; Pollak, Martin R; Mount, David B

2013-12-01

A pregnant woman presented at gestational week 28 with loss of consciousness and profound polyuria. Further characterization revealed osmotic diuresis due to massive glycosuria without hyperglycemia. Glycosuria reduced substantially postpartum, from approximately 100 to approximately 30 g/1.73 m2 per day. DNA sequencing analysis of the SLC5A2 gene encoding the renal glucose transporter SGLT2 showed a homozygous frame-shift mutation (occurring after the glutamine at amino acid 168 and leading to premature termination of the protein at amino acid 186) diagnostic of familial renal glycosuria. Pregnant women with familial renal glycosuria can be at risk of profound polyuria during pregnancy due to the associated increase in glycosuria. These findings also have implications for the use of SGLT2 inhibitors in clinical practice. Published by Elsevier Inc.

Dark photon decay beyond the Euler-Heisenberg limit

NASA Astrophysics Data System (ADS)

McDermott, Samuel D.; Patel, Hiren H.; Ramani, Harikrishnan

2018-04-01

We calculate the exact width for a dark photon decaying to three photons at one-loop order for dark photon masses m' below the e+e- production threshold of 2 me. We find substantial deviations from previous results derived from the lowest order Euler-Heisenberg effective Lagrangian in the range me≲m'≤2 me, where higher order terms in the derivative expansion are non-negligible. This mass range is precisely where the three photon decay takes place on cosmologically relevant timescales. Our improved analysis reveals a window for dark photons in the range 850 KeV ≲m'≤2 me , 10-5≲ɛ ≲10-4 that is only constrained by possibly model-dependent bounds on the number of light degrees of freedom in the early Universe.

Patterns and causes of observed piñon pine mortality in the southwestern United States

USGS Publications Warehouse

Meddens, Arjan J.H.; Hicke, Jeff H.; Macalady, Alison K.; Buotte, P.C.; Cowles, T.R.; Allen, Craig D.

2015-01-01

Recently, widespread piñon pine die-off occurred in the southwestern United States. Here we synthesize observational studies of this event and compare findings to expected relationships with biotic and abiotic factors. Agreement exists on the occurrence of drought, presence of bark beetles and increased mortality of larger trees. However, studies disagree about the influences of stem density, elevation and other factors, perhaps related to study design, location and impact of extreme drought. Detailed information about bark beetles is seldom reported and their role is poorly understood. Our analysis reveals substantial limits to our knowledge regarding the processes that produce mortality patterns across space and time, indicating a poor ability to forecast mortality in response to expected increases in future droughts.

Conformational analysis of cellobiose by electronic structure theories.

PubMed

French, Alfred D; Johnson, Glenn P; Cramer, Christopher J; Csonka, Gábor I

2012-03-01

Adiabatic Φ/ψ maps for cellobiose were prepared with B3LYP density functional theory. A mixed basis set was used for minimization, followed with 6-31+G(d) single-point calculations, with and without SMD continuum solvation. Different arrangements of the exocyclic groups (38 starting geometries) were considered for each Φ/ψ point. The vacuum calculations agreed with earlier computational and experimental results on the preferred gas phase conformation (anti-Φ(H), syn-ψ(H)), and the results from the solvated calculations were consistent with the (syn Φ(H)/ψ(H) conformations from condensed phases (crystals or solutions). Results from related studies were compared, and there is substantial dependence on the solvation model as well as arrangements of exocyclic groups. New stabilizing interactions were revealed by Atoms-In-Molecules theory. Published by Elsevier Ltd.

Living arrangements and children's development in low-income White, Black, and Latino families.

PubMed

Foster, E Michael; Kalil, Ariel

2007-01-01

This article uses longitudinal data from approximately 2,000 low-income families participating in the national evaluation of the Comprehensive Child Development Program to examine the associations between preschool children's living arrangements and their cognitive achievement and emotional adjustment. The analysis distinguishes families in which children live only with their mothers from children who live in biological father, blended, and multigenerational households. Linkages are examined separately for White, Black, and Latino children. Fixed effects regression techniques reveal few significant associations between living arrangements and child development. These findings suggest that substantial diversity exists in the developmental contexts among children living in the same family structure. Policies seeking to change the living arrangements of low-income children may do little to improve child well-being.

Understanding Activist Leadership Effort in the Movement Opposing Drinking and Driving

PubMed Central

Dorius, Cassandra R.; McCarthy, John D.

2012-01-01

Why do some social movement leaders work harder than others? And, how does gender affect the patterns we uncover? Utilizing historical case study evidence of local chapters in the emerging movement opposing drinking and driving we are able to develop and test theoretical expectations about predictors of weekly effort among MADD and RID leaders. Taken together, our model explains 45 percent of the variation in leadership effort. We find bureaucratic complexity and victim support activities are more powerful predictors of effort than are individual leader characteristics, although all are important. Further analysis reveals that gender almost wholly conditions the strong effect of bureaucratic complexity on leadership effort so that increasingly complex chapter structures are associated with substantial increases in work hours for women but not men. PMID:22993454

Are smartphones comparable to laptops for image diagnosis in teleophthalmology?

PubMed

John, Sheila; Arun, Vikram; Katti, Nahush; Appukuttan, Bindu; Pearlson, Inbiomedvision Consortium; Badrinath, Sengamedu S

2013-01-01

To assess the reliability and accuracy of smartphones in diagnosing transmitted fundus images in comparison with a laptop. Fundus images captured with a Topcon NW 200 camera were transferred onto a conventional laptop and a smartphone and given to ophthalmologists for diagnosis. The smartphone and the laptop diagnosis were compared with the actual face to face diagnosis statistically to assess their diagnostic accuracy. Fundus images of 228 eyes of 114 patients (mean age 47 years,73.6% males) were included in the study. 92.5% eyes were correctly diagnosed by both smartphones and laptop. Smartphone analysis revealed 98% sensitivity,57% specificity and kappa value of 0.62 in comparison to laptop, suggessting substantial interrater agreement. Smartphones are as effective as the laptop in diagnosing fundus pathologies and hold promise for teleophthalmology in future.

Near-field microscopy of waveguide architectures of InGaN/GaN diode lasers

NASA Astrophysics Data System (ADS)

Friede, Sebastian; Tomm, Jens W.; Kühn, Sergei; Hoffmann, Veit; Wenzel, Hans; Weyers, Markus

2016-11-01

Waveguide (WG) architectures of 420 nm emitting InGaN/GaN diode lasers are analyzed by photoluminescence and photocurrent spectroscopy using a nearfield scanning optical microscope that scans along their front facets. The components of the ‘optical active cavity’, quantum wells, WGs, and cladding layers are individually inspected with a spatial resolution of ∼100 nm. Separate analysis of the p- and n-sections of the WG was achieved, and reveals defect levels in the p-part. Moreover, it is demonstrated that the homogeneity of the n-WG section directly affects the quantum wells that are grown on top of this layer. Substantially increased carrier capture efficiencies into InGaN/GaN-WGs compared to GaN-WGs are demonstrated.

Efficacy and Safety of Indigo Naturalis in Combination with Narrow-Band Ultraviolet B for Treatment of Pityriasis Rosea: A Meta-Analysis

PubMed Central

Xue, Y. N.; Li, Z. W.; Zhang, W.; Ji, X. P.; Fan, Z.

2018-01-01

Pityriasis rosea (PR), a skin rash, causes substantial discomfort in patients. There is a lack of effective therapies for PR. A combination of ultraviolet irradiation and indigo naturalis treatment has been shown to be a safe and effective regime for control of PR; however, the data have been largely inconsistent. Tis meta-analysis further evaluated the efficacy and safety of this combination in patients with PR. The PubMed, Embase, Cochrane Library, CNKI, VIP, and Wan Fang databases were searched for relevant RCTs of this combination therapy in patients with PR. A total of eight studies with a combined study population of 688 patients published between January 2006 and March 2016 were eligible for this meta-analysis. The RevMan 5.3 software was used for the meta-analysis. The regimen of compound indigo naturalis plus NB-UVB showed much better control of PR as compared to that achieved with use of compound indigo naturalis or NB-UVB alone in terms of cure rate or effective rate. However, no significant difference was observed between the two with respect to incidence of adverse effects. The analysis was affected by publication bias as revealed by funnel plot analysis. Further studies with large sample sizes are required to confirm our findings. PMID:29770152

Efficacy and Safety of Indigo Naturalis in Combination with Narrow-Band Ultraviolet B for Treatment of Pityriasis Rosea: A Meta-Analysis.

PubMed

Wang, L; Xue, Y N; Li, Z W; Zhang, W; Ji, X P; Fan, Z; Li, Y J

2018-01-01

Pityriasis rosea (PR), a skin rash, causes substantial discomfort in patients. There is a lack of effective therapies for PR. A combination of ultraviolet irradiation and indigo naturalis treatment has been shown to be a safe and effective regime for control of PR; however, the data have been largely inconsistent. Tis meta-analysis further evaluated the efficacy and safety of this combination in patients with PR. The PubMed, Embase, Cochrane Library, CNKI, VIP, and Wan Fang databases were searched for relevant RCTs of this combination therapy in patients with PR. A total of eight studies with a combined study population of 688 patients published between January 2006 and March 2016 were eligible for this meta-analysis. The RevMan 5.3 software was used for the meta-analysis. The regimen of compound indigo naturalis plus NB-UVB showed much better control of PR as compared to that achieved with use of compound indigo naturalis or NB-UVB alone in terms of cure rate or effective rate. However, no significant difference was observed between the two with respect to incidence of adverse effects. The analysis was affected by publication bias as revealed by funnel plot analysis. Further studies with large sample sizes are required to confirm our findings.

Therapy of bovine endometritis with prostaglandin F2α: a meta-analysis.

PubMed

Haimerl, P; Heuwieser, W; Arlt, S

2013-05-01

The objective of the conducted meta-analysis was to assess the efficacy of the treatment of bovine endometritis with PGF(2α) by statistical means. Postpartum uterine infections have a high prevalence and a very negative effect on reproductive performance in dairy cattle. Because of a wide discordance between research results, a meta-analysis of the efficacy of the treatment of bovine endometritis with PGF(2α) was conducted. A comprehensive literature search was performed using online databases to reveal a total of 2,307 references. In addition, 5 articles were retrieved by reviewing citations. After applying specific exclusion criteria and evaluating specific evidence parameters, 5 publications, comprising 6 trials, were eligible for being analyzed by means of meta-analysis. Data for each trial were extracted and analyzed using meta-analysis software Review Manager (version 5.1; The Nordic Cochrane Centre, Copenhagen, Denmark). Estimated effect sizes of PGF(2α) were calculated on calving to first service and calving to conception interval. Prostaglandin F(2α) treatment of cows with chronic endometritis had a negative effect on both reproductive performance parameters. Heterogeneity was substantial for calving to first service and calving to conception interval [I(2) (measure of variation beyond chance)=100 and 87%, respectively]; therefore, random-effects models were used. Sensitivity analysis as well as subgroup analysis showed that the performance of randomization was influential in modifying effect size of PGF(2α) treatment. The funnel plot illustrated a publication bias toward smaller studies that reported a prolonged calving to conception interval after a PGF(2α) treatment. We conclude that the investigation of this subject by means of meta-analysis did not reveal an improvement of reproductive performance of cows with endometritis after treatment with PGF(2α). Furthermore, there is a shortage of comparable high quality studies investigating reproductive performance after PGF(2α) treatment of cows with chronic endometritis. Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

A Metagenomics Transect into the Deepest Point of the Baltic Sea Reveals Clear Stratification of Microbial Functional Capacities

PubMed Central

Poole, Anthony M.; Sjöberg, Britt-Marie; Sjöling, Sara

2013-01-01

The Baltic Sea is characterized by hyposaline surface waters, hypoxic and anoxic deep waters and sediments. These conditions, which in turn lead to a steep oxygen gradient, are particularly evident at Landsort Deep in the Baltic Proper. Given these substantial differences in environmental parameters at Landsort Deep, we performed a metagenomic census spanning surface to sediment to establish whether the microbial communities at this site are as stratified as the physical environment. We report strong stratification across a depth transect for both functional capacity and taxonomic affiliation, with functional capacity corresponding most closely to key environmental parameters of oxygen, salinity and temperature. We report similarities in functional capacity between the hypoxic community and hadal zone communities, underscoring the substantial degree of eutrophication in the Baltic Proper. Reconstruction of the nitrogen cycle at Landsort deep shows potential for syntrophy between archaeal ammonium oxidizers and bacterial denitrification at anoxic depths, while anaerobic ammonium oxidation genes are absent, despite substantial ammonium levels below the chemocline. Our census also reveals enrichment in genetic prerequisites for a copiotrophic lifestyle and resistance mechanisms reflecting adaptation to prevalent eutrophic conditions and the accumulation of environmental pollutants resulting from ongoing anthropogenic pressures in the Baltic Sea. PMID:24086414

Heat integrated ethanol dehydration flowsheets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hutahaean, L.S.; Shen, W.H.; Brunt, V. Van

1995-04-01

zA theoretical evaluation of heat-integrated heterogeneous-azeotropic ethanol-water distillation flowsheets is presented. Simulations of two column flowsheets using several different hydrocarbon entrainers reveal a region of potential heat integration and substantial reduction in operating energy. In this paper, methods for comparing hydrocarbon entrainers are shown. Two aspects of entrainers are related to operating and capital costs. The binary azeotropic composition of the entrainer-ethanol mixture is related to the energy requirements of the flowsheet. A temperature difference in the azeotrophic column is related to the size of the column and overall process staging requirements. Although the hydrophobicity of an entrainer is essentialmore » for specification of staging in the dehydration column, no substantial increase in operating energy results from an entrainer that has a higher water content. Likewise, liquid-liquid equilibria between several entrainer-ethanol-water mixtures have no substantial effect on either staging or operation. Rather, increasing the alcohol content of the entrainer-ethanol azeotrope limits its recovery in the dehydration column, and increases the recycle and reflux streams. These effects both contribute to increasing the separation energy requirements and reducing the region of potential heat integration. A cost comparison with a multieffect extractive distillation flowsheet reveals that the costs are comparable; however, the extractive distillation flowsheet is more cost effective as operating costs increase.« less

Differential histone modification and protein expression associated with cell wall removal and regeneration in rice (Oryza sativa).

PubMed

Tan, Feng; Zhang, Kangling; Mujahid, Hana; Verma, Desh Pal S; Peng, Zhaohua

2011-02-04

The cell wall is a critical extracellular structure that provides protection and structural support in plant cells. To study the biological function of the cell wall and the regulation of cell wall resynthesis, we examined cellular responses to enzymatic removal of the cell wall in rice (Oryza sativa) suspension cells using proteomic approaches. We find that removal of cell wall stimulates cell wall synthesis from multiple sites in protoplasts instead of from a single site as in cytokinesis. Nucleus DAPI stain and MNase digestion further show that removal of the cell wall is concomitant with substantial chromatin reorganization. Histone post-translational modification studies using both Western blots and isotope labeling assisted quantitative mass spectrometry analyses reveal that substantial histone modification changes, particularly H3K18(AC) and H3K23(AC), are associated with the removal and regeneration of the cell wall. Label-free quantitative proteome analyses further reveal that chromatin associated proteins undergo dramatic changes upon removal of the cell wall, along with cytoskeleton, cell wall metabolism, and stress-response proteins. This study demonstrates that cell wall removal is associated with substantial chromatin change and may lead to stimulation of cell wall synthesis using a novel mechanism.

Coexistence and local μ-stability of multiple equilibrium points for memristive neural networks with nonmonotonic piecewise linear activation functions and unbounded time-varying delays.

PubMed

Nie, Xiaobing; Zheng, Wei Xing; Cao, Jinde

2016-12-01

In this paper, the coexistence and dynamical behaviors of multiple equilibrium points are discussed for a class of memristive neural networks (MNNs) with unbounded time-varying delays and nonmonotonic piecewise linear activation functions. By means of the fixed point theorem, nonsmooth analysis theory and rigorous mathematical analysis, it is proven that under some conditions, such n-neuron MNNs can have 5 n equilibrium points located in ℜ n , and 3 n of them are locally μ-stable. As a direct application, some criteria are also obtained on the multiple exponential stability, multiple power stability, multiple log-stability and multiple log-log-stability. All these results reveal that the addressed neural networks with activation functions introduced in this paper can generate greater storage capacity than the ones with Mexican-hat-type activation function. Numerical simulations are presented to substantiate the theoretical results. Copyright © 2016 Elsevier Ltd. All rights reserved.

Drug information, misinformation, and disinformation on social media: a content analysis study.

PubMed

Al Khaja, Khalid A J; AlKhaja, Alwaleed K; Sequeira, Reginald P

2018-05-24

Dissemination of misleading drug information through social media can be detrimental to the health of the public. This study, carried out in Bahrain, evaluated the truthfulness of 22 social media claims about drugs (72.7%), dietary supplements (22.7%), and toxic bisphenol-A (4.5%). They circulated on WhatsApp platform, as case studies. We categorized claims as objectively true, false, or potentially misleading. The content analysis revealed that "potentially misleading" claims were the most frequent messages (59.1%). They tend to exaggerate the efficacy or safety without sufficient evidence to substantiate claims. False claims (27.3%) were likely due to unfair competition or deception. Overall, 13.6% of the messages were objectively true claims that could withstand regulatory scrutiny. Majority of the drug-related messages on social media were potentially misleading or false claims that lacked credible evidence to support them. In the public interest, regulatory authorities should monitor such information disseminated via social media platforms.

A comparative analysis of whispered and normally phonated speech using an LPC-10 vocoder

NASA Astrophysics Data System (ADS)

Wilson, J. B.; Mosko, J. D.

1985-12-01

The determination of the performance of an LPC-10 vocoder in the processing of adult male and female whispered and normally phonated connected speech was the focus of this study. The LPC-10 vocoder's analysis of whispered speech compared quite favorably with similar studies which used sound spectrographic processing techniques. Shifting from phonated speech to whispered speech caused a substantial increase in the phonomic formant frequencies and formant bandwidths for both male and female speakers. The data from this study showed no evidence that the LPC-10 vocoder's ability to process voices with pitch extremes and quality extremes was limited in any significant manner. A comparison of the unprocessed natural vowel waveforms and qualities with the synthesized vowel waveforms and qualities revealed almost imperceptible differences. An LPC-10 vocoder's ability to process linguistic and dialectical suprasegmental features such as intonation, rate and stress at low bit rates should be a critical issue of concern for future research.

(Per)chlorate in Biology on Earth and Beyond.

PubMed

Youngblut, Matthew D; Wang, Ouwei; Barnum, Tyler P; Coates, John D

2016-09-08

Respiration of perchlorate and chlorate [collectively, (per)chlorate] was only recognized in the last 20 years, yet substantial advances have been made in our understanding of the underlying metabolisms. Although it was once considered solely anthropogenic, pervasive natural sources, both terrestrial and extraterrestrial, indicate an ancient (per)chlorate presence across our solar system. These discoveries stimulated interest in (per)chlorate microbiology, and the application of advanced approaches highlights exciting new facets. Forward and reverse genetics revealed new information regarding underlying molecular biology and associated regulatory mechanisms. Structural and functional analysis characterized core enzymes and identified novel reaction sequences. Comparative genomics elucidated evolutionary aspects, and stress analysis identified novel response mechanisms to reactive chlorine species. Finally, systems biology identified unique metabolic versatility and novel mechanisms of (per)chlorate respiration, including symbiosis and a hybrid enzymatic-abiotic metabolism. While many published studies focus on (per)chlorate and their basic metabolism, this review highlights seminal advances made over the last decade and identifies new directions and potential novel applications.

The financial and economic feasibility of rural household biodigesters for poor communities in South Africa.

PubMed

Smith, Michael T; Goebel, Jessica Schroenn; Blignaut, James N

2014-02-01

Given the persistence of systemic poverty in, most notably, the rural parts of South Africa, the question is whether the use of biodigesters as a source of energy offers potential solutions to some of the difficulties and development needs faced by people in these areas. At the core, this translates into whether this technology would be financially and economically feasible for installation and use by rural households. Here we conduct both a financial and an economic cost-benefit analysis in one such community based on survey data from 120 households. Analysis of these data and supporting literature reveals that a biodigester is not a financially feasible investment for a rural household. Substantial economic benefits are, however, found to make a biodigester a worthwhile investment from a broader societal perspective. This is a compelling argument for further study and the consideration of government support in the light of broader economy-wide benefits. Copyright © 2013 Elsevier Ltd. All rights reserved.

The development of socio-motivational dependency from early to middle adolescence

PubMed Central

Jagenow, Danilo; Raufelder, Diana; Eid, Michael

2015-01-01

Research on students’ motivation has shown that motivation can be enhanced or undermined by social factors. However, when interpreting such findings, interindividual differences, and intraindividual changes underlying students’ perception of peers and teachers as a source of motivation are often neglected. The aim of the present study was to complement our understanding of socio-motivational dependency by investigating differences in the development of students’ socio-motivational dependency from early to middle adolescence. Data from 1088 students on their perceptions of peers and teachers as positive motivators when students were in seventh and eighth grade were compared with data of the same sample 2 years later. Latent class analysis supported four different motivation types (MT): (1) teacher-dependent MT, (2) peer-dependent MT, (3) teacher-and-peer-dependent MT, and (4) teacher-and-peer-independent MT. Latent transition analysis revealed substantial changes between the groups. The perceived teacher influence on students’ academic motivation increased from early to middle adolescence. Divergent roles of peers and teachers on students’ academic motivation are discussed. PMID:25762966

Meta-analysis of technology-assisted interventions for social anxiety disorder.

PubMed

Kampmann, Isabel L; Emmelkamp, Paul M G; Morina, Nexhmedin

2016-08-01

This meta-analysis investigated the efficacy of technology-assisted interventions for individuals with social anxiety disorder (SAD). A systematic literature search in the databases Medline, PsychInfo, and Web of Science revealed 37 randomized controlled trials (2991 participants) that were grouped into internet delivered cognitive behavior therapy (ICBT; 21 trials), virtual reality exposure therapy (VRET; 3 trials), and cognitive bias modification (CBM; 13 trials). Patients undergoing ICBT and VRET showed significantly less SAD symptoms at postassessment than passive control conditions (g=0.84 and 0.82, respectively). Compared to active control conditions, ICBT had a small advantage (g=0.38) and VRET showed comparable effects (p>0.05). CBM was not more effective than passive control conditions, except when delivered in the laboratory (g=0.35). While the efficacy of CBM was limited, substantial evidence for ICBT and preliminary evidence for VRET suggests that both can effectively reduce SAD symptoms indicating the potential of technology-assisted interventions for SAD. Copyright © 2016 Elsevier Ltd. All rights reserved.

Dynamic and kinematic strategies for head movement control

NASA Technical Reports Server (NTRS)

Peterson, B. W.; Choi, H.; Hain, T.; Keshner, E.; Peng, G. C.

2001-01-01

This paper describes our analysis of the complex head-neck system using a combination of experimental and modeling approaches. Dynamical analysis of head movements and EMG activation elicited by perturbation of trunk position has examined functional contributions of biomechanically and neurally generated forces in lumped systems with greatly simplified kinematics. This has revealed that visual and voluntary control of neck muscles and the dynamic and static vestibulocollic and cervicocollic reflexes preferentially govern head-neck system state in different frequency domains. It also documents redundant control, which allows the system to compensate for lesions and creates a potential for substantial variability within and between subjects. Kinematic studies have indicated the existence of reciprocal and co-contraction strategies for voluntary force generation, of a vestibulocollic strategy for stabilizing the head during body perturbations and of at least two strategies for voluntary head tracking. Each strategy appears to be executed by a specific muscle synergy that is presumably optimized to efficiently meet the demands of the task.

Hypocholesterolemic and bioactive potential of exopolysaccharide from a probiotic Enterococcus faecium K1 isolated from kalarei.

PubMed

Bhat, Bilqeesa; Bajaj, Bijender Kumar

2018-04-01

Bioprospecting of novel probiotic strains especially from unexplored eco-niches has been a continuous practice. Enterococcus faecium K1, an isolate from indigenously fermented milk product kalarei possesses numerous desirable functional attributes. In current study, E. faecium K1 has been used for EPS production, and it yielded 355 ± 0.019 mg/L EPS. EPS demonstrates remarkable hypocholesterolemic, antioxidant, antibiofilm, and emulsification characteristics. EPS is constituted of mannose, glucose and galactose. SEM analysis reveals flake like compact structure of EPS while TEM and X-ray diffractogram confirms the amorphous structure of EPS. FTIR substantiates the functional groups/bonds typical of polysaccharides. Thermal analysis indicates adequate stability of EPS at 237 °C with average weight loss of 22%. E. faecium K1 EPS possesses unique functional bioactivities and physicochemical characteristics, and may potentially be explored for applications in food/pharmaceutical industries. Copyright © 2018 Elsevier Ltd. All rights reserved.

Segregation analysis reveals evidence of a major gene for Alzheimer disease.

PubMed Central

Farrer, L A; Myers, R H; Connor, L; Cupples, L A; Growdon, J H

1991-01-01

In an attempt to resolve the relative influences of major genes, multifactorial heritability, and cohort effects on the susceptibility to Alzheimer disease (AD), complex segregation analysis was performed on 232 nuclear families. All families were consecutively ascertained through a single proband who was referred for diagnostic evaluation of a memory disorder. The results suggest that susceptibility to AD is determined, in part, by a major autosomal dominant allele with an additional multifactorial component. Single-locus, polygenic, sporadic, and no-transmission models, as well as recessive inheritance of the major effect, were significantly rejected. Excess transmission from the heterozygote was marginally significant and probably reflects the presence of phenocopies or perhaps the existence of two or more major loci for AD. The frequency of the AD susceptibility allele was estimated to be .038, but the major locus accounts for only 24% of the transmission variance, indicating a substantial role for other genetic and nongenetic mechanisms in the causation of AD. PMID:2035523

Formation Pathways of Carbon Allotropes in Detonation Condensates

NASA Astrophysics Data System (ADS)

Nielsen, Michael; Bagge-Hansen, Michael; Hammons, Josh; Lauderbach, Lisa; Hodgin, Ralph; Bastea, Sorin; Fried, Larry; Lee, Jonathan; van Buuren, Tony; Pagoria, Phil; May, Chadd; Aloni, Shaul; Willey, Trevor

2017-06-01

Time-resolved small-angle scattering (TR-SAXS) data reveal evolution in the size and morphology of nano-carbon particles that form during the first microsecond during the detonation of high explosive (HE) materials, but do not provide chemical or phase information. Herein, we present analysis of complementary post-detonation soots collected with minimal environmental carbon or other contamination: HE samples are detonated whithin clean ice capture layers to yield aqueous dispersions of the carbonaceous soot. We report substantial variation in soots formed through the detonation of HE materials that attain a variety of temperatures and pressures during detonation. Transmission electron microscopy analysis of these recovered soots provides physical and chemical information that we compare directly to TR-SAXS data and SAXS measurements from recovered soots. We observe various structures including graphitic and amorphous carbon, nanodiamond, and spherical carbon onions. These experimental data correlate to models of how products from HE materials traverse the carbon phase diagram during detonation. Prepared by LLNL under Contract DE-AC52-07NA27344.

Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication

PubMed Central

Wu, G. Albert; Prochnik, Simon; Jenkins, Jerry; Salse, Jerome; Hellsten, Uffe; Murat, Florent; Perrier, Xavier; Ruiz, Manuel; Scalabrin, Simone; Terol, Javier; Takita, Marco Aurélio; Labadie, Karine; Poulain, Julie; Couloux, Arnaud; Jabbari, Kamel; Cattonaro, Federica; Del Fabbro, Cristian; Pinosio, Sara; Zuccolo, Andrea; Chapman, Jarrod; Grimwood, Jane; Tadeo, Francisco R.; Estornell, Leandro H.; Muñoz-Sanz, Juan V.; Ibanez, Victoria; Herrero-Ortega, Amparo; Aleza, Pablo; Pérez-Pérez, Julián; Ramón, Daniel; Brunel, Dominique; Luro, François; Chen, Chunxian; Farmerie, William G.; Desany, Brian; Kodira, Chinnappa; Mohiuddin, Mohammed; Harkins, Tim; Fredrikson, Karin; Burns, Paul; Lomsadze, Alexandre; Borodovsky, Mark; Reforgiato, Giuseppe; Freitas-Astúa, Juliana; Quetier, Francis; Navarro, Luis; Roose, Mikeal; Wincker, Patrick; Schmutz, Jeremy; Morgante, Michele; Machado, Marcos Antonio; Talon, Manuel; Jaillon, Olivier; Ollitrault, Patrick; Gmitter, Frederick; Rokhsar, Daniel

2014-01-01

The domestication of citrus, is poorly understood. Cultivated types are selections from, or hybrids of, wild progenitor species, whose identities and contributions remain controversial. By comparative analysis of a collection of citrus genomes, including a high quality haploid reference, we show that cultivated types were derived from two progenitor species. Though cultivated pummelos represent selections from a single progenitor species, C. maxima, cultivated mandarins are introgressions of C. maxima into the ancestral mandarin species, C. reticulata. The most widely cultivated citrus, sweet orange, is the offspring of previously admixed individuals, but sour orange is an F1 hybrid of pure C. maxima and C. reticulata parents, implying that wild mandarins were part of the early breeding germplasm. A wild “mandarin” from China exhibited substantial divergence from C. reticulata, suggesting the possibility of other unrecognized wild citrus species. Understanding citrus phylogeny through genome analysis clarifies taxonomic relationships and enables sequence-directed genetic improvement. PMID:24908277

Solar granulation and statistical crystallography: A modeling approach using size-shape relations

NASA Technical Reports Server (NTRS)

Noever, D. A.

1994-01-01

The irregular polygonal pattern of solar granulation is analyzed for size-shape relations using statistical crystallography. In contrast to previous work which has assumed perfectly hexagonal patterns for granulation, more realistic accounting of cell (granule) shapes reveals a broader basis for quantitative analysis. Several features emerge as noteworthy: (1) a linear correlation between number of cell-sides and neighboring shapes (called Aboav-Weaire's law); (2) a linear correlation between both average cell area and perimeter and the number of cell-sides (called Lewis's law and a perimeter law, respectively) and (3) a linear correlation between cell area and squared perimeter (called convolution index). This statistical picture of granulation is consistent with a finding of no correlation in cell shapes beyond nearest neighbors. A comparative calculation between existing model predictions taken from luminosity data and the present analysis shows substantial agreements for cell-size distributions. A model for understanding grain lifetimes is proposed which links convective times to cell shape using crystallographic results.

Effects of welding heat and travel speed on the impact property and microstructure of FC welds

NASA Astrophysics Data System (ADS)

Lee, Jeong Soo; Jeong, Sang Hoon; Lim, Dong Yong; Yun, Jin Oh; Kim, Myung Hyun

2010-10-01

This paper is concerned with the effects of welding heat (current x voltage = W) and travel speed (v) on the impact property and microstructure of FC (flux cored) welds. Two sets of plate were welded under different welding conditions such as higher W, v and lower W, v, while maintaining identical heat input. We evaluated the effects of each factor by Charpy impact test and observation of the microstructure, and then compared these data with the results of the numerical temperature analysis. The size of the re-heated zone was increased as the v value decreased, and the results of numerical analysis also revealed the same tendency. Cooling rate of welds (both of as-welded and re-heated zones) decreased as the W value increased. Despite identical heat input conditions, the use of lower W and v made the microstructure finer and increased the volume fraction of AF, thereby leading to a substantial improvement of the impact property.

Causes of accidents in terrain parks: an exploratory factor analysis of recreational freestylers' views.

PubMed

Carús, Luis

2014-03-01

This study examines ski and snowboard terrain park users' views on aspects associated with accidents by identifying and assessing variables that may influence the occurrence of accidents and the resulting injuries. The research was conducted in a major resort in the Spanish Pyrenees, using information gathered from freestyle skiers and snowboarders aged 6 or older. To identify interrelationships among variables and to group the variables belonging to unified concepts, an exploratory factor analysis was performed using varimax rotation. The results revealed 5 factors that grouped the measured variables that may influence the occurrence of accidents while freestyling in terrain parks. The park features, conditions of the activity, and the user's personal conditions were found to have the most substantial influence on the freestylers' perceptions. Variables identified as components of the main factors of accident risk in terrain parks should be incorporated into resort management communication and policies. © 2013 Wilderness Medical Society Published by Wilderness Medical Society All rights reserved.

Molecular analysis of leptospires from serogroup Sejroe obtained from asymptomatic cattle in Rio de Janeiro - Brazil reveals genetic proximity to serovar Guaricura.

PubMed

Loureiro, A P; Hamond, C; Pinto, P; Bremont, S; Bourhy, P; Lilenbaum, W

2016-04-01

Bovine leptospirosis causes substantial reproductive failure in cattle, mainly due to infections with serovar (sv) Hardjo infection. Notwithstanding, other serovars from the serogroup (sg) Sejroe could also have important roles in bovine leptospirosis. The objective was to investigate genetic diversity of serogroup Sejroe isolates obtained from asymptomatic cattle in the state of Rio de Janeiro, Brazil. Urine and vaginal fluid (VF) were collected from clinically healthy cattle immediately after slaughter. Five isolates were recovered and characterized (serogrouping) as belonging to sg Sejroe. Sequencing of rrs and secY genes further identified them as Leptospira santarosai. Analysis of secY sequences indicated a high level of sequence homology to sv Guaricura strains. Based on culture and sequence data, we inferred that other members of sg Sejroe may be important in bovine leptospiral infection, particularly genotypes of L. santarosai serovar Guaricura. Copyright © 2016 Elsevier Ltd. All rights reserved.

Near-Earth asteroid satellite spins under spin-orbit coupling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Naidu, Shantanu P.; Margot, Jean-Luc

We develop a fourth-order numerical integrator to simulate the coupled spin and orbital motions of two rigid bodies having arbitrary mass distributions under the influence of their mutual gravitational potential. We simulate the dynamics of components in well-characterized binary and triple near-Earth asteroid systems and use surface of section plots to map the possible spin configurations of the satellites. For asynchronous satellites, the analysis reveals large regions of phase space where the spin state of the satellite is chaotic. For synchronous satellites, we show that libration amplitudes can reach detectable values even for moderately elongated shapes. The presence of chaoticmore » regions in the phase space has important consequences for the evolution of binary asteroids. It may substantially increase spin synchronization timescales, explain the observed fraction of asychronous binaries, delay BYORP-type evolution, and extend the lifetime of binaries. The variations in spin rate due to large librations also affect the analysis and interpretation of light curve and radar observations.« less

The Chemical Shift Baseline for High-Pressure NMR Spectra of Proteins.

PubMed

Frach, Roland; Kibies, Patrick; Böttcher, Saraphina; Pongratz, Tim; Strohfeldt, Steven; Kurrmann, Simon; Koehler, Joerg; Hofmann, Martin; Kremer, Werner; Kalbitzer, Hans Robert; Reiser, Oliver; Horinek, Dominik; Kast, Stefan M

2016-07-18

High-pressure (HP) NMR spectroscopy is an important method for detecting rare functional states of proteins by analyzing the pressure response of chemical shifts. However, for the analysis of the shifts it is mandatory to understand the origin of the observed pressure dependence. Here we present experimental HP NMR data on the (15) N-enriched peptide bond model, N-methylacetamide (NMA), in water, combined with quantum-chemical computations of the magnetic parameters using a pressure-sensitive solvation model. Theoretical analysis of NMA and the experimentally used internal reference standard 4,4-dimethyl-4-silapentane-1-sulfonic (DSS) reveal that a substantial part of observed shifts can be attributed to purely solvent-induced electronic polarization of the backbone. DSS is only marginally responsive to pressure changes and is therefore a reliable sensor for variations in the local magnetic field caused by pressure-induced changes of the magnetic susceptibility of the solvent. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Raman spectroscopy identifies radiation response in human non-small cell lung cancer xenografts

NASA Astrophysics Data System (ADS)

Harder, Samantha J.; Isabelle, Martin; Devorkin, Lindsay; Smazynski, Julian; Beckham, Wayne; Brolo, Alexandre G.; Lum, Julian J.; Jirasek, Andrew

2016-02-01

External beam radiation therapy is a standard form of treatment for numerous cancers. Despite this, there are no approved methods to account for patient specific radiation sensitivity. In this report, Raman spectroscopy (RS) was used to identify radiation-induced biochemical changes in human non-small cell lung cancer xenografts. Chemometric analysis revealed unique radiation-related Raman signatures that were specific to nucleic acid, lipid, protein and carbohydrate spectral features. Among these changes was a dramatic shift in the accumulation of glycogen spectral bands for doses of 5 or 15 Gy when compared to unirradiated tumours. When spatial mapping was applied in this analysis there was considerable variability as we found substantial intra- and inter-tumour heterogeneity in the distribution of glycogen and other RS spectral features. Collectively, these data provide unique insight into the biochemical response of tumours, irradiated in vivo, and demonstrate the utility of RS for detecting distinct radiobiological responses in human tumour xenografts.

Biomedical journal title changes: reasons, trends, and impact.

PubMed Central

Afes, V B; Wrynn, P E

1993-01-01

A study was conducted to document the impact of biomedical journal title changes on medical libraries and to increase awareness of the reasons titles are changed. The study consisted of two parts: a survey of academic health sciences libraries in the United States and Canada and an analysis of title changes from two different years. The survey response rate was 83%. The majority of respondents commented on difficulties in identifying and processing title changes, often resulting in the delay or loss of information. The analysis revealed that a third of title changes were not justified by the journal. The study results substantiate the need to standardize title change reporting by publishers. A standard developed by the National Information Standards Organization requires publishers to conform to standardized practices for notification. This standard precisely reflects the concerns reflected in both the survey and the study of title changes, and librarians are urged to ensure that the standard is implemented by publishers. PMID:8428189

Verification of Anderson Superexchange in MnO via Magnetic Pair Distribution Function Analysis and ab initio Theory

NASA Astrophysics Data System (ADS)

Frandsen, Benjamin A.; Brunelli, Michela; Page, Katharine; Uemura, Yasutomo J.; Staunton, Julie B.; Billinge, Simon J. L.

2016-05-01

We present a temperature-dependent atomic and magnetic pair distribution function (PDF) analysis of neutron total scattering measurements of antiferromagnetic MnO, an archetypal strongly correlated transition-metal oxide. The known antiferromagnetic ground-state structure fits the low-temperature data closely with refined parameters that agree with conventional techniques, confirming the reliability of the newly developed magnetic PDF method. The measurements performed in the paramagnetic phase reveal significant short-range magnetic correlations on a ˜1 nm length scale that differ substantially from the low-temperature long-range spin arrangement. Ab initio calculations using a self-interaction-corrected local spin density approximation of density functional theory predict magnetic interactions dominated by Anderson superexchange and reproduce the measured short-range magnetic correlations to a high degree of accuracy. Further calculations simulating an additional contribution from a direct exchange interaction show much worse agreement with the data. The Anderson superexchange model for MnO is thus verified by experimentation and confirmed by ab initio theory.

One Size Fits All? The Validity of a Composite Poverty Index Across Urban and Rural Households in South Africa.

PubMed

Steinert, Janina Isabel; Cluver, Lucie Dale; Melendez-Torres, G J; Vollmer, Sebastian

2018-01-01

Composite indices have been prominently used in poverty research. However, validity of these indices remains subject to debate. This paper examines the validity of a common type of composite poverty indices using data from a cross-sectional survey of 2477 households in urban and rural KwaZulu-Natal, South Africa. Multiple-group comparisons in structural equation modelling were employed for testing differences in the measurement model across urban and rural groups. The analysis revealed substantial variations between urban and rural respondents both in the conceptualisation of poverty as well as in the weights and importance assigned to individual poverty indicators. The validity of a 'one size fits all' measurement model can therefore not be confirmed. In consequence, it becomes virtually impossible to determine a household's poverty level relative to the full sample. Findings from our analysis have important practical implications in nuancing how we can sensitively use composite poverty indices to identify poor people.

Dynamic Functional Connectivity States Between the Dorsal and Ventral Sensorimotor Networks Revealed by Dynamic Conditional Correlation Analysis of Resting-State Functional Magnetic Resonance Imaging.

PubMed

Syed, Maleeha F; Lindquist, Martin A; Pillai, Jay J; Agarwal, Shruti; Gujar, Sachin K; Choe, Ann S; Caffo, Brian; Sair, Haris I

2017-12-01

Functional connectivity in resting-state functional magnetic resonance imaging (rs-fMRI) has received substantial attention since the initial findings of Biswal et al. Traditional network correlation metrics assume that the functional connectivity in the brain remains stationary over time. However, recent studies have shown that robust temporal fluctuations of functional connectivity among as well as within functional networks exist, challenging this assumption. In this study, these dynamic correlation differences were investigated between the dorsal and ventral sensorimotor networks by applying the dynamic conditional correlation model to rs-fMRI data of 20 healthy subjects. k-Means clustering was used to determine an optimal number of discrete connectivity states (k = 10) of the sensorimotor system across all subjects. Our analysis confirms the existence of differences in dynamic correlation between the dorsal and ventral networks, with highest connectivity found within the ventral motor network.

Dynamics of psychological crisis experience with psychological consulting by gestalt therapy methods.

PubMed

Fahrutdinova, Liliya Raifovna; Nugmanova, Dzhamilia Renatovna

2015-01-01

Dynamics of experience as such and its corporeal, emotional and cognitive elements in the situation of psychological consulting provisioning is covered. The aim of research was to study psychological crisis experience dynamics in the situation when psychological consulting by gestalt therapy methods is provided. Theoretical analysis of the problem of crisis situations, phenomenon and structural, and dynamic organization of experience of the subject of consulting have been carried out. To fulfill research project test subjects experience crisis situation have been selected, studied in the situation when they provided psychological consulting by methods of gestalt therapy, and methodology of study of crisis situations experience has been prepared. Specifics of psychological crisis experience have been revealed and its elements in different stages of psychological consulting by gestalt therapy methods. Dynamics of experience of psychological crisis and its structural elements have been revealed and reliable changes in it have been revealed. Dynamics of psychological crisis experience and its structural elements have been revealed and reliable changes in it have been revealed. "Desiccation" of experience is being observed, releasing its substantiality of negative impression to the end of consulting and development of the new experience of control over crisis situation. Interrelations of structural elements of experience in the process of psychological consulting have been shown. Effecting one structure causes reliable changes in all others structural elements of experience. Giving actual psychological help to clients in crisis situation by methods of gestalt therapy is possible as it was shown in psychological consulting sessions. Structure of client's request has been revealed - problems of personal sense are fixed as the most frequent cause of clients' applications, as well as absence of choices, obtrusiveness of negative thoughts, tend to getting stuck on events took place in the past, drawing into oneself, etc.

On the costs and benefits of emotional labor: a meta-analysis of three decades of research.

PubMed

Hülsheger, Ute R; Schewe, Anna F

2011-07-01

This article provides a quantitative review of the link of emotional labor (emotion-rule dissonance, surface acting, and deep acting) with well-being and performance outcomes. The meta-analysis is based on 494 individual correlations drawn from a final sample of 95 independent studies. Results revealed substantial relationships of emotion-rule dissonance and surface acting with indicators of impaired well-being (ρs between .39 and .48) and job attitudes (ρs between -.24 and -.40) and a small negative relationship with performance outcomes (ρs between -.20 and -.05). Overall, deep acting displayed weak relationships with indicators of impaired well-being and job attitudes but positive relationships with emotional performance and customer satisfaction (ρs .18 and .37). A meta-analytic regression analysis provides information on the unique contribution of emotion-rule dissonance, surface acting, and deep acting in statistically predicting well-being and performance outcomes. Furthermore, a mediation analysis confirms theoretical models of emotional labor which suggest that surface acting partially mediates the relationship of emotion-rule dissonance with well-being. Implications for future research as well as pragmatic ramifications for organizational practices are discussed in conclusion.

Differential item functioning analysis of the Vanderbilt Expertise Test for cars.

PubMed

Lee, Woo-Yeol; Cho, Sun-Joo; McGugin, Rankin W; Van Gulick, Ana Beth; Gauthier, Isabel

2015-01-01

The Vanderbilt Expertise Test for cars (VETcar) is a test of visual learning for contemporary car models. We used item response theory to assess the VETcar and in particular used differential item functioning (DIF) analysis to ask if the test functions the same way in laboratory versus online settings and for different groups based on age and gender. An exploratory factor analysis found evidence of multidimensionality in the VETcar, although a single dimension was deemed sufficient to capture the recognition ability measured by the test. We selected a unidimensional three-parameter logistic item response model to examine item characteristics and subject abilities. The VETcar had satisfactory internal consistency. A substantial number of items showed DIF at a medium effect size for test setting and for age group, whereas gender DIF was negligible. Because online subjects were on average older than those tested in the lab, we focused on the age groups to conduct a multigroup item response theory analysis. This revealed that most items on the test favored the younger group. DIF could be more the rule than the exception when measuring performance with familiar object categories, therefore posing a challenge for the measurement of either domain-general visual abilities or category-specific knowledge.

Economic analysis of new space transportation systems: Executive summary

NASA Technical Reports Server (NTRS)

1971-01-01

An economic analysis of alternative space transportation systems is presented. Results indicate that the expendable systems represent modest investments, but the recurring costs of operation would remain high. The space shuttle and tug system requires a substantial investment, but would substantially reduce the recurring costs of operation. Economic benefits and costs of the different systems are also analyzed. Findings are summarized.

Effectiveness of Internet-Based Interventions on Glycemic Control in Patients With Type 2 Diabetes: Meta-Analysis of Randomized Controlled Trials

PubMed Central

Shen, Ying; Wang, Fengbin; Zhang, Xing; Zhu, Xiaorou; Sun, Qiudan; Fisher, Edwin

2018-01-01

Background The popularity of internet as an area of research has grown manifold over the years. Given its rapid development and increasing coverage worldwide, internet-based interventions seem to offer a promising option to ameliorate huge burdens brought by type 2 diabetes mellitus. However, studies conducted by different researchers have provided contradictory results on the effect of internet-based interventions in glycemic control. Objective This meta-analysis aims to summarize currently available evidence and evaluate the overall impact of internet-based interventions on glycemic management of type 2 diabetic patients. Methods A systematic literature search was performed in PubMed, ScienceDirect, and Web of Science. Randomized controlled trials that used glycosylated hemoglobin values as the outcome measure of glycemic control were considered. Risk of bias and publication bias were evaluated. Results Of the 492 studies, 35 were included in meta-analysis, and results indicated that the weighted mean difference (WMD) between usual care and internet-based interventions at endpoint was –0.426% (95% CI –0.540 to –0.312; P<.001). Subgroup analyses revealed that intervention duration ≤3 months yielded optimal performance (WMD –0.51%; 95% CI –0.71 to –0.31; P<.001). Combined mobile and website interventions were substantially superior to solely Web-based and mobile-based interventions in glycemic control (combined WMD –0.77%, 95% CI –1.07 to –0.47; P<.001; Web only: WMD –0.48%; 95% CI –0.71 to –0.24, P<.001; mobile only WMD –0.31%, 95% CI –0.49 to –0.14; P<.001). Furthermore, the effect of interventions with automated feedbacks was similar to those with manual feedbacks, and studies with internet-based educational contents were more effective in glycemic control. The assessment revealed a low risk of bias. Conclusions In conclusion, utilization of internet-based intervention is beneficial for patients with type 2 diabetes mellitus, and taking full advantage of this type of intervention may substantially reduce the incidence of complications and improve quality of life. Trial Registration International Prospective Register of Systematic Reviews (PROSPERO): CRD42017058032; https://www.crd.york.ac.uk/PROSPERO/display_record.php?RecordID=58032 (Archived by WebCite at http://www.webcitation.org/6yY7eQNHr) PMID:29735475

Identification and prognostic value of anterior gradient protein 2 expression in breast cancer based on tissue microarray.

PubMed

Guo, Jilong; Gong, Guohua; Zhang, Bin

2017-07-01

Breast cancer has attracted substantial attention as one of the major cancers causing death in women. It is crucial to find potential biomarkers of prognostic value in breast cancer. In this study, the expression pattern of anterior gradient protein 2 in breast cancer was identified based on the main molecular subgroups. Through analysis of 69 samples from the Gene Expression Omnibus database, we found that anterior gradient protein 2 expression was significantly higher in non-triple-negative breast cancer tissues compared with normal tissues and triple-negative breast cancer tissues (p < 0.05). The data from a total of 622 patients from The Cancer Genome Atlas were analysed. The data from The Cancer Genome Atlas and results from quantitative reverse transcription polymerase chain reaction also verified the anterior gradient protein 2 expression pattern. Furthermore, we performed immunohistochemical analysis. The quantification results revealed that anterior gradient protein 2 is highly expressed in non-triple-negative breast cancer (grade 3 excluded) and grade 1 + 2 (triple-negative breast cancer excluded) tumours compared with normal tissues. Anterior gradient protein 2 was significantly highly expressed in non-triple-negative breast cancer (grade 3 excluded) and non-triple-negative breast cancer tissues compared with triple-negative breast cancer tissues (p < 0.01). In addition, anterior gradient protein 2 was significantly highly expressed in grade 1 + 2 (triple-negative breast cancer excluded) and grade 1 + 2 tissues compared with grade 3 tissues (p < 0.05). Analysis by Fisher's exact test revealed that anterior gradient protein 2 expression was significantly associated with histologic type, histological grade, oestrogen status and progesterone status. Univariate analysis of clinicopathological variables showed that anterior gradient protein 2 expression, tumour size and lymph node status were significantly correlated with overall survival in patients with grade 1 and 2 tumours. Cox multivariate analysis revealed anterior gradient protein 2 as a putative independent indicator of unfavourable outcomes (p = 0.031). All these data clearly showed that anterior gradient protein 2 is highly expressed in breast cancer and can be regarded as a putative biomarker for breast cancer prognosis.

Child protection decisions to substantiate hospital child protection teams' reports of suspected maltreatment.

PubMed

Jedwab, Merav; Benbenishty, Rami; Chen, Wendy; Glasser, Saralee; Siegal, Gil; Lerner-Geva, Liat

2015-02-01

The present study focuses on the way child protection officers (CPOs) in Israel assess suspected abuse and neglect (SCAN) reports made by hospital child protection teams (CPTs), to determine whether the alleged maltreatment is substantiated. The study was conducted in six medical centers and included 358 reports investigated by CPOs for SCAN. A structured questionnaire was completed by hospital CPTs to capture all relevant information on each child referred to the CPTs. Structured phone interviews were conducted with each of the CPOs who received a CPT report. Bivariate associations and multivariate logistic regressions were conducted to estimate the substantiation rate of cases reported by CPTs and the types of maltreatment substantiated, as well as to identify case characteristics of the child and the family that were associated with the CPOs' substantiation decision. CPO follow-up investigations revealed a substantiation rate of 53.5%. The maltreatment type most commonly substantiated was neglect. The case characteristics associated with substantiation included socio-demographic background, parents' health and functioning, previous contact with social services, characteristics of the hospital referral, medical findings and an assessment of the parents' behaviors. The findings of the study highlighted the importance of cooperation between the health and welfare services and the policy makers. This cooperation is essential for identifying early signs of maltreatment. Enhanced cooperation and effective information transfer between various professionals would help prevent or at least reduce the recurrence of maltreatment and would ensure that the children and their families are treated appropriately. Copyright © 2014 Elsevier Ltd. All rights reserved.

Novel Analysis Software for Detecting and Classifying Ca2+ Transient Abnormalities in Stem Cell-Derived Cardiomyocytes

PubMed Central

Penttinen, Kirsi; Siirtola, Harri; Àvalos-Salguero, Jorge; Vainio, Tiina; Juhola, Martti; Aalto-Setälä, Katriina

2015-01-01

Comprehensive functioning of Ca2+ cycling is crucial for excitation–contraction coupling of cardiomyocytes (CMs). Abnormal Ca2+ cycling is linked to arrhythmogenesis, which is associated with cardiac disorders and heart failure. Accordingly, we have generated spontaneously beating CMs from induced pluripotent stem cells (iPSC) derived from patients with catecholaminergic polymorphic ventricular tachycardia (CPVT), which is an inherited and severe cardiac disease. Ca2+ cycling studies have revealed substantial abnormalities in these CMs. Ca2+ transient analysis performed manually lacks accepted analysis criteria, and has both low throughput and high variability. To overcome these issues, we have developed a software tool, AnomalyExplorer based on interactive visualization, to assist in the classification of Ca2+ transient patterns detected in CMs. Here, we demonstrate the usability and capability of the software, and we also compare the analysis efficiency to manual analysis. We show that AnomalyExplorer is suitable for detecting normal and abnormal Ca2+ transients; furthermore, this method provides more defined and consistent information regarding the Ca2+ abnormality patterns and cell line specific differences when compared to manual analysis. This tool will facilitate and speed up the analysis of CM Ca2+ transients, making it both more accurate and user-independent. AnomalyExplorer can be exploited in Ca2+ cycling analysis to study basic disease pathology and the effects of different drugs. PMID:26308621

Novel Analysis Software for Detecting and Classifying Ca2+ Transient Abnormalities in Stem Cell-Derived Cardiomyocytes.

