Fine-mapping of qGW4.05, a major QTL for kernel weight and size in maize.

PubMed

Chen, Lin; Li, Yong-xiang; Li, Chunhui; Wu, Xun; Qin, Weiwei; Li, Xin; Jiao, Fuchao; Zhang, Xiaojing; Zhang, Dengfeng; Shi, Yunsu; Song, Yanchun; Li, Yu; Wang, Tianyu

2016-04-12

Kernel weight and size are important components of grain yield in cereals. Although some information is available concerning the map positions of quantitative trait loci (QTL) for kernel weight and size in maize, little is known about the molecular mechanisms of these QTLs. qGW4.05 is a major QTL that is associated with kernel weight and size in maize. We combined linkage analysis and association mapping to fine-map and identify candidate gene(s) at qGW4.05. QTL qGW4.05 was fine-mapped to a 279.6-kb interval in a segregating population derived from a cross of Huangzaosi with LV28. By combining the results of regional association mapping and linkage analysis, we identified GRMZM2G039934 as a candidate gene responsible for qGW4.05. Candidate gene-based association mapping was conducted using a panel of 184 inbred lines with variable kernel weights and kernel sizes. Six polymorphic sites in the gene GRMZM2G039934 were significantly associated with kernel weight and kernel size. The results of linkage analysis and association mapping revealed that GRMZM2G039934 is the most likely candidate gene for qGW4.05. These results will improve our understanding of the genetic architecture and molecular mechanisms underlying kernel development in maize.

The flounder organic anion transporter fOat has sequence, function, and substrate specificity similarity to both mammalian Oat1 and Oat3

PubMed Central

Aslamkhan, Amy G.; Thompson, Deborah M.; Perry, Jennifer L.; Bleasby, Kelly; Wolff, Natascha A.; Barros, Scott; Miller, David S.; Pritchard, John B.

2007-01-01

The flounder renal organic anion transporter (fOat) has substantial sequence homology to mammalian basolateral organic anion transporter orthologs (OAT1/Oat1 and OAT3/Oat3), suggesting that fOat may have functional properties of both mammalian forms. We therefore compared uptake of various substrates by rat Oat1 and Oat3 and human OAT1 and OAT3 with the fOat clone expressed in Xenopus oocytes. These data confirm that estrone sulfate is an excellent substrate for mammalian OAT3/Oat3 transporters but not for OAT1/Oat1 transporters. In contrast, 2,4-dichlorophenoxyacetic acid and adefovir are better transported by mammalian OAT1/Oat1 than by the OAT3/Oat3 clones. All three substrates were well transported by fOat-expressing Xenopus oocytes. fOat Km values were comparable to those obtained for mammalian OAT/Oat1/3 clones. We also characterized the ability of these substrates to inhibit uptake of the fluorescent substrate fluorescein in intact teleost proximal tubules isolated from the winter flounder (Pseudopleuronectes americanus) and killifish (Fundulus heteroclitus). The rank order of the IC50 values for inhibition of cellular fluorescein accumulation was similar to that for the Km values obtained in fOat-expressing oocytes, suggesting that fOat may be the primary teleost renal basolateral Oat. Assessment of the zebrafish (Danio rerio) genome indicated the presence of a single Oat (zfOat) with similarity to both mammalian OAT1/Oat1 and OAT3/Oat3. The puffer fish (Takifugu rubripes) also has an Oat (pfOat) similar to mammalian OAT1/Oat1 and OAT3/Oat3 members. Furthermore, phylogenetic analyses argue that the teleost Oat1/3-like genes diverged from a common ancestral gene in advance of the divergence of the mammalian OAT1/Oat1, OAT3/Oat3, and, possibly, Oat6 genes. PMID:16857889

The Conserved and Unique Genetic Architecture of Kernel Size and Weight in Maize and Rice1[OPEN

PubMed Central

Lan, Liu; Wang, Hongze; Xu, Yuancheng; Yang, Xiaohong; Li, Wenqiang; Tong, Hao; Xiao, Yingjie; Pan, Qingchun; Qiao, Feng; Raihan, Mohammad Sharif; Liu, Haijun; Yang, Ning; Wang, Xiaqing; Deng, Min; Jin, Minliang; Zhao, Lijun; Luo, Xin; Zhan, Wei; Liu, Nannan; Wang, Hong; Chen, Gengshen

2017-01-01

Maize (Zea mays) is a major staple crop. Maize kernel size and weight are important contributors to its yield. Here, we measured kernel length, kernel width, kernel thickness, hundred kernel weight, and kernel test weight in 10 recombinant inbred line populations and dissected their genetic architecture using three statistical models. In total, 729 quantitative trait loci (QTLs) were identified, many of which were identified in all three models, including 22 major QTLs that each can explain more than 10% of phenotypic variation. To provide candidate genes for these QTLs, we identified 30 maize genes that are orthologs of 18 rice (Oryza sativa) genes reported to affect rice seed size or weight. Interestingly, 24 of these 30 genes are located in the identified QTLs or within 1 Mb of the significant single-nucleotide polymorphisms. We further confirmed the effects of five genes on maize kernel size/weight in an independent association mapping panel with 540 lines by candidate gene association analysis. Lastly, the function of ZmINCW1, a homolog of rice GRAIN INCOMPLETE FILLING1 that affects seed size and weight, was characterized in detail. ZmINCW1 is close to QTL peaks for kernel size/weight (less than 1 Mb) and contains significant single-nucleotide polymorphisms affecting kernel size/weight in the association panel. Overexpression of this gene can rescue the reduced weight of the Arabidopsis (Arabidopsis thaliana) homozygous mutant line in the AtcwINV2 gene (Arabidopsis ortholog of ZmINCW1). These results indicate that the molecular mechanisms affecting seed development are conserved in maize, rice, and possibly Arabidopsis. PMID:28811335

Evolution of the Oat Genetic Road Map: From Tetraploid to Hexaploid

USDA-ARS?s Scientific Manuscript database

The development of a genetic linkage map for hexaploid oat (Avena sativa L. 2n = 6 x = 42) that defines all 21 chromosomes has been hindered due to the lack of oat-based markers and the size and complexity of the oat genome. Recent efforts in oat DArT, SSR, and SNP marker development should improve...

QTL detection for wheat kernel size and quality and the responses of these traits to low nitrogen stress.

PubMed

Cui, Fa; Fan, Xiaoli; Chen, Mei; Zhang, Na; Zhao, Chunhua; Zhang, Wei; Han, Jie; Ji, Jun; Zhao, Xueqiang; Yang, Lijuan; Zhao, Zongwu; Tong, Yiping; Wang, Tao; Li, Junming

2016-03-01

QTLs for kernel characteristics and tolerance to N stress were identified, and the functions of ten known genes with regard to these traits were specified. Kernel size and quality characteristics in wheat (Triticum aestivum L.) ultimately determine the end use of the grain and affect its commodity price, both of which are influenced by the application of nitrogen (N) fertilizer. This study characterized quantitative trait loci (QTLs) for kernel size and quality and examined the responses of these traits to low-N stress using a recombinant inbred line population derived from Kenong 9204 × Jing 411. Phenotypic analyses were conducted in five trials that each included low- and high-N treatments. We identified 109 putative additive QTLs for 11 kernel size and quality characteristics and 49 QTLs for tolerance to N stress, 27 and 14 of which were stable across the tested environments, respectively. These QTLs were distributed across all wheat chromosomes except for chromosomes 3A, 4D, 6D, and 7B. Eleven QTL clusters that simultaneously affected kernel size- and quality-related traits were identified. At nine locations, 25 of the 49 QTLs for N deficiency tolerance coincided with the QTLs for kernel characteristics, indicating their genetic independence. The feasibility of indirect selection of a superior genotype for kernel size and quality under high-N conditions in breeding programs designed for a lower input management system are discussed. In addition, we specified the functions of Glu-A1, Glu-B1, Glu-A3, Glu-B3, TaCwi-A1, TaSus2, TaGS2-D1, PPO-D1, Rht-B1, and Ha with regard to kernel characteristics and the sensitivities of these characteristics to N stress. This study provides useful information for the genetic improvement of wheat kernel size, quality, and resistance to N stress.

Sorption of copper, zinc and cobalt by oat and oat products.

PubMed

Górecka, Danuta; Stachowiak, Jadwiga

2002-04-01

We determined copper, zinc and cobalt sorption by oat and its products under variable pH conditions as well as the content of neutral dietary fiber (NDF) and its fractional composition. Adsorbents in a model sorption system were: oat, dehulled oat, oats bran and oats flakes. Three various buffers (pH 1.8, 6.6 and 8.7) were used as dispersing solutions. Results collected during this study indicate that copper, zinc and cobalt sorption is significantly affected by the type of cereal raw material. Zinc and copper ions are subjected to higher sorption than cobalt ions. Examined metal ions were subjected to high sorption under conditions corresponding to the duodenum environment (pH 8.7), regardless of the kind of adsorbent. A little lower sorption capacity is observed under conditions close to the neutral environment, while the lowest one is found in environment reflecting conditions of stomach juice (pH 1.8). Zinc ions are bound intensively by dehulled oat, while oats flakes bound mostly copper and cobalt, independently on environmental conditions. Contents of dietary fiber in oat, dehulled oat, oat bran and oat flakes were: 40.1, 19.3, 20.3 and 14.3%, respectively. The dominating fraction in all oat products was the fraction of hemicelluloses. The content of remaining fractions varies in dependence on the product.

Effects of Wheat and Oat-Based Whole Grain Foods on Serum Lipoprotein Size and Distribution in Overweight Middle Aged People: A Randomised Controlled Trial

PubMed Central

Tighe, Paula; Duthie, Garry; Brittenden, Julie; Vaughan, Nicholas; Mutch, William; Simpson, William G.; Duthie, Susan; Horgan, Graham W.; Thies, Frank

2013-01-01

Introduction Epidemiological studies suggest three daily servings of whole-grain foods (WGF) might lower cardiovascular disease risk, at least partly by lowering serum lipid levels. We have assessed the effects of consuming three daily portions of wholegrain food (provided as wheat or a mixture of wheat and oats) on lipoprotein subclass size and concentration in a dietary randomised controlled trial involving middle aged healthy individuals. Methods After a 4-week run-in period on a refined diet, volunteers were randomly allocated to a control (refined diet), wheat, or wheat + oats group for 12 weeks. Our servings were determined in order to significantly increase the intakes of non starch polysaccharides to the UK Dietary Reference Value of 18 g per day in the whole grain groups (18.5 g and 16.8 g per day in the wheat and wheat + oats groups respectively in comparison with 11.3 g per day in the control group). Outcome measures were serum lipoprotein subclasses' size and concentration. Habitual dietary intake was assessed prior and during the intervention. Of the 233 volunteers recruited, 24 withdrew and 3 were excluded. Results At baseline, significant associations were found between lipoprotein size and subclasses' concentrations and some markers of cardiovascular risk such as insulin resistance, blood pressure and serum Inter cellular adhesion molecule 1 concentration. Furthermore, alcohol and vitamin C intake were positively associated with an anti-atherogenic lipoprotein profile, with regards to lipoprotein size and subclasses' distribution. However, none of the interventions with whole grain affected lipoprotein size and profile. Conclusion Our results indicate that three portions of wholegrain foods, irrelevant of the type (wheat or oat-based) do not reduce cardiovascular risk by beneficially altering the size and distribution of lipoprotein subclasses. Trial Registration www.Controlled-Trials.com ISRCTN 27657880. PMID:23940575

Particle size of wheat, maize, and oat test meals: effects on plasma glucose and insulin responses and on the rate of starch digestion in vitro.

PubMed

Heaton, K W; Marcus, S N; Emmett, P M; Bolton, C H

1988-04-01

When normal volunteers ate isocaloric wheat-based meals, their plasma insulin responses (peak concentration and area under curve) increased stepwise: whole grains less than cracked grains less than coarse flour less than fine flour. Insulin responses were also greater with fine maizemeal than with whole or cracked maize grains but were similar with whole groats, rolled oats, and fine oatmeal. The peak-to-nadir swing of plasma glucose was greater with wheat flour than with cracked or whole grains. In vitro starch hydrolysis by pancreatic amylase was faster with decreasing particle size with all three cereals. Correlation with the in vivo data was imperfect. Oat-based meals evoked smaller glucose and insulin responses than wheat- or maize-based meals. Particle size influences the digestion rate and consequent metabolic effects of wheat and maize but not oats. The increased insulin response to finely ground flour may be relevant to the etiology of diseases associated with hyperinsulinemia and to the management of diabetes.

Effect of kernel size and mill type on protein, milling yield, and baking quality of hard red spring wheat

USDA-ARS?s Scientific Manuscript database

Optimization of flour yield and quality is important in the milling industry. The objective of this study was to determine the effect of kernel size and mill type on flour yield and end-use quality. A hard red spring wheat composite sample was segregated, based on kernel size, into large, medium, ...

Light qualities and dose influence ascorbate pool size in detached oat leaves.

PubMed

Mastropasqua, Linda; Borraccino, Giuseppe; Bianco, Laura; Paciolla, Costantino

2012-02-01

In this work, we studied the mechanism of light influence on AsA pool size in Avena sativa L. under the effects of low intensity light at different wavelengths. Exposure to low intensity light of oat leaf segments incubated in water or in l-galactono-1,4-lactone (GL), resulted in an increase in AsA content compared with the dark control. This increase was due to modulation of l-galactono-1,4-lactone dehydrogenase (GLDH; EC 1.3.2.3) light-dependent activity and was dependent on the size of the endogenous GL pool. Both blue and red light were effective in increasing AsA, and this increase depended on both exposure time and light intensity. Protein biosynthesis, photosynthesis and calcium were involved in controlling the level of light-dependent AsA. We suggest that multiple checkpoints correlated to the presence of light underlie the ascorbate pool size. The presence of a light-activated switch for the maintenance of an adequate AsA level seems to be necessary for the various tasks of scavenging reactive oxygen species, in response to the dark-light cycle which plants experience under natural conditions. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Ornithine aminotransferase (OAT): recombination between an X-linked OAT sequence (7.5 kb) and the Norrie disease locus.

PubMed

Ngo, J T; Bateman, J B; Spence, M A; Cortessis, V; Sparkes, R S; Kivlin, J D; Mohandas, T; Inana, G

1990-01-01

A human ornithine aminotransferase (OAT) locus has been mapped to the Xp11.2, as has the Norrie disease locus. We used a cDNA probe to investigate a 3-generation UCLA family with Norrie disease; a 4.2-kb RFLP was detected and a maximum lod score of 0.602 at zero recombination fraction was calculated. We used the same probe to study a second multigeneration family with Norrie disease from Utah. A different RFLP of 7.5 kb in size was identified and a recombinational event between the OAT locus represented by this RFLP and the disease loci was observed. Linkage analysis of these two loci in this family revealed a maximum load score of 1.88 at a recombination fraction of 0.10. Although both families have affected members with the same disease, the lod scores are reported separately because the 4.2- and 7.5-kb RFLPs may represent two different loci for the X-linked OAT.

Responses of Oat Grains to Fusarium poae and F. langsethiae Infections and Mycotoxin Contaminations

PubMed Central

Martin, Charlotte; Schöneberg, Torsten; Morisoli, Romina; Bertossa, Mario; Bucheli, Thomas D.; Mauch-Mani, Brigitte; Mascher, Fabio

2018-01-01

Recent increases of Fusarium head blight (FHB) disease caused by infections with F. poae (FP) and F. langsethiae (FL) have been observed in oats. These pathogens are producers of nivalenol (NIV) and T-2/HT-2 toxin (T-2/HT-2), respectively, which are now considered major issues for cereal food and feed safety. To date, the impact of FP and FL on oat grains has not yet been identified, and little is known about oat resistance elements against these pathogens. In the present study, the impact of FL and FP on oat grains was assessed under different environmental conditions in field experiments with artificial inoculations. The severity of FP and FL infection on grains were compared across three field sites, and the resistance against NIV and T-2/HT2 accumulation was assessed for seven oat genotypes. Grain weight, β-glucan content, and protein content were compared between infected and non-infected grains. Analyses of grain infection showed that FL was able to cause infection on the grain only in the field site with the highest relative humidity, whereas FP infected grains in all field sites. The FP infection of grains resulted in NIV contamination (between 30–500 μg/kg). The concentration of NIV in grains was not conditioned by environmental conditions. FL provoked an average contamination of grains with T-2/HT-2 (between 15–132 μg/kg). None of the genotypes was able to fully avoid toxin accumulation. The general resistance of oat grains against toxin accumulation was weak, and resistance against NIV accumulation was strongly impacted by the interaction between the genotype and the environment. Only the genotype with hull-less grains showed partial resistance to both NIV and T-2/HT-2 contamination. FP and FL infections could change the β-glucan content in grains, depending on the genotypes and environmental conditions. FP and FL did not have a significant impact on the thousand kernel weight (TKW) and protein content. Hence, resistance against toxin

Suppressors of oat crown rust resistance in interspecific oat crosses

USDA-ARS?s Scientific Manuscript database

Attempts to transfer disease resistance genes between related species may be hindered by suppression, or lack of expression, of the trait in the interspecific combination. In crosses of diploid oat Avena strigosa (Schreb.) accession CI6954SP with resistance to oat crown rust Puccinia coronata f. sp....

In vitro fermentation of oat flours from typical and high beta-glucan oat lines.

PubMed

Kim, Hyun Jung; White, Pamela J

2009-08-26

Two publicly available oat (Avena sativa) lines, "Jim" and "Paul" (5.17 and 5.31% beta-glucan, respectively), and one experimental oat line "N979" (7.70% beta-glucan), were used to study the effect of beta-glucan levels in oat flours during simulated in vitro digestion and fermentation with human fecal flora obtained from different individuals. The oat flours were digested by using human digestion enzymes and fermented by batch fermentation under anaerobic conditions for 24 h. The fermentation progress was monitored by measuring pH, total gas, and short-chain fatty acid (SCFA) production. Significant effects of beta-glucan on the formation of gas and total SCFA were observed compared to the blank without substrate (P < 0.05); however, there were no differences in pH changes, total gas, and total SCFA production among oat lines (P > 0.05). Acetate, propionate, and butyrate were the main SCFA produced from digested oat flours during fermentation. More propionate and less acetate were produced from digested oat flours compared to lactulose. Different human fecal floras obtained from three healthy individuals had similar patterns in the change of pH and the production of gas during fermentation. Total SCFA after 24 h of fermentation were not different, but the formation rates of total SCFA differed between individuals. In vitro fermentation of digested oat flours with beta-glucan could provide favorable environmental conditions for the colon and these findings, thus, will help in developing oat-based food products with desirable health benefits.

Background field removal technique using regularization enabled sophisticated harmonic artifact reduction for phase data with varying kernel sizes.

PubMed

Kan, Hirohito; Kasai, Harumasa; Arai, Nobuyuki; Kunitomo, Hiroshi; Hirose, Yasujiro; Shibamoto, Yuta

2016-09-01

An effective background field removal technique is desired for more accurate quantitative susceptibility mapping (QSM) prior to dipole inversion. The aim of this study was to evaluate the accuracy of regularization enabled sophisticated harmonic artifact reduction for phase data with varying spherical kernel sizes (REV-SHARP) method using a three-dimensional head phantom and human brain data. The proposed REV-SHARP method used the spherical mean value operation and Tikhonov regularization in the deconvolution process, with varying 2-14mm kernel sizes. The kernel sizes were gradually reduced, similar to the SHARP with varying spherical kernel (VSHARP) method. We determined the relative errors and relationships between the true local field and estimated local field in REV-SHARP, VSHARP, projection onto dipole fields (PDF), and regularization enabled SHARP (RESHARP). Human experiment was also conducted using REV-SHARP, VSHARP, PDF, and RESHARP. The relative errors in the numerical phantom study were 0.386, 0.448, 0.838, and 0.452 for REV-SHARP, VSHARP, PDF, and RESHARP. REV-SHARP result exhibited the highest correlation between the true local field and estimated local field. The linear regression slopes were 1.005, 1.124, 0.988, and 0.536 for REV-SHARP, VSHARP, PDF, and RESHARP in regions of interest on the three-dimensional head phantom. In human experiments, no obvious errors due to artifacts were present in REV-SHARP. The proposed REV-SHARP is a new method combined with variable spherical kernel size and Tikhonov regularization. This technique might make it possible to be more accurate backgroud field removal and help to achive better accuracy of QSM. Copyright © 2016 Elsevier Inc. All rights reserved.

Methotrexate-loxoprofen interaction: involvement of human organic anion transporters hOAT1 and hOAT3.

PubMed

Uwai, Yuichi; Taniguchi, Risa; Motohashi, Hideyuki; Saito, Hideyuki; Okuda, Masahiro; Inui, Ken-ichi

2004-10-01

Human organic anion transporters hOAT1 (SLC22A6) and hOAT3 (SLC22A8) are responsible for renal tubular secretion of an antifolic acid methotrexate, and are considered to be involved in drug interaction of methotrexate with nonsteroidal anti-inflammatory drugs (NSAIDs). In our hospital, a delay of methotrexate elimination was experienced in a patient with Hodgkin's disease, who took loxoprofen, a commonly used NSAID in Japan, which suggested a cause. In this study, we examined the drug interaction via hOAT1 and hOAT3, using Xenopus laevis oocytes. hOAT1 and hOAT3 mediated the methotrexate transport with low affinity (K(m) of 724.0 muM) and high affinity (K(m) of 17.2 muM), respectively. Loxoprofen and its trans-OH metabolite, an active major metabolite, markedly inhibited the methotrexate transport by both transporters. Their inhibition concentrations (IC(50)) were in the range of the therapeutic levels. These findings suggest that loxoprofen retards the elimination of methotrexate, at least in part, by inhibiting hOAT1 and hOAT3.

Identification and Quantitative Assessment of Uremic Solutes as Inhibitors of Renal Organic Anion Transporters, OAT1 and OAT3.

PubMed

Hsueh, Chia-Hsiang; Yoshida, Kenta; Zhao, Ping; Meyer, Timothy W; Zhang, Lei; Huang, Shiew-Mei; Giacomini, Kathleen M

2016-09-06

One of the characteristics of chronic kidney disease (CKD) is the accumulation of uremic solutes in the plasma. Less is known about the effects of uremic solutes on transporters that may play critical roles in pharmacokinetics. We evaluated the effect of 72 uremic solutes on organic anion transporter 1 and 3 (OAT1 and OAT3) using a fluorescent probe substrate, 6-carboxyfluorescein. A total of 12 and 13 solutes were identified as inhibitors of OAT1 and OAT3, respectively. Several of them inhibited OAT1 or OAT3 at clinically relevant concentrations and reduced the transport of other OAT1/3 substrates in vitro. Review of clinical studies showed that the active secretion of most drugs that are known substrates of OAT1/3 deteriorated faster than the renal filtration in CKD. Collectively, these data suggest that through inhibition of OAT1 and OAT3, uremic solutes contribute to the decline in renal drug clearance in patients with CKD.

Inhibitory effect of selective cyclooxygenase-2 inhibitor lumiracoxib on human organic anion transporters hOAT1 and hOAT3.

PubMed

Uwai, Yuichi; Honjo, Hiroaki; Iwamoto, Kikuo

2010-01-01

Nonsteroidal anti-inflammatory drugs (NSAIDs) delay renal excretion of antifolate methotrexate by inhibiting human organic anion transporters hOAT1 (SLC22A6) and hOAT3 (SLC22A8). In this study, we performed uptake experiments using Xenopus laevis oocytes to assess the inhibitory effect of selective cyclooxygenase-2 inhibitors on hOAT1 and hOAT3. The uptake of methotrexate into oocytes was increased by the injection of hOAT1 and hOAT3 cRNA, and transport was strongly inhibited by lumiracoxib. The apparent 50% inhibitory concentrations of lumiracoxib were estimated to be 3.3 µM and 1.9 µM for uptake of p-aminohippurate by hOAT1 and of estrone sulfate by hOAT3, respectively. Eadie-Hofstee plot analysis showed that lumiracoxib inhibited hOAT1 and hOAT3 in a competitive manner. For other cyclooxygenase-2 inhibitors celecoxib, etoricoxib, rofecoxib and valdecoxib, slight to moderate inhibition of hOAT3 only was observed. These findings show that lumiracoxib has inhibitory potential toward hOAT1 and hOAT3, comparable to that of nonselective NSAIDs.

Dissection of Genetic Factors underlying Wheat Kernel Shape and Size in an Elite × Nonadapted Cross using a High Density SNP Linkage Map.

PubMed

Kumar, Ajay; Mantovani, E E; Seetan, R; Soltani, A; Echeverry-Solarte, M; Jain, S; Simsek, S; Doehlert, D; Alamri, M S; Elias, E M; Kianian, S F; Mergoum, M

2016-03-01

Wheat kernel shape and size has been under selection since early domestication. Kernel morphology is a major consideration in wheat breeding, as it impacts grain yield and quality. A population of 160 recombinant inbred lines (RIL), developed using an elite (ND 705) and a nonadapted genotype (PI 414566), was extensively phenotyped in replicated field trials and genotyped using Infinium iSelect 90K assay to gain insight into the genetic architecture of kernel shape and size. A high density genetic map consisting of 10,172 single nucleotide polymorphism (SNP) markers, with an average marker density of 0.39 cM/marker, identified a total of 29 genomic regions associated with six grain shape and size traits; ∼80% of these regions were associated with multiple traits. The analyses showed that kernel length (KL) and width (KW) are genetically independent, while a large number (∼59%) of the quantitative trait loci (QTL) for kernel shape traits were in common with genomic regions associated with kernel size traits. The most significant QTL was identified on chromosome 4B, and could be an ortholog of major rice grain size and shape gene or . Major and stable loci also were identified on the homeologous regions of Group 5 chromosomes, and in the regions of (6A) and (7A) genes. Both parental genotypes contributed equivalent positive QTL alleles, suggesting that the nonadapted germplasm has a great potential for enhancing the gene pool for grain shape and size. This study provides new knowledge on the genetic dissection of kernel morphology, with a much higher resolution, which may aid further improvement in wheat yield and quality using genomic tools. Copyright © 2016 Crop Science Society of America.

Functional Properties of a High Protein Beverage Stabilized with Oat-β-Glucan.

PubMed

Vasquez-Orejarena, Eva; Simons, Christopher T; Litchfield, John H; Alvarez, Valente B

2018-05-01

This study evaluated the effect of oat flour and milk protein on the functional properties and sensory acceptability of shelf stable high protein dairy beverages containing at least 0.75 g of oat-β-glucan per serving size. Formulations adjusted to levels of 1.50% to 2.30% oat flour and 2.50% to 4.00% milk protein isolate (MPI) were thermal processed in a rotary retort. The finished product exhibited good suspension stability (>80%). The increase of oat and MPI contents lead to nectar-like beverages (51 to 100 mPas). However, oat flour was the component showing the highest effect on the viscosity coefficient values of the beverages. Sensory evaluation indicated that formulations with less than 1.9% oat flour and 2.5% MPI (thin liquid, <50 mPas) were the most accepted. Mouthfeel (perceived thickness), sweetness and aftertaste had the most influence on overall liking of the beverages. Overall, this study comprises the development of a functional food product. Supplementation of beverages with fiber from oats is an innovative approach to stabilize high protein beverages. Ready to drink protein beverage formulations use gums to stabilize the product and provide a desirable mouthfeel. The levels of oat-β-glucan used in the beverage increased the thickness and meet the requirement of the FDA approved health claim for reduction of the cardiovascular disease risk (21 CFR 101.81). © 2018 Institute of Food Technologists®.

An automatic optimum kernel-size selection technique for edge enhancement

USGS Publications Warehouse

Chavez, Pat S.; Bauer, Brian P.

1982-01-01

Edge enhancement is a technique that can be considered, to a first order, a correction for the modulation transfer function of an imaging system. Digital imaging systems sample a continuous function at discrete intervals so that high-frequency information cannot be recorded at the same precision as lower frequency data. Because of this, fine detail or edge information in digital images is lost. Spatial filtering techniques can be used to enhance the fine detail information that does exist in the digital image, but the filter size is dependent on the type of area being processed. A technique has been developed by the authors that uses the horizontal first difference to automatically select the optimum kernel-size that should be used to enhance the edges that are contained in the image. 

Puccinia coronata f. sp. avenae: a threat to global oat production.

PubMed

Nazareno, Eric S; Li, Feng; Smith, Madeleine; Park, Robert F; Kianian, Shahryar F; Figueroa, Melania

2018-05-01

Puccinia coronata f. sp. avenae (Pca) causes crown rust disease in cultivated and wild oat (Avena spp.). The significant yield losses inflicted by this pathogen make crown rust the most devastating disease in the oat industry. Pca is a basidiomycete fungus with an obligate biotrophic lifestyle, and is classified as a typical macrocyclic and heteroecious fungus. The asexual phase in the life cycle of Pca occurs in oat, whereas the sexual phase takes place primarily in Rhamnus species as the alternative host. Epidemics of crown rust happens in areas with warm temperatures (20-25 °C) and high humidity. Infection by the pathogen leads to plant lodging and shrivelled grain of poor quality. Disease symptoms: Infection of susceptible oat varieties gives rise to orange-yellow round to oblong uredinia (pustules) containing newly formed urediniospores. Pustules vary in size and can be larger than 5 mm in length. Infection occurs primarily on the surfaces of leaves, although occasional symptoms develop in the oat leaf sheaths and/or floral structures, such as awns. Symptoms in resistant oat varieties vary from flecks to small pustules, typically accompanied by chlorotic halos and/or necrosis. The pycnial and aecial stages are mostly present in the leaves of Rhamnus species, but occasionally symptoms can also be observed in petioles, young stems and floral structures. Aecial structures display a characteristic hypertrophy and can differ in size, occasionally reaching more than 5 mm in diameter. Taxonomy: Pca belongs to the kingdom Fungi, phylum Basidiomycota, class Pucciniomycetes, order Pucciniales and family Pucciniaceae. Host range: Puccinia coronata sensu lato can infect 290 species of grass hosts. Pca is prevalent in all oat-growing regions and, compared with other cereal rusts, displays a broad telial host range. The most common grass hosts of Pca include cultivated hexaploid oat (Avena sativa) and wild relatives, such as bluejoint grass, perennial ryegrass and

Molecular cloning and characterization of two novel human renal organic anion transporters (hOAT1 and hOAT3).

PubMed

Race, J E; Grassl, S M; Williams, W J; Holtzman, E J

1999-02-16

The cloned organic anion transporters from rat, mouse, and winter flounder (rOAT1, mOAT1, fROAT) mediate the coupled exchange of alpha-ketoglutarate with multiple organic anions, including p-aminohippurate (PAH). We have isolated two novel gene products from human kidney which bear significant homology to the known OATs and belong to the amphiphilic solute facilitator (ASF) family. The cDNAs, hOAT1 and hOAT3, encode for 550- and 568-amino-acid residue proteins, respectively. hOAT1 and hOAT3 mRNAs are expressed strongly in kidney and weakly in brain. Both genes map to chromosome 11 region q11.7. PAH uptake by Xenopus laevis oocytes injected with hOAT1 mRNA is increased 100-fold compared to water-injected oocytes. PAH uptake is chloride dependent and is not further increased by preincubation of oocytes in 5 mM glutarate. Uptake of PAH is inhibited by probenicid, alpha-ketoglutarate, bumetanide, furosemide, and losartan, but not by salicylate, urate, choline, amilioride, and hydrochlorothiazide. Copyright 1999 Academic Press.

Oats

MedlinePlus

... saturated fat. For each gram of soluble fiber (beta-glucan) consumed, total cholesterol decreases by about 1.42 ... total cholesterol than foods containing oat bran plus beta-glucan soluble fiber. The FDA recommends that approximately 3 ...

Functional properties of teff and oat composites

USDA-ARS?s Scientific Manuscript database

Teff-oat composites were developed using gluten free teff flour containing essential amino acids and minerals along with oat products containing ß-glucan known for lowering blood cholesterol. Teff-oat composites were evaluated for their pasting and rheological properties by a Rapid Visco Analyzer (R...

P-gp, MRP2 and OAT1/OAT3 mediate the drug-drug interaction between resveratrol and methotrexate

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

Jia, Yongming

The purpose of present study was to investigate the effect of resveratrol (Res) on altering methotrexate (MTX) pharmacokinetics and clarify the related molecular mechanism. Res significantly increased rat intestinal absorption of MTX in vivo and in vitro. Simultaneously, Res inhibited MTX efflux transport in MDR1-MDCK and MRP2-MDCK cell monolayers, suggesting that the target of drug interaction was MDR1 and MRP2 in the intestine during the absorption process. Furthermore, there was a significant decrease in renal clearance of MTX after simultaneous intravenous administration. Similarly, MTX uptake was markedly inhibited by Res in rat kidney slices and hOAT1/3-HEK293 cell, indicating that OAT1more » and OAT3 were involved in the drug interaction in the kidney. Additionally, concomitant administration of Res decreased cytotoxic effects of MTX in hOAT1/3-HEK293 cells, and ameliorated nephrotoxicity caused by MTX in rats. Conversely, intestinal damage caused by MTX was not exacerbated after Res treatment. In conclusion, Res enhanced MTX absorption in intestine and decreased MTX renal elimination by inhibiting P-gp, MRP2, OAT1 and OAT3 in vivo and in vitro. Res improved MTX-induced renal damage without increasing intestinal toxicity. - Highlights: • DDI between MTX and Res will occur when they are co-administered. • The first targets of the DDI are P-gp and MRP2 located in intestine. • The second targets of the DDI are OAT1 and OAT3 in kidney. • Res improved MTX-induced renal damage without increasing intestinal toxicity.« less

Forward phenomics of oat panicles

USDA-ARS?s Scientific Manuscript database

There is a growing need for adapted and more productive germplasm to expand oat production, optimize its yield, improve groat quality, and satisfy farmers and consumers demand, especially in the Upper Midwest of the US. Oat germplasm, representing different eco-geographical origins and breeding stat...

ASIC-based architecture for the real-time computation of 2D convolution with large kernel size

NASA Astrophysics Data System (ADS)

Shao, Rui; Zhong, Sheng; Yan, Luxin

2015-12-01

Bidimensional convolution is a low-level processing algorithm of interest in many areas, but its high computational cost constrains the size of the kernels, especially in real-time embedded systems. This paper presents a hardware architecture for the ASIC-based implementation of 2-D convolution with medium-large kernels. Aiming to improve the efficiency of storage resources on-chip, reducing off-chip bandwidth of these two issues, proposed construction of a data cache reuse. Multi-block SPRAM to cross cached images and the on-chip ping-pong operation takes full advantage of the data convolution calculation reuse, design a new ASIC data scheduling scheme and overall architecture. Experimental results show that the structure can achieve 40× 32 size of template real-time convolution operations, and improve the utilization of on-chip memory bandwidth and on-chip memory resources, the experimental results show that the structure satisfies the conditions to maximize data throughput output , reducing the need for off-chip memory bandwidth.

JBP485 improves gentamicin-induced acute renal failure by regulating the expression and function of Oat1 and Oat3 in rats

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

Guo, Xinjin; Meng, Qiang; Liu, Qi

2013-09-01

We investigated the effects of JBP485 (an anti-inflammatory dipeptide and a substrate of OAT) on regulation of the expression and function of renal Oat1 and Oat3, which can accelerate the excretion of accumulated uremic toxins (e.g. indoxyl sulfate) in the kidney to improve gentamicin-induced ARF in rats. JBP485 caused a significant decrease in the accumulation of endogenous substances (creatinine, blood urea nitrogen and indoxyl sulfate) in vivo, an increase in the excretion of exogenous compounds (lisinopril and inulin) into urine, and up-regulation of the expressions of renal Oat1 and Oat3 in the kidney tissues and slices via substrate induction. Tomore » determine the effect of JBP485 on the accelerated excretion of uremic toxins mediated by Oat1 and Oat3, the mRNA and protein expression levels of renal basolateral Oats were assessed by quantitative real-time PCR, western blot, immunohistochemical analysis and an immunofluorescence method. Gentamicin down-regulated the expression of Oats mRNA and protein in rat kidney, and these effects were reversed after administration of JBP485. In addition, JBP485 caused a significant decrease in MPO and MDA levels in the kidney, and improved the pathological condition of rat kidney. These results indicated that JBP485 improved acute renal failure by increasing the expression and function of Oat1 and Oat3, and by decreasing overoxidation of the kidney in gentamicin-induced ARF rats. - Highlights: • JBP485 could up-regulate function and expression of Oat1 and Oat3 in kidney. • Effects of JBP485 on ARF are mediated by stimulating excretion of uremic toxins. • JBP485 protected against gentamicin-induced ARF by decreasing MPO and MDA.« less

PAH clearance after renal ischemia and reperfusion is a function of impaired expression of basolateral Oat1 and Oat3.

PubMed

Bischoff, Ariane; Bucher, Michael; Gekle, Michael; Sauvant, Christoph

2014-02-01

Determination of renal plasma flow (RPF) by para-aminohippurate (PAH) clearance leads to gross underestimation of this respective parameter due to impaired renal extraction of PAH after renal ischemia and reperfusion injury. However, no mechanistic explanation for this phenomenon is available. Based on our own previous studies we hypothesized that this may be due to impairment of expression of the basolateral rate limiting organic anion transporters Oat1 and Oat3. Thus, we investigated this phenomenon in a rat model of renal ischemia and reperfusion by determining PAH clearance, PAH extraction, PAH net secretion, and the expression of rOat1 and rOat3. PAH extraction was seriously impaired after ischemia and reperfusion which led to a threefold underestimation of RPF when PAH extraction ratio was not considered. PAH extraction directly correlated with the expression of basolateral Oat1 and Oat3. Tubular PAH secretion directly correlated with PAH extraction. Consequently, our data offer an explanation for impaired renal PAH extraction by reduced expression of the rate limiting basolateral organic anion transporters Oat1 and Oat3. Moreover, we show that determination of PAH net secretion is suitable to correct PAH clearance for impaired extraction after ischemia and reperfusion in order to get valid results for RPF.

Polyamine binding to proteins in oat and Petunia protoplasts

NASA Technical Reports Server (NTRS)

Mizrahi, Y.; Applewhite, P. B.; Galston, A. W.

1989-01-01

Previous work (A Apelbaum et al. [1988] Plant Physiol 88: 996-998) has demonstrated binding of labeled spermidine (Spd) to a developmentally regulated 18 kilodalton protein in tobacco tissue cultures derived from thin surface layer explants. To assess the general importance of such Spd-protein complexes, we attempted bulk isolation from protoplasts of Petunia and oat (Avena sativa). In Petunia, as in tobacco, fed radioactive Spd is bound to protein, but in oat, Spd is first converted to 1,3,-diaminopropane (DAP), probably by polyamine oxidase action. In oat, binding of DAP to protein depends on age of donor leaf and conditions of illumination and temperature, and the extraction of the DAP-protein complex depends upon buffer and pH. The yield of the DAP-protein complex was maximized by extraction of frozen-thawed protoplasts with a pH 8.8 carbonate buffer containing SDS. Its molecular size, based on Sephacryl column fractionation of ammonium sulfate precipitated material, exceeded 45 kilodaltons. Bound Spd or DAP can be released from their complexes by the action of Pronase, but not DNAse, RNAse, or strong salt solutions, indicating covalent attachment to protein.

Polyamine binding to proteins in oat and Petunia protoplasts.

PubMed

Mizrahi, Y; Applewhite, P B; Galston, A W

1989-01-01

Previous work (A Apelbaum et al. [1988] Plant Physiol 88: 996-998) has demonstrated binding of labeled spermidine (Spd) to a developmentally regulated 18 kilodalton protein in tobacco tissue cultures derived from thin surface layer explants. To assess the general importance of such Spd-protein complexes, we attempted bulk isolation from protoplasts of Petunia and oat (Avena sativa). In Petunia, as in tobacco, fed radioactive Spd is bound to protein, but in oat, Spd is first converted to 1,3,-diaminopropane (DAP), probably by polyamine oxidase action. In oat, binding of DAP to protein depends on age of donor leaf and conditions of illumination and temperature, and the extraction of the DAP-protein complex depends upon buffer and pH. The yield of the DAP-protein complex was maximized by extraction of frozen-thawed protoplasts with a pH 8.8 carbonate buffer containing SDS. Its molecular size, based on Sephacryl column fractionation of ammonium sulfate precipitated material, exceeded 45 kilodaltons. Bound Spd or DAP can be released from their complexes by the action of Pronase, but not DNAse, RNAse, or strong salt solutions, indicating covalent attachment to protein.

A Kernel-based Lagrangian method for imperfectly-mixed chemical reactions

NASA Astrophysics Data System (ADS)

Schmidt, Michael J.; Pankavich, Stephen; Benson, David A.

2017-05-01

Current Lagrangian (particle-tracking) algorithms used to simulate diffusion-reaction equations must employ a certain number of particles to properly emulate the system dynamics-particularly for imperfectly-mixed systems. The number of particles is tied to the statistics of the initial concentration fields of the system at hand. Systems with shorter-range correlation and/or smaller concentration variance require more particles, potentially limiting the computational feasibility of the method. For the well-known problem of bimolecular reaction, we show that using kernel-based, rather than Dirac delta, particles can significantly reduce the required number of particles. We derive the fixed width of a Gaussian kernel for a given reduced number of particles that analytically eliminates the error between kernel and Dirac solutions at any specified time. We also show how to solve for the fixed kernel size by minimizing the squared differences between solutions over any given time interval. Numerical results show that the width of the kernel should be kept below about 12% of the domain size, and that the analytic equations used to derive kernel width suffer significantly from the neglect of higher-order moments. The simulations with a kernel width given by least squares minimization perform better than those made to match at one specific time. A heuristic time-variable kernel size, based on the previous results, performs on par with the least squares fixed kernel size.

Dissection of genetic factors underlying wheat kernel shape and size in an elite x nonadapted cross using a high density SNP linkage map

USDA-ARS?s Scientific Manuscript database

Wheat kernel shape and size has been under selection since early domestication. Kernel morphology is a major consideration in wheat breeding, as it impacts grain yield and quality. A population of 160 recombinant inbred lines (RIL), developed using an elite (ND 705) and a nonadapted genotype (PI 414...

Structural Development of the Oat Plant

NASA Technical Reports Server (NTRS)

Kaufman, Peter B.; Brock, Thomas G.

1992-01-01

The anatomical structure and morphology of the oat plant (Avena sativa L.) have been reviewed previously by Hector (1936), Bonnett (1961a,b) and Coffman (1977). In addition, Bonnett published detailed accounts of oat panicle development (1937, 1961a,b). This work has been summarized by Esau in her book, Anatomy of Seed Plants, in 1977. It is not the purpose of the present authors to simply go over all this same material again in a repetitive fashion, but rather, to emphasize some of the more recent and previously overlooked work on structural development of the oat plant, with emphasis on the major cultivated species, A. sativa (see Stanton, 1955; Coffman, 1977 for descriptions of this species). The material presented here should be of use to oat breeders, agronomists, and plant physiologists.

Grinding energy and physical properties of chopped and hammer-milled barley, wheat, oat, and canola straws

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

J.S. Tumuluru; L.G. Tabil; Y. Song

2014-01-01

In the present study, specific energy for grinding and physical properties of wheat, canola, oat and barley straw grinds were investigated. The initial moisture content of the straw was about 0.13–0.15 (fraction total mass basis). Particle size reduction experiments were conducted in two stages: (1) a chopper without a screen, and (2) a hammer mill using three screen sizes (19.05, 25.4, and 31.75 mm). The lowest grinding energy (1.96 and 2.91 kWh t-1) was recorded for canola straw using a chopper and hammer mill with 19.05-mm screen size, whereas the highest (3.15 and 8.05 kWh t-1) was recorded for barleymore » and oat straws. The physical properties (geometric mean particle diameter, bulk, tapped and particle density, and porosity) of the chopped and hammer-milled wheat, barley, canola, and oat straw grinds measured were in the range of 0.98–4.22 mm, 36–80 kg m-3, 49–119 kg m-3, 600–1220 kg m-3, and 0.9–0.96, respectively. The average mean particle diameter was highest for the chopped wheat straw (4.22-mm) and lowest for the canola grind (0.98-mm). The canola grinds produced using the hammer mill (19.05-mm screen size) had the highest bulk and tapped density of about 80 and 119 kg m-3; whereas, the wheat and oat grinds had the lowest of about 58 and 88–90 kg m-3. The results indicate that the bulk and tapped densities are inversely proportional to the particle size of the grinds. The flow properties of the grinds calculated are better for chopped straws compared to hammer milled using smaller screen size (19.05 mm).« less

Combining kernel matrix optimization and regularization to improve particle size distribution retrieval

NASA Astrophysics Data System (ADS)

Ma, Qian; Xia, Houping; Xu, Qiang; Zhao, Lei

2018-05-01

A new method combining Tikhonov regularization and kernel matrix optimization by multi-wavelength incidence is proposed for retrieving particle size distribution (PSD) in an independent model with improved accuracy and stability. In comparison to individual regularization or multi-wavelength least squares, the proposed method exhibited better anti-noise capability, higher accuracy and stability. While standard regularization typically makes use of the unit matrix, it is not universal for different PSDs, particularly for Junge distributions. Thus, a suitable regularization matrix was chosen by numerical simulation, with the second-order differential matrix found to be appropriate for most PSD types.

Replacing Corn and Wheat in Layer Diets with Hulless Oats Shows Effects on Sensory Properties and Yolk Quality of Eggs.

PubMed

Winkler, Louisa R; Hasenbeck, Aimee; Murphy, Kevin M; Hermes, James C

2017-01-01

US organic poultry producers are under pressure to find feed alternatives to corn and wheat. Hulless oats offer advantages such as wide geographic adaptation of the plant and high concentrations of protein and oil in the grain. They have shown considerable potential in experimental work as a feed grain for poultry, but more research is needed into their influence on the sensory and nutritional properties of eggs. In this study, hulless oats were substituted for corn or wheat at 200 g kg -1 in diets fed to Hy-Line Brown hens and eggs were sampled for sensory evaluation after 8 weeks. Discrimination tests of blended and baked egg samples found evidence of difference between eggs from oat-based diets and those from the oat-free control ( p  < 0.05 for eggs from an oat-corn diet, p  < 0.01 for eggs from an oat-wheat diet). Acceptance tests of similar samples showed that eggs from the oat-wheat diet were significantly less liked than control eggs for their texture ( p  < 0.01) and response to cooking ( p  < 0.01), while eggs from the oat-corn diet were somewhat less liked. Yolk weight was greater ( p  < 0.05) in control eggs (34.1 g) than eggs from oat-corn (31.6 g) or oat-wheat (31.2 g) diets, leading to smaller yolk proportion in the oat-fed eggs. Fatty acid profile differences across treatments were not of nutritional significance, and no evidence was found that the feeding of hulless oats improved storage properties of eggs. In this study, modifying the carbohydrate source in layer diets was shown to change textural properties of cooked eggs in a way that was perceptible to untrained consumers, probably by reducing the yolk proportion. This finding was not commercially relevant owing to small effect size, and results overall add to existing evidence that hulless oats can be fed to poultry at a moderate proportion of the diet with no negative effect on consumer acceptability of eggs. Regardless of the small effect size, however, findings

Replacing Corn and Wheat in Layer Diets with Hulless Oats Shows Effects on Sensory Properties and Yolk Quality of Eggs

PubMed Central

Winkler, Louisa R.; Hasenbeck, Aimee; Murphy, Kevin M.; Hermes, James C.

2017-01-01

US organic poultry producers are under pressure to find feed alternatives to corn and wheat. Hulless oats offer advantages such as wide geographic adaptation of the plant and high concentrations of protein and oil in the grain. They have shown considerable potential in experimental work as a feed grain for poultry, but more research is needed into their influence on the sensory and nutritional properties of eggs. In this study, hulless oats were substituted for corn or wheat at 200 g kg−1 in diets fed to Hy-Line Brown hens and eggs were sampled for sensory evaluation after 8 weeks. Discrimination tests of blended and baked egg samples found evidence of difference between eggs from oat-based diets and those from the oat-free control (p < 0.05 for eggs from an oat-corn diet, p < 0.01 for eggs from an oat-wheat diet). Acceptance tests of similar samples showed that eggs from the oat-wheat diet were significantly less liked than control eggs for their texture (p < 0.01) and response to cooking (p < 0.01), while eggs from the oat-corn diet were somewhat less liked. Yolk weight was greater (p < 0.05) in control eggs (34.1 g) than eggs from oat-corn (31.6 g) or oat-wheat (31.2 g) diets, leading to smaller yolk proportion in the oat-fed eggs. Fatty acid profile differences across treatments were not of nutritional significance, and no evidence was found that the feeding of hulless oats improved storage properties of eggs. In this study, modifying the carbohydrate source in layer diets was shown to change textural properties of cooked eggs in a way that was perceptible to untrained consumers, probably by reducing the yolk proportion. This finding was not commercially relevant owing to small effect size, and results overall add to existing evidence that hulless oats can be fed to poultry at a moderate proportion of the diet with no negative effect on consumer acceptability of eggs. Regardless of the small effect size, however, findings are

Volatile Compounds Produced by Lactobacillus paracasei During Oat Fermentation.

PubMed

Lee, Sang Mi; Oh, Jieun; Hurh, Byung-Serk; Jeong, Gwi-Hwa; Shin, Young-Keum; Kim, Young-Suk

2016-12-01

This study investigated the profiles of volatile compounds produced by Lactobacillus paracasei during oat fermentation using gas chromatography-mass spectrometry coupled with headspace solid-phase microextraction method. A total of 60 compounds, including acids, alcohols, aldehydes, esters, furan derivatives, hydrocarbons, ketones, sulfur-containing compounds, terpenes, and other compounds, were identified in fermented oat. Lipid oxidation products such as 2-pentylfuran, 1-octen-3-ol, hexanal, and nonanal were found to be the main contributors to oat samples fermented by L. paracasei with the level of 2-pentylfuran being the highest. In addition, the contents of ketones, alcohols, acids, and furan derivatives in the oat samples consistently increased with the fermentation time. On the other hand, the contents of degradation products of amino acids, such as 3-methylbutanal, benzaldehyde, acetophenone, dimethyl sulfide, and dimethyl disulfide, decreased in oat samples during fermentation. Principal component analysis (PCA) was applied to discriminate the fermented oat samples according to different fermentation times. The fermented oats were clearly differentiated on PCA plots. The initial fermentation stage was mainly affected by aldehydes, whereas the later samples of fermented oats were strongly associated with acids, alcohols, furan derivatives, and ketones. The application of PCA to data of the volatile profiles revealed that the oat samples fermented by L. paracasei could be distinguished according to fermentation time. © 2016 Institute of Food Technologists®.

SOME ENGINEERING PROPERTIES OF SHELLED AND KERNEL TEA (Camellia sinensis) SEEDS.

PubMed

Altuntas, Ebubekir; Yildiz, Merve

2017-01-01

Camellia sinensis is the source of tea leaves and it is an economic crop now grown around the World. Tea seed oil has been used for cooking in China and other Asian countries for more than a thousand years. Tea is the most widely consumed beverages after water in the world. It is mainly produced in Asia, central Africa, and exported throughout the World. Some engineering properties (size dimensions, sphericity, volume, bulk and true densities, friction coefficient, colour characteristics and mechanical behaviour as rupture force of shelled and kernel tea ( Camellia sinensis ) seeds were determined in this study. This research was carried out for shelled and kernel tea seeds. The shelled tea seeds used in this study were obtained from East-Black Sea Tea Cooperative Institution in Rize city of Turkey. Shelled and kernel tea seeds were characterized as large and small sizes. The average geometric mean diameter and seed mass of the shelled tea seeds were 15.8 mm, 10.7 mm (large size); 1.47 g, 0.49 g (small size); while the average geometric mean diameter and seed mass of the kernel tea seeds were 11.8 mm, 8 mm for large size; 0.97 g, 0.31 g for small size, respectively. The sphericity, surface area and volume values were found to be higher in a larger size than small size for the shelled and kernel tea samples. The shelled tea seed's colour intensity (Chroma) were found between 59.31 and 64.22 for large size, while the kernel tea seed's chroma values were found between 56.04 68.34 for large size, respectively. The rupture force values of kernel tea seeds were higher than shelled tea seeds for the large size along X axis; whereas, the rupture force values of along X axis were higher than Y axis for large size of shelled tea seeds. The static coefficients of friction of shelled and kernel tea seeds for the large and small sizes higher values for rubber than the other friction surfaces. Some engineering properties, such as geometric mean diameter, sphericity, volume, bulk

The U.S. Oats Industry. Agricultural Economic Report Number 573.

ERIC Educational Resources Information Center

Hoffman, Linwood A.; Livezey, Janet

This report describes the United States oats industry from producers to consumers and provides a single source of economic and statistical information on oats. Background information on oats is provided first. The report then examines the basic factors of supply, demand, and price to determine what caused the decline in the importance of oats and…

Characterization of celiac disease related oat proteins: bases for the development of high quality oat varieties suitable for celiac patients.

PubMed

Giménez, María J; Real, Ana; García-Molina, M Dolores; Sousa, Carolina; Barro, Francisco

2017-02-17

Some studies have suggested that the immunogenicity of oats depends on the cultivar. RP-HPLC has been proposed as a useful technique to select varieties of oats with reduced immunogenicity. The aim of this study was to identify both the avenin protein patterns associated with low gluten content and the available variability for the development of new non-toxic oat cultivars. The peaks of alcohol-soluble avenins of a collection of landraces and cultivars of oats have been characterized based on the RP-HPLC elution times. The immunotoxicity of oat varieties for patients with celiac disease (CD) has been tested using a competitive ELISA based on G12 monoclonal antibody. The oat lines show, on average, seven avenin peaks giving profiles with certain similarities. Based on this similarity, most of the accessions have been grouped into avenin patterns. The variability of RP-HPLC profiles of the collection is great, but not sufficient to uniquely identify the different varieties of the set. Overall, the immunogenicity of the collection is less than 20 ppm. However, there is a different distribution of toxicity ranges between the different peak patterns. We conclude that the RP-HPLC technique is useful to establish groups of varieties differing in degree of toxicity for CD patients.