PubMed

Penttinen, Kirsi; Siirtola, Harri; Àvalos-Salguero, Jorge; Vainio, Tiina; Juhola, Martti; Aalto-Setälä, Katriina

2015-01-01

Comprehensive functioning of Ca2+ cycling is crucial for excitation-contraction coupling of cardiomyocytes (CMs). Abnormal Ca2+ cycling is linked to arrhythmogenesis, which is associated with cardiac disorders and heart failure. Accordingly, we have generated spontaneously beating CMs from induced pluripotent stem cells (iPSC) derived from patients with catecholaminergic polymorphic ventricular tachycardia (CPVT), which is an inherited and severe cardiac disease. Ca2+ cycling studies have revealed substantial abnormalities in these CMs. Ca2+ transient analysis performed manually lacks accepted analysis criteria, and has both low throughput and high variability. To overcome these issues, we have developed a software tool, AnomalyExplorer based on interactive visualization, to assist in the classification of Ca2+ transient patterns detected in CMs. Here, we demonstrate the usability and capability of the software, and we also compare the analysis efficiency to manual analysis. We show that AnomalyExplorer is suitable for detecting normal and abnormal Ca2+ transients; furthermore, this method provides more defined and consistent information regarding the Ca2+ abnormality patterns and cell line specific differences when compared to manual analysis. This tool will facilitate and speed up the analysis of CM Ca2+ transients, making it both more accurate and user-independent. AnomalyExplorer can be exploited in Ca2+ cycling analysis to study basic disease pathology and the effects of different drugs.

Older Korean American men's prostate cancer screening behavior: the prime role of culture.

PubMed

Lee, Hee Yun; Jung, Yunkyung

2013-12-01

East and South Asian male immigrants show markedly low odds of prostate cancer screening as compared to U.S.-born men. However, knowledge about these immigrants' culture-based screening behavior and barriers to screening is extremely limited. This study investigates factors influencing receipt of prostate cancer screening among Korean American immigrant men, particularly investigating culture's impact on screening behaviors. Data were collected through a convenience and purposive sampling technique from 134 Korean American males aged 50 and older recruited in New York City. A structured questionnaire was used and cultural variables were measured by adopting items from Tang and colleagues' work. Approximately 60 % of the sample had received a prostate-specific antigen (PSA) test in their lifetime, and of these, about 66 % reported having done so in the previous 12 months. Logistic regression analysis revealed that a crisis-oriented intervention approach was associated with a substantially reduced likelihood of screening. A positive correlation was noted between the use of Eastern medicine and PSA test receipt. Further analysis revealed a significant interaction effect between use of Eastern medicine and age in predicting PSA test uptake. Culture-specific intervention strategies for increasing prostate cancer screening in this group are discussed, with particular attention to increasing pertinent health literacy. Health professionals should consider the cultural domain when working with Korean immigrant men in order to provide culturally competent care.

Comparative Genomics Analysis of Streptococcus Isolates from the Human Small Intestine Reveals their Adaptation to a Highly Dynamic Ecosystem

PubMed Central

Van den Bogert, Bartholomeus; Boekhorst, Jos; Herrmann, Ruth; Smid, Eddy J.; Zoetendal, Erwin G.; Kleerebezem, Michiel

2013-01-01

The human small-intestinal microbiota is characterised by relatively large and dynamic Streptococcus populations. In this study, genome sequences of small-intestinal streptococci from S. mitis, S. bovis, and S. salivarius species-groups were determined and compared with those from 58 Streptococcus strains in public databases. The Streptococcus pangenome consists of 12,403 orthologous groups of which 574 are shared among all sequenced streptococci and are defined as the Streptococcus core genome. Genome mining of the small-intestinal streptococci focused on functions playing an important role in the interaction of these streptococci in the small-intestinal ecosystem, including natural competence and nutrient-transport and metabolism. Analysis of the small-intestinal Streptococcus genomes predicts a high capacity to synthesize amino acids and various vitamins as well as substantial divergence in their carbohydrate transport and metabolic capacities, which is in agreement with observed physiological differences between these Streptococcus strains. Gene-specific PCR-strategies enabled evaluation of conservation of Streptococcus populations in intestinal samples from different human individuals, revealing that the S. salivarius strains were frequently detected in the small-intestine microbiota, supporting the representative value of the genomes provided in this study. Finally, the Streptococcus genomes allow prediction of the effect of dietary substances on Streptococcus population dynamics in the human small-intestine. PMID:24386196

The tryptophan-derived endogenous arylhydrocarbon receptor ligand 6-formylindolo[3,2-b]carbazole (FICZ) is a nanomolar UVA-photosensitizer in epidermal keratinocytes

PubMed Central

Williams, Joshua D.; Cabello, Christopher M.; Qiao, Shuxi; Wondrak, Georg T.

2014-01-01

Endogenous UVA-chromophores may act as sensitizers of oxidative stress underlying cutaneous photoaging and photocarcinogenesis, but the molecular identity of non-DNA key chromophores displaying UVA-driven photodyamic activity in human skin remains largely undefined. Here we report that 6-formylindolo[3,2-b]carbazole (FICZ), a tryptophan photoproduct and endogenous high affinity aryl hydrocarbon receptor (AhR) agonist, acts as a nanomolar photosensitizer potentiating UVA-induced oxidative stress irrespective of AhR ligand activity. In human HaCaT and primary epidermal keratinocytes, photodynamic induction of apoptosis was elicited by the combined action of solar simulated UVA and FICZ, whereas exposure to the isolated action of UVA or FICZ did not impair viability. In a human epidermal tissue reconstruct, FICZ/UVA-cotreatment caused pronounced phototoxicity inducing keratinocyte cell death, and FICZ photodynamic activity was also substantiated in a murine skin exposure model. Array analysis revealed pronounced potentiation of cellular heat shock, ER stress, and oxidative stress response gene expression observed only upon FICZ/UVA-cotreatment. FICZ photosensitization caused intracellular oxidative stress, and comet analysis revealed introduction of formamidopyrimidine-DNA glycosylase (FPG)-sensitive oxidative DNA lesions suppressible by antioxidant cotreatment. Taken together, our data demonstrate that the endogenous AhR ligand FICZ displays nanomolar photodynamic activity representing a molecular mechanism of UVA-induced photooxidative stress potentially operative in human skin. PMID:25431849

Transgenic soya bean seeds accumulating β-carotene exhibit the collateral enhancements of oleate and protein content traits.

PubMed

Schmidt, Monica A; Parrott, Wayne A; Hildebrand, David F; Berg, R Howard; Cooksey, Amanda; Pendarvis, Ken; He, Yonghua; McCarthy, Fiona; Herman, Eliot M

2015-05-01

Transgenic soya bean (Glycine max) plants overexpressing a seed-specific bacterial phytoene synthase gene from Pantoea ananatis modified to target to plastids accumulated 845 μg β carotene g(-1) dry seed weight with a desirable 12:1 ratio of β to α. The β carotene accumulating seeds exhibited a shift in oil composition increasing oleic acid with a concomitant decrease in linoleic acid and an increase in seed protein content by at least 4% (w/w). Elevated β-carotene accumulating soya bean cotyledons contain 40% the amount of abscisic acid compared to nontransgenic cotyledons. Proteomic and nontargeted metabolomic analysis of the mid-maturation β-carotene cotyledons compared to the nontransgenic did not reveal any significant differences that would account for the altered phenotypes of both elevated oleate and protein content. Transcriptomic analysis, confirmed by RT-PCR, revealed a number of significant differences in ABA-responsive transcripton factor gene expression in the crtB transgenics compared to nontransgenic cotyledons of the same maturation stage. The altered seed composition traits seem to be attributed to altered ABA hormone levels varying transcription factor expression. The elevated β-carotene, oleic acid and protein traits in the β-carotene soya beans confer a substantial additive nutritional quality to soya beans. © 2014 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

Molecular homogeneity of heat-stable enterotoxins produced by bovine enterotoxigenic Escherichia coli.

PubMed Central

Saeed, A M; Magnuson, N S; Sriranganathan, N; Burger, D; Cosand, W

1984-01-01

Heat-stable enterotoxins (STs) from four strains of bovine enterotoxigenic Escherichia coli representing four serogroups were purified to homogeneity by utilizing previously published purification schemata. Biochemical characterization of the purified STs showed that they met the basic criteria for the heat-stable enterotoxins of E. coli. Amino acid analysis of the purified STs revealed that they were peptides of identical amino acid composition. This composition consisted of 18 residues of 10 different amino acids, 6 of which were cysteine. The amino acid composition of the four ST peptides was identical to that reported for the STs of human and porcine E. coli. In addition, complete sequence analysis of two of the ST peptides and partial sequencing of several others revealed strong homology to the sequences of STs from human and porcine E. coli and to the sequence predicted from the last 18 codons of the transposon Tn1681. There was also substantial homology to the sequence predicted from the ST-coding genetic element of human E. coli, which may indicate the existence of identical bioactive configuration among ST peptides of E. coli strains of various host origins. These data support the hypothesis that STs produced by human, bovine, and porcine E. coli are coded by a closely related genetic element which may have originated from a single, widely disseminated transposon. Images PMID:6376355

Mangiferin prevents corticosterone-induced behavioural deficits via alleviation of oxido-nitrosative stress and down-regulation of indoleamine 2,3-dioxygenase (IDO) activity.

PubMed

Luo, Gao-Quan; Liu, Ling; Gao, Qu-Wen; Wu, Xiao-Na; Xiang, Wei; Deng, Wen-Ting

2017-08-01

In recent years, a substantial amount of experimental studies have demonstrated that exogenous administration of corticosterone causes anxiety and depressive-like behaviour in rodents which involves hypothalamic-pituitary-adrenal axis dysregulation. Our present study aimed to explore the neuroprotective potential of mangiferin against corticosterone-induced anxiety and depressive-like behaviour. Corticosterone (40 mg/kg; subcutaneously) was administered once daily in swiss albino mice for 21 days. Mice were treated simultaneously with mangiferin (40 mg/kg; p.o.), 30 min prior to the corticosterone injection. Chronic administration of corticosterone caused anxiety and depressive-like behaviour in mice which was significantly alleviated by mangiferin treatment. Biochemical analysis revealed that mangiferin treatment significantly attenuated corticosterone-induced oxido-nitrosative stress and neuroinflammation in the hippocampus region. Furthermore, concomitant treatment with mangiferin significantly enhanced the hippocampal brain-derived neurotrophic factor (BDNF) level and decreased the serum corticosterone level in the corticosterone-treated animals. Western blotting analysis revealed that corticosterone administration significantly up-regulated the indoleamine 2,3-dioxygenase (IDO) protein expression level in the hippocampus which was significantly reduced by mangiferin treatment. Taken together, our results suggest that mangiferin exerts anti-anxiety and antidepressant effect in corticosterone-treated rats, which is probably mediated through up-regulation of BDNF level along with inhibition of oxido-nitrosative stress, neuroinflammation and IDO up-regulation in the hippocampus region.

Effect of glass concentration on stripping of glasphalt.

DOT National Transportation Integrated Search

1998-03-01

Virginia allows up to 15 percent glass to be used in asphalt concrete. However, a literature search revealed that there is not much test data to substantiate this quantity. Because of the smooth surface texture of glass particles and the associated r...

Competence formation of engineering directions students in the field of energy saving as a way to create new generation technologies

NASA Astrophysics Data System (ADS)

Gilmanshin, I. R.; Gilmanshina, S. I.

2017-09-01

The urgency of the formation of competence in the field of energy saving in the process of studying engineering and technical disciplines at the university is substantiated. The author’s definition of the competence in the field of energy saving is given, allowing to consider the necessity of its formation among students - future engineers as a way to create technologies of a new generation. The essence of this competence is revealed. The system of work, pedagogical conditions and technologies of its formation in the conditions of the federal university is substantiated.

Early pregnancy in the mare: old concepts revisited.

PubMed

Klein, C

2016-07-01

"Maternal recognition of pregnancy" (MRP) is commonly used to describe the ongoing embryo-maternal communication during early pregnancy that culminates in prevention of luteolysis and ensures ongoing progestin support. The conceptus-derived pregnancy recognition signal has not yet been identified in the mare. Although equine conceptuses produce substantial amounts of estrogens, there is a lack of evidence that estrogens are the pregnancy recognition signal in mares. Conceptus mobility is integral to MRP and is driven by conceptus-derived prostaglandin production. Cessation of conceptus mobility, referred to as fixation, is caused by increases in conceptus size and uterine tone and reduction in sialic acid content of the embryonic capsule. Gene expression profiling of equine preimplantation conceptuses revealed expression of neuraminidase 2 (NEU2), an enzyme that cleaves sialic acid from polysaccharide chains. Furthermore, secretion of NEU2 by conceptuses in vitro was functionally active; it appears therefore, that the conceptus itself regulates sialic acid content through expression of NEU2. Based on gene expression profiling, equine conceptuses express increasing amounts of fibrinogen during early development. Western blot analysis confirmed secretion of fibrinogen into culture medium when conceptuses were cultured in vitro and with immunohistochemistry, the acellular glycoprotein capsule of the conceptus had particularly intense staining for fibrinogen. Therefore, we hypothesize that conceptus-derived fibrinogen interacts with endometrial integrins to promote cessation of conceptus mobility and fixation. Indeed, next generation sequencing analysis of conceptus and endometrial samples 16 d after ovulation revealed that the integrin signaling pathway is significantly enriched in both sample types. Real-time reverse transcription polymerase chain reaction (RT-PCR) confirmed ITGAVB1 as the most abundant integrin receptor in endometrium; fibrinogen has the highest affinity for ITGAVB1 among integrins receptors to which it binds. Finally, the equine conceptus expresses increasing quantities of relaxin during preimplantation development, with the endometrium expressing relaxin receptors. In the pig, mouse, and human, relaxin is produced by the corpus luteum and is known to promote angiogenesis during early pregnancy. In summary, substantial advances in understanding MRP in the horse are underway. Crown Copyright © 2016. Published by Elsevier Inc. All rights reserved.

The Nitrogen Moieties of Dietary Nonessential Amino Acids Are Distinctively Metabolized in the Gut and Distributed to the Circulation in Rats.

PubMed

Nakamura, Hidehiro; Kawamata, Yasuko; Kuwahara, Tomomi; Sakai, Ryosei

2017-08-01

Background: Although previous growth studies in rodents have indicated the importance of dietary nonessential amino acids (NEAAs) as nitrogen sources, individual NEAAs have different growth-promoting activities. This phenomenon might be attributable to differences in the nitrogen metabolism of individual NEAAs. Objective: The aim of this study was to compare nitrogen metabolism across dietary NEAAs with the use of their 15 N isotopologues. Methods: Male Fischer rats (8 wk old) were given 1.0 g amino acid-defined diets containing either 15 N-labeled glutamate, glutamine (amino or amide), aspartate, alanine, proline, glycine, or serine hourly for 5-6 h. Then, steady-state amino acid concentrations and their 15 N enrichments in the gut and in portal and arterial plasma were measured by an amino acid analyzer and LC tandem mass spectrometry, respectively. Results: The intestinal 15 N distribution and portal-arterial balance of 15 N metabolites indicated that most dietary glutamate nitrogen (>90% of dietary input) was incorporated into various amino acids, including alanine, proline, and citrulline, in the gut. Dietary aspartate nitrogen, alanine nitrogen, and amino nitrogen of glutamine were distributed similarly to other amino acids both in the gut and in the circulation. In contrast, incorporation of the nitrogen moieties of dietary proline, serine, and glycine into other amino acids was less than that of other NEAAs, although interconversion between serine and glycine was very active. Cluster analysis of 15 N enrichment data also indicated that dietary glutamate nitrogen, aspartate nitrogen, alanine nitrogen, and the amino nitrogen of glutamine were distributed similarly to intestinal and circulating amino acids. Further, the analysis revealed close relations between intestinal and arterial 15 N enrichment for each amino acid. The steady-state 15 N enrichment of arterial amino acids indicated that substantial amounts of circulating amino acid nitrogen are derived from dietary NEAAs. Conclusions: The present results revealed similarities and differences among NEAAs in terms of their intestinal nitrogen metabolism in rats and indicated substantial entry of dietary NEAA nitrogen into circulating amino acid nitrogen, presumably primarily through metabolism in the gut. © 2017 American Society for Nutrition.

The etiology of behavior problems in 7-year-old twins: substantial genetic influence and negligible shared environmental influence for parent ratings and ratings by same and different teachers.

PubMed

Saudino, Kimberly J; Ronald, Angelica; Plomin, Robert

2005-02-01

Parent ratings of behavior problems in childhood show substantial genetic influence and modest shared environmental influence. However, few studies have compared these results to teacher ratings and no previous studies have compared same-teacher ratings to different-teacher ratings. 3,714 7-year-old twin pairs in the Twins Early Development Study were rated by parents and teachers on the Strengths and Difficulties Questionnaire. Substantial heritability and negligible shared environmental influence were found for data from all three raters for total behavior problems, hyperactivity, prosocial behavior, peer problems, conduct problems, and emotional symptoms. Sex-limitation models revealed similar results for males and females, although there was some evidence for greater heritability for boys, especially when twins were rated by the same teacher.

Spatial-Temporal Dynamics of High-Resolution Animal Networks: What Can We Learn from Domestic Animals?

PubMed

Chen, Shi; Ilany, Amiyaal; White, Brad J; Sanderson, Michael W; Lanzas, Cristina

2015-01-01

Animal social network is the key to understand many ecological and epidemiological processes. We used real-time location system (RTLS) to accurately track cattle position, analyze their proximity networks, and tested the hypothesis of temporal stationarity and spatial homogeneity in these networks during different daily time periods and in different areas of the pen. The network structure was analyzed using global network characteristics (network density), subgroup clustering (modularity), triadic property (transitivity), and dyadic interactions (correlation coefficient from a quadratic assignment procedure) at hourly level. We demonstrated substantial spatial-temporal heterogeneity in these networks and potential link between indirect animal-environment contact and direct animal-animal contact. But such heterogeneity diminished if data were collected at lower spatial (aggregated at entire pen level) or temporal (aggregated at daily level) resolution. The network structure (described by the characteristics such as density, modularity, transitivity, etc.) also changed substantially at different time and locations. There were certain time (feeding) and location (hay) that the proximity network structures were more consistent based on the dyadic interaction analysis. These results reveal new insights for animal network structure and spatial-temporal dynamics, provide more accurate descriptions of animal social networks, and allow more accurate modeling of multiple (both direct and indirect) disease transmission pathways.

Altered Neural Correlate of the Self-Agency Experience in First-Episode Schizophrenia-Spectrum Patients: An fMRI Study.

PubMed

Spaniel, Filip; Tintera, Jaroslav; Rydlo, Jan; Ibrahim, Ibrahim; Kasparek, Tomas; Horacek, Jiri; Zaytseva, Yuliya; Matejka, Martin; Fialova, Marketa; Slovakova, Andrea; Mikolas, Pavol; Melicher, Tomas; Görnerova, Natalie; Höschl, Cyril; Hajek, Tomas

2016-07-01

The phenomenology of the clinical symptoms indicates that disturbance of the sense of self be a core marker of schizophrenia. To compare neural activity related to the self/other-agency judgment in patients with first-episode schizophrenia-spectrum disorders (FES, n = 35) and healthy controls (HC, n = 35). A functional magnetic resonance imaging (fMRI) using motor task with temporal distortion of the visual feedback was employed. A task-related functional connectivity was analyzed with the use of independent component analysis (ICA). (1) During self-agency experience, FES showed a deficit in cortical activation in medial frontal gyrus (BA 10) and posterior cingulate gyrus, (BA 31; P < .05, Family-Wise Error [FWE] corrected). (2) Pooled-sample task-related ICA revealed that the self/other-agency judgment was dependent upon anti-correlated default mode and central-executive networks (DMN/CEN) dynamic switching. This antagonistic mechanism was substantially impaired in FES during the task. During self-agency experience, FES demonstrate deficit in engagement of cortical midline structures along with substantial attenuation of anti-correlated DMN/CEN activity underlying normal self/other-agency discriminative processes. © The Author 2015. Published by Oxford University Press on behalf of the Maryland Psychiatric Research Center. All rights reserved. For permissions, please email: journals.permissions@oup.com.

The role of HIV integration in viral persistence: no more whistling past the proviral graveyard

PubMed Central

Maldarelli, Frank

2016-01-01

A substantial research effort has been directed to identifying strategies to eradicate or control HIV infection without a requirement for combination antiretroviral therapy (cART). A number of obstacles prevent HIV eradication, including low-level viral persistence during cART, long-term persistence of HIV-infected cells, and latent infection of resting CD4+ T cells. Mechanisms of persistence remain uncertain, but integration of the provirus into the host genome represents a central event in replication and pathogenesis of all retroviruses, including HIV. Analysis of HIV proviruses in CD4+ lymphocytes from individuals after prolonged cART revealed that a substantial proportion of the infected cells that persist have undergone clonal expansion and frequently have proviruses integrated in genes associated with regulation of cell growth. These data suggest that integration may influence persistence and clonal expansion of HIV-infected cells after cART is introduced, and these processes may represent key mechanisms for HIV persistence. Determining the diversity of host genes with integrants in HIV-infected cells that persist for prolonged periods may yield useful information regarding pathways by which infected cells persist for prolonged periods. Moreover, many integrants are defective, and new studies are required to characterize the role of clonal expansion in the persistence of replication-competent HIV. PMID:26829624

Birds in space and time: genetic changes accompanying anthropogenic habitat fragmentation in the endangered black-capped vireo (Vireo atricapilla)

PubMed Central

Athrey, Giridhar; Barr, Kelly R; Lance, Richard F; Leberg, Paul L

2012-01-01

Anthropogenic alterations in the natural environment can be a potent evolutionary force. For species that have specific habitat requirements, habitat loss can result in substantial genetic effects, potentially impeding future adaptability and evolution. The endangered black-capped vireo (Vireo atricapilla) suffered a substantial contraction of breeding habitat and population size during much of the 20th century. In a previous study, we reported significant differentiation between remnant populations, but failed to recover a strong genetic signal of bottlenecks. In this study, we used a combination of historical and contemporary sampling from Oklahoma and Texas to (i) determine whether population structure and genetic diversity have changed over time and (ii) evaluate alternate demographic hypotheses using approximate Bayesian computation (ABC). We found lower genetic diversity and increased differentiation in contemporary samples compared to historical samples, indicating nontrivial impacts of fragmentation. ABC analysis suggests a bottleneck having occurred in the early part of the 20th century, resulting in a magnitude decline in effective population size. Genetic monitoring with temporally spaced samples, such as used in this study, can be highly informative for assessing the genetic impacts of anthropogenic fragmentation on threatened or endangered species, as well as revealing the dynamics of small populations over time. PMID:23028396

Structural and Kinetic Basis for Substrate Selectivity in Populus tremuloides Sinapyl Alcohol Dehydrogenase

PubMed Central

Bomati, Erin K.; Noel, Joseph P.

2005-01-01

We describe the three-dimensional structure of sinapyl alcohol dehydrogenase (SAD) from Populus tremuloides (aspen), a member of the NADP(H)-dependent dehydrogenase family that catalyzes the last reductive step in the formation of monolignols. The active site topology revealed by the crystal structure substantiates kinetic results indicating that SAD maintains highest specificity for the substrate sinapaldehyde. We also report substantial substrate inhibition kinetics for the SAD-catalyzed reduction of hydroxycinnamaldehydes. Although SAD and classical cinnamyl alcohol dehydrogenases (CADs) catalyze the same reaction and share some sequence identity, the active site topology of SAD is strikingly different from that predicted for classical CADs. Kinetic analyses of wild-type SAD and several active site mutants demonstrate the complexity of defining determinants of substrate specificity in these enzymes. These results, along with a phylogenetic analysis, support the inclusion of SAD in a plant alcohol dehydrogenase subfamily that includes cinnamaldehyde and benzaldehyde dehydrogenases. We used the SAD three-dimensional structure to model several of these SAD-like enzymes, and although their active site topologies largely mirror that of SAD, we describe a correlation between substrate specificity and amino acid substitution patterns in their active sites. The SAD structure thus provides a framework for understanding substrate specificity in this family of enzymes and for engineering new enzyme specificities. PMID:15829607

Structural and kinetic basis for substrate selectivity in Populus tremuloides sinapyl alcohol dehydrogenase.

PubMed

Bomati, Erin K; Noel, Joseph P

2005-05-01

We describe the three-dimensional structure of sinapyl alcohol dehydrogenase (SAD) from Populus tremuloides (aspen), a member of the NADP(H)-dependent dehydrogenase family that catalyzes the last reductive step in the formation of monolignols. The active site topology revealed by the crystal structure substantiates kinetic results indicating that SAD maintains highest specificity for the substrate sinapaldehyde. We also report substantial substrate inhibition kinetics for the SAD-catalyzed reduction of hydroxycinnamaldehydes. Although SAD and classical cinnamyl alcohol dehydrogenases (CADs) catalyze the same reaction and share some sequence identity, the active site topology of SAD is strikingly different from that predicted for classical CADs. Kinetic analyses of wild-type SAD and several active site mutants demonstrate the complexity of defining determinants of substrate specificity in these enzymes. These results, along with a phylogenetic analysis, support the inclusion of SAD in a plant alcohol dehydrogenase subfamily that includes cinnamaldehyde and benzaldehyde dehydrogenases. We used the SAD three-dimensional structure to model several of these SAD-like enzymes, and although their active site topologies largely mirror that of SAD, we describe a correlation between substrate specificity and amino acid substitution patterns in their active sites. The SAD structure thus provides a framework for understanding substrate specificity in this family of enzymes and for engineering new enzyme specificities.

Ripening-dependent metabolic changes in the volatiles of pineapple (Ananas comosus (L.) Merr.) fruit: II. Multivariate statistical profiling of pineapple aroma compounds based on comprehensive two-dimensional gas chromatography-mass spectrometry.

PubMed

Steingass, Christof Björn; Jutzi, Manfred; Müller, Jenny; Carle, Reinhold; Schmarr, Hans-Georg

2015-03-01

Ripening-dependent changes of pineapple volatiles were studied in a nontargeted profiling analysis. Volatiles were isolated via headspace solid phase microextraction and analyzed by comprehensive 2D gas chromatography and mass spectrometry (HS-SPME-GC×GC-qMS). Profile patterns presented in the contour plots were evaluated applying image processing techniques and subsequent multivariate statistical data analysis. Statistical methods comprised unsupervised hierarchical cluster analysis (HCA) and principal component analysis (PCA) to classify the samples. Supervised partial least squares discriminant analysis (PLS-DA) and partial least squares (PLS) regression were applied to discriminate different ripening stages and describe the development of volatiles during postharvest storage, respectively. Hereby, substantial chemical markers allowing for class separation were revealed. The workflow permitted the rapid distinction between premature green-ripe pineapples and postharvest-ripened sea-freighted fruits. Volatile profiles of fully ripe air-freighted pineapples were similar to those of green-ripe fruits postharvest ripened for 6 days after simulated sea freight export, after PCA with only two principal components. However, PCA considering also the third principal component allowed differentiation between air-freighted fruits and the four progressing postharvest maturity stages of sea-freighted pineapples.