Characterization of celiac disease related oat proteins: bases for the development of high quality oat varieties suitable for celiac patients

PubMed Central

Giménez, María J.; Real, Ana; García-Molina, M. Dolores; Sousa, Carolina; Barro, Francisco

2017-01-01

Some studies have suggested that the immunogenicity of oats depends on the cultivar. RP-HPLC has been proposed as a useful technique to select varieties of oats with reduced immunogenicity. The aim of this study was to identify both the avenin protein patterns associated with low gluten content and the available variability for the development of new non-toxic oat cultivars. The peaks of alcohol-soluble avenins of a collection of landraces and cultivars of oats have been characterized based on the RP-HPLC elution times. The immunotoxicity of oat varieties for patients with celiac disease (CD) has been tested using a competitive ELISA based on G12 monoclonal antibody. The oat lines show, on average, seven avenin peaks giving profiles with certain similarities. Based on this similarity, most of the accessions have been grouped into avenin patterns. The variability of RP-HPLC profiles of the collection is great, but not sufficient to uniquely identify the different varieties of the set. Overall, the immunogenicity of the collection is less than 20 ppm. However, there is a different distribution of toxicity ranges between the different peak patterns. We conclude that the RP-HPLC technique is useful to establish groups of varieties differing in degree of toxicity for CD patients. PMID:28209962

Molecular Properties of Drugs Interacting with SLC22 Transporters OAT1, OAT3, OCT1, and OCT2: A Machine-Learning Approach

PubMed Central

Liu, Henry C.; Goldenberg, Anne; Chen, Yuchen; Lun, Christina; Wu, Wei; Bush, Kevin T.; Balac, Natasha; Rodriguez, Paul; Abagyan, Ruben

2016-01-01

Statistical analysis was performed on physicochemical descriptors of ∼250 drugs known to interact with one or more SLC22 “drug” transporters (i.e., SLC22A6 or OAT1, SLC22A8 or OAT3, SLC22A1 or OCT1, and SLC22A2 or OCT2), followed by application of machine-learning methods and wet laboratory testing of novel predictions. In addition to molecular charge, organic anion transporters (OATs) were found to prefer interacting with planar structures, whereas organic cation transporters (OCTs) interact with more three-dimensional structures (i.e., greater SP3 character). Moreover, compared with OAT1 ligands, OAT3 ligands possess more acyclic tetravalent bonds and have a more zwitterionic/cationic character. In contrast, OCT1 and OCT2 ligands were not clearly distinquishable form one another by the methods employed. Multiple pharmacophore models were generated on the basis of the drugs and, consistent with the machine-learning analyses, one unique pharmacophore created from ligands of OAT3 possessed cationic properties similar to OCT ligands; this was confirmed by quantitative atomic property field analysis. Virtual screening with this pharmacophore, followed by transport assays, identified several cationic drugs that selectively interact with OAT3 but not OAT1. Although the present analysis may be somewhat limited by the need to rely largely on inhibition data for modeling, wet laboratory/in vitro transport studies, as well as analysis of drug/metabolite handling in Oat and Oct knockout animals, support the general validity of the approach—which can also be applied to other SLC and ATP binding cassette drug transporters. This may make it possible to predict the molecular properties of a drug or metabolite necessary for interaction with the transporter(s), thereby enabling better prediction of drug-drug interactions and drug-metabolite interactions. Furthermore, understanding the overlapping specificities of OATs and OCTs in the context of dynamic transporter tissue

Physical properties of sugar cookies containing chia-oat composites

USDA-ARS?s Scientific Manuscript database

Omega-3 of chia seeds (Salvia hispanica L.) and soluble ß-glucan of oat products could be beneficial for lowering blood cholesterol and preventing coronary heart disease. Nutrim, oat bran concentrate (OBC), and whole oat flour (WOF) were dry-blended with finely ground chia for improving nutritional ...

Identification, introgression, and molecular marker genetic analysis and selection of a highly effective novel oat crown rust resistance from diploid oat, Avena strigosa

USDA-ARS?s Scientific Manuscript database

A new highly effective resistance to oat crown rust (Puccinia coronata f. sp. avenae) was identified in the diploid oat Avena strigosa PI 258731 and introgressed into hexaploid cultivated oat. Young plants with this resistance show moderate susceptibility, whereas older plant tissues and adult plant...

Increasing accuracy of dispersal kernels in grid-based population models

USGS Publications Warehouse

Slone, D.H.

2011-01-01

Dispersal kernels in grid-based population models specify the proportion, distance and direction of movements within the model landscape. Spatial errors in dispersal kernels can have large compounding effects on model accuracy. Circular Gaussian and Laplacian dispersal kernels at a range of spatial resolutions were investigated, and methods for minimizing errors caused by the discretizing process were explored. Kernels of progressively smaller sizes relative to the landscape grid size were calculated using cell-integration and cell-center methods. These kernels were convolved repeatedly, and the final distribution was compared with a reference analytical solution. For large Gaussian kernels (σ > 10 cells), the total kernel error was <10 &sup-11; compared to analytical results. Using an invasion model that tracked the time a population took to reach a defined goal, the discrete model results were comparable to the analytical reference. With Gaussian kernels that had σ ≤ 0.12 using the cell integration method, or σ ≤ 0.22 using the cell center method, the kernel error was greater than 10%, which resulted in invasion times that were orders of magnitude different than theoretical results. A goal-seeking routine was developed to adjust the kernels to minimize overall error. With this, corrections for small kernels were found that decreased overall kernel error to <10-11 and invasion time error to <5%.

Digestive development in neonatal dairy calves with either whole or ground oats in the calf starter.

PubMed

Suarez-Mena, F X; Heinrichs, A J; Jones, C M; Hill, T M; Quigley, J D

2015-05-01

A series of 3 trials was conducted to determine effects of whole or ground oats in starter grain on reticulorumen fermentation and digestive system development of preweaned calves. Male Holstein calves (43.1±2.3kg at birth; n=8, 9, and 7 for trials 1, 2, and 3, respectively) were housed in individual pens in a heated facility; bedding was covered with landscape fabric to prevent consumption of bedding by the calves. In trials 1 and 2 only, calves were fitted with rumen cannulas by wk 2 of life. In all trials, a fixed amount of starter (containing 25% oats either ground and in the pellet or whole) was offered daily; orts were fed through the cannula in trials 1 and 2. Calves were randomly assigned to an all-pelleted starter or pellets plus whole oats. Rumen contents (trials 1 and 2) were sampled weekly at -8, -4, 0, 2, 4, 8, and 12 h after grain feeding for determination of pH and volatile fatty acids. Calves were killed 3 wk (trial 1) or 4 wk (trials 2 and 3) after grain was offered; organs were harvested, emptied, rinsed, and weighed to gauge digestive organ development. Starter intake was not different between treatments. Weekly measurements of rumen digesta pH did not change and only subtle changes were observed in molar proportions of individual volatile fatty acids. Molar proportion of butyrate and pH linearly decreased with age, whereas acetate proportion increased. Reticulorumen weight and papillae length tended to be greater for calves fed pelleted starter, whereas abomasum weight was greater for calves fed pellets plus whole oats. Fecal particle size and starch content were greater for calves fed pellets plus whole oats. Under the conditions of this study, physical form of oats in starter grain did not affect rumen fermentation measurements; greater rumen weight and papillae length in calves fed pelleted starter may be the result of greater nutrient availability of ground oats. Under the conditions of this study with young calves on treatments for <4 wk

Inhibition of organic anion transporter (OAT) activity by cigarette smoke condensate.

PubMed

Sayyed, Katia; Le Vee, Marc; Abdel-Razzak, Ziad; Fardel, Olivier

2017-10-01

Cigarette smoke condensate (CSC) has previously been shown to impair activity and expression of hepatic drug transporters. In the present study, we provided evidence that CSC also hinders activity of organic anion transporters (OATs), notably expressed at the kidney level. CSC thus cis-inhibited OAT substrate uptake in OAT1- and OAT3-transfected HEK293 cells, in a concentration-dependent manner (IC 50 =72.1μg/mL for OAT1 inhibition and IC 50 =27.3μg/mL for OAT3 inhibition). By contrast, OAT4 as well as the renal organic cation transporter (OCT) 2 were less sensitive to the inhibitory effect of CSC (IC 50 =351.5μg/mL and IC 50 =226.2μg/mL, for inhibition of OAT4 and OCT2, respectively). OAT3 activity was further demonstrated to be blocked by some single chemicals present in cigarette smoke such as the heterocyclic amines AαC (IC 50 =11.3μM) and PhIP (IC 50 =1.9μM), whereas other major cigarette smoke components used at 100μM, like nicotine, the nitrosamine NNK and the polycyclic aromatic hydrocarbons benzo(a)pyrene and phenanthrene, were without effect. AαC and PhIP however failed to trans-stimulate activity of OAT3, suggesting that they were not substrates for this transporter. Taken together, these data establish OAT1 and OAT3 transporters as targets of cigarette smoke chemicals, which may contribute to smoking-associated pharmacokinetics alterations. Copyright © 2017 Elsevier Ltd. All rights reserved.

7 CFR 810.1001 - Definition of oats.

Code of Federal Regulations, 2010 CFR

2010-01-01

... Agriculture Regulations of the Department of Agriculture (Continued) GRAIN INSPECTION, PACKERS AND STOCKYARD ADMINISTRATION (FEDERAL GRAIN INSPECTION SERVICE), DEPARTMENT OF AGRICULTURE OFFICIAL UNITED STATES STANDARDS FOR GRAIN United States Standards for Oats Terms Defined § 810.1001 Definition of oats. Grain that consists...

7 CFR 1437.310 - Sea grass and sea oats.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 7 Agriculture 10 2012-01-01 2012-01-01 false Sea grass and sea oats. 1437.310 Section 1437.310 Agriculture Regulations of the Department of Agriculture (Continued) COMMODITY CREDIT CORPORATION, DEPARTMENT... Determining Coverage Using Value § 1437.310 Sea grass and sea oats. (a) Sea grass and sea oats are value loss...

7 CFR 1437.310 - Sea grass and sea oats.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 7 Agriculture 10 2013-01-01 2013-01-01 false Sea grass and sea oats. 1437.310 Section 1437.310 Agriculture Regulations of the Department of Agriculture (Continued) COMMODITY CREDIT CORPORATION, DEPARTMENT... Determining Coverage Using Value § 1437.310 Sea grass and sea oats. (a) Sea grass and sea oats are value loss...

7 CFR 1437.310 - Sea grass and sea oats.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 7 Agriculture 10 2014-01-01 2014-01-01 false Sea grass and sea oats. 1437.310 Section 1437.310 Agriculture Regulations of the Department of Agriculture (Continued) COMMODITY CREDIT CORPORATION, DEPARTMENT... Determining Coverage Using Value § 1437.310 Sea grass and sea oats. (a) Sea grass and sea oats are value loss...

Discovery and Validation of Pyridoxic Acid and Homovanillic Acid as Novel Endogenous Plasma Biomarkers of Organic Anion Transporter (OAT) 1 and OAT3 in Cynomolgus Monkeys.

PubMed

Shen, Hong; Nelson, David M; Oliveira, Regina V; Zhang, Yueping; Mcnaney, Colleen A; Gu, Xiaomei; Chen, Weiqi; Su, Ching; Reily, Michael D; Shipkova, Petia A; Gan, Jinping; Lai, Yurong; Marathe, Punit; Humphreys, W Griffith

2018-02-01

Perturbation of organic anion transporter (OAT) 1- and OAT3-mediated transport can alter the exposure, efficacy, and safety of drugs. Although there have been reports of the endogenous biomarkers for OAT1/3, none of these have all of the characteristics required for a clinical useful biomarker. Cynomolgus monkeys were treated with intravenous probenecid (PROB) at a dose of 40 mg/kg in this study. As expected, PROB increased the area under the plasma concentration-time curve (AUC) of coadministered furosemide, a known substrate of OAT1 and OAT3, by 4.1-fold, consistent with the values reported in humans (3.1- to 3.7-fold). Of the 233 plasma metabolites analyzed using a liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based metabolomics method, 29 metabolites, including pyridoxic acid (PDA) and homovanillic acid (HVA), were significantly increased after either 1 or 3 hours in plasma from the monkeys pretreated with PROB compared with the treated animals. The plasma of animals was then subjected to targeted LC-MS/MS analysis, which confirmed that the PDA and HVA AUCs increased by approximately 2- to 3-fold by PROB pretreatments. PROB also increased the plasma concentrations of hexadecanedioic acid (HDA) and tetradecanedioic acid (TDA), although the increases were not statistically significant. Moreover, transporter profiling assessed using stable cell lines constitutively expressing transporters demonstrated that PDA and HVA are substrates for human OAT1, OAT3, OAT2 (HVA), and OAT4 (PDA), but not OCT2, MATE1, MATE2K, OATP1B1, OATP1B3, and sodium taurocholate cotransporting polypeptide. Collectively, these findings suggest that PDA and HVA might serve as blood-based endogenous probes of cynomolgus monkey OAT1 and OAT3, and investigation of PDA and HVA as circulating endogenous biomarkers of human OAT1 and OAT3 function is warranted. Copyright © 2018 by The American Society for Pharmacology and Experimental Therapeutics.

No harm from five year ingestion of oats in coeliac disease

PubMed Central

Janatuinen, E K; Kemppainen, T A; Julkunen, R J K; Kosma, V-M; Mäki, M; Heikkinen, M; Uusitupa, M I J

2002-01-01

Background: Six to 12 months of ingestion of moderate amounts of oats does not have a harmful effect in adult patients with coeliac disease. As the safety of long term intake of oats in coeliac patients is not known, we continued our previous 6–12 month study for five years. Aim: To assess the safety of long term ingestion of oats in the diet of coeliac patients. Patients: In our previous study, the effects of a gluten free diet and a gluten free diet including oats were compared in a randomised trial involving 92 adult patients with coeliac disease (45 in the oats group, 47 in the control group). After the initial phase of 6–12 months, patients in the oats group were allowed to eat oats freely in conjunction with an otherwise gluten free diet. After five years, 35 patients in the original oats group (23 still on an oats diet) and 28 in the control group on a conventional gluten free diet were examined. Methods: Clinical and nutritional assessment, duodenal biopsies for conventional histopathology and histomorphometry, and measurement of antiendomysial, antireticulin, and antigliadin antibodies. Results: There were no significant differences between controls and those patients consuming oats with respect to duodenal villous architecture, inflammatory cell infiltration of the duodenal mucosa, or antibody titres after five years of follow up. In both groups histological and histomorphometric indexes improved equally with time. Conclusions: This study provides the first evidence of the long term safety of oats as part of a coeliac diet in adult patients with coeliac disease. It also appears that the majority of coeliac patients prefer oats in their diet. PMID:11839710

Why Oats Are Safe and Healthy for Celiac Disease Patients.

PubMed

Gilissen, Luud J W J; van der Meer, Ingrid M; Smulders, Marinus J M

2016-11-26

The water-insoluble storage proteins of cereals (prolamins) are called "gluten" in wheat, barley, and rye, and "avenins" in oat. Gluten can provoke celiac disease (CD) in genetically susceptible individuals (those with human leukocyte antigen (HLA)-DQ2 or HLA-DQ8 serotypes). Avenins are present at a lower concentration (10%-15% of total protein content) in oat as compared to gluten in wheat (80%-85%). The avenins in the genus Avena (cultivated oat as well as various wild species of which gene bank accessions were analyzed) are free of the known CD immunogenic epitopes from wheat, barley, and rye. T cells that recognize avenin-specific epitopes have been found very rarely in CD patients. CD patients that consume oats daily do not show significantly increased levels of intraepithelial lymphocyte (EIL) cells. The safety and the positive health effects of the long-term inclusion of oats in the gluten-free diet have been confirmed in long-term studies. Since 2009 (EC 41/2009) and 2013 (FDA) oat products may be sold as gluten-free in several countries provided a gluten contamination level below 20 ppm. Introduction of oats in the gluten-free diet of celiac patients is advised after the recovery of the intestine. Health effects of oat consumption are reflected in European Food Safety Authority (EFSA)- and Food and Drug Administration (FDA)-approved health claims. Oats can form a healthy, nutritious, fiber-rich, and safe complement to the gluten-free diet.

Molecular Properties of Drugs Interacting with SLC22 Transporters OAT1, OAT3, OCT1, and OCT2: A Machine-Learning Approach.

PubMed

Liu, Henry C; Goldenberg, Anne; Chen, Yuchen; Lun, Christina; Wu, Wei; Bush, Kevin T; Balac, Natasha; Rodriguez, Paul; Abagyan, Ruben; Nigam, Sanjay K

2016-10-01

Statistical analysis was performed on physicochemical descriptors of ∼250 drugs known to interact with one or more SLC22 "drug" transporters (i.e., SLC22A6 or OAT1, SLC22A8 or OAT3, SLC22A1 or OCT1, and SLC22A2 or OCT2), followed by application of machine-learning methods and wet laboratory testing of novel predictions. In addition to molecular charge, organic anion transporters (OATs) were found to prefer interacting with planar structures, whereas organic cation transporters (OCTs) interact with more three-dimensional structures (i.e., greater SP3 character). Moreover, compared with OAT1 ligands, OAT3 ligands possess more acyclic tetravalent bonds and have a more zwitterionic/cationic character. In contrast, OCT1 and OCT2 ligands were not clearly distinquishable form one another by the methods employed. Multiple pharmacophore models were generated on the basis of the drugs and, consistent with the machine-learning analyses, one unique pharmacophore created from ligands of OAT3 possessed cationic properties similar to OCT ligands; this was confirmed by quantitative atomic property field analysis. Virtual screening with this pharmacophore, followed by transport assays, identified several cationic drugs that selectively interact with OAT3 but not OAT1. Although the present analysis may be somewhat limited by the need to rely largely on inhibition data for modeling, wet laboratory/in vitro transport studies, as well as analysis of drug/metabolite handling in Oat and Oct knockout animals, support the general validity of the approach-which can also be applied to other SLC and ATP binding cassette drug transporters. This may make it possible to predict the molecular properties of a drug or metabolite necessary for interaction with the transporter(s), thereby enabling better prediction of drug-drug interactions and drug-metabolite interactions. Furthermore, understanding the overlapping specificities of OATs and OCTs in the context of dynamic transporter tissue

7 CFR 1437.310 - Sea grass and sea oats.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 7 Agriculture 10 2011-01-01 2011-01-01 false Sea grass and sea oats. 1437.310 Section 1437.310... Determining Coverage Using Value § 1437.310 Sea grass and sea oats. (a) Sea grass and sea oats are value loss... paragraphs (c) through (h) of this section, except to the extent that similar provisions apply to claims...

7 CFR 1437.310 - Sea grass and sea oats.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 10 2010-01-01 2010-01-01 false Sea grass and sea oats. 1437.310 Section 1437.310... Determining Coverage Using Value § 1437.310 Sea grass and sea oats. (a) Sea grass and sea oats are value loss... paragraphs (c) through (h) of this section, except to the extent that similar provisions apply to claims...

Physical properties of sugar cookies containing chia-oat composites.

PubMed

Inglett, George E; Chen, Diejun; Liu, Sean

2014-12-01

Omega-3 fatty acids of chia seeds (Salvia hispanica L.) and soluble β-glucan of oat products are known for lowering blood cholesterol and preventing coronary heart disease. Nutrim, oat bran concentrate (OBC), and whole oat flour (WOF) were composited with finely ground chia, and used in cookies at 20% replacement of wheat flour for improved nutritional and physical quality. The objective was to evaluate physical properties of chia-oat composites, dough, and cookies. These composites had improved water-holding capacities compared to the starting materials. The geometrical properties and texture properties of the cookies were not greatly influenced by a 20% flour replacement using chia-OBC or chia-WOF composites. There was a decrease in the cookie diameter, and increases in the height of cookies and dough hardness using 20% Chia- Nutrim composite. These fine-particle chia-oat composites were prepared by a feasible procedure for improved nutritional value and physical properties of foods. The cookies containing chia-oat composites can be considered a health-promoting functional food. Published 2014. This article is a U.S. Government work and is in the public domain in the USA.

Grazing management for fall-grown oat forages

USDA-ARS?s Scientific Manuscript database

Fall forage production of oat generally will out-yield winter wheat or cereal rye by about a 2:1 ratio, regardless of weather conditions or harvest date because oat plants will joint, elongate, and produce a seedhead before winter, while winter wheat or cereal rye will remain vegetative until spring...

In vitro antioxidant capacity and anti-inflammatory activity of seven common oats

USDA-ARS?s Scientific Manuscript database

Oats have received increased scientific and public interest for their purported antioxidant-associated health benefits, however most reported studies have concentrated on oat extracts or specific oat phytochemicals, such as beta-glucans, tocols (vitamin E) or avenanthramides. Studies on whole oat gr...

The Organic Anion Transporter (OAT) Family: A Systems Biology Perspective

PubMed Central

Nigam, Sanjay K.; Bush, Kevin T.; Martovetsky, Gleb; Ahn, Sun-Young; Liu, Henry C.; Richard, Erin; Bhatnagar, Vibha; Wu, Wei

2015-01-01

The organic anion transporter (OAT) subfamily, which constitutes roughly half of the SLC22 (solute carrier 22) transporter family, has received a great deal of attention because of its role in handling of common drugs (antibiotics, antivirals, diuretics, nonsteroidal anti-inflammatory drugs), toxins (mercury, aristolochic acid), and nutrients (vitamins, flavonoids). Oats are expressed in many tissues, including kidney, liver, choroid plexus, olfactory mucosa, brain, retina, and placenta. Recent metabolomics and microarray data from Oat1 [Slc22a6, originally identified as NKT (novel kidney transporter)] and Oat3 (Slc22a8) knockouts, as well as systems biology studies, indicate that this pathway plays a central role in the metabolism and handling of gut microbiome metabolites as well as putative uremic toxins of kidney disease. Nuclear receptors and other transcription factors, such as Hnf4α and Hnf1α, appear to regulate the expression of certain Oats in conjunction with phase I and phase II drug metabolizing enzymes. Some Oats have a strong selectivity for particular signaling molecules, including cyclic nucleotides, conjugated sex steroids, odorants, uric acid, and prostaglandins and/or their metabolites. According to the “Remote Sensing and Signaling Hypothesis,” which is elaborated in detail here, Oats may function in remote interorgan communication by regulating levels of signaling molecules and key metabolites in tissues and body fluids. Oats may also play a major role in interorganismal communication (via movement of small molecules across the intestine, placental barrier, into breast milk, and volatile odorants into the urine). The role of various Oat isoforms in systems physiology appears quite complex, and their ramifications are discussed in the context of remote sensing and signaling. PMID:25540139

Lipid-modifying enzymes in oat and faba bean.

PubMed

Yang, Zhen; Piironen, Vieno; Lampi, Anna-Maija

2017-10-01

The aim was to study lipase, lipoxygenase (LOX) and peroxygenase (POX) activities in oat and faba bean samples to be able to evaluate their potential in formation of lipid-derived off-flavours. Lipase and LOX activities were measured by spectroscopy, and POX activities via the formation of epoxides. An ultra-high performance liquid chromatography method was developed to study the formation of fatty acid epoxides. The epoxides of esters were measured by gas chromatography. Mass spectroscopy was used to verify the identity of the epoxides. Both oat and faba bean possessed high lipase activities. In faba bean, LOX catalysed the formation of hydroperoxides, whose break-down products are the likely cause of off-flavours. Since oat had low LOX activity, autoxidation is needed to initiate lipid oxidation. Oat had high POX activity, which is able to convert hydroperoxides to epoxy and hydroxy fatty acids that could contribute significantly to off-flavours. POX activity in the faba bean was low. Thus, in faba bean volatile lipid oxidation products could rapidly be formed by LOX, whereas in oat reactions are slower due to the need of autoxidation prior to further reactions. Copyright © 2017 Elsevier Ltd. All rights reserved.

Gradient-based adaptation of general gaussian kernels.

PubMed

Glasmachers, Tobias; Igel, Christian

2005-10-01

Gradient-based optimizing of gaussian kernel functions is considered. The gradient for the adaptation of scaling and rotation of the input space is computed to achieve invariance against linear transformations. This is done by using the exponential map as a parameterization of the kernel parameter manifold. By restricting the optimization to a constant trace subspace, the kernel size can be controlled. This is, for example, useful to prevent overfitting when minimizing radius-margin generalization performance measures. The concepts are demonstrated by training hard margin support vector machines on toy data.

Genome-wide association mapping of crown rust resistance in oat elite germplasm

USDA-ARS?s Scientific Manuscript database

Oat crown rust, caused by Puccinia coronata f. sp. avenae, is a major constraint to oat production in many parts of the world. In this first comprehensive multi-environment genome-wide association map of oat crown rust, we used 2,972 SNPs genotyped on 631 oat lines for association mapping of quantit...

Properties of amaranth flour with functional oat products

USDA-ARS?s Scientific Manuscript database

Amaranth flour containing the essential amino acid, lysine, was composited with oat products that contain ß-glucan known for lowering blood cholesterol and preventing heart disease. The pasting and rheological properties of amaranth-oat composites were evaluated. The amaranth-Nutrim composites showe...

Pasting and rheological properties of quinoa-oat composites

USDA-ARS?s Scientific Manuscript database

Quinoa (Chenopodium, quinoa) flour, known for its essential amino acids, was composited with oat products containing ß-glucan known for lowering blood cholesterol and preventing heart disease. Quinoa-oat composites were developed and evaluated for their pasting and rheological properties by a Rapid ...

Quantum kernel applications in medicinal chemistry.

PubMed

Huang, Lulu; Massa, Lou

2012-07-01

Progress in the quantum mechanics of biological molecules is being driven by computational advances. The notion of quantum kernels can be introduced to simplify the formalism of quantum mechanics, making it especially suitable for parallel computation of very large biological molecules. The essential idea is to mathematically break large biological molecules into smaller kernels that are calculationally tractable, and then to represent the full molecule by a summation over the kernels. The accuracy of the kernel energy method (KEM) is shown by systematic application to a great variety of molecular types found in biology. These include peptides, proteins, DNA and RNA. Examples are given that explore the KEM across a variety of chemical models, and to the outer limits of energy accuracy and molecular size. KEM represents an advance in quantum biology applicable to problems in medicine and drug design.

Gis-Based Crop Support System For Common Oatand Naked Oat in China

NASA Astrophysics Data System (ADS)

Wan, Fan; Wang, Zhen; Li, Fengmin; Cao, Huhua; Sun, Guojun

The identification of the suitable areas for common oat (Avena sativa L.) and naked oat (Avena nuda L.) in China using Multi-Criteria Evaluation (MCE) approach based on GIS is presented in the current article. Climate, topography, soil, land use and oat variety databases were created. Relevant criteria,suitability levels and their weights for each factor were defined. Then the criteria maps were obtained and turned into the MCE process, and suitability maps for common oat and naked oat were created. The land use and the suitability maps were crossed to identify the suitable areas for each crop. The results identified 397,720 km2 of suitable areas for common oats of forage purpose distributed in 744 counties in 17 provinces, and 556,232 km2 of suitable areas for naked oats of grain purpose distributed in 779 counties in 19 provinces. This result is in accordance with the distribution of farmingpastoral ecozones located in semi-arid regions of northern China. The mapped areas can help define the working limits and serve as indicative zones for oat in China. The created databases, mapped results, interface of expert system and relevant hardware facilities could construct a complete crop support system for oats.

A role for the organic anion transporter OAT3 in renal creatinine secretion in mice

PubMed Central

Eraly, Satish A.; Rao, Satish Ramachandra; Gerasimova, Maria; Rose, Michael; Nagle, Megha; Anzai, Naohiko; Smith, Travis; Sharma, Kumar; Nigam, Sanjay K.; Rieg, Timo

2012-01-01

Tubular secretion of the organic cation, creatinine, limits its value as a marker of glomerular filtration rate (GFR) but the molecular determinants of this pathway are unclear. The organic anion transporters, OAT1 and OAT3, are expressed on the basolateral membrane of the proximal tubule and transport organic anions but also neutral compounds and cations. Here, we demonstrate specific uptake of creatinine into mouse mOat1- and mOat3-microinjected Xenopus laevis oocytes at a concentration of 10 μM (i.e., similar to physiological plasma levels), which was inhibited by both probenecid and cimetidine, prototypical competitive inhibitors of organic anion and cation transporters, respectively. Renal creatinine clearance was consistently greater than inulin clearance (as a measure of GFR) in wild-type (WT) mice but not in mice lacking OAT1 (Oat1−/−) and OAT3 (Oat3−/−). WT mice presented renal creatinine net secretion (0.23 ± 0.03 μg/min) which represented 45 ± 6% of total renal creatinine excretion. Mean values for renal creatinine net secretion and renal creatinine secretion fraction were not different from zero in Oat1−/− (−0.03 ± 0.10 μg/min; −3 ± 18%) and Oat3−/− (0.01 ± 0.06 μg/min; −6 ± 19%), with greater variability in Oat1−/−. Expression of OAT3 protein in the renal membranes of Oat1−/− mice was reduced to ∼6% of WT levels, and that of OAT1 in Oat3−/− mice to ∼60%, possibly as a consequence of the genes for Oat1 and Oat3 having adjacent chromosomal locations. Plasma creatinine concentrations of Oat3−/− were elevated in clearance studies under anesthesia but not following brief isoflurane anesthesia, indicating that the former condition enhanced the quantitative contribution of OAT3 for renal creatinine secretion. The results are consistent with a contribution of OAT3 and possibly OAT1 to renal creatinine secretion in mice. PMID:22338083

Pasting and rheological properties of oat products dry-blended with ground chia seeds

USDA-ARS?s Scientific Manuscript database

Oat products containing ß-glucan are documented for lowering blood cholesterol that could be beneficial for preventing coronary heart disease. Oat products (oat flour, oat bran concentrate, and Nutrim) were dry-blended with ground chia (Salvia hispanica L.) that contains omega-3 polyunsaturated fatt...

Genetic Analysis of Kernel Traits in Maize-Teosinte Introgression Populations.

PubMed

Liu, Zhengbin; Garcia, Arturo; McMullen, Michael D; Flint-Garcia, Sherry A

2016-08-09

Seed traits have been targeted by human selection during the domestication of crop species as a way to increase the caloric and nutritional content of food during the transition from hunter-gather to early farming societies. The primary seed trait under selection was likely seed size/weight as it is most directly related to overall grain yield. Additional seed traits involved in seed shape may have also contributed to larger grain. Maize (Zea mays ssp. mays) kernel weight has increased more than 10-fold in the 9000 years since domestication from its wild ancestor, teosinte (Z. mays ssp. parviglumis). In order to study how size and shape affect kernel weight, we analyzed kernel morphometric traits in a set of 10 maize-teosinte introgression populations using digital imaging software. We identified quantitative trait loci (QTL) for kernel area and length with moderate allelic effects that colocalize with kernel weight QTL. Several genomic regions with strong effects during maize domestication were detected, and a genetic framework for kernel traits was characterized by complex pleiotropic interactions. Our results both confirm prior reports of kernel domestication loci and identify previously uncharacterized QTL with a range of allelic effects, enabling future research into the genetic basis of these traits. Copyright © 2016 Liu et al.

Genetic Analysis of Kernel Traits in Maize-Teosinte Introgression Populations

PubMed Central

Liu, Zhengbin; Garcia, Arturo; McMullen, Michael D.; Flint-Garcia, Sherry A.

2016-01-01

Seed traits have been targeted by human selection during the domestication of crop species as a way to increase the caloric and nutritional content of food during the transition from hunter-gather to early farming societies. The primary seed trait under selection was likely seed size/weight as it is most directly related to overall grain yield. Additional seed traits involved in seed shape may have also contributed to larger grain. Maize (Zea mays ssp. mays) kernel weight has increased more than 10-fold in the 9000 years since domestication from its wild ancestor, teosinte (Z. mays ssp. parviglumis). In order to study how size and shape affect kernel weight, we analyzed kernel morphometric traits in a set of 10 maize-teosinte introgression populations using digital imaging software. We identified quantitative trait loci (QTL) for kernel area and length with moderate allelic effects that colocalize with kernel weight QTL. Several genomic regions with strong effects during maize domestication were detected, and a genetic framework for kernel traits was characterized by complex pleiotropic interactions. Our results both confirm prior reports of kernel domestication loci and identify previously uncharacterized QTL with a range of allelic effects, enabling future research into the genetic basis of these traits. PMID:27317774

Occurrence of 'super soft' wheat kernel texture in hexaploid and tetraploid wheats

USDA-ARS?s Scientific Manuscript database

Wheat kernel texture is a key trait that governs milling performance, flour starch damage, flour particle size, flour hydration properties, and baking quality. Kernel texture is commonly measured using the Perten Single Kernel Characterization System (SKCS). The SKCS returns texture values (Hardness...

Active impulsive noise control using maximum correntropy with adaptive kernel size

NASA Astrophysics Data System (ADS)

Lu, Lu; Zhao, Haiquan

2017-03-01

The active noise control (ANC) based on the principle of superposition is an attractive method to attenuate the noise signals. However, the impulsive noise in the ANC systems will degrade the performance of the controller. In this paper, a filtered-x recursive maximum correntropy (FxRMC) algorithm is proposed based on the maximum correntropy criterion (MCC) to reduce the effect of outliers. The proposed FxRMC algorithm does not requires any priori information of the noise characteristics and outperforms the filtered-x least mean square (FxLMS) algorithm for impulsive noise. Meanwhile, in order to adjust the kernel size of FxRMC algorithm online, a recursive approach is proposed through taking into account the past estimates of error signals over a sliding window. Simulation and experimental results in the context of active impulsive noise control demonstrate that the proposed algorithms achieve much better performance than the existing algorithms in various noise environments.

Examining Potential Boundary Bias Effects in Kernel Smoothing on Equating: An Introduction for the Adaptive and Epanechnikov Kernels.

PubMed

Cid, Jaime A; von Davier, Alina A

2015-05-01

Test equating is a method of making the test scores from different test forms of the same assessment comparable. In the equating process, an important step involves continuizing the discrete score distributions. In traditional observed-score equating, this step is achieved using linear interpolation (or an unscaled uniform kernel). In the kernel equating (KE) process, this continuization process involves Gaussian kernel smoothing. It has been suggested that the choice of bandwidth in kernel smoothing controls the trade-off between variance and bias. In the literature on estimating density functions using kernels, it has also been suggested that the weight of the kernel depends on the sample size, and therefore, the resulting continuous distribution exhibits bias at the endpoints, where the samples are usually smaller. The purpose of this article is (a) to explore the potential effects of atypical scores (spikes) at the extreme ends (high and low) on the KE method in distributions with different degrees of asymmetry using the randomly equivalent groups equating design (Study I), and (b) to introduce the Epanechnikov and adaptive kernels as potential alternative approaches to reducing boundary bias in smoothing (Study II). The beta-binomial model is used to simulate observed scores reflecting a range of different skewed shapes.

Oat raw materials and bakery products - amino acid composition and celiac immunoreactivity.

PubMed

Mickowska, Barbara; Litwinek, Dorota; Gambuś, Halina

2016-01-01

The aim of this study was to compare the biochemical and immunochemical properties of avenins in some special oat raw materials and additionally the possibility of using them as a raw material for the gluten-free bakery products. The compared oat raw materials were - oat flakes, commercial oat flours (including gluten-free oat flour) and residual oat flour, which is by-product of β-glucan preparation. Biochemical characteristic included amino acid compositions and SDS-PAGE profiles of extracted avenins. The immunochemical reactivity with polyclonal anti-gluten and monoclonal anti-gliadin antibodies was evaluated qualitatively and quantitatively by immunoblotting and ELISA methods. Additionally, experimental bakery products made of examined raw materials were assessed according to their suitability for the celiac patients' diet. The highest protein content was measured in the β-glucan preparation "Betaven" and gluten-free oat flour. Proteins of all materials are rich in glutamic and aspartic acid, leucine and arginine. Proportions of amino acids in avenins extracted from most of oat raw materials are similar, excluding gluten-free oat flour, which has a very low avenin content and proportions of individual amino acids are different. The SDS-PAGE protein pattern consisted of proteins with molecular weight of about 25-35 kDa. Polyclonal anti-gluten anti-body recognized all protein fractions of molecular weight higher than 20 kDa. Quantitative ELISA analysis shows that the majority of samples has a gliadin-like protein content within the range of 80-260 mg/kg, excluding gluten-free flours and corresponding bakery products. Altogether, β-glucan preparation has extremely high level of gliadin-like proteins. In the examined oat raw materials and foods the contents of immunoreactive amino acid sequences exceeded the limit of 20 mg/kg (considered as gluten-free) except for gluten-free flours (oat and  the prepared mixture) and the bakery products based on gluten

Flavonoids Are Inhibitors of Human Organic Anion Transporter 1 (OAT1)–Mediated Transport

PubMed Central

An, Guohua; Wang, Xiaodong

2014-01-01

Organic anion transporter 1 (OAT1) has been reported to be involved in the nephrotoxicity of many anionic xenobiotics. As current clinically used OAT1 inhibitors are often associated with safety issues, identifying potent OAT1 inhibitors with little toxicity is of great value in reducing OAT1-mediated drug nephrotoxicity. Flavonoids are a class of polyphenolic compounds with exceptional safety records. Our objective was to evaluate the effects of 18 naturally occurring flavonoids, and some of their glycosides, on the uptake of para-aminohippuric acid (PAH) in both OAT1-expressing and OAT1-negative LLC-PK1 cells. Most flavonoid aglycones produced substantial decreases in PAH uptake in OAT1-expressing cells. Among the flavonoids screened, fisetin, luteolin, morin, and quercetin exhibited the strongest effect and produced complete inhibition of OAT1-mediated PAH uptake at a concentration of 50 μM. Further concentration-dependent studies revealed that both morin and luteolin are potent OAT1 inhibitors, with IC50 values of <0.3 and 0.47 μM, respectively. In contrast to the tested flavonoid aglycones, all flavonoid glycosides had negligible or small effects on OAT1. In addition, the role of OAT1 in the uptake of fisetin, luteolin, morin, and quercetin was investigated and fisetin was found to be a substrate of OAT1. Taken together, our results indicate that flavonoids are a novel class of OAT1 modulators. Considering the high consumption of flavonoids in the diet and in herbal products, OAT1-mediated flavonoid-drug interactions may be clinically relevant. Further investigation is warranted to evaluate the nephroprotective role of flavonoids in relation to drug-induced nephrotoxicity mediated by the OAT1 pathway. PMID:25002746

Reduction of Ochratoxin A in Oat Flakes by Twin-Screw Extrusion Processing.

PubMed

Lee, Hyun Jung; Dahal, Samjhana; Perez, Enrique Garcia; Kowalski, Ryan Joseph; Ganjyal, Girish M; Ryu, Dojin

2017-10-01

Ochratoxin A (OTA) is one of the most important mycotoxins owing to its widespread occurrence and toxicity, including nephrotoxicity and potential carcinogenicity to humans. OTA has been detected in a wide range of agricultural commodities, including cereal grains and their processed products. In particular, oat-based products show a higher incidence and level of contamination. Extrusion cooking is widely used in the manufacturing of breakfast cereals and snacks and may reduce mycotoxins to varying degrees. Hence, the effects of extrusion cooking on the stability of OTA in spiked (100 μg/kg) oat flake was investigated by using a laboratory-scale twin-screw extruder with a central composite design. Factors examined were moisture content (20, 25, and 30% dry weight basis), temperature (140, 160, and 180°C), screw speed (150, 200, and 250 rpm), and die size (1.5, 2, and 3 mm). Both nonextruded and extruded samples were analyzed for reductions of OTA by high-performance liquid chromatography, coupled with fluorescence detection. The percentage of reductions in OTA in the contaminated oat flakes upon extrusion processing were in the range of 0 to 28%. OTA was partially stable during extrusion, with only screw speed and die size having significant effect on reduction (P < 0.005). The highest reduction of 28% was achieved at 180°C, 20% moisture, 250 rpm screw speed, and a 3-mm die with 193 kJ/kg specific mechanical energy. According to the central composite design analyses, up to 28% of OTA can be reduced by a combination of 162°C, 30% moisture, and 221 rpm, with a 3-mm die.

Multineuron spike train analysis with R-convolution linear combination kernel.

PubMed

Tezuka, Taro

2018-06-01

A spike train kernel provides an effective way of decoding information represented by a spike train. Some spike train kernels have been extended to multineuron spike trains, which are simultaneously recorded spike trains obtained from multiple neurons. However, most of these multineuron extensions were carried out in a kernel-specific manner. In this paper, a general framework is proposed for extending any single-neuron spike train kernel to multineuron spike trains, based on the R-convolution kernel. Special subclasses of the proposed R-convolution linear combination kernel are explored. These subclasses have a smaller number of parameters and make optimization tractable when the size of data is limited. The proposed kernel was evaluated using Gaussian process regression for multineuron spike trains recorded from an animal brain. It was compared with the sum kernel and the population Spikernel, which are existing ways of decoding multineuron spike trains using kernels. The results showed that the proposed approach performs better than these kernels and also other commonly used neural decoding methods. Copyright © 2018 Elsevier Ltd. All rights reserved.

Plant defense activators as elicitors of oat avenanthramide biosynthesis

USDA-ARS?s Scientific Manuscript database

Oats produce a group of phenolic secondary metabolites termed “avenanthramides”. Among food crops these metabolites are unique to oat. In addition to their biological role as phytoalexins, the avenanthramides are potent antioxidants in vitro and have potential as nutraceuticals. In cellular assays ...

Dielectric properties of wheat flour mixed with oat meal

NASA Astrophysics Data System (ADS)

Łuczycka, D.; Czubaszek, A.; Fujarczuk, M.; Pruski, K.

2013-03-01

Possibilities of using electric methods for determining admixtures of oat meal to wheat flour, type 650 are presented. In wheat flour, oat meal and mixtures containing 10, 20 and 30% of the oat meal, moisture, protein, starch and ash content, sedimentation value, yield and softening of wet gluten were determined. In samples containing 0, 5, 10, 15, 20, 25, 30 and 100% of oat meal, the dielectric loss factor and conductivity were determined using an impedance analyzer for electromagnetic field frequency ranging from 0.1-20 kHz. It was found that the dielectric loss factor varied for tested material. The best distinguishing between tested mixtures was obtained at the measuring electromagnetic field frequency of 20 kHz. The loss factor was significantly correlated with the yield of wet gluten and the sedimentation value, parameters indicating the amount and quality of gluten proteins in flour.

Physical properties and FTIR analysis of rice-oat flour and maize-oat flour based extruded food products containing olive pomace.

PubMed

Ying, DanYang; Hlaing, Mya Myintzu; Lerisson, Julie; Pitts, Keith; Cheng, Lijiang; Sanguansri, Luz; Augustin, Mary Ann

2017-10-01

Olive pomace, a waste stream from olive oil processing, was fractionated by centrifugation to obtain a supernatant and a flesh-enriched fraction, and freeze dried to obtain a powder. The dried supernatant contained 5.8% moisture, 4.8% protein, 3.5% fat, 3.5% ash, 82.4% carbohydrate (including 17.2% dietary fiber) and polyphenols (2970mg gallic acid equivalents (GAE)/100g). The dried flesh-enriched fraction, contained 5.9% moisture, 13.4% protein, 14.2% fat, 3.5% ash, 63.1% carbohydrate (including 42.7% dietary fiber) and polyphenols (1960mg GAE/100g). The extruded products using rice-oat flour or maize-oat flour mixtures as the base were formulated to contain 5% or 10% olive pomace fractions (dry basis). The extruded products with added olive pomace fractions has higher fiber (2-7g/100g) and polyphenol contents (67-161mg GAE/100g) compared to the corresponding mixtures of rice-oat flour base (0.92g/100g fiber, 20mg GAE/100g) or maize-oat flour base (3.2g/100g fiber, 20mg GAE/100g) without olive pomace fractions. Addition of olive pomace fractions reduced the die pressure and specific mechanical energy during extrusion and resulted in lower radial expansion in the extruded product. The impact of the addition of olive pomace fraction on physical characteristics of the extruded product is higher for rice-oat flour base than maize-oat flour base. The underlining mechanism was explained by FTIR analysis. FTIR showed that there were significant changes in the carbohydrate components and the structure of the proteins on extrusion, with consequent effects on the expansion and density of the extruded product. This study showed the feasibility of preparing fiber and polyphenol enriched extruded products by incorporation of olive pomace. This shows the potential of recovery and diversion of edible components from waste streams of olive oil processing for formulation of extruded products. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Oat Newsletter: where we've been and where we're going

USDA-ARS?s Scientific Manuscript database

The first Oat Newsletter was published by the National Oat Conference in 1950. It was published once a year and mailed out to “oat workers” only. The newsletter was designed to supplement the Uniform Nursery reports by providing short research updates, meeting information, community information,...

Avenanthramide-enriched oats have an anti-inflammatory action: a pilot clinical trial

USDA-ARS?s Scientific Manuscript database

Regular consumption of oats has been shown to benefit heart health by lowering serum lipids in humans, an effect mediated primarily via beta-glucan. Other components of oats, including the polyphenolic avenanthramides (AV), may also contribute to reducing the risk of atherogenesis. In vivo, oat AV e...

Chromosome-anchored QTL conferring aluminum tolerance in hexaploid oat

USDA-ARS?s Scientific Manuscript database

Abstract Aluminum (Al) toxicity is a major constraint on crop production in acid soils around the world. Hexaploid oat (Avena sativa L.) possesses signi'cant Al tolerance making it a good candidate for production in these environments. Genetic improvement for Al tolerance in oat has traditionally be...

Analysis of genetic diversity using SNP markers in oat

USDA-ARS?s Scientific Manuscript database

A large-scale single nucleotide polymorphism (SNP) discovery was carried out in cultivated oat using Roche 454 sequencing methods. DNA sequences were generated from cDNAs originating from a panel of 20 diverse oat cultivars, and from Diversity Array Technology (DArT) genomic complexity reductions fr...

7 CFR 810.205 - Grades and grade requirements for Two-rowed Malting barley.

Code of Federal Regulations, 2010 CFR

2010-01-01

... (percent) Maximum limits of— Wild oats (percent) Foreign material (percent) Skinned and broken kernels... Injured-by-frost kernels and injured-by-mold kernels are not considered damaged kernels or considered...

7 CFR 810.202 - Definition of other terms.

Code of Federal Regulations, 2014 CFR

2014-01-01

... barley kernels, other grains, and wild oats that are badly shrunken and distinctly discolored black or... kernels. Kernels and pieces of barley kernels that are distinctly indented, immature or shrunken in...

7 CFR 810.202 - Definition of other terms.

Code of Federal Regulations, 2013 CFR

2013-01-01

... barley kernels, other grains, and wild oats that are badly shrunken and distinctly discolored black or... kernels. Kernels and pieces of barley kernels that are distinctly indented, immature or shrunken in...

7 CFR 810.202 - Definition of other terms.

Code of Federal Regulations, 2012 CFR

2012-01-01

... barley kernels, other grains, and wild oats that are badly shrunken and distinctly discolored black or... kernels. Kernels and pieces of barley kernels that are distinctly indented, immature or shrunken in...

Identification and molecular characterization of oat peptides implicated on coeliac immune response

PubMed Central

Comino, Isabel; Bernardo, David; Bancel, Emmanuelle; Moreno, María de Lourdes; Sánchez, Borja; Barro, Francisco; Šuligoj, Tanja; Ciclitira, Paul J.; Cebolla, Ángel; Knight, Stella C.; Branlard, Gérard; Sousa, Carolina

2016-01-01

Background Oats provide important nutritional and pharmacological properties, although their safety in coeliac patients remains controversial. Previous studies have confirmed that the reactivity of the anti-33-mer monoclonal antibody with different oat varieties is proportional to the immune responses in terms of T-cell proliferation. Although the impact of these varieties on the adaptive response has been studied, the role of the dendritic cells (DC) is still poorly understood. The aim of this study is to characterize different oat fractions and to study their effect on DC from coeliac patients. Methods and results Protein fractions were isolated from oat grains and analyzed by SDS–PAGE. Several proteins were characterized in the prolamin fraction using immunological and proteomic tools, and by Nano-LC-MS/MS. These proteins, analogous to α- and γ-gliadin-like, showed reactive sequences to anti-33-mer antibody suggesting their immunogenic potential. That was further confirmed as some of the newly identified oat peptides had a differential stimulatory capacity on circulating DC from coeliac patients compared with healthy controls. Conclusions This is the first time, to our knowledge, where newly identified oat peptides have been shown to elicit a differential stimulatory capacity on circulating DC obtained from coeliac patients, potentially identifying immunogenic properties of these oat peptides. PMID:26853779

Transcriptome analysis of hexaploid hulless oat in response to salinity stress

PubMed Central

Wu, Bin; Hu, Yani; Huo, Pengjie; Zhang, Qian; Chen, Xin; Zhang, Zongwen

2017-01-01

Background Oat is a cereal crop of global importance used for food, feed, and forage. Understanding salinity stress tolerance mechanisms in plants is an important step towards generating crop varieties that can cope with environmental stresses. To date, little is known about the salt tolerance of oat at the molecular level. To better understand the molecular mechanisms underlying salt tolerance in oat, we investigated the transcriptomes of control and salt-treated oat using RNA-Seq. Results Using Illumina HiSeq 4000 platform, we generated 72,291,032 and 356,891,432 reads from non-stressed control and salt-stressed oat, respectively. Assembly of 64 Gb raw sequence data yielded 128,414 putative unique transcripts with an average length of 1,189 bp. Analysis of the assembled unigenes from the salt stressed and control libraries indicated that about 65,000 unigenes were differentially expressed at different stages. Functional annotation showed that ABC transporters, plant hormone signal transduction, plant-pathogen interactions, starch and sucrose metabolism, arginine and proline metabolism, and other secondary metabolite pathways were enriched under salt stress. Based on the RPKM values of assembled unigenes, 24 differentially expressed genes under salt stress were selected for quantitative RT-PCR validation, which successfully confirmed the results of RNA-Seq. Furthermore, we identified 18,039 simple sequence repeats, which may help further elucidate salt tolerance mechanisms in oat. Conclusions Our global survey of transcriptome profiles of oat plants in response to salt stress provides useful insights into the molecular mechanisms underlying salt tolerance in this crop. These findings also represent a rich resource for further analysis of salt tolerance and for breeding oat with improved salt tolerance through the use of salt-related genes. PMID:28192458

Adaptive kernel regression for freehand 3D ultrasound reconstruction

NASA Astrophysics Data System (ADS)

Alshalalfah, Abdel-Latif; Daoud, Mohammad I.; Al-Najar, Mahasen

2017-03-01

Freehand three-dimensional (3D) ultrasound imaging enables low-cost and flexible 3D scanning of arbitrary-shaped organs, where the operator can freely move a two-dimensional (2D) ultrasound probe to acquire a sequence of tracked cross-sectional images of the anatomy. Often, the acquired 2D ultrasound images are irregularly and sparsely distributed in the 3D space. Several 3D reconstruction algorithms have been proposed to synthesize 3D ultrasound volumes based on the acquired 2D images. A challenging task during the reconstruction process is to preserve the texture patterns in the synthesized volume and ensure that all gaps in the volume are correctly filled. This paper presents an adaptive kernel regression algorithm that can effectively reconstruct high-quality freehand 3D ultrasound volumes. The algorithm employs a kernel regression model that enables nonparametric interpolation of the voxel gray-level values. The kernel size of the regression model is adaptively adjusted based on the characteristics of the voxel that is being interpolated. In particular, when the algorithm is employed to interpolate a voxel located in a region with dense ultrasound data samples, the size of the kernel is reduced to preserve the texture patterns. On the other hand, the size of the kernel is increased in areas that include large gaps to enable effective gap filling. The performance of the proposed algorithm was compared with seven previous interpolation approaches by synthesizing freehand 3D ultrasound volumes of a benign breast tumor. The experimental results show that the proposed algorithm outperforms the other interpolation approaches.

Many Molecular Properties from One Kernel in Chemical Space

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

Ramakrishnan, Raghunathan; von Lilienfeld, O. Anatole

We introduce property-independent kernels for machine learning modeling of arbitrarily many molecular properties. The kernels encode molecular structures for training sets of varying size, as well as similarity measures sufficiently diffuse in chemical space to sample over all training molecules. Corresponding molecular reference properties provided, they enable the instantaneous generation of ML models which can systematically be improved through the addition of more data. This idea is exemplified for single kernel based modeling of internal energy, enthalpy, free energy, heat capacity, polarizability, electronic spread, zero-point vibrational energy, energies of frontier orbitals, HOMOLUMO gap, and the highest fundamental vibrational wavenumber. Modelsmore » of these properties are trained and tested using 112 kilo organic molecules of similar size. Resulting models are discussed as well as the kernels’ use for generating and using other property models.« less

Kernel Machine SNP-set Testing under Multiple Candidate Kernels

PubMed Central

Wu, Michael C.; Maity, Arnab; Lee, Seunggeun; Simmons, Elizabeth M.; Harmon, Quaker E.; Lin, Xinyi; Engel, Stephanie M.; Molldrem, Jeffrey J.; Armistead, Paul M.

2013-01-01

Joint testing for the cumulative effect of multiple single nucleotide polymorphisms grouped on the basis of prior biological knowledge has become a popular and powerful strategy for the analysis of large scale genetic association studies. The kernel machine (KM) testing framework is a useful approach that has been proposed for testing associations between multiple genetic variants and many different types of complex traits by comparing pairwise similarity in phenotype between subjects to pairwise similarity in genotype, with similarity in genotype defined via a kernel function. An advantage of the KM framework is its flexibility: choosing different kernel functions allows for different assumptions concerning the underlying model and can allow for improved power. In practice, it is difficult to know which kernel to use a priori since this depends on the unknown underlying trait architecture and selecting the kernel which gives the lowest p-value can lead to inflated type I error. Therefore, we propose practical strategies for KM testing when multiple candidate kernels are present based on constructing composite kernels and based on efficient perturbation procedures. We demonstrate through simulations and real data applications that the procedures protect the type I error rate and can lead to substantially improved power over poor choices of kernels and only modest differences in power versus using the best candidate kernel. PMID:23471868

Avenanthramides, unique polyphenols of oats with potential health effects

USDA-ARS?s Scientific Manuscript database

Oats in addition to being a good source of carbohydrate energy in food and animal feed are considered a grain with several health benefits. It is a grain with a well-accepted healthy heart effect due to its soluble fiber b-glucan content, which reduces blood cholesterol. For a long time, the oat bat...

Physical properties of gluten free sugar cookies containing teff and functional oat products

USDA-ARS?s Scientific Manuscript database

Teff-oat composites were developed using gluten free teff flour containing essential 15 amino acids with oat products containing ß-glucan, known for lowering blood cholesterol and improving texture. The teff-oat composites were used in sugar cookies for improving nutritional and physical properties....

Investigation of various energy deposition kernel refinements for the convolution/superposition method

PubMed Central

Huang, Jessie Y.; Eklund, David; Childress, Nathan L.; Howell, Rebecca M.; Mirkovic, Dragan; Followill, David S.; Kry, Stephen F.

2013-01-01

Purpose: Several simplifications used in clinical implementations of the convolution/superposition (C/S) method, specifically, density scaling of water kernels for heterogeneous media and use of a single polyenergetic kernel, lead to dose calculation inaccuracies. Although these weaknesses of the C/S method are known, it is not well known which of these simplifications has the largest effect on dose calculation accuracy in clinical situations. The purpose of this study was to generate and characterize high-resolution, polyenergetic, and material-specific energy deposition kernels (EDKs), as well as to investigate the dosimetric impact of implementing spatially variant polyenergetic and material-specific kernels in a collapsed cone C/S algorithm. Methods: High-resolution, monoenergetic water EDKs and various material-specific EDKs were simulated using the EGSnrc Monte Carlo code. Polyenergetic kernels, reflecting the primary spectrum of a clinical 6 MV photon beam at different locations in a water phantom, were calculated for different depths, field sizes, and off-axis distances. To investigate the dosimetric impact of implementing spatially variant polyenergetic kernels, depth dose curves in water were calculated using two different implementations of the collapsed cone C/S method. The first method uses a single polyenergetic kernel, while the second method fully takes into account spectral changes in the convolution calculation. To investigate the dosimetric impact of implementing material-specific kernels, depth dose curves were calculated for a simplified titanium implant geometry using both a traditional C/S implementation that performs density scaling of water kernels and a novel implementation using material-specific kernels. Results: For our high-resolution kernels, we found good agreement with the Mackie et al. kernels, with some differences near the interaction site for low photon energies (<500 keV). For our spatially variant polyenergetic kernels, we

High-throughput method for ear phenotyping and kernel weight estimation in maize using ear digital imaging.

PubMed

Makanza, R; Zaman-Allah, M; Cairns, J E; Eyre, J; Burgueño, J; Pacheco, Ángela; Diepenbrock, C; Magorokosho, C; Tarekegne, A; Olsen, M; Prasanna, B M

2018-01-01

Grain yield, ear and kernel attributes can assist to understand the performance of maize plant under different environmental conditions and can be used in the variety development process to address farmer's preferences. These parameters are however still laborious and expensive to measure. A low-cost ear digital imaging method was developed that provides estimates of ear and kernel attributes i.e., ear number and size, kernel number and size as well as kernel weight from photos of ears harvested from field trial plots. The image processing method uses a script that runs in a batch mode on ImageJ; an open source software. Kernel weight was estimated using the total kernel number derived from the number of kernels visible on the image and the average kernel size. Data showed a good agreement in terms of accuracy and precision between ground truth measurements and data generated through image processing. Broad-sense heritability of the estimated parameters was in the range or higher than that for measured grain weight. Limitation of the method for kernel weight estimation is discussed. The method developed in this work provides an opportunity to significantly reduce the cost of selection in the breeding process, especially for resource constrained crop improvement programs and can be used to learn more about the genetic bases of grain yield determinants.

TaGS5-3A, a grain size gene selected during wheat improvement for larger kernel and yield.

PubMed

Ma, Lin; Li, Tian; Hao, Chenyang; Wang, Yuquan; Chen, Xinhong; Zhang, Xueyong

2016-05-01

Grain size is a dominant component of grain weight in cereals. Earlier studies have shown that OsGS5 plays a major role in regulating both grain size and weight in rice via promotion of cell division. In this study, we isolated TaGS5 homoeologues in wheat and mapped them on chromosomes 3A, 3B and 3D. Temporal and spatial expression analysis showed that TaGS5 homoeologues were preferentially expressed in young spikes and developing grains. Two alleles of TaGS5-3A, TaGS5-3A-T and TaGS5-3A-G were identified in wheat accessions, and a functional marker was developed to discriminate them. Association analysis revealed that TaGS5-3A-T was significantly correlated with larger grain size and higher thousand kernel weight. Biochemical assays showed that TaGS5-3A-T possesses a higher enzymatic activity than TaGS5-3A-G. Transgenic rice lines overexpressing TaGS5-3A-T also exhibited larger grain size and higher thousand kernel weight than TaGS5-3A-G lines, and the transcript levels of cell cycle-related genes in TaGS5-3A-T lines were higher than those in TaGS5-3A-G lines. Furthermore, systematic evolution analysis in diploid, tetraploid and hexaploid wheat showed that TaGS5-3A underwent strong artificial selection during wheat polyploidization events and the frequency changes of two alleles demonstrated that TaGS5-3A-T was favoured in global modern wheat cultivars. These results suggest that TaGS5-3A is a positive regulator of grain size and its favoured allele TaGS5-3A-T exhibits a larger potential application in wheat high-yield breeding. © 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

Pollen source effects on growth of kernel structures and embryo chemical compounds in maize.

PubMed

Tanaka, W; Mantese, A I; Maddonni, G A

2009-08-01

Previous studies have reported effects of pollen source on the oil concentration of maize (Zea mays) kernels through modifications to both the embryo/kernel ratio and embryo oil concentration. The present study expands upon previous analyses by addressing pollen source effects on the growth of kernel structures (i.e. pericarp, endosperm and embryo), allocation of embryo chemical constituents (i.e. oil, protein, starch and soluble sugars), and the anatomy and histology of the embryos. Maize kernels with different oil concentration were obtained from pollinations with two parental genotypes of contrasting oil concentration. The dynamics of the growth of kernel structures and allocation of embryo chemical constituents were analysed during the post-flowering period. Mature kernels were dissected to study the anatomy (embryonic axis and scutellum) and histology [cell number and cell size of the scutellums, presence of sub-cellular structures in scutellum tissue (starch granules, oil and protein bodies)] of the embryos. Plants of all crosses exhibited a similar kernel number and kernel weight. Pollen source modified neither the growth period of kernel structures, nor pericarp growth rate. By contrast, pollen source determined a trade-off between embryo and endosperm growth rates, which impacted on the embryo/kernel ratio of mature kernels. Modifications to the embryo size were mediated by scutellum cell number. Pollen source also affected (P < 0.01) allocation of embryo chemical compounds. Negative correlations among embryo oil concentration and those of starch (r = 0.98, P < 0.01) and soluble sugars (r = 0.95, P < 0.05) were found. Coincidently, embryos with low oil concentration had an increased (P < 0.05-0.10) scutellum cell area occupied by starch granules and fewer oil bodies. The effects of pollen source on both embryo/kernel ratio and allocation of embryo chemicals seems to be related to the early established sink strength (i.e. sink size and sink activity) of the

Shaker Oats: Fortifying Musicality

ERIC Educational Resources Information Center

Semmes, Laurie R.

2010-01-01

In this article, the author describes how an experiment in a class she taught called Minority Musics of North America developed into a surprisingly successful and flexible teaching tool known as "Shaker Oats," created to encourage the concepts of ensemble and community. Most music educators in the United States today are familiar with…

Influence of wheat kernel physical properties on the pulverizing process.

PubMed

Dziki, Dariusz; Cacak-Pietrzak, Grażyna; Miś, Antoni; Jończyk, Krzysztof; Gawlik-Dziki, Urszula

2014-10-01

The physical properties of wheat kernel were determined and related to pulverizing performance by correlation analysis. Nineteen samples of wheat cultivars about similar level of protein content (11.2-12.8 % w.b.) and obtained from organic farming system were used for analysis. The kernel (moisture content 10 % w.b.) was pulverized by using the laboratory hammer mill equipped with round holes 1.0 mm screen. The specific grinding energy ranged from 120 kJkg(-1) to 159 kJkg(-1). On the basis of data obtained many of significant correlations (p < 0.05) were found between wheat kernel physical properties and pulverizing process of wheat kernel, especially wheat kernel hardness index (obtained on the basis of Single Kernel Characterization System) and vitreousness significantly and positively correlated with the grinding energy indices and the mass fraction of coarse particles (> 0.5 mm). Among the kernel mechanical properties determined on the basis of uniaxial compression test only the rapture force was correlated with the impact grinding results. The results showed also positive and significant relationships between kernel ash content and grinding energy requirements. On the basis of wheat physical properties the multiple linear regression was proposed for predicting the average particle size of pulverized kernel.

7 CFR 51.2559 - Size classifications.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 7 Agriculture 2 2014-01-01 2014-01-01 false Size classifications. 51.2559 Section 51.2559....2559 Size classifications. (a) The size of pistachio kernels may be specified in connection with the grade in accordance with one of the following size classifications. (1) Jumbo Whole Kernels: 80 percent...

7 CFR 51.2559 - Size classifications.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 7 Agriculture 2 2013-01-01 2013-01-01 false Size classifications. 51.2559 Section 51.2559....2559 Size classifications. (a) The size of pistachio kernels may be specified in connection with the grade in accordance with one of the following size classifications. (1) Jumbo Whole Kernels: 80 percent...

A Fast Reduced Kernel Extreme Learning Machine.

PubMed

Deng, Wan-Yu; Ong, Yew-Soon; Zheng, Qing-Hua

2016-04-01

In this paper, we present a fast and accurate kernel-based supervised algorithm referred to as the Reduced Kernel Extreme Learning Machine (RKELM). In contrast to the work on Support Vector Machine (SVM) or Least Square SVM (LS-SVM), which identifies the support vectors or weight vectors iteratively, the proposed RKELM randomly selects a subset of the available data samples as support vectors (or mapping samples). By avoiding the iterative steps of SVM, significant cost savings in the training process can be readily attained, especially on Big datasets. RKELM is established based on the rigorous proof of universal learning involving reduced kernel-based SLFN. In particular, we prove that RKELM can approximate any nonlinear functions accurately under the condition of support vectors sufficiency. Experimental results on a wide variety of real world small instance size and large instance size applications in the context of binary classification, multi-class problem and regression are then reported to show that RKELM can perform at competitive level of generalized performance as the SVM/LS-SVM at only a fraction of the computational effort incurred. Copyright © 2015 Elsevier Ltd. All rights reserved.

Impact of whole grains on the gut microbiota: the next frontier for oats?

PubMed

Rose, Devin J

2014-10-01

The gut microbiota plays important roles in proper gut function and can contribute to or help prevent disease. Whole grains, including oats, constitute important sources of nutrients for the gut microbiota and contribute to a healthy gut microbiome. In particular, whole grains provide NSP and resistant starch, unsaturated TAG and complex lipids, and phenolics. The composition of these constituents is unique in oats compared with other whole grains. Therefore, oats may contribute distinctive effects on gut health relative to other grains. Studies designed to determine these effects may uncover new human-health benefits of oat consumption.

Total centromere size and genome size are strongly correlated in ten grass species.

PubMed

Zhang, Han; Dawe, R Kelly

2012-05-01

It has been known for decades that centromere size varies across species, but the factors involved in setting centromere boundaries are unknown. As a means to address this question, we estimated centromere sizes in ten species of the grass family including rice, maize, and wheat, which diverged 60~80 million years ago and vary by 40-fold in genome size. Measurements were made using a broadly reactive antibody to rice centromeric histone H3 (CENH3). In species-wide comparisons, we found a clear linear relationship between total centromere size and genome size. Species with large genomes and few chromosomes tend to have the largest centromeres (e.g., rye) while species with small genomes and many chromosomes have the smallest centromeres (e.g., rice). However, within a species, centromere size is surprisingly uniform. We present evidence from three oat-maize addition lines that support this claim, indicating that each of three maize centromeres propagated in oat are not measurably different from each other. In the context of previously published data, our results suggest that the apparent correlation between chromosome and centromere size is incidental to a larger trend that reflects genome size. Centromere size may be determined by a limiting component mechanism similar to that described for Caenorhabditis elegans centrosomes.

New DArT markers for oat provide enhanced map coverage and global germplasm characterization

USDA-ARS?s Scientific Manuscript database

Genomic discovery in oat and its application to oat improvement have been hindered by a lack of common markers on different genetic maps, and by the difficulty of conducting whole-genome analysis using high throughput markers. In this study we developed, characterized, and applied a large set oat g...

Phosphoinositide-specific phospholipase C in oat roots: association with the actin cytoskeleton.

PubMed

Huang, Chiung-Hua; Crain, Richard C

2009-10-01

Phosphoinositide-specific phospholipase C (PI-PLC) activities are involved in mediating plant cell responses to environmental stimuli. Two variants of PI-PLC have been partially purified from the roots of oat seedlings; one cytosolic and one particulate. Although the cytosolic enzyme was significantly purified, the activity still co-migrated with a number of other proteins on heparin HPLC and also on size-exclusion chromatography. The partially purified PI-PLC was tested by Western blotting, and we found that actin and actin-binding proteins, profilin and tropomyosin, co-purified with cytosolic phospholipase C. After a non-ionic detergent (Triton X-100) treatment, PI-PLC activities still remained with the actin cytoskeleton. The effects of phalloidin and F-buffer confirmed this association; these conditions, which favor actin polymerization, decreased the release of PI-PLC from the cytoskeleton. The treatments of latrunculin and G-buffer, the conditions that favor actin depolymerization, increased the release of PI-PLC from the cytoskeleton. These results suggest that oat PI-PLC associates with the actin cytoskeleton.

Development of a model system to identify differences in spring and winter oat.

PubMed

Chawade, Aakash; Lindén, Pernilla; Bräutigam, Marcus; Jonsson, Rickard; Jonsson, Anders; Moritz, Thomas; Olsson, Olof

2012-01-01

Our long-term goal is to develop a Swedish winter oat (Avena sativa). To identify molecular differences that correlate with winter hardiness, a winter oat model comprising of both non-hardy spring lines and winter hardy lines is needed. To achieve this, we selected 294 oat breeding lines, originating from various Russian, German, and American winter oat breeding programs and tested them in the field in south- and western Sweden. By assaying for winter survival and agricultural properties during four consecutive seasons, we identified 14 breeding lines of different origins that not only survived the winter but also were agronomically better than the rest. Laboratory tests including electrolytic leakage, controlled crown freezing assay, expression analysis of the AsVrn1 gene and monitoring of flowering time suggested that the American lines had the highest freezing tolerance, although the German lines performed better in the field. Finally, six lines constituting the two most freezing tolerant lines, two intermediate lines and two spring cultivars were chosen to build a winter oat model system. Metabolic profiling of non-acclimated and cold acclimated leaf tissue samples isolated from the six selected lines revealed differential expression patterns of 245 metabolites including several sugars, amino acids, organic acids and 181 hitherto unknown metabolites. The expression patterns of 107 metabolites showed significant interactions with either a cultivar or a time-point. Further identification, characterisation and validation of these metabolites will lead to an increased understanding of the cold acclimation process in oats. Furthermore, by using the winter oat model system, differential sequencing of crown mRNA populations would lead to identification of various biomarkers to facilitate winter oat breeding.

Tracking multi-walled carbon nanotubes inside oat (Avena sativa L.) plants and assessing their effect on growth, yield, and mammalian (human) cell viability

NASA Astrophysics Data System (ADS)

Joshi, Anjali; Kaur, Simranjeet; Singh, Pargat; Dharamvir, Keya; Nayyar, Harsh; Verma, Gaurav

2018-05-01

Our findings show that oxidized multi-walled carbon nanotubes (MWCNT) having serpent-like morphology and smaller sizes (diameter of 35 nm and lengths of 200-300 nm) are compatible with oat plant tissues. Applied by seed-priming method as 90 µg/ml concentration, these serpentine MWCNT (having open-end caps) enter the oat plant and traverse the cells. Tracking of MWCNT inside sections and tissues during growth of oat plant has been done using special sample preparation. We present clear images of MWCNT inside the primed seeds and vascular bundles, the conducting tissues of root and shoot of oat. A dye fluorescein isothiocyanate non-covalently bonded to MWCNT also helped in detecting the path through circumferential perimeters of the oat channels, using fluorescence and confocal microscopy. The presence of MWCNT inside oat enhanced the growth of xylem cells by about 1.85-fold in vasculature of shoots. Compared to controls, the chlorophyll content increased by 57%, while photosynthetic activity enhanced by 15% for the same sample in MWCNT-primed plants. Overall, the growth factors were also augmented leading to significant increase in yield components. No toxic effects of MWCNT were observed in the DNA of the primed plants, and in the human cell lines treated with grains harvested from the MWCNT-primed plants. Our study provides some new insights about the role of MWCNT in plants and their potential benefits in agriculture.

Excretion of Avenanthramides, Phenolic Acids and their Major Metabolites Following Intake of Oat Bran

PubMed Central

Schär, Manuel Y.; Corona, Giulia; Soycan, Gulten; Dine, Clemence; Kristek, Angelika; Alsharif, Sarah N. S.; Behrends, Volker; Lovegrove, Alison; Shewry, Peter R.

2017-01-01

Scope Wholegrain has been associated with reduced chronic disease mortality, with oat intake particularly notable for lowering blood cholesterol and glycemia. To better understand the complex nutrient profile of oats, we studied urinary excretion of phenolic acids and avenanthramides after ingestion of oat bran in humans. Methods and results After a 2‐d (poly)phenol‐low diet, seven healthy men provided urine 12 h before and 48 h after consuming 60 g oat bran (7.8 μmol avenanthramides, 139.2 μmol phenolic acids) or a phenolic‐low (traces of phenolics) control in a crossover design. Analysis by ultra‐high performance liquid chromatography (UPLC)–MS/MS showed that oat bran intake resulted in an elevation in urinary excretion of 30 phenolics relative to the control, suggesting that they are oat bran‐derived. Mean excretion levels were elevated between 0–2 and 4–8 h, following oat bran intake, and amounted to a total of 33.7 ± 7.3 μmol total excretion (mean recovery: 22.9 ± 5.0%), relative to control. The predominant metabolites included: vanillic acid, 4‐ and 3‐hydroxyhippuric acids, and sulfate‐conjugates of benzoic and ferulic acids, which accounted collectively for two thirds of total excretion. Conclusion Oat bran phenolics follow a relatively rapid urinary excretion, with 30 metabolites excreted within 8 h of intake. These levels of excretion suggest that bound phenolics are, in part, rapidly released by the microbiota. PMID:29024323

Avenanthramide biosynthesis in oat cultivars treated with systemic acquired resistance elicitors

USDA-ARS?s Scientific Manuscript database

The synthetic systemic acquired resistance elicitor benzothiadiazole (BTH) has been shown to elicit avenanthramide biosynthesis in the oat cultivar ‘Belle’. This report investigates the response of multiple oat cultivars to BTH as well as 2,6- dichloroisonicotinic acid (INA) at different growth stag...

Application of an in vitro OAT assay in drug design and optimization of renal clearance.

PubMed

Soars, Matthew G; Barton, Patrick; Elkin, Lisa L; Mosure, Kathleen W; Sproston, Joanne L; Riley, Robert J

2014-07-01

1. Optimization of renal clearance is a complex balance between passive and active processes mediated by renal transporters. This work aimed to characterize the interaction of a series of compounds with rat and human organic anion transporters (OATs) and develop quantitative structure-activity relationships (QSARs) to optimize renal clearance. 2. In vitro inhibition assays were established for human OAT1 and rat Oat3 and rat in vivo renal clearance was obtained. Statistically significant quantitative relationships were explored between the compounds' physical properties, their affinity for OAT1 and oat3 and the inter-relationship with unbound renal clearance (URC) in rat. 3. Many of the compounds were actively secreted and in vitro analysis demonstrated that these were ligands for rat and human OAT transporters (IC50 values ranging from <1 to >100 µM). Application of resultant QSAR models reduced renal clearance in the rat from 24 to <0.1 ml/min/kg. Data analysis indicated that the properties associated with increasing affinity at OATs are the same as those associated with reducing URC but orthogonal in nature. 4. This study has demonstrated that OAT inhibition data and QSAR models can be successfully used to optimize rat renal clearance in vivo and provide confidence of translation to humans.

Screening wild oat accessions from Morocco for resistance to Puccinia coronata

USDA-ARS?s Scientific Manuscript database

Here we report the screening of 338 new accessions of 11 different wild oat species (Avena) from the USDA Small Grains Collection for resistance to crown rust (Puccinia coronata). Wild oat species were originally collected in Morocco by C. Al Faiz, INRAT Rabat: Avena agadiriana, A. atlantica, A. bar...

Puccinia coronata f. sp. avenae: a threat to global oat production

USDA-ARS?s Scientific Manuscript database

Puccinia coronata f. sp. avenae causes crown rust disease in cultivated and wild oat. The significant yield losses inflicted by this pathogen makes crown rust the most devastating disease in the oat industry. P. coronata f. sp. avenae is a basidiomycete fungus with an obligate biotrophic lifestyle a...

New Advances in Marker Assisted Selection for Winter Hardiness in Oats.

USDA-ARS?s Scientific Manuscript database

Oat (Avena sativa L.) breeding and genetics research has lagged behind other small grains, such as wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.), in the development of PCR based markers and map construction due to fewer oat researchers and reduced research funding. As a result, marke...

Image quality of mixed convolution kernel in thoracic computed tomography.

PubMed

Neubauer, Jakob; Spira, Eva Maria; Strube, Juliane; Langer, Mathias; Voss, Christian; Kotter, Elmar

2016-11-01

The mixed convolution kernel alters his properties geographically according to the depicted organ structure, especially for the lung. Therefore, we compared the image quality of the mixed convolution kernel to standard soft and hard kernel reconstructions for different organ structures in thoracic computed tomography (CT) images.Our Ethics Committee approved this prospective study. In total, 31 patients who underwent contrast-enhanced thoracic CT studies were included after informed consent. Axial reconstructions were performed with hard, soft, and mixed convolution kernel. Three independent and blinded observers rated the image quality according to the European Guidelines for Quality Criteria of Thoracic CT for 13 organ structures. The observers rated the depiction of the structures in all reconstructions on a 5-point Likert scale. Statistical analysis was performed with the Friedman Test and post hoc analysis with the Wilcoxon rank-sum test.Compared to the soft convolution kernel, the mixed convolution kernel was rated with a higher image quality for lung parenchyma, segmental bronchi, and the border between the pleura and the thoracic wall (P < 0.03). Compared to the hard convolution kernel, the mixed convolution kernel was rated with a higher image quality for aorta, anterior mediastinal structures, paratracheal soft tissue, hilar lymph nodes, esophagus, pleuromediastinal border, large and medium sized pulmonary vessels and abdomen (P < 0.004) but a lower image quality for trachea, segmental bronchi, lung parenchyma, and skeleton (P < 0.001).The mixed convolution kernel cannot fully substitute the standard CT reconstructions. Hard and soft convolution kernel reconstructions still seem to be mandatory for thoracic CT.

Impact of process conditions on the density and durability of wheat, oat, canola, and barley straw briquettes

DOE PAGES

Tumuluru, J. S.; Tabil, L. G.; Song, Y.; ...

2014-10-01

The present study is to understand the impact of process conditions on the quality attributes of wheat oat, barley, and canola straw briquettes. Analysis of variance indicated that briquette moisture content and initial density immediately after compaction and final density after 2 weeks of storage are strong functions of feedstock moisture content and compression pressure, whereas durability rating is influenced by die temperature and feedstock moisture content. Briquettes produced at a low feedstock moisture content of 9 % (w.b.) yielded maximum densities >700 kg/m3 for wheat, oat, canola, and barley straws. Lower feedstock moisture content of <10 % (w.b.) andmore » higher die temperatures >110 °C and compression pressure >10 MPa minimized the briquette moisture content and maximized densities and durability rating based on surface plots observations. Optimal process conditions indicated that a low feedstock moisture content of about 9 % (w.b.), high die temperature of 120–130 °C, medium-to-large hammer mill screen sizes of about 24 to 31.75 mm, and low to high compression pressures of 7.5 to 12.5 MPa minimized briquette moisture content to <8 % (w.b.) and maximized density to >700 kg/m3. Durability rating >90 % is achievable at higher die temperatures of >123 °C, lower to medium feedstock moisture contents of 9 to 12 % (w.b.), low to high compression pressures of 7.5 to 12.5 MPa, and large hammer mill screen size of 31.75 mm, except for canola where a lower compression pressure of 7.5 to 8.5 MPa and a smaller hammer mill screen size of 19 mm for oat maximized the durability rating values.« less

Fusarium mycotoxin content of UK organic and conventional oats.

PubMed

Edwards, S G

2009-07-01

Every year between 2002 and 2005 approximately 100 samples of oats from fields of known agronomy were analysed by GC/MS for 10 trichothecenes: deoxynivalenol (DON), nivalenol, 3-acetylDON, 15-acetylDON, fusarenone X, T-2 toxin (T2), HT-2 toxin (HT2), diacetoxyscirpenol, neosolaniol and T-2 triol. Samples were also analysed for moniliformin and zearalenone by HPLC. Of the 10 trichothecenes analysed from 458 harvest samples of oat only three, 15-acetylDON, fusarenone X and diacetoxyscirpenol, were not detected. Moniliformin and zearalenone were absent or rarely detected, respectively. HT2 and T2 were the most frequently detected fusarium mycotoxins, present above the limit of quantification (10 microg kg(-1)) in 92 and 84% of samples, respectively, and were usually present at the highest concentrations. The combined mean and median for HT2 and T2 (HT2 + T2) was 570 and 213 microg kg(-1), respectively. There were good correlations between concentrations of HT2 and all other type A trichothecenes detected (T2, T2 triol and neosolaniol). Year and region had a significant effect on HT2 + T2 concentration. There was also a highly significant difference between HT2 + T2 content in organic and conventional samples, with the predicted mean for organic samples five times lower than that of conventional samples. This is the largest difference reported for any mycotoxin level in organic and conventional cereals. No samples exceeded the legal limits for DON or zearalenone in oats intended for human consumption. Legislative limits for HT2 and T2 are currently under consideration by the European Commission. Depending on the limits set for unprocessed oats intended for human consumption, the levels detected here could have serious consequences for the UK oat-processing industry.

Kernel Abortion in Maize 1

PubMed Central

Hanft, Jonathan M.; Jones, Robert J.

1986-01-01

Kernels cultured in vitro were induced to abort by high temperature (35°C) and by culturing six kernels/cob piece. Aborting kernels failed to enter a linear phase of dry mass accumulation and had a final mass that was less than 6% of nonaborting field-grown kernels. Kernels induced to abort by high temperature failed to synthesize starch in the endosperm and had elevated sucrose concentrations and low fructose and glucose concentrations in the pedicel during early growth compared to nonaborting kernels. Kernels induced to abort by high temperature also had much lower pedicel soluble acid invertase activities than did nonaborting kernels. These results suggest that high temperature during the lag phase of kernel growth may impair the process of sucrose unloading in the pedicel by indirectly inhibiting soluble acid invertase activity and prevent starch synthesis in the endosperm. Kernels induced to abort by culturing six kernels/cob piece had reduced pedicel fructose, glucose, and sucrose concentrations compared to kernels from field-grown ears. These aborting kernels also had a lower pedicel soluble acid invertase activity compared to nonaborting kernels from the same cob piece and from field-grown ears. The low invertase activity in pedicel tissue of the aborting kernels was probably caused by a lack of substrate (sucrose) for the invertase to cleave due to the intense competition for available assimilates. In contrast to kernels cultured at 35°C, aborting kernels from cob pieces containing all six kernels accumulated starch in a linear fashion. These results indicate that kernels cultured six/cob piece abort because of an inadequate supply of sugar and are similar to apical kernels from field-grown ears that often abort prior to the onset of linear growth. PMID:16664846

Celiac Disease and Gluten-Free Oats: A Canadian Position Based on a Literature Review.

PubMed

La Vieille, Sébastien; Pulido, Olga M; Abbott, Michael; Koerner, Terence B; Godefroy, Samuel

2016-01-01

This paper provides an overview of the latest scientific data related to the safety of uncontaminated oats (<20 ppm of gluten) in the diet of individuals with celiac disease (CD). It updates the previous Health Canada position posted on the Health Canada website in 2007 and a related paper published in 2009. It considers a number of recent studies published between January 2008 and January 2015. While recognizing that a few people with celiac disease seem to be clinically intolerant to oats, this review concludes that oats uncontaminated by gluten-containing cereals (wheat, rye, and barley) can be safely ingested by most patients with celiac disease and that there is no conclusive evidence that the consumption of uncontaminated or specially produced oats containing no greater than 20 ppm gluten by patients with celiac disease should be limited to a specific daily amount. However, individuals with CD should observe a stabilization phase before introducing uncontaminated oats to the gluten-free diet (GFD). Oats uncontaminated with gluten should only be introduced after all symptoms of celiac disease have resolved and the individual has been on a GFD for a minimum of 6 months. Long-term regular medical follow-up of these patients is recommended but this is no different recommendation to celiac individuals on a GFD without oats.

Approximate kernel competitive learning.

PubMed

Wu, Jian-Sheng; Zheng, Wei-Shi; Lai, Jian-Huang

2015-03-01

Kernel competitive learning has been successfully used to achieve robust clustering. However, kernel competitive learning (KCL) is not scalable for large scale data processing, because (1) it has to calculate and store the full kernel matrix that is too large to be calculated and kept in the memory and (2) it cannot be computed in parallel. In this paper we develop a framework of approximate kernel competitive learning for processing large scale dataset. The proposed framework consists of two parts. First, it derives an approximate kernel competitive learning (AKCL), which learns kernel competitive learning in a subspace via sampling. We provide solid theoretical analysis on why the proposed approximation modelling would work for kernel competitive learning, and furthermore, we show that the computational complexity of AKCL is largely reduced. Second, we propose a pseudo-parallelled approximate kernel competitive learning (PAKCL) based on a set-based kernel competitive learning strategy, which overcomes the obstacle of using parallel programming in kernel competitive learning and significantly accelerates the approximate kernel competitive learning for large scale clustering. The empirical evaluation on publicly available datasets shows that the proposed AKCL and PAKCL can perform comparably as KCL, with a large reduction on computational cost. Also, the proposed methods achieve more effective clustering performance in terms of clustering precision against related approximate clustering approaches. Copyright © 2014 Elsevier Ltd. All rights reserved.

7 CFR 51.2284 - Size classification.

Code of Federal Regulations, 2010 CFR

2010-01-01

...: “Halves”, “Pieces and Halves”, “Pieces” or “Small Pieces”. The size of portions of kernels in the lot... consists of 85 percent or more, by weight, half kernels, and the remainder three-fourths half kernels. (See § 51.2285.) (b) Pieces and halves. Lot consists of 20 percent or more, by weight, half kernels, and the...

The Effect of Chemical Systemic Acquired Resistance Elicitors on Oat Avenanthramide Biosynthesis

USDA-ARS?s Scientific Manuscript database

Abstract. Oats produce a group of phenolic antioxidants termed “avenanthramides”. These metabolites are, among food crops, unique to oats. They are known to be potent antioxidants and have shown certain desirable nutritional characteristics such as inhibiting atherosclerotic plaque formation and ...

KSOS Computer Program Development Specifications (Type B-5). (Kernelized Secure Operating System). I. Security Kernel (CDRL 0002AF). II. UNIX Emulator (CDRL 0002AG). III. Security-Related Software (CDRL 0002AH).

DTIC Science & Technology

1980-12-01

Commun- ications Corporation, Palo Alto, CA (March 1978). g. [Walter at al. 74] Walter, K.G. et al., " Primitive Models for Computer .. Security", ESD-TR...discussion is followed by a presenta- tion of the Kernel primitive operations upon these objects. All Kernel objects shall be referenced by a common...set of sizes. All process segments, regardless of domain, shall be manipulated by the same set of Kernel segment primitives . User domain segments

Dietary fiber and satiety: the effects of oats on satiety

PubMed Central

O’Neil, Carol E.; Greenway, Frank L.

2016-01-01

This review examines the effect of β-glucan, the viscous soluble fiber in oats, on satiety. A literature search for studies that examined delivery of the fiber in whole foods or as an extract was conducted. Viscosity interferes with the peristaltic mixing process in the small intestine to impede digestion and absorption of nutrients, which precipitates satiety signals. From measurements of the physicochemical and rheological properties of β-glucan, it appears that viscosity plays a key role in modulating satiety. However, the lack of standardized methods to measure viscosity and the inherent nature of appetite make it difficult to pinpoint the reasons for inconsistent results of the effects of oats on satiety. Nevertheless, the majority of the evidence suggests that oat β-glucan has a positive effect on perceptions of satiety. PMID:26724486

Classification With Truncated Distance Kernel.

PubMed

Huang, Xiaolin; Suykens, Johan A K; Wang, Shuning; Hornegger, Joachim; Maier, Andreas

2018-05-01

This brief proposes a truncated distance (TL1) kernel, which results in a classifier that is nonlinear in the global region but is linear in each subregion. With this kernel, the subregion structure can be trained using all the training data and local linear classifiers can be established simultaneously. The TL1 kernel has good adaptiveness to nonlinearity and is suitable for problems which require different nonlinearities in different areas. Though the TL1 kernel is not positive semidefinite, some classical kernel learning methods are still applicable which means that the TL1 kernel can be directly used in standard toolboxes by replacing the kernel evaluation. In numerical experiments, the TL1 kernel with a pregiven parameter achieves similar or better performance than the radial basis function kernel with the parameter tuned by cross validation, implying the TL1 kernel a promising nonlinear kernel for classification tasks.

Considering causal genes in the genetic dissection of kernel traits in common wheat.

PubMed

Mohler, Volker; Albrecht, Theresa; Castell, Adelheid; Diethelm, Manuela; Schweizer, Günther; Hartl, Lorenz

2016-11-01

Genetic factors controlling thousand-kernel weight (TKW) were characterized for their association with other seed traits, including kernel width, kernel length, ratio of kernel width to kernel length (KW/KL), kernel area, and spike number per m 2 (SN). For this purpose, a genetic map was established utilizing a doubled haploid population derived from a cross between German winter wheat cultivars Pamier and Format. Association studies in a diversity panel of elite cultivars supplemented genetic analysis of kernel traits. In both populations, genomic signatures of 13 candidate genes for TKW and kernel size were analyzed. Major quantitative trait loci (QTL) for TKW were identified on chromosomes 1B, 2A, 2D, and 4D, and their locations coincided with major QTL for kernel size traits, supporting the common belief that TKW is a function of other kernel traits. The QTL on chromosome 2A was associated with TKW candidate gene TaCwi-A1 and the QTL on chromosome 4D was associated with dwarfing gene Rht-D1. A minor QTL for TKW on chromosome 6B coincided with TaGW2-6B. The QTL for kernel dimensions that did not affect TKW were detected on eight chromosomes. A major QTL for KW/KL located at the distal tip of chromosome arm 5AS is being reported for the first time. TaSus1-7A and TaSAP-A1, closely linked to each other on chromosome 7A, could be related to a minor QTL for KW/KL. Genetic analysis of SN confirmed its negative correlation with TKW in this cross. In the diversity panel, TaSus1-7A was associated with TKW. Compared to the Pamier/Format bi-parental population where TaCwi-A1a was associated with higher TKW, the same allele reduced grain yield in the diversity panel, suggesting opposite effects of TaCwi-A1 on these two traits.

Coupling individual kernel-filling processes with source-sink interactions into GREENLAB-Maize.

PubMed

Ma, Yuntao; Chen, Youjia; Zhu, Jinyu; Meng, Lei; Guo, Yan; Li, Baoguo; Hoogenboom, Gerrit

2018-02-13

Failure to account for the variation of kernel growth in a cereal crop simulation model may cause serious deviations in the estimates of crop yield. The goal of this research was to revise the GREENLAB-Maize model to incorporate source- and sink-limited allocation approaches to simulate the dry matter accumulation of individual kernels of an ear (GREENLAB-Maize-Kernel). The model used potential individual kernel growth rates to characterize the individual potential sink demand. The remobilization of non-structural carbohydrates from reserve organs to kernels was also incorporated. Two years of field experiments were conducted to determine the model parameter values and to evaluate the model using two maize hybrids with different plant densities and pollination treatments. Detailed observations were made on the dimensions and dry weights of individual kernels and other above-ground plant organs throughout the seasons. Three basic traits characterizing an individual kernel were compared on simulated and measured individual kernels: (1) final kernel size; (2) kernel growth rate; and (3) duration of kernel filling. Simulations of individual kernel growth closely corresponded to experimental data. The model was able to reproduce the observed dry weight of plant organs well. Then, the source-sink dynamics and the remobilization of carbohydrates for kernel growth were quantified to show that remobilization processes accompanied source-sink dynamics during the kernel-filling process. We conclude that the model may be used to explore options for optimizing plant kernel yield by matching maize management to the environment, taking into account responses at the level of individual kernels. © The Author(s) 2018. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Cookies elaborated with oat and common bean flours improved serum markers in diabetic rats.

PubMed

Pérez-Ramírez, Iza F; Becerril-Ocampo, Laura J; Reynoso-Camacho, Rosalía; Herrera, Mayra D; Guzmán-Maldonado, S Horacio; Cruz-Bravo, Raquel K

2018-02-01

Common beans have been associated with anti-diabetic effects, due to its high content of bioactive compounds. Nevertheless, its consumption has decreased worldwide. Therefore, there is an increasing interest in the development of novel functional foods elaborated with common beans. The aim of this study was to evaluate the anti-diabetic effect of oat-bean flour cookies, and to analyze its bioactive composition, using commercial oat-wheat cookies for comparative purposes. Oat-bean cookies (1.2 g kg -1 ) slightly decreased serum glucose levels (∼1.1-fold) and increased insulin levels (∼1.2-fold) in diabetic rats, reducing the hyperglycemic peak in healthy rats (∼1.1-fold). Oat-bean cookies (0.8 and 1.2 g kg -1 ) exerted a greater hypolipidemic effect than commercial oat-wheat cookies (1.2 g kg -1 ), as observed in decreased serum triglycerides and low-density lipoprotein cholesterol. Furthermore, the supplementation with 1.2 g kg -1 oat-bean cookies decreased atherogenic index and serum C-reactive protein levels, suggesting their cardioprotective potential. The beneficial effect of oat-bean cookies was associated with their high content of dietary fiber and galacto oligosaccharides, as well as chlorogenic acid, rutin, protocatechuic acid, β-sitosterol and soyasaponins. These results suggest that common beans can be used as functional ingredients for the elaboration of cookies with anti-diabetic effects. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

The effect of thermo-mechanical processing on physical properties of processed amaranth and oat bran composites

USDA-ARS?s Scientific Manuscript database

Amaranth-oat composites were developed using gluten free amaranth flour containing essential amino acids and minerals with oat products containing ß-glucan, known for lowering blood cholesterol. Amaranth flour and oat bran concentrate (OBC) composites (1:4) were processed using different technologie...

Citizen Science: Dune Restoration with Sea Oats by Junior Friends of MacArthur Beach State Park

NASA Astrophysics Data System (ADS)

Allen, S.

2016-12-01

As a crucial part of the dune ecosystem, Sea Oats are a protected species in Florida. They provide excellent habitat for small birds and mammals and prevent dune erosion with their fibrous roots.Citizen science is a research and education tool that involves everyday people in real and meaningful forms of science. My volunteer group, Junior friends of Macarthur Beach State Park, used citizen science to restore dunes by growing and planting Sea Oats. Junior friends is a group of 6-12th grade students whose purpose is to support the park through monthly activities and special events. Junior Friends asked,what is the best way to germinate/grow/and plant Sea Oats to renourish the beach dune. Specifically, what planting medium is most conducive for maximizing growth of Sea Oats? We tested three scenarios: 100% potting soil, 100% sand from the beach, 50% sand-50% potting soil mixture.Using harvested Sea Oat seeds from Macarthur Beach State Park, we separated the seeds from their casings, known as spiklets. We then monitored the plant's weekly over the course of 14 weeks and charted their growth. All the seeds had similar growth rates, but the seeds that grew in 100% potting soil consistently grew the tallest. The second tallest Sea Oats were 100% sand; the 50% sand-50% potting soil mixture produced the least amount of growth. When seedlings reached their desired growth of 6-8 inches and established a root ball, we planted the Sea Oats on the dune for restoration. After planting them,we monitored the growth of the Sea Oats on the MacArthur Beach dune throughout the rest of the year, charting the height of the planted Sea Oats. Using Citizen science we had meaningful data that helped us have a better understanding of restoring Sea Oats on Florida dunes and will help further future restorations.

Production and nitrogen-use efficiency of oat forage receiving slurry or urea

USDA-ARS?s Scientific Manuscript database

Recently, several research projects have evaluated fall-grown oat for use as emergency fall forage throughout the north-central US; however, using fall-grown oat in cropping programs also allows the practical benefit of summer manure distribution that is completely de-coupled from corn production. ‘...

A gene expression atlas of developing oat seeds for enhancing nutritional composition

USDA-ARS?s Scientific Manuscript database

Oat (Avena sativa L.) genome resources are less abundant than for wheat and barley, but next generation sequencing (NGS) technologies have great potential to accelerate new genome information for oat in a cost-effective manner. We are employing RNA-Seq to develop a gene expression atlas of developin...

Genetic progress in oat associated with fungicide use in Rio Grande do Sul, Brazil.

PubMed

Follmann, D N; Cargnelutti Filho, A; Lúcio, A D; de Souza, V Q; Caraffa, M; Wartha, C A

2016-12-19

The State of Rio Grande do Sul (RS) is the largest producer of oat in Brazil with the aid of consolidated breeding programs, which are constantly releasing new cultivars. The main objectives of this study were to: 1) evaluate the annual genetic progress in grain yield and hectoliter weight of the oat cultivars in RS, with and without fungicide use on aerial parts of plants; and 2) evaluate the efficiency of oat breeding programs in introducing disease-resistant genes in the released cultivars through network yield trials conducted with and without fungicide use on aerial plant parts. The data on grain yield and hectoliter weight were obtained from 89 competition field trials of oat cultivars carried out from 2007 to 2014 in nine municipalities of RS. Of the total 89 trials, 44 were carried out with fungicide application on aerial plant parts and 45 were carried out without fungicide application. The annual genetic progress in oat cultivars was studied using the methodology proposed by Vencovsky (1988). The annual genetic progress in oat grain yield was 1.02% with fungicide use and 4.02% without fungicide use during the eight-year study period in RS. The annual genetic progress with respect to the hectoliter weight was 0.08% for trials with fungicide use and 0.71% for trials without fungicide use. Performing network yield trials with and without fungicide use on the aerial plants parts is a feasible method to evaluate the efficiency of oat breeding programs in introducing disease-resistant genes in the released cultivars.

The Gluten-Free Diet: Can Oats and Wheat Starch Be Part of It?

PubMed

Poley, J Rainer

2017-01-01

Objective and Conclusion: Uncertainty still exists about the use of oats and wheat starch as part of a gluten-free diet in patients with celiac disease (CD). This review should help to clarify the issues at hand. Whereas uncontaminated (from gluten/gliadin) oats and oats from cultivars not containing celiac-activating sequences of proline and glutamine can be used without risk of intestinal damage, wheat starch should not be used, unless it is free of gluten-that is, deglutinized-because even small amounts of gluten over time are able to induce small intestinal mucosal damage.

Pathway-Based Kernel Boosting for the Analysis of Genome-Wide Association Studies

PubMed Central

Manitz, Juliane; Burger, Patricia; Amos, Christopher I.; Chang-Claude, Jenny; Wichmann, Heinz-Erich; Kneib, Thomas; Bickeböller, Heike

2017-01-01

The analysis of genome-wide association studies (GWAS) benefits from the investigation of biologically meaningful gene sets, such as gene-interaction networks (pathways). We propose an extension to a successful kernel-based pathway analysis approach by integrating kernel functions into a powerful algorithmic framework for variable selection, to enable investigation of multiple pathways simultaneously. We employ genetic similarity kernels from the logistic kernel machine test (LKMT) as base-learners in a boosting algorithm. A model to explain case-control status is created iteratively by selecting pathways that improve its prediction ability. We evaluated our method in simulation studies adopting 50 pathways for different sample sizes and genetic effect strengths. Additionally, we included an exemplary application of kernel boosting to a rheumatoid arthritis and a lung cancer dataset. Simulations indicate that kernel boosting outperforms the LKMT in certain genetic scenarios. Applications to GWAS data on rheumatoid arthritis and lung cancer resulted in sparse models which were based on pathways interpretable in a clinical sense. Kernel boosting is highly flexible in terms of considered variables and overcomes the problem of multiple testing. Additionally, it enables the prediction of clinical outcomes. Thus, kernel boosting constitutes a new, powerful tool in the analysis of GWAS data and towards the understanding of biological processes involved in disease susceptibility. PMID:28785300

Pathway-Based Kernel Boosting for the Analysis of Genome-Wide Association Studies.

PubMed

Friedrichs, Stefanie; Manitz, Juliane; Burger, Patricia; Amos, Christopher I; Risch, Angela; Chang-Claude, Jenny; Wichmann, Heinz-Erich; Kneib, Thomas; Bickeböller, Heike; Hofner, Benjamin

2017-01-01

The analysis of genome-wide association studies (GWAS) benefits from the investigation of biologically meaningful gene sets, such as gene-interaction networks (pathways). We propose an extension to a successful kernel-based pathway analysis approach by integrating kernel functions into a powerful algorithmic framework for variable selection, to enable investigation of multiple pathways simultaneously. We employ genetic similarity kernels from the logistic kernel machine test (LKMT) as base-learners in a boosting algorithm. A model to explain case-control status is created iteratively by selecting pathways that improve its prediction ability. We evaluated our method in simulation studies adopting 50 pathways for different sample sizes and genetic effect strengths. Additionally, we included an exemplary application of kernel boosting to a rheumatoid arthritis and a lung cancer dataset. Simulations indicate that kernel boosting outperforms the LKMT in certain genetic scenarios. Applications to GWAS data on rheumatoid arthritis and lung cancer resulted in sparse models which were based on pathways interpretable in a clinical sense. Kernel boosting is highly flexible in terms of considered variables and overcomes the problem of multiple testing. Additionally, it enables the prediction of clinical outcomes. Thus, kernel boosting constitutes a new, powerful tool in the analysis of GWAS data and towards the understanding of biological processes involved in disease susceptibility.

Partition coefficient of cadmium between organic soils and bean and oat plants

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

Siddqui, M.F.R.; Courchesne, F.; Kennedy, G.

Environmental fate models require the partition coefficient data of contaminants among two or more environmental compartments. The bioaccumulation of cadmium (Cd) by bean and oat plants grown on organic soils in a controlled growth chamber was investigated to validate the plant/soil partition coefficient. Total Cd was measured in the soils and in the different parts of the plants. The mean total Cd concentrations for soil cultivated with beans and oats were 0.86 and 0.69 {micro}g/g, respectively. Selective extractants (BaCl{sub 2}, Na-pyrophosphate and HNO{sub 3}-hydroxy) were used to evaluate solid phase Cd species in the soil. In the soil cultivated withmore » bean, BaCl{sub 2} exchangeable, Na-pyrophosphate extractable and HNO{sub 3}-NH{sub 2}OH extractable Cd represented 1.2, 1.6 and 50.9% of total soil Cd, respectively. For the soil cultivated with oats, the same extractants gave values of 1.1, 1.8 and 61.9%. Cd concentration levels in bean plants followed the sequence roots > fruits = stems > leaves (p < 0.01) while the following sequence was observed for oat plants: roots > fruits > stems > leaves (p < 0.05). The partition coefficient for total Cd (Cd{sub Plant tissue}/Cd{sub Soil}) was in the range of 0.28--0.55 for bean plants and 1.03--1.86 for oat plants.« less

Reduction of lipid oxidation by formation of caseinate-oil-oat gum emulsions

USDA-ARS?s Scientific Manuscript database

The concentration of oat gum, though important for formation of stable emulsion, has no effect on oxidation of Omega 3 oil; this is most prominent in fish-oil based Omega 3 oil. The optimal concentration of oat gum is about 0.2% wt for emulsion stability and visual appearance. We found that concentr...

QTLs for important breeding characteristics in the doubled haploid oat progeny.

PubMed

Tanhuanpää, Pirjo; Manninen, Outi; Kiviharju, Elina

2010-06-01

A homozygous mapping population, consisting of doubled haploid (DH) oat (Avena sativa L.) plants generated through anther culture of F1 plants from the cross between the Finnish cultivar 'Aslak' and the Swedish cultivar 'Matilda', was used to construct an oat linkage map. Ten agronomic and quality traits were analyzed in the DH plants from field trials in 2005 and 2006. Leaf blotch (caused by Pyrenophora avenae) resistance was also evaluated in a greenhouse test with 2 different isolates. One to 8 quantitative trait loci (QTLs) were found to be associated with each trait studied. Some chromosomal regions affected more than 1 trait; for example, 4 regions affected both protein and oil content. This study gives valuable information to oat breeders concerning the inheritance of important traits, and it provides potential tools to assist breeding.

GPU-accelerated Kernel Regression Reconstruction for Freehand 3D Ultrasound Imaging.

PubMed

Wen, Tiexiang; Li, Ling; Zhu, Qingsong; Qin, Wenjian; Gu, Jia; Yang, Feng; Xie, Yaoqin

2017-07-01

Volume reconstruction method plays an important role in improving reconstructed volumetric image quality for freehand three-dimensional (3D) ultrasound imaging. By utilizing the capability of programmable graphics processing unit (GPU), we can achieve a real-time incremental volume reconstruction at a speed of 25-50 frames per second (fps). After incremental reconstruction and visualization, hole-filling is performed on GPU to fill remaining empty voxels. However, traditional pixel nearest neighbor-based hole-filling fails to reconstruct volume with high image quality. On the contrary, the kernel regression provides an accurate volume reconstruction method for 3D ultrasound imaging but with the cost of heavy computational complexity. In this paper, a GPU-based fast kernel regression method is proposed for high-quality volume after the incremental reconstruction of freehand ultrasound. The experimental results show that improved image quality for speckle reduction and details preservation can be obtained with the parameter setting of kernel window size of [Formula: see text] and kernel bandwidth of 1.0. The computational performance of the proposed GPU-based method can be over 200 times faster than that on central processing unit (CPU), and the volume with size of 50 million voxels in our experiment can be reconstructed within 10 seconds.

Optimized Kernel Entropy Components.

PubMed

Izquierdo-Verdiguier, Emma; Laparra, Valero; Jenssen, Robert; Gomez-Chova, Luis; Camps-Valls, Gustau

2017-06-01

This brief addresses two main issues of the standard kernel entropy component analysis (KECA) algorithm: the optimization of the kernel decomposition and the optimization of the Gaussian kernel parameter. KECA roughly reduces to a sorting of the importance of kernel eigenvectors by entropy instead of variance, as in the kernel principal components analysis. In this brief, we propose an extension of the KECA method, named optimized KECA (OKECA), that directly extracts the optimal features retaining most of the data entropy by means of compacting the information in very few features (often in just one or two). The proposed method produces features which have higher expressive power. In particular, it is based on the independent component analysis framework, and introduces an extra rotation to the eigen decomposition, which is optimized via gradient-ascent search. This maximum entropy preservation suggests that OKECA features are more efficient than KECA features for density estimation. In addition, a critical issue in both the methods is the selection of the kernel parameter, since it critically affects the resulting performance. Here, we analyze the most common kernel length-scale selection criteria. The results of both the methods are illustrated in different synthetic and real problems. Results show that OKECA returns projections with more expressive power than KECA, the most successful rule for estimating the kernel parameter is based on maximum likelihood, and OKECA is more robust to the selection of the length-scale parameter in kernel density estimation.

Oat consumption reduced intestinal fat deposition and improved health span in Caenorhabditis elegans model

PubMed Central

Gao, Chenfei; Gao, Zhanguo; Greenway, Frank L.; Burton, Jeffrey H.; Johnson, William D.; Keenan, Michael J.; Enright, Frederick M.; Martin, Roy J.; Chu, YiFang; Zheng, Jolene

2015-01-01

In addition to their fermentable dietary fiber and the soluble β-glucan fiber, oats have unique avenanthramides that have anti-inflammatory and antioxidant properties that reduce coronary heart disease in human clinical trials. We hypothesized that oat consumption will increase insulin sensitivity, reduce body fat, and improve health span in Caenorhabditis elegans through a mechanism involving the daf-2 gene, which codes for the insulin/insulin-like growth factor-1–like receptor, and that hyperglycemia will attenuate these changes. Caenorhabditis elegans wild type (N2) and the null strains sir-2.1, daf-16, and daf-16/daf-2 were fed Escherichia coli (OP50) and oat flakes (0.5%, 1.0%, or 3%) with and without 2% glucose. Oat feeding decreased intestinal fat deposition in N2, daf-16, or daf-16/daf-2 strains (P < .05); and glucose did not affect intestinal fat deposition response. The N2, daf-16, or sir-2.1 mutant increased the pharyngeal pumping rate (P < .05), a surrogate marker of life span, following oat consumption. Oat consumption increased ckr-1, gcy-8, cpt-1, and cpt-2 mRNA expression in both the N2 and the sir-2.1 mutant, with significantly higher expression in sir-2.1 than in N2 (P < .01). Additional glucose further increased expression 1.5-fold of the 4 genes in N2 (P < .01), decreased the expression of all except cpt-1 in the daf-16 mutant, and reduced mRNA expression of the 4 genes in the daf-16/daf-2 mutant (P < .01). These data suggest that oat consumption reduced fat storage and increased ckr-1, gcy-8, cpt-1, or cpt-2 through the sir-2.1 genetic pathway. Oat consumption may be a beneficial dietary intervention for reducing fat accumulation, augmenting health span, and improving hyperglycemia-impaired lipid metabolism. PMID:26253816

Dietary fiber and satiety: the effects of oats on satiety.

PubMed

Rebello, Candida J; O'Neil, Carol E; Greenway, Frank L

2016-02-01

This review examines the effect of β-glucan, the viscous soluble fiber in oats, on satiety. A literature search for studies that examined delivery of the fiber in whole foods or as an extract was conducted. Viscosity interferes with the peristaltic mixing process in the small intestine to impede digestion and absorption of nutrients, which precipitates satiety signals. From measurements of the physicochemical and rheological properties of β-glucan, it appears that viscosity plays a key role in modulating satiety. However, the lack of standardized methods to measure viscosity and the inherent nature of appetite make it difficult to pinpoint the reasons for inconsistent results of the effects of oats on satiety. Nevertheless, the majority of the evidence suggests that oat β-glucan has a positive effect on perceptions of satiety. © The Author(s) 2016. Published by Oxford University Press on behalf of the International Life Sciences Institute. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Pharmacokinetics of avenanthramides (AV) from AV-enriched malted oats in healthy older adults

USDA-ARS?s Scientific Manuscript database

Avenanthramides (AV) are a unique group of phytochemicals found in oat bran. In vitro studies show both purified AV and concentrated oat AV mixtures have anti-atherogenic and anti-inflammatory activity, suggesting they may have similar effects in vivo if they are sufficiently bioavailable. The bioav...

Genome-Wide Association Mapping of Crown Rust Resistance in Oat Elite Germplasm.