Cluster analysis reveals seasonal variation of sperm subpopulations in extended boar semen

PubMed Central

IBĂNESCU, Iulian; LEIDING, Claus; BOLLWEIN, Heinrich

2017-01-01

This study aimed to identify motile sperm subpopulations in extended boar semen and to observe the presumptive seasonal variation in their distribution. Data from 4837 boar ejaculates collected over a two-year period were analyzed in terms of kinematic parameters by Computer Assisted Sperm Analysis (CASA). Individual sperm data were used to determine subgroups of motile sperm within the ejaculates using cluster analysis. Four motile sperm subpopulations (SP) were identified, with distinct movement patterns: SP1 sperm with high velocity and high linearity; SP2 sperm with high velocity but low linearity; SP3 sperm with low velocity but high linearity; and SP4 sperm with low velocity and low linearity. SP1 constituted the least overall proportion within the ejaculates (P < 0.05). Season of semen collection significantly influenced the different proportions of sperm subpopulations. Spring was characterized by similar proportions of SP1 and SP4 (NS) and higher proportions of SP3. Summer brought a decrease in both subgroups containing fast sperm (SP1 and SP2) (P < 0.05). During autumn, increases in SP2 and SP4 were recorded. Winter substantially affected the proportions of all sperm subpopulations (P < 0.05) and SP2 became the most represented subgroup, while SP1 (fast and linear) reached its highest proportion compared to other seasons. In conclusion, extended boar semen is structured in distinct motile sperm subpopulations whose proportions vary according to the season of collection. Summer and autumn seem to have a negative impact on the fast and linear subpopulation. Cluster analysis can be useful in revealing differences in semen quality that are not normally detected by classical evaluation based on mean values. PMID:29081440

Development and validation of the simulation-based learning evaluation scale.

PubMed

Hung, Chang-Chiao; Liu, Hsiu-Chen; Lin, Chun-Chih; Lee, Bih-O

2016-05-01

The instruments that evaluate a student's perception of receiving simulated training are English versions and have not been tested for reliability or validity. The aim of this study was to develop and validate a Chinese version Simulation-Based Learning Evaluation Scale (SBLES). Four stages were conducted to develop and validate the SBLES. First, specific desired competencies were identified according to the National League for Nursing and Taiwan Nursing Accreditation Council core competencies. Next, the initial item pool was comprised of 50 items related to simulation that were drawn from the literature of core competencies. Content validity was established by use of an expert panel. Finally, exploratory factor analysis and confirmatory factor analysis were conducted for construct validity, and Cronbach's coefficient alpha determined the scale's internal consistency reliability. Two hundred and fifty students who had experienced simulation-based learning were invited to participate in this study. Two hundred and twenty-five students completed and returned questionnaires (response rate=90%). Six items were deleted from the initial item pool and one was added after an expert panel review. Exploratory factor analysis with varimax rotation revealed 37 items remaining in five factors which accounted for 67% of the variance. The construct validity of SBLES was substantiated in a confirmatory factor analysis that revealed a good fit of the hypothesized factor structure. The findings tally with the criterion of convergent and discriminant validity. The range of internal consistency for five subscales was .90 to .93. Items were rated on a 5-point scale from 1 (strongly disagree) to 5 (strongly agree). The results of this study indicate that the SBLES is valid and reliable. The authors recommend that the scale could be applied in the nursing school to evaluate the effectiveness of simulation-based learning curricula. Copyright © 2016 Elsevier Ltd. All rights reserved.

Occurrence of a Sequence in Marine Cyanophages Similar to That of T4 g20 and Its Application to PCR-Based Detection and Quantification Techniques†

PubMed Central

Fuller, Nicholas J.; Wilson, William H.; Joint, Ian R.; Mann, Nicholas H.

1998-01-01

Viruses are ubiquitous components of marine ecosystems and are known to infect unicellular phycoerythrin-containing cyanobacteria belonging to the genus Synechococcus. A conserved region from the cyanophage genome was identified in three genetically distinct cyanomyoviruses, and a sequence analysis revealed that this region exhibited significant similarity to a gene encoding a capsid assembly protein (gp20) from the enteric coliphage T4. The results of a comparison of gene 20 sequences from three cyanomyoviruses and T4 allowed us to design two degenerate PCR primers, CPS1 and CPS2, which specifically amplified a 165-bp region from the majority of cyanomyoviruses tested. A competitive PCR (cPCR) analysis revealed that cyanomyovirus strains could be accurately enumerated, and it was demonstrated that quantification was log-linear over ca. 3 orders of magnitude. Different calibration curves were obtained for each of the three cyanomyovirus strains tested; consequently, cPCR performed with primers CPS1 and CPS2 could lead to substantial inaccuracies in estimates of phage abundance in natural assemblages. Further sequence analysis of cyanomyovirus gene 20 homologs would be necessary in order to design primers which do not exhibit phage-to-phage variability in priming efficiency. It was demonstrated that PCR products of the correct size could be amplified from seawater samples following 100× concentration and even directly without any prior concentration. Hence, the use of degenerate primers in PCR analyses of cyanophage populations should provide valuable data on the diversity of cyanophages in natural assemblages. Further optimization of procedures may ultimately lead to a sensitive assay which can be used to analyze natural cyanophage populations both quantitatively (by cPCR) and qualitatively following phylogenetic analysis of amplified products. PMID:9603813

Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae

PubMed Central

Reguly, Teresa; Breitkreutz, Ashton; Boucher, Lorrie; Breitkreutz, Bobby-Joe; Hon, Gary C; Myers, Chad L; Parsons, Ainslie; Friesen, Helena; Oughtred, Rose; Tong, Amy; Stark, Chris; Ho, Yuen; Botstein, David; Andrews, Brenda; Boone, Charles; Troyanskya, Olga G; Ideker, Trey; Dolinski, Kara; Batada, Nizar N; Tyers, Mike

2006-01-01

Background The study of complex biological networks and prediction of gene function has been enabled by high-throughput (HTP) methods for detection of genetic and protein interactions. Sparse coverage in HTP datasets may, however, distort network properties and confound predictions. Although a vast number of well substantiated interactions are recorded in the scientific literature, these data have not yet been distilled into networks that enable system-level inference. Results We describe here a comprehensive database of genetic and protein interactions, and associated experimental evidence, for the budding yeast Saccharomyces cerevisiae, as manually curated from over 31,793 abstracts and online publications. This literature-curated (LC) dataset contains 33,311 interactions, on the order of all extant HTP datasets combined. Surprisingly, HTP protein-interaction datasets currently achieve only around 14% coverage of the interactions in the literature. The LC network nevertheless shares attributes with HTP networks, including scale-free connectivity and correlations between interactions, abundance, localization, and expression. We find that essential genes or proteins are enriched for interactions with other essential genes or proteins, suggesting that the global network may be functionally unified. This interconnectivity is supported by a substantial overlap of protein and genetic interactions in the LC dataset. We show that the LC dataset considerably improves the predictive power of network-analysis approaches. The full LC dataset is available at the BioGRID () and SGD () databases. Conclusion Comprehensive datasets of biological interactions derived from the primary literature provide critical benchmarks for HTP methods, augment functional prediction, and reveal system-level attributes of biological networks. PMID:16762047

Community preferences for health states associated with intimate partner violence.

PubMed

Wittenberg, Eve; Lichter, Erika L; Ganz, Michael L; McCloskey, Laura A

2006-08-01

One in 4 women is affected by intimate partner violence in her lifetime. This article reports on a cross-sectional survey to estimate community preferences for health states resulting from intimate partner violence. A secondary analysis was conducted of data from a convenience sample of 93 abused and 138 nonabused women (231 total) recruited for in-person interviews from hospital outpatient department waiting rooms in metropolitan Boston, Massachusetts. SF-12 data were converted to utilities to describe community-perspective preferences for health states associated with intimate partner violence. Linear regression analysis was used to explore the association between violence and utility while controlling for other health and demographic factors. Median utility for intimate partner violence was between 0.58 and 0.63 on a scale of 0 (equivalent to death) to 1.0 (equivalent to optimal health), with a range from 0.64 to 0.66 for less severe violence to 0.53 to 0.62 for more severe violence. The data do not reveal whether violence itself is responsible for lower utility or whether a constellation of factors contributes to disutility experienced by women victims of abuse. The utility of health states experienced by women exposed to intimate partner violence is substantially diminished compared with optimal health and even other health conditions. These values quantify the substantial negative health impact of the experience of intimate partner violence in terms that allow comparison across diseases. They can be used in cost-effectiveness analyses to identify the benefits and potential returns from resources allocated to violence prevention and intervention efforts.

Enhanced structural stability and photo responsiveness of CH 3NH 3SnI 3 perovskite via pressure-induced amorphization and recrystallization

DOE PAGES

Lu, Xujie; Wang, Yonggang; Stoumpos, Constantinos C.; ...

2016-10-01

An organic–inorganic halide CH 3NH 3SnI 3 perovskite with significantly improved structural stability is obtained via pressure-induced amorphization and recrystallization. In situ high-pressure resistance measurements reveal an increased electrical conductivity by 300% in the pressure-treated perovskite. Photocurrent measurements also reveal a substantial enhancement in visible-light responsiveness. In conclusion, the mechanism underlying the enhanced properties is shown to be associated with the pressure-induced structural modification.

Teacher Knowledge for Active-Learning Instruction: Expert-Novice Comparison Reveals Differences

ERIC Educational Resources Information Center

Auerbach, A. J.; Higgins, M.; Brickman, P.; Andrews, T. C.

2018-01-01

Active-learning strategies "can" improve science, technology, engineering, and mathematics (STEM) undergraduates' abilities to learn fundamental concepts and skills. However, the results instructors achieve vary substantially. One explanation for this is that instructors commonly implement active learning differently than intended. An…

Drug Use among Pregnant Adolescents.

ERIC Educational Resources Information Center

Gilchrist, Lewayne D.; And Others

1990-01-01

Collected data from first 100 subjects in on-going longitudinal study of drug use before and during pregnancy in adolescence. Findings from unmarried pregnant adolescents revealed that, although lifetime prevalence of drug use was relatively high, substance use declined voluntarily and substantially during pregnancy. Prepregnancy drug use…

Phenotypic and Genetic Divergence among Poison Frog Populations in a Mimetic Radiation

PubMed Central

Twomey, Evan; Yeager, Justin; Brown, Jason Lee; Morales, Victor; Cummings, Molly; Summers, Kyle

2013-01-01

The evolution of Müllerian mimicry is, paradoxically, associated with high levels of diversity in color and pattern. In a mimetic radiation, different populations of a species evolve to resemble different models, which can lead to speciation. Yet there are circumstances under which initial selection for divergence under mimicry may be reversed. Here we provide evidence for the evolution of extensive phenotypic divergence in a mimetic radiation in Ranitomeya imitator, the mimic poison frog, in Peru. Analyses of color hue (spectral reflectance) and pattern reveal substantial divergence between morphs. However, we also report that there is a “transition-zone” with mixed phenotypes. Analyses of genetic structure using microsatellite variation reveals some differentiation between populations, but this does not strictly correspond to color pattern divergence. Analyses of gene flow between populations suggest that, while historical levels of gene flow were low, recent levels are high in some cases, including substantial gene flow between some color pattern morphs. We discuss possible explanations for these observations. PMID:23405150

Genome sequencing of ovine isolates of Mycobacterium avium subspecies paratuberculosis offers insights into host association

PubMed Central

2012-01-01

Background The genome of Mycobacterium avium subspecies paratuberculosis (MAP) is remarkably homogeneous among the genomes of bovine, human and wildlife isolates. However, previous work in our laboratories with the bovine K-10 strain has revealed substantial differences compared to sheep isolates. To systematically characterize all genomic differences that may be associated with the specific hosts, we sequenced the genomes of three U.S. sheep isolates and also obtained an optical map. Results Our analysis of one of the isolates, MAP S397, revealed a genome 4.8 Mb in size with 4,700 open reading frames (ORFs). Comparative analysis of the MAP S397 isolate showed it acquired approximately 10 large sequence regions that are shared with the human M. avium subsp. hominissuis strain 104 and lost 2 large regions that are present in the bovine strain. In addition, optical mapping defined the presence of 7 large inversions between the bovine and ovine genomes (~ 2.36 Mb). Whole-genome sequencing of 2 additional sheep strains of MAP (JTC1074 and JTC7565) further confirmed genomic homogeneity of the sheep isolates despite the presence of polymorphisms on the nucleotide level. Conclusions Comparative sequence analysis employed here provided a better understanding of the host association, evolution of members of the M. avium complex and could help in deciphering the phenotypic differences observed among sheep and cattle strains of MAP. A similar approach based on whole-genome sequencing combined with optical mapping could be employed to examine closely related pathogens. We propose an evolutionary scenario for M. avium complex strains based on these genome sequences. PMID:22409516

Vicenin-2 inhibits Wnt/β-catenin signaling and induces apoptosis in HT-29 human colon cancer cell line.

PubMed

Yang, Dong; Zhang, Xiling; Zhang, Wencun; Rengarajan, Thamaraiselvan

2018-01-01

Colorectal cancer (CRC) is among highest prevailing cancers in the whole world, especially in western countries. For a diverse of reasons, patients prefer naturally occurring dietary substances over synthetic agents to prevent cancer. Vicenin-2 is largely available in a medicinal plant Ocimum sanctum and is an apigenin form, 6,8-di-C-glucoside, which has been reported to have a range of pharmacological values which includes antioxidant, hepatoprotective, anti-inflammatory and anti-cancer. This study was aimed to analyze the anti-proliferative effect of Vicenin-2 on human colon cancer cells via the Wnt/β-catenin signaling inhibition. MTT assay was used to assess the cell viability at different concentrations and time point. Vicenin-2 at a concentration of 50 µM (IC 50 ) decreased the phosphorylated (inactive) glycogen synthase kinase-3β, cyclin D1, and non-p-β-catenin expressions in HT-29 cells, which were evidenced through western blot analysis. Further, Vincenin-2 reduced the T-cell factor (TCF) / Leukocyte erythroid factor (LEF) reporter activity in HT-29 cells. Vicenin-2 also promoted substantial cell cycle arrest at the G 2 M phase of HT-29 cells, as well induced apoptosis in HT-29 cells, as revealed through flow cytometric analysis. Furthermore, immunoblot analysis showed that Vicenin-2 treatment enhanced the expression of Cytochrome C, Bax and caspase-3 whereas suppressed the Bcl-2 expression. Together, these results revealed that Vicenin-2 can act as a potent inhibitor of HT-29 cell proliferation and can be used as an agent against CRC.

Related Giant Viruses in Distant Locations and Different Habitats: Acanthamoeba polyphaga moumouvirus Represents a Third Lineage of the Mimiviridae That Is Close to the Megavirus Lineage

PubMed Central

Yoosuf, Niyaz; Yutin, Natalya; Colson, Philippe; Shabalina, Svetlana A.; Pagnier, Isabelle; Robert, Catherine; Azza, Said; Klose, Thomas; Wong, Jimson; Rossmann, Michael G.; La Scola, Bernard; Raoult, Didier; Koonin, Eugene V.

2012-01-01

The 1,021,348 base pair genome sequence of the Acanthamoeba polyphaga moumouvirus, a new member of the Mimiviridae family infecting Acanthamoeba polyphaga, is reported. The moumouvirus represents a third lineage beside mimivirus and megavirus. Thereby, it is a new member of the recently proposed Megavirales order. This giant virus was isolated from a cooling tower water in southeastern France but is most closely related to Megavirus chiliensis, which was isolated from ocean water off the coast of Chile. The moumouvirus is predicted to encode 930 proteins, of which 879 have detectable homologs. Among these predicted proteins, for 702 the closest homolog was detected in Megavirus chiliensis, with the median amino acid sequence identity of 62%. The evolutionary affinity of moumouvirus and megavirus was further supported by phylogenetic tree analysis of conserved genes. The moumouvirus and megavirus genomes share near perfect orthologous gene collinearity in the central part of the genome, with the variations concentrated in the terminal regions. In addition, genomic comparisons of the Mimiviridae reveal substantial gene loss in the moumouvirus lineage. The majority of the remaining moumouvirus proteins are most similar to homologs from other Mimiviridae members, and for 27 genes the closest homolog was found in bacteria. Phylogenetic analysis of these genes supported gene acquisition from diverse bacteria after the separation of the moumouvirus and megavirus lineages. Comparative genome analysis of the three lineages of the Mimiviridae revealed significant mobility of Group I self-splicing introns, with the highest intron content observed in the moumouvirus genome. PMID:23221609

Comparative Analysis of the Peanut Witches'-Broom Phytoplasma Genome Reveals Horizontal Transfer of Potential Mobile Units and Effectors

PubMed Central

Lo, Wen-Sui; Lin, Chan-Pin; Kuo, Chih-Horng

2013-01-01

Phytoplasmas are a group of bacteria that are associated with hundreds of plant diseases. Due to their economical importance and the difficulties involved in the experimental study of these obligate pathogens, genome sequencing and comparative analysis have been utilized as powerful tools to understand phytoplasma biology. To date four complete phytoplasma genome sequences have been published. However, these four strains represent limited phylogenetic diversity. In this study, we report the shotgun sequencing and evolutionary analysis of a peanut witches'-broom (PnWB) phytoplasma genome. The availability of this genome provides the first representative of the 16SrII group and substantially improves the taxon sampling to investigate genome evolution. The draft genome assembly contains 13 chromosomal contigs with a total size of 562,473 bp, covering ∼90% of the chromosome. Additionally, a complete plasmid sequence is included. Comparisons among the five available phytoplasma genomes reveal the differentiations in gene content and metabolic capacity. Notably, phylogenetic inferences of the potential mobile units (PMUs) in these genomes indicate that horizontal transfer may have occurred between divergent phytoplasma lineages. Because many effectors are associated with PMUs, the horizontal transfer of these transposon-like elements can contribute to the adaptation and diversification of these pathogens. In summary, the findings from this study highlight the importance of improving taxon sampling when investigating genome evolution. Moreover, the currently available sequences are inadequate to fully characterize the pan-genome of phytoplasmas. Future genome sequencing efforts to expand phylogenetic diversity are essential in improving our understanding of phytoplasma evolution. PMID:23626855

Meta-GWAS and Meta-Analysis of Exome Array Studies Do Not Reveal Genetic Determinants of Serum Hepcidin

PubMed Central

Galesloot, Tessel E.; van Dijk, Freerk; Geurts-Moespot, Anneke J.; Girelli, Domenico; Kiemeney, Lambertus A. L. M.; Sweep, Fred C. G. J.; Swertz, Morris A.; van der Meer, Peter; Camaschella, Clara; Toniolo, Daniela; Vermeulen, Sita H.; van der Harst, Pim; Swinkels, Dorine W.

2016-01-01

Serum hepcidin concentration is regulated by iron status, inflammation, erythropoiesis and numerous other factors, but underlying processes are incompletely understood. We studied the association of common and rare single nucleotide variants (SNVs) with serum hepcidin in one Italian study and two large Dutch population-based studies. We genotyped common SNVs with genome-wide association study (GWAS) arrays and subsequently performed imputation using the 1000 Genomes reference panel. Cohort-specific GWAS were performed for log-transformed serum hepcidin, adjusted for age and gender, and results were combined in a fixed-effects meta-analysis (total N 6,096). Six top SNVs (p<5x10-6) were genotyped in 3,821 additional samples, but associations were not replicated. Furthermore, we meta-analyzed cohort-specific exome array association results of rare SNVs with serum hepcidin that were available for two of the three cohorts (total N 3,226), but no exome-wide significant signal (p<1.4x10-6) was identified. Gene-based meta-analyses revealed 19 genes that showed significant association with hepcidin. Our results suggest the absence of common SNVs and rare exonic SNVs explaining a large proportion of phenotypic variation in serum hepcidin. We recommend extension of our study once additional substantial cohorts with hepcidin measurements, GWAS and/or exome array data become available in order to increase power to identify variants that explain a smaller proportion of hepcidin variation. In addition, we encourage follow-up of the potentially interesting genes that resulted from the gene-based analysis of low-frequency and rare variants. PMID:27846281

Structures of mesophilic and extremophilic citrate synthases reveal rigidity and flexibility for function.

PubMed

Wells, Stephen A; Crennell, Susan J; Danson, Michael J

2014-10-01

Citrate synthase (CS) catalyses the entry of carbon into the citric acid cycle and is highly-conserved structurally across the tree of life. Crystal structures of dimeric CSs are known in both "open" and "closed" forms, which differ by a substantial domain motion that closes the substrate-binding clefts. We explore both the static rigidity and the dynamic flexibility of CS structures from mesophilic and extremophilic organisms from all three evolutionary domains. The computational expense of this wide-ranging exploration is kept to a minimum by the use of rigidity analysis and rapid all-atom simulations of flexible motion, combining geometric simulation and elastic network modeling. CS structures from thermophiles display increased structural rigidity compared with the mesophilic enzyme. A CS structure from a psychrophile, stabilized by strong ionic interactions, appears to display likewise increased rigidity in conventional rigidity analysis; however, a novel modified analysis, taking into account the weakening of the hydrophobic effect at low temperatures, shows a more appropriate decreased rigidity. These rigidity variations do not, however, affect the character of the flexible dynamics, which are well conserved across all the structures studied. Simulation trajectories not only duplicate the crystallographically observed symmetric open-to-closed transitions, but also identify motions describing a previously unidentified antisymmetric functional motion. This antisymmetric motion would not be directly observed in crystallography but is revealed as an intrinsic property of the CS structure by modeling of flexible motion. This suggests that the functional motion closing the binding clefts in CS may be independent rather than symmetric and cooperative. © 2014 Wiley Periodicals, Inc.

X-ray motion analysis of the vertebral column during the startle response in striped bass, Morone saxatilis.

PubMed

Nowroozi, B N; Brainerd, E L

2013-08-01

Whole-body stiffness has a substantial impact on propulsive wave speed during axial undulatory locomotion in fishes. The connective tissues of the vertebral column may contribute to body stiffness, but without mechanical and kinematic analysis it is unclear whether the in vivo range of motion of intervertebral joints (IVJs) is great enough to stress IVJ tissues, thus generating stiffness. The present study used 2D videoradiography and 3D X-ray reconstruction of moving morphology (XROMM) to quantify vertebral kinematics during the startle response in striped bass (Morone saxatilis). X-ray video revealed two distinct patterns of bending: pattern I begins in the abdominal region and then proceeds to maximum IVJ angles in the caudal region, whereas pattern II begins in the cervical region and proceeds to maximum IVJ angles in the abdominal and then the caudal joints. In pattern II bends, the cervical joints exhibit a greater in vivo range of motion than previously reported in other species. XROMM analysis of caudal IVJs suggests primarily lateral bending: mean axial and dorsoventral rotations were less than 2 deg and inconsistent across 51 sequences analyzed from five individuals, whereas mean maximum lateral bending angles were 10.4±3.57 deg. These angles, combined with previous investigations of mechanical properties, reveal that the maximum angles all occur within the neutral zone of bending, indicating that little stress is experienced about the joint. This suggests that the IVJs of striped bass are quite compliant and likely do not contribute significantly to whole-body stiffness or elastic recoil during swimming in vivo.

Therapeutic non-adherence: a rational behavior revealing patient preferences?

PubMed

Lamiraud, Karine; Geoffard, Pierre-Yves

2007-11-01

This paper offers an indirect measure of patient welfare based on whether patients comply with the prescription they receive. Adherence behavior is supposed to reveal patients' subjective valuations of particular therapies. We write a simple theoretical model of patient adherence behavior, that reflects the trade-off between perceived costs and observed regimen efficacy. A discrete choice framework is then used for the estimation, i.e. the comparison of the incremental benefit of drug intake between two regimens. Consequently, the empirical analysis is based on the identification of patient and drug characteristics associated with adherence. The econometric approach is implemented through a bivariate panel two-equation simultaneous system studying jointly the factors associated with adherence and response to treatment. The data come from a randomized clinical trial conducted in France between 1999 and 2001 and comparing the efficacy of two tritherapy strategies in HIV disease. Both the theoretical and empirical results suggest that, for comparable clinical efficacy and toxicity levels, a higher adherence level is associated with higher patient welfare, thus adding valuable information to conclusions drawn by a mere biostatistical analysis. Therefore, from the perspective of the patient, the adherence-enhancing drug must be favored. Our results based on panel data also stress that unobserved patient characteristics account substantially for drug valuation and that the assessment evolves during the course of the treatment. Furthermore, we provide a new framework for the analysis of adherence data. The microeconometric framework highlights that non-adherence is an endogenous behavior, thus suggesting new ways for improving adherence. (c) 2007 John Wiley & Sons, Ltd.

Mycobacterium paratuberculosis, Mycobacterium smegmatis, and lipopolysaccharide induce different transcriptional and post-transcriptional regulation of the IRG1 gene in murine macrophages.

PubMed

Basler, Tina; Jeckstadt, Sabine; Valentin-Weigand, Peter; Goethe, Ralph

2006-03-01

Mycobacterium avium subspecies paratuberculosis (MAP) causes a chronic enteritis in ruminants. In addition, MAP is presently the most favored pathogen linked to Crohn's disease. In this study, we were interested in dissecting the molecular mechanisms of macrophage activation or deactivation after infection with MAP. By subtractive hybridization of cDNAs, we identified the immune-responsive gene 1 (IRG1), which was expressed substantially higher in lipopolysaccharide (LPS)-stimulated than in MAP-infected murine macrophage cell lines. A nuclear run-on transcription assay revealed that the IRG1 gene was activated transcriptionally in LPS-stimulated and MAP-infected macrophages with higher expression in LPS-stimulated cells. Analysis of post-transcriptional regulation demonstrated that IRG1 mRNA stability was increased in LPS-stimulated but not in MAP-infected macrophages. Furthermore, IRG1 gene expression of macrophages infected with the nonpathogenic Mycobacterium smegmatis differed from those of LPS-stimulated and MAP-infected macrophages. At 2 h postinfection, M. smegmatis-induced IRG1 gene expression was as low as in MAP-infected, and 8 h postinfection, it increased nearly to the level in LPS-stimulated macrophages. Transient transfection experiments revealed similar IRG1 promoter activities in MAP- and M. smegmatis-infected cells. Northern analysis demonstrated increased IRG1 mRNA stability in M. smegmatis-infected macrophages. IRG1 mRNA stabilization was p38 mitogen-activated protein kinase-independent. Inhibition of protein synthesis revealed that constitutively expressed factors seemed to be responsible for IRG1 mRNA destabilization. Thus, our data demonstrate that transcriptional and post-transcriptional mechanisms are responsible for a differential IRG1 gene expression in murine macrophages treated with LPS, MAP, and M. smegmatis.

Metallomics and NMR-based metabolomics of Chlorella sp. reveal the synergistic role of copper and cadmium in multi-metal toxicity and oxidative stress.