PubMed

Klos, Kathy Esvelt; Yimer, Belayneh A; Babiker, Ebrahiem M; Beattie, Aaron D; Bonman, J Michael; Carson, Martin L; Chong, James; Harrison, Stephen A; Ibrahim, Amir M H; Kolb, Frederic L; McCartney, Curt A; McMullen, Michael; Fetch, Jennifer Mitchell; Mohammadi, Mohsen; Murphy, J Paul; Tinker, Nicholas A

2017-07-01

Oat crown rust, caused by f. sp. , is a major constraint to oat ( L.) production in many parts of the world. In this first comprehensive multienvironment genome-wide association map of oat crown rust, we used 2972 single-nucleotide polymorphisms (SNPs) genotyped on 631 oat lines for association mapping of quantitative trait loci (QTL). Seedling reaction to crown rust in these lines was assessed as infection type (IT) with each of 10 crown rust isolates. Adult plant reaction was assessed in the field in a total of 10 location-years as percentage severity (SV) and as infection reaction (IR) in a 0-to-1 scale. Overall, 29 SNPs on 12 linkage groups were predictive of crown rust reaction in at least one experiment at a genome-wide level of statistical significance. The QTL identified here include those in regions previously shown to be linked with seedling resistance genes , , , , , and and also with adult-plant resistance and adaptation-related QTL. In addition, QTL on linkage groups Mrg03, Mrg08, and Mrg23 were identified in regions not previously associated with crown rust resistance. Evaluation of marker genotypes in a set of crown rust differential lines supported as the identity of . The SNPs with rare alleles associated with lower disease scores may be suitable for use in marker-assisted selection of oat lines for crown rust resistance. Copyright © 2017 Crop Science Society of America.

The effect of replacing fat with oat bran on fatty acid composition and physicochemical properties of meatballs.

PubMed

Yılmaz, İsmail; Dağlıoğlu, Orhan

2003-10-01

Oat bran was used as a fat substitute in the production of meatballs. The effect of oat bran addition on the fatty acid composition, trans fatty acids, total fat, some physicochemical and sensory properties of the samples was studied. Meatballs were produced with four different formulations; the addition of 5, 10, 15 and 20% oat bran. Control samples were formulated with 25% fat addition as in commercial production. The major fatty acids were cis-oleic, palmitic and stearic acid in all the meatball samples, those with oat bran added as well as the control. Meatballs containing oat bran had lower concentrations of total fat and total trans fatty acids than the control samples. Meatballs made with 20% oat bran had the highest protein, salt and ash contents, L value (lightness), b value (yellowness), and the lowest moisture content and a value (redness). There was no significant difference among the meatball samples with respect to sensory properties, and all samples had high acceptability.

Inhibitory effect of selective cyclooxygenase-2 inhibitor etoricoxib on human organic anion transporter 3 (hOAT3).

PubMed

Honjo, Hiroaki; Uwai, Yuichi; Iwamoto, Kikuo

2011-04-01

It is well known that nonsteroidal anti-inflammatory drugs (NSAIDs) delay the elimination of methotrexate. One of the mechanisms is thought to be inhibition of methotrexate uptake via human organic anion transporter 3 (hOAT3, SLC22A8) in the renal proximal tubule by NSAIDs. In this study, we evaluated the inhibitory effects of selective cyclooxygenase-2 inhibitor etoricoxib on hOAT3 by uptake experiments using Xenopus laevis oocytes. The injection of hOAT3 cRNA stimulated the uptake of methotrexate into the oocytes, and its transport was inhibited by etoricoxib. Etoricoxib inhibited estrone sulfate uptake by hOAT3 dose dependently, and the 50% inhibitory concentration was estimated to be 9.8 µM. Eadie-Hofstee plot analysis showed that etoricoxib inhibited hOAT3 in a competitive manner. These findings show that etoricoxib has inhibitory effect on hOAT3, and that the potential is comparable to that of traditional NSAIDs. ©2011 Bentham Science Publishers Ltd.

7 CFR 981.408 - Inedible kernel.

Code of Federal Regulations, 2014 CFR

2014-01-01

... kernel is modified to mean a kernel, piece, or particle of almond kernel with any defect scored as... purposes of determining inedible kernels, pieces, or particles of almond kernels. [59 FR 39419, Aug. 3...

7 CFR 981.408 - Inedible kernel.

Code of Federal Regulations, 2011 CFR

2011-01-01

... kernel is modified to mean a kernel, piece, or particle of almond kernel with any defect scored as... purposes of determining inedible kernels, pieces, or particles of almond kernels. [59 FR 39419, Aug. 3...

7 CFR 981.408 - Inedible kernel.

Code of Federal Regulations, 2012 CFR

2012-01-01

... kernel is modified to mean a kernel, piece, or particle of almond kernel with any defect scored as... purposes of determining inedible kernels, pieces, or particles of almond kernels. [59 FR 39419, Aug. 3...

7 CFR 981.408 - Inedible kernel.

Code of Federal Regulations, 2013 CFR

2013-01-01

... kernel is modified to mean a kernel, piece, or particle of almond kernel with any defect scored as... purposes of determining inedible kernels, pieces, or particles of almond kernels. [59 FR 39419, Aug. 3...

Cellulose fibers extracted from rice and oat husks and their application in hydrogel.

PubMed

Oliveira, Jean Paulo de; Bruni, Graziella Pinheiro; Lima, Karina Oliveira; Halal, Shanise Lisie Mello El; Rosa, Gabriela Silveira da; Dias, Alvaro Renato Guerra; Zavareze, Elessandra da Rosa

2017-04-15

The commercial cellulose fibers and cellulose fibers extracted from rice and oat husks were analyzed by chemical composition, morphology, functional groups, crystallinity and thermal properties. The cellulose fibers from rice and oat husks were used to produce hydrogels with poly (vinyl alcohol). The fibers presented different structural, crystallinity, and thermal properties, depending on the cellulose source. The hydrogel from rice cellulose fibers had a network structure with a similar agglomeration sponge, with more homogeneous pores compared to the hydrogel from oat cellulose fibers. The hydrogels prepared from the cellulose extracted from rice and oat husks showed water absorption capacity of 141.6-392.1% and high opacity. The highest water absorption capacity and maximum stress the compression were presented by rice cellulose hydrogel at 25°C. These results show that the use of agro-industrial residues is promising for the biomaterial field, especially in the preparation of hydrogels. Copyright © 2016 Elsevier Ltd. All rights reserved.

Para-hydrogen and helium cluster size distributions in free jet expansions based on Smoluchowski theory with kernel scaling.

PubMed

Kornilov, Oleg; Toennies, J Peter

2015-02-21

The size distribution of para-H2 (pH2) clusters produced in free jet expansions at a source temperature of T0 = 29.5 K and pressures of P0 = 0.9-1.96 bars is reported and analyzed according to a cluster growth model based on the Smoluchowski theory with kernel scaling. Good overall agreement is found between the measured and predicted, Nk = A k(a) e(-bk), shape of the distribution. The fit yields values for A and b for values of a derived from simple collision models. The small remaining deviations between measured abundances and theory imply a (pH2)k magic number cluster of k = 13 as has been observed previously by Raman spectroscopy. The predicted linear dependence of b(-(a+1)) on source gas pressure was verified and used to determine the value of the basic effective agglomeration reaction rate constant. A comparison of the corresponding effective growth cross sections σ11 with results from a similar analysis of He cluster size distributions indicates that the latter are much larger by a factor 6-10. An analysis of the three body recombination rates, the geometric sizes and the fact that the He clusters are liquid independent of their size can explain the larger cross sections found for He.

UNICOS Kernel Internals Application Development

NASA Technical Reports Server (NTRS)

Caredo, Nicholas; Craw, James M. (Technical Monitor)

1995-01-01

Having an understanding of UNICOS Kernel Internals is valuable information. However, having the knowledge is only half the value. The second half comes with knowing how to use this information and apply it to the development of tools. The kernel contains vast amounts of useful information that can be utilized. This paper discusses the intricacies of developing utilities that utilize kernel information. In addition, algorithms, logic, and code will be discussed for accessing kernel information. Code segments will be provided that demonstrate how to locate and read kernel structures. Types of applications that can utilize kernel information will also be discussed.

Pure Oats as Part of the Canadian Gluten-Free Diet in Celiac Disease: The Need to Revisit the Issue

PubMed Central

de Souza, M. Cristina P.; Deschênes, Marie-Eve; Laurencelle, Suzanne; Godet, Patrick; Roy, Claude C.; Djilali-Saiah, Idriss

2016-01-01

The question about recommending pure, noncontaminated oats as part of the gluten-free diet of patients with celiac disease remains controversial. This might be due to gluten cross contamination and to the possible immunogenicity of some oat cultivars. In view of this controversy, a review of the scientific literature was conducted to highlight the latest findings published between 2008 and 2014 to examine the current knowledge on oats safety and celiac disease in Europe and North America. Results showed that regular oats consumed in Canada are largely contaminated. Overall, the consumption of pure oats has been generally considered to be safe for adults and children. However, it appears that some oat cultivars may trigger an immune response in sensitive individuals. Therefore, further long-term studies on the impact of consumption of oats identifying the cultivar(s) constitute an important step forward for drawing final recommendations. Furthermore, a closer and more accurate monitoring of the dietary intake of noncontaminated oats would be paramount to better determine what its actual contribution in the gluten-free diet of adults and children with celiac disease are in order to draw sound recommendations on the safety of pure oats as part of the gluten-free diet. PMID:27446824

Pure Oats as Part of the Canadian Gluten-Free Diet in Celiac Disease: The Need to Revisit the Issue.

PubMed

de Souza, M Cristina P; Deschênes, Marie-Eve; Laurencelle, Suzanne; Godet, Patrick; Roy, Claude C; Djilali-Saiah, Idriss

2016-01-01

The question about recommending pure, noncontaminated oats as part of the gluten-free diet of patients with celiac disease remains controversial. This might be due to gluten cross contamination and to the possible immunogenicity of some oat cultivars. In view of this controversy, a review of the scientific literature was conducted to highlight the latest findings published between 2008 and 2014 to examine the current knowledge on oats safety and celiac disease in Europe and North America. Results showed that regular oats consumed in Canada are largely contaminated. Overall, the consumption of pure oats has been generally considered to be safe for adults and children. However, it appears that some oat cultivars may trigger an immune response in sensitive individuals. Therefore, further long-term studies on the impact of consumption of oats identifying the cultivar(s) constitute an important step forward for drawing final recommendations. Furthermore, a closer and more accurate monitoring of the dietary intake of noncontaminated oats would be paramount to better determine what its actual contribution in the gluten-free diet of adults and children with celiac disease are in order to draw sound recommendations on the safety of pure oats as part of the gluten-free diet.

7 CFR 51.2113 - Size requirements.

Code of Federal Regulations, 2010 CFR

2010-01-01

... of range in count of whole almond kernels per ounce or in terms of minimum, or minimum and maximum diameter. When a range in count is specified, the whole kernels shall be fairly uniform in size, and the average count per ounce shall be within the range specified. Doubles and broken kernels shall not be used...

Effect of chemical systemic acquired resistance elicitors on avenanthramide biosynthesis in oat (Avena sativa)

USDA-ARS?s Scientific Manuscript database

Oats produce a group of phenolic antioxidants termed avenanthramides. These metabolites are, among food crops, unique to oats and have shown some desirable nutritional characteristics, in experimental systems, such as inhibiting atherosclerotic plaque formation and reducing inflammatory responses. ...

Comparative Analysis of the Antioxidant Capacities and Phenolic Compounds of Oat and Buckwheat Vinegars During Production Processes.

PubMed

Yu, Xiao; Yang, Mei; Dong, Jilin; Shen, Ruiling

2018-03-01

This study aimed to explore the dynamic changes in the antioxidant activities and phenolic acid profiles of oat and buckwheat vinegars during different production stages. The results showed that both oat and buckwheat vinegar products comparably attenuated D-galactose-induced oxidative damage in mice serum and liver, indicating no obvious dose dependence within the tested concentrations. However, oat vinegar product revealed more favorable in vitro antioxidant activities than those in buckwheat vinegar product as evaluated by 2,2-Diphenyl-1-picrylhydrazyl (DPPH) radical scavenging abilities. Moreover, the alcoholic fermentation, acetic acid fermentation and fumigating induced successive increase in DPPH radical scavenging abilities and phenolic acid contents of the fermentation substrates of oat and buckwheat vinegars. Importantly, the different fermentation processes of oat and buckwheat vinegars were accompanied by the dynamic migration and transformation of specific phenolic acids across bound, esterified and free fractions. Thus, the antioxidant activities of oat and buckwheat vinegars could be improved through targeted modulation of the generation of specific phenolic acid fractions during production processes. We had evaluated the in vitro and in vivo antioxidant activities and phenolic acid contents of oat and buckwheat vinegars, and further explored the dynamic changes of bound, esterified and free phenolic acid fractions during successive fermentation processes of oat and buckwheat vinegars. This study provided the theoretical guidance for obtaining minor grain vinegar with the optimal antioxidant activities through targeted modulation of fermentation processes. © 2018 Institute of Food Technologists®.

Protein Subcellular Localization with Gaussian Kernel Discriminant Analysis and Its Kernel Parameter Selection.

PubMed

Wang, Shunfang; Nie, Bing; Yue, Kun; Fei, Yu; Li, Wenjia; Xu, Dongshu

2017-12-15

Kernel discriminant analysis (KDA) is a dimension reduction and classification algorithm based on nonlinear kernel trick, which can be novelly used to treat high-dimensional and complex biological data before undergoing classification processes such as protein subcellular localization. Kernel parameters make a great impact on the performance of the KDA model. Specifically, for KDA with the popular Gaussian kernel, to select the scale parameter is still a challenging problem. Thus, this paper introduces the KDA method and proposes a new method for Gaussian kernel parameter selection depending on the fact that the differences between reconstruction errors of edge normal samples and those of interior normal samples should be maximized for certain suitable kernel parameters. Experiments with various standard data sets of protein subcellular localization show that the overall accuracy of protein classification prediction with KDA is much higher than that without KDA. Meanwhile, the kernel parameter of KDA has a great impact on the efficiency, and the proposed method can produce an optimum parameter, which makes the new algorithm not only perform as effectively as the traditional ones, but also reduce the computational time and thus improve efficiency.

Fortification of yogurt with oat hydrocolloid

USDA-ARS?s Scientific Manuscript database

C-Trim 30, an oat hydrocolloid was added to milk such that fermented yogurt had 0, 0.75, 1.5, 2.25, and 3 g ß-glucan per serving. The fermentation rate and physical characteristics of yogurt were studied. Lactose fermentation was not inhibited by the addition of C-Trim. All yogurt mix reached the...

7 CFR 981.7 - Edible kernel.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 8 2010-01-01 2010-01-01 false Edible kernel. 981.7 Section 981.7 Agriculture... Regulating Handling Definitions § 981.7 Edible kernel. Edible kernel means a kernel, piece, or particle of almond kernel that is not inedible. [41 FR 26852, June 30, 1976] ...

Fractionation of oats into products enriched with protein, beta-glucan, starch, or other carbohydrates

USDA-ARS?s Scientific Manuscript database

A modified wet method was developed to fractionate ground oat groats into 4 fractions enriched with beta-glucan (BG), protein, starch, and other carbohydrates (CHO), respectively. Effects of defatting oats and centrifuge force for separation were also investigated. Results show that, depending on ...

Unconventional protein sources: apricot seed kernels.

PubMed

Gabrial, G N; El-Nahry, F I; Awadalla, M Z; Girgis, S M

1981-09-01

Hamawy apricot seed kernels (sweet), Amar apricot seed kernels (bitter) and treated Amar apricot kernels (bitterness removed) were evaluated biochemically. All kernels were found to be high in fat (42.2--50.91%), protein (23.74--25.70%) and fiber (15.08--18.02%). Phosphorus, calcium, and iron were determined in all experimental samples. The three different apricot seed kernels were used for extensive study including the qualitative determination of the amino acid constituents by acid hydrolysis, quantitative determination of some amino acids, and biological evaluation of the kernel proteins in order to use them as new protein sources. Weanling albino rats failed to grow on diets containing the Amar apricot seed kernels due to low food consumption because of its bitterness. There was no loss in weight in that case. The Protein Efficiency Ratio data and blood analysis results showed the Hamawy apricot seed kernels to be higher in biological value than treated apricot seed kernels. The Net Protein Ratio data which accounts for both weight, maintenance and growth showed the treated apricot seed kernels to be higher in biological value than both Hamawy and Amar kernels. The Net Protein Ratio for the last two kernels were nearly equal.

The Long-Term Consumption of Oats in Celiac Disease Patients Is Safe: A Large Cross-Sectional Study

PubMed Central

Aaltonen, Katri; Laurikka, Pilvi; Huhtala, Heini; Mäki, Markku; Kaukinen, Katri; Kurppa, Kalle

2017-01-01

A strict gluten-free diet (GFD) can be diversified by non-contaminated oats, but there is a shortage of long-term studies concerning its safety. We compared long-term treatment outcomes and factors associated with the introduction of oats between celiac patients on a GFD with or without oats. Eight hundred sixty-nine previously diagnosed celiac patients were interviewed. The validated Gastrointestinal Symptom Rating Scale (GSRS), Psychological General Well-Being (PGWB), and Short-Form 36 Health Survey (SF-36) questionnaires were used to assess symptoms and quality of life, serological tests were performed, and results of histology were confirmed from patient records. We found the median duration of GFD to be 10 years and 82% using oats. Factors predicting the consumption of oats were diagnosis after the year 2000, advice from a dietitian, detection by screening, and mild clinical presentation. Oat consumers and non-consumers did not differ in dietary adherence (96.5% vs. 97.4%, p = 0.746), the prevalence of symptoms (22.9% vs. 22.5%, p = 0.931), positivity for endomysial antibodies (8.8% vs. 6.0%, p = 0.237), histological recovery after one year (63.1% vs. 60.0%, p = 0.773), malignancy (4.8% vs. 3.3%, p = 0.420), osteoporosis/osteopenia (9.2% vs. 11.0%, p = 0.489), or fractures (26.9% vs. 27.9%, p = 0.791). The oat consumers had better SF-36 physical role limitations and general health scores. Based on our results, the long-term consumption of oats in celiac disease patients is safe and may improve quality of life. PMID:28617328

7 CFR 981.8 - Inedible kernel.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 8 2010-01-01 2010-01-01 false Inedible kernel. 981.8 Section 981.8 Agriculture... Regulating Handling Definitions § 981.8 Inedible kernel. Inedible kernel means a kernel, piece, or particle of almond kernel with any defect scored as serious damage, or damage due to mold, gum, shrivel, or...

7 CFR 51.1415 - Inedible kernels.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 2 2010-01-01 2010-01-01 false Inedible kernels. 51.1415 Section 51.1415 Agriculture... Standards for Grades of Pecans in the Shell 1 Definitions § 51.1415 Inedible kernels. Inedible kernels means that the kernel or pieces of kernels are rancid, moldy, decayed, injured by insects or otherwise...

Comparative analysis of homoeoallele expression in the tocol biosynthetic pathway during oat seed development

USDA-ARS?s Scientific Manuscript database

Oats are a rich source of compounds that collectively constitute vitamin E, the tocols. Significant attention has been given to the health benefits of tocols in oats, but little is known about themolecular control of their accumulation during grain development. Next generation sequencing provides an...

7 CFR 981.408 - Inedible kernel.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 8 2010-01-01 2010-01-01 false Inedible kernel. 981.408 Section 981.408 Agriculture... Administrative Rules and Regulations § 981.408 Inedible kernel. Pursuant to § 981.8, the definition of inedible kernel is modified to mean a kernel, piece, or particle of almond kernel with any defect scored as...

Effect of an oats-containing gluten-free diet on symptoms and quality of life in coeliac disease. A randomized study.

PubMed

Peräaho, M; Kaukinen, K; Mustalahti, K; Vuolteenaho, N; Mäki, M; Laippala, P; Collin, P

2004-01-01

Evidence suggests the acceptability of oats in a gluten-free diet in coeliac disease. We investigated the impact of an oats-containing diet on quality of life and gastrointestinal symptoms. Thirty-nine coeliac disease patients on a gluten-free diet were randomized to take either 50 g of oats-containing gluten-free products daily or to continue without oats for 1 year. Quality of life was assessed using the Psychological General Well-Being questionnaire and gastrointestinal symptoms using the Gastrointestinal Symptom Rating Scale. Small-bowel mucosal villous architecture, CD3+, alphabeta+, gammadelta+ intraepithelial lymphocytes, serum endomysial and tissue transglutaminase antibodies were investigated. Twenty-three subjects were randomized to the oats-containing diet and 16 to the traditional gluten-free diet. All adhered strictly to their respective diet. Quality of life did not differ between the groups. In general, there were more gastrointestinal symptoms in the oats-consuming group. Patients taking oats suffered significantly more often from diarrhoea, but there was a simultaneous trend towards a more severe average constipation symptom score. The villous structure did not differ between the groups, but the density of intraepithelial lymphocytes was slightly but significantly higher in the oats group. The severity of symptoms was not dependent on the degree of inflammation. Antibody levels did not increase during the study period. The oats-containing gluten-free diet caused more intestinal symptoms than the traditional diet. Mucosal integrity was not disturbed, but more inflammation was evident in the oats group. Oats provide an alternative in the gluten-free diet, but coeliac patients should be aware of the possible increase in intestinal symptoms.

Genetic diversity and crown rust resistance of oat landraces from various locations throughout Turkey

USDA-ARS?s Scientific Manuscript database

A diversity study was carried out to identify the origin of 375 oat landraces (Avena sativa L. and A. byzantina C. Koch.) collected from Turkey and maintained in various gene banks. New assays interrogating oat-based microsatellite and single-nucleotide polymorphism loci were used to characterize t...

New DArT markers for oat provide enhanced map coverage and global germplasm characterization

USDA-ARS?s Scientific Manuscript database

Background Genomic discovery in oat and its application to oat improvement have been hindered by a lack of genetic markers common to different genetic maps, and by the difficulty of conducting whole-genome analysis using high-throughput markers. This study was intended to develop, characterize, and ...

LZW-Kernel: fast kernel utilizing variable length code blocks from LZW compressors for protein sequence classification.

PubMed

Filatov, Gleb; Bauwens, Bruno; Kertész-Farkas, Attila

2018-05-07

Bioinformatics studies often rely on similarity measures between sequence pairs, which often pose a bottleneck in large-scale sequence analysis. Here, we present a new convolutional kernel function for protein sequences called the LZW-Kernel. It is based on code words identified with the Lempel-Ziv-Welch (LZW) universal text compressor. The LZW-Kernel is an alignment-free method, it is always symmetric, is positive, always provides 1.0 for self-similarity and it can directly be used with Support Vector Machines (SVMs) in classification problems, contrary to normalized compression distance (NCD), which often violates the distance metric properties in practice and requires further techniques to be used with SVMs. The LZW-Kernel is a one-pass algorithm, which makes it particularly plausible for big data applications. Our experimental studies on remote protein homology detection and protein classification tasks reveal that the LZW-Kernel closely approaches the performance of the Local Alignment Kernel (LAK) and the SVM-pairwise method combined with Smith-Waterman (SW) scoring at a fraction of the time. Moreover, the LZW-Kernel outperforms the SVM-pairwise method when combined with BLAST scores, which indicates that the LZW code words might be a better basis for similarity measures than local alignment approximations found with BLAST. In addition, the LZW-Kernel outperforms n-gram based mismatch kernels, hidden Markov model based SAM and Fisher kernel, and protein family based PSI-BLAST, among others. Further advantages include the LZW-Kernel's reliance on a simple idea, its ease of implementation, and its high speed, three times faster than BLAST and several magnitudes faster than SW or LAK in our tests. LZW-Kernel is implemented as a standalone C code and is a free open-source program distributed under GPLv3 license and can be downloaded from https://github.com/kfattila/LZW-Kernel. akerteszfarkas@hse.ru. Supplementary data are available at Bioinformatics Online.

Increasing the Size of a Piece of Popcorn

NASA Astrophysics Data System (ADS)

Quinn, Paul; Hong, Daniel C.; Both, Joseph

2003-03-01

Popcorn is an extremely popular snack food in the world today. Thermodynamics can be used to analyze how popcorn is produced. By treating the popping mechanism of the corn as a thermodynamic expansion, a method of increasing the volume or size of a kernel of popcorn can be studied. By lowering the pressure surrounding the unpopped kernel, one can use a thermodynamic argument to show that the expanded volume of the kernel when it pops must increase. In this project, a variety of experiments are run to test the validity of this theory. The results show that there is a significant increase in the average kernel size when the pressure of the surroundings is reduced.

Increasing the size of a piece of popcorn

NASA Astrophysics Data System (ADS)

Quinn, Paul V.; Hong, Daniel C.; Both, J. A.

2005-08-01

Popcorn is an extremely popular snack food in the world today. Thermodynamics can be used to analyze how popcorn is produced. By treating the popping mechanism of the corn as a thermodynamic expansion, a method of increasing the volume or size of a kernel of popcorn can be studied. By lowering the pressure surrounding the unpopped kernel, one can use a thermodynamic argument to show that the expanded volume of the kernel when it pops must increase. In this project, a variety of experiments are run to test the qualitative validity of this theory. The results show that there is a significant increase in the average kernel size when the pressure of the surroundings is reduced.

7 CFR 810.202 - Definition of other terms.

Code of Federal Regulations, 2011 CFR

2011-01-01

... GRAIN United States Standards for Barley Terms Defined § 810.202 Definition of other terms. (a) Black barley. Barley with black hulls. (b) Broken kernels. Barley with more than 1/4 of the kernel removed. (c... barley kernels, other grains, and wild oats that are badly shrunken and distinctly discolored black or...

Interaction of human organic anion transporter 2 (OAT2) and sodium taurocholate cotransporting polypeptide (NTCP) with antineoplastic drugs.

PubMed

Marada, Venkata V V R; Flörl, Saskia; Kühne, Annett; Müller, Judith; Burckhardt, Gerhard; Hagos, Yohannes

2015-01-01

The ability of an antineoplastic drug to exert its cytostatic effect depends largely on the balance between its uptake into and extrusion from the cancer cells. ATP driven efflux transporter proteins drive the export of antineoplastic drugs and play a pivotal role in the development of chemoresistance. As regards uptake transporters, comparably less is known on their impact in drug action. In the current study, we characterized the interactions of two uptake transporter proteins, expressed mainly in the liver; the organic anion transporter 2 (OAT2, encoded by the SLC22A7 gene) and the sodium taurocholate cotransporting polypeptide (NTCP, encoded by the SLC10A1 gene), stably transfected in human embryonic kidney cells, with some antineoplastic agents that are routinely being used in cancer chemotherapy. Whereas NTCP did not show any strong interactions with the cytostatics tested, we observed a very strong inhibition of OAT2 mediated [(3)H] cGMP uptake in the presence of bendamustine, irinotecan and paclitaxel. The Ki values of OAT2 for bendamustine, irinotecan and paclitaxel were determined to be 43.3±4.33μM, 26.4±2.34μM and 10.4±0.45μM, respectively. Incubation of bendamustine with OAT2 expressing cells increased the caspase-3 activity, and this increase was inhibited by simultaneous incubation with bendamustine and probenecid, a well-known inhibitor of OATs, suggesting that bendamustine is a substrate of OAT2. A higher accumulation of irinotecan was observed in OAT2 expressing cells compared to control pcDNA cells by HPLC analysis of cell lysates. The accumulation was diminished in the presence of cGMP, the substrate we used to functionally characterize OAT2, suggesting specificity of this uptake and the fact that OAT2 mediates uptake of irinotecan. Copyright © 2014 Elsevier Ltd. All rights reserved.

Molecular and Immunological Characterization of Gluten Proteins Isolated from Oat Cultivars That Differ in Toxicity for Celiac Disease

PubMed Central

Real, Ana; Comino, Isabel; de Lorenzo, Laura; Merchán, Francisco; Gil-Humanes, Javier; Giménez, María J.; López-Casado, Miguel Ángel; Cebolla, Ángel; Sousa, Carolina; Barro, Francisco; Pistón, Fernando

2012-01-01

A strict gluten-free diet (GFD) is the only currently available therapeutic treatment for patients with celiac disease (CD). Traditionally, treatment with a GFD has excluded wheat, barley and rye, while the presence of oats is a subject of debate. The most-recent research indicates that some cultivars of oats can be a safe part of a GFD. In order to elucidate the toxicity of the prolamins from oat varieties with low, medium, and high CD toxicity, the avenin genes of these varieties were cloned and sequenced, and their expression quantified throughout the grain development. At the protein level, we have accomplished an exhaustive characterization and quantification of avenins by RP-HPLC and an analysis of immunogenicity of peptides present in prolamins of different oat cultivars. Avenin sequences were classified into three different groups, which have homology with S-rich prolamins of Triticeae. Avenin proteins presented a lower proline content than that of wheat gliadin; this may contribute to the low toxicity shown by oat avenins. The expression of avenin genes throughout the development stages has shown a pattern similar to that of prolamins of wheat and barley. RP-HPLC chromatograms showed protein peaks in the alcohol-soluble and reduced-soluble fractions. Therefore, oat grains had both monomeric and polymeric avenins, termed in this paper gliadin- and glutenin-like avenins. We found a direct correlation between the immunogenicity of the different oat varieties and the presence of the specific peptides with a higher/lower potential immunotoxicity. The specific peptides from the oat variety with the highest toxicity have shown a higher potential immunotoxicity. These results suggest that there is wide range of variation of potential immunotoxicity of oat cultivars that could be due to differences in the degree of immunogenicity in their sequences. PMID:23284616

Partial Deconvolution with Inaccurate Blur Kernel.

PubMed

Ren, Dongwei; Zuo, Wangmeng; Zhang, David; Xu, Jun; Zhang, Lei

2017-10-17

Most non-blind deconvolution methods are developed under the error-free kernel assumption, and are not robust to inaccurate blur kernel. Unfortunately, despite the great progress in blind deconvolution, estimation error remains inevitable during blur kernel estimation. Consequently, severe artifacts such as ringing effects and distortions are likely to be introduced in the non-blind deconvolution stage. In this paper, we tackle this issue by suggesting: (i) a partial map in the Fourier domain for modeling kernel estimation error, and (ii) a partial deconvolution model for robust deblurring with inaccurate blur kernel. The partial map is constructed by detecting the reliable Fourier entries of estimated blur kernel. And partial deconvolution is applied to wavelet-based and learning-based models to suppress the adverse effect of kernel estimation error. Furthermore, an E-M algorithm is developed for estimating the partial map and recovering the latent sharp image alternatively. Experimental results show that our partial deconvolution model is effective in relieving artifacts caused by inaccurate blur kernel, and can achieve favorable deblurring quality on synthetic and real blurry images.Most non-blind deconvolution methods are developed under the error-free kernel assumption, and are not robust to inaccurate blur kernel. Unfortunately, despite the great progress in blind deconvolution, estimation error remains inevitable during blur kernel estimation. Consequently, severe artifacts such as ringing effects and distortions are likely to be introduced in the non-blind deconvolution stage. In this paper, we tackle this issue by suggesting: (i) a partial map in the Fourier domain for modeling kernel estimation error, and (ii) a partial deconvolution model for robust deblurring with inaccurate blur kernel. The partial map is constructed by detecting the reliable Fourier entries of estimated blur kernel. And partial deconvolution is applied to wavelet-based and learning

7 CFR 981.9 - Kernel weight.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 8 2010-01-01 2010-01-01 false Kernel weight. 981.9 Section 981.9 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Marketing Agreements... Regulating Handling Definitions § 981.9 Kernel weight. Kernel weight means the weight of kernels, including...

Indetermination of particle sizing by laser diffraction in the anomalous size ranges

NASA Astrophysics Data System (ADS)

Pan, Linchao; Ge, Baozhen; Zhang, Fugen

2017-09-01

The laser diffraction method is widely used to measure particle size distributions. It is generally accepted that the scattering angle becomes smaller and the angles to the location of the main peak of scattered energy distributions in laser diffraction instruments shift to smaller values with increasing particle size. This specific principle forms the foundation of the laser diffraction method. However, this principle is not entirely correct for non-absorbing particles in certain size ranges and these particle size ranges are called anomalous size ranges. Here, we derive the analytical formulae for the bounds of the anomalous size ranges and discuss the influence of the width of the size segments on the signature of the Mie scattering kernel. This anomalous signature of the Mie scattering kernel will result in an indetermination of the particle size distribution when measured by laser diffraction instruments in the anomalous size ranges. By using the singular-value decomposition method we interpret the mechanism of occurrence of this indetermination in detail and then validate its existence by using inversion simulations.

7 CFR 51.2295 - Half kernel.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 2 2010-01-01 2010-01-01 false Half kernel. 51.2295 Section 51.2295 Agriculture... Standards for Shelled English Walnuts (Juglans Regia) Definitions § 51.2295 Half kernel. Half kernel means the separated half of a kernel with not more than one-eighth broken off. ...

Improved scatter correction using adaptive scatter kernel superposition

NASA Astrophysics Data System (ADS)

Sun, M.; Star-Lack, J. M.

2010-11-01

Accurate scatter correction is required to produce high-quality reconstructions of x-ray cone-beam computed tomography (CBCT) scans. This paper describes new scatter kernel superposition (SKS) algorithms for deconvolving scatter from projection data. The algorithms are designed to improve upon the conventional approach whose accuracy is limited by the use of symmetric kernels that characterize the scatter properties of uniform slabs. To model scatter transport in more realistic objects, nonstationary kernels, whose shapes adapt to local thickness variations in the projection data, are proposed. Two methods are introduced: (1) adaptive scatter kernel superposition (ASKS) requiring spatial domain convolutions and (2) fast adaptive scatter kernel superposition (fASKS) where, through a linearity approximation, convolution is efficiently performed in Fourier space. The conventional SKS algorithm, ASKS, and fASKS, were tested with Monte Carlo simulations and with phantom data acquired on a table-top CBCT system matching the Varian On-Board Imager (OBI). All three models accounted for scatter point-spread broadening due to object thickening, object edge effects, detector scatter properties and an anti-scatter grid. Hounsfield unit (HU) errors in reconstructions of a large pelvis phantom with a measured maximum scatter-to-primary ratio over 200% were reduced from -90 ± 58 HU (mean ± standard deviation) with no scatter correction to 53 ± 82 HU with SKS, to 19 ± 25 HU with fASKS and to 13 ± 21 HU with ASKS. HU accuracies and measured contrast were similarly improved in reconstructions of a body-sized elliptical Catphan phantom. The results show that the adaptive SKS methods offer significant advantages over the conventional scatter deconvolution technique.

Formulation Optimization of Gluten-Free Functional Spaghetti Based on Maize Flour and Oat Bran Enriched in b-Glucans.

PubMed

Padalino, Lucia; Mastromatteo, Marcella; Sepielli, Grazia; Nobile, Matteo Alessandro Del

2011-12-08

The aim of this work concerns the manufacturing process of gluten-free functional spaghetti based on maize flour and oat bran, enriched with b-glucans (22%). More specifically, the goal of the study was to obtain oat bran-loaded maize spaghetti with sensory properties close to unloaded pasta. To this aim, the study has been organized in two subsequent trials. In the first one, the oat bran amount added to spaghetti was continuously increased until the overall sensory quality of pasta reached the set sensory threshold (oat bran concentration = 20%). The second experimental step was aimed to improve the overall sensory quality of oat bran loaded maize spaghetti. In particular, an attempt was made to increase the sensory quality of spaghetti added with 20% oat bran by means of structuring agents. To this aim, the effects of different kinds of some hydrocolloids and egg white powder on the rheological properties of dough, as well as on quality attributes of pasta were examined. The rheological analysis showed that the addition of hydrocolloids and white egg to the dough enriched with 20% oat bran did not cause any substantial difference in the viscoelastic properties, compared to samples without any structuring agents. The best overall quality for both fresh and dry spaghetti was obtained by the addition of carboxymethylcellulose and chitosan at a concentration of 2%.

Detection of gold nanoparticles signal inside wheat (Triticum Aestivum.L) and oats (Avena sativa) seedlings

NASA Astrophysics Data System (ADS)

Joshi, Anjali; Nayyar, Harsh; Dharamvir, Keya; Verma, Gaurav

2018-05-01

Nanostructures have recently been reported by various research groups to induce growth enhancement in variety of crops. In this report 30-40 nm size gold nanoparticles (AuNPs) at two concentrations were found to enhance the total biomass yield of wheat and oats. Treating plants with up to 100 µl /mL and 200 µl /mL of AuNPs shows an increased growth and germination rate. The noticeable difference in fresh weight and relative leaf water content were recorded. The fluorescence and UV-Vis spectroscopy detected the gold nanoparticles inside the seedling.

A SNP genotyping array for hexaploid oat

USDA-ARS?s Scientific Manuscript database

Recognizing a need in cultivated hexaploid oat (Avena sativa L.) for a reliable set of reference SNPs, we have developed a 6K BeadChip design containing 257 Infinium I and 5,486 Infinium II designs corresponding to 5,743 SNPs. Of those, 4,975 SNPs yielded successful assays after array manufacturing...

Community Needs Assessment Office Administration & Technology (OAT).

ERIC Educational Resources Information Center

Pezzoli, J. A.; Lum, Ku'uipo; Meyer, Diane

The purpose of this survey was to obtain from employers the requisite skills and potential employment demand for office workers on Maui. Of particular interest was: (1) the assessment of various clerical skills and computer software in its relevance to the Office Administration & Technology (OAT) curriculum at Maui Community College; and (2)…

Kernel abortion in maize : I. Carbohydrate concentration patterns and Acid invertase activity of maize kernels induced to abort in vitro.

PubMed

Hanft, J M; Jones, R J

1986-06-01

Kernels cultured in vitro were induced to abort by high temperature (35 degrees C) and by culturing six kernels/cob piece. Aborting kernels failed to enter a linear phase of dry mass accumulation and had a final mass that was less than 6% of nonaborting field-grown kernels. Kernels induced to abort by high temperature failed to synthesize starch in the endosperm and had elevated sucrose concentrations and low fructose and glucose concentrations in the pedicel during early growth compared to nonaborting kernels. Kernels induced to abort by high temperature also had much lower pedicel soluble acid invertase activities than did nonaborting kernels. These results suggest that high temperature during the lag phase of kernel growth may impair the process of sucrose unloading in the pedicel by indirectly inhibiting soluble acid invertase activity and prevent starch synthesis in the endosperm. Kernels induced to abort by culturing six kernels/cob piece had reduced pedicel fructose, glucose, and sucrose concentrations compared to kernels from field-grown ears. These aborting kernels also had a lower pedicel soluble acid invertase activity compared to nonaborting kernels from the same cob piece and from field-grown ears. The low invertase activity in pedicel tissue of the aborting kernels was probably caused by a lack of substrate (sucrose) for the invertase to cleave due to the intense competition for available assimilates. In contrast to kernels cultured at 35 degrees C, aborting kernels from cob pieces containing all six kernels accumulated starch in a linear fashion. These results indicate that kernels cultured six/cob piece abort because of an inadequate supply of sugar and are similar to apical kernels from field-grown ears that often abort prior to the onset of linear growth.

An Approximate Approach to Automatic Kernel Selection.

PubMed

Ding, Lizhong; Liao, Shizhong

2016-02-02

Kernel selection is a fundamental problem of kernel-based learning algorithms. In this paper, we propose an approximate approach to automatic kernel selection for regression from the perspective of kernel matrix approximation. We first introduce multilevel circulant matrices into automatic kernel selection, and develop two approximate kernel selection algorithms by exploiting the computational virtues of multilevel circulant matrices. The complexity of the proposed algorithms is quasi-linear in the number of data points. Then, we prove an approximation error bound to measure the effect of the approximation in kernel matrices by multilevel circulant matrices on the hypothesis and further show that the approximate hypothesis produced with multilevel circulant matrices converges to the accurate hypothesis produced with kernel matrices. Experimental evaluations on benchmark datasets demonstrate the effectiveness of approximate kernel selection.

Viscozyme L pretreatment on palm kernels improved the aroma of palm kernel oil after kernel roasting.

PubMed

Zhang, Wencan; Leong, Siew Mun; Zhao, Feifei; Zhao, Fangju; Yang, Tiankui; Liu, Shaoquan

2018-05-01

With an interest to enhance the aroma of palm kernel oil (PKO), Viscozyme L, an enzyme complex containing a wide range of carbohydrases, was applied to alter the carbohydrates in palm kernels (PK) to modulate the formation of volatiles upon kernel roasting. After Viscozyme treatment, the content of simple sugars and free amino acids in PK increased by 4.4-fold and 4.5-fold, respectively. After kernel roasting and oil extraction, significantly more 2,5-dimethylfuran, 2-[(methylthio)methyl]-furan, 1-(2-furanyl)-ethanone, 1-(2-furyl)-2-propanone, 5-methyl-2-furancarboxaldehyde and 2-acetyl-5-methylfuran but less 2-furanmethanol and 2-furanmethanol acetate were found in treated PKO; the correlation between their formation and simple sugar profile was estimated by using partial least square regression (PLS1). Obvious differences in pyrroles and Strecker aldehydes were also found between the control and treated PKOs. Principal component analysis (PCA) clearly discriminated the treated PKOs from that of control PKOs on the basis of all volatile compounds. Such changes in volatiles translated into distinct sensory attributes, whereby treated PKO was more caramelic and burnt after aqueous extraction and more nutty, roasty, caramelic and smoky after solvent extraction. Copyright © 2018 Elsevier Ltd. All rights reserved.

7 CFR 810.2002 - Definition of other terms.

Code of Federal Regulations, 2010 CFR

2010-01-01

... shrunken and broken kernels. The sum of these three factors may not exceed the limit for the factor defects..., and wild oats. (g) Shrunken and broken kernels. All matter that passes through a 0.064×3/8 oblong-hole...

7 CFR 810.2002 - Definition of other terms.

Code of Federal Regulations, 2011 CFR

2011-01-01

... shrunken and broken kernels. The sum of these three factors may not exceed the limit for the factor defects..., and wild oats. (g) Shrunken and broken kernels. All matter that passes through a 0.064×3/8 oblong-hole...

7 CFR 810.2002 - Definition of other terms.

Code of Federal Regulations, 2014 CFR

2014-01-01

... shrunken and broken kernels. The sum of these three factors may not exceed the limit for the factor defects..., and wild oats. (g) Shrunken and broken kernels. All matter that passes through a 0.064×3/8 oblong-hole...

7 CFR 810.2002 - Definition of other terms.

Code of Federal Regulations, 2012 CFR

2012-01-01

... shrunken and broken kernels. The sum of these three factors may not exceed the limit for the factor defects..., and wild oats. (g) Shrunken and broken kernels. All matter that passes through a 0.064×3/8 oblong-hole...

7 CFR 810.2002 - Definition of other terms.

Code of Federal Regulations, 2013 CFR

2013-01-01

... shrunken and broken kernels. The sum of these three factors may not exceed the limit for the factor defects..., and wild oats. (g) Shrunken and broken kernels. All matter that passes through a 0.064×3/8 oblong-hole...

7 CFR 51.1441 - Half-kernel.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 2 2010-01-01 2010-01-01 false Half-kernel. 51.1441 Section 51.1441 Agriculture... Standards for Grades of Shelled Pecans Definitions § 51.1441 Half-kernel. Half-kernel means one of the separated halves of an entire pecan kernel with not more than one-eighth of its original volume missing...

Para-hydrogen and helium cluster size distributions in free jet expansions based on Smoluchowski theory with kernel scaling

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

Kornilov, Oleg; Toennies, J. Peter

The size distribution of para-H{sub 2} (pH{sub 2}) clusters produced in free jet expansions at a source temperature of T{sub 0} = 29.5 K and pressures of P{sub 0} = 0.9–1.96 bars is reported and analyzed according to a cluster growth model based on the Smoluchowski theory with kernel scaling. Good overall agreement is found between the measured and predicted, N{sub k} = A k{sup a} e{sup −bk}, shape of the distribution. The fit yields values for A and b for values of a derived from simple collision models. The small remaining deviations between measured abundances and theory imply a (pH{submore » 2}){sub k} magic number cluster of k = 13 as has been observed previously by Raman spectroscopy. The predicted linear dependence of b{sup −(a+1)} on source gas pressure was verified and used to determine the value of the basic effective agglomeration reaction rate constant. A comparison of the corresponding effective growth cross sections σ{sub 11} with results from a similar analysis of He cluster size distributions indicates that the latter are much larger by a factor 6-10. An analysis of the three body recombination rates, the geometric sizes and the fact that the He clusters are liquid independent of their size can explain the larger cross sections found for He.« less

Effect of natural flocculants on purity and properties of β-glucan extracted from barley and oat.

PubMed

Kurek, Marcin Andrzej; Karp, Sabina; Stelmasiak, Adrian; Pieczykolan, Ewelina; Juszczyk, Karolina; Rieder, Anne

2018-05-15

In this study, β-glucan was extracted from wholegrain oat and barley flours by a novel extraction and purification method employing natural flocculants (chitosan, guar gum and gelatin). The use of flocculants decreased the total amount of extracted gum, which was highest in control samples (9.07 and 7.9% for oat and barley, respectively). The β-glucan specific yield, however, increased with the use of chitosan and guar gum, which were able to remove protein and ash impurities resulting in gums with a higher purity.The highest concentration of chitosan (0.6 %) resulted in gums with the highest β-glucan content (82.0 ± 0.23 and 79.0 ± 0.19 for barley and oat, respectively) and highest β-glucan specific yield (96.9 and 93.3 % for oat and barley, respectively). Explanation is in R&D section. The use of gelatin was not successful. All gum samples had a high content of total dietary fiber (>74%) and a high water holding capacity (4.6-7.4 g/g), but differed in apparent viscosity, which was highest for the oat sample extracted with 0.6% chitosan. This sample also showed the highest β-glucan molecular weight among the oat samples, which were in general 10-fold higher than for the barley samples. Among the barley samples, β-glucan molecular weight was highest for the control. Copyright © 2018 Elsevier Ltd. All rights reserved.

An introduction to kernel-based learning algorithms.

PubMed

Müller, K R; Mika, S; Rätsch, G; Tsuda, K; Schölkopf, B

2001-01-01

This paper provides an introduction to support vector machines, kernel Fisher discriminant analysis, and kernel principal component analysis, as examples for successful kernel-based learning methods. We first give a short background about Vapnik-Chervonenkis theory and kernel feature spaces and then proceed to kernel based learning in supervised and unsupervised scenarios including practical and algorithmic considerations. We illustrate the usefulness of kernel algorithms by discussing applications such as optical character recognition and DNA analysis.

A new discriminative kernel from probabilistic models.

PubMed

Tsuda, Koji; Kawanabe, Motoaki; Rätsch, Gunnar; Sonnenburg, Sören; Müller, Klaus-Robert

2002-10-01

Recently, Jaakkola and Haussler (1999) proposed a method for constructing kernel functions from probabilistic models. Their so-called Fisher kernel has been combined with discriminative classifiers such as support vector machines and applied successfully in, for example, DNA and protein analysis. Whereas the Fisher kernel is calculated from the marginal log-likelihood, we propose the TOP kernel derived; from tangent vectors of posterior log-odds. Furthermore, we develop a theoretical framework on feature extractors from probabilistic models and use it for analyzing the TOP kernel. In experiments, our new discriminative TOP kernel compares favorably to the Fisher kernel.

A locally adaptive kernel regression method for facies delineation

NASA Astrophysics Data System (ADS)

Fernàndez-Garcia, D.; Barahona-Palomo, M.; Henri, C. V.; Sanchez-Vila, X.

2015-12-01

Facies delineation is defined as the separation of geological units with distinct intrinsic characteristics (grain size, hydraulic conductivity, mineralogical composition). A major challenge in this area stems from the fact that only a few scattered pieces of hydrogeological information are available to delineate geological facies. Several methods to delineate facies are available in the literature, ranging from those based only on existing hard data, to those including secondary data or external knowledge about sedimentological patterns. This paper describes a methodology to use kernel regression methods as an effective tool for facies delineation. The method uses both the spatial and the actual sampled values to produce, for each individual hard data point, a locally adaptive steering kernel function, self-adjusting the principal directions of the local anisotropic kernels to the direction of highest local spatial correlation. The method is shown to outperform the nearest neighbor classification method in a number of synthetic aquifers whenever the available number of hard data is small and randomly distributed in space. In the case of exhaustive sampling, the steering kernel regression method converges to the true solution. Simulations ran in a suite of synthetic examples are used to explore the selection of kernel parameters in typical field settings. It is shown that, in practice, a rule of thumb can be used to obtain suboptimal results. The performance of the method is demonstrated to significantly improve when external information regarding facies proportions is incorporated. Remarkably, the method allows for a reasonable reconstruction of the facies connectivity patterns, shown in terms of breakthrough curves performance.

Kernel Abortion in Maize 1

PubMed Central

Hanft, Jonathan M.; Jones, Robert J.

1986-01-01

This study was designed to compare the uptake and distribution of 14C among fructose, glucose, sucrose, and starch in the cob, pedicel, and endosperm tissues of maize (Zea mays L.) kernels induced to abort by high temperature with those that develop normally. Kernels cultured in vitro at 30 and 35°C were transferred to [14C]sucrose media 10 days after pollination. Kernels cultured at 35°C aborted prior to the onset of linear dry matter accumulation. Significant uptake into the cob, pedicel, and endosperm of radioactivity associated with the soluble and starch fractions of the tissues was detected after 24 hours in culture on labeled media. After 8 days in culture on [14C]sucrose media, 48 and 40% of the radioactivity associated with the cob carbohydrates was found in the reducing sugars at 30 and 35°C, respectively. This indicates that some of the sucrose taken up by the cob tissue was cleaved to fructose and glucose in the cob. Of the total carbohydrates, a higher percentage of label was associated with sucrose and a lower percentage with fructose and glucose in pedicel tissue of kernels cultured at 35°C compared to kernels cultured at 30°C. These results indicate that sucrose was not cleaved to fructose and glucose as rapidly during the unloading process in the pedicel of kernels induced to abort by high temperature. Kernels cultured at 35°C had a much lower proportion of label associated with endosperm starch (29%) than did kernels cultured at 30°C (89%). Kernels cultured at 35°C had a correspondingly higher proportion of 14C in endosperm fructose, glucose, and sucrose. These results indicate that starch synthesis in the endosperm is strongly inhibited in kernels induced to abort by high temperature even though there is an adequate supply of sugar. PMID:16664847

Local Observed-Score Kernel Equating

ERIC Educational Resources Information Center

Wiberg, Marie; van der Linden, Wim J.; von Davier, Alina A.

2014-01-01

Three local observed-score kernel equating methods that integrate methods from the local equating and kernel equating frameworks are proposed. The new methods were compared with their earlier counterparts with respect to such measures as bias--as defined by Lord's criterion of equity--and percent relative error. The local kernel item response…

How bandwidth selection algorithms impact exploratory data analysis using kernel density estimation.

PubMed

Harpole, Jared K; Woods, Carol M; Rodebaugh, Thomas L; Levinson, Cheri A; Lenze, Eric J

2014-09-01

Exploratory data analysis (EDA) can reveal important features of underlying distributions, and these features often have an impact on inferences and conclusions drawn from data. Graphical analysis is central to EDA, and graphical representations of distributions often benefit from smoothing. A viable method of estimating and graphing the underlying density in EDA is kernel density estimation (KDE). This article provides an introduction to KDE and examines alternative methods for specifying the smoothing bandwidth in terms of their ability to recover the true density. We also illustrate the comparison and use of KDE methods with 2 empirical examples. Simulations were carried out in which we compared 8 bandwidth selection methods (Sheather-Jones plug-in [SJDP], normal rule of thumb, Silverman's rule of thumb, least squares cross-validation, biased cross-validation, and 3 adaptive kernel estimators) using 5 true density shapes (standard normal, positively skewed, bimodal, skewed bimodal, and standard lognormal) and 9 sample sizes (15, 25, 50, 75, 100, 250, 500, 1,000, 2,000). Results indicate that, overall, SJDP outperformed all methods. However, for smaller sample sizes (25 to 100) either biased cross-validation or Silverman's rule of thumb was recommended, and for larger sample sizes the adaptive kernel estimator with SJDP was recommended. Information is provided about implementing the recommendations in the R computing language. PsycINFO Database Record (c) 2014 APA, all rights reserved.

Effects of seeding rate on the dry matter yield and nutritive value of fall-oat

USDA-ARS?s Scientific Manuscript database

Several recent research projects have evaluated fall-grown oat as a fall-forage option for harvest as silage, or to extend the fall grazing season. Producers frequently ask about the appropriate seeding rates for fall-grown oat and whether or not it is the same as the traditional recommendation for ...

Credit scoring analysis using kernel discriminant

NASA Astrophysics Data System (ADS)

Widiharih, T.; Mukid, M. A.; Mustafid

2018-05-01

Credit scoring model is an important tool for reducing the risk of wrong decisions when granting credit facilities to applicants. This paper investigate the performance of kernel discriminant model in assessing customer credit risk. Kernel discriminant analysis is a non- parametric method which means that it does not require any assumptions about the probability distribution of the input. The main ingredient is a kernel that allows an efficient computation of Fisher discriminant. We use several kernel such as normal, epanechnikov, biweight, and triweight. The models accuracy was compared each other using data from a financial institution in Indonesia. The results show that kernel discriminant can be an alternative method that can be used to determine who is eligible for a credit loan. In the data we use, it shows that a normal kernel is relevant to be selected for credit scoring using kernel discriminant model. Sensitivity and specificity reach to 0.5556 and 0.5488 respectively.

Germination of oat and quinoa and evaluation of the malts as gluten free baking ingredients.

PubMed

Mäkinen, Outi E; Zannini, Emanuele; Arendt, Elke K

2013-03-01

Germination can be used to improve the sensory and nutritional properties of cereal and pseudocereal grains. Oat and quinoa are rich in minerals, vitamins and fibre while quinoa also contains high amounts of protein of a high nutritional value. In this study, oat and quinoa malts were produced and incorporated in a rice and potato based gluten free formulation. Germination of oat led to a drastic increase of α-amylase activity from 0.3 to 48 U/g, and minor increases in proteolytic and lipolytic activities. Little change was observed in quinoa except a decrease in proteolytic activity from 9.6 to 6.9 U/g. Oat malt addition decreased batter viscosities at both proofing temperature and during heating. These changes led to a decrease in bread density from 0.59 to 0.5 g/ml and the formation of a more open crumb, but overdosing of oat malt deteriorated the product as a result of excessive amylolysis during baking. Quinoa malt had no significant effect on the baking properties due to low α-amylase activity. Despite showing a very different impact on the bread quality, both malts influenced the electrophoretic patterns of rice flour protein similarly. This suggests that malt induced proteolysis does not influence the technological properties of a complex gluten free formulation.

Effects of cultivar and grazing initiation date on fall-grown oat for replacement dairy heifers.

PubMed

Coblentz, W K; Brink, G E; Esser, N M; Cavadini, J S

2015-09-01

Fall-grown oat has shown promise for extending the grazing season in Wisconsin, but the optimum date for initiating grazing has not been evaluated. Our objectives for this project were (1) to assess the pasture productivity and nutritive value of 2 oat cultivars [Ogle and ForagePlus (OG and FP, respectively)] with late-September (EG) or mid-October (LG) grazing initiation dates; and (2) to evaluate growth performance by heifers grazing these oat forages compared with heifers reared in confinement (CON). A total of 160 gravid Holstein heifers (80 heifers/yr) were assigned to 10 research groups (8 heifers/group). Mean initial body weight was 509±40.5 kg in 2013 and 517±30.2 kg in 2014. Heifer groups were assigned to specific pastures arranged as a 2×2 factorial of oat cultivars and grazing initiation dates. Grazing heifer groups were allowed to strip-graze oat pastures for 6 h daily before returning to the barn, where they were offered a forage-based basal total mixed ration. Main effects of oat cultivar and sampling date interacted for forage characteristics in 2013, but not in 2014. During 2013, oat forage mass increased until early November before declining in response to freezing weather conditions, thereby exhibiting linear and quadratic effects of sampling date, regardless of oat cultivar. Similar trends over time were observed in 2014. For 2013, the maximum forage mass was 5,329 and 5,046 kg/ha for FP and OG, respectively, whereas the mean maximum forage mass for 2014 was 4,806 kg/ha. ForagePlus did not reach the boot stage of growth during either year of the trial; OG matured more rapidly, reaching the late-heading stage during 2013, but exhibited only minor maturity differences from FP in 2014. For 2013, average daily gain for CON did not differ from grazing heifer groups (overall mean=0.63 kg/d); however, average daily gain from FP was greater than OG (0.68 vs. 0.57 kg/d), and greater from EG compared with LG (0.82 vs. 0.43 kg/d). For 2013, advantages in

Modeling adaptive kernels from probabilistic phylogenetic trees.

PubMed

Nicotra, Luca; Micheli, Alessio

2009-01-01

Modeling phylogenetic interactions is an open issue in many computational biology problems. In the context of gene function prediction we introduce a class of kernels for structured data leveraging on a hierarchical probabilistic modeling of phylogeny among species. We derive three kernels belonging to this setting: a sufficient statistics kernel, a Fisher kernel, and a probability product kernel. The new kernels are used in the context of support vector machine learning. The kernels adaptivity is obtained through the estimation of the parameters of a tree structured model of evolution using as observed data phylogenetic profiles encoding the presence or absence of specific genes in a set of fully sequenced genomes. We report results obtained in the prediction of the functional class of the proteins of the budding yeast Saccharomyces cerevisae which favorably compare to a standard vector based kernel and to a non-adaptive tree kernel function. A further comparative analysis is performed in order to assess the impact of the different components of the proposed approach. We show that the key features of the proposed kernels are the adaptivity to the input domain and the ability to deal with structured data interpreted through a graphical model representation.

Nonlinear Deep Kernel Learning for Image Annotation.

PubMed

Jiu, Mingyuan; Sahbi, Hichem

2017-02-08

Multiple kernel learning (MKL) is a widely used technique for kernel design. Its principle consists in learning, for a given support vector classifier, the most suitable convex (or sparse) linear combination of standard elementary kernels. However, these combinations are shallow and often powerless to capture the actual similarity between highly semantic data, especially for challenging classification tasks such as image annotation. In this paper, we redefine multiple kernels using deep multi-layer networks. In this new contribution, a deep multiple kernel is recursively defined as a multi-layered combination of nonlinear activation functions, each one involves a combination of several elementary or intermediate kernels, and results into a positive semi-definite deep kernel. We propose four different frameworks in order to learn the weights of these networks: supervised, unsupervised, kernel-based semisupervised and Laplacian-based semi-supervised. When plugged into support vector machines (SVMs), the resulting deep kernel networks show clear gain, compared to several shallow kernels for the task of image annotation. Extensive experiments and analysis on the challenging ImageCLEF photo annotation benchmark, the COREL5k database and the Banana dataset validate the effectiveness of the proposed method.

Fall-grown oat to extend the fall grazing season for replacement dairy heifers.

PubMed

Coblentz, W K; Brink, G E; Hoffman, P C; Esser, N M; Bertram, M G

2014-03-01

Our objective was to assess the pasture productivity and forage characteristics of 2 fall-grown oat (Avena sativa L.) cultivars, specifically for extending the grazing season and reducing reliance on harvested forages by replacement dairy heifers. A total of 160 gravid Holstein heifers (80 heifers/yr) were stratified by weight, and assigned to 1 of 10 identical research pens (8 heifers/pen). Initial body weights were 480 ± 43.5 kg in 2011 and 509 ± 39.4 kg in 2012. During both years of the trial, four 1.0-ha pasture replicates were seeded in August with Ogle oat (Schumitsch Seed Inc., Antigo, WI), and 4 separate, but similarly configured, pasture replicates were seeded with Forage Plus oat (Kratz Farms, Slinger, WI). Heifer groups were maintained as units, assigned to specific pastures, and then allowed to graze fall-oat pastures for 6h daily before returning to the barn, where they were offered a forage-based basal total mixed ration. Two heifer groups were retained in confinement (without grazing) as controls and offered the identical total mixed ration as pasture groups. During 2011, available forage mass increased with strong linear and quadratic effects for both cultivars, peaking at almost 9 Mg/ha on October 31. In contrast, forage mass was not affected by evaluation date in 2012, remaining ≤ 2,639 kg/ha across all dates because of droughty climatic conditions. During 2012, Ogle exhibited greater forage mass than Forage Plus across all sampling dates (2,678 vs. 1,856 kg/ha), largely because of its more rapid maturation rate and greater canopy height. Estimates of energy density for oat forage ranged from 59.6 to 69.1% during 2011, and ranged narrowly from 68.4 to 70.4% during 2012. For 2011, responses for both cultivars had strong quadratic character, in which the most energy-dense forages occurred in mid November, largely due to accumulation of water-soluble carbohydrates that reached maximum concentrations of 18.2 and 15.1% for Forage Plus and Ogle

Data-Driven Hierarchical Structure Kernel for Multiscale Part-Based Object Recognition

PubMed Central

Wang, Botao; Xiong, Hongkai; Jiang, Xiaoqian; Zheng, Yuan F.

2017-01-01

Detecting generic object categories in images and videos are a fundamental issue in computer vision. However, it faces the challenges from inter and intraclass diversity, as well as distortions caused by viewpoints, poses, deformations, and so on. To solve object variations, this paper constructs a structure kernel and proposes a multiscale part-based model incorporating the discriminative power of kernels. The structure kernel would measure the resemblance of part-based objects in three aspects: 1) the global similarity term to measure the resemblance of the global visual appearance of relevant objects; 2) the part similarity term to measure the resemblance of the visual appearance of distinctive parts; and 3) the spatial similarity term to measure the resemblance of the spatial layout of parts. In essence, the deformation of parts in the structure kernel is penalized in a multiscale space with respect to horizontal displacement, vertical displacement, and scale difference. Part similarities are combined with different weights, which are optimized efficiently to maximize the intraclass similarities and minimize the interclass similarities by the normalized stochastic gradient ascent algorithm. In addition, the parameters of the structure kernel are learned during the training process with regard to the distribution of the data in a more discriminative way. With flexible part sizes on scale and displacement, it can be more robust to the intraclass variations, poses, and viewpoints. Theoretical analysis and experimental evaluations demonstrate that the proposed multiscale part-based representation model with structure kernel exhibits accurate and robust performance, and outperforms state-of-the-art object classification approaches. PMID:24808345

Graph Kernels for Molecular Similarity.

PubMed

Rupp, Matthias; Schneider, Gisbert

2010-04-12

Molecular similarity measures are important for many cheminformatics applications like ligand-based virtual screening and quantitative structure-property relationships. Graph kernels are formal similarity measures defined directly on graphs, such as the (annotated) molecular structure graph. Graph kernels are positive semi-definite functions, i.e., they correspond to inner products. This property makes them suitable for use with kernel-based machine learning algorithms such as support vector machines and Gaussian processes. We review the major types of kernels between graphs (based on random walks, subgraphs, and optimal assignments, respectively), and discuss their advantages, limitations, and successful applications in cheminformatics. Copyright © 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Relationship of carbohydrates and lignin molecular structure spectral profiles to nutrient profile in newly developed oats cultivars and barley grain

NASA Astrophysics Data System (ADS)

Prates, Luciana Louzada; Refat, Basim; Lei, Yaogeng; Louzada-Prates, Mariana; Yu, Peiqiang

2018-01-01

The objectives of this study were to quantify the chemical profile and the magnitude of differences in the oat and barley grain varieties developed by Crop Development Centre (CDC) in terms of Cornell Net Carbohydrate Protein System (CNCPS) carbohydrate sub-fractions: CA4 (sugars), CB1 (starch), CB2 (soluble fibre), CB3 (available neutral detergent fibre - NDF), and CC (unavailable carbohydrate); to estimate the energy values; to detect the lignin and carbohydrate (CHO) molecular structure profiles in CDC Nasser and CDC Seabiscuit oat and CDC Meredith barley grains by using Fourier transform infrared attenuated total reflectance (FTIR-ATR); to develop a model to predict nutrient supply based on CHO molecular profile. Results showed that NDF, ADF and CHO were greater (P < 0.05) in oat than in barley. The starch content was greater (P < 0.05) in barley than in oat. The CDC Meredith showed greater total rumen degradable carbohydrate (RDC), intestinal digestible fraction carbohydrate (FC) and lower total rumen undegradable carbohydrate (RUC). However, the estimated milk production did not differ for CDC Nasser oat and CDC Meredith barley. Lignin peak area and peak height did not differ (P > 0.05) for oat and barley grains as well as non-structural CHO. However, cellulosic compounds peak area and height were greater (P < 0.05) in oat than barley grains. Multiple regressions were determined to predict nutrient supply by using lignin and CHO molecular profiles. It was concluded that although there were some differences between oat and barley grains, CDC Nasser and CDC Meredith presented similarities related to chemical and molecular profiles, indicating that CDC Meredith barley could be replaced for CDC Nasser as ruminant feed. The FTIR was able to identify functional groups related to CHO molecular spectral in oat and barley grains and FTIR-ATR results could be used to predict nutrient supply in ruminant livestock systems.

Bird cherry-oat aphid: do we have resistance?

USDA-ARS?s Scientific Manuscript database

Bird cherry-oat aphid (BCOA), Rhopalosiphum padi (L.), is a highly efficient, non-propagative, persistent vector of the phloem limited leutovirus BYD-PAV. BYD is the most important viral disease of cereal grains in the world and PAV is the most prevalent strain of BYD in North America. Not all BCO...

Effect of serving size and addition of sugar on the glycemic response elicited by oatmeal: A randomized, cross-over study.

PubMed

Wolever, Thomas M S; van Klinken, B Jan-Willem; Spruill, Susan E; Jenkins, Alexandra L; Chu, YiFang; Harkness, Laura

2016-12-01

We aimed to determine the impact of serving size and addition of sucrose on the glycemic response elicited by oatmeal. We studied 38 healthy subjects (mean ± SD age 40 ± 12 yr, BMI 26.4 ± 3.6 kg/m 2 ) on 8 separate days using a randomized, cross-over design. Capillary blood-glucose responses over 2hr after consuming 30, 40 and 60 g Classic Quaker Quick Oats (18, 24 and 36 g available-carbohydrate [avCHO], respectively) and 30 g Oats plus 9 g sucrose (27 g avCHO) were compared with those after avCHO-matched servings of Cream of Rice cereal (Control) (22, 29, 44 and 33 g cereal, respectively). Blood-glucose incremental area under the curve (iAUC), peak-rise, rate-of-decline, time-to-peak and time-to-baseline were calculated. As serving size increased, iAUC, peak-rise, rate-of-decline and time-to-baseline increased significantly for both cereals, but the rate of increase was significantly greater for Control than for Oats. Time-to-peak increased significantly with serving size only for Oats. Compared to avCHO-matched servings of Control, mean (95%CI) iAUC, peak-rise and rate-of-decline, respectively were 22 (16, 27)%, 22 (19, 26)% and 23 (18, 27)% lower after consuming Oats without sucrose and 26 (18, 34)%, 14 (9, 20)% and 16 (9, 24)% lower after consuming Oats plus sucrose. Oatmeal elicited a significantly lower glycemic response than avCHO-matched servings of Cream of Rice, even when sucrose was added to the oatmeal. Measures of glycemic response tended to increase with increased serving size; although the pattern of change varied between cereal types. These results suggest that oatmeal may be a good choice for minimizing postprandial glycemia. ClinicalTrials.gov (NCT02506972). Copyright © 2016 European Society for Clinical Nutrition and Metabolism. Published by Elsevier Ltd. All rights reserved.

Genome-wide association mapping of barley yellow dwarf virus tolerance in spring oat (Avena sativa L.)

USDA-ARS?s Scientific Manuscript database

Barley yellow dwarf (BYD) is one of the most destructive diseases of cereal crops worldwide. Barley yellow dwarf viruses (BYDVs) are responsible for BYD and affect many cereals including oat (Avena sativa L.). Until recently, the molecular marker technology in oat has not allowed for many marker-t...

Structural characterization and evaluation of antioxidant, anticancer and hypoglycemic activity of radiation degraded oat (Avena sativa) β- glucan

NASA Astrophysics Data System (ADS)

Hussain, Peerzada R.; Rather, Sarver A.; Suradkar, Prashant P.

2018-03-01

Oat β-D-glucan after extraction was degraded at doses of 3, 6, 9, 12 and 15 kGy. The average molecular weight decreased to 45 kDa at dose of 15 kGy from an initial value of 200 kDa in native sample. XRD analysis revealed no significant change in diffraction pattern of irradiated samples when compared with control, except a decrease in intensity of x-ray diffraction. The results of the antioxidant activity revealed decrease in EC50 values and corresponding increase in antioxidant activity of radiation degraded oat β-D-glucan. Results of the anticancer studies indicated that cytotoxicity of gamma irradiated oat β-D-glucan in cancer cell lines was highest against colo-205 and MCF7 cancer cells compared to T47D cell and no cytotoxicity was observed in normal cell lines at all concentrations used. Evaluation of hypoglycemic activity showed highest inhibition in α-glucosidase activity compared to α-amylase activity due to gamma irradiation of oat β-D-glucan. Comparison of the EC50 values of known standards and gamma irradiated oat beta-glucan samples indicates that radiation treatment significantly modified the biological activity of the beta-glucan samples. Therefore, it is suggested that gamma irradiation can be used for producing low molecular weight oat β-D-glucan; which can help in modifying the biological activities.

Comparing Alternative Kernels for the Kernel Method of Test Equating: Gaussian, Logistic, and Uniform Kernels. Research Report. ETS RR-08-12

ERIC Educational Resources Information Center

Lee, Yi-Hsuan; von Davier, Alina A.

2008-01-01

The kernel equating method (von Davier, Holland, & Thayer, 2004) is based on a flexible family of equipercentile-like equating functions that use a Gaussian kernel to continuize the discrete score distributions. While the classical equipercentile, or percentile-rank, equating method carries out the continuization step by linear interpolation,…

Population structure and genome-wide association analysis for frost tolerance in oat using continuous SNP array signal intensity ratios.

PubMed

Tumino, Giorgio; Voorrips, Roeland E; Rizza, Fulvia; Badeck, Franz W; Morcia, Caterina; Ghizzoni, Roberta; Germeier, Christoph U; Paulo, Maria-João; Terzi, Valeria; Smulders, Marinus J M

2016-09-01

Infinium SNP data analysed as continuous intensity ratios enabled associating genotypic and phenotypic data from heterogeneous oat samples, showing that association mapping for frost tolerance is a feasible option. Oat is sensitive to freezing temperatures, which restricts the cultivation of fall-sown or winter oats to regions with milder winters. Fall-sown oats have a longer growth cycle, mature earlier, and have a higher productivity than spring-sown oats, therefore improving frost tolerance is an important goal in oat breeding. Our aim was to test the effectiveness of a Genome-Wide Association Study (GWAS) for mapping QTLs related to frost tolerance, using an approach that tolerates continuously distributed signals from SNPs in bulked samples from heterogeneous accessions. A collection of 138 European oat accessions, including landraces, old and modern varieties from 27 countries was genotyped using the Infinium 6K SNP array. The SNP data were analyzed as continuous intensity ratios, rather than converting them into discrete values by genotype calling. PCA and Ward's clustering of genetic similarities revealed the presence of two main groups of accessions, which roughly corresponded to Continental Europe and Mediterranean/Atlantic Europe, although a total of eight subgroups can be distinguished. The accessions were phenotyped for frost tolerance under controlled conditions by measuring fluorescence quantum yield of photosystem II after a freezing stress. GWAS were performed by a linear mixed model approach, comparing different corrections for population structure. All models detected three robust QTLs, two of which co-mapped with QTLs identified earlier in bi-parental mapping populations. The approach used in the present work shows that SNP array data of heterogeneous hexaploid oat samples can be successfully used to determine genetic similarities and to map associations to quantitative phenotypic traits.

Comparisons of geoid models over Alaska computed with different Stokes' kernel modifications

NASA Astrophysics Data System (ADS)

Li, X.; Wang, Y.

2011-01-01

Various Stokes kernel modification methods have been developed over the years. The goal of this paper is to test the most commonly used Stokes kernel modifications numerically by using Alaska as a test area and EGM08 as a reference model. The tests show that some methods are more sensitive than others to the integration cap sizes. For instance, using the methods of Vaníček and Kleusberg or Featherstone et al. with kernel modification at degree 60, the geoid decreases by 30 cm (on average) when the cap size increases from 1° to 25°. The corresponding changes in the methods of Wong and Gore and Heck and Grüninger are only at the 1 cm level. At high modification degrees, above 360, the methods of Vaníček and Kleusberg and Featherstone et al become unstable because of numerical problems in the modification coefficients; similar conclusions have been reported by Featherstone (2003). In contrast, the methods of Wong and Gore, Heck and Grüninger and the least-squares spectral combination are stable at any modification degree, though they do not provide as good fit as the best case of the Molodenskii-type methods at the GPS/Leveling benchmarks. However, certain tests for choosing the cap size and modification degree have to be performed in advance to avoid abrupt mean geoid changes if the latter methods are applied.

Analysis, annotation, and profiling of the oat seed transcriptome

USDA-ARS?s Scientific Manuscript database

Novel high-throughput next generation sequencing (NGS) technologies are providing opportunities to explore genomes and transcriptomes in a cost-effective manner. To construct a gene expression atlas of developing oat (Avena sativa) seeds, two software packages specifically designed for RNA-seq (Trin...

7 CFR 981.401 - Adjusted kernel weight.

Code of Federal Regulations, 2012 CFR

2012-01-01

... based on the analysis of a 1,000 gram sample taken from a lot of almonds weighing 10,000 pounds with less than 95 percent kernels, and a 1,000 gram sample taken from a lot of almonds weighing 10,000... percent kernels containing the following: Edible kernels, 530 grams; inedible kernels, 120 grams; foreign...

7 CFR 981.401 - Adjusted kernel weight.

Code of Federal Regulations, 2011 CFR

2011-01-01

... based on the analysis of a 1,000 gram sample taken from a lot of almonds weighing 10,000 pounds with less than 95 percent kernels, and a 1,000 gram sample taken from a lot of almonds weighing 10,000... percent kernels containing the following: Edible kernels, 530 grams; inedible kernels, 120 grams; foreign...

7 CFR 981.401 - Adjusted kernel weight.

Code of Federal Regulations, 2013 CFR

2013-01-01

... based on the analysis of a 1,000 gram sample taken from a lot of almonds weighing 10,000 pounds with less than 95 percent kernels, and a 1,000 gram sample taken from a lot of almonds weighing 10,000... percent kernels containing the following: Edible kernels, 530 grams; inedible kernels, 120 grams; foreign...

7 CFR 981.401 - Adjusted kernel weight.

Code of Federal Regulations, 2010 CFR

2010-01-01

... based on the analysis of a 1,000 gram sample taken from a lot of almonds weighing 10,000 pounds with less than 95 percent kernels, and a 1,000 gram sample taken from a lot of almonds weighing 10,000... percent kernels containing the following: Edible kernels, 530 grams; inedible kernels, 120 grams; foreign...

7 CFR 981.401 - Adjusted kernel weight.

Code of Federal Regulations, 2014 CFR

2014-01-01

... based on the analysis of a 1,000 gram sample taken from a lot of almonds weighing 10,000 pounds with less than 95 percent kernels, and a 1,000 gram sample taken from a lot of almonds weighing 10,000... percent kernels containing the following: Edible kernels, 530 grams; inedible kernels, 120 grams; foreign...

7 CFR 51.1403 - Kernel color classification.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 2 2010-01-01 2010-01-01 false Kernel color classification. 51.1403 Section 51.1403... STANDARDS) United States Standards for Grades of Pecans in the Shell 1 Kernel Color Classification § 51.1403 Kernel color classification. (a) The skin color of pecan kernels may be described in terms of the color...

Joint and collaborative representation with local Volterra kernels convolution feature for face recognition

NASA Astrophysics Data System (ADS)

Feng, Guang; Li, Hengjian; Dong, Jiwen; Chen, Xi; Yang, Huiru

2018-04-01

In this paper, we proposed a joint and collaborative representation with Volterra kernel convolution feature (JCRVK) for face recognition. Firstly, the candidate face images are divided into sub-blocks in the equal size. The blocks are extracted feature using the two-dimensional Voltera kernels discriminant analysis, which can better capture the discrimination information from the different faces. Next, the proposed joint and collaborative representation is employed to optimize and classify the local Volterra kernels features (JCR-VK) individually. JCR-VK is very efficiently for its implementation only depending on matrix multiplication. Finally, recognition is completed by using the majority voting principle. Extensive experiments on the Extended Yale B and AR face databases are conducted, and the results show that the proposed approach can outperform other recently presented similar dictionary algorithms on recognition accuracy.

Wholegrain oat-based cereals have prebiotic potential and low glycaemic index.

PubMed

Connolly, M L; Tuohy, K M; Lovegrove, J A

2012-12-28

Population studies show a positive association between increased dietary intake of wholegrains and reduced risk of cardiometabolic disorders. Consumption of wholegrain food has been associated with lower blood glucose and therefore may contribute to a low-glycaemic load diet. The ability to mediate a prebiotic modulation of gut microbiota has recently been suggested to have an inverse correlation with risk of cardiometabolic disease. To date very little work has been carried out on the functionality of wholegrain breakfast cereals in terms of glycaemic response or impact on gut microbiota. An investigation into identifying wholegrain-based breakfast cereals demonstrating both low glycaemic index (GI) and prebiotic attributes was performed. After in vitro digestion, cereal samples were supplemented to pH-controlled anaerobic batch cultures of the human faecal microbiota. Total bacteria populations increased significantly (P < 0·05) in all treated cultures, and the fermentation of a wholegrain oat cluster cereal was associated with proliferation of the Bifidobacterium genus (P = 0·02). Smaller, but significant increases in the Bifidobacterium genus were observed for a further four oat-based cereals. Significant increases in the Lactobacillus-Enterococcus group were observed for granola (P = 0·01), 100 % wholegrain aggregate (P = 0·04) and 70 % wholegrain loops (P = 0·01). Cereals demonstrating prebiotic potential were selected for GI determination in twelve healthy subjects. The wholegrain oat aggregate cereal achieved the lowest GI value (40), three other cereals ranged between 44 and 74, with instant porridge resulting in a GI value similar to the standard glucose control. The present study suggests that wholegrain oat-based breakfast cereals may be prebiotics and have the potential to have low GI.

A consensus map in cultivated hexaploid oat reveals conserved grass synteny with substantial sub-genome rearrangement

USDA-ARS?s Scientific Manuscript database

Hexaploid oat (Avena sativa, 2n = 6x = 42) is a member of the Poaceae family with a very large genome (~13 Gb) containing 21 chromosome pairs: seven from each of two similar ancestral diploids (A and D) and seven from a more diverged ancestral diploid (C). Physical rearrangements among ancestral oat...

Out-of-Sample Extensions for Non-Parametric Kernel Methods.

PubMed

Pan, Binbin; Chen, Wen-Sheng; Chen, Bo; Xu, Chen; Lai, Jianhuang

2017-02-01

Choosing suitable kernels plays an important role in the performance of kernel methods. Recently, a number of studies were devoted to developing nonparametric kernels. Without assuming any parametric form of the target kernel, nonparametric kernel learning offers a flexible scheme to utilize the information of the data, which may potentially characterize the data similarity better. The kernel methods using nonparametric kernels are referred to as nonparametric kernel methods. However, many nonparametric kernel methods are restricted to transductive learning, where the prediction function is defined only over the data points given beforehand. They have no straightforward extension for the out-of-sample data points, and thus cannot be applied to inductive learning. In this paper, we show how to make the nonparametric kernel methods applicable to inductive learning. The key problem of out-of-sample extension is how to extend the nonparametric kernel matrix to the corresponding kernel function. A regression approach in the hyper reproducing kernel Hilbert space is proposed to solve this problem. Empirical results indicate that the out-of-sample performance is comparable to the in-sample performance in most cases. Experiments on face recognition demonstrate the superiority of our nonparametric kernel method over the state-of-the-art parametric kernel methods.

Cost-effectiveness of Maintaining Daily Intake of Oat β-Glucan for Coronary Heart Disease Primary Prevention.

PubMed

Earnshaw, Stephanie R; McDade, Cheryl L; Chu, YiFang; Fleige, Lisa E; Sievenpiper, John L

2017-04-01

Oat β-glucan reduces cholesterol levels and thus reduces the risk for coronary heart disease (CHD). However, its economic impact has not been well studied. We examined the economic impact of daily intake of ≥3 g of oat β-glucan in primary prevention of CHD in patients receiving statins or no pharmacologic treatment. A decision model was developed to compare costs and outcomes associated with lowering cholesterol levels with no pharmacologic treatment and normal diet, no pharmacologic treatment plus ≥3 g/d of oat β-glucan, and statin therapy plus ≥3 g/d of oat β-glucan. The population comprised men 45, 55, or 65 years of age with no history of cardiovascular disease and a 10-year risk for CHD of 5%, 7.5%, or 10%. Clinical efficacy data were gathered from meta-analyses; safety data, costs, and utilities were gathered from published literature. Cost per quality-adjusted life years and number of first events were reported. Maintaining ≥3 g/d of β-glucan may be cost-effective in men aged 45, 55, and 65 years with 10-year CHD risks of 5.0%, 7.5%, and 10.0% taking no pharmacologic treatment or on statins. It may also reduce first events of myocardial infarction and CHD death. Results are sensitive to oat β-glucan cost but insensitive to changes in other parameters. Maintaining ≥3 g of oat β-glucan daily remains cost-effective within plausible range of values. β-glucan may be cost-effective for preventing CHD events in middle-aged men with no history of cardiovascular events whose 10-year CHD risk is ≥5%. Maintaining daily β-glucan intake may have considerable impact on first events. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Computed tomography coronary stent imaging with iterative reconstruction: a trade-off study between medium kernel and sharp kernel.

PubMed

Zhou, Qijing; Jiang, Biao; Dong, Fei; Huang, Peiyu; Liu, Hongtao; Zhang, Minming

2014-01-01

To evaluate the improvement of iterative reconstruction in image space (IRIS) technique in computed tomographic (CT) coronary stent imaging with sharp kernel, and to make a trade-off analysis. Fifty-six patients with 105 stents were examined by 128-slice dual-source CT coronary angiography (CTCA). Images were reconstructed using standard filtered back projection (FBP) and IRIS with both medium kernel and sharp kernel applied. Image noise and the stent diameter were investigated. Image noise was measured both in background vessel and in-stent lumen as objective image evaluation. Image noise score and stent score were performed as subjective image evaluation. The CTCA images reconstructed with IRIS were associated with significant noise reduction compared to that of CTCA images reconstructed using FBP technique in both of background vessel and in-stent lumen (the background noise decreased by approximately 25.4% ± 8.2% in medium kernel (P kernel (P kernel (P kernel (P kernel showed better visualization of the stent struts and in-stent lumen than that with medium kernel. Iterative reconstruction in image space reconstruction can effectively reduce the image noise and improve image quality. The sharp kernel images constructed with iterative reconstruction are considered the optimal images to observe coronary stents in this study.

Genome-Wide Association Mapping of Barley Yellow Dwarf Virus Tolerance in Spring Oat (Avena sativa L.)

PubMed Central

Foresman, Bradley J.; Oliver, Rebekah E.; Jackson, Eric W.; Chao, Shiaoman; Arruda, Marcio P.; Kolb, Frederic L.

2016-01-01

Barley yellow dwarf viruses (BYDVs) are responsible for the disease barley yellow dwarf (BYD) and affect many cereals including oat (Avena sativa L.). Until recently, the molecular marker technology in oat has not allowed for many marker-trait association studies to determine the genetic mechanisms for tolerance. A genome-wide association study (GWAS) was performed on 428 spring oat lines using a recently developed high-density oat single nucleotide polymorphism (SNP) array as well as a SNP-based consensus map. Marker-trait associations were performed using a Q-K mixed model approach to control for population structure and relatedness. Six significant SNP-trait associations representing two QTL were found on chromosomes 3C (Mrg17) and 18D (Mrg04). This is the first report of BYDV tolerance QTL on chromosome 3C (Mrg17) and 18D (Mrg04). Haplotypes using the two QTL were evaluated and distinct classes for tolerance were identified based on the number of favorable alleles. A large number of lines carrying both favorable alleles were observed in the panel. PMID:27175781

Genetic variation and associations involving Fusarium head blight and deoxynivalenol accumulation in cultivated oat (Avena sativa L.)

USDA-ARS?s Scientific Manuscript database

Resistance in oats (Avena sativa L.) to infection by Fusarium graminearum was assessed in field trials in 2011-12 including 424 spring oat lines from North America and Scandinavia. Traits measured were Fusarium Head Blight (FHB), deoxynivalenol (DON) content, days to flowering (DTF) and days to matu...

Anisotropic hydrodynamics with a scalar collisional kernel

NASA Astrophysics Data System (ADS)

Almaalol, Dekrayat; Strickland, Michael

2018-04-01

Prior studies of nonequilibrium dynamics using anisotropic hydrodynamics have used the relativistic Anderson-Witting scattering kernel or some variant thereof. In this paper, we make the first study of the impact of using a more realistic scattering kernel. For this purpose, we consider a conformal system undergoing transversally homogenous and boost-invariant Bjorken expansion and take the collisional kernel to be given by the leading order 2 ↔2 scattering kernel in scalar λ ϕ4 . We consider both classical and quantum statistics to assess the impact of Bose enhancement on the dynamics. We also determine the anisotropic nonequilibrium attractor of a system subject to this collisional kernel. We find that, when the near-equilibrium relaxation-times in the Anderson-Witting and scalar collisional kernels are matched, the scalar kernel results in a higher degree of momentum-space anisotropy during the system's evolution, given the same initial conditions. Additionally, we find that taking into account Bose enhancement further increases the dynamically generated momentum-space anisotropy.

Ranking Support Vector Machine with Kernel Approximation

PubMed Central

Dou, Yong

2017-01-01

Learning to rank algorithm has become important in recent years due to its successful application in information retrieval, recommender system, and computational biology, and so forth. Ranking support vector machine (RankSVM) is one of the state-of-art ranking models and has been favorably used. Nonlinear RankSVM (RankSVM with nonlinear kernels) can give higher accuracy than linear RankSVM (RankSVM with a linear kernel) for complex nonlinear ranking problem. However, the learning methods for nonlinear RankSVM are still time-consuming because of the calculation of kernel matrix. In this paper, we propose a fast ranking algorithm based on kernel approximation to avoid computing the kernel matrix. We explore two types of kernel approximation methods, namely, the Nyström method and random Fourier features. Primal truncated Newton method is used to optimize the pairwise L2-loss (squared Hinge-loss) objective function of the ranking model after the nonlinear kernel approximation. Experimental results demonstrate that our proposed method gets a much faster training speed than kernel RankSVM and achieves comparable or better performance over state-of-the-art ranking algorithms. PMID:28293256

Ranking Support Vector Machine with Kernel Approximation.

PubMed

Chen, Kai; Li, Rongchun; Dou, Yong; Liang, Zhengfa; Lv, Qi

2017-01-01

Learning to rank algorithm has become important in recent years due to its successful application in information retrieval, recommender system, and computational biology, and so forth. Ranking support vector machine (RankSVM) is one of the state-of-art ranking models and has been favorably used. Nonlinear RankSVM (RankSVM with nonlinear kernels) can give higher accuracy than linear RankSVM (RankSVM with a linear kernel) for complex nonlinear ranking problem. However, the learning methods for nonlinear RankSVM are still time-consuming because of the calculation of kernel matrix. In this paper, we propose a fast ranking algorithm based on kernel approximation to avoid computing the kernel matrix. We explore two types of kernel approximation methods, namely, the Nyström method and random Fourier features. Primal truncated Newton method is used to optimize the pairwise L2-loss (squared Hinge-loss) objective function of the ranking model after the nonlinear kernel approximation. Experimental results demonstrate that our proposed method gets a much faster training speed than kernel RankSVM and achieves comparable or better performance over state-of-the-art ranking algorithms.

Population genetics related to adaptation in elite oat germplasm

USDA-ARS?s Scientific Manuscript database

Six hundred thirty five oat lines and 2,635 SNP loci were used to evaluate population structure, linkage disequilibrium (LD) and genotype-phenotype association with heading date. The first five principal components (PC) accounted for 25.3% of genetic variation. Neither the eigenvalues of the first 2...

The art of attrition: development of robust oat microsatellites

USDA-ARS?s Scientific Manuscript database

Microsatellite or simple sequence repeat (SSR) markers are important tools for genetic analyses, especially those targeting diversity, based on the fact that multiple alleles can occur at a given locus. Currently, only 160 genomic-based SSR markers are publicly available for oat, most of which have...

Rare variant testing across methods and thresholds using the multi-kernel sequence kernel association test (MK-SKAT).

PubMed

Urrutia, Eugene; Lee, Seunggeun; Maity, Arnab; Zhao, Ni; Shen, Judong; Li, Yun; Wu, Michael C

Analysis of rare genetic variants has focused on region-based analysis wherein a subset of the variants within a genomic region is tested for association with a complex trait. Two important practical challenges have emerged. First, it is difficult to choose which test to use. Second, it is unclear which group of variants within a region should be tested. Both depend on the unknown true state of nature. Therefore, we develop the Multi-Kernel SKAT (MK-SKAT) which tests across a range of rare variant tests and groupings. Specifically, we demonstrate that several popular rare variant tests are special cases of the sequence kernel association test which compares pair-wise similarity in trait value to similarity in the rare variant genotypes between subjects as measured through a kernel function. Choosing a particular test is equivalent to choosing a kernel. Similarly, choosing which group of variants to test also reduces to choosing a kernel. Thus, MK-SKAT uses perturbation to test across a range of kernels. Simulations and real data analyses show that our framework controls type I error while maintaining high power across settings: MK-SKAT loses power when compared to the kernel for a particular scenario but has much greater power than poor choices.

7 CFR 51.2559 - Size classifications.

Code of Federal Regulations, 2010 CFR

2010-01-01

... STANDARDS) United States Standards for Grades of Shelled Pistachio Nuts § 51.2559 Size classifications. (a) The size of pistachio kernels may be specified in connection with the grade in accordance with one of...

Wigner functions defined with Laplace transform kernels.

PubMed

Oh, Se Baek; Petruccelli, Jonathan C; Tian, Lei; Barbastathis, George

2011-10-24

We propose a new Wigner-type phase-space function using Laplace transform kernels--Laplace kernel Wigner function. Whereas momentum variables are real in the traditional Wigner function, the Laplace kernel Wigner function may have complex momentum variables. Due to the property of the Laplace transform, a broader range of signals can be represented in complex phase-space. We show that the Laplace kernel Wigner function exhibits similar properties in the marginals as the traditional Wigner function. As an example, we use the Laplace kernel Wigner function to analyze evanescent waves supported by surface plasmon polariton. © 2011 Optical Society of America

Metabolic network prediction through pairwise rational kernels.

PubMed

Roche-Lima, Abiel; Domaratzki, Michael; Fristensky, Brian

2014-09-26

Metabolic networks are represented by the set of metabolic pathways. Metabolic pathways are a series of biochemical reactions, in which the product (output) from one reaction serves as the substrate (input) to another reaction. Many pathways remain incompletely characterized. One of the major challenges of computational biology is to obtain better models of metabolic pathways. Existing models are dependent on the annotation of the genes. This propagates error accumulation when the pathways are predicted by incorrectly annotated genes. Pairwise classification methods are supervised learning methods used to classify new pair of entities. Some of these classification methods, e.g., Pairwise Support Vector Machines (SVMs), use pairwise kernels. Pairwise kernels describe similarity measures between two pairs of entities. Using pairwise kernels to handle sequence data requires long processing times and large storage. Rational kernels are kernels based on weighted finite-state transducers that represent similarity measures between sequences or automata. They have been effectively used in problems that handle large amount of sequence information such as protein essentiality, natural language processing and machine translations. We create a new family of pairwise kernels using weighted finite-state transducers (called Pairwise Rational Kernel (PRK)) to predict metabolic pathways from a variety of biological data. PRKs take advantage of the simpler representations and faster algorithms of transducers. Because raw sequence data can be used, the predictor model avoids the errors introduced by incorrect gene annotations. We then developed several experiments with PRKs and Pairwise SVM to validate our methods using the metabolic network of Saccharomyces cerevisiae. As a result, when PRKs are used, our method executes faster in comparison with other pairwise kernels. Also, when we use PRKs combined with other simple kernels that include evolutionary information, the accuracy

GC-TOF-MS-based serum metabolomic investigations of naked oat bran supplementation in high-fat-diet-induced dyslipidemic rats.

PubMed

Gu, Jiaojiao; Jing, Lulu; Ma, Xiaotao; Zhang, Zhaofeng; Guo, Qianying; Li, Yong

2015-12-01

The present study aimed to explore the metabolic response of oat bran consumption in dyslipidemic rats by a high-throughput metabolomics approach. Four groups of Sprague-Dawley rats were used: N group (normal chow diet), M group (dyslipidemia induced by 4-week high-fat feeding, then normal chow diet), OL group and OH group (dyslipidemia induced, then normal chow diet supplemented with 10.8% or 43.4% naked oat bran). Intervention lasted for 12weeks. Gas chromatography quadrupole time-of-flight mass spectrometry was used to identify serum metabolite profiles. Results confirmed the effects of oat bran on improving lipidemic variables and showed distinct metabolomic profiles associated with diet intervention. A number of endogenous molecules were changed by high-fat diet and normalized following supplementation of naked oat bran. Elevated levels of serum unsaturated fatty acids including arachidonic acid (Log2Fold of change=0.70, P=.02 OH vs. M group), palmitoleic acid (Log2Fold of change=1.24, P=.02 OH vs. M group) and oleic acid (Log2Fold of change=0.66, P=.04 OH vs. M group) were detected after oat bran consumption. Furthermore, consumption of oat bran was also characterized by higher levels of methionine and S-adenosylmethionine. Pathway exploration found that most of the discriminant metabolites were involved in fatty acid biosynthesis, biosynthesis and metabolism of amino acids, microbial metabolism in diverse environments and biosynthesis of plant secondary metabolites. These results point to potential biomarkers and underlying benefit of naked oat bran in the context of diet-induced dyslipidemia and offer some insights into the mechanism exploration. Copyright © 2015 Elsevier Inc. All rights reserved.

7 CFR 810.1004 - Grades and grade requirements for oats.

Code of Federal Regulations, 2010 CFR

2010-01-01

... Section 810.1004 Agriculture Regulations of the Department of Agriculture (Continued) GRAIN INSPECTION, PACKERS AND STOCKYARD ADMINISTRATION (FEDERAL GRAIN INSPECTION SERVICE), DEPARTMENT OF AGRICULTURE OFFICIAL UNITED STATES STANDARDS FOR GRAIN United States Standards for Oats Principles Governing the...

High levels of avenanthramides in oat-based diet further suppress high fat diet-induced atherosclerosis in Ldlr-/- mice

USDA-ARS?s Scientific Manuscript database

Background: The consumption of oats reduces plasma cholesterol, a major risk factor for heart disease. Oats, in addition to cholesterol lowering properties through its beta-glucan content, are a good source of several antioxidants including Avenanthramides (Avns), a unique group of polyphenols prese...

Properties of Particle Size Distribution from Milled White Nixtamalized Corn Kernels as a Function of Steeping Time

PubMed Central

Fernández-Muñoz, J. L.; Zapata-Torrez, M.; Márquez-Herrera, A.; Sánchez-Sinencio, F.; Mendoza-Álvarez, J. G.; Meléndez-Lira, M.; Zelaya-Ángel, O.

2016-01-01

This paper focuses on the particle size distribution (PSD) changes during nixtamalized corn kernels (NCK) as a function of the steeping time (ST). The process to obtain powder or corn flour from NCK was as follows: (i) the NCK with different STs were wet-milled in a stone mill, (ii) dehydrated by a Flash type dryer, and (iii) pulverized with a hammer mill and sieved with a 20 mesh. The powder was characterized by measuring the PSD percentage, calcium percentage (CP), peak viscosity at 90°C (PV), and crystallinity percentage (CP). The PSD of the powder as a function of ST was determined by sieving in Ro-TAP equipment. By sieving, five fractions of powder were obtained employing meshes 30, 40, 60, 80, and 100. The final weight of the PSD obtained from the sieving process follows a Gaussian profile with the maximum corresponding to the average particle obtained with mesh 60. The calcium percentage as a function of ST follows a behavior similar to the weight of the PSD. The study of crystallinity versus the mesh number shows that it decreases for smaller mesh number. A similar behavior is observed as steeping time increases, except around ST = 8 h where the gelatinization of starch is observed. The trend of increasing viscosity values of the powder samples occurs when increasing ST and decreasing particle size. The ST significantly changes the crystallinity and viscosity values of the powder and, in both cases, a minimum value is observed in the region 7–9 h. The experimental results show that the viscosity increases (decreases) if the particle size decreases (increases). PMID:27375921

Effects of high-fiber oat and wheat cereals on postprandial glucose and lipid responses in healthy men.

PubMed

Maki, Kevin C; Davidson, Michael H; Witchger, Mary Sue; Dicklin, Mary R; Subbaiah, Papasani V

2007-09-01

This randomized, crossover study compared the effects of consuming high-fiber oat and wheat cereals on postprandial metabolic profiles in healthy men. Twenty-seven subjects received oat (providing 5.7 g/day beta-glucan) or wheat (control) cereal products, in random order, incorporated into their usual diets for two weeks. Total energy and fiber (approximately 14 g/day) contents of the cereals were matched. A meal tolerance test that included the study cereal and a high-fat milkshake (1240 kcal, 105 g fat) was performed at the end of each treatment period. Postprandial insulin and glucose responses over 10 hours did not differ between treatments. Peak triglyceride concentration was lower after oat vs. wheat cereal consumption [2.3 +/- 1.2 (mean +/- standard deviation) vs. 2.9 +/- 1.3 mmol/L, p = 0.016]. Mean area under the triglyceride curve also tended to be lower (15.1 +/- 8.2 vs. 17.6 +/- 8.6 hours x mmol/L, p = 0.068). The free fatty acid area under the curve was elevated after the oat vs. the wheat products (3.64 +/- 0.91 vs. 3.38 +/- 0.98 hours x mmol/L, p = 0.018). These results suggest that high-fiber oat cereal influenced postprandial triglyceride and free fatty acid levels, which may have implications regarding cardiovascular disease risk.

Ideal regularization for learning kernels from labels.

PubMed

Pan, Binbin; Lai, Jianhuang; Shen, Lixin

2014-08-01

In this paper, we propose a new form of regularization that is able to utilize the label information of a data set for learning kernels. The proposed regularization, referred to as ideal regularization, is a linear function of the kernel matrix to be learned. The ideal regularization allows us to develop efficient algorithms to exploit labels. Three applications of the ideal regularization are considered. Firstly, we use the ideal regularization to incorporate the labels into a standard kernel, making the resulting kernel more appropriate for learning tasks. Next, we employ the ideal regularization to learn a data-dependent kernel matrix from an initial kernel matrix (which contains prior similarity information, geometric structures, and labels of the data). Finally, we incorporate the ideal regularization to some state-of-the-art kernel learning problems. With this regularization, these learning problems can be formulated as simpler ones which permit more efficient solvers. Empirical results show that the ideal regularization exploits the labels effectively and efficiently. Copyright © 2014 Elsevier Ltd. All rights reserved.

Abiotic stress growth conditions induce different responses in kernel iron concentration across genotypically distinct maize inbred varieties

PubMed Central

Kandianis, Catherine B.; Michenfelder, Abigail S.; Simmons, Susan J.; Grusak, Michael A.; Stapleton, Ann E.

2013-01-01

The improvement of grain nutrient profiles for essential minerals and vitamins through breeding strategies is a target important for agricultural regions where nutrient poor crops like maize contribute a large proportion of the daily caloric intake. Kernel iron concentration in maize exhibits a broad range. However, the magnitude of genotype by environment (GxE) effects on this trait reduces the efficacy and predictability of selection programs, particularly when challenged with abiotic stress such as water and nitrogen limitations. Selection has also been limited by an inverse correlation between kernel iron concentration and the yield component of kernel size in target environments. Using 25 maize inbred lines for which extensive genome sequence data is publicly available, we evaluated the response of kernel iron density and kernel mass to water and nitrogen limitation in a managed field stress experiment using a factorial design. To further understand GxE interactions we used partition analysis to characterize response of kernel iron and weight to abiotic stressors among all genotypes, and observed two patterns: one characterized by higher kernel iron concentrations in control over stress conditions, and another with higher kernel iron concentration under drought and combined stress conditions. Breeding efforts for this nutritional trait could exploit these complementary responses through combinations of favorable allelic variation from these already well-characterized genetic stocks. PMID:24363659

SEMI-SUPERVISED OBJECT RECOGNITION USING STRUCTURE KERNEL

PubMed Central

Wang, Botao; Xiong, Hongkai; Jiang, Xiaoqian; Ling, Fan

2013-01-01

Object recognition is a fundamental problem in computer vision. Part-based models offer a sparse, flexible representation of objects, but suffer from difficulties in training and often use standard kernels. In this paper, we propose a positive definite kernel called “structure kernel”, which measures the similarity of two part-based represented objects. The structure kernel has three terms: 1) the global term that measures the global visual similarity of two objects; 2) the part term that measures the visual similarity of corresponding parts; 3) the spatial term that measures the spatial similarity of geometric configuration of parts. The contribution of this paper is to generalize the discriminant capability of local kernels to complex part-based object models. Experimental results show that the proposed kernel exhibit higher accuracy than state-of-art approaches using standard kernels. PMID:23666108

The pre-image problem in kernel methods.

PubMed

Kwok, James Tin-yau; Tsang, Ivor Wai-hung

2004-11-01

In this paper, we address the problem of finding the pre-image of a feature vector in the feature space induced by a kernel. This is of central importance in some kernel applications, such as on using kernel principal component analysis (PCA) for image denoising. Unlike the traditional method which relies on nonlinear optimization, our proposed method directly finds the location of the pre-image based on distance constraints in the feature space. It is noniterative, involves only linear algebra and does not suffer from numerical instability or local minimum problems. Evaluations on performing kernel PCA and kernel clustering on the USPS data set show much improved performance.

Exploiting graph kernels for high performance biomedical relation extraction.

PubMed

Panyam, Nagesh C; Verspoor, Karin; Cohn, Trevor; Ramamohanarao, Kotagiri

2018-01-30

Relation extraction from biomedical publications is an important task in the area of semantic mining of text. Kernel methods for supervised relation extraction are often preferred over manual feature engineering methods, when classifying highly ordered structures such as trees and graphs obtained from syntactic parsing of a sentence. Tree kernels such as the Subset Tree Kernel and Partial Tree Kernel have been shown to be effective for classifying constituency parse trees and basic dependency parse graphs of a sentence. Graph kernels such as the All Path Graph kernel (APG) and Approximate Subgraph Matching (ASM) kernel have been shown to be suitable for classifying general graphs with cycles, such as the enhanced dependency parse graph of a sentence. In this work, we present a high performance Chemical-Induced Disease (CID) relation extraction system. We present a comparative study of kernel methods for the CID task and also extend our study to the Protein-Protein Interaction (PPI) extraction task, an important biomedical relation extraction task. We discuss novel modifications to the ASM kernel to boost its performance and a method to apply graph kernels for extracting relations expressed in multiple sentences. Our system for CID relation extraction attains an F-score of 60%, without using external knowledge sources or task specific heuristic or rules. In comparison, the state of the art Chemical-Disease Relation Extraction system achieves an F-score of 56% using an ensemble of multiple machine learning methods, which is then boosted to 61% with a rule based system employing task specific post processing rules. For the CID task, graph kernels outperform tree kernels substantially, and the best performance is obtained with APG kernel that attains an F-score of 60%, followed by the ASM kernel at 57%. The performance difference between the ASM and APG kernels for CID sentence level relation extraction is not significant. In our evaluation of ASM for the PPI task, ASM

Correlation and classification of single kernel fluorescence hyperspectral data with aflatoxin concentration in corn kernels inoculated with Aspergillus flavus spores.

PubMed

Yao, H; Hruska, Z; Kincaid, R; Brown, R; Cleveland, T; Bhatnagar, D

2010-05-01

The objective of this study was to examine the relationship between fluorescence emissions of corn kernels inoculated with Aspergillus flavus and aflatoxin contamination levels within the kernels. Aflatoxin contamination in corn has been a long-standing problem plaguing the grain industry with potentially devastating consequences to corn growers. In this study, aflatoxin-contaminated corn kernels were produced through artificial inoculation of corn ears in the field with toxigenic A. flavus spores. The kernel fluorescence emission data were taken with a fluorescence hyperspectral imaging system when corn kernels were excited with ultraviolet light. Raw fluorescence image data were preprocessed and regions of interest in each image were created for all kernels. The regions of interest were used to extract spectral signatures and statistical information. The aflatoxin contamination level of single corn kernels was then chemically measured using affinity column chromatography. A fluorescence peak shift phenomenon was noted among different groups of kernels with different aflatoxin contamination levels. The fluorescence peak shift was found to move more toward the longer wavelength in the blue region for the highly contaminated kernels and toward the shorter wavelengths for the clean kernels. Highly contaminated kernels were also found to have a lower fluorescence peak magnitude compared with the less contaminated kernels. It was also noted that a general negative correlation exists between measured aflatoxin and the fluorescence image bands in the blue and green regions. The correlation coefficients of determination, r(2), was 0.72 for the multiple linear regression model. The multivariate analysis of variance found that the fluorescence means of four aflatoxin groups, <1, 1-20, 20-100, and >or=100 ng g(-1) (parts per billion), were significantly different from each other at the 0.01 level of alpha. Classification accuracy under a two-class schema ranged from 0.84 to

Adaptive kernel function using line transect sampling

NASA Astrophysics Data System (ADS)

Albadareen, Baker; Ismail, Noriszura

2018-04-01

The estimation of f(0) is crucial in the line transect method which is used for estimating population abundance in wildlife survey's. The classical kernel estimator of f(0) has a high negative bias. Our study proposes an adaptation in the kernel function which is shown to be more efficient than the usual kernel estimator. A simulation study is adopted to compare the performance of the proposed estimators with the classical kernel estimators.

Kernel K-Means Sampling for Nyström Approximation.

PubMed

He, Li; Zhang, Hong

2018-05-01

A fundamental problem in Nyström-based kernel matrix approximation is the sampling method by which training set is built. In this paper, we suggest to use kernel -means sampling, which is shown in our works to minimize the upper bound of a matrix approximation error. We first propose a unified kernel matrix approximation framework, which is able to describe most existing Nyström approximations under many popular kernels, including Gaussian kernel and polynomial kernel. We then show that, the matrix approximation error upper bound, in terms of the Frobenius norm, is equal to the -means error of data points in kernel space plus a constant. Thus, the -means centers of data in kernel space, or the kernel -means centers, are the optimal representative points with respect to the Frobenius norm error upper bound. Experimental results, with both Gaussian kernel and polynomial kernel, on real-world data sets and image segmentation tasks show the superiority of the proposed method over the state-of-the-art methods.

7 CFR 51.2284 - Size classification.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 7 Agriculture 2 2013-01-01 2013-01-01 false Size classification. 51.2284 Section 51.2284...) Size Requirements § 51.2284 Size classification. The following classifications are provided to describe... of kernels in the lot shall conform to the requirements of the specified classification as defined...

7 CFR 51.2284 - Size classification.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 7 Agriculture 2 2014-01-01 2014-01-01 false Size classification. 51.2284 Section 51.2284...) Size Requirements § 51.2284 Size classification. The following classifications are provided to describe... of kernels in the lot shall conform to the requirements of the specified classification as defined...

Benchmarking NWP Kernels on Multi- and Many-core Processors

NASA Astrophysics Data System (ADS)

Michalakes, J.; Vachharajani, M.

2008-12-01

Increased computing power for weather, climate, and atmospheric science has provided direct benefits for defense, agriculture, the economy, the environment, and public welfare and convenience. Today, very large clusters with many thousands of processors are allowing scientists to move forward with simulations of unprecedented size. But time-critical applications such as real-time forecasting or climate prediction need strong scaling: faster nodes and processors, not more of them. Moreover, the need for good cost- performance has never been greater, both in terms of performance per watt and per dollar. For these reasons, the new generations of multi- and many-core processors being mass produced for commercial IT and "graphical computing" (video games) are being scrutinized for their ability to exploit the abundant fine- grain parallelism in atmospheric models. We present results of our work to date identifying key computational kernels within the dynamics and physics of a large community NWP model, the Weather Research and Forecast (WRF) model. We benchmark and optimize these kernels on several different multi- and many-core processors. The goals are to (1) characterize and model performance of the kernels in terms of computational intensity, data parallelism, memory bandwidth pressure, memory footprint, etc. (2) enumerate and classify effective strategies for coding and optimizing for these new processors, (3) assess difficulties and opportunities for tool or higher-level language support, and (4) establish a continuing set of kernel benchmarks that can be used to measure and compare effectiveness of current and future designs of multi- and many-core processors for weather and climate applications.

Effect of amaranth and oat bran on blood serum and liver lipids in rats depending on the kind of dietary fats.