PubMed

Zhang, Wenlin; Tan, Nicole G J; Fu, Baohui; Li, Sam F Y

2015-03-01

Industrial wastewaters often contain high levels of metal mixtures, in which metal mixtures may have synergistic or antagonistic effects on aquatic organisms. A combination of metallomics and nuclear magnetic resonance spectroscopy (NMR)-based metabolomics was employed to understand the consequences of multi-metal systems (Cu, Cd, Pb) on freshwater microalgae. Morphological characterization, cell viability and chlorophyll a determination of metal-spiked Chlorella sp. suggested synergistic effects of Cu and Cd on growth inhibition and toxicity. While Pb has no apparent effect on Chlorella sp. metabolome, a substantial decrease of sucrose, amino acid content and glycerophospholipid precursors in Cu-spiked microalgae revealed Cu-induced oxidative stress. Addition of Cd to Cu-spiked cultures induced more drastic metabolic perturbations, hence we confirmed that Cu and Cd synergistically influenced photosynthesis inhibition, oxidative stress and membrane degradation. Total elemental analysis revealed a significant decrease in K, and an increase in Na, Mg, Zn and Mn concentrations in Cu-spiked cultures. This indicated that Cu is more toxic to Chlorella sp. as compared to Cd or Pb, and the combination of Cu and Cd has a strong synergistic effect on Chlorella sp. oxidative stress induction. Oxidative stress is confirmed by liquid chromatography tandem mass spectrometry analysis, which demonstrated a drastic decrease in the GSH/GSSG ratio solely in Cu-spiked cultures. Interestingly, we observed Cu-facilitated Cd and Pb bioconcentration in Chlorella sp. The absence of phytochelatins and an increment of extracellular polymeric substances (EPS) yields in Cu-spiked cultures suggested that the mode of bioconcentration of Cd and Pb is through adsorption of free metals onto the algal EPS rather than intracellular chelation to phytochelatins.

Kelvin wave-induced trace constituent oscillations in the equatorial stratosphere

NASA Technical Reports Server (NTRS)

Randel, William J.

1990-01-01

Kelvin wave induced oscillations in ozone (O3), water vapor (H2O), nitric acid (HNO3) and nitrogen dioxide (NO2) in the equatorial stratosphere are analyzed using Limb Infrared Monitor of the Stratosphere (LIMS) data. Power and cross-spectrum analyses reveal coherent eastward propagating zonal wave 1 and 2 constituent fluctuations, due to the influence of Kelvin waves previously documented in the LIMS data. Comparison is made between a preliminary and the archival versions of the LIMS data; significant differences are found, demonstrating the sensitivity of constituent retrievals to derived temperature profiles. Because Kelvin waves have vanishing meridional velocity, analysis of tracer transport in the meridional plane is substantially simplified. Kelvin wave vertical advection is demonstrated by coherent, in-phase temperature-tracer oscillations, co-located near regions of strong background vertical gradients.

Asymptomatic and Submicroscopic Carriage of Plasmodium knowlesi Malaria in Household and Community Members of Clinical Cases in Sabah, Malaysia.

PubMed

Fornace, Kimberly M; Nuin, Nor Afizah; Betson, Martha; Grigg, Matthew J; William, Timothy; Anstey, Nicholas M; Yeo, Tsin W; Cox, Jonathan; Ying, Lau Tiek; Drakeley, Chris J

2016-03-01

Although asymptomatic carriage of human malaria species has been widely reported, the extent of asymptomatic, submicroscopic Plasmodium knowlesi parasitemia is unknown. In this study, samples were obtained from individuals residing in households or villages of symptomatic malaria cases with the aim of detecting submicroscopic P. knowlesi in this population. Four published molecular assays were used to confirm the presence of P. knowlesi. Latent class analysis revealed that the estimated proportion of asymptomatic individuals was 6.9% (95% confidence interval, 5.6%-8.4%). This study confirms the presence of a substantial number of asymptomatic monoinfections across all age groups; further work is needed to estimate prevalence in the wider community. © The Author 2015. Published by Oxford University Press for the Infectious Diseases Society of America.

No evidence of suicide increase following terrorist attacks in the United States: an interrupted time-series analysis of September 11 and Oklahoma City.

PubMed

Pridemore, William Alex; Trahan, Adam; Chamlin, Mitchell B

2009-12-01

There is substantial evidence of detrimental psychological sequelae following disasters, including terrorist attacks. The effect of these events on extreme responses such as suicide, however, is unclear. We tested competing hypotheses about such effects by employing autoregressive integrated moving average techniques to model the impact of September 11 and the Oklahoma City bombing on monthly suicide counts at the local, state, and national level. Unlike prior studies that provided conflicting evidence, rigorous time series techniques revealed no support for an increase or decrease in suicides following these events. We conclude that while terrorist attacks produce subsequent psychological morbidity and may affect self and collective efficacy well beyond their immediate impact, these effects are not strong enough to influence levels of suicide mortality.

Estimating the Effects of Parental Divorce and Death With Fixed Effects Models.

PubMed

Amato, Paul R; Anthony, Christopher J

2014-04-01

The authors used child fixed effects models to estimate the effects of parental divorce and death on a variety of outcomes using 2 large national data sets: (a) the Early Childhood Longitudinal Study, Kindergarten Cohort (kindergarten through the 5th grade) and (b) the National Educational Longitudinal Study (8th grade to the senior year of high school). In both data sets, divorce and death were associated with multiple negative outcomes among children. Although evidence for a causal effect of divorce on children was reasonably strong, effect sizes were small in magnitude. A second analysis revealed a substantial degree of variability in children's outcomes following parental divorce, with some children declining, others improving, and most not changing at all. The estimated effects of divorce appeared to be strongest among children with the highest propensity to experience parental divorce.

Evidence for solar wind origin of energetic heavy ions in the earth's radiation belt

NASA Technical Reports Server (NTRS)

Hovestadt, D.; Klecker, B.; Scholer, M.; Gloeckler, G.; Ipavich, F. M.; Fan, C. Y.; Fisk, L. A.; Ogallagher, J. J.

1978-01-01

Analysis of data from our energetic ion composition experiment on ISEE-1 has revealed the presence of substantial fluxes of carbon, oxygen, and heavier ions above 400 keV/nucleon at L values between approximately 2.5 and 4 earth radii. The measured C/O ratio varies systematically from 1.3 at 450 keV/nucleon to 4.1 at 1.3 MeV/nucleon, and no iron is observed above 200 keV/nucleon. These results provide strong evidence for a solar wind origin for energetic ions in the outer radiation belt. The absence of iron and the increase of the carbon-to-oxygen ratio with energy suggest that the condition for the validity of the first adiabatic invariant may have a strong influence on the trapping of these particles.

Sources of Individual Differences in Emerging Competence With Numeration Understanding Versus Multidigit Calculation Skill

PubMed Central

Fuchs, Lynn S.; Geary, David C.; Fuchs, Douglas; Compton, Donald L.; Hamlett, Carol L.

2014-01-01

This study investigated contributions of general cognitive abilities and foundational mathematical competencies to numeration understanding (i.e., base-10 structure) versus multidigit calculation skill. Children (n = 394, M = 6.5 years) were assessed on general cognitive abilities and foundational numerical competencies at start of 1st grade; on the same numerical competencies, multidigit calculation skill, and numeration understanding at end of 2nd grade; and on multidigit calculation skill and numeration understanding at end of 3rd grade. Path-analytic mediation analysis revealed that general cognitive predictors exerted more direct and more substantial effects on numeration understanding than on multidigit calculations. Foundational mathematics competencies contributed to both outcomes, but largely via 2nd-grade mathematics achievement, and results suggest a mutually supportive role between numeration understanding and multidigit calculations. PMID:25284885

Phenotypic Diagnosis of Lineage and Differentiation During Sake Yeast Breeding

PubMed Central

Ohnuki, Shinsuke; Okada, Hiroki; Friedrich, Anne; Kanno, Yoichiro; Goshima, Tetsuya; Hasuda, Hirokazu; Inahashi, Masaaki; Okazaki, Naoto; Tamura, Hiroyasu; Nakamura, Ryo; Hirata, Dai; Fukuda, Hisashi; Shimoi, Hitoshi; Kitamoto, Katsuhiko; Watanabe, Daisuke; Schacherer, Joseph; Akao, Takeshi; Ohya, Yoshikazu

2017-01-01

Sake yeast was developed exclusively in Japan. Its diversification during breeding remains largely uncharacterized. To evaluate the breeding processes of the sake lineage, we thoroughly investigated the phenotypes and differentiation of 27 sake yeast strains using high-dimensional, single-cell, morphological phenotyping. Although the genetic diversity of the sake yeast lineage is relatively low, its morphological diversity has expanded substantially compared to that of the Saccharomyces cerevisiae species as a whole. Evaluation of the different types of breeding processes showed that the generation of hybrids (crossbreeding) has more profound effects on cell morphology than the isolation of mutants (mutation breeding). Analysis of phenotypic robustness revealed that some sake yeast strains are more morphologically heterogeneous, possibly due to impairment of cellular network hubs. This study provides a new perspective for studying yeast breeding genetics and micro-organism breeding strategies. PMID:28642365

Emotion comprehension: the impact of nonverbal intelligence.

PubMed

Albanese, Ottavia; De Stasio, Simona; Di Chiacchio, Carlo; Fiorilli, Caterina; Pons, Francisco

2010-01-01

A substantial body of research has established that emotion understanding develops throughout early childhood and has identified three hierarchical developmental phases: external, mental, and reflexive. The authors analyzed nonverbal intelligence and its effect on children's improvement of emotion understanding and hypothesized that cognitive level is a consistent predictor of emotion comprehension. In all, 366 children (182 girls, 184 boys) between the ages of 3 and 10 years were tested using the Test of Emotion Comprehension and the Coloured Progressive Matrices. The data obtained by using the path analysis model revealed that nonverbal intelligence was statistically associated with the ability to recognize emotions in the 3 developmental phases. The use of this model showed the significant effect that cognitive aspect plays on the reflexive phase. The authors aim to contribute to the debate about the influence of cognitive factors on emotion understanding.

Distribution patterns of the mesozooplankton, principally siphonophores and medusae, in the vicinity of the Antarctic Slope Front (eastern Weddell Sea)

NASA Astrophysics Data System (ADS)

Pagès, Francesc; Schnack-Schiel, Sigrid B.

1996-12-01

The composition, abundance and vertical distribution of mesozooplankton, particularly siphonophores and medusae (27 species), collected along two transects in the eastern Weddell Sea have been analysed. Both transects were characterized by a steep thermocline that on approaching the coastline defined the Antarctic Slope Front. The front acted as a strong boundary in the shelf-slope and caused a pronounced cross frontal gradient in the populations of cnidarians. Few species and low abundances were found in the upper cold waters and most of the populations concentrated in and below the thermocline. The analysis of the gastrozooids of the physonect siphonophore Pyrostephos vanhoeffeni showed a wide variety of prey but the relatively high contribution of krill larvae reveals a substantial trophic impact when both organisms co-occur.

Stem cell hype: media portrayal of therapy translation.

PubMed

Kamenova, Kalina; Caulfield, Timothy

2015-03-11

In this Perspective, we examine the portrayal of translational stem cell research in major daily newspapers in Canada, the United States, and the United Kingdom between 2010 and 2013, focusing on how timelines for stem cell therapies were represented before and after Geron terminated its pioneering stem cell program. Our content analysis reveals that press coverage has shifted from ethical, legal, and social issues to clinical translation issues, and highly optimistic timelines were provided with no substantial change in representation over time. Scientists were the dominant voice with respect to translation timelines. The findings raise questions about the degree to which the media's overly optimistic slant fosters unrealistic expectations regarding the speed of clinical translation and highlight the ethical responsibility of stem cell researchers as public communicators. Copyright © 2015, American Association for the Advancement of Science.

Topology of the South African stock market network across the 2008 financial crisis

NASA Astrophysics Data System (ADS)

Majapa, Mohamed; Gossel, Sean Joss

2016-03-01

This study uses the cross-correlations in the daily closing prices of the South African Top 100 companies listed on the JSE All share index (ALSI) from June 2003 to June 2013 to compute minimum spanning tree maps. In addition to the full sample, the analysis also uses three sub-periods to investigate the topological evolution before, during, and after the 2008 financial crisis. The findings show that although there is substantial clustering and homogeneity on the JSE, the most connected nodes are in the financial and resources sectors. The sub-sample results further reveal that the JSE network tree shrank in the run-up to, and during the financial crisis, and slowly expanded afterwards. In addition, the different clusters in the network are connected by various nodes that are significantly affected by diversification and credit market dynamics.

A Metabolic Probe-Enabled Strategy Reveals Uptake and Protein Targets of Polyunsaturated Aldehydes in the Diatom Phaeodactylum tricornutum

PubMed Central

Wolfram, Stefanie; Wielsch, Natalie; Hupfer, Yvonne; Mönch, Bettina; Lu-Walther, Hui-Wen; Heintzmann, Rainer; Werz, Oliver; Svatoš, Aleš; Pohnert, Georg

2015-01-01

Diatoms are unicellular algae of crucial importance as they belong to the main primary producers in aquatic ecosystems. Several diatom species produce polyunsaturated aldehydes (PUAs) that have been made responsible for chemically mediated interactions in the plankton. PUA-effects include chemical defense by reducing the reproductive success of grazing copepods, allelochemical activity by interfering with the growth of competing phytoplankton and cell to cell signaling. We applied a PUA-derived molecular probe, based on the biologically highly active 2,4-decadienal, with the aim to reveal protein targets of PUAs and affected metabolic pathways. By using fluorescence microscopy, we observed a substantial uptake of the PUA probe into cells of the diatom Phaeodactylum tricornutum in comparison to the uptake of a structurally closely related control probe based on a saturated aldehyde. The specific uptake motivated a chemoproteomic approach to generate a qualitative inventory of proteins covalently targeted by the α,β,γ,δ-unsaturated aldehyde structure element. Activity-based protein profiling revealed selective covalent modification of target proteins by the PUA probe. Analysis of the labeled proteins gave insights into putative affected molecular functions and biological processes such as photosynthesis including ATP generation and catalytic activity in the Calvin cycle or the pentose phosphate pathway. The mechanism of action of PUAs involves covalent reactions with proteins that may result in protein dysfunction and interference of involved pathways. PMID:26496085

The analysis of novel microRNA mimic sequences in cancer cells reveals lack of specificity in stem-loop RT-qPCR-based microRNA detection.

PubMed

Winata, Patrick; Williams, Marissa; McGowan, Eileen; Nassif, Najah; van Zandwijk, Nico; Reid, Glen

2017-11-17

MicroRNAs are frequently downregulated in cancer, and restoring expression has tumour suppressive activity in tumour cells. Our recent phase I clinical trial investigated microRNA-based therapy in patients with malignant pleural mesothelioma. Treatment with TargomiRs, microRNA mimics with novel sequence packaged in EGFR antibody-targeted bacterial minicells, revealed clear signs of clinical activity. In order to detect delivery of microRNA mimics to tumour cells in future clinical trials, we tested hydrolysis probe-based assays specific for the sequence of the novel mimics in transfected mesothelioma cell lines using RT-qPCR. The custom assays efficiently and specifically amplified the consensus mimics. However, we found that these assays gave a signal when total RNA from untransfected and control mimic-transfected cells were used as templates. Further investigation revealed that the reverse transcription step using stem-loop primers appeared to introduce substantial non-specific amplification with either total RNA or synthetic RNA templates. This suggests that reverse transcription using stem-loop primers suffers from an intrinsic lack of specificity for the detection of highly similar microRNAs in the same family, especially when analysing total RNA. These results suggest that RT-qPCR is unlikely to be an effective means to detect delivery of microRNA mimic-based drugs to tumour cells in patients.

Exploring Individual Differences in Preschoolers' Causal Stance

ERIC Educational Resources Information Center

Alvarez, Aubry; Booth, Amy E.

2016-01-01

Preschoolers, as a group, are highly attuned to causality, and this attunement is known to facilitate memory, learning, and problem solving. However, recent work reveals substantial individual variability in the strength of children's "causal stance," as demonstrated by their curiosity about and preference for new causal information. In…

TOXICITY REDUCTION EVALUATION (TRE) AT A MUNICIPAL WASTEWATER TREATMENT PLANT USING MUTAGENICITY AS AN END- POINT

EPA Science Inventory

Previous work revealed substantial levels of mutagenicity in effluents from certain municipal wastewater treatment plants. One of these treatment plants was selected for further study to track the effluent mutagenicity to its sources, to chemically characterize the mutagenicity, ...

Human and Social Capital as Facilitators of Lifelong Learning in Nursing.

ERIC Educational Resources Information Center

Gopee, Neil

2002-01-01

Interviews and focus groups with 27 nurses revealed the influence of health care professionals and nonprofessional acquaintances on participation in lifelong learning. Substantial informal learning occurs through work-based contexts, supported by other significant individuals. These factors constitute human and social capital, a significant…

Home Care Services and the Rural Elderly.

ERIC Educational Resources Information Center

Hayslip, Bert, Jr.; And Others

1980-01-01

Independent studies examined a needs v an agency perspective on home health care service needs within a rural county. Interviews with 299 elderly, aged 60-93, revealed there were substantial needs for home health care services and the desire for services varied with residence within the county. (Author)

Protein NMR Studies of Substrate Binding to Human Blood Group A and B Glycosyltransferases.

PubMed

Grimm, Lena Lisbeth; Weissbach, Sophie; Flügge, Friedemann; Begemann, Nora; Palcic, Monica M; Peters, Thomas

2017-07-04

Donor and acceptor substrate binding to human blood group A and B glycosyltransferases (GTA, GTB) has been studied by a variety of protein NMR experiments. Prior crystallographic studies had shown these enzymes to adopt an open conformation in the absence of substrates. Binding either of the donor substrate UDP-Gal or of UDP induces a semiclosed conformation. In the presence of both donor and acceptor substrates, the enzymes shift towards a closed conformation with ordering of an internal loop and the C-terminal residues, which then completely cover the donor-binding pocket. Chemical-shift titrations of uniformly 2 H, 15 N-labeled GTA or GTB with UDP affected about 20 % of all crosspeaks in 1 H, 15 N TROSY-HSQC spectra, reflecting substantial plasticity of the enzymes. On the other hand, it is this conformational flexibility that impedes NH backbone assignments. Chemical-shift-perturbation experiments with δ1-[ 13 C]methyl-Ile-labeled samples revealed two Ile residues-Ile123 at the bottom of the UDP binding pocket, and Ile192 as part of the internal loop-that were significantly disturbed upon stepwise addition of UDP and H-disaccharide, also revealing long-range perturbations. Finally, methyl TROSY-based relaxation dispersion experiments do not reveal micro- to millisecond timescale motions. Although this study reveals substantial conformational plasticity of GTA and GTB, the matter of how binding of substrates shifts the enzymes into catalytically competent states remains enigmatic. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Using beta coefficients to impute missing correlations in meta-analysis research: Reasons for caution.

PubMed

Roth, Philip L; Le, Huy; Oh, In-Sue; Van Iddekinge, Chad H; Bobko, Philip

2018-06-01

Meta-analysis has become a well-accepted method for synthesizing empirical research about a given phenomenon. Many meta-analyses focus on synthesizing correlations across primary studies, but some primary studies do not report correlations. Peterson and Brown (2005) suggested that researchers could use standardized regression weights (i.e., beta coefficients) to impute missing correlations. Indeed, their beta estimation procedures (BEPs) have been used in meta-analyses in a wide variety of fields. In this study, the authors evaluated the accuracy of BEPs in meta-analysis. We first examined how use of BEPs might affect results from a published meta-analysis. We then developed a series of Monte Carlo simulations that systematically compared the use of existing correlations (that were not missing) to data sets that incorporated BEPs (that impute missing correlations from corresponding beta coefficients). These simulations estimated ρ̄ (mean population correlation) and SDρ (true standard deviation) across a variety of meta-analytic conditions. Results from both the existing meta-analysis and the Monte Carlo simulations revealed that BEPs were associated with potentially large biases when estimating ρ̄ and even larger biases when estimating SDρ. Using only existing correlations often substantially outperformed use of BEPs and virtually never performed worse than BEPs. Overall, the authors urge a return to the standard practice of using only existing correlations in meta-analysis. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Finite Element Analysis Of Influence Of Flank Wear Evolution On Forces In Orthogonal Cutting Of 42CrMo4 Steel

NASA Astrophysics Data System (ADS)

Madajewski, Marek; Nowakowski, Zbigniew

2017-01-01

This paper presents analysis of flank wear influence on forces in orthogonal turning of 42CrMo4 steel and evaluates capacity of finite element model to provide such force values. Data about magnitude of feed and cutting force were obtained from measurements with force tensiometer in experimental test as well as from finite element analysis of chip formation process in ABAQUS/Explicit software. For studies an insert with complex rake face was selected and flank wear was simulated by grinding operation on its flank face. The aim of grinding inset surface was to obtain even flat wear along cutting edge, which after the measurement could be modeled with CAD program and applied in FE analysis for selected range of wear width. By comparing both sets of force values as function of flank wear in given cutting conditions FEA model was validated and it was established that it can be applied to analyze other physical aspects of machining. Force analysis found that progression of wear causes increase in cutting force magnitude and steep boost to feed force magnitude. Analysis of Fc/Ff force ratio revealed that flank wear has significant impact on resultant force in orthogonal cutting and magnitude of this force components in cutting and feed direction. Surge in force values can result in transfer of substantial loads to machine-tool interface.

Mass-Spectrometry-Based Proteomics Reveals Organ-Specific Expression Patterns To Be Used as Forensic Evidence.

PubMed

Dammeier, Sascha; Nahnsen, Sven; Veit, Johannes; Wehner, Frank; Ueffing, Marius; Kohlbacher, Oliver

2016-01-04

Standard forensic procedures to examine bullets after an exchange of fire include a mechanical or ballistic reconstruction of the event. While this is routine to identify which projectile hit a subject by DNA analysis of biological material on the surface of the projectile, it is rather difficult to determine which projectile caused the lethal injury--often the crucial point with regard to legal proceedings. With respect to fundamental law it is the duty of the public authority to make every endeavor to solve every homicide case. To improve forensic examinations, we present a forensic proteomic method to investigate biological material from a projectile's surface and determine the tissues traversed by it. To obtain a range of relevant samples, different major bovine organs were penetrated with projectiles experimentally. After tryptic "on-surface" digestion, mass-spectrometry-based proteome analysis, and statistical data analysis, we were able to achieve a cross-validated organ classification accuracy of >99%. Different types of anticipated external variables exhibited no prominent influence on the findings. In addition, shooting experiments were performed to validate the results. Finally, we show that these concepts could be applied to a real case of murder to substantially improve the forensic reconstruction.

Causal inference with measurement error in outcomes: Bias analysis and estimation methods.

PubMed

Shu, Di; Yi, Grace Y

2017-01-01

Inverse probability weighting estimation has been popularly used to consistently estimate the average treatment effect. Its validity, however, is challenged by the presence of error-prone variables. In this paper, we explore the inverse probability weighting estimation with mismeasured outcome variables. We study the impact of measurement error for both continuous and discrete outcome variables and reveal interesting consequences of the naive analysis which ignores measurement error. When a continuous outcome variable is mismeasured under an additive measurement error model, the naive analysis may still yield a consistent estimator; when the outcome is binary, we derive the asymptotic bias in a closed-form. Furthermore, we develop consistent estimation procedures for practical scenarios where either validation data or replicates are available. With validation data, we propose an efficient method for estimation of average treatment effect; the efficiency gain is substantial relative to usual methods of using validation data. To provide protection against model misspecification, we further propose a doubly robust estimator which is consistent even when either the treatment model or the outcome model is misspecified. Simulation studies are reported to assess the performance of the proposed methods. An application to a smoking cessation dataset is presented.

Malnutrition among women in sub-Saharan Africa: rural-urban disparity.

PubMed

Uthman, O A; Aremu, O

2008-01-01

Malnutrition is a serious public health problem, particularly in developing countries, linked to a substantial increase in the risk of mortality and morbidity. Women and young children are most often affected. Rural disadvantage is a known factor, but little attention has been paid to rural-urban disparity among women. To provide a reliable source of information for policy-makers, the current study used nationally representative data from 26 countries in sub-Saharan Africa to update knowledge about the prevalence malnutrition and its rural-urban disparities among women. The data sources were the demographic and health surveys of 26 countries conducted between 1995 and 2006. The methods included meta-analysis, meta-regression, sub-group and sensitivity. Overall, rural women were 68% more likely to be malnourished compared with their urban counterparts. In the meta-regression analysis, sub-region, sample size, and the year the study was conducted explained the observed heterogeneity. This meta-analysis provided usable data for women in sub-Saharan Africa. The magnitude of rural-urban malnutrition disparity revealed provides a baseline that will be of assistance to clinicians, researchers, and policy-makers in the detection, prevention and treatment of malnutrition among rural women.

Adherence to a Vegetarian Diet and Diabetes Risk: A Systematic Review and Meta-Analysis of Observational Studies.

PubMed

Lee, Yujin; Park, Kyong

2017-06-14

We quantitatively assessed the association between a vegetarian diet and diabetes risk using pooled estimates from observational studies. Electronic database searches for articles published from January 1980 to May 2016 were independently performed by two investigators, and 13 articles (14 studies) were identified. The pooled odds ratio (OR) for diabetes in vegetarians vs. non-vegetarians was 0.726 (95% confidence interval (CI): 0.608, 0.867). In the subgroup analyses, this inverse association was stronger for the studies conducted in the Western Pacific region (OR 0.514, 95% CI: 0.304, 0.871) and Europe/North America (OR 0.756, 95% CI: 0.589, 0.971) than studies conducted in Southeast Asia (OR 0.888, 95% CI: 0.718, 1.099). No study had a substantial effect on the pooled effect size in the influence analysis, and the Egger's ( p = 0.465) and Begg's tests ( p = 0.584) revealed no publication bias. This meta-analysis indicates that a vegetarian diet is inversely associated with diabetes risk. Our results support the need for further investigations into the effects of the motivations for vegetarianism, the duration of the adherence to a vegetarian diet, and type of vegetarian on diabetes risk.

Assessment of pleiotropic transcriptome perturbations in Arabidopsis engineered for indirect insect defence.

PubMed

Houshyani, Benyamin; van der Krol, Alexander R; Bino, Raoul J; Bouwmeester, Harro J

2014-06-19

Molecular characterization is an essential step of risk/safety assessment of genetically modified (GM) crops. Holistic approaches for molecular characterization using omics platforms can be used to confirm the intended impact of the genetic engineering, but can also reveal the unintended changes at the omics level as a first assessment of potential risks. The potential of omics platforms for risk assessment of GM crops has rarely been used for this purpose because of the lack of a consensus reference and statistical methods to judge the significance or importance of the pleiotropic changes in GM plants. Here we propose a meta data analysis approach to the analysis of GM plants, by measuring the transcriptome distance to untransformed wild-types. In the statistical analysis of the transcriptome distance between GM and wild-type plants, values are compared with naturally occurring transcriptome distances in non-GM counterparts obtained from a database. Using this approach we show that the pleiotropic effect of genes involved in indirect insect defence traits is substantially equivalent to the variation in gene expression occurring naturally in Arabidopsis. Transcriptome distance is a useful screening method to obtain insight in the pleiotropic effects of genetic modification.