PubMed

Grajeta, H

1999-04-01

The effect of amaranth and oat bran on the lipids of blood and liver in rats depending on the kind of fats in diet was the subject of our study. Sixty male Buffalo rats were fed for 28 days one of six diet containing 15% of fat (lard or sunflower oil), 20% of protein and 0.5% of cholesterol. Amaranth and oat bran added to diet provided 4-4.5% of dietary fiber, water soluble fraction of which amounted to 30%. Amaranth significantly decreased the level of total cholesterol in rats blood serum (by 10.7% in the case of diet with lard and by 14% with sunflower oil) and in liver (by 20% in the case of diet with lard and by 23% with sunflower oil). Similarly oat bran decreased the level of total cholesterol in the blood serum: by 19% in the case of diet with lard and by 22% with sunflower oil; and in liver by 22 and 27%, respectively. Amaranth and oat bran did not influence HDL-cholesterol in the blood of rats. The influence of amaranth and oat bran on the concentration of triglycerides in the blood serum depended on the kind of fats in a diet. The diets containing amaranth or oat bran with lard did not decrease the concentration of this lipids, however, the same diets but with sunflower oil decreased this concentration significantly (by 22%). In liver significant hypotriglyceridemic effect of amaranth and oat bran was observed for both of the diets: based on lard and sunflower. The decrease of triglycerides concentration under the influence of amaranth amounted to 10% (diet with lard) and 15% (diet with sunflower oil). Oat bran decreased the concentration of triglycerides in liver by 15% (diet with lard) and 20% (diet with sunflower oil). Sunflower oil added to the diets augmented the hypolipemic effect of amaranth and oat bran.

7 CFR 51.2125 - Split or broken kernels.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 2 2010-01-01 2010-01-01 false Split or broken kernels. 51.2125 Section 51.2125 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards... kernels. Split or broken kernels means seven-eighths or less of complete whole kernels but which will not...

Robotic Intelligence Kernel: Driver

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

The INL Robotic Intelligence Kernel-Driver is built on top of the RIK-A and implements a dynamic autonomy structure. The RIK-D is used to orchestrate hardware for sensing and action as well as software components for perception, communication, behavior and world modeling into a single cognitive behavior kernel that provides intrinsic intelligence for a wide variety of unmanned ground vehicle systems.

Using brown midrib 6 dwarf forage sorghum silage and fall-grown oat silage in lactating dairy cow rations.

PubMed

Harper, M T; Oh, J; Giallongo, F; Lopes, J C; Roth, G W; Hristov, A N

2017-07-01

Double cropping and increasing crop diversity could improve dairy farm economic and environmental sustainability. In this experiment, corn silage was partially replaced with 2 alternative forages, brown midrib-6 brachytic dwarf forage sorghum (Sorghum bicolor) or fall-grown oat (Avena sativa) silage, in the diet of lactating dairy cows. We investigated the effect on dry matter (DM) intake, milk yield (MY), milk components and fatty acid profile, apparent total-tract nutrient digestibility, N utilization, enteric methane emissions, and income over feed cost. We analyzed the in situ DM and neutral detergent fiber disappearance of the alternative forages versus corn silage and alfalfa haylage. Sorghum was grown in the summer and harvested in the milk stage. Oats were grown in the fall and harvested in the boot stage. Compared with corn silage, neutral detergent fiber and acid detergent fiber concentrations were higher in the alternative forages. Lignin content was highest for sorghum silage and similar for corn silage and oat silage. The alternative forages had less than 1% starch compared with the approximately 35% starch in the corn silage. Ruminal in situ DM effective degradability was similar, although statistically different, for corn silage and oat silage, but lower for sorghum silage. Diets with the alternative forages were fed in a replicated 3 × 3 Latin square design experiment with three 28-d periods and 12 Holstein cows. The control diet contained 44% (DM basis) corn silage. In the other 2 diets, sorghum or oat silages were included at 10% of dietary DM, replacing corn silage. Sorghum silage inclusion decreased DM intake, MY, and milk protein content but increased milk fat and maintained energy-corrected MY similar to the control. Oat silage had no effect on DM intake, MY, or milk components compared to the control. The oat silage diet increased apparent total-tract digestibility of dietary nutrients, except starch, whereas the sorghum diet slightly

Bell nozzle kernel analysis program

NASA Technical Reports Server (NTRS)

Elliot, J. J.; Stromstra, R. R.

1969-01-01

Bell Nozzle Kernel Analysis Program computes and analyzes the supersonic flowfield in the kernel, or initial expansion region, of a bell or conical nozzle. It analyzes both plane and axisymmetric geometrices for specified gas properties, nozzle throat geometry and input line.

Increasing the Size of Microwave Popcorn

NASA Astrophysics Data System (ADS)

Smoyer, Justin

2005-03-01

Each year Americans consume approximately 17 billion quarts of popcorn. Since the 1940s, microwaves have been the heating source of choice for most. By treating the popcorn mechanism as a thermodynamic system, it has been shown mathematically and experimentally that reducing the surrounding pressure of the unpopped kernels, results in an increased volume of the kernels [Quinn et al, http://xxx.lanl.gov/abs/cond-mat/0409434 v1 2004]. In this project an alternate method of popping with the microwave was used to further test and confirm this hypothesis. Numerous experimental trials where run to test the validity of the theory. The results show that there is a significant increase in the average kernel size as well as a reduction in the number of unpopped kernels.

7 CFR 51.2296 - Three-fourths half kernel.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 2 2010-01-01 2010-01-01 false Three-fourths half kernel. 51.2296 Section 51.2296 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards...-fourths half kernel. Three-fourths half kernel means a portion of a half of a kernel which has more than...

Metabolism of HT-2 Toxin and T-2 Toxin in Oats

PubMed Central

Meng-Reiterer, Jacqueline; Bueschl, Christoph; Rechthaler, Justyna; Berthiller, Franz; Lemmens, Marc; Schuhmacher, Rainer

2016-01-01

The Fusarium mycotoxins HT-2 toxin (HT2) and T-2 toxin (T2) are frequent contaminants in oats. These toxins, but also their plant metabolites, may contribute to toxicological effects. This work describes the use of 13C-assisted liquid chromatography–high-resolution mass spectrometry for the first comprehensive study on the biotransformation of HT2 and T2 in oats. Using this approach, 16 HT2 and 17 T2 metabolites were annotated including novel glycosylated and hydroxylated forms of the toxins, hydrolysis products, and conjugates with acetic acid, putative malic acid, malonic acid, and ferulic acid. Further targeted quantitative analysis was performed to study toxin metabolism over time, as well as toxin and conjugate mobility within non-treated plant tissues. As a result, HT2-3-O-β-d-glucoside was identified as the major detoxification product of both parent toxins, which was rapidly formed (to an extent of 74% in HT2-treated and 48% in T2-treated oats within one day after treatment) and further metabolised. Mobility of the parent toxins appeared to be negligible, while HT2-3-O-β-d-glucoside was partly transported (up to approximately 4%) through panicle side branches and stem. Our findings demonstrate that the presented combination of untargeted and targeted analysis is well suited for the comprehensive elucidation of mycotoxin metabolism in plants. PMID:27929394

Application of kernel method in fluorescence molecular tomography

NASA Astrophysics Data System (ADS)

Zhao, Yue; Baikejiang, Reheman; Li, Changqing

2017-02-01

Reconstruction of fluorescence molecular tomography (FMT) is an ill-posed inverse problem. Anatomical guidance in the FMT reconstruction can improve FMT reconstruction efficiently. We have developed a kernel method to introduce the anatomical guidance into FMT robustly and easily. The kernel method is from machine learning for pattern analysis and is an efficient way to represent anatomical features. For the finite element method based FMT reconstruction, we calculate a kernel function for each finite element node from an anatomical image, such as a micro-CT image. Then the fluorophore concentration at each node is represented by a kernel coefficient vector and the corresponding kernel function. In the FMT forward model, we have a new system matrix by multiplying the sensitivity matrix with the kernel matrix. Thus, the kernel coefficient vector is the unknown to be reconstructed following a standard iterative reconstruction process. We convert the FMT reconstruction problem into the kernel coefficient reconstruction problem. The desired fluorophore concentration at each node can be calculated accordingly. Numerical simulation studies have demonstrated that the proposed kernel-based algorithm can improve the spatial resolution of the reconstructed FMT images. In the proposed kernel method, the anatomical guidance can be obtained directly from the anatomical image and is included in the forward modeling. One of the advantages is that we do not need to segment the anatomical image for the targets and background.

[Effects of legume-oat intercropping on abundance and community structure of soil N2-fixing bacteria].

PubMed

Yang, Ya Dong; Feng, Xiao Min; Hu, Yue Gao; Ren, Chang Zhong; Zeng, Zhao Hai

2017-03-18

In this study, real-time PCR and high-throughput sequencing approaches were employed to investigate the abundance and community structure of N 2 -fixing bacteria in a field experiment with three planting patterns (Oat monoculture, O; Soybean-oat intercropping, OSO; Mung bean-oat intercropping, OMO). The results showed that soil chemical properties varied significantly in different soil samples (P＜0.05). The abundance of nifH gene varied from 1.75×10 10 to 7.37×10 10 copies·g -1 dry soil in all soil samples. The copy numbers of nifH gene in OSO and OMO were 2.18, 2.64, and 1.92, 2.57 times as much as that in O at jointing and mature stages, with a significant decline from jointing to mature stage for all treatments (P＜0.05). Rarefaction curve and cove-rage results proved the nifH gene sequencing results were reliable, and the diversity index showed that the N 2 -fixing bacteria diversity of OSO was much higher than that of O. Azohydromonas, Azotobacter, Bradyrhizobium, Skermanella and other groups that could not be classified are the dominant genera, with significant differences in proportion of these dominant groups observed among all soil samples (P＜0.05). Venn and PCA analysis indicated that there were greater differences of nifH gene communities between jointing and mature stages; however, the OSO and OMO had similar communities in both stages. All these results confirmed that legume-oat intercropping significantly increased the abundance and changed the community composition of N 2 -fixing bacteria in oat soils.

7 CFR 868.254 - Broken kernels determination.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 7 2010-01-01 2010-01-01 false Broken kernels determination. 868.254 Section 868.254 Agriculture Regulations of the Department of Agriculture (Continued) GRAIN INSPECTION, PACKERS AND STOCKYARD... Governing Application of Standards § 868.254 Broken kernels determination. Broken kernels shall be...

Sodium and potassium fluxes and compartmentation in roots of atriplex and oat.

PubMed

Mills, D; Robinson, K; Hodges, T K

1985-07-01

K(+) and Na(+) fluxes and ion content have been studied in roots of Atriplex nummularia Lindl. and Avena sativa L. cv Goodfield grown in 3 millimolar K(+) with or without 3 or 50 millimolar NaCl. Compartmental analysis was carried out with entire root systems under steady-state conditions.Increasing ambient Na(+) concentrations from 0 to 50 millimolar altered K(+), in Atriplex, as follows: slightly decreased the cytoplasmic content (Q(c)), the vacuolar content (Q(v)), and the plasma membrane influx and efflux. Xylem transport for K(+) decreased by 63% in Atriplex. For oat roots, similar increases in Na(+) altered K(+) parameters as follows: plasma membrane influx and efflux decreased by about 80%. Q(c) decreased by 65%, and xylem transport decreased by 91%. No change, however, was observed in Q(v) for K(+). Increasing ambient Na(+) resulted in higher (3 to 5-fold) Na(+) fluxes across the plasma membrane and in Q(c) of both species. In Atriplex, Na(+) fluxes across the tonoplast and Q(v) increased as external Na(+) was increased. In oat, however, no significant change was observed in Na(+) flux across the tonoplast or in Q(v) as external Na(+) was increased. In oat roots, Na(+) reduced K(+) uptake markedly; in Atriplex, this was not as pronounced. However, even at high Na(+) levels, the influx transport system at the plasma membrane of both species preferred K(+) over Na(+).Based upon the Ussing-Teorell equation, it was concluded that active inward transport of K(+) occurred across the plasma membrane, and passive movement of K(+) occurred across the tonoplast in both species. Na(+), in oat roots, was actively pumped out of the cytoplasm to the exterior, whereas, in Atriplex, Na(+) was passively distributed between the free space, cytoplasm, and vacuole.

[Creation of a unit for education in the self-management of oat].

PubMed

Camino Guiu, M Jesús; Cebollero Mata, M Luisa; Bolea Muro, Carmen; Borrel Roncalés, Mercedes

2012-04-01

Oral anticoagulant therapy (OAT) with Vitamin K antagonists requires frequent analytical controls that create a certain degree of dependency and a loss of autonomy in the patient. These drugs have an undesirable variability due to food and drug interactions, febrile processes, etc. which can modify the patient's INR and predispose them to a thromboembolic or hemorrhagic event. OAT self-control is supported by more than 15 years of experience in countries such as Germany and the Netherlands, and by comparative studies that reflect a reduction of thromboembolism and other adverse effects. The reason of this is because these patients are in the correct therapeutic range for longer periods of time due to more frequent controls (once a week against every 4-5 weeks of traditional control) and also to a better understanding of their treatment. In Aragon, OAT is a free health service and in our hospital, OAT has been an institutional aim since 2070. After a training course, the patient is capable to make their own INR determinations at home, to evaluate their results and adjust their own dose. Additionally the patient should acquire the appropriate knowledge to detect any adverse symptom and to know how to react to any problem in their treatment. This article summarizes our experience regarding the implementation of the programme and creation of the specific unit: the organization and training of the professionals involved, establishment of the patient selection criteria, and design of the patients' training course, follow-up strategy and equipment. In addition, the results of the study conducted in our Unit, showing a high degree of patient satisfaction, are included. At this moment 20% of our patients are included in the self-control strategy.

7 CFR 51.2559 - Size classifications.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 7 Agriculture 2 2012-01-01 2012-01-01 false Size classifications. 51.2559 Section 51.2559... STANDARDS) United States Standards for Grades of Shelled Pistachio Nuts § 51.2559 Size classifications. (a... the following size classifications. (1) Jumbo Whole Kernels: 80 percent or more by weight shall be...

7 CFR 51.2559 - Size classifications.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 7 Agriculture 2 2011-01-01 2011-01-01 false Size classifications. 51.2559 Section 51.2559... STANDARDS) United States Standards for Grades of Shelled Pistachio Nuts § 51.2559 Size classifications. (a... the following size classifications. (1) Jumbo Whole Kernels: 80 percent or more by weight shall be...

Evaluating the Gradient of the Thin Wire Kernel

NASA Technical Reports Server (NTRS)

Wilton, Donald R.; Champagne, Nathan J.

2008-01-01

Recently, a formulation for evaluating the thin wire kernel was developed that employed a change of variable to smooth the kernel integrand, canceling the singularity in the integrand. Hence, the typical expansion of the wire kernel in a series for use in the potential integrals is avoided. The new expression for the kernel is exact and may be used directly to determine the gradient of the wire kernel, which consists of components that are parallel and radial to the wire axis.

Effect of Consuming Oat Bran Mixed in Water before a Meal on Glycemic Responses in Healthy Humans-A Pilot Study.

PubMed

Steinert, Robert E; Raederstorff, Daniel; Wolever, Thomas M S

2016-08-26

Viscous dietary fibers including oat β-glucan are one of the most effective classes of functional food ingredients for reducing postprandial blood glucose. The mechanism of action is thought to be via an increase in viscosity of the stomach contents that delays gastric emptying and reduces mixing of food with digestive enzymes, which, in turn, retards glucose absorption. Previous studies suggest that taking viscous fibers separate from a meal may not be effective in reducing postprandial glycemia. We aimed to re-assess the effect of consuming a preload of a commercially available oat-bran (4.5, 13.6 or 27.3 g) containing 22% of high molecular weight oat β-glucan (O22 (OatWell(®)22)) mixed in water before a test-meal of white bread on glycemic responses in 10 healthy humans. We found a significant effect of dose on blood glucose area under the curve (AUC) (p = 0.006) with AUC after 27.3 g of O22 being significantly lower than white bread only. Linear regression analysis showed that each gram of oat β-glucan reduced glucose AUC by 4.35% ± 1.20% (r = 0.507, p = 0.0008, n = 40) and peak rise by 6.57% ± 1.49% (r = 0.582, p < 0.0001). These data suggest the use of oat bran as nutritional preload strategy in the management of postprandial glycemia.

Transgenic Wheat, Barley and Oats: Future Prospects

NASA Astrophysics Data System (ADS)

Dunwell, Jim M.

Following the success of transgenic maize and rice, methods have now been developed for the efficient introduction of genes into wheat, barley and oats. This review summarizes the present position in relation to these three species, and also uses information from field trial databases and the patent literature to assess the future trends in the exploitation of transgenic material. This analysis includes agronomic traits and also discusses opportunities in expanding areas such as biofuels and biopharming.

KITTEN Lightweight Kernel 0.1 Beta

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

Pedretti, Kevin; Levenhagen, Michael; Kelly, Suzanne

2007-12-12

The Kitten Lightweight Kernel is a simplified OS (operating system) kernel that is intended to manage a compute node's hardware resources. It provides a set of mechanisms to user-level applications for utilizing hardware resources (e.g., allocating memory, creating processes, accessing the network). Kitten is much simpler than general-purpose OS kernels, such as Linux or Windows, but includes all of the esssential functionality needed to support HPC (high-performance computing) MPI, PGAS and OpenMP applications. Kitten provides unique capabilities such as physically contiguous application memory, transparent large page support, and noise-free tick-less operation, which enable HPC applications to obtain greater efficiency andmore » scalability than with general purpose OS kernels.« less

Herbicide resistance-endowing ACCase gene mutations in hexaploid wild oat (Avena fatua): insights into resistance evolution in a hexaploid species

PubMed Central

Yu, Q; Ahmad-Hamdani, M S; Han, H; Christoffers, M J; Powles, S B

2013-01-01

Many herbicide-resistant weed species are polyploids, but far too little about the evolution of resistance mutations in polyploids is understood. Hexaploid wild oat (Avena fatua) is a global crop weed and many populations have evolved herbicide resistance. We studied plastidic acetyl-coenzyme A carboxylase (ACCase)-inhibiting herbicide resistance in hexaploid wild oat and revealed that resistant individuals can express one, two or three different plastidic ACCase gene resistance mutations (Ile-1781-Leu, Asp-2078-Gly and Cys-2088-Arg). Using ACCase resistance mutations as molecular markers, combined with genetic, molecular and biochemical approaches, we found in individual resistant wild-oat plants that (1) up to three unlinked ACCase gene loci assort independently following Mendelian laws for disomic inheritance, (2) all three of these homoeologous ACCase genes were transcribed, with each able to carry its own mutation and (3) in a hexaploid background, each individual ACCase resistance mutation confers relatively low-level herbicide resistance, in contrast to high-level resistance conferred by the same mutations in unrelated diploid weed species of the Poaceae (grass) family. Low resistance conferred by individual ACCase resistance mutations is likely due to a dilution effect by susceptible ACCase expressed by homoeologs in hexaploid wild oat and/or differential expression of homoeologous ACCase gene copies. Thus, polyploidy in hexaploid wild oat may slow resistance evolution. Evidence of coexisting non-target-site resistance mechanisms among wild-oat populations was also revealed. In all, these results demonstrate that herbicide resistance and its evolution can be more complex in hexaploid wild oat than in unrelated diploid grass weeds. Our data provide a starting point for the daunting task of understanding resistance evolution in polyploids. PMID:23047200

Implementing Kernel Methods Incrementally by Incremental Nonlinear Projection Trick.

PubMed

Kwak, Nojun

2016-05-20

Recently, the nonlinear projection trick (NPT) was introduced enabling direct computation of coordinates of samples in a reproducing kernel Hilbert space. With NPT, any machine learning algorithm can be extended to a kernel version without relying on the so called kernel trick. However, NPT is inherently difficult to be implemented incrementally because an ever increasing kernel matrix should be treated as additional training samples are introduced. In this paper, an incremental version of the NPT (INPT) is proposed based on the observation that the centerization step in NPT is unnecessary. Because the proposed INPT does not change the coordinates of the old data, the coordinates obtained by INPT can directly be used in any incremental methods to implement a kernel version of the incremental methods. The effectiveness of the INPT is shown by applying it to implement incremental versions of kernel methods such as, kernel singular value decomposition, kernel principal component analysis, and kernel discriminant analysis which are utilized for problems of kernel matrix reconstruction, letter classification, and face image retrieval, respectively.

Structural Make-up, Biopolymer Conformation, and Biodegradation Characteristics of Newly Developed Super Genotype of Oats (CDC SO-I vs. Conventional Varieties): Novel Approach

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

Damiran, D.; Yu, P

Recently, a new 'super' genotype of oats (CDC SO-I or SO-I) has been developed. The objectives of this study were to determine structural makeup (features) of oat grain in endosperm and pericarp regions and to reveal and identify differences in protein amide I and II and carbohydrate structural makeup (conformation) between SO-I and two conventional oats (CDC Dancer and Derby) grown in western Canada in 2006, using advanced synchrotron radiation based Fourier transform infrared microspectroscopy (SRFTIRM). The SRFTIRM experiments were conducted at National Synchrotron Light Sources, Brookhaven National Laboratory (NSLS, BNL, U.S. Department of Energy). From the results, it wasmore » observed that comparison between the new genotype oats and conventional oats showed (1) differences in basic chemical and protein subfraction profiles and energy values with the new SO-I oats containing lower lignin (21 g/kg of DM) and higher soluble crude protein (530 g/kg CP), crude fat (59 g/kg of DM), and energy values (TDN, 820 g/kg of DM; NE{sub L3x}, 7.8 MJ/kg of DM); (2) significant differences in rumen biodegradation kinetics of dry matter, starch, and protein with the new SO-I oats containing lower EDDM (638 g/kg of DM) and higher EDCP (103 g/kg of DM); (3) significant differences in nutrient supply with highest truly absorbed rumen undegraded protein (ARUP, 23 g/kg of DM) and total metabolizable protein supply (MP, 81 g/kg of DM) from the new SO-I oats; and (4) significant differences in structural makeup in terms of protein amide I in the endosperm region (with amide I peak height from 0.13 to 0.22 IR absorbance unit) and cellulosic compounds to carbohydrate ratio in the pericarp region (ratio from 0.02 to 0.06). The results suggest that with the SRFTIRM technique, the structural makeup differences between the new genotype oats (SO-I) and two conventional oats (Dancer and Derby) could be revealed.« less

Mobilization of lipid reserves during germination of oat (Avena sativa L.), a cereal rich in endosperm oil.

PubMed

Leonova, Svetlana; Grimberg, Asa; Marttila, Salla; Stymne, Sten; Carlsson, Anders S

2010-06-01

Since the cereal endosperm is a dead tissue in the mature grain, beta-oxidation is not possible there. This raises the question about the use of the endosperm oil in cereal grains during germination. In this study, mobilization of lipids in different tissues of germinating oat grains was analysed using thin-layer and gas chromatography. The data imply that the oat endosperm oil [triacylglycerol (TAG)] is not a dead-end product as it was absorbed by the scutellum, either as free fatty acids (FFAs) released from TAG or as intact TAG immediately degraded to FFAs. These data were supported by light and transmission electron microscopy (LM and TEM) studies where close contact between endosperm lipid droplets and the scutellum was observed. The appearance of the fused oil in the oat endosperm changed into oil droplets during germination in areas close to the aleurone and the scutellar epithelium. However, according to the data obtained by TEM these oil droplets are unlikely to be oil bodies surrounded by oleosins. Accumulation of FFA pools in the embryo suggested further transport of FFAs from the scutellum. Noticeably high levels of TAG were also accumulated in the embryo but were not synthesized by re-esterification from imported FFAs. Comparison between two oat cultivars with different amounts of oil and starch in the endosperm suggests that an increased oil to starch ratio in oat grains does not significantly impact the germination process.

7 CFR 868.304 - Broken kernels determination.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 7 Agriculture 7 2011-01-01 2011-01-01 false Broken kernels determination. 868.304 Section 868.304 Agriculture Regulations of the Department of Agriculture (Continued) GRAIN INSPECTION, PACKERS AND STOCKYARD... Application of Standards § 868.304 Broken kernels determination. Broken kernels shall be determined by the use...

7 CFR 868.304 - Broken kernels determination.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 7 2010-01-01 2010-01-01 false Broken kernels determination. 868.304 Section 868.304 Agriculture Regulations of the Department of Agriculture (Continued) GRAIN INSPECTION, PACKERS AND STOCKYARD... Application of Standards § 868.304 Broken kernels determination. Broken kernels shall be determined by the use...

QTL Analysis of Kernel-Related Traits in Maize Using an Immortalized F2 Population

PubMed Central

Hu, Yanmin; Li, Weihua; Fu, Zhiyuan; Ding, Dong; Li, Haochuan; Qiao, Mengmeng; Tang, Jihua

2014-01-01

Kernel size and weight are important determinants of grain yield in maize. In this study, multivariate conditional and unconditional quantitative trait loci (QTL), and digenic epistatic analyses were utilized in order to elucidate the genetic basis for these kernel-related traits. Five kernel-related traits, including kernel weight (KW), volume (KV), length (KL), thickness (KT), and width (KWI), were collected from an immortalized F2 (IF2) maize population comprising of 243 crosses performed at two separate locations over a span of two years. A total of 54 unconditional main QTL for these five kernel-related traits were identified, many of which were clustered in chromosomal bins 6.04–6.06, 7.02–7.03, and 10.06–10.07. In addition, qKL3, qKWI6, qKV10a, qKV10b, qKW10a, and qKW7a were detected across multiple environments. Sixteen main QTL were identified for KW conditioned on the other four kernel traits (KL, KWI, KT, and KV). Thirteen main QTL were identified for KV conditioned on three kernel-shape traits. Conditional mapping analysis revealed that KWI and KV had the strongest influence on KW at the individual QTL level, followed by KT, and then KL; KV was mostly strongly influenced by KT, followed by KWI, and was least impacted by KL. Digenic epistatic analysis identified 18 digenic interactions involving 34 loci over the entire genome. However, only a small proportion of them were identical to the main QTL we detected. Additionally, conditional digenic epistatic analysis revealed that the digenic epistasis for KW and KV were entirely determined by their constituent traits. The main QTL identified in this study for determining kernel-related traits with high broad-sense heritability may play important roles during kernel development. Furthermore, digenic interactions were shown to exert relatively large effects on KL (the highest AA and DD effects were 4.6% and 6.7%, respectively) and KT (the highest AA effects were 4.3%). PMID:24586932

Preferential recruitment of the maternal centromere-specific histone H3 (CENH3) in oat (Avena sativa L.) × pearl millet (Pennisetum glaucum L.) hybrid embryos.

PubMed

Ishii, Takayoshi; Sunamura, Naohiro; Matsumoto, Ayaka; Eltayeb, Amin Elsadig; Tsujimoto, Hisashi

2015-12-01

Chromosome elimination occurs frequently in interspecific hybrids between distantly related species in Poaceae. However, chromosomes from both parents behave stably in a hybrid of female oat (Avena sativa L.) pollinated by pearl millet (Pennisetum glaucum L.). To analyze the chromosome behavior in this hybrid, we cloned the centromere-specific histone H3 (CENH3) genes of oat and pearl millet and produced a pearl millet-specific anti-CENH3 antibody. Application of this antibody together with a grass species common anti-CENH3 antibody revealed the dynamic CENH3 composition of the hybrid cells before and after fertilization. Despite co-expression of CENH3 genes encoded by oat and pearl millet, only an oat-type CENH3 was incorporated into the centromeres of both species in the hybrid embryo. Oat CENH3 enables a functional centromere in pearl millet chromosomes in an oat genetic background. Comparison of CENH3 genes among Poaceae species that show chromosome elimination in interspecific hybrids revealed that the loop 1 regions of oat and pearl millet CENH3 exhibit exceptionally high similarity.

Kernel learning at the first level of inference.

PubMed

Cawley, Gavin C; Talbot, Nicola L C

2014-05-01

Kernel learning methods, whether Bayesian or frequentist, typically involve multiple levels of inference, with the coefficients of the kernel expansion being determined at the first level and the kernel and regularisation parameters carefully tuned at the second level, a process known as model selection. Model selection for kernel machines is commonly performed via optimisation of a suitable model selection criterion, often based on cross-validation or theoretical performance bounds. However, if there are a large number of kernel parameters, as for instance in the case of automatic relevance determination (ARD), there is a substantial risk of over-fitting the model selection criterion, resulting in poor generalisation performance. In this paper we investigate the possibility of learning the kernel, for the Least-Squares Support Vector Machine (LS-SVM) classifier, at the first level of inference, i.e. parameter optimisation. The kernel parameters and the coefficients of the kernel expansion are jointly optimised at the first level of inference, minimising a training criterion with an additional regularisation term acting on the kernel parameters. The key advantage of this approach is that the values of only two regularisation parameters need be determined in model selection, substantially alleviating the problem of over-fitting the model selection criterion. The benefits of this approach are demonstrated using a suite of synthetic and real-world binary classification benchmark problems, where kernel learning at the first level of inference is shown to be statistically superior to the conventional approach, improves on our previous work (Cawley and Talbot, 2007) and is competitive with Multiple Kernel Learning approaches, but with reduced computational expense. Copyright © 2014 Elsevier Ltd. All rights reserved.

Multiple kernels learning-based biological entity relationship extraction method.

PubMed

Dongliang, Xu; Jingchang, Pan; Bailing, Wang

2017-09-20

Automatic extracting protein entity interaction information from biomedical literature can help to build protein relation network and design new drugs. There are more than 20 million literature abstracts included in MEDLINE, which is the most authoritative textual database in the field of biomedicine, and follow an exponential growth over time. This frantic expansion of the biomedical literature can often be difficult to absorb or manually analyze. Thus efficient and automated search engines are necessary to efficiently explore the biomedical literature using text mining techniques. The P, R, and F value of tag graph method in Aimed corpus are 50.82, 69.76, and 58.61%, respectively. The P, R, and F value of tag graph kernel method in other four evaluation corpuses are 2-5% higher than that of all-paths graph kernel. And The P, R and F value of feature kernel and tag graph kernel fuse methods is 53.43, 71.62 and 61.30%, respectively. The P, R and F value of feature kernel and tag graph kernel fuse methods is 55.47, 70.29 and 60.37%, respectively. It indicated that the performance of the two kinds of kernel fusion methods is better than that of simple kernel. In comparison with the all-paths graph kernel method, the tag graph kernel method is superior in terms of overall performance. Experiments show that the performance of the multi-kernels method is better than that of the three separate single-kernel method and the dual-mutually fused kernel method used hereof in five corpus sets.

Black oat cover crop management in watermelon production systems

USDA-ARS?s Scientific Manuscript database

Black oats (Avena strigosa Schreb.) were sown as a cover crop near Weslaco, Texas (Lat. 26 deg N) in Fall 2010. The cover crop was allowed to senesce naturally and was planted to watermelons in both the spring and in the fall of 2011. Watermelon transplants planted in the spring into mowed black o...

Evaluation of beneficial use of wood-fired boiler ash on oat and bean growth

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

Krejsl, J.A.; Scanlon, T.M.

An evaluation on the effects of pulp and paper mill combined boiler ashes on growth and nutrient uptake by oat (Avena sativa L., var. 501) and bean (Phaseolus vulgaris L., var. blue pole) was conducted in a greenhouse. Ash with a calcium carbonate equivalent of 29.1% and a pH of 12.1 was applied at the rates 30, 40, and 50 dry Mg ha{sup -1} to Chehalis silty clay loam (fine-silty, mixed, mesic Cumulic Ultic Haploxerolls), with pH 5.4. An agricultural dolomitic lime treatment of 7.4 Mg ha{sup -1} and a nonamended control were also included. Plants grown on ash-amended soilmore » had higher biomass compared to plants grown on lime and control treatments. Ash treatments 30, 40, and 50 dry Mg ha{sup -1} increased the bean (stems and leaves) dry matter (DM) yield over the control by 49, 57, and 64%, respectively. The lime treatment increased the bean DM yield by 31% compared with the control. The ash rate 30 dry Mg ha{sup -1}, equivalent to the recommended agronomic lime rate 7.4 Mg ha{sup -1}, increased oat (shoots) DM yields over the control by 45%, while the lime treatment increased biomass by 8% over control. The highest ash treatment, 50 Mg ha{sup -1}, produced the lowest oat biomass. The ash was as effective as dolomitic lime in raising soil pH. Ash-amended soils contained higher concentrations of P, S, and B for plant growth compared to lime and nonamended soils. Soil Zn, Fe, mn, and Cu concentrations decreased as ash application rates increased. Oat and bean plants grown in the ash-amended soil had increased concentrations of K, S, and B and decreased concentrations of Mn and Cu compared with plants grown in the nonamended control soil. Overall, oat and bean benefited from the increased nutrient availability and soil pH caused by the application of boiler ash. 20 refs., 6 tabs.« less

7 CFR 51.1403 - Kernel color classification.

Code of Federal Regulations, 2013 CFR

2013-01-01

... generally conforms to the “light” or “light amber” classification, that color classification may be used to... 7 Agriculture 2 2013-01-01 2013-01-01 false Kernel color classification. 51.1403 Section 51.1403... Color Classification § 51.1403 Kernel color classification. (a) The skin color of pecan kernels may be...

7 CFR 51.1403 - Kernel color classification.

Code of Federal Regulations, 2014 CFR

2014-01-01

... generally conforms to the “light” or “light amber” classification, that color classification may be used to... 7 Agriculture 2 2014-01-01 2014-01-01 false Kernel color classification. 51.1403 Section 51.1403... Color Classification § 51.1403 Kernel color classification. (a) The skin color of pecan kernels may be...

Evidence-based Kernels: Fundamental Units of Behavioral Influence

PubMed Central

Biglan, Anthony

2008-01-01

This paper describes evidence-based kernels, fundamental units of behavioral influence that appear to underlie effective prevention and treatment for children, adults, and families. A kernel is a behavior–influence procedure shown through experimental analysis to affect a specific behavior and that is indivisible in the sense that removing any of its components would render it inert. Existing evidence shows that a variety of kernels can influence behavior in context, and some evidence suggests that frequent use or sufficient use of some kernels may produce longer lasting behavioral shifts. The analysis of kernels could contribute to an empirically based theory of behavioral influence, augment existing prevention or treatment efforts, facilitate the dissemination of effective prevention and treatment practices, clarify the active ingredients in existing interventions, and contribute to efficiently developing interventions that are more effective. Kernels involve one or more of the following mechanisms of behavior influence: reinforcement, altering antecedents, changing verbal relational responding, or changing physiological states directly. The paper describes 52 of these kernels, and details practical, theoretical, and research implications, including calling for a national database of kernels that influence human behavior. PMID:18712600

Integrating the Gradient of the Thin Wire Kernel

NASA Technical Reports Server (NTRS)

Champagne, Nathan J.; Wilton, Donald R.

2008-01-01

A formulation for integrating the gradient of the thin wire kernel is presented. This approach employs a new expression for the gradient of the thin wire kernel derived from a recent technique for numerically evaluating the exact thin wire kernel. This approach should provide essentially arbitrary accuracy and may be used with higher-order elements and basis functions using the procedure described in [4].When the source and observation points are close, the potential integrals over wire segments involving the wire kernel are split into parts to handle the singular behavior of the integrand [1]. The singularity characteristics of the gradient of the wire kernel are different than those of the wire kernel, and the axial and radial components have different singularities. The characteristics of the gradient of the wire kernel are discussed in [2]. To evaluate the near electric and magnetic fields of a wire, the integration of the gradient of the wire kernel needs to be calculated over the source wire. Since the vector bases for current have constant direction on linear wire segments, these integrals reduce to integrals of the form

THERMOS. 30-Group ENDF/B Scattered Kernels

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

McCrosson, F.J.; Finch, D.R.

1973-12-01

These data are 30-group THERMOS thermal scattering kernels for P0 to P5 Legendre orders for every temperature of every material from s(alpha,beta) data stored in the ENDF/B library. These scattering kernels were generated using the FLANGE2 computer code. To test the kernels, the integral properties of each set of kernels were determined by a precision integration of the diffusion length equation and compared to experimental measurements of these properties. In general, the agreement was very good. Details of the methods used and results obtained are contained in the reference. The scattering kernels are organized into a two volume magnetic tapemore » library from which they may be retrieved easily for use in any 30-group THERMOS library.« less

Impact of planting date on annual clover survival in oat

USDA-ARS?s Scientific Manuscript database

Interseeding annual clovers in cereal grains may help organic producers reduce the need for tillage in their cropping systems. In this study in eastern South Dakota, we evaluated seedling emergence and survival of two annual clovers in oat as affected by planting date. Berseem clover (Trifolium al...

Subgenome-specific assembly of vitamin E biosynthesis genes and expression patterns during seed development provide insight into the evolution of oat genome.

PubMed

Gutierrez-Gonzalez, Juan J; Garvin, David F

2016-11-01

Vitamin E is essential for humans and thus must be a component of a healthy diet. Among the cereal grains, hexaploid oats (Avena sativa L.) have high vitamin E content. To date, no gene sequences in the vitamin E biosynthesis pathway have been reported for oats. Using deep sequencing and orthology-guided assembly, coding sequences of genes for each step in vitamin E synthesis in oats were reconstructed, including resolution of the sequences of homeologs. Three homeologs, presumably representing each of the three oat subgenomes, were identified for the main steps of the pathway. Partial sequences, likely representing pseudogenes, were recovered in some instances as well. Pairwise comparisons among homeologs revealed that two of the three putative subgenome-specific homeologs are almost identical for each gene. Synonymous substitution rates indicate the time of divergence of the two more similar subgenomes from the distinct one at 7.9-8.7 MYA, and a divergence between the similar subgenomes from a common ancestor 1.1 MYA. A new proposed evolutionary model for hexaploid oat formation is discussed. Homeolog-specific gene expression was quantified during oat seed development and compared with vitamin E accumulation. Homeolog expression largely appears to be similar for most of genes; however, for some genes, homoeolog-specific transcriptional bias was observed. The expression of HPPD, as well as certain homoeologs of VTE2 and VTE4, is highly correlated with seed vitamin E accumulation. Our findings expand our understanding of oat genome evolution and will assist efforts to modify vitamin E content and composition in oats. Published 2016. This article is a U.S. Government work and is in the public domain in the USA. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Protein evaluation of four oat (Avena sativa L.) cultivars adapted for cultivation in the south of Brazil.

PubMed

Pedó, I; Sgarbieri, V C; Gutkoski, L C

1999-01-01

Four oat cultivars adapted for soil and climate conditions in the southern region of Brazil were evaluated for protein nutritive value. Evaluations were done both in vitro and in vivo. In vitro evaluation was done by essential amino acid profile, available lysine, amino acid scoring, and protein digestibility corrected amino acid-scoring (PDCAAS). Nitrogen balance indices and PER were determined in vivo with rats. In all four cultivars (UFP-15, UFP-16, CTC-03, UFRGS-14), lysine was the most limiting amino acid. Available lysine, amino acid score and PDCAAS were highest for cultivar UFRGS-14 and lowest for CTC-03. When compared to casein, only nitrogen retention for UFRGS-14 did not differ statistically (p>0.05); all other indices of protein quality were inferior to casein for the oat cultivars. The oat cultivars tended to be identical among themselves, except for apparent protein digestibility which was significantly higher in the UFRGS-14 and CTC-03 cultivars. On average, the PER values of the oat cultivars were 82% of casein; the net protein utilization was 88% of casein as determined in vivo and 49% by the estimation in vitro (PDCAAS).

Structural makeup, biopolymer conformation, and biodegradation characteristics of a newly developed super genotype of oats (CDC SO-I versus conventional varieties): a novel approach.

PubMed

Damiran, Daalkhaijav; Yu, Peiqiang

2010-02-24

Recently, a new "super" genotype of oats (CDC SO-I or SO-I) has been developed. The objectives of this study were to determine structural makeup (features) of oat grain in endosperm and pericarp regions and to reveal and identify differences in protein amide I and II and carbohydrate structural makeup (conformation) between SO-I and two conventional oats (CDC Dancer and Derby) grown in western Canada in 2006, using advanced synchrotron radiation based Fourier transform infrared microspectroscopy (SRFTIRM). The SRFTIRM experiments were conducted at National Synchrotron Light Sources, Brookhaven National Laboratory (NSLS, BNL, U.S. Department of Energy). From the results, it was observed that comparison between the new genotype oats and conventional oats showed (1) differences in basic chemical and protein subfraction profiles and energy values with the new SO-I oats containing lower lignin (21 g/kg of DM) and higher soluble crude protein (530 g/kg CP), crude fat (59 g/kg of DM), and energy values (TDN, 820 g/kg of DM; NE(L3x), 7.8 MJ/kg of DM); (2) significant differences in rumen biodegradation kinetics of dry matter, starch, and protein with the new SO-I oats containing lower EDDM (638 g/kg of DM) and higher EDCP (103 g/kg of DM); (3) significant differences in nutrient supply with highest truly absorbed rumen undegraded protein (ARUP, 23 g/kg of DM) and total metabolizable protein supply (MP, 81 g/kg of DM) from the new SO-I oats; and (4) significant differences in structural makeup in terms of protein amide I in the endosperm region (with amide I peak height from 0.13 to 0.22 IR absorbance unit) and cellulosic compounds to carbohydrate ratio in the pericarp region (ratio from 0.02 to 0.06). The results suggest that with the SRFTIRM technique, the structural makeup differences between the new genotype oats (SO-I) and two conventional oats (Dancer and Derby) could be revealed.

The Classification of Diabetes Mellitus Using Kernel k-means

NASA Astrophysics Data System (ADS)

Alamsyah, M.; Nafisah, Z.; Prayitno, E.; Afida, A. M.; Imah, E. M.

2018-01-01

Diabetes Mellitus is a metabolic disorder which is characterized by chronicle hypertensive glucose. Automatics detection of diabetes mellitus is still challenging. This study detected diabetes mellitus by using kernel k-Means algorithm. Kernel k-means is an algorithm which was developed from k-means algorithm. Kernel k-means used kernel learning that is able to handle non linear separable data; where it differs with a common k-means. The performance of kernel k-means in detecting diabetes mellitus is also compared with SOM algorithms. The experiment result shows that kernel k-means has good performance and a way much better than SOM.

Brain tumor image segmentation using kernel dictionary learning.

PubMed

Jeon Lee; Seung-Jun Kim; Rong Chen; Herskovits, Edward H

2015-08-01

Automated brain tumor image segmentation with high accuracy and reproducibility holds a big potential to enhance the current clinical practice. Dictionary learning (DL) techniques have been applied successfully to various image processing tasks recently. In this work, kernel extensions of the DL approach are adopted. Both reconstructive and discriminative versions of the kernel DL technique are considered, which can efficiently incorporate multi-modal nonlinear feature mappings based on the kernel trick. Our novel discriminative kernel DL formulation allows joint learning of a task-driven kernel-based dictionary and a linear classifier using a K-SVD-type algorithm. The proposed approaches were tested using real brain magnetic resonance (MR) images of patients with high-grade glioma. The obtained preliminary performances are competitive with the state of the art. The discriminative kernel DL approach is seen to reduce computational burden without much sacrifice in performance.

A robust, high-throughput method for computing maize ear, cob, and kernel attributes automatically from images.

PubMed

Miller, Nathan D; Haase, Nicholas J; Lee, Jonghyun; Kaeppler, Shawn M; de Leon, Natalia; Spalding, Edgar P

2017-01-01

Grain yield of the maize plant depends on the sizes, shapes, and numbers of ears and the kernels they bear. An automated pipeline that can measure these components of yield from easily-obtained digital images is needed to advance our understanding of this globally important crop. Here we present three custom algorithms designed to compute such yield components automatically from digital images acquired by a low-cost platform. One algorithm determines the average space each kernel occupies along the cob axis using a sliding-window Fourier transform analysis of image intensity features. A second counts individual kernels removed from ears, including those in clusters. A third measures each kernel's major and minor axis after a Bayesian analysis of contour points identifies the kernel tip. Dimensionless ear and kernel shape traits that may interrelate yield components are measured by principal components analysis of contour point sets. Increased objectivity and speed compared to typical manual methods are achieved without loss of accuracy as evidenced by high correlations with ground truth measurements and simulated data. Millimeter-scale differences among ear, cob, and kernel traits that ranged more than 2.5-fold across a diverse group of inbred maize lines were resolved. This system for measuring maize ear, cob, and kernel attributes is being used by multiple research groups as an automated Web service running on community high-throughput computing and distributed data storage infrastructure. Users may create their own workflow using the source code that is staged for download on a public repository. © 2016 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.

Development of a kernel function for clinical data.

PubMed

Daemen, Anneleen; De Moor, Bart

2009-01-01

For most diseases and examinations, clinical data such as age, gender and medical history guides clinical management, despite the rise of high-throughput technologies. To fully exploit such clinical information, appropriate modeling of relevant parameters is required. As the widely used linear kernel function has several disadvantages when applied to clinical data, we propose a new kernel function specifically developed for this data. This "clinical kernel function" more accurately represents similarities between patients. Evidently, three data sets were studied and significantly better performances were obtained with a Least Squares Support Vector Machine when based on the clinical kernel function compared to the linear kernel function.

Towards the Geometry of Reproducing Kernels

NASA Astrophysics Data System (ADS)

Galé, J. E.

2010-11-01

It is shown here how one is naturally led to consider a category whose objects are reproducing kernels of Hilbert spaces, and how in this way a differential geometry for such kernels may be settled down.

Glycemic potency of muffins made with wheat, rice, corn, oat and barley flours: a comparative study between in vivo and in vitro.

PubMed

Soong, Yean Yean; Quek, Rina Yu Chin; Henry, Christiani Jeyakumar

2015-12-01

Muffins made with wheat flour are a popular snack consumed in western and emerging countries. This study aimed to examine the content of amylose, glycemic response (GR) and glycemic index (GI) of muffins baked with refined wheat and rice flours, as well as wholegrain corn, oat and barley flours. This study adopted a randomized, controlled, crossover, non-blind design. Twelve healthy participants consumed wheat, rice, corn, oat and barley muffins once and the reference glucose solution three times in a random order on non-consecutive day. Capillary blood samples were taken every 15 min in the first 60 min and every 30 min for the remaining 60 min for blood glucose analysis. The Megazyme amylose/amylopectin assay procedure was employed to measure amylose content. The GR elicited from the consumption of wheat, rice and corn muffins was comparable between these samples but significantly greater when compared with oat and barley muffins. Consumption of wholegrain muffins, apart from corn muffin, blunted postprandial GR when compared with muffins baked with refined cereal flours. Muffins baked with wheat, rice, corn, oat and barley flours gave rise to GI values of 74, 79, 74, 53 and 55, respectively. The content of amylose was significantly higher in corn, oat and barley muffins than wheat and rice muffins. The greater content of amylose and fibre may play a part in the reduced glycemic potency of oat and barley muffins. Wheat flour can be substituted with oat and barley flours for healthier muffins and other bakery products.

Super-resolution fusion of complementary panoramic images based on cross-selection kernel regression interpolation.

PubMed

Chen, Lidong; Basu, Anup; Zhang, Maojun; Wang, Wei; Liu, Yu

2014-03-20

A complementary catadioptric imaging technique was proposed to solve the problem of low and nonuniform resolution in omnidirectional imaging. To enhance this research, our paper focuses on how to generate a high-resolution panoramic image from the captured omnidirectional image. To avoid the interference between the inner and outer images while fusing the two complementary views, a cross-selection kernel regression method is proposed. First, in view of the complementarity of sampling resolution in the tangential and radial directions between the inner and the outer images, respectively, the horizontal gradients in the expected panoramic image are estimated based on the scattered neighboring pixels mapped from the outer, while the vertical gradients are estimated using the inner image. Then, the size and shape of the regression kernel are adaptively steered based on the local gradients. Furthermore, the neighboring pixels in the next interpolation step of kernel regression are also selected based on the comparison between the horizontal and vertical gradients. In simulation and real-image experiments, the proposed method outperforms existing kernel regression methods and our previous wavelet-based fusion method in terms of both visual quality and objective evaluation.

Sodium and Potassium Fluxes and Compartmentation in Roots of Atriplex and Oat 1

PubMed Central

Mills, David; Robinson, Kenneth; Hodges, Thomas K.

1985-01-01

K+ and Na+ fluxes and ion content have been studied in roots of Atriplex nummularia Lindl. and Avena sativa L. cv Goodfield grown in 3 millimolar K+ with or without 3 or 50 millimolar NaCl. Compartmental analysis was carried out with entire root systems under steady-state conditions. Increasing ambient Na+ concentrations from 0 to 50 millimolar altered K+, in Atriplex, as follows: slightly decreased the cytoplasmic content (Qc), the vacuolar content (Qv), and the plasma membrane influx and efflux. Xylem transport for K+ decreased by 63% in Atriplex. For oat roots, similar increases in Na+ altered K+ parameters as follows: plasma membrane influx and efflux decreased by about 80%. Qc decreased by 65%, and xylem transport decreased by 91%. No change, however, was observed in Qv for K+. Increasing ambient Na+ resulted in higher (3 to 5-fold) Na+ fluxes across the plasma membrane and in Qc of both species. In Atriplex, Na+ fluxes across the tonoplast and Qv increased as external Na+ was increased. In oat, however, no significant change was observed in Na+ flux across the tonoplast or in Qv as external Na+ was increased. In oat roots, Na+ reduced K+ uptake markedly; in Atriplex, this was not as pronounced. However, even at high Na+ levels, the influx transport system at the plasma membrane of both species preferred K+ over Na+. Based upon the Ussing-Teorell equation, it was concluded that active inward transport of K+ occurred across the plasma membrane, and passive movement of K+ occurred across the tonoplast in both species. Na+, in oat roots, was actively pumped out of the cytoplasm to the exterior, whereas, in Atriplex, Na+ was passively distributed between the free space, cytoplasm, and vacuole. PMID:16664273

Kernel-PCA data integration with enhanced interpretability

PubMed Central

2014-01-01

Background Nowadays, combining the different sources of information to improve the biological knowledge available is a challenge in bioinformatics. One of the most powerful methods for integrating heterogeneous data types are kernel-based methods. Kernel-based data integration approaches consist of two basic steps: firstly the right kernel is chosen for each data set; secondly the kernels from the different data sources are combined to give a complete representation of the available data for a given statistical task. Results We analyze the integration of data from several sources of information using kernel PCA, from the point of view of reducing dimensionality. Moreover, we improve the interpretability of kernel PCA by adding to the plot the representation of the input variables that belong to any dataset. In particular, for each input variable or linear combination of input variables, we can represent the direction of maximum growth locally, which allows us to identify those samples with higher/lower values of the variables analyzed. Conclusions The integration of different datasets and the simultaneous representation of samples and variables together give us a better understanding of biological knowledge. PMID:25032747

Gaussian mass optimization for kernel PCA parameters

NASA Astrophysics Data System (ADS)

Liu, Yong; Wang, Zulin

2011-10-01

This paper proposes a novel kernel parameter optimization method based on Gaussian mass, which aims to overcome the current brute force parameter optimization method in a heuristic way. Generally speaking, the choice of kernel parameter should be tightly related to the target objects while the variance between the samples, the most commonly used kernel parameter, doesn't possess much features of the target, which gives birth to Gaussian mass. Gaussian mass defined in this paper has the property of the invariance of rotation and translation and is capable of depicting the edge, topology and shape information. Simulation results show that Gaussian mass leads a promising heuristic optimization boost up for kernel method. In MNIST handwriting database, the recognition rate improves by 1.6% compared with common kernel method without Gaussian mass optimization. Several promising other directions which Gaussian mass might help are also proposed at the end of the paper.

Design of CT reconstruction kernel specifically for clinical lung imaging

NASA Astrophysics Data System (ADS)

Cody, Dianna D.; Hsieh, Jiang; Gladish, Gregory W.

2005-04-01

In this study we developed a new reconstruction kernel specifically for chest CT imaging. An experimental flat-panel CT scanner was used on large dogs to produce 'ground-truth" reference chest CT images. These dogs were also examined using a clinical 16-slice CT scanner. We concluded from the dog images acquired on the clinical scanner that the loss of subtle lung structures was due mostly to the presence of the background noise texture when using currently available reconstruction kernels. This qualitative evaluation of the dog CT images prompted the design of a new recon kernel. This new kernel consisted of the combination of a low-pass and a high-pass kernel to produce a new reconstruction kernel, called the 'Hybrid" kernel. The performance of this Hybrid kernel fell between the two kernels on which it was based, as expected. This Hybrid kernel was also applied to a set of 50 patient data sets; the analysis of these clinical images is underway. We are hopeful that this Hybrid kernel will produce clinical images with an acceptable tradeoff of lung detail, reliable HU, and image noise.

Quality changes in macadamia kernel between harvest and farm-gate.

PubMed

Walton, David A; Wallace, Helen M

2011-02-01

Macadamia integrifolia, Macadamia tetraphylla and their hybrids are cultivated for their edible kernels. After harvest, nuts-in-shell are partially dried on-farm and sorted to eliminate poor-quality kernels before consignment to a processor. During these operations, kernel quality may be lost. In this study, macadamia nuts-in-shell were sampled at five points of an on-farm postharvest handling chain from dehusking to the final storage silo to assess quality loss prior to consignment. Shoulder damage, weight of pieces and unsound kernel were assessed for raw kernels, and colour, mottled colour and surface damage for roasted kernels. Shoulder damage, weight of pieces and unsound kernel for raw kernels increased significantly between the dehusker and the final silo. Roasted kernels displayed a significant increase in dark colour, mottled colour and surface damage during on-farm handling. Significant loss of macadamia kernel quality occurred on a commercial farm during sorting and storage of nuts-in-shell before nuts were consigned to a processor. Nuts-in-shell should be dried as quickly as possible and on-farm handling minimised to maintain optimum kernel quality. 2010 Society of Chemical Industry.

LoCoH: Non-parameteric kernel methods for constructing home ranges and utilization distributions

USGS Publications Warehouse

Getz, Wayne M.; Fortmann-Roe, Scott; Cross, Paul C.; Lyons, Andrew J.; Ryan, Sadie J.; Wilmers, Christopher C.

2007-01-01

Parametric kernel methods currently dominate the literature regarding the construction of animal home ranges (HRs) and utilization distributions (UDs). These methods frequently fail to capture the kinds of hard boundaries common to many natural systems. Recently a local convex hull (LoCoH) nonparametric kernel method, which generalizes the minimum convex polygon (MCP) method, was shown to be more appropriate than parametric kernel methods for constructing HRs and UDs, because of its ability to identify hard boundaries (e.g., rivers, cliff edges) and convergence to the true distribution as sample size increases. Here we extend the LoCoH in two ways: ‘‘fixed sphere-of-influence,’’ or r -LoCoH (kernels constructed from all points within a fixed radius r of each reference point), and an ‘‘adaptive sphere-of-influence,’’ or a -LoCoH (kernels constructed from all points within a radius a such that the distances of all points within the radius to the reference point sum to a value less than or equal to a ), and compare them to the original ‘‘fixed-number-of-points,’’ or k -LoCoH (all kernels constructed from k -1 nearest neighbors of root points). We also compare these nonparametric LoCoH to parametric kernel methods using manufactured data and data collected from GPS collars on African buffalo in the Kruger National Park, South Africa. Our results demonstrate that LoCoH methods are superior to parametric kernel methods in estimating areas used by animals, excluding unused areas (holes) and, generally, in constructing UDs and HRs arising from the movement of animals influenced by hard boundaries and irregular structures (e.g., rocky outcrops). We also demonstrate that a -LoCoH is generally superior to k - and r -LoCoH (with software for all three methods available at http://locoh.cnr.berkeley.edu).

Unified heat kernel regression for diffusion, kernel smoothing and wavelets on manifolds and its application to mandible growth modeling in CT images.

PubMed

Chung, Moo K; Qiu, Anqi; Seo, Seongho; Vorperian, Houri K

2015-05-01

We present a novel kernel regression framework for smoothing scalar surface data using the Laplace-Beltrami eigenfunctions. Starting with the heat kernel constructed from the eigenfunctions, we formulate a new bivariate kernel regression framework as a weighted eigenfunction expansion with the heat kernel as the weights. The new kernel method is mathematically equivalent to isotropic heat diffusion, kernel smoothing and recently popular diffusion wavelets. The numerical implementation is validated on a unit sphere using spherical harmonics. As an illustration, the method is applied to characterize the localized growth pattern of mandible surfaces obtained in CT images between ages 0 and 20 by regressing the length of displacement vectors with respect to a surface template. Copyright © 2015 Elsevier B.V. All rights reserved.

Generalization Performance of Regularized Ranking With Multiscale Kernels.

PubMed

Zhou, Yicong; Chen, Hong; Lan, Rushi; Pan, Zhibin

2016-05-01

The regularized kernel method for the ranking problem has attracted increasing attentions in machine learning. The previous regularized ranking algorithms are usually based on reproducing kernel Hilbert spaces with a single kernel. In this paper, we go beyond this framework by investigating the generalization performance of the regularized ranking with multiscale kernels. A novel ranking algorithm with multiscale kernels is proposed and its representer theorem is proved. We establish the upper bound of the generalization error in terms of the complexity of hypothesis spaces. It shows that the multiscale ranking algorithm can achieve satisfactory learning rates under mild conditions. Experiments demonstrate the effectiveness of the proposed method for drug discovery and recommendation tasks.

Putting Priors in Mixture Density Mercer Kernels

NASA Technical Reports Server (NTRS)

Srivastava, Ashok N.; Schumann, Johann; Fischer, Bernd

2004-01-01

This paper presents a new methodology for automatic knowledge driven data mining based on the theory of Mercer Kernels, which are highly nonlinear symmetric positive definite mappings from the original image space to a very high, possibly infinite dimensional feature space. We describe a new method called Mixture Density Mercer Kernels to learn kernel function directly from data, rather than using predefined kernels. These data adaptive kernels can en- code prior knowledge in the kernel using a Bayesian formulation, thus allowing for physical information to be encoded in the model. We compare the results with existing algorithms on data from the Sloan Digital Sky Survey (SDSS). The code for these experiments has been generated with the AUTOBAYES tool, which automatically generates efficient and documented C/C++ code from abstract statistical model specifications. The core of the system is a schema library which contains template for learning and knowledge discovery algorithms like different versions of EM, or numeric optimization methods like conjugate gradient methods. The template instantiation is supported by symbolic- algebraic computations, which allows AUTOBAYES to find closed-form solutions and, where possible, to integrate them into the code. The results show that the Mixture Density Mercer-Kernel described here outperforms tree-based classification in distinguishing high-redshift galaxies from low- redshift galaxies by approximately 16% on test data, bagged trees by approximately 7%, and bagged trees built on a much larger sample of data by approximately 2%.

Comparative microstructure study of oil palm fruit bunch fibre, mesocarp and kernels after microwave pre-treatment

NASA Astrophysics Data System (ADS)

Chang, Jessie S. L.; Chan, Y. S.; Law, M. C.; Leo, C. P.

2017-07-01

The implementation of microwave technology in palm oil processing offers numerous advantages; besides elimination of polluted palm oil mill effluent, it also reduces energy consumption, processing time and space. However, microwave exposure could damage a material’s microstructure which affected the quality of fruit that can be related to its physical structure including the texture and appearance. In this work, empty fruit bunches, mesocarp and kernel was microwave dried and their respective microstructures were examined. The microwave pretreatments were conducted at 100W and 200W and the microstructure investigation of both treated and untreated samples were evaluated using scanning electron microscope. The micrographs demonstrated that microwave does not significantly influence kernel and mesocarp but noticeable change was found on the empty fruit bunches where the sizes of the granular starch were reduced and a small portion of the silica bodies were disrupted. From the experimental data, the microwave irradiation was shown to be efficiently applied on empty fruit bunches followed by mesocarp and kernel as significant weight loss and size reduction was observed after the microwave treatments. The current work showed that microwave treatment did not change the physical surfaces of samples but sample shrinkage is observed.

A Review of Extraction and Analysis of Bioactives in Oat and Barley and Scope for Use of Novel Food Processing Technologies.

PubMed

Gangopadhyay, Nirupama; Hossain, Mohammad B; Rai, Dilip K; Brunton, Nigel P

2015-06-12

Oat and barely are cereal crops mainly used as animal feed and for the purposes of malting and brewing, respectively. Some studies have indicated that consumption of oat and barley rich foods may reduce the risk of some chronic diseases such as coronary heart disease, type II diabetes and cancer. Whilst there is no absolute consensus, some of these benefits may be linked to presence of compounds such as phenolics, vitamin E and β-glucan in these cereals. A number of benefits have also been linked to the lipid component (sterols, fatty acids) and the proteins and bioactive peptides in oats and barley. Since the available evidence is pointing toward the possible health benefits of oat and barley components, a number of authors have examined techniques for recovering them from their native sources. In the present review, we summarise and examine the range of conventional techniques that have been used for the purpose of extraction and detection of these bioactives. In addition, the recent advances in use of novel food processing technologies as a substitute to conventional processes for extraction of bioactives from oats and barley, has been discussed.

An SVM model with hybrid kernels for hydrological time series

NASA Astrophysics Data System (ADS)

Wang, C.; Wang, H.; Zhao, X.; Xie, Q.

2017-12-01

Support Vector Machine (SVM) models have been widely applied to the forecast of climate/weather and its impact on other environmental variables such as hydrologic response to climate/weather. When using SVM, the choice of the kernel function plays the key role. Conventional SVM models mostly use one single type of kernel function, e.g., radial basis kernel function. Provided that there are several featured kernel functions available, each having its own advantages and drawbacks, a combination of these kernel functions may give more flexibility and robustness to SVM approach, making it suitable for a wide range of application scenarios. This paper presents such a linear combination of radial basis kernel and polynomial kernel for the forecast of monthly flowrate in two gaging stations using SVM approach. The results indicate significant improvement in the accuracy of predicted series compared to the approach with either individual kernel function, thus demonstrating the feasibility and advantages of such hybrid kernel approach for SVM applications.

Preferred carbon precursors for lipid labelling in the heterotrophic endosperm of developing oat (Avena sativa L.) grains.

PubMed

Grimberg, Åsa

2014-10-01

Oat (Avena sativa L.) is unusual among the cereal grains in storing high amounts of oil in the endosperm; up to 90% of total grain oil. By using oat as a model species for oil metabolism in the cereal endosperm, we can learn how to develop strategies to redirect carbon from starch to achieve high-oil yielding cereal crops. Carbon precursors for lipid synthesis were compared in two genetically close oat cultivars with different endosperm oil content (about 6% and 10% of grain dw, medium-oil; MO, and high-oil; HO cultivar, respectively) by supplying a variety of (14)C-labelled substrates to the grain from both up- and downstream parts of glycolysis, either through detached oat panicles in vitro or by direct injection in planta. When supplied by direct injection, (14)C from acetate was identified to label the lipid fraction of the grain to the highest extent among substrates tested; 46% of net accumulated (14)C, demonstrating its applicability as a marker for lipids in the endosperm. Time course analyses of injected (14)C acetate during grain development suggested a more efficient transfer of fatty acids from polar lipids to triacylglycerol in the HO as compared to the MO cultivar, and turnover of triacylglycerol was suggested to not play a major role for the final oil content of oat grain endosperm despite the low amount of protective oleosins in this tissue. Moreover, availability of light was shown to drastically affect grain net carbon accumulation from (14)C-sucrose when supplied through detached panicles for the HO cultivar. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Graph wavelet alignment kernels for drug virtual screening.

PubMed

Smalter, Aaron; Huan, Jun; Lushington, Gerald

2009-06-01

In this paper, we introduce a novel statistical modeling technique for target property prediction, with applications to virtual screening and drug design. In our method, we use graphs to model chemical structures and apply a wavelet analysis of graphs to summarize features capturing graph local topology. We design a novel graph kernel function to utilize the topology features to build predictive models for chemicals via Support Vector Machine classifier. We call the new graph kernel a graph wavelet-alignment kernel. We have evaluated the efficacy of the wavelet-alignment kernel using a set of chemical structure-activity prediction benchmarks. Our results indicate that the use of the kernel function yields performance profiles comparable to, and sometimes exceeding that of the existing state-of-the-art chemical classification approaches. In addition, our results also show that the use of wavelet functions significantly decreases the computational costs for graph kernel computation with more than ten fold speedup.

Small convolution kernels for high-fidelity image restoration

NASA Technical Reports Server (NTRS)

Reichenbach, Stephen E.; Park, Stephen K.

1991-01-01

An algorithm is developed for computing the mean-square-optimal values for small, image-restoration kernels. The algorithm is based on a comprehensive, end-to-end imaging system model that accounts for the important components of the imaging process: the statistics of the scene, the point-spread function of the image-gathering device, sampling effects, noise, and display reconstruction. Subject to constraints on the spatial support of the kernel, the algorithm generates the kernel values that restore the image with maximum fidelity, that is, the kernel minimizes the expected mean-square restoration error. The algorithm is consistent with the derivation of the spatially unconstrained Wiener filter, but leads to a small, spatially constrained kernel that, unlike the unconstrained filter, can be efficiently implemented by convolution. Simulation experiments demonstrate that for a wide range of imaging systems these small kernels can restore images with fidelity comparable to images restored with the unconstrained Wiener filter.

Reduced multiple empirical kernel learning machine.

PubMed

Wang, Zhe; Lu, MingZhe; Gao, Daqi

2015-02-01

Multiple kernel learning (MKL) is demonstrated to be flexible and effective in depicting heterogeneous data sources since MKL can introduce multiple kernels rather than a single fixed kernel into applications. However, MKL would get a high time and space complexity in contrast to single kernel learning, which is not expected in real-world applications. Meanwhile, it is known that the kernel mapping ways of MKL generally have two forms including implicit kernel mapping and empirical kernel mapping (EKM), where the latter is less attracted. In this paper, we focus on the MKL with the EKM, and propose a reduced multiple empirical kernel learning machine named RMEKLM for short. To the best of our knowledge, it is the first to reduce both time and space complexity of the MKL with EKM. Different from the existing MKL, the proposed RMEKLM adopts the Gauss Elimination technique to extract a set of feature vectors, which is validated that doing so does not lose much information of the original feature space. Then RMEKLM adopts the extracted feature vectors to span a reduced orthonormal subspace of the feature space, which is visualized in terms of the geometry structure. It can be demonstrated that the spanned subspace is isomorphic to the original feature space, which means that the dot product of two vectors in the original feature space is equal to that of the two corresponding vectors in the generated orthonormal subspace. More importantly, the proposed RMEKLM brings a simpler computation and meanwhile needs a less storage space, especially in the processing of testing. Finally, the experimental results show that RMEKLM owns a much efficient and effective performance in terms of both complexity and classification. The contributions of this paper can be given as follows: (1) by mapping the input space into an orthonormal subspace, the geometry of the generated subspace is visualized; (2) this paper first reduces both the time and space complexity of the EKM-based MKL; (3

Application of kernel functions for accurate similarity search in large chemical databases.

PubMed

Wang, Xiaohong; Huan, Jun; Smalter, Aaron; Lushington, Gerald H

2010-04-29

Similarity search in chemical structure databases is an important problem with many applications in chemical genomics, drug design, and efficient chemical probe screening among others. It is widely believed that structure based methods provide an efficient way to do the query. Recently various graph kernel functions have been designed to capture the intrinsic similarity of graphs. Though successful in constructing accurate predictive and classification models, graph kernel functions can not be applied to large chemical compound database due to the high computational complexity and the difficulties in indexing similarity search for large databases. To bridge graph kernel function and similarity search in chemical databases, we applied a novel kernel-based similarity measurement, developed in our team, to measure similarity of graph represented chemicals. In our method, we utilize a hash table to support new graph kernel function definition, efficient storage and fast search. We have applied our method, named G-hash, to large chemical databases. Our results show that the G-hash method achieves state-of-the-art performance for k-nearest neighbor (k-NN) classification. Moreover, the similarity measurement and the index structure is scalable to large chemical databases with smaller indexing size, and faster query processing time as compared to state-of-the-art indexing methods such as Daylight fingerprints, C-tree and GraphGrep. Efficient similarity query processing method for large chemical databases is challenging since we need to balance running time efficiency and similarity search accuracy. Our previous similarity search method, G-hash, provides a new way to perform similarity search in chemical databases. Experimental study validates the utility of G-hash in chemical databases.

A Fast Multiple-Kernel Method With Applications to Detect Gene-Environment Interaction.

PubMed

Marceau, Rachel; Lu, Wenbin; Holloway, Shannon; Sale, Michèle M; Worrall, Bradford B; Williams, Stephen R; Hsu, Fang-Chi; Tzeng, Jung-Ying

2015-09-01

Kernel machine (KM) models are a powerful tool for exploring associations between sets of genetic variants and complex traits. Although most KM methods use a single kernel function to assess the marginal effect of a variable set, KM analyses involving multiple kernels have become increasingly popular. Multikernel analysis allows researchers to study more complex problems, such as assessing gene-gene or gene-environment interactions, incorporating variance-component based methods for population substructure into rare-variant association testing, and assessing the conditional effects of a variable set adjusting for other variable sets. The KM framework is robust, powerful, and provides efficient dimension reduction for multifactor analyses, but requires the estimation of high dimensional nuisance parameters. Traditional estimation techniques, including regularization and the "expectation-maximization (EM)" algorithm, have a large computational cost and are not scalable to large sample sizes needed for rare variant analysis. Therefore, under the context of gene-environment interaction, we propose a computationally efficient and statistically rigorous "fastKM" algorithm for multikernel analysis that is based on a low-rank approximation to the nuisance effect kernel matrices. Our algorithm is applicable to various trait types (e.g., continuous, binary, and survival traits) and can be implemented using any existing single-kernel analysis software. Through extensive simulation studies, we show that our algorithm has similar performance to an EM-based KM approach for quantitative traits while running much faster. We also apply our method to the Vitamin Intervention for Stroke Prevention (VISP) clinical trial, examining gene-by-vitamin effects on recurrent stroke risk and gene-by-age effects on change in homocysteine level. © 2015 WILEY PERIODICALS, INC.

Physical and molecular changes during the storage of gluten-free rice and oat bread.

PubMed

Hager, Anna-Sophie; Bosmans, Geertrui M; Delcour, Jan A

2014-06-18

Gluten-free bread crumb generally firms more rapidly than regular wheat bread crumb. We here combined differential scanning calorimetry (DSC), texture analysis, and time-domain proton nuclear magnetic resonance (TD (1)H NMR) to investigate the mechanisms underlying firming of gluten-free rice and oat bread. The molecular mobility of water and biopolymers in flour/water model systems and changes thereof after heating and subsequent cooling to room temperature were investigated as a basis for underpinning the interpretation of TD (1)H NMR profiles of fresh crumb. The proton distributions of wheat and rice flour/water model systems were comparable, while that of oat flour/water samples showed less resolved peaks and an additional population at higher T2 relaxation times representing lipid protons. No significant crumb moisture loss during storage was observed for the gluten-free bread loaves. Crumb firming was mainly caused by amylopectin retrogradation and water redistribution within bread crumb. DSC, texture, and TD (1)H NMR data correlated well and showed that starch retrogradation and crumb firming are much more pronounced in rice flour bread than in oat flour bread.

7 CFR 981.61 - Redetermination of kernel weight.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 8 2010-01-01 2010-01-01 false Redetermination of kernel weight. 981.61 Section 981... GROWN IN CALIFORNIA Order Regulating Handling Volume Regulation § 981.61 Redetermination of kernel weight. The Board, on the basis of reports by handlers, shall redetermine the kernel weight of almonds...

Enhanced gluten properties in soft kernel durum wheat

USDA-ARS?s Scientific Manuscript database

Soft kernel durum wheat is a relatively recent development (Morris et al. 2011 Crop Sci. 51:114). The soft kernel trait exerts profound effects on kernel texture, flour milling including break flour yield, milling energy, and starch damage, and dough water absorption (DWA). With the caveat of reduce...

Accelerating the Original Profile Kernel.

PubMed

Hamp, Tobias; Goldberg, Tatyana; Rost, Burkhard

2013-01-01

One of the most accurate multi-class protein classification systems continues to be the profile-based SVM kernel introduced by the Leslie group. Unfortunately, its CPU requirements render it too slow for practical applications of large-scale classification tasks. Here, we introduce several software improvements that enable significant acceleration. Using various non-redundant data sets, we demonstrate that our new implementation reaches a maximal speed-up as high as 14-fold for calculating the same kernel matrix. Some predictions are over 200 times faster and render the kernel as possibly the top contender in a low ratio of speed/performance. Additionally, we explain how to parallelize various computations and provide an integrative program that reduces creating a production-quality classifier to a single program call. The new implementation is available as a Debian package under a free academic license and does not depend on commercial software. For non-Debian based distributions, the source package ships with a traditional Makefile-based installer. Download and installation instructions can be found at https://rostlab.org/owiki/index.php/Fast_Profile_Kernel. Bugs and other issues may be reported at https://rostlab.org/bugzilla3/enter_bug.cgi?product=fastprofkernel.

21 CFR 176.350 - Tamarind seed kernel powder.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 3 2014-04-01 2014-04-01 false Tamarind seed kernel powder. 176.350 Section 176... Paperboard § 176.350 Tamarind seed kernel powder. Tamarind seed kernel powder may be safely used as a component of articles intended for use in producing, manufacturing, packing, processing, preparing, treating...

7 CFR 981.60 - Determination of kernel weight.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 8 2010-01-01 2010-01-01 false Determination of kernel weight. 981.60 Section 981.60... Regulating Handling Volume Regulation § 981.60 Determination of kernel weight. (a) Almonds for which settlement is made on kernel weight. All lots of almonds, whether shelled or unshelled, for which settlement...

End-use quality of soft kernel durum wheat

USDA-ARS?s Scientific Manuscript database

Kernel texture is a major determinant of end-use quality of wheat. Durum wheat has very hard kernels. We developed soft kernel durum wheat via Ph1b-mediated homoeologous recombination. The Hardness locus was transferred from Chinese Spring to Svevo durum wheat via back-crossing. ‘Soft Svevo’ had SKC...

Spectral Kernel Approach to Study Radiative Response of Climate Variables and Interannual Variability of Reflected Solar Spectrum

NASA Technical Reports Server (NTRS)

Jin, Zhonghai; Wielicki, Bruce A.; Loukachine, Constantin; Charlock, Thomas P.; Young, David; Noeel, Stefan

2011-01-01

The radiative kernel approach provides a simple way to separate the radiative response to different climate parameters and to decompose the feedback into radiative and climate response components. Using CERES/MODIS/Geostationary data, we calculated and analyzed the solar spectral reflectance kernels for various climate parameters on zonal, regional, and global spatial scales. The kernel linearity is tested. Errors in the kernel due to nonlinearity can vary strongly depending on climate parameter, wavelength, surface, and solar elevation; they are large in some absorption bands for some parameters but are negligible in most conditions. The spectral kernels are used to calculate the radiative responses to different climate parameter changes in different latitudes. The results show that the radiative response in high latitudes is sensitive to the coverage of snow and sea ice. The radiative response in low latitudes is contributed mainly by cloud property changes, especially cloud fraction and optical depth. The large cloud height effect is confined to absorption bands, while the cloud particle size effect is found mainly in the near infrared. The kernel approach, which is based on calculations using CERES retrievals, is then tested by direct comparison with spectral measurements from Scanning Imaging Absorption Spectrometer for Atmospheric Cartography (SCIAMACHY) (a different instrument on a different spacecraft). The monthly mean interannual variability of spectral reflectance based on the kernel technique is consistent with satellite observations over the ocean, but not over land, where both model and data have large uncertainty. RMS errors in kernel ]derived monthly global mean reflectance over the ocean compared to observations are about 0.001, and the sampling error is likely a major component.

Multilevel image recognition using discriminative patches and kernel covariance descriptor

NASA Astrophysics Data System (ADS)

Lu, Le; Yao, Jianhua; Turkbey, Evrim; Summers, Ronald M.

2014-03-01

Computer-aided diagnosis of medical images has emerged as an important tool to objectively improve the performance, accuracy and consistency for clinical workflow. To computerize the medical image diagnostic recognition problem, there are three fundamental problems: where to look (i.e., where is the region of interest from the whole image/volume), image feature description/encoding, and similarity metrics for classification or matching. In this paper, we exploit the motivation, implementation and performance evaluation of task-driven iterative, discriminative image patch mining; covariance matrix based descriptor via intensity, gradient and spatial layout; and log-Euclidean distance kernel for support vector machine, to address these three aspects respectively. To cope with often visually ambiguous image patterns for the region of interest in medical diagnosis, discovery of multilabel selective discriminative patches is desired. Covariance of several image statistics summarizes their second order interactions within an image patch and is proved as an effective image descriptor, with low dimensionality compared with joint statistics and fast computation regardless of the patch size. We extensively evaluate two extended Gaussian kernels using affine-invariant Riemannian metric or log-Euclidean metric with support vector machines (SVM), on two medical image classification problems of degenerative disc disease (DDD) detection on cortical shell unwrapped CT maps and colitis detection on CT key images. The proposed approach is validated with promising quantitative results on these challenging tasks. Our experimental findings and discussion also unveil some interesting insights on the covariance feature composition with or without spatial layout for classification and retrieval, and different kernel constructions for SVM. This will also shed some light on future work using covariance feature and kernel classification for medical image analysis.

Safety of Adding Oats to a Gluten-Free Diet for Patients With Celiac Disease: Systematic Review and Meta-analysis of Clinical and Observational Studies.

PubMed

Pinto-Sánchez, María Inés; Causada-Calo, Natalia; Bercik, Premysl; Ford, Alexander C; Murray, Joseph A; Armstrong, David; Semrad, Carol; Kupfer, Sonia S; Alaedini, Armin; Moayyedi, Paul; Leffler, Daniel A; Verdú, Elena F; Green, Peter

2017-08-01

Patients with celiac disease should maintain a gluten-free diet (GFD), excluding wheat, rye, and barley. Oats might increase the nutritional value of a GFD, but their inclusion is controversial. We performed a systematic review and meta-analysis to evaluate the safety of oats as part of a GFD in patients with celiac disease. We searched the Cochrane Central Register of Controlled Trials, MEDLINE, and EMBASE databases for clinical trials and observational studies of the effects of including oats in GFD of patients with celiac disease. The studies reported patients' symptoms, results from serology tests, and findings from histologic analyses. We used the GRADE approach to assess the quality of evidence. We identified 433 studies; 28 were eligible for analysis. Of these, 6 were randomized and 2 were not randomized controlled trials comprising a total of 661 patients-the remaining studies were observational. All randomized controlled trials used pure/uncontaminated oats. Oat consumption for 12 months did not affect symptoms (standardized mean difference: reduction in symptom scores in patients who did and did not consume oats, -0.22; 95% CI, -0.56 to 0.13; P = .22), histologic scores (relative risk for histologic findings in patients who consumed oats, 0.24; 95% CI, 0.01-4.8; P = .35), intraepithelial lymphocyte counts (standardized mean difference, 0.21; 95% CI, reduction of 1.44 to increase in 1.86), or results from serologic tests. Subgroup analyses of adults vs children did not reveal differences. The overall quality of evidence was low. In a systematic review and meta-analysis, we found no evidence that addition of oats to a GFD affects symptoms, histology, immunity, or serologic features of patients with celiac disease. However, there were few studies for many endpoints, as well as limited geographic distribution and low quality of evidence. Rigorous double-blind, placebo-controlled, randomized controlled trials, using commonly available oats sourced from

Cadmium-induced accumulation of putrescine in oat and bean leaves

NASA Technical Reports Server (NTRS)

Weinstein, L. H.; Kaur-Sawhney, R.; Rajam, M. V.; Wettlaufer, S. H.; Galston, A. W.

1986-01-01

The effects of Cd2+ on putrescine (Put), spermidine (Spd), and spermine (Spm) titers were studied in oat and bean leaves. Treatment with Cd2+ for up to 16 hours in the light or dark resulted in a large increase in Put titer, but had little or no effect on Spd or Spm. The activity of arginine decarboxylase (ADC) followed the pattern of Put accumulation, and experiments with alpha-difluoromethylarginine established that ADC was the enzyme responsible for Put increase. Concentrations of Cd2+ as low as 10 micromolar increased Put titer in oat segments. In bean leaves, there was a Cd(2+)-induced accumulation of Put in the free and soluble conjugated fractions, but not in the insoluble fraction. This suggests a rapid exchange between Put that exists in the free form and Put found in acid soluble conjugate forms. It is concluded that Cd2+ can act like certain other stresses (K+ and Mg2+ deficiency, excess NH4+, low pH, salinity, osmotic stress, wilting) to induce substantial increases in Put in plant cells.

Molecular Basis of the Increase in Invertase Activity Elicited by Gravistimulation of Oat-Shoot Pulvini

NASA Technical Reports Server (NTRS)

Wu, Liu-Lai; Song, Il; Kim, Donghern; Kaufman, Peter B.

1993-01-01

An asymmetric (top vs. bottom) increase in invertase activity is elicited by gravistimulation in oatshoot pulvini starting within 3h after treatment. In order to analyze the regulation of invertase gene expression in this system, we examined the effect of gravistimulation on invertase mRNA induction. Total RNA and poly(A)(+)RNA, isolated from oat pulvini, and two oligonucleotide primers, corresponding to two conserved amino-acid sequences (NDPNG and WECPD) found in invertase from other species, were used for the Polymerase Chain Reaction (PCR). A partial-length cDNA (550 base pairs) was obtained and characterized. There was a 52 % deduced amino-acid sequence homology to that of carrot beta-fructosi- dase and a 48 % homology to that of tomato invertase. Northern blot analysis showed that there was an obvious transient accumulation of invertase mRNA elicited by gravistimulation of oat pulvini. The mRNA was rapidly induced to a maximum level at 1h following gravistimulation treatment and gradually decreased afterwards. The mRNA level in the bottom half of the oat pulvinus was significantly higher (five-fold) than that in the top half of the pulvinus tissue. The induction of invertase mRNA was consistent with the transient enhancement of invertase activity during the graviresponse of the pulvinus. These data indicate that the expression of the invertase gene(s) could be regulated by gravistimulation at the transcriptional and/or translational levels. Southern blot analysis showed that there were four genomic DNA fragments hybridized to the invertase cDNA. This suggests that an invertase gene family may exist in oat plants.

Deep Restricted Kernel Machines Using Conjugate Feature Duality.

PubMed

Suykens, Johan A K

2017-08-01

The aim of this letter is to propose a theory of deep restricted kernel machines offering new foundations for deep learning with kernel machines. From the viewpoint of deep learning, it is partially related to restricted Boltzmann machines, which are characterized by visible and hidden units in a bipartite graph without hidden-to-hidden connections and deep learning extensions as deep belief networks and deep Boltzmann machines. From the viewpoint of kernel machines, it includes least squares support vector machines for classification and regression, kernel principal component analysis (PCA), matrix singular value decomposition, and Parzen-type models. A key element is to first characterize these kernel machines in terms of so-called conjugate feature duality, yielding a representation with visible and hidden units. It is shown how this is related to the energy form in restricted Boltzmann machines, with continuous variables in a nonprobabilistic setting. In this new framework of so-called restricted kernel machine (RKM) representations, the dual variables correspond to hidden features. Deep RKM are obtained by coupling the RKMs. The method is illustrated for deep RKM, consisting of three levels with a least squares support vector machine regression level and two kernel PCA levels. In its primal form also deep feedforward neural networks can be trained within this framework.

Swedish children with celiac disease comply well with a gluten-free diet, and most include oats without reporting any adverse effects: a long-term follow-up study.

PubMed

Tapsas, Dimitrios; Fälth-Magnusson, Karin; Högberg, Lotta; Hammersjö, Jan-Åke; Hollén, Elisabet

2014-05-01

The only known treatment for celiac disease is a gluten-free diet (GFD), which initially meant abstention from wheat, rye, barley, and oats. Recently, oats free from contamination with wheat have been accepted in the GFD. Yet, reports indicate that all celiac disease patients may not tolerate oats. We hypothesized that celiac children comply well with a GFD and that most have included oats in their diet. A food questionnaire was used to check our patients; 316 questionnaires were returned. Mean time on the GFD was 6.9 years, and 96.8% of the children reported that they were trying to keep a strict GFD. However, accidental transgressions occurred in 263 children (83.2%). In 2 of 3 cases, mistakes took place when the patients were not at home. Symptoms after incidental gluten intake were experienced by 162 (61.6%) patients, mostly (87.5%) from the gastrointestinal tract. Small amounts of gluten (<4 g) caused symptoms in 38% of the cases, and 68% reported symptoms during the first 3 hours after gluten consumption. Oats were included in the diet of 89.4% of the children for a mean of 3.4 years. Most (81.9%) ate purified oats, and 45.3% consumed oats less than once a week. Among those who did not consume oats, only 5.9% refrained because of symptoms. General compliance with the GFD was good. Only the duration of the GFD appeared to influence adherence to the diet. Most patients did not report adverse effects after long-term consumption of oats. Copyright © 2014 Elsevier Inc. All rights reserved.

Improved modeling of clinical data with kernel methods.

PubMed

Daemen, Anneleen; Timmerman, Dirk; Van den Bosch, Thierry; Bottomley, Cecilia; Kirk, Emma; Van Holsbeke, Caroline; Valentin, Lil; Bourne, Tom; De Moor, Bart

2012-02-01

Despite the rise of high-throughput technologies, clinical data such as age, gender and medical history guide clinical management for most diseases and examinations. To improve clinical management, available patient information should be fully exploited. This requires appropriate modeling of relevant parameters. When kernel methods are used, traditional kernel functions such as the linear kernel are often applied to the set of clinical parameters. These kernel functions, however, have their disadvantages due to the specific characteristics of clinical data, being a mix of variable types with each variable its own range. We propose a new kernel function specifically adapted to the characteristics of clinical data. The clinical kernel function provides a better representation of patients' similarity by equalizing the influence of all variables and taking into account the range r of the variables. Moreover, it is robust with respect to changes in r. Incorporated in a least squares support vector machine, the new kernel function results in significantly improved diagnosis, prognosis and prediction of therapy response. This is illustrated on four clinical data sets within gynecology, with an average increase in test area under the ROC curve (AUC) of 0.023, 0.021, 0.122 and 0.019, respectively. Moreover, when combining clinical parameters and expression data in three case studies on breast cancer, results improved overall with use of the new kernel function and when considering both data types in a weighted fashion, with a larger weight assigned to the clinical parameters. The increase in AUC with respect to a standard kernel function and/or unweighted data combination was maximum 0.127, 0.042 and 0.118 for the three case studies. For clinical data consisting of variables of different types, the proposed kernel function--which takes into account the type and range of each variable--has shown to be a better alternative for linear and non-linear classification problems

Triso coating development progress for uranium nitride kernels

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

Jolly, Brian C.; Lindemer, Terrence; Terrani, Kurt A.

2015-08-01

In support of fully ceramic matrix (FCM) fuel development [1-2], coating development work is ongoing at the Oak Ridge National Laboratory (ORNL) to produce tri-structural isotropic (TRISO) coated fuel particles with UN kernels [3]. The nitride kernels are used to increase fissile density in these SiC-matrix fuel pellets with details described elsewhere [4]. The advanced gas reactor (AGR) program at ORNL used fluidized bed chemical vapor deposition (FBCVD) techniques for TRISO coating of UCO (two phase mixture of UO2 and UCx) kernels [5]. Similar techniques were employed for coating of the UN kernels, however significant changes in processing conditions weremore » required to maintain acceptable coating properties due to physical property and dimensional differences between the UCO and UN kernels (Table 1).« less

21 CFR 176.350 - Tamarind seed kernel powder.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 3 2011-04-01 2011-04-01 false Tamarind seed kernel powder. 176.350 Section 176... Substances for Use Only as Components of Paper and Paperboard § 176.350 Tamarind seed kernel powder. Tamarind seed kernel powder may be safely used as a component of articles intended for use in producing...

21 CFR 176.350 - Tamarind seed kernel powder.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 3 2012-04-01 2012-04-01 false Tamarind seed kernel powder. 176.350 Section 176... Substances for Use Only as Components of Paper and Paperboard § 176.350 Tamarind seed kernel powder. Tamarind seed kernel powder may be safely used as a component of articles intended for use in producing...

21 CFR 176.350 - Tamarind seed kernel powder.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Tamarind seed kernel powder. 176.350 Section 176... Substances for Use Only as Components of Paper and Paperboard § 176.350 Tamarind seed kernel powder. Tamarind seed kernel powder may be safely used as a component of articles intended for use in producing...

21 CFR 176.350 - Tamarind seed kernel powder.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 3 2013-04-01 2013-04-01 false Tamarind seed kernel powder. 176.350 Section 176... Substances for Use Only as Components of Paper and Paperboard § 176.350 Tamarind seed kernel powder. Tamarind seed kernel powder may be safely used as a component of articles intended for use in producing...

Prediction of heterotrimeric protein complexes by two-phase learning using neighboring kernels

PubMed Central

2014-01-01

Background Protein complexes play important roles in biological systems such as gene regulatory networks and metabolic pathways. Most methods for predicting protein complexes try to find protein complexes with size more than three. It, however, is known that protein complexes with smaller sizes occupy a large part of whole complexes for several species. In our previous work, we developed a method with several feature space mappings and the domain composition kernel for prediction of heterodimeric protein complexes, which outperforms existing methods. Results We propose methods for prediction of heterotrimeric protein complexes by extending techniques in the previous work on the basis of the idea that most heterotrimeric protein complexes are not likely to share the same protein with each other. We make use of the discriminant function in support vector machines (SVMs), and design novel feature space mappings for the second phase. As the second classifier, we examine SVMs and relevance vector machines (RVMs). We perform 10-fold cross-validation computational experiments. The results suggest that our proposed two-phase methods and SVM with the extended features outperform the existing method NWE, which was reported to outperform other existing methods such as MCL, MCODE, DPClus, CMC, COACH, RRW, and PPSampler for prediction of heterotrimeric protein complexes. Conclusions We propose two-phase prediction methods with the extended features, the domain composition kernel, SVMs and RVMs. The two-phase method with the extended features and the domain composition kernel using SVM as the second classifier is particularly useful for prediction of heterotrimeric protein complexes. PMID:24564744

Unified Heat Kernel Regression for Diffusion, Kernel Smoothing and Wavelets on Manifolds and Its Application to Mandible Growth Modeling in CT Images

PubMed Central

Chung, Moo K.; Qiu, Anqi; Seo, Seongho; Vorperian, Houri K.

2014-01-01

We present a novel kernel regression framework for smoothing scalar surface data using the Laplace-Beltrami eigenfunctions. Starting with the heat kernel constructed from the eigenfunctions, we formulate a new bivariate kernel regression framework as a weighted eigenfunction expansion with the heat kernel as the weights. The new kernel regression is mathematically equivalent to isotropic heat diffusion, kernel smoothing and recently popular diffusion wavelets. Unlike many previous partial differential equation based approaches involving diffusion, our approach represents the solution of diffusion analytically, reducing numerical inaccuracy and slow convergence. The numerical implementation is validated on a unit sphere using spherical harmonics. As an illustration, we have applied the method in characterizing the localized growth pattern of mandible surfaces obtained in CT images from subjects between ages 0 and 20 years by regressing the length of displacement vectors with respect to the template surface. PMID:25791435

Organic anion transporter 4 (OAT 4) modifies placental transfer of perfluorinated alkyl acids PFOS and PFOA in human placental ex vivo perfusion system.

PubMed

Kummu, M; Sieppi, E; Koponen, J; Laatio, L; Vähäkangas, K; Kiviranta, H; Rautio, A; Myllynen, P

2015-10-01

Perfluorinated alkyl acids (PFAAs) are widely used in industry and consumer products. Pregnant women are exposed to PFAAs and their presence in umbilical cord blood represents fetal exposure. Interestingly, PFAAs are substrates for organic anion transporters (OAT) of which OAT4 is expressed in human placenta. To evaluate the contribution of OAT4 and ATP-binding cassette transporter G2 (ABCG2) proteins in the transplacental transfer of perfluoro octane sulfonate (PFOS) and perfluoro octanoate (PFOA) an ex vivo dual recirculating human placental perfusion was used. Altogether 8 placentas from healthy mothers with uncomplicated pregnancies were successfully perfused. Both PFOS and PFOA crossed the placenta as suggested by in vivo data in the literature. The expression of OAT4 and ABCG2 proteins were studied by immunoblotting and correlation with the transfer index %(TI %) of PFOS and PFOA at 120 and 240 min (n = 4) was studied. The expression of OAT4 was in negative correlation with TI % of PFOA (R(2) = 0.92, p = 0.043) and PFOS (R(2) = 0.99, p = 0.007) at 120 min while at 240 min the correlation was statistically significant only with PFOA. The expression of ABCG2 did not correlate with TI% of PFOS or PFOA. Data obtained in this study suggest the involvement of OAT4 in placental passage of PFAAs. Placental passage of PFOS and PFOA is modified by the transporter protein OAT4 but not by ABCG2. This is the first study indicating that OAT4 may decrease the fetal exposure to PFAAs and protect the fetus after maternal exposure to PFAAs but further studies are needed to confirm our findings. Copyright © 2015 Elsevier Ltd. All rights reserved.

Molecular mapping of powdery mildew resistance gene Eg-3 in cultivated oat (Avena sativa L. cv. Rollo).

PubMed

Mohler, Volker; Zeller, Friedrich J; Hsam, Sai L K

2012-05-01

Powdery mildew is a prevalent fungal disease affecting oat (Avena sativa L.) production in Europe. Common oat cultivar Rollo was previously shown to carry the powdery mildew resistance gene Eg-3 in common with cultivar Mostyn. The resistance gene was mapped with restriction fragment length polymorphism (RFLP) markers from Triticeae group-1 chromosomes using a population of F(3) lines from a cross between A. byzantina cv. Kanota and A. sativa cv. Rollo. This comparative mapping approach positioned Eg-3 between cDNA-RFLP marker loci cmwg706 and cmwg733. Since both marker loci were derived from the long arm of barley chromosome 1H, the subchromosomal location of Eg-3 was assumed to be on the long arm of oat chromosome 17. Amplified fragment length polymorphism (AFLP) marker technology featured as an efficient means for obtaining markers closely linked to Eg-3.

In vitro characterization of the antivirulence target of Gram-positive pathogens, peptidoglycan O-acetyltransferase A (OatA)

DOE PAGES

Sychantha, David; Jones, Carys S.; Little, Dustin J.; ...

2017-10-27

The O-acetylation of the essential cell wall polymer peptidoglycan occurs in most Gram-positive bacterial pathogens, including species of Staphylococcus, Streptococcus and Enterococcus. This modification to peptidoglycan protects these pathogens from the lytic action of the lysozymes of innate immunity systems and, as such, is recognized as a virulence factor. The key enzyme involved, peptidoglycan O-acetyltransferase A (OatA) represents a particular challenge to biochemical study since it is a membrane associated protein whose substrate is the insoluble peptidoglycan cell wall polymer. OatA is predicted to be bimodular, being comprised of an N-terminal integral membrane domain linked to a C-terminal extracytoplasmic domain.more » We present herein the first biochemical and kinetic characterization of the C-terminal catalytic domain of OatA from two important human pathogens, Staphylococcus aureus and Streptococcus pneumoniae. Using both pseudosubstrates and novel biosynthetically-prepared peptidoglycan polymers, we characterized distinct substrate specificities for the two enzymes. In addition, the high resolution crystal structure of the C-terminal domain reveals an SGNH/GDSL-like hydrolase fold with a catalytic triad of amino acids but with a non-canonical oxyanion hole structure. Site-specific replacements confirmed the identity of the catalytic and oxyanion hole residues. A model is presented for the O-acetylation of peptidoglycan whereby the translocation of acetyl groups from a cytoplasmic source across the cytoplasmic membrane is catalyzed by the N-terminal domain of OatA for their transfer to peptidoglycan by its C-terminal domain. This study on the structure-function relationship of OatA provides a molecular and mechanistic understanding of this bacterial resistance mechanism opening the prospect for novel chemotherapeutic exploration to enhance innate immunity protection against Gram-positive pathogens.« less

In vitro characterization of the antivirulence target of Gram-positive pathogens, peptidoglycan O-acetyltransferase A (OatA)

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

Sychantha, David; Jones, Carys S.; Little, Dustin J.

The O-acetylation of the essential cell wall polymer peptidoglycan occurs in most Gram-positive bacterial pathogens, including species of Staphylococcus, Streptococcus and Enterococcus. This modification to peptidoglycan protects these pathogens from the lytic action of the lysozymes of innate immunity systems and, as such, is recognized as a virulence factor. The key enzyme involved, peptidoglycan O-acetyltransferase A (OatA) represents a particular challenge to biochemical study since it is a membrane associated protein whose substrate is the insoluble peptidoglycan cell wall polymer. OatA is predicted to be bimodular, being comprised of an N-terminal integral membrane domain linked to a C-terminal extracytoplasmic domain.more » We present herein the first biochemical and kinetic characterization of the C-terminal catalytic domain of OatA from two important human pathogens, Staphylococcus aureus and Streptococcus pneumoniae. Using both pseudosubstrates and novel biosynthetically-prepared peptidoglycan polymers, we characterized distinct substrate specificities for the two enzymes. In addition, the high resolution crystal structure of the C-terminal domain reveals an SGNH/GDSL-like hydrolase fold with a catalytic triad of amino acids but with a non-canonical oxyanion hole structure. Site-specific replacements confirmed the identity of the catalytic and oxyanion hole residues. A model is presented for the O-acetylation of peptidoglycan whereby the translocation of acetyl groups from a cytoplasmic source across the cytoplasmic membrane is catalyzed by the N-terminal domain of OatA for their transfer to peptidoglycan by its C-terminal domain. This study on the structure-function relationship of OatA provides a molecular and mechanistic understanding of this bacterial resistance mechanism opening the prospect for novel chemotherapeutic exploration to enhance innate immunity protection against Gram-positive pathogens.« less

In vitro characterization of the antivirulence target of Gram-positive pathogens, peptidoglycan O-acetyltransferase A (OatA)

PubMed Central

Sychantha, David; Jones, Carys S.; Little, Dustin J.; Howell, P. Lynne

2017-01-01

The O-acetylation of the essential cell wall polymer peptidoglycan occurs in most Gram-positive bacterial pathogens, including species of Staphylococcus, Streptococcus and Enterococcus. This modification to peptidoglycan protects these pathogens from the lytic action of the lysozymes of innate immunity systems and, as such, is recognized as a virulence factor. The key enzyme involved, peptidoglycan O-acetyltransferase A (OatA) represents a particular challenge to biochemical study since it is a membrane associated protein whose substrate is the insoluble peptidoglycan cell wall polymer. OatA is predicted to be bimodular, being comprised of an N-terminal integral membrane domain linked to a C-terminal extracytoplasmic domain. We present herein the first biochemical and kinetic characterization of the C-terminal catalytic domain of OatA from two important human pathogens, Staphylococcus aureus and Streptococcus pneumoniae. Using both pseudosubstrates and novel biosynthetically-prepared peptidoglycan polymers, we characterized distinct substrate specificities for the two enzymes. In addition, the high resolution crystal structure of the C-terminal domain reveals an SGNH/GDSL-like hydrolase fold with a catalytic triad of amino acids but with a non-canonical oxyanion hole structure. Site-specific replacements confirmed the identity of the catalytic and oxyanion hole residues. A model is presented for the O-acetylation of peptidoglycan whereby the translocation of acetyl groups from a cytoplasmic source across the cytoplasmic membrane is catalyzed by the N-terminal domain of OatA for their transfer to peptidoglycan by its C-terminal domain. This study on the structure-function relationship of OatA provides a molecular and mechanistic understanding of this bacterial resistance mechanism opening the prospect for novel chemotherapeutic exploration to enhance innate immunity protection against Gram-positive pathogens. PMID:29077761

A dynamic kernel modifier for linux

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

Minnich, R. G.

2002-09-03

Dynamic Kernel Modifier, or DKM, is a kernel module for Linux that allows user-mode programs to modify the execution of functions in the kernel without recompiling or modifying the kernel source in any way. Functions may be traced, either function entry only or function entry and exit; nullified; or replaced with some other function. For the tracing case, function execution results in the activation of a watchpoint. When the watchpoint is activated, the address of the function is logged in a FIFO buffer that is readable by external applications. The watchpoints are time-stamped with the resolution of the processor highmore » resolution timers, which on most modem processors are accurate to a single processor tick. DKM is very similar to earlier systems such as the SunOS trace device or Linux TT. Unlike these two systems, and other similar systems, DKM requires no kernel modifications. DKM allows users to do initial probing of the kernel to look for performance problems, or even to resolve potential problems by turning functions off or replacing them. DKM watchpoints are not without cost: it takes about 200 nanoseconds to make a log entry on an 800 Mhz Pentium-Ill. The overhead numbers are actually competitive with other hardware-based trace systems, although it has less 'Los Alamos National Laboratory is operated by the University of California for the National Nuclear Security Administration of the United States Department of Energy under contract W-7405-ENG-36. accuracy than an In-Circuit Emulator such as the American Arium. Once the user has zeroed in on a problem, other mechanisms with a higher degree of accuracy can be used.« less

Organic anion transporter 1 (OAT1/SLC22A6) enhances bioluminescence based on d-luciferin-luciferase reaction in living cells by facilitating the intracellular accumulation of d-luciferin.

PubMed

Furuya, Takahito; Takehara, Issey; Shimura, Asuka; Kishimoto, Hisanao; Yasujima, Tomoya; Ohta, Kinya; Shirasaka, Yoshiyuki; Yuasa, Hiroaki; Inoue, Katsuhisa

2018-01-15

Bioluminescence (BL) imaging based on d-luciferin (d-luc)-luciferase reaction allows noninvasive and real-time monitoring of luciferase-expressing cells. Because BL intensity depends on photons generated through the d-luc-luciferase reaction, an approach to increase intracellular levels of d-luc could improve the detection sensitivity. In the present study, we showed that organic anion transporter 1 (OAT1) is useful, as a d-luc transporter, in boosting the BL intensity in luciferase-expressing cells. Functional screening of several transporters showed that the expression of OAT1 in HEK293 cells stably expressing Pyrearinus termitilluminans luciferase (HEK293/eLuc) markedly enhanced BL intensity in the presence of d-luc. When OAT1 was transiently expressed in HEK293 cells, intracellular accumulation of d-luc was higher than that in control cells, and the specific d-luc uptake mediated by OAT1 was saturable with a Michaelis constant (K m ) of 0.23 μM. The interaction between OAT1 and d-luc was verified using 6-carboxyfluorescein, a typical substrate of OAT1, which showed that d-luc inhibited the uptake of 6-carboxyfluorescein mediated by OAT1. BL intensity was concentration-dependent at steady states in HEK293/eLuc cells stably expressing OAT1, and followed Michaelis-Menten kinetics with an apparent K m of 0.36 μM. In addition, the enhanced BL was significantly inhibited by OAT1-specific inhibitors. Thus, OAT1-mediated transport of d-luc could be a rate-limiting step in the d-luc-luciferase reaction. Furthermore, we found that expressing OAT1 in HEK293/eLuc cells implanted subcutaneously in mice also significantly increased the BL after intraperitoneal injection of d-luc. Our findings suggest that because OAT1 is capable of transporting d-luc, it can also be used to improve visualization and monitoring of luciferase-expressing cells. Copyright © 2017 Elsevier Inc. All rights reserved.

The difference between oats and beta-glucan extract intake in the management of HbA1c, fasting glucose and insulin sensitivity: a meta-analysis of randomized controlled trials.

PubMed

He, Li-xia; Zhao, Jian; Huang, Yuan-sheng; Li, Yong

2016-03-01

Increasing oats and beta-glucan extract intake has been associated with improved glycemic control, which is associated with the reduction in the development of diabetes. This study aims to assess the different effects between oat (whole and bran) and beta-glucan extract intake on glycemic control and insulin sensitivity. PubMed, Embase, Medline, The Cochrane Library, CINAHL and Web of Science were searched up to February 2014. We included randomized controlled trials with interventions that lasted at least four weeks that compared oats and beta-glucan (extracted from oats or other sources) intake with a control. A total of 1351 articles were screened for eligibility, and relevant data were extracted from 18 studies (n = 1024). Oat product dose ranged from 20 g d(-1) to 136 g d(-1), and beta-glucan extract dose ranged from 3 g d(-1) to 10 g d(-1). Compared with the control, oat intake resulted in a greater decrease in fasting glucose and insulin of subjects (P < 0.05), but beta-glucan extract intake did not. Furthermore, oat intake resulted in a greater decrease in glycosylated hemoglobin (HbA1c) (P < 0.001, I(2) = 0%) and fasting glucose (P < 0.001, I(2) = 68%) after removing one study using a concentrate and a different design and fasting insulin of type 2 diabetes (T2D) (P < 0.001, I(2) = 0%). The intake of oats and beta-glucan extracted from oats were effective in decreasing fasting glucose (P = 0.007, I(2) = 91%) and fasting insulin of T2D (P < 0.001, I(2) = 0%) and tented to lower HbA1c (P = 0.09, I(2) = 92%). Higher consumption of whole oats and oat bran, but not oat or barley beta-glucan extracts, are associated with lower HbA1c, fasting glucose and fasting insulin of T2D, hyperlipidaemic and overweight subjects, especially people with T2D, which supports the need for clinical trials to evaluate the potential role of oats in approaching to the management of glycemic control and insulin sensitivity of diabetes or metabolic syndrome subjects.

OATE Journal: Oklahoma Association of Teacher Educators. Volume 14, Spring 2010

ERIC Educational Resources Information Center

Green, Malinda Hendricks, Ed.

2010-01-01

The "OATE Journal" is published annually by the Oklahoma Association of Teacher Educators. Articles in this issue include: (1) "The Transition of Middle School Students into High School" by Aric Sappington, Malinda Hendricks Green, Jennifer J. R. Endicott, and Susan C. Scott; (2) "Graduate Students' Perceptions of Teacher…

Effects of dietary oat, barley, and guar gums on serum and liver lipid concentrations in diet-induced hypertriglyceridemic rats.

PubMed

Oda, T; Aoe, S; Imanishi, S; Kanazawa, Y; Sanada, H; Ayano, Y

1994-04-01

Effects of dietary oat, barley, and guar gums on serum and liver triglyceride or cholesterol concentrations were examined in diet-induced hypertriglyceridemic rats. Male Sprague-Dawley rats were fed a hypertriglyceridemic diet that contained 20% coconut oil, 17.5% fructose, 17.5% sucrose, and 5% cellulose at 4 weeks of age for 14 days. In the gum-supplemented diets, 2% cellulose was replaced by oat gum, barley gum, or guar gum. Hypertriglyceridemia was observed in the control group, whereas serum cholesterol concentration was not increased. All of the gums lowered serum and liver cholesterol concentrations except barley gum which had no significant effect on liver cholesterol. Both oat and barley gums suppressed the elevation of serum and liver triglyceride concentrations but guar gum had no effect.

Hadamard Kernel SVM with applications for breast cancer outcome predictions.

PubMed

Jiang, Hao; Ching, Wai-Ki; Cheung, Wai-Shun; Hou, Wenpin; Yin, Hong

2017-12-21

Breast cancer is one of the leading causes of deaths for women. It is of great necessity to develop effective methods for breast cancer detection and diagnosis. Recent studies have focused on gene-based signatures for outcome predictions. Kernel SVM for its discriminative power in dealing with small sample pattern recognition problems has attracted a lot attention. But how to select or construct an appropriate kernel for a specified problem still needs further investigation. Here we propose a novel kernel (Hadamard Kernel) in conjunction with Support Vector Machines (SVMs) to address the problem of breast cancer outcome prediction using gene expression data. Hadamard Kernel outperform the classical kernels and correlation kernel in terms of Area under the ROC Curve (AUC) values where a number of real-world data sets are adopted to test the performance of different methods. Hadamard Kernel SVM is effective for breast cancer predictions, either in terms of prognosis or diagnosis. It may benefit patients by guiding therapeutic options. Apart from that, it would be a valuable addition to the current SVM kernel families. We hope it will contribute to the wider biology and related communities.

Kernel Partial Least Squares for Nonlinear Regression and Discrimination

NASA Technical Reports Server (NTRS)

Rosipal, Roman; Clancy, Daniel (Technical Monitor)

2002-01-01

This paper summarizes recent results on applying the method of partial least squares (PLS) in a reproducing kernel Hilbert space (RKHS). A previously proposed kernel PLS regression model was proven to be competitive with other regularized regression methods in RKHS. The family of nonlinear kernel-based PLS models is extended by considering the kernel PLS method for discrimination. Theoretical and experimental results on a two-class discrimination problem indicate usefulness of the method.

Aggressiveness of loose kernel smut isolate from Johnson grass on sorghum line BTx643

USDA-ARS?s Scientific Manuscript database

An isolate of loose kernel smut obtained from Johnson grass was inoculated unto six BTx643 sorghum plants in the greenhouse to determine its aggressiveness. All the BTx643 sorghum plants inoculated with the Johnson grass isolate were infected. Mean size of the teliospores from the Johnson grass, i...