Scanning electron microscope fractography in failure analysis of steels

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wouters, R.; Froyen, L.

1996-04-01

For many failure cases, macroscopic examination of the fracture surface permits discrimination of fatigue fractures from overload fractures. For clarifying fatigue fractures, the practical significance of microfractography is limited to an investigation of the crack initiation areas. Scanning electron microscopy is successfully used in tracing local material abnormalities that act as fatigue crack initiators. The task for the scanning electron microscope, however, is much more substantial in failure analysis of overload fractures, especially for steels. By revealing specific fractographic characteristics, complemented by information about the material and the loading conditions, scanning electron microscopy provides a strong indication of the probablemore » cause of failure. A complete dimple fracture is indicative of acceptable bulk material properties; overloading, by subdimensioning or excessive external loading, has to be verified. The presence of cleavage fracture makes the material properties questionable if external conditions causing embrittlement are absent. Intergranular brittle fracture requires verification of grain-boundary weakening conditions--a sensitized structure, whether or not combined with a local stress state or a specific environment. The role of scanning electron microscopy in failure analysis is illustrated by case histories of the aforementioned fracture types.« less

Association between MTHFR polymorphisms and acute myeloid leukemia risk: a meta-analysis.

PubMed

Qin, Yu-Tao; Zhang, Yong; Wu, Fang; Su, Yan; Lu, Ge-Ning; Wang, Ren-Sheng

2014-01-01

Previous observational studies investigating the association between methylenetetrahydrofolate reductase (MTHFR) polymorphisms and acute myeloid leukemia risk (AML) have yielded inconsistent results. The aim of this study is to derive a more precise estimation of the association between MTHFR (C677T and A1298C) polymorphisms and acute myeloid leukemia risk. PubMed and Embase databases were systematically searched to identify relevant studies from their inception to August 2013. Odds ratios (ORs) with 95% confidence intervals (CIs) were the metric of choice. Thirteen studies were selected for C677T polymorphism (1838 cases and 5318 controls) and 9 studies (1335 patients and 4295 controls) for A1298C polymorphism. Overall, pooled results showed that C677T polymorphism was not significant associated with AML risk(OR, 0.98-1.04; 95% CI, 0.86-0.92 to 1.09-1.25). Similar results were observed for the A1298C polymorphism and in subgroup analysis. All comparisons revealed no substantial heterogeneity nor did we detect evidence of publication bias. In summary, this meta-analysis provides evidence that MTHFR polymorphisms were not associated with AML risk. Further investigations are needed to offer better insight into the role of these polymorphisms in AML carcinogenesis.

Ecological Settings and State Economies as Factor Inputs in the Provision of Outdoor Recreation

NASA Astrophysics Data System (ADS)

Siderelis, Christos; Smith, Jordan W.

2013-09-01

State parks play a substantial role in the provision of outdoor recreation opportunities within the United States. Park operators must make crucial decisions in how they allocate capital expenditures, labor, and parkland to maintain recreation opportunities. Their decisions are influenced, in part, by the ecological characteristics of their state's park system as well as the vitality of their state's economy. In this research, we incorporate the characteristics of states' ecosystems and their local economies into a formal production analysis of the states' park systems from the years 1986 to 2011. Our analysis revealed all three factors of production were positive and inelastic. Expenditures on labor had the largest effect on both park utilization and operational expenditures. Our analysis also found a large degree of variability in the effects of ecological characteristics on both utilization and operating expenditures. Parkland utilization and operational expenditures were more elastic in areas such as Oceania and Mediterranean California relative to other ecological regions. These findings lead us to conclude that state park operators will experience variable levels of difficulty in both accommodating increasing demands for recreation from state parks and maintaining the existing quality of outdoor recreation provided within their system.

Evaluating the evidence base for relational frame theory: a citation analysis.

PubMed

Dymond, Simon; May, Richard J; Munnelly, Anita; Hoon, Alice E

2010-01-01

Relational frame theory (RFT) is a contemporary behavior-analytic account of language and cognition. Since it was first outlined in 1985, RFT has generated considerable controversy and debate, and several claims have been made concerning its evidence base. The present study sought to evaluate the evidence base for RFT by undertaking a citation analysis and by categorizing all articles that cited RFT-related search terms. A total of 174 articles were identified between 1991 and 2008, 62 (36%) of which were empirical and 112 (64%) were nonempirical articles. Further analyses revealed that 42 (68%) of the empirical articles were classified as empirical RFT and 20 (32%) as empirical other, whereas 27 (24%) of the nonempirical articles were assigned to the nonempirical reviews category and 85 (76%) to the nonempirical conceptual category. In addition, the present findings show that the majority of empirical research on RFT has been conducted with typically developing adult populations, on the relational frame of sameness, and has tended to be published in either The Psychological Record or the Journal of the Experimental Analysis of Behavior. Overall, RFT has made a substantial contribution to the literature in a relatively short period of time.

Barely started and already left behind: a descriptive analysis of the mathematics ability demonstrated by young deaf children.

PubMed

Kritzer, Karen L

2009-01-01

This study examined young deaf children's early informal/formal mathematical knowledge as measured by the Test of Early Mathematics Ability (TEMA-3). Findings from this study suggest that prior to the onset of formal schooling, young deaf children might already demonstrate evidence of academic delays. Of these 28 participants (4-6 years of age), for whom data were analyzed, none received a score on the TEMA-3, indicating above-"average" ability according to normative ranking. More than half of participants received scores substantially below average with 11 participants receiving scores a year or more behind normative age-equivalent scores. Upon more focused analysis, specific areas of difficulty were found to include word/story problems, skip counting (i.e., counting by twos, threes, etc.), number comparisons, the reading/writing of two to three digit numbers, and addition/subtraction number facts. A qualitative analysis of the answers participants gave and the behaviors they demonstrated while answering the test items was conducted and revealed possible explanations for why specific test items may have been challenging. Implications of findings for parents, early interventionists, and teachers of young deaf children are discussed.

Polymorphism of 11 Y Chromosome Short Tandem Repeat Markers among Malaysian Aborigines.

PubMed

Mohd Yussup, Sofia Sakina; Marzukhi, Marlia; Md-Zain, Badrul Munir; Mamat, Kamaruddin; Mohd Yusof, Farida Zuraina

2017-01-01

The conventional technique such as patrilocality suggests some substantial effects on population diversity. With that, this particular study investigated the paternal line, specifically Scientific Working Group on DNA Analysis Methods (SWGDAM)-recommended Y-STR markers, namely, DYS19, DYS385, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS438, and DYS439. These markers were tested to compare 184 Orang Asli individuals from 3 tribes found in Peninsular Malaysia. As a result, the haplotype diversity and the discrimination capacity obtained were 0.9987 and 0.9076, respectively. Besides, the most diverse marker was DYS385b, whereas the least was DYS391. Furthermore, the Senoi and Proto-Malay tribes were found to be the most distant, whereas the Senoi and Negrito clans were almost similar to each other. In addition, the analysis of molecular variance analysis revealed 82% of variance within the population, but only 18% of difference between the tribes. Finally, the phylogenetic trees constructed using Neighbour Joining and UPGMA (Unweighted Pair Group Method with Arithmetic Mean) displayed several clusters that were tribe specific. With that, future studies are projected to analyse individuals based on more specific sub-tribes.

Enrichment of Root Endophytic Bacteria from Populus deltoides and Single-Cell-Genomics Analysis

DOE PAGES

Utturkar, Sagar M.; Cude, W. Nathan; Robeson, Jr., Michael S.; ...

2016-07-15

Bacterial endophytes that colonize Populus trees contribute to nutrient acquisition, prime immunity responses, and directly or indirectly increase both above- and below-ground biomasses. Endophytes are embedded within plant material, so physical separation and isolation are difficult tasks. Application of culture-independent methods, such as metagenome or bacterial transcriptome sequencing, has been limited due to the predominance of DNA from the plant biomass. In this paper, we present a modified differential and density gradient centrifugation-based protocol for the separation of endophytic bacteria from Populus roots. This protocol achieved substantial reduction in contaminating plant DNA, allowed enrichment of endophytic bacteria away from themore » plant material, and enabled single-cell genomics analysis. Four single-cell genomes were selected for whole-genome amplification based on their rarity in the microbiome (potentially uncultured taxa) as well as their inferred abilities to form associations with plants. Bioinformatics analyses, including assembly, contamination removal, and completeness estimation, were performed to obtain single-amplified genomes (SAGs) of organisms from the phyla Armatimonadetes, Verrucomicrobia, and Planctomycetes, which were unrepresented in our previous cultivation efforts. Finally, comparative genomic analysis revealed unique characteristics of each SAG that could facilitate future cultivation efforts for these bacteria.« less

Henry Gray, plagiarist.

PubMed

Richardson, Ruth

2016-03-01

The first edition of Anatomy Descriptive and Surgical (1858) was greeted with accolades, but also provoked serious controversy concerning Henry Gray's failure to acknowledge the work of earlier anatomists. A review in the Medical Times (1859) accused Gray of intellectual theft. The journal took the unusual step of substantiating its indictment by publishing twenty parallel texts from Gray and from a pre-existing textbook, Quain's Anatomy. At the recent "Vesalius Continuum" conference in Zakynthos, Greece (2014) Professor Brion Benninger disputed the theft by announcing from the floor the results of a computer analysis of both texts, which he reported exonerated Gray by revealing no evidence of plagiarism. The analysis has not been forthcoming, however, despite requests. Here the historian of Gray's Anatomy supplements the argument set out in the Medical Times 150 years ago with data suggesting unwelcome personality traits in Henry Gray, and demonstrating the utility of others' work to his professional advancement. Fair dealing in the world of anatomy and indeed the genuineness of the lustre of medical fame are important matters, but whether quantitative evidence has anything to add to the discussion concerning Gray's probity can be assessed only if Benninger makes public his computer analysis. © 2015 Wiley Periodicals, Inc.

Understanding the organization of the amphibian egg cytoplasm - Gravitational force as a probe

NASA Technical Reports Server (NTRS)

Neff, Anton W.; Malacinski, George M.; Yokota, Hiroki; Wakahara, Masami

1992-01-01

A combination of hypergravity (centrifugation) and hypogravity (clinostat) studies have been carried out on amphibian (frog, Xenopus) eggs. The results reveal that the twinning caused by centrifugation exhibits substantial spawning to spawning variation. That variation can be attributed to the apparent viscosity of the egg's internal cytoplasm. Simulated hypogravity results in a relocation of the egg's third (horizontal) cleavage furrow, toward the equator. Substantial egg-to-egg variation is also observed in this 'cleavage effect'. For interpreting spaceflight data and for using G-forces as probes for understanding the egg's architecture the egg variation documented herein should be considered.

[Prevalence of gene polymorphisms associated with immune-dependent diseases in the populations of North Eurasia].

PubMed

Cherednichenko, A A; Trifonova, E A; Vagaitseva, K V; Bocharova, A V; Varzari, A M; Radzhabov, M O; Stepanov, V A

2015-01-01

The data on distribution of genetic diversity in gene polymorphisms associated with autoimmune and allergic diseases and with regulation of immunoglobulin E and cytokines levels in 26 populations of the Northern Eurasia is presented. Substantial correlation between the values of average expected heterozygosity by 44 gene polymorphisms with climatic and geographical factors has not been revealed. Clustering of population groups in correspondence with their geographic locations is observed. The degree of gene differentiation among populations and the selective neutrality of gene polymorphisms have been assessed. The results of our work evidence the substantial genetic diversity and differentiation of human populations by studied genes.

Divergent mtDNA lineages of goats in an Early Neolithic site, far from the initial domestication areas

PubMed Central

Fernández, Helena; Hughes, Sandrine; Vigne, Jean-Denis; Helmer, Daniel; Hodgins, Greg; Miquel, Christian; Hänni, Catherine; Luikart, Gordon; Taberlet, Pierre

2006-01-01

Goats were among the first farm animals domesticated, ≈10,500 years ago, contributing to the rise of the “Neolithic revolution.” Previous genetic studies have revealed that contemporary domestic goats (Capra hircus) show far weaker intercontinental population structuring than other livestock species, suggesting that goats have been transported more extensively. However, the timing of these extensive movements in goats remains unknown. To address this question, we analyzed mtDNA sequences from 19 ancient goat bones (7,300–6,900 years old) from one of the earliest Neolithic sites in southwestern Europe. Phylogenetic analysis revealed that two highly divergent goat lineages coexisted in each of the two Early Neolithic layers of this site. This finding indicates that high mtDNA diversity was already present >7,000 years ago in European goats, far from their areas of initial domestication in the Near East. These results argue for substantial gene flow among goat populations dating back to the early neolithisation of Europe and for a dual domestication scenario in the Near East, with two independent but essentially contemporary origins (of both A and C domestic lineages) and several more remote and/or later origins. PMID:17030824

Genomic sequencing of Pleistocene cave bears

DOE Office of Scientific and Technical Information (OSTI.GOV)

Noonan, James P.; Hofreiter, Michael; Smith, Doug

2005-04-01

Despite the information content of genomic DNA, ancient DNA studies to date have largely been limited to amplification of mitochondrial DNA due to technical hurdles such as contamination and degradation of ancient DNAs. In this study, we describe two metagenomic libraries constructed using unamplified DNA extracted from the bones of two 40,000-year-old extinct cave bears. Analysis of {approx}1 Mb of sequence from each library showed that, despite significant microbial contamination, 5.8 percent and 1.1 percent of clones in the libraries contain cave bear inserts, yielding 26,861 bp of cave bear genome sequence. Alignment of this sequence to the dog genome,more » the closest sequenced genome to cave bear in terms of evolutionary distance, revealed roughly the expected ratio of cave bear exons, repeats and conserved noncoding sequences. Only 0.04 percent of all clones sequenced were derived from contamination with modern human DNA. Comparison of cave bear with orthologous sequences from several modern bear species revealed the evolutionary relationship of these lineages. Using the metagenomic approach described here, we have recovered substantial quantities of mammalian genomic sequence more than twice as old as any previously reported, establishing the feasibility of ancient DNA genomic sequencing programs.« less

Cell lineage tracing in the developing enteric nervous system: superstars revealed by experiment and simulation

PubMed Central

Cheeseman, Bevan L.; Zhang, Dongcheng; Binder, Benjamin J.; Newgreen, Donald F.; Landman, Kerry A.

2014-01-01

Cell lineage tracing is a powerful tool for understanding how proliferation and differentiation of individual cells contribute to population behaviour. In the developing enteric nervous system (ENS), enteric neural crest (ENC) cells move and undergo massive population expansion by cell division within self-growing mesenchymal tissue. We show that single ENC cells labelled to follow clonality in the intestine reveal extraordinary and unpredictable variation in number and position of descendant cells, even though ENS development is highly predictable at the population level. We use an agent-based model to simulate ENC colonization and obtain agent lineage tracing data, which we analyse using econometric data analysis tools. In all realizations, a small proportion of identical initial agents accounts for a substantial proportion of the total final agent population. We term these individuals superstars. Their existence is consistent across individual realizations and is robust to changes in model parameters. This inequality of outcome is amplified at elevated proliferation rate. The experiments and model suggest that stochastic competition for resources is an important concept when understanding biological processes which feature high levels of cell proliferation. The results have implications for cell-fate processes in the ENS. PMID:24501272

Integrative modelling reveals mechanisms linking productivity and plant species richness.

PubMed

Grace, James B; Anderson, T Michael; Seabloom, Eric W; Borer, Elizabeth T; Adler, Peter B; Harpole, W Stanley; Hautier, Yann; Hillebrand, Helmut; Lind, Eric M; Pärtel, Meelis; Bakker, Jonathan D; Buckley, Yvonne M; Crawley, Michael J; Damschen, Ellen I; Davies, Kendi F; Fay, Philip A; Firn, Jennifer; Gruner, Daniel S; Hector, Andy; Knops, Johannes M H; MacDougall, Andrew S; Melbourne, Brett A; Morgan, John W; Orrock, John L; Prober, Suzanne M; Smith, Melinda D

2016-01-21

How ecosystem productivity and species richness are interrelated is one of the most debated subjects in the history of ecology. Decades of intensive study have yet to discern the actual mechanisms behind observed global patterns. Here, by integrating the predictions from multiple theories into a single model and using data from 1,126 grassland plots spanning five continents, we detect the clear signals of numerous underlying mechanisms linking productivity and richness. We find that an integrative model has substantially higher explanatory power than traditional bivariate analyses. In addition, the specific results unveil several surprising findings that conflict with classical models. These include the isolation of a strong and consistent enhancement of productivity by richness, an effect in striking contrast with superficial data patterns. Also revealed is a consistent importance of competition across the full range of productivity values, in direct conflict with some (but not all) proposed models. The promotion of local richness by macroecological gradients in climatic favourability, generally seen as a competing hypothesis, is also found to be important in our analysis. The results demonstrate that an integrative modelling approach leads to a major advance in our ability to discern the underlying processes operating in ecological systems.

Phenylpropanoid Scent Compounds in Petunia x hybrida Are Glycosylated and Accumulate in Vacuoles

PubMed Central

Cna'ani, Alon; Shavit, Reut; Ravid, Jasmin; Aravena-Calvo, Javiera; Skaliter, Oded; Masci, Tania; Vainstein, Alexander

2017-01-01

Floral scent has been studied extensively in the model plant Petunia. However, little is known about the intracellular fate of scent compounds. Here, we characterize the glycosylation of phenylpropanoid scent compounds in Petunia x hybrida. This modification reduces scent compounds' volatility, reactivity, and autotoxicity while increasing their water-solubility. Gas chromatography–mass spectrometry (GC–MS) analyses revealed that flowers of petunia cultivars accumulate substantial amounts of glycosylated scent compounds and that their increasing level parallels flower development. In contrast to the pool of accumulated aglycones, which drops considerably at the beginning of the light period, the collective pool of glycosides starts to increase at that time and does not decrease thereafter. The glycoside pool is dynamic and is generated or catabolized during peak scent emission, as inferred from phenylalanine isotope-feeding experiments. Using several approaches, we show that phenylpropanoid scent compounds are stored as glycosides in the vacuoles of petal cells: ectopic expression of Aspergillus niger β-glucosidase-1 targeted to the vacuole resulted in decreased glycoside accumulation; GC–MS analysis of intact vacuoles isolated from petal protoplasts revealed the presence of glycosylated scent compounds. Accumulation of glycosides in the vacuoles seems to be a common mechanism for phenylpropanoid metabolites. PMID:29163617

The structure of (CENP-A-H4) 2 reveals physical features that mark centromeres

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sekulic, Nikolina; Bassett, Emily A; Rogers, Danielle J

2010-09-20

Centromeres are specified epigenetically, and the histone H3 variant CENP-A is assembled into the chromatin of all active centromeres. Divergence from H3 raises the possibility that CENP-A generates unique chromatin features to mark physically centromere location. Here we report the crystal structure of a subnucleosomal heterotetramer, human (CENP-A-H4) 2, that reveals three distinguishing properties encoded by the residues that comprise the CENP-A targeting domain (CATD; ref. 2): (1) a CENP-A-CENP-A interface that is substantially rotated relative to the H3-H3 interface; (2) a protruding loop L1 of the opposite charge as that on H3; and (3) strong hydrophobic contacts that rigidifymore » the CENP-A-H4 interface. Residues involved in the CENP-A-CENP-A rotation are required for efficient incorporation into centromeric chromatin, indicating specificity for an unconventional nucleosome shape. DNA topological analysis indicates that CENP-A-containing nucleosomes are octameric with conventional left-handed DNA wrapping, in contrast to other recent proposals. Our results indicate that CENP-A marks centromere location by restructuring the nucleosome from within its folded histone core.« less

An in-vitro evaluation of Kodak Insight and Ektaspeed Plus film with a CMOS detector for natural proximal caries: ROC analysis.

PubMed

Nair, M K; Nair, U P

2001-01-01

This study compared the diagnostic efficacy of Kodak Ektaspeed Plus film, Kodak Insight film, a newly introduced E/F-speed film, and Schick CMOS-APS digital sensor, with respect to caries detection in 92 proximal surfaces of extracted unrestored teeth, 51 of which were carious. Ground truth was evaluated histologically and the lesions classified as enamel or dentinal. Eight observers read the radiographs using a five-point confidence rating scale to record their diagnoses. Analyses using receiver operating characteristic curves revealed the areas under each curve that indicated the diagnostic accuracy (Ektaspeed Plus - 0.760, Insight - 0.778 and CMOS-APS sensor - 0.732). ANOVA revealed significant differences with respect to caries depth (p<0.031) and observers (p<0.0001). Weighted kappa analyses indicated moderate to substantial inter- and intra-observer agreement (0.42 and 0.66, respectively). The results suggest that none of the imaging modalities evaluated in this study differed in their diagnostic capabilities with respect to proximal decay detection and that the Insight film which was used with 20% less radiation exposure than Ektaspeed Plus film was as good as the other two sensors for this purpose.

Personality of Wild Male Crested Macaques (Macaca nigra)

PubMed Central

Neumann, Christof; Agil, Muhammad; Widdig, Anja; Engelhardt, Antje

2013-01-01

Animal personalities, i.e. consistent differences in behavior across time and/or context, have received increased attention of behavioral biologists over the last years. Recent research shows that personalities represent traits on which natural and sexual selection work and which can have substantial fitness consequences. The aim of this study is to establish the personality structure of crested macaque (Macaca nigra) males as foundation for future studies on its adaptive value. We collected behavioral data through focal animal sampling and additionally conducted two sets of playback experiments. Results of a factor analysis on the behavioral data revealed a four factor structure with components we labeled Anxiety, Sociability, Connectedness and Aggressiveness. Results from the experiments revealed an additional and independent Boldness factor but the absence of Neophilia. Overall, this structure resembles other macaque and animal species with the exception of Connectedness, which might be a consequence of the species' tolerant social style. Our results thus not only form the basis for future studies on the adaptive value of personality in crested macaques but also contribute an important data point for investigating the evolution of personality structure from a comparative perspective by refining, for example, which personality factors characterized the last common ancestor of hominids and macaques. PMID:23940517

Individual Movement Strategies Revealed through Novel Clustering of Emergent Movement Patterns

NASA Astrophysics Data System (ADS)

Valle, Denis; Cvetojevic, Sreten; Robertson, Ellen P.; Reichert, Brian E.; Hochmair, Hartwig H.; Fletcher, Robert J.

2017-03-01

Understanding movement is critical in several disciplines but analysis methods often neglect key information by adopting each location as sampling unit, rather than each individual. We introduce a novel statistical method that, by focusing on individuals, enables better identification of temporal dynamics of connectivity, traits of individuals that explain emergent movement patterns, and sites that play a critical role in connecting subpopulations. We apply this method to two examples that span movement networks that vary considerably in size and questions: movements of an endangered raptor, the snail kite (Rostrhamus sociabilis plumbeus), and human movement in Florida inferred from Twitter. For snail kites, our method reveals substantial differences in movement strategies for different bird cohorts and temporal changes in connectivity driven by the invasion of an exotic food resource, illustrating the challenge of identifying critical connectivity sites for conservation in the presence of global change. For human movement, our method is able to reliably determine the origin of Florida visitors and identify distinct movement patterns within Florida for visitors from different places, providing near real-time information on the spatial and temporal patterns of tourists. These results emphasize the need to integrate individual variation to generate new insights when modeling movement data.

Modified aging of elite athletes revealed by analysis of epigenetic age markers

PubMed Central

Spólnicka, Magdalena; Pośpiech, Ewelina; Adamczyk, Jakub Grzegorz; Freire-Aradas, Ana; Pepłońska, Beata; Zbieć-Piekarska, Renata; Makowska, Żanetta; Pięta, Anna; Lareu, Maria Victoria; Phillips, Christopher; Płoski, Rafał; Żekanowski, Cezary

2018-01-01

Recent progress in epigenomics has led to the development of prediction systems that enable accurate age estimation from DNA methylation data. Our objective was to track responses to intense physical exercise of individual age-correlated DNA methylation markers and to infer their potential impact on the aging processes. The study showed accelerated DNA hypermethylation for two CpG sites in TRIM59 and KLF14. Both markers predicted the investigated elite athletes to be several years older than controls and this effect was more substantial in subjects involved in power sports. Accordingly, the complete 5-CpG model revealed age acceleration of elite athletes (P=1.503x10-7) and the result was more significant amongst power athletes (P=1.051x10-9). The modified methylation of TRIM59 and KLF14 in top athletes may be accounted for by the biological roles played by these genes. Their known anti-tumour and anti-inflammatory activities suggests that intense physical training has a complex influence on aging and potentially launches signalling networks that contribute to the observed lower risk of elite athletes to develop cardiovascular disease and cancer. PMID:29466246

Modified aging of elite athletes revealed by analysis of epigenetic age markers.

PubMed

Spólnicka, Magdalena; Pośpiech, Ewelina; Adamczyk, Jakub Grzegorz; Freire-Aradas, Ana; Pepłońska, Beata; Zbieć-Piekarska, Renata; Makowska, Żanetta; Pięta, Anna; Lareu, Maria Victoria; Phillips, Christopher; Płoski, Rafał; Żekanowski, Cezary; Branicki, Wojciech

2018-02-15

Recent progress in epigenomics has led to the development of prediction systems that enable accurate age estimation from DNA methylation data. Our objective was to track responses to intense physical exercise of individual age-correlated DNA methylation markers and to infer their potential impact on the aging processes. The study showed accelerated DNA hypermethylation for two CpG sites in TRIM59 and KLF14 . Both markers predicted the investigated elite athletes to be several years older than controls and this effect was more substantial in subjects involved in power sports. Accordingly, the complete 5-CpG model revealed age acceleration of elite athletes ( P =1.503x10 -7 ) and the result was more significant amongst power athletes (P=1.051x10 -9 ). The modified methylation of TRIM59 and KLF14 in top athletes may be accounted for by the biological roles played by these genes. Their known anti-tumour and anti-inflammatory activities suggests that intense physical training has a complex influence on aging and potentially launches signalling networks that contribute to the observed lower risk of elite athletes to develop cardiovascular disease and cancer.

Seed transfer zones for a native grass Festuca roemeri: genecological evidence

Treesearch

Barbara L. Wilson; Dale C. Darris; Rob Fiegener; Matthew E. Horning; Keli Kuykendall

2008-01-01

A common-garden study of Festuca roemeri (Pavlick) E. B. Alexeev (Poaceae) revealed substantial genetic variation within and among 47 populations from throughout its range in the Pacific Northwest, USA, for growth, fitness, phenological, and morphological traits. Using climatic and physiographic variables, genetic patterns over the landscape were...