Aflatoxin contamination of developing corn kernels.

PubMed

Amer, M A

2005-01-01

Preharvest of corn and its contamination with aflatoxin is a serious problem. Some environmental and cultural factors responsible for infection and subsequent aflatoxin production were investigated in this study. Stage of growth and location of kernels on corn ears were found to be one of the important factors in the process of kernel infection with A. flavus & A. parasiticus. The results showed positive correlation between the stage of growth and kernel infection. Treatment of corn with aflatoxin reduced germination, protein and total nitrogen contents. Total and reducing soluble sugar was increase in corn kernels as response to infection. Sucrose and protein content were reduced in case of both pathogens. Shoot system length, seeding fresh weigh and seedling dry weigh was also affected. Both pathogens induced reduction of starch content. Healthy corn seedlings treated with aflatoxin solution were badly affected. Their leaves became yellow then, turned brown with further incubation. Moreover, their total chlorophyll and protein contents showed pronounced decrease. On the other hand, total phenolic compounds were increased. Histopathological studies indicated that A. flavus & A. parasiticus could colonize corn silks and invade developing kernels. Germination of A. flavus spores was occurred and hyphae spread rapidly across the silk, producing extensive growth and lateral branching. Conidiophores and conidia had formed in and on the corn silk. Temperature and relative humidity greatly influenced the growth of A. flavus & A. parasiticus and aflatoxin production.

High-density marker profiling confirms ancestral genomes of Avena species and identifies D-genome chromosomes of hexaploid oat.

PubMed

Yan, Honghai; Bekele, Wubishet A; Wight, Charlene P; Peng, Yuanying; Langdon, Tim; Latta, Robert G; Fu, Yong-Bi; Diederichsen, Axel; Howarth, Catherine J; Jellen, Eric N; Boyle, Brian; Wei, Yuming; Tinker, Nicholas A

2016-11-01

Genome analysis of 27 oat species identifies ancestral groups, delineates the D genome, and identifies ancestral origin of 21 mapped chromosomes in hexaploid oat. We investigated genomic relationships among 27 species of the genus Avena using high-density genetic markers revealed by genotyping-by-sequencing (GBS). Two methods of GBS analysis were used: one based on tag-level haplotypes that were previously mapped in cultivated hexaploid oat (A. sativa), and one intended to sample and enumerate tag-level haplotypes originating from all species under investigation. Qualitatively, both methods gave similar predictions regarding the clustering of species and shared ancestral genomes. Furthermore, results were consistent with previous phylogenies of the genus obtained with conventional approaches, supporting the robustness of whole genome GBS analysis. Evidence is presented to justify the final and definitive classification of the tetraploids A. insularis, A. maroccana (=A. magna), and A. murphyi as containing D-plus-C genomes, and not A-plus-C genomes, as is most often specified in past literature. Through electronic painting of the 21 chromosome representations in the hexaploid oat consensus map, we show how the relative frequency of matches between mapped hexaploid-derived haplotypes and AC (DC)-genome tetraploids vs. A- and C-genome diploids can accurately reveal the genome origin of all hexaploid chromosomes, including the approximate positions of inter-genome translocations. Evidence is provided that supports the continued classification of a diverged B genome in AB tetraploids, and it is confirmed that no extant A-genome diploids, including A. canariensis, are similar enough to the D genome of tetraploid and hexaploid oat to warrant consideration as a D-genome diploid.

Anthraquinones isolated from the browned Chinese chestnut kernels (Castanea mollissima blume)

NASA Astrophysics Data System (ADS)

Zhang, Y. L.; Qi, J. H.; Qin, L.; Wang, F.; Pang, M. X.

2016-08-01

Anthraquinones (AQS) represent a group of secondary metallic products in plants. AQS are often naturally occurring in plants and microorganisms. In a previous study, we found that AQS were produced by enzymatic browning reaction in Chinese chestnut kernels. To find out whether non-enzymatic browning reaction in the kernels could produce AQS too, AQS were extracted from three groups of chestnut kernels: fresh kernels, non-enzymatic browned kernels, and browned kernels, and the contents of AQS were determined. High performance liquid chromatography (HPLC) and nuclear magnetic resonance (NMR) methods were used to identify two compounds of AQS, rehein(1) and emodin(2). AQS were barely exists in the fresh kernels, while both browned kernel groups sample contained a high amount of AQS. Thus, we comfirmed that AQS could be produced during both enzymatic and non-enzymatic browning process. Rhein and emodin were the main components of AQS in the browned kernels.

A scalable kernel-based semisupervised metric learning algorithm with out-of-sample generalization ability.

PubMed

Yeung, Dit-Yan; Chang, Hong; Dai, Guang

2008-11-01

In recent years, metric learning in the semisupervised setting has aroused a lot of research interest. One type of semisupervised metric learning utilizes supervisory information in the form of pairwise similarity or dissimilarity constraints. However, most methods proposed so far are either limited to linear metric learning or unable to scale well with the data set size. In this letter, we propose a nonlinear metric learning method based on the kernel approach. By applying low-rank approximation to the kernel matrix, our method can handle significantly larger data sets. Moreover, our low-rank approximation scheme can naturally lead to out-of-sample generalization. Experiments performed on both artificial and real-world data show very promising results.

Performance Characteristics of a Kernel-Space Packet Capture Module

DTIC Science & Technology

2010-03-01

Defense, or the United States Government . AFIT/GCO/ENG/10-03 PERFORMANCE CHARACTERISTICS OF A KERNEL-SPACE PACKET CAPTURE MODULE THESIS Presented to the...3.1.2.3 Prototype. The proof of concept for this research is the design, development, and comparative performance analysis of a kernel level N2d capture...changes to kernel code 5. Can be used for both user-space and kernel-space capture applications in order to control comparative performance analysis to

Physical properties of gluten-free sugar cookies made from amaranth-oat composites

USDA-ARS?s Scientific Manuscript database

Amaranth flour containing the essential amino acid, lysine, was blended with oat products that contain ß-glucan known for lowering blood cholesterol and preventing heart disease. These composites improved nutritional value, water holding capacity and the pasting properties along with their gluten fr...

Functional properties of gluten-free sugar cookies made from amaranth-oat composites

USDA-ARS?s Scientific Manuscript database

Amaranth flour containing the essential amino acid, lysine, was blended with oat products that contain ß-glucan known for lowering blood cholesterol and preventing heart disease. These composites improved nutritional value, water holding capacity and the pasting properties along with their gluten fr...

Anatomically-Aided PET Reconstruction Using the Kernel Method

PubMed Central

Hutchcroft, Will; Wang, Guobao; Chen, Kevin T.; Catana, Ciprian; Qi, Jinyi

2016-01-01

This paper extends the kernel method that was proposed previously for dynamic PET reconstruction, to incorporate anatomical side information into the PET reconstruction model. In contrast to existing methods that incorporate anatomical information using a penalized likelihood framework, the proposed method incorporates this information in the simpler maximum likelihood (ML) formulation and is amenable to ordered subsets. The new method also does not require any segmentation of the anatomical image to obtain edge information. We compare the kernel method with the Bowsher method for anatomically-aided PET image reconstruction through a simulated data set. Computer simulations demonstrate that the kernel method offers advantages over the Bowsher method in region of interest (ROI) quantification. Additionally the kernel method is applied to a 3D patient data set. The kernel method results in reduced noise at a matched contrast level compared with the conventional ML expectation maximization (EM) algorithm. PMID:27541810

Anatomically-aided PET reconstruction using the kernel method.

PubMed

Hutchcroft, Will; Wang, Guobao; Chen, Kevin T; Catana, Ciprian; Qi, Jinyi

2016-09-21

This paper extends the kernel method that was proposed previously for dynamic PET reconstruction, to incorporate anatomical side information into the PET reconstruction model. In contrast to existing methods that incorporate anatomical information using a penalized likelihood framework, the proposed method incorporates this information in the simpler maximum likelihood (ML) formulation and is amenable to ordered subsets. The new method also does not require any segmentation of the anatomical image to obtain edge information. We compare the kernel method with the Bowsher method for anatomically-aided PET image reconstruction through a simulated data set. Computer simulations demonstrate that the kernel method offers advantages over the Bowsher method in region of interest quantification. Additionally the kernel method is applied to a 3D patient data set. The kernel method results in reduced noise at a matched contrast level compared with the conventional ML expectation maximization algorithm.

Anatomically-aided PET reconstruction using the kernel method

NASA Astrophysics Data System (ADS)

Hutchcroft, Will; Wang, Guobao; Chen, Kevin T.; Catana, Ciprian; Qi, Jinyi

2016-09-01

This paper extends the kernel method that was proposed previously for dynamic PET reconstruction, to incorporate anatomical side information into the PET reconstruction model. In contrast to existing methods that incorporate anatomical information using a penalized likelihood framework, the proposed method incorporates this information in the simpler maximum likelihood (ML) formulation and is amenable to ordered subsets. The new method also does not require any segmentation of the anatomical image to obtain edge information. We compare the kernel method with the Bowsher method for anatomically-aided PET image reconstruction through a simulated data set. Computer simulations demonstrate that the kernel method offers advantages over the Bowsher method in region of interest quantification. Additionally the kernel method is applied to a 3D patient data set. The kernel method results in reduced noise at a matched contrast level compared with the conventional ML expectation maximization algorithm.

Digital image sensor-based assessment of the status of oat (Avena sativa L.) crops after frost damage.

PubMed

Macedo-Cruz, Antonia; Pajares, Gonzalo; Santos, Matilde; Villegas-Romero, Isidro

2011-01-01

The aim of this paper is to classify the land covered with oat crops, and the quantification of frost damage on oats, while plants are still in the flowering stage. The images are taken by a digital colour camera CCD-based sensor. Unsupervised classification methods are applied because the plants present different spectral signatures, depending on two main factors: illumination and the affected state. The colour space used in this application is CIELab, based on the decomposition of the colour in three channels, because it is the closest to human colour perception. The histogram of each channel is successively split into regions by thresholding. The best threshold to be applied is automatically obtained as a combination of three thresholding strategies: (a) Otsu's method, (b) Isodata algorithm, and (c) Fuzzy thresholding. The fusion of these automatic thresholding techniques and the design of the classification strategy are some of the main findings of the paper, which allows an estimation of the damages and a prediction of the oat production.

Embedded real-time operating system micro kernel design

NASA Astrophysics Data System (ADS)

Cheng, Xiao-hui; Li, Ming-qiang; Wang, Xin-zheng

2005-12-01

Embedded systems usually require a real-time character. Base on an 8051 microcontroller, an embedded real-time operating system micro kernel is proposed consisting of six parts, including a critical section process, task scheduling, interruption handle, semaphore and message mailbox communication, clock managent and memory managent. Distributed CPU and other resources are among tasks rationally according to the importance and urgency. The design proposed here provides the position, definition, function and principle of micro kernel. The kernel runs on the platform of an ATMEL AT89C51 microcontroller. Simulation results prove that the designed micro kernel is stable and reliable and has quick response while operating in an application system.

Kernel Temporal Differences for Neural Decoding

PubMed Central

Bae, Jihye; Sanchez Giraldo, Luis G.; Pohlmeyer, Eric A.; Francis, Joseph T.; Sanchez, Justin C.; Príncipe, José C.

2015-01-01

We study the feasibility and capability of the kernel temporal difference (KTD)(λ) algorithm for neural decoding. KTD(λ) is an online, kernel-based learning algorithm, which has been introduced to estimate value functions in reinforcement learning. This algorithm combines kernel-based representations with the temporal difference approach to learning. One of our key observations is that by using strictly positive definite kernels, algorithm's convergence can be guaranteed for policy evaluation. The algorithm's nonlinear functional approximation capabilities are shown in both simulations of policy evaluation and neural decoding problems (policy improvement). KTD can handle high-dimensional neural states containing spatial-temporal information at a reasonable computational complexity allowing real-time applications. When the algorithm seeks a proper mapping between a monkey's neural states and desired positions of a computer cursor or a robot arm, in both open-loop and closed-loop experiments, it can effectively learn the neural state to action mapping. Finally, a visualization of the coadaptation process between the decoder and the subject shows the algorithm's capabilities in reinforcement learning brain machine interfaces. PMID:25866504

Online selective kernel-based temporal difference learning.

PubMed

Chen, Xingguo; Gao, Yang; Wang, Ruili

2013-12-01

In this paper, an online selective kernel-based temporal difference (OSKTD) learning algorithm is proposed to deal with large scale and/or continuous reinforcement learning problems. OSKTD includes two online procedures: online sparsification and parameter updating for the selective kernel-based value function. A new sparsification method (i.e., a kernel distance-based online sparsification method) is proposed based on selective ensemble learning, which is computationally less complex compared with other sparsification methods. With the proposed sparsification method, the sparsified dictionary of samples is constructed online by checking if a sample needs to be added to the sparsified dictionary. In addition, based on local validity, a selective kernel-based value function is proposed to select the best samples from the sample dictionary for the selective kernel-based value function approximator. The parameters of the selective kernel-based value function are iteratively updated by using the temporal difference (TD) learning algorithm combined with the gradient descent technique. The complexity of the online sparsification procedure in the OSKTD algorithm is O(n). In addition, two typical experiments (Maze and Mountain Car) are used to compare with both traditional and up-to-date O(n) algorithms (GTD, GTD2, and TDC using the kernel-based value function), and the results demonstrate the effectiveness of our proposed algorithm. In the Maze problem, OSKTD converges to an optimal policy and converges faster than both traditional and up-to-date algorithms. In the Mountain Car problem, OSKTD converges, requires less computation time compared with other sparsification methods, gets a better local optima than the traditional algorithms, and converges much faster than the up-to-date algorithms. In addition, OSKTD can reach a competitive ultimate optima compared with the up-to-date algorithms.

Kernel-based Linux emulation for Plan 9.

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

Minnich, Ronald G.

2010-09-01

CNKemu is a kernel-based system for the 9k variant of the Plan 9 kernel. It is designed to provide transparent binary support for programs compiled for IBM's Compute Node Kernel (CNK) on the Blue Gene series of supercomputers. This support allows users to build applications with the standard Blue Gene toolchain, including C++ and Fortran compilers. While the CNK is not Linux, IBM designed the CNK so that the user interface has much in common with the Linux 2.0 system call interface. The Plan 9 CNK emulator hence provides the foundation of kernel-based Linux system call support on Plan 9.more » In this paper we discuss cnkemu's implementation and some of its more interesting features, such as the ability to easily intermix Plan 9 and Linux system calls.« less

Gabor-based kernel PCA with fractional power polynomial models for face recognition.

PubMed

Liu, Chengjun

2004-05-01

This paper presents a novel Gabor-based kernel Principal Component Analysis (PCA) method by integrating the Gabor wavelet representation of face images and the kernel PCA method for face recognition. Gabor wavelets first derive desirable facial features characterized by spatial frequency, spatial locality, and orientation selectivity to cope with the variations due to illumination and facial expression changes. The kernel PCA method is then extended to include fractional power polynomial models for enhanced face recognition performance. A fractional power polynomial, however, does not necessarily define a kernel function, as it might not define a positive semidefinite Gram matrix. Note that the sigmoid kernels, one of the three classes of widely used kernel functions (polynomial kernels, Gaussian kernels, and sigmoid kernels), do not actually define a positive semidefinite Gram matrix either. Nevertheless, the sigmoid kernels have been successfully used in practice, such as in building support vector machines. In order to derive real kernel PCA features, we apply only those kernel PCA eigenvectors that are associated with positive eigenvalues. The feasibility of the Gabor-based kernel PCA method with fractional power polynomial models has been successfully tested on both frontal and pose-angled face recognition, using two data sets from the FERET database and the CMU PIE database, respectively. The FERET data set contains 600 frontal face images of 200 subjects, while the PIE data set consists of 680 images across five poses (left and right profiles, left and right half profiles, and frontal view) with two different facial expressions (neutral and smiling) of 68 subjects. The effectiveness of the Gabor-based kernel PCA method with fractional power polynomial models is shown in terms of both absolute performance indices and comparative performance against the PCA method, the kernel PCA method with polynomial kernels, the kernel PCA method with fractional power

Carbon balance assessment by eddy covariance method for agroecosystems with potato plants and oats & vetch mixture on sod-podzolic soils of Russia

NASA Astrophysics Data System (ADS)

Meshalkina, J. L.; Yaroslavtsev, A. M.; Vasenev, I. I.; Andreeva, I. V.; Tihonova, M. V.

2018-01-01

The carbon balance for the agroecosystems with potato plants and oats & vetch mixture on sod-podzolics soils was evaluated using the eddy covariance approach. Absorption of carbon was recorded only during the growing season; maximum values were detected for all crops in July. The number of days during the vegetation period, when the carbon stocked in the fields with potatoes and oats & vetch mixture was about the same and accounted for 53-55 days. During this period, the increase in gross primary production (GPP) is well correlated with the crop yields. The curve of the gross primary productivity is closely linked to the phases of development of plants; for potatoes, this graph differs significantly for all phases. Form of oats & vetch mixture biomass curve shown linear increases. Carbon losses were observed for all the studied agroecosystems: for fields with an oats & vetch mixture they were 254 g C m-2 y-1, while for fields with potato plants they were 307 g C m-2 y-1. Values about 250-300 g C m-2 per year may be considered as estimated values for the total carbon uptake for agroecosystems with potato plants and oats & vetch mixture on sod-podzolic soils.

Production of bio-based fiber gums from the waste streams resulting from the commercial processing of corn bran and oat hulls

USDA-ARS?s Scientific Manuscript database

The U.S. food and non-food industries would benefit from the development of a domestically produced crude, semi-pure and pure bio-based fiber gum from corn bran and oat hulls processing waste streams. When corn bran and oat hulls are processed to produce a commercial cellulose enriched fiber gel, th...

Genetic dissection of the maize kernel development process via conditional QTL mapping for three developing kernel-related traits in an immortalized F2 population.

PubMed

Zhang, Zhanhui; Wu, Xiangyuan; Shi, Chaonan; Wang, Rongna; Li, Shengfei; Wang, Zhaohui; Liu, Zonghua; Xue, Yadong; Tang, Guiliang; Tang, Jihua

2016-02-01

Kernel development is an important dynamic trait that determines the final grain yield in maize. To dissect the genetic basis of maize kernel development process, a conditional quantitative trait locus (QTL) analysis was conducted using an immortalized F2 (IF2) population comprising 243 single crosses at two locations over 2 years. Volume (KV) and density (KD) of dried developing kernels, together with kernel weight (KW) at different developmental stages, were used to describe dynamic changes during kernel development. Phenotypic analysis revealed that final KW and KD were determined at DAP22 and KV at DAP29. Unconditional QTL mapping for KW, KV and KD uncovered 97 QTLs at different kernel development stages, of which qKW6b, qKW7a, qKW7b, qKW10b, qKW10c, qKV10a, qKV10b and qKV7 were identified under multiple kernel developmental stages and environments. Among the 26 QTLs detected by conditional QTL mapping, conqKW7a, conqKV7a, conqKV10a, conqKD2, conqKD7 and conqKD8a were conserved between the two mapping methodologies. Furthermore, most of these QTLs were consistent with QTLs and genes for kernel development/grain filling reported in previous studies. These QTLs probably contain major genes associated with the kernel development process, and can be used to improve grain yield and quality through marker-assisted selection.

A trace ratio maximization approach to multiple kernel-based dimensionality reduction.

PubMed

Jiang, Wenhao; Chung, Fu-lai

2014-01-01

Most dimensionality reduction techniques are based on one metric or one kernel, hence it is necessary to select an appropriate kernel for kernel-based dimensionality reduction. Multiple kernel learning for dimensionality reduction (MKL-DR) has been recently proposed to learn a kernel from a set of base kernels which are seen as different descriptions of data. As MKL-DR does not involve regularization, it might be ill-posed under some conditions and consequently its applications are hindered. This paper proposes a multiple kernel learning framework for dimensionality reduction based on regularized trace ratio, termed as MKL-TR. Our method aims at learning a transformation into a space of lower dimension and a corresponding kernel from the given base kernels among which some may not be suitable for the given data. The solutions for the proposed framework can be found based on trace ratio maximization. The experimental results demonstrate its effectiveness in benchmark datasets, which include text, image and sound datasets, for supervised, unsupervised as well as semi-supervised settings. Copyright © 2013 Elsevier Ltd. All rights reserved.

Detection of maize kernels breakage rate based on K-means clustering

NASA Astrophysics Data System (ADS)

Yang, Liang; Wang, Zhuo; Gao, Lei; Bai, Xiaoping

2017-04-01

In order to optimize the recognition accuracy of maize kernels breakage detection and improve the detection efficiency of maize kernels breakage, this paper using computer vision technology and detecting of the maize kernels breakage based on K-means clustering algorithm. First, the collected RGB images are converted into Lab images, then the original images clarity evaluation are evaluated by the energy function of Sobel 8 gradient. Finally, the detection of maize kernels breakage using different pixel acquisition equipments and different shooting angles. In this paper, the broken maize kernels are identified by the color difference between integrity kernels and broken kernels. The original images clarity evaluation and different shooting angles are taken to verify that the clarity and shooting angles of the images have a direct influence on the feature extraction. The results show that K-means clustering algorithm can distinguish the broken maize kernels effectively.

Kernel and Traditional Equipercentile Equating with Degrees of Presmoothing. Research Report. ETS RR-07-15

ERIC Educational Resources Information Center

Moses, Tim; Holland, Paul

2007-01-01

The purpose of this study was to empirically evaluate the impact of loglinear presmoothing accuracy on equating bias and variability across chained and post-stratification equating methods, kernel and percentile-rank continuization methods, and sample sizes. The results of evaluating presmoothing on equating accuracy generally agreed with those of…

Stochastic subset selection for learning with kernel machines.

PubMed

Rhinelander, Jason; Liu, Xiaoping P

2012-06-01

Kernel machines have gained much popularity in applications of machine learning. Support vector machines (SVMs) are a subset of kernel machines and generalize well for classification, regression, and anomaly detection tasks. The training procedure for traditional SVMs involves solving a quadratic programming (QP) problem. The QP problem scales super linearly in computational effort with the number of training samples and is often used for the offline batch processing of data. Kernel machines operate by retaining a subset of observed data during training. The data vectors contained within this subset are referred to as support vectors (SVs). The work presented in this paper introduces a subset selection method for the use of kernel machines in online, changing environments. Our algorithm works by using a stochastic indexing technique when selecting a subset of SVs when computing the kernel expansion. The work described here is novel because it separates the selection of kernel basis functions from the training algorithm used. The subset selection algorithm presented here can be used in conjunction with any online training technique. It is important for online kernel machines to be computationally efficient due to the real-time requirements of online environments. Our algorithm is an important contribution because it scales linearly with the number of training samples and is compatible with current training techniques. Our algorithm outperforms standard techniques in terms of computational efficiency and provides increased recognition accuracy in our experiments. We provide results from experiments using both simulated and real-world data sets to verify our algorithm.

RTOS kernel in portable electrocardiograph

NASA Astrophysics Data System (ADS)

Centeno, C. A.; Voos, J. A.; Riva, G. G.; Zerbini, C.; Gonzalez, E. A.

2011-12-01

This paper presents the use of a Real Time Operating System (RTOS) on a portable electrocardiograph based on a microcontroller platform. All medical device digital functions are performed by the microcontroller. The electrocardiograph CPU is based on the 18F4550 microcontroller, in which an uCOS-II RTOS can be embedded. The decision associated with the kernel use is based on its benefits, the license for educational use and its intrinsic time control and peripherals management. The feasibility of its use on the electrocardiograph is evaluated based on the minimum memory requirements due to the kernel structure. The kernel's own tools were used for time estimation and evaluation of resources used by each process. After this feasibility analysis, the migration from cyclic code to a structure based on separate processes or tasks able to synchronize events is used; resulting in an electrocardiograph running on one Central Processing Unit (CPU) based on RTOS.

Phase behaviour of oat β-glucan/sodium caseinate mixtures varying in molecular weight.

PubMed

Agbenorhevi, Jacob K; Kontogiorgos, Vassilis; Kasapis, Stefan

2013-05-01

The isothermal phase behaviour at 5 °C of mixtures of sodium caseinate and oat β-glucan isolates varying in molecular weight (MW) was investigated by means of phase diagram construction, rheometry, fluorescence microscopy and electrophoresis. Phase diagrams indicated that the compatibility of the β-glucan/sodium caseinate system increases as β-glucan MW decreases. Images of mixtures taken at various biopolymer concentrations revealed phase separated domains. Results also revealed that at the state of thermodynamic equilibrium, lower MW samples yielded considerable viscosity in the mixture. At equivalent hydrodynamic volume of β-glucan in the mixtures, samples varying in molecular weight exhibited similar flow behaviour. A deviation dependent on the protein concentration was observed for the high MW sample in the concentrated regime due to the size of β-glucan aggregates formed. Results demonstrate that by controlling the structural features of β-glucan in mixtures with sodium caseinate, informed manipulation of rheological properties in these systems can be achieved. Copyright © 2012 Elsevier Ltd. All rights reserved.

A Robustness Testing Campaign for IMA-SP Partitioning Kernels

NASA Astrophysics Data System (ADS)

Grixti, Stephen; Lopez Trecastro, Jorge; Sammut, Nicholas; Zammit-Mangion, David

2015-09-01

With time and space partitioned architectures becoming increasingly appealing to the European space sector, the dependability of partitioning kernel technology is a key factor to its applicability in European Space Agency projects. This paper explores the potential of the data type fault model, which injects faults through the Application Program Interface, in partitioning kernel robustness testing. This fault injection methodology has been tailored to investigate its relevance in uncovering vulnerabilities within partitioning kernels and potentially contributing towards fault removal campaigns within this domain. This is demonstrated through a robustness testing case study of the XtratuM partitioning kernel for SPARC LEON3 processors. The robustness campaign exposed a number of vulnerabilities in XtratuM, exhibiting the potential benefits of using such a methodology for the robustness assessment of partitioning kernels.

Shifts in comparative advantages for maize, oat and wheat cropping under climate change in Europe.

PubMed

Elsgaard, L; Børgesen, C D; Olesen, J E; Siebert, S; Ewert, F; Peltonen-Sainio, P; Rötter, R P; Skjelvåg, A O

2012-01-01

Climate change is anticipated to affect European agriculture, including the risk of emerging or re-emerging feed and food hazards. Indirectly, climate change may influence such hazards (e.g. the occurrence of mycotoxins) due to geographic shifts in the distribution of major cereal cropping systems and the consequences this may have for crop rotations. This paper analyses the impact of climate on cropping shares of maize, oat and wheat on a 50-km square grid across Europe (45-65°N) and provides model-based estimates of the changes in cropping shares in response to changes in temperature and precipitation as projected for the time period around 2040 by two regional climate models (RCM) with a moderate and a strong climate change signal, respectively. The projected cropping shares are based on the output from the two RCMs and on algorithms derived for the relation between meteorological data and observed cropping shares of maize, oat and wheat. The observed cropping shares show a south-to-north gradient, where maize had its maximum at 45-55°N, oat had its maximum at 55-65°N, and wheat was more evenly distributed along the latitudes in Europe. Under the projected climate changes, there was a general increase in maize cropping shares, whereas for oat no areas showed distinct increases. For wheat, the projected changes indicated a tendency towards higher cropping shares in the northern parts and lower cropping shares in the southern parts of the study area. The present modelling approach represents a simplification of factors determining the distribution of cereal crops, and also some uncertainties in the data basis were apparent. A promising way of future model improvement could be through a systematic analysis and inclusion of other variables, such as key soil properties and socio-economic conditions, influencing the comparative advantages of specific crops.

Microwave-Assisted Alkali Pre-Treatment, Densification and Enzymatic Saccharification of Canola Straw and Oat Hull

PubMed Central

Agu, Obiora S.; Tabil, Lope G.; Dumonceaux, Tim

2017-01-01

The effects of microwave-assisted alkali pre-treatment on pellets’ characteristics and enzymatic saccharification for bioethanol production using lignocellulosic biomass of canola straw and oat hull were investigated. The ground canola straw and oat hull were immersed in distilled water, sodium hydroxide and potassium hydroxide solutions at two concentrations (0.75% and 1.5% w/v) and exposed to microwave radiation at power level 713 W and three residence times (6, 12 and 18 min). Bulk and particle densities of ground biomass samples were determined. Alkaline-microwave pre-treated and untreated samples were subjected to single pelleting test in an Instron universal machine, pre-set to a load of 4000 N. The measured parameters, pellet density, tensile strength and dimensional stability were evaluated and the results showed that the microwave-assisted alkali pre-treated pellets had a significantly higher density and tensile strength compared to samples that were untreated or pre-treated by microwave alone. The chemical composition analysis showed that microwave-assisted alkali pre-treatment was able to disrupt and break down the lignocellulosic structure of the samples, creating an area of cellulose accessible to cellulase reactivity. The best enzymatic saccharification results gave a high glucose yield of 110.05 mg/g dry sample for canola straw ground in a 1.6 mm screen hammer mill and pre-treated with 1.5% NaOH for 18 min, and a 99.10 mg/g dry sample for oat hull ground in a 1.6 mm screen hammer mill and pre-treated with 0.75% NaOH for 18 min microwave-assisted alkali pre-treatments. The effects of pre-treatment results were supported by SEM analysis. Overall, it was found that microwave-assisted alkali pre-treatment of canola straw and oat hull at a short residence time enhanced glucose yield. PMID:28952504

Microwave-Assisted Alkali Pre-Treatment, Densification and Enzymatic Saccharification of Canola Straw and Oat Hull.

PubMed

Agu, Obiora S; Tabil, Lope G; Dumonceaux, Tim

2017-03-26

The effects of microwave-assisted alkali pre-treatment on pellets' characteristics and enzymatic saccharification for bioethanol production using lignocellulosic biomass of canola straw and oat hull were investigated. The ground canola straw and oat hull were immersed in distilled water, sodium hydroxide and potassium hydroxide solutions at two concentrations (0.75% and 1.5% w/v) and exposed to microwave radiation at power level 713 W and three residence times (6, 12 and 18 min). Bulk and particle densities of ground biomass samples were determined. Alkaline-microwave pre-treated and untreated samples were subjected to single pelleting test in an Instron universal machine, pre-set to a load of 4000 N. The measured parameters, pellet density, tensile strength and dimensional stability were evaluated and the results showed that the microwave-assisted alkali pre-treated pellets had a significantly higher density and tensile strength compared to samples that were untreated or pre-treated by microwave alone. The chemical composition analysis showed that microwave-assisted alkali pre-treatment was able to disrupt and break down the lignocellulosic structure of the samples, creating an area of cellulose accessible to cellulase reactivity. The best enzymatic saccharification results gave a high glucose yield of 110.05 mg/g dry sample for canola straw ground in a 1.6 mm screen hammer mill and pre-treated with 1.5% NaOH for 18 min, and a 99.10 mg/g dry sample for oat hull ground in a 1.6 mm screen hammer mill and pre-treated with 0.75% NaOH for 18 min microwave-assisted alkali pre-treatments. The effects of pre-treatment results were supported by SEM analysis. Overall, it was found that microwave-assisted alkali pre-treatment of canola straw and oat hull at a short residence time enhanced glucose yield.

Effects of oat β-glucan consumption at breakfast on ad libitum eating, appetite, glycemia, insulinemia and GLP-1 concentrations in healthy subjects.

PubMed

Zaremba, Suzanne M M; Gow, Iain F; Drummond, Sandra; McCluskey, Jane T; Steinert, Robert E

2018-06-18

There is evidence that oat β-glucan lowers appetite and ad libitum eating; however, not all studies are consistent, and the underpinning mechanisms are not entirely understood. We investigated the effects of 4 g high molecular weight (MW) oat β-glucan on ad libitum eating, subjective appetite, glycemia, insulinemia and plasma GLP-1 responses in 33 normal-weight subjects (22 female/11 male, mean age (y): 26.9 ± 1.0, BMI (kg/m 2 ): 23.5 ± 0.4). The study followed a randomised double-blind, cross-over design with subjects fed two test breakfasts with and without oat β-glucan followed by an ad libitum test meal on two different days. Blood samples and ratings for subjective appetite were collected postprandially at regular time intervals. Oat β-glucan increased feelings of fullness (p = 0.048) and satiety (p = 0.034), but did not affect energy and amount eaten at the ad libitum test meal. There was a treatment by time interaction for plasma GLP-1, plasma insulin and blood glucose. GLP-1 was significantly reduced at 90 min (p = 0.021), blood glucose at 30 min (p = 0.008) and plasma insulin at 30 and 60 min (p = 0.002 and 0.017, respectively) following the oat β-glucan breakfast when compared with the control breakfast. Four grams of high MW oat β-glucan lowers appetite but not ad libitum eating and beneficially modulates postprandial glycaemia, it does however, not increase plasma GLP-1 secretion. Copyright © 2018 Elsevier Ltd. All rights reserved.

The effect of relatedness and pack size on territory overlap in African wild dogs.

PubMed

Jackson, Craig R; Groom, Rosemary J; Jordan, Neil R; McNutt, J Weldon

2017-01-01

Spacing patterns mediate competitive interactions between conspecifics, ultimately increasing fitness. The degree of territorial overlap between neighbouring African wild dog ( Lycaon pictus ) packs varies greatly, yet the role of factors potentially affecting the degree of overlap, such as relatedness and pack size, remain unclear. We used movement data from 21 wild dog packs to calculate the extent of territory overlap (20 dyads). On average, unrelated neighbouring packs had low levels of overlap restricted to the peripheral regions of their 95% utilisation kernels. Related neighbours had significantly greater levels of peripheral overlap. Only one unrelated dyad included overlap between 75%-75% kernels, but no 50%-50% kernels overlapped. However, eight of 12 related dyads overlapped between their respective 75% kernels and six between the frequented 50% kernels. Overlap between these more frequented kernels confers a heightened likelihood of encounter, as the mean utilisation intensity per unit area within the 50% kernels was 4.93 times greater than in the 95% kernels, and 2.34 times greater than in the 75% kernels. Related packs spent significantly more time in their 95% kernel overlap zones than did unrelated packs. Pack size appeared to have little effect on overlap between related dyads, yet among unrelated neighbours larger packs tended to overlap more onto smaller packs' territories. However, the true effect is unclear given that the model's confidence intervals overlapped zero. Evidence suggests that costly intraspecific aggression is greatly reduced between related packs. Consequently, the tendency for dispersing individuals to establish territories alongside relatives, where intensively utilised portions of ranges regularly overlap, may extend kin selection and inclusive fitness benefits from the intra-pack to inter-pack level. This natural spacing system can affect survival parameters and the carrying capacity of protected areas, having important

Multi-board kernel communication using socket programming for embedded applications

NASA Astrophysics Data System (ADS)

Mishra, Ashish; Girdhar, Neha; Krishnia, Nikita

2016-03-01

It is often seen in large application projects, there is a need to communicate between two different processors or two different kernels. The aim of this paper is to communicate between two different kernels and use efficient method to do so. The TCP/IP protocol is implemented to communicate between two boards via the Ethernet port and use lwIP (lightweight IP) stack, which is a smaller independent implementation of the TCP/IP stack suitable for use in embedded systems. While retaining TCP/IP functionality, lwIP stack reduces the use of memory and even size of the code. In this process of communication we made Raspberry pi as an active client and Field programmable gate array(FPGA) board as a passive server and they are allowed to communicate via Ethernet. Three applications based on TCP/IP client-server network communication have been implemented. The Echo server application is used to communicate between two different kernels of two different boards. Socket programming is used as it is independent of platform and programming language used. TCP transmit and receive throughput test applications are used to measure maximum throughput of the transmission of data. These applications are based on communication to an open source tool called iperf. It is used to measure the throughput transmission rate by sending or receiving some constant piece of data to the client or server according to the test application.

Searching for efficient Markov chain Monte Carlo proposal kernels

PubMed Central

Yang, Ziheng; Rodríguez, Carlos E.

2013-01-01

Markov chain Monte Carlo (MCMC) or the Metropolis–Hastings algorithm is a simulation algorithm that has made modern Bayesian statistical inference possible. Nevertheless, the efficiency of different Metropolis–Hastings proposal kernels has rarely been studied except for the Gaussian proposal. Here we propose a unique class of Bactrian kernels, which avoid proposing values that are very close to the current value, and compare their efficiency with a number of proposals for simulating different target distributions, with efficiency measured by the asymptotic variance of a parameter estimate. The uniform kernel is found to be more efficient than the Gaussian kernel, whereas the Bactrian kernel is even better. When optimal scales are used for both, the Bactrian kernel is at least 50% more efficient than the Gaussian. Implementation in a Bayesian program for molecular clock dating confirms the general applicability of our results to generic MCMC algorithms. Our results refute a previous claim that all proposals had nearly identical performance and will prompt further research into efficient MCMC proposals. PMID:24218600

Comparison of acid-induced cell wall loosening in Valonia ventricosa and in oat coleoptiles

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

Tepfer, M.; Cleland, R.E.

The acid-induced loosening of cell walls of Valonia ventricosa has been compared to that of frozen-thawed oat coleoptiles. The two acid extension responses are similar in regard to the shape of the pH response curve and the increase in plastic compliance induced by acid treatment. In both systems the acid response can be inhibited by Ca/sup 2 +/ and in both the removal of the protons leads to a rapid termination of wall loosening. The two responses differ in several significant ways, however. The acid-induced extension of Valonia walls is more rapid than that of coleoptile walls, but of smallermore » total magnitude. Acid-induced loosening can occur in Valonia without the wall being under tension, but not in coleoptiles. The acid-induced extension of Valonia walls is not inhibited by 8 molar urea, whereas the response in oat coleoptiles is completely inhibited by this treatment. Ethylenediaminetetraacetate (EDTA) can cause wall loosening in Valonia comparable to that produced by low pH, whereas in coleoptiles EDTA causes a much smaller response. These results with Valonia are consistent with a mechanism of acid-induced wall loosening in which a central role is played by the displacement of Ca/sup 2 +/ from the wall, while the larger part of acid-induced wall loosening in oat coleoptiles appears to be via a different mechanism.« less

Spatiotemporal Domain Decomposition for Massive Parallel Computation of Space-Time Kernel Density

NASA Astrophysics Data System (ADS)

Hohl, A.; Delmelle, E. M.; Tang, W.

2015-07-01

Accelerated processing capabilities are deemed critical when conducting analysis on spatiotemporal datasets of increasing size, diversity and availability. High-performance parallel computing offers the capacity to solve computationally demanding problems in a limited timeframe, but likewise poses the challenge of preventing processing inefficiency due to workload imbalance between computing resources. Therefore, when designing new algorithms capable of implementing parallel strategies, careful spatiotemporal domain decomposition is necessary to account for heterogeneity in the data. In this study, we perform octtree-based adaptive decomposition of the spatiotemporal domain for parallel computation of space-time kernel density. In order to avoid edge effects near subdomain boundaries, we establish spatiotemporal buffers to include adjacent data-points that are within the spatial and temporal kernel bandwidths. Then, we quantify computational intensity of each subdomain to balance workloads among processors. We illustrate the benefits of our methodology using a space-time epidemiological dataset of Dengue fever, an infectious vector-borne disease that poses a severe threat to communities in tropical climates. Our parallel implementation of kernel density reaches substantial speedup compared to sequential processing, and achieves high levels of workload balance among processors due to great accuracy in quantifying computational intensity. Our approach is portable of other space-time analytical tests.

Defect Analysis Of Quality Palm Kernel Meal Using Statistical Quality Control In Kernels Factory

NASA Astrophysics Data System (ADS)

Sembiring, M. T.; Marbun, N. J.

2018-04-01

The production quality has an important impact retain the totality of characteristics of a product or service to pay attention to its capabilities to meet the needs that have been established. Quality criteria Palm Kernel Meal (PKM) set Factory kernel is as follows: oil content: max 8.50%, water content: max 12,00% and impurity content: max 4.00% While the average quality of the oil content of 8.94%, the water content of 5.51%, and 8.45% impurity content. To identify the defective product quality PKM produced, then used a method of analysis using Statistical Quality Control (SQC). PKM Plant Quality Kernel shows the oil content was 0.44% excess of a predetermined maximum value, and 4.50% impurity content. With excessive PKM content of oil and dirt cause disability content of production for oil, amounted to 854.6078 kg PKM and 8643.193 kg impurity content of PKM. Analysis of the results of cause and effect diagram and SQC, the factors that lead to poor quality of PKM is Ampere second press oil expeller and hours second press oil expeller.

Scuba: scalable kernel-based gene prioritization.

PubMed

Zampieri, Guido; Tran, Dinh Van; Donini, Michele; Navarin, Nicolò; Aiolli, Fabio; Sperduti, Alessandro; Valle, Giorgio

2018-01-25

The uncovering of genes linked to human diseases is a pressing challenge in molecular biology and precision medicine. This task is often hindered by the large number of candidate genes and by the heterogeneity of the available information. Computational methods for the prioritization of candidate genes can help to cope with these problems. In particular, kernel-based methods are a powerful resource for the integration of heterogeneous biological knowledge, however, their practical implementation is often precluded by their limited scalability. We propose Scuba, a scalable kernel-based method for gene prioritization. It implements a novel multiple kernel learning approach, based on a semi-supervised perspective and on the optimization of the margin distribution. Scuba is optimized to cope with strongly unbalanced settings where known disease genes are few and large scale predictions are required. Importantly, it is able to efficiently deal both with a large amount of candidate genes and with an arbitrary number of data sources. As a direct consequence of scalability, Scuba integrates also a new efficient strategy to select optimal kernel parameters for each data source. We performed cross-validation experiments and simulated a realistic usage setting, showing that Scuba outperforms a wide range of state-of-the-art methods. Scuba achieves state-of-the-art performance and has enhanced scalability compared to existing kernel-based approaches for genomic data. This method can be useful to prioritize candidate genes, particularly when their number is large or when input data is highly heterogeneous. The code is freely available at https://github.com/gzampieri/Scuba .

Genomic Prediction of Genotype × Environment Interaction Kernel Regression Models.

PubMed

Cuevas, Jaime; Crossa, José; Soberanis, Víctor; Pérez-Elizalde, Sergio; Pérez-Rodríguez, Paulino; Campos, Gustavo de Los; Montesinos-López, O A; Burgueño, Juan

2016-11-01

In genomic selection (GS), genotype × environment interaction (G × E) can be modeled by a marker × environment interaction (M × E). The G × E may be modeled through a linear kernel or a nonlinear (Gaussian) kernel. In this study, we propose using two nonlinear Gaussian kernels: the reproducing kernel Hilbert space with kernel averaging (RKHS KA) and the Gaussian kernel with the bandwidth estimated through an empirical Bayesian method (RKHS EB). We performed single-environment analyses and extended to account for G × E interaction (GBLUP-G × E, RKHS KA-G × E and RKHS EB-G × E) in wheat ( L.) and maize ( L.) data sets. For single-environment analyses of wheat and maize data sets, RKHS EB and RKHS KA had higher prediction accuracy than GBLUP for all environments. For the wheat data, the RKHS KA-G × E and RKHS EB-G × E models did show up to 60 to 68% superiority over the corresponding single environment for pairs of environments with positive correlations. For the wheat data set, the models with Gaussian kernels had accuracies up to 17% higher than that of GBLUP-G × E. For the maize data set, the prediction accuracy of RKHS EB-G × E and RKHS KA-G × E was, on average, 5 to 6% higher than that of GBLUP-G × E. The superiority of the Gaussian kernel models over the linear kernel is due to more flexible kernels that accounts for small, more complex marker main effects and marker-specific interaction effects. Copyright © 2016 Crop Science Society of America.

Sepsis mortality prediction with the Quotient Basis Kernel.

PubMed

Ribas Ripoll, Vicent J; Vellido, Alfredo; Romero, Enrique; Ruiz-Rodríguez, Juan Carlos

2014-05-01

This paper presents an algorithm to assess the risk of death in patients with sepsis. Sepsis is a common clinical syndrome in the intensive care unit (ICU) that can lead to severe sepsis, a severe state of septic shock or multi-organ failure. The proposed algorithm may be implemented as part of a clinical decision support system that can be used in combination with the scores deployed in the ICU to improve the accuracy, sensitivity and specificity of mortality prediction for patients with sepsis. In this paper, we used the Simplified Acute Physiology Score (SAPS) for ICU patients and the Sequential Organ Failure Assessment (SOFA) to build our kernels and algorithms. In the proposed method, we embed the available data in a suitable feature space and use algorithms based on linear algebra, geometry and statistics for inference. We present a simplified version of the Fisher kernel (practical Fisher kernel for multinomial distributions), as well as a novel kernel that we named the Quotient Basis Kernel (QBK). These kernels are used as the basis for mortality prediction using soft-margin support vector machines. The two new kernels presented are compared against other generative kernels based on the Jensen-Shannon metric (centred, exponential and inverse) and other widely used kernels (linear, polynomial and Gaussian). Clinical relevance is also evaluated by comparing these results with logistic regression and the standard clinical prediction method based on the initial SAPS score. As described in this paper, we tested the new methods via cross-validation with a cohort of 400 test patients. The results obtained using our methods compare favourably with those obtained using alternative kernels (80.18% accuracy for the QBK) and the standard clinical prediction method, which are based on the basal SAPS score or logistic regression (71.32% and 71.55%, respectively). The QBK presented a sensitivity and specificity of 79.34% and 83.24%, which outperformed the other kernels

Kernel Methods for Mining Instance Data in Ontologies

NASA Astrophysics Data System (ADS)

Bloehdorn, Stephan; Sure, York

The amount of ontologies and meta data available on the Web is constantly growing. The successful application of machine learning techniques for learning of ontologies from textual data, i.e. mining for the Semantic Web, contributes to this trend. However, no principal approaches exist so far for mining from the Semantic Web. We investigate how machine learning algorithms can be made amenable for directly taking advantage of the rich knowledge expressed in ontologies and associated instance data. Kernel methods have been successfully employed in various learning tasks and provide a clean framework for interfacing between non-vectorial data and machine learning algorithms. In this spirit, we express the problem of mining instances in ontologies as the problem of defining valid corresponding kernels. We present a principled framework for designing such kernels by means of decomposing the kernel computation into specialized kernels for selected characteristics of an ontology which can be flexibly assembled and tuned. Initial experiments on real world Semantic Web data enjoy promising results and show the usefulness of our approach.

Biasing anisotropic scattering kernels for deep-penetration Monte Carlo calculations

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

Carter, L.L.; Hendricks, J.S.

1983-01-01

The exponential transform is often used to improve the efficiency of deep-penetration Monte Carlo calculations. This technique is usually implemented by biasing the distance-to-collision kernel of the transport equation, but leaving the scattering kernel unchanged. Dwivedi obtained significant improvements in efficiency by biasing an isotropic scattering kernel as well as the distance-to-collision kernel. This idea is extended to anisotropic scattering, particularly the highly forward Klein-Nishina scattering of gamma rays.

Digestibility of carbohydrates from rice-, oat- and wheat-based ready-to-eat breakfast cereals in children.

PubMed

Brighenti, F; Casiraghi, M C; Ciappellano, S; Crovetti, R; Testolin, G

1994-09-01

To study the effect of the presence and quality of dietary fibre in ready-to-eat (RTE) breakfast cereals on completeness of carbohydrate digestion in children and on starch susceptibility to alpha-amylase in vitro. A controlled intervention study. Eight 3-8-year-old healthy children. Completeness of digestion was evaluated by assessing the amount of carbohydrates apparently fermented into the colon using the breath-H2 technique after consumption in random order, of five breakfast tests containing boiled rice (either alone or supplemented with 3 g of lactulose) as reference food, or RTE cereals based on rice (low-fibre), wheat (high insoluble fibre) and oats (high-soluble fibre). The potential glycaemic impact of the products was estimated in vitro by assessing starch susceptibility to alpha-amylolysis using an enzymatic-dialysis method. Compared to boiled rice and to rice-based RTE cereal, wheat- and oat-based RTE cereals both significantly (P < 0.05) increased the amount of apparently fermented carbohydrates (+1.1 +/- 1.7% of total breakfast carbohydrate fermented for rice, +5.6 +/- 0.9% for wheat and +9.4 +/- 3.7% for oats; mean +/- SEM), calculated using the excess H2 in breath after lactulose as standard. All products showed similar in vitro digestibility, resulting in estimated glycaemic indexes of 117.5 (24.0) for rice, and 105.7 (14.1) for oats-based, 128.4 (17.6) for wheat-based, and 129.8 (16.6) [mean 95% CI)] for rice-based RTE cereals. Results suggest that the presence of fibre in RTE breakfast cereals, in particular soluble fibre, increases colonic fermentation in children whereas it seems not to affect glucose availability.

Direct Measurement of Wave Kernels in Time-Distance Helioseismology

NASA Technical Reports Server (NTRS)

Duvall, T. L., Jr.

2006-01-01

Solar f-mode waves are surface-gravity waves which propagate horizontally in a thin layer near the photosphere with a dispersion relation approximately that of deep water waves. At the power maximum near 3 mHz, the wavelength of 5 Mm is large enough for various wave scattering properties to be observable. Gizon and Birch (2002,ApJ,571,966)h ave calculated kernels, in the Born approximation, for the sensitivity of wave travel times to local changes in damping rate and source strength. In this work, using isolated small magnetic features as approximate point-sourc'e scatterers, such a kernel has been measured. The observed kernel contains similar features to a theoretical damping kernel but not for a source kernel. A full understanding of the effect of small magnetic features on the waves will require more detailed modeling.

Total antioxidant capacity and starch digestibility of muffins baked with rice, wheat, oat, corn and barley flour.

PubMed

Soong, Yean Yean; Tan, Seow Peng; Leong, Lai Peng; Henry, Jeya Kumar

2014-12-01

Muffins are a popular snack consumed in western and emerging countries. Increased glycemic load has been implicated in the aetiology of diabetes. This study examined the starch digestibility of muffins baked with rice, wheat, corn, oat and barley flour. Rapidly digested starch (RDS) was greatest in rice (445 mg/g) and wheat (444 mg/g) muffins, followed by oat (416 mg/g), corn (402 mg/g) and barley (387 mg/g). Total phenolic content was found to be positively correlated with total antioxidative capacity and inversely related to the RDS of muffins. The phenolic content was highest in muffin baked with barley flour (1,687 μg/g), followed by corn (1,454 μg/g), oat (945 μg/g), wheat (705 μg/g), and rice (675 μg/g) flour. Browning was shown not to correlate with free radical scavenging capacity and digestibility of muffins. The presence of high phenolic content and low RDS makes barley muffin an ideal snack to modulate glycemic response. Copyright © 2014 Elsevier Ltd. All rights reserved.

Digital Image Sensor-Based Assessment of the Status of Oat (Avena sativa L.) Crops after Frost Damage

PubMed Central

Macedo-Cruz, Antonia; Pajares, Gonzalo; Santos, Matilde; Villegas-Romero, Isidro

2011-01-01

The aim of this paper is to classify the land covered with oat crops, and the quantification of frost damage on oats, while plants are still in the flowering stage. The images are taken by a digital colour camera CCD-based sensor. Unsupervised classification methods are applied because the plants present different spectral signatures, depending on two main factors: illumination and the affected state. The colour space used in this application is CIELab, based on the decomposition of the colour in three channels, because it is the closest to human colour perception. The histogram of each channel is successively split into regions by thresholding. The best threshold to be applied is automatically obtained as a combination of three thresholding strategies: (a) Otsu’s method, (b) Isodata algorithm, and (c) Fuzzy thresholding. The fusion of these automatic thresholding techniques and the design of the classification strategy are some of the main findings of the paper, which allows an estimation of the damages and a prediction of the oat production. PMID:22163940

Dropping macadamia nuts-in-shell reduces kernel roasting quality.

PubMed

Walton, David A; Wallace, Helen M

2010-10-01

Macadamia nuts ('nuts-in-shell') are subjected to many impacts from dropping during postharvest handling, resulting in damage to the raw kernel. The effect of dropping on roasted kernel quality is unknown. Macadamia nuts-in-shell were dropped in various combinations of moisture content, number of drops and receiving surface in three experiments. After dropping, samples from each treatment and undropped controls were dry oven-roasted for 20 min at 130 °C, and kernels were assessed for colour, mottled colour and surface damage. Dropping nuts-in-shell onto a bed of nuts-in-shell at 3% moisture content or 20% moisture content increased the percentage of dark roasted kernels. Kernels from nuts dropped first at 20%, then 10% moisture content, onto a metal plate had increased mottled colour. Dropping nuts-in-shell at 3% moisture content onto nuts-in-shell significantly increased surface damage. Similarly, surface damage increased for kernels dropped onto a metal plate at 20%, then at 10% moisture content. Postharvest dropping of macadamia nuts-in-shell causes concealed cellular damage to kernels, the effects not evident until roasting. This damage provides the reagents needed for non-enzymatic browning reactions. Improvements in handling, such as reducing the number of drops and improving handling equipment, will reduce cellular damage and after-roast darkening. Copyright © 2010 Society of Chemical Industry.

Compound analysis via graph kernels incorporating chirality.

PubMed

Brown, J B; Urata, Takashi; Tamura, Takeyuki; Arai, Midori A; Kawabata, Takeo; Akutsu, Tatsuya

2010-12-01

High accuracy is paramount when predicting biochemical characteristics using Quantitative Structural-Property Relationships (QSPRs). Although existing graph-theoretic kernel methods combined with machine learning techniques are efficient for QSPR model construction, they cannot distinguish topologically identical chiral compounds which often exhibit different biological characteristics. In this paper, we propose a new method that extends the recently developed tree pattern graph kernel to accommodate stereoisomers. We show that Support Vector Regression (SVR) with a chiral graph kernel is useful for target property prediction by demonstrating its application to a set of human vitamin D receptor ligands currently under consideration for their potential anti-cancer effects.

Kernel-aligned multi-view canonical correlation analysis for image recognition

NASA Astrophysics Data System (ADS)

Su, Shuzhi; Ge, Hongwei; Yuan, Yun-Hao

2016-09-01

Existing kernel-based correlation analysis methods mainly adopt a single kernel in each view. However, only a single kernel is usually insufficient to characterize nonlinear distribution information of a view. To solve the problem, we transform each original feature vector into a 2-dimensional feature matrix by means of kernel alignment, and then propose a novel kernel-aligned multi-view canonical correlation analysis (KAMCCA) method on the basis of the feature matrices. Our proposed method can simultaneously employ multiple kernels to better capture the nonlinear distribution information of each view, so that correlation features learned by KAMCCA can have well discriminating power in real-world image recognition. Extensive experiments are designed on five real-world image datasets, including NIR face images, thermal face images, visible face images, handwritten digit images, and object images. Promising experimental results on the datasets have manifested the effectiveness of our proposed method.