World-System Mobility and Economic Growth, 1980-2000

ERIC Educational Resources Information Center

Clark, Rob

2010-01-01

World-system scholars have traditionally emphasized the stability of the core/periphery hierarchy. However, prior network studies employing both categorical and continuous measures of world-system position reveal substantial mobility across time, whereby a number of developing states have become more integrated in the world economy over the past…

Value Imposition in Day Care: Fact, Fancy, and Irrelevant?

ERIC Educational Resources Information Center

Horner, William C.

1977-01-01

A questionnaire addressed to 70 parents and 30 staff members of an early intervention program revealed no substantial discrepancies in their respective evaluations of a number of child behavior characteristics (mainly social). Even when parents subjectively perceived some value dissonance, their satisfaction with the day care program was not…

Dissociable Stages of Problem Solving (I): Temporal Characteristics Revealed by Eye-Movement Analyses

ERIC Educational Resources Information Center

Nitschke, Kai; Ruh, Nina; Kappler, Sonja; Stahl, Christoph; Kaller, Christoph P.

2012-01-01

Understanding the functional neuroanatomy of planning and problem solving may substantially benefit from better insight into the chronology of the cognitive processes involved. Based on the assumption that regularities in cognitive processing are reflected in overtly observable eye-movement patterns, here we recorded eye movements while…

Treating Adult Marijuana Dependence: A Test of the Relapse Prevention Model.

ERIC Educational Resources Information Center

Stephens, Robert S.; And Others

1994-01-01

Randomly assigned adults (n=212) seeking treatment for marijuana use to relapse prevention (RP) or social support (SSP) group discussion intervention. Data collected at 12 months posttreatment revealed substantial reductions in frequency of marijuana use and associated problems; no significant difference between treatments on days of marijuana…

Long-read sequencing improves assembly of Trichinella genomes 10-fold, revealing substantial synteny between lineages diverged over seven million years

USDA-ARS?s Scientific Manuscript database

Genome evolution influences a parasite’s’s pathogenicity, host-pathogen interactions, environmental constraints, and invasion biology, while genome assemblies form the basis of comparative sequence analyses. Given that closely related organisms typically maintain appreciable synteny, the genome asse...

32 CFR 776.25 - Confidentiality of information.

Code of Federal Regulations, 2010 CFR

2010-07-01

... information: (1) A covered attorney shall not reveal information relating to representation of a client unless... to carry out the representation, and except as stated in paragraphs (a)(2) and (a)(3) of this section... is likely to result in imminent death or substantial bodily harm, or significant impairment of...

The Sources of the Relationship between Sustained Attention and Reasoning

ERIC Educational Resources Information Center

Ren, Xuezhu; Schweizer, Karl; Xu, Fen

2013-01-01

Although a substantial relationship of sustained attention and reasoning was consistently found, little is known about what drives this relationship. The present study aims at revealing the underlying sources that are responsible for the relationship by means of an integrative approach combining experimental manipulation and psychometric modeling.…

Germany's Emerging Multiethnic Society: Old Problems and New.

ERIC Educational Resources Information Center

Gedmin, Jeffrey

1994-01-01

Opinion polls do not indicate a growing neo-Nazism in Germany, but they do reveal substantial hostile attitudes toward Jews and significant bias against other ethnic minorities. Demographic trends suggest that Germany will have an increasingly multiracial society as well as a greater need for foreign labor in the future. (SLD)

Live-sawing: a way to increase lumber grade yield and mill profits

Treesearch

Neil K. Huyler

1974-01-01

A study to compare live-sawing with conventional grade-sawing of factory-grade 3 red oak sawlogs revealed that live-sawing results in substantial increases in production rate, overrun, log value per thousand board feet, and significant reduction in size of the breakeven log diameter.

Occupational Therapy--Real Help for Real Life

ERIC Educational Resources Information Center

Gibbs, Hope J.

2004-01-01

Occupational therapy is one of the hottest growing professions around. The American Occupational Therapy Association (AOTA) cites on its website (www.aota.org) that "the U.S. Department of Labor's Bureau of Labor Statistics reveals that the job outlook for occupational therapists will improve substantially in the next several years and will…

Effect of section shape on frequencies of natural oscillations of tubular springs

NASA Astrophysics Data System (ADS)

Pirogov, S. P.; Chuba, A. Yu; Cherentsov, D. A.

2018-05-01

The necessity of determining the frequencies of natural oscillations of manometric tubular springs is substantiated. Based on the mathematical model and computer program, numerical experiments were performed that allowed us to reveal the effect of geometric parameters on the frequencies of free oscillations of manometric tubular springs.

Representation of Knowledge on Some Management Accounting Techniques in Textbooks

ERIC Educational Resources Information Center

Golyagina, Alena; Valuckas, Danielius

2016-01-01

This paper examines the coverage of management accounting techniques in several popular management accounting texts, assessing each technique's claimed position within practice, its benefits and limitations, and the information sources substantiating these claims. Employing the notion of research genres, the study reveals that textbooks in their…

Translations on Eastern Europe: Political, Sociological and Military Affairs No. 1606.

DTIC Science & Technology

1978-11-07

some extent over to their side. As Dahlem reveals, Friedrich Roetter , a lawyer of German nationality and Jewish descent, above all rendered an...apparatus and, once abroad, to supply him with a substantial sum of foreign currency, Roetter , for one night, turned his Berlin office over to the

The Quality of Life in China

ERIC Educational Resources Information Center

Shu, Xiaoling; Zhu, Yifei

2009-01-01

The Asia Barometer Survey of 2,000 respondents reveals that substantial majorities of the Chinese people experience feelings of happiness, enjoyment, and accomplishment. In fact, the proportion experiencing these indicators of a high quality of life are larger in China than in some more prosperous countries. Favorable historical comparison,…

The Role of the Stratosphere in Explosive Deepening of Extratropical Cyclones

NASA Astrophysics Data System (ADS)

Knippertz, Peter; Wilbraham, Robert; Trzeciak, Tomek; Owen, Jenny; Odell, Luke; Fink, Andreas H.; Pinto, Joaquim G.

2014-05-01

Using a combination of an automatic cyclone tracking method and a special version of the classical pressure tendency equation (PTE), changes in surface core pressure of extra-tropical cyclones can be related to contributions from horizontal temperature advection, vertical motion and diabatic processes, i.e. mainly latent heat release in clouds. Here, the PTE is evaluated in 3°x3° boxes located over the cyclone positions at 6-hourly basis, thus following the movement of a given storm at each time step. PTE calculations are performed from the surface to 100 hPa. Previous work has shown that this approach can be used to quantify the contribution of diabatic processes to cyclone deepening in an automated way, and can easily be applied to large gridded datasets, in this case ERA-Interim reanalyses. In order to close the mass budget in the PTE, geopotential height tendencies at the upper integration boundary (usually 100 hPa) need to be taken into account. Older studies have assumed this term to be negligible, and this has been confirmed with modern re-analysis data for many explosively deepening storms. However, some historical storms show a remarkable contribution from this term, indicating a substantial warming of the levels above 100hPa. An outstanding example is the Braer Storm of January 1993, which reached a record minimum core pressure of 914 hPa near Iceland. A stepwise increase of the upper integration boundary reveals that substantial geopotential height tendencies reach above 1 hPa. This unusual behaviour appears to be related to the propagation of a deep planetary wave trough from North America towards the North Atlantic basin. A similar but somewhat less dramatic behaviour was found for cyclone Wiebke. Another interesting example is storm Emma, which managed to sustain substantial deepening rates despite adverse positive geopotential height tendencies at 100 hPa. Future work will include a more robust statistical analysis of this problem and a better understanding of the nature and physical mechanism of the stratospheric influence on explosive cyclogenesis.

Inefficiency, heterogeneity and spillover effects in maternal care in India: a spatial stochastic frontier analysis.

PubMed

Kinfu, Yohannes; Sawhney, Monika

2015-03-25

Institutional delivery is one of the key and proven strategies to reduce maternal deaths. Since the 1990s, the government of India has made substantial investment on maternal care to reduce the huge burden of maternal deaths in the country. However, despite the effort access to institutional delivery in India remains below the global average. In addition, even in places where health investments have been comparable, inter- and intra-state difference in access to maternal care services remain wide and substantial. This raises a fundamental question on whether the sub-national units themselves differ in terms of the efficiency with which they use available resources, and if so, why? Data obtained from round 3 of the country's District Level Health and Facility Survey was analyzed to measure the level and determinants of inefficiency of institutional delivery in the country. Analysis was conducted using spatial stochastic frontier models that correct for heterogeneity and spatial interactions between sub-national units. Inefficiency differences in maternal care services between and within states are substantial. The top one third of districts in the country has a mean efficiency score of 90 per cent or more, while the bottom 10 per cent of districts exhibit mean inefficiency score of as high as over 75 per cent or more. Overall mean inefficiency is about 30 per cent. The result also reveals the existence of both heterogeneity and spatial correlation in institutional delivery in the country. Given the high level of inefficiency in the system, further progress in improving coverage of institutional delivery in the country should focus both on improving the efficiency of resource utilization--especially where inefficiency levels are extremely high--and on bringing new resources in to the system. The additional investment should specifically focus on those parts of the country where coverage rates are still low but efficiency levels are already at a high level. In addition, given that inefficiency was also associated inversely with literacy and urbanization and positively related with proportion of households belonging to poor households, investment in these areas can also improve coverage of institutional delivery in the country.

Differential item functioning analysis of the Vanderbilt Expertise Test for cars

PubMed Central

Lee, Woo-Yeol; Cho, Sun-Joo; McGugin, Rankin W.; Van Gulick, Ana Beth; Gauthier, Isabel

2015-01-01

The Vanderbilt Expertise Test for cars (VETcar) is a test of visual learning for contemporary car models. We used item response theory to assess the VETcar and in particular used differential item functioning (DIF) analysis to ask if the test functions the same way in laboratory versus online settings and for different groups based on age and gender. An exploratory factor analysis found evidence of multidimensionality in the VETcar, although a single dimension was deemed sufficient to capture the recognition ability measured by the test. We selected a unidimensional three-parameter logistic item response model to examine item characteristics and subject abilities. The VETcar had satisfactory internal consistency. A substantial number of items showed DIF at a medium effect size for test setting and for age group, whereas gender DIF was negligible. Because online subjects were on average older than those tested in the lab, we focused on the age groups to conduct a multigroup item response theory analysis. This revealed that most items on the test favored the younger group. DIF could be more the rule than the exception when measuring performance with familiar object categories, therefore posing a challenge for the measurement of either domain-general visual abilities or category-specific knowledge. PMID:26418499

Analyzing large-scale proteomics projects with latent semantic indexing.

PubMed

Klie, Sebastian; Martens, Lennart; Vizcaíno, Juan Antonio; Côté, Richard; Jones, Phil; Apweiler, Rolf; Hinneburg, Alexander; Hermjakob, Henning

2008-01-01

Since the advent of public data repositories for proteomics data, readily accessible results from high-throughput experiments have been accumulating steadily. Several large-scale projects in particular have contributed substantially to the amount of identifications available to the community. Despite the considerable body of information amassed, very few successful analyses have been performed and published on this data, leveling off the ultimate value of these projects far below their potential. A prominent reason published proteomics data is seldom reanalyzed lies in the heterogeneous nature of the original sample collection and the subsequent data recording and processing. To illustrate that at least part of this heterogeneity can be compensated for, we here apply a latent semantic analysis to the data contributed by the Human Proteome Organization's Plasma Proteome Project (HUPO PPP). Interestingly, despite the broad spectrum of instruments and methodologies applied in the HUPO PPP, our analysis reveals several obvious patterns that can be used to formulate concrete recommendations for optimizing proteomics project planning as well as the choice of technologies used in future experiments. It is clear from these results that the analysis of large bodies of publicly available proteomics data by noise-tolerant algorithms such as the latent semantic analysis holds great promise and is currently underexploited.

Detecting Large-Scale Brain Networks Using EEG: Impact of Electrode Density, Head Modeling and Source Localization

PubMed Central

Liu, Quanying; Ganzetti, Marco; Wenderoth, Nicole; Mantini, Dante

2018-01-01

Resting state networks (RSNs) in the human brain were recently detected using high-density electroencephalography (hdEEG). This was done by using an advanced analysis workflow to estimate neural signals in the cortex and to assess functional connectivity (FC) between distant cortical regions. FC analyses were conducted either using temporal (tICA) or spatial independent component analysis (sICA). Notably, EEG-RSNs obtained with sICA were very similar to RSNs retrieved with sICA from functional magnetic resonance imaging data. It still remains to be clarified, however, what technological aspects of hdEEG acquisition and analysis primarily influence this correspondence. Here we examined to what extent the detection of EEG-RSN maps by sICA depends on the electrode density, the accuracy of the head model, and the source localization algorithm employed. Our analyses revealed that the collection of EEG data using a high-density montage is crucial for RSN detection by sICA, but also the use of appropriate methods for head modeling and source localization have a substantial effect on RSN reconstruction. Overall, our results confirm the potential of hdEEG for mapping the functional architecture of the human brain, and highlight at the same time the interplay between acquisition technology and innovative solutions in data analysis. PMID:29551969

Validity analysis on merged and averaged data using within and between analysis: focus on effect of qualitative social capital on self-rated health.

PubMed

Shin, Sang Soo; Shin, Young-Jeon

2016-01-01

With an increasing number of studies highlighting regional social capital (SC) as a determinant of health, many studies are using multi-level analysis with merged and averaged scores of community residents' survey responses calculated from community SC data. Sufficient examination is required to validate if the merged and averaged data can represent the community. Therefore, this study analyzes the validity of the selected indicators and their applicability in multi-level analysis. Within and between analysis (WABA) was performed after creating community variables using merged and averaged data of community residents' responses from the 2013 Community Health Survey in Korea, using subjective self-rated health assessment as a dependent variable. Further analysis was performed following the model suggested by WABA result. Both E-test results (1) and WABA results (2) revealed that single-level analysis needs to be performed using qualitative SC variable with cluster mean centering. Through single-level multivariate regression analysis, qualitative SC with cluster mean centering showed positive effect on self-rated health (0.054, p<0.001), although there was no substantial difference in comparison to analysis using SC variables without cluster mean centering or multi-level analysis. As modification in qualitative SC was larger within the community than between communities, we validate that relational analysis of individual self-rated health can be performed within the group, using cluster mean centering. Other tests besides the WABA can be performed in the future to confirm the validity of using community variables and their applicability in multi-level analysis.

Enhanced Structural Stability and Photo Responsiveness of CH3 NH3 SnI3 Perovskite via Pressure-Induced Amorphization and Recrystallization.

PubMed

Lü, Xujie; Wang, Yonggang; Stoumpos, Constantinos C; Hu, Qingyang; Guo, Xiaofeng; Chen, Haijie; Yang, Liuxiang; Smith, Jesse S; Yang, Wenge; Zhao, Yusheng; Xu, Hongwu; Kanatzidis, Mercouri G; Jia, Quanxi

2016-10-01

An organic-inorganic halide CH 3 NH 3 SnI 3 perovskite with significantly improved structural stability is obtained via pressure-induced amorphization and recrystallization. In situ high-pressure resistance measurements reveal an increased electrical conductivity by 300% in the pressure-treated perovskite. Photocurrent measurements also reveal a substantial enhancement in visible-light responsiveness. The mechanism underlying the enhanced properties is shown to be associated with the pressure-induced structural modification. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Environmental footprints of brick kiln bottom ashes: Geostatistical approach for assessment of metal toxicity.

PubMed

Mondal, Ananya; Das, Subhasish; Sah, Rajesh Kumar; Bhattacharyya, Pradip; Bhattacharya, Satya Sundar

2017-12-31

Coal fired brick kiln factories generate significant of brick kiln bottom ash (BKBA) that contaminate soil and water environments of areas near the dumping sites through leaching of toxic metals (Pb, Cr, Cd, Zn, Mn, and Cu). However, characteristics and environmental effects of BKBAs are yet unknown. We collected BKBA samples from 32 strategic locations of two rapidly developing States (West Bengal and Assam) of India. Scanning electron microscope images indicated spherical and granular structures of BKBAs produced in West Bengal (WBKBA) and Assam (ABKBA) respectively; while energy dispersive spectroscopy and analytical assessments confirmed substantial occurrence of total organic C and nutrient elements (N, P, K, Ca, Mg, and S) in both the BKBAs. FTIR analysis revealed greater predominance of organic matter in ABKBAs than WBKBAs. Occurrence of toxic metals (Cd, Cr, Pb, Zn, Mn, and Cu) was higher in ABKBAs than in WBKBAs; while organic and residual fractions of metals were highly predominant in most of the BKBAs. Principal component analysis showed that metal contents and pH were the major distinguishing characteristics of the BKBAs generated in the two different environmental locations. Human health risk associated with BKBAs generated in Assam is of significant concern. Finally, geo-statistical tools enabled to predict the spatial distribution patterns of toxic metals contributed by the BKBAs in Assam and West Bengal respectively. Assessment of contamination index, geo-accumulation index, and ecological risk index revealed some BKBAs to be more toxic than others. Copyright © 2017. Published by Elsevier B.V.

Recovery of urinary nanovesicles from ultracentrifugation supernatants.

PubMed

Musante, Luca; Saraswat, Mayank; Ravidà, Alessandra; Byrne, Barry; Holthofer, Harry

2013-06-01

Urinary vesicles represent a newly established source of biological material, widely considered to faithfully represent pathological events in the kidneys and the urogenital epithelium. The majority of currently applied isolation protocols involve cumbersome centrifugation steps to enrich vesicles from urine. To date, the efficiency of these approaches has not been investigated with respect to performing quantitative and qualitative analyses of vesicle populations in the pellet and supernatant (SN) fractions. After the series of differential centrifugations, the final SN was reduced to one-twentieth of the original volume by ammonium sulphate precipitation, with the precipitate pellet subjected to another round of differential centrifugations. Electron microscopy, dynamic light scattering and western blot analysis were used to characterize the vesicles present in individual fractions of interest. Pellets obtained after the second set of centrifugations at 200 000 g revealed the presence of vesicles which share a common marker profile, but with distinct differences from those seen in the initial 200 000 g pellet used as the reference. This suggests an enrichment of previously uncharacterized urinary vesicles still in solution after the initial centrifugation steps. Analysis of protein yields recovered post-ultracentrifugation revealed an additional 40% of vesicles retained from the SN. Moreover, these structures showed a formidable resistance to harsh treatments (e.g. 95% ammonium sulphate saturation, hypotonic dialysis, 0.3 M sodium hydroxide). Methods which employ differential centrifugations of native urine are remarkably ineffective and may lose a substantial population of biologically important vesicle species.

Heterogeneity of long-history migration explains cultural differences in reports of emotional expressivity and the functions of smiles

PubMed Central

Rychlowska, Magdalena; Miyamoto, Yuri; Matsumoto, David; Hess, Ursula; Gilboa-Schechtman, Eva; Kamble, Shanmukh; Muluk, Hamdi; Masuda, Takahiko; Niedenthal, Paula Marie

2015-01-01

A small number of facial expressions may be universal in that they are produced by the same basic affective states and recognized as such throughout the world. However, other aspects of emotionally expressive behavior vary widely across culture. Just why do they vary? We propose that some cultural differences in expressive behavior are determined by historical heterogeneity, or the extent to which a country’s present-day population descended from migration from numerous vs. few source countries over a period of 500 y. Our reanalysis of data on cultural rules for displaying emotion from 32 countries [n = 5,340; Matsumoto D, Yoo S, Fontaine J (2008) J Cross Cult Psychol 39(1):55–74] reveals that historical heterogeneity explains substantial, unique variance in the degree to which individuals believe that emotions should be openly expressed. We also report an original study of the underlying states that people believe are signified by a smile. Cluster analysis applied to data from nine countries (n = 726), including Canada, France, Germany, India, Indonesia, Israel, Japan, New Zealand, and the United States, reveals that countries group into “cultures of smiling” determined by historical heterogeneity. Factor analysis shows that smiles sort into three social-functional subtypes: pleasure, affiliative, and dominance. The relative importance of these smile subtypes varies as a function of historical heterogeneity. These findings thus highlight the power of social-historical factors to explain cross-cultural variation in emotional expression and smile behavior. PMID:25902500

Heterogeneity of long-history migration explains cultural differences in reports of emotional expressivity and the functions of smiles.

PubMed

Rychlowska, Magdalena; Miyamoto, Yuri; Matsumoto, David; Hess, Ursula; Gilboa-Schechtman, Eva; Kamble, Shanmukh; Muluk, Hamdi; Masuda, Takahiko; Niedenthal, Paula Marie

2015-05-12

A small number of facial expressions may be universal in that they are produced by the same basic affective states and recognized as such throughout the world. However, other aspects of emotionally expressive behavior vary widely across culture. Just why do they vary? We propose that some cultural differences in expressive behavior are determined by historical heterogeneity, or the extent to which a country's present-day population descended from migration from numerous vs. few source countries over a period of 500 y. Our reanalysis of data on cultural rules for displaying emotion from 32 countries [n = 5,340; Matsumoto D, Yoo S, Fontaine J (2008) J Cross Cult Psychol 39(1):55-74] reveals that historical heterogeneity explains substantial, unique variance in the degree to which individuals believe that emotions should be openly expressed. We also report an original study of the underlying states that people believe are signified by a smile. Cluster analysis applied to data from nine countries (n = 726), including Canada, France, Germany, India, Indonesia, Israel, Japan, New Zealand, and the United States, reveals that countries group into "cultures of smiling" determined by historical heterogeneity. Factor analysis shows that smiles sort into three social-functional subtypes: pleasure, affiliative, and dominance. The relative importance of these smile subtypes varies as a function of historical heterogeneity. These findings thus highlight the power of social-historical factors to explain cross-cultural variation in emotional expression and smile behavior.

Searching for missing heritability: Designing rare variant association studies

PubMed Central

Zuk, Or; Schaffner, Stephen F.; Samocha, Kaitlin; Do, Ron; Hechter, Eliana; Kathiresan, Sekar; Daly, Mark J.; Neale, Benjamin M.; Sunyaev, Shamil R.; Lander, Eric S.

2014-01-01

Genetic studies have revealed thousands of loci predisposing to hundreds of human diseases and traits, revealing important biological pathways and defining novel therapeutic hypotheses. However, the genes discovered to date typically explain less than half of the apparent heritability. Because efforts have largely focused on common genetic variants, one hypothesis is that much of the missing heritability is due to rare genetic variants. Studies of common variants are typically referred to as genomewide association studies, whereas studies of rare variants are often simply called sequencing studies. Because they are actually closely related, we use the terms common variant association study (CVAS) and rare variant association study (RVAS). In this paper, we outline the similarities and differences between RVAS and CVAS and describe a conceptual framework for the design of RVAS. We apply the framework to address key questions about the sample sizes needed to detect association, the relative merits of testing disruptive alleles vs. missense alleles, frequency thresholds for filtering alleles, the value of predictors of the functional impact of missense alleles, the potential utility of isolated populations, the value of gene-set analysis, and the utility of de novo mutations. The optimal design depends critically on the selection coefficient against deleterious alleles and thus varies across genes. The analysis shows that common variant and rare variant studies require similarly large sample collections. In particular, a well-powered RVAS should involve discovery sets with at least 25,000 cases, together with a substantial replication set. PMID:24443550

Cooperative cytotoxic activity of Zn and Cu in bovine serum albumin-conjugated ZnS/CuS nano-composites in PC12 cancer cells

NASA Astrophysics Data System (ADS)

Wang, Hua-Jie; Yu, Xue-Hong; Wang, Cai-Feng; Cao, Ying

2013-11-01

Series of self-assembled and mono-dispersed bovine serum albumin (BSA)-conjugated ZnS/CuS nano-composites with different Zn/Cu ratios had been successfully synthesized by a combination method of the biomimetic synthesis and ion-exchange strategy under the gentle conditions. High-resolution transmission electron microscopy observation, Fourier transform infrared spectra and zeta potential analysis demonstrated that BSA-conjugated ZnS/CuS nano-composites with well dispersity had the hierarchical structure and BSA was a key factor to control the morphology and surface electro-negativity of final products. The real-time monitoring by atomic absorption spectroscopy and powder X-ray diffraction revealed that the Zn/Cu ratio of nano-composites could be controlled by adjusting the ion-exchange time. In addition, the metabolic and morphological assays indicated that the metabolic proliferation and spread of rat pheochromocytoma (PC12) cells could be inhibited by nano-composites, with the high anti-cancer activity at a low concentration (4 ppm). What were more important, Zn and Cu in nano-composites exhibited a positive cooperativity at inhibiting cancer cell functions. The microscope observation and biochemical marker analysis clearly revealed that the nano-composites-included lipid peroxidation and disintegration of membrane led to the death of PC12 cells. Summarily, the present study substantiated the potential of BSA-conjugated ZnS/CuS nano-composites as anti-cancer drug.

Comparative Transcriptome Analyses Reveal Potential Mechanisms of Enhanced Drought Tolerance in Transgenic Salvia Miltiorrhiza Plants Expressing AtDREB1A from Arabidopsis.

PubMed

Wei, Tao; Deng, Kejun; Wang, Hongbin; Zhang, Lipeng; Wang, Chunguo; Song, Wenqin; Zhang, Yong; Chen, Chengbin

2018-03-12

In our previous study, drought-resistant transgenic plants of Salvia miltiorrhiza were produced via overexpression of the transcription factor AtDREB1A. To unravel the molecular mechanisms underpinning elevated drought tolerance in transgenic plants, in the present study we compared the global transcriptional profiles of wild-type (WT) and AtDREB1A -expressing transgenic plants using RNA-sequencing (RNA-seq). Using cluster analysis, we identified 3904 differentially expressed genes (DEGs). Compared with WT plants, 423 unigenes were up-regulated in pRD29A::AtDREB1A-31 before drought treatment, while 936 were down-regulated and 1580 and 1313 unigenes were up- and down-regulated after six days of drought. COG analysis revealed that the 'signal transduction mechanisms' category was highly enriched among these DEGs both before and after drought stress. Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation, DEGs associated with "ribosome", "plant hormone signal transduction", photosynthesis", "plant-pathogen interaction", "glycolysis/gluconeogenesis" and "carbon fixation" are hypothesized to perform major functions in drought resistance in AtDREB1A -expressing transgenic plants. Furthermore, the number of DEGs associated with different transcription factors increased significantly after drought stress, especially the AP2/ERF, bZIP and MYB protein families. Taken together, this study substantially expands the transcriptomic information for S. miltiorrhiza and provides valuable clues for elucidating the mechanism of AtDREB1A-mediated drought tolerance in transgenic plants.

Perception of Climate Risk among Rural Farmers in Vietnam: Consistency within Households and with the Empirical Record.

PubMed

Cullen, Alison C; Anderson, C Leigh

2017-03-01

Rural farmers in Vietnamese communes perceive climate risk and potential impacts on livelihood within a complex context that may influence individual and household decisions. In a primary survey of 1,145 residents of the Thach Ha district of Ha Tinh province, we gathered data regarding perception about stability in climate, potential risks to livelihood, demographic characteristics, orientation toward risk, and interest in expanding economic activity. Temporal analysis of meteorological and economic indicator data forms an empirical basis for comparison with human perception. We ask the basic question: Are rural farmers' perceptions of climate consistent with the historical record and reproducible within households? We find that respondents do perceive climate anomalies, with some anchoring on recent extreme events as revealed by climate observational data, and further that spouses disproportionately share perceptions relative to randomly simulated pairings. To put climate-related risk perception in a larger context, we examine patterns across a range of risks to livelihood faced by farmers (livestock disease, pests, markets, health), using dimension reduction techniques. We find that our respondents distinguish among potential causes of low economic productivity, with substantial emphasis on climate-related impacts. They do not express uniform concern across risks, but rather average patterns reveal common modes and distinguish climate concern. Still, among those expressing concern about climate-related risks to livelihood we do not find an association with expressed intention to pursue changes in economic activity as a risk management response. © 2016 Society for Risk Analysis.

Differential transcriptome analysis supports Rhodnius montenegrensis and Rhodnius robustus (Hemiptera, Reduviidae, Triatominae) as distinct species.

PubMed

de Carvalho, Danila Blanco; Congrains, Carlos; Chahad-Ehlers, Samira; Pinotti, Heloisa; Brito, Reinaldo Alves de; da Rosa, João Aristeu

2017-01-01

Chagas disease is one of the main parasitic diseases found in Latin America and it is estimated that between six and seven million people are infected worldwide. Its etiologic agent, the protozoan Trypanosoma cruzi, is transmitted by triatomines, some of which from the genus Rhodnius. Twenty species are currently recognized in this genus, including some closely related species with low levels of morphological differentiation, such as Rhodnius montenegrensis and Rhodnius robustus. In order to investigate genetic differences between these two species, we generated large-scale RNA-sequencing data (consisting of four RNA-seq libraries) from the heads and salivary glands of males of R. montenegrensis and R. robustus. Transcriptome assemblies produced for each species resulted in 64,952 contigs for R. montenegrensis and 70,894 contigs for R. robustus, with N50 of approximately 2,100 for both species. SNP calling based on the more complete R. robustus assembly revealed 3,055 fixed interspecific differences and 216 transcripts with high levels of divergence which contained only fixed differences between the two species. A gene ontology enrichment analysis revealed that these highly differentiated transcripts were enriched for eight GO terms related to AP-2 adaptor complex, as well as other interesting genes that could be involved in their differentiation. The results show that R. montenegrensis and R. robustus have a substantial quantity of fixed interspecific polymorphisms, which suggests a high degree of genetic divergence between the two species and likely corroborates the species status of R. montenegrensis.

Adaptation Genomics of a Small-Colony Variant in a Pseudomonas chlororaphis 30-84 Biofilm

PubMed Central

Dorosky, Robert J.; Han, Cliff S.; Lo, Chien-chi; Dichosa, Armand E. K.; Chain, Patrick S.; Yu, Jun Myoung; Pierson, Leland S.

2014-01-01

The rhizosphere-colonizing bacterium Pseudomonas chlororaphis 30-84 is an effective biological control agent against take-all disease of wheat. In this study, we characterize a small-colony variant (SCV) isolated from a P. chlororaphis 30-84 biofilm. The SCV exhibited pleiotropic phenotypes, including small cell size, slow growth and motility, low levels of phenazine production, and increased biofilm formation and resistance to antimicrobials. To better understand the genetic alterations underlying these phenotypes, RNA and whole-genome sequencing analyses were conducted comparing an SCV to the wild-type strain. Of the genome's 5,971 genes, transcriptomic profiling indicated that 1,098 (18.4%) have undergone substantial reprograming of gene expression in the SCV. Whole-genome sequence analysis revealed multiple alterations in the SCV, including mutations in yfiR (cyclic-di-GMP production), fusA (elongation factor), and cyoE (heme synthesis) and a 70-kb deletion. Genetic analysis revealed that the yfiR locus plays a major role in controlling SCV phenotypes, including colony size, growth, motility, and biofilm formation. Moreover, a point mutation in the fusA gene contributed to kanamycin resistance. Interestingly, the SCV can partially switch back to wild-type morphologies under specific conditions. Our data also support the idea that phenotypic switching in P. chlororaphis is not due to simple genetic reversions but may involve multiple secondary mutations. The emergence of these highly adherent and antibiotic-resistant SCVs within the biofilm might play key roles in P. chlororaphis natural persistence. PMID:25416762

Phylogeography of recently emerged DENV-2 in southern Viet Nam.

PubMed

Rabaa, Maia A; Ty Hang, Vu Thi; Wills, Bridget; Farrar, Jeremy; Simmons, Cameron P; Holmes, Edward C

2010-07-27

Revealing the dispersal of dengue viruses (DENV) in time and space is central to understanding their epidemiology. However, the processes that shape DENV transmission patterns at the scale of local populations are not well understood, particularly the impact of such factors as human population movement and urbanization. Herein, we investigated trends in the spatial dynamics of DENV-2 transmission in the highly endemic setting of southern Viet Nam. Through a phylogeographic analysis of 168 full-length DENV-2 genome sequences obtained from hospitalized dengue cases from 10 provinces in southern Viet Nam, we reveal substantial genetic diversity in both urban and rural areas, with multiple lineages identified in individual provinces within a single season, and indicative of frequent viral migration among communities. Focusing on the recently introduced Asian I genotype, we observed particularly high rates of viral exchange between adjacent geographic areas, and between Ho Chi Minh City, the primary urban center of this region, and populations across southern Viet Nam. Within Ho Chi Minh City, patterns of DENV movement appear consistent with a gravity model of virus dispersal, with viruses traveling across a gradient of population density. Overall, our analysis suggests that Ho Chi Minh City may act as a source population for the dispersal of DENV across southern Viet Nam, and provides further evidence that urban areas of Southeast Asia play a primary role in DENV transmission. However, these data also indicate that more rural areas are also capable of maintaining virus populations and hence fueling DENV evolution over multiple seasons.

BARHL2 differentially regulates the development of retinal amacrine and ganglion neurons

PubMed Central

Ding, Qian; Chen, Hui; Xie, Xiaoling; Libby, Richard T.; Tian, Ning; Gan, Lin

2009-01-01

Summary Through transcriptional regulations the BarH family of homeodomain proteins play essential roles in cell fate specification, cell differentiation, migration and survival. Barhl2, a member of the Barh gene family, is expressed in retinal ganglion cells (RGCs), amacrine cells (ACs) and horizontal cells. Here, to investigate the role of Barhl2 in retinal development, Barhl2 deficient mice were generated. Analysis of AC subtypes in Barhl2 deficient retinas suggests that Barhl2 plays a critical role in AC subtype determination. A significant reduction of glycinergic and GABAergic ACs with a substantial increase in the number of cholinergic ACs was observed in Barhl2-null retinas. Barhl2 is also critical for the development of a normal complement of RGCs. Barhl2 deficiency resulted in a 35% increase in RGCs undergoing apoptosis during development. Genetic analysis revealed that Barhl2 functions downstream of the Atoh7-Pou4f3 regulatory pathway and regulates the maturation and/or survival of RGCs. Thus, BARHL2 appears to have numerous roles in retinal development, including regulating neuronal subtype specification, differentiation, and survival. PMID:19339595

Complete genome characterization of a novel enterovirus type EV-B106 isolated in China, 2012.

PubMed

Tang, Jingjing; Tao, Zexin; Ding, Zhengrong; Zhang, Yong; Zhang, Jie; Tian, Bingjun; Zhao, Zhixian; Zhang, Lifen; Xu, Wenbo

2014-03-03

Human enterovirus B106 (EV-B106) is a recently identified member of enterovirus species B. In this study, we report the complete genomic characterization of an EV-B106 strain (148/YN/CHN/12) isolated from an acute flaccid paralysis patient in Yunnan Province, China. The new strain had 79.2-81.3% nucleotide and 89.1-94.8% amino acid similarity in the VP1 region with the other two EV-B106 strains from Bolivia and Pakistan. When compared with other EV serotypes, it had the highest (73.3%) VP1 nucleotide similarity with the EV-B77 prototype strain CF496-99. However, when aligned with all EV-B106 and EV-B77 sequences available from the GenBank database, two major frame shifts were observed in the VP1 coding region, which resulted in substantial (20.5%) VP1 amino acid divergence between the two serotypes. Phylogenetic analysis and similarity plot analysis revealed multiple recombination events in the genome of this strain. This is the first report of the complete genome of EV-B106.

Verification of Anderson Superexchange in MnO via Magnetic Pair Distribution Function Analysis and ab initio Theory.

PubMed

Frandsen, Benjamin A; Brunelli, Michela; Page, Katharine; Uemura, Yasutomo J; Staunton, Julie B; Billinge, Simon J L

2016-05-13

We present a temperature-dependent atomic and magnetic pair distribution function (PDF) analysis of neutron total scattering measurements of antiferromagnetic MnO, an archetypal strongly correlated transition-metal oxide. The known antiferromagnetic ground-state structure fits the low-temperature data closely with refined parameters that agree with conventional techniques, confirming the reliability of the newly developed magnetic PDF method. The measurements performed in the paramagnetic phase reveal significant short-range magnetic correlations on a ∼1  nm length scale that differ substantially from the low-temperature long-range spin arrangement. Ab initio calculations using a self-interaction-corrected local spin density approximation of density functional theory predict magnetic interactions dominated by Anderson superexchange and reproduce the measured short-range magnetic correlations to a high degree of accuracy. Further calculations simulating an additional contribution from a direct exchange interaction show much worse agreement with the data. The Anderson superexchange model for MnO is thus verified by experimentation and confirmed by ab initio theory.

Disambiguating brain functional connectivity.

PubMed

Duff, Eugene P; Makin, Tamar; Cottaar, Michiel; Smith, Stephen M; Woolrich, Mark W

2018-06-01

Functional connectivity (FC) analyses of correlations of neural activity are used extensively in neuroimaging and electrophysiology to gain insights into neural interactions. However, analyses assessing changes in correlation fail to distinguish effects produced by sources as different as changes in neural signal amplitudes or noise levels. This ambiguity substantially diminishes the value of FC for inferring system properties and clinical states. Network modelling approaches may avoid ambiguities, but require specific assumptions. We present an enhancement to FC analysis with improved specificity of inferences, minimal assumptions and no reduction in flexibility. The Additive Signal Change (ASC) approach characterizes FC changes into certain prevalent classes of signal change that involve the input of additional signal to existing activity. With FMRI data, the approach reveals a rich diversity of signal changes underlying measured changes in FC, suggesting that it could clarify our current understanding of FC changes in many contexts. The ASC method can also be used to disambiguate other measures of dependency, such as regression and coherence, providing a flexible tool for the analysis of neural data. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Understanding the motives for food choice in Western Balkan Countries.

PubMed

Milošević, Jasna; Žeželj, Iris; Gorton, Matthew; Barjolle, Dominique

2012-02-01

Substantial empirical evidence exists regarding the importance of different factors underlying food choice in Western Europe. However, research results on eating habits and food choice in the Western Balkan Countries (WBCs) remain scarce. A Food Choice Questionnaire (FCQ), an instrument that measures the reported importance of nine factors underlying food choice, was administered to a representative sample of 3085 adult respondents in six WBCs. The most important factors reported are sensory appeal, purchase convenience, and health and natural content; the least important are ethical concern and familiarity. The ranking of food choice motives across WBCs was strikingly similar. Factor analysis revealed eight factors compared to nine in the original FCQ model: health and natural content scales loaded onto one factor as did familiarity and ethical concern; the convenience scale items generated two factors, one related to purchase convenience and the other to preparation convenience. Groups of consumers with similar motivational profiles were identified using cluster analysis. Each cluster has distinct food purchasing behavior and socio-economic characteristics, for which appropriate public health communication messages can be drawn. Copyright © 2011 Elsevier Ltd. All rights reserved.

Effects of soil and topographic factors on vegetation restoration in opencast coal mine dumps located in a loess area

NASA Astrophysics Data System (ADS)

Wang, Jinman; Wang, Hongdan; Cao, Yingui; Bai, Zhongke; Qin, Qian

2016-02-01

Vegetation plays an important role in improving and restoring fragile ecological environments. In the Antaibao opencast coal mine, located in a loess area, the eco-environment has been substantially disturbed by mining activities, and the relationship between the vegetation and environmental factors is not very clear. Therefore, it is crucial to understand the effects of soil and topographic factors on vegetation restoration to improve the fragile ecosystems of damaged land. An investigation of the soil, topography and vegetation in 50 reclamation sample plots in Shanxi Pingshuo Antaibao opencast coal mine dumps was performed. Statistical analyses in this study included one-way ANOVA and significance testing using SPSS 20.0, and multivariate techniques of detrended correspondence analysis (DCA) and redundancy analysis (RDA) using CANOCO 4.5. The RDA revealed the environmental factors that affected vegetation restoration. Various vegetation and soil variables were significantly correlated. The available K and rock content were good explanatory variables, and they were positively correlated with tree volume. The effects of the soil factors on vegetation restoration were higher than those of the topographic factors.

Effects of soil and topographic factors on vegetation restoration in opencast coal mine dumps located in a loess area

PubMed Central

Wang, Jinman; Wang, Hongdan; Cao, Yingui; Bai, Zhongke; Qin, Qian

2016-01-01

Vegetation plays an important role in improving and restoring fragile ecological environments. In the Antaibao opencast coal mine, located in a loess area, the eco-environment has been substantially disturbed by mining activities, and the relationship between the vegetation and environmental factors is not very clear. Therefore, it is crucial to understand the effects of soil and topographic factors on vegetation restoration to improve the fragile ecosystems of damaged land. An investigation of the soil, topography and vegetation in 50 reclamation sample plots in Shanxi Pingshuo Antaibao opencast coal mine dumps was performed. Statistical analyses in this study included one-way ANOVA and significance testing using SPSS 20.0, and multivariate techniques of detrended correspondence analysis (DCA) and redundancy analysis (RDA) using CANOCO 4.5. The RDA revealed the environmental factors that affected vegetation restoration. Various vegetation and soil variables were significantly correlated. The available K and rock content were good explanatory variables, and they were positively correlated with tree volume. The effects of the soil factors on vegetation restoration were higher than those of the topographic factors. PMID:26916152

Effects of soil and topographic factors on vegetation restoration in opencast coal mine dumps located in a loess area.

PubMed

Wang, Jinman; Wang, Hongdan; Cao, Yingui; Bai, Zhongke; Qin, Qian

2016-02-26

Vegetation plays an important role in improving and restoring fragile ecological environments. In the Antaibao opencast coal mine, located in a loess area, the eco-environment has been substantially disturbed by mining activities, and the relationship between the vegetation and environmental factors is not very clear. Therefore, it is crucial to understand the effects of soil and topographic factors on vegetation restoration to improve the fragile ecosystems of damaged land. An investigation of the soil, topography and vegetation in 50 reclamation sample plots in Shanxi Pingshuo Antaibao opencast coal mine dumps was performed. Statistical analyses in this study included one-way ANOVA and significance testing using SPSS 20.0, and multivariate techniques of detrended correspondence analysis (DCA) and redundancy analysis (RDA) using CANOCO 4.5. The RDA revealed the environmental factors that affected vegetation restoration. Various vegetation and soil variables were significantly correlated. The available K and rock content were good explanatory variables, and they were positively correlated with tree volume. The effects of the soil factors on vegetation restoration were higher than those of the topographic factors.

Synthesis and physicochemical properties of bis(L-asparaginato) zinc(II): A promising new semiorganic crystal with high laser damage threshold for shorter wavelength generation

NASA Astrophysics Data System (ADS)

Subhashini, R.; Arjunan, S.

2018-05-01

An exceedingly apparent nonlinear semiorganic optical crystals of bis(L-asparaginato)zinc(II) [BLAZ], was synthesized by a traditional slow evaporation solution growth technique. The cell parameters were estimated from single crystal X-ray diffraction analysis. Spectroscopic study substantiates the presence of functional groups. The UV spectrum shows the sustenance of wide transparency window and several optical constants, such as extinction coefficient (K), refractive index, optical conductivity and electric susceptibility with real and imaginary parts of dielectric constant were calculated using the transmittance data. The fluorescence emission spectrum of the crystal pronounces red emission. The laser induced surface damage threshold of the crystal was measured using Nd:YAG laser. The output intensity of second harmonic generation was estimated using the Kurtz and Perry powder method. The hardness stability was investigated by Vickers microhardness test. The decomposition and thermal stability of the compound were scrutinized by TGA-DSC studies. Dielectric studies were carried out to anatomize the electrical properties of the crystal. SEM analysis reveals the existence of minute crystallites on the growth surface.

The Effects of Mobile-Computer-Supported Collaborative Learning: Meta-Analysis and Critical Synthesis.

PubMed

Sung, Yao-Ting; Yang, Je-Ming; Lee, Han-Yueh

2017-08-01

One of the trends in collaborative learning is using mobile devices for supporting the process and products of collaboration, which has been forming the field of mobile-computer-supported collaborative learning (mCSCL). Although mobile devices have become valuable collaborative learning tools, evaluative evidence for their substantial contributions to collaborative learning is still scarce. The present meta-analysis, which included 48 peer-reviewed journal articles and doctoral dissertations written over a 16-year period (2000-2015) involving 5,294 participants, revealed that mCSCL has produced meaningful improvements for collaborative learning, with an overall mean effect size of 0.516. Moderator variables, such as domain subject, group size, teaching method, intervention duration, and reward method were related to different effect sizes. The results provided implications for future research and practice, such as suggestions on how to appropriately use the functionalities of mobile devices, how to best leverage mCSCL through effective group learning mechanisms, and what outcome variables should be included in future studies to fully elucidate the process and products of mCSCL.

Technical indicators of economic performance in dairy sheep farming.

PubMed

Theodoridis, A; Ragkos, A; Roustemis, D; Arsenos, G; Abas, Z; Sinapis, E

2014-01-01

In this study, the level of technical efficiency of 58 sheep farms rearing the Chios breed in Greece was measured through the application of the stochastic frontier analysis method. A Translog stochastic frontier production function was estimated using farm accounting data of Chios sheep farms and the impact of various socio-demographic and biophysical factors on the estimated efficiency of the farms was evaluated. The farms were classified into efficiency groups on the basis of the estimated level of efficiency and a technical and economic descriptive analysis was applied in order to illustrate an indicative picture of their structure and productivity. The results of the stochastic frontier model indicate that there are substantial production inefficiencies among the Chios sheep farms and that these farms could increase their production through the improvement of technical efficiency, whereas the results of the inefficiency effects model reveal that the farm-specific explanatory factors can partly explain the observed efficiency differentials. The measurement of technical inefficiency and the detection of its determinants can be used to form the basis of policy recommendations that could contribute to the development of the sector.

MtPAR MYB transcription factor acts as an on switch for proanthocyanidin biosynthesis in Medicago truncatula

PubMed Central

Verdier, Jerome; Zhao, Jian; Torres-Jerez, Ivone; Ge, Shujun; Liu, Chenggang; He, Xianzhi; Mysore, Kirankumar S.; Dixon, Richard A.; Udvardi, Michael K.

2012-01-01

MtPAR (Medicago truncatula proanthocyanidin regulator) is an MYB family transcription factor that functions as a key regulator of proanthocyanidin (PA) biosynthesis in the model legume Medicago truncatula. MtPAR expression is confined to the seed coat, the site of PA accumulation. Loss-of-function par mutants contained substantially less PA in the seed coat than the wild type, whereas levels of anthocyanin and other specialized metabolites were normal in the mutants. In contrast, massive accumulation of PAs occurred when MtPAR was expressed ectopically in transformed hairy roots of Medicago. Transcriptome analysis of par mutants and MtPAR-expressing hairy roots, coupled with yeast one-hybrid analysis, revealed that MtPAR positively regulates genes encoding enzymes of the flavonoid–PA pathway via a probable activation of WD40-1. Expression of MtPAR in the forage legume alfalfa (Medicago sativa) resulted in detectable levels of PA in shoots, highlighting the potential of this gene for biotechnological strategies to increase PAs in forage legumes for reduction of pasture bloat in ruminant animals. PMID:22307644

Modeling the influence of LASIK surgery on optical properties of the human eye

NASA Astrophysics Data System (ADS)

Szul-Pietrzak, Elżbieta; Hachoł, Andrzej; Cieślak, Krzysztof; Drożdż, Ryszard; Podbielska, Halina

2011-11-01

The aim was to model the influence of LASIK surgery on the optical parameters of the human eye and to ascertain which factors besides the central corneal radius of curvature and central thickness play the major role in postsurgical refractive change. Ten patients were included in the study. Pre- and postsurgical measurements included standard refraction, anterior corneal curvature and pachymetry. The optical model used in the analysis was based on the Le Grand and El Hage schematic eye, modified by the measured individual parameters of corneal geometry. A substantial difference between eye refractive error measured after LASIK and estimated from the eye model was observed. In three patients, full correction of the refractive error was achieved. However, analysis of the visual quality in terms of spot diagrams and optical transfer functions of the eye optical system revealed some differences in these measurements. This suggests that other factors besides corneal geometry may play a major role in postsurgical refraction. In this paper we investigated whether the biomechanical properties of the eyeball and changes in intraocular pressure could account for the observed discrepancies.

Verification of Anderson superexchange in MnO via magnetic pair distribution function analysis and ab initio theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Benjamin A. Frandsen; Brunelli, Michela; Page, Katharine

Here, we present a temperature-dependent atomic and magnetic pair distribution function (PDF) analysis of neutron total scattering measurements of antiferromagnetic MnO, an archetypal strongly correlated transition-metal oxide. The known antiferromagnetic ground-state structure fits the low-temperature data closely with refined parameters that agree with conventional techniques, confirming the reliability of the newly developed magnetic PDF method. The measurements performed in the paramagnetic phase reveal significant short-range magnetic correlations on a ~1 nm length scale that differ substantially from the low-temperature long-range spin arrangement. Ab initio calculations using a self-interaction-corrected local spin density approximation of density functional theory predict magnetic interactions dominatedmore » by Anderson superexchange and reproduce the measured short-range magnetic correlations to a high degree of accuracy. Further calculations simulating an additional contribution from a direct exchange interaction show much worse agreement with the data. Furthermore, the Anderson superexchange model for MnO is thus verified by experimentation and confirmed by ab initio theory.« less

Common variant at 16p11.2 conferring risk of psychosis.

PubMed

Steinberg, S; de Jong, S; Mattheisen, M; Costas, J; Demontis, D; Jamain, S; Pietiläinen, O P H; Lin, K; Papiol, S; Huttenlocher, J; Sigurdsson, E; Vassos, E; Giegling, I; Breuer, R; Fraser, G; Walker, N; Melle, I; Djurovic, S; Agartz, I; Tuulio-Henriksson, A; Suvisaari, J; Lönnqvist, J; Paunio, T; Olsen, L; Hansen, T; Ingason, A; Pirinen, M; Strengman, E; Hougaard, D M; Orntoft, T; Didriksen, M; Hollegaard, M V; Nordentoft, M; Abramova, L; Kaleda, V; Arrojo, M; Sanjuán, J; Arango, C; Etain, B; Bellivier, F; Méary, A; Schürhoff, F; Szoke, A; Ribolsi, M; Magni, V; Siracusano, A; Sperling, S; Rossner, M; Christiansen, C; Kiemeney, L A; Franke, B; van den Berg, L H; Veldink, J; Curran, S; Bolton, P; Poot, M; Staal, W; Rehnstrom, K; Kilpinen, H; Freitag, C M; Meyer, J; Magnusson, P; Saemundsen, E; Martsenkovsky, I; Bikshaieva, I; Martsenkovska, I; Vashchenko, O; Raleva, M; Paketchieva, K; Stefanovski, B; Durmishi, N; Pejovic Milovancevic, M; Lecic Tosevski, D; Silagadze, T; Naneishvili, N; Mikeladze, N; Surguladze, S; Vincent, J B; Farmer, A; Mitchell, P B; Wright, A; Schofield, P R; Fullerton, J M; Montgomery, G W; Martin, N G; Rubino, I A; van Winkel, R; Kenis, G; De Hert, M; Réthelyi, J M; Bitter, I; Terenius, L; Jönsson, E G; Bakker, S; van Os, J; Jablensky, A; Leboyer, M; Bramon, E; Powell, J; Murray, R; Corvin, A; Gill, M; Morris, D; O'Neill, F A; Kendler, K; Riley, B; Craddock, N; Owen, M J; O'Donovan, M C; Thorsteinsdottir, U; Kong, A; Ehrenreich, H; Carracedo, A; Golimbet, V; Andreassen, O A; Børglum, A D; Mors, O; Mortensen, P B; Werge, T; Ophoff, R A; Nöthen, M M; Rietschel, M; Cichon, S; Ruggeri, M; Tosato, S; Palotie, A; St Clair, D; Rujescu, D; Collier, D A; Stefansson, H; Stefansson, K

2014-01-01

Epidemiological and genetic data support the notion that schizophrenia and bipolar disorder share genetic risk factors. In our previous genome-wide association study, meta-analysis and follow-up (totaling as many as 18 206 cases and 42 536 controls), we identified four loci showing genome-wide significant association with schizophrenia. Here we consider a mixed schizophrenia and bipolar disorder (psychosis) phenotype (addition of 7469 bipolar disorder cases, 1535 schizophrenia cases, 333 other psychosis cases, 808 unaffected family members and 46 160 controls). Combined analysis reveals a novel variant at 16p11.2 showing genome-wide significant association (rs4583255[T]; odds ratio=1.08; P=6.6 × 10(-11)). The new variant is located within a 593-kb region that substantially increases risk of psychosis when duplicated. In line with the association of the duplication with reduced body mass index (BMI), rs4583255[T] is also associated with lower BMI (P=0.0039 in the public GIANT consortium data set; P=0.00047 in 22 651 additional Icelanders).

[Caricatures of aging in German newspapers and magazine cartoons. Historical comparison between the 1960s and the present].

PubMed

Polanski, F

2014-06-01

The focus of this study was the collective images of aging that were unconsciously used despite rationally led social discourse on aging. Hypothesized was that despite changes in aging over the last 50 years these images went unaltered and thereby negative stereotypes of previous generations were maintained. In an effort to verify this hypothesis images of aging in cartoons were empirically examined, a first in the field of German language. Using a social scientific operationalization of age stereotypes and culturally historical topoi as a basis, a content analysis was conducted on 2,546 cartoons (with 8,882 characters) from the years 1960-1964 and 2007. In general both young and old age are equally encoded with negative connotations by deficient characteristics and acknowledged stereotypes partially significantly more often in the cartoons from 2007 than from 1960-1964. The last 50 years have seen no substantial changes in the images of aging as depicted by magazine and newspaper cartoons. Humor requires more frequent analysis as it often unconsciously reveals socially unacceptable images of aging, even those embedded in science.